Multiple sequence alignment - TraesCS2B01G334500

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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 TraesCS2B01G334500 chr2B 100.000 7715 0 0 1 7715 478112684 478120398 0.000000e+00 14248.0
1 TraesCS2B01G334500 chr2B 82.450 1208 157 37 2990 4155 478104271 478105465 0.000000e+00 1005.0
2 TraesCS2B01G334500 chr2B 81.706 1055 159 23 5043 6073 478106667 478107711 0.000000e+00 848.0
3 TraesCS2B01G334500 chr2B 83.158 285 43 4 926 1210 478101954 478102233 9.940000e-64 255.0
4 TraesCS2B01G334500 chr2B 81.105 344 41 19 248 583 478101096 478101423 3.570000e-63 254.0
5 TraesCS2B01G334500 chr2B 96.000 100 4 0 1687 1786 546976472 546976373 6.190000e-36 163.0
6 TraesCS2B01G334500 chr2B 82.836 134 22 1 4244 4377 478105660 478105792 1.360000e-22 119.0
7 TraesCS2B01G334500 chr2B 90.769 65 3 1 1261 1325 478113881 478113942 4.960000e-12 84.2
8 TraesCS2B01G334500 chr2B 90.769 65 3 1 1198 1259 478113944 478114008 4.960000e-12 84.2
9 TraesCS2B01G334500 chr2A 94.080 5321 221 50 2429 7712 542456334 542461597 0.000000e+00 7995.0
10 TraesCS2B01G334500 chr2A 94.888 1702 75 9 1 1694 542453910 542455607 0.000000e+00 2651.0
11 TraesCS2B01G334500 chr2A 82.951 1132 146 35 2990 4089 542385637 542386753 0.000000e+00 977.0
12 TraesCS2B01G334500 chr2A 95.478 575 23 3 1776 2348 542455606 542456179 0.000000e+00 915.0
13 TraesCS2B01G334500 chr2A 82.381 1067 153 23 5036 6077 542387992 542389048 0.000000e+00 896.0
14 TraesCS2B01G334500 chr2A 83.382 343 32 16 248 582 542382785 542383110 2.110000e-75 294.0
15 TraesCS2B01G334500 chr2A 82.635 334 48 9 926 1255 542383654 542383981 3.520000e-73 287.0
16 TraesCS2B01G334500 chr2A 89.076 119 6 7 2024 2136 483604565 483604682 2.900000e-29 141.0
17 TraesCS2B01G334500 chr2A 83.582 134 21 1 4244 4377 542387026 542387158 2.920000e-24 124.0
18 TraesCS2B01G334500 chr2A 90.769 65 3 1 1261 1325 542455111 542455172 4.960000e-12 84.2
19 TraesCS2B01G334500 chr2D 96.393 3715 113 13 2429 6132 404088007 404091711 0.000000e+00 6098.0
20 TraesCS2B01G334500 chr2D 92.719 1703 72 11 1 1694 404085622 404087281 0.000000e+00 2410.0
21 TraesCS2B01G334500 chr2D 94.680 1203 44 13 6173 7360 404091710 404092907 0.000000e+00 1849.0
22 TraesCS2B01G334500 chr2D 81.716 1247 165 44 2956 4155 404040584 404041814 0.000000e+00 981.0
23 TraesCS2B01G334500 chr2D 92.390 657 25 5 1776 2430 404087280 404087913 0.000000e+00 913.0
24 TraesCS2B01G334500 chr2D 82.408 1063 152 22 5036 6073 404042974 404044026 0.000000e+00 894.0
25 TraesCS2B01G334500 chr2D 83.036 336 49 7 926 1258 404038637 404038967 1.630000e-76 298.0
26 TraesCS2B01G334500 chr2D 82.659 346 41 17 249 583 404037774 404038111 9.800000e-74 289.0
27 TraesCS2B01G334500 chr2D 78.754 353 43 21 7383 7715 404092902 404093242 2.820000e-49 207.0
28 TraesCS2B01G334500 chr2D 95.652 92 4 0 2029 2120 534925464 534925555 1.730000e-31 148.0
29 TraesCS2B01G334500 chr2D 74.419 344 67 13 4244 4587 404042009 404042331 2.260000e-25 128.0
30 TraesCS2B01G334500 chr2D 90.323 62 3 1 1198 1256 404086861 404086922 2.310000e-10 78.7
31 TraesCS2B01G334500 chr7A 84.615 325 37 8 6556 6870 650540524 650540845 2.090000e-80 311.0
32 TraesCS2B01G334500 chr7A 84.308 325 38 10 6556 6870 685399770 685400091 9.730000e-79 305.0
33 TraesCS2B01G334500 chr7D 87.854 247 21 5 6633 6870 94736547 94736301 1.640000e-71 281.0
34 TraesCS2B01G334500 chr4D 87.854 247 21 5 6633 6870 468439364 468439118 1.640000e-71 281.0
35 TraesCS2B01G334500 chr4D 95.745 94 4 0 1684 1777 437508887 437508980 1.340000e-32 152.0
36 TraesCS2B01G334500 chr3D 87.854 247 21 6 6633 6870 562008997 562008751 1.640000e-71 281.0
37 TraesCS2B01G334500 chr3D 85.990 207 25 3 1 203 444916247 444916453 1.300000e-52 219.0
38 TraesCS2B01G334500 chr3D 86.364 198 25 2 1 196 24569502 24569699 1.690000e-51 215.0
39 TraesCS2B01G334500 chr3D 83.019 212 31 3 1 207 444933889 444934100 3.680000e-43 187.0
40 TraesCS2B01G334500 chr1D 87.449 247 22 5 6633 6870 419285198 419284952 7.630000e-70 276.0
41 TraesCS2B01G334500 chr1D 86.735 196 23 3 1 194 466406918 466407112 1.690000e-51 215.0
42 TraesCS2B01G334500 chrUn 86.100 259 27 7 6621 6870 478215795 478216053 3.550000e-68 270.0
43 TraesCS2B01G334500 chrUn 98.913 92 1 0 1687 1778 62690560 62690469 1.720000e-36 165.0
44 TraesCS2B01G334500 chrUn 94.737 95 3 2 2023 2116 101630891 101630798 6.240000e-31 147.0
45 TraesCS2B01G334500 chr5B 87.817 197 22 2 1 195 608713570 608713374 6.020000e-56 230.0
46 TraesCS2B01G334500 chr5B 91.429 105 8 1 2026 2130 399811552 399811655 8.070000e-30 143.0
47 TraesCS2B01G334500 chr1A 87.755 196 22 2 3 196 556086313 556086508 2.170000e-55 228.0
48 TraesCS2B01G334500 chr1A 85.990 207 25 3 1 203 552373254 552373460 1.300000e-52 219.0
49 TraesCS2B01G334500 chr5D 97.826 92 2 0 1692 1783 504793016 504792925 8.010000e-35 159.0
50 TraesCS2B01G334500 chr3B 97.826 92 1 1 1687 1778 6673714 6673804 2.880000e-34 158.0
51 TraesCS2B01G334500 chr6D 94.175 103 4 2 1680 1782 268067208 268067108 1.040000e-33 156.0
52 TraesCS2B01G334500 chr6D 91.667 108 6 3 1681 1787 427966209 427966104 6.240000e-31 147.0
53 TraesCS2B01G334500 chr6A 94.898 98 3 2 1684 1781 15768143 15768238 1.340000e-32 152.0
54 TraesCS2B01G334500 chr7B 94.000 100 5 1 2015 2114 740996254 740996156 4.820000e-32 150.0
55 TraesCS2B01G334500 chr6B 91.667 108 4 5 2013 2115 485061180 485061287 2.240000e-30 145.0
56 TraesCS2B01G334500 chr6B 88.430 121 8 6 1693 1809 96970844 96970726 2.900000e-29 141.0
57 TraesCS2B01G334500 chr4B 91.509 106 5 2 2017 2118 192792847 192792742 8.070000e-30 143.0


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 TraesCS2B01G334500 chr2B 478112684 478120398 7714 False 14248.00 14248 100.00000 1 7715 1 chr2B.!!$F1 7714
1 TraesCS2B01G334500 chr2B 478101096 478107711 6615 False 496.20 1005 82.25100 248 6073 5 chr2B.!!$F2 5825
2 TraesCS2B01G334500 chr2A 542453910 542461597 7687 False 2911.30 7995 93.80375 1 7712 4 chr2A.!!$F3 7711
3 TraesCS2B01G334500 chr2A 542382785 542389048 6263 False 515.60 977 82.98620 248 6077 5 chr2A.!!$F2 5829
4 TraesCS2B01G334500 chr2D 404085622 404093242 7620 False 1925.95 6098 90.87650 1 7715 6 chr2D.!!$F3 7714
5 TraesCS2B01G334500 chr2D 404037774 404044026 6252 False 518.00 981 80.84760 249 6073 5 chr2D.!!$F2 5824

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
683 710 0.373716 GGTCGATCAATTGTGTCGCC 59.626 55.000 22.29 21.32 35.48 5.54 F
1974 2733 0.389296 TTGGCGAGGTATGACACGTG 60.389 55.000 15.48 15.48 0.00 4.49 F
3210 4171 1.204146 TAGGTGATCAAGACAGGGGC 58.796 55.000 0.00 0.00 0.00 5.80 F
4611 5715 1.570501 ACATGTAGGCCCACCAATCAT 59.429 47.619 0.00 0.00 39.06 2.45 F
5321 6765 0.035630 GCTCCAGCAATCCTGTGAGT 60.036 55.000 0.00 0.00 39.28 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 3149 0.734889 CCGGACTGCATTTGCTTAGG 59.265 55.0 0.00 0.00 42.66 2.69 R
3268 4229 0.391263 CCAGAACCCCTACGTGAAGC 60.391 60.0 0.00 0.00 0.00 3.86 R
5164 6608 1.093972 CTGTGTTGACAGTTGTGGCA 58.906 50.0 0.00 0.00 44.15 4.92 R
5872 7340 0.108186 TGCTACAATGGGCTCAGACG 60.108 55.0 0.00 0.00 0.00 4.18 R
7243 8729 0.235665 CGATAAAATCCTGCGCGCAT 59.764 50.0 36.48 21.42 0.00 4.73 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
39 41 5.121105 GGTTGTCTACTACACAAGGTTTGT 58.879 41.667 0.00 0.00 46.75 2.83
103 105 3.188786 CGCTCCGGTGCTTGTAGC 61.189 66.667 24.75 12.56 42.82 3.58
108 110 2.048597 CGGTGCTTGTAGCCGTCA 60.049 61.111 0.00 0.00 41.51 4.35
122 124 1.830279 CCGTCACTAGGTGGTCTACA 58.170 55.000 0.00 0.00 33.87 2.74
123 125 2.376109 CCGTCACTAGGTGGTCTACAT 58.624 52.381 0.00 0.00 33.87 2.29
148 151 5.652452 ACCTGGATGTATTTTTACTTCTGGC 59.348 40.000 0.00 0.00 0.00 4.85
222 230 6.734104 AAAAGAGATAGCAGTGAACATGTC 57.266 37.500 0.00 0.00 0.00 3.06
240 248 2.024414 GTCATGTAACCAGGCCATTCC 58.976 52.381 5.01 0.00 0.00 3.01
300 308 5.126067 CCAGATAGGAAATCAACCGTCATT 58.874 41.667 0.00 0.00 41.22 2.57
499 514 0.749454 CCCAAGAGCTTCCCCAATCG 60.749 60.000 0.00 0.00 0.00 3.34
521 536 1.827394 GAATCCCGACGAATCCCCA 59.173 57.895 0.00 0.00 0.00 4.96
597 618 2.303676 CGAGAAATCTAGCGCGCCC 61.304 63.158 30.33 8.34 0.00 6.13
683 710 0.373716 GGTCGATCAATTGTGTCGCC 59.626 55.000 22.29 21.32 35.48 5.54
806 834 4.765856 TGTACTGTGAGAGAGTTAGGGTTC 59.234 45.833 0.00 0.00 0.00 3.62
969 1212 2.516460 CTGGATCCTGCTGCTGGC 60.516 66.667 19.55 7.55 42.22 4.85
1151 1394 8.545420 CAATTTGCTATTTTGGTGCATATTCTC 58.455 33.333 0.00 0.00 36.66 2.87
1156 1399 6.293407 GCTATTTTGGTGCATATTCTCGCTAA 60.293 38.462 0.00 0.00 0.00 3.09
1161 1404 3.433615 GGTGCATATTCTCGCTAATGGTC 59.566 47.826 0.00 0.00 0.00 4.02
1179 1422 9.764363 CTAATGGTCACTGCTGTTTATAGAATA 57.236 33.333 0.00 0.00 0.00 1.75
1307 1553 4.161565 AGACGTTTCTAGTGGCATTGGATA 59.838 41.667 0.00 0.00 0.00 2.59
1322 1568 1.754803 TGGATAACTCTACACCGGCTG 59.245 52.381 0.00 1.20 0.00 4.85
1445 1694 7.799081 TGATCATTCTTCAGTGTTCCTATCAT 58.201 34.615 0.00 0.00 0.00 2.45
1500 1749 3.493503 ACTTGTACTGTGAAGCGCTTTAC 59.506 43.478 31.56 31.56 0.00 2.01
1519 1773 7.467267 CGCTTTACTTATATGTTGCATGGAACT 60.467 37.037 27.36 16.60 0.00 3.01
1660 1922 3.266510 TGATTATCAGTCTGTGTGCCC 57.733 47.619 0.00 0.00 0.00 5.36
1663 1925 3.334583 TTATCAGTCTGTGTGCCCTTC 57.665 47.619 0.00 0.00 0.00 3.46
1697 1959 9.819267 AGTAAGTGCTGTTAAATTAGATACTCC 57.181 33.333 0.00 0.00 0.00 3.85
1698 1960 9.043079 GTAAGTGCTGTTAAATTAGATACTCCC 57.957 37.037 0.00 0.00 0.00 4.30
1699 1961 7.439108 AGTGCTGTTAAATTAGATACTCCCT 57.561 36.000 0.00 0.00 0.00 4.20
1700 1962 7.501844 AGTGCTGTTAAATTAGATACTCCCTC 58.498 38.462 0.00 0.00 0.00 4.30
1701 1963 6.706716 GTGCTGTTAAATTAGATACTCCCTCC 59.293 42.308 0.00 0.00 0.00 4.30
1702 1964 5.927115 GCTGTTAAATTAGATACTCCCTCCG 59.073 44.000 0.00 0.00 0.00 4.63
1703 1965 6.462628 GCTGTTAAATTAGATACTCCCTCCGT 60.463 42.308 0.00 0.00 0.00 4.69
1704 1966 7.047460 TGTTAAATTAGATACTCCCTCCGTC 57.953 40.000 0.00 0.00 0.00 4.79
1705 1967 6.041296 TGTTAAATTAGATACTCCCTCCGTCC 59.959 42.308 0.00 0.00 0.00 4.79
1706 1968 2.671896 TTAGATACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
1707 1969 1.526315 TAGATACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
1708 1970 0.861155 AGATACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
1709 1971 2.071372 AGATACTCCCTCCGTCCCATA 58.929 52.381 0.00 0.00 0.00 2.74
1710 1972 2.449730 AGATACTCCCTCCGTCCCATAA 59.550 50.000 0.00 0.00 0.00 1.90
1711 1973 3.077695 AGATACTCCCTCCGTCCCATAAT 59.922 47.826 0.00 0.00 0.00 1.28
1712 1974 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1713 1975 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
1714 1976 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
1715 1977 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
1716 1978 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
1717 1979 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1718 1980 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
1720 1982 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
1721 1983 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
1722 1984 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
1723 1985 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1724 1986 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
1772 2034 3.990369 TCCTATATTATGGGACGGAGGG 58.010 50.000 4.74 0.00 34.71 4.30
1773 2035 3.599240 TCCTATATTATGGGACGGAGGGA 59.401 47.826 4.74 0.00 34.71 4.20
1774 2036 3.961408 CCTATATTATGGGACGGAGGGAG 59.039 52.174 0.00 0.00 31.57 4.30
1775 2037 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1776 2038 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
1934 2220 4.854436 AGGGAATACATCAGGATTAGCCAT 59.146 41.667 0.00 0.00 40.02 4.40
1974 2733 0.389296 TTGGCGAGGTATGACACGTG 60.389 55.000 15.48 15.48 0.00 4.49
2037 2809 9.613428 TTGTGAATCTTTGTTATATACTCCCTG 57.387 33.333 0.00 0.00 0.00 4.45
2057 2829 7.857456 TCCCTGTGTAAAGAAATATAAGAGCA 58.143 34.615 0.00 0.00 0.00 4.26
2351 3133 3.775661 GCAATATGTGCGGGTAAACTT 57.224 42.857 0.00 0.00 45.10 2.66
2352 3134 4.886247 GCAATATGTGCGGGTAAACTTA 57.114 40.909 0.00 0.00 45.10 2.24
2353 3135 5.432885 GCAATATGTGCGGGTAAACTTAT 57.567 39.130 0.00 0.00 45.10 1.73
2354 3136 5.827666 GCAATATGTGCGGGTAAACTTATT 58.172 37.500 0.00 0.00 45.10 1.40
2355 3137 6.270064 GCAATATGTGCGGGTAAACTTATTT 58.730 36.000 0.00 0.00 45.10 1.40
2356 3138 6.754675 GCAATATGTGCGGGTAAACTTATTTT 59.245 34.615 0.00 0.00 45.10 1.82
2357 3139 7.276878 GCAATATGTGCGGGTAAACTTATTTTT 59.723 33.333 0.00 0.00 45.10 1.94
2404 3186 3.839490 TCCGGTCTTTCTTACCATAACCA 59.161 43.478 0.00 0.00 36.78 3.67
2440 3222 8.316946 TGCAGACTAGCATATATAAATGAAGCT 58.683 33.333 0.00 0.00 40.11 3.74
2459 3241 9.807649 ATGAAGCTAATGTTGGATGAATTAAAC 57.192 29.630 0.00 0.00 0.00 2.01
2533 3449 2.036346 GCATTTCTTGGCAACCTCACTT 59.964 45.455 0.00 0.00 0.00 3.16
2561 3477 9.301153 ACTTACACAAGTGCTGAAATTTAAAAG 57.699 29.630 0.00 0.00 43.50 2.27
2588 3504 2.810274 CACCAAGAGTTCCATGACACTG 59.190 50.000 0.00 0.00 0.00 3.66
2697 3613 1.800655 GCATGCACTAGACTCGTCCTG 60.801 57.143 14.21 0.00 0.00 3.86
2721 3637 3.397955 AGGGACACAAAGGATACAAGGTT 59.602 43.478 0.00 0.00 41.41 3.50
2750 3698 4.533919 TCATCCGTGCAAATGGAATTTT 57.466 36.364 7.58 0.00 46.10 1.82
2764 3712 1.478105 GAATTTTGCGGATTCCAGGCT 59.522 47.619 3.09 0.00 0.00 4.58
2766 3714 1.305219 TTTTGCGGATTCCAGGCTCG 61.305 55.000 3.09 0.00 0.00 5.03
2769 3717 3.854669 CGGATTCCAGGCTCGGCT 61.855 66.667 3.09 0.00 0.00 5.52
2770 3718 2.592308 GGATTCCAGGCTCGGCTT 59.408 61.111 0.00 0.00 0.00 4.35
2771 3719 1.821332 GGATTCCAGGCTCGGCTTG 60.821 63.158 0.00 1.80 35.37 4.01
2799 3750 5.805486 CGCTGCATACTCTTCTAGTTACAAA 59.195 40.000 0.00 0.00 39.80 2.83
2901 3853 6.460399 GCCTTTTGTGACCTGTGTGTTATTTA 60.460 38.462 0.00 0.00 0.00 1.40
2926 3884 8.622948 ACGACAATGAGATACTGATCATACTA 57.377 34.615 0.00 0.00 35.11 1.82
3028 3986 6.653320 TGTACTTTGCACTTAGTAAGGATTGG 59.347 38.462 14.36 2.97 0.00 3.16
3121 4079 8.668653 TGGTTTAACTGATCATATATGGACCAT 58.331 33.333 12.67 12.67 0.00 3.55
3122 4080 9.167311 GGTTTAACTGATCATATATGGACCATC 57.833 37.037 11.17 8.65 0.00 3.51
3210 4171 1.204146 TAGGTGATCAAGACAGGGGC 58.796 55.000 0.00 0.00 0.00 5.80
3268 4229 2.266055 GGAGCTCCCAACAGTCCG 59.734 66.667 23.19 0.00 34.14 4.79
3418 4379 3.209410 CATGATTGGGAGAGTAGGTTGC 58.791 50.000 0.00 0.00 0.00 4.17
3642 4603 5.582665 GGATAACGATGGGAAGCAAGATATC 59.417 44.000 0.00 0.00 0.00 1.63
3643 4604 4.422073 AACGATGGGAAGCAAGATATCA 57.578 40.909 5.32 0.00 0.00 2.15
3795 4756 4.012374 CTGGTTTATCACATGCTGGTTCT 58.988 43.478 0.00 0.00 0.00 3.01
3893 4854 2.351276 CACCACACCCCAGGTAGC 59.649 66.667 0.00 0.00 36.07 3.58
4146 5142 5.506686 TGTTTGCTGCTTGTGTTATTACA 57.493 34.783 0.00 0.00 0.00 2.41
4159 5155 9.176181 CTTGTGTTATTACAATGGTTGTGTTAC 57.824 33.333 5.64 0.62 45.03 2.50
4222 5307 5.814481 TCATCCACATCATTTGTTCCTACA 58.186 37.500 0.00 0.00 36.00 2.74
4405 5507 1.893801 AGGACTGGTGTCTTTCTACCG 59.106 52.381 0.00 0.00 42.54 4.02
4419 5521 8.714179 TGTCTTTCTACCGTAACAATTTATGTG 58.286 33.333 0.00 0.00 42.99 3.21
4500 5603 9.517609 AGATACTTGTCGAATATTGTGAAGTAC 57.482 33.333 0.00 0.00 29.70 2.73
4600 5704 7.312154 TGAACAAATTTATGACACATGTAGGC 58.688 34.615 0.00 0.00 0.00 3.93
4611 5715 1.570501 ACATGTAGGCCCACCAATCAT 59.429 47.619 0.00 0.00 39.06 2.45
4623 5727 4.644685 CCCACCAATCATTGTTAGGTTAGG 59.355 45.833 0.00 0.00 0.00 2.69
4820 6229 5.241064 GTCTGAGGAGTACACTTCACTGTTA 59.759 44.000 0.96 0.00 0.00 2.41
4978 6387 3.370840 ACTAGGATGCAGGCATTTTCA 57.629 42.857 8.34 0.00 36.70 2.69
4980 6389 3.698040 ACTAGGATGCAGGCATTTTCAAG 59.302 43.478 8.34 5.17 36.70 3.02
5164 6608 4.160329 TCTAATGGTCCTGTGAAGACTGT 58.840 43.478 0.00 0.00 34.56 3.55
5196 6640 1.537202 CAACACAGCCTTCTAACAGCC 59.463 52.381 0.00 0.00 0.00 4.85
5321 6765 0.035630 GCTCCAGCAATCCTGTGAGT 60.036 55.000 0.00 0.00 39.28 3.41
5549 6993 5.677567 TCATCTAGCTTGATTGATGAGCAA 58.322 37.500 8.00 0.00 39.91 3.91
5568 7012 5.290496 AGCAAAAGAACCCCTCTGTTGATC 61.290 45.833 8.54 0.00 43.21 2.92
5627 7071 4.499183 CTGGAAGTAGTTCATGTGAGGAC 58.501 47.826 12.31 0.00 33.93 3.85
5658 7102 1.135915 GTGATGGATCTCAGCGACACT 59.864 52.381 0.00 0.00 33.83 3.55
5669 7113 0.318784 AGCGACACTTCTCCGACAAC 60.319 55.000 0.00 0.00 0.00 3.32
5734 7178 2.578021 AGGGGTTGCATGAGATTGTAGT 59.422 45.455 0.00 0.00 0.00 2.73
5852 7320 1.065345 TCAGTGAGGTCGGACTCTAGG 60.065 57.143 8.23 0.00 38.32 3.02
5872 7340 2.418976 GGTATGACGAAGCCCTTTTGTC 59.581 50.000 0.00 1.25 46.35 3.18
5892 7360 1.373570 GTCTGAGCCCATTGTAGCAC 58.626 55.000 0.00 0.00 0.00 4.40
6163 7632 8.472007 ACTTTTGGGTCATCAACACTATTTTA 57.528 30.769 0.00 0.00 30.14 1.52
6243 7712 8.567948 CCATCAAGTACTCATAGTTTTGTTGTT 58.432 33.333 0.00 0.00 29.27 2.83
6246 7715 7.990886 TCAAGTACTCATAGTTTTGTTGTTCCT 59.009 33.333 0.00 0.00 0.00 3.36
6250 7719 7.404671 ACTCATAGTTTTGTTGTTCCTGTTT 57.595 32.000 0.00 0.00 0.00 2.83
6449 7918 9.274206 GGGTTTAGCAATAAACAAAACCATTTA 57.726 29.630 15.04 0.00 40.63 1.40
6523 7995 7.554118 TGAGATTCAGGATTTGGTAGATGTTTC 59.446 37.037 0.00 0.00 0.00 2.78
6530 8004 6.715264 AGGATTTGGTAGATGTTTCGAGTTTT 59.285 34.615 0.00 0.00 0.00 2.43
6564 8048 3.433274 ACGCGATGGTGCATATCATTTAG 59.567 43.478 15.93 5.67 34.15 1.85
6594 8078 3.656457 TGCACATCAGGAATGCACT 57.344 47.368 7.31 0.00 44.17 4.40
6595 8079 1.456296 TGCACATCAGGAATGCACTC 58.544 50.000 7.31 0.00 44.17 3.51
6600 8084 2.039480 ACATCAGGAATGCACTCACACT 59.961 45.455 0.00 0.00 39.12 3.55
6601 8085 2.936919 TCAGGAATGCACTCACACTT 57.063 45.000 0.00 0.00 0.00 3.16
6604 8088 3.953612 TCAGGAATGCACTCACACTTTTT 59.046 39.130 0.00 0.00 0.00 1.94
6634 8118 6.426587 ACCATCTTTGCCTATCATTTACTGT 58.573 36.000 0.00 0.00 0.00 3.55
6635 8119 6.319658 ACCATCTTTGCCTATCATTTACTGTG 59.680 38.462 0.00 0.00 0.00 3.66
6744 8228 4.881920 ACACATCAACCAAAATTACTGGC 58.118 39.130 6.44 0.00 37.48 4.85
6766 8250 2.362077 GTTGTCAACCATGCTTGGAACT 59.638 45.455 24.48 6.27 46.92 3.01
6778 8262 3.822735 TGCTTGGAACTTTTGGAGATCAG 59.177 43.478 0.00 0.00 0.00 2.90
6841 8325 4.609301 TGGGGTGATTAGCTTAGCAAATT 58.391 39.130 7.07 0.00 0.00 1.82
6878 8362 1.270907 ACTTCAGCTCTGTGGGTAGG 58.729 55.000 0.00 0.00 0.00 3.18
6905 8389 4.591321 TGGGTAGATTGATGCTTTTCCT 57.409 40.909 0.00 0.00 0.00 3.36
6943 8427 4.551671 TGAGGGTTTTCTTCATTTTCCCA 58.448 39.130 0.00 0.00 36.24 4.37
7068 8552 3.372206 CGTGGCTTATCCTTGTTTCAGAG 59.628 47.826 0.00 0.00 35.26 3.35
7145 8630 6.039717 GGCTATCTATGGTCTCAAATTTTGCA 59.960 38.462 4.19 0.00 0.00 4.08
7205 8690 0.599728 TTTGCTTTGATTGGTGGCGC 60.600 50.000 0.00 0.00 0.00 6.53
7233 8719 1.000521 CAGCCTGCCTTCATGGGAA 60.001 57.895 0.00 0.00 35.09 3.97
7249 8735 1.261619 GGGAACAGAAAGATATGCGCG 59.738 52.381 0.00 0.00 0.00 6.86
7261 8747 3.372206 AGATATGCGCGCAGGATTTTATC 59.628 43.478 38.44 33.00 31.61 1.75
7288 8775 8.474025 GGGTCCAGATATCTCATTTAGTCATAG 58.526 40.741 1.03 0.00 0.00 2.23
7329 8816 5.888161 GGTAATCCTGTTTGATCATGAGGTT 59.112 40.000 0.09 9.72 0.00 3.50
7353 8840 1.519498 ATTTAGGCCCCCTCCTACAC 58.481 55.000 0.00 0.00 38.37 2.90
7360 8876 1.074889 GCCCCCTCCTACACTTTCAAA 59.925 52.381 0.00 0.00 0.00 2.69
7361 8877 2.291605 GCCCCCTCCTACACTTTCAAAT 60.292 50.000 0.00 0.00 0.00 2.32
7362 8878 3.817931 GCCCCCTCCTACACTTTCAAATT 60.818 47.826 0.00 0.00 0.00 1.82
7363 8879 4.569015 GCCCCCTCCTACACTTTCAAATTA 60.569 45.833 0.00 0.00 0.00 1.40
7364 8880 5.193679 CCCCCTCCTACACTTTCAAATTAG 58.806 45.833 0.00 0.00 0.00 1.73
7365 8881 5.045140 CCCCCTCCTACACTTTCAAATTAGA 60.045 44.000 0.00 0.00 0.00 2.10
7366 8882 6.116126 CCCCTCCTACACTTTCAAATTAGAG 58.884 44.000 0.00 0.00 0.00 2.43
7367 8883 6.296489 CCCCTCCTACACTTTCAAATTAGAGT 60.296 42.308 0.00 0.00 0.00 3.24
7368 8884 7.093024 CCCCTCCTACACTTTCAAATTAGAGTA 60.093 40.741 0.00 0.00 0.00 2.59
7369 8885 8.319146 CCCTCCTACACTTTCAAATTAGAGTAA 58.681 37.037 0.00 0.00 0.00 2.24
7370 8886 9.720769 CCTCCTACACTTTCAAATTAGAGTAAA 57.279 33.333 0.00 0.00 0.00 2.01
7441 8957 8.967664 TCTTAGTATGTTACTGTTTTGTTGGT 57.032 30.769 0.00 0.00 39.81 3.67
7453 8973 6.657117 ACTGTTTTGTTGGTTTGGCTTTATTT 59.343 30.769 0.00 0.00 0.00 1.40
7476 8996 5.941555 TTTTTACTGGGAAACAATGGTGT 57.058 34.783 0.00 0.00 40.75 4.16
7484 9004 3.056891 GGGAAACAATGGTGTGGTACATG 60.057 47.826 0.00 0.00 44.52 3.21
7486 9006 4.762765 GGAAACAATGGTGTGGTACATGTA 59.237 41.667 0.08 0.08 44.52 2.29
7487 9007 5.241949 GGAAACAATGGTGTGGTACATGTAA 59.758 40.000 7.25 0.00 44.52 2.41
7492 9053 6.094881 ACAATGGTGTGGTACATGTAATTAGC 59.905 38.462 7.25 5.22 44.52 3.09
7518 9079 2.419011 TTTGGCTGCTTTCGGGGCTA 62.419 55.000 0.00 0.00 0.00 3.93
7519 9080 2.514824 GGCTGCTTTCGGGGCTAG 60.515 66.667 0.00 0.00 0.00 3.42
7520 9081 2.584608 GCTGCTTTCGGGGCTAGA 59.415 61.111 0.00 0.00 0.00 2.43
7521 9082 1.522580 GCTGCTTTCGGGGCTAGAG 60.523 63.158 0.00 0.00 0.00 2.43
7522 9083 1.144936 CTGCTTTCGGGGCTAGAGG 59.855 63.158 0.00 0.00 0.00 3.69
7523 9084 1.612442 TGCTTTCGGGGCTAGAGGT 60.612 57.895 0.00 0.00 0.00 3.85
7524 9085 1.198759 TGCTTTCGGGGCTAGAGGTT 61.199 55.000 0.00 0.00 0.00 3.50
7525 9086 0.462225 GCTTTCGGGGCTAGAGGTTC 60.462 60.000 0.00 0.00 0.00 3.62
7526 9087 0.179108 CTTTCGGGGCTAGAGGTTCG 60.179 60.000 0.00 0.00 0.00 3.95
7527 9088 1.610554 TTTCGGGGCTAGAGGTTCGG 61.611 60.000 0.00 0.00 0.00 4.30
7528 9089 4.222847 CGGGGCTAGAGGTTCGGC 62.223 72.222 0.00 0.00 0.00 5.54
7529 9090 2.764547 GGGGCTAGAGGTTCGGCT 60.765 66.667 0.00 0.00 0.00 5.52
7530 9091 2.501610 GGGCTAGAGGTTCGGCTG 59.498 66.667 0.00 0.00 0.00 4.85
7531 9092 2.202946 GGCTAGAGGTTCGGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
7532 9093 2.726351 GGCTAGAGGTTCGGCTGCT 61.726 63.158 0.00 0.00 0.00 4.24
7533 9094 1.392710 GGCTAGAGGTTCGGCTGCTA 61.393 60.000 0.00 0.00 0.00 3.49
7534 9095 0.031449 GCTAGAGGTTCGGCTGCTAG 59.969 60.000 0.00 0.00 33.45 3.42
7535 9096 0.671251 CTAGAGGTTCGGCTGCTAGG 59.329 60.000 0.00 0.00 0.00 3.02
7536 9097 1.392710 TAGAGGTTCGGCTGCTAGGC 61.393 60.000 0.00 0.00 37.44 3.93
7537 9098 3.003173 AGGTTCGGCTGCTAGGCA 61.003 61.111 0.00 0.00 41.44 4.75
7547 9108 3.627690 GCTAGGCAGCTCTGGACT 58.372 61.111 0.00 0.00 44.93 3.85
7571 9132 1.092348 CACTCCCAGACGATGTACGA 58.908 55.000 0.00 0.00 45.77 3.43
7572 9133 1.676529 CACTCCCAGACGATGTACGAT 59.323 52.381 0.00 0.00 45.77 3.73
7573 9134 1.676529 ACTCCCAGACGATGTACGATG 59.323 52.381 0.00 0.00 45.77 3.84
7574 9135 1.676529 CTCCCAGACGATGTACGATGT 59.323 52.381 0.00 0.00 45.77 3.06
7575 9136 2.876550 CTCCCAGACGATGTACGATGTA 59.123 50.000 0.00 0.00 45.77 2.29
7576 9137 2.615447 TCCCAGACGATGTACGATGTAC 59.385 50.000 0.00 0.22 45.77 2.90
7577 9138 2.601504 CCCAGACGATGTACGATGTACG 60.602 54.545 0.00 0.00 45.77 3.67
7593 9154 0.828022 TACGGTAAGTGCCATGAGGG 59.172 55.000 0.00 0.00 40.85 4.30
7602 9163 2.357836 CCATGAGGGCCAGCTGTT 59.642 61.111 13.81 0.00 0.00 3.16
7625 9190 0.537188 CTGAGCCGGTGTGAGGTATT 59.463 55.000 1.90 0.00 0.00 1.89
7631 9196 2.420129 GCCGGTGTGAGGTATTGAATCT 60.420 50.000 1.90 0.00 0.00 2.40
7637 9202 5.294552 GGTGTGAGGTATTGAATCTTAGTGC 59.705 44.000 0.00 0.00 0.00 4.40
7638 9203 5.294552 GTGTGAGGTATTGAATCTTAGTGCC 59.705 44.000 0.00 0.00 0.00 5.01
7639 9204 4.816925 GTGAGGTATTGAATCTTAGTGCCC 59.183 45.833 0.00 0.00 0.00 5.36
7647 9212 2.755952 ATCTTAGTGCCCCATTTCCC 57.244 50.000 0.00 0.00 0.00 3.97
7648 9213 0.629058 TCTTAGTGCCCCATTTCCCC 59.371 55.000 0.00 0.00 0.00 4.81
7649 9214 0.397114 CTTAGTGCCCCATTTCCCCC 60.397 60.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.886563 AGTAGACAACCGGGAAGTCG 59.113 55.000 6.32 0.00 37.36 4.18
13 14 2.353406 CCTTGTGTAGTAGACAACCGGG 60.353 54.545 6.32 5.80 40.66 5.73
39 41 1.153989 CTCCCTCATAGGAGCCGGA 59.846 63.158 5.05 0.54 46.76 5.14
103 105 1.830279 TGTAGACCACCTAGTGACGG 58.170 55.000 0.00 0.00 35.23 4.79
108 110 3.530564 TCCAGGTATGTAGACCACCTAGT 59.469 47.826 0.00 0.00 40.77 2.57
122 124 7.502561 GCCAGAAGTAAAAATACATCCAGGTAT 59.497 37.037 0.00 0.00 35.53 2.73
123 125 6.826741 GCCAGAAGTAAAAATACATCCAGGTA 59.173 38.462 0.00 0.00 0.00 3.08
162 166 3.692791 TCTATTCATCGACTGTCGTGG 57.307 47.619 27.16 20.16 41.35 4.94
165 169 7.356540 ACTTTAGATCTATTCATCGACTGTCG 58.643 38.462 23.33 23.33 42.10 4.35
222 230 1.024271 CGGAATGGCCTGGTTACATG 58.976 55.000 3.32 0.00 0.00 3.21
300 308 2.908015 GCACCTTCCCTATGCCGA 59.092 61.111 0.00 0.00 33.06 5.54
304 312 0.390860 CTCCTCGCACCTTCCCTATG 59.609 60.000 0.00 0.00 0.00 2.23
306 314 1.381327 CCTCCTCGCACCTTCCCTA 60.381 63.158 0.00 0.00 0.00 3.53
328 338 5.404946 CCTATGCAAAATGTGACTTTCAGG 58.595 41.667 0.00 0.00 0.00 3.86
499 514 2.928732 GATTCGTCGGGATTCGCGC 61.929 63.158 17.34 11.66 39.60 6.86
521 536 2.952116 TGGAGGGTTGGAAAATTTCGT 58.048 42.857 0.00 0.00 0.00 3.85
597 618 0.796927 TCAGCGACGACTCTGTGTAG 59.203 55.000 0.00 0.00 31.65 2.74
683 710 2.261172 TATCGGGATATCACGCCGCG 62.261 60.000 22.64 12.14 43.59 6.46
695 722 1.002201 CTCCTCTCGTAGCTATCGGGA 59.998 57.143 14.69 14.69 36.37 5.14
873 1092 1.390123 CGGTTACAGCACACGATTCAG 59.610 52.381 0.00 0.00 0.00 3.02
969 1212 2.350522 GCCACTCACCATCTACACTTG 58.649 52.381 0.00 0.00 0.00 3.16
1151 1394 1.442769 AACAGCAGTGACCATTAGCG 58.557 50.000 0.00 0.00 0.00 4.26
1307 1553 2.829720 TGATTACAGCCGGTGTAGAGTT 59.170 45.455 10.19 0.00 42.75 3.01
1500 1749 6.698008 TCCAAGTTCCATGCAACATATAAG 57.302 37.500 1.63 0.00 0.00 1.73
1519 1773 6.041637 AGTTCGACATATTATACTGGCTCCAA 59.958 38.462 0.00 0.00 0.00 3.53
1617 1879 2.634600 AGTTTAACAAGCACCGACACA 58.365 42.857 0.00 0.00 0.00 3.72
1694 1956 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1695 1957 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
1696 1958 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
1697 1959 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
1698 1960 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
1699 1961 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
1750 2012 3.705072 CCCTCCGTCCCATAATATAGGAC 59.295 52.174 7.65 7.65 45.49 3.85
1751 2013 3.599240 TCCCTCCGTCCCATAATATAGGA 59.401 47.826 0.00 0.00 0.00 2.94
1752 2014 3.961408 CTCCCTCCGTCCCATAATATAGG 59.039 52.174 0.00 0.00 0.00 2.57
1753 2015 4.611367 ACTCCCTCCGTCCCATAATATAG 58.389 47.826 0.00 0.00 0.00 1.31
1754 2016 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1755 2017 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1756 2018 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
1757 2019 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
1758 2020 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
1759 2021 4.687262 ATAATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
1760 2022 3.562108 ATAATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
1761 2023 3.339713 AATAATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
1762 2024 4.701651 AAAATAATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
1763 2025 6.416631 AGTAAAATAATACTCCCTCCGTCC 57.583 41.667 0.00 0.00 30.26 4.79
1764 2026 6.148264 CGAGTAAAATAATACTCCCTCCGTC 58.852 44.000 8.45 0.00 45.87 4.79
1765 2027 5.010415 CCGAGTAAAATAATACTCCCTCCGT 59.990 44.000 8.45 0.00 45.87 4.69
1766 2028 5.242393 TCCGAGTAAAATAATACTCCCTCCG 59.758 44.000 8.45 0.00 45.87 4.63
1767 2029 6.041296 TGTCCGAGTAAAATAATACTCCCTCC 59.959 42.308 8.45 0.00 45.87 4.30
1768 2030 7.047460 TGTCCGAGTAAAATAATACTCCCTC 57.953 40.000 8.45 0.00 45.87 4.30
1769 2031 7.289317 TCATGTCCGAGTAAAATAATACTCCCT 59.711 37.037 8.45 0.00 45.87 4.20
1770 2032 7.439381 TCATGTCCGAGTAAAATAATACTCCC 58.561 38.462 8.45 0.00 45.87 4.30
1771 2033 8.882415 TTCATGTCCGAGTAAAATAATACTCC 57.118 34.615 8.45 0.00 45.87 3.85
1934 2220 9.515020 CGCCAAGAATTTCTTAATAAATGCTTA 57.485 29.630 15.60 0.00 41.03 3.09
1940 2226 7.696992 ACCTCGCCAAGAATTTCTTAATAAA 57.303 32.000 11.21 0.00 33.78 1.40
1941 2227 8.836413 CATACCTCGCCAAGAATTTCTTAATAA 58.164 33.333 11.21 0.00 33.78 1.40
1959 2716 1.068125 TCAACCACGTGTCATACCTCG 60.068 52.381 15.65 0.00 0.00 4.63
2186 2960 0.828677 CCTACCACCCTACCCTTTCG 59.171 60.000 0.00 0.00 0.00 3.46
2354 3136 6.315891 GCATTTGCTTAGGATATTGCCAAAAA 59.684 34.615 0.00 0.00 38.21 1.94
2355 3137 5.816777 GCATTTGCTTAGGATATTGCCAAAA 59.183 36.000 0.00 0.00 38.21 2.44
2356 3138 5.105023 TGCATTTGCTTAGGATATTGCCAAA 60.105 36.000 3.94 0.00 42.66 3.28
2357 3139 4.405036 TGCATTTGCTTAGGATATTGCCAA 59.595 37.500 3.94 0.00 42.66 4.52
2358 3140 3.959449 TGCATTTGCTTAGGATATTGCCA 59.041 39.130 3.94 0.00 42.66 4.92
2359 3141 4.038402 ACTGCATTTGCTTAGGATATTGCC 59.962 41.667 3.94 0.00 42.66 4.52
2360 3142 5.192327 ACTGCATTTGCTTAGGATATTGC 57.808 39.130 3.94 0.00 42.66 3.56
2361 3143 5.561532 CGGACTGCATTTGCTTAGGATATTG 60.562 44.000 3.94 0.00 42.66 1.90
2362 3144 4.516698 CGGACTGCATTTGCTTAGGATATT 59.483 41.667 3.94 0.00 42.66 1.28
2363 3145 4.067896 CGGACTGCATTTGCTTAGGATAT 58.932 43.478 3.94 0.00 42.66 1.63
2364 3146 3.466836 CGGACTGCATTTGCTTAGGATA 58.533 45.455 3.94 0.00 42.66 2.59
2365 3147 2.292267 CGGACTGCATTTGCTTAGGAT 58.708 47.619 3.94 0.00 42.66 3.24
2366 3148 1.678728 CCGGACTGCATTTGCTTAGGA 60.679 52.381 0.00 0.00 42.66 2.94
2367 3149 0.734889 CCGGACTGCATTTGCTTAGG 59.265 55.000 0.00 0.00 42.66 2.69
2368 3150 1.398390 GACCGGACTGCATTTGCTTAG 59.602 52.381 9.46 0.00 42.66 2.18
2369 3151 1.003118 AGACCGGACTGCATTTGCTTA 59.997 47.619 9.46 0.00 42.66 3.09
2404 3186 5.972107 ATGCTAGTCTGCAAATCAAAACT 57.028 34.783 0.00 0.00 46.61 2.66
2434 3216 9.023962 AGTTTAATTCATCCAACATTAGCTTCA 57.976 29.630 0.00 0.00 0.00 3.02
2506 3418 2.064014 GTTGCCAAGAAATGCTGAAGC 58.936 47.619 0.00 0.00 42.50 3.86
2561 3477 4.154918 GTCATGGAACTCTTGGTGACATTC 59.845 45.833 0.00 0.00 42.32 2.67
2588 3504 5.634859 CAGGCCAAAGTGAATAATGTGAAAC 59.365 40.000 5.01 0.00 37.35 2.78
2623 3539 1.070289 GATCCCGATCTACAACCCCAC 59.930 57.143 0.00 0.00 35.04 4.61
2697 3613 2.489938 TGTATCCTTTGTGTCCCTGC 57.510 50.000 0.00 0.00 0.00 4.85
2721 3637 0.250684 TTGCACGGATGAAGCTTGGA 60.251 50.000 2.10 0.00 0.00 3.53
2749 3697 2.125147 CGAGCCTGGAATCCGCAA 60.125 61.111 0.00 0.00 0.00 4.85
2750 3698 4.161295 CCGAGCCTGGAATCCGCA 62.161 66.667 0.00 0.00 0.00 5.69
2901 3853 7.517614 AGTATGATCAGTATCTCATTGTCGT 57.482 36.000 0.09 0.00 34.14 4.34
2926 3884 8.032952 CAGTGACACTGTAATACACATTGAAT 57.967 34.615 24.73 0.00 41.19 2.57
3028 3986 7.199766 TGATTGGTAACTGAACAATTGAACAC 58.800 34.615 13.59 1.09 35.17 3.32
3121 4079 8.169977 AGCACAAAAGAATAGTCAATTCAAGA 57.830 30.769 0.00 0.00 45.58 3.02
3122 4080 8.697067 CAAGCACAAAAGAATAGTCAATTCAAG 58.303 33.333 0.00 0.00 45.58 3.02
3210 4171 2.672874 TGATCGGTTTCTTGATGAAGCG 59.327 45.455 1.74 1.74 36.86 4.68
3268 4229 0.391263 CCAGAACCCCTACGTGAAGC 60.391 60.000 0.00 0.00 0.00 3.86
3562 4523 2.158900 AGATACCACCAGCATCCTTTCG 60.159 50.000 0.00 0.00 0.00 3.46
3795 4756 1.127567 ACACTTCAGGCTGCCTACCA 61.128 55.000 22.90 5.40 29.64 3.25
3832 4793 5.575957 CATTACTGTTTCAGCCATGCTTAG 58.424 41.667 0.00 0.00 36.40 2.18
3940 4904 7.987458 AGTGACTGGAACGAAATATGATTACAT 59.013 33.333 0.00 0.00 40.16 2.29
4146 5142 5.061179 GTCACTGGTAGTAACACAACCATT 58.939 41.667 0.00 0.00 42.23 3.16
4405 5507 7.961855 TGCATTGCATTCACATAAATTGTTAC 58.038 30.769 7.38 0.00 31.96 2.50
4525 5629 3.750371 TGTAGGGAAATATTGCGGATGG 58.250 45.455 0.00 0.00 0.00 3.51
4540 5644 7.047891 TGCAGAGTTAAATAACAGATGTAGGG 58.952 38.462 6.13 0.00 38.62 3.53
4638 5742 8.443176 AGATCAATACAATCCATAATCCTGTGT 58.557 33.333 0.00 0.00 0.00 3.72
4729 5836 6.855763 TGGCAGAACAAAATTCCATCTATT 57.144 33.333 0.00 0.00 0.00 1.73
4788 5895 5.580998 AGTGTACTCCTCAGACAAATAGGA 58.419 41.667 0.00 0.00 37.07 2.94
4820 6229 8.385491 TGACCCAATGCTGATCAAGTAATATAT 58.615 33.333 0.00 0.00 0.00 0.86
4906 6315 8.776376 AAAATAAACTGCAATATCCCACAAAG 57.224 30.769 0.00 0.00 0.00 2.77
4970 6379 4.240096 AGCACATACAAGCTTGAAAATGC 58.760 39.130 32.50 29.39 38.01 3.56
4980 6389 2.356069 GCCTTAGGAAGCACATACAAGC 59.644 50.000 0.69 0.00 0.00 4.01
5164 6608 1.093972 CTGTGTTGACAGTTGTGGCA 58.906 50.000 0.00 0.00 44.15 4.92
5196 6640 3.380479 TTTGACTGGAGTACGAACAGG 57.620 47.619 15.54 2.68 36.57 4.00
5290 6734 1.675801 CTGGAGCAGTCTCTGGCAA 59.324 57.895 0.00 0.00 39.31 4.52
5415 6859 4.641396 TCACCAGATGAACCTTGTTGTAG 58.359 43.478 0.00 0.00 33.02 2.74
5467 6911 3.488721 GCTCCGCAGTAACTCGAAGAATA 60.489 47.826 0.00 0.00 34.09 1.75
5549 6993 3.395941 ACAGATCAACAGAGGGGTTCTTT 59.604 43.478 0.00 0.00 32.41 2.52
5568 7012 5.530915 TGATTCCACTGTTAAACAAGGACAG 59.469 40.000 1.51 1.51 33.72 3.51
5627 7071 4.095334 TGAGATCCATCACAAGAATTTGCG 59.905 41.667 0.00 0.00 37.85 4.85
5658 7102 2.297880 TGATTTCCTCGTTGTCGGAGAA 59.702 45.455 0.00 0.00 39.69 2.87
5669 7113 1.740025 GAAGGTGGCTTGATTTCCTCG 59.260 52.381 0.00 0.00 0.00 4.63
5734 7178 0.736053 GTTGGCGTCCTTGTTGTCAA 59.264 50.000 0.00 0.00 0.00 3.18
5836 7304 2.775960 TCATACCTAGAGTCCGACCTCA 59.224 50.000 0.00 0.00 33.75 3.86
5852 7320 2.093783 CGACAAAAGGGCTTCGTCATAC 59.906 50.000 0.00 0.00 0.00 2.39
5872 7340 0.108186 TGCTACAATGGGCTCAGACG 60.108 55.000 0.00 0.00 0.00 4.18
5892 7360 1.341531 AGGATACGATTCCTCTTGCCG 59.658 52.381 5.28 0.00 42.71 5.69
6126 7594 6.548441 TGACCCAAAAGTTACGAATACTTG 57.452 37.500 0.00 0.00 36.06 3.16
6132 7600 4.882427 TGTTGATGACCCAAAAGTTACGAA 59.118 37.500 0.00 0.00 0.00 3.85
6449 7918 6.044682 GGATTTCATTTCCGCTTCAATTGAT 58.955 36.000 9.40 0.00 0.00 2.57
6460 7929 9.855021 AAACAAAATACTAGGATTTCATTTCCG 57.145 29.630 13.44 0.32 38.36 4.30
6545 8019 5.947228 AACCTAAATGATATGCACCATCG 57.053 39.130 0.00 0.00 0.00 3.84
6549 8023 5.594317 ACCAGAAACCTAAATGATATGCACC 59.406 40.000 0.00 0.00 0.00 5.01
6564 8048 3.129287 CCTGATGTGCATTACCAGAAACC 59.871 47.826 9.09 0.00 0.00 3.27
6617 8101 8.851145 TGTTAAAACACAGTAAATGATAGGCAA 58.149 29.630 0.00 0.00 33.17 4.52
6634 8118 9.226606 CAAAGTAGTGGGAGATATGTTAAAACA 57.773 33.333 0.00 0.00 44.06 2.83
6635 8119 9.227777 ACAAAGTAGTGGGAGATATGTTAAAAC 57.772 33.333 0.00 0.00 0.00 2.43
6744 8228 3.477504 CCAAGCATGGTTGACAACG 57.522 52.632 33.41 16.00 42.18 4.10
6766 8250 2.642311 TGGTACAGCCTGATCTCCAAAA 59.358 45.455 0.00 0.00 38.35 2.44
6841 8325 6.315393 GCTGAAGTTAACGGGAAAATATCTCA 59.685 38.462 0.00 0.00 0.00 3.27
6878 8362 5.841957 AAGCATCAATCTACCCATGAAAC 57.158 39.130 0.00 0.00 0.00 2.78
6905 8389 2.958355 CCCTCAAACCTCTTTTCAGCAA 59.042 45.455 0.00 0.00 0.00 3.91
6943 8427 3.420893 TGTTTCATTCGGCATTCCTTCT 58.579 40.909 0.00 0.00 0.00 2.85
7046 8530 3.334691 TCTGAAACAAGGATAAGCCACG 58.665 45.455 0.00 0.00 40.02 4.94
7157 8642 6.151817 AGGAAGCCAGATTTGAGTAAAACATC 59.848 38.462 0.00 0.00 0.00 3.06
7173 8658 1.613836 AAGCAAAGACAGGAAGCCAG 58.386 50.000 0.00 0.00 0.00 4.85
7205 8690 4.099170 GCAGGCTGCGCAACTGAG 62.099 66.667 33.36 16.02 34.21 3.35
7217 8702 1.304381 TGTTCCCATGAAGGCAGGC 60.304 57.895 0.00 0.00 35.39 4.85
7226 8712 3.304257 GCGCATATCTTTCTGTTCCCATG 60.304 47.826 0.30 0.00 0.00 3.66
7233 8719 0.933097 CTGCGCGCATATCTTTCTGT 59.067 50.000 36.48 0.00 0.00 3.41
7236 8722 1.151668 ATCCTGCGCGCATATCTTTC 58.848 50.000 36.48 0.00 0.00 2.62
7241 8727 2.094258 CGATAAAATCCTGCGCGCATAT 59.906 45.455 36.48 26.69 0.00 1.78
7243 8729 0.235665 CGATAAAATCCTGCGCGCAT 59.764 50.000 36.48 21.42 0.00 4.73
7245 8731 1.082756 CCGATAAAATCCTGCGCGC 60.083 57.895 27.26 27.26 0.00 6.86
7246 8732 1.157870 ACCCGATAAAATCCTGCGCG 61.158 55.000 0.00 0.00 0.00 6.86
7249 8735 2.158813 TCTGGACCCGATAAAATCCTGC 60.159 50.000 0.00 0.00 31.97 4.85
7261 8747 5.243954 TGACTAAATGAGATATCTGGACCCG 59.756 44.000 10.74 0.00 0.00 5.28
7288 8775 2.295253 ACCGAATTGATCACCGTCTC 57.705 50.000 0.00 0.00 0.00 3.36
7297 8784 6.828273 TGATCAAACAGGATTACCGAATTGAT 59.172 34.615 0.00 0.00 41.83 2.57
7329 8816 4.544968 TGTAGGAGGGGGCCTAAATTAAAA 59.455 41.667 0.84 0.00 41.95 1.52
7368 8884 9.829507 TCAAACCATGAAATAACAAATCTGTTT 57.170 25.926 0.00 0.00 39.80 2.83
7412 8928 9.826574 AACAAAACAGTAACATACTAAGAGTCA 57.173 29.630 0.00 0.00 37.23 3.41
7420 8936 7.262048 CCAAACCAACAAAACAGTAACATACT 58.738 34.615 0.00 0.00 40.28 2.12
7422 8938 6.043411 GCCAAACCAACAAAACAGTAACATA 58.957 36.000 0.00 0.00 0.00 2.29
7476 8996 4.116961 GAGTGCGCTAATTACATGTACCA 58.883 43.478 9.73 0.00 0.00 3.25
7484 9004 2.678336 AGCCAAAGAGTGCGCTAATTAC 59.322 45.455 9.73 0.00 33.54 1.89
7486 9006 1.470098 CAGCCAAAGAGTGCGCTAATT 59.530 47.619 9.73 0.00 33.54 1.40
7487 9007 1.089920 CAGCCAAAGAGTGCGCTAAT 58.910 50.000 9.73 0.00 33.54 1.73
7492 9053 0.386478 GAAAGCAGCCAAAGAGTGCG 60.386 55.000 0.00 0.00 42.26 5.34
7518 9079 2.726351 GCCTAGCAGCCGAACCTCT 61.726 63.158 0.00 0.00 0.00 3.69
7519 9080 2.202946 GCCTAGCAGCCGAACCTC 60.203 66.667 0.00 0.00 0.00 3.85
7520 9081 3.003173 TGCCTAGCAGCCGAACCT 61.003 61.111 0.00 0.00 33.32 3.50
7531 9092 1.136695 CTTCAGTCCAGAGCTGCCTAG 59.863 57.143 0.00 0.00 34.21 3.02
7532 9093 1.189752 CTTCAGTCCAGAGCTGCCTA 58.810 55.000 0.00 0.00 34.21 3.93
7533 9094 1.981636 CTTCAGTCCAGAGCTGCCT 59.018 57.895 0.00 0.00 34.21 4.75
7534 9095 1.744741 GCTTCAGTCCAGAGCTGCC 60.745 63.158 0.00 0.00 34.21 4.85
7535 9096 1.004080 TGCTTCAGTCCAGAGCTGC 60.004 57.895 0.00 0.00 34.21 5.25
7536 9097 0.321021 AGTGCTTCAGTCCAGAGCTG 59.679 55.000 0.00 0.00 35.43 4.24
7537 9098 0.607620 GAGTGCTTCAGTCCAGAGCT 59.392 55.000 0.00 0.00 0.00 4.09
7538 9099 3.135942 GAGTGCTTCAGTCCAGAGC 57.864 57.895 0.00 0.00 0.00 4.09
7544 9105 0.389166 CGTCTGGGAGTGCTTCAGTC 60.389 60.000 0.00 0.00 33.45 3.51
7545 9106 0.827925 TCGTCTGGGAGTGCTTCAGT 60.828 55.000 0.00 0.00 0.00 3.41
7546 9107 0.534412 ATCGTCTGGGAGTGCTTCAG 59.466 55.000 0.00 0.00 0.00 3.02
7547 9108 0.247460 CATCGTCTGGGAGTGCTTCA 59.753 55.000 0.00 0.00 0.00 3.02
7570 9131 3.123804 CTCATGGCACTTACCGTACATC 58.876 50.000 0.00 0.00 0.00 3.06
7571 9132 2.158957 CCTCATGGCACTTACCGTACAT 60.159 50.000 0.00 0.00 0.00 2.29
7572 9133 1.206132 CCTCATGGCACTTACCGTACA 59.794 52.381 0.00 0.00 0.00 2.90
7573 9134 1.472728 CCCTCATGGCACTTACCGTAC 60.473 57.143 0.00 0.00 0.00 3.67
7574 9135 0.828022 CCCTCATGGCACTTACCGTA 59.172 55.000 0.00 0.00 0.00 4.02
7575 9136 1.602237 CCCTCATGGCACTTACCGT 59.398 57.895 0.00 0.00 0.00 4.83
7576 9137 4.540153 CCCTCATGGCACTTACCG 57.460 61.111 0.00 0.00 0.00 4.02
7599 9160 1.453015 ACACCGGCTCAGCAAAACA 60.453 52.632 0.00 0.00 0.00 2.83
7602 9163 1.597854 CTCACACCGGCTCAGCAAA 60.598 57.895 0.00 0.00 0.00 3.68
7625 9190 3.627237 GGGAAATGGGGCACTAAGATTCA 60.627 47.826 0.00 0.00 0.00 2.57
7631 9196 1.700985 GGGGGAAATGGGGCACTAA 59.299 57.895 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.