Multiple sequence alignment - TraesCS2A01G340100

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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 TraesCS2A01G340100 chr2A 100.000 6035 0 0 1 6035 574981459 574975425 0.000000e+00 11145.0
1 TraesCS2A01G340100 chr2A 80.707 368 48 12 8 363 221305212 221304856 1.290000e-66 265.0
2 TraesCS2A01G340100 chr2A 78.146 151 27 5 654 798 621376739 621376889 2.320000e-14 91.6
3 TraesCS2A01G340100 chr2B 94.324 2995 97 23 3084 6035 482738183 482735219 0.000000e+00 4521.0
4 TraesCS2A01G340100 chr2B 95.360 1444 57 7 396 1834 482740842 482739404 0.000000e+00 2287.0
5 TraesCS2A01G340100 chr2B 90.336 1190 48 23 1834 2967 482739361 482738183 0.000000e+00 1498.0
6 TraesCS2A01G340100 chr2B 83.503 394 46 9 3 381 754993551 754993162 3.460000e-92 350.0
7 TraesCS2A01G340100 chr2B 85.039 127 17 2 998 1123 70753678 70753803 1.770000e-25 128.0
8 TraesCS2A01G340100 chr2D 94.148 2734 94 28 3082 5778 406957491 406954787 0.000000e+00 4102.0
9 TraesCS2A01G340100 chr2D 94.716 1798 68 11 54 1834 406960581 406958794 0.000000e+00 2769.0
10 TraesCS2A01G340100 chr2D 93.189 1013 33 10 2023 3008 406958533 406957530 0.000000e+00 1456.0
11 TraesCS2A01G340100 chr2D 93.893 262 8 1 5774 6035 406954698 406954445 7.340000e-104 388.0
12 TraesCS2A01G340100 chr2D 84.278 388 43 8 3 375 648170670 648171054 4.450000e-96 363.0
13 TraesCS2A01G340100 chr2D 96.257 187 7 0 1834 2020 406958751 406958565 2.110000e-79 307.0
14 TraesCS2A01G340100 chr2D 80.822 146 23 5 654 798 478831847 478831706 6.400000e-20 110.0
15 TraesCS2A01G340100 chr2D 98.039 51 1 0 3020 3070 15192923 15192973 8.330000e-14 89.8
16 TraesCS2A01G340100 chr2D 88.060 67 3 2 3002 3063 558200781 558200847 2.330000e-09 75.0
17 TraesCS2A01G340100 chr3D 84.536 388 41 11 3 375 591660694 591661077 3.440000e-97 366.0
18 TraesCS2A01G340100 chr6A 84.416 385 42 6 8 378 603089658 603089278 4.450000e-96 363.0
19 TraesCS2A01G340100 chr6A 79.795 391 75 3 4627 5015 346590443 346590055 1.280000e-71 281.0
20 TraesCS2A01G340100 chr3A 83.673 392 44 10 3 379 623194459 623194845 9.620000e-93 351.0
21 TraesCS2A01G340100 chr1D 83.551 383 44 7 8 375 7824530 7824908 2.080000e-89 340.0
22 TraesCS2A01G340100 chr1B 82.776 389 49 10 3 377 584476185 584475801 1.250000e-86 331.0
23 TraesCS2A01G340100 chr1B 83.019 212 31 4 3 213 569514255 569514048 2.870000e-43 187.0
24 TraesCS2A01G340100 chr4A 82.812 384 47 9 8 375 609562814 609563194 5.830000e-85 326.0
25 TraesCS2A01G340100 chr4A 93.651 126 5 3 2023 2147 137187117 137186994 1.030000e-42 185.0
26 TraesCS2A01G340100 chr4A 76.119 335 70 9 4627 4956 679274738 679274409 3.740000e-37 167.0
27 TraesCS2A01G340100 chr4A 86.290 124 15 2 1003 1125 679277209 679277087 3.790000e-27 134.0
28 TraesCS2A01G340100 chr4A 96.552 58 0 2 3006 3063 266960575 266960520 1.790000e-15 95.3
29 TraesCS2A01G340100 chr3B 82.642 386 45 8 11 379 690108987 690108607 7.550000e-84 322.0
30 TraesCS2A01G340100 chr4B 86.039 308 30 4 3 299 427518767 427519072 9.760000e-83 318.0
31 TraesCS2A01G340100 chr4B 81.746 378 49 8 15 378 652763416 652763045 1.270000e-76 298.0
32 TraesCS2A01G340100 chr4B 92.126 127 7 3 2023 2147 413830755 413830880 6.220000e-40 176.0
33 TraesCS2A01G340100 chr4B 86.290 124 15 2 1003 1125 594875643 594875521 3.790000e-27 134.0
34 TraesCS2A01G340100 chr7D 81.865 386 55 9 1 375 264984700 264985081 1.630000e-80 311.0
35 TraesCS2A01G340100 chr7D 84.429 289 32 3 3 282 183030521 183030805 7.710000e-69 272.0
36 TraesCS2A01G340100 chr7D 95.122 123 4 2 2023 2144 623793464 623793585 6.170000e-45 193.0
37 TraesCS2A01G340100 chr7D 87.097 124 14 2 1003 1125 78504969 78504847 8.160000e-29 139.0
38 TraesCS2A01G340100 chr7D 95.000 60 2 1 3006 3064 101475401 101475460 6.440000e-15 93.5
39 TraesCS2A01G340100 chr7D 89.552 67 1 3 3006 3067 554684098 554684163 5.010000e-11 80.5
40 TraesCS2A01G340100 chr7D 100.000 28 0 0 5622 5649 203706220 203706247 1.100000e-02 52.8
41 TraesCS2A01G340100 chr6B 80.977 389 53 9 3 378 708987987 708987607 7.650000e-74 289.0
42 TraesCS2A01G340100 chr6B 82.051 234 42 0 4627 4860 337860837 337861070 3.690000e-47 200.0
43 TraesCS2A01G340100 chr6B 94.444 126 6 1 2022 2147 233039346 233039222 6.170000e-45 193.0
44 TraesCS2A01G340100 chr6B 89.189 74 3 2 3001 3070 95327503 95327575 3.000000e-13 87.9
45 TraesCS2A01G340100 chr6B 100.000 28 0 0 5622 5649 65091714 65091741 1.100000e-02 52.8
46 TraesCS2A01G340100 chr6D 79.949 389 78 0 4627 5015 249961057 249961445 2.750000e-73 287.0
47 TraesCS2A01G340100 chr6D 92.000 125 9 1 2023 2147 134289080 134288957 2.240000e-39 174.0
48 TraesCS2A01G340100 chr5A 92.126 127 10 0 2023 2149 337822958 337822832 4.810000e-41 180.0
49 TraesCS2A01G340100 chr5A 77.876 113 17 4 650 755 528935109 528935220 5.050000e-06 63.9
50 TraesCS2A01G340100 chr4D 92.126 127 6 4 2023 2147 335774315 335774439 6.220000e-40 176.0
51 TraesCS2A01G340100 chr4D 86.290 124 15 2 1003 1125 472522603 472522481 3.790000e-27 134.0
52 TraesCS2A01G340100 chr4D 88.710 62 5 1 3005 3064 1401756 1401695 2.330000e-09 75.0
53 TraesCS2A01G340100 chr7B 93.750 64 2 1 3006 3067 11922466 11922403 1.790000e-15 95.3
54 TraesCS2A01G340100 chr7B 88.060 67 6 2 2999 3064 639262746 639262811 1.800000e-10 78.7
55 TraesCS2A01G340100 chr5B 98.039 51 1 0 3020 3070 127198253 127198203 8.330000e-14 89.8
56 TraesCS2A01G340100 chr5D 91.803 61 3 1 3006 3064 520064541 520064481 3.880000e-12 84.2


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 TraesCS2A01G340100 chr2A 574975425 574981459 6034 True 11145.000000 11145 100.0000 1 6035 1 chr2A.!!$R2 6034
1 TraesCS2A01G340100 chr2B 482735219 482740842 5623 True 2768.666667 4521 93.3400 396 6035 3 chr2B.!!$R2 5639
2 TraesCS2A01G340100 chr2D 406954445 406960581 6136 True 1804.400000 4102 94.4406 54 6035 5 chr2D.!!$R2 5981

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
860 880 0.036952 ACAGTGACTGCTCAATCCCG 60.037 55.000 13.37 0.0 34.37 5.14 F
1271 1291 0.528249 CTTTGTTTGCTTGCGGCTGT 60.528 50.000 0.00 0.0 42.39 4.40 F
2630 2753 1.265635 GTTTGCCGTGCTGTGTAATCA 59.734 47.619 0.00 0.0 0.00 2.57 F
3028 3151 0.033796 CCCTCCGTCCCACTAGTGTA 60.034 60.000 21.18 6.6 0.00 2.90 F
4599 4747 0.541863 AGCTACCATGGGAGGAAACG 59.458 55.000 25.94 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2007 0.317020 GAACAACTGCTTGGCGTGTC 60.317 55.000 0.00 0.0 0.00 3.67 R
3009 3132 0.033796 TACACTAGTGGGACGGAGGG 60.034 60.000 26.12 0.0 34.19 4.30 R
3935 4079 0.463620 TTGGCCAAAGGTTGAACTGC 59.536 50.000 17.98 0.0 0.00 4.40 R
4695 4843 3.125316 GCTGCTCAATGTACTTAAAGCGT 59.875 43.478 0.00 0.0 30.89 5.07 R
5704 5909 1.074727 TGCAAGTTTAAGCCCTAGCCA 59.925 47.619 0.00 0.0 41.25 4.75 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
21 22 4.535526 AACCCTGTATTTTGAATGGTGC 57.464 40.909 0.00 0.00 0.00 5.01
22 23 2.831526 ACCCTGTATTTTGAATGGTGCC 59.168 45.455 0.00 0.00 0.00 5.01
23 24 2.830923 CCCTGTATTTTGAATGGTGCCA 59.169 45.455 0.00 0.00 0.00 4.92
24 25 3.260380 CCCTGTATTTTGAATGGTGCCAA 59.740 43.478 0.00 0.00 0.00 4.52
25 26 4.262808 CCCTGTATTTTGAATGGTGCCAAA 60.263 41.667 0.00 0.00 0.00 3.28
26 27 5.303971 CCTGTATTTTGAATGGTGCCAAAA 58.696 37.500 0.00 0.00 43.59 2.44
28 29 6.128227 CCTGTATTTTGAATGGTGCCAAAATG 60.128 38.462 17.96 6.44 46.35 2.32
29 30 4.769859 ATTTTGAATGGTGCCAAAATGC 57.230 36.364 10.95 0.00 45.65 3.56
30 31 3.488778 TTTGAATGGTGCCAAAATGCT 57.511 38.095 0.00 0.00 30.29 3.79
31 32 4.613925 TTTGAATGGTGCCAAAATGCTA 57.386 36.364 0.00 0.00 30.29 3.49
32 33 4.822685 TTGAATGGTGCCAAAATGCTAT 57.177 36.364 0.00 0.00 0.00 2.97
33 34 4.822685 TGAATGGTGCCAAAATGCTATT 57.177 36.364 0.00 0.00 0.00 1.73
34 35 5.163281 TGAATGGTGCCAAAATGCTATTT 57.837 34.783 0.00 0.00 0.00 1.40
35 36 5.558818 TGAATGGTGCCAAAATGCTATTTT 58.441 33.333 0.00 0.00 0.00 1.82
36 37 5.411977 TGAATGGTGCCAAAATGCTATTTTG 59.588 36.000 19.15 19.15 38.68 2.44
37 38 4.613925 TGGTGCCAAAATGCTATTTTGA 57.386 36.364 23.97 11.08 40.73 2.69
38 39 4.965814 TGGTGCCAAAATGCTATTTTGAA 58.034 34.783 23.97 14.82 40.73 2.69
39 40 5.371526 TGGTGCCAAAATGCTATTTTGAAA 58.628 33.333 23.97 14.59 40.73 2.69
40 41 6.002704 TGGTGCCAAAATGCTATTTTGAAAT 58.997 32.000 23.97 0.00 40.73 2.17
41 42 6.149142 TGGTGCCAAAATGCTATTTTGAAATC 59.851 34.615 23.97 16.37 40.73 2.17
42 43 6.372381 GGTGCCAAAATGCTATTTTGAAATCT 59.628 34.615 23.97 0.00 40.73 2.40
43 44 7.413328 GGTGCCAAAATGCTATTTTGAAATCTC 60.413 37.037 23.97 14.81 40.73 2.75
44 45 7.118101 GTGCCAAAATGCTATTTTGAAATCTCA 59.882 33.333 23.97 14.01 40.73 3.27
45 46 7.660617 TGCCAAAATGCTATTTTGAAATCTCAA 59.339 29.630 23.97 0.00 40.73 3.02
90 91 8.922931 TCAGCATGTTTATGTGGATGTATATT 57.077 30.769 0.00 0.00 36.65 1.28
137 138 7.702348 GCTGAAATAAATAACCATGTGAGTTCC 59.298 37.037 0.00 0.00 0.00 3.62
154 155 7.675478 GTGAGTTCCACAAAAATGAAAAAGTC 58.325 34.615 0.00 0.00 45.03 3.01
155 156 7.330700 GTGAGTTCCACAAAAATGAAAAAGTCA 59.669 33.333 0.00 0.00 45.03 3.41
181 182 7.315142 TGATTTTGGAAAGATGAATAGTGCAC 58.685 34.615 9.40 9.40 0.00 4.57
183 184 3.937814 TGGAAAGATGAATAGTGCACGT 58.062 40.909 12.01 0.96 0.00 4.49
196 197 9.406828 TGAATAGTGCACGTATTATTCAGTATC 57.593 33.333 24.42 8.61 37.51 2.24
208 209 9.778741 GTATTATTCAGTATCTGGAAATCACCA 57.221 33.333 0.00 0.00 38.33 4.17
231 241 9.189156 ACCATTTTGTATAGCTCACATGTTTAT 57.811 29.630 0.00 0.00 0.00 1.40
317 327 9.377312 CCTTTTGGAATTTTCTAAAACTTGTGA 57.623 29.630 9.62 0.00 40.95 3.58
368 381 3.292460 CAATATACCCCGGCTCCAAAAA 58.708 45.455 0.00 0.00 0.00 1.94
375 388 0.527565 CCGGCTCCAAAAATCCACTG 59.472 55.000 0.00 0.00 0.00 3.66
378 391 2.238521 GGCTCCAAAAATCCACTGTCA 58.761 47.619 0.00 0.00 0.00 3.58
420 433 2.237143 TCCTGATGCGGTCAAATCTCTT 59.763 45.455 0.00 0.00 36.14 2.85
422 435 3.264947 CTGATGCGGTCAAATCTCTTCA 58.735 45.455 0.00 0.00 36.14 3.02
434 453 7.415318 GGTCAAATCTCTTCACATCGTCTACTA 60.415 40.741 0.00 0.00 0.00 1.82
435 454 7.429920 GTCAAATCTCTTCACATCGTCTACTAC 59.570 40.741 0.00 0.00 0.00 2.73
436 455 7.337184 TCAAATCTCTTCACATCGTCTACTACT 59.663 37.037 0.00 0.00 0.00 2.57
780 799 3.900892 CTACCCCATCGCGTCGCT 61.901 66.667 16.36 0.00 0.00 4.93
848 868 3.056536 TGAGCTCTTGTCCATACAGTGAC 60.057 47.826 16.19 0.00 36.83 3.67
860 880 0.036952 ACAGTGACTGCTCAATCCCG 60.037 55.000 13.37 0.00 34.37 5.14
1077 1097 4.189188 GGCGAGCGCTACTTCGGA 62.189 66.667 11.50 0.00 41.60 4.55
1215 1235 7.102993 TCTGTGCAGTATACATGTGTAAATGT 58.897 34.615 9.11 0.00 43.21 2.71
1268 1288 2.597713 GCCTTTGTTTGCTTGCGGC 61.598 57.895 0.00 0.00 42.22 6.53
1271 1291 0.528249 CTTTGTTTGCTTGCGGCTGT 60.528 50.000 0.00 0.00 42.39 4.40
1381 1402 3.150767 TGGGTGGAATTTTTCGACGATT 58.849 40.909 0.00 0.00 39.02 3.34
1390 1412 2.288961 TTTCGACGATTCAGCTACCC 57.711 50.000 0.00 0.00 0.00 3.69
1418 1440 7.161404 ACTGTTATGAGTTATGTGACACATGT 58.839 34.615 27.66 14.03 39.53 3.21
1426 1448 6.611381 AGTTATGTGACACATGTATGTTTGC 58.389 36.000 27.66 9.23 39.53 3.68
1439 1461 5.649557 TGTATGTTTGCTTATGATTGCACC 58.350 37.500 0.00 0.00 39.05 5.01
1496 1520 9.561069 AAGAATTTATTACAGCCAGGTATAGTG 57.439 33.333 0.00 0.00 0.00 2.74
1524 1548 2.166254 TCCTACCGTTTGGAATACCGTC 59.834 50.000 0.00 0.00 39.21 4.79
1567 1591 8.499162 CGAATACATTGATACCTCCAAAATCTC 58.501 37.037 0.00 0.00 0.00 2.75
1589 1613 8.246430 TCTCCCGAATTAAACACTGTATATCT 57.754 34.615 0.00 0.00 0.00 1.98
1665 1689 6.970043 TGAAACACACCTTTTTACGAAGATTG 59.030 34.615 0.00 0.00 0.00 2.67
1666 1690 5.432885 ACACACCTTTTTACGAAGATTGG 57.567 39.130 0.00 0.00 0.00 3.16
1726 1750 6.292542 CGTGTCAATATGCCTCTGTTTATCTG 60.293 42.308 0.00 0.00 0.00 2.90
1743 1767 6.771188 TTATCTGCTTCTAATTAAGAGCGC 57.229 37.500 0.00 0.00 35.05 5.92
1756 1780 3.246112 AGCGCCCACTGGGTTGTA 61.246 61.111 16.03 0.00 46.51 2.41
1764 1788 3.430453 CCCACTGGGTTGTATGTCATTT 58.570 45.455 5.85 0.00 38.25 2.32
1775 1799 9.097257 GGGTTGTATGTCATTTTATTTTGATGG 57.903 33.333 0.00 0.00 0.00 3.51
1906 1973 4.488770 TCTAAATTCCTGCCAAACCCTTT 58.511 39.130 0.00 0.00 0.00 3.11
1927 1994 6.183360 CCTTTTTGTGTCTCATGTAAGGTTGT 60.183 38.462 0.00 0.00 0.00 3.32
1929 1996 8.458573 TTTTTGTGTCTCATGTAAGGTTGTAT 57.541 30.769 0.00 0.00 0.00 2.29
1940 2007 7.495606 TCATGTAAGGTTGTATGCTCATTACAG 59.504 37.037 15.95 11.11 35.74 2.74
1966 2033 2.295909 GCCAAGCAGTTGTTCACCAATA 59.704 45.455 0.00 0.00 35.02 1.90
2009 2076 7.698506 ATATAATTCTGCTCCACCATGATTG 57.301 36.000 0.00 0.00 0.00 2.67
2083 2179 9.781834 TTTAGTGTGTTTGTTCACTCATTTTAG 57.218 29.630 1.08 0.00 42.77 1.85
2194 2291 6.534079 GTCCAGTGTAAAATAGTAAGATGCGT 59.466 38.462 0.00 0.00 0.00 5.24
2510 2632 5.865552 GGTTTGTACTGTTCGCAATCTACTA 59.134 40.000 0.00 0.00 0.00 1.82
2514 2636 5.518847 TGTACTGTTCGCAATCTACTAATGC 59.481 40.000 0.00 0.00 36.74 3.56
2559 2682 7.225931 TGTTGTCCAGTTTAGTTATGTTCTGTC 59.774 37.037 0.00 0.00 0.00 3.51
2577 2700 7.338196 TGTTCTGTCCTTTCTTTGTGACAAATA 59.662 33.333 11.58 1.22 37.29 1.40
2596 2719 9.455847 GACAAATATTTTGCTCATATCCTGTTC 57.544 33.333 0.00 0.00 0.00 3.18
2622 2745 1.806542 AGATAGTTGTTTGCCGTGCTG 59.193 47.619 0.00 0.00 0.00 4.41
2630 2753 1.265635 GTTTGCCGTGCTGTGTAATCA 59.734 47.619 0.00 0.00 0.00 2.57
2631 2754 1.598882 TTGCCGTGCTGTGTAATCAA 58.401 45.000 0.00 0.00 0.00 2.57
2794 2917 5.276820 GGAAAATCTTTTGACTTGTTTGGCG 60.277 40.000 0.00 0.00 0.00 5.69
2822 2945 4.365514 TTCATGCAGGTAAAGTGGAGAA 57.634 40.909 0.00 0.00 0.00 2.87
2823 2946 4.365514 TCATGCAGGTAAAGTGGAGAAA 57.634 40.909 0.00 0.00 0.00 2.52
2824 2947 4.724399 TCATGCAGGTAAAGTGGAGAAAA 58.276 39.130 0.00 0.00 0.00 2.29
2825 2948 4.761739 TCATGCAGGTAAAGTGGAGAAAAG 59.238 41.667 0.00 0.00 0.00 2.27
2826 2949 3.486383 TGCAGGTAAAGTGGAGAAAAGG 58.514 45.455 0.00 0.00 0.00 3.11
2827 2950 3.137544 TGCAGGTAAAGTGGAGAAAAGGA 59.862 43.478 0.00 0.00 0.00 3.36
2828 2951 4.202567 TGCAGGTAAAGTGGAGAAAAGGAT 60.203 41.667 0.00 0.00 0.00 3.24
2829 2952 5.013704 TGCAGGTAAAGTGGAGAAAAGGATA 59.986 40.000 0.00 0.00 0.00 2.59
2830 2953 5.944007 GCAGGTAAAGTGGAGAAAAGGATAA 59.056 40.000 0.00 0.00 0.00 1.75
2882 3005 3.419915 CGCAATGAGCATGTTGTTACTC 58.580 45.455 0.00 0.00 46.13 2.59
2897 3020 6.127758 TGTTGTTACTCTGCAAATTGACTTGT 60.128 34.615 0.00 0.00 0.00 3.16
2928 3051 2.016318 TGCTTTGGCCATGTTCTATCG 58.984 47.619 6.09 0.00 37.74 2.92
2939 3062 5.700832 GCCATGTTCTATCGTTATTGATGGA 59.299 40.000 0.00 0.00 34.50 3.41
3010 3133 6.329496 GCTGTCAGCAGATCTATATTACTCC 58.671 44.000 20.16 0.00 45.28 3.85
3011 3134 6.627065 GCTGTCAGCAGATCTATATTACTCCC 60.627 46.154 20.16 0.00 45.28 4.30
3012 3135 6.556639 TGTCAGCAGATCTATATTACTCCCT 58.443 40.000 0.00 0.00 0.00 4.20
3013 3136 6.661377 TGTCAGCAGATCTATATTACTCCCTC 59.339 42.308 0.00 0.00 0.00 4.30
3014 3137 6.096282 GTCAGCAGATCTATATTACTCCCTCC 59.904 46.154 0.00 0.00 0.00 4.30
3015 3138 5.067153 CAGCAGATCTATATTACTCCCTCCG 59.933 48.000 0.00 0.00 0.00 4.63
3016 3139 4.951094 GCAGATCTATATTACTCCCTCCGT 59.049 45.833 0.00 0.00 0.00 4.69
3017 3140 5.066764 GCAGATCTATATTACTCCCTCCGTC 59.933 48.000 0.00 0.00 0.00 4.79
3018 3141 5.591067 CAGATCTATATTACTCCCTCCGTCC 59.409 48.000 0.00 0.00 0.00 4.79
3019 3142 4.313020 TCTATATTACTCCCTCCGTCCC 57.687 50.000 0.00 0.00 0.00 4.46
3020 3143 3.659195 TCTATATTACTCCCTCCGTCCCA 59.341 47.826 0.00 0.00 0.00 4.37
3021 3144 2.077687 TATTACTCCCTCCGTCCCAC 57.922 55.000 0.00 0.00 0.00 4.61
3022 3145 0.338814 ATTACTCCCTCCGTCCCACT 59.661 55.000 0.00 0.00 0.00 4.00
3023 3146 1.002069 TTACTCCCTCCGTCCCACTA 58.998 55.000 0.00 0.00 0.00 2.74
3024 3147 0.549950 TACTCCCTCCGTCCCACTAG 59.450 60.000 0.00 0.00 0.00 2.57
3025 3148 1.306970 CTCCCTCCGTCCCACTAGT 59.693 63.158 0.00 0.00 0.00 2.57
3026 3149 1.000019 TCCCTCCGTCCCACTAGTG 60.000 63.158 16.34 16.34 0.00 2.74
3027 3150 1.305046 CCCTCCGTCCCACTAGTGT 60.305 63.158 21.18 0.00 0.00 3.55
3028 3151 0.033796 CCCTCCGTCCCACTAGTGTA 60.034 60.000 21.18 6.60 0.00 2.90
3029 3152 1.617804 CCCTCCGTCCCACTAGTGTAA 60.618 57.143 21.18 6.25 0.00 2.41
3030 3153 2.173519 CCTCCGTCCCACTAGTGTAAA 58.826 52.381 21.18 3.70 0.00 2.01
3031 3154 2.564062 CCTCCGTCCCACTAGTGTAAAA 59.436 50.000 21.18 1.21 0.00 1.52
3032 3155 3.007182 CCTCCGTCCCACTAGTGTAAAAA 59.993 47.826 21.18 2.07 0.00 1.94
3054 3177 8.446599 AAAAACACTCTTATATTATGGGACGG 57.553 34.615 0.00 0.00 0.00 4.79
3055 3178 6.989155 AACACTCTTATATTATGGGACGGA 57.011 37.500 0.00 0.00 0.00 4.69
3056 3179 6.591750 ACACTCTTATATTATGGGACGGAG 57.408 41.667 0.00 0.00 0.00 4.63
3057 3180 5.480772 ACACTCTTATATTATGGGACGGAGG 59.519 44.000 0.00 0.00 0.00 4.30
3058 3181 5.024118 ACTCTTATATTATGGGACGGAGGG 58.976 45.833 0.00 0.00 0.00 4.30
3059 3182 5.222484 ACTCTTATATTATGGGACGGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
3060 3183 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3083 3206 6.012745 AGTACCATTTTGGCTTCTCATTCTT 58.987 36.000 0.00 0.00 42.67 2.52
3164 3308 3.084039 TCATTGATGGCAAGGTGTCTTC 58.916 45.455 0.00 0.00 37.12 2.87
3214 3358 1.731709 TGTGTATCATCGTTGCTGCAC 59.268 47.619 0.00 10.42 35.81 4.57
3285 3429 7.972832 TTTCCGTTTGTACTGAATTAGTGAT 57.027 32.000 0.00 0.00 40.65 3.06
3340 3484 7.025963 GCTCATAATATTTCATGCAGGTAAGC 58.974 38.462 0.00 0.00 0.00 3.09
3440 3584 3.696051 CAGCTACATGCACCAGGTAATTT 59.304 43.478 0.00 0.00 45.94 1.82
3446 3590 2.235016 TGCACCAGGTAATTTGACACC 58.765 47.619 0.00 0.00 34.86 4.16
3451 3595 5.393027 GCACCAGGTAATTTGACACCTATTG 60.393 44.000 0.00 0.45 43.45 1.90
3458 3602 5.567138 AATTTGACACCTATTGTAGCAGC 57.433 39.130 0.00 0.00 39.17 5.25
3472 3616 0.604780 AGCAGCACATGTCAGTGGTC 60.605 55.000 0.00 0.00 46.31 4.02
3648 3792 9.109393 CAGCCATGTTATATGTAGTAGTGTTTT 57.891 33.333 0.00 0.00 0.00 2.43
3680 3824 5.361857 AGGCATGTGCTTTTATCTGCTATTT 59.638 36.000 4.84 0.00 41.70 1.40
3684 3828 6.271488 TGTGCTTTTATCTGCTATTTTGCT 57.729 33.333 0.00 0.00 0.00 3.91
3687 3831 8.303156 TGTGCTTTTATCTGCTATTTTGCTTTA 58.697 29.630 0.00 0.00 0.00 1.85
3698 3842 8.755696 TGCTATTTTGCTTTAGTTTAACCATG 57.244 30.769 0.00 0.00 0.00 3.66
3775 3919 8.718102 ACAATCGATAAAGCATTACTTGTACT 57.282 30.769 0.00 0.00 39.09 2.73
3776 3920 9.162764 ACAATCGATAAAGCATTACTTGTACTT 57.837 29.630 0.00 0.00 39.09 2.24
3898 4042 1.739562 CAGTGCTGCGAAGGACTCC 60.740 63.158 15.78 0.00 38.42 3.85
3935 4079 3.645687 TCCTGAAAAAGTTCCAAATGGGG 59.354 43.478 0.00 0.00 37.22 4.96
4036 4180 6.469410 ACTTAACGGAAATGACTTGGACATA 58.531 36.000 0.00 0.00 0.00 2.29
4068 4212 6.597280 CCTAGTTTCCTTTCTTCAAGATCCTG 59.403 42.308 0.00 0.00 33.80 3.86
4074 4218 5.765182 TCCTTTCTTCAAGATCCTGTTTGTC 59.235 40.000 0.00 0.00 33.80 3.18
4180 4324 2.104281 AGTAACTGCAAGGGACGAAACT 59.896 45.455 0.00 0.00 39.30 2.66
4267 4411 4.006319 GCTCCACTGAGACTTTAAATGCT 58.994 43.478 0.00 0.00 41.42 3.79
4311 4455 8.458052 TGACAAATGTTGCAGGTTATTACTATG 58.542 33.333 0.00 0.00 0.00 2.23
4326 4470 9.014297 GTTATTACTATGCCATATTTGCCTTCT 57.986 33.333 0.00 0.00 0.00 2.85
4328 4472 8.798859 ATTACTATGCCATATTTGCCTTCTAG 57.201 34.615 0.00 0.00 0.00 2.43
4353 4497 9.778741 AGTACTGTTTTTCTTGTTCTCATCATA 57.221 29.630 0.00 0.00 0.00 2.15
4450 4594 5.913137 TTTTTCTGGTATATGTGGGCAAG 57.087 39.130 0.00 0.00 0.00 4.01
4599 4747 0.541863 AGCTACCATGGGAGGAAACG 59.458 55.000 25.94 0.00 0.00 3.60
4603 4751 0.768622 ACCATGGGAGGAAACGTCAA 59.231 50.000 18.09 0.00 0.00 3.18
5023 5171 2.452491 AGGGCCTTGGTGGGAAGT 60.452 61.111 0.00 0.00 36.00 3.01
5048 5196 5.782893 TTAGGTTGATTTTCCCTGTTGTG 57.217 39.130 0.00 0.00 0.00 3.33
5108 5256 7.824289 ACTGTTGTATGTACACAGCTATTTCAT 59.176 33.333 0.00 0.00 38.10 2.57
5166 5314 2.093447 AGTATGAACCTGAGGAAAGCCG 60.093 50.000 4.99 0.00 39.96 5.52
5273 5424 4.036027 TCGACTATACTTTCCACCGACATC 59.964 45.833 0.00 0.00 0.00 3.06
5355 5506 9.845740 TTTTTATGCACTAGATTTAGCCATCTA 57.154 29.630 0.00 0.00 35.08 1.98
5497 5653 8.579850 TGAGGCTACTTTTGAATTCATGTATT 57.420 30.769 9.40 0.00 0.00 1.89
5533 5689 4.925054 CCAGTTATGTGGATGCAAAAACTG 59.075 41.667 21.03 21.03 40.44 3.16
5603 5778 2.404923 CCAATTGCAATCAATGGGCA 57.595 45.000 17.53 0.00 44.46 5.36
5609 5784 2.458620 TGCAATCAATGGGCATCTCAA 58.541 42.857 0.00 0.00 31.58 3.02
5617 5792 1.808411 TGGGCATCTCAAGTTCGTTC 58.192 50.000 0.00 0.00 0.00 3.95
5622 5797 4.394920 GGGCATCTCAAGTTCGTTCATAAA 59.605 41.667 0.00 0.00 0.00 1.40
5623 5798 5.066505 GGGCATCTCAAGTTCGTTCATAAAT 59.933 40.000 0.00 0.00 0.00 1.40
5624 5799 6.260050 GGGCATCTCAAGTTCGTTCATAAATA 59.740 38.462 0.00 0.00 0.00 1.40
5628 5832 9.478019 CATCTCAAGTTCGTTCATAAATAACAC 57.522 33.333 0.00 0.00 0.00 3.32
5630 5834 7.876068 TCTCAAGTTCGTTCATAAATAACACCT 59.124 33.333 0.00 0.00 0.00 4.00
5704 5909 4.689983 GCTTTCTGCTCTATTTATGGGGGT 60.690 45.833 0.00 0.00 38.95 4.95
5736 5941 2.113774 CTTGCAGTGGTCCTGGCA 59.886 61.111 0.00 0.00 41.81 4.92
5778 5983 1.606737 GGGGCATCTCGTGATCTTAGC 60.607 57.143 0.00 0.00 0.00 3.09
5822 6120 7.334421 GTGCATTCTCCACCGTATATATTCATT 59.666 37.037 0.00 0.00 0.00 2.57
5883 6181 3.522987 CAAAATTGCCGTCGCGCG 61.523 61.111 26.76 26.76 38.08 6.86
5900 6206 1.990563 CGCGTACCCTAAGAAACACAG 59.009 52.381 0.00 0.00 0.00 3.66
5901 6207 1.730612 GCGTACCCTAAGAAACACAGC 59.269 52.381 0.00 0.00 0.00 4.40
5902 6208 2.868839 GCGTACCCTAAGAAACACAGCA 60.869 50.000 0.00 0.00 0.00 4.41
5903 6209 2.735134 CGTACCCTAAGAAACACAGCAC 59.265 50.000 0.00 0.00 0.00 4.40
5904 6210 3.735591 GTACCCTAAGAAACACAGCACA 58.264 45.455 0.00 0.00 0.00 4.57
5905 6211 3.508845 ACCCTAAGAAACACAGCACAT 57.491 42.857 0.00 0.00 0.00 3.21
5906 6212 3.412386 ACCCTAAGAAACACAGCACATC 58.588 45.455 0.00 0.00 0.00 3.06
5907 6213 3.181445 ACCCTAAGAAACACAGCACATCA 60.181 43.478 0.00 0.00 0.00 3.07
5916 6222 3.954200 ACACAGCACATCAATCCACATA 58.046 40.909 0.00 0.00 0.00 2.29
5948 6254 0.179034 ATAGCAGCAGCAGGTAAGGC 60.179 55.000 3.17 0.00 45.49 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.260632 GGCACCATTCAAAATACAGGGTT 59.739 43.478 0.00 0.00 0.00 4.11
1 2 2.831526 GGCACCATTCAAAATACAGGGT 59.168 45.455 0.00 0.00 0.00 4.34
2 3 2.830923 TGGCACCATTCAAAATACAGGG 59.169 45.455 0.00 0.00 0.00 4.45
3 4 4.533919 TTGGCACCATTCAAAATACAGG 57.466 40.909 0.00 0.00 0.00 4.00
4 5 6.621164 GCATTTTGGCACCATTCAAAATACAG 60.621 38.462 11.90 4.30 45.88 2.74
5 6 5.180868 GCATTTTGGCACCATTCAAAATACA 59.819 36.000 11.90 0.00 45.88 2.29
6 7 5.412286 AGCATTTTGGCACCATTCAAAATAC 59.588 36.000 11.90 8.11 45.88 1.89
7 8 5.558818 AGCATTTTGGCACCATTCAAAATA 58.441 33.333 11.90 0.00 45.88 1.40
9 10 3.818180 AGCATTTTGGCACCATTCAAAA 58.182 36.364 0.00 0.00 43.87 2.44
10 11 3.488778 AGCATTTTGGCACCATTCAAA 57.511 38.095 0.00 0.00 35.83 2.69
11 12 4.822685 ATAGCATTTTGGCACCATTCAA 57.177 36.364 0.00 0.00 35.83 2.69
12 13 4.822685 AATAGCATTTTGGCACCATTCA 57.177 36.364 0.00 0.00 35.83 2.57
13 14 5.642919 TCAAAATAGCATTTTGGCACCATTC 59.357 36.000 22.68 0.00 39.25 2.67
14 15 5.558818 TCAAAATAGCATTTTGGCACCATT 58.441 33.333 22.68 0.00 39.25 3.16
15 16 5.163281 TCAAAATAGCATTTTGGCACCAT 57.837 34.783 22.68 0.00 39.25 3.55
16 17 4.613925 TCAAAATAGCATTTTGGCACCA 57.386 36.364 22.68 9.63 39.25 4.17
17 18 5.938438 TTTCAAAATAGCATTTTGGCACC 57.062 34.783 22.68 0.00 39.25 5.01
18 19 7.118101 TGAGATTTCAAAATAGCATTTTGGCAC 59.882 33.333 22.68 15.72 39.25 5.01
19 20 7.160049 TGAGATTTCAAAATAGCATTTTGGCA 58.840 30.769 22.68 15.12 39.25 4.92
20 21 7.599630 TGAGATTTCAAAATAGCATTTTGGC 57.400 32.000 22.68 14.80 39.25 4.52
56 57 8.970020 TCCACATAAACATGCTGATTTATCTTT 58.030 29.630 0.00 0.00 30.31 2.52
59 60 8.355169 ACATCCACATAAACATGCTGATTTATC 58.645 33.333 0.00 0.00 30.31 1.75
90 91 8.851541 TCAGCATCAAAATCTGCACATATATA 57.148 30.769 0.00 0.00 40.88 0.86
92 93 7.571080 TTCAGCATCAAAATCTGCACATATA 57.429 32.000 0.00 0.00 40.88 0.86
94 95 5.900865 TTCAGCATCAAAATCTGCACATA 57.099 34.783 0.00 0.00 40.88 2.29
152 153 9.512435 CACTATTCATCTTTCCAAAATCATGAC 57.488 33.333 0.00 0.00 0.00 3.06
154 155 7.977293 TGCACTATTCATCTTTCCAAAATCATG 59.023 33.333 0.00 0.00 0.00 3.07
155 156 7.977853 GTGCACTATTCATCTTTCCAAAATCAT 59.022 33.333 10.32 0.00 0.00 2.45
176 177 6.213677 TCCAGATACTGAATAATACGTGCAC 58.786 40.000 6.82 6.82 32.44 4.57
181 182 8.926710 GGTGATTTCCAGATACTGAATAATACG 58.073 37.037 0.00 0.00 32.44 3.06
196 197 7.067372 TGAGCTATACAAAATGGTGATTTCCAG 59.933 37.037 0.00 0.00 41.05 3.86
279 289 9.927668 GAAAATTCCAAAAGGAATTCTACATGA 57.072 29.630 19.46 0.00 44.64 3.07
280 290 9.933723 AGAAAATTCCAAAAGGAATTCTACATG 57.066 29.630 19.46 0.00 44.64 3.21
352 365 0.033894 GGATTTTTGGAGCCGGGGTA 60.034 55.000 2.18 0.00 0.00 3.69
354 367 1.304879 TGGATTTTTGGAGCCGGGG 60.305 57.895 2.18 0.00 0.00 5.73
368 381 4.594675 AGTAGTACTCCTGACAGTGGAT 57.405 45.455 0.00 0.00 32.56 3.41
375 388 7.544915 GGATAAACACAAAGTAGTACTCCTGAC 59.455 40.741 15.74 0.00 0.00 3.51
378 391 7.453752 TCAGGATAAACACAAAGTAGTACTCCT 59.546 37.037 2.58 0.00 0.00 3.69
420 433 5.235831 CGATTGGTAGTAGTAGACGATGTGA 59.764 44.000 0.00 0.00 0.00 3.58
422 435 5.121811 ACGATTGGTAGTAGTAGACGATGT 58.878 41.667 0.00 0.00 0.00 3.06
434 453 0.108804 CTGGCGTGACGATTGGTAGT 60.109 55.000 10.10 0.00 0.00 2.73
435 454 0.806102 CCTGGCGTGACGATTGGTAG 60.806 60.000 10.10 0.00 0.00 3.18
436 455 1.216977 CCTGGCGTGACGATTGGTA 59.783 57.895 10.10 0.00 0.00 3.25
561 580 1.408340 TCAGAGTATGAGAGCAGCAGC 59.592 52.381 0.00 0.00 35.54 5.25
562 581 2.223782 GGTCAGAGTATGAGAGCAGCAG 60.224 54.545 0.00 0.00 39.07 4.24
563 582 1.753649 GGTCAGAGTATGAGAGCAGCA 59.246 52.381 0.00 0.00 39.07 4.41
860 880 3.017442 GGGAATTTGTGGAGGTTAGCTC 58.983 50.000 2.39 2.39 0.00 4.09
1215 1235 4.582701 TCGAACTAACACCTAACGGAAA 57.417 40.909 0.00 0.00 0.00 3.13
1268 1288 5.633830 AACAAGGAGCATATTCAACACAG 57.366 39.130 0.00 0.00 0.00 3.66
1271 1291 7.362834 CCAACATAACAAGGAGCATATTCAACA 60.363 37.037 0.00 0.00 0.00 3.33
1357 1378 3.685756 TCGTCGAAAAATTCCACCCATAC 59.314 43.478 0.00 0.00 0.00 2.39
1381 1402 4.286032 ACTCATAACAGTTTGGGTAGCTGA 59.714 41.667 0.00 0.00 34.60 4.26
1390 1412 7.860613 TGTGTCACATAACTCATAACAGTTTG 58.139 34.615 0.18 0.00 37.75 2.93
1418 1440 4.397730 ACGGTGCAATCATAAGCAAACATA 59.602 37.500 0.00 0.00 43.20 2.29
1426 1448 3.188254 TGTGAACACGGTGCAATCATAAG 59.812 43.478 8.30 0.00 0.00 1.73
1439 1461 5.052567 GCTAACGACATACTATGTGAACACG 60.053 44.000 6.41 6.13 45.03 4.49
1496 1520 3.048337 TCCAAACGGTAGGATGTTGTC 57.952 47.619 0.00 0.00 0.00 3.18
1524 1548 6.655062 TGTATTCGTAAAAGACAAGCTTGTG 58.345 36.000 35.67 19.18 42.43 3.33
1567 1591 8.657074 TTCAGATATACAGTGTTTAATTCGGG 57.343 34.615 0.00 0.00 0.00 5.14
1589 1613 3.311322 CCGGCGCACTTAAATCTATTTCA 59.689 43.478 10.83 0.00 0.00 2.69
1665 1689 3.160777 CAATCTTGCTGAAAGGCATCC 57.839 47.619 0.00 0.00 42.09 3.51
1726 1750 2.288186 GTGGGCGCTCTTAATTAGAAGC 59.712 50.000 9.62 9.86 36.45 3.86
1756 1780 7.884354 AGGCAAACCATCAAAATAAAATGACAT 59.116 29.630 0.00 0.00 39.06 3.06
1764 1788 5.559148 ACCAAGGCAAACCATCAAAATAA 57.441 34.783 0.00 0.00 39.06 1.40
1775 1799 5.705905 AGATAGACAAGTTACCAAGGCAAAC 59.294 40.000 0.00 0.00 0.00 2.93
1906 1973 6.072728 GCATACAACCTTACATGAGACACAAA 60.073 38.462 0.00 0.00 0.00 2.83
1927 1994 2.167487 TGGCGTGTCTGTAATGAGCATA 59.833 45.455 0.00 0.00 0.00 3.14
1929 1996 0.320050 TGGCGTGTCTGTAATGAGCA 59.680 50.000 0.00 0.00 0.00 4.26
1940 2007 0.317020 GAACAACTGCTTGGCGTGTC 60.317 55.000 0.00 0.00 0.00 3.67
2047 2143 6.913873 ACAAACACACTAAAACACGTCTAT 57.086 33.333 0.00 0.00 0.00 1.98
2130 2226 2.444421 TGAGAAGTACTCCCTCCGTTC 58.556 52.381 17.51 1.79 44.34 3.95
2171 2268 6.903883 ACGCATCTTACTATTTTACACTGG 57.096 37.500 0.00 0.00 0.00 4.00
2314 2429 5.691305 TCACAAGCATGAAAAGTATTGTTGC 59.309 36.000 0.00 0.00 0.00 4.17
2483 2605 5.488341 AGATTGCGAACAGTACAAACCTAT 58.512 37.500 0.00 0.00 0.00 2.57
2496 2618 7.588143 ATGATAGCATTAGTAGATTGCGAAC 57.412 36.000 0.00 0.00 39.05 3.95
2510 2632 8.818622 ACATATGGCATAAGAATGATAGCATT 57.181 30.769 15.97 5.77 47.00 3.56
2514 2636 8.671921 GGACAACATATGGCATAAGAATGATAG 58.328 37.037 15.97 6.99 39.66 2.08
2534 2657 7.307811 GGACAGAACATAACTAAACTGGACAAC 60.308 40.741 0.00 0.00 0.00 3.32
2559 2682 8.369218 AGCAAAATATTTGTCACAAAGAAAGG 57.631 30.769 9.27 0.00 0.00 3.11
2577 2700 8.985315 TGATAAGAACAGGATATGAGCAAAAT 57.015 30.769 0.00 0.00 0.00 1.82
2596 2719 5.727791 GCACGGCAAACAACTATCTGATAAG 60.728 44.000 0.00 0.00 0.00 1.73
2600 2723 1.804151 GCACGGCAAACAACTATCTGA 59.196 47.619 0.00 0.00 0.00 3.27
2622 2745 9.973246 CATATGTGTTAGAACAGTTGATTACAC 57.027 33.333 9.13 9.13 40.05 2.90
2630 2753 7.307989 GCACTTGTCATATGTGTTAGAACAGTT 60.308 37.037 1.90 0.00 40.05 3.16
2631 2754 6.147821 GCACTTGTCATATGTGTTAGAACAGT 59.852 38.462 1.90 0.00 40.05 3.55
2663 2786 6.311735 ACAAAAGTATGGGTAAGGTTCATGT 58.688 36.000 0.00 0.00 0.00 3.21
2758 2881 4.581309 AAGATTTTCCTCTGCATCTCCA 57.419 40.909 0.00 0.00 0.00 3.86
2794 2917 5.393461 CCACTTTACCTGCATGAAAAGATCC 60.393 44.000 17.00 0.00 33.98 3.36
2897 3020 5.890985 ACATGGCCAAAGCACTATACAATTA 59.109 36.000 10.96 0.00 42.56 1.40
2928 3051 9.487790 TTCATTTTTCAAACCTCCATCAATAAC 57.512 29.630 0.00 0.00 0.00 1.89
2939 3062 6.232581 TGTGTGGATTCATTTTTCAAACCT 57.767 33.333 0.00 0.00 0.00 3.50
3005 3128 0.549950 CTAGTGGGACGGAGGGAGTA 59.450 60.000 0.00 0.00 0.00 2.59
3006 3129 1.306970 CTAGTGGGACGGAGGGAGT 59.693 63.158 0.00 0.00 0.00 3.85
3007 3130 1.038130 CACTAGTGGGACGGAGGGAG 61.038 65.000 15.49 0.00 0.00 4.30
3008 3131 1.000019 CACTAGTGGGACGGAGGGA 60.000 63.158 15.49 0.00 0.00 4.20
3009 3132 0.033796 TACACTAGTGGGACGGAGGG 60.034 60.000 26.12 0.00 34.19 4.30
3010 3133 1.843368 TTACACTAGTGGGACGGAGG 58.157 55.000 26.12 0.00 34.19 4.30
3011 3134 3.947910 TTTTACACTAGTGGGACGGAG 57.052 47.619 26.12 0.00 34.19 4.63
3029 3152 8.269317 TCCGTCCCATAATATAAGAGTGTTTTT 58.731 33.333 0.00 0.00 0.00 1.94
3030 3153 7.798071 TCCGTCCCATAATATAAGAGTGTTTT 58.202 34.615 0.00 0.00 0.00 2.43
3031 3154 7.369551 TCCGTCCCATAATATAAGAGTGTTT 57.630 36.000 0.00 0.00 0.00 2.83
3032 3155 6.014499 CCTCCGTCCCATAATATAAGAGTGTT 60.014 42.308 0.00 0.00 0.00 3.32
3033 3156 5.480772 CCTCCGTCCCATAATATAAGAGTGT 59.519 44.000 0.00 0.00 0.00 3.55
3034 3157 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
3035 3158 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
3036 3159 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3037 3160 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3038 3161 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3039 3162 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3040 3163 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3041 3164 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3042 3165 3.501019 GGTACTCCCTCCGTCCCATAATA 60.501 52.174 0.00 0.00 0.00 0.98
3043 3166 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
3044 3167 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
3045 3168 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
3046 3169 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
3047 3170 1.882189 ATGGTACTCCCTCCGTCCCA 61.882 60.000 0.00 0.00 0.00 4.37
3048 3171 0.690077 AATGGTACTCCCTCCGTCCC 60.690 60.000 0.00 0.00 0.00 4.46
3049 3172 1.201424 AAATGGTACTCCCTCCGTCC 58.799 55.000 0.00 0.00 0.00 4.79
3050 3173 2.629051 CAAAATGGTACTCCCTCCGTC 58.371 52.381 0.00 0.00 0.00 4.79
3051 3174 1.280998 CCAAAATGGTACTCCCTCCGT 59.719 52.381 0.00 0.00 31.35 4.69
3052 3175 2.017113 GCCAAAATGGTACTCCCTCCG 61.017 57.143 0.00 0.00 40.46 4.63
3053 3176 1.285078 AGCCAAAATGGTACTCCCTCC 59.715 52.381 0.00 0.00 40.46 4.30
3054 3177 2.808906 AGCCAAAATGGTACTCCCTC 57.191 50.000 0.00 0.00 40.46 4.30
3055 3178 2.649816 AGAAGCCAAAATGGTACTCCCT 59.350 45.455 0.00 0.00 40.46 4.20
3056 3179 3.017442 GAGAAGCCAAAATGGTACTCCC 58.983 50.000 0.00 0.00 40.46 4.30
3057 3180 3.686016 TGAGAAGCCAAAATGGTACTCC 58.314 45.455 12.87 0.00 40.46 3.85
3058 3181 5.649831 AGAATGAGAAGCCAAAATGGTACTC 59.350 40.000 0.00 5.70 40.46 2.59
3059 3182 5.574188 AGAATGAGAAGCCAAAATGGTACT 58.426 37.500 0.00 0.00 40.46 2.73
3060 3183 5.904362 AGAATGAGAAGCCAAAATGGTAC 57.096 39.130 0.00 0.00 40.46 3.34
3146 3290 2.229792 GTGAAGACACCTTGCCATCAA 58.770 47.619 0.00 0.00 40.74 2.57
3164 3308 7.735917 TGGAGAGTAATAATGAATAGGTGGTG 58.264 38.462 0.00 0.00 0.00 4.17
3244 3388 3.443681 CGGAAATATCCTGCCACAAGTTT 59.556 43.478 0.00 0.00 44.17 2.66
3307 3451 9.457436 TGCATGAAATATTATGAGCTGTCATAT 57.543 29.630 0.00 0.00 43.74 1.78
3315 3459 7.025963 GCTTACCTGCATGAAATATTATGAGC 58.974 38.462 0.00 0.38 0.00 4.26
3340 3484 3.983344 CGCCTGTCTTTTTCTTTGATTGG 59.017 43.478 0.00 0.00 0.00 3.16
3440 3584 2.301583 TGTGCTGCTACAATAGGTGTCA 59.698 45.455 0.00 0.00 41.98 3.58
3446 3590 4.033702 CACTGACATGTGCTGCTACAATAG 59.966 45.833 1.15 4.63 33.69 1.73
3451 3595 1.081892 CCACTGACATGTGCTGCTAC 58.918 55.000 1.15 0.00 36.68 3.58
3458 3602 1.568612 GGCACGACCACTGACATGTG 61.569 60.000 1.15 0.00 38.86 3.21
3536 3680 6.183360 GGATAAGTCACTGCAACATTTAGCAT 60.183 38.462 0.00 0.00 40.42 3.79
3648 3792 2.574006 AAGCACATGCCTGAGAAGAA 57.426 45.000 0.00 0.00 43.38 2.52
3680 3824 6.007703 AGGTAGCATGGTTAAACTAAAGCAA 58.992 36.000 1.12 0.00 40.00 3.91
3684 3828 7.826918 ACAAAGGTAGCATGGTTAAACTAAA 57.173 32.000 1.12 0.00 0.00 1.85
3687 3831 7.826918 TTTACAAAGGTAGCATGGTTAAACT 57.173 32.000 1.12 0.00 0.00 2.66
3698 3842 6.862711 AAGAGACTGTTTTACAAAGGTAGC 57.137 37.500 0.00 0.00 0.00 3.58
3898 4042 2.060275 TCAGGAGATGATGATTGGGGG 58.940 52.381 0.00 0.00 31.12 5.40
3935 4079 0.463620 TTGGCCAAAGGTTGAACTGC 59.536 50.000 17.98 0.00 0.00 4.40
4017 4161 5.253330 ACATTATGTCCAAGTCATTTCCGT 58.747 37.500 0.00 0.00 0.00 4.69
4019 4163 7.339466 AGGTAACATTATGTCCAAGTCATTTCC 59.661 37.037 0.00 0.00 41.41 3.13
4036 4180 8.990163 TTGAAGAAAGGAAACTAGGTAACATT 57.010 30.769 0.00 0.00 42.68 2.71
4096 4240 6.550108 TGCCCTGTGTAGGTTGTAAAAATAAA 59.450 34.615 0.00 0.00 42.96 1.40
4097 4241 6.069331 TGCCCTGTGTAGGTTGTAAAAATAA 58.931 36.000 0.00 0.00 42.96 1.40
4098 4242 5.632118 TGCCCTGTGTAGGTTGTAAAAATA 58.368 37.500 0.00 0.00 42.96 1.40
4099 4243 4.475345 TGCCCTGTGTAGGTTGTAAAAAT 58.525 39.130 0.00 0.00 42.96 1.82
4100 4244 3.899726 TGCCCTGTGTAGGTTGTAAAAA 58.100 40.909 0.00 0.00 42.96 1.94
4101 4245 3.579534 TGCCCTGTGTAGGTTGTAAAA 57.420 42.857 0.00 0.00 42.96 1.52
4102 4246 3.799432 ATGCCCTGTGTAGGTTGTAAA 57.201 42.857 0.00 0.00 42.96 2.01
4267 4411 5.034852 TGTCACAGAAGAATTTGTCCTCA 57.965 39.130 0.00 0.00 0.00 3.86
4326 4470 9.778741 ATGATGAGAACAAGAAAAACAGTACTA 57.221 29.630 0.00 0.00 0.00 1.82
4327 4471 8.682936 ATGATGAGAACAAGAAAAACAGTACT 57.317 30.769 0.00 0.00 0.00 2.73
4354 4498 9.914834 AATAATAGGTCAAAGCAAACCATACTA 57.085 29.630 0.00 0.00 38.06 1.82
4359 4503 5.777732 ACCAATAATAGGTCAAAGCAAACCA 59.222 36.000 0.00 0.00 38.06 3.67
4360 4504 6.280855 ACCAATAATAGGTCAAAGCAAACC 57.719 37.500 0.00 0.00 32.90 3.27
4361 4505 7.655732 ACAAACCAATAATAGGTCAAAGCAAAC 59.344 33.333 0.00 0.00 38.76 2.93
4450 4594 5.707764 GGAGATTACTTGGGGCTTTATGATC 59.292 44.000 0.00 0.00 0.00 2.92
4603 4751 8.428852 ACTGGAACAAGGCAAATTAAGTTAAAT 58.571 29.630 0.00 0.00 38.70 1.40
4695 4843 3.125316 GCTGCTCAATGTACTTAAAGCGT 59.875 43.478 0.00 0.00 30.89 5.07
4782 4930 4.371855 TTCAGTATCCACGTCATCAGAC 57.628 45.455 0.00 0.00 41.46 3.51
4791 4939 6.627395 AAGAGAGAGTATTCAGTATCCACG 57.373 41.667 0.00 0.00 0.00 4.94
5023 5171 5.659079 ACAACAGGGAAAATCAACCTAAACA 59.341 36.000 0.00 0.00 32.22 2.83
5048 5196 7.595311 TGCTCCAAAGAAAAAGAAAAGAAAC 57.405 32.000 0.00 0.00 0.00 2.78
5108 5256 6.953520 AGATTAACAATTTTCCATGGAGGTGA 59.046 34.615 15.53 0.00 39.02 4.02
5248 5399 3.376546 GTCGGTGGAAAGTATAGTCGAGT 59.623 47.826 0.00 0.00 0.00 4.18
5355 5506 0.038744 AAGGGCACTGCTAGCACAAT 59.961 50.000 14.93 0.00 38.04 2.71
5356 5507 0.606401 GAAGGGCACTGCTAGCACAA 60.606 55.000 14.93 0.00 38.04 3.33
5468 5624 8.680903 ACATGAATTCAAAAGTAGCCTCAATAG 58.319 33.333 13.09 0.00 0.00 1.73
5469 5625 8.579850 ACATGAATTCAAAAGTAGCCTCAATA 57.420 30.769 13.09 0.00 0.00 1.90
5470 5626 7.472334 ACATGAATTCAAAAGTAGCCTCAAT 57.528 32.000 13.09 0.00 0.00 2.57
5471 5627 6.899393 ACATGAATTCAAAAGTAGCCTCAA 57.101 33.333 13.09 0.00 0.00 3.02
5472 5628 8.579850 AATACATGAATTCAAAAGTAGCCTCA 57.420 30.769 13.09 0.00 0.00 3.86
5473 5629 8.131731 GGAATACATGAATTCAAAAGTAGCCTC 58.868 37.037 13.09 12.21 37.56 4.70
5474 5630 7.615365 TGGAATACATGAATTCAAAAGTAGCCT 59.385 33.333 13.09 5.36 37.56 4.58
5475 5631 7.771183 TGGAATACATGAATTCAAAAGTAGCC 58.229 34.615 13.09 17.87 37.56 3.93
5497 5653 5.003160 CACATAACTGGAGAAACACATGGA 58.997 41.667 0.00 0.00 0.00 3.41
5533 5689 4.809426 CAGGGACGTACATTTCCTATGAAC 59.191 45.833 0.00 0.00 31.90 3.18
5603 5778 8.665685 GGTGTTATTTATGAACGAACTTGAGAT 58.334 33.333 0.00 0.00 0.00 2.75
5622 5797 8.826765 CCTCTGTCCCATAATATAAGGTGTTAT 58.173 37.037 0.00 0.00 33.25 1.89
5623 5798 8.014263 TCCTCTGTCCCATAATATAAGGTGTTA 58.986 37.037 0.00 0.00 0.00 2.41
5624 5799 6.849697 TCCTCTGTCCCATAATATAAGGTGTT 59.150 38.462 0.00 0.00 0.00 3.32
5628 5832 9.892130 GTATTTCCTCTGTCCCATAATATAAGG 57.108 37.037 0.00 0.00 0.00 2.69
5704 5909 1.074727 TGCAAGTTTAAGCCCTAGCCA 59.925 47.619 0.00 0.00 41.25 4.75
5736 5941 5.497474 CCACTAAGTATTGCTACCTTTGGT 58.503 41.667 0.00 0.00 40.16 3.67
5883 6181 3.735591 TGTGCTGTGTTTCTTAGGGTAC 58.264 45.455 0.00 0.00 0.00 3.34
5888 6186 5.181811 TGGATTGATGTGCTGTGTTTCTTAG 59.818 40.000 0.00 0.00 0.00 2.18
5900 6206 4.156556 ACTGTGTTATGTGGATTGATGTGC 59.843 41.667 0.00 0.00 0.00 4.57
5901 6207 5.885230 ACTGTGTTATGTGGATTGATGTG 57.115 39.130 0.00 0.00 0.00 3.21
5902 6208 7.119699 CACTAACTGTGTTATGTGGATTGATGT 59.880 37.037 0.00 0.00 41.53 3.06
5903 6209 7.334171 TCACTAACTGTGTTATGTGGATTGATG 59.666 37.037 14.03 0.00 46.27 3.07
5904 6210 7.394016 TCACTAACTGTGTTATGTGGATTGAT 58.606 34.615 14.03 0.00 46.27 2.57
5905 6211 6.764379 TCACTAACTGTGTTATGTGGATTGA 58.236 36.000 14.03 0.00 46.27 2.57
5906 6212 7.615582 ATCACTAACTGTGTTATGTGGATTG 57.384 36.000 14.03 0.00 46.27 2.67
5907 6213 7.495934 GCTATCACTAACTGTGTTATGTGGATT 59.504 37.037 14.03 7.46 46.27 3.01
5916 6222 4.248859 CTGCTGCTATCACTAACTGTGTT 58.751 43.478 0.00 0.00 46.27 3.32


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

AutoCloner maintained by Alex Coulton.