Multiple sequence alignment - TraesCS3B01G594700

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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 TraesCS3B01G594700 chr3B 100.000 2453 0 0 1 2453 818053857 818051405 0.000000e+00 4530.0
1 TraesCS3B01G594700 chr3B 88.852 1489 107 25 9 1477 825573298 825571849 0.000000e+00 1775.0
2 TraesCS3B01G594700 chr3B 91.687 1203 80 14 556 1750 809059582 809058392 0.000000e+00 1650.0
3 TraesCS3B01G594700 chr3B 89.452 1223 112 15 532 1750 788406636 788405427 0.000000e+00 1528.0
4 TraesCS3B01G594700 chr3B 90.076 1179 80 18 581 1752 813307664 813306516 0.000000e+00 1495.0
5 TraesCS3B01G594700 chr3B 91.908 828 62 5 927 1752 27487928 27487104 0.000000e+00 1153.0
6 TraesCS3B01G594700 chr3B 92.105 798 61 1 955 1752 788510558 788511353 0.000000e+00 1123.0
7 TraesCS3B01G594700 chr3B 87.563 796 60 17 824 1605 824380186 824379416 0.000000e+00 885.0
8 TraesCS3B01G594700 chr3B 89.974 379 32 3 1840 2212 788511423 788511801 3.670000e-133 484.0
9 TraesCS3B01G594700 chr3B 87.302 378 39 4 1840 2211 813306446 813306072 8.110000e-115 424.0
10 TraesCS3B01G594700 chr3B 87.896 347 31 6 568 914 788510214 788510549 4.910000e-107 398.0
11 TraesCS3B01G594700 chr3B 86.280 379 33 4 1840 2212 27487034 27486669 6.360000e-106 394.0
12 TraesCS3B01G594700 chr3B 90.236 297 28 1 1840 2135 825545515 825545219 1.060000e-103 387.0
13 TraesCS3B01G594700 chr3B 88.442 199 17 4 556 749 764445585 764445388 4.080000e-58 235.0
14 TraesCS3B01G594700 chr3B 86.432 199 23 3 1388 1584 813267011 813266815 5.310000e-52 215.0
15 TraesCS3B01G594700 chr3B 85.377 212 17 6 556 762 824380403 824380201 8.890000e-50 207.0
16 TraesCS3B01G594700 chr3B 90.714 140 11 1 2309 2446 105397124 105396985 4.170000e-43 185.0
17 TraesCS3B01G594700 chr3B 93.137 102 7 0 2209 2310 818045208 818045107 1.520000e-32 150.0
18 TraesCS3B01G594700 chr3B 97.561 41 1 0 1760 1800 788511385 788511425 1.220000e-08 71.3
19 TraesCS3B01G594700 chrUn 88.374 972 78 21 782 1730 364044718 364045677 0.000000e+00 1136.0
20 TraesCS3B01G594700 chrUn 90.254 749 49 16 747 1481 232147738 232147000 0.000000e+00 957.0
21 TraesCS3B01G594700 chrUn 90.254 749 49 16 747 1481 291110909 291111647 0.000000e+00 957.0
22 TraesCS3B01G594700 chrUn 87.907 645 53 8 556 1200 342674459 342673840 0.000000e+00 736.0
23 TraesCS3B01G594700 chrUn 87.597 645 55 8 556 1200 388617789 388618408 0.000000e+00 725.0
24 TraesCS3B01G594700 chrUn 91.842 380 26 3 9 386 329637359 329636983 2.160000e-145 525.0
25 TraesCS3B01G594700 chrUn 91.842 380 26 3 9 386 354043914 354043538 2.160000e-145 525.0
26 TraesCS3B01G594700 chrUn 92.283 311 21 2 1237 1546 209282025 209282333 2.900000e-119 438.0
27 TraesCS3B01G594700 chrUn 90.421 261 25 0 1492 1752 342673099 342672839 6.490000e-91 344.0
28 TraesCS3B01G594700 chrUn 90.421 261 25 0 1492 1752 380530275 380530015 6.490000e-91 344.0
29 TraesCS3B01G594700 chrUn 90.421 261 25 0 1492 1752 473077757 473077497 6.490000e-91 344.0
30 TraesCS3B01G594700 chrUn 88.442 199 17 4 556 749 232152792 232152595 4.080000e-58 235.0
31 TraesCS3B01G594700 chrUn 88.442 199 17 4 556 749 237971831 237971634 4.080000e-58 235.0
32 TraesCS3B01G594700 chrUn 93.548 124 7 1 1840 1962 380529945 380529822 1.500000e-42 183.0
33 TraesCS3B01G594700 chr7B 92.283 311 21 2 1237 1546 642242158 642242466 2.900000e-119 438.0
34 TraesCS3B01G594700 chr7B 87.156 109 13 1 2206 2314 430772592 430772699 3.310000e-24 122.0
35 TraesCS3B01G594700 chr4D 91.781 146 10 1 2305 2448 310901708 310901563 4.140000e-48 202.0
36 TraesCS3B01G594700 chr7D 91.667 144 10 1 2306 2447 207975291 207975434 5.350000e-47 198.0
37 TraesCS3B01G594700 chr2D 90.667 150 12 1 2306 2453 119888101 119888250 5.350000e-47 198.0
38 TraesCS3B01G594700 chr6B 91.096 146 11 1 2306 2449 404347547 404347692 1.920000e-46 196.0
39 TraesCS3B01G594700 chr2B 91.156 147 10 2 2309 2453 518197515 518197370 1.920000e-46 196.0
40 TraesCS3B01G594700 chr1B 92.481 133 10 0 2316 2448 189390251 189390383 8.950000e-45 191.0
41 TraesCS3B01G594700 chr7A 90.411 146 11 2 2309 2452 512293000 512292856 3.220000e-44 189.0
42 TraesCS3B01G594700 chr7A 90.580 138 12 1 2316 2453 461751016 461751152 5.390000e-42 182.0
43 TraesCS3B01G594700 chr7A 87.736 106 13 0 2209 2314 7256781 7256886 9.210000e-25 124.0
44 TraesCS3B01G594700 chr4A 92.000 100 8 0 2210 2309 102948692 102948791 9.150000e-30 141.0
45 TraesCS3B01G594700 chr5D 88.462 104 12 0 2209 2312 346694548 346694651 2.560000e-25 126.0
46 TraesCS3B01G594700 chr6A 89.000 100 11 0 2211 2310 337291877 337291976 9.210000e-25 124.0
47 TraesCS3B01G594700 chr6A 87.129 101 13 0 2209 2309 259250397 259250497 5.540000e-22 115.0
48 TraesCS3B01G594700 chr2A 86.916 107 14 0 2209 2315 764144240 764144346 1.190000e-23 121.0
49 TraesCS3B01G594700 chr1D 87.379 103 13 0 2209 2311 125743541 125743439 4.280000e-23 119.0


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 TraesCS3B01G594700 chr3B 818051405 818053857 2452 True 4530.000 4530 100.000 1 2453 1 chr3B.!!$R7 2452
1 TraesCS3B01G594700 chr3B 825571849 825573298 1449 True 1775.000 1775 88.852 9 1477 1 chr3B.!!$R9 1468
2 TraesCS3B01G594700 chr3B 809058392 809059582 1190 True 1650.000 1650 91.687 556 1750 1 chr3B.!!$R4 1194
3 TraesCS3B01G594700 chr3B 788405427 788406636 1209 True 1528.000 1528 89.452 532 1750 1 chr3B.!!$R3 1218
4 TraesCS3B01G594700 chr3B 813306072 813307664 1592 True 959.500 1495 88.689 581 2211 2 chr3B.!!$R11 1630
5 TraesCS3B01G594700 chr3B 27486669 27487928 1259 True 773.500 1153 89.094 927 2212 2 chr3B.!!$R10 1285
6 TraesCS3B01G594700 chr3B 824379416 824380403 987 True 546.000 885 86.470 556 1605 2 chr3B.!!$R12 1049
7 TraesCS3B01G594700 chr3B 788510214 788511801 1587 False 519.075 1123 91.884 568 2212 4 chr3B.!!$F1 1644
8 TraesCS3B01G594700 chrUn 364044718 364045677 959 False 1136.000 1136 88.374 782 1730 1 chrUn.!!$F3 948
9 TraesCS3B01G594700 chrUn 232147000 232147738 738 True 957.000 957 90.254 747 1481 1 chrUn.!!$R1 734
10 TraesCS3B01G594700 chrUn 291110909 291111647 738 False 957.000 957 90.254 747 1481 1 chrUn.!!$F2 734
11 TraesCS3B01G594700 chrUn 388617789 388618408 619 False 725.000 725 87.597 556 1200 1 chrUn.!!$F4 644
12 TraesCS3B01G594700 chrUn 342672839 342674459 1620 True 540.000 736 89.164 556 1752 2 chrUn.!!$R7 1196

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
815 829 0.17691 GCACTCCAGAGGTAAGCTCC 59.823 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2821 0.039888 TGTGCGTCTCGTCGAAATGA 60.04 50.0 0.0 0.0 0.0 2.57 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 5.482878 AGAACTTGTATTTAGGAACGGAGGA 59.517 40.000 0.00 0.00 0.00 3.71
28 29 6.438425 ACTTGTATTTAGGAACGGAGGAAGTA 59.562 38.462 0.00 0.00 0.00 2.24
46 47 2.684881 AGTAAATCATTCTGCCGCTTGG 59.315 45.455 0.00 0.00 0.00 3.61
50 51 0.543277 TCATTCTGCCGCTTGGATCT 59.457 50.000 0.00 0.00 33.02 2.75
71 72 4.138290 CTGTCATCGGTGTACCTCTAGAT 58.862 47.826 0.00 0.00 0.00 1.98
82 85 5.695816 GTGTACCTCTAGATAGTCCACTACG 59.304 48.000 9.98 0.00 0.00 3.51
268 273 6.431543 TCGACCTTCCATTATACTTGCAAAAA 59.568 34.615 0.00 0.00 0.00 1.94
502 509 3.069586 CCCAGAAACCAAAGGTTCTTTCC 59.930 47.826 1.34 0.00 46.20 3.13
503 510 3.069586 CCAGAAACCAAAGGTTCTTTCCC 59.930 47.826 1.34 0.00 46.20 3.97
505 512 2.858787 AACCAAAGGTTCTTTCCCCA 57.141 45.000 0.00 0.00 43.05 4.96
511 518 4.188462 CAAAGGTTCTTTCCCCAACAAAC 58.812 43.478 0.00 0.00 0.00 2.93
514 521 2.483013 GGTTCTTTCCCCAACAAACTGC 60.483 50.000 0.00 0.00 0.00 4.40
529 536 0.239347 ACTGCTGCTGAAATGAACGC 59.761 50.000 13.69 0.00 0.00 4.84
535 542 2.353889 CTGCTGAAATGAACGCTGCTAT 59.646 45.455 0.00 0.00 0.00 2.97
622 631 1.152777 TTGCACTGGACCAACAGGG 60.153 57.895 0.00 0.00 44.73 4.45
633 642 1.304282 CAACAGGGGTCCCATCAGG 59.696 63.158 10.98 0.00 38.92 3.86
664 677 5.201713 TGCATCACTAGCAGGAGTATTAC 57.798 43.478 0.00 0.00 37.02 1.89
777 790 3.565307 TCCAGACCTTTGCTTTCACATT 58.435 40.909 0.00 0.00 0.00 2.71
799 813 1.276421 TCTTGCTCCAGAGGTAAGCAC 59.724 52.381 0.00 0.00 45.15 4.40
805 819 1.077169 TCCAGAGGTAAGCACTCCAGA 59.923 52.381 0.00 0.00 35.58 3.86
808 822 1.077993 AGAGGTAAGCACTCCAGAGGT 59.922 52.381 0.00 0.00 35.58 3.85
809 823 2.312140 AGAGGTAAGCACTCCAGAGGTA 59.688 50.000 0.00 0.00 35.58 3.08
813 827 1.650528 AAGCACTCCAGAGGTAAGCT 58.349 50.000 0.00 0.64 0.00 3.74
814 828 1.190643 AGCACTCCAGAGGTAAGCTC 58.809 55.000 0.00 0.00 0.00 4.09
815 829 0.176910 GCACTCCAGAGGTAAGCTCC 59.823 60.000 0.00 0.00 0.00 4.70
816 830 1.561643 CACTCCAGAGGTAAGCTCCA 58.438 55.000 0.00 0.00 0.00 3.86
817 831 1.480137 CACTCCAGAGGTAAGCTCCAG 59.520 57.143 0.00 0.00 0.00 3.86
818 832 1.359474 ACTCCAGAGGTAAGCTCCAGA 59.641 52.381 0.00 0.00 0.00 3.86
819 833 2.031120 CTCCAGAGGTAAGCTCCAGAG 58.969 57.143 0.00 0.00 0.00 3.35
820 834 1.118838 CCAGAGGTAAGCTCCAGAGG 58.881 60.000 0.00 0.00 0.00 3.69
821 835 1.621072 CCAGAGGTAAGCTCCAGAGGT 60.621 57.143 0.00 0.00 41.53 3.85
822 836 2.358300 CCAGAGGTAAGCTCCAGAGGTA 60.358 54.545 0.00 0.00 38.35 3.08
953 969 2.755876 TGCATCTCCCGAGCGTCT 60.756 61.111 0.00 0.00 0.00 4.18
1466 1972 0.524414 AAATAAGAAACCACGGCCGC 59.476 50.000 28.58 7.73 0.00 6.53
1605 2154 8.444715 TGTAATACACTAGTTTGGTATTTTGCG 58.555 33.333 17.44 0.00 38.35 4.85
1635 2184 0.811219 TCGCAGCCGATCAGAAATGG 60.811 55.000 0.00 0.00 38.82 3.16
1665 2214 4.427312 CTTTGCATGGCTCCTTAAATCAC 58.573 43.478 0.00 0.00 0.00 3.06
1668 2217 2.360165 GCATGGCTCCTTAAATCACAGG 59.640 50.000 0.00 0.00 0.00 4.00
1730 2279 5.779806 CGATCTAAACGGACACAGATTTT 57.220 39.130 0.00 0.00 0.00 1.82
1731 2280 6.880822 CGATCTAAACGGACACAGATTTTA 57.119 37.500 0.00 0.00 0.00 1.52
1733 2282 7.906160 CGATCTAAACGGACACAGATTTTATT 58.094 34.615 0.00 0.00 0.00 1.40
1736 2285 5.934935 AAACGGACACAGATTTTATTCGT 57.065 34.783 0.00 0.00 0.00 3.85
1738 2287 5.277601 ACGGACACAGATTTTATTCGTTG 57.722 39.130 0.00 0.00 0.00 4.10
1752 2301 0.099082 TCGTTGTTTGTCCGTTTGGC 59.901 50.000 0.00 0.00 34.14 4.52
1753 2302 0.868177 CGTTGTTTGTCCGTTTGGCC 60.868 55.000 0.00 0.00 34.14 5.36
1754 2303 0.868177 GTTGTTTGTCCGTTTGGCCG 60.868 55.000 0.00 0.00 34.14 6.13
1755 2304 2.354188 GTTTGTCCGTTTGGCCGC 60.354 61.111 0.00 0.00 34.14 6.53
1756 2305 2.829003 TTTGTCCGTTTGGCCGCA 60.829 55.556 0.00 0.00 34.14 5.69
1757 2306 2.415608 TTTGTCCGTTTGGCCGCAA 61.416 52.632 0.00 0.00 34.14 4.85
1799 2372 0.764271 CCCAACTGGCAAACCCATTT 59.236 50.000 0.00 0.00 44.33 2.32
1801 2374 1.881591 CAACTGGCAAACCCATTTGG 58.118 50.000 4.95 0.00 45.57 3.28
1810 2383 2.755469 CCCATTTGGTCCGCCTGG 60.755 66.667 0.00 0.00 35.27 4.45
1811 2384 3.451894 CCATTTGGTCCGCCTGGC 61.452 66.667 9.11 9.11 35.27 4.85
1812 2385 3.451894 CATTTGGTCCGCCTGGCC 61.452 66.667 14.12 0.00 35.27 5.36
1828 2401 4.337013 CCGGTAGGCAGCCAAATT 57.663 55.556 15.80 0.00 0.00 1.82
1829 2402 2.578683 CCGGTAGGCAGCCAAATTT 58.421 52.632 15.80 0.00 0.00 1.82
1830 2403 1.757682 CCGGTAGGCAGCCAAATTTA 58.242 50.000 15.80 0.00 0.00 1.40
1831 2404 1.404035 CCGGTAGGCAGCCAAATTTAC 59.596 52.381 15.80 6.73 0.00 2.01
1832 2405 2.088423 CGGTAGGCAGCCAAATTTACA 58.912 47.619 15.80 0.00 0.00 2.41
1833 2406 2.159435 CGGTAGGCAGCCAAATTTACAC 60.159 50.000 15.80 0.87 0.00 2.90
1834 2407 3.089284 GGTAGGCAGCCAAATTTACACT 58.911 45.455 15.80 0.00 0.00 3.55
1835 2408 4.266714 GGTAGGCAGCCAAATTTACACTA 58.733 43.478 15.80 0.00 0.00 2.74
1836 2409 4.887655 GGTAGGCAGCCAAATTTACACTAT 59.112 41.667 15.80 0.00 0.00 2.12
1837 2410 5.359860 GGTAGGCAGCCAAATTTACACTATT 59.640 40.000 15.80 0.00 0.00 1.73
1838 2411 6.127451 GGTAGGCAGCCAAATTTACACTATTT 60.127 38.462 15.80 0.00 0.00 1.40
1839 2412 6.358974 AGGCAGCCAAATTTACACTATTTT 57.641 33.333 15.80 0.00 0.00 1.82
1840 2413 6.768483 AGGCAGCCAAATTTACACTATTTTT 58.232 32.000 15.80 0.00 0.00 1.94
2036 2610 9.632807 GAGCTGGTATATCTATTAGTTGACAAG 57.367 37.037 0.00 0.00 0.00 3.16
2095 2669 7.516198 AGTTGAAACTGAGTTGCTTAATCAT 57.484 32.000 4.71 0.00 37.98 2.45
2102 2676 6.694447 ACTGAGTTGCTTAATCATGCATTTT 58.306 32.000 0.00 0.00 39.07 1.82
2105 2679 6.753279 TGAGTTGCTTAATCATGCATTTTAGC 59.247 34.615 12.88 12.88 39.07 3.09
2117 2691 3.940221 TGCATTTTAGCATGAAATTGGGC 59.060 39.130 0.00 0.00 40.11 5.36
2131 2705 0.179097 TTGGGCGAACTTTGCAAACC 60.179 50.000 8.05 7.51 0.00 3.27
2136 2710 2.792674 GGCGAACTTTGCAAACCTTAAC 59.207 45.455 8.05 0.00 0.00 2.01
2144 2718 0.885196 GCAAACCTTAACGGGCATGA 59.115 50.000 0.00 0.00 36.97 3.07
2163 2742 6.154445 GCATGATCAACTCAACATTTTCACT 58.846 36.000 0.00 0.00 37.44 3.41
2194 2773 5.180117 ACCAAACTCTTGATCGAAGATGTTG 59.820 40.000 15.01 15.02 45.12 3.33
2196 2775 6.293626 CCAAACTCTTGATCGAAGATGTTGTT 60.294 38.462 17.50 12.11 45.12 2.83
2200 2779 6.473778 ACTCTTGATCGAAGATGTTGTTATCG 59.526 38.462 7.69 0.00 45.12 2.92
2212 2791 0.317854 TGTTATCGCGCTCATCCTCG 60.318 55.000 5.56 0.00 0.00 4.63
2213 2792 1.004277 GTTATCGCGCTCATCCTCGG 61.004 60.000 5.56 0.00 0.00 4.63
2214 2793 1.170290 TTATCGCGCTCATCCTCGGA 61.170 55.000 5.56 0.00 0.00 4.55
2215 2794 0.960861 TATCGCGCTCATCCTCGGAT 60.961 55.000 5.56 0.00 34.81 4.18
2216 2795 1.810606 ATCGCGCTCATCCTCGGATT 61.811 55.000 5.56 0.00 31.62 3.01
2217 2796 1.170290 TCGCGCTCATCCTCGGATTA 61.170 55.000 5.56 0.00 31.62 1.75
2218 2797 0.318699 CGCGCTCATCCTCGGATTAA 60.319 55.000 5.56 0.00 31.62 1.40
2219 2798 1.423395 GCGCTCATCCTCGGATTAAG 58.577 55.000 0.00 0.00 31.62 1.85
2220 2799 1.000163 GCGCTCATCCTCGGATTAAGA 60.000 52.381 0.00 0.00 31.62 2.10
2221 2800 2.667137 CGCTCATCCTCGGATTAAGAC 58.333 52.381 8.56 1.80 31.62 3.01
2222 2801 2.667137 GCTCATCCTCGGATTAAGACG 58.333 52.381 8.56 0.00 31.62 4.18
2223 2802 2.293677 GCTCATCCTCGGATTAAGACGA 59.706 50.000 8.56 4.52 37.56 4.20
2224 2803 3.243434 GCTCATCCTCGGATTAAGACGAA 60.243 47.826 8.56 0.00 38.79 3.85
2225 2804 4.559704 GCTCATCCTCGGATTAAGACGAAT 60.560 45.833 8.56 0.00 38.79 3.34
2226 2805 5.531122 TCATCCTCGGATTAAGACGAATT 57.469 39.130 0.00 0.00 38.79 2.17
2227 2806 5.914033 TCATCCTCGGATTAAGACGAATTT 58.086 37.500 0.00 0.00 38.79 1.82
2228 2807 6.346096 TCATCCTCGGATTAAGACGAATTTT 58.654 36.000 0.00 0.00 38.79 1.82
2229 2808 7.494211 TCATCCTCGGATTAAGACGAATTTTA 58.506 34.615 0.00 0.00 38.79 1.52
2230 2809 8.148351 TCATCCTCGGATTAAGACGAATTTTAT 58.852 33.333 0.00 0.00 38.79 1.40
2231 2810 9.419297 CATCCTCGGATTAAGACGAATTTTATA 57.581 33.333 0.00 0.00 38.79 0.98
2233 2812 9.635520 TCCTCGGATTAAGACGAATTTTATATC 57.364 33.333 5.88 0.00 38.79 1.63
2234 2813 9.419297 CCTCGGATTAAGACGAATTTTATATCA 57.581 33.333 5.88 0.00 38.79 2.15
2259 2838 1.545759 GATCATTTCGACGAGACGCA 58.454 50.000 0.00 0.00 0.00 5.24
2260 2839 1.253034 GATCATTTCGACGAGACGCAC 59.747 52.381 0.00 0.00 0.00 5.34
2261 2840 0.039888 TCATTTCGACGAGACGCACA 60.040 50.000 0.00 0.00 0.00 4.57
2262 2841 0.781787 CATTTCGACGAGACGCACAA 59.218 50.000 0.00 0.00 0.00 3.33
2263 2842 0.782384 ATTTCGACGAGACGCACAAC 59.218 50.000 0.00 0.00 0.00 3.32
2264 2843 0.248743 TTTCGACGAGACGCACAACT 60.249 50.000 0.00 0.00 0.00 3.16
2265 2844 0.248743 TTCGACGAGACGCACAACTT 60.249 50.000 0.00 0.00 0.00 2.66
2266 2845 0.248743 TCGACGAGACGCACAACTTT 60.249 50.000 0.00 0.00 0.00 2.66
2267 2846 0.158928 CGACGAGACGCACAACTTTC 59.841 55.000 0.00 0.00 0.00 2.62
2268 2847 1.205657 GACGAGACGCACAACTTTCA 58.794 50.000 0.00 0.00 0.00 2.69
2269 2848 1.792949 GACGAGACGCACAACTTTCAT 59.207 47.619 0.00 0.00 0.00 2.57
2270 2849 1.526887 ACGAGACGCACAACTTTCATG 59.473 47.619 0.00 0.00 0.00 3.07
2271 2850 1.136252 CGAGACGCACAACTTTCATGG 60.136 52.381 0.00 0.00 0.00 3.66
2272 2851 1.873591 GAGACGCACAACTTTCATGGT 59.126 47.619 0.00 0.00 0.00 3.55
2273 2852 1.603802 AGACGCACAACTTTCATGGTG 59.396 47.619 0.00 0.00 0.00 4.17
2274 2853 1.601903 GACGCACAACTTTCATGGTGA 59.398 47.619 2.20 0.00 33.16 4.02
2275 2854 2.020720 ACGCACAACTTTCATGGTGAA 58.979 42.857 2.20 0.00 34.03 3.18
2276 2855 2.425312 ACGCACAACTTTCATGGTGAAA 59.575 40.909 5.17 5.17 43.37 2.69
2277 2856 2.788786 CGCACAACTTTCATGGTGAAAC 59.211 45.455 1.24 0.00 41.02 2.78
2278 2857 3.733380 CGCACAACTTTCATGGTGAAACA 60.733 43.478 1.24 0.00 41.02 2.83
2279 2858 4.370917 GCACAACTTTCATGGTGAAACAT 58.629 39.130 1.24 0.00 41.02 2.71
2280 2859 4.810491 GCACAACTTTCATGGTGAAACATT 59.190 37.500 1.24 0.00 41.02 2.71
2281 2860 5.294060 GCACAACTTTCATGGTGAAACATTT 59.706 36.000 1.24 0.00 41.02 2.32
2282 2861 6.183360 GCACAACTTTCATGGTGAAACATTTT 60.183 34.615 1.24 0.00 41.02 1.82
2283 2862 7.401080 CACAACTTTCATGGTGAAACATTTTC 58.599 34.615 1.24 0.00 41.02 2.29
2284 2863 6.538381 ACAACTTTCATGGTGAAACATTTTCC 59.462 34.615 1.24 0.00 41.02 3.13
2285 2864 6.232581 ACTTTCATGGTGAAACATTTTCCA 57.767 33.333 1.24 5.22 41.02 3.53
2286 2865 6.829849 ACTTTCATGGTGAAACATTTTCCAT 58.170 32.000 1.24 8.33 41.02 3.41
2287 2866 7.281841 ACTTTCATGGTGAAACATTTTCCATT 58.718 30.769 10.35 0.00 41.02 3.16
2288 2867 8.428063 ACTTTCATGGTGAAACATTTTCCATTA 58.572 29.630 10.35 3.74 41.02 1.90
2289 2868 8.830201 TTTCATGGTGAAACATTTTCCATTAG 57.170 30.769 10.35 4.28 41.02 1.73
2290 2869 7.773489 TCATGGTGAAACATTTTCCATTAGA 57.227 32.000 10.35 5.84 39.98 2.10
2291 2870 7.829725 TCATGGTGAAACATTTTCCATTAGAG 58.170 34.615 10.35 3.58 39.98 2.43
2292 2871 6.588719 TGGTGAAACATTTTCCATTAGAGG 57.411 37.500 0.00 0.00 39.98 3.69
2293 2872 5.480073 TGGTGAAACATTTTCCATTAGAGGG 59.520 40.000 0.00 0.00 39.98 4.30
2294 2873 5.410924 GTGAAACATTTTCCATTAGAGGGC 58.589 41.667 0.00 0.00 36.32 5.19
2295 2874 5.047377 GTGAAACATTTTCCATTAGAGGGCA 60.047 40.000 0.00 0.00 36.32 5.36
2296 2875 5.721000 TGAAACATTTTCCATTAGAGGGCAT 59.279 36.000 0.00 0.00 0.00 4.40
2297 2876 5.859205 AACATTTTCCATTAGAGGGCATC 57.141 39.130 0.00 0.00 0.00 3.91
2298 2877 5.134725 ACATTTTCCATTAGAGGGCATCT 57.865 39.130 6.96 6.96 42.47 2.90
2299 2878 5.522641 ACATTTTCCATTAGAGGGCATCTT 58.477 37.500 7.11 0.00 39.64 2.40
2300 2879 6.672593 ACATTTTCCATTAGAGGGCATCTTA 58.327 36.000 7.11 0.00 39.64 2.10
2301 2880 7.125391 ACATTTTCCATTAGAGGGCATCTTAA 58.875 34.615 7.11 0.22 39.64 1.85
2302 2881 7.786464 ACATTTTCCATTAGAGGGCATCTTAAT 59.214 33.333 7.11 2.72 39.64 1.40
2303 2882 8.645110 CATTTTCCATTAGAGGGCATCTTAATT 58.355 33.333 7.11 0.00 39.64 1.40
2304 2883 7.587037 TTTCCATTAGAGGGCATCTTAATTG 57.413 36.000 7.11 0.39 39.64 2.32
2305 2884 6.514012 TCCATTAGAGGGCATCTTAATTGA 57.486 37.500 7.11 4.39 39.64 2.57
2306 2885 6.537355 TCCATTAGAGGGCATCTTAATTGAG 58.463 40.000 7.11 0.00 39.64 3.02
2307 2886 6.101734 TCCATTAGAGGGCATCTTAATTGAGT 59.898 38.462 7.11 0.00 39.64 3.41
2308 2887 6.774656 CCATTAGAGGGCATCTTAATTGAGTT 59.225 38.462 7.11 0.00 39.64 3.01
2309 2888 7.286316 CCATTAGAGGGCATCTTAATTGAGTTT 59.714 37.037 7.11 0.00 39.64 2.66
2310 2889 7.865706 TTAGAGGGCATCTTAATTGAGTTTC 57.134 36.000 7.11 0.00 39.64 2.78
2311 2890 6.072199 AGAGGGCATCTTAATTGAGTTTCT 57.928 37.500 0.00 0.00 32.99 2.52
2312 2891 5.884792 AGAGGGCATCTTAATTGAGTTTCTG 59.115 40.000 0.00 0.00 32.99 3.02
2313 2892 4.952335 AGGGCATCTTAATTGAGTTTCTGG 59.048 41.667 0.00 0.00 0.00 3.86
2314 2893 4.949856 GGGCATCTTAATTGAGTTTCTGGA 59.050 41.667 0.00 0.00 0.00 3.86
2315 2894 5.418840 GGGCATCTTAATTGAGTTTCTGGAA 59.581 40.000 0.00 0.00 0.00 3.53
2316 2895 6.325596 GGCATCTTAATTGAGTTTCTGGAAC 58.674 40.000 0.00 0.00 38.58 3.62
2317 2896 6.071952 GGCATCTTAATTGAGTTTCTGGAACA 60.072 38.462 0.98 0.00 40.84 3.18
2318 2897 6.803807 GCATCTTAATTGAGTTTCTGGAACAC 59.196 38.462 0.98 0.00 40.84 3.32
2319 2898 6.539649 TCTTAATTGAGTTTCTGGAACACG 57.460 37.500 0.98 0.00 40.84 4.49
2320 2899 6.285224 TCTTAATTGAGTTTCTGGAACACGA 58.715 36.000 0.98 0.00 40.84 4.35
2321 2900 6.423905 TCTTAATTGAGTTTCTGGAACACGAG 59.576 38.462 0.98 0.00 40.84 4.18
2322 2901 3.812156 TTGAGTTTCTGGAACACGAGA 57.188 42.857 0.98 0.00 40.84 4.04
2323 2902 3.371102 TGAGTTTCTGGAACACGAGAG 57.629 47.619 0.98 0.00 40.84 3.20
2324 2903 2.035961 TGAGTTTCTGGAACACGAGAGG 59.964 50.000 0.98 0.00 40.84 3.69
2325 2904 2.296471 GAGTTTCTGGAACACGAGAGGA 59.704 50.000 0.98 0.00 40.84 3.71
2326 2905 2.297597 AGTTTCTGGAACACGAGAGGAG 59.702 50.000 0.98 0.00 40.84 3.69
2327 2906 1.257743 TTCTGGAACACGAGAGGAGG 58.742 55.000 0.00 0.00 0.00 4.30
2328 2907 1.216710 CTGGAACACGAGAGGAGGC 59.783 63.158 0.00 0.00 0.00 4.70
2329 2908 2.232298 CTGGAACACGAGAGGAGGCC 62.232 65.000 0.00 0.00 0.00 5.19
2330 2909 1.985116 GGAACACGAGAGGAGGCCT 60.985 63.158 3.86 3.86 36.03 5.19
2331 2910 1.216710 GAACACGAGAGGAGGCCTG 59.783 63.158 12.00 0.00 31.76 4.85
2332 2911 1.534235 AACACGAGAGGAGGCCTGT 60.534 57.895 12.00 0.00 31.76 4.00
2333 2912 1.821061 AACACGAGAGGAGGCCTGTG 61.821 60.000 12.00 14.11 31.76 3.66
2334 2913 2.681778 ACGAGAGGAGGCCTGTGG 60.682 66.667 12.00 0.00 31.76 4.17
2335 2914 3.465403 CGAGAGGAGGCCTGTGGG 61.465 72.222 12.00 0.00 31.76 4.61
2336 2915 3.086600 GAGAGGAGGCCTGTGGGG 61.087 72.222 12.00 0.00 31.76 4.96
2349 2928 4.076509 TGGGGCCCACTATACACC 57.923 61.111 24.76 2.47 0.00 4.16
2350 2929 1.083141 TGGGGCCCACTATACACCA 59.917 57.895 24.76 5.69 0.00 4.17
2351 2930 0.986019 TGGGGCCCACTATACACCAG 60.986 60.000 24.76 0.00 0.00 4.00
2352 2931 1.705997 GGGGCCCACTATACACCAGG 61.706 65.000 26.86 0.00 0.00 4.45
2353 2932 1.705997 GGGCCCACTATACACCAGGG 61.706 65.000 19.95 0.00 42.55 4.45
2355 2934 2.615244 CCCACTATACACCAGGGCA 58.385 57.895 0.00 0.00 31.81 5.36
2356 2935 0.180406 CCCACTATACACCAGGGCAC 59.820 60.000 0.00 0.00 31.81 5.01
2357 2936 0.179084 CCACTATACACCAGGGCACG 60.179 60.000 0.00 0.00 0.00 5.34
2358 2937 0.810031 CACTATACACCAGGGCACGC 60.810 60.000 0.00 0.00 0.00 5.34
2359 2938 1.227556 CTATACACCAGGGCACGCC 60.228 63.158 0.00 0.00 0.00 5.68
2360 2939 1.966901 CTATACACCAGGGCACGCCA 61.967 60.000 10.83 0.00 37.98 5.69
2361 2940 1.966901 TATACACCAGGGCACGCCAG 61.967 60.000 10.83 1.44 37.98 4.85
2394 2973 2.919043 CCTGATGGGTAGTGGGGC 59.081 66.667 0.00 0.00 0.00 5.80
2395 2974 2.757124 CCTGATGGGTAGTGGGGCC 61.757 68.421 0.00 0.00 0.00 5.80
2396 2975 2.694616 TGATGGGTAGTGGGGCCC 60.695 66.667 18.17 18.17 45.04 5.80
2417 2996 4.366684 GGCACCCCCTTGACCCAG 62.367 72.222 0.00 0.00 0.00 4.45
2419 2998 3.260100 CACCCCCTTGACCCAGCT 61.260 66.667 0.00 0.00 0.00 4.24
2420 2999 2.936032 ACCCCCTTGACCCAGCTC 60.936 66.667 0.00 0.00 0.00 4.09
2421 3000 3.732849 CCCCCTTGACCCAGCTCC 61.733 72.222 0.00 0.00 0.00 4.70
2422 3001 4.101448 CCCCTTGACCCAGCTCCG 62.101 72.222 0.00 0.00 0.00 4.63
2423 3002 4.785453 CCCTTGACCCAGCTCCGC 62.785 72.222 0.00 0.00 0.00 5.54
2424 3003 4.785453 CCTTGACCCAGCTCCGCC 62.785 72.222 0.00 0.00 0.00 6.13
2425 3004 3.710722 CTTGACCCAGCTCCGCCT 61.711 66.667 0.00 0.00 0.00 5.52
2426 3005 3.672295 CTTGACCCAGCTCCGCCTC 62.672 68.421 0.00 0.00 0.00 4.70
2427 3006 4.704103 TGACCCAGCTCCGCCTCT 62.704 66.667 0.00 0.00 0.00 3.69
2428 3007 2.442272 GACCCAGCTCCGCCTCTA 60.442 66.667 0.00 0.00 0.00 2.43
2429 3008 1.834822 GACCCAGCTCCGCCTCTAT 60.835 63.158 0.00 0.00 0.00 1.98
2430 3009 0.539901 GACCCAGCTCCGCCTCTATA 60.540 60.000 0.00 0.00 0.00 1.31
2431 3010 0.105658 ACCCAGCTCCGCCTCTATAA 60.106 55.000 0.00 0.00 0.00 0.98
2432 3011 1.048601 CCCAGCTCCGCCTCTATAAA 58.951 55.000 0.00 0.00 0.00 1.40
2433 3012 1.625818 CCCAGCTCCGCCTCTATAAAT 59.374 52.381 0.00 0.00 0.00 1.40
2434 3013 2.832129 CCCAGCTCCGCCTCTATAAATA 59.168 50.000 0.00 0.00 0.00 1.40
2435 3014 3.368531 CCCAGCTCCGCCTCTATAAATAC 60.369 52.174 0.00 0.00 0.00 1.89
2436 3015 3.368531 CCAGCTCCGCCTCTATAAATACC 60.369 52.174 0.00 0.00 0.00 2.73
2437 3016 2.832733 AGCTCCGCCTCTATAAATACCC 59.167 50.000 0.00 0.00 0.00 3.69
2438 3017 2.832733 GCTCCGCCTCTATAAATACCCT 59.167 50.000 0.00 0.00 0.00 4.34
2439 3018 4.021916 GCTCCGCCTCTATAAATACCCTA 58.978 47.826 0.00 0.00 0.00 3.53
2440 3019 4.465305 GCTCCGCCTCTATAAATACCCTAA 59.535 45.833 0.00 0.00 0.00 2.69
2441 3020 5.046807 GCTCCGCCTCTATAAATACCCTAAA 60.047 44.000 0.00 0.00 0.00 1.85
2442 3021 6.519551 GCTCCGCCTCTATAAATACCCTAAAA 60.520 42.308 0.00 0.00 0.00 1.52
2443 3022 7.563724 TCCGCCTCTATAAATACCCTAAAAT 57.436 36.000 0.00 0.00 0.00 1.82
2444 3023 7.618137 TCCGCCTCTATAAATACCCTAAAATC 58.382 38.462 0.00 0.00 0.00 2.17
2445 3024 6.822170 CCGCCTCTATAAATACCCTAAAATCC 59.178 42.308 0.00 0.00 0.00 3.01
2446 3025 6.822170 CGCCTCTATAAATACCCTAAAATCCC 59.178 42.308 0.00 0.00 0.00 3.85
2447 3026 7.528205 CGCCTCTATAAATACCCTAAAATCCCA 60.528 40.741 0.00 0.00 0.00 4.37
2448 3027 8.168058 GCCTCTATAAATACCCTAAAATCCCAA 58.832 37.037 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.727434 TCCTCCGTTCCTAAATACAAGTTC 58.273 41.667 0.00 0.00 0.00 3.01
2 3 5.750352 TCCTCCGTTCCTAAATACAAGTT 57.250 39.130 0.00 0.00 0.00 2.66
3 4 5.247792 ACTTCCTCCGTTCCTAAATACAAGT 59.752 40.000 0.00 0.00 0.00 3.16
4 5 5.731591 ACTTCCTCCGTTCCTAAATACAAG 58.268 41.667 0.00 0.00 0.00 3.16
5 6 5.750352 ACTTCCTCCGTTCCTAAATACAA 57.250 39.130 0.00 0.00 0.00 2.41
6 7 6.855763 TTACTTCCTCCGTTCCTAAATACA 57.144 37.500 0.00 0.00 0.00 2.29
7 8 7.983484 TGATTTACTTCCTCCGTTCCTAAATAC 59.017 37.037 0.00 0.00 0.00 1.89
17 18 4.192317 GCAGAATGATTTACTTCCTCCGT 58.808 43.478 0.00 0.00 39.69 4.69
22 23 2.945668 AGCGGCAGAATGATTTACTTCC 59.054 45.455 1.45 0.00 39.69 3.46
24 25 3.129287 CCAAGCGGCAGAATGATTTACTT 59.871 43.478 1.45 0.00 39.69 2.24
28 29 1.838112 TCCAAGCGGCAGAATGATTT 58.162 45.000 1.45 0.00 39.69 2.17
46 47 2.952978 AGAGGTACACCGATGACAGATC 59.047 50.000 0.00 0.00 42.08 2.75
50 51 3.639672 TCTAGAGGTACACCGATGACA 57.360 47.619 0.00 0.00 42.08 3.58
71 72 7.928307 ATGAGTACTTTAACGTAGTGGACTA 57.072 36.000 4.31 0.00 45.00 2.59
82 85 9.804758 ACACTATTCTGCTATGAGTACTTTAAC 57.195 33.333 0.00 0.00 0.00 2.01
131 134 0.535335 CTCCTAGTTGGTTGCGCCTA 59.465 55.000 4.18 0.00 38.35 3.93
133 136 1.003718 ACTCCTAGTTGGTTGCGCC 60.004 57.895 4.18 0.00 37.07 6.53
244 249 5.811399 TTTGCAAGTATAATGGAAGGTCG 57.189 39.130 0.00 0.00 29.63 4.79
268 273 8.952278 GGGTTATTTTTCTTTTTGTGGAACTTT 58.048 29.630 0.00 0.00 38.04 2.66
343 349 0.976641 AATCAGCGGTGACTTCAGGA 59.023 50.000 21.19 0.00 34.75 3.86
354 360 6.869421 ATTTTCACGAATAAAAATCAGCGG 57.131 33.333 0.00 0.00 31.17 5.52
355 361 9.656834 GTAAATTTTCACGAATAAAAATCAGCG 57.343 29.630 0.00 0.00 34.78 5.18
480 487 3.069586 GGAAAGAACCTTTGGTTTCTGGG 59.930 47.826 3.34 0.00 46.95 4.45
481 488 3.069586 GGGAAAGAACCTTTGGTTTCTGG 59.930 47.826 3.34 0.00 46.95 3.86
502 509 0.746063 TTCAGCAGCAGTTTGTTGGG 59.254 50.000 0.00 0.00 31.15 4.12
503 510 2.582728 TTTCAGCAGCAGTTTGTTGG 57.417 45.000 0.00 0.00 31.15 3.77
505 512 4.114794 GTTCATTTCAGCAGCAGTTTGTT 58.885 39.130 0.00 0.00 0.00 2.83
511 518 0.520404 AGCGTTCATTTCAGCAGCAG 59.480 50.000 0.00 0.00 0.00 4.24
514 521 0.520404 AGCAGCGTTCATTTCAGCAG 59.480 50.000 0.00 0.00 0.00 4.24
529 536 6.153510 TGCTGGTACTAATAGATCCATAGCAG 59.846 42.308 13.27 11.18 39.80 4.24
535 542 4.223144 TGCTGCTGGTACTAATAGATCCA 58.777 43.478 0.00 1.53 0.00 3.41
642 655 4.895889 AGTAATACTCCTGCTAGTGATGCA 59.104 41.667 0.00 0.00 38.81 3.96
664 677 0.517316 GGCGTTGCTGGTAGTTGAAG 59.483 55.000 0.00 0.00 0.00 3.02
738 751 1.354040 GAGTTGAGGCATGACACTCG 58.646 55.000 0.00 0.00 36.53 4.18
777 790 1.827969 GCTTACCTCTGGAGCAAGAGA 59.172 52.381 11.47 0.00 45.59 3.10
799 813 2.031120 CTCTGGAGCTTACCTCTGGAG 58.969 57.143 0.00 0.00 40.57 3.86
805 819 3.476485 ACTTACCTCTGGAGCTTACCT 57.524 47.619 0.00 0.00 0.00 3.08
808 822 6.869206 AATTGTACTTACCTCTGGAGCTTA 57.131 37.500 0.00 0.00 0.00 3.09
809 823 5.763876 AATTGTACTTACCTCTGGAGCTT 57.236 39.130 0.00 0.00 0.00 3.74
822 836 9.525409 ACGCGAACTATATAAGAAATTGTACTT 57.475 29.630 15.93 0.00 0.00 2.24
953 969 3.492102 AAGCAAACTCTGGCTCAACTA 57.508 42.857 0.00 0.00 40.01 2.24
1591 2140 7.422878 TTTAAAATCCCGCAAAATACCAAAC 57.577 32.000 0.00 0.00 0.00 2.93
1605 2154 1.673920 TCGGCTGCGATTTAAAATCCC 59.326 47.619 0.00 0.00 0.00 3.85
1665 2214 4.125703 GGCATGAATGACTAGACTTCCTG 58.874 47.826 0.00 1.34 31.49 3.86
1668 2217 5.065731 CCTTTGGCATGAATGACTAGACTTC 59.934 44.000 0.00 0.00 36.54 3.01
1695 2244 2.332362 TAGATCGGCGCGTTGGAGTC 62.332 60.000 8.43 0.00 0.00 3.36
1723 2272 6.140110 ACGGACAAACAACGAATAAAATCTG 58.860 36.000 0.00 0.00 0.00 2.90
1730 2279 3.548415 GCCAAACGGACAAACAACGAATA 60.548 43.478 0.00 0.00 0.00 1.75
1731 2280 2.796735 GCCAAACGGACAAACAACGAAT 60.797 45.455 0.00 0.00 0.00 3.34
1733 2282 0.099082 GCCAAACGGACAAACAACGA 59.901 50.000 0.00 0.00 0.00 3.85
1736 2285 1.433879 CGGCCAAACGGACAAACAA 59.566 52.632 2.24 0.00 0.00 2.83
1738 2287 2.354188 GCGGCCAAACGGACAAAC 60.354 61.111 2.24 0.00 0.00 2.93
1752 2301 1.536709 GCTAGATTTGGGCAATTGCGG 60.537 52.381 23.48 6.51 43.26 5.69
1753 2302 1.536709 GGCTAGATTTGGGCAATTGCG 60.537 52.381 23.48 7.97 43.26 4.85
1754 2303 1.481772 TGGCTAGATTTGGGCAATTGC 59.518 47.619 22.47 22.47 37.41 3.56
1755 2304 2.762327 ACTGGCTAGATTTGGGCAATTG 59.238 45.455 3.17 0.00 39.81 2.32
1756 2305 2.762327 CACTGGCTAGATTTGGGCAATT 59.238 45.455 3.17 0.00 39.81 2.32
1757 2306 2.381911 CACTGGCTAGATTTGGGCAAT 58.618 47.619 3.17 0.00 39.81 3.56
1811 2384 1.404035 GTAAATTTGGCTGCCTACCGG 59.596 52.381 21.03 0.00 0.00 5.28
1812 2385 2.088423 TGTAAATTTGGCTGCCTACCG 58.912 47.619 21.03 0.00 0.00 4.02
1813 2386 3.089284 AGTGTAAATTTGGCTGCCTACC 58.911 45.455 21.03 7.60 0.00 3.18
1814 2387 6.451064 AATAGTGTAAATTTGGCTGCCTAC 57.549 37.500 21.03 13.53 0.00 3.18
1815 2388 7.475137 AAAATAGTGTAAATTTGGCTGCCTA 57.525 32.000 21.03 9.91 0.00 3.93
1816 2389 6.358974 AAAATAGTGTAAATTTGGCTGCCT 57.641 33.333 21.03 0.83 0.00 4.75
2027 2601 8.972127 AGTATATGTGTACTCATCTTGTCAACT 58.028 33.333 13.44 2.65 28.99 3.16
2051 2625 9.598517 TTCAACTTCAAAATAATTTGCTTGAGT 57.401 25.926 0.00 0.00 44.52 3.41
2057 2631 9.853921 CTCAGTTTCAACTTCAAAATAATTTGC 57.146 29.630 0.00 0.00 40.48 3.68
2079 2653 7.043590 GCTAAAATGCATGATTAAGCAACTCAG 60.044 37.037 0.00 0.00 44.88 3.35
2102 2676 2.722094 AGTTCGCCCAATTTCATGCTA 58.278 42.857 0.00 0.00 0.00 3.49
2105 2679 2.412770 GCAAAGTTCGCCCAATTTCATG 59.587 45.455 0.00 0.00 0.00 3.07
2117 2691 3.040099 CCGTTAAGGTTTGCAAAGTTCG 58.960 45.455 13.26 11.21 34.51 3.95
2131 2705 3.270027 TGAGTTGATCATGCCCGTTAAG 58.730 45.455 0.00 0.00 31.12 1.85
2136 2710 1.452110 TGTTGAGTTGATCATGCCCG 58.548 50.000 0.00 0.00 37.89 6.13
2163 2742 7.659799 TCTTCGATCAAGAGTTTGGTTTTCATA 59.340 33.333 0.00 0.00 36.08 2.15
2171 2750 5.180117 ACAACATCTTCGATCAAGAGTTTGG 59.820 40.000 20.46 13.31 44.71 3.28
2194 2773 1.004277 CCGAGGATGAGCGCGATAAC 61.004 60.000 12.10 0.00 0.00 1.89
2196 2775 0.960861 ATCCGAGGATGAGCGCGATA 60.961 55.000 12.10 0.00 32.98 2.92
2200 2779 1.000163 TCTTAATCCGAGGATGAGCGC 60.000 52.381 5.25 0.00 34.70 5.92
2240 2819 1.253034 GTGCGTCTCGTCGAAATGATC 59.747 52.381 0.00 0.00 0.00 2.92
2241 2820 1.269166 GTGCGTCTCGTCGAAATGAT 58.731 50.000 0.00 0.00 0.00 2.45
2242 2821 0.039888 TGTGCGTCTCGTCGAAATGA 60.040 50.000 0.00 0.00 0.00 2.57
2243 2822 0.781787 TTGTGCGTCTCGTCGAAATG 59.218 50.000 0.00 0.00 0.00 2.32
2244 2823 0.782384 GTTGTGCGTCTCGTCGAAAT 59.218 50.000 0.00 0.00 0.00 2.17
2245 2824 0.248743 AGTTGTGCGTCTCGTCGAAA 60.249 50.000 0.00 0.00 0.00 3.46
2246 2825 0.248743 AAGTTGTGCGTCTCGTCGAA 60.249 50.000 0.00 0.00 0.00 3.71
2247 2826 0.248743 AAAGTTGTGCGTCTCGTCGA 60.249 50.000 0.00 0.00 0.00 4.20
2248 2827 0.158928 GAAAGTTGTGCGTCTCGTCG 59.841 55.000 0.00 0.00 0.00 5.12
2249 2828 1.205657 TGAAAGTTGTGCGTCTCGTC 58.794 50.000 0.00 0.00 0.00 4.20
2250 2829 1.526887 CATGAAAGTTGTGCGTCTCGT 59.473 47.619 0.00 0.00 0.00 4.18
2251 2830 1.136252 CCATGAAAGTTGTGCGTCTCG 60.136 52.381 0.00 0.00 0.00 4.04
2252 2831 1.873591 ACCATGAAAGTTGTGCGTCTC 59.126 47.619 0.00 0.00 0.00 3.36
2253 2832 1.603802 CACCATGAAAGTTGTGCGTCT 59.396 47.619 0.00 0.00 0.00 4.18
2254 2833 1.601903 TCACCATGAAAGTTGTGCGTC 59.398 47.619 0.00 0.00 0.00 5.19
2255 2834 1.674359 TCACCATGAAAGTTGTGCGT 58.326 45.000 0.00 0.00 0.00 5.24
2256 2835 2.772568 TTCACCATGAAAGTTGTGCG 57.227 45.000 0.00 0.00 32.71 5.34
2257 2836 3.779759 TGTTTCACCATGAAAGTTGTGC 58.220 40.909 4.26 0.00 45.83 4.57
2258 2837 6.907206 AAATGTTTCACCATGAAAGTTGTG 57.093 33.333 4.26 0.00 45.83 3.33
2259 2838 6.538381 GGAAAATGTTTCACCATGAAAGTTGT 59.462 34.615 4.26 0.00 45.83 3.32
2260 2839 6.538021 TGGAAAATGTTTCACCATGAAAGTTG 59.462 34.615 4.26 0.00 45.83 3.16
2261 2840 6.648192 TGGAAAATGTTTCACCATGAAAGTT 58.352 32.000 4.26 1.21 45.83 2.66
2262 2841 6.232581 TGGAAAATGTTTCACCATGAAAGT 57.767 33.333 4.26 0.00 45.83 2.66
2263 2842 7.733402 AATGGAAAATGTTTCACCATGAAAG 57.267 32.000 4.26 0.00 45.83 2.62
2264 2843 8.646004 TCTAATGGAAAATGTTTCACCATGAAA 58.354 29.630 13.73 0.00 43.37 2.69
2265 2844 8.187913 TCTAATGGAAAATGTTTCACCATGAA 57.812 30.769 13.73 0.00 37.34 2.57
2266 2845 7.093814 CCTCTAATGGAAAATGTTTCACCATGA 60.094 37.037 13.73 8.57 37.34 3.07
2267 2846 7.037438 CCTCTAATGGAAAATGTTTCACCATG 58.963 38.462 13.73 0.00 37.34 3.66
2268 2847 6.155049 CCCTCTAATGGAAAATGTTTCACCAT 59.845 38.462 0.00 0.00 38.18 3.55
2269 2848 5.480073 CCCTCTAATGGAAAATGTTTCACCA 59.520 40.000 3.35 0.00 33.49 4.17
2270 2849 5.624509 GCCCTCTAATGGAAAATGTTTCACC 60.625 44.000 3.35 0.00 0.00 4.02
2271 2850 5.047377 TGCCCTCTAATGGAAAATGTTTCAC 60.047 40.000 3.35 0.00 0.00 3.18
2272 2851 5.083122 TGCCCTCTAATGGAAAATGTTTCA 58.917 37.500 3.35 0.00 0.00 2.69
2273 2852 5.659440 TGCCCTCTAATGGAAAATGTTTC 57.341 39.130 0.00 0.00 0.00 2.78
2274 2853 5.960202 AGATGCCCTCTAATGGAAAATGTTT 59.040 36.000 0.00 0.00 30.26 2.83
2275 2854 5.522641 AGATGCCCTCTAATGGAAAATGTT 58.477 37.500 0.00 0.00 30.26 2.71
2276 2855 5.134725 AGATGCCCTCTAATGGAAAATGT 57.865 39.130 0.00 0.00 30.26 2.71
2277 2856 7.587037 TTAAGATGCCCTCTAATGGAAAATG 57.413 36.000 0.00 0.00 32.41 2.32
2278 2857 8.645110 CAATTAAGATGCCCTCTAATGGAAAAT 58.355 33.333 0.00 0.00 32.41 1.82
2279 2858 7.838696 TCAATTAAGATGCCCTCTAATGGAAAA 59.161 33.333 0.00 0.00 32.41 2.29
2280 2859 7.353525 TCAATTAAGATGCCCTCTAATGGAAA 58.646 34.615 0.00 0.00 32.41 3.13
2281 2860 6.910191 TCAATTAAGATGCCCTCTAATGGAA 58.090 36.000 0.00 0.00 32.41 3.53
2282 2861 6.101734 ACTCAATTAAGATGCCCTCTAATGGA 59.898 38.462 0.00 0.00 32.41 3.41
2283 2862 6.302269 ACTCAATTAAGATGCCCTCTAATGG 58.698 40.000 0.00 0.00 32.41 3.16
2284 2863 7.814264 AACTCAATTAAGATGCCCTCTAATG 57.186 36.000 0.00 0.00 32.41 1.90
2285 2864 8.277918 AGAAACTCAATTAAGATGCCCTCTAAT 58.722 33.333 0.00 0.00 32.41 1.73
2286 2865 7.554118 CAGAAACTCAATTAAGATGCCCTCTAA 59.446 37.037 0.00 0.00 32.41 2.10
2287 2866 7.050377 CAGAAACTCAATTAAGATGCCCTCTA 58.950 38.462 0.00 0.00 32.41 2.43
2288 2867 5.884792 CAGAAACTCAATTAAGATGCCCTCT 59.115 40.000 0.00 0.00 34.96 3.69
2289 2868 5.067023 CCAGAAACTCAATTAAGATGCCCTC 59.933 44.000 0.00 0.00 0.00 4.30
2290 2869 4.952335 CCAGAAACTCAATTAAGATGCCCT 59.048 41.667 0.00 0.00 0.00 5.19
2291 2870 4.949856 TCCAGAAACTCAATTAAGATGCCC 59.050 41.667 0.00 0.00 0.00 5.36
2292 2871 6.071952 TGTTCCAGAAACTCAATTAAGATGCC 60.072 38.462 0.00 0.00 38.76 4.40
2293 2872 6.803807 GTGTTCCAGAAACTCAATTAAGATGC 59.196 38.462 0.00 0.00 38.76 3.91
2294 2873 7.017645 CGTGTTCCAGAAACTCAATTAAGATG 58.982 38.462 0.00 0.00 38.76 2.90
2295 2874 6.934645 TCGTGTTCCAGAAACTCAATTAAGAT 59.065 34.615 0.00 0.00 38.76 2.40
2296 2875 6.285224 TCGTGTTCCAGAAACTCAATTAAGA 58.715 36.000 0.00 0.00 38.76 2.10
2297 2876 6.423905 TCTCGTGTTCCAGAAACTCAATTAAG 59.576 38.462 0.00 0.00 38.76 1.85
2298 2877 6.285224 TCTCGTGTTCCAGAAACTCAATTAA 58.715 36.000 0.00 0.00 38.76 1.40
2299 2878 5.849510 TCTCGTGTTCCAGAAACTCAATTA 58.150 37.500 0.00 0.00 38.76 1.40
2300 2879 4.703897 TCTCGTGTTCCAGAAACTCAATT 58.296 39.130 0.00 0.00 38.76 2.32
2301 2880 4.310769 CTCTCGTGTTCCAGAAACTCAAT 58.689 43.478 0.00 0.00 38.76 2.57
2302 2881 3.492656 CCTCTCGTGTTCCAGAAACTCAA 60.493 47.826 0.00 0.00 38.76 3.02
2303 2882 2.035961 CCTCTCGTGTTCCAGAAACTCA 59.964 50.000 0.00 0.00 38.76 3.41
2304 2883 2.296471 TCCTCTCGTGTTCCAGAAACTC 59.704 50.000 0.00 0.00 38.76 3.01
2305 2884 2.297597 CTCCTCTCGTGTTCCAGAAACT 59.702 50.000 0.00 0.00 38.76 2.66
2306 2885 2.610727 CCTCCTCTCGTGTTCCAGAAAC 60.611 54.545 0.00 0.00 38.43 2.78
2307 2886 1.618837 CCTCCTCTCGTGTTCCAGAAA 59.381 52.381 0.00 0.00 0.00 2.52
2308 2887 1.257743 CCTCCTCTCGTGTTCCAGAA 58.742 55.000 0.00 0.00 0.00 3.02
2309 2888 1.251527 GCCTCCTCTCGTGTTCCAGA 61.252 60.000 0.00 0.00 0.00 3.86
2310 2889 1.216710 GCCTCCTCTCGTGTTCCAG 59.783 63.158 0.00 0.00 0.00 3.86
2311 2890 2.283529 GGCCTCCTCTCGTGTTCCA 61.284 63.158 0.00 0.00 0.00 3.53
2312 2891 1.985116 AGGCCTCCTCTCGTGTTCC 60.985 63.158 0.00 0.00 0.00 3.62
2313 2892 1.216710 CAGGCCTCCTCTCGTGTTC 59.783 63.158 0.00 0.00 0.00 3.18
2314 2893 1.534235 ACAGGCCTCCTCTCGTGTT 60.534 57.895 0.00 0.00 0.00 3.32
2315 2894 2.118513 ACAGGCCTCCTCTCGTGT 59.881 61.111 0.00 0.00 0.00 4.49
2316 2895 2.575993 CACAGGCCTCCTCTCGTG 59.424 66.667 0.00 2.62 0.00 4.35
2317 2896 2.681778 CCACAGGCCTCCTCTCGT 60.682 66.667 0.00 0.00 0.00 4.18
2318 2897 3.465403 CCCACAGGCCTCCTCTCG 61.465 72.222 0.00 0.00 0.00 4.04
2319 2898 3.086600 CCCCACAGGCCTCCTCTC 61.087 72.222 0.00 0.00 0.00 3.20
2332 2911 0.986019 CTGGTGTATAGTGGGCCCCA 60.986 60.000 22.27 0.00 0.00 4.96
2333 2912 1.705997 CCTGGTGTATAGTGGGCCCC 61.706 65.000 22.27 11.17 0.00 5.80
2334 2913 1.705997 CCCTGGTGTATAGTGGGCCC 61.706 65.000 17.59 17.59 0.00 5.80
2335 2914 1.837090 CCCTGGTGTATAGTGGGCC 59.163 63.158 0.00 0.00 0.00 5.80
2337 2916 0.180406 GTGCCCTGGTGTATAGTGGG 59.820 60.000 0.00 0.00 40.74 4.61
2338 2917 0.179084 CGTGCCCTGGTGTATAGTGG 60.179 60.000 0.00 0.00 0.00 4.00
2339 2918 0.810031 GCGTGCCCTGGTGTATAGTG 60.810 60.000 0.00 0.00 0.00 2.74
2340 2919 1.520666 GCGTGCCCTGGTGTATAGT 59.479 57.895 0.00 0.00 0.00 2.12
2341 2920 1.227556 GGCGTGCCCTGGTGTATAG 60.228 63.158 0.00 0.00 0.00 1.31
2342 2921 1.966901 CTGGCGTGCCCTGGTGTATA 61.967 60.000 8.69 0.00 34.56 1.47
2343 2922 3.326578 TGGCGTGCCCTGGTGTAT 61.327 61.111 8.69 0.00 34.56 2.29
2344 2923 4.015406 CTGGCGTGCCCTGGTGTA 62.015 66.667 8.69 0.00 34.56 2.90
2377 2956 2.757124 GGCCCCACTACCCATCAGG 61.757 68.421 0.00 0.00 43.78 3.86
2378 2957 2.757124 GGGCCCCACTACCCATCAG 61.757 68.421 12.23 0.00 46.22 2.90
2379 2958 2.694616 GGGCCCCACTACCCATCA 60.695 66.667 12.23 0.00 46.22 3.07
2400 2979 4.366684 CTGGGTCAAGGGGGTGCC 62.367 72.222 0.00 0.00 0.00 5.01
2402 2981 3.260100 AGCTGGGTCAAGGGGGTG 61.260 66.667 0.00 0.00 0.00 4.61
2403 2982 2.936032 GAGCTGGGTCAAGGGGGT 60.936 66.667 0.00 0.00 0.00 4.95
2404 2983 3.732849 GGAGCTGGGTCAAGGGGG 61.733 72.222 0.00 0.00 0.00 5.40
2405 2984 4.101448 CGGAGCTGGGTCAAGGGG 62.101 72.222 0.00 0.00 0.00 4.79
2418 2997 6.600882 TTTAGGGTATTTATAGAGGCGGAG 57.399 41.667 0.00 0.00 0.00 4.63
2419 2998 6.999705 TTTTAGGGTATTTATAGAGGCGGA 57.000 37.500 0.00 0.00 0.00 5.54
2420 2999 6.822170 GGATTTTAGGGTATTTATAGAGGCGG 59.178 42.308 0.00 0.00 0.00 6.13
2421 3000 6.822170 GGGATTTTAGGGTATTTATAGAGGCG 59.178 42.308 0.00 0.00 0.00 5.52
2422 3001 7.696017 TGGGATTTTAGGGTATTTATAGAGGC 58.304 38.462 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.