Multiple sequence alignment - TraesCS6A01G345000

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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 TraesCS6A01G345000 chr6A 100.000 2854 0 0 1 2854 578941127 578943980 0.000000e+00 5271
1 TraesCS6A01G345000 chr6A 94.412 859 43 4 1997 2854 65663370 65662516 0.000000e+00 1315
2 TraesCS6A01G345000 chr6A 74.442 403 65 32 1247 1642 578954863 578955234 3.830000e-29 139
3 TraesCS6A01G345000 chr6D 88.375 1858 127 46 149 1968 432822937 432824743 0.000000e+00 2152
4 TraesCS6A01G345000 chr6D 74.690 403 64 33 1247 1642 432852866 432853237 8.240000e-31 145
5 TraesCS6A01G345000 chr6B 91.795 1365 81 16 629 1968 652944868 652946226 0.000000e+00 1871
6 TraesCS6A01G345000 chr6B 74.442 403 65 30 1247 1642 652983780 652984151 3.830000e-29 139
7 TraesCS6A01G345000 chr1B 95.349 860 35 5 1997 2854 683375065 683374209 0.000000e+00 1362
8 TraesCS6A01G345000 chr2D 94.890 861 40 4 1997 2854 432018034 432017175 0.000000e+00 1343
9 TraesCS6A01G345000 chr2A 94.457 866 42 5 1994 2854 619909654 619910518 0.000000e+00 1328
10 TraesCS6A01G345000 chr2A 94.296 859 47 2 1997 2854 672765490 672766347 0.000000e+00 1314
11 TraesCS6A01G345000 chr7D 94.419 860 41 6 1997 2854 604364444 604363590 0.000000e+00 1315
12 TraesCS6A01G345000 chr7A 94.206 863 45 4 1997 2854 114014885 114015747 0.000000e+00 1312
13 TraesCS6A01G345000 chr7A 94.172 858 46 2 1997 2854 19090712 19089859 0.000000e+00 1304
14 TraesCS6A01G345000 chr3A 94.206 863 43 3 1999 2854 732624460 732625322 0.000000e+00 1310
15 TraesCS6A01G345000 chr3D 97.674 43 1 0 1490 1532 6434559 6434517 1.100000e-09 75


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 TraesCS6A01G345000 chr6A 578941127 578943980 2853 False 5271 5271 100.000 1 2854 1 chr6A.!!$F1 2853
1 TraesCS6A01G345000 chr6A 65662516 65663370 854 True 1315 1315 94.412 1997 2854 1 chr6A.!!$R1 857
2 TraesCS6A01G345000 chr6D 432822937 432824743 1806 False 2152 2152 88.375 149 1968 1 chr6D.!!$F1 1819
3 TraesCS6A01G345000 chr6B 652944868 652946226 1358 False 1871 1871 91.795 629 1968 1 chr6B.!!$F1 1339
4 TraesCS6A01G345000 chr1B 683374209 683375065 856 True 1362 1362 95.349 1997 2854 1 chr1B.!!$R1 857
5 TraesCS6A01G345000 chr2D 432017175 432018034 859 True 1343 1343 94.890 1997 2854 1 chr2D.!!$R1 857
6 TraesCS6A01G345000 chr2A 619909654 619910518 864 False 1328 1328 94.457 1994 2854 1 chr2A.!!$F1 860
7 TraesCS6A01G345000 chr2A 672765490 672766347 857 False 1314 1314 94.296 1997 2854 1 chr2A.!!$F2 857
8 TraesCS6A01G345000 chr7D 604363590 604364444 854 True 1315 1315 94.419 1997 2854 1 chr7D.!!$R1 857
9 TraesCS6A01G345000 chr7A 114014885 114015747 862 False 1312 1312 94.206 1997 2854 1 chr7A.!!$F1 857
10 TraesCS6A01G345000 chr7A 19089859 19090712 853 True 1304 1304 94.172 1997 2854 1 chr7A.!!$R1 857
11 TraesCS6A01G345000 chr3A 732624460 732625322 862 False 1310 1310 94.206 1999 2854 1 chr3A.!!$F1 855

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
107 108 0.249911 AAGTGAGTGTTGACCGGAGC 60.25 55.0 9.46 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2016 0.178068 ATAACGCGGCTGTTGGAGAT 59.822 50.0 12.47 3.74 33.32 2.75 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
70 71 8.879759 AGTGGAAACATATACAAAGTGAATACG 58.120 33.333 0.00 0.00 46.14 3.06
71 72 8.662141 GTGGAAACATATACAAAGTGAATACGT 58.338 33.333 0.00 0.00 46.14 3.57
72 73 8.661257 TGGAAACATATACAAAGTGAATACGTG 58.339 33.333 0.00 0.00 33.40 4.49
73 74 7.638683 GGAAACATATACAAAGTGAATACGTGC 59.361 37.037 0.00 0.00 0.00 5.34
74 75 7.603963 AACATATACAAAGTGAATACGTGCA 57.396 32.000 0.00 0.00 0.00 4.57
75 76 7.234187 ACATATACAAAGTGAATACGTGCAG 57.766 36.000 0.00 0.00 0.00 4.41
76 77 6.257849 ACATATACAAAGTGAATACGTGCAGG 59.742 38.462 4.53 4.53 0.00 4.85
77 78 1.535462 ACAAAGTGAATACGTGCAGGC 59.465 47.619 6.26 0.00 0.00 4.85
78 79 1.535028 CAAAGTGAATACGTGCAGGCA 59.465 47.619 6.26 0.00 0.00 4.75
79 80 1.442769 AAGTGAATACGTGCAGGCAG 58.557 50.000 6.26 0.00 0.00 4.85
80 81 0.391661 AGTGAATACGTGCAGGCAGG 60.392 55.000 11.98 11.98 37.77 4.85
81 82 0.391130 GTGAATACGTGCAGGCAGGA 60.391 55.000 19.49 5.05 35.94 3.86
82 83 0.541392 TGAATACGTGCAGGCAGGAT 59.459 50.000 19.49 6.95 35.94 3.24
83 84 1.760029 TGAATACGTGCAGGCAGGATA 59.240 47.619 19.49 9.15 35.94 2.59
84 85 2.169561 TGAATACGTGCAGGCAGGATAA 59.830 45.455 19.49 6.04 35.94 1.75
85 86 2.240493 ATACGTGCAGGCAGGATAAC 57.760 50.000 19.49 0.00 35.94 1.89
86 87 1.191535 TACGTGCAGGCAGGATAACT 58.808 50.000 19.49 0.70 35.94 2.24
100 101 5.808366 AGGATAACTGAAGTGAGTGTTGA 57.192 39.130 0.00 0.00 0.00 3.18
101 102 5.542779 AGGATAACTGAAGTGAGTGTTGAC 58.457 41.667 0.00 0.00 0.00 3.18
102 103 4.691216 GGATAACTGAAGTGAGTGTTGACC 59.309 45.833 0.00 0.00 0.00 4.02
103 104 2.225068 ACTGAAGTGAGTGTTGACCG 57.775 50.000 0.00 0.00 0.00 4.79
104 105 1.202533 ACTGAAGTGAGTGTTGACCGG 60.203 52.381 0.00 0.00 0.00 5.28
105 106 1.068588 CTGAAGTGAGTGTTGACCGGA 59.931 52.381 9.46 0.00 0.00 5.14
106 107 1.068588 TGAAGTGAGTGTTGACCGGAG 59.931 52.381 9.46 0.00 0.00 4.63
107 108 0.249911 AAGTGAGTGTTGACCGGAGC 60.250 55.000 9.46 0.00 0.00 4.70
108 109 1.115930 AGTGAGTGTTGACCGGAGCT 61.116 55.000 9.46 0.00 0.00 4.09
109 110 0.249911 GTGAGTGTTGACCGGAGCTT 60.250 55.000 9.46 0.00 0.00 3.74
110 111 1.000506 GTGAGTGTTGACCGGAGCTTA 59.999 52.381 9.46 0.00 0.00 3.09
111 112 1.272490 TGAGTGTTGACCGGAGCTTAG 59.728 52.381 9.46 0.00 0.00 2.18
112 113 1.544691 GAGTGTTGACCGGAGCTTAGA 59.455 52.381 9.46 0.00 0.00 2.10
113 114 1.968493 AGTGTTGACCGGAGCTTAGAA 59.032 47.619 9.46 0.00 0.00 2.10
114 115 2.367567 AGTGTTGACCGGAGCTTAGAAA 59.632 45.455 9.46 0.00 0.00 2.52
115 116 2.737252 GTGTTGACCGGAGCTTAGAAAG 59.263 50.000 9.46 0.00 0.00 2.62
116 117 2.289444 TGTTGACCGGAGCTTAGAAAGG 60.289 50.000 9.46 0.00 0.00 3.11
117 118 1.640917 TGACCGGAGCTTAGAAAGGT 58.359 50.000 9.46 0.00 42.93 3.50
118 119 1.975680 TGACCGGAGCTTAGAAAGGTT 59.024 47.619 9.46 0.00 39.77 3.50
119 120 2.289444 TGACCGGAGCTTAGAAAGGTTG 60.289 50.000 9.46 0.00 39.77 3.77
120 121 1.975680 ACCGGAGCTTAGAAAGGTTGA 59.024 47.619 9.46 0.00 39.77 3.18
121 122 2.370849 ACCGGAGCTTAGAAAGGTTGAA 59.629 45.455 9.46 0.00 39.77 2.69
122 123 2.742589 CCGGAGCTTAGAAAGGTTGAAC 59.257 50.000 0.00 0.00 39.77 3.18
123 124 3.557264 CCGGAGCTTAGAAAGGTTGAACT 60.557 47.826 0.00 0.00 39.77 3.01
124 125 3.433615 CGGAGCTTAGAAAGGTTGAACTG 59.566 47.826 0.00 0.00 39.77 3.16
125 126 4.390264 GGAGCTTAGAAAGGTTGAACTGT 58.610 43.478 0.00 0.00 39.77 3.55
126 127 5.548406 GGAGCTTAGAAAGGTTGAACTGTA 58.452 41.667 0.00 0.00 39.77 2.74
127 128 5.639931 GGAGCTTAGAAAGGTTGAACTGTAG 59.360 44.000 0.00 0.00 39.77 2.74
128 129 6.420913 AGCTTAGAAAGGTTGAACTGTAGA 57.579 37.500 0.00 0.00 35.27 2.59
129 130 6.459923 AGCTTAGAAAGGTTGAACTGTAGAG 58.540 40.000 0.00 0.00 35.27 2.43
130 131 6.267928 AGCTTAGAAAGGTTGAACTGTAGAGA 59.732 38.462 0.00 0.00 35.27 3.10
131 132 6.929606 GCTTAGAAAGGTTGAACTGTAGAGAA 59.070 38.462 0.00 0.00 0.00 2.87
132 133 7.441458 GCTTAGAAAGGTTGAACTGTAGAGAAA 59.559 37.037 0.00 0.00 0.00 2.52
133 134 9.326413 CTTAGAAAGGTTGAACTGTAGAGAAAA 57.674 33.333 0.00 0.00 0.00 2.29
134 135 7.555306 AGAAAGGTTGAACTGTAGAGAAAAC 57.445 36.000 0.00 0.00 0.00 2.43
135 136 7.110155 AGAAAGGTTGAACTGTAGAGAAAACA 58.890 34.615 0.00 0.00 0.00 2.83
136 137 6.679327 AAGGTTGAACTGTAGAGAAAACAC 57.321 37.500 0.00 0.00 0.00 3.32
137 138 5.741011 AGGTTGAACTGTAGAGAAAACACA 58.259 37.500 0.00 0.00 0.00 3.72
138 139 6.177610 AGGTTGAACTGTAGAGAAAACACAA 58.822 36.000 0.00 0.00 0.00 3.33
139 140 6.093633 AGGTTGAACTGTAGAGAAAACACAAC 59.906 38.462 0.00 0.00 33.75 3.32
140 141 5.712217 TGAACTGTAGAGAAAACACAACG 57.288 39.130 0.00 0.00 0.00 4.10
141 142 5.412640 TGAACTGTAGAGAAAACACAACGA 58.587 37.500 0.00 0.00 0.00 3.85
142 143 5.870433 TGAACTGTAGAGAAAACACAACGAA 59.130 36.000 0.00 0.00 0.00 3.85
143 144 6.369340 TGAACTGTAGAGAAAACACAACGAAA 59.631 34.615 0.00 0.00 0.00 3.46
144 145 6.103222 ACTGTAGAGAAAACACAACGAAAC 57.897 37.500 0.00 0.00 0.00 2.78
145 146 5.064325 ACTGTAGAGAAAACACAACGAAACC 59.936 40.000 0.00 0.00 0.00 3.27
146 147 4.936411 TGTAGAGAAAACACAACGAAACCA 59.064 37.500 0.00 0.00 0.00 3.67
147 148 5.411977 TGTAGAGAAAACACAACGAAACCAA 59.588 36.000 0.00 0.00 0.00 3.67
153 154 7.317390 AGAAAACACAACGAAACCAACTAATT 58.683 30.769 0.00 0.00 0.00 1.40
210 211 2.711542 AGGTTAGCAACTTAGCGCAAT 58.288 42.857 11.47 0.00 40.15 3.56
223 224 7.375106 ACTTAGCGCAATATCGTAGTAGTAT 57.625 36.000 11.47 0.00 0.00 2.12
230 231 6.859508 CGCAATATCGTAGTAGTATTGGACAA 59.140 38.462 0.00 0.00 36.69 3.18
250 251 9.470399 TGGACAATTGTGTATAGAGTCTAGTTA 57.530 33.333 17.58 0.00 38.41 2.24
260 261 3.107601 AGAGTCTAGTTAAGGGCATGCA 58.892 45.455 21.36 0.00 0.00 3.96
261 262 3.713764 AGAGTCTAGTTAAGGGCATGCAT 59.286 43.478 21.36 7.59 0.00 3.96
262 263 4.061596 GAGTCTAGTTAAGGGCATGCATC 58.938 47.826 21.36 11.12 0.00 3.91
263 264 3.455910 AGTCTAGTTAAGGGCATGCATCA 59.544 43.478 21.36 0.00 0.00 3.07
264 265 4.103785 AGTCTAGTTAAGGGCATGCATCAT 59.896 41.667 21.36 6.64 0.00 2.45
265 266 5.307976 AGTCTAGTTAAGGGCATGCATCATA 59.692 40.000 21.36 5.61 0.00 2.15
266 267 5.997746 GTCTAGTTAAGGGCATGCATCATAA 59.002 40.000 21.36 11.35 0.00 1.90
267 268 6.656693 GTCTAGTTAAGGGCATGCATCATAAT 59.343 38.462 21.36 3.34 0.00 1.28
268 269 7.824289 GTCTAGTTAAGGGCATGCATCATAATA 59.176 37.037 21.36 4.37 0.00 0.98
269 270 8.043113 TCTAGTTAAGGGCATGCATCATAATAG 58.957 37.037 21.36 13.43 0.00 1.73
270 271 6.782986 AGTTAAGGGCATGCATCATAATAGA 58.217 36.000 21.36 0.00 0.00 1.98
271 272 7.233632 AGTTAAGGGCATGCATCATAATAGAA 58.766 34.615 21.36 0.00 0.00 2.10
299 300 5.070847 GGGTTTCATATGGGCATTCTTTCAT 59.929 40.000 2.13 0.00 0.00 2.57
317 318 5.862924 TTCATGAGCTTTGCTACACTTAC 57.137 39.130 0.00 0.00 39.88 2.34
330 331 9.703892 TTTGCTACACTTACGTAAAATTACCTA 57.296 29.630 9.68 0.00 0.00 3.08
331 332 8.915871 TGCTACACTTACGTAAAATTACCTAG 57.084 34.615 9.68 0.00 0.00 3.02
333 334 7.436376 GCTACACTTACGTAAAATTACCTAGGG 59.564 40.741 14.81 0.00 0.00 3.53
348 349 4.891992 CCTAGGGAGGTTATGTACATGG 57.108 50.000 18.81 2.99 38.16 3.66
352 353 3.454812 AGGGAGGTTATGTACATGGTGAC 59.545 47.826 18.81 10.87 0.00 3.67
375 376 4.439426 CGTGGAGTTGTTTGATTGGACAAA 60.439 41.667 0.00 0.00 37.49 2.83
379 380 5.872070 GGAGTTGTTTGATTGGACAAAACAA 59.128 36.000 8.43 8.43 40.62 2.83
383 384 4.081198 TGTTTGATTGGACAAAACAAGGCT 60.081 37.500 0.00 0.00 40.62 4.58
391 392 1.750778 ACAAAACAAGGCTCCACACTG 59.249 47.619 0.00 0.00 0.00 3.66
399 400 3.228188 AGGCTCCACACTGAAATGAAA 57.772 42.857 0.00 0.00 0.00 2.69
401 402 2.229784 GGCTCCACACTGAAATGAAAGG 59.770 50.000 0.00 0.00 0.00 3.11
403 404 3.490348 CTCCACACTGAAATGAAAGGGT 58.510 45.455 0.00 0.00 0.00 4.34
411 412 9.226606 CACACTGAAATGAAAGGGTAATTAGTA 57.773 33.333 0.00 0.00 0.00 1.82
419 420 9.690913 AATGAAAGGGTAATTAGTAAGGGTTAC 57.309 33.333 0.00 0.00 36.38 2.50
427 428 2.629017 AGTAAGGGTTACGGAAGGGA 57.371 50.000 0.00 0.00 41.01 4.20
428 429 2.906568 AGTAAGGGTTACGGAAGGGAA 58.093 47.619 0.00 0.00 41.01 3.97
429 430 3.457836 AGTAAGGGTTACGGAAGGGAAT 58.542 45.455 0.00 0.00 41.01 3.01
430 431 2.801077 AAGGGTTACGGAAGGGAATG 57.199 50.000 0.00 0.00 0.00 2.67
431 432 0.916809 AGGGTTACGGAAGGGAATGG 59.083 55.000 0.00 0.00 0.00 3.16
432 433 0.750546 GGGTTACGGAAGGGAATGGC 60.751 60.000 0.00 0.00 0.00 4.40
433 434 0.255033 GGTTACGGAAGGGAATGGCT 59.745 55.000 0.00 0.00 0.00 4.75
434 435 1.340697 GGTTACGGAAGGGAATGGCTT 60.341 52.381 0.00 0.00 0.00 4.35
435 436 2.443416 GTTACGGAAGGGAATGGCTTT 58.557 47.619 0.00 0.00 0.00 3.51
436 437 2.823747 GTTACGGAAGGGAATGGCTTTT 59.176 45.455 0.00 0.00 0.00 2.27
437 438 2.009681 ACGGAAGGGAATGGCTTTTT 57.990 45.000 0.00 0.00 0.00 1.94
438 439 1.893137 ACGGAAGGGAATGGCTTTTTC 59.107 47.619 0.00 0.00 0.00 2.29
487 489 6.544197 TGTAGGTGTAGCATTTTTGTTCTTCA 59.456 34.615 0.00 0.00 0.00 3.02
492 494 8.726988 GGTGTAGCATTTTTGTTCTTCACTATA 58.273 33.333 0.00 0.00 30.77 1.31
516 518 7.754069 ATAATTGTGTGTTGTTTTGTGACTG 57.246 32.000 0.00 0.00 0.00 3.51
517 519 4.837896 TTGTGTGTTGTTTTGTGACTGA 57.162 36.364 0.00 0.00 0.00 3.41
518 520 4.418013 TGTGTGTTGTTTTGTGACTGAG 57.582 40.909 0.00 0.00 0.00 3.35
519 521 3.171277 GTGTGTTGTTTTGTGACTGAGC 58.829 45.455 0.00 0.00 0.00 4.26
520 522 3.081061 TGTGTTGTTTTGTGACTGAGCT 58.919 40.909 0.00 0.00 0.00 4.09
521 523 4.094294 GTGTGTTGTTTTGTGACTGAGCTA 59.906 41.667 0.00 0.00 0.00 3.32
522 524 4.881273 TGTGTTGTTTTGTGACTGAGCTAT 59.119 37.500 0.00 0.00 0.00 2.97
523 525 6.018262 GTGTGTTGTTTTGTGACTGAGCTATA 60.018 38.462 0.00 0.00 0.00 1.31
524 526 6.540551 TGTGTTGTTTTGTGACTGAGCTATAA 59.459 34.615 0.00 0.00 0.00 0.98
525 527 7.066404 TGTGTTGTTTTGTGACTGAGCTATAAA 59.934 33.333 0.00 0.00 0.00 1.40
526 528 7.587757 GTGTTGTTTTGTGACTGAGCTATAAAG 59.412 37.037 0.00 0.00 0.00 1.85
527 529 7.282224 TGTTGTTTTGTGACTGAGCTATAAAGT 59.718 33.333 0.00 0.00 0.00 2.66
539 541 6.315714 TGAGCTATAAAGTAGTCATAGGCCT 58.684 40.000 11.78 11.78 0.00 5.19
593 595 4.966850 TTCTCGTCGAAAAACACTGATC 57.033 40.909 0.00 0.00 0.00 2.92
594 596 4.238761 TCTCGTCGAAAAACACTGATCT 57.761 40.909 0.00 0.00 0.00 2.75
595 597 3.981416 TCTCGTCGAAAAACACTGATCTG 59.019 43.478 0.00 0.00 0.00 2.90
609 611 6.324819 ACACTGATCTGTTTTTGTTTCTGTG 58.675 36.000 1.95 0.00 38.33 3.66
611 613 7.120579 ACACTGATCTGTTTTTGTTTCTGTGTA 59.879 33.333 1.95 0.00 41.41 2.90
612 614 7.967854 CACTGATCTGTTTTTGTTTCTGTGTAA 59.032 33.333 1.95 0.00 32.06 2.41
613 615 8.519526 ACTGATCTGTTTTTGTTTCTGTGTAAA 58.480 29.630 0.00 0.00 0.00 2.01
614 616 9.352784 CTGATCTGTTTTTGTTTCTGTGTAAAA 57.647 29.630 0.00 0.00 0.00 1.52
615 617 9.698309 TGATCTGTTTTTGTTTCTGTGTAAAAA 57.302 25.926 0.00 0.00 0.00 1.94
651 661 7.530863 GGTTTGGTTTTGCAAATTTCTGTTTA 58.469 30.769 13.65 0.00 0.00 2.01
792 803 1.807165 CGTCATGGTCTGGCAGTCG 60.807 63.158 15.27 5.74 0.00 4.18
801 812 3.144120 CTGGCAGTCGGAGGATCGG 62.144 68.421 6.28 0.00 34.37 4.18
818 829 1.105457 CGGTCCCTGGATACGTACAA 58.895 55.000 0.00 0.00 42.51 2.41
829 840 6.100404 TGGATACGTACAACCCCATATAAC 57.900 41.667 0.00 0.00 42.51 1.89
956 970 1.004560 CACTCCTTCGCTCCAGCAA 60.005 57.895 0.00 0.00 42.21 3.91
957 971 1.004440 ACTCCTTCGCTCCAGCAAC 60.004 57.895 0.00 0.00 42.21 4.17
958 972 1.294780 CTCCTTCGCTCCAGCAACT 59.705 57.895 0.00 0.00 42.21 3.16
961 975 1.078759 CCTTCGCTCCAGCAACTACG 61.079 60.000 0.00 0.00 42.21 3.51
970 984 3.431725 GCAACTACGCCTGCCCAC 61.432 66.667 0.00 0.00 32.18 4.61
1026 1040 1.440938 TACCACACGCAGCAAACCAC 61.441 55.000 0.00 0.00 0.00 4.16
1062 1076 3.353836 GGCACGCACGTTGGTCAT 61.354 61.111 0.00 0.00 0.00 3.06
1071 1085 1.079819 CGTTGGTCATCCACGAGCT 60.080 57.895 0.00 0.00 44.22 4.09
1072 1086 0.172578 CGTTGGTCATCCACGAGCTA 59.827 55.000 0.00 0.00 44.22 3.32
1073 1087 1.799181 CGTTGGTCATCCACGAGCTAG 60.799 57.143 0.00 0.00 44.22 3.42
1097 1111 2.338500 CTGGTCTACCAAAAGCTCGAC 58.662 52.381 2.97 0.00 46.97 4.20
1164 1190 4.593864 GCCGTCATCCTCCTCGCC 62.594 72.222 0.00 0.00 0.00 5.54
1167 1193 4.933064 GTCATCCTCCTCGCCGCG 62.933 72.222 6.39 6.39 0.00 6.46
1697 1724 1.080705 GGACACGTTCGTGAGGGAG 60.081 63.158 27.77 4.69 39.25 4.30
1706 1733 4.436998 GTGAGGGAGACGGTGGCG 62.437 72.222 0.00 0.00 0.00 5.69
1859 1897 5.394553 GCTTGGTGAAATGGAGGAAATAAGG 60.395 44.000 0.00 0.00 0.00 2.69
1874 1912 9.578439 GAGGAAATAAGGTGATTTTTCATTCTG 57.422 33.333 0.00 0.00 31.29 3.02
1939 1979 3.033764 GCGACGTGCCTTTCGTGA 61.034 61.111 0.00 0.00 41.64 4.35
1968 2008 4.798574 AGAATTGGCACGAAGATTTGTTC 58.201 39.130 0.00 0.00 0.00 3.18
1969 2009 4.520492 AGAATTGGCACGAAGATTTGTTCT 59.480 37.500 0.00 0.00 35.70 3.01
1971 2011 4.647424 TTGGCACGAAGATTTGTTCTTT 57.353 36.364 0.00 0.00 44.88 2.52
1972 2012 5.759506 TTGGCACGAAGATTTGTTCTTTA 57.240 34.783 0.00 0.00 44.88 1.85
1973 2013 5.759506 TGGCACGAAGATTTGTTCTTTAA 57.240 34.783 0.00 0.00 44.88 1.52
1974 2014 5.757886 TGGCACGAAGATTTGTTCTTTAAG 58.242 37.500 0.00 0.00 44.88 1.85
1975 2015 4.617223 GGCACGAAGATTTGTTCTTTAAGC 59.383 41.667 0.00 0.00 44.88 3.09
1976 2016 5.212194 GCACGAAGATTTGTTCTTTAAGCA 58.788 37.500 0.00 0.00 44.88 3.91
1977 2017 5.858581 GCACGAAGATTTGTTCTTTAAGCAT 59.141 36.000 0.00 0.00 44.88 3.79
1978 2018 6.032880 GCACGAAGATTTGTTCTTTAAGCATC 59.967 38.462 0.00 0.00 44.88 3.91
1979 2019 7.301054 CACGAAGATTTGTTCTTTAAGCATCT 58.699 34.615 0.00 0.00 44.88 2.90
1980 2020 7.479916 CACGAAGATTTGTTCTTTAAGCATCTC 59.520 37.037 0.00 0.00 44.88 2.75
1981 2021 6.963805 CGAAGATTTGTTCTTTAAGCATCTCC 59.036 38.462 0.00 0.00 44.88 3.71
1982 2022 7.361201 CGAAGATTTGTTCTTTAAGCATCTCCA 60.361 37.037 0.00 0.00 44.88 3.86
1983 2023 7.765695 AGATTTGTTCTTTAAGCATCTCCAA 57.234 32.000 0.00 0.00 0.00 3.53
1984 2024 7.597386 AGATTTGTTCTTTAAGCATCTCCAAC 58.403 34.615 0.00 0.00 0.00 3.77
1985 2025 6.707440 TTTGTTCTTTAAGCATCTCCAACA 57.293 33.333 0.00 0.00 0.00 3.33
1986 2026 5.947228 TGTTCTTTAAGCATCTCCAACAG 57.053 39.130 0.00 0.00 0.00 3.16
1987 2027 4.216257 TGTTCTTTAAGCATCTCCAACAGC 59.784 41.667 0.00 0.00 0.00 4.40
1988 2028 3.347216 TCTTTAAGCATCTCCAACAGCC 58.653 45.455 0.00 0.00 0.00 4.85
1989 2029 1.737838 TTAAGCATCTCCAACAGCCG 58.262 50.000 0.00 0.00 0.00 5.52
1990 2030 0.744414 TAAGCATCTCCAACAGCCGC 60.744 55.000 0.00 0.00 0.00 6.53
1991 2031 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
1992 2032 2.434884 CATCTCCAACAGCCGCGT 60.435 61.111 4.92 0.00 0.00 6.01
2054 2094 9.487790 CAAAGCCCAACTAAAATTCTGAAATTA 57.512 29.630 0.00 0.00 33.93 1.40
2113 2153 4.536489 AGTGAGGCTAAAGTTTAGTCCCAT 59.464 41.667 20.94 5.52 0.00 4.00
2116 2156 4.112331 AGGCTAAAGTTTAGTCCCATCCT 58.888 43.478 20.94 14.98 0.00 3.24
2125 2165 2.887151 AGTCCCATCCTGAAAGTTGG 57.113 50.000 0.00 0.00 35.67 3.77
2149 2189 6.408662 GGGAGAGAGTTGCACCTCTTTATAAT 60.409 42.308 15.62 0.00 41.85 1.28
2155 2195 6.476378 AGTTGCACCTCTTTATAATGTGAGT 58.524 36.000 0.00 1.42 0.00 3.41
2300 2357 4.793216 CACGTTGTCTATATTTTTGCTGCC 59.207 41.667 0.00 0.00 0.00 4.85
2305 2365 2.173782 TCTATATTTTTGCTGCCCGGGA 59.826 45.455 29.31 8.79 0.00 5.14
2363 2425 4.083908 GCGTTAATTACTGAACCGTTTCCA 60.084 41.667 0.00 0.00 0.00 3.53
2442 2504 3.445450 CCGCACTATATAGTCAGGCAGAT 59.555 47.826 12.62 0.00 33.46 2.90
2520 2582 0.603707 CCGCCAAGCAAGTCTTCTCA 60.604 55.000 0.00 0.00 31.27 3.27
2545 2607 1.300620 CCTTTCGACGTGCACCAGA 60.301 57.895 12.15 5.33 0.00 3.86
2784 2846 1.741706 TCCTGTTCGAGATCGTGGTAC 59.258 52.381 1.70 0.00 40.80 3.34
2792 2854 5.761165 TCGAGATCGTGGTACAATTCATA 57.239 39.130 1.70 0.00 44.16 2.15
2820 2882 3.580458 AGTATGTGCCCTAGATGTGATCC 59.420 47.826 0.00 0.00 0.00 3.36
2835 2897 3.384467 TGTGATCCGTTCATCTGCTATGA 59.616 43.478 0.00 0.00 36.54 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.879759 CGTATTCACTTTGTATATGTTTCCACT 58.120 33.333 0.00 0.00 0.00 4.00
45 46 8.662141 ACGTATTCACTTTGTATATGTTTCCAC 58.338 33.333 0.00 0.00 29.33 4.02
46 47 8.661257 CACGTATTCACTTTGTATATGTTTCCA 58.339 33.333 0.00 0.00 30.66 3.53
47 48 7.638683 GCACGTATTCACTTTGTATATGTTTCC 59.361 37.037 0.00 0.00 30.66 3.13
48 49 8.172484 TGCACGTATTCACTTTGTATATGTTTC 58.828 33.333 0.00 0.00 30.66 2.78
49 50 8.035165 TGCACGTATTCACTTTGTATATGTTT 57.965 30.769 0.00 0.00 30.66 2.83
50 51 7.201609 CCTGCACGTATTCACTTTGTATATGTT 60.202 37.037 0.00 0.00 30.66 2.71
51 52 6.257849 CCTGCACGTATTCACTTTGTATATGT 59.742 38.462 0.00 0.00 32.43 2.29
52 53 6.649436 CCTGCACGTATTCACTTTGTATATG 58.351 40.000 0.00 0.00 0.00 1.78
53 54 5.236478 GCCTGCACGTATTCACTTTGTATAT 59.764 40.000 0.00 0.00 0.00 0.86
54 55 4.569162 GCCTGCACGTATTCACTTTGTATA 59.431 41.667 0.00 0.00 0.00 1.47
55 56 3.374058 GCCTGCACGTATTCACTTTGTAT 59.626 43.478 0.00 0.00 0.00 2.29
56 57 2.739913 GCCTGCACGTATTCACTTTGTA 59.260 45.455 0.00 0.00 0.00 2.41
57 58 1.535462 GCCTGCACGTATTCACTTTGT 59.465 47.619 0.00 0.00 0.00 2.83
58 59 1.535028 TGCCTGCACGTATTCACTTTG 59.465 47.619 0.00 0.00 0.00 2.77
59 60 1.806542 CTGCCTGCACGTATTCACTTT 59.193 47.619 0.00 0.00 0.00 2.66
60 61 1.442769 CTGCCTGCACGTATTCACTT 58.557 50.000 0.00 0.00 0.00 3.16
61 62 0.391661 CCTGCCTGCACGTATTCACT 60.392 55.000 0.00 0.00 0.00 3.41
62 63 0.391130 TCCTGCCTGCACGTATTCAC 60.391 55.000 0.00 0.00 0.00 3.18
63 64 0.541392 ATCCTGCCTGCACGTATTCA 59.459 50.000 0.00 0.00 0.00 2.57
64 65 2.526304 TATCCTGCCTGCACGTATTC 57.474 50.000 0.00 0.00 0.00 1.75
65 66 2.170607 AGTTATCCTGCCTGCACGTATT 59.829 45.455 0.00 0.00 0.00 1.89
66 67 1.762957 AGTTATCCTGCCTGCACGTAT 59.237 47.619 0.00 0.00 0.00 3.06
67 68 1.134818 CAGTTATCCTGCCTGCACGTA 60.135 52.381 0.00 0.00 33.59 3.57
68 69 0.391661 CAGTTATCCTGCCTGCACGT 60.392 55.000 0.00 0.00 33.59 4.49
69 70 0.108186 TCAGTTATCCTGCCTGCACG 60.108 55.000 0.00 0.00 41.25 5.34
70 71 2.012673 CTTCAGTTATCCTGCCTGCAC 58.987 52.381 0.00 0.00 41.25 4.57
71 72 1.630369 ACTTCAGTTATCCTGCCTGCA 59.370 47.619 0.00 0.00 41.25 4.41
72 73 2.012673 CACTTCAGTTATCCTGCCTGC 58.987 52.381 0.00 0.00 41.25 4.85
73 74 3.055530 ACTCACTTCAGTTATCCTGCCTG 60.056 47.826 0.00 0.00 41.25 4.85
74 75 3.055530 CACTCACTTCAGTTATCCTGCCT 60.056 47.826 0.00 0.00 41.25 4.75
75 76 3.265791 CACTCACTTCAGTTATCCTGCC 58.734 50.000 0.00 0.00 41.25 4.85
76 77 3.931578 ACACTCACTTCAGTTATCCTGC 58.068 45.455 0.00 0.00 41.25 4.85
77 78 5.406780 GTCAACACTCACTTCAGTTATCCTG 59.593 44.000 0.00 0.00 42.97 3.86
78 79 5.511545 GGTCAACACTCACTTCAGTTATCCT 60.512 44.000 0.00 0.00 0.00 3.24
79 80 4.691216 GGTCAACACTCACTTCAGTTATCC 59.309 45.833 0.00 0.00 0.00 2.59
80 81 4.386049 CGGTCAACACTCACTTCAGTTATC 59.614 45.833 0.00 0.00 0.00 1.75
81 82 4.307432 CGGTCAACACTCACTTCAGTTAT 58.693 43.478 0.00 0.00 0.00 1.89
82 83 3.491964 CCGGTCAACACTCACTTCAGTTA 60.492 47.826 0.00 0.00 0.00 2.24
83 84 2.550978 CGGTCAACACTCACTTCAGTT 58.449 47.619 0.00 0.00 0.00 3.16
84 85 1.202533 CCGGTCAACACTCACTTCAGT 60.203 52.381 0.00 0.00 0.00 3.41
85 86 1.068588 TCCGGTCAACACTCACTTCAG 59.931 52.381 0.00 0.00 0.00 3.02
86 87 1.068588 CTCCGGTCAACACTCACTTCA 59.931 52.381 0.00 0.00 0.00 3.02
87 88 1.784525 CTCCGGTCAACACTCACTTC 58.215 55.000 0.00 0.00 0.00 3.01
88 89 0.249911 GCTCCGGTCAACACTCACTT 60.250 55.000 0.00 0.00 0.00 3.16
89 90 1.115930 AGCTCCGGTCAACACTCACT 61.116 55.000 0.00 0.00 0.00 3.41
90 91 0.249911 AAGCTCCGGTCAACACTCAC 60.250 55.000 0.00 0.00 0.00 3.51
91 92 1.272490 CTAAGCTCCGGTCAACACTCA 59.728 52.381 0.00 0.00 0.00 3.41
92 93 1.544691 TCTAAGCTCCGGTCAACACTC 59.455 52.381 0.00 0.00 0.00 3.51
93 94 1.629043 TCTAAGCTCCGGTCAACACT 58.371 50.000 0.00 0.00 0.00 3.55
94 95 2.450609 TTCTAAGCTCCGGTCAACAC 57.549 50.000 0.00 0.00 0.00 3.32
95 96 2.289444 CCTTTCTAAGCTCCGGTCAACA 60.289 50.000 0.00 0.00 0.00 3.33
96 97 2.289506 ACCTTTCTAAGCTCCGGTCAAC 60.290 50.000 0.00 0.00 0.00 3.18
97 98 1.975680 ACCTTTCTAAGCTCCGGTCAA 59.024 47.619 0.00 0.00 0.00 3.18
98 99 1.640917 ACCTTTCTAAGCTCCGGTCA 58.359 50.000 0.00 0.00 0.00 4.02
99 100 2.028385 TCAACCTTTCTAAGCTCCGGTC 60.028 50.000 0.00 0.00 0.00 4.79
100 101 1.975680 TCAACCTTTCTAAGCTCCGGT 59.024 47.619 0.00 0.00 0.00 5.28
101 102 2.742589 GTTCAACCTTTCTAAGCTCCGG 59.257 50.000 0.00 0.00 0.00 5.14
102 103 3.433615 CAGTTCAACCTTTCTAAGCTCCG 59.566 47.826 0.00 0.00 0.00 4.63
103 104 4.390264 ACAGTTCAACCTTTCTAAGCTCC 58.610 43.478 0.00 0.00 0.00 4.70
104 105 6.456501 TCTACAGTTCAACCTTTCTAAGCTC 58.543 40.000 0.00 0.00 0.00 4.09
105 106 6.267928 TCTCTACAGTTCAACCTTTCTAAGCT 59.732 38.462 0.00 0.00 0.00 3.74
106 107 6.456501 TCTCTACAGTTCAACCTTTCTAAGC 58.543 40.000 0.00 0.00 0.00 3.09
107 108 8.888579 TTTCTCTACAGTTCAACCTTTCTAAG 57.111 34.615 0.00 0.00 0.00 2.18
108 109 9.106070 GTTTTCTCTACAGTTCAACCTTTCTAA 57.894 33.333 0.00 0.00 0.00 2.10
109 110 8.262227 TGTTTTCTCTACAGTTCAACCTTTCTA 58.738 33.333 0.00 0.00 0.00 2.10
110 111 7.065923 GTGTTTTCTCTACAGTTCAACCTTTCT 59.934 37.037 0.00 0.00 0.00 2.52
111 112 7.148306 TGTGTTTTCTCTACAGTTCAACCTTTC 60.148 37.037 0.00 0.00 0.00 2.62
112 113 6.657541 TGTGTTTTCTCTACAGTTCAACCTTT 59.342 34.615 0.00 0.00 0.00 3.11
113 114 6.177610 TGTGTTTTCTCTACAGTTCAACCTT 58.822 36.000 0.00 0.00 0.00 3.50
114 115 5.741011 TGTGTTTTCTCTACAGTTCAACCT 58.259 37.500 0.00 0.00 0.00 3.50
115 116 6.255950 GTTGTGTTTTCTCTACAGTTCAACC 58.744 40.000 0.00 0.00 30.22 3.77
116 117 5.957796 CGTTGTGTTTTCTCTACAGTTCAAC 59.042 40.000 0.00 0.00 31.76 3.18
117 118 5.870433 TCGTTGTGTTTTCTCTACAGTTCAA 59.130 36.000 0.00 0.00 0.00 2.69
118 119 5.412640 TCGTTGTGTTTTCTCTACAGTTCA 58.587 37.500 0.00 0.00 0.00 3.18
119 120 5.961395 TCGTTGTGTTTTCTCTACAGTTC 57.039 39.130 0.00 0.00 0.00 3.01
120 121 6.402875 GGTTTCGTTGTGTTTTCTCTACAGTT 60.403 38.462 0.00 0.00 0.00 3.16
121 122 5.064325 GGTTTCGTTGTGTTTTCTCTACAGT 59.936 40.000 0.00 0.00 0.00 3.55
122 123 5.064198 TGGTTTCGTTGTGTTTTCTCTACAG 59.936 40.000 0.00 0.00 0.00 2.74
123 124 4.936411 TGGTTTCGTTGTGTTTTCTCTACA 59.064 37.500 0.00 0.00 0.00 2.74
124 125 5.473796 TGGTTTCGTTGTGTTTTCTCTAC 57.526 39.130 0.00 0.00 0.00 2.59
125 126 5.644636 AGTTGGTTTCGTTGTGTTTTCTCTA 59.355 36.000 0.00 0.00 0.00 2.43
126 127 4.457949 AGTTGGTTTCGTTGTGTTTTCTCT 59.542 37.500 0.00 0.00 0.00 3.10
127 128 4.729595 AGTTGGTTTCGTTGTGTTTTCTC 58.270 39.130 0.00 0.00 0.00 2.87
128 129 4.776795 AGTTGGTTTCGTTGTGTTTTCT 57.223 36.364 0.00 0.00 0.00 2.52
129 130 7.514573 AATTAGTTGGTTTCGTTGTGTTTTC 57.485 32.000 0.00 0.00 0.00 2.29
130 131 7.892778 AAATTAGTTGGTTTCGTTGTGTTTT 57.107 28.000 0.00 0.00 0.00 2.43
131 132 8.983307 TTAAATTAGTTGGTTTCGTTGTGTTT 57.017 26.923 0.00 0.00 0.00 2.83
132 133 9.240159 GATTAAATTAGTTGGTTTCGTTGTGTT 57.760 29.630 0.00 0.00 0.00 3.32
133 134 7.863877 GGATTAAATTAGTTGGTTTCGTTGTGT 59.136 33.333 0.00 0.00 0.00 3.72
134 135 7.863375 TGGATTAAATTAGTTGGTTTCGTTGTG 59.137 33.333 0.00 0.00 0.00 3.33
135 136 7.942990 TGGATTAAATTAGTTGGTTTCGTTGT 58.057 30.769 0.00 0.00 0.00 3.32
136 137 8.980143 ATGGATTAAATTAGTTGGTTTCGTTG 57.020 30.769 0.00 0.00 0.00 4.10
137 138 9.418045 CAATGGATTAAATTAGTTGGTTTCGTT 57.582 29.630 0.00 0.00 0.00 3.85
138 139 8.581578 ACAATGGATTAAATTAGTTGGTTTCGT 58.418 29.630 0.00 0.00 0.00 3.85
139 140 8.980143 ACAATGGATTAAATTAGTTGGTTTCG 57.020 30.769 0.00 0.00 0.00 3.46
147 148 9.816354 GCCATGTTAACAATGGATTAAATTAGT 57.184 29.630 27.36 2.35 37.66 2.24
153 154 6.596309 TGTGCCATGTTAACAATGGATTAA 57.404 33.333 27.36 14.27 37.66 1.40
203 204 5.182570 TCCAATACTACTACGATATTGCGCT 59.817 40.000 9.73 0.00 35.75 5.92
210 211 8.689061 ACACAATTGTCCAATACTACTACGATA 58.311 33.333 8.48 0.00 0.00 2.92
223 224 8.362464 ACTAGACTCTATACACAATTGTCCAA 57.638 34.615 8.48 0.00 37.15 3.53
230 231 7.563924 TGCCCTTAACTAGACTCTATACACAAT 59.436 37.037 0.00 0.00 0.00 2.71
233 234 6.956202 TGCCCTTAACTAGACTCTATACAC 57.044 41.667 0.00 0.00 0.00 2.90
244 245 8.043113 TCTATTATGATGCATGCCCTTAACTAG 58.957 37.037 16.68 15.41 0.00 2.57
250 251 5.638133 ACTTCTATTATGATGCATGCCCTT 58.362 37.500 16.68 7.92 0.00 3.95
253 254 5.336213 CCCAACTTCTATTATGATGCATGCC 60.336 44.000 16.68 0.28 0.00 4.40
261 262 9.573166 CCATATGAAACCCAACTTCTATTATGA 57.427 33.333 3.65 0.00 0.00 2.15
262 263 8.796475 CCCATATGAAACCCAACTTCTATTATG 58.204 37.037 3.65 0.00 0.00 1.90
263 264 7.451566 GCCCATATGAAACCCAACTTCTATTAT 59.548 37.037 3.65 0.00 0.00 1.28
264 265 6.775629 GCCCATATGAAACCCAACTTCTATTA 59.224 38.462 3.65 0.00 0.00 0.98
265 266 5.598417 GCCCATATGAAACCCAACTTCTATT 59.402 40.000 3.65 0.00 0.00 1.73
266 267 5.140454 GCCCATATGAAACCCAACTTCTAT 58.860 41.667 3.65 0.00 0.00 1.98
267 268 4.017958 TGCCCATATGAAACCCAACTTCTA 60.018 41.667 3.65 0.00 0.00 2.10
268 269 3.245586 TGCCCATATGAAACCCAACTTCT 60.246 43.478 3.65 0.00 0.00 2.85
269 270 3.096092 TGCCCATATGAAACCCAACTTC 58.904 45.455 3.65 0.00 0.00 3.01
270 271 3.182887 TGCCCATATGAAACCCAACTT 57.817 42.857 3.65 0.00 0.00 2.66
271 272 2.917713 TGCCCATATGAAACCCAACT 57.082 45.000 3.65 0.00 0.00 3.16
330 331 3.454812 GTCACCATGTACATAACCTCCCT 59.545 47.826 8.32 0.00 0.00 4.20
331 332 3.740141 CGTCACCATGTACATAACCTCCC 60.740 52.174 8.32 0.00 0.00 4.30
333 334 3.863424 CACGTCACCATGTACATAACCTC 59.137 47.826 8.32 0.00 0.00 3.85
336 337 3.852286 TCCACGTCACCATGTACATAAC 58.148 45.455 8.32 4.18 0.00 1.89
338 339 3.093814 ACTCCACGTCACCATGTACATA 58.906 45.455 8.32 0.00 0.00 2.29
339 340 1.899814 ACTCCACGTCACCATGTACAT 59.100 47.619 1.41 1.41 0.00 2.29
340 341 1.334160 ACTCCACGTCACCATGTACA 58.666 50.000 0.00 0.00 0.00 2.90
341 342 2.066262 CAACTCCACGTCACCATGTAC 58.934 52.381 0.00 0.00 0.00 2.90
342 343 1.689813 ACAACTCCACGTCACCATGTA 59.310 47.619 0.00 0.00 0.00 2.29
343 344 0.468226 ACAACTCCACGTCACCATGT 59.532 50.000 0.00 0.00 0.00 3.21
344 345 1.593196 AACAACTCCACGTCACCATG 58.407 50.000 0.00 0.00 0.00 3.66
345 346 1.946768 CAAACAACTCCACGTCACCAT 59.053 47.619 0.00 0.00 0.00 3.55
346 347 1.066071 TCAAACAACTCCACGTCACCA 60.066 47.619 0.00 0.00 0.00 4.17
347 348 1.658994 TCAAACAACTCCACGTCACC 58.341 50.000 0.00 0.00 0.00 4.02
348 349 3.548014 CCAATCAAACAACTCCACGTCAC 60.548 47.826 0.00 0.00 0.00 3.67
352 353 2.616376 TGTCCAATCAAACAACTCCACG 59.384 45.455 0.00 0.00 0.00 4.94
357 358 5.874261 CCTTGTTTTGTCCAATCAAACAACT 59.126 36.000 5.54 0.00 37.10 3.16
375 376 2.435372 TTTCAGTGTGGAGCCTTGTT 57.565 45.000 0.00 0.00 0.00 2.83
379 380 2.957402 TTCATTTCAGTGTGGAGCCT 57.043 45.000 0.00 0.00 0.00 4.58
383 384 3.593442 ACCCTTTCATTTCAGTGTGGA 57.407 42.857 0.00 0.00 0.00 4.02
391 392 8.818622 ACCCTTACTAATTACCCTTTCATTTC 57.181 34.615 0.00 0.00 0.00 2.17
399 400 5.528337 TCCGTAACCCTTACTAATTACCCT 58.472 41.667 0.00 0.00 33.98 4.34
401 402 6.283694 CCTTCCGTAACCCTTACTAATTACC 58.716 44.000 0.00 0.00 33.98 2.85
403 404 6.201591 TCCCTTCCGTAACCCTTACTAATTA 58.798 40.000 0.00 0.00 33.98 1.40
411 412 1.283905 CCATTCCCTTCCGTAACCCTT 59.716 52.381 0.00 0.00 0.00 3.95
419 420 1.135402 CGAAAAAGCCATTCCCTTCCG 60.135 52.381 0.00 0.00 0.00 4.30
455 456 7.450323 ACAAAAATGCTACACCTACAAACCTAT 59.550 33.333 0.00 0.00 0.00 2.57
492 494 7.542890 TCAGTCACAAAACAACACACAATTAT 58.457 30.769 0.00 0.00 0.00 1.28
495 497 5.384063 TCAGTCACAAAACAACACACAAT 57.616 34.783 0.00 0.00 0.00 2.71
514 516 6.435904 AGGCCTATGACTACTTTATAGCTCAG 59.564 42.308 1.29 0.00 0.00 3.35
516 518 6.844097 AGGCCTATGACTACTTTATAGCTC 57.156 41.667 1.29 0.00 0.00 4.09
517 519 9.992442 TTATAGGCCTATGACTACTTTATAGCT 57.008 33.333 31.81 5.72 0.00 3.32
555 557 9.104965 TCGACGAGAAAAACATAAATATGGAAT 57.895 29.630 0.00 0.00 38.00 3.01
614 616 5.671577 GCAAAACCAAACCGAAACGATTTTT 60.672 36.000 0.00 0.00 0.00 1.94
615 617 4.201734 GCAAAACCAAACCGAAACGATTTT 60.202 37.500 0.00 0.00 0.00 1.82
616 618 3.307512 GCAAAACCAAACCGAAACGATTT 59.692 39.130 0.00 0.00 0.00 2.17
617 619 2.861335 GCAAAACCAAACCGAAACGATT 59.139 40.909 0.00 0.00 0.00 3.34
619 621 1.201647 TGCAAAACCAAACCGAAACGA 59.798 42.857 0.00 0.00 0.00 3.85
620 622 1.630148 TGCAAAACCAAACCGAAACG 58.370 45.000 0.00 0.00 0.00 3.60
621 623 4.608073 ATTTGCAAAACCAAACCGAAAC 57.392 36.364 17.19 0.00 37.51 2.78
625 627 4.094146 ACAGAAATTTGCAAAACCAAACCG 59.906 37.500 17.19 3.12 37.51 4.44
626 628 5.559427 ACAGAAATTTGCAAAACCAAACC 57.441 34.783 17.19 1.92 37.51 3.27
792 803 0.114560 TATCCAGGGACCGATCCTCC 59.885 60.000 0.00 0.00 45.46 4.30
801 812 1.137675 GGGTTGTACGTATCCAGGGAC 59.862 57.143 0.00 0.00 0.00 4.46
818 829 3.431207 CGAAGTTGGACGTTATATGGGGT 60.431 47.826 0.00 0.00 0.00 4.95
829 840 3.777925 CTGGCGCGAAGTTGGACG 61.778 66.667 12.10 0.00 0.00 4.79
924 935 1.517257 GAGTGGCGTCCATGTCGAG 60.517 63.158 10.87 0.00 35.28 4.04
925 936 2.571757 GAGTGGCGTCCATGTCGA 59.428 61.111 10.87 0.00 35.28 4.20
956 970 3.009115 ATGGTGGGCAGGCGTAGT 61.009 61.111 0.00 0.00 0.00 2.73
957 971 2.514592 CATGGTGGGCAGGCGTAG 60.515 66.667 0.00 0.00 0.00 3.51
958 972 2.130821 TTTCATGGTGGGCAGGCGTA 62.131 55.000 0.00 0.00 0.00 4.42
961 975 1.598701 GAGTTTCATGGTGGGCAGGC 61.599 60.000 0.00 0.00 0.00 4.85
970 984 2.464459 GCGCGGGAGAGTTTCATGG 61.464 63.158 8.83 0.00 0.00 3.66
1001 1015 4.481463 GTTTGCTGCGTGTGGTATTTATT 58.519 39.130 0.00 0.00 0.00 1.40
1056 1070 0.970427 TGCTAGCTCGTGGATGACCA 60.970 55.000 17.23 0.00 44.76 4.02
1062 1076 2.351244 CCAGGTGCTAGCTCGTGGA 61.351 63.158 37.36 9.19 43.76 4.02
1097 1111 2.897350 GAGGAGGCGGCATTTCGG 60.897 66.667 13.08 0.00 0.00 4.30
1445 1471 3.953775 CCTTCACCACCCACGCCT 61.954 66.667 0.00 0.00 0.00 5.52
1667 1693 2.920912 GTGTCCGGTGTCCCTCCA 60.921 66.667 0.00 0.00 0.00 3.86
1716 1743 2.891461 GATCATGCACGCACGCACAG 62.891 60.000 0.00 0.00 46.56 3.66
1874 1912 8.432359 GGCAGCAACAAAAGTAATAATTGTAAC 58.568 33.333 0.00 0.00 36.33 2.50
1879 1917 7.714813 AGTTTGGCAGCAACAAAAGTAATAATT 59.285 29.630 4.98 0.00 39.29 1.40
1893 1933 1.674359 TTCTTCGAGTTTGGCAGCAA 58.326 45.000 0.00 0.00 0.00 3.91
1897 1937 1.329292 CGTGTTTCTTCGAGTTTGGCA 59.671 47.619 0.00 0.00 0.00 4.92
1932 1972 3.664107 CCAATTCTCCTGAGTCACGAAA 58.336 45.455 0.00 0.00 0.00 3.46
1939 1979 0.976641 TCGTGCCAATTCTCCTGAGT 59.023 50.000 0.00 0.00 0.00 3.41
1968 2008 2.096496 CGGCTGTTGGAGATGCTTAAAG 59.904 50.000 0.00 0.00 0.00 1.85
1969 2009 2.083774 CGGCTGTTGGAGATGCTTAAA 58.916 47.619 0.00 0.00 0.00 1.52
1970 2010 1.737838 CGGCTGTTGGAGATGCTTAA 58.262 50.000 0.00 0.00 0.00 1.85
1971 2011 0.744414 GCGGCTGTTGGAGATGCTTA 60.744 55.000 0.00 0.00 0.00 3.09
1972 2012 2.042831 GCGGCTGTTGGAGATGCTT 61.043 57.895 0.00 0.00 0.00 3.91
1973 2013 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
1974 2014 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
1975 2015 0.739462 TAACGCGGCTGTTGGAGATG 60.739 55.000 12.47 0.00 33.32 2.90
1976 2016 0.178068 ATAACGCGGCTGTTGGAGAT 59.822 50.000 12.47 3.74 33.32 2.75
1977 2017 0.818938 TATAACGCGGCTGTTGGAGA 59.181 50.000 12.47 1.91 33.32 3.71
1978 2018 1.865865 ATATAACGCGGCTGTTGGAG 58.134 50.000 12.47 0.00 33.32 3.86
1979 2019 1.937223 CAATATAACGCGGCTGTTGGA 59.063 47.619 12.47 7.67 33.32 3.53
1980 2020 1.668751 ACAATATAACGCGGCTGTTGG 59.331 47.619 12.47 0.00 33.32 3.77
1981 2021 3.097910 CAACAATATAACGCGGCTGTTG 58.902 45.455 12.47 15.35 38.13 3.33
1982 2022 2.096819 CCAACAATATAACGCGGCTGTT 59.903 45.455 12.47 13.07 35.86 3.16
1983 2023 1.668751 CCAACAATATAACGCGGCTGT 59.331 47.619 12.47 0.87 0.00 4.40
1984 2024 1.937223 TCCAACAATATAACGCGGCTG 59.063 47.619 12.47 0.18 0.00 4.85
1985 2025 2.319136 TCCAACAATATAACGCGGCT 57.681 45.000 12.47 0.00 0.00 5.52
1986 2026 3.619233 ATTCCAACAATATAACGCGGC 57.381 42.857 12.47 0.00 0.00 6.53
1987 2027 5.276161 GCAAAATTCCAACAATATAACGCGG 60.276 40.000 12.47 0.00 0.00 6.46
1988 2028 5.514914 AGCAAAATTCCAACAATATAACGCG 59.485 36.000 3.53 3.53 0.00 6.01
1989 2029 6.885735 AGCAAAATTCCAACAATATAACGC 57.114 33.333 0.00 0.00 0.00 4.84
2054 2094 1.117150 GTGCATGAATGGGCCAAGAT 58.883 50.000 11.89 0.00 0.00 2.40
2113 2153 2.977808 ACTCTCTCCCAACTTTCAGGA 58.022 47.619 0.00 0.00 0.00 3.86
2116 2156 2.172505 TGCAACTCTCTCCCAACTTTCA 59.827 45.455 0.00 0.00 0.00 2.69
2125 2165 2.849294 AAAGAGGTGCAACTCTCTCC 57.151 50.000 33.62 7.05 46.70 3.71
2149 2189 6.266786 TCATACAAGTGGTAGAAGAACTCACA 59.733 38.462 0.00 0.00 34.92 3.58
2155 2195 5.738619 TGCTCATACAAGTGGTAGAAGAA 57.261 39.130 0.00 0.00 34.92 2.52
2363 2425 4.315803 AGTCGTCACGATCCAAAAGAATT 58.684 39.130 1.61 0.00 38.42 2.17
2442 2504 2.831742 CGGCGGCTAGGGTAGACA 60.832 66.667 7.61 0.00 31.54 3.41
2520 2582 0.391263 GCACGTCGAAAGGAGGGATT 60.391 55.000 0.00 0.00 34.85 3.01
2545 2607 0.540597 GAGGCCTGCTGTCCCTTTTT 60.541 55.000 12.00 0.00 0.00 1.94
2581 2643 1.688311 CCCTCTCCCGTACAGGATCAA 60.688 57.143 0.00 0.00 45.00 2.57
2761 2823 1.472878 CCACGATCTCGAACAGGAAGA 59.527 52.381 6.60 0.00 43.02 2.87
2784 2846 8.627208 AGGGCACATACTAGAAATATGAATTG 57.373 34.615 0.00 0.00 34.65 2.32
2792 2854 6.554982 TCACATCTAGGGCACATACTAGAAAT 59.445 38.462 0.00 0.00 46.12 2.17
2820 2882 5.979517 TGTGAACTATCATAGCAGATGAACG 59.020 40.000 5.52 3.20 38.01 3.95


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

AutoCloner maintained by Alex Coulton.