Multiple sequence alignment - TraesCS1A01G110400

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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 TraesCS1A01G110400 chr1A 100.000 2314 0 0 1 2314 110072002 110074315 0.000000e+00 4274
1 TraesCS1A01G110400 chr1A 100.000 347 0 0 2522 2868 110074523 110074869 2.410000e-180 641
2 TraesCS1A01G110400 chr1A 92.357 157 12 0 2687 2843 110079691 110079847 1.030000e-54 224
3 TraesCS1A01G110400 chr1B 91.723 2356 127 30 3 2314 159205266 159202935 0.000000e+00 3208
4 TraesCS1A01G110400 chr1D 94.856 1905 81 9 222 2113 107501640 107503540 0.000000e+00 2959
5 TraesCS1A01G110400 chr1D 93.659 205 12 1 2108 2312 107509074 107509277 3.590000e-79 305
6 TraesCS1A01G110400 chr1D 95.122 164 6 2 2523 2686 107509319 107509480 1.020000e-64 257
7 TraesCS1A01G110400 chr6D 93.085 188 10 2 2684 2868 25997066 25997253 3.640000e-69 272
8 TraesCS1A01G110400 chr6D 94.268 157 8 1 2687 2843 472130704 472130859 3.690000e-59 239
9 TraesCS1A01G110400 chr6D 89.894 188 13 3 2682 2868 472125648 472125830 1.330000e-58 237
10 TraesCS1A01G110400 chr6D 92.994 157 9 1 2687 2843 26001605 26001759 7.990000e-56 228
11 TraesCS1A01G110400 chr3D 95.706 163 6 1 2688 2849 56707135 56706973 7.880000e-66 261
12 TraesCS1A01G110400 chr3D 90.659 182 12 2 2687 2868 51753268 51753444 1.330000e-58 237
13 TraesCS1A01G110400 chr3D 92.994 157 11 0 2687 2843 56689948 56689792 2.220000e-56 230
14 TraesCS1A01G110400 chr3B 89.617 183 14 5 2687 2866 159940003 159940183 7.990000e-56 228


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 TraesCS1A01G110400 chr1A 110072002 110074869 2867 False 2457.5 4274 100.000 1 2868 2 chr1A.!!$F2 2867
1 TraesCS1A01G110400 chr1B 159202935 159205266 2331 True 3208.0 3208 91.723 3 2314 1 chr1B.!!$R1 2311
2 TraesCS1A01G110400 chr1D 107501640 107503540 1900 False 2959.0 2959 94.856 222 2113 1 chr1D.!!$F1 1891

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
22 23 0.179029 AGCTGGCCGTACAAACAACT 60.179 50.0 0.00 0.0 0.00 3.16 F
1093 1126 0.461961 GTCGCTGAAGGTCCATAGCT 59.538 55.0 9.46 0.0 34.13 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1150 0.535102 GCCAGGTGGGTATTGATCCG 60.535 60.0 0.0 0.0 39.65 4.18 R
2787 2855 0.402121 GCCCACCTCCTGTTTTCTCT 59.598 55.0 0.0 0.0 0.00 3.10 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
22 23 0.179029 AGCTGGCCGTACAAACAACT 60.179 50.000 0.00 0.00 0.00 3.16
29 30 2.095919 GCCGTACAAACAACTTAGGCAG 60.096 50.000 0.00 0.00 42.57 4.85
43 44 4.940046 ACTTAGGCAGTCAATCATGTTCTG 59.060 41.667 0.00 0.00 34.93 3.02
62 63 3.843619 TCTGTGTGGGATTTCTCATACCA 59.156 43.478 5.06 0.00 0.00 3.25
69 70 5.652014 GTGGGATTTCTCATACCAATCACAA 59.348 40.000 0.00 0.00 41.02 3.33
75 76 5.434182 TCTCATACCAATCACAATGTGGA 57.566 39.130 13.95 0.79 36.23 4.02
78 79 6.891361 TCTCATACCAATCACAATGTGGAATT 59.109 34.615 13.95 4.06 36.23 2.17
80 81 6.662663 TCATACCAATCACAATGTGGAATTCA 59.337 34.615 13.95 0.00 36.23 2.57
83 84 7.479352 ACCAATCACAATGTGGAATTCATAA 57.521 32.000 13.95 0.00 36.23 1.90
89 90 5.577945 CACAATGTGGAATTCATAAGCAACC 59.422 40.000 5.29 0.00 0.00 3.77
105 106 2.888594 CAACCGGCTTCGATCTCTTAA 58.111 47.619 0.00 0.00 35.61 1.85
108 109 4.138487 ACCGGCTTCGATCTCTTAAAAT 57.862 40.909 0.00 0.00 35.61 1.82
141 142 8.809468 ATAGGATGATGTAGACGAGCTATAAA 57.191 34.615 0.00 0.00 0.00 1.40
146 147 8.978564 ATGATGTAGACGAGCTATAAAAGATG 57.021 34.615 0.00 0.00 0.00 2.90
150 151 7.941919 TGTAGACGAGCTATAAAAGATGTCAT 58.058 34.615 0.00 0.00 29.53 3.06
155 156 8.978564 ACGAGCTATAAAAGATGTCATATCAG 57.021 34.615 0.00 0.00 0.00 2.90
186 187 8.918202 TGCCTAGTTGAAATAGAAAAGAAAGA 57.082 30.769 0.62 0.00 0.00 2.52
334 367 4.878397 GTGAGTGAGCTATTACATTGGCTT 59.122 41.667 0.00 0.00 35.01 4.35
337 370 7.227512 GTGAGTGAGCTATTACATTGGCTTTAT 59.772 37.037 0.00 0.00 35.01 1.40
450 483 8.730680 ACATCAAAACAGATAGATGGTTGTTAC 58.269 33.333 0.00 0.00 41.55 2.50
451 484 8.950210 CATCAAAACAGATAGATGGTTGTTACT 58.050 33.333 0.00 0.00 35.42 2.24
471 504 2.871633 CTGGAAGTTTTGCCGCAAAAAT 59.128 40.909 28.27 25.26 43.50 1.82
587 620 2.430694 TCATGACAGGTCCCAAGATACG 59.569 50.000 0.00 0.00 0.00 3.06
680 713 2.282462 CTTGAGTGGGGGTGGTGC 60.282 66.667 0.00 0.00 0.00 5.01
686 719 3.099841 TGGGGGTGGTGCTTGTCA 61.100 61.111 0.00 0.00 0.00 3.58
730 763 5.892160 ACATGCACATTATATCATGAGGC 57.108 39.130 0.09 7.41 38.77 4.70
835 868 8.844244 TGCACTAGTTAGTATACTACCTTTAGC 58.156 37.037 14.39 14.68 34.13 3.09
925 958 4.082841 TGTTCGTTCCATCCATCATTTGTG 60.083 41.667 0.00 0.00 0.00 3.33
935 968 4.979335 TCCATCATTTGTGTGTTCCACTA 58.021 39.130 0.00 0.00 44.81 2.74
1093 1126 0.461961 GTCGCTGAAGGTCCATAGCT 59.538 55.000 9.46 0.00 34.13 3.32
1094 1127 1.134670 GTCGCTGAAGGTCCATAGCTT 60.135 52.381 0.00 0.00 45.93 3.74
1205 1238 9.353999 ACTTCTTGTTTTGTTCATACTGAAAAC 57.646 29.630 0.00 0.00 38.22 2.43
1313 1346 4.678742 GCTGCTGAAACAACTTCATTCTTC 59.321 41.667 0.00 0.00 43.20 2.87
1933 1969 3.532792 CCACACACGTCGATCGCG 61.533 66.667 23.61 23.61 44.19 5.87
1967 2003 0.179073 CAGTCGAGCCAGGGTATTGG 60.179 60.000 0.00 0.00 41.35 3.16
2028 2093 2.159296 TGGTATGTCATGGTCTCGTTCG 60.159 50.000 0.00 0.00 0.00 3.95
2032 2097 1.336517 TGTCATGGTCTCGTTCGGAAC 60.337 52.381 10.83 10.83 0.00 3.62
2037 2102 3.663995 TGGTCTCGTTCGGAACAAATA 57.336 42.857 19.91 2.52 0.00 1.40
2115 2180 9.123902 TCATTCCTGTATTTGGTTGAAGATATG 57.876 33.333 0.00 0.00 0.00 1.78
2255 2323 6.438741 TCCCAGCAACATTTCCATTGTATTTA 59.561 34.615 0.00 0.00 0.00 1.40
2297 2365 9.624697 GAAGTATACAATGTCAAGCAAAATTCA 57.375 29.630 5.50 0.00 0.00 2.57
2299 2367 8.796475 AGTATACAATGTCAAGCAAAATTCAGT 58.204 29.630 5.50 0.00 0.00 3.41
2300 2368 7.878477 ATACAATGTCAAGCAAAATTCAGTG 57.122 32.000 0.00 0.00 0.00 3.66
2308 2376 6.703165 GTCAAGCAAAATTCAGTGGAAAGAAT 59.297 34.615 0.00 0.00 36.43 2.40
2562 2630 6.978674 TCGATAAGAGAGGAATAACCATGT 57.021 37.500 0.00 0.00 42.04 3.21
2563 2631 6.749139 TCGATAAGAGAGGAATAACCATGTG 58.251 40.000 0.00 0.00 42.04 3.21
2564 2632 6.549736 TCGATAAGAGAGGAATAACCATGTGA 59.450 38.462 0.00 0.00 42.04 3.58
2565 2633 7.233553 TCGATAAGAGAGGAATAACCATGTGAT 59.766 37.037 0.00 0.00 42.04 3.06
2566 2634 7.875041 CGATAAGAGAGGAATAACCATGTGATT 59.125 37.037 0.00 0.00 42.04 2.57
2567 2635 9.213799 GATAAGAGAGGAATAACCATGTGATTC 57.786 37.037 0.00 0.00 42.04 2.52
2572 2640 5.424121 GGAATAACCATGTGATTCCTTCG 57.576 43.478 13.86 0.00 45.55 3.79
2573 2641 5.123227 GGAATAACCATGTGATTCCTTCGA 58.877 41.667 13.86 0.00 45.55 3.71
2574 2642 5.765182 GGAATAACCATGTGATTCCTTCGAT 59.235 40.000 13.86 0.00 45.55 3.59
2575 2643 6.263168 GGAATAACCATGTGATTCCTTCGATT 59.737 38.462 13.86 0.00 45.55 3.34
2576 2644 7.201821 GGAATAACCATGTGATTCCTTCGATTT 60.202 37.037 13.86 0.00 45.55 2.17
2577 2645 4.970662 ACCATGTGATTCCTTCGATTTG 57.029 40.909 0.00 0.00 0.00 2.32
2578 2646 3.696051 ACCATGTGATTCCTTCGATTTGG 59.304 43.478 0.00 0.00 0.00 3.28
2579 2647 3.696051 CCATGTGATTCCTTCGATTTGGT 59.304 43.478 0.00 0.00 0.00 3.67
2580 2648 4.439153 CCATGTGATTCCTTCGATTTGGTG 60.439 45.833 0.00 0.00 0.00 4.17
2581 2649 3.081061 TGTGATTCCTTCGATTTGGTGG 58.919 45.455 0.00 0.00 0.00 4.61
2582 2650 3.244735 TGTGATTCCTTCGATTTGGTGGA 60.245 43.478 0.00 0.00 0.00 4.02
2583 2651 3.756434 GTGATTCCTTCGATTTGGTGGAA 59.244 43.478 0.00 0.00 40.49 3.53
2584 2652 4.399303 GTGATTCCTTCGATTTGGTGGAAT 59.601 41.667 5.38 5.38 46.43 3.01
2593 2661 3.699067 GATTTGGTGGAATCGCTTGATG 58.301 45.455 0.00 0.00 31.07 3.07
2594 2662 2.488204 TTGGTGGAATCGCTTGATGA 57.512 45.000 0.00 0.00 31.07 2.92
2595 2663 2.488204 TGGTGGAATCGCTTGATGAA 57.512 45.000 0.00 0.00 31.07 2.57
2596 2664 2.358957 TGGTGGAATCGCTTGATGAAG 58.641 47.619 0.00 0.00 31.07 3.02
2607 2675 3.777465 CTTGATGAAGCACATGAAGGG 57.223 47.619 0.00 0.00 43.18 3.95
2608 2676 3.349927 CTTGATGAAGCACATGAAGGGA 58.650 45.455 0.00 0.00 43.18 4.20
2609 2677 3.438216 TGATGAAGCACATGAAGGGAA 57.562 42.857 0.00 0.00 39.56 3.97
2610 2678 3.972133 TGATGAAGCACATGAAGGGAAT 58.028 40.909 0.00 0.00 39.56 3.01
2611 2679 5.114764 TGATGAAGCACATGAAGGGAATA 57.885 39.130 0.00 0.00 39.56 1.75
2612 2680 5.698104 TGATGAAGCACATGAAGGGAATAT 58.302 37.500 0.00 0.00 39.56 1.28
2613 2681 6.131264 TGATGAAGCACATGAAGGGAATATT 58.869 36.000 0.00 0.00 39.56 1.28
2614 2682 6.263842 TGATGAAGCACATGAAGGGAATATTC 59.736 38.462 6.93 6.93 39.56 1.75
2615 2683 4.889409 TGAAGCACATGAAGGGAATATTCC 59.111 41.667 24.14 24.14 46.82 3.01
2616 2684 4.803329 AGCACATGAAGGGAATATTCCT 57.197 40.909 29.24 14.34 46.72 3.36
2617 2685 5.134725 AGCACATGAAGGGAATATTCCTT 57.865 39.130 29.24 21.97 46.72 3.36
2625 2693 5.903198 AAGGGAATATTCCTTCTCTGAGG 57.097 43.478 29.24 0.00 46.72 3.86
2626 2694 5.163259 AGGGAATATTCCTTCTCTGAGGA 57.837 43.478 29.24 0.00 46.72 3.71
2627 2695 5.736237 AGGGAATATTCCTTCTCTGAGGAT 58.264 41.667 29.24 3.65 44.98 3.24
2628 2696 5.784906 AGGGAATATTCCTTCTCTGAGGATC 59.215 44.000 29.24 11.36 44.98 3.36
2629 2697 5.545723 GGGAATATTCCTTCTCTGAGGATCA 59.454 44.000 29.24 0.00 44.98 2.92
2630 2698 6.463360 GGAATATTCCTTCTCTGAGGATCAC 58.537 44.000 24.74 0.00 44.98 3.06
2631 2699 6.042552 GGAATATTCCTTCTCTGAGGATCACA 59.957 42.308 24.74 0.00 44.98 3.58
2632 2700 7.256619 GGAATATTCCTTCTCTGAGGATCACAT 60.257 40.741 24.74 0.00 44.98 3.21
2633 2701 4.750021 TTCCTTCTCTGAGGATCACATG 57.250 45.455 4.59 0.00 42.56 3.21
2634 2702 3.036819 TCCTTCTCTGAGGATCACATGG 58.963 50.000 4.59 0.00 42.56 3.66
2635 2703 2.770802 CCTTCTCTGAGGATCACATGGT 59.229 50.000 4.59 0.00 42.56 3.55
2636 2704 3.199508 CCTTCTCTGAGGATCACATGGTT 59.800 47.826 4.59 0.00 42.56 3.67
2637 2705 4.324099 CCTTCTCTGAGGATCACATGGTTT 60.324 45.833 4.59 0.00 42.56 3.27
2638 2706 4.478206 TCTCTGAGGATCACATGGTTTC 57.522 45.455 4.59 0.00 42.56 2.78
2639 2707 4.099633 TCTCTGAGGATCACATGGTTTCT 58.900 43.478 4.59 0.00 42.56 2.52
2640 2708 4.081254 TCTCTGAGGATCACATGGTTTCTG 60.081 45.833 4.59 0.00 42.56 3.02
2641 2709 3.584406 TCTGAGGATCACATGGTTTCTGT 59.416 43.478 0.00 0.00 42.56 3.41
2642 2710 4.042062 TCTGAGGATCACATGGTTTCTGTT 59.958 41.667 0.00 0.00 42.56 3.16
2643 2711 4.728772 TGAGGATCACATGGTTTCTGTTT 58.271 39.130 0.00 0.00 42.56 2.83
2644 2712 4.761739 TGAGGATCACATGGTTTCTGTTTC 59.238 41.667 0.00 0.00 42.56 2.78
2645 2713 4.728772 AGGATCACATGGTTTCTGTTTCA 58.271 39.130 0.00 0.00 0.00 2.69
2646 2714 5.327732 AGGATCACATGGTTTCTGTTTCAT 58.672 37.500 0.00 0.00 0.00 2.57
2647 2715 5.416952 AGGATCACATGGTTTCTGTTTCATC 59.583 40.000 0.00 0.00 0.00 2.92
2648 2716 5.393461 GGATCACATGGTTTCTGTTTCATCC 60.393 44.000 0.00 0.00 0.00 3.51
2649 2717 4.728772 TCACATGGTTTCTGTTTCATCCT 58.271 39.130 0.00 0.00 0.00 3.24
2650 2718 4.761739 TCACATGGTTTCTGTTTCATCCTC 59.238 41.667 0.00 0.00 0.00 3.71
2651 2719 4.520111 CACATGGTTTCTGTTTCATCCTCA 59.480 41.667 0.00 0.00 0.00 3.86
2652 2720 5.009911 CACATGGTTTCTGTTTCATCCTCAA 59.990 40.000 0.00 0.00 0.00 3.02
2653 2721 5.010012 ACATGGTTTCTGTTTCATCCTCAAC 59.990 40.000 0.00 0.00 0.00 3.18
2654 2722 4.792068 TGGTTTCTGTTTCATCCTCAACT 58.208 39.130 0.00 0.00 0.00 3.16
2655 2723 5.935945 TGGTTTCTGTTTCATCCTCAACTA 58.064 37.500 0.00 0.00 0.00 2.24
2656 2724 6.361433 TGGTTTCTGTTTCATCCTCAACTAA 58.639 36.000 0.00 0.00 0.00 2.24
2657 2725 6.831353 TGGTTTCTGTTTCATCCTCAACTAAA 59.169 34.615 0.00 0.00 0.00 1.85
2658 2726 7.139392 GGTTTCTGTTTCATCCTCAACTAAAC 58.861 38.462 0.00 0.00 33.42 2.01
2659 2727 7.201785 GGTTTCTGTTTCATCCTCAACTAAACA 60.202 37.037 0.00 0.00 37.62 2.83
2660 2728 6.861065 TCTGTTTCATCCTCAACTAAACAC 57.139 37.500 0.00 0.00 35.69 3.32
2661 2729 6.591935 TCTGTTTCATCCTCAACTAAACACT 58.408 36.000 0.00 0.00 35.69 3.55
2662 2730 6.483307 TCTGTTTCATCCTCAACTAAACACTG 59.517 38.462 0.00 0.00 35.69 3.66
2663 2731 6.353323 TGTTTCATCCTCAACTAAACACTGA 58.647 36.000 0.00 0.00 35.69 3.41
2664 2732 6.826231 TGTTTCATCCTCAACTAAACACTGAA 59.174 34.615 0.00 0.00 35.69 3.02
2665 2733 7.338196 TGTTTCATCCTCAACTAAACACTGAAA 59.662 33.333 0.00 0.00 35.69 2.69
2666 2734 8.352942 GTTTCATCCTCAACTAAACACTGAAAT 58.647 33.333 0.00 0.00 34.00 2.17
2667 2735 7.439157 TCATCCTCAACTAAACACTGAAATG 57.561 36.000 0.00 0.00 0.00 2.32
2668 2736 6.430925 TCATCCTCAACTAAACACTGAAATGG 59.569 38.462 0.00 0.00 0.00 3.16
2669 2737 5.690865 TCCTCAACTAAACACTGAAATGGT 58.309 37.500 0.00 0.00 0.00 3.55
2670 2738 5.530915 TCCTCAACTAAACACTGAAATGGTG 59.469 40.000 0.00 0.00 40.19 4.17
2671 2739 5.278463 CCTCAACTAAACACTGAAATGGTGG 60.278 44.000 0.00 0.00 38.83 4.61
2672 2740 4.582656 TCAACTAAACACTGAAATGGTGGG 59.417 41.667 0.00 0.00 38.83 4.61
2673 2741 2.890945 ACTAAACACTGAAATGGTGGGC 59.109 45.455 0.00 0.00 38.83 5.36
2674 2742 2.086610 AAACACTGAAATGGTGGGCT 57.913 45.000 0.00 0.00 38.83 5.19
2675 2743 2.969821 AACACTGAAATGGTGGGCTA 57.030 45.000 0.00 0.00 38.83 3.93
2676 2744 2.496899 ACACTGAAATGGTGGGCTAG 57.503 50.000 0.00 0.00 38.83 3.42
2677 2745 1.004745 ACACTGAAATGGTGGGCTAGG 59.995 52.381 0.00 0.00 38.83 3.02
2678 2746 0.625849 ACTGAAATGGTGGGCTAGGG 59.374 55.000 0.00 0.00 0.00 3.53
2679 2747 0.918983 CTGAAATGGTGGGCTAGGGA 59.081 55.000 0.00 0.00 0.00 4.20
2680 2748 0.623723 TGAAATGGTGGGCTAGGGAC 59.376 55.000 0.00 0.00 0.00 4.46
2681 2749 0.463833 GAAATGGTGGGCTAGGGACG 60.464 60.000 0.00 0.00 0.00 4.79
2682 2750 1.921869 AAATGGTGGGCTAGGGACGG 61.922 60.000 0.00 0.00 0.00 4.79
2683 2751 2.833151 AATGGTGGGCTAGGGACGGA 62.833 60.000 0.00 0.00 0.00 4.69
2684 2752 2.686106 GGTGGGCTAGGGACGGAA 60.686 66.667 0.00 0.00 0.00 4.30
2685 2753 2.070650 GGTGGGCTAGGGACGGAAT 61.071 63.158 0.00 0.00 0.00 3.01
2686 2754 1.632965 GGTGGGCTAGGGACGGAATT 61.633 60.000 0.00 0.00 0.00 2.17
2687 2755 0.463833 GTGGGCTAGGGACGGAATTG 60.464 60.000 0.00 0.00 0.00 2.32
2688 2756 0.912487 TGGGCTAGGGACGGAATTGT 60.912 55.000 0.00 0.00 0.00 2.71
2689 2757 1.125633 GGGCTAGGGACGGAATTGTA 58.874 55.000 0.00 0.00 0.00 2.41
2690 2758 1.070289 GGGCTAGGGACGGAATTGTAG 59.930 57.143 0.00 0.00 0.00 2.74
2691 2759 2.037144 GGCTAGGGACGGAATTGTAGA 58.963 52.381 0.00 0.00 0.00 2.59
2692 2760 2.036089 GGCTAGGGACGGAATTGTAGAG 59.964 54.545 0.00 0.00 0.00 2.43
2693 2761 2.957006 GCTAGGGACGGAATTGTAGAGA 59.043 50.000 0.00 0.00 0.00 3.10
2694 2762 3.004944 GCTAGGGACGGAATTGTAGAGAG 59.995 52.174 0.00 0.00 0.00 3.20
2695 2763 3.383698 AGGGACGGAATTGTAGAGAGA 57.616 47.619 0.00 0.00 0.00 3.10
2696 2764 3.025262 AGGGACGGAATTGTAGAGAGAC 58.975 50.000 0.00 0.00 0.00 3.36
2697 2765 2.758979 GGGACGGAATTGTAGAGAGACA 59.241 50.000 0.00 0.00 0.00 3.41
2698 2766 3.194968 GGGACGGAATTGTAGAGAGACAA 59.805 47.826 0.00 0.00 43.23 3.18
2699 2767 4.425520 GGACGGAATTGTAGAGAGACAAG 58.574 47.826 0.00 0.00 42.38 3.16
2700 2768 4.082136 GGACGGAATTGTAGAGAGACAAGT 60.082 45.833 0.00 0.00 42.38 3.16
2701 2769 5.470047 ACGGAATTGTAGAGAGACAAGTT 57.530 39.130 0.00 0.00 42.38 2.66
2702 2770 6.349944 GGACGGAATTGTAGAGAGACAAGTTA 60.350 42.308 0.00 0.00 42.38 2.24
2703 2771 7.171630 ACGGAATTGTAGAGAGACAAGTTAT 57.828 36.000 0.00 0.00 42.38 1.89
2704 2772 7.036220 ACGGAATTGTAGAGAGACAAGTTATG 58.964 38.462 0.00 0.00 42.38 1.90
2705 2773 6.477033 CGGAATTGTAGAGAGACAAGTTATGG 59.523 42.308 0.00 0.00 42.38 2.74
2706 2774 6.763610 GGAATTGTAGAGAGACAAGTTATGGG 59.236 42.308 0.00 0.00 42.38 4.00
2707 2775 4.737855 TGTAGAGAGACAAGTTATGGGC 57.262 45.455 0.00 0.00 0.00 5.36
2708 2776 4.353777 TGTAGAGAGACAAGTTATGGGCT 58.646 43.478 0.00 0.00 0.00 5.19
2709 2777 3.902881 AGAGAGACAAGTTATGGGCTG 57.097 47.619 0.00 0.00 0.00 4.85
2710 2778 3.177228 AGAGAGACAAGTTATGGGCTGT 58.823 45.455 0.00 0.00 0.00 4.40
2711 2779 3.055530 AGAGAGACAAGTTATGGGCTGTG 60.056 47.826 0.00 0.00 0.00 3.66
2712 2780 1.740025 GAGACAAGTTATGGGCTGTGC 59.260 52.381 0.00 0.00 0.00 4.57
2713 2781 1.073763 AGACAAGTTATGGGCTGTGCA 59.926 47.619 0.00 0.00 0.00 4.57
2714 2782 1.885887 GACAAGTTATGGGCTGTGCAA 59.114 47.619 0.00 0.00 0.00 4.08
2715 2783 2.493278 GACAAGTTATGGGCTGTGCAAT 59.507 45.455 0.00 0.00 0.00 3.56
2716 2784 2.493278 ACAAGTTATGGGCTGTGCAATC 59.507 45.455 0.00 0.00 0.00 2.67
2717 2785 2.492881 CAAGTTATGGGCTGTGCAATCA 59.507 45.455 0.00 0.00 0.00 2.57
2718 2786 2.094675 AGTTATGGGCTGTGCAATCAC 58.905 47.619 0.00 0.00 43.40 3.06
2732 2800 4.971830 GTGCAATCACAATGTATTGATCGG 59.028 41.667 11.29 0.00 42.66 4.18
2733 2801 4.639755 TGCAATCACAATGTATTGATCGGT 59.360 37.500 11.29 0.00 40.14 4.69
2734 2802 5.819901 TGCAATCACAATGTATTGATCGGTA 59.180 36.000 11.29 0.00 40.14 4.02
2735 2803 6.136071 GCAATCACAATGTATTGATCGGTAC 58.864 40.000 11.29 1.49 40.14 3.34
2736 2804 6.238347 GCAATCACAATGTATTGATCGGTACA 60.238 38.462 11.29 11.10 40.14 2.90
2737 2805 7.520453 GCAATCACAATGTATTGATCGGTACAT 60.520 37.037 11.29 13.92 41.85 2.29
2738 2806 7.658179 ATCACAATGTATTGATCGGTACATC 57.342 36.000 17.87 0.00 39.83 3.06
2739 2807 6.578023 TCACAATGTATTGATCGGTACATCA 58.422 36.000 17.87 0.00 39.83 3.07
2740 2808 6.701400 TCACAATGTATTGATCGGTACATCAG 59.299 38.462 17.87 15.92 39.83 2.90
2741 2809 6.701400 CACAATGTATTGATCGGTACATCAGA 59.299 38.462 17.87 0.00 39.83 3.27
2742 2810 6.701841 ACAATGTATTGATCGGTACATCAGAC 59.298 38.462 17.87 0.20 39.83 3.51
2743 2811 5.845391 TGTATTGATCGGTACATCAGACA 57.155 39.130 6.05 2.67 34.22 3.41
2744 2812 5.588240 TGTATTGATCGGTACATCAGACAC 58.412 41.667 6.05 0.00 34.22 3.67
2745 2813 4.736126 ATTGATCGGTACATCAGACACA 57.264 40.909 0.00 0.00 34.22 3.72
2746 2814 4.736126 TTGATCGGTACATCAGACACAT 57.264 40.909 0.00 0.00 34.22 3.21
2747 2815 5.845391 TTGATCGGTACATCAGACACATA 57.155 39.130 0.00 0.00 34.22 2.29
2748 2816 6.405278 TTGATCGGTACATCAGACACATAT 57.595 37.500 0.00 0.00 34.22 1.78
2749 2817 7.519032 TTGATCGGTACATCAGACACATATA 57.481 36.000 0.00 0.00 34.22 0.86
2750 2818 7.703058 TGATCGGTACATCAGACACATATAT 57.297 36.000 0.00 0.00 0.00 0.86
2751 2819 8.801882 TGATCGGTACATCAGACACATATATA 57.198 34.615 0.00 0.00 0.00 0.86
2752 2820 9.408648 TGATCGGTACATCAGACACATATATAT 57.591 33.333 0.00 0.00 0.00 0.86
2767 2835 9.702253 ACACATATATATAAGTACAGAGGGAGG 57.298 37.037 0.49 0.00 0.00 4.30
2768 2836 9.137459 CACATATATATAAGTACAGAGGGAGGG 57.863 40.741 0.49 0.00 0.00 4.30
2769 2837 7.785506 ACATATATATAAGTACAGAGGGAGGGC 59.214 40.741 0.00 0.00 0.00 5.19
2770 2838 2.104669 ATAAGTACAGAGGGAGGGCC 57.895 55.000 0.00 0.00 0.00 5.80
2771 2839 0.714180 TAAGTACAGAGGGAGGGCCA 59.286 55.000 6.18 0.00 35.15 5.36
2772 2840 0.910088 AAGTACAGAGGGAGGGCCAC 60.910 60.000 6.18 0.00 35.15 5.01
2773 2841 1.612442 GTACAGAGGGAGGGCCACA 60.612 63.158 6.18 0.00 35.15 4.17
2774 2842 0.983378 GTACAGAGGGAGGGCCACAT 60.983 60.000 6.18 0.00 35.15 3.21
2775 2843 0.691078 TACAGAGGGAGGGCCACATC 60.691 60.000 6.18 5.44 35.15 3.06
2776 2844 2.367512 AGAGGGAGGGCCACATCC 60.368 66.667 6.18 8.87 35.15 3.51
2777 2845 2.367512 GAGGGAGGGCCACATCCT 60.368 66.667 17.58 12.18 35.80 3.24
2782 2850 4.257890 AGGGCCACATCCTCAACT 57.742 55.556 6.18 0.00 0.00 3.16
2783 2851 3.417330 AGGGCCACATCCTCAACTA 57.583 52.632 6.18 0.00 0.00 2.24
2784 2852 1.898863 AGGGCCACATCCTCAACTAT 58.101 50.000 6.18 0.00 0.00 2.12
2785 2853 3.060479 AGGGCCACATCCTCAACTATA 57.940 47.619 6.18 0.00 0.00 1.31
2786 2854 2.706190 AGGGCCACATCCTCAACTATAC 59.294 50.000 6.18 0.00 0.00 1.47
2787 2855 2.438021 GGGCCACATCCTCAACTATACA 59.562 50.000 4.39 0.00 0.00 2.29
2788 2856 3.495100 GGGCCACATCCTCAACTATACAG 60.495 52.174 4.39 0.00 0.00 2.74
2789 2857 3.388024 GGCCACATCCTCAACTATACAGA 59.612 47.826 0.00 0.00 0.00 3.41
2790 2858 4.502259 GGCCACATCCTCAACTATACAGAG 60.502 50.000 0.00 0.00 0.00 3.35
2791 2859 4.342378 GCCACATCCTCAACTATACAGAGA 59.658 45.833 0.00 0.00 0.00 3.10
2792 2860 5.163405 GCCACATCCTCAACTATACAGAGAA 60.163 44.000 0.00 0.00 0.00 2.87
2793 2861 6.630413 GCCACATCCTCAACTATACAGAGAAA 60.630 42.308 0.00 0.00 0.00 2.52
2794 2862 7.331026 CCACATCCTCAACTATACAGAGAAAA 58.669 38.462 0.00 0.00 0.00 2.29
2795 2863 7.278868 CCACATCCTCAACTATACAGAGAAAAC 59.721 40.741 0.00 0.00 0.00 2.43
2796 2864 7.819415 CACATCCTCAACTATACAGAGAAAACA 59.181 37.037 0.00 0.00 0.00 2.83
2797 2865 8.037758 ACATCCTCAACTATACAGAGAAAACAG 58.962 37.037 0.00 0.00 0.00 3.16
2798 2866 6.936279 TCCTCAACTATACAGAGAAAACAGG 58.064 40.000 0.00 0.00 0.00 4.00
2799 2867 6.724441 TCCTCAACTATACAGAGAAAACAGGA 59.276 38.462 0.00 0.00 0.00 3.86
2800 2868 7.038659 CCTCAACTATACAGAGAAAACAGGAG 58.961 42.308 0.00 0.00 0.00 3.69
2801 2869 6.936279 TCAACTATACAGAGAAAACAGGAGG 58.064 40.000 0.00 0.00 0.00 4.30
2802 2870 6.497259 TCAACTATACAGAGAAAACAGGAGGT 59.503 38.462 0.00 0.00 0.00 3.85
2803 2871 6.287589 ACTATACAGAGAAAACAGGAGGTG 57.712 41.667 0.00 0.00 0.00 4.00
2804 2872 2.938956 ACAGAGAAAACAGGAGGTGG 57.061 50.000 0.00 0.00 0.00 4.61
2805 2873 1.421646 ACAGAGAAAACAGGAGGTGGG 59.578 52.381 0.00 0.00 0.00 4.61
2806 2874 0.402121 AGAGAAAACAGGAGGTGGGC 59.598 55.000 0.00 0.00 0.00 5.36
2807 2875 0.609406 GAGAAAACAGGAGGTGGGCC 60.609 60.000 0.00 0.00 0.00 5.80
2808 2876 1.606601 GAAAACAGGAGGTGGGCCC 60.607 63.158 17.59 17.59 34.57 5.80
2810 2878 0.774491 AAAACAGGAGGTGGGCCCTA 60.774 55.000 25.70 6.58 46.51 3.53
2811 2879 0.552615 AAACAGGAGGTGGGCCCTAT 60.553 55.000 25.70 8.74 46.51 2.57
2812 2880 0.345502 AACAGGAGGTGGGCCCTATA 59.654 55.000 25.70 0.00 46.51 1.31
2813 2881 0.400093 ACAGGAGGTGGGCCCTATAC 60.400 60.000 25.70 13.34 46.51 1.47
2814 2882 0.399949 CAGGAGGTGGGCCCTATACA 60.400 60.000 25.70 0.00 46.51 2.29
2815 2883 0.400093 AGGAGGTGGGCCCTATACAC 60.400 60.000 25.70 12.48 46.51 2.90
2816 2884 0.693092 GGAGGTGGGCCCTATACACA 60.693 60.000 25.70 0.00 46.51 3.72
2817 2885 1.209621 GAGGTGGGCCCTATACACAA 58.790 55.000 25.70 0.00 46.51 3.33
2818 2886 1.774856 GAGGTGGGCCCTATACACAAT 59.225 52.381 25.70 4.52 46.51 2.71
2819 2887 2.976882 GAGGTGGGCCCTATACACAATA 59.023 50.000 25.70 0.00 46.51 1.90
2820 2888 3.587506 GAGGTGGGCCCTATACACAATAT 59.412 47.826 25.70 0.00 46.51 1.28
2821 2889 4.770193 AGGTGGGCCCTATACACAATATA 58.230 43.478 25.70 0.00 43.87 0.86
2822 2890 5.359173 AGGTGGGCCCTATACACAATATAT 58.641 41.667 25.70 0.00 43.87 0.86
2823 2891 6.517614 AGGTGGGCCCTATACACAATATATA 58.482 40.000 25.70 0.00 43.87 0.86
2824 2892 6.386050 AGGTGGGCCCTATACACAATATATAC 59.614 42.308 25.70 6.25 43.87 1.47
2825 2893 6.278363 GTGGGCCCTATACACAATATATACG 58.722 44.000 25.70 0.00 35.30 3.06
2826 2894 5.959594 TGGGCCCTATACACAATATATACGT 59.040 40.000 25.70 0.00 0.00 3.57
2827 2895 7.068593 GTGGGCCCTATACACAATATATACGTA 59.931 40.741 25.70 0.00 35.30 3.57
2828 2896 7.068593 TGGGCCCTATACACAATATATACGTAC 59.931 40.741 25.70 0.00 0.00 3.67
2829 2897 7.068593 GGGCCCTATACACAATATATACGTACA 59.931 40.741 17.04 0.00 0.00 2.90
2830 2898 8.636213 GGCCCTATACACAATATATACGTACAT 58.364 37.037 0.00 0.00 0.00 2.29
2846 2914 6.350629 ACGTACATAATATACTCAACCCCC 57.649 41.667 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.682852 TGTTTGTACGGCCAGCTACT 59.317 50.000 2.24 0.00 0.00 2.57
1 2 1.196127 GTTGTTTGTACGGCCAGCTAC 59.804 52.381 2.24 0.00 0.00 3.58
22 23 4.696877 CACAGAACATGATTGACTGCCTAA 59.303 41.667 0.00 0.00 35.73 2.69
29 30 3.411446 TCCCACACAGAACATGATTGAC 58.589 45.455 0.00 0.00 0.00 3.18
43 44 5.066505 GTGATTGGTATGAGAAATCCCACAC 59.933 44.000 0.00 0.00 30.75 3.82
62 63 7.172868 TGCTTATGAATTCCACATTGTGATT 57.827 32.000 18.33 10.47 35.23 2.57
69 70 3.381272 CCGGTTGCTTATGAATTCCACAT 59.619 43.478 2.27 0.00 0.00 3.21
89 90 6.830114 ACTTATTTTAAGAGATCGAAGCCG 57.170 37.500 0.00 0.00 37.07 5.52
141 142 9.887629 CTAGGCAAATATCTGATATGACATCTT 57.112 33.333 10.76 0.00 0.00 2.40
146 147 9.494271 TTCAACTAGGCAAATATCTGATATGAC 57.506 33.333 10.76 3.69 0.00 3.06
208 209 2.283145 ACAGCCAGCTGAAATTCAGT 57.717 45.000 25.66 8.27 45.94 3.41
209 210 2.097142 GCTACAGCCAGCTGAAATTCAG 59.903 50.000 25.66 18.02 46.30 3.02
212 213 1.815003 GTGCTACAGCCAGCTGAAATT 59.185 47.619 25.66 6.20 46.30 1.82
213 214 1.271543 TGTGCTACAGCCAGCTGAAAT 60.272 47.619 25.66 6.56 46.30 2.17
214 215 0.108396 TGTGCTACAGCCAGCTGAAA 59.892 50.000 25.66 12.08 46.30 2.69
215 216 0.108396 TTGTGCTACAGCCAGCTGAA 59.892 50.000 25.66 5.91 46.30 3.02
300 312 9.021863 GTAATAGCTCACTCACACAATAGTTAC 57.978 37.037 0.00 0.00 0.00 2.50
311 323 4.446371 AGCCAATGTAATAGCTCACTCAC 58.554 43.478 0.00 0.00 31.06 3.51
357 390 1.122849 GTGCACGCAACAACAGATTG 58.877 50.000 0.00 0.00 41.98 2.67
432 465 6.213600 ACTTCCAGTAACAACCATCTATCTGT 59.786 38.462 0.00 0.00 0.00 3.41
450 483 1.933247 TTTTGCGGCAAAACTTCCAG 58.067 45.000 30.89 0.00 38.24 3.86
451 484 2.386661 TTTTTGCGGCAAAACTTCCA 57.613 40.000 33.47 19.75 42.02 3.53
587 620 5.560375 GCATGCATGTTATGTCAGTCATCTC 60.560 44.000 26.79 1.13 37.91 2.75
667 700 3.103213 ACAAGCACCACCCCCACT 61.103 61.111 0.00 0.00 0.00 4.00
707 740 5.106436 CGCCTCATGATATAATGTGCATGTT 60.106 40.000 13.98 0.00 39.22 2.71
730 763 0.242286 CTGCGATAGTGAGGGGATCG 59.758 60.000 0.00 0.00 44.11 3.69
835 868 1.227973 GCGAGGGGATGGCTAAAGG 60.228 63.158 0.00 0.00 0.00 3.11
935 968 3.688694 AGTCTCTACTCACTCAGTCGT 57.311 47.619 0.00 0.00 36.43 4.34
1070 1103 1.949847 ATGGACCTTCAGCGACCTCG 61.950 60.000 0.00 0.00 43.27 4.63
1117 1150 0.535102 GCCAGGTGGGTATTGATCCG 60.535 60.000 0.00 0.00 39.65 4.18
1205 1238 2.099263 TCGAAACGGATCTCTGGCTAAG 59.901 50.000 0.00 0.00 0.00 2.18
1232 1265 2.289506 GGTTTCGTCCTCTGGCTAACTT 60.290 50.000 0.00 0.00 0.00 2.66
1239 1272 1.679032 GGGATTGGTTTCGTCCTCTGG 60.679 57.143 0.00 0.00 32.55 3.86
1313 1346 7.665561 TTTTCAGGAAAAAGGTGTTTCTTTG 57.334 32.000 4.79 0.00 37.35 2.77
1383 1416 4.777366 TGTCCATCTGGTCATACAAGAAGA 59.223 41.667 0.00 0.00 36.34 2.87
1384 1417 5.089970 TGTCCATCTGGTCATACAAGAAG 57.910 43.478 0.00 0.00 36.34 2.85
1385 1418 5.491070 CTTGTCCATCTGGTCATACAAGAA 58.509 41.667 17.37 0.00 43.43 2.52
1510 1546 2.737359 GCAATGGACGGTGATCTCGTTA 60.737 50.000 13.96 8.52 41.22 3.18
1786 1822 2.815211 CCACCGCACACCATCTCG 60.815 66.667 0.00 0.00 0.00 4.04
1933 1969 2.126580 CTGCTTGCTCGCTTTGGC 60.127 61.111 0.00 0.00 0.00 4.52
1967 2003 3.023832 CCAAACACATCCCAAGGTATCC 58.976 50.000 0.00 0.00 0.00 2.59
2028 2093 6.993079 AGAATGAAACCAACCTATTTGTTCC 58.007 36.000 0.00 0.00 32.71 3.62
2032 2097 7.209475 ACACAAGAATGAAACCAACCTATTTG 58.791 34.615 0.00 0.00 34.63 2.32
2037 2102 4.202010 CGAACACAAGAATGAAACCAACCT 60.202 41.667 0.00 0.00 0.00 3.50
2123 2188 7.168637 CACAAGGTGAGTTGAATCAGATTTTTG 59.831 37.037 0.00 0.00 35.23 2.44
2220 2288 9.378504 TGGAAATGTTGCTGGGATTTATATAAT 57.621 29.630 0.00 0.00 0.00 1.28
2223 2291 7.860649 ATGGAAATGTTGCTGGGATTTATAT 57.139 32.000 0.00 0.00 0.00 0.86
2224 2292 7.125507 ACAATGGAAATGTTGCTGGGATTTATA 59.874 33.333 0.00 0.00 0.00 0.98
2225 2293 6.070078 ACAATGGAAATGTTGCTGGGATTTAT 60.070 34.615 0.00 0.00 0.00 1.40
2226 2294 5.248020 ACAATGGAAATGTTGCTGGGATTTA 59.752 36.000 0.00 0.00 0.00 1.40
2227 2295 4.041938 ACAATGGAAATGTTGCTGGGATTT 59.958 37.500 0.00 0.00 0.00 2.17
2228 2296 3.583966 ACAATGGAAATGTTGCTGGGATT 59.416 39.130 0.00 0.00 0.00 3.01
2229 2297 3.175594 ACAATGGAAATGTTGCTGGGAT 58.824 40.909 0.00 0.00 0.00 3.85
2230 2298 2.607499 ACAATGGAAATGTTGCTGGGA 58.393 42.857 0.00 0.00 0.00 4.37
2231 2299 4.741321 ATACAATGGAAATGTTGCTGGG 57.259 40.909 0.00 0.00 32.27 4.45
2272 2340 9.630098 CTGAATTTTGCTTGACATTGTATACTT 57.370 29.630 4.17 0.00 0.00 2.24
2274 2342 8.853345 CACTGAATTTTGCTTGACATTGTATAC 58.147 33.333 0.00 0.00 0.00 1.47
2276 2344 6.869913 CCACTGAATTTTGCTTGACATTGTAT 59.130 34.615 0.00 0.00 0.00 2.29
2534 2602 7.467650 TGGTTATTCCTCTCTTATCGATAGGA 58.532 38.462 15.59 15.59 41.71 2.94
2535 2603 7.704578 TGGTTATTCCTCTCTTATCGATAGG 57.295 40.000 8.19 8.19 37.35 2.57
2536 2604 8.744652 ACATGGTTATTCCTCTCTTATCGATAG 58.255 37.037 5.09 0.00 37.07 2.08
2537 2605 8.523658 CACATGGTTATTCCTCTCTTATCGATA 58.476 37.037 0.00 0.00 37.07 2.92
2538 2606 7.233553 TCACATGGTTATTCCTCTCTTATCGAT 59.766 37.037 2.16 2.16 37.07 3.59
2539 2607 6.549736 TCACATGGTTATTCCTCTCTTATCGA 59.450 38.462 0.00 0.00 37.07 3.59
2540 2608 6.749139 TCACATGGTTATTCCTCTCTTATCG 58.251 40.000 0.00 0.00 37.07 2.92
2541 2609 9.213799 GAATCACATGGTTATTCCTCTCTTATC 57.786 37.037 0.00 0.00 37.07 1.75
2542 2610 8.160106 GGAATCACATGGTTATTCCTCTCTTAT 58.840 37.037 20.39 0.00 40.88 1.73
2543 2611 7.509546 GGAATCACATGGTTATTCCTCTCTTA 58.490 38.462 20.39 0.00 40.88 2.10
2544 2612 6.360618 GGAATCACATGGTTATTCCTCTCTT 58.639 40.000 20.39 0.00 40.88 2.85
2545 2613 5.934781 GGAATCACATGGTTATTCCTCTCT 58.065 41.667 20.39 0.00 40.88 3.10
2550 2618 5.123227 TCGAAGGAATCACATGGTTATTCC 58.877 41.667 20.21 20.21 43.02 3.01
2551 2619 6.867662 ATCGAAGGAATCACATGGTTATTC 57.132 37.500 0.00 3.19 0.00 1.75
2552 2620 7.416664 CCAAATCGAAGGAATCACATGGTTATT 60.417 37.037 0.00 0.00 0.00 1.40
2553 2621 6.039717 CCAAATCGAAGGAATCACATGGTTAT 59.960 38.462 0.00 0.00 0.00 1.89
2554 2622 5.356751 CCAAATCGAAGGAATCACATGGTTA 59.643 40.000 0.00 0.00 0.00 2.85
2555 2623 4.158394 CCAAATCGAAGGAATCACATGGTT 59.842 41.667 0.00 0.00 0.00 3.67
2556 2624 3.696051 CCAAATCGAAGGAATCACATGGT 59.304 43.478 0.00 0.00 0.00 3.55
2557 2625 3.696051 ACCAAATCGAAGGAATCACATGG 59.304 43.478 8.68 0.00 0.00 3.66
2558 2626 4.439153 CCACCAAATCGAAGGAATCACATG 60.439 45.833 8.68 0.00 0.00 3.21
2559 2627 3.696051 CCACCAAATCGAAGGAATCACAT 59.304 43.478 8.68 0.00 0.00 3.21
2560 2628 3.081061 CCACCAAATCGAAGGAATCACA 58.919 45.455 8.68 0.00 0.00 3.58
2561 2629 3.343617 TCCACCAAATCGAAGGAATCAC 58.656 45.455 8.68 0.00 0.00 3.06
2562 2630 3.712016 TCCACCAAATCGAAGGAATCA 57.288 42.857 8.68 0.00 0.00 2.57
2572 2640 3.378112 TCATCAAGCGATTCCACCAAATC 59.622 43.478 0.00 0.00 33.22 2.17
2573 2641 3.355378 TCATCAAGCGATTCCACCAAAT 58.645 40.909 0.00 0.00 0.00 2.32
2574 2642 2.789213 TCATCAAGCGATTCCACCAAA 58.211 42.857 0.00 0.00 0.00 3.28
2575 2643 2.488204 TCATCAAGCGATTCCACCAA 57.512 45.000 0.00 0.00 0.00 3.67
2576 2644 2.358957 CTTCATCAAGCGATTCCACCA 58.641 47.619 0.00 0.00 0.00 4.17
2577 2645 1.064654 GCTTCATCAAGCGATTCCACC 59.935 52.381 0.00 0.00 45.67 4.61
2578 2646 2.465210 GCTTCATCAAGCGATTCCAC 57.535 50.000 0.00 0.00 45.67 4.02
2587 2655 3.349927 TCCCTTCATGTGCTTCATCAAG 58.650 45.455 0.00 0.82 34.99 3.02
2588 2656 3.438216 TCCCTTCATGTGCTTCATCAA 57.562 42.857 0.00 0.00 34.09 2.57
2589 2657 3.438216 TTCCCTTCATGTGCTTCATCA 57.562 42.857 0.00 0.00 34.09 3.07
2590 2658 6.294397 GGAATATTCCCTTCATGTGCTTCATC 60.294 42.308 22.09 0.00 41.62 2.92
2591 2659 5.537674 GGAATATTCCCTTCATGTGCTTCAT 59.462 40.000 22.09 0.00 41.62 2.57
2592 2660 4.889409 GGAATATTCCCTTCATGTGCTTCA 59.111 41.667 22.09 0.00 41.62 3.02
2593 2661 5.444663 GGAATATTCCCTTCATGTGCTTC 57.555 43.478 22.09 0.00 41.62 3.86
2614 2682 2.770802 ACCATGTGATCCTCAGAGAAGG 59.229 50.000 0.00 0.00 37.81 3.46
2615 2683 4.484537 AACCATGTGATCCTCAGAGAAG 57.515 45.455 0.00 0.00 0.00 2.85
2616 2684 4.533707 AGAAACCATGTGATCCTCAGAGAA 59.466 41.667 0.00 0.00 0.00 2.87
2617 2685 4.081254 CAGAAACCATGTGATCCTCAGAGA 60.081 45.833 0.00 0.00 0.00 3.10
2618 2686 4.190001 CAGAAACCATGTGATCCTCAGAG 58.810 47.826 0.00 0.00 0.00 3.35
2619 2687 3.584406 ACAGAAACCATGTGATCCTCAGA 59.416 43.478 0.00 0.00 0.00 3.27
2620 2688 3.947868 ACAGAAACCATGTGATCCTCAG 58.052 45.455 0.00 0.00 0.00 3.35
2621 2689 4.371624 AACAGAAACCATGTGATCCTCA 57.628 40.909 0.00 0.00 0.00 3.86
2622 2690 4.761739 TGAAACAGAAACCATGTGATCCTC 59.238 41.667 0.00 0.00 0.00 3.71
2623 2691 4.728772 TGAAACAGAAACCATGTGATCCT 58.271 39.130 0.00 0.00 0.00 3.24
2624 2692 5.393461 GGATGAAACAGAAACCATGTGATCC 60.393 44.000 0.00 0.00 30.65 3.36
2625 2693 5.416952 AGGATGAAACAGAAACCATGTGATC 59.583 40.000 0.00 0.00 0.00 2.92
2626 2694 5.327732 AGGATGAAACAGAAACCATGTGAT 58.672 37.500 0.00 0.00 0.00 3.06
2627 2695 4.728772 AGGATGAAACAGAAACCATGTGA 58.271 39.130 0.00 0.00 0.00 3.58
2628 2696 4.520111 TGAGGATGAAACAGAAACCATGTG 59.480 41.667 0.00 0.00 0.00 3.21
2629 2697 4.728772 TGAGGATGAAACAGAAACCATGT 58.271 39.130 0.00 0.00 0.00 3.21
2630 2698 5.242393 AGTTGAGGATGAAACAGAAACCATG 59.758 40.000 0.00 0.00 0.00 3.66
2631 2699 5.388654 AGTTGAGGATGAAACAGAAACCAT 58.611 37.500 0.00 0.00 0.00 3.55
2632 2700 4.792068 AGTTGAGGATGAAACAGAAACCA 58.208 39.130 0.00 0.00 0.00 3.67
2633 2701 6.877611 TTAGTTGAGGATGAAACAGAAACC 57.122 37.500 0.00 0.00 0.00 3.27
2634 2702 7.644157 GTGTTTAGTTGAGGATGAAACAGAAAC 59.356 37.037 0.00 0.00 36.23 2.78
2635 2703 7.556275 AGTGTTTAGTTGAGGATGAAACAGAAA 59.444 33.333 0.00 0.00 30.56 2.52
2636 2704 7.012327 CAGTGTTTAGTTGAGGATGAAACAGAA 59.988 37.037 0.00 0.00 30.56 3.02
2637 2705 6.483307 CAGTGTTTAGTTGAGGATGAAACAGA 59.517 38.462 0.00 0.00 30.56 3.41
2638 2706 6.483307 TCAGTGTTTAGTTGAGGATGAAACAG 59.517 38.462 0.00 0.00 30.56 3.16
2639 2707 6.353323 TCAGTGTTTAGTTGAGGATGAAACA 58.647 36.000 0.00 0.00 0.00 2.83
2640 2708 6.861065 TCAGTGTTTAGTTGAGGATGAAAC 57.139 37.500 0.00 0.00 0.00 2.78
2641 2709 7.873719 TTTCAGTGTTTAGTTGAGGATGAAA 57.126 32.000 0.00 0.00 0.00 2.69
2642 2710 7.040478 CCATTTCAGTGTTTAGTTGAGGATGAA 60.040 37.037 0.00 0.00 0.00 2.57
2643 2711 6.430925 CCATTTCAGTGTTTAGTTGAGGATGA 59.569 38.462 0.00 0.00 0.00 2.92
2644 2712 6.207417 ACCATTTCAGTGTTTAGTTGAGGATG 59.793 38.462 0.00 0.00 0.00 3.51
2645 2713 6.207417 CACCATTTCAGTGTTTAGTTGAGGAT 59.793 38.462 0.00 0.00 0.00 3.24
2646 2714 5.530915 CACCATTTCAGTGTTTAGTTGAGGA 59.469 40.000 0.00 0.00 0.00 3.71
2647 2715 5.278463 CCACCATTTCAGTGTTTAGTTGAGG 60.278 44.000 0.00 0.00 33.20 3.86
2648 2716 5.278463 CCCACCATTTCAGTGTTTAGTTGAG 60.278 44.000 0.00 0.00 33.20 3.02
2649 2717 4.582656 CCCACCATTTCAGTGTTTAGTTGA 59.417 41.667 0.00 0.00 33.20 3.18
2650 2718 4.795962 GCCCACCATTTCAGTGTTTAGTTG 60.796 45.833 0.00 0.00 33.20 3.16
2651 2719 3.320826 GCCCACCATTTCAGTGTTTAGTT 59.679 43.478 0.00 0.00 33.20 2.24
2652 2720 2.890945 GCCCACCATTTCAGTGTTTAGT 59.109 45.455 0.00 0.00 33.20 2.24
2653 2721 3.157087 AGCCCACCATTTCAGTGTTTAG 58.843 45.455 0.00 0.00 33.20 1.85
2654 2722 3.237268 AGCCCACCATTTCAGTGTTTA 57.763 42.857 0.00 0.00 33.20 2.01
2655 2723 2.086610 AGCCCACCATTTCAGTGTTT 57.913 45.000 0.00 0.00 33.20 2.83
2656 2724 2.555227 CCTAGCCCACCATTTCAGTGTT 60.555 50.000 0.00 0.00 33.20 3.32
2657 2725 1.004745 CCTAGCCCACCATTTCAGTGT 59.995 52.381 0.00 0.00 33.20 3.55
2658 2726 1.683011 CCCTAGCCCACCATTTCAGTG 60.683 57.143 0.00 0.00 34.91 3.66
2659 2727 0.625849 CCCTAGCCCACCATTTCAGT 59.374 55.000 0.00 0.00 0.00 3.41
2660 2728 0.918983 TCCCTAGCCCACCATTTCAG 59.081 55.000 0.00 0.00 0.00 3.02
2661 2729 0.623723 GTCCCTAGCCCACCATTTCA 59.376 55.000 0.00 0.00 0.00 2.69
2662 2730 0.463833 CGTCCCTAGCCCACCATTTC 60.464 60.000 0.00 0.00 0.00 2.17
2663 2731 1.607612 CGTCCCTAGCCCACCATTT 59.392 57.895 0.00 0.00 0.00 2.32
2664 2732 2.375345 CCGTCCCTAGCCCACCATT 61.375 63.158 0.00 0.00 0.00 3.16
2665 2733 2.768344 CCGTCCCTAGCCCACCAT 60.768 66.667 0.00 0.00 0.00 3.55
2666 2734 2.833151 ATTCCGTCCCTAGCCCACCA 62.833 60.000 0.00 0.00 0.00 4.17
2667 2735 1.632965 AATTCCGTCCCTAGCCCACC 61.633 60.000 0.00 0.00 0.00 4.61
2668 2736 0.463833 CAATTCCGTCCCTAGCCCAC 60.464 60.000 0.00 0.00 0.00 4.61
2669 2737 0.912487 ACAATTCCGTCCCTAGCCCA 60.912 55.000 0.00 0.00 0.00 5.36
2670 2738 1.070289 CTACAATTCCGTCCCTAGCCC 59.930 57.143 0.00 0.00 0.00 5.19
2671 2739 2.036089 CTCTACAATTCCGTCCCTAGCC 59.964 54.545 0.00 0.00 0.00 3.93
2672 2740 2.957006 TCTCTACAATTCCGTCCCTAGC 59.043 50.000 0.00 0.00 0.00 3.42
2673 2741 4.276431 GTCTCTCTACAATTCCGTCCCTAG 59.724 50.000 0.00 0.00 0.00 3.02
2674 2742 4.205587 GTCTCTCTACAATTCCGTCCCTA 58.794 47.826 0.00 0.00 0.00 3.53
2675 2743 3.025262 GTCTCTCTACAATTCCGTCCCT 58.975 50.000 0.00 0.00 0.00 4.20
2676 2744 2.758979 TGTCTCTCTACAATTCCGTCCC 59.241 50.000 0.00 0.00 0.00 4.46
2677 2745 4.082136 ACTTGTCTCTCTACAATTCCGTCC 60.082 45.833 0.00 0.00 38.61 4.79
2678 2746 5.061920 ACTTGTCTCTCTACAATTCCGTC 57.938 43.478 0.00 0.00 38.61 4.79
2679 2747 5.470047 AACTTGTCTCTCTACAATTCCGT 57.530 39.130 0.00 0.00 38.61 4.69
2680 2748 6.477033 CCATAACTTGTCTCTCTACAATTCCG 59.523 42.308 0.00 0.00 38.61 4.30
2681 2749 6.763610 CCCATAACTTGTCTCTCTACAATTCC 59.236 42.308 0.00 0.00 38.61 3.01
2682 2750 6.258947 GCCCATAACTTGTCTCTCTACAATTC 59.741 42.308 0.00 0.00 38.61 2.17
2683 2751 6.069963 AGCCCATAACTTGTCTCTCTACAATT 60.070 38.462 0.00 0.00 38.61 2.32
2684 2752 5.426833 AGCCCATAACTTGTCTCTCTACAAT 59.573 40.000 0.00 0.00 38.61 2.71
2685 2753 4.777896 AGCCCATAACTTGTCTCTCTACAA 59.222 41.667 0.00 0.00 37.75 2.41
2686 2754 4.160439 CAGCCCATAACTTGTCTCTCTACA 59.840 45.833 0.00 0.00 0.00 2.74
2687 2755 4.160626 ACAGCCCATAACTTGTCTCTCTAC 59.839 45.833 0.00 0.00 0.00 2.59
2688 2756 4.160439 CACAGCCCATAACTTGTCTCTCTA 59.840 45.833 0.00 0.00 0.00 2.43
2689 2757 3.055530 CACAGCCCATAACTTGTCTCTCT 60.056 47.826 0.00 0.00 0.00 3.10
2690 2758 3.265791 CACAGCCCATAACTTGTCTCTC 58.734 50.000 0.00 0.00 0.00 3.20
2691 2759 2.616510 GCACAGCCCATAACTTGTCTCT 60.617 50.000 0.00 0.00 0.00 3.10
2692 2760 1.740025 GCACAGCCCATAACTTGTCTC 59.260 52.381 0.00 0.00 0.00 3.36
2693 2761 1.073763 TGCACAGCCCATAACTTGTCT 59.926 47.619 0.00 0.00 0.00 3.41
2694 2762 1.533625 TGCACAGCCCATAACTTGTC 58.466 50.000 0.00 0.00 0.00 3.18
2695 2763 1.993956 TTGCACAGCCCATAACTTGT 58.006 45.000 0.00 0.00 0.00 3.16
2696 2764 2.492881 TGATTGCACAGCCCATAACTTG 59.507 45.455 0.00 0.00 0.00 3.16
2697 2765 2.493278 GTGATTGCACAGCCCATAACTT 59.507 45.455 0.00 0.00 44.51 2.66
2698 2766 2.094675 GTGATTGCACAGCCCATAACT 58.905 47.619 0.00 0.00 44.51 2.24
2699 2767 2.566952 GTGATTGCACAGCCCATAAC 57.433 50.000 0.00 0.00 44.51 1.89
2709 2777 4.971830 CCGATCAATACATTGTGATTGCAC 59.028 41.667 0.00 0.00 45.35 4.57
2710 2778 4.639755 ACCGATCAATACATTGTGATTGCA 59.360 37.500 0.00 0.00 38.84 4.08
2711 2779 5.173774 ACCGATCAATACATTGTGATTGC 57.826 39.130 0.00 0.00 38.84 3.56
2712 2780 7.245419 TGTACCGATCAATACATTGTGATTG 57.755 36.000 0.00 6.19 38.84 2.67
2713 2781 7.714813 TGATGTACCGATCAATACATTGTGATT 59.285 33.333 16.19 0.00 41.12 2.57
2714 2782 7.216494 TGATGTACCGATCAATACATTGTGAT 58.784 34.615 16.19 0.00 41.12 3.06
2715 2783 6.578023 TGATGTACCGATCAATACATTGTGA 58.422 36.000 16.19 0.00 41.12 3.58
2716 2784 6.701400 TCTGATGTACCGATCAATACATTGTG 59.299 38.462 16.19 11.17 41.12 3.33
2717 2785 6.701841 GTCTGATGTACCGATCAATACATTGT 59.298 38.462 16.19 0.00 41.12 2.71
2718 2786 6.701400 TGTCTGATGTACCGATCAATACATTG 59.299 38.462 16.19 13.08 41.12 2.82
2719 2787 6.701841 GTGTCTGATGTACCGATCAATACATT 59.298 38.462 16.19 4.92 41.12 2.71
2720 2788 6.183360 TGTGTCTGATGTACCGATCAATACAT 60.183 38.462 15.40 15.40 43.19 2.29
2721 2789 5.126384 TGTGTCTGATGTACCGATCAATACA 59.874 40.000 8.16 8.16 35.82 2.29
2722 2790 5.588240 TGTGTCTGATGTACCGATCAATAC 58.412 41.667 0.00 0.00 31.90 1.89
2723 2791 5.845391 TGTGTCTGATGTACCGATCAATA 57.155 39.130 0.00 0.00 31.90 1.90
2724 2792 4.736126 TGTGTCTGATGTACCGATCAAT 57.264 40.909 0.00 0.00 31.90 2.57
2725 2793 4.736126 ATGTGTCTGATGTACCGATCAA 57.264 40.909 0.00 0.00 31.90 2.57
2726 2794 7.703058 ATATATGTGTCTGATGTACCGATCA 57.297 36.000 0.00 0.00 0.00 2.92
2741 2809 9.702253 CCTCCCTCTGTACTTATATATATGTGT 57.298 37.037 17.38 6.59 0.00 3.72
2742 2810 9.137459 CCCTCCCTCTGTACTTATATATATGTG 57.863 40.741 17.38 5.36 0.00 3.21
2743 2811 7.785506 GCCCTCCCTCTGTACTTATATATATGT 59.214 40.741 13.92 13.92 0.00 2.29
2744 2812 7.233757 GGCCCTCCCTCTGTACTTATATATATG 59.766 44.444 5.44 4.50 0.00 1.78
2745 2813 7.091030 TGGCCCTCCCTCTGTACTTATATATAT 60.091 40.741 0.00 0.00 0.00 0.86
2746 2814 6.221029 TGGCCCTCCCTCTGTACTTATATATA 59.779 42.308 0.00 0.00 0.00 0.86
2747 2815 5.017431 TGGCCCTCCCTCTGTACTTATATAT 59.983 44.000 0.00 0.00 0.00 0.86
2748 2816 4.358918 TGGCCCTCCCTCTGTACTTATATA 59.641 45.833 0.00 0.00 0.00 0.86
2749 2817 3.144125 TGGCCCTCCCTCTGTACTTATAT 59.856 47.826 0.00 0.00 0.00 0.86
2750 2818 2.520980 TGGCCCTCCCTCTGTACTTATA 59.479 50.000 0.00 0.00 0.00 0.98
2751 2819 1.294068 TGGCCCTCCCTCTGTACTTAT 59.706 52.381 0.00 0.00 0.00 1.73
2752 2820 0.714180 TGGCCCTCCCTCTGTACTTA 59.286 55.000 0.00 0.00 0.00 2.24
2753 2821 0.910088 GTGGCCCTCCCTCTGTACTT 60.910 60.000 0.00 0.00 0.00 2.24
2754 2822 1.306226 GTGGCCCTCCCTCTGTACT 60.306 63.158 0.00 0.00 0.00 2.73
2755 2823 0.983378 ATGTGGCCCTCCCTCTGTAC 60.983 60.000 0.00 0.00 0.00 2.90
2756 2824 0.691078 GATGTGGCCCTCCCTCTGTA 60.691 60.000 0.00 0.00 0.00 2.74
2757 2825 1.997874 GATGTGGCCCTCCCTCTGT 60.998 63.158 0.00 0.00 0.00 3.41
2758 2826 2.750657 GGATGTGGCCCTCCCTCTG 61.751 68.421 0.00 0.00 0.00 3.35
2759 2827 2.367512 GGATGTGGCCCTCCCTCT 60.368 66.667 0.00 0.00 0.00 3.69
2760 2828 2.367512 AGGATGTGGCCCTCCCTC 60.368 66.667 0.00 0.00 31.49 4.30
2761 2829 2.367512 GAGGATGTGGCCCTCCCT 60.368 66.667 0.00 0.75 43.37 4.20
2765 2833 1.898863 ATAGTTGAGGATGTGGCCCT 58.101 50.000 0.00 0.00 36.57 5.19
2766 2834 2.438021 TGTATAGTTGAGGATGTGGCCC 59.562 50.000 0.00 0.00 0.00 5.80
2767 2835 3.388024 TCTGTATAGTTGAGGATGTGGCC 59.612 47.826 0.00 0.00 0.00 5.36
2768 2836 4.342378 TCTCTGTATAGTTGAGGATGTGGC 59.658 45.833 0.00 0.00 0.00 5.01
2769 2837 6.471233 TTCTCTGTATAGTTGAGGATGTGG 57.529 41.667 0.00 0.00 0.00 4.17
2770 2838 7.819415 TGTTTTCTCTGTATAGTTGAGGATGTG 59.181 37.037 0.00 0.00 0.00 3.21
2771 2839 7.907389 TGTTTTCTCTGTATAGTTGAGGATGT 58.093 34.615 0.00 0.00 0.00 3.06
2772 2840 7.493971 CCTGTTTTCTCTGTATAGTTGAGGATG 59.506 40.741 0.00 0.00 0.00 3.51
2773 2841 7.400339 TCCTGTTTTCTCTGTATAGTTGAGGAT 59.600 37.037 0.00 0.00 0.00 3.24
2774 2842 6.724441 TCCTGTTTTCTCTGTATAGTTGAGGA 59.276 38.462 0.00 0.00 0.00 3.71
2775 2843 6.936279 TCCTGTTTTCTCTGTATAGTTGAGG 58.064 40.000 0.00 0.00 0.00 3.86
2776 2844 7.038659 CCTCCTGTTTTCTCTGTATAGTTGAG 58.961 42.308 0.00 0.00 0.00 3.02
2777 2845 6.497259 ACCTCCTGTTTTCTCTGTATAGTTGA 59.503 38.462 0.00 0.00 0.00 3.18
2778 2846 6.591834 CACCTCCTGTTTTCTCTGTATAGTTG 59.408 42.308 0.00 0.00 0.00 3.16
2779 2847 6.295916 CCACCTCCTGTTTTCTCTGTATAGTT 60.296 42.308 0.00 0.00 0.00 2.24
2780 2848 5.187967 CCACCTCCTGTTTTCTCTGTATAGT 59.812 44.000 0.00 0.00 0.00 2.12
2781 2849 5.395768 CCCACCTCCTGTTTTCTCTGTATAG 60.396 48.000 0.00 0.00 0.00 1.31
2782 2850 4.469945 CCCACCTCCTGTTTTCTCTGTATA 59.530 45.833 0.00 0.00 0.00 1.47
2783 2851 3.264450 CCCACCTCCTGTTTTCTCTGTAT 59.736 47.826 0.00 0.00 0.00 2.29
2784 2852 2.637872 CCCACCTCCTGTTTTCTCTGTA 59.362 50.000 0.00 0.00 0.00 2.74
2785 2853 1.421646 CCCACCTCCTGTTTTCTCTGT 59.578 52.381 0.00 0.00 0.00 3.41
2786 2854 1.884067 GCCCACCTCCTGTTTTCTCTG 60.884 57.143 0.00 0.00 0.00 3.35
2787 2855 0.402121 GCCCACCTCCTGTTTTCTCT 59.598 55.000 0.00 0.00 0.00 3.10
2788 2856 0.609406 GGCCCACCTCCTGTTTTCTC 60.609 60.000 0.00 0.00 0.00 2.87
2789 2857 1.460699 GGCCCACCTCCTGTTTTCT 59.539 57.895 0.00 0.00 0.00 2.52
2790 2858 1.606601 GGGCCCACCTCCTGTTTTC 60.607 63.158 19.95 0.00 35.85 2.29
2791 2859 2.526110 GGGCCCACCTCCTGTTTT 59.474 61.111 19.95 0.00 35.85 2.43
2800 2868 5.710409 ATATATTGTGTATAGGGCCCACC 57.290 43.478 27.56 8.92 40.67 4.61
2801 2869 6.127253 ACGTATATATTGTGTATAGGGCCCAC 60.127 42.308 27.56 14.86 0.00 4.61
2802 2870 5.959594 ACGTATATATTGTGTATAGGGCCCA 59.040 40.000 27.56 10.89 0.00 5.36
2803 2871 6.475596 ACGTATATATTGTGTATAGGGCCC 57.524 41.667 16.46 16.46 0.00 5.80
2804 2872 7.999679 TGTACGTATATATTGTGTATAGGGCC 58.000 38.462 0.00 0.00 0.00 5.80
2820 2888 9.189156 GGGGGTTGAGTATATTATGTACGTATA 57.811 37.037 0.00 0.00 0.00 1.47
2821 2889 8.071177 GGGGGTTGAGTATATTATGTACGTAT 57.929 38.462 0.00 0.00 0.00 3.06
2822 2890 7.466746 GGGGGTTGAGTATATTATGTACGTA 57.533 40.000 0.00 0.00 0.00 3.57
2823 2891 6.350629 GGGGGTTGAGTATATTATGTACGT 57.649 41.667 0.00 0.00 0.00 3.57


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

AutoCloner maintained by Alex Coulton.