Multiple sequence alignment - TraesCS1A01G149800

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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 TraesCS1A01G149800 chr1A 100.000 8445 0 0 1 8445 257550896 257559340 0.000000e+00 15596.0
1 TraesCS1A01G149800 chr1A 93.220 59 4 0 2581 2639 257553320 257553378 4.200000e-13 87.9
2 TraesCS1A01G149800 chr1A 93.220 59 4 0 2425 2483 257553476 257553534 4.200000e-13 87.9
3 TraesCS1A01G149800 chr1B 97.371 3271 54 16 2351 5613 297094025 297097271 0.000000e+00 5535.0
4 TraesCS1A01G149800 chr1B 94.189 2461 82 22 5781 8217 297097603 297100026 0.000000e+00 3696.0
5 TraesCS1A01G149800 chr1B 91.478 1631 70 17 760 2353 297092346 297093944 0.000000e+00 2178.0
6 TraesCS1A01G149800 chr1B 86.194 804 81 10 1 779 297091544 297092342 0.000000e+00 843.0
7 TraesCS1A01G149800 chr1B 93.785 177 10 1 8269 8445 297100011 297100186 1.810000e-66 265.0
8 TraesCS1A01G149800 chr1B 94.675 169 5 1 5616 5784 297097326 297097490 8.410000e-65 259.0
9 TraesCS1A01G149800 chr1D 93.999 2233 58 26 5616 7818 203290779 203292965 0.000000e+00 3312.0
10 TraesCS1A01G149800 chr1D 98.217 1795 22 7 2397 4185 203285639 203287429 0.000000e+00 3129.0
11 TraesCS1A01G149800 chr1D 98.196 1441 17 2 4172 5612 203289292 203290723 0.000000e+00 2508.0
12 TraesCS1A01G149800 chr1D 93.290 1535 60 18 792 2311 203284136 203285642 0.000000e+00 2224.0
13 TraesCS1A01G149800 chr1D 84.754 833 68 24 1 787 203283208 203284027 0.000000e+00 780.0
14 TraesCS1A01G149800 chr1D 94.681 470 22 1 7976 8445 203293079 203293545 0.000000e+00 726.0
15 TraesCS1A01G149800 chr1D 95.098 102 5 0 7890 7991 203292964 203293065 2.440000e-35 161.0
16 TraesCS1A01G149800 chr1D 94.915 59 3 0 2425 2483 203285823 203285881 9.030000e-15 93.5
17 TraesCS1A01G149800 chr1D 93.220 59 4 0 2581 2639 203285667 203285725 4.200000e-13 87.9
18 TraesCS1A01G149800 chr6D 75.161 620 114 32 4980 5570 47662474 47661866 1.090000e-63 255.0
19 TraesCS1A01G149800 chr6B 75.161 620 113 30 4980 5570 123843275 123843882 3.910000e-63 254.0
20 TraesCS1A01G149800 chr2B 89.431 123 12 1 4530 4652 707609879 707610000 4.080000e-33 154.0
21 TraesCS1A01G149800 chr2B 96.000 75 3 0 6228 6302 227855163 227855089 1.150000e-23 122.0
22 TraesCS1A01G149800 chr2B 81.897 116 20 1 2183 2298 258639425 258639311 6.980000e-16 97.1
23 TraesCS1A01G149800 chr2B 91.525 59 3 2 8217 8273 166612749 166612691 7.030000e-11 80.5
24 TraesCS1A01G149800 chr2B 91.379 58 3 2 8213 8269 513267182 513267238 2.530000e-10 78.7
25 TraesCS1A01G149800 chr5B 96.154 78 3 0 6228 6305 574956515 574956438 2.470000e-25 128.0
26 TraesCS1A01G149800 chr3D 94.186 86 2 3 6228 6310 422517724 422517809 2.470000e-25 128.0
27 TraesCS1A01G149800 chr3A 97.297 74 2 0 6225 6298 353624523 353624596 8.900000e-25 126.0
28 TraesCS1A01G149800 chr3A 94.444 54 2 1 8217 8269 669772476 669772529 1.950000e-11 82.4
29 TraesCS1A01G149800 chr5D 94.872 78 4 0 6228 6305 468170539 468170462 1.150000e-23 122.0
30 TraesCS1A01G149800 chr2D 94.872 78 4 0 6225 6302 169965058 169965135 1.150000e-23 122.0
31 TraesCS1A01G149800 chr2A 96.000 75 3 0 6228 6302 180354942 180354868 1.150000e-23 122.0
32 TraesCS1A01G149800 chr2A 80.405 148 28 1 5889 6035 750108162 750108309 2.490000e-20 111.0
33 TraesCS1A01G149800 chr2A 94.545 55 2 1 8217 8270 133466983 133466929 5.430000e-12 84.2
34 TraesCS1A01G149800 chr6A 81.752 137 16 6 2196 2325 137379849 137379715 1.160000e-18 106.0
35 TraesCS1A01G149800 chr7D 94.643 56 2 1 8217 8271 535848576 535848521 1.510000e-12 86.1
36 TraesCS1A01G149800 chr7B 94.444 54 2 1 8213 8265 703708310 703708363 1.950000e-11 82.4
37 TraesCS1A01G149800 chr4D 90.000 60 4 2 8217 8275 29181781 29181839 9.090000e-10 76.8
38 TraesCS1A01G149800 chr3B 89.831 59 4 2 8213 8270 167066009 167065952 3.270000e-09 75.0


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 TraesCS1A01G149800 chr1A 257550896 257559340 8444 False 15596.000000 15596 100.000000 1 8445 1 chr1A.!!$F1 8444
1 TraesCS1A01G149800 chr1B 297091544 297100186 8642 False 2129.333333 5535 92.948667 1 8445 6 chr1B.!!$F1 8444
2 TraesCS1A01G149800 chr1D 203283208 203293545 10337 False 1446.822222 3312 94.041111 1 8445 9 chr1D.!!$F1 8444
3 TraesCS1A01G149800 chr6D 47661866 47662474 608 True 255.000000 255 75.161000 4980 5570 1 chr6D.!!$R1 590
4 TraesCS1A01G149800 chr6B 123843275 123843882 607 False 254.000000 254 75.161000 4980 5570 1 chr6B.!!$F1 590

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
400 444 0.107897 TTGTCTGTTGTCGCCTGTGT 60.108 50.000 0.00 0.00 0.00 3.72 F
401 445 0.107897 TGTCTGTTGTCGCCTGTGTT 60.108 50.000 0.00 0.00 0.00 3.32 F
1644 1826 0.182537 ATACTATTGCGGGCCAAGCA 59.817 50.000 19.45 19.45 43.59 3.91 F
1898 2083 0.251787 AGGGGCCTTCATTGGTTGAC 60.252 55.000 0.84 0.00 32.84 3.18 F
2914 3189 1.915078 ATTCACCAAGAGAGCCCCGG 61.915 60.000 0.00 0.00 0.00 5.73 F
3405 3685 1.607178 CTTTGGTGGATGCCTGGCA 60.607 57.895 25.65 25.65 44.86 4.92 F
4369 6526 2.032030 ACAGACGTACAGTTGCATTTGC 60.032 45.455 0.00 0.00 42.50 3.68 F
4943 7100 2.710377 TCATGCCAACCACTGTATGTC 58.290 47.619 0.00 0.00 0.00 3.06 F
6540 8910 1.946768 GCTGTGCCTTCTGTAACAACA 59.053 47.619 0.00 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1905 0.822121 GGGTCTTTGCGTCCCTTTGT 60.822 55.000 0.00 0.00 37.91 2.83 R
2080 2265 0.971386 CAAAGGCCCTGCAAATGAGT 59.029 50.000 0.00 0.00 0.00 3.41 R
3145 3423 1.216710 GGCGGACAGAAGACCTCAG 59.783 63.158 0.00 0.00 0.00 3.35 R
3232 3512 5.117406 ACTTATCCCTGATTTCCCTTCAC 57.883 43.478 0.00 0.00 0.00 3.18 R
4352 6509 0.237235 CGGCAAATGCAACTGTACGT 59.763 50.000 7.80 0.00 44.36 3.57 R
4893 7050 0.250338 GAAAACACCGGACTGGCTCT 60.250 55.000 9.46 0.00 43.94 4.09 R
5691 7918 1.485066 AGTTCCGTGTGGTGAAACTCT 59.515 47.619 0.00 0.00 36.74 3.24 R
6835 9206 0.248825 CCTGCGGAGATCTCGAGTTG 60.249 60.000 16.46 9.49 0.00 3.16 R
7929 10306 0.036732 CAGGTAGCCAGCAGGTTCAA 59.963 55.000 0.00 0.00 37.19 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
38 39 6.208599 ACTTTTTGGAAATGATTCGAGCCTTA 59.791 34.615 0.00 0.00 36.36 2.69
107 108 4.836825 CAGATTGTGTGGACCTGATTACT 58.163 43.478 0.00 0.00 0.00 2.24
121 122 7.170393 ACCTGATTACTTTAATTGGGAAAGC 57.830 36.000 0.08 0.00 37.41 3.51
124 125 7.169158 TGATTACTTTAATTGGGAAAGCAGG 57.831 36.000 0.08 0.00 37.41 4.85
125 126 6.723977 TGATTACTTTAATTGGGAAAGCAGGT 59.276 34.615 0.08 0.00 37.41 4.00
145 167 1.202758 TCGTTTGGTGTGATCCAAGCT 60.203 47.619 9.72 0.00 46.27 3.74
163 186 1.309950 CTCGATGTCTTCCGCTCCTA 58.690 55.000 0.00 0.00 0.00 2.94
194 217 6.681729 TCTCTTTAAGTAGTGTTGTCCCAT 57.318 37.500 0.00 0.00 0.00 4.00
248 271 1.476477 TCCGACGTGGATGGTTGATA 58.524 50.000 0.00 0.00 43.74 2.15
252 275 2.347452 CGACGTGGATGGTTGATAACAC 59.653 50.000 0.00 0.00 0.00 3.32
283 306 1.665679 CTGATTTATCGCGGCTGTTGT 59.334 47.619 6.13 0.00 0.00 3.32
284 307 1.663643 TGATTTATCGCGGCTGTTGTC 59.336 47.619 6.13 0.00 0.00 3.18
315 359 1.926490 GCAACACTTTTGCCTTGCG 59.074 52.632 0.00 0.00 39.38 4.85
317 361 1.227234 AACACTTTTGCCTTGCGCC 60.227 52.632 4.18 0.00 36.24 6.53
328 372 3.695022 CTTGCGCCTGATGCTTGCC 62.695 63.158 4.18 0.00 38.05 4.52
337 381 1.276989 CTGATGCTTGCCCCATTTTGT 59.723 47.619 0.00 0.00 0.00 2.83
344 388 0.324285 TGCCCCATTTTGTTGCCATC 59.676 50.000 0.00 0.00 0.00 3.51
347 391 1.672441 CCCCATTTTGTTGCCATCACG 60.672 52.381 0.00 0.00 0.00 4.35
348 392 1.672441 CCCATTTTGTTGCCATCACGG 60.672 52.381 0.00 0.00 38.11 4.94
400 444 0.107897 TTGTCTGTTGTCGCCTGTGT 60.108 50.000 0.00 0.00 0.00 3.72
401 445 0.107897 TGTCTGTTGTCGCCTGTGTT 60.108 50.000 0.00 0.00 0.00 3.32
467 511 2.752354 ACAATGCGAAATCGAAATGGGA 59.248 40.909 7.06 0.00 43.02 4.37
468 512 3.381272 ACAATGCGAAATCGAAATGGGAT 59.619 39.130 7.06 0.00 43.02 3.85
472 516 1.675483 CGAAATCGAAATGGGATGGCA 59.325 47.619 0.00 0.00 43.02 4.92
477 521 0.740737 CGAAATGGGATGGCAGTTCC 59.259 55.000 0.00 0.00 0.00 3.62
482 526 1.891933 TGGGATGGCAGTTCCTATGA 58.108 50.000 7.06 0.00 35.26 2.15
488 532 2.827755 TGGCAGTTCCTATGAGGTGTA 58.172 47.619 0.00 0.00 36.53 2.90
506 550 4.096382 GGTGTACATGATTGAAGCGGAATT 59.904 41.667 0.00 0.00 0.00 2.17
544 589 2.859165 TCGAGCATTGGAAGGAAGTT 57.141 45.000 0.00 0.00 0.00 2.66
568 613 2.676342 ACTTGGTGAAACGACTCAACAC 59.324 45.455 8.43 0.00 42.69 3.32
602 647 2.380084 TTGAGTGGACCTGATTACGC 57.620 50.000 0.00 0.00 0.00 4.42
637 682 9.860898 AAGGCTTTTTAAGTTGTTCATGATATC 57.139 29.630 0.00 0.00 0.00 1.63
639 684 8.181573 GGCTTTTTAAGTTGTTCATGATATCGA 58.818 33.333 0.00 0.00 0.00 3.59
679 725 1.008327 TGGGTCCATGAAGCTCCTAGA 59.992 52.381 0.00 0.00 0.00 2.43
708 754 2.160219 TGAGCAAACTGATTGACGATGC 59.840 45.455 1.49 0.00 41.85 3.91
754 800 0.403271 AGCTTGTCACATGGCCTTCT 59.597 50.000 3.32 0.00 0.00 2.85
784 856 4.972751 AAAACCACTAATTTGCATGGGT 57.027 36.364 6.71 0.00 36.47 4.51
912 1062 2.819595 CACCCCAATCACTCGCCG 60.820 66.667 0.00 0.00 0.00 6.46
913 1063 4.778143 ACCCCAATCACTCGCCGC 62.778 66.667 0.00 0.00 0.00 6.53
986 1151 3.509442 TCTCCAACCCAAAAGCATCATT 58.491 40.909 0.00 0.00 0.00 2.57
987 1152 3.903090 TCTCCAACCCAAAAGCATCATTT 59.097 39.130 0.00 0.00 0.00 2.32
1155 1320 1.002544 AGAAACAGGAGCGGGAAGAAG 59.997 52.381 0.00 0.00 0.00 2.85
1209 1374 1.303799 TGGAGCCTCTGTACGACGAC 61.304 60.000 0.00 0.00 0.00 4.34
1443 1625 0.750546 GCATGATGGAGGCAGCTCAA 60.751 55.000 0.00 0.00 0.00 3.02
1484 1666 1.022451 TTCGCGGTTACCTGAATGGC 61.022 55.000 6.13 0.00 40.22 4.40
1492 1674 2.683362 GTTACCTGAATGGCTAAGTGGC 59.317 50.000 0.00 0.00 40.22 5.01
1605 1787 6.878317 AGTGAGTATGCTGTTGCTTTCTATA 58.122 36.000 0.00 0.00 40.48 1.31
1606 1788 7.504403 AGTGAGTATGCTGTTGCTTTCTATAT 58.496 34.615 0.00 0.00 40.48 0.86
1607 1789 8.642432 AGTGAGTATGCTGTTGCTTTCTATATA 58.358 33.333 0.00 0.00 40.48 0.86
1608 1790 8.704234 GTGAGTATGCTGTTGCTTTCTATATAC 58.296 37.037 0.00 0.00 40.48 1.47
1612 1794 7.875316 ATGCTGTTGCTTTCTATATACGTAG 57.125 36.000 0.08 0.00 40.48 3.51
1614 1796 7.933396 TGCTGTTGCTTTCTATATACGTAGTA 58.067 34.615 0.08 0.00 43.78 1.82
1634 1816 9.189723 CGTAGTACTTTAGGGAAATACTATTGC 57.810 37.037 0.00 0.00 31.41 3.56
1635 1817 9.189723 GTAGTACTTTAGGGAAATACTATTGCG 57.810 37.037 0.00 0.00 31.41 4.85
1636 1818 7.215085 AGTACTTTAGGGAAATACTATTGCGG 58.785 38.462 0.00 0.00 0.00 5.69
1637 1819 5.374071 ACTTTAGGGAAATACTATTGCGGG 58.626 41.667 0.00 0.00 0.00 6.13
1638 1820 2.271944 AGGGAAATACTATTGCGGGC 57.728 50.000 0.00 0.00 0.00 6.13
1639 1821 1.202891 AGGGAAATACTATTGCGGGCC 60.203 52.381 0.00 0.00 0.00 5.80
1640 1822 1.477923 GGGAAATACTATTGCGGGCCA 60.478 52.381 4.39 0.00 0.00 5.36
1641 1823 2.303175 GGAAATACTATTGCGGGCCAA 58.697 47.619 4.39 0.00 37.94 4.52
1642 1824 2.293399 GGAAATACTATTGCGGGCCAAG 59.707 50.000 4.39 0.00 36.76 3.61
1643 1825 1.318576 AATACTATTGCGGGCCAAGC 58.681 50.000 14.68 14.68 36.76 4.01
1644 1826 0.182537 ATACTATTGCGGGCCAAGCA 59.817 50.000 19.45 19.45 43.59 3.91
1645 1827 0.463654 TACTATTGCGGGCCAAGCAG 60.464 55.000 21.64 14.56 46.01 4.24
1646 1828 2.440065 TATTGCGGGCCAAGCAGG 60.440 61.111 21.64 0.00 46.01 4.85
1647 1829 2.891941 CTATTGCGGGCCAAGCAGGA 62.892 60.000 21.64 11.33 46.01 3.86
1746 1929 3.047877 GGACGCAAAGACCCACCG 61.048 66.667 0.00 0.00 0.00 4.94
1752 1935 1.980052 CAAAGACCCACCGAGCCTA 59.020 57.895 0.00 0.00 0.00 3.93
1882 2067 5.733620 TGTTGTCCAGTACTTAAGTAGGG 57.266 43.478 15.68 18.40 0.00 3.53
1883 2068 4.529377 TGTTGTCCAGTACTTAAGTAGGGG 59.471 45.833 23.47 21.62 30.96 4.79
1884 2069 3.102204 TGTCCAGTACTTAAGTAGGGGC 58.898 50.000 22.37 22.37 33.68 5.80
1885 2070 2.433604 GTCCAGTACTTAAGTAGGGGCC 59.566 54.545 23.47 12.94 29.41 5.80
1886 2071 2.316982 TCCAGTACTTAAGTAGGGGCCT 59.683 50.000 23.47 12.75 30.96 5.19
1888 2073 3.134262 CCAGTACTTAAGTAGGGGCCTTC 59.866 52.174 15.68 1.91 0.00 3.46
1889 2074 3.773119 CAGTACTTAAGTAGGGGCCTTCA 59.227 47.826 15.68 0.00 0.00 3.02
1898 2083 0.251787 AGGGGCCTTCATTGGTTGAC 60.252 55.000 0.84 0.00 32.84 3.18
1913 2098 8.095792 TCATTGGTTGACATTATTTGCAAGATT 58.904 29.630 0.00 0.00 0.00 2.40
1936 2121 4.270008 AGTCCAATAAACCGGAAATGAGG 58.730 43.478 9.46 3.08 31.67 3.86
1937 2122 3.380320 GTCCAATAAACCGGAAATGAGGG 59.620 47.826 9.46 0.88 31.67 4.30
1938 2123 3.267291 TCCAATAAACCGGAAATGAGGGA 59.733 43.478 9.46 3.67 0.00 4.20
2080 2265 9.715121 ATTGAAGTCTAATAAAACCTCACGTTA 57.285 29.630 0.00 0.00 33.05 3.18
2084 2269 7.889469 AGTCTAATAAAACCTCACGTTACTCA 58.111 34.615 0.00 0.00 33.05 3.41
2146 2331 7.012327 CCAGTAAATGATCGTACACCATTTGAT 59.988 37.037 19.10 10.09 39.80 2.57
2404 2678 7.051623 TCTACATACCAACTCACAACAAAGTT 58.948 34.615 0.00 0.00 36.16 2.66
2837 3112 2.019807 TCCCACCTAAACGAGTCCTT 57.980 50.000 0.00 0.00 0.00 3.36
2914 3189 1.915078 ATTCACCAAGAGAGCCCCGG 61.915 60.000 0.00 0.00 0.00 5.73
3275 3555 2.987232 ACCCCGAAAGCTTCTATTGAC 58.013 47.619 0.00 0.00 0.00 3.18
3405 3685 1.607178 CTTTGGTGGATGCCTGGCA 60.607 57.895 25.65 25.65 44.86 4.92
3713 3993 2.687935 TGTGCTTTCTTCCAGTTGTTCC 59.312 45.455 0.00 0.00 0.00 3.62
4369 6526 2.032030 ACAGACGTACAGTTGCATTTGC 60.032 45.455 0.00 0.00 42.50 3.68
4653 6810 4.164843 AGTTCTGTTTCTTGCCAGGTAA 57.835 40.909 0.00 0.00 0.00 2.85
4701 6858 7.487822 TCCTCATTCTCTAGTCTTGTTTGAT 57.512 36.000 0.00 0.00 0.00 2.57
4893 7050 5.180367 TCACAATTCATCAAAGCGTTTCA 57.820 34.783 0.00 0.00 0.00 2.69
4943 7100 2.710377 TCATGCCAACCACTGTATGTC 58.290 47.619 0.00 0.00 0.00 3.06
5613 7788 3.785887 AGCCTTGACATAACCATTAGGGA 59.214 43.478 0.00 0.00 41.15 4.20
5684 7911 5.049405 CACAGAATACCACTCTTCCAAACAC 60.049 44.000 0.00 0.00 0.00 3.32
5691 7918 3.390135 CACTCTTCCAAACACGCTCTTA 58.610 45.455 0.00 0.00 0.00 2.10
5713 7940 2.798847 GAGTTTCACCACACGGAACTAC 59.201 50.000 0.00 0.00 29.36 2.73
5834 8177 3.818773 CCACAAGGACCACGACTTAAAAT 59.181 43.478 0.00 0.00 36.89 1.82
5835 8178 4.998672 CCACAAGGACCACGACTTAAAATA 59.001 41.667 0.00 0.00 36.89 1.40
5836 8179 5.106830 CCACAAGGACCACGACTTAAAATAC 60.107 44.000 0.00 0.00 36.89 1.89
5838 8181 6.148811 CACAAGGACCACGACTTAAAATACAT 59.851 38.462 0.00 0.00 0.00 2.29
5993 8344 2.685897 GCAAGGTTTGGTGTTACAGTCA 59.314 45.455 0.00 0.00 0.00 3.41
6124 8475 5.997732 ATCACTGAAAATCGAAATTTGCG 57.002 34.783 0.00 0.00 33.61 4.85
6164 8515 8.690884 TCATTTGAAATCTTAACCAGTTGAACA 58.309 29.630 0.00 0.00 0.00 3.18
6214 8565 2.800250 CCTTTTTCTCAGTGGAGCCAT 58.200 47.619 0.00 0.00 41.13 4.40
6489 8842 1.969713 AACCGGGACATAAACCCCTA 58.030 50.000 6.32 0.00 44.09 3.53
6540 8910 1.946768 GCTGTGCCTTCTGTAACAACA 59.053 47.619 0.00 0.00 0.00 3.33
6544 8914 2.221055 GTGCCTTCTGTAACAACACTCG 59.779 50.000 0.00 0.00 0.00 4.18
6548 8918 4.307432 CCTTCTGTAACAACACTCGTGAT 58.693 43.478 3.74 0.00 0.00 3.06
6602 8972 7.092079 CCTGCATACATGATTGAACTTTTTGA 58.908 34.615 0.00 0.00 0.00 2.69
6703 9074 2.779742 AAATACCGCTGCAGCCCCAA 62.780 55.000 32.07 15.89 37.91 4.12
6724 9095 5.394115 CCAACCAAGCTGAAGTTTTGTAGTT 60.394 40.000 0.00 0.00 0.00 2.24
6734 9105 7.755373 GCTGAAGTTTTGTAGTTTTCAGAAGTT 59.245 33.333 14.65 0.00 44.58 2.66
6767 9138 6.688385 CGATTACATAAAGGTGAAAGCATGTG 59.312 38.462 0.00 0.00 36.26 3.21
6774 9145 4.685169 AGGTGAAAGCATGTGTTATTCG 57.315 40.909 0.00 0.00 36.26 3.34
6835 9206 8.705048 ACTTCGAAGATATAGAAAAAGACACC 57.295 34.615 31.08 0.00 35.04 4.16
6866 9237 3.256936 CGCAGGACATGTGTGGTG 58.743 61.111 1.15 0.00 34.56 4.17
6867 9238 1.301637 CGCAGGACATGTGTGGTGA 60.302 57.895 1.15 0.00 34.56 4.02
6868 9239 0.674581 CGCAGGACATGTGTGGTGAT 60.675 55.000 1.15 0.00 34.56 3.06
6869 9240 1.405391 CGCAGGACATGTGTGGTGATA 60.405 52.381 1.15 0.00 34.56 2.15
6870 9241 2.710377 GCAGGACATGTGTGGTGATAA 58.290 47.619 1.15 0.00 0.00 1.75
6940 9311 7.611213 AAGCTATACCAAGTGTATTTGTGTC 57.389 36.000 0.00 0.00 40.64 3.67
7201 9573 3.054434 TGCACATACCTGCTATTGTTCCT 60.054 43.478 0.00 0.00 38.07 3.36
7343 9715 3.308595 CGAGAACGCAATGGCATACTTAA 59.691 43.478 0.00 0.00 41.24 1.85
7549 9921 8.474006 CACAGTACATAATGTGTAGCTAACAA 57.526 34.615 10.55 0.11 44.51 2.83
7670 10046 8.459635 GTTCACAATAAAGGGTCTCTTTTATCC 58.540 37.037 2.29 0.00 42.62 2.59
7671 10047 7.928873 TCACAATAAAGGGTCTCTTTTATCCT 58.071 34.615 2.29 0.00 42.62 3.24
7672 10048 7.829211 TCACAATAAAGGGTCTCTTTTATCCTG 59.171 37.037 2.29 0.00 42.62 3.86
7673 10049 7.611855 CACAATAAAGGGTCTCTTTTATCCTGT 59.388 37.037 2.29 0.00 42.62 4.00
7674 10050 8.832735 ACAATAAAGGGTCTCTTTTATCCTGTA 58.167 33.333 2.29 0.00 42.62 2.74
7675 10051 9.110502 CAATAAAGGGTCTCTTTTATCCTGTAC 57.889 37.037 2.29 0.00 42.62 2.90
7676 10052 6.954352 AAAGGGTCTCTTTTATCCTGTACT 57.046 37.500 0.00 0.00 42.62 2.73
7677 10053 9.725206 ATAAAGGGTCTCTTTTATCCTGTACTA 57.275 33.333 2.29 0.00 42.62 1.82
7678 10054 7.663043 AAGGGTCTCTTTTATCCTGTACTAG 57.337 40.000 0.00 0.00 29.99 2.57
7679 10055 6.743788 AGGGTCTCTTTTATCCTGTACTAGT 58.256 40.000 0.00 0.00 0.00 2.57
7680 10056 7.880623 AGGGTCTCTTTTATCCTGTACTAGTA 58.119 38.462 0.00 0.00 0.00 1.82
7681 10057 7.779326 AGGGTCTCTTTTATCCTGTACTAGTAC 59.221 40.741 23.58 23.58 36.63 2.73
7682 10058 7.779326 GGGTCTCTTTTATCCTGTACTAGTACT 59.221 40.741 28.56 14.41 37.00 2.73
7683 10059 8.839343 GGTCTCTTTTATCCTGTACTAGTACTC 58.161 40.741 28.56 8.80 37.00 2.59
7706 10082 8.812972 ACTCCTACTATGTAGTCAATGTGAAAA 58.187 33.333 0.00 0.00 37.73 2.29
7750 10126 3.503363 TGCATCAGATGTGTTCACCTTTC 59.497 43.478 12.18 0.00 0.00 2.62
7751 10127 3.119708 GCATCAGATGTGTTCACCTTTCC 60.120 47.826 12.18 0.00 0.00 3.13
7840 10217 0.677731 AGGCAAGCGCTTAAGCATGA 60.678 50.000 27.40 0.00 42.21 3.07
7851 10228 3.862642 GCTTAAGCATGACTAGGCGCTAT 60.863 47.826 22.59 0.00 38.93 2.97
7888 10265 4.950479 CCTTGAGGGCTGCTAGTG 57.050 61.111 0.00 0.00 0.00 2.74
7929 10306 6.153942 AGGAATTTAGACCTAGGGCTTTTT 57.846 37.500 25.89 14.19 34.47 1.94
7949 10326 1.127567 TGAACCTGCTGGCTACCTGT 61.128 55.000 9.95 0.00 36.63 4.00
7996 10402 3.275999 AGGTGGTTTGACACACAGTAAC 58.724 45.455 0.00 0.00 43.08 2.50
8097 10503 6.618287 TTCACACTTCAACATTTCTACCTG 57.382 37.500 0.00 0.00 0.00 4.00
8159 10565 2.527624 TGTGGTCTCAGCAGCCCT 60.528 61.111 0.00 0.00 0.00 5.19
8175 10581 0.820871 CCCTAGAGAACAAGAGCGCT 59.179 55.000 11.27 11.27 0.00 5.92
8176 10582 1.470632 CCCTAGAGAACAAGAGCGCTG 60.471 57.143 18.48 3.41 0.00 5.18
8188 10594 3.475566 AGAGCGCTGCCATTATTTCTA 57.524 42.857 18.48 0.00 0.00 2.10
8232 10705 9.927668 ACTTAAATGTTAATGAAATGGTTCAGG 57.072 29.630 0.00 0.00 46.75 3.86
8233 10706 8.770438 TTAAATGTTAATGAAATGGTTCAGGC 57.230 30.769 0.00 0.00 46.75 4.85
8234 10707 6.610075 AATGTTAATGAAATGGTTCAGGCT 57.390 33.333 0.00 0.00 46.75 4.58
8235 10708 5.389859 TGTTAATGAAATGGTTCAGGCTG 57.610 39.130 8.58 8.58 46.75 4.85
8236 10709 4.220382 TGTTAATGAAATGGTTCAGGCTGG 59.780 41.667 15.73 0.00 46.75 4.85
8237 10710 1.188863 ATGAAATGGTTCAGGCTGGC 58.811 50.000 15.73 8.02 46.75 4.85
8238 10711 1.243342 TGAAATGGTTCAGGCTGGCG 61.243 55.000 15.73 0.00 38.88 5.69
8239 10712 1.228552 AAATGGTTCAGGCTGGCGT 60.229 52.632 15.73 0.00 0.00 5.68
8240 10713 0.037590 AAATGGTTCAGGCTGGCGTA 59.962 50.000 15.73 0.00 0.00 4.42
8241 10714 0.037590 AATGGTTCAGGCTGGCGTAA 59.962 50.000 15.73 0.00 0.00 3.18
8242 10715 0.392998 ATGGTTCAGGCTGGCGTAAG 60.393 55.000 15.73 0.00 43.44 2.34
8254 10727 2.125991 CGTAAGCCCGCCGTAACA 60.126 61.111 0.00 0.00 0.00 2.41
8255 10728 2.447070 CGTAAGCCCGCCGTAACAC 61.447 63.158 0.00 0.00 0.00 3.32
8256 10729 2.102438 GTAAGCCCGCCGTAACACC 61.102 63.158 0.00 0.00 0.00 4.16
8257 10730 3.646023 TAAGCCCGCCGTAACACCG 62.646 63.158 0.00 0.00 0.00 4.94
8260 10733 4.360964 CCCGCCGTAACACCGTCA 62.361 66.667 0.00 0.00 0.00 4.35
8261 10734 2.356075 CCGCCGTAACACCGTCAA 60.356 61.111 0.00 0.00 0.00 3.18
8262 10735 1.955157 CCGCCGTAACACCGTCAAA 60.955 57.895 0.00 0.00 0.00 2.69
8263 10736 1.497223 CCGCCGTAACACCGTCAAAA 61.497 55.000 0.00 0.00 0.00 2.44
8264 10737 0.304098 CGCCGTAACACCGTCAAAAA 59.696 50.000 0.00 0.00 0.00 1.94
8265 10738 1.069771 CGCCGTAACACCGTCAAAAAT 60.070 47.619 0.00 0.00 0.00 1.82
8266 10739 2.157279 CGCCGTAACACCGTCAAAAATA 59.843 45.455 0.00 0.00 0.00 1.40
8267 10740 3.363772 CGCCGTAACACCGTCAAAAATAA 60.364 43.478 0.00 0.00 0.00 1.40
8268 10741 4.535116 GCCGTAACACCGTCAAAAATAAA 58.465 39.130 0.00 0.00 0.00 1.40
8269 10742 5.155643 GCCGTAACACCGTCAAAAATAAAT 58.844 37.500 0.00 0.00 0.00 1.40
8270 10743 6.313252 GCCGTAACACCGTCAAAAATAAATA 58.687 36.000 0.00 0.00 0.00 1.40
8271 10744 6.800892 GCCGTAACACCGTCAAAAATAAATAA 59.199 34.615 0.00 0.00 0.00 1.40
8272 10745 7.325579 GCCGTAACACCGTCAAAAATAAATAAA 59.674 33.333 0.00 0.00 0.00 1.40
8273 10746 9.178427 CCGTAACACCGTCAAAAATAAATAAAA 57.822 29.630 0.00 0.00 0.00 1.52
8274 10747 9.977490 CGTAACACCGTCAAAAATAAATAAAAC 57.023 29.630 0.00 0.00 0.00 2.43
8301 10774 1.338020 GTTTGACAGAAAGCCACTGGG 59.662 52.381 0.00 0.00 39.38 4.45
8327 10800 2.485795 GGCACAACGGCTGGTTTGA 61.486 57.895 0.00 0.00 36.49 2.69
8349 10823 9.712305 TTTGAAAACACCAGAAAATAACTCAAA 57.288 25.926 0.00 0.00 0.00 2.69
8402 10876 3.121279 CGACTGGTTGATAACACGTCTTG 59.879 47.826 0.00 0.00 33.01 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.859245 GCTCGAATCATTTCCAAAAAGTCC 59.141 41.667 0.00 0.00 0.00 3.85
16 17 6.582677 TTAAGGCTCGAATCATTTCCAAAA 57.417 33.333 0.00 0.00 0.00 2.44
51 52 3.214328 GTTGAGTCAATCCACCAAGTGT 58.786 45.455 9.18 0.00 0.00 3.55
54 55 5.458041 AATTGTTGAGTCAATCCACCAAG 57.542 39.130 9.18 0.00 37.09 3.61
64 65 7.094508 TCTGCAAAACTAAATTGTTGAGTCA 57.905 32.000 0.00 0.00 0.00 3.41
107 108 3.492337 ACGACCTGCTTTCCCAATTAAA 58.508 40.909 0.00 0.00 0.00 1.52
121 122 1.156736 GGATCACACCAAACGACCTG 58.843 55.000 0.00 0.00 0.00 4.00
145 167 1.880675 GATAGGAGCGGAAGACATCGA 59.119 52.381 0.00 0.00 0.00 3.59
163 186 8.652290 ACAACACTACTTAAAGAGAAGGAAGAT 58.348 33.333 0.00 0.00 0.00 2.40
213 236 2.169769 GTCGGATCATCCAACCTAACCA 59.830 50.000 4.06 0.00 35.91 3.67
237 260 4.058817 GAGGATCGTGTTATCAACCATCC 58.941 47.826 0.00 0.00 0.00 3.51
243 266 3.384789 CAGGGAGAGGATCGTGTTATCAA 59.615 47.826 0.00 0.00 42.67 2.57
248 271 2.166907 ATCAGGGAGAGGATCGTGTT 57.833 50.000 0.00 0.00 42.67 3.32
252 275 3.674682 GCGATAAATCAGGGAGAGGATCG 60.675 52.174 0.00 0.00 42.67 3.69
315 359 1.619807 AAATGGGGCAAGCATCAGGC 61.620 55.000 0.00 0.00 45.30 4.85
317 361 1.276989 ACAAAATGGGGCAAGCATCAG 59.723 47.619 0.00 0.00 0.00 2.90
344 388 0.783579 CCAAATTCAAAAGCGCCGTG 59.216 50.000 2.29 0.00 0.00 4.94
347 391 1.460743 GAAGCCAAATTCAAAAGCGCC 59.539 47.619 2.29 0.00 0.00 6.53
348 392 1.460743 GGAAGCCAAATTCAAAAGCGC 59.539 47.619 0.00 0.00 0.00 5.92
382 426 0.107897 AACACAGGCGACAACAGACA 60.108 50.000 0.00 0.00 0.00 3.41
467 511 2.200081 ACACCTCATAGGAACTGCCAT 58.800 47.619 0.00 0.00 41.52 4.40
468 512 1.656587 ACACCTCATAGGAACTGCCA 58.343 50.000 0.00 0.00 41.52 4.92
472 516 6.384015 TCAATCATGTACACCTCATAGGAACT 59.616 38.462 0.00 0.00 46.37 3.01
477 521 5.176406 CGCTTCAATCATGTACACCTCATAG 59.824 44.000 0.00 0.00 0.00 2.23
482 526 2.236146 TCCGCTTCAATCATGTACACCT 59.764 45.455 0.00 0.00 0.00 4.00
488 532 6.375455 AGAGTTTAATTCCGCTTCAATCATGT 59.625 34.615 0.00 0.00 0.00 3.21
506 550 5.107220 GCTCGAATCGTTTCCAAAGAGTTTA 60.107 40.000 1.52 0.00 0.00 2.01
544 589 5.693104 GTGTTGAGTCGTTTCACCAAGTATA 59.307 40.000 0.00 0.00 0.00 1.47
578 623 4.142160 CGTAATCAGGTCCACTCAATCTGA 60.142 45.833 0.00 0.00 38.59 3.27
602 647 7.441836 ACAACTTAAAAAGCCTTCCCAATTAG 58.558 34.615 0.00 0.00 0.00 1.73
637 682 7.926555 ACCCAATTACAAGAAGTATGTCTATCG 59.073 37.037 0.00 0.00 31.53 2.92
639 684 8.211629 GGACCCAATTACAAGAAGTATGTCTAT 58.788 37.037 0.00 0.00 31.53 1.98
643 688 6.134535 TGGACCCAATTACAAGAAGTATGT 57.865 37.500 0.00 0.00 31.53 2.29
679 725 8.081633 TCGTCAATCAGTTTGCTCAAAATAAAT 58.918 29.630 0.00 0.00 35.16 1.40
784 856 9.996554 ACTTTCTTTTTCCTCTTTTTCTTGAAA 57.003 25.926 0.00 0.00 0.00 2.69
836 986 1.303317 CGGGGAAACAGACAAGGGG 60.303 63.158 0.00 0.00 0.00 4.79
912 1062 3.813724 CTGTGGAGGGGATGGGGC 61.814 72.222 0.00 0.00 0.00 5.80
913 1063 2.042762 TCTGTGGAGGGGATGGGG 59.957 66.667 0.00 0.00 0.00 4.96
986 1151 1.634973 TGGACATTGCTGGAGATGGAA 59.365 47.619 0.00 0.00 0.00 3.53
987 1152 1.288188 TGGACATTGCTGGAGATGGA 58.712 50.000 0.00 0.00 0.00 3.41
1113 1278 3.246112 CCCACCTCCCCGTTCACA 61.246 66.667 0.00 0.00 0.00 3.58
1155 1320 3.358076 CTCCTTCACCGCGTCCTCC 62.358 68.421 4.92 0.00 0.00 4.30
1197 1362 1.868997 GAACCCGTCGTCGTACAGA 59.131 57.895 0.71 0.00 35.01 3.41
1394 1576 3.648982 TGGAGCGCACAAAGCACG 61.649 61.111 11.47 0.00 46.13 5.34
1484 1666 2.227388 CAGAAGCAAACTGGCCACTTAG 59.773 50.000 0.00 0.00 0.00 2.18
1492 1674 5.059833 ACTCTTAGAACAGAAGCAAACTGG 58.940 41.667 0.00 0.00 39.38 4.00
1608 1790 9.189723 GCAATAGTATTTCCCTAAAGTACTACG 57.810 37.037 0.00 0.00 31.51 3.51
1612 1794 6.426025 CCCGCAATAGTATTTCCCTAAAGTAC 59.574 42.308 0.00 0.00 0.00 2.73
1614 1796 5.374071 CCCGCAATAGTATTTCCCTAAAGT 58.626 41.667 0.00 0.00 0.00 2.66
1632 1814 4.594854 TTTCCTGCTTGGCCCGCA 62.595 61.111 15.12 15.12 35.26 5.69
1633 1815 3.752339 CTTTCCTGCTTGGCCCGC 61.752 66.667 0.00 3.19 35.26 6.13
1634 1816 3.752339 GCTTTCCTGCTTGGCCCG 61.752 66.667 0.00 0.00 35.26 6.13
1635 1817 3.385384 GGCTTTCCTGCTTGGCCC 61.385 66.667 0.00 0.00 37.12 5.80
1636 1818 2.283460 AGGCTTTCCTGCTTGGCC 60.283 61.111 0.00 0.00 42.34 5.36
1644 1826 1.168714 CGCTAAAAGCAGGCTTTCCT 58.831 50.000 18.59 7.79 44.50 3.36
1645 1827 0.881796 ACGCTAAAAGCAGGCTTTCC 59.118 50.000 18.59 9.91 44.50 3.13
1646 1828 2.706555 AACGCTAAAAGCAGGCTTTC 57.293 45.000 18.59 6.77 44.50 2.62
1647 1829 3.146847 AGTAACGCTAAAAGCAGGCTTT 58.853 40.909 13.20 13.20 46.90 3.51
1707 1889 7.096230 CGTCCCTTTGTTTTGACATTGATTAAC 60.096 37.037 0.00 0.00 0.00 2.01
1716 1898 1.464734 TGCGTCCCTTTGTTTTGACA 58.535 45.000 0.00 0.00 0.00 3.58
1718 1900 2.755655 TCTTTGCGTCCCTTTGTTTTGA 59.244 40.909 0.00 0.00 0.00 2.69
1723 1905 0.822121 GGGTCTTTGCGTCCCTTTGT 60.822 55.000 0.00 0.00 37.91 2.83
1808 1991 7.913674 ATAGGTCTTCTAAAAGTCAGCTTTG 57.086 36.000 0.00 0.00 43.52 2.77
1813 1996 6.642950 CCGCATATAGGTCTTCTAAAAGTCAG 59.357 42.308 0.00 0.00 33.95 3.51
1882 2067 5.343307 AATAATGTCAACCAATGAAGGCC 57.657 39.130 0.00 0.00 40.50 5.19
1883 2068 5.063817 GCAAATAATGTCAACCAATGAAGGC 59.936 40.000 0.00 0.00 40.50 4.35
1884 2069 6.164876 TGCAAATAATGTCAACCAATGAAGG 58.835 36.000 0.00 0.00 40.50 3.46
1885 2070 7.599621 TCTTGCAAATAATGTCAACCAATGAAG 59.400 33.333 0.00 0.00 40.50 3.02
1886 2071 7.440198 TCTTGCAAATAATGTCAACCAATGAA 58.560 30.769 0.00 0.00 40.50 2.57
1888 2073 7.837202 ATCTTGCAAATAATGTCAACCAATG 57.163 32.000 0.00 0.00 0.00 2.82
1889 2074 9.590451 CTAATCTTGCAAATAATGTCAACCAAT 57.410 29.630 0.00 0.00 0.00 3.16
1913 2098 5.433526 CCTCATTTCCGGTTTATTGGACTA 58.566 41.667 0.00 0.00 32.95 2.59
1936 2121 4.580580 CACATTGGGTAGGCTTATTCTTCC 59.419 45.833 0.00 0.00 0.00 3.46
1937 2122 5.297029 GTCACATTGGGTAGGCTTATTCTTC 59.703 44.000 0.00 0.00 0.00 2.87
1938 2123 5.193679 GTCACATTGGGTAGGCTTATTCTT 58.806 41.667 0.00 0.00 0.00 2.52
2080 2265 0.971386 CAAAGGCCCTGCAAATGAGT 59.029 50.000 0.00 0.00 0.00 3.41
2084 2269 1.720781 ACTTCAAAGGCCCTGCAAAT 58.279 45.000 0.00 0.00 0.00 2.32
2146 2331 5.754782 AGGTGAATAATGCAAGTCATACCA 58.245 37.500 11.45 0.00 33.31 3.25
2158 2343 9.209175 GTAATAGTGAAGCCTAGGTGAATAATG 57.791 37.037 11.31 0.00 0.00 1.90
2227 2417 7.834068 AACATGCGTCTATATACATCCAATC 57.166 36.000 0.00 0.00 0.00 2.67
2623 2897 5.538813 GGGGAAACAAAACTAGACTTGGATT 59.461 40.000 0.00 0.00 0.00 3.01
2837 3112 1.476833 GGGTGCAACAAACTCAGGAGA 60.477 52.381 3.06 0.00 39.98 3.71
2914 3189 3.727726 CAAACTTGTGGGTTGATTTCCC 58.272 45.455 0.00 0.00 44.88 3.97
3145 3423 1.216710 GGCGGACAGAAGACCTCAG 59.783 63.158 0.00 0.00 0.00 3.35
3232 3512 5.117406 ACTTATCCCTGATTTCCCTTCAC 57.883 43.478 0.00 0.00 0.00 3.18
3275 3555 6.567050 AGCATTTATGTTCATTGCTGTTAGG 58.433 36.000 8.91 0.00 41.79 2.69
3893 4173 9.205513 ACATCCTTGGCTCATAAAAAGATAATT 57.794 29.630 0.00 0.00 0.00 1.40
3895 4175 8.593945 AACATCCTTGGCTCATAAAAAGATAA 57.406 30.769 0.00 0.00 0.00 1.75
3897 4177 7.486407 AAACATCCTTGGCTCATAAAAAGAT 57.514 32.000 0.00 0.00 0.00 2.40
3898 4178 6.916360 AAACATCCTTGGCTCATAAAAAGA 57.084 33.333 0.00 0.00 0.00 2.52
3899 4179 7.223387 GCATAAACATCCTTGGCTCATAAAAAG 59.777 37.037 0.00 0.00 0.00 2.27
4164 4446 7.966753 GCATATATGTTTCTTGCACTCCATATG 59.033 37.037 14.14 0.00 33.58 1.78
4165 4447 7.886970 AGCATATATGTTTCTTGCACTCCATAT 59.113 33.333 14.14 0.00 35.79 1.78
4166 4448 7.226441 AGCATATATGTTTCTTGCACTCCATA 58.774 34.615 14.14 0.00 35.79 2.74
4167 4449 6.066690 AGCATATATGTTTCTTGCACTCCAT 58.933 36.000 14.14 0.00 35.79 3.41
4168 4450 5.439721 AGCATATATGTTTCTTGCACTCCA 58.560 37.500 14.14 0.00 35.79 3.86
4352 6509 0.237235 CGGCAAATGCAACTGTACGT 59.763 50.000 7.80 0.00 44.36 3.57
4353 6510 0.454285 CCGGCAAATGCAACTGTACG 60.454 55.000 7.80 0.74 44.36 3.67
4354 6511 0.878416 TCCGGCAAATGCAACTGTAC 59.122 50.000 7.80 0.00 44.36 2.90
4355 6512 1.610363 TTCCGGCAAATGCAACTGTA 58.390 45.000 7.80 0.00 44.36 2.74
4356 6513 0.749649 TTTCCGGCAAATGCAACTGT 59.250 45.000 7.80 0.00 44.36 3.55
4357 6514 1.421382 CTTTCCGGCAAATGCAACTG 58.579 50.000 7.80 0.00 44.36 3.16
4358 6515 0.318120 CCTTTCCGGCAAATGCAACT 59.682 50.000 7.80 0.00 44.36 3.16
4359 6516 0.316841 TCCTTTCCGGCAAATGCAAC 59.683 50.000 7.80 0.00 44.36 4.17
4369 6526 4.423625 AATGGATACTTCTCCTTTCCGG 57.576 45.455 0.00 0.00 36.20 5.14
4512 6669 5.187381 TGCCAATTGCTGATAAATGAAAGGA 59.813 36.000 0.00 0.00 42.00 3.36
4653 6810 7.123247 GGATTTAGGCAGCACCATTATAATGAT 59.877 37.037 24.17 6.77 43.14 2.45
4709 6866 8.637986 GGAGAGTATCAGATCAAACAGTTAGAT 58.362 37.037 0.00 0.00 37.82 1.98
4893 7050 0.250338 GAAAACACCGGACTGGCTCT 60.250 55.000 9.46 0.00 43.94 4.09
5613 7788 8.576442 CAAATTTGACTTAAATACCAGTCCTGT 58.424 33.333 13.08 0.00 38.01 4.00
5684 7911 2.731976 GTGTGGTGAAACTCTAAGAGCG 59.268 50.000 0.00 0.00 36.74 5.03
5691 7918 1.485066 AGTTCCGTGTGGTGAAACTCT 59.515 47.619 0.00 0.00 36.74 3.24
5713 7940 6.478344 TGTGCTAAATTAGGTGTTTGCAAAAG 59.522 34.615 14.67 4.66 30.45 2.27
5908 8259 5.186256 TGTATTCTTCACCCTGCCAAATA 57.814 39.130 0.00 0.00 0.00 1.40
5953 8304 1.748493 GCCGCCATCCTTACAAATTCA 59.252 47.619 0.00 0.00 0.00 2.57
5993 8344 2.825532 CTCCGACAAACCCAAATGGAAT 59.174 45.455 0.00 0.00 37.39 3.01
6106 8457 5.804449 TGAACGCAAATTTCGATTTTCAG 57.196 34.783 14.21 0.00 0.00 3.02
6114 8465 7.798052 TGATATGACATATGAACGCAAATTTCG 59.202 33.333 12.74 8.01 0.00 3.46
6489 8842 3.560636 AGCGGCTCAAATGTATTACCT 57.439 42.857 0.00 0.00 0.00 3.08
6544 8914 4.264614 CGTGTACGAGTTGGATGTAATCAC 59.735 45.833 0.00 0.00 43.70 3.06
6663 9033 5.518848 TTTGGTCTATTTGGCTATGCATG 57.481 39.130 10.16 0.26 0.00 4.06
6703 9074 5.914898 AAACTACAAAACTTCAGCTTGGT 57.085 34.783 0.00 0.00 0.00 3.67
6724 9095 9.715121 ATGTAATCGGTAAGTTAACTTCTGAAA 57.285 29.630 23.76 14.17 37.40 2.69
6734 9105 9.941325 TTTCACCTTTATGTAATCGGTAAGTTA 57.059 29.630 0.00 0.00 0.00 2.24
6774 9145 6.036408 GCCATGCTTTCATGTTATTTTTCCTC 59.964 38.462 4.80 0.00 46.64 3.71
6835 9206 0.248825 CCTGCGGAGATCTCGAGTTG 60.249 60.000 16.46 9.49 0.00 3.16
6864 9235 9.769093 GGTTACAAATGTGTTATCACTTATCAC 57.231 33.333 0.00 0.00 44.14 3.06
6865 9236 9.508642 TGGTTACAAATGTGTTATCACTTATCA 57.491 29.630 0.00 0.00 44.14 2.15
6868 9239 8.788806 CCTTGGTTACAAATGTGTTATCACTTA 58.211 33.333 0.00 0.00 39.49 2.24
6869 9240 7.286775 ACCTTGGTTACAAATGTGTTATCACTT 59.713 33.333 0.00 0.00 39.49 3.16
6870 9241 6.775629 ACCTTGGTTACAAATGTGTTATCACT 59.224 34.615 0.00 0.00 39.49 3.41
6940 9311 3.004106 CCAGAACCAACTGCAGAAAGAAG 59.996 47.826 23.35 5.10 36.67 2.85
7201 9573 4.526970 AGTAGAATCGTCCGGGTACTTTA 58.473 43.478 0.00 0.00 0.00 1.85
7343 9715 2.561069 GGTCTTCCTCCCTCTTCCTCTT 60.561 54.545 0.00 0.00 0.00 2.85
7670 10046 9.912634 GACTACATAGTAGGAGTACTAGTACAG 57.087 40.741 29.87 17.66 43.55 2.74
7671 10047 9.426534 TGACTACATAGTAGGAGTACTAGTACA 57.573 37.037 29.87 11.75 43.55 2.90
7674 10050 9.781633 CATTGACTACATAGTAGGAGTACTAGT 57.218 37.037 0.00 0.00 43.55 2.57
7675 10051 9.781633 ACATTGACTACATAGTAGGAGTACTAG 57.218 37.037 8.83 0.00 43.55 2.57
7676 10052 9.557061 CACATTGACTACATAGTAGGAGTACTA 57.443 37.037 8.83 0.00 44.26 1.82
7677 10053 8.272889 TCACATTGACTACATAGTAGGAGTACT 58.727 37.037 0.00 0.00 42.49 2.73
7678 10054 8.447924 TCACATTGACTACATAGTAGGAGTAC 57.552 38.462 8.83 0.00 36.50 2.73
7679 10055 9.470399 TTTCACATTGACTACATAGTAGGAGTA 57.530 33.333 8.83 0.00 36.50 2.59
7680 10056 7.956328 TTCACATTGACTACATAGTAGGAGT 57.044 36.000 8.83 0.00 36.50 3.85
7681 10057 9.088512 GTTTTCACATTGACTACATAGTAGGAG 57.911 37.037 8.83 0.00 36.50 3.69
7682 10058 8.590204 TGTTTTCACATTGACTACATAGTAGGA 58.410 33.333 8.83 0.00 36.50 2.94
7683 10059 8.771920 TGTTTTCACATTGACTACATAGTAGG 57.228 34.615 8.83 0.00 36.50 3.18
7706 10082 2.158813 CCTGTCACTTTAGGTGGTGTGT 60.159 50.000 0.00 0.00 45.38 3.72
7750 10126 5.847670 CTTCTCCTAAAAGAAGTTGTCGG 57.152 43.478 5.66 0.00 44.75 4.79
7824 10201 2.286294 CCTAGTCATGCTTAAGCGCTTG 59.714 50.000 32.23 17.70 45.83 4.01
7825 10202 2.555199 CCTAGTCATGCTTAAGCGCTT 58.445 47.619 27.97 27.97 45.83 4.68
7826 10203 1.808133 GCCTAGTCATGCTTAAGCGCT 60.808 52.381 21.97 17.75 45.83 5.92
7829 10206 0.583917 GCGCCTAGTCATGCTTAAGC 59.416 55.000 20.84 20.84 42.50 3.09
7859 10236 0.460987 CCTCAAGGCTAGGCGTTCTG 60.461 60.000 11.10 7.43 34.33 3.02
7882 10259 1.068921 GCCTCTGCCTAGCACTAGC 59.931 63.158 0.00 0.00 42.56 3.42
7883 10260 0.826715 TTGCCTCTGCCTAGCACTAG 59.173 55.000 0.00 0.00 35.96 2.57
7884 10261 1.275666 TTTGCCTCTGCCTAGCACTA 58.724 50.000 0.00 0.00 35.96 2.74
7885 10262 0.401738 TTTTGCCTCTGCCTAGCACT 59.598 50.000 0.00 0.00 35.96 4.40
7886 10263 1.467920 ATTTTGCCTCTGCCTAGCAC 58.532 50.000 0.00 0.00 35.96 4.40
7887 10264 2.421952 CCTATTTTGCCTCTGCCTAGCA 60.422 50.000 0.00 0.00 36.33 3.49
7888 10265 2.158755 TCCTATTTTGCCTCTGCCTAGC 60.159 50.000 0.00 0.00 36.33 3.42
7929 10306 0.036732 CAGGTAGCCAGCAGGTTCAA 59.963 55.000 0.00 0.00 37.19 2.69
7949 10326 8.945481 ACATGTGAAATCTTTTCAAAACATGA 57.055 26.923 24.07 0.00 35.64 3.07
8075 10481 5.924356 TCAGGTAGAAATGTTGAAGTGTGA 58.076 37.500 0.00 0.00 0.00 3.58
8159 10565 0.108615 GGCAGCGCTCTTGTTCTCTA 60.109 55.000 7.13 0.00 0.00 2.43
8175 10581 5.172687 TCACCAGTGTAGAAATAATGGCA 57.827 39.130 0.00 0.00 35.57 4.92
8176 10582 6.318648 TCATTCACCAGTGTAGAAATAATGGC 59.681 38.462 0.00 0.00 35.57 4.40
8188 10594 9.912634 CATTTAAGTTTTATCATTCACCAGTGT 57.087 29.630 0.00 0.00 0.00 3.55
8217 10690 1.551883 GCCAGCCTGAACCATTTCATT 59.448 47.619 0.00 0.00 41.05 2.57
8218 10691 1.188863 GCCAGCCTGAACCATTTCAT 58.811 50.000 0.00 0.00 41.05 2.57
8219 10692 1.243342 CGCCAGCCTGAACCATTTCA 61.243 55.000 0.00 0.00 39.55 2.69
8220 10693 1.244019 ACGCCAGCCTGAACCATTTC 61.244 55.000 0.00 0.00 0.00 2.17
8221 10694 0.037590 TACGCCAGCCTGAACCATTT 59.962 50.000 0.00 0.00 0.00 2.32
8222 10695 0.037590 TTACGCCAGCCTGAACCATT 59.962 50.000 0.00 0.00 0.00 3.16
8223 10696 0.392998 CTTACGCCAGCCTGAACCAT 60.393 55.000 0.00 0.00 0.00 3.55
8224 10697 1.003839 CTTACGCCAGCCTGAACCA 60.004 57.895 0.00 0.00 0.00 3.67
8225 10698 2.399356 GCTTACGCCAGCCTGAACC 61.399 63.158 0.00 0.00 33.21 3.62
8226 10699 3.178539 GCTTACGCCAGCCTGAAC 58.821 61.111 0.00 0.00 33.21 3.18
8237 10710 2.125991 TGTTACGGCGGGCTTACG 60.126 61.111 13.24 0.00 0.00 3.18
8238 10711 2.102438 GGTGTTACGGCGGGCTTAC 61.102 63.158 13.24 3.37 0.00 2.34
8239 10712 2.265424 GGTGTTACGGCGGGCTTA 59.735 61.111 13.24 0.00 0.00 3.09
8246 10719 2.691984 ATTTTTGACGGTGTTACGGC 57.308 45.000 0.00 0.00 43.68 5.68
8247 10720 8.725212 TTTATTTATTTTTGACGGTGTTACGG 57.275 30.769 0.00 0.00 38.39 4.02
8248 10721 9.977490 GTTTTATTTATTTTTGACGGTGTTACG 57.023 29.630 0.00 0.00 40.31 3.18
8269 10742 9.308318 GGCTTTCTGTCAAACATTTAAGTTTTA 57.692 29.630 0.00 0.00 39.55 1.52
8270 10743 7.821846 TGGCTTTCTGTCAAACATTTAAGTTTT 59.178 29.630 0.00 0.00 39.55 2.43
8271 10744 7.277760 GTGGCTTTCTGTCAAACATTTAAGTTT 59.722 33.333 0.00 0.00 42.10 2.66
8272 10745 6.756542 GTGGCTTTCTGTCAAACATTTAAGTT 59.243 34.615 0.00 0.00 28.98 2.66
8273 10746 6.096846 AGTGGCTTTCTGTCAAACATTTAAGT 59.903 34.615 0.00 0.00 28.98 2.24
8274 10747 6.418819 CAGTGGCTTTCTGTCAAACATTTAAG 59.581 38.462 0.00 0.00 28.98 1.85
8275 10748 6.272318 CAGTGGCTTTCTGTCAAACATTTAA 58.728 36.000 0.00 0.00 28.98 1.52
8276 10749 5.221224 CCAGTGGCTTTCTGTCAAACATTTA 60.221 40.000 0.00 0.00 28.98 1.40
8277 10750 4.441913 CCAGTGGCTTTCTGTCAAACATTT 60.442 41.667 0.00 0.00 28.98 2.32
8278 10751 3.068590 CCAGTGGCTTTCTGTCAAACATT 59.931 43.478 0.00 0.00 28.98 2.71
8279 10752 2.624838 CCAGTGGCTTTCTGTCAAACAT 59.375 45.455 0.00 0.00 28.98 2.71
8280 10753 2.023673 CCAGTGGCTTTCTGTCAAACA 58.976 47.619 0.00 0.00 28.98 2.83
8281 10754 1.338020 CCCAGTGGCTTTCTGTCAAAC 59.662 52.381 2.61 0.00 28.98 2.93
8282 10755 1.214175 TCCCAGTGGCTTTCTGTCAAA 59.786 47.619 2.61 0.00 28.98 2.69
8283 10756 0.843309 TCCCAGTGGCTTTCTGTCAA 59.157 50.000 2.61 0.00 28.98 3.18
8301 10774 1.135402 CAGCCGTTGTGCCCTTATTTC 60.135 52.381 0.00 0.00 0.00 2.17
8327 10800 9.719355 AAACTTTGAGTTATTTTCTGGTGTTTT 57.281 25.926 0.00 0.00 37.47 2.43
8349 10823 7.272244 CCCTTATTTTCCTGTTTTCACAAACT 58.728 34.615 0.00 0.00 42.61 2.66
8396 10870 7.329471 TGTTACTGATTTCTGATCTTCAAGACG 59.671 37.037 0.00 0.00 0.00 4.18
8402 10876 8.994429 TCTTCTGTTACTGATTTCTGATCTTC 57.006 34.615 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.