Multiple sequence alignment - TraesCS7A01G093200

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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 TraesCS7A01G093200 chr7A 100.000 3187 0 0 1 3187 56725068 56728254 0.000000e+00 5886.0
1 TraesCS7A01G093200 chr7A 90.962 1029 83 4 271 1299 56974355 56975373 0.000000e+00 1376.0
2 TraesCS7A01G093200 chr7A 94.357 443 25 0 2717 3159 56978053 56978495 0.000000e+00 680.0
3 TraesCS7A01G093200 chr7A 90.497 463 38 3 1661 2118 664368645 664369106 9.780000e-170 606.0
4 TraesCS7A01G093200 chr7A 84.291 522 66 13 784 1298 55930419 55930931 2.210000e-136 496.0
5 TraesCS7A01G093200 chr7A 97.193 285 4 2 2245 2526 56977627 56977910 2.220000e-131 479.0
6 TraesCS7A01G093200 chr7A 80.686 554 75 21 759 1299 56245095 56245629 4.950000e-108 401.0
7 TraesCS7A01G093200 chr7A 85.978 271 33 2 2119 2389 56377641 56377906 5.200000e-73 285.0
8 TraesCS7A01G093200 chr7A 84.982 273 36 2 2117 2389 56460619 56460886 4.050000e-69 272.0
9 TraesCS7A01G093200 chr7A 89.640 222 10 8 2218 2434 56422337 56422550 1.460000e-68 270.0
10 TraesCS7A01G093200 chr7A 81.424 323 43 14 985 1298 56460314 56460628 6.830000e-62 248.0
11 TraesCS7A01G093200 chr7A 89.560 182 16 3 1118 1298 56240989 56241168 8.890000e-56 228.0
12 TraesCS7A01G093200 chr7A 93.243 148 8 2 2490 2635 56977907 56978054 1.930000e-52 217.0
13 TraesCS7A01G093200 chr7A 80.952 273 41 5 2118 2389 56913704 56913966 4.170000e-49 206.0
14 TraesCS7A01G093200 chr7A 86.486 148 18 2 2460 2606 56422474 56422620 9.150000e-36 161.0
15 TraesCS7A01G093200 chr7A 88.991 109 11 1 477 584 607561520 607561628 1.990000e-27 134.0
16 TraesCS7A01G093200 chr7A 86.170 94 11 1 784 877 56235479 56235570 2.020000e-17 100.0
17 TraesCS7A01G093200 chr7A 96.774 31 1 0 3052 3082 123235900 123235930 6.000000e-03 52.8
18 TraesCS7A01G093200 chr5B 98.417 821 12 1 1299 2118 256596612 256597432 0.000000e+00 1443.0
19 TraesCS7A01G093200 chr5B 89.338 619 62 4 1300 1917 3944438 3943823 0.000000e+00 774.0
20 TraesCS7A01G093200 chr5B 92.777 443 29 3 1300 1741 403109713 403110153 3.470000e-179 638.0
21 TraesCS7A01G093200 chr5B 91.443 409 33 2 1303 1710 542696698 542696291 7.720000e-156 560.0
22 TraesCS7A01G093200 chr5B 91.483 317 26 1 1802 2118 403110171 403110486 4.880000e-118 435.0
23 TraesCS7A01G093200 chr5B 87.454 271 30 3 206 476 495004123 495004389 3.090000e-80 309.0
24 TraesCS7A01G093200 chr5B 84.470 264 33 8 216 476 639666862 639666604 1.470000e-63 254.0
25 TraesCS7A01G093200 chr5B 73.085 457 94 16 2630 3082 27462055 27462486 5.550000e-28 135.0
26 TraesCS7A01G093200 chr5B 84.270 89 14 0 604 692 589873704 589873792 1.570000e-13 87.9
27 TraesCS7A01G093200 chr2B 98.291 819 14 0 1300 2118 610115077 610114259 0.000000e+00 1435.0
28 TraesCS7A01G093200 chr2B 97.805 820 17 1 1300 2118 752836230 752835411 0.000000e+00 1413.0
29 TraesCS7A01G093200 chr2B 92.375 459 34 1 1619 2077 67536434 67535977 0.000000e+00 652.0
30 TraesCS7A01G093200 chr2A 97.927 820 16 1 1300 2118 44392314 44393133 0.000000e+00 1419.0
31 TraesCS7A01G093200 chr2A 96.532 173 6 0 1300 1472 44393133 44392961 1.450000e-73 287.0
32 TraesCS7A01G093200 chr2A 88.235 102 9 3 478 577 29730310 29730410 5.580000e-23 119.0
33 TraesCS7A01G093200 chr6B 92.346 797 33 16 1300 2096 707154478 707155246 0.000000e+00 1109.0
34 TraesCS7A01G093200 chr6B 86.873 259 28 6 206 463 616862568 616862821 5.200000e-73 285.0
35 TraesCS7A01G093200 chr3A 87.985 824 54 8 1300 2119 272799709 272798927 0.000000e+00 931.0
36 TraesCS7A01G093200 chr6D 82.203 826 62 37 1299 2119 403653568 403652823 1.610000e-177 632.0
37 TraesCS7A01G093200 chr6D 86.264 182 22 1 2 183 436241942 436241764 9.020000e-46 195.0
38 TraesCS7A01G093200 chr6D 92.727 110 8 0 475 584 469816551 469816442 3.290000e-35 159.0
39 TraesCS7A01G093200 chr7D 83.681 527 67 16 784 1299 53558309 53558827 2.220000e-131 479.0
40 TraesCS7A01G093200 chr7D 85.495 455 39 12 2171 2607 53700438 53700883 1.740000e-122 449.0
41 TraesCS7A01G093200 chr7D 83.815 346 39 9 2118 2462 53575027 53575356 2.390000e-81 313.0
42 TraesCS7A01G093200 chr7D 79.279 444 71 6 2717 3157 53700918 53701343 1.120000e-74 291.0
43 TraesCS7A01G093200 chr7D 92.818 181 12 1 1118 1298 53539590 53539769 8.770000e-66 261.0
44 TraesCS7A01G093200 chr7D 92.265 181 13 1 1118 1298 53524925 53525104 4.080000e-64 255.0
45 TraesCS7A01G093200 chr7D 92.697 178 12 1 1118 1295 53530169 53530345 4.080000e-64 255.0
46 TraesCS7A01G093200 chr7D 91.176 170 15 0 1130 1299 53700201 53700370 6.880000e-57 231.0
47 TraesCS7A01G093200 chr7D 86.813 182 21 2 2 183 569024279 569024101 1.940000e-47 200.0
48 TraesCS7A01G093200 chr7D 85.938 192 17 5 690 872 53633876 53634066 2.510000e-46 196.0
49 TraesCS7A01G093200 chr7D 94.737 95 5 0 2633 2727 519264545 519264639 7.120000e-32 148.0
50 TraesCS7A01G093200 chr7D 96.774 31 1 0 3052 3082 119055353 119055383 6.000000e-03 52.8
51 TraesCS7A01G093200 chr4A 86.025 322 32 8 2118 2435 668319578 668319890 1.830000e-87 333.0
52 TraesCS7A01G093200 chr4A 81.366 322 49 11 984 1299 668285333 668285649 5.280000e-63 252.0
53 TraesCS7A01G093200 chr4A 83.598 189 16 12 690 877 668358736 668358910 2.540000e-36 163.0
54 TraesCS7A01G093200 chr4A 91.346 104 9 0 475 578 701282622 701282725 3.310000e-30 143.0
55 TraesCS7A01G093200 chr7B 87.097 279 27 4 199 476 79029945 79030215 1.110000e-79 307.0
56 TraesCS7A01G093200 chr7B 92.593 108 8 0 477 584 176239404 176239297 4.260000e-34 156.0
57 TraesCS7A01G093200 chr7B 92.593 108 8 0 477 584 741940784 741940677 4.260000e-34 156.0
58 TraesCS7A01G093200 chr2D 86.765 272 33 3 206 476 78047225 78047494 1.860000e-77 300.0
59 TraesCS7A01G093200 chr2D 85.401 274 32 7 206 476 118469771 118469503 8.710000e-71 278.0
60 TraesCS7A01G093200 chr2D 87.151 179 20 2 2 180 431918615 431918790 1.940000e-47 200.0
61 TraesCS7A01G093200 chr2D 86.813 182 20 2 2 183 619207759 619207936 1.940000e-47 200.0
62 TraesCS7A01G093200 chr2D 86.264 182 22 2 2 183 34535837 34536015 9.020000e-46 195.0
63 TraesCS7A01G093200 chr2D 86.264 182 21 2 2 183 78046921 78047098 9.020000e-46 195.0
64 TraesCS7A01G093200 chr2D 93.069 101 7 0 2633 2733 619321094 619320994 7.120000e-32 148.0
65 TraesCS7A01G093200 chr2D 90.411 73 7 0 620 692 417614845 417614773 2.620000e-16 97.1
66 TraesCS7A01G093200 chr1D 86.765 272 28 4 206 476 439219093 439219357 2.400000e-76 296.0
67 TraesCS7A01G093200 chr1D 87.363 182 19 2 2 183 6322953 6322776 4.170000e-49 206.0
68 TraesCS7A01G093200 chr1D 94.845 97 5 0 2625 2721 337065180 337065276 5.510000e-33 152.0
69 TraesCS7A01G093200 chr1D 93.617 94 6 0 2633 2726 355081216 355081123 1.190000e-29 141.0
70 TraesCS7A01G093200 chr1B 85.091 275 35 6 205 476 377927063 377927334 3.130000e-70 276.0
71 TraesCS7A01G093200 chr4B 83.150 273 44 2 205 476 15638885 15639156 6.830000e-62 248.0
72 TraesCS7A01G093200 chr4B 91.176 102 8 1 2633 2733 29662591 29662490 1.540000e-28 137.0
73 TraesCS7A01G093200 chr4B 88.043 92 9 2 605 695 530012608 530012518 1.210000e-19 108.0
74 TraesCS7A01G093200 chr3D 87.912 182 19 2 2 183 496668853 496669031 8.960000e-51 211.0
75 TraesCS7A01G093200 chr4D 87.363 182 19 2 2 183 8925706 8925883 4.170000e-49 206.0
76 TraesCS7A01G093200 chr4D 92.929 99 6 1 2634 2731 478671852 478671950 3.310000e-30 143.0
77 TraesCS7A01G093200 chr4D 89.623 106 11 0 2621 2726 333063260 333063365 5.550000e-28 135.0
78 TraesCS7A01G093200 chr5D 95.745 94 4 0 2634 2727 294640319 294640226 5.510000e-33 152.0
79 TraesCS7A01G093200 chr5D 96.629 89 3 0 2632 2720 62715156 62715244 7.120000e-32 148.0
80 TraesCS7A01G093200 chr5A 89.815 108 11 0 477 584 706667784 706667891 4.290000e-29 139.0
81 TraesCS7A01G093200 chrUn 87.037 108 14 0 477 584 92755996 92756103 4.320000e-24 122.0


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 TraesCS7A01G093200 chr7A 56725068 56728254 3186 False 5886.000000 5886 100.000000 1 3187 1 chr7A.!!$F4 3186
1 TraesCS7A01G093200 chr7A 56974355 56978495 4140 False 688.000000 1376 93.938750 271 3159 4 chr7A.!!$F12 2888
2 TraesCS7A01G093200 chr7A 55930419 55930931 512 False 496.000000 496 84.291000 784 1298 1 chr7A.!!$F1 514
3 TraesCS7A01G093200 chr7A 56240989 56245629 4640 False 314.500000 401 85.123000 759 1299 2 chr7A.!!$F9 540
4 TraesCS7A01G093200 chr7A 56460314 56460886 572 False 260.000000 272 83.203000 985 2389 2 chr7A.!!$F11 1404
5 TraesCS7A01G093200 chr5B 256596612 256597432 820 False 1443.000000 1443 98.417000 1299 2118 1 chr5B.!!$F2 819
6 TraesCS7A01G093200 chr5B 3943823 3944438 615 True 774.000000 774 89.338000 1300 1917 1 chr5B.!!$R1 617
7 TraesCS7A01G093200 chr5B 403109713 403110486 773 False 536.500000 638 92.130000 1300 2118 2 chr5B.!!$F5 818
8 TraesCS7A01G093200 chr2B 610114259 610115077 818 True 1435.000000 1435 98.291000 1300 2118 1 chr2B.!!$R2 818
9 TraesCS7A01G093200 chr2B 752835411 752836230 819 True 1413.000000 1413 97.805000 1300 2118 1 chr2B.!!$R3 818
10 TraesCS7A01G093200 chr2A 44392314 44393133 819 False 1419.000000 1419 97.927000 1300 2118 1 chr2A.!!$F2 818
11 TraesCS7A01G093200 chr6B 707154478 707155246 768 False 1109.000000 1109 92.346000 1300 2096 1 chr6B.!!$F2 796
12 TraesCS7A01G093200 chr3A 272798927 272799709 782 True 931.000000 931 87.985000 1300 2119 1 chr3A.!!$R1 819
13 TraesCS7A01G093200 chr6D 403652823 403653568 745 True 632.000000 632 82.203000 1299 2119 1 chr6D.!!$R1 820
14 TraesCS7A01G093200 chr7D 53558309 53558827 518 False 479.000000 479 83.681000 784 1299 1 chr7D.!!$F4 515
15 TraesCS7A01G093200 chr7D 53700201 53701343 1142 False 323.666667 449 85.316667 1130 3157 3 chr7D.!!$F9 2027
16 TraesCS7A01G093200 chr2D 78046921 78047494 573 False 247.500000 300 86.514500 2 476 2 chr2D.!!$F4 474

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
255 256 0.448593 CGGGCGGCGAATTTCTTTTA 59.551 50.0 12.98 0.0 0.0 1.52 F
1127 4521 0.458370 CATCTGATGTCGTCCGTGCA 60.458 55.0 9.50 0.0 0.0 4.57 F
2096 5757 0.028110 GTCATTTCGATTCGGCAGGC 59.972 55.0 6.18 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1198 4601 0.249657 GACGGTGGAGATGATGAGCC 60.250 60.0 0.0 0.0 0.0 4.70 R
2123 5784 0.250770 GGGTGTTCTTGAGGTGGTCC 60.251 60.0 0.0 0.0 0.0 4.46 R
3162 9063 0.249573 TCGTCGGTGTTCTTGGGTTC 60.250 55.0 0.0 0.0 0.0 3.62 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
18 19 3.516578 CGAGGAGGTGTTGGAGAAC 57.483 57.895 0.00 0.00 0.00 3.01
19 20 0.679505 CGAGGAGGTGTTGGAGAACA 59.320 55.000 0.00 0.00 39.88 3.18
27 28 0.534203 TGTTGGAGAACAAGCCCGTC 60.534 55.000 0.00 0.00 39.20 4.79
76 77 4.314440 GGTGGAGCTGGTCGTGCA 62.314 66.667 0.00 0.00 0.00 4.57
77 78 2.046892 GTGGAGCTGGTCGTGCAT 60.047 61.111 0.00 0.00 0.00 3.96
80 81 2.046892 GAGCTGGTCGTGCATGGT 60.047 61.111 5.98 0.00 0.00 3.55
81 82 1.672356 GAGCTGGTCGTGCATGGTT 60.672 57.895 5.98 0.00 0.00 3.67
83 84 1.965930 GCTGGTCGTGCATGGTTCA 60.966 57.895 5.98 1.68 0.00 3.18
84 85 1.915614 GCTGGTCGTGCATGGTTCAG 61.916 60.000 5.98 11.86 0.00 3.02
85 86 1.300971 CTGGTCGTGCATGGTTCAGG 61.301 60.000 5.98 0.00 0.00 3.86
86 87 1.003839 GGTCGTGCATGGTTCAGGA 60.004 57.895 5.98 0.00 0.00 3.86
87 88 1.021390 GGTCGTGCATGGTTCAGGAG 61.021 60.000 5.98 0.00 0.00 3.69
90 91 1.012086 CGTGCATGGTTCAGGAGATG 58.988 55.000 0.00 0.00 0.00 2.90
91 92 1.386533 GTGCATGGTTCAGGAGATGG 58.613 55.000 0.00 0.00 0.00 3.51
94 95 0.816825 CATGGTTCAGGAGATGGCCG 60.817 60.000 0.00 0.00 0.00 6.13
95 96 0.982852 ATGGTTCAGGAGATGGCCGA 60.983 55.000 0.00 0.00 0.00 5.54
98 99 3.371097 TTCAGGAGATGGCCGACGC 62.371 63.158 0.00 0.00 0.00 5.19
118 119 2.046314 CGGGGGCGTGAGTGAAAT 60.046 61.111 0.00 0.00 0.00 2.17
119 120 2.398554 CGGGGGCGTGAGTGAAATG 61.399 63.158 0.00 0.00 0.00 2.32
120 121 2.046285 GGGGGCGTGAGTGAAATGG 61.046 63.158 0.00 0.00 0.00 3.16
121 122 1.303317 GGGGCGTGAGTGAAATGGT 60.303 57.895 0.00 0.00 0.00 3.55
122 123 1.586154 GGGGCGTGAGTGAAATGGTG 61.586 60.000 0.00 0.00 0.00 4.17
123 124 1.210155 GGCGTGAGTGAAATGGTGC 59.790 57.895 0.00 0.00 0.00 5.01
124 125 1.237285 GGCGTGAGTGAAATGGTGCT 61.237 55.000 0.00 0.00 0.00 4.40
152 153 3.838271 GCGATCACCGGAGCAGGA 61.838 66.667 9.46 0.00 39.04 3.86
154 155 2.818132 GATCACCGGAGCAGGAGG 59.182 66.667 9.46 0.00 34.73 4.30
155 156 3.453070 GATCACCGGAGCAGGAGGC 62.453 68.421 9.46 0.00 45.30 4.70
171 172 2.556287 GCGTCGCCACAAAAGGAG 59.444 61.111 5.75 0.00 0.00 3.69
173 174 1.597027 CGTCGCCACAAAAGGAGGT 60.597 57.895 0.00 0.00 0.00 3.85
181 182 0.468029 ACAAAAGGAGGTGGTGCAGG 60.468 55.000 0.00 0.00 0.00 4.85
182 183 1.531602 AAAAGGAGGTGGTGCAGGC 60.532 57.895 0.00 0.00 0.00 4.85
183 184 2.011617 AAAAGGAGGTGGTGCAGGCT 62.012 55.000 0.00 0.00 0.00 4.58
185 186 4.767255 GGAGGTGGTGCAGGCTCG 62.767 72.222 0.00 0.00 0.00 5.03
186 187 4.767255 GAGGTGGTGCAGGCTCGG 62.767 72.222 0.00 0.00 0.00 4.63
190 191 4.020617 TGGTGCAGGCTCGGAAGG 62.021 66.667 0.00 0.00 0.00 3.46
192 193 2.125350 GTGCAGGCTCGGAAGGAG 60.125 66.667 0.00 0.00 46.06 3.69
199 200 3.532155 CTCGGAAGGAGCGGGAGG 61.532 72.222 0.00 0.00 35.63 4.30
210 211 4.838152 CGGGAGGCATCACCACGG 62.838 72.222 0.00 0.00 43.14 4.94
212 213 4.408821 GGAGGCATCACCACGGCA 62.409 66.667 0.00 0.00 43.14 5.69
213 214 2.124570 GAGGCATCACCACGGCAT 60.125 61.111 0.00 0.00 43.14 4.40
214 215 2.124570 AGGCATCACCACGGCATC 60.125 61.111 0.00 0.00 43.14 3.91
216 217 2.511373 GCATCACCACGGCATCGA 60.511 61.111 0.00 0.00 40.11 3.59
217 218 2.813179 GCATCACCACGGCATCGAC 61.813 63.158 0.00 0.00 40.11 4.20
218 219 2.202743 ATCACCACGGCATCGACG 60.203 61.111 0.00 0.00 41.40 5.12
219 220 3.716539 ATCACCACGGCATCGACGG 62.717 63.158 0.00 0.00 39.02 4.79
253 254 2.874751 CGGGCGGCGAATTTCTTT 59.125 55.556 12.98 0.00 0.00 2.52
254 255 1.211709 CGGGCGGCGAATTTCTTTT 59.788 52.632 12.98 0.00 0.00 2.27
255 256 0.448593 CGGGCGGCGAATTTCTTTTA 59.551 50.000 12.98 0.00 0.00 1.52
256 257 1.064952 CGGGCGGCGAATTTCTTTTAT 59.935 47.619 12.98 0.00 0.00 1.40
257 258 2.478879 CGGGCGGCGAATTTCTTTTATT 60.479 45.455 12.98 0.00 0.00 1.40
258 259 3.517602 GGGCGGCGAATTTCTTTTATTT 58.482 40.909 12.98 0.00 0.00 1.40
260 261 3.924073 GGCGGCGAATTTCTTTTATTTGT 59.076 39.130 12.98 0.00 0.00 2.83
262 263 5.107259 GGCGGCGAATTTCTTTTATTTGTTT 60.107 36.000 12.98 0.00 0.00 2.83
266 267 9.459276 CGGCGAATTTCTTTTATTTGTTTTATG 57.541 29.630 0.00 0.00 0.00 1.90
296 297 4.412843 TGTCTATGTGGACTGTGGAACTA 58.587 43.478 0.00 0.00 37.16 2.24
301 302 1.218316 GGACTGTGGAACTAGGCCG 59.782 63.158 0.00 0.00 34.33 6.13
306 307 1.535462 CTGTGGAACTAGGCCGTTTTG 59.465 52.381 0.00 0.00 38.04 2.44
332 333 7.542824 GTGGCCGTAATGTTTAATTATGTTGTT 59.457 33.333 0.00 0.00 0.00 2.83
432 433 3.797353 ATGATTCGGGGTGCGGCT 61.797 61.111 0.00 0.00 0.00 5.52
456 457 4.947147 TGGGCGCACTGACAACCC 62.947 66.667 12.74 0.00 41.24 4.11
578 579 1.668419 GTGATCATTTAGCGGCACCT 58.332 50.000 1.45 0.00 0.00 4.00
611 612 7.011950 TGACTATTTAAAACTATGGCGGACATG 59.988 37.037 6.59 0.00 40.82 3.21
612 613 7.051623 ACTATTTAAAACTATGGCGGACATGA 58.948 34.615 6.59 0.00 40.82 3.07
615 616 1.651987 AACTATGGCGGACATGAACG 58.348 50.000 6.59 4.41 40.82 3.95
616 617 0.535335 ACTATGGCGGACATGAACGT 59.465 50.000 6.59 0.00 40.82 3.99
619 620 0.460284 ATGGCGGACATGAACGTCTC 60.460 55.000 16.44 7.87 38.70 3.36
624 625 1.660607 CGGACATGAACGTCTCCATTG 59.339 52.381 0.00 0.00 36.12 2.82
636 637 3.309506 CCATTGCCGCCCCAAACA 61.310 61.111 0.00 0.00 0.00 2.83
654 655 5.339990 CAAACAGACGAAAACAGACCAAAT 58.660 37.500 0.00 0.00 0.00 2.32
663 664 2.457366 ACAGACCAAATCAGACGTCC 57.543 50.000 13.01 0.00 0.00 4.79
679 680 3.943691 CCGTTTGGGGTCGTGGGA 61.944 66.667 0.00 0.00 0.00 4.37
684 685 1.847798 TTTGGGGTCGTGGGATGGAG 61.848 60.000 0.00 0.00 0.00 3.86
692 693 1.077429 GTGGGATGGAGTTGGCCTC 60.077 63.158 3.32 0.00 39.67 4.70
760 761 4.758674 AGCTACGTGTACTTGAGTTCACTA 59.241 41.667 15.69 8.55 41.99 2.74
809 4162 1.677217 GCTCTCTCCGGCAAAGATGTT 60.677 52.381 0.00 0.00 0.00 2.71
837 4190 4.124351 CGCGCCTACCTCGACCAA 62.124 66.667 0.00 0.00 0.00 3.67
845 4198 0.896940 TACCTCGACCAAAGGCTCGT 60.897 55.000 0.00 0.00 37.42 4.18
995 4350 4.761739 CCATTTAACTCAAACTGCAGAGGA 59.238 41.667 23.35 13.15 36.20 3.71
1020 4375 4.096003 GCCGGAGCCAAGGTAGCA 62.096 66.667 5.05 0.00 0.00 3.49
1021 4376 2.668632 CCGGAGCCAAGGTAGCAA 59.331 61.111 0.00 0.00 0.00 3.91
1027 4382 0.764890 AGCCAAGGTAGCAACTGTCA 59.235 50.000 0.00 0.00 0.00 3.58
1127 4521 0.458370 CATCTGATGTCGTCCGTGCA 60.458 55.000 9.50 0.00 0.00 4.57
1161 4564 2.182791 CGAGCGTGAGGATGCTGT 59.817 61.111 0.00 0.00 44.95 4.40
1189 4592 4.467084 GGCGCACCTCATCCCGAA 62.467 66.667 10.83 0.00 0.00 4.30
1218 4621 0.461548 GCTCATCATCTCCACCGTCA 59.538 55.000 0.00 0.00 0.00 4.35
1245 4648 0.106708 GGCCTACTTCATCATCGCCA 59.893 55.000 0.00 0.00 34.98 5.69
1380 4783 7.461749 TGAATTAGATTGACAAAAGAGACCCT 58.538 34.615 0.00 0.00 0.00 4.34
1423 4833 4.367023 GGCGACACGTGGCACCTA 62.367 66.667 21.44 0.00 35.94 3.08
1622 5033 2.440409 GGTCACTGAGTGGCATCATTT 58.560 47.619 19.78 0.00 40.26 2.32
1723 5135 1.676014 GCTGCTATGTCCGGTTCAAGT 60.676 52.381 0.00 0.00 0.00 3.16
2096 5757 0.028110 GTCATTTCGATTCGGCAGGC 59.972 55.000 6.18 0.00 0.00 4.85
2142 5803 0.250770 GGACCACCTCAAGAACACCC 60.251 60.000 0.00 0.00 0.00 4.61
2143 5804 0.765510 GACCACCTCAAGAACACCCT 59.234 55.000 0.00 0.00 0.00 4.34
2153 5814 1.807814 AGAACACCCTCTTCCACTGT 58.192 50.000 0.00 0.00 0.00 3.55
2166 5827 6.201044 CCTCTTCCACTGTTTACGCTATAATG 59.799 42.308 0.00 0.00 0.00 1.90
2205 5905 4.408270 TGTAATAAACTATACCGTGGCCCA 59.592 41.667 0.00 0.00 0.00 5.36
2236 6721 4.256110 CACCTGTCTGCTGAATGATACAA 58.744 43.478 0.00 0.00 0.00 2.41
2239 6724 6.539826 CACCTGTCTGCTGAATGATACAATAA 59.460 38.462 0.00 0.00 0.00 1.40
2520 8407 4.284829 TCACTCATCTTACATGTGCCAA 57.715 40.909 9.11 0.00 0.00 4.52
2553 8443 5.514500 AAAGACCAAACTAAGGGCATCTA 57.486 39.130 0.00 0.00 36.27 1.98
2579 8469 2.561569 CCAGCCCCTAAAACAGATACG 58.438 52.381 0.00 0.00 0.00 3.06
2635 8533 7.099764 TCAAACTCCAGAAACATCTCAGATAC 58.900 38.462 0.00 0.00 0.00 2.24
2636 8534 6.865834 AACTCCAGAAACATCTCAGATACT 57.134 37.500 0.00 0.00 0.00 2.12
2637 8535 6.463995 ACTCCAGAAACATCTCAGATACTC 57.536 41.667 0.00 0.00 0.00 2.59
2638 8536 5.362430 ACTCCAGAAACATCTCAGATACTCC 59.638 44.000 0.00 0.00 0.00 3.85
2639 8537 4.651503 TCCAGAAACATCTCAGATACTCCC 59.348 45.833 0.00 0.00 0.00 4.30
2640 8538 4.653341 CCAGAAACATCTCAGATACTCCCT 59.347 45.833 0.00 0.00 0.00 4.20
2641 8539 5.221422 CCAGAAACATCTCAGATACTCCCTC 60.221 48.000 0.00 0.00 0.00 4.30
2642 8540 4.898861 AGAAACATCTCAGATACTCCCTCC 59.101 45.833 0.00 0.00 0.00 4.30
2643 8541 2.870175 ACATCTCAGATACTCCCTCCG 58.130 52.381 0.00 0.00 0.00 4.63
2644 8542 2.175931 ACATCTCAGATACTCCCTCCGT 59.824 50.000 0.00 0.00 0.00 4.69
2645 8543 2.642154 TCTCAGATACTCCCTCCGTC 57.358 55.000 0.00 0.00 0.00 4.79
2646 8544 1.143277 TCTCAGATACTCCCTCCGTCC 59.857 57.143 0.00 0.00 0.00 4.79
2647 8545 1.144093 CTCAGATACTCCCTCCGTCCT 59.856 57.143 0.00 0.00 0.00 3.85
2648 8546 2.372504 CTCAGATACTCCCTCCGTCCTA 59.627 54.545 0.00 0.00 0.00 2.94
2649 8547 2.987437 TCAGATACTCCCTCCGTCCTAT 59.013 50.000 0.00 0.00 0.00 2.57
2650 8548 4.173594 TCAGATACTCCCTCCGTCCTATA 58.826 47.826 0.00 0.00 0.00 1.31
2651 8549 4.600547 TCAGATACTCCCTCCGTCCTATAA 59.399 45.833 0.00 0.00 0.00 0.98
2652 8550 5.253330 TCAGATACTCCCTCCGTCCTATAAT 59.747 44.000 0.00 0.00 0.00 1.28
2653 8551 6.446110 TCAGATACTCCCTCCGTCCTATAATA 59.554 42.308 0.00 0.00 0.00 0.98
2654 8552 7.129038 TCAGATACTCCCTCCGTCCTATAATAT 59.871 40.741 0.00 0.00 0.00 1.28
2655 8553 8.438373 CAGATACTCCCTCCGTCCTATAATATA 58.562 40.741 0.00 0.00 0.00 0.86
2656 8554 9.011860 AGATACTCCCTCCGTCCTATAATATAA 57.988 37.037 0.00 0.00 0.00 0.98
2657 8555 9.287373 GATACTCCCTCCGTCCTATAATATAAG 57.713 40.741 0.00 0.00 0.00 1.73
2658 8556 7.281366 ACTCCCTCCGTCCTATAATATAAGA 57.719 40.000 0.00 0.00 0.00 2.10
2659 8557 7.348033 ACTCCCTCCGTCCTATAATATAAGAG 58.652 42.308 0.00 0.00 0.00 2.85
2660 8558 6.127793 TCCCTCCGTCCTATAATATAAGAGC 58.872 44.000 0.00 0.00 0.00 4.09
2661 8559 5.892119 CCCTCCGTCCTATAATATAAGAGCA 59.108 44.000 0.00 0.00 0.00 4.26
2662 8560 6.551601 CCCTCCGTCCTATAATATAAGAGCAT 59.448 42.308 0.00 0.00 0.00 3.79
2663 8561 7.070074 CCCTCCGTCCTATAATATAAGAGCATT 59.930 40.741 0.00 0.00 0.00 3.56
2664 8562 8.478877 CCTCCGTCCTATAATATAAGAGCATTT 58.521 37.037 0.00 0.00 0.00 2.32
2665 8563 9.877178 CTCCGTCCTATAATATAAGAGCATTTT 57.123 33.333 0.00 0.00 0.00 1.82
2708 8606 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2709 8607 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2710 8608 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2711 8609 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2712 8610 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2713 8611 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2714 8612 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2715 8613 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2716 8614 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2717 8615 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2731 8629 7.173032 ACGGAGGGAGTAGAATTTAAACAAAT 58.827 34.615 0.00 0.00 0.00 2.32
2901 8801 0.842030 TGTCTTCCCCATGTCCAGCT 60.842 55.000 0.00 0.00 0.00 4.24
2936 8837 3.318275 ACGAGCTCTGTGAAGTGAAGTTA 59.682 43.478 12.85 0.00 0.00 2.24
3053 8954 3.458163 ATGTGGACGTCGCCGGAT 61.458 61.111 5.05 0.00 38.78 4.18
3054 8955 3.716539 ATGTGGACGTCGCCGGATG 62.717 63.158 5.05 0.00 38.78 3.51
3086 8987 4.595538 TCGTGGTCGTTGCGGCTT 62.596 61.111 0.00 0.00 38.33 4.35
3121 9022 3.853330 CGGCGCGACCAACATGAG 61.853 66.667 12.10 0.00 39.03 2.90
3159 9060 1.349026 TCCTTGTGCCTCCTCTTCTTG 59.651 52.381 0.00 0.00 0.00 3.02
3160 9061 1.072965 CCTTGTGCCTCCTCTTCTTGT 59.927 52.381 0.00 0.00 0.00 3.16
3161 9062 2.487986 CCTTGTGCCTCCTCTTCTTGTT 60.488 50.000 0.00 0.00 0.00 2.83
3162 9063 2.260844 TGTGCCTCCTCTTCTTGTTG 57.739 50.000 0.00 0.00 0.00 3.33
3163 9064 1.768275 TGTGCCTCCTCTTCTTGTTGA 59.232 47.619 0.00 0.00 0.00 3.18
3164 9065 2.172505 TGTGCCTCCTCTTCTTGTTGAA 59.827 45.455 0.00 0.00 0.00 2.69
3165 9066 2.550180 GTGCCTCCTCTTCTTGTTGAAC 59.450 50.000 0.00 0.00 0.00 3.18
3166 9067 2.155279 GCCTCCTCTTCTTGTTGAACC 58.845 52.381 0.00 0.00 0.00 3.62
3167 9068 2.784347 CCTCCTCTTCTTGTTGAACCC 58.216 52.381 0.00 0.00 0.00 4.11
3168 9069 2.106511 CCTCCTCTTCTTGTTGAACCCA 59.893 50.000 0.00 0.00 0.00 4.51
3169 9070 3.435026 CCTCCTCTTCTTGTTGAACCCAA 60.435 47.826 0.00 0.00 0.00 4.12
3170 9071 3.817647 CTCCTCTTCTTGTTGAACCCAAG 59.182 47.826 0.00 0.00 40.51 3.61
3171 9072 3.458118 TCCTCTTCTTGTTGAACCCAAGA 59.542 43.478 0.00 0.00 44.83 3.02
3176 9077 3.020984 TCTTGTTGAACCCAAGAACACC 58.979 45.455 0.62 0.00 43.87 4.16
3177 9078 1.384525 TGTTGAACCCAAGAACACCG 58.615 50.000 0.00 0.00 32.06 4.94
3178 9079 1.065345 TGTTGAACCCAAGAACACCGA 60.065 47.619 0.00 0.00 32.06 4.69
3179 9080 1.332686 GTTGAACCCAAGAACACCGAC 59.667 52.381 0.00 0.00 32.06 4.79
3180 9081 0.531090 TGAACCCAAGAACACCGACG 60.531 55.000 0.00 0.00 0.00 5.12
3181 9082 0.249573 GAACCCAAGAACACCGACGA 60.250 55.000 0.00 0.00 0.00 4.20
3182 9083 0.249741 AACCCAAGAACACCGACGAG 60.250 55.000 0.00 0.00 0.00 4.18
3184 9085 2.027625 CCAAGAACACCGACGAGGC 61.028 63.158 0.00 0.00 46.52 4.70
3185 9086 2.027625 CAAGAACACCGACGAGGCC 61.028 63.158 0.00 0.00 46.52 5.19
3186 9087 2.207924 AAGAACACCGACGAGGCCT 61.208 57.895 3.86 3.86 46.52 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.301401 CGACGGGCTTGTTCTCCAA 60.301 57.895 0.00 0.00 0.00 3.53
59 60 3.612247 ATGCACGACCAGCTCCACC 62.612 63.158 0.00 0.00 0.00 4.61
60 61 2.046892 ATGCACGACCAGCTCCAC 60.047 61.111 0.00 0.00 0.00 4.02
61 62 2.046988 CATGCACGACCAGCTCCA 60.047 61.111 0.00 0.00 0.00 3.86
62 63 2.821366 CCATGCACGACCAGCTCC 60.821 66.667 0.00 0.00 0.00 4.70
63 64 1.639298 GAACCATGCACGACCAGCTC 61.639 60.000 0.00 0.00 0.00 4.09
65 66 1.915614 CTGAACCATGCACGACCAGC 61.916 60.000 0.00 0.00 0.00 4.85
67 68 1.302431 CCTGAACCATGCACGACCA 60.302 57.895 0.00 0.00 0.00 4.02
68 69 1.003839 TCCTGAACCATGCACGACC 60.004 57.895 0.00 0.00 0.00 4.79
69 70 0.037326 TCTCCTGAACCATGCACGAC 60.037 55.000 0.00 0.00 0.00 4.34
70 71 0.904649 ATCTCCTGAACCATGCACGA 59.095 50.000 0.00 0.00 0.00 4.35
72 73 1.386533 CCATCTCCTGAACCATGCAC 58.613 55.000 0.00 0.00 0.00 4.57
73 74 0.394762 GCCATCTCCTGAACCATGCA 60.395 55.000 0.00 0.00 0.00 3.96
75 76 0.816825 CGGCCATCTCCTGAACCATG 60.817 60.000 2.24 0.00 0.00 3.66
76 77 0.982852 TCGGCCATCTCCTGAACCAT 60.983 55.000 2.24 0.00 0.00 3.55
77 78 1.612146 TCGGCCATCTCCTGAACCA 60.612 57.895 2.24 0.00 0.00 3.67
80 81 2.892640 CGTCGGCCATCTCCTGAA 59.107 61.111 2.24 0.00 0.00 3.02
81 82 3.838271 GCGTCGGCCATCTCCTGA 61.838 66.667 2.24 0.00 0.00 3.86
102 103 2.046285 CCATTTCACTCACGCCCCC 61.046 63.158 0.00 0.00 0.00 5.40
106 107 0.166814 GAGCACCATTTCACTCACGC 59.833 55.000 0.00 0.00 0.00 5.34
107 108 0.798776 GGAGCACCATTTCACTCACG 59.201 55.000 0.00 0.00 35.97 4.35
130 131 4.873129 CTCCGGTGATCGCGGTGG 62.873 72.222 6.13 8.45 37.59 4.61
135 136 3.781770 CTCCTGCTCCGGTGATCGC 62.782 68.421 7.92 0.00 37.59 4.58
136 137 2.415010 CTCCTGCTCCGGTGATCG 59.585 66.667 7.92 0.00 38.88 3.69
137 138 2.818132 CCTCCTGCTCCGGTGATC 59.182 66.667 7.92 0.00 0.00 2.92
138 139 3.474570 GCCTCCTGCTCCGGTGAT 61.475 66.667 7.92 0.00 36.87 3.06
154 155 2.556287 CTCCTTTTGTGGCGACGC 59.444 61.111 12.43 12.43 42.66 5.19
155 156 1.597027 ACCTCCTTTTGTGGCGACG 60.597 57.895 0.00 0.00 0.00 5.12
157 158 1.228124 CCACCTCCTTTTGTGGCGA 60.228 57.895 0.00 0.00 44.98 5.54
158 159 3.354678 CCACCTCCTTTTGTGGCG 58.645 61.111 0.00 0.00 44.98 5.69
162 163 0.468029 CCTGCACCACCTCCTTTTGT 60.468 55.000 0.00 0.00 0.00 2.83
163 164 1.809567 GCCTGCACCACCTCCTTTTG 61.810 60.000 0.00 0.00 0.00 2.44
164 165 1.531602 GCCTGCACCACCTCCTTTT 60.532 57.895 0.00 0.00 0.00 2.27
165 166 2.116125 GCCTGCACCACCTCCTTT 59.884 61.111 0.00 0.00 0.00 3.11
166 167 2.856000 AGCCTGCACCACCTCCTT 60.856 61.111 0.00 0.00 0.00 3.36
171 172 4.329545 TTCCGAGCCTGCACCACC 62.330 66.667 0.00 0.00 0.00 4.61
173 174 4.020617 CCTTCCGAGCCTGCACCA 62.021 66.667 0.00 0.00 0.00 4.17
175 176 2.125350 CTCCTTCCGAGCCTGCAC 60.125 66.667 0.00 0.00 0.00 4.57
182 183 3.532155 CCTCCCGCTCCTTCCGAG 61.532 72.222 0.00 0.00 42.04 4.63
185 186 3.468326 GATGCCTCCCGCTCCTTCC 62.468 68.421 0.00 0.00 38.78 3.46
186 187 2.110006 GATGCCTCCCGCTCCTTC 59.890 66.667 0.00 0.00 38.78 3.46
190 191 3.785859 TGGTGATGCCTCCCGCTC 61.786 66.667 0.00 0.00 38.78 5.03
193 194 4.838152 CCGTGGTGATGCCTCCCG 62.838 72.222 0.00 0.00 38.35 5.14
195 196 3.704231 ATGCCGTGGTGATGCCTCC 62.704 63.158 0.00 0.00 38.35 4.30
196 197 2.124570 ATGCCGTGGTGATGCCTC 60.125 61.111 0.00 0.00 38.35 4.70
197 198 2.124570 GATGCCGTGGTGATGCCT 60.125 61.111 0.00 0.00 38.35 4.75
198 199 3.576356 CGATGCCGTGGTGATGCC 61.576 66.667 0.00 0.00 37.90 4.40
199 200 2.511373 TCGATGCCGTGGTGATGC 60.511 61.111 0.00 0.00 37.05 3.91
200 201 2.516589 CGTCGATGCCGTGGTGATG 61.517 63.158 0.00 0.00 37.05 3.07
201 202 2.202743 CGTCGATGCCGTGGTGAT 60.203 61.111 0.00 0.00 37.05 3.06
202 203 4.429212 CCGTCGATGCCGTGGTGA 62.429 66.667 0.00 0.00 37.05 4.02
236 237 0.448593 TAAAAGAAATTCGCCGCCCG 59.551 50.000 0.00 0.00 38.61 6.13
238 239 3.924073 ACAAATAAAAGAAATTCGCCGCC 59.076 39.130 0.00 0.00 0.00 6.13
266 267 7.985184 TCCACAGTCCACATAGACATAATTAAC 59.015 37.037 0.00 0.00 39.34 2.01
267 268 8.084985 TCCACAGTCCACATAGACATAATTAA 57.915 34.615 0.00 0.00 39.34 1.40
301 302 6.772770 AATTAAACATTACGGCCACAAAAC 57.227 33.333 2.24 0.00 0.00 2.43
306 307 7.030768 ACAACATAATTAAACATTACGGCCAC 58.969 34.615 2.24 0.00 0.00 5.01
414 415 3.585990 GCCGCACCCCGAATCATG 61.586 66.667 0.00 0.00 40.02 3.07
448 449 4.589675 GGGGCCGTTGGGTTGTCA 62.590 66.667 0.00 0.00 34.97 3.58
476 477 8.918961 TTCATAGCCCGTTATTTAAAACATTG 57.081 30.769 0.00 0.00 0.00 2.82
578 579 7.628366 GCCATAGTTTTAAATAGTCAGCAGCAA 60.628 37.037 0.00 0.00 0.00 3.91
584 585 6.537301 TGTCCGCCATAGTTTTAAATAGTCAG 59.463 38.462 0.00 0.00 0.00 3.51
585 586 6.408035 TGTCCGCCATAGTTTTAAATAGTCA 58.592 36.000 0.00 0.00 0.00 3.41
611 612 2.750888 GGCGGCAATGGAGACGTTC 61.751 63.158 3.07 0.00 37.50 3.95
612 613 2.746277 GGCGGCAATGGAGACGTT 60.746 61.111 3.07 0.00 41.24 3.99
615 616 3.936772 TTGGGGCGGCAATGGAGAC 62.937 63.158 12.47 0.00 0.00 3.36
616 617 3.216985 TTTGGGGCGGCAATGGAGA 62.217 57.895 12.47 0.00 0.00 3.71
619 620 3.299524 CTGTTTGGGGCGGCAATGG 62.300 63.158 12.47 0.00 0.00 3.16
631 632 4.349663 TTGGTCTGTTTTCGTCTGTTTG 57.650 40.909 0.00 0.00 0.00 2.93
636 637 4.511826 GTCTGATTTGGTCTGTTTTCGTCT 59.488 41.667 0.00 0.00 0.00 4.18
654 655 2.091102 GACCCCAAACGGACGTCTGA 62.091 60.000 30.55 0.00 0.00 3.27
663 664 2.038269 CATCCCACGACCCCAAACG 61.038 63.158 0.00 0.00 0.00 3.60
679 680 1.302285 CAGCTGAGGCCAACTCCAT 59.698 57.895 8.42 0.00 46.01 3.41
684 685 0.807496 GATGAACAGCTGAGGCCAAC 59.193 55.000 23.35 7.24 39.73 3.77
692 693 4.059511 GAGATGAGATGGATGAACAGCTG 58.940 47.826 13.48 13.48 37.20 4.24
857 4210 3.074412 CGTTGATTACCTTTGGAGCAGT 58.926 45.455 0.00 0.00 0.00 4.40
893 4246 4.389576 GCAAGAGTGCGTTGGCCG 62.390 66.667 0.00 0.00 41.93 6.13
1016 4371 0.032952 GACGGTGGTGACAGTTGCTA 59.967 55.000 0.00 0.00 44.46 3.49
1017 4372 1.227556 GACGGTGGTGACAGTTGCT 60.228 57.895 0.00 0.00 44.46 3.91
1020 4375 2.279918 GCGACGGTGGTGACAGTT 60.280 61.111 0.00 0.00 44.46 3.16
1021 4376 3.224324 AGCGACGGTGGTGACAGT 61.224 61.111 0.00 0.00 44.46 3.55
1127 4521 0.321919 TCGCCAGCTGCAGAGAAATT 60.322 50.000 20.43 0.00 41.33 1.82
1198 4601 0.249657 GACGGTGGAGATGATGAGCC 60.250 60.000 0.00 0.00 0.00 4.70
1218 4621 0.694444 ATGAAGTAGGCCATCCCGGT 60.694 55.000 5.01 0.00 39.21 5.28
1245 4648 3.875369 GCCATTGAGAGGATGGTCTTGTT 60.875 47.826 5.16 0.00 44.75 2.83
1493 4904 3.390521 CTGTGTGGCGAGGGGCTA 61.391 66.667 0.00 0.00 42.94 3.93
1622 5033 3.394674 TCTAGTCAAAACCGTGCATGA 57.605 42.857 7.72 0.00 0.00 3.07
1723 5135 1.155889 CACACACTGGAGCGCATTTA 58.844 50.000 11.47 0.00 0.00 1.40
2119 5780 3.234630 TTCTTGAGGTGGTCCGGCG 62.235 63.158 0.00 0.00 39.05 6.46
2120 5781 1.671379 GTTCTTGAGGTGGTCCGGC 60.671 63.158 0.00 0.00 39.05 6.13
2121 5782 0.602905 GTGTTCTTGAGGTGGTCCGG 60.603 60.000 0.00 0.00 39.05 5.14
2122 5783 0.602905 GGTGTTCTTGAGGTGGTCCG 60.603 60.000 0.00 0.00 39.05 4.79
2123 5784 0.250770 GGGTGTTCTTGAGGTGGTCC 60.251 60.000 0.00 0.00 0.00 4.46
2124 5785 0.765510 AGGGTGTTCTTGAGGTGGTC 59.234 55.000 0.00 0.00 0.00 4.02
2125 5786 0.765510 GAGGGTGTTCTTGAGGTGGT 59.234 55.000 0.00 0.00 0.00 4.16
2126 5787 1.059913 AGAGGGTGTTCTTGAGGTGG 58.940 55.000 0.00 0.00 0.00 4.61
2142 5803 6.201044 CCATTATAGCGTAAACAGTGGAAGAG 59.799 42.308 0.00 0.00 0.00 2.85
2143 5804 6.046593 CCATTATAGCGTAAACAGTGGAAGA 58.953 40.000 0.00 0.00 0.00 2.87
2182 5867 4.408270 TGGGCCACGGTATAGTTTATTACA 59.592 41.667 0.00 0.00 0.00 2.41
2184 5869 5.829062 ATGGGCCACGGTATAGTTTATTA 57.171 39.130 9.28 0.00 0.00 0.98
2205 5905 3.075005 AGACAGGTGCGGCCGTAT 61.075 61.111 28.70 6.95 43.70 3.06
2236 6721 7.038659 GCCTCTCTCGCTGAACATTATATTAT 58.961 38.462 0.00 0.00 0.00 1.28
2239 6724 4.617067 CGCCTCTCTCGCTGAACATTATAT 60.617 45.833 0.00 0.00 0.00 0.86
2537 8425 3.181510 GCGTTGTAGATGCCCTTAGTTTG 60.182 47.826 0.00 0.00 34.03 2.93
2553 8443 1.151908 TTTTAGGGGCTGGCGTTGT 59.848 52.632 0.00 0.00 0.00 3.32
2561 8451 5.046520 GGATATCGTATCTGTTTTAGGGGCT 60.047 44.000 0.00 0.00 0.00 5.19
2579 8469 2.059541 GCCTGCTCGTAAACGGATATC 58.940 52.381 2.24 0.00 40.29 1.63
2635 8533 6.263617 GCTCTTATATTATAGGACGGAGGGAG 59.736 46.154 0.00 0.00 0.00 4.30
2636 8534 6.127793 GCTCTTATATTATAGGACGGAGGGA 58.872 44.000 0.00 0.00 0.00 4.20
2637 8535 5.892119 TGCTCTTATATTATAGGACGGAGGG 59.108 44.000 0.00 0.00 0.00 4.30
2638 8536 7.589958 ATGCTCTTATATTATAGGACGGAGG 57.410 40.000 0.00 0.00 0.00 4.30
2639 8537 9.877178 AAAATGCTCTTATATTATAGGACGGAG 57.123 33.333 0.00 0.00 0.00 4.63
2684 8582 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2685 8583 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2686 8584 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2687 8585 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2688 8586 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2689 8587 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2690 8588 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2691 8589 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2692 8590 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2693 8591 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2694 8592 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2695 8593 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2696 8594 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2697 8595 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
2698 8596 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2699 8597 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2700 8598 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
2701 8599 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
2702 8600 0.635009 ATTCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2703 8601 1.790818 AATTCTACTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
2704 8602 5.114780 GTTTAAATTCTACTCCCTCCGTCC 58.885 45.833 0.00 0.00 0.00 4.79
2705 8603 5.727434 TGTTTAAATTCTACTCCCTCCGTC 58.273 41.667 0.00 0.00 0.00 4.79
2706 8604 5.750352 TGTTTAAATTCTACTCCCTCCGT 57.250 39.130 0.00 0.00 0.00 4.69
2707 8605 7.625828 ATTTGTTTAAATTCTACTCCCTCCG 57.374 36.000 0.00 0.00 32.70 4.63
2757 8655 8.620116 ATTTTGATCCGGTTTGAATGAAAATT 57.380 26.923 0.00 0.00 0.00 1.82
2800 8698 4.086105 CGTCCGCTTTCGTTTAATTGAAAC 59.914 41.667 0.00 0.00 43.51 2.78
2819 8717 3.007635 CTGGGATAAAAAGGTGTCGTCC 58.992 50.000 0.00 0.00 0.00 4.79
2901 8801 0.613260 AGCTCGTGGCCATTGAACTA 59.387 50.000 9.72 0.00 43.05 2.24
2936 8837 2.047830 GTCATATTCTTCCCCTCCCGT 58.952 52.381 0.00 0.00 0.00 5.28
2966 8867 1.448540 CTCGTGTCCCATGTGAGCC 60.449 63.158 0.00 0.00 0.00 4.70
3053 8954 3.399181 GAGGCCGACCCATCCACA 61.399 66.667 0.00 0.00 36.11 4.17
3054 8955 4.530857 CGAGGCCGACCCATCCAC 62.531 72.222 0.00 0.00 38.22 4.02
3086 8987 1.585267 CGCTAGCATGGTTTGTGCCA 61.585 55.000 16.45 0.00 43.50 4.92
3159 9060 1.332686 GTCGGTGTTCTTGGGTTCAAC 59.667 52.381 0.00 0.00 0.00 3.18
3160 9061 1.670791 GTCGGTGTTCTTGGGTTCAA 58.329 50.000 0.00 0.00 0.00 2.69
3161 9062 0.531090 CGTCGGTGTTCTTGGGTTCA 60.531 55.000 0.00 0.00 0.00 3.18
3162 9063 0.249573 TCGTCGGTGTTCTTGGGTTC 60.250 55.000 0.00 0.00 0.00 3.62
3163 9064 0.249741 CTCGTCGGTGTTCTTGGGTT 60.250 55.000 0.00 0.00 0.00 4.11
3164 9065 1.366366 CTCGTCGGTGTTCTTGGGT 59.634 57.895 0.00 0.00 0.00 4.51
3165 9066 1.374252 CCTCGTCGGTGTTCTTGGG 60.374 63.158 0.00 0.00 0.00 4.12
3166 9067 2.027625 GCCTCGTCGGTGTTCTTGG 61.028 63.158 0.00 0.00 34.25 3.61
3167 9068 2.027625 GGCCTCGTCGGTGTTCTTG 61.028 63.158 0.00 0.00 34.25 3.02
3168 9069 2.207924 AGGCCTCGTCGGTGTTCTT 61.208 57.895 0.00 0.00 34.25 2.52
3169 9070 2.600769 AGGCCTCGTCGGTGTTCT 60.601 61.111 0.00 0.00 34.25 3.01


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

AutoCloner maintained by Alex Coulton.