Multiple sequence alignment - TraesCS3B01G076400

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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 TraesCS3B01G076400 chr3B 100.000 3152 0 0 1 3152 47191685 47194836 0.000000e+00 5821.0
1 TraesCS3B01G076400 chr3B 100.000 1420 0 0 3500 4919 47195184 47196603 0.000000e+00 2623.0
2 TraesCS3B01G076400 chr3B 76.519 971 178 29 1356 2312 47121670 47122604 7.400000e-133 484.0
3 TraesCS3B01G076400 chr3B 76.313 971 176 30 1361 2315 46365619 46364687 2.070000e-128 470.0
4 TraesCS3B01G076400 chr3B 79.091 330 51 9 3722 4050 47122893 47123205 1.390000e-50 211.0
5 TraesCS3B01G076400 chr3B 80.488 205 24 7 3849 4052 46364079 46363890 5.130000e-30 143.0
6 TraesCS3B01G076400 chr3B 78.289 152 30 3 3807 3957 46307758 46307907 1.460000e-15 95.3
7 TraesCS3B01G076400 chr3B 94.000 50 2 1 572 621 68407730 68407682 1.900000e-09 75.0
8 TraesCS3B01G076400 chr3B 93.750 48 3 0 4555 4602 47205283 47205330 6.830000e-09 73.1
9 TraesCS3B01G076400 chr3D 93.463 1285 59 13 3659 4919 27678191 27676908 0.000000e+00 1884.0
10 TraesCS3B01G076400 chr3D 93.494 830 48 1 1481 2310 27681531 27680708 0.000000e+00 1229.0
11 TraesCS3B01G076400 chr3D 92.490 759 48 7 2398 3152 27679247 27678494 0.000000e+00 1077.0
12 TraesCS3B01G076400 chr3D 87.263 581 62 7 920 1491 27682128 27681551 0.000000e+00 652.0
13 TraesCS3B01G076400 chr3D 91.213 478 18 10 393 849 27688795 27688321 3.230000e-176 628.0
14 TraesCS3B01G076400 chr3D 85.455 385 38 10 1 379 27689352 27688980 7.720000e-103 385.0
15 TraesCS3B01G076400 chr3D 93.902 164 10 0 3500 3663 27678448 27678285 1.060000e-61 248.0
16 TraesCS3B01G076400 chr3D 80.455 220 36 5 3722 3939 27950092 27950306 1.420000e-35 161.0
17 TraesCS3B01G076400 chr3D 77.586 232 37 12 3741 3965 4924881 4924658 5.170000e-25 126.0
18 TraesCS3B01G076400 chr3D 98.276 58 1 0 865 922 27682211 27682154 8.710000e-18 102.0
19 TraesCS3B01G076400 chr3D 83.871 93 11 3 4173 4261 324311072 324311164 8.770000e-13 86.1
20 TraesCS3B01G076400 chr3D 86.364 66 7 2 4181 4245 363324933 363324869 2.460000e-08 71.3
21 TraesCS3B01G076400 chr3A 77.002 974 174 24 1356 2315 37823519 37822582 3.400000e-141 512.0
22 TraesCS3B01G076400 chr3A 78.049 328 52 9 3725 4050 37822293 37821984 6.500000e-44 189.0
23 TraesCS3B01G076400 chr3A 88.764 89 5 4 4177 4261 58929337 58929424 2.420000e-18 104.0
24 TraesCS3B01G076400 chr3A 88.333 60 7 0 153 212 531961517 531961458 6.830000e-09 73.1
25 TraesCS3B01G076400 chr6D 91.398 372 31 1 2360 2730 437338665 437338294 4.390000e-140 508.0
26 TraesCS3B01G076400 chr6D 87.952 415 45 5 2355 2764 119162855 119163269 7.400000e-133 484.0
27 TraesCS3B01G076400 chr6D 77.647 170 26 7 135 302 2898994 2899153 5.240000e-15 93.5
28 TraesCS3B01G076400 chr7A 89.216 408 38 4 2352 2755 30253963 30254368 5.680000e-139 505.0
29 TraesCS3B01G076400 chr7A 83.146 89 11 2 4182 4266 433736426 433736514 1.470000e-10 78.7
30 TraesCS3B01G076400 chr2D 90.981 377 31 3 2356 2730 114817816 114818191 5.680000e-139 505.0
31 TraesCS3B01G076400 chr2D 88.416 423 41 6 2351 2769 66822600 66823018 2.040000e-138 503.0
32 TraesCS3B01G076400 chr2D 88.943 407 40 3 2353 2755 61308365 61307960 9.510000e-137 497.0
33 TraesCS3B01G076400 chr2D 88.378 413 42 4 2347 2755 40785176 40784766 4.420000e-135 492.0
34 TraesCS3B01G076400 chr2D 88.642 405 40 4 2356 2755 22789330 22788927 5.720000e-134 488.0
35 TraesCS3B01G076400 chr2D 75.934 241 53 4 1051 1287 35035104 35034865 8.650000e-23 119.0
36 TraesCS3B01G076400 chr2D 86.567 67 8 1 4181 4246 383553884 383553818 6.830000e-09 73.1
37 TraesCS3B01G076400 chr2D 91.667 48 4 0 4189 4236 493194381 493194428 3.180000e-07 67.6
38 TraesCS3B01G076400 chrUn 79.275 193 38 2 1922 2113 306115748 306115557 3.090000e-27 134.0
39 TraesCS3B01G076400 chrUn 76.250 160 28 5 144 302 323395994 323396144 5.280000e-10 76.8
40 TraesCS3B01G076400 chrUn 76.250 160 28 5 144 302 323399194 323399344 5.280000e-10 76.8
41 TraesCS3B01G076400 chrUn 76.250 160 28 5 144 302 382807225 382807075 5.280000e-10 76.8
42 TraesCS3B01G076400 chr2B 72.727 473 99 19 1746 2203 787034390 787033933 1.110000e-26 132.0
43 TraesCS3B01G076400 chr2B 75.519 241 54 4 1051 1287 57791138 57790899 4.020000e-21 113.0
44 TraesCS3B01G076400 chr2B 91.304 69 5 1 4179 4246 771822009 771821941 5.240000e-15 93.5
45 TraesCS3B01G076400 chr2B 92.453 53 3 1 569 621 63858173 63858224 1.900000e-09 75.0
46 TraesCS3B01G076400 chr7D 78.659 164 23 7 144 305 56623132 56622979 1.130000e-16 99.0
47 TraesCS3B01G076400 chr7D 88.060 67 7 1 4180 4245 424708820 424708886 1.470000e-10 78.7
48 TraesCS3B01G076400 chr2A 92.537 67 5 0 4180 4246 758599098 758599164 4.050000e-16 97.1
49 TraesCS3B01G076400 chr5A 84.694 98 10 5 4175 4268 27728003 27727907 5.240000e-15 93.5
50 TraesCS3B01G076400 chr5A 86.567 67 7 2 4181 4246 700441681 700441616 6.830000e-09 73.1
51 TraesCS3B01G076400 chr4B 85.882 85 8 2 4181 4261 420202873 420202957 2.440000e-13 87.9
52 TraesCS3B01G076400 chr1D 85.393 89 8 4 4177 4261 59875944 59876031 2.440000e-13 87.9
53 TraesCS3B01G076400 chr5B 89.706 68 6 1 4180 4246 580289204 580289137 8.770000e-13 86.1
54 TraesCS3B01G076400 chr1A 90.164 61 5 1 4187 4246 466899791 466899851 1.470000e-10 78.7
55 TraesCS3B01G076400 chr1B 76.543 162 23 8 146 306 133162682 133162535 1.900000e-09 75.0
56 TraesCS3B01G076400 chr1B 83.117 77 10 2 4188 4261 70499496 70499572 3.180000e-07 67.6
57 TraesCS3B01G076400 chr6A 91.837 49 2 2 4189 4236 68894627 68894580 3.180000e-07 67.6
58 TraesCS3B01G076400 chr5D 97.368 38 1 0 4188 4225 460038787 460038824 1.140000e-06 65.8
59 TraesCS3B01G076400 chr4A 81.707 82 11 3 144 222 620594580 620594500 1.140000e-06 65.8


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 TraesCS3B01G076400 chr3B 47191685 47196603 4918 False 4222.000000 5821 100.0000 1 4919 2 chr3B.!!$F4 4918
1 TraesCS3B01G076400 chr3B 47121670 47123205 1535 False 347.500000 484 77.8050 1356 4050 2 chr3B.!!$F3 2694
2 TraesCS3B01G076400 chr3B 46363890 46365619 1729 True 306.500000 470 78.4005 1361 4052 2 chr3B.!!$R2 2691
3 TraesCS3B01G076400 chr3D 27676908 27682211 5303 True 865.333333 1884 93.1480 865 4919 6 chr3D.!!$R3 4054
4 TraesCS3B01G076400 chr3D 27688321 27689352 1031 True 506.500000 628 88.3340 1 849 2 chr3D.!!$R4 848
5 TraesCS3B01G076400 chr3A 37821984 37823519 1535 True 350.500000 512 77.5255 1356 4050 2 chr3A.!!$R2 2694

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
558 741 0.037734 ATTTCTTGGGACGTGGGACC 59.962 55.0 0.00 0.0 0.0 4.46 F
1217 1443 0.038159 CTCCTCGGCGTCTTTGAGTT 60.038 55.0 6.85 0.0 0.0 3.01 F
1840 2102 0.178767 TTGTCAGATCATCCAGGCCG 59.821 55.0 0.00 0.0 0.0 6.13 F
2523 4191 0.179137 CATTCGGCGAGCTCTGTACA 60.179 55.0 10.46 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 4064 0.031994 ATGTTTTCTTGCGTGGGTGC 59.968 50.000 0.00 0.00 0.00 5.01 R
2500 4168 1.137086 ACAGAGCTCGCCGAATGTTAT 59.863 47.619 8.37 0.00 0.00 1.89 R
3650 5536 0.603569 CCGGACTCAATAGATCCCGG 59.396 60.000 0.00 7.31 42.52 5.73 R
4354 6353 0.952984 GACAGCAGTCACAAGAGCCC 60.953 60.000 4.10 0.00 44.34 5.19 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
26 27 2.036387 TGGAGAACTTCCTCGACAACA 58.964 47.619 0.00 0.00 46.92 3.33
28 29 2.801111 GGAGAACTTCCTCGACAACAAC 59.199 50.000 0.00 0.00 43.16 3.32
29 30 3.454375 GAGAACTTCCTCGACAACAACA 58.546 45.455 0.00 0.00 0.00 3.33
30 31 4.058817 GAGAACTTCCTCGACAACAACAT 58.941 43.478 0.00 0.00 0.00 2.71
53 54 9.039165 ACATCATCATGGGATTAAAAGAAGTTT 57.961 29.630 0.00 0.00 33.82 2.66
111 112 1.305219 TTGGCCATGTTGTAGCTCGC 61.305 55.000 6.09 0.00 0.00 5.03
116 118 1.432514 CATGTTGTAGCTCGCTGTGT 58.567 50.000 0.85 0.00 0.00 3.72
124 126 1.082756 GCTCGCTGTGTCAAAACCG 60.083 57.895 0.00 0.00 0.00 4.44
125 127 1.082756 CTCGCTGTGTCAAAACCGC 60.083 57.895 0.00 0.00 0.00 5.68
128 130 1.008538 GCTGTGTCAAAACCGCTGG 60.009 57.895 0.00 0.00 0.00 4.85
189 193 9.289303 TCTGAGCAATTTTTCGCTAAATAAATC 57.711 29.630 0.00 0.00 38.99 2.17
226 230 8.554528 GTCTCACTAATACTACACTATAACGCA 58.445 37.037 0.00 0.00 0.00 5.24
274 278 6.653989 AGCATATTTTAAGAGTGGTGCTACT 58.346 36.000 0.00 0.00 39.64 2.57
279 283 1.512926 AAGAGTGGTGCTACTTTGCG 58.487 50.000 0.00 0.00 35.36 4.85
325 329 3.249559 GTCAAAACTGAAGAGCCTGAGTG 59.750 47.826 0.00 0.00 0.00 3.51
327 331 3.567478 AAACTGAAGAGCCTGAGTGTT 57.433 42.857 0.00 0.00 0.00 3.32
328 332 4.689612 AAACTGAAGAGCCTGAGTGTTA 57.310 40.909 0.00 0.00 0.00 2.41
342 349 6.583806 GCCTGAGTGTTAATTTCTCAATTGTG 59.416 38.462 5.13 2.93 37.68 3.33
345 352 7.362662 TGAGTGTTAATTTCTCAATTGTGCTC 58.637 34.615 5.13 2.84 35.65 4.26
391 560 5.717178 CCTACTCTTATAGATAGCAAGGGCA 59.283 44.000 0.00 0.00 44.61 5.36
395 564 6.726299 ACTCTTATAGATAGCAAGGGCATGTA 59.274 38.462 0.00 0.00 44.61 2.29
396 565 6.936279 TCTTATAGATAGCAAGGGCATGTAC 58.064 40.000 0.00 0.00 44.61 2.90
397 566 6.496911 TCTTATAGATAGCAAGGGCATGTACA 59.503 38.462 0.00 0.00 44.61 2.90
488 668 5.066893 CACATGATTGATTCAGTAACCAGGG 59.933 44.000 0.00 0.00 37.89 4.45
489 669 5.044919 ACATGATTGATTCAGTAACCAGGGA 60.045 40.000 0.00 0.00 37.89 4.20
490 670 5.512942 TGATTGATTCAGTAACCAGGGAA 57.487 39.130 0.00 0.00 0.00 3.97
520 703 0.680280 CCGAGACTCGAGGAGGGAAA 60.680 60.000 26.11 0.00 43.74 3.13
537 720 3.952628 AAGCGGCGCTGAGGTTACC 62.953 63.158 37.09 0.00 39.62 2.85
558 741 0.037734 ATTTCTTGGGACGTGGGACC 59.962 55.000 0.00 0.00 0.00 4.46
593 776 1.137675 TCAGATCAGGCTGATGAACCG 59.862 52.381 33.30 16.18 39.84 4.44
619 802 6.267817 GGTGGTTCCAACTAGTTTGTTTTAC 58.732 40.000 5.07 2.19 35.97 2.01
637 820 5.600908 TTTACATTACAAGACGCCAAGAC 57.399 39.130 0.00 0.00 0.00 3.01
658 841 2.128507 TGTGTTGGTTTTCCCCGGC 61.129 57.895 0.00 0.00 39.73 6.13
699 882 4.877378 AGCATCTTGATTGGCAGAAAAA 57.123 36.364 0.00 0.00 0.00 1.94
727 910 5.106396 ACACTGCATCTTCTTAAGAATGTGC 60.106 40.000 29.62 29.62 41.63 4.57
736 919 8.181904 TCTTCTTAAGAATGTGCCTTGAATTT 57.818 30.769 18.02 0.00 33.83 1.82
752 935 6.038714 CCTTGAATTTAAGTAGGGAGCACATC 59.961 42.308 8.94 0.00 0.00 3.06
753 936 5.116180 TGAATTTAAGTAGGGAGCACATCG 58.884 41.667 0.00 0.00 0.00 3.84
767 950 2.363276 ATCGGTAGTGCACGGGGA 60.363 61.111 12.01 8.23 0.00 4.81
768 951 2.423898 ATCGGTAGTGCACGGGGAG 61.424 63.158 12.01 3.66 0.00 4.30
770 953 3.702048 GGTAGTGCACGGGGAGCA 61.702 66.667 12.01 0.00 40.19 4.26
803 988 1.661112 GATTCTCCGGCGACAGAAAAG 59.339 52.381 20.33 0.00 32.40 2.27
849 1046 3.063997 GTCCAATAGGAGCATTTCACACG 59.936 47.826 0.00 0.00 46.92 4.49
850 1047 3.055458 TCCAATAGGAGCATTTCACACGA 60.055 43.478 0.00 0.00 39.61 4.35
851 1048 3.310774 CCAATAGGAGCATTTCACACGAG 59.689 47.826 0.00 0.00 36.89 4.18
852 1049 3.895232 ATAGGAGCATTTCACACGAGT 57.105 42.857 0.00 0.00 0.00 4.18
853 1050 2.086054 AGGAGCATTTCACACGAGTC 57.914 50.000 0.00 0.00 0.00 3.36
854 1051 1.620819 AGGAGCATTTCACACGAGTCT 59.379 47.619 0.00 0.00 0.00 3.24
855 1052 2.826128 AGGAGCATTTCACACGAGTCTA 59.174 45.455 0.00 0.00 0.00 2.59
856 1053 2.924290 GGAGCATTTCACACGAGTCTAC 59.076 50.000 0.00 0.00 0.00 2.59
857 1054 2.924290 GAGCATTTCACACGAGTCTACC 59.076 50.000 0.00 0.00 0.00 3.18
858 1055 1.654105 GCATTTCACACGAGTCTACCG 59.346 52.381 0.00 0.00 0.00 4.02
859 1056 2.259618 CATTTCACACGAGTCTACCGG 58.740 52.381 0.00 0.00 0.00 5.28
860 1057 1.608055 TTTCACACGAGTCTACCGGA 58.392 50.000 9.46 0.00 0.00 5.14
861 1058 1.608055 TTCACACGAGTCTACCGGAA 58.392 50.000 9.46 0.00 0.00 4.30
862 1059 1.162698 TCACACGAGTCTACCGGAAG 58.837 55.000 9.46 0.00 0.00 3.46
863 1060 0.456312 CACACGAGTCTACCGGAAGC 60.456 60.000 9.46 0.00 0.00 3.86
919 1116 2.761767 TCCTACGGCACAGCTATACAAA 59.238 45.455 0.00 0.00 0.00 2.83
922 1119 1.299541 CGGCACAGCTATACAAAGGG 58.700 55.000 0.00 0.00 0.00 3.95
923 1120 1.406887 CGGCACAGCTATACAAAGGGT 60.407 52.381 0.00 0.00 0.00 4.34
924 1121 2.289565 GGCACAGCTATACAAAGGGTC 58.710 52.381 0.00 0.00 0.00 4.46
925 1122 1.933853 GCACAGCTATACAAAGGGTCG 59.066 52.381 0.00 0.00 0.00 4.79
926 1123 2.418197 GCACAGCTATACAAAGGGTCGA 60.418 50.000 0.00 0.00 0.00 4.20
927 1124 3.741388 GCACAGCTATACAAAGGGTCGAT 60.741 47.826 0.00 0.00 0.00 3.59
928 1125 4.051922 CACAGCTATACAAAGGGTCGATC 58.948 47.826 0.00 0.00 0.00 3.69
929 1126 3.243434 ACAGCTATACAAAGGGTCGATCG 60.243 47.826 9.36 9.36 0.00 3.69
930 1127 2.059541 GCTATACAAAGGGTCGATCGC 58.940 52.381 11.09 5.58 0.00 4.58
932 1129 0.874607 ATACAAAGGGTCGATCGCGC 60.875 55.000 11.09 13.72 37.46 6.86
933 1130 2.894240 TACAAAGGGTCGATCGCGCC 62.894 60.000 11.09 14.62 37.46 6.53
961 1187 1.903404 AACCTTGCCTTTGCCCTCG 60.903 57.895 0.00 0.00 36.33 4.63
972 1198 4.208686 GCCCTCGGCGTCTTCGAT 62.209 66.667 6.85 0.00 39.62 3.59
976 1202 2.752640 TCGGCGTCTTCGATCCCA 60.753 61.111 6.85 0.00 39.71 4.37
978 1204 2.893398 GGCGTCTTCGATCCCAGT 59.107 61.111 0.00 0.00 39.71 4.00
985 1211 1.195115 CTTCGATCCCAGTTCCCTCA 58.805 55.000 0.00 0.00 0.00 3.86
990 1216 0.759346 ATCCCAGTTCCCTCATACGC 59.241 55.000 0.00 0.00 0.00 4.42
992 1218 1.227263 CCAGTTCCCTCATACGCCG 60.227 63.158 0.00 0.00 0.00 6.46
1034 1260 3.190849 CGCCGACATGACCTGCTG 61.191 66.667 0.00 0.00 0.00 4.41
1039 1265 1.812922 GACATGACCTGCTGCTCCG 60.813 63.158 0.00 0.00 0.00 4.63
1066 1292 2.174319 GGCGACGATCTCCTTTGGC 61.174 63.158 0.00 0.00 0.00 4.52
1085 1311 2.920384 GATCCTCCTCCGCCTCCC 60.920 72.222 0.00 0.00 0.00 4.30
1136 1362 4.389576 GTTCTGCAAGCGGTGGCG 62.390 66.667 9.83 4.51 46.35 5.69
1154 1380 3.459063 GCCCTTCGCTACCGACCT 61.459 66.667 0.00 0.00 44.30 3.85
1165 1391 1.409427 CTACCGACCTCATGTTCCTCC 59.591 57.143 0.00 0.00 0.00 4.30
1167 1393 1.519455 CGACCTCATGTTCCTCCGC 60.519 63.158 0.00 0.00 0.00 5.54
1168 1394 1.596934 GACCTCATGTTCCTCCGCA 59.403 57.895 0.00 0.00 0.00 5.69
1177 1403 1.336517 TGTTCCTCCGCAACTTCTACG 60.337 52.381 0.00 0.00 0.00 3.51
1217 1443 0.038159 CTCCTCGGCGTCTTTGAGTT 60.038 55.000 6.85 0.00 0.00 3.01
1221 1447 2.861006 GGCGTCTTTGAGTTCCGC 59.139 61.111 0.00 0.00 43.35 5.54
1224 1450 1.773496 CGTCTTTGAGTTCCGCGAC 59.227 57.895 8.23 0.00 0.00 5.19
1243 1469 1.002888 ACAGCATGGTCTTCACCTCTG 59.997 52.381 0.00 0.00 44.17 3.35
1252 1478 1.202891 TCTTCACCTCTGTCCTCGACA 60.203 52.381 0.00 0.00 40.50 4.35
1255 1481 1.606889 ACCTCTGTCCTCGACACCC 60.607 63.158 0.00 0.00 37.67 4.61
1271 1497 3.849951 CCCGGACCACATCCCTCG 61.850 72.222 0.73 0.00 46.04 4.63
1272 1498 3.075005 CCGGACCACATCCCTCGT 61.075 66.667 0.00 0.00 46.04 4.18
1282 1508 3.417275 ATCCCTCGTGAGCGCTTCG 62.417 63.158 23.23 23.23 38.14 3.79
1296 1522 1.077089 GCTTCGACCTCCAACGCTAC 61.077 60.000 0.00 0.00 0.00 3.58
1299 1525 1.805945 CGACCTCCAACGCTACAGC 60.806 63.158 0.00 0.00 37.78 4.40
1315 1541 3.925238 GCTGCCGCCACGAATACG 61.925 66.667 0.00 0.00 45.75 3.06
1327 1553 2.435938 AATACGGCACACCCAGCG 60.436 61.111 0.00 0.00 0.00 5.18
1353 1579 1.230635 CCCACAGGAACGAAGTGCTG 61.231 60.000 0.00 0.00 45.00 4.41
1386 1612 1.270625 GGTCGTGTCCTCACCATTGAA 60.271 52.381 0.00 0.00 41.09 2.69
1412 1638 2.036604 TGTGCAAGGAACTCATCGTGTA 59.963 45.455 0.00 0.00 38.49 2.90
1419 1645 1.274167 GAACTCATCGTGTACACCCCA 59.726 52.381 20.11 4.97 0.00 4.96
1425 1651 1.372499 CGTGTACACCCCAGTCACG 60.372 63.158 20.11 1.33 43.77 4.35
1453 1679 1.745115 CGTCACATGGCCATTCCGT 60.745 57.895 17.92 8.65 37.80 4.69
1471 1703 3.120477 TCCGTCCGATTTCAAAACATTCG 60.120 43.478 0.00 0.00 0.00 3.34
1484 1716 5.408299 TCAAAACATTCGTCTACCACATCAG 59.592 40.000 0.00 0.00 0.00 2.90
1518 1780 2.914097 GCTGCCAGCAACCAAGGT 60.914 61.111 12.82 0.00 41.89 3.50
1530 1792 2.587753 CAAGGTCACGTGCACGGT 60.588 61.111 39.21 23.69 44.95 4.83
1655 1917 3.755378 GGCAAACTCATCTCAACAGACAT 59.245 43.478 0.00 0.00 0.00 3.06
1702 1964 3.353836 CCGGGTCACTTGTTGGCG 61.354 66.667 0.00 0.00 0.00 5.69
1703 1965 3.353836 CGGGTCACTTGTTGGCGG 61.354 66.667 0.00 0.00 0.00 6.13
1708 1970 2.026014 CACTTGTTGGCGGTGCAC 59.974 61.111 8.80 8.80 0.00 4.57
1736 1998 4.562082 TGGTTGGTTACTACGATGAGTTG 58.438 43.478 0.00 0.00 0.00 3.16
1840 2102 0.178767 TTGTCAGATCATCCAGGCCG 59.821 55.000 0.00 0.00 0.00 6.13
1907 2169 2.738743 CTTACAAATGTGGCAGGGGAT 58.261 47.619 0.00 0.00 0.00 3.85
1965 2227 5.841810 TGGAAGACCATTGAAATGAACAAC 58.158 37.500 4.58 0.00 41.77 3.32
2031 2293 5.223449 TCGAAACCATACTGGGATATTCC 57.777 43.478 0.00 0.00 43.37 3.01
2069 2331 7.439955 TGCTATTTTTATATACGTGGACACCAG 59.560 37.037 0.00 0.00 32.34 4.00
2071 2333 6.971527 TTTTTATATACGTGGACACCAGTG 57.028 37.500 0.00 0.00 32.34 3.66
2203 2465 5.661458 TCCTAGTCTTTGTATTGTAGCAGC 58.339 41.667 0.00 0.00 0.00 5.25
2220 2482 2.471749 GCAGCGACGTTATGTTGTGTAC 60.472 50.000 0.00 0.00 34.15 2.90
2222 2484 2.727798 AGCGACGTTATGTTGTGTACAC 59.272 45.455 19.36 19.36 40.19 2.90
2302 2570 7.174946 TCAACAAGTTTCCTTTTGCTAGATAGG 59.825 37.037 0.00 0.00 0.00 2.57
2323 3985 2.817258 GCACACTTAACTTGTGGCCATA 59.183 45.455 9.72 1.91 43.90 2.74
2326 3988 5.566627 GCACACTTAACTTGTGGCCATATTT 60.567 40.000 9.72 5.34 43.90 1.40
2362 4029 9.332502 ACATGGGTAAAAATGTAAAAGGAAAAC 57.667 29.630 0.00 0.00 35.28 2.43
2375 4042 0.881796 GGAAAACTAGTGGCTGCACC 59.118 55.000 0.50 0.00 39.84 5.01
2383 4050 4.641645 TGGCTGCACCCACCTTCG 62.642 66.667 0.50 0.00 37.83 3.79
2385 4052 4.643387 GCTGCACCCACCTTCGGT 62.643 66.667 0.00 0.00 35.62 4.69
2394 4061 4.619227 ACCTTCGGTGCACCCACG 62.619 66.667 29.95 18.33 43.00 4.94
2395 4062 4.308458 CCTTCGGTGCACCCACGA 62.308 66.667 29.95 20.39 43.00 4.35
2396 4063 2.738521 CTTCGGTGCACCCACGAG 60.739 66.667 29.95 17.45 43.00 4.18
2397 4064 4.308458 TTCGGTGCACCCACGAGG 62.308 66.667 29.95 14.84 43.00 4.63
2418 4085 2.287909 GCACCCACGCAAGAAAACATAA 60.288 45.455 0.00 0.00 43.62 1.90
2419 4086 3.305110 CACCCACGCAAGAAAACATAAC 58.695 45.455 0.00 0.00 43.62 1.89
2467 4135 8.074613 ACTTCATGGAAATGATCATCAACAAT 57.925 30.769 9.06 0.15 0.00 2.71
2510 4178 6.620678 AGTTTGGTGATCAAATAACATTCGG 58.379 36.000 0.00 0.00 45.79 4.30
2512 4180 3.064682 TGGTGATCAAATAACATTCGGCG 59.935 43.478 0.00 0.00 0.00 6.46
2523 4191 0.179137 CATTCGGCGAGCTCTGTACA 60.179 55.000 10.46 0.00 0.00 2.90
2555 4223 8.947055 ACAAAATTACAAAATCTGCTCAAACT 57.053 26.923 0.00 0.00 0.00 2.66
2573 4241 6.033341 TCAAACTGTGCACTTACATTTTGAC 58.967 36.000 19.41 0.00 46.26 3.18
2661 4329 3.364621 GCAAGCGTCCATAACATTTGTTG 59.635 43.478 6.21 0.00 38.90 3.33
2671 4339 9.590451 GTCCATAACATTTGTTGATGATCATTT 57.410 29.630 10.14 0.00 38.90 2.32
2683 4351 7.652909 TGTTGATGATCATTTCCACAAAGTTTC 59.347 33.333 10.14 0.00 0.00 2.78
2735 4403 4.063967 CGTGGGTGCACCGAGCTA 62.064 66.667 29.08 10.27 45.94 3.32
2736 4404 2.345991 GTGGGTGCACCGAGCTAA 59.654 61.111 29.08 7.78 45.94 3.09
2747 4415 1.823610 ACCGAGCTAAGGGTGTAGAAC 59.176 52.381 11.85 0.00 34.58 3.01
2748 4416 5.535874 CACCGAGCTAAGGGTGTAGAACC 62.536 56.522 18.37 0.00 46.79 3.62
2765 4436 8.660373 GTGTAGAACCACTCTCTAAATCAAATG 58.340 37.037 0.00 0.00 35.41 2.32
2829 4500 8.911247 AACTTAATTGGCATTTTCGTAATCTC 57.089 30.769 0.00 0.00 0.00 2.75
2830 4501 8.050778 ACTTAATTGGCATTTTCGTAATCTCA 57.949 30.769 0.00 0.00 0.00 3.27
2832 4503 8.682128 TTAATTGGCATTTTCGTAATCTCAAC 57.318 30.769 0.00 0.00 0.00 3.18
2835 4506 3.098636 GCATTTTCGTAATCTCAACGCC 58.901 45.455 0.00 0.00 40.12 5.68
2844 4515 5.180492 TCGTAATCTCAACGCCTTTTCAAAT 59.820 36.000 0.00 0.00 40.12 2.32
2898 4569 9.630098 CATACCATCAGAAATAATATGTTTGCC 57.370 33.333 0.00 0.00 0.00 4.52
2906 4577 8.246180 CAGAAATAATATGTTTGCCTCACTTGT 58.754 33.333 0.00 0.00 0.00 3.16
2919 4590 1.420138 TCACTTGTTGAAGACCCTCCC 59.580 52.381 0.00 0.00 32.98 4.30
2939 4610 3.452755 CGCAGGTGACCAAGACATATA 57.547 47.619 3.63 0.00 0.00 0.86
2945 4616 6.586344 CAGGTGACCAAGACATATAGAACAT 58.414 40.000 3.63 0.00 0.00 2.71
2950 4621 8.150945 GTGACCAAGACATATAGAACATACCAT 58.849 37.037 0.00 0.00 0.00 3.55
3012 4683 0.399833 AAACCCGCATGCCCAAAATT 59.600 45.000 13.15 0.00 0.00 1.82
3025 4696 7.118971 GCATGCCCAAAATTACTTTTGTTGATA 59.881 33.333 6.36 1.05 46.43 2.15
3084 4755 2.869237 GCTTGATATGATGAGGAGCGCA 60.869 50.000 11.47 0.00 0.00 6.09
3103 4774 2.095516 GCAAAAAGGAAAGAGGAGCGAG 60.096 50.000 0.00 0.00 0.00 5.03
3612 5286 4.870123 AGGCACATTCTTGCATTTACAA 57.130 36.364 0.00 0.00 44.94 2.41
3614 5288 5.797051 AGGCACATTCTTGCATTTACAATT 58.203 33.333 0.00 0.00 44.94 2.32
3615 5289 5.640357 AGGCACATTCTTGCATTTACAATTG 59.360 36.000 3.24 3.24 44.94 2.32
3727 5711 2.790468 GCCTGCTACGTACACTAGTTCG 60.790 54.545 0.00 1.34 43.13 3.95
3765 5750 6.972328 TGAGTTATTTTGCTCAAGTTGTGTTC 59.028 34.615 2.11 0.00 38.61 3.18
3795 5780 1.690352 ACAGTGTAACCGCCTTACTGT 59.310 47.619 0.00 0.00 44.99 3.55
3797 5782 3.321682 ACAGTGTAACCGCCTTACTGTTA 59.678 43.478 0.00 0.00 46.96 2.41
3825 5810 8.434589 TTTCATTATCCATTTGTCCTTTCCTT 57.565 30.769 0.00 0.00 0.00 3.36
3960 5946 4.669206 ATGTGTTGGAATGTTTCAGCAA 57.331 36.364 0.00 0.00 0.00 3.91
4006 5993 4.335416 ACGATTTGTGAGATTTGGACCAT 58.665 39.130 0.00 0.00 0.00 3.55
4069 6056 8.983702 AGGTAGTGAAAACTATTGTTGGTTAA 57.016 30.769 0.00 0.00 36.39 2.01
4082 6069 5.843673 TGTTGGTTAAAAGTGCAGAATCA 57.156 34.783 0.00 0.00 0.00 2.57
4138 6126 4.331168 GCTTTCTCCAGCTATATATTGGCG 59.669 45.833 8.05 3.78 36.79 5.69
4150 6138 1.128200 TATTGGCGGGCAGTCTGTAT 58.872 50.000 2.09 0.00 0.00 2.29
4186 6174 9.967346 AAAATCTGAAAGTTAAAAGCTACTTCC 57.033 29.630 0.18 0.00 33.66 3.46
4199 6187 2.605257 CTACTTCCCCGTCCCATCATA 58.395 52.381 0.00 0.00 0.00 2.15
4202 6190 3.593942 ACTTCCCCGTCCCATCATATAA 58.406 45.455 0.00 0.00 0.00 0.98
4207 6195 3.181475 CCCCGTCCCATCATATAAGATCG 60.181 52.174 0.00 0.00 0.00 3.69
4302 6293 5.072741 GTGCATATCAGGTTACCAATGGAT 58.927 41.667 6.16 3.84 0.00 3.41
4321 6312 5.540911 TGGATTGATGTTCTTGCTTTTTCC 58.459 37.500 0.00 0.00 0.00 3.13
4459 6459 3.942748 TGGCCTAATTTACCATCAACGTC 59.057 43.478 3.32 0.00 0.00 4.34
4507 6507 3.006110 GTGTGTAGGTTACTGTGCTACCA 59.994 47.826 10.02 0.00 34.32 3.25
4545 6545 9.423061 GGCAACAGAAAAGTCACATTATAAATT 57.577 29.630 0.00 0.00 0.00 1.82
4688 6688 1.139989 CACACACTAACACAGGAGCG 58.860 55.000 0.00 0.00 0.00 5.03
4697 6697 0.034896 ACACAGGAGCGTTGTTAGGG 59.965 55.000 0.00 0.00 0.00 3.53
4707 6707 3.055094 AGCGTTGTTAGGGAACTGATGAT 60.055 43.478 0.00 0.00 43.88 2.45
4765 6766 7.068962 GTGGCTAAGAAGTCTCTAGGAGTAAAT 59.931 40.741 0.00 0.00 0.00 1.40
4779 6780 8.475639 TCTAGGAGTAAATAATCACCAGAACAC 58.524 37.037 0.00 0.00 0.00 3.32
4826 6827 6.211587 TGTATGGCTTCCTGATTTCATTTG 57.788 37.500 0.00 0.00 0.00 2.32
4827 6828 5.716228 TGTATGGCTTCCTGATTTCATTTGT 59.284 36.000 0.00 0.00 0.00 2.83
4829 6830 6.855763 ATGGCTTCCTGATTTCATTTGTAA 57.144 33.333 0.00 0.00 0.00 2.41
4831 6832 7.243604 TGGCTTCCTGATTTCATTTGTAATT 57.756 32.000 0.00 0.00 0.00 1.40
4832 6833 7.322664 TGGCTTCCTGATTTCATTTGTAATTC 58.677 34.615 0.00 0.00 0.00 2.17
4834 6835 7.490402 GGCTTCCTGATTTCATTTGTAATTCTG 59.510 37.037 0.00 0.00 0.00 3.02
4835 6836 8.031277 GCTTCCTGATTTCATTTGTAATTCTGT 58.969 33.333 0.00 0.00 0.00 3.41
4837 6838 7.829725 TCCTGATTTCATTTGTAATTCTGTGG 58.170 34.615 0.00 0.00 0.00 4.17
4838 6839 7.451255 TCCTGATTTCATTTGTAATTCTGTGGT 59.549 33.333 0.00 0.00 0.00 4.16
4894 6904 0.678048 ATTTCGGCTTCCAGAGTGGC 60.678 55.000 0.00 0.00 37.47 5.01
4904 6914 2.180276 TCCAGAGTGGCTTCTTACCTC 58.820 52.381 0.00 0.00 37.47 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.001618 TGATGATGTTGTTGTCGAGGAA 57.998 40.909 0.00 0.00 0.00 3.36
26 27 8.599624 ACTTCTTTTAATCCCATGATGATGTT 57.400 30.769 0.00 0.00 0.00 2.71
28 29 9.880157 AAAACTTCTTTTAATCCCATGATGATG 57.120 29.630 0.00 0.00 0.00 3.07
111 112 1.021202 TTCCAGCGGTTTTGACACAG 58.979 50.000 0.00 0.00 0.00 3.66
161 165 2.626088 AGCGAAAAATTGCTCAGAGC 57.374 45.000 16.21 16.21 42.82 4.09
162 166 8.673626 TTTATTTAGCGAAAAATTGCTCAGAG 57.326 30.769 0.00 0.00 42.48 3.35
218 222 9.659830 CGTGCTATATCACTATATTGCGTTATA 57.340 33.333 5.26 0.00 44.71 0.98
219 223 8.188799 ACGTGCTATATCACTATATTGCGTTAT 58.811 33.333 5.26 0.00 44.71 1.89
220 224 7.532571 ACGTGCTATATCACTATATTGCGTTA 58.467 34.615 5.26 0.00 44.71 3.18
221 225 6.387465 ACGTGCTATATCACTATATTGCGTT 58.613 36.000 5.26 0.00 44.71 4.84
240 244 9.370126 CACTCTTAAAATATGCTATTAACGTGC 57.630 33.333 0.00 0.00 0.00 5.34
243 247 9.864034 CACCACTCTTAAAATATGCTATTAACG 57.136 33.333 0.00 0.00 0.00 3.18
252 256 7.698130 GCAAAGTAGCACCACTCTTAAAATATG 59.302 37.037 0.00 0.00 0.00 1.78
253 257 7.414098 CGCAAAGTAGCACCACTCTTAAAATAT 60.414 37.037 0.00 0.00 0.00 1.28
325 329 8.895932 ATTACGAGCACAATTGAGAAATTAAC 57.104 30.769 13.59 0.00 0.00 2.01
328 332 8.677300 ACATATTACGAGCACAATTGAGAAATT 58.323 29.630 13.59 0.00 0.00 1.82
342 349 5.849858 TGTTTGTCGAAACATATTACGAGC 58.150 37.500 0.00 0.00 45.26 5.03
501 684 0.680280 TTTCCCTCCTCGAGTCTCGG 60.680 60.000 21.63 12.22 40.88 4.63
520 703 4.452733 GGTAACCTCAGCGCCGCT 62.453 66.667 5.39 5.39 40.77 5.52
537 720 0.036765 TCCCACGTCCCAAGAAATCG 60.037 55.000 0.00 0.00 0.00 3.34
558 741 6.073167 GCCTGATCTGATGTGATTTGTCATAG 60.073 42.308 0.38 0.00 0.00 2.23
593 776 2.235891 CAAACTAGTTGGAACCACCCC 58.764 52.381 9.34 0.00 38.00 4.95
619 802 1.393539 CCGTCTTGGCGTCTTGTAATG 59.606 52.381 0.00 0.00 0.00 1.90
637 820 1.737201 GGGGAAAACCAACACACCG 59.263 57.895 0.00 0.00 42.91 4.94
665 848 3.432051 GATGCTAGTCGGCGCAGGT 62.432 63.158 10.83 0.00 39.82 4.00
699 882 9.236006 ACATTCTTAAGAAGATGCAGTGTTATT 57.764 29.630 21.75 0.00 37.38 1.40
708 891 5.124457 TCAAGGCACATTCTTAAGAAGATGC 59.876 40.000 30.58 30.58 42.96 3.91
727 910 5.253330 TGTGCTCCCTACTTAAATTCAAGG 58.747 41.667 0.00 0.00 0.00 3.61
736 919 2.154567 ACCGATGTGCTCCCTACTTA 57.845 50.000 0.00 0.00 0.00 2.24
752 935 4.814294 GCTCCCCGTGCACTACCG 62.814 72.222 16.19 0.67 0.00 4.02
753 936 3.702048 TGCTCCCCGTGCACTACC 61.702 66.667 16.19 0.00 35.31 3.18
767 950 0.815213 AATCATATGCGTGCCGTGCT 60.815 50.000 0.00 0.00 0.00 4.40
768 951 0.384725 GAATCATATGCGTGCCGTGC 60.385 55.000 0.00 0.00 0.00 5.34
770 953 1.502231 GAGAATCATATGCGTGCCGT 58.498 50.000 0.00 0.00 33.17 5.68
771 954 0.792640 GGAGAATCATATGCGTGCCG 59.207 55.000 0.00 0.00 36.25 5.69
829 1026 3.270027 TCGTGTGAAATGCTCCTATTGG 58.730 45.455 0.00 0.00 0.00 3.16
849 1046 1.516423 GTGGGCTTCCGGTAGACTC 59.484 63.158 14.28 4.75 0.00 3.36
850 1047 2.348888 CGTGGGCTTCCGGTAGACT 61.349 63.158 14.28 0.00 0.00 3.24
851 1048 2.163601 AACGTGGGCTTCCGGTAGAC 62.164 60.000 12.94 9.20 0.00 2.59
852 1049 1.474332 AAACGTGGGCTTCCGGTAGA 61.474 55.000 12.94 0.00 0.00 2.59
853 1050 1.004200 AAACGTGGGCTTCCGGTAG 60.004 57.895 3.26 3.26 0.00 3.18
854 1051 1.301874 CAAACGTGGGCTTCCGGTA 60.302 57.895 0.00 0.00 0.00 4.02
855 1052 2.593436 CAAACGTGGGCTTCCGGT 60.593 61.111 0.00 0.00 0.00 5.28
856 1053 1.730451 AAACAAACGTGGGCTTCCGG 61.730 55.000 0.00 0.00 0.00 5.14
857 1054 0.593773 CAAACAAACGTGGGCTTCCG 60.594 55.000 0.00 0.00 0.00 4.30
858 1055 0.874175 GCAAACAAACGTGGGCTTCC 60.874 55.000 0.00 0.00 0.00 3.46
859 1056 0.102300 AGCAAACAAACGTGGGCTTC 59.898 50.000 0.00 0.00 29.71 3.86
860 1057 0.102300 GAGCAAACAAACGTGGGCTT 59.898 50.000 0.00 0.00 32.87 4.35
861 1058 1.733526 GAGCAAACAAACGTGGGCT 59.266 52.632 0.00 0.00 34.65 5.19
862 1059 1.657181 CGAGCAAACAAACGTGGGC 60.657 57.895 0.00 0.00 0.00 5.36
863 1060 1.008995 CCGAGCAAACAAACGTGGG 60.009 57.895 0.00 0.00 0.00 4.61
919 1116 4.814294 GTTGGCGCGATCGACCCT 62.814 66.667 21.57 0.00 44.89 4.34
922 1119 2.398800 GATTCGTTGGCGCGATCGAC 62.399 60.000 22.44 9.84 45.94 4.20
923 1120 2.202690 ATTCGTTGGCGCGATCGA 60.203 55.556 21.57 19.51 40.76 3.59
924 1121 2.242670 GATTCGTTGGCGCGATCG 59.757 61.111 12.10 15.56 40.76 3.69
925 1122 1.701545 TTGGATTCGTTGGCGCGATC 61.702 55.000 12.10 0.88 40.76 3.69
926 1123 1.743623 TTGGATTCGTTGGCGCGAT 60.744 52.632 12.10 0.00 40.76 4.58
927 1124 2.357638 TTGGATTCGTTGGCGCGA 60.358 55.556 12.10 0.00 39.28 5.87
928 1125 2.202298 GTTGGATTCGTTGGCGCG 60.202 61.111 0.00 0.00 38.14 6.86
929 1126 1.862602 AAGGTTGGATTCGTTGGCGC 61.863 55.000 0.00 0.00 38.14 6.53
930 1127 0.109781 CAAGGTTGGATTCGTTGGCG 60.110 55.000 0.00 0.00 39.92 5.69
932 1129 0.243636 GGCAAGGTTGGATTCGTTGG 59.756 55.000 0.00 0.00 33.23 3.77
933 1130 1.247567 AGGCAAGGTTGGATTCGTTG 58.752 50.000 0.00 0.00 34.94 4.10
937 1163 1.338105 GGCAAAGGCAAGGTTGGATTC 60.338 52.381 0.00 0.00 43.71 2.52
961 1187 0.806492 GAACTGGGATCGAAGACGCC 60.806 60.000 0.00 0.00 42.51 5.68
963 1189 0.179108 GGGAACTGGGATCGAAGACG 60.179 60.000 0.00 0.00 42.51 4.18
972 1198 1.335132 GGCGTATGAGGGAACTGGGA 61.335 60.000 0.00 0.00 44.43 4.37
978 1204 4.884257 GCGCGGCGTATGAGGGAA 62.884 66.667 24.46 0.00 0.00 3.97
996 1222 1.310933 CCTTGCTTTCGCTCATGGCT 61.311 55.000 0.00 0.00 39.13 4.75
997 1223 1.138247 CCTTGCTTTCGCTCATGGC 59.862 57.895 0.00 0.00 36.97 4.40
1006 1232 4.103103 GTCGGCGCCCTTGCTTTC 62.103 66.667 23.46 0.00 34.43 2.62
1050 1276 0.173481 TCTGCCAAAGGAGATCGTCG 59.827 55.000 0.00 0.00 0.00 5.12
1062 1288 2.735772 GCGGAGGAGGATCTGCCAA 61.736 63.158 7.07 0.00 44.35 4.52
1066 1292 2.206536 GGAGGCGGAGGAGGATCTG 61.207 68.421 0.00 0.00 33.73 2.90
1088 1314 2.686835 GGAGGGAGGACAGCTGCT 60.687 66.667 15.27 3.06 0.00 4.24
1089 1315 3.791586 GGGAGGGAGGACAGCTGC 61.792 72.222 15.27 6.61 0.00 5.25
1136 1362 4.525949 GGTCGGTAGCGAAGGGCC 62.526 72.222 19.94 12.19 45.17 5.80
1139 1365 0.249073 CATGAGGTCGGTAGCGAAGG 60.249 60.000 19.94 0.84 0.00 3.46
1140 1366 0.456221 ACATGAGGTCGGTAGCGAAG 59.544 55.000 19.94 7.48 0.00 3.79
1141 1367 0.892755 AACATGAGGTCGGTAGCGAA 59.107 50.000 19.94 3.43 0.00 4.70
1144 1370 0.824759 AGGAACATGAGGTCGGTAGC 59.175 55.000 0.00 0.00 0.00 3.58
1146 1372 1.481871 GGAGGAACATGAGGTCGGTA 58.518 55.000 0.00 0.00 0.00 4.02
1167 1393 1.491563 GTGGTGCGCGTAGAAGTTG 59.508 57.895 8.43 0.00 0.00 3.16
1168 1394 2.019951 CGTGGTGCGCGTAGAAGTT 61.020 57.895 8.43 0.00 32.40 2.66
1217 1443 2.835701 GAAGACCATGCTGTCGCGGA 62.836 60.000 6.13 0.00 40.26 5.54
1221 1447 0.036952 AGGTGAAGACCATGCTGTCG 60.037 55.000 0.00 0.00 45.98 4.35
1224 1450 1.002888 ACAGAGGTGAAGACCATGCTG 59.997 52.381 0.00 0.00 45.98 4.41
1243 1469 3.756727 GTCCGGGGTGTCGAGGAC 61.757 72.222 0.00 3.79 45.07 3.85
1271 1497 2.507324 GGAGGTCGAAGCGCTCAC 60.507 66.667 12.06 8.07 0.00 3.51
1272 1498 2.570284 TTGGAGGTCGAAGCGCTCA 61.570 57.895 12.06 0.00 0.00 4.26
1282 1508 4.187056 GCTGTAGCGTTGGAGGTC 57.813 61.111 0.00 0.00 0.00 3.85
1296 1522 2.511373 TATTCGTGGCGGCAGCTG 60.511 61.111 13.91 10.11 44.37 4.24
1299 1525 3.261951 CCGTATTCGTGGCGGCAG 61.262 66.667 13.91 7.03 38.99 4.85
1327 1553 2.955881 CGTTCCTGTGGGGAGGACC 61.956 68.421 0.00 0.00 46.01 4.46
1365 1591 0.321671 CAATGGTGAGGACACGACCT 59.678 55.000 0.00 0.00 46.77 3.85
1386 1612 2.346766 TGAGTTCCTTGCACACATGT 57.653 45.000 0.00 0.00 0.00 3.21
1439 1665 1.983119 ATCGGACGGAATGGCCATGT 61.983 55.000 21.63 13.49 35.94 3.21
1453 1679 5.121142 GGTAGACGAATGTTTTGAAATCGGA 59.879 40.000 4.07 0.00 37.81 4.55
1484 1716 4.347453 CGCAAAGCACAGCCCCAC 62.347 66.667 0.00 0.00 0.00 4.61
1510 1772 2.177580 CGTGCACGTGACCTTGGTT 61.178 57.895 30.50 0.00 34.11 3.67
1518 1780 2.892914 CAACCACCGTGCACGTGA 60.893 61.111 34.81 1.04 37.74 4.35
1530 1792 0.399949 AGGGACTGGAGTGACAACCA 60.400 55.000 2.04 2.04 37.18 3.67
1655 1917 7.465353 TGAGCAGTGAAAATCAAATATGGAA 57.535 32.000 0.00 0.00 0.00 3.53
1702 1964 0.396811 ACCAACCAGTAGAGTGCACC 59.603 55.000 14.63 5.12 0.00 5.01
1703 1965 2.256117 AACCAACCAGTAGAGTGCAC 57.744 50.000 9.40 9.40 0.00 4.57
1708 1970 5.356190 TCATCGTAGTAACCAACCAGTAGAG 59.644 44.000 0.00 0.00 0.00 2.43
1736 1998 4.708726 AACTTAAGCATGTCATTCCTGC 57.291 40.909 1.29 0.00 37.83 4.85
1822 2084 0.687427 TCGGCCTGGATGATCTGACA 60.687 55.000 0.00 0.00 0.00 3.58
1845 2107 3.457610 AAACCAACAGCACCATCTTTG 57.542 42.857 0.00 0.00 0.00 2.77
1846 2108 4.441792 GAAAAACCAACAGCACCATCTTT 58.558 39.130 0.00 0.00 0.00 2.52
1907 2169 5.514169 TGGCAACACCAGGAATATTCATAA 58.486 37.500 17.07 0.00 46.36 1.90
1965 2227 0.182299 GAGGAGGGAGCCCAAGAATG 59.818 60.000 8.53 0.00 38.92 2.67
2069 2331 8.094798 TGATTTAAGTTGAACCATGTAGACAC 57.905 34.615 0.00 0.00 0.00 3.67
2071 2333 9.559958 CATTGATTTAAGTTGAACCATGTAGAC 57.440 33.333 0.00 0.00 0.00 2.59
2182 2444 5.230306 GTCGCTGCTACAATACAAAGACTAG 59.770 44.000 0.00 0.00 0.00 2.57
2187 2449 2.666508 ACGTCGCTGCTACAATACAAAG 59.333 45.455 5.14 0.00 0.00 2.77
2203 2465 2.089427 CCGTGTACACAACATAACGTCG 59.911 50.000 24.98 6.94 41.10 5.12
2220 2482 5.163663 ACAATATAGATGTTTGGCAACCGTG 60.164 40.000 0.00 0.00 31.02 4.94
2222 2484 5.273170 CACAATATAGATGTTTGGCAACCG 58.727 41.667 0.00 0.00 31.02 4.44
2302 2570 1.028905 TGGCCACAAGTTAAGTGTGC 58.971 50.000 0.00 8.50 44.13 4.57
2380 4047 4.308458 CCTCGTGGGTGCACCGAA 62.308 66.667 29.08 17.49 44.64 4.30
2392 4059 4.988598 CTTGCGTGGGTGCCTCGT 62.989 66.667 0.00 0.00 41.72 4.18
2393 4060 4.680237 TCTTGCGTGGGTGCCTCG 62.680 66.667 0.00 0.00 42.44 4.63
2394 4061 1.452145 TTTTCTTGCGTGGGTGCCTC 61.452 55.000 0.00 0.00 0.00 4.70
2395 4062 1.454847 TTTTCTTGCGTGGGTGCCT 60.455 52.632 0.00 0.00 0.00 4.75
2396 4063 1.299850 GTTTTCTTGCGTGGGTGCC 60.300 57.895 0.00 0.00 0.00 5.01
2397 4064 0.031994 ATGTTTTCTTGCGTGGGTGC 59.968 50.000 0.00 0.00 0.00 5.01
2398 4065 3.243234 TGTTATGTTTTCTTGCGTGGGTG 60.243 43.478 0.00 0.00 0.00 4.61
2399 4066 2.952978 TGTTATGTTTTCTTGCGTGGGT 59.047 40.909 0.00 0.00 0.00 4.51
2400 4067 3.634568 TGTTATGTTTTCTTGCGTGGG 57.365 42.857 0.00 0.00 0.00 4.61
2401 4068 5.289675 TGTTTTGTTATGTTTTCTTGCGTGG 59.710 36.000 0.00 0.00 0.00 4.94
2402 4069 6.324522 TGTTTTGTTATGTTTTCTTGCGTG 57.675 33.333 0.00 0.00 0.00 5.34
2403 4070 7.532682 AATGTTTTGTTATGTTTTCTTGCGT 57.467 28.000 0.00 0.00 0.00 5.24
2404 4071 9.907576 TTAAATGTTTTGTTATGTTTTCTTGCG 57.092 25.926 0.00 0.00 0.00 4.85
2451 4119 8.542080 ACCCATAACAATTGTTGATGATCATTT 58.458 29.630 29.72 5.27 38.90 2.32
2467 4135 2.697751 ACTTTGCAAGCACCCATAACAA 59.302 40.909 0.00 0.00 0.00 2.83
2495 4163 3.206150 AGCTCGCCGAATGTTATTTGAT 58.794 40.909 0.00 0.00 0.00 2.57
2500 4168 1.137086 ACAGAGCTCGCCGAATGTTAT 59.863 47.619 8.37 0.00 0.00 1.89
2528 4196 9.034544 GTTTGAGCAGATTTTGTAATTTTGTCT 57.965 29.630 0.00 0.00 0.00 3.41
2555 4223 9.243637 GAAAATTAGTCAAAATGTAAGTGCACA 57.756 29.630 21.04 0.00 0.00 4.57
2661 4329 5.801947 CCGAAACTTTGTGGAAATGATCATC 59.198 40.000 9.06 0.00 0.00 2.92
2735 4403 3.261818 AGAGAGTGGTTCTACACCCTT 57.738 47.619 0.00 0.00 46.68 3.95
2736 4404 4.399483 TTAGAGAGTGGTTCTACACCCT 57.601 45.455 0.00 0.00 46.68 4.34
2747 4415 7.335171 TCATGTGACATTTGATTTAGAGAGTGG 59.665 37.037 0.00 0.00 0.00 4.00
2748 4416 8.260270 TCATGTGACATTTGATTTAGAGAGTG 57.740 34.615 0.00 0.00 0.00 3.51
2750 4418 8.489990 ACTCATGTGACATTTGATTTAGAGAG 57.510 34.615 10.88 6.51 0.00 3.20
2807 4478 7.483375 CGTTGAGATTACGAAAATGCCAATTAA 59.517 33.333 0.00 0.00 41.33 1.40
2818 4489 4.512198 TGAAAAGGCGTTGAGATTACGAAA 59.488 37.500 0.00 0.00 41.33 3.46
2829 4500 7.816945 ATTATTGAGATTTGAAAAGGCGTTG 57.183 32.000 0.00 0.00 0.00 4.10
2830 4501 9.921637 TTTATTATTGAGATTTGAAAAGGCGTT 57.078 25.926 0.00 0.00 0.00 4.84
2871 4542 9.630098 GCAAACATATTATTTCTGATGGTATGG 57.370 33.333 0.00 0.00 0.00 2.74
2872 4543 9.630098 GGCAAACATATTATTTCTGATGGTATG 57.370 33.333 0.00 0.00 0.00 2.39
2874 4545 8.995027 AGGCAAACATATTATTTCTGATGGTA 57.005 30.769 0.00 0.00 0.00 3.25
2875 4546 7.560991 TGAGGCAAACATATTATTTCTGATGGT 59.439 33.333 0.00 0.00 0.00 3.55
2876 4547 7.864379 GTGAGGCAAACATATTATTTCTGATGG 59.136 37.037 0.00 0.00 0.00 3.51
2877 4548 8.627403 AGTGAGGCAAACATATTATTTCTGATG 58.373 33.333 0.00 0.00 0.00 3.07
2878 4549 8.757982 AGTGAGGCAAACATATTATTTCTGAT 57.242 30.769 0.00 0.00 0.00 2.90
2881 4552 8.353423 ACAAGTGAGGCAAACATATTATTTCT 57.647 30.769 0.00 0.00 0.00 2.52
2898 4569 2.551071 GGGAGGGTCTTCAACAAGTGAG 60.551 54.545 0.00 0.00 37.61 3.51
2906 4577 2.592993 CCTGCGGGAGGGTCTTCAA 61.593 63.158 5.28 0.00 38.36 2.69
2919 4590 2.315925 ATATGTCTTGGTCACCTGCG 57.684 50.000 0.00 0.00 0.00 5.18
2945 4616 9.432982 AGCCATGAAAGGAAATTTAATATGGTA 57.567 29.630 0.00 0.00 38.25 3.25
2950 4621 9.920946 AGTAGAGCCATGAAAGGAAATTTAATA 57.079 29.630 0.00 0.00 0.00 0.98
2961 4632 4.187694 GAGTCCAAGTAGAGCCATGAAAG 58.812 47.826 0.00 0.00 0.00 2.62
3025 4696 8.661257 GCAAAACACACCAAACTAATAAACTTT 58.339 29.630 0.00 0.00 0.00 2.66
3084 4755 3.493767 ACTCGCTCCTCTTTCCTTTTT 57.506 42.857 0.00 0.00 0.00 1.94
3507 5178 4.215399 CGGAATGTTCCTGAAAGCAGTTTA 59.785 41.667 9.90 0.00 45.33 2.01
3576 5249 8.159344 AGAATGTGCCTAAAAATAGTATGCTC 57.841 34.615 0.00 0.00 0.00 4.26
3578 5251 7.168135 GCAAGAATGTGCCTAAAAATAGTATGC 59.832 37.037 0.00 0.00 38.66 3.14
3586 5259 7.212976 TGTAAATGCAAGAATGTGCCTAAAAA 58.787 30.769 0.00 0.00 44.26 1.94
3650 5536 0.603569 CCGGACTCAATAGATCCCGG 59.396 60.000 0.00 7.31 42.52 5.73
3651 5537 0.603569 CCCGGACTCAATAGATCCCG 59.396 60.000 0.73 0.00 35.29 5.14
3657 5543 2.883026 AGGATCTCCCGGACTCAATAG 58.117 52.381 0.73 0.00 40.87 1.73
3765 5750 2.334838 GGTTACACTGTTGAGCCTACG 58.665 52.381 0.00 0.00 0.00 3.51
3797 5782 8.699130 GGAAAGGACAAATGGATAATGAAAGAT 58.301 33.333 0.00 0.00 0.00 2.40
3976 5962 7.390440 TCCAAATCTCACAAATCGTAATCAAGT 59.610 33.333 0.00 0.00 0.00 3.16
4166 6154 4.758165 CGGGGAAGTAGCTTTTAACTTTCA 59.242 41.667 7.53 0.00 36.10 2.69
4184 6172 3.553375 TCTTATATGATGGGACGGGGA 57.447 47.619 0.00 0.00 0.00 4.81
4186 6174 3.447586 ACGATCTTATATGATGGGACGGG 59.552 47.826 13.01 0.00 0.00 5.28
4228 6216 9.703892 CTCCGTTTCATATAAGATCATTTCTCT 57.296 33.333 0.00 0.00 31.78 3.10
4246 6234 5.301298 ACATAGTACATACTCCCTCCGTTTC 59.699 44.000 0.00 0.00 37.73 2.78
4247 6235 5.206587 ACATAGTACATACTCCCTCCGTTT 58.793 41.667 0.00 0.00 37.73 3.60
4248 6236 4.801164 ACATAGTACATACTCCCTCCGTT 58.199 43.478 0.00 0.00 37.73 4.44
4249 6237 4.450305 ACATAGTACATACTCCCTCCGT 57.550 45.455 0.00 0.00 37.73 4.69
4250 6238 7.463961 AATAACATAGTACATACTCCCTCCG 57.536 40.000 0.00 0.00 37.73 4.63
4251 6239 9.531158 ACTAATAACATAGTACATACTCCCTCC 57.469 37.037 0.00 0.00 37.73 4.30
4302 6293 3.243704 CGGGGAAAAAGCAAGAACATCAA 60.244 43.478 0.00 0.00 0.00 2.57
4321 6312 4.523083 TGAATTCTGATTCTAAACCCGGG 58.477 43.478 22.25 22.25 41.80 5.73
4352 6351 0.954449 CAGCAGTCACAAGAGCCCTG 60.954 60.000 0.00 0.00 0.00 4.45
4354 6353 0.952984 GACAGCAGTCACAAGAGCCC 60.953 60.000 4.10 0.00 44.34 5.19
4414 6413 6.183360 CCAGTCAACATAGTACAGGTCGAATA 60.183 42.308 0.00 0.00 0.00 1.75
4415 6414 5.394224 CCAGTCAACATAGTACAGGTCGAAT 60.394 44.000 0.00 0.00 0.00 3.34
4416 6415 4.082408 CCAGTCAACATAGTACAGGTCGAA 60.082 45.833 0.00 0.00 0.00 3.71
4418 6417 3.770666 CCAGTCAACATAGTACAGGTCG 58.229 50.000 0.00 0.00 0.00 4.79
4419 6418 3.522553 GCCAGTCAACATAGTACAGGTC 58.477 50.000 0.00 0.00 0.00 3.85
4421 6420 2.501723 AGGCCAGTCAACATAGTACAGG 59.498 50.000 5.01 0.00 0.00 4.00
4427 6427 6.119536 TGGTAAATTAGGCCAGTCAACATAG 58.880 40.000 5.01 0.00 0.00 2.23
4430 6430 4.374689 TGGTAAATTAGGCCAGTCAACA 57.625 40.909 5.01 0.00 0.00 3.33
4459 6459 4.998788 TGAGACTTACATCTTGATCACCG 58.001 43.478 0.00 0.00 0.00 4.94
4545 6545 6.454848 CGTTGCAAAACACAAGCTGAATTTTA 60.455 34.615 0.00 0.00 0.00 1.52
4546 6546 5.630061 GTTGCAAAACACAAGCTGAATTTT 58.370 33.333 0.00 0.00 0.00 1.82
4556 6556 4.563184 GGAACATAACGTTGCAAAACACAA 59.437 37.500 11.99 0.00 44.80 3.33
4626 6626 4.953940 AGGAAATGCACTTTGCCTTAAA 57.046 36.364 0.00 0.00 44.23 1.52
4628 6628 4.662278 AGTAGGAAATGCACTTTGCCTTA 58.338 39.130 4.85 0.00 44.23 2.69
4688 6688 4.755411 TCGATCATCAGTTCCCTAACAAC 58.245 43.478 0.00 0.00 38.12 3.32
4765 6766 8.806429 ATATCAATTGTGTGTTCTGGTGATTA 57.194 30.769 5.13 0.00 0.00 1.75
4799 6800 6.855763 TGAAATCAGGAAGCCATACAAATT 57.144 33.333 0.00 0.00 0.00 1.82
4800 6801 7.427989 AATGAAATCAGGAAGCCATACAAAT 57.572 32.000 0.00 0.00 0.00 2.32
4812 6813 7.451255 ACCACAGAATTACAAATGAAATCAGGA 59.549 33.333 0.00 0.00 0.00 3.86
4826 6827 5.886960 AAATGAGCTGACCACAGAATTAC 57.113 39.130 0.00 0.00 46.03 1.89
4827 6828 5.122239 CGAAAATGAGCTGACCACAGAATTA 59.878 40.000 0.00 0.00 46.03 1.40
4829 6830 3.438087 CGAAAATGAGCTGACCACAGAAT 59.562 43.478 0.00 0.00 46.03 2.40
4831 6832 2.224281 ACGAAAATGAGCTGACCACAGA 60.224 45.455 0.00 0.00 46.03 3.41
4832 6833 2.146342 ACGAAAATGAGCTGACCACAG 58.854 47.619 0.00 0.00 45.91 3.66
4834 6835 2.918131 GCAACGAAAATGAGCTGACCAC 60.918 50.000 0.00 0.00 0.00 4.16
4835 6836 1.266718 GCAACGAAAATGAGCTGACCA 59.733 47.619 0.00 0.00 0.00 4.02
4837 6838 2.686558 TGCAACGAAAATGAGCTGAC 57.313 45.000 0.00 0.00 0.00 3.51
4838 6839 2.357323 TGTTGCAACGAAAATGAGCTGA 59.643 40.909 23.79 0.00 0.00 4.26
4894 6904 5.183228 TGGCTTAATTTCGGAGGTAAGAAG 58.817 41.667 7.98 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.