Multiple sequence alignment - TraesCS6B01G091400

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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 TraesCS6B01G091400 chr6B 100.000 5862 0 0 1 5862 67132937 67127076 0.000000e+00 10826.0
1 TraesCS6B01G091400 chr6B 96.875 3744 110 6 1407 5146 67324055 67320315 0.000000e+00 6259.0
2 TraesCS6B01G091400 chr6B 81.510 3218 506 69 1851 5009 66991894 66988707 0.000000e+00 2564.0
3 TraesCS6B01G091400 chr6B 78.517 2644 431 90 1851 4437 66971097 66968534 0.000000e+00 1609.0
4 TraesCS6B01G091400 chr6B 84.518 1337 172 16 1851 3177 68783248 68781937 0.000000e+00 1290.0
5 TraesCS6B01G091400 chr6B 79.238 1941 312 69 1862 3769 66755673 66753791 0.000000e+00 1267.0
6 TraesCS6B01G091400 chr6B 78.521 1988 326 75 1856 3800 66786269 66784340 0.000000e+00 1212.0
7 TraesCS6B01G091400 chr6B 79.578 1611 280 34 3820 5400 67409326 67407735 0.000000e+00 1107.0
8 TraesCS6B01G091400 chr6B 79.752 1615 249 60 2913 4482 67229129 67227548 0.000000e+00 1099.0
9 TraesCS6B01G091400 chr6B 80.942 1317 217 27 3842 5137 68751196 68752499 0.000000e+00 1011.0
10 TraesCS6B01G091400 chr6B 80.265 1358 236 25 3842 5178 68780505 68779159 0.000000e+00 994.0
11 TraesCS6B01G091400 chr6B 93.440 564 31 6 5174 5735 67320320 67319761 0.000000e+00 832.0
12 TraesCS6B01G091400 chr6B 93.540 387 15 6 1 378 66973653 66973268 8.530000e-158 568.0
13 TraesCS6B01G091400 chr6B 93.838 357 15 5 1051 1407 67324457 67324108 1.120000e-146 531.0
14 TraesCS6B01G091400 chr6B 81.195 686 48 29 376 1050 66973108 66972493 1.480000e-130 477.0
15 TraesCS6B01G091400 chr6B 83.690 374 26 23 685 1050 67324768 67324422 2.640000e-83 320.0
16 TraesCS6B01G091400 chr6B 91.534 189 12 2 1051 1235 66972528 66972340 2.100000e-64 257.0
17 TraesCS6B01G091400 chr6B 83.212 274 40 5 1048 1319 68748402 68748671 4.540000e-61 246.0
18 TraesCS6B01G091400 chr6B 83.209 268 39 5 1054 1319 68783740 68783477 2.110000e-59 241.0
19 TraesCS6B01G091400 chr6B 81.690 284 36 11 1054 1330 66992384 66992110 7.650000e-54 222.0
20 TraesCS6B01G091400 chr6B 96.899 129 4 0 5734 5862 230318942 230319070 3.560000e-52 217.0
21 TraesCS6B01G091400 chr6B 77.273 264 30 13 810 1050 66863304 66863048 1.710000e-25 128.0
22 TraesCS6B01G091400 chr6B 77.273 264 30 13 810 1050 66921185 66920929 1.710000e-25 128.0
23 TraesCS6B01G091400 chr6B 80.978 184 15 6 806 969 66945765 66945582 1.710000e-25 128.0
24 TraesCS6B01G091400 chr6B 80.749 187 13 14 866 1033 66992551 66992369 2.220000e-24 124.0
25 TraesCS6B01G091400 chr6B 90.123 81 8 0 807 887 66756567 66756487 8.030000e-19 106.0
26 TraesCS6B01G091400 chr6B 94.118 51 3 0 638 688 560706183 560706133 1.750000e-10 78.7
27 TraesCS6B01G091400 chr6B 94.118 51 3 0 638 688 560745634 560745584 1.750000e-10 78.7
28 TraesCS6B01G091400 chr6B 97.727 44 1 0 639 682 59870688 59870731 6.300000e-10 76.8
29 TraesCS6B01G091400 chr6D 92.572 4389 263 36 1051 5404 31755252 31750892 0.000000e+00 6240.0
30 TraesCS6B01G091400 chr6D 83.497 1933 267 39 1851 3751 31770570 31768658 0.000000e+00 1755.0
31 TraesCS6B01G091400 chr6D 83.170 1937 270 41 1851 3751 23440453 23438537 0.000000e+00 1720.0
32 TraesCS6B01G091400 chr6D 81.715 1143 186 16 3850 4977 23438469 23437335 0.000000e+00 931.0
33 TraesCS6B01G091400 chr6D 81.627 1143 187 16 3850 4977 31768590 31767456 0.000000e+00 926.0
34 TraesCS6B01G091400 chr6D 94.314 598 30 3 1 594 31755769 31756366 0.000000e+00 913.0
35 TraesCS6B01G091400 chr6D 94.157 599 30 3 1 594 23425787 23426385 0.000000e+00 907.0
36 TraesCS6B01G091400 chr6D 92.179 358 19 8 1051 1407 23425267 23424918 1.130000e-136 497.0
37 TraesCS6B01G091400 chr6D 89.474 380 19 8 677 1050 31755581 31755217 1.490000e-125 460.0
38 TraesCS6B01G091400 chr6D 88.158 380 21 9 677 1050 23425593 23425232 1.170000e-116 431.0
39 TraesCS6B01G091400 chr6D 79.817 218 28 8 806 1022 23441126 23440924 1.700000e-30 145.0
40 TraesCS6B01G091400 chr6D 79.817 218 28 8 806 1022 31771243 31771041 1.700000e-30 145.0
41 TraesCS6B01G091400 chr6D 100.000 45 0 0 596 640 23425647 23425603 3.760000e-12 84.2
42 TraesCS6B01G091400 chr6D 97.727 44 1 0 639 682 293177565 293177522 6.300000e-10 76.8
43 TraesCS6B01G091400 chr6D 88.000 50 4 2 5410 5458 193255195 193255147 2.280000e-04 58.4
44 TraesCS6B01G091400 chr2B 80.617 3080 476 79 1873 4881 696670289 696673318 0.000000e+00 2268.0
45 TraesCS6B01G091400 chr6A 79.410 3084 510 93 1851 4879 36108982 36105969 0.000000e+00 2061.0
46 TraesCS6B01G091400 chr6A 83.239 1945 274 39 1851 3756 36252880 36250949 0.000000e+00 1738.0
47 TraesCS6B01G091400 chr6A 88.335 1063 57 34 3 1050 36111387 36110377 0.000000e+00 1214.0
48 TraesCS6B01G091400 chr6A 78.414 1992 324 77 1860 3797 36055817 36053878 0.000000e+00 1199.0
49 TraesCS6B01G091400 chr6A 78.281 1989 332 74 1860 3797 35990424 35988485 0.000000e+00 1188.0
50 TraesCS6B01G091400 chr6A 79.261 1596 281 34 3835 5395 36250928 36249348 0.000000e+00 1068.0
51 TraesCS6B01G091400 chr6A 92.593 189 10 2 1051 1235 36110412 36110224 9.680000e-68 268.0
52 TraesCS6B01G091400 chr6A 82.206 281 39 7 1054 1330 36253357 36253084 1.270000e-56 231.0
53 TraesCS6B01G091400 chr6A 78.616 159 30 4 1975 2132 36407599 36407444 1.040000e-17 102.0
54 TraesCS6B01G091400 chr2D 79.864 2647 404 81 2303 4881 579386981 579389566 0.000000e+00 1816.0
55 TraesCS6B01G091400 chr2D 80.769 442 73 8 1874 2311 579386524 579386957 9.410000e-88 335.0
56 TraesCS6B01G091400 chr2A 80.164 2193 332 62 2303 4437 717137789 717139936 0.000000e+00 1544.0
57 TraesCS6B01G091400 chr7B 88.462 338 25 5 5402 5735 68839580 68839907 4.260000e-106 396.0
58 TraesCS6B01G091400 chr1B 97.656 128 3 0 5735 5862 304339214 304339341 2.750000e-53 220.0
59 TraesCS6B01G091400 chr1B 97.727 44 1 0 638 681 426073344 426073301 6.300000e-10 76.8
60 TraesCS6B01G091400 chr5B 96.899 129 4 0 5734 5862 76253834 76253962 3.560000e-52 217.0
61 TraesCS6B01G091400 chr3B 95.522 134 6 0 5729 5862 167828910 167828777 1.280000e-51 215.0
62 TraesCS6B01G091400 chr3B 93.023 43 3 0 1411 1453 494710357 494710399 4.900000e-06 63.9
63 TraesCS6B01G091400 chr1A 95.522 134 6 0 5729 5862 423364373 423364506 1.280000e-51 215.0
64 TraesCS6B01G091400 chr1A 81.197 117 18 3 5515 5627 6475868 6475752 2.250000e-14 91.6
65 TraesCS6B01G091400 chrUn 94.286 140 6 2 5723 5860 50807575 50807714 4.600000e-51 213.0
66 TraesCS6B01G091400 chrUn 94.161 137 8 0 5726 5862 62731041 62730905 5.950000e-50 209.0
67 TraesCS6B01G091400 chr5A 93.056 144 9 1 5719 5862 519585597 519585455 5.950000e-50 209.0
68 TraesCS6B01G091400 chr4A 94.161 137 8 0 5726 5862 635113194 635113058 5.950000e-50 209.0
69 TraesCS6B01G091400 chr4A 97.872 47 1 0 636 682 699892980 699892934 1.350000e-11 82.4
70 TraesCS6B01G091400 chr5D 79.861 144 27 2 1410 1551 41601524 41601381 2.890000e-18 104.0
71 TraesCS6B01G091400 chr5D 95.833 48 2 0 635 682 503136560 503136607 1.750000e-10 78.7
72 TraesCS6B01G091400 chr5D 97.727 44 1 0 639 682 320627427 320627384 6.300000e-10 76.8
73 TraesCS6B01G091400 chr5D 90.698 43 3 1 1400 1441 468830875 468830917 8.210000e-04 56.5
74 TraesCS6B01G091400 chr3A 81.818 110 16 3 5515 5620 177677244 177677353 8.090000e-14 89.8
75 TraesCS6B01G091400 chr7D 97.727 44 1 0 639 682 127220712 127220669 6.300000e-10 76.8
76 TraesCS6B01G091400 chr7A 88.462 52 6 0 1412 1463 85901272 85901323 4.900000e-06 63.9
77 TraesCS6B01G091400 chr1D 86.275 51 7 0 1412 1462 8792877 8792927 8.210000e-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 TraesCS6B01G091400 chr6B 67127076 67132937 5861 True 10826.000000 10826 100.000000 1 5862 1 chr6B.!!$R5 5861
1 TraesCS6B01G091400 chr6B 67319761 67324768 5007 True 1985.500000 6259 91.960750 685 5735 4 chr6B.!!$R13 5050
2 TraesCS6B01G091400 chr6B 66784340 66786269 1929 True 1212.000000 1212 78.521000 1856 3800 1 chr6B.!!$R1 1944
3 TraesCS6B01G091400 chr6B 67407735 67409326 1591 True 1107.000000 1107 79.578000 3820 5400 1 chr6B.!!$R7 1580
4 TraesCS6B01G091400 chr6B 67227548 67229129 1581 True 1099.000000 1099 79.752000 2913 4482 1 chr6B.!!$R6 1569
5 TraesCS6B01G091400 chr6B 66988707 66992551 3844 True 970.000000 2564 81.316333 866 5009 3 chr6B.!!$R12 4143
6 TraesCS6B01G091400 chr6B 68779159 68783740 4581 True 841.666667 1290 82.664000 1054 5178 3 chr6B.!!$R14 4124
7 TraesCS6B01G091400 chr6B 66968534 66973653 5119 True 727.750000 1609 86.196500 1 4437 4 chr6B.!!$R11 4436
8 TraesCS6B01G091400 chr6B 66753791 66756567 2776 True 686.500000 1267 84.680500 807 3769 2 chr6B.!!$R10 2962
9 TraesCS6B01G091400 chr6B 68748402 68752499 4097 False 628.500000 1011 82.077000 1048 5137 2 chr6B.!!$F3 4089
10 TraesCS6B01G091400 chr6D 31750892 31755581 4689 True 3350.000000 6240 91.023000 677 5404 2 chr6D.!!$R5 4727
11 TraesCS6B01G091400 chr6D 31767456 31771243 3787 True 942.000000 1755 81.647000 806 4977 3 chr6D.!!$R6 4171
12 TraesCS6B01G091400 chr6D 23437335 23441126 3791 True 932.000000 1720 81.567333 806 4977 3 chr6D.!!$R4 4171
13 TraesCS6B01G091400 chr6D 31755769 31756366 597 False 913.000000 913 94.314000 1 594 1 chr6D.!!$F2 593
14 TraesCS6B01G091400 chr6D 23425787 23426385 598 False 907.000000 907 94.157000 1 594 1 chr6D.!!$F1 593
15 TraesCS6B01G091400 chr6D 23424918 23425647 729 True 337.400000 497 93.445667 596 1407 3 chr6D.!!$R3 811
16 TraesCS6B01G091400 chr2B 696670289 696673318 3029 False 2268.000000 2268 80.617000 1873 4881 1 chr2B.!!$F1 3008
17 TraesCS6B01G091400 chr6A 36053878 36055817 1939 True 1199.000000 1199 78.414000 1860 3797 1 chr6A.!!$R2 1937
18 TraesCS6B01G091400 chr6A 35988485 35990424 1939 True 1188.000000 1188 78.281000 1860 3797 1 chr6A.!!$R1 1937
19 TraesCS6B01G091400 chr6A 36105969 36111387 5418 True 1181.000000 2061 86.779333 3 4879 3 chr6A.!!$R4 4876
20 TraesCS6B01G091400 chr6A 36249348 36253357 4009 True 1012.333333 1738 81.568667 1054 5395 3 chr6A.!!$R5 4341
21 TraesCS6B01G091400 chr2D 579386524 579389566 3042 False 1075.500000 1816 80.316500 1874 4881 2 chr2D.!!$F1 3007
22 TraesCS6B01G091400 chr2A 717137789 717139936 2147 False 1544.000000 1544 80.164000 2303 4437 1 chr2A.!!$F1 2134

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
654 837 0.033011 AGCTACTCCCTCCGTCACAT 60.033 55.000 0.00 0.00 0.00 3.21 F
1589 2598 0.038166 CTTGAACCTTGGCTAGCCCA 59.962 55.000 30.81 19.65 43.51 5.36 F
2366 3575 0.469070 AGAGCCCATCTGCATGACTC 59.531 55.000 0.00 0.00 36.69 3.36 F
2503 3712 1.209019 AGCCATCACTCTACAAGGCAG 59.791 52.381 0.00 0.00 44.34 4.85 F
2900 4129 1.253100 TTCCCGCAATTGAAAGGGTC 58.747 50.000 24.19 1.51 44.13 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 3184 0.108186 GCACATGACTCCACGATGGA 60.108 55.000 0.00 6.57 45.98 3.41 R
2668 3877 3.119245 GCACATGCCAGATTCTCAATTGT 60.119 43.478 5.13 0.00 34.31 2.71 R
4358 6546 3.200825 AGGAGATGACCCGATGAATGTTT 59.799 43.478 0.00 0.00 0.00 2.83 R
4442 6630 9.913310 TCCTAATGTGTTATTTGATTACATCCA 57.087 29.630 0.00 0.00 31.30 3.41 R
4950 7154 5.936686 ACACATATGCTAATGATGCAGAC 57.063 39.130 1.58 0.00 44.04 3.51 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
52 53 3.308323 GTCTTCTTCATCTTGCATCCGTC 59.692 47.826 0.00 0.00 0.00 4.79
78 81 7.059945 CGACGGCCTTTTTACTTACGTATATAG 59.940 40.741 0.00 0.00 32.84 1.31
80 83 7.014230 ACGGCCTTTTTACTTACGTATATAGGA 59.986 37.037 9.36 0.00 31.94 2.94
415 590 7.530010 TGCTTTATTCTTCTTAGTTGCATGTC 58.470 34.615 0.00 0.00 0.00 3.06
447 622 3.076621 GCCATGACAGATTCTGTGAACA 58.923 45.455 23.57 15.27 45.44 3.18
498 674 2.170817 GGCCCTCCCTGTTACTCTAAAG 59.829 54.545 0.00 0.00 0.00 1.85
510 686 9.280174 CCTGTTACTCTAAAGAAACATGGTTAA 57.720 33.333 0.00 0.00 31.88 2.01
640 823 3.190535 GCATGGAGTCTCTAGCTAGCTAC 59.809 52.174 20.67 13.52 0.00 3.58
642 825 4.345859 TGGAGTCTCTAGCTAGCTACTC 57.654 50.000 29.25 29.25 35.68 2.59
644 827 3.558533 GGAGTCTCTAGCTAGCTACTCCC 60.559 56.522 36.05 26.67 42.69 4.30
645 828 3.323775 AGTCTCTAGCTAGCTACTCCCT 58.676 50.000 20.67 11.11 0.00 4.20
646 829 3.326880 AGTCTCTAGCTAGCTACTCCCTC 59.673 52.174 20.67 9.05 0.00 4.30
647 830 2.640826 TCTCTAGCTAGCTACTCCCTCC 59.359 54.545 20.67 0.00 0.00 4.30
649 832 1.072648 CTAGCTAGCTACTCCCTCCGT 59.927 57.143 20.67 0.00 0.00 4.69
650 833 0.179012 AGCTAGCTACTCCCTCCGTC 60.179 60.000 17.69 0.00 0.00 4.79
652 835 1.310904 CTAGCTACTCCCTCCGTCAC 58.689 60.000 0.00 0.00 0.00 3.67
653 836 0.622136 TAGCTACTCCCTCCGTCACA 59.378 55.000 0.00 0.00 0.00 3.58
654 837 0.033011 AGCTACTCCCTCCGTCACAT 60.033 55.000 0.00 0.00 0.00 3.21
655 838 1.214673 AGCTACTCCCTCCGTCACATA 59.785 52.381 0.00 0.00 0.00 2.29
656 839 2.029623 GCTACTCCCTCCGTCACATAA 58.970 52.381 0.00 0.00 0.00 1.90
657 840 2.628657 GCTACTCCCTCCGTCACATAAT 59.371 50.000 0.00 0.00 0.00 1.28
658 841 3.825014 GCTACTCCCTCCGTCACATAATA 59.175 47.826 0.00 0.00 0.00 0.98
659 842 4.463186 GCTACTCCCTCCGTCACATAATAT 59.537 45.833 0.00 0.00 0.00 1.28
660 843 5.651139 GCTACTCCCTCCGTCACATAATATA 59.349 44.000 0.00 0.00 0.00 0.86
661 844 6.152323 GCTACTCCCTCCGTCACATAATATAA 59.848 42.308 0.00 0.00 0.00 0.98
662 845 6.989155 ACTCCCTCCGTCACATAATATAAA 57.011 37.500 0.00 0.00 0.00 1.40
663 846 7.369551 ACTCCCTCCGTCACATAATATAAAA 57.630 36.000 0.00 0.00 0.00 1.52
664 847 7.798071 ACTCCCTCCGTCACATAATATAAAAA 58.202 34.615 0.00 0.00 0.00 1.94
665 848 7.713942 ACTCCCTCCGTCACATAATATAAAAAC 59.286 37.037 0.00 0.00 0.00 2.43
666 849 6.702723 TCCCTCCGTCACATAATATAAAAACG 59.297 38.462 0.00 0.00 0.00 3.60
667 850 6.480981 CCCTCCGTCACATAATATAAAAACGT 59.519 38.462 0.00 0.00 0.00 3.99
668 851 7.011669 CCCTCCGTCACATAATATAAAAACGTT 59.988 37.037 0.00 0.00 0.00 3.99
669 852 8.392612 CCTCCGTCACATAATATAAAAACGTTT 58.607 33.333 7.96 7.96 0.00 3.60
670 853 9.763465 CTCCGTCACATAATATAAAAACGTTTT 57.237 29.630 20.26 20.26 0.00 2.43
691 874 2.941428 TGACACTACACACGTATGCTG 58.059 47.619 0.00 0.00 0.00 4.41
718 903 6.225318 AGTGCATGTTTAGTGAATTTTGCAT 58.775 32.000 0.00 0.00 0.00 3.96
747 935 0.614979 GGGCAGACAGTCCACTCCTA 60.615 60.000 0.00 0.00 43.39 2.94
776 964 2.109126 GGATCCACGGAGCTGCAAC 61.109 63.158 6.95 0.00 0.00 4.17
777 965 2.045926 ATCCACGGAGCTGCAACC 60.046 61.111 5.91 4.03 0.00 3.77
778 966 2.527951 GATCCACGGAGCTGCAACCT 62.528 60.000 5.91 0.00 0.00 3.50
779 967 2.527951 ATCCACGGAGCTGCAACCTC 62.528 60.000 5.91 5.66 0.00 3.85
780 968 2.345244 CACGGAGCTGCAACCTCT 59.655 61.111 5.91 0.00 0.00 3.69
781 969 2.031516 CACGGAGCTGCAACCTCTG 61.032 63.158 17.11 17.11 40.68 3.35
790 978 4.613929 CAACCTCTGCTCTGCTCC 57.386 61.111 0.00 0.00 0.00 4.70
791 979 1.447489 CAACCTCTGCTCTGCTCCG 60.447 63.158 0.00 0.00 0.00 4.63
792 980 3.308014 AACCTCTGCTCTGCTCCGC 62.308 63.158 0.00 0.00 0.00 5.54
793 981 3.459965 CCTCTGCTCTGCTCCGCT 61.460 66.667 0.00 0.00 0.00 5.52
794 982 2.104729 CTCTGCTCTGCTCCGCTC 59.895 66.667 0.00 0.00 0.00 5.03
795 983 2.362247 TCTGCTCTGCTCCGCTCT 60.362 61.111 0.00 0.00 0.00 4.09
804 997 2.489275 GCTCCGCTCTCCTCTCCTG 61.489 68.421 0.00 0.00 0.00 3.86
960 1191 4.097437 CCTACTTAGCCGATCTGTAACACA 59.903 45.833 0.00 0.00 0.00 3.72
1040 1275 0.327259 TTCTCCTTCTCCTCGGTCGA 59.673 55.000 0.00 0.00 0.00 4.20
1041 1276 0.107606 TCTCCTTCTCCTCGGTCGAG 60.108 60.000 12.87 12.87 41.63 4.04
1042 1277 1.720694 CTCCTTCTCCTCGGTCGAGC 61.721 65.000 14.21 4.06 40.69 5.03
1043 1278 2.776913 CCTTCTCCTCGGTCGAGCC 61.777 68.421 14.21 1.35 40.69 4.70
1044 1279 2.035155 TTCTCCTCGGTCGAGCCA 59.965 61.111 14.21 0.00 40.69 4.75
1045 1280 2.272918 CTTCTCCTCGGTCGAGCCAC 62.273 65.000 14.21 0.00 40.69 5.01
1046 1281 2.752238 CTCCTCGGTCGAGCCACT 60.752 66.667 14.21 0.00 40.69 4.00
1047 1282 3.057547 CTCCTCGGTCGAGCCACTG 62.058 68.421 14.21 1.67 40.69 3.66
1048 1283 4.803426 CCTCGGTCGAGCCACTGC 62.803 72.222 14.21 0.00 40.69 4.40
1058 1293 3.769201 GCCACTGCTTGCCTTCTT 58.231 55.556 0.00 0.00 33.53 2.52
1059 1294 1.583477 GCCACTGCTTGCCTTCTTC 59.417 57.895 0.00 0.00 33.53 2.87
1060 1295 1.174712 GCCACTGCTTGCCTTCTTCA 61.175 55.000 0.00 0.00 33.53 3.02
1061 1296 0.595095 CCACTGCTTGCCTTCTTCAC 59.405 55.000 0.00 0.00 0.00 3.18
1067 1302 1.809547 GCTTGCCTTCTTCACCTTCTC 59.190 52.381 0.00 0.00 0.00 2.87
1071 1306 1.404851 GCCTTCTTCACCTTCTCCTCG 60.405 57.143 0.00 0.00 0.00 4.63
1074 1309 1.546961 TCTTCACCTTCTCCTCGGTC 58.453 55.000 0.00 0.00 0.00 4.79
1442 2451 6.804677 AGTCGATGCTATATTCATGAGATCC 58.195 40.000 0.00 0.00 0.00 3.36
1465 2474 2.542411 GCATTGAGATCCGTGCAAATCC 60.542 50.000 0.00 0.00 37.52 3.01
1513 2522 6.821388 ACATGGTATCTCACTTGATAAGACC 58.179 40.000 0.00 0.00 31.61 3.85
1526 2535 8.759641 CACTTGATAAGACCTGATTAAATCTCG 58.240 37.037 0.00 0.00 0.00 4.04
1589 2598 0.038166 CTTGAACCTTGGCTAGCCCA 59.962 55.000 30.81 19.65 43.51 5.36
1751 2761 6.828273 TCTTTTGAATGAGGACAGTTCTCAAA 59.172 34.615 15.97 3.04 43.43 2.69
1946 3100 3.379372 AGCATTGCTACATCAACATCCAC 59.621 43.478 10.00 0.00 36.99 4.02
2027 3184 6.039941 CCACTATTTCCAAGACGAGATAGACT 59.960 42.308 0.00 0.00 33.34 3.24
2366 3575 0.469070 AGAGCCCATCTGCATGACTC 59.531 55.000 0.00 0.00 36.69 3.36
2374 3583 3.059099 TGCATGACTCGGCAGACA 58.941 55.556 0.00 0.00 34.58 3.41
2391 3600 4.261197 GCAGACAATGTTCTTCGGAAGTTT 60.261 41.667 16.78 5.23 34.28 2.66
2441 3650 2.610727 GGCTCAGCAAAGACGTTAGAGT 60.611 50.000 0.00 0.00 0.00 3.24
2503 3712 1.209019 AGCCATCACTCTACAAGGCAG 59.791 52.381 0.00 0.00 44.34 4.85
2668 3877 1.985159 ACTTGCCCACTAGGAACATGA 59.015 47.619 0.00 0.00 38.24 3.07
2900 4129 1.253100 TTCCCGCAATTGAAAGGGTC 58.747 50.000 24.19 1.51 44.13 4.46
2905 4134 1.265635 CGCAATTGAAAGGGTCGTTGA 59.734 47.619 10.34 0.00 30.11 3.18
3133 4363 1.552337 GCCACACAAGAGGAGATCTCA 59.448 52.381 23.85 0.00 44.81 3.27
3262 4518 7.701924 TGTCCAATCGCATATTCAAATTTCTTC 59.298 33.333 0.00 0.00 0.00 2.87
3565 5681 1.375098 GGATCTTGCAGCTGCTGACC 61.375 60.000 36.61 27.91 42.66 4.02
4358 6546 5.596361 TGATTTAACAGAGGGCAACAAAGAA 59.404 36.000 0.00 0.00 39.74 2.52
4442 6630 5.133221 AGTGCAAAGGTTAGAACACAGAAT 58.867 37.500 0.00 0.00 0.00 2.40
4557 6746 6.560711 GTCGACATTAACCAAAATAGGCATT 58.439 36.000 11.55 0.00 0.00 3.56
4950 7154 4.100035 TGCCATCTAGGATGTTGACTACAG 59.900 45.833 6.75 0.00 41.22 2.74
5015 7219 3.629142 ATACCCGGAGAAAAGTTCTGG 57.371 47.619 0.73 0.00 40.87 3.86
5058 7262 3.000041 TGTTGCGGTGTGTGATAAGATC 59.000 45.455 0.00 0.00 0.00 2.75
5142 7347 7.633018 ATGTATGAGAATAGTATTGGGTGGT 57.367 36.000 0.00 0.00 0.00 4.16
5164 7369 2.789092 GCAGCTTTATGACGATGTGCAC 60.789 50.000 10.75 10.75 0.00 4.57
5173 7378 0.516877 ACGATGTGCACATTGTTCGG 59.483 50.000 36.67 21.94 46.03 4.30
5190 7428 0.462047 CGGGTGCAATAGGTGACTCC 60.462 60.000 0.00 0.00 43.67 3.85
5203 7441 5.319043 AGGTGACTCCAATTTAGTTCCAA 57.681 39.130 0.00 0.00 39.02 3.53
5208 7446 7.433680 GTGACTCCAATTTAGTTCCAACAATT 58.566 34.615 0.00 0.00 0.00 2.32
5242 7481 7.877612 ACATATCAAAGAAAATGGGGTCAAAAC 59.122 33.333 0.00 0.00 0.00 2.43
5275 7524 3.195396 GCACCAATCTCATAAGGGCAAAA 59.805 43.478 0.00 0.00 0.00 2.44
5276 7525 4.141869 GCACCAATCTCATAAGGGCAAAAT 60.142 41.667 0.00 0.00 0.00 1.82
5332 7581 1.203758 CGGGGTTTTGCTATTTCCCAC 59.796 52.381 0.00 0.00 39.85 4.61
5340 7589 5.379732 TTTGCTATTTCCCACTTTTACGG 57.620 39.130 0.00 0.00 0.00 4.02
5361 7610 0.630673 AGGGGCCATGCATAGACAAA 59.369 50.000 4.39 0.00 0.00 2.83
5405 7654 2.551287 GCCCACATAACCGGCATACATA 60.551 50.000 0.00 0.00 42.52 2.29
5527 7777 0.090676 CACATCGTTCGTTTCGTCCG 59.909 55.000 0.00 0.00 0.00 4.79
5544 7794 5.358922 TCGTCCGGTAAAAAGAGAGAAAAA 58.641 37.500 0.00 0.00 0.00 1.94
5574 7824 1.679559 GATTGCCCAGCCACCATTCC 61.680 60.000 0.00 0.00 0.00 3.01
5609 7859 2.107366 CTCTCCCTCTCCCTTGTCTTC 58.893 57.143 0.00 0.00 0.00 2.87
5640 7890 2.574399 GACGACCTCCTCACAGCC 59.426 66.667 0.00 0.00 0.00 4.85
5722 7972 0.460987 CTTCTCCTCACCATCCACGC 60.461 60.000 0.00 0.00 0.00 5.34
5740 7990 3.120191 CCCCCTCCCCTCACTACT 58.880 66.667 0.00 0.00 0.00 2.57
5741 7991 2.339796 CCCCCTCCCCTCACTACTA 58.660 63.158 0.00 0.00 0.00 1.82
5742 7992 0.188834 CCCCCTCCCCTCACTACTAG 59.811 65.000 0.00 0.00 0.00 2.57
5743 7993 1.232909 CCCCTCCCCTCACTACTAGA 58.767 60.000 0.00 0.00 0.00 2.43
5744 7994 1.574339 CCCCTCCCCTCACTACTAGAA 59.426 57.143 0.00 0.00 0.00 2.10
5745 7995 2.023307 CCCCTCCCCTCACTACTAGAAA 60.023 54.545 0.00 0.00 0.00 2.52
5746 7996 3.568109 CCCCTCCCCTCACTACTAGAAAA 60.568 52.174 0.00 0.00 0.00 2.29
5747 7997 4.101856 CCCTCCCCTCACTACTAGAAAAA 58.898 47.826 0.00 0.00 0.00 1.94
5764 8014 2.500392 AAAACCCTACTAATGGCGCA 57.500 45.000 10.83 0.00 0.00 6.09
5765 8015 1.746470 AAACCCTACTAATGGCGCAC 58.254 50.000 10.83 0.00 0.00 5.34
5766 8016 0.107361 AACCCTACTAATGGCGCACC 60.107 55.000 10.83 0.00 0.00 5.01
5767 8017 0.981277 ACCCTACTAATGGCGCACCT 60.981 55.000 10.83 0.00 36.63 4.00
5768 8018 1.045407 CCCTACTAATGGCGCACCTA 58.955 55.000 10.83 0.00 36.63 3.08
5769 8019 1.414919 CCCTACTAATGGCGCACCTAA 59.585 52.381 10.83 0.00 36.63 2.69
5770 8020 2.158871 CCCTACTAATGGCGCACCTAAA 60.159 50.000 10.83 0.00 36.63 1.85
5771 8021 3.537580 CCTACTAATGGCGCACCTAAAA 58.462 45.455 10.83 0.00 36.63 1.52
5772 8022 4.134563 CCTACTAATGGCGCACCTAAAAT 58.865 43.478 10.83 0.00 36.63 1.82
5773 8023 4.024048 CCTACTAATGGCGCACCTAAAATG 60.024 45.833 10.83 0.00 36.63 2.32
5774 8024 2.687935 ACTAATGGCGCACCTAAAATGG 59.312 45.455 10.83 0.00 36.63 3.16
5775 8025 0.175531 AATGGCGCACCTAAAATGGC 59.824 50.000 10.83 0.00 36.63 4.40
5776 8026 1.675720 ATGGCGCACCTAAAATGGCC 61.676 55.000 10.83 0.00 40.88 5.36
5777 8027 2.347322 GGCGCACCTAAAATGGCCA 61.347 57.895 8.56 8.56 40.24 5.36
5778 8028 1.675720 GGCGCACCTAAAATGGCCAT 61.676 55.000 14.09 14.09 40.24 4.40
5779 8029 0.175531 GCGCACCTAAAATGGCCATT 59.824 50.000 25.73 25.73 0.00 3.16
5780 8030 1.407258 GCGCACCTAAAATGGCCATTA 59.593 47.619 30.84 15.76 0.00 1.90
5781 8031 2.159170 GCGCACCTAAAATGGCCATTAA 60.159 45.455 30.84 20.22 0.00 1.40
5782 8032 3.492482 GCGCACCTAAAATGGCCATTAAT 60.492 43.478 30.84 23.44 0.00 1.40
5783 8033 4.050553 CGCACCTAAAATGGCCATTAATG 58.949 43.478 30.84 22.38 0.00 1.90
5794 8044 2.410785 CCATTAATGGCGCATCTGTG 57.589 50.000 21.32 0.00 41.75 3.66
5795 8045 1.001048 CCATTAATGGCGCATCTGTGG 60.001 52.381 21.32 6.13 41.75 4.17
5796 8046 1.677576 CATTAATGGCGCATCTGTGGT 59.322 47.619 10.83 0.00 0.00 4.16
5797 8047 1.093972 TTAATGGCGCATCTGTGGTG 58.906 50.000 10.83 0.00 0.00 4.17
5798 8048 1.375853 TAATGGCGCATCTGTGGTGC 61.376 55.000 10.83 0.00 40.91 5.01
5799 8049 3.923782 ATGGCGCATCTGTGGTGCA 62.924 57.895 10.83 0.00 43.32 4.57
5800 8050 3.136123 GGCGCATCTGTGGTGCAT 61.136 61.111 10.83 0.00 43.32 3.96
5801 8051 2.406401 GCGCATCTGTGGTGCATC 59.594 61.111 0.30 0.00 42.62 3.91
5802 8052 2.400962 GCGCATCTGTGGTGCATCA 61.401 57.895 0.30 0.00 42.62 3.07
5803 8053 1.721664 GCGCATCTGTGGTGCATCAT 61.722 55.000 1.27 0.00 42.62 2.45
5804 8054 0.736636 CGCATCTGTGGTGCATCATT 59.263 50.000 1.27 0.00 42.62 2.57
5805 8055 1.533129 CGCATCTGTGGTGCATCATTG 60.533 52.381 1.27 0.00 42.62 2.82
5806 8056 1.746787 GCATCTGTGGTGCATCATTGA 59.253 47.619 1.27 5.04 42.08 2.57
5807 8057 2.361119 GCATCTGTGGTGCATCATTGAT 59.639 45.455 1.27 7.39 42.08 2.57
5808 8058 3.566742 GCATCTGTGGTGCATCATTGATA 59.433 43.478 1.27 0.00 42.08 2.15
5809 8059 4.320275 GCATCTGTGGTGCATCATTGATAG 60.320 45.833 1.27 6.59 42.08 2.08
5810 8060 3.208594 TCTGTGGTGCATCATTGATAGC 58.791 45.455 1.27 6.50 0.00 2.97
5811 8061 2.946990 CTGTGGTGCATCATTGATAGCA 59.053 45.455 1.27 15.31 34.10 3.49
5814 8064 2.028287 GTGCATCATTGATAGCACGC 57.972 50.000 24.75 14.77 46.35 5.34
5815 8065 0.946528 TGCATCATTGATAGCACGCC 59.053 50.000 15.31 0.00 31.05 5.68
5816 8066 0.946528 GCATCATTGATAGCACGCCA 59.053 50.000 13.00 0.00 0.00 5.69
5817 8067 1.538512 GCATCATTGATAGCACGCCAT 59.461 47.619 13.00 0.00 0.00 4.40
5818 8068 2.030540 GCATCATTGATAGCACGCCATT 60.031 45.455 13.00 0.00 0.00 3.16
5819 8069 3.189080 GCATCATTGATAGCACGCCATTA 59.811 43.478 13.00 0.00 0.00 1.90
5820 8070 4.670992 GCATCATTGATAGCACGCCATTAG 60.671 45.833 13.00 0.00 0.00 1.73
5821 8071 4.071961 TCATTGATAGCACGCCATTAGT 57.928 40.909 0.00 0.00 0.00 2.24
5822 8072 5.208463 TCATTGATAGCACGCCATTAGTA 57.792 39.130 0.00 0.00 0.00 1.82
5823 8073 5.606505 TCATTGATAGCACGCCATTAGTAA 58.393 37.500 0.00 0.00 0.00 2.24
5824 8074 6.230472 TCATTGATAGCACGCCATTAGTAAT 58.770 36.000 0.00 0.00 0.00 1.89
5825 8075 6.710295 TCATTGATAGCACGCCATTAGTAATT 59.290 34.615 0.00 0.00 0.00 1.40
5826 8076 6.935741 TTGATAGCACGCCATTAGTAATTT 57.064 33.333 0.00 0.00 0.00 1.82
5827 8077 6.935741 TGATAGCACGCCATTAGTAATTTT 57.064 33.333 0.00 0.00 0.00 1.82
5828 8078 7.328277 TGATAGCACGCCATTAGTAATTTTT 57.672 32.000 0.00 0.00 0.00 1.94
5829 8079 8.439993 TGATAGCACGCCATTAGTAATTTTTA 57.560 30.769 0.00 0.00 0.00 1.52
5830 8080 8.339714 TGATAGCACGCCATTAGTAATTTTTAC 58.660 33.333 0.00 0.00 0.00 2.01
5831 8081 6.753107 AGCACGCCATTAGTAATTTTTACT 57.247 33.333 5.36 5.36 0.00 2.24
5832 8082 7.852971 AGCACGCCATTAGTAATTTTTACTA 57.147 32.000 3.59 3.59 0.00 1.82
5833 8083 8.271312 AGCACGCCATTAGTAATTTTTACTAA 57.729 30.769 17.53 17.53 42.18 2.24
5834 8084 8.899771 AGCACGCCATTAGTAATTTTTACTAAT 58.100 29.630 19.63 19.63 46.06 1.73
5842 8092 5.886992 AGTAATTTTTACTAATGGCGCACC 58.113 37.500 10.83 0.00 0.00 5.01
5858 8108 2.045438 CCACCTGGTGCGCCATTA 60.045 61.111 21.54 0.00 45.05 1.90
5859 8109 2.114670 CCACCTGGTGCGCCATTAG 61.115 63.158 21.54 14.16 45.05 1.73
5860 8110 1.377202 CACCTGGTGCGCCATTAGT 60.377 57.895 21.54 14.84 45.05 2.24
5861 8111 0.107897 CACCTGGTGCGCCATTAGTA 60.108 55.000 21.54 0.00 45.05 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.744795 AGATGAAGAAGACTACGGCATT 57.255 40.909 0.00 0.00 0.00 3.56
52 53 2.774864 CGTAAGTAAAAAGGCCGTCG 57.225 50.000 0.00 0.00 0.00 5.12
66 67 9.160496 ACCTCGAAGTATTCCTATATACGTAAG 57.840 37.037 0.00 0.00 43.81 2.34
282 288 1.143813 ATTGGATCCAAGATCCGGCT 58.856 50.000 29.98 10.05 41.03 5.52
447 622 3.069872 TGCACTGAAAATGAAGCCAACAT 59.930 39.130 0.00 0.00 0.00 2.71
498 674 4.244066 TGCATGCACATTAACCATGTTTC 58.756 39.130 18.46 0.00 44.40 2.78
510 686 0.448990 GTCACGTCATGCATGCACAT 59.551 50.000 25.37 4.95 0.00 3.21
640 823 7.095774 CGTTTTTATATTATGTGACGGAGGGAG 60.096 40.741 0.00 0.00 0.00 4.30
642 825 6.480981 ACGTTTTTATATTATGTGACGGAGGG 59.519 38.462 0.00 0.00 33.95 4.30
644 827 9.763465 AAAACGTTTTTATATTATGTGACGGAG 57.237 29.630 20.26 0.00 33.95 4.63
657 840 9.488124 GTGTGTAGTGTCAAAAACGTTTTTATA 57.512 29.630 32.12 22.38 38.23 0.98
658 841 7.216693 CGTGTGTAGTGTCAAAAACGTTTTTAT 59.783 33.333 32.12 19.76 38.23 1.40
659 842 6.519078 CGTGTGTAGTGTCAAAAACGTTTTTA 59.481 34.615 32.12 18.43 38.23 1.52
660 843 5.340138 CGTGTGTAGTGTCAAAAACGTTTTT 59.660 36.000 28.62 28.62 40.75 1.94
661 844 4.847217 CGTGTGTAGTGTCAAAAACGTTTT 59.153 37.500 20.26 20.26 0.00 2.43
662 845 4.083908 ACGTGTGTAGTGTCAAAAACGTTT 60.084 37.500 7.96 7.96 0.00 3.60
663 846 3.432933 ACGTGTGTAGTGTCAAAAACGTT 59.567 39.130 0.00 0.00 0.00 3.99
664 847 2.995258 ACGTGTGTAGTGTCAAAAACGT 59.005 40.909 0.00 0.00 0.00 3.99
665 848 3.644805 ACGTGTGTAGTGTCAAAAACG 57.355 42.857 0.00 0.00 0.00 3.60
666 849 4.901881 GCATACGTGTGTAGTGTCAAAAAC 59.098 41.667 14.10 0.00 33.17 2.43
667 850 4.812091 AGCATACGTGTGTAGTGTCAAAAA 59.188 37.500 14.10 0.00 33.17 1.94
668 851 4.210328 CAGCATACGTGTGTAGTGTCAAAA 59.790 41.667 14.10 0.00 33.17 2.44
669 852 3.738791 CAGCATACGTGTGTAGTGTCAAA 59.261 43.478 14.10 0.00 33.17 2.69
670 853 3.313690 CAGCATACGTGTGTAGTGTCAA 58.686 45.455 14.10 0.00 33.17 3.18
671 854 2.924880 GCAGCATACGTGTGTAGTGTCA 60.925 50.000 14.10 0.00 33.17 3.58
672 855 1.654105 GCAGCATACGTGTGTAGTGTC 59.346 52.381 14.10 0.00 33.17 3.67
673 856 1.000394 TGCAGCATACGTGTGTAGTGT 60.000 47.619 14.10 0.00 33.17 3.55
674 857 1.708822 TGCAGCATACGTGTGTAGTG 58.291 50.000 14.10 9.98 33.17 2.74
675 858 2.288825 ACTTGCAGCATACGTGTGTAGT 60.289 45.455 14.10 7.13 33.17 2.73
676 859 2.092681 CACTTGCAGCATACGTGTGTAG 59.907 50.000 14.10 7.82 33.17 2.74
677 860 2.065512 CACTTGCAGCATACGTGTGTA 58.934 47.619 14.10 0.00 34.45 2.90
678 861 0.867746 CACTTGCAGCATACGTGTGT 59.132 50.000 14.10 0.00 0.00 3.72
679 862 0.453282 GCACTTGCAGCATACGTGTG 60.453 55.000 8.09 8.09 41.59 3.82
680 863 1.868997 GCACTTGCAGCATACGTGT 59.131 52.632 16.68 0.00 41.59 4.49
681 864 4.751539 GCACTTGCAGCATACGTG 57.248 55.556 13.04 13.04 41.59 4.49
691 874 6.357198 CAAAATTCACTAAACATGCACTTGC 58.643 36.000 0.00 0.00 42.50 4.01
700 885 8.791675 TGAGTCATATGCAAAATTCACTAAACA 58.208 29.630 0.00 0.00 0.00 2.83
718 903 0.817654 CTGTCTGCCCGTGAGTCATA 59.182 55.000 0.00 0.00 0.00 2.15
787 975 1.077068 ACAGGAGAGGAGAGCGGAG 60.077 63.158 0.00 0.00 0.00 4.63
788 976 1.077357 GACAGGAGAGGAGAGCGGA 60.077 63.158 0.00 0.00 0.00 5.54
789 977 2.124693 GGACAGGAGAGGAGAGCGG 61.125 68.421 0.00 0.00 0.00 5.52
790 978 1.077068 AGGACAGGAGAGGAGAGCG 60.077 63.158 0.00 0.00 0.00 5.03
791 979 0.258774 AGAGGACAGGAGAGGAGAGC 59.741 60.000 0.00 0.00 0.00 4.09
792 980 1.133792 GGAGAGGACAGGAGAGGAGAG 60.134 61.905 0.00 0.00 0.00 3.20
793 981 0.923358 GGAGAGGACAGGAGAGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
794 982 0.926293 AGGAGAGGACAGGAGAGGAG 59.074 60.000 0.00 0.00 0.00 3.69
795 983 0.923358 GAGGAGAGGACAGGAGAGGA 59.077 60.000 0.00 0.00 0.00 3.71
804 997 5.714806 CAGATTTATAGGGAGAGGAGAGGAC 59.285 48.000 0.00 0.00 0.00 3.85
837 1030 3.270169 TGGGGGATATGAGCAATGCATAT 59.730 43.478 8.35 2.69 40.60 1.78
960 1191 0.526662 GCTGACTAGCGTAGTGTGGT 59.473 55.000 2.96 0.00 40.67 4.16
1042 1277 0.595095 GTGAAGAAGGCAAGCAGTGG 59.405 55.000 0.00 0.00 0.00 4.00
1043 1278 0.595095 GGTGAAGAAGGCAAGCAGTG 59.405 55.000 0.00 0.00 0.00 3.66
1044 1279 0.475906 AGGTGAAGAAGGCAAGCAGT 59.524 50.000 0.00 0.00 0.00 4.40
1045 1280 1.538950 GAAGGTGAAGAAGGCAAGCAG 59.461 52.381 0.00 0.00 0.00 4.24
1046 1281 1.143684 AGAAGGTGAAGAAGGCAAGCA 59.856 47.619 0.00 0.00 0.00 3.91
1047 1282 1.809547 GAGAAGGTGAAGAAGGCAAGC 59.190 52.381 0.00 0.00 0.00 4.01
1048 1283 2.039613 AGGAGAAGGTGAAGAAGGCAAG 59.960 50.000 0.00 0.00 0.00 4.01
1049 1284 2.039084 GAGGAGAAGGTGAAGAAGGCAA 59.961 50.000 0.00 0.00 0.00 4.52
1050 1285 1.625818 GAGGAGAAGGTGAAGAAGGCA 59.374 52.381 0.00 0.00 0.00 4.75
1051 1286 1.404851 CGAGGAGAAGGTGAAGAAGGC 60.405 57.143 0.00 0.00 0.00 4.35
1052 1287 1.205893 CCGAGGAGAAGGTGAAGAAGG 59.794 57.143 0.00 0.00 0.00 3.46
1053 1288 1.896465 ACCGAGGAGAAGGTGAAGAAG 59.104 52.381 0.00 0.00 39.66 2.85
1054 1289 1.893801 GACCGAGGAGAAGGTGAAGAA 59.106 52.381 0.00 0.00 41.51 2.52
1055 1290 1.546961 GACCGAGGAGAAGGTGAAGA 58.453 55.000 0.00 0.00 41.51 2.87
1056 1291 0.171455 CGACCGAGGAGAAGGTGAAG 59.829 60.000 0.00 0.00 41.51 3.02
1057 1292 0.251033 TCGACCGAGGAGAAGGTGAA 60.251 55.000 0.00 0.00 41.51 3.18
1058 1293 0.677098 CTCGACCGAGGAGAAGGTGA 60.677 60.000 11.28 0.00 41.51 4.02
1059 1294 1.803943 CTCGACCGAGGAGAAGGTG 59.196 63.158 11.28 0.00 41.51 4.00
1060 1295 2.047443 GCTCGACCGAGGAGAAGGT 61.047 63.158 19.35 0.00 44.64 3.50
1061 1296 2.776913 GGCTCGACCGAGGAGAAGG 61.777 68.421 19.35 0.00 42.19 3.46
1067 1302 4.803426 GCAGTGGCTCGACCGAGG 62.803 72.222 19.35 5.16 43.94 4.63
1229 1473 1.408702 GCATTCACCGGCCATAACAAT 59.591 47.619 0.00 0.00 0.00 2.71
1287 2230 3.959535 GGTTTGAAATCAATCCCTGCA 57.040 42.857 10.79 0.00 38.93 4.41
1431 2440 4.765813 TCTCAATGCAGGATCTCATGAA 57.234 40.909 0.00 0.00 0.00 2.57
1442 2451 2.771435 TGCACGGATCTCAATGCAG 58.229 52.632 8.86 0.00 42.92 4.41
1513 2522 4.921547 TCAGTCGACCGAGATTTAATCAG 58.078 43.478 13.01 1.07 0.00 2.90
1589 2598 5.911178 TGAGGGTATAGAAAATGAGGTGGAT 59.089 40.000 0.00 0.00 0.00 3.41
1946 3100 0.460311 AATAAGCCTCGTCCACTCGG 59.540 55.000 0.00 0.00 0.00 4.63
2027 3184 0.108186 GCACATGACTCCACGATGGA 60.108 55.000 0.00 6.57 45.98 3.41
2038 3195 3.189618 TGGATGAGATCTGCACATGAC 57.810 47.619 0.00 0.00 0.00 3.06
2084 3241 6.095160 GCTTCTCTCATCAACCTCAATGAAAT 59.905 38.462 0.00 0.00 31.81 2.17
2271 3443 6.679843 ACACTCCACAAGAAAACGTTAAAAA 58.320 32.000 0.00 0.00 0.00 1.94
2366 3575 0.443869 CCGAAGAACATTGTCTGCCG 59.556 55.000 0.00 0.00 0.00 5.69
2374 3583 4.647424 TTGCAAACTTCCGAAGAACATT 57.353 36.364 15.23 2.04 0.00 2.71
2391 3600 6.817641 GGTTGAAATCACCATTATCATTTGCA 59.182 34.615 0.00 0.00 0.00 4.08
2503 3712 5.502153 AGATGCTTGCTTGAGAATTCATC 57.498 39.130 8.44 3.31 32.27 2.92
2668 3877 3.119245 GCACATGCCAGATTCTCAATTGT 60.119 43.478 5.13 0.00 34.31 2.71
3133 4363 5.947228 TTTTGATCGCTTCATTGAAGAGT 57.053 34.783 26.72 15.13 41.71 3.24
3565 5681 5.928976 TGATATCATGTAGTTGGGAAGTGG 58.071 41.667 0.00 0.00 0.00 4.00
4358 6546 3.200825 AGGAGATGACCCGATGAATGTTT 59.799 43.478 0.00 0.00 0.00 2.83
4442 6630 9.913310 TCCTAATGTGTTATTTGATTACATCCA 57.087 29.630 0.00 0.00 31.30 3.41
4950 7154 5.936686 ACACATATGCTAATGATGCAGAC 57.063 39.130 1.58 0.00 44.04 3.51
5058 7262 7.543172 CCAATTCCCTTAAATTCATATGCATCG 59.457 37.037 0.19 0.00 0.00 3.84
5142 7347 1.398041 GCACATCGTCATAAAGCTGCA 59.602 47.619 1.02 0.00 0.00 4.41
5164 7369 2.091541 ACCTATTGCACCCGAACAATG 58.908 47.619 0.00 0.00 37.11 2.82
5172 7377 0.618458 TGGAGTCACCTATTGCACCC 59.382 55.000 0.00 0.00 39.86 4.61
5173 7378 2.489938 TTGGAGTCACCTATTGCACC 57.510 50.000 0.00 0.00 39.86 5.01
5225 7464 6.607019 TGTAGTAGTTTTGACCCCATTTTCT 58.393 36.000 0.00 0.00 0.00 2.52
5227 7466 6.266786 CCTTGTAGTAGTTTTGACCCCATTTT 59.733 38.462 0.00 0.00 0.00 1.82
5235 7474 3.501062 GGTGCCCTTGTAGTAGTTTTGAC 59.499 47.826 0.00 0.00 0.00 3.18
5242 7481 3.197766 TGAGATTGGTGCCCTTGTAGTAG 59.802 47.826 0.00 0.00 0.00 2.57
5275 7524 6.461509 GGTCTTCCACAAATGAGTGTTTTGAT 60.462 38.462 3.39 0.00 37.48 2.57
5276 7525 5.163561 GGTCTTCCACAAATGAGTGTTTTGA 60.164 40.000 3.39 0.00 37.48 2.69
5324 7573 2.167662 CCTGCCGTAAAAGTGGGAAAT 58.832 47.619 0.00 0.00 0.00 2.17
5325 7574 1.611519 CCTGCCGTAAAAGTGGGAAA 58.388 50.000 0.00 0.00 0.00 3.13
5328 7577 1.677633 CCCCTGCCGTAAAAGTGGG 60.678 63.158 0.00 0.00 34.68 4.61
5340 7589 1.900498 GTCTATGCATGGCCCCTGC 60.900 63.158 18.07 18.07 40.10 4.85
5361 7610 5.294552 GCGTCAGCTCTAGGTTTTATTTCAT 59.705 40.000 0.00 0.00 41.01 2.57
5405 7654 3.666902 GCGCGACTGTTAATGTGTTCAAT 60.667 43.478 12.10 0.00 0.00 2.57
5478 7727 1.500396 GGCGGCGAAAGAAAATCGT 59.500 52.632 12.98 0.00 42.15 3.73
5479 7728 1.226295 GGGCGGCGAAAGAAAATCG 60.226 57.895 12.98 0.00 42.99 3.34
5544 7794 1.613437 CTGGGCAATCCGTTTCTTTGT 59.387 47.619 0.00 0.00 38.76 2.83
5553 7803 4.738998 TGGTGGCTGGGCAATCCG 62.739 66.667 0.00 0.00 38.76 4.18
5574 7824 0.972883 GAGAGGAATCGAGGGATGGG 59.027 60.000 0.00 0.00 31.83 4.00
5624 7874 3.374402 CGGCTGTGAGGAGGTCGT 61.374 66.667 0.00 0.00 0.00 4.34
5671 7921 3.650950 GAAGGGGTGGCAGCCTCA 61.651 66.667 32.43 0.00 35.71 3.86
5744 7994 2.490509 GTGCGCCATTAGTAGGGTTTTT 59.509 45.455 4.18 0.00 0.00 1.94
5745 7995 2.089201 GTGCGCCATTAGTAGGGTTTT 58.911 47.619 4.18 0.00 0.00 2.43
5746 7996 1.680860 GGTGCGCCATTAGTAGGGTTT 60.681 52.381 12.58 0.00 34.09 3.27
5747 7997 0.107361 GGTGCGCCATTAGTAGGGTT 60.107 55.000 12.58 0.00 34.09 4.11
5748 7998 0.981277 AGGTGCGCCATTAGTAGGGT 60.981 55.000 20.59 0.00 37.19 4.34
5749 7999 1.045407 TAGGTGCGCCATTAGTAGGG 58.955 55.000 20.59 0.00 37.19 3.53
5750 8000 2.902705 TTAGGTGCGCCATTAGTAGG 57.097 50.000 20.59 0.00 37.19 3.18
5751 8001 4.024048 CCATTTTAGGTGCGCCATTAGTAG 60.024 45.833 20.59 2.34 37.19 2.57
5752 8002 3.880490 CCATTTTAGGTGCGCCATTAGTA 59.120 43.478 20.59 0.00 37.19 1.82
5753 8003 2.687935 CCATTTTAGGTGCGCCATTAGT 59.312 45.455 20.59 0.00 37.19 2.24
5754 8004 2.543653 GCCATTTTAGGTGCGCCATTAG 60.544 50.000 20.59 2.79 37.19 1.73
5755 8005 1.407258 GCCATTTTAGGTGCGCCATTA 59.593 47.619 20.59 0.00 37.19 1.90
5756 8006 0.175531 GCCATTTTAGGTGCGCCATT 59.824 50.000 20.59 0.20 37.19 3.16
5757 8007 1.675720 GGCCATTTTAGGTGCGCCAT 61.676 55.000 20.59 6.28 37.19 4.40
5758 8008 2.347322 GGCCATTTTAGGTGCGCCA 61.347 57.895 20.59 1.18 37.19 5.69
5759 8009 1.675720 ATGGCCATTTTAGGTGCGCC 61.676 55.000 14.09 8.71 35.09 6.53
5760 8010 0.175531 AATGGCCATTTTAGGTGCGC 59.824 50.000 25.73 0.00 0.00 6.09
5761 8011 3.791973 TTAATGGCCATTTTAGGTGCG 57.208 42.857 34.85 0.00 32.50 5.34
5762 8012 4.379652 CCATTAATGGCCATTTTAGGTGC 58.620 43.478 34.85 0.00 41.75 5.01
5776 8026 1.677576 ACCACAGATGCGCCATTAATG 59.322 47.619 4.18 8.58 0.00 1.90
5777 8027 1.677576 CACCACAGATGCGCCATTAAT 59.322 47.619 4.18 0.00 0.00 1.40
5778 8028 1.093972 CACCACAGATGCGCCATTAA 58.906 50.000 4.18 0.00 0.00 1.40
5779 8029 1.375853 GCACCACAGATGCGCCATTA 61.376 55.000 4.18 0.00 32.45 1.90
5780 8030 2.703798 GCACCACAGATGCGCCATT 61.704 57.895 4.18 0.00 32.45 3.16
5781 8031 3.136123 GCACCACAGATGCGCCAT 61.136 61.111 4.18 0.00 32.45 4.40
5782 8032 3.923782 ATGCACCACAGATGCGCCA 62.924 57.895 4.18 0.00 46.49 5.69
5783 8033 3.117175 GATGCACCACAGATGCGCC 62.117 63.158 4.18 0.00 46.49 6.53
5784 8034 1.721664 ATGATGCACCACAGATGCGC 61.722 55.000 0.00 0.00 46.49 6.09
5785 8035 0.736636 AATGATGCACCACAGATGCG 59.263 50.000 0.00 0.00 46.49 4.73
5786 8036 1.746787 TCAATGATGCACCACAGATGC 59.253 47.619 0.00 0.00 43.68 3.91
5787 8037 4.320275 GCTATCAATGATGCACCACAGATG 60.320 45.833 5.91 4.30 0.00 2.90
5788 8038 3.819337 GCTATCAATGATGCACCACAGAT 59.181 43.478 5.91 2.87 0.00 2.90
5789 8039 3.208594 GCTATCAATGATGCACCACAGA 58.791 45.455 5.91 0.00 0.00 3.41
5790 8040 2.946990 TGCTATCAATGATGCACCACAG 59.053 45.455 5.91 0.00 0.00 3.66
5791 8041 2.684374 GTGCTATCAATGATGCACCACA 59.316 45.455 25.84 7.94 46.84 4.17
5792 8042 3.344904 GTGCTATCAATGATGCACCAC 57.655 47.619 25.84 15.45 46.84 4.16
5796 8046 0.946528 GGCGTGCTATCAATGATGCA 59.053 50.000 5.91 10.58 0.00 3.96
5797 8047 0.946528 TGGCGTGCTATCAATGATGC 59.053 50.000 5.91 8.16 0.00 3.91
5798 8048 3.909776 AATGGCGTGCTATCAATGATG 57.090 42.857 5.91 0.00 0.00 3.07
5799 8049 4.645535 ACTAATGGCGTGCTATCAATGAT 58.354 39.130 0.00 0.00 0.00 2.45
5800 8050 4.071961 ACTAATGGCGTGCTATCAATGA 57.928 40.909 0.00 0.00 0.00 2.57
5801 8051 5.922739 TTACTAATGGCGTGCTATCAATG 57.077 39.130 0.00 0.00 0.00 2.82
5802 8052 7.510549 AAATTACTAATGGCGTGCTATCAAT 57.489 32.000 0.00 0.00 0.00 2.57
5803 8053 6.935741 AAATTACTAATGGCGTGCTATCAA 57.064 33.333 0.00 0.00 0.00 2.57
5804 8054 6.935741 AAAATTACTAATGGCGTGCTATCA 57.064 33.333 0.00 0.00 0.00 2.15
5805 8055 8.557029 AGTAAAAATTACTAATGGCGTGCTATC 58.443 33.333 1.06 0.00 0.00 2.08
5806 8056 8.446599 AGTAAAAATTACTAATGGCGTGCTAT 57.553 30.769 1.06 0.00 0.00 2.97
5807 8057 7.852971 AGTAAAAATTACTAATGGCGTGCTA 57.147 32.000 1.06 0.00 0.00 3.49
5808 8058 6.753107 AGTAAAAATTACTAATGGCGTGCT 57.247 33.333 1.06 0.00 0.00 4.40
5816 8066 8.132995 GGTGCGCCATTAGTAAAAATTACTAAT 58.867 33.333 21.36 21.36 46.06 1.73
5817 8067 7.120873 TGGTGCGCCATTAGTAAAAATTACTAA 59.879 33.333 16.89 19.41 42.18 2.24
5818 8068 6.598457 TGGTGCGCCATTAGTAAAAATTACTA 59.402 34.615 16.89 6.00 40.46 1.82
5819 8069 5.416326 TGGTGCGCCATTAGTAAAAATTACT 59.584 36.000 16.89 7.80 40.46 2.24
5820 8070 5.642686 TGGTGCGCCATTAGTAAAAATTAC 58.357 37.500 16.89 0.00 40.46 1.89
5821 8071 5.899120 TGGTGCGCCATTAGTAAAAATTA 57.101 34.783 16.89 0.00 40.46 1.40
5822 8072 4.792521 TGGTGCGCCATTAGTAAAAATT 57.207 36.364 16.89 0.00 40.46 1.82


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

AutoCloner maintained by Alex Coulton.