Multiple sequence alignment - TraesCS3A01G504100

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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 TraesCS3A01G504100 chr3A 100.000 2675 0 0 1 2675 726411744 726409070 0.000000e+00 4940
1 TraesCS3A01G504100 chr3A 84.552 1340 141 43 475 1777 726515269 726516579 0.000000e+00 1267
2 TraesCS3A01G504100 chr3A 84.224 1198 137 29 587 1752 726457917 726459094 0.000000e+00 1118
3 TraesCS3A01G504100 chr3A 86.232 138 16 3 2333 2470 726444676 726444810 2.150000e-31 147
4 TraesCS3A01G504100 chr3A 95.238 63 2 1 475 536 726457852 726457914 6.090000e-17 99
5 TraesCS3A01G504100 chr3D 93.740 1789 78 11 1 1777 595287539 595285773 0.000000e+00 2652
6 TraesCS3A01G504100 chr3D 83.018 1584 168 52 248 1752 595704540 595706101 0.000000e+00 1341
7 TraesCS3A01G504100 chr3D 84.021 1333 131 48 475 1768 595738653 595739942 0.000000e+00 1206
8 TraesCS3A01G504100 chr3D 86.693 1007 99 24 789 1768 595674257 595675255 0.000000e+00 1085
9 TraesCS3A01G504100 chr3D 85.658 1011 105 19 789 1768 595302941 595303942 0.000000e+00 1027
10 TraesCS3A01G504100 chr3D 87.112 838 95 4 956 1791 596097024 596096198 0.000000e+00 937
11 TraesCS3A01G504100 chr3D 90.948 464 17 11 2209 2668 595285772 595285330 3.810000e-168 601
12 TraesCS3A01G504100 chr3D 84.756 328 39 4 475 791 595302447 595302774 4.300000e-83 318
13 TraesCS3A01G504100 chr3D 86.598 291 35 4 475 763 595673797 595674085 4.300000e-83 318
14 TraesCS3A01G504100 chr3D 84.255 235 22 5 248 468 595673525 595673758 5.800000e-52 215
15 TraesCS3A01G504100 chr3D 88.506 174 20 0 295 468 595738441 595738614 7.500000e-51 211
16 TraesCS3A01G504100 chr3D 92.308 104 8 0 351 454 595302130 595302233 5.970000e-32 148
17 TraesCS3A01G504100 chr3D 78.866 194 29 5 6 195 595704338 595704523 1.300000e-23 121
18 TraesCS3A01G504100 chr3B 84.140 1198 133 30 475 1636 798686163 798687339 0.000000e+00 1107
19 TraesCS3A01G504100 chr3B 86.152 946 100 10 835 1752 798648158 798649100 0.000000e+00 992
20 TraesCS3A01G504100 chr3B 95.281 445 20 1 1777 2221 677604261 677604704 0.000000e+00 704
21 TraesCS3A01G504100 chr3B 96.065 432 14 2 1777 2208 785668243 785667815 0.000000e+00 701
22 TraesCS3A01G504100 chr3B 78.285 1073 162 36 747 1777 798639541 798640584 2.260000e-175 625
23 TraesCS3A01G504100 chr3B 86.100 259 30 5 475 729 798647702 798647958 9.430000e-70 274
24 TraesCS3A01G504100 chr3B 83.729 295 34 8 185 468 799523218 799522927 1.580000e-67 267
25 TraesCS3A01G504100 chr3B 84.615 169 19 5 573 738 799522682 799522518 7.660000e-36 161
26 TraesCS3A01G504100 chr3B 81.481 216 21 7 266 468 798647455 798647664 2.760000e-35 159
27 TraesCS3A01G504100 chr4A 96.171 444 14 3 1777 2219 701424696 701424255 0.000000e+00 723
28 TraesCS3A01G504100 chr7B 96.322 435 13 2 1777 2211 362413647 362413216 0.000000e+00 712
29 TraesCS3A01G504100 chr6A 96.110 437 14 2 1777 2213 569460384 569460817 0.000000e+00 710
30 TraesCS3A01G504100 chr4B 94.737 456 20 4 1768 2221 266060450 266060903 0.000000e+00 706
31 TraesCS3A01G504100 chr4B 95.455 440 18 2 1777 2216 660362259 660361822 0.000000e+00 701
32 TraesCS3A01G504100 chr4D 95.270 444 18 2 1777 2220 234383196 234383636 0.000000e+00 701
33 TraesCS3A01G504100 chr4D 95.291 446 12 7 1777 2218 221295859 221295419 0.000000e+00 699


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 TraesCS3A01G504100 chr3A 726409070 726411744 2674 True 4940.000000 4940 100.000000 1 2675 1 chr3A.!!$R1 2674
1 TraesCS3A01G504100 chr3A 726515269 726516579 1310 False 1267.000000 1267 84.552000 475 1777 1 chr3A.!!$F2 1302
2 TraesCS3A01G504100 chr3A 726457852 726459094 1242 False 608.500000 1118 89.731000 475 1752 2 chr3A.!!$F3 1277
3 TraesCS3A01G504100 chr3D 595285330 595287539 2209 True 1626.500000 2652 92.344000 1 2668 2 chr3D.!!$R2 2667
4 TraesCS3A01G504100 chr3D 596096198 596097024 826 True 937.000000 937 87.112000 956 1791 1 chr3D.!!$R1 835
5 TraesCS3A01G504100 chr3D 595704338 595706101 1763 False 731.000000 1341 80.942000 6 1752 2 chr3D.!!$F3 1746
6 TraesCS3A01G504100 chr3D 595738441 595739942 1501 False 708.500000 1206 86.263500 295 1768 2 chr3D.!!$F4 1473
7 TraesCS3A01G504100 chr3D 595673525 595675255 1730 False 539.333333 1085 85.848667 248 1768 3 chr3D.!!$F2 1520
8 TraesCS3A01G504100 chr3D 595302130 595303942 1812 False 497.666667 1027 87.574000 351 1768 3 chr3D.!!$F1 1417
9 TraesCS3A01G504100 chr3B 798686163 798687339 1176 False 1107.000000 1107 84.140000 475 1636 1 chr3B.!!$F3 1161
10 TraesCS3A01G504100 chr3B 798639541 798640584 1043 False 625.000000 625 78.285000 747 1777 1 chr3B.!!$F2 1030
11 TraesCS3A01G504100 chr3B 798647455 798649100 1645 False 475.000000 992 84.577667 266 1752 3 chr3B.!!$F4 1486
12 TraesCS3A01G504100 chr3B 799522518 799523218 700 True 214.000000 267 84.172000 185 738 2 chr3B.!!$R2 553

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
931 1786 1.002773 TGGGCCCTTTCTACGTTCTTC 59.997 52.381 25.7 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 3472 0.034186 CCAGCTCTTACCCAATGCCA 60.034 55.0 0.0 0.0 0.0 4.92 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
61 66 5.067153 CCTGTGTTCATGTTGTCAAAGGTTA 59.933 40.000 0.00 0.00 32.40 2.85
99 104 5.009310 TGCTCTCATGGCAAATATCATTCAC 59.991 40.000 0.00 0.00 36.71 3.18
135 140 2.093288 CAGCCCATGTAAGCTCTTCTGA 60.093 50.000 0.00 0.00 37.18 3.27
138 143 4.410228 AGCCCATGTAAGCTCTTCTGATTA 59.590 41.667 0.00 0.00 32.71 1.75
143 148 6.481644 CCATGTAAGCTCTTCTGATTAGGTTC 59.518 42.308 7.28 2.82 33.37 3.62
144 149 5.978814 TGTAAGCTCTTCTGATTAGGTTCC 58.021 41.667 7.28 0.00 33.37 3.62
153 161 8.337118 TCTTCTGATTAGGTTCCTTCCATAAT 57.663 34.615 0.00 0.00 0.00 1.28
162 170 2.782922 TCCTTCCATAATAGGCCACCA 58.217 47.619 5.01 0.00 0.00 4.17
184 192 6.439562 CATCGTCTGGATTGGGAACCTCTT 62.440 50.000 0.00 0.00 41.52 2.85
241 249 3.628032 CCTGTCGTGCTCTCAGTATCTAA 59.372 47.826 6.94 0.00 0.00 2.10
245 253 5.357032 TGTCGTGCTCTCAGTATCTAATTGA 59.643 40.000 0.00 0.00 0.00 2.57
248 256 6.920210 TCGTGCTCTCAGTATCTAATTGATTG 59.080 38.462 0.00 0.00 36.65 2.67
307 332 5.179452 TCTTAAGCTGGTGCCTTAAATCT 57.821 39.130 0.00 0.00 40.80 2.40
336 361 5.357878 TGTGCATTCATTTCTCTTATCCACC 59.642 40.000 0.00 0.00 0.00 4.61
348 373 5.366477 TCTCTTATCCACCTGATTATGCACA 59.634 40.000 0.00 0.00 34.76 4.57
383 408 8.846943 TCATCAGCTGTCTTTGTAAATCTTTA 57.153 30.769 14.67 0.00 0.00 1.85
549 784 4.578105 AGCAGCAATATTCTCCTTTAGTGC 59.422 41.667 0.00 0.00 39.12 4.40
602 957 9.944376 ACAATTTGGCGAGTATATATACTGATT 57.056 29.630 26.51 14.11 43.27 2.57
655 1011 2.588620 TGTTGCTACCCGGTGAAAAAT 58.411 42.857 0.00 0.00 0.00 1.82
677 1033 1.542915 GCACTTGACAGGCATGTTCAT 59.457 47.619 5.07 0.00 40.68 2.57
678 1034 2.749076 GCACTTGACAGGCATGTTCATA 59.251 45.455 5.07 0.00 40.68 2.15
777 1298 8.997323 AGTCTCTTCAATTTACAGAATTGAGTG 58.003 33.333 12.32 10.32 44.49 3.51
778 1299 8.993121 GTCTCTTCAATTTACAGAATTGAGTGA 58.007 33.333 12.32 12.92 44.49 3.41
779 1300 9.559732 TCTCTTCAATTTACAGAATTGAGTGAA 57.440 29.630 12.32 0.78 44.49 3.18
780 1301 9.604626 CTCTTCAATTTACAGAATTGAGTGAAC 57.395 33.333 12.32 0.00 44.49 3.18
781 1302 8.567948 TCTTCAATTTACAGAATTGAGTGAACC 58.432 33.333 12.32 0.00 44.49 3.62
782 1303 6.898041 TCAATTTACAGAATTGAGTGAACCG 58.102 36.000 9.44 0.00 40.53 4.44
783 1304 6.485313 TCAATTTACAGAATTGAGTGAACCGT 59.515 34.615 9.44 0.00 40.53 4.83
784 1305 5.666969 TTTACAGAATTGAGTGAACCGTG 57.333 39.130 0.00 0.00 0.00 4.94
785 1306 1.873591 ACAGAATTGAGTGAACCGTGC 59.126 47.619 0.00 0.00 0.00 5.34
786 1307 1.872952 CAGAATTGAGTGAACCGTGCA 59.127 47.619 0.00 0.00 0.00 4.57
787 1308 2.485426 CAGAATTGAGTGAACCGTGCAT 59.515 45.455 0.00 0.00 0.00 3.96
831 1541 5.049405 TCAAGACTTAACTTTGCAAGCTAGC 60.049 40.000 6.62 6.62 0.00 3.42
845 1692 4.114659 CAAGCTAGCTTTAGTGTGGCACT 61.115 47.826 27.34 6.99 40.09 4.40
846 1693 2.039084 AGCTAGCTTTAGTGTGGCACTT 59.961 45.455 19.83 9.69 42.59 3.16
886 1733 9.601217 ACGAAGTATTTATGCAGTAGATTTCTT 57.399 29.630 0.00 0.00 41.94 2.52
916 1771 6.096282 TGCTTCTACTGTTTTAATAATGGGCC 59.904 38.462 0.00 0.00 0.00 5.80
924 1779 7.123697 ACTGTTTTAATAATGGGCCCTTTCTAC 59.876 37.037 25.40 14.91 0.00 2.59
925 1780 6.095720 TGTTTTAATAATGGGCCCTTTCTACG 59.904 38.462 25.40 0.00 0.00 3.51
926 1781 3.945640 AATAATGGGCCCTTTCTACGT 57.054 42.857 25.40 4.35 0.00 3.57
927 1782 3.945640 ATAATGGGCCCTTTCTACGTT 57.054 42.857 25.40 5.92 0.00 3.99
928 1783 2.124277 AATGGGCCCTTTCTACGTTC 57.876 50.000 25.70 0.00 0.00 3.95
929 1784 1.286248 ATGGGCCCTTTCTACGTTCT 58.714 50.000 25.70 0.00 0.00 3.01
930 1785 1.061546 TGGGCCCTTTCTACGTTCTT 58.938 50.000 25.70 0.00 0.00 2.52
931 1786 1.002773 TGGGCCCTTTCTACGTTCTTC 59.997 52.381 25.70 0.00 0.00 2.87
932 1787 1.278413 GGGCCCTTTCTACGTTCTTCT 59.722 52.381 17.04 0.00 0.00 2.85
933 1788 2.347731 GGCCCTTTCTACGTTCTTCTG 58.652 52.381 0.00 0.00 0.00 3.02
934 1789 2.289506 GGCCCTTTCTACGTTCTTCTGT 60.290 50.000 0.00 0.00 0.00 3.41
935 1790 3.056322 GGCCCTTTCTACGTTCTTCTGTA 60.056 47.826 0.00 0.00 0.00 2.74
936 1791 4.382793 GGCCCTTTCTACGTTCTTCTGTAT 60.383 45.833 0.00 0.00 0.00 2.29
937 1792 5.176592 GCCCTTTCTACGTTCTTCTGTATT 58.823 41.667 0.00 0.00 0.00 1.89
938 1793 5.063564 GCCCTTTCTACGTTCTTCTGTATTG 59.936 44.000 0.00 0.00 0.00 1.90
939 1794 6.164176 CCCTTTCTACGTTCTTCTGTATTGT 58.836 40.000 0.00 0.00 0.00 2.71
940 1795 6.649557 CCCTTTCTACGTTCTTCTGTATTGTT 59.350 38.462 0.00 0.00 0.00 2.83
941 1796 7.148623 CCCTTTCTACGTTCTTCTGTATTGTTC 60.149 40.741 0.00 0.00 0.00 3.18
942 1797 7.599245 CCTTTCTACGTTCTTCTGTATTGTTCT 59.401 37.037 0.00 0.00 0.00 3.01
943 1798 9.622004 CTTTCTACGTTCTTCTGTATTGTTCTA 57.378 33.333 0.00 0.00 0.00 2.10
984 1880 7.700234 TGTCTAACAATTGTTGATGTTTGTGTC 59.300 33.333 29.72 12.15 40.14 3.67
1038 1934 2.035626 CCCACCGGCAGGACAATT 59.964 61.111 10.86 0.00 41.02 2.32
1041 1937 2.046314 ACCGGCAGGACAATTCGG 60.046 61.111 10.86 0.00 45.42 4.30
1042 1938 2.267642 CCGGCAGGACAATTCGGA 59.732 61.111 0.00 0.00 42.94 4.55
1066 1965 1.203237 AGGTCCACTCATCAGACACCT 60.203 52.381 0.00 0.00 31.99 4.00
1115 2015 1.939838 GCAGTACCACCTCGTCTTTGG 60.940 57.143 0.00 0.00 36.39 3.28
1209 2109 5.466393 CCAGGAAAAGATGCAAATTTTCGTT 59.534 36.000 22.18 15.21 43.28 3.85
1419 2320 3.003173 CTCCTTGTCCTCCGCCCA 61.003 66.667 0.00 0.00 0.00 5.36
1467 2371 1.421646 CACCTCTTTGTCAGGACCCTT 59.578 52.381 0.00 0.00 34.75 3.95
1517 2421 0.320771 AGCTCGGACACCATCAACAC 60.321 55.000 0.00 0.00 0.00 3.32
1777 2694 9.270640 ACTATCATTCTAGTACTGTACGTTAGG 57.729 37.037 11.97 3.01 30.16 2.69
1778 2695 9.486497 CTATCATTCTAGTACTGTACGTTAGGA 57.514 37.037 11.97 5.22 0.00 2.94
1779 2696 8.743085 ATCATTCTAGTACTGTACGTTAGGAA 57.257 34.615 11.97 12.22 0.00 3.36
1780 2697 8.565896 TCATTCTAGTACTGTACGTTAGGAAA 57.434 34.615 11.97 2.70 0.00 3.13
1781 2698 9.013229 TCATTCTAGTACTGTACGTTAGGAAAA 57.987 33.333 11.97 2.12 0.00 2.29
1782 2699 9.798994 CATTCTAGTACTGTACGTTAGGAAAAT 57.201 33.333 11.97 3.99 0.00 1.82
1784 2701 7.989826 TCTAGTACTGTACGTTAGGAAAATCC 58.010 38.462 11.97 0.00 36.58 3.01
1785 2702 6.594788 AGTACTGTACGTTAGGAAAATCCA 57.405 37.500 11.97 0.00 39.61 3.41
1786 2703 7.179076 AGTACTGTACGTTAGGAAAATCCAT 57.821 36.000 11.97 0.00 39.61 3.41
1787 2704 7.263496 AGTACTGTACGTTAGGAAAATCCATC 58.737 38.462 11.97 0.00 39.61 3.51
1788 2705 5.425630 ACTGTACGTTAGGAAAATCCATCC 58.574 41.667 0.00 0.00 39.61 3.51
1790 2707 6.381994 ACTGTACGTTAGGAAAATCCATCCTA 59.618 38.462 0.00 0.00 45.51 2.94
1791 2708 7.070821 ACTGTACGTTAGGAAAATCCATCCTAT 59.929 37.037 0.00 0.00 46.29 2.57
1792 2709 7.439381 TGTACGTTAGGAAAATCCATCCTATC 58.561 38.462 0.00 2.62 46.29 2.08
1793 2710 6.494666 ACGTTAGGAAAATCCATCCTATCA 57.505 37.500 3.31 0.00 46.29 2.15
1794 2711 6.289064 ACGTTAGGAAAATCCATCCTATCAC 58.711 40.000 3.31 0.00 46.29 3.06
1795 2712 5.701290 CGTTAGGAAAATCCATCCTATCACC 59.299 44.000 3.31 0.00 46.29 4.02
1796 2713 4.731313 AGGAAAATCCATCCTATCACCC 57.269 45.455 0.00 0.00 45.51 4.61
1797 2714 3.073062 AGGAAAATCCATCCTATCACCCG 59.927 47.826 0.00 0.00 45.51 5.28
1798 2715 3.412386 GAAAATCCATCCTATCACCCGG 58.588 50.000 0.00 0.00 0.00 5.73
1799 2716 2.118403 AATCCATCCTATCACCCGGT 57.882 50.000 0.00 0.00 0.00 5.28
1800 2717 1.352083 ATCCATCCTATCACCCGGTG 58.648 55.000 11.73 11.73 34.45 4.94
1801 2718 0.762842 TCCATCCTATCACCCGGTGG 60.763 60.000 17.76 1.28 33.87 4.61
1803 2720 1.712056 CATCCTATCACCCGGTGGTA 58.288 55.000 17.76 13.93 45.57 3.25
1804 2721 1.618837 CATCCTATCACCCGGTGGTAG 59.381 57.143 25.67 25.67 45.57 3.18
1805 2722 0.632835 TCCTATCACCCGGTGGTAGT 59.367 55.000 28.64 12.18 45.57 2.73
1806 2723 1.007479 TCCTATCACCCGGTGGTAGTT 59.993 52.381 28.64 9.25 45.57 2.24
1807 2724 2.244510 TCCTATCACCCGGTGGTAGTTA 59.755 50.000 28.64 17.64 45.57 2.24
1808 2725 2.363359 CCTATCACCCGGTGGTAGTTAC 59.637 54.545 28.64 0.00 45.57 2.50
1809 2726 1.197812 ATCACCCGGTGGTAGTTACC 58.802 55.000 17.76 1.25 45.57 2.85
1810 2727 0.904394 TCACCCGGTGGTAGTTACCC 60.904 60.000 17.76 0.00 45.57 3.69
1811 2728 1.613332 ACCCGGTGGTAGTTACCCC 60.613 63.158 0.00 5.97 45.45 4.95
1812 2729 1.613035 CCCGGTGGTAGTTACCCCA 60.613 63.158 0.00 0.00 45.87 4.96
1819 2736 2.910544 TGGTAGTTACCCCACATGTCT 58.089 47.619 0.00 0.00 45.87 3.41
1820 2737 2.835764 TGGTAGTTACCCCACATGTCTC 59.164 50.000 0.00 0.00 45.87 3.36
1824 2741 5.307196 GGTAGTTACCCCACATGTCTCATAT 59.693 44.000 0.00 0.00 40.53 1.78
1833 2750 6.401394 CCCACATGTCTCATATACTACCATG 58.599 44.000 0.00 0.00 0.00 3.66
1834 2751 6.014242 CCCACATGTCTCATATACTACCATGT 60.014 42.308 0.00 0.00 0.00 3.21
1835 2752 6.870439 CCACATGTCTCATATACTACCATGTG 59.130 42.308 18.17 18.17 43.80 3.21
1836 2753 6.870439 CACATGTCTCATATACTACCATGTGG 59.130 42.308 17.61 0.00 41.82 4.17
1935 2852 6.736110 AAAAATTGCATATGAGCCCATAGT 57.264 33.333 6.97 0.00 38.53 2.12
1936 2853 6.736110 AAAATTGCATATGAGCCCATAGTT 57.264 33.333 6.97 0.00 38.53 2.24
1937 2854 6.736110 AAATTGCATATGAGCCCATAGTTT 57.264 33.333 6.97 0.00 38.53 2.66
1938 2855 6.736110 AATTGCATATGAGCCCATAGTTTT 57.264 33.333 6.97 0.00 38.53 2.43
1939 2856 6.736110 ATTGCATATGAGCCCATAGTTTTT 57.264 33.333 6.97 0.00 38.53 1.94
1940 2857 5.518848 TGCATATGAGCCCATAGTTTTTG 57.481 39.130 6.97 0.00 38.53 2.44
1941 2858 4.955450 TGCATATGAGCCCATAGTTTTTGT 59.045 37.500 6.97 0.00 38.53 2.83
1942 2859 5.421693 TGCATATGAGCCCATAGTTTTTGTT 59.578 36.000 6.97 0.00 38.53 2.83
1943 2860 6.605194 TGCATATGAGCCCATAGTTTTTGTTA 59.395 34.615 6.97 0.00 38.53 2.41
1944 2861 7.287466 TGCATATGAGCCCATAGTTTTTGTTAT 59.713 33.333 6.97 0.00 38.53 1.89
1945 2862 8.792633 GCATATGAGCCCATAGTTTTTGTTATA 58.207 33.333 6.97 0.00 38.53 0.98
1950 2867 9.030452 TGAGCCCATAGTTTTTGTTATATTTGT 57.970 29.630 0.00 0.00 0.00 2.83
2062 2979 9.940166 TCATTGTTATGTACTACATACTACACG 57.060 33.333 8.22 6.09 40.47 4.49
2063 2980 9.726232 CATTGTTATGTACTACATACTACACGT 57.274 33.333 8.22 0.00 40.47 4.49
2066 2983 9.377312 TGTTATGTACTACATACTACACGTACA 57.623 33.333 8.22 5.53 40.47 2.90
2070 2987 9.770097 ATGTACTACATACTACACGTACATACT 57.230 33.333 10.17 0.00 43.04 2.12
2071 2988 9.249457 TGTACTACATACTACACGTACATACTC 57.751 37.037 0.00 0.00 34.18 2.59
2072 2989 9.469807 GTACTACATACTACACGTACATACTCT 57.530 37.037 0.00 0.00 0.00 3.24
2073 2990 8.586570 ACTACATACTACACGTACATACTCTC 57.413 38.462 0.00 0.00 0.00 3.20
2074 2991 6.522233 ACATACTACACGTACATACTCTCG 57.478 41.667 0.00 0.00 0.00 4.04
2075 2992 5.464722 ACATACTACACGTACATACTCTCGG 59.535 44.000 0.00 0.00 0.00 4.63
2076 2993 3.866651 ACTACACGTACATACTCTCGGT 58.133 45.455 0.00 0.00 0.00 4.69
2077 2994 4.256920 ACTACACGTACATACTCTCGGTT 58.743 43.478 0.00 0.00 0.00 4.44
2078 2995 3.754188 ACACGTACATACTCTCGGTTC 57.246 47.619 0.00 0.00 0.00 3.62
2079 2996 2.421424 ACACGTACATACTCTCGGTTCC 59.579 50.000 0.00 0.00 0.00 3.62
2080 2997 1.667724 ACGTACATACTCTCGGTTCCG 59.332 52.381 4.74 4.74 0.00 4.30
2081 2998 1.935873 CGTACATACTCTCGGTTCCGA 59.064 52.381 13.34 13.34 36.95 4.55
2082 2999 2.286067 CGTACATACTCTCGGTTCCGAC 60.286 54.545 10.00 0.00 34.59 4.79
2083 3000 1.830279 ACATACTCTCGGTTCCGACA 58.170 50.000 10.00 0.00 34.59 4.35
2084 3001 1.743958 ACATACTCTCGGTTCCGACAG 59.256 52.381 10.00 11.88 34.59 3.51
2085 3002 2.014857 CATACTCTCGGTTCCGACAGA 58.985 52.381 19.84 11.81 34.59 3.41
2086 3003 2.414994 TACTCTCGGTTCCGACAGAT 57.585 50.000 19.84 9.17 34.59 2.90
2087 3004 2.414994 ACTCTCGGTTCCGACAGATA 57.585 50.000 19.84 0.00 34.59 1.98
2088 3005 2.015587 ACTCTCGGTTCCGACAGATAC 58.984 52.381 19.84 0.00 34.59 2.24
2089 3006 2.290464 CTCTCGGTTCCGACAGATACT 58.710 52.381 10.00 0.00 34.59 2.12
2090 3007 3.118482 ACTCTCGGTTCCGACAGATACTA 60.118 47.826 19.84 0.00 34.59 1.82
2091 3008 3.201290 TCTCGGTTCCGACAGATACTAC 58.799 50.000 10.00 0.00 34.59 2.73
2092 3009 2.941064 CTCGGTTCCGACAGATACTACA 59.059 50.000 10.00 0.00 34.59 2.74
2093 3010 3.548770 TCGGTTCCGACAGATACTACAT 58.451 45.455 10.00 0.00 33.26 2.29
2094 3011 4.707105 TCGGTTCCGACAGATACTACATA 58.293 43.478 10.00 0.00 33.26 2.29
2095 3012 4.512944 TCGGTTCCGACAGATACTACATAC 59.487 45.833 10.00 0.00 33.26 2.39
2096 3013 4.274214 CGGTTCCGACAGATACTACATACA 59.726 45.833 5.19 0.00 0.00 2.29
2097 3014 5.220912 CGGTTCCGACAGATACTACATACAA 60.221 44.000 5.19 0.00 0.00 2.41
2098 3015 5.975939 GGTTCCGACAGATACTACATACAAC 59.024 44.000 0.00 0.00 0.00 3.32
2099 3016 6.405065 GGTTCCGACAGATACTACATACAACA 60.405 42.308 0.00 0.00 0.00 3.33
2100 3017 6.954487 TCCGACAGATACTACATACAACAT 57.046 37.500 0.00 0.00 0.00 2.71
2101 3018 8.347771 GTTCCGACAGATACTACATACAACATA 58.652 37.037 0.00 0.00 0.00 2.29
2102 3019 7.868775 TCCGACAGATACTACATACAACATAC 58.131 38.462 0.00 0.00 0.00 2.39
2103 3020 7.499895 TCCGACAGATACTACATACAACATACA 59.500 37.037 0.00 0.00 0.00 2.29
2104 3021 8.132995 CCGACAGATACTACATACAACATACAA 58.867 37.037 0.00 0.00 0.00 2.41
2105 3022 9.511144 CGACAGATACTACATACAACATACAAA 57.489 33.333 0.00 0.00 0.00 2.83
2109 3026 8.814235 AGATACTACATACAACATACAAAACGC 58.186 33.333 0.00 0.00 0.00 4.84
2110 3027 6.788684 ACTACATACAACATACAAAACGCA 57.211 33.333 0.00 0.00 0.00 5.24
2111 3028 7.192148 ACTACATACAACATACAAAACGCAA 57.808 32.000 0.00 0.00 0.00 4.85
2113 3030 5.457140 ACATACAACATACAAAACGCAAGG 58.543 37.500 0.00 0.00 46.39 3.61
2114 3031 5.009210 ACATACAACATACAAAACGCAAGGT 59.991 36.000 0.00 0.00 46.39 3.50
2115 3032 3.701241 ACAACATACAAAACGCAAGGTG 58.299 40.909 0.00 0.00 46.39 4.00
2116 3033 3.049206 CAACATACAAAACGCAAGGTGG 58.951 45.455 0.00 0.00 46.39 4.61
2117 3034 2.303175 ACATACAAAACGCAAGGTGGT 58.697 42.857 0.00 0.00 46.39 4.16
2118 3035 2.034053 ACATACAAAACGCAAGGTGGTG 59.966 45.455 0.00 0.00 46.39 4.17
2119 3036 1.025812 TACAAAACGCAAGGTGGTGG 58.974 50.000 0.00 0.00 46.39 4.61
2120 3037 0.968393 ACAAAACGCAAGGTGGTGGT 60.968 50.000 0.00 0.00 46.39 4.16
2121 3038 1.025812 CAAAACGCAAGGTGGTGGTA 58.974 50.000 0.00 0.00 46.39 3.25
2122 3039 1.405821 CAAAACGCAAGGTGGTGGTAA 59.594 47.619 0.00 0.00 46.39 2.85
2123 3040 1.026584 AAACGCAAGGTGGTGGTAAC 58.973 50.000 0.00 0.00 46.39 2.50
2124 3041 0.181824 AACGCAAGGTGGTGGTAACT 59.818 50.000 0.00 0.00 46.39 2.24
2125 3042 1.050204 ACGCAAGGTGGTGGTAACTA 58.950 50.000 0.00 0.00 46.39 2.24
2126 3043 1.270465 ACGCAAGGTGGTGGTAACTAC 60.270 52.381 0.00 0.00 46.39 2.73
2139 3056 3.858247 GGTAACTACCACTGCTTGTAGG 58.142 50.000 0.80 0.00 45.73 3.18
2140 3057 3.512724 GGTAACTACCACTGCTTGTAGGA 59.487 47.826 0.80 0.00 45.73 2.94
2141 3058 4.020839 GGTAACTACCACTGCTTGTAGGAA 60.021 45.833 0.80 0.00 45.73 3.36
2142 3059 4.699925 AACTACCACTGCTTGTAGGAAA 57.300 40.909 0.00 0.00 38.98 3.13
2143 3060 4.004196 ACTACCACTGCTTGTAGGAAAC 57.996 45.455 0.00 0.00 38.98 2.78
2144 3061 3.389983 ACTACCACTGCTTGTAGGAAACA 59.610 43.478 0.00 0.00 38.98 2.83
2145 3062 3.508845 ACCACTGCTTGTAGGAAACAT 57.491 42.857 0.00 0.00 38.10 2.71
2146 3063 3.832527 ACCACTGCTTGTAGGAAACATT 58.167 40.909 0.00 0.00 38.10 2.71
2147 3064 4.215109 ACCACTGCTTGTAGGAAACATTT 58.785 39.130 0.00 0.00 38.10 2.32
2148 3065 4.037923 ACCACTGCTTGTAGGAAACATTTG 59.962 41.667 0.00 0.00 38.10 2.32
2149 3066 4.037923 CCACTGCTTGTAGGAAACATTTGT 59.962 41.667 0.00 0.00 38.10 2.83
2150 3067 5.215160 CACTGCTTGTAGGAAACATTTGTC 58.785 41.667 0.00 0.00 38.10 3.18
2151 3068 4.278419 ACTGCTTGTAGGAAACATTTGTCC 59.722 41.667 0.00 0.00 38.10 4.02
2152 3069 3.252215 TGCTTGTAGGAAACATTTGTCCG 59.748 43.478 0.00 0.00 38.10 4.79
2153 3070 3.252458 GCTTGTAGGAAACATTTGTCCGT 59.748 43.478 0.00 0.00 38.10 4.69
2154 3071 4.261447 GCTTGTAGGAAACATTTGTCCGTT 60.261 41.667 0.00 0.00 38.10 4.44
2155 3072 5.049267 GCTTGTAGGAAACATTTGTCCGTTA 60.049 40.000 0.00 0.00 38.10 3.18
2156 3073 6.349033 GCTTGTAGGAAACATTTGTCCGTTAT 60.349 38.462 0.00 0.00 38.10 1.89
2157 3074 7.148373 GCTTGTAGGAAACATTTGTCCGTTATA 60.148 37.037 0.00 0.00 38.10 0.98
2158 3075 8.795842 TTGTAGGAAACATTTGTCCGTTATAT 57.204 30.769 0.00 0.00 38.10 0.86
2159 3076 9.887629 TTGTAGGAAACATTTGTCCGTTATATA 57.112 29.630 0.00 0.00 38.10 0.86
2246 3163 4.468510 TCCGGTATTGTTCCTTCACAGTAT 59.531 41.667 0.00 0.00 0.00 2.12
2265 3182 7.981789 CACAGTATAAGTGTGGAGTGTTATCAT 59.018 37.037 6.93 0.00 43.86 2.45
2283 3200 7.430211 TGTTATCATCAAAACTACGTACTAGCG 59.570 37.037 0.00 0.00 37.94 4.26
2305 3222 6.542370 AGCGGTATCATTTAGCAGTTTGTTAT 59.458 34.615 0.00 0.00 0.00 1.89
2340 3257 5.934043 TGTGTTGAGTCTGTTTATCCATCTG 59.066 40.000 0.00 0.00 0.00 2.90
2385 3302 4.346418 AGTCCCTGGATCTGTATTGTCATC 59.654 45.833 0.00 0.00 0.00 2.92
2444 3361 5.183228 CCGACAAATAGCCTCCTTTCTTTA 58.817 41.667 0.00 0.00 0.00 1.85
2458 3379 9.467796 CCTCCTTTCTTTACTCATTTATTTCCT 57.532 33.333 0.00 0.00 0.00 3.36
2508 3429 7.172019 TCCATGTTTTCGATCATCTATGACATG 59.828 37.037 0.00 11.29 40.03 3.21
2528 3449 7.701924 TGACATGACAGTCAAAATTTGAAGAAC 59.298 33.333 10.27 0.00 44.92 3.01
2540 3461 6.423776 AATTTGAAGAACCCACATGAATGT 57.576 33.333 0.00 0.00 42.84 2.71
2544 3465 3.795688 AGAACCCACATGAATGTCACT 57.204 42.857 0.00 0.00 39.39 3.41
2547 3468 4.279169 AGAACCCACATGAATGTCACTTTG 59.721 41.667 0.00 0.00 39.39 2.77
2548 3469 3.831323 ACCCACATGAATGTCACTTTGA 58.169 40.909 0.00 0.00 39.39 2.69
2549 3470 3.822735 ACCCACATGAATGTCACTTTGAG 59.177 43.478 0.00 0.00 39.39 3.02
2550 3471 3.366679 CCCACATGAATGTCACTTTGAGC 60.367 47.826 0.00 0.00 39.39 4.26
2551 3472 3.504906 CCACATGAATGTCACTTTGAGCT 59.495 43.478 0.00 0.00 39.39 4.09
2552 3473 4.473199 CACATGAATGTCACTTTGAGCTG 58.527 43.478 0.00 0.00 39.39 4.24
2553 3474 3.504906 ACATGAATGTCACTTTGAGCTGG 59.495 43.478 0.00 0.00 35.87 4.85
2554 3475 1.881973 TGAATGTCACTTTGAGCTGGC 59.118 47.619 0.00 0.00 0.00 4.85
2555 3476 1.881973 GAATGTCACTTTGAGCTGGCA 59.118 47.619 0.00 0.00 0.00 4.92
2556 3477 2.211250 ATGTCACTTTGAGCTGGCAT 57.789 45.000 0.00 0.00 0.00 4.40
2557 3478 1.985473 TGTCACTTTGAGCTGGCATT 58.015 45.000 0.00 0.00 0.00 3.56
2558 3479 1.610038 TGTCACTTTGAGCTGGCATTG 59.390 47.619 0.00 0.00 0.00 2.82
2559 3480 1.068055 GTCACTTTGAGCTGGCATTGG 60.068 52.381 0.00 0.00 0.00 3.16
2560 3481 0.245539 CACTTTGAGCTGGCATTGGG 59.754 55.000 0.00 0.00 0.00 4.12
2561 3482 0.178953 ACTTTGAGCTGGCATTGGGT 60.179 50.000 0.00 0.00 0.00 4.51
2562 3483 1.075374 ACTTTGAGCTGGCATTGGGTA 59.925 47.619 0.00 0.00 0.00 3.69
2563 3484 2.170166 CTTTGAGCTGGCATTGGGTAA 58.830 47.619 0.00 0.00 0.00 2.85
2580 3501 3.691609 GGGTAAGAGCTGGAATCAAGTTG 59.308 47.826 0.00 0.00 0.00 3.16
2595 3516 1.122019 AGTTGTCCTCGTCCTTGCCT 61.122 55.000 0.00 0.00 0.00 4.75
2661 3582 1.575788 TGGAGGATGAGAAGGAGGCTA 59.424 52.381 0.00 0.00 0.00 3.93
2664 3585 2.566724 GAGGATGAGAAGGAGGCTATGG 59.433 54.545 0.00 0.00 0.00 2.74
2665 3586 2.180973 AGGATGAGAAGGAGGCTATGGA 59.819 50.000 0.00 0.00 0.00 3.41
2666 3587 2.301583 GGATGAGAAGGAGGCTATGGAC 59.698 54.545 0.00 0.00 0.00 4.02
2667 3588 2.856760 TGAGAAGGAGGCTATGGACT 57.143 50.000 0.00 0.00 0.00 3.85
2668 3589 3.121929 TGAGAAGGAGGCTATGGACTT 57.878 47.619 0.00 0.00 0.00 3.01
2669 3590 3.034635 TGAGAAGGAGGCTATGGACTTC 58.965 50.000 0.00 0.00 38.20 3.01
2670 3591 2.367241 GAGAAGGAGGCTATGGACTTCC 59.633 54.545 0.00 0.00 38.58 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.616679 TACTGGTGGTAGGCTGACCC 60.617 60.000 0.00 0.00 38.89 4.46
99 104 1.154205 GGCTGGATGGTCGTGATTCG 61.154 60.000 0.00 0.00 41.41 3.34
135 140 5.615261 TGGCCTATTATGGAAGGAACCTAAT 59.385 40.000 3.32 0.00 34.58 1.73
138 143 3.138468 GTGGCCTATTATGGAAGGAACCT 59.862 47.826 3.32 0.00 34.58 3.50
143 148 3.690460 GATGGTGGCCTATTATGGAAGG 58.310 50.000 3.32 0.00 35.86 3.46
144 149 3.244561 ACGATGGTGGCCTATTATGGAAG 60.245 47.826 3.32 0.00 0.00 3.46
153 161 3.628989 CCAGACGATGGTGGCCTA 58.371 61.111 3.32 0.00 44.91 3.93
162 170 1.486726 GAGGTTCCCAATCCAGACGAT 59.513 52.381 0.00 0.00 0.00 3.73
184 192 4.358851 CAAGAAATTTGCGGACACTTGAA 58.641 39.130 0.00 0.00 36.43 2.69
241 249 6.540189 GTCAGGATAGCAACAGTACAATCAAT 59.460 38.462 0.00 0.00 0.00 2.57
245 253 4.384208 GGGTCAGGATAGCAACAGTACAAT 60.384 45.833 0.00 0.00 0.00 2.71
248 256 2.158943 GGGGTCAGGATAGCAACAGTAC 60.159 54.545 0.00 0.00 0.00 2.73
307 332 8.246180 GGATAAGAGAAATGAATGCACAAAAGA 58.754 33.333 0.00 0.00 0.00 2.52
336 361 9.241317 GATGAAAGGTAAATTGTGCATAATCAG 57.759 33.333 9.29 0.00 0.00 2.90
348 373 7.014615 ACAAAGACAGCTGATGAAAGGTAAATT 59.985 33.333 23.35 0.00 0.00 1.82
383 408 2.354805 GCTCTGAATTTCAGTACCGGGT 60.355 50.000 22.44 4.46 44.58 5.28
549 784 1.131126 CCCTGCGCAAACTTAGTGATG 59.869 52.381 13.05 0.00 0.00 3.07
646 1002 3.803778 CCTGTCAAGTGCAATTTTTCACC 59.196 43.478 0.00 0.00 33.90 4.02
655 1011 1.337703 GAACATGCCTGTCAAGTGCAA 59.662 47.619 0.00 0.00 38.69 4.08
713 1069 7.573096 CGTGAGTTGCTAGGAATAAAACACAAT 60.573 37.037 0.00 0.00 0.00 2.71
716 1072 5.390567 CCGTGAGTTGCTAGGAATAAAACAC 60.391 44.000 0.00 6.06 0.00 3.32
771 1292 2.535012 TACATGCACGGTTCACTCAA 57.465 45.000 0.00 0.00 0.00 3.02
775 1296 9.541724 CATTAATAATATACATGCACGGTTCAC 57.458 33.333 0.00 0.00 0.00 3.18
776 1297 9.495572 TCATTAATAATATACATGCACGGTTCA 57.504 29.630 0.00 0.00 0.00 3.18
780 1301 9.225201 GCAATCATTAATAATATACATGCACGG 57.775 33.333 0.00 0.00 0.00 4.94
781 1302 9.992910 AGCAATCATTAATAATATACATGCACG 57.007 29.630 0.00 0.00 0.00 5.34
916 1771 7.599245 AGAACAATACAGAAGAACGTAGAAAGG 59.401 37.037 0.00 0.00 0.00 3.11
984 1880 3.189618 TGCATTCTGGATGAGCTACAG 57.810 47.619 0.00 0.00 38.03 2.74
1038 1934 1.757118 GATGAGTGGACCTTGATCCGA 59.243 52.381 0.00 0.00 42.24 4.55
1041 1937 3.196469 TGTCTGATGAGTGGACCTTGATC 59.804 47.826 0.00 0.00 0.00 2.92
1042 1938 3.055530 GTGTCTGATGAGTGGACCTTGAT 60.056 47.826 0.00 0.00 0.00 2.57
1066 1965 1.944024 CTTTGCCTTGACGGTGTACAA 59.056 47.619 0.00 0.00 34.25 2.41
1115 2015 1.270839 TGTCTTCTAGCTGCAACCCAC 60.271 52.381 1.02 0.00 0.00 4.61
1209 2109 2.697761 GCCTGACAGCGTCTCCGTA 61.698 63.158 0.00 0.00 36.15 4.02
1324 2225 0.874390 TGTTTGCTGGCGAAGATGAC 59.126 50.000 0.00 0.00 0.00 3.06
1419 2320 3.041946 CCTACTTTCTCCTGGCCTACAT 58.958 50.000 3.32 0.00 0.00 2.29
1482 2386 1.079750 GCTCCTGACGTCAAGGTCC 60.080 63.158 20.49 13.15 36.07 4.46
1517 2421 4.396478 TCTCGTAGATCTTCACCTTGACAG 59.604 45.833 0.00 0.00 33.89 3.51
1777 2694 3.181443 ACCGGGTGATAGGATGGATTTTC 60.181 47.826 6.32 0.00 0.00 2.29
1778 2695 2.783510 ACCGGGTGATAGGATGGATTTT 59.216 45.455 6.32 0.00 0.00 1.82
1779 2696 2.106511 CACCGGGTGATAGGATGGATTT 59.893 50.000 22.77 0.00 35.23 2.17
1780 2697 1.699634 CACCGGGTGATAGGATGGATT 59.300 52.381 22.77 0.00 35.23 3.01
1781 2698 1.352083 CACCGGGTGATAGGATGGAT 58.648 55.000 22.77 0.00 35.23 3.41
1782 2699 0.762842 CCACCGGGTGATAGGATGGA 60.763 60.000 28.36 0.00 35.23 3.41
1783 2700 1.754745 CCACCGGGTGATAGGATGG 59.245 63.158 28.36 5.14 35.23 3.51
1800 2717 2.835764 TGAGACATGTGGGGTAACTACC 59.164 50.000 1.15 0.00 45.71 3.18
1801 2718 4.755266 ATGAGACATGTGGGGTAACTAC 57.245 45.455 1.15 0.00 0.00 2.73
1802 2719 7.302948 AGTATATGAGACATGTGGGGTAACTA 58.697 38.462 1.15 0.00 0.00 2.24
1803 2720 6.143915 AGTATATGAGACATGTGGGGTAACT 58.856 40.000 1.15 0.00 0.00 2.24
1804 2721 6.420913 AGTATATGAGACATGTGGGGTAAC 57.579 41.667 1.15 0.00 0.00 2.50
1805 2722 6.495872 GGTAGTATATGAGACATGTGGGGTAA 59.504 42.308 1.15 0.00 0.00 2.85
1806 2723 6.014647 GGTAGTATATGAGACATGTGGGGTA 58.985 44.000 1.15 0.00 0.00 3.69
1807 2724 4.838986 GGTAGTATATGAGACATGTGGGGT 59.161 45.833 1.15 0.00 0.00 4.95
1808 2725 4.838423 TGGTAGTATATGAGACATGTGGGG 59.162 45.833 1.15 0.00 0.00 4.96
1809 2726 6.014242 ACATGGTAGTATATGAGACATGTGGG 60.014 42.308 1.15 0.00 43.84 4.61
1810 2727 6.997655 ACATGGTAGTATATGAGACATGTGG 58.002 40.000 1.15 0.00 43.84 4.17
1812 2729 6.997655 CCACATGGTAGTATATGAGACATGT 58.002 40.000 0.00 0.00 45.67 3.21
1912 2829 6.736110 ACTATGGGCTCATATGCAATTTTT 57.264 33.333 6.77 0.00 35.53 1.94
1913 2830 6.736110 AACTATGGGCTCATATGCAATTTT 57.264 33.333 6.77 0.00 35.53 1.82
1914 2831 6.736110 AAACTATGGGCTCATATGCAATTT 57.264 33.333 6.77 1.06 35.53 1.82
1915 2832 6.736110 AAAACTATGGGCTCATATGCAATT 57.264 33.333 6.77 0.00 35.53 2.32
1916 2833 6.098695 ACAAAAACTATGGGCTCATATGCAAT 59.901 34.615 6.77 0.00 35.53 3.56
1917 2834 5.421693 ACAAAAACTATGGGCTCATATGCAA 59.578 36.000 6.77 0.00 35.53 4.08
1918 2835 4.955450 ACAAAAACTATGGGCTCATATGCA 59.045 37.500 6.77 0.00 35.53 3.96
1919 2836 5.520376 ACAAAAACTATGGGCTCATATGC 57.480 39.130 6.77 0.00 35.53 3.14
1924 2841 9.030452 ACAAATATAACAAAAACTATGGGCTCA 57.970 29.630 0.00 0.00 0.00 4.26
2036 2953 9.940166 CGTGTAGTATGTAGTACATAACAATGA 57.060 33.333 21.78 0.48 42.15 2.57
2037 2954 9.726232 ACGTGTAGTATGTAGTACATAACAATG 57.274 33.333 21.78 18.97 42.15 2.82
2040 2957 9.377312 TGTACGTGTAGTATGTAGTACATAACA 57.623 33.333 21.78 19.64 42.15 2.41
2045 2962 9.249457 GAGTATGTACGTGTAGTATGTAGTACA 57.751 37.037 5.24 5.24 45.25 2.90
2046 2963 9.469807 AGAGTATGTACGTGTAGTATGTAGTAC 57.530 37.037 0.00 0.00 37.69 2.73
2047 2964 9.684448 GAGAGTATGTACGTGTAGTATGTAGTA 57.316 37.037 0.00 0.00 37.69 1.82
2048 2965 7.380870 CGAGAGTATGTACGTGTAGTATGTAGT 59.619 40.741 0.00 0.00 37.69 2.73
2049 2966 7.148836 CCGAGAGTATGTACGTGTAGTATGTAG 60.149 44.444 0.00 0.00 37.69 2.74
2050 2967 6.642540 CCGAGAGTATGTACGTGTAGTATGTA 59.357 42.308 0.00 0.00 37.69 2.29
2051 2968 5.464722 CCGAGAGTATGTACGTGTAGTATGT 59.535 44.000 0.00 0.00 37.69 2.29
2052 2969 5.464722 ACCGAGAGTATGTACGTGTAGTATG 59.535 44.000 0.00 0.00 37.69 2.39
2053 2970 5.605534 ACCGAGAGTATGTACGTGTAGTAT 58.394 41.667 0.00 0.00 37.69 2.12
2054 2971 5.011090 ACCGAGAGTATGTACGTGTAGTA 57.989 43.478 0.00 0.00 0.00 1.82
2055 2972 3.866651 ACCGAGAGTATGTACGTGTAGT 58.133 45.455 0.00 0.00 0.00 2.73
2056 2973 4.260538 GGAACCGAGAGTATGTACGTGTAG 60.261 50.000 0.00 0.00 0.00 2.74
2057 2974 3.623060 GGAACCGAGAGTATGTACGTGTA 59.377 47.826 0.00 0.00 0.00 2.90
2058 2975 2.421424 GGAACCGAGAGTATGTACGTGT 59.579 50.000 0.00 0.00 0.00 4.49
2059 2976 2.538333 CGGAACCGAGAGTATGTACGTG 60.538 54.545 7.53 0.00 42.83 4.49
2060 2977 1.667724 CGGAACCGAGAGTATGTACGT 59.332 52.381 7.53 0.00 42.83 3.57
2061 2978 1.935873 TCGGAACCGAGAGTATGTACG 59.064 52.381 12.04 0.00 44.01 3.67
2072 2989 2.989909 TGTAGTATCTGTCGGAACCGA 58.010 47.619 12.04 12.04 46.87 4.69
2073 2990 3.984508 ATGTAGTATCTGTCGGAACCG 57.015 47.619 6.94 6.94 41.35 4.44
2074 2991 5.762825 TGTATGTAGTATCTGTCGGAACC 57.237 43.478 0.00 0.00 0.00 3.62
2075 2992 6.558009 TGTTGTATGTAGTATCTGTCGGAAC 58.442 40.000 0.00 0.00 0.00 3.62
2076 2993 6.762702 TGTTGTATGTAGTATCTGTCGGAA 57.237 37.500 0.00 0.00 0.00 4.30
2077 2994 6.954487 ATGTTGTATGTAGTATCTGTCGGA 57.046 37.500 0.00 0.00 0.00 4.55
2078 2995 7.645402 TGTATGTTGTATGTAGTATCTGTCGG 58.355 38.462 0.00 0.00 0.00 4.79
2079 2996 9.511144 TTTGTATGTTGTATGTAGTATCTGTCG 57.489 33.333 0.00 0.00 0.00 4.35
2083 3000 8.814235 GCGTTTTGTATGTTGTATGTAGTATCT 58.186 33.333 0.00 0.00 0.00 1.98
2084 3001 8.597227 TGCGTTTTGTATGTTGTATGTAGTATC 58.403 33.333 0.00 0.00 0.00 2.24
2085 3002 8.481974 TGCGTTTTGTATGTTGTATGTAGTAT 57.518 30.769 0.00 0.00 0.00 2.12
2086 3003 7.886405 TGCGTTTTGTATGTTGTATGTAGTA 57.114 32.000 0.00 0.00 0.00 1.82
2087 3004 6.788684 TGCGTTTTGTATGTTGTATGTAGT 57.211 33.333 0.00 0.00 0.00 2.73
2088 3005 6.740905 CCTTGCGTTTTGTATGTTGTATGTAG 59.259 38.462 0.00 0.00 0.00 2.74
2089 3006 6.205076 ACCTTGCGTTTTGTATGTTGTATGTA 59.795 34.615 0.00 0.00 0.00 2.29
2090 3007 5.009210 ACCTTGCGTTTTGTATGTTGTATGT 59.991 36.000 0.00 0.00 0.00 2.29
2091 3008 5.341993 CACCTTGCGTTTTGTATGTTGTATG 59.658 40.000 0.00 0.00 0.00 2.39
2092 3009 5.457140 CACCTTGCGTTTTGTATGTTGTAT 58.543 37.500 0.00 0.00 0.00 2.29
2093 3010 4.261238 CCACCTTGCGTTTTGTATGTTGTA 60.261 41.667 0.00 0.00 0.00 2.41
2094 3011 3.490078 CCACCTTGCGTTTTGTATGTTGT 60.490 43.478 0.00 0.00 0.00 3.32
2095 3012 3.049206 CCACCTTGCGTTTTGTATGTTG 58.951 45.455 0.00 0.00 0.00 3.33
2096 3013 2.691011 ACCACCTTGCGTTTTGTATGTT 59.309 40.909 0.00 0.00 0.00 2.71
2097 3014 2.034053 CACCACCTTGCGTTTTGTATGT 59.966 45.455 0.00 0.00 0.00 2.29
2098 3015 2.606795 CCACCACCTTGCGTTTTGTATG 60.607 50.000 0.00 0.00 0.00 2.39
2099 3016 1.611491 CCACCACCTTGCGTTTTGTAT 59.389 47.619 0.00 0.00 0.00 2.29
2100 3017 1.025812 CCACCACCTTGCGTTTTGTA 58.974 50.000 0.00 0.00 0.00 2.41
2101 3018 0.968393 ACCACCACCTTGCGTTTTGT 60.968 50.000 0.00 0.00 0.00 2.83
2102 3019 1.025812 TACCACCACCTTGCGTTTTG 58.974 50.000 0.00 0.00 0.00 2.44
2103 3020 1.406180 GTTACCACCACCTTGCGTTTT 59.594 47.619 0.00 0.00 0.00 2.43
2104 3021 1.026584 GTTACCACCACCTTGCGTTT 58.973 50.000 0.00 0.00 0.00 3.60
2105 3022 0.181824 AGTTACCACCACCTTGCGTT 59.818 50.000 0.00 0.00 0.00 4.84
2106 3023 1.050204 TAGTTACCACCACCTTGCGT 58.950 50.000 0.00 0.00 0.00 5.24
2107 3024 1.435577 GTAGTTACCACCACCTTGCG 58.564 55.000 0.00 0.00 0.00 4.85
2108 3025 1.817357 GGTAGTTACCACCACCTTGC 58.183 55.000 3.45 0.00 45.73 4.01
2118 3035 3.512724 TCCTACAAGCAGTGGTAGTTACC 59.487 47.826 0.00 1.25 46.62 2.85
2119 3036 4.796038 TCCTACAAGCAGTGGTAGTTAC 57.204 45.455 0.00 0.00 36.17 2.50
2120 3037 5.070714 TGTTTCCTACAAGCAGTGGTAGTTA 59.929 40.000 0.00 0.00 36.17 2.24
2121 3038 4.141574 TGTTTCCTACAAGCAGTGGTAGTT 60.142 41.667 0.00 0.00 36.17 2.24
2122 3039 3.389983 TGTTTCCTACAAGCAGTGGTAGT 59.610 43.478 0.00 0.00 36.17 2.73
2123 3040 4.002906 TGTTTCCTACAAGCAGTGGTAG 57.997 45.455 0.00 0.00 37.36 3.18
2124 3041 4.634012 ATGTTTCCTACAAGCAGTGGTA 57.366 40.909 0.00 0.00 40.89 3.25
2125 3042 3.508845 ATGTTTCCTACAAGCAGTGGT 57.491 42.857 0.00 0.00 40.89 4.16
2126 3043 4.037923 ACAAATGTTTCCTACAAGCAGTGG 59.962 41.667 0.00 0.00 40.89 4.00
2127 3044 5.186996 ACAAATGTTTCCTACAAGCAGTG 57.813 39.130 0.00 0.00 40.89 3.66
2128 3045 4.278419 GGACAAATGTTTCCTACAAGCAGT 59.722 41.667 0.00 0.00 40.89 4.40
2129 3046 4.613622 CGGACAAATGTTTCCTACAAGCAG 60.614 45.833 0.00 0.00 40.89 4.24
2130 3047 3.252215 CGGACAAATGTTTCCTACAAGCA 59.748 43.478 0.00 0.00 40.89 3.91
2131 3048 3.252458 ACGGACAAATGTTTCCTACAAGC 59.748 43.478 0.00 0.00 40.89 4.01
2132 3049 5.432885 AACGGACAAATGTTTCCTACAAG 57.567 39.130 0.00 0.00 40.89 3.16
2133 3050 8.795842 ATATAACGGACAAATGTTTCCTACAA 57.204 30.769 0.00 0.00 40.89 2.41
2246 3163 7.936847 AGTTTTGATGATAACACTCCACACTTA 59.063 33.333 0.00 0.00 0.00 2.24
2265 3182 5.353956 TGATACCGCTAGTACGTAGTTTTGA 59.646 40.000 8.48 0.00 37.78 2.69
2305 3222 6.636705 ACAGACTCAACACACTAACAAACTA 58.363 36.000 0.00 0.00 0.00 2.24
2340 3257 6.505272 ACTCTTAATAGTAGTTCGGCATGAC 58.495 40.000 0.00 0.00 0.00 3.06
2385 3302 7.664082 ACAGACTGTTATTCTCAATCAACTG 57.336 36.000 1.07 0.00 0.00 3.16
2444 3361 9.628500 GGGTATGTAGAAAGGAAATAAATGAGT 57.372 33.333 0.00 0.00 0.00 3.41
2481 3402 7.219322 TGTCATAGATGATCGAAAACATGGAT 58.781 34.615 0.00 0.00 39.30 3.41
2508 3429 5.748630 GTGGGTTCTTCAAATTTTGACTGTC 59.251 40.000 11.30 0.00 39.87 3.51
2519 3440 4.892345 TGACATTCATGTGGGTTCTTCAAA 59.108 37.500 0.00 0.00 41.95 2.69
2528 3449 3.366679 GCTCAAAGTGACATTCATGTGGG 60.367 47.826 0.00 0.00 41.95 4.61
2540 3461 1.250328 CCAATGCCAGCTCAAAGTGA 58.750 50.000 0.00 0.00 0.00 3.41
2544 3465 2.170166 CTTACCCAATGCCAGCTCAAA 58.830 47.619 0.00 0.00 0.00 2.69
2547 3468 1.673168 CTCTTACCCAATGCCAGCTC 58.327 55.000 0.00 0.00 0.00 4.09
2548 3469 0.394899 GCTCTTACCCAATGCCAGCT 60.395 55.000 0.00 0.00 0.00 4.24
2549 3470 0.394899 AGCTCTTACCCAATGCCAGC 60.395 55.000 0.00 0.00 0.00 4.85
2550 3471 1.386533 CAGCTCTTACCCAATGCCAG 58.613 55.000 0.00 0.00 0.00 4.85
2551 3472 0.034186 CCAGCTCTTACCCAATGCCA 60.034 55.000 0.00 0.00 0.00 4.92
2552 3473 0.255890 TCCAGCTCTTACCCAATGCC 59.744 55.000 0.00 0.00 0.00 4.40
2553 3474 2.128771 TTCCAGCTCTTACCCAATGC 57.871 50.000 0.00 0.00 0.00 3.56
2554 3475 3.889815 TGATTCCAGCTCTTACCCAATG 58.110 45.455 0.00 0.00 0.00 2.82
2555 3476 4.018050 ACTTGATTCCAGCTCTTACCCAAT 60.018 41.667 0.00 0.00 0.00 3.16
2556 3477 3.330701 ACTTGATTCCAGCTCTTACCCAA 59.669 43.478 0.00 0.00 0.00 4.12
2557 3478 2.912956 ACTTGATTCCAGCTCTTACCCA 59.087 45.455 0.00 0.00 0.00 4.51
2558 3479 3.636153 ACTTGATTCCAGCTCTTACCC 57.364 47.619 0.00 0.00 0.00 3.69
2559 3480 4.327680 ACAACTTGATTCCAGCTCTTACC 58.672 43.478 0.00 0.00 0.00 2.85
2560 3481 4.393371 GGACAACTTGATTCCAGCTCTTAC 59.607 45.833 0.00 0.00 0.00 2.34
2561 3482 4.287067 AGGACAACTTGATTCCAGCTCTTA 59.713 41.667 0.00 0.00 0.00 2.10
2562 3483 3.073650 AGGACAACTTGATTCCAGCTCTT 59.926 43.478 0.00 0.00 0.00 2.85
2563 3484 2.641815 AGGACAACTTGATTCCAGCTCT 59.358 45.455 0.00 0.00 0.00 4.09
2580 3501 0.955919 CCAAAGGCAAGGACGAGGAC 60.956 60.000 0.00 0.00 0.00 3.85
2595 3516 2.291043 GCCGTCCTCCTCCTCCAAA 61.291 63.158 0.00 0.00 0.00 3.28
2631 3552 2.042930 ATCCTCCACCACTCCCCC 59.957 66.667 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.