Multiple sequence alignment - TraesCS6B01G059400

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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 TraesCS6B01G059400 chr6B 100.000 4050 0 0 1 4050 39200866 39196817 0.000000e+00 7480.0
1 TraesCS6B01G059400 chr6B 86.952 1027 97 21 1802 2794 39339895 39338872 0.000000e+00 1120.0
2 TraesCS6B01G059400 chr6B 83.024 377 59 4 1062 1434 336900624 336900249 1.800000e-88 337.0
3 TraesCS6B01G059400 chr6B 86.722 241 19 3 1512 1739 336892487 336892247 5.190000e-64 255.0
4 TraesCS6B01G059400 chr6B 88.667 150 15 1 1256 1405 39340501 39340354 8.940000e-42 182.0
5 TraesCS6B01G059400 chr6B 87.500 72 7 2 2944 3014 39197823 39197753 9.330000e-12 82.4
6 TraesCS6B01G059400 chr6B 87.500 72 7 2 3044 3114 39197923 39197853 9.330000e-12 82.4
7 TraesCS6B01G059400 chr6D 90.723 3126 136 42 921 3931 24232347 24229261 0.000000e+00 4024.0
8 TraesCS6B01G059400 chr6D 87.731 1027 91 12 1809 2803 24262717 24261694 0.000000e+00 1166.0
9 TraesCS6B01G059400 chr6D 94.186 344 17 2 1 342 24233140 24232798 4.640000e-144 521.0
10 TraesCS6B01G059400 chr6D 90.313 351 34 0 536 886 24232800 24232450 1.030000e-125 460.0
11 TraesCS6B01G059400 chr6D 95.935 123 5 0 3928 4050 160204644 160204522 2.470000e-47 200.0
12 TraesCS6B01G059400 chr6D 93.182 44 1 2 3249 3290 24230815 24230858 3.380000e-06 63.9
13 TraesCS6B01G059400 chr6D 97.297 37 1 0 1464 1500 24263116 24263080 3.380000e-06 63.9
14 TraesCS6B01G059400 chr6D 100.000 32 0 0 883 914 15360990 15360959 4.370000e-05 60.2
15 TraesCS6B01G059400 chr6D 100.000 32 0 0 883 914 456275168 456275137 4.370000e-05 60.2
16 TraesCS6B01G059400 chr6D 90.909 44 2 2 3249 3290 24262128 24262171 1.570000e-04 58.4
17 TraesCS6B01G059400 chr6A 90.402 3032 178 35 921 3931 22697275 22694336 0.000000e+00 3882.0
18 TraesCS6B01G059400 chr6A 87.353 1020 95 11 1809 2797 22804472 22803456 0.000000e+00 1138.0
19 TraesCS6B01G059400 chr6A 88.501 887 82 10 1 886 22698246 22697379 0.000000e+00 1055.0
20 TraesCS6B01G059400 chr6A 82.800 250 25 6 1256 1487 22805364 22805115 1.480000e-49 207.0
21 TraesCS6B01G059400 chr6A 95.935 123 5 0 3928 4050 110073122 110073244 2.470000e-47 200.0
22 TraesCS6B01G059400 chr6A 79.661 236 28 12 1285 1501 583766455 583766221 7.010000e-33 152.0
23 TraesCS6B01G059400 chr6A 78.325 203 32 8 2801 2994 22803395 22803196 1.980000e-23 121.0
24 TraesCS6B01G059400 chr6A 84.722 72 9 2 3044 3114 22695307 22695237 2.020000e-08 71.3
25 TraesCS6B01G059400 chr6A 97.297 37 1 0 1464 1500 22804868 22804832 3.380000e-06 63.9
26 TraesCS6B01G059400 chr6A 90.909 44 2 2 3249 3290 22803883 22803926 1.570000e-04 58.4
27 TraesCS6B01G059400 chr6A 100.000 30 0 0 3770 3799 22689120 22689149 5.650000e-04 56.5
28 TraesCS6B01G059400 chr3B 88.205 585 66 3 1832 2415 607385481 607384899 0.000000e+00 695.0
29 TraesCS6B01G059400 chr3B 79.612 412 44 21 2619 3017 607384661 607384277 4.020000e-65 259.0
30 TraesCS6B01G059400 chr3B 84.653 202 26 2 3022 3223 607384371 607384175 3.190000e-46 196.0
31 TraesCS6B01G059400 chr3B 84.756 164 16 4 1258 1412 530702718 530702555 5.420000e-34 156.0
32 TraesCS6B01G059400 chr3B 94.872 39 2 0 2544 2582 607384712 607384674 1.220000e-05 62.1
33 TraesCS6B01G059400 chr3B 100.000 28 0 0 1760 1787 244388883 244388910 7.000000e-03 52.8
34 TraesCS6B01G059400 chr3A 87.692 585 70 2 1832 2415 601555426 601556009 0.000000e+00 680.0
35 TraesCS6B01G059400 chr3A 77.974 681 112 26 17 679 661641808 661642468 3.790000e-105 392.0
36 TraesCS6B01G059400 chr3A 78.641 412 48 19 2619 3017 601556247 601556631 1.880000e-58 237.0
37 TraesCS6B01G059400 chr3A 84.158 202 27 2 3022 3223 601556537 601556733 1.490000e-44 191.0
38 TraesCS6B01G059400 chr3A 94.872 39 2 0 2544 2582 601556196 601556234 1.220000e-05 62.1
39 TraesCS6B01G059400 chr3A 96.970 33 1 0 3767 3799 728885014 728884982 5.650000e-04 56.5
40 TraesCS6B01G059400 chr3A 96.970 33 1 0 3767 3799 728892939 728892907 5.650000e-04 56.5
41 TraesCS6B01G059400 chr3A 94.444 36 1 1 2689 2723 601556127 601556162 2.000000e-03 54.7
42 TraesCS6B01G059400 chr3A 100.000 28 0 0 3772 3799 744253654 744253627 7.000000e-03 52.8
43 TraesCS6B01G059400 chr5B 83.356 733 99 12 1802 2513 166168017 166167287 0.000000e+00 656.0
44 TraesCS6B01G059400 chr5B 83.220 733 100 12 1802 2513 165776682 165775952 0.000000e+00 651.0
45 TraesCS6B01G059400 chr5B 75.843 712 150 15 191 884 679769589 679770296 3.880000e-90 342.0
46 TraesCS6B01G059400 chr5B 96.774 124 4 0 3927 4050 280024418 280024295 1.480000e-49 207.0
47 TraesCS6B01G059400 chr5B 77.811 338 47 13 1243 1553 166308028 166307692 2.490000e-42 183.0
48 TraesCS6B01G059400 chr5B 78.369 282 29 13 1243 1498 205585237 205585512 1.950000e-33 154.0
49 TraesCS6B01G059400 chr5A 82.880 736 98 7 1802 2513 465111016 465111747 1.590000e-178 636.0
50 TraesCS6B01G059400 chr5A 97.500 40 1 0 1747 1786 580186965 580186926 7.260000e-08 69.4
51 TraesCS6B01G059400 chr7A 78.579 901 146 26 11 886 215931445 215930567 5.920000e-153 551.0
52 TraesCS6B01G059400 chr7A 92.683 41 3 0 1747 1787 366871645 366871685 4.370000e-05 60.2
53 TraesCS6B01G059400 chr7A 100.000 32 0 0 883 914 700097310 700097279 4.370000e-05 60.2
54 TraesCS6B01G059400 chr7D 77.227 887 166 24 17 884 12914090 12913221 1.690000e-133 486.0
55 TraesCS6B01G059400 chr7D 75.985 787 149 25 121 886 497044620 497043853 1.780000e-98 370.0
56 TraesCS6B01G059400 chr7D 100.000 36 0 0 1701 1736 109922145 109922180 2.610000e-07 67.6
57 TraesCS6B01G059400 chr7D 94.872 39 2 0 1701 1739 60105565 60105527 1.220000e-05 62.1
58 TraesCS6B01G059400 chr7D 92.683 41 3 0 1747 1787 227691736 227691776 4.370000e-05 60.2
59 TraesCS6B01G059400 chr4A 89.965 289 29 0 1080 1368 696667136 696667424 1.370000e-99 374.0
60 TraesCS6B01G059400 chr4A 89.965 289 29 0 1080 1368 696691186 696691474 1.370000e-99 374.0
61 TraesCS6B01G059400 chr4A 88.927 289 32 0 1080 1368 696647199 696647487 1.380000e-94 357.0
62 TraesCS6B01G059400 chr4A 87.983 233 14 3 1512 1731 696668129 696668360 3.100000e-66 263.0
63 TraesCS6B01G059400 chr4A 87.983 233 14 3 1512 1731 696692179 696692410 3.100000e-66 263.0
64 TraesCS6B01G059400 chr4A 86.975 238 17 8 1512 1736 696648191 696648427 5.190000e-64 255.0
65 TraesCS6B01G059400 chr4A 81.786 280 44 5 610 886 622292522 622292247 1.130000e-55 228.0
66 TraesCS6B01G059400 chr7B 74.699 830 172 22 76 886 735911205 735910395 6.490000e-88 335.0
67 TraesCS6B01G059400 chr7B 75.698 716 143 21 191 886 572029810 572030514 3.020000e-86 329.0
68 TraesCS6B01G059400 chr7B 74.334 713 150 21 190 880 151427699 151428400 5.160000e-69 272.0
69 TraesCS6B01G059400 chr7B 95.968 124 5 0 3927 4050 697307789 697307912 6.860000e-48 202.0
70 TraesCS6B01G059400 chr3D 75.770 714 146 19 191 884 436679227 436678521 6.490000e-88 335.0
71 TraesCS6B01G059400 chr3D 78.832 411 51 19 2619 3017 459467950 459467564 1.120000e-60 244.0
72 TraesCS6B01G059400 chr3D 85.279 197 24 2 3027 3223 459467653 459467462 8.880000e-47 198.0
73 TraesCS6B01G059400 chr3D 94.872 39 2 0 2544 2582 459468001 459467963 1.220000e-05 62.1
74 TraesCS6B01G059400 chr3D 100.000 32 0 0 883 914 20906803 20906834 4.370000e-05 60.2
75 TraesCS6B01G059400 chr3D 100.000 32 0 0 883 914 100984475 100984506 4.370000e-05 60.2
76 TraesCS6B01G059400 chr3D 94.444 36 1 1 2689 2723 459468070 459468035 2.000000e-03 54.7
77 TraesCS6B01G059400 chr2A 77.737 539 103 14 10 543 40085888 40086414 8.450000e-82 315.0
78 TraesCS6B01G059400 chr2A 77.365 539 105 11 10 543 40091679 40092205 1.830000e-78 303.0
79 TraesCS6B01G059400 chr2A 73.543 858 180 37 54 886 523446572 523447407 2.380000e-72 283.0
80 TraesCS6B01G059400 chr2A 80.685 321 32 11 1258 1553 425814005 425813690 5.270000e-54 222.0
81 TraesCS6B01G059400 chr2A 77.293 229 33 11 1282 1491 780149916 780150144 2.560000e-22 117.0
82 TraesCS6B01G059400 chr1B 75.498 653 137 16 249 884 94478217 94478863 8.510000e-77 298.0
83 TraesCS6B01G059400 chr1B 93.684 95 5 1 1646 1739 179580982 179580888 1.520000e-29 141.0
84 TraesCS6B01G059400 chrUn 95.935 123 5 0 3928 4050 83943649 83943771 2.470000e-47 200.0
85 TraesCS6B01G059400 chrUn 95.935 123 5 0 3928 4050 332284875 332284997 2.470000e-47 200.0
86 TraesCS6B01G059400 chrUn 97.368 38 1 0 1747 1784 31029652 31029689 9.400000e-07 65.8
87 TraesCS6B01G059400 chr4B 95.935 123 5 0 3928 4050 185228044 185228166 2.470000e-47 200.0
88 TraesCS6B01G059400 chr4B 95.935 123 5 0 3928 4050 438514849 438514971 2.470000e-47 200.0
89 TraesCS6B01G059400 chr4B 92.308 39 3 0 1749 1787 4187405 4187443 5.650000e-04 56.5
90 TraesCS6B01G059400 chr1A 95.935 123 5 0 3928 4050 222361988 222361866 2.470000e-47 200.0
91 TraesCS6B01G059400 chr1A 93.182 44 3 0 1744 1787 42645388 42645431 9.400000e-07 65.8
92 TraesCS6B01G059400 chr1A 94.444 36 2 0 2980 3015 487093015 487092980 5.650000e-04 56.5
93 TraesCS6B01G059400 chr2B 80.072 276 31 10 1247 1500 693801743 693802016 2.490000e-42 183.0
94 TraesCS6B01G059400 chr4D 90.411 73 6 1 2986 3058 381837081 381837152 1.200000e-15 95.3
95 TraesCS6B01G059400 chr4D 100.000 28 0 0 3087 3114 381837082 381837109 7.000000e-03 52.8
96 TraesCS6B01G059400 chr2D 100.000 32 0 0 883 914 11506466 11506497 4.370000e-05 60.2
97 TraesCS6B01G059400 chr2D 100.000 32 0 0 883 914 391803098 391803067 4.370000e-05 60.2
98 TraesCS6B01G059400 chr1D 100.000 32 0 0 883 914 418302630 418302661 4.370000e-05 60.2
99 TraesCS6B01G059400 chr1D 100.000 32 0 0 883 914 453427831 453427862 4.370000e-05 60.2
100 TraesCS6B01G059400 chr1D 94.444 36 2 0 2980 3015 387427560 387427525 5.650000e-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 TraesCS6B01G059400 chr6B 39196817 39200866 4049 True 2548.266667 7480 91.666667 1 4050 3 chr6B.!!$R3 4049
1 TraesCS6B01G059400 chr6B 39338872 39340501 1629 True 651.000000 1120 87.809500 1256 2794 2 chr6B.!!$R4 1538
2 TraesCS6B01G059400 chr6D 24229261 24233140 3879 True 1668.333333 4024 91.740667 1 3931 3 chr6D.!!$R4 3930
3 TraesCS6B01G059400 chr6D 24261694 24263116 1422 True 614.950000 1166 92.514000 1464 2803 2 chr6D.!!$R5 1339
4 TraesCS6B01G059400 chr6A 22694336 22698246 3910 True 1669.433333 3882 87.875000 1 3931 3 chr6A.!!$R2 3930
5 TraesCS6B01G059400 chr6A 22803196 22805364 2168 True 382.475000 1138 86.443750 1256 2994 4 chr6A.!!$R3 1738
6 TraesCS6B01G059400 chr3B 607384175 607385481 1306 True 303.025000 695 86.835500 1832 3223 4 chr3B.!!$R2 1391
7 TraesCS6B01G059400 chr3A 661641808 661642468 660 False 392.000000 392 77.974000 17 679 1 chr3A.!!$F1 662
8 TraesCS6B01G059400 chr3A 601555426 601556733 1307 False 244.960000 680 87.961400 1832 3223 5 chr3A.!!$F2 1391
9 TraesCS6B01G059400 chr5B 166167287 166168017 730 True 656.000000 656 83.356000 1802 2513 1 chr5B.!!$R2 711
10 TraesCS6B01G059400 chr5B 165775952 165776682 730 True 651.000000 651 83.220000 1802 2513 1 chr5B.!!$R1 711
11 TraesCS6B01G059400 chr5B 679769589 679770296 707 False 342.000000 342 75.843000 191 884 1 chr5B.!!$F2 693
12 TraesCS6B01G059400 chr5A 465111016 465111747 731 False 636.000000 636 82.880000 1802 2513 1 chr5A.!!$F1 711
13 TraesCS6B01G059400 chr7A 215930567 215931445 878 True 551.000000 551 78.579000 11 886 1 chr7A.!!$R1 875
14 TraesCS6B01G059400 chr7D 12913221 12914090 869 True 486.000000 486 77.227000 17 884 1 chr7D.!!$R1 867
15 TraesCS6B01G059400 chr7D 497043853 497044620 767 True 370.000000 370 75.985000 121 886 1 chr7D.!!$R3 765
16 TraesCS6B01G059400 chr4A 696667136 696668360 1224 False 318.500000 374 88.974000 1080 1731 2 chr4A.!!$F2 651
17 TraesCS6B01G059400 chr4A 696691186 696692410 1224 False 318.500000 374 88.974000 1080 1731 2 chr4A.!!$F3 651
18 TraesCS6B01G059400 chr4A 696647199 696648427 1228 False 306.000000 357 87.951000 1080 1736 2 chr4A.!!$F1 656
19 TraesCS6B01G059400 chr7B 735910395 735911205 810 True 335.000000 335 74.699000 76 886 1 chr7B.!!$R1 810
20 TraesCS6B01G059400 chr7B 572029810 572030514 704 False 329.000000 329 75.698000 191 886 1 chr7B.!!$F2 695
21 TraesCS6B01G059400 chr7B 151427699 151428400 701 False 272.000000 272 74.334000 190 880 1 chr7B.!!$F1 690
22 TraesCS6B01G059400 chr3D 436678521 436679227 706 True 335.000000 335 75.770000 191 884 1 chr3D.!!$R1 693
23 TraesCS6B01G059400 chr2A 40085888 40086414 526 False 315.000000 315 77.737000 10 543 1 chr2A.!!$F1 533
24 TraesCS6B01G059400 chr2A 40091679 40092205 526 False 303.000000 303 77.365000 10 543 1 chr2A.!!$F2 533
25 TraesCS6B01G059400 chr2A 523446572 523447407 835 False 283.000000 283 73.543000 54 886 1 chr2A.!!$F3 832
26 TraesCS6B01G059400 chr1B 94478217 94478863 646 False 298.000000 298 75.498000 249 884 1 chr1B.!!$F1 635

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
978 1095 0.935837 ACCCATCCCCATTTCCCCAT 60.936 55.0 0.00 0.00 0.00 4.00 F
1633 2779 0.179111 TACAGCAGTCTGGCGCATAC 60.179 55.0 10.83 3.48 44.54 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 3318 0.171455 AGCGGTGATCAACTCGAGAC 59.829 55.0 21.68 5.18 0.0 3.36 R
3393 4759 0.671781 CCGTCTCAGGAAGCAAGGTG 60.672 60.0 0.00 0.00 0.0 4.00 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
72 73 2.941025 CCACCACCACCATCCCCT 60.941 66.667 0.00 0.00 0.00 4.79
109 113 2.591753 CGATGGGCATGGACCTGT 59.408 61.111 0.00 0.00 0.00 4.00
188 194 2.809601 GCGCTCTTTTCGGCTCGA 60.810 61.111 0.00 0.00 0.00 4.04
216 223 3.760035 GGCTCGTTGGCTCCTCGA 61.760 66.667 6.61 6.61 38.32 4.04
545 572 4.827087 AGTCGCAGCTCCGGCATG 62.827 66.667 3.65 0.00 41.70 4.06
578 606 2.480419 CACCTCTTCGACAATGTTCCAC 59.520 50.000 0.00 0.00 0.00 4.02
580 608 2.549992 CCTCTTCGACAATGTTCCACCA 60.550 50.000 0.00 0.00 0.00 4.17
581 609 3.138304 CTCTTCGACAATGTTCCACCAA 58.862 45.455 0.00 0.00 0.00 3.67
859 906 5.072055 TGATTGGATTGCTTCTTCAGTTGA 58.928 37.500 0.00 0.00 0.00 3.18
886 933 4.742438 TTAGCCGTGTTCTTCATTGTTC 57.258 40.909 0.00 0.00 0.00 3.18
887 934 2.571212 AGCCGTGTTCTTCATTGTTCA 58.429 42.857 0.00 0.00 0.00 3.18
888 935 2.290641 AGCCGTGTTCTTCATTGTTCAC 59.709 45.455 0.00 0.00 0.00 3.18
893 983 1.068541 GTTCTTCATTGTTCACGCCCC 60.069 52.381 0.00 0.00 0.00 5.80
916 1006 1.659211 GCGTCCGTGTCATGTGTTTTC 60.659 52.381 0.00 0.00 0.00 2.29
917 1007 1.595328 CGTCCGTGTCATGTGTTTTCA 59.405 47.619 0.00 0.00 0.00 2.69
918 1008 2.223144 CGTCCGTGTCATGTGTTTTCAT 59.777 45.455 0.00 0.00 0.00 2.57
919 1009 3.554524 GTCCGTGTCATGTGTTTTCATG 58.445 45.455 0.00 0.00 44.36 3.07
920 1010 3.003275 GTCCGTGTCATGTGTTTTCATGT 59.997 43.478 6.57 0.00 43.70 3.21
921 1011 4.212425 GTCCGTGTCATGTGTTTTCATGTA 59.788 41.667 6.57 0.00 43.70 2.29
961 1078 7.009357 TGCGTATTGGCGAAAAATAAATAAACC 59.991 33.333 0.00 0.00 35.06 3.27
970 1087 7.505258 CGAAAAATAAATAAACCCATCCCCAT 58.495 34.615 0.00 0.00 0.00 4.00
978 1095 0.935837 ACCCATCCCCATTTCCCCAT 60.936 55.000 0.00 0.00 0.00 4.00
1223 1340 0.752009 CCCTCCATCTTCCTCGACGA 60.752 60.000 0.00 0.00 0.00 4.20
1278 1395 1.442184 CTCGACAACGACCCGACTG 60.442 63.158 0.00 0.00 43.81 3.51
1291 1408 2.888863 GACTGTGCCTCCTCTCCG 59.111 66.667 0.00 0.00 0.00 4.63
1510 2322 1.895131 AGTGGGCATTTTACTTGGCAG 59.105 47.619 0.00 0.00 41.14 4.85
1564 2376 7.278868 GCTCTGTTGTTTGTAGATAGTGCTTAT 59.721 37.037 0.00 0.00 0.00 1.73
1569 2381 8.391106 GTTGTTTGTAGATAGTGCTTATTGGAG 58.609 37.037 0.00 0.00 0.00 3.86
1575 2387 8.946085 TGTAGATAGTGCTTATTGGAGTTTTTG 58.054 33.333 0.00 0.00 0.00 2.44
1633 2779 0.179111 TACAGCAGTCTGGCGCATAC 60.179 55.000 10.83 3.48 44.54 2.39
1698 2857 7.387643 AGTGTTCCCTAAATGAAAGTAGAGAC 58.612 38.462 0.00 0.00 0.00 3.36
1699 2858 7.016268 AGTGTTCCCTAAATGAAAGTAGAGACA 59.984 37.037 0.00 0.00 0.00 3.41
1746 2905 4.081406 TGATGTGCAGTGCTTCCTAAATT 58.919 39.130 17.60 0.00 0.00 1.82
1755 2914 4.783227 AGTGCTTCCTAAATTACTCCCTCA 59.217 41.667 0.00 0.00 0.00 3.86
1772 2931 8.560124 ACTCCCTCAGTCTCAAAATATAAGAT 57.440 34.615 0.00 0.00 0.00 2.40
1805 2965 2.165437 CTGAGACAGAGGGAGTACAAGC 59.835 54.545 0.00 0.00 32.44 4.01
1863 3023 8.510243 TGACTCATCAAAATACTGCATTGTAT 57.490 30.769 0.00 0.00 34.91 2.29
1872 3032 8.853345 CAAAATACTGCATTGTATCTGTGAAAC 58.147 33.333 0.00 0.00 32.55 2.78
1916 3086 7.151999 TGTTCTTTGAGTTTTCTTGCTTACA 57.848 32.000 0.00 0.00 0.00 2.41
1984 3154 7.012799 GGATGTTTCTAGCTAAATCCAAGGAAG 59.987 40.741 0.00 0.00 0.00 3.46
2035 3205 1.067283 AGGACATGCAAGAGTCAGACG 60.067 52.381 16.05 0.00 36.50 4.18
2092 3262 3.704800 TCGTTATCAATGGTGTCCCAA 57.295 42.857 0.00 0.00 46.04 4.12
2148 3318 0.596083 CAGTAAGAGATGCTCCGCGG 60.596 60.000 22.12 22.12 0.00 6.46
2163 3333 1.134530 CGCGGTCTCGAGTTGATCAC 61.135 60.000 13.13 1.42 39.00 3.06
2232 3402 4.434520 GAGACAAGTACTATGCAGGGAAC 58.565 47.826 0.00 0.00 0.00 3.62
2239 3409 1.623811 ACTATGCAGGGAACGTTGTCT 59.376 47.619 5.00 0.00 0.00 3.41
2252 3422 2.364324 ACGTTGTCTGGTATGACAGTGT 59.636 45.455 0.00 0.00 46.02 3.55
2283 3455 4.321452 TGGTACACCGTTGTCTATGAAGAC 60.321 45.833 0.00 0.00 44.96 3.01
2381 3553 5.443185 ACACTTGTGATGGACAAATTCAG 57.557 39.130 7.83 0.00 44.14 3.02
2392 3564 6.748333 TGGACAAATTCAGACATCAGAATC 57.252 37.500 0.58 0.00 32.03 2.52
2413 3609 1.629043 TGCTCCCGACTACAGAACTT 58.371 50.000 0.00 0.00 0.00 2.66
2449 3672 0.179108 GATGGTGGTCAGAGCGGTAC 60.179 60.000 0.00 0.00 0.00 3.34
2471 3694 0.104120 GGCCAACAGTCAAACAACCC 59.896 55.000 0.00 0.00 0.00 4.11
2609 3865 2.684881 CAGGTGATATTCAACCTGTGCC 59.315 50.000 18.38 0.00 39.08 5.01
2640 3920 8.576442 ACAACAGGTGATATTCAACCTAAAAAG 58.424 33.333 0.00 0.00 33.71 2.27
2781 4070 8.295288 GGAAGCCAGTCATTCTAATAATCAATG 58.705 37.037 0.00 0.00 0.00 2.82
2804 4150 7.348080 TGTCACTGTTCCAATATCTAGTAGG 57.652 40.000 0.00 0.00 0.00 3.18
2894 4251 6.920569 ACCCAGCGTACTTTTAAATCTATG 57.079 37.500 0.00 0.00 0.00 2.23
2931 4291 7.337167 ACTGCTGTCATATCAATTTCTTCTCT 58.663 34.615 0.00 0.00 0.00 3.10
3017 4383 3.089284 GGAAATGGAACCTAGTTGTGGG 58.911 50.000 0.00 0.00 0.00 4.61
3039 4405 5.465390 GGGTTAATTTCTTTTCCTGTGCAAC 59.535 40.000 0.00 0.00 37.35 4.17
3114 4480 3.153919 TGTGGAAATGGAACCTAGTTGC 58.846 45.455 0.00 0.00 34.50 4.17
3160 4526 6.122277 TGAAAGATCCTTGAGTTGTTTCACT 58.878 36.000 0.00 0.00 29.76 3.41
3330 4696 4.363999 AGTTCTTGTGAGTTCAGAGAACG 58.636 43.478 20.80 0.00 45.32 3.95
3337 4703 1.921230 GAGTTCAGAGAACGATTCGCC 59.079 52.381 5.86 0.00 34.02 5.54
3351 4717 0.323629 TTCGCCCCAGTTAGGTCTTG 59.676 55.000 0.00 0.00 34.66 3.02
3352 4718 0.834687 TCGCCCCAGTTAGGTCTTGT 60.835 55.000 0.00 0.00 34.66 3.16
3353 4719 0.673644 CGCCCCAGTTAGGTCTTGTG 60.674 60.000 0.00 0.00 34.66 3.33
3378 4744 5.940595 AGTGTGTACGAATCTACAAGAGAC 58.059 41.667 0.00 0.00 36.87 3.36
3393 4759 4.211374 ACAAGAGACGTATCAGCAACAAAC 59.789 41.667 13.45 0.00 0.00 2.93
3464 4830 2.361104 AACCATGGCAATCGGCGT 60.361 55.556 13.04 0.00 46.16 5.68
3482 4848 2.742372 GGTGAATCGCCTGCGTGT 60.742 61.111 11.68 0.33 40.74 4.49
3509 4875 2.226330 CTGGTGGAGACGGAGATCTAG 58.774 57.143 0.00 0.00 0.00 2.43
3515 4881 2.875933 GGAGACGGAGATCTAGTCTGTG 59.124 54.545 27.94 4.88 44.30 3.66
3569 4935 3.102972 TCTCAGCTCTTCCATGCTTACT 58.897 45.455 0.00 0.00 37.44 2.24
3570 4936 4.281657 TCTCAGCTCTTCCATGCTTACTA 58.718 43.478 0.00 0.00 37.44 1.82
3571 4937 4.098654 TCTCAGCTCTTCCATGCTTACTAC 59.901 45.833 0.00 0.00 37.44 2.73
3572 4938 3.133003 TCAGCTCTTCCATGCTTACTACC 59.867 47.826 0.00 0.00 37.44 3.18
3573 4939 3.133721 CAGCTCTTCCATGCTTACTACCT 59.866 47.826 0.00 0.00 37.44 3.08
3600 4967 5.473162 CAGGAAAACAGAACACCATGACATA 59.527 40.000 0.00 0.00 0.00 2.29
3601 4968 5.707298 AGGAAAACAGAACACCATGACATAG 59.293 40.000 0.00 0.00 0.00 2.23
3602 4969 5.473504 GGAAAACAGAACACCATGACATAGT 59.526 40.000 0.00 0.00 0.00 2.12
3664 5031 5.163913 CGTTGAGTTGCTCTTAAGAAGATGG 60.164 44.000 6.63 0.00 36.82 3.51
3667 5034 7.187824 TGAGTTGCTCTTAAGAAGATGGTAT 57.812 36.000 6.63 0.00 36.82 2.73
3681 5048 5.808366 AGATGGTATGATACAACGGTGAT 57.192 39.130 7.88 0.00 0.00 3.06
3692 5059 3.861840 ACAACGGTGATGAACTGATAGG 58.138 45.455 7.88 0.00 38.65 2.57
3822 5217 2.307768 CTAGTGGGGTTAGCGATCAGA 58.692 52.381 0.00 0.00 0.00 3.27
3854 5249 7.181125 AGTTTATTCTTCAGGTGAGATAGTGGT 59.819 37.037 0.00 0.00 0.00 4.16
3873 5268 5.241506 AGTGGTTGATGGTCAATTTGTACTG 59.758 40.000 0.00 0.00 38.79 2.74
3877 5272 6.238897 GGTTGATGGTCAATTTGTACTGTGAA 60.239 38.462 0.00 0.00 38.79 3.18
3879 5274 6.734137 TGATGGTCAATTTGTACTGTGAAAC 58.266 36.000 0.00 0.00 37.35 2.78
3903 5298 3.512680 CCACGGTAGATTCTGAACAGTC 58.487 50.000 0.00 0.00 0.00 3.51
3907 5302 4.283722 ACGGTAGATTCTGAACAGTCCTTT 59.716 41.667 0.00 0.00 0.00 3.11
3933 5328 9.985730 TTAATTTCAGATCATAATTTGGATGGC 57.014 29.630 0.00 0.00 0.00 4.40
3934 5329 7.850935 ATTTCAGATCATAATTTGGATGGCT 57.149 32.000 0.00 0.00 0.00 4.75
3935 5330 8.945195 ATTTCAGATCATAATTTGGATGGCTA 57.055 30.769 0.00 0.00 0.00 3.93
3936 5331 8.765488 TTTCAGATCATAATTTGGATGGCTAA 57.235 30.769 0.00 0.00 0.00 3.09
3937 5332 8.765488 TTCAGATCATAATTTGGATGGCTAAA 57.235 30.769 0.00 0.00 0.00 1.85
3938 5333 8.400184 TCAGATCATAATTTGGATGGCTAAAG 57.600 34.615 0.00 0.00 0.00 1.85
3939 5334 7.040201 TCAGATCATAATTTGGATGGCTAAAGC 60.040 37.037 0.00 0.00 41.14 3.51
3940 5335 5.437289 TCATAATTTGGATGGCTAAAGCG 57.563 39.130 0.00 0.00 43.26 4.68
3941 5336 4.887071 TCATAATTTGGATGGCTAAAGCGT 59.113 37.500 0.00 0.00 43.26 5.07
3942 5337 3.508744 AATTTGGATGGCTAAAGCGTG 57.491 42.857 0.00 0.00 43.26 5.34
3943 5338 0.525761 TTTGGATGGCTAAAGCGTGC 59.474 50.000 0.00 0.00 43.26 5.34
3944 5339 1.643868 TTGGATGGCTAAAGCGTGCG 61.644 55.000 0.00 0.00 43.26 5.34
3945 5340 2.709475 GATGGCTAAAGCGTGCGG 59.291 61.111 0.00 0.00 43.26 5.69
3946 5341 1.813753 GATGGCTAAAGCGTGCGGA 60.814 57.895 0.00 0.00 43.26 5.54
3947 5342 1.766143 GATGGCTAAAGCGTGCGGAG 61.766 60.000 0.00 0.00 43.26 4.63
3948 5343 2.125673 GGCTAAAGCGTGCGGAGA 60.126 61.111 0.00 0.00 43.26 3.71
3949 5344 1.740296 GGCTAAAGCGTGCGGAGAA 60.740 57.895 0.00 0.00 43.26 2.87
3950 5345 1.090052 GGCTAAAGCGTGCGGAGAAT 61.090 55.000 0.00 0.00 43.26 2.40
3951 5346 0.026803 GCTAAAGCGTGCGGAGAATG 59.973 55.000 0.00 0.00 0.00 2.67
3952 5347 1.359848 CTAAAGCGTGCGGAGAATGT 58.640 50.000 0.00 0.00 0.00 2.71
3953 5348 1.324736 CTAAAGCGTGCGGAGAATGTC 59.675 52.381 0.00 0.00 0.00 3.06
3954 5349 0.602638 AAAGCGTGCGGAGAATGTCA 60.603 50.000 0.00 0.00 0.00 3.58
3955 5350 0.602638 AAGCGTGCGGAGAATGTCAA 60.603 50.000 0.00 0.00 0.00 3.18
3956 5351 1.016130 AGCGTGCGGAGAATGTCAAG 61.016 55.000 0.00 0.00 0.00 3.02
3957 5352 1.014044 GCGTGCGGAGAATGTCAAGA 61.014 55.000 0.00 0.00 0.00 3.02
3958 5353 0.994995 CGTGCGGAGAATGTCAAGAG 59.005 55.000 0.00 0.00 0.00 2.85
3959 5354 1.402852 CGTGCGGAGAATGTCAAGAGA 60.403 52.381 0.00 0.00 0.00 3.10
3960 5355 2.266554 GTGCGGAGAATGTCAAGAGAG 58.733 52.381 0.00 0.00 0.00 3.20
3961 5356 1.205655 TGCGGAGAATGTCAAGAGAGG 59.794 52.381 0.00 0.00 0.00 3.69
3962 5357 1.472376 GCGGAGAATGTCAAGAGAGGG 60.472 57.143 0.00 0.00 0.00 4.30
3963 5358 1.472376 CGGAGAATGTCAAGAGAGGGC 60.472 57.143 0.00 0.00 0.00 5.19
3964 5359 1.472376 GGAGAATGTCAAGAGAGGGCG 60.472 57.143 0.00 0.00 0.00 6.13
3965 5360 0.539051 AGAATGTCAAGAGAGGGCGG 59.461 55.000 0.00 0.00 0.00 6.13
3966 5361 0.462759 GAATGTCAAGAGAGGGCGGG 60.463 60.000 0.00 0.00 0.00 6.13
3967 5362 1.915078 AATGTCAAGAGAGGGCGGGG 61.915 60.000 0.00 0.00 0.00 5.73
3968 5363 3.003763 GTCAAGAGAGGGCGGGGT 61.004 66.667 0.00 0.00 0.00 4.95
3969 5364 2.683933 TCAAGAGAGGGCGGGGTC 60.684 66.667 0.00 0.00 0.00 4.46
3970 5365 4.148825 CAAGAGAGGGCGGGGTCG 62.149 72.222 0.00 0.00 39.81 4.79
3971 5366 4.377760 AAGAGAGGGCGGGGTCGA 62.378 66.667 0.00 0.00 39.00 4.20
3982 5377 2.463592 GGGGTCGACCGAATTTGAC 58.536 57.895 27.68 11.35 41.60 3.18
3983 5378 0.320946 GGGGTCGACCGAATTTGACA 60.321 55.000 27.68 0.00 41.60 3.58
3984 5379 1.677820 GGGGTCGACCGAATTTGACAT 60.678 52.381 27.68 0.00 41.60 3.06
3985 5380 1.396996 GGGTCGACCGAATTTGACATG 59.603 52.381 27.68 0.00 36.71 3.21
3986 5381 2.343101 GGTCGACCGAATTTGACATGA 58.657 47.619 20.85 0.00 33.04 3.07
3987 5382 2.348666 GGTCGACCGAATTTGACATGAG 59.651 50.000 20.85 0.00 33.04 2.90
3988 5383 3.250744 GTCGACCGAATTTGACATGAGA 58.749 45.455 3.51 0.00 0.00 3.27
3989 5384 3.865745 GTCGACCGAATTTGACATGAGAT 59.134 43.478 3.51 0.00 0.00 2.75
3990 5385 3.865164 TCGACCGAATTTGACATGAGATG 59.135 43.478 0.00 0.00 0.00 2.90
3991 5386 3.865164 CGACCGAATTTGACATGAGATGA 59.135 43.478 0.00 0.00 0.00 2.92
3992 5387 4.026228 CGACCGAATTTGACATGAGATGAG 60.026 45.833 0.00 0.00 0.00 2.90
3993 5388 4.836825 ACCGAATTTGACATGAGATGAGT 58.163 39.130 0.00 0.00 0.00 3.41
3994 5389 4.872691 ACCGAATTTGACATGAGATGAGTC 59.127 41.667 0.00 0.00 0.00 3.36
3995 5390 4.272018 CCGAATTTGACATGAGATGAGTCC 59.728 45.833 0.00 0.00 0.00 3.85
3996 5391 4.872124 CGAATTTGACATGAGATGAGTCCA 59.128 41.667 0.00 0.00 0.00 4.02
3997 5392 5.526479 CGAATTTGACATGAGATGAGTCCAT 59.474 40.000 0.00 0.00 35.29 3.41
3998 5393 6.037940 CGAATTTGACATGAGATGAGTCCATT 59.962 38.462 0.00 0.00 32.09 3.16
3999 5394 7.225341 CGAATTTGACATGAGATGAGTCCATTA 59.775 37.037 0.00 0.00 32.09 1.90
4000 5395 8.812513 AATTTGACATGAGATGAGTCCATTAA 57.187 30.769 0.00 0.00 32.09 1.40
4001 5396 7.854557 TTTGACATGAGATGAGTCCATTAAG 57.145 36.000 0.00 0.00 32.09 1.85
4002 5397 6.796785 TGACATGAGATGAGTCCATTAAGA 57.203 37.500 0.00 0.00 32.09 2.10
4003 5398 6.814043 TGACATGAGATGAGTCCATTAAGAG 58.186 40.000 0.00 0.00 32.09 2.85
4004 5399 6.608808 TGACATGAGATGAGTCCATTAAGAGA 59.391 38.462 0.00 0.00 32.09 3.10
4005 5400 7.053316 ACATGAGATGAGTCCATTAAGAGAG 57.947 40.000 0.00 0.00 32.09 3.20
4006 5401 6.838090 ACATGAGATGAGTCCATTAAGAGAGA 59.162 38.462 0.00 0.00 32.09 3.10
4007 5402 6.707440 TGAGATGAGTCCATTAAGAGAGAC 57.293 41.667 0.00 0.00 32.09 3.36
4008 5403 5.596361 TGAGATGAGTCCATTAAGAGAGACC 59.404 44.000 0.00 0.00 32.09 3.85
4009 5404 5.776358 AGATGAGTCCATTAAGAGAGACCT 58.224 41.667 0.00 0.00 32.09 3.85
4010 5405 5.598005 AGATGAGTCCATTAAGAGAGACCTG 59.402 44.000 0.00 0.00 32.09 4.00
4011 5406 4.935578 TGAGTCCATTAAGAGAGACCTGA 58.064 43.478 0.00 0.00 0.00 3.86
4012 5407 5.333581 TGAGTCCATTAAGAGAGACCTGAA 58.666 41.667 0.00 0.00 0.00 3.02
4013 5408 5.420421 TGAGTCCATTAAGAGAGACCTGAAG 59.580 44.000 0.00 0.00 0.00 3.02
4014 5409 5.584913 AGTCCATTAAGAGAGACCTGAAGA 58.415 41.667 0.00 0.00 0.00 2.87
4015 5410 6.019748 AGTCCATTAAGAGAGACCTGAAGAA 58.980 40.000 0.00 0.00 0.00 2.52
4016 5411 6.671779 AGTCCATTAAGAGAGACCTGAAGAAT 59.328 38.462 0.00 0.00 0.00 2.40
4017 5412 7.181845 AGTCCATTAAGAGAGACCTGAAGAATT 59.818 37.037 0.00 0.00 0.00 2.17
4018 5413 7.279758 GTCCATTAAGAGAGACCTGAAGAATTG 59.720 40.741 0.00 0.00 0.00 2.32
4019 5414 6.541641 CCATTAAGAGAGACCTGAAGAATTGG 59.458 42.308 0.00 0.00 0.00 3.16
4020 5415 6.935240 TTAAGAGAGACCTGAAGAATTGGA 57.065 37.500 0.00 0.00 0.00 3.53
4021 5416 5.419239 AAGAGAGACCTGAAGAATTGGAG 57.581 43.478 0.00 0.00 0.00 3.86
4022 5417 4.424842 AGAGAGACCTGAAGAATTGGAGT 58.575 43.478 0.00 0.00 0.00 3.85
4023 5418 5.584913 AGAGAGACCTGAAGAATTGGAGTA 58.415 41.667 0.00 0.00 0.00 2.59
4024 5419 6.201591 AGAGAGACCTGAAGAATTGGAGTAT 58.798 40.000 0.00 0.00 0.00 2.12
4025 5420 6.323739 AGAGAGACCTGAAGAATTGGAGTATC 59.676 42.308 0.00 0.00 0.00 2.24
4026 5421 5.068460 AGAGACCTGAAGAATTGGAGTATCG 59.932 44.000 0.00 0.00 34.37 2.92
4027 5422 4.956700 AGACCTGAAGAATTGGAGTATCGA 59.043 41.667 0.00 0.00 34.37 3.59
4028 5423 5.012328 ACCTGAAGAATTGGAGTATCGAC 57.988 43.478 0.00 0.00 34.37 4.20
4029 5424 4.466370 ACCTGAAGAATTGGAGTATCGACA 59.534 41.667 0.00 0.00 34.37 4.35
4030 5425 5.046591 ACCTGAAGAATTGGAGTATCGACAA 60.047 40.000 0.00 0.00 34.37 3.18
4031 5426 5.874810 CCTGAAGAATTGGAGTATCGACAAA 59.125 40.000 0.00 0.00 34.37 2.83
4032 5427 6.036517 CCTGAAGAATTGGAGTATCGACAAAG 59.963 42.308 0.00 0.00 34.37 2.77
4033 5428 6.697395 TGAAGAATTGGAGTATCGACAAAGA 58.303 36.000 0.00 0.00 34.37 2.52
4034 5429 6.813649 TGAAGAATTGGAGTATCGACAAAGAG 59.186 38.462 0.00 0.00 34.37 2.85
4035 5430 5.112686 AGAATTGGAGTATCGACAAAGAGC 58.887 41.667 0.00 0.00 34.37 4.09
4036 5431 4.744795 ATTGGAGTATCGACAAAGAGCT 57.255 40.909 0.00 0.00 34.37 4.09
4037 5432 5.854010 ATTGGAGTATCGACAAAGAGCTA 57.146 39.130 0.00 0.00 34.37 3.32
4038 5433 4.902443 TGGAGTATCGACAAAGAGCTAG 57.098 45.455 0.00 0.00 34.37 3.42
4039 5434 3.066900 TGGAGTATCGACAAAGAGCTAGC 59.933 47.826 6.62 6.62 34.37 3.42
4040 5435 3.316868 GGAGTATCGACAAAGAGCTAGCT 59.683 47.826 19.45 19.45 34.37 3.32
4041 5436 4.515944 GGAGTATCGACAAAGAGCTAGCTA 59.484 45.833 19.38 0.00 34.37 3.32
4042 5437 5.182380 GGAGTATCGACAAAGAGCTAGCTAT 59.818 44.000 19.38 12.73 34.37 2.97
4043 5438 6.007936 AGTATCGACAAAGAGCTAGCTATG 57.992 41.667 19.38 18.66 0.00 2.23
4044 5439 3.717400 TCGACAAAGAGCTAGCTATGG 57.283 47.619 19.38 13.23 0.00 2.74
4045 5440 3.288092 TCGACAAAGAGCTAGCTATGGA 58.712 45.455 19.38 8.12 0.00 3.41
4046 5441 3.066900 TCGACAAAGAGCTAGCTATGGAC 59.933 47.826 19.38 10.10 0.00 4.02
4047 5442 3.181486 CGACAAAGAGCTAGCTATGGACA 60.181 47.826 19.38 0.00 0.00 4.02
4048 5443 4.367450 GACAAAGAGCTAGCTATGGACAG 58.633 47.826 19.38 6.25 0.00 3.51
4049 5444 3.133721 ACAAAGAGCTAGCTATGGACAGG 59.866 47.826 19.38 4.81 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.003173 CTGAAGACGCCCCTGGGA 61.003 66.667 16.20 0.00 37.50 4.37
94 98 0.773644 GGATACAGGTCCATGCCCAT 59.226 55.000 0.00 0.00 38.20 4.00
109 113 2.611751 CCGTGAACGCATGAAATGGATA 59.388 45.455 0.00 0.00 46.86 2.59
188 194 0.883833 CAACGAGCCAAAAGAGCCAT 59.116 50.000 0.00 0.00 0.00 4.40
216 223 2.520536 GGTGGTGGTGCAGAGAGGT 61.521 63.158 0.00 0.00 0.00 3.85
364 379 0.179936 GATCTGGAAGGAGGCACAGG 59.820 60.000 0.00 0.00 0.00 4.00
545 572 4.736896 GAGGTGGTCGTCGGGCAC 62.737 72.222 0.00 0.00 0.00 5.01
558 585 2.550208 GGTGGAACATTGTCGAAGAGGT 60.550 50.000 0.00 0.00 44.52 3.85
859 906 2.223876 TGAAGAACACGGCTAAACTCGT 60.224 45.455 0.00 0.00 40.49 4.18
961 1078 0.178924 GGATGGGGAAATGGGGATGG 60.179 60.000 0.00 0.00 0.00 3.51
970 1087 1.280998 GAAAGGAGTCGGATGGGGAAA 59.719 52.381 0.00 0.00 0.00 3.13
978 1095 3.895656 TCTTGAAGAAGAAAGGAGTCGGA 59.104 43.478 0.00 0.00 35.14 4.55
1006 1123 3.006217 GCAAGCAAGAGGGAAATGAGTTT 59.994 43.478 0.00 0.00 0.00 2.66
1210 1327 0.757188 AGGGCATCGTCGAGGAAGAT 60.757 55.000 11.71 0.00 31.49 2.40
1278 1395 4.500116 GCGTCGGAGAGGAGGCAC 62.500 72.222 0.00 0.00 46.48 5.01
1510 2322 5.049818 GCACACTATCTCCACAAATATCAGC 60.050 44.000 0.00 0.00 0.00 4.26
1564 2376 6.094325 AGTGTATCAAACGACAAAAACTCCAA 59.906 34.615 0.00 0.00 0.00 3.53
1569 2381 8.542132 TGTACTAGTGTATCAAACGACAAAAAC 58.458 33.333 5.39 0.00 0.00 2.43
1575 2387 7.807687 ACAATGTACTAGTGTATCAAACGAC 57.192 36.000 5.39 0.00 35.52 4.34
1633 2779 4.890378 CAGATGCATTTCTGTACTTCACG 58.110 43.478 8.85 0.00 38.64 4.35
1658 2816 5.253096 AGGGAACACTTGGATATTAACCAGT 59.747 40.000 0.00 0.00 38.70 4.00
1746 2905 9.661954 ATCTTATATTTTGAGACTGAGGGAGTA 57.338 33.333 0.00 0.00 33.83 2.59
1829 2989 3.421919 TTTGATGAGTCAGGCATGTCA 57.578 42.857 0.00 0.00 35.39 3.58
1863 3023 7.275888 AGCATAAATCAAACAGTTTCACAGA 57.724 32.000 0.00 0.00 0.00 3.41
1872 3032 6.643770 AGAACAAGCAAGCATAAATCAAACAG 59.356 34.615 0.00 0.00 0.00 3.16
1937 3107 3.760684 CCTGGAGGAGAAAGAAAATGGTG 59.239 47.826 0.00 0.00 37.39 4.17
1984 3154 4.392047 TCCATGACCTGATATTGCATCAC 58.608 43.478 0.00 0.00 0.00 3.06
2035 3205 0.740737 ACTTGAACAACAGGTGCAGC 59.259 50.000 8.11 8.11 36.08 5.25
2092 3262 3.140325 TGCGAAATCAGGAGGAAAGTT 57.860 42.857 0.00 0.00 0.00 2.66
2148 3318 0.171455 AGCGGTGATCAACTCGAGAC 59.829 55.000 21.68 5.18 0.00 3.36
2163 3333 0.734889 CTAGCCATTCACCAAAGCGG 59.265 55.000 0.00 0.00 42.50 5.52
2232 3402 3.026630 ACACTGTCATACCAGACAACG 57.973 47.619 0.00 0.00 46.90 4.10
2239 3409 6.065374 ACCAATTGTTTACACTGTCATACCA 58.935 36.000 4.43 0.00 0.00 3.25
2252 3422 5.124645 AGACAACGGTGTACCAATTGTTTA 58.875 37.500 5.82 0.00 42.00 2.01
2283 3455 2.100584 CTCAAGATCTTCCTGGTCTCCG 59.899 54.545 4.57 0.00 0.00 4.63
2381 3553 2.159043 TCGGGAGCAAGATTCTGATGTC 60.159 50.000 0.00 0.00 0.00 3.06
2392 3564 1.546476 AGTTCTGTAGTCGGGAGCAAG 59.454 52.381 0.00 0.00 0.00 4.01
2413 3609 4.818005 CACCATCTGATTGCTAGCAACATA 59.182 41.667 31.51 21.57 38.88 2.29
2449 3672 2.472816 GTTGTTTGACTGTTGGCCATG 58.527 47.619 6.09 2.33 0.00 3.66
2609 3865 5.925969 GGTTGAATATCACCTGTTGTTTTGG 59.074 40.000 0.00 0.00 0.00 3.28
2781 4070 7.349412 ACCTACTAGATATTGGAACAGTGAC 57.651 40.000 0.00 0.00 42.39 3.67
2894 4251 3.909019 GACAGCAGTCGCATAGTAAAC 57.091 47.619 0.00 0.00 42.27 2.01
2931 4291 6.820335 ACAGCATGCAGATATACTTGTCTAA 58.180 36.000 21.98 0.00 42.53 2.10
3017 4383 6.292328 GCAGTTGCACAGGAAAAGAAATTAAC 60.292 38.462 0.00 0.00 41.59 2.01
3077 4443 1.242076 CACAAGGAGAAGTTGCAGGG 58.758 55.000 0.00 0.00 0.00 4.45
3079 4445 2.260844 TCCACAAGGAGAAGTTGCAG 57.739 50.000 0.00 0.00 39.61 4.41
3114 4480 1.714794 AGAATTCAGCCAGACGAACG 58.285 50.000 8.44 0.00 0.00 3.95
3330 4696 0.831307 AGACCTAACTGGGGCGAATC 59.169 55.000 0.00 0.00 39.91 2.52
3337 4703 3.181454 ACACTTCACAAGACCTAACTGGG 60.181 47.826 0.00 0.00 41.11 4.45
3351 4717 6.147581 TCTTGTAGATTCGTACACACTTCAC 58.852 40.000 0.00 0.00 32.53 3.18
3352 4718 6.206048 TCTCTTGTAGATTCGTACACACTTCA 59.794 38.462 0.00 0.00 32.53 3.02
3353 4719 6.523893 GTCTCTTGTAGATTCGTACACACTTC 59.476 42.308 0.00 0.00 36.36 3.01
3378 4744 3.554524 CAAGGTGTTTGTTGCTGATACG 58.445 45.455 0.00 0.00 31.92 3.06
3393 4759 0.671781 CCGTCTCAGGAAGCAAGGTG 60.672 60.000 0.00 0.00 0.00 4.00
3464 4830 2.741985 CACGCAGGCGATTCACCA 60.742 61.111 21.62 0.00 42.83 4.17
3482 4848 1.532604 CCGTCTCCACCAGTAGCACA 61.533 60.000 0.00 0.00 0.00 4.57
3515 4881 2.883253 GAGAAGAGAGGTGCGCGC 60.883 66.667 27.26 27.26 0.00 6.86
3527 4893 7.273712 TGAGAAGGAATCATCATTCAGAGAAG 58.726 38.462 6.08 0.00 46.22 2.85
3528 4894 7.191593 TGAGAAGGAATCATCATTCAGAGAA 57.808 36.000 6.08 0.00 46.22 2.87
3569 4935 4.448210 GTGTTCTGTTTTCCTGTCAGGTA 58.552 43.478 18.65 6.43 36.53 3.08
3570 4936 3.279434 GTGTTCTGTTTTCCTGTCAGGT 58.721 45.455 18.65 0.00 36.53 4.00
3571 4937 2.618709 GGTGTTCTGTTTTCCTGTCAGG 59.381 50.000 13.21 13.21 36.46 3.86
3572 4938 3.278574 TGGTGTTCTGTTTTCCTGTCAG 58.721 45.455 0.00 0.00 0.00 3.51
3573 4939 3.358111 TGGTGTTCTGTTTTCCTGTCA 57.642 42.857 0.00 0.00 0.00 3.58
3641 5008 5.703130 ACCATCTTCTTAAGAGCAACTCAAC 59.297 40.000 5.12 0.00 41.61 3.18
3664 5031 6.040247 TCAGTTCATCACCGTTGTATCATAC 58.960 40.000 0.00 0.00 0.00 2.39
3667 5034 4.529109 TCAGTTCATCACCGTTGTATCA 57.471 40.909 0.00 0.00 0.00 2.15
3681 5048 8.146053 TCCTGAAGTTTAATCCTATCAGTTCA 57.854 34.615 0.00 0.00 34.03 3.18
3692 5059 6.349694 CCAAGCTCCTTTCCTGAAGTTTAATC 60.350 42.308 0.00 0.00 33.29 1.75
3794 5189 3.310193 GCTAACCCCACTAGGAATCTCT 58.690 50.000 0.00 0.00 38.24 3.10
3822 5217 7.453393 TCTCACCTGAAGAATAAACTGATTGT 58.547 34.615 0.00 0.00 0.00 2.71
3854 5249 6.951062 TTCACAGTACAAATTGACCATCAA 57.049 33.333 0.00 0.00 41.09 2.57
3873 5268 2.467566 ATCTACCGTGGGTGTTTCAC 57.532 50.000 0.00 0.00 36.19 3.18
3877 5272 2.253610 TCAGAATCTACCGTGGGTGTT 58.746 47.619 0.00 0.00 36.19 3.32
3879 5274 2.028476 TGTTCAGAATCTACCGTGGGTG 60.028 50.000 0.00 0.00 36.19 4.61
3907 5302 9.985730 GCCATCCAAATTATGATCTGAAATTAA 57.014 29.630 0.00 0.00 0.00 1.40
3922 5317 2.417243 GCACGCTTTAGCCATCCAAATT 60.417 45.455 0.00 0.00 37.91 1.82
3931 5326 1.090052 ATTCTCCGCACGCTTTAGCC 61.090 55.000 0.00 0.00 37.91 3.93
3932 5327 0.026803 CATTCTCCGCACGCTTTAGC 59.973 55.000 0.00 0.00 37.78 3.09
3933 5328 1.324736 GACATTCTCCGCACGCTTTAG 59.675 52.381 0.00 0.00 0.00 1.85
3934 5329 1.337354 TGACATTCTCCGCACGCTTTA 60.337 47.619 0.00 0.00 0.00 1.85
3935 5330 0.602638 TGACATTCTCCGCACGCTTT 60.603 50.000 0.00 0.00 0.00 3.51
3936 5331 0.602638 TTGACATTCTCCGCACGCTT 60.603 50.000 0.00 0.00 0.00 4.68
3937 5332 1.005037 TTGACATTCTCCGCACGCT 60.005 52.632 0.00 0.00 0.00 5.07
3938 5333 1.014044 TCTTGACATTCTCCGCACGC 61.014 55.000 0.00 0.00 0.00 5.34
3939 5334 0.994995 CTCTTGACATTCTCCGCACG 59.005 55.000 0.00 0.00 0.00 5.34
3940 5335 2.266554 CTCTCTTGACATTCTCCGCAC 58.733 52.381 0.00 0.00 0.00 5.34
3941 5336 1.205655 CCTCTCTTGACATTCTCCGCA 59.794 52.381 0.00 0.00 0.00 5.69
3942 5337 1.472376 CCCTCTCTTGACATTCTCCGC 60.472 57.143 0.00 0.00 0.00 5.54
3943 5338 1.472376 GCCCTCTCTTGACATTCTCCG 60.472 57.143 0.00 0.00 0.00 4.63
3944 5339 1.472376 CGCCCTCTCTTGACATTCTCC 60.472 57.143 0.00 0.00 0.00 3.71
3945 5340 1.472376 CCGCCCTCTCTTGACATTCTC 60.472 57.143 0.00 0.00 0.00 2.87
3946 5341 0.539051 CCGCCCTCTCTTGACATTCT 59.461 55.000 0.00 0.00 0.00 2.40
3947 5342 0.462759 CCCGCCCTCTCTTGACATTC 60.463 60.000 0.00 0.00 0.00 2.67
3948 5343 1.604378 CCCGCCCTCTCTTGACATT 59.396 57.895 0.00 0.00 0.00 2.71
3949 5344 2.370445 CCCCGCCCTCTCTTGACAT 61.370 63.158 0.00 0.00 0.00 3.06
3950 5345 3.003173 CCCCGCCCTCTCTTGACA 61.003 66.667 0.00 0.00 0.00 3.58
3951 5346 3.003763 ACCCCGCCCTCTCTTGAC 61.004 66.667 0.00 0.00 0.00 3.18
3952 5347 2.683933 GACCCCGCCCTCTCTTGA 60.684 66.667 0.00 0.00 0.00 3.02
3953 5348 4.148825 CGACCCCGCCCTCTCTTG 62.149 72.222 0.00 0.00 0.00 3.02
3954 5349 4.377760 TCGACCCCGCCCTCTCTT 62.378 66.667 0.00 0.00 35.37 2.85
3964 5359 0.320946 TGTCAAATTCGGTCGACCCC 60.321 55.000 28.52 5.39 0.00 4.95
3965 5360 1.396996 CATGTCAAATTCGGTCGACCC 59.603 52.381 28.52 12.33 0.00 4.46
3966 5361 2.343101 TCATGTCAAATTCGGTCGACC 58.657 47.619 25.28 25.28 0.00 4.79
3967 5362 3.250744 TCTCATGTCAAATTCGGTCGAC 58.749 45.455 7.13 7.13 0.00 4.20
3968 5363 3.586100 TCTCATGTCAAATTCGGTCGA 57.414 42.857 0.00 0.00 0.00 4.20
3969 5364 3.865164 TCATCTCATGTCAAATTCGGTCG 59.135 43.478 0.00 0.00 0.00 4.79
3970 5365 4.872691 ACTCATCTCATGTCAAATTCGGTC 59.127 41.667 0.00 0.00 0.00 4.79
3971 5366 4.836825 ACTCATCTCATGTCAAATTCGGT 58.163 39.130 0.00 0.00 0.00 4.69
3972 5367 4.272018 GGACTCATCTCATGTCAAATTCGG 59.728 45.833 0.00 0.00 32.84 4.30
3973 5368 4.872124 TGGACTCATCTCATGTCAAATTCG 59.128 41.667 0.00 0.00 32.84 3.34
3974 5369 6.939132 ATGGACTCATCTCATGTCAAATTC 57.061 37.500 0.00 0.00 32.84 2.17
3975 5370 8.812513 TTAATGGACTCATCTCATGTCAAATT 57.187 30.769 0.00 0.00 32.24 1.82
3976 5371 8.270030 TCTTAATGGACTCATCTCATGTCAAAT 58.730 33.333 0.00 0.00 32.24 2.32
3977 5372 7.623630 TCTTAATGGACTCATCTCATGTCAAA 58.376 34.615 0.00 0.00 32.24 2.69
3978 5373 7.124750 TCTCTTAATGGACTCATCTCATGTCAA 59.875 37.037 0.00 0.00 32.24 3.18
3979 5374 6.608808 TCTCTTAATGGACTCATCTCATGTCA 59.391 38.462 0.00 0.00 32.24 3.58
3980 5375 7.014134 TCTCTCTTAATGGACTCATCTCATGTC 59.986 40.741 0.00 0.00 32.24 3.06
3981 5376 6.838090 TCTCTCTTAATGGACTCATCTCATGT 59.162 38.462 0.00 0.00 32.24 3.21
3982 5377 7.147312 GTCTCTCTTAATGGACTCATCTCATG 58.853 42.308 0.00 0.00 32.24 3.07
3983 5378 6.267471 GGTCTCTCTTAATGGACTCATCTCAT 59.733 42.308 0.00 0.00 32.24 2.90
3984 5379 5.596361 GGTCTCTCTTAATGGACTCATCTCA 59.404 44.000 0.00 0.00 32.24 3.27
3985 5380 5.833131 AGGTCTCTCTTAATGGACTCATCTC 59.167 44.000 0.00 0.00 32.24 2.75
3986 5381 5.598005 CAGGTCTCTCTTAATGGACTCATCT 59.402 44.000 0.00 0.00 32.24 2.90
3987 5382 5.596361 TCAGGTCTCTCTTAATGGACTCATC 59.404 44.000 0.00 0.00 32.24 2.92
3988 5383 5.523588 TCAGGTCTCTCTTAATGGACTCAT 58.476 41.667 0.00 0.00 34.56 2.90
3989 5384 4.935578 TCAGGTCTCTCTTAATGGACTCA 58.064 43.478 0.00 0.00 0.00 3.41
3990 5385 5.654650 TCTTCAGGTCTCTCTTAATGGACTC 59.345 44.000 0.00 0.00 0.00 3.36
3991 5386 5.584913 TCTTCAGGTCTCTCTTAATGGACT 58.415 41.667 0.00 0.00 0.00 3.85
3992 5387 5.923733 TCTTCAGGTCTCTCTTAATGGAC 57.076 43.478 0.00 0.00 0.00 4.02
3993 5388 7.334090 CAATTCTTCAGGTCTCTCTTAATGGA 58.666 38.462 0.00 0.00 0.00 3.41
3994 5389 6.541641 CCAATTCTTCAGGTCTCTCTTAATGG 59.458 42.308 0.00 0.00 0.00 3.16
3995 5390 7.334090 TCCAATTCTTCAGGTCTCTCTTAATG 58.666 38.462 0.00 0.00 0.00 1.90
3996 5391 7.181845 ACTCCAATTCTTCAGGTCTCTCTTAAT 59.818 37.037 0.00 0.00 0.00 1.40
3997 5392 6.498651 ACTCCAATTCTTCAGGTCTCTCTTAA 59.501 38.462 0.00 0.00 0.00 1.85
3998 5393 6.019748 ACTCCAATTCTTCAGGTCTCTCTTA 58.980 40.000 0.00 0.00 0.00 2.10
3999 5394 4.843516 ACTCCAATTCTTCAGGTCTCTCTT 59.156 41.667 0.00 0.00 0.00 2.85
4000 5395 4.424842 ACTCCAATTCTTCAGGTCTCTCT 58.575 43.478 0.00 0.00 0.00 3.10
4001 5396 4.817318 ACTCCAATTCTTCAGGTCTCTC 57.183 45.455 0.00 0.00 0.00 3.20
4002 5397 5.068460 CGATACTCCAATTCTTCAGGTCTCT 59.932 44.000 0.00 0.00 0.00 3.10
4003 5398 5.067936 TCGATACTCCAATTCTTCAGGTCTC 59.932 44.000 0.00 0.00 0.00 3.36
4004 5399 4.956700 TCGATACTCCAATTCTTCAGGTCT 59.043 41.667 0.00 0.00 0.00 3.85
4005 5400 5.044558 GTCGATACTCCAATTCTTCAGGTC 58.955 45.833 0.00 0.00 0.00 3.85
4006 5401 4.466370 TGTCGATACTCCAATTCTTCAGGT 59.534 41.667 0.00 0.00 0.00 4.00
4007 5402 5.011090 TGTCGATACTCCAATTCTTCAGG 57.989 43.478 0.00 0.00 0.00 3.86
4008 5403 6.813649 TCTTTGTCGATACTCCAATTCTTCAG 59.186 38.462 0.00 0.00 0.00 3.02
4009 5404 6.697395 TCTTTGTCGATACTCCAATTCTTCA 58.303 36.000 0.00 0.00 0.00 3.02
4010 5405 6.237969 GCTCTTTGTCGATACTCCAATTCTTC 60.238 42.308 0.00 0.00 0.00 2.87
4011 5406 5.582665 GCTCTTTGTCGATACTCCAATTCTT 59.417 40.000 0.00 0.00 0.00 2.52
4012 5407 5.105146 AGCTCTTTGTCGATACTCCAATTCT 60.105 40.000 0.00 0.00 0.00 2.40
4013 5408 5.112686 AGCTCTTTGTCGATACTCCAATTC 58.887 41.667 0.00 0.00 0.00 2.17
4014 5409 5.091261 AGCTCTTTGTCGATACTCCAATT 57.909 39.130 0.00 0.00 0.00 2.32
4015 5410 4.744795 AGCTCTTTGTCGATACTCCAAT 57.255 40.909 0.00 0.00 0.00 3.16
4016 5411 4.440250 GCTAGCTCTTTGTCGATACTCCAA 60.440 45.833 7.70 0.00 0.00 3.53
4017 5412 3.066900 GCTAGCTCTTTGTCGATACTCCA 59.933 47.826 7.70 0.00 0.00 3.86
4018 5413 3.316868 AGCTAGCTCTTTGTCGATACTCC 59.683 47.826 12.68 0.00 0.00 3.85
4019 5414 4.561735 AGCTAGCTCTTTGTCGATACTC 57.438 45.455 12.68 0.00 0.00 2.59
4020 5415 5.048364 CCATAGCTAGCTCTTTGTCGATACT 60.048 44.000 23.26 0.00 0.00 2.12
4021 5416 5.048643 TCCATAGCTAGCTCTTTGTCGATAC 60.049 44.000 23.26 0.00 0.00 2.24
4022 5417 5.048643 GTCCATAGCTAGCTCTTTGTCGATA 60.049 44.000 23.26 0.00 0.00 2.92
4023 5418 3.891977 TCCATAGCTAGCTCTTTGTCGAT 59.108 43.478 23.26 3.19 0.00 3.59
4024 5419 3.066900 GTCCATAGCTAGCTCTTTGTCGA 59.933 47.826 23.26 8.50 0.00 4.20
4025 5420 3.181486 TGTCCATAGCTAGCTCTTTGTCG 60.181 47.826 23.26 6.37 0.00 4.35
4026 5421 4.367450 CTGTCCATAGCTAGCTCTTTGTC 58.633 47.826 23.26 12.44 0.00 3.18
4027 5422 3.133721 CCTGTCCATAGCTAGCTCTTTGT 59.866 47.826 23.26 0.00 0.00 2.83
4028 5423 3.726607 CCTGTCCATAGCTAGCTCTTTG 58.273 50.000 23.26 16.78 0.00 2.77


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

AutoCloner maintained by Alex Coulton.