Multiple sequence alignment - TraesCS7D01G431100

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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 TraesCS7D01G431100 chr7D 100.000 3030 0 0 1 3030 550461993 550465022 0.000000e+00 5596.0
1 TraesCS7D01G431100 chr7D 89.222 1837 116 32 301 2099 550552367 550554159 0.000000e+00 2220.0
2 TraesCS7D01G431100 chr7D 94.353 1399 53 7 1 1395 550642281 550643657 0.000000e+00 2122.0
3 TraesCS7D01G431100 chr7D 90.309 1228 96 12 913 2134 550800374 550801584 0.000000e+00 1587.0
4 TraesCS7D01G431100 chr7D 89.970 668 55 11 2078 2739 550554170 550554831 0.000000e+00 852.0
5 TraesCS7D01G431100 chr7D 77.287 929 73 70 1 868 550799524 550800375 1.300000e-113 420.0
6 TraesCS7D01G431100 chr7D 91.358 243 16 5 1 241 550551987 550552226 8.100000e-86 327.0
7 TraesCS7D01G431100 chr7D 82.000 350 40 11 2259 2591 550656085 550656428 2.980000e-70 276.0
8 TraesCS7D01G431100 chr7D 92.308 78 2 1 236 313 550552278 550552351 1.150000e-19 108.0
9 TraesCS7D01G431100 chr7A 89.062 2496 191 38 287 2739 635859649 635862105 0.000000e+00 3022.0
10 TraesCS7D01G431100 chr7A 90.605 1916 111 23 236 2129 636126158 636128026 0.000000e+00 2477.0
11 TraesCS7D01G431100 chr7A 86.196 1985 121 60 250 2134 636628254 636630185 0.000000e+00 2006.0
12 TraesCS7D01G431100 chr7A 90.438 251 14 4 1 241 636125882 636126132 3.770000e-84 322.0
13 TraesCS7D01G431100 chr7A 89.879 247 19 2 1 241 635859156 635859402 2.270000e-81 313.0
14 TraesCS7D01G431100 chr7A 87.097 217 24 4 2378 2591 636206655 636206870 3.020000e-60 243.0
15 TraesCS7D01G431100 chr7A 87.923 207 18 7 2269 2469 636141468 636141673 1.400000e-58 237.0
16 TraesCS7D01G431100 chr7A 86.636 217 25 4 2378 2591 636144783 636144998 1.400000e-58 237.0
17 TraesCS7D01G431100 chr7A 92.982 57 2 2 236 290 635859442 635859498 6.960000e-12 82.4
18 TraesCS7D01G431100 chr7B 90.081 1976 101 33 236 2134 595006641 595008598 0.000000e+00 2475.0
19 TraesCS7D01G431100 chr7B 88.127 1735 128 31 451 2132 595079986 595081695 0.000000e+00 1991.0
20 TraesCS7D01G431100 chr7B 88.799 1366 100 28 787 2134 595307136 595308466 0.000000e+00 1626.0
21 TraesCS7D01G431100 chr7B 92.320 651 47 2 1485 2132 595172825 595173475 0.000000e+00 922.0
22 TraesCS7D01G431100 chr7B 84.748 872 73 32 351 1178 595165875 595166730 0.000000e+00 819.0
23 TraesCS7D01G431100 chr7B 85.838 346 36 10 2259 2591 595081690 595082035 3.720000e-94 355.0
24 TraesCS7D01G431100 chr7B 85.890 326 38 6 2259 2580 595173470 595173791 1.040000e-89 340.0
25 TraesCS7D01G431100 chr7B 92.025 163 12 1 72 234 595165524 595165685 8.450000e-56 228.0
26 TraesCS7D01G431100 chr7B 88.000 200 14 4 1292 1491 595166773 595166962 8.450000e-56 228.0
27 TraesCS7D01G431100 chr7B 93.103 145 9 1 602 745 595306704 595306848 8.510000e-51 211.0
28 TraesCS7D01G431100 chr7B 82.990 194 28 5 2287 2476 595308482 595308674 1.440000e-38 171.0
29 TraesCS7D01G431100 chr7B 100.000 35 0 0 749 783 595306872 595306906 7.010000e-07 65.8
30 TraesCS7D01G431100 chr3A 87.640 89 10 1 2141 2229 681474684 681474771 5.340000e-18 102.0
31 TraesCS7D01G431100 chr6D 82.203 118 9 8 238 350 77171802 77171912 1.160000e-14 91.6
32 TraesCS7D01G431100 chr3D 91.304 46 2 1 698 743 551346681 551346638 9.070000e-06 62.1
33 TraesCS7D01G431100 chr3D 80.208 96 3 7 698 780 551429979 551430071 1.170000e-04 58.4


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 TraesCS7D01G431100 chr7D 550461993 550465022 3029 False 5596.000000 5596 100.000000 1 3030 1 chr7D.!!$F1 3029
1 TraesCS7D01G431100 chr7D 550642281 550643657 1376 False 2122.000000 2122 94.353000 1 1395 1 chr7D.!!$F2 1394
2 TraesCS7D01G431100 chr7D 550799524 550801584 2060 False 1003.500000 1587 83.798000 1 2134 2 chr7D.!!$F5 2133
3 TraesCS7D01G431100 chr7D 550551987 550554831 2844 False 876.750000 2220 90.714500 1 2739 4 chr7D.!!$F4 2738
4 TraesCS7D01G431100 chr7A 636628254 636630185 1931 False 2006.000000 2006 86.196000 250 2134 1 chr7A.!!$F2 1884
5 TraesCS7D01G431100 chr7A 636125882 636128026 2144 False 1399.500000 2477 90.521500 1 2129 2 chr7A.!!$F4 2128
6 TraesCS7D01G431100 chr7A 635859156 635862105 2949 False 1139.133333 3022 90.641000 1 2739 3 chr7A.!!$F3 2738
7 TraesCS7D01G431100 chr7A 636141468 636144998 3530 False 237.000000 237 87.279500 2269 2591 2 chr7A.!!$F5 322
8 TraesCS7D01G431100 chr7B 595006641 595008598 1957 False 2475.000000 2475 90.081000 236 2134 1 chr7B.!!$F1 1898
9 TraesCS7D01G431100 chr7B 595079986 595082035 2049 False 1173.000000 1991 86.982500 451 2591 2 chr7B.!!$F2 2140
10 TraesCS7D01G431100 chr7B 595172825 595173791 966 False 631.000000 922 89.105000 1485 2580 2 chr7B.!!$F4 1095
11 TraesCS7D01G431100 chr7B 595306704 595308674 1970 False 518.450000 1626 91.223000 602 2476 4 chr7B.!!$F5 1874
12 TraesCS7D01G431100 chr7B 595165524 595166962 1438 False 425.000000 819 88.257667 72 1491 3 chr7B.!!$F3 1419

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
38 39 3.187842 CGACGTGATTATCTGTATCCCGA 59.812 47.826 0.0 0.0 29.43 5.14 F
1226 1949 1.266178 TCAGAGTTCTTGGCGATGGA 58.734 50.000 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 2333 0.179065 TGCTCCTGATCCGCTCAATG 60.179 55.0 0.00 0.0 32.14 2.82 R
2973 6974 0.039888 GCGTGTGGGCGTTAACATTT 60.040 50.0 6.39 0.0 0.00 2.32 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
38 39 3.187842 CGACGTGATTATCTGTATCCCGA 59.812 47.826 0.00 0.00 29.43 5.14
143 157 3.317149 GCCCAAATTAAACGTAGGGATCC 59.683 47.826 1.92 1.92 38.60 3.36
194 208 5.450965 GCCAAGAATGAATGAATGGTCGATT 60.451 40.000 0.00 0.00 0.00 3.34
1023 1719 2.594592 GTGGACCTGCAACGCCTT 60.595 61.111 0.00 0.00 0.00 4.35
1049 1745 1.537814 ATGTTACTCACCACCGGCGA 61.538 55.000 9.30 0.00 0.00 5.54
1072 1774 4.008933 GCGGTCACCACCAGCTCT 62.009 66.667 0.00 0.00 44.02 4.09
1226 1949 1.266178 TCAGAGTTCTTGGCGATGGA 58.734 50.000 0.00 0.00 0.00 3.41
1256 1979 2.045340 GGCTAAGAAGGGCGGCAA 60.045 61.111 12.47 0.00 0.00 4.52
1302 2025 4.803426 AAGAAGCGGAGGCGCGAG 62.803 66.667 12.10 0.00 46.35 5.03
1372 2095 1.517257 CAGCAGACCATCGACGTCC 60.517 63.158 10.58 0.00 0.00 4.79
1446 2171 2.346376 CCGATCGATACTTTGCGTTTCG 60.346 50.000 18.66 0.00 44.86 3.46
1588 2333 0.620556 TCAAGGCCAAGGATGAGGAC 59.379 55.000 5.01 0.00 0.00 3.85
1643 2388 1.153804 GAGCGTCTTCGGAACCTCC 60.154 63.158 0.00 0.00 37.56 4.30
1669 2414 2.587194 GCTCAGATGTGGCGCGAT 60.587 61.111 12.10 0.00 0.00 4.58
1684 2429 2.202932 GATGTCGCGCAGTCCCAT 60.203 61.111 8.75 0.67 0.00 4.00
1807 2555 1.078567 GTGCTGCTGGGGAGAGAAG 60.079 63.158 0.00 0.00 0.00 2.85
2053 2801 4.957954 TGCGGGAGGAATAGTTTTAGAGTA 59.042 41.667 0.00 0.00 0.00 2.59
2134 2916 7.757624 TGTTCACTTTTTCTATTGTTGTTGACC 59.242 33.333 0.00 0.00 0.00 4.02
2136 2918 6.316640 TCACTTTTTCTATTGTTGTTGACCGA 59.683 34.615 0.00 0.00 0.00 4.69
2174 2956 4.643387 GCCGTGTGAGGTTGGGCT 62.643 66.667 0.00 0.00 40.59 5.19
2175 2957 2.669569 CCGTGTGAGGTTGGGCTG 60.670 66.667 0.00 0.00 0.00 4.85
2204 2986 1.830847 GGCCAGGTTTTCAACGGGT 60.831 57.895 0.00 0.00 0.00 5.28
2215 2997 0.470341 TCAACGGGTCCACATGTCAA 59.530 50.000 0.00 0.00 0.00 3.18
2227 3009 4.081142 TCCACATGTCAATGGTAGAACGAT 60.081 41.667 0.00 0.00 38.19 3.73
2239 3021 0.460311 AGAACGATAGGGTGCCGAAG 59.540 55.000 0.00 0.00 43.77 3.79
2262 3044 6.130569 AGGTTAGAGTATCCTCCTACTTGTG 58.869 44.000 0.00 0.00 38.58 3.33
2263 3045 5.892686 GGTTAGAGTATCCTCCTACTTGTGT 59.107 44.000 0.00 0.00 38.58 3.72
2264 3046 6.380560 GGTTAGAGTATCCTCCTACTTGTGTT 59.619 42.308 0.00 0.00 38.58 3.32
2265 3047 5.923733 AGAGTATCCTCCTACTTGTGTTG 57.076 43.478 0.00 0.00 38.58 3.33
2266 3048 5.580998 AGAGTATCCTCCTACTTGTGTTGA 58.419 41.667 0.00 0.00 38.58 3.18
2267 3049 5.419471 AGAGTATCCTCCTACTTGTGTTGAC 59.581 44.000 0.00 0.00 38.58 3.18
2271 3053 1.616865 CTCCTACTTGTGTTGACGGGA 59.383 52.381 0.00 0.00 0.00 5.14
2277 3059 4.280436 ACTTGTGTTGACGGGATGATAA 57.720 40.909 0.00 0.00 0.00 1.75
2296 3078 7.020827 TGATAAATAGGAGGATGGTTGGATC 57.979 40.000 0.00 0.00 0.00 3.36
2391 3181 8.655651 TTGTTCAACAAGAAGAAAAACAGTTT 57.344 26.923 0.00 0.00 36.65 2.66
2394 3184 7.636259 TCAACAAGAAGAAAAACAGTTTGTG 57.364 32.000 0.00 0.00 0.00 3.33
2403 3194 5.810074 AGAAAAACAGTTTGTGGTATTGCAC 59.190 36.000 0.00 0.00 0.00 4.57
2406 6399 6.398234 AAACAGTTTGTGGTATTGCACATA 57.602 33.333 0.00 0.00 0.00 2.29
2515 6512 4.686554 GGTCAAAGATAGGAATCCGATTCG 59.313 45.833 13.74 0.00 40.17 3.34
2617 6617 8.597662 ACTGTCCAAAGATTGATTTGAATTTG 57.402 30.769 0.91 0.00 41.71 2.32
2634 6634 9.810545 TTTGAATTTGTAGAAATTTTTCTCGGT 57.189 25.926 11.49 0.00 43.72 4.69
2637 6637 9.458374 GAATTTGTAGAAATTTTTCTCGGTTGA 57.542 29.630 11.49 0.00 43.72 3.18
2638 6638 9.981114 AATTTGTAGAAATTTTTCTCGGTTGAT 57.019 25.926 8.76 0.00 43.72 2.57
2656 6656 4.487714 TGATAAGAGGTTGGTGCCTAAG 57.512 45.455 0.00 0.00 39.34 2.18
2744 6745 3.813724 GGTGGAGGGAGGGCCATG 61.814 72.222 6.18 0.00 36.41 3.66
2745 6746 3.813724 GTGGAGGGAGGGCCATGG 61.814 72.222 7.63 7.63 36.41 3.66
2756 6757 4.722700 GCCATGGCGACCACCAGT 62.723 66.667 23.48 0.00 44.71 4.00
2757 6758 2.034066 CCATGGCGACCACCAGTT 59.966 61.111 0.00 0.00 44.71 3.16
2758 6759 2.040544 CCATGGCGACCACCAGTTC 61.041 63.158 0.00 0.00 44.71 3.01
2759 6760 2.040544 CATGGCGACCACCAGTTCC 61.041 63.158 0.50 0.00 44.71 3.62
2760 6761 3.268103 ATGGCGACCACCAGTTCCC 62.268 63.158 0.50 0.00 44.71 3.97
2761 6762 4.717313 GGCGACCACCAGTTCCCC 62.717 72.222 0.00 0.00 0.00 4.81
2762 6763 3.948719 GCGACCACCAGTTCCCCA 61.949 66.667 0.00 0.00 0.00 4.96
2763 6764 2.833227 CGACCACCAGTTCCCCAA 59.167 61.111 0.00 0.00 0.00 4.12
2764 6765 1.149627 CGACCACCAGTTCCCCAAA 59.850 57.895 0.00 0.00 0.00 3.28
2765 6766 0.889186 CGACCACCAGTTCCCCAAAG 60.889 60.000 0.00 0.00 0.00 2.77
2766 6767 0.539669 GACCACCAGTTCCCCAAAGG 60.540 60.000 0.00 0.00 0.00 3.11
2767 6768 1.293683 ACCACCAGTTCCCCAAAGGT 61.294 55.000 0.00 0.00 36.75 3.50
2768 6769 0.539669 CCACCAGTTCCCCAAAGGTC 60.540 60.000 0.00 0.00 36.75 3.85
2769 6770 0.539669 CACCAGTTCCCCAAAGGTCC 60.540 60.000 0.00 0.00 36.75 4.46
2770 6771 0.996762 ACCAGTTCCCCAAAGGTCCA 60.997 55.000 0.00 0.00 36.75 4.02
2771 6772 0.539669 CCAGTTCCCCAAAGGTCCAC 60.540 60.000 0.00 0.00 36.75 4.02
2772 6773 0.478507 CAGTTCCCCAAAGGTCCACT 59.521 55.000 0.00 0.00 36.75 4.00
2773 6774 1.702957 CAGTTCCCCAAAGGTCCACTA 59.297 52.381 0.00 0.00 36.75 2.74
2774 6775 2.107552 CAGTTCCCCAAAGGTCCACTAA 59.892 50.000 0.00 0.00 36.75 2.24
2775 6776 2.787035 AGTTCCCCAAAGGTCCACTAAA 59.213 45.455 0.00 0.00 36.75 1.85
2776 6777 3.401342 AGTTCCCCAAAGGTCCACTAAAT 59.599 43.478 0.00 0.00 36.75 1.40
2777 6778 4.604490 AGTTCCCCAAAGGTCCACTAAATA 59.396 41.667 0.00 0.00 36.75 1.40
2778 6779 5.255443 AGTTCCCCAAAGGTCCACTAAATAT 59.745 40.000 0.00 0.00 36.75 1.28
2779 6780 5.124036 TCCCCAAAGGTCCACTAAATATG 57.876 43.478 0.00 0.00 36.75 1.78
2780 6781 4.542525 TCCCCAAAGGTCCACTAAATATGT 59.457 41.667 0.00 0.00 36.75 2.29
2781 6782 5.015817 TCCCCAAAGGTCCACTAAATATGTT 59.984 40.000 0.00 0.00 36.75 2.71
2782 6783 6.217900 TCCCCAAAGGTCCACTAAATATGTTA 59.782 38.462 0.00 0.00 36.75 2.41
2783 6784 7.066781 CCCCAAAGGTCCACTAAATATGTTAT 58.933 38.462 0.00 0.00 0.00 1.89
2784 6785 7.563556 CCCCAAAGGTCCACTAAATATGTTATT 59.436 37.037 0.00 0.00 0.00 1.40
2785 6786 8.977412 CCCAAAGGTCCACTAAATATGTTATTT 58.023 33.333 0.00 0.00 0.00 1.40
2839 6840 5.989551 AAAAAGCCACAAAAGTTGCTATG 57.010 34.783 0.00 0.00 32.82 2.23
2840 6841 4.670896 AAAGCCACAAAAGTTGCTATGT 57.329 36.364 0.00 0.00 32.82 2.29
2841 6842 4.670896 AAGCCACAAAAGTTGCTATGTT 57.329 36.364 0.00 0.00 32.82 2.71
2842 6843 5.782893 AAGCCACAAAAGTTGCTATGTTA 57.217 34.783 0.00 0.00 32.82 2.41
2843 6844 5.982890 AGCCACAAAAGTTGCTATGTTAT 57.017 34.783 0.00 0.00 30.97 1.89
2844 6845 6.345096 AGCCACAAAAGTTGCTATGTTATT 57.655 33.333 0.00 0.00 30.97 1.40
2845 6846 6.758254 AGCCACAAAAGTTGCTATGTTATTT 58.242 32.000 0.00 0.00 30.97 1.40
2846 6847 6.646240 AGCCACAAAAGTTGCTATGTTATTTG 59.354 34.615 0.00 0.00 30.97 2.32
2847 6848 6.423604 GCCACAAAAGTTGCTATGTTATTTGT 59.576 34.615 0.00 0.00 39.36 2.83
2848 6849 7.359181 GCCACAAAAGTTGCTATGTTATTTGTC 60.359 37.037 0.00 0.00 37.40 3.18
2849 6850 7.651304 CCACAAAAGTTGCTATGTTATTTGTCA 59.349 33.333 0.00 0.00 37.40 3.58
2850 6851 9.195411 CACAAAAGTTGCTATGTTATTTGTCAT 57.805 29.630 0.00 0.00 37.40 3.06
2854 6855 9.855021 AAAGTTGCTATGTTATTTGTCATAACC 57.145 29.630 2.96 0.00 34.51 2.85
2855 6856 7.996385 AGTTGCTATGTTATTTGTCATAACCC 58.004 34.615 2.96 0.00 34.51 4.11
2856 6857 7.613801 AGTTGCTATGTTATTTGTCATAACCCA 59.386 33.333 2.96 0.00 34.51 4.51
2857 6858 7.946381 TGCTATGTTATTTGTCATAACCCAA 57.054 32.000 2.96 0.00 34.51 4.12
2858 6859 8.354711 TGCTATGTTATTTGTCATAACCCAAA 57.645 30.769 2.96 0.00 34.51 3.28
2859 6860 8.807118 TGCTATGTTATTTGTCATAACCCAAAA 58.193 29.630 2.96 0.00 34.52 2.44
2860 6861 9.646427 GCTATGTTATTTGTCATAACCCAAAAA 57.354 29.630 2.96 0.00 34.52 1.94
2867 6868 7.489574 TTTGTCATAACCCAAAAATCTTTGC 57.510 32.000 0.00 0.00 40.61 3.68
2868 6869 6.166984 TGTCATAACCCAAAAATCTTTGCA 57.833 33.333 0.00 0.00 40.61 4.08
2869 6870 6.586344 TGTCATAACCCAAAAATCTTTGCAA 58.414 32.000 0.00 0.00 40.61 4.08
2870 6871 7.050377 TGTCATAACCCAAAAATCTTTGCAAA 58.950 30.769 12.14 12.14 40.61 3.68
2871 6872 7.554118 TGTCATAACCCAAAAATCTTTGCAAAA 59.446 29.630 13.84 5.01 40.61 2.44
2872 6873 8.401709 GTCATAACCCAAAAATCTTTGCAAAAA 58.598 29.630 13.84 0.00 40.61 1.94
2873 6874 9.129532 TCATAACCCAAAAATCTTTGCAAAAAT 57.870 25.926 13.84 2.11 40.61 1.82
2876 6877 8.518430 AACCCAAAAATCTTTGCAAAAATAGT 57.482 26.923 13.84 0.00 40.61 2.12
2877 6878 8.153479 ACCCAAAAATCTTTGCAAAAATAGTC 57.847 30.769 13.84 0.00 40.61 2.59
2878 6879 7.042119 ACCCAAAAATCTTTGCAAAAATAGTCG 60.042 33.333 13.84 0.00 40.61 4.18
2879 6880 7.290118 CCAAAAATCTTTGCAAAAATAGTCGG 58.710 34.615 13.84 5.92 40.61 4.79
2880 6881 7.042119 CCAAAAATCTTTGCAAAAATAGTCGGT 60.042 33.333 13.84 0.00 40.61 4.69
2881 6882 8.973378 CAAAAATCTTTGCAAAAATAGTCGGTA 58.027 29.630 13.84 0.00 35.81 4.02
2882 6883 9.535878 AAAAATCTTTGCAAAAATAGTCGGTAA 57.464 25.926 13.84 0.00 0.00 2.85
2883 6884 9.535878 AAAATCTTTGCAAAAATAGTCGGTAAA 57.464 25.926 13.84 0.00 0.00 2.01
2884 6885 8.515473 AATCTTTGCAAAAATAGTCGGTAAAC 57.485 30.769 13.84 0.00 0.00 2.01
2885 6886 7.028926 TCTTTGCAAAAATAGTCGGTAAACA 57.971 32.000 13.84 0.00 0.00 2.83
2886 6887 7.481642 TCTTTGCAAAAATAGTCGGTAAACAA 58.518 30.769 13.84 0.00 0.00 2.83
2887 6888 7.974501 TCTTTGCAAAAATAGTCGGTAAACAAA 59.025 29.630 13.84 0.00 0.00 2.83
2888 6889 8.475331 TTTGCAAAAATAGTCGGTAAACAAAA 57.525 26.923 10.02 0.00 0.00 2.44
2889 6890 8.475331 TTGCAAAAATAGTCGGTAAACAAAAA 57.525 26.923 0.00 0.00 0.00 1.94
2890 6891 8.649973 TGCAAAAATAGTCGGTAAACAAAAAT 57.350 26.923 0.00 0.00 0.00 1.82
2891 6892 8.543774 TGCAAAAATAGTCGGTAAACAAAAATG 58.456 29.630 0.00 0.00 0.00 2.32
2892 6893 7.529185 GCAAAAATAGTCGGTAAACAAAAATGC 59.471 33.333 0.00 0.00 0.00 3.56
2893 6894 8.543774 CAAAAATAGTCGGTAAACAAAAATGCA 58.456 29.630 0.00 0.00 0.00 3.96
2894 6895 8.649973 AAAATAGTCGGTAAACAAAAATGCAA 57.350 26.923 0.00 0.00 0.00 4.08
2895 6896 7.631915 AATAGTCGGTAAACAAAAATGCAAC 57.368 32.000 0.00 0.00 0.00 4.17
2896 6897 4.364860 AGTCGGTAAACAAAAATGCAACC 58.635 39.130 0.00 0.00 0.00 3.77
2897 6898 4.098807 AGTCGGTAAACAAAAATGCAACCT 59.901 37.500 0.00 0.00 0.00 3.50
2898 6899 4.443063 GTCGGTAAACAAAAATGCAACCTC 59.557 41.667 0.00 0.00 0.00 3.85
2899 6900 4.339814 TCGGTAAACAAAAATGCAACCTCT 59.660 37.500 0.00 0.00 0.00 3.69
2900 6901 4.679654 CGGTAAACAAAAATGCAACCTCTC 59.320 41.667 0.00 0.00 0.00 3.20
2901 6902 5.596845 GGTAAACAAAAATGCAACCTCTCA 58.403 37.500 0.00 0.00 0.00 3.27
2902 6903 6.045955 GGTAAACAAAAATGCAACCTCTCAA 58.954 36.000 0.00 0.00 0.00 3.02
2903 6904 6.705825 GGTAAACAAAAATGCAACCTCTCAAT 59.294 34.615 0.00 0.00 0.00 2.57
2904 6905 7.870445 GGTAAACAAAAATGCAACCTCTCAATA 59.130 33.333 0.00 0.00 0.00 1.90
2905 6906 9.423061 GTAAACAAAAATGCAACCTCTCAATAT 57.577 29.630 0.00 0.00 0.00 1.28
2906 6907 8.907222 AAACAAAAATGCAACCTCTCAATATT 57.093 26.923 0.00 0.00 0.00 1.28
2907 6908 9.995003 AAACAAAAATGCAACCTCTCAATATTA 57.005 25.926 0.00 0.00 0.00 0.98
2908 6909 9.995003 AACAAAAATGCAACCTCTCAATATTAA 57.005 25.926 0.00 0.00 0.00 1.40
2909 6910 9.423061 ACAAAAATGCAACCTCTCAATATTAAC 57.577 29.630 0.00 0.00 0.00 2.01
2910 6911 8.872845 CAAAAATGCAACCTCTCAATATTAACC 58.127 33.333 0.00 0.00 0.00 2.85
2911 6912 7.961326 AAATGCAACCTCTCAATATTAACCT 57.039 32.000 0.00 0.00 0.00 3.50
2912 6913 9.474313 AAAATGCAACCTCTCAATATTAACCTA 57.526 29.630 0.00 0.00 0.00 3.08
2913 6914 9.646522 AAATGCAACCTCTCAATATTAACCTAT 57.353 29.630 0.00 0.00 0.00 2.57
2914 6915 9.646522 AATGCAACCTCTCAATATTAACCTATT 57.353 29.630 0.00 0.00 0.00 1.73
2940 6941 8.959734 AAAATAATAAAAACTAGCACGTGACC 57.040 30.769 22.23 1.65 0.00 4.02
2941 6942 6.673154 ATAATAAAAACTAGCACGTGACCC 57.327 37.500 22.23 0.78 0.00 4.46
2942 6943 2.335316 AAAAACTAGCACGTGACCCA 57.665 45.000 22.23 0.00 0.00 4.51
2943 6944 2.561478 AAAACTAGCACGTGACCCAT 57.439 45.000 22.23 0.00 0.00 4.00
2944 6945 1.808411 AAACTAGCACGTGACCCATG 58.192 50.000 22.23 4.87 0.00 3.66
2945 6946 0.673644 AACTAGCACGTGACCCATGC 60.674 55.000 22.23 0.85 39.74 4.06
2946 6947 1.079197 CTAGCACGTGACCCATGCA 60.079 57.895 22.23 0.00 41.97 3.96
2947 6948 0.462581 CTAGCACGTGACCCATGCAT 60.463 55.000 22.23 0.00 41.97 3.96
2948 6949 0.461870 TAGCACGTGACCCATGCATC 60.462 55.000 22.23 0.00 41.97 3.91
2949 6950 1.746615 GCACGTGACCCATGCATCT 60.747 57.895 22.23 0.00 39.23 2.90
2950 6951 1.985447 GCACGTGACCCATGCATCTG 61.985 60.000 22.23 0.00 39.23 2.90
2951 6952 1.746615 ACGTGACCCATGCATCTGC 60.747 57.895 0.00 0.00 42.50 4.26
2952 6953 2.816360 CGTGACCCATGCATCTGCG 61.816 63.158 0.00 0.00 45.83 5.18
2953 6954 2.825387 TGACCCATGCATCTGCGC 60.825 61.111 0.00 0.00 45.83 6.09
2954 6955 3.945434 GACCCATGCATCTGCGCG 61.945 66.667 0.00 0.00 45.83 6.86
2958 6959 2.968697 CATGCATCTGCGCGGCTA 60.969 61.111 12.58 0.00 45.83 3.93
2959 6960 2.664185 ATGCATCTGCGCGGCTAG 60.664 61.111 12.58 4.61 45.83 3.42
2960 6961 3.451556 ATGCATCTGCGCGGCTAGT 62.452 57.895 12.58 0.00 45.83 2.57
2961 6962 3.333969 GCATCTGCGCGGCTAGTC 61.334 66.667 12.58 0.00 0.00 2.59
2962 6963 2.415010 CATCTGCGCGGCTAGTCT 59.585 61.111 12.58 0.00 0.00 3.24
2963 6964 1.227089 CATCTGCGCGGCTAGTCTT 60.227 57.895 12.58 0.00 0.00 3.01
2964 6965 0.807667 CATCTGCGCGGCTAGTCTTT 60.808 55.000 12.58 0.00 0.00 2.52
2965 6966 0.108138 ATCTGCGCGGCTAGTCTTTT 60.108 50.000 12.58 0.00 0.00 2.27
2966 6967 0.320421 TCTGCGCGGCTAGTCTTTTT 60.320 50.000 12.58 0.00 0.00 1.94
2987 6988 5.707242 TTTATCACAAATGTTAACGCCCA 57.293 34.783 0.26 0.00 0.00 5.36
2988 6989 3.569250 ATCACAAATGTTAACGCCCAC 57.431 42.857 0.26 0.00 0.00 4.61
2989 6990 2.298610 TCACAAATGTTAACGCCCACA 58.701 42.857 0.26 0.00 0.00 4.17
2990 6991 2.033550 TCACAAATGTTAACGCCCACAC 59.966 45.455 0.26 0.00 0.00 3.82
2991 6992 1.002251 ACAAATGTTAACGCCCACACG 60.002 47.619 0.26 0.00 39.50 4.49
2992 6993 0.039888 AAATGTTAACGCCCACACGC 60.040 50.000 0.26 0.00 36.19 5.34
3003 7004 4.354212 CACACGCGTGGCACGAAG 62.354 66.667 40.94 32.66 46.05 3.79
3010 7011 4.539152 GTGGCACGAAGCAACATG 57.461 55.556 0.00 0.00 46.95 3.21
3011 7012 1.081242 GTGGCACGAAGCAACATGG 60.081 57.895 0.00 0.00 46.95 3.66
3013 7014 2.126346 GCACGAAGCAACATGGCC 60.126 61.111 0.00 0.00 44.79 5.36
3014 7015 2.568090 CACGAAGCAACATGGCCC 59.432 61.111 0.00 0.00 0.00 5.80
3015 7016 2.115052 ACGAAGCAACATGGCCCA 59.885 55.556 0.00 0.00 0.00 5.36
3016 7017 1.530419 ACGAAGCAACATGGCCCAA 60.530 52.632 0.00 0.00 0.00 4.12
3017 7018 1.080569 CGAAGCAACATGGCCCAAC 60.081 57.895 0.00 0.00 0.00 3.77
3018 7019 1.293179 GAAGCAACATGGCCCAACC 59.707 57.895 0.00 0.00 39.84 3.77
3019 7020 2.171209 GAAGCAACATGGCCCAACCC 62.171 60.000 0.00 0.00 37.83 4.11
3020 7021 3.705289 GCAACATGGCCCAACCCC 61.705 66.667 0.00 0.00 37.83 4.95
3021 7022 3.381136 CAACATGGCCCAACCCCG 61.381 66.667 0.00 0.00 37.83 5.73
3022 7023 4.694987 AACATGGCCCAACCCCGG 62.695 66.667 0.00 0.00 37.83 5.73
3024 7025 3.733972 CATGGCCCAACCCCGGTA 61.734 66.667 0.00 0.00 37.83 4.02
3025 7026 2.698406 ATGGCCCAACCCCGGTAT 60.698 61.111 0.00 0.00 37.83 2.73
3026 7027 2.763645 ATGGCCCAACCCCGGTATC 61.764 63.158 0.00 0.00 37.83 2.24
3027 7028 3.413300 GGCCCAACCCCGGTATCA 61.413 66.667 0.00 0.00 0.00 2.15
3028 7029 2.763645 GGCCCAACCCCGGTATCAT 61.764 63.158 0.00 0.00 0.00 2.45
3029 7030 1.229076 GCCCAACCCCGGTATCATT 59.771 57.895 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.798994 AGTATAGTGTCGATCGTCTTTTAATTT 57.201 29.630 15.94 0.00 0.00 1.82
143 157 2.408835 GTGCAAATCCGGCCGATG 59.591 61.111 30.73 20.15 0.00 3.84
194 208 8.637986 AGCTAGTAATTGATTTGGTGAAAACAA 58.362 29.630 0.00 0.00 37.98 2.83
951 1636 3.251245 CCGCTCGCTCCTATATATACAGG 59.749 52.174 0.07 0.07 0.00 4.00
1023 1719 0.682292 TGGTGAGTAACATGTGGCGA 59.318 50.000 0.00 0.00 0.00 5.54
1184 1892 1.672854 CTGATACGGGGCCGAAGTCA 61.673 60.000 0.00 0.00 42.83 3.41
1188 1908 1.546589 AACACTGATACGGGGCCGAA 61.547 55.000 0.00 0.00 42.83 4.30
1226 1949 0.460284 CTTAGCCAGATCAACCGCGT 60.460 55.000 4.92 0.00 0.00 6.01
1232 1955 1.134401 CGCCCTTCTTAGCCAGATCAA 60.134 52.381 0.00 0.00 0.00 2.57
1302 2025 2.332362 TAAGCATCGACGACCGCTCC 62.332 60.000 20.32 0.00 38.37 4.70
1446 2171 3.063045 CGACCACGTAGAAATTAAAGCCC 59.937 47.826 0.00 0.00 34.56 5.19
1537 2282 4.394712 CTGGCCTCCACGGTCCAC 62.395 72.222 3.32 0.00 36.18 4.02
1582 2327 1.137675 CTGATCCGCTCAATGTCCTCA 59.862 52.381 0.00 0.00 32.14 3.86
1588 2333 0.179065 TGCTCCTGATCCGCTCAATG 60.179 55.000 0.00 0.00 32.14 2.82
1630 2375 1.195115 CCATGAGGAGGTTCCGAAGA 58.805 55.000 0.00 0.00 42.75 2.87
1643 2388 1.202663 CCACATCTGAGCCTCCATGAG 60.203 57.143 7.55 0.87 0.00 2.90
1669 2414 3.647649 CTCATGGGACTGCGCGACA 62.648 63.158 12.10 6.68 0.00 4.35
1761 2509 3.054503 CGTCCTCCTGACCGTCGT 61.055 66.667 0.00 0.00 41.18 4.34
2007 2755 2.220824 CACGAAAAGTTGATGCAGACGA 59.779 45.455 0.00 0.00 0.00 4.20
2122 2904 2.399396 CGCTTTCGGTCAACAACAAT 57.601 45.000 0.00 0.00 0.00 2.71
2134 2916 3.191539 GCAGAGGAGCCGCTTTCG 61.192 66.667 0.00 0.00 0.00 3.46
2153 2935 3.049674 CAACCTCACACGGCGCAT 61.050 61.111 10.83 0.00 0.00 4.73
2166 2948 1.604593 ACATGTCAGCAGCCCAACC 60.605 57.895 0.00 0.00 0.00 3.77
2174 2956 2.034532 CTGGCCCACATGTCAGCA 59.965 61.111 16.33 4.48 0.00 4.41
2175 2957 2.753043 CCTGGCCCACATGTCAGC 60.753 66.667 0.00 7.90 0.00 4.26
2204 2986 3.259625 TCGTTCTACCATTGACATGTGGA 59.740 43.478 1.15 0.00 38.86 4.02
2215 2997 1.692519 GGCACCCTATCGTTCTACCAT 59.307 52.381 0.00 0.00 0.00 3.55
2227 3009 1.272872 ACTCTAACCTTCGGCACCCTA 60.273 52.381 0.00 0.00 0.00 3.53
2256 3038 2.859165 ATCATCCCGTCAACACAAGT 57.141 45.000 0.00 0.00 0.00 3.16
2262 3044 5.011738 TCCTCCTATTTATCATCCCGTCAAC 59.988 44.000 0.00 0.00 0.00 3.18
2263 3045 5.152193 TCCTCCTATTTATCATCCCGTCAA 58.848 41.667 0.00 0.00 0.00 3.18
2264 3046 4.747583 TCCTCCTATTTATCATCCCGTCA 58.252 43.478 0.00 0.00 0.00 4.35
2265 3047 5.395768 CCATCCTCCTATTTATCATCCCGTC 60.396 48.000 0.00 0.00 0.00 4.79
2266 3048 4.471386 CCATCCTCCTATTTATCATCCCGT 59.529 45.833 0.00 0.00 0.00 5.28
2267 3049 4.471386 ACCATCCTCCTATTTATCATCCCG 59.529 45.833 0.00 0.00 0.00 5.14
2271 3053 7.240405 TGATCCAACCATCCTCCTATTTATCAT 59.760 37.037 0.00 0.00 0.00 2.45
2277 3059 4.047166 TGTGATCCAACCATCCTCCTATT 58.953 43.478 0.00 0.00 0.00 1.73
2296 3078 8.465999 GGATACAAGTCCTCTCATATCTATGTG 58.534 40.741 0.00 0.00 35.32 3.21
2340 3127 3.631250 TCCAACAGCTTCAGGAAAAAGT 58.369 40.909 0.00 0.00 0.00 2.66
2515 6512 2.076863 CACTCTTTGACGGTTGGATCC 58.923 52.381 4.20 4.20 0.00 3.36
2617 6617 9.974750 CTCTTATCAACCGAGAAAAATTTCTAC 57.025 33.333 8.32 2.80 46.84 2.59
2624 6624 5.472137 CCAACCTCTTATCAACCGAGAAAAA 59.528 40.000 0.00 0.00 0.00 1.94
2634 6634 4.288626 ACTTAGGCACCAACCTCTTATCAA 59.711 41.667 0.00 0.00 41.50 2.57
2637 6637 4.623171 CGAACTTAGGCACCAACCTCTTAT 60.623 45.833 0.00 0.00 41.50 1.73
2638 6638 3.306502 CGAACTTAGGCACCAACCTCTTA 60.307 47.826 0.00 0.00 41.50 2.10
2656 6656 8.470040 TCTTCTGTATATTTGGTTGTACGAAC 57.530 34.615 0.00 0.00 0.00 3.95
2739 6740 4.722700 ACTGGTGGTCGCCATGGC 62.723 66.667 27.67 27.67 37.96 4.40
2740 6741 2.034066 AACTGGTGGTCGCCATGG 59.966 61.111 7.63 7.63 37.96 3.66
2741 6742 2.040544 GGAACTGGTGGTCGCCATG 61.041 63.158 3.52 1.85 37.96 3.66
2742 6743 2.351276 GGAACTGGTGGTCGCCAT 59.649 61.111 3.52 0.00 37.96 4.40
2743 6744 3.948719 GGGAACTGGTGGTCGCCA 61.949 66.667 3.07 3.07 36.97 5.69
2744 6745 4.717313 GGGGAACTGGTGGTCGCC 62.717 72.222 1.54 1.54 0.00 5.54
2745 6746 2.969300 TTTGGGGAACTGGTGGTCGC 62.969 60.000 0.00 0.00 0.00 5.19
2746 6747 0.889186 CTTTGGGGAACTGGTGGTCG 60.889 60.000 0.00 0.00 0.00 4.79
2747 6748 0.539669 CCTTTGGGGAACTGGTGGTC 60.540 60.000 0.00 0.00 37.23 4.02
2748 6749 1.293683 ACCTTTGGGGAACTGGTGGT 61.294 55.000 0.00 0.00 38.76 4.16
2749 6750 0.539669 GACCTTTGGGGAACTGGTGG 60.540 60.000 0.00 0.00 38.76 4.61
2750 6751 0.539669 GGACCTTTGGGGAACTGGTG 60.540 60.000 0.00 0.00 38.76 4.17
2751 6752 0.996762 TGGACCTTTGGGGAACTGGT 60.997 55.000 0.00 0.00 38.76 4.00
2752 6753 0.539669 GTGGACCTTTGGGGAACTGG 60.540 60.000 0.00 0.00 38.76 4.00
2753 6754 0.478507 AGTGGACCTTTGGGGAACTG 59.521 55.000 0.00 0.00 38.76 3.16
2754 6755 2.127651 TAGTGGACCTTTGGGGAACT 57.872 50.000 0.00 0.00 38.76 3.01
2755 6756 2.963599 TTAGTGGACCTTTGGGGAAC 57.036 50.000 0.00 0.00 38.76 3.62
2756 6757 5.015817 ACATATTTAGTGGACCTTTGGGGAA 59.984 40.000 0.00 0.00 38.76 3.97
2757 6758 4.542525 ACATATTTAGTGGACCTTTGGGGA 59.457 41.667 0.00 0.00 38.76 4.81
2758 6759 4.867086 ACATATTTAGTGGACCTTTGGGG 58.133 43.478 0.00 0.00 41.89 4.96
2759 6760 8.533569 AATAACATATTTAGTGGACCTTTGGG 57.466 34.615 0.00 0.00 38.88 4.12
2823 6824 7.651304 TGACAAATAACATAGCAACTTTTGTGG 59.349 33.333 3.17 0.00 36.33 4.17
2824 6825 8.572828 TGACAAATAACATAGCAACTTTTGTG 57.427 30.769 3.17 0.00 36.33 3.33
2828 6829 9.855021 GGTTATGACAAATAACATAGCAACTTT 57.145 29.630 9.69 0.00 36.49 2.66
2829 6830 8.466798 GGGTTATGACAAATAACATAGCAACTT 58.533 33.333 9.69 0.00 36.49 2.66
2830 6831 7.613801 TGGGTTATGACAAATAACATAGCAACT 59.386 33.333 9.69 0.00 36.49 3.16
2831 6832 7.767261 TGGGTTATGACAAATAACATAGCAAC 58.233 34.615 9.69 0.00 36.49 4.17
2832 6833 7.946381 TGGGTTATGACAAATAACATAGCAA 57.054 32.000 9.69 0.00 36.49 3.91
2833 6834 7.946381 TTGGGTTATGACAAATAACATAGCA 57.054 32.000 9.69 0.00 36.49 3.49
2834 6835 9.646427 TTTTTGGGTTATGACAAATAACATAGC 57.354 29.630 9.69 0.00 36.57 2.97
2841 6842 9.213799 GCAAAGATTTTTGGGTTATGACAAATA 57.786 29.630 10.43 0.00 43.12 1.40
2842 6843 7.718753 TGCAAAGATTTTTGGGTTATGACAAAT 59.281 29.630 10.43 0.00 43.12 2.32
2843 6844 7.050377 TGCAAAGATTTTTGGGTTATGACAAA 58.950 30.769 10.43 0.00 43.12 2.83
2844 6845 6.586344 TGCAAAGATTTTTGGGTTATGACAA 58.414 32.000 10.43 0.00 43.12 3.18
2845 6846 6.166984 TGCAAAGATTTTTGGGTTATGACA 57.833 33.333 10.43 0.00 43.12 3.58
2846 6847 7.489574 TTTGCAAAGATTTTTGGGTTATGAC 57.510 32.000 8.05 0.00 43.12 3.06
2847 6848 8.511604 TTTTTGCAAAGATTTTTGGGTTATGA 57.488 26.923 12.41 0.00 43.12 2.15
2850 6851 9.620259 ACTATTTTTGCAAAGATTTTTGGGTTA 57.380 25.926 19.10 0.00 43.12 2.85
2851 6852 8.518430 ACTATTTTTGCAAAGATTTTTGGGTT 57.482 26.923 19.10 0.00 43.12 4.11
2852 6853 7.042119 CGACTATTTTTGCAAAGATTTTTGGGT 60.042 33.333 19.10 9.55 43.12 4.51
2853 6854 7.290118 CGACTATTTTTGCAAAGATTTTTGGG 58.710 34.615 19.10 7.06 43.12 4.12
2854 6855 7.042119 ACCGACTATTTTTGCAAAGATTTTTGG 60.042 33.333 19.10 18.91 43.12 3.28
2855 6856 7.850501 ACCGACTATTTTTGCAAAGATTTTTG 58.149 30.769 19.10 10.68 45.17 2.44
2856 6857 9.535878 TTACCGACTATTTTTGCAAAGATTTTT 57.464 25.926 19.10 5.51 0.00 1.94
2857 6858 9.535878 TTTACCGACTATTTTTGCAAAGATTTT 57.464 25.926 19.10 7.78 0.00 1.82
2858 6859 8.974408 GTTTACCGACTATTTTTGCAAAGATTT 58.026 29.630 19.10 8.11 0.00 2.17
2859 6860 8.138712 TGTTTACCGACTATTTTTGCAAAGATT 58.861 29.630 19.10 3.74 0.00 2.40
2860 6861 7.653647 TGTTTACCGACTATTTTTGCAAAGAT 58.346 30.769 18.12 18.12 0.00 2.40
2861 6862 7.028926 TGTTTACCGACTATTTTTGCAAAGA 57.971 32.000 12.41 8.58 0.00 2.52
2862 6863 7.687005 TTGTTTACCGACTATTTTTGCAAAG 57.313 32.000 12.41 2.98 0.00 2.77
2863 6864 8.475331 TTTTGTTTACCGACTATTTTTGCAAA 57.525 26.923 8.05 8.05 0.00 3.68
2864 6865 8.475331 TTTTTGTTTACCGACTATTTTTGCAA 57.525 26.923 0.00 0.00 0.00 4.08
2865 6866 8.543774 CATTTTTGTTTACCGACTATTTTTGCA 58.456 29.630 0.00 0.00 0.00 4.08
2866 6867 7.529185 GCATTTTTGTTTACCGACTATTTTTGC 59.471 33.333 0.00 0.00 0.00 3.68
2867 6868 8.543774 TGCATTTTTGTTTACCGACTATTTTTG 58.456 29.630 0.00 0.00 0.00 2.44
2868 6869 8.649973 TGCATTTTTGTTTACCGACTATTTTT 57.350 26.923 0.00 0.00 0.00 1.94
2869 6870 8.544597 GTTGCATTTTTGTTTACCGACTATTTT 58.455 29.630 0.00 0.00 0.00 1.82
2870 6871 7.170151 GGTTGCATTTTTGTTTACCGACTATTT 59.830 33.333 0.00 0.00 0.00 1.40
2871 6872 6.643360 GGTTGCATTTTTGTTTACCGACTATT 59.357 34.615 0.00 0.00 0.00 1.73
2872 6873 6.015772 AGGTTGCATTTTTGTTTACCGACTAT 60.016 34.615 0.00 0.00 0.00 2.12
2873 6874 5.299782 AGGTTGCATTTTTGTTTACCGACTA 59.700 36.000 0.00 0.00 0.00 2.59
2874 6875 4.098807 AGGTTGCATTTTTGTTTACCGACT 59.901 37.500 0.00 0.00 0.00 4.18
2875 6876 4.364860 AGGTTGCATTTTTGTTTACCGAC 58.635 39.130 0.00 0.00 0.00 4.79
2876 6877 4.339814 AGAGGTTGCATTTTTGTTTACCGA 59.660 37.500 0.00 0.00 0.00 4.69
2877 6878 4.616953 AGAGGTTGCATTTTTGTTTACCG 58.383 39.130 0.00 0.00 0.00 4.02
2878 6879 5.596845 TGAGAGGTTGCATTTTTGTTTACC 58.403 37.500 0.00 0.00 0.00 2.85
2879 6880 7.713764 ATTGAGAGGTTGCATTTTTGTTTAC 57.286 32.000 0.00 0.00 0.00 2.01
2880 6881 9.995003 AATATTGAGAGGTTGCATTTTTGTTTA 57.005 25.926 0.00 0.00 0.00 2.01
2881 6882 8.907222 AATATTGAGAGGTTGCATTTTTGTTT 57.093 26.923 0.00 0.00 0.00 2.83
2882 6883 9.995003 TTAATATTGAGAGGTTGCATTTTTGTT 57.005 25.926 0.00 0.00 0.00 2.83
2883 6884 9.423061 GTTAATATTGAGAGGTTGCATTTTTGT 57.577 29.630 0.00 0.00 0.00 2.83
2884 6885 8.872845 GGTTAATATTGAGAGGTTGCATTTTTG 58.127 33.333 0.00 0.00 0.00 2.44
2885 6886 8.815912 AGGTTAATATTGAGAGGTTGCATTTTT 58.184 29.630 0.00 0.00 0.00 1.94
2886 6887 8.366359 AGGTTAATATTGAGAGGTTGCATTTT 57.634 30.769 0.00 0.00 0.00 1.82
2887 6888 7.961326 AGGTTAATATTGAGAGGTTGCATTT 57.039 32.000 0.00 0.00 0.00 2.32
2888 6889 9.646522 AATAGGTTAATATTGAGAGGTTGCATT 57.353 29.630 0.00 0.00 0.00 3.56
2915 6916 8.024865 GGGTCACGTGCTAGTTTTTATTATTTT 58.975 33.333 11.67 0.00 0.00 1.82
2916 6917 7.175293 TGGGTCACGTGCTAGTTTTTATTATTT 59.825 33.333 11.67 0.00 0.00 1.40
2917 6918 6.655848 TGGGTCACGTGCTAGTTTTTATTATT 59.344 34.615 11.67 0.00 0.00 1.40
2918 6919 6.174760 TGGGTCACGTGCTAGTTTTTATTAT 58.825 36.000 11.67 0.00 0.00 1.28
2919 6920 5.549347 TGGGTCACGTGCTAGTTTTTATTA 58.451 37.500 11.67 0.00 0.00 0.98
2920 6921 4.391155 TGGGTCACGTGCTAGTTTTTATT 58.609 39.130 11.67 0.00 0.00 1.40
2921 6922 4.010667 TGGGTCACGTGCTAGTTTTTAT 57.989 40.909 11.67 0.00 0.00 1.40
2922 6923 3.472283 TGGGTCACGTGCTAGTTTTTA 57.528 42.857 11.67 0.00 0.00 1.52
2923 6924 2.335316 TGGGTCACGTGCTAGTTTTT 57.665 45.000 11.67 0.00 0.00 1.94
2924 6925 2.151202 CATGGGTCACGTGCTAGTTTT 58.849 47.619 11.67 0.00 0.00 2.43
2925 6926 1.808411 CATGGGTCACGTGCTAGTTT 58.192 50.000 11.67 0.00 0.00 2.66
2926 6927 3.532896 CATGGGTCACGTGCTAGTT 57.467 52.632 11.67 0.00 0.00 2.24
2932 6933 1.985447 GCAGATGCATGGGTCACGTG 61.985 60.000 9.94 9.94 41.59 4.49
2933 6934 1.746615 GCAGATGCATGGGTCACGT 60.747 57.895 2.46 0.00 41.59 4.49
2934 6935 2.816360 CGCAGATGCATGGGTCACG 61.816 63.158 2.46 0.00 42.21 4.35
2935 6936 3.104766 CGCAGATGCATGGGTCAC 58.895 61.111 2.46 0.00 42.21 3.67
2936 6937 2.825387 GCGCAGATGCATGGGTCA 60.825 61.111 2.46 0.00 42.21 4.02
2937 6938 3.945434 CGCGCAGATGCATGGGTC 61.945 66.667 2.46 0.00 42.21 4.46
2941 6942 2.951315 CTAGCCGCGCAGATGCATG 61.951 63.158 2.46 0.00 42.21 4.06
2942 6943 2.664185 CTAGCCGCGCAGATGCAT 60.664 61.111 8.75 0.00 42.21 3.96
2943 6944 4.147449 ACTAGCCGCGCAGATGCA 62.147 61.111 8.75 0.00 42.21 3.96
2944 6945 3.333969 GACTAGCCGCGCAGATGC 61.334 66.667 8.75 3.90 37.78 3.91
2945 6946 0.807667 AAAGACTAGCCGCGCAGATG 60.808 55.000 8.75 0.00 0.00 2.90
2946 6947 0.108138 AAAAGACTAGCCGCGCAGAT 60.108 50.000 8.75 0.00 0.00 2.90
2947 6948 0.320421 AAAAAGACTAGCCGCGCAGA 60.320 50.000 8.75 0.00 0.00 4.26
2948 6949 2.162716 AAAAAGACTAGCCGCGCAG 58.837 52.632 8.75 0.00 0.00 5.18
2949 6950 4.371975 AAAAAGACTAGCCGCGCA 57.628 50.000 8.75 0.00 0.00 6.09
2963 6964 6.421202 GTGGGCGTTAACATTTGTGATAAAAA 59.579 34.615 6.39 0.00 0.00 1.94
2964 6965 5.921408 GTGGGCGTTAACATTTGTGATAAAA 59.079 36.000 6.39 0.00 0.00 1.52
2965 6966 5.009710 TGTGGGCGTTAACATTTGTGATAAA 59.990 36.000 6.39 0.00 0.00 1.40
2966 6967 4.519350 TGTGGGCGTTAACATTTGTGATAA 59.481 37.500 6.39 0.00 0.00 1.75
2967 6968 4.072839 TGTGGGCGTTAACATTTGTGATA 58.927 39.130 6.39 0.00 0.00 2.15
2968 6969 2.887783 TGTGGGCGTTAACATTTGTGAT 59.112 40.909 6.39 0.00 0.00 3.06
2969 6970 2.033550 GTGTGGGCGTTAACATTTGTGA 59.966 45.455 6.39 0.00 0.00 3.58
2970 6971 2.389998 GTGTGGGCGTTAACATTTGTG 58.610 47.619 6.39 0.00 0.00 3.33
2971 6972 1.002251 CGTGTGGGCGTTAACATTTGT 60.002 47.619 6.39 0.00 0.00 2.83
2972 6973 1.680668 CGTGTGGGCGTTAACATTTG 58.319 50.000 6.39 0.00 0.00 2.32
2973 6974 0.039888 GCGTGTGGGCGTTAACATTT 60.040 50.000 6.39 0.00 0.00 2.32
2974 6975 1.577421 GCGTGTGGGCGTTAACATT 59.423 52.632 6.39 0.00 0.00 2.71
2975 6976 3.259930 GCGTGTGGGCGTTAACAT 58.740 55.556 6.39 0.00 0.00 2.71
2986 6987 4.354212 CTTCGTGCCACGCGTGTG 62.354 66.667 34.81 26.49 46.00 3.82
2991 6992 3.254014 ATGTTGCTTCGTGCCACGC 62.254 57.895 13.39 0.00 42.21 5.34
2992 6993 1.440850 CATGTTGCTTCGTGCCACG 60.441 57.895 11.80 11.80 44.19 4.94
2993 6994 1.081242 CCATGTTGCTTCGTGCCAC 60.081 57.895 0.00 0.00 42.00 5.01
2994 6995 2.918345 GCCATGTTGCTTCGTGCCA 61.918 57.895 0.00 0.00 42.00 4.92
2995 6996 2.126346 GCCATGTTGCTTCGTGCC 60.126 61.111 0.00 0.00 42.00 5.01
2996 6997 2.126346 GGCCATGTTGCTTCGTGC 60.126 61.111 0.00 0.00 43.25 5.34
2997 6998 1.804396 TTGGGCCATGTTGCTTCGTG 61.804 55.000 7.26 0.00 0.00 4.35
2998 6999 1.530419 TTGGGCCATGTTGCTTCGT 60.530 52.632 7.26 0.00 0.00 3.85
2999 7000 1.080569 GTTGGGCCATGTTGCTTCG 60.081 57.895 7.26 0.00 0.00 3.79
3000 7001 1.293179 GGTTGGGCCATGTTGCTTC 59.707 57.895 7.26 0.00 37.17 3.86
3001 7002 2.216331 GGGTTGGGCCATGTTGCTT 61.216 57.895 7.26 0.00 39.65 3.91
3002 7003 2.604382 GGGTTGGGCCATGTTGCT 60.604 61.111 7.26 0.00 39.65 3.91
3003 7004 3.705289 GGGGTTGGGCCATGTTGC 61.705 66.667 7.26 0.00 39.65 4.17
3004 7005 3.381136 CGGGGTTGGGCCATGTTG 61.381 66.667 7.26 0.00 39.65 3.33
3005 7006 4.694987 CCGGGGTTGGGCCATGTT 62.695 66.667 7.26 0.00 39.65 2.71
3007 7008 2.976494 GATACCGGGGTTGGGCCATG 62.976 65.000 7.26 0.00 39.65 3.66
3008 7009 2.698406 ATACCGGGGTTGGGCCAT 60.698 61.111 7.26 0.00 39.65 4.40
3009 7010 3.413300 GATACCGGGGTTGGGCCA 61.413 66.667 6.32 0.00 39.65 5.36
3010 7011 2.292785 AATGATACCGGGGTTGGGCC 62.293 60.000 6.32 0.00 0.00 5.80
3011 7012 1.229076 AATGATACCGGGGTTGGGC 59.771 57.895 6.32 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.