Multiple sequence alignment - TraesCS6D01G012300

Loading Multiple Alignment...

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 TraesCS6D01G012300 chr6D 100.000 2810 0 0 1 2810 4780224 4777415 0.000000e+00 5190.0
1 TraesCS6D01G012300 chr6B 88.105 992 64 20 848 1810 8996928 8997894 0.000000e+00 1129.0
2 TraesCS6D01G012300 chr6B 88.725 204 15 3 603 805 8996727 8996923 2.800000e-60 243.0
3 TraesCS6D01G012300 chr6B 83.582 134 12 3 1766 1889 8999743 8999876 1.770000e-22 117.0
4 TraesCS6D01G012300 chr6A 86.767 1058 61 27 842 1847 3856213 3855183 0.000000e+00 1105.0
5 TraesCS6D01G012300 chr6A 87.284 637 61 10 1 635 3856968 3856350 0.000000e+00 710.0
6 TraesCS6D01G012300 chr6A 91.753 97 6 2 2658 2754 3854138 3854044 1.760000e-27 134.0
7 TraesCS6D01G012300 chr6A 75.191 262 36 18 1 258 600137469 600137705 2.300000e-16 97.1
8 TraesCS6D01G012300 chr2D 85.312 320 45 2 364 681 517079458 517079139 2.090000e-86 329.0
9 TraesCS6D01G012300 chr2D 84.615 325 48 2 357 679 330454707 330455031 3.490000e-84 322.0
10 TraesCS6D01G012300 chr2D 79.178 365 55 13 1 361 350072149 350072496 1.680000e-57 233.0
11 TraesCS6D01G012300 chr5D 82.429 387 44 16 1 382 70634045 70634412 1.620000e-82 316.0
12 TraesCS6D01G012300 chr4B 82.038 373 58 8 312 682 417768135 417768500 2.720000e-80 309.0
13 TraesCS6D01G012300 chr4B 87.050 139 15 3 1992 2128 295542671 295542808 1.350000e-33 154.0
14 TraesCS6D01G012300 chr3D 81.061 396 63 7 260 650 16377784 16378172 3.520000e-79 305.0
15 TraesCS6D01G012300 chr3D 93.878 49 3 0 1081 1129 32743487 32743439 1.080000e-09 75.0
16 TraesCS6D01G012300 chr4D 81.510 384 58 10 303 679 338834798 338835175 1.260000e-78 303.0
17 TraesCS6D01G012300 chr5A 81.606 386 51 12 1 382 60456336 60456705 4.550000e-78 302.0
18 TraesCS6D01G012300 chr2B 83.601 311 46 4 371 678 398653974 398653666 1.270000e-73 287.0
19 TraesCS6D01G012300 chrUn 80.720 389 48 14 4 382 29862782 29862411 7.670000e-71 278.0
20 TraesCS6D01G012300 chr7B 80.526 380 55 15 315 688 123868264 123867898 9.920000e-70 274.0
21 TraesCS6D01G012300 chr3B 83.039 283 42 4 273 550 532211808 532212089 4.650000e-63 252.0
22 TraesCS6D01G012300 chr3B 86.957 92 11 1 2038 2128 55642120 55642029 4.950000e-18 102.0
23 TraesCS6D01G012300 chr3B 93.878 49 3 0 1081 1129 55371665 55371617 1.080000e-09 75.0
24 TraesCS6D01G012300 chr3B 93.878 49 3 0 1081 1129 55394136 55394088 1.080000e-09 75.0
25 TraesCS6D01G012300 chr2A 82.807 285 43 4 271 550 452784020 452784303 1.670000e-62 250.0
26 TraesCS6D01G012300 chr2A 78.036 387 66 12 1 383 596150869 596151240 2.820000e-55 226.0
27 TraesCS6D01G012300 chr4A 82.332 283 44 4 273 550 741964984 741964703 1.010000e-59 241.0
28 TraesCS6D01G012300 chr3A 93.878 49 3 0 1081 1129 45171258 45171210 1.080000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G012300 chr6D 4777415 4780224 2809 True 5190.000000 5190 100.000000 1 2810 1 chr6D.!!$R1 2809
1 TraesCS6D01G012300 chr6B 8996727 8999876 3149 False 496.333333 1129 86.804000 603 1889 3 chr6B.!!$F1 1286
2 TraesCS6D01G012300 chr6A 3854044 3856968 2924 True 649.666667 1105 88.601333 1 2754 3 chr6A.!!$R1 2753

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
145 148 0.101040 CCAAGGGCGTAACATGCATG 59.899 55.0 25.09 25.09 0.0 4.06 F
814 818 0.105964 TGGGTTCTCAGTTGTCACCG 59.894 55.0 0.00 0.00 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1396 0.037232 AGGCTGCGTAGTTGAAGGAC 60.037 55.0 1.53 0.0 0.0 3.85 R
2087 2166 0.249447 CGCTCCGTTGGATCATGCTA 60.249 55.0 0.00 0.0 0.0 3.49 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
87 89 5.500645 AAAAGAACGGGAGACTCAAAAAG 57.499 39.130 4.53 0.00 0.00 2.27
89 91 3.467803 AGAACGGGAGACTCAAAAAGTG 58.532 45.455 4.53 0.00 38.74 3.16
108 111 8.545229 AAAAGTGAGATGAGAGAATAACACAG 57.455 34.615 0.00 0.00 0.00 3.66
121 124 9.823647 AGAGAATAACACAGAGTAATTGGTATG 57.176 33.333 0.00 0.00 0.00 2.39
133 136 3.662290 TGGTATGAACACCAAGGGC 57.338 52.632 0.00 0.00 45.65 5.19
136 139 1.065998 GGTATGAACACCAAGGGCGTA 60.066 52.381 0.00 0.00 38.55 4.42
137 140 2.616001 GGTATGAACACCAAGGGCGTAA 60.616 50.000 0.00 0.00 38.55 3.18
142 145 1.241315 ACACCAAGGGCGTAACATGC 61.241 55.000 0.00 0.00 0.00 4.06
143 146 1.074072 ACCAAGGGCGTAACATGCA 59.926 52.632 0.00 0.00 0.00 3.96
144 147 0.323360 ACCAAGGGCGTAACATGCAT 60.323 50.000 0.00 0.00 0.00 3.96
145 148 0.101040 CCAAGGGCGTAACATGCATG 59.899 55.000 25.09 25.09 0.00 4.06
146 149 0.526096 CAAGGGCGTAACATGCATGC 60.526 55.000 26.53 11.82 0.00 4.06
147 150 0.964860 AAGGGCGTAACATGCATGCA 60.965 50.000 26.53 25.04 0.00 3.96
148 151 0.964860 AGGGCGTAACATGCATGCAA 60.965 50.000 26.68 11.98 0.00 4.08
149 152 0.108898 GGGCGTAACATGCATGCAAA 60.109 50.000 26.68 9.31 0.00 3.68
150 153 1.471327 GGGCGTAACATGCATGCAAAT 60.471 47.619 26.68 15.86 0.00 2.32
151 154 1.589320 GGCGTAACATGCATGCAAATG 59.411 47.619 26.68 21.54 0.00 2.32
164 167 0.376852 GCAAATGCCATGCAATGCAG 59.623 50.000 14.98 1.61 46.85 4.41
165 168 0.376852 CAAATGCCATGCAATGCAGC 59.623 50.000 14.98 13.22 44.97 5.25
196 199 5.717078 AGGAATTAATACCGAGCGATGTA 57.283 39.130 0.00 0.00 0.00 2.29
225 228 1.601903 ACCCATATATGCGTTGTTGCG 59.398 47.619 7.24 0.00 37.81 4.85
249 252 0.179225 GTGCGACCGTTATGTGCAAG 60.179 55.000 0.00 0.00 37.30 4.01
252 255 1.463528 GCGACCGTTATGTGCAAGAAC 60.464 52.381 0.00 0.00 0.00 3.01
261 264 5.734498 CGTTATGTGCAAGAACAATAAGAGC 59.266 40.000 0.00 0.00 32.81 4.09
271 274 3.299340 ACAATAAGAGCGTCGAGTTGT 57.701 42.857 0.00 0.00 0.00 3.32
272 275 4.430137 ACAATAAGAGCGTCGAGTTGTA 57.570 40.909 0.00 0.00 0.00 2.41
273 276 4.995124 ACAATAAGAGCGTCGAGTTGTAT 58.005 39.130 0.00 0.00 0.00 2.29
274 277 4.798907 ACAATAAGAGCGTCGAGTTGTATG 59.201 41.667 0.00 0.00 0.00 2.39
275 278 1.630148 AAGAGCGTCGAGTTGTATGC 58.370 50.000 0.00 0.00 0.00 3.14
276 279 0.526211 AGAGCGTCGAGTTGTATGCA 59.474 50.000 0.00 0.00 0.00 3.96
277 280 1.067846 AGAGCGTCGAGTTGTATGCAA 60.068 47.619 0.00 0.00 0.00 4.08
296 299 0.387750 ACGAACTAGGGTCGTTTCGC 60.388 55.000 15.61 0.00 36.67 4.70
308 311 1.736126 TCGTTTCGCTCAGACGTAGAT 59.264 47.619 0.00 0.00 37.95 1.98
318 321 6.691818 TCGCTCAGACGTAGATAATTCTTTTC 59.308 38.462 0.00 0.00 33.17 2.29
337 340 7.974675 TCTTTTCTTAATCTTCAAGCGTATGG 58.025 34.615 0.00 0.00 0.00 2.74
425 428 8.977505 GCAGATTTAAAACATTGCTTCAACTTA 58.022 29.630 0.00 0.00 0.00 2.24
438 441 8.830201 TTGCTTCAACTTACAAATAATGCATT 57.170 26.923 17.56 17.56 0.00 3.56
441 444 7.593875 TTCAACTTACAAATAATGCATTGGC 57.406 32.000 22.27 0.00 41.68 4.52
481 484 5.153950 AGGCTCTTTAAGAACAGAATCGT 57.846 39.130 0.00 0.00 0.00 3.73
499 502 2.123342 CGTCGTACAAAAACCGTACCA 58.877 47.619 0.00 0.00 36.66 3.25
513 516 5.806366 ACCGTACCAAAAGTATTGTATGC 57.194 39.130 0.00 0.00 32.28 3.14
546 549 7.283807 TGCTTCCTAACGTACTACTGATATGAA 59.716 37.037 0.00 0.00 0.00 2.57
560 563 7.372260 ACTGATATGAATTTCTGCTAGACCT 57.628 36.000 0.00 0.00 0.00 3.85
564 567 5.946942 ATGAATTTCTGCTAGACCTCAGA 57.053 39.130 0.00 0.00 37.54 3.27
569 572 1.005332 TCTGCTAGACCTCAGAGTGCT 59.995 52.381 0.00 0.00 34.69 4.40
585 588 3.073735 CTCCTCTCTGCCGTGGCT 61.074 66.667 12.84 0.00 42.51 4.75
586 589 1.754621 CTCCTCTCTGCCGTGGCTA 60.755 63.158 12.84 0.00 42.51 3.93
596 599 2.098293 CCGTGGCTAGGCACAATTC 58.902 57.895 38.66 19.31 0.00 2.17
605 608 0.527565 AGGCACAATTCGGATGTTGC 59.472 50.000 1.75 1.75 0.00 4.17
611 614 2.086869 CAATTCGGATGTTGCTGGACT 58.913 47.619 0.00 0.00 0.00 3.85
628 631 5.160607 TGGACTGTTCTGACGGATATTTT 57.839 39.130 0.00 0.00 36.01 1.82
629 632 4.935205 TGGACTGTTCTGACGGATATTTTG 59.065 41.667 0.00 0.00 36.01 2.44
650 653 3.195661 GGTGGACACGTCAATTATCTCC 58.804 50.000 0.00 0.00 0.00 3.71
654 657 0.852777 CACGTCAATTATCTCCCGCG 59.147 55.000 0.00 0.00 0.00 6.46
658 661 2.546778 GTCAATTATCTCCCGCGTTGA 58.453 47.619 4.92 2.56 0.00 3.18
660 663 3.560068 GTCAATTATCTCCCGCGTTGAAT 59.440 43.478 4.92 0.00 0.00 2.57
661 664 3.559655 TCAATTATCTCCCGCGTTGAATG 59.440 43.478 4.92 0.00 0.00 2.67
662 665 1.295792 TTATCTCCCGCGTTGAATGC 58.704 50.000 4.92 0.00 0.00 3.56
663 666 0.176910 TATCTCCCGCGTTGAATGCA 59.823 50.000 10.29 0.00 0.00 3.96
805 809 0.617413 AGCTCACCATGGGTTCTCAG 59.383 55.000 18.09 3.26 31.02 3.35
806 810 0.326264 GCTCACCATGGGTTCTCAGT 59.674 55.000 18.09 0.00 31.02 3.41
807 811 1.271597 GCTCACCATGGGTTCTCAGTT 60.272 52.381 18.09 0.00 31.02 3.16
808 812 2.430465 CTCACCATGGGTTCTCAGTTG 58.570 52.381 18.09 1.44 31.02 3.16
809 813 1.774254 TCACCATGGGTTCTCAGTTGT 59.226 47.619 18.09 0.00 31.02 3.32
810 814 2.154462 CACCATGGGTTCTCAGTTGTC 58.846 52.381 18.09 0.00 31.02 3.18
811 815 1.774254 ACCATGGGTTCTCAGTTGTCA 59.226 47.619 18.09 0.00 27.29 3.58
812 816 2.154462 CCATGGGTTCTCAGTTGTCAC 58.846 52.381 2.85 0.00 0.00 3.67
813 817 2.154462 CATGGGTTCTCAGTTGTCACC 58.846 52.381 0.00 0.00 0.00 4.02
814 818 0.105964 TGGGTTCTCAGTTGTCACCG 59.894 55.000 0.00 0.00 0.00 4.94
815 819 0.106149 GGGTTCTCAGTTGTCACCGT 59.894 55.000 0.00 0.00 0.00 4.83
816 820 1.217882 GGTTCTCAGTTGTCACCGTG 58.782 55.000 0.00 0.00 0.00 4.94
817 821 1.202486 GGTTCTCAGTTGTCACCGTGA 60.202 52.381 0.00 0.00 0.00 4.35
819 823 0.387929 TCTCAGTTGTCACCGTGACC 59.612 55.000 25.39 13.20 46.40 4.02
820 824 0.389391 CTCAGTTGTCACCGTGACCT 59.611 55.000 25.39 15.06 46.40 3.85
821 825 0.828022 TCAGTTGTCACCGTGACCTT 59.172 50.000 25.39 10.65 46.40 3.50
822 826 1.208535 TCAGTTGTCACCGTGACCTTT 59.791 47.619 25.39 10.33 46.40 3.11
823 827 1.330521 CAGTTGTCACCGTGACCTTTG 59.669 52.381 25.39 17.00 46.40 2.77
824 828 1.208535 AGTTGTCACCGTGACCTTTGA 59.791 47.619 25.39 6.85 46.40 2.69
825 829 1.597663 GTTGTCACCGTGACCTTTGAG 59.402 52.381 25.39 0.00 46.40 3.02
826 830 1.116308 TGTCACCGTGACCTTTGAGA 58.884 50.000 25.39 5.48 46.40 3.27
827 831 1.691976 TGTCACCGTGACCTTTGAGAT 59.308 47.619 25.39 0.00 46.40 2.75
828 832 2.104111 TGTCACCGTGACCTTTGAGATT 59.896 45.455 25.39 0.00 46.40 2.40
829 833 2.737252 GTCACCGTGACCTTTGAGATTC 59.263 50.000 19.30 0.00 41.37 2.52
830 834 2.076863 CACCGTGACCTTTGAGATTCC 58.923 52.381 0.00 0.00 0.00 3.01
831 835 1.337823 ACCGTGACCTTTGAGATTCCG 60.338 52.381 0.00 0.00 0.00 4.30
832 836 0.721718 CGTGACCTTTGAGATTCCGC 59.278 55.000 0.00 0.00 0.00 5.54
833 837 0.721718 GTGACCTTTGAGATTCCGCG 59.278 55.000 0.00 0.00 0.00 6.46
834 838 1.019278 TGACCTTTGAGATTCCGCGC 61.019 55.000 0.00 0.00 0.00 6.86
835 839 2.025359 GACCTTTGAGATTCCGCGCG 62.025 60.000 25.67 25.67 0.00 6.86
836 840 2.703409 CTTTGAGATTCCGCGCGG 59.297 61.111 42.13 42.13 0.00 6.46
837 841 3.440356 CTTTGAGATTCCGCGCGGC 62.440 63.158 42.78 28.99 34.68 6.53
867 871 3.053455 GGAAAGCAGAGGATACGATTCG 58.947 50.000 4.14 4.14 46.39 3.34
959 984 4.240881 TCCATTCCCTCCAAGAAATCAG 57.759 45.455 0.00 0.00 0.00 2.90
1131 1156 1.455248 CCGTCGACTTCCTCTTCTCT 58.545 55.000 14.70 0.00 0.00 3.10
1360 1385 2.747855 CCTTCTTCACCTGCGGCC 60.748 66.667 0.00 0.00 0.00 6.13
1373 1398 3.365265 CGGCCCCAGCAACAAGTC 61.365 66.667 0.00 0.00 42.56 3.01
1384 1409 3.059597 CAGCAACAAGTCCTTCAACTACG 60.060 47.826 0.00 0.00 0.00 3.51
1385 1410 2.349532 GCAACAAGTCCTTCAACTACGC 60.350 50.000 0.00 0.00 0.00 4.42
1388 1413 1.461127 CAAGTCCTTCAACTACGCAGC 59.539 52.381 0.00 0.00 0.00 5.25
1454 1479 3.983494 CGGGAGCGAGATGGCGAT 61.983 66.667 0.00 0.00 38.18 4.58
1459 1484 1.846849 GAGCGAGATGGCGATCGAGA 61.847 60.000 21.57 3.81 41.40 4.04
1460 1485 1.008424 GCGAGATGGCGATCGAGAA 60.008 57.895 21.57 2.95 41.40 2.87
1668 1717 1.988406 GCTCGGGTACAAGGAGGGT 60.988 63.158 0.00 0.00 0.00 4.34
1678 1727 0.749649 CAAGGAGGGTCTGGAGATCG 59.250 60.000 0.00 0.00 0.00 3.69
1812 1867 2.980233 GCCTGGCGTGTTTGAGCT 60.980 61.111 1.35 0.00 0.00 4.09
1823 1880 1.956477 TGTTTGAGCTTGAAGCCTTCC 59.044 47.619 14.45 1.67 43.77 3.46
1829 1886 0.962855 GCTTGAAGCCTTCCCTGACC 60.963 60.000 5.74 0.00 34.48 4.02
1871 1935 4.119862 GGTACAATTCTGCAGCGAATAGA 58.880 43.478 9.47 0.00 33.47 1.98
1872 1936 4.210120 GGTACAATTCTGCAGCGAATAGAG 59.790 45.833 9.47 2.09 33.47 2.43
1880 1944 1.539929 GCAGCGAATAGAGCAGTGGAT 60.540 52.381 0.00 0.00 37.01 3.41
1893 1957 4.910195 AGCAGTGGATGATTGTAAAGACA 58.090 39.130 0.00 0.00 0.00 3.41
1908 1972 8.810652 TTGTAAAGACAAAATGCATAACTTCC 57.189 30.769 0.00 0.00 42.66 3.46
1909 1973 7.375053 TGTAAAGACAAAATGCATAACTTCCC 58.625 34.615 0.00 0.00 30.68 3.97
1910 1974 5.405935 AAGACAAAATGCATAACTTCCCC 57.594 39.130 0.00 0.00 0.00 4.81
1911 1975 4.415596 AGACAAAATGCATAACTTCCCCA 58.584 39.130 0.00 0.00 0.00 4.96
1912 1976 4.220602 AGACAAAATGCATAACTTCCCCAC 59.779 41.667 0.00 0.00 0.00 4.61
1913 1977 4.159557 ACAAAATGCATAACTTCCCCACT 58.840 39.130 0.00 0.00 0.00 4.00
1914 1978 4.592778 ACAAAATGCATAACTTCCCCACTT 59.407 37.500 0.00 0.00 0.00 3.16
1915 1979 5.777732 ACAAAATGCATAACTTCCCCACTTA 59.222 36.000 0.00 0.00 0.00 2.24
1916 1980 6.440328 ACAAAATGCATAACTTCCCCACTTAT 59.560 34.615 0.00 0.00 0.00 1.73
1917 1981 6.715347 AAATGCATAACTTCCCCACTTATC 57.285 37.500 0.00 0.00 0.00 1.75
1919 1983 5.387113 TGCATAACTTCCCCACTTATCAT 57.613 39.130 0.00 0.00 0.00 2.45
1920 1984 6.508030 TGCATAACTTCCCCACTTATCATA 57.492 37.500 0.00 0.00 0.00 2.15
1921 1985 6.905736 TGCATAACTTCCCCACTTATCATAA 58.094 36.000 0.00 0.00 0.00 1.90
1922 1986 6.998074 TGCATAACTTCCCCACTTATCATAAG 59.002 38.462 2.58 2.58 0.00 1.73
1923 1987 6.431234 GCATAACTTCCCCACTTATCATAAGG 59.569 42.308 9.31 0.00 0.00 2.69
1924 1988 5.388599 AACTTCCCCACTTATCATAAGGG 57.611 43.478 9.31 4.43 39.29 3.95
1961 2032 5.660864 TGTGGAATCAGGGGATTTATTTTCC 59.339 40.000 0.00 0.00 43.69 3.13
2005 2084 8.883954 TGCTTGATATATCTATCATAGCTTGC 57.116 34.615 21.59 3.88 42.51 4.01
2006 2085 7.930325 TGCTTGATATATCTATCATAGCTTGCC 59.070 37.037 21.59 7.01 42.51 4.52
2007 2086 7.930325 GCTTGATATATCTATCATAGCTTGCCA 59.070 37.037 13.79 0.00 42.51 4.92
2008 2087 9.258826 CTTGATATATCTATCATAGCTTGCCAC 57.741 37.037 13.79 0.00 42.51 5.01
2009 2088 7.730084 TGATATATCTATCATAGCTTGCCACC 58.270 38.462 13.79 0.00 39.03 4.61
2010 2089 2.820059 TCTATCATAGCTTGCCACCG 57.180 50.000 0.00 0.00 0.00 4.94
2011 2090 2.316108 TCTATCATAGCTTGCCACCGA 58.684 47.619 0.00 0.00 0.00 4.69
2012 2091 2.698274 TCTATCATAGCTTGCCACCGAA 59.302 45.455 0.00 0.00 0.00 4.30
2013 2092 1.668419 ATCATAGCTTGCCACCGAAC 58.332 50.000 0.00 0.00 0.00 3.95
2014 2093 0.613260 TCATAGCTTGCCACCGAACT 59.387 50.000 0.00 0.00 0.00 3.01
2015 2094 1.828595 TCATAGCTTGCCACCGAACTA 59.171 47.619 0.00 0.00 0.00 2.24
2016 2095 2.235155 TCATAGCTTGCCACCGAACTAA 59.765 45.455 0.00 0.00 0.00 2.24
2017 2096 3.118408 TCATAGCTTGCCACCGAACTAAT 60.118 43.478 0.00 0.00 0.00 1.73
2018 2097 2.200373 AGCTTGCCACCGAACTAATT 57.800 45.000 0.00 0.00 0.00 1.40
2019 2098 3.343941 AGCTTGCCACCGAACTAATTA 57.656 42.857 0.00 0.00 0.00 1.40
2020 2099 3.681593 AGCTTGCCACCGAACTAATTAA 58.318 40.909 0.00 0.00 0.00 1.40
2021 2100 3.689649 AGCTTGCCACCGAACTAATTAAG 59.310 43.478 0.00 0.00 0.00 1.85
2022 2101 3.439129 GCTTGCCACCGAACTAATTAAGT 59.561 43.478 0.00 0.00 41.49 2.24
2041 2120 9.642327 AATTAAGTTTTTGAACGGTGTAAAAGT 57.358 25.926 0.00 0.00 0.00 2.66
2045 2124 8.009984 AGTTTTTGAACGGTGTAAAAGTTTTC 57.990 30.769 3.60 0.00 0.00 2.29
2049 2128 6.497785 TGAACGGTGTAAAAGTTTTCAGAA 57.502 33.333 3.60 0.00 0.00 3.02
2051 2130 7.540299 TGAACGGTGTAAAAGTTTTCAGAAAT 58.460 30.769 3.60 0.00 0.00 2.17
2052 2131 7.698970 TGAACGGTGTAAAAGTTTTCAGAAATC 59.301 33.333 3.60 0.00 0.00 2.17
2053 2132 6.500910 ACGGTGTAAAAGTTTTCAGAAATCC 58.499 36.000 3.60 0.65 0.00 3.01
2054 2133 5.918576 CGGTGTAAAAGTTTTCAGAAATCCC 59.081 40.000 3.60 0.05 0.00 3.85
2055 2134 5.918576 GGTGTAAAAGTTTTCAGAAATCCCG 59.081 40.000 3.60 0.00 0.00 5.14
2056 2135 6.238814 GGTGTAAAAGTTTTCAGAAATCCCGA 60.239 38.462 3.60 0.00 0.00 5.14
2057 2136 7.197703 GTGTAAAAGTTTTCAGAAATCCCGAA 58.802 34.615 3.60 0.00 0.00 4.30
2058 2137 7.703197 GTGTAAAAGTTTTCAGAAATCCCGAAA 59.297 33.333 3.60 0.00 0.00 3.46
2090 2169 9.326413 ACTGAAACAACACACCTATAATATAGC 57.674 33.333 1.81 0.00 0.00 2.97
2091 2170 9.325198 CTGAAACAACACACCTATAATATAGCA 57.675 33.333 1.81 0.00 0.00 3.49
2092 2171 9.845740 TGAAACAACACACCTATAATATAGCAT 57.154 29.630 1.81 0.00 0.00 3.79
2094 2173 9.845740 AAACAACACACCTATAATATAGCATGA 57.154 29.630 13.40 0.00 0.00 3.07
2096 2175 9.658799 ACAACACACCTATAATATAGCATGATC 57.341 33.333 13.40 0.00 0.00 2.92
2097 2176 9.102757 CAACACACCTATAATATAGCATGATCC 57.897 37.037 13.40 0.00 0.00 3.36
2098 2177 8.379428 ACACACCTATAATATAGCATGATCCA 57.621 34.615 13.40 0.00 0.00 3.41
2099 2178 8.825774 ACACACCTATAATATAGCATGATCCAA 58.174 33.333 13.40 0.00 0.00 3.53
2100 2179 9.102757 CACACCTATAATATAGCATGATCCAAC 57.897 37.037 13.40 0.00 0.00 3.77
2101 2180 7.981789 ACACCTATAATATAGCATGATCCAACG 59.018 37.037 13.40 0.00 0.00 4.10
2102 2181 7.439356 CACCTATAATATAGCATGATCCAACGG 59.561 40.741 0.00 0.00 0.00 4.44
2103 2182 7.344612 ACCTATAATATAGCATGATCCAACGGA 59.655 37.037 0.00 0.00 35.55 4.69
2104 2183 7.869937 CCTATAATATAGCATGATCCAACGGAG 59.130 40.741 0.00 0.00 34.05 4.63
2105 2184 2.175878 ATAGCATGATCCAACGGAGC 57.824 50.000 0.00 0.00 38.78 4.70
2106 2185 0.249447 TAGCATGATCCAACGGAGCG 60.249 55.000 0.00 0.00 41.58 5.03
2107 2186 1.521457 GCATGATCCAACGGAGCGA 60.521 57.895 0.00 0.00 41.58 4.93
2108 2187 0.882042 GCATGATCCAACGGAGCGAT 60.882 55.000 0.00 0.00 41.58 4.58
2109 2188 1.586422 CATGATCCAACGGAGCGATT 58.414 50.000 0.00 0.00 41.58 3.34
2110 2189 1.262417 CATGATCCAACGGAGCGATTG 59.738 52.381 0.00 0.00 41.58 2.67
2111 2190 0.534873 TGATCCAACGGAGCGATTGA 59.465 50.000 0.00 0.00 41.58 2.57
2112 2191 1.066502 TGATCCAACGGAGCGATTGAA 60.067 47.619 0.00 0.00 41.58 2.69
2113 2192 2.006888 GATCCAACGGAGCGATTGAAA 58.993 47.619 0.00 0.00 34.05 2.69
2114 2193 1.885560 TCCAACGGAGCGATTGAAAA 58.114 45.000 0.00 0.00 0.00 2.29
2115 2194 2.222886 TCCAACGGAGCGATTGAAAAA 58.777 42.857 0.00 0.00 0.00 1.94
2205 2285 8.716646 AAAATTTTGAATATTTCCGGATGGTC 57.283 30.769 4.15 0.00 36.30 4.02
2224 2304 8.749354 GGATGGTCTGGAATAATTAAAGTTGTT 58.251 33.333 0.00 0.00 0.00 2.83
2227 2307 8.356657 TGGTCTGGAATAATTAAAGTTGTTGTG 58.643 33.333 0.00 0.00 0.00 3.33
2241 2321 4.096382 AGTTGTTGTGAAATGTCTGTGGTC 59.904 41.667 0.00 0.00 0.00 4.02
2242 2322 3.884895 TGTTGTGAAATGTCTGTGGTCT 58.115 40.909 0.00 0.00 0.00 3.85
2257 2337 9.672086 TGTCTGTGGTCTTTTTATTAAAATTCG 57.328 29.630 2.57 0.00 33.05 3.34
2260 2340 7.434492 TGTGGTCTTTTTATTAAAATTCGCCA 58.566 30.769 2.57 6.65 33.05 5.69
2275 2355 2.524306 TCGCCAAAATGGGTCTCAAAT 58.476 42.857 0.00 0.00 38.19 2.32
2290 2370 9.253832 TGGGTCTCAAATTATTGAAATATGTGT 57.746 29.630 0.00 0.00 44.64 3.72
2498 2599 7.172532 TGTGCTTCTAAAACGATACTGAAATGT 59.827 33.333 0.00 0.00 0.00 2.71
2500 2601 8.227791 TGCTTCTAAAACGATACTGAAATGTTC 58.772 33.333 0.00 0.00 0.00 3.18
2501 2602 8.227791 GCTTCTAAAACGATACTGAAATGTTCA 58.772 33.333 0.00 0.00 38.17 3.18
2539 2640 8.486383 TCATTGCTTGTTTTAATTGAACAATCG 58.514 29.630 17.08 10.82 43.64 3.34
2542 2643 6.478344 TGCTTGTTTTAATTGAACAATCGCTT 59.522 30.769 20.85 0.00 43.64 4.68
2544 2645 7.318674 GCTTGTTTTAATTGAACAATCGCTTTG 59.681 33.333 17.08 8.88 43.64 2.77
2557 2658 6.373779 ACAATCGCTTTGTTTGTTGATAGAG 58.626 36.000 0.00 0.00 46.51 2.43
2558 2659 6.017109 ACAATCGCTTTGTTTGTTGATAGAGT 60.017 34.615 0.00 0.00 46.51 3.24
2564 3012 9.180678 CGCTTTGTTTGTTGATAGAGTTAAAAT 57.819 29.630 0.00 0.00 0.00 1.82
2628 3104 1.955778 AGCAGCTTGTTACAATGCACA 59.044 42.857 20.95 0.00 39.34 4.57
2629 3105 2.053627 GCAGCTTGTTACAATGCACAC 58.946 47.619 16.00 5.31 36.88 3.82
2631 3107 3.858129 GCAGCTTGTTACAATGCACACAT 60.858 43.478 16.00 0.00 38.49 3.21
2647 3163 4.563976 GCACACATTGTAGCAATGGATTTC 59.436 41.667 21.19 7.03 32.14 2.17
2648 3164 5.104374 CACACATTGTAGCAATGGATTTCC 58.896 41.667 21.19 0.00 32.14 3.13
2720 3236 8.953990 CAAAATACTTGAAACTACGAAAAGTGG 58.046 33.333 0.00 0.00 37.35 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 6.862209 ACTCTGTGTTATTCTCTCATCTCAC 58.138 40.000 0.00 0.00 0.00 3.51
99 102 9.733556 TGTTCATACCAATTACTCTGTGTTATT 57.266 29.630 0.00 0.00 0.00 1.40
102 105 6.430000 GGTGTTCATACCAATTACTCTGTGTT 59.570 38.462 0.00 0.00 40.54 3.32
121 124 1.199097 CATGTTACGCCCTTGGTGTTC 59.801 52.381 4.44 0.52 44.78 3.18
132 135 2.982919 CATTTGCATGCATGTTACGC 57.017 45.000 26.79 13.39 0.00 4.42
145 148 0.376852 CTGCATTGCATGGCATTTGC 59.623 50.000 12.53 15.51 43.50 3.68
146 149 0.376852 GCTGCATTGCATGGCATTTG 59.623 50.000 12.53 0.00 38.76 2.32
147 150 0.035915 TGCTGCATTGCATGGCATTT 60.036 45.000 18.42 0.00 38.76 2.32
148 151 0.035915 TTGCTGCATTGCATGGCATT 60.036 45.000 21.67 0.00 38.96 3.56
149 152 0.180171 ATTGCTGCATTGCATGGCAT 59.820 45.000 21.67 11.91 38.96 4.40
150 153 0.824759 TATTGCTGCATTGCATGGCA 59.175 45.000 18.42 18.42 42.96 4.92
151 154 1.942677 TTATTGCTGCATTGCATGGC 58.057 45.000 12.53 13.48 42.96 4.40
152 155 4.948608 TTTTTATTGCTGCATTGCATGG 57.051 36.364 12.53 2.45 42.96 3.66
182 185 1.535833 CCTCCTACATCGCTCGGTAT 58.464 55.000 0.00 0.00 0.00 2.73
190 193 2.808206 GGGTGCCCCTCCTACATCG 61.808 68.421 3.16 0.00 41.34 3.84
196 199 1.673767 CATATATGGGTGCCCCTCCT 58.326 55.000 4.68 0.38 45.70 3.69
249 252 3.673809 ACAACTCGACGCTCTTATTGTTC 59.326 43.478 0.00 0.00 0.00 3.18
252 255 4.317418 GCATACAACTCGACGCTCTTATTG 60.317 45.833 0.00 0.00 0.00 1.90
271 274 1.820519 ACGACCCTAGTTCGTTGCATA 59.179 47.619 10.11 0.00 36.67 3.14
272 275 0.606604 ACGACCCTAGTTCGTTGCAT 59.393 50.000 10.11 0.00 36.67 3.96
273 276 0.390124 AACGACCCTAGTTCGTTGCA 59.610 50.000 22.01 0.00 46.35 4.08
274 277 3.206090 AACGACCCTAGTTCGTTGC 57.794 52.632 22.01 0.00 46.35 4.17
277 280 0.387750 GCGAAACGACCCTAGTTCGT 60.388 55.000 10.11 10.11 42.20 3.85
278 281 0.109412 AGCGAAACGACCCTAGTTCG 60.109 55.000 8.96 8.96 0.00 3.95
286 289 0.110056 TACGTCTGAGCGAAACGACC 60.110 55.000 10.17 0.00 39.59 4.79
318 321 6.507900 TCTCTCCATACGCTTGAAGATTAAG 58.492 40.000 0.00 0.00 0.00 1.85
322 325 4.798924 GCATCTCTCCATACGCTTGAAGAT 60.799 45.833 0.00 0.00 0.00 2.40
332 335 5.874810 TGTGTTTTAGTGCATCTCTCCATAC 59.125 40.000 0.00 0.00 0.00 2.39
390 393 8.924691 GCAATGTTTTAAATCTGCACTAAATCA 58.075 29.630 5.91 0.00 0.00 2.57
438 441 8.860780 AGCCTAATTTTTAATTTTTCATGCCA 57.139 26.923 0.00 0.00 0.00 4.92
472 475 3.182972 CGGTTTTTGTACGACGATTCTGT 59.817 43.478 0.00 0.00 0.00 3.41
475 478 3.776043 ACGGTTTTTGTACGACGATTC 57.224 42.857 0.00 0.00 0.00 2.52
478 481 2.223595 TGGTACGGTTTTTGTACGACGA 60.224 45.455 0.00 0.00 42.42 4.20
481 484 4.633565 ACTTTTGGTACGGTTTTTGTACGA 59.366 37.500 0.00 0.00 42.42 3.43
513 516 1.922570 ACGTTAGGAAGCATGCTACG 58.077 50.000 29.07 29.07 33.59 3.51
546 549 3.118811 GCACTCTGAGGTCTAGCAGAAAT 60.119 47.826 9.85 0.00 40.33 2.17
564 567 2.283532 ACGGCAGAGAGGAGCACT 60.284 61.111 0.00 0.00 0.00 4.40
569 572 1.754621 CTAGCCACGGCAGAGAGGA 60.755 63.158 11.35 0.00 44.88 3.71
578 581 1.705337 CGAATTGTGCCTAGCCACGG 61.705 60.000 0.00 0.00 38.55 4.94
585 588 1.742831 GCAACATCCGAATTGTGCCTA 59.257 47.619 0.00 0.00 0.00 3.93
586 589 0.527565 GCAACATCCGAATTGTGCCT 59.472 50.000 0.00 0.00 0.00 4.75
589 592 1.811965 TCCAGCAACATCCGAATTGTG 59.188 47.619 0.00 0.00 0.00 3.33
596 599 0.798776 GAACAGTCCAGCAACATCCG 59.201 55.000 0.00 0.00 0.00 4.18
605 608 4.392921 AATATCCGTCAGAACAGTCCAG 57.607 45.455 0.00 0.00 0.00 3.86
611 614 4.006989 CCACCAAAATATCCGTCAGAACA 58.993 43.478 0.00 0.00 0.00 3.18
628 631 3.369052 GGAGATAATTGACGTGTCCACCA 60.369 47.826 0.00 0.00 0.00 4.17
629 632 3.195661 GGAGATAATTGACGTGTCCACC 58.804 50.000 0.00 0.00 0.00 4.61
650 653 2.102749 CCCATGCATTCAACGCGG 59.897 61.111 12.47 0.00 0.00 6.46
787 791 0.326264 ACTGAGAACCCATGGTGAGC 59.674 55.000 11.73 0.00 35.34 4.26
808 812 2.457366 ATCTCAAAGGTCACGGTGAC 57.543 50.000 28.65 28.65 46.23 3.67
809 813 2.289444 GGAATCTCAAAGGTCACGGTGA 60.289 50.000 6.76 6.76 0.00 4.02
810 814 2.076863 GGAATCTCAAAGGTCACGGTG 58.923 52.381 0.56 0.56 0.00 4.94
811 815 1.337823 CGGAATCTCAAAGGTCACGGT 60.338 52.381 0.00 0.00 0.00 4.83
812 816 1.359848 CGGAATCTCAAAGGTCACGG 58.640 55.000 0.00 0.00 0.00 4.94
813 817 0.721718 GCGGAATCTCAAAGGTCACG 59.278 55.000 0.00 0.00 0.00 4.35
814 818 0.721718 CGCGGAATCTCAAAGGTCAC 59.278 55.000 0.00 0.00 0.00 3.67
815 819 1.019278 GCGCGGAATCTCAAAGGTCA 61.019 55.000 8.83 0.00 0.00 4.02
816 820 1.716172 GCGCGGAATCTCAAAGGTC 59.284 57.895 8.83 0.00 0.00 3.85
817 821 2.100631 CGCGCGGAATCTCAAAGGT 61.101 57.895 24.84 0.00 0.00 3.50
818 822 2.703409 CGCGCGGAATCTCAAAGG 59.297 61.111 24.84 0.00 0.00 3.11
819 823 2.703409 CCGCGCGGAATCTCAAAG 59.297 61.111 44.86 12.52 37.50 2.77
831 835 4.770874 TCCCTTGTAAGGCCGCGC 62.771 66.667 0.00 0.00 45.10 6.86
832 836 1.644786 CTTTCCCTTGTAAGGCCGCG 61.645 60.000 0.00 0.00 45.10 6.46
833 837 1.934220 GCTTTCCCTTGTAAGGCCGC 61.934 60.000 5.11 1.52 45.10 6.53
834 838 0.608035 TGCTTTCCCTTGTAAGGCCG 60.608 55.000 5.11 0.00 45.10 6.13
835 839 1.177401 CTGCTTTCCCTTGTAAGGCC 58.823 55.000 5.11 0.00 45.10 5.19
836 840 2.087646 CTCTGCTTTCCCTTGTAAGGC 58.912 52.381 5.11 0.00 45.10 4.35
837 841 2.305927 TCCTCTGCTTTCCCTTGTAAGG 59.694 50.000 3.61 3.61 46.06 2.69
838 842 3.703001 TCCTCTGCTTTCCCTTGTAAG 57.297 47.619 0.00 0.00 0.00 2.34
839 843 4.382685 CGTATCCTCTGCTTTCCCTTGTAA 60.383 45.833 0.00 0.00 0.00 2.41
840 844 3.132289 CGTATCCTCTGCTTTCCCTTGTA 59.868 47.826 0.00 0.00 0.00 2.41
867 871 1.444119 TTGTCTGTCGGGCAACAAGC 61.444 55.000 0.00 0.00 44.65 4.01
933 937 1.063717 TCTTGGAGGGAATGGAATGGC 60.064 52.381 0.00 0.00 0.00 4.40
959 984 1.208293 CAACTTCCACTCTCCCTAGGC 59.792 57.143 2.05 0.00 0.00 3.93
1360 1385 1.338020 GTTGAAGGACTTGTTGCTGGG 59.662 52.381 0.00 0.00 0.00 4.45
1364 1389 2.349532 GCGTAGTTGAAGGACTTGTTGC 60.350 50.000 0.00 0.00 0.00 4.17
1369 1394 1.608283 GGCTGCGTAGTTGAAGGACTT 60.608 52.381 1.53 0.00 0.00 3.01
1371 1396 0.037232 AGGCTGCGTAGTTGAAGGAC 60.037 55.000 1.53 0.00 0.00 3.85
1372 1397 0.037326 CAGGCTGCGTAGTTGAAGGA 60.037 55.000 0.00 0.00 0.00 3.36
1373 1398 1.639298 GCAGGCTGCGTAGTTGAAGG 61.639 60.000 25.47 0.00 31.71 3.46
1442 1467 1.008424 TTCTCGATCGCCATCTCGC 60.008 57.895 11.09 0.00 34.94 5.03
1454 1479 1.582968 GGCACGTACTGGTTCTCGA 59.417 57.895 0.00 0.00 0.00 4.04
1668 1717 0.324738 AGGCCTTGACGATCTCCAGA 60.325 55.000 0.00 0.00 0.00 3.86
1811 1866 0.695347 AGGTCAGGGAAGGCTTCAAG 59.305 55.000 27.17 16.17 0.00 3.02
1812 1867 0.401738 CAGGTCAGGGAAGGCTTCAA 59.598 55.000 27.17 8.02 0.00 2.69
1829 1886 1.260825 CATAGATGAAGCTGCACGCAG 59.739 52.381 14.73 14.73 46.15 5.18
1871 1935 4.910195 TGTCTTTACAATCATCCACTGCT 58.090 39.130 0.00 0.00 30.91 4.24
1872 1936 5.627499 TTGTCTTTACAATCATCCACTGC 57.373 39.130 0.00 0.00 40.69 4.40
1880 1944 9.979578 AAGTTATGCATTTTGTCTTTACAATCA 57.020 25.926 3.54 0.00 44.85 2.57
1893 1957 6.667414 TGATAAGTGGGGAAGTTATGCATTTT 59.333 34.615 3.54 0.00 35.01 1.82
1894 1958 6.194235 TGATAAGTGGGGAAGTTATGCATTT 58.806 36.000 3.54 0.00 35.01 2.32
1896 1960 5.387113 TGATAAGTGGGGAAGTTATGCAT 57.613 39.130 3.79 3.79 35.01 3.96
1897 1961 4.853468 TGATAAGTGGGGAAGTTATGCA 57.147 40.909 0.00 0.00 35.01 3.96
1901 1965 6.509523 CCCTTATGATAAGTGGGGAAGTTA 57.490 41.667 10.98 0.00 36.17 2.24
1902 1966 5.388599 CCCTTATGATAAGTGGGGAAGTT 57.611 43.478 10.98 0.00 36.17 2.66
1908 1972 7.675161 AAAAATTCCCCTTATGATAAGTGGG 57.325 36.000 22.58 22.58 37.68 4.61
1933 1997 7.566658 AATAAATCCCCTGATTCCACAAAAA 57.433 32.000 0.00 0.00 40.34 1.94
1934 1998 7.566658 AAATAAATCCCCTGATTCCACAAAA 57.433 32.000 0.00 0.00 40.34 2.44
1936 2000 6.156083 GGAAAATAAATCCCCTGATTCCACAA 59.844 38.462 0.00 0.00 40.34 3.33
1937 2001 5.660864 GGAAAATAAATCCCCTGATTCCACA 59.339 40.000 0.00 0.00 40.34 4.17
1938 2002 6.161855 GGAAAATAAATCCCCTGATTCCAC 57.838 41.667 0.00 0.00 40.34 4.02
1992 2071 2.802816 GTTCGGTGGCAAGCTATGATAG 59.197 50.000 0.00 0.00 0.00 2.08
1997 2076 3.560636 ATTAGTTCGGTGGCAAGCTAT 57.439 42.857 0.00 0.00 0.00 2.97
1998 2077 3.343941 AATTAGTTCGGTGGCAAGCTA 57.656 42.857 0.00 0.00 0.00 3.32
1999 2078 2.200373 AATTAGTTCGGTGGCAAGCT 57.800 45.000 0.00 0.00 0.00 3.74
2000 2079 3.439129 ACTTAATTAGTTCGGTGGCAAGC 59.561 43.478 0.00 0.00 31.29 4.01
2001 2080 5.622770 AACTTAATTAGTTCGGTGGCAAG 57.377 39.130 0.00 0.00 43.67 4.01
2002 2081 6.394025 AAAACTTAATTAGTTCGGTGGCAA 57.606 33.333 0.00 0.00 46.34 4.52
2003 2082 6.039493 TCAAAAACTTAATTAGTTCGGTGGCA 59.961 34.615 0.00 0.00 46.34 4.92
2004 2083 6.440436 TCAAAAACTTAATTAGTTCGGTGGC 58.560 36.000 0.00 0.00 46.34 5.01
2005 2084 7.112426 CGTTCAAAAACTTAATTAGTTCGGTGG 59.888 37.037 0.00 0.00 46.34 4.61
2006 2085 7.112426 CCGTTCAAAAACTTAATTAGTTCGGTG 59.888 37.037 0.00 0.00 46.34 4.94
2007 2086 7.134163 CCGTTCAAAAACTTAATTAGTTCGGT 58.866 34.615 0.00 0.00 46.34 4.69
2008 2087 7.112426 CACCGTTCAAAAACTTAATTAGTTCGG 59.888 37.037 14.50 14.50 46.34 4.30
2009 2088 7.641020 ACACCGTTCAAAAACTTAATTAGTTCG 59.359 33.333 0.00 0.00 46.34 3.95
2010 2089 8.845942 ACACCGTTCAAAAACTTAATTAGTTC 57.154 30.769 0.00 0.00 46.34 3.01
2015 2094 9.642327 ACTTTTACACCGTTCAAAAACTTAATT 57.358 25.926 0.00 0.00 32.95 1.40
2016 2095 9.642327 AACTTTTACACCGTTCAAAAACTTAAT 57.358 25.926 0.00 0.00 32.95 1.40
2017 2096 9.473640 AAACTTTTACACCGTTCAAAAACTTAA 57.526 25.926 0.00 0.00 32.95 1.85
2018 2097 9.473640 AAAACTTTTACACCGTTCAAAAACTTA 57.526 25.926 0.00 0.00 32.95 2.24
2019 2098 7.949903 AAACTTTTACACCGTTCAAAAACTT 57.050 28.000 0.00 0.00 32.95 2.66
2020 2099 7.652507 TGAAAACTTTTACACCGTTCAAAAACT 59.347 29.630 0.00 0.00 32.95 2.66
2021 2100 7.785144 TGAAAACTTTTACACCGTTCAAAAAC 58.215 30.769 0.00 0.00 0.00 2.43
2022 2101 7.866393 TCTGAAAACTTTTACACCGTTCAAAAA 59.134 29.630 0.00 0.00 0.00 1.94
2023 2102 7.368833 TCTGAAAACTTTTACACCGTTCAAAA 58.631 30.769 0.00 0.00 0.00 2.44
2024 2103 6.910995 TCTGAAAACTTTTACACCGTTCAAA 58.089 32.000 0.00 0.00 0.00 2.69
2030 2109 5.918576 GGGATTTCTGAAAACTTTTACACCG 59.081 40.000 6.95 0.00 0.00 4.94
2031 2110 5.918576 CGGGATTTCTGAAAACTTTTACACC 59.081 40.000 6.95 0.00 0.00 4.16
2032 2111 6.731164 TCGGGATTTCTGAAAACTTTTACAC 58.269 36.000 6.95 0.00 0.00 2.90
2064 2143 9.326413 GCTATATTATAGGTGTGTTGTTTCAGT 57.674 33.333 11.72 0.00 0.00 3.41
2065 2144 9.325198 TGCTATATTATAGGTGTGTTGTTTCAG 57.675 33.333 11.72 0.00 0.00 3.02
2068 2147 9.845740 TCATGCTATATTATAGGTGTGTTGTTT 57.154 29.630 11.72 0.00 0.00 2.83
2070 2149 9.658799 GATCATGCTATATTATAGGTGTGTTGT 57.341 33.333 11.72 0.00 0.00 3.32
2071 2150 9.102757 GGATCATGCTATATTATAGGTGTGTTG 57.897 37.037 11.72 0.00 0.00 3.33
2072 2151 8.825774 TGGATCATGCTATATTATAGGTGTGTT 58.174 33.333 11.72 0.00 0.00 3.32
2073 2152 8.379428 TGGATCATGCTATATTATAGGTGTGT 57.621 34.615 11.72 0.00 0.00 3.72
2074 2153 9.102757 GTTGGATCATGCTATATTATAGGTGTG 57.897 37.037 11.72 0.00 0.00 3.82
2075 2154 7.981789 CGTTGGATCATGCTATATTATAGGTGT 59.018 37.037 11.72 0.00 0.00 4.16
2076 2155 7.439356 CCGTTGGATCATGCTATATTATAGGTG 59.561 40.741 11.72 0.00 0.00 4.00
2077 2156 7.344612 TCCGTTGGATCATGCTATATTATAGGT 59.655 37.037 11.72 0.00 0.00 3.08
2078 2157 7.726216 TCCGTTGGATCATGCTATATTATAGG 58.274 38.462 11.72 0.00 0.00 2.57
2079 2158 7.383572 GCTCCGTTGGATCATGCTATATTATAG 59.616 40.741 6.37 6.37 0.00 1.31
2080 2159 7.210174 GCTCCGTTGGATCATGCTATATTATA 58.790 38.462 0.00 0.00 0.00 0.98
2081 2160 6.051717 GCTCCGTTGGATCATGCTATATTAT 58.948 40.000 0.00 0.00 0.00 1.28
2082 2161 5.419542 GCTCCGTTGGATCATGCTATATTA 58.580 41.667 0.00 0.00 0.00 0.98
2083 2162 4.256920 GCTCCGTTGGATCATGCTATATT 58.743 43.478 0.00 0.00 0.00 1.28
2084 2163 3.677148 CGCTCCGTTGGATCATGCTATAT 60.677 47.826 0.00 0.00 0.00 0.86
2085 2164 2.352715 CGCTCCGTTGGATCATGCTATA 60.353 50.000 0.00 0.00 0.00 1.31
2086 2165 1.606480 CGCTCCGTTGGATCATGCTAT 60.606 52.381 0.00 0.00 0.00 2.97
2087 2166 0.249447 CGCTCCGTTGGATCATGCTA 60.249 55.000 0.00 0.00 0.00 3.49
2088 2167 1.522355 CGCTCCGTTGGATCATGCT 60.522 57.895 0.00 0.00 0.00 3.79
2089 2168 0.882042 ATCGCTCCGTTGGATCATGC 60.882 55.000 0.00 0.00 0.00 4.06
2090 2169 1.262417 CAATCGCTCCGTTGGATCATG 59.738 52.381 0.00 0.00 0.00 3.07
2091 2170 1.138859 TCAATCGCTCCGTTGGATCAT 59.861 47.619 0.00 0.00 0.00 2.45
2092 2171 0.534873 TCAATCGCTCCGTTGGATCA 59.465 50.000 0.00 0.00 0.00 2.92
2093 2172 1.651987 TTCAATCGCTCCGTTGGATC 58.348 50.000 0.00 0.00 0.00 3.36
2094 2173 2.107950 TTTCAATCGCTCCGTTGGAT 57.892 45.000 0.00 0.00 0.00 3.41
2095 2174 1.885560 TTTTCAATCGCTCCGTTGGA 58.114 45.000 0.00 0.00 0.00 3.53
2096 2175 2.697431 TTTTTCAATCGCTCCGTTGG 57.303 45.000 0.00 0.00 0.00 3.77
2180 2260 8.539544 AGACCATCCGGAAATATTCAAAATTTT 58.460 29.630 9.01 0.00 35.59 1.82
2184 2264 5.359576 CCAGACCATCCGGAAATATTCAAAA 59.640 40.000 9.01 0.00 35.59 2.44
2195 2275 5.897851 TTAATTATTCCAGACCATCCGGA 57.102 39.130 6.61 6.61 35.59 5.14
2197 2277 7.067008 ACAACTTTAATTATTCCAGACCATCCG 59.933 37.037 0.00 0.00 0.00 4.18
2199 2279 9.573133 CAACAACTTTAATTATTCCAGACCATC 57.427 33.333 0.00 0.00 0.00 3.51
2224 2304 5.913137 AAAAAGACCACAGACATTTCACA 57.087 34.783 0.00 0.00 0.00 3.58
2234 2314 7.596995 TGGCGAATTTTAATAAAAAGACCACAG 59.403 33.333 2.03 0.00 37.97 3.66
2241 2321 9.553418 CCCATTTTGGCGAATTTTAATAAAAAG 57.447 29.630 2.03 0.00 35.65 2.27
2242 2322 9.067986 ACCCATTTTGGCGAATTTTAATAAAAA 57.932 25.926 2.03 0.00 36.20 1.94
2257 2337 6.405538 TCAATAATTTGAGACCCATTTTGGC 58.594 36.000 0.00 0.00 36.94 4.52
2461 2545 9.340695 TCGTTTTAGAAGCACATATTTCAAATG 57.659 29.630 0.00 0.00 0.00 2.32
2466 2550 9.638300 CAGTATCGTTTTAGAAGCACATATTTC 57.362 33.333 0.00 0.00 0.00 2.17
2518 2619 6.452244 AGCGATTGTTCAATTAAAACAAGC 57.548 33.333 17.45 17.45 46.45 4.01
2519 2620 8.684141 CAAAGCGATTGTTCAATTAAAACAAG 57.316 30.769 17.99 10.32 46.45 3.16
2534 2635 6.373779 ACTCTATCAACAAACAAAGCGATTG 58.626 36.000 4.04 4.04 44.95 2.67
2535 2636 6.560253 ACTCTATCAACAAACAAAGCGATT 57.440 33.333 0.00 0.00 0.00 3.34
2578 3026 9.672086 TTCGAATTATTTCACAAAACGAATCTT 57.328 25.926 0.00 0.00 33.55 2.40
2628 3104 5.999205 TTGGAAATCCATTGCTACAATGT 57.001 34.783 16.67 0.00 46.97 2.71
2678 3194 9.715123 CAAGTATTTTGGAATTGTTTTGGAAAC 57.285 29.630 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.