Multiple sequence alignment - TraesCS3D01G111300

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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 TraesCS3D01G111300 chr3D 100.000 4125 0 0 1 4125 64760830 64764954 0.000000e+00 7618.0
1 TraesCS3D01G111300 chr3D 88.043 276 26 6 3799 4070 10339560 10339288 1.850000e-83 320.0
2 TraesCS3D01G111300 chr3D 87.956 274 28 3 3799 4069 601044273 601044002 6.650000e-83 318.0
3 TraesCS3D01G111300 chr3D 76.842 475 89 15 1148 1608 106736796 106737263 8.850000e-62 248.0
4 TraesCS3D01G111300 chr3D 75.714 210 41 9 2536 2740 424351192 424350988 3.390000e-16 97.1
5 TraesCS3D01G111300 chr3B 92.175 2901 107 35 772 3610 107958511 107961353 0.000000e+00 3989.0
6 TraesCS3D01G111300 chr3B 84.770 348 28 10 210 540 107957905 107958244 3.980000e-85 326.0
7 TraesCS3D01G111300 chr3B 78.528 326 57 10 1287 1601 157377253 157377576 6.990000e-48 202.0
8 TraesCS3D01G111300 chr3B 76.190 210 40 9 2536 2740 554117584 554117380 7.300000e-18 102.0
9 TraesCS3D01G111300 chr3A 93.764 1748 58 23 1854 3557 75546404 75548144 0.000000e+00 2577.0
10 TraesCS3D01G111300 chr3A 96.134 957 24 4 840 1787 75545446 75546398 0.000000e+00 1550.0
11 TraesCS3D01G111300 chr3A 92.332 639 33 7 204 840 75542785 75543409 0.000000e+00 894.0
12 TraesCS3D01G111300 chr3A 95.789 190 8 0 1 190 75542614 75542803 1.440000e-79 307.0
13 TraesCS3D01G111300 chr3A 86.147 231 21 8 3610 3838 466040976 466040755 5.330000e-59 239.0
14 TraesCS3D01G111300 chr3A 85.185 216 19 12 3591 3800 701344684 701344476 4.180000e-50 209.0
15 TraesCS3D01G111300 chr3A 92.537 67 5 0 4059 4125 75548220 75548286 3.390000e-16 97.1
16 TraesCS3D01G111300 chr3A 76.042 192 36 9 2536 2722 564440432 564440618 1.580000e-14 91.6
17 TraesCS3D01G111300 chr4D 88.636 264 24 4 3801 4060 43773617 43773878 2.390000e-82 316.0
18 TraesCS3D01G111300 chr4B 88.889 261 23 5 3794 4051 631583951 631584208 2.390000e-82 316.0
19 TraesCS3D01G111300 chr5B 88.593 263 25 4 3801 4060 352304792 352305052 8.610000e-82 315.0
20 TraesCS3D01G111300 chr2D 87.681 276 27 5 3800 4071 481282195 481281923 8.610000e-82 315.0
21 TraesCS3D01G111300 chr2D 88.770 187 17 4 3610 3794 620298291 620298107 4.150000e-55 226.0
22 TraesCS3D01G111300 chr7B 87.546 273 28 5 3792 4060 59608969 59609239 1.110000e-80 311.0
23 TraesCS3D01G111300 chr6D 87.319 276 29 5 3800 4071 151317212 151317485 1.110000e-80 311.0
24 TraesCS3D01G111300 chr6B 87.778 270 28 4 3800 4066 550778183 550777916 1.110000e-80 311.0
25 TraesCS3D01G111300 chr1A 89.583 192 15 3 3610 3797 202093037 202093227 5.330000e-59 239.0
26 TraesCS3D01G111300 chr1A 87.565 193 20 4 3606 3796 420573036 420572846 1.930000e-53 220.0
27 TraesCS3D01G111300 chr6A 89.674 184 17 2 3611 3794 23679312 23679493 2.480000e-57 233.0
28 TraesCS3D01G111300 chr6A 87.081 209 17 10 3597 3800 180309144 180309347 1.150000e-55 228.0
29 TraesCS3D01G111300 chr4A 87.562 201 21 4 3601 3799 519575481 519575679 3.210000e-56 230.0
30 TraesCS3D01G111300 chr4A 88.830 188 14 7 3609 3793 11366021 11366204 1.490000e-54 224.0
31 TraesCS3D01G111300 chr7A 86.058 208 20 9 3600 3803 130378185 130378387 8.980000e-52 215.0
32 TraesCS3D01G111300 chr7A 79.661 118 15 7 604 715 706985065 706984951 4.420000e-10 76.8


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 TraesCS3D01G111300 chr3D 64760830 64764954 4124 False 7618.00 7618 100.0000 1 4125 1 chr3D.!!$F1 4124
1 TraesCS3D01G111300 chr3B 107957905 107961353 3448 False 2157.50 3989 88.4725 210 3610 2 chr3B.!!$F2 3400
2 TraesCS3D01G111300 chr3A 75542614 75548286 5672 False 1085.02 2577 94.1112 1 4125 5 chr3A.!!$F2 4124

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
410 414 0.871057 CACACACACACACACACACA 59.129 50.000 0.0 0.0 0.0 3.72 F
413 417 1.265365 CACACACACACACACACACAA 59.735 47.619 0.0 0.0 0.0 3.33 F
1625 3761 1.356624 GCACGATATGGGCAAGCAC 59.643 57.895 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 3703 2.303549 GATGACGTCCAGCTCCAGGG 62.304 65.000 14.12 0.00 0.00 4.45 R
1626 3762 4.409218 CGTGGTGCATGCTGGTGC 62.409 66.667 20.33 4.64 45.25 5.01 R
3435 5655 0.105090 CCCTTACCCCCTAGGAGGTC 60.105 65.000 19.93 0.00 39.89 3.85 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
43 44 6.929049 TGTTGTAGAACTTTATGGTGACTCAG 59.071 38.462 4.21 0.00 32.79 3.35
93 94 7.818930 CACCAGCTGTTGTATTTGGATTAAATT 59.181 33.333 13.81 0.00 39.61 1.82
97 98 8.470002 AGCTGTTGTATTTGGATTAAATTCTCC 58.530 33.333 0.00 0.00 39.61 3.71
130 131 6.324042 GCAAATTGCCAAATTAAATTCCAGG 58.676 36.000 6.72 0.00 37.42 4.45
145 146 6.983906 AATTCCAGGATATTTTAGCCCAAG 57.016 37.500 0.00 0.00 33.87 3.61
168 169 7.812309 AGTGCTAAACAACTTTCAAAGAAAC 57.188 32.000 3.49 0.00 0.00 2.78
186 187 6.187727 AGAAACTAGGTGAGGTGATGAAAA 57.812 37.500 0.00 0.00 0.00 2.29
187 188 5.998363 AGAAACTAGGTGAGGTGATGAAAAC 59.002 40.000 0.00 0.00 0.00 2.43
188 189 5.568620 AACTAGGTGAGGTGATGAAAACT 57.431 39.130 0.00 0.00 0.00 2.66
189 190 5.568620 ACTAGGTGAGGTGATGAAAACTT 57.431 39.130 0.00 0.00 0.00 2.66
190 191 5.941788 ACTAGGTGAGGTGATGAAAACTTT 58.058 37.500 0.00 0.00 0.00 2.66
191 192 6.365520 ACTAGGTGAGGTGATGAAAACTTTT 58.634 36.000 0.00 0.00 0.00 2.27
192 193 6.833933 ACTAGGTGAGGTGATGAAAACTTTTT 59.166 34.615 0.00 0.00 0.00 1.94
239 243 8.137437 TGAAAACTTGATCTCTTTTGTCCAATC 58.863 33.333 0.00 0.00 0.00 2.67
368 372 5.009631 TCCATGGTGGTCAAATGTTTAGAG 58.990 41.667 12.58 0.00 39.03 2.43
410 414 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
413 417 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
414 418 1.950216 ACACACACACACACACACAAA 59.050 42.857 0.00 0.00 0.00 2.83
415 419 2.359214 ACACACACACACACACACAAAA 59.641 40.909 0.00 0.00 0.00 2.44
507 523 3.653539 AACAAGCACGTATTTTTCCCC 57.346 42.857 0.00 0.00 0.00 4.81
568 584 7.941790 GCCCTTCCTTTGATATAGAGAAATCTT 59.058 37.037 0.00 0.00 0.00 2.40
614 671 9.189723 CTTTGAAGACTTTGAAGAATTGGATTC 57.810 33.333 0.00 0.00 39.56 2.52
654 741 7.698130 GGATTTGTTTCTATCCTTCACATTTCG 59.302 37.037 0.00 0.00 37.83 3.46
694 787 6.595716 GCTCAGAGCTAACAGAAAAATTCCTA 59.404 38.462 15.78 0.00 38.45 2.94
695 788 7.413548 GCTCAGAGCTAACAGAAAAATTCCTAC 60.414 40.741 15.78 0.00 38.45 3.18
697 790 8.157476 TCAGAGCTAACAGAAAAATTCCTACTT 58.843 33.333 0.00 0.00 0.00 2.24
832 925 2.202932 CCGCCGTAGCAGCATCTT 60.203 61.111 0.00 0.00 39.83 2.40
976 3108 1.599071 CATCATCACATTAACGCGCCT 59.401 47.619 5.73 0.00 0.00 5.52
1344 3476 2.813908 GTGGTCGTCGACATGCCC 60.814 66.667 25.64 9.62 33.68 5.36
1571 3703 2.710902 GCCCCCAGATTTCCAACGC 61.711 63.158 0.00 0.00 0.00 4.84
1624 3760 2.179547 CGCACGATATGGGCAAGCA 61.180 57.895 0.00 0.00 34.01 3.91
1625 3761 1.356624 GCACGATATGGGCAAGCAC 59.643 57.895 0.00 0.00 0.00 4.40
1626 3762 1.643292 CACGATATGGGCAAGCACG 59.357 57.895 0.00 0.00 0.00 5.34
1627 3763 2.180204 ACGATATGGGCAAGCACGC 61.180 57.895 0.00 0.00 0.00 5.34
1976 4151 2.489722 GACTTTGACATTTCCCCTCTGC 59.510 50.000 0.00 0.00 0.00 4.26
2107 4294 1.736645 CAACGCGGACCTGTTCGAT 60.737 57.895 12.47 0.00 0.00 3.59
2112 4299 3.195698 GGACCTGTTCGATGCGGC 61.196 66.667 0.00 0.00 0.00 6.53
2380 4567 2.579787 GACGTCGCCAGGATCGTG 60.580 66.667 8.47 8.47 34.25 4.35
2426 4613 0.445043 CACCGTGTACGTCATCGAGA 59.555 55.000 0.00 0.00 40.62 4.04
2445 4632 0.110328 ACGACGCTCAACTACGACAG 60.110 55.000 0.00 0.00 0.00 3.51
2602 4789 3.706373 AAGATCGGGCTGTGGCGT 61.706 61.111 0.00 0.00 39.81 5.68
2622 4809 4.431131 CCCGCACCCTTGGCTCAT 62.431 66.667 0.00 0.00 0.00 2.90
2660 4847 3.255379 GCATCGCCGACTTCGACC 61.255 66.667 0.00 0.00 43.02 4.79
2878 5081 1.592400 CGGAGGAGGTGTTCTACGCA 61.592 60.000 0.00 0.00 0.00 5.24
3242 5452 5.963586 GCAAATTTGATAGTAGGTTGTACGC 59.036 40.000 22.31 0.00 0.00 4.42
3291 5505 5.936187 TCTCCACATGTACCCGTTATTAA 57.064 39.130 0.00 0.00 0.00 1.40
3297 5511 8.359642 TCCACATGTACCCGTTATTAATAGTAC 58.640 37.037 0.00 12.51 0.00 2.73
3329 5543 4.493547 CAAAAGTGTGAACAAAGCTCCAA 58.506 39.130 0.00 0.00 0.00 3.53
3363 5577 8.225107 CACTTTGCCAGATAAATGTTTCATTTG 58.775 33.333 15.18 2.63 0.00 2.32
3435 5655 7.013083 AGCTCTTTTATATGATTGCTCCAACTG 59.987 37.037 0.00 0.00 0.00 3.16
3452 5676 1.291335 ACTGACCTCCTAGGGGGTAAG 59.709 57.143 36.27 36.27 40.58 2.34
3453 5677 0.640495 TGACCTCCTAGGGGGTAAGG 59.360 60.000 34.29 21.62 40.58 2.69
3522 5755 2.189594 TGAGCATCCACTTTCACTGG 57.810 50.000 0.00 0.00 0.00 4.00
3557 5815 5.628134 CGTCCACTTAAGGCAAGTTATTTC 58.372 41.667 7.53 0.00 45.54 2.17
3558 5816 5.180492 CGTCCACTTAAGGCAAGTTATTTCA 59.820 40.000 7.53 0.00 45.54 2.69
3564 5822 7.867403 CACTTAAGGCAAGTTATTTCAATGTGT 59.133 33.333 7.53 0.00 45.54 3.72
3571 5829 9.644993 GGCAAGTTATTTCAATGTGTTAAAAAC 57.355 29.630 0.00 0.00 0.00 2.43
3577 5835 7.707774 ATTTCAATGTGTTAAAAACGGAAGG 57.292 32.000 0.00 0.00 0.00 3.46
3578 5836 6.452494 TTCAATGTGTTAAAAACGGAAGGA 57.548 33.333 0.00 0.00 0.00 3.36
3590 5848 6.954487 AAAACGGAAGGATTTTAGTTGACT 57.046 33.333 0.00 0.00 0.00 3.41
3619 5877 8.850454 TTGTCATTTTCTACTACAGTTTTTGC 57.150 30.769 0.00 0.00 0.00 3.68
3620 5878 8.220755 TGTCATTTTCTACTACAGTTTTTGCT 57.779 30.769 0.00 0.00 0.00 3.91
3621 5879 9.332502 TGTCATTTTCTACTACAGTTTTTGCTA 57.667 29.630 0.00 0.00 0.00 3.49
3625 5883 9.678941 ATTTTCTACTACAGTTTTTGCTAAAGC 57.321 29.630 0.00 0.00 42.50 3.51
3651 5909 7.651808 ACATCTAAATGTGCCATAAGTATTGC 58.348 34.615 0.00 0.00 44.51 3.56
3652 5910 7.285172 ACATCTAAATGTGCCATAAGTATTGCA 59.715 33.333 0.00 0.00 44.51 4.08
3660 5918 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
3661 5919 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
3662 5920 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
3663 5921 6.708054 GCCATAAGTATTGCACATCTAAGTCT 59.292 38.462 0.00 0.00 0.00 3.24
3664 5922 7.227512 GCCATAAGTATTGCACATCTAAGTCTT 59.772 37.037 0.00 0.00 0.00 3.01
3665 5923 9.764363 CCATAAGTATTGCACATCTAAGTCTTA 57.236 33.333 0.00 0.00 0.00 2.10
3707 5965 8.880768 CGAAGATTCGTGTGAATATTTTTCTT 57.119 30.769 6.81 0.00 43.94 2.52
3708 5966 9.329913 CGAAGATTCGTGTGAATATTTTTCTTT 57.670 29.630 6.81 0.00 43.94 2.52
3734 5992 9.533253 TTCTTTTCCTTTTTCTTTCTATGCTTG 57.467 29.630 0.00 0.00 0.00 4.01
3735 5993 7.653311 TCTTTTCCTTTTTCTTTCTATGCTTGC 59.347 33.333 0.00 0.00 0.00 4.01
3736 5994 6.655078 TTCCTTTTTCTTTCTATGCTTGCT 57.345 33.333 0.00 0.00 0.00 3.91
3737 5995 6.655078 TCCTTTTTCTTTCTATGCTTGCTT 57.345 33.333 0.00 0.00 0.00 3.91
3738 5996 6.449698 TCCTTTTTCTTTCTATGCTTGCTTG 58.550 36.000 0.00 0.00 0.00 4.01
3739 5997 6.040842 TCCTTTTTCTTTCTATGCTTGCTTGT 59.959 34.615 0.00 0.00 0.00 3.16
3740 5998 6.145048 CCTTTTTCTTTCTATGCTTGCTTGTG 59.855 38.462 0.00 0.00 0.00 3.33
3741 5999 5.772825 TTTCTTTCTATGCTTGCTTGTGT 57.227 34.783 0.00 0.00 0.00 3.72
3742 6000 5.362556 TTCTTTCTATGCTTGCTTGTGTC 57.637 39.130 0.00 0.00 0.00 3.67
3743 6001 4.388485 TCTTTCTATGCTTGCTTGTGTCA 58.612 39.130 0.00 0.00 0.00 3.58
3744 6002 4.214119 TCTTTCTATGCTTGCTTGTGTCAC 59.786 41.667 0.00 0.00 0.00 3.67
3745 6003 3.407424 TCTATGCTTGCTTGTGTCACT 57.593 42.857 4.27 0.00 0.00 3.41
3746 6004 3.743521 TCTATGCTTGCTTGTGTCACTT 58.256 40.909 4.27 0.00 0.00 3.16
3747 6005 2.787601 ATGCTTGCTTGTGTCACTTG 57.212 45.000 4.27 0.00 0.00 3.16
3748 6006 0.740149 TGCTTGCTTGTGTCACTTGG 59.260 50.000 4.27 0.00 0.00 3.61
3749 6007 1.024271 GCTTGCTTGTGTCACTTGGA 58.976 50.000 4.27 0.00 0.00 3.53
3750 6008 1.610522 GCTTGCTTGTGTCACTTGGAT 59.389 47.619 4.27 0.00 0.00 3.41
3751 6009 2.606308 GCTTGCTTGTGTCACTTGGATG 60.606 50.000 4.27 2.47 0.00 3.51
3752 6010 2.346766 TGCTTGTGTCACTTGGATGT 57.653 45.000 4.27 0.00 0.00 3.06
3753 6011 1.948834 TGCTTGTGTCACTTGGATGTG 59.051 47.619 4.27 0.00 39.15 3.21
3754 6012 1.335324 GCTTGTGTCACTTGGATGTGC 60.335 52.381 4.27 0.00 37.81 4.57
3755 6013 1.948834 CTTGTGTCACTTGGATGTGCA 59.051 47.619 4.27 0.00 37.81 4.57
3756 6014 2.049888 TGTGTCACTTGGATGTGCAA 57.950 45.000 4.27 0.00 37.81 4.08
3757 6015 2.585330 TGTGTCACTTGGATGTGCAAT 58.415 42.857 4.27 0.00 37.81 3.56
3758 6016 3.749226 TGTGTCACTTGGATGTGCAATA 58.251 40.909 4.27 0.00 37.81 1.90
3759 6017 3.752747 TGTGTCACTTGGATGTGCAATAG 59.247 43.478 4.27 0.00 37.81 1.73
3760 6018 2.749076 TGTCACTTGGATGTGCAATAGC 59.251 45.455 0.00 0.00 42.57 2.97
3761 6019 3.012518 GTCACTTGGATGTGCAATAGCT 58.987 45.455 0.00 0.00 42.74 3.32
3762 6020 3.011818 TCACTTGGATGTGCAATAGCTG 58.988 45.455 0.00 0.00 42.74 4.24
3763 6021 3.011818 CACTTGGATGTGCAATAGCTGA 58.988 45.455 0.00 0.00 42.74 4.26
3764 6022 3.064958 CACTTGGATGTGCAATAGCTGAG 59.935 47.826 0.00 0.00 42.74 3.35
3765 6023 2.336945 TGGATGTGCAATAGCTGAGG 57.663 50.000 0.00 0.00 42.74 3.86
3766 6024 0.950116 GGATGTGCAATAGCTGAGGC 59.050 55.000 0.00 0.00 42.74 4.70
3767 6025 1.671979 GATGTGCAATAGCTGAGGCA 58.328 50.000 0.00 0.00 42.74 4.75
3770 6028 3.888424 TGCAATAGCTGAGGCACAT 57.112 47.368 0.00 0.00 42.74 3.21
3771 6029 1.671979 TGCAATAGCTGAGGCACATC 58.328 50.000 0.00 0.00 42.74 3.06
3772 6030 1.211212 TGCAATAGCTGAGGCACATCT 59.789 47.619 0.00 0.00 42.74 2.90
3773 6031 2.435437 TGCAATAGCTGAGGCACATCTA 59.565 45.455 0.00 0.00 42.74 1.98
3774 6032 3.065655 GCAATAGCTGAGGCACATCTAG 58.934 50.000 0.00 0.00 41.70 2.43
3775 6033 3.244009 GCAATAGCTGAGGCACATCTAGA 60.244 47.826 0.00 0.00 41.70 2.43
3776 6034 4.563168 GCAATAGCTGAGGCACATCTAGAT 60.563 45.833 0.00 0.00 41.70 1.98
3777 6035 4.804868 ATAGCTGAGGCACATCTAGATG 57.195 45.455 27.63 27.63 41.70 2.90
3778 6036 8.903316 GCAATAGCTGAGGCACATCTAGATGT 62.903 46.154 28.95 28.95 44.46 3.06
3779 6037 9.611521 GCAATAGCTGAGGCACATCTAGATGTA 62.612 44.444 32.57 18.77 43.02 2.29
3792 6050 6.750148 CATCTAGATGTACCCTAGACAAACC 58.250 44.000 22.42 0.00 43.57 3.27
3793 6051 5.206587 TCTAGATGTACCCTAGACAAACCC 58.793 45.833 14.52 0.00 38.08 4.11
3794 6052 4.076175 AGATGTACCCTAGACAAACCCT 57.924 45.455 0.00 0.00 0.00 4.34
3795 6053 4.436079 AGATGTACCCTAGACAAACCCTT 58.564 43.478 0.00 0.00 0.00 3.95
3796 6054 4.850386 AGATGTACCCTAGACAAACCCTTT 59.150 41.667 0.00 0.00 0.00 3.11
3797 6055 4.628963 TGTACCCTAGACAAACCCTTTC 57.371 45.455 0.00 0.00 0.00 2.62
3798 6056 4.237018 TGTACCCTAGACAAACCCTTTCT 58.763 43.478 0.00 0.00 0.00 2.52
3799 6057 5.405279 TGTACCCTAGACAAACCCTTTCTA 58.595 41.667 0.00 0.00 0.00 2.10
3800 6058 6.027482 TGTACCCTAGACAAACCCTTTCTAT 58.973 40.000 0.00 0.00 0.00 1.98
3801 6059 7.191210 TGTACCCTAGACAAACCCTTTCTATA 58.809 38.462 0.00 0.00 0.00 1.31
3802 6060 6.556974 ACCCTAGACAAACCCTTTCTATAC 57.443 41.667 0.00 0.00 0.00 1.47
3803 6061 6.269974 ACCCTAGACAAACCCTTTCTATACT 58.730 40.000 0.00 0.00 0.00 2.12
3804 6062 6.383436 ACCCTAGACAAACCCTTTCTATACTC 59.617 42.308 0.00 0.00 0.00 2.59
3805 6063 6.183360 CCCTAGACAAACCCTTTCTATACTCC 60.183 46.154 0.00 0.00 0.00 3.85
3806 6064 5.695424 AGACAAACCCTTTCTATACTCCC 57.305 43.478 0.00 0.00 0.00 4.30
3807 6065 5.351405 AGACAAACCCTTTCTATACTCCCT 58.649 41.667 0.00 0.00 0.00 4.20
3808 6066 5.425862 AGACAAACCCTTTCTATACTCCCTC 59.574 44.000 0.00 0.00 0.00 4.30
3809 6067 4.473922 ACAAACCCTTTCTATACTCCCTCC 59.526 45.833 0.00 0.00 0.00 4.30
3810 6068 2.960163 ACCCTTTCTATACTCCCTCCG 58.040 52.381 0.00 0.00 0.00 4.63
3811 6069 2.246849 ACCCTTTCTATACTCCCTCCGT 59.753 50.000 0.00 0.00 0.00 4.69
3812 6070 3.306613 CCCTTTCTATACTCCCTCCGTT 58.693 50.000 0.00 0.00 0.00 4.44
3813 6071 3.321396 CCCTTTCTATACTCCCTCCGTTC 59.679 52.174 0.00 0.00 0.00 3.95
3814 6072 3.321396 CCTTTCTATACTCCCTCCGTTCC 59.679 52.174 0.00 0.00 0.00 3.62
3815 6073 3.675348 TTCTATACTCCCTCCGTTCCA 57.325 47.619 0.00 0.00 0.00 3.53
3816 6074 3.897657 TCTATACTCCCTCCGTTCCAT 57.102 47.619 0.00 0.00 0.00 3.41
3817 6075 5.329191 TTCTATACTCCCTCCGTTCCATA 57.671 43.478 0.00 0.00 0.00 2.74
3818 6076 5.329191 TCTATACTCCCTCCGTTCCATAA 57.671 43.478 0.00 0.00 0.00 1.90
3819 6077 5.900437 TCTATACTCCCTCCGTTCCATAAT 58.100 41.667 0.00 0.00 0.00 1.28
3820 6078 4.891992 ATACTCCCTCCGTTCCATAATG 57.108 45.455 0.00 0.00 0.00 1.90
3821 6079 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
3822 6080 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
3823 6081 3.641906 ACTCCCTCCGTTCCATAATGTAG 59.358 47.826 0.00 0.00 0.00 2.74
3824 6082 3.641906 CTCCCTCCGTTCCATAATGTAGT 59.358 47.826 0.00 0.00 0.00 2.73
3825 6083 3.386726 TCCCTCCGTTCCATAATGTAGTG 59.613 47.826 0.00 0.00 0.00 2.74
3826 6084 3.131396 CCTCCGTTCCATAATGTAGTGC 58.869 50.000 0.00 0.00 0.00 4.40
3827 6085 3.431626 CCTCCGTTCCATAATGTAGTGCA 60.432 47.826 0.00 0.00 0.00 4.57
3828 6086 4.380531 CTCCGTTCCATAATGTAGTGCAT 58.619 43.478 0.00 0.00 40.03 3.96
3829 6087 5.510690 CCTCCGTTCCATAATGTAGTGCATA 60.511 44.000 0.00 0.00 36.67 3.14
3830 6088 6.109156 TCCGTTCCATAATGTAGTGCATAT 57.891 37.500 0.00 0.00 36.67 1.78
3831 6089 7.234661 TCCGTTCCATAATGTAGTGCATATA 57.765 36.000 0.00 0.00 36.67 0.86
3832 6090 7.320399 TCCGTTCCATAATGTAGTGCATATAG 58.680 38.462 0.00 0.00 36.67 1.31
3833 6091 7.039293 TCCGTTCCATAATGTAGTGCATATAGT 60.039 37.037 0.00 0.00 36.67 2.12
3834 6092 7.602644 CCGTTCCATAATGTAGTGCATATAGTT 59.397 37.037 0.00 0.00 36.67 2.24
3835 6093 8.988934 CGTTCCATAATGTAGTGCATATAGTTT 58.011 33.333 0.00 0.00 36.67 2.66
3870 6128 8.889849 AAGTCGAACATTATAAATTTTGACCG 57.110 30.769 18.05 9.43 34.21 4.79
3871 6129 8.036273 AGTCGAACATTATAAATTTTGACCGT 57.964 30.769 18.05 6.21 34.21 4.83
3872 6130 8.508875 AGTCGAACATTATAAATTTTGACCGTT 58.491 29.630 18.05 0.00 34.21 4.44
3873 6131 9.120422 GTCGAACATTATAAATTTTGACCGTTT 57.880 29.630 13.94 0.00 0.00 3.60
3889 6147 9.729281 TTTGACCGTTTATAGAGAAAAATAGGT 57.271 29.630 0.00 0.00 33.83 3.08
3891 6149 9.807649 TGACCGTTTATAGAGAAAAATAGGTAC 57.192 33.333 0.00 0.00 32.38 3.34
3892 6150 9.807649 GACCGTTTATAGAGAAAAATAGGTACA 57.192 33.333 0.00 0.00 32.38 2.90
3911 6169 7.897864 AGGTACATCTAGAATACCTAATGCAC 58.102 38.462 26.60 8.36 45.56 4.57
3912 6170 7.509318 AGGTACATCTAGAATACCTAATGCACA 59.491 37.037 26.60 0.00 45.56 4.57
3913 6171 8.314751 GGTACATCTAGAATACCTAATGCACAT 58.685 37.037 21.45 0.00 36.26 3.21
3914 6172 9.360093 GTACATCTAGAATACCTAATGCACATC 57.640 37.037 0.00 0.00 0.00 3.06
3915 6173 7.966812 ACATCTAGAATACCTAATGCACATCA 58.033 34.615 0.00 0.00 0.00 3.07
3916 6174 8.600668 ACATCTAGAATACCTAATGCACATCAT 58.399 33.333 0.00 0.00 36.87 2.45
3917 6175 9.445878 CATCTAGAATACCTAATGCACATCATT 57.554 33.333 0.00 0.00 46.48 2.57
3918 6176 8.837788 TCTAGAATACCTAATGCACATCATTG 57.162 34.615 0.00 0.00 44.62 2.82
3919 6177 6.889301 AGAATACCTAATGCACATCATTGG 57.111 37.500 0.00 0.00 44.62 3.16
3920 6178 6.604171 AGAATACCTAATGCACATCATTGGA 58.396 36.000 0.00 0.00 43.78 3.53
3921 6179 7.236529 AGAATACCTAATGCACATCATTGGAT 58.763 34.615 0.00 0.00 43.78 3.41
3922 6180 8.385491 AGAATACCTAATGCACATCATTGGATA 58.615 33.333 0.00 0.00 43.78 2.59
3923 6181 7.928307 ATACCTAATGCACATCATTGGATAC 57.072 36.000 0.00 0.00 43.78 2.24
3943 6201 9.631257 TGGATACATCATGAGTTATGTTTTCAT 57.369 29.630 5.07 0.00 46.17 2.57
3958 6216 6.474819 TGTTTTCATAATGTACGTGTCTGG 57.525 37.500 0.00 0.00 0.00 3.86
3959 6217 5.992829 TGTTTTCATAATGTACGTGTCTGGT 59.007 36.000 0.00 0.00 0.00 4.00
3960 6218 7.153315 TGTTTTCATAATGTACGTGTCTGGTA 58.847 34.615 0.00 0.00 0.00 3.25
3961 6219 7.329962 TGTTTTCATAATGTACGTGTCTGGTAG 59.670 37.037 0.00 0.00 0.00 3.18
3962 6220 6.519679 TTCATAATGTACGTGTCTGGTAGT 57.480 37.500 0.00 0.00 0.00 2.73
3963 6221 5.886992 TCATAATGTACGTGTCTGGTAGTG 58.113 41.667 0.00 0.00 0.00 2.74
3964 6222 5.416639 TCATAATGTACGTGTCTGGTAGTGT 59.583 40.000 0.00 0.00 0.00 3.55
3965 6223 6.598850 TCATAATGTACGTGTCTGGTAGTGTA 59.401 38.462 0.00 0.00 0.00 2.90
3966 6224 4.959596 ATGTACGTGTCTGGTAGTGTAG 57.040 45.455 0.00 0.00 0.00 2.74
3967 6225 4.006780 TGTACGTGTCTGGTAGTGTAGA 57.993 45.455 0.00 0.00 0.00 2.59
3968 6226 4.582869 TGTACGTGTCTGGTAGTGTAGAT 58.417 43.478 0.00 0.00 0.00 1.98
3969 6227 4.393990 TGTACGTGTCTGGTAGTGTAGATG 59.606 45.833 0.00 0.00 0.00 2.90
3970 6228 3.418995 ACGTGTCTGGTAGTGTAGATGT 58.581 45.455 0.00 0.00 0.00 3.06
3971 6229 4.582869 ACGTGTCTGGTAGTGTAGATGTA 58.417 43.478 0.00 0.00 0.00 2.29
3972 6230 4.634883 ACGTGTCTGGTAGTGTAGATGTAG 59.365 45.833 0.00 0.00 0.00 2.74
3973 6231 4.874396 CGTGTCTGGTAGTGTAGATGTAGA 59.126 45.833 0.00 0.00 0.00 2.59
3974 6232 5.220624 CGTGTCTGGTAGTGTAGATGTAGAC 60.221 48.000 0.00 0.00 35.20 2.59
3975 6233 5.646793 GTGTCTGGTAGTGTAGATGTAGACA 59.353 44.000 0.00 0.00 40.43 3.41
3976 6234 6.319152 GTGTCTGGTAGTGTAGATGTAGACAT 59.681 42.308 0.00 0.00 43.29 3.06
3977 6235 6.890268 TGTCTGGTAGTGTAGATGTAGACATT 59.110 38.462 0.00 0.00 38.55 2.71
3978 6236 7.396339 TGTCTGGTAGTGTAGATGTAGACATTT 59.604 37.037 0.00 0.00 38.55 2.32
3979 6237 8.251721 GTCTGGTAGTGTAGATGTAGACATTTT 58.748 37.037 0.00 0.00 36.57 1.82
3980 6238 8.812972 TCTGGTAGTGTAGATGTAGACATTTTT 58.187 33.333 0.00 0.00 36.57 1.94
3981 6239 8.997621 TGGTAGTGTAGATGTAGACATTTTTC 57.002 34.615 0.00 0.00 36.57 2.29
3982 6240 8.812972 TGGTAGTGTAGATGTAGACATTTTTCT 58.187 33.333 0.00 0.00 36.57 2.52
3983 6241 9.303537 GGTAGTGTAGATGTAGACATTTTTCTC 57.696 37.037 0.00 0.00 36.57 2.87
4013 6271 5.981174 CTTGATCAAAGTTGGCACATTTTG 58.019 37.500 9.88 9.89 41.48 2.44
4015 6273 5.049167 TGATCAAAGTTGGCACATTTTGAC 58.951 37.500 17.30 13.18 46.79 3.18
4016 6274 4.734398 TCAAAGTTGGCACATTTTGACT 57.266 36.364 13.21 0.00 42.82 3.41
4017 6275 5.083533 TCAAAGTTGGCACATTTTGACTT 57.916 34.783 13.21 4.81 42.82 3.01
4018 6276 6.214191 TCAAAGTTGGCACATTTTGACTTA 57.786 33.333 13.21 0.00 42.82 2.24
4019 6277 6.634805 TCAAAGTTGGCACATTTTGACTTAA 58.365 32.000 13.21 0.00 42.82 1.85
4020 6278 7.099764 TCAAAGTTGGCACATTTTGACTTAAA 58.900 30.769 13.21 0.00 42.82 1.52
4021 6279 7.604164 TCAAAGTTGGCACATTTTGACTTAAAA 59.396 29.630 13.21 0.00 42.82 1.52
4022 6280 7.913674 AAGTTGGCACATTTTGACTTAAAAA 57.086 28.000 0.00 0.00 41.29 1.94
4051 6309 9.842775 ATCTATATGCACTATATTGTGGAATGG 57.157 33.333 14.64 11.25 41.34 3.16
4052 6310 9.045745 TCTATATGCACTATATTGTGGAATGGA 57.954 33.333 14.64 12.86 41.34 3.41
4053 6311 9.671279 CTATATGCACTATATTGTGGAATGGAA 57.329 33.333 14.64 1.02 41.34 3.53
4054 6312 6.889301 ATGCACTATATTGTGGAATGGAAG 57.111 37.500 14.64 0.00 41.34 3.46
4055 6313 5.132502 TGCACTATATTGTGGAATGGAAGG 58.867 41.667 17.22 0.00 35.42 3.46
4056 6314 5.104151 TGCACTATATTGTGGAATGGAAGGA 60.104 40.000 17.22 0.00 35.42 3.36
4057 6315 5.471456 GCACTATATTGTGGAATGGAAGGAG 59.529 44.000 17.22 0.00 38.31 3.69
4060 6318 8.210946 CACTATATTGTGGAATGGAAGGAGTAA 58.789 37.037 9.17 0.00 34.56 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.642131 GTCACCATAAAGTTCTACAACACGTA 59.358 38.462 0.00 0.00 34.60 3.57
43 44 3.569250 ACCATTTTCGTGTTGCCATAC 57.431 42.857 0.00 0.00 0.00 2.39
93 94 2.288152 GCAATTTGCCGTTTTCTGGAGA 60.288 45.455 10.34 0.00 37.42 3.71
145 146 7.812309 AGTTTCTTTGAAAGTTGTTTAGCAC 57.188 32.000 4.68 0.00 0.00 4.40
168 169 6.884280 AAAAGTTTTCATCACCTCACCTAG 57.116 37.500 0.00 0.00 0.00 3.02
195 196 2.865079 TCATCACCTTACCCGCAAAAA 58.135 42.857 0.00 0.00 0.00 1.94
196 197 2.570415 TCATCACCTTACCCGCAAAA 57.430 45.000 0.00 0.00 0.00 2.44
197 198 2.570415 TTCATCACCTTACCCGCAAA 57.430 45.000 0.00 0.00 0.00 3.68
198 199 2.554893 GTTTTCATCACCTTACCCGCAA 59.445 45.455 0.00 0.00 0.00 4.85
199 200 2.156098 GTTTTCATCACCTTACCCGCA 58.844 47.619 0.00 0.00 0.00 5.69
200 201 2.433436 AGTTTTCATCACCTTACCCGC 58.567 47.619 0.00 0.00 0.00 6.13
201 202 4.069304 TCAAGTTTTCATCACCTTACCCG 58.931 43.478 0.00 0.00 0.00 5.28
202 203 5.946377 AGATCAAGTTTTCATCACCTTACCC 59.054 40.000 0.00 0.00 0.00 3.69
203 204 6.881602 AGAGATCAAGTTTTCATCACCTTACC 59.118 38.462 0.00 0.00 0.00 2.85
204 205 7.913674 AGAGATCAAGTTTTCATCACCTTAC 57.086 36.000 0.00 0.00 0.00 2.34
205 206 8.924511 AAAGAGATCAAGTTTTCATCACCTTA 57.075 30.769 0.00 0.00 0.00 2.69
206 207 7.830099 AAAGAGATCAAGTTTTCATCACCTT 57.170 32.000 0.00 0.00 0.00 3.50
207 208 7.286316 ACAAAAGAGATCAAGTTTTCATCACCT 59.714 33.333 0.00 0.00 0.00 4.00
208 209 7.428826 ACAAAAGAGATCAAGTTTTCATCACC 58.571 34.615 0.00 0.00 0.00 4.02
209 210 7.592903 GGACAAAAGAGATCAAGTTTTCATCAC 59.407 37.037 0.00 0.00 0.00 3.06
210 211 7.285172 TGGACAAAAGAGATCAAGTTTTCATCA 59.715 33.333 0.00 0.00 0.00 3.07
211 212 7.651808 TGGACAAAAGAGATCAAGTTTTCATC 58.348 34.615 0.00 0.00 0.00 2.92
338 342 0.184692 TGACCACCATGGACAGCAAA 59.815 50.000 21.47 0.00 40.96 3.68
368 372 2.184579 GGTACTGCAGGCCGACTC 59.815 66.667 19.93 0.00 0.00 3.36
415 419 8.537728 TGCACTGATAATATTGGATCCTTTTT 57.462 30.769 14.23 4.94 0.00 1.94
507 523 4.675146 CGCCTTGTTTATTGATTGACCAGG 60.675 45.833 0.00 0.00 0.00 4.45
743 836 7.128077 AGGGAAGTCATGATAAATGAAATGGT 58.872 34.615 0.00 0.00 0.00 3.55
976 3108 1.836383 GCTTCGCGTTTAGCTAGCTA 58.164 50.000 20.67 20.67 43.38 3.32
1571 3703 2.303549 GATGACGTCCAGCTCCAGGG 62.304 65.000 14.12 0.00 0.00 4.45
1626 3762 4.409218 CGTGGTGCATGCTGGTGC 62.409 66.667 20.33 4.64 45.25 5.01
1627 3763 4.409218 GCGTGGTGCATGCTGGTG 62.409 66.667 20.33 6.22 42.44 4.17
1825 3996 9.383519 CACTATCAATTTACACTGTACTCCATT 57.616 33.333 0.00 0.00 0.00 3.16
1826 3997 7.987458 CCACTATCAATTTACACTGTACTCCAT 59.013 37.037 0.00 0.00 0.00 3.41
1827 3998 7.038587 ACCACTATCAATTTACACTGTACTCCA 60.039 37.037 0.00 0.00 0.00 3.86
1828 3999 7.328737 ACCACTATCAATTTACACTGTACTCC 58.671 38.462 0.00 0.00 0.00 3.85
1829 4000 9.517609 CTACCACTATCAATTTACACTGTACTC 57.482 37.037 0.00 0.00 0.00 2.59
1830 4001 9.032624 ACTACCACTATCAATTTACACTGTACT 57.967 33.333 0.00 0.00 0.00 2.73
1831 4002 9.649167 AACTACCACTATCAATTTACACTGTAC 57.351 33.333 0.00 0.00 0.00 2.90
1976 4151 7.380602 CGGGTAGAGTAATGGAGTAATTTAACG 59.619 40.741 0.00 0.00 0.00 3.18
2426 4613 0.110328 CTGTCGTAGTTGAGCGTCGT 60.110 55.000 0.00 0.00 0.00 4.34
2614 4801 1.737735 CACGAGCACGATGAGCCAA 60.738 57.895 11.40 0.00 42.66 4.52
2785 4975 4.864806 CAGTGTCAGTTAAGTGCGTGATAT 59.135 41.667 5.35 0.00 0.00 1.63
2878 5081 1.211449 CGAGAAGAGCAGCGACACT 59.789 57.895 0.00 0.00 0.00 3.55
2991 5194 2.431942 CGTGGGCCGTGTAGTGTC 60.432 66.667 0.00 0.00 0.00 3.67
2992 5195 3.998672 CCGTGGGCCGTGTAGTGT 61.999 66.667 0.00 0.00 33.66 3.55
3010 5213 2.847234 AAGTGGCGGACCCAGTCA 60.847 61.111 0.00 0.00 46.80 3.41
3022 5225 2.949106 CACTTGCTGCCGAAGTGG 59.051 61.111 19.55 6.49 44.41 4.00
3032 5235 3.360340 GAAGCGCTGCCACTTGCT 61.360 61.111 12.58 0.40 42.00 3.91
3236 5446 6.072893 TCGACAGAGCATATTATTAGCGTACA 60.073 38.462 0.00 0.00 0.00 2.90
3291 5505 8.582437 TCACACTTTTGCTTACAGTAGTACTAT 58.418 33.333 5.75 0.00 0.00 2.12
3297 5511 6.358118 TGTTCACACTTTTGCTTACAGTAG 57.642 37.500 0.00 0.00 0.00 2.57
3329 5543 6.892658 TTTATCTGGCAAAGTGTACATTGT 57.107 33.333 10.16 0.00 0.00 2.71
3363 5577 2.934801 GCCAAAGTCCTCTTCTGAGCTC 60.935 54.545 6.82 6.82 38.93 4.09
3421 5641 1.003580 GGAGGTCAGTTGGAGCAATCA 59.996 52.381 0.00 0.00 46.51 2.57
3435 5655 0.105090 CCCTTACCCCCTAGGAGGTC 60.105 65.000 19.93 0.00 39.89 3.85
3452 5676 1.903183 AGCTCAGACTAAACACTCCCC 59.097 52.381 0.00 0.00 0.00 4.81
3453 5677 4.202172 GGATAGCTCAGACTAAACACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
3529 5762 0.685097 TGCCTTAAGTGGACGCTCTT 59.315 50.000 0.97 0.00 0.00 2.85
3530 5763 0.685097 TTGCCTTAAGTGGACGCTCT 59.315 50.000 0.97 0.00 0.00 4.09
3557 5815 7.707774 AAATCCTTCCGTTTTTAACACATTG 57.292 32.000 0.00 0.00 0.00 2.82
3558 5816 9.471084 CTAAAATCCTTCCGTTTTTAACACATT 57.529 29.630 0.00 0.00 29.44 2.71
3564 5822 8.905850 AGTCAACTAAAATCCTTCCGTTTTTAA 58.094 29.630 0.00 0.00 29.44 1.52
3571 5829 8.512138 ACAATTAAGTCAACTAAAATCCTTCCG 58.488 33.333 0.00 0.00 0.00 4.30
3637 5895 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
3638 5896 6.708054 AGACTTAGATGTGCAATACTTATGGC 59.292 38.462 0.00 0.00 33.16 4.40
3639 5897 8.668510 AAGACTTAGATGTGCAATACTTATGG 57.331 34.615 0.00 0.00 0.00 2.74
3708 5966 9.533253 CAAGCATAGAAAGAAAAAGGAAAAGAA 57.467 29.630 0.00 0.00 0.00 2.52
3709 5967 7.653311 GCAAGCATAGAAAGAAAAAGGAAAAGA 59.347 33.333 0.00 0.00 0.00 2.52
3710 5968 7.654923 AGCAAGCATAGAAAGAAAAAGGAAAAG 59.345 33.333 0.00 0.00 0.00 2.27
3711 5969 7.500141 AGCAAGCATAGAAAGAAAAAGGAAAA 58.500 30.769 0.00 0.00 0.00 2.29
3712 5970 7.054491 AGCAAGCATAGAAAGAAAAAGGAAA 57.946 32.000 0.00 0.00 0.00 3.13
3713 5971 6.655078 AGCAAGCATAGAAAGAAAAAGGAA 57.345 33.333 0.00 0.00 0.00 3.36
3714 5972 6.040842 ACAAGCAAGCATAGAAAGAAAAAGGA 59.959 34.615 0.00 0.00 0.00 3.36
3715 5973 6.145048 CACAAGCAAGCATAGAAAGAAAAAGG 59.855 38.462 0.00 0.00 0.00 3.11
3716 5974 6.698766 ACACAAGCAAGCATAGAAAGAAAAAG 59.301 34.615 0.00 0.00 0.00 2.27
3717 5975 6.572519 ACACAAGCAAGCATAGAAAGAAAAA 58.427 32.000 0.00 0.00 0.00 1.94
3718 5976 6.147864 ACACAAGCAAGCATAGAAAGAAAA 57.852 33.333 0.00 0.00 0.00 2.29
3719 5977 5.299028 TGACACAAGCAAGCATAGAAAGAAA 59.701 36.000 0.00 0.00 0.00 2.52
3720 5978 4.821260 TGACACAAGCAAGCATAGAAAGAA 59.179 37.500 0.00 0.00 0.00 2.52
3721 5979 4.214119 GTGACACAAGCAAGCATAGAAAGA 59.786 41.667 0.00 0.00 0.00 2.52
3722 5980 4.214971 AGTGACACAAGCAAGCATAGAAAG 59.785 41.667 8.59 0.00 0.00 2.62
3723 5981 4.136796 AGTGACACAAGCAAGCATAGAAA 58.863 39.130 8.59 0.00 0.00 2.52
3724 5982 3.743521 AGTGACACAAGCAAGCATAGAA 58.256 40.909 8.59 0.00 0.00 2.10
3725 5983 3.407424 AGTGACACAAGCAAGCATAGA 57.593 42.857 8.59 0.00 0.00 1.98
3726 5984 3.365666 CCAAGTGACACAAGCAAGCATAG 60.366 47.826 8.59 0.00 0.00 2.23
3727 5985 2.553602 CCAAGTGACACAAGCAAGCATA 59.446 45.455 8.59 0.00 0.00 3.14
3728 5986 1.338973 CCAAGTGACACAAGCAAGCAT 59.661 47.619 8.59 0.00 0.00 3.79
3729 5987 0.740149 CCAAGTGACACAAGCAAGCA 59.260 50.000 8.59 0.00 0.00 3.91
3730 5988 1.024271 TCCAAGTGACACAAGCAAGC 58.976 50.000 8.59 0.00 0.00 4.01
3731 5989 2.620115 ACATCCAAGTGACACAAGCAAG 59.380 45.455 8.59 0.00 0.00 4.01
3732 5990 2.358582 CACATCCAAGTGACACAAGCAA 59.641 45.455 8.59 0.00 42.05 3.91
3733 5991 1.948834 CACATCCAAGTGACACAAGCA 59.051 47.619 8.59 0.00 42.05 3.91
3734 5992 1.335324 GCACATCCAAGTGACACAAGC 60.335 52.381 8.59 0.00 42.05 4.01
3735 5993 1.948834 TGCACATCCAAGTGACACAAG 59.051 47.619 8.59 0.00 42.05 3.16
3736 5994 2.049888 TGCACATCCAAGTGACACAA 57.950 45.000 8.59 0.00 42.05 3.33
3737 5995 2.049888 TTGCACATCCAAGTGACACA 57.950 45.000 8.59 0.00 42.05 3.72
3738 5996 3.426695 GCTATTGCACATCCAAGTGACAC 60.427 47.826 0.00 0.00 42.05 3.67
3739 5997 2.749076 GCTATTGCACATCCAAGTGACA 59.251 45.455 0.00 0.00 42.05 3.58
3740 5998 3.012518 AGCTATTGCACATCCAAGTGAC 58.987 45.455 1.12 0.00 42.05 3.67
3741 5999 3.011818 CAGCTATTGCACATCCAAGTGA 58.988 45.455 1.12 0.00 42.05 3.41
3742 6000 3.011818 TCAGCTATTGCACATCCAAGTG 58.988 45.455 1.12 0.00 42.74 3.16
3743 6001 3.276857 CTCAGCTATTGCACATCCAAGT 58.723 45.455 1.12 0.00 42.74 3.16
3744 6002 2.617308 CCTCAGCTATTGCACATCCAAG 59.383 50.000 1.12 0.00 42.74 3.61
3745 6003 2.646930 CCTCAGCTATTGCACATCCAA 58.353 47.619 1.12 0.00 42.74 3.53
3746 6004 1.748244 GCCTCAGCTATTGCACATCCA 60.748 52.381 1.12 0.00 42.74 3.41
3747 6005 0.950116 GCCTCAGCTATTGCACATCC 59.050 55.000 1.12 0.00 42.74 3.51
3748 6006 1.671979 TGCCTCAGCTATTGCACATC 58.328 50.000 1.12 0.00 42.74 3.06
3749 6007 3.888424 TGCCTCAGCTATTGCACAT 57.112 47.368 1.12 0.00 42.74 3.21
3752 6010 1.211212 AGATGTGCCTCAGCTATTGCA 59.789 47.619 1.12 0.00 41.29 4.08
3753 6011 1.964552 AGATGTGCCTCAGCTATTGC 58.035 50.000 0.00 0.00 41.29 3.56
3754 6012 4.597404 TCTAGATGTGCCTCAGCTATTG 57.403 45.455 4.84 0.00 42.89 1.90
3755 6013 5.149973 CATCTAGATGTGCCTCAGCTATT 57.850 43.478 22.42 0.00 42.89 1.73
3756 6014 4.804868 CATCTAGATGTGCCTCAGCTAT 57.195 45.455 22.42 0.00 42.89 2.97
3768 6026 6.239345 GGGTTTGTCTAGGGTACATCTAGATG 60.239 46.154 27.63 27.63 43.25 2.90
3769 6027 5.839606 GGGTTTGTCTAGGGTACATCTAGAT 59.160 44.000 20.70 0.00 43.25 1.98
3770 6028 5.043582 AGGGTTTGTCTAGGGTACATCTAGA 60.044 44.000 16.45 16.45 40.38 2.43
3771 6029 5.209659 AGGGTTTGTCTAGGGTACATCTAG 58.790 45.833 13.29 13.29 36.46 2.43
3772 6030 5.216665 AGGGTTTGTCTAGGGTACATCTA 57.783 43.478 0.00 0.00 0.00 1.98
3773 6031 4.076175 AGGGTTTGTCTAGGGTACATCT 57.924 45.455 0.00 0.00 0.00 2.90
3774 6032 4.838904 AAGGGTTTGTCTAGGGTACATC 57.161 45.455 0.00 0.00 0.00 3.06
3775 6033 4.850386 AGAAAGGGTTTGTCTAGGGTACAT 59.150 41.667 0.00 0.00 0.00 2.29
3776 6034 4.237018 AGAAAGGGTTTGTCTAGGGTACA 58.763 43.478 0.00 0.00 0.00 2.90
3777 6035 4.904895 AGAAAGGGTTTGTCTAGGGTAC 57.095 45.455 0.00 0.00 0.00 3.34
3778 6036 7.425003 AGTATAGAAAGGGTTTGTCTAGGGTA 58.575 38.462 0.00 0.00 0.00 3.69
3779 6037 6.269974 AGTATAGAAAGGGTTTGTCTAGGGT 58.730 40.000 0.00 0.00 0.00 4.34
3780 6038 6.183360 GGAGTATAGAAAGGGTTTGTCTAGGG 60.183 46.154 0.00 0.00 0.00 3.53
3781 6039 6.183360 GGGAGTATAGAAAGGGTTTGTCTAGG 60.183 46.154 0.00 0.00 0.00 3.02
3782 6040 6.612049 AGGGAGTATAGAAAGGGTTTGTCTAG 59.388 42.308 0.00 0.00 0.00 2.43
3783 6041 6.509386 AGGGAGTATAGAAAGGGTTTGTCTA 58.491 40.000 0.00 0.00 0.00 2.59
3784 6042 5.351405 AGGGAGTATAGAAAGGGTTTGTCT 58.649 41.667 0.00 0.00 0.00 3.41
3785 6043 5.396548 GGAGGGAGTATAGAAAGGGTTTGTC 60.397 48.000 0.00 0.00 0.00 3.18
3786 6044 4.473922 GGAGGGAGTATAGAAAGGGTTTGT 59.526 45.833 0.00 0.00 0.00 2.83
3787 6045 4.443034 CGGAGGGAGTATAGAAAGGGTTTG 60.443 50.000 0.00 0.00 0.00 2.93
3788 6046 3.710165 CGGAGGGAGTATAGAAAGGGTTT 59.290 47.826 0.00 0.00 0.00 3.27
3789 6047 3.306613 CGGAGGGAGTATAGAAAGGGTT 58.693 50.000 0.00 0.00 0.00 4.11
3790 6048 2.246849 ACGGAGGGAGTATAGAAAGGGT 59.753 50.000 0.00 0.00 0.00 4.34
3791 6049 2.960163 ACGGAGGGAGTATAGAAAGGG 58.040 52.381 0.00 0.00 0.00 3.95
3792 6050 3.321396 GGAACGGAGGGAGTATAGAAAGG 59.679 52.174 0.00 0.00 0.00 3.11
3793 6051 3.958798 TGGAACGGAGGGAGTATAGAAAG 59.041 47.826 0.00 0.00 0.00 2.62
3794 6052 3.985127 TGGAACGGAGGGAGTATAGAAA 58.015 45.455 0.00 0.00 0.00 2.52
3795 6053 3.675348 TGGAACGGAGGGAGTATAGAA 57.325 47.619 0.00 0.00 0.00 2.10
3796 6054 3.897657 ATGGAACGGAGGGAGTATAGA 57.102 47.619 0.00 0.00 0.00 1.98
3797 6055 5.480772 ACATTATGGAACGGAGGGAGTATAG 59.519 44.000 0.00 0.00 0.00 1.31
3798 6056 5.399991 ACATTATGGAACGGAGGGAGTATA 58.600 41.667 0.00 0.00 0.00 1.47
3799 6057 4.232091 ACATTATGGAACGGAGGGAGTAT 58.768 43.478 0.00 0.00 0.00 2.12
3800 6058 3.649843 ACATTATGGAACGGAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
3801 6059 2.478292 ACATTATGGAACGGAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
3802 6060 3.641906 ACTACATTATGGAACGGAGGGAG 59.358 47.826 0.00 0.00 0.00 4.30
3803 6061 3.386726 CACTACATTATGGAACGGAGGGA 59.613 47.826 0.00 0.00 0.00 4.20
3804 6062 3.728845 CACTACATTATGGAACGGAGGG 58.271 50.000 0.00 0.00 0.00 4.30
3805 6063 3.131396 GCACTACATTATGGAACGGAGG 58.869 50.000 0.00 0.00 0.00 4.30
3806 6064 3.792401 TGCACTACATTATGGAACGGAG 58.208 45.455 0.00 0.00 0.00 4.63
3807 6065 3.897141 TGCACTACATTATGGAACGGA 57.103 42.857 0.00 0.00 0.00 4.69
3808 6066 7.097192 ACTATATGCACTACATTATGGAACGG 58.903 38.462 0.00 0.00 40.38 4.44
3809 6067 8.534333 AACTATATGCACTACATTATGGAACG 57.466 34.615 0.00 0.00 40.38 3.95
3844 6102 9.337091 CGGTCAAAATTTATAATGTTCGACTTT 57.663 29.630 0.00 0.00 0.00 2.66
3845 6103 8.508875 ACGGTCAAAATTTATAATGTTCGACTT 58.491 29.630 0.00 0.00 0.00 3.01
3846 6104 8.036273 ACGGTCAAAATTTATAATGTTCGACT 57.964 30.769 0.00 0.00 0.00 4.18
3847 6105 8.663771 AACGGTCAAAATTTATAATGTTCGAC 57.336 30.769 0.00 0.00 0.00 4.20
3863 6121 9.729281 ACCTATTTTTCTCTATAAACGGTCAAA 57.271 29.630 0.00 0.00 0.00 2.69
3865 6123 9.807649 GTACCTATTTTTCTCTATAAACGGTCA 57.192 33.333 0.00 0.00 0.00 4.02
3866 6124 9.807649 TGTACCTATTTTTCTCTATAAACGGTC 57.192 33.333 0.00 0.00 0.00 4.79
3884 6142 9.769677 TGCATTAGGTATTCTAGATGTACCTAT 57.230 33.333 28.09 20.44 45.55 2.57
3885 6143 9.021807 GTGCATTAGGTATTCTAGATGTACCTA 57.978 37.037 25.95 25.95 44.76 3.08
3887 6145 7.667557 TGTGCATTAGGTATTCTAGATGTACC 58.332 38.462 19.81 19.81 38.49 3.34
3888 6146 9.360093 GATGTGCATTAGGTATTCTAGATGTAC 57.640 37.037 0.00 0.27 35.46 2.90
3889 6147 9.088987 TGATGTGCATTAGGTATTCTAGATGTA 57.911 33.333 0.00 0.00 0.00 2.29
3890 6148 7.966812 TGATGTGCATTAGGTATTCTAGATGT 58.033 34.615 0.00 0.00 0.00 3.06
3891 6149 9.445878 AATGATGTGCATTAGGTATTCTAGATG 57.554 33.333 0.00 0.00 45.16 2.90
3892 6150 9.445878 CAATGATGTGCATTAGGTATTCTAGAT 57.554 33.333 0.00 0.00 45.23 1.98
3893 6151 7.879677 CCAATGATGTGCATTAGGTATTCTAGA 59.120 37.037 0.00 0.00 45.23 2.43
3894 6152 7.879677 TCCAATGATGTGCATTAGGTATTCTAG 59.120 37.037 0.00 0.00 45.23 2.43
3895 6153 7.744733 TCCAATGATGTGCATTAGGTATTCTA 58.255 34.615 0.00 0.00 45.23 2.10
3896 6154 6.604171 TCCAATGATGTGCATTAGGTATTCT 58.396 36.000 0.00 0.00 45.23 2.40
3897 6155 6.882610 TCCAATGATGTGCATTAGGTATTC 57.117 37.500 0.00 0.00 45.23 1.75
3898 6156 7.944000 TGTATCCAATGATGTGCATTAGGTATT 59.056 33.333 0.00 0.00 45.23 1.89
3899 6157 7.460910 TGTATCCAATGATGTGCATTAGGTAT 58.539 34.615 0.00 0.00 45.23 2.73
3900 6158 6.836242 TGTATCCAATGATGTGCATTAGGTA 58.164 36.000 0.00 0.00 45.23 3.08
3901 6159 5.693961 TGTATCCAATGATGTGCATTAGGT 58.306 37.500 0.00 0.00 45.23 3.08
3902 6160 6.431852 TGATGTATCCAATGATGTGCATTAGG 59.568 38.462 0.00 0.00 45.23 2.69
3903 6161 7.443259 TGATGTATCCAATGATGTGCATTAG 57.557 36.000 0.00 0.00 45.23 1.73
3904 6162 7.666388 TCATGATGTATCCAATGATGTGCATTA 59.334 33.333 0.00 0.00 45.23 1.90
3906 6164 6.007703 TCATGATGTATCCAATGATGTGCAT 58.992 36.000 0.00 0.00 39.43 3.96
3907 6165 5.378332 TCATGATGTATCCAATGATGTGCA 58.622 37.500 0.00 0.00 32.18 4.57
3908 6166 5.472478 ACTCATGATGTATCCAATGATGTGC 59.528 40.000 0.00 0.00 32.18 4.57
3909 6167 7.506328 AACTCATGATGTATCCAATGATGTG 57.494 36.000 0.00 0.00 32.18 3.21
3910 6168 9.227777 CATAACTCATGATGTATCCAATGATGT 57.772 33.333 0.00 0.00 36.69 3.06
3911 6169 9.227777 ACATAACTCATGATGTATCCAATGATG 57.772 33.333 0.00 0.00 38.10 3.07
3912 6170 9.803507 AACATAACTCATGATGTATCCAATGAT 57.196 29.630 0.00 0.00 38.10 2.45
3913 6171 9.631257 AAACATAACTCATGATGTATCCAATGA 57.369 29.630 0.00 0.00 38.10 2.57
3916 6174 9.460019 TGAAAACATAACTCATGATGTATCCAA 57.540 29.630 0.00 0.00 38.10 3.53
3917 6175 9.631257 ATGAAAACATAACTCATGATGTATCCA 57.369 29.630 0.00 0.00 38.10 3.41
3928 6186 9.210329 ACACGTACATTATGAAAACATAACTCA 57.790 29.630 0.00 0.00 30.81 3.41
3929 6187 9.685005 GACACGTACATTATGAAAACATAACTC 57.315 33.333 0.00 0.00 30.81 3.01
3930 6188 9.431887 AGACACGTACATTATGAAAACATAACT 57.568 29.630 0.00 0.00 30.81 2.24
3931 6189 9.472995 CAGACACGTACATTATGAAAACATAAC 57.527 33.333 0.00 0.00 30.81 1.89
3932 6190 8.661257 CCAGACACGTACATTATGAAAACATAA 58.339 33.333 0.00 0.00 0.00 1.90
3933 6191 7.820386 ACCAGACACGTACATTATGAAAACATA 59.180 33.333 0.00 0.00 0.00 2.29
3934 6192 6.653320 ACCAGACACGTACATTATGAAAACAT 59.347 34.615 0.00 0.00 0.00 2.71
3935 6193 5.992829 ACCAGACACGTACATTATGAAAACA 59.007 36.000 0.00 0.00 0.00 2.83
3936 6194 6.476243 ACCAGACACGTACATTATGAAAAC 57.524 37.500 0.00 0.00 0.00 2.43
3937 6195 7.329962 CACTACCAGACACGTACATTATGAAAA 59.670 37.037 0.00 0.00 0.00 2.29
3938 6196 6.809689 CACTACCAGACACGTACATTATGAAA 59.190 38.462 0.00 0.00 0.00 2.69
3939 6197 6.071784 ACACTACCAGACACGTACATTATGAA 60.072 38.462 0.00 0.00 0.00 2.57
3940 6198 5.416639 ACACTACCAGACACGTACATTATGA 59.583 40.000 0.00 0.00 0.00 2.15
3941 6199 5.647589 ACACTACCAGACACGTACATTATG 58.352 41.667 0.00 0.00 0.00 1.90
3942 6200 5.909621 ACACTACCAGACACGTACATTAT 57.090 39.130 0.00 0.00 0.00 1.28
3943 6201 6.172630 TCTACACTACCAGACACGTACATTA 58.827 40.000 0.00 0.00 0.00 1.90
3944 6202 5.005740 TCTACACTACCAGACACGTACATT 58.994 41.667 0.00 0.00 0.00 2.71
3945 6203 4.582869 TCTACACTACCAGACACGTACAT 58.417 43.478 0.00 0.00 0.00 2.29
3946 6204 4.006780 TCTACACTACCAGACACGTACA 57.993 45.455 0.00 0.00 0.00 2.90
3947 6205 4.394300 ACATCTACACTACCAGACACGTAC 59.606 45.833 0.00 0.00 0.00 3.67
3948 6206 4.582869 ACATCTACACTACCAGACACGTA 58.417 43.478 0.00 0.00 0.00 3.57
3949 6207 3.418995 ACATCTACACTACCAGACACGT 58.581 45.455 0.00 0.00 0.00 4.49
3950 6208 4.874396 TCTACATCTACACTACCAGACACG 59.126 45.833 0.00 0.00 0.00 4.49
3951 6209 5.646793 TGTCTACATCTACACTACCAGACAC 59.353 44.000 0.00 0.00 36.99 3.67
3952 6210 5.812286 TGTCTACATCTACACTACCAGACA 58.188 41.667 0.00 0.00 38.95 3.41
3953 6211 6.945938 ATGTCTACATCTACACTACCAGAC 57.054 41.667 0.00 0.00 33.43 3.51
3954 6212 7.956328 AAATGTCTACATCTACACTACCAGA 57.044 36.000 0.00 0.00 35.10 3.86
3955 6213 9.088512 GAAAAATGTCTACATCTACACTACCAG 57.911 37.037 0.00 0.00 35.10 4.00
3956 6214 8.812972 AGAAAAATGTCTACATCTACACTACCA 58.187 33.333 0.00 0.00 35.10 3.25
3957 6215 9.303537 GAGAAAAATGTCTACATCTACACTACC 57.696 37.037 0.00 0.00 35.10 3.18
3990 6248 5.754406 TCAAAATGTGCCAACTTTGATCAAG 59.246 36.000 8.41 5.87 33.90 3.02
3991 6249 5.523188 GTCAAAATGTGCCAACTTTGATCAA 59.477 36.000 3.38 3.38 39.32 2.57
3992 6250 5.049167 GTCAAAATGTGCCAACTTTGATCA 58.951 37.500 13.67 0.00 39.32 2.92
3993 6251 5.291971 AGTCAAAATGTGCCAACTTTGATC 58.708 37.500 13.67 0.00 39.32 2.92
3994 6252 5.280654 AGTCAAAATGTGCCAACTTTGAT 57.719 34.783 13.67 6.10 39.32 2.57
3995 6253 4.734398 AGTCAAAATGTGCCAACTTTGA 57.266 36.364 9.64 9.64 35.88 2.69
3996 6254 6.900568 TTAAGTCAAAATGTGCCAACTTTG 57.099 33.333 0.00 0.00 0.00 2.77
3997 6255 7.913674 TTTTAAGTCAAAATGTGCCAACTTT 57.086 28.000 0.00 0.00 31.05 2.66
3998 6256 7.913674 TTTTTAAGTCAAAATGTGCCAACTT 57.086 28.000 0.00 0.00 36.04 2.66
4025 6283 9.842775 CCATTCCACAATATAGTGCATATAGAT 57.157 33.333 0.00 0.00 38.18 1.98
4026 6284 9.045745 TCCATTCCACAATATAGTGCATATAGA 57.954 33.333 0.00 0.00 38.18 1.98
4027 6285 9.671279 TTCCATTCCACAATATAGTGCATATAG 57.329 33.333 0.00 0.00 38.18 1.31
4028 6286 9.671279 CTTCCATTCCACAATATAGTGCATATA 57.329 33.333 0.00 0.00 38.18 0.86
4029 6287 7.613022 CCTTCCATTCCACAATATAGTGCATAT 59.387 37.037 0.00 0.00 38.18 1.78
4030 6288 6.942005 CCTTCCATTCCACAATATAGTGCATA 59.058 38.462 0.00 0.00 38.18 3.14
4031 6289 5.771666 CCTTCCATTCCACAATATAGTGCAT 59.228 40.000 0.00 0.00 38.18 3.96
4032 6290 5.104151 TCCTTCCATTCCACAATATAGTGCA 60.104 40.000 0.00 0.00 38.18 4.57
4033 6291 5.376625 TCCTTCCATTCCACAATATAGTGC 58.623 41.667 0.00 0.00 38.18 4.40
4034 6292 6.595682 ACTCCTTCCATTCCACAATATAGTG 58.404 40.000 0.00 0.00 39.21 2.74
4035 6293 6.831664 ACTCCTTCCATTCCACAATATAGT 57.168 37.500 0.00 0.00 0.00 2.12
4090 6348 6.751514 TGAAATAAAGTGCGATGGTGTTAT 57.248 33.333 0.00 0.00 0.00 1.89
4091 6349 6.751514 ATGAAATAAAGTGCGATGGTGTTA 57.248 33.333 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.