Multiple sequence alignment - TraesCS7D01G393700

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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 TraesCS7D01G393700 chr7D 100.000 3149 0 0 1 3149 509199255 509202403 0.000000e+00 5816.0
1 TraesCS7D01G393700 chr7D 81.556 347 35 16 2826 3149 622542296 622541956 3.120000e-65 259.0
2 TraesCS7D01G393700 chr7D 85.965 114 11 1 101 209 625034703 625034590 1.980000e-22 117.0
3 TraesCS7D01G393700 chr7D 83.871 124 13 5 3028 3149 574296637 574296519 9.230000e-21 111.0
4 TraesCS7D01G393700 chr7A 92.870 1613 86 16 789 2397 579732537 579734124 0.000000e+00 2314.0
5 TraesCS7D01G393700 chr7A 91.815 672 50 4 2481 3148 579734122 579734792 0.000000e+00 931.0
6 TraesCS7D01G393700 chr7A 90.132 608 35 12 209 796 579729543 579730145 0.000000e+00 767.0
7 TraesCS7D01G393700 chr7A 90.566 106 8 2 2385 2488 51360354 51360459 4.240000e-29 139.0
8 TraesCS7D01G393700 chr7A 81.967 122 13 4 96 209 647173660 647173780 9.300000e-16 95.3
9 TraesCS7D01G393700 chr7B 93.270 1471 75 9 864 2328 537384072 537385524 0.000000e+00 2146.0
10 TraesCS7D01G393700 chr7B 85.421 535 37 19 208 730 537383457 537383962 4.660000e-143 518.0
11 TraesCS7D01G393700 chr7B 96.875 96 3 0 716 811 537383979 537384074 9.040000e-36 161.0
12 TraesCS7D01G393700 chr1D 81.341 343 47 10 2822 3149 59302915 59303255 2.410000e-66 263.0
13 TraesCS7D01G393700 chr5A 83.688 282 31 7 2882 3149 452125859 452125579 5.210000e-63 252.0
14 TraesCS7D01G393700 chr5A 76.900 329 47 18 2837 3149 343963527 343963212 3.250000e-35 159.0
15 TraesCS7D01G393700 chr5A 94.681 94 3 2 2389 2481 18658576 18658668 9.100000e-31 145.0
16 TraesCS7D01G393700 chr5B 79.765 341 48 12 2822 3148 499387225 499387558 8.790000e-56 228.0
17 TraesCS7D01G393700 chr5B 87.805 82 8 2 135 214 605957931 605957850 9.300000e-16 95.3
18 TraesCS7D01G393700 chr2B 81.509 265 32 8 2827 3075 644843683 644843420 5.330000e-48 202.0
19 TraesCS7D01G393700 chr3A 91.743 109 6 3 2382 2488 127972383 127972276 7.040000e-32 148.0
20 TraesCS7D01G393700 chr3A 93.684 95 4 2 2396 2488 641469084 641468990 1.180000e-29 141.0
21 TraesCS7D01G393700 chr3A 90.566 106 8 2 2385 2488 9970349 9970244 4.240000e-29 139.0
22 TraesCS7D01G393700 chr3A 100.000 35 0 0 3113 3147 725069949 725069983 7.290000e-07 65.8
23 TraesCS7D01G393700 chr3B 83.529 170 14 10 2488 2645 711541153 711540986 2.530000e-31 147.0
24 TraesCS7D01G393700 chr3B 92.000 100 7 1 2390 2488 696703687 696703786 4.240000e-29 139.0
25 TraesCS7D01G393700 chr3B 83.200 125 12 5 94 209 726745346 726745470 4.300000e-19 106.0
26 TraesCS7D01G393700 chr3B 82.787 122 14 3 96 210 813590636 813590757 5.560000e-18 102.0
27 TraesCS7D01G393700 chr3B 81.148 122 16 3 96 210 813465992 813466113 1.200000e-14 91.6
28 TraesCS7D01G393700 chr3B 100.000 35 0 0 3113 3147 797728433 797728467 7.290000e-07 65.8
29 TraesCS7D01G393700 chr3B 94.872 39 2 0 3111 3149 797729413 797729451 9.430000e-06 62.1
30 TraesCS7D01G393700 chr3D 93.750 96 5 1 2386 2481 528183640 528183546 3.270000e-30 143.0
31 TraesCS7D01G393700 chr4A 83.544 158 19 6 2488 2641 722929261 722929415 1.180000e-29 141.0
32 TraesCS7D01G393700 chr4A 91.139 79 5 1 2591 2667 723476157 723476079 4.300000e-19 106.0
33 TraesCS7D01G393700 chr1A 92.857 98 6 1 2384 2481 44363428 44363332 1.180000e-29 141.0
34 TraesCS7D01G393700 chr1A 94.444 90 4 1 2400 2488 258741943 258741854 1.520000e-28 137.0
35 TraesCS7D01G393700 chr1B 83.200 125 19 1 2545 2667 632766523 632766647 2.570000e-21 113.0
36 TraesCS7D01G393700 chr1B 97.222 36 1 0 2629 2664 448528129 448528164 9.430000e-06 62.1
37 TraesCS7D01G393700 chr5D 83.333 120 16 3 96 214 6105733 6105849 1.190000e-19 108.0
38 TraesCS7D01G393700 chr4D 81.967 122 16 3 96 211 7705735 7705856 7.190000e-17 99.0
39 TraesCS7D01G393700 chr2A 80.328 122 22 1 2545 2664 611003654 611003775 1.200000e-14 91.6
40 TraesCS7D01G393700 chr6D 77.901 181 7 13 2488 2635 129709020 129709200 7.240000e-12 82.4
41 TraesCS7D01G393700 chr6A 91.379 58 3 1 2586 2641 168008156 168008213 9.360000e-11 78.7
42 TraesCS7D01G393700 chr6A 100.000 33 0 0 2545 2577 168008098 168008130 9.430000e-06 62.1
43 TraesCS7D01G393700 chr6B 80.556 108 6 7 2488 2580 156664098 156663991 5.640000e-08 69.4


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 TraesCS7D01G393700 chr7D 509199255 509202403 3148 False 5816.000000 5816 100.000000 1 3149 1 chr7D.!!$F1 3148
1 TraesCS7D01G393700 chr7A 579729543 579734792 5249 False 1337.333333 2314 91.605667 209 3148 3 chr7A.!!$F3 2939
2 TraesCS7D01G393700 chr7B 537383457 537385524 2067 False 941.666667 2146 91.855333 208 2328 3 chr7B.!!$F1 2120

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
865 3319 0.320771 AGGCAACGTCTGTCATGACC 60.321 55.0 22.85 6.94 46.39 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2852 5326 0.249398 ACCACACGAGATAAGCCACC 59.751 55.0 0.0 0.0 0.0 4.61 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
56 57 9.621629 TTTAGTTTTCTCTAAATGGTTGAGACA 57.378 29.630 0.00 0.00 36.69 3.41
57 58 9.793259 TTAGTTTTCTCTAAATGGTTGAGACAT 57.207 29.630 0.00 0.00 36.69 3.06
58 59 8.697507 AGTTTTCTCTAAATGGTTGAGACATT 57.302 30.769 0.00 0.00 40.07 2.71
59 60 9.136323 AGTTTTCTCTAAATGGTTGAGACATTT 57.864 29.630 8.25 8.25 46.76 2.32
60 61 9.399403 GTTTTCTCTAAATGGTTGAGACATTTC 57.601 33.333 6.66 0.00 44.75 2.17
61 62 7.687941 TTCTCTAAATGGTTGAGACATTTCC 57.312 36.000 6.66 0.00 44.75 3.13
62 63 6.180472 TCTCTAAATGGTTGAGACATTTCCC 58.820 40.000 6.66 0.00 44.75 3.97
63 64 6.012508 TCTCTAAATGGTTGAGACATTTCCCT 60.013 38.462 6.66 0.00 44.75 4.20
64 65 6.552008 TCTAAATGGTTGAGACATTTCCCTT 58.448 36.000 6.66 0.00 44.75 3.95
65 66 7.010160 TCTAAATGGTTGAGACATTTCCCTTT 58.990 34.615 6.66 0.00 44.75 3.11
66 67 6.499106 AAATGGTTGAGACATTTCCCTTTT 57.501 33.333 0.00 0.00 43.03 2.27
67 68 6.499106 AATGGTTGAGACATTTCCCTTTTT 57.501 33.333 0.00 0.00 35.11 1.94
68 69 5.529581 TGGTTGAGACATTTCCCTTTTTC 57.470 39.130 0.00 0.00 0.00 2.29
69 70 5.208121 TGGTTGAGACATTTCCCTTTTTCT 58.792 37.500 0.00 0.00 0.00 2.52
70 71 5.660864 TGGTTGAGACATTTCCCTTTTTCTT 59.339 36.000 0.00 0.00 0.00 2.52
71 72 6.156083 TGGTTGAGACATTTCCCTTTTTCTTT 59.844 34.615 0.00 0.00 0.00 2.52
72 73 7.047891 GGTTGAGACATTTCCCTTTTTCTTTT 58.952 34.615 0.00 0.00 0.00 2.27
73 74 7.552687 GGTTGAGACATTTCCCTTTTTCTTTTT 59.447 33.333 0.00 0.00 0.00 1.94
74 75 8.390354 GTTGAGACATTTCCCTTTTTCTTTTTG 58.610 33.333 0.00 0.00 0.00 2.44
75 76 7.846066 TGAGACATTTCCCTTTTTCTTTTTGA 58.154 30.769 0.00 0.00 0.00 2.69
76 77 7.981225 TGAGACATTTCCCTTTTTCTTTTTGAG 59.019 33.333 0.00 0.00 0.00 3.02
77 78 8.078060 AGACATTTCCCTTTTTCTTTTTGAGA 57.922 30.769 0.00 0.00 0.00 3.27
78 79 8.539544 AGACATTTCCCTTTTTCTTTTTGAGAA 58.460 29.630 0.00 0.00 42.56 2.87
131 132 3.491581 GTCCACGTGACACGAGAAT 57.508 52.632 33.12 9.07 46.05 2.40
132 133 1.779569 GTCCACGTGACACGAGAATT 58.220 50.000 33.12 8.67 46.05 2.17
133 134 1.455786 GTCCACGTGACACGAGAATTG 59.544 52.381 33.12 19.76 46.05 2.32
134 135 1.067974 TCCACGTGACACGAGAATTGT 59.932 47.619 33.12 7.10 46.05 2.71
135 136 2.293955 TCCACGTGACACGAGAATTGTA 59.706 45.455 33.12 5.86 46.05 2.41
136 137 3.054166 CCACGTGACACGAGAATTGTAA 58.946 45.455 33.12 0.00 46.05 2.41
137 138 3.678072 CCACGTGACACGAGAATTGTAAT 59.322 43.478 33.12 4.76 46.05 1.89
138 139 4.151689 CCACGTGACACGAGAATTGTAATT 59.848 41.667 33.12 4.21 46.05 1.40
139 140 5.333798 CCACGTGACACGAGAATTGTAATTT 60.334 40.000 33.12 4.00 46.05 1.82
140 141 6.133392 CACGTGACACGAGAATTGTAATTTT 58.867 36.000 33.12 3.54 46.05 1.82
141 142 6.084939 CACGTGACACGAGAATTGTAATTTTG 59.915 38.462 33.12 12.36 46.05 2.44
142 143 6.018588 ACGTGACACGAGAATTGTAATTTTGA 60.019 34.615 33.12 0.00 46.05 2.69
143 144 6.516355 CGTGACACGAGAATTGTAATTTTGAG 59.484 38.462 23.39 0.00 46.05 3.02
144 145 7.568679 CGTGACACGAGAATTGTAATTTTGAGA 60.569 37.037 23.39 0.00 46.05 3.27
145 146 8.230486 GTGACACGAGAATTGTAATTTTGAGAT 58.770 33.333 0.00 0.00 0.00 2.75
146 147 8.229811 TGACACGAGAATTGTAATTTTGAGATG 58.770 33.333 0.00 0.00 0.00 2.90
147 148 8.322906 ACACGAGAATTGTAATTTTGAGATGA 57.677 30.769 0.00 0.00 0.00 2.92
148 149 8.783093 ACACGAGAATTGTAATTTTGAGATGAA 58.217 29.630 0.00 0.00 0.00 2.57
149 150 9.270576 CACGAGAATTGTAATTTTGAGATGAAG 57.729 33.333 0.00 0.00 0.00 3.02
150 151 8.454106 ACGAGAATTGTAATTTTGAGATGAAGG 58.546 33.333 0.00 0.00 0.00 3.46
151 152 8.454106 CGAGAATTGTAATTTTGAGATGAAGGT 58.546 33.333 0.00 0.00 0.00 3.50
152 153 9.565213 GAGAATTGTAATTTTGAGATGAAGGTG 57.435 33.333 0.00 0.00 0.00 4.00
153 154 9.300681 AGAATTGTAATTTTGAGATGAAGGTGA 57.699 29.630 0.00 0.00 0.00 4.02
154 155 9.565213 GAATTGTAATTTTGAGATGAAGGTGAG 57.435 33.333 0.00 0.00 0.00 3.51
155 156 7.452880 TTGTAATTTTGAGATGAAGGTGAGG 57.547 36.000 0.00 0.00 0.00 3.86
156 157 6.542821 TGTAATTTTGAGATGAAGGTGAGGT 58.457 36.000 0.00 0.00 0.00 3.85
157 158 5.972107 AATTTTGAGATGAAGGTGAGGTG 57.028 39.130 0.00 0.00 0.00 4.00
158 159 2.479566 TTGAGATGAAGGTGAGGTGC 57.520 50.000 0.00 0.00 0.00 5.01
159 160 1.351076 TGAGATGAAGGTGAGGTGCA 58.649 50.000 0.00 0.00 0.00 4.57
160 161 1.002430 TGAGATGAAGGTGAGGTGCAC 59.998 52.381 8.80 8.80 46.98 4.57
171 172 3.660621 GGTGCACACAGCTTCCTC 58.339 61.111 20.43 0.00 45.94 3.71
172 173 1.227943 GGTGCACACAGCTTCCTCA 60.228 57.895 20.43 0.00 45.94 3.86
173 174 0.607489 GGTGCACACAGCTTCCTCAT 60.607 55.000 20.43 0.00 45.94 2.90
174 175 1.339055 GGTGCACACAGCTTCCTCATA 60.339 52.381 20.43 0.00 45.94 2.15
175 176 2.426522 GTGCACACAGCTTCCTCATAA 58.573 47.619 13.17 0.00 45.94 1.90
176 177 2.417933 GTGCACACAGCTTCCTCATAAG 59.582 50.000 13.17 0.00 45.94 1.73
182 183 2.993539 GCTTCCTCATAAGCGGTCC 58.006 57.895 0.00 0.00 42.21 4.46
183 184 0.876342 GCTTCCTCATAAGCGGTCCG 60.876 60.000 6.99 6.99 42.21 4.79
206 207 4.796495 GCGGGCCCCAACCACTAG 62.796 72.222 18.66 0.00 0.00 2.57
217 218 3.118261 CCCAACCACTAGTCACATAGCAT 60.118 47.826 0.00 0.00 0.00 3.79
246 248 2.017049 GGTATCATGGTTGCTGGTCAC 58.983 52.381 0.00 0.00 0.00 3.67
272 274 2.695359 TCAGCCTTAACTGTAAAGCGG 58.305 47.619 0.00 0.00 38.84 5.52
398 400 6.881017 TCGAGCGATCAAATGATTAGATTTG 58.119 36.000 0.00 0.00 42.40 2.32
406 408 7.218228 TCAAATGATTAGATTTGCACACACT 57.782 32.000 0.00 0.00 41.31 3.55
407 409 7.307694 TCAAATGATTAGATTTGCACACACTC 58.692 34.615 0.00 0.00 41.31 3.51
408 410 6.822667 AATGATTAGATTTGCACACACTCA 57.177 33.333 0.00 0.00 0.00 3.41
409 411 6.822667 ATGATTAGATTTGCACACACTCAA 57.177 33.333 0.00 0.00 0.00 3.02
412 424 3.213206 AGATTTGCACACACTCAAGGA 57.787 42.857 0.00 0.00 0.00 3.36
437 449 6.487668 ACCGTATTTTGGTTAGCAAAACTAGT 59.512 34.615 21.92 14.65 35.82 2.57
480 492 0.743688 TGCGTGCATGTTCTTGGTTT 59.256 45.000 7.93 0.00 0.00 3.27
481 493 1.135915 TGCGTGCATGTTCTTGGTTTT 59.864 42.857 7.93 0.00 0.00 2.43
506 519 2.632996 ACTCCAGGAGTCGTTGAATCAA 59.367 45.455 17.31 0.00 38.71 2.57
507 520 3.071023 ACTCCAGGAGTCGTTGAATCAAA 59.929 43.478 17.31 0.00 38.71 2.69
513 526 3.062234 GGAGTCGTTGAATCAAACCGATC 59.938 47.826 10.97 9.48 31.11 3.69
537 550 3.864944 GCAATGCAATGCAAGCGT 58.135 50.000 21.74 6.70 43.62 5.07
538 551 3.033114 GCAATGCAATGCAAGCGTA 57.967 47.368 21.74 0.00 43.62 4.42
539 552 0.641783 GCAATGCAATGCAAGCGTAC 59.358 50.000 21.74 0.00 43.62 3.67
540 553 1.979897 CAATGCAATGCAAGCGTACA 58.020 45.000 13.45 0.00 43.62 2.90
568 581 1.153539 TGGTTGATTGGAGTTCCCCA 58.846 50.000 0.00 0.00 34.29 4.96
569 582 1.715931 TGGTTGATTGGAGTTCCCCAT 59.284 47.619 0.00 0.00 35.87 4.00
570 583 2.102578 GGTTGATTGGAGTTCCCCATG 58.897 52.381 0.00 0.00 35.87 3.66
571 584 2.557452 GGTTGATTGGAGTTCCCCATGT 60.557 50.000 0.00 0.00 35.87 3.21
572 585 3.308832 GGTTGATTGGAGTTCCCCATGTA 60.309 47.826 0.00 0.00 35.87 2.29
604 628 4.096532 TGACTACGATGGAGCAACTAAGAG 59.903 45.833 0.00 0.00 0.00 2.85
618 642 5.179368 GCAACTAAGAGTGTTTGTCTGCATA 59.821 40.000 12.62 0.00 0.00 3.14
621 645 5.877012 ACTAAGAGTGTTTGTCTGCATATGG 59.123 40.000 4.56 0.00 0.00 2.74
624 648 3.424703 AGTGTTTGTCTGCATATGGCTT 58.575 40.909 4.56 0.00 45.15 4.35
626 650 4.281688 AGTGTTTGTCTGCATATGGCTTTT 59.718 37.500 4.56 0.00 45.15 2.27
630 654 7.432252 GTGTTTGTCTGCATATGGCTTTTATAC 59.568 37.037 4.56 0.00 45.15 1.47
644 668 6.537301 TGGCTTTTATACGTACAATTCTGGAG 59.463 38.462 0.00 0.00 0.00 3.86
740 795 4.461781 AGTTAGTTAGTACTGTCCACGCAT 59.538 41.667 5.39 0.00 35.78 4.73
772 827 2.558359 CAAAGATTTCAGTGACCCCACC 59.442 50.000 0.00 0.00 44.22 4.61
812 3266 5.920273 TGCACTTAATTTGCAGCTTTACTTC 59.080 36.000 7.61 0.00 45.06 3.01
820 3274 2.938451 TGCAGCTTTACTTCCATCGATG 59.062 45.455 18.76 18.76 0.00 3.84
843 3297 6.351711 TGGATCAACCATACAAGATGAAGAG 58.648 40.000 0.00 0.00 44.64 2.85
844 3298 6.156775 TGGATCAACCATACAAGATGAAGAGA 59.843 38.462 0.00 0.00 44.64 3.10
845 3299 6.705381 GGATCAACCATACAAGATGAAGAGAG 59.295 42.308 0.00 0.00 38.79 3.20
846 3300 6.857437 TCAACCATACAAGATGAAGAGAGA 57.143 37.500 0.00 0.00 0.00 3.10
847 3301 6.871844 TCAACCATACAAGATGAAGAGAGAG 58.128 40.000 0.00 0.00 0.00 3.20
849 3303 4.100808 ACCATACAAGATGAAGAGAGAGGC 59.899 45.833 0.00 0.00 0.00 4.70
850 3304 4.100653 CCATACAAGATGAAGAGAGAGGCA 59.899 45.833 0.00 0.00 0.00 4.75
851 3305 5.396101 CCATACAAGATGAAGAGAGAGGCAA 60.396 44.000 0.00 0.00 0.00 4.52
852 3306 3.936564 ACAAGATGAAGAGAGAGGCAAC 58.063 45.455 0.00 0.00 0.00 4.17
853 3307 2.928757 CAAGATGAAGAGAGAGGCAACG 59.071 50.000 0.00 0.00 46.39 4.10
854 3308 2.175202 AGATGAAGAGAGAGGCAACGT 58.825 47.619 0.00 0.00 46.39 3.99
855 3309 2.165437 AGATGAAGAGAGAGGCAACGTC 59.835 50.000 0.00 0.00 46.39 4.34
856 3310 1.621992 TGAAGAGAGAGGCAACGTCT 58.378 50.000 0.00 0.00 46.39 4.18
857 3311 1.270826 TGAAGAGAGAGGCAACGTCTG 59.729 52.381 0.00 0.00 46.39 3.51
858 3312 1.271102 GAAGAGAGAGGCAACGTCTGT 59.729 52.381 0.00 0.00 46.39 3.41
859 3313 0.885196 AGAGAGAGGCAACGTCTGTC 59.115 55.000 6.39 6.39 46.39 3.51
860 3314 0.598562 GAGAGAGGCAACGTCTGTCA 59.401 55.000 8.92 0.00 46.39 3.58
861 3315 1.203523 GAGAGAGGCAACGTCTGTCAT 59.796 52.381 8.92 0.00 46.39 3.06
862 3316 1.067283 AGAGAGGCAACGTCTGTCATG 60.067 52.381 3.27 0.00 46.39 3.07
863 3317 0.969149 AGAGGCAACGTCTGTCATGA 59.031 50.000 0.00 0.00 46.39 3.07
864 3318 1.071605 GAGGCAACGTCTGTCATGAC 58.928 55.000 19.27 19.27 46.39 3.06
865 3319 0.320771 AGGCAACGTCTGTCATGACC 60.321 55.000 22.85 6.94 46.39 4.02
883 3337 2.819019 GACCCCTATTAGTAGTCGAGGC 59.181 54.545 0.00 0.00 0.00 4.70
1301 3773 1.599047 CCACTGACTCCGCTCCAAT 59.401 57.895 0.00 0.00 0.00 3.16
1384 3856 2.045280 CTCCTACGCCTCCTCATGG 58.955 63.158 0.00 0.00 0.00 3.66
1397 3869 3.197790 CATGGTTCGGAGCAGCGG 61.198 66.667 0.47 0.00 36.60 5.52
1434 3906 3.604629 GCACTCGACTGCCTCCTA 58.395 61.111 5.81 0.00 0.00 2.94
1446 3918 4.253257 CTCCTAGCGTCGCCGTCC 62.253 72.222 14.86 0.00 36.15 4.79
1509 3981 1.681486 CCTCCTCCTTCGCCTTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
1510 3982 1.681486 CTCCTCCTTCGCCTTCCTCC 61.681 65.000 0.00 0.00 0.00 4.30
1512 3984 1.519719 CTCCTTCGCCTTCCTCCTG 59.480 63.158 0.00 0.00 0.00 3.86
1518 3990 0.967887 TCGCCTTCCTCCTGAGACAG 60.968 60.000 0.00 0.00 0.00 3.51
1538 4010 1.002011 GGAGCCCCAAGGTCAAGAC 60.002 63.158 0.00 0.00 45.21 3.01
1541 4013 1.973812 GCCCCAAGGTCAAGACAGC 60.974 63.158 2.29 0.00 34.57 4.40
1572 4044 0.968901 TAATCCACACCGTCGGAGCT 60.969 55.000 20.51 0.00 33.97 4.09
1632 4104 2.352422 GTCATGGGAGCACTGGCA 59.648 61.111 0.00 0.00 44.61 4.92
1712 4184 3.062466 CCTCTGCTCGTCGGACCA 61.062 66.667 1.91 0.00 0.00 4.02
1812 4284 3.084579 CCGTCTTCATGTGCGCTC 58.915 61.111 9.73 5.51 0.00 5.03
1830 4302 2.284921 TGGACCCTGGCTCTGGAG 60.285 66.667 0.00 0.00 0.00 3.86
2177 4649 6.179906 TCATCCCATCAATCTTAGAACCTC 57.820 41.667 0.00 0.00 0.00 3.85
2199 4671 9.909644 ACCTCATGTAAATACAGTATCGAATAC 57.090 33.333 0.00 0.00 39.92 1.89
2289 4761 1.156736 AGTCGCACGCTGCTATTTTT 58.843 45.000 0.00 0.00 42.25 1.94
2303 4775 7.358023 CGCTGCTATTTTTCGTGTAACAAATTT 60.358 33.333 0.00 0.00 35.74 1.82
2316 4788 6.736853 GTGTAACAAATTTCCGAATTCTCTCG 59.263 38.462 3.52 0.00 34.44 4.04
2328 4800 0.888619 TTCTCTCGAGTGGCAACGAT 59.111 50.000 13.13 0.00 37.86 3.73
2332 4804 0.179137 CTCGAGTGGCAACGATAGCA 60.179 55.000 16.00 0.00 37.86 3.49
2408 4880 9.816354 AAGTCACATTTTTATAACAGTTTTGCT 57.184 25.926 0.00 0.00 0.00 3.91
2442 4914 8.245195 TCTAGATGTACCATAAGTATTGCACA 57.755 34.615 0.00 0.00 32.28 4.57
2443 4915 8.870116 TCTAGATGTACCATAAGTATTGCACAT 58.130 33.333 0.00 0.00 32.28 3.21
2444 4916 7.969536 AGATGTACCATAAGTATTGCACATC 57.030 36.000 7.30 7.30 33.07 3.06
2445 4917 7.739825 AGATGTACCATAAGTATTGCACATCT 58.260 34.615 10.42 10.42 36.06 2.90
2446 4918 8.870116 AGATGTACCATAAGTATTGCACATCTA 58.130 33.333 13.03 0.00 37.71 1.98
2447 4919 9.489084 GATGTACCATAAGTATTGCACATCTAA 57.511 33.333 7.84 0.00 31.49 2.10
2448 4920 9.845740 ATGTACCATAAGTATTGCACATCTAAA 57.154 29.630 0.00 0.00 32.28 1.85
2449 4921 9.845740 TGTACCATAAGTATTGCACATCTAAAT 57.154 29.630 0.00 0.00 32.28 1.40
2451 4923 8.396272 ACCATAAGTATTGCACATCTAAATCC 57.604 34.615 0.00 0.00 0.00 3.01
2452 4924 8.220559 ACCATAAGTATTGCACATCTAAATCCT 58.779 33.333 0.00 0.00 0.00 3.24
2453 4925 9.725019 CCATAAGTATTGCACATCTAAATCCTA 57.275 33.333 0.00 0.00 0.00 2.94
2475 4947 9.297037 TCCTATATCATTGATCTTACGTTGAGA 57.703 33.333 1.55 0.00 0.00 3.27
2479 4951 6.812481 TCATTGATCTTACGTTGAGATTCG 57.188 37.500 13.35 5.46 34.13 3.34
2480 4952 6.330278 TCATTGATCTTACGTTGAGATTCGT 58.670 36.000 13.35 0.00 42.82 3.85
2481 4953 7.477494 TCATTGATCTTACGTTGAGATTCGTA 58.523 34.615 13.35 0.00 40.70 3.43
2482 4954 8.135529 TCATTGATCTTACGTTGAGATTCGTAT 58.864 33.333 13.35 5.06 41.10 3.06
2483 4955 9.394477 CATTGATCTTACGTTGAGATTCGTATA 57.606 33.333 13.35 0.00 41.10 1.47
2504 4976 8.011673 CGTATAATATCATTCTGCAAGTGTTGG 58.988 37.037 0.00 0.00 33.76 3.77
2515 4987 2.682856 GCAAGTGTTGGTCTCACAAGAA 59.317 45.455 0.00 0.00 38.16 2.52
2523 4995 6.759827 GTGTTGGTCTCACAAGAAAGTAGTAA 59.240 38.462 0.00 0.00 36.05 2.24
2560 5032 9.209175 TGTTTGTTTTAGTAAAAGCACATTTGT 57.791 25.926 8.33 0.00 35.80 2.83
2654 5128 1.202758 TCCCACACATGAACTCACCAC 60.203 52.381 0.00 0.00 0.00 4.16
2658 5132 2.033299 CACACATGAACTCACCACCAAC 59.967 50.000 0.00 0.00 0.00 3.77
2687 5161 9.787532 CAACCTACATGGAGTATTTGTTTAATG 57.212 33.333 3.73 0.00 39.71 1.90
2706 5180 2.749600 TGTTCTGCATATTTGGGGCAT 58.250 42.857 0.00 0.00 36.87 4.40
2717 5191 1.935799 TTGGGGCATGCTACATGTTT 58.064 45.000 18.92 0.00 0.00 2.83
2738 5212 8.467963 TGTTTGCTGATTAATACATGGATCAT 57.532 30.769 0.00 0.00 0.00 2.45
2751 5225 0.107945 GGATCATATCAGCCGCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
2753 5227 1.002430 GATCATATCAGCCGCCTCCAA 59.998 52.381 0.00 0.00 0.00 3.53
2773 5247 1.033746 AGCCGTTGGATTCTGCATGG 61.034 55.000 0.00 0.00 0.00 3.66
2790 5264 2.171725 GGCACACGTCTAATCGCCC 61.172 63.158 0.00 0.00 33.31 6.13
2798 5272 2.663188 CTAATCGCCCGCTCCAGC 60.663 66.667 0.00 0.00 37.78 4.85
2826 5300 0.322816 AGCATGGCTTCCATTGTCGT 60.323 50.000 0.00 0.00 42.23 4.34
2845 5319 2.284150 CGTGGTATTTGCACGGTAGATG 59.716 50.000 0.00 0.00 38.50 2.90
2847 5321 1.602377 GGTATTTGCACGGTAGATGCC 59.398 52.381 0.00 0.00 42.69 4.40
2852 5326 2.238942 TGCACGGTAGATGCCATAAG 57.761 50.000 0.00 0.00 42.69 1.73
2879 5353 0.321671 ATCTCGTGTGGTTGGGACTG 59.678 55.000 0.00 0.00 0.00 3.51
2938 5412 1.073216 GCACCGATGACACAGAGACG 61.073 60.000 0.00 0.00 0.00 4.18
2948 5422 0.966920 CACAGAGACGTACCCAGGTT 59.033 55.000 0.00 0.00 0.00 3.50
2950 5424 0.531200 CAGAGACGTACCCAGGTTCC 59.469 60.000 0.00 0.00 0.00 3.62
2971 5445 1.037579 GGCCCTTGCATGGAGGTAAC 61.038 60.000 19.85 0.31 40.13 2.50
2983 5457 3.677156 GGAGGTAACACCCTAGTCCTA 57.323 52.381 0.00 0.00 42.26 2.94
3014 5488 1.523758 ATGAAGAACACGGTTGCTCC 58.476 50.000 0.00 0.00 0.00 4.70
3025 5499 2.230750 ACGGTTGCTCCTAGAGTTGTAC 59.769 50.000 0.00 0.00 31.39 2.90
3027 5501 2.416972 GGTTGCTCCTAGAGTTGTACCG 60.417 54.545 0.00 0.00 31.39 4.02
3067 5542 0.179032 TAGCTCTGCTCTCTCCCTCG 60.179 60.000 0.00 0.00 40.44 4.63
3084 5559 1.546923 CTCGTGTATGTGGGTGTGGTA 59.453 52.381 0.00 0.00 0.00 3.25
3098 5573 3.502920 GTGTGGTAGTGAGAATGAGTCG 58.497 50.000 0.00 0.00 0.00 4.18
3099 5574 3.190744 GTGTGGTAGTGAGAATGAGTCGA 59.809 47.826 0.00 0.00 0.00 4.20
3100 5575 3.190744 TGTGGTAGTGAGAATGAGTCGAC 59.809 47.826 7.70 7.70 0.00 4.20
3103 5578 1.187087 AGTGAGAATGAGTCGACCCC 58.813 55.000 13.01 5.21 0.00 4.95
3105 5580 0.041238 TGAGAATGAGTCGACCCCCT 59.959 55.000 13.01 2.55 0.00 4.79
3107 5582 1.137282 GAGAATGAGTCGACCCCCTTC 59.863 57.143 13.01 12.64 0.00 3.46
3108 5583 1.196012 GAATGAGTCGACCCCCTTCT 58.804 55.000 13.01 0.00 0.00 2.85
3109 5584 2.024273 AGAATGAGTCGACCCCCTTCTA 60.024 50.000 13.01 0.00 0.00 2.10
3110 5585 2.074729 ATGAGTCGACCCCCTTCTAG 57.925 55.000 13.01 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.621629 TGTCTCAACCATTTAGAGAAAACTAAA 57.378 29.630 0.00 0.00 43.39 1.85
31 32 9.793259 ATGTCTCAACCATTTAGAGAAAACTAA 57.207 29.630 0.00 0.00 39.85 2.24
32 33 9.793259 AATGTCTCAACCATTTAGAGAAAACTA 57.207 29.630 0.00 0.00 39.85 2.24
33 34 8.697507 AATGTCTCAACCATTTAGAGAAAACT 57.302 30.769 0.00 0.00 39.85 2.66
34 35 9.399403 GAAATGTCTCAACCATTTAGAGAAAAC 57.601 33.333 0.00 0.00 41.34 2.43
35 36 8.576442 GGAAATGTCTCAACCATTTAGAGAAAA 58.424 33.333 0.00 0.00 41.34 2.29
36 37 7.176690 GGGAAATGTCTCAACCATTTAGAGAAA 59.823 37.037 0.00 0.00 41.34 2.52
37 38 6.659242 GGGAAATGTCTCAACCATTTAGAGAA 59.341 38.462 0.00 0.00 41.34 2.87
38 39 6.012508 AGGGAAATGTCTCAACCATTTAGAGA 60.013 38.462 0.00 0.00 41.34 3.10
39 40 6.183347 AGGGAAATGTCTCAACCATTTAGAG 58.817 40.000 0.00 0.00 41.34 2.43
40 41 6.139679 AGGGAAATGTCTCAACCATTTAGA 57.860 37.500 0.00 0.00 41.34 2.10
41 42 6.840780 AAGGGAAATGTCTCAACCATTTAG 57.159 37.500 0.00 0.00 41.34 1.85
42 43 7.610580 AAAAGGGAAATGTCTCAACCATTTA 57.389 32.000 0.00 0.00 41.34 1.40
43 44 6.499106 AAAAGGGAAATGTCTCAACCATTT 57.501 33.333 0.00 0.00 43.33 2.32
44 45 6.327365 AGAAAAAGGGAAATGTCTCAACCATT 59.673 34.615 0.00 0.00 34.07 3.16
45 46 5.840693 AGAAAAAGGGAAATGTCTCAACCAT 59.159 36.000 0.00 0.00 0.00 3.55
46 47 5.208121 AGAAAAAGGGAAATGTCTCAACCA 58.792 37.500 0.00 0.00 0.00 3.67
47 48 5.791336 AGAAAAAGGGAAATGTCTCAACC 57.209 39.130 0.00 0.00 0.00 3.77
48 49 8.390354 CAAAAAGAAAAAGGGAAATGTCTCAAC 58.610 33.333 0.00 0.00 0.00 3.18
49 50 8.317679 TCAAAAAGAAAAAGGGAAATGTCTCAA 58.682 29.630 0.00 0.00 0.00 3.02
50 51 7.846066 TCAAAAAGAAAAAGGGAAATGTCTCA 58.154 30.769 0.00 0.00 0.00 3.27
51 52 8.197439 TCTCAAAAAGAAAAAGGGAAATGTCTC 58.803 33.333 0.00 0.00 0.00 3.36
52 53 8.078060 TCTCAAAAAGAAAAAGGGAAATGTCT 57.922 30.769 0.00 0.00 0.00 3.41
53 54 8.716646 TTCTCAAAAAGAAAAAGGGAAATGTC 57.283 30.769 0.00 0.00 41.10 3.06
69 70 6.394809 AGCCTCGAAAAACTTTTCTCAAAAA 58.605 32.000 11.94 0.00 43.27 1.94
70 71 5.961272 AGCCTCGAAAAACTTTTCTCAAAA 58.039 33.333 11.94 0.00 43.27 2.44
71 72 5.576447 AGCCTCGAAAAACTTTTCTCAAA 57.424 34.783 11.94 0.00 43.27 2.69
72 73 5.576447 AAGCCTCGAAAAACTTTTCTCAA 57.424 34.783 11.94 0.00 43.27 3.02
73 74 5.576447 AAAGCCTCGAAAAACTTTTCTCA 57.424 34.783 11.94 0.12 43.27 3.27
74 75 6.887376 AAAAAGCCTCGAAAAACTTTTCTC 57.113 33.333 11.94 1.26 43.27 2.87
95 96 7.277760 CACGTGGACATCACATCTATCTAAAAA 59.722 37.037 7.95 0.00 46.36 1.94
96 97 6.756542 CACGTGGACATCACATCTATCTAAAA 59.243 38.462 7.95 0.00 46.36 1.52
97 98 6.096282 TCACGTGGACATCACATCTATCTAAA 59.904 38.462 17.00 0.00 46.36 1.85
98 99 5.592688 TCACGTGGACATCACATCTATCTAA 59.407 40.000 17.00 0.00 46.36 2.10
99 100 5.008712 GTCACGTGGACATCACATCTATCTA 59.991 44.000 17.00 0.00 46.36 1.98
100 101 3.954258 TCACGTGGACATCACATCTATCT 59.046 43.478 17.00 0.00 46.36 1.98
101 102 4.045104 GTCACGTGGACATCACATCTATC 58.955 47.826 17.00 0.00 46.36 2.08
102 103 4.046938 GTCACGTGGACATCACATCTAT 57.953 45.455 17.00 0.00 46.36 1.98
103 104 3.503827 GTCACGTGGACATCACATCTA 57.496 47.619 17.00 0.00 46.36 1.98
104 105 2.370281 GTCACGTGGACATCACATCT 57.630 50.000 17.00 0.00 46.36 2.90
114 115 1.067974 ACAATTCTCGTGTCACGTGGA 59.932 47.619 23.82 17.30 43.14 4.02
115 116 1.497991 ACAATTCTCGTGTCACGTGG 58.502 50.000 23.82 17.35 43.14 4.94
116 117 4.903638 ATTACAATTCTCGTGTCACGTG 57.096 40.909 23.82 21.22 43.14 4.49
117 118 5.917541 AAATTACAATTCTCGTGTCACGT 57.082 34.783 23.82 6.46 43.14 4.49
118 119 6.359545 TCAAAATTACAATTCTCGTGTCACG 58.640 36.000 19.38 19.38 44.19 4.35
119 120 7.572759 TCTCAAAATTACAATTCTCGTGTCAC 58.427 34.615 0.00 0.00 0.00 3.67
120 121 7.722795 TCTCAAAATTACAATTCTCGTGTCA 57.277 32.000 0.00 0.00 0.00 3.58
121 122 8.443160 TCATCTCAAAATTACAATTCTCGTGTC 58.557 33.333 0.00 0.00 0.00 3.67
122 123 8.322906 TCATCTCAAAATTACAATTCTCGTGT 57.677 30.769 0.00 0.00 0.00 4.49
123 124 9.270576 CTTCATCTCAAAATTACAATTCTCGTG 57.729 33.333 0.00 0.00 0.00 4.35
124 125 8.454106 CCTTCATCTCAAAATTACAATTCTCGT 58.546 33.333 0.00 0.00 0.00 4.18
125 126 8.454106 ACCTTCATCTCAAAATTACAATTCTCG 58.546 33.333 0.00 0.00 0.00 4.04
126 127 9.565213 CACCTTCATCTCAAAATTACAATTCTC 57.435 33.333 0.00 0.00 0.00 2.87
127 128 9.300681 TCACCTTCATCTCAAAATTACAATTCT 57.699 29.630 0.00 0.00 0.00 2.40
128 129 9.565213 CTCACCTTCATCTCAAAATTACAATTC 57.435 33.333 0.00 0.00 0.00 2.17
129 130 8.526147 CCTCACCTTCATCTCAAAATTACAATT 58.474 33.333 0.00 0.00 0.00 2.32
130 131 7.671398 ACCTCACCTTCATCTCAAAATTACAAT 59.329 33.333 0.00 0.00 0.00 2.71
131 132 7.004086 ACCTCACCTTCATCTCAAAATTACAA 58.996 34.615 0.00 0.00 0.00 2.41
132 133 6.430925 CACCTCACCTTCATCTCAAAATTACA 59.569 38.462 0.00 0.00 0.00 2.41
133 134 6.623767 GCACCTCACCTTCATCTCAAAATTAC 60.624 42.308 0.00 0.00 0.00 1.89
134 135 5.415701 GCACCTCACCTTCATCTCAAAATTA 59.584 40.000 0.00 0.00 0.00 1.40
135 136 4.219288 GCACCTCACCTTCATCTCAAAATT 59.781 41.667 0.00 0.00 0.00 1.82
136 137 3.760684 GCACCTCACCTTCATCTCAAAAT 59.239 43.478 0.00 0.00 0.00 1.82
137 138 3.149196 GCACCTCACCTTCATCTCAAAA 58.851 45.455 0.00 0.00 0.00 2.44
138 139 2.106338 TGCACCTCACCTTCATCTCAAA 59.894 45.455 0.00 0.00 0.00 2.69
139 140 1.699083 TGCACCTCACCTTCATCTCAA 59.301 47.619 0.00 0.00 0.00 3.02
140 141 1.002430 GTGCACCTCACCTTCATCTCA 59.998 52.381 5.22 0.00 39.79 3.27
141 142 1.002430 TGTGCACCTCACCTTCATCTC 59.998 52.381 15.69 0.00 45.03 2.75
142 143 1.059098 TGTGCACCTCACCTTCATCT 58.941 50.000 15.69 0.00 45.03 2.90
143 144 1.160137 GTGTGCACCTCACCTTCATC 58.840 55.000 15.69 0.00 45.03 2.92
144 145 0.473755 TGTGTGCACCTCACCTTCAT 59.526 50.000 15.69 0.00 45.03 2.57
145 146 0.179048 CTGTGTGCACCTCACCTTCA 60.179 55.000 15.69 0.36 45.03 3.02
146 147 1.510480 GCTGTGTGCACCTCACCTTC 61.510 60.000 15.69 0.00 45.03 3.46
147 148 1.526917 GCTGTGTGCACCTCACCTT 60.527 57.895 15.69 0.00 45.03 3.50
148 149 1.987807 AAGCTGTGTGCACCTCACCT 61.988 55.000 15.69 7.67 45.03 4.00
149 150 1.510480 GAAGCTGTGTGCACCTCACC 61.510 60.000 15.69 5.43 45.03 4.02
150 151 1.510480 GGAAGCTGTGTGCACCTCAC 61.510 60.000 15.69 6.69 45.94 3.51
151 152 1.227943 GGAAGCTGTGTGCACCTCA 60.228 57.895 15.69 12.62 45.94 3.86
152 153 1.072159 AGGAAGCTGTGTGCACCTC 59.928 57.895 15.69 8.29 43.32 3.85
153 154 1.072159 GAGGAAGCTGTGTGCACCT 59.928 57.895 15.69 0.22 46.97 4.00
154 155 0.607489 ATGAGGAAGCTGTGTGCACC 60.607 55.000 15.69 6.37 45.94 5.01
155 156 2.099141 TATGAGGAAGCTGTGTGCAC 57.901 50.000 10.75 10.75 45.94 4.57
156 157 2.703416 CTTATGAGGAAGCTGTGTGCA 58.297 47.619 0.00 0.00 45.94 4.57
157 158 1.399791 GCTTATGAGGAAGCTGTGTGC 59.600 52.381 0.94 0.00 46.85 4.57
159 160 5.787092 GACCGCTTATGAGGAAGCTGTGT 62.787 52.174 9.48 3.06 46.08 3.72
160 161 3.310790 GACCGCTTATGAGGAAGCTGTG 61.311 54.545 9.48 0.25 46.08 3.66
164 165 0.876342 CGGACCGCTTATGAGGAAGC 60.876 60.000 0.00 0.00 46.90 3.86
165 166 3.274393 CGGACCGCTTATGAGGAAG 57.726 57.895 0.00 0.00 36.60 3.46
189 190 4.796495 CTAGTGGTTGGGGCCCGC 62.796 72.222 19.83 13.46 0.00 6.13
190 191 3.325201 GACTAGTGGTTGGGGCCCG 62.325 68.421 19.83 2.78 0.00 6.13
191 192 2.228480 TGACTAGTGGTTGGGGCCC 61.228 63.158 18.17 18.17 0.00 5.80
192 193 1.002502 GTGACTAGTGGTTGGGGCC 60.003 63.158 0.00 0.00 0.00 5.80
193 194 0.328258 ATGTGACTAGTGGTTGGGGC 59.672 55.000 0.00 0.00 0.00 5.80
194 195 2.420129 GCTATGTGACTAGTGGTTGGGG 60.420 54.545 0.00 0.00 0.00 4.96
195 196 2.236146 TGCTATGTGACTAGTGGTTGGG 59.764 50.000 0.00 0.00 0.00 4.12
196 197 3.610040 TGCTATGTGACTAGTGGTTGG 57.390 47.619 0.00 0.00 0.00 3.77
197 198 3.873361 CCATGCTATGTGACTAGTGGTTG 59.127 47.826 0.00 0.00 0.00 3.77
198 199 3.774766 TCCATGCTATGTGACTAGTGGTT 59.225 43.478 0.00 0.00 0.00 3.67
199 200 3.374764 TCCATGCTATGTGACTAGTGGT 58.625 45.455 0.00 0.00 0.00 4.16
200 201 3.244009 CCTCCATGCTATGTGACTAGTGG 60.244 52.174 0.00 0.00 0.00 4.00
201 202 3.386078 ACCTCCATGCTATGTGACTAGTG 59.614 47.826 0.00 0.00 0.00 2.74
202 203 3.647636 ACCTCCATGCTATGTGACTAGT 58.352 45.455 0.00 0.00 0.00 2.57
203 204 5.279206 CCTTACCTCCATGCTATGTGACTAG 60.279 48.000 0.00 0.00 0.00 2.57
204 205 4.588951 CCTTACCTCCATGCTATGTGACTA 59.411 45.833 0.00 0.00 0.00 2.59
205 206 3.389329 CCTTACCTCCATGCTATGTGACT 59.611 47.826 0.00 0.00 0.00 3.41
206 207 3.134804 ACCTTACCTCCATGCTATGTGAC 59.865 47.826 0.00 0.00 0.00 3.67
217 218 3.118038 GCAACCATGATACCTTACCTCCA 60.118 47.826 0.00 0.00 0.00 3.86
246 248 5.863935 GCTTTACAGTTAAGGCTGATTTTGG 59.136 40.000 1.61 0.00 37.33 3.28
272 274 4.632538 AAACACCTTTTGTCTAGTGTGC 57.367 40.909 0.00 0.00 42.40 4.57
398 400 0.032952 TACGGTCCTTGAGTGTGTGC 59.967 55.000 0.00 0.00 0.00 4.57
406 408 4.004982 GCTAACCAAAATACGGTCCTTGA 58.995 43.478 0.00 0.00 34.99 3.02
407 409 3.754323 TGCTAACCAAAATACGGTCCTTG 59.246 43.478 0.00 0.00 34.99 3.61
408 410 4.023726 TGCTAACCAAAATACGGTCCTT 57.976 40.909 0.00 0.00 34.99 3.36
409 411 3.706600 TGCTAACCAAAATACGGTCCT 57.293 42.857 0.00 0.00 34.99 3.85
437 449 2.362397 TGGTTTGCTTAATTGAACGGCA 59.638 40.909 0.00 0.00 0.00 5.69
480 492 4.675976 TCAACGACTCCTGGAGTAAAAA 57.324 40.909 28.41 11.16 43.53 1.94
481 493 4.675976 TTCAACGACTCCTGGAGTAAAA 57.324 40.909 28.41 14.98 43.53 1.52
491 503 2.409975 TCGGTTTGATTCAACGACTCC 58.590 47.619 7.73 2.40 0.00 3.85
506 519 1.202177 GCATTGCATGTTCGATCGGTT 60.202 47.619 16.41 0.00 0.00 4.44
507 520 0.378257 GCATTGCATGTTCGATCGGT 59.622 50.000 16.41 0.00 0.00 4.69
535 548 0.911856 CAACCATACTCGCGTGTACG 59.088 55.000 21.87 14.68 43.27 3.67
536 549 2.267188 TCAACCATACTCGCGTGTAC 57.733 50.000 21.87 0.00 0.00 2.90
537 550 3.183754 CAATCAACCATACTCGCGTGTA 58.816 45.455 21.71 21.71 0.00 2.90
538 551 1.999735 CAATCAACCATACTCGCGTGT 59.000 47.619 18.61 18.61 0.00 4.49
539 552 1.327460 CCAATCAACCATACTCGCGTG 59.673 52.381 5.77 6.24 0.00 5.34
540 553 1.206132 TCCAATCAACCATACTCGCGT 59.794 47.619 5.77 0.00 0.00 6.01
569 582 8.027189 GCTCCATCGTAGTCAAACATATATACA 58.973 37.037 0.00 0.00 0.00 2.29
570 583 8.027189 TGCTCCATCGTAGTCAAACATATATAC 58.973 37.037 0.00 0.00 0.00 1.47
571 584 8.117813 TGCTCCATCGTAGTCAAACATATATA 57.882 34.615 0.00 0.00 0.00 0.86
572 585 6.993079 TGCTCCATCGTAGTCAAACATATAT 58.007 36.000 0.00 0.00 0.00 0.86
604 628 3.855689 AAGCCATATGCAGACAAACAC 57.144 42.857 0.00 0.00 44.83 3.32
618 642 7.051623 TCCAGAATTGTACGTATAAAAGCCAT 58.948 34.615 8.90 0.00 0.00 4.40
621 645 7.535489 ACTCCAGAATTGTACGTATAAAAGC 57.465 36.000 8.90 2.14 0.00 3.51
626 650 9.618890 AACTACTACTCCAGAATTGTACGTATA 57.381 33.333 0.00 0.00 0.00 1.47
630 654 8.206325 TCTAACTACTACTCCAGAATTGTACG 57.794 38.462 0.00 0.00 0.00 3.67
644 668 8.507249 TCGTTTTGGTCTAACTCTAACTACTAC 58.493 37.037 0.00 0.00 0.00 2.73
740 795 6.942532 ACTGAAATCTTTGCAGTGTTCTTA 57.057 33.333 0.01 0.00 41.02 2.10
820 3274 6.586344 TCTCTTCATCTTGTATGGTTGATCC 58.414 40.000 0.00 0.00 0.00 3.36
827 3281 4.100653 TGCCTCTCTCTTCATCTTGTATGG 59.899 45.833 0.00 0.00 0.00 2.74
843 3297 1.067565 TCATGACAGACGTTGCCTCTC 60.068 52.381 0.00 0.00 0.00 3.20
844 3298 0.969149 TCATGACAGACGTTGCCTCT 59.031 50.000 0.00 0.00 0.00 3.69
845 3299 1.071605 GTCATGACAGACGTTGCCTC 58.928 55.000 21.07 0.00 0.00 4.70
846 3300 0.320771 GGTCATGACAGACGTTGCCT 60.321 55.000 26.47 0.00 39.42 4.75
847 3301 1.298859 GGGTCATGACAGACGTTGCC 61.299 60.000 26.47 12.32 39.42 4.52
849 3303 0.321671 AGGGGTCATGACAGACGTTG 59.678 55.000 26.47 0.00 39.42 4.10
850 3304 1.933021 TAGGGGTCATGACAGACGTT 58.067 50.000 26.47 10.55 39.42 3.99
851 3305 2.160721 ATAGGGGTCATGACAGACGT 57.839 50.000 26.47 18.24 39.42 4.34
852 3306 3.637229 ACTAATAGGGGTCATGACAGACG 59.363 47.826 26.47 8.92 39.42 4.18
853 3307 5.834204 ACTACTAATAGGGGTCATGACAGAC 59.166 44.000 26.47 15.55 33.76 3.51
854 3308 6.027025 ACTACTAATAGGGGTCATGACAGA 57.973 41.667 26.47 9.16 32.08 3.41
855 3309 5.048643 CGACTACTAATAGGGGTCATGACAG 60.049 48.000 26.47 15.47 32.08 3.51
856 3310 4.825634 CGACTACTAATAGGGGTCATGACA 59.174 45.833 26.47 7.13 32.08 3.58
857 3311 5.068636 TCGACTACTAATAGGGGTCATGAC 58.931 45.833 17.91 17.91 32.08 3.06
858 3312 5.314529 CTCGACTACTAATAGGGGTCATGA 58.685 45.833 12.58 0.00 32.08 3.07
859 3313 4.459685 CCTCGACTACTAATAGGGGTCATG 59.540 50.000 12.58 0.00 32.08 3.07
860 3314 4.664392 CCTCGACTACTAATAGGGGTCAT 58.336 47.826 12.58 0.00 32.08 3.06
861 3315 3.749954 GCCTCGACTACTAATAGGGGTCA 60.750 52.174 12.58 3.25 32.08 4.02
862 3316 2.819019 GCCTCGACTACTAATAGGGGTC 59.181 54.545 0.00 0.00 32.08 4.46
863 3317 2.813354 CGCCTCGACTACTAATAGGGGT 60.813 54.545 0.00 0.00 35.99 4.95
864 3318 1.811359 CGCCTCGACTACTAATAGGGG 59.189 57.143 0.00 0.00 34.47 4.79
865 3319 2.502295 ACGCCTCGACTACTAATAGGG 58.498 52.381 0.00 0.00 32.08 3.53
906 3360 2.030185 GCAGGCAAGGCAGATGATAATG 60.030 50.000 0.00 0.00 0.00 1.90
907 3361 2.158505 AGCAGGCAAGGCAGATGATAAT 60.159 45.455 0.00 0.00 0.00 1.28
908 3362 1.213678 AGCAGGCAAGGCAGATGATAA 59.786 47.619 0.00 0.00 0.00 1.75
909 3363 0.841961 AGCAGGCAAGGCAGATGATA 59.158 50.000 0.00 0.00 0.00 2.15
910 3364 0.752009 CAGCAGGCAAGGCAGATGAT 60.752 55.000 0.00 0.00 0.00 2.45
911 3365 1.378119 CAGCAGGCAAGGCAGATGA 60.378 57.895 0.00 0.00 0.00 2.92
952 3406 4.100373 GGCCAGGAGAGGAGTATGAATAT 58.900 47.826 0.00 0.00 0.00 1.28
953 3407 3.511477 GGCCAGGAGAGGAGTATGAATA 58.489 50.000 0.00 0.00 0.00 1.75
954 3408 2.334023 GGCCAGGAGAGGAGTATGAAT 58.666 52.381 0.00 0.00 0.00 2.57
955 3409 1.794714 GGCCAGGAGAGGAGTATGAA 58.205 55.000 0.00 0.00 0.00 2.57
956 3410 0.468214 CGGCCAGGAGAGGAGTATGA 60.468 60.000 2.24 0.00 0.00 2.15
957 3411 1.467678 CCGGCCAGGAGAGGAGTATG 61.468 65.000 2.24 0.00 45.00 2.39
1079 3542 3.834799 GGCGGTCGTAGGTCTGGG 61.835 72.222 0.00 0.00 0.00 4.45
1285 3757 1.194781 ACCATTGGAGCGGAGTCAGT 61.195 55.000 10.37 0.00 0.00 3.41
1384 3856 2.125512 ATCACCGCTGCTCCGAAC 60.126 61.111 0.00 0.00 0.00 3.95
1531 4003 1.968540 GGCACAGGGCTGTCTTGAC 60.969 63.158 0.00 0.00 42.83 3.18
1541 4013 2.203209 GGATTAGGCGGCACAGGG 60.203 66.667 13.08 0.00 0.00 4.45
1797 4269 0.390340 TCCAGAGCGCACATGAAGAC 60.390 55.000 11.47 0.00 0.00 3.01
1812 4284 2.284921 TCCAGAGCCAGGGTCCAG 60.285 66.667 15.46 8.29 0.00 3.86
1830 4302 2.049063 AGCACGAGTTCCAGCGTC 60.049 61.111 0.00 0.00 38.92 5.19
2237 4709 6.244552 TCAAATAAGATGACCATGAGCTCT 57.755 37.500 16.19 0.00 0.00 4.09
2289 4761 6.425721 AGAGAATTCGGAAATTTGTTACACGA 59.574 34.615 0.00 0.00 35.21 4.35
2303 4775 0.456221 GCCACTCGAGAGAATTCGGA 59.544 55.000 21.68 0.00 41.32 4.55
2316 4788 1.438651 TTGTGCTATCGTTGCCACTC 58.561 50.000 0.00 0.00 0.00 3.51
2332 4804 0.601576 TAGCAACGCACGGACATTGT 60.602 50.000 0.00 0.00 0.00 2.71
2418 4890 9.144747 GATGTGCAATACTTATGGTACATCTAG 57.855 37.037 19.82 0.00 46.94 2.43
2420 4892 7.969536 GATGTGCAATACTTATGGTACATCT 57.030 36.000 19.82 0.00 46.94 2.90
2425 4897 9.502091 GGATTTAGATGTGCAATACTTATGGTA 57.498 33.333 0.00 0.00 34.62 3.25
2426 4898 8.220559 AGGATTTAGATGTGCAATACTTATGGT 58.779 33.333 0.00 0.00 0.00 3.55
2427 4899 8.627208 AGGATTTAGATGTGCAATACTTATGG 57.373 34.615 0.00 0.00 0.00 2.74
2449 4921 9.297037 TCTCAACGTAAGATCAATGATATAGGA 57.703 33.333 12.27 0.00 43.62 2.94
2453 4925 9.133627 CGAATCTCAACGTAAGATCAATGATAT 57.866 33.333 12.34 0.00 43.62 1.63
2454 4926 8.135529 ACGAATCTCAACGTAAGATCAATGATA 58.864 33.333 12.34 0.00 40.92 2.15
2455 4927 6.980978 ACGAATCTCAACGTAAGATCAATGAT 59.019 34.615 12.34 0.00 40.92 2.45
2456 4928 6.330278 ACGAATCTCAACGTAAGATCAATGA 58.670 36.000 12.34 0.00 40.92 2.57
2457 4929 6.575083 ACGAATCTCAACGTAAGATCAATG 57.425 37.500 12.34 6.83 40.92 2.82
2458 4930 9.961265 TTATACGAATCTCAACGTAAGATCAAT 57.039 29.630 12.34 7.60 45.49 2.57
2459 4931 9.961265 ATTATACGAATCTCAACGTAAGATCAA 57.039 29.630 12.34 2.11 45.49 2.57
2470 4942 9.927668 TGCAGAATGATATTATACGAATCTCAA 57.072 29.630 0.00 0.00 39.69 3.02
2471 4943 9.927668 TTGCAGAATGATATTATACGAATCTCA 57.072 29.630 0.00 0.00 39.69 3.27
2473 4945 9.935241 ACTTGCAGAATGATATTATACGAATCT 57.065 29.630 0.00 0.00 39.69 2.40
2474 4946 9.964253 CACTTGCAGAATGATATTATACGAATC 57.036 33.333 0.00 0.00 39.69 2.52
2475 4947 9.494271 ACACTTGCAGAATGATATTATACGAAT 57.506 29.630 0.00 0.00 39.69 3.34
2476 4948 8.887036 ACACTTGCAGAATGATATTATACGAA 57.113 30.769 0.00 0.00 39.69 3.85
2477 4949 8.764287 CAACACTTGCAGAATGATATTATACGA 58.236 33.333 0.00 0.00 39.69 3.43
2478 4950 8.011673 CCAACACTTGCAGAATGATATTATACG 58.988 37.037 1.38 0.00 39.69 3.06
2479 4951 8.840321 ACCAACACTTGCAGAATGATATTATAC 58.160 33.333 1.38 0.00 39.69 1.47
2480 4952 8.978874 ACCAACACTTGCAGAATGATATTATA 57.021 30.769 1.38 0.00 39.69 0.98
2481 4953 7.776969 AGACCAACACTTGCAGAATGATATTAT 59.223 33.333 1.38 0.00 39.69 1.28
2482 4954 7.112122 AGACCAACACTTGCAGAATGATATTA 58.888 34.615 1.38 0.00 39.69 0.98
2483 4955 5.948162 AGACCAACACTTGCAGAATGATATT 59.052 36.000 1.38 0.00 39.69 1.28
2528 5000 9.523730 GTGCTTTTACTAAAACAAACAAACAAG 57.476 29.630 0.00 0.00 0.00 3.16
2579 5051 2.357154 CCATTTGTGGGGCTAGTAGCTT 60.357 50.000 21.20 0.00 41.99 3.74
2582 5054 2.348411 CCCATTTGTGGGGCTAGTAG 57.652 55.000 5.56 0.00 45.34 2.57
2621 5093 1.880027 GTGTGGGACCAACACTTCATC 59.120 52.381 23.00 0.00 39.52 2.92
2633 5107 1.202758 TGGTGAGTTCATGTGTGGGAC 60.203 52.381 0.00 0.00 0.00 4.46
2687 5161 2.804212 GCATGCCCCAAATATGCAGAAC 60.804 50.000 6.36 0.00 44.88 3.01
2706 5180 7.622893 TGTATTAATCAGCAAACATGTAGCA 57.377 32.000 21.03 5.98 0.00 3.49
2717 5191 9.609346 CTGATATGATCCATGTATTAATCAGCA 57.391 33.333 0.00 0.00 33.63 4.41
2738 5212 1.153168 GCTTTGGAGGCGGCTGATA 60.153 57.895 19.63 0.00 0.00 2.15
2751 5225 0.597568 TGCAGAATCCAACGGCTTTG 59.402 50.000 0.00 0.00 34.63 2.77
2753 5227 0.813184 CATGCAGAATCCAACGGCTT 59.187 50.000 0.00 0.00 0.00 4.35
2760 5234 1.307355 CGTGTGCCATGCAGAATCCA 61.307 55.000 0.00 0.00 40.08 3.41
2773 5247 2.514013 CGGGCGATTAGACGTGTGC 61.514 63.158 0.00 0.00 35.59 4.57
2790 5264 1.153901 CTGCAAATTGGCTGGAGCG 60.154 57.895 6.34 0.00 43.26 5.03
2798 5272 1.365699 GAAGCCATGCTGCAAATTGG 58.634 50.000 14.84 14.84 39.62 3.16
2826 5300 2.285083 GCATCTACCGTGCAAATACCA 58.715 47.619 0.00 0.00 42.08 3.25
2847 5321 3.804325 CACACGAGATAAGCCACCTTATG 59.196 47.826 1.04 0.00 42.76 1.90
2852 5326 0.249398 ACCACACGAGATAAGCCACC 59.751 55.000 0.00 0.00 0.00 4.61
2898 5372 1.961277 GTGCCTAATCCCGCATCCG 60.961 63.158 0.00 0.00 37.33 4.18
2900 5374 0.946221 CTCGTGCCTAATCCCGCATC 60.946 60.000 0.00 0.00 37.33 3.91
2905 5379 1.523938 GGTGCTCGTGCCTAATCCC 60.524 63.158 7.05 0.00 38.71 3.85
2953 5427 0.323360 TGTTACCTCCATGCAAGGGC 60.323 55.000 8.36 0.00 37.98 5.19
2958 5432 1.837439 CTAGGGTGTTACCTCCATGCA 59.163 52.381 0.00 0.00 42.09 3.96
2967 5441 4.347607 TCCTTGTAGGACTAGGGTGTTAC 58.652 47.826 7.16 0.00 40.06 2.50
2983 5457 5.171476 CGTGTTCTTCATAGTGATCCTTGT 58.829 41.667 0.00 0.00 0.00 3.16
2999 5473 1.546476 CTCTAGGAGCAACCGTGTTCT 59.454 52.381 0.00 0.00 44.74 3.01
3014 5488 2.092538 TCCTCCTCCGGTACAACTCTAG 60.093 54.545 0.00 0.00 0.00 2.43
3025 5499 1.398692 CTCTCTTCTTCCTCCTCCGG 58.601 60.000 0.00 0.00 0.00 5.14
3027 5501 2.031870 GAGCTCTCTTCTTCCTCCTCC 58.968 57.143 6.43 0.00 0.00 4.30
3067 5542 2.300723 TCACTACCACACCCACATACAC 59.699 50.000 0.00 0.00 0.00 2.90
3084 5559 1.187087 GGGGTCGACTCATTCTCACT 58.813 55.000 18.98 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.