Multiple sequence alignment - TraesCS1D01G351800

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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 TraesCS1D01G351800 chr1D 100.000 4115 0 0 1 4115 437002712 436998598 0.000000e+00 7600
1 TraesCS1D01G351800 chr1B 94.598 1518 62 9 413 1926 592174634 592173133 0.000000e+00 2331
2 TraesCS1D01G351800 chr1B 94.174 1253 58 12 2048 3294 592173010 592171767 0.000000e+00 1895
3 TraesCS1D01G351800 chr1B 95.248 463 21 1 3356 3817 592171764 592171302 0.000000e+00 732
4 TraesCS1D01G351800 chr1B 92.405 79 5 1 1925 2002 592173089 592173011 1.210000e-20 111
5 TraesCS1D01G351800 chr1A 95.150 1237 52 5 2216 3449 534051259 534050028 0.000000e+00 1945
6 TraesCS1D01G351800 chr1A 91.243 1336 83 20 592 1899 534052854 534051525 0.000000e+00 1788
7 TraesCS1D01G351800 chr3B 83.811 908 136 8 2217 3117 828421026 828420123 0.000000e+00 852
8 TraesCS1D01G351800 chr3B 83.589 914 133 12 2214 3114 828764314 828765223 0.000000e+00 841
9 TraesCS1D01G351800 chr3B 78.545 811 145 19 1098 1892 828421956 828421159 1.320000e-139 507
10 TraesCS1D01G351800 chr3B 91.803 305 17 8 3813 4115 39934379 39934081 6.360000e-113 418
11 TraesCS1D01G351800 chr3D 83.680 913 131 11 2217 3117 610805036 610804130 0.000000e+00 845
12 TraesCS1D01G351800 chr3A 82.842 915 142 10 2217 3117 745513533 745512620 0.000000e+00 806
13 TraesCS1D01G351800 chr7B 88.619 536 58 3 1 533 64007127 64007662 0.000000e+00 649
14 TraesCS1D01G351800 chr2D 88.598 535 54 5 1 533 625113461 625113990 0.000000e+00 643
15 TraesCS1D01G351800 chr2D 76.351 888 185 18 2215 3084 174324526 174325406 1.740000e-123 453
16 TraesCS1D01G351800 chr2D 91.531 307 25 1 3810 4115 8153929 8153623 4.920000e-114 422
17 TraesCS1D01G351800 chr2D 90.645 310 28 1 3807 4115 458741506 458741815 1.060000e-110 411
18 TraesCS1D01G351800 chr2D 90.789 76 4 2 2970 3043 174388369 174388443 9.410000e-17 99
19 TraesCS1D01G351800 chr2B 88.390 534 57 3 1 533 71225759 71226288 4.490000e-179 638
20 TraesCS1D01G351800 chr2B 87.763 523 62 2 12 533 520898684 520899205 9.780000e-171 610
21 TraesCS1D01G351800 chr2B 86.932 528 68 1 7 533 732113439 732113966 3.540000e-165 592
22 TraesCS1D01G351800 chr4D 87.977 524 61 2 1 522 77177191 77177714 5.840000e-173 617
23 TraesCS1D01G351800 chr4D 90.397 302 26 3 3815 4114 488792680 488792380 1.070000e-105 394
24 TraesCS1D01G351800 chr4B 87.500 536 64 2 1 533 404802009 404802544 2.100000e-172 616
25 TraesCS1D01G351800 chr4B 89.389 311 29 4 3808 4115 546576545 546576854 4.990000e-104 388
26 TraesCS1D01G351800 chr4B 89.389 311 29 4 3808 4115 546598921 546599230 4.990000e-104 388
27 TraesCS1D01G351800 chr7D 87.103 535 67 2 1 533 205228915 205228381 4.550000e-169 604
28 TraesCS1D01G351800 chr4A 87.238 525 64 2 1 522 508178130 508177606 2.740000e-166 595
29 TraesCS1D01G351800 chr2A 76.180 890 184 20 2215 3084 174027288 174028169 1.050000e-120 444
30 TraesCS1D01G351800 chr2A 76.214 824 172 16 2220 3024 174245677 174246495 8.230000e-112 414
31 TraesCS1D01G351800 chr2A 75.668 711 154 13 2389 3084 174195615 174196321 1.830000e-88 337
32 TraesCS1D01G351800 chr6D 90.820 305 25 3 3813 4115 449382331 449382028 4.950000e-109 405
33 TraesCS1D01G351800 chr6D 90.492 305 25 4 3811 4114 141586023 141586324 2.300000e-107 399
34 TraesCS1D01G351800 chr5D 90.789 304 25 3 3813 4115 543401313 543401614 1.780000e-108 403


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 TraesCS1D01G351800 chr1D 436998598 437002712 4114 True 7600.00 7600 100.00000 1 4115 1 chr1D.!!$R1 4114
1 TraesCS1D01G351800 chr1B 592171302 592174634 3332 True 1267.25 2331 94.10625 413 3817 4 chr1B.!!$R1 3404
2 TraesCS1D01G351800 chr1A 534050028 534052854 2826 True 1866.50 1945 93.19650 592 3449 2 chr1A.!!$R1 2857
3 TraesCS1D01G351800 chr3B 828764314 828765223 909 False 841.00 841 83.58900 2214 3114 1 chr3B.!!$F1 900
4 TraesCS1D01G351800 chr3B 828420123 828421956 1833 True 679.50 852 81.17800 1098 3117 2 chr3B.!!$R2 2019
5 TraesCS1D01G351800 chr3D 610804130 610805036 906 True 845.00 845 83.68000 2217 3117 1 chr3D.!!$R1 900
6 TraesCS1D01G351800 chr3A 745512620 745513533 913 True 806.00 806 82.84200 2217 3117 1 chr3A.!!$R1 900
7 TraesCS1D01G351800 chr7B 64007127 64007662 535 False 649.00 649 88.61900 1 533 1 chr7B.!!$F1 532
8 TraesCS1D01G351800 chr2D 625113461 625113990 529 False 643.00 643 88.59800 1 533 1 chr2D.!!$F4 532
9 TraesCS1D01G351800 chr2D 174324526 174325406 880 False 453.00 453 76.35100 2215 3084 1 chr2D.!!$F1 869
10 TraesCS1D01G351800 chr2B 71225759 71226288 529 False 638.00 638 88.39000 1 533 1 chr2B.!!$F1 532
11 TraesCS1D01G351800 chr2B 520898684 520899205 521 False 610.00 610 87.76300 12 533 1 chr2B.!!$F2 521
12 TraesCS1D01G351800 chr2B 732113439 732113966 527 False 592.00 592 86.93200 7 533 1 chr2B.!!$F3 526
13 TraesCS1D01G351800 chr4D 77177191 77177714 523 False 617.00 617 87.97700 1 522 1 chr4D.!!$F1 521
14 TraesCS1D01G351800 chr4B 404802009 404802544 535 False 616.00 616 87.50000 1 533 1 chr4B.!!$F1 532
15 TraesCS1D01G351800 chr7D 205228381 205228915 534 True 604.00 604 87.10300 1 533 1 chr7D.!!$R1 532
16 TraesCS1D01G351800 chr4A 508177606 508178130 524 True 595.00 595 87.23800 1 522 1 chr4A.!!$R1 521
17 TraesCS1D01G351800 chr2A 174027288 174028169 881 False 444.00 444 76.18000 2215 3084 1 chr2A.!!$F1 869
18 TraesCS1D01G351800 chr2A 174245677 174246495 818 False 414.00 414 76.21400 2220 3024 1 chr2A.!!$F3 804
19 TraesCS1D01G351800 chr2A 174195615 174196321 706 False 337.00 337 75.66800 2389 3084 1 chr2A.!!$F2 695

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
979 1007 0.108615 CACCCACCACTAGCTTCTCG 60.109 60.0 0.0 0.0 0.00 4.04 F
1566 1594 0.109597 GCCTGCATTCAGTTGTTCCG 60.110 55.0 0.0 0.0 38.66 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2256 0.107945 CTCTGCTGGCAACTACTCCC 60.108 60.0 0.0 0.0 37.61 4.30 R
3204 3421 1.583495 GGTGACTAAAACCTGCCGCC 61.583 60.0 0.0 0.0 34.66 6.13 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
55 57 3.113514 TTGGGGTGCGAGCTGAACA 62.114 57.895 0.00 0.00 0.00 3.18
79 81 3.265791 CATCAACCTCCTCACTAAGTGC 58.734 50.000 0.00 0.00 32.98 4.40
112 114 2.470821 CATCGTTCCCCTACTAAAGCG 58.529 52.381 0.00 0.00 0.00 4.68
165 167 6.976925 GTCTGTAATACTGTAGCCACGTAATT 59.023 38.462 0.00 0.00 0.00 1.40
195 197 4.274950 ACGTTGCACAATATTATACAGGGC 59.725 41.667 0.00 0.00 0.00 5.19
207 209 2.627148 TACAGGGCAGGGTACTGTAA 57.373 50.000 0.00 0.00 46.62 2.41
255 257 1.408969 TCCTCCCAAAACCTTGTTGC 58.591 50.000 0.00 0.00 0.00 4.17
295 297 4.941873 ACGAATTTCACCCTATGGAAGAAC 59.058 41.667 0.00 0.00 31.98 3.01
318 321 4.202202 CGACTCTTTTATCCTCATGAGCCT 60.202 45.833 17.76 8.69 0.00 4.58
352 355 4.398673 GGTGAGTCAGTAGGTCTTACGATT 59.601 45.833 0.00 0.00 37.35 3.34
360 363 5.589452 CAGTAGGTCTTACGATTACCTGAGT 59.411 44.000 11.82 0.00 43.47 3.41
363 366 5.014858 AGGTCTTACGATTACCTGAGTCAA 58.985 41.667 0.00 0.00 42.08 3.18
421 424 1.303236 CCACATGCCTTCCGGTTCA 60.303 57.895 0.00 0.00 0.00 3.18
439 442 9.922477 TCCGGTTCATGAGATAATCTATATAGT 57.078 33.333 9.58 0.00 0.00 2.12
504 510 7.601942 TCAATCTCTAGACCCCCTAATCTTTA 58.398 38.462 0.00 0.00 0.00 1.85
524 530 9.627395 ATCTTTAGGTCGACAAATAATATCTCG 57.373 33.333 18.91 0.00 0.00 4.04
554 560 3.125656 TCTTTGGGTCCATGATCCATCT 58.874 45.455 0.00 0.00 42.95 2.90
556 562 4.726317 TCTTTGGGTCCATGATCCATCTTA 59.274 41.667 0.00 0.00 42.95 2.10
557 563 4.437682 TTGGGTCCATGATCCATCTTAC 57.562 45.455 0.00 0.00 42.95 2.34
568 577 3.482722 TCCATCTTACTGTTCGACGAC 57.517 47.619 0.00 0.00 0.00 4.34
656 665 0.250038 TCTGACCTCACACAAGCAGC 60.250 55.000 0.00 0.00 0.00 5.25
737 746 5.776208 TCCCCTTTAATTTAACCACCAAGAC 59.224 40.000 0.00 0.00 0.00 3.01
777 786 5.514834 CCAAGATCCTTACTCCTTTGGAACA 60.515 44.000 0.00 0.00 31.87 3.18
812 822 1.169661 TGGCATGGTTTGACCGACAC 61.170 55.000 0.00 0.00 42.58 3.67
911 921 7.773224 AGTGAGACCTCTATATATCCAGAATCG 59.227 40.741 0.00 0.00 0.00 3.34
954 982 2.746362 CAGTCCTGCATCACCTTTCTTC 59.254 50.000 0.00 0.00 0.00 2.87
955 983 2.641815 AGTCCTGCATCACCTTTCTTCT 59.358 45.455 0.00 0.00 0.00 2.85
956 984 3.006247 GTCCTGCATCACCTTTCTTCTC 58.994 50.000 0.00 0.00 0.00 2.87
957 985 2.639347 TCCTGCATCACCTTTCTTCTCA 59.361 45.455 0.00 0.00 0.00 3.27
979 1007 0.108615 CACCCACCACTAGCTTCTCG 60.109 60.000 0.00 0.00 0.00 4.04
980 1008 1.153549 CCCACCACTAGCTTCTCGC 60.154 63.158 0.00 0.00 39.57 5.03
981 1009 1.517257 CCACCACTAGCTTCTCGCG 60.517 63.158 0.00 0.00 45.59 5.87
997 1025 2.650116 GCGGGAGTGAGGAGCAGAA 61.650 63.158 0.00 0.00 0.00 3.02
998 1026 1.216710 CGGGAGTGAGGAGCAGAAC 59.783 63.158 0.00 0.00 0.00 3.01
1028 1056 1.217882 GAACTGTTGTGGAGTGGTCG 58.782 55.000 0.00 0.00 0.00 4.79
1043 1071 1.445238 GTCGACCTGCACTCTCAGC 60.445 63.158 3.51 0.00 32.87 4.26
1525 1553 0.912487 ACTCAACCCCGCCTTCCATA 60.912 55.000 0.00 0.00 0.00 2.74
1546 1574 2.166664 ACCGAGAAGCTCAAGGTACATC 59.833 50.000 0.00 0.00 32.76 3.06
1550 1578 0.905357 AAGCTCAAGGTACATCGCCT 59.095 50.000 0.00 0.00 38.11 5.52
1554 1582 0.541392 TCAAGGTACATCGCCTGCAT 59.459 50.000 0.00 0.00 36.30 3.96
1558 1586 0.940126 GGTACATCGCCTGCATTCAG 59.060 55.000 0.00 0.00 40.02 3.02
1559 1587 1.656652 GTACATCGCCTGCATTCAGT 58.343 50.000 0.00 0.00 38.66 3.41
1561 1589 0.806868 ACATCGCCTGCATTCAGTTG 59.193 50.000 0.00 0.00 38.66 3.16
1562 1590 0.806868 CATCGCCTGCATTCAGTTGT 59.193 50.000 0.00 0.00 38.66 3.32
1563 1591 1.200716 CATCGCCTGCATTCAGTTGTT 59.799 47.619 0.00 0.00 38.66 2.83
1566 1594 0.109597 GCCTGCATTCAGTTGTTCCG 60.110 55.000 0.00 0.00 38.66 4.30
1646 1712 1.442520 CTCATGTTGCCGGCGTTTG 60.443 57.895 23.90 16.41 0.00 2.93
1732 1798 2.202987 GATGTCTGCCCGGAGCTG 60.203 66.667 0.73 9.33 44.23 4.24
1913 1988 8.441312 TTTTAACTTTTGGTAGTAGACTGGTG 57.559 34.615 0.00 0.00 0.00 4.17
1917 1992 5.783875 ACTTTTGGTAGTAGACTGGTGGTAT 59.216 40.000 0.00 0.00 0.00 2.73
1919 1994 5.927281 TTGGTAGTAGACTGGTGGTATTC 57.073 43.478 0.00 0.00 0.00 1.75
1941 2061 5.361135 CACTGAATAAATCTGTGTGTGCA 57.639 39.130 7.15 0.00 46.90 4.57
1998 2121 7.598278 TCATTCGGCAGTAAAATTTACACAAT 58.402 30.769 17.00 5.63 0.00 2.71
2002 2125 7.016466 TCGGCAGTAAAATTTACACAATTACG 58.984 34.615 17.00 11.00 32.99 3.18
2005 2128 9.777575 GGCAGTAAAATTTACACAATTACGTAT 57.222 29.630 17.00 0.00 32.99 3.06
2074 2239 4.966965 TTTGAACTGCCAAAACGTCTTA 57.033 36.364 0.00 0.00 33.56 2.10
2081 2246 6.178239 ACTGCCAAAACGTCTTATACATTC 57.822 37.500 0.00 0.00 0.00 2.67
2090 2255 8.827177 AAACGTCTTATACATTCAAGAACAGA 57.173 30.769 0.00 0.00 32.79 3.41
2091 2256 8.467402 AACGTCTTATACATTCAAGAACAGAG 57.533 34.615 0.00 0.00 32.79 3.35
2118 2285 3.960571 AGTTGCCAGCAGAGTGATATTT 58.039 40.909 0.00 0.00 0.00 1.40
2146 2313 4.142469 CCCTTACAACCTTATTTTCCGCAG 60.142 45.833 0.00 0.00 0.00 5.18
2147 2314 4.412207 CTTACAACCTTATTTTCCGCAGC 58.588 43.478 0.00 0.00 0.00 5.25
2155 2322 2.927553 ATTTTCCGCAGCTGCTTTAG 57.072 45.000 34.22 19.55 39.32 1.85
2156 2323 1.890876 TTTTCCGCAGCTGCTTTAGA 58.109 45.000 34.22 22.21 39.32 2.10
2166 2333 2.634940 AGCTGCTTTAGAGTGAACCTCA 59.365 45.455 0.00 0.00 43.12 3.86
2172 2340 5.527582 TGCTTTAGAGTGAACCTCAGTTTTC 59.472 40.000 0.00 0.00 43.12 2.29
2657 2841 7.534723 TTTGCTAGAAAGAACTAGAGGTACA 57.465 36.000 0.00 0.00 41.42 2.90
3008 3225 1.814394 GTTGTGCATGATCCTTCAGCA 59.186 47.619 0.00 0.00 34.73 4.41
3167 3384 4.441792 TCTTTGTAGTATCATGCGCATGT 58.558 39.130 40.57 30.95 39.72 3.21
3243 3460 6.486993 GTCACCATCTGTTTTCTTTTCCTACT 59.513 38.462 0.00 0.00 0.00 2.57
3311 3528 9.048446 ACTTACGACAACTATTTTGTATTGTGT 57.952 29.630 0.00 0.00 35.47 3.72
3329 3548 9.233232 GTATTGTGTTTCTCTTGTGTTTTTAGG 57.767 33.333 0.00 0.00 0.00 2.69
3451 3671 5.300034 CCATAATTGGCTAGACATTGAGCAA 59.700 40.000 0.00 0.00 40.64 3.91
3550 3770 4.447724 CACCGGGTGACAATAAATAGATCG 59.552 45.833 22.77 0.00 35.23 3.69
3591 3811 6.430616 TGACATGATATTCAAAGCAGTTGTCA 59.569 34.615 0.00 0.00 35.41 3.58
3597 3817 4.572985 TTCAAAGCAGTTGTCAGATTGG 57.427 40.909 0.68 0.00 38.47 3.16
3611 3832 8.873830 GTTGTCAGATTGGATTATATACGATGG 58.126 37.037 0.00 0.00 0.00 3.51
3630 3851 3.325870 TGGACAACTTAGACGATTGCAG 58.674 45.455 0.00 0.00 0.00 4.41
3662 3883 5.048364 GCACTGATCTCGGACTATAAGACAT 60.048 44.000 0.00 0.00 0.00 3.06
3663 3884 6.515862 GCACTGATCTCGGACTATAAGACATT 60.516 42.308 0.00 0.00 0.00 2.71
3680 3901 6.889301 AGACATTGTTGTGATGAGACAAAT 57.111 33.333 0.00 0.00 37.58 2.32
3705 3926 5.528043 TTATATGGCGCAAAAATGACCAT 57.472 34.783 10.83 2.16 43.42 3.55
3786 4007 2.061848 TGGACTGAAAAGGATCACCCA 58.938 47.619 0.00 0.00 37.41 4.51
3792 4013 2.111613 TGAAAAGGATCACCCAACCCAT 59.888 45.455 0.00 0.00 37.41 4.00
3801 4022 0.555769 ACCCAACCCATCAAGTGTGT 59.444 50.000 0.00 0.00 0.00 3.72
3817 4038 3.259374 AGTGTGTGACCATGGTCTTAGAG 59.741 47.826 37.92 3.10 44.80 2.43
3818 4039 2.028112 TGTGTGACCATGGTCTTAGAGC 60.028 50.000 37.92 23.64 44.80 4.09
3819 4040 2.028112 GTGTGACCATGGTCTTAGAGCA 60.028 50.000 37.92 24.58 44.80 4.26
3820 4041 2.637382 TGTGACCATGGTCTTAGAGCAA 59.363 45.455 37.92 18.11 43.29 3.91
3821 4042 3.003480 GTGACCATGGTCTTAGAGCAAC 58.997 50.000 37.92 24.34 43.29 4.17
3822 4043 2.906389 TGACCATGGTCTTAGAGCAACT 59.094 45.455 37.92 4.33 43.29 3.16
3823 4044 3.055819 TGACCATGGTCTTAGAGCAACTC 60.056 47.826 37.92 14.30 43.29 3.01
3824 4045 3.177228 ACCATGGTCTTAGAGCAACTCT 58.823 45.455 18.17 2.23 43.29 3.24
3825 4046 4.353777 ACCATGGTCTTAGAGCAACTCTA 58.646 43.478 18.17 0.16 43.29 2.43
3826 4047 4.404073 ACCATGGTCTTAGAGCAACTCTAG 59.596 45.833 18.17 6.26 42.92 2.43
3827 4048 4.367450 CATGGTCTTAGAGCAACTCTAGC 58.633 47.826 18.17 0.00 42.92 3.42
3828 4049 3.431415 TGGTCTTAGAGCAACTCTAGCA 58.569 45.455 11.98 0.03 42.92 3.49
3829 4050 3.445450 TGGTCTTAGAGCAACTCTAGCAG 59.555 47.826 11.98 1.69 42.92 4.24
3830 4051 3.697045 GGTCTTAGAGCAACTCTAGCAGA 59.303 47.826 6.55 3.80 42.92 4.26
3831 4052 4.439563 GGTCTTAGAGCAACTCTAGCAGAC 60.440 50.000 19.29 19.29 43.30 3.51
3832 4053 3.697045 TCTTAGAGCAACTCTAGCAGACC 59.303 47.826 4.64 0.00 42.92 3.85
3833 4054 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
3834 4055 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
3835 4056 1.153549 GCAACTCTAGCAGACCCCG 60.154 63.158 0.00 0.00 0.00 5.73
3836 4057 1.153549 CAACTCTAGCAGACCCCGC 60.154 63.158 0.00 0.00 0.00 6.13
3837 4058 1.609501 AACTCTAGCAGACCCCGCA 60.610 57.895 0.00 0.00 0.00 5.69
3838 4059 0.978146 AACTCTAGCAGACCCCGCAT 60.978 55.000 0.00 0.00 0.00 4.73
3839 4060 1.365633 CTCTAGCAGACCCCGCATC 59.634 63.158 0.00 0.00 0.00 3.91
3840 4061 2.093537 CTCTAGCAGACCCCGCATCC 62.094 65.000 0.00 0.00 0.00 3.51
3841 4062 3.506059 CTAGCAGACCCCGCATCCG 62.506 68.421 0.00 0.00 0.00 4.18
3881 4102 2.715536 GCTAAAATGCGGGTAGGGG 58.284 57.895 0.00 0.00 0.00 4.79
3882 4103 1.452953 GCTAAAATGCGGGTAGGGGC 61.453 60.000 0.00 0.00 0.00 5.80
3883 4104 1.153127 TAAAATGCGGGTAGGGGCG 60.153 57.895 0.00 0.00 0.00 6.13
3884 4105 2.612095 TAAAATGCGGGTAGGGGCGG 62.612 60.000 0.00 0.00 0.00 6.13
3888 4109 4.413565 GCGGGTAGGGGCGGAAAA 62.414 66.667 0.00 0.00 0.00 2.29
3889 4110 2.352039 CGGGTAGGGGCGGAAAAA 59.648 61.111 0.00 0.00 0.00 1.94
3890 4111 2.042259 CGGGTAGGGGCGGAAAAAC 61.042 63.158 0.00 0.00 0.00 2.43
3891 4112 1.679977 GGGTAGGGGCGGAAAAACC 60.680 63.158 0.00 0.00 0.00 3.27
3892 4113 1.381463 GGTAGGGGCGGAAAAACCT 59.619 57.895 0.00 0.00 37.13 3.50
3893 4114 0.963856 GGTAGGGGCGGAAAAACCTG 60.964 60.000 0.00 0.00 34.59 4.00
3894 4115 1.303806 TAGGGGCGGAAAAACCTGC 60.304 57.895 0.00 0.00 37.42 4.85
3897 4118 2.650778 GGCGGAAAAACCTGCCTG 59.349 61.111 6.50 0.00 46.66 4.85
3898 4119 1.901464 GGCGGAAAAACCTGCCTGA 60.901 57.895 6.50 0.00 46.66 3.86
3899 4120 1.250840 GGCGGAAAAACCTGCCTGAT 61.251 55.000 6.50 0.00 46.66 2.90
3900 4121 0.171231 GCGGAAAAACCTGCCTGATC 59.829 55.000 0.00 0.00 36.31 2.92
3901 4122 1.533625 CGGAAAAACCTGCCTGATCA 58.466 50.000 0.00 0.00 36.31 2.92
3902 4123 1.470098 CGGAAAAACCTGCCTGATCAG 59.530 52.381 16.24 16.24 36.31 2.90
3903 4124 2.795329 GGAAAAACCTGCCTGATCAGA 58.205 47.619 24.62 3.99 36.19 3.27
3904 4125 2.489722 GGAAAAACCTGCCTGATCAGAC 59.510 50.000 24.62 13.69 36.19 3.51
3905 4126 2.206576 AAAACCTGCCTGATCAGACC 57.793 50.000 24.62 14.38 36.19 3.85
3906 4127 0.329596 AAACCTGCCTGATCAGACCC 59.670 55.000 24.62 11.95 36.19 4.46
3907 4128 1.566298 AACCTGCCTGATCAGACCCC 61.566 60.000 24.62 9.57 36.19 4.95
3908 4129 2.503061 CTGCCTGATCAGACCCCG 59.497 66.667 24.62 7.90 36.19 5.73
3909 4130 3.746949 CTGCCTGATCAGACCCCGC 62.747 68.421 24.62 17.74 36.19 6.13
3910 4131 3.785859 GCCTGATCAGACCCCGCA 61.786 66.667 24.62 0.00 0.00 5.69
3911 4132 3.112205 GCCTGATCAGACCCCGCAT 62.112 63.158 24.62 0.00 0.00 4.73
3912 4133 1.758440 GCCTGATCAGACCCCGCATA 61.758 60.000 24.62 0.00 0.00 3.14
3913 4134 0.034059 CCTGATCAGACCCCGCATAC 59.966 60.000 24.62 0.00 0.00 2.39
3914 4135 0.034059 CTGATCAGACCCCGCATACC 59.966 60.000 18.34 0.00 0.00 2.73
3915 4136 1.006102 GATCAGACCCCGCATACCG 60.006 63.158 0.00 0.00 0.00 4.02
3916 4137 3.165160 ATCAGACCCCGCATACCGC 62.165 63.158 0.00 0.00 35.03 5.68
3917 4138 4.910585 CAGACCCCGCATACCGCC 62.911 72.222 0.00 0.00 37.30 6.13
3949 4170 3.907894 AAAATTTTAAGAGGCGCGACA 57.092 38.095 17.71 0.00 0.00 4.35
3950 4171 3.907894 AAATTTTAAGAGGCGCGACAA 57.092 38.095 17.71 0.00 0.00 3.18
3951 4172 3.907894 AATTTTAAGAGGCGCGACAAA 57.092 38.095 17.71 5.63 0.00 2.83
3952 4173 3.907894 ATTTTAAGAGGCGCGACAAAA 57.092 38.095 17.71 13.00 0.00 2.44
3953 4174 3.907894 TTTTAAGAGGCGCGACAAAAT 57.092 38.095 17.71 0.00 0.00 1.82
3954 4175 3.465122 TTTAAGAGGCGCGACAAAATC 57.535 42.857 17.71 1.67 0.00 2.17
3955 4176 2.380084 TAAGAGGCGCGACAAAATCT 57.620 45.000 17.71 4.81 0.00 2.40
3956 4177 1.079503 AAGAGGCGCGACAAAATCTC 58.920 50.000 17.71 0.22 0.00 2.75
3957 4178 0.037326 AGAGGCGCGACAAAATCTCA 60.037 50.000 17.71 0.00 0.00 3.27
3958 4179 0.371645 GAGGCGCGACAAAATCTCAG 59.628 55.000 17.71 0.00 0.00 3.35
3959 4180 1.226128 GGCGCGACAAAATCTCAGC 60.226 57.895 12.10 0.00 0.00 4.26
3960 4181 1.226128 GCGCGACAAAATCTCAGCC 60.226 57.895 12.10 0.00 0.00 4.85
3961 4182 1.425428 CGCGACAAAATCTCAGCCC 59.575 57.895 0.00 0.00 0.00 5.19
3962 4183 1.803289 GCGACAAAATCTCAGCCCC 59.197 57.895 0.00 0.00 0.00 5.80
3963 4184 0.960364 GCGACAAAATCTCAGCCCCA 60.960 55.000 0.00 0.00 0.00 4.96
3964 4185 1.533625 CGACAAAATCTCAGCCCCAA 58.466 50.000 0.00 0.00 0.00 4.12
3965 4186 1.200020 CGACAAAATCTCAGCCCCAAC 59.800 52.381 0.00 0.00 0.00 3.77
3966 4187 1.546029 GACAAAATCTCAGCCCCAACC 59.454 52.381 0.00 0.00 0.00 3.77
3967 4188 0.897621 CAAAATCTCAGCCCCAACCC 59.102 55.000 0.00 0.00 0.00 4.11
3968 4189 0.611896 AAAATCTCAGCCCCAACCCG 60.612 55.000 0.00 0.00 0.00 5.28
3969 4190 1.789576 AAATCTCAGCCCCAACCCGT 61.790 55.000 0.00 0.00 0.00 5.28
3970 4191 2.484287 AATCTCAGCCCCAACCCGTG 62.484 60.000 0.00 0.00 0.00 4.94
3971 4192 3.636231 CTCAGCCCCAACCCGTGA 61.636 66.667 0.00 0.00 0.00 4.35
3972 4193 3.172106 TCAGCCCCAACCCGTGAA 61.172 61.111 0.00 0.00 0.00 3.18
3973 4194 2.035626 CAGCCCCAACCCGTGAAT 59.964 61.111 0.00 0.00 0.00 2.57
3974 4195 1.202099 TCAGCCCCAACCCGTGAATA 61.202 55.000 0.00 0.00 0.00 1.75
3975 4196 1.029947 CAGCCCCAACCCGTGAATAC 61.030 60.000 0.00 0.00 0.00 1.89
3985 4206 3.573515 CGTGAATACGCGGGTTTTC 57.426 52.632 22.80 22.80 44.11 2.29
3986 4207 0.095762 CGTGAATACGCGGGTTTTCC 59.904 55.000 25.21 17.76 44.11 3.13
3996 4217 2.034221 GGTTTTCCCCTCGCAGCT 59.966 61.111 0.00 0.00 0.00 4.24
3997 4218 2.335712 GGTTTTCCCCTCGCAGCTG 61.336 63.158 10.11 10.11 0.00 4.24
3998 4219 2.672996 TTTTCCCCTCGCAGCTGC 60.673 61.111 29.12 29.12 37.78 5.25
4015 4236 3.434319 CGGTGCCCTGCATCACAC 61.434 66.667 13.50 9.52 40.05 3.82
4016 4237 2.282391 GGTGCCCTGCATCACACA 60.282 61.111 13.18 0.00 41.91 3.72
4017 4238 1.902918 GGTGCCCTGCATCACACAA 60.903 57.895 13.18 0.00 41.91 3.33
4018 4239 1.462731 GGTGCCCTGCATCACACAAA 61.463 55.000 13.18 0.00 41.91 2.83
4019 4240 0.038892 GTGCCCTGCATCACACAAAG 60.039 55.000 7.92 0.00 41.91 2.77
4020 4241 1.080298 GCCCTGCATCACACAAAGC 60.080 57.895 0.00 0.00 0.00 3.51
4021 4242 1.808531 GCCCTGCATCACACAAAGCA 61.809 55.000 0.00 0.00 35.43 3.91
4022 4243 0.892755 CCCTGCATCACACAAAGCAT 59.107 50.000 0.00 0.00 36.28 3.79
4023 4244 1.274167 CCCTGCATCACACAAAGCATT 59.726 47.619 0.00 0.00 36.28 3.56
4024 4245 2.289195 CCCTGCATCACACAAAGCATTT 60.289 45.455 0.00 0.00 40.26 2.32
4036 4257 3.140814 GCATTTGGCGGGAGGGAC 61.141 66.667 0.00 0.00 0.00 4.46
4037 4258 2.354729 CATTTGGCGGGAGGGACA 59.645 61.111 0.00 0.00 0.00 4.02
4038 4259 1.076777 CATTTGGCGGGAGGGACAT 60.077 57.895 0.00 0.00 0.00 3.06
4039 4260 0.684153 CATTTGGCGGGAGGGACATT 60.684 55.000 0.00 0.00 0.00 2.71
4040 4261 0.041090 ATTTGGCGGGAGGGACATTT 59.959 50.000 0.00 0.00 0.00 2.32
4041 4262 0.178947 TTTGGCGGGAGGGACATTTT 60.179 50.000 0.00 0.00 0.00 1.82
4042 4263 0.699399 TTGGCGGGAGGGACATTTTA 59.301 50.000 0.00 0.00 0.00 1.52
4043 4264 0.254747 TGGCGGGAGGGACATTTTAG 59.745 55.000 0.00 0.00 0.00 1.85
4044 4265 1.101635 GGCGGGAGGGACATTTTAGC 61.102 60.000 0.00 0.00 0.00 3.09
4045 4266 1.101635 GCGGGAGGGACATTTTAGCC 61.102 60.000 0.00 0.00 0.00 3.93
4046 4267 0.465642 CGGGAGGGACATTTTAGCCC 60.466 60.000 0.00 0.00 42.37 5.19
4047 4268 0.465642 GGGAGGGACATTTTAGCCCG 60.466 60.000 0.00 0.00 46.68 6.13
4048 4269 1.101635 GGAGGGACATTTTAGCCCGC 61.102 60.000 0.00 0.00 46.68 6.13
4049 4270 1.436983 GAGGGACATTTTAGCCCGCG 61.437 60.000 0.00 0.00 46.68 6.46
4050 4271 2.407616 GGACATTTTAGCCCGCGC 59.592 61.111 0.00 0.00 0.00 6.86
4051 4272 2.022762 GACATTTTAGCCCGCGCG 59.977 61.111 25.67 25.67 41.18 6.86
4052 4273 4.174129 ACATTTTAGCCCGCGCGC 62.174 61.111 27.36 23.91 41.18 6.86
4053 4274 4.905193 CATTTTAGCCCGCGCGCC 62.905 66.667 27.36 17.65 41.18 6.53
4067 4288 3.979497 CGCCTTTTCCCCACCCCT 61.979 66.667 0.00 0.00 0.00 4.79
4068 4289 2.531326 GCCTTTTCCCCACCCCTT 59.469 61.111 0.00 0.00 0.00 3.95
4069 4290 1.609501 GCCTTTTCCCCACCCCTTC 60.610 63.158 0.00 0.00 0.00 3.46
4070 4291 1.078528 CCTTTTCCCCACCCCTTCC 59.921 63.158 0.00 0.00 0.00 3.46
4071 4292 1.304134 CTTTTCCCCACCCCTTCCG 60.304 63.158 0.00 0.00 0.00 4.30
4072 4293 3.516949 TTTTCCCCACCCCTTCCGC 62.517 63.158 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 4.163078 CACTTAGTGAGGAGGTTGATGGAT 59.837 45.833 6.50 0.00 35.23 3.41
112 114 0.531974 TGAATATCCAGTTCCGGCGC 60.532 55.000 0.00 0.00 0.00 6.53
139 141 3.760151 ACGTGGCTACAGTATTACAGACA 59.240 43.478 0.00 0.00 0.00 3.41
165 167 8.198778 TGTATAATATTGTGCAACGTAAGGAGA 58.801 33.333 0.55 0.00 42.39 3.71
195 197 1.067212 CGCTAGCCTTACAGTACCCTG 59.933 57.143 9.66 0.00 44.68 4.45
255 257 0.239879 CGTTGTTGGGGATGAAACGG 59.760 55.000 0.00 0.00 39.80 4.44
295 297 4.054671 GGCTCATGAGGATAAAAGAGTCG 58.945 47.826 23.89 0.00 0.00 4.18
318 321 3.242867 ACTGACTCACCATTCTGGAAGA 58.757 45.455 0.00 0.00 44.68 2.87
352 355 7.120923 ACACTCTAAAACTTTGACTCAGGTA 57.879 36.000 0.00 0.00 0.00 3.08
439 442 3.423539 AAATACCTGCTGAGCAAGTGA 57.576 42.857 18.33 3.75 38.41 3.41
442 445 9.807649 ATTAAAAATAAATACCTGCTGAGCAAG 57.192 29.630 9.07 4.73 38.41 4.01
504 510 6.636562 AGACGAGATATTATTTGTCGACCT 57.363 37.500 14.12 0.00 34.72 3.85
522 528 0.400213 ACCCAAAGATGGCAAGACGA 59.600 50.000 0.00 0.00 46.09 4.20
524 530 1.177401 GGACCCAAAGATGGCAAGAC 58.823 55.000 0.00 0.00 46.09 3.01
554 560 5.342433 TCAAAAAGAGTCGTCGAACAGTAA 58.658 37.500 0.00 0.00 0.00 2.24
556 562 3.777478 TCAAAAAGAGTCGTCGAACAGT 58.223 40.909 0.00 0.00 0.00 3.55
557 563 4.042398 TCTCAAAAAGAGTCGTCGAACAG 58.958 43.478 0.00 0.00 44.98 3.16
568 577 7.011828 TCGGTGTAAAAAGTCTCAAAAAGAG 57.988 36.000 0.00 0.00 46.14 2.85
656 665 1.201647 CAGTTTCATGGCTGCTTCCTG 59.798 52.381 0.00 0.00 0.00 3.86
697 706 2.506472 GACGAAGGAGGATGGCCC 59.494 66.667 0.00 0.00 33.31 5.80
777 786 0.681175 GCCACAGGGTCAATTGCTTT 59.319 50.000 0.00 0.00 36.17 3.51
782 791 0.114954 ACCATGCCACAGGGTCAATT 59.885 50.000 0.00 0.00 45.92 2.32
789 798 1.865788 CGGTCAAACCATGCCACAGG 61.866 60.000 0.00 0.00 38.47 4.00
790 799 0.888736 TCGGTCAAACCATGCCACAG 60.889 55.000 0.00 0.00 38.47 3.66
911 921 4.202202 TGGATTGGTGATGTTTTTGGTCAC 60.202 41.667 0.00 0.00 41.07 3.67
954 982 0.247736 GCTAGTGGTGGGTGAGTGAG 59.752 60.000 0.00 0.00 0.00 3.51
955 983 0.178932 AGCTAGTGGTGGGTGAGTGA 60.179 55.000 0.00 0.00 0.00 3.41
956 984 0.687354 AAGCTAGTGGTGGGTGAGTG 59.313 55.000 0.00 0.00 0.00 3.51
957 985 0.977395 GAAGCTAGTGGTGGGTGAGT 59.023 55.000 0.00 0.00 0.00 3.41
979 1007 2.650116 TTCTGCTCCTCACTCCCGC 61.650 63.158 0.00 0.00 0.00 6.13
980 1008 1.216710 GTTCTGCTCCTCACTCCCG 59.783 63.158 0.00 0.00 0.00 5.14
981 1009 0.687354 TTGTTCTGCTCCTCACTCCC 59.313 55.000 0.00 0.00 0.00 4.30
997 1025 4.279169 CCACAACAGTTCAAGATCCATTGT 59.721 41.667 0.00 0.00 0.00 2.71
998 1026 4.520111 TCCACAACAGTTCAAGATCCATTG 59.480 41.667 0.00 0.00 0.00 2.82
1028 1056 0.669932 CAGTGCTGAGAGTGCAGGTC 60.670 60.000 0.00 0.00 41.41 3.85
1043 1071 2.184830 CCGCAGATCCATGGCAGTG 61.185 63.158 6.96 4.75 0.00 3.66
1525 1553 1.629043 TGTACCTTGAGCTTCTCGGT 58.371 50.000 0.00 0.00 32.35 4.69
1546 1574 0.109597 GGAACAACTGAATGCAGGCG 60.110 55.000 5.47 0.00 46.60 5.52
1550 1578 1.234821 GGACGGAACAACTGAATGCA 58.765 50.000 0.00 0.00 0.00 3.96
1554 1582 0.176219 ACACGGACGGAACAACTGAA 59.824 50.000 0.00 0.00 0.00 3.02
1558 1586 2.174969 TGCACACGGACGGAACAAC 61.175 57.895 0.00 0.00 0.00 3.32
1559 1587 2.174969 GTGCACACGGACGGAACAA 61.175 57.895 13.17 0.00 0.00 2.83
1646 1712 3.117171 CTCCTCACAGCACGCAGC 61.117 66.667 0.00 0.00 46.19 5.25
1732 1798 2.430610 ATCTCCGGTGAGGCTCTGC 61.431 63.158 16.72 8.49 39.23 4.26
1913 1988 8.177663 CACACACAGATTTATTCAGTGAATACC 58.822 37.037 22.44 15.03 42.74 2.73
1917 1992 5.530543 TGCACACACAGATTTATTCAGTGAA 59.469 36.000 8.27 8.27 42.74 3.18
1919 1994 5.361135 TGCACACACAGATTTATTCAGTG 57.639 39.130 0.00 0.00 44.89 3.66
2038 2203 6.036470 GCAGTTCAAAACAGAGCTACTTTTT 58.964 36.000 0.00 0.00 30.93 1.94
2039 2204 5.450550 GGCAGTTCAAAACAGAGCTACTTTT 60.451 40.000 0.00 0.00 0.00 2.27
2040 2205 4.036852 GGCAGTTCAAAACAGAGCTACTTT 59.963 41.667 0.00 0.00 0.00 2.66
2042 2207 3.142174 GGCAGTTCAAAACAGAGCTACT 58.858 45.455 0.00 0.00 0.00 2.57
2043 2208 2.878406 TGGCAGTTCAAAACAGAGCTAC 59.122 45.455 0.00 0.00 0.00 3.58
2044 2209 3.207265 TGGCAGTTCAAAACAGAGCTA 57.793 42.857 0.00 0.00 0.00 3.32
2045 2210 2.057137 TGGCAGTTCAAAACAGAGCT 57.943 45.000 0.00 0.00 0.00 4.09
2046 2211 2.869233 TTGGCAGTTCAAAACAGAGC 57.131 45.000 0.00 0.00 0.00 4.09
2074 2239 6.670027 ACTACTCCCTCTGTTCTTGAATGTAT 59.330 38.462 0.00 0.00 0.00 2.29
2081 2246 3.330267 GCAACTACTCCCTCTGTTCTTG 58.670 50.000 0.00 0.00 0.00 3.02
2090 2255 0.545309 TCTGCTGGCAACTACTCCCT 60.545 55.000 0.00 0.00 37.61 4.20
2091 2256 0.107945 CTCTGCTGGCAACTACTCCC 60.108 60.000 0.00 0.00 37.61 4.30
2118 2285 7.435305 CGGAAAATAAGGTTGTAAGGGAAAAA 58.565 34.615 0.00 0.00 0.00 1.94
2146 2313 2.999355 CTGAGGTTCACTCTAAAGCAGC 59.001 50.000 0.00 0.00 46.72 5.25
2147 2314 4.264460 ACTGAGGTTCACTCTAAAGCAG 57.736 45.455 0.00 0.00 46.72 4.24
2155 2322 2.835027 ACCGAAAACTGAGGTTCACTC 58.165 47.619 0.00 0.00 46.78 3.51
2156 2323 3.277142 AACCGAAAACTGAGGTTCACT 57.723 42.857 0.00 0.00 44.13 3.41
2166 2333 6.861055 CAGTACATGCAAATTAACCGAAAACT 59.139 34.615 0.00 0.00 0.00 2.66
2192 2360 2.742053 GGCATGGCATACCGTTACATAG 59.258 50.000 15.47 0.00 39.70 2.23
2193 2361 2.104963 TGGCATGGCATACCGTTACATA 59.895 45.455 19.43 0.00 39.70 2.29
2194 2362 1.133945 TGGCATGGCATACCGTTACAT 60.134 47.619 19.43 0.00 39.70 2.29
2195 2363 0.253327 TGGCATGGCATACCGTTACA 59.747 50.000 19.43 0.00 39.70 2.41
2196 2364 1.604604 ATGGCATGGCATACCGTTAC 58.395 50.000 31.41 0.00 39.70 2.50
2197 2365 2.356665 AATGGCATGGCATACCGTTA 57.643 45.000 32.36 4.56 39.70 3.18
2198 2366 1.484038 AAATGGCATGGCATACCGTT 58.516 45.000 32.36 20.76 39.70 4.44
2200 2368 1.408340 TGAAAATGGCATGGCATACCG 59.592 47.619 32.36 0.00 39.70 4.02
2203 2373 2.694628 GACCTGAAAATGGCATGGCATA 59.305 45.455 32.36 17.37 0.00 3.14
2640 2814 8.834749 AAGACATTTGTACCTCTAGTTCTTTC 57.165 34.615 0.00 0.00 0.00 2.62
2657 2841 8.192774 CCTGCACATCATGTTAATAAGACATTT 58.807 33.333 0.00 0.00 35.64 2.32
3008 3225 2.030805 GGTGCGAGCTCAAACTCAAAAT 60.031 45.455 15.40 0.00 36.42 1.82
3167 3384 4.528206 ACATATCACATAGGAGGCGAATGA 59.472 41.667 0.00 0.00 0.00 2.57
3204 3421 1.583495 GGTGACTAAAACCTGCCGCC 61.583 60.000 0.00 0.00 34.66 6.13
3311 3528 9.744468 GCTATTTTCCTAAAAACACAAGAGAAA 57.256 29.630 0.00 0.00 37.20 2.52
3451 3671 6.363065 AGATTGAGCTTGATCACAATATGGT 58.637 36.000 8.74 0.00 35.37 3.55
3550 3770 5.886992 TCATGTCATGCATTTCACTTGATC 58.113 37.500 8.03 0.00 35.19 2.92
3563 3783 5.828747 ACTGCTTTGAATATCATGTCATGC 58.171 37.500 8.03 0.00 0.00 4.06
3564 3784 7.255569 ACAACTGCTTTGAATATCATGTCATG 58.744 34.615 6.47 6.47 38.73 3.07
3591 3811 8.816894 AGTTGTCCATCGTATATAATCCAATCT 58.183 33.333 0.00 0.00 0.00 2.40
3597 3817 9.275231 CGTCTAAGTTGTCCATCGTATATAATC 57.725 37.037 0.00 0.00 0.00 1.75
3611 3832 3.614616 CCTCTGCAATCGTCTAAGTTGTC 59.385 47.826 0.00 0.00 0.00 3.18
3630 3851 0.935898 CGAGATCAGTGCATTGCCTC 59.064 55.000 16.08 16.08 0.00 4.70
3680 3901 7.043961 TGGTCATTTTTGCGCCATATAAATA 57.956 32.000 4.18 0.00 0.00 1.40
3685 3906 4.405116 AATGGTCATTTTTGCGCCATAT 57.595 36.364 4.18 0.00 38.82 1.78
3705 3926 3.745480 GCTCCATCGAGATCCCAATGAAA 60.745 47.826 0.00 0.00 38.52 2.69
3786 4007 1.214175 TGGTCACACACTTGATGGGTT 59.786 47.619 0.00 0.00 45.28 4.11
3792 4013 1.768275 AGACCATGGTCACACACTTGA 59.232 47.619 39.38 0.00 46.76 3.02
3801 4022 2.906389 AGTTGCTCTAAGACCATGGTCA 59.094 45.455 39.38 23.22 46.76 4.02
3817 4038 1.153549 CGGGGTCTGCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
3818 4039 1.153549 GCGGGGTCTGCTAGAGTTG 60.154 63.158 0.00 0.00 0.00 3.16
3819 4040 0.978146 ATGCGGGGTCTGCTAGAGTT 60.978 55.000 0.00 0.00 0.00 3.01
3820 4041 1.381872 ATGCGGGGTCTGCTAGAGT 60.382 57.895 0.00 0.00 0.00 3.24
3821 4042 1.365633 GATGCGGGGTCTGCTAGAG 59.634 63.158 0.00 0.00 0.00 2.43
3822 4043 2.134287 GGATGCGGGGTCTGCTAGA 61.134 63.158 0.00 0.00 0.00 2.43
3823 4044 2.423446 GGATGCGGGGTCTGCTAG 59.577 66.667 0.30 0.00 0.00 3.42
3824 4045 3.536917 CGGATGCGGGGTCTGCTA 61.537 66.667 0.00 0.00 0.00 3.49
3846 4067 0.741927 AGCGGTTATTTTCCGGGTCG 60.742 55.000 0.00 0.00 46.90 4.79
3847 4068 2.314323 TAGCGGTTATTTTCCGGGTC 57.686 50.000 0.00 0.00 46.90 4.46
3848 4069 2.785540 TTAGCGGTTATTTTCCGGGT 57.214 45.000 0.00 0.00 46.90 5.28
3849 4070 4.356289 CATTTTAGCGGTTATTTTCCGGG 58.644 43.478 0.00 0.00 46.90 5.73
3850 4071 3.794564 GCATTTTAGCGGTTATTTTCCGG 59.205 43.478 0.00 0.00 46.90 5.14
3863 4084 1.452953 GCCCCTACCCGCATTTTAGC 61.453 60.000 0.00 0.00 0.00 3.09
3864 4085 1.164041 CGCCCCTACCCGCATTTTAG 61.164 60.000 0.00 0.00 0.00 1.85
3865 4086 1.153127 CGCCCCTACCCGCATTTTA 60.153 57.895 0.00 0.00 0.00 1.52
3866 4087 2.439519 CGCCCCTACCCGCATTTT 60.440 61.111 0.00 0.00 0.00 1.82
3867 4088 4.499633 CCGCCCCTACCCGCATTT 62.500 66.667 0.00 0.00 0.00 2.32
3871 4092 3.923782 TTTTTCCGCCCCTACCCGC 62.924 63.158 0.00 0.00 0.00 6.13
3872 4093 2.042259 GTTTTTCCGCCCCTACCCG 61.042 63.158 0.00 0.00 0.00 5.28
3873 4094 1.679977 GGTTTTTCCGCCCCTACCC 60.680 63.158 0.00 0.00 0.00 3.69
3874 4095 0.963856 CAGGTTTTTCCGCCCCTACC 60.964 60.000 0.00 0.00 41.99 3.18
3875 4096 1.592400 GCAGGTTTTTCCGCCCCTAC 61.592 60.000 0.00 0.00 41.99 3.18
3876 4097 1.303806 GCAGGTTTTTCCGCCCCTA 60.304 57.895 0.00 0.00 41.99 3.53
3877 4098 2.600470 GCAGGTTTTTCCGCCCCT 60.600 61.111 0.00 0.00 41.99 4.79
3878 4099 3.691342 GGCAGGTTTTTCCGCCCC 61.691 66.667 7.95 0.00 44.24 5.80
3881 4102 0.171231 GATCAGGCAGGTTTTTCCGC 59.829 55.000 0.00 0.00 41.99 5.54
3882 4103 1.470098 CTGATCAGGCAGGTTTTTCCG 59.530 52.381 15.38 0.00 41.99 4.30
3883 4104 2.489722 GTCTGATCAGGCAGGTTTTTCC 59.510 50.000 22.39 0.00 36.55 3.13
3884 4105 2.489722 GGTCTGATCAGGCAGGTTTTTC 59.510 50.000 27.64 4.98 36.55 2.29
3885 4106 2.519013 GGTCTGATCAGGCAGGTTTTT 58.481 47.619 27.64 0.00 36.55 1.94
3886 4107 1.272147 GGGTCTGATCAGGCAGGTTTT 60.272 52.381 27.64 0.00 36.55 2.43
3887 4108 0.329596 GGGTCTGATCAGGCAGGTTT 59.670 55.000 27.64 0.00 36.55 3.27
3888 4109 1.566298 GGGGTCTGATCAGGCAGGTT 61.566 60.000 27.64 0.00 36.55 3.50
3889 4110 1.997874 GGGGTCTGATCAGGCAGGT 60.998 63.158 27.64 0.00 36.55 4.00
3890 4111 2.914289 GGGGTCTGATCAGGCAGG 59.086 66.667 27.64 0.77 36.55 4.85
3891 4112 2.503061 CGGGGTCTGATCAGGCAG 59.497 66.667 27.64 14.78 33.98 4.85
3892 4113 3.785859 GCGGGGTCTGATCAGGCA 61.786 66.667 27.64 4.75 33.98 4.75
3893 4114 1.758440 TATGCGGGGTCTGATCAGGC 61.758 60.000 22.42 20.93 0.00 4.85
3894 4115 0.034059 GTATGCGGGGTCTGATCAGG 59.966 60.000 22.42 7.19 0.00 3.86
3895 4116 0.034059 GGTATGCGGGGTCTGATCAG 59.966 60.000 17.07 17.07 0.00 2.90
3896 4117 1.744320 CGGTATGCGGGGTCTGATCA 61.744 60.000 0.00 0.00 0.00 2.92
3897 4118 1.006102 CGGTATGCGGGGTCTGATC 60.006 63.158 0.00 0.00 0.00 2.92
3898 4119 3.138625 CGGTATGCGGGGTCTGAT 58.861 61.111 0.00 0.00 0.00 2.90
3899 4120 3.845259 GCGGTATGCGGGGTCTGA 61.845 66.667 0.00 0.00 0.00 3.27
3928 4149 4.231718 TGTCGCGCCTCTTAAAATTTTT 57.768 36.364 9.06 0.00 0.00 1.94
3929 4150 3.907894 TGTCGCGCCTCTTAAAATTTT 57.092 38.095 8.75 8.75 0.00 1.82
3930 4151 3.907894 TTGTCGCGCCTCTTAAAATTT 57.092 38.095 0.00 0.00 0.00 1.82
3931 4152 3.907894 TTTGTCGCGCCTCTTAAAATT 57.092 38.095 0.00 0.00 0.00 1.82
3932 4153 3.907894 TTTTGTCGCGCCTCTTAAAAT 57.092 38.095 0.00 0.00 0.00 1.82
3933 4154 3.500680 AGATTTTGTCGCGCCTCTTAAAA 59.499 39.130 0.00 3.57 0.00 1.52
3934 4155 3.071479 AGATTTTGTCGCGCCTCTTAAA 58.929 40.909 0.00 0.00 0.00 1.52
3935 4156 2.671396 GAGATTTTGTCGCGCCTCTTAA 59.329 45.455 0.00 0.00 0.00 1.85
3936 4157 2.268298 GAGATTTTGTCGCGCCTCTTA 58.732 47.619 0.00 0.00 0.00 2.10
3937 4158 1.079503 GAGATTTTGTCGCGCCTCTT 58.920 50.000 0.00 0.00 0.00 2.85
3938 4159 0.037326 TGAGATTTTGTCGCGCCTCT 60.037 50.000 0.00 0.00 0.00 3.69
3939 4160 0.371645 CTGAGATTTTGTCGCGCCTC 59.628 55.000 0.00 0.00 0.00 4.70
3940 4161 1.639298 GCTGAGATTTTGTCGCGCCT 61.639 55.000 0.00 0.00 0.00 5.52
3941 4162 1.226128 GCTGAGATTTTGTCGCGCC 60.226 57.895 0.00 0.00 0.00 6.53
3942 4163 1.226128 GGCTGAGATTTTGTCGCGC 60.226 57.895 0.00 0.00 0.00 6.86
3943 4164 1.425428 GGGCTGAGATTTTGTCGCG 59.575 57.895 0.00 0.00 0.00 5.87
3944 4165 0.960364 TGGGGCTGAGATTTTGTCGC 60.960 55.000 0.00 0.00 0.00 5.19
3945 4166 1.200020 GTTGGGGCTGAGATTTTGTCG 59.800 52.381 0.00 0.00 0.00 4.35
3946 4167 1.546029 GGTTGGGGCTGAGATTTTGTC 59.454 52.381 0.00 0.00 0.00 3.18
3947 4168 1.632589 GGTTGGGGCTGAGATTTTGT 58.367 50.000 0.00 0.00 0.00 2.83
3948 4169 0.897621 GGGTTGGGGCTGAGATTTTG 59.102 55.000 0.00 0.00 0.00 2.44
3949 4170 0.611896 CGGGTTGGGGCTGAGATTTT 60.612 55.000 0.00 0.00 0.00 1.82
3950 4171 1.000896 CGGGTTGGGGCTGAGATTT 60.001 57.895 0.00 0.00 0.00 2.17
3951 4172 2.231380 ACGGGTTGGGGCTGAGATT 61.231 57.895 0.00 0.00 0.00 2.40
3952 4173 2.610859 ACGGGTTGGGGCTGAGAT 60.611 61.111 0.00 0.00 0.00 2.75
3953 4174 3.636231 CACGGGTTGGGGCTGAGA 61.636 66.667 0.00 0.00 0.00 3.27
3954 4175 2.484287 ATTCACGGGTTGGGGCTGAG 62.484 60.000 0.00 0.00 0.00 3.35
3955 4176 1.202099 TATTCACGGGTTGGGGCTGA 61.202 55.000 0.00 0.00 0.00 4.26
3956 4177 1.029947 GTATTCACGGGTTGGGGCTG 61.030 60.000 0.00 0.00 0.00 4.85
3957 4178 1.301954 GTATTCACGGGTTGGGGCT 59.698 57.895 0.00 0.00 0.00 5.19
3958 4179 2.110352 CGTATTCACGGGTTGGGGC 61.110 63.158 0.00 0.00 44.59 5.80
3959 4180 4.211986 CGTATTCACGGGTTGGGG 57.788 61.111 0.00 0.00 44.59 4.96
3968 4189 0.448990 GGGAAAACCCGCGTATTCAC 59.551 55.000 4.92 0.90 35.07 3.18
3969 4190 2.857254 GGGAAAACCCGCGTATTCA 58.143 52.632 4.92 0.00 35.07 2.57
3979 4200 2.034221 AGCTGCGAGGGGAAAACC 59.966 61.111 0.00 0.00 39.11 3.27
3980 4201 2.982744 GCAGCTGCGAGGGGAAAAC 61.983 63.158 25.23 0.00 0.00 2.43
3981 4202 2.672996 GCAGCTGCGAGGGGAAAA 60.673 61.111 25.23 0.00 0.00 2.29
4000 4221 0.038892 CTTTGTGTGATGCAGGGCAC 60.039 55.000 9.46 9.46 43.04 5.01
4001 4222 1.808531 GCTTTGTGTGATGCAGGGCA 61.809 55.000 0.00 0.00 44.86 5.36
4002 4223 1.080298 GCTTTGTGTGATGCAGGGC 60.080 57.895 0.00 0.00 0.00 5.19
4003 4224 0.892755 ATGCTTTGTGTGATGCAGGG 59.107 50.000 0.00 0.00 38.87 4.45
4004 4225 2.734606 CAAATGCTTTGTGTGATGCAGG 59.265 45.455 0.00 0.00 38.87 4.85
4005 4226 2.734606 CCAAATGCTTTGTGTGATGCAG 59.265 45.455 0.00 0.00 38.98 4.41
4006 4227 2.756829 CCAAATGCTTTGTGTGATGCA 58.243 42.857 0.00 0.00 38.98 3.96
4007 4228 1.461897 GCCAAATGCTTTGTGTGATGC 59.538 47.619 7.53 0.00 38.98 3.91
4008 4229 1.722464 CGCCAAATGCTTTGTGTGATG 59.278 47.619 7.53 0.00 38.98 3.07
4009 4230 1.337074 CCGCCAAATGCTTTGTGTGAT 60.337 47.619 7.53 0.00 38.98 3.06
4010 4231 0.031857 CCGCCAAATGCTTTGTGTGA 59.968 50.000 7.53 0.00 38.98 3.58
4011 4232 0.945265 CCCGCCAAATGCTTTGTGTG 60.945 55.000 7.53 6.09 38.98 3.82
4012 4233 1.112315 TCCCGCCAAATGCTTTGTGT 61.112 50.000 7.53 0.00 38.98 3.72
4013 4234 0.388907 CTCCCGCCAAATGCTTTGTG 60.389 55.000 7.53 0.01 38.98 3.33
4014 4235 1.535204 CCTCCCGCCAAATGCTTTGT 61.535 55.000 7.53 0.00 38.98 2.83
4015 4236 1.216178 CCTCCCGCCAAATGCTTTG 59.784 57.895 2.70 2.70 40.32 2.77
4016 4237 1.984026 CCCTCCCGCCAAATGCTTT 60.984 57.895 0.00 0.00 38.05 3.51
4017 4238 2.362889 CCCTCCCGCCAAATGCTT 60.363 61.111 0.00 0.00 38.05 3.91
4018 4239 3.338250 TCCCTCCCGCCAAATGCT 61.338 61.111 0.00 0.00 38.05 3.79
4019 4240 3.140814 GTCCCTCCCGCCAAATGC 61.141 66.667 0.00 0.00 0.00 3.56
4020 4241 0.684153 AATGTCCCTCCCGCCAAATG 60.684 55.000 0.00 0.00 0.00 2.32
4021 4242 0.041090 AAATGTCCCTCCCGCCAAAT 59.959 50.000 0.00 0.00 0.00 2.32
4022 4243 0.178947 AAAATGTCCCTCCCGCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
4023 4244 0.699399 TAAAATGTCCCTCCCGCCAA 59.301 50.000 0.00 0.00 0.00 4.52
4024 4245 0.254747 CTAAAATGTCCCTCCCGCCA 59.745 55.000 0.00 0.00 0.00 5.69
4025 4246 1.101635 GCTAAAATGTCCCTCCCGCC 61.102 60.000 0.00 0.00 0.00 6.13
4026 4247 1.101635 GGCTAAAATGTCCCTCCCGC 61.102 60.000 0.00 0.00 0.00 6.13
4027 4248 0.465642 GGGCTAAAATGTCCCTCCCG 60.466 60.000 0.00 0.00 37.08 5.14
4028 4249 0.465642 CGGGCTAAAATGTCCCTCCC 60.466 60.000 0.00 0.00 37.89 4.30
4029 4250 1.101635 GCGGGCTAAAATGTCCCTCC 61.102 60.000 0.00 0.00 37.89 4.30
4030 4251 1.436983 CGCGGGCTAAAATGTCCCTC 61.437 60.000 0.00 0.00 37.89 4.30
4031 4252 1.451387 CGCGGGCTAAAATGTCCCT 60.451 57.895 0.00 0.00 37.89 4.20
4032 4253 3.107447 CGCGGGCTAAAATGTCCC 58.893 61.111 0.00 0.00 36.68 4.46
4033 4254 2.407616 GCGCGGGCTAAAATGTCC 59.592 61.111 18.33 0.00 35.83 4.02
4034 4255 2.022762 CGCGCGGGCTAAAATGTC 59.977 61.111 24.84 0.00 36.88 3.06
4035 4256 4.174129 GCGCGCGGGCTAAAATGT 62.174 61.111 37.00 0.00 36.88 2.71
4036 4257 4.905193 GGCGCGCGGGCTAAAATG 62.905 66.667 40.61 6.65 38.40 2.32
4050 4271 3.523374 AAGGGGTGGGGAAAAGGCG 62.523 63.158 0.00 0.00 0.00 5.52
4051 4272 1.609501 GAAGGGGTGGGGAAAAGGC 60.610 63.158 0.00 0.00 0.00 4.35
4052 4273 1.078528 GGAAGGGGTGGGGAAAAGG 59.921 63.158 0.00 0.00 0.00 3.11
4053 4274 1.304134 CGGAAGGGGTGGGGAAAAG 60.304 63.158 0.00 0.00 0.00 2.27
4054 4275 2.848032 CGGAAGGGGTGGGGAAAA 59.152 61.111 0.00 0.00 0.00 2.29
4055 4276 3.974293 GCGGAAGGGGTGGGGAAA 61.974 66.667 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.