Multiple sequence alignment - TraesCS5D01G040300

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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 TraesCS5D01G040300 chr5D 100.000 4157 0 0 1 4157 41290550 41294706 0.000000e+00 7677.0
1 TraesCS5D01G040300 chr5D 89.076 357 34 4 1519 1873 25852939 25852586 4.930000e-119 438.0
2 TraesCS5D01G040300 chr5D 75.123 611 77 45 3553 4127 41120226 41119655 2.520000e-52 217.0
3 TraesCS5D01G040300 chr5B 93.119 1744 81 15 1097 2817 35283205 35284932 0.000000e+00 2519.0
4 TraesCS5D01G040300 chr5B 90.855 1345 62 20 2824 4157 35285147 35286441 0.000000e+00 1746.0
5 TraesCS5D01G040300 chr5B 92.067 479 24 9 464 936 35282309 35282779 0.000000e+00 662.0
6 TraesCS5D01G040300 chr5B 91.329 346 24 3 1 340 35281970 35282315 6.290000e-128 468.0
7 TraesCS5D01G040300 chr5B 88.515 357 35 5 1519 1873 517822282 517822634 1.070000e-115 427.0
8 TraesCS5D01G040300 chr5B 90.722 194 18 0 1207 1400 517822096 517822289 4.120000e-65 259.0
9 TraesCS5D01G040300 chr5B 73.492 630 83 41 3553 4127 35189910 35189310 1.200000e-35 161.0
10 TraesCS5D01G040300 chr5B 88.288 111 13 0 7 117 667569965 667570075 2.610000e-27 134.0
11 TraesCS5D01G040300 chr5A 89.143 1179 79 23 1 1158 29613182 29614332 0.000000e+00 1423.0
12 TraesCS5D01G040300 chr5A 88.889 387 32 5 1604 1982 3470657 3470274 2.260000e-127 466.0
13 TraesCS5D01G040300 chr5A 86.667 435 40 10 3195 3622 29618567 29618990 2.260000e-127 466.0
14 TraesCS5D01G040300 chr5A 88.372 387 33 5 1604 1982 702048251 702047869 4.900000e-124 455.0
15 TraesCS5D01G040300 chr5A 86.188 362 43 5 1519 1877 669938660 669939017 6.520000e-103 385.0
16 TraesCS5D01G040300 chr5A 88.430 242 19 3 1748 1982 541372795 541372556 2.450000e-72 283.0
17 TraesCS5D01G040300 chr5A 80.843 261 34 10 3881 4127 29515387 29515129 1.530000e-44 191.0
18 TraesCS5D01G040300 chr5A 91.667 132 11 0 1399 1530 687680924 687681055 2.550000e-42 183.0
19 TraesCS5D01G040300 chr3D 88.601 386 34 6 1604 1982 440212350 440211968 1.050000e-125 460.0
20 TraesCS5D01G040300 chr3D 81.313 396 56 11 1611 2005 25519571 25519949 5.220000e-79 305.0
21 TraesCS5D01G040300 chr3D 91.429 140 11 1 1393 1532 351086759 351086621 1.530000e-44 191.0
22 TraesCS5D01G040300 chr4B 88.220 382 39 5 1604 1982 597481668 597482046 6.340000e-123 451.0
23 TraesCS5D01G040300 chr6B 87.855 387 34 7 1604 1982 219880515 219880896 3.810000e-120 442.0
24 TraesCS5D01G040300 chr6B 86.957 115 15 0 3 117 204159130 204159244 3.370000e-26 130.0
25 TraesCS5D01G040300 chr2D 88.767 365 36 3 1604 1965 29674253 29673891 3.810000e-120 442.0
26 TraesCS5D01G040300 chr2D 93.651 126 8 0 1398 1523 62293293 62293418 5.490000e-44 189.0
27 TraesCS5D01G040300 chr2D 92.969 128 9 0 1396 1523 300887311 300887438 1.970000e-43 187.0
28 TraesCS5D01G040300 chr3A 89.106 358 31 6 1519 1873 242902226 242901874 4.930000e-119 438.0
29 TraesCS5D01G040300 chr3A 91.837 196 16 0 1205 1400 242902414 242902219 1.470000e-69 274.0
30 TraesCS5D01G040300 chr2B 87.395 357 37 5 1519 1873 65242961 65243311 1.800000e-108 403.0
31 TraesCS5D01G040300 chr2B 88.358 335 33 4 1550 1880 764014477 764014145 8.370000e-107 398.0
32 TraesCS5D01G040300 chr2B 92.784 194 14 0 1207 1400 65242775 65242968 8.800000e-72 281.0
33 TraesCS5D01G040300 chr2B 88.667 150 14 3 1398 1546 423662812 423662665 3.300000e-41 180.0
34 TraesCS5D01G040300 chr6A 87.252 353 39 4 1519 1868 120275674 120275325 8.370000e-107 398.0
35 TraesCS5D01G040300 chr6A 86.188 362 43 5 1519 1877 120355298 120355655 6.520000e-103 385.0
36 TraesCS5D01G040300 chr6A 91.327 196 17 0 1205 1400 120355110 120355305 6.850000e-68 268.0
37 TraesCS5D01G040300 chr6A 91.053 190 17 0 1211 1400 120275856 120275667 1.480000e-64 257.0
38 TraesCS5D01G040300 chr6A 86.957 115 15 0 3 117 84916864 84916750 3.370000e-26 130.0
39 TraesCS5D01G040300 chr4A 85.912 362 43 6 1519 1877 231001055 231001411 3.030000e-101 379.0
40 TraesCS5D01G040300 chr4A 92.347 196 15 0 1205 1400 231000867 231001062 3.160000e-71 279.0
41 TraesCS5D01G040300 chr4A 78.571 336 56 9 2824 3150 687314380 687314708 1.510000e-49 207.0
42 TraesCS5D01G040300 chr4A 100.000 28 0 0 1034 1061 469197470 469197443 8.000000e-03 52.8
43 TraesCS5D01G040300 chr7D 81.818 396 54 11 1611 2005 37667640 37667262 2.410000e-82 316.0
44 TraesCS5D01G040300 chr7D 92.105 190 15 0 1211 1400 48133236 48133047 6.850000e-68 268.0
45 TraesCS5D01G040300 chr7D 90.306 196 19 0 1205 1400 508068990 508068795 1.480000e-64 257.0
46 TraesCS5D01G040300 chr7D 95.082 122 6 0 1402 1523 585713918 585714039 4.240000e-45 193.0
47 TraesCS5D01G040300 chr7B 92.857 126 9 0 1398 1523 680907435 680907560 2.550000e-42 183.0
48 TraesCS5D01G040300 chr6D 91.667 132 11 0 1400 1531 435990509 435990640 2.550000e-42 183.0
49 TraesCS5D01G040300 chrUn 89.091 110 12 0 8 117 94181869 94181978 2.020000e-28 137.0
50 TraesCS5D01G040300 chr2A 88.991 109 12 0 9 117 449280139 449280031 7.250000e-28 135.0
51 TraesCS5D01G040300 chr1D 87.288 118 15 0 1 118 465596795 465596912 7.250000e-28 135.0
52 TraesCS5D01G040300 chr1A 88.288 111 13 0 7 117 498166878 498166988 2.610000e-27 134.0


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 TraesCS5D01G040300 chr5D 41290550 41294706 4156 False 7677.00 7677 100.0000 1 4157 1 chr5D.!!$F1 4156
1 TraesCS5D01G040300 chr5D 41119655 41120226 571 True 217.00 217 75.1230 3553 4127 1 chr5D.!!$R2 574
2 TraesCS5D01G040300 chr5B 35281970 35286441 4471 False 1348.75 2519 91.8425 1 4157 4 chr5B.!!$F2 4156
3 TraesCS5D01G040300 chr5B 517822096 517822634 538 False 343.00 427 89.6185 1207 1873 2 chr5B.!!$F3 666
4 TraesCS5D01G040300 chr5A 29613182 29614332 1150 False 1423.00 1423 89.1430 1 1158 1 chr5A.!!$F1 1157
5 TraesCS5D01G040300 chr3A 242901874 242902414 540 True 356.00 438 90.4715 1205 1873 2 chr3A.!!$R1 668
6 TraesCS5D01G040300 chr2B 65242775 65243311 536 False 342.00 403 90.0895 1207 1873 2 chr2B.!!$F1 666
7 TraesCS5D01G040300 chr6A 120275325 120275856 531 True 327.50 398 89.1525 1211 1868 2 chr6A.!!$R2 657
8 TraesCS5D01G040300 chr6A 120355110 120355655 545 False 326.50 385 88.7575 1205 1877 2 chr6A.!!$F1 672
9 TraesCS5D01G040300 chr4A 231000867 231001411 544 False 329.00 379 89.1295 1205 1877 2 chr4A.!!$F2 672

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
242 247 0.828022 TGTCAAATAGTCGGCCGGAT 59.172 50.0 27.83 16.91 0.00 4.18 F
1548 1883 0.463654 TATCTGTTCATGCCCCACGC 60.464 55.0 0.00 0.00 38.31 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1908 0.042731 AGGTGGGCTAGGTGCTTAGA 59.957 55.0 0.0 0.0 42.39 2.10 R
3265 3827 0.179062 AACGATGCTCCCTCTCATGC 60.179 55.0 0.0 0.0 0.00 4.06 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
24 25 7.589958 CTTATGTACTACTCCCTCTGTTCAT 57.410 40.000 0.00 0.00 0.00 2.57
76 77 2.094234 ACATACAAAGCGGCCCATTTTC 60.094 45.455 0.00 0.00 0.00 2.29
89 90 3.985279 GCCCATTTTCGGTTGTCTAAAAC 59.015 43.478 0.00 0.00 0.00 2.43
90 91 4.500035 GCCCATTTTCGGTTGTCTAAAACA 60.500 41.667 0.00 0.00 35.59 2.83
206 211 2.227388 CCTGCATCTCCACTGTTTTGTC 59.773 50.000 0.00 0.00 0.00 3.18
242 247 0.828022 TGTCAAATAGTCGGCCGGAT 59.172 50.000 27.83 16.91 0.00 4.18
302 309 5.525378 GTGTGATCCTAGCAAGGTGATTTAG 59.475 44.000 0.00 0.00 44.09 1.85
303 310 4.513318 GTGATCCTAGCAAGGTGATTTAGC 59.487 45.833 0.00 0.00 44.09 3.09
312 319 4.213059 GCAAGGTGATTTAGCATAGAGAGC 59.787 45.833 0.00 0.00 0.00 4.09
373 380 7.209475 TCTCATTCATTTTCCCAGAAAAACAC 58.791 34.615 6.59 0.00 31.35 3.32
374 381 6.882656 TCATTCATTTTCCCAGAAAAACACA 58.117 32.000 6.59 0.00 31.35 3.72
657 675 6.094881 ACAAGAACATTTTTGAAGTTCGGAGA 59.905 34.615 2.19 0.00 44.67 3.71
860 881 2.664851 CCGTTCCGCTTCTGTGCA 60.665 61.111 0.00 0.00 0.00 4.57
901 922 1.663695 ATAGGAAAATGCCGTCCGTG 58.336 50.000 0.00 0.00 39.06 4.94
973 994 1.220236 CATCTCCTCCCCTCTCCTTCT 59.780 57.143 0.00 0.00 0.00 2.85
1004 1025 1.375908 GCACCGCTCTCACCATGAA 60.376 57.895 0.00 0.00 0.00 2.57
1024 1053 2.915137 CCTCCTCTAGCTCCGGCC 60.915 72.222 0.00 0.00 39.73 6.13
1026 1055 2.123683 TCCTCTAGCTCCGGCCAG 60.124 66.667 2.24 0.00 39.73 4.85
1027 1056 3.230245 CCTCTAGCTCCGGCCAGG 61.230 72.222 2.24 5.27 39.73 4.45
1429 1764 2.038033 TCCGTCCCGAAATTCTTGTCTT 59.962 45.455 0.00 0.00 0.00 3.01
1431 1766 3.617263 CCGTCCCGAAATTCTTGTCTTAG 59.383 47.826 0.00 0.00 0.00 2.18
1432 1767 4.491676 CGTCCCGAAATTCTTGTCTTAGA 58.508 43.478 0.00 0.00 0.00 2.10
1436 1771 7.244192 GTCCCGAAATTCTTGTCTTAGATTTG 58.756 38.462 0.00 0.00 0.00 2.32
1481 1816 8.684973 AGTCACGTTTTAGTGTTAGATACATC 57.315 34.615 0.00 0.00 42.40 3.06
1527 1862 5.603170 AGAATTTTCGGTCGGAGGTAATA 57.397 39.130 0.00 0.00 0.00 0.98
1528 1863 5.598769 AGAATTTTCGGTCGGAGGTAATAG 58.401 41.667 0.00 0.00 0.00 1.73
1532 1867 5.695851 TTTCGGTCGGAGGTAATAGTATC 57.304 43.478 0.00 0.00 0.00 2.24
1546 1881 2.717639 AGTATCTGTTCATGCCCCAC 57.282 50.000 0.00 0.00 0.00 4.61
1547 1882 1.134401 AGTATCTGTTCATGCCCCACG 60.134 52.381 0.00 0.00 0.00 4.94
1548 1883 0.463654 TATCTGTTCATGCCCCACGC 60.464 55.000 0.00 0.00 38.31 5.34
1559 1894 2.435586 CCCACGCTCCTGCTGAAG 60.436 66.667 0.00 0.00 36.97 3.02
1562 1897 1.447489 CACGCTCCTGCTGAAGAGG 60.447 63.158 0.00 0.00 36.97 3.69
1573 1908 4.141665 CCTGCTGAAGAGGAGATGATCTTT 60.142 45.833 0.00 0.00 40.04 2.52
1672 2010 6.232692 CACCATGAACTTGAATTGGGAAATT 58.767 36.000 0.00 0.00 0.00 1.82
1716 2054 2.353704 GGGTTAGCCTGGAATTTGTTGC 60.354 50.000 0.00 0.00 34.45 4.17
1719 2057 0.883833 AGCCTGGAATTTGTTGCGAG 59.116 50.000 0.00 0.00 0.00 5.03
1743 2087 6.313905 AGTTGTAAGATGCTTCGAGTAAATGG 59.686 38.462 0.00 0.00 0.00 3.16
1822 2166 2.733945 GAGGAGGATGGCGAGCTC 59.266 66.667 2.73 2.73 0.00 4.09
1895 2240 2.863809 CCCCCTGCACTAATGTATTCC 58.136 52.381 0.00 0.00 0.00 3.01
1913 2258 8.891671 TGTATTCCGTTTTTACAAGTAAGACT 57.108 30.769 0.00 0.00 0.00 3.24
1950 2295 7.012661 TCATGATCATCTGCCATGTAGTAAT 57.987 36.000 4.86 0.00 38.88 1.89
1951 2296 7.101700 TCATGATCATCTGCCATGTAGTAATC 58.898 38.462 4.86 0.00 38.88 1.75
1959 2304 5.703592 TCTGCCATGTAGTAATCGTTGTTTT 59.296 36.000 0.00 0.00 0.00 2.43
1989 2334 8.630917 TGTAACTGCTAAGAGGATTAGTCATAC 58.369 37.037 0.00 0.00 0.00 2.39
2008 2353 7.839200 AGTCATACAAAAGGGGCACTAATTAAT 59.161 33.333 0.00 0.00 0.00 1.40
2155 2500 5.240844 GCTTTGTCAGTATTACAACCCTGTT 59.759 40.000 0.00 0.00 36.61 3.16
2208 2553 7.219484 ACAATAAACTTGTCATTTCAGGGAG 57.781 36.000 0.00 0.00 0.00 4.30
2209 2554 5.904362 ATAAACTTGTCATTTCAGGGAGC 57.096 39.130 0.00 0.00 0.00 4.70
2247 2593 7.404671 ACATGTTTTGTCTCAGTTTTAAGGT 57.595 32.000 0.00 0.00 30.89 3.50
2259 2605 9.151471 TCTCAGTTTTAAGGTCATATTTTCGAG 57.849 33.333 0.00 0.00 0.00 4.04
2261 2607 7.389330 TCAGTTTTAAGGTCATATTTTCGAGCA 59.611 33.333 0.00 0.00 32.05 4.26
2387 2741 1.202615 GCATGTGATCTGCTAGCCTCA 60.203 52.381 13.29 9.81 36.68 3.86
2390 2744 3.465742 TGTGATCTGCTAGCCTCATTC 57.534 47.619 13.29 2.96 0.00 2.67
2416 2770 5.237815 TCATCAAGTGAATTCTAGTTGCGT 58.762 37.500 7.05 3.27 32.78 5.24
2553 2907 7.706607 CGAAGTCTCAGGTATTTGATTGTGATA 59.293 37.037 0.00 0.00 0.00 2.15
2557 2911 7.168302 GTCTCAGGTATTTGATTGTGATACTCG 59.832 40.741 0.00 0.00 0.00 4.18
2568 2922 3.925379 TGTGATACTCGTGTTTGCATCT 58.075 40.909 0.00 0.00 0.00 2.90
2587 2941 2.040278 TCTTCTCCTGAATGGGTTGGTG 59.960 50.000 0.00 0.00 36.20 4.17
2592 2946 2.311542 TCCTGAATGGGTTGGTGCTAAT 59.688 45.455 0.00 0.00 36.20 1.73
2688 3042 7.558604 ACTAAAACGTATGGAAAGGCTACATA 58.441 34.615 0.00 0.00 0.00 2.29
2705 3059 5.696724 GCTACATATACATTTCTCAAGCGGT 59.303 40.000 0.00 0.00 0.00 5.68
2744 3098 4.691216 GGAGTCATAAGCGGTATCATTTCC 59.309 45.833 0.00 0.00 0.00 3.13
2761 3115 2.754946 TCCGTTCCCAACATACTGTC 57.245 50.000 0.00 0.00 0.00 3.51
2764 3118 4.028131 TCCGTTCCCAACATACTGTCTAT 58.972 43.478 0.00 0.00 0.00 1.98
2798 3152 4.527509 TCTGAGCAAGTGGAAGAACTAG 57.472 45.455 0.00 0.00 0.00 2.57
2804 3158 2.464157 AGTGGAAGAACTAGCACTGC 57.536 50.000 0.00 0.00 0.00 4.40
2812 3166 2.494073 AGAACTAGCACTGCTCACCTAC 59.506 50.000 6.86 0.00 40.44 3.18
2817 3171 3.601443 AGCACTGCTCACCTACTAAAG 57.399 47.619 0.00 0.00 30.62 1.85
2818 3172 3.165875 AGCACTGCTCACCTACTAAAGA 58.834 45.455 0.00 0.00 30.62 2.52
2847 3409 1.067295 TTCCACCTCTGCCTTGTCAT 58.933 50.000 0.00 0.00 0.00 3.06
2848 3410 1.067295 TCCACCTCTGCCTTGTCATT 58.933 50.000 0.00 0.00 0.00 2.57
2856 3418 2.622942 TCTGCCTTGTCATTGTTTGTCC 59.377 45.455 0.00 0.00 0.00 4.02
2901 3463 6.620733 GCGCAAACATATTGATATACCTGGAC 60.621 42.308 0.30 0.00 0.00 4.02
2906 3468 3.936372 ATTGATATACCTGGACGTCCG 57.064 47.619 28.70 21.91 39.43 4.79
2928 3490 0.469917 AGGCGCTGCAAGGTATGTAT 59.530 50.000 7.64 0.00 0.00 2.29
2938 3500 3.304928 GCAAGGTATGTATCAATGCTGCC 60.305 47.826 0.00 0.00 0.00 4.85
2939 3501 3.862877 AGGTATGTATCAATGCTGCCA 57.137 42.857 0.00 0.00 0.00 4.92
2941 3503 3.117926 AGGTATGTATCAATGCTGCCACA 60.118 43.478 0.00 0.00 0.00 4.17
2942 3504 3.003689 GGTATGTATCAATGCTGCCACAC 59.996 47.826 0.00 0.00 0.00 3.82
2943 3505 1.462616 TGTATCAATGCTGCCACACC 58.537 50.000 0.00 0.00 0.00 4.16
2944 3506 0.740737 GTATCAATGCTGCCACACCC 59.259 55.000 0.00 0.00 0.00 4.61
2945 3507 0.625316 TATCAATGCTGCCACACCCT 59.375 50.000 0.00 0.00 0.00 4.34
2946 3508 0.682209 ATCAATGCTGCCACACCCTC 60.682 55.000 0.00 0.00 0.00 4.30
2947 3509 2.036256 AATGCTGCCACACCCTCC 59.964 61.111 0.00 0.00 0.00 4.30
2948 3510 3.925630 AATGCTGCCACACCCTCCG 62.926 63.158 0.00 0.00 0.00 4.63
2951 3513 4.641645 CTGCCACACCCTCCGCAA 62.642 66.667 0.00 0.00 0.00 4.85
2952 3514 4.641645 TGCCACACCCTCCGCAAG 62.642 66.667 0.00 0.00 0.00 4.01
2955 3517 4.680237 CACACCCTCCGCAAGCGA 62.680 66.667 16.97 1.31 42.83 4.93
2956 3518 3.706373 ACACCCTCCGCAAGCGAT 61.706 61.111 16.97 0.00 42.83 4.58
2957 3519 2.436646 CACCCTCCGCAAGCGATT 60.437 61.111 16.97 0.00 42.83 3.34
2958 3520 2.125106 ACCCTCCGCAAGCGATTC 60.125 61.111 16.97 0.00 42.83 2.52
2959 3521 3.264897 CCCTCCGCAAGCGATTCG 61.265 66.667 16.97 0.62 42.83 3.34
2975 3537 6.561614 AGCGATTCGAGTTCTTCATTTACTA 58.438 36.000 10.88 0.00 0.00 1.82
2991 3553 8.766000 TCATTTACTATCTCGCTAGACTAGAG 57.234 38.462 13.91 10.28 33.57 2.43
3061 3623 1.270839 ACATCTCCGACAACAAGGTGG 60.271 52.381 0.00 0.00 0.00 4.61
3069 3631 2.132762 GACAACAAGGTGGTACTGACG 58.867 52.381 0.00 0.00 0.00 4.35
3081 3643 0.883833 TACTGACGGAGGGTTTCGAC 59.116 55.000 0.00 0.00 0.00 4.20
3118 3680 5.186021 GTCAAGTACTTGGAGAAGATGGAGA 59.814 44.000 30.35 8.03 40.78 3.71
3124 3686 1.272480 TGGAGAAGATGGAGACGTGGA 60.272 52.381 0.00 0.00 0.00 4.02
3137 3699 2.997897 GTGGACAGGACGCCCTCT 60.998 66.667 0.00 0.00 42.02 3.69
3144 3706 1.828660 AGGACGCCCTCTGATACCG 60.829 63.158 0.00 0.00 38.86 4.02
3183 3745 1.468520 GGCTTTGCGTTGATAGCTTGA 59.531 47.619 0.00 0.00 34.16 3.02
3203 3765 2.170187 GAGATGCACTCACTCCCTTGAT 59.830 50.000 10.30 0.00 44.36 2.57
3210 3772 3.684788 CACTCACTCCCTTGATTAAACCG 59.315 47.826 0.00 0.00 0.00 4.44
3225 3787 7.497595 TGATTAAACCGTGCTGTAATATCTCT 58.502 34.615 0.00 0.00 0.00 3.10
3226 3788 7.652105 TGATTAAACCGTGCTGTAATATCTCTC 59.348 37.037 0.00 0.00 0.00 3.20
3227 3789 5.599999 AAACCGTGCTGTAATATCTCTCT 57.400 39.130 0.00 0.00 0.00 3.10
3228 3790 4.576216 ACCGTGCTGTAATATCTCTCTG 57.424 45.455 0.00 0.00 0.00 3.35
3229 3791 4.207955 ACCGTGCTGTAATATCTCTCTGA 58.792 43.478 0.00 0.00 0.00 3.27
3230 3792 4.645136 ACCGTGCTGTAATATCTCTCTGAA 59.355 41.667 0.00 0.00 0.00 3.02
3231 3793 4.979197 CCGTGCTGTAATATCTCTCTGAAC 59.021 45.833 0.00 0.00 0.00 3.18
3232 3794 5.221145 CCGTGCTGTAATATCTCTCTGAACT 60.221 44.000 0.00 0.00 0.00 3.01
3246 3808 4.224594 TCTCTGAACTCTGAAGGCATCATT 59.775 41.667 0.00 0.00 37.44 2.57
3252 3814 4.401022 ACTCTGAAGGCATCATTTGACAA 58.599 39.130 0.00 0.00 37.44 3.18
3256 3818 4.873817 TGAAGGCATCATTTGACAAACAG 58.126 39.130 1.94 0.00 34.87 3.16
3265 3827 6.549912 TCATTTGACAAACAGACTCTGATG 57.450 37.500 13.25 12.65 35.18 3.07
3270 3832 3.999001 GACAAACAGACTCTGATGCATGA 59.001 43.478 13.25 0.00 35.18 3.07
3278 3840 0.757512 TCTGATGCATGAGAGGGAGC 59.242 55.000 12.19 0.00 0.00 4.70
3294 3856 1.363744 GAGCATCGTTCTGGACCTTG 58.636 55.000 0.00 0.00 0.00 3.61
3298 3860 2.611971 GCATCGTTCTGGACCTTGTACA 60.612 50.000 0.00 0.00 0.00 2.90
3348 3913 1.915489 TGATGATAACCTGCACCTGGT 59.085 47.619 0.00 0.00 37.28 4.00
3359 3924 3.995597 ACCTGGTGGTGGTGCTTA 58.004 55.556 0.00 0.00 46.51 3.09
3363 3928 2.092429 ACCTGGTGGTGGTGCTTATATG 60.092 50.000 0.00 0.00 46.51 1.78
3364 3929 2.092429 CCTGGTGGTGGTGCTTATATGT 60.092 50.000 0.00 0.00 0.00 2.29
3365 3930 3.620488 CTGGTGGTGGTGCTTATATGTT 58.380 45.455 0.00 0.00 0.00 2.71
3367 3932 3.761218 TGGTGGTGGTGCTTATATGTTTG 59.239 43.478 0.00 0.00 0.00 2.93
3368 3933 3.428862 GGTGGTGGTGCTTATATGTTTGC 60.429 47.826 0.00 0.00 0.00 3.68
3369 3934 3.443681 GTGGTGGTGCTTATATGTTTGCT 59.556 43.478 0.00 0.00 0.00 3.91
3370 3935 3.443329 TGGTGGTGCTTATATGTTTGCTG 59.557 43.478 0.00 0.00 0.00 4.41
3371 3936 3.694072 GGTGGTGCTTATATGTTTGCTGA 59.306 43.478 0.00 0.00 0.00 4.26
3372 3937 4.157656 GGTGGTGCTTATATGTTTGCTGAA 59.842 41.667 0.00 0.00 0.00 3.02
3373 3938 5.163519 GGTGGTGCTTATATGTTTGCTGAAT 60.164 40.000 0.00 0.00 0.00 2.57
3374 3939 5.973565 GTGGTGCTTATATGTTTGCTGAATC 59.026 40.000 0.00 0.00 0.00 2.52
3375 3940 5.067674 TGGTGCTTATATGTTTGCTGAATCC 59.932 40.000 0.00 0.00 0.00 3.01
3376 3941 5.067674 GGTGCTTATATGTTTGCTGAATCCA 59.932 40.000 0.00 0.00 0.00 3.41
3377 3942 6.239120 GGTGCTTATATGTTTGCTGAATCCAT 60.239 38.462 0.00 0.00 0.00 3.41
3378 3943 6.639686 GTGCTTATATGTTTGCTGAATCCATG 59.360 38.462 0.00 0.00 0.00 3.66
3379 3944 6.154445 GCTTATATGTTTGCTGAATCCATGG 58.846 40.000 4.97 4.97 0.00 3.66
3380 3945 6.016024 GCTTATATGTTTGCTGAATCCATGGA 60.016 38.462 18.88 18.88 0.00 3.41
3381 3946 5.779529 ATATGTTTGCTGAATCCATGGAC 57.220 39.130 18.99 5.93 0.00 4.02
3382 3947 2.874014 TGTTTGCTGAATCCATGGACA 58.126 42.857 18.99 10.92 0.00 4.02
3383 3948 3.229293 TGTTTGCTGAATCCATGGACAA 58.771 40.909 18.99 13.58 0.00 3.18
3384 3949 3.833650 TGTTTGCTGAATCCATGGACAAT 59.166 39.130 18.99 6.39 0.00 2.71
3385 3950 4.283978 TGTTTGCTGAATCCATGGACAATT 59.716 37.500 18.99 7.83 0.00 2.32
3386 3951 5.221682 TGTTTGCTGAATCCATGGACAATTT 60.222 36.000 18.99 7.40 0.00 1.82
3387 3952 5.486735 TTGCTGAATCCATGGACAATTTT 57.513 34.783 18.99 6.96 0.00 1.82
3388 3953 5.075858 TGCTGAATCCATGGACAATTTTC 57.924 39.130 18.99 16.72 0.00 2.29
3389 3954 4.773674 TGCTGAATCCATGGACAATTTTCT 59.226 37.500 18.99 0.00 0.00 2.52
3390 3955 5.105635 TGCTGAATCCATGGACAATTTTCTC 60.106 40.000 18.99 12.37 0.00 2.87
3391 3956 5.680665 GCTGAATCCATGGACAATTTTCTCC 60.681 44.000 18.99 7.94 0.00 3.71
3428 3993 2.981140 CGTCTCGTTTCTTCTGAAGGAC 59.019 50.000 16.83 14.04 33.28 3.85
3429 3994 3.550233 CGTCTCGTTTCTTCTGAAGGACA 60.550 47.826 16.83 0.00 33.28 4.02
3434 3999 6.017934 TCTCGTTTCTTCTGAAGGACATTTTG 60.018 38.462 16.83 4.61 33.28 2.44
3436 4001 4.853924 TTCTTCTGAAGGACATTTTGGC 57.146 40.909 16.83 0.00 0.00 4.52
3445 4010 2.092375 AGGACATTTTGGCTAGCTACCC 60.092 50.000 15.72 0.00 0.00 3.69
3446 4011 2.092375 GGACATTTTGGCTAGCTACCCT 60.092 50.000 15.72 0.00 0.00 4.34
3447 4012 3.206964 GACATTTTGGCTAGCTACCCTC 58.793 50.000 15.72 0.00 0.00 4.30
3449 4014 0.916809 TTTTGGCTAGCTACCCTCCC 59.083 55.000 15.72 0.00 0.00 4.30
3450 4015 0.252974 TTTGGCTAGCTACCCTCCCA 60.253 55.000 15.72 0.00 0.00 4.37
3451 4016 0.030092 TTGGCTAGCTACCCTCCCAT 60.030 55.000 15.72 0.00 0.00 4.00
3452 4017 0.764369 TGGCTAGCTACCCTCCCATG 60.764 60.000 15.72 0.00 0.00 3.66
3454 4019 1.132500 GCTAGCTACCCTCCCATGTT 58.868 55.000 7.70 0.00 0.00 2.71
3455 4020 1.070914 GCTAGCTACCCTCCCATGTTC 59.929 57.143 7.70 0.00 0.00 3.18
3456 4021 2.683768 CTAGCTACCCTCCCATGTTCT 58.316 52.381 0.00 0.00 0.00 3.01
3457 4022 1.207791 AGCTACCCTCCCATGTTCTG 58.792 55.000 0.00 0.00 0.00 3.02
3458 4023 0.464554 GCTACCCTCCCATGTTCTGC 60.465 60.000 0.00 0.00 0.00 4.26
3459 4024 0.911769 CTACCCTCCCATGTTCTGCA 59.088 55.000 0.00 0.00 0.00 4.41
3496 4061 6.524101 TTTCCAAAGTTGTGAAGTAAAGCT 57.476 33.333 0.00 0.00 0.00 3.74
3539 4104 8.121305 AGTAGCAAATTTGGTTTATGATGTGA 57.879 30.769 26.32 3.32 39.88 3.58
3550 4117 6.127925 TGGTTTATGATGTGAGTCTGCAAATC 60.128 38.462 0.00 0.00 33.89 2.17
3561 4128 2.627699 GTCTGCAAATCTGGGGTTTTCA 59.372 45.455 0.00 0.00 0.00 2.69
3567 4134 4.081476 GCAAATCTGGGGTTTTCAGCTTAT 60.081 41.667 0.00 0.00 32.63 1.73
3790 4377 1.264826 CACAAGCTGCAATTTTTGGGC 59.735 47.619 1.02 0.00 0.00 5.36
3795 4382 1.632422 CTGCAATTTTTGGGCGCTAG 58.368 50.000 7.64 0.00 0.00 3.42
3816 4404 5.153950 AGACAACTCATTTACCAGAGGAC 57.846 43.478 0.00 0.00 36.20 3.85
3837 4425 5.222048 GGACAAGGGTCATTGGGCTATATAA 60.222 44.000 0.55 0.00 46.17 0.98
3897 4489 3.179048 GTTGTTTTGACTGTGCAGAACC 58.821 45.455 6.17 0.00 33.38 3.62
3921 4513 8.306761 ACCTTTTAATTGCAAATCTCCTGTAAG 58.693 33.333 1.71 0.00 0.00 2.34
3923 4515 9.565213 CTTTTAATTGCAAATCTCCTGTAAGAG 57.435 33.333 1.71 0.00 34.07 2.85
4010 4602 2.974148 TTCGTGCCACAGCTGCAG 60.974 61.111 15.27 10.11 39.87 4.41
4023 4615 2.987149 CAGCTGCAGCATTTCTCAAAAG 59.013 45.455 38.24 10.42 45.16 2.27
4055 4655 4.888326 TTTTGCAAGATTGGGTGCTAAT 57.112 36.364 0.00 0.00 41.48 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.865090 TGAAATGTCTTCAAGGCCTTATAAAAA 58.135 29.630 20.00 6.94 0.00 1.94
89 90 7.120726 ACTCCCTCCGTTCATTTTTATAAGTTG 59.879 37.037 0.00 0.00 0.00 3.16
90 91 7.173032 ACTCCCTCCGTTCATTTTTATAAGTT 58.827 34.615 0.00 0.00 0.00 2.66
183 188 0.403271 AAACAGTGGAGATGCAGGCT 59.597 50.000 0.00 0.00 0.00 4.58
206 211 4.619227 ACAACCCGTCACGGCTGG 62.619 66.667 12.05 4.01 46.86 4.85
223 228 0.828022 ATCCGGCCGACTATTTGACA 59.172 50.000 30.73 0.00 0.00 3.58
302 309 0.666913 TAACGACCGGCTCTCTATGC 59.333 55.000 0.00 0.00 0.00 3.14
303 310 1.948145 AGTAACGACCGGCTCTCTATG 59.052 52.381 0.00 0.00 0.00 2.23
312 319 3.705043 AACTGCTATAGTAACGACCGG 57.295 47.619 0.00 0.00 39.18 5.28
342 349 6.985117 TCTGGGAAAATGAATGAGAAAACTG 58.015 36.000 0.00 0.00 0.00 3.16
414 422 5.576447 AATGACCGTGTTTCTCAAAAACT 57.424 34.783 2.73 0.00 0.00 2.66
415 423 6.641176 AAAATGACCGTGTTTCTCAAAAAC 57.359 33.333 0.00 0.00 0.00 2.43
511 520 8.745837 GTTCACATATTTGAAAAGTGTTCAGTG 58.254 33.333 5.88 6.18 37.24 3.66
628 645 8.227119 CCGAACTTCAAAAATGTTCTTGTTTTT 58.773 29.630 0.00 0.00 37.85 1.94
767 788 1.377612 GGTCCGGCTTTTACTGGGT 59.622 57.895 0.00 0.00 36.66 4.51
778 799 4.542075 GGAAGATTCTGGTCCGGC 57.458 61.111 0.00 0.00 0.00 6.13
848 869 1.135315 CCGAATTGCACAGAAGCGG 59.865 57.895 0.00 0.00 37.31 5.52
961 982 1.199615 GTTGAGGAGAAGGAGAGGGG 58.800 60.000 0.00 0.00 0.00 4.79
1004 1025 1.076632 CCGGAGCTAGAGGAGGTGT 60.077 63.158 0.00 0.00 35.50 4.16
1101 1432 4.776322 TTGCTCCCATCGCCACGG 62.776 66.667 0.00 0.00 0.00 4.94
1102 1433 3.499737 GTTGCTCCCATCGCCACG 61.500 66.667 0.00 0.00 0.00 4.94
1103 1434 3.134127 GGTTGCTCCCATCGCCAC 61.134 66.667 0.00 0.00 0.00 5.01
1104 1435 4.776322 CGGTTGCTCCCATCGCCA 62.776 66.667 0.00 0.00 0.00 5.69
1108 1439 3.195698 GACGCGGTTGCTCCCATC 61.196 66.667 12.47 0.00 39.65 3.51
1203 1538 2.341101 CGGCCGTGAGTGAGTACCT 61.341 63.158 19.50 0.00 0.00 3.08
1282 1617 4.891037 GCTCCTCATGCCCAGCCC 62.891 72.222 0.00 0.00 0.00 5.19
1284 1619 4.166888 TCGCTCCTCATGCCCAGC 62.167 66.667 0.00 0.00 0.00 4.85
1436 1771 8.899776 CGTGACTAGATAAATCCGTATTTACAC 58.100 37.037 0.00 0.00 39.71 2.90
1481 1816 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
1514 1849 5.533903 TGAACAGATACTATTACCTCCGACC 59.466 44.000 0.00 0.00 0.00 4.79
1527 1862 1.134401 CGTGGGGCATGAACAGATACT 60.134 52.381 0.00 0.00 0.00 2.12
1528 1863 1.299541 CGTGGGGCATGAACAGATAC 58.700 55.000 0.00 0.00 0.00 2.24
1559 1894 5.070313 AGGTGCTTAGAAAGATCATCTCCTC 59.930 44.000 4.49 0.00 0.00 3.71
1562 1897 5.925969 GCTAGGTGCTTAGAAAGATCATCTC 59.074 44.000 4.49 0.00 38.95 2.75
1573 1908 0.042731 AGGTGGGCTAGGTGCTTAGA 59.957 55.000 0.00 0.00 42.39 2.10
1702 2040 2.034558 ACAACTCGCAACAAATTCCAGG 59.965 45.455 0.00 0.00 0.00 4.45
1716 2054 3.502920 ACTCGAAGCATCTTACAACTCG 58.497 45.455 0.00 0.00 0.00 4.18
1719 2057 6.092259 ACCATTTACTCGAAGCATCTTACAAC 59.908 38.462 0.00 0.00 0.00 3.32
1760 2104 3.417275 CTCGCCTGACCGCCTACAG 62.417 68.421 0.00 0.00 0.00 2.74
1822 2166 3.386543 CTGGTTAGCCCGAATCAGG 57.613 57.895 0.00 0.00 34.45 3.86
1909 2254 7.845037 TGATCATGAAGAGTATGAACAAGTCT 58.155 34.615 0.00 0.00 38.01 3.24
1912 2257 8.766151 CAGATGATCATGAAGAGTATGAACAAG 58.234 37.037 14.30 0.00 39.63 3.16
1913 2258 7.226128 GCAGATGATCATGAAGAGTATGAACAA 59.774 37.037 14.30 0.00 39.63 2.83
1918 2263 5.548406 TGGCAGATGATCATGAAGAGTATG 58.452 41.667 14.30 0.00 0.00 2.39
1959 2304 9.216117 GACTAATCCTCTTAGCAGTTACAAAAA 57.784 33.333 0.00 0.00 0.00 1.94
1961 2306 7.903145 TGACTAATCCTCTTAGCAGTTACAAA 58.097 34.615 0.00 0.00 0.00 2.83
1962 2307 7.476540 TGACTAATCCTCTTAGCAGTTACAA 57.523 36.000 0.00 0.00 0.00 2.41
1963 2308 7.661536 ATGACTAATCCTCTTAGCAGTTACA 57.338 36.000 0.00 0.00 0.00 2.41
1964 2309 8.630917 TGTATGACTAATCCTCTTAGCAGTTAC 58.369 37.037 0.00 0.00 0.00 2.50
1966 2311 7.661536 TGTATGACTAATCCTCTTAGCAGTT 57.338 36.000 0.00 0.00 0.00 3.16
1981 2326 5.765576 TTAGTGCCCCTTTTGTATGACTA 57.234 39.130 0.00 0.00 0.00 2.59
1984 2329 9.349713 CTATTAATTAGTGCCCCTTTTGTATGA 57.650 33.333 0.00 0.00 0.00 2.15
2008 2353 0.108992 GGGTTCGACGCATGACACTA 60.109 55.000 0.00 0.00 0.00 2.74
2188 2533 4.761739 CAGCTCCCTGAAATGACAAGTTTA 59.238 41.667 0.00 0.00 41.77 2.01
2189 2534 3.571401 CAGCTCCCTGAAATGACAAGTTT 59.429 43.478 0.00 0.00 41.77 2.66
2198 2543 4.379302 AAAGAAGACAGCTCCCTGAAAT 57.621 40.909 0.00 0.00 41.77 2.17
2232 2577 8.932791 TCGAAAATATGACCTTAAAACTGAGAC 58.067 33.333 0.00 0.00 0.00 3.36
2235 2580 7.389330 TGCTCGAAAATATGACCTTAAAACTGA 59.611 33.333 0.00 0.00 0.00 3.41
2247 2593 6.114187 AGGGTATGATGCTCGAAAATATGA 57.886 37.500 0.00 0.00 0.00 2.15
2256 2602 7.905604 TGATTAAATTAGGGTATGATGCTCG 57.094 36.000 0.00 0.00 0.00 5.03
2390 2744 7.223582 ACGCAACTAGAATTCACTTGATGATAG 59.776 37.037 8.44 0.00 37.11 2.08
2416 2770 3.706600 AATTCCACTAAGCGGGTTACA 57.293 42.857 0.00 0.00 0.00 2.41
2450 2804 6.719370 AGGTTTACAGGATCATTACAAAAGCA 59.281 34.615 0.00 0.00 0.00 3.91
2553 2907 2.037772 AGGAGAAGATGCAAACACGAGT 59.962 45.455 0.00 0.00 0.00 4.18
2557 2911 4.380233 CCATTCAGGAGAAGATGCAAACAC 60.380 45.833 0.00 0.00 41.22 3.32
2568 2922 1.547675 GCACCAACCCATTCAGGAGAA 60.548 52.381 0.00 0.00 41.22 2.87
2688 3042 3.119495 GGCAAACCGCTTGAGAAATGTAT 60.119 43.478 0.07 0.00 41.91 2.29
2705 3059 1.347707 ACTCCTTCGTCTGATGGCAAA 59.652 47.619 0.00 0.00 38.88 3.68
2761 3115 7.337942 ACTTGCTCAGAAGAATAAACCCAATAG 59.662 37.037 0.00 0.00 0.00 1.73
2764 3118 5.241506 CACTTGCTCAGAAGAATAAACCCAA 59.758 40.000 0.00 0.00 0.00 4.12
2798 3152 3.594603 TCTTTAGTAGGTGAGCAGTGC 57.405 47.619 7.13 7.13 0.00 4.40
2804 3158 6.231211 ACAAACCACATCTTTAGTAGGTGAG 58.769 40.000 0.00 0.00 37.13 3.51
2847 3409 4.072131 GCATACCTGAAGAGGACAAACAA 58.928 43.478 0.00 0.00 42.93 2.83
2848 3410 3.674997 GCATACCTGAAGAGGACAAACA 58.325 45.455 0.00 0.00 42.93 2.83
2856 3418 0.384309 TACGCCGCATACCTGAAGAG 59.616 55.000 0.00 0.00 0.00 2.85
2893 3455 2.642254 CCTTGCGGACGTCCAGGTA 61.642 63.158 32.80 15.32 35.14 3.08
2906 3468 2.409870 ATACCTTGCAGCGCCTTGC 61.410 57.895 14.21 14.21 46.98 4.01
2928 3490 1.303561 GAGGGTGTGGCAGCATTGA 60.304 57.895 0.00 0.00 33.07 2.57
2938 3500 3.958147 ATCGCTTGCGGAGGGTGTG 62.958 63.158 15.10 0.00 39.25 3.82
2939 3501 3.254024 AATCGCTTGCGGAGGGTGT 62.254 57.895 15.10 0.00 39.25 4.16
2941 3503 2.125106 GAATCGCTTGCGGAGGGT 60.125 61.111 15.10 0.00 39.25 4.34
2942 3504 3.264897 CGAATCGCTTGCGGAGGG 61.265 66.667 15.10 0.00 39.55 4.30
2943 3505 2.202743 TCGAATCGCTTGCGGAGG 60.203 61.111 15.10 3.04 0.00 4.30
2944 3506 1.078759 AACTCGAATCGCTTGCGGAG 61.079 55.000 15.10 14.55 0.00 4.63
2945 3507 1.076533 GAACTCGAATCGCTTGCGGA 61.077 55.000 15.10 3.59 0.00 5.54
2946 3508 1.078759 AGAACTCGAATCGCTTGCGG 61.079 55.000 15.10 0.39 0.00 5.69
2947 3509 0.716108 AAGAACTCGAATCGCTTGCG 59.284 50.000 8.87 8.87 0.00 4.85
2948 3510 1.726791 TGAAGAACTCGAATCGCTTGC 59.273 47.619 0.00 0.00 0.00 4.01
2949 3511 4.590400 AATGAAGAACTCGAATCGCTTG 57.410 40.909 0.00 0.00 0.00 4.01
2950 3512 5.869888 AGTAAATGAAGAACTCGAATCGCTT 59.130 36.000 0.00 0.00 0.00 4.68
2951 3513 5.411781 AGTAAATGAAGAACTCGAATCGCT 58.588 37.500 0.00 0.00 0.00 4.93
2952 3514 5.704217 AGTAAATGAAGAACTCGAATCGC 57.296 39.130 0.00 0.00 0.00 4.58
2953 3515 8.789881 AGATAGTAAATGAAGAACTCGAATCG 57.210 34.615 0.00 0.00 0.00 3.34
2954 3516 8.897809 CGAGATAGTAAATGAAGAACTCGAATC 58.102 37.037 0.00 0.00 44.41 2.52
2955 3517 7.380065 GCGAGATAGTAAATGAAGAACTCGAAT 59.620 37.037 1.07 0.00 44.41 3.34
2956 3518 6.691818 GCGAGATAGTAAATGAAGAACTCGAA 59.308 38.462 1.07 0.00 44.41 3.71
2957 3519 6.038382 AGCGAGATAGTAAATGAAGAACTCGA 59.962 38.462 1.07 0.00 44.41 4.04
2958 3520 6.202937 AGCGAGATAGTAAATGAAGAACTCG 58.797 40.000 0.00 0.00 44.45 4.18
2959 3521 8.561212 TCTAGCGAGATAGTAAATGAAGAACTC 58.439 37.037 0.00 0.00 0.00 3.01
2975 3537 4.286297 AGCATCTCTAGTCTAGCGAGAT 57.714 45.455 0.00 5.92 43.32 2.75
2991 3553 4.179926 TCGGCAATCAGATACTAGCATC 57.820 45.455 0.00 0.00 0.00 3.91
3061 3623 0.883833 TCGAAACCCTCCGTCAGTAC 59.116 55.000 0.00 0.00 0.00 2.73
3069 3631 4.368543 ACGCCGTCGAAACCCTCC 62.369 66.667 0.00 0.00 39.41 4.30
3124 3686 1.043673 GGTATCAGAGGGCGTCCTGT 61.044 60.000 16.74 6.59 45.05 4.00
3137 3699 5.352016 CGGTTTTATCTTTGGAACGGTATCA 59.648 40.000 0.00 0.00 0.00 2.15
3144 3706 3.254903 AGCCACGGTTTTATCTTTGGAAC 59.745 43.478 0.00 0.00 0.00 3.62
3183 3745 1.649321 TCAAGGGAGTGAGTGCATCT 58.351 50.000 0.00 0.00 0.00 2.90
3203 3765 6.978659 CAGAGAGATATTACAGCACGGTTTAA 59.021 38.462 0.00 0.00 0.00 1.52
3210 3772 6.917477 CAGAGTTCAGAGAGATATTACAGCAC 59.083 42.308 0.00 0.00 0.00 4.40
3225 3787 4.564782 AATGATGCCTTCAGAGTTCAGA 57.435 40.909 0.00 0.00 37.89 3.27
3226 3788 4.698780 TCAAATGATGCCTTCAGAGTTCAG 59.301 41.667 0.00 0.00 37.89 3.02
3227 3789 4.456911 GTCAAATGATGCCTTCAGAGTTCA 59.543 41.667 0.00 0.00 37.89 3.18
3228 3790 4.456911 TGTCAAATGATGCCTTCAGAGTTC 59.543 41.667 0.00 0.00 37.89 3.01
3229 3791 4.401022 TGTCAAATGATGCCTTCAGAGTT 58.599 39.130 0.00 0.00 37.89 3.01
3230 3792 4.025040 TGTCAAATGATGCCTTCAGAGT 57.975 40.909 0.00 0.00 37.89 3.24
3231 3793 5.159209 GTTTGTCAAATGATGCCTTCAGAG 58.841 41.667 0.40 0.00 37.89 3.35
3232 3794 4.583907 TGTTTGTCAAATGATGCCTTCAGA 59.416 37.500 0.40 0.00 37.89 3.27
3246 3808 3.807553 TGCATCAGAGTCTGTTTGTCAA 58.192 40.909 19.53 0.00 32.61 3.18
3252 3814 3.118702 CCTCTCATGCATCAGAGTCTGTT 60.119 47.826 23.96 8.98 35.29 3.16
3256 3818 2.036217 CTCCCTCTCATGCATCAGAGTC 59.964 54.545 23.96 0.00 35.29 3.36
3265 3827 0.179062 AACGATGCTCCCTCTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
3270 3832 0.324738 TCCAGAACGATGCTCCCTCT 60.325 55.000 0.00 0.00 0.00 3.69
3278 3840 3.313012 TGTACAAGGTCCAGAACGATG 57.687 47.619 0.00 0.00 0.00 3.84
3294 3856 3.839293 TGTTTTGCACAACCACTTGTAC 58.161 40.909 12.96 0.00 38.66 2.90
3322 3884 3.544684 GTGCAGGTTATCATCATCACCA 58.455 45.455 0.00 0.00 29.45 4.17
3324 3886 3.562973 CAGGTGCAGGTTATCATCATCAC 59.437 47.826 0.00 0.00 0.00 3.06
3348 3913 3.443329 CAGCAAACATATAAGCACCACCA 59.557 43.478 0.00 0.00 0.00 4.17
3359 3924 5.202765 TGTCCATGGATTCAGCAAACATAT 58.797 37.500 19.62 0.00 0.00 1.78
3363 3928 3.940209 TTGTCCATGGATTCAGCAAAC 57.060 42.857 19.62 2.31 0.00 2.93
3364 3929 5.486735 AAATTGTCCATGGATTCAGCAAA 57.513 34.783 19.62 4.83 0.00 3.68
3365 3930 5.246656 AGAAAATTGTCCATGGATTCAGCAA 59.753 36.000 19.62 16.83 0.00 3.91
3367 3932 5.334724 AGAAAATTGTCCATGGATTCAGC 57.665 39.130 19.62 4.90 0.00 4.26
3368 3933 5.163478 GGGAGAAAATTGTCCATGGATTCAG 60.163 44.000 19.62 0.00 42.10 3.02
3369 3934 4.711355 GGGAGAAAATTGTCCATGGATTCA 59.289 41.667 19.62 9.55 42.10 2.57
3370 3935 4.958581 AGGGAGAAAATTGTCCATGGATTC 59.041 41.667 19.62 16.63 42.10 2.52
3371 3936 4.713321 CAGGGAGAAAATTGTCCATGGATT 59.287 41.667 19.62 7.57 45.33 3.01
3372 3937 4.284178 CAGGGAGAAAATTGTCCATGGAT 58.716 43.478 19.62 0.00 45.33 3.41
3373 3938 3.700538 CAGGGAGAAAATTGTCCATGGA 58.299 45.455 11.44 11.44 45.33 3.41
3376 3941 5.582953 TGATTCAGGGAGAAAATTGTCCAT 58.417 37.500 11.03 1.29 42.10 3.41
3377 3942 4.996793 TGATTCAGGGAGAAAATTGTCCA 58.003 39.130 11.03 0.00 42.10 4.02
3378 3943 5.573337 CTGATTCAGGGAGAAAATTGTCC 57.427 43.478 5.73 0.82 40.22 4.02
3428 3993 2.576615 GGAGGGTAGCTAGCCAAAATG 58.423 52.381 36.59 0.00 46.03 2.32
3429 3994 1.495148 GGGAGGGTAGCTAGCCAAAAT 59.505 52.381 36.59 20.76 46.03 1.82
3434 3999 0.764752 ACATGGGAGGGTAGCTAGCC 60.765 60.000 30.68 30.68 44.02 3.93
3436 4001 2.366916 CAGAACATGGGAGGGTAGCTAG 59.633 54.545 0.00 0.00 0.00 3.42
3455 4020 8.264981 TTTGGAAAAACAAAGTGCACATGCAG 62.265 38.462 21.04 6.43 42.35 4.41
3456 4021 6.543089 TTTGGAAAAACAAAGTGCACATGCA 61.543 36.000 21.04 1.49 40.88 3.96
3457 4022 2.935201 TGGAAAAACAAAGTGCACATGC 59.065 40.909 21.04 4.39 42.50 4.06
3458 4023 5.542616 TTTGGAAAAACAAAGTGCACATG 57.457 34.783 21.04 19.23 35.57 3.21
3496 4061 4.080863 GCTACTCCAGAAAAGATTCCCTCA 60.081 45.833 0.00 0.00 36.12 3.86
3539 4104 2.683211 AAACCCCAGATTTGCAGACT 57.317 45.000 0.00 0.00 0.00 3.24
3550 4117 2.807676 ACCATAAGCTGAAAACCCCAG 58.192 47.619 0.00 0.00 34.88 4.45
3561 4128 7.713073 GCAAGAAAGTAGAGATAACCATAAGCT 59.287 37.037 0.00 0.00 0.00 3.74
3567 4134 7.956328 TCTAGCAAGAAAGTAGAGATAACCA 57.044 36.000 0.00 0.00 0.00 3.67
3790 4377 4.744570 TCTGGTAAATGAGTTGTCTAGCG 58.255 43.478 0.00 0.00 0.00 4.26
3795 4382 4.894784 TGTCCTCTGGTAAATGAGTTGTC 58.105 43.478 0.00 0.00 0.00 3.18
3816 4404 6.126863 TCTTATATAGCCCAATGACCCTTG 57.873 41.667 0.00 0.00 0.00 3.61
3871 4463 2.983136 TGCACAGTCAAAACAACAAACG 59.017 40.909 0.00 0.00 0.00 3.60
3897 4489 9.565213 CTCTTACAGGAGATTTGCAATTAAAAG 57.435 33.333 0.00 0.00 35.52 2.27
3947 4539 9.702726 GCTTTAAACAACAAAAATCTTCCTTTC 57.297 29.630 0.00 0.00 0.00 2.62
3972 4564 1.462670 CTCAAGTTCTTGAAGCGAGGC 59.537 52.381 14.76 0.00 0.00 4.70
4023 4615 6.293027 CCCAATCTTGCAAAAACATTGAACTC 60.293 38.462 16.19 0.00 0.00 3.01
4055 4655 4.830600 GGGGTAGGATTCACAACAAAAAGA 59.169 41.667 0.00 0.00 0.00 2.52
4127 4732 2.338785 GCAGTCCAGCAAAGGGAGC 61.339 63.158 0.00 0.00 34.44 4.70


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

AutoCloner maintained by Alex Coulton.