Multiple sequence alignment - TraesCS3B01G151300

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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 TraesCS3B01G151300 chr3B 100.000 3555 0 0 1 3555 142728277 142731831 0.000000e+00 6565.0
1 TraesCS3B01G151300 chr3B 79.141 163 22 9 1102 1258 466297169 466297325 6.280000e-18 102.0
2 TraesCS3B01G151300 chr3D 93.434 929 24 14 900 1791 93361474 93360546 0.000000e+00 1343.0
3 TraesCS3B01G151300 chr3D 91.516 884 45 16 1880 2754 93360491 93359629 0.000000e+00 1190.0
4 TraesCS3B01G151300 chr3D 88.679 477 42 10 431 896 93362046 93361571 3.980000e-159 571.0
5 TraesCS3B01G151300 chr3D 86.836 433 49 6 1 429 93363625 93363197 8.930000e-131 477.0
6 TraesCS3B01G151300 chr3D 81.690 142 20 5 3 141 93363773 93363635 2.900000e-21 113.0
7 TraesCS3B01G151300 chr3A 92.779 914 30 15 900 1777 546597983 546598896 0.000000e+00 1290.0
8 TraesCS3B01G151300 chr3A 92.963 810 34 7 1881 2683 546598920 546599713 0.000000e+00 1158.0
9 TraesCS3B01G151300 chr3A 85.635 905 64 15 1 884 546597025 546597884 0.000000e+00 891.0
10 TraesCS3B01G151300 chr3A 87.540 618 66 9 2937 3547 742609693 742609080 0.000000e+00 704.0
11 TraesCS3B01G151300 chr3A 90.909 99 8 1 1777 1874 228579109 228579011 8.010000e-27 132.0
12 TraesCS3B01G151300 chr3A 79.141 163 22 9 1102 1258 479781192 479781348 6.280000e-18 102.0
13 TraesCS3B01G151300 chr4D 91.974 623 48 2 2934 3555 40175966 40176587 0.000000e+00 872.0
14 TraesCS3B01G151300 chr4D 90.909 99 6 3 1778 1874 19689988 19689891 2.880000e-26 130.0
15 TraesCS3B01G151300 chr7D 89.068 622 59 6 2935 3554 91115995 91115381 0.000000e+00 763.0
16 TraesCS3B01G151300 chr7D 96.629 89 2 1 1790 1877 159658149 159658061 2.860000e-31 147.0
17 TraesCS3B01G151300 chr7D 75.796 157 32 6 1094 1247 541494837 541494990 1.370000e-09 75.0
18 TraesCS3B01G151300 chr2D 88.853 619 66 3 2939 3555 337502653 337502036 0.000000e+00 758.0
19 TraesCS3B01G151300 chr2D 96.591 88 3 0 1787 1874 475134422 475134509 2.860000e-31 147.0
20 TraesCS3B01G151300 chr2D 94.624 93 5 0 1782 1874 207410665 207410757 1.030000e-30 145.0
21 TraesCS3B01G151300 chr1B 88.443 623 59 9 2936 3555 162306730 162307342 0.000000e+00 739.0
22 TraesCS3B01G151300 chr1B 95.604 91 3 1 1785 1874 371456333 371456423 1.030000e-30 145.0
23 TraesCS3B01G151300 chr7B 87.722 619 62 10 2932 3547 535452137 535452744 0.000000e+00 710.0
24 TraesCS3B01G151300 chr5A 87.480 623 65 8 2935 3555 103901567 103900956 0.000000e+00 706.0
25 TraesCS3B01G151300 chr5A 95.604 91 3 1 1786 1876 444563048 444563137 1.030000e-30 145.0
26 TraesCS3B01G151300 chr5D 87.159 623 70 7 2928 3548 432766921 432767535 0.000000e+00 699.0
27 TraesCS3B01G151300 chr5D 89.796 98 8 2 1778 1874 229934118 229934214 1.340000e-24 124.0
28 TraesCS3B01G151300 chr1A 87.154 615 73 6 2934 3547 124182407 124183016 0.000000e+00 693.0
29 TraesCS3B01G151300 chrUn 94.737 95 5 0 1787 1881 19198134 19198228 7.950000e-32 148.0
30 TraesCS3B01G151300 chr6D 94.624 93 5 0 1782 1874 157328017 157328109 1.030000e-30 145.0
31 TraesCS3B01G151300 chr6D 87.838 74 4 5 1621 1692 269741014 269741084 8.180000e-12 82.4
32 TraesCS3B01G151300 chr2B 94.565 92 5 0 1783 1874 135374768 135374677 3.700000e-30 143.0
33 TraesCS3B01G151300 chr2B 84.127 126 17 3 1763 1887 470530711 470530834 6.230000e-23 119.0
34 TraesCS3B01G151300 chr1D 94.565 92 4 1 1785 1875 225701729 225701820 1.330000e-29 141.0
35 TraesCS3B01G151300 chr1D 90.426 94 6 3 1778 1869 272923322 272923230 1.730000e-23 121.0
36 TraesCS3B01G151300 chr7A 90.000 100 10 0 1775 1874 9539671 9539770 2.880000e-26 130.0
37 TraesCS3B01G151300 chr2A 86.667 105 10 4 1777 1879 721607958 721607856 2.900000e-21 113.0
38 TraesCS3B01G151300 chr4A 86.139 101 14 0 1775 1875 285490002 285490102 3.750000e-20 110.0
39 TraesCS3B01G151300 chr4A 85.577 104 13 2 1778 1879 581294457 581294560 1.350000e-19 108.0
40 TraesCS3B01G151300 chr6B 87.671 73 4 5 1622 1692 422353625 422353694 2.940000e-11 80.5
41 TraesCS3B01G151300 chr6A 87.671 73 4 5 1622 1692 383974776 383974845 2.940000e-11 80.5
42 TraesCS3B01G151300 chr5B 96.970 33 1 0 1405 1437 576249625 576249657 4.960000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G151300 chr3B 142728277 142731831 3554 False 6565.0 6565 100.000 1 3555 1 chr3B.!!$F1 3554
1 TraesCS3B01G151300 chr3D 93359629 93363773 4144 True 738.8 1343 88.431 1 2754 5 chr3D.!!$R1 2753
2 TraesCS3B01G151300 chr3A 546597025 546599713 2688 False 1113.0 1290 90.459 1 2683 3 chr3A.!!$F2 2682
3 TraesCS3B01G151300 chr3A 742609080 742609693 613 True 704.0 704 87.540 2937 3547 1 chr3A.!!$R2 610
4 TraesCS3B01G151300 chr4D 40175966 40176587 621 False 872.0 872 91.974 2934 3555 1 chr4D.!!$F1 621
5 TraesCS3B01G151300 chr7D 91115381 91115995 614 True 763.0 763 89.068 2935 3554 1 chr7D.!!$R1 619
6 TraesCS3B01G151300 chr2D 337502036 337502653 617 True 758.0 758 88.853 2939 3555 1 chr2D.!!$R1 616
7 TraesCS3B01G151300 chr1B 162306730 162307342 612 False 739.0 739 88.443 2936 3555 1 chr1B.!!$F1 619
8 TraesCS3B01G151300 chr7B 535452137 535452744 607 False 710.0 710 87.722 2932 3547 1 chr7B.!!$F1 615
9 TraesCS3B01G151300 chr5A 103900956 103901567 611 True 706.0 706 87.480 2935 3555 1 chr5A.!!$R1 620
10 TraesCS3B01G151300 chr5D 432766921 432767535 614 False 699.0 699 87.159 2928 3548 1 chr5D.!!$F2 620
11 TraesCS3B01G151300 chr1A 124182407 124183016 609 False 693.0 693 87.154 2934 3547 1 chr1A.!!$F1 613

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
731 2052 0.692476 TAGGTCTTGCAGTGTGCCAT 59.308 50.0 0.00 0.0 44.23 4.40 F
1048 2483 0.322008 CCTCCTGACCTTGGTCTTGC 60.322 60.0 19.11 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 3705 0.037232 GAGGTTCCTGACGTCTTGGG 60.037 60.0 17.92 15.45 39.48 4.12 R
2804 4295 0.038251 CGTGTGGCAAGCTGAGAGTA 60.038 55.0 0.00 0.00 0.00 2.59 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
153 302 6.875948 GACAAAATTTGGCCAATAAAAGGT 57.124 33.333 21.26 13.49 30.38 3.50
163 312 2.352323 CCAATAAAAGGTTGACGTGGGC 60.352 50.000 0.00 0.00 0.00 5.36
174 323 2.509336 CGTGGGCGCTTACTGGAG 60.509 66.667 7.64 0.00 0.00 3.86
206 355 1.226030 CGGTCAACGGGTCAAACCTC 61.226 60.000 0.00 0.00 38.64 3.85
249 402 1.299939 GGGAGGGAAGGGTTGAATCT 58.700 55.000 0.00 0.00 0.00 2.40
340 499 6.403092 GCCCATTTTGAAAATACCATTTTCCG 60.403 38.462 17.36 5.48 37.55 4.30
346 505 5.566469 TGAAAATACCATTTTCCGGAGAGT 58.434 37.500 17.36 0.00 37.55 3.24
349 508 6.997239 AAATACCATTTTCCGGAGAGTAAC 57.003 37.500 3.34 0.00 0.00 2.50
350 509 2.968675 ACCATTTTCCGGAGAGTAACG 58.031 47.619 3.34 0.00 0.00 3.18
433 1743 8.914328 TCATAACGATTAACTTTCATACGTGA 57.086 30.769 0.00 0.00 33.05 4.35
438 1748 6.801377 ACGATTAACTTTCATACGTGACGTAA 59.199 34.615 22.28 4.69 45.39 3.18
448 1758 7.410800 TCATACGTGACGTAAACAAAAAGAT 57.589 32.000 22.28 0.00 45.39 2.40
557 1871 6.076607 CGAAAAATTACAGATCAATCGCGAAC 60.077 38.462 15.24 2.59 0.00 3.95
684 2005 4.893241 CGTTGCAACGTGGACTTC 57.107 55.556 37.16 5.85 46.63 3.01
693 2014 3.251004 GCAACGTGGACTTCTCTCATTTT 59.749 43.478 0.00 0.00 0.00 1.82
731 2052 0.692476 TAGGTCTTGCAGTGTGCCAT 59.308 50.000 0.00 0.00 44.23 4.40
834 2162 1.201647 CAACAAGCTCTTGGCCTCATG 59.798 52.381 3.32 0.00 44.45 3.07
873 2201 1.028868 GCAGTCCACCTGATTCAGCC 61.029 60.000 8.23 0.00 44.49 4.85
888 2216 4.617875 GCCGAAGCTTAGCTCCAA 57.382 55.556 7.36 0.00 38.25 3.53
893 2221 2.427506 CGAAGCTTAGCTCCAAAACCT 58.572 47.619 7.36 0.00 38.25 3.50
896 2224 4.324267 GAAGCTTAGCTCCAAAACCTACA 58.676 43.478 7.36 0.00 38.25 2.74
897 2225 3.944087 AGCTTAGCTCCAAAACCTACAG 58.056 45.455 0.00 0.00 30.62 2.74
898 2226 2.420372 GCTTAGCTCCAAAACCTACAGC 59.580 50.000 0.00 0.00 0.00 4.40
924 2345 5.941788 AGTACATAAGAAATCATCCCACCC 58.058 41.667 0.00 0.00 0.00 4.61
977 2401 4.323333 CCTGACAACACATCCAGATCTTCT 60.323 45.833 0.00 0.00 0.00 2.85
978 2402 5.105187 CCTGACAACACATCCAGATCTTCTA 60.105 44.000 0.00 0.00 0.00 2.10
1048 2483 0.322008 CCTCCTGACCTTGGTCTTGC 60.322 60.000 19.11 0.00 0.00 4.01
1276 2711 0.617935 GCCAAGCTTCTCCTCTTCCT 59.382 55.000 0.00 0.00 0.00 3.36
1334 2778 0.456312 CGAGACGAGTTTTCTCCGGG 60.456 60.000 0.00 0.00 43.49 5.73
1471 2915 2.125552 TCCTGCAGAACGCCATCG 60.126 61.111 17.39 0.00 41.33 3.84
1615 3090 4.020218 TCTGCTTACTCCTGCTGTGTTTAT 60.020 41.667 0.00 0.00 0.00 1.40
1688 3163 1.622232 GGAACGACTACAACTACGCC 58.378 55.000 0.00 0.00 0.00 5.68
1772 3247 2.251642 GGACGTCGCAAAGGCAAGT 61.252 57.895 9.92 0.00 41.24 3.16
1787 3262 3.492102 GCAAGTGGCATCCCTTAGATA 57.508 47.619 0.00 0.00 43.97 1.98
1791 3266 5.412904 GCAAGTGGCATCCCTTAGATATTAC 59.587 44.000 0.00 0.00 43.97 1.89
1792 3267 6.745474 GCAAGTGGCATCCCTTAGATATTACT 60.745 42.308 0.00 0.00 43.97 2.24
1793 3268 6.613153 AGTGGCATCCCTTAGATATTACTC 57.387 41.667 0.00 0.00 32.37 2.59
1794 3269 5.485708 AGTGGCATCCCTTAGATATTACTCC 59.514 44.000 0.00 0.00 32.37 3.85
1795 3270 4.783227 TGGCATCCCTTAGATATTACTCCC 59.217 45.833 0.00 0.00 32.37 4.30
1796 3271 5.033522 GGCATCCCTTAGATATTACTCCCT 58.966 45.833 0.00 0.00 32.37 4.20
1797 3272 5.129650 GGCATCCCTTAGATATTACTCCCTC 59.870 48.000 0.00 0.00 32.37 4.30
1798 3273 5.129650 GCATCCCTTAGATATTACTCCCTCC 59.870 48.000 0.00 0.00 32.37 4.30
1799 3274 4.931914 TCCCTTAGATATTACTCCCTCCG 58.068 47.826 0.00 0.00 0.00 4.63
1800 3275 4.356190 TCCCTTAGATATTACTCCCTCCGT 59.644 45.833 0.00 0.00 0.00 4.69
1801 3276 5.553162 TCCCTTAGATATTACTCCCTCCGTA 59.447 44.000 0.00 0.00 0.00 4.02
1802 3277 6.045931 TCCCTTAGATATTACTCCCTCCGTAA 59.954 42.308 0.00 0.00 0.00 3.18
1803 3278 6.723052 CCCTTAGATATTACTCCCTCCGTAAA 59.277 42.308 0.00 0.00 31.36 2.01
1804 3279 7.309683 CCCTTAGATATTACTCCCTCCGTAAAC 60.310 44.444 0.00 0.00 31.36 2.01
1805 3280 7.450944 CCTTAGATATTACTCCCTCCGTAAACT 59.549 40.741 0.00 0.00 31.36 2.66
1806 3281 9.512588 CTTAGATATTACTCCCTCCGTAAACTA 57.487 37.037 0.00 0.00 31.36 2.24
1808 3283 8.953223 AGATATTACTCCCTCCGTAAACTAAT 57.047 34.615 0.00 0.00 31.36 1.73
1816 3291 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
1817 3292 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
1818 3293 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
1819 3294 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
1899 3376 2.096218 GCAATCAATCGATCTAACCCGC 60.096 50.000 0.00 0.00 0.00 6.13
1917 3394 1.360931 GCACGGGCATTTGCATTTCC 61.361 55.000 3.77 0.00 44.36 3.13
1924 3401 2.485038 GGCATTTGCATTTCCTTGGTTG 59.515 45.455 4.74 0.00 44.36 3.77
1925 3402 2.095617 GCATTTGCATTTCCTTGGTTGC 60.096 45.455 0.00 0.00 41.59 4.17
1926 3403 3.404899 CATTTGCATTTCCTTGGTTGCT 58.595 40.909 0.00 0.00 36.10 3.91
1927 3404 2.818130 TTGCATTTCCTTGGTTGCTC 57.182 45.000 0.00 0.00 36.10 4.26
1928 3405 1.702182 TGCATTTCCTTGGTTGCTCA 58.298 45.000 11.07 0.00 36.10 4.26
2200 3677 4.680537 ACCTCCTCGACCACGCCT 62.681 66.667 0.00 0.00 39.58 5.52
2214 3691 1.034292 ACGCCTCCGTCCTAGGTAAC 61.034 60.000 9.08 0.00 46.39 2.50
2216 3693 0.685458 GCCTCCGTCCTAGGTAACCA 60.685 60.000 9.08 0.00 36.43 3.67
2228 3705 6.594547 GTCCTAGGTAACCAATCAAAGTTCTC 59.405 42.308 9.08 0.00 37.17 2.87
2257 3734 0.605589 CAGGAACCTCAACGAGAGCT 59.394 55.000 0.00 0.00 43.31 4.09
2273 3750 3.753434 CTGAGAGCTGACCCGCGT 61.753 66.667 4.92 0.00 34.40 6.01
2274 3751 3.978723 CTGAGAGCTGACCCGCGTG 62.979 68.421 4.92 0.00 34.40 5.34
2461 3938 2.662596 GACGGCATCCACCTCACA 59.337 61.111 0.00 0.00 0.00 3.58
2509 3986 2.092914 GTCGATCCTCATGGAAGGGTTT 60.093 50.000 0.82 0.00 46.80 3.27
2536 4013 3.127533 GCCGAAAGCGTGCAGGAT 61.128 61.111 11.29 0.00 34.99 3.24
2551 4028 2.680221 GCAGGATATATGGAGCTGCTGG 60.680 54.545 7.01 0.00 34.04 4.85
2557 4034 3.977134 ATATGGAGCTGCTGGTGATAG 57.023 47.619 7.01 0.00 0.00 2.08
2587 4071 3.110178 GCGCGCGTTGTTCTAGGT 61.110 61.111 32.35 0.00 0.00 3.08
2667 4152 1.203994 GCTTGCAAATGTCAGCTCCAT 59.796 47.619 0.00 0.00 0.00 3.41
2692 4183 3.191791 TCGGTTACGATCACACAATCTCA 59.808 43.478 0.00 0.00 45.59 3.27
2701 4192 1.741706 CACACAATCTCACAGCATCCC 59.258 52.381 0.00 0.00 0.00 3.85
2703 4194 2.286872 CACAATCTCACAGCATCCCTC 58.713 52.381 0.00 0.00 0.00 4.30
2710 4201 1.280133 TCACAGCATCCCTCTTCTTGG 59.720 52.381 0.00 0.00 0.00 3.61
2722 4213 4.649218 CCCTCTTCTTGGTTTCCTTGAAAA 59.351 41.667 0.00 0.00 33.14 2.29
2723 4214 5.305386 CCCTCTTCTTGGTTTCCTTGAAAAT 59.695 40.000 0.00 0.00 33.14 1.82
2735 4226 4.151883 TCCTTGAAAATATAGGGCCATGC 58.848 43.478 6.18 0.00 0.00 4.06
2736 4227 9.777173 GTTTCCTTGAAAATATAGGGCCATGCC 62.777 44.444 6.18 0.00 39.55 4.40
2754 4245 6.735694 GCCATGCCTTAATTTATCGTTCACAT 60.736 38.462 0.00 0.00 0.00 3.21
2755 4246 6.638063 CCATGCCTTAATTTATCGTTCACATG 59.362 38.462 0.00 0.00 0.00 3.21
2756 4247 5.577835 TGCCTTAATTTATCGTTCACATGC 58.422 37.500 0.00 0.00 0.00 4.06
2757 4248 4.976116 GCCTTAATTTATCGTTCACATGCC 59.024 41.667 0.00 0.00 0.00 4.40
2758 4249 5.449862 GCCTTAATTTATCGTTCACATGCCA 60.450 40.000 0.00 0.00 0.00 4.92
2759 4250 6.201517 CCTTAATTTATCGTTCACATGCCAG 58.798 40.000 0.00 0.00 0.00 4.85
2760 4251 4.637483 AATTTATCGTTCACATGCCAGG 57.363 40.909 0.00 0.00 0.00 4.45
2761 4252 1.378531 TTATCGTTCACATGCCAGGC 58.621 50.000 3.66 3.66 0.00 4.85
2762 4253 0.809636 TATCGTTCACATGCCAGGCG 60.810 55.000 7.03 0.00 0.00 5.52
2763 4254 3.803082 CGTTCACATGCCAGGCGG 61.803 66.667 7.03 3.91 0.00 6.13
2764 4255 2.672996 GTTCACATGCCAGGCGGT 60.673 61.111 7.03 4.66 33.28 5.68
2765 4256 2.672651 TTCACATGCCAGGCGGTG 60.673 61.111 23.76 23.76 37.64 4.94
2789 4280 2.508439 CGGTGCGCGTTGTAGGAT 60.508 61.111 8.43 0.00 0.00 3.24
2790 4281 2.798501 CGGTGCGCGTTGTAGGATG 61.799 63.158 8.43 0.00 0.00 3.51
2791 4282 2.399611 GTGCGCGTTGTAGGATGC 59.600 61.111 8.43 0.00 0.00 3.91
2792 4283 2.100631 GTGCGCGTTGTAGGATGCT 61.101 57.895 8.43 0.00 0.00 3.79
2793 4284 1.375396 TGCGCGTTGTAGGATGCTT 60.375 52.632 8.43 0.00 0.00 3.91
2794 4285 0.108567 TGCGCGTTGTAGGATGCTTA 60.109 50.000 8.43 0.00 0.00 3.09
2795 4286 1.003851 GCGCGTTGTAGGATGCTTAA 58.996 50.000 8.43 0.00 0.00 1.85
2796 4287 1.395608 GCGCGTTGTAGGATGCTTAAA 59.604 47.619 8.43 0.00 0.00 1.52
2797 4288 2.786700 GCGCGTTGTAGGATGCTTAAAC 60.787 50.000 8.43 0.00 0.00 2.01
2798 4289 2.222953 CGCGTTGTAGGATGCTTAAACC 60.223 50.000 0.00 0.00 0.00 3.27
2799 4290 3.007635 GCGTTGTAGGATGCTTAAACCT 58.992 45.455 0.00 0.00 37.76 3.50
2800 4291 3.181510 GCGTTGTAGGATGCTTAAACCTG 60.182 47.826 0.00 0.00 35.52 4.00
2801 4292 4.000988 CGTTGTAGGATGCTTAAACCTGT 58.999 43.478 0.00 0.00 35.52 4.00
2802 4293 4.454504 CGTTGTAGGATGCTTAAACCTGTT 59.545 41.667 0.00 0.00 35.52 3.16
2803 4294 5.616866 CGTTGTAGGATGCTTAAACCTGTTG 60.617 44.000 0.00 0.00 35.52 3.33
2804 4295 4.980573 TGTAGGATGCTTAAACCTGTTGT 58.019 39.130 0.00 0.00 35.52 3.32
2805 4296 6.116711 TGTAGGATGCTTAAACCTGTTGTA 57.883 37.500 0.00 0.00 35.52 2.41
2806 4297 5.935789 TGTAGGATGCTTAAACCTGTTGTAC 59.064 40.000 0.00 0.00 35.52 2.90
2807 4298 5.242795 AGGATGCTTAAACCTGTTGTACT 57.757 39.130 0.00 0.00 32.39 2.73
2808 4299 5.246307 AGGATGCTTAAACCTGTTGTACTC 58.754 41.667 0.00 0.00 32.39 2.59
2809 4300 5.013183 AGGATGCTTAAACCTGTTGTACTCT 59.987 40.000 0.00 0.00 32.39 3.24
2810 4301 5.351740 GGATGCTTAAACCTGTTGTACTCTC 59.648 44.000 0.00 0.00 0.00 3.20
2811 4302 5.284861 TGCTTAAACCTGTTGTACTCTCA 57.715 39.130 0.00 0.00 0.00 3.27
2812 4303 5.297547 TGCTTAAACCTGTTGTACTCTCAG 58.702 41.667 0.00 0.33 0.00 3.35
2813 4304 4.152580 GCTTAAACCTGTTGTACTCTCAGC 59.847 45.833 0.00 0.00 0.00 4.26
2814 4305 5.542779 CTTAAACCTGTTGTACTCTCAGCT 58.457 41.667 0.00 0.00 0.00 4.24
2815 4306 4.423625 AAACCTGTTGTACTCTCAGCTT 57.576 40.909 0.00 0.00 0.00 3.74
2816 4307 3.393089 ACCTGTTGTACTCTCAGCTTG 57.607 47.619 0.00 0.00 0.00 4.01
2817 4308 2.072298 CCTGTTGTACTCTCAGCTTGC 58.928 52.381 0.00 0.00 0.00 4.01
2818 4309 2.072298 CTGTTGTACTCTCAGCTTGCC 58.928 52.381 0.00 0.00 0.00 4.52
2819 4310 1.416030 TGTTGTACTCTCAGCTTGCCA 59.584 47.619 0.00 0.00 0.00 4.92
2820 4311 1.801178 GTTGTACTCTCAGCTTGCCAC 59.199 52.381 0.00 0.00 0.00 5.01
2821 4312 1.047801 TGTACTCTCAGCTTGCCACA 58.952 50.000 0.00 0.00 0.00 4.17
2822 4313 1.270305 TGTACTCTCAGCTTGCCACAC 60.270 52.381 0.00 0.00 0.00 3.82
2823 4314 0.038251 TACTCTCAGCTTGCCACACG 60.038 55.000 0.00 0.00 0.00 4.49
2824 4315 2.031012 TCTCAGCTTGCCACACGG 59.969 61.111 0.00 0.00 0.00 4.94
2825 4316 3.052082 CTCAGCTTGCCACACGGG 61.052 66.667 0.00 0.00 40.85 5.28
2826 4317 4.641645 TCAGCTTGCCACACGGGG 62.642 66.667 0.00 0.00 37.04 5.73
2841 4332 4.724262 GGGGGCTTCTTGAGTCAC 57.276 61.111 0.00 0.00 30.48 3.67
2842 4333 2.070639 GGGGGCTTCTTGAGTCACT 58.929 57.895 0.00 0.00 32.53 3.41
2843 4334 0.322008 GGGGGCTTCTTGAGTCACTG 60.322 60.000 0.00 0.00 32.53 3.66
2844 4335 0.322008 GGGGCTTCTTGAGTCACTGG 60.322 60.000 0.00 0.00 28.01 4.00
2845 4336 0.398318 GGGCTTCTTGAGTCACTGGT 59.602 55.000 0.00 0.00 0.00 4.00
2846 4337 1.202818 GGGCTTCTTGAGTCACTGGTT 60.203 52.381 0.00 0.00 0.00 3.67
2847 4338 2.576615 GGCTTCTTGAGTCACTGGTTT 58.423 47.619 0.00 0.00 0.00 3.27
2848 4339 3.496160 GGGCTTCTTGAGTCACTGGTTTA 60.496 47.826 0.00 0.00 0.00 2.01
2849 4340 3.748568 GGCTTCTTGAGTCACTGGTTTAG 59.251 47.826 0.00 0.00 0.00 1.85
2850 4341 4.503296 GGCTTCTTGAGTCACTGGTTTAGA 60.503 45.833 0.00 0.00 0.00 2.10
2851 4342 5.241662 GCTTCTTGAGTCACTGGTTTAGAT 58.758 41.667 0.00 0.00 0.00 1.98
2852 4343 5.121454 GCTTCTTGAGTCACTGGTTTAGATG 59.879 44.000 0.00 0.00 0.00 2.90
2853 4344 6.419484 TTCTTGAGTCACTGGTTTAGATGA 57.581 37.500 0.00 0.00 0.00 2.92
2854 4345 6.611613 TCTTGAGTCACTGGTTTAGATGAT 57.388 37.500 0.00 0.00 0.00 2.45
2855 4346 6.401394 TCTTGAGTCACTGGTTTAGATGATG 58.599 40.000 0.00 0.00 0.00 3.07
2856 4347 5.745312 TGAGTCACTGGTTTAGATGATGT 57.255 39.130 0.00 0.00 0.00 3.06
2857 4348 6.114187 TGAGTCACTGGTTTAGATGATGTT 57.886 37.500 0.00 0.00 0.00 2.71
2858 4349 6.533730 TGAGTCACTGGTTTAGATGATGTTT 58.466 36.000 0.00 0.00 0.00 2.83
2859 4350 6.427853 TGAGTCACTGGTTTAGATGATGTTTG 59.572 38.462 0.00 0.00 0.00 2.93
2860 4351 6.299141 AGTCACTGGTTTAGATGATGTTTGT 58.701 36.000 0.00 0.00 0.00 2.83
2861 4352 6.772716 AGTCACTGGTTTAGATGATGTTTGTT 59.227 34.615 0.00 0.00 0.00 2.83
2862 4353 6.857964 GTCACTGGTTTAGATGATGTTTGTTG 59.142 38.462 0.00 0.00 0.00 3.33
2863 4354 6.770303 TCACTGGTTTAGATGATGTTTGTTGA 59.230 34.615 0.00 0.00 0.00 3.18
2864 4355 7.448161 TCACTGGTTTAGATGATGTTTGTTGAT 59.552 33.333 0.00 0.00 0.00 2.57
2865 4356 7.539710 CACTGGTTTAGATGATGTTTGTTGATG 59.460 37.037 0.00 0.00 0.00 3.07
2866 4357 6.389091 TGGTTTAGATGATGTTTGTTGATGC 58.611 36.000 0.00 0.00 0.00 3.91
2867 4358 5.512788 GGTTTAGATGATGTTTGTTGATGCG 59.487 40.000 0.00 0.00 0.00 4.73
2868 4359 6.314018 GTTTAGATGATGTTTGTTGATGCGA 58.686 36.000 0.00 0.00 0.00 5.10
2869 4360 6.682423 TTAGATGATGTTTGTTGATGCGAT 57.318 33.333 0.00 0.00 0.00 4.58
2870 4361 5.165911 AGATGATGTTTGTTGATGCGATC 57.834 39.130 0.00 0.00 0.00 3.69
2871 4362 4.637091 AGATGATGTTTGTTGATGCGATCA 59.363 37.500 0.00 0.00 37.55 2.92
2872 4363 4.345271 TGATGTTTGTTGATGCGATCAG 57.655 40.909 0.00 0.00 40.94 2.90
2873 4364 3.127376 TGATGTTTGTTGATGCGATCAGG 59.873 43.478 0.00 0.00 40.94 3.86
2874 4365 2.777094 TGTTTGTTGATGCGATCAGGA 58.223 42.857 0.00 0.00 40.94 3.86
2875 4366 3.346315 TGTTTGTTGATGCGATCAGGAT 58.654 40.909 0.00 0.00 40.94 3.24
2876 4367 4.512484 TGTTTGTTGATGCGATCAGGATA 58.488 39.130 0.00 0.00 40.94 2.59
2877 4368 5.125356 TGTTTGTTGATGCGATCAGGATAT 58.875 37.500 0.00 0.00 40.94 1.63
2878 4369 6.287525 TGTTTGTTGATGCGATCAGGATATA 58.712 36.000 0.00 0.00 40.94 0.86
2879 4370 6.936335 TGTTTGTTGATGCGATCAGGATATAT 59.064 34.615 0.00 0.00 40.94 0.86
2880 4371 7.118245 TGTTTGTTGATGCGATCAGGATATATC 59.882 37.037 3.96 3.96 40.94 1.63
2881 4372 6.535963 TGTTGATGCGATCAGGATATATCT 57.464 37.500 12.42 0.00 40.94 1.98
2882 4373 6.939622 TGTTGATGCGATCAGGATATATCTT 58.060 36.000 12.42 1.81 40.94 2.40
2883 4374 7.389232 TGTTGATGCGATCAGGATATATCTTT 58.611 34.615 12.42 0.00 40.94 2.52
2884 4375 8.531146 TGTTGATGCGATCAGGATATATCTTTA 58.469 33.333 12.42 0.00 40.94 1.85
2885 4376 9.539825 GTTGATGCGATCAGGATATATCTTTAT 57.460 33.333 12.42 2.10 40.94 1.40
2911 4402 7.542534 TTTGTAGGTGTAGTAGTTGTGTTTG 57.457 36.000 0.00 0.00 0.00 2.93
2912 4403 5.051816 TGTAGGTGTAGTAGTTGTGTTTGC 58.948 41.667 0.00 0.00 0.00 3.68
2913 4404 3.473625 AGGTGTAGTAGTTGTGTTTGCC 58.526 45.455 0.00 0.00 0.00 4.52
2914 4405 3.135895 AGGTGTAGTAGTTGTGTTTGCCT 59.864 43.478 0.00 0.00 0.00 4.75
2915 4406 3.497262 GGTGTAGTAGTTGTGTTTGCCTC 59.503 47.826 0.00 0.00 0.00 4.70
2916 4407 4.124238 GTGTAGTAGTTGTGTTTGCCTCA 58.876 43.478 0.00 0.00 0.00 3.86
2917 4408 4.025145 GTGTAGTAGTTGTGTTTGCCTCAC 60.025 45.833 0.00 0.00 36.48 3.51
2918 4409 3.560636 AGTAGTTGTGTTTGCCTCACT 57.439 42.857 0.00 0.00 36.83 3.41
2919 4410 3.206150 AGTAGTTGTGTTTGCCTCACTG 58.794 45.455 0.00 0.00 36.83 3.66
2920 4411 2.418368 AGTTGTGTTTGCCTCACTGA 57.582 45.000 0.00 0.00 36.83 3.41
2921 4412 2.017049 AGTTGTGTTTGCCTCACTGAC 58.983 47.619 0.00 0.00 36.83 3.51
2922 4413 2.017049 GTTGTGTTTGCCTCACTGACT 58.983 47.619 0.00 0.00 36.83 3.41
2923 4414 1.953559 TGTGTTTGCCTCACTGACTC 58.046 50.000 0.00 0.00 36.83 3.36
2924 4415 1.486310 TGTGTTTGCCTCACTGACTCT 59.514 47.619 0.00 0.00 36.83 3.24
2925 4416 1.869767 GTGTTTGCCTCACTGACTCTG 59.130 52.381 0.00 0.00 33.59 3.35
2926 4417 1.486310 TGTTTGCCTCACTGACTCTGT 59.514 47.619 0.00 0.00 0.00 3.41
2927 4418 2.092968 TGTTTGCCTCACTGACTCTGTT 60.093 45.455 0.00 0.00 0.00 3.16
2928 4419 3.133901 TGTTTGCCTCACTGACTCTGTTA 59.866 43.478 0.00 0.00 0.00 2.41
2929 4420 4.127171 GTTTGCCTCACTGACTCTGTTAA 58.873 43.478 0.00 0.00 0.00 2.01
2930 4421 4.415881 TTGCCTCACTGACTCTGTTAAA 57.584 40.909 0.00 0.00 0.00 1.52
2947 4440 9.296400 CTCTGTTAAAGATTGTAGAAGACTAGC 57.704 37.037 0.00 0.00 33.29 3.42
2953 4447 7.906199 AAGATTGTAGAAGACTAGCATAGGT 57.094 36.000 0.00 0.00 44.97 3.08
2978 4472 3.244156 GCAACACAATTGCATTGATCGA 58.756 40.909 20.80 0.00 44.34 3.59
3025 4521 1.833630 CAGGATAGAGCCACAACCTCA 59.166 52.381 0.00 0.00 0.00 3.86
3041 4537 7.106239 CACAACCTCAAACTATACAGGAGAAT 58.894 38.462 0.00 0.00 0.00 2.40
3058 4554 1.006639 GAATTAGGAGGTGGGCCCAAA 59.993 52.381 30.64 17.37 34.66 3.28
3153 4660 1.204941 CTGGAACGGAACTCCTCGAAT 59.795 52.381 0.00 0.00 36.31 3.34
3180 4687 3.725634 AGTAGGCAGTCCCTTAGTCATT 58.274 45.455 0.00 0.00 43.06 2.57
3215 4722 0.107643 TGTGCAGTCGGAACATGGAA 59.892 50.000 0.00 0.00 26.64 3.53
3339 4846 3.043586 CACAGAGACGTTGTCACAGTAC 58.956 50.000 0.00 0.00 34.60 2.73
3358 4866 0.108615 CACAACCGTAGCCTGGAGAG 60.109 60.000 0.00 0.00 0.00 3.20
3387 4895 2.104792 TGCAACTCCTGAAGTAGCTGTT 59.895 45.455 0.00 0.00 37.17 3.16
3474 4982 0.393808 AACTGTGGGTTGTCGCTTGT 60.394 50.000 0.00 0.00 36.70 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 186 7.378181 TGGGAAAGTTTCAGATATTTTTGCTC 58.622 34.615 17.16 0.00 0.00 4.26
128 277 6.003326 CCTTTTATTGGCCAAATTTTGTCCT 58.997 36.000 24.71 4.81 0.00 3.85
153 302 1.666553 CAGTAAGCGCCCACGTCAA 60.667 57.895 2.29 0.00 42.83 3.18
163 312 1.746220 AGTCAGCTACTCCAGTAAGCG 59.254 52.381 0.00 0.00 30.33 4.68
174 323 0.601558 TTGACCGTCCAGTCAGCTAC 59.398 55.000 0.00 0.00 46.90 3.58
206 355 0.895530 TCCTGGTTTCTGAGTAGGCG 59.104 55.000 0.00 0.00 0.00 5.52
249 402 3.370103 CCTGGACTATCAAAACCGCCTAA 60.370 47.826 0.00 0.00 0.00 2.69
407 568 9.524106 TCACGTATGAAAGTTAATCGTTATGAT 57.476 29.630 0.00 0.00 39.67 2.45
415 576 8.427012 TGTTTACGTCACGTATGAAAGTTAATC 58.573 33.333 11.64 0.00 41.97 1.75
418 579 7.691430 TTGTTTACGTCACGTATGAAAGTTA 57.309 32.000 11.64 0.00 41.97 2.24
448 1758 7.904558 TGGCCCATTTTCATGTACATATTTA 57.095 32.000 8.32 0.00 0.00 1.40
454 1764 6.805016 ATAATTGGCCCATTTTCATGTACA 57.195 33.333 7.46 0.00 0.00 2.90
538 1852 4.811024 ACATGTTCGCGATTGATCTGTAAT 59.189 37.500 10.88 0.00 0.00 1.89
548 1862 7.528481 TGTAAACTTATACATGTTCGCGATT 57.472 32.000 10.88 0.00 31.03 3.34
583 1902 7.560368 TGGCTTTTCCAAGTTTCAAAGAAATA 58.440 30.769 0.00 0.00 43.21 1.40
616 1935 8.922931 ACATGAAGCCCTTTATTTCAAAATTT 57.077 26.923 0.00 0.00 34.80 1.82
618 1937 7.765819 GCTACATGAAGCCCTTTATTTCAAAAT 59.234 33.333 0.00 0.00 36.45 1.82
684 2005 5.819901 CCCTAGAGGCAAACTAAAATGAGAG 59.180 44.000 0.00 0.00 0.00 3.20
693 2014 6.046881 AGACCTATATCCCTAGAGGCAAACTA 59.953 42.308 0.00 0.00 39.55 2.24
731 2052 1.899814 GACAGGGTGACATACTGACCA 59.100 52.381 14.10 0.00 36.17 4.02
834 2162 3.005897 TGCTTGTCTACTCTGGTTGACTC 59.994 47.826 10.71 3.41 44.39 3.36
873 2201 2.427506 AGGTTTTGGAGCTAAGCTTCG 58.572 47.619 0.00 0.00 39.88 3.79
884 2212 3.644265 TGTACTCAGCTGTAGGTTTTGGA 59.356 43.478 14.67 0.00 0.00 3.53
886 2214 7.097192 TCTTATGTACTCAGCTGTAGGTTTTG 58.903 38.462 14.67 0.00 0.00 2.44
888 2216 6.852420 TCTTATGTACTCAGCTGTAGGTTT 57.148 37.500 14.67 0.00 0.00 3.27
893 2221 8.144478 GGATGATTTCTTATGTACTCAGCTGTA 58.856 37.037 14.67 0.00 0.00 2.74
896 2224 6.100279 TGGGATGATTTCTTATGTACTCAGCT 59.900 38.462 0.00 0.00 0.00 4.24
897 2225 6.203723 GTGGGATGATTTCTTATGTACTCAGC 59.796 42.308 0.00 0.00 0.00 4.26
898 2226 6.708054 GGTGGGATGATTTCTTATGTACTCAG 59.292 42.308 0.00 0.00 0.00 3.35
924 2345 5.183969 AGATGGAGATTGTTCTGTGTGATG 58.816 41.667 0.00 0.00 30.30 3.07
977 2401 3.807209 GCTTGGTTGCCAGAACTTCTCTA 60.807 47.826 0.00 0.00 33.81 2.43
978 2402 2.856222 CTTGGTTGCCAGAACTTCTCT 58.144 47.619 0.00 0.00 33.81 3.10
1005 2440 1.742880 GGCACGAGAAGATGCAGCA 60.743 57.895 4.07 0.00 43.93 4.41
1014 2449 1.293498 GAGGAGCTTGGCACGAGAA 59.707 57.895 0.00 0.00 0.00 2.87
1048 2483 2.046507 GTCCCACAGAGCCTGCAG 60.047 66.667 6.78 6.78 34.37 4.41
1276 2711 1.205460 GGCTACCTCTGTCCCCCAAA 61.205 60.000 0.00 0.00 0.00 3.28
1615 3090 1.280982 CAGCTTCTTCGCGCAATCTA 58.719 50.000 8.75 0.00 34.40 1.98
1772 3247 4.783227 GGGAGTAATATCTAAGGGATGCCA 59.217 45.833 5.86 0.00 35.98 4.92
1777 3252 4.356190 ACGGAGGGAGTAATATCTAAGGGA 59.644 45.833 0.00 0.00 0.00 4.20
1779 3254 7.450944 AGTTTACGGAGGGAGTAATATCTAAGG 59.549 40.741 0.00 0.00 34.50 2.69
1791 3266 7.115947 CGCTTTTATATTAGTTTACGGAGGGAG 59.884 40.741 0.00 0.00 0.00 4.30
1792 3267 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
1793 3268 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
1794 3269 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
1853 3328 9.662947 GCCTTTTACTTCCTCTGTAAACTAATA 57.337 33.333 0.00 0.00 38.91 0.98
1854 3329 8.161425 TGCCTTTTACTTCCTCTGTAAACTAAT 58.839 33.333 0.00 0.00 38.91 1.73
1855 3330 7.511268 TGCCTTTTACTTCCTCTGTAAACTAA 58.489 34.615 0.00 0.00 38.91 2.24
1856 3331 7.069877 TGCCTTTTACTTCCTCTGTAAACTA 57.930 36.000 0.00 0.00 38.91 2.24
1857 3332 5.937111 TGCCTTTTACTTCCTCTGTAAACT 58.063 37.500 0.00 0.00 38.91 2.66
1858 3333 6.628919 TTGCCTTTTACTTCCTCTGTAAAC 57.371 37.500 0.00 0.00 38.91 2.01
1859 3334 7.001674 TGATTGCCTTTTACTTCCTCTGTAAA 58.998 34.615 0.00 0.00 37.88 2.01
1860 3335 6.539173 TGATTGCCTTTTACTTCCTCTGTAA 58.461 36.000 0.00 0.00 0.00 2.41
1861 3336 6.121776 TGATTGCCTTTTACTTCCTCTGTA 57.878 37.500 0.00 0.00 0.00 2.74
1862 3337 4.985538 TGATTGCCTTTTACTTCCTCTGT 58.014 39.130 0.00 0.00 0.00 3.41
1863 3338 5.964958 TTGATTGCCTTTTACTTCCTCTG 57.035 39.130 0.00 0.00 0.00 3.35
1864 3339 5.355350 CGATTGATTGCCTTTTACTTCCTCT 59.645 40.000 0.00 0.00 0.00 3.69
1865 3340 5.354234 TCGATTGATTGCCTTTTACTTCCTC 59.646 40.000 0.00 0.00 0.00 3.71
1866 3341 5.253330 TCGATTGATTGCCTTTTACTTCCT 58.747 37.500 0.00 0.00 0.00 3.36
1867 3342 5.560966 TCGATTGATTGCCTTTTACTTCC 57.439 39.130 0.00 0.00 0.00 3.46
1868 3343 7.020914 AGATCGATTGATTGCCTTTTACTTC 57.979 36.000 0.00 0.00 34.09 3.01
1869 3344 8.398665 GTTAGATCGATTGATTGCCTTTTACTT 58.601 33.333 0.00 0.00 34.09 2.24
1870 3345 7.012421 GGTTAGATCGATTGATTGCCTTTTACT 59.988 37.037 0.00 0.00 34.09 2.24
1871 3346 7.132863 GGTTAGATCGATTGATTGCCTTTTAC 58.867 38.462 0.00 0.00 34.09 2.01
1872 3347 6.262273 GGGTTAGATCGATTGATTGCCTTTTA 59.738 38.462 0.00 0.00 34.09 1.52
1873 3348 5.067805 GGGTTAGATCGATTGATTGCCTTTT 59.932 40.000 0.00 0.00 34.09 2.27
1874 3349 4.580580 GGGTTAGATCGATTGATTGCCTTT 59.419 41.667 0.00 0.00 34.09 3.11
1875 3350 4.137543 GGGTTAGATCGATTGATTGCCTT 58.862 43.478 0.00 0.00 34.09 4.35
1876 3351 3.744660 GGGTTAGATCGATTGATTGCCT 58.255 45.455 0.00 0.00 34.09 4.75
1877 3352 2.480419 CGGGTTAGATCGATTGATTGCC 59.520 50.000 0.00 0.00 34.09 4.52
1878 3353 2.096218 GCGGGTTAGATCGATTGATTGC 60.096 50.000 0.00 0.00 34.09 3.56
1899 3376 0.247185 AGGAAATGCAAATGCCCGTG 59.753 50.000 2.46 0.00 41.18 4.94
1917 3394 3.881688 CCTCCTGATTATGAGCAACCAAG 59.118 47.826 0.00 0.00 0.00 3.61
1924 3401 3.256879 TCGATCACCTCCTGATTATGAGC 59.743 47.826 0.00 0.00 39.96 4.26
1925 3402 4.617995 GCTCGATCACCTCCTGATTATGAG 60.618 50.000 0.00 0.00 39.96 2.90
1926 3403 3.256879 GCTCGATCACCTCCTGATTATGA 59.743 47.826 0.00 0.00 39.96 2.15
1927 3404 3.257873 AGCTCGATCACCTCCTGATTATG 59.742 47.826 0.00 0.00 39.96 1.90
1928 3405 3.257873 CAGCTCGATCACCTCCTGATTAT 59.742 47.826 0.00 0.00 39.96 1.28
2049 3526 3.710722 CTCTTGAGGCAGCCCCGT 61.711 66.667 8.22 0.00 39.21 5.28
2151 3628 1.280982 CGTAGTAGTCGGCGTAGACA 58.719 55.000 6.85 0.00 43.24 3.41
2200 3677 3.104519 TGATTGGTTACCTAGGACGGA 57.895 47.619 17.98 0.00 0.00 4.69
2214 3691 3.189287 CGTCTTGGGAGAACTTTGATTGG 59.811 47.826 0.00 0.00 32.66 3.16
2216 3693 4.065789 GACGTCTTGGGAGAACTTTGATT 58.934 43.478 8.70 0.00 32.66 2.57
2228 3705 0.037232 GAGGTTCCTGACGTCTTGGG 60.037 60.000 17.92 15.45 39.48 4.12
2257 3734 4.056125 CACGCGGGTCAGCTCTCA 62.056 66.667 12.47 0.00 34.40 3.27
2535 4012 4.141756 GCTATCACCAGCAGCTCCATATAT 60.142 45.833 0.00 0.00 41.40 0.86
2536 4013 3.196469 GCTATCACCAGCAGCTCCATATA 59.804 47.826 0.00 0.00 41.40 0.86
2692 4183 1.366319 ACCAAGAAGAGGGATGCTGT 58.634 50.000 0.00 0.00 0.00 4.40
2703 4194 8.470002 CCCTATATTTTCAAGGAAACCAAGAAG 58.530 37.037 0.00 0.00 30.83 2.85
2710 4201 6.515832 CATGGCCCTATATTTTCAAGGAAAC 58.484 40.000 0.00 0.00 30.83 2.78
2735 4226 6.130298 TGGCATGTGAACGATAAATTAAGG 57.870 37.500 0.00 0.00 0.00 2.69
2736 4227 6.201517 CCTGGCATGTGAACGATAAATTAAG 58.798 40.000 0.00 0.00 0.00 1.85
2737 4228 5.449862 GCCTGGCATGTGAACGATAAATTAA 60.450 40.000 15.17 0.00 0.00 1.40
2747 4238 2.672996 ACCGCCTGGCATGTGAAC 60.673 61.111 20.29 0.00 39.70 3.18
2772 4263 2.508439 ATCCTACAACGCGCACCG 60.508 61.111 5.73 0.00 44.21 4.94
2773 4264 3.089784 CATCCTACAACGCGCACC 58.910 61.111 5.73 0.00 0.00 5.01
2774 4265 1.635663 AAGCATCCTACAACGCGCAC 61.636 55.000 5.73 0.00 0.00 5.34
2775 4266 0.108567 TAAGCATCCTACAACGCGCA 60.109 50.000 5.73 0.00 0.00 6.09
2776 4267 1.003851 TTAAGCATCCTACAACGCGC 58.996 50.000 5.73 0.00 0.00 6.86
2777 4268 2.222953 GGTTTAAGCATCCTACAACGCG 60.223 50.000 3.53 3.53 0.00 6.01
2778 4269 3.007635 AGGTTTAAGCATCCTACAACGC 58.992 45.455 0.00 0.00 0.00 4.84
2779 4270 4.000988 ACAGGTTTAAGCATCCTACAACG 58.999 43.478 0.00 0.00 0.00 4.10
2780 4271 5.240844 ACAACAGGTTTAAGCATCCTACAAC 59.759 40.000 0.00 0.00 0.00 3.32
2781 4272 5.381757 ACAACAGGTTTAAGCATCCTACAA 58.618 37.500 0.00 0.00 0.00 2.41
2782 4273 4.980573 ACAACAGGTTTAAGCATCCTACA 58.019 39.130 0.00 0.00 0.00 2.74
2783 4274 6.171213 AGTACAACAGGTTTAAGCATCCTAC 58.829 40.000 0.00 0.00 0.00 3.18
2784 4275 6.212791 AGAGTACAACAGGTTTAAGCATCCTA 59.787 38.462 0.00 0.00 0.00 2.94
2785 4276 5.013183 AGAGTACAACAGGTTTAAGCATCCT 59.987 40.000 0.00 0.00 0.00 3.24
2786 4277 5.246307 AGAGTACAACAGGTTTAAGCATCC 58.754 41.667 0.00 0.00 0.00 3.51
2787 4278 5.932303 TGAGAGTACAACAGGTTTAAGCATC 59.068 40.000 0.00 0.00 0.00 3.91
2788 4279 5.865085 TGAGAGTACAACAGGTTTAAGCAT 58.135 37.500 0.00 0.00 0.00 3.79
2789 4280 5.284861 TGAGAGTACAACAGGTTTAAGCA 57.715 39.130 0.00 0.00 0.00 3.91
2790 4281 4.152580 GCTGAGAGTACAACAGGTTTAAGC 59.847 45.833 13.09 0.00 33.00 3.09
2791 4282 5.542779 AGCTGAGAGTACAACAGGTTTAAG 58.457 41.667 11.02 0.00 38.88 1.85
2792 4283 5.546621 AGCTGAGAGTACAACAGGTTTAA 57.453 39.130 11.02 0.00 38.88 1.52
2793 4284 5.297547 CAAGCTGAGAGTACAACAGGTTTA 58.702 41.667 20.25 0.00 45.62 2.01
2794 4285 4.130118 CAAGCTGAGAGTACAACAGGTTT 58.870 43.478 20.25 9.75 45.62 3.27
2796 4287 2.548920 GCAAGCTGAGAGTACAACAGGT 60.549 50.000 11.02 11.02 42.75 4.00
2797 4288 2.072298 GCAAGCTGAGAGTACAACAGG 58.928 52.381 13.09 2.24 33.00 4.00
2798 4289 2.072298 GGCAAGCTGAGAGTACAACAG 58.928 52.381 0.00 2.74 35.14 3.16
2799 4290 1.416030 TGGCAAGCTGAGAGTACAACA 59.584 47.619 0.00 0.00 0.00 3.33
2800 4291 1.801178 GTGGCAAGCTGAGAGTACAAC 59.199 52.381 0.00 0.00 0.00 3.32
2801 4292 1.416030 TGTGGCAAGCTGAGAGTACAA 59.584 47.619 0.00 0.00 0.00 2.41
2802 4293 1.047801 TGTGGCAAGCTGAGAGTACA 58.952 50.000 0.00 0.00 0.00 2.90
2803 4294 1.433534 GTGTGGCAAGCTGAGAGTAC 58.566 55.000 0.00 0.00 0.00 2.73
2804 4295 0.038251 CGTGTGGCAAGCTGAGAGTA 60.038 55.000 0.00 0.00 0.00 2.59
2805 4296 1.301244 CGTGTGGCAAGCTGAGAGT 60.301 57.895 0.00 0.00 0.00 3.24
2806 4297 2.031516 CCGTGTGGCAAGCTGAGAG 61.032 63.158 0.00 0.00 0.00 3.20
2807 4298 2.031012 CCGTGTGGCAAGCTGAGA 59.969 61.111 0.00 0.00 0.00 3.27
2808 4299 3.052082 CCCGTGTGGCAAGCTGAG 61.052 66.667 0.00 0.00 0.00 3.35
2809 4300 4.641645 CCCCGTGTGGCAAGCTGA 62.642 66.667 0.00 0.00 0.00 4.26
2824 4315 0.322008 CAGTGACTCAAGAAGCCCCC 60.322 60.000 0.00 0.00 0.00 5.40
2825 4316 0.322008 CCAGTGACTCAAGAAGCCCC 60.322 60.000 0.00 0.00 0.00 5.80
2826 4317 0.398318 ACCAGTGACTCAAGAAGCCC 59.602 55.000 0.00 0.00 0.00 5.19
2827 4318 2.262423 AACCAGTGACTCAAGAAGCC 57.738 50.000 0.00 0.00 0.00 4.35
2828 4319 4.632153 TCTAAACCAGTGACTCAAGAAGC 58.368 43.478 0.00 0.00 0.00 3.86
2829 4320 6.459066 TCATCTAAACCAGTGACTCAAGAAG 58.541 40.000 0.00 0.00 0.00 2.85
2830 4321 6.419484 TCATCTAAACCAGTGACTCAAGAA 57.581 37.500 0.00 0.00 0.00 2.52
2831 4322 6.014242 ACATCATCTAAACCAGTGACTCAAGA 60.014 38.462 0.00 0.00 0.00 3.02
2832 4323 6.169094 ACATCATCTAAACCAGTGACTCAAG 58.831 40.000 0.00 0.00 0.00 3.02
2833 4324 6.114187 ACATCATCTAAACCAGTGACTCAA 57.886 37.500 0.00 0.00 0.00 3.02
2834 4325 5.745312 ACATCATCTAAACCAGTGACTCA 57.255 39.130 0.00 0.00 0.00 3.41
2835 4326 6.428159 ACAAACATCATCTAAACCAGTGACTC 59.572 38.462 0.00 0.00 0.00 3.36
2836 4327 6.299141 ACAAACATCATCTAAACCAGTGACT 58.701 36.000 0.00 0.00 0.00 3.41
2837 4328 6.560253 ACAAACATCATCTAAACCAGTGAC 57.440 37.500 0.00 0.00 0.00 3.67
2838 4329 6.770303 TCAACAAACATCATCTAAACCAGTGA 59.230 34.615 0.00 0.00 0.00 3.41
2839 4330 6.969366 TCAACAAACATCATCTAAACCAGTG 58.031 36.000 0.00 0.00 0.00 3.66
2840 4331 7.596494 CATCAACAAACATCATCTAAACCAGT 58.404 34.615 0.00 0.00 0.00 4.00
2841 4332 6.529125 GCATCAACAAACATCATCTAAACCAG 59.471 38.462 0.00 0.00 0.00 4.00
2842 4333 6.389091 GCATCAACAAACATCATCTAAACCA 58.611 36.000 0.00 0.00 0.00 3.67
2843 4334 5.512788 CGCATCAACAAACATCATCTAAACC 59.487 40.000 0.00 0.00 0.00 3.27
2844 4335 6.314018 TCGCATCAACAAACATCATCTAAAC 58.686 36.000 0.00 0.00 0.00 2.01
2845 4336 6.493449 TCGCATCAACAAACATCATCTAAA 57.507 33.333 0.00 0.00 0.00 1.85
2846 4337 6.315891 TGATCGCATCAACAAACATCATCTAA 59.684 34.615 0.00 0.00 36.11 2.10
2847 4338 5.816777 TGATCGCATCAACAAACATCATCTA 59.183 36.000 0.00 0.00 36.11 1.98
2848 4339 4.637091 TGATCGCATCAACAAACATCATCT 59.363 37.500 0.00 0.00 36.11 2.90
2849 4340 4.912214 TGATCGCATCAACAAACATCATC 58.088 39.130 0.00 0.00 36.11 2.92
2850 4341 4.201980 CCTGATCGCATCAACAAACATCAT 60.202 41.667 1.44 0.00 39.11 2.45
2851 4342 3.127376 CCTGATCGCATCAACAAACATCA 59.873 43.478 1.44 0.00 39.11 3.07
2852 4343 3.374988 TCCTGATCGCATCAACAAACATC 59.625 43.478 1.44 0.00 39.11 3.06
2853 4344 3.346315 TCCTGATCGCATCAACAAACAT 58.654 40.909 1.44 0.00 39.11 2.71
2854 4345 2.777094 TCCTGATCGCATCAACAAACA 58.223 42.857 1.44 0.00 39.11 2.83
2855 4346 5.679734 ATATCCTGATCGCATCAACAAAC 57.320 39.130 1.44 0.00 39.11 2.93
2856 4347 7.389232 AGATATATCCTGATCGCATCAACAAA 58.611 34.615 9.18 0.00 39.11 2.83
2857 4348 6.939622 AGATATATCCTGATCGCATCAACAA 58.060 36.000 9.18 0.00 39.11 2.83
2858 4349 6.535963 AGATATATCCTGATCGCATCAACA 57.464 37.500 9.18 0.00 39.11 3.33
2859 4350 7.840342 AAAGATATATCCTGATCGCATCAAC 57.160 36.000 9.18 0.00 39.11 3.18
2885 4376 9.263538 CAAACACAACTACTACACCTACAAATA 57.736 33.333 0.00 0.00 0.00 1.40
2886 4377 7.255001 GCAAACACAACTACTACACCTACAAAT 60.255 37.037 0.00 0.00 0.00 2.32
2887 4378 6.037391 GCAAACACAACTACTACACCTACAAA 59.963 38.462 0.00 0.00 0.00 2.83
2888 4379 5.524646 GCAAACACAACTACTACACCTACAA 59.475 40.000 0.00 0.00 0.00 2.41
2889 4380 5.051816 GCAAACACAACTACTACACCTACA 58.948 41.667 0.00 0.00 0.00 2.74
2890 4381 4.450080 GGCAAACACAACTACTACACCTAC 59.550 45.833 0.00 0.00 0.00 3.18
2891 4382 4.345837 AGGCAAACACAACTACTACACCTA 59.654 41.667 0.00 0.00 0.00 3.08
2892 4383 3.135895 AGGCAAACACAACTACTACACCT 59.864 43.478 0.00 0.00 0.00 4.00
2893 4384 3.473625 AGGCAAACACAACTACTACACC 58.526 45.455 0.00 0.00 0.00 4.16
2894 4385 4.025145 GTGAGGCAAACACAACTACTACAC 60.025 45.833 0.00 0.00 38.05 2.90
2895 4386 4.124238 GTGAGGCAAACACAACTACTACA 58.876 43.478 0.00 0.00 38.05 2.74
2896 4387 4.211374 CAGTGAGGCAAACACAACTACTAC 59.789 45.833 10.85 0.00 40.25 2.73
2897 4388 4.100344 TCAGTGAGGCAAACACAACTACTA 59.900 41.667 10.85 0.00 40.25 1.82
2898 4389 3.118408 TCAGTGAGGCAAACACAACTACT 60.118 43.478 10.85 0.00 40.25 2.57
2899 4390 3.002348 GTCAGTGAGGCAAACACAACTAC 59.998 47.826 0.00 0.00 40.25 2.73
2900 4391 3.118408 AGTCAGTGAGGCAAACACAACTA 60.118 43.478 0.00 0.00 40.25 2.24
2901 4392 2.017049 GTCAGTGAGGCAAACACAACT 58.983 47.619 0.00 0.00 40.25 3.16
2902 4393 2.017049 AGTCAGTGAGGCAAACACAAC 58.983 47.619 0.00 8.62 40.25 3.32
2903 4394 2.092968 AGAGTCAGTGAGGCAAACACAA 60.093 45.455 0.00 0.00 40.25 3.33
2904 4395 1.486310 AGAGTCAGTGAGGCAAACACA 59.514 47.619 0.00 0.00 40.25 3.72
2905 4396 1.869767 CAGAGTCAGTGAGGCAAACAC 59.130 52.381 0.00 0.00 38.38 3.32
2906 4397 1.486310 ACAGAGTCAGTGAGGCAAACA 59.514 47.619 0.00 0.00 0.00 2.83
2907 4398 2.246719 ACAGAGTCAGTGAGGCAAAC 57.753 50.000 0.00 0.00 0.00 2.93
2908 4399 4.415881 TTAACAGAGTCAGTGAGGCAAA 57.584 40.909 0.00 0.00 0.00 3.68
2909 4400 4.100963 TCTTTAACAGAGTCAGTGAGGCAA 59.899 41.667 0.00 0.00 0.00 4.52
2910 4401 3.641436 TCTTTAACAGAGTCAGTGAGGCA 59.359 43.478 0.00 0.00 0.00 4.75
2911 4402 4.258702 TCTTTAACAGAGTCAGTGAGGC 57.741 45.455 0.00 0.00 0.00 4.70
2912 4403 6.226787 ACAATCTTTAACAGAGTCAGTGAGG 58.773 40.000 0.00 0.00 33.87 3.86
2913 4404 8.300286 TCTACAATCTTTAACAGAGTCAGTGAG 58.700 37.037 0.00 0.00 33.87 3.51
2914 4405 8.178313 TCTACAATCTTTAACAGAGTCAGTGA 57.822 34.615 0.00 0.00 33.87 3.41
2915 4406 8.818141 TTCTACAATCTTTAACAGAGTCAGTG 57.182 34.615 0.00 0.00 33.87 3.66
2916 4407 8.861086 TCTTCTACAATCTTTAACAGAGTCAGT 58.139 33.333 0.00 0.00 33.87 3.41
2917 4408 9.134734 GTCTTCTACAATCTTTAACAGAGTCAG 57.865 37.037 0.00 0.00 33.87 3.51
2918 4409 8.861086 AGTCTTCTACAATCTTTAACAGAGTCA 58.139 33.333 0.00 0.00 33.87 3.41
2921 4412 9.296400 GCTAGTCTTCTACAATCTTTAACAGAG 57.704 37.037 0.00 0.00 33.87 3.35
2922 4413 8.803235 TGCTAGTCTTCTACAATCTTTAACAGA 58.197 33.333 0.00 0.00 35.33 3.41
2923 4414 8.988064 TGCTAGTCTTCTACAATCTTTAACAG 57.012 34.615 0.00 0.00 0.00 3.16
2927 4418 9.422681 ACCTATGCTAGTCTTCTACAATCTTTA 57.577 33.333 0.00 0.00 0.00 1.85
2928 4419 8.312669 ACCTATGCTAGTCTTCTACAATCTTT 57.687 34.615 0.00 0.00 0.00 2.52
2929 4420 7.255312 CGACCTATGCTAGTCTTCTACAATCTT 60.255 40.741 0.00 0.00 0.00 2.40
2930 4421 6.205853 CGACCTATGCTAGTCTTCTACAATCT 59.794 42.308 0.00 0.00 0.00 2.40
2947 4440 3.491356 CAATTGTGTTGCACGACCTATG 58.509 45.455 0.00 0.00 37.14 2.23
3025 4521 7.071321 CCACCTCCTAATTCTCCTGTATAGTTT 59.929 40.741 0.00 0.00 0.00 2.66
3041 4537 0.113580 GTTTTGGGCCCACCTCCTAA 59.886 55.000 28.70 12.94 41.11 2.69
3124 4631 2.125912 CCGTTCCAGTCTCTGCGG 60.126 66.667 0.00 0.00 31.04 5.69
3153 4660 0.178903 AGGGACTGCCTACTTCCACA 60.179 55.000 0.00 0.00 37.18 4.17
3180 4687 1.424403 CACAACAGTTCGCCGATGTA 58.576 50.000 0.00 0.00 0.00 2.29
3215 4722 1.241315 CCTTGGACGCATTCGGGTTT 61.241 55.000 0.00 0.00 38.64 3.27
3339 4846 0.108615 CTCTCCAGGCTACGGTTGTG 60.109 60.000 0.00 0.00 0.00 3.33
3358 4866 4.197750 ACTTCAGGAGTTGCATCATGATC 58.802 43.478 4.86 1.82 39.51 2.92
3387 4895 2.656646 CGAGTGCACCTGGCTACA 59.343 61.111 14.63 0.00 45.15 2.74
3442 4950 0.882042 CACAGTTTCGTGCTCCAGCT 60.882 55.000 0.00 0.00 42.66 4.24
3474 4982 1.742880 CCCTCGTCTCGTGGTCGTA 60.743 63.158 8.91 0.00 38.62 3.43
3530 5038 3.050275 GGCTTCCCTGACACACGC 61.050 66.667 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.