Multiple sequence alignment - TraesCS5A01G238000

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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 TraesCS5A01G238000 chr5A 100.000 4678 0 0 1 4678 454438430 454433753 0.000000e+00 8639.0
1 TraesCS5A01G238000 chr5B 91.576 3763 162 56 197 3897 417553363 417549694 0.000000e+00 5049.0
2 TraesCS5A01G238000 chr5B 86.905 420 41 7 3938 4343 417549609 417549190 4.270000e-125 459.0
3 TraesCS5A01G238000 chr5B 92.188 192 11 3 1 190 417553682 417553493 7.720000e-68 268.0
4 TraesCS5A01G238000 chr5B 87.302 189 22 2 4485 4671 417548958 417548770 1.020000e-51 215.0
5 TraesCS5A01G238000 chr5B 90.435 115 11 0 4370 4484 417549194 417549080 8.110000e-33 152.0
6 TraesCS5A01G238000 chr5D 92.487 3381 120 54 572 3897 353513877 353510576 0.000000e+00 4713.0
7 TraesCS5A01G238000 chr5D 88.309 556 50 8 3943 4484 353510409 353509855 0.000000e+00 652.0
8 TraesCS5A01G238000 chr5D 86.747 166 20 2 4508 4671 353509570 353509405 2.870000e-42 183.0
9 TraesCS5A01G238000 chr7B 100.000 28 0 0 2012 2039 62508792 62508819 8.000000e-03 52.8
10 TraesCS5A01G238000 chr6D 100.000 28 0 0 2016 2043 60131823 60131850 8.000000e-03 52.8
11 TraesCS5A01G238000 chr6B 100.000 28 0 0 2017 2044 71347607 71347634 8.000000e-03 52.8
12 TraesCS5A01G238000 chr6B 100.000 28 0 0 2017 2044 71487407 71487434 8.000000e-03 52.8


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 TraesCS5A01G238000 chr5A 454433753 454438430 4677 True 8639.000000 8639 100.0000 1 4678 1 chr5A.!!$R1 4677
1 TraesCS5A01G238000 chr5B 417548770 417553682 4912 True 1228.600000 5049 89.6812 1 4671 5 chr5B.!!$R1 4670
2 TraesCS5A01G238000 chr5D 353509405 353513877 4472 True 1849.333333 4713 89.1810 572 4671 3 chr5D.!!$R1 4099

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
772 916 0.033699 AGCCCAAGAGCCTCCAAATC 60.034 55.0 0.00 0.00 0.0 2.17 F
1593 1757 0.316204 CGTAGTTGTTGTCCGGGAGT 59.684 55.0 0.00 0.00 0.0 3.85 F
1598 1762 0.605319 TTGTTGTCCGGGAGTGATGC 60.605 55.0 0.00 0.00 0.0 3.91 F
3334 3549 0.578683 CCGATCGTGTCATGTCATGC 59.421 55.0 15.09 4.35 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2768 2946 0.179225 CACGATTTTCAGTTCGGCCG 60.179 55.0 22.12 22.12 39.61 6.13 R
2885 3067 0.036388 CACCGTGTTCACCAGGCTAT 60.036 55.0 0.00 0.00 0.00 2.97 R
3410 3634 0.461516 CATGGCAGCGAGTGATCAGT 60.462 55.0 1.67 1.67 0.00 3.41 R
4504 5154 0.326595 TTGGAGCAATACGAAGCCCA 59.673 50.0 0.00 0.00 31.98 5.36 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
40 41 5.160699 ACTATGTTGTGATGCGCTTATTG 57.839 39.130 9.73 0.00 0.00 1.90
49 50 6.045955 TGTGATGCGCTTATTGTATGAACTA 58.954 36.000 9.73 0.00 0.00 2.24
102 105 9.823647 TTCAAGCAAACAAACATTAAAATAGGA 57.176 25.926 0.00 0.00 0.00 2.94
144 147 6.884832 ACAAGATTATCGTAATCCACCAGAA 58.115 36.000 11.62 0.00 0.00 3.02
156 159 7.148323 CGTAATCCACCAGAATATCAAACACAA 60.148 37.037 0.00 0.00 0.00 3.33
160 163 5.353956 CCACCAGAATATCAAACACAATCGA 59.646 40.000 0.00 0.00 0.00 3.59
190 193 4.949238 ACAGTACATGCCATGCAAAATAGA 59.051 37.500 4.17 0.00 43.62 1.98
191 194 5.418524 ACAGTACATGCCATGCAAAATAGAA 59.581 36.000 4.17 0.00 43.62 2.10
192 195 6.071447 ACAGTACATGCCATGCAAAATAGAAA 60.071 34.615 4.17 0.00 43.62 2.52
194 197 5.410355 ACATGCCATGCAAAATAGAAACT 57.590 34.783 4.17 0.00 43.62 2.66
205 331 6.317140 TGCAAAATAGAAACTCTCCTGCTATG 59.683 38.462 0.00 0.00 0.00 2.23
208 334 2.476199 AGAAACTCTCCTGCTATGCCT 58.524 47.619 0.00 0.00 0.00 4.75
213 339 6.327626 AGAAACTCTCCTGCTATGCCTTAATA 59.672 38.462 0.00 0.00 0.00 0.98
227 353 6.969993 TGCCTTAATAAGAAAACCTTGTGT 57.030 33.333 0.83 0.00 36.34 3.72
228 354 6.744112 TGCCTTAATAAGAAAACCTTGTGTG 58.256 36.000 0.83 0.00 36.34 3.82
236 362 4.997565 AGAAAACCTTGTGTGAATGTGTG 58.002 39.130 0.00 0.00 0.00 3.82
239 365 2.722094 ACCTTGTGTGAATGTGTGTGT 58.278 42.857 0.00 0.00 0.00 3.72
241 367 4.460263 ACCTTGTGTGAATGTGTGTGTAT 58.540 39.130 0.00 0.00 0.00 2.29
246 372 8.726068 CCTTGTGTGAATGTGTGTGTATAAATA 58.274 33.333 0.00 0.00 0.00 1.40
304 430 2.028839 TGCGAAATTTCTACTCCCGACA 60.029 45.455 15.92 2.41 0.00 4.35
310 436 0.535335 TTCTACTCCCGACACATGCC 59.465 55.000 0.00 0.00 0.00 4.40
324 450 2.866156 CACATGCCTAATCACCGTAGTG 59.134 50.000 0.00 0.00 46.00 2.74
357 485 7.801716 TTGCATGTTAGAACCTATTACATCC 57.198 36.000 0.00 0.00 0.00 3.51
358 486 6.296026 TGCATGTTAGAACCTATTACATCCC 58.704 40.000 0.00 0.00 0.00 3.85
370 498 8.762481 ACCTATTACATCCCTTTAAATCCAAC 57.238 34.615 0.00 0.00 0.00 3.77
371 499 8.340757 ACCTATTACATCCCTTTAAATCCAACA 58.659 33.333 0.00 0.00 0.00 3.33
385 513 6.635030 AAATCCAACAAGTCCTAAAGTGAC 57.365 37.500 0.00 0.00 0.00 3.67
408 536 2.226437 AGTCAAATGTTAGCTGCCAACG 59.774 45.455 6.47 0.00 0.00 4.10
425 553 2.471607 GATGTGCGTGCGTGTCTG 59.528 61.111 0.00 0.00 0.00 3.51
431 559 2.738139 CGTGCGTGTCTGATGCCA 60.738 61.111 0.00 0.00 35.48 4.92
505 641 5.431765 AGTGTGAGCTCTTTCTTCTTCAAA 58.568 37.500 16.19 0.00 0.00 2.69
545 688 3.914435 AGTTCCCTCTTAAAGCTTACCCA 59.086 43.478 0.00 0.00 0.00 4.51
549 692 2.952310 CCTCTTAAAGCTTACCCATGGC 59.048 50.000 6.09 0.00 0.00 4.40
570 714 1.003355 GGGCAACACTAGCTCTGCA 60.003 57.895 11.36 0.00 36.50 4.41
588 732 1.000060 GCAAAGCATCAGTGGAAGCAA 60.000 47.619 5.43 0.00 40.12 3.91
638 782 3.976169 TGTAATGCAACTTGACTTTGGC 58.024 40.909 0.00 0.00 0.00 4.52
688 832 3.374220 TGTTGCTCCAGAAAAATGCAG 57.626 42.857 0.00 0.00 35.02 4.41
738 882 5.924356 TCACTTTGACATTTCACACCTAGA 58.076 37.500 0.00 0.00 0.00 2.43
739 883 5.991606 TCACTTTGACATTTCACACCTAGAG 59.008 40.000 0.00 0.00 0.00 2.43
740 884 4.757149 ACTTTGACATTTCACACCTAGAGC 59.243 41.667 0.00 0.00 0.00 4.09
772 916 0.033699 AGCCCAAGAGCCTCCAAATC 60.034 55.000 0.00 0.00 0.00 2.17
892 1036 1.987704 CTCGACCTCACAGCTCTCCG 61.988 65.000 0.00 0.00 0.00 4.63
893 1037 2.336478 CGACCTCACAGCTCTCCGT 61.336 63.158 0.00 0.00 0.00 4.69
894 1038 1.509004 GACCTCACAGCTCTCCGTC 59.491 63.158 0.00 0.00 0.00 4.79
895 1039 0.963355 GACCTCACAGCTCTCCGTCT 60.963 60.000 0.00 0.00 0.00 4.18
896 1040 0.963355 ACCTCACAGCTCTCCGTCTC 60.963 60.000 0.00 0.00 0.00 3.36
897 1041 1.662438 CCTCACAGCTCTCCGTCTCC 61.662 65.000 0.00 0.00 0.00 3.71
898 1042 1.662438 CTCACAGCTCTCCGTCTCCC 61.662 65.000 0.00 0.00 0.00 4.30
899 1043 2.752238 ACAGCTCTCCGTCTCCCG 60.752 66.667 0.00 0.00 0.00 5.14
900 1044 2.438614 CAGCTCTCCGTCTCCCGA 60.439 66.667 0.00 0.00 39.56 5.14
901 1045 1.826054 CAGCTCTCCGTCTCCCGAT 60.826 63.158 0.00 0.00 39.56 4.18
902 1046 1.527380 AGCTCTCCGTCTCCCGATC 60.527 63.158 0.00 0.00 39.56 3.69
903 1047 1.527380 GCTCTCCGTCTCCCGATCT 60.527 63.158 0.00 0.00 39.56 2.75
904 1048 1.512156 GCTCTCCGTCTCCCGATCTC 61.512 65.000 0.00 0.00 39.56 2.75
905 1049 0.887387 CTCTCCGTCTCCCGATCTCC 60.887 65.000 0.00 0.00 39.56 3.71
1040 1184 2.306805 TCCTGTGCATCCTCATTTCTGT 59.693 45.455 0.00 0.00 0.00 3.41
1481 1631 3.822192 CGTGCCGGACATCGAGGA 61.822 66.667 5.05 0.00 42.43 3.71
1574 1738 2.440569 GCTATAGCTAGCTGCGCGC 61.441 63.158 27.68 27.26 45.78 6.86
1582 1746 3.620300 TAGCTGCGCGCGTAGTTGT 62.620 57.895 40.29 29.17 45.59 3.32
1588 1752 2.468532 GCGCGTAGTTGTTGTCCG 59.531 61.111 8.43 0.00 0.00 4.79
1590 1754 2.377310 CGCGTAGTTGTTGTCCGGG 61.377 63.158 0.00 0.00 0.00 5.73
1592 1756 1.012486 GCGTAGTTGTTGTCCGGGAG 61.012 60.000 0.00 0.00 0.00 4.30
1593 1757 0.316204 CGTAGTTGTTGTCCGGGAGT 59.684 55.000 0.00 0.00 0.00 3.85
1595 1759 1.342174 GTAGTTGTTGTCCGGGAGTGA 59.658 52.381 0.00 0.00 0.00 3.41
1598 1762 0.605319 TTGTTGTCCGGGAGTGATGC 60.605 55.000 0.00 0.00 0.00 3.91
1599 1763 1.745489 GTTGTCCGGGAGTGATGCC 60.745 63.158 0.00 0.00 0.00 4.40
1600 1764 2.220586 TTGTCCGGGAGTGATGCCA 61.221 57.895 0.00 0.00 0.00 4.92
1601 1765 2.184020 TTGTCCGGGAGTGATGCCAG 62.184 60.000 0.00 0.00 0.00 4.85
1602 1766 2.284625 TCCGGGAGTGATGCCAGT 60.285 61.111 0.00 0.00 0.00 4.00
1603 1767 2.124983 CCGGGAGTGATGCCAGTG 60.125 66.667 0.00 0.00 0.00 3.66
1604 1768 2.124983 CGGGAGTGATGCCAGTGG 60.125 66.667 4.20 4.20 0.00 4.00
1711 1875 4.521062 CGGCGGAAGGAGGAGCTG 62.521 72.222 0.00 0.00 0.00 4.24
1712 1876 3.077556 GGCGGAAGGAGGAGCTGA 61.078 66.667 0.00 0.00 0.00 4.26
1760 1924 1.944430 GCTACAACTCCTTCCCCAACG 60.944 57.143 0.00 0.00 0.00 4.10
1857 2024 4.260656 CGTCGTGGTGTATACGTCTTTAAC 59.739 45.833 0.00 0.00 41.91 2.01
1859 2026 5.284660 GTCGTGGTGTATACGTCTTTAACAG 59.715 44.000 0.00 0.00 41.91 3.16
1860 2027 5.048782 TCGTGGTGTATACGTCTTTAACAGT 60.049 40.000 0.00 0.00 41.91 3.55
1862 2029 6.968904 CGTGGTGTATACGTCTTTAACAGTAT 59.031 38.462 0.00 0.00 36.83 2.12
1876 2043 8.717821 TCTTTAACAGTATCAGCACAACAATAC 58.282 33.333 0.00 0.00 0.00 1.89
1880 2047 5.939883 ACAGTATCAGCACAACAATACACAT 59.060 36.000 0.00 0.00 0.00 3.21
1900 2067 4.742417 CATGAATGCCATGTAACGGAAAA 58.258 39.130 0.00 0.00 45.83 2.29
1908 2082 1.595466 TGTAACGGAAAACCGCATGT 58.405 45.000 8.59 0.00 36.58 3.21
2015 2189 4.758251 CTCATGCGGTCACGGGCA 62.758 66.667 0.00 0.00 44.29 5.36
2042 2216 2.394912 GACGACGACGACGAGGAG 59.605 66.667 25.15 4.59 42.66 3.69
2304 2478 4.631813 CCATACACTTCAAGGCTTACAGTC 59.368 45.833 0.00 0.00 0.00 3.51
2306 2480 3.467803 ACACTTCAAGGCTTACAGTCAC 58.532 45.455 0.00 0.00 0.00 3.67
2310 2484 3.769739 TCAAGGCTTACAGTCACATGT 57.230 42.857 0.00 0.00 37.19 3.21
2326 2500 1.522258 CATGTTTTTCTTGTGCCGTGC 59.478 47.619 0.00 0.00 0.00 5.34
2345 2519 1.227089 GGCTGCTGATCGATGTCGT 60.227 57.895 0.54 0.00 40.80 4.34
2550 2728 5.278604 GTTACCGTGCATGGGATTTAATTC 58.721 41.667 28.37 4.30 0.00 2.17
2551 2729 2.693074 ACCGTGCATGGGATTTAATTCC 59.307 45.455 28.37 7.72 34.83 3.01
2575 2753 0.872021 GGTGCGACGATGATGAGGAC 60.872 60.000 0.00 0.00 0.00 3.85
2580 2758 1.664302 CGACGATGATGAGGACGATGG 60.664 57.143 0.00 0.00 0.00 3.51
2649 2827 1.220749 GTGGAAGGTGATGCCGCTA 59.779 57.895 0.00 0.00 43.70 4.26
2768 2946 1.592669 CCTCGATGTGGATGCGTCC 60.593 63.158 18.69 18.69 45.31 4.79
2842 3020 4.634004 TCCTTTCGATGCATTAAATCGTGT 59.366 37.500 0.00 0.00 45.53 4.49
2851 3033 4.033932 TGCATTAAATCGTGTCCTTCATCG 59.966 41.667 0.00 0.00 0.00 3.84
2860 3042 3.674955 CGTGTCCTTCATCGGTCAATACA 60.675 47.826 0.00 0.00 0.00 2.29
2874 3056 5.431765 GGTCAATACACTCCATTCATGAGT 58.568 41.667 0.00 0.00 0.00 3.41
2875 3057 6.582636 GGTCAATACACTCCATTCATGAGTA 58.417 40.000 0.00 0.00 0.00 2.59
2876 3058 6.480320 GGTCAATACACTCCATTCATGAGTAC 59.520 42.308 0.00 0.00 0.00 2.73
2877 3059 6.199154 GTCAATACACTCCATTCATGAGTACG 59.801 42.308 0.00 0.00 0.00 3.67
2878 3060 3.526931 ACACTCCATTCATGAGTACGG 57.473 47.619 0.00 0.00 0.00 4.02
2879 3061 2.205074 CACTCCATTCATGAGTACGGC 58.795 52.381 0.00 0.00 0.00 5.68
2880 3062 1.831106 ACTCCATTCATGAGTACGGCA 59.169 47.619 0.00 0.00 0.00 5.69
2881 3063 2.159043 ACTCCATTCATGAGTACGGCAG 60.159 50.000 0.00 0.00 0.00 4.85
2882 3064 0.940126 CCATTCATGAGTACGGCAGC 59.060 55.000 0.00 0.00 0.00 5.25
2883 3065 1.655484 CATTCATGAGTACGGCAGCA 58.345 50.000 0.00 0.00 0.00 4.41
2884 3066 2.009051 CATTCATGAGTACGGCAGCAA 58.991 47.619 0.00 0.00 0.00 3.91
2885 3067 2.177394 TTCATGAGTACGGCAGCAAA 57.823 45.000 0.00 0.00 0.00 3.68
2991 3191 4.698304 CGCCTTTGTTTCCCAGATTAGTAA 59.302 41.667 0.00 0.00 0.00 2.24
2993 3193 6.294286 CGCCTTTGTTTCCCAGATTAGTAAAA 60.294 38.462 0.00 0.00 0.00 1.52
2999 3199 7.064229 TGTTTCCCAGATTAGTAAAACCAACT 58.936 34.615 0.00 0.00 0.00 3.16
3036 3236 5.908341 TCATTTTCTTGTGGTGGTAAAACC 58.092 37.500 0.00 0.00 40.94 3.27
3146 3346 4.625800 GTGCTCATCCACCACCTC 57.374 61.111 0.00 0.00 0.00 3.85
3191 3399 0.743688 CCTCTCCACACAGATCCTCG 59.256 60.000 0.00 0.00 0.00 4.63
3198 3406 5.883115 TCTCCACACAGATCCTCGATATATC 59.117 44.000 2.34 2.34 0.00 1.63
3210 3425 1.647213 CGATATATCGCCGTTTGTCCG 59.353 52.381 21.28 0.00 43.84 4.79
3213 3428 1.426041 ATATCGCCGTTTGTCCGTGC 61.426 55.000 0.00 0.00 0.00 5.34
3232 3447 4.617875 GACAGGAACGTCCCATGG 57.382 61.111 4.14 4.14 37.19 3.66
3233 3448 1.745489 GACAGGAACGTCCCATGGC 60.745 63.158 6.09 0.00 37.19 4.40
3334 3549 0.578683 CCGATCGTGTCATGTCATGC 59.421 55.000 15.09 4.35 0.00 4.06
3357 3572 3.583882 AAAGCCCGGGTGGTCCATG 62.584 63.158 24.63 0.00 36.04 3.66
3407 3631 0.814410 CCTGCCTATGAGCTGTGCTG 60.814 60.000 0.00 0.00 39.88 4.41
3410 3634 1.222661 CCTATGAGCTGTGCTGCCA 59.777 57.895 0.00 0.00 39.88 4.92
3445 3669 3.233980 TGGCGACAGCTGTGGAGT 61.234 61.111 30.28 2.84 44.37 3.85
3447 3671 2.320587 GGCGACAGCTGTGGAGTTG 61.321 63.158 30.28 8.51 44.37 3.16
3448 3672 1.595382 GCGACAGCTGTGGAGTTGT 60.595 57.895 30.28 1.34 45.53 3.32
3450 3674 1.419374 CGACAGCTGTGGAGTTGTAC 58.581 55.000 27.27 5.11 43.14 2.90
3451 3675 1.419374 GACAGCTGTGGAGTTGTACG 58.581 55.000 27.27 0.00 43.14 3.67
3452 3676 0.750850 ACAGCTGTGGAGTTGTACGT 59.249 50.000 20.97 0.00 41.47 3.57
3453 3677 1.139989 CAGCTGTGGAGTTGTACGTG 58.860 55.000 5.25 0.00 0.00 4.49
3454 3678 0.750850 AGCTGTGGAGTTGTACGTGT 59.249 50.000 0.00 0.00 0.00 4.49
3455 3679 0.859232 GCTGTGGAGTTGTACGTGTG 59.141 55.000 0.00 0.00 0.00 3.82
3456 3680 0.859232 CTGTGGAGTTGTACGTGTGC 59.141 55.000 0.00 0.00 0.00 4.57
3457 3681 0.462375 TGTGGAGTTGTACGTGTGCT 59.538 50.000 0.00 0.00 0.00 4.40
3458 3682 1.682323 TGTGGAGTTGTACGTGTGCTA 59.318 47.619 0.00 0.00 0.00 3.49
3491 3715 2.005370 ATGGGGGTGATGATTGATGC 57.995 50.000 0.00 0.00 0.00 3.91
3581 3805 3.804329 GTTCCCCGCCATGGCCTA 61.804 66.667 30.79 10.91 37.98 3.93
3645 3869 2.509336 GGTGCCCGACTGATGACG 60.509 66.667 0.00 0.00 0.00 4.35
3732 3956 4.707448 TCTCCCTTTTTGTTGTTGTTGCTA 59.293 37.500 0.00 0.00 0.00 3.49
3782 4012 7.750229 AATCATTAGAGAAGAAACAACAGCA 57.250 32.000 0.00 0.00 0.00 4.41
3783 4013 7.934855 ATCATTAGAGAAGAAACAACAGCAT 57.065 32.000 0.00 0.00 0.00 3.79
3784 4014 7.137490 TCATTAGAGAAGAAACAACAGCATG 57.863 36.000 0.00 0.00 46.00 4.06
3819 4049 2.628178 GGAGGACGATGATCATGTACCA 59.372 50.000 14.30 0.00 0.00 3.25
3903 4145 6.567687 TTTTTCGAAATATTGCACTCCAGA 57.432 33.333 12.12 0.00 0.00 3.86
3912 4154 2.368011 GCACTCCAGACCCCCTACC 61.368 68.421 0.00 0.00 0.00 3.18
3928 4177 0.034337 TACCACCACACTCGAAAGCC 59.966 55.000 0.00 0.00 0.00 4.35
3963 4338 4.782691 TCTCTCTCTCTCTCTCTCTCCAAA 59.217 45.833 0.00 0.00 0.00 3.28
3986 4361 5.332743 AGGTCTCAGGGAGATCTATCAATC 58.667 45.833 7.23 0.00 46.86 2.67
4034 4420 0.241481 GCCGAGTTGACTTCGTCTCT 59.759 55.000 0.00 0.00 33.15 3.10
4038 4424 3.366476 CCGAGTTGACTTCGTCTCTGATT 60.366 47.826 0.00 0.00 33.15 2.57
4050 4436 1.227823 TCTGATTTATGGGCGGCGG 60.228 57.895 9.78 0.00 0.00 6.13
4069 4455 0.738762 GGCCTACTCGTTTTCCGGTC 60.739 60.000 0.00 0.00 37.11 4.79
4139 4525 4.403976 GAGGAGCCGTTCATCGAC 57.596 61.111 0.00 0.00 42.86 4.20
4176 4562 1.455959 AGGACCGATTCGAGGAGGG 60.456 63.158 7.83 0.00 0.00 4.30
4194 4580 0.988678 GGAGGCCTGGTATGTTCCCT 60.989 60.000 12.00 0.00 0.00 4.20
4203 4589 3.517901 CTGGTATGTTCCCTTGTCACCTA 59.482 47.826 0.00 0.00 0.00 3.08
4204 4590 3.517901 TGGTATGTTCCCTTGTCACCTAG 59.482 47.826 0.00 0.00 0.00 3.02
4213 4599 3.321111 CCCTTGTCACCTAGCACGTATAT 59.679 47.826 0.00 0.00 0.00 0.86
4217 4603 3.067601 TGTCACCTAGCACGTATATGTGG 59.932 47.826 23.30 11.43 40.26 4.17
4221 4607 2.404215 CTAGCACGTATATGTGGGCAC 58.596 52.381 23.30 9.20 40.26 5.01
4239 4625 3.788766 GTGGACCACGATGCACGC 61.789 66.667 9.33 0.00 46.94 5.34
4255 4641 2.258591 GCGAGGCGAAGTGTCTCA 59.741 61.111 0.00 0.00 0.00 3.27
4267 4655 2.540383 AGTGTCTCAATGAGTGCCCTA 58.460 47.619 10.36 0.00 0.00 3.53
4268 4656 2.234908 AGTGTCTCAATGAGTGCCCTAC 59.765 50.000 10.36 0.48 0.00 3.18
4270 4658 2.840038 TGTCTCAATGAGTGCCCTACAT 59.160 45.455 10.36 0.00 0.00 2.29
4333 4722 2.164026 GCGAGCGCTCTCCTTTCTG 61.164 63.158 32.88 16.90 35.94 3.02
4339 4728 0.649475 CGCTCTCCTTTCTGCATTCG 59.351 55.000 0.00 0.00 0.00 3.34
4376 4765 2.695359 GTGCAACCGAATCCAGTTCTA 58.305 47.619 0.00 0.00 34.56 2.10
4377 4766 2.673368 GTGCAACCGAATCCAGTTCTAG 59.327 50.000 0.00 0.00 34.56 2.43
4383 4772 2.103094 CCGAATCCAGTTCTAGCCATGA 59.897 50.000 0.00 0.00 34.56 3.07
4465 4854 0.749649 CGAATGAGGTCCTCTCCTGG 59.250 60.000 19.82 2.30 41.76 4.45
4471 4860 1.996187 GGTCCTCTCCTGGTTCCCC 60.996 68.421 0.00 0.00 0.00 4.81
4474 4863 0.104144 TCCTCTCCTGGTTCCCCAAA 60.104 55.000 0.00 0.00 41.27 3.28
4484 4873 1.423921 GGTTCCCCAAAGTGAAGGAGA 59.576 52.381 0.00 0.00 0.00 3.71
4486 4875 3.348119 GTTCCCCAAAGTGAAGGAGATC 58.652 50.000 0.00 0.00 0.00 2.75
4487 4876 1.916181 TCCCCAAAGTGAAGGAGATCC 59.084 52.381 0.00 0.00 0.00 3.36
4491 5001 3.341823 CCAAAGTGAAGGAGATCCAGTG 58.658 50.000 0.92 0.00 38.89 3.66
4517 5167 1.766143 GCTCGCTGGGCTTCGTATTG 61.766 60.000 0.00 0.00 0.00 1.90
4526 5176 2.565841 GGCTTCGTATTGCTCCAAGAT 58.434 47.619 0.00 0.00 0.00 2.40
4527 5177 2.945668 GGCTTCGTATTGCTCCAAGATT 59.054 45.455 0.00 0.00 0.00 2.40
4544 5194 0.779997 ATTGGCAACCCTCAGAACCT 59.220 50.000 0.00 0.00 0.00 3.50
4551 5201 3.347216 CAACCCTCAGAACCTACCAATG 58.653 50.000 0.00 0.00 0.00 2.82
4556 5206 3.200825 CCTCAGAACCTACCAATGGATGT 59.799 47.826 6.16 0.00 0.00 3.06
4562 5212 3.290710 ACCTACCAATGGATGTGAATGC 58.709 45.455 6.16 0.00 0.00 3.56
4570 5220 3.739782 GATGTGAATGCGGTGGCGC 62.740 63.158 0.00 0.00 44.10 6.53
4572 5222 2.817834 GTGAATGCGGTGGCGCTA 60.818 61.111 7.64 0.00 44.10 4.26
4583 5233 2.279252 GGCGCTAGCGATTCCGAA 60.279 61.111 39.52 0.00 46.35 4.30
4589 5239 2.474816 GCTAGCGATTCCGAAATCACT 58.525 47.619 0.00 0.00 41.22 3.41
4635 5287 5.680922 GCCTCTATCATGAATAGGTCATCCG 60.681 48.000 17.77 0.00 44.01 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.106197 GCATCACAACATAGTTCAATCACCA 60.106 40.000 0.00 0.00 0.00 4.17
116 119 8.343168 TGGTGGATTACGATAATCTTGTTTTT 57.657 30.769 13.67 0.00 0.00 1.94
156 159 3.623060 GGCATGTACTGTGACAATTCGAT 59.377 43.478 0.00 0.00 31.83 3.59
160 163 3.119388 GCATGGCATGTACTGTGACAATT 60.119 43.478 26.94 0.00 38.28 2.32
175 178 4.158394 GGAGAGTTTCTATTTTGCATGGCA 59.842 41.667 0.00 0.00 36.47 4.92
176 179 4.400567 AGGAGAGTTTCTATTTTGCATGGC 59.599 41.667 0.00 0.00 0.00 4.40
190 193 4.844349 TTAAGGCATAGCAGGAGAGTTT 57.156 40.909 0.00 0.00 0.00 2.66
191 194 6.327626 TCTTATTAAGGCATAGCAGGAGAGTT 59.672 38.462 3.66 0.00 0.00 3.01
192 195 5.841237 TCTTATTAAGGCATAGCAGGAGAGT 59.159 40.000 3.66 0.00 0.00 3.24
194 197 6.747414 TTCTTATTAAGGCATAGCAGGAGA 57.253 37.500 3.66 0.00 0.00 3.71
205 331 6.977213 TCACACAAGGTTTTCTTATTAAGGC 58.023 36.000 3.66 0.00 33.68 4.35
208 334 9.743057 CACATTCACACAAGGTTTTCTTATTAA 57.257 29.630 0.00 0.00 33.68 1.40
213 339 5.047377 ACACACATTCACACAAGGTTTTCTT 60.047 36.000 0.00 0.00 35.79 2.52
228 354 9.849607 CGATCTTGTATTTATACACACACATTC 57.150 33.333 2.16 0.00 42.48 2.67
241 367 8.155821 TGGTGTTTGTTTCGATCTTGTATTTA 57.844 30.769 0.00 0.00 0.00 1.40
246 372 4.319477 CGATGGTGTTTGTTTCGATCTTGT 60.319 41.667 0.00 0.00 31.74 3.16
304 430 2.741878 GCACTACGGTGATTAGGCATGT 60.742 50.000 0.00 0.00 45.61 3.21
310 436 7.513132 CAAATGATATGCACTACGGTGATTAG 58.487 38.462 0.00 0.00 45.61 1.73
324 450 6.742109 AGGTTCTAACATGCAAATGATATGC 58.258 36.000 0.00 0.00 44.08 3.14
351 479 6.661805 GGACTTGTTGGATTTAAAGGGATGTA 59.338 38.462 0.00 0.00 0.00 2.29
353 481 5.716703 AGGACTTGTTGGATTTAAAGGGATG 59.283 40.000 0.00 0.00 0.00 3.51
357 485 8.082242 CACTTTAGGACTTGTTGGATTTAAAGG 58.918 37.037 0.00 0.00 33.44 3.11
358 486 8.846211 TCACTTTAGGACTTGTTGGATTTAAAG 58.154 33.333 0.00 0.00 34.63 1.85
370 498 4.238761 TGACTCGTCACTTTAGGACTTG 57.761 45.455 0.00 0.00 34.14 3.16
371 499 4.931661 TTGACTCGTCACTTTAGGACTT 57.068 40.909 0.00 0.00 39.66 3.01
385 513 2.076100 TGGCAGCTAACATTTGACTCG 58.924 47.619 0.00 0.00 0.00 4.18
408 536 1.354337 ATCAGACACGCACGCACATC 61.354 55.000 0.00 0.00 0.00 3.06
425 553 5.329035 ACCACTATCAAAATGTTGGCATC 57.671 39.130 0.00 0.00 35.29 3.91
431 559 8.375506 TCAGAGAACTACCACTATCAAAATGTT 58.624 33.333 0.00 0.00 0.00 2.71
481 617 5.028549 TGAAGAAGAAAGAGCTCACACTT 57.971 39.130 17.77 16.36 0.00 3.16
482 618 4.679373 TGAAGAAGAAAGAGCTCACACT 57.321 40.909 17.77 8.54 0.00 3.55
525 668 4.325030 CCATGGGTAAGCTTTAAGAGGGAA 60.325 45.833 3.20 0.00 0.00 3.97
526 669 3.202151 CCATGGGTAAGCTTTAAGAGGGA 59.798 47.826 3.20 0.00 0.00 4.20
527 670 3.555966 CCATGGGTAAGCTTTAAGAGGG 58.444 50.000 3.20 0.00 0.00 4.30
528 671 2.952310 GCCATGGGTAAGCTTTAAGAGG 59.048 50.000 15.13 1.61 0.00 3.69
545 688 0.967380 GCTAGTGTTGCCCAAGCCAT 60.967 55.000 0.00 0.00 38.69 4.40
549 692 1.446907 CAGAGCTAGTGTTGCCCAAG 58.553 55.000 0.00 0.00 0.00 3.61
558 701 2.352034 CTGATGCTTTGCAGAGCTAGTG 59.648 50.000 27.37 13.01 43.65 2.74
570 714 1.615392 GGTTGCTTCCACTGATGCTTT 59.385 47.619 0.00 0.00 41.10 3.51
588 732 1.828595 ACCGGCAAAAGAAAAACAGGT 59.171 42.857 0.00 0.00 0.00 4.00
638 782 5.824624 ACCACAGCTTCATATATGGTGAAAG 59.175 40.000 12.78 9.63 38.99 2.62
688 832 6.739112 AGGACAACTTTTCTTCTTACATTGC 58.261 36.000 0.00 0.00 0.00 3.56
892 1036 1.460273 GGCAGAGGAGATCGGGAGAC 61.460 65.000 0.00 0.00 44.82 3.36
893 1037 1.152652 GGCAGAGGAGATCGGGAGA 60.153 63.158 0.00 0.00 46.90 3.71
894 1038 1.456518 TGGCAGAGGAGATCGGGAG 60.457 63.158 0.00 0.00 0.00 4.30
895 1039 1.456518 CTGGCAGAGGAGATCGGGA 60.457 63.158 9.42 0.00 0.00 5.14
896 1040 3.136750 CTGGCAGAGGAGATCGGG 58.863 66.667 9.42 0.00 0.00 5.14
897 1041 2.366480 CTGCTGGCAGAGGAGATCGG 62.366 65.000 20.86 0.00 46.30 4.18
898 1042 1.067749 CTGCTGGCAGAGGAGATCG 59.932 63.158 20.86 0.00 46.30 3.69
899 1043 1.227615 GCTGCTGGCAGAGGAGATC 60.228 63.158 24.40 0.00 46.30 2.75
900 1044 2.909577 GCTGCTGGCAGAGGAGAT 59.090 61.111 24.40 0.00 46.30 2.75
901 1045 3.767806 CGCTGCTGGCAGAGGAGA 61.768 66.667 24.40 0.00 46.30 3.71
1106 1256 3.056313 GCTTTCTCATGGCGGCCAC 62.056 63.158 26.48 4.89 35.80 5.01
1120 1270 2.674380 CAGCTTGAGGGCGGCTTT 60.674 61.111 9.56 0.00 37.29 3.51
1302 1452 3.767230 CGCGACACCAGCACGAAG 61.767 66.667 0.00 0.00 34.19 3.79
1374 1524 1.807573 GTGGAAGAAGAGCGCCGAG 60.808 63.158 2.29 0.00 0.00 4.63
1533 1683 0.322456 CCCTCTTCATGGCGTGGAAA 60.322 55.000 6.90 0.00 0.00 3.13
1574 1738 0.316204 ACTCCCGGACAACAACTACG 59.684 55.000 0.73 0.00 0.00 3.51
1582 1746 2.184020 CTGGCATCACTCCCGGACAA 62.184 60.000 0.73 0.00 0.00 3.18
1595 1759 6.800229 TGATTAATATCATACGCCACTGGCAT 60.800 38.462 20.28 7.45 41.32 4.40
1598 1762 6.091305 CACTGATTAATATCATACGCCACTGG 59.909 42.308 0.00 0.00 39.94 4.00
1599 1763 6.401474 GCACTGATTAATATCATACGCCACTG 60.401 42.308 0.00 0.00 39.94 3.66
1600 1764 5.639506 GCACTGATTAATATCATACGCCACT 59.360 40.000 0.00 0.00 39.94 4.00
1601 1765 5.408299 TGCACTGATTAATATCATACGCCAC 59.592 40.000 0.00 0.00 39.94 5.01
1602 1766 5.546526 TGCACTGATTAATATCATACGCCA 58.453 37.500 0.00 0.00 39.94 5.69
1603 1767 6.668541 ATGCACTGATTAATATCATACGCC 57.331 37.500 0.00 0.00 39.94 5.68
1857 2024 5.861222 TGTGTATTGTTGTGCTGATACTG 57.139 39.130 0.00 0.00 0.00 2.74
1859 2026 6.421377 TCATGTGTATTGTTGTGCTGATAC 57.579 37.500 0.00 0.00 0.00 2.24
1860 2027 7.474190 CATTCATGTGTATTGTTGTGCTGATA 58.526 34.615 0.00 0.00 0.00 2.15
1862 2029 5.701855 CATTCATGTGTATTGTTGTGCTGA 58.298 37.500 0.00 0.00 0.00 4.26
1880 2047 3.057174 GGTTTTCCGTTACATGGCATTCA 60.057 43.478 0.00 0.00 0.00 2.57
2024 2198 3.403249 CTCCTCGTCGTCGTCGTCG 62.403 68.421 14.18 14.18 46.06 5.12
2025 2199 2.394912 CTCCTCGTCGTCGTCGTC 59.605 66.667 11.41 0.00 38.33 4.20
2026 2200 3.117171 CCTCCTCGTCGTCGTCGT 61.117 66.667 11.41 0.00 38.33 4.34
2027 2201 2.800581 CTCCTCCTCGTCGTCGTCG 61.801 68.421 5.50 5.50 38.33 5.12
2304 2478 2.535166 CACGGCACAAGAAAAACATGTG 59.465 45.455 0.00 0.00 46.68 3.21
2306 2480 1.522258 GCACGGCACAAGAAAAACATG 59.478 47.619 0.00 0.00 0.00 3.21
2310 2484 1.064946 CCGCACGGCACAAGAAAAA 59.935 52.632 0.00 0.00 0.00 1.94
2326 2500 2.298629 CGACATCGATCAGCAGCCG 61.299 63.158 0.00 0.00 43.02 5.52
2329 2503 0.932123 CGGACGACATCGATCAGCAG 60.932 60.000 8.54 0.00 43.02 4.24
2551 2729 3.751401 ATCATCGTCGCACCGTCCG 62.751 63.158 0.00 0.00 0.00 4.79
2575 2753 2.373540 TTTTACGTCAGGTCCCATCG 57.626 50.000 0.00 0.00 0.00 3.84
2580 2758 3.254903 AGGCAAAATTTTACGTCAGGTCC 59.745 43.478 2.44 0.00 0.00 4.46
2649 2827 3.285484 GCTGTGATGGATGTTCCTGAAT 58.715 45.455 0.00 0.00 37.46 2.57
2768 2946 0.179225 CACGATTTTCAGTTCGGCCG 60.179 55.000 22.12 22.12 39.61 6.13
2773 2951 5.418310 TTGAAGGTCACGATTTTCAGTTC 57.582 39.130 0.00 0.00 31.85 3.01
2842 3020 3.132289 GGAGTGTATTGACCGATGAAGGA 59.868 47.826 0.00 0.00 34.73 3.36
2851 3033 5.431765 ACTCATGAATGGAGTGTATTGACC 58.568 41.667 0.00 0.00 43.65 4.02
2860 3042 1.831106 TGCCGTACTCATGAATGGAGT 59.169 47.619 9.47 0.22 46.71 3.85
2878 3060 1.135286 GTTCACCAGGCTATTTGCTGC 60.135 52.381 0.00 0.00 42.39 5.25
2879 3061 2.095059 GTGTTCACCAGGCTATTTGCTG 60.095 50.000 0.00 0.00 42.39 4.41
2880 3062 2.162681 GTGTTCACCAGGCTATTTGCT 58.837 47.619 0.00 0.00 42.39 3.91
2881 3063 1.135689 CGTGTTCACCAGGCTATTTGC 60.136 52.381 0.00 0.00 41.94 3.68
2882 3064 1.468520 CCGTGTTCACCAGGCTATTTG 59.531 52.381 0.00 0.00 0.00 2.32
2883 3065 1.073284 ACCGTGTTCACCAGGCTATTT 59.927 47.619 0.00 0.00 0.00 1.40
2884 3066 0.690762 ACCGTGTTCACCAGGCTATT 59.309 50.000 0.00 0.00 0.00 1.73
2885 3067 0.036388 CACCGTGTTCACCAGGCTAT 60.036 55.000 0.00 0.00 0.00 2.97
2898 3091 5.007823 TGTTCAAGTGGTATTTAACACCGTG 59.992 40.000 2.19 0.00 39.04 4.94
3011 3211 5.782893 TTTACCACCACAAGAAAATGAGG 57.217 39.130 0.00 0.00 37.13 3.86
3191 3399 2.407361 CACGGACAAACGGCGATATATC 59.593 50.000 16.62 2.34 38.39 1.63
3219 3434 2.438434 CCAGCCATGGGACGTTCC 60.438 66.667 15.13 5.70 43.54 3.62
3230 3445 4.960866 CACTGCACCAGCCAGCCA 62.961 66.667 0.00 0.00 41.13 4.75
3334 3549 2.755469 CCACCCGGGCTTTCATGG 60.755 66.667 24.08 16.54 0.00 3.66
3407 3631 2.459442 GCAGCGAGTGATCAGTGGC 61.459 63.158 25.21 25.21 35.98 5.01
3410 3634 0.461516 CATGGCAGCGAGTGATCAGT 60.462 55.000 1.67 1.67 0.00 3.41
3443 3667 5.047519 ACCTAAATCTAGCACACGTACAACT 60.048 40.000 0.00 0.00 0.00 3.16
3444 3668 5.166398 ACCTAAATCTAGCACACGTACAAC 58.834 41.667 0.00 0.00 0.00 3.32
3445 3669 5.395682 ACCTAAATCTAGCACACGTACAA 57.604 39.130 0.00 0.00 0.00 2.41
3447 3671 5.297776 TCCTACCTAAATCTAGCACACGTAC 59.702 44.000 0.00 0.00 0.00 3.67
3448 3672 5.439721 TCCTACCTAAATCTAGCACACGTA 58.560 41.667 0.00 0.00 0.00 3.57
3450 3674 4.913335 TCCTACCTAAATCTAGCACACG 57.087 45.455 0.00 0.00 0.00 4.49
3451 3675 5.992217 CCATTCCTACCTAAATCTAGCACAC 59.008 44.000 0.00 0.00 0.00 3.82
3452 3676 5.071788 CCCATTCCTACCTAAATCTAGCACA 59.928 44.000 0.00 0.00 0.00 4.57
3453 3677 5.513267 CCCCATTCCTACCTAAATCTAGCAC 60.513 48.000 0.00 0.00 0.00 4.40
3454 3678 4.597507 CCCCATTCCTACCTAAATCTAGCA 59.402 45.833 0.00 0.00 0.00 3.49
3455 3679 4.019231 CCCCCATTCCTACCTAAATCTAGC 60.019 50.000 0.00 0.00 0.00 3.42
3456 3680 5.013183 CACCCCCATTCCTACCTAAATCTAG 59.987 48.000 0.00 0.00 0.00 2.43
3457 3681 4.911522 CACCCCCATTCCTACCTAAATCTA 59.088 45.833 0.00 0.00 0.00 1.98
3458 3682 3.722101 CACCCCCATTCCTACCTAAATCT 59.278 47.826 0.00 0.00 0.00 2.40
3491 3715 1.658095 CAAAAACCAAGCACCAACACG 59.342 47.619 0.00 0.00 0.00 4.49
3645 3869 0.710567 TCGTCTTCGTCGTCGTAGTC 59.289 55.000 8.32 2.89 36.23 2.59
3732 3956 6.182627 TCATAGAGAAGAATGCCACAACAAT 58.817 36.000 0.00 0.00 0.00 2.71
3782 4012 7.472334 TCGTCCTCCTAAAAAGTAGTAACAT 57.528 36.000 0.00 0.00 0.00 2.71
3783 4013 6.899393 TCGTCCTCCTAAAAAGTAGTAACA 57.101 37.500 0.00 0.00 0.00 2.41
3784 4014 7.542025 TCATCGTCCTCCTAAAAAGTAGTAAC 58.458 38.462 0.00 0.00 0.00 2.50
3785 4015 7.707624 TCATCGTCCTCCTAAAAAGTAGTAA 57.292 36.000 0.00 0.00 0.00 2.24
3786 4016 7.558807 TGATCATCGTCCTCCTAAAAAGTAGTA 59.441 37.037 0.00 0.00 0.00 1.82
3789 4019 6.785337 TGATCATCGTCCTCCTAAAAAGTA 57.215 37.500 0.00 0.00 0.00 2.24
3819 4049 7.870509 ACATCATTGACAACATAAGCACTAT 57.129 32.000 0.00 0.00 0.00 2.12
3883 4113 3.938963 GGTCTGGAGTGCAATATTTCGAA 59.061 43.478 0.00 0.00 0.00 3.71
3884 4114 3.531538 GGTCTGGAGTGCAATATTTCGA 58.468 45.455 0.00 0.00 0.00 3.71
3885 4115 2.614057 GGGTCTGGAGTGCAATATTTCG 59.386 50.000 0.00 0.00 0.00 3.46
3890 4132 0.253160 AGGGGGTCTGGAGTGCAATA 60.253 55.000 0.00 0.00 0.00 1.90
3892 4134 1.159905 TAGGGGGTCTGGAGTGCAA 59.840 57.895 0.00 0.00 0.00 4.08
3894 4136 2.368011 GGTAGGGGGTCTGGAGTGC 61.368 68.421 0.00 0.00 0.00 4.40
3899 4141 2.124085 TGGTGGTAGGGGGTCTGG 59.876 66.667 0.00 0.00 0.00 3.86
3903 4145 1.538135 GAGTGTGGTGGTAGGGGGT 60.538 63.158 0.00 0.00 0.00 4.95
3912 4154 1.966451 GGGGCTTTCGAGTGTGGTG 60.966 63.158 0.00 0.00 0.00 4.17
3934 4183 2.370189 GAGAGAGAGAGAGAGAGAGGGG 59.630 59.091 0.00 0.00 0.00 4.79
3936 4185 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
3963 4338 4.823364 TTGATAGATCTCCCTGAGACCT 57.177 45.455 0.00 0.00 41.76 3.85
3983 4358 2.923121 CACATCATCAACTCCCCGATT 58.077 47.619 0.00 0.00 0.00 3.34
3986 4361 1.431488 CGCACATCATCAACTCCCCG 61.431 60.000 0.00 0.00 0.00 5.73
4034 4420 2.203280 CCCGCCGCCCATAAATCA 60.203 61.111 0.00 0.00 0.00 2.57
4069 4455 2.436115 GCCGGAGAAGGAAACCCG 60.436 66.667 5.05 0.00 41.47 5.28
4097 4483 3.168528 AGCAACACCACCCTCCGT 61.169 61.111 0.00 0.00 0.00 4.69
4139 4525 4.504916 CACTCGGCTCCTCGGCTG 62.505 72.222 0.00 0.00 39.72 4.85
4145 4531 2.363147 GTCCTCCACTCGGCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
4176 4562 0.919710 AAGGGAACATACCAGGCCTC 59.080 55.000 0.00 0.00 0.00 4.70
4194 4580 4.440940 CCACATATACGTGCTAGGTGACAA 60.441 45.833 19.78 0.00 33.82 3.18
4203 4589 0.529773 CGTGCCCACATATACGTGCT 60.530 55.000 0.00 0.00 35.47 4.40
4204 4590 0.808453 ACGTGCCCACATATACGTGC 60.808 55.000 0.00 0.00 46.55 5.34
4213 4599 4.555709 GTGGTCCACGTGCCCACA 62.556 66.667 33.30 18.68 46.33 4.17
4239 4625 0.994995 CATTGAGACACTTCGCCTCG 59.005 55.000 0.00 0.00 0.00 4.63
4244 4630 1.728971 GGCACTCATTGAGACACTTCG 59.271 52.381 20.33 1.34 33.32 3.79
4251 4637 2.840038 ACATGTAGGGCACTCATTGAGA 59.160 45.455 20.33 0.00 33.32 3.27
4255 4641 1.064463 CCCACATGTAGGGCACTCATT 60.064 52.381 17.10 0.00 39.96 2.57
4267 4655 1.681666 CTCTCACAGCCCCACATGT 59.318 57.895 0.00 0.00 0.00 3.21
4268 4656 1.077930 CCTCTCACAGCCCCACATG 60.078 63.158 0.00 0.00 0.00 3.21
4270 4658 2.930019 CCCTCTCACAGCCCCACA 60.930 66.667 0.00 0.00 0.00 4.17
4333 4722 0.874390 TCTTCACTGCAACCGAATGC 59.126 50.000 5.56 5.56 46.58 3.56
4339 4728 1.269257 GCACCTTTCTTCACTGCAACC 60.269 52.381 0.00 0.00 0.00 3.77
4349 4738 1.886542 GGATTCGGTTGCACCTTTCTT 59.113 47.619 0.00 0.00 35.66 2.52
4383 4772 3.842923 CGTGCTCCGCTCCATCCT 61.843 66.667 0.00 0.00 0.00 3.24
4398 4787 1.298667 GCATACACCTCCAACCCGT 59.701 57.895 0.00 0.00 0.00 5.28
4465 4854 2.951229 TCTCCTTCACTTTGGGGAAC 57.049 50.000 0.00 0.00 28.39 3.62
4471 4860 2.746362 GCACTGGATCTCCTTCACTTTG 59.254 50.000 0.00 0.00 36.82 2.77
4474 4863 1.554160 CTGCACTGGATCTCCTTCACT 59.446 52.381 0.00 0.00 36.82 3.41
4504 5154 0.326595 TTGGAGCAATACGAAGCCCA 59.673 50.000 0.00 0.00 31.98 5.36
4526 5176 1.073284 GTAGGTTCTGAGGGTTGCCAA 59.927 52.381 0.00 0.00 0.00 4.52
4527 5177 0.690762 GTAGGTTCTGAGGGTTGCCA 59.309 55.000 0.00 0.00 0.00 4.92
4531 5181 2.308866 CCATTGGTAGGTTCTGAGGGTT 59.691 50.000 0.00 0.00 0.00 4.11
4544 5194 2.296792 CCGCATTCACATCCATTGGTA 58.703 47.619 1.86 0.00 0.00 3.25
4551 5201 2.800736 GCCACCGCATTCACATCC 59.199 61.111 0.00 0.00 34.03 3.51
4562 5212 3.330853 GAATCGCTAGCGCCACCG 61.331 66.667 31.82 5.40 39.59 4.94
4589 5239 6.419980 GCAAAAATATGCCTTGTTATGCAA 57.580 33.333 0.00 0.00 41.50 4.08
4611 5261 5.669477 GGATGACCTATTCATGATAGAGGC 58.331 45.833 14.85 9.98 45.67 4.70
4621 5273 2.637872 GGGGATTCGGATGACCTATTCA 59.362 50.000 0.00 0.00 39.11 2.57
4635 5287 9.143155 ACAAAAATATAATGTAGGTGGGGATTC 57.857 33.333 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.