Multiple sequence alignment - TraesCS2A01G372000

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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 TraesCS2A01G372000 chr2A 100.000 3945 0 0 1 3945 614396624 614392680 0.000000e+00 7286.0
1 TraesCS2A01G372000 chr2A 95.652 46 1 1 2611 2656 205917662 205917706 5.470000e-09 73.1
2 TraesCS2A01G372000 chr2D 88.866 1904 105 37 1 1893 472946555 472944748 0.000000e+00 2242.0
3 TraesCS2A01G372000 chr2D 92.371 1088 56 13 2109 3195 472944531 472943470 0.000000e+00 1524.0
4 TraesCS2A01G372000 chr2D 83.178 749 114 8 3204 3945 472943362 472942619 0.000000e+00 675.0
5 TraesCS2A01G372000 chr2D 98.010 201 4 0 1881 2081 472944729 472944529 2.260000e-92 350.0
6 TraesCS2A01G372000 chr2D 93.478 46 2 1 2611 2656 29686609 29686565 2.540000e-07 67.6
7 TraesCS2A01G372000 chr2D 91.489 47 3 1 2610 2656 192181749 192181704 3.290000e-06 63.9
8 TraesCS2A01G372000 chr2B 91.897 1592 88 13 1606 3195 552262105 552260553 0.000000e+00 2187.0
9 TraesCS2A01G372000 chr2B 86.942 1501 125 31 62 1547 552263558 552262114 0.000000e+00 1620.0
10 TraesCS2A01G372000 chr2B 80.774 749 118 14 3204 3942 552260433 552259701 2.660000e-156 562.0
11 TraesCS2A01G372000 chr2B 91.111 45 3 1 2612 2656 6176710 6176753 4.260000e-05 60.2
12 TraesCS2A01G372000 chr1B 100.000 28 0 0 2611 2638 380888232 380888259 7.000000e-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 TraesCS2A01G372000 chr2A 614392680 614396624 3944 True 7286.000000 7286 100.000000 1 3945 1 chr2A.!!$R1 3944
1 TraesCS2A01G372000 chr2D 472942619 472946555 3936 True 1197.750000 2242 90.606250 1 3945 4 chr2D.!!$R3 3944
2 TraesCS2A01G372000 chr2B 552259701 552263558 3857 True 1456.333333 2187 86.537667 62 3942 3 chr2B.!!$R1 3880

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
755 776 0.040067 CTTCGGCAAGTTGGCAAGTC 60.040 55.0 26.86 0.0 43.94 3.01 F
1991 2078 0.459489 AGCTCGTCATCAAGCTCCTC 59.541 55.0 0.00 0.0 45.57 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2174 0.038166 GTTGGCCACATCTTCAGGGA 59.962 55.0 3.88 0.0 0.0 4.20 R
3683 3917 0.240945 GCAACAACATGAGAACCCGG 59.759 55.0 0.00 0.0 0.0 5.73 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
111 112 9.643652 TTTTAAATGCGAACAAATTGTGAAATC 57.356 25.926 0.00 0.00 0.00 2.17
112 113 8.586570 TTAAATGCGAACAAATTGTGAAATCT 57.413 26.923 0.00 0.00 0.00 2.40
117 118 6.700960 TGCGAACAAATTGTGAAATCTCAATT 59.299 30.769 14.45 14.45 45.99 2.32
172 174 6.567769 AGTAAGCATTTTTGTGAAAACACG 57.432 33.333 0.00 0.00 37.56 4.49
173 175 3.923827 AGCATTTTTGTGAAAACACGC 57.076 38.095 0.00 0.00 37.56 5.34
411 428 0.603707 CCTGGCAGTTTTCTCGCTCA 60.604 55.000 14.43 0.00 0.00 4.26
553 570 3.159298 GTCCATGGACGATGCAACT 57.841 52.632 28.52 0.00 35.30 3.16
606 627 2.664851 CAGACTGGGCGCGTCAAA 60.665 61.111 14.93 0.00 33.89 2.69
623 644 3.587170 AACCCGTCCTCTCGCTCCT 62.587 63.158 0.00 0.00 0.00 3.69
683 704 2.858158 CGAAACCGGCGGAAGAAC 59.142 61.111 35.78 16.78 0.00 3.01
741 762 0.391263 GGTACTTGACCTGCCTTCGG 60.391 60.000 0.00 0.00 45.89 4.30
755 776 0.040067 CTTCGGCAAGTTGGCAAGTC 60.040 55.000 26.86 0.00 43.94 3.01
785 806 2.773397 TACCACACACCGCGTCCATG 62.773 60.000 4.92 0.00 0.00 3.66
786 807 2.664851 CACACACCGCGTCCATGT 60.665 61.111 4.92 0.53 0.00 3.21
788 809 2.356913 CACACCGCGTCCATGTGA 60.357 61.111 19.34 0.00 45.34 3.58
789 810 2.357034 ACACCGCGTCCATGTGAC 60.357 61.111 17.43 4.71 40.81 3.67
796 817 2.430244 GTCCATGTGACGCGACGT 60.430 61.111 15.93 0.00 45.10 4.34
797 818 2.430075 TCCATGTGACGCGACGTG 60.430 61.111 15.93 13.42 41.37 4.49
798 819 3.478394 CCATGTGACGCGACGTGG 61.478 66.667 20.72 20.72 44.63 4.94
799 820 3.478394 CATGTGACGCGACGTGGG 61.478 66.667 15.93 0.00 41.37 4.61
800 821 4.735132 ATGTGACGCGACGTGGGG 62.735 66.667 15.93 13.02 41.37 4.96
897 937 2.229062 TCGGATCGGATCTACAGCAATC 59.771 50.000 16.96 0.00 0.00 2.67
924 964 1.185618 ACCTTCAGTCGTGCTGCCTA 61.186 55.000 0.00 0.00 44.66 3.93
926 966 0.737715 CTTCAGTCGTGCTGCCTACC 60.738 60.000 0.00 0.00 44.66 3.18
978 1018 1.398692 GAGAGGAAGGCGAGATCAGT 58.601 55.000 0.00 0.00 0.00 3.41
979 1019 1.336755 GAGAGGAAGGCGAGATCAGTC 59.663 57.143 0.00 0.00 0.00 3.51
980 1020 1.107114 GAGGAAGGCGAGATCAGTCA 58.893 55.000 0.00 0.00 0.00 3.41
981 1021 1.066908 GAGGAAGGCGAGATCAGTCAG 59.933 57.143 0.00 0.00 0.00 3.51
982 1022 1.107114 GGAAGGCGAGATCAGTCAGA 58.893 55.000 0.00 0.00 0.00 3.27
983 1023 1.686052 GGAAGGCGAGATCAGTCAGAT 59.314 52.381 0.00 0.00 40.48 2.90
1044 1084 3.068691 CTCGTCGGAGCCAAGGGA 61.069 66.667 0.00 0.00 32.61 4.20
1108 1148 0.898320 CTCCCCACATCGAGTTCTGT 59.102 55.000 0.00 0.00 0.00 3.41
1138 1178 2.358737 CGGCTCTGCTTTCCCGTT 60.359 61.111 0.00 0.00 36.18 4.44
1165 1205 2.089201 TCGATCAAGTAGCTCGGTGAA 58.911 47.619 0.00 0.00 36.57 3.18
1166 1206 2.097629 TCGATCAAGTAGCTCGGTGAAG 59.902 50.000 0.00 0.00 36.57 3.02
1167 1207 2.159366 CGATCAAGTAGCTCGGTGAAGT 60.159 50.000 0.00 0.00 32.50 3.01
1168 1208 2.724977 TCAAGTAGCTCGGTGAAGTG 57.275 50.000 0.00 0.00 0.00 3.16
1169 1209 2.235891 TCAAGTAGCTCGGTGAAGTGA 58.764 47.619 0.00 0.00 0.00 3.41
1177 1217 1.450312 CGGTGAAGTGATGGCCTCC 60.450 63.158 3.32 0.00 0.00 4.30
1210 1250 1.202371 TCGGCGCAATATTCTCGAGTT 60.202 47.619 13.13 4.09 0.00 3.01
1225 1265 1.477105 GAGTTGTTTGTGCTTTCGCC 58.523 50.000 0.00 0.00 34.43 5.54
1235 1276 1.372128 GCTTTCGCCTTTGCTGGTG 60.372 57.895 0.00 0.00 38.85 4.17
1242 1283 1.812571 CGCCTTTGCTGGTGTCTAATT 59.187 47.619 0.00 0.00 34.43 1.40
1244 1285 2.094545 GCCTTTGCTGGTGTCTAATTGG 60.095 50.000 0.00 0.00 33.53 3.16
1245 1286 2.094545 CCTTTGCTGGTGTCTAATTGGC 60.095 50.000 0.00 0.00 0.00 4.52
1289 1330 1.003262 CCGTGGCTGCGAATTGTTTG 61.003 55.000 3.81 0.00 0.00 2.93
1330 1371 1.231221 ACGCGGTTCTAAAATGCACA 58.769 45.000 12.47 0.00 0.00 4.57
1368 1409 0.611714 ACCGTCGCCTCAGGTAAATT 59.388 50.000 0.00 0.00 36.34 1.82
1382 1423 7.129109 TCAGGTAAATTTCTTCGTTAGCTTG 57.871 36.000 0.00 0.00 34.28 4.01
1394 1435 6.307800 TCTTCGTTAGCTTGCAAATATTTTGC 59.692 34.615 16.03 16.03 45.11 3.68
1396 1437 5.799936 TCGTTAGCTTGCAAATATTTTGCTC 59.200 36.000 21.50 12.70 45.13 4.26
1403 1450 6.532657 GCTTGCAAATATTTTGCTCACAGTAT 59.467 34.615 21.50 0.00 45.13 2.12
1552 1606 4.098654 CACTGGTACTGAATGAGTCCTAGG 59.901 50.000 0.82 0.82 35.96 3.02
1571 1625 1.508632 GTTCCACGTGCTGCTAGAAA 58.491 50.000 10.91 0.00 0.00 2.52
1603 1657 3.758755 TGAAGCTTGAGTCTGTCATGT 57.241 42.857 2.10 0.00 34.17 3.21
1720 1774 3.546002 TGCGCTAAAAGCACGTTAATT 57.454 38.095 9.73 0.00 42.58 1.40
1721 1775 4.665281 TGCGCTAAAAGCACGTTAATTA 57.335 36.364 9.73 0.00 42.58 1.40
1722 1776 5.032100 TGCGCTAAAAGCACGTTAATTAA 57.968 34.783 9.73 0.00 42.58 1.40
1829 1885 5.112220 TCAAGACATGTTAAAAGCAGCAG 57.888 39.130 0.00 0.00 0.00 4.24
1991 2078 0.459489 AGCTCGTCATCAAGCTCCTC 59.541 55.000 0.00 0.00 45.57 3.71
2080 2167 2.624838 AGCAATTTTGGTCCTGTGTCAG 59.375 45.455 0.00 0.00 32.71 3.51
2081 2168 2.362077 GCAATTTTGGTCCTGTGTCAGT 59.638 45.455 0.00 0.00 0.00 3.41
2082 2169 3.181476 GCAATTTTGGTCCTGTGTCAGTT 60.181 43.478 0.00 0.00 0.00 3.16
2083 2170 4.680440 GCAATTTTGGTCCTGTGTCAGTTT 60.680 41.667 0.00 0.00 0.00 2.66
2084 2171 4.918810 ATTTTGGTCCTGTGTCAGTTTC 57.081 40.909 0.00 0.00 0.00 2.78
2085 2172 3.644966 TTTGGTCCTGTGTCAGTTTCT 57.355 42.857 0.00 0.00 0.00 2.52
2086 2173 4.764050 TTTGGTCCTGTGTCAGTTTCTA 57.236 40.909 0.00 0.00 0.00 2.10
2087 2174 4.974645 TTGGTCCTGTGTCAGTTTCTAT 57.025 40.909 0.00 0.00 0.00 1.98
2088 2175 4.537135 TGGTCCTGTGTCAGTTTCTATC 57.463 45.455 0.00 0.00 0.00 2.08
2089 2176 3.260884 TGGTCCTGTGTCAGTTTCTATCC 59.739 47.826 0.00 0.00 0.00 2.59
2090 2177 3.369576 GGTCCTGTGTCAGTTTCTATCCC 60.370 52.174 0.00 0.00 0.00 3.85
2091 2178 3.515901 GTCCTGTGTCAGTTTCTATCCCT 59.484 47.826 0.00 0.00 0.00 4.20
2092 2179 3.515502 TCCTGTGTCAGTTTCTATCCCTG 59.484 47.826 0.00 0.00 0.00 4.45
2093 2180 3.515502 CCTGTGTCAGTTTCTATCCCTGA 59.484 47.826 0.00 0.00 33.03 3.86
2094 2181 4.020218 CCTGTGTCAGTTTCTATCCCTGAA 60.020 45.833 0.00 0.00 37.01 3.02
2095 2182 5.152623 TGTGTCAGTTTCTATCCCTGAAG 57.847 43.478 0.00 0.00 37.01 3.02
2096 2183 4.838423 TGTGTCAGTTTCTATCCCTGAAGA 59.162 41.667 0.00 0.00 37.01 2.87
2097 2184 5.485353 TGTGTCAGTTTCTATCCCTGAAGAT 59.515 40.000 0.00 0.00 37.01 2.40
2098 2185 5.814705 GTGTCAGTTTCTATCCCTGAAGATG 59.185 44.000 0.00 0.00 37.01 2.90
2099 2186 5.485353 TGTCAGTTTCTATCCCTGAAGATGT 59.515 40.000 0.00 0.00 37.01 3.06
2100 2187 5.814705 GTCAGTTTCTATCCCTGAAGATGTG 59.185 44.000 0.00 0.00 37.01 3.21
2101 2188 5.104776 TCAGTTTCTATCCCTGAAGATGTGG 60.105 44.000 0.00 0.00 32.55 4.17
2102 2189 3.845781 TTCTATCCCTGAAGATGTGGC 57.154 47.619 0.00 0.00 0.00 5.01
2103 2190 2.050144 TCTATCCCTGAAGATGTGGCC 58.950 52.381 0.00 0.00 0.00 5.36
2104 2191 1.770658 CTATCCCTGAAGATGTGGCCA 59.229 52.381 0.00 0.00 0.00 5.36
2105 2192 1.002069 ATCCCTGAAGATGTGGCCAA 58.998 50.000 7.24 0.00 0.00 4.52
2106 2193 0.038166 TCCCTGAAGATGTGGCCAAC 59.962 55.000 7.24 2.03 0.00 3.77
2107 2194 0.967380 CCCTGAAGATGTGGCCAACC 60.967 60.000 7.24 0.00 0.00 3.77
2108 2195 0.967380 CCTGAAGATGTGGCCAACCC 60.967 60.000 7.24 0.00 33.59 4.11
2109 2196 0.251297 CTGAAGATGTGGCCAACCCA 60.251 55.000 7.24 0.57 42.79 4.51
2274 2391 4.497006 GCAGATTGCATCATCCACTACAAC 60.497 45.833 0.00 0.00 44.26 3.32
2275 2392 4.880120 CAGATTGCATCATCCACTACAACT 59.120 41.667 0.00 0.00 0.00 3.16
2448 2565 8.398767 ACATTCATGTTCAGGGACTAAACCCA 62.399 42.308 0.00 0.00 44.68 4.51
2544 2661 2.640184 AGGGCCTTATTCGCTGTTAAC 58.360 47.619 0.00 0.00 0.00 2.01
2545 2662 2.026636 AGGGCCTTATTCGCTGTTAACA 60.027 45.455 8.28 8.28 0.00 2.41
2546 2663 2.354821 GGGCCTTATTCGCTGTTAACAG 59.645 50.000 27.85 27.85 46.40 3.16
2547 2664 3.007635 GGCCTTATTCGCTGTTAACAGT 58.992 45.455 30.90 17.17 45.45 3.55
2548 2665 3.439129 GGCCTTATTCGCTGTTAACAGTT 59.561 43.478 30.90 18.23 45.45 3.16
2549 2666 4.082949 GGCCTTATTCGCTGTTAACAGTTT 60.083 41.667 30.90 17.94 45.45 2.66
2550 2667 5.458015 GCCTTATTCGCTGTTAACAGTTTT 58.542 37.500 30.90 18.22 45.45 2.43
2581 2698 1.967319 AACTGATCACCACCACACAC 58.033 50.000 0.00 0.00 0.00 3.82
2584 2701 1.875514 CTGATCACCACCACACACTTG 59.124 52.381 0.00 0.00 0.00 3.16
2598 2715 4.275689 CACACACTTGGCTGTAATTCTTCA 59.724 41.667 0.00 0.00 0.00 3.02
2609 2726 4.906618 TGTAATTCTTCAACTCCCTCCAC 58.093 43.478 0.00 0.00 0.00 4.02
2617 2734 3.724478 TCAACTCCCTCCACAGATACAT 58.276 45.455 0.00 0.00 0.00 2.29
2685 2802 8.837389 TCTTTTAGCCTTTCAACTTCTAGTTTC 58.163 33.333 0.00 0.00 36.03 2.78
2686 2803 8.514330 TTTTAGCCTTTCAACTTCTAGTTTCA 57.486 30.769 0.00 0.00 36.03 2.69
2687 2804 7.730364 TTAGCCTTTCAACTTCTAGTTTCAG 57.270 36.000 0.00 0.00 36.03 3.02
2688 2805 4.517075 AGCCTTTCAACTTCTAGTTTCAGC 59.483 41.667 0.00 0.00 36.03 4.26
2689 2806 4.275936 GCCTTTCAACTTCTAGTTTCAGCA 59.724 41.667 0.00 0.00 36.03 4.41
2690 2807 5.752712 CCTTTCAACTTCTAGTTTCAGCAC 58.247 41.667 0.00 0.00 36.03 4.40
2691 2808 5.278022 CCTTTCAACTTCTAGTTTCAGCACC 60.278 44.000 0.00 0.00 36.03 5.01
2692 2809 4.415881 TCAACTTCTAGTTTCAGCACCA 57.584 40.909 0.00 0.00 36.03 4.17
2693 2810 4.127171 TCAACTTCTAGTTTCAGCACCAC 58.873 43.478 0.00 0.00 36.03 4.16
2694 2811 4.130118 CAACTTCTAGTTTCAGCACCACT 58.870 43.478 0.00 0.00 36.03 4.00
2695 2812 5.069914 TCAACTTCTAGTTTCAGCACCACTA 59.930 40.000 0.00 0.00 36.03 2.74
2696 2813 5.546621 ACTTCTAGTTTCAGCACCACTAA 57.453 39.130 0.00 0.00 0.00 2.24
2709 2826 6.154534 TCAGCACCACTAATTGTGTAGAGTAT 59.845 38.462 7.09 0.00 44.81 2.12
2712 2829 5.977725 CACCACTAATTGTGTAGAGTATCCG 59.022 44.000 7.09 0.00 44.81 4.18
2719 2836 4.508551 TGTGTAGAGTATCCGGGTCTTA 57.491 45.455 0.00 0.00 33.66 2.10
2720 2837 5.057843 TGTGTAGAGTATCCGGGTCTTAT 57.942 43.478 0.00 0.00 33.66 1.73
2734 2851 5.359860 CCGGGTCTTATTTTTATGCTCCTTT 59.640 40.000 0.00 0.00 0.00 3.11
2735 2852 6.265577 CGGGTCTTATTTTTATGCTCCTTTG 58.734 40.000 0.00 0.00 0.00 2.77
2739 2856 7.436376 GGTCTTATTTTTATGCTCCTTTGATGC 59.564 37.037 0.00 0.00 0.00 3.91
2740 2857 7.436376 GTCTTATTTTTATGCTCCTTTGATGCC 59.564 37.037 0.00 0.00 0.00 4.40
2747 2864 2.174360 GCTCCTTTGATGCCTTCCTTT 58.826 47.619 0.00 0.00 0.00 3.11
2748 2865 2.564504 GCTCCTTTGATGCCTTCCTTTT 59.435 45.455 0.00 0.00 0.00 2.27
2749 2866 3.367806 GCTCCTTTGATGCCTTCCTTTTC 60.368 47.826 0.00 0.00 0.00 2.29
2750 2867 4.085009 CTCCTTTGATGCCTTCCTTTTCT 58.915 43.478 0.00 0.00 0.00 2.52
2751 2868 4.482990 TCCTTTGATGCCTTCCTTTTCTT 58.517 39.130 0.00 0.00 0.00 2.52
2752 2869 4.901250 TCCTTTGATGCCTTCCTTTTCTTT 59.099 37.500 0.00 0.00 0.00 2.52
2753 2870 5.366477 TCCTTTGATGCCTTCCTTTTCTTTT 59.634 36.000 0.00 0.00 0.00 2.27
2754 2871 5.698089 CCTTTGATGCCTTCCTTTTCTTTTC 59.302 40.000 0.00 0.00 0.00 2.29
2786 2903 0.882927 GTCAACTGCGGGCTTACACA 60.883 55.000 0.00 0.00 0.00 3.72
2787 2904 0.179043 TCAACTGCGGGCTTACACAA 60.179 50.000 0.00 0.00 0.00 3.33
2841 2958 1.403514 CGAGCTGGTCCTTCTTCTGAC 60.404 57.143 0.00 0.00 0.00 3.51
2859 2976 8.816894 TCTTCTGACCTCAATACTTACATTTCT 58.183 33.333 0.00 0.00 0.00 2.52
2862 2979 6.711277 TGACCTCAATACTTACATTTCTGCT 58.289 36.000 0.00 0.00 0.00 4.24
2868 2985 9.443283 CTCAATACTTACATTTCTGCTAAATGC 57.557 33.333 18.95 0.00 40.35 3.56
2897 3014 0.247460 TTCACAGGAGGCTCGTGATG 59.753 55.000 35.91 28.21 39.29 3.07
2952 3069 5.942826 GGAACCAATCATCTTGAGAAGAAGT 59.057 40.000 0.00 0.00 41.63 3.01
2970 3087 2.498167 AGTAGGTGCTTTGCTGAACTG 58.502 47.619 0.00 0.00 0.00 3.16
3095 3212 9.542462 TCCTTATTGATTGGTATCGTTTTCTAG 57.458 33.333 0.00 0.00 33.23 2.43
3163 3280 6.721318 TGAGCCCTCTTTAATGTCACTAAAT 58.279 36.000 0.00 0.00 0.00 1.40
3167 3284 7.836183 AGCCCTCTTTAATGTCACTAAATTGAT 59.164 33.333 0.00 0.00 0.00 2.57
3177 3294 6.757237 TGTCACTAAATTGATTTGCAATGGT 58.243 32.000 0.00 0.00 46.25 3.55
3195 3312 2.043664 TGGTGATGGCCCCATTTCTTAA 59.956 45.455 0.00 0.00 36.70 1.85
3196 3313 3.308401 GGTGATGGCCCCATTTCTTAAT 58.692 45.455 0.00 0.00 36.70 1.40
3197 3314 4.078922 TGGTGATGGCCCCATTTCTTAATA 60.079 41.667 0.00 0.00 36.70 0.98
3198 3315 4.524328 GGTGATGGCCCCATTTCTTAATAG 59.476 45.833 0.00 0.00 36.70 1.73
3202 3430 5.725551 TGGCCCCATTTCTTAATAGAGAA 57.274 39.130 0.00 0.00 34.00 2.87
3233 3461 3.601435 CATCAATTGATGCAAAGGCCAA 58.399 40.909 30.11 0.00 44.44 4.52
3234 3462 3.766068 TCAATTGATGCAAAGGCCAAA 57.234 38.095 5.01 0.00 40.13 3.28
3280 3510 7.867909 CCTTTTTGGAAAGAGTACATTTTCTCC 59.132 37.037 16.68 7.28 44.03 3.71
3281 3511 8.533569 TTTTTGGAAAGAGTACATTTTCTCCT 57.466 30.769 16.68 0.00 34.52 3.69
3286 3516 7.998964 TGGAAAGAGTACATTTTCTCCTTTCTT 59.001 33.333 16.68 2.20 34.52 2.52
3309 3542 1.880027 GTCGATGGTGCTTCCTTTGTT 59.120 47.619 0.00 0.00 37.07 2.83
3329 3562 9.553064 CTTTGTTGTAGATATTCAATCTAGCCT 57.447 33.333 0.00 0.00 31.90 4.58
3346 3579 4.785346 AGCCTACATGTGAGGATGAAAT 57.215 40.909 19.53 2.04 35.99 2.17
3364 3598 8.159344 GATGAAATCCTCTTATAACAACCCTG 57.841 38.462 0.00 0.00 37.38 4.45
3406 3640 8.970691 ACCAATTTTCTATCTTTTGAATGTCG 57.029 30.769 0.00 0.00 0.00 4.35
3427 3661 7.218614 TGTCGAAGTGGGAACTAAAAAGAATA 58.781 34.615 0.00 0.00 0.00 1.75
3456 3690 2.032071 GTGACACTTCCACCGGGG 59.968 66.667 6.32 0.00 38.37 5.73
3471 3705 0.912968 CGGGGGAAAGAGTTAGGGGT 60.913 60.000 0.00 0.00 0.00 4.95
3515 3749 7.561237 TTACAAGTTTAATCATGCTTTTCGC 57.439 32.000 0.00 0.00 39.77 4.70
3526 3760 1.337823 TGCTTTTCGCCTCTAGTGGTC 60.338 52.381 12.31 4.33 38.05 4.02
3534 3768 1.672145 GCCTCTAGTGGTCGTGGTTTC 60.672 57.143 12.31 0.00 0.00 2.78
3540 3774 0.935196 GTGGTCGTGGTTTCACTGAC 59.065 55.000 10.57 10.57 41.75 3.51
3542 3776 3.372795 GTCGTGGTTTCACTGACCA 57.627 52.632 0.00 0.00 44.59 4.02
3588 3822 9.553064 TTCAATAGTGGTACTAACGGTTTAAAA 57.447 29.630 0.00 0.00 33.89 1.52
3594 3828 5.526846 TGGTACTAACGGTTTAAAACTGGTG 59.473 40.000 0.00 0.00 42.15 4.17
3600 3834 4.959723 ACGGTTTAAAACTGGTGCTACTA 58.040 39.130 1.03 0.00 42.15 1.82
3604 3838 6.148150 CGGTTTAAAACTGGTGCTACTATGAA 59.852 38.462 1.03 0.00 34.07 2.57
3614 3848 5.045942 TGGTGCTACTATGAAAATGACCTCA 60.046 40.000 0.00 0.00 0.00 3.86
3615 3849 5.525378 GGTGCTACTATGAAAATGACCTCAG 59.475 44.000 0.00 0.00 0.00 3.35
3618 3852 6.070824 TGCTACTATGAAAATGACCTCAGTGA 60.071 38.462 0.00 0.00 0.00 3.41
3619 3853 6.256757 GCTACTATGAAAATGACCTCAGTGAC 59.743 42.308 0.00 0.00 0.00 3.67
3620 3854 6.114187 ACTATGAAAATGACCTCAGTGACA 57.886 37.500 0.00 0.00 0.00 3.58
3624 3858 4.042062 TGAAAATGACCTCAGTGACAGGAT 59.958 41.667 5.46 0.00 34.75 3.24
3625 3859 4.647564 AAATGACCTCAGTGACAGGATT 57.352 40.909 5.46 0.00 34.75 3.01
3651 3885 4.237018 AGAACCTAGTAGTTTGGGGTTGA 58.763 43.478 0.00 0.00 39.92 3.18
3652 3886 4.850386 AGAACCTAGTAGTTTGGGGTTGAT 59.150 41.667 0.00 0.00 39.92 2.57
3653 3887 4.569719 ACCTAGTAGTTTGGGGTTGATG 57.430 45.455 0.00 0.00 0.00 3.07
3655 3889 5.095809 ACCTAGTAGTTTGGGGTTGATGTA 58.904 41.667 0.00 0.00 0.00 2.29
3668 3902 4.537015 GGTTGATGTAGTTGTTGTGCTTC 58.463 43.478 0.00 0.00 0.00 3.86
3670 3904 2.805671 TGATGTAGTTGTTGTGCTTCGG 59.194 45.455 0.00 0.00 0.00 4.30
3675 3909 2.365582 AGTTGTTGTGCTTCGGAAGTT 58.634 42.857 18.32 0.00 0.00 2.66
3683 3917 2.479275 GTGCTTCGGAAGTTGGAACTAC 59.521 50.000 18.32 0.17 38.57 2.73
3697 3931 2.027469 GGAACTACCGGGTTCTCATGTT 60.027 50.000 19.09 1.81 43.43 2.71
3699 3933 1.975680 ACTACCGGGTTCTCATGTTGT 59.024 47.619 4.31 0.00 0.00 3.32
3706 3940 2.508526 GGTTCTCATGTTGTTGCCTCT 58.491 47.619 0.00 0.00 0.00 3.69
3708 3942 2.189594 TCTCATGTTGTTGCCTCTGG 57.810 50.000 0.00 0.00 0.00 3.86
3728 3962 3.275143 GGGAAGCCTTTCTCTTCTTAGC 58.725 50.000 0.00 0.00 39.75 3.09
3740 3974 4.959210 TCTCTTCTTAGCTGCTAAGTCCAT 59.041 41.667 35.53 4.35 42.66 3.41
3746 3980 0.103937 GCTGCTAAGTCCATCGCTCT 59.896 55.000 0.00 0.00 0.00 4.09
3750 3984 1.135139 GCTAAGTCCATCGCTCTGTCA 59.865 52.381 0.00 0.00 0.00 3.58
3759 3994 0.598419 TCGCTCTGTCAACACTGCAG 60.598 55.000 13.48 13.48 0.00 4.41
3781 4016 3.313690 GTTTTGGTTTGGTATTGCCGAG 58.686 45.455 0.00 0.00 41.21 4.63
3815 4050 2.297701 TCTGGGTTTGTTGACTGCTTC 58.702 47.619 0.00 0.00 0.00 3.86
3820 4055 3.447742 GGTTTGTTGACTGCTTCCTTTG 58.552 45.455 0.00 0.00 0.00 2.77
3823 4058 1.939934 TGTTGACTGCTTCCTTTGTCG 59.060 47.619 0.00 0.00 32.64 4.35
3825 4060 0.250295 TGACTGCTTCCTTTGTCGGG 60.250 55.000 0.00 0.00 32.64 5.14
3836 4071 2.683867 CCTTTGTCGGGTTTTGTGTACA 59.316 45.455 0.00 0.00 0.00 2.90
3852 4087 5.616270 TGTGTACAGTAGCTCCATGAAAAA 58.384 37.500 0.00 0.00 0.00 1.94
3868 4103 2.086054 AAAAGTTTTGTTGTGCGGCA 57.914 40.000 0.00 0.00 0.00 5.69
3881 4116 0.804364 TGCGGCATGAATCACACTTC 59.196 50.000 0.00 0.00 0.00 3.01
3886 4121 3.578688 GGCATGAATCACACTTCAAACC 58.421 45.455 0.00 0.00 38.55 3.27
3887 4122 3.256631 GGCATGAATCACACTTCAAACCT 59.743 43.478 0.00 0.00 38.55 3.50
3888 4123 4.479619 GCATGAATCACACTTCAAACCTC 58.520 43.478 0.00 0.00 38.55 3.85
3889 4124 4.715896 CATGAATCACACTTCAAACCTCG 58.284 43.478 0.00 0.00 38.55 4.63
3891 4126 4.641396 TGAATCACACTTCAAACCTCGAT 58.359 39.130 0.00 0.00 32.35 3.59
3893 4128 5.869344 TGAATCACACTTCAAACCTCGATAG 59.131 40.000 0.00 0.00 32.35 2.08
3894 4129 4.866508 TCACACTTCAAACCTCGATAGT 57.133 40.909 0.00 0.00 37.40 2.12
3895 4130 5.970317 TCACACTTCAAACCTCGATAGTA 57.030 39.130 0.00 0.00 37.40 1.82
3917 4154 2.159226 TCGATTTTGTGCCGTTGGTTTT 60.159 40.909 0.00 0.00 0.00 2.43
3925 4162 3.632604 TGTGCCGTTGGTTTTAATCTCAA 59.367 39.130 0.00 0.00 0.00 3.02
3927 4164 5.221342 TGTGCCGTTGGTTTTAATCTCAATT 60.221 36.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 164 5.196809 TCAAATTTTGTGCGTGTTTTCAC 57.803 34.783 8.89 0.00 46.33 3.18
165 167 6.430451 TGTTTTCAAATTTTGTGCGTGTTTT 58.570 28.000 8.89 0.00 0.00 2.43
169 171 8.060679 TGATTATGTTTTCAAATTTTGTGCGTG 58.939 29.630 8.89 0.00 0.00 5.34
170 172 8.136057 TGATTATGTTTTCAAATTTTGTGCGT 57.864 26.923 8.89 3.14 0.00 5.24
171 173 9.596677 AATGATTATGTTTTCAAATTTTGTGCG 57.403 25.926 8.89 0.00 0.00 5.34
366 383 6.171213 CCGATTTTACAAGGTTCCTAAGAGT 58.829 40.000 0.00 0.00 0.00 3.24
368 385 6.117975 ACCGATTTTACAAGGTTCCTAAGA 57.882 37.500 0.00 0.00 32.17 2.10
387 404 0.034896 GAGAAAACTGCCAGGACCGA 59.965 55.000 0.00 0.00 0.00 4.69
544 561 2.345641 GTGCAGTGTAGTAGTTGCATCG 59.654 50.000 1.09 0.00 46.80 3.84
606 627 3.999297 GAGGAGCGAGAGGACGGGT 62.999 68.421 0.00 0.00 0.00 5.28
623 644 1.298602 CGTGCCGATTGGATGATTGA 58.701 50.000 1.98 0.00 37.49 2.57
648 669 4.415332 CGCGTGTCTGCCCGTAGT 62.415 66.667 0.00 0.00 0.00 2.73
722 743 0.391263 CCGAAGGCAGGTCAAGTACC 60.391 60.000 0.00 0.00 46.80 3.34
739 760 2.252260 CGACTTGCCAACTTGCCG 59.748 61.111 0.00 0.00 0.00 5.69
755 776 1.227556 GTGTGGTAGGGCATAGGCG 60.228 63.158 0.00 0.00 42.47 5.52
796 817 4.649705 TTCCTCGCACCTCCCCCA 62.650 66.667 0.00 0.00 0.00 4.96
797 818 3.787001 CTTCCTCGCACCTCCCCC 61.787 72.222 0.00 0.00 0.00 5.40
798 819 2.683933 TCTTCCTCGCACCTCCCC 60.684 66.667 0.00 0.00 0.00 4.81
799 820 2.579738 GTCTTCCTCGCACCTCCC 59.420 66.667 0.00 0.00 0.00 4.30
800 821 2.182030 CGTCTTCCTCGCACCTCC 59.818 66.667 0.00 0.00 0.00 4.30
924 964 5.848286 TCAGGAATTATATGCTGATGGGT 57.152 39.130 0.00 0.00 42.02 4.51
978 1018 1.456518 CTCTCCGGGCCTGATCTGA 60.457 63.158 15.09 0.00 0.00 3.27
979 1019 1.045350 TTCTCTCCGGGCCTGATCTG 61.045 60.000 15.09 0.00 0.00 2.90
980 1020 0.758685 CTTCTCTCCGGGCCTGATCT 60.759 60.000 15.09 0.00 0.00 2.75
981 1021 0.757188 TCTTCTCTCCGGGCCTGATC 60.757 60.000 15.09 0.00 0.00 2.92
982 1022 0.105246 ATCTTCTCTCCGGGCCTGAT 60.105 55.000 15.09 0.00 0.00 2.90
983 1023 1.045350 CATCTTCTCTCCGGGCCTGA 61.045 60.000 15.09 3.98 0.00 3.86
984 1024 1.445095 CATCTTCTCTCCGGGCCTG 59.555 63.158 3.88 3.88 0.00 4.85
985 1025 1.764054 CCATCTTCTCTCCGGGCCT 60.764 63.158 0.84 0.00 0.00 5.19
986 1026 2.825264 CCATCTTCTCTCCGGGCC 59.175 66.667 0.00 0.00 0.00 5.80
990 1030 1.591059 CTGCGCCATCTTCTCTCCG 60.591 63.158 4.18 0.00 0.00 4.63
1044 1084 1.163554 GGTAGTCGGTGTTCTCGAGT 58.836 55.000 13.13 0.00 42.16 4.18
1095 1135 3.062763 CAAGCAGAACAGAACTCGATGT 58.937 45.455 0.00 0.00 0.00 3.06
1108 1148 2.079158 CAGAGCCGAATTCAAGCAGAA 58.921 47.619 17.14 0.00 41.28 3.02
1138 1178 1.735376 GCTACTTGATCGAGCGGGGA 61.735 60.000 10.09 0.00 0.00 4.81
1165 1205 1.383109 TGATCGGGAGGCCATCACT 60.383 57.895 5.01 0.00 0.00 3.41
1166 1206 1.070445 CTGATCGGGAGGCCATCAC 59.930 63.158 5.01 0.00 0.00 3.06
1167 1207 2.811514 GCTGATCGGGAGGCCATCA 61.812 63.158 5.01 3.74 0.00 3.07
1168 1208 2.031768 GCTGATCGGGAGGCCATC 59.968 66.667 5.01 0.00 0.00 3.51
1169 1209 3.564218 GGCTGATCGGGAGGCCAT 61.564 66.667 5.01 0.00 43.59 4.40
1225 1265 2.414559 CGCCAATTAGACACCAGCAAAG 60.415 50.000 0.00 0.00 0.00 2.77
1235 1276 2.457366 ATCGATCCCGCCAATTAGAC 57.543 50.000 0.00 0.00 35.37 2.59
1289 1330 2.570181 GTCCATGTTGCCTGCAGC 59.430 61.111 8.66 4.57 44.14 5.25
1330 1371 1.143620 GCTCTTCTGCTCCTGCGAT 59.856 57.895 0.00 0.00 43.34 4.58
1368 1409 7.148820 GCAAAATATTTGCAAGCTAACGAAGAA 60.149 33.333 19.73 0.00 44.34 2.52
1382 1423 9.831737 CCTATATACTGTGAGCAAAATATTTGC 57.168 33.333 17.62 17.62 45.22 3.68
1421 1470 6.042777 AGCGTTGATCGATAAATTGAAGAGA 58.957 36.000 0.00 0.00 42.86 3.10
1536 1590 3.515901 GTGGAACCTAGGACTCATTCAGT 59.484 47.826 17.98 0.00 38.45 3.41
1552 1606 1.461127 CTTTCTAGCAGCACGTGGAAC 59.539 52.381 18.88 0.00 0.00 3.62
1576 1630 1.163554 GACTCAAGCTTCAAGCCTGG 58.836 55.000 5.53 0.37 43.77 4.45
1586 1640 3.482156 AACACATGACAGACTCAAGCT 57.518 42.857 0.00 0.00 30.60 3.74
1603 1657 4.826733 AGACATTACTGACATGGCAAAACA 59.173 37.500 1.11 0.00 31.22 2.83
1720 1774 9.101655 GGGAAAATAAGATGCGTTAACTACTTA 57.898 33.333 3.71 8.16 0.00 2.24
1721 1775 7.608761 TGGGAAAATAAGATGCGTTAACTACTT 59.391 33.333 3.71 6.41 0.00 2.24
1722 1776 7.065443 GTGGGAAAATAAGATGCGTTAACTACT 59.935 37.037 3.71 0.00 0.00 2.57
1732 1786 3.279434 ACGAGGTGGGAAAATAAGATGC 58.721 45.455 0.00 0.00 0.00 3.91
1797 1853 9.695526 CTTTTAACATGTCTTGATGATTTCCAA 57.304 29.630 0.00 0.00 0.00 3.53
1803 1859 6.071784 TGCTGCTTTTAACATGTCTTGATGAT 60.072 34.615 0.00 0.00 0.00 2.45
1871 1927 9.424319 GAGTGAAGTCAAGTTACATCTCATAAA 57.576 33.333 0.00 0.00 0.00 1.40
1928 2015 3.697045 TGAACACAAAGGTTTCGTTCCAT 59.303 39.130 9.95 0.00 36.07 3.41
1988 2075 1.448540 GCCACCATCACTGTCGAGG 60.449 63.158 0.00 0.00 0.00 4.63
1991 2078 2.382746 CGTGCCACCATCACTGTCG 61.383 63.158 0.00 0.00 32.54 4.35
2072 2159 4.808414 TCAGGGATAGAAACTGACACAG 57.192 45.455 0.00 0.00 36.41 3.66
2080 2167 3.879892 GCCACATCTTCAGGGATAGAAAC 59.120 47.826 0.00 0.00 0.00 2.78
2081 2168 3.117888 GGCCACATCTTCAGGGATAGAAA 60.118 47.826 0.00 0.00 0.00 2.52
2082 2169 2.439507 GGCCACATCTTCAGGGATAGAA 59.560 50.000 0.00 0.00 0.00 2.10
2083 2170 2.050144 GGCCACATCTTCAGGGATAGA 58.950 52.381 0.00 0.00 0.00 1.98
2084 2171 1.770658 TGGCCACATCTTCAGGGATAG 59.229 52.381 0.00 0.00 0.00 2.08
2085 2172 1.891933 TGGCCACATCTTCAGGGATA 58.108 50.000 0.00 0.00 0.00 2.59
2086 2173 1.002069 TTGGCCACATCTTCAGGGAT 58.998 50.000 3.88 0.00 0.00 3.85
2087 2174 0.038166 GTTGGCCACATCTTCAGGGA 59.962 55.000 3.88 0.00 0.00 4.20
2088 2175 0.967380 GGTTGGCCACATCTTCAGGG 60.967 60.000 3.88 0.00 34.09 4.45
2089 2176 0.967380 GGGTTGGCCACATCTTCAGG 60.967 60.000 3.88 0.00 36.17 3.86
2090 2177 0.251297 TGGGTTGGCCACATCTTCAG 60.251 55.000 3.88 0.00 36.17 3.02
2091 2178 0.251297 CTGGGTTGGCCACATCTTCA 60.251 55.000 3.88 0.00 36.17 3.02
2092 2179 0.038166 TCTGGGTTGGCCACATCTTC 59.962 55.000 3.88 0.00 36.17 2.87
2093 2180 0.038744 CTCTGGGTTGGCCACATCTT 59.961 55.000 3.88 0.00 36.17 2.40
2094 2181 1.136329 ACTCTGGGTTGGCCACATCT 61.136 55.000 3.88 0.00 36.17 2.90
2095 2182 0.962356 CACTCTGGGTTGGCCACATC 60.962 60.000 3.88 0.00 36.17 3.06
2096 2183 1.075482 CACTCTGGGTTGGCCACAT 59.925 57.895 3.88 0.00 36.17 3.21
2097 2184 1.932156 AACACTCTGGGTTGGCCACA 61.932 55.000 3.88 0.00 36.17 4.17
2098 2185 1.152756 AACACTCTGGGTTGGCCAC 60.153 57.895 3.88 0.00 36.17 5.01
2099 2186 1.150536 GAACACTCTGGGTTGGCCA 59.849 57.895 0.00 0.00 36.17 5.36
2100 2187 1.603739 GGAACACTCTGGGTTGGCC 60.604 63.158 0.00 0.00 0.00 5.36
2101 2188 0.178990 AAGGAACACTCTGGGTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
2102 2189 1.956477 CAAAGGAACACTCTGGGTTGG 59.044 52.381 0.00 0.00 0.00 3.77
2103 2190 2.880890 CTCAAAGGAACACTCTGGGTTG 59.119 50.000 0.00 0.00 0.00 3.77
2104 2191 2.509964 ACTCAAAGGAACACTCTGGGTT 59.490 45.455 0.00 0.00 0.00 4.11
2105 2192 2.127708 ACTCAAAGGAACACTCTGGGT 58.872 47.619 0.00 0.00 0.00 4.51
2106 2193 2.938956 ACTCAAAGGAACACTCTGGG 57.061 50.000 0.00 0.00 0.00 4.45
2107 2194 4.962155 ACTAACTCAAAGGAACACTCTGG 58.038 43.478 0.00 0.00 0.00 3.86
2108 2195 5.817816 ACAACTAACTCAAAGGAACACTCTG 59.182 40.000 0.00 0.00 0.00 3.35
2109 2196 5.817816 CACAACTAACTCAAAGGAACACTCT 59.182 40.000 0.00 0.00 0.00 3.24
2274 2391 8.961294 ATCCTGAAAGAATCAAATACTCAGAG 57.039 34.615 0.00 0.00 37.67 3.35
2275 2392 7.989741 GGATCCTGAAAGAATCAAATACTCAGA 59.010 37.037 3.84 0.00 37.67 3.27
2422 2539 6.177610 GGTTTAGTCCCTGAACATGAATGTA 58.822 40.000 0.00 0.00 40.80 2.29
2448 2565 4.202326 ACAGAGGACACGGTAAAGTGAAAT 60.202 41.667 4.00 0.00 44.43 2.17
2546 2663 9.722056 GGTGATCAGTTTATCATATGTGAAAAC 57.278 33.333 15.64 15.64 38.13 2.43
2547 2664 9.460019 TGGTGATCAGTTTATCATATGTGAAAA 57.540 29.630 0.00 0.00 38.13 2.29
2548 2665 8.892723 GTGGTGATCAGTTTATCATATGTGAAA 58.107 33.333 0.00 1.99 38.13 2.69
2549 2666 7.498900 GGTGGTGATCAGTTTATCATATGTGAA 59.501 37.037 0.00 0.00 38.13 3.18
2550 2667 6.992123 GGTGGTGATCAGTTTATCATATGTGA 59.008 38.462 0.00 0.00 38.13 3.58
2581 2698 4.156739 GGGAGTTGAAGAATTACAGCCAAG 59.843 45.833 0.00 0.00 0.00 3.61
2584 2701 3.942115 GAGGGAGTTGAAGAATTACAGCC 59.058 47.826 0.00 0.00 0.00 4.85
2598 2715 3.456277 GGAATGTATCTGTGGAGGGAGTT 59.544 47.826 0.00 0.00 0.00 3.01
2609 2726 3.000322 GTCGCTCAAACGGAATGTATCTG 60.000 47.826 0.00 0.00 40.53 2.90
2617 2734 2.512485 TACTTGTCGCTCAAACGGAA 57.488 45.000 0.00 0.00 35.48 4.30
2692 2809 5.206587 ACCCGGATACTCTACACAATTAGT 58.793 41.667 0.73 0.00 0.00 2.24
2693 2810 5.535406 AGACCCGGATACTCTACACAATTAG 59.465 44.000 0.73 0.00 0.00 1.73
2694 2811 5.452255 AGACCCGGATACTCTACACAATTA 58.548 41.667 0.73 0.00 0.00 1.40
2695 2812 4.287552 AGACCCGGATACTCTACACAATT 58.712 43.478 0.73 0.00 0.00 2.32
2696 2813 3.912248 AGACCCGGATACTCTACACAAT 58.088 45.455 0.73 0.00 0.00 2.71
2709 2826 4.165372 AGGAGCATAAAAATAAGACCCGGA 59.835 41.667 0.73 0.00 0.00 5.14
2712 2829 7.404671 TCAAAGGAGCATAAAAATAAGACCC 57.595 36.000 0.00 0.00 0.00 4.46
2719 2836 5.945144 AGGCATCAAAGGAGCATAAAAAT 57.055 34.783 0.00 0.00 0.00 1.82
2720 2837 5.337491 GGAAGGCATCAAAGGAGCATAAAAA 60.337 40.000 0.00 0.00 0.00 1.94
2734 2851 6.484364 AAAGAAAAGAAAAGGAAGGCATCA 57.516 33.333 0.00 0.00 0.00 3.07
2735 2852 7.792374 AAAAAGAAAAGAAAAGGAAGGCATC 57.208 32.000 0.00 0.00 0.00 3.91
2766 2883 1.666553 TGTAAGCCCGCAGTTGACG 60.667 57.895 0.00 0.00 0.00 4.35
2841 2958 9.941664 CATTTAGCAGAAATGTAAGTATTGAGG 57.058 33.333 13.31 0.00 34.01 3.86
2859 2976 6.513884 CTGTGAACAGAGAAAAGCATTTAGCA 60.514 38.462 4.36 0.00 46.06 3.49
2862 2979 6.061441 TCCTGTGAACAGAGAAAAGCATTTA 58.939 36.000 12.05 0.00 46.59 1.40
2868 2985 2.810852 GCCTCCTGTGAACAGAGAAAAG 59.189 50.000 12.05 2.00 46.59 2.27
2897 3014 2.027100 AGTTTTCCTCGGGTTGATCCTC 60.027 50.000 0.00 0.00 36.25 3.71
2952 3069 2.221169 CACAGTTCAGCAAAGCACCTA 58.779 47.619 0.00 0.00 0.00 3.08
2970 3087 1.881252 ACGACTTGTCACGCACCAC 60.881 57.895 0.00 0.00 0.00 4.16
3163 3280 2.354906 GGCCATCACCATTGCAAATCAA 60.355 45.455 1.71 0.00 39.32 2.57
3167 3284 1.551908 GGGGCCATCACCATTGCAAA 61.552 55.000 4.39 0.00 0.00 3.68
3175 3292 2.452600 TAAGAAATGGGGCCATCACC 57.547 50.000 4.39 0.00 35.31 4.02
3177 3294 5.372363 TCTCTATTAAGAAATGGGGCCATCA 59.628 40.000 4.39 2.02 35.31 3.07
3195 3312 4.558226 TGATGCACACAACCTTCTCTAT 57.442 40.909 0.00 0.00 0.00 1.98
3196 3313 4.350368 TTGATGCACACAACCTTCTCTA 57.650 40.909 0.00 0.00 0.00 2.43
3197 3314 2.936919 TGATGCACACAACCTTCTCT 57.063 45.000 0.00 0.00 0.00 3.10
3198 3315 4.022935 TCAATTGATGCACACAACCTTCTC 60.023 41.667 3.38 0.00 0.00 2.87
3202 3430 4.182693 CATCAATTGATGCACACAACCT 57.817 40.909 30.11 0.00 44.44 3.50
3233 3461 1.680338 AGAAAACAAGCGAGTGCCTT 58.320 45.000 0.00 0.00 44.31 4.35
3234 3462 1.604278 GAAGAAAACAAGCGAGTGCCT 59.396 47.619 0.00 0.00 44.31 4.75
3266 3496 7.798982 CGACAAAAGAAAGGAGAAAATGTACTC 59.201 37.037 0.00 0.00 0.00 2.59
3270 3500 6.693315 TCGACAAAAGAAAGGAGAAAATGT 57.307 33.333 0.00 0.00 0.00 2.71
3271 3501 6.583806 CCATCGACAAAAGAAAGGAGAAAATG 59.416 38.462 0.00 0.00 0.00 2.32
3274 3504 5.008613 CACCATCGACAAAAGAAAGGAGAAA 59.991 40.000 0.00 0.00 0.00 2.52
3280 3510 3.904136 AGCACCATCGACAAAAGAAAG 57.096 42.857 0.00 0.00 0.00 2.62
3281 3511 3.004315 GGAAGCACCATCGACAAAAGAAA 59.996 43.478 0.00 0.00 38.79 2.52
3286 3516 2.270352 AAGGAAGCACCATCGACAAA 57.730 45.000 0.00 0.00 42.04 2.83
3288 3518 1.202758 ACAAAGGAAGCACCATCGACA 60.203 47.619 0.00 0.00 42.04 4.35
3309 3542 9.314133 ACATGTAGGCTAGATTGAATATCTACA 57.686 33.333 0.66 0.00 39.66 2.74
3325 3558 4.445448 GGATTTCATCCTCACATGTAGGCT 60.445 45.833 13.53 0.00 46.19 4.58
3346 3579 5.280317 GGACAACAGGGTTGTTATAAGAGGA 60.280 44.000 15.10 0.00 45.53 3.71
3390 3624 5.874810 TCCCACTTCGACATTCAAAAGATAG 59.125 40.000 0.00 0.00 0.00 2.08
3391 3625 5.800296 TCCCACTTCGACATTCAAAAGATA 58.200 37.500 0.00 0.00 0.00 1.98
3392 3626 4.651778 TCCCACTTCGACATTCAAAAGAT 58.348 39.130 0.00 0.00 0.00 2.40
3398 3632 4.610605 TTAGTTCCCACTTCGACATTCA 57.389 40.909 0.00 0.00 34.06 2.57
3406 3640 8.617290 TGTCTATTCTTTTTAGTTCCCACTTC 57.383 34.615 0.00 0.00 34.06 3.01
3427 3661 4.532126 TGGAAGTGTCACCATATCTTGTCT 59.468 41.667 0.00 0.00 0.00 3.41
3440 3674 3.246112 CCCCCGGTGGAAGTGTCA 61.246 66.667 0.00 0.00 35.39 3.58
3515 3749 1.616865 TGAAACCACGACCACTAGAGG 59.383 52.381 4.44 4.44 0.00 3.69
3526 3760 0.307760 GCTTGGTCAGTGAAACCACG 59.692 55.000 3.22 3.52 46.27 4.94
3534 3768 1.972872 AGGTTGAAGCTTGGTCAGTG 58.027 50.000 2.10 0.00 0.00 3.66
3540 3774 3.196685 AGCTCTACTAGGTTGAAGCTTGG 59.803 47.826 2.10 0.00 29.36 3.61
3542 3776 4.528596 TGAAGCTCTACTAGGTTGAAGCTT 59.471 41.667 15.47 15.47 45.83 3.74
3588 3822 5.045578 AGGTCATTTTCATAGTAGCACCAGT 60.046 40.000 0.00 0.00 0.00 4.00
3594 3828 6.256757 GTCACTGAGGTCATTTTCATAGTAGC 59.743 42.308 0.00 0.00 0.00 3.58
3600 3834 4.042062 TCCTGTCACTGAGGTCATTTTCAT 59.958 41.667 0.00 0.00 31.85 2.57
3604 3838 4.647564 AATCCTGTCACTGAGGTCATTT 57.352 40.909 0.00 0.00 31.85 2.32
3614 3848 6.257586 ACTAGGTTCTCTAAATCCTGTCACT 58.742 40.000 0.00 0.00 0.00 3.41
3615 3849 6.532988 ACTAGGTTCTCTAAATCCTGTCAC 57.467 41.667 0.00 0.00 0.00 3.67
3618 3852 8.532819 CAAACTACTAGGTTCTCTAAATCCTGT 58.467 37.037 0.00 0.00 0.00 4.00
3619 3853 7.982354 CCAAACTACTAGGTTCTCTAAATCCTG 59.018 40.741 0.00 0.00 0.00 3.86
3620 3854 7.125963 CCCAAACTACTAGGTTCTCTAAATCCT 59.874 40.741 0.00 0.00 0.00 3.24
3624 3858 6.086775 ACCCCAAACTACTAGGTTCTCTAAA 58.913 40.000 0.00 0.00 0.00 1.85
3625 3859 5.658474 ACCCCAAACTACTAGGTTCTCTAA 58.342 41.667 0.00 0.00 0.00 2.10
3651 3885 3.120321 TCCGAAGCACAACAACTACAT 57.880 42.857 0.00 0.00 0.00 2.29
3652 3886 2.605837 TCCGAAGCACAACAACTACA 57.394 45.000 0.00 0.00 0.00 2.74
3653 3887 2.870411 ACTTCCGAAGCACAACAACTAC 59.130 45.455 8.11 0.00 0.00 2.73
3655 3889 2.038387 ACTTCCGAAGCACAACAACT 57.962 45.000 8.11 0.00 0.00 3.16
3670 3904 2.038164 AGAACCCGGTAGTTCCAACTTC 59.962 50.000 17.01 0.00 46.00 3.01
3675 3909 1.553248 CATGAGAACCCGGTAGTTCCA 59.447 52.381 17.01 14.85 46.00 3.53
3683 3917 0.240945 GCAACAACATGAGAACCCGG 59.759 55.000 0.00 0.00 0.00 5.73
3697 3931 1.719063 AAGGCTTCCCAGAGGCAACA 61.719 55.000 0.00 0.00 44.07 3.33
3699 3933 0.251341 GAAAGGCTTCCCAGAGGCAA 60.251 55.000 0.00 0.00 44.07 4.52
3706 3940 3.307762 GCTAAGAAGAGAAAGGCTTCCCA 60.308 47.826 0.00 0.00 42.04 4.37
3708 3942 3.938334 CAGCTAAGAAGAGAAAGGCTTCC 59.062 47.826 0.00 0.00 42.04 3.46
3728 3962 1.135915 ACAGAGCGATGGACTTAGCAG 59.864 52.381 0.00 0.00 0.00 4.24
3740 3974 0.598419 CTGCAGTGTTGACAGAGCGA 60.598 55.000 5.25 0.00 33.22 4.93
3746 3980 1.476085 CCAAAACCTGCAGTGTTGACA 59.524 47.619 17.70 0.00 45.34 3.58
3750 3984 2.354604 CCAAACCAAAACCTGCAGTGTT 60.355 45.455 13.81 13.32 0.00 3.32
3759 3994 2.036089 TCGGCAATACCAAACCAAAACC 59.964 45.455 0.00 0.00 39.03 3.27
3781 4016 5.476945 ACAAACCCAGATCCAGAATACAAAC 59.523 40.000 0.00 0.00 0.00 2.93
3815 4050 2.683867 TGTACACAAAACCCGACAAAGG 59.316 45.455 0.00 0.00 0.00 3.11
3820 4055 2.477754 GCTACTGTACACAAAACCCGAC 59.522 50.000 0.00 0.00 0.00 4.79
3823 4058 3.072211 GGAGCTACTGTACACAAAACCC 58.928 50.000 0.00 0.00 0.00 4.11
3825 4060 4.994852 TCATGGAGCTACTGTACACAAAAC 59.005 41.667 0.00 0.00 0.00 2.43
3836 4071 6.715347 ACAAAACTTTTTCATGGAGCTACT 57.285 33.333 0.00 0.00 0.00 2.57
3852 4087 0.743688 TCATGCCGCACAACAAAACT 59.256 45.000 0.00 0.00 0.00 2.66
3868 4103 4.641396 TCGAGGTTTGAAGTGTGATTCAT 58.359 39.130 0.00 0.00 38.90 2.57
3889 4124 5.432157 CAACGGCACAAAATCGATACTATC 58.568 41.667 0.00 0.00 0.00 2.08
3891 4126 3.619483 CCAACGGCACAAAATCGATACTA 59.381 43.478 0.00 0.00 0.00 1.82
3893 4128 2.160813 ACCAACGGCACAAAATCGATAC 59.839 45.455 0.00 0.00 0.00 2.24
3894 4129 2.428491 ACCAACGGCACAAAATCGATA 58.572 42.857 0.00 0.00 0.00 2.92
3895 4130 1.243902 ACCAACGGCACAAAATCGAT 58.756 45.000 0.00 0.00 0.00 3.59
3898 4133 5.694458 AGATTAAAACCAACGGCACAAAATC 59.306 36.000 0.00 0.00 0.00 2.17
3899 4134 5.606505 AGATTAAAACCAACGGCACAAAAT 58.393 33.333 0.00 0.00 0.00 1.82
3900 4135 5.012328 AGATTAAAACCAACGGCACAAAA 57.988 34.783 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.