Multiple sequence alignment - TraesCS3B01G044300

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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 TraesCS3B01G044300 chr3B 100.000 4770 0 0 1 4770 22515617 22520386 0.000000e+00 8809.0
1 TraesCS3B01G044300 chr3B 82.661 1090 160 15 2754 3842 22459169 22458108 0.000000e+00 939.0
2 TraesCS3B01G044300 chr3B 81.517 1147 176 21 2754 3899 22321271 22320160 0.000000e+00 911.0
3 TraesCS3B01G044300 chr3B 78.947 1463 205 55 1026 2417 22323141 22321711 0.000000e+00 900.0
4 TraesCS3B01G044300 chr3B 81.243 837 124 11 1029 1859 22461465 22460656 0.000000e+00 645.0
5 TraesCS3B01G044300 chr3B 88.172 279 29 2 2476 2750 22459491 22459213 3.560000e-86 329.0
6 TraesCS3B01G044300 chr3B 100.000 29 0 0 1854 1882 22460643 22460615 2.000000e-03 54.7
7 TraesCS3B01G044300 chr3A 91.987 3594 190 43 827 4383 20913882 20917414 0.000000e+00 4951.0
8 TraesCS3B01G044300 chr3A 86.784 1869 152 32 928 2749 20841687 20843507 0.000000e+00 1995.0
9 TraesCS3B01G044300 chr3A 92.155 1211 78 9 2752 3958 20843546 20844743 0.000000e+00 1694.0
10 TraesCS3B01G044300 chr3A 90.335 776 60 8 2 765 20913110 20913882 0.000000e+00 1003.0
11 TraesCS3B01G044300 chr3A 83.043 1091 154 17 2754 3842 20938667 20939728 0.000000e+00 961.0
12 TraesCS3B01G044300 chr3A 81.766 872 114 16 1029 1882 20936815 20937659 0.000000e+00 688.0
13 TraesCS3B01G044300 chr3A 92.276 246 19 0 2506 2751 20938379 20938624 2.730000e-92 350.0
14 TraesCS3B01G044300 chr3A 93.043 230 12 3 4543 4770 20917412 20917639 2.750000e-87 333.0
15 TraesCS3B01G044300 chr3A 98.171 164 3 0 4381 4544 20900244 20900407 2.170000e-73 287.0
16 TraesCS3B01G044300 chr3A 97.576 165 4 0 4381 4545 30057936 30058100 2.810000e-72 283.0
17 TraesCS3B01G044300 chr3A 94.413 179 10 0 4380 4558 222451035 222450857 4.700000e-70 276.0
18 TraesCS3B01G044300 chr3D 93.768 3209 149 20 1014 4196 15368061 15364878 0.000000e+00 4771.0
19 TraesCS3B01G044300 chr3D 87.245 1913 163 43 877 2758 15389774 15387912 0.000000e+00 2106.0
20 TraesCS3B01G044300 chr3D 92.739 1212 69 9 2752 3958 15387882 15386685 0.000000e+00 1733.0
21 TraesCS3B01G044300 chr3D 90.569 668 51 5 32 689 15368748 15368083 0.000000e+00 874.0
22 TraesCS3B01G044300 chr3D 84.743 662 88 8 2754 3414 15342049 15341400 0.000000e+00 651.0
23 TraesCS3B01G044300 chr3D 81.123 837 125 10 1029 1859 15345030 15344221 1.450000e-179 640.0
24 TraesCS3B01G044300 chr3D 88.530 279 28 2 2476 2750 15342371 15342093 7.650000e-88 335.0
25 TraesCS3B01G044300 chr3D 75.182 274 57 7 3634 3906 15341389 15341126 8.390000e-23 119.0
26 TraesCS3B01G044300 chr3D 100.000 29 0 0 1854 1882 15344202 15344174 2.000000e-03 54.7
27 TraesCS3B01G044300 chr5D 84.059 1217 161 22 2493 3708 558340697 558339513 0.000000e+00 1142.0
28 TraesCS3B01G044300 chr5D 80.849 872 119 21 1015 1870 558342305 558341466 4.020000e-180 641.0
29 TraesCS3B01G044300 chr5D 79.147 422 45 24 1958 2343 558341300 558340886 7.920000e-63 252.0
30 TraesCS3B01G044300 chr4A 83.974 1223 153 26 2493 3708 611265367 611264181 0.000000e+00 1133.0
31 TraesCS3B01G044300 chr4A 80.523 421 42 25 1956 2343 611265972 611265559 2.170000e-73 287.0
32 TraesCS3B01G044300 chr5B 83.387 1252 172 23 2493 3742 704311695 704312912 0.000000e+00 1127.0
33 TraesCS3B01G044300 chr5B 80.229 875 122 24 1015 1870 704310141 704310983 1.130000e-170 610.0
34 TraesCS3B01G044300 chr5B 96.175 183 7 0 4365 4547 545902441 545902259 2.790000e-77 300.0
35 TraesCS3B01G044300 chr5B 96.450 169 6 0 4378 4546 548073326 548073494 3.640000e-71 279.0
36 TraesCS3B01G044300 chr5B 79.858 422 45 22 1956 2343 704311090 704311505 6.080000e-69 272.0
37 TraesCS3B01G044300 chr7D 82.414 580 80 13 170 731 617516694 617516119 2.000000e-133 486.0
38 TraesCS3B01G044300 chr7D 77.076 554 77 30 189 731 116468688 116469202 1.690000e-69 274.0
39 TraesCS3B01G044300 chr7D 73.791 786 160 29 1039 1813 14590579 14591329 7.870000e-68 268.0
40 TraesCS3B01G044300 chr7B 82.264 530 73 12 170 682 711738500 711737975 5.670000e-119 438.0
41 TraesCS3B01G044300 chr7B 97.576 165 4 0 4380 4544 244134812 244134976 2.810000e-72 283.0
42 TraesCS3B01G044300 chr7B 85.714 119 15 2 617 735 686856042 686856158 1.800000e-24 124.0
43 TraesCS3B01G044300 chr6B 98.788 165 2 0 4380 4544 160917218 160917054 1.300000e-75 294.0
44 TraesCS3B01G044300 chr7A 97.576 165 4 0 4380 4544 13105430 13105266 2.810000e-72 283.0
45 TraesCS3B01G044300 chr1B 95.930 172 7 0 4376 4547 146949874 146950045 3.640000e-71 279.0
46 TraesCS3B01G044300 chr2A 77.578 446 80 13 188 625 597865116 597864683 7.920000e-63 252.0
47 TraesCS3B01G044300 chr2D 86.061 165 19 3 2176 2338 2450240 2450078 1.760000e-39 174.0
48 TraesCS3B01G044300 chrUn 85.350 157 19 4 2180 2334 358520442 358520288 4.940000e-35 159.0
49 TraesCS3B01G044300 chrUn 84.713 157 20 4 2180 2334 15442167 15442013 2.300000e-33 154.0
50 TraesCS3B01G044300 chrUn 84.375 160 21 4 2177 2334 283167219 283167376 2.300000e-33 154.0
51 TraesCS3B01G044300 chrUn 84.375 160 20 5 2177 2334 15722670 15722826 8.270000e-33 152.0
52 TraesCS3B01G044300 chrUn 85.600 125 14 4 2212 2334 357010893 357011015 1.390000e-25 128.0


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 TraesCS3B01G044300 chr3B 22515617 22520386 4769 False 8809.000000 8809 100.000000 1 4770 1 chr3B.!!$F1 4769
1 TraesCS3B01G044300 chr3B 22320160 22323141 2981 True 905.500000 911 80.232000 1026 3899 2 chr3B.!!$R1 2873
2 TraesCS3B01G044300 chr3B 22458108 22461465 3357 True 491.925000 939 88.019000 1029 3842 4 chr3B.!!$R2 2813
3 TraesCS3B01G044300 chr3A 20913110 20917639 4529 False 2095.666667 4951 91.788333 2 4770 3 chr3A.!!$F4 4768
4 TraesCS3B01G044300 chr3A 20841687 20844743 3056 False 1844.500000 1995 89.469500 928 3958 2 chr3A.!!$F3 3030
5 TraesCS3B01G044300 chr3A 20936815 20939728 2913 False 666.333333 961 85.695000 1029 3842 3 chr3A.!!$F5 2813
6 TraesCS3B01G044300 chr3D 15364878 15368748 3870 True 2822.500000 4771 92.168500 32 4196 2 chr3D.!!$R2 4164
7 TraesCS3B01G044300 chr3D 15386685 15389774 3089 True 1919.500000 2106 89.992000 877 3958 2 chr3D.!!$R3 3081
8 TraesCS3B01G044300 chr3D 15341126 15345030 3904 True 359.940000 651 85.915600 1029 3906 5 chr3D.!!$R1 2877
9 TraesCS3B01G044300 chr5D 558339513 558342305 2792 True 678.333333 1142 81.351667 1015 3708 3 chr5D.!!$R1 2693
10 TraesCS3B01G044300 chr4A 611264181 611265972 1791 True 710.000000 1133 82.248500 1956 3708 2 chr4A.!!$R1 1752
11 TraesCS3B01G044300 chr5B 704310141 704312912 2771 False 669.666667 1127 81.158000 1015 3742 3 chr5B.!!$F2 2727
12 TraesCS3B01G044300 chr7D 617516119 617516694 575 True 486.000000 486 82.414000 170 731 1 chr7D.!!$R1 561
13 TraesCS3B01G044300 chr7D 116468688 116469202 514 False 274.000000 274 77.076000 189 731 1 chr7D.!!$F2 542
14 TraesCS3B01G044300 chr7D 14590579 14591329 750 False 268.000000 268 73.791000 1039 1813 1 chr7D.!!$F1 774
15 TraesCS3B01G044300 chr7B 711737975 711738500 525 True 438.000000 438 82.264000 170 682 1 chr7B.!!$R1 512

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
837 858 0.038159 AGCGTGTAAGTGAGGTGAGC 60.038 55.0 0.0 0.0 0.00 4.26 F
918 940 0.108585 TTCCACCAGCCTCAGTGAAC 59.891 55.0 0.0 0.0 36.01 3.18 F
2015 2369 0.613260 TATCGGTGGCTGCTTCTGTT 59.387 50.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2514 4533 0.322816 TCCACTCCATCAGCAAAGCC 60.323 55.000 0.0 0.0 0.00 4.35 R
2520 4539 1.690893 TGCTATCTCCACTCCATCAGC 59.309 52.381 0.0 0.0 0.00 4.26 R
3932 6208 0.898789 ATGGTGGAGAGTTCGTCCGT 60.899 55.000 0.0 0.0 36.82 4.69 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
22 23 3.366577 GCAAAATACCGGAATTTGGACGT 60.367 43.478 22.92 0.00 35.21 4.34
24 25 2.320745 ATACCGGAATTTGGACGTCC 57.679 50.000 28.17 28.17 0.00 4.79
25 26 0.975135 TACCGGAATTTGGACGTCCA 59.025 50.000 33.23 33.23 45.94 4.02
40 41 0.820871 GTCCAGACAGCTTCGAGGAT 59.179 55.000 0.00 0.00 36.21 3.24
58 59 5.221843 CGAGGATTGATAAAGGTCCCCATTA 60.222 44.000 0.00 0.00 0.00 1.90
60 61 7.179460 AGGATTGATAAAGGTCCCCATTAAT 57.821 36.000 0.00 0.00 0.00 1.40
63 64 9.374711 GGATTGATAAAGGTCCCCATTAATTTA 57.625 33.333 0.00 0.00 0.00 1.40
89 90 5.850557 AAGTGAACAAATGTGTCCAATCA 57.149 34.783 0.00 0.00 36.80 2.57
110 111 8.906693 CAATCAGACATATACTAGTACTTTGCG 58.093 37.037 4.31 0.00 0.00 4.85
116 117 6.323225 ACATATACTAGTACTTTGCGGGTCTT 59.677 38.462 4.31 0.00 0.00 3.01
117 118 5.672421 ATACTAGTACTTTGCGGGTCTTT 57.328 39.130 4.31 0.00 0.00 2.52
137 138 5.653769 TCTTTCTTGGAGATGCCCTAAAATG 59.346 40.000 0.00 0.00 34.97 2.32
138 139 3.290710 TCTTGGAGATGCCCTAAAATGC 58.709 45.455 0.00 0.00 34.97 3.56
145 146 3.703052 AGATGCCCTAAAATGCCTGAAAG 59.297 43.478 0.00 0.00 0.00 2.62
149 150 3.448660 GCCCTAAAATGCCTGAAAGACAT 59.551 43.478 0.00 0.00 34.07 3.06
154 155 6.150976 CCTAAAATGCCTGAAAGACATGTACA 59.849 38.462 0.00 0.00 34.07 2.90
226 229 2.616842 ACTTACGTTGTCCAAAAGGCTG 59.383 45.455 0.00 0.00 0.00 4.85
337 344 0.102481 CCTCGGACGGTGTTCTATGG 59.898 60.000 0.00 0.00 0.00 2.74
341 348 3.025978 TCGGACGGTGTTCTATGGTTAT 58.974 45.455 0.00 0.00 0.00 1.89
350 357 7.451877 ACGGTGTTCTATGGTTATATGAGAGAT 59.548 37.037 0.00 0.00 0.00 2.75
455 464 2.762887 TCCAGGCAGTCTGAGTTGATAG 59.237 50.000 2.64 0.00 46.18 2.08
465 474 7.978975 GCAGTCTGAGTTGATAGTTATCTTCTT 59.021 37.037 3.32 0.00 33.88 2.52
498 514 3.084039 ACATGCCACGATGAGTTTCAAT 58.916 40.909 0.00 0.00 0.00 2.57
504 520 2.912967 CACGATGAGTTTCAATGCTTGC 59.087 45.455 0.00 0.00 0.00 4.01
510 526 3.066621 TGAGTTTCAATGCTTGCGTTTCT 59.933 39.130 0.00 0.00 0.00 2.52
537 557 3.740115 AGCAACCGAGTTTACATGTTCT 58.260 40.909 2.30 0.17 0.00 3.01
542 562 6.674760 GCAACCGAGTTTACATGTTCTATTCC 60.675 42.308 2.30 0.00 0.00 3.01
612 632 1.218196 CTAGTAGCCCCCTTCTCCTCA 59.782 57.143 0.00 0.00 0.00 3.86
690 710 3.052036 CCAACCTTTGTTTCTTGATGCG 58.948 45.455 0.00 0.00 30.42 4.73
692 712 1.680735 ACCTTTGTTTCTTGATGCGCA 59.319 42.857 14.96 14.96 0.00 6.09
705 725 2.104622 TGATGCGCATCTTCCTATCCAA 59.895 45.455 40.90 20.89 38.60 3.53
728 748 1.069022 CCTTCATGTGGTTTGCAGTCG 60.069 52.381 0.00 0.00 0.00 4.18
738 758 2.546368 GGTTTGCAGTCGAACACATGTA 59.454 45.455 0.00 0.00 38.15 2.29
739 759 3.541711 GTTTGCAGTCGAACACATGTAC 58.458 45.455 0.00 0.00 36.74 2.90
740 760 1.414378 TGCAGTCGAACACATGTACG 58.586 50.000 0.00 5.48 0.00 3.67
765 786 8.879759 CGCTAGTTTTTAACCTAGAATGATGAA 58.120 33.333 0.00 0.00 0.00 2.57
776 797 9.972106 AACCTAGAATGATGAAAAGAGATTTCT 57.028 29.630 0.00 0.00 46.27 2.52
787 808 9.972106 ATGAAAAGAGATTTCTATTCTGTTCCT 57.028 29.630 2.98 0.00 46.27 3.36
788 809 9.224267 TGAAAAGAGATTTCTATTCTGTTCCTG 57.776 33.333 2.98 0.00 46.27 3.86
789 810 7.622893 AAAGAGATTTCTATTCTGTTCCTGC 57.377 36.000 0.00 0.00 31.96 4.85
790 811 5.679601 AGAGATTTCTATTCTGTTCCTGCC 58.320 41.667 0.00 0.00 0.00 4.85
791 812 4.446371 AGATTTCTATTCTGTTCCTGCCG 58.554 43.478 0.00 0.00 0.00 5.69
792 813 2.691409 TTCTATTCTGTTCCTGCCGG 57.309 50.000 0.00 0.00 0.00 6.13
793 814 1.860641 TCTATTCTGTTCCTGCCGGA 58.139 50.000 5.05 0.00 37.60 5.14
794 815 1.480954 TCTATTCTGTTCCTGCCGGAC 59.519 52.381 5.05 0.00 39.60 4.79
795 816 0.539986 TATTCTGTTCCTGCCGGACC 59.460 55.000 5.05 0.00 39.60 4.46
796 817 2.521958 ATTCTGTTCCTGCCGGACCG 62.522 60.000 5.05 6.99 39.60 4.79
813 834 4.767255 GGACACCGGAGCTGGCAG 62.767 72.222 9.46 10.94 0.00 4.85
814 835 3.695606 GACACCGGAGCTGGCAGA 61.696 66.667 20.86 0.00 0.00 4.26
815 836 3.941657 GACACCGGAGCTGGCAGAC 62.942 68.421 20.86 11.09 0.00 3.51
816 837 4.767255 CACCGGAGCTGGCAGACC 62.767 72.222 20.86 18.66 0.00 3.85
819 840 4.504916 CGGAGCTGGCAGACCGAG 62.505 72.222 33.57 15.74 46.94 4.63
820 841 4.828925 GGAGCTGGCAGACCGAGC 62.829 72.222 20.86 1.61 39.70 5.03
824 845 4.363990 CTGGCAGACCGAGCGTGT 62.364 66.667 9.42 0.00 39.70 4.49
825 846 2.986979 TGGCAGACCGAGCGTGTA 60.987 61.111 0.00 0.00 39.70 2.90
826 847 2.260434 GGCAGACCGAGCGTGTAA 59.740 61.111 0.00 0.00 0.00 2.41
836 857 1.729472 CGAGCGTGTAAGTGAGGTGAG 60.729 57.143 0.00 0.00 0.00 3.51
837 858 0.038159 AGCGTGTAAGTGAGGTGAGC 60.038 55.000 0.00 0.00 0.00 4.26
839 860 1.872237 GCGTGTAAGTGAGGTGAGCAA 60.872 52.381 0.00 0.00 0.00 3.91
849 870 4.452455 AGTGAGGTGAGCAATTTTAAGTCG 59.548 41.667 0.00 0.00 0.00 4.18
862 883 9.827411 GCAATTTTAAGTCGAGAGAAATTAACT 57.173 29.630 7.81 0.00 45.01 2.24
875 896 8.329203 AGAGAAATTAACTGAGTGTTTGATCC 57.671 34.615 0.00 0.00 39.89 3.36
907 929 6.148480 CACTTCATAGACTTTCTTTCCACCAG 59.852 42.308 0.00 0.00 0.00 4.00
918 940 0.108585 TTCCACCAGCCTCAGTGAAC 59.891 55.000 0.00 0.00 36.01 3.18
919 941 1.302832 CCACCAGCCTCAGTGAACC 60.303 63.158 0.00 0.00 36.01 3.62
950 972 3.008485 ACCTGATGACCTTGACTTTCTCC 59.992 47.826 0.00 0.00 0.00 3.71
997 1021 2.706339 AGCAGAGGCAATTAGGACAG 57.294 50.000 0.00 0.00 44.61 3.51
1138 1182 1.971695 GGCCAACAGCACCTACCAC 60.972 63.158 0.00 0.00 46.50 4.16
1206 1292 2.048222 CCCGCAGCTCTTCGTCAA 60.048 61.111 0.00 0.00 0.00 3.18
1832 1995 1.793414 TCCATCTCCGACATCCATGT 58.207 50.000 0.00 0.00 45.16 3.21
1840 2003 2.501128 ACATCCATGTCTCCGGCG 59.499 61.111 0.00 0.00 35.87 6.46
1942 2284 7.194112 TGTATGATAATTCCTTGACACTGGA 57.806 36.000 0.00 0.00 0.00 3.86
2015 2369 0.613260 TATCGGTGGCTGCTTCTGTT 59.387 50.000 0.00 0.00 0.00 3.16
2041 2404 2.253603 GGTTGCAATCTGTTTCATCGC 58.746 47.619 0.59 0.00 0.00 4.58
2162 3073 5.468746 TGATAGCGCCATAATTTTCAGGTAC 59.531 40.000 2.29 0.00 0.00 3.34
2196 3119 2.484889 ACTCACGAGTTTCAAGAAGGC 58.515 47.619 0.00 0.00 38.83 4.35
2289 3212 5.187186 AGAGGCTACAGATAACTTTTCCGAA 59.813 40.000 0.00 0.00 0.00 4.30
2514 4533 6.464222 TGATATATGTTTTTCTCCTAGGGCG 58.536 40.000 9.46 0.36 0.00 6.13
2520 4539 0.035439 TTTCTCCTAGGGCGGCTTTG 60.035 55.000 9.46 1.42 0.00 2.77
2675 4694 6.783708 TCTCAAGGAGAGGAGAAAATACTC 57.216 41.667 0.00 0.00 44.81 2.59
2862 5123 4.476479 AGAAAAGCTCTATTGGACTGGGAT 59.524 41.667 0.00 0.00 30.22 3.85
3201 5462 2.360138 TGCATCCCACGGCATTTTT 58.640 47.368 0.00 0.00 34.58 1.94
3656 5926 3.714144 AGAAGCACCCACTACTACTCAT 58.286 45.455 0.00 0.00 0.00 2.90
3749 6021 8.836268 TGTGTTAATTTAGATGTTCGGTAGTT 57.164 30.769 0.00 0.00 0.00 2.24
3905 6179 2.270858 TCCTACCAATGGTTGTAGGCA 58.729 47.619 11.41 0.00 37.09 4.75
3961 6237 3.724478 ACTCTCCACCATCCAGATTACA 58.276 45.455 0.00 0.00 0.00 2.41
4009 6285 5.249780 TGGAAAAATCAAGGTAGGCACTA 57.750 39.130 0.00 0.00 41.75 2.74
4063 6339 7.556733 AAGTTGATGTACACCGTTTAGAAAA 57.443 32.000 0.00 0.00 0.00 2.29
4107 6383 3.881220 TCGTGGTTTTGAGAAGGAAGTT 58.119 40.909 0.00 0.00 0.00 2.66
4115 6391 6.350194 GGTTTTGAGAAGGAAGTTGTTTGACT 60.350 38.462 0.00 0.00 0.00 3.41
4139 6415 4.832560 AGGGGTGCAGGGAAAAATATAT 57.167 40.909 0.00 0.00 0.00 0.86
4223 6500 2.413862 TCTTTGCCGAGTGTCAAAGGC 61.414 52.381 12.84 7.34 45.45 4.35
4243 6520 0.602106 CAGTGCTAGGCATCATCCCG 60.602 60.000 0.00 0.00 41.91 5.14
4264 6541 5.816777 CCCGGATGATGTTTGCAAAATTTAT 59.183 36.000 14.67 6.52 0.00 1.40
4291 6568 2.832201 GCAGCCTTGGGATGGAGC 60.832 66.667 4.00 0.00 39.79 4.70
4313 6590 4.389077 GCCTATCCAACGATCCTAATTTCG 59.611 45.833 0.00 0.00 41.04 3.46
4314 6591 5.779922 CCTATCCAACGATCCTAATTTCGA 58.220 41.667 4.37 0.00 38.67 3.71
4318 6595 3.246226 CCAACGATCCTAATTTCGAGCTG 59.754 47.826 4.37 0.00 38.67 4.24
4321 6598 3.130516 ACGATCCTAATTTCGAGCTGACA 59.869 43.478 4.37 0.00 38.67 3.58
4325 6602 2.854777 CCTAATTTCGAGCTGACAGACG 59.145 50.000 6.65 11.05 0.00 4.18
4329 6606 0.456824 TTCGAGCTGACAGACGCATC 60.457 55.000 6.65 0.00 0.00 3.91
4371 6648 3.434319 ACCCGCTTTCTGCATGCG 61.434 61.111 14.09 8.20 46.17 4.73
4378 6655 1.000233 CTTTCTGCATGCGCACACAC 61.000 55.000 14.90 2.50 45.36 3.82
4379 6656 1.722636 TTTCTGCATGCGCACACACA 61.723 50.000 14.90 7.86 45.36 3.72
4380 6657 1.517210 TTCTGCATGCGCACACACAT 61.517 50.000 14.90 0.00 45.36 3.21
4381 6658 0.673022 TCTGCATGCGCACACACATA 60.673 50.000 14.90 0.00 45.36 2.29
4382 6659 0.521867 CTGCATGCGCACACACATAC 60.522 55.000 14.90 0.00 45.36 2.39
4383 6660 0.954938 TGCATGCGCACACACATACT 60.955 50.000 14.90 0.00 45.36 2.12
4384 6661 0.247814 GCATGCGCACACACATACTC 60.248 55.000 14.90 0.00 38.36 2.59
4385 6662 0.374758 CATGCGCACACACATACTCC 59.625 55.000 14.90 0.00 0.00 3.85
4386 6663 0.744414 ATGCGCACACACATACTCCC 60.744 55.000 14.90 0.00 0.00 4.30
4387 6664 1.079127 GCGCACACACATACTCCCT 60.079 57.895 0.30 0.00 0.00 4.20
4388 6665 1.084370 GCGCACACACATACTCCCTC 61.084 60.000 0.30 0.00 0.00 4.30
4389 6666 0.460284 CGCACACACATACTCCCTCC 60.460 60.000 0.00 0.00 0.00 4.30
4390 6667 0.460284 GCACACACATACTCCCTCCG 60.460 60.000 0.00 0.00 0.00 4.63
4391 6668 0.895530 CACACACATACTCCCTCCGT 59.104 55.000 0.00 0.00 0.00 4.69
4392 6669 1.275291 CACACACATACTCCCTCCGTT 59.725 52.381 0.00 0.00 0.00 4.44
4393 6670 1.549170 ACACACATACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
4394 6671 1.134788 CACACATACTCCCTCCGTTCC 60.135 57.143 0.00 0.00 0.00 3.62
4395 6672 0.464452 CACATACTCCCTCCGTTCCC 59.536 60.000 0.00 0.00 0.00 3.97
4396 6673 0.042131 ACATACTCCCTCCGTTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
4397 6674 1.200519 CATACTCCCTCCGTTCCCAA 58.799 55.000 0.00 0.00 0.00 4.12
4398 6675 1.557832 CATACTCCCTCCGTTCCCAAA 59.442 52.381 0.00 0.00 0.00 3.28
4399 6676 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
4400 6677 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4401 6678 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
4402 6679 1.838077 CTCCCTCCGTTCCCAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
4403 6680 2.238898 CTCCCTCCGTTCCCAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
4404 6681 2.026636 TCCCTCCGTTCCCAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
4405 6682 2.290705 CCCTCCGTTCCCAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
4406 6683 3.007635 CCTCCGTTCCCAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
4407 6684 3.307480 CCTCCGTTCCCAAATACTTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
4408 6685 4.324267 CTCCGTTCCCAAATACTTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
4409 6686 4.721132 TCCGTTCCCAAATACTTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
4410 6687 4.758165 TCCGTTCCCAAATACTTGTCTTTC 59.242 41.667 0.00 0.00 0.00 2.62
4411 6688 4.760204 CCGTTCCCAAATACTTGTCTTTCT 59.240 41.667 0.00 0.00 0.00 2.52
4412 6689 5.935789 CCGTTCCCAAATACTTGTCTTTCTA 59.064 40.000 0.00 0.00 0.00 2.10
4413 6690 6.092259 CCGTTCCCAAATACTTGTCTTTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
4414 6691 6.092259 CGTTCCCAAATACTTGTCTTTCTAGG 59.908 42.308 0.00 0.00 0.00 3.02
4415 6692 5.497474 TCCCAAATACTTGTCTTTCTAGGC 58.503 41.667 0.00 0.00 0.00 3.93
4416 6693 5.013704 TCCCAAATACTTGTCTTTCTAGGCA 59.986 40.000 0.00 0.00 33.22 4.75
4417 6694 5.888161 CCCAAATACTTGTCTTTCTAGGCAT 59.112 40.000 0.00 0.00 35.56 4.40
4418 6695 6.378280 CCCAAATACTTGTCTTTCTAGGCATT 59.622 38.462 0.00 0.00 35.56 3.56
4419 6696 7.093771 CCCAAATACTTGTCTTTCTAGGCATTT 60.094 37.037 0.00 0.00 35.56 2.32
4420 6697 8.306761 CCAAATACTTGTCTTTCTAGGCATTTT 58.693 33.333 0.00 0.00 35.56 1.82
4426 6703 9.077885 ACTTGTCTTTCTAGGCATTTTAAATGA 57.922 29.630 20.37 0.11 35.56 2.57
4427 6704 9.912634 CTTGTCTTTCTAGGCATTTTAAATGAA 57.087 29.630 20.37 3.61 35.56 2.57
4428 6705 9.691362 TTGTCTTTCTAGGCATTTTAAATGAAC 57.309 29.630 20.37 12.07 35.56 3.18
4429 6706 9.077885 TGTCTTTCTAGGCATTTTAAATGAACT 57.922 29.630 20.37 17.62 29.10 3.01
4430 6707 9.561270 GTCTTTCTAGGCATTTTAAATGAACTC 57.439 33.333 20.37 7.12 0.00 3.01
4431 6708 9.295825 TCTTTCTAGGCATTTTAAATGAACTCA 57.704 29.630 20.37 6.21 0.00 3.41
4432 6709 9.912634 CTTTCTAGGCATTTTAAATGAACTCAA 57.087 29.630 20.37 10.72 0.00 3.02
4433 6710 9.691362 TTTCTAGGCATTTTAAATGAACTCAAC 57.309 29.630 20.37 1.88 0.00 3.18
4434 6711 8.402798 TCTAGGCATTTTAAATGAACTCAACA 57.597 30.769 20.37 3.29 0.00 3.33
4435 6712 9.023962 TCTAGGCATTTTAAATGAACTCAACAT 57.976 29.630 20.37 2.42 0.00 2.71
4437 6714 8.986477 AGGCATTTTAAATGAACTCAACATAC 57.014 30.769 20.37 0.00 0.00 2.39
4438 6715 7.754924 AGGCATTTTAAATGAACTCAACATACG 59.245 33.333 20.37 0.00 0.00 3.06
4439 6716 7.009174 GGCATTTTAAATGAACTCAACATACGG 59.991 37.037 20.37 0.00 0.00 4.02
4440 6717 7.753132 GCATTTTAAATGAACTCAACATACGGA 59.247 33.333 20.37 0.00 0.00 4.69
4441 6718 9.787532 CATTTTAAATGAACTCAACATACGGAT 57.212 29.630 11.89 0.00 0.00 4.18
4442 6719 9.787532 ATTTTAAATGAACTCAACATACGGATG 57.212 29.630 5.94 5.94 39.16 3.51
4444 6721 9.438228 TTTAAATGAACTCAACATACGGATGTA 57.562 29.630 15.10 0.00 45.93 2.29
4445 6722 9.607988 TTAAATGAACTCAACATACGGATGTAT 57.392 29.630 15.10 0.00 45.93 2.29
4447 6724 9.778741 AAATGAACTCAACATACGGATGTATAT 57.221 29.630 15.10 0.00 45.93 0.86
4450 6727 9.292195 TGAACTCAACATACGGATGTATATAGA 57.708 33.333 15.10 6.65 45.93 1.98
4451 6728 9.557338 GAACTCAACATACGGATGTATATAGAC 57.443 37.037 15.10 0.06 45.93 2.59
4452 6729 8.631480 ACTCAACATACGGATGTATATAGACA 57.369 34.615 15.10 2.07 45.93 3.41
4453 6730 9.244292 ACTCAACATACGGATGTATATAGACAT 57.756 33.333 15.10 12.70 45.93 3.06
4483 6760 7.801547 AAAATGTAGATTCACTCATTTTGCG 57.198 32.000 17.26 0.00 40.40 4.85
4484 6761 4.340894 TGTAGATTCACTCATTTTGCGC 57.659 40.909 0.00 0.00 0.00 6.09
4485 6762 2.927553 AGATTCACTCATTTTGCGCC 57.072 45.000 4.18 0.00 0.00 6.53
4486 6763 1.131126 AGATTCACTCATTTTGCGCCG 59.869 47.619 4.18 0.00 0.00 6.46
4487 6764 0.881118 ATTCACTCATTTTGCGCCGT 59.119 45.000 4.18 0.00 0.00 5.68
4488 6765 1.514003 TTCACTCATTTTGCGCCGTA 58.486 45.000 4.18 0.00 0.00 4.02
4489 6766 1.732941 TCACTCATTTTGCGCCGTAT 58.267 45.000 4.18 0.00 0.00 3.06
4490 6767 1.396648 TCACTCATTTTGCGCCGTATG 59.603 47.619 4.18 5.63 0.00 2.39
4491 6768 1.130373 CACTCATTTTGCGCCGTATGT 59.870 47.619 4.18 0.00 0.00 2.29
4492 6769 2.350192 CACTCATTTTGCGCCGTATGTA 59.650 45.455 4.18 0.00 0.00 2.29
4493 6770 2.607635 ACTCATTTTGCGCCGTATGTAG 59.392 45.455 4.18 7.56 0.00 2.74
4494 6771 2.607635 CTCATTTTGCGCCGTATGTAGT 59.392 45.455 4.18 0.00 0.00 2.73
4495 6772 2.605818 TCATTTTGCGCCGTATGTAGTC 59.394 45.455 4.18 0.00 0.00 2.59
4496 6773 2.081725 TTTTGCGCCGTATGTAGTCA 57.918 45.000 4.18 0.00 0.00 3.41
4497 6774 1.352114 TTTGCGCCGTATGTAGTCAC 58.648 50.000 4.18 0.00 0.00 3.67
4498 6775 0.528924 TTGCGCCGTATGTAGTCACT 59.471 50.000 4.18 0.00 0.00 3.41
4499 6776 0.528924 TGCGCCGTATGTAGTCACTT 59.471 50.000 4.18 0.00 0.00 3.16
4500 6777 0.921347 GCGCCGTATGTAGTCACTTG 59.079 55.000 0.00 0.00 0.00 3.16
4501 6778 1.734707 GCGCCGTATGTAGTCACTTGT 60.735 52.381 0.00 0.00 0.00 3.16
4502 6779 2.602878 CGCCGTATGTAGTCACTTGTT 58.397 47.619 0.00 0.00 0.00 2.83
4503 6780 2.344441 CGCCGTATGTAGTCACTTGTTG 59.656 50.000 0.00 0.00 0.00 3.33
4504 6781 3.581755 GCCGTATGTAGTCACTTGTTGA 58.418 45.455 0.00 0.00 0.00 3.18
4505 6782 3.991773 GCCGTATGTAGTCACTTGTTGAA 59.008 43.478 0.00 0.00 35.39 2.69
4506 6783 4.449743 GCCGTATGTAGTCACTTGTTGAAA 59.550 41.667 0.00 0.00 35.39 2.69
4507 6784 5.121768 GCCGTATGTAGTCACTTGTTGAAAT 59.878 40.000 0.00 0.00 35.39 2.17
4508 6785 6.672357 GCCGTATGTAGTCACTTGTTGAAATC 60.672 42.308 0.00 0.00 35.39 2.17
4509 6786 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
4510 6787 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
4511 6788 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
4512 6789 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
4514 6791 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
4515 6792 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
4518 6795 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
4519 6796 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
4520 6797 9.173021 TCACTTGTTGAAATCTCTAAAAAGACA 57.827 29.630 0.00 0.00 0.00 3.41
4521 6798 9.787532 CACTTGTTGAAATCTCTAAAAAGACAA 57.212 29.630 0.00 0.00 0.00 3.18
4535 6812 9.211485 TCTAAAAAGACAAGTATTTAGGAACGG 57.789 33.333 0.00 0.00 36.48 4.44
4536 6813 9.211485 CTAAAAAGACAAGTATTTAGGAACGGA 57.789 33.333 0.00 0.00 33.69 4.69
4537 6814 7.668525 AAAAGACAAGTATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
4538 6815 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
4539 6816 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
4540 6817 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4541 6818 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
4545 6822 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
4637 6916 6.556495 AGACTCCATGAATACACATGTATCCT 59.444 38.462 0.00 0.00 44.00 3.24
4656 6935 7.936847 TGTATCCTTGTTTCTACATGAAAGTGT 59.063 33.333 0.00 0.00 44.36 3.55
4681 6960 2.949644 AGTTGTCACCTTAGTTGTTGCC 59.050 45.455 0.00 0.00 0.00 4.52
4682 6961 2.685897 GTTGTCACCTTAGTTGTTGCCA 59.314 45.455 0.00 0.00 0.00 4.92
4711 6990 6.273825 AGTATCACCATTAGTCATTCACGTC 58.726 40.000 0.00 0.00 0.00 4.34
4760 7039 2.809665 GCCCATTGCAACAATTGGTGAA 60.810 45.455 27.54 14.89 40.77 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.175929 CGTCCAAATTCCGGTATTTTGC 58.824 45.455 15.62 8.46 30.46 3.68
10 11 2.076863 CTGTCTGGACGTCCAAATTCC 58.923 52.381 35.36 21.21 46.97 3.01
17 18 1.444553 CGAAGCTGTCTGGACGTCC 60.445 63.158 28.17 28.17 0.00 4.79
22 23 1.205655 CAATCCTCGAAGCTGTCTGGA 59.794 52.381 0.00 0.00 33.11 3.86
24 25 2.662006 TCAATCCTCGAAGCTGTCTG 57.338 50.000 0.00 0.00 0.00 3.51
25 26 5.344743 TTTATCAATCCTCGAAGCTGTCT 57.655 39.130 0.00 0.00 0.00 3.41
58 59 8.878769 GGACACATTTGTTCACTTTTGTAAATT 58.121 29.630 0.00 0.00 35.47 1.82
60 61 7.378966 TGGACACATTTGTTCACTTTTGTAAA 58.621 30.769 0.00 0.00 36.19 2.01
63 64 5.398603 TGGACACATTTGTTCACTTTTGT 57.601 34.783 0.00 0.00 36.19 2.83
89 90 5.832060 ACCCGCAAAGTACTAGTATATGTCT 59.168 40.000 5.75 0.00 0.00 3.41
94 95 6.604795 AGAAAGACCCGCAAAGTACTAGTATA 59.395 38.462 5.75 0.00 0.00 1.47
99 100 4.312443 CAAGAAAGACCCGCAAAGTACTA 58.688 43.478 0.00 0.00 0.00 1.82
104 105 1.537202 CTCCAAGAAAGACCCGCAAAG 59.463 52.381 0.00 0.00 0.00 2.77
110 111 1.683319 GGGCATCTCCAAGAAAGACCC 60.683 57.143 0.00 0.00 36.21 4.46
116 117 3.701040 GCATTTTAGGGCATCTCCAAGAA 59.299 43.478 0.00 0.00 36.21 2.52
117 118 3.290710 GCATTTTAGGGCATCTCCAAGA 58.709 45.455 0.00 0.00 36.21 3.02
137 138 6.743575 AAAGTATGTACATGTCTTTCAGGC 57.256 37.500 23.09 0.00 0.00 4.85
167 168 0.035915 TCGCCATGGTGGATTTTCGA 60.036 50.000 24.82 13.55 40.96 3.71
168 169 0.098728 GTCGCCATGGTGGATTTTCG 59.901 55.000 24.82 11.35 40.96 3.46
226 229 3.466836 TCCTCCGTGATTCATTGTATGC 58.533 45.455 0.00 0.00 0.00 3.14
310 315 2.196229 CCGTCCGAGGGAGAGGAT 59.804 66.667 0.40 0.00 38.97 3.24
341 348 7.730332 TGTTCTTAGCTGGGAATATCTCTCATA 59.270 37.037 0.00 0.00 32.64 2.15
350 357 4.777896 AGAGTGTGTTCTTAGCTGGGAATA 59.222 41.667 0.00 0.00 0.00 1.75
356 363 3.643763 ACGAAGAGTGTGTTCTTAGCTG 58.356 45.455 0.00 0.00 37.53 4.24
455 464 5.470098 TGTCAAGTTGGAGCAAGAAGATAAC 59.530 40.000 2.34 0.00 0.00 1.89
465 474 0.178995 TGGCATGTCAAGTTGGAGCA 60.179 50.000 0.00 0.84 0.00 4.26
498 514 0.867746 CTACTGCAGAAACGCAAGCA 59.132 50.000 23.35 0.00 42.45 3.91
537 557 2.429610 GGCTCCGAGTAACAGTGGAATA 59.570 50.000 0.00 0.00 0.00 1.75
542 562 0.317160 TGTGGCTCCGAGTAACAGTG 59.683 55.000 0.00 0.00 0.00 3.66
612 632 2.676839 CGATGCTGCTTTCTGTCTTCAT 59.323 45.455 0.00 0.00 0.00 2.57
677 697 2.162208 GGAAGATGCGCATCAAGAAACA 59.838 45.455 42.35 6.15 40.22 2.83
690 710 4.949856 TGAAGGTTTTGGATAGGAAGATGC 59.050 41.667 0.00 0.00 0.00 3.91
692 712 6.604795 CACATGAAGGTTTTGGATAGGAAGAT 59.395 38.462 0.00 0.00 0.00 2.40
728 748 6.793680 GGTTAAAAACTAGCGTACATGTGTTC 59.206 38.462 9.11 0.00 0.00 3.18
738 758 8.038944 TCATCATTCTAGGTTAAAAACTAGCGT 58.961 33.333 9.51 0.00 37.26 5.07
739 759 8.420374 TCATCATTCTAGGTTAAAAACTAGCG 57.580 34.615 9.51 2.31 37.26 4.26
765 786 6.601217 GGCAGGAACAGAATAGAAATCTCTTT 59.399 38.462 0.00 0.00 32.70 2.52
766 787 6.118852 GGCAGGAACAGAATAGAAATCTCTT 58.881 40.000 0.00 0.00 32.70 2.85
767 788 5.679601 GGCAGGAACAGAATAGAAATCTCT 58.320 41.667 0.00 0.00 35.52 3.10
768 789 4.509600 CGGCAGGAACAGAATAGAAATCTC 59.490 45.833 0.00 0.00 0.00 2.75
769 790 4.446371 CGGCAGGAACAGAATAGAAATCT 58.554 43.478 0.00 0.00 0.00 2.40
770 791 3.561725 CCGGCAGGAACAGAATAGAAATC 59.438 47.826 0.00 0.00 41.02 2.17
771 792 3.199946 TCCGGCAGGAACAGAATAGAAAT 59.800 43.478 1.89 0.00 45.12 2.17
772 793 2.569853 TCCGGCAGGAACAGAATAGAAA 59.430 45.455 1.89 0.00 45.12 2.52
773 794 2.184533 TCCGGCAGGAACAGAATAGAA 58.815 47.619 1.89 0.00 45.12 2.10
774 795 1.860641 TCCGGCAGGAACAGAATAGA 58.139 50.000 1.89 0.00 45.12 1.98
796 817 4.767255 CTGCCAGCTCCGGTGTCC 62.767 72.222 0.00 0.00 0.00 4.02
797 818 3.695606 TCTGCCAGCTCCGGTGTC 61.696 66.667 0.00 0.00 0.00 3.67
798 819 4.008933 GTCTGCCAGCTCCGGTGT 62.009 66.667 0.00 0.00 0.00 4.16
799 820 4.767255 GGTCTGCCAGCTCCGGTG 62.767 72.222 0.00 0.00 34.09 4.94
802 823 4.504916 CTCGGTCTGCCAGCTCCG 62.505 72.222 17.60 17.60 43.65 4.63
803 824 4.828925 GCTCGGTCTGCCAGCTCC 62.829 72.222 0.00 0.00 36.58 4.70
807 828 2.486636 TTACACGCTCGGTCTGCCAG 62.487 60.000 0.00 0.00 34.09 4.85
808 829 2.486636 CTTACACGCTCGGTCTGCCA 62.487 60.000 0.00 0.00 34.09 4.92
809 830 1.805945 CTTACACGCTCGGTCTGCC 60.806 63.158 0.00 0.00 0.00 4.85
810 831 1.080705 ACTTACACGCTCGGTCTGC 60.081 57.895 0.00 0.00 0.00 4.26
811 832 0.240145 TCACTTACACGCTCGGTCTG 59.760 55.000 0.00 0.00 0.00 3.51
812 833 0.522180 CTCACTTACACGCTCGGTCT 59.478 55.000 0.00 0.00 0.00 3.85
813 834 0.456312 CCTCACTTACACGCTCGGTC 60.456 60.000 0.00 0.00 0.00 4.79
814 835 1.177256 ACCTCACTTACACGCTCGGT 61.177 55.000 0.00 0.00 0.00 4.69
815 836 0.732880 CACCTCACTTACACGCTCGG 60.733 60.000 0.00 0.00 0.00 4.63
816 837 0.240145 TCACCTCACTTACACGCTCG 59.760 55.000 0.00 0.00 0.00 5.03
817 838 1.983972 CTCACCTCACTTACACGCTC 58.016 55.000 0.00 0.00 0.00 5.03
818 839 0.038159 GCTCACCTCACTTACACGCT 60.038 55.000 0.00 0.00 0.00 5.07
819 840 0.319555 TGCTCACCTCACTTACACGC 60.320 55.000 0.00 0.00 0.00 5.34
820 841 2.148916 TTGCTCACCTCACTTACACG 57.851 50.000 0.00 0.00 0.00 4.49
821 842 5.438761 AAAATTGCTCACCTCACTTACAC 57.561 39.130 0.00 0.00 0.00 2.90
822 843 6.770785 ACTTAAAATTGCTCACCTCACTTACA 59.229 34.615 0.00 0.00 0.00 2.41
823 844 7.203255 ACTTAAAATTGCTCACCTCACTTAC 57.797 36.000 0.00 0.00 0.00 2.34
824 845 6.147164 CGACTTAAAATTGCTCACCTCACTTA 59.853 38.462 0.00 0.00 0.00 2.24
825 846 5.049405 CGACTTAAAATTGCTCACCTCACTT 60.049 40.000 0.00 0.00 0.00 3.16
826 847 4.452455 CGACTTAAAATTGCTCACCTCACT 59.548 41.667 0.00 0.00 0.00 3.41
836 857 9.827411 AGTTAATTTCTCTCGACTTAAAATTGC 57.173 29.630 10.81 6.29 33.12 3.56
849 870 8.447053 GGATCAAACACTCAGTTAATTTCTCTC 58.553 37.037 0.00 0.00 40.26 3.20
875 896 9.657121 GAAAGAAAGTCTATGAAGTGTTTGAAG 57.343 33.333 0.00 0.00 0.00 3.02
886 907 4.565652 GGCTGGTGGAAAGAAAGTCTATGA 60.566 45.833 0.00 0.00 0.00 2.15
907 929 1.827399 TTCTCGGGGTTCACTGAGGC 61.827 60.000 10.50 0.00 42.78 4.70
918 940 0.461961 GTCATCAGGTCTTCTCGGGG 59.538 60.000 0.00 0.00 0.00 5.73
919 941 0.461961 GGTCATCAGGTCTTCTCGGG 59.538 60.000 0.00 0.00 0.00 5.14
950 972 5.442402 GTTGCTTTAACATGGCAAAATGTG 58.558 37.500 7.73 0.00 45.49 3.21
1110 1154 1.852067 GCTGTTGGCCGTGTAGTTGG 61.852 60.000 0.00 0.00 34.27 3.77
1138 1182 4.379243 AGCACGGCGAGGTTGGAG 62.379 66.667 16.62 0.00 0.00 3.86
1823 1986 2.501128 CGCCGGAGACATGGATGT 59.499 61.111 5.05 0.00 45.16 3.06
1852 2051 1.026718 ACATACTCTTGCTTGCCGGC 61.027 55.000 22.73 22.73 0.00 6.13
1951 2293 5.183904 ACTCCATGTCCTTCAAAATTAGCAC 59.816 40.000 0.00 0.00 0.00 4.40
2041 2404 2.202756 GCCGCCGAAGACAGTAGG 60.203 66.667 0.00 0.00 0.00 3.18
2122 3016 6.459024 GGCGCTATCAGTATCGATCTCTTAAT 60.459 42.308 7.64 1.55 0.00 1.40
2137 3043 4.516698 ACCTGAAAATTATGGCGCTATCAG 59.483 41.667 10.46 11.13 34.33 2.90
2162 3073 1.455786 CGTGAGTACGCTTTCCTTGTG 59.544 52.381 0.00 0.00 44.11 3.33
2196 3119 4.022416 TCCATTTCCCAAACTTGTTCATCG 60.022 41.667 0.00 0.00 0.00 3.84
2289 3212 2.758423 ACCTTCGCCAAGTTTGTTTTCT 59.242 40.909 0.00 0.00 0.00 2.52
2354 3439 9.688592 CCTAGAAAACGAGGATTATTACGTAAT 57.311 33.333 23.36 23.36 38.00 1.89
2436 3530 7.175347 TGGATCAATATTCTCCCTCTTATCG 57.825 40.000 9.94 0.00 0.00 2.92
2504 4523 2.514824 GCAAAGCCGCCCTAGGAG 60.515 66.667 11.48 3.57 0.00 3.69
2514 4533 0.322816 TCCACTCCATCAGCAAAGCC 60.323 55.000 0.00 0.00 0.00 4.35
2520 4539 1.690893 TGCTATCTCCACTCCATCAGC 59.309 52.381 0.00 0.00 0.00 4.26
2675 4694 3.676172 TGTTTGGCAAGTATTCGTAGACG 59.324 43.478 0.00 0.00 34.32 4.18
2881 5142 4.479786 GAAGTCCTTCTGCTGTTCCTAT 57.520 45.455 0.00 0.00 36.69 2.57
3201 5462 7.445121 AGCTGAATACATCCGATTTGATAGAA 58.555 34.615 0.00 0.00 0.00 2.10
3341 5602 3.949113 TCACGGACTAAACAAAGCCTTTT 59.051 39.130 0.00 0.00 0.00 2.27
3356 5622 9.916397 CAAATACTTAATTAGTTGATCACGGAC 57.084 33.333 7.09 0.00 38.33 4.79
3509 5779 4.259570 CGATCAACTGCATTCTCTTGTACG 60.260 45.833 0.00 0.00 0.00 3.67
3905 6179 7.562135 ACCATACAACTATCGGTAGTTTGATT 58.438 34.615 18.43 6.24 46.40 2.57
3932 6208 0.898789 ATGGTGGAGAGTTCGTCCGT 60.899 55.000 0.00 0.00 36.82 4.69
4063 6339 0.898789 ACACTCGGAGATGGTTCGGT 60.899 55.000 12.86 0.00 33.89 4.69
4107 6383 0.257328 TGCACCCCTTCAGTCAAACA 59.743 50.000 0.00 0.00 0.00 2.83
4115 6391 0.263172 TTTTTCCCTGCACCCCTTCA 59.737 50.000 0.00 0.00 0.00 3.02
4187 6464 4.808895 GGCAAAGATTTTCGACACCTTTTT 59.191 37.500 0.00 0.00 0.00 1.94
4188 6465 4.368315 GGCAAAGATTTTCGACACCTTTT 58.632 39.130 0.00 0.00 0.00 2.27
4195 6472 2.223377 ACACTCGGCAAAGATTTTCGAC 59.777 45.455 0.00 0.00 0.00 4.20
4223 6500 0.250640 GGGATGATGCCTAGCACTGG 60.251 60.000 0.00 0.00 43.04 4.00
4243 6520 7.906527 GCAGAATAAATTTTGCAAACATCATCC 59.093 33.333 12.39 0.00 44.49 3.51
4291 6568 5.779922 TCGAAATTAGGATCGTTGGATAGG 58.220 41.667 0.00 0.00 39.91 2.57
4306 6583 2.259618 GCGTCTGTCAGCTCGAAATTA 58.740 47.619 17.09 0.00 0.00 1.40
4313 6590 1.409227 CGTGATGCGTCTGTCAGCTC 61.409 60.000 7.58 0.00 35.54 4.09
4314 6591 1.445066 CGTGATGCGTCTGTCAGCT 60.445 57.895 7.58 0.00 35.54 4.24
4371 6648 0.460284 CGGAGGGAGTATGTGTGTGC 60.460 60.000 0.00 0.00 0.00 4.57
4378 6655 1.200519 TTGGGAACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
4379 6656 1.961133 TTTGGGAACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
4380 6657 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4381 6658 1.558294 GTATTTGGGAACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
4382 6659 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
4383 6660 1.961133 AGTATTTGGGAACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
4384 6661 2.290705 ACAAGTATTTGGGAACGGAGGG 60.291 50.000 2.81 0.00 38.66 4.30
4385 6662 3.007635 GACAAGTATTTGGGAACGGAGG 58.992 50.000 2.81 0.00 38.66 4.30
4386 6663 3.939066 AGACAAGTATTTGGGAACGGAG 58.061 45.455 2.81 0.00 38.66 4.63
4387 6664 4.360951 AAGACAAGTATTTGGGAACGGA 57.639 40.909 2.81 0.00 38.66 4.69
4388 6665 4.760204 AGAAAGACAAGTATTTGGGAACGG 59.240 41.667 2.81 0.00 38.66 4.44
4389 6666 5.941948 AGAAAGACAAGTATTTGGGAACG 57.058 39.130 2.81 0.00 38.66 3.95
4390 6667 6.127980 GCCTAGAAAGACAAGTATTTGGGAAC 60.128 42.308 2.81 0.00 38.66 3.62
4391 6668 5.944007 GCCTAGAAAGACAAGTATTTGGGAA 59.056 40.000 2.81 0.00 38.66 3.97
4392 6669 5.013704 TGCCTAGAAAGACAAGTATTTGGGA 59.986 40.000 2.81 0.00 38.66 4.37
4393 6670 5.253330 TGCCTAGAAAGACAAGTATTTGGG 58.747 41.667 2.81 0.00 38.66 4.12
4394 6671 7.396540 AATGCCTAGAAAGACAAGTATTTGG 57.603 36.000 2.81 0.00 38.66 3.28
4400 6677 9.077885 TCATTTAAAATGCCTAGAAAGACAAGT 57.922 29.630 0.00 0.00 0.00 3.16
4401 6678 9.912634 TTCATTTAAAATGCCTAGAAAGACAAG 57.087 29.630 0.00 0.00 0.00 3.16
4402 6679 9.691362 GTTCATTTAAAATGCCTAGAAAGACAA 57.309 29.630 0.00 0.00 0.00 3.18
4403 6680 9.077885 AGTTCATTTAAAATGCCTAGAAAGACA 57.922 29.630 0.00 0.00 0.00 3.41
4404 6681 9.561270 GAGTTCATTTAAAATGCCTAGAAAGAC 57.439 33.333 0.00 0.00 0.00 3.01
4405 6682 9.295825 TGAGTTCATTTAAAATGCCTAGAAAGA 57.704 29.630 0.00 0.00 0.00 2.52
4406 6683 9.912634 TTGAGTTCATTTAAAATGCCTAGAAAG 57.087 29.630 0.00 0.00 0.00 2.62
4407 6684 9.691362 GTTGAGTTCATTTAAAATGCCTAGAAA 57.309 29.630 0.00 0.00 0.00 2.52
4408 6685 8.855110 TGTTGAGTTCATTTAAAATGCCTAGAA 58.145 29.630 0.00 0.00 0.00 2.10
4409 6686 8.402798 TGTTGAGTTCATTTAAAATGCCTAGA 57.597 30.769 0.00 0.00 0.00 2.43
4412 6689 7.754924 CGTATGTTGAGTTCATTTAAAATGCCT 59.245 33.333 0.00 0.00 0.00 4.75
4413 6690 7.009174 CCGTATGTTGAGTTCATTTAAAATGCC 59.991 37.037 0.00 0.00 0.00 4.40
4414 6691 7.753132 TCCGTATGTTGAGTTCATTTAAAATGC 59.247 33.333 0.00 0.00 0.00 3.56
4415 6692 9.787532 ATCCGTATGTTGAGTTCATTTAAAATG 57.212 29.630 0.00 0.00 0.00 2.32
4416 6693 9.787532 CATCCGTATGTTGAGTTCATTTAAAAT 57.212 29.630 0.00 0.00 0.00 1.82
4417 6694 8.788806 ACATCCGTATGTTGAGTTCATTTAAAA 58.211 29.630 0.00 0.00 44.07 1.52
4418 6695 8.330466 ACATCCGTATGTTGAGTTCATTTAAA 57.670 30.769 0.00 0.00 44.07 1.52
4419 6696 7.915293 ACATCCGTATGTTGAGTTCATTTAA 57.085 32.000 0.00 0.00 44.07 1.52
4421 6698 9.778741 ATATACATCCGTATGTTGAGTTCATTT 57.221 29.630 0.00 0.00 44.07 2.32
4424 6701 9.292195 TCTATATACATCCGTATGTTGAGTTCA 57.708 33.333 0.00 0.00 44.07 3.18
4425 6702 9.557338 GTCTATATACATCCGTATGTTGAGTTC 57.443 37.037 0.00 0.00 44.07 3.01
4426 6703 9.074576 TGTCTATATACATCCGTATGTTGAGTT 57.925 33.333 0.00 0.00 44.07 3.01
4427 6704 8.631480 TGTCTATATACATCCGTATGTTGAGT 57.369 34.615 0.00 0.00 44.07 3.41
4457 6734 9.340695 CGCAAAATGAGTGAATCTACATTTTAA 57.659 29.630 17.18 0.00 45.06 1.52
4458 6735 7.484641 GCGCAAAATGAGTGAATCTACATTTTA 59.515 33.333 0.30 0.00 45.06 1.52
4459 6736 6.308766 GCGCAAAATGAGTGAATCTACATTTT 59.691 34.615 0.30 0.00 46.58 1.82
4460 6737 5.801947 GCGCAAAATGAGTGAATCTACATTT 59.198 36.000 0.30 0.00 42.25 2.32
4461 6738 5.335127 GCGCAAAATGAGTGAATCTACATT 58.665 37.500 0.30 0.00 34.99 2.71
4462 6739 4.201950 GGCGCAAAATGAGTGAATCTACAT 60.202 41.667 10.83 0.00 0.00 2.29
4463 6740 3.126858 GGCGCAAAATGAGTGAATCTACA 59.873 43.478 10.83 0.00 0.00 2.74
4464 6741 3.685058 GGCGCAAAATGAGTGAATCTAC 58.315 45.455 10.83 0.00 0.00 2.59
4465 6742 2.351418 CGGCGCAAAATGAGTGAATCTA 59.649 45.455 10.83 0.00 0.00 1.98
4466 6743 1.131126 CGGCGCAAAATGAGTGAATCT 59.869 47.619 10.83 0.00 0.00 2.40
4467 6744 1.135689 ACGGCGCAAAATGAGTGAATC 60.136 47.619 10.83 0.00 0.00 2.52
4468 6745 0.881118 ACGGCGCAAAATGAGTGAAT 59.119 45.000 10.83 0.00 0.00 2.57
4469 6746 1.514003 TACGGCGCAAAATGAGTGAA 58.486 45.000 10.83 0.00 0.00 3.18
4470 6747 1.396648 CATACGGCGCAAAATGAGTGA 59.603 47.619 10.83 0.00 0.00 3.41
4471 6748 1.130373 ACATACGGCGCAAAATGAGTG 59.870 47.619 10.83 0.00 0.00 3.51
4472 6749 1.448985 ACATACGGCGCAAAATGAGT 58.551 45.000 10.83 0.00 0.00 3.41
4473 6750 2.607635 ACTACATACGGCGCAAAATGAG 59.392 45.455 10.83 10.39 0.00 2.90
4474 6751 2.605818 GACTACATACGGCGCAAAATGA 59.394 45.455 10.83 0.00 0.00 2.57
4475 6752 2.350192 TGACTACATACGGCGCAAAATG 59.650 45.455 10.83 11.57 0.00 2.32
4476 6753 2.350498 GTGACTACATACGGCGCAAAAT 59.650 45.455 10.83 0.00 0.00 1.82
4477 6754 1.727880 GTGACTACATACGGCGCAAAA 59.272 47.619 10.83 0.00 0.00 2.44
4478 6755 1.067425 AGTGACTACATACGGCGCAAA 60.067 47.619 10.83 0.00 0.00 3.68
4479 6756 0.528924 AGTGACTACATACGGCGCAA 59.471 50.000 10.83 0.00 0.00 4.85
4480 6757 0.528924 AAGTGACTACATACGGCGCA 59.471 50.000 10.83 0.00 0.00 6.09
4481 6758 0.921347 CAAGTGACTACATACGGCGC 59.079 55.000 6.90 0.00 0.00 6.53
4482 6759 2.273370 ACAAGTGACTACATACGGCG 57.727 50.000 4.80 4.80 0.00 6.46
4483 6760 3.581755 TCAACAAGTGACTACATACGGC 58.418 45.455 0.00 0.00 0.00 5.68
4484 6761 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
4485 6762 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
4486 6763 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
4488 6765 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
4489 6766 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
4492 6769 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
4493 6770 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
4494 6771 9.173021 TGTCTTTTTAGAGATTTCAACAAGTGA 57.827 29.630 0.00 0.00 0.00 3.41
4495 6772 9.787532 TTGTCTTTTTAGAGATTTCAACAAGTG 57.212 29.630 0.00 0.00 0.00 3.16
4509 6786 9.211485 CCGTTCCTAAATACTTGTCTTTTTAGA 57.789 33.333 0.00 0.00 34.90 2.10
4510 6787 9.211485 TCCGTTCCTAAATACTTGTCTTTTTAG 57.789 33.333 0.00 0.00 33.47 1.85
4511 6788 9.211485 CTCCGTTCCTAAATACTTGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
4512 6789 7.174426 CCTCCGTTCCTAAATACTTGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
4513 6790 6.653740 CCTCCGTTCCTAAATACTTGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
4514 6791 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
4515 6792 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
4516 6793 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
4517 6794 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
4518 6795 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
4519 6796 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
4520 6797 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
4521 6798 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
4522 6799 4.646492 TGTACTCCCTCCGTTCCTAAATAC 59.354 45.833 0.00 0.00 0.00 1.89
4523 6800 4.646492 GTGTACTCCCTCCGTTCCTAAATA 59.354 45.833 0.00 0.00 0.00 1.40
4524 6801 3.450096 GTGTACTCCCTCCGTTCCTAAAT 59.550 47.826 0.00 0.00 0.00 1.40
4525 6802 2.827921 GTGTACTCCCTCCGTTCCTAAA 59.172 50.000 0.00 0.00 0.00 1.85
4526 6803 2.450476 GTGTACTCCCTCCGTTCCTAA 58.550 52.381 0.00 0.00 0.00 2.69
4527 6804 1.679944 CGTGTACTCCCTCCGTTCCTA 60.680 57.143 0.00 0.00 0.00 2.94
4528 6805 0.964358 CGTGTACTCCCTCCGTTCCT 60.964 60.000 0.00 0.00 0.00 3.36
4529 6806 1.246737 ACGTGTACTCCCTCCGTTCC 61.247 60.000 0.00 0.00 0.00 3.62
4530 6807 0.169894 GACGTGTACTCCCTCCGTTC 59.830 60.000 0.00 0.00 0.00 3.95
4531 6808 0.538057 TGACGTGTACTCCCTCCGTT 60.538 55.000 0.00 0.00 0.00 4.44
4532 6809 0.538057 TTGACGTGTACTCCCTCCGT 60.538 55.000 0.00 0.00 0.00 4.69
4533 6810 0.109412 GTTGACGTGTACTCCCTCCG 60.109 60.000 0.00 0.00 0.00 4.63
4534 6811 1.201880 GAGTTGACGTGTACTCCCTCC 59.798 57.143 13.22 0.00 35.78 4.30
4535 6812 1.884579 TGAGTTGACGTGTACTCCCTC 59.115 52.381 18.77 5.12 40.00 4.30
4536 6813 1.612463 GTGAGTTGACGTGTACTCCCT 59.388 52.381 18.77 0.00 40.00 4.20
4537 6814 1.612463 AGTGAGTTGACGTGTACTCCC 59.388 52.381 18.77 11.01 40.00 4.30
4538 6815 2.662700 CAGTGAGTTGACGTGTACTCC 58.337 52.381 18.77 12.45 40.00 3.85
4539 6816 2.052157 GCAGTGAGTTGACGTGTACTC 58.948 52.381 16.08 16.08 40.89 2.59
4540 6817 1.407618 TGCAGTGAGTTGACGTGTACT 59.592 47.619 0.00 0.00 0.00 2.73
4541 6818 1.847818 TGCAGTGAGTTGACGTGTAC 58.152 50.000 0.00 0.00 0.00 2.90
4545 6822 0.532640 TGCATGCAGTGAGTTGACGT 60.533 50.000 18.46 0.00 0.00 4.34
4599 6878 1.801913 GAGTCTATATGCGCGGCCG 60.802 63.158 24.05 24.05 37.57 6.13
4602 6881 1.202348 TCATGGAGTCTATATGCGCGG 59.798 52.381 8.83 0.00 0.00 6.46
4604 6883 5.289675 GTGTATTCATGGAGTCTATATGCGC 59.710 44.000 0.00 0.00 0.00 6.09
4635 6914 9.450807 CTTAAACACTTTCATGTAGAAACAAGG 57.549 33.333 0.00 0.00 41.17 3.61
4656 6935 6.404954 GGCAACAACTAAGGTGACAACTTAAA 60.405 38.462 13.81 0.00 30.68 1.52
4681 6960 9.933723 TGAATGACTAATGGTGATACTATGATG 57.066 33.333 0.00 0.00 0.00 3.07
4682 6961 9.935241 GTGAATGACTAATGGTGATACTATGAT 57.065 33.333 0.00 0.00 0.00 2.45
4726 7005 0.680921 AATGGGCAGGGATGACAACG 60.681 55.000 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.