Multiple sequence alignment - TraesCS3A01G187000

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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 TraesCS3A01G187000 chr3A 100.000 5816 0 0 1 5816 221951405 221945590 0.000000e+00 10741.0
1 TraesCS3A01G187000 chr3A 84.545 220 29 4 92 308 689483222 689483439 4.570000e-51 213.0
2 TraesCS3A01G187000 chr3A 87.218 133 11 2 2371 2503 588937732 588937858 4.700000e-31 147.0
3 TraesCS3A01G187000 chr3A 84.564 149 17 4 2370 2514 750297090 750297236 6.080000e-30 143.0
4 TraesCS3A01G187000 chr3B 95.830 2254 60 14 2519 4752 257282027 257279788 0.000000e+00 3611.0
5 TraesCS3A01G187000 chr3B 88.262 2019 82 49 475 2420 257284017 257282081 0.000000e+00 2272.0
6 TraesCS3A01G187000 chr3B 88.364 593 54 12 5237 5816 257279218 257278628 0.000000e+00 699.0
7 TraesCS3A01G187000 chr3B 92.276 246 13 5 4996 5236 257279651 257279407 1.550000e-90 344.0
8 TraesCS3A01G187000 chr3B 86.667 135 18 0 2376 2510 111565408 111565274 3.630000e-32 150.0
9 TraesCS3A01G187000 chr3B 92.045 88 7 0 1 88 225966028 225966115 2.200000e-24 124.0
10 TraesCS3A01G187000 chr3D 97.614 1551 27 6 2516 4063 179180435 179178892 0.000000e+00 2651.0
11 TraesCS3A01G187000 chr3D 93.724 1705 64 19 731 2416 179182159 179180479 0.000000e+00 2516.0
12 TraesCS3A01G187000 chr3D 93.144 1196 38 13 4059 5236 179173555 179172386 0.000000e+00 1714.0
13 TraesCS3A01G187000 chr3D 82.690 803 74 23 1 743 179182976 179182179 0.000000e+00 652.0
14 TraesCS3A01G187000 chr3D 85.772 246 32 2 5568 5812 179171958 179171715 2.080000e-64 257.0
15 TraesCS3A01G187000 chr3D 82.028 217 38 1 94 310 412093337 412093552 3.580000e-42 183.0
16 TraesCS3A01G187000 chr5B 83.333 210 33 1 102 309 600032427 600032218 5.950000e-45 193.0
17 TraesCS3A01G187000 chr5B 82.857 210 34 1 102 309 599989538 599989329 2.770000e-43 187.0
18 TraesCS3A01G187000 chr5B 88.636 132 10 4 2371 2502 532184640 532184514 7.800000e-34 156.0
19 TraesCS3A01G187000 chrUn 82.857 210 34 1 102 309 452675026 452675235 2.770000e-43 187.0
20 TraesCS3A01G187000 chrUn 89.286 140 8 4 2364 2503 310358345 310358477 1.000000e-37 169.0
21 TraesCS3A01G187000 chr7B 76.786 336 73 5 92 424 556754995 556754662 3.580000e-42 183.0
22 TraesCS3A01G187000 chr1D 81.776 214 37 2 92 303 322163476 322163689 1.670000e-40 178.0
23 TraesCS3A01G187000 chr1D 93.162 117 2 4 2388 2502 150952488 150952376 3.600000e-37 167.0
24 TraesCS3A01G187000 chr1D 85.455 110 12 3 5471 5578 22102105 22101998 1.710000e-20 111.0
25 TraesCS3A01G187000 chr6A 78.676 272 51 5 126 394 431067226 431067493 2.150000e-39 174.0
26 TraesCS3A01G187000 chr7A 90.226 133 10 2 2370 2502 7041151 7041022 2.790000e-38 171.0
27 TraesCS3A01G187000 chr4D 98.936 94 1 0 2416 2509 182067337 182067430 1.000000e-37 169.0
28 TraesCS3A01G187000 chr6B 88.722 133 14 1 2371 2502 34316504 34316636 1.680000e-35 161.0
29 TraesCS3A01G187000 chr2D 77.007 274 57 6 125 396 37640823 37641092 1.010000e-32 152.0
30 TraesCS3A01G187000 chr6D 93.258 89 6 0 1 89 212997785 212997697 1.320000e-26 132.0
31 TraesCS3A01G187000 chr6D 92.308 91 5 2 1 89 471091869 471091959 1.700000e-25 128.0
32 TraesCS3A01G187000 chr6D 92.135 89 7 0 1 89 344289503 344289591 6.120000e-25 126.0
33 TraesCS3A01G187000 chr1B 92.222 90 7 0 1 90 421866875 421866786 1.700000e-25 128.0
34 TraesCS3A01G187000 chr5A 90.526 95 9 0 1 95 95877185 95877091 6.120000e-25 126.0
35 TraesCS3A01G187000 chr2B 91.954 87 7 0 1 87 207435665 207435751 7.910000e-24 122.0
36 TraesCS3A01G187000 chr2A 91.954 87 7 0 1 87 160201013 160200927 7.910000e-24 122.0
37 TraesCS3A01G187000 chr4B 76.923 130 30 0 289 418 634181902 634181773 2.250000e-09 75.0
38 TraesCS3A01G187000 chr1A 97.222 36 1 0 4958 4993 130742238 130742203 1.750000e-05 62.1


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 TraesCS3A01G187000 chr3A 221945590 221951405 5815 True 10741.000000 10741 100.000000 1 5816 1 chr3A.!!$R1 5815
1 TraesCS3A01G187000 chr3B 257278628 257284017 5389 True 1731.500000 3611 91.183000 475 5816 4 chr3B.!!$R2 5341
2 TraesCS3A01G187000 chr3D 179178892 179182976 4084 True 1939.666667 2651 91.342667 1 4063 3 chr3D.!!$R2 4062
3 TraesCS3A01G187000 chr3D 179171715 179173555 1840 True 985.500000 1714 89.458000 4059 5812 2 chr3D.!!$R1 1753

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
57 58 0.043183 TGCATCTCCCCTCCTCTTCA 59.957 55.0 0.00 0.0 0.00 3.02 F
815 908 0.108377 ACACACACAGTTGACGCAGA 60.108 50.0 0.00 0.0 0.00 4.26 F
1820 1953 0.030638 GCTTCGCTTCCAACTTGCAA 59.969 50.0 0.00 0.0 0.00 4.08 F
2062 2212 0.036306 AGTTACTGGGGGAAGCAACG 59.964 55.0 0.00 0.0 0.00 4.10 F
3170 3358 0.108520 GTGCATTGCATGGGGTTCAG 60.109 55.0 15.49 0.0 41.91 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1013 1114 0.103208 AGCGAGGTAGCCATTCTTCG 59.897 55.000 0.00 0.0 38.01 3.79 R
2105 2255 1.341531 GACGATATAGCCCTGCAGTGT 59.658 52.381 13.81 0.0 0.00 3.55 R
3004 3192 3.140623 CAAAACCCATCCAAAAGCCTTG 58.859 45.455 0.00 0.0 0.00 3.61 R
3594 3783 4.093556 GTCGAATCTCCACTCACCAATTTC 59.906 45.833 0.00 0.0 0.00 2.17 R
4882 5089 0.106335 TCCGCCGGTGAAACTGTTTA 59.894 50.000 18.79 0.0 43.33 2.01 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
27 28 8.336235 TGGTTCTCACTGAGGGAAATAATTATT 58.664 33.333 4.81 4.81 0.00 1.40
48 49 4.689612 TTCTATTGTACTGCATCTCCCC 57.310 45.455 0.00 0.00 0.00 4.81
51 52 1.204146 TTGTACTGCATCTCCCCTCC 58.796 55.000 0.00 0.00 0.00 4.30
52 53 0.339859 TGTACTGCATCTCCCCTCCT 59.660 55.000 0.00 0.00 0.00 3.69
53 54 1.044611 GTACTGCATCTCCCCTCCTC 58.955 60.000 0.00 0.00 0.00 3.71
56 57 0.758123 CTGCATCTCCCCTCCTCTTC 59.242 60.000 0.00 0.00 0.00 2.87
57 58 0.043183 TGCATCTCCCCTCCTCTTCA 59.957 55.000 0.00 0.00 0.00 3.02
80 81 0.965363 AAAATCCCAACGCGGCTCAT 60.965 50.000 12.47 0.00 0.00 2.90
91 92 1.258982 CGCGGCTCATAAGTAGCAAAG 59.741 52.381 0.00 0.00 41.93 2.77
94 95 2.866762 CGGCTCATAAGTAGCAAAGGAC 59.133 50.000 0.00 0.00 41.93 3.85
95 96 3.430929 CGGCTCATAAGTAGCAAAGGACT 60.431 47.826 0.00 0.00 41.93 3.85
111 112 0.320697 GACTAGGTGGACGCAACCTT 59.679 55.000 10.61 0.00 46.14 3.50
116 117 1.098712 GGTGGACGCAACCTTTGTCA 61.099 55.000 0.00 0.00 34.66 3.58
119 120 1.278637 GACGCAACCTTTGTCACGG 59.721 57.895 0.00 0.00 32.91 4.94
123 124 1.008538 CAACCTTTGTCACGGCAGC 60.009 57.895 0.00 0.00 0.00 5.25
175 176 4.334118 TCGGGACCGACGGTGAGA 62.334 66.667 27.26 17.20 44.01 3.27
179 180 1.601419 GGGACCGACGGTGAGAATGA 61.601 60.000 27.26 0.00 35.25 2.57
184 185 0.811915 CGACGGTGAGAATGAGGAGT 59.188 55.000 0.00 0.00 0.00 3.85
199 200 2.283388 AGTAAGGGTGGCGGACGA 60.283 61.111 0.00 0.00 0.00 4.20
200 201 2.125793 GTAAGGGTGGCGGACGAC 60.126 66.667 0.00 0.00 0.00 4.34
228 229 2.032071 ACGCGGGAAAGGTTGGAG 59.968 61.111 12.47 0.00 0.00 3.86
230 231 2.754375 GCGGGAAAGGTTGGAGGA 59.246 61.111 0.00 0.00 0.00 3.71
242 243 0.253347 TTGGAGGAAGGCAGGAGGAT 60.253 55.000 0.00 0.00 0.00 3.24
275 278 8.014070 AGTGATGGATTTGATGCAATTTATGA 57.986 30.769 0.00 0.00 33.18 2.15
284 287 5.078949 TGATGCAATTTATGATGGGGTAGG 58.921 41.667 0.00 0.00 0.00 3.18
286 289 3.230134 GCAATTTATGATGGGGTAGGCA 58.770 45.455 0.00 0.00 0.00 4.75
338 341 1.805428 GCGCCCGGGCATTTTCATAT 61.805 55.000 42.78 0.00 42.06 1.78
340 343 0.603065 GCCCGGGCATTTTCATATCC 59.397 55.000 40.73 5.21 41.49 2.59
343 346 1.238439 CGGGCATTTTCATATCCGCT 58.762 50.000 0.00 0.00 0.00 5.52
347 350 3.437049 GGGCATTTTCATATCCGCTCTAC 59.563 47.826 0.00 0.00 0.00 2.59
348 351 4.065088 GGCATTTTCATATCCGCTCTACA 58.935 43.478 0.00 0.00 0.00 2.74
352 355 7.094805 GGCATTTTCATATCCGCTCTACATTTA 60.095 37.037 0.00 0.00 0.00 1.40
355 358 6.911250 TTCATATCCGCTCTACATTTAGGA 57.089 37.500 0.00 0.00 0.00 2.94
358 361 6.437477 TCATATCCGCTCTACATTTAGGATGT 59.563 38.462 5.17 0.00 38.73 3.06
383 386 3.865383 TGATGCCGGCCAGCCTAG 61.865 66.667 26.77 0.00 0.00 3.02
399 402 1.002087 CCTAGACGTTTGAGGCCTGTT 59.998 52.381 12.00 0.00 0.00 3.16
401 404 0.468226 AGACGTTTGAGGCCTGTTCA 59.532 50.000 12.00 0.00 0.00 3.18
412 415 1.966451 CCTGTTCAAGGTGCCCGTC 60.966 63.158 0.00 0.00 41.74 4.79
413 416 1.071471 CTGTTCAAGGTGCCCGTCT 59.929 57.895 0.00 0.00 0.00 4.18
414 417 0.320374 CTGTTCAAGGTGCCCGTCTA 59.680 55.000 0.00 0.00 0.00 2.59
415 418 0.981183 TGTTCAAGGTGCCCGTCTAT 59.019 50.000 0.00 0.00 0.00 1.98
416 419 1.338674 TGTTCAAGGTGCCCGTCTATG 60.339 52.381 0.00 0.00 0.00 2.23
418 421 0.981183 TCAAGGTGCCCGTCTATGTT 59.019 50.000 0.00 0.00 0.00 2.71
444 459 0.395173 TGACCGATCTGTCCATCCGA 60.395 55.000 13.91 0.00 34.25 4.55
446 461 0.460311 ACCGATCTGTCCATCCGAAC 59.540 55.000 0.00 0.00 0.00 3.95
454 469 1.076332 GTCCATCCGAACGTTTGAGG 58.924 55.000 17.38 14.59 0.00 3.86
455 470 0.672401 TCCATCCGAACGTTTGAGGC 60.672 55.000 17.38 0.00 0.00 4.70
458 473 3.342627 CCGAACGTTTGAGGCGCA 61.343 61.111 17.38 0.00 0.00 6.09
460 475 2.307309 CGAACGTTTGAGGCGCAGA 61.307 57.895 10.83 0.00 0.00 4.26
485 525 9.134734 GACTGTAGATGCTCTAAAATATGCTAC 57.865 37.037 0.00 0.00 29.58 3.58
543 584 7.724061 AGAGGTTTTCCATAGCAAAAAGAAGTA 59.276 33.333 0.00 0.00 43.73 2.24
544 585 7.658261 AGGTTTTCCATAGCAAAAAGAAGTAC 58.342 34.615 0.00 0.00 43.73 2.73
545 586 7.505923 AGGTTTTCCATAGCAAAAAGAAGTACT 59.494 33.333 0.00 0.00 43.73 2.73
550 591 6.588756 TCCATAGCAAAAAGAAGTACTACACG 59.411 38.462 0.00 0.00 0.00 4.49
653 713 3.843999 TCCATTTGCTTGCGTAAATTCC 58.156 40.909 0.00 0.00 33.91 3.01
666 726 3.736252 CGTAAATTCCGATGAGCAGTAGG 59.264 47.826 0.00 0.00 0.00 3.18
758 851 4.028490 CAAGCGGGCCCACACCTA 62.028 66.667 24.92 0.00 0.00 3.08
815 908 0.108377 ACACACACAGTTGACGCAGA 60.108 50.000 0.00 0.00 0.00 4.26
832 925 2.390938 CAGAGCACAGACGACGTTTTA 58.609 47.619 0.13 0.00 0.00 1.52
838 931 2.867975 CACAGACGACGTTTTACCCTTT 59.132 45.455 0.13 0.00 0.00 3.11
847 946 2.309613 GTTTTACCCTTTTCCACCCGT 58.690 47.619 0.00 0.00 0.00 5.28
865 964 3.112709 GCACACGTTCCTCCTCGC 61.113 66.667 0.00 0.00 0.00 5.03
890 989 2.276740 CTCATGGCCCCACCTTCC 59.723 66.667 0.00 0.00 40.22 3.46
891 990 3.346734 TCATGGCCCCACCTTCCC 61.347 66.667 0.00 0.00 40.22 3.97
930 1030 0.673644 GACAGTGGGGTTCGACATGG 60.674 60.000 0.00 0.00 0.00 3.66
954 1054 1.536662 AGAACACCCCCGCTTCTCT 60.537 57.895 0.00 0.00 0.00 3.10
963 1063 4.521062 CGCTTCTCTCTGGGCGGG 62.521 72.222 0.00 0.00 43.25 6.13
964 1064 4.168291 GCTTCTCTCTGGGCGGGG 62.168 72.222 0.00 0.00 0.00 5.73
993 1093 0.887933 ACGGTGATGCCATTTGTTCC 59.112 50.000 0.00 0.00 36.97 3.62
1007 1108 7.772757 TGCCATTTGTTCCTTCTTAATTTGTTT 59.227 29.630 0.00 0.00 0.00 2.83
1008 1109 9.267084 GCCATTTGTTCCTTCTTAATTTGTTTA 57.733 29.630 0.00 0.00 0.00 2.01
1013 1114 8.173542 TGTTCCTTCTTAATTTGTTTAGTCCC 57.826 34.615 0.00 0.00 0.00 4.46
1014 1115 7.040961 TGTTCCTTCTTAATTTGTTTAGTCCCG 60.041 37.037 0.00 0.00 0.00 5.14
1015 1116 6.771573 TCCTTCTTAATTTGTTTAGTCCCGA 58.228 36.000 0.00 0.00 0.00 5.14
1073 1174 4.282873 CGAGCACTTTCTTTCTTTTCCAC 58.717 43.478 0.00 0.00 0.00 4.02
1074 1175 4.611943 GAGCACTTTCTTTCTTTTCCACC 58.388 43.478 0.00 0.00 0.00 4.61
1075 1176 3.384789 AGCACTTTCTTTCTTTTCCACCC 59.615 43.478 0.00 0.00 0.00 4.61
1076 1177 3.384789 GCACTTTCTTTCTTTTCCACCCT 59.615 43.478 0.00 0.00 0.00 4.34
1077 1178 4.141937 GCACTTTCTTTCTTTTCCACCCTT 60.142 41.667 0.00 0.00 0.00 3.95
1078 1179 5.592054 CACTTTCTTTCTTTTCCACCCTTC 58.408 41.667 0.00 0.00 0.00 3.46
1101 1202 3.157949 CTCCGCTTCTCCCTCCCC 61.158 72.222 0.00 0.00 0.00 4.81
1104 1205 2.840102 CGCTTCTCCCTCCCCGAT 60.840 66.667 0.00 0.00 0.00 4.18
1106 1207 2.862223 GCTTCTCCCTCCCCGATCG 61.862 68.421 8.51 8.51 0.00 3.69
1107 1208 1.152735 CTTCTCCCTCCCCGATCGA 60.153 63.158 18.66 0.00 0.00 3.59
1108 1209 0.540830 CTTCTCCCTCCCCGATCGAT 60.541 60.000 18.66 0.00 0.00 3.59
1109 1210 0.539901 TTCTCCCTCCCCGATCGATC 60.540 60.000 18.66 15.68 0.00 3.69
1111 1212 2.997897 CCCTCCCCGATCGATCCC 60.998 72.222 18.66 0.00 0.00 3.85
1112 1213 3.374402 CCTCCCCGATCGATCCCG 61.374 72.222 18.66 9.58 37.07 5.14
1113 1214 3.374402 CTCCCCGATCGATCCCGG 61.374 72.222 18.66 17.87 44.94 5.73
1154 1256 1.256812 CACTGATTCCAAACCCACCC 58.743 55.000 0.00 0.00 0.00 4.61
1158 1260 1.595093 GATTCCAAACCCACCCAGCG 61.595 60.000 0.00 0.00 0.00 5.18
1311 1414 2.125147 GTGCTCGCCATGGTGCTA 60.125 61.111 20.97 3.28 0.00 3.49
1362 1465 4.035102 GGAGGAACTGCGGGGCTT 62.035 66.667 0.00 0.00 41.55 4.35
1587 1690 3.710722 CTGCACTCGGGGAAGCCT 61.711 66.667 0.00 0.00 0.00 4.58
1624 1727 0.870307 GATCCCCACATTCGTCGTCG 60.870 60.000 0.00 0.00 38.55 5.12
1715 1834 4.674362 GCTCTCTGTTTCGGTTTGTTTGTT 60.674 41.667 0.00 0.00 0.00 2.83
1719 1838 5.290386 TCTGTTTCGGTTTGTTTGTTTGTT 58.710 33.333 0.00 0.00 0.00 2.83
1759 1889 3.282745 CTACGTGTGCAGACGGGCT 62.283 63.158 35.35 20.12 43.84 5.19
1760 1890 3.277211 TACGTGTGCAGACGGGCTC 62.277 63.158 35.35 0.08 43.84 4.70
1767 1897 4.900154 CAGACGGGCTCTGTCTTC 57.100 61.111 12.41 0.00 44.00 2.87
1779 1909 3.623510 GCTCTGTCTTCGGGATTTTAAGG 59.376 47.826 0.00 0.00 0.00 2.69
1820 1953 0.030638 GCTTCGCTTCCAACTTGCAA 59.969 50.000 0.00 0.00 0.00 4.08
1910 2048 1.906966 GCATGTCGAATTTTGTCTGCG 59.093 47.619 0.00 0.00 0.00 5.18
1932 2070 1.967319 TGAGAATCCCTTTATGCCGC 58.033 50.000 0.00 0.00 0.00 6.53
2015 2165 3.630312 TGCCCTGTCAGTTTGAACTTTAC 59.370 43.478 0.00 0.00 37.08 2.01
2062 2212 0.036306 AGTTACTGGGGGAAGCAACG 59.964 55.000 0.00 0.00 0.00 4.10
2163 2313 0.240678 TTTGTACAATGGCTGCAGCG 59.759 50.000 31.19 20.03 43.26 5.18
2214 2364 3.769300 ACTGATATGCCCTTTTGGTTTCC 59.231 43.478 0.00 0.00 38.10 3.13
2416 2566 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
2417 2567 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
2418 2568 8.503458 AGAGCGTTTAGATCACTAAAGTAGTA 57.497 34.615 0.00 0.00 45.42 1.82
2419 2569 8.397148 AGAGCGTTTAGATCACTAAAGTAGTAC 58.603 37.037 0.00 0.00 45.42 2.73
2420 2570 8.278729 AGCGTTTAGATCACTAAAGTAGTACT 57.721 34.615 0.00 0.00 45.42 2.73
2421 2571 8.397148 AGCGTTTAGATCACTAAAGTAGTACTC 58.603 37.037 2.58 0.00 45.42 2.59
2422 2572 7.643371 GCGTTTAGATCACTAAAGTAGTACTCC 59.357 40.741 2.58 0.00 45.42 3.85
2423 2573 8.127954 CGTTTAGATCACTAAAGTAGTACTCCC 58.872 40.741 2.58 0.00 45.42 4.30
2424 2574 9.187996 GTTTAGATCACTAAAGTAGTACTCCCT 57.812 37.037 2.58 0.00 45.42 4.20
2425 2575 8.977267 TTAGATCACTAAAGTAGTACTCCCTC 57.023 38.462 2.58 0.00 37.23 4.30
2426 2576 7.215743 AGATCACTAAAGTAGTACTCCCTCT 57.784 40.000 2.58 0.00 37.23 3.69
2427 2577 7.057894 AGATCACTAAAGTAGTACTCCCTCTG 58.942 42.308 2.58 0.00 37.23 3.35
2428 2578 6.137104 TCACTAAAGTAGTACTCCCTCTGT 57.863 41.667 2.58 0.00 37.23 3.41
2429 2579 7.262990 TCACTAAAGTAGTACTCCCTCTGTA 57.737 40.000 2.58 0.00 37.23 2.74
2430 2580 7.693132 TCACTAAAGTAGTACTCCCTCTGTAA 58.307 38.462 2.58 0.00 37.23 2.41
2431 2581 8.166061 TCACTAAAGTAGTACTCCCTCTGTAAA 58.834 37.037 2.58 0.00 37.23 2.01
2432 2582 8.242739 CACTAAAGTAGTACTCCCTCTGTAAAC 58.757 40.741 2.58 0.00 37.23 2.01
2433 2583 8.169393 ACTAAAGTAGTACTCCCTCTGTAAACT 58.831 37.037 2.58 0.00 37.23 2.66
2434 2584 9.678260 CTAAAGTAGTACTCCCTCTGTAAACTA 57.322 37.037 2.58 0.00 0.00 2.24
2435 2585 8.946797 AAAGTAGTACTCCCTCTGTAAACTAA 57.053 34.615 2.58 0.00 0.00 2.24
2436 2586 9.544579 AAAGTAGTACTCCCTCTGTAAACTAAT 57.455 33.333 2.58 0.00 0.00 1.73
2444 2594 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2445 2595 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2446 2596 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2447 2597 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2448 2598 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2463 2613 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
2464 2614 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
2478 2628 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2479 2629 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2480 2630 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2481 2631 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2496 2646 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2497 2647 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2560 2748 9.719355 TTATAACTGTTCTGTTCTGCTTGAATA 57.281 29.630 0.00 0.00 36.99 1.75
2792 2980 6.831868 AGGTAATTCACTGTTGTTAACTTGGT 59.168 34.615 7.22 0.00 0.00 3.67
2978 3166 5.936372 CCCACATGGATGAATGTATCACTAG 59.064 44.000 0.00 0.00 41.93 2.57
3004 3192 5.398603 TGAAAGAGGATCAAGAGACTGAC 57.601 43.478 0.00 0.00 37.82 3.51
3170 3358 0.108520 GTGCATTGCATGGGGTTCAG 60.109 55.000 15.49 0.00 41.91 3.02
3538 3727 0.527817 GTCGGTCTTCTGGCCATACG 60.528 60.000 5.51 5.18 0.00 3.06
3594 3783 1.964223 AGGGCGTACTGACATATGGAG 59.036 52.381 7.80 5.13 0.00 3.86
3865 4056 9.379791 AGTTTAGGTAACAGATTAATACAGTGC 57.620 33.333 0.00 0.00 39.30 4.40
3935 4126 3.727970 GCTTAATGCGAGTTGGTAACTGC 60.728 47.826 0.00 4.51 43.03 4.40
3952 4143 5.673337 AACTGCGTGTTAGCCATATAATG 57.327 39.130 0.00 0.00 37.07 1.90
3953 4144 4.703897 ACTGCGTGTTAGCCATATAATGT 58.296 39.130 0.00 0.00 36.02 2.71
4085 4276 3.792401 TGGTAAGTCTTGGCATACATCG 58.208 45.455 0.00 0.00 0.00 3.84
4119 4310 0.392193 CGGAAGCTGGAATGCTCTGT 60.392 55.000 0.00 0.00 43.24 3.41
4178 4369 0.251916 CCCTTGCGTTGATGTCCCTA 59.748 55.000 0.00 0.00 0.00 3.53
4233 4424 7.414540 CCACTGTTATCTATGGACTGAAAAAGC 60.415 40.741 0.00 0.00 33.80 3.51
4236 4427 7.324935 TGTTATCTATGGACTGAAAAAGCGTA 58.675 34.615 0.00 0.00 0.00 4.42
4250 4441 2.747446 AAAGCGTATGCGTTTTCATCCT 59.253 40.909 11.90 0.00 45.78 3.24
4251 4442 2.825086 GCGTATGCGTTTTCATCCTT 57.175 45.000 4.81 0.00 40.81 3.36
4252 4443 2.705154 GCGTATGCGTTTTCATCCTTC 58.295 47.619 4.81 0.00 40.81 3.46
4253 4444 2.351726 GCGTATGCGTTTTCATCCTTCT 59.648 45.455 4.81 0.00 40.81 2.85
4254 4445 3.785505 GCGTATGCGTTTTCATCCTTCTG 60.786 47.826 4.81 0.00 40.81 3.02
4255 4446 3.370978 CGTATGCGTTTTCATCCTTCTGT 59.629 43.478 0.00 0.00 0.00 3.41
4256 4447 4.142902 CGTATGCGTTTTCATCCTTCTGTT 60.143 41.667 0.00 0.00 0.00 3.16
4257 4448 4.853924 ATGCGTTTTCATCCTTCTGTTT 57.146 36.364 0.00 0.00 0.00 2.83
4258 4449 5.957842 ATGCGTTTTCATCCTTCTGTTTA 57.042 34.783 0.00 0.00 0.00 2.01
4259 4450 5.759506 TGCGTTTTCATCCTTCTGTTTAA 57.240 34.783 0.00 0.00 0.00 1.52
4324 4515 8.855110 TGCTGGTTCTCAATAAAAGTCATTAAA 58.145 29.630 0.00 0.00 0.00 1.52
4525 4716 3.812156 ATGTGGACGTCAAATATCCGA 57.188 42.857 18.91 0.00 35.06 4.55
4745 4952 9.793259 TTTTCTGACTGGTAAGATTGAAATAGT 57.207 29.630 0.00 0.00 0.00 2.12
4746 4953 9.436957 TTTCTGACTGGTAAGATTGAAATAGTC 57.563 33.333 0.00 0.00 35.20 2.59
4747 4954 8.134202 TCTGACTGGTAAGATTGAAATAGTCA 57.866 34.615 0.00 0.00 40.43 3.41
4748 4955 8.762645 TCTGACTGGTAAGATTGAAATAGTCAT 58.237 33.333 0.00 0.00 41.42 3.06
4761 4968 7.880059 TGAAATAGTCATATGATTCGAGCAG 57.120 36.000 9.02 0.00 0.00 4.24
4791 4998 2.996734 ACCCCTTTGGCAATGCGG 60.997 61.111 13.55 13.55 37.83 5.69
4882 5089 7.268586 GTTCAACTATACCATCTCACTGACAT 58.731 38.462 0.00 0.00 0.00 3.06
4894 5101 6.844696 TCTCACTGACATAAACAGTTTCAC 57.155 37.500 0.48 0.00 44.69 3.18
4896 5103 4.509970 TCACTGACATAAACAGTTTCACCG 59.490 41.667 0.48 0.00 44.69 4.94
4897 5104 3.813166 ACTGACATAAACAGTTTCACCGG 59.187 43.478 0.48 0.00 44.69 5.28
4917 5124 0.744414 CGGAACAGAATCCATGGCGT 60.744 55.000 6.96 0.00 39.61 5.68
5026 5237 1.673760 CAAAAGGCGTGTCATGTTCG 58.326 50.000 0.00 0.00 0.00 3.95
5035 5246 1.154413 GTCATGTTCGGCTTGTGCG 60.154 57.895 0.00 0.00 40.82 5.34
5041 5252 0.040425 GTTCGGCTTGTGCGTTTCAT 60.040 50.000 0.00 0.00 40.82 2.57
5147 5358 5.529800 ACCTACACAAACAGTATCAACAACC 59.470 40.000 0.00 0.00 0.00 3.77
5151 5362 3.562557 ACAAACAGTATCAACAACCGGAC 59.437 43.478 9.46 0.00 0.00 4.79
5227 5445 3.625745 CACCTACCAGTGTCCCAAC 57.374 57.895 0.00 0.00 32.89 3.77
5229 5447 1.375523 CCTACCAGTGTCCCAACGC 60.376 63.158 0.00 0.00 36.09 4.84
5230 5448 1.369692 CTACCAGTGTCCCAACGCA 59.630 57.895 0.00 0.00 38.41 5.24
5231 5449 0.670546 CTACCAGTGTCCCAACGCAG 60.671 60.000 0.00 0.00 38.41 5.18
5232 5450 1.116536 TACCAGTGTCCCAACGCAGA 61.117 55.000 0.00 0.00 38.41 4.26
5233 5451 1.669115 CCAGTGTCCCAACGCAGAG 60.669 63.158 0.00 0.00 38.41 3.35
5234 5452 2.031163 AGTGTCCCAACGCAGAGC 59.969 61.111 0.00 0.00 38.41 4.09
5235 5453 2.280797 GTGTCCCAACGCAGAGCA 60.281 61.111 0.00 0.00 35.90 4.26
5260 5667 2.100916 GTCTATGGCGGTGACATGTAGT 59.899 50.000 0.00 0.00 31.56 2.73
5268 5675 1.609061 GGTGACATGTAGTGCTGCTGT 60.609 52.381 0.00 0.00 0.00 4.40
5277 5684 0.250901 AGTGCTGCTGTGTTTAGGGG 60.251 55.000 0.00 0.00 0.00 4.79
5286 5693 1.602323 TGTTTAGGGGTGCAAGCGG 60.602 57.895 0.00 0.00 33.03 5.52
5317 5725 4.638421 TGTATCCCCGAAACTAGCAAATTG 59.362 41.667 0.00 0.00 0.00 2.32
5363 5771 1.065126 CGCTTCCATTTTCCTCCTCCT 60.065 52.381 0.00 0.00 0.00 3.69
5384 5794 0.323957 AACCTCGTAAGCTTCACCCC 59.676 55.000 0.00 0.00 37.18 4.95
5386 5796 0.613777 CCTCGTAAGCTTCACCCCTT 59.386 55.000 0.00 0.00 37.18 3.95
5388 5798 2.076863 CTCGTAAGCTTCACCCCTTTG 58.923 52.381 0.00 0.00 37.18 2.77
5395 5805 3.801068 TTCACCCCTTTGCCACCCG 62.801 63.158 0.00 0.00 0.00 5.28
5454 5876 3.311110 GCCTGACTCCGTCCACCA 61.311 66.667 0.00 0.00 0.00 4.17
5494 5916 2.863809 ACTGGAATTTCCGAGTTTGCT 58.136 42.857 10.79 0.00 40.17 3.91
5513 5935 7.871463 AGTTTGCTGAGTACTATAAAAACTCGT 59.129 33.333 15.33 1.74 42.05 4.18
5520 5942 7.272084 TGAGTACTATAAAAACTCGTCGAAAGC 59.728 37.037 0.00 0.00 42.05 3.51
5586 6063 1.697982 AGGGTACTCGGCAAAGACTTT 59.302 47.619 0.00 0.00 0.00 2.66
5587 6064 2.105993 AGGGTACTCGGCAAAGACTTTT 59.894 45.455 0.00 0.00 0.00 2.27
5602 6079 6.619801 AAGACTTTTTCGAGCACTAAACAT 57.380 33.333 0.00 0.00 0.00 2.71
5608 6085 1.899814 TCGAGCACTAAACATGGGACT 59.100 47.619 0.00 0.00 0.00 3.85
5701 6178 4.735132 GCACGCAGGTACTCGGCA 62.735 66.667 0.00 0.00 34.60 5.69
5707 6184 1.202371 CGCAGGTACTCGGCAAATCTA 60.202 52.381 0.00 0.00 34.60 1.98
5709 6186 2.608090 GCAGGTACTCGGCAAATCTAAC 59.392 50.000 0.00 0.00 34.60 2.34
5719 6196 2.446435 GCAAATCTAACAGCCCAGGAA 58.554 47.619 0.00 0.00 0.00 3.36
5723 6200 1.344065 TCTAACAGCCCAGGAACGAA 58.656 50.000 0.00 0.00 0.00 3.85
5777 6254 3.414269 TCGACAAATCTTGGTAAACCCC 58.586 45.455 0.00 0.00 34.29 4.95
5805 6283 2.883574 CCGAGTATTGTTTGCCGAGTA 58.116 47.619 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.298626 AGGGGAGATGCAGTACAATAGAA 58.701 43.478 0.00 0.00 0.00 2.10
32 33 1.204146 GGAGGGGAGATGCAGTACAA 58.796 55.000 0.00 0.00 0.00 2.41
74 75 4.143986 AGTCCTTTGCTACTTATGAGCC 57.856 45.455 0.00 0.00 39.30 4.70
80 81 4.465305 GTCCACCTAGTCCTTTGCTACTTA 59.535 45.833 0.00 0.00 0.00 2.24
91 92 1.079336 GGTTGCGTCCACCTAGTCC 60.079 63.158 0.00 0.00 0.00 3.85
94 95 1.156736 CAAAGGTTGCGTCCACCTAG 58.843 55.000 3.14 0.00 32.81 3.02
95 96 0.470766 ACAAAGGTTGCGTCCACCTA 59.529 50.000 3.14 0.00 32.81 3.08
123 124 4.275508 CATCCAGCCCATCCCCGG 62.276 72.222 0.00 0.00 0.00 5.73
125 126 1.723128 ATGTCATCCAGCCCATCCCC 61.723 60.000 0.00 0.00 0.00 4.81
126 127 0.251077 GATGTCATCCAGCCCATCCC 60.251 60.000 0.90 0.00 0.00 3.85
130 131 1.427809 CCTAGATGTCATCCAGCCCA 58.572 55.000 9.29 0.00 0.00 5.36
139 140 2.063979 CCCACCGCCCTAGATGTCA 61.064 63.158 0.00 0.00 0.00 3.58
175 176 0.541863 CGCCACCCTTACTCCTCATT 59.458 55.000 0.00 0.00 0.00 2.57
179 180 1.988406 GTCCGCCACCCTTACTCCT 60.988 63.158 0.00 0.00 0.00 3.69
184 185 3.751246 CGTCGTCCGCCACCCTTA 61.751 66.667 0.00 0.00 0.00 2.69
228 229 2.203126 CGCATCCTCCTGCCTTCC 60.203 66.667 0.00 0.00 39.00 3.46
230 231 2.262774 CTTCCGCATCCTCCTGCCTT 62.263 60.000 0.00 0.00 39.00 4.35
242 243 2.027285 TCAAATCCATCACTCTTCCGCA 60.027 45.455 0.00 0.00 0.00 5.69
246 247 5.571784 TTGCATCAAATCCATCACTCTTC 57.428 39.130 0.00 0.00 0.00 2.87
275 278 2.452064 CCCGACATGCCTACCCCAT 61.452 63.158 0.00 0.00 0.00 4.00
317 320 4.496927 GAAAATGCCCGGGCGCAG 62.497 66.667 39.00 5.50 43.26 5.18
332 335 6.911250 TCCTAAATGTAGAGCGGATATGAA 57.089 37.500 0.00 0.00 0.00 2.57
333 336 6.437477 ACATCCTAAATGTAGAGCGGATATGA 59.563 38.462 0.00 0.00 30.56 2.15
335 338 6.859112 ACATCCTAAATGTAGAGCGGATAT 57.141 37.500 0.00 0.00 30.56 1.63
338 341 7.614192 TCATATACATCCTAAATGTAGAGCGGA 59.386 37.037 4.43 0.00 37.84 5.54
340 343 8.462811 ACTCATATACATCCTAAATGTAGAGCG 58.537 37.037 10.46 0.00 37.84 5.03
347 350 7.010830 CGGCATCACTCATATACATCCTAAATG 59.989 40.741 0.00 0.00 0.00 2.32
348 351 7.044181 CGGCATCACTCATATACATCCTAAAT 58.956 38.462 0.00 0.00 0.00 1.40
352 355 3.196469 CCGGCATCACTCATATACATCCT 59.804 47.826 0.00 0.00 0.00 3.24
355 358 2.355108 GGCCGGCATCACTCATATACAT 60.355 50.000 30.85 0.00 0.00 2.29
358 361 1.276138 CTGGCCGGCATCACTCATATA 59.724 52.381 30.85 0.00 0.00 0.86
368 371 3.866582 GTCTAGGCTGGCCGGCAT 61.867 66.667 36.64 32.95 41.95 4.40
383 386 1.264288 CTTGAACAGGCCTCAAACGTC 59.736 52.381 0.00 0.00 32.57 4.34
424 427 0.676184 CGGATGGACAGATCGGTCAT 59.324 55.000 24.43 16.34 39.59 3.06
426 429 0.744874 TTCGGATGGACAGATCGGTC 59.255 55.000 16.66 16.66 37.06 4.79
427 430 0.460311 GTTCGGATGGACAGATCGGT 59.540 55.000 0.00 0.00 0.00 4.69
428 431 0.595053 CGTTCGGATGGACAGATCGG 60.595 60.000 0.00 0.00 34.24 4.18
429 432 0.100682 ACGTTCGGATGGACAGATCG 59.899 55.000 0.00 0.00 40.04 3.69
430 433 2.295253 AACGTTCGGATGGACAGATC 57.705 50.000 0.00 0.00 0.00 2.75
431 434 2.028476 TCAAACGTTCGGATGGACAGAT 60.028 45.455 0.00 0.00 0.00 2.90
432 435 1.341852 TCAAACGTTCGGATGGACAGA 59.658 47.619 0.00 0.00 0.00 3.41
433 436 1.726791 CTCAAACGTTCGGATGGACAG 59.273 52.381 0.00 0.00 0.00 3.51
434 437 1.606994 CCTCAAACGTTCGGATGGACA 60.607 52.381 0.00 0.00 0.00 4.02
439 454 2.388232 GCGCCTCAAACGTTCGGAT 61.388 57.895 0.00 0.00 0.00 4.18
444 459 1.227556 AGTCTGCGCCTCAAACGTT 60.228 52.632 4.18 0.00 0.00 3.99
446 461 0.666274 TACAGTCTGCGCCTCAAACG 60.666 55.000 4.18 0.00 0.00 3.60
454 469 2.587574 GAGCATCTACAGTCTGCGC 58.412 57.895 0.00 0.00 40.78 6.09
543 584 7.661127 TGCTGATTTATTACAAACGTGTAGT 57.339 32.000 0.00 0.00 41.25 2.73
653 713 0.678395 AGGCATCCTACTGCTCATCG 59.322 55.000 0.00 0.00 41.95 3.84
666 726 2.805099 GTCTCATTCATCGGAAGGCATC 59.195 50.000 0.00 0.00 36.25 3.91
710 770 1.200252 AGCGATCGACGAGGGAATATG 59.800 52.381 21.57 0.00 45.77 1.78
758 851 1.409661 GGTTGACTTGACCCCAACTGT 60.410 52.381 0.00 0.00 39.84 3.55
815 908 1.494824 GGTAAAACGTCGTCTGTGCT 58.505 50.000 0.00 0.00 0.00 4.40
832 925 2.203437 GCACGGGTGGAAAAGGGT 60.203 61.111 0.43 0.00 0.00 4.34
847 946 2.338620 CGAGGAGGAACGTGTGCA 59.661 61.111 0.00 0.00 0.00 4.57
865 964 4.489771 GGGCCATGAGGTCGGTGG 62.490 72.222 4.39 0.00 41.80 4.61
891 990 4.016706 GTGGACCCCCGTGTCTGG 62.017 72.222 0.00 0.00 35.54 3.86
930 1030 2.438434 CGGGGGTGTTCTGGATGC 60.438 66.667 0.00 0.00 0.00 3.91
993 1093 8.319143 TCTTCGGGACTAAACAAATTAAGAAG 57.681 34.615 0.00 0.00 33.61 2.85
1007 1108 2.037144 GGTAGCCATTCTTCGGGACTA 58.963 52.381 0.00 0.00 0.00 2.59
1008 1109 0.831307 GGTAGCCATTCTTCGGGACT 59.169 55.000 0.00 0.00 0.00 3.85
1009 1110 0.831307 AGGTAGCCATTCTTCGGGAC 59.169 55.000 0.00 0.00 0.00 4.46
1010 1111 1.120530 GAGGTAGCCATTCTTCGGGA 58.879 55.000 0.00 0.00 0.00 5.14
1013 1114 0.103208 AGCGAGGTAGCCATTCTTCG 59.897 55.000 0.00 0.00 38.01 3.79
1014 1115 2.205911 GAAGCGAGGTAGCCATTCTTC 58.794 52.381 0.00 0.00 38.01 2.87
1015 1116 1.134371 GGAAGCGAGGTAGCCATTCTT 60.134 52.381 0.00 0.00 38.01 2.52
1073 1174 0.176910 GAAGCGGAGAAGGAGAAGGG 59.823 60.000 0.00 0.00 0.00 3.95
1074 1175 1.136110 GAGAAGCGGAGAAGGAGAAGG 59.864 57.143 0.00 0.00 0.00 3.46
1075 1176 1.136110 GGAGAAGCGGAGAAGGAGAAG 59.864 57.143 0.00 0.00 0.00 2.85
1076 1177 1.187087 GGAGAAGCGGAGAAGGAGAA 58.813 55.000 0.00 0.00 0.00 2.87
1077 1178 0.684805 GGGAGAAGCGGAGAAGGAGA 60.685 60.000 0.00 0.00 0.00 3.71
1078 1179 0.686112 AGGGAGAAGCGGAGAAGGAG 60.686 60.000 0.00 0.00 0.00 3.69
1101 1202 1.498865 CTTTTGGCCGGGATCGATCG 61.499 60.000 18.81 9.36 39.00 3.69
1102 1203 1.166531 CCTTTTGGCCGGGATCGATC 61.167 60.000 17.36 17.36 39.00 3.69
1103 1204 1.152963 CCTTTTGGCCGGGATCGAT 60.153 57.895 2.18 0.00 39.00 3.59
1104 1205 2.270850 CCTTTTGGCCGGGATCGA 59.729 61.111 2.18 0.00 39.00 3.59
1154 1256 0.460987 ATTCTTTCTCTCGCCCGCTG 60.461 55.000 0.00 0.00 0.00 5.18
1330 1433 2.683933 TCCTCCTCCTCCGTTGCC 60.684 66.667 0.00 0.00 0.00 4.52
1331 1434 2.726351 CCTCCTCCTCCTCCGTTGC 61.726 68.421 0.00 0.00 0.00 4.17
1333 1436 0.615261 GTTCCTCCTCCTCCTCCGTT 60.615 60.000 0.00 0.00 0.00 4.44
1334 1437 1.000612 GTTCCTCCTCCTCCTCCGT 59.999 63.158 0.00 0.00 0.00 4.69
1335 1438 1.040339 CAGTTCCTCCTCCTCCTCCG 61.040 65.000 0.00 0.00 0.00 4.63
1336 1439 1.334384 GCAGTTCCTCCTCCTCCTCC 61.334 65.000 0.00 0.00 0.00 4.30
1337 1440 1.671901 CGCAGTTCCTCCTCCTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
1338 1441 1.684049 CGCAGTTCCTCCTCCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
1360 1463 4.148825 CCTCGCTCCCGTCCCAAG 62.149 72.222 0.00 0.00 35.54 3.61
1443 1546 3.414700 GTGAGCGCCACGTGGAAG 61.415 66.667 38.30 28.86 35.86 3.46
1587 1690 2.678580 TCGTCCATGAGGCCGTCA 60.679 61.111 0.00 1.68 40.38 4.35
1715 1834 3.060272 CACGTTGCACAACAAACAAACAA 60.060 39.130 13.52 0.00 40.82 2.83
1719 1838 1.670087 CCCACGTTGCACAACAAACAA 60.670 47.619 13.52 0.00 40.82 2.83
1759 1889 3.606687 GCCTTAAAATCCCGAAGACAGA 58.393 45.455 0.00 0.00 0.00 3.41
1760 1890 2.351726 CGCCTTAAAATCCCGAAGACAG 59.648 50.000 0.00 0.00 0.00 3.51
1767 1897 5.507974 GTTTTATCTCGCCTTAAAATCCCG 58.492 41.667 0.00 0.00 31.90 5.14
1779 1909 4.019867 CACCGATTTTCGTTTTATCTCGC 58.980 43.478 0.00 0.00 38.40 5.03
1910 2048 2.291741 CGGCATAAAGGGATTCTCAAGC 59.708 50.000 0.00 0.00 0.00 4.01
2015 2165 3.000727 GGGTGTACATGAACGAAGGAAG 58.999 50.000 0.00 0.00 0.00 3.46
2062 2212 3.626028 ACGGAGCATTTCAAAACTGAC 57.374 42.857 0.00 0.00 0.00 3.51
2105 2255 1.341531 GACGATATAGCCCTGCAGTGT 59.658 52.381 13.81 0.00 0.00 3.55
2163 2313 5.707764 ACTTACTCTTCTTCAATCTTTGCCC 59.292 40.000 0.00 0.00 0.00 5.36
2418 2568 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2419 2569 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2420 2570 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2421 2571 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2422 2572 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2437 2587 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
2438 2588 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
2439 2589 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
2440 2590 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
2454 2604 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2455 2605 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2470 2620 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2471 2621 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2472 2622 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2473 2623 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2474 2624 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2485 2635 8.871125 CCATATTATGTACTCCCTCTGTAAACT 58.129 37.037 3.10 0.00 0.00 2.66
2486 2636 8.867097 TCCATATTATGTACTCCCTCTGTAAAC 58.133 37.037 3.10 0.00 0.00 2.01
2487 2637 9.615660 ATCCATATTATGTACTCCCTCTGTAAA 57.384 33.333 3.10 0.00 0.00 2.01
2488 2638 9.615660 AATCCATATTATGTACTCCCTCTGTAA 57.384 33.333 3.10 0.00 0.00 2.41
2489 2639 9.615660 AAATCCATATTATGTACTCCCTCTGTA 57.384 33.333 3.10 0.00 0.00 2.74
2490 2640 8.511748 AAATCCATATTATGTACTCCCTCTGT 57.488 34.615 3.10 0.00 0.00 3.41
2491 2641 8.820831 AGAAATCCATATTATGTACTCCCTCTG 58.179 37.037 3.10 0.00 0.00 3.35
2492 2642 8.980832 AGAAATCCATATTATGTACTCCCTCT 57.019 34.615 3.10 0.00 0.00 3.69
2493 2643 9.041354 AGAGAAATCCATATTATGTACTCCCTC 57.959 37.037 3.10 0.00 0.00 4.30
2494 2644 8.980832 AGAGAAATCCATATTATGTACTCCCT 57.019 34.615 3.10 0.00 0.00 4.20
2495 2645 9.041354 AGAGAGAAATCCATATTATGTACTCCC 57.959 37.037 3.10 0.00 0.00 4.30
2507 2657 6.267242 CACATGGAGAGAGAGAGAAATCCATA 59.733 42.308 4.32 0.00 43.86 2.74
2560 2748 3.711190 TGCCATCAGTATGTACCTGTGAT 59.289 43.478 0.00 0.00 37.40 3.06
2978 3166 7.064490 GTCAGTCTCTTGATCCTCTTTCATTTC 59.936 40.741 0.00 0.00 0.00 2.17
3004 3192 3.140623 CAAAACCCATCCAAAAGCCTTG 58.859 45.455 0.00 0.00 0.00 3.61
3170 3358 8.087982 TCATGAAATCTTTACGAAGGATATGC 57.912 34.615 0.00 0.00 33.56 3.14
3538 3727 6.238759 GCCAGGATATTGTCAAATACCTTGTC 60.239 42.308 0.00 0.00 36.34 3.18
3594 3783 4.093556 GTCGAATCTCCACTCACCAATTTC 59.906 45.833 0.00 0.00 0.00 2.17
3760 3949 7.956508 TTGTAAACGTTGAACACATAAACAG 57.043 32.000 14.38 0.00 0.00 3.16
3865 4056 6.624423 ACAGCAGCAGTAAATAAAATTCCTG 58.376 36.000 0.00 0.00 0.00 3.86
3935 4126 7.703328 AGGAAAAACATTATATGGCTAACACG 58.297 34.615 0.00 0.00 33.60 4.49
3952 4143 7.973944 ACATTTTCGGCTTGATATAGGAAAAAC 59.026 33.333 1.52 0.00 37.07 2.43
3953 4144 8.062065 ACATTTTCGGCTTGATATAGGAAAAA 57.938 30.769 1.52 0.00 37.07 1.94
4085 4276 2.819984 TTCCGATCCCAAGCACAGCC 62.820 60.000 0.00 0.00 0.00 4.85
4119 4310 7.377766 AGAAGCGCTTAAATAGAAAACATCA 57.622 32.000 25.11 0.00 0.00 3.07
4236 4427 4.853924 AAACAGAAGGATGAAAACGCAT 57.146 36.364 0.00 0.00 0.00 4.73
4250 4441 5.640147 ACCATCCATTGACCTTAAACAGAA 58.360 37.500 0.00 0.00 0.00 3.02
4251 4442 5.255397 ACCATCCATTGACCTTAAACAGA 57.745 39.130 0.00 0.00 0.00 3.41
4252 4443 5.982890 AACCATCCATTGACCTTAAACAG 57.017 39.130 0.00 0.00 0.00 3.16
4253 4444 6.325028 TCAAAACCATCCATTGACCTTAAACA 59.675 34.615 0.00 0.00 0.00 2.83
4254 4445 6.754193 TCAAAACCATCCATTGACCTTAAAC 58.246 36.000 0.00 0.00 0.00 2.01
4255 4446 6.985653 TCAAAACCATCCATTGACCTTAAA 57.014 33.333 0.00 0.00 0.00 1.52
4256 4447 6.985653 TTCAAAACCATCCATTGACCTTAA 57.014 33.333 0.00 0.00 33.13 1.85
4257 4448 6.985653 TTTCAAAACCATCCATTGACCTTA 57.014 33.333 0.00 0.00 33.13 2.69
4258 4449 5.885449 TTTCAAAACCATCCATTGACCTT 57.115 34.783 0.00 0.00 33.13 3.50
4259 4450 5.543405 TGATTTCAAAACCATCCATTGACCT 59.457 36.000 0.00 0.00 33.13 3.85
4324 4515 7.214467 ACGATCCTTGTTAAATTCAACATGT 57.786 32.000 0.00 0.00 38.18 3.21
4744 4951 5.046529 ACAACTCTGCTCGAATCATATGAC 58.953 41.667 7.78 0.00 0.00 3.06
4745 4952 5.045872 CACAACTCTGCTCGAATCATATGA 58.954 41.667 8.10 8.10 0.00 2.15
4746 4953 4.318618 GCACAACTCTGCTCGAATCATATG 60.319 45.833 0.00 0.00 34.06 1.78
4747 4954 3.806521 GCACAACTCTGCTCGAATCATAT 59.193 43.478 0.00 0.00 34.06 1.78
4748 4955 3.118992 AGCACAACTCTGCTCGAATCATA 60.119 43.478 0.00 0.00 44.58 2.15
4751 4958 1.719600 AGCACAACTCTGCTCGAATC 58.280 50.000 0.00 0.00 44.58 2.52
4761 4968 1.109323 AAGGGGTGCAAGCACAACTC 61.109 55.000 24.67 9.97 42.94 3.01
4882 5089 0.106335 TCCGCCGGTGAAACTGTTTA 59.894 50.000 18.79 0.00 43.33 2.01
4894 5101 1.153168 ATGGATTCTGTTCCGCCGG 60.153 57.895 0.00 0.00 38.74 6.13
4896 5103 1.728490 GCCATGGATTCTGTTCCGCC 61.728 60.000 18.40 0.00 38.74 6.13
4897 5104 1.729881 GCCATGGATTCTGTTCCGC 59.270 57.895 18.40 0.00 38.74 5.54
4917 5124 5.468746 GCACTAATTTCAGACACCAGTACAA 59.531 40.000 0.00 0.00 0.00 2.41
5026 5237 1.284297 GGCAATGAAACGCACAAGCC 61.284 55.000 0.00 0.00 37.52 4.35
5035 5246 2.650608 GTTGACAGACGGCAATGAAAC 58.349 47.619 0.00 0.00 0.00 2.78
5041 5252 1.771073 CTTGCGTTGACAGACGGCAA 61.771 55.000 0.00 12.23 42.98 4.52
5147 5358 1.290203 ACATAGATGCTTTGCGTCCG 58.710 50.000 7.99 1.22 44.75 4.79
5151 5362 5.469373 TTGAAGTACATAGATGCTTTGCG 57.531 39.130 0.00 0.00 0.00 4.85
5188 5406 0.916086 AGGTGGTGTTGGACTGTTGA 59.084 50.000 0.00 0.00 0.00 3.18
5227 5445 0.031857 CCATAGACCTCTGCTCTGCG 59.968 60.000 0.00 0.00 0.00 5.18
5229 5447 0.031857 CGCCATAGACCTCTGCTCTG 59.968 60.000 0.00 0.00 0.00 3.35
5230 5448 1.112315 CCGCCATAGACCTCTGCTCT 61.112 60.000 0.00 0.00 0.00 4.09
5231 5449 1.365633 CCGCCATAGACCTCTGCTC 59.634 63.158 0.00 0.00 0.00 4.26
5232 5450 1.381872 ACCGCCATAGACCTCTGCT 60.382 57.895 0.00 0.00 0.00 4.24
5233 5451 1.227380 CACCGCCATAGACCTCTGC 60.227 63.158 0.00 0.00 0.00 4.26
5234 5452 0.103208 GTCACCGCCATAGACCTCTG 59.897 60.000 0.00 0.00 0.00 3.35
5235 5453 0.324368 TGTCACCGCCATAGACCTCT 60.324 55.000 0.00 0.00 0.00 3.69
5260 5667 0.537143 CACCCCTAAACACAGCAGCA 60.537 55.000 0.00 0.00 0.00 4.41
5268 5675 1.602323 CCGCTTGCACCCCTAAACA 60.602 57.895 0.00 0.00 0.00 2.83
5293 5700 2.973694 TGCTAGTTTCGGGGATACAC 57.026 50.000 0.00 0.00 39.74 2.90
5344 5752 2.025887 TGAGGAGGAGGAAAATGGAAGC 60.026 50.000 0.00 0.00 0.00 3.86
5363 5771 1.001633 GGGTGAAGCTTACGAGGTTGA 59.998 52.381 0.00 0.00 43.27 3.18
5399 5809 4.821589 GAGAGGCGGCAAGGTCGG 62.822 72.222 13.08 0.00 0.00 4.79
5454 5876 0.175760 AGTGATGCTACGCCGAATGT 59.824 50.000 0.00 0.00 0.00 2.71
5494 5916 7.272084 GCTTTCGACGAGTTTTTATAGTACTCA 59.728 37.037 0.00 0.00 38.52 3.41
5513 5935 2.798283 CCGAGTGTAAAACAGCTTTCGA 59.202 45.455 0.00 0.00 0.00 3.71
5520 5942 3.994392 ACAGTATGCCGAGTGTAAAACAG 59.006 43.478 0.00 0.00 42.53 3.16
5586 6063 3.071479 GTCCCATGTTTAGTGCTCGAAA 58.929 45.455 0.00 0.00 0.00 3.46
5587 6064 2.301870 AGTCCCATGTTTAGTGCTCGAA 59.698 45.455 0.00 0.00 0.00 3.71
5633 6110 2.406401 CGCCGTCTCCGTACGATT 59.594 61.111 18.76 0.00 45.68 3.34
5701 6178 2.304761 TCGTTCCTGGGCTGTTAGATTT 59.695 45.455 0.00 0.00 0.00 2.17
5707 6184 1.600916 GCTTCGTTCCTGGGCTGTT 60.601 57.895 0.00 0.00 0.00 3.16
5709 6186 2.032528 TGCTTCGTTCCTGGGCTG 59.967 61.111 0.00 0.00 0.00 4.85
5723 6200 3.119849 GCAAATATTTCAGGTGACGTGCT 60.120 43.478 0.00 0.00 0.00 4.40
5731 6208 5.469479 CAAAACTCGGCAAATATTTCAGGT 58.531 37.500 0.00 0.00 0.00 4.00
5767 6244 1.888826 CGGCAAAGATGGGGTTTACCA 60.889 52.381 0.69 0.00 46.24 3.25
5770 6247 1.353022 ACTCGGCAAAGATGGGGTTTA 59.647 47.619 0.00 0.00 0.00 2.01
5777 6254 3.853671 GCAAACAATACTCGGCAAAGATG 59.146 43.478 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.