Multiple sequence alignment - TraesCS4B01G051600

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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 TraesCS4B01G051600 chr4B 100.000 4360 0 0 1 4360 40237605 40233246 0.000000e+00 8052.0
1 TraesCS4B01G051600 chr4B 88.364 1461 82 40 2935 4348 40437506 40438925 0.000000e+00 1676.0
2 TraesCS4B01G051600 chr4B 83.312 767 75 21 3580 4322 40419655 40420392 0.000000e+00 658.0
3 TraesCS4B01G051600 chr4B 90.449 178 17 0 1792 1969 10860707 10860530 7.290000e-58 235.0
4 TraesCS4B01G051600 chr4B 88.636 132 14 1 1838 1969 120130426 120130296 4.510000e-35 159.0
5 TraesCS4B01G051600 chr4B 100.000 28 0 0 2487 2514 10860487 10860460 8.000000e-03 52.8
6 TraesCS4B01G051600 chr4B 100.000 28 0 0 2487 2514 120130253 120130226 8.000000e-03 52.8
7 TraesCS4B01G051600 chr4A 88.252 2060 140 52 2358 4359 575736466 575734451 0.000000e+00 2370.0
8 TraesCS4B01G051600 chr4A 88.409 1760 112 38 440 2158 575738349 575736641 0.000000e+00 2036.0
9 TraesCS4B01G051600 chr4A 90.860 186 16 1 1789 1974 743708699 743708883 9.360000e-62 248.0
10 TraesCS4B01G051600 chr4A 77.985 268 29 17 17 266 575738729 575738474 1.630000e-29 141.0
11 TraesCS4B01G051600 chr4D 87.321 1885 119 39 2403 4238 27560557 27562370 0.000000e+00 2047.0
12 TraesCS4B01G051600 chr4D 85.475 1673 141 41 532 2165 27558854 27560463 0.000000e+00 1650.0
13 TraesCS4B01G051600 chr4D 86.643 569 27 20 1 531 27558232 27558789 6.280000e-163 584.0
14 TraesCS4B01G051600 chr4D 82.365 499 32 14 3743 4210 27562944 27563417 2.460000e-102 383.0
15 TraesCS4B01G051600 chr4D 84.000 100 14 2 2778 2876 28243934 28243836 1.290000e-15 95.3
16 TraesCS4B01G051600 chr4D 92.500 40 2 1 2411 2450 28253860 28253822 6.090000e-04 56.5
17 TraesCS4B01G051600 chr2B 87.237 619 47 12 1304 1914 69350474 69351068 0.000000e+00 676.0
18 TraesCS4B01G051600 chr2B 90.710 183 16 1 1792 1974 201242790 201242609 4.360000e-60 243.0
19 TraesCS4B01G051600 chr2B 91.209 91 8 0 2068 2158 69351239 69351329 1.650000e-24 124.0
20 TraesCS4B01G051600 chr1B 83.033 389 29 11 1789 2165 2839126 2839489 7.040000e-83 318.0
21 TraesCS4B01G051600 chr1B 90.710 183 16 1 1792 1974 627870708 627870527 4.360000e-60 243.0
22 TraesCS4B01G051600 chr1B 90.323 186 17 1 1789 1974 677582201 677582385 4.360000e-60 243.0
23 TraesCS4B01G051600 chr1B 98.462 65 1 0 2450 2514 2839674 2839738 9.910000e-22 115.0
24 TraesCS4B01G051600 chr1B 100.000 28 0 0 2487 2514 15263085 15263112 8.000000e-03 52.8
25 TraesCS4B01G051600 chr1B 100.000 28 0 0 2487 2514 609698222 609698249 8.000000e-03 52.8
26 TraesCS4B01G051600 chr7B 95.783 166 7 0 2213 2378 728967355 728967520 7.190000e-68 268.0
27 TraesCS4B01G051600 chr7B 94.220 173 9 1 2214 2386 712514073 712514244 3.340000e-66 263.0
28 TraesCS4B01G051600 chr7B 90.860 186 16 1 1789 1974 742023430 742023614 9.360000e-62 248.0
29 TraesCS4B01G051600 chr5B 95.783 166 7 0 2214 2379 441127871 441127706 7.190000e-68 268.0
30 TraesCS4B01G051600 chr5B 90.055 181 18 0 1789 1969 453110950 453111130 7.290000e-58 235.0
31 TraesCS4B01G051600 chr5B 89.888 178 18 0 1792 1969 667221873 667221696 3.390000e-56 230.0
32 TraesCS4B01G051600 chr5B 88.550 131 14 1 1839 1969 237663687 237663816 1.620000e-34 158.0
33 TraesCS4B01G051600 chr5B 87.879 132 15 1 1838 1969 105174895 105175025 2.100000e-33 154.0
34 TraesCS4B01G051600 chr5B 100.000 28 0 0 2487 2514 453111173 453111200 8.000000e-03 52.8
35 TraesCS4B01G051600 chr5B 100.000 28 0 0 2487 2514 500099357 500099384 8.000000e-03 52.8
36 TraesCS4B01G051600 chr6B 93.296 179 10 2 2203 2379 47282676 47282854 3.340000e-66 263.0
37 TraesCS4B01G051600 chr6B 90.710 183 16 1 1792 1974 659283116 659282935 4.360000e-60 243.0
38 TraesCS4B01G051600 chr1D 93.064 173 10 2 2209 2381 490423320 490423150 7.240000e-63 252.0
39 TraesCS4B01G051600 chr2A 91.758 182 11 4 2207 2386 753655286 753655465 2.600000e-62 250.0
40 TraesCS4B01G051600 chr5D 91.667 180 13 2 2207 2386 66671954 66671777 9.360000e-62 248.0
41 TraesCS4B01G051600 chr3A 91.667 180 12 3 2208 2387 12424433 12424257 3.370000e-61 246.0
42 TraesCS4B01G051600 chr5A 90.052 191 14 5 2210 2397 493338459 493338647 4.360000e-60 243.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G051600 chr4B 40233246 40237605 4359 True 8052.000000 8052 100.0000 1 4360 1 chr4B.!!$R1 4359
1 TraesCS4B01G051600 chr4B 40437506 40438925 1419 False 1676.000000 1676 88.3640 2935 4348 1 chr4B.!!$F2 1413
2 TraesCS4B01G051600 chr4B 40419655 40420392 737 False 658.000000 658 83.3120 3580 4322 1 chr4B.!!$F1 742
3 TraesCS4B01G051600 chr4A 575734451 575738729 4278 True 1515.666667 2370 84.8820 17 4359 3 chr4A.!!$R1 4342
4 TraesCS4B01G051600 chr4D 27558232 27563417 5185 False 1166.000000 2047 85.4510 1 4238 4 chr4D.!!$F1 4237
5 TraesCS4B01G051600 chr2B 69350474 69351329 855 False 400.000000 676 89.2230 1304 2158 2 chr2B.!!$F1 854
6 TraesCS4B01G051600 chr1B 2839126 2839738 612 False 216.500000 318 90.7475 1789 2514 2 chr1B.!!$F4 725

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
698 832 1.138671 GAGAGAGAGCAGCGACACC 59.861 63.158 0.0 0.0 0.0 4.16 F
981 1144 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.0 0.0 0.0 3.69 F
1672 1854 0.249120 ATGATCACCTGGCGAAACGA 59.751 50.000 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1842 0.179225 CGTTCAATCGTTTCGCCAGG 60.179 55.0 0.00 0.0 0.00 4.45 R
2978 3378 0.032267 GGTACCTCGGTGCTATCAGC 59.968 60.0 4.06 0.0 42.82 4.26 R
3631 4065 0.976641 TGGGAACAGAGCAATCTCGT 59.023 50.0 0.00 0.0 44.02 4.18 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
73 78 3.618690 ACAAGGCCTGTTCATAGAGTC 57.381 47.619 5.69 0.00 32.99 3.36
91 104 4.814294 GCCACGACCACGCCTAGG 62.814 72.222 3.67 3.67 43.96 3.02
103 116 4.972875 CCTAGGGCAAGAGCAAGG 57.027 61.111 0.00 0.00 44.61 3.61
110 123 2.694760 GCAAGAGCAAGGGAAGCGG 61.695 63.158 0.00 0.00 41.58 5.52
131 161 1.215014 GCAAAGCAAGAAACACCGCC 61.215 55.000 0.00 0.00 0.00 6.13
135 165 3.283684 CAAGAAACACCGCCCGCA 61.284 61.111 0.00 0.00 0.00 5.69
157 187 1.807495 CGCCTCCCTCGACCTTATCC 61.807 65.000 0.00 0.00 0.00 2.59
191 227 1.895231 GTTCACCGGCCGTCCTTTT 60.895 57.895 26.12 0.00 0.00 2.27
272 308 2.355209 GCTCTCCCGAATTTTCCAGACT 60.355 50.000 0.00 0.00 0.00 3.24
303 349 2.600475 CGTCCGTCCGTTTGTTGGG 61.600 63.158 0.00 0.00 0.00 4.12
324 382 4.016706 CTCCCCCACCACCACGAC 62.017 72.222 0.00 0.00 0.00 4.34
575 701 1.153329 TATAAAGCACACGCCCCGG 60.153 57.895 0.00 0.00 39.83 5.73
688 822 4.096255 TCGTCGAGCGAGAGAGAG 57.904 61.111 6.09 0.00 45.68 3.20
689 823 2.168503 TCGTCGAGCGAGAGAGAGC 61.169 63.158 6.09 0.00 45.68 4.09
690 824 2.456948 CGTCGAGCGAGAGAGAGCA 61.457 63.158 0.00 0.00 44.77 4.26
692 826 2.024588 CGAGCGAGAGAGAGCAGC 59.975 66.667 0.00 0.00 35.48 5.25
693 827 2.024588 GAGCGAGAGAGAGCAGCG 59.975 66.667 0.00 0.00 35.48 5.18
694 828 2.437537 AGCGAGAGAGAGCAGCGA 60.438 61.111 0.00 0.00 35.48 4.93
695 829 2.277884 GCGAGAGAGAGCAGCGAC 60.278 66.667 0.00 0.00 0.00 5.19
696 830 3.045277 GCGAGAGAGAGCAGCGACA 62.045 63.158 0.00 0.00 0.00 4.35
697 831 1.226267 CGAGAGAGAGCAGCGACAC 60.226 63.158 0.00 0.00 0.00 3.67
698 832 1.138671 GAGAGAGAGCAGCGACACC 59.861 63.158 0.00 0.00 0.00 4.16
772 906 4.174411 CGAAAGACGGCAGGATATATCA 57.826 45.455 14.60 0.00 38.46 2.15
773 907 4.748892 CGAAAGACGGCAGGATATATCAT 58.251 43.478 14.60 4.42 38.46 2.45
774 908 5.891451 CGAAAGACGGCAGGATATATCATA 58.109 41.667 14.60 0.00 38.46 2.15
775 909 5.974158 CGAAAGACGGCAGGATATATCATAG 59.026 44.000 14.60 5.33 38.46 2.23
776 910 4.927978 AGACGGCAGGATATATCATAGC 57.072 45.455 14.60 13.29 0.00 2.97
777 911 4.541705 AGACGGCAGGATATATCATAGCT 58.458 43.478 14.60 0.00 0.00 3.32
778 912 4.340666 AGACGGCAGGATATATCATAGCTG 59.659 45.833 21.13 21.13 31.88 4.24
779 913 3.181471 ACGGCAGGATATATCATAGCTGC 60.181 47.826 23.15 23.15 37.52 5.25
781 915 4.378774 GGCAGGATATATCATAGCTGCTG 58.621 47.826 26.85 18.30 38.00 4.41
782 916 4.100653 GGCAGGATATATCATAGCTGCTGA 59.899 45.833 26.85 2.86 38.00 4.26
783 917 5.221682 GGCAGGATATATCATAGCTGCTGAT 60.222 44.000 26.85 10.84 38.00 2.90
784 918 6.014755 GGCAGGATATATCATAGCTGCTGATA 60.015 42.308 26.85 17.93 38.00 2.15
785 919 7.092079 GCAGGATATATCATAGCTGCTGATAG 58.908 42.308 23.59 10.40 38.59 2.08
786 920 7.092079 CAGGATATATCATAGCTGCTGATAGC 58.908 42.308 13.43 13.54 44.01 2.97
825 976 5.531122 TTCTGTTCCGGAATAGATTCGAT 57.469 39.130 35.27 0.00 38.15 3.59
826 977 5.531122 TCTGTTCCGGAATAGATTCGATT 57.469 39.130 32.62 0.00 37.67 3.34
832 983 5.081728 TCCGGAATAGATTCGATTCCCTTA 58.918 41.667 24.40 12.61 46.63 2.69
833 984 5.541101 TCCGGAATAGATTCGATTCCCTTAA 59.459 40.000 24.40 10.78 46.63 1.85
853 1004 2.125673 ATTCTTGCGGTCGGTCGG 60.126 61.111 1.10 0.00 0.00 4.79
895 1046 1.951631 GATCGTTGCTAGCCCGAGC 60.952 63.158 24.65 22.93 43.16 5.03
914 1065 1.441016 GCTTTTGTTGGAGCGAGCG 60.441 57.895 0.00 0.00 0.00 5.03
916 1067 2.786564 CTTTTGTTGGAGCGAGCGCC 62.787 60.000 11.66 10.95 43.17 6.53
917 1068 4.617520 TTGTTGGAGCGAGCGCCA 62.618 61.111 16.33 16.33 43.94 5.69
919 1070 4.742201 GTTGGAGCGAGCGCCAGA 62.742 66.667 19.05 9.09 46.01 3.86
946 1109 2.974698 GTGCCTTGTGCGTCTGCT 60.975 61.111 0.00 0.00 45.60 4.24
947 1110 2.974148 TGCCTTGTGCGTCTGCTG 60.974 61.111 0.00 0.00 45.60 4.41
950 1113 3.730761 CTTGTGCGTCTGCTGCCC 61.731 66.667 0.00 0.00 43.34 5.36
977 1140 3.024356 AGCCGAGGAGGAGGAGGA 61.024 66.667 0.00 0.00 45.00 3.71
978 1141 2.520741 GCCGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 45.00 3.69
979 1142 2.197324 CCGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 45.00 4.30
980 1143 2.387772 CCGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 45.00 3.71
981 1144 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
982 1145 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1381 1556 4.824515 ACGCCTCCTCCTCCTCCG 62.825 72.222 0.00 0.00 0.00 4.63
1407 1582 1.912862 AGCCCAGGTAGGAATCCATT 58.087 50.000 0.61 0.00 41.22 3.16
1411 1586 3.627237 GCCCAGGTAGGAATCCATTCAAA 60.627 47.826 0.61 0.00 41.22 2.69
1412 1587 4.609301 CCCAGGTAGGAATCCATTCAAAA 58.391 43.478 0.61 0.00 41.22 2.44
1440 1615 3.452474 TCCACGCAAAATTTGTCCTTTG 58.548 40.909 7.60 0.00 0.00 2.77
1480 1656 1.265635 GTTGTTGCCGTGCTGATTGTA 59.734 47.619 0.00 0.00 0.00 2.41
1567 1743 2.236395 TGAGAATTCGGTTCCCTTCCTC 59.764 50.000 0.00 0.00 37.56 3.71
1576 1752 2.108425 GGTTCCCTTCCTCCTCTGTTTT 59.892 50.000 0.00 0.00 0.00 2.43
1578 1754 3.790089 TCCCTTCCTCCTCTGTTTTTC 57.210 47.619 0.00 0.00 0.00 2.29
1579 1755 3.327439 TCCCTTCCTCCTCTGTTTTTCT 58.673 45.455 0.00 0.00 0.00 2.52
1580 1756 3.722101 TCCCTTCCTCCTCTGTTTTTCTT 59.278 43.478 0.00 0.00 0.00 2.52
1660 1842 1.202698 GGCAGTGGGAGGTATGATCAC 60.203 57.143 0.00 0.00 0.00 3.06
1672 1854 0.249120 ATGATCACCTGGCGAAACGA 59.751 50.000 0.00 0.00 0.00 3.85
1699 1881 2.097466 CGCCATGGATGTCAAGGTTTAC 59.903 50.000 18.40 0.00 36.64 2.01
1742 1924 6.768381 TGAGTTTCTCTTTCCTTTTTCCTCTC 59.232 38.462 0.00 0.00 0.00 3.20
1747 1929 7.142995 TCTCTTTCCTTTTTCCTCTCTTCTT 57.857 36.000 0.00 0.00 0.00 2.52
1774 1959 5.412640 TCATTTTGGTTGCATGATGCTTAG 58.587 37.500 19.19 0.00 45.31 2.18
1777 1962 4.963276 TTGGTTGCATGATGCTTAGTAC 57.037 40.909 19.19 8.45 45.31 2.73
1779 1964 2.936498 GGTTGCATGATGCTTAGTACGT 59.064 45.455 19.19 0.00 45.31 3.57
1780 1965 4.116961 GGTTGCATGATGCTTAGTACGTA 58.883 43.478 19.19 0.00 45.31 3.57
1783 1968 6.128902 GGTTGCATGATGCTTAGTACGTATAC 60.129 42.308 19.19 0.00 45.31 1.47
1786 1971 5.628193 GCATGATGCTTAGTACGTATACGTT 59.372 40.000 33.47 20.25 45.03 3.99
1787 1972 6.798476 GCATGATGCTTAGTACGTATACGTTA 59.202 38.462 33.47 19.22 45.03 3.18
1830 2015 7.397892 TGACGGAAAATATTGAAGGCAATTA 57.602 32.000 0.00 0.00 41.87 1.40
1861 2052 7.624360 TGAATTGCGTATAAAAGAGACCAAT 57.376 32.000 0.00 0.00 0.00 3.16
1891 2082 7.091533 TGAATTCTCTTCTAAGTTTCCCCTT 57.908 36.000 7.05 0.00 0.00 3.95
1918 2109 7.920738 ACTGAATGAATTAAGGCGATTTACTC 58.079 34.615 0.00 0.00 0.00 2.59
1935 2126 6.525121 TTTACTCGTGAATCTGAACACTTG 57.475 37.500 13.45 9.55 35.23 3.16
1952 2143 2.295885 CTTGAGGGATTGGATGAGTGC 58.704 52.381 0.00 0.00 0.00 4.40
1969 2160 7.201565 GGATGAGTGCTACATACTCTGTTTTTC 60.202 40.741 0.00 0.00 43.79 2.29
1970 2161 6.759272 TGAGTGCTACATACTCTGTTTTTCT 58.241 36.000 0.00 0.00 43.79 2.52
1971 2162 6.646653 TGAGTGCTACATACTCTGTTTTTCTG 59.353 38.462 0.00 0.00 43.79 3.02
1976 2184 7.715249 TGCTACATACTCTGTTTTTCTGTTCTT 59.285 33.333 0.00 0.00 39.39 2.52
1977 2185 8.224437 GCTACATACTCTGTTTTTCTGTTCTTC 58.776 37.037 0.00 0.00 39.39 2.87
1978 2186 7.178712 ACATACTCTGTTTTTCTGTTCTTCG 57.821 36.000 0.00 0.00 32.90 3.79
1979 2187 6.984474 ACATACTCTGTTTTTCTGTTCTTCGA 59.016 34.615 0.00 0.00 32.90 3.71
1980 2188 7.494625 ACATACTCTGTTTTTCTGTTCTTCGAA 59.505 33.333 0.00 0.00 32.90 3.71
1981 2189 6.108097 ACTCTGTTTTTCTGTTCTTCGAAC 57.892 37.500 0.00 0.00 0.00 3.95
1982 2190 5.138800 TCTGTTTTTCTGTTCTTCGAACG 57.861 39.130 0.00 0.00 0.00 3.95
1983 2191 4.865925 TCTGTTTTTCTGTTCTTCGAACGA 59.134 37.500 0.00 0.00 0.00 3.85
1984 2192 5.522460 TCTGTTTTTCTGTTCTTCGAACGAT 59.478 36.000 0.00 0.00 0.00 3.73
1985 2193 6.036735 TCTGTTTTTCTGTTCTTCGAACGATT 59.963 34.615 0.00 0.00 0.00 3.34
1986 2194 6.548171 TGTTTTTCTGTTCTTCGAACGATTT 58.452 32.000 0.00 0.00 0.00 2.17
1987 2195 6.467682 TGTTTTTCTGTTCTTCGAACGATTTG 59.532 34.615 0.00 0.00 0.00 2.32
1988 2196 5.728351 TTTCTGTTCTTCGAACGATTTGT 57.272 34.783 0.00 0.00 0.00 2.83
1989 2197 6.831727 TTTCTGTTCTTCGAACGATTTGTA 57.168 33.333 0.00 0.00 0.00 2.41
1990 2198 6.448053 TTCTGTTCTTCGAACGATTTGTAG 57.552 37.500 0.00 0.00 0.00 2.74
1991 2199 5.526115 TCTGTTCTTCGAACGATTTGTAGT 58.474 37.500 0.00 0.00 0.00 2.73
1992 2200 6.671190 TCTGTTCTTCGAACGATTTGTAGTA 58.329 36.000 0.00 0.00 0.00 1.82
1993 2201 6.580041 TCTGTTCTTCGAACGATTTGTAGTAC 59.420 38.462 0.00 0.00 0.00 2.73
2066 2274 7.461156 CGTCGACAGTTAAGTATAGTTCTTTGC 60.461 40.741 17.16 0.00 0.00 3.68
2088 2355 5.163468 TGCCAATCAAGCTGTCAACTTAAAA 60.163 36.000 0.00 0.00 0.00 1.52
2142 2409 9.852091 ACTCTGAAGATCAATAAAAATTTCTGC 57.148 29.630 0.00 0.00 0.00 4.26
2171 2494 2.689983 CAGCCAATGGTTACCATCTTCC 59.310 50.000 18.03 6.74 44.40 3.46
2175 2498 4.892934 GCCAATGGTTACCATCTTCCATAA 59.107 41.667 18.03 0.00 44.40 1.90
2177 2500 5.301805 CCAATGGTTACCATCTTCCATAACC 59.698 44.000 18.03 5.28 44.40 2.85
2228 2581 5.998128 ACTATACTACTCCCTCTGTTCCT 57.002 43.478 0.00 0.00 0.00 3.36
2235 2588 9.900112 ATACTACTCCCTCTGTTCCTAAATATT 57.100 33.333 0.00 0.00 0.00 1.28
2238 2591 7.272144 ACTCCCTCTGTTCCTAAATATTTGT 57.728 36.000 11.05 0.00 0.00 2.83
2241 2594 7.928873 TCCCTCTGTTCCTAAATATTTGTCTT 58.071 34.615 11.05 0.00 0.00 3.01
2242 2595 8.390921 TCCCTCTGTTCCTAAATATTTGTCTTT 58.609 33.333 11.05 0.00 0.00 2.52
2243 2596 9.025041 CCCTCTGTTCCTAAATATTTGTCTTTT 57.975 33.333 11.05 0.00 0.00 2.27
2264 2617 9.921637 TCTTTTTAAACATTTCAACAAGTGACT 57.078 25.926 0.00 0.00 35.39 3.41
2273 2626 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2274 2627 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2275 2628 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2276 2629 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2277 2630 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2278 2631 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2279 2632 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2280 2633 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2281 2634 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2282 2635 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2283 2636 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2284 2637 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2285 2638 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2286 2639 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2287 2640 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2288 2641 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2289 2642 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2290 2643 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2291 2644 4.074970 ACGGAGCAAAATGAGTGAATCTT 58.925 39.130 0.00 0.00 0.00 2.40
2292 2645 4.154918 ACGGAGCAAAATGAGTGAATCTTC 59.845 41.667 0.00 0.00 0.00 2.87
2293 2646 4.154737 CGGAGCAAAATGAGTGAATCTTCA 59.845 41.667 0.00 0.00 34.20 3.02
2308 2661 7.910304 GTGAATCTTCACGCTAAAATATGTCT 58.090 34.615 7.27 0.00 46.80 3.41
2309 2662 9.031360 GTGAATCTTCACGCTAAAATATGTCTA 57.969 33.333 7.27 0.00 46.80 2.59
2310 2663 9.031360 TGAATCTTCACGCTAAAATATGTCTAC 57.969 33.333 0.00 0.00 31.01 2.59
2311 2664 8.942338 AATCTTCACGCTAAAATATGTCTACA 57.058 30.769 0.00 0.00 0.00 2.74
2312 2665 9.547753 AATCTTCACGCTAAAATATGTCTACAT 57.452 29.630 0.63 0.63 40.22 2.29
2314 2667 9.459640 TCTTCACGCTAAAATATGTCTACATAC 57.540 33.333 4.98 0.00 41.15 2.39
2315 2668 7.847166 TCACGCTAAAATATGTCTACATACG 57.153 36.000 4.98 6.10 41.15 3.06
2316 2669 6.859508 TCACGCTAAAATATGTCTACATACGG 59.140 38.462 4.98 0.13 41.15 4.02
2317 2670 6.859508 CACGCTAAAATATGTCTACATACGGA 59.140 38.462 4.98 0.00 41.15 4.69
2318 2671 7.541091 CACGCTAAAATATGTCTACATACGGAT 59.459 37.037 4.98 0.00 41.15 4.18
2319 2672 7.541091 ACGCTAAAATATGTCTACATACGGATG 59.459 37.037 5.94 5.94 41.15 3.51
2321 2674 9.850628 GCTAAAATATGTCTACATACGGATGTA 57.149 33.333 19.32 19.32 44.77 2.29
2336 2689 6.726490 ACGGATGTATGTAGTAGTCCATTT 57.274 37.500 0.00 0.00 0.00 2.32
2337 2690 6.513180 ACGGATGTATGTAGTAGTCCATTTG 58.487 40.000 0.00 0.00 0.00 2.32
2338 2691 6.322969 ACGGATGTATGTAGTAGTCCATTTGA 59.677 38.462 0.00 0.00 0.00 2.69
2339 2692 7.147794 ACGGATGTATGTAGTAGTCCATTTGAA 60.148 37.037 0.00 0.00 0.00 2.69
2340 2693 7.709182 CGGATGTATGTAGTAGTCCATTTGAAA 59.291 37.037 0.00 0.00 0.00 2.69
2341 2694 9.561069 GGATGTATGTAGTAGTCCATTTGAAAT 57.439 33.333 0.00 0.00 0.00 2.17
2343 2696 9.905713 ATGTATGTAGTAGTCCATTTGAAATGT 57.094 29.630 15.93 1.43 0.00 2.71
2344 2697 9.378551 TGTATGTAGTAGTCCATTTGAAATGTC 57.621 33.333 15.93 9.10 0.00 3.06
2345 2698 9.601217 GTATGTAGTAGTCCATTTGAAATGTCT 57.399 33.333 15.93 14.81 0.00 3.41
2347 2700 9.823647 ATGTAGTAGTCCATTTGAAATGTCTAG 57.176 33.333 15.93 1.90 0.00 2.43
2348 2701 9.031537 TGTAGTAGTCCATTTGAAATGTCTAGA 57.968 33.333 15.93 4.16 0.00 2.43
2349 2702 9.871238 GTAGTAGTCCATTTGAAATGTCTAGAA 57.129 33.333 15.93 7.10 0.00 2.10
2351 2704 9.442047 AGTAGTCCATTTGAAATGTCTAGAAAG 57.558 33.333 15.93 0.00 0.00 2.62
2352 2705 9.436957 GTAGTCCATTTGAAATGTCTAGAAAGA 57.563 33.333 15.93 1.84 0.00 2.52
2389 2742 5.452255 ACGGAGGGAGTACATGAGTATAAA 58.548 41.667 0.00 0.00 31.84 1.40
2470 2854 2.505407 CCATGGTGGAAGTGATGGTCTA 59.495 50.000 2.57 0.00 40.96 2.59
2529 2913 5.954150 AGGACATGGTATGAGCAAAGAAATT 59.046 36.000 0.00 0.00 0.00 1.82
2538 2922 8.178313 GGTATGAGCAAAGAAATTGACTAGTTC 58.822 37.037 0.00 0.00 41.85 3.01
2542 2926 7.041098 TGAGCAAAGAAATTGACTAGTTCTTCC 60.041 37.037 11.66 7.30 39.97 3.46
2587 2974 8.344831 GCACAAATTCTTATTCAAAGGCTTTTT 58.655 29.630 10.36 0.96 0.00 1.94
2695 3084 1.771255 AGGCATCATCCTCAAGGTACC 59.229 52.381 2.73 2.73 36.34 3.34
2755 3148 8.742554 TGTGTATGCAACTCGTATATCTTATG 57.257 34.615 0.00 0.00 0.00 1.90
2762 3155 6.145696 GCAACTCGTATATCTTATGGTGTTCC 59.854 42.308 0.00 0.00 0.00 3.62
2764 3157 7.216973 ACTCGTATATCTTATGGTGTTCCTC 57.783 40.000 0.00 0.00 34.23 3.71
2877 3270 2.954868 CTGTCGTCGCGGTATGCC 60.955 66.667 6.13 0.00 42.08 4.40
2878 3271 3.693382 CTGTCGTCGCGGTATGCCA 62.693 63.158 6.13 0.00 42.08 4.92
2880 3273 3.750155 TCGTCGCGGTATGCCACA 61.750 61.111 6.13 0.00 42.08 4.17
2882 3275 2.125673 GTCGCGGTATGCCACAGT 60.126 61.111 6.13 0.00 42.08 3.55
2889 3285 2.544903 GCGGTATGCCACAGTTTTTGTT 60.545 45.455 0.00 0.00 38.16 2.83
2902 3298 6.737750 CACAGTTTTTGTTGAAAGAAATGCAC 59.262 34.615 0.00 0.00 38.16 4.57
2904 3300 6.737750 CAGTTTTTGTTGAAAGAAATGCACAC 59.262 34.615 0.00 0.00 0.00 3.82
2922 3318 4.261741 GCACACCAACATCTTCAGAAACAT 60.262 41.667 0.00 0.00 0.00 2.71
2925 3321 7.246311 CACACCAACATCTTCAGAAACATATC 58.754 38.462 0.00 0.00 0.00 1.63
2926 3322 6.942005 ACACCAACATCTTCAGAAACATATCA 59.058 34.615 0.00 0.00 0.00 2.15
2927 3323 7.448161 ACACCAACATCTTCAGAAACATATCAA 59.552 33.333 0.00 0.00 0.00 2.57
2978 3378 4.398598 CTTGCCCCGGTTTTCGCG 62.399 66.667 0.00 0.00 37.59 5.87
2987 3387 1.692148 CGGTTTTCGCGCTGATAGCA 61.692 55.000 5.56 0.00 42.58 3.49
2990 3390 1.692148 TTTTCGCGCTGATAGCACCG 61.692 55.000 5.56 3.48 42.58 4.94
2991 3391 2.551097 TTTCGCGCTGATAGCACCGA 62.551 55.000 5.56 8.75 42.58 4.69
3089 3489 4.619227 CCGCTGGTGTTCACGGGT 62.619 66.667 0.00 0.00 41.95 5.28
3323 3723 1.674057 CGAGAAGGAGGTGGTGCTT 59.326 57.895 0.00 0.00 40.07 3.91
3361 3765 1.143684 GCTCAGCCCCAGGATTTGATA 59.856 52.381 0.00 0.00 0.00 2.15
3404 3812 4.020617 CGTGGGCTGAGGCAGGAA 62.021 66.667 8.68 0.00 40.87 3.36
3409 3817 2.270527 GCTGAGGCAGGAAGGTCC 59.729 66.667 0.00 0.00 38.54 4.46
3460 3873 3.518552 AACCTCCGTCTGTCCCCGA 62.519 63.158 0.00 0.00 0.00 5.14
3462 3875 2.675423 CTCCGTCTGTCCCCGACA 60.675 66.667 0.00 0.00 40.50 4.35
3566 3991 4.673298 TTTGCGAGCGCGGGAAGA 62.673 61.111 12.86 0.00 45.51 2.87
3631 4065 2.504274 GGTGACGACTGGTGGTGGA 61.504 63.158 0.00 0.00 0.00 4.02
3645 4079 0.247736 GGTGGACGAGATTGCTCTGT 59.752 55.000 0.00 0.00 39.06 3.41
3835 4282 2.614057 ACGGCAGAATCGATTGATTTCC 59.386 45.455 16.96 8.19 44.79 3.13
3843 4290 7.490402 GCAGAATCGATTGATTTCCTTGAATTT 59.510 33.333 16.96 0.00 44.79 1.82
3845 4292 8.193438 AGAATCGATTGATTTCCTTGAATTTCC 58.807 33.333 16.96 0.00 44.79 3.13
3847 4294 7.466746 TCGATTGATTTCCTTGAATTTCCTT 57.533 32.000 0.00 0.00 0.00 3.36
3853 4300 4.871933 TTCCTTGAATTTCCTTGGCTTC 57.128 40.909 0.00 0.00 0.00 3.86
3858 4311 1.745653 GAATTTCCTTGGCTTCTCCCG 59.254 52.381 0.00 0.00 0.00 5.14
3871 4324 0.756294 TCTCCCGTGTCACAATGTGT 59.244 50.000 13.55 0.00 34.79 3.72
3894 4347 1.031029 TTGTGTTGCTCACTGCTGCA 61.031 50.000 0.88 0.88 46.27 4.41
3895 4348 1.281960 GTGTTGCTCACTGCTGCAG 59.718 57.895 27.02 27.02 43.13 4.41
3896 4349 1.146707 TGTTGCTCACTGCTGCAGA 59.853 52.632 34.28 13.74 43.37 4.26
3897 4350 1.162181 TGTTGCTCACTGCTGCAGAC 61.162 55.000 34.28 20.83 43.37 3.51
3898 4351 1.598962 TTGCTCACTGCTGCAGACC 60.599 57.895 34.28 18.49 43.37 3.85
3899 4352 3.117171 GCTCACTGCTGCAGACCG 61.117 66.667 34.28 21.15 38.95 4.79
3900 4353 2.433838 CTCACTGCTGCAGACCGG 60.434 66.667 34.28 19.61 35.18 5.28
3901 4354 4.687215 TCACTGCTGCAGACCGGC 62.687 66.667 34.28 2.17 46.38 6.13
3908 4361 4.007644 TGCAGACCGGCAGTGGAG 62.008 66.667 0.00 0.00 39.25 3.86
3910 4363 3.699894 CAGACCGGCAGTGGAGCT 61.700 66.667 0.00 0.00 34.17 4.09
3911 4364 2.925170 AGACCGGCAGTGGAGCTT 60.925 61.111 0.00 0.00 34.17 3.74
3912 4365 2.032681 GACCGGCAGTGGAGCTTT 59.967 61.111 0.00 0.00 34.17 3.51
3913 4366 1.600916 GACCGGCAGTGGAGCTTTT 60.601 57.895 0.00 0.00 34.17 2.27
3914 4367 1.856265 GACCGGCAGTGGAGCTTTTG 61.856 60.000 0.00 0.00 34.17 2.44
3915 4368 2.629656 CCGGCAGTGGAGCTTTTGG 61.630 63.158 0.00 0.00 34.17 3.28
3916 4369 2.653115 GGCAGTGGAGCTTTTGGC 59.347 61.111 0.00 0.00 42.19 4.52
4019 4493 1.209019 TCTCAGGATTTCTCTGGCTGC 59.791 52.381 0.00 0.00 33.36 5.25
4024 4498 1.065564 GGATTTCTCTGGCTGCACTCT 60.066 52.381 0.50 0.00 0.00 3.24
4025 4499 2.617532 GGATTTCTCTGGCTGCACTCTT 60.618 50.000 0.50 0.00 0.00 2.85
4067 4541 2.805353 CGACTGCTTCACGACGGG 60.805 66.667 0.00 0.00 0.00 5.28
4126 4626 1.298859 GCGGCCAAGAGTCGTGATTT 61.299 55.000 7.72 0.00 0.00 2.17
4129 4633 1.339151 GGCCAAGAGTCGTGATTTCCT 60.339 52.381 7.72 0.00 0.00 3.36
4189 4699 2.209690 TGTGTGAGGTCAGGTATCGA 57.790 50.000 0.00 0.00 0.00 3.59
4204 4714 3.004524 GGTATCGACATCGGCTAACTCTT 59.995 47.826 0.73 0.00 40.29 2.85
4238 4748 0.963962 GGTCGGCTATCGGGTATTGA 59.036 55.000 0.00 0.00 39.77 2.57
4239 4749 1.336609 GGTCGGCTATCGGGTATTGAC 60.337 57.143 0.00 0.00 39.77 3.18
4241 4751 1.611977 TCGGCTATCGGGTATTGACTG 59.388 52.381 0.00 0.00 39.77 3.51
4242 4752 1.336887 CGGCTATCGGGTATTGACTGG 60.337 57.143 0.00 0.00 34.75 4.00
4299 5047 3.228017 TGCCGTCCGTCCTTGTCA 61.228 61.111 0.00 0.00 0.00 3.58
4302 5050 1.080705 CCGTCCGTCCTTGTCAGAC 60.081 63.158 0.00 0.00 0.00 3.51
4305 5053 0.959553 GTCCGTCCTTGTCAGACTGA 59.040 55.000 0.00 0.00 31.83 3.41
4322 5073 2.559668 ACTGATTCAATGGCACCACAAG 59.440 45.455 0.00 0.00 0.00 3.16
4339 5090 6.795114 CACCACAAGTTATTACACGTTTGATC 59.205 38.462 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.778470 TTTGTGTTGGATTGGTAAACAAATC 57.222 32.000 2.12 2.12 43.46 2.17
91 104 2.694760 CGCTTCCCTTGCTCTTGCC 61.695 63.158 0.00 0.00 38.71 4.52
97 110 2.697147 TTTGCTCCGCTTCCCTTGCT 62.697 55.000 0.00 0.00 0.00 3.91
98 111 2.205243 CTTTGCTCCGCTTCCCTTGC 62.205 60.000 0.00 0.00 0.00 4.01
99 112 1.878775 CTTTGCTCCGCTTCCCTTG 59.121 57.895 0.00 0.00 0.00 3.61
100 113 1.973812 GCTTTGCTCCGCTTCCCTT 60.974 57.895 0.00 0.00 0.00 3.95
101 114 2.360475 GCTTTGCTCCGCTTCCCT 60.360 61.111 0.00 0.00 0.00 4.20
102 115 2.205243 CTTGCTTTGCTCCGCTTCCC 62.205 60.000 0.00 0.00 0.00 3.97
103 116 1.211190 CTTGCTTTGCTCCGCTTCC 59.789 57.895 0.00 0.00 0.00 3.46
110 123 1.758783 CGGTGTTTCTTGCTTTGCTC 58.241 50.000 0.00 0.00 0.00 4.26
121 151 3.810896 GGATGCGGGCGGTGTTTC 61.811 66.667 0.00 0.00 0.00 2.78
135 165 2.294170 TAAGGTCGAGGGAGGCGGAT 62.294 60.000 0.00 0.00 0.00 4.18
217 253 2.172659 GAGCGGCCGAACGTTTTC 59.827 61.111 33.48 8.41 35.98 2.29
228 264 3.771491 CATATGCGAGCGAGCGGC 61.771 66.667 7.11 7.11 40.67 6.53
229 265 3.771491 GCATATGCGAGCGAGCGG 61.771 66.667 12.82 0.00 40.67 5.52
303 349 2.856988 TGGTGGTGGGGGAGGAAC 60.857 66.667 0.00 0.00 0.00 3.62
365 428 0.738975 GCCGTCCCTTATCTTTTGGC 59.261 55.000 0.00 0.00 0.00 4.52
571 697 3.157949 GAGAAGGAGGGAGCCGGG 61.158 72.222 2.18 0.00 0.00 5.73
575 701 1.223211 GCTTGGAGAAGGAGGGAGC 59.777 63.158 0.00 0.00 0.00 4.70
577 703 0.473694 TGTGCTTGGAGAAGGAGGGA 60.474 55.000 0.00 0.00 28.76 4.20
579 705 1.882623 GTTTGTGCTTGGAGAAGGAGG 59.117 52.381 0.00 0.00 28.76 4.30
584 710 2.092429 AGTCTGGTTTGTGCTTGGAGAA 60.092 45.455 0.00 0.00 0.00 2.87
636 762 1.003355 ATTGCCTGTCCCGAGTGTG 60.003 57.895 0.00 0.00 0.00 3.82
716 850 4.873129 CGGACCGGATGCTCGTGG 62.873 72.222 9.46 0.00 0.00 4.94
775 909 2.371158 CGCGCTAGCTATCAGCAGC 61.371 63.158 13.93 9.83 45.56 5.25
776 910 0.109365 ATCGCGCTAGCTATCAGCAG 60.109 55.000 13.93 5.30 45.56 4.24
777 911 0.109551 GATCGCGCTAGCTATCAGCA 60.110 55.000 13.93 0.23 45.56 4.41
778 912 1.131037 CGATCGCGCTAGCTATCAGC 61.131 60.000 13.93 7.33 43.34 4.26
779 913 0.444260 TCGATCGCGCTAGCTATCAG 59.556 55.000 13.93 9.28 43.34 2.90
781 915 0.854037 CGTCGATCGCGCTAGCTATC 60.854 60.000 13.93 11.59 40.80 2.08
782 916 1.132844 CGTCGATCGCGCTAGCTAT 59.867 57.895 13.93 3.41 42.32 2.97
783 917 2.549778 CGTCGATCGCGCTAGCTA 59.450 61.111 13.93 0.00 42.32 3.32
805 956 4.686554 GGAATCGAATCTATTCCGGAACAG 59.313 45.833 21.56 18.96 42.14 3.16
825 976 2.224917 ACCGCAAGAATGGTTAAGGGAA 60.225 45.455 0.00 0.00 43.02 3.97
826 977 1.353022 ACCGCAAGAATGGTTAAGGGA 59.647 47.619 0.00 0.00 43.02 4.20
832 983 0.953960 GACCGACCGCAAGAATGGTT 60.954 55.000 0.00 0.00 38.99 3.67
833 984 1.375523 GACCGACCGCAAGAATGGT 60.376 57.895 0.00 0.00 42.42 3.55
853 1004 1.749063 CTAAAAATGGGCGAACCTCCC 59.251 52.381 0.00 0.00 44.17 4.30
930 1093 2.974148 CAGCAGACGCACAAGGCA 60.974 61.111 0.00 0.00 45.17 4.75
931 1094 4.395583 GCAGCAGACGCACAAGGC 62.396 66.667 0.00 0.00 42.27 4.35
1302 1471 1.101635 TGGGGATGAGCTCGTAGTCG 61.102 60.000 8.83 0.00 38.55 4.18
1381 1556 2.125106 CTACCTGGGCTTGACGGC 60.125 66.667 0.00 0.00 37.49 5.68
1411 1586 6.188400 ACAAATTTTGCGTGGATTTGTTTT 57.812 29.167 9.04 0.00 46.24 2.43
1412 1587 5.809719 ACAAATTTTGCGTGGATTTGTTT 57.190 30.435 9.04 0.00 46.24 2.83
1440 1615 3.607370 GAGGACACCCGGGCTGAAC 62.607 68.421 24.08 15.25 37.58 3.18
1598 1776 2.852495 AATCAGCTACCGGCCACACG 62.852 60.000 0.00 0.00 43.05 4.49
1660 1842 0.179225 CGTTCAATCGTTTCGCCAGG 60.179 55.000 0.00 0.00 0.00 4.45
1672 1854 2.127271 TGACATCCATGGCGTTCAAT 57.873 45.000 6.96 0.00 39.17 2.57
1699 1881 2.124983 CCAGTCCAGTCCATGCCG 60.125 66.667 0.00 0.00 0.00 5.69
1742 1924 8.537049 TCATGCAACCAAAATGAAATAAGAAG 57.463 30.769 0.00 0.00 0.00 2.85
1747 1929 6.665474 GCATCATGCAACCAAAATGAAATA 57.335 33.333 4.20 0.00 44.26 1.40
1777 1962 9.773670 CAATGTTAAGCACTAATAACGTATACG 57.226 33.333 23.24 23.24 46.33 3.06
1779 1964 9.537192 AGCAATGTTAAGCACTAATAACGTATA 57.463 29.630 0.00 0.00 35.30 1.47
1780 1965 8.433421 AGCAATGTTAAGCACTAATAACGTAT 57.567 30.769 0.00 0.00 35.30 3.06
1783 1968 7.216317 GTCAAGCAATGTTAAGCACTAATAACG 59.784 37.037 0.00 0.00 35.30 3.18
1786 1971 6.183360 CCGTCAAGCAATGTTAAGCACTAATA 60.183 38.462 0.00 0.00 0.00 0.98
1787 1972 5.391950 CCGTCAAGCAATGTTAAGCACTAAT 60.392 40.000 0.00 0.00 0.00 1.73
1861 2052 9.003658 GGAAACTTAGAAGAGAATTCAACATCA 57.996 33.333 8.44 0.00 0.00 3.07
1891 2082 6.757897 AAATCGCCTTAATTCATTCAGTCA 57.242 33.333 0.00 0.00 0.00 3.41
1918 2109 2.738846 CCCTCAAGTGTTCAGATTCACG 59.261 50.000 0.00 0.00 39.25 4.35
1935 2126 2.435805 TGTAGCACTCATCCAATCCCTC 59.564 50.000 0.00 0.00 0.00 4.30
1952 2143 8.428536 CGAAGAACAGAAAAACAGAGTATGTAG 58.571 37.037 0.00 0.00 43.00 2.74
1969 2160 5.824243 ACTACAAATCGTTCGAAGAACAG 57.176 39.130 12.56 6.19 45.90 3.16
1970 2161 6.142798 GTGTACTACAAATCGTTCGAAGAACA 59.857 38.462 12.56 0.00 45.90 3.18
1971 2162 6.361748 AGTGTACTACAAATCGTTCGAAGAAC 59.638 38.462 0.00 3.04 45.90 3.01
1976 2184 5.112220 ACAGTGTACTACAAATCGTTCGA 57.888 39.130 0.00 0.00 0.00 3.71
1977 2185 5.400188 TGAACAGTGTACTACAAATCGTTCG 59.600 40.000 0.00 0.00 34.41 3.95
1978 2186 6.758593 TGAACAGTGTACTACAAATCGTTC 57.241 37.500 0.00 11.09 0.00 3.95
1979 2187 7.542534 TTTGAACAGTGTACTACAAATCGTT 57.457 32.000 0.00 0.00 0.00 3.85
1980 2188 6.292703 GCTTTGAACAGTGTACTACAAATCGT 60.293 38.462 0.00 0.00 0.00 3.73
1981 2189 6.071463 GCTTTGAACAGTGTACTACAAATCG 58.929 40.000 0.00 0.00 0.00 3.34
1982 2190 6.954944 TGCTTTGAACAGTGTACTACAAATC 58.045 36.000 0.00 4.54 0.00 2.17
1983 2191 6.935741 TGCTTTGAACAGTGTACTACAAAT 57.064 33.333 0.00 0.00 0.00 2.32
1984 2192 6.935741 ATGCTTTGAACAGTGTACTACAAA 57.064 33.333 0.00 6.89 0.00 2.83
1985 2193 8.615878 ATTATGCTTTGAACAGTGTACTACAA 57.384 30.769 0.00 0.00 0.00 2.41
1986 2194 8.615878 AATTATGCTTTGAACAGTGTACTACA 57.384 30.769 0.00 0.00 0.00 2.74
1987 2195 9.893305 AAAATTATGCTTTGAACAGTGTACTAC 57.107 29.630 0.00 0.00 0.00 2.73
2066 2274 7.652909 TCAATTTTAAGTTGACAGCTTGATTGG 59.347 33.333 22.27 12.94 31.07 3.16
2088 2355 6.949352 AAAATCCGCATGATTAGTCTCAAT 57.051 33.333 0.00 0.00 42.97 2.57
2142 2409 1.518056 AACCATTGGCTGCACGTCAG 61.518 55.000 1.54 9.73 45.62 3.51
2152 2419 2.733956 TGGAAGATGGTAACCATTGGC 58.266 47.619 1.54 0.00 45.26 4.52
2171 2494 7.672983 ATAAAAGATGTATCGCCAGGTTATG 57.327 36.000 0.00 0.00 0.00 1.90
2175 2498 7.450074 TCATTATAAAAGATGTATCGCCAGGT 58.550 34.615 0.00 0.00 0.00 4.00
2210 2563 9.725206 AAATATTTAGGAACAGAGGGAGTAGTA 57.275 33.333 0.00 0.00 0.00 1.82
2211 2564 8.487028 CAAATATTTAGGAACAGAGGGAGTAGT 58.513 37.037 0.00 0.00 0.00 2.73
2238 2591 9.921637 AGTCACTTGTTGAAATGTTTAAAAAGA 57.078 25.926 3.25 0.00 35.39 2.52
2245 2598 8.067784 CGTATGTAGTCACTTGTTGAAATGTTT 58.932 33.333 0.00 0.00 35.39 2.83
2246 2599 7.307751 CCGTATGTAGTCACTTGTTGAAATGTT 60.308 37.037 0.00 0.00 35.39 2.71
2247 2600 6.147164 CCGTATGTAGTCACTTGTTGAAATGT 59.853 38.462 0.00 0.00 35.39 2.71
2248 2601 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
2249 2602 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2250 2603 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2251 2604 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2253 2606 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2256 2609 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2257 2610 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2258 2611 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2259 2612 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2260 2613 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2261 2614 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2264 2617 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2266 2619 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2267 2620 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2269 2622 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2270 2623 4.154737 TGAAGATTCACTCATTTTGCTCCG 59.845 41.667 0.00 0.00 31.01 4.63
2284 2637 9.031360 GTAGACATATTTTAGCGTGAAGATTCA 57.969 33.333 0.00 0.00 34.20 2.57
2285 2638 9.031360 TGTAGACATATTTTAGCGTGAAGATTC 57.969 33.333 0.00 0.00 0.00 2.52
2286 2639 8.942338 TGTAGACATATTTTAGCGTGAAGATT 57.058 30.769 0.00 0.00 0.00 2.40
2288 2641 9.459640 GTATGTAGACATATTTTAGCGTGAAGA 57.540 33.333 5.69 0.00 40.53 2.87
2289 2642 8.417928 CGTATGTAGACATATTTTAGCGTGAAG 58.582 37.037 5.69 0.00 40.53 3.02
2290 2643 7.380333 CCGTATGTAGACATATTTTAGCGTGAA 59.620 37.037 5.69 0.00 40.53 3.18
2291 2644 6.859508 CCGTATGTAGACATATTTTAGCGTGA 59.140 38.462 5.69 0.00 40.53 4.35
2292 2645 6.859508 TCCGTATGTAGACATATTTTAGCGTG 59.140 38.462 5.69 0.27 40.53 5.34
2293 2646 6.973843 TCCGTATGTAGACATATTTTAGCGT 58.026 36.000 5.69 0.00 40.53 5.07
2294 2647 7.541091 ACATCCGTATGTAGACATATTTTAGCG 59.459 37.037 5.69 3.99 44.66 4.26
2295 2648 8.758633 ACATCCGTATGTAGACATATTTTAGC 57.241 34.615 5.69 0.00 44.66 3.09
2311 2664 8.304596 CAAATGGACTACTACATACATCCGTAT 58.695 37.037 0.00 0.00 38.96 3.06
2312 2665 7.503230 TCAAATGGACTACTACATACATCCGTA 59.497 37.037 0.00 0.00 0.00 4.02
2313 2666 6.322969 TCAAATGGACTACTACATACATCCGT 59.677 38.462 0.00 0.00 0.00 4.69
2314 2667 6.745116 TCAAATGGACTACTACATACATCCG 58.255 40.000 0.00 0.00 0.00 4.18
2315 2668 8.958119 TTTCAAATGGACTACTACATACATCC 57.042 34.615 0.00 0.00 0.00 3.51
2317 2670 9.905713 ACATTTCAAATGGACTACTACATACAT 57.094 29.630 14.70 0.00 0.00 2.29
2318 2671 9.378551 GACATTTCAAATGGACTACTACATACA 57.621 33.333 14.70 0.00 0.00 2.29
2319 2672 9.601217 AGACATTTCAAATGGACTACTACATAC 57.399 33.333 14.70 0.00 0.00 2.39
2321 2674 9.823647 CTAGACATTTCAAATGGACTACTACAT 57.176 33.333 14.70 0.00 0.00 2.29
2322 2675 9.031537 TCTAGACATTTCAAATGGACTACTACA 57.968 33.333 14.70 0.00 0.00 2.74
2323 2676 9.871238 TTCTAGACATTTCAAATGGACTACTAC 57.129 33.333 14.70 0.00 0.00 2.73
2325 2678 9.442047 CTTTCTAGACATTTCAAATGGACTACT 57.558 33.333 14.70 7.81 0.00 2.57
2326 2679 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
2343 2696 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2344 2697 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2345 2698 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2346 2699 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2347 2700 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2348 2701 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2349 2702 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2350 2703 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2351 2704 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2352 2705 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2353 2706 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2354 2707 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2355 2708 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
2356 2709 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2362 2715 1.006758 TCATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
2529 2913 7.121463 GTCTCAGATAACAGGAAGAACTAGTCA 59.879 40.741 0.00 0.00 0.00 3.41
2538 2922 5.599732 CAGATGGTCTCAGATAACAGGAAG 58.400 45.833 0.00 0.00 0.00 3.46
2542 2926 4.118410 GTGCAGATGGTCTCAGATAACAG 58.882 47.826 0.00 0.00 0.00 3.16
2587 2974 9.230122 TCAGATACATTTTCTGCATTGAGTAAA 57.770 29.630 0.00 0.00 40.35 2.01
2589 2976 8.791327 TTCAGATACATTTTCTGCATTGAGTA 57.209 30.769 0.00 0.00 40.35 2.59
2590 2977 7.609146 TCTTCAGATACATTTTCTGCATTGAGT 59.391 33.333 0.00 0.00 40.35 3.41
2591 2978 7.982224 TCTTCAGATACATTTTCTGCATTGAG 58.018 34.615 0.00 0.00 40.35 3.02
2695 3084 0.877071 GCAAGTCACAGGTGATGGTG 59.123 55.000 5.29 5.67 42.18 4.17
2755 3148 1.886886 TAGCCAAAACGAGGAACACC 58.113 50.000 0.00 0.00 0.00 4.16
2762 3155 2.609459 CACAGCCTATAGCCAAAACGAG 59.391 50.000 0.00 0.00 45.47 4.18
2764 3157 1.064060 GCACAGCCTATAGCCAAAACG 59.936 52.381 0.00 0.00 45.47 3.60
2801 3194 1.089112 TGATGCCATTGACAAGAGCG 58.911 50.000 7.49 0.00 0.00 5.03
2877 3270 6.737750 GTGCATTTCTTTCAACAAAAACTGTG 59.262 34.615 0.00 0.00 38.67 3.66
2878 3271 6.426328 TGTGCATTTCTTTCAACAAAAACTGT 59.574 30.769 0.00 0.00 41.27 3.55
2880 3273 6.128309 GGTGTGCATTTCTTTCAACAAAAACT 60.128 34.615 0.00 0.00 0.00 2.66
2882 3275 5.702670 TGGTGTGCATTTCTTTCAACAAAAA 59.297 32.000 0.00 0.00 0.00 1.94
2889 3285 4.341806 AGATGTTGGTGTGCATTTCTTTCA 59.658 37.500 0.00 0.00 0.00 2.69
2902 3298 7.381766 TGATATGTTTCTGAAGATGTTGGTG 57.618 36.000 0.00 0.00 0.00 4.17
2930 3326 8.891671 ACAGCAAACATTCAAAATCAGTTATT 57.108 26.923 0.00 0.00 0.00 1.40
2931 3327 9.630098 CTACAGCAAACATTCAAAATCAGTTAT 57.370 29.630 0.00 0.00 0.00 1.89
2932 3328 8.081633 CCTACAGCAAACATTCAAAATCAGTTA 58.918 33.333 0.00 0.00 0.00 2.24
2933 3329 6.925165 CCTACAGCAAACATTCAAAATCAGTT 59.075 34.615 0.00 0.00 0.00 3.16
2941 3337 1.068610 GCGCCTACAGCAAACATTCAA 60.069 47.619 0.00 0.00 44.04 2.69
2945 3341 0.523072 CAAGCGCCTACAGCAAACAT 59.477 50.000 2.29 0.00 44.04 2.71
2978 3378 0.032267 GGTACCTCGGTGCTATCAGC 59.968 60.000 4.06 0.00 42.82 4.26
2987 3387 1.530013 CCGTGAACTGGTACCTCGGT 61.530 60.000 14.36 2.34 33.20 4.69
2990 3390 1.190178 ACCCCGTGAACTGGTACCTC 61.190 60.000 14.36 2.82 0.00 3.85
2991 3391 1.152183 ACCCCGTGAACTGGTACCT 60.152 57.895 14.36 0.00 0.00 3.08
3404 3812 3.606662 CGGCGGATGATCGGACCT 61.607 66.667 0.00 0.00 0.00 3.85
3452 3864 1.873270 CGTCATCACTGTCGGGGACA 61.873 60.000 0.00 0.00 40.50 4.02
3460 3873 2.126463 CGACCGCGTCATCACTGT 60.126 61.111 4.92 0.00 32.09 3.55
3462 3875 3.338126 GACCGACCGCGTCATCACT 62.338 63.158 4.92 0.00 35.23 3.41
3566 3991 7.848128 AGTTGTAGTGGTAGTTACTAATGCAT 58.152 34.615 0.00 0.00 32.84 3.96
3631 4065 0.976641 TGGGAACAGAGCAATCTCGT 59.023 50.000 0.00 0.00 44.02 4.18
3645 4079 1.529796 GGGACACACACACTGGGAA 59.470 57.895 0.00 0.00 0.00 3.97
3720 4154 4.309950 ACACCGGGCGACTCCAAC 62.310 66.667 6.32 0.00 36.21 3.77
3814 4261 2.614057 GGAAATCAATCGATTCTGCCGT 59.386 45.455 7.92 0.00 41.12 5.68
3835 4282 3.194329 GGGAGAAGCCAAGGAAATTCAAG 59.806 47.826 0.00 0.00 38.95 3.02
3843 4290 1.827399 GACACGGGAGAAGCCAAGGA 61.827 60.000 0.00 0.00 38.95 3.36
3845 4292 0.951040 GTGACACGGGAGAAGCCAAG 60.951 60.000 0.00 0.00 38.95 3.61
3847 4294 1.691195 TTGTGACACGGGAGAAGCCA 61.691 55.000 0.00 0.00 38.95 4.75
3853 4300 1.593196 AACACATTGTGACACGGGAG 58.407 50.000 23.12 0.00 36.96 4.30
3894 4347 2.056906 AAAAGCTCCACTGCCGGTCT 62.057 55.000 1.90 0.00 0.00 3.85
3895 4348 1.600916 AAAAGCTCCACTGCCGGTC 60.601 57.895 1.90 0.00 0.00 4.79
3896 4349 1.898574 CAAAAGCTCCACTGCCGGT 60.899 57.895 1.90 0.00 0.00 5.28
3897 4350 2.629656 CCAAAAGCTCCACTGCCGG 61.630 63.158 0.00 0.00 0.00 6.13
3898 4351 2.956987 CCAAAAGCTCCACTGCCG 59.043 61.111 0.00 0.00 0.00 5.69
3899 4352 2.653115 GCCAAAAGCTCCACTGCC 59.347 61.111 0.00 0.00 38.99 4.85
3908 4361 1.538849 CCACTCACCAAAGCCAAAAGC 60.539 52.381 0.00 0.00 44.25 3.51
3909 4362 2.031120 TCCACTCACCAAAGCCAAAAG 58.969 47.619 0.00 0.00 0.00 2.27
3910 4363 2.031120 CTCCACTCACCAAAGCCAAAA 58.969 47.619 0.00 0.00 0.00 2.44
3911 4364 1.691196 CTCCACTCACCAAAGCCAAA 58.309 50.000 0.00 0.00 0.00 3.28
3912 4365 0.823356 GCTCCACTCACCAAAGCCAA 60.823 55.000 0.00 0.00 0.00 4.52
3913 4366 1.228245 GCTCCACTCACCAAAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
3914 4367 0.538287 AAGCTCCACTCACCAAAGCC 60.538 55.000 0.00 0.00 33.43 4.35
3915 4368 1.268079 GAAAGCTCCACTCACCAAAGC 59.732 52.381 0.00 0.00 0.00 3.51
3916 4369 1.532868 CGAAAGCTCCACTCACCAAAG 59.467 52.381 0.00 0.00 0.00 2.77
3917 4370 1.593196 CGAAAGCTCCACTCACCAAA 58.407 50.000 0.00 0.00 0.00 3.28
3918 4371 0.250295 CCGAAAGCTCCACTCACCAA 60.250 55.000 0.00 0.00 0.00 3.67
3919 4372 1.371183 CCGAAAGCTCCACTCACCA 59.629 57.895 0.00 0.00 0.00 4.17
3920 4373 2.035442 GCCGAAAGCTCCACTCACC 61.035 63.158 0.00 0.00 38.99 4.02
3921 4374 3.567473 GCCGAAAGCTCCACTCAC 58.433 61.111 0.00 0.00 38.99 3.51
4019 4493 2.630098 TCTCTGGACAGAACCAAGAGTG 59.370 50.000 3.35 0.00 39.59 3.51
4024 4498 2.029020 CGACATCTCTGGACAGAACCAA 60.029 50.000 3.35 0.00 39.59 3.67
4025 4499 1.546029 CGACATCTCTGGACAGAACCA 59.454 52.381 3.35 0.00 36.94 3.67
4067 4541 0.326264 TTTTGCCCTCTCAGCTCTCC 59.674 55.000 0.00 0.00 0.00 3.71
4126 4626 2.587522 CCATCCACTCGTAGATCAGGA 58.412 52.381 0.00 0.00 35.64 3.86
4129 4633 1.040646 GGCCATCCACTCGTAGATCA 58.959 55.000 0.00 0.00 33.89 2.92
4189 4699 3.630769 TCACGATAAGAGTTAGCCGATGT 59.369 43.478 0.00 0.00 0.00 3.06
4204 4714 1.426621 GACCTCGCACGTCACGATA 59.573 57.895 2.91 0.00 39.12 2.92
4238 4748 1.484240 GAGGCTGAGCTAATCACCAGT 59.516 52.381 3.72 0.00 33.79 4.00
4239 4749 1.761784 AGAGGCTGAGCTAATCACCAG 59.238 52.381 3.72 0.00 33.79 4.00
4241 4751 1.069978 GGAGAGGCTGAGCTAATCACC 59.930 57.143 3.72 5.08 33.22 4.02
4242 4752 1.759445 TGGAGAGGCTGAGCTAATCAC 59.241 52.381 3.72 0.00 33.22 3.06
4256 5004 3.197790 CGGTTGCGGCATGGAGAG 61.198 66.667 2.28 0.00 0.00 3.20
4299 5047 2.224843 TGTGGTGCCATTGAATCAGTCT 60.225 45.455 0.00 0.00 0.00 3.24
4302 5050 2.559668 ACTTGTGGTGCCATTGAATCAG 59.440 45.455 0.00 0.00 0.00 2.90
4305 5053 5.743636 AATAACTTGTGGTGCCATTGAAT 57.256 34.783 0.00 0.00 0.00 2.57
4322 5073 7.041187 TGAACTCGATCAAACGTGTAATAAC 57.959 36.000 0.00 0.00 38.65 1.89


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

AutoCloner maintained by Alex Coulton.