Multiple sequence alignment - TraesCS6A01G242400

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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 TraesCS6A01G242400 chr6A 100.000 4368 0 0 1 4368 454090478 454094845 0.000000e+00 8067.0
1 TraesCS6A01G242400 chr6B 95.136 3125 115 10 845 3950 508537974 508534868 0.000000e+00 4894.0
2 TraesCS6A01G242400 chr6B 78.058 515 91 13 206 713 230661948 230662447 5.490000e-79 305.0
3 TraesCS6A01G242400 chr6B 94.286 175 10 0 3941 4115 11193177 11193003 7.200000e-68 268.0
4 TraesCS6A01G242400 chr6B 92.063 63 5 0 22 84 508538109 508538047 6.020000e-14 89.8
5 TraesCS6A01G242400 chr6D 94.133 1943 75 20 3 1941 316228184 316230091 0.000000e+00 2920.0
6 TraesCS6A01G242400 chr6D 94.766 1834 70 10 1940 3770 316230428 316232238 0.000000e+00 2832.0
7 TraesCS6A01G242400 chr6D 95.556 180 7 1 3771 3950 316232527 316232705 1.990000e-73 287.0
8 TraesCS6A01G242400 chr4D 93.654 520 23 1 2359 2878 354990611 354991120 0.000000e+00 769.0
9 TraesCS6A01G242400 chr4D 95.266 169 8 0 3951 4119 477898795 477898963 7.200000e-68 268.0
10 TraesCS6A01G242400 chr4D 93.296 179 10 2 3945 4121 69494134 69494312 3.350000e-66 263.0
11 TraesCS6A01G242400 chr3B 85.880 602 78 5 88 686 564201031 564200434 6.160000e-178 634.0
12 TraesCS6A01G242400 chr2A 86.911 573 64 9 88 654 527378415 527377848 2.220000e-177 632.0
13 TraesCS6A01G242400 chr2A 86.387 573 66 8 88 654 754348121 754347555 2.230000e-172 616.0
14 TraesCS6A01G242400 chr5D 85.911 582 62 14 78 654 543615691 543615125 1.740000e-168 603.0
15 TraesCS6A01G242400 chr5D 84.245 603 83 7 88 686 400417446 400416852 1.050000e-160 577.0
16 TraesCS6A01G242400 chr3D 85.464 571 70 8 88 654 460450870 460450309 2.260000e-162 582.0
17 TraesCS6A01G242400 chr3D 85.289 571 70 9 88 654 460452034 460451474 1.050000e-160 577.0
18 TraesCS6A01G242400 chr7D 85.095 577 72 8 81 654 579329659 579330224 1.050000e-160 577.0
19 TraesCS6A01G242400 chr7B 94.886 176 8 1 3942 4116 92046032 92045857 1.550000e-69 274.0
20 TraesCS6A01G242400 chr7B 83.146 89 12 3 514 601 619168651 619168565 1.300000e-10 78.7
21 TraesCS6A01G242400 chr1D 95.808 167 7 0 3950 4116 206955702 206955536 2.000000e-68 270.0
22 TraesCS6A01G242400 chr1D 75.896 502 96 16 190 684 487903870 487904353 2.630000e-57 233.0
23 TraesCS6A01G242400 chr4A 92.553 188 12 2 3951 4137 18115555 18115369 7.200000e-68 268.0
24 TraesCS6A01G242400 chr2D 94.253 174 10 0 3943 4116 89441274 89441447 2.590000e-67 267.0
25 TraesCS6A01G242400 chr4B 91.534 189 12 4 3950 4135 71600623 71600810 1.560000e-64 257.0
26 TraesCS6A01G242400 chr1B 90.576 191 15 3 3926 4115 480970190 480970378 2.610000e-62 250.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G242400 chr6A 454090478 454094845 4367 False 8067.0 8067 100.000000 1 4368 1 chr6A.!!$F1 4367
1 TraesCS6A01G242400 chr6B 508534868 508538109 3241 True 2491.9 4894 93.599500 22 3950 2 chr6B.!!$R2 3928
2 TraesCS6A01G242400 chr6D 316228184 316232705 4521 False 2013.0 2920 94.818333 3 3950 3 chr6D.!!$F1 3947
3 TraesCS6A01G242400 chr4D 354990611 354991120 509 False 769.0 769 93.654000 2359 2878 1 chr4D.!!$F2 519
4 TraesCS6A01G242400 chr3B 564200434 564201031 597 True 634.0 634 85.880000 88 686 1 chr3B.!!$R1 598
5 TraesCS6A01G242400 chr2A 527377848 527378415 567 True 632.0 632 86.911000 88 654 1 chr2A.!!$R1 566
6 TraesCS6A01G242400 chr2A 754347555 754348121 566 True 616.0 616 86.387000 88 654 1 chr2A.!!$R2 566
7 TraesCS6A01G242400 chr5D 543615125 543615691 566 True 603.0 603 85.911000 78 654 1 chr5D.!!$R2 576
8 TraesCS6A01G242400 chr5D 400416852 400417446 594 True 577.0 577 84.245000 88 686 1 chr5D.!!$R1 598
9 TraesCS6A01G242400 chr3D 460450309 460452034 1725 True 579.5 582 85.376500 88 654 2 chr3D.!!$R1 566
10 TraesCS6A01G242400 chr7D 579329659 579330224 565 False 577.0 577 85.095000 81 654 1 chr7D.!!$F1 573

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
748 1931 0.178767 CTCATCCAATGACGCAGGGA 59.821 55.000 0.00 5.82 35.06 4.20 F
837 2021 0.611714 TACCCGGAGCAAAGAGAACC 59.388 55.000 0.73 0.00 0.00 3.62 F
840 2024 0.674895 CCGGAGCAAAGAGAACCTGG 60.675 60.000 0.00 0.00 0.00 4.45 F
2002 3549 0.822164 AATTGCCATCTTCCAGCTGC 59.178 50.000 8.66 0.00 0.00 5.25 F
2621 4171 1.689813 TCCACTCTTACGTGCCTTTGA 59.310 47.619 0.00 0.00 33.60 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 4161 2.672961 TCAGTATCCTCAAAGGCACG 57.327 50.000 0.00 0.0 34.61 5.34 R
2749 4300 1.273327 CCCAGCAAGAATTCCACCAAC 59.727 52.381 0.65 0.0 0.00 3.77 R
2949 4500 0.463620 GAGTCCCCAGATCAGCAGAC 59.536 60.000 0.00 0.0 0.00 3.51 R
3202 4753 0.445043 GTTCCATTCGGCGTGTTACC 59.555 55.000 6.85 0.0 0.00 2.85 R
3993 5841 2.068519 TGCTTCGTATGCAGTCACTTG 58.931 47.619 0.00 0.0 35.31 3.16 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
120 121 2.125310 CAGCCGGCGGATAACACA 60.125 61.111 33.44 0.00 0.00 3.72
132 133 2.157668 GGATAACACACACTGCGTCAAG 59.842 50.000 0.00 0.00 0.00 3.02
148 149 3.742327 CGTCAAGCACCTCATATGTCCAT 60.742 47.826 1.90 0.00 0.00 3.41
298 299 1.894756 CTAGACTCCCCTCTCGCCG 60.895 68.421 0.00 0.00 0.00 6.46
316 317 3.608662 TCCGTCGTTGCTCCGGTT 61.609 61.111 0.00 0.00 42.30 4.44
323 324 2.361104 TTGCTCCGGTTGGGATGC 60.361 61.111 0.00 0.00 46.04 3.91
364 367 1.061857 CAACGGGTTTGTTGCAAAAGC 59.938 47.619 0.00 2.18 42.34 3.51
415 424 1.002900 CTTGATTCACACCGCAAACGT 60.003 47.619 0.00 0.00 37.70 3.99
417 426 0.450482 GATTCACACCGCAAACGTCG 60.450 55.000 0.00 0.00 37.70 5.12
473 1653 1.068333 CCATGTTGCAAAAGTCCTCCG 60.068 52.381 0.00 0.00 0.00 4.63
556 1737 5.888161 CCACTATTATTGCAAAAGTCCTCCT 59.112 40.000 1.71 0.00 0.00 3.69
628 1811 4.273969 TCTGACAAAAATAACGCTTCGGTT 59.726 37.500 0.00 0.00 0.00 4.44
664 1847 5.631026 AGTAATTGTTGCAATGCGAGTTAG 58.369 37.500 0.59 0.00 0.00 2.34
709 1892 2.235650 TCAGAGGCACCTCATTTGAGAG 59.764 50.000 18.67 2.91 44.74 3.20
710 1893 2.235650 CAGAGGCACCTCATTTGAGAGA 59.764 50.000 18.67 0.00 44.74 3.10
711 1894 3.113824 AGAGGCACCTCATTTGAGAGAT 58.886 45.455 18.67 0.00 44.74 2.75
713 1896 3.113824 AGGCACCTCATTTGAGAGATCT 58.886 45.455 9.15 0.00 44.74 2.75
714 1897 3.522750 AGGCACCTCATTTGAGAGATCTT 59.477 43.478 9.15 0.00 44.74 2.40
716 1899 3.065095 GCACCTCATTTGAGAGATCTTGC 59.935 47.826 9.15 0.00 44.74 4.01
717 1900 3.309138 CACCTCATTTGAGAGATCTTGCG 59.691 47.826 9.15 0.00 44.74 4.85
719 1902 3.555139 CCTCATTTGAGAGATCTTGCGTC 59.445 47.826 9.15 0.00 44.74 5.19
720 1903 3.525537 TCATTTGAGAGATCTTGCGTCC 58.474 45.455 0.00 0.00 0.00 4.79
727 1910 4.342092 TGAGAGATCTTGCGTCCATTCATA 59.658 41.667 0.00 0.00 0.00 2.15
747 1930 1.442526 GCTCATCCAATGACGCAGGG 61.443 60.000 6.54 0.00 35.19 4.45
748 1931 0.178767 CTCATCCAATGACGCAGGGA 59.821 55.000 0.00 5.82 35.06 4.20
784 1967 3.323751 ACGTAGCGTGACCCTATTTTT 57.676 42.857 0.00 0.00 39.18 1.94
837 2021 0.611714 TACCCGGAGCAAAGAGAACC 59.388 55.000 0.73 0.00 0.00 3.62
840 2024 0.674895 CCGGAGCAAAGAGAACCTGG 60.675 60.000 0.00 0.00 0.00 4.45
1421 2621 4.154347 CTCCCTGCACTCCCTCGC 62.154 72.222 0.00 0.00 0.00 5.03
1632 2832 1.599797 CTGGTCGTTTGTGGTCCCC 60.600 63.158 0.00 0.00 0.00 4.81
1922 3131 4.612264 TCTACTTGACCCAAACTGGTAC 57.388 45.455 0.00 0.00 39.24 3.34
1941 3150 2.617274 GCCCACCTGTTGCGACTTC 61.617 63.158 5.50 0.00 0.00 3.01
1977 3524 6.649436 CGATGCACGTTATGACATTAGATTT 58.351 36.000 0.00 0.00 37.22 2.17
2002 3549 0.822164 AATTGCCATCTTCCAGCTGC 59.178 50.000 8.66 0.00 0.00 5.25
2049 3596 9.712305 ATTAACAGTGCATCTATATCCTGTTAC 57.288 33.333 17.09 0.00 42.08 2.50
2088 3635 7.933577 TCAGAATTGACTTTGATGTAGTTGACT 59.066 33.333 0.00 0.00 0.00 3.41
2092 3639 9.725019 AATTGACTTTGATGTAGTTGACTATGA 57.275 29.630 0.00 0.00 0.00 2.15
2093 3640 8.763049 TTGACTTTGATGTAGTTGACTATGAG 57.237 34.615 0.00 0.00 0.00 2.90
2557 4107 6.291377 TCTAACTGCCTTCTTATATTGCTGG 58.709 40.000 0.00 0.00 0.00 4.85
2589 4139 4.764172 AGGCTGCAACTTTAGTAGATCTG 58.236 43.478 5.18 0.00 0.00 2.90
2611 4161 8.410673 TCTGTCCTATATTCATCCACTCTTAC 57.589 38.462 0.00 0.00 0.00 2.34
2621 4171 1.689813 TCCACTCTTACGTGCCTTTGA 59.310 47.619 0.00 0.00 33.60 2.69
2626 4176 3.767673 ACTCTTACGTGCCTTTGAGGATA 59.232 43.478 0.00 0.00 37.67 2.59
2675 4226 9.322773 GTTCTACTTACGCCCTTTTATATTTCT 57.677 33.333 0.00 0.00 0.00 2.52
2728 4279 4.926238 CGGATGCTGGTTATCTATCAGTTC 59.074 45.833 0.00 0.00 0.00 3.01
2749 4300 3.315470 TCTGTTCGATGTAGGAGGAATCG 59.685 47.826 0.00 0.00 43.47 3.34
2949 4500 3.069289 TGCTCTGATAACAACTGCAGTG 58.931 45.455 22.49 16.62 0.00 3.66
3104 4655 3.012518 CTGGATGGGATTCAGTGTTCAC 58.987 50.000 0.00 0.00 0.00 3.18
3105 4656 2.009774 GGATGGGATTCAGTGTTCACG 58.990 52.381 0.00 0.00 0.00 4.35
3172 4723 5.353678 GGTCTTGTGAAATCAGAGATTCAGG 59.646 44.000 2.40 0.00 36.31 3.86
3202 4753 2.393271 AAACTGGAGGAATCGCTCAG 57.607 50.000 0.00 0.00 0.00 3.35
3512 5071 5.904941 AGATAGCATCTGTTGTCTTCTCTG 58.095 41.667 0.00 0.00 38.44 3.35
3533 5092 8.661345 TCTCTGTGTCACAGGATAGTATAGTAT 58.339 37.037 28.47 0.00 45.94 2.12
3534 5093 9.945904 CTCTGTGTCACAGGATAGTATAGTATA 57.054 37.037 28.47 7.03 45.94 1.47
3564 5123 7.987458 ACCTCCTGTAACATCTTGTAATGTATG 59.013 37.037 0.00 0.00 38.92 2.39
3617 5176 8.713737 TCATAGATGAACATGAAAGAGTCAAG 57.286 34.615 0.00 0.00 35.09 3.02
3664 5224 3.119531 TGAACTCTGGCCATTTTTATGCG 60.120 43.478 5.51 0.00 0.00 4.73
3751 5311 6.985645 ACTTTGAATCAGCATCAGTATCTCTC 59.014 38.462 0.00 0.00 0.00 3.20
3756 5316 7.710044 TGAATCAGCATCAGTATCTCTCTTTTC 59.290 37.037 0.00 0.00 0.00 2.29
3766 5326 7.174426 TCAGTATCTCTCTTTTCGTGTGAAGTA 59.826 37.037 0.00 0.00 35.06 2.24
3835 5683 4.941263 TGCGCTCTTATTTCTGTGGTAAAT 59.059 37.500 9.73 0.00 0.00 1.40
3840 5688 9.256477 CGCTCTTATTTCTGTGGTAAATACATA 57.744 33.333 0.00 0.00 30.52 2.29
3955 5803 6.981722 TGAGCTTTCCTTTTTCAAATACTCC 58.018 36.000 0.00 0.00 0.00 3.85
3956 5804 6.015434 TGAGCTTTCCTTTTTCAAATACTCCC 60.015 38.462 0.00 0.00 0.00 4.30
3957 5805 6.077993 AGCTTTCCTTTTTCAAATACTCCCT 58.922 36.000 0.00 0.00 0.00 4.20
3958 5806 6.209589 AGCTTTCCTTTTTCAAATACTCCCTC 59.790 38.462 0.00 0.00 0.00 4.30
3959 5807 6.572509 GCTTTCCTTTTTCAAATACTCCCTCC 60.573 42.308 0.00 0.00 0.00 4.30
3960 5808 4.585879 TCCTTTTTCAAATACTCCCTCCG 58.414 43.478 0.00 0.00 0.00 4.63
3961 5809 4.042435 TCCTTTTTCAAATACTCCCTCCGT 59.958 41.667 0.00 0.00 0.00 4.69
3962 5810 4.765339 CCTTTTTCAAATACTCCCTCCGTT 59.235 41.667 0.00 0.00 0.00 4.44
3963 5811 5.106277 CCTTTTTCAAATACTCCCTCCGTTC 60.106 44.000 0.00 0.00 0.00 3.95
3964 5812 3.622166 TTCAAATACTCCCTCCGTTCC 57.378 47.619 0.00 0.00 0.00 3.62
3965 5813 2.829023 TCAAATACTCCCTCCGTTCCT 58.171 47.619 0.00 0.00 0.00 3.36
3966 5814 3.985127 TCAAATACTCCCTCCGTTCCTA 58.015 45.455 0.00 0.00 0.00 2.94
3967 5815 4.355549 TCAAATACTCCCTCCGTTCCTAA 58.644 43.478 0.00 0.00 0.00 2.69
3968 5816 4.778958 TCAAATACTCCCTCCGTTCCTAAA 59.221 41.667 0.00 0.00 0.00 1.85
3969 5817 5.427481 TCAAATACTCCCTCCGTTCCTAAAT 59.573 40.000 0.00 0.00 0.00 1.40
3970 5818 6.612456 TCAAATACTCCCTCCGTTCCTAAATA 59.388 38.462 0.00 0.00 0.00 1.40
3971 5819 7.291651 TCAAATACTCCCTCCGTTCCTAAATAT 59.708 37.037 0.00 0.00 0.00 1.28
3972 5820 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
3973 5821 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3974 5822 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3975 5823 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3976 5824 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3977 5825 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3978 5826 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3979 5827 6.260271 CCCTCCGTTCCTAAATATTTGTCTTC 59.740 42.308 11.05 0.00 0.00 2.87
3980 5828 6.260271 CCTCCGTTCCTAAATATTTGTCTTCC 59.740 42.308 11.05 0.00 0.00 3.46
3981 5829 6.954232 TCCGTTCCTAAATATTTGTCTTCCT 58.046 36.000 11.05 0.00 0.00 3.36
3982 5830 8.081517 TCCGTTCCTAAATATTTGTCTTCCTA 57.918 34.615 11.05 0.00 0.00 2.94
3983 5831 8.202137 TCCGTTCCTAAATATTTGTCTTCCTAG 58.798 37.037 11.05 0.00 0.00 3.02
3984 5832 8.202137 CCGTTCCTAAATATTTGTCTTCCTAGA 58.798 37.037 11.05 0.00 0.00 2.43
3985 5833 9.250624 CGTTCCTAAATATTTGTCTTCCTAGAG 57.749 37.037 11.05 0.00 0.00 2.43
3995 5843 8.924511 ATTTGTCTTCCTAGAGATTTCAACAA 57.075 30.769 0.00 0.00 0.00 2.83
3996 5844 7.969536 TTGTCTTCCTAGAGATTTCAACAAG 57.030 36.000 0.00 0.00 0.00 3.16
3997 5845 7.067496 TGTCTTCCTAGAGATTTCAACAAGT 57.933 36.000 0.00 0.00 0.00 3.16
3998 5846 6.931281 TGTCTTCCTAGAGATTTCAACAAGTG 59.069 38.462 0.00 0.00 0.00 3.16
3999 5847 7.155328 GTCTTCCTAGAGATTTCAACAAGTGA 58.845 38.462 0.00 0.00 0.00 3.41
4000 5848 7.117092 GTCTTCCTAGAGATTTCAACAAGTGAC 59.883 40.741 0.00 0.00 35.39 3.67
4001 5849 6.672266 TCCTAGAGATTTCAACAAGTGACT 57.328 37.500 0.00 0.00 35.39 3.41
4002 5850 6.459066 TCCTAGAGATTTCAACAAGTGACTG 58.541 40.000 0.00 0.00 35.39 3.51
4003 5851 5.121454 CCTAGAGATTTCAACAAGTGACTGC 59.879 44.000 0.00 0.00 35.39 4.40
4004 5852 4.454678 AGAGATTTCAACAAGTGACTGCA 58.545 39.130 0.00 0.00 35.39 4.41
4005 5853 5.068636 AGAGATTTCAACAAGTGACTGCAT 58.931 37.500 0.00 0.00 35.39 3.96
4006 5854 6.233434 AGAGATTTCAACAAGTGACTGCATA 58.767 36.000 0.00 0.00 35.39 3.14
4007 5855 6.148480 AGAGATTTCAACAAGTGACTGCATAC 59.852 38.462 0.00 0.00 35.39 2.39
4008 5856 4.466567 TTTCAACAAGTGACTGCATACG 57.533 40.909 0.00 0.00 35.39 3.06
4009 5857 3.378911 TCAACAAGTGACTGCATACGA 57.621 42.857 0.00 0.00 0.00 3.43
4010 5858 3.723260 TCAACAAGTGACTGCATACGAA 58.277 40.909 0.00 0.00 0.00 3.85
4011 5859 3.740832 TCAACAAGTGACTGCATACGAAG 59.259 43.478 0.00 0.00 0.00 3.79
4012 5860 2.069273 ACAAGTGACTGCATACGAAGC 58.931 47.619 0.00 0.00 0.00 3.86
4013 5861 2.068519 CAAGTGACTGCATACGAAGCA 58.931 47.619 0.00 0.00 40.19 3.91
4014 5862 2.455674 AGTGACTGCATACGAAGCAA 57.544 45.000 0.00 0.00 42.17 3.91
4015 5863 2.766313 AGTGACTGCATACGAAGCAAA 58.234 42.857 0.00 0.00 42.17 3.68
4016 5864 3.138304 AGTGACTGCATACGAAGCAAAA 58.862 40.909 0.00 0.00 42.17 2.44
4017 5865 3.753272 AGTGACTGCATACGAAGCAAAAT 59.247 39.130 0.00 0.00 42.17 1.82
4018 5866 3.848019 GTGACTGCATACGAAGCAAAATG 59.152 43.478 0.00 0.00 42.17 2.32
4019 5867 3.750652 TGACTGCATACGAAGCAAAATGA 59.249 39.130 0.00 0.00 42.17 2.57
4020 5868 4.215185 TGACTGCATACGAAGCAAAATGAA 59.785 37.500 0.00 0.00 42.17 2.57
4021 5869 5.106197 TGACTGCATACGAAGCAAAATGAAT 60.106 36.000 0.00 0.00 42.17 2.57
4022 5870 5.097529 ACTGCATACGAAGCAAAATGAATG 58.902 37.500 0.00 0.00 42.17 2.67
4023 5871 5.106197 ACTGCATACGAAGCAAAATGAATGA 60.106 36.000 0.00 0.00 42.17 2.57
4024 5872 5.707931 TGCATACGAAGCAAAATGAATGAA 58.292 33.333 0.00 0.00 39.39 2.57
4025 5873 6.331845 TGCATACGAAGCAAAATGAATGAAT 58.668 32.000 0.00 0.00 39.39 2.57
4026 5874 6.473131 TGCATACGAAGCAAAATGAATGAATC 59.527 34.615 0.00 0.00 39.39 2.52
4027 5875 6.694411 GCATACGAAGCAAAATGAATGAATCT 59.306 34.615 0.00 0.00 0.00 2.40
4028 5876 7.857389 GCATACGAAGCAAAATGAATGAATCTA 59.143 33.333 0.00 0.00 0.00 1.98
4029 5877 9.888878 CATACGAAGCAAAATGAATGAATCTAT 57.111 29.630 0.00 0.00 0.00 1.98
4032 5880 9.113838 ACGAAGCAAAATGAATGAATCTATACT 57.886 29.630 0.00 0.00 0.00 2.12
4033 5881 9.941664 CGAAGCAAAATGAATGAATCTATACTT 57.058 29.630 0.00 0.00 0.00 2.24
4075 5923 8.687292 ACATCCGTATGTAGTAGTCTATTTGA 57.313 34.615 0.00 0.00 44.66 2.69
4076 5924 9.128404 ACATCCGTATGTAGTAGTCTATTTGAA 57.872 33.333 0.00 0.00 44.66 2.69
4077 5925 9.961265 CATCCGTATGTAGTAGTCTATTTGAAA 57.039 33.333 0.00 0.00 0.00 2.69
4109 5957 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
4110 5958 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4111 5959 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4112 5960 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4113 5961 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
4114 5962 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
4115 5963 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
4116 5964 4.957684 ATTTAGGAACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
4117 5965 3.393426 TTAGGAACGGAGGGAGTATGT 57.607 47.619 0.00 0.00 0.00 2.29
4118 5966 2.249309 AGGAACGGAGGGAGTATGTT 57.751 50.000 0.00 0.00 0.00 2.71
4119 5967 2.547990 AGGAACGGAGGGAGTATGTTT 58.452 47.619 0.00 0.00 0.00 2.83
4120 5968 2.236395 AGGAACGGAGGGAGTATGTTTG 59.764 50.000 0.00 0.00 0.00 2.93
4121 5969 2.235402 GGAACGGAGGGAGTATGTTTGA 59.765 50.000 0.00 0.00 0.00 2.69
4122 5970 3.307199 GGAACGGAGGGAGTATGTTTGAA 60.307 47.826 0.00 0.00 0.00 2.69
4123 5971 3.611766 ACGGAGGGAGTATGTTTGAAG 57.388 47.619 0.00 0.00 0.00 3.02
4124 5972 3.170717 ACGGAGGGAGTATGTTTGAAGA 58.829 45.455 0.00 0.00 0.00 2.87
4125 5973 3.581332 ACGGAGGGAGTATGTTTGAAGAA 59.419 43.478 0.00 0.00 0.00 2.52
4126 5974 3.933332 CGGAGGGAGTATGTTTGAAGAAC 59.067 47.826 0.00 0.00 0.00 3.01
4127 5975 3.933332 GGAGGGAGTATGTTTGAAGAACG 59.067 47.826 0.00 0.00 0.00 3.95
4128 5976 3.335579 AGGGAGTATGTTTGAAGAACGC 58.664 45.455 0.00 0.00 0.00 4.84
4129 5977 3.071479 GGGAGTATGTTTGAAGAACGCA 58.929 45.455 0.00 0.00 0.00 5.24
4130 5978 3.689649 GGGAGTATGTTTGAAGAACGCAT 59.310 43.478 0.00 0.00 0.00 4.73
4131 5979 4.437390 GGGAGTATGTTTGAAGAACGCATG 60.437 45.833 0.00 0.00 0.00 4.06
4132 5980 4.391830 GGAGTATGTTTGAAGAACGCATGA 59.608 41.667 0.00 0.00 0.00 3.07
4133 5981 5.106712 GGAGTATGTTTGAAGAACGCATGAA 60.107 40.000 0.00 0.00 0.00 2.57
4134 5982 6.403636 GGAGTATGTTTGAAGAACGCATGAAT 60.404 38.462 0.00 0.00 0.00 2.57
4135 5983 6.913170 AGTATGTTTGAAGAACGCATGAATT 58.087 32.000 0.00 0.00 0.00 2.17
4136 5984 7.370383 AGTATGTTTGAAGAACGCATGAATTT 58.630 30.769 0.00 0.00 0.00 1.82
4137 5985 7.867403 AGTATGTTTGAAGAACGCATGAATTTT 59.133 29.630 0.00 0.00 0.00 1.82
4138 5986 6.900568 TGTTTGAAGAACGCATGAATTTTT 57.099 29.167 0.00 0.00 0.00 1.94
4185 6033 9.331282 GGGGTATATATGAATACTTCTTGATGC 57.669 37.037 0.00 0.00 33.62 3.91
4186 6034 9.890629 GGGTATATATGAATACTTCTTGATGCA 57.109 33.333 0.00 0.00 33.62 3.96
4193 6041 7.558161 TGAATACTTCTTGATGCAACATAGG 57.442 36.000 0.00 0.00 0.00 2.57
4194 6042 7.112122 TGAATACTTCTTGATGCAACATAGGT 58.888 34.615 0.00 0.00 0.00 3.08
4195 6043 8.264347 TGAATACTTCTTGATGCAACATAGGTA 58.736 33.333 0.00 1.32 0.00 3.08
4196 6044 9.277783 GAATACTTCTTGATGCAACATAGGTAT 57.722 33.333 0.00 3.57 0.00 2.73
4200 6048 9.632638 ACTTCTTGATGCAACATAGGTATATTT 57.367 29.630 0.00 0.00 0.00 1.40
4201 6049 9.888878 CTTCTTGATGCAACATAGGTATATTTG 57.111 33.333 0.00 0.00 0.00 2.32
4202 6050 8.978874 TCTTGATGCAACATAGGTATATTTGT 57.021 30.769 0.00 0.00 0.00 2.83
4203 6051 9.407380 TCTTGATGCAACATAGGTATATTTGTT 57.593 29.630 0.00 0.00 32.76 2.83
4205 6053 9.800433 TTGATGCAACATAGGTATATTTGTTTG 57.200 29.630 0.00 0.00 30.23 2.93
4206 6054 8.965819 TGATGCAACATAGGTATATTTGTTTGT 58.034 29.630 0.00 0.00 30.23 2.83
4207 6055 9.450807 GATGCAACATAGGTATATTTGTTTGTC 57.549 33.333 0.00 0.00 30.23 3.18
4208 6056 8.574251 TGCAACATAGGTATATTTGTTTGTCT 57.426 30.769 0.00 0.00 30.23 3.41
4209 6057 9.019656 TGCAACATAGGTATATTTGTTTGTCTT 57.980 29.630 0.00 0.00 30.23 3.01
4266 6114 9.605955 TTTGAACATGAGAACATATGTTTTACG 57.394 29.630 21.63 12.06 44.88 3.18
4267 6115 8.541133 TGAACATGAGAACATATGTTTTACGA 57.459 30.769 21.63 5.22 44.88 3.43
4268 6116 9.161629 TGAACATGAGAACATATGTTTTACGAT 57.838 29.630 21.63 7.13 44.88 3.73
4308 6156 8.690203 ATACTAATGGCTTAACAATACATGCA 57.310 30.769 0.00 0.00 0.00 3.96
4309 6157 7.587037 ACTAATGGCTTAACAATACATGCAT 57.413 32.000 0.00 0.00 0.00 3.96
4310 6158 8.010733 ACTAATGGCTTAACAATACATGCATT 57.989 30.769 0.00 0.00 0.00 3.56
4311 6159 8.477256 ACTAATGGCTTAACAATACATGCATTT 58.523 29.630 0.00 0.00 0.00 2.32
4312 6160 9.316730 CTAATGGCTTAACAATACATGCATTTT 57.683 29.630 0.00 0.00 0.00 1.82
4314 6162 9.664332 AATGGCTTAACAATACATGCATTTTAA 57.336 25.926 0.00 0.32 0.00 1.52
4315 6163 9.835389 ATGGCTTAACAATACATGCATTTTAAT 57.165 25.926 0.00 0.00 0.00 1.40
4342 6190 9.893305 AAGTTGATATTTCTCTTTTTACAACGG 57.107 29.630 0.00 0.00 39.58 4.44
4343 6191 9.280174 AGTTGATATTTCTCTTTTTACAACGGA 57.720 29.630 0.00 0.00 39.58 4.69
4344 6192 9.326339 GTTGATATTTCTCTTTTTACAACGGAC 57.674 33.333 0.00 0.00 0.00 4.79
4345 6193 8.610248 TGATATTTCTCTTTTTACAACGGACA 57.390 30.769 0.00 0.00 0.00 4.02
4346 6194 9.058174 TGATATTTCTCTTTTTACAACGGACAA 57.942 29.630 0.00 0.00 0.00 3.18
4347 6195 9.887406 GATATTTCTCTTTTTACAACGGACAAA 57.113 29.630 0.00 0.00 0.00 2.83
4348 6196 7.980742 ATTTCTCTTTTTACAACGGACAAAC 57.019 32.000 0.00 0.00 0.00 2.93
4349 6197 6.497785 TTCTCTTTTTACAACGGACAAACA 57.502 33.333 0.00 0.00 0.00 2.83
4350 6198 6.114221 TCTCTTTTTACAACGGACAAACAG 57.886 37.500 0.00 0.00 0.00 3.16
4351 6199 5.644636 TCTCTTTTTACAACGGACAAACAGT 59.355 36.000 0.00 0.00 0.00 3.55
4352 6200 6.149807 TCTCTTTTTACAACGGACAAACAGTT 59.850 34.615 0.00 0.00 37.38 3.16
4353 6201 6.679843 TCTTTTTACAACGGACAAACAGTTT 58.320 32.000 0.00 0.00 34.95 2.66
4354 6202 6.802834 TCTTTTTACAACGGACAAACAGTTTC 59.197 34.615 0.00 0.00 34.95 2.78
4355 6203 5.883503 TTTACAACGGACAAACAGTTTCT 57.116 34.783 0.00 0.00 34.95 2.52
4356 6204 6.981762 TTTACAACGGACAAACAGTTTCTA 57.018 33.333 0.00 0.00 34.95 2.10
4357 6205 6.592798 TTACAACGGACAAACAGTTTCTAG 57.407 37.500 0.00 0.00 34.95 2.43
4358 6206 4.510571 ACAACGGACAAACAGTTTCTAGT 58.489 39.130 0.00 0.00 34.95 2.57
4359 6207 4.939439 ACAACGGACAAACAGTTTCTAGTT 59.061 37.500 0.00 0.00 34.95 2.24
4360 6208 6.108015 ACAACGGACAAACAGTTTCTAGTTA 58.892 36.000 0.00 0.00 34.95 2.24
4361 6209 6.764560 ACAACGGACAAACAGTTTCTAGTTAT 59.235 34.615 0.00 0.00 34.95 1.89
4362 6210 7.281549 ACAACGGACAAACAGTTTCTAGTTATT 59.718 33.333 0.00 0.00 34.95 1.40
4363 6211 8.767085 CAACGGACAAACAGTTTCTAGTTATTA 58.233 33.333 0.00 0.00 34.95 0.98
4364 6212 8.891671 ACGGACAAACAGTTTCTAGTTATTAA 57.108 30.769 0.00 0.00 0.00 1.40
4365 6213 9.328845 ACGGACAAACAGTTTCTAGTTATTAAA 57.671 29.630 0.00 0.00 0.00 1.52
4366 6214 9.590088 CGGACAAACAGTTTCTAGTTATTAAAC 57.410 33.333 0.00 0.00 35.72 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.672983 GGATACAATCATTCGGATACAACAT 57.327 36.000 0.00 0.00 34.28 2.71
51 52 9.927668 TCAATTTCTTTTCTTTTGTGAGAAAGT 57.072 25.926 0.00 0.00 44.05 2.66
84 85 4.427312 GCTGAACAATAGCATTTTCCCAG 58.573 43.478 0.00 0.00 40.81 4.45
132 133 2.138320 CGTGATGGACATATGAGGTGC 58.862 52.381 10.38 0.00 0.00 5.01
139 140 5.279506 GGATAAGGACACGTGATGGACATAT 60.280 44.000 25.01 10.51 0.00 1.78
148 149 4.583489 GGATAAGAGGATAAGGACACGTGA 59.417 45.833 25.01 0.00 0.00 4.35
276 277 0.181587 CGAGAGGGGAGTCTAGAGCA 59.818 60.000 0.00 0.00 0.00 4.26
364 367 0.469917 ACATAGATGTTGCGGGAGGG 59.530 55.000 0.00 0.00 37.90 4.30
536 1717 7.885922 TGTTGTAGGAGGACTTTTGCAATAATA 59.114 33.333 0.00 0.00 0.00 0.98
540 1721 4.469657 TGTTGTAGGAGGACTTTTGCAAT 58.530 39.130 0.00 0.00 0.00 3.56
602 1784 6.148150 ACCGAAGCGTTATTTTTGTCAGAATA 59.852 34.615 0.00 0.00 0.00 1.75
709 1892 3.397482 AGCTATGAATGGACGCAAGATC 58.603 45.455 0.00 0.00 43.62 2.75
710 1893 3.181462 TGAGCTATGAATGGACGCAAGAT 60.181 43.478 0.00 0.00 43.62 2.40
711 1894 2.168313 TGAGCTATGAATGGACGCAAGA 59.832 45.455 0.00 0.00 43.62 3.02
713 1896 2.689553 TGAGCTATGAATGGACGCAA 57.310 45.000 0.00 0.00 0.00 4.85
714 1897 2.548707 GGATGAGCTATGAATGGACGCA 60.549 50.000 0.00 0.00 0.00 5.24
716 1899 3.391506 TGGATGAGCTATGAATGGACG 57.608 47.619 0.00 0.00 0.00 4.79
717 1900 5.180868 GTCATTGGATGAGCTATGAATGGAC 59.819 44.000 0.00 0.00 40.53 4.02
719 1902 4.153655 CGTCATTGGATGAGCTATGAATGG 59.846 45.833 0.00 0.00 40.53 3.16
720 1903 4.378149 GCGTCATTGGATGAGCTATGAATG 60.378 45.833 0.00 0.00 40.53 2.67
727 1910 0.463295 CCTGCGTCATTGGATGAGCT 60.463 55.000 0.00 0.00 40.53 4.09
764 1947 3.323751 AAAAATAGGGTCACGCTACGT 57.676 42.857 3.22 0.00 42.36 3.57
798 1981 6.693545 CGGGTAATCGCTATATCAATCTTCTC 59.306 42.308 0.00 0.00 0.00 2.87
837 2021 5.962433 TCTTTATACACGGTCTTTCTCCAG 58.038 41.667 0.00 0.00 0.00 3.86
840 2024 6.583806 TCGTTTCTTTATACACGGTCTTTCTC 59.416 38.462 0.00 0.00 33.39 2.87
1977 3524 4.139786 GCTGGAAGATGGCAATTCAGATA 58.860 43.478 15.16 1.68 34.07 1.98
2002 3549 6.808008 AATCATACCAATAAATCTCCTGCG 57.192 37.500 0.00 0.00 0.00 5.18
2088 3635 6.939730 TGCACTGTTAATTCTGAAACCTCATA 59.060 34.615 0.00 0.00 0.00 2.15
2092 3639 6.040842 ACAATGCACTGTTAATTCTGAAACCT 59.959 34.615 0.00 0.00 0.00 3.50
2093 3640 6.215845 ACAATGCACTGTTAATTCTGAAACC 58.784 36.000 0.00 0.00 0.00 3.27
2211 3761 8.514594 ACCATAATGCACATTATTACAGCATAC 58.485 33.333 12.17 0.00 44.40 2.39
2557 4107 4.783764 AAGTTGCAGCCTTTTATGGTAC 57.216 40.909 0.00 0.00 0.00 3.34
2589 4139 7.085116 CACGTAAGAGTGGATGAATATAGGAC 58.915 42.308 0.00 0.00 43.62 3.85
2611 4161 2.672961 TCAGTATCCTCAAAGGCACG 57.327 50.000 0.00 0.00 34.61 5.34
2626 4176 9.687210 GAACCGTAAAAGGATTTAAAATTCAGT 57.313 29.630 0.00 0.00 37.28 3.41
2675 4226 2.940158 TGTACTCGCCTCCAATAGCTA 58.060 47.619 0.00 0.00 0.00 3.32
2728 4279 3.066900 ACGATTCCTCCTACATCGAACAG 59.933 47.826 7.72 0.00 41.96 3.16
2749 4300 1.273327 CCCAGCAAGAATTCCACCAAC 59.727 52.381 0.65 0.00 0.00 3.77
2949 4500 0.463620 GAGTCCCCAGATCAGCAGAC 59.536 60.000 0.00 0.00 0.00 3.51
3061 4612 2.559698 TTTGAGATGAAGCCCGTCAA 57.440 45.000 0.00 0.00 33.19 3.18
3104 4655 5.809464 TCAATGCACAAAGTATAAGCATCG 58.191 37.500 0.00 0.00 44.40 3.84
3105 4656 8.057812 CAATCAATGCACAAAGTATAAGCATC 57.942 34.615 0.00 0.00 44.40 3.91
3172 4723 7.634522 CGATTCCTCCAGTTTTGAATAATCTC 58.365 38.462 0.00 0.00 0.00 2.75
3202 4753 0.445043 GTTCCATTCGGCGTGTTACC 59.555 55.000 6.85 0.00 0.00 2.85
3225 4776 5.312079 AGCTGAGCATCTTTATCATTACCC 58.688 41.667 7.39 0.00 34.92 3.69
3346 4905 4.383226 CCTCAACTACTCCCCTCTAAAAGC 60.383 50.000 0.00 0.00 0.00 3.51
3437 4996 4.353737 CACCAACATATTGAATGCCTTCG 58.646 43.478 0.00 0.00 38.15 3.79
3533 5092 8.598202 TTACAAGATGTTACAGGAGGTGTATA 57.402 34.615 0.00 0.00 41.45 1.47
3534 5093 7.490657 TTACAAGATGTTACAGGAGGTGTAT 57.509 36.000 0.00 0.00 41.45 2.29
3535 5094 6.921486 TTACAAGATGTTACAGGAGGTGTA 57.079 37.500 0.00 0.00 40.94 2.90
3536 5095 5.818678 TTACAAGATGTTACAGGAGGTGT 57.181 39.130 0.00 0.00 43.86 4.16
3537 5096 6.173339 ACATTACAAGATGTTACAGGAGGTG 58.827 40.000 0.00 0.00 36.92 4.00
3538 5097 6.374417 ACATTACAAGATGTTACAGGAGGT 57.626 37.500 0.00 0.00 36.92 3.85
3539 5098 8.204160 TCATACATTACAAGATGTTACAGGAGG 58.796 37.037 0.00 0.00 40.54 4.30
3540 5099 9.599866 TTCATACATTACAAGATGTTACAGGAG 57.400 33.333 0.00 0.00 40.54 3.69
3564 5123 3.637694 GACAGGGGTCCTACAGTAGATTC 59.362 52.174 9.38 0.00 38.12 2.52
3579 5138 3.969976 TCATCTATGAGAAAGGACAGGGG 59.030 47.826 0.00 0.00 32.11 4.79
3756 5316 8.029642 ACCAGAAGAAATAAATACTTCACACG 57.970 34.615 0.00 0.00 41.37 4.49
3950 5798 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3951 5799 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3952 5800 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3953 5801 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3954 5802 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3955 5803 6.260271 GGAAGACAAATATTTAGGAACGGAGG 59.740 42.308 0.00 0.00 0.00 4.30
3956 5804 7.048512 AGGAAGACAAATATTTAGGAACGGAG 58.951 38.462 0.00 0.00 0.00 4.63
3957 5805 6.954232 AGGAAGACAAATATTTAGGAACGGA 58.046 36.000 0.00 0.00 0.00 4.69
3958 5806 8.202137 TCTAGGAAGACAAATATTTAGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
3959 5807 9.250624 CTCTAGGAAGACAAATATTTAGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
3970 5818 8.924511 TTGTTGAAATCTCTAGGAAGACAAAT 57.075 30.769 0.00 0.00 0.00 2.32
3971 5819 7.993183 ACTTGTTGAAATCTCTAGGAAGACAAA 59.007 33.333 0.00 0.00 0.00 2.83
3972 5820 7.442364 CACTTGTTGAAATCTCTAGGAAGACAA 59.558 37.037 0.00 0.00 0.00 3.18
3973 5821 6.931281 CACTTGTTGAAATCTCTAGGAAGACA 59.069 38.462 0.00 0.00 0.00 3.41
3974 5822 7.117092 GTCACTTGTTGAAATCTCTAGGAAGAC 59.883 40.741 0.00 0.00 35.39 3.01
3975 5823 7.015682 AGTCACTTGTTGAAATCTCTAGGAAGA 59.984 37.037 0.00 0.00 35.39 2.87
3976 5824 7.117523 CAGTCACTTGTTGAAATCTCTAGGAAG 59.882 40.741 0.00 0.00 35.39 3.46
3977 5825 6.931281 CAGTCACTTGTTGAAATCTCTAGGAA 59.069 38.462 0.00 0.00 35.39 3.36
3978 5826 6.459066 CAGTCACTTGTTGAAATCTCTAGGA 58.541 40.000 0.00 0.00 35.39 2.94
3979 5827 5.121454 GCAGTCACTTGTTGAAATCTCTAGG 59.879 44.000 0.00 0.00 35.39 3.02
3980 5828 5.698089 TGCAGTCACTTGTTGAAATCTCTAG 59.302 40.000 0.00 0.00 35.39 2.43
3981 5829 5.610398 TGCAGTCACTTGTTGAAATCTCTA 58.390 37.500 0.00 0.00 35.39 2.43
3982 5830 4.454678 TGCAGTCACTTGTTGAAATCTCT 58.545 39.130 0.00 0.00 35.39 3.10
3983 5831 4.818534 TGCAGTCACTTGTTGAAATCTC 57.181 40.909 0.00 0.00 35.39 2.75
3984 5832 5.106948 CGTATGCAGTCACTTGTTGAAATCT 60.107 40.000 0.00 0.00 35.39 2.40
3985 5833 5.082059 CGTATGCAGTCACTTGTTGAAATC 58.918 41.667 0.00 0.00 35.39 2.17
3986 5834 4.754618 TCGTATGCAGTCACTTGTTGAAAT 59.245 37.500 0.00 0.00 35.39 2.17
3987 5835 4.123506 TCGTATGCAGTCACTTGTTGAAA 58.876 39.130 0.00 0.00 35.39 2.69
3988 5836 3.723260 TCGTATGCAGTCACTTGTTGAA 58.277 40.909 0.00 0.00 35.39 2.69
3989 5837 3.378911 TCGTATGCAGTCACTTGTTGA 57.621 42.857 0.00 0.00 0.00 3.18
3990 5838 3.665323 GCTTCGTATGCAGTCACTTGTTG 60.665 47.826 0.00 0.00 0.00 3.33
3991 5839 2.480419 GCTTCGTATGCAGTCACTTGTT 59.520 45.455 0.00 0.00 0.00 2.83
3992 5840 2.069273 GCTTCGTATGCAGTCACTTGT 58.931 47.619 0.00 0.00 0.00 3.16
3993 5841 2.068519 TGCTTCGTATGCAGTCACTTG 58.931 47.619 0.00 0.00 35.31 3.16
3994 5842 2.455674 TGCTTCGTATGCAGTCACTT 57.544 45.000 0.00 0.00 35.31 3.16
3995 5843 2.455674 TTGCTTCGTATGCAGTCACT 57.544 45.000 0.00 0.00 41.71 3.41
3996 5844 3.536158 TTTTGCTTCGTATGCAGTCAC 57.464 42.857 0.00 0.00 41.71 3.67
3997 5845 3.750652 TCATTTTGCTTCGTATGCAGTCA 59.249 39.130 0.00 0.00 41.71 3.41
3998 5846 4.340894 TCATTTTGCTTCGTATGCAGTC 57.659 40.909 0.00 0.00 41.71 3.51
3999 5847 4.764679 TTCATTTTGCTTCGTATGCAGT 57.235 36.364 0.00 0.00 41.71 4.40
4000 5848 5.334319 TCATTCATTTTGCTTCGTATGCAG 58.666 37.500 0.00 0.00 41.71 4.41
4001 5849 5.307926 TCATTCATTTTGCTTCGTATGCA 57.692 34.783 0.00 0.00 38.80 3.96
4002 5850 6.694411 AGATTCATTCATTTTGCTTCGTATGC 59.306 34.615 0.00 0.00 0.00 3.14
4003 5851 9.888878 ATAGATTCATTCATTTTGCTTCGTATG 57.111 29.630 0.00 0.00 0.00 2.39
4006 5854 9.113838 AGTATAGATTCATTCATTTTGCTTCGT 57.886 29.630 0.00 0.00 0.00 3.85
4007 5855 9.941664 AAGTATAGATTCATTCATTTTGCTTCG 57.058 29.630 0.00 0.00 0.00 3.79
4049 5897 9.783081 TCAAATAGACTACTACATACGGATGTA 57.217 33.333 19.32 19.32 44.77 2.29
4051 5899 9.961265 TTTCAAATAGACTACTACATACGGATG 57.039 33.333 5.94 5.94 39.16 3.51
4083 5931 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
4084 5932 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
4085 5933 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4086 5934 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4087 5935 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4088 5936 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4089 5937 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4090 5938 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4091 5939 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4092 5940 6.557633 ACATACTCCCTCCGTTCCTAAATATT 59.442 38.462 0.00 0.00 0.00 1.28
4093 5941 6.082707 ACATACTCCCTCCGTTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
4094 5942 5.461327 ACATACTCCCTCCGTTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
4095 5943 4.296056 ACATACTCCCTCCGTTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
4096 5944 3.716431 ACATACTCCCTCCGTTCCTAAA 58.284 45.455 0.00 0.00 0.00 1.85
4097 5945 3.393426 ACATACTCCCTCCGTTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
4098 5946 3.393426 AACATACTCCCTCCGTTCCTA 57.607 47.619 0.00 0.00 0.00 2.94
4099 5947 2.236395 CAAACATACTCCCTCCGTTCCT 59.764 50.000 0.00 0.00 0.00 3.36
4100 5948 2.235402 TCAAACATACTCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
4101 5949 3.604875 TCAAACATACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
4102 5950 3.581332 TCTTCAAACATACTCCCTCCGTT 59.419 43.478 0.00 0.00 0.00 4.44
4103 5951 3.170717 TCTTCAAACATACTCCCTCCGT 58.829 45.455 0.00 0.00 0.00 4.69
4104 5952 3.887621 TCTTCAAACATACTCCCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
4105 5953 3.933332 CGTTCTTCAAACATACTCCCTCC 59.067 47.826 0.00 0.00 0.00 4.30
4106 5954 3.371285 GCGTTCTTCAAACATACTCCCTC 59.629 47.826 0.00 0.00 0.00 4.30
4107 5955 3.244422 TGCGTTCTTCAAACATACTCCCT 60.244 43.478 0.00 0.00 0.00 4.20
4108 5956 3.071479 TGCGTTCTTCAAACATACTCCC 58.929 45.455 0.00 0.00 0.00 4.30
4109 5957 4.391830 TCATGCGTTCTTCAAACATACTCC 59.608 41.667 0.00 0.00 0.00 3.85
4110 5958 5.530519 TCATGCGTTCTTCAAACATACTC 57.469 39.130 0.00 0.00 0.00 2.59
4111 5959 5.940192 TTCATGCGTTCTTCAAACATACT 57.060 34.783 0.00 0.00 0.00 2.12
4112 5960 7.566858 AAATTCATGCGTTCTTCAAACATAC 57.433 32.000 0.00 0.00 0.00 2.39
4113 5961 8.586570 AAAAATTCATGCGTTCTTCAAACATA 57.413 26.923 0.00 0.00 0.00 2.29
4114 5962 7.481275 AAAAATTCATGCGTTCTTCAAACAT 57.519 28.000 0.00 0.00 0.00 2.71
4115 5963 6.900568 AAAAATTCATGCGTTCTTCAAACA 57.099 29.167 0.00 0.00 0.00 2.83
4174 6022 9.632638 AAATATACCTATGTTGCATCAAGAAGT 57.367 29.630 0.75 0.75 0.00 3.01
4175 6023 9.888878 CAAATATACCTATGTTGCATCAAGAAG 57.111 33.333 0.75 0.59 0.00 2.85
4176 6024 9.407380 ACAAATATACCTATGTTGCATCAAGAA 57.593 29.630 0.75 0.00 0.00 2.52
4177 6025 8.978874 ACAAATATACCTATGTTGCATCAAGA 57.021 30.769 0.75 0.00 0.00 3.02
4179 6027 9.800433 CAAACAAATATACCTATGTTGCATCAA 57.200 29.630 0.75 0.00 36.23 2.57
4180 6028 8.965819 ACAAACAAATATACCTATGTTGCATCA 58.034 29.630 0.00 0.00 36.23 3.07
4181 6029 9.450807 GACAAACAAATATACCTATGTTGCATC 57.549 33.333 0.00 0.00 36.23 3.91
4182 6030 9.189156 AGACAAACAAATATACCTATGTTGCAT 57.811 29.630 0.00 0.00 36.23 3.96
4183 6031 8.574251 AGACAAACAAATATACCTATGTTGCA 57.426 30.769 0.00 0.00 36.23 4.08
4240 6088 9.605955 CGTAAAACATATGTTCTCATGTTCAAA 57.394 29.630 21.02 0.00 42.93 2.69
4241 6089 8.994170 TCGTAAAACATATGTTCTCATGTTCAA 58.006 29.630 21.02 0.00 42.93 2.69
4242 6090 8.541133 TCGTAAAACATATGTTCTCATGTTCA 57.459 30.769 21.02 0.00 42.93 3.18
4282 6130 9.785982 TGCATGTATTGTTAAGCCATTAGTATA 57.214 29.630 0.00 0.00 0.00 1.47
4283 6131 8.690203 TGCATGTATTGTTAAGCCATTAGTAT 57.310 30.769 0.00 0.00 0.00 2.12
4284 6132 8.690203 ATGCATGTATTGTTAAGCCATTAGTA 57.310 30.769 0.00 0.00 0.00 1.82
4285 6133 7.587037 ATGCATGTATTGTTAAGCCATTAGT 57.413 32.000 0.00 0.00 0.00 2.24
4286 6134 8.876275 AAATGCATGTATTGTTAAGCCATTAG 57.124 30.769 9.95 0.00 0.00 1.73
4288 6136 9.664332 TTAAAATGCATGTATTGTTAAGCCATT 57.336 25.926 9.95 0.35 0.00 3.16
4289 6137 9.835389 ATTAAAATGCATGTATTGTTAAGCCAT 57.165 25.926 9.95 1.36 0.00 4.40
4316 6164 9.893305 CCGTTGTAAAAAGAGAAATATCAACTT 57.107 29.630 0.00 0.00 33.13 2.66
4317 6165 9.280174 TCCGTTGTAAAAAGAGAAATATCAACT 57.720 29.630 0.00 0.00 33.13 3.16
4318 6166 9.326339 GTCCGTTGTAAAAAGAGAAATATCAAC 57.674 33.333 0.00 0.00 0.00 3.18
4319 6167 9.058174 TGTCCGTTGTAAAAAGAGAAATATCAA 57.942 29.630 0.00 0.00 0.00 2.57
4320 6168 8.610248 TGTCCGTTGTAAAAAGAGAAATATCA 57.390 30.769 0.00 0.00 0.00 2.15
4321 6169 9.887406 TTTGTCCGTTGTAAAAAGAGAAATATC 57.113 29.630 0.00 0.00 0.00 1.63
4322 6170 9.673454 GTTTGTCCGTTGTAAAAAGAGAAATAT 57.327 29.630 0.00 0.00 29.42 1.28
4323 6171 8.675504 TGTTTGTCCGTTGTAAAAAGAGAAATA 58.324 29.630 0.00 0.00 29.42 1.40
4324 6172 7.540299 TGTTTGTCCGTTGTAAAAAGAGAAAT 58.460 30.769 0.00 0.00 29.42 2.17
4325 6173 6.910995 TGTTTGTCCGTTGTAAAAAGAGAAA 58.089 32.000 0.00 0.00 0.00 2.52
4326 6174 6.149807 ACTGTTTGTCCGTTGTAAAAAGAGAA 59.850 34.615 0.00 0.00 0.00 2.87
4327 6175 5.644636 ACTGTTTGTCCGTTGTAAAAAGAGA 59.355 36.000 0.00 0.00 0.00 3.10
4328 6176 5.875930 ACTGTTTGTCCGTTGTAAAAAGAG 58.124 37.500 0.00 0.00 0.00 2.85
4329 6177 5.883503 ACTGTTTGTCCGTTGTAAAAAGA 57.116 34.783 0.00 0.00 0.00 2.52
4330 6178 6.804783 AGAAACTGTTTGTCCGTTGTAAAAAG 59.195 34.615 11.03 0.00 0.00 2.27
4331 6179 6.679843 AGAAACTGTTTGTCCGTTGTAAAAA 58.320 32.000 11.03 0.00 0.00 1.94
4332 6180 6.256912 AGAAACTGTTTGTCCGTTGTAAAA 57.743 33.333 11.03 0.00 0.00 1.52
4333 6181 5.883503 AGAAACTGTTTGTCCGTTGTAAA 57.116 34.783 11.03 0.00 0.00 2.01
4334 6182 6.108015 ACTAGAAACTGTTTGTCCGTTGTAA 58.892 36.000 11.03 0.00 0.00 2.41
4335 6183 5.663456 ACTAGAAACTGTTTGTCCGTTGTA 58.337 37.500 11.03 0.00 0.00 2.41
4336 6184 4.510571 ACTAGAAACTGTTTGTCCGTTGT 58.489 39.130 11.03 0.00 0.00 3.32
4337 6185 5.479716 AACTAGAAACTGTTTGTCCGTTG 57.520 39.130 11.03 0.00 0.00 4.10
4338 6186 7.797038 AATAACTAGAAACTGTTTGTCCGTT 57.203 32.000 11.03 14.57 0.00 4.44
4339 6187 8.891671 TTAATAACTAGAAACTGTTTGTCCGT 57.108 30.769 11.03 5.14 0.00 4.69
4340 6188 9.590088 GTTTAATAACTAGAAACTGTTTGTCCG 57.410 33.333 11.03 4.53 31.71 4.79


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

AutoCloner maintained by Alex Coulton.