Multiple sequence alignment - TraesCS1A01G295400

Loading Multiple Alignment...

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 TraesCS1A01G295400 chr1A 100.000 1804 0 0 716 2519 490417959 490419762 0.000000e+00 3332
1 TraesCS1A01G295400 chr1A 85.878 1225 109 40 789 1992 62794771 62793590 0.000000e+00 1245
2 TraesCS1A01G295400 chr1A 87.399 992 75 20 768 1732 490759741 490760709 0.000000e+00 1094
3 TraesCS1A01G295400 chr1A 92.832 558 38 2 841 1398 487568496 487569051 0.000000e+00 808
4 TraesCS1A01G295400 chr1A 100.000 371 0 0 1 371 490417244 490417614 0.000000e+00 686
5 TraesCS1A01G295400 chr1A 92.121 330 22 2 2192 2519 490778344 490778671 1.770000e-126 462
6 TraesCS1A01G295400 chr1A 90.909 341 28 2 1 339 490759354 490759693 2.950000e-124 455
7 TraesCS1A01G295400 chr1A 88.953 344 26 5 2180 2519 62793606 62793271 5.010000e-112 414
8 TraesCS1A01G295400 chr1A 87.712 236 22 6 1726 1959 490777846 490778076 4.130000e-68 268
9 TraesCS1A01G295400 chr1B 86.574 1147 99 34 859 1992 104481696 104480592 0.000000e+00 1214
10 TraesCS1A01G295400 chr1B 86.501 1126 100 27 749 1841 527287966 527289072 0.000000e+00 1190
11 TraesCS1A01G295400 chr1B 91.182 567 41 6 841 1406 521352209 521352767 0.000000e+00 761
12 TraesCS1A01G295400 chr1B 87.356 609 62 11 866 1471 608335832 608335236 0.000000e+00 684
13 TraesCS1A01G295400 chr1B 91.167 317 24 3 2204 2517 527289882 527290197 6.440000e-116 427
14 TraesCS1A01G295400 chr1B 86.047 344 25 6 2180 2519 104480608 104480284 5.160000e-92 348
15 TraesCS1A01G295400 chr1B 96.825 189 6 0 1992 2180 110622812 110623000 1.450000e-82 316
16 TraesCS1A01G295400 chr1D 86.927 1048 95 23 859 1894 63682289 63681272 0.000000e+00 1138
17 TraesCS1A01G295400 chr1D 90.619 565 51 2 841 1405 388024381 388024943 0.000000e+00 749
18 TraesCS1A01G295400 chr1D 89.394 198 15 5 1775 1970 394490469 394490276 6.960000e-61 244
19 TraesCS1A01G295400 chr1D 90.076 131 13 0 2389 2519 394490181 394490051 1.200000e-38 171
20 TraesCS1A01G295400 chr6B 85.580 1061 80 30 787 1808 679983726 679982700 0.000000e+00 1044
21 TraesCS1A01G295400 chr6B 85.404 322 39 6 24 342 679984117 679983801 6.720000e-86 327
22 TraesCS1A01G295400 chr6B 96.809 188 6 0 1992 2179 475722681 475722868 5.230000e-82 315
23 TraesCS1A01G295400 chr6B 87.200 125 4 6 1879 1992 679982685 679982562 5.650000e-27 132
24 TraesCS1A01G295400 chr3A 96.392 194 7 0 1991 2184 642038941 642038748 1.120000e-83 320
25 TraesCS1A01G295400 chr7A 96.354 192 7 0 1991 2182 105168996 105168805 1.450000e-82 316
26 TraesCS1A01G295400 chr5A 96.809 188 6 0 1993 2180 219371603 219371790 5.230000e-82 315
27 TraesCS1A01G295400 chr4A 96.809 188 6 0 1993 2180 20234536 20234723 5.230000e-82 315
28 TraesCS1A01G295400 chr2B 96.335 191 7 0 1990 2180 409336568 409336378 5.230000e-82 315
29 TraesCS1A01G295400 chr6A 96.791 187 6 0 1994 2180 7980290 7980476 1.880000e-81 313
30 TraesCS1A01G295400 chr7B 94.554 202 7 3 1991 2189 68862024 68862224 2.430000e-80 309


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 TraesCS1A01G295400 chr1A 490417244 490419762 2518 False 2009.0 3332 100.000000 1 2519 2 chr1A.!!$F2 2518
1 TraesCS1A01G295400 chr1A 62793271 62794771 1500 True 829.5 1245 87.415500 789 2519 2 chr1A.!!$R1 1730
2 TraesCS1A01G295400 chr1A 487568496 487569051 555 False 808.0 808 92.832000 841 1398 1 chr1A.!!$F1 557
3 TraesCS1A01G295400 chr1A 490759354 490760709 1355 False 774.5 1094 89.154000 1 1732 2 chr1A.!!$F3 1731
4 TraesCS1A01G295400 chr1A 490777846 490778671 825 False 365.0 462 89.916500 1726 2519 2 chr1A.!!$F4 793
5 TraesCS1A01G295400 chr1B 527287966 527290197 2231 False 808.5 1190 88.834000 749 2517 2 chr1B.!!$F3 1768
6 TraesCS1A01G295400 chr1B 104480284 104481696 1412 True 781.0 1214 86.310500 859 2519 2 chr1B.!!$R2 1660
7 TraesCS1A01G295400 chr1B 521352209 521352767 558 False 761.0 761 91.182000 841 1406 1 chr1B.!!$F2 565
8 TraesCS1A01G295400 chr1B 608335236 608335832 596 True 684.0 684 87.356000 866 1471 1 chr1B.!!$R1 605
9 TraesCS1A01G295400 chr1D 63681272 63682289 1017 True 1138.0 1138 86.927000 859 1894 1 chr1D.!!$R1 1035
10 TraesCS1A01G295400 chr1D 388024381 388024943 562 False 749.0 749 90.619000 841 1405 1 chr1D.!!$F1 564
11 TraesCS1A01G295400 chr6B 679982562 679984117 1555 True 501.0 1044 86.061333 24 1992 3 chr6B.!!$R1 1968


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
782 787 0.036765 TTCCTAGTTCGCGCCATTGT 60.037 50.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2472 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.0 0.0 0.0 0.0 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
34 35 3.628487 TCGTTCGGTTTGTTTCAAATCCT 59.372 39.130 0.00 0.00 0.00 3.24
35 36 4.815308 TCGTTCGGTTTGTTTCAAATCCTA 59.185 37.500 0.00 0.00 0.00 2.94
51 52 1.757306 CTATTGGATGGCCGGCTCT 59.243 57.895 28.56 14.25 36.79 4.09
59 60 4.615815 GGCCGGCTCTCGCATCAT 62.616 66.667 28.56 0.00 38.10 2.45
64 65 0.529337 CGGCTCTCGCATCATTGTCT 60.529 55.000 0.00 0.00 38.10 3.41
87 88 1.149987 GTGTCCGCGAACAAATACCA 58.850 50.000 8.23 0.00 0.00 3.25
91 92 3.253677 TGTCCGCGAACAAATACCATTTT 59.746 39.130 8.23 0.00 0.00 1.82
92 93 3.849708 GTCCGCGAACAAATACCATTTTC 59.150 43.478 8.23 0.00 0.00 2.29
104 107 7.868922 ACAAATACCATTTTCGTTAGGGTTTTC 59.131 33.333 0.00 0.00 33.14 2.29
133 136 5.254115 GAGTTGCCCTTAGACTTACCAAAT 58.746 41.667 0.00 0.00 0.00 2.32
185 189 3.689161 CGCTCCACCTCACAATTTTCATA 59.311 43.478 0.00 0.00 0.00 2.15
359 363 4.153958 TCTCAAAAACACACACACACAC 57.846 40.909 0.00 0.00 0.00 3.82
360 364 3.565902 TCTCAAAAACACACACACACACA 59.434 39.130 0.00 0.00 0.00 3.72
361 365 3.633235 TCAAAAACACACACACACACAC 58.367 40.909 0.00 0.00 0.00 3.82
362 366 3.066760 TCAAAAACACACACACACACACA 59.933 39.130 0.00 0.00 0.00 3.72
363 367 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
364 368 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
365 369 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
366 370 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
367 371 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
368 372 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
742 746 5.761165 ATATTTTGGTAAAATCGACGGGG 57.239 39.130 3.06 0.00 41.16 5.73
745 749 5.641330 ATTTTGGTAAAATCGACGGGGACC 61.641 45.833 0.00 0.00 40.45 4.46
782 787 0.036765 TTCCTAGTTCGCGCCATTGT 60.037 50.000 0.00 0.00 0.00 2.71
785 790 0.095245 CTAGTTCGCGCCATTGTGTG 59.905 55.000 0.00 0.00 0.00 3.82
945 992 2.096406 CATCGAACGGCAGCAACG 59.904 61.111 0.00 0.00 37.36 4.10
989 1046 1.643811 CCTTAAAATCCCCTCCCCACA 59.356 52.381 0.00 0.00 0.00 4.17
1001 1059 1.076777 CCCCACATCCGGCAAATCT 60.077 57.895 0.00 0.00 0.00 2.40
1002 1060 1.103398 CCCCACATCCGGCAAATCTC 61.103 60.000 0.00 0.00 0.00 2.75
1028 1088 0.321564 CAATTCACCACCGCTCCTCA 60.322 55.000 0.00 0.00 0.00 3.86
1038 1103 2.896443 GCTCCTCAACCTCCTCCG 59.104 66.667 0.00 0.00 0.00 4.63
1297 1363 2.503375 GACGCCGTCACCTACACG 60.503 66.667 13.23 0.00 36.99 4.49
1405 1471 4.475135 GCTCTTCCTCGCCACCCC 62.475 72.222 0.00 0.00 0.00 4.95
1406 1472 3.003173 CTCTTCCTCGCCACCCCA 61.003 66.667 0.00 0.00 0.00 4.96
1418 1488 3.402681 ACCCCACTGCAGATCCCG 61.403 66.667 23.35 5.88 0.00 5.14
1451 1521 0.662374 ACCGCGACTTGTGTAGTTCG 60.662 55.000 8.23 0.00 37.17 3.95
1455 1525 1.912110 GCGACTTGTGTAGTTCGCTAG 59.088 52.381 7.53 0.00 43.60 3.42
1490 1561 5.258456 TCGCTATTTCCTCTGTATTTCGT 57.742 39.130 0.00 0.00 0.00 3.85
1502 1573 4.796830 TCTGTATTTCGTACTGAATCGTGC 59.203 41.667 0.00 0.00 38.03 5.34
1553 1628 8.641498 AAATCAAACATGTCTCTGAAATACCT 57.359 30.769 0.00 0.00 0.00 3.08
1563 1638 6.096695 GTCTCTGAAATACCTTGTCTCTGAC 58.903 44.000 0.00 0.00 0.00 3.51
1579 1654 3.216800 TCTGACTTTGTTCTGCTGCATT 58.783 40.909 1.31 0.00 0.00 3.56
1587 1662 4.488126 TGTTCTGCTGCATTTCTGTTAC 57.512 40.909 1.31 0.00 0.00 2.50
1598 1675 7.535940 GCTGCATTTCTGTTACGTAAAATTGTA 59.464 33.333 10.11 6.65 0.00 2.41
1650 1727 2.676748 TGGGAGTTGGATTGTTTTGCT 58.323 42.857 0.00 0.00 0.00 3.91
1667 1744 5.897377 TTTGCTATTCTTTTACCAGGAGC 57.103 39.130 0.00 0.00 0.00 4.70
1679 1756 2.041265 AGGAGCCCCTGACGGATT 59.959 61.111 0.00 0.00 42.42 3.01
1681 1758 2.514824 GAGCCCCTGACGGATTGC 60.515 66.667 0.00 0.00 0.00 3.56
1683 1760 2.124151 GCCCCTGACGGATTGCAT 60.124 61.111 0.00 0.00 0.00 3.96
1692 1769 0.733566 ACGGATTGCATTTGCTTGCG 60.734 50.000 14.57 14.57 45.77 4.85
1696 1773 2.273557 GATTGCATTTGCTTGCGGAAT 58.726 42.857 3.94 0.00 45.77 3.01
1698 1775 2.565210 TGCATTTGCTTGCGGAATAG 57.435 45.000 3.94 0.00 45.77 1.73
1701 1779 3.441922 TGCATTTGCTTGCGGAATAGTTA 59.558 39.130 3.94 0.00 45.77 2.24
1705 1783 2.006888 TGCTTGCGGAATAGTTAGTGC 58.993 47.619 0.00 0.00 0.00 4.40
1712 1790 2.744823 CGGAATAGTTAGTGCATGGCCA 60.745 50.000 8.56 8.56 0.00 5.36
1727 1805 2.449464 TGGCCAAATCAGGAACATCAG 58.551 47.619 0.61 0.00 0.00 2.90
1732 1810 3.367703 CCAAATCAGGAACATCAGTTGCC 60.368 47.826 0.00 0.00 46.06 4.52
1748 1828 1.917872 TGCCCCGTTTCTGCTATTTT 58.082 45.000 0.00 0.00 0.00 1.82
1766 1846 8.901793 TGCTATTTTATCTGATGCATTTGTACA 58.098 29.630 0.00 0.00 0.00 2.90
1767 1847 9.734620 GCTATTTTATCTGATGCATTTGTACAA 57.265 29.630 3.59 3.59 0.00 2.41
1772 1852 4.018490 TCTGATGCATTTGTACAAGGCAT 58.982 39.130 32.50 32.50 42.08 4.40
1784 1864 8.929827 TTTGTACAAGGCATCATTTATGATTG 57.070 30.769 8.56 3.06 44.70 2.67
1789 1873 7.262772 ACAAGGCATCATTTATGATTGTTCTG 58.737 34.615 2.51 1.32 44.70 3.02
1812 1896 7.976175 TCTGTGTTGCAACAATGTGTTTAATTA 59.024 29.630 32.61 2.99 38.77 1.40
1815 1899 8.061268 GTGTTGCAACAATGTGTTTAATTAAGG 58.939 33.333 32.61 0.00 38.77 2.69
1834 1918 9.990868 AATTAAGGTTGGGATTAGTCTGTATTT 57.009 29.630 0.00 0.00 0.00 1.40
1835 1919 9.628500 ATTAAGGTTGGGATTAGTCTGTATTTC 57.372 33.333 0.00 0.00 0.00 2.17
1836 1920 6.636454 AGGTTGGGATTAGTCTGTATTTCA 57.364 37.500 0.00 0.00 0.00 2.69
1838 1922 8.331931 AGGTTGGGATTAGTCTGTATTTCATA 57.668 34.615 0.00 0.00 0.00 2.15
1862 1950 7.798596 ACATCGATTTCTAGATTGATTTGCT 57.201 32.000 0.00 0.00 29.52 3.91
1894 1982 3.119602 GCTCTGTGCAAATCATCATGTGT 60.120 43.478 0.00 0.00 42.31 3.72
1898 1986 4.558178 TGTGCAAATCATCATGTGTTTCC 58.442 39.130 0.00 0.00 0.00 3.13
1908 1996 7.757941 TCATCATGTGTTTCCTGTTAATCAA 57.242 32.000 0.00 0.00 0.00 2.57
1910 1998 8.805175 TCATCATGTGTTTCCTGTTAATCAAAT 58.195 29.630 0.00 0.00 0.00 2.32
1913 2001 8.081633 TCATGTGTTTCCTGTTAATCAAATGTC 58.918 33.333 0.00 0.00 30.64 3.06
1914 2002 7.340122 TGTGTTTCCTGTTAATCAAATGTCA 57.660 32.000 0.00 0.00 0.00 3.58
1916 2004 7.068103 TGTGTTTCCTGTTAATCAAATGTCACT 59.932 33.333 0.00 0.00 0.00 3.41
1974 2329 7.041576 GCAGTAATACTTCATCTGATGCATCAA 60.042 37.037 28.39 19.41 36.18 2.57
1985 2340 3.336468 TGATGCATCAAACATTTTGGCC 58.664 40.909 26.87 0.00 33.08 5.36
1986 2341 1.793258 TGCATCAAACATTTTGGCCG 58.207 45.000 0.00 0.00 0.00 6.13
1987 2342 1.069823 TGCATCAAACATTTTGGCCGT 59.930 42.857 0.00 0.00 0.00 5.68
1988 2343 1.460359 GCATCAAACATTTTGGCCGTG 59.540 47.619 0.00 0.00 0.00 4.94
1989 2344 2.067766 CATCAAACATTTTGGCCGTGG 58.932 47.619 0.00 0.00 0.00 4.94
1990 2345 0.249657 TCAAACATTTTGGCCGTGGC 60.250 50.000 1.16 1.16 41.06 5.01
1991 2346 0.531532 CAAACATTTTGGCCGTGGCA 60.532 50.000 13.76 0.00 44.11 4.92
1992 2347 0.179000 AAACATTTTGGCCGTGGCAA 59.821 45.000 13.76 4.81 46.03 4.52
2018 2373 3.078836 GGCAGCCCCAATGCATGT 61.079 61.111 0.00 0.00 45.68 3.21
2019 2374 1.757731 GGCAGCCCCAATGCATGTA 60.758 57.895 0.00 0.00 45.68 2.29
2020 2375 1.737816 GCAGCCCCAATGCATGTAG 59.262 57.895 0.00 0.00 43.31 2.74
2021 2376 1.737816 CAGCCCCAATGCATGTAGC 59.262 57.895 0.00 1.14 45.96 3.58
2022 2377 0.754217 CAGCCCCAATGCATGTAGCT 60.754 55.000 0.00 3.80 45.94 3.32
2023 2378 0.466922 AGCCCCAATGCATGTAGCTC 60.467 55.000 0.00 0.00 45.94 4.09
2024 2379 1.458639 GCCCCAATGCATGTAGCTCC 61.459 60.000 0.00 0.00 45.94 4.70
2025 2380 0.825010 CCCCAATGCATGTAGCTCCC 60.825 60.000 0.00 0.00 45.94 4.30
2026 2381 1.168407 CCCAATGCATGTAGCTCCCG 61.168 60.000 0.00 0.00 45.94 5.14
2027 2382 1.650912 CAATGCATGTAGCTCCCGC 59.349 57.895 0.00 0.00 45.94 6.13
2029 2384 0.107017 AATGCATGTAGCTCCCGCTT 60.107 50.000 0.00 0.00 46.47 4.68
2030 2385 0.816825 ATGCATGTAGCTCCCGCTTG 60.817 55.000 0.00 0.00 46.47 4.01
2031 2386 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2032 2387 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2035 2390 4.386951 TAGCTCCCGCTTGCGCAA 62.387 61.111 23.48 23.48 46.47 4.85
2041 2396 2.434185 CCGCTTGCGCAAGGTCTA 60.434 61.111 41.83 14.50 38.80 2.59
2042 2397 2.456119 CCGCTTGCGCAAGGTCTAG 61.456 63.158 41.83 23.74 38.80 2.43
2043 2398 2.456119 CGCTTGCGCAAGGTCTAGG 61.456 63.158 41.83 22.68 38.80 3.02
2044 2399 1.376037 GCTTGCGCAAGGTCTAGGT 60.376 57.895 41.83 0.00 38.80 3.08
2045 2400 0.108329 GCTTGCGCAAGGTCTAGGTA 60.108 55.000 41.83 11.45 38.80 3.08
2046 2401 1.674817 GCTTGCGCAAGGTCTAGGTAA 60.675 52.381 41.83 10.91 38.80 2.85
2047 2402 2.271800 CTTGCGCAAGGTCTAGGTAAG 58.728 52.381 36.86 12.36 34.87 2.34
2048 2403 0.535335 TGCGCAAGGTCTAGGTAAGG 59.465 55.000 8.16 0.00 38.28 2.69
2049 2404 0.179081 GCGCAAGGTCTAGGTAAGGG 60.179 60.000 0.30 0.00 38.28 3.95
2050 2405 1.192428 CGCAAGGTCTAGGTAAGGGT 58.808 55.000 0.00 0.00 0.00 4.34
2051 2406 1.136500 CGCAAGGTCTAGGTAAGGGTC 59.864 57.143 0.00 0.00 0.00 4.46
2052 2407 1.485480 GCAAGGTCTAGGTAAGGGTCC 59.515 57.143 0.00 0.00 0.00 4.46
2053 2408 1.755380 CAAGGTCTAGGTAAGGGTCCG 59.245 57.143 0.00 0.00 0.00 4.79
2054 2409 1.302907 AGGTCTAGGTAAGGGTCCGA 58.697 55.000 0.00 0.00 0.00 4.55
2055 2410 1.064091 AGGTCTAGGTAAGGGTCCGAC 60.064 57.143 0.00 0.00 0.00 4.79
2056 2411 1.397672 GTCTAGGTAAGGGTCCGACC 58.602 60.000 9.30 9.30 37.60 4.79
2057 2412 1.002069 TCTAGGTAAGGGTCCGACCA 58.998 55.000 19.43 0.00 41.02 4.02
2058 2413 1.109609 CTAGGTAAGGGTCCGACCAC 58.890 60.000 19.43 8.76 41.02 4.16
2059 2414 0.706433 TAGGTAAGGGTCCGACCACT 59.294 55.000 19.43 10.80 41.02 4.00
2060 2415 0.178912 AGGTAAGGGTCCGACCACTT 60.179 55.000 19.43 19.32 41.02 3.16
2061 2416 0.689055 GGTAAGGGTCCGACCACTTT 59.311 55.000 19.43 12.03 41.02 2.66
2062 2417 1.609841 GGTAAGGGTCCGACCACTTTG 60.610 57.143 19.43 0.00 41.02 2.77
2063 2418 0.688487 TAAGGGTCCGACCACTTTGG 59.312 55.000 19.43 0.00 41.02 3.28
2064 2419 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2065 2420 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2076 2431 4.270008 ACCACTTTGGGTCTATTGTATGC 58.730 43.478 0.00 0.00 43.37 3.14
2077 2432 4.263727 ACCACTTTGGGTCTATTGTATGCA 60.264 41.667 0.00 0.00 43.37 3.96
2078 2433 4.336433 CCACTTTGGGTCTATTGTATGCAG 59.664 45.833 0.00 0.00 32.67 4.41
2079 2434 3.947834 ACTTTGGGTCTATTGTATGCAGC 59.052 43.478 0.00 0.00 0.00 5.25
2080 2435 2.638480 TGGGTCTATTGTATGCAGCC 57.362 50.000 0.00 0.00 0.00 4.85
2081 2436 2.126882 TGGGTCTATTGTATGCAGCCT 58.873 47.619 0.00 0.00 0.00 4.58
2082 2437 2.509548 TGGGTCTATTGTATGCAGCCTT 59.490 45.455 0.00 0.00 0.00 4.35
2083 2438 3.053693 TGGGTCTATTGTATGCAGCCTTT 60.054 43.478 0.00 0.00 0.00 3.11
2084 2439 3.565902 GGGTCTATTGTATGCAGCCTTTC 59.434 47.826 0.00 0.00 0.00 2.62
2085 2440 3.565902 GGTCTATTGTATGCAGCCTTTCC 59.434 47.826 0.00 0.00 0.00 3.13
2086 2441 3.565902 GTCTATTGTATGCAGCCTTTCCC 59.434 47.826 0.00 0.00 0.00 3.97
2087 2442 2.834638 ATTGTATGCAGCCTTTCCCT 57.165 45.000 0.00 0.00 0.00 4.20
2088 2443 3.951563 ATTGTATGCAGCCTTTCCCTA 57.048 42.857 0.00 0.00 0.00 3.53
2089 2444 2.710096 TGTATGCAGCCTTTCCCTAC 57.290 50.000 0.00 0.00 0.00 3.18
2090 2445 1.912731 TGTATGCAGCCTTTCCCTACA 59.087 47.619 0.00 0.00 0.00 2.74
2091 2446 2.509548 TGTATGCAGCCTTTCCCTACAT 59.490 45.455 0.00 0.00 0.00 2.29
2092 2447 2.834638 ATGCAGCCTTTCCCTACATT 57.165 45.000 0.00 0.00 0.00 2.71
2093 2448 2.603075 TGCAGCCTTTCCCTACATTT 57.397 45.000 0.00 0.00 0.00 2.32
2094 2449 2.446435 TGCAGCCTTTCCCTACATTTC 58.554 47.619 0.00 0.00 0.00 2.17
2095 2450 2.041620 TGCAGCCTTTCCCTACATTTCT 59.958 45.455 0.00 0.00 0.00 2.52
2096 2451 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2097 2452 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
2098 2453 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
2099 2454 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
2100 2455 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
2101 2456 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
2111 2466 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
2112 2467 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
2113 2468 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
2114 2469 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
2115 2470 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
2116 2471 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
2117 2472 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
2118 2473 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2119 2474 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2120 2475 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2121 2476 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2122 2477 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2123 2478 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2124 2479 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2125 2480 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2126 2481 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2127 2482 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2128 2483 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2129 2484 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2130 2485 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2131 2486 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2132 2487 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2133 2488 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2134 2489 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2135 2490 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2146 2501 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2147 2502 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2148 2503 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2149 2504 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2150 2505 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2151 2506 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2152 2507 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2153 2508 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2154 2509 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2155 2510 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2156 2511 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2157 2512 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2158 2513 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2159 2514 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2160 2515 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2161 2516 0.984230 AGGCAGCAGCTTTACCACTA 59.016 50.000 0.00 0.00 41.70 2.74
2162 2517 1.087501 GGCAGCAGCTTTACCACTAC 58.912 55.000 0.00 0.00 41.70 2.73
2163 2518 0.721718 GCAGCAGCTTTACCACTACG 59.278 55.000 0.00 0.00 37.91 3.51
2164 2519 0.721718 CAGCAGCTTTACCACTACGC 59.278 55.000 0.00 0.00 0.00 4.42
2165 2520 0.391263 AGCAGCTTTACCACTACGCC 60.391 55.000 0.00 0.00 0.00 5.68
2166 2521 0.672401 GCAGCTTTACCACTACGCCA 60.672 55.000 0.00 0.00 0.00 5.69
2167 2522 1.803334 CAGCTTTACCACTACGCCAA 58.197 50.000 0.00 0.00 0.00 4.52
2168 2523 1.732259 CAGCTTTACCACTACGCCAAG 59.268 52.381 0.00 0.00 0.00 3.61
2169 2524 1.084289 GCTTTACCACTACGCCAAGG 58.916 55.000 0.00 0.00 0.00 3.61
2170 2525 1.084289 CTTTACCACTACGCCAAGGC 58.916 55.000 0.00 0.00 37.85 4.35
2171 2526 0.688487 TTTACCACTACGCCAAGGCT 59.312 50.000 9.73 0.00 39.32 4.58
2172 2527 0.248289 TTACCACTACGCCAAGGCTC 59.752 55.000 9.73 0.00 39.32 4.70
2173 2528 1.610554 TACCACTACGCCAAGGCTCC 61.611 60.000 9.73 0.00 39.32 4.70
2174 2529 2.125106 CACTACGCCAAGGCTCCC 60.125 66.667 9.73 0.00 39.32 4.30
2175 2530 3.400054 ACTACGCCAAGGCTCCCC 61.400 66.667 9.73 0.00 39.32 4.81
2176 2531 3.083997 CTACGCCAAGGCTCCCCT 61.084 66.667 9.73 0.00 45.77 4.79
2186 2541 1.928868 AGGCTCCCCTTCACATTTTG 58.071 50.000 0.00 0.00 38.74 2.44
2187 2542 0.897621 GGCTCCCCTTCACATTTTGG 59.102 55.000 0.00 0.00 0.00 3.28
2188 2543 0.247460 GCTCCCCTTCACATTTTGGC 59.753 55.000 0.00 0.00 0.00 4.52
2189 2544 0.897621 CTCCCCTTCACATTTTGGCC 59.102 55.000 0.00 0.00 0.00 5.36
2216 3285 4.479619 CAGCAACAACTTAATCCTTCAGC 58.520 43.478 0.00 0.00 0.00 4.26
2217 3286 3.507622 AGCAACAACTTAATCCTTCAGCC 59.492 43.478 0.00 0.00 0.00 4.85
2348 3417 5.295540 GGGAAGATCAGTTCTTACTTGATGC 59.704 44.000 3.82 0.00 44.88 3.91
2418 3491 6.220201 GTGAATCCTAGAATCCTACAGAAGC 58.780 44.000 0.00 0.00 0.00 3.86
2445 3518 3.194116 ACCAGCGAGCAATGAAAAATGAT 59.806 39.130 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.305110 ACAAACCGAACGAATTTCATGC 58.695 40.909 0.00 0.00 33.24 4.06
34 35 1.754745 GAGAGCCGGCCATCCAATA 59.245 57.895 26.15 0.00 0.00 1.90
35 36 2.512896 GAGAGCCGGCCATCCAAT 59.487 61.111 26.15 0.94 0.00 3.16
59 60 2.339100 TTCGCGGACACGTCAGACAA 62.339 55.000 6.13 0.00 43.45 3.18
64 65 0.876777 ATTTGTTCGCGGACACGTCA 60.877 50.000 22.39 1.72 43.45 4.35
87 88 5.540719 TCCAATGGAAAACCCTAACGAAAAT 59.459 36.000 0.00 0.00 35.38 1.82
91 92 3.073356 ACTCCAATGGAAAACCCTAACGA 59.927 43.478 2.61 0.00 35.38 3.85
92 93 3.418047 ACTCCAATGGAAAACCCTAACG 58.582 45.455 2.61 0.00 35.38 3.18
104 107 2.025887 AGTCTAAGGGCAACTCCAATGG 60.026 50.000 0.00 0.00 36.21 3.16
160 164 0.321653 AATTGTGAGGTGGAGCGGAC 60.322 55.000 0.00 0.00 0.00 4.79
342 346 3.181486 TGTGTGTGTGTGTGTGTGTTTTT 60.181 39.130 0.00 0.00 0.00 1.94
343 347 2.359214 TGTGTGTGTGTGTGTGTGTTTT 59.641 40.909 0.00 0.00 0.00 2.43
344 348 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
347 351 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
349 353 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
351 355 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
715 719 7.024768 CCGTCGATTTTACCAAAATATTGTGT 58.975 34.615 4.91 0.00 40.97 3.72
716 720 6.470877 CCCGTCGATTTTACCAAAATATTGTG 59.529 38.462 0.00 0.00 40.97 3.33
717 721 6.404954 CCCCGTCGATTTTACCAAAATATTGT 60.405 38.462 0.00 0.00 40.97 2.71
718 722 5.974751 CCCCGTCGATTTTACCAAAATATTG 59.025 40.000 0.00 0.00 40.97 1.90
719 723 5.887035 TCCCCGTCGATTTTACCAAAATATT 59.113 36.000 0.00 0.00 40.97 1.28
720 724 5.297527 GTCCCCGTCGATTTTACCAAAATAT 59.702 40.000 0.00 0.00 40.97 1.28
721 725 4.635324 GTCCCCGTCGATTTTACCAAAATA 59.365 41.667 0.00 0.00 40.97 1.40
722 726 3.441222 GTCCCCGTCGATTTTACCAAAAT 59.559 43.478 0.00 0.00 43.43 1.82
723 727 2.813172 GTCCCCGTCGATTTTACCAAAA 59.187 45.455 0.00 0.00 34.41 2.44
724 728 2.425539 GTCCCCGTCGATTTTACCAAA 58.574 47.619 0.00 0.00 0.00 3.28
725 729 1.338960 GGTCCCCGTCGATTTTACCAA 60.339 52.381 0.00 0.00 0.00 3.67
726 730 0.249955 GGTCCCCGTCGATTTTACCA 59.750 55.000 0.00 0.00 0.00 3.25
727 731 0.807275 CGGTCCCCGTCGATTTTACC 60.807 60.000 0.00 0.00 42.73 2.85
728 732 0.807275 CCGGTCCCCGTCGATTTTAC 60.807 60.000 0.00 0.00 46.80 2.01
730 734 2.266689 CCGGTCCCCGTCGATTTT 59.733 61.111 0.00 0.00 46.80 1.82
762 766 0.373716 CAATGGCGCGAACTAGGAAC 59.626 55.000 12.10 0.00 0.00 3.62
782 787 3.205536 TTTTCGCGCTGGTGCACA 61.206 55.556 20.43 3.92 39.64 4.57
785 790 1.797537 GATGTTTTCGCGCTGGTGC 60.798 57.895 5.56 0.00 0.00 5.01
890 936 2.280865 GATTGCGATCCGGGGGAC 60.281 66.667 0.00 0.00 32.98 4.46
989 1046 1.812571 GTGTTGTGAGATTTGCCGGAT 59.187 47.619 5.05 0.00 0.00 4.18
1001 1059 1.673400 CGGTGGTGAATTGTGTTGTGA 59.327 47.619 0.00 0.00 0.00 3.58
1002 1060 1.863624 GCGGTGGTGAATTGTGTTGTG 60.864 52.381 0.00 0.00 0.00 3.33
1028 1088 3.069318 GAGCGGACGGAGGAGGTT 61.069 66.667 0.00 0.00 0.00 3.50
1401 1467 3.402681 CGGGATCTGCAGTGGGGT 61.403 66.667 14.67 0.00 0.00 4.95
1405 1471 1.813513 AACTTTCGGGATCTGCAGTG 58.186 50.000 14.67 0.10 0.00 3.66
1406 1472 2.154462 CAAACTTTCGGGATCTGCAGT 58.846 47.619 14.67 0.42 0.00 4.40
1418 1488 3.617263 AGTCGCGGTATCATCAAACTTTC 59.383 43.478 6.13 0.00 0.00 2.62
1451 1521 2.424246 AGCGAACTACAGAGGAACTAGC 59.576 50.000 0.00 0.00 41.55 3.42
1455 1525 4.804665 GGAAATAGCGAACTACAGAGGAAC 59.195 45.833 0.00 0.00 0.00 3.62
1490 1561 2.766313 ACTTTGCTGCACGATTCAGTA 58.234 42.857 0.00 0.00 34.21 2.74
1502 1573 4.290155 ACAAACTGCGAATAACTTTGCTG 58.710 39.130 0.00 3.70 41.61 4.41
1537 1610 6.438741 TCAGAGACAAGGTATTTCAGAGACAT 59.561 38.462 0.00 0.00 0.00 3.06
1553 1628 3.873361 CAGCAGAACAAAGTCAGAGACAA 59.127 43.478 0.00 0.00 34.60 3.18
1563 1638 3.973657 ACAGAAATGCAGCAGAACAAAG 58.026 40.909 0.00 0.00 0.00 2.77
1598 1675 7.040201 ACACAATTTTGCATCACAGAAGATAGT 60.040 33.333 0.00 0.00 0.00 2.12
1601 1678 5.924254 CACACAATTTTGCATCACAGAAGAT 59.076 36.000 0.00 0.00 0.00 2.40
1650 1727 3.470868 AGGGGCTCCTGGTAAAAGAATA 58.529 45.455 2.82 0.00 42.98 1.75
1667 1744 0.457035 CAAATGCAATCCGTCAGGGG 59.543 55.000 0.00 0.00 38.33 4.79
1679 1756 1.818060 ACTATTCCGCAAGCAAATGCA 59.182 42.857 8.28 0.00 46.76 3.96
1681 1758 5.030295 CACTAACTATTCCGCAAGCAAATG 58.970 41.667 0.00 0.00 0.00 2.32
1683 1760 3.119990 GCACTAACTATTCCGCAAGCAAA 60.120 43.478 0.00 0.00 0.00 3.68
1692 1769 2.930950 TGGCCATGCACTAACTATTCC 58.069 47.619 0.00 0.00 0.00 3.01
1696 1773 3.947196 CTGATTTGGCCATGCACTAACTA 59.053 43.478 6.09 0.00 0.00 2.24
1698 1775 2.159198 CCTGATTTGGCCATGCACTAAC 60.159 50.000 6.09 0.00 0.00 2.34
1701 1779 0.040058 TCCTGATTTGGCCATGCACT 59.960 50.000 6.09 0.00 0.00 4.40
1705 1783 2.761767 TGATGTTCCTGATTTGGCCATG 59.238 45.455 6.09 0.00 0.00 3.66
1712 1790 2.827921 GGGCAACTGATGTTCCTGATTT 59.172 45.455 0.00 0.00 33.52 2.17
1727 1805 1.173913 AATAGCAGAAACGGGGCAAC 58.826 50.000 0.00 0.00 0.00 4.17
1732 1810 6.662616 CATCAGATAAAATAGCAGAAACGGG 58.337 40.000 0.00 0.00 0.00 5.28
1748 1828 5.192176 TGCCTTGTACAAATGCATCAGATA 58.808 37.500 22.02 4.65 0.00 1.98
1766 1846 7.093640 ACACAGAACAATCATAAATGATGCCTT 60.094 33.333 6.22 0.00 46.22 4.35
1767 1847 6.379133 ACACAGAACAATCATAAATGATGCCT 59.621 34.615 6.22 0.10 46.22 4.75
1772 1852 6.979465 TGCAACACAGAACAATCATAAATGA 58.021 32.000 0.00 0.00 41.70 2.57
1784 1864 3.510719 ACACATTGTTGCAACACAGAAC 58.489 40.909 31.17 3.32 38.92 3.01
1789 1873 8.061268 CCTTAATTAAACACATTGTTGCAACAC 58.939 33.333 31.17 6.69 40.14 3.32
1812 1896 7.027874 TGAAATACAGACTAATCCCAACCTT 57.972 36.000 0.00 0.00 0.00 3.50
1835 1919 9.539139 GCAAATCAATCTAGAAATCGATGTATG 57.461 33.333 0.00 0.07 0.00 2.39
1836 1920 9.499479 AGCAAATCAATCTAGAAATCGATGTAT 57.501 29.630 0.00 0.00 0.00 2.29
1838 1922 7.798596 AGCAAATCAATCTAGAAATCGATGT 57.201 32.000 0.00 0.00 0.00 3.06
1894 1982 7.437862 GCAAAGTGACATTTGATTAACAGGAAA 59.562 33.333 10.31 0.00 41.71 3.13
1898 1986 7.365741 AGAGCAAAGTGACATTTGATTAACAG 58.634 34.615 10.31 0.00 41.71 3.16
1908 1996 5.709164 AGCAGAAATAGAGCAAAGTGACATT 59.291 36.000 0.00 0.00 0.00 2.71
1910 1998 4.453478 CAGCAGAAATAGAGCAAAGTGACA 59.547 41.667 0.00 0.00 0.00 3.58
1913 2001 5.368256 AACAGCAGAAATAGAGCAAAGTG 57.632 39.130 0.00 0.00 0.00 3.16
1914 2002 6.396829 AAAACAGCAGAAATAGAGCAAAGT 57.603 33.333 0.00 0.00 0.00 2.66
1941 2041 7.265673 TCAGATGAAGTATTACTGCAGTAACC 58.734 38.462 35.31 27.88 37.15 2.85
1974 2329 0.179000 TTTGCCACGGCCAAAATGTT 59.821 45.000 2.24 0.00 41.09 2.71
1995 2350 2.068915 CATTGGGGCTGCCCTTTTT 58.931 52.632 34.99 16.16 44.66 1.94
1996 2351 2.595884 GCATTGGGGCTGCCCTTTT 61.596 57.895 34.99 17.92 44.66 2.27
1997 2352 3.004946 GCATTGGGGCTGCCCTTT 61.005 61.111 34.99 18.28 44.66 3.11
1998 2353 3.629035 ATGCATTGGGGCTGCCCTT 62.629 57.895 34.99 18.63 44.66 3.95
1999 2354 4.084147 ATGCATTGGGGCTGCCCT 62.084 61.111 34.99 15.15 44.66 5.19
2000 2355 3.857038 CATGCATTGGGGCTGCCC 61.857 66.667 29.93 29.93 44.51 5.36
2001 2356 1.741327 CTACATGCATTGGGGCTGCC 61.741 60.000 11.05 11.05 38.89 4.85
2002 2357 1.737816 CTACATGCATTGGGGCTGC 59.262 57.895 0.00 0.00 40.10 5.25
2003 2358 0.754217 AGCTACATGCATTGGGGCTG 60.754 55.000 0.00 0.00 45.94 4.85
2004 2359 0.466922 GAGCTACATGCATTGGGGCT 60.467 55.000 11.39 11.39 45.94 5.19
2005 2360 1.458639 GGAGCTACATGCATTGGGGC 61.459 60.000 0.00 0.00 45.94 5.80
2006 2361 0.825010 GGGAGCTACATGCATTGGGG 60.825 60.000 0.00 0.00 45.94 4.96
2007 2362 1.168407 CGGGAGCTACATGCATTGGG 61.168 60.000 0.00 0.00 45.94 4.12
2008 2363 2.324215 CGGGAGCTACATGCATTGG 58.676 57.895 0.00 0.00 45.94 3.16
2027 2382 2.271800 CTTACCTAGACCTTGCGCAAG 58.728 52.381 37.33 37.33 38.14 4.01
2028 2383 1.066430 CCTTACCTAGACCTTGCGCAA 60.066 52.381 23.48 23.48 0.00 4.85
2029 2384 0.535335 CCTTACCTAGACCTTGCGCA 59.465 55.000 5.66 5.66 0.00 6.09
2030 2385 0.179081 CCCTTACCTAGACCTTGCGC 60.179 60.000 0.00 0.00 0.00 6.09
2031 2386 1.136500 GACCCTTACCTAGACCTTGCG 59.864 57.143 0.00 0.00 0.00 4.85
2032 2387 1.485480 GGACCCTTACCTAGACCTTGC 59.515 57.143 0.00 0.00 0.00 4.01
2033 2388 1.755380 CGGACCCTTACCTAGACCTTG 59.245 57.143 0.00 0.00 0.00 3.61
2034 2389 1.642762 TCGGACCCTTACCTAGACCTT 59.357 52.381 0.00 0.00 0.00 3.50
2035 2390 1.064091 GTCGGACCCTTACCTAGACCT 60.064 57.143 0.00 0.00 0.00 3.85
2036 2391 1.397672 GTCGGACCCTTACCTAGACC 58.602 60.000 0.00 0.00 0.00 3.85
2037 2392 1.341383 TGGTCGGACCCTTACCTAGAC 60.341 57.143 23.81 0.00 37.50 2.59
2038 2393 1.002069 TGGTCGGACCCTTACCTAGA 58.998 55.000 23.81 0.00 37.50 2.43
2039 2394 1.109609 GTGGTCGGACCCTTACCTAG 58.890 60.000 23.81 0.00 37.50 3.02
2040 2395 0.706433 AGTGGTCGGACCCTTACCTA 59.294 55.000 23.81 0.61 37.50 3.08
2041 2396 0.178912 AAGTGGTCGGACCCTTACCT 60.179 55.000 23.81 9.20 37.50 3.08
2042 2397 0.689055 AAAGTGGTCGGACCCTTACC 59.311 55.000 23.81 7.17 37.50 2.85
2043 2398 1.609841 CCAAAGTGGTCGGACCCTTAC 60.610 57.143 23.81 15.33 37.50 2.34
2044 2399 0.688487 CCAAAGTGGTCGGACCCTTA 59.312 55.000 23.81 2.97 37.50 2.69
2045 2400 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2046 2401 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2047 2402 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2048 2403 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2049 2404 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2054 2409 4.263727 TGCATACAATAGACCCAAAGTGGT 60.264 41.667 0.00 0.00 42.79 4.16
2055 2410 4.269183 TGCATACAATAGACCCAAAGTGG 58.731 43.478 0.00 0.00 37.25 4.00
2056 2411 4.201950 GCTGCATACAATAGACCCAAAGTG 60.202 45.833 0.00 0.00 0.00 3.16
2057 2412 3.947834 GCTGCATACAATAGACCCAAAGT 59.052 43.478 0.00 0.00 0.00 2.66
2058 2413 3.316308 GGCTGCATACAATAGACCCAAAG 59.684 47.826 0.50 0.00 0.00 2.77
2059 2414 3.053693 AGGCTGCATACAATAGACCCAAA 60.054 43.478 0.50 0.00 0.00 3.28
2060 2415 2.509548 AGGCTGCATACAATAGACCCAA 59.490 45.455 0.50 0.00 0.00 4.12
2061 2416 2.126882 AGGCTGCATACAATAGACCCA 58.873 47.619 0.50 0.00 0.00 4.51
2062 2417 2.938956 AGGCTGCATACAATAGACCC 57.061 50.000 0.50 0.00 0.00 4.46
2063 2418 3.565902 GGAAAGGCTGCATACAATAGACC 59.434 47.826 0.50 0.00 0.00 3.85
2064 2419 3.565902 GGGAAAGGCTGCATACAATAGAC 59.434 47.826 0.50 0.00 0.00 2.59
2065 2420 3.459598 AGGGAAAGGCTGCATACAATAGA 59.540 43.478 0.50 0.00 0.00 1.98
2066 2421 3.825328 AGGGAAAGGCTGCATACAATAG 58.175 45.455 0.50 0.00 0.00 1.73
2067 2422 3.951563 AGGGAAAGGCTGCATACAATA 57.048 42.857 0.50 0.00 0.00 1.90
2068 2423 2.834638 AGGGAAAGGCTGCATACAAT 57.165 45.000 0.50 0.00 0.00 2.71
2069 2424 2.307392 TGTAGGGAAAGGCTGCATACAA 59.693 45.455 0.50 0.00 39.32 2.41
2070 2425 1.912731 TGTAGGGAAAGGCTGCATACA 59.087 47.619 0.50 0.00 39.88 2.29
2071 2426 2.710096 TGTAGGGAAAGGCTGCATAC 57.290 50.000 0.50 0.00 33.66 2.39
2072 2427 3.951563 AATGTAGGGAAAGGCTGCATA 57.048 42.857 0.50 0.00 0.00 3.14
2073 2428 2.834638 AATGTAGGGAAAGGCTGCAT 57.165 45.000 0.50 0.00 0.00 3.96
2074 2429 2.041620 AGAAATGTAGGGAAAGGCTGCA 59.958 45.455 0.50 0.00 0.00 4.41
2075 2430 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2076 2431 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
2077 2432 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
2078 2433 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
2079 2434 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
2080 2435 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
2081 2436 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
2082 2437 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
2083 2438 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
2084 2439 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
2085 2440 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
2086 2441 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
2087 2442 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
2088 2443 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
2089 2444 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
2090 2445 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
2091 2446 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
2092 2447 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
2093 2448 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
2094 2449 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
2105 2460 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2106 2461 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2107 2462 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2108 2463 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2109 2464 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2110 2465 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2111 2466 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2112 2467 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2113 2468 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2114 2469 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2115 2470 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2116 2471 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2117 2472 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2118 2473 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2119 2474 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2129 2484 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2130 2485 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2131 2486 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2132 2487 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2133 2488 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2134 2489 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2135 2490 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2136 2491 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2137 2492 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2138 2493 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2139 2494 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2140 2495 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2141 2496 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2142 2497 0.984230 TAGTGGTAAAGCTGCTGCCT 59.016 50.000 12.44 2.45 40.80 4.75
2143 2498 1.087501 GTAGTGGTAAAGCTGCTGCC 58.912 55.000 12.44 7.07 40.80 4.85
2144 2499 0.721718 CGTAGTGGTAAAGCTGCTGC 59.278 55.000 1.35 7.62 40.05 5.25
2145 2500 0.721718 GCGTAGTGGTAAAGCTGCTG 59.278 55.000 1.35 0.00 0.00 4.41
2146 2501 0.391263 GGCGTAGTGGTAAAGCTGCT 60.391 55.000 0.00 0.00 0.00 4.24
2147 2502 0.672401 TGGCGTAGTGGTAAAGCTGC 60.672 55.000 0.00 0.00 0.00 5.25
2148 2503 1.732259 CTTGGCGTAGTGGTAAAGCTG 59.268 52.381 0.00 0.00 0.00 4.24
2149 2504 1.338769 CCTTGGCGTAGTGGTAAAGCT 60.339 52.381 0.00 0.00 0.00 3.74
2150 2505 1.084289 CCTTGGCGTAGTGGTAAAGC 58.916 55.000 0.00 0.00 0.00 3.51
2151 2506 1.084289 GCCTTGGCGTAGTGGTAAAG 58.916 55.000 0.00 0.00 0.00 1.85
2152 2507 0.688487 AGCCTTGGCGTAGTGGTAAA 59.312 50.000 5.95 0.00 0.00 2.01
2153 2508 0.248289 GAGCCTTGGCGTAGTGGTAA 59.752 55.000 5.95 0.00 0.00 2.85
2154 2509 1.610554 GGAGCCTTGGCGTAGTGGTA 61.611 60.000 5.95 0.00 0.00 3.25
2155 2510 2.663196 GAGCCTTGGCGTAGTGGT 59.337 61.111 5.95 0.00 0.00 4.16
2156 2511 2.125106 GGAGCCTTGGCGTAGTGG 60.125 66.667 5.95 0.00 0.00 4.00
2157 2512 2.125106 GGGAGCCTTGGCGTAGTG 60.125 66.667 5.95 0.00 0.00 2.74
2158 2513 3.400054 GGGGAGCCTTGGCGTAGT 61.400 66.667 5.95 0.00 0.00 2.73
2159 2514 2.595009 GAAGGGGAGCCTTGGCGTAG 62.595 65.000 5.95 0.00 0.00 3.51
2160 2515 2.609610 AAGGGGAGCCTTGGCGTA 60.610 61.111 5.95 0.00 0.00 4.42
2161 2516 4.035102 GAAGGGGAGCCTTGGCGT 62.035 66.667 5.95 0.00 0.00 5.68
2162 2517 4.033776 TGAAGGGGAGCCTTGGCG 62.034 66.667 5.95 0.00 0.00 5.69
2163 2518 2.361737 GTGAAGGGGAGCCTTGGC 60.362 66.667 2.97 2.97 0.00 4.52
2164 2519 0.040204 AATGTGAAGGGGAGCCTTGG 59.960 55.000 0.00 0.00 0.00 3.61
2165 2520 1.928868 AAATGTGAAGGGGAGCCTTG 58.071 50.000 0.00 0.00 0.00 3.61
2166 2521 2.250924 CAAAATGTGAAGGGGAGCCTT 58.749 47.619 0.00 0.00 0.00 4.35
2167 2522 1.550869 CCAAAATGTGAAGGGGAGCCT 60.551 52.381 0.00 0.00 0.00 4.58
2168 2523 0.897621 CCAAAATGTGAAGGGGAGCC 59.102 55.000 0.00 0.00 0.00 4.70
2169 2524 0.247460 GCCAAAATGTGAAGGGGAGC 59.753 55.000 0.00 0.00 0.00 4.70
2170 2525 0.897621 GGCCAAAATGTGAAGGGGAG 59.102 55.000 0.00 0.00 0.00 4.30
2171 2526 0.897863 CGGCCAAAATGTGAAGGGGA 60.898 55.000 2.24 0.00 0.00 4.81
2172 2527 1.184970 ACGGCCAAAATGTGAAGGGG 61.185 55.000 2.24 0.00 0.00 4.79
2173 2528 0.038343 CACGGCCAAAATGTGAAGGG 60.038 55.000 2.24 0.00 35.66 3.95
2174 2529 0.038343 CCACGGCCAAAATGTGAAGG 60.038 55.000 2.24 0.00 35.66 3.46
2175 2530 0.667184 GCCACGGCCAAAATGTGAAG 60.667 55.000 2.24 0.00 35.66 3.02
2176 2531 1.365633 GCCACGGCCAAAATGTGAA 59.634 52.632 2.24 0.00 35.66 3.18
2177 2532 1.804396 CTGCCACGGCCAAAATGTGA 61.804 55.000 2.24 0.00 41.09 3.58
2178 2533 1.373246 CTGCCACGGCCAAAATGTG 60.373 57.895 2.24 1.52 41.09 3.21
2179 2534 3.050339 CTGCCACGGCCAAAATGT 58.950 55.556 2.24 0.00 41.09 2.71
2180 2535 2.432972 GCTGCCACGGCCAAAATG 60.433 61.111 2.24 0.00 41.09 2.32
2181 2536 2.506061 TTGCTGCCACGGCCAAAAT 61.506 52.632 2.24 0.00 41.09 1.82
2182 2537 3.150335 TTGCTGCCACGGCCAAAA 61.150 55.556 2.24 0.00 41.09 2.44
2183 2538 3.910490 GTTGCTGCCACGGCCAAA 61.910 61.111 2.24 0.00 41.09 3.28
2186 2541 4.645921 GTTGTTGCTGCCACGGCC 62.646 66.667 5.42 0.00 41.09 6.13
2187 2542 1.791103 TAAGTTGTTGCTGCCACGGC 61.791 55.000 0.00 0.00 42.35 5.68
2188 2543 0.665835 TTAAGTTGTTGCTGCCACGG 59.334 50.000 0.00 0.00 0.00 4.94
2189 2544 2.584791 GATTAAGTTGTTGCTGCCACG 58.415 47.619 0.00 0.00 0.00 4.94
2278 3347 6.738635 TGTCACTAAACTCCCCTAATCTAGA 58.261 40.000 0.00 0.00 0.00 2.43
2348 3417 7.534085 TTCATTCCTGCTAATACAGTAAACG 57.466 36.000 0.00 0.00 35.83 3.60
2418 3491 1.133253 CATTGCTCGCTGGTGTTCG 59.867 57.895 0.00 0.00 0.00 3.95
2445 3518 8.436778 ACCCAATGCAATGTATCACTACTATTA 58.563 33.333 0.21 0.00 0.00 0.98
2458 3531 3.642848 AGAAACTTGACCCAATGCAATGT 59.357 39.130 0.21 0.00 0.00 2.71



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

AutoCloner maintained by Alex Coulton.