Multiple sequence alignment - TraesCS2D01G480000

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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 TraesCS2D01G480000 chr2D 100.000 3363 0 0 1 3363 580782803 580786165 0.000000e+00 6211.0
1 TraesCS2D01G480000 chr2D 84.733 262 27 6 1281 1542 428579645 428579397 2.000000e-62 250.0
2 TraesCS2D01G480000 chr2D 100.000 90 0 0 2 91 198759305 198759394 2.080000e-37 167.0
3 TraesCS2D01G480000 chr2D 77.907 258 47 8 659 910 618070911 618071164 5.810000e-33 152.0
4 TraesCS2D01G480000 chr2D 77.612 134 22 7 346 475 615173061 615172932 1.290000e-09 75.0
5 TraesCS2D01G480000 chr5A 95.784 2894 100 10 475 3363 499170979 499168103 0.000000e+00 4649.0
6 TraesCS2D01G480000 chr5A 83.969 262 28 8 1281 1542 439834426 439834179 4.340000e-59 239.0
7 TraesCS2D01G480000 chr5A 83.969 262 29 6 1281 1542 707718364 707718612 4.340000e-59 239.0
8 TraesCS2D01G480000 chr4A 98.576 2317 22 5 1057 3363 374405148 374407463 0.000000e+00 4085.0
9 TraesCS2D01G480000 chrUn 95.880 801 31 2 2482 3281 15414232 15413433 0.000000e+00 1295.0
10 TraesCS2D01G480000 chrUn 95.506 801 34 2 2482 3281 15749843 15750642 0.000000e+00 1279.0
11 TraesCS2D01G480000 chrUn 95.579 769 33 1 2482 3249 448849596 448850364 0.000000e+00 1230.0
12 TraesCS2D01G480000 chrUn 95.886 632 25 1 2482 3112 401659383 401660014 0.000000e+00 1022.0
13 TraesCS2D01G480000 chrUn 94.877 527 26 1 2755 3281 428561217 428560692 0.000000e+00 822.0
14 TraesCS2D01G480000 chrUn 96.891 386 11 1 2482 2866 336472582 336472967 0.000000e+00 645.0
15 TraesCS2D01G480000 chrUn 96.891 386 11 1 2482 2866 336478781 336478396 0.000000e+00 645.0
16 TraesCS2D01G480000 chrUn 83.846 260 28 8 1281 1540 372800650 372800895 5.610000e-58 235.0
17 TraesCS2D01G480000 chr2B 95.880 801 31 2 2482 3281 8403175 8402376 0.000000e+00 1295.0
18 TraesCS2D01G480000 chr6B 85.099 812 97 6 659 1470 614591210 614591997 0.000000e+00 808.0
19 TraesCS2D01G480000 chr6B 91.169 385 28 5 97 475 535444589 535444973 4.970000e-143 518.0
20 TraesCS2D01G480000 chr6B 88.654 379 36 6 88 461 661064861 661064485 3.960000e-124 455.0
21 TraesCS2D01G480000 chr6B 83.969 262 28 8 1281 1542 232748280 232748527 4.340000e-59 239.0
22 TraesCS2D01G480000 chr6B 80.189 106 15 6 370 473 585923778 585923879 1.290000e-09 75.0
23 TraesCS2D01G480000 chr7D 89.897 584 42 10 2762 3341 212242890 212242320 0.000000e+00 736.0
24 TraesCS2D01G480000 chr7D 84.783 230 23 8 1066 1284 23078798 23079026 1.570000e-53 220.0
25 TraesCS2D01G480000 chr7D 100.000 91 0 0 1 91 466338958 466339048 5.770000e-38 169.0
26 TraesCS2D01G480000 chr7D 100.000 91 0 0 1 91 581488344 581488254 5.770000e-38 169.0
27 TraesCS2D01G480000 chr6D 89.383 405 26 6 88 475 410081656 410081252 8.380000e-136 494.0
28 TraesCS2D01G480000 chr6D 100.000 91 0 0 1 91 352176540 352176630 5.770000e-38 169.0
29 TraesCS2D01G480000 chr7B 89.313 393 36 6 88 475 537549087 537548696 3.900000e-134 488.0
30 TraesCS2D01G480000 chr7B 84.043 94 12 3 96 187 565654941 565654849 1.660000e-13 87.9
31 TraesCS2D01G480000 chr3D 87.909 397 38 6 87 475 501268830 501268436 3.060000e-125 459.0
32 TraesCS2D01G480000 chr3D 100.000 91 0 0 1 91 399342586 399342676 5.770000e-38 169.0
33 TraesCS2D01G480000 chr4B 83.969 262 28 8 1281 1542 1762563 1762810 4.340000e-59 239.0
34 TraesCS2D01G480000 chr4B 81.185 287 36 11 1926 2201 144928643 144928364 7.310000e-52 215.0
35 TraesCS2D01G480000 chr3A 83.846 260 28 8 1281 1540 95547176 95546931 5.610000e-58 235.0
36 TraesCS2D01G480000 chr1B 80.836 287 37 12 1926 2201 488713734 488713455 3.400000e-50 209.0
37 TraesCS2D01G480000 chr1B 80.139 287 39 7 1926 2201 561882226 561882505 7.360000e-47 198.0
38 TraesCS2D01G480000 chr1B 82.979 94 13 3 96 187 100155258 100155166 7.730000e-12 82.4
39 TraesCS2D01G480000 chr1B 77.778 135 22 7 346 476 684686354 684686484 3.600000e-10 76.8
40 TraesCS2D01G480000 chr5D 100.000 91 0 0 1 91 464956380 464956290 5.770000e-38 169.0
41 TraesCS2D01G480000 chr4D 100.000 91 0 0 1 91 369742578 369742488 5.770000e-38 169.0
42 TraesCS2D01G480000 chr4D 100.000 91 0 0 1 91 393524771 393524681 5.770000e-38 169.0
43 TraesCS2D01G480000 chr1D 100.000 91 0 0 1 91 83107947 83108037 5.770000e-38 169.0
44 TraesCS2D01G480000 chr1A 84.337 166 15 3 2028 2182 566609402 566609237 5.810000e-33 152.0
45 TraesCS2D01G480000 chr1A 77.037 135 23 6 346 476 32540423 32540293 1.670000e-08 71.3


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 TraesCS2D01G480000 chr2D 580782803 580786165 3362 False 6211 6211 100.000 1 3363 1 chr2D.!!$F2 3362
1 TraesCS2D01G480000 chr5A 499168103 499170979 2876 True 4649 4649 95.784 475 3363 1 chr5A.!!$R2 2888
2 TraesCS2D01G480000 chr4A 374405148 374407463 2315 False 4085 4085 98.576 1057 3363 1 chr4A.!!$F1 2306
3 TraesCS2D01G480000 chrUn 15413433 15414232 799 True 1295 1295 95.880 2482 3281 1 chrUn.!!$R1 799
4 TraesCS2D01G480000 chrUn 15749843 15750642 799 False 1279 1279 95.506 2482 3281 1 chrUn.!!$F1 799
5 TraesCS2D01G480000 chrUn 448849596 448850364 768 False 1230 1230 95.579 2482 3249 1 chrUn.!!$F5 767
6 TraesCS2D01G480000 chrUn 401659383 401660014 631 False 1022 1022 95.886 2482 3112 1 chrUn.!!$F4 630
7 TraesCS2D01G480000 chrUn 428560692 428561217 525 True 822 822 94.877 2755 3281 1 chrUn.!!$R3 526
8 TraesCS2D01G480000 chr2B 8402376 8403175 799 True 1295 1295 95.880 2482 3281 1 chr2B.!!$R1 799
9 TraesCS2D01G480000 chr6B 614591210 614591997 787 False 808 808 85.099 659 1470 1 chr6B.!!$F4 811
10 TraesCS2D01G480000 chr7D 212242320 212242890 570 True 736 736 89.897 2762 3341 1 chr7D.!!$R1 579

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
362 363 0.034574 ACCGCTCATATTGTTGGGCA 60.035 50.000 0.0 0.0 43.57 5.36 F
364 365 1.001048 CCGCTCATATTGTTGGGCATG 60.001 52.381 0.0 0.0 43.57 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2113 4.883585 TCCTGACATATGAAATGTGCTTCC 59.116 41.667 10.38 0.0 39.27 3.46 R
3070 3088 3.118000 TGAGGAGCAGCATCAATCAGAAT 60.118 43.478 0.00 0.0 33.80 2.40 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
21 22 4.889832 CAAAGATGGCAACACCTAGATC 57.110 45.455 0.00 0.00 42.88 2.75
22 23 4.521146 CAAAGATGGCAACACCTAGATCT 58.479 43.478 0.00 0.00 42.88 2.75
23 24 5.674525 CAAAGATGGCAACACCTAGATCTA 58.325 41.667 1.69 1.69 42.88 1.98
24 25 6.294473 CAAAGATGGCAACACCTAGATCTAT 58.706 40.000 2.11 0.00 42.88 1.98
25 26 6.107901 AAGATGGCAACACCTAGATCTATC 57.892 41.667 2.11 0.00 42.88 2.08
26 27 5.012561 AAGATGGCAACACCTAGATCTATCC 59.987 44.000 2.11 0.00 42.88 2.59
27 28 3.928754 TGGCAACACCTAGATCTATCCT 58.071 45.455 2.11 0.00 46.17 3.24
28 29 4.298626 TGGCAACACCTAGATCTATCCTT 58.701 43.478 2.11 0.00 46.17 3.36
29 30 4.101585 TGGCAACACCTAGATCTATCCTTG 59.898 45.833 2.11 4.45 46.17 3.61
30 31 4.061596 GCAACACCTAGATCTATCCTTGC 58.938 47.826 2.11 10.07 0.00 4.01
31 32 4.636249 CAACACCTAGATCTATCCTTGCC 58.364 47.826 2.11 0.00 0.00 4.52
32 33 4.206244 ACACCTAGATCTATCCTTGCCT 57.794 45.455 2.11 0.00 0.00 4.75
33 34 4.561752 ACACCTAGATCTATCCTTGCCTT 58.438 43.478 2.11 0.00 0.00 4.35
34 35 4.971924 ACACCTAGATCTATCCTTGCCTTT 59.028 41.667 2.11 0.00 0.00 3.11
35 36 6.143915 ACACCTAGATCTATCCTTGCCTTTA 58.856 40.000 2.11 0.00 0.00 1.85
36 37 6.789959 ACACCTAGATCTATCCTTGCCTTTAT 59.210 38.462 2.11 0.00 0.00 1.40
37 38 7.102346 CACCTAGATCTATCCTTGCCTTTATG 58.898 42.308 2.11 0.00 0.00 1.90
38 39 6.112058 CCTAGATCTATCCTTGCCTTTATGC 58.888 44.000 2.11 0.00 0.00 3.14
39 40 4.916183 AGATCTATCCTTGCCTTTATGCC 58.084 43.478 0.00 0.00 0.00 4.40
40 41 4.600983 AGATCTATCCTTGCCTTTATGCCT 59.399 41.667 0.00 0.00 0.00 4.75
41 42 5.787494 AGATCTATCCTTGCCTTTATGCCTA 59.213 40.000 0.00 0.00 0.00 3.93
42 43 5.489792 TCTATCCTTGCCTTTATGCCTAG 57.510 43.478 0.00 0.00 0.00 3.02
43 44 2.348411 TCCTTGCCTTTATGCCTAGC 57.652 50.000 0.00 0.00 0.00 3.42
44 45 1.846439 TCCTTGCCTTTATGCCTAGCT 59.154 47.619 0.00 0.00 0.00 3.32
45 46 3.045634 TCCTTGCCTTTATGCCTAGCTA 58.954 45.455 0.00 0.00 0.00 3.32
46 47 3.071602 TCCTTGCCTTTATGCCTAGCTAG 59.928 47.826 14.20 14.20 0.00 3.42
47 48 3.406764 CTTGCCTTTATGCCTAGCTAGG 58.593 50.000 32.12 32.12 46.42 3.02
48 49 1.699634 TGCCTTTATGCCTAGCTAGGG 59.300 52.381 35.44 20.54 43.82 3.53
49 50 1.003696 GCCTTTATGCCTAGCTAGGGG 59.996 57.143 35.44 27.46 43.82 4.79
59 60 1.406539 CTAGCTAGGGGCGTTAAACGA 59.593 52.381 13.32 0.00 46.05 3.85
60 61 0.828677 AGCTAGGGGCGTTAAACGAT 59.171 50.000 0.00 0.00 46.05 3.73
61 62 2.034124 AGCTAGGGGCGTTAAACGATA 58.966 47.619 0.00 0.00 46.05 2.92
62 63 2.035576 AGCTAGGGGCGTTAAACGATAG 59.964 50.000 0.00 0.00 46.05 2.08
63 64 2.401351 CTAGGGGCGTTAAACGATAGC 58.599 52.381 0.00 0.00 46.05 2.97
64 65 0.529119 AGGGGCGTTAAACGATAGCG 60.529 55.000 0.00 0.00 46.05 4.26
65 66 1.274770 GGGCGTTAAACGATAGCGC 59.725 57.895 19.47 19.47 46.05 5.92
66 67 1.149964 GGGCGTTAAACGATAGCGCT 61.150 55.000 17.26 17.26 46.05 5.92
67 68 0.648958 GGCGTTAAACGATAGCGCTT 59.351 50.000 18.68 2.89 46.05 4.68
68 69 1.591394 GGCGTTAAACGATAGCGCTTG 60.591 52.381 18.68 9.06 46.05 4.01
69 70 1.060122 GCGTTAAACGATAGCGCTTGT 59.940 47.619 18.68 9.82 46.05 3.16
70 71 2.473376 GCGTTAAACGATAGCGCTTGTT 60.473 45.455 18.68 15.85 46.05 2.83
71 72 3.081445 CGTTAAACGATAGCGCTTGTTG 58.919 45.455 18.68 11.82 46.05 3.33
72 73 3.413558 GTTAAACGATAGCGCTTGTTGG 58.586 45.455 18.68 5.13 42.48 3.77
73 74 0.802494 AAACGATAGCGCTTGTTGGG 59.198 50.000 18.68 1.82 42.48 4.12
74 75 0.036765 AACGATAGCGCTTGTTGGGA 60.037 50.000 18.68 0.00 42.48 4.37
75 76 0.460284 ACGATAGCGCTTGTTGGGAG 60.460 55.000 18.68 1.34 42.48 4.30
76 77 1.154205 CGATAGCGCTTGTTGGGAGG 61.154 60.000 18.68 0.00 0.00 4.30
77 78 1.440145 GATAGCGCTTGTTGGGAGGC 61.440 60.000 18.68 0.00 0.00 4.70
78 79 2.196997 ATAGCGCTTGTTGGGAGGCA 62.197 55.000 18.68 0.00 0.00 4.75
79 80 2.404566 TAGCGCTTGTTGGGAGGCAA 62.405 55.000 18.68 0.00 0.00 4.52
80 81 2.644992 CGCTTGTTGGGAGGCAAC 59.355 61.111 0.00 0.00 0.00 4.17
81 82 2.919494 CGCTTGTTGGGAGGCAACC 61.919 63.158 0.00 0.00 37.17 3.77
95 96 6.478512 GGAGGCAACCCAATTTTATAATCA 57.521 37.500 0.00 0.00 37.17 2.57
96 97 7.066307 GGAGGCAACCCAATTTTATAATCAT 57.934 36.000 0.00 0.00 37.17 2.45
97 98 7.154656 GGAGGCAACCCAATTTTATAATCATC 58.845 38.462 0.00 0.00 37.17 2.92
98 99 7.201992 GGAGGCAACCCAATTTTATAATCATCA 60.202 37.037 0.00 0.00 37.17 3.07
99 100 8.266363 AGGCAACCCAATTTTATAATCATCAT 57.734 30.769 0.00 0.00 37.17 2.45
100 101 9.378504 AGGCAACCCAATTTTATAATCATCATA 57.621 29.630 0.00 0.00 37.17 2.15
117 118 9.950496 AATCATCATATAGGTTATCTTGTGGTC 57.050 33.333 0.00 0.00 0.00 4.02
118 119 8.727100 TCATCATATAGGTTATCTTGTGGTCT 57.273 34.615 0.00 0.00 0.00 3.85
119 120 8.807118 TCATCATATAGGTTATCTTGTGGTCTC 58.193 37.037 0.00 0.00 0.00 3.36
120 121 7.540474 TCATATAGGTTATCTTGTGGTCTCC 57.460 40.000 0.00 0.00 0.00 3.71
121 122 7.306013 TCATATAGGTTATCTTGTGGTCTCCT 58.694 38.462 0.00 0.00 0.00 3.69
122 123 5.878406 ATAGGTTATCTTGTGGTCTCCTG 57.122 43.478 0.00 0.00 0.00 3.86
123 124 2.840651 AGGTTATCTTGTGGTCTCCTGG 59.159 50.000 0.00 0.00 0.00 4.45
124 125 2.838202 GGTTATCTTGTGGTCTCCTGGA 59.162 50.000 0.00 0.00 0.00 3.86
125 126 3.456277 GGTTATCTTGTGGTCTCCTGGAT 59.544 47.826 0.00 0.00 0.00 3.41
126 127 4.446371 GTTATCTTGTGGTCTCCTGGATG 58.554 47.826 0.00 0.00 0.00 3.51
127 128 2.030027 TCTTGTGGTCTCCTGGATGT 57.970 50.000 0.00 0.00 0.00 3.06
128 129 2.338809 TCTTGTGGTCTCCTGGATGTT 58.661 47.619 0.00 0.00 0.00 2.71
129 130 3.516586 TCTTGTGGTCTCCTGGATGTTA 58.483 45.455 0.00 0.00 0.00 2.41
130 131 3.907474 TCTTGTGGTCTCCTGGATGTTAA 59.093 43.478 0.00 0.00 0.00 2.01
131 132 4.349636 TCTTGTGGTCTCCTGGATGTTAAA 59.650 41.667 0.00 0.00 0.00 1.52
132 133 4.927267 TGTGGTCTCCTGGATGTTAAAT 57.073 40.909 0.00 0.00 0.00 1.40
133 134 5.255397 TGTGGTCTCCTGGATGTTAAATT 57.745 39.130 0.00 0.00 0.00 1.82
134 135 5.640147 TGTGGTCTCCTGGATGTTAAATTT 58.360 37.500 0.00 0.00 0.00 1.82
135 136 6.785076 TGTGGTCTCCTGGATGTTAAATTTA 58.215 36.000 0.00 0.00 0.00 1.40
136 137 7.410174 TGTGGTCTCCTGGATGTTAAATTTAT 58.590 34.615 0.00 0.00 0.00 1.40
137 138 7.339212 TGTGGTCTCCTGGATGTTAAATTTATG 59.661 37.037 0.00 0.00 0.00 1.90
138 139 6.833416 TGGTCTCCTGGATGTTAAATTTATGG 59.167 38.462 0.00 0.00 0.00 2.74
139 140 7.060421 GGTCTCCTGGATGTTAAATTTATGGA 58.940 38.462 0.00 0.00 0.00 3.41
140 141 7.229506 GGTCTCCTGGATGTTAAATTTATGGAG 59.770 40.741 0.00 0.00 38.80 3.86
141 142 7.775561 GTCTCCTGGATGTTAAATTTATGGAGT 59.224 37.037 0.00 0.00 38.63 3.85
142 143 8.998814 TCTCCTGGATGTTAAATTTATGGAGTA 58.001 33.333 0.00 0.00 38.63 2.59
143 144 8.974060 TCCTGGATGTTAAATTTATGGAGTAC 57.026 34.615 0.00 0.00 0.00 2.73
144 145 8.778059 TCCTGGATGTTAAATTTATGGAGTACT 58.222 33.333 0.00 0.00 0.00 2.73
145 146 9.408648 CCTGGATGTTAAATTTATGGAGTACTT 57.591 33.333 0.00 0.00 0.00 2.24
147 148 9.967451 TGGATGTTAAATTTATGGAGTACTTCA 57.033 29.630 6.25 6.25 0.00 3.02
149 150 9.916397 GATGTTAAATTTATGGAGTACTTCACG 57.084 33.333 5.84 0.00 0.00 4.35
150 151 8.259049 TGTTAAATTTATGGAGTACTTCACGG 57.741 34.615 5.84 0.00 0.00 4.94
151 152 7.334921 TGTTAAATTTATGGAGTACTTCACGGG 59.665 37.037 5.84 0.00 0.00 5.28
152 153 5.687166 AATTTATGGAGTACTTCACGGGA 57.313 39.130 5.84 0.00 0.00 5.14
153 154 4.730949 TTTATGGAGTACTTCACGGGAG 57.269 45.455 5.84 0.00 0.00 4.30
154 155 2.526888 ATGGAGTACTTCACGGGAGA 57.473 50.000 5.84 0.00 0.00 3.71
155 156 2.526888 TGGAGTACTTCACGGGAGAT 57.473 50.000 0.00 0.00 0.00 2.75
156 157 3.657398 TGGAGTACTTCACGGGAGATA 57.343 47.619 0.00 0.00 0.00 1.98
157 158 4.180377 TGGAGTACTTCACGGGAGATAT 57.820 45.455 0.00 0.00 0.00 1.63
158 159 4.543689 TGGAGTACTTCACGGGAGATATT 58.456 43.478 0.00 0.00 0.00 1.28
159 160 4.960469 TGGAGTACTTCACGGGAGATATTT 59.040 41.667 0.00 0.00 0.00 1.40
160 161 5.424252 TGGAGTACTTCACGGGAGATATTTT 59.576 40.000 0.00 0.00 0.00 1.82
161 162 5.753921 GGAGTACTTCACGGGAGATATTTTG 59.246 44.000 0.00 0.00 0.00 2.44
162 163 6.295719 AGTACTTCACGGGAGATATTTTGT 57.704 37.500 0.00 0.00 0.00 2.83
163 164 6.338937 AGTACTTCACGGGAGATATTTTGTC 58.661 40.000 0.00 0.00 0.00 3.18
164 165 4.514401 ACTTCACGGGAGATATTTTGTCC 58.486 43.478 0.00 0.00 0.00 4.02
165 166 3.173668 TCACGGGAGATATTTTGTCCG 57.826 47.619 0.00 0.00 42.69 4.79
166 167 2.761767 TCACGGGAGATATTTTGTCCGA 59.238 45.455 6.57 0.00 40.53 4.55
167 168 2.864343 CACGGGAGATATTTTGTCCGAC 59.136 50.000 6.57 0.00 40.53 4.79
168 169 2.498481 ACGGGAGATATTTTGTCCGACA 59.502 45.455 6.57 0.00 40.53 4.35
169 170 3.055675 ACGGGAGATATTTTGTCCGACAA 60.056 43.478 9.99 9.99 40.53 3.18
170 171 4.127171 CGGGAGATATTTTGTCCGACAAT 58.873 43.478 14.64 3.86 38.00 2.71
171 172 4.211374 CGGGAGATATTTTGTCCGACAATC 59.789 45.833 14.64 9.25 38.00 2.67
172 173 5.368989 GGGAGATATTTTGTCCGACAATCT 58.631 41.667 14.64 13.58 38.00 2.40
173 174 5.237344 GGGAGATATTTTGTCCGACAATCTG 59.763 44.000 14.64 0.00 38.00 2.90
174 175 5.237344 GGAGATATTTTGTCCGACAATCTGG 59.763 44.000 14.64 0.00 38.00 3.86
175 176 5.989477 AGATATTTTGTCCGACAATCTGGA 58.011 37.500 14.64 0.00 38.00 3.86
176 177 6.051717 AGATATTTTGTCCGACAATCTGGAG 58.948 40.000 14.64 0.00 38.00 3.86
177 178 3.762407 TTTTGTCCGACAATCTGGAGA 57.238 42.857 14.64 0.00 38.00 3.71
178 179 3.319137 TTTGTCCGACAATCTGGAGAG 57.681 47.619 14.64 0.00 38.00 3.20
179 180 1.186200 TGTCCGACAATCTGGAGAGG 58.814 55.000 0.00 0.00 34.21 3.69
180 181 1.187087 GTCCGACAATCTGGAGAGGT 58.813 55.000 0.00 0.00 34.21 3.85
181 182 2.291346 TGTCCGACAATCTGGAGAGGTA 60.291 50.000 0.00 0.00 34.21 3.08
182 183 2.959707 GTCCGACAATCTGGAGAGGTAT 59.040 50.000 0.00 0.00 34.21 2.73
183 184 4.142790 GTCCGACAATCTGGAGAGGTATA 58.857 47.826 0.00 0.00 34.21 1.47
184 185 4.767928 GTCCGACAATCTGGAGAGGTATAT 59.232 45.833 0.00 0.00 34.21 0.86
185 186 5.244178 GTCCGACAATCTGGAGAGGTATATT 59.756 44.000 0.00 0.00 34.21 1.28
186 187 5.839063 TCCGACAATCTGGAGAGGTATATTT 59.161 40.000 0.00 0.00 0.00 1.40
187 188 6.326583 TCCGACAATCTGGAGAGGTATATTTT 59.673 38.462 0.00 0.00 0.00 1.82
188 189 6.425114 CCGACAATCTGGAGAGGTATATTTTG 59.575 42.308 0.00 0.00 0.00 2.44
189 190 6.073548 CGACAATCTGGAGAGGTATATTTTGC 60.074 42.308 0.00 0.00 0.00 3.68
190 191 6.662755 ACAATCTGGAGAGGTATATTTTGCA 58.337 36.000 0.00 0.00 0.00 4.08
191 192 7.293073 ACAATCTGGAGAGGTATATTTTGCAT 58.707 34.615 0.00 0.00 0.00 3.96
192 193 7.446625 ACAATCTGGAGAGGTATATTTTGCATC 59.553 37.037 0.00 0.00 0.00 3.91
193 194 5.541845 TCTGGAGAGGTATATTTTGCATCG 58.458 41.667 0.00 0.00 0.00 3.84
194 195 5.070446 TCTGGAGAGGTATATTTTGCATCGT 59.930 40.000 0.00 0.00 0.00 3.73
195 196 6.266786 TCTGGAGAGGTATATTTTGCATCGTA 59.733 38.462 0.00 0.00 0.00 3.43
196 197 7.004555 TGGAGAGGTATATTTTGCATCGTAT 57.995 36.000 0.00 0.00 0.00 3.06
197 198 7.097192 TGGAGAGGTATATTTTGCATCGTATC 58.903 38.462 0.00 0.00 0.00 2.24
198 199 7.097192 GGAGAGGTATATTTTGCATCGTATCA 58.903 38.462 0.00 0.00 0.00 2.15
199 200 7.766278 GGAGAGGTATATTTTGCATCGTATCAT 59.234 37.037 0.00 0.00 0.00 2.45
200 201 8.709386 AGAGGTATATTTTGCATCGTATCATC 57.291 34.615 0.00 0.00 0.00 2.92
201 202 8.314021 AGAGGTATATTTTGCATCGTATCATCA 58.686 33.333 0.00 0.00 0.00 3.07
202 203 9.102757 GAGGTATATTTTGCATCGTATCATCAT 57.897 33.333 0.00 0.00 0.00 2.45
265 266 9.661563 TTATGGTATGTATATTTTGGATCCGAC 57.338 33.333 7.39 0.00 0.00 4.79
266 267 7.068686 TGGTATGTATATTTTGGATCCGACA 57.931 36.000 7.39 0.00 0.00 4.35
267 268 6.932400 TGGTATGTATATTTTGGATCCGACAC 59.068 38.462 7.39 0.00 0.00 3.67
268 269 6.370718 GGTATGTATATTTTGGATCCGACACC 59.629 42.308 7.39 0.00 0.00 4.16
269 270 4.710324 TGTATATTTTGGATCCGACACCC 58.290 43.478 7.39 0.00 0.00 4.61
270 271 2.721425 TATTTTGGATCCGACACCCC 57.279 50.000 7.39 0.00 0.00 4.95
271 272 0.999712 ATTTTGGATCCGACACCCCT 59.000 50.000 7.39 0.00 0.00 4.79
272 273 0.037590 TTTTGGATCCGACACCCCTG 59.962 55.000 7.39 0.00 0.00 4.45
273 274 0.838554 TTTGGATCCGACACCCCTGA 60.839 55.000 7.39 0.00 0.00 3.86
274 275 0.620410 TTGGATCCGACACCCCTGAT 60.620 55.000 7.39 0.00 0.00 2.90
275 276 1.048724 TGGATCCGACACCCCTGATC 61.049 60.000 7.39 0.00 34.28 2.92
276 277 1.048724 GGATCCGACACCCCTGATCA 61.049 60.000 0.00 0.00 36.24 2.92
277 278 0.390860 GATCCGACACCCCTGATCAG 59.609 60.000 16.24 16.24 34.97 2.90
292 293 6.174451 CCTGATCAGGTATATTTTGCATCG 57.826 41.667 30.55 2.08 43.61 3.84
293 294 5.702670 CCTGATCAGGTATATTTTGCATCGT 59.297 40.000 30.55 0.00 43.61 3.73
294 295 6.873605 CCTGATCAGGTATATTTTGCATCGTA 59.126 38.462 30.55 0.00 43.61 3.43
295 296 7.550551 CCTGATCAGGTATATTTTGCATCGTAT 59.449 37.037 30.55 0.00 43.61 3.06
296 297 8.479313 TGATCAGGTATATTTTGCATCGTATC 57.521 34.615 0.00 0.00 0.00 2.24
297 298 8.093927 TGATCAGGTATATTTTGCATCGTATCA 58.906 33.333 0.00 0.00 0.00 2.15
298 299 9.102757 GATCAGGTATATTTTGCATCGTATCAT 57.897 33.333 0.00 0.00 0.00 2.45
300 301 9.936759 TCAGGTATATTTTGCATCGTATCATAA 57.063 29.630 0.00 0.00 0.00 1.90
337 338 7.639113 ATGGTGTGTTATTATTTTGGATCGT 57.361 32.000 0.00 0.00 0.00 3.73
338 339 7.455641 TGGTGTGTTATTATTTTGGATCGTT 57.544 32.000 0.00 0.00 0.00 3.85
339 340 7.887381 TGGTGTGTTATTATTTTGGATCGTTT 58.113 30.769 0.00 0.00 0.00 3.60
340 341 9.011095 TGGTGTGTTATTATTTTGGATCGTTTA 57.989 29.630 0.00 0.00 0.00 2.01
341 342 9.843334 GGTGTGTTATTATTTTGGATCGTTTAA 57.157 29.630 0.00 0.00 0.00 1.52
345 346 9.843334 TGTTATTATTTTGGATCGTTTAACACC 57.157 29.630 0.00 0.00 0.00 4.16
346 347 9.002080 GTTATTATTTTGGATCGTTTAACACCG 57.998 33.333 0.00 0.00 0.00 4.94
347 348 2.973419 TTTGGATCGTTTAACACCGC 57.027 45.000 0.00 0.00 0.00 5.68
348 349 2.172851 TTGGATCGTTTAACACCGCT 57.827 45.000 0.00 0.00 0.00 5.52
349 350 1.717194 TGGATCGTTTAACACCGCTC 58.283 50.000 0.00 0.00 0.00 5.03
350 351 1.001068 TGGATCGTTTAACACCGCTCA 59.999 47.619 0.00 0.00 0.00 4.26
351 352 2.277084 GGATCGTTTAACACCGCTCAT 58.723 47.619 0.00 0.00 0.00 2.90
352 353 3.119065 TGGATCGTTTAACACCGCTCATA 60.119 43.478 0.00 0.00 0.00 2.15
353 354 4.056050 GGATCGTTTAACACCGCTCATAT 58.944 43.478 0.00 0.00 0.00 1.78
354 355 4.510340 GGATCGTTTAACACCGCTCATATT 59.490 41.667 0.00 0.00 0.00 1.28
355 356 4.850859 TCGTTTAACACCGCTCATATTG 57.149 40.909 0.00 0.00 0.00 1.90
356 357 4.247258 TCGTTTAACACCGCTCATATTGT 58.753 39.130 0.00 0.00 0.00 2.71
357 358 4.691685 TCGTTTAACACCGCTCATATTGTT 59.308 37.500 0.00 0.00 36.23 2.83
358 359 4.786068 CGTTTAACACCGCTCATATTGTTG 59.214 41.667 0.00 0.00 34.15 3.33
359 360 4.955925 TTAACACCGCTCATATTGTTGG 57.044 40.909 0.00 0.00 34.15 3.77
360 361 1.750193 ACACCGCTCATATTGTTGGG 58.250 50.000 0.00 0.00 0.00 4.12
361 362 0.381801 CACCGCTCATATTGTTGGGC 59.618 55.000 0.00 0.00 39.83 5.36
362 363 0.034574 ACCGCTCATATTGTTGGGCA 60.035 50.000 0.00 0.00 43.57 5.36
363 364 1.321474 CCGCTCATATTGTTGGGCAT 58.679 50.000 0.00 0.00 43.57 4.40
364 365 1.001048 CCGCTCATATTGTTGGGCATG 60.001 52.381 0.00 0.00 43.57 4.06
365 366 1.948834 CGCTCATATTGTTGGGCATGA 59.051 47.619 0.00 0.00 43.57 3.07
366 367 2.031420 CGCTCATATTGTTGGGCATGAG 60.031 50.000 0.00 6.15 43.57 2.90
367 368 2.295349 GCTCATATTGTTGGGCATGAGG 59.705 50.000 11.26 0.00 42.88 3.86
368 369 2.295349 CTCATATTGTTGGGCATGAGGC 59.705 50.000 0.00 0.00 40.35 4.70
382 383 5.817616 GCATGAGGCATTTAAATGATTCG 57.182 39.130 28.33 14.24 43.97 3.34
383 384 4.682860 GCATGAGGCATTTAAATGATTCGG 59.317 41.667 28.33 19.22 43.97 4.30
384 385 5.737063 GCATGAGGCATTTAAATGATTCGGT 60.737 40.000 28.33 14.72 43.97 4.69
385 386 6.514870 GCATGAGGCATTTAAATGATTCGGTA 60.515 38.462 28.33 11.20 43.97 4.02
386 387 7.424803 CATGAGGCATTTAAATGATTCGGTAA 58.575 34.615 28.33 10.91 38.70 2.85
387 388 7.397892 TGAGGCATTTAAATGATTCGGTAAA 57.602 32.000 28.33 8.26 38.70 2.01
388 389 7.831753 TGAGGCATTTAAATGATTCGGTAAAA 58.168 30.769 28.33 7.69 38.70 1.52
389 390 8.307483 TGAGGCATTTAAATGATTCGGTAAAAA 58.693 29.630 28.33 7.12 38.70 1.94
412 413 9.743581 AAAAATGATTGAAAGGGAAATAAGCAT 57.256 25.926 0.00 0.00 0.00 3.79
413 414 8.953368 AAATGATTGAAAGGGAAATAAGCATC 57.047 30.769 0.00 0.00 0.00 3.91
414 415 7.664552 ATGATTGAAAGGGAAATAAGCATCA 57.335 32.000 0.00 0.00 0.00 3.07
415 416 7.479352 TGATTGAAAGGGAAATAAGCATCAA 57.521 32.000 0.00 0.00 0.00 2.57
416 417 7.905265 TGATTGAAAGGGAAATAAGCATCAAA 58.095 30.769 0.00 0.00 0.00 2.69
417 418 8.542080 TGATTGAAAGGGAAATAAGCATCAAAT 58.458 29.630 0.00 0.00 0.00 2.32
419 420 9.822185 ATTGAAAGGGAAATAAGCATCAAATAC 57.178 29.630 0.00 0.00 0.00 1.89
420 421 8.359875 TGAAAGGGAAATAAGCATCAAATACA 57.640 30.769 0.00 0.00 0.00 2.29
421 422 8.980596 TGAAAGGGAAATAAGCATCAAATACAT 58.019 29.630 0.00 0.00 0.00 2.29
453 454 9.634163 TTTCATTATAGATTATGATACGTGCGT 57.366 29.630 0.00 2.05 31.34 5.24
454 455 9.634163 TTCATTATAGATTATGATACGTGCGTT 57.366 29.630 1.66 0.00 31.34 4.84
455 456 9.072294 TCATTATAGATTATGATACGTGCGTTG 57.928 33.333 1.66 0.00 0.00 4.10
456 457 5.763444 ATAGATTATGATACGTGCGTTGC 57.237 39.130 1.66 0.00 0.00 4.17
457 458 3.453424 AGATTATGATACGTGCGTTGCA 58.547 40.909 1.66 2.31 35.60 4.08
540 541 1.281899 CCTTTGTCTCGAGCGAATCC 58.718 55.000 7.81 0.00 0.00 3.01
831 832 3.217743 CGACCCTACCGCCCTCTC 61.218 72.222 0.00 0.00 0.00 3.20
1041 1043 3.062466 GGCCGCTTCACCTTTCCC 61.062 66.667 0.00 0.00 0.00 3.97
1630 1634 7.416777 GGGAAGCAAATCTTAGTTAATTGGGAG 60.417 40.741 0.00 0.00 34.56 4.30
2105 2113 1.072331 ACCCTGCTACAACCAGTGAAG 59.928 52.381 0.00 0.00 0.00 3.02
3070 3088 3.427909 GCGAATTTGTTCATGCTGGATCA 60.428 43.478 0.00 0.00 0.00 2.92
3151 3172 2.024176 ATTAGGCGAATCGTTGCTGT 57.976 45.000 4.07 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.521146 AGATCTAGGTGTTGCCATCTTTG 58.479 43.478 0.00 0.00 40.61 2.77
1 2 4.851639 AGATCTAGGTGTTGCCATCTTT 57.148 40.909 0.00 0.00 40.61 2.52
2 3 5.012561 GGATAGATCTAGGTGTTGCCATCTT 59.987 44.000 8.70 0.00 40.61 2.40
3 4 4.530161 GGATAGATCTAGGTGTTGCCATCT 59.470 45.833 8.70 0.00 40.61 2.90
4 5 4.530161 AGGATAGATCTAGGTGTTGCCATC 59.470 45.833 8.70 0.00 40.61 3.51
5 6 4.497516 AGGATAGATCTAGGTGTTGCCAT 58.502 43.478 8.70 0.00 40.61 4.40
6 7 3.928754 AGGATAGATCTAGGTGTTGCCA 58.071 45.455 8.70 0.00 40.61 4.92
7 8 4.636249 CAAGGATAGATCTAGGTGTTGCC 58.364 47.826 8.70 1.54 37.58 4.52
8 9 4.061596 GCAAGGATAGATCTAGGTGTTGC 58.938 47.826 18.51 18.51 0.00 4.17
9 10 4.346418 AGGCAAGGATAGATCTAGGTGTTG 59.654 45.833 8.70 9.78 0.00 3.33
10 11 4.561752 AGGCAAGGATAGATCTAGGTGTT 58.438 43.478 8.70 0.00 0.00 3.32
11 12 4.206244 AGGCAAGGATAGATCTAGGTGT 57.794 45.455 8.70 0.00 0.00 4.16
12 13 5.559148 AAAGGCAAGGATAGATCTAGGTG 57.441 43.478 8.70 4.78 0.00 4.00
13 14 6.296145 GCATAAAGGCAAGGATAGATCTAGGT 60.296 42.308 8.70 0.00 0.00 3.08
14 15 6.112058 GCATAAAGGCAAGGATAGATCTAGG 58.888 44.000 8.70 0.00 0.00 3.02
15 16 6.112058 GGCATAAAGGCAAGGATAGATCTAG 58.888 44.000 8.70 0.00 43.51 2.43
16 17 6.054860 GGCATAAAGGCAAGGATAGATCTA 57.945 41.667 4.57 4.57 43.51 1.98
17 18 4.916183 GGCATAAAGGCAAGGATAGATCT 58.084 43.478 0.00 0.00 43.51 2.75
29 30 1.003696 CCCCTAGCTAGGCATAAAGGC 59.996 57.143 31.33 0.00 42.26 4.35
37 38 0.466963 TTTAACGCCCCTAGCTAGGC 59.533 55.000 31.33 21.92 46.17 3.93
38 39 1.537562 CGTTTAACGCCCCTAGCTAGG 60.538 57.143 30.05 30.05 40.39 3.02
39 40 1.406539 TCGTTTAACGCCCCTAGCTAG 59.593 52.381 14.20 14.20 42.21 3.42
40 41 1.473258 TCGTTTAACGCCCCTAGCTA 58.527 50.000 13.06 0.00 42.21 3.32
41 42 0.828677 ATCGTTTAACGCCCCTAGCT 59.171 50.000 13.06 0.00 42.21 3.32
42 43 2.401351 CTATCGTTTAACGCCCCTAGC 58.599 52.381 13.06 0.00 42.21 3.42
43 44 2.401351 GCTATCGTTTAACGCCCCTAG 58.599 52.381 13.06 11.03 42.21 3.02
44 45 1.269206 CGCTATCGTTTAACGCCCCTA 60.269 52.381 13.06 0.00 42.21 3.53
45 46 0.529119 CGCTATCGTTTAACGCCCCT 60.529 55.000 13.06 0.31 42.21 4.79
46 47 1.929376 CGCTATCGTTTAACGCCCC 59.071 57.895 13.06 0.51 42.21 5.80
47 48 1.274770 GCGCTATCGTTTAACGCCC 59.725 57.895 13.06 0.17 43.58 6.13
48 49 4.866301 GCGCTATCGTTTAACGCC 57.134 55.556 13.06 0.51 43.58 5.68
50 51 3.081445 CAACAAGCGCTATCGTTTAACG 58.919 45.455 12.05 11.60 44.19 3.18
51 52 3.413558 CCAACAAGCGCTATCGTTTAAC 58.586 45.455 12.05 0.00 37.02 2.01
52 53 2.417239 CCCAACAAGCGCTATCGTTTAA 59.583 45.455 12.05 0.00 37.02 1.52
53 54 2.004017 CCCAACAAGCGCTATCGTTTA 58.996 47.619 12.05 0.00 37.02 2.01
54 55 0.802494 CCCAACAAGCGCTATCGTTT 59.198 50.000 12.05 0.00 39.71 3.60
55 56 0.036765 TCCCAACAAGCGCTATCGTT 60.037 50.000 12.05 12.35 38.14 3.85
56 57 0.460284 CTCCCAACAAGCGCTATCGT 60.460 55.000 12.05 5.66 38.14 3.73
57 58 1.154205 CCTCCCAACAAGCGCTATCG 61.154 60.000 12.05 4.88 39.07 2.92
58 59 1.440145 GCCTCCCAACAAGCGCTATC 61.440 60.000 12.05 0.00 0.00 2.08
59 60 1.452108 GCCTCCCAACAAGCGCTAT 60.452 57.895 12.05 0.00 0.00 2.97
60 61 2.046314 GCCTCCCAACAAGCGCTA 60.046 61.111 12.05 0.00 0.00 4.26
61 62 3.790416 TTGCCTCCCAACAAGCGCT 62.790 57.895 2.64 2.64 0.00 5.92
62 63 3.294493 TTGCCTCCCAACAAGCGC 61.294 61.111 0.00 0.00 0.00 5.92
72 73 6.478512 TGATTATAAAATTGGGTTGCCTCC 57.521 37.500 0.00 0.00 0.00 4.30
73 74 7.725251 TGATGATTATAAAATTGGGTTGCCTC 58.275 34.615 0.00 0.00 0.00 4.70
74 75 7.673641 TGATGATTATAAAATTGGGTTGCCT 57.326 32.000 0.00 0.00 0.00 4.75
91 92 9.950496 GACCACAAGATAACCTATATGATGATT 57.050 33.333 0.00 0.00 0.00 2.57
92 93 9.331466 AGACCACAAGATAACCTATATGATGAT 57.669 33.333 0.00 0.00 0.00 2.45
93 94 8.727100 AGACCACAAGATAACCTATATGATGA 57.273 34.615 0.00 0.00 0.00 2.92
94 95 8.037758 GGAGACCACAAGATAACCTATATGATG 58.962 40.741 0.00 0.00 0.00 3.07
95 96 7.958583 AGGAGACCACAAGATAACCTATATGAT 59.041 37.037 0.00 0.00 0.00 2.45
96 97 7.233553 CAGGAGACCACAAGATAACCTATATGA 59.766 40.741 0.00 0.00 0.00 2.15
97 98 7.382110 CAGGAGACCACAAGATAACCTATATG 58.618 42.308 0.00 0.00 0.00 1.78
98 99 6.498651 CCAGGAGACCACAAGATAACCTATAT 59.501 42.308 0.00 0.00 0.00 0.86
99 100 5.839063 CCAGGAGACCACAAGATAACCTATA 59.161 44.000 0.00 0.00 0.00 1.31
100 101 4.656112 CCAGGAGACCACAAGATAACCTAT 59.344 45.833 0.00 0.00 0.00 2.57
101 102 4.030913 CCAGGAGACCACAAGATAACCTA 58.969 47.826 0.00 0.00 0.00 3.08
102 103 2.840651 CCAGGAGACCACAAGATAACCT 59.159 50.000 0.00 0.00 0.00 3.50
103 104 2.838202 TCCAGGAGACCACAAGATAACC 59.162 50.000 0.00 0.00 0.00 2.85
104 105 4.080863 ACATCCAGGAGACCACAAGATAAC 60.081 45.833 0.00 0.00 0.00 1.89
105 106 4.104086 ACATCCAGGAGACCACAAGATAA 58.896 43.478 0.00 0.00 0.00 1.75
106 107 3.724478 ACATCCAGGAGACCACAAGATA 58.276 45.455 0.00 0.00 0.00 1.98
107 108 2.555664 ACATCCAGGAGACCACAAGAT 58.444 47.619 0.00 0.00 0.00 2.40
108 109 2.030027 ACATCCAGGAGACCACAAGA 57.970 50.000 0.00 0.00 0.00 3.02
109 110 2.867109 AACATCCAGGAGACCACAAG 57.133 50.000 0.00 0.00 0.00 3.16
110 111 4.715534 TTTAACATCCAGGAGACCACAA 57.284 40.909 0.00 0.00 0.00 3.33
111 112 4.927267 ATTTAACATCCAGGAGACCACA 57.073 40.909 0.00 0.00 0.00 4.17
112 113 7.201821 CCATAAATTTAACATCCAGGAGACCAC 60.202 40.741 1.21 0.00 0.00 4.16
113 114 6.833416 CCATAAATTTAACATCCAGGAGACCA 59.167 38.462 1.21 0.00 0.00 4.02
114 115 7.060421 TCCATAAATTTAACATCCAGGAGACC 58.940 38.462 1.21 0.00 0.00 3.85
115 116 7.775561 ACTCCATAAATTTAACATCCAGGAGAC 59.224 37.037 20.61 0.00 40.97 3.36
116 117 7.872138 ACTCCATAAATTTAACATCCAGGAGA 58.128 34.615 20.61 0.00 40.97 3.71
117 118 9.057089 GTACTCCATAAATTTAACATCCAGGAG 57.943 37.037 1.21 11.58 43.38 3.69
118 119 8.778059 AGTACTCCATAAATTTAACATCCAGGA 58.222 33.333 1.21 0.00 0.00 3.86
119 120 8.980481 AGTACTCCATAAATTTAACATCCAGG 57.020 34.615 1.21 0.00 0.00 4.45
121 122 9.967451 TGAAGTACTCCATAAATTTAACATCCA 57.033 29.630 1.21 0.00 0.00 3.41
123 124 9.916397 CGTGAAGTACTCCATAAATTTAACATC 57.084 33.333 1.21 0.00 0.00 3.06
124 125 8.889717 CCGTGAAGTACTCCATAAATTTAACAT 58.110 33.333 1.21 0.00 0.00 2.71
125 126 7.334921 CCCGTGAAGTACTCCATAAATTTAACA 59.665 37.037 1.21 0.00 0.00 2.41
126 127 7.550196 TCCCGTGAAGTACTCCATAAATTTAAC 59.450 37.037 1.21 0.00 0.00 2.01
127 128 7.622713 TCCCGTGAAGTACTCCATAAATTTAA 58.377 34.615 1.21 0.00 0.00 1.52
128 129 7.124599 TCTCCCGTGAAGTACTCCATAAATTTA 59.875 37.037 0.00 0.00 0.00 1.40
129 130 6.057321 TCCCGTGAAGTACTCCATAAATTT 57.943 37.500 0.00 0.00 0.00 1.82
130 131 5.424252 TCTCCCGTGAAGTACTCCATAAATT 59.576 40.000 0.00 0.00 0.00 1.82
131 132 4.960469 TCTCCCGTGAAGTACTCCATAAAT 59.040 41.667 0.00 0.00 0.00 1.40
132 133 4.346730 TCTCCCGTGAAGTACTCCATAAA 58.653 43.478 0.00 0.00 0.00 1.40
133 134 3.972133 TCTCCCGTGAAGTACTCCATAA 58.028 45.455 0.00 0.00 0.00 1.90
134 135 3.657398 TCTCCCGTGAAGTACTCCATA 57.343 47.619 0.00 0.00 0.00 2.74
135 136 2.526888 TCTCCCGTGAAGTACTCCAT 57.473 50.000 0.00 0.00 0.00 3.41
136 137 2.526888 ATCTCCCGTGAAGTACTCCA 57.473 50.000 0.00 0.00 0.00 3.86
137 138 5.532664 AAATATCTCCCGTGAAGTACTCC 57.467 43.478 0.00 0.00 0.00 3.85
138 139 6.338937 ACAAAATATCTCCCGTGAAGTACTC 58.661 40.000 0.00 0.00 0.00 2.59
139 140 6.295719 ACAAAATATCTCCCGTGAAGTACT 57.704 37.500 0.00 0.00 0.00 2.73
140 141 5.522824 GGACAAAATATCTCCCGTGAAGTAC 59.477 44.000 0.00 0.00 0.00 2.73
141 142 5.667466 GGACAAAATATCTCCCGTGAAGTA 58.333 41.667 0.00 0.00 0.00 2.24
142 143 4.514401 GGACAAAATATCTCCCGTGAAGT 58.486 43.478 0.00 0.00 0.00 3.01
143 144 3.555956 CGGACAAAATATCTCCCGTGAAG 59.444 47.826 0.00 0.00 33.02 3.02
144 145 3.196039 TCGGACAAAATATCTCCCGTGAA 59.804 43.478 0.00 0.00 38.25 3.18
145 146 2.761767 TCGGACAAAATATCTCCCGTGA 59.238 45.455 0.00 0.00 38.25 4.35
146 147 2.864343 GTCGGACAAAATATCTCCCGTG 59.136 50.000 2.62 0.00 38.25 4.94
147 148 2.498481 TGTCGGACAAAATATCTCCCGT 59.502 45.455 8.68 0.00 38.25 5.28
148 149 3.173668 TGTCGGACAAAATATCTCCCG 57.826 47.619 8.68 0.00 38.41 5.14
149 150 5.237344 CAGATTGTCGGACAAAATATCTCCC 59.763 44.000 25.64 8.08 41.96 4.30
150 151 5.237344 CCAGATTGTCGGACAAAATATCTCC 59.763 44.000 25.64 8.94 41.96 3.71
151 152 6.049149 TCCAGATTGTCGGACAAAATATCTC 58.951 40.000 25.64 17.27 41.96 2.75
152 153 5.989477 TCCAGATTGTCGGACAAAATATCT 58.011 37.500 25.64 19.99 41.96 1.98
153 154 6.049149 TCTCCAGATTGTCGGACAAAATATC 58.951 40.000 25.64 18.25 41.96 1.63
154 155 5.989477 TCTCCAGATTGTCGGACAAAATAT 58.011 37.500 25.64 10.77 41.96 1.28
155 156 5.414789 TCTCCAGATTGTCGGACAAAATA 57.585 39.130 25.64 5.17 41.96 1.40
156 157 4.256920 CTCTCCAGATTGTCGGACAAAAT 58.743 43.478 25.64 15.01 41.96 1.82
157 158 3.557054 CCTCTCCAGATTGTCGGACAAAA 60.557 47.826 25.64 6.31 41.96 2.44
158 159 2.028112 CCTCTCCAGATTGTCGGACAAA 60.028 50.000 25.64 9.51 41.96 2.83
159 160 1.550524 CCTCTCCAGATTGTCGGACAA 59.449 52.381 24.32 24.32 42.95 3.18
160 161 1.186200 CCTCTCCAGATTGTCGGACA 58.814 55.000 6.76 6.76 0.00 4.02
161 162 1.187087 ACCTCTCCAGATTGTCGGAC 58.813 55.000 0.00 0.00 0.00 4.79
162 163 2.820728 TACCTCTCCAGATTGTCGGA 57.179 50.000 0.00 0.00 0.00 4.55
163 164 5.730296 AATATACCTCTCCAGATTGTCGG 57.270 43.478 0.00 0.00 0.00 4.79
164 165 6.073548 GCAAAATATACCTCTCCAGATTGTCG 60.074 42.308 0.00 0.00 0.00 4.35
165 166 6.767902 TGCAAAATATACCTCTCCAGATTGTC 59.232 38.462 0.00 0.00 0.00 3.18
166 167 6.662755 TGCAAAATATACCTCTCCAGATTGT 58.337 36.000 0.00 0.00 0.00 2.71
167 168 7.360691 CGATGCAAAATATACCTCTCCAGATTG 60.361 40.741 0.00 0.00 0.00 2.67
168 169 6.652481 CGATGCAAAATATACCTCTCCAGATT 59.348 38.462 0.00 0.00 0.00 2.40
169 170 6.169094 CGATGCAAAATATACCTCTCCAGAT 58.831 40.000 0.00 0.00 0.00 2.90
170 171 5.070446 ACGATGCAAAATATACCTCTCCAGA 59.930 40.000 0.00 0.00 0.00 3.86
171 172 5.300752 ACGATGCAAAATATACCTCTCCAG 58.699 41.667 0.00 0.00 0.00 3.86
172 173 5.290493 ACGATGCAAAATATACCTCTCCA 57.710 39.130 0.00 0.00 0.00 3.86
173 174 7.097192 TGATACGATGCAAAATATACCTCTCC 58.903 38.462 0.00 0.00 0.00 3.71
174 175 8.709386 ATGATACGATGCAAAATATACCTCTC 57.291 34.615 0.00 0.00 0.00 3.20
175 176 8.314021 TGATGATACGATGCAAAATATACCTCT 58.686 33.333 0.00 0.00 0.00 3.69
176 177 8.479313 TGATGATACGATGCAAAATATACCTC 57.521 34.615 0.00 0.00 0.00 3.85
239 240 9.661563 GTCGGATCCAAAATATACATACCATAA 57.338 33.333 13.41 0.00 0.00 1.90
240 241 8.817876 TGTCGGATCCAAAATATACATACCATA 58.182 33.333 13.41 0.00 0.00 2.74
241 242 7.606456 GTGTCGGATCCAAAATATACATACCAT 59.394 37.037 13.41 0.00 0.00 3.55
242 243 6.932400 GTGTCGGATCCAAAATATACATACCA 59.068 38.462 13.41 0.00 0.00 3.25
243 244 6.370718 GGTGTCGGATCCAAAATATACATACC 59.629 42.308 13.41 0.30 0.00 2.73
244 245 6.370718 GGGTGTCGGATCCAAAATATACATAC 59.629 42.308 13.41 2.31 0.00 2.39
245 246 6.469410 GGGTGTCGGATCCAAAATATACATA 58.531 40.000 13.41 0.00 0.00 2.29
246 247 5.313712 GGGTGTCGGATCCAAAATATACAT 58.686 41.667 13.41 0.00 0.00 2.29
247 248 4.445162 GGGGTGTCGGATCCAAAATATACA 60.445 45.833 13.41 1.21 0.00 2.29
248 249 4.070009 GGGGTGTCGGATCCAAAATATAC 58.930 47.826 13.41 0.47 0.00 1.47
249 250 3.977999 AGGGGTGTCGGATCCAAAATATA 59.022 43.478 13.41 0.00 0.00 0.86
250 251 2.783510 AGGGGTGTCGGATCCAAAATAT 59.216 45.455 13.41 0.00 0.00 1.28
251 252 2.092646 CAGGGGTGTCGGATCCAAAATA 60.093 50.000 13.41 0.00 0.00 1.40
252 253 0.999712 AGGGGTGTCGGATCCAAAAT 59.000 50.000 13.41 0.00 0.00 1.82
253 254 0.037590 CAGGGGTGTCGGATCCAAAA 59.962 55.000 13.41 0.00 0.00 2.44
254 255 0.838554 TCAGGGGTGTCGGATCCAAA 60.839 55.000 13.41 0.00 0.00 3.28
255 256 0.620410 ATCAGGGGTGTCGGATCCAA 60.620 55.000 13.41 0.00 0.00 3.53
256 257 1.002921 ATCAGGGGTGTCGGATCCA 59.997 57.895 13.41 0.00 0.00 3.41
257 258 1.048724 TGATCAGGGGTGTCGGATCC 61.049 60.000 0.00 0.00 36.24 3.36
258 259 0.390860 CTGATCAGGGGTGTCGGATC 59.609 60.000 15.38 0.00 37.31 3.36
259 260 1.050988 CCTGATCAGGGGTGTCGGAT 61.051 60.000 31.14 0.00 44.87 4.18
260 261 1.685765 CCTGATCAGGGGTGTCGGA 60.686 63.158 31.14 0.00 44.87 4.55
261 262 2.903357 CCTGATCAGGGGTGTCGG 59.097 66.667 31.14 6.42 44.87 4.79
270 271 6.791887 ACGATGCAAAATATACCTGATCAG 57.208 37.500 16.24 16.24 0.00 2.90
271 272 8.093927 TGATACGATGCAAAATATACCTGATCA 58.906 33.333 0.00 0.00 0.00 2.92
272 273 8.479313 TGATACGATGCAAAATATACCTGATC 57.521 34.615 0.00 0.00 0.00 2.92
274 275 9.936759 TTATGATACGATGCAAAATATACCTGA 57.063 29.630 0.00 0.00 0.00 3.86
311 312 9.179909 ACGATCCAAAATAATAACACACCATAA 57.820 29.630 0.00 0.00 0.00 1.90
312 313 8.740123 ACGATCCAAAATAATAACACACCATA 57.260 30.769 0.00 0.00 0.00 2.74
313 314 7.639113 ACGATCCAAAATAATAACACACCAT 57.361 32.000 0.00 0.00 0.00 3.55
314 315 7.455641 AACGATCCAAAATAATAACACACCA 57.544 32.000 0.00 0.00 0.00 4.17
315 316 9.843334 TTAAACGATCCAAAATAATAACACACC 57.157 29.630 0.00 0.00 0.00 4.16
319 320 9.843334 GGTGTTAAACGATCCAAAATAATAACA 57.157 29.630 0.00 0.00 0.00 2.41
320 321 9.002080 CGGTGTTAAACGATCCAAAATAATAAC 57.998 33.333 0.00 0.00 0.00 1.89
321 322 7.697291 GCGGTGTTAAACGATCCAAAATAATAA 59.303 33.333 0.00 0.00 0.00 1.40
322 323 7.066043 AGCGGTGTTAAACGATCCAAAATAATA 59.934 33.333 0.00 0.00 0.00 0.98
323 324 6.031471 GCGGTGTTAAACGATCCAAAATAAT 58.969 36.000 0.00 0.00 0.00 1.28
324 325 5.181622 AGCGGTGTTAAACGATCCAAAATAA 59.818 36.000 0.00 0.00 0.00 1.40
325 326 4.696402 AGCGGTGTTAAACGATCCAAAATA 59.304 37.500 0.00 0.00 0.00 1.40
326 327 3.504520 AGCGGTGTTAAACGATCCAAAAT 59.495 39.130 0.00 0.00 0.00 1.82
327 328 2.879646 AGCGGTGTTAAACGATCCAAAA 59.120 40.909 0.00 0.00 0.00 2.44
328 329 2.481185 GAGCGGTGTTAAACGATCCAAA 59.519 45.455 0.00 0.00 39.36 3.28
329 330 2.070783 GAGCGGTGTTAAACGATCCAA 58.929 47.619 0.00 0.00 39.36 3.53
330 331 1.001068 TGAGCGGTGTTAAACGATCCA 59.999 47.619 10.03 0.00 44.05 3.41
331 332 1.717194 TGAGCGGTGTTAAACGATCC 58.283 50.000 10.03 0.00 44.05 3.36
332 333 5.006358 ACAATATGAGCGGTGTTAAACGATC 59.994 40.000 0.00 6.74 44.82 3.69
333 334 4.873827 ACAATATGAGCGGTGTTAAACGAT 59.126 37.500 0.00 0.00 0.00 3.73
334 335 4.247258 ACAATATGAGCGGTGTTAAACGA 58.753 39.130 0.00 0.00 0.00 3.85
335 336 4.593597 ACAATATGAGCGGTGTTAAACG 57.406 40.909 0.00 0.00 0.00 3.60
336 337 5.092781 CCAACAATATGAGCGGTGTTAAAC 58.907 41.667 0.00 0.00 33.04 2.01
337 338 4.156922 CCCAACAATATGAGCGGTGTTAAA 59.843 41.667 0.00 0.00 33.04 1.52
338 339 3.692101 CCCAACAATATGAGCGGTGTTAA 59.308 43.478 0.00 0.00 33.04 2.01
339 340 3.275143 CCCAACAATATGAGCGGTGTTA 58.725 45.455 0.00 0.00 33.04 2.41
340 341 2.091541 CCCAACAATATGAGCGGTGTT 58.908 47.619 0.00 0.00 34.60 3.32
341 342 1.750193 CCCAACAATATGAGCGGTGT 58.250 50.000 0.00 0.00 0.00 4.16
342 343 0.381801 GCCCAACAATATGAGCGGTG 59.618 55.000 0.00 0.00 0.00 4.94
343 344 0.034574 TGCCCAACAATATGAGCGGT 60.035 50.000 0.00 0.00 0.00 5.68
344 345 1.001048 CATGCCCAACAATATGAGCGG 60.001 52.381 0.00 0.00 0.00 5.52
345 346 1.948834 TCATGCCCAACAATATGAGCG 59.051 47.619 0.00 0.00 0.00 5.03
346 347 2.295349 CCTCATGCCCAACAATATGAGC 59.705 50.000 0.00 0.00 43.12 4.26
347 348 2.295349 GCCTCATGCCCAACAATATGAG 59.705 50.000 0.00 0.00 43.74 2.90
348 349 2.309613 GCCTCATGCCCAACAATATGA 58.690 47.619 0.00 0.00 0.00 2.15
349 350 2.033372 TGCCTCATGCCCAACAATATG 58.967 47.619 0.00 0.00 40.16 1.78
350 351 2.457813 TGCCTCATGCCCAACAATAT 57.542 45.000 0.00 0.00 40.16 1.28
351 352 2.457813 ATGCCTCATGCCCAACAATA 57.542 45.000 0.00 0.00 40.16 1.90
352 353 1.575419 AATGCCTCATGCCCAACAAT 58.425 45.000 0.00 0.00 40.16 2.71
353 354 1.350071 AAATGCCTCATGCCCAACAA 58.650 45.000 0.00 0.00 40.16 2.83
354 355 2.228545 TAAATGCCTCATGCCCAACA 57.771 45.000 0.00 0.00 40.16 3.33
355 356 3.608316 TTTAAATGCCTCATGCCCAAC 57.392 42.857 0.00 0.00 40.16 3.77
356 357 3.773667 TCATTTAAATGCCTCATGCCCAA 59.226 39.130 21.15 0.00 40.16 4.12
357 358 3.372897 TCATTTAAATGCCTCATGCCCA 58.627 40.909 21.15 0.00 40.16 5.36
358 359 4.612264 ATCATTTAAATGCCTCATGCCC 57.388 40.909 21.15 0.00 40.16 5.36
359 360 4.682860 CGAATCATTTAAATGCCTCATGCC 59.317 41.667 21.15 6.71 40.16 4.40
360 361 4.682860 CCGAATCATTTAAATGCCTCATGC 59.317 41.667 21.15 8.90 41.77 4.06
361 362 5.835257 ACCGAATCATTTAAATGCCTCATG 58.165 37.500 21.15 14.77 36.36 3.07
362 363 7.581213 TTACCGAATCATTTAAATGCCTCAT 57.419 32.000 21.15 8.48 36.36 2.90
363 364 7.397892 TTTACCGAATCATTTAAATGCCTCA 57.602 32.000 21.15 6.54 36.36 3.86
364 365 8.696410 TTTTTACCGAATCATTTAAATGCCTC 57.304 30.769 21.15 17.37 36.36 4.70
386 387 9.743581 ATGCTTATTTCCCTTTCAATCATTTTT 57.256 25.926 0.00 0.00 0.00 1.94
387 388 9.387257 GATGCTTATTTCCCTTTCAATCATTTT 57.613 29.630 0.00 0.00 0.00 1.82
388 389 8.542080 TGATGCTTATTTCCCTTTCAATCATTT 58.458 29.630 0.00 0.00 0.00 2.32
389 390 8.081517 TGATGCTTATTTCCCTTTCAATCATT 57.918 30.769 0.00 0.00 0.00 2.57
390 391 7.664552 TGATGCTTATTTCCCTTTCAATCAT 57.335 32.000 0.00 0.00 0.00 2.45
391 392 7.479352 TTGATGCTTATTTCCCTTTCAATCA 57.521 32.000 0.00 0.00 0.00 2.57
392 393 8.953368 ATTTGATGCTTATTTCCCTTTCAATC 57.047 30.769 0.00 0.00 0.00 2.67
393 394 9.822185 GTATTTGATGCTTATTTCCCTTTCAAT 57.178 29.630 0.00 0.00 0.00 2.57
394 395 8.811017 TGTATTTGATGCTTATTTCCCTTTCAA 58.189 29.630 0.00 0.00 0.00 2.69
395 396 8.359875 TGTATTTGATGCTTATTTCCCTTTCA 57.640 30.769 0.00 0.00 0.00 2.69
427 428 9.634163 ACGCACGTATCATAATCTATAATGAAA 57.366 29.630 0.00 0.00 35.82 2.69
428 429 9.634163 AACGCACGTATCATAATCTATAATGAA 57.366 29.630 0.00 0.00 35.82 2.57
429 430 9.072294 CAACGCACGTATCATAATCTATAATGA 57.928 33.333 0.00 0.00 36.60 2.57
430 431 7.841277 GCAACGCACGTATCATAATCTATAATG 59.159 37.037 0.00 0.00 0.00 1.90
431 432 7.544217 TGCAACGCACGTATCATAATCTATAAT 59.456 33.333 0.00 0.00 31.71 1.28
432 433 6.864165 TGCAACGCACGTATCATAATCTATAA 59.136 34.615 0.00 0.00 31.71 0.98
433 434 6.383415 TGCAACGCACGTATCATAATCTATA 58.617 36.000 0.00 0.00 31.71 1.31
434 435 5.227152 TGCAACGCACGTATCATAATCTAT 58.773 37.500 0.00 0.00 31.71 1.98
435 436 4.612943 TGCAACGCACGTATCATAATCTA 58.387 39.130 0.00 0.00 31.71 1.98
436 437 3.453424 TGCAACGCACGTATCATAATCT 58.547 40.909 0.00 0.00 31.71 2.40
437 438 3.852471 TGCAACGCACGTATCATAATC 57.148 42.857 0.00 0.00 31.71 1.75
455 456 1.429463 ACTAGTAAGCTTGCACGTGC 58.571 50.000 33.11 33.11 42.50 5.34
456 457 5.779806 ATTAACTAGTAAGCTTGCACGTG 57.220 39.130 17.21 12.28 0.00 4.49
457 458 8.488651 AATAATTAACTAGTAAGCTTGCACGT 57.511 30.769 17.21 9.78 0.00 4.49
496 497 2.494591 CCTCGAGCGCGTACGAAAC 61.495 63.158 21.65 6.99 43.93 2.78
518 519 3.843240 CGCTCGAGACAAAGGCGC 61.843 66.667 18.75 0.00 39.42 6.53
519 520 1.078759 ATTCGCTCGAGACAAAGGCG 61.079 55.000 18.75 11.87 45.93 5.52
559 560 4.468689 GTGGGGTCCGGCTGTAGC 62.469 72.222 0.00 0.00 41.14 3.58
736 737 2.664436 CGCCGTCGACCAGGAAAAC 61.664 63.158 10.58 0.00 38.10 2.43
831 832 1.987855 TTGTAGAGCTCCCACCGGG 60.988 63.158 10.93 0.00 46.11 5.73
834 835 0.108756 GTCGTTGTAGAGCTCCCACC 60.109 60.000 10.93 0.00 0.00 4.61
951 953 2.954611 GGCTTTGTGGAGGAACGC 59.045 61.111 0.00 0.00 0.00 4.84
1027 1029 0.108138 AGATCGGGAAAGGTGAAGCG 60.108 55.000 0.00 0.00 0.00 4.68
1041 1043 2.289002 GCAATGCTGGTTTCCTAGATCG 59.711 50.000 0.00 0.00 0.00 3.69
1630 1634 5.941788 AGAATGGATAAACATACAGTCCCC 58.058 41.667 0.00 0.00 0.00 4.81
2105 2113 4.883585 TCCTGACATATGAAATGTGCTTCC 59.116 41.667 10.38 0.00 39.27 3.46
3070 3088 3.118000 TGAGGAGCAGCATCAATCAGAAT 60.118 43.478 0.00 0.00 33.80 2.40
3151 3172 3.370527 GCCTAGTTATCACCCAGCAAGAA 60.371 47.826 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.