Multiple sequence alignment - TraesCS7B01G385200

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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 TraesCS7B01G385200 chr7B 100.000 2402 0 0 1 2402 650541050 650538649 0.000000e+00 4436.0
1 TraesCS7B01G385200 chr7B 98.085 1932 36 1 50 1980 650551552 650549621 0.000000e+00 3362.0
2 TraesCS7B01G385200 chr7B 97.219 1978 49 3 4 1980 650585903 650583931 0.000000e+00 3343.0
3 TraesCS7B01G385200 chr7B 97.017 1978 44 3 4 1980 650563122 650561159 0.000000e+00 3312.0
4 TraesCS7B01G385200 chr7B 96.990 1329 40 0 652 1980 650574329 650573001 0.000000e+00 2233.0
5 TraesCS7B01G385200 chr7B 99.866 745 1 0 1 745 650552307 650551563 0.000000e+00 1371.0
6 TraesCS7B01G385200 chr7B 98.871 620 6 1 4 623 650574944 650574326 0.000000e+00 1105.0
7 TraesCS7B01G385200 chr7B 93.827 405 21 2 1983 2387 95310444 95310844 7.340000e-170 606.0
8 TraesCS7B01G385200 chr7B 93.627 408 21 4 1981 2387 285870472 285870875 2.640000e-169 604.0
9 TraesCS7B01G385200 chr7B 93.580 405 22 3 1983 2387 691506768 691506368 3.420000e-168 601.0
10 TraesCS7B01G385200 chr7B 82.819 227 36 3 12 237 663742504 663742280 1.460000e-47 200.0
11 TraesCS7B01G385200 chr7B 91.176 102 9 0 242 343 650601700 650601599 3.220000e-29 139.0
12 TraesCS7B01G385200 chr7B 97.222 36 1 0 369 404 650594819 650594784 7.170000e-06 62.1
13 TraesCS7B01G385200 chr7A 90.803 1457 125 7 422 1871 674803080 674801626 0.000000e+00 1940.0
14 TraesCS7B01G385200 chr7A 89.719 1459 126 9 422 1871 674672456 674671013 0.000000e+00 1842.0
15 TraesCS7B01G385200 chr7A 89.975 1197 104 8 427 1611 674609032 674607840 0.000000e+00 1531.0
16 TraesCS7B01G385200 chr7A 89.115 1231 117 8 427 1644 674797393 674796167 0.000000e+00 1515.0
17 TraesCS7B01G385200 chr7A 82.984 382 47 15 431 808 674522960 674522593 1.780000e-86 329.0
18 TraesCS7B01G385200 chr7A 81.937 382 50 15 431 808 674527229 674526863 3.000000e-79 305.0
19 TraesCS7B01G385200 chr7A 89.216 102 10 1 242 343 674803260 674803160 2.510000e-25 126.0
20 TraesCS7B01G385200 chr7D 91.424 1201 87 7 683 1871 582667168 582665972 0.000000e+00 1633.0
21 TraesCS7B01G385200 chr7D 91.341 1201 87 8 683 1871 582561842 582560647 0.000000e+00 1626.0
22 TraesCS7B01G385200 chr7D 92.308 195 15 0 422 616 582562040 582561846 6.540000e-71 278.0
23 TraesCS7B01G385200 chr7D 92.308 195 15 0 422 616 582667366 582667172 6.540000e-71 278.0
24 TraesCS7B01G385200 chr7D 80.176 227 42 3 12 237 364371067 364371291 1.480000e-37 167.0
25 TraesCS7B01G385200 chr7D 85.088 114 16 1 1868 1980 540373141 540373254 5.430000e-22 115.0
26 TraesCS7B01G385200 chr7D 76.522 115 21 2 431 545 582745180 582745072 9.270000e-05 58.4
27 TraesCS7B01G385200 chr2B 94.335 406 19 3 1983 2387 735776606 735776204 9.430000e-174 619.0
28 TraesCS7B01G385200 chr2B 92.402 408 27 3 1982 2387 650378200 650378605 1.600000e-161 579.0
29 TraesCS7B01G385200 chr4B 93.069 404 23 3 1985 2387 609657745 609657346 9.570000e-164 586.0
30 TraesCS7B01G385200 chr4B 92.629 407 25 3 1983 2387 250319635 250319232 4.450000e-162 580.0
31 TraesCS7B01G385200 chr4B 78.281 221 46 2 18 237 601746259 601746040 8.950000e-30 141.0
32 TraesCS7B01G385200 chr4B 80.000 190 34 4 50 236 22952356 22952544 1.160000e-28 137.0
33 TraesCS7B01G385200 chr5B 92.822 404 27 1 1984 2387 60916960 60917361 3.440000e-163 584.0
34 TraesCS7B01G385200 chr5B 79.828 233 43 4 2 233 381720995 381720766 1.480000e-37 167.0
35 TraesCS7B01G385200 chr5B 88.182 110 10 3 1873 1980 687108721 687108613 6.970000e-26 128.0
36 TraesCS7B01G385200 chr1B 92.308 416 23 4 1979 2387 605786567 605786980 1.240000e-162 582.0
37 TraesCS7B01G385200 chrUn 92.264 349 17 5 1533 1871 478357893 478357545 9.980000e-134 486.0
38 TraesCS7B01G385200 chrUn 91.525 59 4 1 158 215 305090087 305090029 1.980000e-11 80.5
39 TraesCS7B01G385200 chrUn 92.727 55 4 0 275 329 328271498 328271444 1.980000e-11 80.5
40 TraesCS7B01G385200 chrUn 92.727 55 4 0 275 329 403575796 403575742 1.980000e-11 80.5
41 TraesCS7B01G385200 chrUn 92.157 51 3 1 279 329 35545856 35545807 1.190000e-08 71.3
42 TraesCS7B01G385200 chrUn 92.157 51 3 1 279 329 320056662 320056613 1.190000e-08 71.3
43 TraesCS7B01G385200 chr3D 84.052 232 34 3 7 237 580128287 580128516 1.120000e-53 220.0
44 TraesCS7B01G385200 chr5D 83.582 201 31 2 17 216 565183486 565183685 1.130000e-43 187.0
45 TraesCS7B01G385200 chr5D 79.167 216 40 3 1 215 120922693 120922904 6.920000e-31 145.0
46 TraesCS7B01G385200 chr4D 80.932 236 41 4 3 236 417812644 417812877 1.470000e-42 183.0
47 TraesCS7B01G385200 chr4D 78.814 236 34 10 1 235 404666911 404667131 6.920000e-31 145.0
48 TraesCS7B01G385200 chr4D 77.586 232 46 6 7 236 49926359 49926132 4.170000e-28 135.0
49 TraesCS7B01G385200 chr4D 77.830 212 42 5 7 216 49912160 49911952 2.510000e-25 126.0
50 TraesCS7B01G385200 chr4D 79.167 192 28 10 9 195 30143514 30143698 3.240000e-24 122.0
51 TraesCS7B01G385200 chr4D 77.358 212 43 5 7 216 49910377 49910169 1.170000e-23 121.0
52 TraesCS7B01G385200 chr4D 78.049 205 26 14 14 214 71060434 71060623 7.020000e-21 111.0
53 TraesCS7B01G385200 chr4D 82.906 117 15 3 99 215 411555006 411555117 1.520000e-17 100.0
54 TraesCS7B01G385200 chr6A 81.778 225 32 6 7 227 570385798 570386017 1.900000e-41 180.0
55 TraesCS7B01G385200 chr6B 80.335 239 43 4 1 237 169161178 169161414 6.820000e-41 178.0
56 TraesCS7B01G385200 chr6D 80.087 231 41 5 7 235 337847059 337847286 1.480000e-37 167.0
57 TraesCS7B01G385200 chr6D 79.372 223 39 7 17 237 39070609 39070392 1.490000e-32 150.0
58 TraesCS7B01G385200 chr6D 85.321 109 15 1 1873 1980 51984493 51984385 7.020000e-21 111.0
59 TraesCS7B01G385200 chr1D 80.952 210 35 5 30 236 221084007 221084214 6.870000e-36 161.0
60 TraesCS7B01G385200 chr2D 78.632 234 44 5 7 239 616500221 616499993 1.490000e-32 150.0
61 TraesCS7B01G385200 chr2D 84.685 111 14 3 1873 1980 542877621 542877731 9.080000e-20 108.0
62 TraesCS7B01G385200 chr2D 87.143 70 8 1 275 343 60187444 60187375 7.120000e-11 78.7
63 TraesCS7B01G385200 chr1A 90.426 94 8 1 1873 1965 559543142 559543235 3.240000e-24 122.0
64 TraesCS7B01G385200 chr1A 84.466 103 15 1 242 343 302930948 302931050 1.520000e-17 100.0
65 TraesCS7B01G385200 chr3B 84.884 86 13 0 244 329 10307850 10307935 1.180000e-13 87.9


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 TraesCS7B01G385200 chr7B 650538649 650541050 2401 True 4436.0 4436 100.0000 1 2402 1 chr7B.!!$R1 2401
1 TraesCS7B01G385200 chr7B 650583931 650585903 1972 True 3343.0 3343 97.2190 4 1980 1 chr7B.!!$R3 1976
2 TraesCS7B01G385200 chr7B 650561159 650563122 1963 True 3312.0 3312 97.0170 4 1980 1 chr7B.!!$R2 1976
3 TraesCS7B01G385200 chr7B 650549621 650552307 2686 True 2366.5 3362 98.9755 1 1980 2 chr7B.!!$R8 1979
4 TraesCS7B01G385200 chr7B 650573001 650574944 1943 True 1669.0 2233 97.9305 4 1980 2 chr7B.!!$R9 1976
5 TraesCS7B01G385200 chr7A 674671013 674672456 1443 True 1842.0 1842 89.7190 422 1871 1 chr7A.!!$R2 1449
6 TraesCS7B01G385200 chr7A 674607840 674609032 1192 True 1531.0 1531 89.9750 427 1611 1 chr7A.!!$R1 1184
7 TraesCS7B01G385200 chr7A 674796167 674797393 1226 True 1515.0 1515 89.1150 427 1644 1 chr7A.!!$R3 1217
8 TraesCS7B01G385200 chr7A 674801626 674803260 1634 True 1033.0 1940 90.0095 242 1871 2 chr7A.!!$R5 1629
9 TraesCS7B01G385200 chr7A 674522593 674527229 4636 True 317.0 329 82.4605 431 808 2 chr7A.!!$R4 377
10 TraesCS7B01G385200 chr7D 582665972 582667366 1394 True 955.5 1633 91.8660 422 1871 2 chr7D.!!$R3 1449
11 TraesCS7B01G385200 chr7D 582560647 582562040 1393 True 952.0 1626 91.8245 422 1871 2 chr7D.!!$R2 1449

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
797 1549 2.762116 CGTACACACGTAACATGCTG 57.238 50.0 0.0 0.0 43.31 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 5930 0.033504 ATCGGTGCGCCATTAGTAGG 59.966 55.0 18.18 0.0 34.09 3.18 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
797 1549 2.762116 CGTACACACGTAACATGCTG 57.238 50.000 0.00 0.00 43.31 4.41
1054 2604 3.547787 AACCTGGTCCTCCTCGCCT 62.548 63.158 0.00 0.00 34.23 5.52
1100 2668 0.338814 CCACCTGTAGTCCCTACCCT 59.661 60.000 0.00 0.00 36.24 4.34
1161 2729 1.672030 CAGCTGCCCGATGAACACA 60.672 57.895 0.00 0.00 0.00 3.72
1168 2736 1.878102 GCCCGATGAACACACTGAAGT 60.878 52.381 0.00 0.00 0.00 3.01
1170 2738 3.659786 CCCGATGAACACACTGAAGTTA 58.340 45.455 0.00 0.00 0.00 2.24
1179 2758 3.906720 ACACTGAAGTTAGGTGTGTGT 57.093 42.857 11.11 0.00 41.75 3.72
1188 2767 0.751452 TAGGTGTGTGTGCCAACGTA 59.249 50.000 0.00 0.00 0.00 3.57
1326 3565 2.408271 TTCTCGGCATCAAGCTCAAT 57.592 45.000 0.00 0.00 44.79 2.57
1434 4325 8.701908 ATCCATGGATGAATATTATACATGCC 57.298 34.615 26.78 9.10 42.81 4.40
1885 5794 4.074970 CACCTTTTGGAGCATCTACAACT 58.925 43.478 0.00 0.00 44.07 3.16
1990 5922 6.467723 GTGTTGTCCACATTTCACTACTAG 57.532 41.667 0.00 0.00 43.92 2.57
1991 5923 5.408604 GTGTTGTCCACATTTCACTACTAGG 59.591 44.000 0.00 0.00 43.92 3.02
1992 5924 5.305902 TGTTGTCCACATTTCACTACTAGGA 59.694 40.000 0.00 0.00 0.00 2.94
1993 5925 6.183361 TGTTGTCCACATTTCACTACTAGGAA 60.183 38.462 0.00 0.00 0.00 3.36
1994 5926 6.428083 TGTCCACATTTCACTACTAGGAAA 57.572 37.500 0.00 0.00 37.41 3.13
1995 5927 6.833041 TGTCCACATTTCACTACTAGGAAAA 58.167 36.000 0.00 0.00 36.67 2.29
1996 5928 6.934645 TGTCCACATTTCACTACTAGGAAAAG 59.065 38.462 0.00 0.00 36.67 2.27
1997 5929 6.371825 GTCCACATTTCACTACTAGGAAAAGG 59.628 42.308 0.00 0.00 36.67 3.11
1998 5930 5.123979 CCACATTTCACTACTAGGAAAAGGC 59.876 44.000 0.00 0.00 36.67 4.35
1999 5931 5.123979 CACATTTCACTACTAGGAAAAGGCC 59.876 44.000 0.00 0.00 36.67 5.19
2000 5932 5.014228 ACATTTCACTACTAGGAAAAGGCCT 59.986 40.000 0.00 0.00 42.15 5.19
2002 5934 5.672421 TTCACTACTAGGAAAAGGCCTAC 57.328 43.478 5.16 0.00 39.50 3.18
2003 5935 4.944177 TCACTACTAGGAAAAGGCCTACT 58.056 43.478 5.16 4.94 39.50 2.57
2004 5936 6.083487 TCACTACTAGGAAAAGGCCTACTA 57.917 41.667 5.16 5.95 39.50 1.82
2008 5940 5.632034 ACTAGGAAAAGGCCTACTAATGG 57.368 43.478 5.16 0.00 39.50 3.16
2014 5946 3.732470 GCCTACTAATGGCGCACC 58.268 61.111 10.83 0.00 41.03 5.01
2015 5947 2.244651 GCCTACTAATGGCGCACCG 61.245 63.158 10.83 0.00 41.03 4.94
2016 5948 1.440060 CCTACTAATGGCGCACCGA 59.560 57.895 10.83 0.00 39.70 4.69
2018 5950 1.540363 CCTACTAATGGCGCACCGATT 60.540 52.381 10.83 4.05 39.70 3.34
2019 5951 2.210116 CTACTAATGGCGCACCGATTT 58.790 47.619 10.83 0.00 39.70 2.17
2020 5952 1.459450 ACTAATGGCGCACCGATTTT 58.541 45.000 10.83 0.00 39.70 1.82
2021 5953 1.132262 ACTAATGGCGCACCGATTTTG 59.868 47.619 10.83 1.60 39.70 2.44
2022 5954 0.179150 TAATGGCGCACCGATTTTGC 60.179 50.000 10.83 0.00 39.70 3.68
2023 5955 2.834034 AATGGCGCACCGATTTTGCC 62.834 55.000 10.83 0.00 45.91 4.52
2024 5956 3.747976 GGCGCACCGATTTTGCCT 61.748 61.111 10.83 0.00 42.44 4.75
2025 5957 2.403378 GGCGCACCGATTTTGCCTA 61.403 57.895 10.83 0.00 42.44 3.93
2026 5958 1.226295 GCGCACCGATTTTGCCTAC 60.226 57.895 0.30 0.00 36.57 3.18
2027 5959 1.644786 GCGCACCGATTTTGCCTACT 61.645 55.000 0.30 0.00 36.57 2.57
2028 5960 1.647346 CGCACCGATTTTGCCTACTA 58.353 50.000 0.00 0.00 36.57 1.82
2030 5962 2.612212 CGCACCGATTTTGCCTACTAAT 59.388 45.455 0.00 0.00 36.57 1.73
2031 5963 3.546020 CGCACCGATTTTGCCTACTAATG 60.546 47.826 0.00 0.00 36.57 1.90
2032 5964 3.243068 GCACCGATTTTGCCTACTAATGG 60.243 47.826 0.00 0.00 33.58 3.16
2038 5970 4.857251 GCCTACTAATGGCGCACT 57.143 55.556 10.83 0.00 41.03 4.40
2039 5971 3.980583 GCCTACTAATGGCGCACTA 57.019 52.632 10.83 0.00 41.03 2.74
2040 5972 1.499049 GCCTACTAATGGCGCACTAC 58.501 55.000 10.83 0.00 41.03 2.73
2041 5973 1.872653 GCCTACTAATGGCGCACTACC 60.873 57.143 10.83 0.00 41.03 3.18
2042 5974 1.602165 CCTACTAATGGCGCACTACCG 60.602 57.143 10.83 0.00 0.00 4.02
2043 5975 0.386476 TACTAATGGCGCACTACCGG 59.614 55.000 10.83 0.00 0.00 5.28
2044 5976 1.143183 CTAATGGCGCACTACCGGT 59.857 57.895 13.98 13.98 0.00 5.28
2046 5978 2.581208 TAATGGCGCACTACCGGTGG 62.581 60.000 19.93 18.66 45.44 4.61
2051 5983 4.109675 GCACTACCGGTGGGCCAT 62.110 66.667 23.02 0.00 45.44 4.40
2052 5984 2.124736 CACTACCGGTGGGCCATG 60.125 66.667 23.02 7.41 41.90 3.66
2053 5985 2.285069 ACTACCGGTGGGCCATGA 60.285 61.111 23.02 0.00 36.48 3.07
2054 5986 2.367202 ACTACCGGTGGGCCATGAG 61.367 63.158 23.02 9.07 36.48 2.90
2055 5987 2.285069 TACCGGTGGGCCATGAGT 60.285 61.111 19.93 10.09 36.48 3.41
2056 5988 1.001888 TACCGGTGGGCCATGAGTA 59.998 57.895 19.93 8.98 36.48 2.59
2057 5989 1.046472 TACCGGTGGGCCATGAGTAG 61.046 60.000 19.93 0.00 36.48 2.57
2058 5990 2.203070 CGGTGGGCCATGAGTAGC 60.203 66.667 10.70 0.00 34.09 3.58
2059 5991 2.998097 GGTGGGCCATGAGTAGCA 59.002 61.111 10.70 0.00 34.09 3.49
2060 5992 1.452108 GGTGGGCCATGAGTAGCAC 60.452 63.158 10.70 0.00 34.09 4.40
2061 5993 1.815421 GTGGGCCATGAGTAGCACG 60.815 63.158 10.70 0.00 34.16 5.34
2062 5994 2.897350 GGGCCATGAGTAGCACGC 60.897 66.667 4.39 0.00 0.00 5.34
2063 5995 2.897350 GGCCATGAGTAGCACGCC 60.897 66.667 0.00 0.00 37.90 5.68
2064 5996 2.125147 GCCATGAGTAGCACGCCA 60.125 61.111 0.00 0.00 0.00 5.69
2065 5997 2.464459 GCCATGAGTAGCACGCCAC 61.464 63.158 0.00 0.00 0.00 5.01
2066 5998 1.219124 CCATGAGTAGCACGCCACT 59.781 57.895 0.00 0.00 0.00 4.00
2067 5999 0.459899 CCATGAGTAGCACGCCACTA 59.540 55.000 0.00 0.00 0.00 2.74
2068 6000 1.536922 CCATGAGTAGCACGCCACTAG 60.537 57.143 0.00 0.00 0.00 2.57
2069 6001 1.135139 CATGAGTAGCACGCCACTAGT 59.865 52.381 0.00 0.00 0.00 2.57
2070 6002 2.118313 TGAGTAGCACGCCACTAGTA 57.882 50.000 0.00 0.00 0.00 1.82
2071 6003 2.651455 TGAGTAGCACGCCACTAGTAT 58.349 47.619 0.00 0.00 0.00 2.12
2072 6004 3.021695 TGAGTAGCACGCCACTAGTATT 58.978 45.455 0.00 0.00 0.00 1.89
2073 6005 3.446161 TGAGTAGCACGCCACTAGTATTT 59.554 43.478 0.00 0.00 0.00 1.40
2074 6006 4.081862 TGAGTAGCACGCCACTAGTATTTT 60.082 41.667 0.00 0.00 0.00 1.82
2075 6007 4.828829 AGTAGCACGCCACTAGTATTTTT 58.171 39.130 0.00 0.00 0.00 1.94
2110 6042 4.041617 TGGCGCGCCATTAGTATG 57.958 55.556 46.88 0.00 41.89 2.39
2111 6043 1.145156 TGGCGCGCCATTAGTATGT 59.855 52.632 46.88 0.00 41.89 2.29
2112 6044 0.389757 TGGCGCGCCATTAGTATGTA 59.610 50.000 46.88 22.38 41.89 2.29
2113 6045 1.202545 TGGCGCGCCATTAGTATGTAA 60.203 47.619 46.88 21.79 41.89 2.41
2114 6046 1.459592 GGCGCGCCATTAGTATGTAAG 59.540 52.381 43.55 0.00 35.81 2.34
2115 6047 2.400399 GCGCGCCATTAGTATGTAAGA 58.600 47.619 23.24 0.00 0.00 2.10
2116 6048 2.798283 GCGCGCCATTAGTATGTAAGAA 59.202 45.455 23.24 0.00 0.00 2.52
2117 6049 3.432252 GCGCGCCATTAGTATGTAAGAAT 59.568 43.478 23.24 0.00 0.00 2.40
2118 6050 4.624024 GCGCGCCATTAGTATGTAAGAATA 59.376 41.667 23.24 0.00 0.00 1.75
2119 6051 5.291128 GCGCGCCATTAGTATGTAAGAATAT 59.709 40.000 23.24 0.00 0.00 1.28
2120 6052 6.696198 CGCGCCATTAGTATGTAAGAATATG 58.304 40.000 0.00 0.00 0.00 1.78
2121 6053 6.478588 GCGCCATTAGTATGTAAGAATATGC 58.521 40.000 0.00 0.00 0.00 3.14
2122 6054 6.696198 CGCCATTAGTATGTAAGAATATGCG 58.304 40.000 0.00 0.00 0.00 4.73
2123 6055 6.478588 GCCATTAGTATGTAAGAATATGCGC 58.521 40.000 0.00 0.00 0.00 6.09
2124 6056 6.456988 GCCATTAGTATGTAAGAATATGCGCC 60.457 42.308 4.18 0.00 0.00 6.53
2125 6057 6.593770 CCATTAGTATGTAAGAATATGCGCCA 59.406 38.462 4.18 0.00 0.00 5.69
2126 6058 7.280876 CCATTAGTATGTAAGAATATGCGCCAT 59.719 37.037 4.18 0.63 0.00 4.40
2127 6059 8.668353 CATTAGTATGTAAGAATATGCGCCATT 58.332 33.333 4.18 4.18 0.00 3.16
2128 6060 9.884636 ATTAGTATGTAAGAATATGCGCCATTA 57.115 29.630 4.18 0.00 0.00 1.90
2129 6061 7.834068 AGTATGTAAGAATATGCGCCATTAG 57.166 36.000 4.18 0.00 0.00 1.73
2130 6062 7.386851 AGTATGTAAGAATATGCGCCATTAGT 58.613 34.615 4.18 0.00 0.00 2.24
2131 6063 8.528643 AGTATGTAAGAATATGCGCCATTAGTA 58.471 33.333 4.18 0.00 0.00 1.82
2132 6064 9.314321 GTATGTAAGAATATGCGCCATTAGTAT 57.686 33.333 4.18 0.00 0.00 2.12
2133 6065 7.595311 TGTAAGAATATGCGCCATTAGTATG 57.405 36.000 4.18 0.00 0.00 2.39
2134 6066 5.551760 AAGAATATGCGCCATTAGTATGC 57.448 39.130 4.18 0.00 0.00 3.14
2135 6067 3.941483 AGAATATGCGCCATTAGTATGCC 59.059 43.478 4.18 0.00 0.00 4.40
2136 6068 3.634397 ATATGCGCCATTAGTATGCCT 57.366 42.857 4.18 0.00 0.00 4.75
2137 6069 1.813513 ATGCGCCATTAGTATGCCTC 58.186 50.000 4.18 0.00 0.00 4.70
2138 6070 0.250295 TGCGCCATTAGTATGCCTCC 60.250 55.000 4.18 0.00 0.00 4.30
2139 6071 0.955919 GCGCCATTAGTATGCCTCCC 60.956 60.000 0.00 0.00 0.00 4.30
2140 6072 0.670546 CGCCATTAGTATGCCTCCCG 60.671 60.000 0.00 0.00 0.00 5.14
2141 6073 0.321653 GCCATTAGTATGCCTCCCGG 60.322 60.000 0.00 0.00 0.00 5.73
2142 6074 0.324943 CCATTAGTATGCCTCCCGGG 59.675 60.000 16.85 16.85 38.36 5.73
2143 6075 0.324943 CATTAGTATGCCTCCCGGGG 59.675 60.000 23.50 6.77 35.12 5.73
2144 6076 0.840722 ATTAGTATGCCTCCCGGGGG 60.841 60.000 23.50 19.89 35.12 5.40
2158 6090 3.322533 GGGGGCCATACGTAACCA 58.677 61.111 4.39 0.00 0.00 3.67
2159 6091 1.841302 GGGGGCCATACGTAACCAT 59.159 57.895 4.39 0.00 0.00 3.55
2160 6092 0.536460 GGGGGCCATACGTAACCATG 60.536 60.000 4.39 0.00 0.00 3.66
2161 6093 0.181824 GGGGCCATACGTAACCATGT 59.818 55.000 4.39 0.00 0.00 3.21
2162 6094 1.305201 GGGCCATACGTAACCATGTG 58.695 55.000 4.39 0.00 0.00 3.21
2163 6095 0.661020 GGCCATACGTAACCATGTGC 59.339 55.000 0.00 0.54 0.00 4.57
2164 6096 1.663695 GCCATACGTAACCATGTGCT 58.336 50.000 0.00 0.00 0.00 4.40
2165 6097 2.014128 GCCATACGTAACCATGTGCTT 58.986 47.619 0.00 0.00 0.00 3.91
2166 6098 2.422127 GCCATACGTAACCATGTGCTTT 59.578 45.455 0.00 0.00 0.00 3.51
2167 6099 3.730662 GCCATACGTAACCATGTGCTTTG 60.731 47.826 0.00 0.00 0.00 2.77
2168 6100 3.438781 CCATACGTAACCATGTGCTTTGT 59.561 43.478 0.00 0.00 0.00 2.83
2169 6101 4.436852 CCATACGTAACCATGTGCTTTGTC 60.437 45.833 0.00 0.00 0.00 3.18
2170 6102 2.566913 ACGTAACCATGTGCTTTGTCA 58.433 42.857 0.00 0.00 0.00 3.58
2171 6103 3.146066 ACGTAACCATGTGCTTTGTCAT 58.854 40.909 0.00 0.00 0.00 3.06
2172 6104 4.320023 ACGTAACCATGTGCTTTGTCATA 58.680 39.130 0.00 0.00 0.00 2.15
2173 6105 4.153475 ACGTAACCATGTGCTTTGTCATAC 59.847 41.667 0.00 0.00 0.00 2.39
2174 6106 4.391830 CGTAACCATGTGCTTTGTCATACT 59.608 41.667 0.00 0.00 0.00 2.12
2175 6107 5.579119 CGTAACCATGTGCTTTGTCATACTA 59.421 40.000 0.00 0.00 0.00 1.82
2176 6108 6.091577 CGTAACCATGTGCTTTGTCATACTAA 59.908 38.462 0.00 0.00 0.00 2.24
2177 6109 7.201609 CGTAACCATGTGCTTTGTCATACTAAT 60.202 37.037 0.00 0.00 0.00 1.73
2178 6110 6.441093 ACCATGTGCTTTGTCATACTAATG 57.559 37.500 0.00 0.00 0.00 1.90
2179 6111 5.357878 ACCATGTGCTTTGTCATACTAATGG 59.642 40.000 0.00 0.00 33.61 3.16
2180 6112 4.963276 TGTGCTTTGTCATACTAATGGC 57.037 40.909 0.00 0.00 38.26 4.40
2181 6113 4.331108 TGTGCTTTGTCATACTAATGGCA 58.669 39.130 0.00 0.00 45.85 4.92
2196 6128 2.118313 TGGCACAATCTGAGGTGATG 57.882 50.000 14.25 3.95 37.18 3.07
2197 6129 0.737219 GGCACAATCTGAGGTGATGC 59.263 55.000 14.25 11.08 37.18 3.91
2198 6130 0.376152 GCACAATCTGAGGTGATGCG 59.624 55.000 14.25 0.00 37.18 4.73
2199 6131 0.376152 CACAATCTGAGGTGATGCGC 59.624 55.000 0.00 0.00 37.18 6.09
2200 6132 0.745845 ACAATCTGAGGTGATGCGCC 60.746 55.000 4.18 0.00 0.00 6.53
2201 6133 0.745486 CAATCTGAGGTGATGCGCCA 60.745 55.000 4.18 0.00 36.32 5.69
2202 6134 0.182061 AATCTGAGGTGATGCGCCAT 59.818 50.000 4.18 0.00 36.32 4.40
2203 6135 0.182061 ATCTGAGGTGATGCGCCATT 59.818 50.000 4.18 0.00 36.32 3.16
2204 6136 0.829990 TCTGAGGTGATGCGCCATTA 59.170 50.000 4.18 0.00 36.32 1.90
2205 6137 1.202568 TCTGAGGTGATGCGCCATTAG 60.203 52.381 4.18 0.00 36.32 1.73
2206 6138 0.541392 TGAGGTGATGCGCCATTAGT 59.459 50.000 4.18 0.00 36.32 2.24
2207 6139 1.760029 TGAGGTGATGCGCCATTAGTA 59.240 47.619 4.18 0.00 36.32 1.82
2208 6140 2.368548 TGAGGTGATGCGCCATTAGTAT 59.631 45.455 4.18 0.00 36.32 2.12
2209 6141 2.996621 GAGGTGATGCGCCATTAGTATC 59.003 50.000 4.18 0.00 36.32 2.24
2210 6142 2.076863 GGTGATGCGCCATTAGTATCC 58.923 52.381 4.18 0.00 33.65 2.59
2211 6143 2.289694 GGTGATGCGCCATTAGTATCCT 60.290 50.000 4.18 0.00 33.65 3.24
2212 6144 3.403038 GTGATGCGCCATTAGTATCCTT 58.597 45.455 4.18 0.00 31.13 3.36
2213 6145 3.815401 GTGATGCGCCATTAGTATCCTTT 59.185 43.478 4.18 0.00 31.13 3.11
2214 6146 3.814842 TGATGCGCCATTAGTATCCTTTG 59.185 43.478 4.18 0.00 31.13 2.77
2215 6147 2.571212 TGCGCCATTAGTATCCTTTGG 58.429 47.619 4.18 0.00 0.00 3.28
2216 6148 1.266989 GCGCCATTAGTATCCTTTGGC 59.733 52.381 0.00 2.19 41.71 4.52
2217 6149 2.571212 CGCCATTAGTATCCTTTGGCA 58.429 47.619 12.24 0.00 43.67 4.92
2218 6150 3.149196 CGCCATTAGTATCCTTTGGCAT 58.851 45.455 12.24 0.00 43.67 4.40
2219 6151 4.323417 CGCCATTAGTATCCTTTGGCATA 58.677 43.478 12.24 0.00 43.67 3.14
2220 6152 4.154195 CGCCATTAGTATCCTTTGGCATAC 59.846 45.833 12.24 0.00 43.67 2.39
2221 6153 5.316987 GCCATTAGTATCCTTTGGCATACT 58.683 41.667 7.34 3.47 43.29 2.12
2222 6154 6.472887 GCCATTAGTATCCTTTGGCATACTA 58.527 40.000 7.34 1.73 43.29 1.82
2223 6155 6.940298 GCCATTAGTATCCTTTGGCATACTAA 59.060 38.462 15.98 15.98 45.55 2.24
2233 6165 3.006672 GCATACTAATGGCGCACCT 57.993 52.632 10.83 0.00 36.63 4.00
2234 6166 0.588252 GCATACTAATGGCGCACCTG 59.412 55.000 10.83 0.00 36.63 4.00
2235 6167 1.229428 CATACTAATGGCGCACCTGG 58.771 55.000 10.83 0.00 36.63 4.45
2236 6168 1.128200 ATACTAATGGCGCACCTGGA 58.872 50.000 10.83 0.00 36.63 3.86
2237 6169 0.464036 TACTAATGGCGCACCTGGAG 59.536 55.000 10.83 0.27 36.63 3.86
2238 6170 1.524621 CTAATGGCGCACCTGGAGG 60.525 63.158 10.83 0.00 42.17 4.30
2248 6180 4.100084 CCTGGAGGTGATGCGCCA 62.100 66.667 4.18 0.00 36.32 5.69
2249 6181 2.191375 CTGGAGGTGATGCGCCAT 59.809 61.111 4.18 0.00 36.32 4.40
2250 6182 1.452651 CTGGAGGTGATGCGCCATT 60.453 57.895 4.18 0.00 36.32 3.16
2251 6183 0.179048 CTGGAGGTGATGCGCCATTA 60.179 55.000 4.18 0.00 36.32 1.90
2252 6184 0.179048 TGGAGGTGATGCGCCATTAG 60.179 55.000 4.18 0.00 36.32 1.73
2253 6185 0.179045 GGAGGTGATGCGCCATTAGT 60.179 55.000 4.18 0.00 36.32 2.24
2254 6186 0.940126 GAGGTGATGCGCCATTAGTG 59.060 55.000 4.18 0.00 36.32 2.74
2255 6187 0.253044 AGGTGATGCGCCATTAGTGT 59.747 50.000 4.18 0.00 36.32 3.55
2256 6188 0.378257 GGTGATGCGCCATTAGTGTG 59.622 55.000 4.18 0.00 33.65 3.82
2257 6189 1.368641 GTGATGCGCCATTAGTGTGA 58.631 50.000 4.18 0.00 0.00 3.58
2258 6190 1.737236 GTGATGCGCCATTAGTGTGAA 59.263 47.619 4.18 0.00 0.00 3.18
2259 6191 2.355756 GTGATGCGCCATTAGTGTGAAT 59.644 45.455 4.18 0.00 0.00 2.57
2260 6192 3.559655 GTGATGCGCCATTAGTGTGAATA 59.440 43.478 4.18 0.00 0.00 1.75
2261 6193 4.214119 GTGATGCGCCATTAGTGTGAATAT 59.786 41.667 4.18 0.00 0.00 1.28
2262 6194 4.821260 TGATGCGCCATTAGTGTGAATATT 59.179 37.500 4.18 0.00 0.00 1.28
2263 6195 5.299028 TGATGCGCCATTAGTGTGAATATTT 59.701 36.000 4.18 0.00 0.00 1.40
2264 6196 4.919206 TGCGCCATTAGTGTGAATATTTG 58.081 39.130 4.18 0.00 0.00 2.32
2265 6197 4.397730 TGCGCCATTAGTGTGAATATTTGT 59.602 37.500 4.18 0.00 0.00 2.83
2266 6198 5.105957 TGCGCCATTAGTGTGAATATTTGTT 60.106 36.000 4.18 0.00 0.00 2.83
2267 6199 5.804979 GCGCCATTAGTGTGAATATTTGTTT 59.195 36.000 0.00 0.00 0.00 2.83
2268 6200 6.310224 GCGCCATTAGTGTGAATATTTGTTTT 59.690 34.615 0.00 0.00 0.00 2.43
2269 6201 7.148656 GCGCCATTAGTGTGAATATTTGTTTTT 60.149 33.333 0.00 0.00 0.00 1.94
2296 6228 7.769272 TTTACTTTTCTGATTTTTGCACAGG 57.231 32.000 1.84 0.00 33.19 4.00
2297 6229 5.343307 ACTTTTCTGATTTTTGCACAGGT 57.657 34.783 1.84 0.00 33.19 4.00
2298 6230 5.733676 ACTTTTCTGATTTTTGCACAGGTT 58.266 33.333 1.84 0.00 33.19 3.50
2299 6231 6.872920 ACTTTTCTGATTTTTGCACAGGTTA 58.127 32.000 1.84 0.00 33.19 2.85
2300 6232 6.756542 ACTTTTCTGATTTTTGCACAGGTTAC 59.243 34.615 1.84 0.00 33.19 2.50
2301 6233 5.843673 TTCTGATTTTTGCACAGGTTACA 57.156 34.783 1.84 0.00 33.19 2.41
2302 6234 5.843673 TCTGATTTTTGCACAGGTTACAA 57.156 34.783 1.84 0.00 33.19 2.41
2303 6235 6.214191 TCTGATTTTTGCACAGGTTACAAA 57.786 33.333 1.84 0.00 33.19 2.83
2304 6236 6.634805 TCTGATTTTTGCACAGGTTACAAAA 58.365 32.000 1.84 6.18 40.47 2.44
2305 6237 7.271511 TCTGATTTTTGCACAGGTTACAAAAT 58.728 30.769 9.59 2.04 41.44 1.82
2306 6238 8.417106 TCTGATTTTTGCACAGGTTACAAAATA 58.583 29.630 9.59 4.27 41.44 1.40
2307 6239 9.206870 CTGATTTTTGCACAGGTTACAAAATAT 57.793 29.630 9.59 7.36 41.44 1.28
2333 6265 8.668510 ATTATTGGACAAAGTATAGACAGCAG 57.331 34.615 0.00 0.00 0.00 4.24
2334 6266 3.861840 TGGACAAAGTATAGACAGCAGC 58.138 45.455 0.00 0.00 0.00 5.25
2335 6267 3.260632 TGGACAAAGTATAGACAGCAGCA 59.739 43.478 0.00 0.00 0.00 4.41
2336 6268 3.619038 GGACAAAGTATAGACAGCAGCAC 59.381 47.826 0.00 0.00 0.00 4.40
2337 6269 4.245660 GACAAAGTATAGACAGCAGCACA 58.754 43.478 0.00 0.00 0.00 4.57
2338 6270 3.997021 ACAAAGTATAGACAGCAGCACAC 59.003 43.478 0.00 0.00 0.00 3.82
2339 6271 3.961480 AAGTATAGACAGCAGCACACA 57.039 42.857 0.00 0.00 0.00 3.72
2340 6272 3.961480 AGTATAGACAGCAGCACACAA 57.039 42.857 0.00 0.00 0.00 3.33
2341 6273 3.589988 AGTATAGACAGCAGCACACAAC 58.410 45.455 0.00 0.00 0.00 3.32
2342 6274 2.549064 ATAGACAGCAGCACACAACA 57.451 45.000 0.00 0.00 0.00 3.33
2343 6275 2.323968 TAGACAGCAGCACACAACAA 57.676 45.000 0.00 0.00 0.00 2.83
2344 6276 1.683943 AGACAGCAGCACACAACAAT 58.316 45.000 0.00 0.00 0.00 2.71
2345 6277 2.849942 AGACAGCAGCACACAACAATA 58.150 42.857 0.00 0.00 0.00 1.90
2346 6278 2.810274 AGACAGCAGCACACAACAATAG 59.190 45.455 0.00 0.00 0.00 1.73
2347 6279 1.267806 ACAGCAGCACACAACAATAGC 59.732 47.619 0.00 0.00 0.00 2.97
2348 6280 1.267533 CAGCAGCACACAACAATAGCA 59.732 47.619 0.00 0.00 0.00 3.49
2349 6281 1.538512 AGCAGCACACAACAATAGCAG 59.461 47.619 0.00 0.00 0.00 4.24
2350 6282 1.536766 GCAGCACACAACAATAGCAGA 59.463 47.619 0.00 0.00 0.00 4.26
2351 6283 2.163010 GCAGCACACAACAATAGCAGAT 59.837 45.455 0.00 0.00 0.00 2.90
2352 6284 3.366679 GCAGCACACAACAATAGCAGATT 60.367 43.478 0.00 0.00 0.00 2.40
2353 6285 4.409570 CAGCACACAACAATAGCAGATTC 58.590 43.478 0.00 0.00 0.00 2.52
2354 6286 4.074259 AGCACACAACAATAGCAGATTCA 58.926 39.130 0.00 0.00 0.00 2.57
2355 6287 4.703575 AGCACACAACAATAGCAGATTCAT 59.296 37.500 0.00 0.00 0.00 2.57
2356 6288 5.032863 GCACACAACAATAGCAGATTCATC 58.967 41.667 0.00 0.00 0.00 2.92
2357 6289 5.260900 CACACAACAATAGCAGATTCATCG 58.739 41.667 0.00 0.00 0.00 3.84
2358 6290 5.063817 CACACAACAATAGCAGATTCATCGA 59.936 40.000 0.00 0.00 0.00 3.59
2359 6291 5.643348 ACACAACAATAGCAGATTCATCGAA 59.357 36.000 0.00 0.00 0.00 3.71
2360 6292 6.317140 ACACAACAATAGCAGATTCATCGAAT 59.683 34.615 0.00 0.00 34.71 3.34
2361 6293 7.495606 ACACAACAATAGCAGATTCATCGAATA 59.504 33.333 0.00 0.00 31.89 1.75
2362 6294 7.795734 CACAACAATAGCAGATTCATCGAATAC 59.204 37.037 0.00 0.00 31.89 1.89
2363 6295 7.495606 ACAACAATAGCAGATTCATCGAATACA 59.504 33.333 0.00 0.00 31.89 2.29
2364 6296 8.337532 CAACAATAGCAGATTCATCGAATACAA 58.662 33.333 0.00 0.00 31.89 2.41
2365 6297 8.613060 ACAATAGCAGATTCATCGAATACAAT 57.387 30.769 0.00 0.00 31.89 2.71
2366 6298 9.060347 ACAATAGCAGATTCATCGAATACAATT 57.940 29.630 0.00 0.00 31.89 2.32
2367 6299 9.539139 CAATAGCAGATTCATCGAATACAATTC 57.461 33.333 0.00 0.00 31.89 2.17
2368 6300 8.837788 ATAGCAGATTCATCGAATACAATTCA 57.162 30.769 0.00 0.00 31.89 2.57
2369 6301 7.741027 AGCAGATTCATCGAATACAATTCAT 57.259 32.000 0.00 0.00 31.89 2.57
2370 6302 7.804712 AGCAGATTCATCGAATACAATTCATC 58.195 34.615 0.00 0.00 31.89 2.92
2371 6303 7.443272 AGCAGATTCATCGAATACAATTCATCA 59.557 33.333 0.00 0.00 31.89 3.07
2372 6304 8.235226 GCAGATTCATCGAATACAATTCATCAT 58.765 33.333 0.00 0.00 31.89 2.45
2387 6319 9.784531 ACAATTCATCATATTAGTCTCCGAATT 57.215 29.630 0.00 0.00 32.37 2.17
2397 6329 6.956299 TTAGTCTCCGAATTTAAAAGACCG 57.044 37.500 11.59 4.77 37.63 4.79
2398 6330 5.143376 AGTCTCCGAATTTAAAAGACCGA 57.857 39.130 11.59 0.00 37.63 4.69
2399 6331 5.544650 AGTCTCCGAATTTAAAAGACCGAA 58.455 37.500 11.59 0.00 37.63 4.30
2400 6332 5.407691 AGTCTCCGAATTTAAAAGACCGAAC 59.592 40.000 11.59 0.00 37.63 3.95
2401 6333 5.178067 GTCTCCGAATTTAAAAGACCGAACA 59.822 40.000 5.91 0.00 32.13 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1161 2729 2.561569 GCACACACACCTAACTTCAGT 58.438 47.619 0.00 0.00 0.00 3.41
1168 2736 0.107606 ACGTTGGCACACACACCTAA 60.108 50.000 0.00 0.00 39.29 2.69
1170 2738 0.107831 ATACGTTGGCACACACACCT 59.892 50.000 0.00 0.00 39.29 4.00
1179 2758 0.878416 GCAGGTTCAATACGTTGGCA 59.122 50.000 0.00 0.00 35.99 4.92
1188 2767 2.574006 TGAGCTTCAGCAGGTTCAAT 57.426 45.000 0.75 0.00 45.16 2.57
1434 4325 9.208169 CAAACTAGTTACGAGTAGAACGATTAG 57.792 37.037 8.92 0.00 33.74 1.73
1980 5912 5.339477 AGTAGGCCTTTTCCTAGTAGTGAA 58.661 41.667 12.58 0.00 39.85 3.18
1981 5913 4.944177 AGTAGGCCTTTTCCTAGTAGTGA 58.056 43.478 12.58 0.00 39.85 3.41
1982 5914 6.786967 TTAGTAGGCCTTTTCCTAGTAGTG 57.213 41.667 12.58 0.00 42.48 2.74
1984 5916 6.741801 GCCATTAGTAGGCCTTTTCCTAGTAG 60.742 46.154 12.58 0.00 46.50 2.57
1985 5917 5.071384 GCCATTAGTAGGCCTTTTCCTAGTA 59.929 44.000 12.58 0.00 46.50 1.82
1987 5919 4.390264 GCCATTAGTAGGCCTTTTCCTAG 58.610 47.826 12.58 0.00 46.50 3.02
1989 5921 3.298686 GCCATTAGTAGGCCTTTTCCT 57.701 47.619 12.58 4.76 46.50 3.36
1998 5930 0.033504 ATCGGTGCGCCATTAGTAGG 59.966 55.000 18.18 0.00 34.09 3.18
1999 5931 1.865865 AATCGGTGCGCCATTAGTAG 58.134 50.000 18.18 0.00 34.09 2.57
2000 5932 2.319136 AAATCGGTGCGCCATTAGTA 57.681 45.000 18.18 0.00 34.09 1.82
2002 5934 1.826327 CAAAATCGGTGCGCCATTAG 58.174 50.000 18.18 0.00 34.09 1.73
2003 5935 0.179150 GCAAAATCGGTGCGCCATTA 60.179 50.000 18.18 0.70 31.20 1.90
2004 5936 1.445926 GCAAAATCGGTGCGCCATT 60.446 52.632 18.18 12.09 31.20 3.16
2008 5940 1.226295 GTAGGCAAAATCGGTGCGC 60.226 57.895 0.00 0.00 43.18 6.09
2009 5941 1.647346 TAGTAGGCAAAATCGGTGCG 58.353 50.000 0.00 0.00 43.18 5.34
2010 5942 3.243068 CCATTAGTAGGCAAAATCGGTGC 60.243 47.826 0.00 0.00 41.45 5.01
2022 5954 1.602165 CGGTAGTGCGCCATTAGTAGG 60.602 57.143 4.18 0.00 0.00 3.18
2023 5955 1.602165 CCGGTAGTGCGCCATTAGTAG 60.602 57.143 4.18 0.00 0.00 2.57
2024 5956 0.386476 CCGGTAGTGCGCCATTAGTA 59.614 55.000 4.18 0.00 0.00 1.82
2025 5957 1.143183 CCGGTAGTGCGCCATTAGT 59.857 57.895 4.18 0.00 0.00 2.24
2026 5958 1.143183 ACCGGTAGTGCGCCATTAG 59.857 57.895 4.49 0.00 0.00 1.73
2027 5959 1.153529 CACCGGTAGTGCGCCATTA 60.154 57.895 6.87 0.00 40.28 1.90
2028 5960 2.435938 CACCGGTAGTGCGCCATT 60.436 61.111 6.87 0.00 40.28 3.16
2034 5966 4.109675 ATGGCCCACCGGTAGTGC 62.110 66.667 6.87 10.45 45.83 4.40
2035 5967 2.124736 CATGGCCCACCGGTAGTG 60.125 66.667 6.87 0.00 46.83 2.74
2036 5968 2.285069 TCATGGCCCACCGGTAGT 60.285 61.111 6.87 0.00 39.70 2.73
2037 5969 1.046472 TACTCATGGCCCACCGGTAG 61.046 60.000 6.87 0.00 39.70 3.18
2038 5970 1.001888 TACTCATGGCCCACCGGTA 59.998 57.895 6.87 0.00 39.70 4.02
2039 5971 2.285069 TACTCATGGCCCACCGGT 60.285 61.111 0.00 0.00 39.70 5.28
2040 5972 2.505982 CTACTCATGGCCCACCGG 59.494 66.667 0.00 0.00 39.70 5.28
2041 5973 2.203070 GCTACTCATGGCCCACCG 60.203 66.667 0.00 0.00 39.70 4.94
2042 5974 1.452108 GTGCTACTCATGGCCCACC 60.452 63.158 0.00 0.00 0.00 4.61
2043 5975 1.815421 CGTGCTACTCATGGCCCAC 60.815 63.158 0.00 0.00 0.00 4.61
2044 5976 2.584064 CGTGCTACTCATGGCCCA 59.416 61.111 0.00 0.00 0.00 5.36
2045 5977 2.897350 GCGTGCTACTCATGGCCC 60.897 66.667 0.00 0.00 32.31 5.80
2048 5980 0.459899 TAGTGGCGTGCTACTCATGG 59.540 55.000 14.37 0.00 38.66 3.66
2049 5981 1.135139 ACTAGTGGCGTGCTACTCATG 59.865 52.381 14.37 8.80 38.66 3.07
2050 5982 1.475403 ACTAGTGGCGTGCTACTCAT 58.525 50.000 14.37 1.51 38.66 2.90
2051 5983 2.118313 TACTAGTGGCGTGCTACTCA 57.882 50.000 14.37 0.00 38.66 3.41
2052 5984 3.712091 AATACTAGTGGCGTGCTACTC 57.288 47.619 14.37 0.00 38.66 2.59
2053 5985 4.467198 AAAATACTAGTGGCGTGCTACT 57.533 40.909 15.27 15.27 40.78 2.57
2094 6026 1.459592 CTTACATACTAATGGCGCGCC 59.540 52.381 42.35 42.35 37.43 6.53
2095 6027 2.400399 TCTTACATACTAATGGCGCGC 58.600 47.619 25.94 25.94 37.43 6.86
2096 6028 6.696198 CATATTCTTACATACTAATGGCGCG 58.304 40.000 0.00 0.00 37.43 6.86
2097 6029 6.478588 GCATATTCTTACATACTAATGGCGC 58.521 40.000 0.00 0.00 37.43 6.53
2098 6030 6.696198 CGCATATTCTTACATACTAATGGCG 58.304 40.000 0.00 0.00 37.43 5.69
2099 6031 6.456988 GGCGCATATTCTTACATACTAATGGC 60.457 42.308 10.83 0.00 37.43 4.40
2100 6032 6.593770 TGGCGCATATTCTTACATACTAATGG 59.406 38.462 10.83 0.00 37.43 3.16
2101 6033 7.595311 TGGCGCATATTCTTACATACTAATG 57.405 36.000 10.83 0.00 39.17 1.90
2102 6034 8.792830 AATGGCGCATATTCTTACATACTAAT 57.207 30.769 10.83 0.00 0.00 1.73
2103 6035 9.366216 CTAATGGCGCATATTCTTACATACTAA 57.634 33.333 10.83 0.00 0.00 2.24
2104 6036 8.528643 ACTAATGGCGCATATTCTTACATACTA 58.471 33.333 10.83 0.00 0.00 1.82
2105 6037 7.386851 ACTAATGGCGCATATTCTTACATACT 58.613 34.615 10.83 0.00 0.00 2.12
2106 6038 7.596749 ACTAATGGCGCATATTCTTACATAC 57.403 36.000 10.83 0.00 0.00 2.39
2107 6039 9.313118 CATACTAATGGCGCATATTCTTACATA 57.687 33.333 10.83 0.00 0.00 2.29
2108 6040 7.201644 GCATACTAATGGCGCATATTCTTACAT 60.202 37.037 10.83 0.00 33.38 2.29
2109 6041 6.092122 GCATACTAATGGCGCATATTCTTACA 59.908 38.462 10.83 0.00 33.38 2.41
2110 6042 6.478588 GCATACTAATGGCGCATATTCTTAC 58.521 40.000 10.83 0.00 33.38 2.34
2111 6043 6.662414 GCATACTAATGGCGCATATTCTTA 57.338 37.500 10.83 4.87 33.38 2.10
2112 6044 5.551760 GCATACTAATGGCGCATATTCTT 57.448 39.130 10.83 2.77 33.38 2.52
2141 6073 0.536460 CATGGTTACGTATGGCCCCC 60.536 60.000 0.00 0.00 0.00 5.40
2142 6074 0.181824 ACATGGTTACGTATGGCCCC 59.818 55.000 0.00 0.00 0.00 5.80
2143 6075 1.305201 CACATGGTTACGTATGGCCC 58.695 55.000 0.00 0.00 0.00 5.80
2144 6076 0.661020 GCACATGGTTACGTATGGCC 59.339 55.000 0.00 0.00 0.00 5.36
2145 6077 1.663695 AGCACATGGTTACGTATGGC 58.336 50.000 0.00 0.00 0.00 4.40
2146 6078 3.438781 ACAAAGCACATGGTTACGTATGG 59.561 43.478 0.00 0.00 35.00 2.74
2147 6079 4.153296 TGACAAAGCACATGGTTACGTATG 59.847 41.667 0.00 0.00 35.00 2.39
2148 6080 4.320023 TGACAAAGCACATGGTTACGTAT 58.680 39.130 0.00 0.00 35.00 3.06
2149 6081 3.729966 TGACAAAGCACATGGTTACGTA 58.270 40.909 0.00 0.00 35.00 3.57
2150 6082 2.566913 TGACAAAGCACATGGTTACGT 58.433 42.857 0.00 0.00 35.00 3.57
2151 6083 3.829886 ATGACAAAGCACATGGTTACG 57.170 42.857 0.00 0.00 35.00 3.18
2152 6084 5.880054 AGTATGACAAAGCACATGGTTAC 57.120 39.130 0.00 0.00 35.00 2.50
2153 6085 7.066887 CCATTAGTATGACAAAGCACATGGTTA 59.933 37.037 0.00 0.00 32.81 2.85
2154 6086 6.127647 CCATTAGTATGACAAAGCACATGGTT 60.128 38.462 0.00 0.00 33.81 3.67
2155 6087 5.357878 CCATTAGTATGACAAAGCACATGGT 59.642 40.000 0.00 0.00 33.37 3.55
2156 6088 5.734220 GCCATTAGTATGACAAAGCACATGG 60.734 44.000 0.00 0.00 33.37 3.66
2157 6089 5.163632 TGCCATTAGTATGACAAAGCACATG 60.164 40.000 0.00 0.00 33.37 3.21
2158 6090 4.949238 TGCCATTAGTATGACAAAGCACAT 59.051 37.500 0.00 0.00 33.37 3.21
2159 6091 4.155826 GTGCCATTAGTATGACAAAGCACA 59.844 41.667 6.44 0.00 41.04 4.57
2160 6092 4.155826 TGTGCCATTAGTATGACAAAGCAC 59.844 41.667 0.00 0.00 41.40 4.40
2161 6093 4.331108 TGTGCCATTAGTATGACAAAGCA 58.669 39.130 0.00 0.00 33.37 3.91
2162 6094 4.963276 TGTGCCATTAGTATGACAAAGC 57.037 40.909 0.00 0.00 33.37 3.51
2163 6095 7.066163 TCAGATTGTGCCATTAGTATGACAAAG 59.934 37.037 0.00 0.00 34.27 2.77
2164 6096 6.883756 TCAGATTGTGCCATTAGTATGACAAA 59.116 34.615 0.00 0.00 34.27 2.83
2165 6097 6.413892 TCAGATTGTGCCATTAGTATGACAA 58.586 36.000 0.00 0.00 34.75 3.18
2166 6098 5.988287 TCAGATTGTGCCATTAGTATGACA 58.012 37.500 0.00 0.00 33.37 3.58
2167 6099 5.468072 CCTCAGATTGTGCCATTAGTATGAC 59.532 44.000 0.00 0.00 33.37 3.06
2168 6100 5.130975 ACCTCAGATTGTGCCATTAGTATGA 59.869 40.000 0.00 0.00 33.37 2.15
2169 6101 5.237996 CACCTCAGATTGTGCCATTAGTATG 59.762 44.000 0.00 0.00 0.00 2.39
2170 6102 5.130975 TCACCTCAGATTGTGCCATTAGTAT 59.869 40.000 0.00 0.00 32.51 2.12
2171 6103 4.469586 TCACCTCAGATTGTGCCATTAGTA 59.530 41.667 0.00 0.00 32.51 1.82
2172 6104 3.264193 TCACCTCAGATTGTGCCATTAGT 59.736 43.478 0.00 0.00 32.51 2.24
2173 6105 3.877559 TCACCTCAGATTGTGCCATTAG 58.122 45.455 0.00 0.00 32.51 1.73
2174 6106 3.998913 TCACCTCAGATTGTGCCATTA 57.001 42.857 0.00 0.00 32.51 1.90
2175 6107 2.885135 TCACCTCAGATTGTGCCATT 57.115 45.000 0.00 0.00 32.51 3.16
2176 6108 2.651455 CATCACCTCAGATTGTGCCAT 58.349 47.619 0.00 0.00 32.51 4.40
2177 6109 1.951895 GCATCACCTCAGATTGTGCCA 60.952 52.381 0.00 0.00 32.51 4.92
2178 6110 0.737219 GCATCACCTCAGATTGTGCC 59.263 55.000 0.00 0.00 32.51 5.01
2179 6111 0.376152 CGCATCACCTCAGATTGTGC 59.624 55.000 0.00 0.00 32.51 4.57
2180 6112 0.376152 GCGCATCACCTCAGATTGTG 59.624 55.000 0.30 0.00 0.00 3.33
2181 6113 0.745845 GGCGCATCACCTCAGATTGT 60.746 55.000 10.83 0.00 0.00 2.71
2182 6114 0.745486 TGGCGCATCACCTCAGATTG 60.745 55.000 10.83 0.00 0.00 2.67
2183 6115 0.182061 ATGGCGCATCACCTCAGATT 59.818 50.000 10.83 0.00 0.00 2.40
2184 6116 0.182061 AATGGCGCATCACCTCAGAT 59.818 50.000 10.83 0.00 0.00 2.90
2185 6117 0.829990 TAATGGCGCATCACCTCAGA 59.170 50.000 10.83 0.00 0.00 3.27
2186 6118 1.224075 CTAATGGCGCATCACCTCAG 58.776 55.000 10.83 0.00 0.00 3.35
2187 6119 0.541392 ACTAATGGCGCATCACCTCA 59.459 50.000 10.83 0.00 0.00 3.86
2188 6120 2.526304 TACTAATGGCGCATCACCTC 57.474 50.000 10.83 0.00 0.00 3.85
2189 6121 2.289694 GGATACTAATGGCGCATCACCT 60.290 50.000 10.83 0.00 0.00 4.00
2190 6122 2.076863 GGATACTAATGGCGCATCACC 58.923 52.381 10.83 0.00 0.00 4.02
2205 6137 4.154195 CGCCATTAGTATGCCAAAGGATAC 59.846 45.833 0.00 0.00 0.00 2.24
2206 6138 4.323417 CGCCATTAGTATGCCAAAGGATA 58.677 43.478 0.00 0.00 0.00 2.59
2207 6139 3.149196 CGCCATTAGTATGCCAAAGGAT 58.851 45.455 0.00 0.00 0.00 3.24
2208 6140 2.571212 CGCCATTAGTATGCCAAAGGA 58.429 47.619 0.00 0.00 0.00 3.36
2209 6141 1.001378 GCGCCATTAGTATGCCAAAGG 60.001 52.381 0.00 0.00 0.00 3.11
2210 6142 1.675483 TGCGCCATTAGTATGCCAAAG 59.325 47.619 4.18 0.00 0.00 2.77
2211 6143 1.403679 GTGCGCCATTAGTATGCCAAA 59.596 47.619 4.18 0.00 0.00 3.28
2212 6144 1.021202 GTGCGCCATTAGTATGCCAA 58.979 50.000 4.18 0.00 0.00 4.52
2213 6145 0.817634 GGTGCGCCATTAGTATGCCA 60.818 55.000 12.58 0.00 34.09 4.92
2214 6146 0.535102 AGGTGCGCCATTAGTATGCC 60.535 55.000 20.59 0.00 37.19 4.40
2215 6147 0.588252 CAGGTGCGCCATTAGTATGC 59.412 55.000 20.59 0.00 37.19 3.14
2216 6148 1.202639 TCCAGGTGCGCCATTAGTATG 60.203 52.381 20.59 5.73 37.19 2.39
2217 6149 1.070758 CTCCAGGTGCGCCATTAGTAT 59.929 52.381 20.59 0.00 37.19 2.12
2218 6150 0.464036 CTCCAGGTGCGCCATTAGTA 59.536 55.000 20.59 0.00 37.19 1.82
2219 6151 1.221840 CTCCAGGTGCGCCATTAGT 59.778 57.895 20.59 0.00 37.19 2.24
2220 6152 1.524621 CCTCCAGGTGCGCCATTAG 60.525 63.158 20.59 11.65 37.19 1.73
2221 6153 2.589540 CCTCCAGGTGCGCCATTA 59.410 61.111 20.59 1.38 37.19 1.90
2231 6163 2.898920 AATGGCGCATCACCTCCAGG 62.899 60.000 10.83 0.00 42.17 4.45
2232 6164 0.179048 TAATGGCGCATCACCTCCAG 60.179 55.000 10.83 0.00 31.36 3.86
2233 6165 0.179048 CTAATGGCGCATCACCTCCA 60.179 55.000 10.83 0.00 0.00 3.86
2234 6166 0.179045 ACTAATGGCGCATCACCTCC 60.179 55.000 10.83 0.00 0.00 4.30
2235 6167 0.940126 CACTAATGGCGCATCACCTC 59.060 55.000 10.83 0.00 0.00 3.85
2236 6168 0.253044 ACACTAATGGCGCATCACCT 59.747 50.000 10.83 0.00 0.00 4.00
2237 6169 0.378257 CACACTAATGGCGCATCACC 59.622 55.000 10.83 0.00 0.00 4.02
2238 6170 1.368641 TCACACTAATGGCGCATCAC 58.631 50.000 10.83 0.00 0.00 3.06
2239 6171 2.106477 TTCACACTAATGGCGCATCA 57.894 45.000 10.83 0.00 0.00 3.07
2240 6172 5.362556 AATATTCACACTAATGGCGCATC 57.637 39.130 10.83 0.00 0.00 3.91
2241 6173 5.067674 ACAAATATTCACACTAATGGCGCAT 59.932 36.000 10.83 0.00 0.00 4.73
2242 6174 4.397730 ACAAATATTCACACTAATGGCGCA 59.602 37.500 10.83 0.00 0.00 6.09
2243 6175 4.920376 ACAAATATTCACACTAATGGCGC 58.080 39.130 0.00 0.00 0.00 6.53
2244 6176 7.810766 AAAACAAATATTCACACTAATGGCG 57.189 32.000 0.00 0.00 0.00 5.69
2270 6202 8.663911 CCTGTGCAAAAATCAGAAAAGTAAAAA 58.336 29.630 2.98 0.00 0.00 1.94
2271 6203 7.821846 ACCTGTGCAAAAATCAGAAAAGTAAAA 59.178 29.630 2.98 0.00 0.00 1.52
2272 6204 7.327214 ACCTGTGCAAAAATCAGAAAAGTAAA 58.673 30.769 2.98 0.00 0.00 2.01
2273 6205 6.872920 ACCTGTGCAAAAATCAGAAAAGTAA 58.127 32.000 2.98 0.00 0.00 2.24
2274 6206 6.463995 ACCTGTGCAAAAATCAGAAAAGTA 57.536 33.333 2.98 0.00 0.00 2.24
2275 6207 5.343307 ACCTGTGCAAAAATCAGAAAAGT 57.657 34.783 2.98 0.00 0.00 2.66
2276 6208 6.756074 TGTAACCTGTGCAAAAATCAGAAAAG 59.244 34.615 2.98 0.00 0.00 2.27
2277 6209 6.634805 TGTAACCTGTGCAAAAATCAGAAAA 58.365 32.000 2.98 0.00 0.00 2.29
2278 6210 6.214191 TGTAACCTGTGCAAAAATCAGAAA 57.786 33.333 2.98 0.00 0.00 2.52
2279 6211 5.843673 TGTAACCTGTGCAAAAATCAGAA 57.156 34.783 2.98 0.00 0.00 3.02
2280 6212 5.843673 TTGTAACCTGTGCAAAAATCAGA 57.156 34.783 2.98 0.00 0.00 3.27
2281 6213 6.900568 TTTTGTAACCTGTGCAAAAATCAG 57.099 33.333 0.00 0.00 38.59 2.90
2307 6239 9.764363 CTGCTGTCTATACTTTGTCCAATAATA 57.236 33.333 0.00 0.00 0.00 0.98
2308 6240 7.227512 GCTGCTGTCTATACTTTGTCCAATAAT 59.772 37.037 0.00 0.00 0.00 1.28
2309 6241 6.538742 GCTGCTGTCTATACTTTGTCCAATAA 59.461 38.462 0.00 0.00 0.00 1.40
2310 6242 6.049149 GCTGCTGTCTATACTTTGTCCAATA 58.951 40.000 0.00 0.00 0.00 1.90
2311 6243 4.878397 GCTGCTGTCTATACTTTGTCCAAT 59.122 41.667 0.00 0.00 0.00 3.16
2312 6244 4.253685 GCTGCTGTCTATACTTTGTCCAA 58.746 43.478 0.00 0.00 0.00 3.53
2313 6245 3.260632 TGCTGCTGTCTATACTTTGTCCA 59.739 43.478 0.00 0.00 0.00 4.02
2314 6246 3.619038 GTGCTGCTGTCTATACTTTGTCC 59.381 47.826 0.00 0.00 0.00 4.02
2315 6247 4.092091 GTGTGCTGCTGTCTATACTTTGTC 59.908 45.833 0.00 0.00 0.00 3.18
2316 6248 3.997021 GTGTGCTGCTGTCTATACTTTGT 59.003 43.478 0.00 0.00 0.00 2.83
2317 6249 3.996363 TGTGTGCTGCTGTCTATACTTTG 59.004 43.478 0.00 0.00 0.00 2.77
2318 6250 4.271696 TGTGTGCTGCTGTCTATACTTT 57.728 40.909 0.00 0.00 0.00 2.66
2319 6251 3.961480 TGTGTGCTGCTGTCTATACTT 57.039 42.857 0.00 0.00 0.00 2.24
2320 6252 3.006859 TGTTGTGTGCTGCTGTCTATACT 59.993 43.478 0.00 0.00 0.00 2.12
2321 6253 3.325870 TGTTGTGTGCTGCTGTCTATAC 58.674 45.455 0.00 0.00 0.00 1.47
2322 6254 3.676291 TGTTGTGTGCTGCTGTCTATA 57.324 42.857 0.00 0.00 0.00 1.31
2323 6255 2.549064 TGTTGTGTGCTGCTGTCTAT 57.451 45.000 0.00 0.00 0.00 1.98
2324 6256 2.323968 TTGTTGTGTGCTGCTGTCTA 57.676 45.000 0.00 0.00 0.00 2.59
2325 6257 1.683943 ATTGTTGTGTGCTGCTGTCT 58.316 45.000 0.00 0.00 0.00 3.41
2326 6258 2.666619 GCTATTGTTGTGTGCTGCTGTC 60.667 50.000 0.00 0.00 0.00 3.51
2327 6259 1.267806 GCTATTGTTGTGTGCTGCTGT 59.732 47.619 0.00 0.00 0.00 4.40
2328 6260 1.267533 TGCTATTGTTGTGTGCTGCTG 59.732 47.619 0.00 0.00 0.00 4.41
2329 6261 1.538512 CTGCTATTGTTGTGTGCTGCT 59.461 47.619 0.00 0.00 0.00 4.24
2330 6262 1.536766 TCTGCTATTGTTGTGTGCTGC 59.463 47.619 0.00 0.00 0.00 5.25
2331 6263 4.083164 TGAATCTGCTATTGTTGTGTGCTG 60.083 41.667 0.00 0.00 0.00 4.41
2332 6264 4.074259 TGAATCTGCTATTGTTGTGTGCT 58.926 39.130 0.00 0.00 0.00 4.40
2333 6265 4.424061 TGAATCTGCTATTGTTGTGTGC 57.576 40.909 0.00 0.00 0.00 4.57
2334 6266 5.063817 TCGATGAATCTGCTATTGTTGTGTG 59.936 40.000 0.00 0.00 0.00 3.82
2335 6267 5.178061 TCGATGAATCTGCTATTGTTGTGT 58.822 37.500 0.00 0.00 0.00 3.72
2336 6268 5.723492 TCGATGAATCTGCTATTGTTGTG 57.277 39.130 0.00 0.00 0.00 3.33
2337 6269 6.932356 ATTCGATGAATCTGCTATTGTTGT 57.068 33.333 0.00 0.00 0.00 3.32
2338 6270 7.854534 TGTATTCGATGAATCTGCTATTGTTG 58.145 34.615 0.00 0.00 33.95 3.33
2339 6271 8.437360 TTGTATTCGATGAATCTGCTATTGTT 57.563 30.769 0.00 0.00 33.95 2.83
2340 6272 8.613060 ATTGTATTCGATGAATCTGCTATTGT 57.387 30.769 0.00 0.00 33.95 2.71
2341 6273 9.539139 GAATTGTATTCGATGAATCTGCTATTG 57.461 33.333 0.00 0.00 33.95 1.90
2342 6274 9.276590 TGAATTGTATTCGATGAATCTGCTATT 57.723 29.630 0.00 0.00 33.95 1.73
2343 6275 8.837788 TGAATTGTATTCGATGAATCTGCTAT 57.162 30.769 0.00 0.00 33.95 2.97
2344 6276 8.837788 ATGAATTGTATTCGATGAATCTGCTA 57.162 30.769 0.00 0.00 33.95 3.49
2345 6277 7.443272 TGATGAATTGTATTCGATGAATCTGCT 59.557 33.333 0.00 0.00 33.95 4.24
2346 6278 7.578852 TGATGAATTGTATTCGATGAATCTGC 58.421 34.615 0.00 0.00 33.95 4.26
2361 6293 9.784531 AATTCGGAGACTAATATGATGAATTGT 57.215 29.630 0.00 0.00 34.32 2.71
2371 6303 9.257651 CGGTCTTTTAAATTCGGAGACTAATAT 57.742 33.333 13.84 0.00 37.48 1.28
2372 6304 8.469200 TCGGTCTTTTAAATTCGGAGACTAATA 58.531 33.333 13.84 0.04 37.48 0.98
2373 6305 7.325694 TCGGTCTTTTAAATTCGGAGACTAAT 58.674 34.615 13.84 0.00 37.48 1.73
2374 6306 6.690530 TCGGTCTTTTAAATTCGGAGACTAA 58.309 36.000 13.84 3.67 37.48 2.24
2375 6307 6.271488 TCGGTCTTTTAAATTCGGAGACTA 57.729 37.500 13.84 3.91 37.48 2.59
2376 6308 5.143376 TCGGTCTTTTAAATTCGGAGACT 57.857 39.130 13.84 0.00 37.48 3.24
2377 6309 5.178067 TGTTCGGTCTTTTAAATTCGGAGAC 59.822 40.000 8.01 8.01 34.32 3.36
2378 6310 5.299148 TGTTCGGTCTTTTAAATTCGGAGA 58.701 37.500 0.00 0.00 0.00 3.71
2379 6311 5.600908 TGTTCGGTCTTTTAAATTCGGAG 57.399 39.130 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.