Multiple sequence alignment - TraesCS3A01G006800

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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 TraesCS3A01G006800 chr3A 100.000 4751 0 0 1 4751 7316041 7311291 0.000000e+00 8774.0
1 TraesCS3A01G006800 chr3A 88.494 1521 151 11 3238 4751 7386325 7384822 0.000000e+00 1818.0
2 TraesCS3A01G006800 chr3A 92.323 1003 57 12 976 1973 7389086 7388099 0.000000e+00 1408.0
3 TraesCS3A01G006800 chr3A 93.124 858 50 7 1 851 489614146 489615001 0.000000e+00 1249.0
4 TraesCS3A01G006800 chr3A 85.897 234 30 3 2392 2624 45585392 45585623 3.670000e-61 246.0
5 TraesCS3A01G006800 chr3A 77.640 161 29 4 3063 3220 550145046 550144890 1.820000e-14 91.6
6 TraesCS3A01G006800 chr3A 78.289 152 26 4 3063 3211 690219861 690220008 1.820000e-14 91.6
7 TraesCS3A01G006800 chr3A 75.497 151 30 5 3063 3210 691401075 691401221 3.070000e-07 67.6
8 TraesCS3A01G006800 chr3B 89.290 1522 138 12 3238 4751 4703715 4705219 0.000000e+00 1884.0
9 TraesCS3A01G006800 chr3B 89.166 1523 138 14 3238 4751 3805235 3806739 0.000000e+00 1873.0
10 TraesCS3A01G006800 chr3B 83.643 1021 125 31 983 1979 3803384 3804386 0.000000e+00 922.0
11 TraesCS3A01G006800 chr3B 83.366 1022 125 33 983 1979 4701863 4702864 0.000000e+00 904.0
12 TraesCS3A01G006800 chr3B 85.366 246 32 3 2381 2623 813317746 813317990 7.890000e-63 252.0
13 TraesCS3A01G006800 chr3B 85.629 167 21 2 2013 2179 104590776 104590613 6.320000e-39 172.0
14 TraesCS3A01G006800 chr3D 93.517 1234 73 3 3522 4751 1658169 1659399 0.000000e+00 1829.0
15 TraesCS3A01G006800 chr3D 85.528 1071 115 23 976 2028 1655921 1656969 0.000000e+00 1083.0
16 TraesCS3A01G006800 chr3D 85.501 869 65 25 2621 3439 1656947 1657804 0.000000e+00 850.0
17 TraesCS3A01G006800 chr3D 96.667 60 2 0 4273 4332 1708269 1708328 3.030000e-17 100.0
18 TraesCS3A01G006800 chr1A 93.450 855 50 6 1 850 67196620 67195767 0.000000e+00 1264.0
19 TraesCS3A01G006800 chr1A 76.489 655 103 34 2014 2649 2538309 2538931 4.620000e-80 309.0
20 TraesCS3A01G006800 chr1A 74.242 660 97 39 2016 2620 531026640 531025999 4.820000e-50 209.0
21 TraesCS3A01G006800 chr1A 78.289 152 26 5 3063 3211 30569762 30569909 1.820000e-14 91.6
22 TraesCS3A01G006800 chr7A 93.450 855 49 7 1 850 526995359 526994507 0.000000e+00 1262.0
23 TraesCS3A01G006800 chr7A 93.091 854 53 6 1 850 566749085 566748234 0.000000e+00 1245.0
24 TraesCS3A01G006800 chr7A 87.037 162 16 4 2008 2167 8231154 8231312 1.360000e-40 178.0
25 TraesCS3A01G006800 chr6A 93.333 855 50 7 1 850 433944677 433943825 0.000000e+00 1256.0
26 TraesCS3A01G006800 chr6A 93.248 859 44 11 1 850 126542580 126541727 0.000000e+00 1253.0
27 TraesCS3A01G006800 chr6A 93.107 856 52 7 1 850 387041905 387042759 0.000000e+00 1247.0
28 TraesCS3A01G006800 chr6A 79.054 1036 189 20 3638 4662 574526099 574525081 0.000000e+00 686.0
29 TraesCS3A01G006800 chr6A 78.378 666 65 37 2016 2620 614871215 614871862 4.520000e-95 359.0
30 TraesCS3A01G006800 chr6A 77.848 158 28 4 3063 3217 588365493 588365340 1.820000e-14 91.6
31 TraesCS3A01G006800 chr5A 93.232 857 50 8 1 851 614878792 614879646 0.000000e+00 1254.0
32 TraesCS3A01G006800 chr5A 81.250 288 36 11 2345 2618 672336195 672336478 2.880000e-52 217.0
33 TraesCS3A01G006800 chr4A 93.216 855 53 5 1 850 374607580 374608434 0.000000e+00 1253.0
34 TraesCS3A01G006800 chr4A 77.439 164 29 5 3063 3222 556629259 556629100 1.820000e-14 91.6
35 TraesCS3A01G006800 chrUn 82.512 852 111 27 998 1827 426378073 426377238 0.000000e+00 713.0
36 TraesCS3A01G006800 chr6B 79.138 1021 185 19 3638 4647 646742446 646741443 0.000000e+00 680.0
37 TraesCS3A01G006800 chr6B 78.658 909 150 33 1076 1951 2072247 2073144 8.930000e-157 564.0
38 TraesCS3A01G006800 chr6B 78.733 884 148 32 1097 1951 5790395 5791267 5.370000e-154 555.0
39 TraesCS3A01G006800 chr6D 79.054 888 132 32 1097 1951 606130 605264 1.150000e-155 560.0
40 TraesCS3A01G006800 chr6D 81.211 479 72 9 1476 1951 1489192 1489655 2.090000e-98 370.0
41 TraesCS3A01G006800 chr6D 84.195 348 32 18 2148 2487 78818921 78818589 2.760000e-82 316.0
42 TraesCS3A01G006800 chr6D 84.483 174 21 4 2016 2189 411408231 411408064 2.940000e-37 167.0
43 TraesCS3A01G006800 chr2B 77.677 878 152 30 1099 1951 755591393 755592251 3.300000e-136 496.0
44 TraesCS3A01G006800 chr2B 78.737 649 61 32 2020 2620 569126109 569126728 3.490000e-96 363.0
45 TraesCS3A01G006800 chr2B 81.102 254 21 11 2013 2247 180568181 180567936 1.360000e-40 178.0
46 TraesCS3A01G006800 chr4B 79.522 669 81 28 2008 2634 630641103 630640449 4.390000e-115 425.0
47 TraesCS3A01G006800 chr4B 81.915 282 29 11 2346 2626 23813739 23813479 8.010000e-53 219.0
48 TraesCS3A01G006800 chr4B 83.983 231 30 6 2392 2620 665417781 665418006 1.040000e-51 215.0
49 TraesCS3A01G006800 chr2D 86.104 403 43 11 2226 2617 624782137 624782537 5.680000e-114 422.0
50 TraesCS3A01G006800 chr2D 79.936 623 83 26 2024 2627 562165810 562166409 2.040000e-113 420.0
51 TraesCS3A01G006800 chr2D 79.412 102 15 5 2863 2958 45687457 45687356 3.070000e-07 67.6
52 TraesCS3A01G006800 chr5D 79.811 634 63 33 2014 2620 482384262 482384857 7.410000e-108 401.0
53 TraesCS3A01G006800 chr5D 81.034 290 45 9 2342 2627 454832057 454831774 6.190000e-54 222.0
54 TraesCS3A01G006800 chr5D 89.571 163 14 2 2014 2176 491269290 491269449 2.240000e-48 204.0
55 TraesCS3A01G006800 chr2A 81.569 510 60 20 2017 2504 40473540 40473043 1.600000e-104 390.0
56 TraesCS3A01G006800 chr2A 77.215 632 100 33 2017 2617 40472610 40471992 3.540000e-86 329.0
57 TraesCS3A01G006800 chr2A 77.863 131 26 3 2993 3120 724421537 724421407 1.420000e-10 78.7
58 TraesCS3A01G006800 chr1B 75.146 684 98 43 2009 2649 3663661 3663007 6.100000e-64 255.0
59 TraesCS3A01G006800 chr1B 87.421 159 17 2 2009 2167 420236689 420236844 3.780000e-41 180.0
60 TraesCS3A01G006800 chr7D 79.261 352 40 14 2160 2491 634722715 634722377 1.040000e-51 215.0
61 TraesCS3A01G006800 chr7D 81.569 255 23 11 2009 2247 567337898 567338144 6.280000e-44 189.0
62 TraesCS3A01G006800 chr7D 88.889 153 12 4 2016 2167 95103677 95103825 2.920000e-42 183.0
63 TraesCS3A01G006800 chr4D 75.527 237 38 15 2394 2620 78834999 78834773 1.090000e-16 99.0
64 TraesCS3A01G006800 chr7B 75.758 198 40 6 2985 3178 468404041 468404234 5.060000e-15 93.5
65 TraesCS3A01G006800 chr1D 78.676 136 18 11 2985 3113 240665934 240666065 3.940000e-11 80.5


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 TraesCS3A01G006800 chr3A 7311291 7316041 4750 True 8774.0 8774 100.0000 1 4751 1 chr3A.!!$R1 4750
1 TraesCS3A01G006800 chr3A 7384822 7389086 4264 True 1613.0 1818 90.4085 976 4751 2 chr3A.!!$R3 3775
2 TraesCS3A01G006800 chr3A 489614146 489615001 855 False 1249.0 1249 93.1240 1 851 1 chr3A.!!$F2 850
3 TraesCS3A01G006800 chr3B 3803384 3806739 3355 False 1397.5 1873 86.4045 983 4751 2 chr3B.!!$F2 3768
4 TraesCS3A01G006800 chr3B 4701863 4705219 3356 False 1394.0 1884 86.3280 983 4751 2 chr3B.!!$F3 3768
5 TraesCS3A01G006800 chr3D 1655921 1659399 3478 False 1254.0 1829 88.1820 976 4751 3 chr3D.!!$F2 3775
6 TraesCS3A01G006800 chr1A 67195767 67196620 853 True 1264.0 1264 93.4500 1 850 1 chr1A.!!$R1 849
7 TraesCS3A01G006800 chr1A 2538309 2538931 622 False 309.0 309 76.4890 2014 2649 1 chr1A.!!$F1 635
8 TraesCS3A01G006800 chr1A 531025999 531026640 641 True 209.0 209 74.2420 2016 2620 1 chr1A.!!$R2 604
9 TraesCS3A01G006800 chr7A 526994507 526995359 852 True 1262.0 1262 93.4500 1 850 1 chr7A.!!$R1 849
10 TraesCS3A01G006800 chr7A 566748234 566749085 851 True 1245.0 1245 93.0910 1 850 1 chr7A.!!$R2 849
11 TraesCS3A01G006800 chr6A 433943825 433944677 852 True 1256.0 1256 93.3330 1 850 1 chr6A.!!$R2 849
12 TraesCS3A01G006800 chr6A 126541727 126542580 853 True 1253.0 1253 93.2480 1 850 1 chr6A.!!$R1 849
13 TraesCS3A01G006800 chr6A 387041905 387042759 854 False 1247.0 1247 93.1070 1 850 1 chr6A.!!$F1 849
14 TraesCS3A01G006800 chr6A 574525081 574526099 1018 True 686.0 686 79.0540 3638 4662 1 chr6A.!!$R3 1024
15 TraesCS3A01G006800 chr6A 614871215 614871862 647 False 359.0 359 78.3780 2016 2620 1 chr6A.!!$F2 604
16 TraesCS3A01G006800 chr5A 614878792 614879646 854 False 1254.0 1254 93.2320 1 851 1 chr5A.!!$F1 850
17 TraesCS3A01G006800 chr4A 374607580 374608434 854 False 1253.0 1253 93.2160 1 850 1 chr4A.!!$F1 849
18 TraesCS3A01G006800 chrUn 426377238 426378073 835 True 713.0 713 82.5120 998 1827 1 chrUn.!!$R1 829
19 TraesCS3A01G006800 chr6B 646741443 646742446 1003 True 680.0 680 79.1380 3638 4647 1 chr6B.!!$R1 1009
20 TraesCS3A01G006800 chr6B 2072247 2073144 897 False 564.0 564 78.6580 1076 1951 1 chr6B.!!$F1 875
21 TraesCS3A01G006800 chr6B 5790395 5791267 872 False 555.0 555 78.7330 1097 1951 1 chr6B.!!$F2 854
22 TraesCS3A01G006800 chr6D 605264 606130 866 True 560.0 560 79.0540 1097 1951 1 chr6D.!!$R1 854
23 TraesCS3A01G006800 chr2B 755591393 755592251 858 False 496.0 496 77.6770 1099 1951 1 chr2B.!!$F2 852
24 TraesCS3A01G006800 chr2B 569126109 569126728 619 False 363.0 363 78.7370 2020 2620 1 chr2B.!!$F1 600
25 TraesCS3A01G006800 chr4B 630640449 630641103 654 True 425.0 425 79.5220 2008 2634 1 chr4B.!!$R2 626
26 TraesCS3A01G006800 chr2D 562165810 562166409 599 False 420.0 420 79.9360 2024 2627 1 chr2D.!!$F1 603
27 TraesCS3A01G006800 chr5D 482384262 482384857 595 False 401.0 401 79.8110 2014 2620 1 chr5D.!!$F1 606
28 TraesCS3A01G006800 chr2A 40471992 40473540 1548 True 359.5 390 79.3920 2017 2617 2 chr2A.!!$R2 600
29 TraesCS3A01G006800 chr1B 3663007 3663661 654 True 255.0 255 75.1460 2009 2649 1 chr1B.!!$R1 640

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
818 827 0.043334 AGCCTCTCCATACACACCCT 59.957 55.0 0.00 0.0 0.0 4.34 F
935 944 0.101040 TTCAAGTCGTCGTTGGTCGT 59.899 50.0 0.00 0.0 40.8 4.34 F
936 945 0.317269 TCAAGTCGTCGTTGGTCGTC 60.317 55.0 0.00 0.0 40.8 4.20 F
1719 1803 0.390124 AAACAACCTACGCGACCTCA 59.610 50.0 15.93 0.0 0.0 3.86 F
2725 4443 0.250553 TTGTGGTGGTAAGAAGCGGG 60.251 55.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1807 0.395312 CCGTAGGTGGTGTTGAACCT 59.605 55.000 0.0 0.0 45.62 3.50 R
2243 2630 0.960364 CGCACCAAGCATACCCAAGT 60.960 55.000 0.0 0.0 46.13 3.16 R
2470 3183 2.362077 GCATGTTGACCAGGTTTGACTT 59.638 45.455 0.0 0.0 0.00 3.01 R
3427 5644 1.066716 GGCATAAGGTGTGGACGTACA 60.067 52.381 0.0 0.0 0.00 2.90 R
4423 6949 0.108585 TTTGACAGCGGCTTCTTCCT 59.891 50.000 0.0 0.0 0.00 3.36 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
51 52 4.160635 CGCGCGCTTCCCGAAATT 62.161 61.111 30.48 0.00 40.02 1.82
87 88 2.970974 GCGGGCTGCAGAACAACTC 61.971 63.158 20.43 0.00 45.45 3.01
102 103 5.817816 AGAACAACTCGTCAAAACAGAAGAT 59.182 36.000 0.00 0.00 0.00 2.40
325 327 6.814146 GGCTAATGATGAAGCTATGTACCTAC 59.186 42.308 0.00 0.00 38.80 3.18
364 367 0.991920 CCAAAGAGCCCTACCCAAGA 59.008 55.000 0.00 0.00 0.00 3.02
448 451 3.449018 ACACTCGACCAAGAAGCTATCAT 59.551 43.478 0.00 0.00 0.00 2.45
494 497 4.036518 ACTGCCAGGAGATCTAAAGTCAT 58.963 43.478 0.00 0.00 0.00 3.06
498 501 4.102367 GCCAGGAGATCTAAAGTCATTCCT 59.898 45.833 0.00 0.00 34.03 3.36
515 518 2.027625 CTCAGGCAAACGGTCGGTC 61.028 63.158 0.00 0.00 0.00 4.79
516 519 2.030562 CAGGCAAACGGTCGGTCT 59.969 61.111 0.00 0.00 0.00 3.85
529 532 4.083057 ACGGTCGGTCTTTAAGTAGTCTTC 60.083 45.833 0.00 0.00 35.36 2.87
697 701 7.600375 CCTCTGTTATTCACACGCATATAATCT 59.400 37.037 0.00 0.00 0.00 2.40
761 766 3.491652 GCGAAGGCCTGAACTCGC 61.492 66.667 28.19 28.19 39.33 5.03
764 769 2.032681 AAGGCCTGAACTCGCACC 59.967 61.111 5.69 0.00 0.00 5.01
765 770 3.553095 AAGGCCTGAACTCGCACCC 62.553 63.158 5.69 0.00 0.00 4.61
766 771 4.021925 GGCCTGAACTCGCACCCT 62.022 66.667 0.00 0.00 0.00 4.34
780 788 0.309612 CACCCTGCGTGTTTACAACC 59.690 55.000 0.00 0.00 37.73 3.77
818 827 0.043334 AGCCTCTCCATACACACCCT 59.957 55.000 0.00 0.00 0.00 4.34
851 860 4.038763 TGTCAGAGTTAGAACCACGACAAT 59.961 41.667 0.00 0.00 0.00 2.71
852 861 4.989168 GTCAGAGTTAGAACCACGACAATT 59.011 41.667 0.00 0.00 0.00 2.32
853 862 5.465724 GTCAGAGTTAGAACCACGACAATTT 59.534 40.000 0.00 0.00 0.00 1.82
854 863 6.643770 GTCAGAGTTAGAACCACGACAATTTA 59.356 38.462 0.00 0.00 0.00 1.40
855 864 7.331193 GTCAGAGTTAGAACCACGACAATTTAT 59.669 37.037 0.00 0.00 0.00 1.40
856 865 8.525316 TCAGAGTTAGAACCACGACAATTTATA 58.475 33.333 0.00 0.00 0.00 0.98
857 866 9.314321 CAGAGTTAGAACCACGACAATTTATAT 57.686 33.333 0.00 0.00 0.00 0.86
858 867 9.886132 AGAGTTAGAACCACGACAATTTATATT 57.114 29.630 0.00 0.00 0.00 1.28
864 873 9.675464 AGAACCACGACAATTTATATTTAGGAA 57.325 29.630 0.00 0.00 0.00 3.36
865 874 9.712359 GAACCACGACAATTTATATTTAGGAAC 57.288 33.333 0.00 0.00 0.00 3.62
866 875 8.217131 ACCACGACAATTTATATTTAGGAACC 57.783 34.615 0.00 0.00 0.00 3.62
867 876 7.011669 ACCACGACAATTTATATTTAGGAACCG 59.988 37.037 0.00 0.00 0.00 4.44
868 877 7.225145 CCACGACAATTTATATTTAGGAACCGA 59.775 37.037 0.00 0.00 0.00 4.69
869 878 8.273557 CACGACAATTTATATTTAGGAACCGAG 58.726 37.037 0.00 0.00 0.00 4.63
870 879 7.440255 ACGACAATTTATATTTAGGAACCGAGG 59.560 37.037 0.00 0.00 0.00 4.63
871 880 7.654520 CGACAATTTATATTTAGGAACCGAGGA 59.345 37.037 0.00 0.00 0.00 3.71
872 881 9.333724 GACAATTTATATTTAGGAACCGAGGAA 57.666 33.333 0.00 0.00 0.00 3.36
873 882 9.689501 ACAATTTATATTTAGGAACCGAGGAAA 57.310 29.630 0.00 0.00 0.00 3.13
877 886 8.685838 TTATATTTAGGAACCGAGGAAAATGG 57.314 34.615 0.00 0.00 0.00 3.16
878 887 4.644163 TTTAGGAACCGAGGAAAATGGA 57.356 40.909 0.00 0.00 0.00 3.41
879 888 4.855298 TTAGGAACCGAGGAAAATGGAT 57.145 40.909 0.00 0.00 0.00 3.41
880 889 3.739401 AGGAACCGAGGAAAATGGATT 57.261 42.857 0.00 0.00 0.00 3.01
881 890 3.356290 AGGAACCGAGGAAAATGGATTG 58.644 45.455 0.00 0.00 0.00 2.67
882 891 3.010138 AGGAACCGAGGAAAATGGATTGA 59.990 43.478 0.00 0.00 0.00 2.57
883 892 3.761752 GGAACCGAGGAAAATGGATTGAA 59.238 43.478 0.00 0.00 0.00 2.69
884 893 4.402474 GGAACCGAGGAAAATGGATTGAAT 59.598 41.667 0.00 0.00 0.00 2.57
885 894 4.989279 ACCGAGGAAAATGGATTGAATG 57.011 40.909 0.00 0.00 0.00 2.67
886 895 4.599041 ACCGAGGAAAATGGATTGAATGA 58.401 39.130 0.00 0.00 0.00 2.57
887 896 5.203528 ACCGAGGAAAATGGATTGAATGAT 58.796 37.500 0.00 0.00 0.00 2.45
888 897 5.658190 ACCGAGGAAAATGGATTGAATGATT 59.342 36.000 0.00 0.00 0.00 2.57
889 898 5.981315 CCGAGGAAAATGGATTGAATGATTG 59.019 40.000 0.00 0.00 0.00 2.67
890 899 5.461078 CGAGGAAAATGGATTGAATGATTGC 59.539 40.000 0.00 0.00 0.00 3.56
891 900 6.302535 AGGAAAATGGATTGAATGATTGCA 57.697 33.333 0.00 0.00 0.00 4.08
892 901 6.346096 AGGAAAATGGATTGAATGATTGCAG 58.654 36.000 0.00 0.00 0.00 4.41
893 902 5.526111 GGAAAATGGATTGAATGATTGCAGG 59.474 40.000 0.00 0.00 0.00 4.85
894 903 3.746045 ATGGATTGAATGATTGCAGGC 57.254 42.857 0.00 0.00 0.00 4.85
895 904 2.458620 TGGATTGAATGATTGCAGGCA 58.541 42.857 0.00 0.00 0.00 4.75
896 905 2.832733 TGGATTGAATGATTGCAGGCAA 59.167 40.909 9.38 9.38 40.47 4.52
898 907 4.080807 TGGATTGAATGATTGCAGGCAATT 60.081 37.500 19.44 6.04 45.50 2.32
899 908 4.510340 GGATTGAATGATTGCAGGCAATTC 59.490 41.667 19.44 14.42 45.50 2.17
900 909 3.530265 TGAATGATTGCAGGCAATTCC 57.470 42.857 19.44 9.36 45.50 3.01
911 920 2.657336 GCAATTCCTGCGTGATTGC 58.343 52.632 9.92 9.92 42.37 3.56
912 921 0.109179 GCAATTCCTGCGTGATTGCA 60.109 50.000 16.84 0.00 44.79 4.08
913 922 1.669502 GCAATTCCTGCGTGATTGCAA 60.670 47.619 16.84 0.00 45.74 4.08
914 923 2.256174 CAATTCCTGCGTGATTGCAAG 58.744 47.619 4.94 0.00 45.74 4.01
915 924 0.171903 ATTCCTGCGTGATTGCAAGC 59.828 50.000 7.99 7.99 45.74 4.01
920 929 3.477504 GCGTGATTGCAAGCTTCAA 57.522 47.368 16.73 11.88 44.57 2.69
921 930 1.334054 GCGTGATTGCAAGCTTCAAG 58.666 50.000 16.73 12.45 44.57 3.02
922 931 1.335324 GCGTGATTGCAAGCTTCAAGT 60.335 47.619 16.73 0.00 44.57 3.16
923 932 2.578495 CGTGATTGCAAGCTTCAAGTC 58.422 47.619 16.73 0.66 0.00 3.01
924 933 2.578495 GTGATTGCAAGCTTCAAGTCG 58.422 47.619 16.73 0.00 0.00 4.18
925 934 2.031682 GTGATTGCAAGCTTCAAGTCGT 60.032 45.455 16.73 0.00 0.00 4.34
926 935 2.224079 TGATTGCAAGCTTCAAGTCGTC 59.776 45.455 16.73 0.00 0.00 4.20
927 936 0.581529 TTGCAAGCTTCAAGTCGTCG 59.418 50.000 0.00 0.00 0.00 5.12
928 937 0.529773 TGCAAGCTTCAAGTCGTCGT 60.530 50.000 0.00 0.00 0.00 4.34
929 938 0.582005 GCAAGCTTCAAGTCGTCGTT 59.418 50.000 0.00 0.00 0.00 3.85
930 939 1.657538 GCAAGCTTCAAGTCGTCGTTG 60.658 52.381 0.00 0.00 0.00 4.10
931 940 1.070577 CAAGCTTCAAGTCGTCGTTGG 60.071 52.381 0.00 0.00 0.00 3.77
932 941 0.104304 AGCTTCAAGTCGTCGTTGGT 59.896 50.000 0.00 0.00 0.00 3.67
933 942 0.507358 GCTTCAAGTCGTCGTTGGTC 59.493 55.000 0.00 0.00 0.00 4.02
934 943 0.776451 CTTCAAGTCGTCGTTGGTCG 59.224 55.000 0.00 0.00 41.41 4.79
935 944 0.101040 TTCAAGTCGTCGTTGGTCGT 59.899 50.000 0.00 0.00 40.80 4.34
936 945 0.317269 TCAAGTCGTCGTTGGTCGTC 60.317 55.000 0.00 0.00 40.80 4.20
938 947 2.722130 AAGTCGTCGTTGGTCGTCGG 62.722 60.000 6.96 0.00 46.85 4.79
939 948 2.971959 TCGTCGTTGGTCGTCGGA 60.972 61.111 6.96 0.00 46.85 4.55
940 949 2.051076 CGTCGTTGGTCGTCGGAA 60.051 61.111 0.00 0.00 44.30 4.30
941 950 2.359791 CGTCGTTGGTCGTCGGAAC 61.360 63.158 0.00 0.00 44.30 3.62
958 967 3.514645 GGAACGGCTCGAGTATTAAACA 58.485 45.455 15.13 0.00 0.00 2.83
959 968 3.928375 GGAACGGCTCGAGTATTAAACAA 59.072 43.478 15.13 0.00 0.00 2.83
960 969 4.201656 GGAACGGCTCGAGTATTAAACAAC 60.202 45.833 15.13 0.00 0.00 3.32
961 970 4.184079 ACGGCTCGAGTATTAAACAACT 57.816 40.909 15.13 0.00 0.00 3.16
962 971 4.171754 ACGGCTCGAGTATTAAACAACTC 58.828 43.478 15.13 6.10 39.00 3.01
970 979 6.882458 GAGTATTAAACAACTCGTACCCAG 57.118 41.667 1.61 0.00 33.38 4.45
971 980 6.594788 AGTATTAAACAACTCGTACCCAGA 57.405 37.500 0.00 0.00 0.00 3.86
972 981 6.628185 AGTATTAAACAACTCGTACCCAGAG 58.372 40.000 0.00 0.00 41.27 3.35
973 982 2.165319 AAACAACTCGTACCCAGAGC 57.835 50.000 0.00 0.00 39.23 4.09
974 983 1.045407 AACAACTCGTACCCAGAGCA 58.955 50.000 0.00 0.00 39.23 4.26
975 984 0.603569 ACAACTCGTACCCAGAGCAG 59.396 55.000 0.00 0.00 39.23 4.24
976 985 0.737715 CAACTCGTACCCAGAGCAGC 60.738 60.000 0.00 0.00 39.23 5.25
977 986 1.185618 AACTCGTACCCAGAGCAGCA 61.186 55.000 0.00 0.00 39.23 4.41
978 987 1.185618 ACTCGTACCCAGAGCAGCAA 61.186 55.000 0.00 0.00 39.23 3.91
979 988 0.459237 CTCGTACCCAGAGCAGCAAG 60.459 60.000 0.00 0.00 0.00 4.01
980 989 1.448540 CGTACCCAGAGCAGCAAGG 60.449 63.158 0.00 0.00 0.00 3.61
990 999 3.437795 CAGCAAGGCAAGCCCTCG 61.438 66.667 7.62 0.00 45.62 4.63
992 1001 2.439156 GCAAGGCAAGCCCTCGAT 60.439 61.111 7.62 0.00 45.62 3.59
1040 1049 3.062585 CTGCTTCTCTACTGGCAGC 57.937 57.895 15.89 0.00 44.03 5.25
1457 1502 0.739462 CAAACGCTGGCCTACATCGA 60.739 55.000 3.32 0.00 40.95 3.59
1513 1594 2.334946 GCCATGTGCCGAGCAGAAA 61.335 57.895 0.00 0.00 40.08 2.52
1526 1607 3.188786 AGAAAGCGACGGCGATGC 61.189 61.111 18.90 17.24 46.35 3.91
1547 1628 4.373116 GTCGGCCCTCAGCAACGA 62.373 66.667 0.00 0.00 46.50 3.85
1563 1644 2.427245 CGACTCCTGCTCCGGGATT 61.427 63.158 0.00 0.00 38.36 3.01
1603 1684 4.473520 CCAGGGGCCTGCAGTACG 62.474 72.222 13.81 0.00 42.35 3.67
1636 1720 2.203280 CCGGCTTCAACACCACCA 60.203 61.111 0.00 0.00 0.00 4.17
1686 1770 1.215382 CGTTCTCATGGACGCCTCA 59.785 57.895 0.00 0.00 0.00 3.86
1704 1788 3.699038 CCTCAAACTTCACCTTCCAAACA 59.301 43.478 0.00 0.00 0.00 2.83
1719 1803 0.390124 AAACAACCTACGCGACCTCA 59.610 50.000 15.93 0.00 0.00 3.86
1723 1807 3.129502 CCTACGCGACCTCACCGA 61.130 66.667 15.93 0.00 0.00 4.69
1743 1827 1.232621 GGTTCAACACCACCTACGGC 61.233 60.000 0.00 0.00 46.42 5.68
1744 1828 1.301087 TTCAACACCACCTACGGCG 60.301 57.895 4.80 4.80 0.00 6.46
1745 1829 2.718747 TTCAACACCACCTACGGCGG 62.719 60.000 13.24 0.00 0.00 6.13
1746 1830 2.918802 AACACCACCTACGGCGGA 60.919 61.111 13.24 0.00 0.00 5.54
1747 1831 2.939261 AACACCACCTACGGCGGAG 61.939 63.158 13.43 13.43 0.00 4.63
1748 1832 3.379445 CACCACCTACGGCGGAGT 61.379 66.667 19.35 5.58 0.00 3.85
1957 2041 4.853924 CAAGGATGCAAAGGTTTGTAGT 57.146 40.909 4.45 0.00 40.24 2.73
2053 2369 1.899814 GGTCCCTCAAATTCCCCAAAC 59.100 52.381 0.00 0.00 0.00 2.93
2066 2382 2.502538 TCCCCAAACGTATAGACTTGGG 59.497 50.000 21.65 21.65 46.60 4.12
2125 2442 7.773224 TCAAGTCTCAAAACCTGATAAGTTTGA 59.227 33.333 0.00 0.00 37.50 2.69
2243 2630 6.071896 TGTGAACTTTTGTGACAACCAACATA 60.072 34.615 0.00 0.00 0.00 2.29
2251 2638 4.141459 TGTGACAACCAACATACTTGGGTA 60.141 41.667 4.19 0.00 43.71 3.69
2252 2639 5.007682 GTGACAACCAACATACTTGGGTAT 58.992 41.667 4.19 0.00 43.71 2.73
2277 2664 4.111375 TGGTGCGTGTAAATTTTTGTGT 57.889 36.364 0.00 0.00 0.00 3.72
2306 2696 1.134401 CATCCGAGGAGCTTTAGCCAA 60.134 52.381 0.00 0.00 43.38 4.52
2507 3311 7.226523 GGTCAACATGCTTAAAATCTGGTTTTT 59.773 33.333 3.68 0.00 40.40 1.94
2510 3314 8.610896 CAACATGCTTAAAATCTGGTTTTTGAA 58.389 29.630 3.68 0.00 40.40 2.69
2535 3340 6.017357 ACAAACTTATCCGGTTTTGAGACTTC 60.017 38.462 16.47 0.00 35.09 3.01
2655 4373 9.320352 CCATCAAAAATCTATGCAATGATTCAA 57.680 29.630 14.98 5.22 32.43 2.69
2675 4393 9.214953 GATTCAAGTAGATTTTTGTTATGAGCG 57.785 33.333 0.00 0.00 0.00 5.03
2677 4395 8.766000 TCAAGTAGATTTTTGTTATGAGCGTA 57.234 30.769 0.00 0.00 0.00 4.42
2678 4396 8.653338 TCAAGTAGATTTTTGTTATGAGCGTAC 58.347 33.333 0.00 0.00 0.00 3.67
2682 4400 9.821662 GTAGATTTTTGTTATGAGCGTACTTTT 57.178 29.630 0.00 0.00 0.00 2.27
2713 4431 3.320541 TGCTGGGAAAGTTTATTGTGGTG 59.679 43.478 0.00 0.00 0.00 4.17
2722 4440 5.959618 AGTTTATTGTGGTGGTAAGAAGC 57.040 39.130 0.00 0.00 0.00 3.86
2725 4443 0.250553 TTGTGGTGGTAAGAAGCGGG 60.251 55.000 0.00 0.00 0.00 6.13
2800 4974 6.421202 GTCTTGTCTAACGAAGGCCTATATTG 59.579 42.308 5.16 0.00 0.00 1.90
2850 5024 7.837505 TCTTATAGATACGTCGCAAATTGTTG 58.162 34.615 0.00 0.00 37.83 3.33
2872 5055 4.649674 TGCTATAATACATCCTCCGATCCC 59.350 45.833 0.00 0.00 0.00 3.85
2882 5065 3.112263 TCCTCCGATCCCAAATAAGTGT 58.888 45.455 0.00 0.00 0.00 3.55
2884 5067 3.118408 CCTCCGATCCCAAATAAGTGTCA 60.118 47.826 0.00 0.00 0.00 3.58
2886 5069 3.262151 TCCGATCCCAAATAAGTGTCACA 59.738 43.478 5.62 0.00 0.00 3.58
2890 5073 3.674997 TCCCAAATAAGTGTCACAGCTC 58.325 45.455 5.62 0.00 0.00 4.09
2891 5074 3.327757 TCCCAAATAAGTGTCACAGCTCT 59.672 43.478 5.62 0.00 0.00 4.09
2894 5077 5.122396 CCCAAATAAGTGTCACAGCTCTAAC 59.878 44.000 5.62 0.00 0.00 2.34
2904 5093 6.144724 GTGTCACAGCTCTAACTAAAGTTGAG 59.855 42.308 5.62 10.51 38.90 3.02
2905 5094 5.635700 GTCACAGCTCTAACTAAAGTTGAGG 59.364 44.000 16.78 8.95 38.90 3.86
2936 5125 8.514136 TTAGTTCAAAGTTGTGACACTTTTTG 57.486 30.769 16.81 16.81 43.17 2.44
2937 5126 6.744112 AGTTCAAAGTTGTGACACTTTTTGA 58.256 32.000 19.43 19.43 43.17 2.69
2938 5127 7.206687 AGTTCAAAGTTGTGACACTTTTTGAA 58.793 30.769 24.79 24.79 43.17 2.69
2939 5128 7.872483 AGTTCAAAGTTGTGACACTTTTTGAAT 59.128 29.630 27.77 20.31 43.17 2.57
2940 5129 7.810766 TCAAAGTTGTGACACTTTTTGAATC 57.189 32.000 20.30 0.00 43.17 2.52
2941 5130 6.526325 TCAAAGTTGTGACACTTTTTGAATCG 59.474 34.615 20.30 2.73 43.17 3.34
2956 5147 8.817092 TTTTTGAATCGGAGGGAGTATATTTT 57.183 30.769 0.00 0.00 0.00 1.82
2963 5154 8.666129 ATCGGAGGGAGTATATTTTATTGAGA 57.334 34.615 0.00 0.00 0.00 3.27
2982 5173 6.669125 TGAGATTTGGTTCATTGTTTGGAT 57.331 33.333 0.00 0.00 0.00 3.41
2986 5177 9.657419 GAGATTTGGTTCATTGTTTGGATTAAT 57.343 29.630 0.00 0.00 0.00 1.40
3173 5390 4.788840 GCTGAAGTGATATGCTTGCATGTC 60.789 45.833 20.40 20.40 0.00 3.06
3189 5406 5.730550 TGCATGTCGAGAAATAGGTTAGTT 58.269 37.500 0.00 0.00 0.00 2.24
3190 5407 5.580691 TGCATGTCGAGAAATAGGTTAGTTG 59.419 40.000 0.00 0.00 0.00 3.16
3191 5408 5.006746 GCATGTCGAGAAATAGGTTAGTTGG 59.993 44.000 0.00 0.00 0.00 3.77
3192 5409 5.080969 TGTCGAGAAATAGGTTAGTTGGG 57.919 43.478 0.00 0.00 0.00 4.12
3193 5410 4.081309 TGTCGAGAAATAGGTTAGTTGGGG 60.081 45.833 0.00 0.00 0.00 4.96
3201 5418 8.823794 AGAAATAGGTTAGTTGGGGCTATATAC 58.176 37.037 0.00 0.00 0.00 1.47
3336 5553 1.864669 ATTTGCCCGGTGGATTCAAT 58.135 45.000 0.00 0.00 0.00 2.57
3426 5643 6.713276 TGGTCTTGGAGAAAAATTCGGTATA 58.287 36.000 0.00 0.00 34.02 1.47
3427 5644 7.343357 TGGTCTTGGAGAAAAATTCGGTATAT 58.657 34.615 0.00 0.00 34.02 0.86
3439 5656 3.969117 TCGGTATATGTACGTCCACAC 57.031 47.619 0.00 0.00 0.00 3.82
3442 5659 3.067180 CGGTATATGTACGTCCACACCTT 59.933 47.826 0.00 0.00 0.00 3.50
3443 5660 4.275689 CGGTATATGTACGTCCACACCTTA 59.724 45.833 0.00 0.00 0.00 2.69
3444 5661 5.048504 CGGTATATGTACGTCCACACCTTAT 60.049 44.000 0.00 0.00 0.00 1.73
3445 5662 6.154445 GGTATATGTACGTCCACACCTTATG 58.846 44.000 0.00 0.00 0.00 1.90
3447 5664 1.066716 TGTACGTCCACACCTTATGCC 60.067 52.381 0.00 0.00 0.00 4.40
3450 5667 1.206371 ACGTCCACACCTTATGCCTAC 59.794 52.381 0.00 0.00 0.00 3.18
3451 5668 1.480954 CGTCCACACCTTATGCCTACT 59.519 52.381 0.00 0.00 0.00 2.57
3452 5669 2.691526 CGTCCACACCTTATGCCTACTA 59.308 50.000 0.00 0.00 0.00 1.82
3498 6012 7.792374 ATCAACATTATGTGTACCAGATCAC 57.208 36.000 0.00 0.00 41.14 3.06
3500 6014 8.073467 TCAACATTATGTGTACCAGATCACTA 57.927 34.615 0.00 0.00 41.14 2.74
3502 6016 8.768019 CAACATTATGTGTACCAGATCACTATG 58.232 37.037 0.00 0.00 41.14 2.23
3515 6029 9.911788 ACCAGATCACTATGTTTAATTTCATCT 57.088 29.630 0.00 0.00 0.00 2.90
3533 6047 8.498054 TTTCATCTAAGATTCTTAGTGCCAAG 57.502 34.615 25.49 13.99 0.00 3.61
3589 6105 2.528564 TCTCTTTTGCCCCAAATGAGG 58.471 47.619 22.47 11.62 46.35 3.86
3611 6131 2.380084 TGACGACTAACCTTGGCATC 57.620 50.000 0.00 0.00 0.00 3.91
3708 6228 3.791973 AGGAGTATCAAGAGACAAGCG 57.208 47.619 0.00 0.00 36.25 4.68
3715 6235 1.005340 CAAGAGACAAGCGCTGATCC 58.995 55.000 12.58 6.14 0.00 3.36
3748 6268 3.196901 TGAATACTATCAACAGCACGGGT 59.803 43.478 0.00 0.00 0.00 5.28
3749 6269 4.403113 TGAATACTATCAACAGCACGGGTA 59.597 41.667 0.00 0.00 0.00 3.69
3750 6270 5.105269 TGAATACTATCAACAGCACGGGTAA 60.105 40.000 0.00 0.00 0.00 2.85
3918 6444 3.103911 GTCGACGGCAAGGACACG 61.104 66.667 0.00 0.00 0.00 4.49
3948 6474 3.127030 CGGTAAAAAGATGCAAGGAGGTC 59.873 47.826 0.00 0.00 0.00 3.85
3951 6477 3.356529 AAAAGATGCAAGGAGGTCGAT 57.643 42.857 0.00 0.00 0.00 3.59
3972 6498 1.273886 GAGAGCAGGACGAAGGACTTT 59.726 52.381 0.00 0.00 0.00 2.66
4113 6639 2.680805 GCAGGAGCTATTGTACAGCCAA 60.681 50.000 0.00 0.00 39.99 4.52
4197 6723 2.488355 GCGTACCTGCACTCGCTA 59.512 61.111 11.09 0.00 44.28 4.26
4199 6725 1.801332 CGTACCTGCACTCGCTAGT 59.199 57.895 0.00 0.00 39.64 2.57
4423 6949 1.078823 TCCTTCTGGAGCTCCTAACCA 59.921 52.381 32.28 12.59 37.46 3.67
4485 7011 4.162320 GTGATGGTTCAAGAGTCTATGGGA 59.838 45.833 0.00 0.00 32.48 4.37
4593 7119 1.270094 CGATGCTTAGTTATGCCGGGA 60.270 52.381 2.18 0.00 0.00 5.14
4662 7188 2.595463 GACCAAGTGCAGCAGCCA 60.595 61.111 0.00 0.00 41.13 4.75
4677 7203 0.681175 AGCCATTGGTTTTGGAGTGC 59.319 50.000 4.26 0.00 36.26 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.125431 GGGTTTCGCGGGATTCGA 60.125 61.111 6.13 0.00 42.43 3.71
87 88 3.403038 AGTGGGATCTTCTGTTTTGACG 58.597 45.455 0.00 0.00 0.00 4.35
116 117 8.638685 TTCTTTACTTGTAATATACCGAGTGC 57.361 34.615 5.18 0.00 0.00 4.40
127 128 7.527457 GCCGAGTGAATTTCTTTACTTGTAAT 58.473 34.615 0.00 0.00 32.83 1.89
129 130 5.119588 CGCCGAGTGAATTTCTTTACTTGTA 59.880 40.000 0.00 0.00 32.83 2.41
215 216 1.202758 ACATGAGTGCCTCGTTTTGGA 60.203 47.619 0.00 0.00 32.35 3.53
364 367 4.430441 AGGTGACTTCTTCTAGGGATGTT 58.570 43.478 0.00 0.00 37.44 2.71
408 411 0.313043 GTCTTGAACCCGTCGAGTGA 59.687 55.000 0.00 0.00 38.72 3.41
448 451 0.109532 TGGTTGGCTTCATGGTCGAA 59.890 50.000 0.00 0.00 0.00 3.71
494 497 1.301401 CGACCGTTTGCCTGAGGAA 60.301 57.895 0.65 0.00 0.00 3.36
498 501 2.029964 GACCGACCGTTTGCCTGA 59.970 61.111 0.00 0.00 0.00 3.86
542 545 5.046807 ACTGGTAACGCTCCTAATAAAGTGT 60.047 40.000 0.00 0.00 37.83 3.55
571 574 6.720748 GGGTTTAAGGTACATTTAAGGTTGGA 59.279 38.462 0.00 0.00 0.00 3.53
654 658 0.252197 AGGTGCGAACCCTTCATACC 59.748 55.000 9.68 0.00 36.25 2.73
780 788 3.696051 GGCTAGATCTCAGCTATGGAGAG 59.304 52.174 17.89 0.52 44.04 3.20
818 827 6.151312 GGTTCTAACTCTGACAGTGATGTAGA 59.849 42.308 11.37 10.83 34.56 2.59
851 860 9.127277 CCATTTTCCTCGGTTCCTAAATATAAA 57.873 33.333 0.00 0.00 0.00 1.40
852 861 8.496088 TCCATTTTCCTCGGTTCCTAAATATAA 58.504 33.333 0.00 0.00 0.00 0.98
853 862 8.036585 TCCATTTTCCTCGGTTCCTAAATATA 57.963 34.615 0.00 0.00 0.00 0.86
854 863 6.906848 TCCATTTTCCTCGGTTCCTAAATAT 58.093 36.000 0.00 0.00 0.00 1.28
855 864 6.316280 TCCATTTTCCTCGGTTCCTAAATA 57.684 37.500 0.00 0.00 0.00 1.40
856 865 5.187621 TCCATTTTCCTCGGTTCCTAAAT 57.812 39.130 0.00 0.00 0.00 1.40
857 866 4.644163 TCCATTTTCCTCGGTTCCTAAA 57.356 40.909 0.00 0.00 0.00 1.85
858 867 4.855298 ATCCATTTTCCTCGGTTCCTAA 57.145 40.909 0.00 0.00 0.00 2.69
859 868 4.226394 TCAATCCATTTTCCTCGGTTCCTA 59.774 41.667 0.00 0.00 0.00 2.94
860 869 3.010138 TCAATCCATTTTCCTCGGTTCCT 59.990 43.478 0.00 0.00 0.00 3.36
861 870 3.352648 TCAATCCATTTTCCTCGGTTCC 58.647 45.455 0.00 0.00 0.00 3.62
862 871 5.125417 TCATTCAATCCATTTTCCTCGGTTC 59.875 40.000 0.00 0.00 0.00 3.62
863 872 5.016173 TCATTCAATCCATTTTCCTCGGTT 58.984 37.500 0.00 0.00 0.00 4.44
864 873 4.599041 TCATTCAATCCATTTTCCTCGGT 58.401 39.130 0.00 0.00 0.00 4.69
865 874 5.779529 ATCATTCAATCCATTTTCCTCGG 57.220 39.130 0.00 0.00 0.00 4.63
866 875 5.461078 GCAATCATTCAATCCATTTTCCTCG 59.539 40.000 0.00 0.00 0.00 4.63
867 876 6.342906 TGCAATCATTCAATCCATTTTCCTC 58.657 36.000 0.00 0.00 0.00 3.71
868 877 6.302535 TGCAATCATTCAATCCATTTTCCT 57.697 33.333 0.00 0.00 0.00 3.36
869 878 5.526111 CCTGCAATCATTCAATCCATTTTCC 59.474 40.000 0.00 0.00 0.00 3.13
870 879 5.007332 GCCTGCAATCATTCAATCCATTTTC 59.993 40.000 0.00 0.00 0.00 2.29
871 880 4.879545 GCCTGCAATCATTCAATCCATTTT 59.120 37.500 0.00 0.00 0.00 1.82
872 881 4.080807 TGCCTGCAATCATTCAATCCATTT 60.081 37.500 0.00 0.00 0.00 2.32
873 882 3.452990 TGCCTGCAATCATTCAATCCATT 59.547 39.130 0.00 0.00 0.00 3.16
874 883 3.035363 TGCCTGCAATCATTCAATCCAT 58.965 40.909 0.00 0.00 0.00 3.41
875 884 2.458620 TGCCTGCAATCATTCAATCCA 58.541 42.857 0.00 0.00 0.00 3.41
876 885 3.530265 TTGCCTGCAATCATTCAATCC 57.470 42.857 0.00 0.00 0.00 3.01
877 886 4.510340 GGAATTGCCTGCAATCATTCAATC 59.490 41.667 16.99 9.28 44.86 2.67
878 887 4.448210 GGAATTGCCTGCAATCATTCAAT 58.552 39.130 16.99 0.56 44.86 2.57
879 888 3.864243 GGAATTGCCTGCAATCATTCAA 58.136 40.909 16.99 0.00 44.86 2.69
880 889 3.530265 GGAATTGCCTGCAATCATTCA 57.470 42.857 16.99 0.00 44.86 2.57
894 903 2.256174 CTTGCAATCACGCAGGAATTG 58.744 47.619 0.00 0.00 44.14 2.32
895 904 1.403249 GCTTGCAATCACGCAGGAATT 60.403 47.619 0.00 0.00 44.14 2.17
896 905 0.171903 GCTTGCAATCACGCAGGAAT 59.828 50.000 0.00 0.00 44.14 3.01
897 906 0.890542 AGCTTGCAATCACGCAGGAA 60.891 50.000 10.59 0.00 44.14 3.36
898 907 0.890542 AAGCTTGCAATCACGCAGGA 60.891 50.000 10.59 0.00 44.14 3.86
899 908 0.455633 GAAGCTTGCAATCACGCAGG 60.456 55.000 2.10 0.00 44.14 4.85
900 909 0.239082 TGAAGCTTGCAATCACGCAG 59.761 50.000 2.10 0.00 44.14 5.18
901 910 0.667453 TTGAAGCTTGCAATCACGCA 59.333 45.000 2.10 0.00 39.64 5.24
902 911 1.334054 CTTGAAGCTTGCAATCACGC 58.666 50.000 2.10 0.00 37.70 5.34
903 912 2.578495 GACTTGAAGCTTGCAATCACG 58.422 47.619 2.10 1.30 0.00 4.35
904 913 2.031682 ACGACTTGAAGCTTGCAATCAC 60.032 45.455 2.10 0.00 0.00 3.06
905 914 2.221169 ACGACTTGAAGCTTGCAATCA 58.779 42.857 2.10 0.00 0.00 2.57
906 915 2.723010 CGACGACTTGAAGCTTGCAATC 60.723 50.000 2.10 0.00 0.00 2.67
907 916 1.195448 CGACGACTTGAAGCTTGCAAT 59.805 47.619 2.10 0.00 0.00 3.56
908 917 0.581529 CGACGACTTGAAGCTTGCAA 59.418 50.000 2.10 7.40 0.00 4.08
909 918 0.529773 ACGACGACTTGAAGCTTGCA 60.530 50.000 2.10 0.00 0.00 4.08
910 919 0.582005 AACGACGACTTGAAGCTTGC 59.418 50.000 2.10 0.00 0.00 4.01
911 920 1.070577 CCAACGACGACTTGAAGCTTG 60.071 52.381 2.10 0.00 0.00 4.01
912 921 1.217882 CCAACGACGACTTGAAGCTT 58.782 50.000 0.00 0.00 0.00 3.74
913 922 0.104304 ACCAACGACGACTTGAAGCT 59.896 50.000 0.00 0.00 0.00 3.74
914 923 0.507358 GACCAACGACGACTTGAAGC 59.493 55.000 0.00 0.00 0.00 3.86
915 924 0.776451 CGACCAACGACGACTTGAAG 59.224 55.000 0.00 0.00 45.77 3.02
916 925 0.101040 ACGACCAACGACGACTTGAA 59.899 50.000 0.00 0.00 45.77 2.69
917 926 0.317269 GACGACCAACGACGACTTGA 60.317 55.000 0.00 0.00 45.77 3.02
918 927 2.130711 GACGACCAACGACGACTTG 58.869 57.895 0.00 0.00 45.77 3.16
919 928 4.622364 GACGACCAACGACGACTT 57.378 55.556 0.00 0.00 45.77 3.01
924 933 3.530666 GTTCCGACGACCAACGAC 58.469 61.111 0.00 0.00 45.77 4.34
934 943 0.100146 AATACTCGAGCCGTTCCGAC 59.900 55.000 13.61 0.00 0.00 4.79
935 944 1.667236 TAATACTCGAGCCGTTCCGA 58.333 50.000 13.61 0.00 0.00 4.55
936 945 2.480224 TTAATACTCGAGCCGTTCCG 57.520 50.000 13.61 0.00 0.00 4.30
937 946 3.514645 TGTTTAATACTCGAGCCGTTCC 58.485 45.455 13.61 0.00 0.00 3.62
938 947 4.624452 AGTTGTTTAATACTCGAGCCGTTC 59.376 41.667 13.61 0.00 0.00 3.95
939 948 4.563061 AGTTGTTTAATACTCGAGCCGTT 58.437 39.130 13.61 7.53 0.00 4.44
940 949 4.171754 GAGTTGTTTAATACTCGAGCCGT 58.828 43.478 13.61 0.00 32.31 5.68
941 950 4.756868 GAGTTGTTTAATACTCGAGCCG 57.243 45.455 13.61 0.00 32.31 5.52
947 956 6.624423 TCTGGGTACGAGTTGTTTAATACTC 58.376 40.000 0.00 0.00 37.90 2.59
948 957 6.594788 TCTGGGTACGAGTTGTTTAATACT 57.405 37.500 0.00 0.00 35.07 2.12
949 958 5.290400 GCTCTGGGTACGAGTTGTTTAATAC 59.710 44.000 0.00 0.00 35.07 1.89
950 959 5.047164 TGCTCTGGGTACGAGTTGTTTAATA 60.047 40.000 0.00 0.00 35.07 0.98
951 960 4.251268 GCTCTGGGTACGAGTTGTTTAAT 58.749 43.478 0.00 0.00 35.07 1.40
952 961 3.069872 TGCTCTGGGTACGAGTTGTTTAA 59.930 43.478 0.00 0.00 35.07 1.52
953 962 2.629137 TGCTCTGGGTACGAGTTGTTTA 59.371 45.455 0.00 0.00 35.07 2.01
954 963 1.414919 TGCTCTGGGTACGAGTTGTTT 59.585 47.619 0.00 0.00 35.07 2.83
955 964 1.000955 CTGCTCTGGGTACGAGTTGTT 59.999 52.381 0.00 0.00 35.07 2.83
956 965 0.603569 CTGCTCTGGGTACGAGTTGT 59.396 55.000 0.00 0.00 35.07 3.32
957 966 0.737715 GCTGCTCTGGGTACGAGTTG 60.738 60.000 0.00 0.00 35.07 3.16
958 967 1.185618 TGCTGCTCTGGGTACGAGTT 61.186 55.000 0.00 0.00 35.07 3.01
959 968 1.185618 TTGCTGCTCTGGGTACGAGT 61.186 55.000 0.00 0.00 35.07 4.18
960 969 0.459237 CTTGCTGCTCTGGGTACGAG 60.459 60.000 0.00 0.00 34.70 4.18
961 970 1.591703 CTTGCTGCTCTGGGTACGA 59.408 57.895 0.00 0.00 0.00 3.43
962 971 1.448540 CCTTGCTGCTCTGGGTACG 60.449 63.158 0.00 0.00 0.00 3.67
963 972 1.746991 GCCTTGCTGCTCTGGGTAC 60.747 63.158 0.00 0.00 0.00 3.34
964 973 1.778017 TTGCCTTGCTGCTCTGGGTA 61.778 55.000 0.00 0.00 0.00 3.69
965 974 3.137385 TTGCCTTGCTGCTCTGGGT 62.137 57.895 0.00 0.00 0.00 4.51
966 975 2.282674 TTGCCTTGCTGCTCTGGG 60.283 61.111 0.00 0.00 0.00 4.45
967 976 2.991076 GCTTGCCTTGCTGCTCTGG 61.991 63.158 0.00 1.49 0.00 3.86
968 977 2.567049 GCTTGCCTTGCTGCTCTG 59.433 61.111 0.00 0.00 0.00 3.35
969 978 2.675772 GGCTTGCCTTGCTGCTCT 60.676 61.111 4.11 0.00 0.00 4.09
970 979 3.756727 GGGCTTGCCTTGCTGCTC 61.757 66.667 11.71 0.00 0.00 4.26
971 980 4.296729 AGGGCTTGCCTTGCTGCT 62.297 61.111 11.71 0.00 0.00 4.24
972 981 3.756727 GAGGGCTTGCCTTGCTGC 61.757 66.667 11.71 0.00 0.00 5.25
973 982 3.437795 CGAGGGCTTGCCTTGCTG 61.438 66.667 11.71 0.00 0.00 4.41
974 983 2.883267 GATCGAGGGCTTGCCTTGCT 62.883 60.000 11.71 0.00 0.00 3.91
975 984 2.439156 ATCGAGGGCTTGCCTTGC 60.439 61.111 11.71 0.85 0.00 4.01
976 985 1.821332 GGATCGAGGGCTTGCCTTG 60.821 63.158 11.71 2.20 0.00 3.61
977 986 2.300967 TGGATCGAGGGCTTGCCTT 61.301 57.895 11.71 3.40 0.00 4.35
978 987 2.688666 TGGATCGAGGGCTTGCCT 60.689 61.111 11.71 0.00 0.00 4.75
979 988 2.514824 GTGGATCGAGGGCTTGCC 60.515 66.667 2.49 2.49 0.00 4.52
980 989 1.522580 GAGTGGATCGAGGGCTTGC 60.523 63.158 0.00 0.00 0.00 4.01
990 999 1.227674 GGACGGCATGGAGTGGATC 60.228 63.158 0.00 0.00 0.00 3.36
992 1001 3.399181 GGGACGGCATGGAGTGGA 61.399 66.667 0.00 0.00 0.00 4.02
1449 1494 4.569023 TGCGCGCCCTCGATGTAG 62.569 66.667 30.77 0.00 38.10 2.74
1463 1508 2.019951 GTGTACTCGTGGGTGTGCG 61.020 63.158 0.00 0.00 0.00 5.34
1468 1549 2.927580 CGCTGGTGTACTCGTGGGT 61.928 63.158 0.00 0.00 0.00 4.51
1471 1552 2.809601 GCCGCTGGTGTACTCGTG 60.810 66.667 0.00 0.00 0.00 4.35
1506 1587 3.649277 ATCGCCGTCGCTTTCTGCT 62.649 57.895 0.00 0.00 40.11 4.24
1508 1589 2.697425 CATCGCCGTCGCTTTCTG 59.303 61.111 0.00 0.00 35.26 3.02
1547 1628 2.370445 CCAATCCCGGAGCAGGAGT 61.370 63.158 0.73 0.00 36.67 3.85
1593 1674 0.603569 ACTCCACTTCGTACTGCAGG 59.396 55.000 19.93 0.00 0.00 4.85
1636 1720 0.670546 CGGCTGACGTTGTGGATCTT 60.671 55.000 0.00 0.00 37.93 2.40
1671 1755 0.976641 AGTTTGAGGCGTCCATGAGA 59.023 50.000 3.56 0.00 0.00 3.27
1686 1770 4.093743 AGGTTGTTTGGAAGGTGAAGTTT 58.906 39.130 0.00 0.00 0.00 2.66
1704 1788 2.968206 GGTGAGGTCGCGTAGGTT 59.032 61.111 5.77 0.00 0.00 3.50
1723 1807 0.395312 CCGTAGGTGGTGTTGAACCT 59.605 55.000 0.00 0.00 45.62 3.50
1951 2035 8.508883 AGTATTGTTTTGTGTTGGTACTACAA 57.491 30.769 3.48 0.00 32.93 2.41
1952 2036 9.781633 ATAGTATTGTTTTGTGTTGGTACTACA 57.218 29.630 0.00 0.00 0.00 2.74
2053 2369 1.410004 TGAGGGCCCAAGTCTATACG 58.590 55.000 27.56 0.00 0.00 3.06
2216 2603 6.071896 TGTTGGTTGTCACAAAAGTTCACATA 60.072 34.615 0.00 0.00 0.00 2.29
2217 2604 5.167845 GTTGGTTGTCACAAAAGTTCACAT 58.832 37.500 0.00 0.00 0.00 3.21
2218 2605 4.038042 TGTTGGTTGTCACAAAAGTTCACA 59.962 37.500 0.00 0.00 0.00 3.58
2219 2606 4.551388 TGTTGGTTGTCACAAAAGTTCAC 58.449 39.130 0.00 0.00 0.00 3.18
2224 2611 5.748152 CCAAGTATGTTGGTTGTCACAAAAG 59.252 40.000 0.00 0.00 34.92 2.27
2243 2630 0.960364 CGCACCAAGCATACCCAAGT 60.960 55.000 0.00 0.00 46.13 3.16
2251 2638 3.658757 AAATTTACACGCACCAAGCAT 57.341 38.095 0.00 0.00 46.13 3.79
2252 2639 3.444703 AAAATTTACACGCACCAAGCA 57.555 38.095 0.00 0.00 46.13 3.91
2277 2664 4.487714 AGCTCCTCGGATGTTATTTGAA 57.512 40.909 0.00 0.00 0.00 2.69
2470 3183 2.362077 GCATGTTGACCAGGTTTGACTT 59.638 45.455 0.00 0.00 0.00 3.01
2507 3311 5.823570 TCTCAAAACCGGATAAGTTTGTTCA 59.176 36.000 9.46 0.00 37.50 3.18
2510 3314 5.374071 AGTCTCAAAACCGGATAAGTTTGT 58.626 37.500 9.46 0.00 37.50 2.83
2574 4290 7.403231 TCCCTCAAGTTCTCCAAAAGTATAGAT 59.597 37.037 0.00 0.00 0.00 1.98
2655 4373 8.773404 AAGTACGCTCATAACAAAAATCTACT 57.227 30.769 0.00 0.00 0.00 2.57
2713 4431 3.819337 AGAAAAAGTTCCCGCTTCTTACC 59.181 43.478 0.00 0.00 33.92 2.85
2780 4954 8.521176 TCTAATCAATATAGGCCTTCGTTAGAC 58.479 37.037 12.58 0.00 0.00 2.59
2782 4956 9.307121 CATCTAATCAATATAGGCCTTCGTTAG 57.693 37.037 12.58 10.44 0.00 2.34
2822 4996 8.700644 ACAATTTGCGACGTATCTATAAGATTC 58.299 33.333 0.00 0.00 36.20 2.52
2850 5024 4.649674 TGGGATCGGAGGATGTATTATAGC 59.350 45.833 0.00 0.00 31.51 2.97
2851 5025 6.791867 TTGGGATCGGAGGATGTATTATAG 57.208 41.667 0.00 0.00 31.51 1.31
2860 5043 3.716872 ACACTTATTTGGGATCGGAGGAT 59.283 43.478 0.00 0.00 34.96 3.24
2861 5044 3.112263 ACACTTATTTGGGATCGGAGGA 58.888 45.455 0.00 0.00 0.00 3.71
2866 5049 3.063997 GCTGTGACACTTATTTGGGATCG 59.936 47.826 7.20 0.00 0.00 3.69
2872 5055 8.534333 TTAGTTAGAGCTGTGACACTTATTTG 57.466 34.615 8.54 0.00 0.00 2.32
2882 5065 5.304614 ACCTCAACTTTAGTTAGAGCTGTGA 59.695 40.000 0.00 0.00 36.32 3.58
2884 5067 5.810080 ACCTCAACTTTAGTTAGAGCTGT 57.190 39.130 0.00 0.00 36.32 4.40
2886 5069 6.497606 AGGTTACCTCAACTTTAGTTAGAGCT 59.502 38.462 0.00 0.00 36.32 4.09
2904 5093 6.316890 TGTCACAACTTTGAACTAAGGTTACC 59.683 38.462 0.00 0.00 36.55 2.85
2905 5094 7.065443 AGTGTCACAACTTTGAACTAAGGTTAC 59.935 37.037 5.62 0.00 36.55 2.50
2936 5125 9.372369 CTCAATAAAATATACTCCCTCCGATTC 57.628 37.037 0.00 0.00 0.00 2.52
2937 5126 9.101325 TCTCAATAAAATATACTCCCTCCGATT 57.899 33.333 0.00 0.00 0.00 3.34
2938 5127 8.666129 TCTCAATAAAATATACTCCCTCCGAT 57.334 34.615 0.00 0.00 0.00 4.18
2939 5128 8.666129 ATCTCAATAAAATATACTCCCTCCGA 57.334 34.615 0.00 0.00 0.00 4.55
2940 5129 9.726438 AAATCTCAATAAAATATACTCCCTCCG 57.274 33.333 0.00 0.00 0.00 4.63
2956 5147 8.187913 TCCAAACAATGAACCAAATCTCAATA 57.812 30.769 0.00 0.00 0.00 1.90
2958 5149 6.477053 TCCAAACAATGAACCAAATCTCAA 57.523 33.333 0.00 0.00 0.00 3.02
3132 5349 5.678132 TCAGCATGCAACATACATACATC 57.322 39.130 21.98 0.00 34.76 3.06
3173 5390 3.118371 AGCCCCAACTAACCTATTTCTCG 60.118 47.826 0.00 0.00 0.00 4.04
3324 5541 2.850321 CAACGACAATTGAATCCACCG 58.150 47.619 13.59 6.18 0.00 4.94
3372 5589 2.315925 TTCTCTCGCATGTCCCATTC 57.684 50.000 0.00 0.00 0.00 2.67
3426 5643 2.419574 GGCATAAGGTGTGGACGTACAT 60.420 50.000 2.42 0.00 32.43 2.29
3427 5644 1.066716 GGCATAAGGTGTGGACGTACA 60.067 52.381 0.00 0.00 0.00 2.90
3486 6000 9.952030 TGAAATTAAACATAGTGATCTGGTACA 57.048 29.630 0.00 0.00 0.00 2.90
3513 6027 9.601217 GAATTACTTGGCACTAAGAATCTTAGA 57.399 33.333 30.30 10.36 0.00 2.10
3514 6028 8.831550 GGAATTACTTGGCACTAAGAATCTTAG 58.168 37.037 24.09 24.09 0.00 2.18
3515 6029 8.325787 TGGAATTACTTGGCACTAAGAATCTTA 58.674 33.333 2.44 2.44 0.00 2.10
3516 6030 7.175104 TGGAATTACTTGGCACTAAGAATCTT 58.825 34.615 0.00 0.00 0.00 2.40
3517 6031 6.721318 TGGAATTACTTGGCACTAAGAATCT 58.279 36.000 0.34 0.00 0.00 2.40
3518 6032 7.500559 AGATGGAATTACTTGGCACTAAGAATC 59.499 37.037 0.34 0.00 0.00 2.52
3519 6033 7.349598 AGATGGAATTACTTGGCACTAAGAAT 58.650 34.615 0.34 0.00 0.00 2.40
3520 6034 6.721318 AGATGGAATTACTTGGCACTAAGAA 58.279 36.000 0.34 0.00 0.00 2.52
3557 6073 4.507756 GGGCAAAAGAGAACATGTGTTTTC 59.492 41.667 0.00 8.01 38.56 2.29
3560 6076 2.365293 GGGGCAAAAGAGAACATGTGTT 59.635 45.455 0.00 0.00 41.64 3.32
3561 6077 1.963515 GGGGCAAAAGAGAACATGTGT 59.036 47.619 0.00 0.00 0.00 3.72
3589 6105 2.695359 TGCCAAGGTTAGTCGTCATTC 58.305 47.619 0.00 0.00 0.00 2.67
3626 6146 3.800604 GCCAACCAGAATAACGCCAAAAA 60.801 43.478 0.00 0.00 0.00 1.94
3677 6197 3.328382 TGATACTCCTTTTGTGACGGG 57.672 47.619 0.00 0.00 0.00 5.28
3708 6228 1.406898 TCATCACTCTGTCGGATCAGC 59.593 52.381 0.00 0.00 35.63 4.26
3715 6235 7.196331 TGTTGATAGTATTCATCACTCTGTCG 58.804 38.462 0.00 0.00 32.23 4.35
3774 6294 3.259876 TGAACCCAATGTTACGCTCTACT 59.740 43.478 0.00 0.00 37.29 2.57
3918 6444 2.595386 CATCTTTTTACCGCCACAAGC 58.405 47.619 0.00 0.00 38.52 4.01
3948 6474 0.248825 CCTTCGTCCTGCTCTCATCG 60.249 60.000 0.00 0.00 0.00 3.84
3951 6477 0.251386 AGTCCTTCGTCCTGCTCTCA 60.251 55.000 0.00 0.00 0.00 3.27
3972 6498 0.250234 GTATCACCAGCTCCTGCACA 59.750 55.000 0.00 0.00 42.74 4.57
4197 6723 1.898154 GTGGAGTATCGGGTGCACT 59.102 57.895 17.98 0.00 34.37 4.40
4199 6725 2.717044 CCGTGGAGTATCGGGTGCA 61.717 63.158 0.00 0.00 42.61 4.57
4423 6949 0.108585 TTTGACAGCGGCTTCTTCCT 59.891 50.000 0.00 0.00 0.00 3.36
4449 6975 1.637553 ACCATCACCATGAGGCTCTTT 59.362 47.619 16.72 0.00 39.06 2.52
4566 7092 3.633235 CATAACTAAGCATCGAGTCGCT 58.367 45.455 7.92 0.00 41.20 4.93
4593 7119 1.079127 CATCGCCGGTCTCCTGTTT 60.079 57.895 1.90 0.00 0.00 2.83
4677 7203 7.046652 CCATATCTTTGATAGTGAGGCTATGG 58.953 42.308 0.00 0.00 40.30 2.74


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

AutoCloner maintained by Alex Coulton.