Multiple sequence alignment - TraesCS7B01G056600

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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 TraesCS7B01G056600 chr7B 100.000 4427 0 0 1 4427 59604149 59608575 0.000000e+00 8176.0
1 TraesCS7B01G056600 chr7B 86.301 73 10 0 5 77 169294157 169294229 3.670000e-11 80.5
2 TraesCS7B01G056600 chr7B 93.750 48 3 0 34 81 425224400 425224353 6.140000e-09 73.1
3 TraesCS7B01G056600 chr7B 82.857 70 12 0 1 70 432904393 432904462 3.700000e-06 63.9
4 TraesCS7B01G056600 chrUn 91.797 3316 184 44 1165 4427 91567381 91564101 0.000000e+00 4536.0
5 TraesCS7B01G056600 chrUn 87.621 1034 80 31 155 1165 91568418 91567410 0.000000e+00 1157.0
6 TraesCS7B01G056600 chr7A 94.720 1231 53 10 3141 4367 106201778 106203000 0.000000e+00 1903.0
7 TraesCS7B01G056600 chr7A 90.152 1320 63 25 1165 2445 106199562 106200853 0.000000e+00 1655.0
8 TraesCS7B01G056600 chr7A 91.457 714 43 9 2436 3143 106201007 106201708 0.000000e+00 965.0
9 TraesCS7B01G056600 chr7A 86.829 782 66 23 396 1159 106198765 106199527 0.000000e+00 839.0
10 TraesCS7B01G056600 chr7A 85.714 77 11 0 1 77 481570765 481570841 1.020000e-11 82.4
11 TraesCS7B01G056600 chr7A 86.957 69 9 0 9 77 216829823 216829891 1.320000e-10 78.7
12 TraesCS7B01G056600 chr3B 85.526 76 11 0 1 76 760472700 760472625 3.670000e-11 80.5
13 TraesCS7B01G056600 chr7D 84.416 77 12 0 1 77 416948193 416948269 4.750000e-10 76.8
14 TraesCS7B01G056600 chr6A 84.416 77 12 0 1 77 73668506 73668430 4.750000e-10 76.8


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 TraesCS7B01G056600 chr7B 59604149 59608575 4426 False 8176.0 8176 100.0000 1 4427 1 chr7B.!!$F1 4426
1 TraesCS7B01G056600 chrUn 91564101 91568418 4317 True 2846.5 4536 89.7090 155 4427 2 chrUn.!!$R1 4272
2 TraesCS7B01G056600 chr7A 106198765 106203000 4235 False 1340.5 1903 90.7895 396 4367 4 chr7A.!!$F3 3971

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
37 38 0.10576 TTTGGGGTGGTTGCATGACT 60.106 50.000 0.00 0.0 0.00 3.41 F
1159 1217 0.17927 CGAATTGCACGTTTACGCGA 60.179 50.000 15.93 0.0 44.43 5.87 F
1904 2024 1.06406 GCTTTTGTGTGAACGTGCTCT 59.936 47.619 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1552 0.108186 TGACCAGCCGTGCTAGAATG 60.108 55.0 0.0 0.0 36.40 2.67 R
2752 3069 2.040278 CTCAACCATGAAGGGAGAACCA 59.960 50.0 0.0 0.0 43.89 3.67 R
3681 4078 0.738412 TAGCCAGCCGACGCTTTTAC 60.738 55.0 0.0 0.0 45.55 2.01 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
35 36 1.500474 TTTTTGGGGTGGTTGCATGA 58.500 45.000 0.00 0.00 0.00 3.07
36 37 0.755686 TTTTGGGGTGGTTGCATGAC 59.244 50.000 0.00 0.00 0.00 3.06
37 38 0.105760 TTTGGGGTGGTTGCATGACT 60.106 50.000 0.00 0.00 0.00 3.41
38 39 0.774276 TTGGGGTGGTTGCATGACTA 59.226 50.000 0.00 0.00 0.00 2.59
39 40 0.327924 TGGGGTGGTTGCATGACTAG 59.672 55.000 0.00 0.00 0.00 2.57
40 41 0.394352 GGGGTGGTTGCATGACTAGG 60.394 60.000 0.00 0.00 0.00 3.02
41 42 0.618458 GGGTGGTTGCATGACTAGGA 59.382 55.000 0.00 0.00 0.00 2.94
42 43 1.004277 GGGTGGTTGCATGACTAGGAA 59.996 52.381 0.00 0.00 0.00 3.36
43 44 2.554344 GGGTGGTTGCATGACTAGGAAA 60.554 50.000 0.00 0.00 0.00 3.13
44 45 3.153919 GGTGGTTGCATGACTAGGAAAA 58.846 45.455 0.00 0.00 0.00 2.29
45 46 3.572255 GGTGGTTGCATGACTAGGAAAAA 59.428 43.478 0.00 0.00 0.00 1.94
46 47 4.220602 GGTGGTTGCATGACTAGGAAAAAT 59.779 41.667 0.00 0.00 0.00 1.82
47 48 5.417580 GGTGGTTGCATGACTAGGAAAAATA 59.582 40.000 0.00 0.00 0.00 1.40
48 49 6.404734 GGTGGTTGCATGACTAGGAAAAATAG 60.405 42.308 0.00 0.00 0.00 1.73
49 50 5.652014 TGGTTGCATGACTAGGAAAAATAGG 59.348 40.000 0.00 0.00 0.00 2.57
50 51 5.652452 GGTTGCATGACTAGGAAAAATAGGT 59.348 40.000 0.00 0.00 0.00 3.08
51 52 6.826741 GGTTGCATGACTAGGAAAAATAGGTA 59.173 38.462 0.00 0.00 0.00 3.08
52 53 7.012421 GGTTGCATGACTAGGAAAAATAGGTAG 59.988 40.741 0.00 0.00 0.00 3.18
53 54 7.195374 TGCATGACTAGGAAAAATAGGTAGT 57.805 36.000 0.00 0.00 0.00 2.73
54 55 7.047891 TGCATGACTAGGAAAAATAGGTAGTG 58.952 38.462 0.00 0.00 0.00 2.74
55 56 6.483640 GCATGACTAGGAAAAATAGGTAGTGG 59.516 42.308 0.00 0.00 0.00 4.00
56 57 6.555463 TGACTAGGAAAAATAGGTAGTGGG 57.445 41.667 0.00 0.00 0.00 4.61
57 58 6.027482 TGACTAGGAAAAATAGGTAGTGGGT 58.973 40.000 0.00 0.00 0.00 4.51
58 59 6.502863 TGACTAGGAAAAATAGGTAGTGGGTT 59.497 38.462 0.00 0.00 0.00 4.11
59 60 6.718294 ACTAGGAAAAATAGGTAGTGGGTTG 58.282 40.000 0.00 0.00 0.00 3.77
60 61 5.594199 AGGAAAAATAGGTAGTGGGTTGT 57.406 39.130 0.00 0.00 0.00 3.32
61 62 6.707273 AGGAAAAATAGGTAGTGGGTTGTA 57.293 37.500 0.00 0.00 0.00 2.41
62 63 6.718294 AGGAAAAATAGGTAGTGGGTTGTAG 58.282 40.000 0.00 0.00 0.00 2.74
63 64 5.356190 GGAAAAATAGGTAGTGGGTTGTAGC 59.644 44.000 0.00 0.00 0.00 3.58
64 65 5.774102 AAAATAGGTAGTGGGTTGTAGCT 57.226 39.130 0.00 0.00 0.00 3.32
65 66 6.879367 AAAATAGGTAGTGGGTTGTAGCTA 57.121 37.500 0.00 0.00 34.59 3.32
66 67 7.447510 AAAATAGGTAGTGGGTTGTAGCTAT 57.552 36.000 0.00 0.00 40.19 2.97
67 68 7.447510 AAATAGGTAGTGGGTTGTAGCTATT 57.552 36.000 0.00 7.63 45.38 1.73
68 69 7.447510 AATAGGTAGTGGGTTGTAGCTATTT 57.552 36.000 0.00 0.00 42.90 1.40
69 70 8.557304 AATAGGTAGTGGGTTGTAGCTATTTA 57.443 34.615 0.00 0.00 42.90 1.40
70 71 6.481434 AGGTAGTGGGTTGTAGCTATTTAG 57.519 41.667 0.00 0.00 0.00 1.85
88 89 6.910536 ATTTAGCAATAGAAGACACGAAGG 57.089 37.500 0.00 0.00 0.00 3.46
89 90 2.622436 AGCAATAGAAGACACGAAGGC 58.378 47.619 0.00 0.00 0.00 4.35
90 91 2.028112 AGCAATAGAAGACACGAAGGCA 60.028 45.455 0.00 0.00 0.00 4.75
91 92 2.094417 GCAATAGAAGACACGAAGGCAC 59.906 50.000 0.00 0.00 0.00 5.01
93 94 4.744570 CAATAGAAGACACGAAGGCACTA 58.255 43.478 0.00 0.00 38.49 2.74
94 95 5.352284 CAATAGAAGACACGAAGGCACTAT 58.648 41.667 0.00 0.00 38.49 2.12
95 96 3.238108 AGAAGACACGAAGGCACTATG 57.762 47.619 0.00 0.00 38.49 2.23
96 97 2.563179 AGAAGACACGAAGGCACTATGT 59.437 45.455 0.00 0.00 38.49 2.29
97 98 3.762288 AGAAGACACGAAGGCACTATGTA 59.238 43.478 0.00 0.00 38.49 2.29
98 99 3.505464 AGACACGAAGGCACTATGTAC 57.495 47.619 0.00 0.00 38.49 2.90
99 100 2.165845 AGACACGAAGGCACTATGTACC 59.834 50.000 0.00 0.00 38.49 3.34
100 101 1.206371 ACACGAAGGCACTATGTACCC 59.794 52.381 0.00 0.00 38.49 3.69
101 102 0.828677 ACGAAGGCACTATGTACCCC 59.171 55.000 0.00 0.00 38.49 4.95
102 103 1.120530 CGAAGGCACTATGTACCCCT 58.879 55.000 0.00 0.00 38.49 4.79
103 104 1.068741 CGAAGGCACTATGTACCCCTC 59.931 57.143 0.00 0.00 38.49 4.30
104 105 2.399580 GAAGGCACTATGTACCCCTCT 58.600 52.381 0.00 0.00 38.49 3.69
105 106 3.573695 GAAGGCACTATGTACCCCTCTA 58.426 50.000 0.00 0.00 38.49 2.43
106 107 3.246416 AGGCACTATGTACCCCTCTAG 57.754 52.381 0.00 0.00 36.02 2.43
107 108 1.619332 GGCACTATGTACCCCTCTAGC 59.381 57.143 0.00 0.00 0.00 3.42
108 109 1.269998 GCACTATGTACCCCTCTAGCG 59.730 57.143 0.00 0.00 0.00 4.26
109 110 1.887198 CACTATGTACCCCTCTAGCGG 59.113 57.143 0.00 0.00 0.00 5.52
110 111 0.889306 CTATGTACCCCTCTAGCGGC 59.111 60.000 0.00 0.00 0.00 6.53
111 112 0.186630 TATGTACCCCTCTAGCGGCA 59.813 55.000 1.45 0.00 0.00 5.69
112 113 0.471971 ATGTACCCCTCTAGCGGCAT 60.472 55.000 1.45 0.00 0.00 4.40
113 114 1.367840 GTACCCCTCTAGCGGCATG 59.632 63.158 1.45 0.00 0.00 4.06
114 115 1.837051 TACCCCTCTAGCGGCATGG 60.837 63.158 1.45 0.00 0.00 3.66
115 116 2.306715 TACCCCTCTAGCGGCATGGA 62.307 60.000 1.45 0.00 0.00 3.41
116 117 2.423446 CCCTCTAGCGGCATGGAC 59.577 66.667 1.45 0.00 0.00 4.02
117 118 2.136878 CCCTCTAGCGGCATGGACT 61.137 63.158 1.45 0.00 0.00 3.85
118 119 0.827925 CCCTCTAGCGGCATGGACTA 60.828 60.000 1.45 0.00 0.00 2.59
119 120 0.600557 CCTCTAGCGGCATGGACTAG 59.399 60.000 1.45 0.00 35.71 2.57
120 121 1.610363 CTCTAGCGGCATGGACTAGA 58.390 55.000 1.45 0.00 39.97 2.43
121 122 1.268352 CTCTAGCGGCATGGACTAGAC 59.732 57.143 1.45 0.00 37.94 2.59
122 123 0.315568 CTAGCGGCATGGACTAGACC 59.684 60.000 1.45 4.09 36.33 3.85
123 124 0.396556 TAGCGGCATGGACTAGACCA 60.397 55.000 16.36 16.36 44.41 4.02
124 125 1.220749 GCGGCATGGACTAGACCAA 59.779 57.895 17.88 2.21 43.47 3.67
125 126 0.811616 GCGGCATGGACTAGACCAAG 60.812 60.000 17.88 14.45 43.47 3.61
128 129 2.409948 GCATGGACTAGACCAAGCTT 57.590 50.000 26.84 6.71 46.71 3.74
129 130 2.012673 GCATGGACTAGACCAAGCTTG 58.987 52.381 26.84 19.93 46.71 4.01
130 131 2.012673 CATGGACTAGACCAAGCTTGC 58.987 52.381 21.43 8.45 43.47 4.01
131 132 1.055849 TGGACTAGACCAAGCTTGCA 58.944 50.000 21.43 7.93 36.96 4.08
132 133 1.630369 TGGACTAGACCAAGCTTGCAT 59.370 47.619 21.43 11.04 36.96 3.96
133 134 2.040278 TGGACTAGACCAAGCTTGCATT 59.960 45.455 21.43 10.10 36.96 3.56
134 135 2.680339 GGACTAGACCAAGCTTGCATTC 59.320 50.000 21.43 15.44 0.00 2.67
135 136 3.604582 GACTAGACCAAGCTTGCATTCT 58.395 45.455 21.43 20.95 0.00 2.40
136 137 4.383118 GGACTAGACCAAGCTTGCATTCTA 60.383 45.833 21.43 20.95 0.00 2.10
137 138 5.363939 GACTAGACCAAGCTTGCATTCTAT 58.636 41.667 21.43 13.73 0.00 1.98
138 139 5.121811 ACTAGACCAAGCTTGCATTCTATG 58.878 41.667 21.43 17.62 0.00 2.23
139 140 3.960571 AGACCAAGCTTGCATTCTATGT 58.039 40.909 21.43 10.51 0.00 2.29
140 141 3.944015 AGACCAAGCTTGCATTCTATGTC 59.056 43.478 21.43 18.15 0.00 3.06
141 142 3.019564 ACCAAGCTTGCATTCTATGTCC 58.980 45.455 21.43 0.00 0.00 4.02
142 143 3.285484 CCAAGCTTGCATTCTATGTCCT 58.715 45.455 21.43 0.00 0.00 3.85
143 144 3.698040 CCAAGCTTGCATTCTATGTCCTT 59.302 43.478 21.43 0.00 0.00 3.36
144 145 4.159135 CCAAGCTTGCATTCTATGTCCTTT 59.841 41.667 21.43 0.00 0.00 3.11
145 146 5.337009 CCAAGCTTGCATTCTATGTCCTTTT 60.337 40.000 21.43 0.00 0.00 2.27
146 147 6.127647 CCAAGCTTGCATTCTATGTCCTTTTA 60.128 38.462 21.43 0.00 0.00 1.52
147 148 7.315142 CAAGCTTGCATTCTATGTCCTTTTAA 58.685 34.615 14.65 0.00 0.00 1.52
148 149 7.093322 AGCTTGCATTCTATGTCCTTTTAAG 57.907 36.000 0.00 0.00 0.00 1.85
149 150 6.660949 AGCTTGCATTCTATGTCCTTTTAAGT 59.339 34.615 0.00 0.00 0.00 2.24
150 151 7.177392 AGCTTGCATTCTATGTCCTTTTAAGTT 59.823 33.333 0.00 0.00 0.00 2.66
151 152 8.458843 GCTTGCATTCTATGTCCTTTTAAGTTA 58.541 33.333 0.00 0.00 0.00 2.24
154 155 9.461312 TGCATTCTATGTCCTTTTAAGTTATGT 57.539 29.630 0.00 0.00 0.00 2.29
188 189 9.799106 CATGTTATTCTCTTTTATATCCCCACT 57.201 33.333 0.00 0.00 0.00 4.00
232 234 7.712204 TTATTTCACCACTTCCCTATTTTCC 57.288 36.000 0.00 0.00 0.00 3.13
238 240 7.242359 TCACCACTTCCCTATTTTCCATTTTA 58.758 34.615 0.00 0.00 0.00 1.52
303 307 6.183361 ACGAATACTACTATTTGGGAAGCCAT 60.183 38.462 0.00 0.00 30.38 4.40
305 309 8.041323 CGAATACTACTATTTGGGAAGCCATAT 58.959 37.037 0.00 0.00 0.00 1.78
315 320 8.731591 ATTTGGGAAGCCATATCATCTATTTT 57.268 30.769 0.00 0.00 0.00 1.82
322 327 7.154435 AGCCATATCATCTATTTTCATGCAC 57.846 36.000 0.00 0.00 0.00 4.57
329 334 6.287525 TCATCTATTTTCATGCACGGACATA 58.712 36.000 0.00 0.00 0.00 2.29
332 337 7.566760 TCTATTTTCATGCACGGACATATTT 57.433 32.000 0.00 0.00 0.00 1.40
333 338 7.995289 TCTATTTTCATGCACGGACATATTTT 58.005 30.769 0.00 0.00 0.00 1.82
386 417 9.619316 TTTTGAGACATTGTCATTTTATAACCG 57.381 29.630 18.57 0.00 34.60 4.44
387 418 8.554835 TTGAGACATTGTCATTTTATAACCGA 57.445 30.769 18.57 0.00 34.60 4.69
388 419 8.554835 TGAGACATTGTCATTTTATAACCGAA 57.445 30.769 18.57 0.00 34.60 4.30
389 420 8.447833 TGAGACATTGTCATTTTATAACCGAAC 58.552 33.333 18.57 0.00 34.60 3.95
390 421 7.758495 AGACATTGTCATTTTATAACCGAACC 58.242 34.615 18.57 0.00 34.60 3.62
391 422 7.392113 AGACATTGTCATTTTATAACCGAACCA 59.608 33.333 18.57 0.00 34.60 3.67
392 423 7.535139 ACATTGTCATTTTATAACCGAACCAG 58.465 34.615 0.00 0.00 0.00 4.00
393 424 7.175990 ACATTGTCATTTTATAACCGAACCAGT 59.824 33.333 0.00 0.00 0.00 4.00
394 425 6.730960 TGTCATTTTATAACCGAACCAGTC 57.269 37.500 0.00 0.00 0.00 3.51
395 426 6.469410 TGTCATTTTATAACCGAACCAGTCT 58.531 36.000 0.00 0.00 0.00 3.24
396 427 6.938030 TGTCATTTTATAACCGAACCAGTCTT 59.062 34.615 0.00 0.00 0.00 3.01
397 428 7.446013 TGTCATTTTATAACCGAACCAGTCTTT 59.554 33.333 0.00 0.00 0.00 2.52
398 429 7.961283 GTCATTTTATAACCGAACCAGTCTTTC 59.039 37.037 0.00 0.00 0.00 2.62
399 430 7.662258 TCATTTTATAACCGAACCAGTCTTTCA 59.338 33.333 0.00 0.00 0.00 2.69
400 431 7.989416 TTTTATAACCGAACCAGTCTTTCAT 57.011 32.000 0.00 0.00 0.00 2.57
401 432 7.989416 TTTATAACCGAACCAGTCTTTCATT 57.011 32.000 0.00 0.00 0.00 2.57
402 433 7.989416 TTATAACCGAACCAGTCTTTCATTT 57.011 32.000 0.00 0.00 0.00 2.32
403 434 6.894339 ATAACCGAACCAGTCTTTCATTTT 57.106 33.333 0.00 0.00 0.00 1.82
404 435 4.568152 ACCGAACCAGTCTTTCATTTTG 57.432 40.909 0.00 0.00 0.00 2.44
405 436 4.204012 ACCGAACCAGTCTTTCATTTTGA 58.796 39.130 0.00 0.00 0.00 2.69
406 437 4.642885 ACCGAACCAGTCTTTCATTTTGAA 59.357 37.500 0.00 0.00 34.03 2.69
477 509 1.533625 CATTCGGGTGAGGCTTTTCA 58.466 50.000 0.00 0.00 0.00 2.69
500 532 2.772287 CGGAGCCTTCTTCTTTGTTCT 58.228 47.619 0.00 0.00 0.00 3.01
516 548 2.028125 TTCTTCCCGCTCATAGCCCG 62.028 60.000 0.00 0.00 38.18 6.13
595 627 4.389576 CGTGCCCAGCGCTCAAAC 62.390 66.667 7.13 2.62 36.86 2.93
683 715 2.511600 GTGCATCTTCCCCGTCCG 60.512 66.667 0.00 0.00 0.00 4.79
720 760 2.756283 CTTCCTCCTCCTCGCCGT 60.756 66.667 0.00 0.00 0.00 5.68
722 762 3.283812 TTCCTCCTCCTCGCCGTCT 62.284 63.158 0.00 0.00 0.00 4.18
756 803 3.807538 GCGTCGCGTCCCTACAGA 61.808 66.667 5.77 0.00 0.00 3.41
792 849 2.829458 CGACCGGTCCCCTCTCTC 60.829 72.222 28.52 1.12 0.00 3.20
793 850 2.829458 GACCGGTCCCCTCTCTCG 60.829 72.222 24.75 0.00 0.00 4.04
797 854 4.467107 GGTCCCCTCTCTCGCCCT 62.467 72.222 0.00 0.00 0.00 5.19
798 855 3.151022 GTCCCCTCTCTCGCCCTG 61.151 72.222 0.00 0.00 0.00 4.45
799 856 3.673597 TCCCCTCTCTCGCCCTGT 61.674 66.667 0.00 0.00 0.00 4.00
800 857 2.685380 CCCCTCTCTCGCCCTGTT 60.685 66.667 0.00 0.00 0.00 3.16
805 862 0.456995 CTCTCTCGCCCTGTTTCGAC 60.457 60.000 0.00 0.00 0.00 4.20
810 867 2.943978 CGCCCTGTTTCGACCTCCT 61.944 63.158 0.00 0.00 0.00 3.69
901 958 3.805891 GAGCTCCAGATCTGCCGCC 62.806 68.421 22.93 14.60 0.00 6.13
917 974 2.529619 GCCTTCGGCTCGATTGCTC 61.530 63.158 0.00 0.00 46.69 4.26
923 980 2.102357 GCTCGATTGCTCCGACGA 59.898 61.111 0.00 0.00 32.18 4.20
930 987 1.590238 GATTGCTCCGACGATCTGTTG 59.410 52.381 0.00 0.00 0.00 3.33
949 1006 0.521735 GGATTTTTCGCCTGCTTCGT 59.478 50.000 0.00 0.00 0.00 3.85
969 1026 3.865745 CGTTGAAATCTAATGGCTCTCGT 59.134 43.478 0.00 0.00 0.00 4.18
978 1035 0.670546 ATGGCTCTCGTTGTTGTCGG 60.671 55.000 0.00 0.00 0.00 4.79
988 1045 1.412453 TTGTTGTCGGCAGGTAGGGT 61.412 55.000 0.00 0.00 0.00 4.34
998 1055 3.001406 GGTAGGGTGGTCCGCTGT 61.001 66.667 1.66 0.00 41.52 4.40
1083 1140 3.411351 CGCGTGTTCGGGGTTCTG 61.411 66.667 0.00 0.00 44.34 3.02
1132 1190 0.317160 TTCTCCGCGATTGTCACTGT 59.683 50.000 8.23 0.00 0.00 3.55
1140 1198 1.634702 GATTGTCACTGTCTCCGCTC 58.365 55.000 0.00 0.00 0.00 5.03
1159 1217 0.179270 CGAATTGCACGTTTACGCGA 60.179 50.000 15.93 0.00 44.43 5.87
1194 1281 2.519013 GGCTGACAGTTTTCAGGGAAT 58.481 47.619 3.99 0.00 42.95 3.01
1232 1319 2.455674 TAGATGAGTTTGCGCACTGT 57.544 45.000 11.12 0.00 0.00 3.55
1236 1323 2.162319 TGAGTTTGCGCACTGTCATA 57.838 45.000 11.12 0.00 0.00 2.15
1372 1475 8.143193 AGATTTTTGTTGTCATGCTACAATTCA 58.857 29.630 14.08 3.44 41.10 2.57
1475 1589 2.959707 GTCATCCCTCGGTGAACTCTAT 59.040 50.000 0.00 0.00 0.00 1.98
1487 1601 5.749109 CGGTGAACTCTATCTTGTGTAATCC 59.251 44.000 0.00 0.00 0.00 3.01
1504 1618 2.609427 TCCTGTCATCAGCTGCATAC 57.391 50.000 9.47 7.01 40.09 2.39
1506 1620 3.299503 TCCTGTCATCAGCTGCATACTA 58.700 45.455 9.47 0.00 40.09 1.82
1515 1630 5.440234 TCAGCTGCATACTAACTAGTAGC 57.560 43.478 9.47 0.00 41.62 3.58
1586 1705 5.048083 TGTGGCCAATTTACTGAATCTGAAC 60.048 40.000 7.24 0.00 0.00 3.18
1590 1709 6.587608 GGCCAATTTACTGAATCTGAACTTTG 59.412 38.462 0.00 0.00 0.00 2.77
1639 1758 7.439655 CCATGAAGTACCTCTAGAATTGCTTAC 59.560 40.741 0.00 0.00 0.00 2.34
1649 1768 7.246171 TCTAGAATTGCTTACTTTCCTGACT 57.754 36.000 0.00 0.00 0.00 3.41
1685 1805 4.883585 ACACATCACCTAAGCATGGTTATG 59.116 41.667 17.19 16.33 42.05 1.90
1739 1859 2.736400 GCCTGTGCTGATACAATTTGCC 60.736 50.000 0.00 0.00 33.53 4.52
1904 2024 1.064060 GCTTTTGTGTGAACGTGCTCT 59.936 47.619 0.00 0.00 0.00 4.09
1909 2029 3.592898 TGTGTGAACGTGCTCTATCAT 57.407 42.857 0.00 0.00 0.00 2.45
1972 2118 7.988737 TGAATGTTAGATCATAGGCTGTTTTG 58.011 34.615 0.00 0.00 0.00 2.44
2008 2154 6.044054 AGAGAATGTCCATCATATCACATGGT 59.956 38.462 0.00 0.00 40.59 3.55
2138 2284 6.911250 ATGACACATTTGCATATCCATGAT 57.089 33.333 0.00 0.00 33.67 2.45
2146 2292 4.548451 TGCATATCCATGATCCTGTCTC 57.452 45.455 0.00 0.00 33.67 3.36
2501 2814 8.924303 TCCTGTTATACTTTGCTGATATGTAGT 58.076 33.333 0.00 0.00 0.00 2.73
2531 2844 6.954487 ACTATCACACATGATCATGCAAAT 57.046 33.333 31.17 21.47 42.15 2.32
2546 2859 5.234972 TCATGCAAATGATTAGTGACTAGCG 59.765 40.000 0.00 0.00 0.00 4.26
2547 2860 3.309682 TGCAAATGATTAGTGACTAGCGC 59.690 43.478 0.00 0.00 0.00 5.92
2553 2866 4.871513 TGATTAGTGACTAGCGCCAATAG 58.128 43.478 2.29 1.45 0.00 1.73
2558 2871 7.514784 TTAGTGACTAGCGCCAATAGTATTA 57.485 36.000 2.29 0.00 33.64 0.98
2607 2924 5.757320 ACATGATGAGCAATCTACTTGTAGC 59.243 40.000 0.00 0.00 37.18 3.58
2679 2996 2.288642 ATATGCTGTGGGGGTGGCTG 62.289 60.000 0.00 0.00 0.00 4.85
2681 2998 4.603535 GCTGTGGGGGTGGCTGTT 62.604 66.667 0.00 0.00 0.00 3.16
2711 3028 4.191544 GCTACATGCAGTTCCAGACATTA 58.808 43.478 0.00 0.00 42.31 1.90
2717 3034 4.517285 TGCAGTTCCAGACATTATCTTCC 58.483 43.478 0.00 0.00 34.41 3.46
2748 3065 8.508601 TCTACCTGTTAGATGTTAATCCTCCTA 58.491 37.037 0.00 0.00 31.28 2.94
2750 3067 8.568617 ACCTGTTAGATGTTAATCCTCCTATT 57.431 34.615 0.00 0.00 32.77 1.73
2752 3069 9.853177 CCTGTTAGATGTTAATCCTCCTATTTT 57.147 33.333 0.00 0.00 32.77 1.82
2754 3071 9.627123 TGTTAGATGTTAATCCTCCTATTTTGG 57.373 33.333 0.00 0.00 32.77 3.28
2760 3077 7.116736 TGTTAATCCTCCTATTTTGGTTCTCC 58.883 38.462 0.00 0.00 0.00 3.71
2780 3097 4.030913 TCCCTTCATGGTTGAGTAGTAGG 58.969 47.826 0.00 0.00 32.27 3.18
2781 3098 3.775316 CCCTTCATGGTTGAGTAGTAGGT 59.225 47.826 0.00 0.00 32.27 3.08
2784 3101 5.421056 CCTTCATGGTTGAGTAGTAGGTGTA 59.579 44.000 0.00 0.00 32.27 2.90
2986 3304 4.905429 TGTGCTACATTAAGCTCCTCAAA 58.095 39.130 0.00 0.00 43.19 2.69
3074 3393 2.284417 GTCGGAAGGTTTTAGCGCATAG 59.716 50.000 11.47 0.00 0.00 2.23
3088 3407 4.884247 AGCGCATAGAAAGAATACCCTAC 58.116 43.478 11.47 0.00 0.00 3.18
3129 3448 6.592798 ATTGTTTGTCACATTTGCTTCTTG 57.407 33.333 0.00 0.00 34.43 3.02
3146 3537 5.447010 GCTTCTTGTGCTAAATCTGTAGCTG 60.447 44.000 0.00 0.00 45.65 4.24
3151 3542 7.824289 TCTTGTGCTAAATCTGTAGCTGTATTT 59.176 33.333 0.00 0.00 45.65 1.40
3385 3781 9.632638 AAGGATTTCTACTGTATGTAATGCATT 57.367 29.630 17.56 17.56 38.57 3.56
3411 3807 7.288389 TGTTACTATTATGGTTCCAGGTATCGT 59.712 37.037 0.00 0.00 0.00 3.73
3520 3916 2.111613 TGTCCCCCATTTGAAACATCCT 59.888 45.455 0.00 0.00 0.00 3.24
3562 3958 7.678207 TTGGTTAAGTTCCCCATAACTTTTT 57.322 32.000 7.24 0.00 45.20 1.94
3564 3960 7.070629 TGGTTAAGTTCCCCATAACTTTTTCT 58.929 34.615 7.24 0.00 45.20 2.52
3587 3983 4.461081 TGCCCTATTATGGTTGTGTTTGAC 59.539 41.667 0.00 0.00 0.00 3.18
3681 4078 3.857854 GCATCGTCCTGCACTGCG 61.858 66.667 0.00 0.00 41.87 5.18
3832 4229 2.659757 CGCGTGTTCTTCGTTGAAGATA 59.340 45.455 9.83 0.98 46.20 1.98
3863 4260 4.636648 TCAAAAAGCAGTAACGACCTTTCA 59.363 37.500 0.00 0.00 0.00 2.69
3896 4293 5.806654 ATTGGTAAGGTTTGATTGTGCTT 57.193 34.783 0.00 0.00 0.00 3.91
3987 4384 1.065564 GCTTGCTTCTCTGGGACTGAT 60.066 52.381 0.00 0.00 35.31 2.90
4113 4510 0.528017 CAAGCCTGTCTAGACTGCGA 59.472 55.000 23.01 2.48 35.80 5.10
4114 4511 0.528470 AAGCCTGTCTAGACTGCGAC 59.472 55.000 23.01 13.95 35.80 5.19
4117 4514 1.502190 CTGTCTAGACTGCGACGCA 59.498 57.895 22.99 22.99 36.92 5.24
4142 4539 2.551270 GCAGTTGGCGTCGTTCTG 59.449 61.111 0.00 2.38 0.00 3.02
4183 4580 4.100084 CCCCGACATGCTGCCTGA 62.100 66.667 11.93 0.00 0.00 3.86
4186 4583 1.450848 CCGACATGCTGCCTGATGT 60.451 57.895 11.93 7.81 35.46 3.06
4218 4615 0.532640 TCTGCTTTCTTCACTGCGCA 60.533 50.000 10.98 10.98 0.00 6.09
4262 4660 7.372260 AGCTTATATCTTCCAGTCACATTCT 57.628 36.000 0.00 0.00 0.00 2.40
4325 4723 3.874392 ATAATTTGGTTGAGCCTGCAC 57.126 42.857 0.00 0.00 38.35 4.57
4384 4782 6.785488 GACATTGAAGTGTCAGACATGTTA 57.215 37.500 6.51 0.00 46.04 2.41
4385 4783 7.369803 GACATTGAAGTGTCAGACATGTTAT 57.630 36.000 6.51 0.00 46.04 1.89
4386 4784 8.479313 GACATTGAAGTGTCAGACATGTTATA 57.521 34.615 6.51 0.00 46.04 0.98
4406 4805 9.330063 TGTTATATAACCTTGATCTGCTTTCTG 57.670 33.333 20.35 0.00 35.37 3.02
4409 4808 6.749923 ATAACCTTGATCTGCTTTCTGTTC 57.250 37.500 0.00 0.00 0.00 3.18
4414 4813 5.240183 CCTTGATCTGCTTTCTGTTCTCAAA 59.760 40.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.139853 GTCATGCAACCACCCCAAAAA 59.860 47.619 0.00 0.00 0.00 1.94
17 18 0.755686 GTCATGCAACCACCCCAAAA 59.244 50.000 0.00 0.00 0.00 2.44
18 19 0.105760 AGTCATGCAACCACCCCAAA 60.106 50.000 0.00 0.00 0.00 3.28
19 20 0.774276 TAGTCATGCAACCACCCCAA 59.226 50.000 0.00 0.00 0.00 4.12
20 21 0.327924 CTAGTCATGCAACCACCCCA 59.672 55.000 0.00 0.00 0.00 4.96
21 22 0.394352 CCTAGTCATGCAACCACCCC 60.394 60.000 0.00 0.00 0.00 4.95
22 23 0.618458 TCCTAGTCATGCAACCACCC 59.382 55.000 0.00 0.00 0.00 4.61
23 24 2.489938 TTCCTAGTCATGCAACCACC 57.510 50.000 0.00 0.00 0.00 4.61
24 25 4.846779 TTTTTCCTAGTCATGCAACCAC 57.153 40.909 0.00 0.00 0.00 4.16
25 26 5.652014 CCTATTTTTCCTAGTCATGCAACCA 59.348 40.000 0.00 0.00 0.00 3.67
26 27 5.652452 ACCTATTTTTCCTAGTCATGCAACC 59.348 40.000 0.00 0.00 0.00 3.77
27 28 6.759497 ACCTATTTTTCCTAGTCATGCAAC 57.241 37.500 0.00 0.00 0.00 4.17
28 29 7.552687 CACTACCTATTTTTCCTAGTCATGCAA 59.447 37.037 0.00 0.00 0.00 4.08
29 30 7.047891 CACTACCTATTTTTCCTAGTCATGCA 58.952 38.462 0.00 0.00 0.00 3.96
30 31 6.483640 CCACTACCTATTTTTCCTAGTCATGC 59.516 42.308 0.00 0.00 0.00 4.06
31 32 6.992715 CCCACTACCTATTTTTCCTAGTCATG 59.007 42.308 0.00 0.00 0.00 3.07
32 33 6.677076 ACCCACTACCTATTTTTCCTAGTCAT 59.323 38.462 0.00 0.00 0.00 3.06
33 34 6.027482 ACCCACTACCTATTTTTCCTAGTCA 58.973 40.000 0.00 0.00 0.00 3.41
34 35 6.556974 ACCCACTACCTATTTTTCCTAGTC 57.443 41.667 0.00 0.00 0.00 2.59
35 36 6.273965 ACAACCCACTACCTATTTTTCCTAGT 59.726 38.462 0.00 0.00 0.00 2.57
36 37 6.718294 ACAACCCACTACCTATTTTTCCTAG 58.282 40.000 0.00 0.00 0.00 3.02
37 38 6.707273 ACAACCCACTACCTATTTTTCCTA 57.293 37.500 0.00 0.00 0.00 2.94
38 39 5.594199 ACAACCCACTACCTATTTTTCCT 57.406 39.130 0.00 0.00 0.00 3.36
39 40 5.356190 GCTACAACCCACTACCTATTTTTCC 59.644 44.000 0.00 0.00 0.00 3.13
40 41 6.178324 AGCTACAACCCACTACCTATTTTTC 58.822 40.000 0.00 0.00 0.00 2.29
41 42 6.135819 AGCTACAACCCACTACCTATTTTT 57.864 37.500 0.00 0.00 0.00 1.94
42 43 5.774102 AGCTACAACCCACTACCTATTTT 57.226 39.130 0.00 0.00 0.00 1.82
43 44 7.447510 AATAGCTACAACCCACTACCTATTT 57.552 36.000 0.00 0.00 0.00 1.40
44 45 7.447510 AAATAGCTACAACCCACTACCTATT 57.552 36.000 0.00 0.00 0.00 1.73
45 46 7.256225 GCTAAATAGCTACAACCCACTACCTAT 60.256 40.741 0.00 0.00 45.62 2.57
46 47 6.041296 GCTAAATAGCTACAACCCACTACCTA 59.959 42.308 0.00 0.00 45.62 3.08
47 48 5.163332 GCTAAATAGCTACAACCCACTACCT 60.163 44.000 0.00 0.00 45.62 3.08
48 49 5.055144 GCTAAATAGCTACAACCCACTACC 58.945 45.833 0.00 0.00 45.62 3.18
63 64 7.306866 GCCTTCGTGTCTTCTATTGCTAAATAG 60.307 40.741 0.00 0.00 44.58 1.73
64 65 6.479001 GCCTTCGTGTCTTCTATTGCTAAATA 59.521 38.462 0.00 0.00 0.00 1.40
65 66 5.294552 GCCTTCGTGTCTTCTATTGCTAAAT 59.705 40.000 0.00 0.00 0.00 1.40
66 67 4.630069 GCCTTCGTGTCTTCTATTGCTAAA 59.370 41.667 0.00 0.00 0.00 1.85
67 68 4.181578 GCCTTCGTGTCTTCTATTGCTAA 58.818 43.478 0.00 0.00 0.00 3.09
68 69 3.194755 TGCCTTCGTGTCTTCTATTGCTA 59.805 43.478 0.00 0.00 0.00 3.49
69 70 2.028112 TGCCTTCGTGTCTTCTATTGCT 60.028 45.455 0.00 0.00 0.00 3.91
70 71 2.094417 GTGCCTTCGTGTCTTCTATTGC 59.906 50.000 0.00 0.00 0.00 3.56
71 72 3.589988 AGTGCCTTCGTGTCTTCTATTG 58.410 45.455 0.00 0.00 0.00 1.90
72 73 3.963428 AGTGCCTTCGTGTCTTCTATT 57.037 42.857 0.00 0.00 0.00 1.73
73 74 4.402793 ACATAGTGCCTTCGTGTCTTCTAT 59.597 41.667 0.00 0.00 0.00 1.98
74 75 3.762288 ACATAGTGCCTTCGTGTCTTCTA 59.238 43.478 0.00 0.00 0.00 2.10
75 76 2.563179 ACATAGTGCCTTCGTGTCTTCT 59.437 45.455 0.00 0.00 0.00 2.85
76 77 2.960819 ACATAGTGCCTTCGTGTCTTC 58.039 47.619 0.00 0.00 0.00 2.87
77 78 3.368116 GGTACATAGTGCCTTCGTGTCTT 60.368 47.826 0.00 0.00 35.44 3.01
78 79 2.165845 GGTACATAGTGCCTTCGTGTCT 59.834 50.000 0.00 0.00 35.44 3.41
79 80 2.537401 GGTACATAGTGCCTTCGTGTC 58.463 52.381 0.00 0.00 35.44 3.67
80 81 1.206371 GGGTACATAGTGCCTTCGTGT 59.794 52.381 4.33 0.00 38.37 4.49
81 82 1.472728 GGGGTACATAGTGCCTTCGTG 60.473 57.143 4.33 0.00 38.37 4.35
82 83 0.828677 GGGGTACATAGTGCCTTCGT 59.171 55.000 4.33 0.00 38.37 3.85
83 84 1.068741 GAGGGGTACATAGTGCCTTCG 59.931 57.143 4.33 0.00 38.37 3.79
84 85 2.399580 AGAGGGGTACATAGTGCCTTC 58.600 52.381 4.33 3.48 38.37 3.46
85 86 2.570386 AGAGGGGTACATAGTGCCTT 57.430 50.000 4.33 0.00 38.37 4.35
86 87 2.756919 GCTAGAGGGGTACATAGTGCCT 60.757 54.545 4.33 0.00 38.37 4.75
87 88 1.619332 GCTAGAGGGGTACATAGTGCC 59.381 57.143 0.00 0.00 37.58 5.01
88 89 1.269998 CGCTAGAGGGGTACATAGTGC 59.730 57.143 0.00 0.00 0.00 4.40
89 90 1.887198 CCGCTAGAGGGGTACATAGTG 59.113 57.143 4.27 0.00 42.54 2.74
90 91 2.289592 CCGCTAGAGGGGTACATAGT 57.710 55.000 4.27 0.00 42.54 2.12
99 100 0.827925 TAGTCCATGCCGCTAGAGGG 60.828 60.000 14.91 5.27 0.00 4.30
100 101 0.600557 CTAGTCCATGCCGCTAGAGG 59.399 60.000 8.37 8.37 35.48 3.69
101 102 1.268352 GTCTAGTCCATGCCGCTAGAG 59.732 57.143 15.01 0.00 40.99 2.43
102 103 1.319541 GTCTAGTCCATGCCGCTAGA 58.680 55.000 12.22 12.22 38.91 2.43
103 104 0.315568 GGTCTAGTCCATGCCGCTAG 59.684 60.000 0.64 9.00 34.96 3.42
104 105 0.396556 TGGTCTAGTCCATGCCGCTA 60.397 55.000 4.43 0.00 31.96 4.26
105 106 1.264749 TTGGTCTAGTCCATGCCGCT 61.265 55.000 9.63 0.00 37.33 5.52
106 107 0.811616 CTTGGTCTAGTCCATGCCGC 60.812 60.000 9.63 0.00 37.33 6.53
107 108 0.811616 GCTTGGTCTAGTCCATGCCG 60.812 60.000 26.21 11.22 46.26 5.69
108 109 3.086733 GCTTGGTCTAGTCCATGCC 57.913 57.895 26.21 14.25 46.26 4.40
110 111 2.012673 GCAAGCTTGGTCTAGTCCATG 58.987 52.381 27.10 12.65 37.33 3.66
111 112 1.630369 TGCAAGCTTGGTCTAGTCCAT 59.370 47.619 27.10 0.00 37.33 3.41
112 113 1.055849 TGCAAGCTTGGTCTAGTCCA 58.944 50.000 27.10 11.37 35.49 4.02
113 114 2.409948 ATGCAAGCTTGGTCTAGTCC 57.590 50.000 27.10 8.86 0.00 3.85
114 115 3.604582 AGAATGCAAGCTTGGTCTAGTC 58.395 45.455 27.10 9.58 0.00 2.59
115 116 3.710209 AGAATGCAAGCTTGGTCTAGT 57.290 42.857 27.10 2.97 0.00 2.57
116 117 5.121811 ACATAGAATGCAAGCTTGGTCTAG 58.878 41.667 27.10 1.45 0.00 2.43
117 118 5.102953 ACATAGAATGCAAGCTTGGTCTA 57.897 39.130 27.10 11.36 0.00 2.59
118 119 3.944015 GACATAGAATGCAAGCTTGGTCT 59.056 43.478 27.10 9.78 0.00 3.85
119 120 3.065925 GGACATAGAATGCAAGCTTGGTC 59.934 47.826 27.10 20.49 0.00 4.02
120 121 3.019564 GGACATAGAATGCAAGCTTGGT 58.980 45.455 27.10 13.81 0.00 3.67
121 122 3.285484 AGGACATAGAATGCAAGCTTGG 58.715 45.455 27.10 10.68 0.00 3.61
122 123 4.978083 AAGGACATAGAATGCAAGCTTG 57.022 40.909 22.44 22.44 0.00 4.01
123 124 5.990120 AAAAGGACATAGAATGCAAGCTT 57.010 34.783 0.00 0.00 0.00 3.74
124 125 6.660949 ACTTAAAAGGACATAGAATGCAAGCT 59.339 34.615 0.00 0.00 0.00 3.74
125 126 6.856895 ACTTAAAAGGACATAGAATGCAAGC 58.143 36.000 0.00 0.00 0.00 4.01
128 129 9.461312 ACATAACTTAAAAGGACATAGAATGCA 57.539 29.630 0.00 0.00 0.00 3.96
161 162 9.793259 GTGGGGATATAAAAGAGAATAACATGA 57.207 33.333 0.00 0.00 0.00 3.07
162 163 9.799106 AGTGGGGATATAAAAGAGAATAACATG 57.201 33.333 0.00 0.00 0.00 3.21
200 201 5.452636 GGGAAGTGGTGAAATAAAACAAGCA 60.453 40.000 0.00 0.00 0.00 3.91
201 202 4.988540 GGGAAGTGGTGAAATAAAACAAGC 59.011 41.667 0.00 0.00 0.00 4.01
286 290 7.574021 AGATGATATGGCTTCCCAAATAGTA 57.426 36.000 0.00 0.00 46.14 1.82
287 291 6.460103 AGATGATATGGCTTCCCAAATAGT 57.540 37.500 0.00 0.00 46.14 2.12
288 292 9.471702 AAATAGATGATATGGCTTCCCAAATAG 57.528 33.333 0.00 0.00 46.14 1.73
289 293 9.827198 AAAATAGATGATATGGCTTCCCAAATA 57.173 29.630 0.00 0.00 46.14 1.40
290 294 8.731591 AAAATAGATGATATGGCTTCCCAAAT 57.268 30.769 0.00 0.00 46.14 2.32
294 298 7.630082 GCATGAAAATAGATGATATGGCTTCCC 60.630 40.741 0.00 0.00 0.00 3.97
303 307 6.287525 TGTCCGTGCATGAAAATAGATGATA 58.712 36.000 7.72 0.00 0.00 2.15
305 309 4.512484 TGTCCGTGCATGAAAATAGATGA 58.488 39.130 7.72 0.00 0.00 2.92
368 399 7.535139 ACTGGTTCGGTTATAAAATGACAATG 58.465 34.615 0.00 0.00 0.00 2.82
369 400 7.610305 AGACTGGTTCGGTTATAAAATGACAAT 59.390 33.333 0.00 0.00 0.00 2.71
372 403 6.980051 AGACTGGTTCGGTTATAAAATGAC 57.020 37.500 0.00 0.00 0.00 3.06
374 405 7.812648 TGAAAGACTGGTTCGGTTATAAAATG 58.187 34.615 0.00 0.00 0.00 2.32
380 411 6.488683 TCAAAATGAAAGACTGGTTCGGTTAT 59.511 34.615 0.00 0.00 0.00 1.89
381 412 5.823570 TCAAAATGAAAGACTGGTTCGGTTA 59.176 36.000 0.00 0.00 0.00 2.85
382 413 4.642885 TCAAAATGAAAGACTGGTTCGGTT 59.357 37.500 0.00 0.00 0.00 4.44
383 414 4.204012 TCAAAATGAAAGACTGGTTCGGT 58.796 39.130 0.00 0.00 0.00 4.69
384 415 4.829064 TCAAAATGAAAGACTGGTTCGG 57.171 40.909 0.00 0.00 0.00 4.30
385 416 7.518731 TTTTTCAAAATGAAAGACTGGTTCG 57.481 32.000 5.75 0.00 45.77 3.95
405 436 9.657419 CCCTGTTAAAAATGCTCATCTATTTTT 57.343 29.630 11.08 11.08 44.28 1.94
406 437 8.815912 ACCCTGTTAAAAATGCTCATCTATTTT 58.184 29.630 0.00 0.00 37.92 1.82
453 485 2.966732 GCCTCACCCGAATGGACCA 61.967 63.158 0.00 0.00 37.49 4.02
488 520 2.104111 TGAGCGGGAAGAACAAAGAAGA 59.896 45.455 0.00 0.00 0.00 2.87
494 526 1.406887 GGCTATGAGCGGGAAGAACAA 60.407 52.381 0.00 0.00 43.62 2.83
497 529 1.830145 GGGCTATGAGCGGGAAGAA 59.170 57.895 0.00 0.00 43.62 2.52
500 532 1.816863 GATCGGGCTATGAGCGGGAA 61.817 60.000 0.00 0.00 43.62 3.97
516 548 2.123982 CTGGGCTTGCCCTGGATC 60.124 66.667 28.37 4.47 0.00 3.36
590 622 6.177610 GGATATATTGCTATTCGGGGTTTGA 58.822 40.000 0.00 0.00 0.00 2.69
595 627 5.373812 AAGGGATATATTGCTATTCGGGG 57.626 43.478 0.00 0.00 0.00 5.73
635 667 2.282446 GTGATCGGGAGGGGAGGA 59.718 66.667 0.00 0.00 0.00 3.71
670 702 3.528370 CGAGCGGACGGGGAAGAT 61.528 66.667 0.00 0.00 0.00 2.40
704 736 2.754658 GACGGCGAGGAGGAGGAA 60.755 66.667 16.62 0.00 0.00 3.36
752 799 0.178958 ACCTTCTCCGGTCTGTCTGT 60.179 55.000 0.00 0.00 29.14 3.41
756 803 1.536943 GCTCACCTTCTCCGGTCTGT 61.537 60.000 0.00 0.00 34.29 3.41
781 828 3.151022 CAGGGCGAGAGAGGGGAC 61.151 72.222 0.00 0.00 0.00 4.46
782 829 2.748641 AAACAGGGCGAGAGAGGGGA 62.749 60.000 0.00 0.00 0.00 4.81
789 846 1.874345 GAGGTCGAAACAGGGCGAGA 61.874 60.000 0.00 0.00 37.18 4.04
790 847 1.446272 GAGGTCGAAACAGGGCGAG 60.446 63.158 0.00 0.00 37.18 5.03
791 848 2.654877 GAGGTCGAAACAGGGCGA 59.345 61.111 0.00 0.00 0.00 5.54
792 849 2.434359 GGAGGTCGAAACAGGGCG 60.434 66.667 0.00 0.00 0.00 6.13
793 850 1.079057 GAGGAGGTCGAAACAGGGC 60.079 63.158 0.00 0.00 0.00 5.19
794 851 1.192146 TGGAGGAGGTCGAAACAGGG 61.192 60.000 0.00 0.00 0.00 4.45
795 852 0.685097 TTGGAGGAGGTCGAAACAGG 59.315 55.000 0.00 0.00 0.00 4.00
796 853 2.543777 TTTGGAGGAGGTCGAAACAG 57.456 50.000 0.00 0.00 28.68 3.16
799 856 0.399075 GGGTTTGGAGGAGGTCGAAA 59.601 55.000 0.00 0.00 31.02 3.46
800 857 0.473117 AGGGTTTGGAGGAGGTCGAA 60.473 55.000 0.00 0.00 0.00 3.71
805 862 3.053359 AGATCTAGGGTTTGGAGGAGG 57.947 52.381 0.00 0.00 0.00 4.30
810 867 6.078664 GGAGAGATTAGATCTAGGGTTTGGA 58.921 44.000 2.02 0.00 40.38 3.53
880 937 1.519719 GGCAGATCTGGAGCTCGTT 59.480 57.895 23.89 0.00 0.00 3.85
881 938 2.780094 CGGCAGATCTGGAGCTCGT 61.780 63.158 23.89 0.00 0.00 4.18
901 958 2.233654 CGGAGCAATCGAGCCGAAG 61.234 63.158 0.00 0.00 46.29 3.79
917 974 3.483574 CGAAAAATCCAACAGATCGTCGG 60.484 47.826 0.00 0.00 32.47 4.79
923 980 2.094545 GCAGGCGAAAAATCCAACAGAT 60.095 45.455 0.00 0.00 36.48 2.90
930 987 0.521735 ACGAAGCAGGCGAAAAATCC 59.478 50.000 0.00 0.00 0.00 3.01
949 1006 5.245531 ACAACGAGAGCCATTAGATTTCAA 58.754 37.500 0.00 0.00 0.00 2.69
969 1026 1.373435 CCCTACCTGCCGACAACAA 59.627 57.895 0.00 0.00 0.00 2.83
978 1035 4.468689 GCGGACCACCCTACCTGC 62.469 72.222 0.00 0.00 0.00 4.85
1083 1140 4.732106 CGGATGACTAACCTCCGC 57.268 61.111 0.00 0.00 46.08 5.54
1132 1190 1.805539 CGTGCAATTCGAGCGGAGA 60.806 57.895 0.00 0.00 33.85 3.71
1140 1198 2.243562 CGCGTAAACGTGCAATTCG 58.756 52.632 0.00 0.00 43.06 3.34
1159 1217 2.203070 GCCGTTCCGCCATCTCAT 60.203 61.111 0.00 0.00 0.00 2.90
1177 1264 9.123902 CATTATATCATTCCCTGAAAACTGTCA 57.876 33.333 0.00 0.00 37.44 3.58
1194 1281 7.330262 TCATCTATCGCCAAAGCATTATATCA 58.670 34.615 0.00 0.00 39.83 2.15
1287 1376 4.714308 AGCAGCTAGAATTCTAGAACCTGT 59.286 41.667 36.09 22.24 46.80 4.00
1424 1536 6.186420 TGCTAGAATGCACCCAGATTTATA 57.814 37.500 0.00 0.00 38.12 0.98
1438 1552 0.108186 TGACCAGCCGTGCTAGAATG 60.108 55.000 0.00 0.00 36.40 2.67
1475 1589 4.223700 AGCTGATGACAGGATTACACAAGA 59.776 41.667 0.00 0.00 43.62 3.02
1487 1601 4.691175 AGTTAGTATGCAGCTGATGACAG 58.309 43.478 20.43 0.00 45.91 3.51
1504 1618 6.490381 TGGACATGTATCCAGCTACTAGTTAG 59.510 42.308 0.00 0.00 44.14 2.34
1506 1620 5.208890 TGGACATGTATCCAGCTACTAGTT 58.791 41.667 0.00 0.00 44.14 2.24
1549 1664 5.874897 ATTGGCCACATATTTTGCTGTAT 57.125 34.783 3.88 0.00 0.00 2.29
1586 1705 1.528309 AGTGGGCCGGAACACAAAG 60.528 57.895 24.78 0.00 39.99 2.77
1615 1734 8.312669 AGTAAGCAATTCTAGAGGTACTTCAT 57.687 34.615 7.82 0.00 41.55 2.57
1639 1758 7.168135 GTGTTTATCAAAAGCAAGTCAGGAAAG 59.832 37.037 0.00 0.00 0.00 2.62
1649 1768 6.403866 AGGTGATGTGTTTATCAAAAGCAA 57.596 33.333 0.00 0.00 38.69 3.91
1714 1834 2.391616 TTGTATCAGCACAGGCAGAG 57.608 50.000 0.00 0.00 44.61 3.35
1739 1859 2.283298 AGCAAACTGTATCAGCATCCG 58.717 47.619 0.00 0.00 34.37 4.18
1949 2071 7.944729 ACAAAACAGCCTATGATCTAACATT 57.055 32.000 0.00 0.00 0.00 2.71
1950 2072 7.611467 TGAACAAAACAGCCTATGATCTAACAT 59.389 33.333 0.00 0.00 0.00 2.71
1951 2073 6.939730 TGAACAAAACAGCCTATGATCTAACA 59.060 34.615 0.00 0.00 0.00 2.41
1952 2074 7.119846 ACTGAACAAAACAGCCTATGATCTAAC 59.880 37.037 0.00 0.00 38.74 2.34
1972 2118 6.650807 TGATGGACATTCTCTGTTAACTGAAC 59.349 38.462 15.06 4.59 38.54 3.18
2008 2154 8.655092 GTGAACAAAATCAAATGTCACAAAGAA 58.345 29.630 0.00 0.00 32.65 2.52
2112 2258 7.878036 TCATGGATATGCAAATGTGTCATTAG 58.122 34.615 0.00 0.00 34.21 1.73
2138 2284 3.849002 GCAGATGCAAGAGACAGGA 57.151 52.632 0.00 0.00 41.59 3.86
2466 2779 9.612620 CAGCAAAGTATAACAGGAACTTTTTAG 57.387 33.333 0.00 0.00 40.52 1.85
2467 2780 9.344772 TCAGCAAAGTATAACAGGAACTTTTTA 57.655 29.630 0.00 0.00 40.52 1.52
2501 2814 8.562052 GCATGATCATGTGTGATAGTAATGAAA 58.438 33.333 31.09 0.00 44.96 2.69
2531 2844 3.819564 ATTGGCGCTAGTCACTAATCA 57.180 42.857 7.64 0.00 0.00 2.57
2546 2859 9.748708 TTCAAATTGCAGAATAATACTATTGGC 57.251 29.630 0.00 0.00 0.00 4.52
2553 2866 8.872845 CAAAGGGTTCAAATTGCAGAATAATAC 58.127 33.333 0.00 0.00 0.00 1.89
2558 2871 5.549742 TCAAAGGGTTCAAATTGCAGAAT 57.450 34.783 0.00 0.00 0.00 2.40
2607 2924 6.843069 AATTTTGAAACAAATCAGGGAACG 57.157 33.333 0.00 0.00 0.00 3.95
2711 3028 7.070074 ACATCTAACAGGTAGAAATCGGAAGAT 59.930 37.037 0.00 0.00 46.16 2.40
2717 3034 8.979574 GGATTAACATCTAACAGGTAGAAATCG 58.020 37.037 0.00 0.00 42.24 3.34
2748 3065 4.132122 ACCATGAAGGGAGAACCAAAAT 57.868 40.909 0.00 0.00 43.89 1.82
2750 3067 3.117322 TCAACCATGAAGGGAGAACCAAA 60.117 43.478 0.00 0.00 43.89 3.28
2752 3069 2.040278 CTCAACCATGAAGGGAGAACCA 59.960 50.000 0.00 0.00 43.89 3.67
2754 3071 3.425162 ACTCAACCATGAAGGGAGAAC 57.575 47.619 0.00 0.00 43.89 3.01
2760 3077 4.223032 ACACCTACTACTCAACCATGAAGG 59.777 45.833 0.00 0.00 45.67 3.46
2780 3097 6.975772 TGCAATTACAAACACCTTTTCTACAC 59.024 34.615 0.00 0.00 0.00 2.90
2781 3098 7.101652 TGCAATTACAAACACCTTTTCTACA 57.898 32.000 0.00 0.00 0.00 2.74
2784 3101 5.990996 CCATGCAATTACAAACACCTTTTCT 59.009 36.000 0.00 0.00 0.00 2.52
2860 3177 2.672874 GCATCATTGAGCGTACTTCACA 59.327 45.455 0.00 0.00 0.00 3.58
2869 3186 2.190161 CACAATTGGCATCATTGAGCG 58.810 47.619 16.62 3.59 0.00 5.03
2944 3261 3.133691 CAAGCTCAAGTAGTTCTGCACA 58.866 45.455 0.00 0.00 0.00 4.57
3029 3347 3.756434 TGACTACCCAAAATGCAACTAGC 59.244 43.478 0.00 0.00 45.96 3.42
3044 3362 3.397849 AAACCTTCCGACTTGACTACC 57.602 47.619 0.00 0.00 0.00 3.18
3074 3393 9.057089 CAGATTTGGTATGTAGGGTATTCTTTC 57.943 37.037 0.00 0.00 0.00 2.62
3101 3420 6.826893 AGCAAATGTGACAAACAATAACAC 57.173 33.333 0.00 0.00 43.61 3.32
3361 3756 8.840321 ACAATGCATTACATACAGTAGAAATCC 58.160 33.333 12.53 0.00 38.34 3.01
3385 3781 7.288389 ACGATACCTGGAACCATAATAGTAACA 59.712 37.037 0.00 0.00 0.00 2.41
3434 3830 4.169508 CAGAACACTCTCCAGACATAACG 58.830 47.826 0.00 0.00 0.00 3.18
3520 3916 2.416747 CAAACTCAAGCAGTCGATGGA 58.583 47.619 0.00 0.00 32.30 3.41
3562 3958 4.584638 AACACAACCATAATAGGGCAGA 57.415 40.909 0.00 0.00 0.00 4.26
3564 3960 4.461081 GTCAAACACAACCATAATAGGGCA 59.539 41.667 0.00 0.00 0.00 5.36
3681 4078 0.738412 TAGCCAGCCGACGCTTTTAC 60.738 55.000 0.00 0.00 45.55 2.01
3695 4092 2.027561 ACATAACTGAAAGCCGTAGCCA 60.028 45.455 0.00 0.00 41.25 4.75
3708 4105 6.017400 AGCAAAACCATGAAGACATAACTG 57.983 37.500 0.00 0.00 35.09 3.16
3778 4175 4.337555 GGTCGTCTGCAGGAACTAATACTA 59.662 45.833 15.13 0.00 36.02 1.82
3779 4176 3.130693 GGTCGTCTGCAGGAACTAATACT 59.869 47.826 15.13 0.00 36.02 2.12
3863 4260 7.278875 TCAAACCTTACCAATTTGCAAAAGAT 58.721 30.769 17.19 1.22 34.09 2.40
3896 4293 9.494271 CTAATACTTCCAGAAGCTGCATTTATA 57.506 33.333 7.32 0.00 41.99 0.98
3987 4384 4.159506 GCCATTCAACTAAATACCTTGCCA 59.840 41.667 0.00 0.00 0.00 4.92
4113 4510 1.956170 CAACTGCCGAACTCTGCGT 60.956 57.895 0.00 0.00 0.00 5.24
4114 4511 2.671177 CCAACTGCCGAACTCTGCG 61.671 63.158 0.00 0.00 0.00 5.18
4117 4514 2.357517 CGCCAACTGCCGAACTCT 60.358 61.111 0.00 0.00 36.24 3.24
4142 4539 2.072298 AGTTGAGAACGAAGAGCATGC 58.928 47.619 10.51 10.51 36.23 4.06
4183 4580 4.298103 AGCAGAATGTGGAGAAGAACAT 57.702 40.909 0.00 0.00 39.31 2.71
4186 4583 4.978099 AGAAAGCAGAATGTGGAGAAGAA 58.022 39.130 0.00 0.00 39.31 2.52
4218 4615 3.243907 GCTACCAAGGAGCTCAATCGTAT 60.244 47.826 17.19 0.00 36.96 3.06
4376 4774 8.839310 AGCAGATCAAGGTTATATAACATGTC 57.161 34.615 23.59 18.65 37.92 3.06
4377 4775 9.632638 AAAGCAGATCAAGGTTATATAACATGT 57.367 29.630 23.59 13.36 37.92 3.21
4380 4778 9.330063 CAGAAAGCAGATCAAGGTTATATAACA 57.670 33.333 23.59 6.85 37.92 2.41
4381 4779 9.331282 ACAGAAAGCAGATCAAGGTTATATAAC 57.669 33.333 15.98 15.98 35.50 1.89
4382 4780 9.905713 AACAGAAAGCAGATCAAGGTTATATAA 57.094 29.630 0.00 0.00 0.00 0.98
4384 4782 8.270744 AGAACAGAAAGCAGATCAAGGTTATAT 58.729 33.333 0.00 0.00 0.00 0.86
4385 4783 7.624549 AGAACAGAAAGCAGATCAAGGTTATA 58.375 34.615 0.00 0.00 0.00 0.98
4386 4784 6.479884 AGAACAGAAAGCAGATCAAGGTTAT 58.520 36.000 0.00 0.00 0.00 1.89
4388 4786 4.723309 AGAACAGAAAGCAGATCAAGGTT 58.277 39.130 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.