Multiple sequence alignment - TraesCS5D01G328400

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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 TraesCS5D01G328400 chr5D 100.000 5511 0 0 1 5511 420923532 420918022 0.000000e+00 10178.0
1 TraesCS5D01G328400 chr5D 78.650 637 95 32 4 621 524512647 524512033 8.660000e-103 385.0
2 TraesCS5D01G328400 chr5D 92.308 65 4 1 1786 1850 420921685 420921622 2.110000e-14 91.6
3 TraesCS5D01G328400 chr5D 92.308 65 4 1 1848 1911 420921747 420921683 2.110000e-14 91.6
4 TraesCS5D01G328400 chr5B 93.145 2013 82 24 2700 4689 507007736 507005757 0.000000e+00 2902.0
5 TraesCS5D01G328400 chr5B 94.889 763 28 7 1090 1849 507009082 507008328 0.000000e+00 1182.0
6 TraesCS5D01G328400 chr5B 89.247 837 43 10 4687 5509 507005733 507004930 0.000000e+00 1003.0
7 TraesCS5D01G328400 chr5B 93.723 462 25 2 2196 2657 507008198 507007741 0.000000e+00 689.0
8 TraesCS5D01G328400 chr5B 91.282 195 14 2 1846 2037 507008392 507008198 4.230000e-66 263.0
9 TraesCS5D01G328400 chr5A 90.015 2033 144 37 37 2046 534276682 534274686 0.000000e+00 2575.0
10 TraesCS5D01G328400 chr5A 91.734 1851 99 18 2118 3952 534274578 534272766 0.000000e+00 2521.0
11 TraesCS5D01G328400 chr5A 89.466 712 40 20 3949 4650 534272735 534272049 0.000000e+00 867.0
12 TraesCS5D01G328400 chr5A 87.215 571 45 10 4687 5231 534271911 534271343 4.690000e-175 625.0
13 TraesCS5D01G328400 chr5A 89.320 206 13 3 5258 5455 534271342 534271138 3.300000e-62 250.0
14 TraesCS5D01G328400 chr5A 93.548 62 4 0 1846 1907 534274950 534274889 5.880000e-15 93.5
15 TraesCS5D01G328400 chr5A 100.000 32 0 0 1026 1057 359694402 359694371 5.960000e-05 60.2
16 TraesCS5D01G328400 chr1D 80.804 771 102 34 4 747 257510166 257509415 3.730000e-156 562.0
17 TraesCS5D01G328400 chr7A 84.561 570 72 15 4 563 20733574 20733011 8.070000e-153 551.0
18 TraesCS5D01G328400 chr7A 96.970 33 1 0 1024 1056 660447788 660447820 7.710000e-04 56.5
19 TraesCS5D01G328400 chr3D 80.640 625 97 22 6 623 110530260 110530867 3.890000e-126 462.0
20 TraesCS5D01G328400 chr3D 81.128 514 73 22 7 509 19532914 19532414 1.860000e-104 390.0
21 TraesCS5D01G328400 chr3D 92.857 42 3 0 1014 1055 537042798 537042757 1.660000e-05 62.1
22 TraesCS5D01G328400 chr3D 92.857 42 3 0 1014 1055 537042985 537042944 1.660000e-05 62.1
23 TraesCS5D01G328400 chr2B 79.939 658 107 22 4 650 785903585 785904228 1.400000e-125 460.0
24 TraesCS5D01G328400 chr1B 79.016 691 97 29 5 686 480652361 480651710 3.940000e-116 429.0
25 TraesCS5D01G328400 chr2D 81.356 472 60 24 61 517 42701095 42701553 5.250000e-95 359.0
26 TraesCS5D01G328400 chr6D 85.000 120 17 1 952 1070 152187731 152187850 2.700000e-23 121.0
27 TraesCS5D01G328400 chr4D 89.831 59 6 0 993 1051 508335806 508335864 5.920000e-10 76.8
28 TraesCS5D01G328400 chr3A 95.238 42 2 0 1014 1055 710242566 710242525 3.560000e-07 67.6
29 TraesCS5D01G328400 chr1A 92.500 40 2 1 1023 1062 36190212 36190174 7.710000e-04 56.5


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 TraesCS5D01G328400 chr5D 420918022 420923532 5510 True 3453.733333 10178 94.872000 1 5511 3 chr5D.!!$R2 5510
1 TraesCS5D01G328400 chr5D 524512033 524512647 614 True 385.000000 385 78.650000 4 621 1 chr5D.!!$R1 617
2 TraesCS5D01G328400 chr5B 507004930 507009082 4152 True 1207.800000 2902 92.457200 1090 5509 5 chr5B.!!$R1 4419
3 TraesCS5D01G328400 chr5A 534271138 534276682 5544 True 1155.250000 2575 90.216333 37 5455 6 chr5A.!!$R2 5418
4 TraesCS5D01G328400 chr1D 257509415 257510166 751 True 562.000000 562 80.804000 4 747 1 chr1D.!!$R1 743
5 TraesCS5D01G328400 chr7A 20733011 20733574 563 True 551.000000 551 84.561000 4 563 1 chr7A.!!$R1 559
6 TraesCS5D01G328400 chr3D 110530260 110530867 607 False 462.000000 462 80.640000 6 623 1 chr3D.!!$F1 617
7 TraesCS5D01G328400 chr3D 19532414 19532914 500 True 390.000000 390 81.128000 7 509 1 chr3D.!!$R1 502
8 TraesCS5D01G328400 chr2B 785903585 785904228 643 False 460.000000 460 79.939000 4 650 1 chr2B.!!$F1 646
9 TraesCS5D01G328400 chr1B 480651710 480652361 651 True 429.000000 429 79.016000 5 686 1 chr1B.!!$R1 681

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
886 1029 0.465460 GGAGGCGGCATGGTATCAAA 60.465 55.000 13.08 0.00 0.00 2.69 F
1894 2053 0.030638 TGAAGTTTTCCTGCAAGCGC 59.969 50.000 0.00 0.00 39.24 5.92 F
2188 2429 0.622136 AGTTGATGATCTGCTGGCCA 59.378 50.000 4.71 4.71 0.00 5.36 F
3567 3827 1.471684 CACAAGAAAGATGGAGCCTGC 59.528 52.381 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2417 0.178998 ATGGACATGGCCAGCAGATC 60.179 55.0 27.68 3.7 42.15 2.75 R
2895 3144 1.968704 TCCCGCAACAACAACATACA 58.031 45.0 0.00 0.0 0.00 2.29 R
4093 4403 0.252761 TGCAAGATTGGAGCGGATGA 59.747 50.0 0.00 0.0 0.00 2.92 R
4583 4903 0.394565 ACTGAAGCTCGCCAGAAAGT 59.605 50.0 15.01 0.0 34.65 2.66 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
167 176 3.441496 ACAAAGCTTGACCATGTGTTG 57.559 42.857 0.00 0.00 0.00 3.33
547 659 9.522804 ACGTGTATTACAAAAATGTTGTTGATT 57.477 25.926 0.00 0.00 34.11 2.57
735 877 1.448013 GCGCCTCCTCTGTAACCAC 60.448 63.158 0.00 0.00 0.00 4.16
754 896 3.556775 CCACGAACGGAGAAAGTAACAAA 59.443 43.478 0.00 0.00 0.00 2.83
816 958 2.829458 GTAGTCCGCGCCTCCTCT 60.829 66.667 0.00 0.00 0.00 3.69
819 961 2.261430 TAGTCCGCGCCTCCTCTGTA 62.261 60.000 0.00 0.00 0.00 2.74
851 993 2.189594 ACAATTGTGCAGCTGCTAGA 57.810 45.000 36.61 22.71 42.66 2.43
862 1004 1.137614 CTGCTAGAAGCTCGTCGCA 59.862 57.895 0.00 0.00 42.97 5.10
864 1006 1.874466 GCTAGAAGCTCGTCGCACC 60.874 63.158 0.00 0.00 42.61 5.01
866 1008 2.254703 CTAGAAGCTCGTCGCACCGT 62.255 60.000 0.00 0.00 42.61 4.83
886 1029 0.465460 GGAGGCGGCATGGTATCAAA 60.465 55.000 13.08 0.00 0.00 2.69
887 1030 0.663153 GAGGCGGCATGGTATCAAAC 59.337 55.000 13.08 0.00 0.00 2.93
945 1088 2.942376 TCTTTGTATGTGCTAATGGCCG 59.058 45.455 0.00 0.00 40.92 6.13
984 1127 8.848474 TCTATTCTTTATATGTGCTTAAGGGC 57.152 34.615 4.29 0.00 0.00 5.19
986 1129 4.385825 TCTTTATATGTGCTTAAGGGCCG 58.614 43.478 4.29 0.00 0.00 6.13
987 1130 4.101898 TCTTTATATGTGCTTAAGGGCCGA 59.898 41.667 4.29 0.00 0.00 5.54
988 1131 2.256117 ATATGTGCTTAAGGGCCGAC 57.744 50.000 4.29 0.00 0.00 4.79
1008 1160 2.094338 ACCCGATTACTCCAGACGTTTC 60.094 50.000 0.00 0.00 0.00 2.78
1012 1164 3.673594 CGATTACTCCAGACGTTTCAGCT 60.674 47.826 0.00 0.00 0.00 4.24
1020 1172 3.246619 CAGACGTTTCAGCTAGAGAACC 58.753 50.000 0.00 0.00 0.00 3.62
1027 1179 2.025155 TCAGCTAGAGAACCATCCGTC 58.975 52.381 0.00 0.00 0.00 4.79
1053 1205 2.949451 AATGCGAGATATAGCTCCCG 57.051 50.000 12.27 3.69 0.00 5.14
1054 1206 0.457851 ATGCGAGATATAGCTCCCGC 59.542 55.000 14.95 14.95 42.52 6.13
1056 1208 1.226435 CGAGATATAGCTCCCGCGC 60.226 63.158 12.27 0.00 42.32 6.86
1068 1220 0.468226 TCCCGCGCTCAAATAGGATT 59.532 50.000 5.56 0.00 0.00 3.01
1069 1221 1.134220 TCCCGCGCTCAAATAGGATTT 60.134 47.619 5.56 0.00 0.00 2.17
1070 1222 1.676006 CCCGCGCTCAAATAGGATTTT 59.324 47.619 5.56 0.00 0.00 1.82
1071 1223 2.099098 CCCGCGCTCAAATAGGATTTTT 59.901 45.455 5.56 0.00 0.00 1.94
1132 1284 1.971357 ACTCCGAACAAGAGATGTGGT 59.029 47.619 0.00 0.00 42.99 4.16
1146 1298 2.442212 TGTGGTCGACGCAGAAAATA 57.558 45.000 9.92 0.00 33.95 1.40
1197 1349 1.594293 CGTGCCCTACCGCCATTAG 60.594 63.158 0.00 0.00 0.00 1.73
1198 1350 1.227853 GTGCCCTACCGCCATTAGG 60.228 63.158 0.00 0.00 36.58 2.69
1225 1377 2.481568 TGCTGCAATCTTGTCTCGAAAG 59.518 45.455 0.00 0.00 0.00 2.62
1226 1378 2.738846 GCTGCAATCTTGTCTCGAAAGA 59.261 45.455 0.73 0.73 38.01 2.52
1644 1801 1.027357 CCATTGTGATAGCACCAGGC 58.973 55.000 8.95 0.00 44.51 4.85
1727 1884 4.282449 CCAATGGCATATCATCCAACATGT 59.718 41.667 0.00 0.00 35.75 3.21
1735 1892 8.308931 GGCATATCATCCAACATGTAATCATTT 58.691 33.333 0.00 0.00 31.15 2.32
1784 1943 5.116180 TGAGAAGCTCTTTTCAAAGTCGAA 58.884 37.500 0.99 0.00 37.31 3.71
1834 1993 4.742438 TTAAGTTTTCCTGCAAGCGTAG 57.258 40.909 0.00 0.00 0.00 3.51
1851 2010 2.540101 CGTAGCATTCGTTCAAGGATCC 59.460 50.000 2.48 2.48 0.00 3.36
1894 2053 0.030638 TGAAGTTTTCCTGCAAGCGC 59.969 50.000 0.00 0.00 39.24 5.92
1943 2103 6.800341 GATTGCACAATCAGCGACAGATCG 62.800 50.000 16.57 0.00 46.55 3.69
2039 2201 8.299570 TGATTCTTTTGGCTCTTAGATGTTTTC 58.700 33.333 0.00 0.00 0.00 2.29
2046 2208 8.958119 TTGGCTCTTAGATGTTTTCGTATTAT 57.042 30.769 0.00 0.00 0.00 1.28
2050 2212 9.959775 GCTCTTAGATGTTTTCGTATTATATGC 57.040 33.333 0.00 0.00 0.00 3.14
2052 2214 9.135843 TCTTAGATGTTTTCGTATTATATGCGG 57.864 33.333 0.00 0.00 38.93 5.69
2053 2215 9.135843 CTTAGATGTTTTCGTATTATATGCGGA 57.864 33.333 0.00 0.00 38.93 5.54
2054 2216 9.647797 TTAGATGTTTTCGTATTATATGCGGAT 57.352 29.630 0.00 0.00 38.93 4.18
2055 2217 7.963981 AGATGTTTTCGTATTATATGCGGATG 58.036 34.615 0.00 0.00 38.93 3.51
2056 2218 7.817478 AGATGTTTTCGTATTATATGCGGATGA 59.183 33.333 0.00 0.00 38.93 2.92
2057 2219 7.346208 TGTTTTCGTATTATATGCGGATGAG 57.654 36.000 0.00 0.00 38.93 2.90
2058 2220 6.367695 TGTTTTCGTATTATATGCGGATGAGG 59.632 38.462 0.00 0.00 38.93 3.86
2059 2221 5.654603 TTCGTATTATATGCGGATGAGGT 57.345 39.130 0.00 0.00 38.93 3.85
2060 2222 6.762702 TTCGTATTATATGCGGATGAGGTA 57.237 37.500 0.00 0.00 38.93 3.08
2061 2223 6.762702 TCGTATTATATGCGGATGAGGTAA 57.237 37.500 0.00 0.00 38.93 2.85
2062 2224 7.160547 TCGTATTATATGCGGATGAGGTAAA 57.839 36.000 0.00 0.00 38.93 2.01
2063 2225 7.778083 TCGTATTATATGCGGATGAGGTAAAT 58.222 34.615 0.00 0.00 38.93 1.40
2064 2226 7.919091 TCGTATTATATGCGGATGAGGTAAATC 59.081 37.037 0.00 0.00 38.93 2.17
2065 2227 7.921214 CGTATTATATGCGGATGAGGTAAATCT 59.079 37.037 0.00 0.00 34.66 2.40
2066 2228 9.250624 GTATTATATGCGGATGAGGTAAATCTC 57.749 37.037 0.00 0.00 0.00 2.75
2067 2229 2.910688 TGCGGATGAGGTAAATCTCC 57.089 50.000 0.00 0.00 33.04 3.71
2068 2230 2.398588 TGCGGATGAGGTAAATCTCCT 58.601 47.619 0.00 0.00 38.09 3.69
2069 2231 2.103094 TGCGGATGAGGTAAATCTCCTG 59.897 50.000 0.00 0.00 35.20 3.86
2070 2232 2.103263 GCGGATGAGGTAAATCTCCTGT 59.897 50.000 0.00 0.00 35.20 4.00
2071 2233 3.432326 GCGGATGAGGTAAATCTCCTGTT 60.432 47.826 0.00 0.00 35.20 3.16
2072 2234 4.372656 CGGATGAGGTAAATCTCCTGTTC 58.627 47.826 0.00 0.00 35.20 3.18
2073 2235 4.141937 CGGATGAGGTAAATCTCCTGTTCA 60.142 45.833 0.00 0.00 35.20 3.18
2074 2236 5.119694 GGATGAGGTAAATCTCCTGTTCAC 58.880 45.833 0.00 0.00 35.20 3.18
2075 2237 4.188247 TGAGGTAAATCTCCTGTTCACG 57.812 45.455 0.00 0.00 35.20 4.35
2076 2238 3.830178 TGAGGTAAATCTCCTGTTCACGA 59.170 43.478 0.00 0.00 35.20 4.35
2077 2239 4.282449 TGAGGTAAATCTCCTGTTCACGAA 59.718 41.667 0.00 0.00 35.20 3.85
2078 2240 4.822026 AGGTAAATCTCCTGTTCACGAAG 58.178 43.478 0.00 0.00 33.62 3.79
2079 2241 3.933332 GGTAAATCTCCTGTTCACGAAGG 59.067 47.826 0.00 0.00 34.65 3.46
2080 2242 3.771577 AAATCTCCTGTTCACGAAGGT 57.228 42.857 0.00 0.00 34.94 3.50
2081 2243 4.884668 AAATCTCCTGTTCACGAAGGTA 57.115 40.909 0.00 0.00 34.94 3.08
2082 2244 4.884668 AATCTCCTGTTCACGAAGGTAA 57.115 40.909 0.00 0.00 34.94 2.85
2083 2245 3.655276 TCTCCTGTTCACGAAGGTAAC 57.345 47.619 0.00 0.00 34.94 2.50
2084 2246 2.960384 TCTCCTGTTCACGAAGGTAACA 59.040 45.455 0.00 0.00 41.41 2.41
2085 2247 3.005472 TCTCCTGTTCACGAAGGTAACAG 59.995 47.826 7.32 7.32 46.18 3.16
2095 2257 6.263344 TCACGAAGGTAACAGATAATCTTCG 58.737 40.000 17.80 17.80 45.27 3.79
2143 2384 4.687483 GGTGCAAATCATTTGGTCTTTCTG 59.313 41.667 12.14 0.00 40.94 3.02
2145 2386 5.984926 GTGCAAATCATTTGGTCTTTCTGAA 59.015 36.000 12.14 0.00 40.94 3.02
2146 2387 6.647895 GTGCAAATCATTTGGTCTTTCTGAAT 59.352 34.615 12.14 0.00 40.94 2.57
2147 2388 7.814107 GTGCAAATCATTTGGTCTTTCTGAATA 59.186 33.333 12.14 0.00 40.94 1.75
2148 2389 7.814107 TGCAAATCATTTGGTCTTTCTGAATAC 59.186 33.333 12.14 0.00 40.94 1.89
2149 2390 7.276438 GCAAATCATTTGGTCTTTCTGAATACC 59.724 37.037 12.14 12.96 40.94 2.73
2150 2391 6.683974 ATCATTTGGTCTTTCTGAATACCG 57.316 37.500 14.24 4.39 35.39 4.02
2151 2392 5.800296 TCATTTGGTCTTTCTGAATACCGA 58.200 37.500 14.24 11.16 35.39 4.69
2152 2393 6.414732 TCATTTGGTCTTTCTGAATACCGAT 58.585 36.000 14.24 9.80 35.39 4.18
2153 2394 6.884295 TCATTTGGTCTTTCTGAATACCGATT 59.116 34.615 14.24 8.58 35.39 3.34
2154 2395 8.044309 TCATTTGGTCTTTCTGAATACCGATTA 58.956 33.333 14.24 3.59 35.39 1.75
2176 2417 4.326504 AAGAGTTGGCCAAAAGTTGATG 57.673 40.909 22.47 0.00 0.00 3.07
2188 2429 0.622136 AGTTGATGATCTGCTGGCCA 59.378 50.000 4.71 4.71 0.00 5.36
2271 2512 8.770828 CGACAAGTATATAACCATAACTTTGGG 58.229 37.037 0.00 0.00 41.35 4.12
2291 2532 4.519350 TGGGTATCTTGTAGATGTAGAGCG 59.481 45.833 0.00 0.00 35.37 5.03
2319 2560 5.531287 ACAAGCTTTACTCCTTGTTAGGTTG 59.469 40.000 0.00 0.00 46.86 3.77
2418 2659 3.241067 TCGAAACAGGGAAACGATAGG 57.759 47.619 0.00 0.00 43.77 2.57
2419 2660 2.827322 TCGAAACAGGGAAACGATAGGA 59.173 45.455 0.00 0.00 43.77 2.94
2420 2661 2.928116 CGAAACAGGGAAACGATAGGAC 59.072 50.000 0.00 0.00 43.77 3.85
2452 2693 7.680982 GTTAATTTAAAAACGATGGGCCAATC 58.319 34.615 11.89 10.46 0.00 2.67
2493 2734 2.124778 GCTTCTGCCTCTCCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
2602 2843 2.747446 GAGGCGCATTTGTTTCTCCTTA 59.253 45.455 10.83 0.00 0.00 2.69
2673 2922 2.164338 TCACGGGGCCTTAAACATTTC 58.836 47.619 0.84 0.00 0.00 2.17
2695 2944 9.834628 ATTTCTACGTTTTTATTGTACATGGTG 57.165 29.630 0.00 0.00 0.00 4.17
2803 3052 9.965824 AGTAAAAGTAATGTTGATTTTGTCTGG 57.034 29.630 0.00 0.00 0.00 3.86
2847 3096 4.202398 TGGGATGATAGAACCTGATTGAGC 60.202 45.833 0.00 0.00 0.00 4.26
2880 3129 2.584835 AAATAGCAGAGGTGGTGCAA 57.415 45.000 0.00 0.00 43.82 4.08
2895 3144 6.041979 AGGTGGTGCAATAAGAAATCTGTTTT 59.958 34.615 0.00 0.00 0.00 2.43
2921 3170 1.906333 GTTGTTGCGGGATTGGGGT 60.906 57.895 0.00 0.00 0.00 4.95
3098 3350 4.958581 GGGAATGGGTCTCAGAAATGAAAT 59.041 41.667 0.00 0.00 0.00 2.17
3147 3399 9.944376 AATCTTCAGTTAGTATTGCTAAGTCAA 57.056 29.630 0.00 0.00 40.38 3.18
3247 3499 6.441604 ACATCATCTTCTTTGGCCCTTAAAAT 59.558 34.615 0.00 0.00 0.00 1.82
3373 3626 3.194062 ACACTTCCGCCATTTGTTTTTG 58.806 40.909 0.00 0.00 0.00 2.44
3392 3645 8.143193 TGTTTTTGTTCAATGACATCTGCTATT 58.857 29.630 0.00 0.00 0.00 1.73
3563 3823 2.095364 CACAGCACAAGAAAGATGGAGC 60.095 50.000 0.00 0.00 0.00 4.70
3567 3827 1.471684 CACAAGAAAGATGGAGCCTGC 59.528 52.381 0.00 0.00 0.00 4.85
3569 3829 2.015587 CAAGAAAGATGGAGCCTGCTC 58.984 52.381 10.68 10.68 42.04 4.26
3776 4036 8.693504 CAACATCAACATTAACTTTGCTGTTAG 58.306 33.333 14.85 9.23 39.06 2.34
3984 4293 4.711846 GGGTCTTCTAGAATGGCCAATTTT 59.288 41.667 10.96 0.00 0.00 1.82
4093 4403 1.840635 GCTTCCCCTTCCTGTACTGAT 59.159 52.381 0.60 0.00 0.00 2.90
4197 4507 2.740826 GCCAGCGCCAACTAACGA 60.741 61.111 2.29 0.00 0.00 3.85
4250 4560 4.727179 CGAAGAAACGAGCATTTCATCATG 59.273 41.667 9.82 0.00 40.43 3.07
4299 4609 3.631686 TGGTCCAATAATCCTCATTTGCG 59.368 43.478 0.00 0.00 0.00 4.85
4354 4664 7.545615 CCTCATCGAATCCAATAATCGTTGATA 59.454 37.037 8.14 0.00 41.59 2.15
4414 4724 3.365265 CCGGCTTGTCAAGTGGCC 61.365 66.667 14.03 9.08 41.02 5.36
4421 4731 2.112297 GTCAAGTGGCCCGAACCA 59.888 61.111 0.00 0.00 37.38 3.67
4429 4739 0.893270 TGGCCCGAACCATTGTCTTG 60.893 55.000 0.00 0.00 33.75 3.02
4452 4765 3.243068 GCAACAATTTCGTCCTTGTCAGT 60.243 43.478 0.00 0.00 34.61 3.41
4473 4786 5.922544 CAGTGAACAATCTTTGTCCCATTTC 59.077 40.000 0.00 0.00 44.59 2.17
4494 4807 2.095853 CGGATTTGATCACTGTTTCGGG 59.904 50.000 0.00 0.00 0.00 5.14
4499 4812 2.627945 TGATCACTGTTTCGGGTATGC 58.372 47.619 0.00 0.00 0.00 3.14
4516 4830 3.907894 ATGCGTGAAAATAAACACCGT 57.092 38.095 0.00 0.00 34.05 4.83
4531 4845 4.508128 CGTGGTCCGTGGGATCCG 62.508 72.222 5.45 0.00 30.39 4.18
4532 4846 4.832608 GTGGTCCGTGGGATCCGC 62.833 72.222 5.45 0.00 30.39 5.54
4534 4848 2.836360 GGTCCGTGGGATCCGCTA 60.836 66.667 5.45 0.00 32.73 4.26
4535 4849 2.428925 GGTCCGTGGGATCCGCTAA 61.429 63.158 5.45 0.00 32.73 3.09
4536 4850 1.518774 GTCCGTGGGATCCGCTAAA 59.481 57.895 5.45 0.00 32.73 1.85
4537 4851 0.108041 GTCCGTGGGATCCGCTAAAA 60.108 55.000 5.45 0.00 32.73 1.52
4538 4852 0.834612 TCCGTGGGATCCGCTAAAAT 59.165 50.000 5.45 0.00 0.00 1.82
4539 4853 1.202604 TCCGTGGGATCCGCTAAAATC 60.203 52.381 5.45 0.00 0.00 2.17
4540 4854 1.226746 CGTGGGATCCGCTAAAATCC 58.773 55.000 5.45 0.00 40.69 3.01
4548 4862 4.340950 GGATCCGCTAAAATCCAAATCCAA 59.659 41.667 0.00 0.00 41.02 3.53
4574 4894 3.802685 GCTGTTTGGATACTGTCGGATAC 59.197 47.826 0.00 0.00 37.61 2.24
4651 5045 7.254117 CGAACTCTTGGCATAATACAGTACTTG 60.254 40.741 0.00 0.00 0.00 3.16
4664 5058 2.485426 CAGTACTTGCACACATCCCAAG 59.515 50.000 0.00 0.00 41.20 3.61
4676 5070 1.867595 ATCCCAAGAGGCCCCAACAG 61.868 60.000 0.00 0.00 34.51 3.16
4750 5170 2.060980 GGCTCAGAGACGACCCCAT 61.061 63.158 0.00 0.00 0.00 4.00
4753 5173 1.186200 CTCAGAGACGACCCCATCAA 58.814 55.000 0.00 0.00 0.00 2.57
4806 5226 5.427378 TCAAAATCTAACCGCATCATCTGA 58.573 37.500 0.00 0.00 0.00 3.27
4946 5376 1.882912 TCGTTGGATCTATGCATGCC 58.117 50.000 16.68 6.13 0.00 4.40
5074 5508 2.028476 TCATCCAAAGATCGACGGTGTT 60.028 45.455 0.00 0.00 0.00 3.32
5138 5589 0.908198 AGGTCTGAATGGCTCTGGAC 59.092 55.000 0.00 0.00 0.00 4.02
5161 5612 2.751436 GCCAAATCGCTCCTGCCA 60.751 61.111 0.00 0.00 35.36 4.92
5232 5684 7.042335 GGAATACTACTGCTGAATACACACTT 58.958 38.462 0.00 0.00 0.00 3.16
5233 5685 7.222999 GGAATACTACTGCTGAATACACACTTC 59.777 40.741 0.00 0.00 0.00 3.01
5235 5687 6.042638 ACTACTGCTGAATACACACTTCAT 57.957 37.500 0.00 0.00 32.50 2.57
5236 5688 5.871524 ACTACTGCTGAATACACACTTCATG 59.128 40.000 0.00 0.00 32.50 3.07
5252 5704 4.160252 ACTTCATGAACTTGTGCTTGGTTT 59.840 37.500 3.38 0.00 0.00 3.27
5253 5705 4.044336 TCATGAACTTGTGCTTGGTTTG 57.956 40.909 0.00 0.00 0.00 2.93
5277 5729 8.718158 TGTGTGAGAGGATTCTATCATTATCT 57.282 34.615 0.69 0.00 42.35 1.98
5282 5735 9.828691 TGAGAGGATTCTATCATTATCTTACCA 57.171 33.333 0.00 0.00 36.44 3.25
5284 5737 9.041354 AGAGGATTCTATCATTATCTTACCACC 57.959 37.037 0.00 0.00 0.00 4.61
5289 5742 1.418637 TCATTATCTTACCACCGCCCC 59.581 52.381 0.00 0.00 0.00 5.80
5306 5770 4.077184 CCGCTCCACGCCAAGGTA 62.077 66.667 0.00 0.00 41.76 3.08
5307 5771 2.186903 CGCTCCACGCCAAGGTAT 59.813 61.111 0.00 0.00 34.21 2.73
5308 5772 1.440060 CGCTCCACGCCAAGGTATA 59.560 57.895 0.00 0.00 34.21 1.47
5349 5813 1.611006 CTCCATCGATCGATCACCTGT 59.389 52.381 27.20 3.21 31.62 4.00
5361 5825 0.821517 TCACCTGTTCCGCATCGTAT 59.178 50.000 0.00 0.00 0.00 3.06
5509 5978 5.070685 AGGACTTGACTTTCGGCTTTTATT 58.929 37.500 0.00 0.00 0.00 1.40
5510 5979 5.048713 AGGACTTGACTTTCGGCTTTTATTG 60.049 40.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
510 619 8.563289 TTTTGTAATACACGTCCAACATTTTC 57.437 30.769 0.00 0.00 0.00 2.29
511 620 8.928270 TTTTTGTAATACACGTCCAACATTTT 57.072 26.923 0.00 0.00 0.00 1.82
698 840 3.235195 CGCGGACTACTTGATACATAGC 58.765 50.000 0.00 0.00 0.00 2.97
790 932 0.384669 GCGCGGACTACTTGAGGTAT 59.615 55.000 8.83 0.00 0.00 2.73
816 958 4.576873 ACAATTGTTGTGTTCGTGGATACA 59.423 37.500 4.92 0.00 44.47 2.29
844 986 1.136872 GTGCGACGAGCTTCTAGCAG 61.137 60.000 0.00 0.00 45.56 4.24
845 987 1.154016 GTGCGACGAGCTTCTAGCA 60.154 57.895 0.00 4.19 45.56 3.49
864 1006 3.460672 ATACCATGCCGCCTCCACG 62.461 63.158 0.00 0.00 0.00 4.94
866 1008 1.631071 TTGATACCATGCCGCCTCCA 61.631 55.000 0.00 0.00 0.00 3.86
870 1012 1.733526 GGTTTGATACCATGCCGCC 59.266 57.895 0.00 0.00 46.92 6.13
887 1030 4.694987 AAATGGGGGTGCGTGGGG 62.695 66.667 0.00 0.00 0.00 4.96
938 1081 2.143876 AAATTAGCAGTCCGGCCATT 57.856 45.000 2.24 0.00 0.00 3.16
942 1085 5.297029 AGAATAGAAAAATTAGCAGTCCGGC 59.703 40.000 0.00 0.00 0.00 6.13
983 1126 1.067582 CTGGAGTAATCGGGTCGGC 59.932 63.158 0.00 0.00 0.00 5.54
984 1127 0.384669 GTCTGGAGTAATCGGGTCGG 59.615 60.000 0.00 0.00 0.00 4.79
986 1129 1.101331 ACGTCTGGAGTAATCGGGTC 58.899 55.000 0.00 0.00 0.00 4.46
987 1130 1.553706 AACGTCTGGAGTAATCGGGT 58.446 50.000 0.00 0.00 0.00 5.28
988 1131 2.094390 TGAAACGTCTGGAGTAATCGGG 60.094 50.000 0.00 0.00 0.00 5.14
1008 1160 2.028130 AGACGGATGGTTCTCTAGCTG 58.972 52.381 0.00 0.00 0.00 4.24
1012 1164 1.022735 GCGAGACGGATGGTTCTCTA 58.977 55.000 0.00 0.00 0.00 2.43
1132 1284 2.256174 CTCCGTTATTTTCTGCGTCGA 58.744 47.619 0.00 0.00 0.00 4.20
1136 1288 2.073816 ACCACTCCGTTATTTTCTGCG 58.926 47.619 0.00 0.00 0.00 5.18
1146 1298 3.168528 ACAGCCCACCACTCCGTT 61.169 61.111 0.00 0.00 0.00 4.44
1197 1349 1.379576 AAGATTGCAGCAGGAGGCC 60.380 57.895 0.00 0.00 46.50 5.19
1198 1350 0.964358 ACAAGATTGCAGCAGGAGGC 60.964 55.000 0.00 0.00 45.30 4.70
1199 1351 1.093159 GACAAGATTGCAGCAGGAGG 58.907 55.000 0.00 0.00 0.00 4.30
1200 1352 2.008329 GAGACAAGATTGCAGCAGGAG 58.992 52.381 0.00 0.00 0.00 3.69
1201 1353 1.673923 CGAGACAAGATTGCAGCAGGA 60.674 52.381 0.00 0.00 0.00 3.86
1205 1357 2.738846 TCTTTCGAGACAAGATTGCAGC 59.261 45.455 0.00 0.00 0.00 5.25
1391 1544 4.127907 GCCCTAAAATTAGAACGAGGAGG 58.872 47.826 1.75 0.00 32.47 4.30
1644 1801 7.069331 ACTCCCTTTCTATCTGACATCTTACTG 59.931 40.741 0.00 0.00 0.00 2.74
1699 1856 5.794726 TGGATGATATGCCATTGGAAAAG 57.205 39.130 6.95 0.00 0.00 2.27
1735 1892 7.124573 TCCAGCTATTCTAAATTCTGCACTA 57.875 36.000 0.00 0.00 0.00 2.74
1784 1943 8.924511 TTTCTTCAGTTTTATCAACTGGATCT 57.075 30.769 13.42 0.00 45.66 2.75
1814 1973 2.482721 GCTACGCTTGCAGGAAAACTTA 59.517 45.455 0.00 0.00 0.00 2.24
1834 1993 2.359900 ACTGGATCCTTGAACGAATGC 58.640 47.619 14.23 0.00 0.00 3.56
1839 1998 6.149474 AGTTTTATCAACTGGATCCTTGAACG 59.851 38.462 17.63 1.23 37.44 3.95
1848 2007 9.082313 ACATTTCTTCAGTTTTATCAACTGGAT 57.918 29.630 13.42 0.00 45.66 3.41
1851 2010 9.734620 TCAACATTTCTTCAGTTTTATCAACTG 57.265 29.630 8.20 8.20 46.67 3.16
1894 2053 4.510711 GTCACATATCCTGAACTGATGCTG 59.489 45.833 0.00 0.00 0.00 4.41
1900 2059 6.457934 GCAATCAAGTCACATATCCTGAACTG 60.458 42.308 0.00 0.00 0.00 3.16
1943 2103 5.194432 TGACATAGGTTCCTCTACACTCTC 58.806 45.833 0.00 0.00 0.00 3.20
1992 2154 9.921637 GAATCACACATAAAAGGGTAATTTGAA 57.078 29.630 0.00 0.00 0.00 2.69
2039 2201 7.921214 AGATTTACCTCATCCGCATATAATACG 59.079 37.037 0.00 0.00 0.00 3.06
2046 2208 4.021104 CAGGAGATTTACCTCATCCGCATA 60.021 45.833 0.00 0.00 35.35 3.14
2047 2209 2.975489 AGGAGATTTACCTCATCCGCAT 59.025 45.455 0.00 0.00 35.13 4.73
2048 2210 2.103094 CAGGAGATTTACCTCATCCGCA 59.897 50.000 0.00 0.00 35.35 5.69
2049 2211 2.103263 ACAGGAGATTTACCTCATCCGC 59.897 50.000 0.00 0.00 35.35 5.54
2050 2212 4.141937 TGAACAGGAGATTTACCTCATCCG 60.142 45.833 0.00 0.00 35.35 4.18
2051 2213 5.119694 GTGAACAGGAGATTTACCTCATCC 58.880 45.833 0.00 0.00 35.35 3.51
2052 2214 4.806247 CGTGAACAGGAGATTTACCTCATC 59.194 45.833 0.00 0.00 35.35 2.92
2053 2215 4.466370 TCGTGAACAGGAGATTTACCTCAT 59.534 41.667 0.00 0.00 35.35 2.90
2054 2216 3.830178 TCGTGAACAGGAGATTTACCTCA 59.170 43.478 0.00 0.00 35.35 3.86
2055 2217 4.451629 TCGTGAACAGGAGATTTACCTC 57.548 45.455 0.00 0.00 35.35 3.85
2056 2218 4.322801 CCTTCGTGAACAGGAGATTTACCT 60.323 45.833 0.00 0.00 38.40 3.08
2057 2219 3.933332 CCTTCGTGAACAGGAGATTTACC 59.067 47.826 0.00 0.00 30.81 2.85
2058 2220 4.566987 ACCTTCGTGAACAGGAGATTTAC 58.433 43.478 0.00 0.00 33.90 2.01
2059 2221 4.884668 ACCTTCGTGAACAGGAGATTTA 57.115 40.909 0.00 0.00 33.90 1.40
2060 2222 3.771577 ACCTTCGTGAACAGGAGATTT 57.228 42.857 0.00 0.00 33.90 2.17
2061 2223 4.039973 TGTTACCTTCGTGAACAGGAGATT 59.960 41.667 0.00 0.00 33.90 2.40
2062 2224 3.576982 TGTTACCTTCGTGAACAGGAGAT 59.423 43.478 0.00 0.00 33.90 2.75
2063 2225 2.960384 TGTTACCTTCGTGAACAGGAGA 59.040 45.455 0.00 0.00 33.90 3.71
2064 2226 3.005472 TCTGTTACCTTCGTGAACAGGAG 59.995 47.826 12.61 0.00 46.53 3.69
2065 2227 2.960384 TCTGTTACCTTCGTGAACAGGA 59.040 45.455 12.61 0.00 46.53 3.86
2066 2228 3.380479 TCTGTTACCTTCGTGAACAGG 57.620 47.619 12.61 0.00 46.53 4.00
2068 2230 6.931838 AGATTATCTGTTACCTTCGTGAACA 58.068 36.000 0.00 0.00 0.00 3.18
2069 2231 7.253684 CGAAGATTATCTGTTACCTTCGTGAAC 60.254 40.741 12.42 0.00 44.32 3.18
2070 2232 6.750501 CGAAGATTATCTGTTACCTTCGTGAA 59.249 38.462 12.42 0.00 44.32 3.18
2071 2233 6.263344 CGAAGATTATCTGTTACCTTCGTGA 58.737 40.000 12.42 0.00 44.32 4.35
2072 2234 6.497939 CGAAGATTATCTGTTACCTTCGTG 57.502 41.667 12.42 0.00 44.32 4.35
2075 2237 8.138712 ACTCATCGAAGATTATCTGTTACCTTC 58.861 37.037 0.00 0.00 45.12 3.46
2076 2238 8.012957 ACTCATCGAAGATTATCTGTTACCTT 57.987 34.615 0.00 0.00 45.12 3.50
2077 2239 7.589958 ACTCATCGAAGATTATCTGTTACCT 57.410 36.000 0.00 0.00 45.12 3.08
2078 2240 9.347934 CATACTCATCGAAGATTATCTGTTACC 57.652 37.037 0.00 0.00 45.12 2.85
2081 2243 9.469807 GTTCATACTCATCGAAGATTATCTGTT 57.530 33.333 0.00 0.00 45.12 3.16
2082 2244 8.085296 GGTTCATACTCATCGAAGATTATCTGT 58.915 37.037 0.00 0.00 45.12 3.41
2083 2245 8.303156 AGGTTCATACTCATCGAAGATTATCTG 58.697 37.037 0.00 0.00 45.12 2.90
2084 2246 8.415950 AGGTTCATACTCATCGAAGATTATCT 57.584 34.615 0.00 0.00 45.12 1.98
2085 2247 9.562583 GTAGGTTCATACTCATCGAAGATTATC 57.437 37.037 0.00 0.00 45.12 1.75
2086 2248 8.524487 GGTAGGTTCATACTCATCGAAGATTAT 58.476 37.037 0.00 0.00 45.12 1.28
2087 2249 7.504574 TGGTAGGTTCATACTCATCGAAGATTA 59.495 37.037 0.00 0.00 45.12 1.75
2088 2250 6.323996 TGGTAGGTTCATACTCATCGAAGATT 59.676 38.462 0.00 0.00 45.12 2.40
2091 2253 5.299531 TCTGGTAGGTTCATACTCATCGAAG 59.700 44.000 0.00 0.00 0.00 3.79
2095 2257 7.309499 CCATAGTCTGGTAGGTTCATACTCATC 60.309 44.444 0.00 0.00 40.49 2.92
2122 2363 5.787953 TCAGAAAGACCAAATGATTTGCA 57.212 34.783 12.26 0.00 39.31 4.08
2131 2372 8.624367 TTTAATCGGTATTCAGAAAGACCAAA 57.376 30.769 14.92 7.26 45.33 3.28
2143 2384 4.879545 TGGCCAACTCTTTAATCGGTATTC 59.120 41.667 0.61 0.00 0.00 1.75
2145 2386 4.497291 TGGCCAACTCTTTAATCGGTAT 57.503 40.909 0.61 0.00 0.00 2.73
2146 2387 3.985019 TGGCCAACTCTTTAATCGGTA 57.015 42.857 0.61 0.00 0.00 4.02
2147 2388 2.871096 TGGCCAACTCTTTAATCGGT 57.129 45.000 0.61 0.00 0.00 4.69
2148 2389 4.022329 ACTTTTGGCCAACTCTTTAATCGG 60.022 41.667 20.35 0.00 0.00 4.18
2149 2390 5.121221 ACTTTTGGCCAACTCTTTAATCG 57.879 39.130 20.35 0.37 0.00 3.34
2150 2391 6.512297 TCAACTTTTGGCCAACTCTTTAATC 58.488 36.000 20.35 0.00 0.00 1.75
2151 2392 6.478512 TCAACTTTTGGCCAACTCTTTAAT 57.521 33.333 20.35 0.00 0.00 1.40
2152 2393 5.923733 TCAACTTTTGGCCAACTCTTTAA 57.076 34.783 20.35 7.83 0.00 1.52
2153 2394 5.596361 TCATCAACTTTTGGCCAACTCTTTA 59.404 36.000 20.35 0.00 0.00 1.85
2154 2395 4.405358 TCATCAACTTTTGGCCAACTCTTT 59.595 37.500 20.35 6.32 0.00 2.52
2176 2417 0.178998 ATGGACATGGCCAGCAGATC 60.179 55.000 27.68 3.70 42.15 2.75
2259 2500 7.993183 ACATCTACAAGATACCCAAAGTTATGG 59.007 37.037 0.00 0.00 35.15 2.74
2271 2512 5.109662 TGCGCTCTACATCTACAAGATAC 57.890 43.478 9.73 0.00 32.12 2.24
2273 2514 4.862902 ATGCGCTCTACATCTACAAGAT 57.137 40.909 9.73 0.00 34.74 2.40
2291 2532 5.629079 AACAAGGAGTAAAGCTTGTATGC 57.371 39.130 0.00 0.00 38.85 3.14
2319 2560 8.000780 AGAGCTCCAATAATAAACATGGAAAC 57.999 34.615 10.93 0.00 41.20 2.78
2420 2661 7.111041 CCCATCGTTTTTAAATTAACGCTATCG 59.889 37.037 16.63 3.65 44.87 2.92
2452 2693 1.500474 TACCAGGATGCCTCTCCTTG 58.500 55.000 0.00 0.00 43.33 3.61
2493 2734 1.606885 GGGTGGAATGTGGCATGTGG 61.607 60.000 0.00 0.00 0.00 4.17
2563 2804 3.759581 CCTCCACCTTCATCCAATATGG 58.240 50.000 0.00 0.00 39.43 2.74
2577 2818 0.388520 GAAACAAATGCGCCTCCACC 60.389 55.000 4.18 0.00 0.00 4.61
2657 2898 3.349927 ACGTAGAAATGTTTAAGGCCCC 58.650 45.455 0.00 0.00 0.00 5.80
2673 2922 8.246908 TCTCACCATGTACAATAAAAACGTAG 57.753 34.615 0.00 0.00 0.00 3.51
2688 2937 2.425143 ATCCGCAAATCTCACCATGT 57.575 45.000 0.00 0.00 0.00 3.21
2695 2944 4.816925 ACCTTTTAGCTATCCGCAAATCTC 59.183 41.667 0.00 0.00 42.61 2.75
2792 3041 5.355350 CCATCTCTACAACCCAGACAAAATC 59.645 44.000 0.00 0.00 0.00 2.17
2803 3052 5.221461 CCCAGTACATACCATCTCTACAACC 60.221 48.000 0.00 0.00 0.00 3.77
2847 3096 6.183360 CCTCTGCTATTTACCTAAACAAACCG 60.183 42.308 0.00 0.00 0.00 4.44
2895 3144 1.968704 TCCCGCAACAACAACATACA 58.031 45.000 0.00 0.00 0.00 2.29
2921 3170 5.428457 AGTGATGATGTCCCTGTAACCATAA 59.572 40.000 0.00 0.00 0.00 1.90
2958 3210 9.627123 CTATACATAAAAAGGTCCATTTGAGGA 57.373 33.333 0.00 0.00 34.64 3.71
3025 3277 3.684788 CGGTGAACAGAAGATTTACCTGG 59.315 47.826 0.00 0.00 34.38 4.45
3147 3399 4.024670 AGTTATAGGACGGAGCAAGAAGT 58.975 43.478 0.00 0.00 0.00 3.01
3247 3499 6.303839 ACTTTTGGACTGGCAAATAGTAGAA 58.696 36.000 0.00 0.00 0.00 2.10
3373 3626 6.589830 ACGTAATAGCAGATGTCATTGAAC 57.410 37.500 0.00 0.00 0.00 3.18
3392 3645 5.299782 AGCATGTTTAAGGGTCAAAAACGTA 59.700 36.000 0.00 0.00 36.19 3.57
3563 3823 4.767928 ACCTAAATATACCTCTCGAGCAGG 59.232 45.833 22.01 22.01 37.03 4.85
3776 4036 6.476706 GCATTGATAACATAACAAGAAAGGCC 59.523 38.462 0.00 0.00 0.00 5.19
3912 4186 0.526954 AACGTGTGAGACACCACGAC 60.527 55.000 17.74 6.84 45.93 4.34
3930 4204 6.246919 TCGGTTATCCTTCCAATTGGTTAAA 58.753 36.000 23.76 10.37 36.34 1.52
3932 4206 5.438698 TCGGTTATCCTTCCAATTGGTTA 57.561 39.130 23.76 12.34 36.34 2.85
4093 4403 0.252761 TGCAAGATTGGAGCGGATGA 59.747 50.000 0.00 0.00 0.00 2.92
4193 4503 2.536761 TCTTTCATGGTCCGTTCGTT 57.463 45.000 0.00 0.00 0.00 3.85
4194 4504 2.536761 TTCTTTCATGGTCCGTTCGT 57.463 45.000 0.00 0.00 0.00 3.85
4195 4505 2.412847 GCTTTCTTTCATGGTCCGTTCG 60.413 50.000 0.00 0.00 0.00 3.95
4196 4506 2.412847 CGCTTTCTTTCATGGTCCGTTC 60.413 50.000 0.00 0.00 0.00 3.95
4197 4507 1.535462 CGCTTTCTTTCATGGTCCGTT 59.465 47.619 0.00 0.00 0.00 4.44
4250 4560 3.917870 CGTCACGGATGCGGATAC 58.082 61.111 12.44 4.91 0.00 2.24
4299 4609 2.364002 ACCACACCATGTTTAAAGCACC 59.636 45.455 0.00 0.00 0.00 5.01
4354 4664 3.795688 ACCAAGTTCCACATCATGTCT 57.204 42.857 0.00 0.00 0.00 3.41
4414 4724 0.958091 TTGCCAAGACAATGGTTCGG 59.042 50.000 0.00 0.00 42.75 4.30
4421 4731 4.298332 GACGAAATTGTTGCCAAGACAAT 58.702 39.130 0.00 0.00 46.58 2.71
4429 4739 2.034053 TGACAAGGACGAAATTGTTGCC 59.966 45.455 0.00 0.00 39.66 4.52
4440 4750 3.393800 AGATTGTTCACTGACAAGGACG 58.606 45.455 0.00 0.00 42.28 4.79
4473 4786 2.095853 CCCGAAACAGTGATCAAATCCG 59.904 50.000 0.00 0.00 0.00 4.18
4494 4807 4.551892 CACGGTGTTTATTTTCACGCATAC 59.448 41.667 0.00 0.00 35.67 2.39
4499 4812 3.547601 GACCACGGTGTTTATTTTCACG 58.452 45.455 7.45 0.00 35.67 4.35
4516 4830 3.665515 TAGCGGATCCCACGGACCA 62.666 63.158 6.06 0.00 32.98 4.02
4548 4862 3.009723 CGACAGTATCCAAACAGCCAAT 58.990 45.455 0.00 0.00 0.00 3.16
4578 4898 3.880490 TGAAGCTCGCCAGAAAGTAAAAA 59.120 39.130 0.00 0.00 0.00 1.94
4583 4903 0.394565 ACTGAAGCTCGCCAGAAAGT 59.605 50.000 15.01 0.00 34.65 2.66
4651 5045 2.048603 GGCCTCTTGGGATGTGTGC 61.049 63.158 0.00 0.00 37.23 4.57
4750 5170 9.231297 CCTAGAAAAATATGAAGTCTTGGTTGA 57.769 33.333 0.00 0.00 0.00 3.18
4753 5173 8.606830 ACTCCTAGAAAAATATGAAGTCTTGGT 58.393 33.333 0.00 0.00 34.23 3.67
4806 5226 5.407387 GCAACAAACAAATCAGATGCAGATT 59.593 36.000 0.00 0.00 37.30 2.40
4937 5367 2.421314 CCGTCGGAGGCATGCATA 59.579 61.111 21.36 0.00 0.00 3.14
4946 5376 2.126071 AATGCGTCACCGTCGGAG 60.126 61.111 20.51 10.94 36.15 4.63
4959 5389 1.245732 GCCAGATCAGATGGGAATGC 58.754 55.000 0.00 0.00 38.33 3.56
4961 5391 0.399454 CGGCCAGATCAGATGGGAAT 59.601 55.000 2.24 0.00 38.33 3.01
4962 5392 0.982852 ACGGCCAGATCAGATGGGAA 60.983 55.000 2.24 0.00 38.33 3.97
5074 5508 4.163268 GGCCCCTATCAATGGCTTTAAAAA 59.837 41.667 0.00 0.00 44.71 1.94
5161 5612 0.618981 GTACCCCTAGCCAAGCAACT 59.381 55.000 0.00 0.00 0.00 3.16
5193 5645 3.182152 AGTATTCCCACTACAACCAGCT 58.818 45.455 0.00 0.00 0.00 4.24
5194 5646 3.629142 AGTATTCCCACTACAACCAGC 57.371 47.619 0.00 0.00 0.00 4.85
5232 5684 3.446873 ACAAACCAAGCACAAGTTCATGA 59.553 39.130 0.00 0.00 0.00 3.07
5233 5685 3.552699 CACAAACCAAGCACAAGTTCATG 59.447 43.478 0.00 0.00 0.00 3.07
5235 5687 2.560542 ACACAAACCAAGCACAAGTTCA 59.439 40.909 0.00 0.00 0.00 3.18
5236 5688 2.923020 CACACAAACCAAGCACAAGTTC 59.077 45.455 0.00 0.00 0.00 3.01
5252 5704 8.718158 AGATAATGATAGAATCCTCTCACACA 57.282 34.615 0.00 0.00 29.84 3.72
5307 5771 9.492730 TGGAGCACATTATCTTCTGGATATATA 57.507 33.333 0.00 0.00 36.86 0.86
5308 5772 8.384693 TGGAGCACATTATCTTCTGGATATAT 57.615 34.615 0.00 0.00 36.86 0.86
5349 5813 5.462068 CACAAGAGATTTATACGATGCGGAA 59.538 40.000 0.00 0.00 0.00 4.30
5361 5825 6.017109 GCAGTTTCAACTCCACAAGAGATTTA 60.017 38.462 0.00 0.00 46.50 1.40
5429 5893 1.530293 CGCAGATGCTCCAAGATAAGC 59.470 52.381 2.95 0.00 39.32 3.09


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

AutoCloner maintained by Alex Coulton.