Multiple sequence alignment - TraesCS2B01G628400

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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 TraesCS2B01G628400 chr2B 100.000 2525 0 0 1 2525 799967753 799970277 0.000000e+00 4663.0
1 TraesCS2B01G628400 chr2B 100.000 1927 0 0 3004 4930 799970756 799972682 0.000000e+00 3559.0
2 TraesCS2B01G628400 chr2B 99.458 553 3 0 1 553 799960908 799961460 0.000000e+00 1005.0
3 TraesCS2B01G628400 chr2B 98.553 553 8 0 1 553 797895982 797895430 0.000000e+00 977.0
4 TraesCS2B01G628400 chr2B 98.373 553 9 0 1 553 745105659 745106211 0.000000e+00 972.0
5 TraesCS2B01G628400 chr2B 98.373 553 9 0 1 553 797902823 797902271 0.000000e+00 972.0
6 TraesCS2B01G628400 chr2B 94.920 374 19 0 1777 2150 799289217 799289590 2.180000e-163 586.0
7 TraesCS2B01G628400 chr2B 88.393 112 12 1 4767 4877 789267271 789267160 3.410000e-27 134.0
8 TraesCS2B01G628400 chr2B 100.000 55 0 0 5377 5431 799973129 799973183 9.620000e-18 102.0
9 TraesCS2B01G628400 chr2D 97.577 1238 19 3 3004 4241 597895244 597894018 0.000000e+00 2109.0
10 TraesCS2B01G628400 chr2D 95.511 891 25 3 3367 4257 641948865 641947990 0.000000e+00 1410.0
11 TraesCS2B01G628400 chr2D 87.623 1220 70 28 1016 2171 597897036 597895834 0.000000e+00 1341.0
12 TraesCS2B01G628400 chr2D 89.479 979 57 18 1229 2171 641950721 641949753 0.000000e+00 1195.0
13 TraesCS2B01G628400 chr2D 79.657 1165 176 33 3035 4165 641881177 641880040 0.000000e+00 782.0
14 TraesCS2B01G628400 chr2D 95.991 449 14 2 4319 4764 641879962 641879515 0.000000e+00 726.0
15 TraesCS2B01G628400 chr2D 78.985 1123 178 28 3035 4123 597825660 597824562 0.000000e+00 713.0
16 TraesCS2B01G628400 chr2D 88.500 600 32 19 554 1128 641609833 641610420 0.000000e+00 691.0
17 TraesCS2B01G628400 chr2D 98.228 395 6 1 3004 3398 641949192 641948799 0.000000e+00 689.0
18 TraesCS2B01G628400 chr2D 93.583 374 23 1 1777 2150 597826134 597825762 1.710000e-154 556.0
19 TraesCS2B01G628400 chr2D 98.371 307 3 1 2174 2480 641949607 641949303 6.190000e-149 538.0
20 TraesCS2B01G628400 chr2D 91.444 374 22 3 1777 2150 641881642 641881279 6.280000e-139 505.0
21 TraesCS2B01G628400 chr2D 99.270 274 2 0 2174 2447 597895745 597895472 3.780000e-136 496.0
22 TraesCS2B01G628400 chr2D 94.118 221 8 3 557 772 641951172 641950952 1.130000e-86 331.0
23 TraesCS2B01G628400 chr2D 88.806 268 22 5 4307 4566 641947991 641947724 6.790000e-84 322.0
24 TraesCS2B01G628400 chr2D 93.213 221 10 3 557 772 597897288 597897068 2.440000e-83 320.0
25 TraesCS2B01G628400 chr2D 93.220 118 7 1 4587 4703 641947734 641947617 7.230000e-39 172.0
26 TraesCS2B01G628400 chr2D 95.062 81 3 1 4587 4666 597893644 597893564 5.710000e-25 126.0
27 TraesCS2B01G628400 chr2D 88.785 107 7 2 1016 1119 641950919 641950815 5.710000e-25 126.0
28 TraesCS2B01G628400 chr2D 83.133 83 7 2 3332 3407 641880842 641880760 9.760000e-08 69.4
29 TraesCS2B01G628400 chr2D 81.928 83 8 2 3332 3407 597825325 597825243 4.540000e-06 63.9
30 TraesCS2B01G628400 chr5B 99.096 553 5 0 1 553 531228947 531228395 0.000000e+00 994.0
31 TraesCS2B01G628400 chr5B 98.734 553 7 0 1 553 531235811 531235259 0.000000e+00 983.0
32 TraesCS2B01G628400 chr5B 97.834 554 11 1 1 553 85971134 85971687 0.000000e+00 955.0
33 TraesCS2B01G628400 chr5B 92.593 54 1 2 4256 4309 711188676 711188626 2.100000e-09 75.0
34 TraesCS2B01G628400 chr7B 98.387 558 8 1 1 558 233886826 233887382 0.000000e+00 979.0
35 TraesCS2B01G628400 chr7B 90.909 110 9 1 4775 4883 695340530 695340639 4.380000e-31 147.0
36 TraesCS2B01G628400 chr6B 98.014 554 10 1 1 553 17880747 17880194 0.000000e+00 961.0
37 TraesCS2B01G628400 chr2A 80.343 1165 180 24 3035 4165 766848125 766846976 0.000000e+00 837.0
38 TraesCS2B01G628400 chr2A 96.644 447 14 1 4319 4764 766846898 766846452 0.000000e+00 741.0
39 TraesCS2B01G628400 chr2A 87.147 389 32 7 1777 2150 766848612 766848227 5.030000e-115 425.0
40 TraesCS2B01G628400 chr2A 82.540 378 25 10 892 1248 766712828 766713185 1.480000e-75 294.0
41 TraesCS2B01G628400 chr2A 97.778 90 2 0 554 643 766712741 766712830 7.280000e-34 156.0
42 TraesCS2B01G628400 chr3B 85.556 360 27 9 2174 2524 434404595 434404252 2.410000e-93 353.0
43 TraesCS2B01G628400 chr3B 94.444 54 2 1 4256 4308 485387351 485387298 1.250000e-11 82.4
44 TraesCS2B01G628400 chr3A 82.865 356 20 16 2174 2525 453820158 453819840 1.150000e-71 281.0
45 TraesCS2B01G628400 chr3A 100.000 28 0 0 3004 3031 453819754 453819727 1.000000e-02 52.8
46 TraesCS2B01G628400 chr3D 82.535 355 23 16 2174 2524 336538704 336538385 5.360000e-70 276.0
47 TraesCS2B01G628400 chr3D 96.296 54 1 1 4256 4309 574387772 574387824 2.690000e-13 87.9
48 TraesCS2B01G628400 chr3D 83.516 91 5 6 4223 4308 12253053 12253138 5.830000e-10 76.8
49 TraesCS2B01G628400 chr3D 100.000 28 0 0 3004 3031 336538301 336538274 1.000000e-02 52.8
50 TraesCS2B01G628400 chr5D 85.714 161 19 3 4767 4925 27352363 27352205 3.360000e-37 167.0
51 TraesCS2B01G628400 chr6D 86.466 133 17 1 4767 4899 469798428 469798297 1.580000e-30 145.0
52 TraesCS2B01G628400 chr6D 87.805 123 14 1 4764 4885 1929749 1929871 5.670000e-30 143.0
53 TraesCS2B01G628400 chr6D 92.727 55 2 1 4256 4308 455902770 455902716 1.620000e-10 78.7
54 TraesCS2B01G628400 chr1D 89.286 112 11 1 4764 4874 46475996 46476107 7.340000e-29 139.0
55 TraesCS2B01G628400 chr1D 91.935 62 4 1 4256 4316 10816054 10816115 9.690000e-13 86.1
56 TraesCS2B01G628400 chr4B 89.333 75 7 1 4851 4924 400687646 400687720 5.790000e-15 93.5
57 TraesCS2B01G628400 chr7D 94.444 54 3 0 4256 4309 400855179 400855232 3.490000e-12 84.2
58 TraesCS2B01G628400 chr7D 92.453 53 4 0 4767 4819 264318722 264318670 5.830000e-10 76.8
59 TraesCS2B01G628400 chr4D 92.857 56 1 1 4256 4308 505989116 505989061 1.620000e-10 78.7
60 TraesCS2B01G628400 chr6A 87.302 63 7 1 4247 4308 616816305 616816367 2.710000e-08 71.3


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 TraesCS2B01G628400 chr2B 799967753 799973183 5430 False 2774.666667 4663 100.000000 1 5431 3 chr2B.!!$F4 5430
1 TraesCS2B01G628400 chr2B 799960908 799961460 552 False 1005.000000 1005 99.458000 1 553 1 chr2B.!!$F3 552
2 TraesCS2B01G628400 chr2B 797895430 797895982 552 True 977.000000 977 98.553000 1 553 1 chr2B.!!$R2 552
3 TraesCS2B01G628400 chr2B 745105659 745106211 552 False 972.000000 972 98.373000 1 553 1 chr2B.!!$F1 552
4 TraesCS2B01G628400 chr2B 797902271 797902823 552 True 972.000000 972 98.373000 1 553 1 chr2B.!!$R3 552
5 TraesCS2B01G628400 chr2D 597893564 597897288 3724 True 878.400000 2109 94.549000 557 4666 5 chr2D.!!$R2 4109
6 TraesCS2B01G628400 chr2D 641609833 641610420 587 False 691.000000 691 88.500000 554 1128 1 chr2D.!!$F1 574
7 TraesCS2B01G628400 chr2D 641947617 641951172 3555 True 597.875000 1410 93.314750 557 4703 8 chr2D.!!$R4 4146
8 TraesCS2B01G628400 chr2D 641879515 641881642 2127 True 520.600000 782 87.556250 1777 4764 4 chr2D.!!$R3 2987
9 TraesCS2B01G628400 chr2D 597824562 597826134 1572 True 444.300000 713 84.832000 1777 4123 3 chr2D.!!$R1 2346
10 TraesCS2B01G628400 chr5B 531228395 531228947 552 True 994.000000 994 99.096000 1 553 1 chr5B.!!$R1 552
11 TraesCS2B01G628400 chr5B 531235259 531235811 552 True 983.000000 983 98.734000 1 553 1 chr5B.!!$R2 552
12 TraesCS2B01G628400 chr5B 85971134 85971687 553 False 955.000000 955 97.834000 1 553 1 chr5B.!!$F1 552
13 TraesCS2B01G628400 chr7B 233886826 233887382 556 False 979.000000 979 98.387000 1 558 1 chr7B.!!$F1 557
14 TraesCS2B01G628400 chr6B 17880194 17880747 553 True 961.000000 961 98.014000 1 553 1 chr6B.!!$R1 552
15 TraesCS2B01G628400 chr2A 766846452 766848612 2160 True 667.666667 837 88.044667 1777 4764 3 chr2A.!!$R1 2987

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
814 830 0.186873 GGAGTGATGCCATGGGGAAT 59.813 55.000 15.13 0.00 33.87 3.01 F
1131 1160 0.039708 GGACTGAGCTTGCTTGTTGC 60.040 55.000 0.00 0.00 43.25 4.17 F
1415 1474 0.249676 AGATGGACTCACAGCAGCAG 59.750 55.000 0.00 0.00 0.00 4.24 F
1611 1700 1.766143 CTGCAATTCTACCGAGGCGC 61.766 60.000 0.00 0.00 0.00 6.53 F
1641 1730 2.043450 CAGCCGAGGAGGAGAGGT 60.043 66.667 0.00 0.00 45.00 3.85 F
2495 2745 2.276732 TTAGCCAGCTGAAGTTGCTT 57.723 45.000 17.39 2.56 38.92 3.91 F
2498 2748 0.169894 GCCAGCTGAAGTTGCTTAGC 59.830 55.000 17.39 1.39 38.92 3.09 F
3703 4015 1.201647 CGGAGTCGAGGTTTGAGCTTA 59.798 52.381 0.00 0.00 39.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1806 0.523966 CCGAGTCTGCTTCGTCTTCT 59.476 55.000 0.00 0.00 0.00 2.85 R
2172 2279 0.973632 TCCGCACCTTATGACACACT 59.026 50.000 0.00 0.00 0.00 3.55 R
2480 2730 1.467734 CTGCTAAGCAACTTCAGCTGG 59.532 52.381 15.13 0.36 42.53 4.85 R
2481 2731 2.896243 CTGCTAAGCAACTTCAGCTG 57.104 50.000 7.63 7.63 42.53 4.24 R
2497 2747 5.499139 TTATACCACATTAAAGCTGCTGC 57.501 39.130 1.35 7.62 40.05 5.25 R
3703 4015 0.683504 AGCTGGACCGTCGTAGGAAT 60.684 55.000 5.97 0.00 34.73 3.01 R
4267 4688 1.619827 ACCCACGACGAGTAATTTGGA 59.380 47.619 0.00 0.00 0.00 3.53 R
4810 5245 0.952984 GAGCTGTGGCACTGGACTTC 60.953 60.000 23.39 8.48 41.70 3.01 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
58 59 1.549037 GCCCAGAGATACCTCTCCGAT 60.549 57.143 0.00 0.00 46.38 4.18
554 557 4.103153 CCTCTAGGGCATATTTCCTTCACA 59.897 45.833 0.00 0.00 34.75 3.58
725 741 3.662759 ATCCCCGGAACACAATGTTAT 57.337 42.857 0.73 0.00 41.28 1.89
726 742 2.717390 TCCCCGGAACACAATGTTATG 58.283 47.619 0.73 0.00 41.28 1.90
755 771 3.215244 CGTAACAATTCAACACGAGTGC 58.785 45.455 2.76 0.00 34.66 4.40
772 788 3.661944 AGTGCAGAAGAGAAGACATGTG 58.338 45.455 1.15 0.00 0.00 3.21
773 789 2.740981 GTGCAGAAGAGAAGACATGTGG 59.259 50.000 1.15 0.00 0.00 4.17
796 812 2.265683 GCGGGTAGAAAAGAGTTACGG 58.734 52.381 0.00 0.00 0.00 4.02
811 827 1.695114 TACGGAGTGATGCCATGGGG 61.695 60.000 15.13 0.00 45.73 4.96
813 829 1.614711 GGAGTGATGCCATGGGGAA 59.385 57.895 15.13 0.00 35.59 3.97
814 830 0.186873 GGAGTGATGCCATGGGGAAT 59.813 55.000 15.13 0.00 33.87 3.01
815 831 1.325355 GAGTGATGCCATGGGGAATG 58.675 55.000 15.13 0.00 29.90 2.67
816 832 0.632835 AGTGATGCCATGGGGAATGT 59.367 50.000 15.13 0.00 29.90 2.71
817 833 1.035139 GTGATGCCATGGGGAATGTC 58.965 55.000 15.13 0.00 29.90 3.06
833 849 6.756542 GGGGAATGTCAACAACAAAATATAGC 59.243 38.462 0.00 0.00 42.37 2.97
876 892 8.821147 AAATGTAAGTCACGACATAACTAACA 57.179 30.769 0.00 0.00 35.21 2.41
950 968 4.460948 AAATAGGAAAGCACCTGCATTG 57.539 40.909 0.00 0.00 45.16 2.82
954 972 3.230134 AGGAAAGCACCTGCATTGTTTA 58.770 40.909 0.00 0.00 45.16 2.01
955 973 3.640967 AGGAAAGCACCTGCATTGTTTAA 59.359 39.130 0.00 0.00 45.16 1.52
956 974 3.989817 GGAAAGCACCTGCATTGTTTAAG 59.010 43.478 0.00 0.00 45.16 1.85
1026 1049 0.889186 GGGCGCGGATGTTAATGGAT 60.889 55.000 8.83 0.00 0.00 3.41
1030 1053 1.813862 CGCGGATGTTAATGGATGGGT 60.814 52.381 0.00 0.00 0.00 4.51
1053 1076 3.553095 AAGCGGAGAACTGGGCCAC 62.553 63.158 0.00 0.00 0.00 5.01
1056 1079 1.966451 CGGAGAACTGGGCCACAAC 60.966 63.158 0.00 0.00 0.00 3.32
1059 1082 1.339151 GGAGAACTGGGCCACAACTAG 60.339 57.143 0.00 0.00 0.00 2.57
1128 1157 1.302033 CCGGACTGAGCTTGCTTGT 60.302 57.895 0.00 0.00 0.00 3.16
1129 1158 0.886490 CCGGACTGAGCTTGCTTGTT 60.886 55.000 0.00 0.00 0.00 2.83
1130 1159 0.236711 CGGACTGAGCTTGCTTGTTG 59.763 55.000 0.00 0.00 0.00 3.33
1131 1160 0.039708 GGACTGAGCTTGCTTGTTGC 60.040 55.000 0.00 0.00 43.25 4.17
1132 1161 0.039708 GACTGAGCTTGCTTGTTGCC 60.040 55.000 0.00 0.00 42.00 4.52
1133 1162 0.466922 ACTGAGCTTGCTTGTTGCCT 60.467 50.000 0.00 0.00 42.00 4.75
1134 1163 0.672342 CTGAGCTTGCTTGTTGCCTT 59.328 50.000 0.00 0.00 42.00 4.35
1150 1179 3.897239 TGCCTTTATACAACCATCCCAG 58.103 45.455 0.00 0.00 0.00 4.45
1168 1197 4.823419 CCCGGCCGCATCGTTGTA 62.823 66.667 22.85 0.00 0.00 2.41
1192 1226 1.222115 CGCTGCTAGGTTATTCGCCC 61.222 60.000 0.00 0.00 0.00 6.13
1204 1238 4.262292 GGTTATTCGCCCCAAAGAAAAAGT 60.262 41.667 0.00 0.00 0.00 2.66
1376 1435 0.602562 GGGATCAGATCTCTGGAGCG 59.397 60.000 10.36 0.00 43.91 5.03
1413 1472 2.680312 TAAGATGGACTCACAGCAGC 57.320 50.000 0.00 0.00 0.00 5.25
1414 1473 0.689055 AAGATGGACTCACAGCAGCA 59.311 50.000 0.00 0.00 0.00 4.41
1415 1474 0.249676 AGATGGACTCACAGCAGCAG 59.750 55.000 0.00 0.00 0.00 4.24
1449 1538 6.018425 GGTATACTTGACAGACGACTTCGATA 60.018 42.308 5.47 0.00 43.02 2.92
1451 1540 4.911053 ACTTGACAGACGACTTCGATATC 58.089 43.478 5.47 0.00 43.02 1.63
1594 1683 2.753296 GAGGATCTCGCTGGATTTCTG 58.247 52.381 0.00 0.00 0.00 3.02
1611 1700 1.766143 CTGCAATTCTACCGAGGCGC 61.766 60.000 0.00 0.00 0.00 6.53
1628 1717 2.123982 CCAATGGAGGAGGCAGCC 60.124 66.667 1.84 1.84 0.00 4.85
1641 1730 2.043450 CAGCCGAGGAGGAGAGGT 60.043 66.667 0.00 0.00 45.00 3.85
1714 1806 7.419518 GGAGTTGGATGAAGAGATGGAGATAAA 60.420 40.741 0.00 0.00 0.00 1.40
1732 1824 2.339728 AAGAAGACGAAGCAGACTCG 57.660 50.000 0.00 0.00 0.00 4.18
2036 2143 2.483876 TCTCAAACGGAGCAACTCAAG 58.516 47.619 0.00 0.00 43.70 3.02
2171 2278 3.071479 TGTCCACGCTCAACTTTATTCC 58.929 45.455 0.00 0.00 0.00 3.01
2172 2279 3.071479 GTCCACGCTCAACTTTATTCCA 58.929 45.455 0.00 0.00 0.00 3.53
2274 2524 7.328737 GCTTGACCTACTAAATTCCAGTAAGA 58.671 38.462 0.00 0.00 0.00 2.10
2485 2735 9.996554 AAAGTGTTAAAATTTAATTAGCCAGCT 57.003 25.926 1.21 0.00 0.00 4.24
2486 2736 8.986477 AGTGTTAAAATTTAATTAGCCAGCTG 57.014 30.769 6.78 6.78 0.00 4.24
2487 2737 8.802267 AGTGTTAAAATTTAATTAGCCAGCTGA 58.198 29.630 17.39 0.00 0.00 4.26
2488 2738 9.418045 GTGTTAAAATTTAATTAGCCAGCTGAA 57.582 29.630 17.39 1.24 0.00 3.02
2489 2739 9.638239 TGTTAAAATTTAATTAGCCAGCTGAAG 57.362 29.630 17.39 0.00 0.00 3.02
2490 2740 9.639601 GTTAAAATTTAATTAGCCAGCTGAAGT 57.360 29.630 17.39 3.31 0.00 3.01
2492 2742 8.538409 AAAATTTAATTAGCCAGCTGAAGTTG 57.462 30.769 17.39 0.00 0.00 3.16
2493 2743 4.701956 TTAATTAGCCAGCTGAAGTTGC 57.298 40.909 17.39 9.76 0.00 4.17
2494 2744 2.503895 ATTAGCCAGCTGAAGTTGCT 57.496 45.000 17.39 17.09 42.06 3.91
2495 2745 2.276732 TTAGCCAGCTGAAGTTGCTT 57.723 45.000 17.39 2.56 38.92 3.91
2496 2746 3.417069 TTAGCCAGCTGAAGTTGCTTA 57.583 42.857 17.39 5.88 38.92 3.09
2497 2747 1.818642 AGCCAGCTGAAGTTGCTTAG 58.181 50.000 17.39 0.00 38.92 2.18
2498 2748 0.169894 GCCAGCTGAAGTTGCTTAGC 59.830 55.000 17.39 1.39 38.92 3.09
2499 2749 1.527034 CCAGCTGAAGTTGCTTAGCA 58.473 50.000 17.39 1.39 38.92 3.49
2500 2750 1.467734 CCAGCTGAAGTTGCTTAGCAG 59.532 52.381 17.39 0.00 40.61 4.24
3580 3874 8.058667 TGAACTAAAAGTACGTGATGGAGATA 57.941 34.615 0.00 0.00 0.00 1.98
3639 3948 3.134804 AGCGGTATAAAGAAGCAGATGGT 59.865 43.478 0.00 0.00 0.00 3.55
3678 3990 2.224161 ACTCTTCGATAGCCCATTCTGC 60.224 50.000 0.00 0.00 0.00 4.26
3689 4001 1.364626 CCATTCTGCACTGCGGAGTC 61.365 60.000 6.61 2.98 45.12 3.36
3703 4015 1.201647 CGGAGTCGAGGTTTGAGCTTA 59.798 52.381 0.00 0.00 39.00 3.09
3909 4224 2.061740 ACGCCGTTTCAGTAGAGTTC 57.938 50.000 0.00 0.00 0.00 3.01
3944 4259 2.985896 TGTTGAGGTAACAGCCTATGC 58.014 47.619 0.00 0.00 44.07 3.14
4044 4359 2.496070 TGGTTCTGAGGTGGAGATTACG 59.504 50.000 0.00 0.00 0.00 3.18
4101 4416 1.523938 GTTGCTGGAGGGATACGCC 60.524 63.158 0.00 0.00 37.60 5.68
4125 4440 2.497675 CCAGGTGTAGTGTGCTATCTGT 59.502 50.000 0.00 0.00 0.00 3.41
4126 4441 3.429547 CCAGGTGTAGTGTGCTATCTGTC 60.430 52.174 0.00 0.00 0.00 3.51
4127 4442 3.445450 CAGGTGTAGTGTGCTATCTGTCT 59.555 47.826 0.00 0.00 0.00 3.41
4128 4443 3.445450 AGGTGTAGTGTGCTATCTGTCTG 59.555 47.826 0.00 0.00 0.00 3.51
4153 4468 8.325787 TGTAATCAGGAGTGGTAATTGTATGTT 58.674 33.333 0.00 0.00 0.00 2.71
4265 4686 5.593679 TTATTTGACTCTTACTCCCTCCG 57.406 43.478 0.00 0.00 0.00 4.63
4266 4687 2.599408 TTGACTCTTACTCCCTCCGT 57.401 50.000 0.00 0.00 0.00 4.69
4267 4688 2.599408 TGACTCTTACTCCCTCCGTT 57.401 50.000 0.00 0.00 0.00 4.44
4268 4689 2.444421 TGACTCTTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 0.00 3.95
4269 4690 1.750206 GACTCTTACTCCCTCCGTTCC 59.250 57.143 0.00 0.00 0.00 3.62
4270 4691 1.076677 ACTCTTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 0.00 3.53
4271 4692 2.176889 CTCTTACTCCCTCCGTTCCAA 58.823 52.381 0.00 0.00 0.00 3.53
4272 4693 2.565834 CTCTTACTCCCTCCGTTCCAAA 59.434 50.000 0.00 0.00 0.00 3.28
4273 4694 3.178865 TCTTACTCCCTCCGTTCCAAAT 58.821 45.455 0.00 0.00 0.00 2.32
4274 4695 3.585732 TCTTACTCCCTCCGTTCCAAATT 59.414 43.478 0.00 0.00 0.00 1.82
4275 4696 4.778958 TCTTACTCCCTCCGTTCCAAATTA 59.221 41.667 0.00 0.00 0.00 1.40
4276 4697 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4277 4698 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4278 4699 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4279 4700 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4280 4701 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4281 4702 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4282 4703 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4283 4704 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
4284 4705 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
4285 4706 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
4286 4707 2.373540 TCCAAATTACTCGTCGTGGG 57.626 50.000 0.00 0.00 0.00 4.61
4287 4708 1.619827 TCCAAATTACTCGTCGTGGGT 59.380 47.619 0.00 0.00 0.00 4.51
4288 4709 2.824936 TCCAAATTACTCGTCGTGGGTA 59.175 45.455 0.00 0.00 0.00 3.69
4289 4710 3.257873 TCCAAATTACTCGTCGTGGGTAA 59.742 43.478 5.57 5.57 0.00 2.85
4290 4711 4.081531 TCCAAATTACTCGTCGTGGGTAAT 60.082 41.667 9.05 9.05 37.63 1.89
4291 4712 4.632688 CCAAATTACTCGTCGTGGGTAATT 59.367 41.667 17.08 17.08 43.51 1.40
4293 4714 5.789710 AATTACTCGTCGTGGGTAATTTG 57.210 39.130 17.08 0.00 40.80 2.32
4294 4715 4.517952 TTACTCGTCGTGGGTAATTTGA 57.482 40.909 0.00 0.00 0.00 2.69
4295 4716 3.389925 ACTCGTCGTGGGTAATTTGAA 57.610 42.857 0.00 0.00 0.00 2.69
4296 4717 3.731089 ACTCGTCGTGGGTAATTTGAAA 58.269 40.909 0.00 0.00 0.00 2.69
4297 4718 3.495753 ACTCGTCGTGGGTAATTTGAAAC 59.504 43.478 0.00 0.00 0.00 2.78
4298 4719 2.475864 TCGTCGTGGGTAATTTGAAACG 59.524 45.455 0.00 0.00 0.00 3.60
4299 4720 2.411806 CGTCGTGGGTAATTTGAAACGG 60.412 50.000 0.00 0.00 0.00 4.44
4300 4721 2.807392 GTCGTGGGTAATTTGAAACGGA 59.193 45.455 0.00 0.00 0.00 4.69
4301 4722 3.068560 TCGTGGGTAATTTGAAACGGAG 58.931 45.455 0.00 0.00 0.00 4.63
4302 4723 2.160813 CGTGGGTAATTTGAAACGGAGG 59.839 50.000 0.00 0.00 0.00 4.30
4303 4724 2.490509 GTGGGTAATTTGAAACGGAGGG 59.509 50.000 0.00 0.00 0.00 4.30
4304 4725 2.375845 TGGGTAATTTGAAACGGAGGGA 59.624 45.455 0.00 0.00 0.00 4.20
4305 4726 3.014623 GGGTAATTTGAAACGGAGGGAG 58.985 50.000 0.00 0.00 0.00 4.30
4306 4727 3.560668 GGGTAATTTGAAACGGAGGGAGT 60.561 47.826 0.00 0.00 0.00 3.85
4307 4728 4.323715 GGGTAATTTGAAACGGAGGGAGTA 60.324 45.833 0.00 0.00 0.00 2.59
4390 4815 7.862372 AGTTTGCTTGTACTGACATTATGTTTG 59.138 33.333 0.00 0.00 34.86 2.93
4632 5065 5.179182 GTCACAGCCCAAACAAAATAATTGG 59.821 40.000 0.00 0.00 42.59 3.16
4771 5206 6.140303 TGTATTAGTAACAAGACTAGCCCG 57.860 41.667 0.00 0.00 33.52 6.13
4772 5207 3.515330 TTAGTAACAAGACTAGCCCGC 57.485 47.619 0.00 0.00 33.52 6.13
4773 5208 0.535797 AGTAACAAGACTAGCCCGCC 59.464 55.000 0.00 0.00 0.00 6.13
4774 5209 0.804933 GTAACAAGACTAGCCCGCCG 60.805 60.000 0.00 0.00 0.00 6.46
4775 5210 2.567564 TAACAAGACTAGCCCGCCGC 62.568 60.000 0.00 0.00 37.98 6.53
4805 5240 3.123620 CTGCCGAGCTGCTGAACC 61.124 66.667 7.01 0.00 32.50 3.62
4806 5241 4.704833 TGCCGAGCTGCTGAACCC 62.705 66.667 7.01 0.00 0.00 4.11
4813 5248 3.121030 CTGCTGAACCCCGCGAAG 61.121 66.667 8.23 0.00 0.00 3.79
4814 5249 3.883744 CTGCTGAACCCCGCGAAGT 62.884 63.158 8.23 0.08 0.00 3.01
4815 5250 3.119096 GCTGAACCCCGCGAAGTC 61.119 66.667 8.23 0.00 0.00 3.01
4816 5251 2.434359 CTGAACCCCGCGAAGTCC 60.434 66.667 8.23 0.00 0.00 3.85
4817 5252 3.234630 CTGAACCCCGCGAAGTCCA 62.235 63.158 8.23 0.00 0.00 4.02
4818 5253 2.434359 GAACCCCGCGAAGTCCAG 60.434 66.667 8.23 0.00 0.00 3.86
4819 5254 3.236003 GAACCCCGCGAAGTCCAGT 62.236 63.158 8.23 0.00 0.00 4.00
4820 5255 3.530910 AACCCCGCGAAGTCCAGTG 62.531 63.158 8.23 0.00 0.00 3.66
4823 5258 4.680237 CCGCGAAGTCCAGTGCCA 62.680 66.667 8.23 0.00 0.00 4.92
4824 5259 3.414700 CGCGAAGTCCAGTGCCAC 61.415 66.667 0.00 0.00 0.00 5.01
4825 5260 2.280797 GCGAAGTCCAGTGCCACA 60.281 61.111 0.00 0.00 0.00 4.17
4826 5261 2.320587 GCGAAGTCCAGTGCCACAG 61.321 63.158 0.00 0.00 0.00 3.66
4827 5262 2.320587 CGAAGTCCAGTGCCACAGC 61.321 63.158 0.00 0.00 40.48 4.40
4828 5263 1.072159 GAAGTCCAGTGCCACAGCT 59.928 57.895 0.00 0.00 40.80 4.24
4829 5264 0.952984 GAAGTCCAGTGCCACAGCTC 60.953 60.000 0.00 0.00 40.80 4.09
4830 5265 2.359230 GTCCAGTGCCACAGCTCC 60.359 66.667 0.00 0.00 40.80 4.70
4831 5266 2.848679 TCCAGTGCCACAGCTCCA 60.849 61.111 0.00 0.00 40.80 3.86
4832 5267 2.359602 CCAGTGCCACAGCTCCAG 60.360 66.667 0.00 0.00 40.80 3.86
4833 5268 2.359602 CAGTGCCACAGCTCCAGG 60.360 66.667 0.00 0.00 40.80 4.45
4834 5269 2.527624 AGTGCCACAGCTCCAGGA 60.528 61.111 0.00 0.00 40.80 3.86
4835 5270 2.149383 AGTGCCACAGCTCCAGGAA 61.149 57.895 0.00 0.00 40.80 3.36
4836 5271 1.673665 GTGCCACAGCTCCAGGAAG 60.674 63.158 0.00 0.00 40.80 3.46
4837 5272 2.749441 GCCACAGCTCCAGGAAGC 60.749 66.667 0.00 0.00 42.82 3.86
4838 5273 2.045536 CCACAGCTCCAGGAAGCC 60.046 66.667 7.15 0.00 43.56 4.35
4839 5274 2.435586 CACAGCTCCAGGAAGCCG 60.436 66.667 7.15 1.15 43.56 5.52
4840 5275 4.400961 ACAGCTCCAGGAAGCCGC 62.401 66.667 7.15 0.00 43.56 6.53
4872 5307 3.003173 CCACGAGCAGGGGGAGAA 61.003 66.667 0.00 0.00 40.70 2.87
4873 5308 2.581354 CACGAGCAGGGGGAGAAG 59.419 66.667 0.00 0.00 0.00 2.85
4874 5309 2.685380 ACGAGCAGGGGGAGAAGG 60.685 66.667 0.00 0.00 0.00 3.46
4875 5310 3.474570 CGAGCAGGGGGAGAAGGG 61.475 72.222 0.00 0.00 0.00 3.95
4876 5311 3.803162 GAGCAGGGGGAGAAGGGC 61.803 72.222 0.00 0.00 0.00 5.19
4877 5312 4.682714 AGCAGGGGGAGAAGGGCA 62.683 66.667 0.00 0.00 0.00 5.36
4878 5313 4.432741 GCAGGGGGAGAAGGGCAC 62.433 72.222 0.00 0.00 0.00 5.01
5398 5833 5.789643 GAGCCCCAATGCTAATTAATCAA 57.210 39.130 0.00 0.00 42.95 2.57
5399 5834 5.776744 GAGCCCCAATGCTAATTAATCAAG 58.223 41.667 0.00 0.00 42.95 3.02
5400 5835 5.457686 AGCCCCAATGCTAATTAATCAAGA 58.542 37.500 2.70 0.00 40.56 3.02
5401 5836 5.537674 AGCCCCAATGCTAATTAATCAAGAG 59.462 40.000 2.70 0.00 40.56 2.85
5402 5837 5.302823 GCCCCAATGCTAATTAATCAAGAGT 59.697 40.000 2.70 0.00 0.00 3.24
5403 5838 6.515696 GCCCCAATGCTAATTAATCAAGAGTC 60.516 42.308 2.70 0.00 0.00 3.36
5404 5839 6.547141 CCCCAATGCTAATTAATCAAGAGTCA 59.453 38.462 0.00 0.00 0.00 3.41
5405 5840 7.232127 CCCCAATGCTAATTAATCAAGAGTCAT 59.768 37.037 0.00 0.00 0.00 3.06
5406 5841 9.288576 CCCAATGCTAATTAATCAAGAGTCATA 57.711 33.333 0.00 0.00 0.00 2.15
5420 5855 8.201554 TCAAGAGTCATACTATCATTTGTTGC 57.798 34.615 0.00 0.00 0.00 4.17
5421 5856 7.823799 TCAAGAGTCATACTATCATTTGTTGCA 59.176 33.333 0.00 0.00 0.00 4.08
5422 5857 8.453320 CAAGAGTCATACTATCATTTGTTGCAA 58.547 33.333 0.00 0.00 0.00 4.08
5423 5858 8.565896 AGAGTCATACTATCATTTGTTGCAAA 57.434 30.769 0.00 0.00 0.00 3.68
5424 5859 9.013229 AGAGTCATACTATCATTTGTTGCAAAA 57.987 29.630 0.00 0.00 0.00 2.44
5425 5860 9.793252 GAGTCATACTATCATTTGTTGCAAAAT 57.207 29.630 0.00 0.00 0.00 1.82
5428 5863 9.715123 TCATACTATCATTTGTTGCAAAATACG 57.285 29.630 0.00 0.00 0.00 3.06
5429 5864 9.502145 CATACTATCATTTGTTGCAAAATACGT 57.498 29.630 0.00 0.00 0.00 3.57
5430 5865 9.716507 ATACTATCATTTGTTGCAAAATACGTC 57.283 29.630 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.710907 CGAGATTAGGATTTGTCACTCCATTTA 59.289 37.037 3.96 0.00 33.75 1.40
554 557 7.832769 ACACTACTACAAAACCAAACACAAAT 58.167 30.769 0.00 0.00 0.00 2.32
725 741 6.846786 CGTGTTGAATTGTTACGTGATTTACA 59.153 34.615 0.00 0.65 0.00 2.41
726 742 7.064674 TCGTGTTGAATTGTTACGTGATTTAC 58.935 34.615 0.00 0.00 36.28 2.01
741 757 3.062763 CTCTTCTGCACTCGTGTTGAAT 58.937 45.455 0.00 0.00 0.00 2.57
755 771 2.354259 GGCCACATGTCTTCTCTTCTG 58.646 52.381 0.00 0.00 0.00 3.02
772 788 1.814169 CTCTTTTCTACCCGCGGCC 60.814 63.158 22.85 0.00 0.00 6.13
773 789 0.672711 AACTCTTTTCTACCCGCGGC 60.673 55.000 22.85 0.00 0.00 6.53
796 812 1.325355 CATTCCCCATGGCATCACTC 58.675 55.000 6.09 0.00 0.00 3.51
811 827 9.410556 ACTTGCTATATTTTGTTGTTGACATTC 57.589 29.630 0.00 0.00 38.26 2.67
858 874 7.724305 AAACATTGTTAGTTATGTCGTGACT 57.276 32.000 1.76 0.00 34.04 3.41
925 943 6.796785 ATGCAGGTGCTTTCCTATTTTATT 57.203 33.333 3.18 0.00 42.66 1.40
1003 1026 0.470766 ATTAACATCCGCGCCCCTTA 59.529 50.000 0.00 0.00 0.00 2.69
1011 1034 1.880027 GACCCATCCATTAACATCCGC 59.120 52.381 0.00 0.00 0.00 5.54
1030 1053 2.048222 CAGTTCTCCGCTTGCCGA 60.048 61.111 0.00 0.00 40.02 5.54
1053 1076 6.702329 ACCTATTCTTCTCCACAACTAGTTG 58.298 40.000 29.76 29.76 45.58 3.16
1056 1079 7.176589 AGAACCTATTCTTCTCCACAACTAG 57.823 40.000 0.00 0.00 42.91 2.57
1128 1157 4.277476 CTGGGATGGTTGTATAAAGGCAA 58.723 43.478 0.00 0.00 0.00 4.52
1129 1158 3.897239 CTGGGATGGTTGTATAAAGGCA 58.103 45.455 0.00 0.00 0.00 4.75
1130 1159 2.623416 GCTGGGATGGTTGTATAAAGGC 59.377 50.000 0.00 0.00 0.00 4.35
1131 1160 3.222603 GGCTGGGATGGTTGTATAAAGG 58.777 50.000 0.00 0.00 0.00 3.11
1132 1161 3.222603 GGGCTGGGATGGTTGTATAAAG 58.777 50.000 0.00 0.00 0.00 1.85
1133 1162 2.422235 CGGGCTGGGATGGTTGTATAAA 60.422 50.000 0.00 0.00 0.00 1.40
1134 1163 1.142060 CGGGCTGGGATGGTTGTATAA 59.858 52.381 0.00 0.00 0.00 0.98
1163 1192 2.685100 ACCTAGCAGCGTTTCTACAAC 58.315 47.619 0.00 0.00 0.00 3.32
1164 1193 3.396260 AACCTAGCAGCGTTTCTACAA 57.604 42.857 0.00 0.00 0.00 2.41
1168 1197 3.187700 CGAATAACCTAGCAGCGTTTCT 58.812 45.455 0.00 0.00 0.00 2.52
1192 1226 4.742440 GCCTGGGGTTTACTTTTTCTTTGG 60.742 45.833 0.00 0.00 0.00 3.28
1245 1304 4.933064 CGAGATCGACCCGCTGCC 62.933 72.222 0.00 0.00 43.02 4.85
1270 1329 1.062658 TCTCCTCCATCAGCATCTCCA 60.063 52.381 0.00 0.00 0.00 3.86
1271 1330 1.714541 TCTCCTCCATCAGCATCTCC 58.285 55.000 0.00 0.00 0.00 3.71
1342 1401 2.848694 TGATCCCTCCAGCAAGAAATCT 59.151 45.455 0.00 0.00 0.00 2.40
1376 1435 2.910688 TATGGAAGGACGAGATTGCC 57.089 50.000 0.00 0.00 0.00 4.52
1410 1469 0.179065 TATACCTGCTGCTGCTGCTG 60.179 55.000 27.67 25.97 40.48 4.41
1411 1470 0.179062 GTATACCTGCTGCTGCTGCT 60.179 55.000 27.67 13.59 40.48 4.24
1412 1471 0.179062 AGTATACCTGCTGCTGCTGC 60.179 55.000 22.51 22.51 40.48 5.25
1413 1472 1.938577 CAAGTATACCTGCTGCTGCTG 59.061 52.381 17.00 15.58 40.48 4.41
1414 1473 1.833630 TCAAGTATACCTGCTGCTGCT 59.166 47.619 17.00 0.00 40.48 4.24
1415 1474 1.936547 GTCAAGTATACCTGCTGCTGC 59.063 52.381 8.89 8.89 40.20 5.25
1451 1540 1.038130 AATCCTCGACGTCCTCCAGG 61.038 60.000 10.58 10.25 0.00 4.45
1594 1683 2.534903 GGCGCCTCGGTAGAATTGC 61.535 63.158 22.15 0.00 0.00 3.56
1611 1700 2.123982 GGCTGCCTCCTCCATTGG 60.124 66.667 12.43 0.00 0.00 3.16
1628 1717 3.264706 TCATCCTATACCTCTCCTCCTCG 59.735 52.174 0.00 0.00 0.00 4.63
1641 1730 6.378564 GTCTTCCGAATCTCCATCATCCTATA 59.621 42.308 0.00 0.00 0.00 1.31
1714 1806 0.523966 CCGAGTCTGCTTCGTCTTCT 59.476 55.000 0.00 0.00 0.00 2.85
1732 1824 5.071519 TCATCATTCCTCATCTTCTTCTCCC 59.928 44.000 0.00 0.00 0.00 4.30
1774 1866 2.807967 TGCAAGAATTCGTTGGACAGAG 59.192 45.455 15.09 0.00 0.00 3.35
1933 2025 1.362406 CTTCTTTCTTCTCCGCCGCC 61.362 60.000 0.00 0.00 0.00 6.13
2036 2143 1.698532 AGCTCATCATCCATCCACTCC 59.301 52.381 0.00 0.00 0.00 3.85
2151 2258 3.071479 TGGAATAAAGTTGAGCGTGGAC 58.929 45.455 0.00 0.00 0.00 4.02
2171 2278 1.078709 CCGCACCTTATGACACACTG 58.921 55.000 0.00 0.00 0.00 3.66
2172 2279 0.973632 TCCGCACCTTATGACACACT 59.026 50.000 0.00 0.00 0.00 3.55
2274 2524 4.589908 CAAGTCCCATAGTTAACTTGCCT 58.410 43.478 14.49 5.56 41.31 4.75
2473 2723 3.955471 AGCAACTTCAGCTGGCTAATTA 58.045 40.909 15.13 0.00 41.61 1.40
2480 2730 1.467734 CTGCTAAGCAACTTCAGCTGG 59.532 52.381 15.13 0.36 42.53 4.85
2481 2731 2.896243 CTGCTAAGCAACTTCAGCTG 57.104 50.000 7.63 7.63 42.53 4.24
2497 2747 5.499139 TTATACCACATTAAAGCTGCTGC 57.501 39.130 1.35 7.62 40.05 5.25
2498 2748 5.822519 TCCTTATACCACATTAAAGCTGCTG 59.177 40.000 1.35 0.00 0.00 4.41
2499 2749 5.823045 GTCCTTATACCACATTAAAGCTGCT 59.177 40.000 0.00 0.00 0.00 4.24
2500 2750 5.823045 AGTCCTTATACCACATTAAAGCTGC 59.177 40.000 0.00 0.00 0.00 5.25
3035 3285 7.823745 ATTAAACAAAGACCATCAGTTCACT 57.176 32.000 0.00 0.00 0.00 3.41
3401 3695 5.582689 AAAAGAACCAGTGGACAAAGAAG 57.417 39.130 18.40 0.00 0.00 2.85
3580 3874 5.706833 TCAACTGTGTATCATTGTGCTCATT 59.293 36.000 0.00 0.00 0.00 2.57
3678 3990 1.006102 AAACCTCGACTCCGCAGTG 60.006 57.895 0.00 0.00 30.63 3.66
3689 4001 3.797256 CGTAGGAATAAGCTCAAACCTCG 59.203 47.826 5.89 6.60 0.00 4.63
3703 4015 0.683504 AGCTGGACCGTCGTAGGAAT 60.684 55.000 5.97 0.00 34.73 3.01
3853 4168 7.176690 AGGAACATAACCATCCAAAACTACTTG 59.823 37.037 0.00 0.00 35.62 3.16
3909 4224 3.248602 CCTCAACAGTCACTCCTTTTTCG 59.751 47.826 0.00 0.00 0.00 3.46
3944 4259 6.016360 ACGATCAGAGATAGAACCAGAATCAG 60.016 42.308 0.00 0.00 0.00 2.90
4044 4359 3.879180 AACCCGGGACCATGCAACC 62.879 63.158 32.02 0.00 0.00 3.77
4125 4440 6.620877 ACAATTACCACTCCTGATTACAGA 57.379 37.500 0.00 0.00 46.03 3.41
4126 4441 7.987458 ACATACAATTACCACTCCTGATTACAG 59.013 37.037 0.00 0.00 43.12 2.74
4127 4442 7.857456 ACATACAATTACCACTCCTGATTACA 58.143 34.615 0.00 0.00 0.00 2.41
4128 4443 8.612619 CAACATACAATTACCACTCCTGATTAC 58.387 37.037 0.00 0.00 0.00 1.89
4257 4678 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4258 4679 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4259 4680 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4260 4681 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4261 4682 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4262 4683 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
4263 4684 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
4264 4685 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
4265 4686 2.414138 CCCACGACGAGTAATTTGGAAC 59.586 50.000 0.00 0.00 0.00 3.62
4266 4687 2.037511 ACCCACGACGAGTAATTTGGAA 59.962 45.455 0.00 0.00 0.00 3.53
4267 4688 1.619827 ACCCACGACGAGTAATTTGGA 59.380 47.619 0.00 0.00 0.00 3.53
4268 4689 2.088950 ACCCACGACGAGTAATTTGG 57.911 50.000 0.00 0.00 0.00 3.28
4269 4690 5.789710 AATTACCCACGACGAGTAATTTG 57.210 39.130 19.75 2.30 41.56 2.32
4271 4692 5.481105 TCAAATTACCCACGACGAGTAATT 58.519 37.500 19.75 19.75 44.50 1.40
4272 4693 5.075858 TCAAATTACCCACGACGAGTAAT 57.924 39.130 0.00 9.07 38.10 1.89
4273 4694 4.517952 TCAAATTACCCACGACGAGTAA 57.482 40.909 0.00 7.07 0.00 2.24
4274 4695 4.517952 TTCAAATTACCCACGACGAGTA 57.482 40.909 0.00 0.00 0.00 2.59
4275 4696 3.389925 TTCAAATTACCCACGACGAGT 57.610 42.857 0.00 0.00 0.00 4.18
4276 4697 3.422603 CGTTTCAAATTACCCACGACGAG 60.423 47.826 0.00 0.00 0.00 4.18
4277 4698 2.475864 CGTTTCAAATTACCCACGACGA 59.524 45.455 0.00 0.00 0.00 4.20
4278 4699 2.411806 CCGTTTCAAATTACCCACGACG 60.412 50.000 0.00 0.00 0.00 5.12
4279 4700 2.807392 TCCGTTTCAAATTACCCACGAC 59.193 45.455 0.00 0.00 0.00 4.34
4280 4701 3.068560 CTCCGTTTCAAATTACCCACGA 58.931 45.455 0.00 0.00 0.00 4.35
4281 4702 2.160813 CCTCCGTTTCAAATTACCCACG 59.839 50.000 0.00 0.00 0.00 4.94
4282 4703 2.490509 CCCTCCGTTTCAAATTACCCAC 59.509 50.000 0.00 0.00 0.00 4.61
4283 4704 2.375845 TCCCTCCGTTTCAAATTACCCA 59.624 45.455 0.00 0.00 0.00 4.51
4284 4705 3.014623 CTCCCTCCGTTTCAAATTACCC 58.985 50.000 0.00 0.00 0.00 3.69
4285 4706 3.682696 ACTCCCTCCGTTTCAAATTACC 58.317 45.455 0.00 0.00 0.00 2.85
4286 4707 5.878669 ACATACTCCCTCCGTTTCAAATTAC 59.121 40.000 0.00 0.00 0.00 1.89
4287 4708 5.878116 CACATACTCCCTCCGTTTCAAATTA 59.122 40.000 0.00 0.00 0.00 1.40
4288 4709 4.700213 CACATACTCCCTCCGTTTCAAATT 59.300 41.667 0.00 0.00 0.00 1.82
4289 4710 4.261801 CACATACTCCCTCCGTTTCAAAT 58.738 43.478 0.00 0.00 0.00 2.32
4290 4711 3.071892 ACACATACTCCCTCCGTTTCAAA 59.928 43.478 0.00 0.00 0.00 2.69
4291 4712 2.635915 ACACATACTCCCTCCGTTTCAA 59.364 45.455 0.00 0.00 0.00 2.69
4292 4713 2.253610 ACACATACTCCCTCCGTTTCA 58.746 47.619 0.00 0.00 0.00 2.69
4293 4714 3.329929 AACACATACTCCCTCCGTTTC 57.670 47.619 0.00 0.00 0.00 2.78
4294 4715 4.895668 TTAACACATACTCCCTCCGTTT 57.104 40.909 0.00 0.00 0.00 3.60
4295 4716 4.468510 TCATTAACACATACTCCCTCCGTT 59.531 41.667 0.00 0.00 0.00 4.44
4296 4717 4.028131 TCATTAACACATACTCCCTCCGT 58.972 43.478 0.00 0.00 0.00 4.69
4297 4718 4.621991 CTCATTAACACATACTCCCTCCG 58.378 47.826 0.00 0.00 0.00 4.63
4298 4719 4.141711 TGCTCATTAACACATACTCCCTCC 60.142 45.833 0.00 0.00 0.00 4.30
4299 4720 5.023533 TGCTCATTAACACATACTCCCTC 57.976 43.478 0.00 0.00 0.00 4.30
4300 4721 4.471386 ACTGCTCATTAACACATACTCCCT 59.529 41.667 0.00 0.00 0.00 4.20
4301 4722 4.770795 ACTGCTCATTAACACATACTCCC 58.229 43.478 0.00 0.00 0.00 4.30
4302 4723 4.504461 CGACTGCTCATTAACACATACTCC 59.496 45.833 0.00 0.00 0.00 3.85
4303 4724 5.004821 CACGACTGCTCATTAACACATACTC 59.995 44.000 0.00 0.00 0.00 2.59
4304 4725 4.864806 CACGACTGCTCATTAACACATACT 59.135 41.667 0.00 0.00 0.00 2.12
4305 4726 4.625742 ACACGACTGCTCATTAACACATAC 59.374 41.667 0.00 0.00 0.00 2.39
4306 4727 4.816392 ACACGACTGCTCATTAACACATA 58.184 39.130 0.00 0.00 0.00 2.29
4307 4728 3.664107 ACACGACTGCTCATTAACACAT 58.336 40.909 0.00 0.00 0.00 3.21
4379 4804 4.507388 GCACACAACAAGCAAACATAATGT 59.493 37.500 0.00 0.00 0.00 2.71
4632 5065 5.622233 GCATCCCAACTTGTTAATTGACTCC 60.622 44.000 1.75 0.00 0.00 3.85
4788 5223 3.123620 GGTTCAGCAGCTCGGCAG 61.124 66.667 0.00 0.00 35.83 4.85
4789 5224 4.704833 GGGTTCAGCAGCTCGGCA 62.705 66.667 0.00 0.00 35.83 5.69
4796 5231 3.121030 CTTCGCGGGGTTCAGCAG 61.121 66.667 6.13 0.00 0.00 4.24
4797 5232 3.876589 GACTTCGCGGGGTTCAGCA 62.877 63.158 6.13 0.00 0.00 4.41
4798 5233 3.119096 GACTTCGCGGGGTTCAGC 61.119 66.667 6.13 0.00 0.00 4.26
4799 5234 2.434359 GGACTTCGCGGGGTTCAG 60.434 66.667 6.13 0.00 0.00 3.02
4800 5235 3.234630 CTGGACTTCGCGGGGTTCA 62.235 63.158 6.13 9.68 0.00 3.18
4801 5236 2.434359 CTGGACTTCGCGGGGTTC 60.434 66.667 6.13 4.91 0.00 3.62
4802 5237 3.239253 ACTGGACTTCGCGGGGTT 61.239 61.111 6.13 0.00 0.00 4.11
4803 5238 4.003788 CACTGGACTTCGCGGGGT 62.004 66.667 6.13 5.28 0.00 4.95
4806 5241 4.680237 TGGCACTGGACTTCGCGG 62.680 66.667 6.13 0.00 0.00 6.46
4807 5242 3.414700 GTGGCACTGGACTTCGCG 61.415 66.667 11.13 0.00 0.00 5.87
4808 5243 2.280797 TGTGGCACTGGACTTCGC 60.281 61.111 19.83 0.00 0.00 4.70
4809 5244 2.320587 GCTGTGGCACTGGACTTCG 61.321 63.158 23.39 2.45 38.54 3.79
4810 5245 0.952984 GAGCTGTGGCACTGGACTTC 60.953 60.000 23.39 8.48 41.70 3.01
4811 5246 1.072159 GAGCTGTGGCACTGGACTT 59.928 57.895 23.39 2.49 41.70 3.01
4812 5247 2.746359 GAGCTGTGGCACTGGACT 59.254 61.111 23.39 14.02 41.70 3.85
4813 5248 2.359230 GGAGCTGTGGCACTGGAC 60.359 66.667 23.39 9.79 41.70 4.02
4814 5249 2.848679 TGGAGCTGTGGCACTGGA 60.849 61.111 23.39 1.27 41.70 3.86
4815 5250 2.359602 CTGGAGCTGTGGCACTGG 60.360 66.667 23.39 14.96 41.70 4.00
4816 5251 2.359602 CCTGGAGCTGTGGCACTG 60.360 66.667 19.83 19.34 41.70 3.66
4817 5252 2.121992 CTTCCTGGAGCTGTGGCACT 62.122 60.000 19.83 0.00 41.70 4.40
4818 5253 1.673665 CTTCCTGGAGCTGTGGCAC 60.674 63.158 11.55 11.55 41.70 5.01
4819 5254 2.752358 CTTCCTGGAGCTGTGGCA 59.248 61.111 0.00 0.00 41.70 4.92
4820 5255 2.749441 GCTTCCTGGAGCTGTGGC 60.749 66.667 0.00 1.16 39.57 5.01
4821 5256 2.045536 GGCTTCCTGGAGCTGTGG 60.046 66.667 14.77 0.00 42.32 4.17
4822 5257 2.435586 CGGCTTCCTGGAGCTGTG 60.436 66.667 14.90 5.53 42.73 3.66
4855 5290 3.003173 TTCTCCCCCTGCTCGTGG 61.003 66.667 0.00 0.00 0.00 4.94
4856 5291 2.581354 CTTCTCCCCCTGCTCGTG 59.419 66.667 0.00 0.00 0.00 4.35
4857 5292 2.685380 CCTTCTCCCCCTGCTCGT 60.685 66.667 0.00 0.00 0.00 4.18
4858 5293 3.474570 CCCTTCTCCCCCTGCTCG 61.475 72.222 0.00 0.00 0.00 5.03
4859 5294 3.803162 GCCCTTCTCCCCCTGCTC 61.803 72.222 0.00 0.00 0.00 4.26
4860 5295 4.682714 TGCCCTTCTCCCCCTGCT 62.683 66.667 0.00 0.00 0.00 4.24
4861 5296 4.432741 GTGCCCTTCTCCCCCTGC 62.433 72.222 0.00 0.00 0.00 4.85
4862 5297 3.732849 GGTGCCCTTCTCCCCCTG 61.733 72.222 0.00 0.00 0.00 4.45
4900 5335 4.090057 GTGCTCCGCGGACAAAGC 62.090 66.667 27.28 26.16 33.62 3.51
4901 5336 3.777925 CGTGCTCCGCGGACAAAG 61.778 66.667 27.28 16.39 32.85 2.77
5376 5811 5.536161 TCTTGATTAATTAGCATTGGGGCTC 59.464 40.000 0.00 0.00 44.54 4.70
5378 5813 5.302823 ACTCTTGATTAATTAGCATTGGGGC 59.697 40.000 0.00 0.00 0.00 5.80
5379 5814 6.547141 TGACTCTTGATTAATTAGCATTGGGG 59.453 38.462 0.00 0.00 0.00 4.96
5380 5815 7.572523 TGACTCTTGATTAATTAGCATTGGG 57.427 36.000 0.00 0.00 0.00 4.12
5394 5829 8.834465 GCAACAAATGATAGTATGACTCTTGAT 58.166 33.333 0.00 0.00 0.00 2.57
5395 5830 7.823799 TGCAACAAATGATAGTATGACTCTTGA 59.176 33.333 0.00 0.00 0.00 3.02
5396 5831 7.977904 TGCAACAAATGATAGTATGACTCTTG 58.022 34.615 0.00 0.00 0.00 3.02
5397 5832 8.565896 TTGCAACAAATGATAGTATGACTCTT 57.434 30.769 0.00 0.00 0.00 2.85
5398 5833 8.565896 TTTGCAACAAATGATAGTATGACTCT 57.434 30.769 0.00 0.00 0.00 3.24
5399 5834 9.793252 ATTTTGCAACAAATGATAGTATGACTC 57.207 29.630 0.00 0.00 0.00 3.36
5402 5837 9.715123 CGTATTTTGCAACAAATGATAGTATGA 57.285 29.630 0.00 0.00 0.00 2.15
5403 5838 9.502145 ACGTATTTTGCAACAAATGATAGTATG 57.498 29.630 0.00 0.00 0.00 2.39
5404 5839 9.716507 GACGTATTTTGCAACAAATGATAGTAT 57.283 29.630 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.