Multiple sequence alignment - TraesCS6A01G213200

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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 TraesCS6A01G213200 chr6A 100.000 6196 0 0 1 6196 387287683 387281488 0.000000e+00 11442.0
1 TraesCS6A01G213200 chr6A 97.953 342 7 0 1 342 113822966 113822625 1.490000e-165 593.0
2 TraesCS6A01G213200 chr6A 99.219 128 1 0 8 135 100731825 100731952 1.340000e-56 231.0
3 TraesCS6A01G213200 chr6A 97.391 115 3 0 229 343 100732340 100732454 4.900000e-46 196.0
4 TraesCS6A01G213200 chr6A 98.198 111 2 0 133 243 100732216 100732326 1.760000e-45 195.0
5 TraesCS6A01G213200 chr6D 91.347 2473 138 39 1672 4115 270050447 270052872 0.000000e+00 3312.0
6 TraesCS6A01G213200 chr6D 93.702 1969 78 17 4245 6196 270053345 270055284 0.000000e+00 2907.0
7 TraesCS6A01G213200 chr6D 91.699 1289 57 17 336 1593 270049179 270050448 0.000000e+00 1742.0
8 TraesCS6A01G213200 chr6D 92.532 308 21 2 3 310 93627234 93627539 2.050000e-119 440.0
9 TraesCS6A01G213200 chr6B 90.628 2486 140 51 1672 4115 422649087 422651521 0.000000e+00 3214.0
10 TraesCS6A01G213200 chr6B 95.704 1164 38 4 4276 5437 422651817 422652970 0.000000e+00 1862.0
11 TraesCS6A01G213200 chr6B 93.838 779 26 7 336 1102 422647874 422648642 0.000000e+00 1153.0
12 TraesCS6A01G213200 chr6B 94.894 705 30 6 5493 6196 422652988 422653687 0.000000e+00 1098.0
13 TraesCS6A01G213200 chr6B 96.479 426 15 0 1168 1593 422648663 422649088 0.000000e+00 704.0
14 TraesCS6A01G213200 chr6B 93.421 76 5 0 4204 4279 422651682 422651757 5.080000e-21 113.0
15 TraesCS6A01G213200 chr6B 85.714 63 8 1 1592 1653 29919930 29919868 1.440000e-06 65.8
16 TraesCS6A01G213200 chr7B 93.860 342 21 0 1 342 554550891 554550550 3.310000e-142 516.0
17 TraesCS6A01G213200 chrUn 93.314 344 21 2 1 344 16910382 16910041 1.990000e-139 507.0
18 TraesCS6A01G213200 chr5D 93.195 338 22 1 6 343 116185553 116185217 4.310000e-136 496.0
19 TraesCS6A01G213200 chr5D 84.694 294 30 7 5608 5890 445008253 445007964 4.730000e-71 279.0
20 TraesCS6A01G213200 chr1A 89.308 318 29 4 29 342 247333147 247333463 1.620000e-105 394.0
21 TraesCS6A01G213200 chr1A 93.023 86 5 1 4118 4203 533166539 533166623 2.350000e-24 124.0
22 TraesCS6A01G213200 chr1A 90.000 60 5 1 1592 1650 61012519 61012578 6.660000e-10 76.8
23 TraesCS6A01G213200 chr1A 90.741 54 3 2 1598 1650 542002560 542002612 3.100000e-08 71.3
24 TraesCS6A01G213200 chr1A 91.489 47 3 1 1604 1649 587672842 587672888 5.190000e-06 63.9
25 TraesCS6A01G213200 chr1B 84.354 294 31 7 5608 5890 680994877 680995166 2.200000e-69 274.0
26 TraesCS6A01G213200 chr7A 83.562 292 31 8 5608 5890 576774635 576774352 2.220000e-64 257.0
27 TraesCS6A01G213200 chr7A 83.219 292 32 8 5608 5890 658277974 658278257 1.030000e-62 252.0
28 TraesCS6A01G213200 chr2B 80.456 307 43 7 29 333 155134331 155134622 1.050000e-52 219.0
29 TraesCS6A01G213200 chr2B 96.386 83 2 1 4118 4200 154831125 154831206 1.080000e-27 135.0
30 TraesCS6A01G213200 chr2B 100.000 73 0 0 4118 4190 475485611 475485539 1.080000e-27 135.0
31 TraesCS6A01G213200 chr2B 95.294 85 3 1 4118 4202 419999626 419999543 3.900000e-27 134.0
32 TraesCS6A01G213200 chr2B 94.118 85 5 0 4118 4202 133013674 133013590 5.040000e-26 130.0
33 TraesCS6A01G213200 chr4B 81.347 193 28 7 155 343 454673653 454673841 3.870000e-32 150.0
34 TraesCS6A01G213200 chr4B 100.000 73 0 0 4118 4190 85349920 85349992 1.080000e-27 135.0
35 TraesCS6A01G213200 chr4B 95.181 83 4 0 4118 4200 601534780 601534862 1.400000e-26 132.0
36 TraesCS6A01G213200 chr1D 96.250 80 2 1 4118 4197 73714896 73714974 5.040000e-26 130.0
37 TraesCS6A01G213200 chr5A 93.182 88 5 1 4118 4205 632877144 632877230 1.810000e-25 128.0
38 TraesCS6A01G213200 chr3D 97.727 44 1 0 1590 1633 457021517 457021560 6.660000e-10 76.8
39 TraesCS6A01G213200 chr3D 95.238 42 2 0 1587 1628 520821163 520821204 4.010000e-07 67.6
40 TraesCS6A01G213200 chr3D 95.000 40 2 0 1589 1628 154613853 154613892 5.190000e-06 63.9
41 TraesCS6A01G213200 chr4A 84.932 73 7 3 1604 1673 515667831 515667760 3.100000e-08 71.3
42 TraesCS6A01G213200 chr4A 86.885 61 6 2 1592 1651 618286366 618286307 4.010000e-07 67.6
43 TraesCS6A01G213200 chr3A 91.111 45 4 0 1640 1684 201478318 201478274 1.860000e-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 TraesCS6A01G213200 chr6A 387281488 387287683 6195 True 11442.000000 11442 100.000000 1 6196 1 chr6A.!!$R2 6195
1 TraesCS6A01G213200 chr6A 100731825 100732454 629 False 207.333333 231 98.269333 8 343 3 chr6A.!!$F1 335
2 TraesCS6A01G213200 chr6D 270049179 270055284 6105 False 2653.666667 3312 92.249333 336 6196 3 chr6D.!!$F2 5860
3 TraesCS6A01G213200 chr6B 422647874 422653687 5813 False 1357.333333 3214 94.160667 336 6196 6 chr6B.!!$F1 5860

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
244 511 0.040204 ATTGTGAAGGGAAGGGCTGG 59.960 55.0 0.00 0.0 0.00 4.85 F
403 698 0.108756 CCGTCCCTTTCGTCTTCCTC 60.109 60.0 0.00 0.0 0.00 3.71 F
684 1009 0.893727 TTTCTCGCTTCCCCTTTGGC 60.894 55.0 0.00 0.0 0.00 4.52 F
1603 1949 0.106819 TCTGTAGTACTCCCTCCGCC 60.107 60.0 0.00 0.0 0.00 6.13 F
1616 1962 0.107848 CTCCGCCCCGAATTACTTGT 60.108 55.0 0.00 0.0 0.00 3.16 F
1617 1963 0.108041 TCCGCCCCGAATTACTTGTC 60.108 55.0 0.00 0.0 0.00 3.18 F
1618 1964 0.107848 CCGCCCCGAATTACTTGTCT 60.108 55.0 0.00 0.0 0.00 3.41 F
2379 2726 0.598065 AAAGGCCACTCGTTCATTGC 59.402 50.0 5.01 0.0 0.00 3.56 F
3983 4372 0.890996 AAAGAAAGCTCCAGCACGGG 60.891 55.0 0.48 0.0 45.16 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1943 0.107848 ACAAGTAATTCGGGGCGGAG 60.108 55.000 0.00 0.0 0.00 4.63 R
1599 1945 0.107848 AGACAAGTAATTCGGGGCGG 60.108 55.000 0.00 0.0 0.00 6.13 R
2029 2376 0.251341 GCATAGGCCATAACCCCAGG 60.251 60.000 5.01 0.0 0.00 4.45 R
3420 3801 0.402121 AAGGTCCTTCTCTGCCAACC 59.598 55.000 0.00 0.0 0.00 3.77 R
3441 3822 1.835483 GCACACACGCTGTCTCAAGG 61.835 60.000 0.00 0.0 0.00 3.61 R
3627 4008 2.673368 GGCTTCACCTTTGATACGTCAG 59.327 50.000 0.00 0.0 33.33 3.51 R
3639 4026 2.925170 AGCTCCGTGGCTTCACCT 60.925 61.111 0.00 0.0 39.86 4.00 R
4173 4668 0.115745 TGGAAGGTACTCCCTCCGTT 59.884 55.000 0.00 0.0 45.47 4.44 R
5780 6768 0.249120 ATGTAACGCCAGCTGCACTA 59.751 50.000 8.66 0.0 41.33 2.74 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
170 437 6.583427 GCAAAGGAATATACCGTTTCGTTTTT 59.417 34.615 3.06 0.00 37.66 1.94
218 485 3.010144 CTGCCATACCCCCAGCTT 58.990 61.111 0.00 0.00 0.00 3.74
243 510 1.180029 CATTGTGAAGGGAAGGGCTG 58.820 55.000 0.00 0.00 0.00 4.85
244 511 0.040204 ATTGTGAAGGGAAGGGCTGG 59.960 55.000 0.00 0.00 0.00 4.85
279 574 5.198602 AGCTCCATCCCTAAAATGAGTTT 57.801 39.130 0.00 0.00 0.00 2.66
343 638 1.067565 GCAAAAGAACTGGCCCTTAGC 60.068 52.381 0.00 0.75 42.60 3.09
344 639 2.238521 CAAAAGAACTGGCCCTTAGCA 58.761 47.619 0.00 0.00 46.50 3.49
352 647 3.278157 GCCCTTAGCAGCCACAAC 58.722 61.111 0.00 0.00 42.97 3.32
403 698 0.108756 CCGTCCCTTTCGTCTTCCTC 60.109 60.000 0.00 0.00 0.00 3.71
435 730 3.615709 GCACCCCACCAGCAAACC 61.616 66.667 0.00 0.00 0.00 3.27
568 876 4.057432 GTGGCTTAGCATCAGATTCTCTC 58.943 47.826 6.53 0.00 0.00 3.20
684 1009 0.893727 TTTCTCGCTTCCCCTTTGGC 60.894 55.000 0.00 0.00 0.00 4.52
700 1025 3.552604 TTGGCGCTGATTCTTGTTTAC 57.447 42.857 7.64 0.00 0.00 2.01
770 1101 3.892162 CCGAACCCCAACCACCCA 61.892 66.667 0.00 0.00 0.00 4.51
771 1102 2.438795 CGAACCCCAACCACCCAT 59.561 61.111 0.00 0.00 0.00 4.00
925 1264 1.082756 CGTCTTGCCAAGTTCGTGC 60.083 57.895 4.04 0.00 0.00 5.34
935 1274 1.393539 CAAGTTCGTGCGGTTGGATAG 59.606 52.381 0.00 0.00 0.00 2.08
963 1302 5.649395 TGATTGCTCTTGAAGGGAATACAAG 59.351 40.000 0.00 0.00 41.27 3.16
968 1307 3.920197 TCTTGAAGGGAATACAAGGGGAA 59.080 43.478 0.00 0.00 40.60 3.97
970 1309 4.965283 TGAAGGGAATACAAGGGGAATT 57.035 40.909 0.00 0.00 0.00 2.17
981 1320 3.198853 ACAAGGGGAATTAGCAGAGTCTC 59.801 47.826 0.00 0.00 0.00 3.36
1012 1351 1.442526 GCTTGTCATGGAGCCATCGG 61.443 60.000 0.00 0.00 33.90 4.18
1131 1470 5.967088 TGCTCCTGTCTATTACTTCACTTC 58.033 41.667 0.00 0.00 0.00 3.01
1146 1485 1.196354 CACTTCGCTTCTCTTTGCTGG 59.804 52.381 0.00 0.00 0.00 4.85
1184 1529 3.770388 TGGATTGGAATTGCATCACATGT 59.230 39.130 0.00 0.00 0.00 3.21
1232 1577 5.182950 TGGCAATTTTACACATCAGTACCTG 59.817 40.000 0.00 0.00 0.00 4.00
1498 1844 5.418840 CCTATGTGGTACTTTTGGCTTCAAT 59.581 40.000 0.00 0.00 0.00 2.57
1598 1944 3.970842 CAGGTCTTCTGTAGTACTCCCT 58.029 50.000 0.00 0.00 38.64 4.20
1599 1945 3.949113 CAGGTCTTCTGTAGTACTCCCTC 59.051 52.174 0.00 0.00 38.64 4.30
1600 1946 3.053470 AGGTCTTCTGTAGTACTCCCTCC 60.053 52.174 0.00 0.00 0.00 4.30
1601 1947 2.944349 GTCTTCTGTAGTACTCCCTCCG 59.056 54.545 0.00 0.00 0.00 4.63
1602 1948 1.677052 CTTCTGTAGTACTCCCTCCGC 59.323 57.143 0.00 0.00 0.00 5.54
1603 1949 0.106819 TCTGTAGTACTCCCTCCGCC 60.107 60.000 0.00 0.00 0.00 6.13
1604 1950 1.076485 TGTAGTACTCCCTCCGCCC 60.076 63.158 0.00 0.00 0.00 6.13
1605 1951 1.831726 GTAGTACTCCCTCCGCCCC 60.832 68.421 0.00 0.00 0.00 5.80
1606 1952 3.426309 TAGTACTCCCTCCGCCCCG 62.426 68.421 0.00 0.00 0.00 5.73
1607 1953 4.828296 GTACTCCCTCCGCCCCGA 62.828 72.222 0.00 0.00 0.00 5.14
1608 1954 4.064768 TACTCCCTCCGCCCCGAA 62.065 66.667 0.00 0.00 0.00 4.30
1609 1955 3.384555 TACTCCCTCCGCCCCGAAT 62.385 63.158 0.00 0.00 0.00 3.34
1610 1956 2.884179 TACTCCCTCCGCCCCGAATT 62.884 60.000 0.00 0.00 0.00 2.17
1611 1957 2.041715 TCCCTCCGCCCCGAATTA 60.042 61.111 0.00 0.00 0.00 1.40
1612 1958 2.110420 CCCTCCGCCCCGAATTAC 59.890 66.667 0.00 0.00 0.00 1.89
1613 1959 2.440817 CCCTCCGCCCCGAATTACT 61.441 63.158 0.00 0.00 0.00 2.24
1614 1960 1.525442 CCTCCGCCCCGAATTACTT 59.475 57.895 0.00 0.00 0.00 2.24
1615 1961 0.814010 CCTCCGCCCCGAATTACTTG 60.814 60.000 0.00 0.00 0.00 3.16
1616 1962 0.107848 CTCCGCCCCGAATTACTTGT 60.108 55.000 0.00 0.00 0.00 3.16
1617 1963 0.108041 TCCGCCCCGAATTACTTGTC 60.108 55.000 0.00 0.00 0.00 3.18
1618 1964 0.107848 CCGCCCCGAATTACTTGTCT 60.108 55.000 0.00 0.00 0.00 3.41
1619 1965 1.677820 CCGCCCCGAATTACTTGTCTT 60.678 52.381 0.00 0.00 0.00 3.01
1620 1966 2.419021 CCGCCCCGAATTACTTGTCTTA 60.419 50.000 0.00 0.00 0.00 2.10
1621 1967 2.864343 CGCCCCGAATTACTTGTCTTAG 59.136 50.000 0.00 0.00 0.00 2.18
1622 1968 3.429822 CGCCCCGAATTACTTGTCTTAGA 60.430 47.826 0.00 0.00 0.00 2.10
1623 1969 4.704965 GCCCCGAATTACTTGTCTTAGAT 58.295 43.478 0.00 0.00 0.00 1.98
1624 1970 5.123936 GCCCCGAATTACTTGTCTTAGATT 58.876 41.667 0.00 0.00 0.00 2.40
1625 1971 5.589050 GCCCCGAATTACTTGTCTTAGATTT 59.411 40.000 0.00 0.00 0.00 2.17
1626 1972 6.458342 GCCCCGAATTACTTGTCTTAGATTTG 60.458 42.308 0.00 0.00 0.00 2.32
1627 1973 6.598064 CCCCGAATTACTTGTCTTAGATTTGT 59.402 38.462 0.00 0.00 0.00 2.83
1628 1974 7.120726 CCCCGAATTACTTGTCTTAGATTTGTT 59.879 37.037 0.00 0.00 0.00 2.83
1629 1975 8.512138 CCCGAATTACTTGTCTTAGATTTGTTT 58.488 33.333 0.00 0.00 0.00 2.83
1659 2005 9.698309 ATGAATGTATCTAGACAAGTAATTCGG 57.302 33.333 0.00 0.00 31.83 4.30
1660 2006 8.909923 TGAATGTATCTAGACAAGTAATTCGGA 58.090 33.333 0.00 0.00 31.83 4.55
1661 2007 9.745880 GAATGTATCTAGACAAGTAATTCGGAA 57.254 33.333 0.00 0.00 31.83 4.30
1662 2008 9.530633 AATGTATCTAGACAAGTAATTCGGAAC 57.469 33.333 0.00 0.00 31.83 3.62
1663 2009 7.861372 ATGTATCTAGACAAGTAATTCGGAACG 59.139 37.037 0.00 0.00 43.46 3.95
1709 2055 9.927668 AGTTTTCTTTCTTGTTTCTGAAAATGA 57.072 25.926 4.09 1.21 36.34 2.57
1715 2061 9.472361 CTTTCTTGTTTCTGAAAATGATCATGT 57.528 29.630 9.46 0.00 32.69 3.21
1716 2062 8.806177 TTCTTGTTTCTGAAAATGATCATGTG 57.194 30.769 9.46 0.00 0.00 3.21
1719 2065 5.921976 TGTTTCTGAAAATGATCATGTGCAC 59.078 36.000 10.75 10.75 0.00 4.57
1764 2111 4.499526 CCTGCTTCAACTTTTGTATGTGCA 60.500 41.667 0.00 0.00 0.00 4.57
1772 2119 8.888332 TCAACTTTTGTATGTGCAATATAACG 57.112 30.769 0.00 0.00 0.00 3.18
1774 2121 6.791303 ACTTTTGTATGTGCAATATAACGGG 58.209 36.000 0.00 0.00 0.00 5.28
1778 2125 3.708563 ATGTGCAATATAACGGGTTGC 57.291 42.857 0.00 2.61 46.24 4.17
1781 2128 3.623960 TGTGCAATATAACGGGTTGCTAC 59.376 43.478 10.20 7.55 46.22 3.58
1785 2132 4.448210 CAATATAACGGGTTGCTACTGGT 58.552 43.478 0.00 0.00 0.00 4.00
1808 2155 5.400485 GTCATTGCAACTGACAATTCAAGTC 59.600 40.000 24.67 0.00 42.08 3.01
1809 2156 4.979943 TTGCAACTGACAATTCAAGTCA 57.020 36.364 0.00 0.00 43.23 3.41
1838 2185 8.598916 TCAAAGGAAAGATATGTAACTGTGGTA 58.401 33.333 0.00 0.00 0.00 3.25
1853 2200 9.005777 GTAACTGTGGTATTGGAAGTAAATGAA 57.994 33.333 0.00 0.00 0.00 2.57
1855 2202 6.148811 ACTGTGGTATTGGAAGTAAATGAACG 59.851 38.462 0.00 0.00 0.00 3.95
1865 2212 3.686016 AGTAAATGAACGCAAGGGTGAT 58.314 40.909 0.00 0.00 46.39 3.06
1900 2247 4.590222 ACTTCCAGAAATCAAAGTTGCCAT 59.410 37.500 0.00 0.00 0.00 4.40
1901 2248 5.070847 ACTTCCAGAAATCAAAGTTGCCATT 59.929 36.000 0.00 0.00 0.00 3.16
1915 2262 3.300852 TGCCATTTTGCTACACATGTG 57.699 42.857 24.25 24.25 0.00 3.21
1926 2273 6.625873 TGCTACACATGTGTTGTTTCATAA 57.374 33.333 34.66 13.81 41.83 1.90
1933 2280 8.579006 ACACATGTGTTGTTTCATAATCTGATT 58.421 29.630 25.76 8.14 41.83 2.57
1937 2284 7.660112 TGTGTTGTTTCATAATCTGATTTGCT 58.340 30.769 8.38 0.00 32.72 3.91
1944 2291 9.674824 GTTTCATAATCTGATTTGCTAATCCTG 57.325 33.333 16.61 10.42 39.56 3.86
1956 2303 3.253188 TGCTAATCCTGTGTTCTTGTTGC 59.747 43.478 0.00 0.00 0.00 4.17
2005 2352 2.311542 CCCATGGGCCTGGCTTATTATA 59.688 50.000 20.41 0.00 34.77 0.98
2014 2361 3.119101 CCTGGCTTATTATAGCGATCGGT 60.119 47.826 24.56 24.56 42.15 4.69
2017 2364 6.216801 TGGCTTATTATAGCGATCGGTATT 57.783 37.500 36.16 24.88 42.15 1.89
2029 2376 2.273370 TCGGTATTTCTGCACTCGTC 57.727 50.000 0.00 0.00 0.00 4.20
2035 2382 2.111999 TTTCTGCACTCGTCCTGGGG 62.112 60.000 0.00 0.00 0.00 4.96
2062 2409 2.287188 GCCTATGCATGTGATTTGGACG 60.287 50.000 10.16 0.00 37.47 4.79
2077 2424 5.585820 TTTGGACGTACTACTGCATCATA 57.414 39.130 0.00 0.00 0.00 2.15
2168 2515 0.815213 TGTGCTGAGTTGCTGACCAC 60.815 55.000 0.00 0.00 0.00 4.16
2181 2528 2.819348 GCTGACCACTGATCCCCTTTTT 60.819 50.000 0.00 0.00 0.00 1.94
2182 2529 3.084786 CTGACCACTGATCCCCTTTTTC 58.915 50.000 0.00 0.00 0.00 2.29
2278 2625 0.940126 GTGGCTGATAGTTGGCATCG 59.060 55.000 0.00 0.00 40.72 3.84
2286 2633 1.448985 TAGTTGGCATCGTTGGAAGC 58.551 50.000 0.00 0.00 36.19 3.86
2359 2706 2.045561 TGCACTCGGTGAAGGAAAAA 57.954 45.000 8.04 0.00 35.23 1.94
2379 2726 0.598065 AAAGGCCACTCGTTCATTGC 59.402 50.000 5.01 0.00 0.00 3.56
2390 2737 4.083324 ACTCGTTCATTGCTTTGTGGTATG 60.083 41.667 0.00 0.00 0.00 2.39
2393 2740 4.616802 CGTTCATTGCTTTGTGGTATGTTC 59.383 41.667 0.00 0.00 0.00 3.18
2403 2750 7.812191 TGCTTTGTGGTATGTTCATGATTTTAC 59.188 33.333 0.00 0.00 0.00 2.01
2431 2778 8.925161 TTTATGGTGCTACTTTGAAATTATGC 57.075 30.769 0.00 0.00 0.00 3.14
2438 2785 9.405587 GTGCTACTTTGAAATTATGCTGTTTAA 57.594 29.630 0.00 0.00 0.00 1.52
2458 2805 8.203485 TGTTTAAGCACCTCTCAAATTTTCAAT 58.797 29.630 0.00 0.00 0.00 2.57
2461 2808 6.165700 AGCACCTCTCAAATTTTCAATTGT 57.834 33.333 5.13 0.00 0.00 2.71
2608 2956 7.589954 ACAAAATACTGTACAAGAAATTCACGC 59.410 33.333 0.00 0.00 0.00 5.34
2617 2965 8.346300 TGTACAAGAAATTCACGCTCAAATTAA 58.654 29.630 0.00 0.00 0.00 1.40
2771 3120 8.929260 TGAAAGACATGCTATTCCATTCATAT 57.071 30.769 0.00 0.00 0.00 1.78
2895 3244 3.256631 TCCAAGAAGGCTGCAAATTTCTC 59.743 43.478 0.50 0.00 37.29 2.87
2919 3268 5.933617 TGTGCTAGCTTTTCCATCTGATAT 58.066 37.500 17.23 0.00 0.00 1.63
3026 3376 3.342377 TGTAAGCGTGGAATCATGGAA 57.658 42.857 0.00 0.00 0.00 3.53
3035 3385 5.065914 CGTGGAATCATGGAACCTTCATAT 58.934 41.667 0.00 0.00 0.00 1.78
3039 3389 6.183347 GGAATCATGGAACCTTCATATAGGG 58.817 44.000 0.00 0.00 39.76 3.53
3040 3390 6.012508 GGAATCATGGAACCTTCATATAGGGA 60.013 42.308 0.00 0.00 39.76 4.20
3041 3391 7.312183 GGAATCATGGAACCTTCATATAGGGAT 60.312 40.741 0.00 0.00 39.76 3.85
3042 3392 6.378661 TCATGGAACCTTCATATAGGGATG 57.621 41.667 0.00 0.00 39.76 3.51
3043 3393 4.640771 TGGAACCTTCATATAGGGATGC 57.359 45.455 0.00 0.00 39.76 3.91
3044 3394 4.242811 TGGAACCTTCATATAGGGATGCT 58.757 43.478 0.00 0.00 39.76 3.79
3046 3396 5.849475 TGGAACCTTCATATAGGGATGCTAA 59.151 40.000 0.00 0.00 39.76 3.09
3047 3397 6.505344 TGGAACCTTCATATAGGGATGCTAAT 59.495 38.462 0.00 0.00 39.76 1.73
3048 3398 7.018550 TGGAACCTTCATATAGGGATGCTAATT 59.981 37.037 0.00 0.00 39.76 1.40
3049 3399 7.337942 GGAACCTTCATATAGGGATGCTAATTG 59.662 40.741 0.00 0.00 39.76 2.32
3050 3400 6.183347 ACCTTCATATAGGGATGCTAATTGC 58.817 40.000 0.00 0.00 39.76 3.56
3051 3401 6.012157 ACCTTCATATAGGGATGCTAATTGCT 60.012 38.462 0.00 0.00 40.05 3.91
3052 3402 7.182749 ACCTTCATATAGGGATGCTAATTGCTA 59.817 37.037 0.00 0.00 40.05 3.49
3053 3403 8.049117 CCTTCATATAGGGATGCTAATTGCTAA 58.951 37.037 0.00 0.00 43.37 3.09
3054 3404 9.624373 CTTCATATAGGGATGCTAATTGCTAAT 57.376 33.333 0.00 0.00 43.37 1.73
3123 3483 4.063689 TGGTGCATTTGTTTTTGCTATGG 58.936 39.130 0.00 0.00 39.60 2.74
3124 3484 4.202295 TGGTGCATTTGTTTTTGCTATGGA 60.202 37.500 0.00 0.00 39.60 3.41
3125 3485 4.152223 GGTGCATTTGTTTTTGCTATGGAC 59.848 41.667 0.00 0.00 39.60 4.02
3126 3486 4.749099 GTGCATTTGTTTTTGCTATGGACA 59.251 37.500 0.00 0.00 39.60 4.02
3127 3487 5.236047 GTGCATTTGTTTTTGCTATGGACAA 59.764 36.000 0.00 0.00 39.60 3.18
3131 3491 7.520292 GCATTTGTTTTTGCTATGGACAAACAT 60.520 33.333 4.84 0.00 41.34 2.71
3143 3503 3.244976 GGACAAACATTTCAGGATTGCG 58.755 45.455 0.00 0.00 0.00 4.85
3146 3506 2.988493 CAAACATTTCAGGATTGCGGTG 59.012 45.455 0.00 0.00 0.00 4.94
3150 3510 2.270352 TTTCAGGATTGCGGTGAAGT 57.730 45.000 0.00 0.00 32.00 3.01
3151 3511 3.410631 TTTCAGGATTGCGGTGAAGTA 57.589 42.857 0.00 0.00 32.00 2.24
3152 3512 3.410631 TTCAGGATTGCGGTGAAGTAA 57.589 42.857 0.00 0.00 0.00 2.24
3161 3521 7.339466 AGGATTGCGGTGAAGTAAAGAATAATT 59.661 33.333 0.00 0.00 0.00 1.40
3163 3523 8.911247 ATTGCGGTGAAGTAAAGAATAATTTC 57.089 30.769 0.00 0.00 0.00 2.17
3165 3525 8.780846 TGCGGTGAAGTAAAGAATAATTTCTA 57.219 30.769 0.00 0.00 41.42 2.10
3166 3526 9.391006 TGCGGTGAAGTAAAGAATAATTTCTAT 57.609 29.630 0.00 0.00 41.42 1.98
3167 3527 9.651718 GCGGTGAAGTAAAGAATAATTTCTATG 57.348 33.333 0.00 0.00 41.42 2.23
3179 3550 9.023962 AGAATAATTTCTATGTGAAGTTTGCCA 57.976 29.630 0.00 0.00 40.47 4.92
3210 3588 9.550406 AAATGAAATTCCACCATGCTATATTTG 57.450 29.630 0.00 0.00 33.67 2.32
3216 3594 7.759489 TTCCACCATGCTATATTTGAATACC 57.241 36.000 0.00 0.00 0.00 2.73
3390 3771 3.706086 ACAAGTTCCCTGTGATGCTTTTT 59.294 39.130 0.00 0.00 0.00 1.94
3420 3801 3.555139 GGAAGCGACTGATTGAAGATCTG 59.445 47.826 0.00 0.00 0.00 2.90
3441 3822 2.155279 GTTGGCAGAGAAGGACCTTTC 58.845 52.381 8.49 8.08 0.00 2.62
3452 3833 1.814793 GGACCTTTCCTTGAGACAGC 58.185 55.000 0.00 0.00 39.13 4.40
3639 4026 2.455674 AGCTGCACTGACGTATCAAA 57.544 45.000 1.02 0.00 33.30 2.69
3693 4080 1.489649 CTGATGTGCCAGGAATCCTCT 59.510 52.381 0.00 0.00 0.00 3.69
3808 4195 8.903820 GCTTTCCTAGGTACAAATGATGTATTT 58.096 33.333 9.08 0.00 45.87 1.40
3888 4277 5.904984 ATCATGCCTAGGTTTGTATACCA 57.095 39.130 11.31 0.00 40.82 3.25
3896 4285 6.483640 GCCTAGGTTTGTATACCAGAAGAATG 59.516 42.308 11.31 0.00 40.82 2.67
3914 4303 3.695830 ATGAAGCTTCCGTGGAAAGTA 57.304 42.857 23.42 1.02 33.34 2.24
3915 4304 2.762745 TGAAGCTTCCGTGGAAAGTAC 58.237 47.619 23.42 0.00 33.34 2.73
3983 4372 0.890996 AAAGAAAGCTCCAGCACGGG 60.891 55.000 0.48 0.00 45.16 5.28
4046 4435 4.607293 AAGGTGAATTTTTCCTGGCTTC 57.393 40.909 0.00 0.00 0.00 3.86
4049 4438 3.366374 GGTGAATTTTTCCTGGCTTCGAG 60.366 47.826 0.00 0.00 0.00 4.04
4084 4480 5.356751 ACTCTGTGTTCACTGCACAATTTTA 59.643 36.000 4.59 0.00 44.86 1.52
4086 4482 6.804677 TCTGTGTTCACTGCACAATTTTATT 58.195 32.000 4.59 0.00 44.86 1.40
4110 4514 1.832883 TGCTGCCGTTTGGTTGATAT 58.167 45.000 0.00 0.00 37.67 1.63
4115 4519 4.755123 GCTGCCGTTTGGTTGATATATACT 59.245 41.667 0.00 0.00 37.67 2.12
4116 4520 5.107065 GCTGCCGTTTGGTTGATATATACTC 60.107 44.000 0.00 0.00 37.67 2.59
4118 4522 5.989168 TGCCGTTTGGTTGATATATACTCTG 59.011 40.000 0.00 0.00 37.67 3.35
4119 4523 5.989777 GCCGTTTGGTTGATATATACTCTGT 59.010 40.000 0.00 0.00 37.67 3.41
4122 4526 9.355215 CCGTTTGGTTGATATATACTCTGTATC 57.645 37.037 0.00 0.00 0.00 2.24
4157 4652 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
4158 4653 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
4167 4662 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
4173 4668 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
4184 4679 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
4185 4680 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
4186 4681 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
4187 4682 0.967380 TTCCGAACGGAGGGAGTACC 60.967 60.000 15.34 0.00 46.06 3.34
4201 4696 5.632034 GGGAGTACCTTCCATGTATTCTT 57.368 43.478 3.75 0.00 39.09 2.52
4202 4697 6.742559 GGGAGTACCTTCCATGTATTCTTA 57.257 41.667 3.75 0.00 39.09 2.10
4207 4702 9.372369 GAGTACCTTCCATGTATTCTTATATGC 57.628 37.037 0.00 0.00 0.00 3.14
4234 4729 1.606668 TGGCGCCTGTTTTAGACTTTG 59.393 47.619 29.70 0.00 0.00 2.77
4300 5273 1.176527 GCAAGGCAGGCTACAATTCA 58.823 50.000 0.00 0.00 0.00 2.57
4375 5351 4.436242 TCACCTATTCGAAGAGTGTCAC 57.564 45.455 17.88 0.00 38.43 3.67
4426 5402 6.750148 AGGAGTGATAACACCGAAAGATATC 58.250 40.000 0.00 0.00 46.99 1.63
4543 5519 2.224378 TGATTCCGATGGCCTGATTCTC 60.224 50.000 3.32 0.00 0.00 2.87
4557 5534 6.823689 GGCCTGATTCTCAGTGAGTAAAAATA 59.176 38.462 19.53 0.00 42.80 1.40
4581 5558 4.019771 GGTCTTCTTCTCCATTCAAGAGGT 60.020 45.833 0.00 0.00 30.32 3.85
4613 5590 0.606401 TAGCTTGACTTGCCCTGTGC 60.606 55.000 0.00 0.00 41.77 4.57
4924 5902 7.415653 GGGAAATGCACCAATTTTTGTTTTGTA 60.416 33.333 0.00 0.00 29.89 2.41
4976 5954 5.363868 AGGGATCACAAAGTCGATATCAAGA 59.636 40.000 0.00 0.00 0.00 3.02
4987 5965 5.477291 AGTCGATATCAAGATACCCGACATT 59.523 40.000 28.35 17.20 45.09 2.71
5012 5990 1.069378 GCCGTTTCGACGACCTAGTG 61.069 60.000 0.00 0.00 34.64 2.74
5018 5996 1.241165 TCGACGACCTAGTGAAAGCA 58.759 50.000 0.00 0.00 0.00 3.91
5135 6113 1.000827 CAGAGATCGATGGGGAAGACG 60.001 57.143 0.54 0.00 0.00 4.18
5188 6166 1.151777 CTCACAAACGACGCTGGTGT 61.152 55.000 5.71 0.00 0.00 4.16
5228 6207 0.173481 CGGTGAAGAGAAGATCGCCA 59.827 55.000 6.23 0.00 44.65 5.69
5271 6250 7.645340 CCTGAGTTGATTTTCACTAACTTTGTG 59.355 37.037 0.00 0.00 33.83 3.33
5299 6278 4.868268 AGCTGACTCTAGTGTATGGGTTA 58.132 43.478 0.00 0.00 0.00 2.85
5431 6413 8.650143 AAATGGTGTTACACTGAAAATAGGAT 57.350 30.769 15.44 0.00 34.40 3.24
5452 6440 5.832060 GGATGAGTCCAAATTTGAGGATCAT 59.168 40.000 19.86 19.46 44.75 2.45
5453 6441 6.323225 GGATGAGTCCAAATTTGAGGATCATT 59.677 38.462 19.86 7.98 44.75 2.57
5478 6466 6.915300 TCATTCGAGTTTGTGTTATTTTGGTG 59.085 34.615 0.00 0.00 0.00 4.17
5480 6468 3.733727 CGAGTTTGTGTTATTTTGGTGCC 59.266 43.478 0.00 0.00 0.00 5.01
5533 6521 6.228258 ACAAACACGAATATCCAGTAGTTGT 58.772 36.000 0.00 0.00 0.00 3.32
5569 6557 6.656270 TCATGATTGTTGCACTAATGAGTCTT 59.344 34.615 0.00 0.00 31.73 3.01
5814 6802 6.375736 TGGCGTTACATTCATTTGGAGATAAA 59.624 34.615 0.00 0.00 0.00 1.40
5834 6822 7.611855 AGATAAAGTATTACAGGCTTGTGCTTT 59.388 33.333 12.40 16.48 38.23 3.51
5848 6836 1.070376 GTGCTTTCGTAACCGTGGAAC 60.070 52.381 0.00 0.00 35.01 3.62
5938 6932 8.627403 GCTACAAGTACTAGTCCATTACACATA 58.373 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 437 1.999735 CTTCTCGCGGCAATCACTTAA 59.000 47.619 6.13 0.00 0.00 1.85
218 485 3.645687 CCCTTCCCTTCACAATGGAAAAA 59.354 43.478 0.00 0.00 37.69 1.94
243 510 4.827835 GGATGGAGCTTAACTTATTTCCCC 59.172 45.833 0.00 0.00 0.00 4.81
244 511 4.827835 GGGATGGAGCTTAACTTATTTCCC 59.172 45.833 0.00 0.00 0.00 3.97
279 574 7.607991 TGTGAAAATAAGCCAAAAGTCCAAAAA 59.392 29.630 0.00 0.00 0.00 1.94
343 638 1.218875 TTCGTGCGTAGTTGTGGCTG 61.219 55.000 0.00 0.00 0.00 4.85
344 639 0.320421 ATTCGTGCGTAGTTGTGGCT 60.320 50.000 0.00 0.00 0.00 4.75
349 644 2.058798 ACACAGATTCGTGCGTAGTTG 58.941 47.619 8.05 0.00 40.73 3.16
352 647 1.649171 GTCACACAGATTCGTGCGTAG 59.351 52.381 8.05 0.00 40.73 3.51
435 730 2.521547 AAAGGAAAGGAGCCCAGATG 57.478 50.000 0.00 0.00 0.00 2.90
441 736 3.834813 AGATTTGGAAAAGGAAAGGAGCC 59.165 43.478 0.00 0.00 0.00 4.70
568 876 2.583520 GGCTGTGCCCTGAGAGAG 59.416 66.667 0.00 0.00 44.06 3.20
623 947 2.669569 TGGAACTGGCTTCGCAGC 60.670 61.111 0.00 0.00 46.52 5.25
624 948 3.257933 GTGGAACTGGCTTCGCAG 58.742 61.111 0.00 0.00 0.00 5.18
684 1009 7.955864 GGTTAACTAAGTAAACAAGAATCAGCG 59.044 37.037 5.42 0.00 0.00 5.18
700 1025 1.471501 GGGTACGGGCGGTTAACTAAG 60.472 57.143 5.42 0.00 0.00 2.18
755 1086 0.683179 GCTATGGGTGGTTGGGGTTC 60.683 60.000 0.00 0.00 0.00 3.62
770 1101 1.222936 GGGCTGTGCTGACTGCTAT 59.777 57.895 5.87 0.00 44.33 2.97
771 1102 2.665000 GGGCTGTGCTGACTGCTA 59.335 61.111 5.87 0.00 44.33 3.49
925 1264 1.268032 GCAATCAACGCTATCCAACCG 60.268 52.381 0.00 0.00 0.00 4.44
935 1274 1.135575 CCCTTCAAGAGCAATCAACGC 60.136 52.381 0.00 0.00 0.00 4.84
963 1302 2.032620 TCGAGACTCTGCTAATTCCCC 58.967 52.381 0.03 0.00 0.00 4.81
968 1307 3.129638 GGTCAACTCGAGACTCTGCTAAT 59.870 47.826 21.68 0.00 36.29 1.73
970 1309 2.085320 GGTCAACTCGAGACTCTGCTA 58.915 52.381 21.68 0.00 36.29 3.49
981 1320 0.318699 TGACAAGCTCGGTCAACTCG 60.319 55.000 16.31 0.00 41.96 4.18
1131 1470 0.391661 TAGGCCAGCAAAGAGAAGCG 60.392 55.000 5.01 0.00 35.48 4.68
1146 1485 6.827727 TCCAATCCATAGTACTTTCTTAGGC 58.172 40.000 0.00 0.00 0.00 3.93
1184 1529 9.964354 CCATCCTATGGTCATATGAGAAAATAA 57.036 33.333 5.42 0.00 45.54 1.40
1300 1645 5.361857 AGATGGAATGAAGCCCAAATACTTG 59.638 40.000 0.00 0.00 35.85 3.16
1463 1808 5.699143 AGTACCACATAGGGTCGTTACTAT 58.301 41.667 0.00 0.00 43.89 2.12
1498 1844 6.867519 TGAACTCTATTGGTTCCATCACTA 57.132 37.500 0.00 0.00 41.42 2.74
1588 1934 2.605299 GGGGCGGAGGGAGTACTA 59.395 66.667 0.00 0.00 0.00 1.82
1593 1939 2.138179 TAATTCGGGGCGGAGGGAG 61.138 63.158 0.00 0.00 0.00 4.30
1594 1940 2.041715 TAATTCGGGGCGGAGGGA 60.042 61.111 0.00 0.00 0.00 4.20
1595 1941 1.979619 AAGTAATTCGGGGCGGAGGG 61.980 60.000 0.00 0.00 0.00 4.30
1596 1942 0.814010 CAAGTAATTCGGGGCGGAGG 60.814 60.000 0.00 0.00 0.00 4.30
1597 1943 0.107848 ACAAGTAATTCGGGGCGGAG 60.108 55.000 0.00 0.00 0.00 4.63
1598 1944 0.108041 GACAAGTAATTCGGGGCGGA 60.108 55.000 0.00 0.00 0.00 5.54
1599 1945 0.107848 AGACAAGTAATTCGGGGCGG 60.108 55.000 0.00 0.00 0.00 6.13
1600 1946 1.734163 AAGACAAGTAATTCGGGGCG 58.266 50.000 0.00 0.00 0.00 6.13
1601 1947 4.133013 TCTAAGACAAGTAATTCGGGGC 57.867 45.455 0.00 0.00 0.00 5.80
1602 1948 6.598064 ACAAATCTAAGACAAGTAATTCGGGG 59.402 38.462 0.00 0.00 0.00 5.73
1603 1949 7.611213 ACAAATCTAAGACAAGTAATTCGGG 57.389 36.000 0.00 0.00 0.00 5.14
1633 1979 9.698309 CCGAATTACTTGTCTAGATACATTCAT 57.302 33.333 0.00 0.00 0.00 2.57
1634 1980 8.909923 TCCGAATTACTTGTCTAGATACATTCA 58.090 33.333 0.00 0.00 0.00 2.57
1635 1981 9.745880 TTCCGAATTACTTGTCTAGATACATTC 57.254 33.333 0.00 0.00 0.00 2.67
1636 1982 9.530633 GTTCCGAATTACTTGTCTAGATACATT 57.469 33.333 0.00 0.00 0.00 2.71
1637 1983 7.861372 CGTTCCGAATTACTTGTCTAGATACAT 59.139 37.037 0.00 0.00 0.00 2.29
1638 1984 7.191551 CGTTCCGAATTACTTGTCTAGATACA 58.808 38.462 0.00 0.00 0.00 2.29
1639 1985 6.636044 CCGTTCCGAATTACTTGTCTAGATAC 59.364 42.308 0.00 0.00 0.00 2.24
1640 1986 6.543465 TCCGTTCCGAATTACTTGTCTAGATA 59.457 38.462 0.00 0.00 0.00 1.98
1641 1987 5.359009 TCCGTTCCGAATTACTTGTCTAGAT 59.641 40.000 0.00 0.00 0.00 1.98
1642 1988 4.701651 TCCGTTCCGAATTACTTGTCTAGA 59.298 41.667 0.00 0.00 0.00 2.43
1643 1989 4.990257 TCCGTTCCGAATTACTTGTCTAG 58.010 43.478 0.00 0.00 0.00 2.43
1644 1990 4.142315 CCTCCGTTCCGAATTACTTGTCTA 60.142 45.833 0.00 0.00 0.00 2.59
1645 1991 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
1646 1992 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1647 1993 2.301009 ACCTCCGTTCCGAATTACTTGT 59.699 45.455 0.00 0.00 0.00 3.16
1648 1994 2.968675 ACCTCCGTTCCGAATTACTTG 58.031 47.619 0.00 0.00 0.00 3.16
1649 1995 4.806640 TTACCTCCGTTCCGAATTACTT 57.193 40.909 0.00 0.00 0.00 2.24
1650 1996 6.661304 ATATTACCTCCGTTCCGAATTACT 57.339 37.500 0.00 0.00 0.00 2.24
1651 1997 6.524586 CGTATATTACCTCCGTTCCGAATTAC 59.475 42.308 0.00 0.00 0.00 1.89
1652 1998 6.429692 TCGTATATTACCTCCGTTCCGAATTA 59.570 38.462 0.00 0.00 0.00 1.40
1653 1999 5.241506 TCGTATATTACCTCCGTTCCGAATT 59.758 40.000 0.00 0.00 0.00 2.17
1654 2000 4.761739 TCGTATATTACCTCCGTTCCGAAT 59.238 41.667 0.00 0.00 0.00 3.34
1655 2001 4.133820 TCGTATATTACCTCCGTTCCGAA 58.866 43.478 0.00 0.00 0.00 4.30
1656 2002 3.738982 TCGTATATTACCTCCGTTCCGA 58.261 45.455 0.00 0.00 0.00 4.55
1657 2003 4.691860 ATCGTATATTACCTCCGTTCCG 57.308 45.455 0.00 0.00 0.00 4.30
1658 2004 7.765307 TCATTATCGTATATTACCTCCGTTCC 58.235 38.462 0.00 0.00 0.00 3.62
1659 2005 8.457261 ACTCATTATCGTATATTACCTCCGTTC 58.543 37.037 0.00 0.00 0.00 3.95
1660 2006 8.345724 ACTCATTATCGTATATTACCTCCGTT 57.654 34.615 0.00 0.00 0.00 4.44
1661 2007 7.934855 ACTCATTATCGTATATTACCTCCGT 57.065 36.000 0.00 0.00 0.00 4.69
1662 2008 9.635520 AAAACTCATTATCGTATATTACCTCCG 57.364 33.333 0.00 0.00 0.00 4.63
1674 2020 9.665264 GAAACAAGAAAGAAAACTCATTATCGT 57.335 29.630 0.00 0.00 0.00 3.73
1675 2021 9.884465 AGAAACAAGAAAGAAAACTCATTATCG 57.116 29.630 0.00 0.00 0.00 2.92
1696 2042 6.154445 AGTGCACATGATCATTTTCAGAAAC 58.846 36.000 21.04 0.00 0.00 2.78
1709 2055 5.565439 GCTTAAAGTCCAAAGTGCACATGAT 60.565 40.000 21.04 4.65 0.00 2.45
1715 2061 2.660572 TGGCTTAAAGTCCAAAGTGCA 58.339 42.857 0.00 0.00 0.00 4.57
1716 2062 3.942130 ATGGCTTAAAGTCCAAAGTGC 57.058 42.857 0.00 0.00 35.75 4.40
1719 2065 5.012046 AGGGAAAATGGCTTAAAGTCCAAAG 59.988 40.000 0.00 0.00 35.75 2.77
1764 2111 4.162698 TGACCAGTAGCAACCCGTTATATT 59.837 41.667 0.00 0.00 0.00 1.28
1772 2119 0.811281 GCAATGACCAGTAGCAACCC 59.189 55.000 0.00 0.00 0.00 4.11
1778 2125 3.402110 TGTCAGTTGCAATGACCAGTAG 58.598 45.455 25.65 4.51 45.24 2.57
1781 2128 3.928727 ATTGTCAGTTGCAATGACCAG 57.071 42.857 25.65 5.53 45.24 4.00
1785 2132 5.067544 TGACTTGAATTGTCAGTTGCAATGA 59.932 36.000 0.59 4.94 39.23 2.57
1838 2185 4.082245 CCCTTGCGTTCATTTACTTCCAAT 60.082 41.667 0.00 0.00 0.00 3.16
1853 2200 1.821216 AATTTCGATCACCCTTGCGT 58.179 45.000 0.00 0.00 0.00 5.24
1855 2202 3.575965 ACAAATTTCGATCACCCTTGC 57.424 42.857 0.00 0.00 0.00 4.01
1865 2212 8.160521 TGATTTCTGGAAGTAACAAATTTCGA 57.839 30.769 0.00 0.00 33.76 3.71
1900 2247 5.714047 TGAAACAACACATGTGTAGCAAAA 58.286 33.333 30.75 13.54 44.13 2.44
1901 2248 5.316327 TGAAACAACACATGTGTAGCAAA 57.684 34.783 30.75 13.04 44.13 3.68
1926 2273 6.421485 AGAACACAGGATTAGCAAATCAGAT 58.579 36.000 0.99 0.00 42.88 2.90
1933 2280 4.261572 GCAACAAGAACACAGGATTAGCAA 60.262 41.667 0.00 0.00 0.00 3.91
1937 2284 6.272318 CAAAAGCAACAAGAACACAGGATTA 58.728 36.000 0.00 0.00 0.00 1.75
1944 2291 2.892374 AGGCAAAAGCAACAAGAACAC 58.108 42.857 0.00 0.00 0.00 3.32
1993 2340 4.111375 ACCGATCGCTATAATAAGCCAG 57.889 45.455 10.32 0.00 39.43 4.85
2005 2352 1.137086 AGTGCAGAAATACCGATCGCT 59.863 47.619 10.32 0.00 0.00 4.93
2014 2361 1.207089 CCCAGGACGAGTGCAGAAATA 59.793 52.381 0.00 0.00 0.00 1.40
2017 2364 2.583441 CCCCAGGACGAGTGCAGAA 61.583 63.158 0.00 0.00 0.00 3.02
2029 2376 0.251341 GCATAGGCCATAACCCCAGG 60.251 60.000 5.01 0.00 0.00 4.45
2035 2382 5.224888 CAAATCACATGCATAGGCCATAAC 58.775 41.667 5.01 0.00 40.13 1.89
2062 2409 5.154932 CGCTACCTTATGATGCAGTAGTAC 58.845 45.833 8.34 0.00 34.29 2.73
2077 2424 3.275999 ACAAAACTGTGAACGCTACCTT 58.724 40.909 0.00 0.00 0.00 3.50
2128 2475 8.476447 AGCACATCTATCTACATAGATCCATTG 58.524 37.037 4.66 3.11 45.74 2.82
2129 2476 8.476447 CAGCACATCTATCTACATAGATCCATT 58.524 37.037 4.66 0.00 45.74 3.16
2143 2490 3.555139 GTCAGCAACTCAGCACATCTATC 59.445 47.826 0.00 0.00 36.85 2.08
2168 2515 3.131755 GCCTTCATGAAAAAGGGGATCAG 59.868 47.826 9.88 0.00 43.00 2.90
2181 2528 1.074405 AGCTTGGTTCTGCCTTCATGA 59.926 47.619 0.00 0.00 38.35 3.07
2182 2529 1.201647 CAGCTTGGTTCTGCCTTCATG 59.798 52.381 0.00 0.00 38.35 3.07
2278 2625 0.517316 CCAGCAAGTACGCTTCCAAC 59.483 55.000 0.00 0.00 41.38 3.77
2359 2706 1.000274 GCAATGAACGAGTGGCCTTTT 60.000 47.619 3.32 0.00 0.00 2.27
2370 2717 4.159377 ACATACCACAAAGCAATGAACG 57.841 40.909 0.00 0.00 0.00 3.95
2379 2726 9.912634 AAGTAAAATCATGAACATACCACAAAG 57.087 29.630 0.00 0.00 0.00 2.77
2390 2737 9.423061 AGCACCATAAAAAGTAAAATCATGAAC 57.577 29.630 0.00 0.00 0.00 3.18
2413 2760 9.624697 CTTAAACAGCATAATTTCAAAGTAGCA 57.375 29.630 0.00 0.00 0.00 3.49
2431 2778 7.202526 TGAAAATTTGAGAGGTGCTTAAACAG 58.797 34.615 0.00 0.00 35.27 3.16
2438 2785 6.165700 ACAATTGAAAATTTGAGAGGTGCT 57.834 33.333 13.59 0.00 0.00 4.40
2451 2798 7.013083 CCCAACATGGATTTTGACAATTGAAAA 59.987 33.333 13.59 9.80 40.96 2.29
2458 2805 2.038295 GCCCCAACATGGATTTTGACAA 59.962 45.455 0.00 0.00 40.96 3.18
2461 2808 1.274712 GGCCCCAACATGGATTTTGA 58.725 50.000 0.00 0.00 40.96 2.69
2590 2938 4.990543 TGAGCGTGAATTTCTTGTACAG 57.009 40.909 0.00 0.00 0.00 2.74
2617 2965 5.182487 GGAATATTTGACCGGCCAATTTTT 58.818 37.500 3.27 2.41 0.00 1.94
2625 2973 3.202829 TGTAGGGAATATTTGACCGGC 57.797 47.619 0.00 0.00 0.00 6.13
2654 3003 4.469657 TCATGTAAAACAAGCACTCCCTT 58.530 39.130 0.00 0.00 0.00 3.95
2771 3120 6.381133 ACCGTAGATCATCCATATATGCAAGA 59.619 38.462 7.24 4.70 0.00 3.02
2883 3232 3.439476 AGCTAGCACAGAGAAATTTGCAG 59.561 43.478 18.83 0.00 37.44 4.41
2895 3244 3.603532 TCAGATGGAAAAGCTAGCACAG 58.396 45.455 18.83 0.00 0.00 3.66
2940 3290 4.705507 TGCACTACTCAAGTTAGTCCTAGG 59.294 45.833 0.82 0.82 35.76 3.02
2995 3345 8.898761 TGATTCCACGCTTACAATTACATATTT 58.101 29.630 0.00 0.00 0.00 1.40
2996 3346 8.445275 TGATTCCACGCTTACAATTACATATT 57.555 30.769 0.00 0.00 0.00 1.28
2997 3347 8.506437 CATGATTCCACGCTTACAATTACATAT 58.494 33.333 0.00 0.00 0.00 1.78
2998 3348 7.041440 CCATGATTCCACGCTTACAATTACATA 60.041 37.037 0.00 0.00 0.00 2.29
2999 3349 6.238731 CCATGATTCCACGCTTACAATTACAT 60.239 38.462 0.00 0.00 0.00 2.29
3003 3353 4.269183 TCCATGATTCCACGCTTACAATT 58.731 39.130 0.00 0.00 0.00 2.32
3011 3361 1.401905 GAAGGTTCCATGATTCCACGC 59.598 52.381 0.00 0.00 0.00 5.34
3012 3362 2.710377 TGAAGGTTCCATGATTCCACG 58.290 47.619 0.00 0.00 0.00 4.94
3026 3376 6.183347 GCAATTAGCATCCCTATATGAAGGT 58.817 40.000 0.00 0.00 44.79 3.50
3085 3435 9.153721 CAAATGCACCATATAACAAAAGAACAT 57.846 29.630 0.00 0.00 0.00 2.71
3123 3483 3.244976 CCGCAATCCTGAAATGTTTGTC 58.755 45.455 0.00 0.00 0.00 3.18
3124 3484 2.627699 ACCGCAATCCTGAAATGTTTGT 59.372 40.909 0.00 0.00 0.00 2.83
3125 3485 2.988493 CACCGCAATCCTGAAATGTTTG 59.012 45.455 0.00 0.00 0.00 2.93
3126 3486 2.890311 TCACCGCAATCCTGAAATGTTT 59.110 40.909 0.00 0.00 0.00 2.83
3127 3487 2.513753 TCACCGCAATCCTGAAATGTT 58.486 42.857 0.00 0.00 0.00 2.71
3131 3491 2.270352 ACTTCACCGCAATCCTGAAA 57.730 45.000 0.00 0.00 0.00 2.69
3152 3512 9.860898 GGCAAACTTCACATAGAAATTATTCTT 57.139 29.630 0.00 0.00 43.43 2.52
3161 3521 5.069318 TGACATGGCAAACTTCACATAGAA 58.931 37.500 0.00 0.00 34.41 2.10
3163 3523 5.375417 TTGACATGGCAAACTTCACATAG 57.625 39.130 12.79 0.00 0.00 2.23
3165 3525 4.669206 TTTGACATGGCAAACTTCACAT 57.331 36.364 22.97 0.00 33.16 3.21
3166 3526 4.099113 TCATTTGACATGGCAAACTTCACA 59.901 37.500 28.63 5.36 40.23 3.58
3167 3527 4.619973 TCATTTGACATGGCAAACTTCAC 58.380 39.130 28.63 0.00 40.23 3.18
3169 3529 6.790285 ATTTCATTTGACATGGCAAACTTC 57.210 33.333 28.63 0.00 40.23 3.01
3172 3543 5.469421 TGGAATTTCATTTGACATGGCAAAC 59.531 36.000 28.63 13.76 40.23 2.93
3179 3550 5.046159 AGCATGGTGGAATTTCATTTGACAT 60.046 36.000 0.00 0.00 0.00 3.06
3244 3625 9.482627 AGTTAACTGTTTGAATTTGTTCAACAA 57.517 25.926 7.48 0.00 40.29 2.83
3390 3771 4.081142 TCAATCAGTCGCTTCCATCCTTTA 60.081 41.667 0.00 0.00 0.00 1.85
3420 3801 0.402121 AAGGTCCTTCTCTGCCAACC 59.598 55.000 0.00 0.00 0.00 3.77
3441 3822 1.835483 GCACACACGCTGTCTCAAGG 61.835 60.000 0.00 0.00 0.00 3.61
3627 4008 2.673368 GGCTTCACCTTTGATACGTCAG 59.327 50.000 0.00 0.00 33.33 3.51
3639 4026 2.925170 AGCTCCGTGGCTTCACCT 60.925 61.111 0.00 0.00 39.86 4.00
3664 4051 1.816835 CTGGCACATCAGCAAGATTGT 59.183 47.619 0.00 0.00 37.80 2.71
3667 4054 0.622136 TCCTGGCACATCAGCAAGAT 59.378 50.000 0.00 0.00 37.80 2.40
3693 4080 6.899089 TGCATAAGATAGTCCCATGAAAAGA 58.101 36.000 0.00 0.00 0.00 2.52
3808 4195 5.764686 ACGCAAGGAGAATAATGCAATATGA 59.235 36.000 0.00 0.00 46.39 2.15
3888 4277 2.303022 TCCACGGAAGCTTCATTCTTCT 59.697 45.455 27.02 0.00 39.75 2.85
3896 4285 2.074576 GGTACTTTCCACGGAAGCTTC 58.925 52.381 18.54 18.54 35.38 3.86
3937 4326 1.202687 TGCTTATCCCTGAATGAGGCG 60.203 52.381 0.00 0.00 41.19 5.52
4084 4480 1.134551 ACCAAACGGCAGCAACAAAAT 60.135 42.857 0.00 0.00 0.00 1.82
4086 4482 0.247736 AACCAAACGGCAGCAACAAA 59.752 45.000 0.00 0.00 0.00 2.83
4132 4536 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
4133 4537 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
4135 4539 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
4136 4540 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
4137 4541 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
4141 4545 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
4142 4546 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
4143 4547 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
4144 4548 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
4145 4549 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
4146 4550 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
4149 4644 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
4155 4650 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
4156 4651 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
4157 4652 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
4158 4653 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
4167 4662 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
4173 4668 0.115745 TGGAAGGTACTCCCTCCGTT 59.884 55.000 0.00 0.00 45.47 4.44
4184 4679 8.321353 CCAGCATATAAGAATACATGGAAGGTA 58.679 37.037 0.00 0.00 37.57 3.08
4185 4680 7.170965 CCAGCATATAAGAATACATGGAAGGT 58.829 38.462 0.00 0.00 32.53 3.50
4186 4681 6.600822 CCCAGCATATAAGAATACATGGAAGG 59.399 42.308 0.00 0.00 0.00 3.46
4187 4682 7.397221 TCCCAGCATATAAGAATACATGGAAG 58.603 38.462 0.00 0.00 0.00 3.46
4188 4683 7.328404 TCCCAGCATATAAGAATACATGGAA 57.672 36.000 0.00 0.00 0.00 3.53
4189 4684 6.950860 TCCCAGCATATAAGAATACATGGA 57.049 37.500 0.00 0.00 0.00 3.41
4190 4685 7.067859 CCATTCCCAGCATATAAGAATACATGG 59.932 40.741 0.00 0.00 0.00 3.66
4191 4686 7.415989 GCCATTCCCAGCATATAAGAATACATG 60.416 40.741 0.00 0.00 0.00 3.21
4192 4687 6.604795 GCCATTCCCAGCATATAAGAATACAT 59.395 38.462 0.00 0.00 0.00 2.29
4193 4688 5.945784 GCCATTCCCAGCATATAAGAATACA 59.054 40.000 0.00 0.00 0.00 2.29
4194 4689 5.065218 CGCCATTCCCAGCATATAAGAATAC 59.935 44.000 0.00 0.00 0.00 1.89
4195 4690 5.185454 CGCCATTCCCAGCATATAAGAATA 58.815 41.667 0.00 0.00 0.00 1.75
4196 4691 4.012374 CGCCATTCCCAGCATATAAGAAT 58.988 43.478 0.00 0.00 0.00 2.40
4197 4692 3.411446 CGCCATTCCCAGCATATAAGAA 58.589 45.455 0.00 0.00 0.00 2.52
4198 4693 2.875672 GCGCCATTCCCAGCATATAAGA 60.876 50.000 0.00 0.00 0.00 2.10
4199 4694 1.470098 GCGCCATTCCCAGCATATAAG 59.530 52.381 0.00 0.00 0.00 1.73
4200 4695 1.533625 GCGCCATTCCCAGCATATAA 58.466 50.000 0.00 0.00 0.00 0.98
4201 4696 0.322456 GGCGCCATTCCCAGCATATA 60.322 55.000 24.80 0.00 0.00 0.86
4202 4697 1.604593 GGCGCCATTCCCAGCATAT 60.605 57.895 24.80 0.00 0.00 1.78
4207 4702 1.535204 AAAACAGGCGCCATTCCCAG 61.535 55.000 31.54 11.20 0.00 4.45
4300 5273 6.940831 AAACTGCACAAATTTAAGCCAATT 57.059 29.167 10.45 1.91 0.00 2.32
4426 5402 3.691049 TTGCCTGACTTTGTTTCTTCG 57.309 42.857 0.00 0.00 0.00 3.79
4471 5447 4.342092 AGAATAACATATGCTGGCAAACCC 59.658 41.667 1.58 0.00 33.59 4.11
4543 5519 9.145865 GAGAAGAAGACCTATTTTTACTCACTG 57.854 37.037 0.00 0.00 0.00 3.66
4557 5534 4.224818 CCTCTTGAATGGAGAAGAAGACCT 59.775 45.833 0.00 0.00 33.03 3.85
4581 5558 3.056107 AGTCAAGCTAAGCCATAACGACA 60.056 43.478 0.00 0.00 0.00 4.35
4613 5590 1.822990 ACAGCCATCTCCTGCAAATTG 59.177 47.619 0.00 0.00 33.65 2.32
4814 5791 3.009723 GTTTTCGCTCATTCAGGGATGA 58.990 45.455 0.00 0.00 43.35 2.92
4924 5902 8.072567 GCAATCTAGCACAAGATCGAAATAATT 58.927 33.333 0.00 0.00 35.10 1.40
4976 5954 0.814010 GGCGCTTGAATGTCGGGTAT 60.814 55.000 7.64 0.00 0.00 2.73
5012 5990 2.483491 CAGCTCCTCAGAAAGTGCTTTC 59.517 50.000 14.80 14.80 46.85 2.62
5018 5996 2.178580 CTCTCCAGCTCCTCAGAAAGT 58.821 52.381 0.00 0.00 0.00 2.66
5096 6074 3.002791 CTGGCTAAGCATTCGAACAAGA 58.997 45.455 0.00 0.00 0.00 3.02
5135 6113 2.203126 CCTCCTCGGATGCTTGCC 60.203 66.667 0.00 0.00 33.16 4.52
5228 6207 5.819991 ACTCAGGAAACACATATGGACAAT 58.180 37.500 7.80 0.00 0.00 2.71
5318 6297 5.302823 ACTTTGCTTTCTAAAACATGGAGCT 59.697 36.000 0.00 0.00 0.00 4.09
5330 6309 2.066262 CGAGGCGAACTTTGCTTTCTA 58.934 47.619 0.92 0.00 0.00 2.10
5419 6401 8.742777 TCAAATTTGGACTCATCCTATTTTCAG 58.257 33.333 17.90 0.00 46.43 3.02
5431 6413 6.247676 TGAATGATCCTCAAATTTGGACTCA 58.752 36.000 17.90 14.72 34.90 3.41
5452 6440 7.433719 CACCAAAATAACACAAACTCGAATGAA 59.566 33.333 0.08 0.00 0.00 2.57
5453 6441 6.915300 CACCAAAATAACACAAACTCGAATGA 59.085 34.615 0.08 0.00 0.00 2.57
5455 6443 5.689961 GCACCAAAATAACACAAACTCGAAT 59.310 36.000 0.00 0.00 0.00 3.34
5458 6446 3.733727 GGCACCAAAATAACACAAACTCG 59.266 43.478 0.00 0.00 0.00 4.18
5478 6466 2.029649 AGTGCAACATTCATGTGAAGGC 60.030 45.455 7.26 6.08 41.61 4.35
5480 6468 8.969121 TTATTTAGTGCAACATTCATGTGAAG 57.031 30.769 1.65 0.00 41.61 3.02
5510 6498 6.721571 ACAACTACTGGATATTCGTGTTTG 57.278 37.500 0.00 0.00 0.00 2.93
5511 6499 7.739498 AAACAACTACTGGATATTCGTGTTT 57.261 32.000 0.00 0.00 0.00 2.83
5541 6529 6.656270 ACTCATTAGTGCAACAATCATGAAGA 59.344 34.615 0.00 0.00 41.43 2.87
5597 6585 1.571955 TGAGCCAGCTGGACTTCATA 58.428 50.000 37.21 15.88 37.39 2.15
5602 6590 1.303155 GCTTTGAGCCAGCTGGACT 60.303 57.895 37.21 29.80 34.48 3.85
5780 6768 0.249120 ATGTAACGCCAGCTGCACTA 59.751 50.000 8.66 0.00 41.33 2.74
5814 6802 3.684788 CGAAAGCACAAGCCTGTAATACT 59.315 43.478 0.00 0.00 43.56 2.12
5834 6822 0.383590 TGTTCGTTCCACGGTTACGA 59.616 50.000 10.60 10.60 42.81 3.43
5848 6836 2.936498 AGGTTGAGACTGTTGTTGTTCG 59.064 45.455 0.00 0.00 0.00 3.95
5938 6932 5.258841 TGAGATCTGCCATGTTTCTTCATT 58.741 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.