Multiple sequence alignment - TraesCS7A01G549500

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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 TraesCS7A01G549500 chr7A 100.000 4474 0 0 1 4474 723308513 723304040 0.000000e+00 8263
1 TraesCS7A01G549500 chr7A 89.971 339 13 7 1592 1917 637066459 637066789 6.920000e-113 418
2 TraesCS7A01G549500 chr7A 89.676 339 13 8 1592 1917 724282253 724282582 3.220000e-111 412
3 TraesCS7A01G549500 chr7D 90.641 4028 165 82 1 3918 627435386 627431461 0.000000e+00 5155
4 TraesCS7A01G549500 chr7D 83.183 333 24 12 4070 4385 627431251 627430934 4.410000e-70 276
5 TraesCS7A01G549500 chr7D 93.714 175 7 4 1474 1644 636513724 636513898 4.440000e-65 259
6 TraesCS7A01G549500 chr7D 85.976 164 4 9 1316 1479 350791321 350791465 1.670000e-34 158
7 TraesCS7A01G549500 chr7D 87.234 141 6 3 3154 3282 195416783 195416643 2.790000e-32 150
8 TraesCS7A01G549500 chr7D 92.233 103 4 3 3970 4069 627431443 627431342 4.670000e-30 143
9 TraesCS7A01G549500 chr7B 88.703 2390 99 65 1795 4063 728836719 728834380 0.000000e+00 2760
10 TraesCS7A01G549500 chr7B 91.419 944 40 18 888 1799 728837787 728836853 0.000000e+00 1256
11 TraesCS7A01G549500 chr7B 86.364 902 43 23 1 861 728838647 728837785 0.000000e+00 911
12 TraesCS7A01G549500 chr7B 85.885 503 19 22 3605 4063 701398299 701398793 5.200000e-134 488
13 TraesCS7A01G549500 chr7B 86.755 151 8 3 3141 3279 164619558 164619708 1.670000e-34 158
14 TraesCS7A01G549500 chr7B 85.926 135 8 1 4099 4222 728834382 728834248 2.810000e-27 134
15 TraesCS7A01G549500 chr7B 85.821 134 8 1 4099 4221 701398791 701398924 1.010000e-26 132
16 TraesCS7A01G549500 chr1A 88.264 605 29 16 1327 1917 199209352 199208776 0.000000e+00 686
17 TraesCS7A01G549500 chr1A 85.045 448 58 4 2159 2605 189659095 189658656 8.830000e-122 448
18 TraesCS7A01G549500 chr1A 82.895 456 63 8 2157 2605 243093717 243093270 3.240000e-106 396
19 TraesCS7A01G549500 chr1A 88.820 161 16 2 1812 1971 212155370 212155211 3.530000e-46 196
20 TraesCS7A01G549500 chr1A 92.079 101 7 1 3141 3240 488677484 488677384 1.680000e-29 141
21 TraesCS7A01G549500 chr5D 87.277 448 46 5 2159 2605 430747992 430748429 6.680000e-138 501
22 TraesCS7A01G549500 chr5D 85.976 164 4 3 1316 1479 178105194 178105338 1.670000e-34 158
23 TraesCS7A01G549500 chr4B 84.891 503 24 22 3605 4063 626990216 626990710 1.130000e-125 460
24 TraesCS7A01G549500 chr4B 92.254 142 9 2 1831 1972 144286307 144286446 2.730000e-47 200
25 TraesCS7A01G549500 chr4B 91.919 99 7 1 3141 3238 452090487 452090585 2.170000e-28 137
26 TraesCS7A01G549500 chr4B 86.567 134 7 1 4099 4221 626990708 626990841 2.170000e-28 137
27 TraesCS7A01G549500 chr4B 85.507 138 8 4 3154 3279 346916622 346916759 2.810000e-27 134
28 TraesCS7A01G549500 chr1B 85.120 457 24 16 1327 1776 41211874 41212293 1.150000e-115 427
29 TraesCS7A01G549500 chr1B 84.768 453 25 16 1331 1776 41173866 41174281 8.950000e-112 414
30 TraesCS7A01G549500 chr5A 89.971 339 13 7 1592 1917 178827553 178827223 6.920000e-113 418
31 TraesCS7A01G549500 chr5A 89.381 339 15 7 1592 1917 568932064 568932394 1.500000e-109 407
32 TraesCS7A01G549500 chr5A 83.151 457 60 10 2157 2605 573739674 573740121 6.970000e-108 401
33 TraesCS7A01G549500 chr5A 91.379 290 10 6 1635 1917 568912671 568912952 2.520000e-102 383
34 TraesCS7A01G549500 chr5A 92.079 101 7 1 3141 3240 622169317 622169417 1.680000e-29 141
35 TraesCS7A01G549500 chr3D 89.143 350 14 6 1318 1662 596006371 596006701 8.950000e-112 414
36 TraesCS7A01G549500 chr3D 83.594 256 28 8 1405 1652 405719168 405719417 1.250000e-55 228
37 TraesCS7A01G549500 chr3D 86.585 164 3 9 1316 1479 409591446 409591302 3.580000e-36 163
38 TraesCS7A01G549500 chr3D 85.366 164 5 12 1316 1479 19402705 19402849 7.750000e-33 152
39 TraesCS7A01G549500 chr6A 83.589 457 58 10 2157 2605 119185835 119185388 3.220000e-111 412
40 TraesCS7A01G549500 chr6A 89.506 162 15 2 1812 1972 87407604 87407444 2.110000e-48 204
41 TraesCS7A01G549500 chr6A 87.654 162 18 2 1812 1972 587390538 587390698 2.120000e-43 187
42 TraesCS7A01G549500 chr6A 78.151 238 31 11 3009 3246 426298698 426298482 1.010000e-26 132
43 TraesCS7A01G549500 chrUn 89.118 340 16 7 1590 1916 151562116 151562447 1.940000e-108 403
44 TraesCS7A01G549500 chrUn 94.301 193 7 2 2112 2301 170964678 170964487 4.380000e-75 292
45 TraesCS7A01G549500 chrUn 86.283 226 9 5 1331 1555 151561912 151562116 4.500000e-55 226
46 TraesCS7A01G549500 chrUn 85.841 226 10 5 1331 1555 146623967 146624171 2.100000e-53 220
47 TraesCS7A01G549500 chr3B 81.333 450 58 8 2157 2605 167208554 167208978 4.290000e-90 342
48 TraesCS7A01G549500 chr5B 93.878 196 8 2 2109 2301 382084 382278 4.380000e-75 292
49 TraesCS7A01G549500 chr5B 86.131 137 7 4 3154 3278 225208101 225207965 2.170000e-28 137
50 TraesCS7A01G549500 chr5B 85.507 138 8 4 3154 3279 195336245 195336382 2.810000e-27 134
51 TraesCS7A01G549500 chr3A 83.271 269 29 7 1719 1972 354898701 354898968 2.690000e-57 233
52 TraesCS7A01G549500 chr3A 82.879 257 29 11 1405 1652 354898320 354898570 2.710000e-52 217
53 TraesCS7A01G549500 chr3A 94.059 101 5 1 3141 3240 142213279 142213379 7.750000e-33 152
54 TraesCS7A01G549500 chr2D 83.529 255 30 8 1405 1652 488415539 488415290 1.250000e-55 228
55 TraesCS7A01G549500 chr2D 83.254 209 34 1 3039 3246 648900421 648900629 1.640000e-44 191
56 TraesCS7A01G549500 chr2D 85.976 164 4 3 1316 1479 617454302 617454446 1.670000e-34 158
57 TraesCS7A01G549500 chr4D 83.465 254 30 8 1406 1652 201807911 201807663 4.500000e-55 226
58 TraesCS7A01G549500 chr2A 88.889 162 16 2 1812 1972 714802956 714802796 9.820000e-47 198
59 TraesCS7A01G549500 chr4A 88.272 162 17 2 1812 1972 519261389 519261229 4.570000e-45 193
60 TraesCS7A01G549500 chr1D 85.366 164 5 3 1316 1479 26748028 26748172 7.750000e-33 152
61 TraesCS7A01G549500 chr2B 86.957 138 6 4 3154 3279 633595459 633595596 1.300000e-30 145


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 TraesCS7A01G549500 chr7A 723304040 723308513 4473 True 8263.00 8263 100.000000 1 4474 1 chr7A.!!$R1 4473
1 TraesCS7A01G549500 chr7D 627430934 627435386 4452 True 1858.00 5155 88.685667 1 4385 3 chr7D.!!$R2 4384
2 TraesCS7A01G549500 chr7B 728834248 728838647 4399 True 1265.25 2760 88.103000 1 4222 4 chr7B.!!$R1 4221
3 TraesCS7A01G549500 chr7B 701398299 701398924 625 False 310.00 488 85.853000 3605 4221 2 chr7B.!!$F2 616
4 TraesCS7A01G549500 chr1A 199208776 199209352 576 True 686.00 686 88.264000 1327 1917 1 chr1A.!!$R2 590
5 TraesCS7A01G549500 chr4B 626990216 626990841 625 False 298.50 460 85.729000 3605 4221 2 chr4B.!!$F4 616
6 TraesCS7A01G549500 chrUn 151561912 151562447 535 False 314.50 403 87.700500 1331 1916 2 chrUn.!!$F2 585
7 TraesCS7A01G549500 chr3A 354898320 354898968 648 False 225.00 233 83.075000 1405 1972 2 chr3A.!!$F2 567

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
285 305 0.103390 GCGAGCTACTTTCCTCCCTC 59.897 60.0 0.00 0.00 0.00 4.30 F
648 703 0.237235 TTGCGTCGAATTGGAGCAAC 59.763 50.0 17.01 0.00 42.02 4.17 F
2044 2386 0.025898 CATTGCACGATCAGCACGAG 59.974 55.0 9.16 0.12 42.54 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2362 1.293924 GCTGATCGTGCAATGCTAGT 58.706 50.000 6.82 0.0 0.00 2.57 R
2624 2978 1.449246 CTGGAGCTTCTTCCTGGCG 60.449 63.158 0.00 0.0 38.12 5.69 R
3986 4455 1.082879 AGATCTTCCCTCCCCCTTTCA 59.917 52.381 0.00 0.0 0.00 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.782044 CCCGTTTTGAAAGCACATGG 58.218 50.000 0.00 0.00 0.00 3.66
48 49 1.339610 CCCGTTTTGAAAGCACATGGA 59.660 47.619 0.00 0.00 0.00 3.41
49 50 2.223923 CCCGTTTTGAAAGCACATGGAA 60.224 45.455 0.00 0.00 0.00 3.53
280 300 2.184579 GCGGCGAGCTACTTTCCT 59.815 61.111 12.98 0.00 44.04 3.36
281 301 1.878975 GCGGCGAGCTACTTTCCTC 60.879 63.158 12.98 0.00 44.04 3.71
282 302 1.227002 CGGCGAGCTACTTTCCTCC 60.227 63.158 0.00 0.00 0.00 4.30
283 303 1.144276 GGCGAGCTACTTTCCTCCC 59.856 63.158 0.00 0.00 0.00 4.30
284 304 1.331399 GGCGAGCTACTTTCCTCCCT 61.331 60.000 0.00 0.00 0.00 4.20
285 305 0.103390 GCGAGCTACTTTCCTCCCTC 59.897 60.000 0.00 0.00 0.00 4.30
286 306 0.382515 CGAGCTACTTTCCTCCCTCG 59.617 60.000 0.00 0.00 36.65 4.63
287 307 1.765230 GAGCTACTTTCCTCCCTCGA 58.235 55.000 0.00 0.00 0.00 4.04
288 308 1.406180 GAGCTACTTTCCTCCCTCGAC 59.594 57.143 0.00 0.00 0.00 4.20
289 309 0.460722 GCTACTTTCCTCCCTCGACC 59.539 60.000 0.00 0.00 0.00 4.79
290 310 1.960953 GCTACTTTCCTCCCTCGACCT 60.961 57.143 0.00 0.00 0.00 3.85
291 311 2.686118 GCTACTTTCCTCCCTCGACCTA 60.686 54.545 0.00 0.00 0.00 3.08
297 317 1.534697 CTCCCTCGACCTAGAGCCT 59.465 63.158 0.00 0.00 36.95 4.58
306 326 0.555769 ACCTAGAGCCTGGGAGAGAG 59.444 60.000 10.80 0.00 35.58 3.20
332 355 3.803162 GCAGCTCCCCCTTCTCCC 61.803 72.222 0.00 0.00 0.00 4.30
438 483 2.548480 GGGGTCGTTTCTTGTTCTTGAG 59.452 50.000 0.00 0.00 0.00 3.02
600 654 1.318576 AGGTTCTTTGGCGTTCTTGG 58.681 50.000 0.00 0.00 0.00 3.61
633 688 2.613506 GGTCCCGGTTGTTCTTGCG 61.614 63.158 0.00 0.00 0.00 4.85
635 690 1.595929 TCCCGGTTGTTCTTGCGTC 60.596 57.895 0.00 0.00 0.00 5.19
641 696 2.307049 GGTTGTTCTTGCGTCGAATTG 58.693 47.619 0.00 0.00 0.00 2.32
647 702 0.516877 CTTGCGTCGAATTGGAGCAA 59.483 50.000 18.64 18.64 44.24 3.91
648 703 0.237235 TTGCGTCGAATTGGAGCAAC 59.763 50.000 17.01 0.00 42.02 4.17
660 731 1.202915 TGGAGCAACAGATTCTTGGCA 60.203 47.619 4.40 0.00 0.00 4.92
664 735 0.455633 CAACAGATTCTTGGCAGCGC 60.456 55.000 0.00 0.00 0.00 5.92
694 765 0.898320 GGTAGAGTTCCAGCTGCTCA 59.102 55.000 18.39 5.61 0.00 4.26
746 818 1.555533 GTTTCTTCCTGGATCTCCCGT 59.444 52.381 0.00 0.00 37.93 5.28
763 835 3.005539 TGCCAGAGCAGAGGGTCC 61.006 66.667 0.00 0.00 46.52 4.46
764 836 2.686835 GCCAGAGCAGAGGGTCCT 60.687 66.667 0.00 0.00 42.52 3.85
765 837 3.028921 GCCAGAGCAGAGGGTCCTG 62.029 68.421 0.00 0.00 42.52 3.86
766 838 1.305633 CCAGAGCAGAGGGTCCTGA 60.306 63.158 0.00 0.00 42.52 3.86
767 839 0.906756 CCAGAGCAGAGGGTCCTGAA 60.907 60.000 0.00 0.00 42.52 3.02
768 840 0.536260 CAGAGCAGAGGGTCCTGAAG 59.464 60.000 0.00 0.00 42.52 3.02
769 841 1.220477 GAGCAGAGGGTCCTGAAGC 59.780 63.158 0.00 0.00 36.29 3.86
770 842 2.125350 GCAGAGGGTCCTGAAGCG 60.125 66.667 0.00 0.00 36.29 4.68
771 843 2.948720 GCAGAGGGTCCTGAAGCGT 61.949 63.158 0.00 0.00 36.29 5.07
772 844 1.079543 CAGAGGGTCCTGAAGCGTG 60.080 63.158 0.00 0.00 36.29 5.34
773 845 2.266055 GAGGGTCCTGAAGCGTGG 59.734 66.667 0.00 0.00 0.00 4.94
774 846 3.959991 GAGGGTCCTGAAGCGTGGC 62.960 68.421 0.00 0.00 0.00 5.01
775 847 4.021925 GGGTCCTGAAGCGTGGCT 62.022 66.667 0.00 0.00 42.56 4.75
776 848 2.656069 GGGTCCTGAAGCGTGGCTA 61.656 63.158 0.00 0.00 38.25 3.93
777 849 1.153549 GGTCCTGAAGCGTGGCTAG 60.154 63.158 0.00 0.00 38.25 3.42
778 850 1.592223 GTCCTGAAGCGTGGCTAGT 59.408 57.895 0.00 0.00 38.25 2.57
779 851 0.458716 GTCCTGAAGCGTGGCTAGTC 60.459 60.000 0.00 0.00 38.25 2.59
780 852 0.612174 TCCTGAAGCGTGGCTAGTCT 60.612 55.000 0.00 0.00 38.25 3.24
832 904 3.564027 CGCGAGGTTTCCCATCGC 61.564 66.667 0.00 10.87 45.64 4.58
861 933 1.821136 CCAAATCCAGAGTTCTTGGCC 59.179 52.381 0.00 0.00 30.84 5.36
921 993 2.962421 ACCAAAAGATCCCGCTTTTTCA 59.038 40.909 0.00 0.00 43.50 2.69
922 994 3.386402 ACCAAAAGATCCCGCTTTTTCAA 59.614 39.130 0.00 0.00 43.50 2.69
923 995 4.141824 ACCAAAAGATCCCGCTTTTTCAAA 60.142 37.500 0.00 0.00 43.50 2.69
924 996 4.448732 CCAAAAGATCCCGCTTTTTCAAAG 59.551 41.667 0.00 0.00 43.50 2.77
966 1038 4.527816 TCCCCTGTTTCTGAATTTGGATTG 59.472 41.667 0.00 0.00 0.00 2.67
975 1049 2.234414 TGAATTTGGATTGCCCTCTTGC 59.766 45.455 0.00 0.00 35.38 4.01
1029 1104 1.227002 GAGATCCGAGAACCACCGC 60.227 63.158 0.00 0.00 0.00 5.68
1113 1188 3.960571 CCTGAGGGACATCAAGAACATT 58.039 45.455 0.00 0.00 33.58 2.71
1188 1263 0.466007 CAATCCACCGATCCATGGCA 60.466 55.000 6.96 0.00 35.81 4.92
1216 1303 4.560128 TCGAACTCCAGTTTGATTCAGAG 58.440 43.478 5.42 0.00 41.97 3.35
1242 1329 3.422417 TCTCTAATCGCTCCGAGTTTG 57.578 47.619 0.00 0.00 39.91 2.93
1373 1460 2.437716 AAACGCCCCGCTGGTATG 60.438 61.111 0.00 0.00 36.04 2.39
1799 1984 5.574443 GCTGTAGATTTTCCATCTTTTGCAC 59.426 40.000 0.00 0.00 0.00 4.57
1800 1985 6.571150 GCTGTAGATTTTCCATCTTTTGCACT 60.571 38.462 0.00 0.00 0.00 4.40
1801 1986 6.913170 TGTAGATTTTCCATCTTTTGCACTC 58.087 36.000 0.00 0.00 0.00 3.51
1810 2044 4.927425 CCATCTTTTGCACTCAGATTTTGG 59.073 41.667 0.00 0.00 0.00 3.28
1930 2272 1.899142 AGTGAGAGGCAGAAGAGGAAC 59.101 52.381 0.00 0.00 0.00 3.62
1942 2284 1.300931 GAGGAACGCTGACACTGCA 60.301 57.895 0.00 0.00 0.00 4.41
2017 2359 5.422012 TGATGAGATGGTAAGCAGAGTAACA 59.578 40.000 0.00 0.00 0.00 2.41
2020 2362 5.011635 TGAGATGGTAAGCAGAGTAACACAA 59.988 40.000 0.00 0.00 0.00 3.33
2024 2366 5.779922 TGGTAAGCAGAGTAACACAACTAG 58.220 41.667 0.00 0.00 0.00 2.57
2041 2383 1.004185 CTAGCATTGCACGATCAGCAC 60.004 52.381 11.91 0.00 42.54 4.40
2042 2384 1.581912 GCATTGCACGATCAGCACG 60.582 57.895 9.16 5.59 42.54 5.34
2043 2385 1.969809 GCATTGCACGATCAGCACGA 61.970 55.000 9.16 0.00 42.54 4.35
2044 2386 0.025898 CATTGCACGATCAGCACGAG 59.974 55.000 9.16 0.12 42.54 4.18
2045 2387 1.699656 ATTGCACGATCAGCACGAGC 61.700 55.000 9.16 0.00 42.54 5.03
2078 2421 1.731709 TGGTGTTTTCATCGCTCATCG 59.268 47.619 0.00 0.00 40.15 3.84
2291 2637 7.574404 CGGTCAAGTTATCTACAGAGTTGTGTA 60.574 40.741 0.00 0.00 38.23 2.90
2301 2647 2.365617 CAGAGTTGTGTACCTGACCTGT 59.634 50.000 0.00 0.00 30.87 4.00
2315 2666 7.598759 ACCTGACCTGTTATGGTAGTAATAG 57.401 40.000 0.00 0.00 41.00 1.73
2319 2670 8.461249 TGACCTGTTATGGTAGTAATAGTCTC 57.539 38.462 0.00 0.00 41.00 3.36
2333 2684 8.814038 AGTAATAGTCTCATTGCCAAATTCTT 57.186 30.769 0.00 0.00 0.00 2.52
2347 2698 4.616835 CCAAATTCTTTGTGCTGTAGGAGC 60.617 45.833 0.00 0.00 41.82 4.70
2445 2796 3.134458 GCTGATTGAGGTAAGGATTCCG 58.866 50.000 0.00 0.00 0.00 4.30
2486 2837 5.589192 TCGGCAAAGTAGTCTTATCTTAGC 58.411 41.667 0.00 0.00 33.09 3.09
2624 2978 2.266055 CTGGCCAGGGAGAACGTC 59.734 66.667 26.14 0.00 0.00 4.34
2705 3059 1.956170 GGTCAGTGTGCCAGTCGTG 60.956 63.158 0.00 0.00 0.00 4.35
2750 3104 2.783288 CGCCTACTCCCGGGAAGAC 61.783 68.421 26.68 11.78 0.00 3.01
2756 3110 1.657804 ACTCCCGGGAAGACATTCTT 58.342 50.000 26.68 0.00 39.87 2.52
2758 3112 0.618458 TCCCGGGAAGACATTCTTGG 59.382 55.000 24.50 0.00 36.73 3.61
2768 3122 3.009723 AGACATTCTTGGCATGGTAACG 58.990 45.455 0.00 0.00 32.93 3.18
2779 3133 3.056107 GGCATGGTAACGATCCTGCTATA 60.056 47.826 0.00 0.00 42.51 1.31
2781 3135 3.909776 TGGTAACGATCCTGCTATACG 57.090 47.619 0.00 0.00 42.51 3.06
2782 3136 3.216800 TGGTAACGATCCTGCTATACGT 58.783 45.455 0.00 0.00 42.51 3.57
2783 3137 3.633525 TGGTAACGATCCTGCTATACGTT 59.366 43.478 0.00 0.00 46.15 3.99
2784 3138 3.979495 GGTAACGATCCTGCTATACGTTG 59.021 47.826 0.00 0.00 44.59 4.10
2794 3148 7.116075 TCCTGCTATACGTTGTATACCTTTT 57.884 36.000 0.00 0.00 0.00 2.27
2806 3160 7.463648 CGTTGTATACCTTTTGTCGATTCGATT 60.464 37.037 12.54 0.00 38.42 3.34
2850 3204 6.756074 GTCTTCAGAGAATTGACACTAGGATG 59.244 42.308 0.00 0.00 32.66 3.51
2853 3207 5.716703 TCAGAGAATTGACACTAGGATGTGA 59.283 40.000 1.47 0.00 40.12 3.58
2872 3226 4.657504 TGTGATAATTCTGCAGGAGAGGAT 59.342 41.667 15.13 0.11 30.18 3.24
2879 3233 2.842496 TCTGCAGGAGAGGATGATTGTT 59.158 45.455 15.13 0.00 0.00 2.83
2918 3272 4.820775 ACATGTCAGTCCCTACTCCATAT 58.179 43.478 0.00 0.00 31.97 1.78
2971 3325 4.468153 AGGGTCTGACAAGAAGGTAAGATC 59.532 45.833 10.38 0.00 31.01 2.75
2973 3327 5.172205 GGTCTGACAAGAAGGTAAGATCAC 58.828 45.833 10.38 0.00 30.78 3.06
3001 3362 4.021719 CACCTTGGATCATTGCTCTGTTTT 60.022 41.667 0.00 0.00 0.00 2.43
3002 3363 4.021719 ACCTTGGATCATTGCTCTGTTTTG 60.022 41.667 0.00 0.00 0.00 2.44
3007 3371 5.711506 TGGATCATTGCTCTGTTTTGTATGT 59.288 36.000 0.00 0.00 0.00 2.29
3267 3650 6.146837 CACTGTCTTTCATTCAGACCAACTAG 59.853 42.308 0.00 0.00 40.12 2.57
3295 3681 3.324846 AGTGAGTGAGTGATGCCTTTGTA 59.675 43.478 0.00 0.00 0.00 2.41
3296 3682 3.433615 GTGAGTGAGTGATGCCTTTGTAC 59.566 47.826 0.00 0.00 0.00 2.90
3297 3683 3.324846 TGAGTGAGTGATGCCTTTGTACT 59.675 43.478 0.00 0.00 0.00 2.73
3301 3693 3.070878 TGAGTGATGCCTTTGTACTCACA 59.929 43.478 10.62 0.00 41.82 3.58
3303 3695 3.071602 AGTGATGCCTTTGTACTCACAGT 59.928 43.478 10.62 0.00 38.90 3.55
3362 3755 4.729918 GTGGAGCTGCACCAGGGG 62.730 72.222 26.46 0.00 38.14 4.79
3426 3819 3.166490 TTCAAGTACGGGTGCGCCA 62.166 57.895 19.98 0.00 36.17 5.69
3484 3877 3.998672 GGCCTGACCGACCGACAA 61.999 66.667 0.00 0.00 0.00 3.18
3485 3878 2.737376 GCCTGACCGACCGACAAC 60.737 66.667 0.00 0.00 0.00 3.32
3486 3879 3.048602 CCTGACCGACCGACAACT 58.951 61.111 0.00 0.00 0.00 3.16
3504 3911 3.026630 ACTTACATCACCGTGTCTGTG 57.973 47.619 15.35 6.94 33.62 3.66
3746 4179 6.705381 CCAATTACATGTGTTGGAATGTGTTT 59.295 34.615 27.79 0.00 43.98 2.83
3885 4336 3.616956 TGATCTTGTCCTGGTAGCAAG 57.383 47.619 16.32 16.32 40.47 4.01
3886 4337 2.906389 TGATCTTGTCCTGGTAGCAAGT 59.094 45.455 19.35 11.89 40.14 3.16
3887 4338 4.093743 TGATCTTGTCCTGGTAGCAAGTA 58.906 43.478 19.35 11.77 40.14 2.24
3926 4385 9.820725 AGAATTTGAAATTTGACTTGATGTGAA 57.179 25.926 4.46 0.00 0.00 3.18
3928 4387 9.820725 AATTTGAAATTTGACTTGATGTGAAGA 57.179 25.926 0.00 0.00 0.00 2.87
3929 4388 9.991906 ATTTGAAATTTGACTTGATGTGAAGAT 57.008 25.926 0.00 0.00 0.00 2.40
3932 4391 7.231115 TGAAATTTGACTTGATGTGAAGATGGA 59.769 33.333 0.00 0.00 0.00 3.41
3975 4444 2.771089 ACATGTGGCTGAGTTGTACTG 58.229 47.619 0.00 0.00 0.00 2.74
3976 4445 2.368548 ACATGTGGCTGAGTTGTACTGA 59.631 45.455 0.00 0.00 0.00 3.41
3983 4452 6.544197 TGTGGCTGAGTTGTACTGAAAATTTA 59.456 34.615 0.00 0.00 0.00 1.40
3984 4453 7.067615 TGTGGCTGAGTTGTACTGAAAATTTAA 59.932 33.333 0.00 0.00 0.00 1.52
3985 4454 7.918562 GTGGCTGAGTTGTACTGAAAATTTAAA 59.081 33.333 0.00 0.00 0.00 1.52
3986 4455 8.637986 TGGCTGAGTTGTACTGAAAATTTAAAT 58.362 29.630 0.00 0.00 0.00 1.40
3987 4456 8.915654 GGCTGAGTTGTACTGAAAATTTAAATG 58.084 33.333 0.39 0.00 0.00 2.32
4042 4515 5.393027 GGATGTGTGAACTTGTTTGACTTGT 60.393 40.000 0.00 0.00 0.00 3.16
4046 4519 3.442273 GTGAACTTGTTTGACTTGTGGGA 59.558 43.478 0.00 0.00 0.00 4.37
4178 4758 8.688747 ATTTGGGTTTGAATTCAAATTTAGCA 57.311 26.923 30.63 16.73 46.12 3.49
4240 4820 3.637821 AGTAGGAGGAATCTGGGCATA 57.362 47.619 0.00 0.00 0.00 3.14
4241 4821 3.941629 AGTAGGAGGAATCTGGGCATAA 58.058 45.455 0.00 0.00 0.00 1.90
4242 4822 3.906846 AGTAGGAGGAATCTGGGCATAAG 59.093 47.826 0.00 0.00 0.00 1.73
4245 4825 2.173569 GGAGGAATCTGGGCATAAGTGT 59.826 50.000 0.00 0.00 0.00 3.55
4247 4827 4.381411 GAGGAATCTGGGCATAAGTGTAC 58.619 47.826 0.00 0.00 0.00 2.90
4248 4828 4.040755 AGGAATCTGGGCATAAGTGTACT 58.959 43.478 0.00 0.00 0.00 2.73
4249 4829 4.475016 AGGAATCTGGGCATAAGTGTACTT 59.525 41.667 2.51 2.51 39.85 2.24
4250 4830 4.576463 GGAATCTGGGCATAAGTGTACTTG 59.424 45.833 7.50 0.00 37.40 3.16
4251 4831 2.985896 TCTGGGCATAAGTGTACTTGC 58.014 47.619 7.50 4.09 37.40 4.01
4252 4832 2.017049 CTGGGCATAAGTGTACTTGCC 58.983 52.381 15.98 15.98 41.61 4.52
4254 4834 2.420058 GGCATAAGTGTACTTGCCCT 57.580 50.000 14.12 0.00 38.43 5.19
4289 4869 6.105397 TGGGAAAACTTGTACTGGTAGTAG 57.895 41.667 0.00 0.00 30.12 2.57
4290 4870 5.603813 TGGGAAAACTTGTACTGGTAGTAGT 59.396 40.000 0.00 0.00 30.12 2.73
4291 4871 6.782000 TGGGAAAACTTGTACTGGTAGTAGTA 59.218 38.462 0.00 0.00 30.12 1.82
4292 4872 7.289782 TGGGAAAACTTGTACTGGTAGTAGTAA 59.710 37.037 0.00 0.00 35.12 2.24
4322 4902 5.114081 AGGCATTGTAATTCGTGTAGTACC 58.886 41.667 0.00 0.00 0.00 3.34
4325 4908 5.501897 GCATTGTAATTCGTGTAGTACCTGC 60.502 44.000 0.00 0.00 0.00 4.85
4343 4926 3.008813 CCTGCCAAGCCTGTAGATATGAT 59.991 47.826 0.00 0.00 0.00 2.45
4349 4932 6.295575 GCCAAGCCTGTAGATATGATTCTACT 60.296 42.308 11.63 0.00 45.48 2.57
4385 4968 4.631377 GGAATGCCAAGGAAAATTAACAGC 59.369 41.667 0.00 0.00 0.00 4.40
4386 4969 3.676291 TGCCAAGGAAAATTAACAGCC 57.324 42.857 0.00 0.00 0.00 4.85
4387 4970 2.301583 TGCCAAGGAAAATTAACAGCCC 59.698 45.455 0.00 0.00 0.00 5.19
4388 4971 2.354704 GCCAAGGAAAATTAACAGCCCC 60.355 50.000 0.00 0.00 0.00 5.80
4389 4972 3.173151 CCAAGGAAAATTAACAGCCCCT 58.827 45.455 0.00 0.00 0.00 4.79
4390 4973 3.195610 CCAAGGAAAATTAACAGCCCCTC 59.804 47.826 0.00 0.00 0.00 4.30
4391 4974 3.825908 AGGAAAATTAACAGCCCCTCA 57.174 42.857 0.00 0.00 0.00 3.86
4392 4975 3.431415 AGGAAAATTAACAGCCCCTCAC 58.569 45.455 0.00 0.00 0.00 3.51
4393 4976 3.161866 GGAAAATTAACAGCCCCTCACA 58.838 45.455 0.00 0.00 0.00 3.58
4394 4977 3.576550 GGAAAATTAACAGCCCCTCACAA 59.423 43.478 0.00 0.00 0.00 3.33
4395 4978 4.222810 GGAAAATTAACAGCCCCTCACAAT 59.777 41.667 0.00 0.00 0.00 2.71
4396 4979 4.806640 AAATTAACAGCCCCTCACAATG 57.193 40.909 0.00 0.00 0.00 2.82
4397 4980 2.969821 TTAACAGCCCCTCACAATGT 57.030 45.000 0.00 0.00 0.00 2.71
4398 4981 2.198827 TAACAGCCCCTCACAATGTG 57.801 50.000 7.12 7.12 34.45 3.21
4399 4982 1.181098 AACAGCCCCTCACAATGTGC 61.181 55.000 8.78 0.00 32.98 4.57
4400 4983 2.036256 AGCCCCTCACAATGTGCC 59.964 61.111 8.78 0.00 32.98 5.01
4401 4984 3.070576 GCCCCTCACAATGTGCCC 61.071 66.667 8.78 0.00 32.98 5.36
4402 4985 2.765969 CCCCTCACAATGTGCCCT 59.234 61.111 8.78 0.00 32.98 5.19
4403 4986 1.679977 CCCCTCACAATGTGCCCTG 60.680 63.158 8.78 0.00 32.98 4.45
4404 4987 1.679977 CCCTCACAATGTGCCCTGG 60.680 63.158 8.78 7.85 32.98 4.45
4405 4988 2.345760 CCTCACAATGTGCCCTGGC 61.346 63.158 8.78 0.00 42.35 4.85
4415 4998 3.704151 GCCCTGGCAGCAAAATCT 58.296 55.556 9.56 0.00 41.49 2.40
4416 4999 1.514553 GCCCTGGCAGCAAAATCTC 59.485 57.895 9.56 0.00 41.49 2.75
4417 5000 0.969409 GCCCTGGCAGCAAAATCTCT 60.969 55.000 9.56 0.00 41.49 3.10
4418 5001 1.683011 GCCCTGGCAGCAAAATCTCTA 60.683 52.381 9.56 0.00 41.49 2.43
4419 5002 2.019984 CCCTGGCAGCAAAATCTCTAC 58.980 52.381 9.56 0.00 0.00 2.59
4420 5003 2.019984 CCTGGCAGCAAAATCTCTACC 58.980 52.381 9.56 0.00 0.00 3.18
4421 5004 1.667724 CTGGCAGCAAAATCTCTACCG 59.332 52.381 0.00 0.00 0.00 4.02
4422 5005 1.017387 GGCAGCAAAATCTCTACCGG 58.983 55.000 0.00 0.00 0.00 5.28
4423 5006 1.679032 GGCAGCAAAATCTCTACCGGT 60.679 52.381 13.98 13.98 0.00 5.28
4424 5007 2.084546 GCAGCAAAATCTCTACCGGTT 58.915 47.619 15.04 0.00 0.00 4.44
4425 5008 3.267483 GCAGCAAAATCTCTACCGGTTA 58.733 45.455 15.04 0.00 0.00 2.85
4426 5009 3.063588 GCAGCAAAATCTCTACCGGTTAC 59.936 47.826 15.04 0.00 0.00 2.50
4427 5010 3.621715 CAGCAAAATCTCTACCGGTTACC 59.378 47.826 15.04 0.00 0.00 2.85
4429 5012 3.853475 CAAAATCTCTACCGGTTACCGT 58.147 45.455 22.78 12.86 46.80 4.83
4430 5013 4.248058 CAAAATCTCTACCGGTTACCGTT 58.752 43.478 22.78 11.51 46.80 4.44
4431 5014 3.515330 AATCTCTACCGGTTACCGTTG 57.485 47.619 22.78 10.68 46.80 4.10
4432 5015 1.176527 TCTCTACCGGTTACCGTTGG 58.823 55.000 22.78 10.95 46.80 3.77
4433 5016 1.176527 CTCTACCGGTTACCGTTGGA 58.823 55.000 22.78 14.98 46.80 3.53
4434 5017 1.545582 CTCTACCGGTTACCGTTGGAA 59.454 52.381 22.78 3.24 46.80 3.53
4435 5018 2.167075 CTCTACCGGTTACCGTTGGAAT 59.833 50.000 22.78 3.41 46.80 3.01
4436 5019 2.566724 TCTACCGGTTACCGTTGGAATT 59.433 45.455 22.78 0.46 46.80 2.17
4437 5020 1.812235 ACCGGTTACCGTTGGAATTC 58.188 50.000 22.78 0.00 46.80 2.17
4438 5021 0.722848 CCGGTTACCGTTGGAATTCG 59.277 55.000 22.78 0.00 46.80 3.34
4439 5022 1.672441 CCGGTTACCGTTGGAATTCGA 60.672 52.381 22.78 0.00 46.80 3.71
4440 5023 2.067766 CGGTTACCGTTGGAATTCGAA 58.932 47.619 16.53 0.00 42.73 3.71
4441 5024 2.674357 CGGTTACCGTTGGAATTCGAAT 59.326 45.455 16.53 4.39 42.73 3.34
4442 5025 3.125658 CGGTTACCGTTGGAATTCGAATT 59.874 43.478 22.93 22.93 42.73 2.17
4443 5026 4.655027 GGTTACCGTTGGAATTCGAATTC 58.345 43.478 33.25 33.25 43.12 2.17
4444 5027 4.154556 GGTTACCGTTGGAATTCGAATTCA 59.845 41.667 38.08 26.39 45.10 2.57
4445 5028 5.335035 GGTTACCGTTGGAATTCGAATTCAA 60.335 40.000 38.08 30.86 45.10 2.69
4446 5029 4.839668 ACCGTTGGAATTCGAATTCAAA 57.160 36.364 38.08 33.70 45.10 2.69
4447 5030 5.385509 ACCGTTGGAATTCGAATTCAAAT 57.614 34.783 38.08 23.31 45.10 2.32
4448 5031 5.778862 ACCGTTGGAATTCGAATTCAAATT 58.221 33.333 38.08 24.33 45.10 1.82
4449 5032 5.861787 ACCGTTGGAATTCGAATTCAAATTC 59.138 36.000 38.08 26.04 45.10 2.17
4453 5036 4.420168 GGAATTCGAATTCAAATTCCGCA 58.580 39.130 38.08 0.00 46.48 5.69
4454 5037 5.043248 GGAATTCGAATTCAAATTCCGCAT 58.957 37.500 38.08 10.87 46.48 4.73
4455 5038 5.051508 GGAATTCGAATTCAAATTCCGCATG 60.052 40.000 38.08 0.00 46.48 4.06
4456 5039 3.419264 TCGAATTCAAATTCCGCATGG 57.581 42.857 6.22 0.00 41.30 3.66
4457 5040 3.013219 TCGAATTCAAATTCCGCATGGA 58.987 40.909 6.22 0.00 44.61 3.41
4458 5041 3.631686 TCGAATTCAAATTCCGCATGGAT 59.368 39.130 6.22 0.00 45.91 3.41
4459 5042 3.732219 CGAATTCAAATTCCGCATGGATG 59.268 43.478 6.22 0.00 45.91 3.51
4460 5043 3.738830 ATTCAAATTCCGCATGGATGG 57.261 42.857 0.00 0.00 45.91 3.51
4461 5044 0.746063 TCAAATTCCGCATGGATGGC 59.254 50.000 0.00 0.00 45.91 4.40
4462 5045 0.748450 CAAATTCCGCATGGATGGCT 59.252 50.000 0.00 0.00 45.91 4.75
4463 5046 1.137479 CAAATTCCGCATGGATGGCTT 59.863 47.619 0.00 0.00 45.91 4.35
4464 5047 0.748450 AATTCCGCATGGATGGCTTG 59.252 50.000 0.00 0.00 45.91 4.01
4465 5048 0.396139 ATTCCGCATGGATGGCTTGT 60.396 50.000 0.00 0.00 45.91 3.16
4466 5049 1.031571 TTCCGCATGGATGGCTTGTC 61.032 55.000 0.00 0.00 45.91 3.18
4467 5050 2.484062 CCGCATGGATGGCTTGTCC 61.484 63.158 0.00 0.00 37.49 4.02
4468 5051 2.827051 CGCATGGATGGCTTGTCCG 61.827 63.158 0.00 0.00 38.64 4.79
4469 5052 2.484062 GCATGGATGGCTTGTCCGG 61.484 63.158 0.00 0.00 38.64 5.14
4470 5053 1.825191 CATGGATGGCTTGTCCGGG 60.825 63.158 0.00 0.00 38.64 5.73
4471 5054 3.721370 ATGGATGGCTTGTCCGGGC 62.721 63.158 0.00 0.00 38.64 6.13
4472 5055 4.424711 GGATGGCTTGTCCGGGCA 62.425 66.667 3.51 3.51 43.10 5.36
4473 5056 2.825836 GATGGCTTGTCCGGGCAG 60.826 66.667 9.61 4.86 42.26 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.179702 CCTTAACGGCTAGGGGGTTC 59.820 60.000 0.00 0.00 0.00 3.62
48 49 2.304069 CCTTAACGGCTAGGGGGTT 58.696 57.895 0.00 0.00 0.00 4.11
49 50 4.061699 CCTTAACGGCTAGGGGGT 57.938 61.111 0.00 0.00 0.00 4.95
276 296 0.106619 GCTCTAGGTCGAGGGAGGAA 60.107 60.000 0.00 0.00 0.00 3.36
277 297 1.532728 GCTCTAGGTCGAGGGAGGA 59.467 63.158 0.00 0.00 0.00 3.71
279 299 0.821711 CAGGCTCTAGGTCGAGGGAG 60.822 65.000 0.00 0.00 0.00 4.30
280 300 1.227664 CAGGCTCTAGGTCGAGGGA 59.772 63.158 0.00 0.00 0.00 4.20
281 301 1.830408 CCAGGCTCTAGGTCGAGGG 60.830 68.421 0.00 0.00 0.00 4.30
282 302 1.830408 CCCAGGCTCTAGGTCGAGG 60.830 68.421 0.00 0.00 0.00 4.63
283 303 0.821711 CTCCCAGGCTCTAGGTCGAG 60.822 65.000 0.00 0.00 0.00 4.04
284 304 1.227664 CTCCCAGGCTCTAGGTCGA 59.772 63.158 0.00 0.00 0.00 4.20
285 305 0.821711 CTCTCCCAGGCTCTAGGTCG 60.822 65.000 0.00 0.00 0.00 4.79
286 306 0.553819 TCTCTCCCAGGCTCTAGGTC 59.446 60.000 0.00 0.00 0.00 3.85
287 307 0.555769 CTCTCTCCCAGGCTCTAGGT 59.444 60.000 0.00 0.00 0.00 3.08
288 308 0.850100 TCTCTCTCCCAGGCTCTAGG 59.150 60.000 0.00 0.00 0.00 3.02
289 309 1.202927 CCTCTCTCTCCCAGGCTCTAG 60.203 61.905 0.00 0.00 0.00 2.43
290 310 0.850100 CCTCTCTCTCCCAGGCTCTA 59.150 60.000 0.00 0.00 0.00 2.43
291 311 1.620259 CCTCTCTCTCCCAGGCTCT 59.380 63.158 0.00 0.00 0.00 4.09
321 344 4.845307 GGGAGGGGGAGAAGGGGG 62.845 77.778 0.00 0.00 0.00 5.40
349 375 4.719369 ACCTCGTTGCTCGGCGAC 62.719 66.667 4.99 3.81 39.38 5.19
438 483 0.614697 CACCAAAGAACCCCATCCCC 60.615 60.000 0.00 0.00 0.00 4.81
600 654 1.153147 GACCTCCAAAGATCCGCCC 60.153 63.158 0.00 0.00 0.00 6.13
633 688 3.686726 AGAATCTGTTGCTCCAATTCGAC 59.313 43.478 0.00 0.00 32.82 4.20
635 690 4.409570 CAAGAATCTGTTGCTCCAATTCG 58.590 43.478 0.00 0.00 32.82 3.34
641 696 1.471684 CTGCCAAGAATCTGTTGCTCC 59.528 52.381 0.00 0.00 0.00 4.70
647 702 2.393768 CGCGCTGCCAAGAATCTGT 61.394 57.895 5.56 0.00 0.00 3.41
648 703 2.402388 CGCGCTGCCAAGAATCTG 59.598 61.111 5.56 0.00 0.00 2.90
664 735 0.603569 AACTCTACCAGCACAGACCG 59.396 55.000 0.00 0.00 0.00 4.79
759 831 1.153549 CTAGCCACGCTTCAGGACC 60.154 63.158 0.00 0.00 40.44 4.46
760 832 0.458716 GACTAGCCACGCTTCAGGAC 60.459 60.000 0.00 0.00 40.44 3.85
761 833 0.612174 AGACTAGCCACGCTTCAGGA 60.612 55.000 0.00 0.00 40.44 3.86
762 834 1.066303 CTAGACTAGCCACGCTTCAGG 59.934 57.143 0.00 0.00 40.44 3.86
763 835 1.746220 ACTAGACTAGCCACGCTTCAG 59.254 52.381 9.52 0.00 40.44 3.02
764 836 1.835494 ACTAGACTAGCCACGCTTCA 58.165 50.000 9.52 0.00 40.44 3.02
765 837 2.291190 CCTACTAGACTAGCCACGCTTC 59.709 54.545 9.52 0.00 40.44 3.86
766 838 2.299521 CCTACTAGACTAGCCACGCTT 58.700 52.381 9.52 0.00 40.44 4.68
767 839 1.477195 CCCTACTAGACTAGCCACGCT 60.477 57.143 9.52 0.00 43.41 5.07
768 840 0.953003 CCCTACTAGACTAGCCACGC 59.047 60.000 9.52 0.00 0.00 5.34
769 841 0.953003 GCCCTACTAGACTAGCCACG 59.047 60.000 9.52 0.00 0.00 4.94
770 842 0.953003 CGCCCTACTAGACTAGCCAC 59.047 60.000 9.52 0.00 0.00 5.01
771 843 0.549950 ACGCCCTACTAGACTAGCCA 59.450 55.000 9.52 0.00 0.00 4.75
772 844 1.608109 GAACGCCCTACTAGACTAGCC 59.392 57.143 9.52 0.00 0.00 3.93
773 845 2.574450 AGAACGCCCTACTAGACTAGC 58.426 52.381 9.52 0.00 0.00 3.42
774 846 3.243134 GCAAGAACGCCCTACTAGACTAG 60.243 52.174 8.00 8.00 0.00 2.57
775 847 2.686915 GCAAGAACGCCCTACTAGACTA 59.313 50.000 0.00 0.00 0.00 2.59
776 848 1.477295 GCAAGAACGCCCTACTAGACT 59.523 52.381 0.00 0.00 0.00 3.24
777 849 1.477295 AGCAAGAACGCCCTACTAGAC 59.523 52.381 0.00 0.00 0.00 2.59
778 850 1.749634 GAGCAAGAACGCCCTACTAGA 59.250 52.381 0.00 0.00 0.00 2.43
779 851 1.534175 CGAGCAAGAACGCCCTACTAG 60.534 57.143 0.00 0.00 0.00 2.57
780 852 0.454600 CGAGCAAGAACGCCCTACTA 59.545 55.000 0.00 0.00 0.00 1.82
832 904 3.160269 ACTCTGGATTTGGCCAAGAAAG 58.840 45.455 19.48 14.57 37.52 2.62
921 993 0.798776 CGCATCCGCAGAAGAACTTT 59.201 50.000 0.00 0.00 38.40 2.66
922 994 0.320771 ACGCATCCGCAGAAGAACTT 60.321 50.000 0.00 0.00 38.40 2.66
923 995 0.320771 AACGCATCCGCAGAAGAACT 60.321 50.000 0.00 0.00 38.40 3.01
924 996 0.517316 AAACGCATCCGCAGAAGAAC 59.483 50.000 0.00 0.00 38.40 3.01
946 1018 4.248058 GGCAATCCAAATTCAGAAACAGG 58.752 43.478 0.00 0.00 0.00 4.00
966 1038 1.871126 GAAACCTGCAGCAAGAGGGC 61.871 60.000 8.66 0.00 33.16 5.19
975 1049 0.035458 ACGGAAGAGGAAACCTGCAG 59.965 55.000 6.78 6.78 31.76 4.41
1074 1149 3.670377 GCCCTGCGGTTGGTGTTC 61.670 66.667 0.00 0.00 0.00 3.18
1137 1212 3.710722 CCCCTCTTGCTGACGGCT 61.711 66.667 7.96 0.00 42.39 5.52
1188 1263 6.486657 TGAATCAAACTGGAGTTCGAAATTCT 59.513 34.615 5.37 0.00 37.25 2.40
1216 1303 1.402194 CGGAGCGATTAGAGATCCAGC 60.402 57.143 1.45 0.00 0.00 4.85
1242 1329 4.048504 CGGGTTTTCTGAAACATGGAAAC 58.951 43.478 1.58 0.00 45.52 2.78
1610 1722 5.924825 GCATGCTCAAATCTCTGAAGTTTTT 59.075 36.000 11.37 0.00 0.00 1.94
1614 1726 3.015327 GGCATGCTCAAATCTCTGAAGT 58.985 45.455 18.92 0.00 0.00 3.01
1810 2044 8.915654 CAAACAAGGCAAGTAAAATAATCTGAC 58.084 33.333 0.00 0.00 0.00 3.51
1930 2272 1.891178 CATTGAATGCAGTGTCAGCG 58.109 50.000 0.00 0.00 33.85 5.18
1942 2284 3.952323 CCATGTCTGAAGGAGCATTGAAT 59.048 43.478 0.00 0.00 0.00 2.57
2017 2359 2.674852 CTGATCGTGCAATGCTAGTTGT 59.325 45.455 6.82 0.00 0.00 3.32
2020 2362 1.293924 GCTGATCGTGCAATGCTAGT 58.706 50.000 6.82 0.00 0.00 2.57
2024 2366 1.581912 CGTGCTGATCGTGCAATGC 60.582 57.895 13.59 0.00 42.41 3.56
2052 2394 3.652274 AGCGATGAAAACACCAAAATGG 58.348 40.909 0.00 0.00 45.02 3.16
2053 2395 4.297510 TGAGCGATGAAAACACCAAAATG 58.702 39.130 0.00 0.00 0.00 2.32
2054 2396 4.582701 TGAGCGATGAAAACACCAAAAT 57.417 36.364 0.00 0.00 0.00 1.82
2078 2421 3.568007 TGGAGTAACAACAAAGCATGGAC 59.432 43.478 0.00 0.00 0.00 4.02
2291 2637 7.130775 ACTATTACTACCATAACAGGTCAGGT 58.869 38.462 0.00 0.00 42.06 4.00
2301 2647 8.257602 TGGCAATGAGACTATTACTACCATAA 57.742 34.615 0.00 0.00 0.00 1.90
2347 2698 2.348998 GGGGGACACACAGCTCAG 59.651 66.667 0.00 0.00 0.00 3.35
2457 2808 3.914426 AGACTACTTTGCCGAATCCAT 57.086 42.857 0.00 0.00 0.00 3.41
2486 2837 4.015084 AGAACTTTCCATTCCAGAGCATG 58.985 43.478 0.00 0.00 0.00 4.06
2576 2930 7.156000 TGTCGATGATGTTTACAGTAAGGAAA 58.844 34.615 0.00 0.00 0.00 3.13
2582 2936 7.284716 AGGTATCTGTCGATGATGTTTACAGTA 59.715 37.037 12.28 0.00 38.88 2.74
2624 2978 1.449246 CTGGAGCTTCTTCCTGGCG 60.449 63.158 0.00 0.00 38.12 5.69
2750 3104 3.003689 GGATCGTTACCATGCCAAGAATG 59.996 47.826 0.00 0.00 0.00 2.67
2756 3110 0.463654 GCAGGATCGTTACCATGCCA 60.464 55.000 0.00 0.00 0.00 4.92
2758 3112 2.526304 TAGCAGGATCGTTACCATGC 57.474 50.000 0.00 0.00 34.38 4.06
2768 3122 6.512342 AGGTATACAACGTATAGCAGGATC 57.488 41.667 19.79 0.00 32.15 3.36
2779 3133 5.061311 CGAATCGACAAAAGGTATACAACGT 59.939 40.000 5.01 0.00 0.00 3.99
2781 3135 6.636666 TCGAATCGACAAAAGGTATACAAC 57.363 37.500 0.00 0.00 0.00 3.32
2782 3136 7.201574 CCAATCGAATCGACAAAAGGTATACAA 60.202 37.037 7.77 0.00 39.18 2.41
2783 3137 6.256975 CCAATCGAATCGACAAAAGGTATACA 59.743 38.462 7.77 0.00 39.18 2.29
2784 3138 6.257193 ACCAATCGAATCGACAAAAGGTATAC 59.743 38.462 7.77 0.00 39.18 1.47
2794 3148 2.421073 ACTCGTACCAATCGAATCGACA 59.579 45.455 7.77 0.00 39.18 4.35
2806 3160 4.761975 AGACAAAACAAGAACTCGTACCA 58.238 39.130 0.00 0.00 0.00 3.25
2850 3204 4.679373 TCCTCTCCTGCAGAATTATCAC 57.321 45.455 17.39 0.00 0.00 3.06
2853 3207 6.183361 ACAATCATCCTCTCCTGCAGAATTAT 60.183 38.462 17.39 0.00 0.00 1.28
2872 3226 4.583907 TGAATTCAAGCCTGTCAACAATCA 59.416 37.500 5.45 0.00 0.00 2.57
2879 3233 3.890756 ACATGTTGAATTCAAGCCTGTCA 59.109 39.130 21.05 14.13 36.39 3.58
2918 3272 5.169992 TGAGGAATCTTCTCATGAAGCAA 57.830 39.130 0.00 0.00 46.81 3.91
2933 3287 1.305623 CCCTGCTGCCTTGAGGAAT 59.694 57.895 5.39 0.00 37.39 3.01
2971 3325 2.414994 ATGATCCAAGGTGAGCTGTG 57.585 50.000 0.00 0.00 0.00 3.66
2973 3327 1.404391 GCAATGATCCAAGGTGAGCTG 59.596 52.381 0.00 0.00 0.00 4.24
3001 3362 3.058085 CAGACAAGCAATGCACACATACA 60.058 43.478 8.35 0.00 34.62 2.29
3002 3363 3.189080 TCAGACAAGCAATGCACACATAC 59.811 43.478 8.35 0.00 34.62 2.39
3007 3371 1.334556 GTGTCAGACAAGCAATGCACA 59.665 47.619 8.35 0.00 0.00 4.57
3267 3650 2.159234 GCATCACTCACTCACTGAAAGC 59.841 50.000 0.00 0.00 37.60 3.51
3295 3681 2.017049 GTGAGCCAAACAACTGTGAGT 58.983 47.619 0.00 0.00 0.00 3.41
3296 3682 2.032550 CAGTGAGCCAAACAACTGTGAG 59.967 50.000 0.00 0.00 0.00 3.51
3297 3683 2.016318 CAGTGAGCCAAACAACTGTGA 58.984 47.619 0.00 0.00 0.00 3.58
3301 3693 2.143876 AACCAGTGAGCCAAACAACT 57.856 45.000 0.00 0.00 0.00 3.16
3303 3695 1.134848 GCAAACCAGTGAGCCAAACAA 60.135 47.619 0.00 0.00 0.00 2.83
3338 3731 2.877975 GTGCAGCTCCACCATCATT 58.122 52.632 0.00 0.00 0.00 2.57
3466 3859 4.988716 TGTCGGTCGGTCAGGCCT 62.989 66.667 0.00 0.00 44.20 5.19
3484 3877 2.626266 TCACAGACACGGTGATGTAAGT 59.374 45.455 16.29 1.77 40.16 2.24
3485 3878 2.987149 GTCACAGACACGGTGATGTAAG 59.013 50.000 16.29 8.31 46.01 2.34
3486 3879 2.362717 TGTCACAGACACGGTGATGTAA 59.637 45.455 16.29 2.62 46.01 2.41
3504 3911 3.188460 TCGCCATCTTTTTAGCAGTTGTC 59.812 43.478 0.00 0.00 0.00 3.18
3885 4336 2.755952 ATTCTGGGGCCCAAGAATAC 57.244 50.000 42.21 17.97 33.24 1.89
3886 4337 3.012274 TCAAATTCTGGGGCCCAAGAATA 59.988 43.478 42.63 29.85 33.57 1.75
3887 4338 2.190538 CAAATTCTGGGGCCCAAGAAT 58.809 47.619 39.26 39.26 34.97 2.40
3926 4385 5.390387 GTTCCTCCTACTCTACATCCATCT 58.610 45.833 0.00 0.00 0.00 2.90
3928 4387 4.171044 AGGTTCCTCCTACTCTACATCCAT 59.829 45.833 0.00 0.00 46.10 3.41
3929 4388 3.532232 AGGTTCCTCCTACTCTACATCCA 59.468 47.826 0.00 0.00 46.10 3.41
3932 4391 4.883021 TCAGGTTCCTCCTACTCTACAT 57.117 45.455 0.00 0.00 46.24 2.29
3975 4444 6.214615 TCCCTCCCCCTTTCATTTAAATTTTC 59.785 38.462 0.00 0.00 0.00 2.29
3976 4445 6.094991 TCCCTCCCCCTTTCATTTAAATTTT 58.905 36.000 0.00 0.00 0.00 1.82
3983 4452 2.368170 TCTTCCCTCCCCCTTTCATTT 58.632 47.619 0.00 0.00 0.00 2.32
3984 4453 2.074922 TCTTCCCTCCCCCTTTCATT 57.925 50.000 0.00 0.00 0.00 2.57
3985 4454 2.139382 GATCTTCCCTCCCCCTTTCAT 58.861 52.381 0.00 0.00 0.00 2.57
3986 4455 1.082879 AGATCTTCCCTCCCCCTTTCA 59.917 52.381 0.00 0.00 0.00 2.69
3987 4456 1.492599 CAGATCTTCCCTCCCCCTTTC 59.507 57.143 0.00 0.00 0.00 2.62
3991 4462 1.135960 CTTCAGATCTTCCCTCCCCC 58.864 60.000 0.00 0.00 0.00 5.40
4042 4515 3.806380 TGCTTACGTACAAGTTTTCCCA 58.194 40.909 0.00 0.00 0.00 4.37
4046 4519 8.822652 AATAGTACTGCTTACGTACAAGTTTT 57.177 30.769 5.39 2.69 39.66 2.43
4088 4657 3.063510 TCAAAGATGCTGAACAGGGAG 57.936 47.619 3.99 0.00 0.00 4.30
4097 4666 4.796038 ACCAGGAAATTCAAAGATGCTG 57.204 40.909 0.00 0.00 0.00 4.41
4178 4758 1.661463 TTCTGAGACAAGCTCCCCAT 58.339 50.000 0.00 0.00 43.26 4.00
4240 4820 2.362077 CAAAGCAAGGGCAAGTACACTT 59.638 45.455 0.00 0.00 44.61 3.16
4241 4821 1.956477 CAAAGCAAGGGCAAGTACACT 59.044 47.619 0.00 0.00 44.61 3.55
4242 4822 1.953686 TCAAAGCAAGGGCAAGTACAC 59.046 47.619 0.00 0.00 44.61 2.90
4245 4825 2.656947 AGTCAAAGCAAGGGCAAGTA 57.343 45.000 0.00 0.00 44.61 2.24
4247 4827 2.476821 CAAAGTCAAAGCAAGGGCAAG 58.523 47.619 0.00 0.00 44.61 4.01
4248 4828 1.138661 CCAAAGTCAAAGCAAGGGCAA 59.861 47.619 0.00 0.00 44.61 4.52
4249 4829 0.752054 CCAAAGTCAAAGCAAGGGCA 59.248 50.000 0.00 0.00 44.61 5.36
4250 4830 0.033920 CCCAAAGTCAAAGCAAGGGC 59.966 55.000 0.00 0.00 41.61 5.19
4251 4831 1.703411 TCCCAAAGTCAAAGCAAGGG 58.297 50.000 0.00 0.00 36.15 3.95
4252 4832 3.817709 TTTCCCAAAGTCAAAGCAAGG 57.182 42.857 0.00 0.00 0.00 3.61
4253 4833 4.758688 AGTTTTCCCAAAGTCAAAGCAAG 58.241 39.130 0.00 0.00 0.00 4.01
4254 4834 4.817318 AGTTTTCCCAAAGTCAAAGCAA 57.183 36.364 0.00 0.00 0.00 3.91
4289 4869 6.183360 ACGAATTACAATGCCTTGCTAGTTAC 60.183 38.462 1.19 0.00 35.69 2.50
4290 4870 5.878116 ACGAATTACAATGCCTTGCTAGTTA 59.122 36.000 1.19 0.00 35.69 2.24
4291 4871 4.700213 ACGAATTACAATGCCTTGCTAGTT 59.300 37.500 1.19 0.00 35.69 2.24
4292 4872 4.094887 CACGAATTACAATGCCTTGCTAGT 59.905 41.667 1.19 0.00 35.69 2.57
4322 4902 3.758755 TCATATCTACAGGCTTGGCAG 57.241 47.619 0.00 0.00 0.00 4.85
4343 4926 6.484643 GCATTCCAGATCTTGCAATAGTAGAA 59.515 38.462 11.42 0.00 35.22 2.10
4349 4932 3.900971 TGGCATTCCAGATCTTGCAATA 58.099 40.909 16.78 0.00 37.47 1.90
4385 4968 1.679977 CAGGGCACATTGTGAGGGG 60.680 63.158 20.77 3.10 35.23 4.79
4386 4969 1.679977 CCAGGGCACATTGTGAGGG 60.680 63.158 20.77 10.76 35.23 4.30
4387 4970 2.345760 GCCAGGGCACATTGTGAGG 61.346 63.158 20.77 15.19 41.49 3.86
4388 4971 3.281240 GCCAGGGCACATTGTGAG 58.719 61.111 20.77 6.50 41.49 3.51
4398 4981 0.969409 AGAGATTTTGCTGCCAGGGC 60.969 55.000 2.62 2.62 42.35 5.19
4399 4982 2.019984 GTAGAGATTTTGCTGCCAGGG 58.980 52.381 0.00 0.00 0.00 4.45
4400 4983 2.019984 GGTAGAGATTTTGCTGCCAGG 58.980 52.381 0.00 0.00 36.94 4.45
4401 4984 1.667724 CGGTAGAGATTTTGCTGCCAG 59.332 52.381 0.00 0.00 36.80 4.85
4402 4985 1.678728 CCGGTAGAGATTTTGCTGCCA 60.679 52.381 0.00 0.00 36.80 4.92
4403 4986 1.017387 CCGGTAGAGATTTTGCTGCC 58.983 55.000 0.00 0.00 34.08 4.85
4404 4987 1.739067 ACCGGTAGAGATTTTGCTGC 58.261 50.000 4.49 0.00 0.00 5.25
4405 4988 3.621715 GGTAACCGGTAGAGATTTTGCTG 59.378 47.826 8.00 0.00 0.00 4.41
4406 4989 3.677976 CGGTAACCGGTAGAGATTTTGCT 60.678 47.826 8.00 0.00 44.15 3.91
4407 4990 2.606272 CGGTAACCGGTAGAGATTTTGC 59.394 50.000 8.00 0.00 44.15 3.68
4419 5002 7.637628 GAATTCGAATTCCAACGGTAACCGG 62.638 48.000 31.77 0.00 43.68 5.28
4420 5003 4.725737 GAATTCGAATTCCAACGGTAACCG 60.726 45.833 31.77 0.00 44.28 4.44
4421 5004 4.154556 TGAATTCGAATTCCAACGGTAACC 59.845 41.667 35.88 16.37 43.19 2.85
4422 5005 5.285798 TGAATTCGAATTCCAACGGTAAC 57.714 39.130 35.88 16.79 43.19 2.50
4423 5006 5.943706 TTGAATTCGAATTCCAACGGTAA 57.056 34.783 35.88 23.62 43.19 2.85
4424 5007 5.943706 TTTGAATTCGAATTCCAACGGTA 57.056 34.783 35.88 20.08 43.19 4.02
4425 5008 4.839668 TTTGAATTCGAATTCCAACGGT 57.160 36.364 35.88 10.90 43.19 4.83
4426 5009 6.317910 GAATTTGAATTCGAATTCCAACGG 57.682 37.500 35.88 0.00 44.92 4.44
4433 5016 4.805192 CCATGCGGAATTTGAATTCGAATT 59.195 37.500 26.80 26.80 44.43 2.17
4434 5017 4.097741 TCCATGCGGAATTTGAATTCGAAT 59.902 37.500 14.21 14.21 44.43 3.34
4435 5018 3.441922 TCCATGCGGAATTTGAATTCGAA 59.558 39.130 10.57 10.57 44.43 3.71
4436 5019 3.013219 TCCATGCGGAATTTGAATTCGA 58.987 40.909 9.61 0.00 44.43 3.71
4437 5020 3.419264 TCCATGCGGAATTTGAATTCG 57.581 42.857 9.61 7.00 44.43 3.34
4449 5032 2.484062 GGACAAGCCATCCATGCGG 61.484 63.158 0.00 0.00 36.15 5.69
4450 5033 2.827051 CGGACAAGCCATCCATGCG 61.827 63.158 0.00 0.00 35.83 4.73
4451 5034 2.484062 CCGGACAAGCCATCCATGC 61.484 63.158 0.00 0.00 35.83 4.06
4452 5035 1.825191 CCCGGACAAGCCATCCATG 60.825 63.158 0.73 0.00 35.83 3.66
4453 5036 2.597340 CCCGGACAAGCCATCCAT 59.403 61.111 0.73 0.00 35.83 3.41
4454 5037 4.424711 GCCCGGACAAGCCATCCA 62.425 66.667 0.73 0.00 35.83 3.41
4455 5038 4.424711 TGCCCGGACAAGCCATCC 62.425 66.667 0.73 0.00 35.94 3.51
4456 5039 2.825836 CTGCCCGGACAAGCCATC 60.826 66.667 0.73 0.00 35.94 3.51


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

AutoCloner maintained by Alex Coulton.