Multiple sequence alignment - TraesCS2D01G094200

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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 TraesCS2D01G094200 chr2D 100.000 3023 0 0 1 3023 45798198 45801220 0.000000e+00 5583.0
1 TraesCS2D01G094200 chr2D 91.690 361 19 6 2448 2800 45802948 45803305 9.740000e-135 490.0
2 TraesCS2D01G094200 chr2D 84.496 129 17 3 500 627 45798602 45798728 1.140000e-24 124.0
3 TraesCS2D01G094200 chr2D 84.496 129 17 3 405 531 45798697 45798824 1.140000e-24 124.0
4 TraesCS2D01G094200 chr2D 85.321 109 12 3 431 536 219893725 219893832 3.190000e-20 110.0
5 TraesCS2D01G094200 chr2B 92.740 2383 95 33 398 2733 72894558 72896909 0.000000e+00 3371.0
6 TraesCS2D01G094200 chr2B 87.000 600 48 12 1 577 72894049 72894641 0.000000e+00 649.0
7 TraesCS2D01G094200 chr2A 92.674 2375 106 35 405 2734 49220507 49222858 0.000000e+00 3360.0
8 TraesCS2D01G094200 chr2A 86.718 655 54 13 1 624 49219977 49220629 0.000000e+00 697.0
9 TraesCS2D01G094200 chr6D 87.500 224 26 2 2802 3023 127906681 127906458 1.080000e-64 257.0
10 TraesCS2D01G094200 chr6D 83.568 213 30 5 2800 3009 262785222 262785432 8.550000e-46 195.0
11 TraesCS2D01G094200 chr6D 91.538 130 11 0 2800 2929 57788606 57788735 2.390000e-41 180.0
12 TraesCS2D01G094200 chr6A 85.650 223 31 1 2802 3023 150247113 150247335 1.810000e-57 233.0
13 TraesCS2D01G094200 chr6A 90.698 129 12 0 2801 2929 327298907 327299035 4.010000e-39 172.0
14 TraesCS2D01G094200 chr3D 85.463 227 29 3 2801 3023 463542189 463542415 1.810000e-57 233.0
15 TraesCS2D01G094200 chr3D 82.819 227 35 3 2800 3023 346756258 346756033 1.840000e-47 200.0
16 TraesCS2D01G094200 chr3D 86.486 111 9 4 526 633 140762394 140762287 1.900000e-22 117.0
17 TraesCS2D01G094200 chr3D 85.321 109 12 3 431 536 339679824 339679931 3.190000e-20 110.0
18 TraesCS2D01G094200 chr7D 84.914 232 27 5 2800 3023 143538658 143538889 8.430000e-56 228.0
19 TraesCS2D01G094200 chr5D 84.211 228 32 4 2800 3023 464531108 464530881 5.070000e-53 219.0
20 TraesCS2D01G094200 chr5D 83.700 227 31 5 2802 3023 292814750 292814525 3.050000e-50 209.0
21 TraesCS2D01G094200 chr4D 82.716 243 22 5 2801 3023 351068468 351068226 6.610000e-47 198.0
22 TraesCS2D01G094200 chr4D 82.231 242 24 7 2801 3023 444259426 444259185 1.110000e-44 191.0
23 TraesCS2D01G094200 chr4D 82.305 243 22 9 2801 3023 487656620 487656861 1.110000e-44 191.0
24 TraesCS2D01G094200 chr4D 82.083 240 22 8 2800 3020 230660048 230660285 5.150000e-43 185.0
25 TraesCS2D01G094200 chr4D 81.818 242 25 8 2801 3023 444274983 444274742 5.150000e-43 185.0
26 TraesCS2D01G094200 chr4D 80.952 231 36 4 2800 3023 154024445 154024216 3.100000e-40 176.0
27 TraesCS2D01G094200 chr4D 89.922 129 13 0 2801 2929 254698991 254699119 1.860000e-37 167.0
28 TraesCS2D01G094200 chr4D 90.000 130 11 2 2801 2929 472131767 472131895 1.860000e-37 167.0
29 TraesCS2D01G094200 chr4D 86.111 144 18 2 2799 2941 6430217 6430075 1.450000e-33 154.0
30 TraesCS2D01G094200 chr4D 85.321 109 12 3 431 536 64796195 64796088 3.190000e-20 110.0
31 TraesCS2D01G094200 chr4A 82.883 222 35 2 2800 3018 161654459 161654238 2.380000e-46 196.0
32 TraesCS2D01G094200 chr4B 82.377 244 21 9 2800 3023 33512009 33511768 3.080000e-45 193.0
33 TraesCS2D01G094200 chr4B 87.037 108 12 2 526 633 551728851 551728956 1.470000e-23 121.0
34 TraesCS2D01G094200 chr1A 82.589 224 32 4 2795 3012 220747712 220747934 1.110000e-44 191.0
35 TraesCS2D01G094200 chr1A 82.305 243 18 12 2801 3023 78522567 78522330 1.430000e-43 187.0
36 TraesCS2D01G094200 chr1D 91.538 130 9 2 2801 2929 119005386 119005258 8.610000e-41 178.0
37 TraesCS2D01G094200 chr1D 81.034 232 36 4 2799 3023 134561815 134562045 8.610000e-41 178.0
38 TraesCS2D01G094200 chr1D 90.698 129 12 0 2801 2929 285014700 285014828 4.010000e-39 172.0
39 TraesCS2D01G094200 chr7B 87.500 104 11 2 530 633 107644658 107644759 5.290000e-23 119.0
40 TraesCS2D01G094200 chr7A 87.500 104 11 2 525 628 36322209 36322108 5.290000e-23 119.0
41 TraesCS2D01G094200 chr5B 86.364 110 11 4 526 633 320746256 320746149 1.900000e-22 117.0
42 TraesCS2D01G094200 chr5A 88.542 96 11 0 432 527 350268454 350268549 1.900000e-22 117.0
43 TraesCS2D01G094200 chrUn 86.111 108 13 2 526 633 41734265 41734370 6.850000e-22 115.0
44 TraesCS2D01G094200 chrUn 87.629 97 12 0 431 527 82485358 82485454 2.460000e-21 113.0
45 TraesCS2D01G094200 chr3A 87.000 100 13 0 440 539 16620489 16620390 2.460000e-21 113.0
46 TraesCS2D01G094200 chr6B 100.000 28 0 0 405 432 567847525 567847552 5.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G094200 chr2D 45798198 45801220 3022 False 1943.666667 5583 89.664 1 3023 3 chr2D.!!$F3 3022
1 TraesCS2D01G094200 chr2B 72894049 72896909 2860 False 2010.000000 3371 89.870 1 2733 2 chr2B.!!$F1 2732
2 TraesCS2D01G094200 chr2A 49219977 49222858 2881 False 2028.500000 3360 89.696 1 2734 2 chr2A.!!$F1 2733

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
851 985 1.137825 CGAGTCCTTCGTCTGCTCC 59.862 63.158 0.0 0.0 44.27 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2810 3012 0.033504 CGCCTCATACGCTACCCATT 59.966 55.0 0.0 0.0 0.0 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
81 86 3.136443 TGGATTCATTCGGTGGCTAGATT 59.864 43.478 0.00 0.00 0.00 2.40
353 379 5.426509 TGATGACACATACTCCCTTCATTCT 59.573 40.000 0.00 0.00 0.00 2.40
396 422 9.661954 TTAGAGATTCCAGTATGAATTACTCCT 57.338 33.333 0.00 0.00 39.19 3.69
398 424 8.997734 AGAGATTCCAGTATGAATTACTCCTTT 58.002 33.333 0.00 0.00 39.19 3.11
455 587 5.473504 ACCTACGAAGCAAAATGAGTGAATT 59.526 36.000 0.00 0.00 0.00 2.17
545 679 5.673029 ACTTACGTACGAAGCAAAATGAAC 58.327 37.500 24.41 0.00 0.00 3.18
549 683 3.592383 CGTACGAAGCAAAATGAACGAAC 59.408 43.478 10.44 0.00 0.00 3.95
815 949 3.706373 CCCTAGCCACTGCCACGT 61.706 66.667 0.00 0.00 38.69 4.49
850 984 4.775746 CGAGTCCTTCGTCTGCTC 57.224 61.111 0.00 0.00 44.27 4.26
851 985 1.137825 CGAGTCCTTCGTCTGCTCC 59.862 63.158 0.00 0.00 44.27 4.70
852 986 1.309499 CGAGTCCTTCGTCTGCTCCT 61.309 60.000 0.00 0.00 44.27 3.69
885 1019 1.735920 CGCTCACTCCACAGCAGAC 60.736 63.158 0.00 0.00 35.15 3.51
992 1139 2.776536 AGGGTCAATTAGCAGCTGATCT 59.223 45.455 20.43 8.63 0.00 2.75
994 1141 3.539604 GGTCAATTAGCAGCTGATCTGT 58.460 45.455 20.43 0.00 44.66 3.41
995 1142 3.559242 GGTCAATTAGCAGCTGATCTGTC 59.441 47.826 20.43 7.54 44.66 3.51
1014 1161 1.076192 GATCATGGGCATGGAGGGG 59.924 63.158 0.00 0.00 39.24 4.79
2048 2202 2.107750 ATCGCCAGCAGACATCGG 59.892 61.111 0.00 0.00 0.00 4.18
2106 2264 7.148137 ACCGATTAATATTTGCCCGATTAATCC 60.148 37.037 9.87 0.00 43.42 3.01
2140 2298 6.611381 ACATACATGCATGGTAATAATTCGC 58.389 36.000 29.41 0.00 0.00 4.70
2171 2333 1.901591 CATGGATGGATGTGGCTACC 58.098 55.000 0.00 0.00 0.00 3.18
2177 2339 4.910913 TGGATGGATGTGGCTACCTATTTA 59.089 41.667 0.00 0.00 0.00 1.40
2178 2340 5.221843 TGGATGGATGTGGCTACCTATTTAC 60.222 44.000 0.00 0.00 0.00 2.01
2179 2341 4.699925 TGGATGTGGCTACCTATTTACC 57.300 45.455 0.00 0.00 0.00 2.85
2383 2556 4.002982 CTGCCTGCTGTTGTAATAAGTGA 58.997 43.478 0.00 0.00 0.00 3.41
2404 2577 8.939201 AGTGATTTTGACACTCTATATGACTG 57.061 34.615 0.00 0.00 43.84 3.51
2473 2663 4.829064 TTGATTCCCTTGTTTCAACGAG 57.171 40.909 0.00 0.38 39.63 4.18
2477 2667 1.673920 TCCCTTGTTTCAACGAGTTGC 59.326 47.619 10.83 0.00 38.50 4.17
2481 2671 2.842208 TGTTTCAACGAGTTGCCTTG 57.158 45.000 10.83 0.00 40.24 3.61
2522 2718 9.567848 TTAAGAAAATAATTGTCTCGATTTGCC 57.432 29.630 0.00 0.00 0.00 4.52
2523 2719 7.156876 AGAAAATAATTGTCTCGATTTGCCA 57.843 32.000 0.00 0.00 0.00 4.92
2543 2743 1.563111 TGCGATTTACCCGATCGTTC 58.437 50.000 15.09 0.47 45.99 3.95
2565 2765 8.700644 CGTTCCAGTTAGTCAGCAAATATATAC 58.299 37.037 0.00 0.00 0.00 1.47
2566 2766 9.765795 GTTCCAGTTAGTCAGCAAATATATACT 57.234 33.333 0.00 0.00 0.00 2.12
2599 2799 3.126831 GCAAAGTGCGAGCTCATATAGT 58.873 45.455 15.40 0.00 31.71 2.12
2600 2800 4.299155 GCAAAGTGCGAGCTCATATAGTA 58.701 43.478 15.40 0.00 31.71 1.82
2601 2801 4.384247 GCAAAGTGCGAGCTCATATAGTAG 59.616 45.833 15.40 0.00 31.71 2.57
2602 2802 4.775058 AAGTGCGAGCTCATATAGTAGG 57.225 45.455 15.40 0.00 0.00 3.18
2688 2890 2.733218 CGACCGTGCTGCTCGAAA 60.733 61.111 23.74 0.00 0.00 3.46
2699 2901 0.534877 TGCTCGAAATGTGTGCCAGT 60.535 50.000 0.00 0.00 0.00 4.00
2702 2904 1.872952 CTCGAAATGTGTGCCAGTCAA 59.127 47.619 0.00 0.00 0.00 3.18
2736 2938 6.072112 GGAATTTTCCTTTTCTTTTTGGCC 57.928 37.500 0.00 0.00 44.11 5.36
2737 2939 5.277779 GGAATTTTCCTTTTCTTTTTGGCCG 60.278 40.000 0.00 0.00 44.11 6.13
2738 2940 2.900716 TTCCTTTTCTTTTTGGCCGG 57.099 45.000 0.00 0.00 0.00 6.13
2739 2941 1.044611 TCCTTTTCTTTTTGGCCGGG 58.955 50.000 2.18 0.00 0.00 5.73
2740 2942 1.044611 CCTTTTCTTTTTGGCCGGGA 58.955 50.000 2.18 0.00 0.00 5.14
2741 2943 1.000843 CCTTTTCTTTTTGGCCGGGAG 59.999 52.381 2.18 0.00 0.00 4.30
2742 2944 1.960689 CTTTTCTTTTTGGCCGGGAGA 59.039 47.619 2.18 0.00 0.00 3.71
2743 2945 2.302587 TTTCTTTTTGGCCGGGAGAT 57.697 45.000 2.18 0.00 0.00 2.75
2744 2946 1.544724 TTCTTTTTGGCCGGGAGATG 58.455 50.000 2.18 0.00 0.00 2.90
2745 2947 0.695924 TCTTTTTGGCCGGGAGATGA 59.304 50.000 2.18 0.00 0.00 2.92
2746 2948 1.284785 TCTTTTTGGCCGGGAGATGAT 59.715 47.619 2.18 0.00 0.00 2.45
2747 2949 1.406539 CTTTTTGGCCGGGAGATGATG 59.593 52.381 2.18 0.00 0.00 3.07
2748 2950 0.395586 TTTTGGCCGGGAGATGATGG 60.396 55.000 2.18 0.00 0.00 3.51
2749 2951 1.278302 TTTGGCCGGGAGATGATGGA 61.278 55.000 2.18 0.00 0.00 3.41
2750 2952 1.278302 TTGGCCGGGAGATGATGGAA 61.278 55.000 2.18 0.00 0.00 3.53
2751 2953 1.061905 TGGCCGGGAGATGATGGAAT 61.062 55.000 2.18 0.00 0.00 3.01
2752 2954 0.111253 GGCCGGGAGATGATGGAATT 59.889 55.000 2.18 0.00 0.00 2.17
2753 2955 1.479389 GGCCGGGAGATGATGGAATTT 60.479 52.381 2.18 0.00 0.00 1.82
2754 2956 1.610522 GCCGGGAGATGATGGAATTTG 59.389 52.381 2.18 0.00 0.00 2.32
2755 2957 1.610522 CCGGGAGATGATGGAATTTGC 59.389 52.381 0.00 0.00 0.00 3.68
2756 2958 2.579873 CGGGAGATGATGGAATTTGCT 58.420 47.619 0.00 0.00 0.00 3.91
2757 2959 3.496692 CCGGGAGATGATGGAATTTGCTA 60.497 47.826 0.00 0.00 0.00 3.49
2758 2960 3.499918 CGGGAGATGATGGAATTTGCTAC 59.500 47.826 0.00 0.00 0.00 3.58
2759 2961 4.723309 GGGAGATGATGGAATTTGCTACT 58.277 43.478 0.00 0.00 0.00 2.57
2760 2962 5.136105 GGGAGATGATGGAATTTGCTACTT 58.864 41.667 0.00 0.00 0.00 2.24
2761 2963 5.009410 GGGAGATGATGGAATTTGCTACTTG 59.991 44.000 0.00 0.00 0.00 3.16
2762 2964 5.591877 GGAGATGATGGAATTTGCTACTTGT 59.408 40.000 0.00 0.00 0.00 3.16
2763 2965 6.446781 AGATGATGGAATTTGCTACTTGTG 57.553 37.500 0.00 0.00 0.00 3.33
2764 2966 5.948162 AGATGATGGAATTTGCTACTTGTGT 59.052 36.000 0.00 0.00 0.00 3.72
2765 2967 5.627499 TGATGGAATTTGCTACTTGTGTC 57.373 39.130 0.00 0.00 0.00 3.67
2766 2968 5.316167 TGATGGAATTTGCTACTTGTGTCT 58.684 37.500 0.00 0.00 0.00 3.41
2767 2969 5.769662 TGATGGAATTTGCTACTTGTGTCTT 59.230 36.000 0.00 0.00 0.00 3.01
2768 2970 6.265196 TGATGGAATTTGCTACTTGTGTCTTT 59.735 34.615 0.00 0.00 0.00 2.52
2769 2971 6.463995 TGGAATTTGCTACTTGTGTCTTTT 57.536 33.333 0.00 0.00 0.00 2.27
2770 2972 6.872920 TGGAATTTGCTACTTGTGTCTTTTT 58.127 32.000 0.00 0.00 0.00 1.94
2771 2973 8.001881 TGGAATTTGCTACTTGTGTCTTTTTA 57.998 30.769 0.00 0.00 0.00 1.52
2772 2974 8.134895 TGGAATTTGCTACTTGTGTCTTTTTAG 58.865 33.333 0.00 0.00 0.00 1.85
2773 2975 7.114953 GGAATTTGCTACTTGTGTCTTTTTAGC 59.885 37.037 0.00 0.00 0.00 3.09
2774 2976 4.725556 TGCTACTTGTGTCTTTTTAGCG 57.274 40.909 0.00 0.00 32.51 4.26
2775 2977 3.496884 TGCTACTTGTGTCTTTTTAGCGG 59.503 43.478 0.00 0.00 32.51 5.52
2776 2978 3.744426 GCTACTTGTGTCTTTTTAGCGGA 59.256 43.478 0.00 0.00 0.00 5.54
2777 2979 4.212636 GCTACTTGTGTCTTTTTAGCGGAA 59.787 41.667 0.00 0.00 0.00 4.30
2778 2980 5.106673 GCTACTTGTGTCTTTTTAGCGGAAT 60.107 40.000 0.00 0.00 0.00 3.01
2779 2981 5.767816 ACTTGTGTCTTTTTAGCGGAATT 57.232 34.783 0.00 0.00 0.00 2.17
2780 2982 6.144078 ACTTGTGTCTTTTTAGCGGAATTT 57.856 33.333 0.00 0.00 0.00 1.82
2781 2983 5.977129 ACTTGTGTCTTTTTAGCGGAATTTG 59.023 36.000 0.00 0.00 0.00 2.32
2782 2984 4.295051 TGTGTCTTTTTAGCGGAATTTGC 58.705 39.130 0.00 0.00 0.00 3.68
2783 2985 4.037446 TGTGTCTTTTTAGCGGAATTTGCT 59.963 37.500 10.49 10.49 46.29 3.91
2784 2986 5.239744 TGTGTCTTTTTAGCGGAATTTGCTA 59.760 36.000 8.73 8.73 43.71 3.49
2785 2987 5.567915 GTGTCTTTTTAGCGGAATTTGCTAC 59.432 40.000 11.57 4.61 44.16 3.58
2786 2988 5.472137 TGTCTTTTTAGCGGAATTTGCTACT 59.528 36.000 11.57 0.00 44.16 2.57
2787 2989 6.016610 TGTCTTTTTAGCGGAATTTGCTACTT 60.017 34.615 11.57 0.00 44.16 2.24
2788 2990 6.305638 GTCTTTTTAGCGGAATTTGCTACTTG 59.694 38.462 11.57 5.06 44.16 3.16
2789 2991 5.699097 TTTTAGCGGAATTTGCTACTTGT 57.301 34.783 11.57 0.00 44.16 3.16
2790 2992 4.678509 TTAGCGGAATTTGCTACTTGTG 57.321 40.909 11.57 0.00 44.16 3.33
2791 2993 1.200020 AGCGGAATTTGCTACTTGTGC 59.800 47.619 4.49 0.00 41.87 4.57
2792 2994 1.882198 CGGAATTTGCTACTTGTGCG 58.118 50.000 0.00 0.00 0.00 5.34
2793 2995 1.463056 CGGAATTTGCTACTTGTGCGA 59.537 47.619 0.00 0.00 0.00 5.10
2794 2996 2.095853 CGGAATTTGCTACTTGTGCGAT 59.904 45.455 0.00 0.00 0.00 4.58
2795 2997 3.685058 GGAATTTGCTACTTGTGCGATC 58.315 45.455 0.00 0.00 0.00 3.69
2796 2998 3.375299 GGAATTTGCTACTTGTGCGATCT 59.625 43.478 0.00 0.00 0.00 2.75
2797 2999 4.570772 GGAATTTGCTACTTGTGCGATCTA 59.429 41.667 0.00 0.00 0.00 1.98
2798 3000 5.470845 AATTTGCTACTTGTGCGATCTAC 57.529 39.130 0.00 0.00 0.00 2.59
2799 3001 2.579207 TGCTACTTGTGCGATCTACC 57.421 50.000 0.00 0.00 0.00 3.18
2800 3002 2.100197 TGCTACTTGTGCGATCTACCT 58.900 47.619 0.00 0.00 0.00 3.08
2801 3003 3.284617 TGCTACTTGTGCGATCTACCTA 58.715 45.455 0.00 0.00 0.00 3.08
2802 3004 3.697542 TGCTACTTGTGCGATCTACCTAA 59.302 43.478 0.00 0.00 0.00 2.69
2803 3005 4.202020 TGCTACTTGTGCGATCTACCTAAG 60.202 45.833 0.00 0.00 0.00 2.18
2804 3006 3.802948 ACTTGTGCGATCTACCTAAGG 57.197 47.619 0.00 0.00 0.00 2.69
2805 3007 3.362706 ACTTGTGCGATCTACCTAAGGA 58.637 45.455 0.00 0.00 0.00 3.36
2806 3008 3.961408 ACTTGTGCGATCTACCTAAGGAT 59.039 43.478 0.00 0.00 0.00 3.24
2807 3009 4.202161 ACTTGTGCGATCTACCTAAGGATG 60.202 45.833 0.00 0.00 0.00 3.51
2808 3010 2.628178 TGTGCGATCTACCTAAGGATGG 59.372 50.000 0.00 0.00 0.00 3.51
2809 3011 2.891580 GTGCGATCTACCTAAGGATGGA 59.108 50.000 0.00 0.00 0.00 3.41
2810 3012 3.321111 GTGCGATCTACCTAAGGATGGAA 59.679 47.826 0.00 0.00 0.00 3.53
2811 3013 3.964688 TGCGATCTACCTAAGGATGGAAA 59.035 43.478 0.00 0.00 0.00 3.13
2812 3014 4.593206 TGCGATCTACCTAAGGATGGAAAT 59.407 41.667 0.00 0.00 0.00 2.17
2813 3015 4.932200 GCGATCTACCTAAGGATGGAAATG 59.068 45.833 0.00 0.00 0.00 2.32
2814 3016 5.482908 CGATCTACCTAAGGATGGAAATGG 58.517 45.833 0.00 0.00 0.00 3.16
2815 3017 5.569630 CGATCTACCTAAGGATGGAAATGGG 60.570 48.000 0.00 0.00 0.00 4.00
2816 3018 4.641868 TCTACCTAAGGATGGAAATGGGT 58.358 43.478 0.00 0.00 0.00 4.51
2817 3019 5.795079 TCTACCTAAGGATGGAAATGGGTA 58.205 41.667 0.00 0.00 0.00 3.69
2818 3020 5.844516 TCTACCTAAGGATGGAAATGGGTAG 59.155 44.000 0.00 0.00 43.50 3.18
2819 3021 3.138468 ACCTAAGGATGGAAATGGGTAGC 59.862 47.826 0.00 0.00 0.00 3.58
2820 3022 2.348411 AAGGATGGAAATGGGTAGCG 57.652 50.000 0.00 0.00 0.00 4.26
2821 3023 1.213296 AGGATGGAAATGGGTAGCGT 58.787 50.000 0.00 0.00 0.00 5.07
2822 3024 2.404559 AGGATGGAAATGGGTAGCGTA 58.595 47.619 0.00 0.00 0.00 4.42
2823 3025 2.979678 AGGATGGAAATGGGTAGCGTAT 59.020 45.455 0.00 0.00 0.00 3.06
2824 3026 3.074412 GGATGGAAATGGGTAGCGTATG 58.926 50.000 0.00 0.00 0.00 2.39
2825 3027 3.244422 GGATGGAAATGGGTAGCGTATGA 60.244 47.826 0.00 0.00 0.00 2.15
2826 3028 3.469008 TGGAAATGGGTAGCGTATGAG 57.531 47.619 0.00 0.00 0.00 2.90
2827 3029 2.104111 TGGAAATGGGTAGCGTATGAGG 59.896 50.000 0.00 0.00 0.00 3.86
2828 3030 2.143925 GAAATGGGTAGCGTATGAGGC 58.856 52.381 0.00 0.00 0.00 4.70
2829 3031 0.033504 AATGGGTAGCGTATGAGGCG 59.966 55.000 0.00 0.00 33.62 5.52
2830 3032 1.816863 ATGGGTAGCGTATGAGGCGG 61.817 60.000 0.00 0.00 33.62 6.13
2831 3033 2.338984 GGTAGCGTATGAGGCGGG 59.661 66.667 0.00 0.00 33.62 6.13
2832 3034 2.496291 GGTAGCGTATGAGGCGGGT 61.496 63.158 0.00 0.00 33.62 5.28
2833 3035 1.174712 GGTAGCGTATGAGGCGGGTA 61.175 60.000 0.00 0.00 33.62 3.69
2834 3036 0.240411 GTAGCGTATGAGGCGGGTAG 59.760 60.000 0.00 0.00 33.62 3.18
2835 3037 0.109153 TAGCGTATGAGGCGGGTAGA 59.891 55.000 0.00 0.00 33.62 2.59
2836 3038 1.173444 AGCGTATGAGGCGGGTAGAG 61.173 60.000 0.00 0.00 33.62 2.43
2837 3039 1.286260 CGTATGAGGCGGGTAGAGC 59.714 63.158 0.00 0.00 0.00 4.09
2838 3040 1.452953 CGTATGAGGCGGGTAGAGCA 61.453 60.000 0.00 0.00 36.08 4.26
2839 3041 0.750850 GTATGAGGCGGGTAGAGCAA 59.249 55.000 0.00 0.00 36.08 3.91
2840 3042 1.344763 GTATGAGGCGGGTAGAGCAAT 59.655 52.381 0.00 0.00 36.08 3.56
2841 3043 1.717032 ATGAGGCGGGTAGAGCAATA 58.283 50.000 0.00 0.00 36.08 1.90
2842 3044 0.750850 TGAGGCGGGTAGAGCAATAC 59.249 55.000 0.00 0.00 36.08 1.89
2843 3045 0.033642 GAGGCGGGTAGAGCAATACC 59.966 60.000 8.50 8.50 43.90 2.73
2844 3046 0.689745 AGGCGGGTAGAGCAATACCA 60.690 55.000 16.56 0.00 46.04 3.25
2845 3047 0.396811 GGCGGGTAGAGCAATACCAT 59.603 55.000 16.56 0.00 46.04 3.55
2846 3048 1.621814 GGCGGGTAGAGCAATACCATA 59.378 52.381 16.56 0.00 46.04 2.74
2847 3049 2.612221 GGCGGGTAGAGCAATACCATAC 60.612 54.545 16.56 7.14 46.04 2.39
2848 3050 2.612221 GCGGGTAGAGCAATACCATACC 60.612 54.545 16.56 4.24 46.04 2.73
2849 3051 3.697619 GGGTAGAGCAATACCATACCC 57.302 52.381 16.56 3.12 46.04 3.69
2851 3053 4.910458 GGTAGAGCAATACCATACCCAT 57.090 45.455 11.42 0.00 44.04 4.00
2853 3055 5.731591 GGTAGAGCAATACCATACCCATAC 58.268 45.833 11.42 0.00 44.04 2.39
2854 3056 4.910458 AGAGCAATACCATACCCATACC 57.090 45.455 0.00 0.00 0.00 2.73
2855 3057 3.587506 AGAGCAATACCATACCCATACCC 59.412 47.826 0.00 0.00 0.00 3.69
2856 3058 3.329520 GAGCAATACCATACCCATACCCA 59.670 47.826 0.00 0.00 0.00 4.51
2857 3059 3.922778 AGCAATACCATACCCATACCCAT 59.077 43.478 0.00 0.00 0.00 4.00
2858 3060 4.016444 GCAATACCATACCCATACCCATG 58.984 47.826 0.00 0.00 0.00 3.66
2859 3061 4.508405 GCAATACCATACCCATACCCATGT 60.508 45.833 0.00 0.00 0.00 3.21
2860 3062 5.280779 GCAATACCATACCCATACCCATGTA 60.281 44.000 0.00 0.00 0.00 2.29
2861 3063 6.414732 CAATACCATACCCATACCCATGTAG 58.585 44.000 0.00 0.00 0.00 2.74
2862 3064 3.949430 ACCATACCCATACCCATGTAGT 58.051 45.455 0.00 0.00 0.00 2.73
2863 3065 3.908103 ACCATACCCATACCCATGTAGTC 59.092 47.826 0.00 0.00 0.00 2.59
2864 3066 3.907474 CCATACCCATACCCATGTAGTCA 59.093 47.826 0.00 0.00 0.00 3.41
2865 3067 4.349636 CCATACCCATACCCATGTAGTCAA 59.650 45.833 0.00 0.00 0.00 3.18
2866 3068 5.014123 CCATACCCATACCCATGTAGTCAAT 59.986 44.000 0.00 0.00 0.00 2.57
2867 3069 4.437682 ACCCATACCCATGTAGTCAATG 57.562 45.455 0.00 0.00 0.00 2.82
2868 3070 3.138283 ACCCATACCCATGTAGTCAATGG 59.862 47.826 7.49 7.49 35.31 3.16
2869 3071 3.394274 CCCATACCCATGTAGTCAATGGA 59.606 47.826 13.04 0.00 37.66 3.41
2870 3072 4.043310 CCCATACCCATGTAGTCAATGGAT 59.957 45.833 13.04 0.00 37.66 3.41
2871 3073 5.250543 CCCATACCCATGTAGTCAATGGATA 59.749 44.000 13.04 0.00 37.66 2.59
2872 3074 6.409704 CCATACCCATGTAGTCAATGGATAG 58.590 44.000 4.00 0.00 37.66 2.08
2873 3075 6.213397 CCATACCCATGTAGTCAATGGATAGA 59.787 42.308 4.00 0.00 37.66 1.98
2874 3076 7.256655 CCATACCCATGTAGTCAATGGATAGAA 60.257 40.741 4.00 0.00 37.66 2.10
2875 3077 6.575244 ACCCATGTAGTCAATGGATAGAAA 57.425 37.500 4.00 0.00 37.66 2.52
2876 3078 6.969043 ACCCATGTAGTCAATGGATAGAAAA 58.031 36.000 4.00 0.00 37.66 2.29
2877 3079 7.586349 ACCCATGTAGTCAATGGATAGAAAAT 58.414 34.615 4.00 0.00 37.66 1.82
2878 3080 8.061304 ACCCATGTAGTCAATGGATAGAAAATT 58.939 33.333 4.00 0.00 37.66 1.82
2879 3081 8.571336 CCCATGTAGTCAATGGATAGAAAATTC 58.429 37.037 4.00 0.00 37.66 2.17
2880 3082 9.347240 CCATGTAGTCAATGGATAGAAAATTCT 57.653 33.333 0.77 0.77 38.20 2.40
2895 3097 6.766429 AGAAAATTCTATCCATACCCGTACC 58.234 40.000 0.00 0.00 35.34 3.34
2896 3098 5.494390 AAATTCTATCCATACCCGTACCC 57.506 43.478 0.00 0.00 0.00 3.69
2897 3099 3.616343 TTCTATCCATACCCGTACCCA 57.384 47.619 0.00 0.00 0.00 4.51
2898 3100 3.839323 TCTATCCATACCCGTACCCAT 57.161 47.619 0.00 0.00 0.00 4.00
2899 3101 3.437213 TCTATCCATACCCGTACCCATG 58.563 50.000 0.00 0.00 0.00 3.66
2900 3102 1.358152 ATCCATACCCGTACCCATGG 58.642 55.000 4.14 4.14 39.48 3.66
2919 3121 8.698973 CCCATGGGTATAAAACATTACATGTA 57.301 34.615 23.93 0.08 44.07 2.29
2920 3122 8.573035 CCCATGGGTATAAAACATTACATGTAC 58.427 37.037 23.93 0.00 44.07 2.90
2921 3123 8.573035 CCATGGGTATAAAACATTACATGTACC 58.427 37.037 4.68 1.64 44.07 3.34
2928 3130 8.700439 ATAAAACATTACATGTACCCATACCC 57.300 34.615 4.68 0.00 44.07 3.69
2929 3131 5.718801 AACATTACATGTACCCATACCCA 57.281 39.130 4.68 0.00 44.07 4.51
2930 3132 5.922960 ACATTACATGTACCCATACCCAT 57.077 39.130 4.68 0.00 42.78 4.00
2931 3133 6.274322 ACATTACATGTACCCATACCCATT 57.726 37.500 4.68 0.00 42.78 3.16
2932 3134 7.395525 ACATTACATGTACCCATACCCATTA 57.604 36.000 4.68 0.00 42.78 1.90
2933 3135 7.458397 ACATTACATGTACCCATACCCATTAG 58.542 38.462 4.68 0.00 42.78 1.73
2934 3136 4.993705 ACATGTACCCATACCCATTAGG 57.006 45.455 0.00 0.00 43.78 2.69
2944 3146 3.792712 CCCATTAGGTACCCAACGG 57.207 57.895 8.74 2.64 0.00 4.44
2960 3162 5.886992 CCCAACGGGTAAATCAAAGAATAC 58.113 41.667 0.00 0.00 38.25 1.89
2961 3163 5.416326 CCCAACGGGTAAATCAAAGAATACA 59.584 40.000 0.00 0.00 38.25 2.29
2962 3164 6.319399 CCAACGGGTAAATCAAAGAATACAC 58.681 40.000 0.00 0.00 0.00 2.90
2963 3165 6.072397 CCAACGGGTAAATCAAAGAATACACA 60.072 38.462 0.00 0.00 0.00 3.72
2964 3166 6.490566 ACGGGTAAATCAAAGAATACACAC 57.509 37.500 0.00 0.00 0.00 3.82
2965 3167 5.998981 ACGGGTAAATCAAAGAATACACACA 59.001 36.000 0.00 0.00 0.00 3.72
2966 3168 6.657541 ACGGGTAAATCAAAGAATACACACAT 59.342 34.615 0.00 0.00 0.00 3.21
2967 3169 7.175990 ACGGGTAAATCAAAGAATACACACATT 59.824 33.333 0.00 0.00 0.00 2.71
2968 3170 8.670135 CGGGTAAATCAAAGAATACACACATTA 58.330 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.579753 CCTGTTTTTCCAAAATGCAATGGT 59.420 37.500 14.12 0.00 37.94 3.55
81 86 3.298958 CCTGCTCAGGTCCGCTTA 58.701 61.111 7.75 0.00 43.61 3.09
130 140 2.163412 TCGTGCAAATGGCTAAATGGAC 59.837 45.455 0.00 1.18 45.15 4.02
132 142 2.423185 TCTCGTGCAAATGGCTAAATGG 59.577 45.455 0.00 0.00 45.15 3.16
474 606 8.803201 ATGTGAACGAAGTACAGATGTATATG 57.197 34.615 0.00 0.00 45.00 1.78
484 616 8.827177 AGAGATTTTAATGTGAACGAAGTACA 57.173 30.769 0.00 0.00 45.00 2.90
528 662 3.904234 GGTTCGTTCATTTTGCTTCGTAC 59.096 43.478 0.00 0.00 0.00 3.67
545 679 9.448294 GTAGACATATTTTAGAGTGTAGGTTCG 57.552 37.037 0.00 0.00 0.00 3.95
607 741 9.886132 ACTCCGTTACTAAATATGAGTCATTTT 57.114 29.630 11.68 13.14 0.00 1.82
611 745 7.776969 ACCTACTCCGTTACTAAATATGAGTCA 59.223 37.037 0.00 0.00 33.89 3.41
616 750 7.047460 ACCACCTACTCCGTTACTAAATATG 57.953 40.000 0.00 0.00 0.00 1.78
850 984 4.929808 GTGAGCGATGGGTGTTTATATAGG 59.070 45.833 0.00 0.00 0.00 2.57
851 985 5.784177 AGTGAGCGATGGGTGTTTATATAG 58.216 41.667 0.00 0.00 0.00 1.31
852 986 5.279306 GGAGTGAGCGATGGGTGTTTATATA 60.279 44.000 0.00 0.00 0.00 0.86
966 1100 1.133790 GCTGCTAATTGACCCTTGCTG 59.866 52.381 0.00 0.00 0.00 4.41
970 1117 3.201708 AGATCAGCTGCTAATTGACCCTT 59.798 43.478 9.47 0.00 0.00 3.95
992 1139 0.107268 CTCCATGCCCATGATCGACA 59.893 55.000 9.73 0.00 41.20 4.35
994 1141 1.756665 CCTCCATGCCCATGATCGA 59.243 57.895 9.73 0.00 41.20 3.59
995 1142 1.303074 CCCTCCATGCCCATGATCG 60.303 63.158 9.73 0.00 41.20 3.69
1014 1161 0.880278 TCACCTTCTTGTCGCAGCAC 60.880 55.000 0.00 0.00 0.00 4.40
1021 1168 2.093235 CCTCCTCCATCACCTTCTTGTC 60.093 54.545 0.00 0.00 0.00 3.18
2106 2264 0.708370 GCATGTATGTATCGGTCGCG 59.292 55.000 0.00 0.00 0.00 5.87
2140 2298 1.954382 CCATCCATGCATGAGGACAAG 59.046 52.381 28.31 9.32 36.60 3.16
2177 2339 7.233348 CAGGCAAGGATTAATAATTATGGTGGT 59.767 37.037 0.00 0.00 0.00 4.16
2178 2340 7.605449 CAGGCAAGGATTAATAATTATGGTGG 58.395 38.462 0.00 0.00 0.00 4.61
2179 2341 7.092716 GCAGGCAAGGATTAATAATTATGGTG 58.907 38.462 0.00 0.00 0.00 4.17
2383 2556 9.376075 CACTTCAGTCATATAGAGTGTCAAAAT 57.624 33.333 0.00 0.00 45.93 1.82
2404 2577 4.397103 TCTTGCATTGGTGATGATCACTTC 59.603 41.667 23.28 9.80 46.19 3.01
2432 2609 9.294030 GAATCAATTAAGAAAGCATAGGTGTTG 57.706 33.333 0.00 0.00 0.00 3.33
2518 2714 0.393132 TCGGGTAAATCGCATGGCAA 60.393 50.000 0.00 0.00 0.00 4.52
2519 2715 0.179032 ATCGGGTAAATCGCATGGCA 60.179 50.000 0.00 0.00 0.00 4.92
2520 2716 0.517316 GATCGGGTAAATCGCATGGC 59.483 55.000 0.00 0.00 0.00 4.40
2521 2717 0.790207 CGATCGGGTAAATCGCATGG 59.210 55.000 7.38 0.00 39.50 3.66
2565 2765 0.523072 ACTTTGCCAGCACGCATAAG 59.477 50.000 0.00 8.00 38.87 1.73
2566 2766 0.240678 CACTTTGCCAGCACGCATAA 59.759 50.000 0.00 0.00 38.87 1.90
2567 2767 1.875262 CACTTTGCCAGCACGCATA 59.125 52.632 0.00 0.00 38.87 3.14
2568 2768 2.646719 CACTTTGCCAGCACGCAT 59.353 55.556 0.00 0.00 38.87 4.73
2571 2771 3.584250 CTCGCACTTTGCCAGCACG 62.584 63.158 0.00 0.00 41.12 5.34
2587 2787 5.490159 ACCGTACTCCTACTATATGAGCTC 58.510 45.833 6.82 6.82 0.00 4.09
2599 2799 1.180029 GGCAGTTGACCGTACTCCTA 58.820 55.000 0.00 0.00 0.00 2.94
2600 2800 0.830444 TGGCAGTTGACCGTACTCCT 60.830 55.000 0.00 0.00 0.00 3.69
2601 2801 0.389948 CTGGCAGTTGACCGTACTCC 60.390 60.000 6.28 0.00 0.00 3.85
2602 2802 1.014564 GCTGGCAGTTGACCGTACTC 61.015 60.000 17.16 0.00 0.00 2.59
2688 2890 5.981088 TCATTAAATTGACTGGCACACAT 57.019 34.783 0.00 0.00 0.00 3.21
2720 2922 1.044611 CCCGGCCAAAAAGAAAAGGA 58.955 50.000 2.24 0.00 0.00 3.36
2722 2924 1.960689 TCTCCCGGCCAAAAAGAAAAG 59.039 47.619 2.24 0.00 0.00 2.27
2727 2929 1.406539 CATCATCTCCCGGCCAAAAAG 59.593 52.381 2.24 0.00 0.00 2.27
2733 2935 0.111253 AATTCCATCATCTCCCGGCC 59.889 55.000 0.00 0.00 0.00 6.13
2734 2936 1.610522 CAAATTCCATCATCTCCCGGC 59.389 52.381 0.00 0.00 0.00 6.13
2735 2937 1.610522 GCAAATTCCATCATCTCCCGG 59.389 52.381 0.00 0.00 0.00 5.73
2736 2938 2.579873 AGCAAATTCCATCATCTCCCG 58.420 47.619 0.00 0.00 0.00 5.14
2737 2939 4.723309 AGTAGCAAATTCCATCATCTCCC 58.277 43.478 0.00 0.00 0.00 4.30
2738 2940 5.591877 ACAAGTAGCAAATTCCATCATCTCC 59.408 40.000 0.00 0.00 0.00 3.71
2739 2941 6.094603 ACACAAGTAGCAAATTCCATCATCTC 59.905 38.462 0.00 0.00 0.00 2.75
2740 2942 5.948162 ACACAAGTAGCAAATTCCATCATCT 59.052 36.000 0.00 0.00 0.00 2.90
2741 2943 6.094603 AGACACAAGTAGCAAATTCCATCATC 59.905 38.462 0.00 0.00 0.00 2.92
2742 2944 5.948162 AGACACAAGTAGCAAATTCCATCAT 59.052 36.000 0.00 0.00 0.00 2.45
2743 2945 5.316167 AGACACAAGTAGCAAATTCCATCA 58.684 37.500 0.00 0.00 0.00 3.07
2744 2946 5.886960 AGACACAAGTAGCAAATTCCATC 57.113 39.130 0.00 0.00 0.00 3.51
2745 2947 6.655078 AAAGACACAAGTAGCAAATTCCAT 57.345 33.333 0.00 0.00 0.00 3.41
2746 2948 6.463995 AAAAGACACAAGTAGCAAATTCCA 57.536 33.333 0.00 0.00 0.00 3.53
2747 2949 7.114953 GCTAAAAAGACACAAGTAGCAAATTCC 59.885 37.037 0.00 0.00 35.22 3.01
2748 2950 7.149128 CGCTAAAAAGACACAAGTAGCAAATTC 60.149 37.037 0.00 0.00 34.89 2.17
2749 2951 6.636850 CGCTAAAAAGACACAAGTAGCAAATT 59.363 34.615 0.00 0.00 34.89 1.82
2750 2952 6.142817 CGCTAAAAAGACACAAGTAGCAAAT 58.857 36.000 0.00 0.00 34.89 2.32
2751 2953 5.504994 CCGCTAAAAAGACACAAGTAGCAAA 60.505 40.000 0.00 0.00 34.89 3.68
2752 2954 4.024387 CCGCTAAAAAGACACAAGTAGCAA 60.024 41.667 0.00 0.00 34.89 3.91
2753 2955 3.496884 CCGCTAAAAAGACACAAGTAGCA 59.503 43.478 0.00 0.00 34.89 3.49
2754 2956 3.744426 TCCGCTAAAAAGACACAAGTAGC 59.256 43.478 0.00 0.00 0.00 3.58
2755 2957 5.917541 TTCCGCTAAAAAGACACAAGTAG 57.082 39.130 0.00 0.00 0.00 2.57
2756 2958 6.870971 AATTCCGCTAAAAAGACACAAGTA 57.129 33.333 0.00 0.00 0.00 2.24
2757 2959 5.767816 AATTCCGCTAAAAAGACACAAGT 57.232 34.783 0.00 0.00 0.00 3.16
2758 2960 5.107875 GCAAATTCCGCTAAAAAGACACAAG 60.108 40.000 0.00 0.00 0.00 3.16
2759 2961 4.742659 GCAAATTCCGCTAAAAAGACACAA 59.257 37.500 0.00 0.00 0.00 3.33
2760 2962 4.037446 AGCAAATTCCGCTAAAAAGACACA 59.963 37.500 0.63 0.00 38.15 3.72
2761 2963 4.546570 AGCAAATTCCGCTAAAAAGACAC 58.453 39.130 0.63 0.00 38.15 3.67
2762 2964 4.846779 AGCAAATTCCGCTAAAAAGACA 57.153 36.364 0.63 0.00 38.15 3.41
2763 2965 5.939457 AGTAGCAAATTCCGCTAAAAAGAC 58.061 37.500 10.27 1.91 43.30 3.01
2764 2966 6.016610 ACAAGTAGCAAATTCCGCTAAAAAGA 60.017 34.615 10.27 0.00 43.30 2.52
2765 2967 6.088085 CACAAGTAGCAAATTCCGCTAAAAAG 59.912 38.462 10.27 5.29 43.30 2.27
2766 2968 5.918011 CACAAGTAGCAAATTCCGCTAAAAA 59.082 36.000 10.27 0.00 43.30 1.94
2767 2969 5.457140 CACAAGTAGCAAATTCCGCTAAAA 58.543 37.500 10.27 0.00 43.30 1.52
2768 2970 4.614993 GCACAAGTAGCAAATTCCGCTAAA 60.615 41.667 10.27 0.00 43.30 1.85
2769 2971 3.119990 GCACAAGTAGCAAATTCCGCTAA 60.120 43.478 10.27 0.00 43.30 3.09
2770 2972 2.418628 GCACAAGTAGCAAATTCCGCTA 59.581 45.455 5.63 5.63 40.96 4.26
2771 2973 1.200020 GCACAAGTAGCAAATTCCGCT 59.800 47.619 7.42 7.42 43.62 5.52
2772 2974 1.617740 GCACAAGTAGCAAATTCCGC 58.382 50.000 0.00 0.00 0.00 5.54
2773 2975 1.463056 TCGCACAAGTAGCAAATTCCG 59.537 47.619 0.00 0.00 0.00 4.30
2774 2976 3.375299 AGATCGCACAAGTAGCAAATTCC 59.625 43.478 0.00 0.00 0.00 3.01
2775 2977 4.606457 AGATCGCACAAGTAGCAAATTC 57.394 40.909 0.00 0.00 0.00 2.17
2776 2978 4.332819 GGTAGATCGCACAAGTAGCAAATT 59.667 41.667 3.38 0.00 0.00 1.82
2777 2979 3.871594 GGTAGATCGCACAAGTAGCAAAT 59.128 43.478 3.38 0.00 0.00 2.32
2778 2980 3.056107 AGGTAGATCGCACAAGTAGCAAA 60.056 43.478 3.38 0.00 0.00 3.68
2779 2981 2.496070 AGGTAGATCGCACAAGTAGCAA 59.504 45.455 3.38 0.00 0.00 3.91
2780 2982 2.100197 AGGTAGATCGCACAAGTAGCA 58.900 47.619 3.38 0.00 0.00 3.49
2781 2983 2.873133 AGGTAGATCGCACAAGTAGC 57.127 50.000 3.38 0.00 0.00 3.58
2782 2984 4.579340 TCCTTAGGTAGATCGCACAAGTAG 59.421 45.833 0.00 0.00 0.00 2.57
2783 2985 4.529897 TCCTTAGGTAGATCGCACAAGTA 58.470 43.478 0.00 0.00 0.00 2.24
2784 2986 3.362706 TCCTTAGGTAGATCGCACAAGT 58.637 45.455 0.00 0.00 0.00 3.16
2785 2987 4.302455 CATCCTTAGGTAGATCGCACAAG 58.698 47.826 0.00 0.20 0.00 3.16
2786 2988 3.069586 CCATCCTTAGGTAGATCGCACAA 59.930 47.826 0.00 0.00 0.00 3.33
2787 2989 2.628178 CCATCCTTAGGTAGATCGCACA 59.372 50.000 0.00 0.00 0.00 4.57
2788 2990 2.891580 TCCATCCTTAGGTAGATCGCAC 59.108 50.000 0.00 0.00 0.00 5.34
2789 2991 3.238788 TCCATCCTTAGGTAGATCGCA 57.761 47.619 0.00 0.00 0.00 5.10
2790 2992 4.602340 TTTCCATCCTTAGGTAGATCGC 57.398 45.455 0.00 0.00 0.00 4.58
2791 2993 5.482908 CCATTTCCATCCTTAGGTAGATCG 58.517 45.833 0.00 0.00 0.00 3.69
2792 2994 5.310857 ACCCATTTCCATCCTTAGGTAGATC 59.689 44.000 0.00 0.00 0.00 2.75
2793 2995 5.235534 ACCCATTTCCATCCTTAGGTAGAT 58.764 41.667 0.00 0.00 0.00 1.98
2794 2996 4.641868 ACCCATTTCCATCCTTAGGTAGA 58.358 43.478 0.00 0.00 0.00 2.59
2795 2997 5.513267 GCTACCCATTTCCATCCTTAGGTAG 60.513 48.000 8.23 8.23 45.45 3.18
2796 2998 4.349930 GCTACCCATTTCCATCCTTAGGTA 59.650 45.833 0.00 0.00 0.00 3.08
2797 2999 3.138468 GCTACCCATTTCCATCCTTAGGT 59.862 47.826 0.00 0.00 0.00 3.08
2798 3000 3.756117 GCTACCCATTTCCATCCTTAGG 58.244 50.000 0.00 0.00 0.00 2.69
2799 3001 3.181454 ACGCTACCCATTTCCATCCTTAG 60.181 47.826 0.00 0.00 0.00 2.18
2800 3002 2.775384 ACGCTACCCATTTCCATCCTTA 59.225 45.455 0.00 0.00 0.00 2.69
2801 3003 1.564348 ACGCTACCCATTTCCATCCTT 59.436 47.619 0.00 0.00 0.00 3.36
2802 3004 1.213296 ACGCTACCCATTTCCATCCT 58.787 50.000 0.00 0.00 0.00 3.24
2803 3005 2.922740 TACGCTACCCATTTCCATCC 57.077 50.000 0.00 0.00 0.00 3.51
2804 3006 3.997021 CTCATACGCTACCCATTTCCATC 59.003 47.826 0.00 0.00 0.00 3.51
2805 3007 3.244561 CCTCATACGCTACCCATTTCCAT 60.245 47.826 0.00 0.00 0.00 3.41
2806 3008 2.104111 CCTCATACGCTACCCATTTCCA 59.896 50.000 0.00 0.00 0.00 3.53
2807 3009 2.767505 CCTCATACGCTACCCATTTCC 58.232 52.381 0.00 0.00 0.00 3.13
2808 3010 2.143925 GCCTCATACGCTACCCATTTC 58.856 52.381 0.00 0.00 0.00 2.17
2809 3011 1.540363 CGCCTCATACGCTACCCATTT 60.540 52.381 0.00 0.00 0.00 2.32
2810 3012 0.033504 CGCCTCATACGCTACCCATT 59.966 55.000 0.00 0.00 0.00 3.16
2811 3013 1.666011 CGCCTCATACGCTACCCAT 59.334 57.895 0.00 0.00 0.00 4.00
2812 3014 2.495409 CCGCCTCATACGCTACCCA 61.495 63.158 0.00 0.00 0.00 4.51
2813 3015 2.338984 CCGCCTCATACGCTACCC 59.661 66.667 0.00 0.00 0.00 3.69
2814 3016 1.174712 TACCCGCCTCATACGCTACC 61.175 60.000 0.00 0.00 0.00 3.18
2815 3017 0.240411 CTACCCGCCTCATACGCTAC 59.760 60.000 0.00 0.00 0.00 3.58
2816 3018 0.109153 TCTACCCGCCTCATACGCTA 59.891 55.000 0.00 0.00 0.00 4.26
2817 3019 1.152819 TCTACCCGCCTCATACGCT 60.153 57.895 0.00 0.00 0.00 5.07
2818 3020 1.286260 CTCTACCCGCCTCATACGC 59.714 63.158 0.00 0.00 0.00 4.42
2819 3021 1.286260 GCTCTACCCGCCTCATACG 59.714 63.158 0.00 0.00 0.00 3.06
2820 3022 0.750850 TTGCTCTACCCGCCTCATAC 59.249 55.000 0.00 0.00 0.00 2.39
2821 3023 1.717032 ATTGCTCTACCCGCCTCATA 58.283 50.000 0.00 0.00 0.00 2.15
2822 3024 1.344763 GTATTGCTCTACCCGCCTCAT 59.655 52.381 0.00 0.00 0.00 2.90
2823 3025 0.750850 GTATTGCTCTACCCGCCTCA 59.249 55.000 0.00 0.00 0.00 3.86
2824 3026 0.033642 GGTATTGCTCTACCCGCCTC 59.966 60.000 4.46 0.00 36.00 4.70
2825 3027 0.689745 TGGTATTGCTCTACCCGCCT 60.690 55.000 11.32 0.00 40.47 5.52
2826 3028 0.396811 ATGGTATTGCTCTACCCGCC 59.603 55.000 11.32 0.00 40.47 6.13
2827 3029 2.612221 GGTATGGTATTGCTCTACCCGC 60.612 54.545 11.32 3.80 40.47 6.13
2828 3030 2.028385 GGGTATGGTATTGCTCTACCCG 60.028 54.545 11.32 0.00 41.46 5.28
2829 3031 3.697619 GGGTATGGTATTGCTCTACCC 57.302 52.381 11.32 0.61 43.42 3.69
2830 3032 4.910458 ATGGGTATGGTATTGCTCTACC 57.090 45.455 7.99 7.99 41.39 3.18
2831 3033 5.338137 GGGTATGGGTATGGTATTGCTCTAC 60.338 48.000 0.00 0.00 0.00 2.59
2832 3034 4.781087 GGGTATGGGTATGGTATTGCTCTA 59.219 45.833 0.00 0.00 0.00 2.43
2833 3035 3.587506 GGGTATGGGTATGGTATTGCTCT 59.412 47.826 0.00 0.00 0.00 4.09
2834 3036 3.329520 TGGGTATGGGTATGGTATTGCTC 59.670 47.826 0.00 0.00 0.00 4.26
2835 3037 3.332044 TGGGTATGGGTATGGTATTGCT 58.668 45.455 0.00 0.00 0.00 3.91
2836 3038 3.799432 TGGGTATGGGTATGGTATTGC 57.201 47.619 0.00 0.00 0.00 3.56
2837 3039 5.255397 ACATGGGTATGGGTATGGTATTG 57.745 43.478 0.00 0.00 38.66 1.90
2838 3040 6.095680 ACTACATGGGTATGGGTATGGTATT 58.904 40.000 0.00 0.00 38.66 1.89
2839 3041 5.671941 ACTACATGGGTATGGGTATGGTAT 58.328 41.667 0.00 0.00 38.66 2.73
2840 3042 5.088730 GACTACATGGGTATGGGTATGGTA 58.911 45.833 0.00 0.00 38.66 3.25
2841 3043 3.908103 GACTACATGGGTATGGGTATGGT 59.092 47.826 0.00 0.00 38.66 3.55
2842 3044 3.907474 TGACTACATGGGTATGGGTATGG 59.093 47.826 0.00 0.00 38.66 2.74
2843 3045 5.560722 TTGACTACATGGGTATGGGTATG 57.439 43.478 0.00 0.00 38.66 2.39
2844 3046 5.014123 CCATTGACTACATGGGTATGGGTAT 59.986 44.000 0.00 0.00 38.66 2.73
2845 3047 4.349636 CCATTGACTACATGGGTATGGGTA 59.650 45.833 0.00 0.00 38.66 3.69
2846 3048 3.138283 CCATTGACTACATGGGTATGGGT 59.862 47.826 0.00 0.00 38.66 4.51
2847 3049 3.394274 TCCATTGACTACATGGGTATGGG 59.606 47.826 16.15 7.84 38.66 4.00
2848 3050 4.705110 TCCATTGACTACATGGGTATGG 57.295 45.455 12.71 12.71 38.66 2.74
2849 3051 7.244886 TCTATCCATTGACTACATGGGTATG 57.755 40.000 0.00 0.00 40.24 2.39
2850 3052 7.872061 TTCTATCCATTGACTACATGGGTAT 57.128 36.000 0.00 0.00 36.18 2.73
2851 3053 7.684317 TTTCTATCCATTGACTACATGGGTA 57.316 36.000 0.00 0.00 36.18 3.69
2852 3054 6.575244 TTTCTATCCATTGACTACATGGGT 57.425 37.500 0.00 0.00 36.18 4.51
2853 3055 8.469309 AATTTTCTATCCATTGACTACATGGG 57.531 34.615 0.00 0.00 36.18 4.00
2854 3056 9.347240 AGAATTTTCTATCCATTGACTACATGG 57.653 33.333 0.00 0.00 35.34 3.66
2870 3072 7.038799 GGGTACGGGTATGGATAGAATTTTCTA 60.039 40.741 2.68 2.68 43.35 2.10
2871 3073 6.239800 GGGTACGGGTATGGATAGAATTTTCT 60.240 42.308 0.00 0.00 41.24 2.52
2872 3074 5.936372 GGGTACGGGTATGGATAGAATTTTC 59.064 44.000 0.00 0.00 0.00 2.29
2873 3075 5.370289 TGGGTACGGGTATGGATAGAATTTT 59.630 40.000 0.00 0.00 0.00 1.82
2874 3076 4.909088 TGGGTACGGGTATGGATAGAATTT 59.091 41.667 0.00 0.00 0.00 1.82
2875 3077 4.495565 TGGGTACGGGTATGGATAGAATT 58.504 43.478 0.00 0.00 0.00 2.17
2876 3078 4.136341 TGGGTACGGGTATGGATAGAAT 57.864 45.455 0.00 0.00 0.00 2.40
2877 3079 3.616343 TGGGTACGGGTATGGATAGAA 57.384 47.619 0.00 0.00 0.00 2.10
2878 3080 3.437213 CATGGGTACGGGTATGGATAGA 58.563 50.000 0.00 0.00 0.00 1.98
2879 3081 2.500098 CCATGGGTACGGGTATGGATAG 59.500 54.545 2.85 0.00 42.05 2.08
2880 3082 2.542550 CCATGGGTACGGGTATGGATA 58.457 52.381 2.85 0.00 42.05 2.59
2881 3083 1.358152 CCATGGGTACGGGTATGGAT 58.642 55.000 2.85 0.00 42.05 3.41
2882 3084 0.765135 CCCATGGGTACGGGTATGGA 60.765 60.000 23.93 0.00 42.05 3.41
2883 3085 1.758592 CCCATGGGTACGGGTATGG 59.241 63.158 23.93 8.50 39.77 2.74
2891 3093 8.573035 CATGTAATGTTTTATACCCATGGGTAC 58.427 37.037 40.14 30.67 45.51 3.34
2892 3094 8.698973 CATGTAATGTTTTATACCCATGGGTA 57.301 34.615 39.50 39.50 46.14 3.69
2893 3095 7.595819 CATGTAATGTTTTATACCCATGGGT 57.404 36.000 37.92 37.92 45.17 4.51
2910 3112 7.027874 CCTAATGGGTATGGGTACATGTAAT 57.972 40.000 7.25 0.24 37.97 1.89
2911 3113 6.442541 CCTAATGGGTATGGGTACATGTAA 57.557 41.667 7.25 0.00 37.97 2.41
2913 3115 4.993705 CCTAATGGGTATGGGTACATGT 57.006 45.455 2.69 2.69 37.97 3.21
2938 3140 6.072397 TGTGTATTCTTTGATTTACCCGTTGG 60.072 38.462 0.00 0.00 37.80 3.77
2939 3141 6.799925 GTGTGTATTCTTTGATTTACCCGTTG 59.200 38.462 0.00 0.00 0.00 4.10
2940 3142 6.487331 TGTGTGTATTCTTTGATTTACCCGTT 59.513 34.615 0.00 0.00 0.00 4.44
2941 3143 5.998981 TGTGTGTATTCTTTGATTTACCCGT 59.001 36.000 0.00 0.00 0.00 5.28
2942 3144 6.489127 TGTGTGTATTCTTTGATTTACCCG 57.511 37.500 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.