Multiple sequence alignment - TraesCS7D01G555000

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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 TraesCS7D01G555000 chr7D 100.000 3986 0 0 2887 6872 638472055 638476040 0.000000e+00 7361.0
1 TraesCS7D01G555000 chr7D 100.000 2584 0 0 1 2584 638469169 638471752 0.000000e+00 4772.0
2 TraesCS7D01G555000 chr7D 83.036 1232 160 33 3148 4362 638560565 638561764 0.000000e+00 1072.0
3 TraesCS7D01G555000 chr7D 90.217 736 59 7 1853 2581 638559150 638559879 0.000000e+00 948.0
4 TraesCS7D01G555000 chr7D 86.916 214 21 2 1584 1790 638558849 638559062 4.140000e-57 233.0
5 TraesCS7D01G555000 chr7D 87.879 132 6 2 1058 1179 638558638 638558769 5.550000e-31 147.0
6 TraesCS7D01G555000 chr7D 97.297 37 1 0 459 495 124512644 124512680 5.750000e-06 63.9
7 TraesCS7D01G555000 chr7B 86.771 3394 301 79 2893 6231 734251700 734248400 0.000000e+00 3644.0
8 TraesCS7D01G555000 chr7B 87.380 1355 82 40 1 1319 734253909 734252608 0.000000e+00 1472.0
9 TraesCS7D01G555000 chr7B 91.618 859 67 4 1553 2409 734252552 734251697 0.000000e+00 1182.0
10 TraesCS7D01G555000 chr7A 93.571 2131 127 8 4106 6230 727431696 727429570 0.000000e+00 3168.0
11 TraesCS7D01G555000 chr7A 89.906 1278 67 25 6 1247 727435279 727434028 0.000000e+00 1589.0
12 TraesCS7D01G555000 chr7A 90.580 966 73 12 1551 2513 727433954 727433004 0.000000e+00 1264.0
13 TraesCS7D01G555000 chr7A 90.594 404 32 6 6257 6657 727429572 727429172 1.310000e-146 531.0
14 TraesCS7D01G555000 chr7A 91.713 181 11 2 6693 6869 727428603 727428423 1.480000e-61 248.0
15 TraesCS7D01G555000 chr7A 89.941 169 14 1 1318 1483 580506868 580506700 1.500000e-51 215.0
16 TraesCS7D01G555000 chr7A 89.231 65 6 1 610 674 663769558 663769621 5.710000e-11 80.5
17 TraesCS7D01G555000 chr7A 100.000 33 0 0 1 33 727435312 727435280 2.070000e-05 62.1
18 TraesCS7D01G555000 chrUn 91.224 2279 142 25 3997 6264 317234040 317231809 0.000000e+00 3048.0
19 TraesCS7D01G555000 chrUn 92.308 962 70 2 1604 2562 88118654 88117694 0.000000e+00 1363.0
20 TraesCS7D01G555000 chrUn 91.506 518 34 8 5788 6299 88108657 88108144 0.000000e+00 704.0
21 TraesCS7D01G555000 chrUn 90.766 509 43 3 1553 2060 88137092 88136587 0.000000e+00 676.0
22 TraesCS7D01G555000 chrUn 94.089 203 9 3 6295 6494 88102984 88102782 8.660000e-79 305.0
23 TraesCS7D01G555000 chrUn 92.386 197 15 0 6676 6872 88102399 88102203 1.460000e-71 281.0
24 TraesCS7D01G555000 chrUn 76.087 506 68 29 699 1182 88119666 88119192 1.500000e-51 215.0
25 TraesCS7D01G555000 chrUn 76.087 506 68 29 699 1182 88974942 88974468 1.500000e-51 215.0
26 TraesCS7D01G555000 chr2D 89.356 1569 164 2 4258 5826 180087354 180085789 0.000000e+00 1969.0
27 TraesCS7D01G555000 chr2D 87.393 1642 203 3 4183 5824 639396639 639398276 0.000000e+00 1882.0
28 TraesCS7D01G555000 chr2D 84.822 929 117 16 1587 2503 639393858 639394774 0.000000e+00 913.0
29 TraesCS7D01G555000 chr2D 83.919 740 111 5 1609 2341 180088266 180087528 0.000000e+00 701.0
30 TraesCS7D01G555000 chr2D 83.445 743 107 9 1604 2341 639666399 639667130 0.000000e+00 676.0
31 TraesCS7D01G555000 chr2D 92.025 163 13 0 1319 1481 526524959 526525121 5.360000e-56 230.0
32 TraesCS7D01G555000 chr2D 90.909 165 15 0 1317 1481 367502165 367502001 8.970000e-54 222.0
33 TraesCS7D01G555000 chr2D 85.246 122 12 5 1061 1179 639665816 639665934 3.370000e-23 121.0
34 TraesCS7D01G555000 chr2D 89.744 78 8 0 597 674 302425715 302425638 4.390000e-17 100.0
35 TraesCS7D01G555000 chr2A 89.229 1569 166 2 4258 5826 194423278 194421713 0.000000e+00 1958.0
36 TraesCS7D01G555000 chr2A 87.085 1657 211 3 4163 5819 765040439 765042092 0.000000e+00 1871.0
37 TraesCS7D01G555000 chr2A 85.386 739 99 7 1604 2336 765039663 765040398 0.000000e+00 758.0
38 TraesCS7D01G555000 chr2A 84.211 741 107 8 1609 2341 194424189 194423451 0.000000e+00 712.0
39 TraesCS7D01G555000 chr2A 86.486 185 23 2 1298 1481 766004651 766004834 1.170000e-47 202.0
40 TraesCS7D01G555000 chr2A 84.874 119 15 3 1061 1179 765039118 765039233 4.350000e-22 117.0
41 TraesCS7D01G555000 chr2B 88.725 1561 173 2 4258 5818 236776593 236775036 0.000000e+00 1905.0
42 TraesCS7D01G555000 chr2B 87.087 1665 206 8 4163 5824 798318352 798316694 0.000000e+00 1875.0
43 TraesCS7D01G555000 chr2B 85.333 750 100 7 1592 2336 798615190 798614446 0.000000e+00 767.0
44 TraesCS7D01G555000 chr2B 85.095 738 103 5 1604 2336 798723289 798724024 0.000000e+00 747.0
45 TraesCS7D01G555000 chr2B 89.820 167 15 1 1318 1482 769078004 769078170 5.400000e-51 213.0
46 TraesCS7D01G555000 chr2B 85.246 122 12 5 1061 1179 798615727 798615609 3.370000e-23 121.0
47 TraesCS7D01G555000 chr2B 84.034 119 16 3 1061 1179 798722749 798722864 2.030000e-20 111.0
48 TraesCS7D01G555000 chr2B 91.935 62 4 1 611 672 680023211 680023151 1.230000e-12 86.1
49 TraesCS7D01G555000 chr3D 90.698 172 15 1 1310 1481 498263632 498263802 1.930000e-55 228.0
50 TraesCS7D01G555000 chr3D 90.964 166 15 0 1314 1479 473421001 473420836 2.490000e-54 224.0
51 TraesCS7D01G555000 chr3B 90.909 165 15 0 1317 1481 428703659 428703823 8.970000e-54 222.0
52 TraesCS7D01G555000 chr3B 93.103 58 4 0 610 667 156725203 156725260 1.230000e-12 86.1
53 TraesCS7D01G555000 chr3B 89.394 66 5 2 610 674 762342230 762342166 1.590000e-11 82.4
54 TraesCS7D01G555000 chr1B 90.303 165 15 1 1318 1481 626100554 626100390 1.500000e-51 215.0
55 TraesCS7D01G555000 chr5D 80.420 143 24 4 1826 1966 115949132 115949272 9.430000e-19 106.0
56 TraesCS7D01G555000 chr5D 97.143 35 0 1 1486 1519 345936220 345936254 2.680000e-04 58.4
57 TraesCS7D01G555000 chr6B 89.041 73 8 0 602 674 690558349 690558277 2.640000e-14 91.6
58 TraesCS7D01G555000 chr6A 92.308 65 4 1 610 674 464618532 464618595 2.640000e-14 91.6
59 TraesCS7D01G555000 chr6A 92.063 63 5 0 610 672 183367415 183367477 9.490000e-14 89.8
60 TraesCS7D01G555000 chr6A 86.364 66 5 4 6487 6551 298971544 298971606 1.240000e-07 69.4
61 TraesCS7D01G555000 chr5A 75.243 206 37 12 6142 6343 3262782 3262977 1.230000e-12 86.1
62 TraesCS7D01G555000 chr5A 87.838 74 6 3 6482 6554 420235172 420235101 4.420000e-12 84.2
63 TraesCS7D01G555000 chr1D 91.803 61 5 0 610 670 216328996 216328936 1.230000e-12 86.1
64 TraesCS7D01G555000 chr5B 91.304 46 3 1 1479 1524 441645818 441645862 2.070000e-05 62.1


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 TraesCS7D01G555000 chr7D 638469169 638476040 6871 False 6066.500000 7361 100.000000 1 6872 2 chr7D.!!$F2 6871
1 TraesCS7D01G555000 chr7D 638558638 638561764 3126 False 600.000000 1072 87.012000 1058 4362 4 chr7D.!!$F3 3304
2 TraesCS7D01G555000 chr7B 734248400 734253909 5509 True 2099.333333 3644 88.589667 1 6231 3 chr7B.!!$R1 6230
3 TraesCS7D01G555000 chr7A 727428423 727435312 6889 True 1143.683333 3168 92.727333 1 6869 6 chr7A.!!$R2 6868
4 TraesCS7D01G555000 chrUn 317231809 317234040 2231 True 3048.000000 3048 91.224000 3997 6264 1 chrUn.!!$R4 2267
5 TraesCS7D01G555000 chrUn 88117694 88119666 1972 True 789.000000 1363 84.197500 699 2562 2 chrUn.!!$R6 1863
6 TraesCS7D01G555000 chrUn 88108144 88108657 513 True 704.000000 704 91.506000 5788 6299 1 chrUn.!!$R1 511
7 TraesCS7D01G555000 chrUn 88136587 88137092 505 True 676.000000 676 90.766000 1553 2060 1 chrUn.!!$R2 507
8 TraesCS7D01G555000 chrUn 88102203 88102984 781 True 293.000000 305 93.237500 6295 6872 2 chrUn.!!$R5 577
9 TraesCS7D01G555000 chr2D 639393858 639398276 4418 False 1397.500000 1882 86.107500 1587 5824 2 chr2D.!!$F2 4237
10 TraesCS7D01G555000 chr2D 180085789 180088266 2477 True 1335.000000 1969 86.637500 1609 5826 2 chr2D.!!$R3 4217
11 TraesCS7D01G555000 chr2D 639665816 639667130 1314 False 398.500000 676 84.345500 1061 2341 2 chr2D.!!$F3 1280
12 TraesCS7D01G555000 chr2A 194421713 194424189 2476 True 1335.000000 1958 86.720000 1609 5826 2 chr2A.!!$R1 4217
13 TraesCS7D01G555000 chr2A 765039118 765042092 2974 False 915.333333 1871 85.781667 1061 5819 3 chr2A.!!$F2 4758
14 TraesCS7D01G555000 chr2B 236775036 236776593 1557 True 1905.000000 1905 88.725000 4258 5818 1 chr2B.!!$R1 1560
15 TraesCS7D01G555000 chr2B 798316694 798318352 1658 True 1875.000000 1875 87.087000 4163 5824 1 chr2B.!!$R3 1661
16 TraesCS7D01G555000 chr2B 798614446 798615727 1281 True 444.000000 767 85.289500 1061 2336 2 chr2B.!!$R4 1275
17 TraesCS7D01G555000 chr2B 798722749 798724024 1275 False 429.000000 747 84.564500 1061 2336 2 chr2B.!!$F2 1275

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
857 911 0.106719 TTTAGTATGGCTGCCAGGGC 60.107 55.0 27.20 17.92 36.75 5.19 F
1647 2186 0.815213 GCTTGGTCGCCATCATAGCA 60.815 55.0 12.47 0.00 31.53 3.49 F
2581 3244 0.785979 CAAAAACAGCAAGGCGATGC 59.214 50.0 9.86 9.86 46.78 3.91 F
3448 4639 0.550914 AACAAGCAAGGTGTCCCTCA 59.449 50.0 0.00 0.00 41.56 3.86 F
4885 7386 0.107703 CGAGGGGCTTAGCAATGACA 60.108 55.0 6.53 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2591 1.000385 CCCACAAAGCAGCGAAATGAA 60.000 47.619 0.00 0.0 0.00 2.57 R
3442 4633 0.833287 GCTCTGGCACTAATGAGGGA 59.167 55.000 3.29 0.0 38.54 4.20 R
4398 6899 1.243902 CGCCTGCCTTCTTTTGGTTA 58.756 50.000 0.00 0.0 0.00 2.85 R
5121 7622 0.884704 GAGCGTTGCTGTGGGAGAAA 60.885 55.000 0.00 0.0 39.88 2.52 R
6634 9434 0.036294 GGACTCTTCGGTTGGGAAGG 60.036 60.000 2.81 0.0 42.88 3.46 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
50 79 5.869579 TCTCTAAGCTCAAAAACCATGTCT 58.130 37.500 0.00 0.00 0.00 3.41
229 263 2.431419 TCAACAAGACAACACGAGGGTA 59.569 45.455 0.00 0.00 0.00 3.69
231 265 2.830104 ACAAGACAACACGAGGGTAAC 58.170 47.619 0.00 0.00 0.00 2.50
232 266 2.168936 ACAAGACAACACGAGGGTAACA 59.831 45.455 0.00 0.00 39.74 2.41
513 555 3.216800 AGTATCATACCTCCGTAACGCA 58.783 45.455 0.00 0.00 0.00 5.24
566 608 9.712305 TTTGTTTTTGAACTATTTGTTTCTCCA 57.288 25.926 0.00 0.00 39.30 3.86
567 609 9.712305 TTGTTTTTGAACTATTTGTTTCTCCAA 57.288 25.926 0.00 0.00 39.30 3.53
568 610 9.145865 TGTTTTTGAACTATTTGTTTCTCCAAC 57.854 29.630 0.00 0.00 39.30 3.77
569 611 9.366216 GTTTTTGAACTATTTGTTTCTCCAACT 57.634 29.630 0.00 0.00 39.30 3.16
592 634 3.090790 TGCCTCAGAAATAGCAAATGCA 58.909 40.909 8.28 0.00 45.16 3.96
631 673 2.559668 TCCGTCCTGAATTACTTGTCGT 59.440 45.455 0.00 0.00 0.00 4.34
639 681 7.544566 GTCCTGAATTACTTGTCGTAGAAATGA 59.455 37.037 0.00 0.00 39.69 2.57
649 691 9.653287 ACTTGTCGTAGAAATGAATAGAAATGA 57.347 29.630 0.00 0.00 39.69 2.57
697 743 2.158490 AGGACGGAGGGAGTACTTATCC 60.158 54.545 0.00 4.42 35.99 2.59
759 805 3.588842 ACTCTGAAATGTGATCCTTCCCA 59.411 43.478 0.00 0.00 0.00 4.37
760 806 4.229123 ACTCTGAAATGTGATCCTTCCCAT 59.771 41.667 0.00 0.00 0.00 4.00
850 904 1.873591 GCCGATGGTTTAGTATGGCTG 59.126 52.381 0.00 0.00 38.00 4.85
854 908 2.418368 TGGTTTAGTATGGCTGCCAG 57.582 50.000 27.20 0.00 36.75 4.85
856 910 1.680338 GTTTAGTATGGCTGCCAGGG 58.320 55.000 27.20 0.00 36.75 4.45
857 911 0.106719 TTTAGTATGGCTGCCAGGGC 60.107 55.000 27.20 17.92 36.75 5.19
858 912 0.988145 TTAGTATGGCTGCCAGGGCT 60.988 55.000 27.20 23.27 42.51 5.19
945 1000 3.230134 CAAGCTAGCTAGGGAGATCAGT 58.770 50.000 19.70 0.00 0.00 3.41
1184 1268 4.323485 CCTGCATCCTTACAGGTCAGTTTA 60.323 45.833 0.79 0.00 46.95 2.01
1187 1271 5.186198 GCATCCTTACAGGTCAGTTTACAT 58.814 41.667 0.00 0.00 36.53 2.29
1189 1273 4.575885 TCCTTACAGGTCAGTTTACATGC 58.424 43.478 0.00 0.00 36.53 4.06
1195 1296 2.751259 AGGTCAGTTTACATGCATGCTG 59.249 45.455 26.53 22.70 0.00 4.41
1207 1308 8.599055 TTACATGCATGCTGTTTTTATTTCAA 57.401 26.923 26.53 5.89 0.00 2.69
1209 1310 8.101654 ACATGCATGCTGTTTTTATTTCAATT 57.898 26.923 26.53 0.00 0.00 2.32
1210 1311 9.217278 ACATGCATGCTGTTTTTATTTCAATTA 57.783 25.926 26.53 0.00 0.00 1.40
1262 1364 9.706691 TTATAAGATATGCTAACCTTTTCCGAG 57.293 33.333 0.00 0.00 0.00 4.63
1328 1850 4.252570 AGTCCATATATACTCCCTCCGG 57.747 50.000 0.00 0.00 0.00 5.14
1332 1854 3.052793 CCATATATACTCCCTCCGGTCCT 60.053 52.174 0.00 0.00 0.00 3.85
1338 1860 3.632420 ACTCCCTCCGGTCCTAAATAT 57.368 47.619 0.00 0.00 0.00 1.28
1340 1862 5.083953 ACTCCCTCCGGTCCTAAATATAA 57.916 43.478 0.00 0.00 0.00 0.98
1344 1866 5.085219 CCCTCCGGTCCTAAATATAAGTCT 58.915 45.833 0.00 0.00 0.00 3.24
1346 1868 6.042897 CCCTCCGGTCCTAAATATAAGTCTTT 59.957 42.308 0.00 0.00 0.00 2.52
1347 1869 7.419865 CCCTCCGGTCCTAAATATAAGTCTTTT 60.420 40.741 0.00 0.00 0.00 2.27
1348 1870 8.645110 CCTCCGGTCCTAAATATAAGTCTTTTA 58.355 37.037 0.00 0.00 0.00 1.52
1373 1895 8.699283 AAAAGATTTCACTATGGACTACGTAC 57.301 34.615 0.00 0.00 0.00 3.67
1377 1899 3.461061 TCACTATGGACTACGTACGGAG 58.539 50.000 25.90 25.90 0.00 4.63
1380 1902 1.466856 ATGGACTACGTACGGAGCAA 58.533 50.000 27.33 13.89 0.00 3.91
1382 1904 1.612950 TGGACTACGTACGGAGCAAAA 59.387 47.619 27.33 8.00 0.00 2.44
1383 1905 2.231964 TGGACTACGTACGGAGCAAAAT 59.768 45.455 27.33 7.40 0.00 1.82
1384 1906 2.601763 GGACTACGTACGGAGCAAAATG 59.398 50.000 27.33 3.03 0.00 2.32
1388 1910 2.762745 ACGTACGGAGCAAAATGAGTT 58.237 42.857 21.06 0.00 0.00 3.01
1389 1911 3.916761 ACGTACGGAGCAAAATGAGTTA 58.083 40.909 21.06 0.00 0.00 2.24
1391 1913 4.151157 ACGTACGGAGCAAAATGAGTTAAC 59.849 41.667 21.06 0.00 0.00 2.01
1392 1914 4.435121 CGTACGGAGCAAAATGAGTTAACC 60.435 45.833 7.57 0.00 0.00 2.85
1393 1915 3.751518 ACGGAGCAAAATGAGTTAACCT 58.248 40.909 0.88 0.00 0.00 3.50
1396 1918 6.646267 ACGGAGCAAAATGAGTTAACCTATA 58.354 36.000 0.88 0.00 0.00 1.31
1397 1919 6.537660 ACGGAGCAAAATGAGTTAACCTATAC 59.462 38.462 0.88 0.00 0.00 1.47
1398 1920 6.761714 CGGAGCAAAATGAGTTAACCTATACT 59.238 38.462 0.88 0.00 0.00 2.12
1399 1921 7.042658 CGGAGCAAAATGAGTTAACCTATACTC 60.043 40.741 0.88 0.00 40.89 2.59
1400 1922 7.988028 GGAGCAAAATGAGTTAACCTATACTCT 59.012 37.037 0.88 0.00 41.05 3.24
1407 1929 9.833917 AATGAGTTAACCTATACTCTAAAAGGC 57.166 33.333 0.88 0.00 41.05 4.35
1408 1930 7.486647 TGAGTTAACCTATACTCTAAAAGGCG 58.513 38.462 0.88 0.00 41.05 5.52
1410 1932 7.487484 AGTTAACCTATACTCTAAAAGGCGTC 58.513 38.462 0.88 0.00 31.98 5.19
1411 1933 7.341512 AGTTAACCTATACTCTAAAAGGCGTCT 59.658 37.037 0.88 0.00 31.98 4.18
1413 1935 7.836479 AACCTATACTCTAAAAGGCGTCTAT 57.164 36.000 0.00 0.00 31.98 1.98
1415 1937 9.531158 AACCTATACTCTAAAAGGCGTCTATAT 57.469 33.333 0.00 0.00 31.98 0.86
1422 1944 7.450634 ACTCTAAAAGGCGTCTATATACATCCA 59.549 37.037 0.00 0.00 0.00 3.41
1425 1947 9.436957 CTAAAAGGCGTCTATATACATCCAAAT 57.563 33.333 0.00 0.00 0.00 2.32
1426 1948 7.672983 AAAGGCGTCTATATACATCCAAATG 57.327 36.000 0.00 0.00 38.93 2.32
1478 2000 9.780186 AAGATTTATATTTAGGAACGAAGGGAG 57.220 33.333 0.00 0.00 0.00 4.30
1499 2021 9.232882 AGGGAGTAGTTCATATTAAAATACCCA 57.767 33.333 0.00 0.00 29.75 4.51
1540 2062 8.666129 TGAAATGGAGGGAGTAGTATATTAGG 57.334 38.462 0.00 0.00 0.00 2.69
1541 2063 8.461854 TGAAATGGAGGGAGTAGTATATTAGGA 58.538 37.037 0.00 0.00 0.00 2.94
1542 2064 8.903059 AAATGGAGGGAGTAGTATATTAGGAG 57.097 38.462 0.00 0.00 0.00 3.69
1543 2065 7.606892 ATGGAGGGAGTAGTATATTAGGAGT 57.393 40.000 0.00 0.00 0.00 3.85
1544 2066 8.712168 ATGGAGGGAGTAGTATATTAGGAGTA 57.288 38.462 0.00 0.00 0.00 2.59
1545 2067 7.926705 TGGAGGGAGTAGTATATTAGGAGTAC 58.073 42.308 0.00 0.00 0.00 2.73
1546 2068 7.047271 GGAGGGAGTAGTATATTAGGAGTACG 58.953 46.154 0.00 0.00 0.00 3.67
1547 2069 7.310983 GGAGGGAGTAGTATATTAGGAGTACGT 60.311 44.444 0.00 0.00 0.00 3.57
1548 2070 8.671987 AGGGAGTAGTATATTAGGAGTACGTA 57.328 38.462 0.00 0.00 0.00 3.57
1549 2071 8.536175 AGGGAGTAGTATATTAGGAGTACGTAC 58.464 40.741 18.10 18.10 0.00 3.67
1550 2072 8.314751 GGGAGTAGTATATTAGGAGTACGTACA 58.685 40.741 26.55 6.82 0.00 2.90
1551 2073 9.883142 GGAGTAGTATATTAGGAGTACGTACAT 57.117 37.037 26.55 13.57 0.00 2.29
1559 2098 9.750783 ATATTAGGAGTACGTACATATCCAGTT 57.249 33.333 26.55 14.45 32.21 3.16
1582 2121 6.169419 TCTACACTTCTGAATTTGAATGCG 57.831 37.500 6.24 0.00 0.00 4.73
1647 2186 0.815213 GCTTGGTCGCCATCATAGCA 60.815 55.000 12.47 0.00 31.53 3.49
1974 2565 1.216977 CGACGGTGGCTCATTGGTA 59.783 57.895 0.00 0.00 0.00 3.25
1996 2587 3.134623 ACACTATGAGGCGATGATCCAAA 59.865 43.478 0.00 0.00 0.00 3.28
2000 2591 3.003394 TGAGGCGATGATCCAAATTGT 57.997 42.857 0.00 0.00 0.00 2.71
2168 2759 4.223032 AGAATACGGTGAGTTCAAGGTGAT 59.777 41.667 0.00 0.00 0.00 3.06
2336 2945 5.018809 ACATGCTGGAATTGTTCAGGTAAT 58.981 37.500 0.00 0.00 0.00 1.89
2374 2993 7.816640 TGTTCATTCAGGTCAAACTTATAAGC 58.183 34.615 12.54 0.00 0.00 3.09
2505 3140 9.599866 AACACAAAAGGAAAAGGAAATAAGAAG 57.400 29.630 0.00 0.00 0.00 2.85
2509 3144 9.468532 CAAAAGGAAAAGGAAATAAGAAGTCTG 57.531 33.333 0.00 0.00 0.00 3.51
2581 3244 0.785979 CAAAAACAGCAAGGCGATGC 59.214 50.000 9.86 9.86 46.78 3.91
2931 3596 6.940298 TCGTTTTCTTCTCATTTACCTCCATT 59.060 34.615 0.00 0.00 0.00 3.16
2932 3597 7.023575 CGTTTTCTTCTCATTTACCTCCATTG 58.976 38.462 0.00 0.00 0.00 2.82
2980 3652 8.556213 TGTATACATTTCCAAGGTGTAACTTC 57.444 34.615 0.08 0.00 36.74 3.01
2982 3654 3.818773 ACATTTCCAAGGTGTAACTTCGG 59.181 43.478 0.00 0.00 36.74 4.30
2984 3656 3.564053 TTCCAAGGTGTAACTTCGGTT 57.436 42.857 0.00 0.00 41.52 4.44
2985 3657 4.686191 TTCCAAGGTGTAACTTCGGTTA 57.314 40.909 0.00 0.00 39.17 2.85
2991 3694 7.718753 TCCAAGGTGTAACTTCGGTTATTTTAA 59.281 33.333 0.00 0.00 41.66 1.52
3072 3778 5.437289 TTCATGTGTGATCTGTTTTGGTC 57.563 39.130 0.00 0.00 33.56 4.02
3075 3781 3.831323 TGTGTGATCTGTTTTGGTCCAT 58.169 40.909 0.00 0.00 0.00 3.41
3090 3796 6.813293 TTGGTCCATCTCTGAAGATCAATA 57.187 37.500 0.00 0.00 40.38 1.90
3126 4253 7.918536 ATCTAGCAATAGTTATGAATGCCTG 57.081 36.000 0.00 0.00 37.73 4.85
3127 4254 4.843220 AGCAATAGTTATGAATGCCTGC 57.157 40.909 0.00 0.00 37.73 4.85
3128 4255 4.467769 AGCAATAGTTATGAATGCCTGCT 58.532 39.130 0.00 0.00 37.73 4.24
3129 4256 4.277672 AGCAATAGTTATGAATGCCTGCTG 59.722 41.667 0.00 0.00 36.33 4.41
3130 4257 4.558095 GCAATAGTTATGAATGCCTGCTGG 60.558 45.833 5.03 5.03 0.00 4.85
3131 4258 2.814805 AGTTATGAATGCCTGCTGGT 57.185 45.000 11.69 0.00 35.27 4.00
3132 4259 3.091633 AGTTATGAATGCCTGCTGGTT 57.908 42.857 11.69 0.00 35.27 3.67
3133 4260 4.235079 AGTTATGAATGCCTGCTGGTTA 57.765 40.909 11.69 1.40 35.27 2.85
3134 4261 4.599041 AGTTATGAATGCCTGCTGGTTAA 58.401 39.130 11.69 0.00 35.27 2.01
3135 4262 4.641989 AGTTATGAATGCCTGCTGGTTAAG 59.358 41.667 11.69 0.00 35.27 1.85
3136 4263 2.877097 TGAATGCCTGCTGGTTAAGA 57.123 45.000 11.69 0.00 35.27 2.10
3137 4264 3.370840 TGAATGCCTGCTGGTTAAGAT 57.629 42.857 11.69 0.00 35.27 2.40
3138 4265 4.502105 TGAATGCCTGCTGGTTAAGATA 57.498 40.909 11.69 0.00 35.27 1.98
3139 4266 5.052693 TGAATGCCTGCTGGTTAAGATAT 57.947 39.130 11.69 0.00 35.27 1.63
3140 4267 4.823442 TGAATGCCTGCTGGTTAAGATATG 59.177 41.667 11.69 0.00 35.27 1.78
3141 4268 3.931907 TGCCTGCTGGTTAAGATATGT 57.068 42.857 11.69 0.00 35.27 2.29
3142 4269 4.235079 TGCCTGCTGGTTAAGATATGTT 57.765 40.909 11.69 0.00 35.27 2.71
3143 4270 4.599041 TGCCTGCTGGTTAAGATATGTTT 58.401 39.130 11.69 0.00 35.27 2.83
3144 4271 5.750524 TGCCTGCTGGTTAAGATATGTTTA 58.249 37.500 11.69 0.00 35.27 2.01
3145 4272 5.822519 TGCCTGCTGGTTAAGATATGTTTAG 59.177 40.000 11.69 0.00 35.27 1.85
3146 4273 5.239525 GCCTGCTGGTTAAGATATGTTTAGG 59.760 44.000 11.69 0.00 35.27 2.69
3147 4274 6.357367 CCTGCTGGTTAAGATATGTTTAGGT 58.643 40.000 0.51 0.00 0.00 3.08
3243 4431 8.792830 ATAGGTATGTTTAGGGACAACTATGA 57.207 34.615 0.00 0.00 32.47 2.15
3244 4432 6.885922 AGGTATGTTTAGGGACAACTATGAC 58.114 40.000 0.00 0.00 32.47 3.06
3326 4514 9.823647 CTTTAGGTACAGTTATGTTGATCAGAT 57.176 33.333 0.00 0.00 41.01 2.90
3328 4516 6.051717 AGGTACAGTTATGTTGATCAGATGC 58.948 40.000 0.00 0.00 41.01 3.91
3353 4541 8.774586 GCATACGATCTGTTTATAGATGGTTTT 58.225 33.333 8.84 0.00 41.46 2.43
3390 4578 8.589335 TGTTGCGATTTACTAATAAGGAGATC 57.411 34.615 0.00 0.00 0.00 2.75
3410 4598 7.571071 AGATCATCCATCAGATTAATGACCT 57.429 36.000 6.62 1.15 33.29 3.85
3442 4633 4.440112 GCTTTCTTGTAACAAGCAAGGTGT 60.440 41.667 2.14 0.00 42.18 4.16
3448 4639 0.550914 AACAAGCAAGGTGTCCCTCA 59.449 50.000 0.00 0.00 41.56 3.86
3450 4641 1.145738 ACAAGCAAGGTGTCCCTCATT 59.854 47.619 0.00 0.00 41.56 2.57
3452 4643 3.012518 CAAGCAAGGTGTCCCTCATTAG 58.987 50.000 0.00 0.00 41.56 1.73
3456 4647 0.912486 AGGTGTCCCTCATTAGTGCC 59.088 55.000 0.00 0.00 35.62 5.01
3480 4671 6.854892 CCAGAGCATTATCTTTTAATCTTGCG 59.145 38.462 0.00 0.00 0.00 4.85
3563 4755 9.941325 TTCCATTGCATATTAGACAACATTTTT 57.059 25.926 0.00 0.00 0.00 1.94
3587 4779 3.060602 GCACCGATACATCTCTAAAGGC 58.939 50.000 0.00 0.00 0.00 4.35
3637 4829 7.026631 TGAGCATATGGTTTATGTTGCTAAC 57.973 36.000 9.14 0.00 38.74 2.34
3642 4834 9.743057 GCATATGGTTTATGTTGCTAACAAATA 57.257 29.630 4.56 0.00 45.86 1.40
3717 4912 4.817987 CTGTTTATACAGTCGTCCGTTG 57.182 45.455 5.25 0.00 45.46 4.10
3718 4913 4.478699 CTGTTTATACAGTCGTCCGTTGA 58.521 43.478 5.25 0.00 45.46 3.18
3719 4914 4.478699 TGTTTATACAGTCGTCCGTTGAG 58.521 43.478 2.13 0.00 0.00 3.02
3720 4915 4.022935 TGTTTATACAGTCGTCCGTTGAGT 60.023 41.667 2.13 0.00 0.00 3.41
3740 4940 4.072131 AGTTGCAGATACACCAACGAAAT 58.928 39.130 0.00 0.00 42.60 2.17
3744 4944 5.933790 TGCAGATACACCAACGAAATTAAC 58.066 37.500 0.00 0.00 0.00 2.01
3747 4947 6.013085 CAGATACACCAACGAAATTAACACG 58.987 40.000 0.00 0.00 0.00 4.49
3840 5042 8.059798 GCCATTTTGTGATTGGCTATATAGAT 57.940 34.615 14.16 0.00 46.50 1.98
3880 5112 4.320608 TCCAAATTTGTCCTTCTTGCAC 57.679 40.909 16.73 0.00 0.00 4.57
3906 5138 5.008619 TGTTGCTTGCATATACATTTGGG 57.991 39.130 0.00 0.00 0.00 4.12
3912 5144 5.221501 GCTTGCATATACATTTGGGTCCATT 60.222 40.000 0.00 0.00 0.00 3.16
3953 5196 2.554142 TCACAAGCATATCCTGAAGCG 58.446 47.619 0.00 0.00 0.00 4.68
4031 5568 5.303333 TGGTGCTAATCGTTACTCCATCATA 59.697 40.000 0.00 0.00 0.00 2.15
4086 5625 6.303496 CGTCGATAGCACTAATTGTCTACATC 59.697 42.308 0.00 0.00 0.00 3.06
4252 6753 9.744468 ACAAAATTGTTGAAACTACTATGTTCC 57.256 29.630 0.00 0.00 38.47 3.62
4311 6812 0.895530 AACTTGGATCTTCGGCGAGA 59.104 50.000 10.46 10.53 0.00 4.04
4332 6833 6.072728 CGAGAACCAACAATCCAATTGACTTA 60.073 38.462 7.12 0.00 42.83 2.24
4398 6899 2.975489 AGAGAAGCATCCCGGTTATGAT 59.025 45.455 16.13 8.36 34.82 2.45
4875 7376 2.920912 TTGGTCGACGAGGGGCTT 60.921 61.111 9.92 0.00 0.00 4.35
4885 7386 0.107703 CGAGGGGCTTAGCAATGACA 60.108 55.000 6.53 0.00 0.00 3.58
4906 7407 1.378911 GCCACCCTGATGACATGCA 60.379 57.895 0.00 0.00 0.00 3.96
4911 7412 3.548770 CACCCTGATGACATGCACTTAT 58.451 45.455 0.00 0.00 0.00 1.73
4920 7421 1.555075 ACATGCACTTATGAGGACGGT 59.445 47.619 0.00 0.00 0.00 4.83
5070 7571 1.003839 GGCACCGATCAACCTCACA 60.004 57.895 0.00 0.00 0.00 3.58
5121 7622 2.943978 CGGCTCCCTCGAGGTGTTT 61.944 63.158 29.25 0.00 36.55 2.83
5205 7706 3.587061 ACCTCAACATGTCAATCTACCCA 59.413 43.478 0.00 0.00 0.00 4.51
5229 7730 0.392863 CCACGATGTTCATCCTGGCA 60.393 55.000 14.36 0.00 0.00 4.92
5318 7819 2.477357 CGTTCATCATGTACCTCGTCGT 60.477 50.000 0.00 0.00 0.00 4.34
5883 8408 3.266510 TCTGGGTAGACACGTACGTAT 57.733 47.619 22.34 10.64 0.00 3.06
5942 8470 9.806203 CAATAATTTGAGTATTTGAGGAATGCA 57.194 29.630 0.00 0.00 34.60 3.96
6072 8601 2.411904 TGCAAAAATCGGTGGCATTTC 58.588 42.857 0.00 0.00 0.00 2.17
6113 8642 5.163478 GCATTTACCTCTCTGATGGCATTTT 60.163 40.000 0.00 0.00 0.00 1.82
6250 8814 1.814394 TCTTCCGTAGCTCGCTTGTTA 59.186 47.619 0.00 0.00 38.35 2.41
6251 8815 2.229543 TCTTCCGTAGCTCGCTTGTTAA 59.770 45.455 0.00 0.00 38.35 2.01
6252 8816 1.986698 TCCGTAGCTCGCTTGTTAAC 58.013 50.000 0.00 0.00 38.35 2.01
6266 8830 5.559417 CGCTTGTTAACGTATTTCACCACTT 60.559 40.000 0.26 0.00 0.00 3.16
6303 8867 9.076596 CACATGTATACTACATTCATATGACCG 57.923 37.037 4.48 1.84 46.69 4.79
6468 9035 2.289631 TGGTCATTGTGTGCTACTCCTG 60.290 50.000 0.00 0.00 0.00 3.86
6540 9340 2.803030 ATTCTCTCAACATGCAGCCT 57.197 45.000 0.00 0.00 0.00 4.58
6589 9389 4.449068 TCTGCATTCTTTTCTCAGTCGTTC 59.551 41.667 0.00 0.00 0.00 3.95
6592 9392 4.212214 GCATTCTTTTCTCAGTCGTTCAGT 59.788 41.667 0.00 0.00 0.00 3.41
6599 9399 4.131649 TCTCAGTCGTTCAGTTTTTCCA 57.868 40.909 0.00 0.00 0.00 3.53
6632 9432 2.482490 GGTATGTAGGACGCATCGGTTT 60.482 50.000 0.00 0.00 0.00 3.27
6634 9434 0.108520 TGTAGGACGCATCGGTTTCC 60.109 55.000 0.00 0.00 0.00 3.13
6659 9459 3.391955 TCCCAACCGAAGAGTCCTAAAAA 59.608 43.478 0.00 0.00 0.00 1.94
6786 10119 2.954318 CTCCATGGAAGATCGGCAAAAT 59.046 45.455 17.00 0.00 0.00 1.82
6790 10123 4.282068 CATGGAAGATCGGCAAAATTACG 58.718 43.478 0.00 0.00 0.00 3.18
6865 10201 1.306482 TCTAGCAGCTCTGGCCCTT 60.306 57.895 0.00 0.00 39.73 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 79 1.919240 TCGTTTAGAGCACAGGGAGA 58.081 50.000 0.00 0.00 0.00 3.71
171 202 7.127012 TGACCGTTATCAATAATACAAGGGA 57.873 36.000 0.00 0.00 0.00 4.20
249 283 4.781934 AGTAAAATTCGCTCCTAATGCCT 58.218 39.130 0.00 0.00 0.00 4.75
250 284 5.500645 AAGTAAAATTCGCTCCTAATGCC 57.499 39.130 0.00 0.00 0.00 4.40
259 293 7.977293 ACTTTGTGGTAAAAAGTAAAATTCGCT 59.023 29.630 0.00 0.00 44.10 4.93
454 493 6.845908 ACCCACTACGAGAGGTCTTATATAA 58.154 40.000 0.00 0.00 0.00 0.98
549 591 7.121315 AGGCATAGTTGGAGAAACAAATAGTTC 59.879 37.037 0.00 0.00 40.26 3.01
552 594 6.599244 TGAGGCATAGTTGGAGAAACAAATAG 59.401 38.462 0.00 0.00 41.61 1.73
553 595 6.480763 TGAGGCATAGTTGGAGAAACAAATA 58.519 36.000 0.00 0.00 41.61 1.40
554 596 5.324409 TGAGGCATAGTTGGAGAAACAAAT 58.676 37.500 0.00 0.00 41.61 2.32
555 597 4.724399 TGAGGCATAGTTGGAGAAACAAA 58.276 39.130 0.00 0.00 41.61 2.83
558 600 4.207891 TCTGAGGCATAGTTGGAGAAAC 57.792 45.455 0.00 0.00 39.24 2.78
560 602 4.908601 TTTCTGAGGCATAGTTGGAGAA 57.091 40.909 0.00 0.00 0.00 2.87
561 603 5.453903 GCTATTTCTGAGGCATAGTTGGAGA 60.454 44.000 0.00 0.00 0.00 3.71
562 604 4.754114 GCTATTTCTGAGGCATAGTTGGAG 59.246 45.833 0.00 0.00 0.00 3.86
564 606 4.454678 TGCTATTTCTGAGGCATAGTTGG 58.545 43.478 0.00 0.00 0.00 3.77
565 607 6.441093 TTTGCTATTTCTGAGGCATAGTTG 57.559 37.500 0.00 0.00 34.59 3.16
566 608 6.460676 GCATTTGCTATTTCTGAGGCATAGTT 60.461 38.462 0.00 0.00 38.21 2.24
567 609 5.009410 GCATTTGCTATTTCTGAGGCATAGT 59.991 40.000 0.00 0.00 38.21 2.12
568 610 5.009310 TGCATTTGCTATTTCTGAGGCATAG 59.991 40.000 3.94 0.00 42.66 2.23
569 611 4.888823 TGCATTTGCTATTTCTGAGGCATA 59.111 37.500 3.94 0.00 42.66 3.14
570 612 3.702548 TGCATTTGCTATTTCTGAGGCAT 59.297 39.130 3.94 0.00 42.66 4.40
592 634 9.823647 CAGGACGGAGCAATTATATATTTCTAT 57.176 33.333 0.00 0.00 0.00 1.98
697 743 0.318107 CGGCCAAAACTCAACAGCTG 60.318 55.000 13.48 13.48 0.00 4.24
759 805 1.066430 CCCGTACTTACAGTGCACCAT 60.066 52.381 14.63 4.21 29.68 3.55
760 806 0.319083 CCCGTACTTACAGTGCACCA 59.681 55.000 14.63 0.00 29.68 4.17
782 836 2.202932 CAACTGGATCGAGGCCGG 60.203 66.667 9.72 12.95 37.80 6.13
850 904 4.849329 CGTCGTCGTAGCCCTGGC 62.849 72.222 0.00 0.00 42.33 4.85
854 908 3.490759 TCGTCGTCGTCGTAGCCC 61.491 66.667 11.41 0.00 38.33 5.19
856 910 0.366871 TAAGTCGTCGTCGTCGTAGC 59.633 55.000 11.41 4.30 38.33 3.58
857 911 1.588551 GCTAAGTCGTCGTCGTCGTAG 60.589 57.143 11.41 14.38 38.89 3.51
858 912 0.366871 GCTAAGTCGTCGTCGTCGTA 59.633 55.000 11.41 0.00 38.33 3.43
1184 1268 7.675962 ATTGAAATAAAAACAGCATGCATGT 57.324 28.000 26.79 17.58 42.53 3.21
1207 1308 7.770662 TGAGAGGAGGGAGTACTCATAATAAT 58.229 38.462 23.91 5.22 39.27 1.28
1209 1310 6.781857 TGAGAGGAGGGAGTACTCATAATA 57.218 41.667 23.91 0.00 39.27 0.98
1210 1311 5.671463 TGAGAGGAGGGAGTACTCATAAT 57.329 43.478 23.91 6.64 39.27 1.28
1259 1361 4.004314 ACCATCTCTATACATCCGACTCG 58.996 47.826 0.00 0.00 0.00 4.18
1262 1364 8.399425 CACTATAACCATCTCTATACATCCGAC 58.601 40.741 0.00 0.00 0.00 4.79
1347 1869 9.793252 GTACGTAGTCCATAGTGAAATCTTTTA 57.207 33.333 0.00 0.00 43.93 1.52
1348 1870 7.487189 CGTACGTAGTCCATAGTGAAATCTTTT 59.513 37.037 7.22 0.00 43.93 2.27
1349 1871 6.971184 CGTACGTAGTCCATAGTGAAATCTTT 59.029 38.462 7.22 0.00 43.93 2.52
1350 1872 6.459298 CCGTACGTAGTCCATAGTGAAATCTT 60.459 42.308 15.21 0.00 43.93 2.40
1351 1873 5.008415 CCGTACGTAGTCCATAGTGAAATCT 59.992 44.000 15.21 0.00 43.93 2.40
1352 1874 5.008019 TCCGTACGTAGTCCATAGTGAAATC 59.992 44.000 15.21 0.00 43.93 2.17
1353 1875 4.883585 TCCGTACGTAGTCCATAGTGAAAT 59.116 41.667 15.21 0.00 43.93 2.17
1357 1879 2.032204 GCTCCGTACGTAGTCCATAGTG 60.032 54.545 15.21 0.00 43.93 2.74
1360 1882 2.330440 TGCTCCGTACGTAGTCCATA 57.670 50.000 15.21 0.00 43.93 2.74
1361 1883 1.466856 TTGCTCCGTACGTAGTCCAT 58.533 50.000 15.21 0.00 43.93 3.41
1362 1884 1.246649 TTTGCTCCGTACGTAGTCCA 58.753 50.000 15.21 0.00 43.93 4.02
1363 1885 2.352503 TTTTGCTCCGTACGTAGTCC 57.647 50.000 15.21 0.00 43.93 3.85
1364 1886 3.504863 TCATTTTGCTCCGTACGTAGTC 58.495 45.455 15.21 5.03 43.93 2.59
1368 1890 2.450609 ACTCATTTTGCTCCGTACGT 57.549 45.000 15.21 0.00 0.00 3.57
1369 1891 4.435121 GGTTAACTCATTTTGCTCCGTACG 60.435 45.833 8.69 8.69 0.00 3.67
1372 1894 3.751518 AGGTTAACTCATTTTGCTCCGT 58.248 40.909 5.42 0.00 0.00 4.69
1373 1895 6.761714 AGTATAGGTTAACTCATTTTGCTCCG 59.238 38.462 5.42 0.00 0.00 4.63
1382 1904 8.142551 CGCCTTTTAGAGTATAGGTTAACTCAT 58.857 37.037 5.42 1.96 43.74 2.90
1383 1905 7.123247 ACGCCTTTTAGAGTATAGGTTAACTCA 59.877 37.037 5.42 0.00 43.74 3.41
1384 1906 7.487484 ACGCCTTTTAGAGTATAGGTTAACTC 58.513 38.462 5.42 0.00 42.02 3.01
1388 1910 8.930846 ATAGACGCCTTTTAGAGTATAGGTTA 57.069 34.615 0.00 0.00 0.00 2.85
1389 1911 7.836479 ATAGACGCCTTTTAGAGTATAGGTT 57.164 36.000 0.00 0.00 0.00 3.50
1396 1918 7.450634 TGGATGTATATAGACGCCTTTTAGAGT 59.549 37.037 9.68 0.00 0.00 3.24
1397 1919 7.827701 TGGATGTATATAGACGCCTTTTAGAG 58.172 38.462 9.68 0.00 0.00 2.43
1398 1920 7.770366 TGGATGTATATAGACGCCTTTTAGA 57.230 36.000 9.68 0.00 0.00 2.10
1399 1921 8.827177 TTTGGATGTATATAGACGCCTTTTAG 57.173 34.615 9.68 0.00 0.00 1.85
1400 1922 9.214957 CATTTGGATGTATATAGACGCCTTTTA 57.785 33.333 9.68 0.00 0.00 1.52
1401 1923 7.719633 ACATTTGGATGTATATAGACGCCTTTT 59.280 33.333 9.68 0.00 44.51 2.27
1402 1924 7.224297 ACATTTGGATGTATATAGACGCCTTT 58.776 34.615 9.68 0.00 44.51 3.11
1405 1927 7.321153 ACTACATTTGGATGTATATAGACGCC 58.679 38.462 0.23 3.08 45.20 5.68
1406 1928 8.244802 AGACTACATTTGGATGTATATAGACGC 58.755 37.037 0.23 0.00 45.20 5.19
1452 1974 9.780186 CTCCCTTCGTTCCTAAATATAAATCTT 57.220 33.333 0.00 0.00 0.00 2.40
1453 1975 8.935741 ACTCCCTTCGTTCCTAAATATAAATCT 58.064 33.333 0.00 0.00 0.00 2.40
1456 1978 9.205513 ACTACTCCCTTCGTTCCTAAATATAAA 57.794 33.333 0.00 0.00 0.00 1.40
1457 1979 8.773033 ACTACTCCCTTCGTTCCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
1458 1980 8.773033 AACTACTCCCTTCGTTCCTAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
1459 1981 7.343833 TGAACTACTCCCTTCGTTCCTAAATAT 59.656 37.037 0.00 0.00 35.97 1.28
1460 1982 6.664816 TGAACTACTCCCTTCGTTCCTAAATA 59.335 38.462 0.00 0.00 35.97 1.40
1461 1983 5.482878 TGAACTACTCCCTTCGTTCCTAAAT 59.517 40.000 0.00 0.00 35.97 1.40
1462 1984 4.834496 TGAACTACTCCCTTCGTTCCTAAA 59.166 41.667 0.00 0.00 35.97 1.85
1463 1985 4.410099 TGAACTACTCCCTTCGTTCCTAA 58.590 43.478 0.00 0.00 35.97 2.69
1464 1986 4.038271 TGAACTACTCCCTTCGTTCCTA 57.962 45.455 0.00 0.00 35.97 2.94
1465 1987 2.885616 TGAACTACTCCCTTCGTTCCT 58.114 47.619 0.00 0.00 35.97 3.36
1466 1988 3.889520 ATGAACTACTCCCTTCGTTCC 57.110 47.619 0.00 0.00 35.97 3.62
1467 1989 8.937634 TTTAATATGAACTACTCCCTTCGTTC 57.062 34.615 0.00 0.00 37.02 3.95
1468 1990 9.901172 ATTTTAATATGAACTACTCCCTTCGTT 57.099 29.630 0.00 0.00 0.00 3.85
1473 1995 9.232882 TGGGTATTTTAATATGAACTACTCCCT 57.767 33.333 0.00 0.00 0.00 4.20
1474 1996 9.856162 TTGGGTATTTTAATATGAACTACTCCC 57.144 33.333 0.00 0.00 0.00 4.30
1515 2037 8.461854 TCCTAATATACTACTCCCTCCATTTCA 58.538 37.037 0.00 0.00 0.00 2.69
1536 2058 7.285566 AGAACTGGATATGTACGTACTCCTAA 58.714 38.462 25.12 6.22 0.00 2.69
1537 2059 6.835174 AGAACTGGATATGTACGTACTCCTA 58.165 40.000 25.12 14.51 0.00 2.94
1538 2060 5.692928 AGAACTGGATATGTACGTACTCCT 58.307 41.667 25.12 12.94 0.00 3.69
1539 2061 6.484643 TGTAGAACTGGATATGTACGTACTCC 59.515 42.308 25.12 22.41 0.00 3.85
1540 2062 7.226325 AGTGTAGAACTGGATATGTACGTACTC 59.774 40.741 25.12 14.83 37.88 2.59
1541 2063 7.052873 AGTGTAGAACTGGATATGTACGTACT 58.947 38.462 25.12 13.70 37.88 2.73
1542 2064 7.256756 AGTGTAGAACTGGATATGTACGTAC 57.743 40.000 18.90 18.90 37.88 3.67
1543 2065 7.772292 AGAAGTGTAGAACTGGATATGTACGTA 59.228 37.037 0.00 0.00 39.81 3.57
1544 2066 6.602406 AGAAGTGTAGAACTGGATATGTACGT 59.398 38.462 0.00 0.00 39.81 3.57
1545 2067 6.913132 CAGAAGTGTAGAACTGGATATGTACG 59.087 42.308 0.00 0.00 39.81 3.67
1546 2068 7.997482 TCAGAAGTGTAGAACTGGATATGTAC 58.003 38.462 0.00 0.00 39.81 2.90
1547 2069 8.589701 TTCAGAAGTGTAGAACTGGATATGTA 57.410 34.615 0.00 0.00 39.81 2.29
1548 2070 7.482169 TTCAGAAGTGTAGAACTGGATATGT 57.518 36.000 0.00 0.00 39.81 2.29
1549 2071 8.954950 AATTCAGAAGTGTAGAACTGGATATG 57.045 34.615 0.00 0.00 39.81 1.78
1550 2072 9.388506 CAAATTCAGAAGTGTAGAACTGGATAT 57.611 33.333 0.00 0.00 39.81 1.63
1551 2073 8.593679 TCAAATTCAGAAGTGTAGAACTGGATA 58.406 33.333 0.00 0.00 39.81 2.59
1559 2098 5.700832 ACGCATTCAAATTCAGAAGTGTAGA 59.299 36.000 0.00 0.00 0.00 2.59
1582 2121 4.123276 TGTTGCAAAAAGACGATCGTAC 57.877 40.909 22.79 14.56 0.00 3.67
1642 2181 2.311294 GCCACGCGAAGAATGCTAT 58.689 52.632 15.93 0.00 0.00 2.97
1824 2371 1.835494 AGACGTCGATTCCTGGAAGA 58.165 50.000 15.34 4.81 34.07 2.87
1974 2565 2.319844 TGGATCATCGCCTCATAGTGT 58.680 47.619 0.00 0.00 0.00 3.55
1996 2587 3.737266 CACAAAGCAGCGAAATGAACAAT 59.263 39.130 0.00 0.00 0.00 2.71
2000 2591 1.000385 CCCACAAAGCAGCGAAATGAA 60.000 47.619 0.00 0.00 0.00 2.57
2168 2759 8.437575 GGATGGTTGTAGAAAGGGAATCTATTA 58.562 37.037 0.00 0.00 32.37 0.98
2518 3181 9.379770 TCTAAGTAGATGTGATTATCCATTGGA 57.620 33.333 8.08 8.08 35.55 3.53
2551 3214 6.037062 GCCTTGCTGTTTTTGTTATTTCACTT 59.963 34.615 0.00 0.00 0.00 3.16
2558 3221 4.236935 CATCGCCTTGCTGTTTTTGTTAT 58.763 39.130 0.00 0.00 0.00 1.89
2899 3562 5.633830 AATGAGAAGAAAACGATGCATGT 57.366 34.783 2.46 0.00 0.00 3.21
2908 3571 6.808704 GCAATGGAGGTAAATGAGAAGAAAAC 59.191 38.462 0.00 0.00 0.00 2.43
2932 3597 8.188531 ACAAGTATAAAACATCATGCATTTGC 57.811 30.769 0.00 0.00 42.50 3.68
3053 3759 3.831323 TGGACCAAAACAGATCACACAT 58.169 40.909 0.00 0.00 0.00 3.21
3068 3774 6.138967 TCTATTGATCTTCAGAGATGGACCA 58.861 40.000 0.00 0.00 42.66 4.02
3072 3778 9.557061 TCAAAATCTATTGATCTTCAGAGATGG 57.443 33.333 0.00 0.00 42.66 3.51
3109 3815 4.796606 ACCAGCAGGCATTCATAACTATT 58.203 39.130 0.00 0.00 39.06 1.73
3116 4243 3.370840 TCTTAACCAGCAGGCATTCAT 57.629 42.857 0.00 0.00 39.06 2.57
3117 4244 2.877097 TCTTAACCAGCAGGCATTCA 57.123 45.000 0.00 0.00 39.06 2.57
3118 4245 4.823989 ACATATCTTAACCAGCAGGCATTC 59.176 41.667 0.00 0.00 39.06 2.67
3119 4246 4.796606 ACATATCTTAACCAGCAGGCATT 58.203 39.130 0.00 0.00 39.06 3.56
3120 4247 4.443978 ACATATCTTAACCAGCAGGCAT 57.556 40.909 0.00 0.00 39.06 4.40
3121 4248 3.931907 ACATATCTTAACCAGCAGGCA 57.068 42.857 0.00 0.00 39.06 4.75
3122 4249 5.239525 CCTAAACATATCTTAACCAGCAGGC 59.760 44.000 0.00 0.00 39.06 4.85
3123 4250 6.357367 ACCTAAACATATCTTAACCAGCAGG 58.643 40.000 0.00 0.00 42.21 4.85
3124 4251 7.985184 TGTACCTAAACATATCTTAACCAGCAG 59.015 37.037 0.00 0.00 0.00 4.24
3125 4252 7.853299 TGTACCTAAACATATCTTAACCAGCA 58.147 34.615 0.00 0.00 0.00 4.41
3126 4253 8.726870 TTGTACCTAAACATATCTTAACCAGC 57.273 34.615 0.00 0.00 0.00 4.85
3127 4254 9.886132 ACTTGTACCTAAACATATCTTAACCAG 57.114 33.333 0.00 0.00 0.00 4.00
3218 4378 8.648693 GTCATAGTTGTCCCTAAACATACCTAT 58.351 37.037 0.00 0.00 0.00 2.57
3326 4514 6.993079 ACCATCTATAAACAGATCGTATGCA 58.007 36.000 0.00 0.00 32.83 3.96
3424 4615 2.293399 GGGACACCTTGCTTGTTACAAG 59.707 50.000 19.66 19.66 43.36 3.16
3442 4633 0.833287 GCTCTGGCACTAATGAGGGA 59.167 55.000 3.29 0.00 38.54 4.20
3456 4647 7.633621 TCGCAAGATTAAAAGATAATGCTCTG 58.366 34.615 0.00 0.00 45.01 3.35
3539 4731 9.590451 AGAAAAATGTTGTCTAATATGCAATGG 57.410 29.630 0.00 0.00 0.00 3.16
3563 4755 4.038042 CCTTTAGAGATGTATCGGTGCAGA 59.962 45.833 0.00 0.00 0.00 4.26
3711 4906 2.611971 GGTGTATCTGCAACTCAACGGA 60.612 50.000 0.00 0.00 0.00 4.69
3715 4910 2.805671 CGTTGGTGTATCTGCAACTCAA 59.194 45.455 0.00 0.00 0.00 3.02
3716 4911 2.036604 TCGTTGGTGTATCTGCAACTCA 59.963 45.455 0.00 0.00 0.00 3.41
3717 4912 2.683968 TCGTTGGTGTATCTGCAACTC 58.316 47.619 0.00 0.00 0.00 3.01
3718 4913 2.831685 TCGTTGGTGTATCTGCAACT 57.168 45.000 0.00 0.00 0.00 3.16
3719 4914 3.889196 TTTCGTTGGTGTATCTGCAAC 57.111 42.857 0.00 0.00 0.00 4.17
3720 4915 6.017026 TGTTAATTTCGTTGGTGTATCTGCAA 60.017 34.615 0.00 0.00 0.00 4.08
3760 4960 4.036498 AGCATACGACAACTAATCTAGCGT 59.964 41.667 0.00 0.00 0.00 5.07
3808 5010 3.768757 CCAATCACAAAATGGCTAAGGGA 59.231 43.478 0.00 0.00 0.00 4.20
3869 5101 1.266718 GCAACAATCGTGCAAGAAGGA 59.733 47.619 6.39 0.00 0.00 3.36
3871 5103 2.693797 AGCAACAATCGTGCAAGAAG 57.306 45.000 6.39 5.20 0.00 2.85
3872 5104 2.730069 CAAGCAACAATCGTGCAAGAA 58.270 42.857 6.39 0.00 0.00 2.52
3873 5105 1.600164 GCAAGCAACAATCGTGCAAGA 60.600 47.619 4.40 4.40 38.49 3.02
3880 5112 6.074729 CCAAATGTATATGCAAGCAACAATCG 60.075 38.462 0.00 0.00 0.00 3.34
3925 5157 9.716531 CTTCAGGATATGCTTGTGATCTATTTA 57.283 33.333 0.00 0.00 0.00 1.40
3931 5174 3.186001 CGCTTCAGGATATGCTTGTGATC 59.814 47.826 0.00 0.00 0.00 2.92
3934 5177 2.283298 ACGCTTCAGGATATGCTTGTG 58.717 47.619 0.00 0.00 0.00 3.33
3942 5185 3.793797 TGATTCGAACGCTTCAGGATA 57.206 42.857 0.00 0.00 0.00 2.59
3948 5191 5.795766 TCAATTACATGATTCGAACGCTTC 58.204 37.500 0.00 0.00 0.00 3.86
3953 5196 6.064846 AGGCATCAATTACATGATTCGAAC 57.935 37.500 0.00 0.00 37.96 3.95
4054 5593 9.338291 GACAATTAGTGCTATCGACGATTTATA 57.662 33.333 16.73 0.00 0.00 0.98
4058 5597 5.833082 AGACAATTAGTGCTATCGACGATT 58.167 37.500 16.73 0.00 0.00 3.34
4187 6687 2.770164 AAATTGCTAGCTGACGGTCT 57.230 45.000 17.23 0.00 0.00 3.85
4311 6812 6.183360 TGCTTAAGTCAATTGGATTGTTGGTT 60.183 34.615 5.42 0.00 41.02 3.67
4332 6833 2.351726 GAGTCTTGTGTCAACGTTGCTT 59.648 45.455 23.47 0.84 0.00 3.91
4398 6899 1.243902 CGCCTGCCTTCTTTTGGTTA 58.756 50.000 0.00 0.00 0.00 2.85
4797 7298 2.270352 TTGAGTTCAGGAATGGCGTT 57.730 45.000 0.00 0.00 0.00 4.84
4875 7376 2.126882 AGGGTGGCTATGTCATTGCTA 58.873 47.619 17.01 9.83 0.00 3.49
4885 7386 1.202855 GCATGTCATCAGGGTGGCTAT 60.203 52.381 0.00 0.00 0.00 2.97
4906 7407 4.099573 CCATGAACTACCGTCCTCATAAGT 59.900 45.833 0.00 0.00 0.00 2.24
4911 7412 1.191535 CCCATGAACTACCGTCCTCA 58.808 55.000 0.00 0.00 0.00 3.86
4920 7421 1.006758 ACGTCTCTCCCCCATGAACTA 59.993 52.381 0.00 0.00 0.00 2.24
5121 7622 0.884704 GAGCGTTGCTGTGGGAGAAA 60.885 55.000 0.00 0.00 39.88 2.52
5161 7662 2.437359 GATGCGCTGCAGAGGGTT 60.437 61.111 20.43 0.00 43.65 4.11
5205 7706 1.134401 AGGATGAACATCGTGGCGATT 60.134 47.619 8.81 0.00 44.59 3.34
5229 7730 1.568504 TCACCGGGAAGAAGCTGTAT 58.431 50.000 6.32 0.00 0.00 2.29
5318 7819 1.860326 CGTGCATCATCGCTATGACAA 59.140 47.619 2.58 0.00 44.79 3.18
5883 8408 9.956640 AATGCAAATAAAATAAAAGATGGGTCA 57.043 25.926 0.00 0.00 0.00 4.02
5942 8470 1.279271 ACAGGCTCCGAGCACTAAAAT 59.721 47.619 21.76 0.00 44.75 1.82
6059 8588 3.071874 TCAAAGAGAAATGCCACCGAT 57.928 42.857 0.00 0.00 0.00 4.18
6061 8590 3.012518 AGATCAAAGAGAAATGCCACCG 58.987 45.455 0.00 0.00 0.00 4.94
6072 8601 7.284034 AGGTAAATGCCATGTTAGATCAAAGAG 59.716 37.037 0.00 0.00 0.00 2.85
6113 8642 7.225931 AGCTGACTTGTTAACTTATTTCAACGA 59.774 33.333 7.22 0.00 0.00 3.85
6135 8664 4.861389 TTTTGTCATTTTTGTGCAGCTG 57.139 36.364 10.11 10.11 0.00 4.24
6193 8729 9.357652 CAAAATCGGTGATTTTCTACAATGAAT 57.642 29.630 13.09 0.00 45.45 2.57
6234 8798 0.638746 CGTTAACAAGCGAGCTACGG 59.361 55.000 6.39 0.82 42.83 4.02
6235 8799 1.334054 ACGTTAACAAGCGAGCTACG 58.666 50.000 13.61 13.61 45.66 3.51
6243 8807 5.352643 AGTGGTGAAATACGTTAACAAGC 57.647 39.130 6.39 0.00 0.00 4.01
6250 8814 8.838365 TGTACAATTTAAGTGGTGAAATACGTT 58.162 29.630 0.00 0.00 0.00 3.99
6251 8815 8.284693 GTGTACAATTTAAGTGGTGAAATACGT 58.715 33.333 0.00 0.00 0.00 3.57
6252 8816 8.283992 TGTGTACAATTTAAGTGGTGAAATACG 58.716 33.333 0.00 0.00 0.00 3.06
6507 9307 6.719829 TGTTGAGAGAATTAGGTGTAGTGAGA 59.280 38.462 0.00 0.00 0.00 3.27
6599 9399 6.865205 GCGTCCTACATACCGATTAATAACTT 59.135 38.462 0.00 0.00 0.00 2.66
6632 9432 0.473117 ACTCTTCGGTTGGGAAGGGA 60.473 55.000 9.03 0.00 45.49 4.20
6634 9434 0.036294 GGACTCTTCGGTTGGGAAGG 60.036 60.000 2.81 0.00 42.88 3.46


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

AutoCloner maintained by Alex Coulton.