Multiple sequence alignment - TraesCS1A01G155300

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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 TraesCS1A01G155300 chr1A 100.000 3428 0 0 1 3428 272986600 272983173 0.000000e+00 6331.0
1 TraesCS1A01G155300 chr1A 84.452 283 39 4 179 459 272986273 272985994 1.330000e-69 274.0
2 TraesCS1A01G155300 chr1A 84.452 283 39 4 328 607 272986422 272986142 1.330000e-69 274.0
3 TraesCS1A01G155300 chr1A 100.000 100 0 0 3652 3751 272982949 272982850 6.400000e-43 185.0
4 TraesCS1A01G155300 chr1A 98.864 88 1 0 2786 2873 548772380 548772293 1.390000e-34 158.0
5 TraesCS1A01G155300 chr1B 92.322 2123 97 28 707 2788 307483039 307480942 0.000000e+00 2957.0
6 TraesCS1A01G155300 chr1B 92.919 692 47 2 3 693 307483713 307483023 0.000000e+00 1005.0
7 TraesCS1A01G155300 chr1B 92.373 236 17 1 3193 3428 307480736 307480502 6.000000e-88 335.0
8 TraesCS1A01G155300 chr1B 85.121 289 37 5 179 464 307483388 307483103 1.320000e-74 291.0
9 TraesCS1A01G155300 chr1B 83.557 298 43 5 328 622 307483537 307483243 1.330000e-69 274.0
10 TraesCS1A01G155300 chr1B 90.431 209 13 2 2869 3070 307480944 307480736 6.180000e-68 268.0
11 TraesCS1A01G155300 chr1B 94.245 139 8 0 3058 3196 409879801 409879939 2.930000e-51 213.0
12 TraesCS1A01G155300 chr1B 77.703 148 27 5 179 323 307483239 307483095 6.680000e-13 86.1
13 TraesCS1A01G155300 chr1D 94.100 1356 56 13 707 2039 214602453 214601099 0.000000e+00 2039.0
14 TraesCS1A01G155300 chr1D 93.838 714 24 6 2075 2788 214601102 214600409 0.000000e+00 1057.0
15 TraesCS1A01G155300 chr1D 91.236 696 54 3 3 693 214603130 214602437 0.000000e+00 941.0
16 TraesCS1A01G155300 chr1D 82.886 298 39 7 328 618 214602954 214602662 1.340000e-64 257.0
17 TraesCS1A01G155300 chr1D 88.182 220 11 5 2869 3074 214600411 214600193 8.050000e-62 248.0
18 TraesCS1A01G155300 chr1D 82.253 293 43 6 179 464 214602807 214602517 1.040000e-60 244.0
19 TraesCS1A01G155300 chr1D 92.308 143 9 2 3063 3203 178459641 178459499 6.350000e-48 202.0
20 TraesCS1A01G155300 chr1D 90.909 110 5 4 2776 2881 11973559 11973451 3.910000e-30 143.0
21 TraesCS1A01G155300 chr1D 78.000 150 24 7 179 323 214602654 214602509 6.680000e-13 86.1
22 TraesCS1A01G155300 chr1D 100.000 28 0 0 1880 1907 408449694 408449721 7.000000e-03 52.8
23 TraesCS1A01G155300 chr7B 92.254 142 11 0 3063 3204 650133243 650133102 6.350000e-48 202.0
24 TraesCS1A01G155300 chr7B 89.172 157 10 7 3040 3192 646052819 646052666 4.950000e-44 189.0
25 TraesCS1A01G155300 chr7A 93.284 134 9 0 3063 3196 166489306 166489439 8.220000e-47 198.0
26 TraesCS1A01G155300 chr7A 94.000 100 5 1 2780 2878 20732921 20733020 2.330000e-32 150.0
27 TraesCS1A01G155300 chr5B 91.667 144 10 2 3066 3208 498828756 498828614 8.220000e-47 198.0
28 TraesCS1A01G155300 chr5B 87.200 125 8 7 2752 2872 655839884 655840004 6.540000e-28 135.0
29 TraesCS1A01G155300 chr6B 90.972 144 11 2 3059 3202 719923438 719923579 3.820000e-45 193.0
30 TraesCS1A01G155300 chr6B 96.739 92 3 0 2786 2877 48548635 48548726 1.800000e-33 154.0
31 TraesCS1A01G155300 chr3B 91.489 141 11 1 3059 3198 650361168 650361308 3.820000e-45 193.0
32 TraesCS1A01G155300 chr4B 88.816 152 15 2 3052 3202 55925892 55926042 6.400000e-43 185.0
33 TraesCS1A01G155300 chr5D 97.826 92 2 0 2780 2871 137915245 137915336 3.880000e-35 159.0
34 TraesCS1A01G155300 chr3A 98.851 87 1 0 2785 2871 711064915 711064829 5.020000e-34 156.0
35 TraesCS1A01G155300 chr3A 100.000 29 0 0 3316 3344 427335694 427335666 2.000000e-03 54.7
36 TraesCS1A01G155300 chr6A 94.898 98 5 0 2785 2882 562819479 562819382 1.800000e-33 154.0
37 TraesCS1A01G155300 chr7D 95.699 93 4 0 2785 2877 615461467 615461375 2.330000e-32 150.0


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 TraesCS1A01G155300 chr1A 272982850 272986600 3750 True 1766.000000 6331 92.226000 1 3751 4 chr1A.!!$R2 3750
1 TraesCS1A01G155300 chr1B 307480502 307483713 3211 True 745.157143 2957 87.775143 3 3428 7 chr1B.!!$R1 3425
2 TraesCS1A01G155300 chr1D 214600193 214603130 2937 True 696.014286 2039 87.213571 3 3074 7 chr1D.!!$R3 3071

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
922 933 0.251922 TATAGCTAATCCCCGGCCGT 60.252 55.0 26.12 7.53 0.0 5.68 F
1578 1614 0.512952 CTGTCTTGCCAGCGTACAAC 59.487 55.0 0.00 0.00 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2671 2724 0.247460 CTGGTCATCGCTCCAGTTCA 59.753 55.0 3.38 0.0 44.19 3.18 R
2918 2971 0.319555 TCGTCAAGAAGGTGAAGGCG 60.320 55.0 0.00 0.0 0.00 5.52 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
114 115 5.818857 ACTTACCACACTATTTGTTGACGTT 59.181 36.000 0.00 0.00 35.67 3.99
133 134 4.569966 ACGTTGAGAATCGTCGTAGAGTAT 59.430 41.667 0.00 0.00 42.89 2.12
286 287 2.675348 TCACATTCATGTAATCGCGCAA 59.325 40.909 8.75 0.00 39.39 4.85
287 288 2.777845 CACATTCATGTAATCGCGCAAC 59.222 45.455 8.75 0.00 39.39 4.17
313 314 8.489559 CAAACCACACAATTTTCATCAACATAG 58.510 33.333 0.00 0.00 0.00 2.23
374 375 1.153549 GGCTTCTTGACGATCGGCT 60.154 57.895 23.76 0.00 0.00 5.52
398 399 3.695060 TCACATTGGTTTAACGGTTGTGT 59.305 39.130 16.50 4.52 35.63 3.72
464 469 6.368516 ACCACACAGTTTTCATCAACAAAAAG 59.631 34.615 0.00 0.00 0.00 2.27
466 471 5.931146 ACACAGTTTTCATCAACAAAAAGCA 59.069 32.000 0.00 0.00 0.00 3.91
469 474 7.427030 CACAGTTTTCATCAACAAAAAGCATTG 59.573 33.333 0.00 0.00 36.37 2.82
552 558 1.001181 GTCTAACGGTTGTGCCCTACA 59.999 52.381 3.07 0.00 37.56 2.74
555 561 2.863132 AACGGTTGTGCCCTACATAA 57.137 45.000 0.00 0.00 39.48 1.90
608 614 1.533756 CCACACAGTTTTCAGCAACGG 60.534 52.381 0.00 0.00 0.00 4.44
619 625 5.776173 TTTCAGCAACGGAAAATCCTTAA 57.224 34.783 0.00 0.00 33.30 1.85
621 627 5.975693 TCAGCAACGGAAAATCCTTAAAT 57.024 34.783 0.00 0.00 33.30 1.40
658 664 6.387192 TCCAGGAGAACTCAATTATGGAAA 57.613 37.500 4.23 0.00 32.84 3.13
677 683 8.593945 ATGGAAAGAAATAAATACTTGGCTGA 57.406 30.769 0.00 0.00 0.00 4.26
678 684 8.415950 TGGAAAGAAATAAATACTTGGCTGAA 57.584 30.769 0.00 0.00 0.00 3.02
679 685 9.034800 TGGAAAGAAATAAATACTTGGCTGAAT 57.965 29.630 0.00 0.00 0.00 2.57
680 686 9.875691 GGAAAGAAATAAATACTTGGCTGAATT 57.124 29.630 0.00 0.00 0.00 2.17
697 703 6.224665 CTGAATTAATTTTCAGCCATCCCA 57.775 37.500 1.43 0.00 44.30 4.37
698 704 5.976458 TGAATTAATTTTCAGCCATCCCAC 58.024 37.500 1.43 0.00 32.07 4.61
699 705 5.483231 TGAATTAATTTTCAGCCATCCCACA 59.517 36.000 1.43 0.00 32.07 4.17
700 706 6.013898 TGAATTAATTTTCAGCCATCCCACAA 60.014 34.615 1.43 0.00 32.07 3.33
701 707 5.815233 TTAATTTTCAGCCATCCCACAAA 57.185 34.783 0.00 0.00 0.00 2.83
702 708 4.703379 AATTTTCAGCCATCCCACAAAA 57.297 36.364 0.00 0.00 0.00 2.44
703 709 4.703379 ATTTTCAGCCATCCCACAAAAA 57.297 36.364 0.00 0.00 0.00 1.94
739 745 1.858458 GCCAAAGAAAACAACGCCTTC 59.142 47.619 0.00 0.00 0.00 3.46
856 867 1.236616 CCAGCAGGCATCACGTTTGA 61.237 55.000 0.00 0.00 35.73 2.69
871 882 2.632136 TTTGACACGTTCCCGTCGCT 62.632 55.000 0.00 0.00 46.28 4.93
884 895 1.484356 CGTCGCTCTTAAATACCCCG 58.516 55.000 0.00 0.00 0.00 5.73
922 933 0.251922 TATAGCTAATCCCCGGCCGT 60.252 55.000 26.12 7.53 0.00 5.68
978 989 0.544120 GCAGGGAGGAGGATAGGAGG 60.544 65.000 0.00 0.00 0.00 4.30
1156 1167 1.741401 TTCCGCATCTTGCTGACGG 60.741 57.895 0.00 0.00 42.25 4.79
1175 1186 1.807886 CGACGACGGATTCCCTCTT 59.192 57.895 0.00 0.00 35.72 2.85
1209 1236 3.746045 ACCGCCGATTACTATCATTGT 57.254 42.857 0.00 0.00 0.00 2.71
1340 1367 0.683412 CATCATCCGCCTCCATCAGA 59.317 55.000 0.00 0.00 0.00 3.27
1352 1379 1.450312 CATCAGACCCTCGGCAACC 60.450 63.158 0.00 0.00 0.00 3.77
1549 1585 4.347876 TGAGCCAGCCTAGAAATTGCTATA 59.652 41.667 0.00 0.00 33.16 1.31
1572 1608 2.226437 ACATTTAACTGTCTTGCCAGCG 59.774 45.455 0.00 0.00 35.83 5.18
1578 1614 0.512952 CTGTCTTGCCAGCGTACAAC 59.487 55.000 0.00 0.00 0.00 3.32
1703 1739 3.692101 TCCAAAGAAGACAAAAGCGTTCA 59.308 39.130 0.00 0.00 0.00 3.18
1822 1858 1.202675 TCTCGTTTGGCCTTTAACGGT 60.203 47.619 26.44 0.00 45.19 4.83
2049 2085 9.507280 CAAGAGCATTTGTAAATTACATGTAGG 57.493 33.333 6.67 0.00 38.68 3.18
2050 2086 9.461312 AAGAGCATTTGTAAATTACATGTAGGA 57.539 29.630 6.67 0.00 38.68 2.94
2051 2087 9.113838 AGAGCATTTGTAAATTACATGTAGGAG 57.886 33.333 6.67 0.00 38.68 3.69
2052 2088 8.225603 AGCATTTGTAAATTACATGTAGGAGG 57.774 34.615 6.67 0.00 38.68 4.30
2062 2114 4.067944 ACATGTAGGAGGAGGAGAAGTT 57.932 45.455 0.00 0.00 0.00 2.66
2099 2151 3.927142 ACCATCTCTACGCTTTTCGAAAG 59.073 43.478 10.98 6.81 41.67 2.62
2100 2152 3.307242 CCATCTCTACGCTTTTCGAAAGG 59.693 47.826 15.13 15.13 41.67 3.11
2175 2227 1.067425 GGCTTGCATGCAGTTGATGAA 60.067 47.619 21.50 2.04 34.04 2.57
2206 2259 4.660789 AACAGTTGCAGCTCTGAATTTT 57.339 36.364 19.76 5.86 35.84 1.82
2207 2260 5.772825 AACAGTTGCAGCTCTGAATTTTA 57.227 34.783 19.76 0.00 35.84 1.52
2208 2261 5.772825 ACAGTTGCAGCTCTGAATTTTAA 57.227 34.783 19.76 0.00 35.84 1.52
2409 2462 3.792047 CCACCGTCGACGCTCGTA 61.792 66.667 31.73 0.00 41.35 3.43
2520 2573 0.930310 CGATAACGCCACCATCACAG 59.070 55.000 0.00 0.00 0.00 3.66
2522 2575 0.908910 ATAACGCCACCATCACAGGA 59.091 50.000 0.00 0.00 0.00 3.86
2635 2688 0.753262 ATGATAGACCTCGGTGCCAC 59.247 55.000 0.00 0.00 0.00 5.01
2656 2709 2.362329 GACGAGGATCTGAGCCTGGC 62.362 65.000 20.84 11.65 35.44 4.85
2789 2842 6.797454 GCTTGATTAGCTACAGTACTGTACT 58.203 40.000 27.99 27.21 46.77 2.73
2790 2843 6.913673 GCTTGATTAGCTACAGTACTGTACTC 59.086 42.308 27.99 21.72 46.77 2.59
2791 2844 6.939132 TGATTAGCTACAGTACTGTACTCC 57.061 41.667 27.99 19.17 44.42 3.85
2792 2845 5.826737 TGATTAGCTACAGTACTGTACTCCC 59.173 44.000 27.99 19.74 44.42 4.30
2793 2846 5.447778 TTAGCTACAGTACTGTACTCCCT 57.552 43.478 27.99 21.78 44.42 4.20
2794 2847 3.888583 AGCTACAGTACTGTACTCCCTC 58.111 50.000 27.99 14.16 44.42 4.30
2795 2848 2.950975 GCTACAGTACTGTACTCCCTCC 59.049 54.545 27.99 9.56 44.42 4.30
2796 2849 2.125773 ACAGTACTGTACTCCCTCCG 57.874 55.000 26.91 8.12 42.90 4.63
2797 2850 1.353694 ACAGTACTGTACTCCCTCCGT 59.646 52.381 26.91 8.73 42.90 4.69
2798 2851 2.573462 ACAGTACTGTACTCCCTCCGTA 59.427 50.000 26.91 0.00 42.90 4.02
2799 2852 3.009473 ACAGTACTGTACTCCCTCCGTAA 59.991 47.826 26.91 0.00 42.90 3.18
2800 2853 4.012374 CAGTACTGTACTCCCTCCGTAAA 58.988 47.826 17.22 0.00 36.76 2.01
2801 2854 4.013050 AGTACTGTACTCCCTCCGTAAAC 58.987 47.826 14.53 0.00 32.47 2.01
2802 2855 3.166560 ACTGTACTCCCTCCGTAAACT 57.833 47.619 0.00 0.00 0.00 2.66
2803 2856 4.307032 ACTGTACTCCCTCCGTAAACTA 57.693 45.455 0.00 0.00 0.00 2.24
2804 2857 4.666512 ACTGTACTCCCTCCGTAAACTAA 58.333 43.478 0.00 0.00 0.00 2.24
2805 2858 5.267587 ACTGTACTCCCTCCGTAAACTAAT 58.732 41.667 0.00 0.00 0.00 1.73
2806 2859 6.426587 ACTGTACTCCCTCCGTAAACTAATA 58.573 40.000 0.00 0.00 0.00 0.98
2807 2860 7.065504 ACTGTACTCCCTCCGTAAACTAATAT 58.934 38.462 0.00 0.00 0.00 1.28
2808 2861 8.220559 ACTGTACTCCCTCCGTAAACTAATATA 58.779 37.037 0.00 0.00 0.00 0.86
2809 2862 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2810 2863 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2811 2864 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2812 2865 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2813 2866 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2814 2867 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2815 2868 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2816 2869 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2817 2870 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2818 2871 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2819 2872 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2835 2888 6.941218 GCGTTTAGCTTACTAAAGTAGTGT 57.059 37.500 0.00 0.00 46.45 3.55
2836 2889 7.343614 GCGTTTAGCTTACTAAAGTAGTGTT 57.656 36.000 0.00 0.00 46.45 3.32
2837 2890 7.443450 GCGTTTAGCTTACTAAAGTAGTGTTC 58.557 38.462 0.00 0.00 46.45 3.18
2838 2891 7.328005 GCGTTTAGCTTACTAAAGTAGTGTTCT 59.672 37.037 0.00 0.00 46.45 3.01
2839 2892 9.831737 CGTTTAGCTTACTAAAGTAGTGTTCTA 57.168 33.333 0.00 0.00 46.45 2.10
2843 2896 8.739649 AGCTTACTAAAGTAGTGTTCTAAACG 57.260 34.615 0.00 0.00 39.81 3.60
2844 2897 7.328005 AGCTTACTAAAGTAGTGTTCTAAACGC 59.672 37.037 0.00 0.00 39.81 4.84
2845 2898 7.328005 GCTTACTAAAGTAGTGTTCTAAACGCT 59.672 37.037 10.40 10.40 42.58 5.07
2865 2918 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2866 2919 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2867 2920 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2896 2949 5.924769 TTTTCTCCTCTTTTTACCTCCCT 57.075 39.130 0.00 0.00 0.00 4.20
2913 2966 2.236395 TCCCTTCTTCGGGTGAGAAATC 59.764 50.000 0.00 0.00 44.95 2.17
2918 2971 0.108329 TTCGGGTGAGAAATCGAGGC 60.108 55.000 0.00 0.00 33.11 4.70
2973 3026 3.414700 CAGTCGGCAGTCGCAACC 61.415 66.667 0.00 0.00 41.24 3.77
2974 3027 3.923864 AGTCGGCAGTCGCAACCA 61.924 61.111 0.00 0.00 41.24 3.67
3019 3085 6.727824 ATAAATCAGATGCAGCGGTATTAC 57.272 37.500 1.21 0.00 0.00 1.89
3077 3143 7.748691 CTAGTTAACTAGTACTCCCTCCATC 57.251 44.000 27.67 0.00 40.72 3.51
3078 3144 5.456779 AGTTAACTAGTACTCCCTCCATCC 58.543 45.833 6.26 0.00 0.00 3.51
3079 3145 2.660670 ACTAGTACTCCCTCCATCCG 57.339 55.000 0.00 0.00 0.00 4.18
3080 3146 2.133520 ACTAGTACTCCCTCCATCCGA 58.866 52.381 0.00 0.00 0.00 4.55
3081 3147 2.512896 ACTAGTACTCCCTCCATCCGAA 59.487 50.000 0.00 0.00 0.00 4.30
3082 3148 2.544844 AGTACTCCCTCCATCCGAAA 57.455 50.000 0.00 0.00 0.00 3.46
3083 3149 2.829023 AGTACTCCCTCCATCCGAAAA 58.171 47.619 0.00 0.00 0.00 2.29
3084 3150 3.385115 AGTACTCCCTCCATCCGAAAAT 58.615 45.455 0.00 0.00 0.00 1.82
3085 3151 4.553678 AGTACTCCCTCCATCCGAAAATA 58.446 43.478 0.00 0.00 0.00 1.40
3086 3152 3.840124 ACTCCCTCCATCCGAAAATAC 57.160 47.619 0.00 0.00 0.00 1.89
3087 3153 3.385115 ACTCCCTCCATCCGAAAATACT 58.615 45.455 0.00 0.00 0.00 2.12
3088 3154 3.780850 ACTCCCTCCATCCGAAAATACTT 59.219 43.478 0.00 0.00 0.00 2.24
3089 3155 4.130118 CTCCCTCCATCCGAAAATACTTG 58.870 47.826 0.00 0.00 0.00 3.16
3090 3156 3.521937 TCCCTCCATCCGAAAATACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
3091 3157 3.877508 CCCTCCATCCGAAAATACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
3092 3158 4.513442 CCTCCATCCGAAAATACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
3093 3159 5.126067 CCTCCATCCGAAAATACTTGTCAT 58.874 41.667 0.00 0.00 0.00 3.06
3094 3160 5.237344 CCTCCATCCGAAAATACTTGTCATC 59.763 44.000 0.00 0.00 0.00 2.92
3095 3161 5.739959 TCCATCCGAAAATACTTGTCATCA 58.260 37.500 0.00 0.00 0.00 3.07
3096 3162 6.176896 TCCATCCGAAAATACTTGTCATCAA 58.823 36.000 0.00 0.00 0.00 2.57
3097 3163 6.657117 TCCATCCGAAAATACTTGTCATCAAA 59.343 34.615 0.00 0.00 32.87 2.69
3098 3164 7.175816 TCCATCCGAAAATACTTGTCATCAAAA 59.824 33.333 0.00 0.00 32.87 2.44
3099 3165 7.975616 CCATCCGAAAATACTTGTCATCAAAAT 59.024 33.333 0.00 0.00 32.87 1.82
3100 3166 8.800972 CATCCGAAAATACTTGTCATCAAAATG 58.199 33.333 0.00 0.00 32.87 2.32
3101 3167 8.105097 TCCGAAAATACTTGTCATCAAAATGA 57.895 30.769 0.00 0.00 39.63 2.57
3102 3168 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
3103 3169 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
3149 3215 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
3157 3223 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
3171 3237 9.942850 CCCCTTTTATTCATTTTAATGACAAGT 57.057 29.630 4.70 0.00 44.54 3.16
3181 3247 9.834628 TCATTTTAATGACAAGTATTTTCGGAC 57.165 29.630 1.12 0.00 40.32 4.79
3182 3248 8.785101 CATTTTAATGACAAGTATTTTCGGACG 58.215 33.333 0.00 0.00 38.70 4.79
3183 3249 4.939509 AATGACAAGTATTTTCGGACGG 57.060 40.909 0.00 0.00 0.00 4.79
3184 3250 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3185 3251 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3186 3252 3.256383 TGACAAGTATTTTCGGACGGAGA 59.744 43.478 0.00 0.00 0.00 3.71
3187 3253 4.240096 GACAAGTATTTTCGGACGGAGAA 58.760 43.478 0.00 0.00 0.00 2.87
3188 3254 4.634199 ACAAGTATTTTCGGACGGAGAAA 58.366 39.130 0.00 0.00 36.00 2.52
3189 3255 4.689345 ACAAGTATTTTCGGACGGAGAAAG 59.311 41.667 0.00 0.00 38.61 2.62
3190 3256 4.532314 AGTATTTTCGGACGGAGAAAGT 57.468 40.909 0.00 0.00 38.61 2.66
3191 3257 5.649782 AGTATTTTCGGACGGAGAAAGTA 57.350 39.130 0.00 0.00 38.61 2.24
3192 3258 5.405797 AGTATTTTCGGACGGAGAAAGTAC 58.594 41.667 18.22 18.22 44.21 2.73
3211 3277 6.344232 AGTACTACCTCAGTCCTCCTTTAT 57.656 41.667 0.00 0.00 38.80 1.40
3222 3288 5.894393 CAGTCCTCCTTTATTAGTCTCCTCA 59.106 44.000 0.00 0.00 0.00 3.86
3264 3330 8.964476 TGATCATGATTTTAAGTACTTCCTCC 57.036 34.615 12.39 0.04 0.00 4.30
3265 3331 7.710907 TGATCATGATTTTAAGTACTTCCTCCG 59.289 37.037 12.39 0.42 0.00 4.63
3267 3333 7.391620 TCATGATTTTAAGTACTTCCTCCGTT 58.608 34.615 12.39 0.00 0.00 4.44
3268 3334 7.548075 TCATGATTTTAAGTACTTCCTCCGTTC 59.452 37.037 12.39 2.63 0.00 3.95
3280 3346 2.361757 TCCTCCGTTCACTTTTGTACGA 59.638 45.455 5.51 0.00 46.28 3.43
3281 3347 3.006110 TCCTCCGTTCACTTTTGTACGAT 59.994 43.478 5.51 0.00 46.28 3.73
3372 3438 4.374689 TTGGTAGTCAAAGCATTGGGTA 57.625 40.909 1.24 0.00 37.15 3.69
3389 3455 3.195471 GGTAACCTCCTAGTGGAATGC 57.805 52.381 6.09 0.00 42.66 3.56
3400 3466 1.135373 AGTGGAATGCGTCTACACTCG 60.135 52.381 6.50 0.00 40.12 4.18
3407 3473 3.998924 CGTCTACACTCGCATCACT 57.001 52.632 0.00 0.00 0.00 3.41
3409 3475 1.914051 CGTCTACACTCGCATCACTTG 59.086 52.381 0.00 0.00 0.00 3.16
3420 3486 2.456989 GCATCACTTGGCATGAAATCG 58.543 47.619 7.45 0.00 0.00 3.34
3668 3734 4.193653 GGCTTCTTCGACTGGCTC 57.806 61.111 0.00 0.00 0.00 4.70
3669 3735 1.807573 GGCTTCTTCGACTGGCTCG 60.808 63.158 0.00 0.00 44.44 5.03
3670 3736 2.448705 GCTTCTTCGACTGGCTCGC 61.449 63.158 0.00 0.00 42.62 5.03
3671 3737 2.126463 TTCTTCGACTGGCTCGCG 60.126 61.111 0.00 0.00 42.62 5.87
3672 3738 3.626680 TTCTTCGACTGGCTCGCGG 62.627 63.158 6.13 0.00 42.62 6.46
3677 3743 4.129737 GACTGGCTCGCGGCTACA 62.130 66.667 17.07 8.41 41.46 2.74
3678 3744 3.642778 GACTGGCTCGCGGCTACAA 62.643 63.158 17.07 3.19 41.46 2.41
3679 3745 2.202932 CTGGCTCGCGGCTACAAT 60.203 61.111 17.07 0.00 41.46 2.71
3680 3746 2.511373 TGGCTCGCGGCTACAATG 60.511 61.111 17.07 0.00 41.46 2.82
3681 3747 3.272334 GGCTCGCGGCTACAATGG 61.272 66.667 17.07 0.00 41.46 3.16
3682 3748 2.202878 GCTCGCGGCTACAATGGA 60.203 61.111 6.13 0.00 38.06 3.41
3683 3749 2.240500 GCTCGCGGCTACAATGGAG 61.241 63.158 6.13 0.00 38.06 3.86
3684 3750 1.592669 CTCGCGGCTACAATGGAGG 60.593 63.158 6.13 0.00 0.00 4.30
3685 3751 3.272334 CGCGGCTACAATGGAGGC 61.272 66.667 9.24 9.24 36.18 4.70
3686 3752 2.124736 GCGGCTACAATGGAGGCA 60.125 61.111 19.41 0.00 39.38 4.75
3687 3753 2.472909 GCGGCTACAATGGAGGCAC 61.473 63.158 19.41 5.48 39.38 5.01
3689 3755 0.464036 CGGCTACAATGGAGGCACTA 59.536 55.000 19.41 0.00 41.55 2.74
3690 3756 1.806623 CGGCTACAATGGAGGCACTAC 60.807 57.143 19.41 0.00 41.55 2.73
3691 3757 1.475213 GGCTACAATGGAGGCACTACC 60.475 57.143 14.70 0.00 39.75 3.18
3692 3758 1.475213 GCTACAATGGAGGCACTACCC 60.475 57.143 0.00 0.00 39.75 3.69
3693 3759 1.141053 CTACAATGGAGGCACTACCCC 59.859 57.143 0.00 0.00 39.75 4.95
3694 3760 1.227383 CAATGGAGGCACTACCCCC 59.773 63.158 0.00 0.00 39.75 5.40
3695 3761 1.084842 AATGGAGGCACTACCCCCT 59.915 57.895 0.00 0.00 39.75 4.79
3696 3762 0.552615 AATGGAGGCACTACCCCCTT 60.553 55.000 0.00 0.00 39.75 3.95
3697 3763 0.988678 ATGGAGGCACTACCCCCTTC 60.989 60.000 0.00 0.00 39.75 3.46
3698 3764 1.307084 GGAGGCACTACCCCCTTCT 60.307 63.158 0.00 0.00 41.55 2.85
3699 3765 1.627297 GGAGGCACTACCCCCTTCTG 61.627 65.000 0.00 0.00 41.55 3.02
3700 3766 2.258748 GAGGCACTACCCCCTTCTGC 62.259 65.000 0.00 0.00 41.55 4.26
3701 3767 2.125106 GCACTACCCCCTTCTGCG 60.125 66.667 0.00 0.00 0.00 5.18
3702 3768 2.656069 GCACTACCCCCTTCTGCGA 61.656 63.158 0.00 0.00 0.00 5.10
3703 3769 1.517832 CACTACCCCCTTCTGCGAG 59.482 63.158 0.00 0.00 0.00 5.03
3704 3770 2.359967 ACTACCCCCTTCTGCGAGC 61.360 63.158 0.00 0.00 0.00 5.03
3705 3771 2.284331 TACCCCCTTCTGCGAGCA 60.284 61.111 0.00 0.00 0.00 4.26
3706 3772 1.899437 CTACCCCCTTCTGCGAGCAA 61.899 60.000 0.00 0.00 0.00 3.91
3707 3773 1.899437 TACCCCCTTCTGCGAGCAAG 61.899 60.000 0.00 0.00 0.00 4.01
3708 3774 2.437359 CCCCTTCTGCGAGCAAGG 60.437 66.667 8.46 8.46 39.24 3.61
3710 3776 3.130160 CCTTCTGCGAGCAAGGGC 61.130 66.667 7.70 0.00 36.29 5.19
3711 3777 2.359107 CTTCTGCGAGCAAGGGCA 60.359 61.111 0.00 0.00 44.61 5.36
3712 3778 1.748122 CTTCTGCGAGCAAGGGCAT 60.748 57.895 0.00 0.00 44.61 4.40
3713 3779 0.462581 CTTCTGCGAGCAAGGGCATA 60.463 55.000 0.00 0.00 44.61 3.14
3714 3780 0.462581 TTCTGCGAGCAAGGGCATAG 60.463 55.000 0.00 0.00 44.61 2.23
3715 3781 1.144716 CTGCGAGCAAGGGCATAGA 59.855 57.895 0.00 0.00 44.61 1.98
3716 3782 0.250209 CTGCGAGCAAGGGCATAGAT 60.250 55.000 0.00 0.00 44.61 1.98
3717 3783 0.181114 TGCGAGCAAGGGCATAGATT 59.819 50.000 0.00 0.00 44.61 2.40
3718 3784 1.416030 TGCGAGCAAGGGCATAGATTA 59.584 47.619 0.00 0.00 44.61 1.75
3719 3785 2.038952 TGCGAGCAAGGGCATAGATTAT 59.961 45.455 0.00 0.00 44.61 1.28
3720 3786 3.077359 GCGAGCAAGGGCATAGATTATT 58.923 45.455 0.00 0.00 44.61 1.40
3721 3787 3.503748 GCGAGCAAGGGCATAGATTATTT 59.496 43.478 0.00 0.00 44.61 1.40
3722 3788 4.378874 GCGAGCAAGGGCATAGATTATTTC 60.379 45.833 0.00 0.00 44.61 2.17
3723 3789 4.143030 CGAGCAAGGGCATAGATTATTTCG 60.143 45.833 0.00 0.00 44.61 3.46
3724 3790 3.503748 AGCAAGGGCATAGATTATTTCGC 59.496 43.478 0.00 0.00 44.61 4.70
3725 3791 3.366374 GCAAGGGCATAGATTATTTCGCC 60.366 47.826 0.00 0.00 40.72 5.54
3726 3792 3.788227 AGGGCATAGATTATTTCGCCA 57.212 42.857 0.00 0.00 41.41 5.69
3727 3793 4.307032 AGGGCATAGATTATTTCGCCAT 57.693 40.909 0.00 0.00 41.41 4.40
3728 3794 4.265073 AGGGCATAGATTATTTCGCCATC 58.735 43.478 0.00 0.00 41.41 3.51
3729 3795 3.378427 GGGCATAGATTATTTCGCCATCC 59.622 47.826 0.00 0.00 41.41 3.51
3730 3796 4.265073 GGCATAGATTATTTCGCCATCCT 58.735 43.478 0.00 0.00 39.38 3.24
3731 3797 4.333926 GGCATAGATTATTTCGCCATCCTC 59.666 45.833 0.00 0.00 39.38 3.71
3732 3798 4.937620 GCATAGATTATTTCGCCATCCTCA 59.062 41.667 0.00 0.00 0.00 3.86
3733 3799 5.163814 GCATAGATTATTTCGCCATCCTCAC 60.164 44.000 0.00 0.00 0.00 3.51
3734 3800 3.744660 AGATTATTTCGCCATCCTCACC 58.255 45.455 0.00 0.00 0.00 4.02
3735 3801 1.948104 TTATTTCGCCATCCTCACCG 58.052 50.000 0.00 0.00 0.00 4.94
3736 3802 0.531974 TATTTCGCCATCCTCACCGC 60.532 55.000 0.00 0.00 0.00 5.68
3737 3803 3.840102 TATTTCGCCATCCTCACCGCC 62.840 57.143 0.00 0.00 0.00 6.13
3740 3806 4.864334 GCCATCCTCACCGCCTGG 62.864 72.222 0.00 0.00 42.84 4.45
3750 3816 2.597217 CCGCCTGGTGCCTTTGAA 60.597 61.111 0.55 0.00 36.24 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.202526 AGACAACAAAACTACAATGGTTCATG 58.797 34.615 0.00 0.00 0.00 3.07
1 2 7.346751 AGACAACAAAACTACAATGGTTCAT 57.653 32.000 0.00 0.00 0.00 2.57
114 115 4.063689 GGGATACTCTACGACGATTCTCA 58.936 47.826 0.00 0.00 0.00 3.27
159 160 3.944015 GGAGATGGATGAACAAGGTGAAG 59.056 47.826 0.00 0.00 0.00 3.02
251 252 7.099120 ACATGAATGTGATTGCGCTATATAGA 58.901 34.615 14.16 0.00 40.03 1.98
255 256 7.411804 CGATTACATGAATGTGATTGCGCTATA 60.412 37.037 9.73 0.00 41.89 1.31
256 257 6.564709 ATTACATGAATGTGATTGCGCTAT 57.435 33.333 9.73 6.47 41.89 2.97
286 287 6.169094 TGTTGATGAAAATTGTGTGGTTTGT 58.831 32.000 0.00 0.00 0.00 2.83
287 288 6.659361 TGTTGATGAAAATTGTGTGGTTTG 57.341 33.333 0.00 0.00 0.00 2.93
374 375 5.103000 CACAACCGTTAAACCAATGTGAAA 58.897 37.500 0.00 0.00 39.10 2.69
398 399 1.760029 TGTGATTGCCGCTACATAGGA 59.240 47.619 0.00 0.00 0.00 2.94
464 469 3.959478 CATGGAGGTCATGCAATGC 57.041 52.632 0.00 0.00 46.21 3.56
482 487 5.921408 CCTATGTATACAAGACTTCTTCGGC 59.079 44.000 10.14 0.00 33.11 5.54
485 490 8.417884 AGAAGCCTATGTATACAAGACTTCTTC 58.582 37.037 24.18 21.26 38.46 2.87
552 558 0.618458 ATGGGTGTGACTGGCGTTAT 59.382 50.000 0.00 0.00 0.00 1.89
555 561 2.032528 CATGGGTGTGACTGGCGT 59.967 61.111 0.00 0.00 0.00 5.68
608 614 7.272978 GGCCCTTTTAGGATTTAAGGATTTTC 58.727 38.462 0.00 0.00 40.71 2.29
619 625 1.570979 CTGGAGGGCCCTTTTAGGATT 59.429 52.381 29.39 0.00 37.67 3.01
621 627 0.919289 CCTGGAGGGCCCTTTTAGGA 60.919 60.000 31.56 12.67 37.67 2.94
676 682 5.976458 TGTGGGATGGCTGAAAATTAATTC 58.024 37.500 0.10 0.00 0.00 2.17
677 683 6.371595 TTGTGGGATGGCTGAAAATTAATT 57.628 33.333 0.00 0.00 0.00 1.40
678 684 6.371595 TTTGTGGGATGGCTGAAAATTAAT 57.628 33.333 0.00 0.00 0.00 1.40
679 685 5.815233 TTTGTGGGATGGCTGAAAATTAA 57.185 34.783 0.00 0.00 0.00 1.40
680 686 5.815233 TTTTGTGGGATGGCTGAAAATTA 57.185 34.783 0.00 0.00 0.00 1.40
681 687 4.703379 TTTTGTGGGATGGCTGAAAATT 57.297 36.364 0.00 0.00 0.00 1.82
682 688 4.703379 TTTTTGTGGGATGGCTGAAAAT 57.297 36.364 0.00 0.00 0.00 1.82
705 711 9.612066 TGTTTTCTTTGGCTGAAAATTAATTCT 57.388 25.926 0.10 0.00 42.76 2.40
725 731 1.663739 GGGGGAAGGCGTTGTTTTC 59.336 57.895 0.00 0.00 0.00 2.29
775 786 2.129607 GCCGATTTCGTTCGCCTATTA 58.870 47.619 0.00 0.00 37.80 0.98
837 848 1.210931 CAAACGTGATGCCTGCTGG 59.789 57.895 5.03 5.03 0.00 4.85
871 882 1.227321 CGCGGCGGGGTATTTAAGA 60.227 57.895 15.84 0.00 0.00 2.10
922 933 1.620798 CCTGTGTGAGAGGAGATGGGA 60.621 57.143 0.00 0.00 31.48 4.37
978 989 0.037605 ACCGATCCAAACTCACCGTC 60.038 55.000 0.00 0.00 0.00 4.79
1156 1167 2.278661 GAGGGAATCCGTCGTCGC 60.279 66.667 6.21 0.00 38.33 5.19
1182 1195 2.521105 AGTAATCGGCGGTAATCACC 57.479 50.000 7.21 0.00 41.93 4.02
1192 1205 4.574828 ACACCAACAATGATAGTAATCGGC 59.425 41.667 0.00 0.00 34.60 5.54
1198 1211 4.155826 GCAGCAACACCAACAATGATAGTA 59.844 41.667 0.00 0.00 0.00 1.82
1200 1213 3.057386 TGCAGCAACACCAACAATGATAG 60.057 43.478 0.00 0.00 0.00 2.08
1209 1236 3.225798 GCCCTGCAGCAACACCAA 61.226 61.111 8.66 0.00 0.00 3.67
1482 1514 5.540400 ATTGGATAACCATGAAGGCAATG 57.460 39.130 0.00 0.00 46.34 2.82
1525 1557 1.674962 GCAATTTCTAGGCTGGCTCAG 59.325 52.381 7.13 4.30 34.12 3.35
1549 1585 4.620982 GCTGGCAAGACAGTTAAATGTTT 58.379 39.130 10.27 1.13 40.59 2.83
1578 1614 1.072331 ACTGACTAGGCCCACAACAAG 59.928 52.381 0.00 0.00 0.00 3.16
1674 1710 5.631096 GCTTTTGTCTTCTTTGGAGTATTGC 59.369 40.000 0.00 0.00 0.00 3.56
1859 1895 5.352293 CCGCTGCTGCATCTATATGAAAATA 59.648 40.000 16.29 0.00 39.64 1.40
1894 1930 4.864334 CCGGGAGATGGTGCTGCC 62.864 72.222 0.00 0.00 42.39 4.85
2043 2079 3.772025 CACAACTTCTCCTCCTCCTACAT 59.228 47.826 0.00 0.00 0.00 2.29
2044 2080 3.165875 CACAACTTCTCCTCCTCCTACA 58.834 50.000 0.00 0.00 0.00 2.74
2045 2081 2.093921 GCACAACTTCTCCTCCTCCTAC 60.094 54.545 0.00 0.00 0.00 3.18
2046 2082 2.180276 GCACAACTTCTCCTCCTCCTA 58.820 52.381 0.00 0.00 0.00 2.94
2047 2083 0.980423 GCACAACTTCTCCTCCTCCT 59.020 55.000 0.00 0.00 0.00 3.69
2048 2084 0.980423 AGCACAACTTCTCCTCCTCC 59.020 55.000 0.00 0.00 0.00 4.30
2049 2085 2.849294 AAGCACAACTTCTCCTCCTC 57.151 50.000 0.00 0.00 30.77 3.71
2062 2114 5.809001 AGAGATGGTTTAATCTGAAGCACA 58.191 37.500 0.00 0.00 37.03 4.57
2635 2688 1.826054 AGGCTCAGATCCTCGTCCG 60.826 63.158 0.00 0.00 0.00 4.79
2671 2724 0.247460 CTGGTCATCGCTCCAGTTCA 59.753 55.000 3.38 0.00 44.19 3.18
2785 2838 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
2786 2839 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2787 2840 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2788 2841 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2789 2842 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2790 2843 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2791 2844 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2792 2845 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2793 2846 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2794 2847 8.423215 GCTAAACGCTCTTATATTAGTTTACGG 58.577 37.037 0.00 0.00 34.29 4.02
2808 2861 7.541437 CACTACTTTAGTAAGCTAAACGCTCTT 59.459 37.037 0.00 0.00 42.48 2.85
2809 2862 7.028361 CACTACTTTAGTAAGCTAAACGCTCT 58.972 38.462 0.00 0.00 42.48 4.09
2810 2863 6.805760 ACACTACTTTAGTAAGCTAAACGCTC 59.194 38.462 0.00 0.00 42.48 5.03
2811 2864 6.685657 ACACTACTTTAGTAAGCTAAACGCT 58.314 36.000 0.00 0.00 44.26 5.07
2812 2865 6.941218 ACACTACTTTAGTAAGCTAAACGC 57.059 37.500 0.00 0.00 40.94 4.84
2813 2866 8.739649 AGAACACTACTTTAGTAAGCTAAACG 57.260 34.615 0.00 0.00 40.94 3.60
2817 2870 9.831737 CGTTTAGAACACTACTTTAGTAAGCTA 57.168 33.333 0.00 0.00 37.23 3.32
2818 2871 7.328005 GCGTTTAGAACACTACTTTAGTAAGCT 59.672 37.037 0.00 0.00 37.23 3.74
2819 2872 7.328005 AGCGTTTAGAACACTACTTTAGTAAGC 59.672 37.037 0.00 0.00 37.23 3.09
2820 2873 8.739649 AGCGTTTAGAACACTACTTTAGTAAG 57.260 34.615 0.00 0.00 37.23 2.34
2821 2874 8.571336 AGAGCGTTTAGAACACTACTTTAGTAA 58.429 33.333 0.00 0.00 37.23 2.24
2822 2875 8.103948 AGAGCGTTTAGAACACTACTTTAGTA 57.896 34.615 0.00 0.00 37.23 1.82
2823 2876 6.979465 AGAGCGTTTAGAACACTACTTTAGT 58.021 36.000 0.00 0.00 40.28 2.24
2824 2877 7.870588 AAGAGCGTTTAGAACACTACTTTAG 57.129 36.000 0.00 0.00 0.00 1.85
2839 2892 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2840 2893 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2841 2894 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2842 2895 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2843 2896 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2896 2949 2.094182 CCTCGATTTCTCACCCGAAGAA 60.094 50.000 0.00 0.00 0.00 2.52
2918 2971 0.319555 TCGTCAAGAAGGTGAAGGCG 60.320 55.000 0.00 0.00 0.00 5.52
2988 3054 6.312487 CGCTGCATCTGATTTATTCTTATGG 58.688 40.000 0.00 0.00 0.00 2.74
2998 3064 3.815401 GGTAATACCGCTGCATCTGATTT 59.185 43.478 0.00 0.00 0.00 2.17
3019 3085 4.806640 AGAATTGGCAAATAGTTGTGGG 57.193 40.909 3.01 0.00 37.06 4.61
3074 3140 8.800972 CATTTTGATGACAAGTATTTTCGGATG 58.199 33.333 0.00 0.00 37.32 3.51
3075 3141 8.739039 TCATTTTGATGACAAGTATTTTCGGAT 58.261 29.630 0.00 0.00 37.32 4.18
3076 3142 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
3077 3143 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
3123 3189 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
3131 3197 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
3145 3211 9.942850 ACTTGTCATTAAAATGAATAAAAGGGG 57.057 29.630 6.95 0.00 46.13 4.79
3155 3221 9.834628 GTCCGAAAATACTTGTCATTAAAATGA 57.165 29.630 1.23 1.23 42.78 2.57
3156 3222 8.785101 CGTCCGAAAATACTTGTCATTAAAATG 58.215 33.333 0.00 0.00 37.75 2.32
3157 3223 7.966204 CCGTCCGAAAATACTTGTCATTAAAAT 59.034 33.333 0.00 0.00 0.00 1.82
3158 3224 7.172875 TCCGTCCGAAAATACTTGTCATTAAAA 59.827 33.333 0.00 0.00 0.00 1.52
3159 3225 6.649973 TCCGTCCGAAAATACTTGTCATTAAA 59.350 34.615 0.00 0.00 0.00 1.52
3160 3226 6.164876 TCCGTCCGAAAATACTTGTCATTAA 58.835 36.000 0.00 0.00 0.00 1.40
3161 3227 5.722263 TCCGTCCGAAAATACTTGTCATTA 58.278 37.500 0.00 0.00 0.00 1.90
3162 3228 4.571919 TCCGTCCGAAAATACTTGTCATT 58.428 39.130 0.00 0.00 0.00 2.57
3163 3229 4.081862 TCTCCGTCCGAAAATACTTGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
3164 3230 3.256383 TCTCCGTCCGAAAATACTTGTCA 59.744 43.478 0.00 0.00 0.00 3.58
3165 3231 3.841643 TCTCCGTCCGAAAATACTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
3166 3232 3.947910 TCTCCGTCCGAAAATACTTGT 57.052 42.857 0.00 0.00 0.00 3.16
3167 3233 4.689345 ACTTTCTCCGTCCGAAAATACTTG 59.311 41.667 0.00 0.00 30.73 3.16
3168 3234 4.891260 ACTTTCTCCGTCCGAAAATACTT 58.109 39.130 0.00 0.00 30.73 2.24
3169 3235 4.532314 ACTTTCTCCGTCCGAAAATACT 57.468 40.909 0.00 0.00 30.73 2.12
3170 3236 5.405797 AGTACTTTCTCCGTCCGAAAATAC 58.594 41.667 0.00 0.00 34.86 1.89
3171 3237 5.649782 AGTACTTTCTCCGTCCGAAAATA 57.350 39.130 0.00 0.00 30.73 1.40
3172 3238 4.532314 AGTACTTTCTCCGTCCGAAAAT 57.468 40.909 0.00 0.00 30.73 1.82
3173 3239 4.321230 GGTAGTACTTTCTCCGTCCGAAAA 60.321 45.833 0.00 0.00 30.73 2.29
3174 3240 3.191371 GGTAGTACTTTCTCCGTCCGAAA 59.809 47.826 0.00 0.00 0.00 3.46
3175 3241 2.749621 GGTAGTACTTTCTCCGTCCGAA 59.250 50.000 0.00 0.00 0.00 4.30
3176 3242 2.026822 AGGTAGTACTTTCTCCGTCCGA 60.027 50.000 0.00 0.00 0.00 4.55
3177 3243 2.354199 GAGGTAGTACTTTCTCCGTCCG 59.646 54.545 0.00 0.00 0.00 4.79
3178 3244 3.350833 TGAGGTAGTACTTTCTCCGTCC 58.649 50.000 17.19 3.63 0.00 4.79
3179 3245 4.009002 ACTGAGGTAGTACTTTCTCCGTC 58.991 47.826 17.19 7.08 38.04 4.79
3180 3246 4.009002 GACTGAGGTAGTACTTTCTCCGT 58.991 47.826 16.27 16.27 40.53 4.69
3181 3247 3.377798 GGACTGAGGTAGTACTTTCTCCG 59.622 52.174 17.19 14.52 40.53 4.63
3182 3248 4.987408 GGACTGAGGTAGTACTTTCTCC 57.013 50.000 17.19 9.25 40.53 3.71
3189 3255 7.779326 ACTAATAAAGGAGGACTGAGGTAGTAC 59.221 40.741 0.00 0.00 40.53 2.73
3190 3256 7.880623 ACTAATAAAGGAGGACTGAGGTAGTA 58.119 38.462 0.00 0.00 40.53 1.82
3191 3257 6.743788 ACTAATAAAGGAGGACTGAGGTAGT 58.256 40.000 0.00 0.00 44.02 2.73
3192 3258 7.064229 AGACTAATAAAGGAGGACTGAGGTAG 58.936 42.308 0.00 0.00 0.00 3.18
3240 3306 7.711339 ACGGAGGAAGTACTTAAAATCATGATC 59.289 37.037 9.06 0.00 0.00 2.92
3259 3325 2.361757 TCGTACAAAAGTGAACGGAGGA 59.638 45.455 0.00 0.00 36.08 3.71
3261 3327 3.739300 ACATCGTACAAAAGTGAACGGAG 59.261 43.478 0.00 0.00 36.08 4.63
3262 3328 3.719924 ACATCGTACAAAAGTGAACGGA 58.280 40.909 0.00 0.00 36.08 4.69
3264 3330 7.317269 GTCTAAAACATCGTACAAAAGTGAACG 59.683 37.037 0.00 0.00 36.71 3.95
3265 3331 8.117988 TGTCTAAAACATCGTACAAAAGTGAAC 58.882 33.333 0.00 0.00 31.20 3.18
3267 3333 7.773864 TGTCTAAAACATCGTACAAAAGTGA 57.226 32.000 0.00 0.00 31.20 3.41
3363 3429 2.421529 CCACTAGGAGGTTACCCAATGC 60.422 54.545 0.00 0.00 36.89 3.56
3372 3438 1.207329 GACGCATTCCACTAGGAGGTT 59.793 52.381 0.00 0.00 46.74 3.50
3381 3447 1.269166 CGAGTGTAGACGCATTCCAC 58.731 55.000 0.00 0.00 0.00 4.02
3389 3455 1.914051 CAAGTGATGCGAGTGTAGACG 59.086 52.381 0.00 0.00 0.00 4.18
3400 3466 2.159338 ACGATTTCATGCCAAGTGATGC 60.159 45.455 0.00 0.00 0.00 3.91
3402 3468 3.614092 AGACGATTTCATGCCAAGTGAT 58.386 40.909 0.00 0.00 0.00 3.06
3407 3473 1.731709 CACGAGACGATTTCATGCCAA 59.268 47.619 0.00 0.00 0.00 4.52
3651 3717 4.193653 GAGCCAGTCGAAGAAGCC 57.806 61.111 0.00 0.00 39.69 4.35
3660 3726 2.907897 ATTGTAGCCGCGAGCCAGTC 62.908 60.000 8.23 1.26 45.47 3.51
3661 3727 3.019003 ATTGTAGCCGCGAGCCAGT 62.019 57.895 8.23 0.00 45.47 4.00
3662 3728 2.202932 ATTGTAGCCGCGAGCCAG 60.203 61.111 8.23 0.00 45.47 4.85
3663 3729 2.511373 CATTGTAGCCGCGAGCCA 60.511 61.111 8.23 0.76 45.47 4.75
3664 3730 3.272334 CCATTGTAGCCGCGAGCC 61.272 66.667 8.23 0.00 45.47 4.70
3665 3731 2.202878 TCCATTGTAGCCGCGAGC 60.203 61.111 8.23 9.98 44.25 5.03
3666 3732 1.592669 CCTCCATTGTAGCCGCGAG 60.593 63.158 8.23 0.00 0.00 5.03
3667 3733 2.499205 CCTCCATTGTAGCCGCGA 59.501 61.111 8.23 0.00 0.00 5.87
3668 3734 3.272334 GCCTCCATTGTAGCCGCG 61.272 66.667 0.00 0.00 0.00 6.46
3669 3735 2.124736 TGCCTCCATTGTAGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
3670 3736 0.464036 TAGTGCCTCCATTGTAGCCG 59.536 55.000 0.00 0.00 0.00 5.52
3671 3737 1.475213 GGTAGTGCCTCCATTGTAGCC 60.475 57.143 0.00 0.00 0.00 3.93
3672 3738 1.475213 GGGTAGTGCCTCCATTGTAGC 60.475 57.143 0.00 0.00 37.43 3.58
3673 3739 1.141053 GGGGTAGTGCCTCCATTGTAG 59.859 57.143 0.00 0.00 37.43 2.74
3674 3740 1.209621 GGGGTAGTGCCTCCATTGTA 58.790 55.000 0.00 0.00 37.43 2.41
3675 3741 1.999346 GGGGTAGTGCCTCCATTGT 59.001 57.895 0.00 0.00 37.43 2.71
3676 3742 4.986467 GGGGTAGTGCCTCCATTG 57.014 61.111 0.00 0.00 37.43 2.82
3681 3747 1.908483 CAGAAGGGGGTAGTGCCTC 59.092 63.158 0.00 0.00 36.85 4.70
3682 3748 2.301738 GCAGAAGGGGGTAGTGCCT 61.302 63.158 0.00 0.00 37.43 4.75
3683 3749 2.272471 GCAGAAGGGGGTAGTGCC 59.728 66.667 0.00 0.00 0.00 5.01
3684 3750 2.125106 CGCAGAAGGGGGTAGTGC 60.125 66.667 0.00 0.00 0.00 4.40
3685 3751 1.517832 CTCGCAGAAGGGGGTAGTG 59.482 63.158 0.00 0.00 34.09 2.74
3686 3752 2.359967 GCTCGCAGAAGGGGGTAGT 61.360 63.158 0.00 0.00 34.09 2.73
3687 3753 1.899437 TTGCTCGCAGAAGGGGGTAG 61.899 60.000 0.00 0.00 34.09 3.18
3688 3754 1.899437 CTTGCTCGCAGAAGGGGGTA 61.899 60.000 0.00 0.00 34.09 3.69
3689 3755 3.249189 TTGCTCGCAGAAGGGGGT 61.249 61.111 0.00 0.00 34.09 4.95
3690 3756 2.437359 CTTGCTCGCAGAAGGGGG 60.437 66.667 0.00 0.00 34.09 5.40
3691 3757 2.437359 CCTTGCTCGCAGAAGGGG 60.437 66.667 2.37 0.00 35.93 4.79
3693 3759 3.130160 GCCCTTGCTCGCAGAAGG 61.130 66.667 3.21 3.21 38.84 3.46
3694 3760 0.462581 TATGCCCTTGCTCGCAGAAG 60.463 55.000 0.00 0.00 38.64 2.85
3695 3761 0.462581 CTATGCCCTTGCTCGCAGAA 60.463 55.000 0.00 0.00 38.64 3.02
3696 3762 1.144716 CTATGCCCTTGCTCGCAGA 59.855 57.895 0.00 0.00 38.64 4.26
3697 3763 0.250209 ATCTATGCCCTTGCTCGCAG 60.250 55.000 0.00 0.00 38.64 5.18
3698 3764 0.181114 AATCTATGCCCTTGCTCGCA 59.819 50.000 0.00 0.00 39.79 5.10
3699 3765 2.169832 TAATCTATGCCCTTGCTCGC 57.830 50.000 0.00 0.00 38.71 5.03
3700 3766 4.143030 CGAAATAATCTATGCCCTTGCTCG 60.143 45.833 0.00 0.00 38.71 5.03
3701 3767 4.378874 GCGAAATAATCTATGCCCTTGCTC 60.379 45.833 0.00 0.00 38.71 4.26
3702 3768 3.503748 GCGAAATAATCTATGCCCTTGCT 59.496 43.478 0.00 0.00 38.71 3.91
3703 3769 3.366374 GGCGAAATAATCTATGCCCTTGC 60.366 47.826 0.00 0.00 36.51 4.01
3704 3770 3.820467 TGGCGAAATAATCTATGCCCTTG 59.180 43.478 0.00 0.00 41.77 3.61
3705 3771 4.098914 TGGCGAAATAATCTATGCCCTT 57.901 40.909 0.00 0.00 41.77 3.95
3706 3772 3.788227 TGGCGAAATAATCTATGCCCT 57.212 42.857 0.00 0.00 41.77 5.19
3707 3773 3.378427 GGATGGCGAAATAATCTATGCCC 59.622 47.826 0.00 0.00 41.77 5.36
3708 3774 4.265073 AGGATGGCGAAATAATCTATGCC 58.735 43.478 0.00 0.00 42.76 4.40
3709 3775 4.937620 TGAGGATGGCGAAATAATCTATGC 59.062 41.667 0.00 0.00 0.00 3.14
3710 3776 5.352569 GGTGAGGATGGCGAAATAATCTATG 59.647 44.000 0.00 0.00 0.00 2.23
3711 3777 5.491982 GGTGAGGATGGCGAAATAATCTAT 58.508 41.667 0.00 0.00 0.00 1.98
3712 3778 4.560716 CGGTGAGGATGGCGAAATAATCTA 60.561 45.833 0.00 0.00 0.00 1.98
3713 3779 3.744660 GGTGAGGATGGCGAAATAATCT 58.255 45.455 0.00 0.00 0.00 2.40
3714 3780 2.480419 CGGTGAGGATGGCGAAATAATC 59.520 50.000 0.00 0.00 0.00 1.75
3715 3781 2.494059 CGGTGAGGATGGCGAAATAAT 58.506 47.619 0.00 0.00 0.00 1.28
3716 3782 1.948104 CGGTGAGGATGGCGAAATAA 58.052 50.000 0.00 0.00 0.00 1.40
3717 3783 0.531974 GCGGTGAGGATGGCGAAATA 60.532 55.000 0.00 0.00 0.00 1.40
3718 3784 1.819632 GCGGTGAGGATGGCGAAAT 60.820 57.895 0.00 0.00 0.00 2.17
3719 3785 2.435938 GCGGTGAGGATGGCGAAA 60.436 61.111 0.00 0.00 0.00 3.46
3720 3786 4.467084 GGCGGTGAGGATGGCGAA 62.467 66.667 0.00 0.00 0.00 4.70
3723 3789 4.864334 CCAGGCGGTGAGGATGGC 62.864 72.222 0.00 0.00 0.00 4.40
3724 3790 3.402681 ACCAGGCGGTGAGGATGG 61.403 66.667 0.23 0.00 46.79 3.51
3733 3799 2.597217 TTCAAAGGCACCAGGCGG 60.597 61.111 0.00 0.00 46.16 6.13


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

AutoCloner maintained by Alex Coulton.