Multiple sequence alignment - TraesCS7D01G232900

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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 TraesCS7D01G232900 chr7D 100.000 4669 0 0 1 4669 194253417 194248749 0.000000e+00 8623.0
1 TraesCS7D01G232900 chr7D 89.286 84 3 3 2328 2410 53428492 53428414 2.970000e-17 100.0
2 TraesCS7D01G232900 chr7A 93.407 1820 77 20 2470 4278 203970959 203969172 0.000000e+00 2656.0
3 TraesCS7D01G232900 chr7A 91.529 1452 56 30 871 2277 203972380 203970951 0.000000e+00 1938.0
4 TraesCS7D01G232900 chr7A 86.111 684 71 8 131 803 203973053 203972383 0.000000e+00 715.0
5 TraesCS7D01G232900 chr7A 93.646 362 19 2 4310 4669 203969171 203968812 5.320000e-149 538.0
6 TraesCS7D01G232900 chr7A 87.255 102 7 3 2313 2413 27360622 27360526 1.370000e-20 111.0
7 TraesCS7D01G232900 chr7A 83.838 99 13 3 631 728 678931053 678931149 1.790000e-14 91.6
8 TraesCS7D01G232900 chr7A 100.000 28 0 0 2032 2059 203971236 203971209 8.000000e-03 52.8
9 TraesCS7D01G232900 chr7B 89.044 1579 91 32 359 1874 158184283 158182724 0.000000e+00 1882.0
10 TraesCS7D01G232900 chr7B 96.082 1021 35 4 3074 4091 158175367 158174349 0.000000e+00 1659.0
11 TraesCS7D01G232900 chr7B 94.272 611 32 3 2470 3079 158181665 158181057 0.000000e+00 931.0
12 TraesCS7D01G232900 chr7B 87.707 423 26 15 1867 2277 158182065 158181657 1.970000e-128 470.0
13 TraesCS7D01G232900 chr7B 87.683 341 36 4 8 345 158186065 158185728 4.380000e-105 392.0
14 TraesCS7D01G232900 chr7B 93.173 249 17 0 4421 4669 158174059 158173811 2.650000e-97 366.0
15 TraesCS7D01G232900 chr7B 85.417 192 6 5 4088 4278 158174310 158174140 3.710000e-41 180.0
16 TraesCS7D01G232900 chr7B 95.238 84 4 0 4310 4393 158174139 158174056 2.930000e-27 134.0
17 TraesCS7D01G232900 chr7B 83.544 79 7 4 2313 2390 749396007 749396080 8.380000e-08 69.4
18 TraesCS7D01G232900 chr4D 86.397 272 31 6 27 295 484411401 484411133 4.570000e-75 292.0
19 TraesCS7D01G232900 chr4D 91.892 74 5 1 1285 1357 419829454 419829381 8.270000e-18 102.0
20 TraesCS7D01G232900 chr4D 85.542 83 12 0 691 773 7739604 7739686 2.310000e-13 87.9
21 TraesCS7D01G232900 chr4D 87.500 72 7 2 780 849 441645312 441645241 1.080000e-11 82.4
22 TraesCS7D01G232900 chr4D 91.228 57 4 1 3270 3326 363570845 363570790 5.010000e-10 76.8
23 TraesCS7D01G232900 chr3D 83.774 265 33 6 27 289 523338521 523338265 4.670000e-60 243.0
24 TraesCS7D01G232900 chr5D 83.142 261 29 8 27 286 388328636 388328882 1.690000e-54 224.0
25 TraesCS7D01G232900 chr5D 86.458 96 12 1 65 159 44904645 44904550 2.300000e-18 104.0
26 TraesCS7D01G232900 chr5D 77.679 112 23 2 660 770 26787609 26787719 3.020000e-07 67.6
27 TraesCS7D01G232900 chr2D 90.588 170 13 2 1191 1357 338958026 338958195 6.080000e-54 222.0
28 TraesCS7D01G232900 chr2D 85.106 94 11 3 781 872 176106847 176106939 4.970000e-15 93.5
29 TraesCS7D01G232900 chr2D 83.133 83 14 0 691 773 440185590 440185508 5.010000e-10 76.8
30 TraesCS7D01G232900 chr6A 77.778 288 46 12 4391 4666 617345380 617345099 1.340000e-35 161.0
31 TraesCS7D01G232900 chr5A 76.894 264 53 8 31 289 7024083 7023823 4.870000e-30 143.0
32 TraesCS7D01G232900 chr5A 92.157 51 4 0 3270 3320 243808089 243808139 6.480000e-09 73.1
33 TraesCS7D01G232900 chr5A 89.474 57 5 1 3270 3326 675528553 675528608 2.330000e-08 71.3
34 TraesCS7D01G232900 chr6B 79.798 198 32 7 4471 4666 717407123 717407314 2.270000e-28 137.0
35 TraesCS7D01G232900 chr6B 76.030 267 41 14 1511 1764 105366025 105365769 2.950000e-22 117.0
36 TraesCS7D01G232900 chr6B 86.364 88 7 5 2352 2436 155264060 155264145 1.790000e-14 91.6
37 TraesCS7D01G232900 chr6B 92.157 51 4 0 3270 3320 164819697 164819647 6.480000e-09 73.1
38 TraesCS7D01G232900 chr1A 81.143 175 25 7 4471 4643 2662032 2662200 2.930000e-27 134.0
39 TraesCS7D01G232900 chr1A 91.071 56 5 0 2355 2410 132698624 132698679 5.010000e-10 76.8
40 TraesCS7D01G232900 chr1A 79.798 99 18 2 644 741 60078355 60078452 2.330000e-08 71.3
41 TraesCS7D01G232900 chr1A 85.714 56 8 0 822 877 34722188 34722133 5.050000e-05 60.2
42 TraesCS7D01G232900 chr1D 89.796 98 5 2 2313 2410 11686820 11686912 2.280000e-23 121.0
43 TraesCS7D01G232900 chr1D 81.897 116 17 4 660 773 409996045 409995932 1.380000e-15 95.3
44 TraesCS7D01G232900 chr1D 90.000 60 2 4 779 834 425526726 425526667 1.800000e-09 75.0
45 TraesCS7D01G232900 chr6D 78.010 191 35 6 4477 4666 472488023 472488207 3.820000e-21 113.0
46 TraesCS7D01G232900 chr6D 79.661 118 21 3 657 773 9373295 9373180 1.080000e-11 82.4
47 TraesCS7D01G232900 chr6D 92.453 53 4 0 3270 3322 60308765 60308817 5.010000e-10 76.8
48 TraesCS7D01G232900 chr1B 80.000 130 26 0 644 773 98975798 98975927 3.850000e-16 97.1
49 TraesCS7D01G232900 chr1B 80.208 96 8 8 782 873 577992017 577991929 1.400000e-05 62.1
50 TraesCS7D01G232900 chr3A 91.667 60 5 0 2351 2410 740070161 740070220 2.990000e-12 84.2
51 TraesCS7D01G232900 chr3B 82.474 97 14 3 779 873 215604506 215604601 1.080000e-11 82.4
52 TraesCS7D01G232900 chr3B 94.118 51 3 0 3270 3320 796469131 796469181 1.390000e-10 78.7
53 TraesCS7D01G232900 chr4A 89.474 57 5 1 3270 3326 467310458 467310513 2.330000e-08 71.3
54 TraesCS7D01G232900 chrUn 97.059 34 0 1 779 811 43289563 43289596 6.530000e-04 56.5


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 TraesCS7D01G232900 chr7D 194248749 194253417 4668 True 8623.00 8623 100.0000 1 4669 1 chr7D.!!$R2 4668
1 TraesCS7D01G232900 chr7A 203968812 203973053 4241 True 1179.96 2656 92.9386 131 4669 5 chr7A.!!$R2 4538
2 TraesCS7D01G232900 chr7B 158181057 158186065 5008 True 918.75 1882 89.6765 8 3079 4 chr7B.!!$R2 3071
3 TraesCS7D01G232900 chr7B 158173811 158175367 1556 True 584.75 1659 92.4775 3074 4669 4 chr7B.!!$R1 1595

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
52 53 0.389426 GCCGTTCCACGATGTAGTGT 60.389 55.000 0.00 0.00 46.05 3.55 F
796 2243 0.400093 GGGTGCTCATAGGGGTAGGT 60.400 60.000 0.00 0.00 0.00 3.08 F
2467 4669 0.106819 CAGCTATCCTGGCCAGCTTT 60.107 55.000 28.39 15.64 42.95 3.51 F
2522 4724 3.290710 CCCACAAGCTTTGGCATAGTAT 58.709 45.455 17.37 0.00 41.70 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 2611 0.620556 GGAGCATGGAGGTGAAGGAA 59.379 55.000 0.00 0.00 0.00 3.36 R
2591 4793 0.040499 GAGTCCCTGACCTCTCCTGT 59.960 60.000 0.00 0.00 32.18 4.00 R
3507 5720 0.176680 ACGTCTATGCTGAGGCCAAG 59.823 55.000 5.01 2.69 37.74 3.61 R
4302 6560 1.001406 CAGAAGCTCCAAAGTCTCCGT 59.999 52.381 0.00 0.00 0.00 4.69 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
33 34 3.611766 AGGTCAAAACTCATACTCCCG 57.388 47.619 0.00 0.00 0.00 5.14
36 37 1.006832 CAAAACTCATACTCCCGCCG 58.993 55.000 0.00 0.00 0.00 6.46
37 38 0.611714 AAAACTCATACTCCCGCCGT 59.388 50.000 0.00 0.00 0.00 5.68
43 44 3.072486 ATACTCCCGCCGTTCCACG 62.072 63.158 0.00 0.00 42.11 4.94
45 46 4.143333 CTCCCGCCGTTCCACGAT 62.143 66.667 0.00 0.00 46.05 3.73
52 53 0.389426 GCCGTTCCACGATGTAGTGT 60.389 55.000 0.00 0.00 46.05 3.55
53 54 1.135315 GCCGTTCCACGATGTAGTGTA 60.135 52.381 0.00 0.00 46.05 2.90
56 57 4.558095 GCCGTTCCACGATGTAGTGTATAT 60.558 45.833 0.00 0.00 46.05 0.86
60 61 8.121086 CCGTTCCACGATGTAGTGTATATATAG 58.879 40.741 0.00 0.00 46.05 1.31
61 62 8.663025 CGTTCCACGATGTAGTGTATATATAGT 58.337 37.037 0.00 0.00 46.05 2.12
113 114 8.188799 AGCTTAACCAAGTTTGTAGAGAAAAAC 58.811 33.333 0.00 0.00 36.69 2.43
193 194 8.153479 TCATATTGTATACATTCTGGTGTTGC 57.847 34.615 6.36 0.00 33.62 4.17
286 289 7.737869 TGCACTATATTATAAAACGGAGGGAA 58.262 34.615 0.00 0.00 0.00 3.97
314 317 2.710220 TACGCACTCATAACACACGT 57.290 45.000 0.00 0.00 36.17 4.49
316 319 2.592194 ACGCACTCATAACACACGTAG 58.408 47.619 0.00 0.00 0.00 3.51
362 375 3.440522 GCTAACTGTTGAATGTTCCCTCC 59.559 47.826 2.69 0.00 0.00 4.30
533 1979 4.961435 TGCATGATAATTTGAGCGTTCA 57.039 36.364 0.00 0.00 0.00 3.18
638 2084 5.434352 CGAAGATAACTCGGATGGTTAGA 57.566 43.478 0.00 0.00 33.50 2.10
639 2085 6.015027 CGAAGATAACTCGGATGGTTAGAT 57.985 41.667 0.00 0.00 33.50 1.98
676 2122 2.781174 TCAACCCACCAAGAGTTAAGGT 59.219 45.455 0.00 0.00 35.65 3.50
718 2165 9.667989 GTGCTTGCATTTTTCTGAATTTATTTT 57.332 25.926 0.00 0.00 0.00 1.82
750 2197 4.441079 CGGTGATATTCGTTTAGTGGGAGT 60.441 45.833 0.00 0.00 0.00 3.85
774 2221 5.133941 AGATGCTTCCATAGACTACGAGAA 58.866 41.667 0.00 0.00 0.00 2.87
796 2243 0.400093 GGGTGCTCATAGGGGTAGGT 60.400 60.000 0.00 0.00 0.00 3.08
803 2250 0.539986 CATAGGGGTAGGTTGTGCGT 59.460 55.000 0.00 0.00 0.00 5.24
807 2254 2.663852 GGTAGGTTGTGCGTGCGT 60.664 61.111 0.00 0.00 0.00 5.24
817 2264 1.811679 TGCGTGCGTTGTCTTCACA 60.812 52.632 0.00 0.00 0.00 3.58
842 2289 3.249917 TGAGTGTATGTGCGTGTATGTG 58.750 45.455 0.00 0.00 0.00 3.21
843 2290 2.603110 GAGTGTATGTGCGTGTATGTGG 59.397 50.000 0.00 0.00 0.00 4.17
844 2291 1.663643 GTGTATGTGCGTGTATGTGGG 59.336 52.381 0.00 0.00 0.00 4.61
845 2292 0.655733 GTATGTGCGTGTATGTGGGC 59.344 55.000 0.00 0.00 0.00 5.36
859 2306 5.820423 TGTATGTGGGCATCTGTATTTGTAC 59.180 40.000 0.00 0.00 36.58 2.90
861 2308 4.260985 TGTGGGCATCTGTATTTGTACTG 58.739 43.478 0.00 0.00 0.00 2.74
907 2382 9.466497 AAAAAGGTATGTGACATTGACATATCT 57.534 29.630 2.29 5.77 45.63 1.98
908 2383 8.668510 AAAGGTATGTGACATTGACATATCTC 57.331 34.615 2.29 3.55 43.81 2.75
998 2474 2.614969 TGGATTGGGCCCAGAGCT 60.615 61.111 26.87 11.40 43.05 4.09
1027 2503 2.352127 GCTGAAGCAAGACCACATTTCC 60.352 50.000 0.00 0.00 41.59 3.13
1221 2701 1.614824 CACCCTGGCCCTCTCTTCT 60.615 63.158 0.00 0.00 0.00 2.85
1233 2713 3.559171 CCCTCTCTTCTCTATCCTCCTCG 60.559 56.522 0.00 0.00 0.00 4.63
1242 2728 0.397187 TATCCTCCTCGTCCTCCTCG 59.603 60.000 0.00 0.00 0.00 4.63
1427 2914 6.652481 CCTCTTGCTTCTAATCTTGTTTCTCA 59.348 38.462 0.00 0.00 0.00 3.27
1431 2918 5.989168 TGCTTCTAATCTTGTTTCTCAACGA 59.011 36.000 0.00 0.00 35.40 3.85
1480 2972 3.674997 TCCTCTGGTTGCTTACATGTTC 58.325 45.455 2.30 0.00 0.00 3.18
1488 2988 4.988540 GGTTGCTTACATGTTCCTTTTTCC 59.011 41.667 2.30 0.00 0.00 3.13
1532 3032 3.039988 CGGACACTGTCACCGTCT 58.960 61.111 11.34 0.00 41.47 4.18
1637 3152 1.292992 GTGGGCGTAATTTAGGTCCG 58.707 55.000 13.44 0.00 41.03 4.79
1638 3153 1.134729 GTGGGCGTAATTTAGGTCCGA 60.135 52.381 13.44 2.68 41.03 4.55
1646 3163 4.217983 CGTAATTTAGGTCCGAGCTATCCT 59.782 45.833 8.12 0.00 0.00 3.24
1681 3198 5.721960 ACACTCCATGGTCTAGACTTGTAAT 59.278 40.000 21.88 6.34 0.00 1.89
1685 3202 6.406370 TCCATGGTCTAGACTTGTAATTGTG 58.594 40.000 21.88 7.96 0.00 3.33
1688 3205 5.479306 TGGTCTAGACTTGTAATTGTGCTC 58.521 41.667 21.88 1.35 0.00 4.26
1689 3206 5.011635 TGGTCTAGACTTGTAATTGTGCTCA 59.988 40.000 21.88 3.95 0.00 4.26
1690 3207 5.932303 GGTCTAGACTTGTAATTGTGCTCAA 59.068 40.000 21.88 3.31 37.98 3.02
1691 3208 6.091441 GGTCTAGACTTGTAATTGTGCTCAAG 59.909 42.308 21.88 0.00 41.74 3.02
1692 3209 4.756084 AGACTTGTAATTGTGCTCAAGC 57.244 40.909 7.35 0.00 40.29 4.01
1894 4086 7.014615 AGGAAGGATGCATAAAATGGATGTAAC 59.985 37.037 0.00 0.00 41.66 2.50
1968 4160 9.774742 GATACATGATGTAAACTTTTGAGGAAC 57.225 33.333 9.61 0.00 36.31 3.62
1969 4161 6.981722 ACATGATGTAAACTTTTGAGGAACC 58.018 36.000 0.00 0.00 0.00 3.62
1970 4162 6.015434 ACATGATGTAAACTTTTGAGGAACCC 60.015 38.462 0.00 0.00 0.00 4.11
2065 4263 4.680537 AGCCAGGGTCTCGGACGT 62.681 66.667 0.00 0.00 32.65 4.34
2107 4305 2.186903 CATAGCGGGGCGTCAACT 59.813 61.111 0.00 0.00 0.00 3.16
2146 4347 1.971481 AGCAATGACAACTGCAGTGA 58.029 45.000 22.49 5.31 41.17 3.41
2185 4386 6.480524 TGTTAGCAACGATGGATATAATGC 57.519 37.500 0.00 0.00 0.00 3.56
2263 4465 1.131638 TGGAGGACTTGTGCAGACTT 58.868 50.000 0.00 0.00 0.00 3.01
2265 4467 2.703536 TGGAGGACTTGTGCAGACTTAA 59.296 45.455 0.00 0.00 0.00 1.85
2266 4468 3.244215 TGGAGGACTTGTGCAGACTTAAG 60.244 47.826 0.00 0.00 0.00 1.85
2267 4469 3.006967 GGAGGACTTGTGCAGACTTAAGA 59.993 47.826 10.09 0.00 0.00 2.10
2268 4470 3.991121 GAGGACTTGTGCAGACTTAAGAC 59.009 47.826 10.09 2.62 0.00 3.01
2269 4471 3.388024 AGGACTTGTGCAGACTTAAGACA 59.612 43.478 10.09 0.00 0.00 3.41
2270 4472 3.495001 GGACTTGTGCAGACTTAAGACAC 59.505 47.826 10.09 11.67 0.00 3.67
2271 4473 3.467803 ACTTGTGCAGACTTAAGACACC 58.532 45.455 10.09 0.00 0.00 4.16
2272 4474 2.543777 TGTGCAGACTTAAGACACCC 57.456 50.000 10.09 0.00 0.00 4.61
2273 4475 2.047061 TGTGCAGACTTAAGACACCCT 58.953 47.619 10.09 0.00 0.00 4.34
2274 4476 3.236047 TGTGCAGACTTAAGACACCCTA 58.764 45.455 10.09 0.00 0.00 3.53
2275 4477 3.838317 TGTGCAGACTTAAGACACCCTAT 59.162 43.478 10.09 0.00 0.00 2.57
2276 4478 4.286032 TGTGCAGACTTAAGACACCCTATT 59.714 41.667 10.09 0.00 0.00 1.73
2277 4479 5.482526 TGTGCAGACTTAAGACACCCTATTA 59.517 40.000 10.09 0.00 0.00 0.98
2278 4480 6.156256 TGTGCAGACTTAAGACACCCTATTAT 59.844 38.462 10.09 0.00 0.00 1.28
2279 4481 7.343574 TGTGCAGACTTAAGACACCCTATTATA 59.656 37.037 10.09 0.00 0.00 0.98
2280 4482 8.202137 GTGCAGACTTAAGACACCCTATTATAA 58.798 37.037 10.09 0.00 0.00 0.98
2281 4483 8.764558 TGCAGACTTAAGACACCCTATTATAAA 58.235 33.333 10.09 0.00 0.00 1.40
2282 4484 9.043079 GCAGACTTAAGACACCCTATTATAAAC 57.957 37.037 10.09 0.00 0.00 2.01
2283 4485 9.245962 CAGACTTAAGACACCCTATTATAAACG 57.754 37.037 10.09 0.00 0.00 3.60
2284 4486 8.419442 AGACTTAAGACACCCTATTATAAACGG 58.581 37.037 10.09 0.00 0.00 4.44
2285 4487 8.310122 ACTTAAGACACCCTATTATAAACGGA 57.690 34.615 10.09 0.00 0.00 4.69
2286 4488 8.200120 ACTTAAGACACCCTATTATAAACGGAC 58.800 37.037 10.09 0.00 0.00 4.79
2287 4489 6.549433 AAGACACCCTATTATAAACGGACA 57.451 37.500 5.27 0.00 0.00 4.02
2288 4490 6.742559 AGACACCCTATTATAAACGGACAT 57.257 37.500 5.27 0.00 0.00 3.06
2289 4491 7.844493 AGACACCCTATTATAAACGGACATA 57.156 36.000 5.27 0.00 0.00 2.29
2290 4492 8.431910 AGACACCCTATTATAAACGGACATAT 57.568 34.615 5.27 0.00 0.00 1.78
2291 4493 8.877195 AGACACCCTATTATAAACGGACATATT 58.123 33.333 5.27 0.00 0.00 1.28
2303 4505 5.786264 ACGGACATATTAAGTAGTGGAGG 57.214 43.478 0.00 0.00 0.00 4.30
2304 4506 5.452255 ACGGACATATTAAGTAGTGGAGGA 58.548 41.667 0.00 0.00 0.00 3.71
2305 4507 5.301298 ACGGACATATTAAGTAGTGGAGGAC 59.699 44.000 0.00 0.00 0.00 3.85
2306 4508 5.535406 CGGACATATTAAGTAGTGGAGGACT 59.465 44.000 0.00 0.00 38.88 3.85
2307 4509 6.040616 CGGACATATTAAGTAGTGGAGGACTT 59.959 42.308 0.00 0.00 39.25 3.01
2308 4510 7.210873 GGACATATTAAGTAGTGGAGGACTTG 58.789 42.308 0.00 0.00 36.58 3.16
2309 4511 7.147707 GGACATATTAAGTAGTGGAGGACTTGT 60.148 40.741 0.00 0.00 36.58 3.16
2310 4512 7.783042 ACATATTAAGTAGTGGAGGACTTGTC 58.217 38.462 0.00 0.00 36.58 3.18
2311 4513 5.678955 ATTAAGTAGTGGAGGACTTGTCC 57.321 43.478 11.59 11.59 36.58 4.02
2312 4514 2.696526 AGTAGTGGAGGACTTGTCCA 57.303 50.000 20.36 0.11 42.06 4.02
2313 4515 2.972348 AGTAGTGGAGGACTTGTCCAA 58.028 47.619 20.36 4.48 45.85 3.53
2314 4516 3.314693 AGTAGTGGAGGACTTGTCCAAA 58.685 45.455 20.36 4.15 45.85 3.28
2315 4517 3.714798 AGTAGTGGAGGACTTGTCCAAAA 59.285 43.478 20.36 3.82 45.85 2.44
2316 4518 3.884037 AGTGGAGGACTTGTCCAAAAT 57.116 42.857 20.36 1.02 45.85 1.82
2317 4519 3.756117 AGTGGAGGACTTGTCCAAAATC 58.244 45.455 20.36 9.75 45.85 2.17
2318 4520 2.820197 GTGGAGGACTTGTCCAAAATCC 59.180 50.000 20.36 17.40 45.85 3.01
2319 4521 2.716424 TGGAGGACTTGTCCAAAATCCT 59.284 45.455 20.36 10.72 41.32 3.24
2320 4522 3.913799 TGGAGGACTTGTCCAAAATCCTA 59.086 43.478 20.36 7.78 41.32 2.94
2321 4523 4.352595 TGGAGGACTTGTCCAAAATCCTAA 59.647 41.667 20.36 3.00 41.32 2.69
2322 4524 5.163034 TGGAGGACTTGTCCAAAATCCTAAA 60.163 40.000 20.36 2.40 41.32 1.85
2323 4525 5.952347 GGAGGACTTGTCCAAAATCCTAAAT 59.048 40.000 20.36 0.00 36.59 1.40
2324 4526 7.116736 GGAGGACTTGTCCAAAATCCTAAATA 58.883 38.462 20.36 0.00 36.59 1.40
2325 4527 7.614192 GGAGGACTTGTCCAAAATCCTAAATAA 59.386 37.037 20.36 0.00 36.59 1.40
2326 4528 8.581253 AGGACTTGTCCAAAATCCTAAATAAG 57.419 34.615 20.36 0.00 35.41 1.73
2327 4529 8.390921 AGGACTTGTCCAAAATCCTAAATAAGA 58.609 33.333 20.36 0.00 35.41 2.10
2328 4530 9.020731 GGACTTGTCCAAAATCCTAAATAAGAA 57.979 33.333 14.34 0.00 0.00 2.52
2351 4553 9.783256 AGAATAAAATAAATAAACGGACTGTGC 57.217 29.630 0.00 0.00 0.00 4.57
2352 4554 8.920509 AATAAAATAAATAAACGGACTGTGCC 57.079 30.769 0.00 0.00 0.00 5.01
2360 4562 4.367023 GGACTGTGCCGTGCCGTA 62.367 66.667 0.00 0.00 0.00 4.02
2361 4563 3.110178 GACTGTGCCGTGCCGTAC 61.110 66.667 0.00 0.00 0.00 3.67
2362 4564 4.675029 ACTGTGCCGTGCCGTACC 62.675 66.667 0.00 0.00 0.00 3.34
2384 4586 3.485431 CGCGTGCTCAGCCTTCAG 61.485 66.667 0.00 0.00 0.00 3.02
2385 4587 3.123620 GCGTGCTCAGCCTTCAGG 61.124 66.667 0.00 0.00 38.53 3.86
2416 4618 4.047059 CCTGGCGTGCCTTGCAAG 62.047 66.667 19.93 19.93 41.47 4.01
2421 4623 4.688419 CGTGCCTTGCAAGCCGTG 62.688 66.667 21.43 8.47 41.47 4.94
2465 4667 3.238438 CAGCTATCCTGGCCAGCT 58.762 61.111 28.39 19.06 46.36 4.24
2466 4668 1.530771 CAGCTATCCTGGCCAGCTT 59.469 57.895 28.39 18.22 42.95 3.74
2467 4669 0.106819 CAGCTATCCTGGCCAGCTTT 60.107 55.000 28.39 15.64 42.95 3.51
2468 4670 0.106819 AGCTATCCTGGCCAGCTTTG 60.107 55.000 28.39 17.13 42.95 2.77
2522 4724 3.290710 CCCACAAGCTTTGGCATAGTAT 58.709 45.455 17.37 0.00 41.70 2.12
2591 4793 4.326504 TCGATGAGCAATGAAGCTATCA 57.673 40.909 0.00 0.00 46.75 2.15
2709 4911 9.828852 TTAATTTTGTGTTAACGTGATATGGAC 57.171 29.630 0.26 0.00 0.00 4.02
2886 5088 4.721132 ACGGTGAAACTAAATTCCAAGGA 58.279 39.130 0.00 0.00 36.74 3.36
2888 5090 5.240844 ACGGTGAAACTAAATTCCAAGGAAG 59.759 40.000 7.69 0.00 35.56 3.46
3000 5210 9.914131 GCAGACATCACTTAGATACATATTACA 57.086 33.333 0.00 0.00 34.43 2.41
3023 5233 8.311395 ACAACCATCTCTCTACTATTTCATGA 57.689 34.615 0.00 0.00 0.00 3.07
3080 5292 7.653311 ACACTGAAAAGAGATAAAAATGGCAAC 59.347 33.333 0.00 0.00 0.00 4.17
3116 5328 6.038936 TGCCATGATTGACATCAGAAGTTATG 59.961 38.462 0.00 0.00 42.93 1.90
3124 5336 5.869344 TGACATCAGAAGTTATGAACCTTCG 59.131 40.000 3.97 0.00 0.00 3.79
3188 5400 3.686227 ATCAGGCATTTTCCATACCCA 57.314 42.857 0.00 0.00 0.00 4.51
3307 5520 6.416514 GTAATTCTACAATTACGGAAAGCCG 58.583 40.000 2.34 2.34 46.16 5.52
3507 5720 6.289064 TCTGAAACTAGACTTGTCCCTTTTC 58.711 40.000 0.00 4.87 0.00 2.29
3605 5818 4.307259 AGGTTATATGGGAGGAGCTTCAA 58.693 43.478 0.00 0.00 0.00 2.69
3708 5921 5.529060 TGGCAAAAATTAAATTTGGAACGCT 59.471 32.000 15.04 0.00 38.04 5.07
3802 6015 5.006358 ACTTTTCATGTACACGTCAACTGAC 59.994 40.000 0.00 0.00 41.47 3.51
3849 6062 7.548196 TTGGCATTACTTCCGTAAGAAATAG 57.452 36.000 0.00 0.00 38.87 1.73
3850 6063 6.646267 TGGCATTACTTCCGTAAGAAATAGT 58.354 36.000 0.00 0.00 38.87 2.12
3851 6064 7.784037 TGGCATTACTTCCGTAAGAAATAGTA 58.216 34.615 0.00 0.00 38.87 1.82
3852 6065 8.426489 TGGCATTACTTCCGTAAGAAATAGTAT 58.574 33.333 0.00 0.00 38.87 2.12
3853 6066 9.918630 GGCATTACTTCCGTAAGAAATAGTATA 57.081 33.333 0.00 0.00 38.87 1.47
3927 6140 6.917477 CAGAGGATTCAAGAGTTAGAATCTCG 59.083 42.308 13.02 0.00 45.83 4.04
4141 6399 6.256321 GTCTCGGCAATAAGGTAAATTACGAA 59.744 38.462 0.00 0.00 30.02 3.85
4143 6401 7.170320 TCTCGGCAATAAGGTAAATTACGAATC 59.830 37.037 0.00 0.00 30.02 2.52
4216 6474 4.382291 TGCTTTTTCATTGAGCAAGCAAT 58.618 34.783 22.66 0.00 45.22 3.56
4278 6536 0.174845 CGTGCGAGGGTTATCTTGGA 59.825 55.000 0.00 0.00 0.00 3.53
4279 6537 1.404986 CGTGCGAGGGTTATCTTGGAA 60.405 52.381 0.00 0.00 0.00 3.53
4280 6538 2.280628 GTGCGAGGGTTATCTTGGAAG 58.719 52.381 0.00 0.00 0.00 3.46
4281 6539 1.300481 GCGAGGGTTATCTTGGAAGC 58.700 55.000 0.00 0.00 0.00 3.86
4282 6540 1.134371 GCGAGGGTTATCTTGGAAGCT 60.134 52.381 0.00 0.00 0.00 3.74
4283 6541 2.681097 GCGAGGGTTATCTTGGAAGCTT 60.681 50.000 0.00 0.00 0.00 3.74
4284 6542 3.431766 GCGAGGGTTATCTTGGAAGCTTA 60.432 47.826 0.00 0.00 0.00 3.09
4285 6543 4.372656 CGAGGGTTATCTTGGAAGCTTAG 58.627 47.826 0.00 0.00 0.00 2.18
4286 6544 4.141914 CGAGGGTTATCTTGGAAGCTTAGT 60.142 45.833 0.00 0.00 0.00 2.24
4287 6545 5.068723 CGAGGGTTATCTTGGAAGCTTAGTA 59.931 44.000 0.00 0.00 0.00 1.82
4288 6546 6.236558 AGGGTTATCTTGGAAGCTTAGTAC 57.763 41.667 0.00 0.00 0.00 2.73
4289 6547 5.130643 AGGGTTATCTTGGAAGCTTAGTACC 59.869 44.000 0.00 0.00 0.00 3.34
4290 6548 5.104652 GGGTTATCTTGGAAGCTTAGTACCA 60.105 44.000 0.00 0.00 0.00 3.25
4291 6549 6.412214 GGTTATCTTGGAAGCTTAGTACCAA 58.588 40.000 14.65 14.65 39.60 3.67
4292 6550 6.882678 GGTTATCTTGGAAGCTTAGTACCAAA 59.117 38.462 15.83 9.22 41.00 3.28
4293 6551 7.148289 GGTTATCTTGGAAGCTTAGTACCAAAC 60.148 40.741 15.83 11.61 41.00 2.93
4294 6552 5.562298 TCTTGGAAGCTTAGTACCAAACT 57.438 39.130 15.83 0.00 41.00 2.66
4295 6553 5.305585 TCTTGGAAGCTTAGTACCAAACTG 58.694 41.667 15.83 7.21 41.00 3.16
4296 6554 4.967084 TGGAAGCTTAGTACCAAACTGA 57.033 40.909 0.00 0.00 39.39 3.41
4297 6555 5.499004 TGGAAGCTTAGTACCAAACTGAT 57.501 39.130 0.00 0.00 39.39 2.90
4298 6556 5.876357 TGGAAGCTTAGTACCAAACTGATT 58.124 37.500 0.00 0.00 39.39 2.57
4299 6557 6.303839 TGGAAGCTTAGTACCAAACTGATTT 58.696 36.000 0.00 0.00 39.39 2.17
4300 6558 7.455058 TGGAAGCTTAGTACCAAACTGATTTA 58.545 34.615 0.00 0.00 39.39 1.40
4301 6559 7.940137 TGGAAGCTTAGTACCAAACTGATTTAA 59.060 33.333 0.00 0.00 39.39 1.52
4302 6560 8.789762 GGAAGCTTAGTACCAAACTGATTTAAA 58.210 33.333 0.00 0.00 39.39 1.52
4303 6561 9.608617 GAAGCTTAGTACCAAACTGATTTAAAC 57.391 33.333 0.00 0.00 39.39 2.01
4304 6562 7.803724 AGCTTAGTACCAAACTGATTTAAACG 58.196 34.615 0.00 0.00 39.39 3.60
4305 6563 7.019418 GCTTAGTACCAAACTGATTTAAACGG 58.981 38.462 0.00 0.00 39.39 4.44
4306 6564 7.095102 GCTTAGTACCAAACTGATTTAAACGGA 60.095 37.037 0.00 0.00 39.39 4.69
4307 6565 6.796705 AGTACCAAACTGATTTAAACGGAG 57.203 37.500 0.00 0.00 36.93 4.63
4308 6566 6.527423 AGTACCAAACTGATTTAAACGGAGA 58.473 36.000 0.00 0.00 36.93 3.71
4345 6605 0.538584 ATCTTCTGGTGCATGAGCGA 59.461 50.000 0.00 0.00 46.23 4.93
4346 6606 0.108472 TCTTCTGGTGCATGAGCGAG 60.108 55.000 0.00 0.00 46.23 5.03
4372 6632 1.594518 CGTGGTGCGTTTTCTCTGTTG 60.595 52.381 0.00 0.00 35.54 3.33
4405 6667 7.482654 TGAGTGTGAACAGATAAAAGACAAG 57.517 36.000 0.00 0.00 0.00 3.16
4408 6670 6.318648 AGTGTGAACAGATAAAAGACAAGCAA 59.681 34.615 0.00 0.00 0.00 3.91
4464 6726 8.001881 AGCTATATAGATACCGACAATCCAAG 57.998 38.462 14.16 0.00 0.00 3.61
4479 6741 5.827797 ACAATCCAAGACTTTGTACACACAT 59.172 36.000 0.00 0.00 33.76 3.21
4536 6798 1.227002 GCGACCATCCTTCCTCGAC 60.227 63.158 0.00 0.00 0.00 4.20
4611 6873 2.223377 CACAGGGAAGCGAAACAACTAC 59.777 50.000 0.00 0.00 0.00 2.73
4626 6888 0.108804 ACTACGCTCCCACGTTCATG 60.109 55.000 0.00 0.00 45.75 3.07
4632 6894 1.877637 CTCCCACGTTCATGTTGTCA 58.122 50.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.457436 GGGAGTATGAGTTTTGACCTTAATTTA 57.543 33.333 0.00 0.00 0.00 1.40
24 25 1.520787 GTGGAACGGCGGGAGTATG 60.521 63.158 13.24 0.00 0.00 2.39
92 93 9.403583 TCTATGTTTTTCTCTACAAACTTGGTT 57.596 29.630 0.00 0.00 34.52 3.67
215 216 5.123661 ACTTTGCAACCTTTGACCAAATTTG 59.876 36.000 11.40 11.40 0.00 2.32
278 281 4.863131 GTGCGTATCTAAATATTCCCTCCG 59.137 45.833 0.00 0.00 0.00 4.63
286 289 9.193133 GTGTGTTATGAGTGCGTATCTAAATAT 57.807 33.333 0.00 0.00 0.00 1.28
297 300 2.592194 ACTACGTGTGTTATGAGTGCG 58.408 47.619 0.00 0.00 0.00 5.34
334 347 6.273071 GGAACATTCAACAGTTAGCACTTTT 58.727 36.000 0.00 0.00 0.00 2.27
341 354 3.684788 CGGAGGGAACATTCAACAGTTAG 59.315 47.826 0.00 0.00 0.00 2.34
362 375 1.364171 CATTCGCTAGGACCTCCCG 59.636 63.158 0.00 1.86 40.87 5.14
420 1866 4.922692 CACAAAAATGCCAGCGATCTAAAA 59.077 37.500 0.00 0.00 0.00 1.52
610 2056 1.197910 CCGAGTTATCTTCGGTTCGC 58.802 55.000 5.56 0.00 41.62 4.70
634 2080 8.956426 GGTTGATTTCACCACAAGAATATCTAA 58.044 33.333 0.00 0.00 0.00 2.10
638 2084 6.015918 TGGGTTGATTTCACCACAAGAATAT 58.984 36.000 0.00 0.00 0.00 1.28
639 2085 5.389520 TGGGTTGATTTCACCACAAGAATA 58.610 37.500 0.00 0.00 0.00 1.75
668 2114 2.832733 GTGCCCAGTCTAGACCTTAACT 59.167 50.000 19.38 0.00 0.00 2.24
676 2122 2.671145 CACCAGTGCCCAGTCTAGA 58.329 57.895 0.00 0.00 0.00 2.43
718 2165 9.590451 ACTAAACGAATATCACCGAAAAATCTA 57.410 29.630 0.00 0.00 0.00 1.98
722 2169 6.128227 CCCACTAAACGAATATCACCGAAAAA 60.128 38.462 0.00 0.00 0.00 1.94
727 2174 4.049186 CTCCCACTAAACGAATATCACCG 58.951 47.826 0.00 0.00 0.00 4.94
734 2181 4.406003 AGCATCTACTCCCACTAAACGAAT 59.594 41.667 0.00 0.00 0.00 3.34
750 2197 5.866207 TCTCGTAGTCTATGGAAGCATCTA 58.134 41.667 0.00 0.00 0.00 1.98
796 2243 1.350319 GAAGACAACGCACGCACAA 59.650 52.632 0.00 0.00 0.00 3.33
803 2250 1.069978 TCATCCTGTGAAGACAACGCA 59.930 47.619 0.00 0.00 32.78 5.24
807 2254 5.012046 ACATACACTCATCCTGTGAAGACAA 59.988 40.000 0.00 0.00 38.65 3.18
817 2264 1.550524 ACACGCACATACACTCATCCT 59.449 47.619 0.00 0.00 0.00 3.24
842 2289 2.287915 CGCAGTACAAATACAGATGCCC 59.712 50.000 0.00 0.00 33.30 5.36
843 2290 2.936498 ACGCAGTACAAATACAGATGCC 59.064 45.455 0.00 0.00 41.94 4.40
844 2291 4.600012 AACGCAGTACAAATACAGATGC 57.400 40.909 0.00 0.00 45.00 3.91
845 2292 8.942669 TTTTTAACGCAGTACAAATACAGATG 57.057 30.769 0.00 0.00 45.00 2.90
900 2375 9.282569 GCCAATTCATTAAGAAGAGAGATATGT 57.717 33.333 0.00 0.00 40.15 2.29
901 2376 8.441608 CGCCAATTCATTAAGAAGAGAGATATG 58.558 37.037 0.00 0.00 40.15 1.78
902 2377 7.605691 CCGCCAATTCATTAAGAAGAGAGATAT 59.394 37.037 0.00 0.00 40.15 1.63
903 2378 6.931281 CCGCCAATTCATTAAGAAGAGAGATA 59.069 38.462 0.00 0.00 40.15 1.98
904 2379 5.762218 CCGCCAATTCATTAAGAAGAGAGAT 59.238 40.000 0.00 0.00 40.15 2.75
907 2382 3.627577 GCCGCCAATTCATTAAGAAGAGA 59.372 43.478 0.00 0.00 40.15 3.10
908 2383 3.243201 GGCCGCCAATTCATTAAGAAGAG 60.243 47.826 3.91 0.00 40.15 2.85
969 2445 0.811281 CCAATCCAGGTCCGAAAAGC 59.189 55.000 0.00 0.00 0.00 3.51
994 2470 1.780025 GCTTCAGCGGCCATTAGCTC 61.780 60.000 2.24 0.00 42.52 4.09
998 2474 0.035534 TCTTGCTTCAGCGGCCATTA 60.036 50.000 2.24 0.00 45.83 1.90
1131 2611 0.620556 GGAGCATGGAGGTGAAGGAA 59.379 55.000 0.00 0.00 0.00 3.36
1221 2701 1.700739 GAGGAGGACGAGGAGGATAGA 59.299 57.143 0.00 0.00 0.00 1.98
1233 2713 1.975660 ATCTAGCAGACGAGGAGGAC 58.024 55.000 0.00 0.00 0.00 3.85
1242 2728 2.419297 CCAGGTGGTGAATCTAGCAGAC 60.419 54.545 0.00 0.00 0.00 3.51
1381 2867 1.830408 CCAACGGGGTGCCAAGAAA 60.830 57.895 0.00 0.00 0.00 2.52
1427 2914 1.215647 GACATCGGCTCCACTCGTT 59.784 57.895 0.00 0.00 0.00 3.85
1480 2972 4.184079 CTTGATCTGCCAAGGAAAAAGG 57.816 45.455 0.00 0.00 39.74 3.11
1488 2988 1.380524 CTGCTCCTTGATCTGCCAAG 58.619 55.000 0.00 0.00 42.28 3.61
1532 3032 2.363795 ATCCCCTGAGGCGTCGAA 60.364 61.111 0.00 0.00 34.51 3.71
1637 3152 3.055819 TGTGTGTTCTCCAAGGATAGCTC 60.056 47.826 0.00 0.00 0.00 4.09
1638 3153 2.906389 TGTGTGTTCTCCAAGGATAGCT 59.094 45.455 0.00 0.00 0.00 3.32
1685 3202 1.800805 TCTACTGCTTGTGCTTGAGC 58.199 50.000 0.00 0.00 40.48 4.26
1688 3205 2.703416 TCCATCTACTGCTTGTGCTTG 58.297 47.619 0.00 0.00 40.48 4.01
1689 3206 3.423539 TTCCATCTACTGCTTGTGCTT 57.576 42.857 0.00 0.00 40.48 3.91
1690 3207 3.641434 ATTCCATCTACTGCTTGTGCT 57.359 42.857 0.00 0.00 40.48 4.40
1691 3208 5.818136 TTAATTCCATCTACTGCTTGTGC 57.182 39.130 0.00 0.00 40.20 4.57
1692 3209 7.281774 ACAGATTAATTCCATCTACTGCTTGTG 59.718 37.037 0.00 0.00 29.36 3.33
1693 3210 7.281774 CACAGATTAATTCCATCTACTGCTTGT 59.718 37.037 0.00 0.00 29.36 3.16
1859 3385 8.908786 TTTTATGCATCCTTCCTAGTCTAATG 57.091 34.615 0.19 0.00 0.00 1.90
1970 4162 1.065701 CTGTCCCCGATAACTCAGTCG 59.934 57.143 0.00 0.00 37.58 4.18
1984 4182 1.192146 TCTGGCACTACCACTGTCCC 61.192 60.000 0.00 0.00 46.36 4.46
2006 4204 1.830477 ACAGAGCAGATTCAGACCCTC 59.170 52.381 0.00 0.00 0.00 4.30
2107 4305 4.137116 CTAATAGGTAGCTTGTGCCACA 57.863 45.455 0.00 0.00 40.80 4.17
2146 4347 3.189287 GCTAACAACACAACTGCTAGCAT 59.811 43.478 19.72 0.28 0.00 3.79
2263 4465 7.658525 TGTCCGTTTATAATAGGGTGTCTTA 57.341 36.000 6.83 0.00 0.00 2.10
2265 4467 6.742559 ATGTCCGTTTATAATAGGGTGTCT 57.257 37.500 6.83 0.00 0.00 3.41
2277 4479 8.365647 CCTCCACTACTTAATATGTCCGTTTAT 58.634 37.037 0.00 0.00 0.00 1.40
2278 4480 7.560991 TCCTCCACTACTTAATATGTCCGTTTA 59.439 37.037 0.00 0.00 0.00 2.01
2279 4481 6.381994 TCCTCCACTACTTAATATGTCCGTTT 59.618 38.462 0.00 0.00 0.00 3.60
2280 4482 5.895534 TCCTCCACTACTTAATATGTCCGTT 59.104 40.000 0.00 0.00 0.00 4.44
2281 4483 5.301298 GTCCTCCACTACTTAATATGTCCGT 59.699 44.000 0.00 0.00 0.00 4.69
2282 4484 5.535406 AGTCCTCCACTACTTAATATGTCCG 59.465 44.000 0.00 0.00 31.37 4.79
2283 4485 6.980416 AGTCCTCCACTACTTAATATGTCC 57.020 41.667 0.00 0.00 31.37 4.02
2284 4486 7.783042 ACAAGTCCTCCACTACTTAATATGTC 58.217 38.462 0.00 0.00 34.23 3.06
2285 4487 7.147707 GGACAAGTCCTCCACTACTTAATATGT 60.148 40.741 11.94 0.00 46.16 2.29
2286 4488 7.210873 GGACAAGTCCTCCACTACTTAATATG 58.789 42.308 11.94 0.00 46.16 1.78
2287 4489 7.362802 GGACAAGTCCTCCACTACTTAATAT 57.637 40.000 11.94 0.00 46.16 1.28
2288 4490 6.786967 GGACAAGTCCTCCACTACTTAATA 57.213 41.667 11.94 0.00 46.16 0.98
2289 4491 5.678955 GGACAAGTCCTCCACTACTTAAT 57.321 43.478 11.94 0.00 46.16 1.40
2325 4527 9.783256 GCACAGTCCGTTTATTTATTTTATTCT 57.217 29.630 0.00 0.00 0.00 2.40
2326 4528 9.016623 GGCACAGTCCGTTTATTTATTTTATTC 57.983 33.333 0.00 0.00 0.00 1.75
2327 4529 7.698970 CGGCACAGTCCGTTTATTTATTTTATT 59.301 33.333 3.91 0.00 44.18 1.40
2328 4530 7.190871 CGGCACAGTCCGTTTATTTATTTTAT 58.809 34.615 3.91 0.00 44.18 1.40
2329 4531 6.544622 CGGCACAGTCCGTTTATTTATTTTA 58.455 36.000 3.91 0.00 44.18 1.52
2330 4532 5.395642 CGGCACAGTCCGTTTATTTATTTT 58.604 37.500 3.91 0.00 44.18 1.82
2331 4533 4.976987 CGGCACAGTCCGTTTATTTATTT 58.023 39.130 3.91 0.00 44.18 1.40
2332 4534 4.609691 CGGCACAGTCCGTTTATTTATT 57.390 40.909 3.91 0.00 44.18 1.40
2367 4569 3.485431 CTGAAGGCTGAGCACGCG 61.485 66.667 6.82 3.53 0.00 6.01
2368 4570 3.123620 CCTGAAGGCTGAGCACGC 61.124 66.667 6.82 0.00 0.00 5.34
2378 4580 2.441532 CATGCCTGGGCCTGAAGG 60.442 66.667 12.58 8.09 38.70 3.46
2379 4581 2.441532 CCATGCCTGGGCCTGAAG 60.442 66.667 16.42 0.00 38.70 3.02
2380 4582 4.764771 GCCATGCCTGGGCCTGAA 62.765 66.667 16.42 0.00 45.87 3.02
2399 4601 4.047059 CTTGCAAGGCACGCCAGG 62.047 66.667 19.14 2.63 38.71 4.45
2400 4602 4.712425 GCTTGCAAGGCACGCCAG 62.712 66.667 27.10 3.43 45.86 4.85
2442 4644 2.834688 CCAGGATAGCTGGGCCAG 59.165 66.667 29.44 29.44 38.28 4.85
2443 4645 3.492353 GCCAGGATAGCTGGGCCA 61.492 66.667 5.85 5.85 42.02 5.36
2446 4648 2.834688 CTGGCCAGGATAGCTGGG 59.165 66.667 26.14 0.00 42.02 4.45
2447 4649 1.992519 AAGCTGGCCAGGATAGCTGG 61.993 60.000 33.46 6.68 46.34 4.85
2448 4650 0.106819 AAAGCTGGCCAGGATAGCTG 60.107 55.000 33.46 7.49 46.34 4.24
2450 4652 1.732417 GCAAAGCTGGCCAGGATAGC 61.732 60.000 33.46 20.06 37.71 2.97
2451 4653 0.394762 TGCAAAGCTGGCCAGGATAG 60.395 55.000 33.46 9.95 0.00 2.08
2452 4654 0.680921 GTGCAAAGCTGGCCAGGATA 60.681 55.000 33.46 7.37 0.00 2.59
2453 4655 1.980772 GTGCAAAGCTGGCCAGGAT 60.981 57.895 33.46 11.06 0.00 3.24
2454 4656 2.598394 GTGCAAAGCTGGCCAGGA 60.598 61.111 33.46 7.00 0.00 3.86
2455 4657 3.688159 GGTGCAAAGCTGGCCAGG 61.688 66.667 33.46 18.03 0.00 4.45
2456 4658 0.966875 TATGGTGCAAAGCTGGCCAG 60.967 55.000 29.34 29.34 32.04 4.85
2457 4659 0.324552 ATATGGTGCAAAGCTGGCCA 60.325 50.000 4.71 4.71 32.70 5.36
2458 4660 0.826062 AATATGGTGCAAAGCTGGCC 59.174 50.000 8.04 0.00 0.00 5.36
2459 4661 1.477700 TCAATATGGTGCAAAGCTGGC 59.522 47.619 3.76 3.76 0.00 4.85
2460 4662 2.480759 GCTCAATATGGTGCAAAGCTGG 60.481 50.000 0.00 0.00 0.00 4.85
2461 4663 2.164827 TGCTCAATATGGTGCAAAGCTG 59.835 45.455 4.34 0.00 32.12 4.24
2462 4664 2.449464 TGCTCAATATGGTGCAAAGCT 58.551 42.857 4.34 0.00 32.12 3.74
2463 4665 2.945447 TGCTCAATATGGTGCAAAGC 57.055 45.000 4.34 0.00 32.12 3.51
2464 4666 6.982141 ACATAATTGCTCAATATGGTGCAAAG 59.018 34.615 20.35 13.79 46.31 2.77
2465 4667 6.876155 ACATAATTGCTCAATATGGTGCAAA 58.124 32.000 20.35 8.32 46.31 3.68
2467 4669 7.579761 TTACATAATTGCTCAATATGGTGCA 57.420 32.000 2.64 2.64 0.00 4.57
2468 4670 8.352201 TCTTTACATAATTGCTCAATATGGTGC 58.648 33.333 0.00 0.00 0.00 5.01
2498 4700 1.538687 ATGCCAAAGCTTGTGGGCTC 61.539 55.000 27.36 13.81 46.53 4.70
2522 4724 6.015265 TCTCAGATTGTCATTGGCATGAAAAA 60.015 34.615 0.00 3.95 39.64 1.94
2591 4793 0.040499 GAGTCCCTGACCTCTCCTGT 59.960 60.000 0.00 0.00 32.18 4.00
2685 4887 7.877003 TGTCCATATCACGTTAACACAAAATT 58.123 30.769 6.39 0.00 0.00 1.82
2709 4911 2.353579 TGCGATGATGCTCAATGAACTG 59.646 45.455 0.00 0.00 35.36 3.16
2728 4930 3.866910 CCACTGCAATAAACCATGAATGC 59.133 43.478 0.00 0.00 0.00 3.56
2774 4976 1.134401 CGGGAACAGGTAGCATGTCAT 60.134 52.381 0.00 0.00 0.00 3.06
2813 5015 7.769970 ACCAAACTCATTGAACATCAATTTTGT 59.230 29.630 18.18 10.00 44.03 2.83
3000 5210 9.995003 GATTCATGAAATAGTAGAGAGATGGTT 57.005 33.333 13.09 0.00 0.00 3.67
3001 5211 9.152327 TGATTCATGAAATAGTAGAGAGATGGT 57.848 33.333 13.09 0.00 0.00 3.55
3023 5233 8.827832 TTCTAGAATTTCCACAATCCATGATT 57.172 30.769 0.00 0.00 31.86 2.57
3080 5292 6.157904 TGTCAATCATGGCAATTAAGTTGTG 58.842 36.000 0.00 0.00 38.47 3.33
3116 5328 5.324697 GTTTGATGCAGAATACGAAGGTTC 58.675 41.667 0.00 0.00 0.00 3.62
3124 5336 6.749923 AAGAGAAGGTTTGATGCAGAATAC 57.250 37.500 0.00 0.00 0.00 1.89
3188 5400 7.675062 TGAAAATGGTAAAAATGCCTACACAT 58.325 30.769 0.00 0.00 0.00 3.21
3307 5520 3.904586 GCTAGCAGCAGACTATCCC 57.095 57.895 10.63 0.00 41.89 3.85
3362 5575 9.824216 AAGCACCCTACAGATCTAGTTATAATA 57.176 33.333 0.00 0.00 0.00 0.98
3370 5583 6.412362 AACATAAGCACCCTACAGATCTAG 57.588 41.667 0.00 0.00 0.00 2.43
3428 5641 9.582431 AATCAAGCATCAGTTAATGAAAGAATG 57.418 29.630 0.00 0.00 42.53 2.67
3507 5720 0.176680 ACGTCTATGCTGAGGCCAAG 59.823 55.000 5.01 2.69 37.74 3.61
3708 5921 5.761234 GGTCTTGGTGTACAACAGTTTATCA 59.239 40.000 14.34 0.00 34.76 2.15
3802 6015 3.146066 CACACCCCATATTATTGACCCG 58.854 50.000 0.00 0.00 0.00 5.28
3805 6018 5.278957 GCCAATCACACCCCATATTATTGAC 60.279 44.000 0.00 0.00 0.00 3.18
3814 6027 2.024080 AGTAATGCCAATCACACCCCAT 60.024 45.455 0.00 0.00 0.00 4.00
3927 6140 7.259290 TGAAAAGCATATAAAGATCGAACCC 57.741 36.000 0.00 0.00 0.00 4.11
4161 6419 6.616260 GCTGGTTGCTTGAAAATAAAATGTCG 60.616 38.462 0.00 0.00 38.95 4.35
4216 6474 5.062809 GCAAAGTTGTCCGTTTTCAATTTCA 59.937 36.000 0.00 0.00 0.00 2.69
4217 6475 5.290885 AGCAAAGTTGTCCGTTTTCAATTTC 59.709 36.000 0.00 0.00 0.00 2.17
4218 6476 5.175127 AGCAAAGTTGTCCGTTTTCAATTT 58.825 33.333 0.00 0.00 0.00 1.82
4278 6536 8.287503 CGTTTAAATCAGTTTGGTACTAAGCTT 58.712 33.333 5.58 3.48 34.56 3.74
4279 6537 7.094933 CCGTTTAAATCAGTTTGGTACTAAGCT 60.095 37.037 2.40 2.40 34.56 3.74
4280 6538 7.019418 CCGTTTAAATCAGTTTGGTACTAAGC 58.981 38.462 0.00 0.00 34.56 3.09
4281 6539 8.314143 TCCGTTTAAATCAGTTTGGTACTAAG 57.686 34.615 0.00 0.00 34.56 2.18
4282 6540 8.149647 TCTCCGTTTAAATCAGTTTGGTACTAA 58.850 33.333 0.00 0.00 34.56 2.24
4283 6541 7.599998 GTCTCCGTTTAAATCAGTTTGGTACTA 59.400 37.037 0.00 0.00 34.56 1.82
4284 6542 6.426025 GTCTCCGTTTAAATCAGTTTGGTACT 59.574 38.462 0.00 0.00 37.68 2.73
4285 6543 6.426025 AGTCTCCGTTTAAATCAGTTTGGTAC 59.574 38.462 0.00 0.00 0.00 3.34
4286 6544 6.527423 AGTCTCCGTTTAAATCAGTTTGGTA 58.473 36.000 0.00 0.00 0.00 3.25
4287 6545 5.374071 AGTCTCCGTTTAAATCAGTTTGGT 58.626 37.500 0.00 0.00 0.00 3.67
4288 6546 5.941948 AGTCTCCGTTTAAATCAGTTTGG 57.058 39.130 0.00 0.00 0.00 3.28
4289 6547 6.636850 CCAAAGTCTCCGTTTAAATCAGTTTG 59.363 38.462 0.00 0.92 0.00 2.93
4290 6548 6.544564 TCCAAAGTCTCCGTTTAAATCAGTTT 59.455 34.615 0.00 0.00 0.00 2.66
4291 6549 6.059484 TCCAAAGTCTCCGTTTAAATCAGTT 58.941 36.000 0.00 0.00 0.00 3.16
4292 6550 5.617252 TCCAAAGTCTCCGTTTAAATCAGT 58.383 37.500 0.00 0.00 0.00 3.41
4293 6551 5.390991 GCTCCAAAGTCTCCGTTTAAATCAG 60.391 44.000 0.00 0.00 0.00 2.90
4294 6552 4.454504 GCTCCAAAGTCTCCGTTTAAATCA 59.545 41.667 0.00 0.00 0.00 2.57
4295 6553 4.695928 AGCTCCAAAGTCTCCGTTTAAATC 59.304 41.667 0.00 0.00 0.00 2.17
4296 6554 4.652822 AGCTCCAAAGTCTCCGTTTAAAT 58.347 39.130 0.00 0.00 0.00 1.40
4297 6555 4.081322 AGCTCCAAAGTCTCCGTTTAAA 57.919 40.909 0.00 0.00 0.00 1.52
4298 6556 3.764237 AGCTCCAAAGTCTCCGTTTAA 57.236 42.857 0.00 0.00 0.00 1.52
4299 6557 3.323979 AGAAGCTCCAAAGTCTCCGTTTA 59.676 43.478 0.00 0.00 0.00 2.01
4300 6558 2.104963 AGAAGCTCCAAAGTCTCCGTTT 59.895 45.455 0.00 0.00 0.00 3.60
4301 6559 1.694696 AGAAGCTCCAAAGTCTCCGTT 59.305 47.619 0.00 0.00 0.00 4.44
4302 6560 1.001406 CAGAAGCTCCAAAGTCTCCGT 59.999 52.381 0.00 0.00 0.00 4.69
4303 6561 1.719600 CAGAAGCTCCAAAGTCTCCG 58.280 55.000 0.00 0.00 0.00 4.63
4304 6562 1.271054 TGCAGAAGCTCCAAAGTCTCC 60.271 52.381 0.00 0.00 42.74 3.71
4305 6563 2.175878 TGCAGAAGCTCCAAAGTCTC 57.824 50.000 0.00 0.00 42.74 3.36
4306 6564 2.645838 TTGCAGAAGCTCCAAAGTCT 57.354 45.000 0.00 0.00 42.74 3.24
4307 6565 3.505293 AGATTTGCAGAAGCTCCAAAGTC 59.495 43.478 0.00 0.00 42.74 3.01
4308 6566 3.494332 AGATTTGCAGAAGCTCCAAAGT 58.506 40.909 0.00 0.00 42.74 2.66
4372 6632 9.515020 TTTATCTGTTCACACTCAACAATTTTC 57.485 29.630 0.00 0.00 33.36 2.29
4405 6667 3.242712 CGAATGTTGTTTTCTGGTGTTGC 59.757 43.478 0.00 0.00 0.00 4.17
4408 6670 3.945285 AGACGAATGTTGTTTTCTGGTGT 59.055 39.130 0.00 0.00 0.00 4.16
4464 6726 4.811555 TTGCTGATGTGTGTACAAAGTC 57.188 40.909 0.00 0.00 40.84 3.01
4479 6741 1.792367 CGATGTCGACTTGTTTGCTGA 59.208 47.619 17.92 0.00 43.02 4.26
4536 6798 2.500229 TGTTTGCTTAGGAACTTCCGG 58.500 47.619 0.00 0.00 42.75 5.14
4571 6833 0.712222 GCGCTTCGGTGTGTACTTAC 59.288 55.000 0.00 0.00 0.00 2.34
4577 6839 2.967076 CTGTGCGCTTCGGTGTGT 60.967 61.111 9.73 0.00 0.00 3.72
4582 6844 3.121030 CTTCCCTGTGCGCTTCGG 61.121 66.667 9.73 6.99 0.00 4.30
4611 6873 1.227999 ACAACATGAACGTGGGAGCG 61.228 55.000 0.00 0.00 37.94 5.03
4626 6888 4.090930 GCAAATGAAGCACATGATGACAAC 59.909 41.667 0.00 0.00 39.39 3.32
4632 6894 2.888594 GCTGCAAATGAAGCACATGAT 58.111 42.857 8.55 0.00 46.14 2.45


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

AutoCloner maintained by Alex Coulton.