Multiple sequence alignment - TraesCS2B01G424400

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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 TraesCS2B01G424400 chr2B 100.000 4487 0 0 1 4487 610424436 610419950 0.000000e+00 8287.0
1 TraesCS2B01G424400 chr2D 90.324 1726 115 31 710 2415 518273235 518271542 0.000000e+00 2215.0
2 TraesCS2B01G424400 chr2D 92.138 1539 84 14 2961 4487 518270886 518269373 0.000000e+00 2137.0
3 TraesCS2B01G424400 chr2D 95.021 482 22 2 2443 2923 518271548 518271068 0.000000e+00 756.0
4 TraesCS2B01G424400 chr2D 83.396 530 82 4 169 694 639674929 639675456 1.880000e-133 486.0
5 TraesCS2B01G424400 chr2A 90.435 1265 71 21 1025 2270 662346117 662344884 0.000000e+00 1620.0
6 TraesCS2B01G424400 chr2A 90.849 1213 63 23 814 2016 662346292 662345118 0.000000e+00 1581.0
7 TraesCS2B01G424400 chr2A 89.192 879 67 16 3618 4487 662343474 662342615 0.000000e+00 1072.0
8 TraesCS2B01G424400 chr2A 93.959 629 27 4 2956 3574 662344102 662343475 0.000000e+00 941.0
9 TraesCS2B01G424400 chr2A 94.867 487 24 1 2443 2928 662344587 662344101 0.000000e+00 760.0
10 TraesCS2B01G424400 chr2A 83.519 540 83 4 164 700 66767786 66767250 2.410000e-137 499.0
11 TraesCS2B01G424400 chr2A 83.333 534 83 4 171 700 765574452 765573921 5.220000e-134 488.0
12 TraesCS2B01G424400 chr2A 89.506 162 9 1 2259 2420 662344729 662344576 9.850000e-47 198.0
13 TraesCS2B01G424400 chr2A 90.541 74 5 2 714 785 771756325 771756398 3.690000e-16 97.1
14 TraesCS2B01G424400 chr1A 83.985 537 76 8 170 700 447640061 447639529 1.440000e-139 507.0
15 TraesCS2B01G424400 chr1A 90.667 75 6 1 710 784 550315070 550314997 1.030000e-16 99.0
16 TraesCS2B01G424400 chr6D 83.396 536 83 4 169 700 253754356 253753823 4.030000e-135 492.0
17 TraesCS2B01G424400 chr6D 83.119 545 85 5 171 710 389920564 389921106 1.450000e-134 490.0
18 TraesCS2B01G424400 chr4D 83.459 532 84 2 172 700 504283869 504283339 4.030000e-135 492.0
19 TraesCS2B01G424400 chr4D 83.209 536 80 8 171 700 12696475 12695944 2.430000e-132 483.0
20 TraesCS2B01G424400 chr4D 89.610 77 7 1 710 785 99207542 99207618 3.690000e-16 97.1
21 TraesCS2B01G424400 chr3A 83.488 539 75 12 165 695 134257094 134257626 1.450000e-134 490.0
22 TraesCS2B01G424400 chr5B 90.789 76 5 2 710 783 690864705 690864630 2.860000e-17 100.0
23 TraesCS2B01G424400 chr3B 91.781 73 5 1 710 781 826973881 826973953 2.860000e-17 100.0
24 TraesCS2B01G424400 chrUn 88.750 80 7 2 710 789 126737866 126737943 3.690000e-16 97.1
25 TraesCS2B01G424400 chr5D 88.750 80 8 1 709 787 329504490 329504569 3.690000e-16 97.1
26 TraesCS2B01G424400 chr5A 87.805 82 10 0 710 791 30634835 30634754 3.690000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G424400 chr2B 610419950 610424436 4486 True 8287.000000 8287 100.000000 1 4487 1 chr2B.!!$R1 4486
1 TraesCS2B01G424400 chr2D 518269373 518273235 3862 True 1702.666667 2215 92.494333 710 4487 3 chr2D.!!$R1 3777
2 TraesCS2B01G424400 chr2D 639674929 639675456 527 False 486.000000 486 83.396000 169 694 1 chr2D.!!$F1 525
3 TraesCS2B01G424400 chr2A 662342615 662346292 3677 True 1028.666667 1620 91.468000 814 4487 6 chr2A.!!$R3 3673
4 TraesCS2B01G424400 chr2A 66767250 66767786 536 True 499.000000 499 83.519000 164 700 1 chr2A.!!$R1 536
5 TraesCS2B01G424400 chr2A 765573921 765574452 531 True 488.000000 488 83.333000 171 700 1 chr2A.!!$R2 529
6 TraesCS2B01G424400 chr1A 447639529 447640061 532 True 507.000000 507 83.985000 170 700 1 chr1A.!!$R1 530
7 TraesCS2B01G424400 chr6D 253753823 253754356 533 True 492.000000 492 83.396000 169 700 1 chr6D.!!$R1 531
8 TraesCS2B01G424400 chr6D 389920564 389921106 542 False 490.000000 490 83.119000 171 710 1 chr6D.!!$F1 539
9 TraesCS2B01G424400 chr4D 504283339 504283869 530 True 492.000000 492 83.459000 172 700 1 chr4D.!!$R2 528
10 TraesCS2B01G424400 chr4D 12695944 12696475 531 True 483.000000 483 83.209000 171 700 1 chr4D.!!$R1 529
11 TraesCS2B01G424400 chr3A 134257094 134257626 532 False 490.000000 490 83.488000 165 695 1 chr3A.!!$F1 530

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
566 570 0.511653 CGACGACTTCTCGACTGTCA 59.488 55.0 8.73 0.0 43.06 3.58 F
992 1014 0.706729 GCAACACGCGTACAGAGTAC 59.293 55.0 13.44 0.0 0.00 2.73 F
2249 2300 0.678395 ACTGCCACTCTCACAGACAG 59.322 55.0 0.00 0.0 35.38 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 1991 0.471022 TACCATAGGGCTCATCCGCA 60.471 55.0 0.0 0.0 37.9 5.69 R
2941 3331 0.635009 AAGATACTCCCTCCGTCCCA 59.365 55.0 0.0 0.0 0.0 4.37 R
3737 4139 0.184933 CCTCACAACCACCCCTGAAA 59.815 55.0 0.0 0.0 0.0 2.69 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
20 21 3.462483 TTTAGACTCGCCACAACAAGA 57.538 42.857 0.00 0.00 0.00 3.02
21 22 3.462483 TTAGACTCGCCACAACAAGAA 57.538 42.857 0.00 0.00 0.00 2.52
22 23 2.550830 AGACTCGCCACAACAAGAAT 57.449 45.000 0.00 0.00 0.00 2.40
23 24 3.678056 AGACTCGCCACAACAAGAATA 57.322 42.857 0.00 0.00 0.00 1.75
24 25 4.207891 AGACTCGCCACAACAAGAATAT 57.792 40.909 0.00 0.00 0.00 1.28
25 26 5.339008 AGACTCGCCACAACAAGAATATA 57.661 39.130 0.00 0.00 0.00 0.86
26 27 5.730550 AGACTCGCCACAACAAGAATATAA 58.269 37.500 0.00 0.00 0.00 0.98
27 28 6.170506 AGACTCGCCACAACAAGAATATAAA 58.829 36.000 0.00 0.00 0.00 1.40
28 29 6.653320 AGACTCGCCACAACAAGAATATAAAA 59.347 34.615 0.00 0.00 0.00 1.52
29 30 7.336931 AGACTCGCCACAACAAGAATATAAAAT 59.663 33.333 0.00 0.00 0.00 1.82
30 31 7.250569 ACTCGCCACAACAAGAATATAAAATG 58.749 34.615 0.00 0.00 0.00 2.32
31 32 6.559810 TCGCCACAACAAGAATATAAAATGG 58.440 36.000 0.00 0.00 0.00 3.16
32 33 5.748152 CGCCACAACAAGAATATAAAATGGG 59.252 40.000 0.00 0.00 0.00 4.00
33 34 6.405286 CGCCACAACAAGAATATAAAATGGGA 60.405 38.462 0.00 0.00 0.00 4.37
34 35 7.500141 GCCACAACAAGAATATAAAATGGGAT 58.500 34.615 0.00 0.00 0.00 3.85
35 36 7.439056 GCCACAACAAGAATATAAAATGGGATG 59.561 37.037 0.00 0.00 0.00 3.51
36 37 8.694540 CCACAACAAGAATATAAAATGGGATGA 58.305 33.333 0.00 0.00 0.00 2.92
41 42 9.136323 ACAAGAATATAAAATGGGATGAACTCC 57.864 33.333 0.00 0.00 44.11 3.85
42 43 9.359653 CAAGAATATAAAATGGGATGAACTCCT 57.640 33.333 0.00 0.00 44.28 3.69
43 44 9.579932 AAGAATATAAAATGGGATGAACTCCTC 57.420 33.333 0.00 0.00 44.28 3.71
44 45 8.953665 AGAATATAAAATGGGATGAACTCCTCT 58.046 33.333 0.00 0.00 44.28 3.69
49 50 7.468141 AAAATGGGATGAACTCCTCTAAAAC 57.532 36.000 0.00 0.00 44.28 2.43
50 51 5.779241 ATGGGATGAACTCCTCTAAAACA 57.221 39.130 0.00 0.00 44.28 2.83
51 52 5.576563 TGGGATGAACTCCTCTAAAACAA 57.423 39.130 0.00 0.00 44.28 2.83
52 53 5.947663 TGGGATGAACTCCTCTAAAACAAA 58.052 37.500 0.00 0.00 44.28 2.83
53 54 6.552008 TGGGATGAACTCCTCTAAAACAAAT 58.448 36.000 0.00 0.00 44.28 2.32
54 55 6.659242 TGGGATGAACTCCTCTAAAACAAATC 59.341 38.462 0.00 0.00 44.28 2.17
55 56 6.659242 GGGATGAACTCCTCTAAAACAAATCA 59.341 38.462 0.00 0.00 44.28 2.57
56 57 7.362142 GGGATGAACTCCTCTAAAACAAATCAC 60.362 40.741 0.00 0.00 44.28 3.06
57 58 7.174946 GGATGAACTCCTCTAAAACAAATCACA 59.825 37.037 0.00 0.00 41.29 3.58
58 59 8.641498 ATGAACTCCTCTAAAACAAATCACAT 57.359 30.769 0.00 0.00 0.00 3.21
59 60 7.874940 TGAACTCCTCTAAAACAAATCACATG 58.125 34.615 0.00 0.00 0.00 3.21
60 61 7.719193 TGAACTCCTCTAAAACAAATCACATGA 59.281 33.333 0.00 0.00 0.00 3.07
61 62 8.641498 AACTCCTCTAAAACAAATCACATGAT 57.359 30.769 0.00 0.00 36.07 2.45
62 63 9.739276 AACTCCTCTAAAACAAATCACATGATA 57.261 29.630 0.00 0.00 33.73 2.15
63 64 9.167311 ACTCCTCTAAAACAAATCACATGATAC 57.833 33.333 0.00 0.00 33.73 2.24
64 65 9.166173 CTCCTCTAAAACAAATCACATGATACA 57.834 33.333 0.00 0.00 33.73 2.29
65 66 9.513906 TCCTCTAAAACAAATCACATGATACAA 57.486 29.630 0.00 0.00 33.73 2.41
70 71 8.470040 AAAACAAATCACATGATACAATGAGC 57.530 30.769 0.00 0.00 33.73 4.26
71 72 7.400599 AACAAATCACATGATACAATGAGCT 57.599 32.000 0.00 0.00 33.73 4.09
72 73 8.510243 AACAAATCACATGATACAATGAGCTA 57.490 30.769 0.00 0.00 33.73 3.32
73 74 8.151141 ACAAATCACATGATACAATGAGCTAG 57.849 34.615 0.00 0.00 33.73 3.42
74 75 7.772292 ACAAATCACATGATACAATGAGCTAGT 59.228 33.333 0.00 0.00 33.73 2.57
75 76 9.264719 CAAATCACATGATACAATGAGCTAGTA 57.735 33.333 0.00 0.00 33.73 1.82
76 77 9.486497 AAATCACATGATACAATGAGCTAGTAG 57.514 33.333 0.00 0.00 33.73 2.57
77 78 7.823745 TCACATGATACAATGAGCTAGTAGA 57.176 36.000 0.00 0.00 0.00 2.59
78 79 7.880105 TCACATGATACAATGAGCTAGTAGAG 58.120 38.462 0.00 0.00 0.00 2.43
79 80 7.503902 TCACATGATACAATGAGCTAGTAGAGT 59.496 37.037 0.00 0.00 0.00 3.24
80 81 7.594386 CACATGATACAATGAGCTAGTAGAGTG 59.406 40.741 0.00 0.00 0.00 3.51
81 82 6.641169 TGATACAATGAGCTAGTAGAGTGG 57.359 41.667 0.00 0.00 0.00 4.00
82 83 6.129874 TGATACAATGAGCTAGTAGAGTGGT 58.870 40.000 0.00 0.00 0.00 4.16
83 84 4.727507 ACAATGAGCTAGTAGAGTGGTG 57.272 45.455 0.00 0.00 0.00 4.17
84 85 4.344978 ACAATGAGCTAGTAGAGTGGTGA 58.655 43.478 0.00 0.00 0.00 4.02
85 86 4.158764 ACAATGAGCTAGTAGAGTGGTGAC 59.841 45.833 0.00 0.00 0.00 3.67
86 87 3.722908 TGAGCTAGTAGAGTGGTGACT 57.277 47.619 0.00 0.00 33.98 3.41
87 88 4.035612 TGAGCTAGTAGAGTGGTGACTT 57.964 45.455 0.00 0.00 30.16 3.01
88 89 4.408276 TGAGCTAGTAGAGTGGTGACTTT 58.592 43.478 0.00 0.00 30.16 2.66
89 90 4.833380 TGAGCTAGTAGAGTGGTGACTTTT 59.167 41.667 0.00 0.00 30.16 2.27
90 91 5.304614 TGAGCTAGTAGAGTGGTGACTTTTT 59.695 40.000 0.00 0.00 30.16 1.94
129 130 4.830826 GGTGACCTTTGTTTTCTAGGTG 57.169 45.455 0.00 0.00 42.21 4.00
130 131 3.004419 GGTGACCTTTGTTTTCTAGGTGC 59.996 47.826 0.00 0.00 42.21 5.01
131 132 3.004419 GTGACCTTTGTTTTCTAGGTGCC 59.996 47.826 0.00 0.00 42.21 5.01
132 133 3.219281 GACCTTTGTTTTCTAGGTGCCA 58.781 45.455 0.00 0.00 42.21 4.92
133 134 2.956333 ACCTTTGTTTTCTAGGTGCCAC 59.044 45.455 0.00 0.00 40.68 5.01
134 135 2.955660 CCTTTGTTTTCTAGGTGCCACA 59.044 45.455 0.00 0.00 0.00 4.17
135 136 3.573967 CCTTTGTTTTCTAGGTGCCACAT 59.426 43.478 0.00 0.00 0.00 3.21
136 137 4.321230 CCTTTGTTTTCTAGGTGCCACATC 60.321 45.833 0.00 0.00 0.00 3.06
137 138 3.500448 TGTTTTCTAGGTGCCACATCA 57.500 42.857 0.00 0.00 0.00 3.07
138 139 3.826524 TGTTTTCTAGGTGCCACATCAA 58.173 40.909 0.00 0.00 0.00 2.57
139 140 3.820467 TGTTTTCTAGGTGCCACATCAAG 59.180 43.478 0.00 0.00 0.00 3.02
140 141 2.787473 TTCTAGGTGCCACATCAAGG 57.213 50.000 0.00 0.00 0.00 3.61
141 142 1.951209 TCTAGGTGCCACATCAAGGA 58.049 50.000 0.00 0.00 0.00 3.36
142 143 2.265367 TCTAGGTGCCACATCAAGGAA 58.735 47.619 0.00 0.00 0.00 3.36
143 144 2.846206 TCTAGGTGCCACATCAAGGAAT 59.154 45.455 0.00 0.00 0.00 3.01
144 145 4.037222 TCTAGGTGCCACATCAAGGAATA 58.963 43.478 0.00 0.00 0.00 1.75
145 146 3.737559 AGGTGCCACATCAAGGAATAA 57.262 42.857 0.00 0.00 0.00 1.40
146 147 3.624777 AGGTGCCACATCAAGGAATAAG 58.375 45.455 0.00 0.00 0.00 1.73
147 148 3.266772 AGGTGCCACATCAAGGAATAAGA 59.733 43.478 0.00 0.00 0.00 2.10
148 149 4.079558 AGGTGCCACATCAAGGAATAAGAT 60.080 41.667 0.00 0.00 0.00 2.40
149 150 4.646492 GGTGCCACATCAAGGAATAAGATT 59.354 41.667 0.00 0.00 0.00 2.40
150 151 5.221126 GGTGCCACATCAAGGAATAAGATTC 60.221 44.000 0.00 0.00 0.00 2.52
151 152 5.357878 GTGCCACATCAAGGAATAAGATTCA 59.642 40.000 0.00 0.00 0.00 2.57
152 153 5.357878 TGCCACATCAAGGAATAAGATTCAC 59.642 40.000 1.90 0.00 0.00 3.18
153 154 5.591877 GCCACATCAAGGAATAAGATTCACT 59.408 40.000 1.90 0.00 0.00 3.41
154 155 6.767902 GCCACATCAAGGAATAAGATTCACTA 59.232 38.462 1.90 0.00 0.00 2.74
155 156 7.283127 GCCACATCAAGGAATAAGATTCACTAA 59.717 37.037 1.90 0.00 0.00 2.24
156 157 9.177608 CCACATCAAGGAATAAGATTCACTAAA 57.822 33.333 1.90 0.00 0.00 1.85
158 159 9.401058 ACATCAAGGAATAAGATTCACTAAAGG 57.599 33.333 1.90 0.00 0.00 3.11
159 160 9.401058 CATCAAGGAATAAGATTCACTAAAGGT 57.599 33.333 1.90 0.00 0.00 3.50
160 161 9.981460 ATCAAGGAATAAGATTCACTAAAGGTT 57.019 29.630 1.90 0.00 0.00 3.50
161 162 9.231297 TCAAGGAATAAGATTCACTAAAGGTTG 57.769 33.333 1.90 0.00 0.00 3.77
162 163 9.014297 CAAGGAATAAGATTCACTAAAGGTTGT 57.986 33.333 1.90 0.00 0.00 3.32
258 259 4.766404 AGGGCTTCGTTTTTAGATGTTG 57.234 40.909 0.00 0.00 0.00 3.33
273 274 8.770438 TTTAGATGTTGCTTTGAGTTTTGTTT 57.230 26.923 0.00 0.00 0.00 2.83
282 283 5.639931 GCTTTGAGTTTTGTTTGGGTTTGTA 59.360 36.000 0.00 0.00 0.00 2.41
291 292 2.107950 TTGGGTTTGTATCCTGCTCG 57.892 50.000 0.00 0.00 0.00 5.03
292 293 1.271856 TGGGTTTGTATCCTGCTCGA 58.728 50.000 0.00 0.00 0.00 4.04
299 300 3.953712 TGTATCCTGCTCGAAAAGACA 57.046 42.857 0.00 0.00 0.00 3.41
306 307 2.281517 TGCTCGAAAAGACAAAACGGA 58.718 42.857 0.00 0.00 0.00 4.69
310 311 1.334689 CGAAAAGACAAAACGGAGGCC 60.335 52.381 0.00 0.00 0.00 5.19
372 373 0.955178 ATCTCGATGGTGCGTCTAGG 59.045 55.000 0.00 0.00 0.00 3.02
380 381 1.434622 GGTGCGTCTAGGATCGTCGA 61.435 60.000 0.00 0.00 0.00 4.20
394 395 1.221840 GTCGATGGGCATGTGGAGT 59.778 57.895 0.00 0.00 0.00 3.85
397 398 1.811860 GATGGGCATGTGGAGTTGC 59.188 57.895 0.00 0.00 38.14 4.17
416 417 1.657751 CGTCTCTGGCGGATCTGTCA 61.658 60.000 8.88 8.88 0.00 3.58
491 495 6.333416 TCAGATTTCCTTCTGATCTACGTTG 58.667 40.000 0.00 0.00 45.49 4.10
507 511 4.617520 TGCTCTTCAACGGCGGCA 62.618 61.111 13.24 6.20 0.00 5.69
539 543 1.381191 TGCGCTGGTCCTATGAGGA 60.381 57.895 9.73 0.00 43.43 3.71
557 561 1.199558 GGACTTAGCACGACGACTTCT 59.800 52.381 0.00 0.00 0.00 2.85
566 570 0.511653 CGACGACTTCTCGACTGTCA 59.488 55.000 8.73 0.00 43.06 3.58
591 595 3.849064 CAAGTTTTGCCCGACCCA 58.151 55.556 0.00 0.00 0.00 4.51
611 615 3.125376 GCAAGGGAGGGGCGATGAT 62.125 63.158 0.00 0.00 0.00 2.45
649 653 1.071605 CGCTTCAGTGCTTGTAGTCC 58.928 55.000 0.00 0.00 0.00 3.85
654 658 0.737715 CAGTGCTTGTAGTCCTCGCC 60.738 60.000 0.00 0.00 0.00 5.54
670 674 2.280552 GCCAGGTGGTCTACGGACA 61.281 63.158 0.00 0.00 43.77 4.02
677 681 1.933853 GTGGTCTACGGACATGAATGC 59.066 52.381 0.00 0.00 43.77 3.56
679 683 1.933853 GGTCTACGGACATGAATGCAC 59.066 52.381 0.00 0.00 43.77 4.57
751 755 8.246908 TGTTCGTTGTACTACCATGATTAAAG 57.753 34.615 0.00 0.00 0.00 1.85
901 905 4.985538 ACTTATTTGATCCTCGACGACT 57.014 40.909 0.00 0.00 0.00 4.18
966 988 3.852205 GCGTTTCCTACTGCAAAAGAACC 60.852 47.826 0.00 0.00 0.00 3.62
967 989 3.564225 CGTTTCCTACTGCAAAAGAACCT 59.436 43.478 0.00 0.00 0.00 3.50
968 990 4.554723 CGTTTCCTACTGCAAAAGAACCTG 60.555 45.833 0.00 0.00 0.00 4.00
969 991 4.431416 TTCCTACTGCAAAAGAACCTGA 57.569 40.909 0.00 0.00 0.00 3.86
970 992 4.640771 TCCTACTGCAAAAGAACCTGAT 57.359 40.909 0.00 0.00 0.00 2.90
971 993 5.755409 TCCTACTGCAAAAGAACCTGATA 57.245 39.130 0.00 0.00 0.00 2.15
972 994 6.121776 TCCTACTGCAAAAGAACCTGATAA 57.878 37.500 0.00 0.00 0.00 1.75
973 995 6.173339 TCCTACTGCAAAAGAACCTGATAAG 58.827 40.000 0.00 0.00 0.00 1.73
974 996 4.773323 ACTGCAAAAGAACCTGATAAGC 57.227 40.909 0.00 0.00 0.00 3.09
975 997 4.144297 ACTGCAAAAGAACCTGATAAGCA 58.856 39.130 0.00 0.00 0.00 3.91
976 998 4.584325 ACTGCAAAAGAACCTGATAAGCAA 59.416 37.500 0.00 0.00 0.00 3.91
977 999 4.870363 TGCAAAAGAACCTGATAAGCAAC 58.130 39.130 0.00 0.00 0.00 4.17
992 1014 0.706729 GCAACACGCGTACAGAGTAC 59.293 55.000 13.44 0.00 0.00 2.73
1000 1022 2.554806 CGTACAGAGTACGCCATTCA 57.445 50.000 15.49 0.00 34.07 2.57
1055 1082 0.808755 CAAACCTTCCCGAAATCCCG 59.191 55.000 0.00 0.00 0.00 5.14
1069 1096 1.806496 ATCCCGATCCAGACCATCAA 58.194 50.000 0.00 0.00 0.00 2.57
1121 1151 2.018866 CCGATCGAGCGCAGAATCC 61.019 63.158 19.24 2.07 0.00 3.01
1593 1623 1.458777 ACCAACAGGGACGACTCCA 60.459 57.895 0.00 0.00 38.52 3.86
1759 1789 0.867746 TTGCTTACTGAACTGCTGCG 59.132 50.000 0.00 0.00 0.00 5.18
1760 1790 1.133458 GCTTACTGAACTGCTGCGC 59.867 57.895 0.00 0.00 0.00 6.09
1772 1802 1.925847 CTGCTGCGCAAGTTTGAAAAA 59.074 42.857 13.05 0.00 38.41 1.94
1776 1806 3.001127 GCTGCGCAAGTTTGAAAAATTGA 59.999 39.130 13.05 0.00 44.19 2.57
1777 1807 4.508052 CTGCGCAAGTTTGAAAAATTGAC 58.492 39.130 13.05 10.06 44.19 3.18
1778 1808 3.000277 TGCGCAAGTTTGAAAAATTGACG 60.000 39.130 8.16 18.27 44.19 4.35
1782 1812 5.610124 CGCAAGTTTGAAAAATTGACGATGG 60.610 40.000 17.41 0.00 44.19 3.51
1798 1828 7.631915 TGACGATGGTTACATTATAATCACG 57.368 36.000 0.00 0.00 37.47 4.35
1799 1829 7.427214 TGACGATGGTTACATTATAATCACGA 58.573 34.615 0.00 0.00 37.47 4.35
1801 1831 8.651391 ACGATGGTTACATTATAATCACGAAA 57.349 30.769 0.00 0.00 37.47 3.46
1830 1868 5.048713 AGGATTTTTGTGCTAAGCAGTGTAC 60.049 40.000 0.00 0.00 40.08 2.90
1845 1883 4.155280 GCAGTGTACGATTAACCAAACCAT 59.845 41.667 0.00 0.00 0.00 3.55
1887 1925 1.725641 CGCATTAGGTCTGCTGACAA 58.274 50.000 23.12 11.63 44.61 3.18
1903 1941 9.534565 TCTGCTGACAATGATAGTTATAGTTTC 57.465 33.333 0.00 0.00 0.00 2.78
1905 1943 8.194769 TGCTGACAATGATAGTTATAGTTTCGA 58.805 33.333 0.00 0.00 0.00 3.71
1953 1991 5.834204 AGTGACTTCTTCTGGTACTAACTGT 59.166 40.000 0.00 0.00 0.00 3.55
1956 1994 3.570926 TCTTCTGGTACTAACTGTGCG 57.429 47.619 0.00 0.00 31.78 5.34
1980 2018 5.163237 GGATGAGCCCTATGGTACTTGTTTA 60.163 44.000 0.00 0.00 0.00 2.01
2017 2055 3.116300 CCATGAACACGATTAGAGACGG 58.884 50.000 0.00 0.00 0.00 4.79
2030 2068 3.340814 AGAGACGGTGAGCAATCAAAT 57.659 42.857 0.00 0.00 0.00 2.32
2033 2071 4.154918 AGAGACGGTGAGCAATCAAATTTC 59.845 41.667 0.00 0.00 0.00 2.17
2068 2106 2.606725 GAGAGGACGCAATGAGTTGATG 59.393 50.000 0.00 0.00 37.53 3.07
2073 2111 1.466167 ACGCAATGAGTTGATGTCTGC 59.534 47.619 0.00 0.00 37.53 4.26
2132 2170 8.235359 AGTGGAGTATCTTGTATGGTAGTTAC 57.765 38.462 0.00 0.00 33.73 2.50
2159 2210 7.719483 GGTTTATTACTAAAAACCCATAGGCC 58.281 38.462 0.00 0.00 45.86 5.19
2160 2211 7.342541 GGTTTATTACTAAAAACCCATAGGCCA 59.657 37.037 5.01 0.00 45.86 5.36
2194 2245 1.753073 GAAATTCATCCACAGGGCCAG 59.247 52.381 6.18 0.00 0.00 4.85
2205 2256 1.985895 ACAGGGCCAGTTAGCTAGTTT 59.014 47.619 6.18 0.00 0.00 2.66
2237 2288 1.071699 TCTTACCACTTCCACTGCCAC 59.928 52.381 0.00 0.00 0.00 5.01
2249 2300 0.678395 ACTGCCACTCTCACAGACAG 59.322 55.000 0.00 0.00 35.38 3.51
2290 2506 7.192913 TGCATTTAATCTTACGATTTTGCGAT 58.807 30.769 0.00 0.00 39.30 4.58
2303 2519 6.183360 ACGATTTTGCGATTACCTTAGTTCAG 60.183 38.462 0.00 0.00 34.83 3.02
2415 2631 5.969423 ACTTTGCAAATCCTACATTGGATG 58.031 37.500 13.23 0.00 45.35 3.51
2417 2633 2.358582 TGCAAATCCTACATTGGATGCG 59.641 45.455 0.00 0.00 45.35 4.73
2418 2634 2.618241 GCAAATCCTACATTGGATGCGA 59.382 45.455 0.00 0.00 45.35 5.10
2419 2635 3.254166 GCAAATCCTACATTGGATGCGAT 59.746 43.478 0.00 0.00 45.35 4.58
2420 2636 4.455533 GCAAATCCTACATTGGATGCGATA 59.544 41.667 0.00 0.00 45.35 2.92
2421 2637 5.124457 GCAAATCCTACATTGGATGCGATAT 59.876 40.000 0.00 0.00 45.35 1.63
2422 2638 6.349611 GCAAATCCTACATTGGATGCGATATT 60.350 38.462 0.00 0.00 45.35 1.28
2423 2639 7.596494 CAAATCCTACATTGGATGCGATATTT 58.404 34.615 0.00 0.00 45.35 1.40
2424 2640 7.765695 AATCCTACATTGGATGCGATATTTT 57.234 32.000 0.00 0.00 45.35 1.82
2425 2641 7.765695 ATCCTACATTGGATGCGATATTTTT 57.234 32.000 0.00 0.00 44.48 1.94
2465 2681 7.807977 AATTGGATGCGATTTATTGTACTCT 57.192 32.000 0.00 0.00 0.00 3.24
2507 2723 3.616219 TGTGGTATGCTATGGTTGGAAC 58.384 45.455 0.00 0.00 0.00 3.62
2543 2760 6.818644 TGGAGATCTGTTGCTTAAGTACATTC 59.181 38.462 0.00 8.80 0.00 2.67
2634 2851 6.204882 GCCTAACACTGAAACAGTACAAAGAT 59.795 38.462 4.08 0.00 43.43 2.40
2861 3078 2.837498 TCAATACATCACCGGCATCTG 58.163 47.619 0.00 0.00 0.00 2.90
2933 3323 8.995027 TGCATCACATTTATTTAATACTCCCT 57.005 30.769 0.00 0.00 0.00 4.20
2934 3324 9.066892 TGCATCACATTTATTTAATACTCCCTC 57.933 33.333 0.00 0.00 0.00 4.30
2935 3325 9.066892 GCATCACATTTATTTAATACTCCCTCA 57.933 33.333 0.00 0.00 0.00 3.86
2945 3335 7.699709 TTTAATACTCCCTCACATTATGGGA 57.300 36.000 0.00 0.00 46.78 4.37
2946 3336 5.568620 AATACTCCCTCACATTATGGGAC 57.431 43.478 0.00 0.00 44.37 4.46
2947 3337 1.762957 ACTCCCTCACATTATGGGACG 59.237 52.381 0.00 0.00 44.37 4.79
2948 3338 1.070758 CTCCCTCACATTATGGGACGG 59.929 57.143 6.20 6.20 44.37 4.79
2949 3339 1.128200 CCCTCACATTATGGGACGGA 58.872 55.000 6.64 0.00 43.47 4.69
2950 3340 1.070758 CCCTCACATTATGGGACGGAG 59.929 57.143 6.64 1.15 43.47 4.63
2951 3341 1.070758 CCTCACATTATGGGACGGAGG 59.929 57.143 7.00 6.10 35.03 4.30
2952 3342 1.070758 CTCACATTATGGGACGGAGGG 59.929 57.143 0.00 0.00 0.00 4.30
2953 3343 1.128200 CACATTATGGGACGGAGGGA 58.872 55.000 0.00 0.00 0.00 4.20
2954 3344 1.070758 CACATTATGGGACGGAGGGAG 59.929 57.143 0.00 0.00 0.00 4.30
2955 3345 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2956 3346 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2957 3347 3.173965 CATTATGGGACGGAGGGAGTAT 58.826 50.000 0.00 0.00 0.00 2.12
2958 3348 2.599408 TATGGGACGGAGGGAGTATC 57.401 55.000 0.00 0.00 0.00 2.24
2972 3362 9.726438 CGGAGGGAGTATCTTTAATGAAAATAT 57.274 33.333 0.00 0.00 33.73 1.28
2994 3384 9.816354 AATATTTTCCAACAGAAATTAATCCCG 57.184 29.630 0.00 0.00 43.93 5.14
3063 3454 6.260936 CAGAAGGGTGGTGTATGAATTATGAC 59.739 42.308 0.00 0.00 0.00 3.06
3096 3487 3.627395 TTGTTGTCTCACCTGAGTTGT 57.373 42.857 2.25 0.00 42.60 3.32
3149 3544 1.203994 CAGTCCCAGTTTCGTACCGAT 59.796 52.381 0.00 0.00 35.23 4.18
3185 3580 3.690460 AGGTGAGTTTCCATGGCTTTAG 58.310 45.455 6.96 0.00 0.00 1.85
3304 3704 2.160219 CGTGGAGTGAAATGATGTGTGG 59.840 50.000 0.00 0.00 0.00 4.17
3354 3754 8.400947 GCTTCTCAGCTAATAATCAACAAATCA 58.599 33.333 0.00 0.00 43.51 2.57
3494 3894 6.401047 ACAGGATGATTATGCCATTTTCTG 57.599 37.500 0.00 0.00 39.69 3.02
3523 3924 7.544566 GTCTATGTCTTCCGTAATCTTTGTGAA 59.455 37.037 0.00 0.00 0.00 3.18
3542 3943 7.053316 TGTGAATTTTTCATCTGGTCATTGT 57.947 32.000 0.00 0.00 42.47 2.71
3579 3980 6.090483 AGTAGTAATGGTGATGAATCGAGG 57.910 41.667 0.00 0.00 0.00 4.63
3606 4007 2.700897 AGCACTTGAGGTTACACTCTGT 59.299 45.455 0.00 0.00 38.32 3.41
3607 4008 3.895656 AGCACTTGAGGTTACACTCTGTA 59.104 43.478 0.00 0.00 38.32 2.74
3613 4014 6.207025 ACTTGAGGTTACACTCTGTAGTACTG 59.793 42.308 5.39 1.05 38.32 2.74
3678 4079 9.578439 CTGAAAACAAATCCTTCCTGAAATATC 57.422 33.333 0.00 0.00 0.00 1.63
3683 4084 8.461249 ACAAATCCTTCCTGAAATATCTCATG 57.539 34.615 0.00 0.00 0.00 3.07
3737 4139 1.512156 GGCGTGACGATGGTTTTGGT 61.512 55.000 10.10 0.00 0.00 3.67
3738 4140 0.309612 GCGTGACGATGGTTTTGGTT 59.690 50.000 10.10 0.00 0.00 3.67
3741 4143 2.032302 CGTGACGATGGTTTTGGTTTCA 59.968 45.455 0.00 0.00 0.00 2.69
3898 4301 0.980231 CTCTGGCCTAGAAGGGTGCT 60.980 60.000 3.32 0.00 35.37 4.40
3905 4308 1.553704 CCTAGAAGGGTGCTACGGTTT 59.446 52.381 0.00 0.00 0.00 3.27
3987 4390 4.519540 AATGTGTTTGGCTGGTCAATAC 57.480 40.909 0.00 0.00 0.00 1.89
4008 4411 7.865706 ATACATTGATTTACAACTGTCTCCC 57.134 36.000 0.00 0.00 41.52 4.30
4009 4412 4.695455 ACATTGATTTACAACTGTCTCCCG 59.305 41.667 0.00 0.00 41.52 5.14
4014 4417 2.885135 TACAACTGTCTCCCGGTAGA 57.115 50.000 0.00 0.00 30.42 2.59
4062 4465 2.542020 TGTTGTCTTCAGCGATTCCA 57.458 45.000 0.00 0.00 0.00 3.53
4156 4563 1.875963 CGGGGCGGATAATGATTGC 59.124 57.895 0.00 0.00 0.00 3.56
4208 4615 7.277760 AGTTTGTTAAAATTTGAGACCTTGTGC 59.722 33.333 0.00 0.00 0.00 4.57
4222 4629 2.932614 CCTTGTGCCAAGTAGATTCTCG 59.067 50.000 12.18 0.00 0.00 4.04
4333 4740 4.333649 CGATGCAATAAAGATCCACACACT 59.666 41.667 0.00 0.00 0.00 3.55
4362 4769 3.243359 ACAAATCCCACACCAATCACT 57.757 42.857 0.00 0.00 0.00 3.41
4373 4780 3.753272 ACACCAATCACTTCACACTATGC 59.247 43.478 0.00 0.00 0.00 3.14
4377 4784 5.125356 CCAATCACTTCACACTATGCCATA 58.875 41.667 0.00 0.00 0.00 2.74
4422 4831 3.944015 GCATCTTGCTCCAGAGTACAATT 59.056 43.478 0.00 0.00 40.96 2.32
4452 4861 4.794278 TCTGTAGCCGTTCTGTTCATAA 57.206 40.909 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.462483 TCTTGTTGTGGCGAGTCTAAA 57.538 42.857 0.00 0.00 0.00 1.85
3 4 2.550830 ATTCTTGTTGTGGCGAGTCT 57.449 45.000 0.00 0.00 0.00 3.24
4 5 6.417191 TTTATATTCTTGTTGTGGCGAGTC 57.583 37.500 0.00 0.00 0.00 3.36
5 6 6.811253 TTTTATATTCTTGTTGTGGCGAGT 57.189 33.333 0.00 0.00 0.00 4.18
6 7 6.692681 CCATTTTATATTCTTGTTGTGGCGAG 59.307 38.462 0.00 0.00 0.00 5.03
7 8 6.405286 CCCATTTTATATTCTTGTTGTGGCGA 60.405 38.462 0.00 0.00 0.00 5.54
8 9 5.748152 CCCATTTTATATTCTTGTTGTGGCG 59.252 40.000 0.00 0.00 0.00 5.69
9 10 6.872920 TCCCATTTTATATTCTTGTTGTGGC 58.127 36.000 0.00 0.00 0.00 5.01
10 11 8.694540 TCATCCCATTTTATATTCTTGTTGTGG 58.305 33.333 0.00 0.00 0.00 4.17
15 16 9.136323 GGAGTTCATCCCATTTTATATTCTTGT 57.864 33.333 0.00 0.00 43.01 3.16
32 33 8.099364 TGTGATTTGTTTTAGAGGAGTTCATC 57.901 34.615 0.00 0.00 0.00 2.92
33 34 8.517878 CATGTGATTTGTTTTAGAGGAGTTCAT 58.482 33.333 0.00 0.00 0.00 2.57
34 35 7.719193 TCATGTGATTTGTTTTAGAGGAGTTCA 59.281 33.333 0.00 0.00 0.00 3.18
35 36 8.099364 TCATGTGATTTGTTTTAGAGGAGTTC 57.901 34.615 0.00 0.00 0.00 3.01
36 37 8.641498 ATCATGTGATTTGTTTTAGAGGAGTT 57.359 30.769 0.00 0.00 0.00 3.01
37 38 9.167311 GTATCATGTGATTTGTTTTAGAGGAGT 57.833 33.333 0.19 0.00 36.05 3.85
38 39 9.166173 TGTATCATGTGATTTGTTTTAGAGGAG 57.834 33.333 0.19 0.00 36.05 3.69
39 40 9.513906 TTGTATCATGTGATTTGTTTTAGAGGA 57.486 29.630 0.19 0.00 36.05 3.71
44 45 9.571810 GCTCATTGTATCATGTGATTTGTTTTA 57.428 29.630 0.19 0.00 36.05 1.52
45 46 8.308931 AGCTCATTGTATCATGTGATTTGTTTT 58.691 29.630 0.19 0.00 36.05 2.43
46 47 7.833786 AGCTCATTGTATCATGTGATTTGTTT 58.166 30.769 0.19 0.00 36.05 2.83
47 48 7.400599 AGCTCATTGTATCATGTGATTTGTT 57.599 32.000 0.19 0.00 36.05 2.83
48 49 7.772292 ACTAGCTCATTGTATCATGTGATTTGT 59.228 33.333 0.19 0.00 36.05 2.83
49 50 8.151141 ACTAGCTCATTGTATCATGTGATTTG 57.849 34.615 0.19 0.00 36.05 2.32
50 51 9.486497 CTACTAGCTCATTGTATCATGTGATTT 57.514 33.333 0.19 0.00 36.05 2.17
51 52 8.864087 TCTACTAGCTCATTGTATCATGTGATT 58.136 33.333 0.19 0.00 36.05 2.57
52 53 8.414629 TCTACTAGCTCATTGTATCATGTGAT 57.585 34.615 0.00 0.68 38.51 3.06
53 54 7.503902 ACTCTACTAGCTCATTGTATCATGTGA 59.496 37.037 0.00 0.00 0.00 3.58
54 55 7.594386 CACTCTACTAGCTCATTGTATCATGTG 59.406 40.741 0.00 0.00 0.00 3.21
55 56 7.255766 CCACTCTACTAGCTCATTGTATCATGT 60.256 40.741 0.00 0.00 0.00 3.21
56 57 7.089538 CCACTCTACTAGCTCATTGTATCATG 58.910 42.308 0.00 0.00 0.00 3.07
57 58 6.780031 ACCACTCTACTAGCTCATTGTATCAT 59.220 38.462 0.00 0.00 0.00 2.45
58 59 6.039829 CACCACTCTACTAGCTCATTGTATCA 59.960 42.308 0.00 0.00 0.00 2.15
59 60 6.263392 TCACCACTCTACTAGCTCATTGTATC 59.737 42.308 0.00 0.00 0.00 2.24
60 61 6.039941 GTCACCACTCTACTAGCTCATTGTAT 59.960 42.308 0.00 0.00 0.00 2.29
61 62 5.357314 GTCACCACTCTACTAGCTCATTGTA 59.643 44.000 0.00 0.00 0.00 2.41
62 63 4.158764 GTCACCACTCTACTAGCTCATTGT 59.841 45.833 0.00 0.00 0.00 2.71
63 64 4.400884 AGTCACCACTCTACTAGCTCATTG 59.599 45.833 0.00 0.00 0.00 2.82
64 65 4.605183 AGTCACCACTCTACTAGCTCATT 58.395 43.478 0.00 0.00 0.00 2.57
65 66 4.243793 AGTCACCACTCTACTAGCTCAT 57.756 45.455 0.00 0.00 0.00 2.90
66 67 3.722908 AGTCACCACTCTACTAGCTCA 57.277 47.619 0.00 0.00 0.00 4.26
67 68 5.394224 AAAAGTCACCACTCTACTAGCTC 57.606 43.478 0.00 0.00 29.93 4.09
68 69 5.810080 AAAAAGTCACCACTCTACTAGCT 57.190 39.130 0.00 0.00 29.93 3.32
100 101 3.190391 AAAGGTCACCCCCACCCC 61.190 66.667 0.00 0.00 33.96 4.95
101 102 2.117423 CAAAGGTCACCCCCACCC 59.883 66.667 0.00 0.00 33.96 4.61
102 103 0.397957 AAACAAAGGTCACCCCCACC 60.398 55.000 0.00 0.00 0.00 4.61
103 104 1.411246 GAAAACAAAGGTCACCCCCAC 59.589 52.381 0.00 0.00 0.00 4.61
104 105 1.289530 AGAAAACAAAGGTCACCCCCA 59.710 47.619 0.00 0.00 0.00 4.96
105 106 2.082140 AGAAAACAAAGGTCACCCCC 57.918 50.000 0.00 0.00 0.00 5.40
106 107 3.154710 CCTAGAAAACAAAGGTCACCCC 58.845 50.000 0.00 0.00 0.00 4.95
107 108 3.568430 CACCTAGAAAACAAAGGTCACCC 59.432 47.826 0.00 0.00 41.75 4.61
108 109 3.004419 GCACCTAGAAAACAAAGGTCACC 59.996 47.826 0.00 0.00 41.75 4.02
109 110 3.004419 GGCACCTAGAAAACAAAGGTCAC 59.996 47.826 0.00 0.00 41.75 3.67
110 111 3.219281 GGCACCTAGAAAACAAAGGTCA 58.781 45.455 0.00 0.00 41.75 4.02
111 112 3.004419 GTGGCACCTAGAAAACAAAGGTC 59.996 47.826 6.29 0.00 41.75 3.85
112 113 2.956333 GTGGCACCTAGAAAACAAAGGT 59.044 45.455 6.29 0.00 44.54 3.50
113 114 2.955660 TGTGGCACCTAGAAAACAAAGG 59.044 45.455 16.26 0.00 36.42 3.11
114 115 4.278170 TGATGTGGCACCTAGAAAACAAAG 59.722 41.667 16.26 0.00 0.00 2.77
115 116 4.211125 TGATGTGGCACCTAGAAAACAAA 58.789 39.130 16.26 0.00 0.00 2.83
116 117 3.826524 TGATGTGGCACCTAGAAAACAA 58.173 40.909 16.26 0.00 0.00 2.83
117 118 3.500448 TGATGTGGCACCTAGAAAACA 57.500 42.857 16.26 0.00 0.00 2.83
118 119 3.191371 CCTTGATGTGGCACCTAGAAAAC 59.809 47.826 16.26 0.00 0.00 2.43
119 120 3.073798 TCCTTGATGTGGCACCTAGAAAA 59.926 43.478 16.26 0.00 0.00 2.29
120 121 2.642311 TCCTTGATGTGGCACCTAGAAA 59.358 45.455 16.26 1.92 0.00 2.52
121 122 2.265367 TCCTTGATGTGGCACCTAGAA 58.735 47.619 16.26 0.00 0.00 2.10
122 123 1.951209 TCCTTGATGTGGCACCTAGA 58.049 50.000 16.26 0.00 0.00 2.43
123 124 2.787473 TTCCTTGATGTGGCACCTAG 57.213 50.000 16.26 6.76 0.00 3.02
124 125 4.473196 TCTTATTCCTTGATGTGGCACCTA 59.527 41.667 16.26 0.00 0.00 3.08
125 126 3.266772 TCTTATTCCTTGATGTGGCACCT 59.733 43.478 16.26 4.83 0.00 4.00
126 127 3.620488 TCTTATTCCTTGATGTGGCACC 58.380 45.455 16.26 0.43 0.00 5.01
127 128 5.357878 TGAATCTTATTCCTTGATGTGGCAC 59.642 40.000 11.55 11.55 0.00 5.01
128 129 5.357878 GTGAATCTTATTCCTTGATGTGGCA 59.642 40.000 0.00 0.00 0.00 4.92
129 130 5.591877 AGTGAATCTTATTCCTTGATGTGGC 59.408 40.000 0.00 0.00 0.00 5.01
130 131 8.737168 TTAGTGAATCTTATTCCTTGATGTGG 57.263 34.615 0.00 0.00 0.00 4.17
132 133 9.401058 CCTTTAGTGAATCTTATTCCTTGATGT 57.599 33.333 0.00 0.00 0.00 3.06
133 134 9.401058 ACCTTTAGTGAATCTTATTCCTTGATG 57.599 33.333 0.00 0.00 0.00 3.07
134 135 9.981460 AACCTTTAGTGAATCTTATTCCTTGAT 57.019 29.630 0.00 0.00 0.00 2.57
135 136 9.231297 CAACCTTTAGTGAATCTTATTCCTTGA 57.769 33.333 0.00 0.00 0.00 3.02
136 137 9.014297 ACAACCTTTAGTGAATCTTATTCCTTG 57.986 33.333 0.00 0.00 0.00 3.61
137 138 9.232473 GACAACCTTTAGTGAATCTTATTCCTT 57.768 33.333 0.00 0.00 0.00 3.36
138 139 7.549488 CGACAACCTTTAGTGAATCTTATTCCT 59.451 37.037 0.00 0.00 0.00 3.36
139 140 7.676572 GCGACAACCTTTAGTGAATCTTATTCC 60.677 40.741 0.00 0.00 0.00 3.01
140 141 7.180748 GCGACAACCTTTAGTGAATCTTATTC 58.819 38.462 0.00 0.00 0.00 1.75
141 142 6.093633 GGCGACAACCTTTAGTGAATCTTATT 59.906 38.462 0.00 0.00 0.00 1.40
142 143 5.585047 GGCGACAACCTTTAGTGAATCTTAT 59.415 40.000 0.00 0.00 0.00 1.73
143 144 4.933400 GGCGACAACCTTTAGTGAATCTTA 59.067 41.667 0.00 0.00 0.00 2.10
144 145 3.751698 GGCGACAACCTTTAGTGAATCTT 59.248 43.478 0.00 0.00 0.00 2.40
145 146 3.244422 TGGCGACAACCTTTAGTGAATCT 60.244 43.478 0.00 0.00 37.44 2.40
146 147 3.071479 TGGCGACAACCTTTAGTGAATC 58.929 45.455 0.00 0.00 37.44 2.52
147 148 2.812011 GTGGCGACAACCTTTAGTGAAT 59.188 45.455 0.00 0.00 46.06 2.57
148 149 2.215196 GTGGCGACAACCTTTAGTGAA 58.785 47.619 0.00 0.00 46.06 3.18
149 150 1.541670 GGTGGCGACAACCTTTAGTGA 60.542 52.381 0.00 0.00 44.45 3.41
150 151 0.872388 GGTGGCGACAACCTTTAGTG 59.128 55.000 0.00 0.00 44.45 2.74
151 152 3.317449 GGTGGCGACAACCTTTAGT 57.683 52.632 0.00 0.00 44.45 2.24
159 160 4.980805 GCAGACCGGTGGCGACAA 62.981 66.667 14.63 0.00 46.06 3.18
206 207 3.127533 GCCAAGATCAACCGCGCT 61.128 61.111 5.56 0.00 0.00 5.92
231 232 0.822121 AAAAACGAAGCCCTTCCGCT 60.822 50.000 2.66 0.00 42.22 5.52
258 259 4.454161 ACAAACCCAAACAAAACTCAAAGC 59.546 37.500 0.00 0.00 0.00 3.51
273 274 1.271856 TCGAGCAGGATACAAACCCA 58.728 50.000 0.00 0.00 41.41 4.51
282 283 3.058914 CGTTTTGTCTTTTCGAGCAGGAT 60.059 43.478 0.00 0.00 0.00 3.24
291 292 1.334689 CGGCCTCCGTTTTGTCTTTTC 60.335 52.381 0.00 0.00 42.73 2.29
292 293 0.666374 CGGCCTCCGTTTTGTCTTTT 59.334 50.000 0.00 0.00 42.73 2.27
306 307 2.467880 TCATCTTTAAGGAGACGGCCT 58.532 47.619 0.00 0.00 40.93 5.19
310 311 8.494016 AACCTTATTTCATCTTTAAGGAGACG 57.506 34.615 13.40 0.00 43.03 4.18
312 313 9.892130 GAGAACCTTATTTCATCTTTAAGGAGA 57.108 33.333 13.40 0.00 43.03 3.71
353 354 0.955178 CCTAGACGCACCATCGAGAT 59.045 55.000 0.00 0.00 0.00 2.75
372 373 1.224069 CCACATGCCCATCGACGATC 61.224 60.000 7.54 0.00 0.00 3.69
380 381 2.048023 CGCAACTCCACATGCCCAT 61.048 57.895 0.00 0.00 39.39 4.00
394 395 2.184322 GATCCGCCAGAGACGCAA 59.816 61.111 0.00 0.00 0.00 4.85
397 398 1.064946 GACAGATCCGCCAGAGACG 59.935 63.158 0.00 0.00 0.00 4.18
416 417 2.092212 AGATCCGAGCAAATCCACCAAT 60.092 45.455 0.00 0.00 0.00 3.16
457 458 5.303971 AGAAGGAAATCTGAAGACACACAG 58.696 41.667 0.00 0.00 35.72 3.66
491 495 2.200170 AATTGCCGCCGTTGAAGAGC 62.200 55.000 0.00 0.00 0.00 4.09
507 511 1.032014 AGCGCACCAGAACAACAATT 58.968 45.000 11.47 0.00 0.00 2.32
539 543 1.136029 CGAGAAGTCGTCGTGCTAAGT 60.136 52.381 0.00 0.00 41.57 2.24
649 653 2.490217 CGTAGACCACCTGGCGAG 59.510 66.667 0.00 0.00 39.32 5.03
654 658 1.182667 TCATGTCCGTAGACCACCTG 58.817 55.000 0.00 0.00 42.81 4.00
717 721 7.604549 TGGTAGTACAACGAACATCAGAAATA 58.395 34.615 2.06 0.00 0.00 1.40
730 734 8.642908 TCATCTTTAATCATGGTAGTACAACG 57.357 34.615 2.06 0.00 0.00 4.10
966 988 1.989864 TGTACGCGTGTTGCTTATCAG 59.010 47.619 24.59 0.00 43.27 2.90
967 989 1.989864 CTGTACGCGTGTTGCTTATCA 59.010 47.619 24.59 5.97 43.27 2.15
968 990 2.256174 TCTGTACGCGTGTTGCTTATC 58.744 47.619 24.59 1.55 43.27 1.75
969 991 2.259618 CTCTGTACGCGTGTTGCTTAT 58.740 47.619 24.59 0.00 43.27 1.73
970 992 1.001048 ACTCTGTACGCGTGTTGCTTA 60.001 47.619 24.59 0.00 43.27 3.09
971 993 0.249322 ACTCTGTACGCGTGTTGCTT 60.249 50.000 24.59 0.00 43.27 3.91
972 994 0.594602 TACTCTGTACGCGTGTTGCT 59.405 50.000 24.59 2.03 43.27 3.91
973 995 0.706729 GTACTCTGTACGCGTGTTGC 59.293 55.000 24.59 9.91 41.47 4.17
974 996 0.972717 CGTACTCTGTACGCGTGTTG 59.027 55.000 24.59 11.38 34.07 3.33
975 997 3.373020 CGTACTCTGTACGCGTGTT 57.627 52.632 24.59 0.00 34.07 3.32
989 1011 1.787155 CTCTATGCGTGAATGGCGTAC 59.213 52.381 0.00 0.00 0.00 3.67
992 1014 0.249447 TCCTCTATGCGTGAATGGCG 60.249 55.000 0.00 0.00 0.00 5.69
1000 1022 1.043673 GTCTGGGGTCCTCTATGCGT 61.044 60.000 0.00 0.00 0.00 5.24
1055 1082 2.422093 GGGGAAGTTGATGGTCTGGATC 60.422 54.545 0.00 0.00 0.00 3.36
1069 1096 0.116342 GTGGGGAATTTGGGGGAAGT 59.884 55.000 0.00 0.00 0.00 3.01
1632 1662 1.663643 GTCTGTGTCAACAAGCGACAA 59.336 47.619 0.00 0.00 44.58 3.18
1726 1756 8.349983 GTTCAGTAAGCAAATCTAAACTTTGGA 58.650 33.333 0.00 0.00 34.81 3.53
1735 1765 4.393062 GCAGCAGTTCAGTAAGCAAATCTA 59.607 41.667 0.00 0.00 0.00 1.98
1759 1789 5.234116 ACCATCGTCAATTTTTCAAACTTGC 59.766 36.000 0.00 0.00 31.12 4.01
1760 1790 6.826893 ACCATCGTCAATTTTTCAAACTTG 57.173 33.333 0.00 0.00 31.97 3.16
1772 1802 8.708742 CGTGATTATAATGTAACCATCGTCAAT 58.291 33.333 1.78 0.00 0.00 2.57
1776 1806 8.651391 TTTCGTGATTATAATGTAACCATCGT 57.349 30.769 1.78 0.00 0.00 3.73
1777 1807 9.923786 TTTTTCGTGATTATAATGTAACCATCG 57.076 29.630 1.78 2.30 0.00 3.84
1807 1845 4.243007 ACACTGCTTAGCACAAAAATCC 57.757 40.909 1.39 0.00 33.79 3.01
1810 1848 3.872182 TCGTACACTGCTTAGCACAAAAA 59.128 39.130 1.39 0.00 33.79 1.94
1811 1849 3.459145 TCGTACACTGCTTAGCACAAAA 58.541 40.909 1.39 0.00 33.79 2.44
1823 1861 5.391523 CCATGGTTTGGTTAATCGTACACTG 60.392 44.000 2.57 0.00 40.99 3.66
1903 1941 4.516321 TGGGCATTCTCACAATTCATATCG 59.484 41.667 0.00 0.00 0.00 2.92
1905 1943 6.989155 ATTGGGCATTCTCACAATTCATAT 57.011 33.333 0.00 0.00 29.89 1.78
1907 1945 5.895534 ACTATTGGGCATTCTCACAATTCAT 59.104 36.000 0.00 0.00 35.40 2.57
1953 1991 0.471022 TACCATAGGGCTCATCCGCA 60.471 55.000 0.00 0.00 37.90 5.69
1956 1994 2.706190 ACAAGTACCATAGGGCTCATCC 59.294 50.000 0.00 0.00 37.90 3.51
2045 2083 2.300152 TCAACTCATTGCGTCCTCTCTT 59.700 45.455 0.00 0.00 35.63 2.85
2054 2092 1.736126 AGCAGACATCAACTCATTGCG 59.264 47.619 0.00 0.00 35.63 4.85
2056 2094 5.366460 AGGATAGCAGACATCAACTCATTG 58.634 41.667 0.00 0.00 37.14 2.82
2068 2106 5.167845 GCAATTAGCTCTAGGATAGCAGAC 58.832 45.833 4.87 0.00 42.62 3.51
2159 2210 4.280819 TGAATTTCCCCTTATGCTCCTTG 58.719 43.478 0.00 0.00 0.00 3.61
2160 2211 4.608170 TGAATTTCCCCTTATGCTCCTT 57.392 40.909 0.00 0.00 0.00 3.36
2194 2245 2.747989 GTTGCCTCCCAAACTAGCTAAC 59.252 50.000 0.00 0.00 34.68 2.34
2205 2256 1.004277 GTGGTAAGATGTTGCCTCCCA 59.996 52.381 11.02 0.00 39.15 4.37
2237 2288 7.542890 AGTACATCAAATACTGTCTGTGAGAG 58.457 38.462 0.00 0.00 31.54 3.20
2286 2502 5.408356 TGAACTCTGAACTAAGGTAATCGC 58.592 41.667 0.00 0.00 0.00 4.58
2290 2506 7.332557 TGTGTTTGAACTCTGAACTAAGGTAA 58.667 34.615 0.00 0.00 0.00 2.85
2303 2519 6.473455 CCAATCAGAAGTTTGTGTTTGAACTC 59.527 38.462 11.97 0.00 34.77 3.01
2348 2564 8.753133 AGAATACTCTTGTAAGTGACATGATCA 58.247 33.333 0.00 0.00 40.41 2.92
2349 2565 9.029243 CAGAATACTCTTGTAAGTGACATGATC 57.971 37.037 0.00 0.00 40.41 2.92
2350 2566 7.493971 GCAGAATACTCTTGTAAGTGACATGAT 59.506 37.037 0.00 0.00 40.41 2.45
2351 2567 6.813649 GCAGAATACTCTTGTAAGTGACATGA 59.186 38.462 0.00 0.00 39.30 3.07
2431 2647 7.727331 AAATCGCATCCAATTTTCTCAAAAA 57.273 28.000 0.00 0.00 38.66 1.94
2432 2648 9.434420 AATAAATCGCATCCAATTTTCTCAAAA 57.566 25.926 0.00 0.00 34.41 2.44
2433 2649 8.871862 CAATAAATCGCATCCAATTTTCTCAAA 58.128 29.630 0.00 0.00 0.00 2.69
2434 2650 8.034215 ACAATAAATCGCATCCAATTTTCTCAA 58.966 29.630 0.00 0.00 0.00 3.02
2435 2651 7.546358 ACAATAAATCGCATCCAATTTTCTCA 58.454 30.769 0.00 0.00 0.00 3.27
2436 2652 7.992180 ACAATAAATCGCATCCAATTTTCTC 57.008 32.000 0.00 0.00 0.00 2.87
2437 2653 8.686334 AGTACAATAAATCGCATCCAATTTTCT 58.314 29.630 0.00 0.00 0.00 2.52
2438 2654 8.856490 AGTACAATAAATCGCATCCAATTTTC 57.144 30.769 0.00 0.00 0.00 2.29
2439 2655 8.686334 AGAGTACAATAAATCGCATCCAATTTT 58.314 29.630 0.00 0.00 0.00 1.82
2440 2656 8.225603 AGAGTACAATAAATCGCATCCAATTT 57.774 30.769 0.00 0.00 0.00 1.82
2441 2657 7.807977 AGAGTACAATAAATCGCATCCAATT 57.192 32.000 0.00 0.00 0.00 2.32
2442 2658 7.807977 AAGAGTACAATAAATCGCATCCAAT 57.192 32.000 0.00 0.00 0.00 3.16
2443 2659 8.725405 TTAAGAGTACAATAAATCGCATCCAA 57.275 30.769 0.00 0.00 0.00 3.53
2444 2660 8.773645 CATTAAGAGTACAATAAATCGCATCCA 58.226 33.333 0.00 0.00 0.00 3.41
2445 2661 8.988934 TCATTAAGAGTACAATAAATCGCATCC 58.011 33.333 0.00 0.00 0.00 3.51
2465 2681 9.295825 ACCACATGAAACTAAATGACTCATTAA 57.704 29.630 4.65 0.00 32.43 1.40
2507 2723 5.277876 GCAACAGATCTCCAATGAGCATAAG 60.278 44.000 0.00 0.00 38.58 1.73
2543 2760 9.778993 CAAATGCCTATCATAAAGATAATTCGG 57.221 33.333 0.00 0.00 38.69 4.30
2560 2777 2.681976 GCTCTGCCTCTTCAAATGCCTA 60.682 50.000 0.00 0.00 0.00 3.93
2634 2851 9.896645 GATTTCTTCCATAGCTTCCATATCATA 57.103 33.333 0.00 0.00 0.00 2.15
2818 3035 5.518848 TTACCGTCAGTTCTTTGTAGACA 57.481 39.130 0.00 0.00 0.00 3.41
2861 3078 6.406288 CCCCCATTCTCTTTCTATTCTTTTGC 60.406 42.308 0.00 0.00 0.00 3.68
2895 3112 2.029200 TGTGATGCAATTGCCGATTGTT 60.029 40.909 26.94 3.74 45.62 2.83
2930 3320 1.070758 CTCCGTCCCATAATGTGAGGG 59.929 57.143 0.00 0.00 44.22 4.30
2931 3321 1.070758 CCTCCGTCCCATAATGTGAGG 59.929 57.143 0.00 0.00 32.70 3.86
2932 3322 1.070758 CCCTCCGTCCCATAATGTGAG 59.929 57.143 0.00 0.00 0.00 3.51
2933 3323 1.128200 CCCTCCGTCCCATAATGTGA 58.872 55.000 0.00 0.00 0.00 3.58
2934 3324 1.070758 CTCCCTCCGTCCCATAATGTG 59.929 57.143 0.00 0.00 0.00 3.21
2935 3325 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2936 3326 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2937 3327 3.077695 AGATACTCCCTCCGTCCCATAAT 59.922 47.826 0.00 0.00 0.00 1.28
2938 3328 2.449730 AGATACTCCCTCCGTCCCATAA 59.550 50.000 0.00 0.00 0.00 1.90
2939 3329 2.071372 AGATACTCCCTCCGTCCCATA 58.929 52.381 0.00 0.00 0.00 2.74
2940 3330 0.861155 AGATACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
2941 3331 0.635009 AAGATACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2942 3332 1.790818 AAAGATACTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
2943 3333 4.587684 TCATTAAAGATACTCCCTCCGTCC 59.412 45.833 0.00 0.00 0.00 4.79
2944 3334 5.786264 TCATTAAAGATACTCCCTCCGTC 57.214 43.478 0.00 0.00 0.00 4.79
2945 3335 6.555463 TTTCATTAAAGATACTCCCTCCGT 57.445 37.500 0.00 0.00 0.00 4.69
2946 3336 9.726438 ATATTTTCATTAAAGATACTCCCTCCG 57.274 33.333 0.00 0.00 0.00 4.63
2972 3362 6.902771 TCGGGATTAATTTCTGTTGGAAAA 57.097 33.333 0.00 0.00 45.56 2.29
2990 3380 2.466846 TCCAGAATCATCACTTCGGGA 58.533 47.619 1.54 1.54 42.32 5.14
3063 3454 4.527038 TGAGACAACAAACCCCTAGAGTAG 59.473 45.833 0.00 0.00 0.00 2.57
3096 3487 3.379057 CAGTTGCCTGCACATGATAATCA 59.621 43.478 0.00 0.00 0.00 2.57
3142 3537 7.545965 CACCTTAGAATCCATATCAATCGGTAC 59.454 40.741 0.00 0.00 0.00 3.34
3149 3544 7.993183 GGAAACTCACCTTAGAATCCATATCAA 59.007 37.037 0.00 0.00 0.00 2.57
3207 3607 4.016444 AGGCACGTTATTGTTCCATGAAT 58.984 39.130 0.00 0.00 0.00 2.57
3304 3704 5.818136 TGAGTATTTGGTTCAAGCTATGC 57.182 39.130 0.00 0.00 0.00 3.14
3354 3754 7.685155 GCAAACCCTCAGAATATACATTGCATT 60.685 37.037 0.00 0.00 39.25 3.56
3494 3894 5.189659 AGATTACGGAAGACATAGACAGC 57.810 43.478 0.00 0.00 0.00 4.40
3523 3924 7.673180 ACAATCACAATGACCAGATGAAAAAT 58.327 30.769 0.00 0.00 0.00 1.82
3542 3943 7.064134 CACCATTACTACTTTTCGCTACAATCA 59.936 37.037 0.00 0.00 0.00 2.57
3595 3996 4.082679 AGCAGCAGTACTACAGAGTGTAAC 60.083 45.833 0.00 0.00 36.28 2.50
3606 4007 1.474330 TAGCAGCAGCAGCAGTACTA 58.526 50.000 12.92 0.00 45.49 1.82
3607 4008 0.610174 TTAGCAGCAGCAGCAGTACT 59.390 50.000 12.92 0.00 45.49 2.73
3700 4101 1.476833 GCCTCCGCATTTTCTATCCCA 60.477 52.381 0.00 0.00 34.03 4.37
3737 4139 0.184933 CCTCACAACCACCCCTGAAA 59.815 55.000 0.00 0.00 0.00 2.69
3738 4140 1.843421 CCTCACAACCACCCCTGAA 59.157 57.895 0.00 0.00 0.00 3.02
3741 4143 3.953775 CGCCTCACAACCACCCCT 61.954 66.667 0.00 0.00 0.00 4.79
3768 4170 2.354259 CATCTGAGCAAACAGGGAGAC 58.646 52.381 0.00 0.00 38.31 3.36
3769 4171 1.280133 CCATCTGAGCAAACAGGGAGA 59.720 52.381 0.00 0.00 38.31 3.71
3770 4172 1.280133 TCCATCTGAGCAAACAGGGAG 59.720 52.381 0.00 0.00 38.31 4.30
3771 4173 1.361204 TCCATCTGAGCAAACAGGGA 58.639 50.000 0.00 0.00 38.31 4.20
3772 4174 2.295885 GATCCATCTGAGCAAACAGGG 58.704 52.381 0.00 0.00 38.31 4.45
3773 4175 2.995283 TGATCCATCTGAGCAAACAGG 58.005 47.619 0.00 0.00 36.19 4.00
3774 4176 3.315470 CCATGATCCATCTGAGCAAACAG 59.685 47.826 0.00 0.00 43.76 3.16
3775 4177 3.054213 TCCATGATCCATCTGAGCAAACA 60.054 43.478 0.00 0.00 43.76 2.83
3776 4178 3.548770 TCCATGATCCATCTGAGCAAAC 58.451 45.455 0.00 0.00 43.76 2.93
3777 4179 3.937778 TCCATGATCCATCTGAGCAAA 57.062 42.857 0.00 0.00 43.76 3.68
3778 4180 3.651423 AGATCCATGATCCATCTGAGCAA 59.349 43.478 0.00 0.00 43.76 3.91
3779 4181 3.008049 CAGATCCATGATCCATCTGAGCA 59.992 47.826 14.16 0.00 44.35 4.26
3780 4182 3.601435 CAGATCCATGATCCATCTGAGC 58.399 50.000 14.16 0.00 44.35 4.26
3781 4183 3.583526 ACCAGATCCATGATCCATCTGAG 59.416 47.826 18.22 13.14 44.35 3.35
3782 4184 3.326880 CACCAGATCCATGATCCATCTGA 59.673 47.826 18.22 0.00 44.35 3.27
3898 4301 3.055458 TCAGATGGATGCAAGAAACCGTA 60.055 43.478 0.00 0.00 0.00 4.02
3905 4308 1.554617 TCGGTTCAGATGGATGCAAGA 59.445 47.619 0.00 0.00 0.00 3.02
3987 4390 4.094887 CCGGGAGACAGTTGTAAATCAATG 59.905 45.833 0.00 0.00 38.38 2.82
4033 4436 5.036737 CGCTGAAGACAACAAACAGAAAAT 58.963 37.500 0.00 0.00 0.00 1.82
4041 4444 3.210227 TGGAATCGCTGAAGACAACAAA 58.790 40.909 0.00 0.00 0.00 2.83
4042 4445 2.844946 TGGAATCGCTGAAGACAACAA 58.155 42.857 0.00 0.00 0.00 2.83
4108 4511 6.886459 AGCACTCCAACTTACAATGTATGAAT 59.114 34.615 12.40 0.00 0.00 2.57
4156 4563 9.806203 TTAAATGAGATATCAATTTGCCTTGTG 57.194 29.630 19.21 0.00 0.00 3.33
4188 4595 5.860941 TGGCACAAGGTCTCAAATTTTAA 57.139 34.783 0.00 0.00 31.92 1.52
4208 4615 2.617308 TCTACGCCGAGAATCTACTTGG 59.383 50.000 0.00 0.00 42.63 3.61
4222 4629 5.545658 TGATTGAAGATTTGTTCTACGCC 57.454 39.130 0.00 0.00 33.05 5.68
4280 4687 9.522804 GTTGTTTGGAAACATGTAACAAAGATA 57.477 29.630 20.07 9.68 45.19 1.98
4333 4740 4.222366 TGGTGTGGGATTTGTATACGTGTA 59.778 41.667 0.00 0.00 0.00 2.90
4373 4780 8.948936 CGCAGCTCGATTCATTCCATTTATGG 62.949 46.154 2.19 2.19 44.66 2.74
4377 4784 2.032550 CGCAGCTCGATTCATTCCATTT 59.967 45.455 0.00 0.00 41.67 2.32
4422 4831 5.593095 ACAGAACGGCTACAGATGAACTATA 59.407 40.000 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.