Multiple sequence alignment - TraesCS3B01G118500

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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 TraesCS3B01G118500 chr3B 100.000 4930 0 0 1 4930 85225550 85220621 0.000000e+00 9105.0
1 TraesCS3B01G118500 chr3B 87.910 1282 127 22 861 2128 85108313 85107046 0.000000e+00 1483.0
2 TraesCS3B01G118500 chr3B 91.317 1048 60 13 1230 2267 85453857 85454883 0.000000e+00 1402.0
3 TraesCS3B01G118500 chr3B 81.144 1119 161 35 1023 2127 207738781 207739863 0.000000e+00 852.0
4 TraesCS3B01G118500 chr3B 80.323 1052 167 27 1020 2063 205775416 205776435 0.000000e+00 760.0
5 TraesCS3B01G118500 chr3B 84.892 556 59 15 3559 4109 85470546 85471081 5.620000e-149 538.0
6 TraesCS3B01G118500 chr3B 95.439 285 11 2 4192 4475 85216373 85216090 2.090000e-123 453.0
7 TraesCS3B01G118500 chr3B 86.260 393 37 7 3082 3474 85470015 85470390 1.280000e-110 411.0
8 TraesCS3B01G118500 chr3B 84.469 367 46 4 850 1216 86134272 86134627 7.850000e-93 351.0
9 TraesCS3B01G118500 chr3B 81.714 350 22 18 829 1174 85453545 85453856 2.280000e-63 254.0
10 TraesCS3B01G118500 chr3B 77.612 469 61 30 2377 2831 85106639 85106201 1.370000e-60 244.0
11 TraesCS3B01G118500 chr3B 92.593 162 5 4 2672 2831 85469507 85469663 4.970000e-55 226.0
12 TraesCS3B01G118500 chr3B 87.912 182 18 3 2834 3014 85469807 85469985 1.390000e-50 211.0
13 TraesCS3B01G118500 chr3B 86.957 115 7 2 3448 3555 85470391 85470504 6.700000e-24 122.0
14 TraesCS3B01G118500 chr3B 87.037 108 10 3 584 689 85453355 85453460 8.670000e-23 119.0
15 TraesCS3B01G118500 chr3D 89.888 1345 88 22 578 1913 55577011 55578316 0.000000e+00 1687.0
16 TraesCS3B01G118500 chr3D 87.696 1276 129 20 867 2128 55742077 55743338 0.000000e+00 1461.0
17 TraesCS3B01G118500 chr3D 88.516 1193 116 16 945 2128 55085009 55083829 0.000000e+00 1424.0
18 TraesCS3B01G118500 chr3D 88.581 613 50 8 3583 4195 55672681 55673273 0.000000e+00 726.0
19 TraesCS3B01G118500 chr3D 87.923 414 26 9 2062 2467 55646617 55647014 2.690000e-127 466.0
20 TraesCS3B01G118500 chr3D 84.421 475 51 11 3084 3556 55672170 55672623 3.500000e-121 446.0
21 TraesCS3B01G118500 chr3D 92.469 239 17 1 2 239 55344669 55344431 1.700000e-89 340.0
22 TraesCS3B01G118500 chr3D 89.286 252 23 4 2830 3080 55664867 55665115 3.710000e-81 313.0
23 TraesCS3B01G118500 chr3D 84.026 313 23 12 2528 2824 55647042 55647343 4.860000e-70 276.0
24 TraesCS3B01G118500 chr3D 82.317 328 29 8 2291 2604 55665149 55665461 1.760000e-64 257.0
25 TraesCS3B01G118500 chr3D 81.588 277 30 11 2377 2633 55083538 55083263 5.000000e-50 209.0
26 TraesCS3B01G118500 chr3D 80.973 226 37 5 2 223 46622554 46622777 1.820000e-39 174.0
27 TraesCS3B01G118500 chr3D 90.090 111 9 2 444 554 55344130 55344022 5.140000e-30 143.0
28 TraesCS3B01G118500 chr3D 91.509 106 6 1 2531 2633 55743747 55743852 5.140000e-30 143.0
29 TraesCS3B01G118500 chr3D 85.263 95 9 2 4034 4124 55745792 55745885 5.250000e-15 93.5
30 TraesCS3B01G118500 chr3D 98.039 51 1 0 4037 4087 55079765 55079715 6.800000e-14 89.8
31 TraesCS3B01G118500 chr3A 87.343 1272 132 23 868 2128 65480887 65479634 0.000000e+00 1430.0
32 TraesCS3B01G118500 chr3A 91.667 684 34 11 4270 4930 535725023 535724340 0.000000e+00 926.0
33 TraesCS3B01G118500 chr3A 81.081 1110 165 29 1020 2120 164610963 164612036 0.000000e+00 845.0
34 TraesCS3B01G118500 chr3A 81.836 1035 156 25 1107 2128 164614502 164615517 0.000000e+00 841.0
35 TraesCS3B01G118500 chr3A 89.627 241 19 5 3 239 65774686 65774924 8.020000e-78 302.0
36 TraesCS3B01G118500 chr3A 87.179 273 22 7 2837 3106 65537076 65536814 1.040000e-76 298.0
37 TraesCS3B01G118500 chr3A 82.759 290 42 6 3559 3840 65478130 65477841 8.190000e-63 252.0
38 TraesCS3B01G118500 chr3A 85.169 236 24 5 3327 3556 65499747 65499517 1.070000e-56 231.0
39 TraesCS3B01G118500 chr1B 96.199 684 25 1 4246 4929 1283807 1284489 0.000000e+00 1118.0
40 TraesCS3B01G118500 chr1B 93.213 221 14 1 4246 4466 1288696 1288915 1.710000e-84 324.0
41 TraesCS3B01G118500 chr1B 92.308 221 16 1 4246 4466 1315621 1315840 3.710000e-81 313.0
42 TraesCS3B01G118500 chr1B 84.314 204 21 7 2528 2727 292206195 292205999 6.510000e-44 189.0
43 TraesCS3B01G118500 chr1B 92.771 83 6 0 4246 4328 1310750 1310832 2.410000e-23 121.0
44 TraesCS3B01G118500 chr1B 83.636 110 18 0 974 1083 98461745 98461636 2.430000e-18 104.0
45 TraesCS3B01G118500 chr7B 95.940 665 27 0 4265 4929 504402478 504401814 0.000000e+00 1079.0
46 TraesCS3B01G118500 chr2B 91.155 701 42 9 4244 4928 707628622 707627926 0.000000e+00 933.0
47 TraesCS3B01G118500 chr2B 90.612 703 41 15 4252 4930 10807263 10807964 0.000000e+00 909.0
48 TraesCS3B01G118500 chr5B 90.909 704 39 15 4252 4930 70570952 70570249 0.000000e+00 922.0
49 TraesCS3B01G118500 chr5B 87.097 248 25 6 4226 4467 180874580 180874334 1.750000e-69 274.0
50 TraesCS3B01G118500 chr5B 85.714 259 27 7 4215 4463 180891160 180890902 1.050000e-66 265.0
51 TraesCS3B01G118500 chr5B 91.071 56 5 0 97 152 278042717 278042662 5.290000e-10 76.8
52 TraesCS3B01G118500 chr1A 90.741 702 41 15 4252 4930 584854575 584853875 0.000000e+00 915.0
53 TraesCS3B01G118500 chr1A 83.117 154 14 6 2540 2687 481143534 481143681 4.000000e-26 130.0
54 TraesCS3B01G118500 chr4A 88.939 660 50 14 4278 4930 19585205 19585848 0.000000e+00 793.0
55 TraesCS3B01G118500 chr2A 95.688 487 21 0 4444 4930 736303173 736302687 0.000000e+00 784.0
56 TraesCS3B01G118500 chr6A 85.185 162 12 5 2528 2685 337993571 337993724 6.610000e-34 156.0
57 TraesCS3B01G118500 chr7A 87.037 108 6 3 2531 2633 151360443 151360547 1.120000e-21 115.0


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 TraesCS3B01G118500 chr3B 85220621 85225550 4929 True 9105.000000 9105 100.000000 1 4930 1 chr3B.!!$R2 4929
1 TraesCS3B01G118500 chr3B 85106201 85108313 2112 True 863.500000 1483 82.761000 861 2831 2 chr3B.!!$R3 1970
2 TraesCS3B01G118500 chr3B 207738781 207739863 1082 False 852.000000 852 81.144000 1023 2127 1 chr3B.!!$F3 1104
3 TraesCS3B01G118500 chr3B 205775416 205776435 1019 False 760.000000 760 80.323000 1020 2063 1 chr3B.!!$F2 1043
4 TraesCS3B01G118500 chr3B 85453355 85454883 1528 False 591.666667 1402 86.689333 584 2267 3 chr3B.!!$F4 1683
5 TraesCS3B01G118500 chr3B 85469507 85471081 1574 False 301.600000 538 87.722800 2672 4109 5 chr3B.!!$F5 1437
6 TraesCS3B01G118500 chr3D 55577011 55578316 1305 False 1687.000000 1687 89.888000 578 1913 1 chr3D.!!$F2 1335
7 TraesCS3B01G118500 chr3D 55672170 55673273 1103 False 586.000000 726 86.501000 3084 4195 2 chr3D.!!$F5 1111
8 TraesCS3B01G118500 chr3D 55079715 55085009 5294 True 574.266667 1424 89.381000 945 4087 3 chr3D.!!$R1 3142
9 TraesCS3B01G118500 chr3D 55742077 55745885 3808 False 565.833333 1461 88.156000 867 4124 3 chr3D.!!$F6 3257
10 TraesCS3B01G118500 chr3D 55646617 55647343 726 False 371.000000 466 85.974500 2062 2824 2 chr3D.!!$F3 762
11 TraesCS3B01G118500 chr3D 55664867 55665461 594 False 285.000000 313 85.801500 2291 3080 2 chr3D.!!$F4 789
12 TraesCS3B01G118500 chr3D 55344022 55344669 647 True 241.500000 340 91.279500 2 554 2 chr3D.!!$R2 552
13 TraesCS3B01G118500 chr3A 535724340 535725023 683 True 926.000000 926 91.667000 4270 4930 1 chr3A.!!$R3 660
14 TraesCS3B01G118500 chr3A 164610963 164615517 4554 False 843.000000 845 81.458500 1020 2128 2 chr3A.!!$F2 1108
15 TraesCS3B01G118500 chr3A 65477841 65480887 3046 True 841.000000 1430 85.051000 868 3840 2 chr3A.!!$R4 2972
16 TraesCS3B01G118500 chr1B 1283807 1284489 682 False 1118.000000 1118 96.199000 4246 4929 1 chr1B.!!$F1 683
17 TraesCS3B01G118500 chr7B 504401814 504402478 664 True 1079.000000 1079 95.940000 4265 4929 1 chr7B.!!$R1 664
18 TraesCS3B01G118500 chr2B 707627926 707628622 696 True 933.000000 933 91.155000 4244 4928 1 chr2B.!!$R1 684
19 TraesCS3B01G118500 chr2B 10807263 10807964 701 False 909.000000 909 90.612000 4252 4930 1 chr2B.!!$F1 678
20 TraesCS3B01G118500 chr5B 70570249 70570952 703 True 922.000000 922 90.909000 4252 4930 1 chr5B.!!$R1 678
21 TraesCS3B01G118500 chr1A 584853875 584854575 700 True 915.000000 915 90.741000 4252 4930 1 chr1A.!!$R1 678
22 TraesCS3B01G118500 chr4A 19585205 19585848 643 False 793.000000 793 88.939000 4278 4930 1 chr4A.!!$F1 652

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
645 744 0.312102 GTCCAACTGCTTTCTGTGCC 59.688 55.0 0.00 0.0 0.00 5.01 F
2213 5841 0.597568 TGGAAATGCTGCGTTTCTGG 59.402 50.0 33.69 0.0 38.82 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 5844 0.324943 GGACTGTTAGCCCTTCTGCA 59.675 55.0 0.0 0.0 0.0 4.41 R
4145 10643 0.537653 GAGCCTCCTACAAGTGGTCC 59.462 60.0 0.0 0.0 0.0 4.46 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
39 40 8.522542 AGGGCATTGGTATAACGTAAAATAAA 57.477 30.769 0.00 0.00 0.00 1.40
40 41 9.138596 AGGGCATTGGTATAACGTAAAATAAAT 57.861 29.630 0.00 0.00 0.00 1.40
87 88 5.063880 ACCATGGACAAAACTTGTACTCTC 58.936 41.667 21.47 0.00 45.00 3.20
88 89 4.455877 CCATGGACAAAACTTGTACTCTCC 59.544 45.833 5.56 0.00 45.00 3.71
108 109 2.095059 CCCATAGTGTGCAAGAACAAGC 60.095 50.000 0.00 0.00 0.00 4.01
116 117 3.872182 TGTGCAAGAACAAGCGTAAACTA 59.128 39.130 0.00 0.00 0.00 2.24
119 120 4.025229 TGCAAGAACAAGCGTAAACTAGTG 60.025 41.667 0.00 0.00 0.00 2.74
223 225 2.967362 ACGATTGCAGTATCAAACCGA 58.033 42.857 0.00 0.00 0.00 4.69
225 227 4.689071 ACGATTGCAGTATCAAACCGATA 58.311 39.130 0.00 0.00 35.39 2.92
251 293 1.004628 TGCACAACTATCAGCATGGGT 59.995 47.619 0.00 0.00 36.16 4.51
314 358 3.641437 TTTTCAGGAAACGAAGCCATG 57.359 42.857 0.00 0.00 0.00 3.66
334 378 9.646522 AGCCATGTAGAAACATAAAAGGATTAT 57.353 29.630 0.00 0.00 44.70 1.28
485 584 8.682936 ACTTGGTAATCTTCCATATCATGAAC 57.317 34.615 0.00 0.00 34.75 3.18
554 653 8.630278 AGTGCAACATTAGTAATTACTACGAG 57.370 34.615 22.22 16.87 41.43 4.18
555 654 8.248945 AGTGCAACATTAGTAATTACTACGAGT 58.751 33.333 22.22 17.40 41.43 4.18
556 655 9.507280 GTGCAACATTAGTAATTACTACGAGTA 57.493 33.333 22.22 10.01 36.15 2.59
597 696 1.069636 CAACAGAAAAGAGCTGGCGAC 60.070 52.381 0.00 0.00 37.69 5.19
603 702 2.859273 AAAGAGCTGGCGACCGGATG 62.859 60.000 9.46 0.00 29.82 3.51
611 710 0.672401 GGCGACCGGATGAAAACAGA 60.672 55.000 9.46 0.00 0.00 3.41
612 711 0.442699 GCGACCGGATGAAAACAGAC 59.557 55.000 9.46 0.00 0.00 3.51
645 744 0.312102 GTCCAACTGCTTTCTGTGCC 59.688 55.000 0.00 0.00 0.00 5.01
652 753 2.979676 CTTTCTGTGCCGCAGCCA 60.980 61.111 0.00 0.00 44.66 4.75
689 794 2.179204 ACCCAAAAGCCTCCCTACTTTT 59.821 45.455 0.00 0.00 44.72 2.27
695 800 4.592997 AAGCCTCCCTACTTTTTATGCT 57.407 40.909 0.00 0.00 0.00 3.79
697 802 2.359214 GCCTCCCTACTTTTTATGCTGC 59.641 50.000 0.00 0.00 0.00 5.25
699 804 3.372025 CCTCCCTACTTTTTATGCTGCCT 60.372 47.826 0.00 0.00 0.00 4.75
700 805 3.879892 CTCCCTACTTTTTATGCTGCCTC 59.120 47.826 0.00 0.00 0.00 4.70
701 806 2.952310 CCCTACTTTTTATGCTGCCTCC 59.048 50.000 0.00 0.00 0.00 4.30
703 808 2.907458 ACTTTTTATGCTGCCTCCCT 57.093 45.000 0.00 0.00 0.00 4.20
705 810 1.135721 CTTTTTATGCTGCCTCCCTGC 59.864 52.381 0.00 0.00 38.72 4.85
707 812 2.572333 TTTATGCTGCCTCCCTGCCC 62.572 60.000 0.00 0.00 37.58 5.36
732 837 3.499737 CGGAGCCGTGCCAACATC 61.500 66.667 0.00 0.00 34.35 3.06
805 911 1.584495 CATCGTCTCACCGTCACCA 59.416 57.895 0.00 0.00 0.00 4.17
806 912 0.732880 CATCGTCTCACCGTCACCAC 60.733 60.000 0.00 0.00 0.00 4.16
807 913 1.874345 ATCGTCTCACCGTCACCACC 61.874 60.000 0.00 0.00 0.00 4.61
808 914 2.852180 CGTCTCACCGTCACCACCA 61.852 63.158 0.00 0.00 0.00 4.17
817 923 1.224069 CGTCACCACCAGTTGAGCAG 61.224 60.000 0.00 0.00 0.00 4.24
820 926 0.886490 CACCACCAGTTGAGCAGGAC 60.886 60.000 0.00 0.00 0.00 3.85
822 928 1.451504 CACCAGTTGAGCAGGACCA 59.548 57.895 0.00 0.00 0.00 4.02
823 929 0.604780 CACCAGTTGAGCAGGACCAG 60.605 60.000 0.00 0.00 0.00 4.00
824 930 1.002868 CCAGTTGAGCAGGACCAGG 60.003 63.158 0.00 0.00 0.00 4.45
825 931 1.673665 CAGTTGAGCAGGACCAGGC 60.674 63.158 0.00 0.00 0.00 4.85
826 932 2.360475 GTTGAGCAGGACCAGGCC 60.360 66.667 0.00 0.00 0.00 5.19
827 933 4.020617 TTGAGCAGGACCAGGCCG 62.021 66.667 0.00 0.00 0.00 6.13
834 940 4.410400 GGACCAGGCCGGGTTCAG 62.410 72.222 29.27 1.32 42.53 3.02
846 952 4.717313 GTTCAGTCCACCCGGCCC 62.717 72.222 0.00 0.00 0.00 5.80
847 953 4.974438 TTCAGTCCACCCGGCCCT 62.974 66.667 0.00 0.00 0.00 5.19
894 1000 1.020861 GCCACCGTAAAACCCTACCG 61.021 60.000 0.00 0.00 0.00 4.02
1124 1245 3.132139 CGCCGACTTCTCCCTCGA 61.132 66.667 0.00 0.00 31.24 4.04
1536 1660 1.194781 GGGAGTGGGTCAGCAAGAGA 61.195 60.000 0.00 0.00 0.00 3.10
1683 1807 3.637273 ACCCGTGTCAAGCTCCCC 61.637 66.667 0.00 0.00 0.00 4.81
1789 1916 1.004785 CGTCGACATGTACCGCAACA 61.005 55.000 17.16 0.00 0.00 3.33
1869 1996 3.681835 ACCGAGTGGACGCTGGAC 61.682 66.667 7.88 0.00 39.21 4.02
2074 5676 3.958147 CTGGTTGATGAGCCGCCGT 62.958 63.158 0.00 0.00 0.00 5.68
2202 5830 3.938963 TCCTCGTTAGTGATTGGAAATGC 59.061 43.478 0.00 0.00 0.00 3.56
2213 5841 0.597568 TGGAAATGCTGCGTTTCTGG 59.402 50.000 33.69 0.00 38.82 3.86
2214 5842 0.881118 GGAAATGCTGCGTTTCTGGA 59.119 50.000 33.69 1.14 38.82 3.86
2215 5843 1.269448 GGAAATGCTGCGTTTCTGGAA 59.731 47.619 33.69 0.43 38.82 3.53
2216 5844 2.094545 GGAAATGCTGCGTTTCTGGAAT 60.095 45.455 33.69 9.37 38.82 3.01
2217 5845 2.642139 AATGCTGCGTTTCTGGAATG 57.358 45.000 0.24 0.00 0.00 2.67
2234 5872 2.409948 ATGCAGAAGGGCTAACAGTC 57.590 50.000 0.00 0.00 34.04 3.51
2315 6005 3.264947 TGTTGATGCTGCAGCTAGTAAG 58.735 45.455 36.61 0.00 42.66 2.34
2333 6023 9.303537 GCTAGTAAGTTACTCCTGTTTGATTAG 57.696 37.037 18.77 7.59 40.14 1.73
2355 6045 6.477053 AGCTACATGATCTTATCTGTGTGT 57.523 37.500 0.00 0.00 33.31 3.72
2361 6056 6.537660 ACATGATCTTATCTGTGTGTGATGTG 59.462 38.462 0.00 0.00 31.18 3.21
2412 6206 7.488187 ACAAGATCTGATGCACATTATGTAC 57.512 36.000 0.00 0.00 0.00 2.90
2445 6243 3.634397 TGCCTAAGCATATGCCCTATC 57.366 47.619 23.96 11.32 46.52 2.08
2474 6272 9.480538 CATTTTTATGCTTAAATTGATGTGTGC 57.519 29.630 5.70 0.00 0.00 4.57
2483 6281 7.010738 GCTTAAATTGATGTGTGCATATGCTTT 59.989 33.333 27.13 17.34 42.66 3.51
2632 6466 3.709653 CTGTATTCAACACTAGCCCCCTA 59.290 47.826 0.00 0.00 33.45 3.53
2635 6469 6.088819 TGTATTCAACACTAGCCCCCTATAT 58.911 40.000 0.00 0.00 31.43 0.86
2637 6471 7.904564 TGTATTCAACACTAGCCCCCTATATAT 59.095 37.037 0.00 0.00 31.43 0.86
2638 6472 9.430399 GTATTCAACACTAGCCCCCTATATATA 57.570 37.037 0.00 0.00 0.00 0.86
2639 6473 7.729124 TTCAACACTAGCCCCCTATATATAC 57.271 40.000 0.00 0.00 0.00 1.47
2640 6474 6.807286 TCAACACTAGCCCCCTATATATACA 58.193 40.000 0.00 0.00 0.00 2.29
2641 6475 6.666546 TCAACACTAGCCCCCTATATATACAC 59.333 42.308 0.00 0.00 0.00 2.90
2642 6476 5.526434 ACACTAGCCCCCTATATATACACC 58.474 45.833 0.00 0.00 0.00 4.16
2643 6477 4.583489 CACTAGCCCCCTATATATACACCG 59.417 50.000 0.00 0.00 0.00 4.94
2644 6478 3.771071 AGCCCCCTATATATACACCGT 57.229 47.619 0.00 0.00 0.00 4.83
2645 6479 4.886755 AGCCCCCTATATATACACCGTA 57.113 45.455 0.00 0.00 0.00 4.02
2646 6480 5.211078 AGCCCCCTATATATACACCGTAA 57.789 43.478 0.00 0.00 0.00 3.18
2673 6510 0.825410 TGGCATGGGCATGTGAATTC 59.175 50.000 0.00 0.00 43.71 2.17
2744 6599 1.482593 CTTACTGCCCCGATGTTCTCT 59.517 52.381 0.00 0.00 0.00 3.10
2745 6600 1.568504 TACTGCCCCGATGTTCTCTT 58.431 50.000 0.00 0.00 0.00 2.85
2746 6601 0.250513 ACTGCCCCGATGTTCTCTTC 59.749 55.000 0.00 0.00 0.00 2.87
2747 6602 0.539051 CTGCCCCGATGTTCTCTTCT 59.461 55.000 0.00 0.00 0.00 2.85
2748 6603 0.537188 TGCCCCGATGTTCTCTTCTC 59.463 55.000 0.00 0.00 0.00 2.87
2824 6682 0.254178 AGATGCATGGGTCTGACACC 59.746 55.000 2.46 7.88 45.97 4.16
2831 6689 0.485543 TGGGTCTGACACCTCCAGTA 59.514 55.000 7.72 0.00 45.95 2.74
2863 8580 0.819259 TGTGCCTCCTTGAGTTGTGC 60.819 55.000 0.00 0.00 0.00 4.57
2969 8754 7.575505 TCTCTCTTACTTGTACCTAGTATGCT 58.424 38.462 5.96 0.00 0.00 3.79
2973 8758 8.991783 TCTTACTTGTACCTAGTATGCTGTAT 57.008 34.615 5.96 0.00 0.00 2.29
3008 8805 6.636447 TCATGTGCTTTTATGTTTTCAAGACG 59.364 34.615 0.00 0.00 0.00 4.18
3014 8811 6.237701 GCTTTTATGTTTTCAAGACGTGCAAA 60.238 34.615 0.00 0.00 0.00 3.68
3015 8812 7.516627 GCTTTTATGTTTTCAAGACGTGCAAAT 60.517 33.333 0.00 0.00 0.00 2.32
3016 8813 8.858003 TTTTATGTTTTCAAGACGTGCAAATA 57.142 26.923 0.00 0.00 0.00 1.40
3018 8815 6.932901 ATGTTTTCAAGACGTGCAAATATG 57.067 33.333 0.00 0.00 26.47 1.78
3042 8839 9.845740 ATGCATAATAGTAGGTGATTTGTTACA 57.154 29.630 0.00 0.00 0.00 2.41
3043 8840 9.325198 TGCATAATAGTAGGTGATTTGTTACAG 57.675 33.333 0.00 0.00 0.00 2.74
3044 8841 9.326413 GCATAATAGTAGGTGATTTGTTACAGT 57.674 33.333 0.00 0.00 0.00 3.55
3048 8845 6.420913 AGTAGGTGATTTGTTACAGTGAGT 57.579 37.500 0.00 0.00 0.00 3.41
3049 8846 6.827727 AGTAGGTGATTTGTTACAGTGAGTT 58.172 36.000 0.00 0.00 0.00 3.01
3050 8847 7.280356 AGTAGGTGATTTGTTACAGTGAGTTT 58.720 34.615 0.00 0.00 0.00 2.66
3051 8848 7.773690 AGTAGGTGATTTGTTACAGTGAGTTTT 59.226 33.333 0.00 0.00 0.00 2.43
3056 8853 9.301153 GTGATTTGTTACAGTGAGTTTTCAAAT 57.699 29.630 0.00 5.37 36.85 2.32
3063 8860 8.690840 GTTACAGTGAGTTTTCAAATTATGCAC 58.309 33.333 0.00 0.00 34.49 4.57
3080 8877 4.811555 TGCACAATGAGTCAGTTGTTAC 57.188 40.909 14.45 11.54 36.48 2.50
3081 8878 4.450976 TGCACAATGAGTCAGTTGTTACT 58.549 39.130 14.45 0.00 36.48 2.24
3139 8936 8.995027 ATTCAGTTGGATTGCCATTAAGTATA 57.005 30.769 0.00 0.00 45.46 1.47
3166 8990 8.359642 CCTTTTGTGGTTTCATTCAGAAGATTA 58.640 33.333 0.00 0.00 37.57 1.75
3183 9007 4.056740 AGATTATCTGATGCGCTTCACTG 58.943 43.478 20.86 13.01 0.00 3.66
3189 9015 2.270923 TGATGCGCTTCACTGTGTATC 58.729 47.619 20.86 6.03 39.09 2.24
3204 9030 8.764287 TCACTGTGTATCTATATGCAAATTTCG 58.236 33.333 7.79 0.00 28.83 3.46
3276 9102 4.660789 AATTATCAGAATGCTTGTGCCC 57.339 40.909 0.00 0.00 38.71 5.36
3278 9104 0.333993 ATCAGAATGCTTGTGCCCCT 59.666 50.000 0.00 0.00 38.71 4.79
3279 9105 0.609957 TCAGAATGCTTGTGCCCCTG 60.610 55.000 0.00 0.00 38.71 4.45
3280 9106 0.896940 CAGAATGCTTGTGCCCCTGT 60.897 55.000 0.00 0.00 38.71 4.00
3283 9109 0.469705 AATGCTTGTGCCCCTGTTCA 60.470 50.000 0.00 0.00 38.71 3.18
3311 9143 4.662468 TTGTTTGCCTTCAGTTTGCATA 57.338 36.364 0.00 0.00 34.51 3.14
3318 9150 3.928375 GCCTTCAGTTTGCATATTTGTGG 59.072 43.478 0.00 0.00 0.00 4.17
3327 9159 2.421775 TGCATATTTGTGGCAACGGTAG 59.578 45.455 0.00 0.00 42.51 3.18
3328 9160 2.223479 GCATATTTGTGGCAACGGTAGG 60.223 50.000 0.00 0.00 42.51 3.18
3329 9161 2.863132 TATTTGTGGCAACGGTAGGT 57.137 45.000 0.00 0.00 42.51 3.08
3330 9162 2.863132 ATTTGTGGCAACGGTAGGTA 57.137 45.000 0.00 0.00 42.51 3.08
3332 9164 3.977134 TTTGTGGCAACGGTAGGTATA 57.023 42.857 0.00 0.00 42.51 1.47
3334 9166 4.490899 TTGTGGCAACGGTAGGTATATT 57.509 40.909 0.00 0.00 42.51 1.28
3335 9167 3.799366 TGTGGCAACGGTAGGTATATTG 58.201 45.455 0.00 0.00 42.51 1.90
3336 9168 2.546789 GTGGCAACGGTAGGTATATTGC 59.453 50.000 0.00 0.00 43.88 3.56
3338 9170 2.841215 GCAACGGTAGGTATATTGCCA 58.159 47.619 0.00 0.00 39.78 4.92
3339 9171 3.207778 GCAACGGTAGGTATATTGCCAA 58.792 45.455 0.00 0.00 39.78 4.52
3340 9172 3.002965 GCAACGGTAGGTATATTGCCAAC 59.997 47.826 0.00 0.00 39.78 3.77
3387 9219 8.079809 GCTAAATTAGTCTCCTAGCTACTTCAG 58.920 40.741 1.68 0.00 33.68 3.02
3518 9384 2.485479 GGTTCTGCAAAGGAGACAGTCA 60.485 50.000 2.66 0.00 33.12 3.41
3556 9441 7.548097 TCTGTACGATTATCTGAAAAGAAGCT 58.452 34.615 0.00 0.00 0.00 3.74
3557 9442 8.035394 TCTGTACGATTATCTGAAAAGAAGCTT 58.965 33.333 0.00 0.00 0.00 3.74
3573 9510 0.598065 GCTTCAGGTGACGCCAATTT 59.402 50.000 7.99 0.00 40.61 1.82
3586 9714 3.753842 CGCCAATTTAGTTGTATGCGTT 58.246 40.909 0.00 0.00 39.53 4.84
3684 9820 7.367828 TCAGGTAGGGGAAGTAATACTACATT 58.632 38.462 0.00 0.00 36.60 2.71
3717 9853 1.354040 GTTCTGATGCTGAGTGACCG 58.646 55.000 0.00 0.00 0.00 4.79
3755 9892 2.476185 GGCTGAAATGTTTCGGTGATCG 60.476 50.000 14.01 0.00 43.74 3.69
3770 9908 3.003275 GGTGATCGCTGTTTTGTTGAGAA 59.997 43.478 6.18 0.00 0.00 2.87
3774 9914 4.273005 TCGCTGTTTTGTTGAGAAGTTC 57.727 40.909 0.00 0.00 0.00 3.01
3781 9921 7.011109 GCTGTTTTGTTGAGAAGTTCAGTACTA 59.989 37.037 5.50 0.00 37.07 1.82
3783 9923 8.255206 TGTTTTGTTGAGAAGTTCAGTACTAGA 58.745 33.333 5.50 0.00 37.07 2.43
3855 10003 3.274288 CTGAAGGCAGTATTCCAGTTCC 58.726 50.000 0.00 0.00 37.37 3.62
3856 10004 2.642311 TGAAGGCAGTATTCCAGTTCCA 59.358 45.455 0.00 0.00 0.00 3.53
3930 10113 8.974060 TGTTTCTATCTCCTGTTAACTTTGTT 57.026 30.769 7.22 0.00 0.00 2.83
3943 10126 3.208747 ACTTTGTTGATCCGTCAGGTT 57.791 42.857 0.00 0.00 39.05 3.50
4001 10263 3.062639 CCGAAAATTCATCCGAGTCTGTG 59.937 47.826 0.00 0.00 0.00 3.66
4086 10584 1.811266 TGATTTCTGCCGAGCGAGC 60.811 57.895 0.00 0.00 0.00 5.03
4137 10635 9.791820 TGCAACTTAGTTTCCTTTAAGTTTTAC 57.208 29.630 0.00 2.47 43.79 2.01
4145 10643 8.347771 AGTTTCCTTTAAGTTTTACTTTAGCCG 58.652 33.333 0.00 0.00 39.51 5.52
4162 10660 1.218316 CGGACCACTTGTAGGAGGC 59.782 63.158 0.00 0.00 0.00 4.70
4195 10693 2.632377 CACTATCAACATGCCGAGGTT 58.368 47.619 0.00 0.00 0.00 3.50
4196 10694 2.352651 CACTATCAACATGCCGAGGTTG 59.647 50.000 0.00 0.00 43.73 3.77
4197 10695 2.027192 ACTATCAACATGCCGAGGTTGT 60.027 45.455 0.00 0.00 43.04 3.32
4198 10696 1.909700 ATCAACATGCCGAGGTTGTT 58.090 45.000 0.00 6.73 43.04 2.83
4199 10697 2.552599 TCAACATGCCGAGGTTGTTA 57.447 45.000 10.64 1.45 43.04 2.41
4200 10698 2.852449 TCAACATGCCGAGGTTGTTAA 58.148 42.857 10.64 0.00 43.04 2.01
4201 10699 3.215151 TCAACATGCCGAGGTTGTTAAA 58.785 40.909 10.64 3.01 43.04 1.52
4202 10700 3.823873 TCAACATGCCGAGGTTGTTAAAT 59.176 39.130 10.64 0.00 43.04 1.40
4203 10701 5.004448 TCAACATGCCGAGGTTGTTAAATA 58.996 37.500 10.64 0.00 43.04 1.40
4204 10702 4.957759 ACATGCCGAGGTTGTTAAATAC 57.042 40.909 0.00 0.00 0.00 1.89
4205 10703 4.328536 ACATGCCGAGGTTGTTAAATACA 58.671 39.130 0.00 0.00 34.12 2.29
4206 10704 4.762765 ACATGCCGAGGTTGTTAAATACAA 59.237 37.500 0.00 0.00 44.31 2.41
4219 10717 7.865875 TGTTAAATACAACATTGCATGTCAC 57.134 32.000 0.00 0.00 44.07 3.67
4220 10718 6.580416 TGTTAAATACAACATTGCATGTCACG 59.420 34.615 0.00 0.00 44.07 4.35
4221 10719 5.369685 AAATACAACATTGCATGTCACGA 57.630 34.783 0.00 0.00 44.07 4.35
4222 10720 5.565592 AATACAACATTGCATGTCACGAT 57.434 34.783 0.00 0.00 44.07 3.73
4223 10721 3.476295 ACAACATTGCATGTCACGATC 57.524 42.857 0.00 0.00 44.07 3.69
4224 10722 2.162208 ACAACATTGCATGTCACGATCC 59.838 45.455 0.00 0.00 44.07 3.36
4225 10723 1.382522 ACATTGCATGTCACGATCCC 58.617 50.000 0.00 0.00 39.92 3.85
4226 10724 1.339920 ACATTGCATGTCACGATCCCA 60.340 47.619 0.00 0.00 39.92 4.37
4227 10725 1.744522 CATTGCATGTCACGATCCCAA 59.255 47.619 0.00 0.00 0.00 4.12
4228 10726 1.164411 TTGCATGTCACGATCCCAAC 58.836 50.000 0.00 0.00 0.00 3.77
4229 10727 0.676466 TGCATGTCACGATCCCAACC 60.676 55.000 0.00 0.00 0.00 3.77
4230 10728 0.676466 GCATGTCACGATCCCAACCA 60.676 55.000 0.00 0.00 0.00 3.67
4231 10729 1.372582 CATGTCACGATCCCAACCAG 58.627 55.000 0.00 0.00 0.00 4.00
4232 10730 1.066215 CATGTCACGATCCCAACCAGA 60.066 52.381 0.00 0.00 0.00 3.86
4233 10731 1.052617 TGTCACGATCCCAACCAGAA 58.947 50.000 0.00 0.00 0.00 3.02
4234 10732 1.001974 TGTCACGATCCCAACCAGAAG 59.998 52.381 0.00 0.00 0.00 2.85
4235 10733 0.613260 TCACGATCCCAACCAGAAGG 59.387 55.000 0.00 0.00 42.21 3.46
4298 10799 9.435570 AGGTTTAGAGATAGATTTGGCTAGTAA 57.564 33.333 0.00 0.00 0.00 2.24
4394 10923 5.977725 TCCTGATTCTTTGTATCGATCGTTC 59.022 40.000 15.94 7.42 0.00 3.95
4504 11039 3.370527 CCTTTTCCCATCCGAAGCTTCTA 60.371 47.826 23.50 12.33 0.00 2.10
4843 11379 3.608662 GACCACGGTCACCACGGA 61.609 66.667 11.43 0.00 44.02 4.69
4888 11424 1.291877 GCCATGTTCTCGTCGCACTT 61.292 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.505625 GGTTCGGAAGTGTACATGTTTTATTTA 58.494 33.333 2.30 0.00 0.00 1.40
44 45 5.366460 TGGTTCGGAAGTGTACATGTTTTA 58.634 37.500 2.30 0.00 0.00 1.52
50 51 2.569853 TCCATGGTTCGGAAGTGTACAT 59.430 45.455 12.58 0.00 0.00 2.29
87 88 2.095059 GCTTGTTCTTGCACACTATGGG 60.095 50.000 0.00 0.00 0.00 4.00
88 89 2.413239 CGCTTGTTCTTGCACACTATGG 60.413 50.000 0.00 0.00 0.00 2.74
223 225 3.434641 GCTGATAGTTGTGCATGCGATAT 59.565 43.478 14.09 6.44 0.00 1.63
225 227 1.600957 GCTGATAGTTGTGCATGCGAT 59.399 47.619 14.09 0.00 0.00 4.58
300 344 3.500680 TGTTTCTACATGGCTTCGTTTCC 59.499 43.478 0.00 0.00 0.00 3.13
306 350 7.391148 TCCTTTTATGTTTCTACATGGCTTC 57.609 36.000 0.00 0.00 44.56 3.86
460 559 8.274322 TGTTCATGATATGGAAGATTACCAAGT 58.726 33.333 0.00 0.00 40.93 3.16
461 560 8.681486 TGTTCATGATATGGAAGATTACCAAG 57.319 34.615 0.00 0.00 40.93 3.61
463 562 9.473007 TTTTGTTCATGATATGGAAGATTACCA 57.527 29.630 0.00 0.00 41.83 3.25
464 563 9.736023 GTTTTGTTCATGATATGGAAGATTACC 57.264 33.333 0.00 0.00 0.00 2.85
468 567 9.028284 ACAAGTTTTGTTCATGATATGGAAGAT 57.972 29.630 0.00 0.00 42.22 2.40
485 584 8.955061 CACACTATGGAAGAATACAAGTTTTG 57.045 34.615 0.00 0.00 0.00 2.44
505 604 5.506708 AGTTTACACCTTTTCTTCCACACT 58.493 37.500 0.00 0.00 0.00 3.55
511 610 6.613755 TGCACTAGTTTACACCTTTTCTTC 57.386 37.500 0.00 0.00 0.00 2.87
517 616 6.996282 ACTAATGTTGCACTAGTTTACACCTT 59.004 34.615 0.00 0.00 0.00 3.50
519 618 6.796705 ACTAATGTTGCACTAGTTTACACC 57.203 37.500 0.00 0.00 0.00 4.16
564 663 9.036671 GCTCTTTTCTGTTGATAGGAGTATAAC 57.963 37.037 0.00 0.00 32.72 1.89
565 664 8.982723 AGCTCTTTTCTGTTGATAGGAGTATAA 58.017 33.333 0.00 0.00 32.72 0.98
566 665 8.417106 CAGCTCTTTTCTGTTGATAGGAGTATA 58.583 37.037 0.00 0.00 32.72 1.47
567 666 7.271511 CAGCTCTTTTCTGTTGATAGGAGTAT 58.728 38.462 0.00 0.00 32.72 2.12
568 667 6.351371 CCAGCTCTTTTCTGTTGATAGGAGTA 60.351 42.308 0.00 0.00 32.72 2.59
569 668 5.486526 CAGCTCTTTTCTGTTGATAGGAGT 58.513 41.667 0.00 0.00 32.72 3.85
570 669 4.874966 CCAGCTCTTTTCTGTTGATAGGAG 59.125 45.833 0.00 0.00 33.08 3.69
571 670 4.836825 CCAGCTCTTTTCTGTTGATAGGA 58.163 43.478 0.00 0.00 0.00 2.94
572 671 3.376546 GCCAGCTCTTTTCTGTTGATAGG 59.623 47.826 0.00 0.00 0.00 2.57
573 672 3.063180 CGCCAGCTCTTTTCTGTTGATAG 59.937 47.826 0.00 0.00 0.00 2.08
574 673 3.002791 CGCCAGCTCTTTTCTGTTGATA 58.997 45.455 0.00 0.00 0.00 2.15
575 674 1.808945 CGCCAGCTCTTTTCTGTTGAT 59.191 47.619 0.00 0.00 0.00 2.57
576 675 1.202639 TCGCCAGCTCTTTTCTGTTGA 60.203 47.619 0.00 0.00 0.00 3.18
581 680 1.374758 CGGTCGCCAGCTCTTTTCT 60.375 57.895 0.00 0.00 0.00 2.52
597 696 2.289694 ACCAGAGTCTGTTTTCATCCGG 60.290 50.000 18.74 0.00 0.00 5.14
611 710 0.178950 TGGACTGCAGAGACCAGAGT 60.179 55.000 23.35 0.00 38.87 3.24
612 711 0.972134 TTGGACTGCAGAGACCAGAG 59.028 55.000 23.35 0.00 43.65 3.35
662 763 1.574702 GGAGGCTTTTGGGTTCGTCG 61.575 60.000 0.00 0.00 0.00 5.12
689 794 2.597340 GGCAGGGAGGCAGCATAA 59.403 61.111 0.00 0.00 43.51 1.90
715 820 3.499737 GATGTTGGCACGGCTCCG 61.500 66.667 6.79 6.79 46.03 4.63
716 821 3.134127 GGATGTTGGCACGGCTCC 61.134 66.667 0.00 0.00 0.00 4.70
717 822 3.499737 CGGATGTTGGCACGGCTC 61.500 66.667 0.00 0.00 0.00 4.70
718 823 3.329542 ATCGGATGTTGGCACGGCT 62.330 57.895 0.00 0.00 0.00 5.52
719 824 2.823829 GATCGGATGTTGGCACGGC 61.824 63.158 0.00 0.00 0.00 5.68
720 825 2.525248 CGATCGGATGTTGGCACGG 61.525 63.158 7.38 0.00 0.00 4.94
721 826 2.525248 CCGATCGGATGTTGGCACG 61.525 63.158 30.62 0.00 37.50 5.34
722 827 2.823829 GCCGATCGGATGTTGGCAC 61.824 63.158 37.64 12.57 45.06 5.01
723 828 2.513666 GCCGATCGGATGTTGGCA 60.514 61.111 37.64 0.00 45.06 4.92
724 829 2.513666 TGCCGATCGGATGTTGGC 60.514 61.111 37.64 19.80 45.91 4.52
725 830 2.180204 GGTGCCGATCGGATGTTGG 61.180 63.158 37.64 9.71 37.50 3.77
726 831 1.431488 CTGGTGCCGATCGGATGTTG 61.431 60.000 37.64 18.77 37.50 3.33
727 832 1.153369 CTGGTGCCGATCGGATGTT 60.153 57.895 37.64 0.00 37.50 2.71
728 833 2.501128 CTGGTGCCGATCGGATGT 59.499 61.111 37.64 0.00 37.50 3.06
729 834 2.969238 GCTGGTGCCGATCGGATG 60.969 66.667 37.64 20.35 37.50 3.51
730 835 3.157252 AGCTGGTGCCGATCGGAT 61.157 61.111 37.64 4.85 40.80 4.18
731 836 4.147449 CAGCTGGTGCCGATCGGA 62.147 66.667 37.64 19.39 40.80 4.55
781 886 2.577059 GGTGAGACGATGGCCGAA 59.423 61.111 0.00 0.00 41.76 4.30
783 888 4.129737 ACGGTGAGACGATGGCCG 62.130 66.667 0.00 0.00 46.83 6.13
785 890 1.805945 GTGACGGTGAGACGATGGC 60.806 63.158 0.00 0.00 37.61 4.40
786 891 1.153823 GGTGACGGTGAGACGATGG 60.154 63.158 0.00 0.00 37.61 3.51
787 892 0.732880 GTGGTGACGGTGAGACGATG 60.733 60.000 0.00 0.00 37.61 3.84
788 893 1.585006 GTGGTGACGGTGAGACGAT 59.415 57.895 0.00 0.00 37.61 3.73
789 894 2.558286 GGTGGTGACGGTGAGACGA 61.558 63.158 0.00 0.00 37.61 4.20
805 911 1.757306 CTGGTCCTGCTCAACTGGT 59.243 57.895 0.00 0.00 38.49 4.00
806 912 1.002868 CCTGGTCCTGCTCAACTGG 60.003 63.158 0.00 0.00 38.71 4.00
807 913 1.673665 GCCTGGTCCTGCTCAACTG 60.674 63.158 0.00 0.00 0.00 3.16
808 914 2.753029 GCCTGGTCCTGCTCAACT 59.247 61.111 0.00 0.00 0.00 3.16
817 923 4.410400 CTGAACCCGGCCTGGTCC 62.410 72.222 20.36 7.63 37.76 4.46
820 926 4.410400 GGACTGAACCCGGCCTGG 62.410 72.222 12.40 12.40 37.55 4.45
822 928 3.637273 GTGGACTGAACCCGGCCT 61.637 66.667 0.00 0.00 0.00 5.19
823 929 4.717313 GGTGGACTGAACCCGGCC 62.717 72.222 0.00 0.00 0.00 6.13
849 955 4.479993 CAGGCGAGGGAAGGCAGG 62.480 72.222 0.00 0.00 36.55 4.85
926 1034 1.282653 TGGGGAGGTGTGGTGTGAAA 61.283 55.000 0.00 0.00 0.00 2.69
1106 1227 4.856607 CGAGGGAGAAGTCGGCGC 62.857 72.222 0.00 0.00 32.40 6.53
1491 1615 2.878429 GACGAGAAGCGCAGGAGA 59.122 61.111 11.47 0.00 46.04 3.71
1662 1786 1.374758 GAGCTTGACACGGGTGAGG 60.375 63.158 0.00 0.00 0.00 3.86
1728 1852 2.431942 CCGACGCAGCGGTACTTT 60.432 61.111 21.15 0.00 46.07 2.66
2074 5676 2.261671 GGAAGAGACGCCTTCGCA 59.738 61.111 0.00 0.00 42.53 5.10
2202 5830 3.689224 CTGCATTCCAGAAACGCAG 57.311 52.632 16.19 16.19 44.64 5.18
2213 5841 2.680339 GACTGTTAGCCCTTCTGCATTC 59.320 50.000 0.00 0.00 0.00 2.67
2214 5842 2.619074 GGACTGTTAGCCCTTCTGCATT 60.619 50.000 0.00 0.00 0.00 3.56
2215 5843 1.065126 GGACTGTTAGCCCTTCTGCAT 60.065 52.381 0.00 0.00 0.00 3.96
2216 5844 0.324943 GGACTGTTAGCCCTTCTGCA 59.675 55.000 0.00 0.00 0.00 4.41
2217 5845 0.324943 TGGACTGTTAGCCCTTCTGC 59.675 55.000 0.00 0.00 0.00 4.26
2218 5846 1.625818 ACTGGACTGTTAGCCCTTCTG 59.374 52.381 0.00 0.00 0.00 3.02
2219 5847 1.903183 GACTGGACTGTTAGCCCTTCT 59.097 52.381 0.00 0.00 0.00 2.85
2274 5912 6.993308 TCAACAAACACACAAGGTAAGCTATA 59.007 34.615 0.00 0.00 0.00 1.31
2275 5913 5.825679 TCAACAAACACACAAGGTAAGCTAT 59.174 36.000 0.00 0.00 0.00 2.97
2277 5915 4.013728 TCAACAAACACACAAGGTAAGCT 58.986 39.130 0.00 0.00 0.00 3.74
2287 5925 2.121786 CTGCAGCATCAACAAACACAC 58.878 47.619 0.00 0.00 0.00 3.82
2315 6005 7.764443 TCATGTAGCTAATCAAACAGGAGTAAC 59.236 37.037 0.00 0.00 30.11 2.50
2333 6023 6.276091 TCACACACAGATAAGATCATGTAGC 58.724 40.000 0.00 0.00 31.94 3.58
2412 6206 3.006752 TGCTTAGGCAATTTTTGGTGGAG 59.993 43.478 0.00 0.00 46.36 3.86
2474 6272 6.906157 ATGGAAACCCATAGAAAGCATATG 57.094 37.500 0.00 0.00 42.41 1.78
2483 6281 7.638444 TGAGAATACAAATGGAAACCCATAGA 58.362 34.615 0.00 0.00 43.38 1.98
2526 6338 9.289782 ACTAAGCTTTTTGACAGATACAGAAAT 57.710 29.630 3.20 0.00 0.00 2.17
2635 6469 7.820386 CCATGCCATACTTAATTACGGTGTATA 59.180 37.037 0.00 0.00 0.00 1.47
2637 6471 5.992829 CCATGCCATACTTAATTACGGTGTA 59.007 40.000 0.00 0.00 0.00 2.90
2638 6472 4.819630 CCATGCCATACTTAATTACGGTGT 59.180 41.667 0.00 0.00 0.00 4.16
2639 6473 4.215399 CCCATGCCATACTTAATTACGGTG 59.785 45.833 0.00 0.00 0.00 4.94
2640 6474 4.394729 CCCATGCCATACTTAATTACGGT 58.605 43.478 0.00 0.00 0.00 4.83
2641 6475 3.190535 GCCCATGCCATACTTAATTACGG 59.809 47.826 0.00 0.00 0.00 4.02
2642 6476 3.818210 TGCCCATGCCATACTTAATTACG 59.182 43.478 0.00 0.00 36.33 3.18
2643 6477 5.243730 ACATGCCCATGCCATACTTAATTAC 59.756 40.000 8.11 0.00 42.39 1.89
2644 6478 5.243507 CACATGCCCATGCCATACTTAATTA 59.756 40.000 8.11 0.00 42.39 1.40
2645 6479 4.039488 CACATGCCCATGCCATACTTAATT 59.961 41.667 8.11 0.00 42.39 1.40
2646 6480 3.575256 CACATGCCCATGCCATACTTAAT 59.425 43.478 8.11 0.00 42.39 1.40
2656 6490 3.673173 GGAATTCACATGCCCATGC 57.327 52.632 7.93 0.00 42.39 4.06
2673 6510 4.384208 CCATAAAGAACTACAGGACTGGGG 60.384 50.000 4.14 0.00 34.19 4.96
2734 6589 9.672086 CCTTTATAAGTAGAGAAGAGAACATCG 57.328 37.037 0.00 0.00 0.00 3.84
2848 6847 1.068055 GCATTGCACAACTCAAGGAGG 60.068 52.381 3.15 0.00 33.35 4.30
2863 8580 5.494632 TCTATCAGAAACATGCTGCATTG 57.505 39.130 13.38 8.63 33.45 2.82
2936 8721 6.605594 AGGTACAAGTAAGAGAGAGAATCCTG 59.394 42.308 0.00 0.00 33.66 3.86
2939 8724 8.741603 ACTAGGTACAAGTAAGAGAGAGAATC 57.258 38.462 0.00 0.00 0.00 2.52
2984 8769 6.417635 ACGTCTTGAAAACATAAAAGCACATG 59.582 34.615 0.00 0.00 0.00 3.21
3016 8813 9.845740 TGTAACAAATCACCTACTATTATGCAT 57.154 29.630 3.79 3.79 0.00 3.96
3018 8815 9.326413 ACTGTAACAAATCACCTACTATTATGC 57.674 33.333 0.00 0.00 0.00 3.14
3022 8819 8.594550 ACTCACTGTAACAAATCACCTACTATT 58.405 33.333 0.00 0.00 0.00 1.73
3023 8820 8.135382 ACTCACTGTAACAAATCACCTACTAT 57.865 34.615 0.00 0.00 0.00 2.12
3024 8821 7.534723 ACTCACTGTAACAAATCACCTACTA 57.465 36.000 0.00 0.00 0.00 1.82
3025 8822 6.420913 ACTCACTGTAACAAATCACCTACT 57.579 37.500 0.00 0.00 0.00 2.57
3026 8823 7.492352 AAACTCACTGTAACAAATCACCTAC 57.508 36.000 0.00 0.00 0.00 3.18
3027 8824 7.771361 TGAAAACTCACTGTAACAAATCACCTA 59.229 33.333 0.00 0.00 0.00 3.08
3028 8825 6.601613 TGAAAACTCACTGTAACAAATCACCT 59.398 34.615 0.00 0.00 0.00 4.00
3029 8826 6.791303 TGAAAACTCACTGTAACAAATCACC 58.209 36.000 0.00 0.00 0.00 4.02
3030 8827 8.682128 TTTGAAAACTCACTGTAACAAATCAC 57.318 30.769 0.00 0.00 0.00 3.06
3031 8828 9.868277 AATTTGAAAACTCACTGTAACAAATCA 57.132 25.926 0.00 0.00 36.19 2.57
3035 8832 9.243637 GCATAATTTGAAAACTCACTGTAACAA 57.756 29.630 0.00 0.00 0.00 2.83
3036 8833 8.409371 TGCATAATTTGAAAACTCACTGTAACA 58.591 29.630 0.00 0.00 0.00 2.41
3037 8834 8.690840 GTGCATAATTTGAAAACTCACTGTAAC 58.309 33.333 0.00 0.00 0.00 2.50
3038 8835 8.409371 TGTGCATAATTTGAAAACTCACTGTAA 58.591 29.630 0.00 0.00 0.00 2.41
3039 8836 7.935520 TGTGCATAATTTGAAAACTCACTGTA 58.064 30.769 0.00 0.00 0.00 2.74
3040 8837 6.804677 TGTGCATAATTTGAAAACTCACTGT 58.195 32.000 0.00 0.00 0.00 3.55
3041 8838 7.697352 TTGTGCATAATTTGAAAACTCACTG 57.303 32.000 0.00 0.00 0.00 3.66
3042 8839 8.143193 TCATTGTGCATAATTTGAAAACTCACT 58.857 29.630 5.87 0.00 0.00 3.41
3043 8840 8.296799 TCATTGTGCATAATTTGAAAACTCAC 57.703 30.769 5.87 0.00 0.00 3.51
3044 8841 8.143193 ACTCATTGTGCATAATTTGAAAACTCA 58.857 29.630 5.87 0.00 0.00 3.41
3045 8842 8.524870 ACTCATTGTGCATAATTTGAAAACTC 57.475 30.769 5.87 0.00 0.00 3.01
3046 8843 8.143193 TGACTCATTGTGCATAATTTGAAAACT 58.857 29.630 5.87 0.00 0.00 2.66
3047 8844 8.296799 TGACTCATTGTGCATAATTTGAAAAC 57.703 30.769 5.87 0.00 0.00 2.43
3048 8845 8.143193 ACTGACTCATTGTGCATAATTTGAAAA 58.857 29.630 5.87 0.00 0.00 2.29
3049 8846 7.660112 ACTGACTCATTGTGCATAATTTGAAA 58.340 30.769 5.87 0.00 0.00 2.69
3050 8847 7.218228 ACTGACTCATTGTGCATAATTTGAA 57.782 32.000 5.87 0.00 0.00 2.69
3051 8848 6.822667 ACTGACTCATTGTGCATAATTTGA 57.177 33.333 5.87 2.77 0.00 2.69
3056 8853 6.710295 AGTAACAACTGACTCATTGTGCATAA 59.290 34.615 0.00 0.00 39.00 1.90
3063 8860 8.276325 GTCTAACAAGTAACAACTGACTCATTG 58.724 37.037 0.00 0.00 0.00 2.82
3081 8878 9.261180 GCTCTATGCAGTATTTATGTCTAACAA 57.739 33.333 0.00 0.00 42.31 2.83
3108 8905 3.633525 TGGCAATCCAACTGAATATGCTC 59.366 43.478 0.00 0.00 39.99 4.26
3139 8936 5.656416 TCTTCTGAATGAAACCACAAAAGGT 59.344 36.000 0.00 0.00 45.91 3.50
3157 8954 4.748600 TGAAGCGCATCAGATAATCTTCTG 59.251 41.667 11.93 0.00 43.70 3.02
3166 8990 1.338484 ACACAGTGAAGCGCATCAGAT 60.338 47.619 16.73 4.95 0.00 2.90
3189 9015 9.507280 AACAGTCATTTCGAAATTTGCATATAG 57.493 29.630 20.56 6.68 0.00 1.31
3204 9030 5.344207 ACTTCGCTAACAACAGTCATTTC 57.656 39.130 0.00 0.00 0.00 2.17
3207 9033 4.574828 ACAAACTTCGCTAACAACAGTCAT 59.425 37.500 0.00 0.00 0.00 3.06
3276 9102 3.002553 GGCAAACAAAGCAAATGAACAGG 59.997 43.478 0.00 0.00 0.00 4.00
3278 9104 3.871485 AGGCAAACAAAGCAAATGAACA 58.129 36.364 0.00 0.00 0.00 3.18
3279 9105 4.332268 TGAAGGCAAACAAAGCAAATGAAC 59.668 37.500 0.00 0.00 0.00 3.18
3280 9106 4.511527 TGAAGGCAAACAAAGCAAATGAA 58.488 34.783 0.00 0.00 0.00 2.57
3283 9109 4.141233 ACTGAAGGCAAACAAAGCAAAT 57.859 36.364 0.00 0.00 0.00 2.32
3311 9143 2.863132 TACCTACCGTTGCCACAAAT 57.137 45.000 0.00 0.00 0.00 2.32
3318 9150 2.841215 TGGCAATATACCTACCGTTGC 58.159 47.619 0.00 0.00 43.17 4.17
3327 9159 5.629079 GCCTATTCAGTTGGCAATATACC 57.371 43.478 1.92 0.00 46.41 2.73
3335 9167 9.538298 CTGATTCATTCAGCCTATTCAGTTGGC 62.538 44.444 0.00 0.00 45.16 4.52
3336 9168 5.591472 TGATTCATTCAGCCTATTCAGTTGG 59.409 40.000 0.00 0.00 0.00 3.77
3337 9169 6.688637 TGATTCATTCAGCCTATTCAGTTG 57.311 37.500 0.00 0.00 0.00 3.16
3338 9170 6.939132 CTGATTCATTCAGCCTATTCAGTT 57.061 37.500 0.00 0.00 45.16 3.16
3518 9384 4.182693 TCGTACAGATTCCATCAACGTT 57.817 40.909 0.00 0.00 35.28 3.99
3556 9441 3.134574 ACTAAATTGGCGTCACCTGAA 57.865 42.857 0.00 0.00 40.22 3.02
3557 9442 2.811431 CAACTAAATTGGCGTCACCTGA 59.189 45.455 0.00 0.00 40.22 3.86
3573 9510 5.163673 TGTGGTATACGAACGCATACAACTA 60.164 40.000 19.24 8.68 34.13 2.24
3586 9714 9.419297 GCAAGAGATATTTAATGTGGTATACGA 57.581 33.333 0.00 0.00 0.00 3.43
3755 9892 4.986622 ACTGAACTTCTCAACAAAACAGC 58.013 39.130 0.00 0.00 32.17 4.40
3774 9914 9.640963 AGTGCTAAACTACAAAATCTAGTACTG 57.359 33.333 5.39 0.00 37.36 2.74
3781 9921 5.530915 TGCACAGTGCTAAACTACAAAATCT 59.469 36.000 25.83 0.00 45.31 2.40
3783 9923 5.766150 TGCACAGTGCTAAACTACAAAAT 57.234 34.783 25.83 0.00 45.31 1.82
3855 10003 3.169512 AGTTCCACCCATAAACCCTTG 57.830 47.619 0.00 0.00 0.00 3.61
3856 10004 4.264217 CCTTAGTTCCACCCATAAACCCTT 60.264 45.833 0.00 0.00 0.00 3.95
3930 10113 2.496070 CAGAACCTAACCTGACGGATCA 59.504 50.000 0.00 0.00 32.37 2.92
3943 10126 0.905357 GAAGGCCAGAGCAGAACCTA 59.095 55.000 5.01 0.00 42.56 3.08
3973 10235 3.521560 TCGGATGAATTTTCGGAGACAG 58.478 45.455 0.00 0.00 34.32 3.51
4001 10263 5.070446 TGGGTAATGGACTGTGTCATATCTC 59.930 44.000 0.07 0.00 33.68 2.75
4086 10584 3.315191 ACAACCTGATGTCCAAAAACTCG 59.685 43.478 0.00 0.00 0.00 4.18
4137 10635 2.618053 CTACAAGTGGTCCGGCTAAAG 58.382 52.381 0.00 0.00 0.00 1.85
4145 10643 0.537653 GAGCCTCCTACAAGTGGTCC 59.462 60.000 0.00 0.00 0.00 4.46
4176 10674 2.027192 ACAACCTCGGCATGTTGATAGT 60.027 45.455 15.07 0.00 43.50 2.12
4183 10681 4.328536 TGTATTTAACAACCTCGGCATGT 58.671 39.130 0.00 0.00 34.29 3.21
4208 10706 1.745087 GTTGGGATCGTGACATGCAAT 59.255 47.619 0.00 0.00 0.00 3.56
4209 10707 1.164411 GTTGGGATCGTGACATGCAA 58.836 50.000 0.00 0.00 0.00 4.08
4210 10708 0.676466 GGTTGGGATCGTGACATGCA 60.676 55.000 0.00 0.00 0.00 3.96
4211 10709 0.676466 TGGTTGGGATCGTGACATGC 60.676 55.000 0.00 0.00 0.00 4.06
4212 10710 1.066215 TCTGGTTGGGATCGTGACATG 60.066 52.381 0.00 0.00 0.00 3.21
4213 10711 1.275666 TCTGGTTGGGATCGTGACAT 58.724 50.000 0.00 0.00 0.00 3.06
4214 10712 1.001974 CTTCTGGTTGGGATCGTGACA 59.998 52.381 0.00 0.00 0.00 3.58
4215 10713 1.676014 CCTTCTGGTTGGGATCGTGAC 60.676 57.143 0.00 0.00 0.00 3.67
4216 10714 0.613260 CCTTCTGGTTGGGATCGTGA 59.387 55.000 0.00 0.00 0.00 4.35
4217 10715 0.324943 ACCTTCTGGTTGGGATCGTG 59.675 55.000 0.00 0.00 46.05 4.35
4218 10716 0.324943 CACCTTCTGGTTGGGATCGT 59.675 55.000 0.00 0.00 46.05 3.73
4219 10717 0.324943 ACACCTTCTGGTTGGGATCG 59.675 55.000 0.00 0.00 46.05 3.69
4220 10718 2.437413 GAACACCTTCTGGTTGGGATC 58.563 52.381 0.00 0.00 46.05 3.36
4221 10719 1.271379 CGAACACCTTCTGGTTGGGAT 60.271 52.381 0.00 0.00 46.05 3.85
4222 10720 0.107831 CGAACACCTTCTGGTTGGGA 59.892 55.000 0.00 0.00 46.05 4.37
4223 10721 0.889186 CCGAACACCTTCTGGTTGGG 60.889 60.000 0.00 0.00 46.05 4.12
4224 10722 0.179029 ACCGAACACCTTCTGGTTGG 60.179 55.000 0.00 0.00 46.05 3.77
4225 10723 1.226746 GACCGAACACCTTCTGGTTG 58.773 55.000 0.00 0.00 46.05 3.77
4226 10724 0.108019 GGACCGAACACCTTCTGGTT 59.892 55.000 0.00 0.00 46.05 3.67
4228 10726 1.003718 GGGACCGAACACCTTCTGG 60.004 63.158 0.00 0.00 39.83 3.86
4229 10727 0.107831 TTGGGACCGAACACCTTCTG 59.892 55.000 0.00 0.00 0.00 3.02
4230 10728 0.108019 GTTGGGACCGAACACCTTCT 59.892 55.000 13.97 0.00 0.00 2.85
4231 10729 0.887836 GGTTGGGACCGAACACCTTC 60.888 60.000 19.58 0.00 35.91 3.46
4232 10730 1.149854 GGTTGGGACCGAACACCTT 59.850 57.895 19.58 0.00 35.91 3.50
4233 10731 2.833957 GGTTGGGACCGAACACCT 59.166 61.111 19.58 0.00 35.91 4.00
4241 10739 1.212195 GAATACCTCCTGGTTGGGACC 59.788 57.143 11.76 0.00 46.05 4.46
4242 10740 1.134491 CGAATACCTCCTGGTTGGGAC 60.134 57.143 11.76 2.07 46.05 4.46
4243 10741 1.200519 CGAATACCTCCTGGTTGGGA 58.799 55.000 11.76 4.98 46.05 4.37
4244 10742 0.180406 CCGAATACCTCCTGGTTGGG 59.820 60.000 11.76 7.30 46.05 4.12
4258 10756 2.579410 AAACCTAACCACAGCCGAAT 57.421 45.000 0.00 0.00 0.00 3.34
4315 10818 7.660208 GGAGAGGAGAGATAGAAGTAGTTACAG 59.340 44.444 0.00 0.00 0.00 2.74
4441 10976 3.717350 CGATAGCGGAAAACGTCTTTT 57.283 42.857 0.00 0.00 46.52 2.27
4504 11039 3.196685 GGCTAGGCTTAGATGGATTCGAT 59.803 47.826 9.46 0.00 0.00 3.59
4865 11401 1.737735 CGACGAGAACATGGCAGCA 60.738 57.895 0.00 0.00 0.00 4.41
4899 11435 0.517316 GAGGTGCGGATGTTGTTGAC 59.483 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.