Multiple sequence alignment - TraesCS2D01G449500

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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 TraesCS2D01G449500 chr2D 100.000 2789 0 0 1 2789 559003233 559000445 0.000000e+00 5151.0
1 TraesCS2D01G449500 chr2D 91.250 1040 70 15 984 2011 558977888 558976858 0.000000e+00 1397.0
2 TraesCS2D01G449500 chr2D 83.042 401 41 7 2295 2670 558976857 558976459 3.440000e-89 339.0
3 TraesCS2D01G449500 chr2D 90.099 202 11 6 2100 2293 39574579 39574779 1.280000e-63 254.0
4 TraesCS2D01G449500 chr2D 88.119 202 14 7 2100 2293 322920709 322920908 6.010000e-57 231.0
5 TraesCS2D01G449500 chr2A 93.101 1232 30 14 771 1985 699642245 699641052 0.000000e+00 1753.0
6 TraesCS2D01G449500 chr2A 89.651 773 65 10 1248 2011 699605833 699605067 0.000000e+00 970.0
7 TraesCS2D01G449500 chr2A 94.366 426 22 1 2364 2789 699641055 699640632 0.000000e+00 652.0
8 TraesCS2D01G449500 chr2A 88.484 521 45 11 1 506 699643730 699643210 1.420000e-172 616.0
9 TraesCS2D01G449500 chr2A 83.060 366 39 13 847 1209 699606175 699605830 7.500000e-81 311.0
10 TraesCS2D01G449500 chr2B 90.863 1182 76 14 855 2011 668052701 668051527 0.000000e+00 1555.0
11 TraesCS2D01G449500 chr2B 87.336 1295 106 24 775 2031 668172098 668170824 0.000000e+00 1430.0
12 TraesCS2D01G449500 chr2B 87.673 649 47 15 2164 2789 668165681 668165043 0.000000e+00 725.0
13 TraesCS2D01G449500 chr2B 86.617 269 36 0 2295 2563 668051526 668051258 5.840000e-77 298.0
14 TraesCS2D01G449500 chr2B 84.568 162 19 5 449 606 627801818 627801659 3.720000e-34 156.0
15 TraesCS2D01G449500 chr2B 89.286 56 4 1 463 516 309191771 309191826 4.980000e-08 69.4
16 TraesCS2D01G449500 chrUn 89.604 202 12 6 2100 2293 229492589 229492389 5.970000e-62 248.0
17 TraesCS2D01G449500 chr5D 89.109 202 13 6 2100 2293 324468094 324468294 2.780000e-60 243.0
18 TraesCS2D01G449500 chr1B 88.614 202 14 6 2100 2293 491496399 491496599 1.290000e-58 237.0
19 TraesCS2D01G449500 chr3D 88.718 195 18 4 2100 2293 72452633 72452442 4.640000e-58 235.0
20 TraesCS2D01G449500 chr3D 88.321 137 14 1 472 606 538570494 538570630 2.220000e-36 163.0
21 TraesCS2D01G449500 chr3D 84.071 113 13 2 492 599 8980224 8980112 1.370000e-18 104.0
22 TraesCS2D01G449500 chr4B 88.119 202 15 6 2100 2293 653388998 653389198 6.010000e-57 231.0
23 TraesCS2D01G449500 chr5A 87.685 203 15 8 2100 2293 647033312 647033111 7.770000e-56 228.0
24 TraesCS2D01G449500 chr7D 84.568 162 23 2 974 1133 184536744 184536905 2.880000e-35 159.0
25 TraesCS2D01G449500 chr6A 84.375 160 19 4 449 606 613372350 613372505 4.810000e-33 152.0
26 TraesCS2D01G449500 chr3A 88.000 100 9 2 510 607 352492208 352492306 6.310000e-22 115.0
27 TraesCS2D01G449500 chr3A 88.571 70 8 0 537 606 421773397 421773466 4.950000e-13 86.1
28 TraesCS2D01G449500 chr1A 89.041 73 8 0 2714 2786 32458604 32458532 1.060000e-14 91.6
29 TraesCS2D01G449500 chr6B 93.023 43 3 0 2743 2785 632237900 632237858 2.320000e-06 63.9


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 TraesCS2D01G449500 chr2D 559000445 559003233 2788 True 5151.0 5151 100.000000 1 2789 1 chr2D.!!$R1 2788
1 TraesCS2D01G449500 chr2D 558976459 558977888 1429 True 868.0 1397 87.146000 984 2670 2 chr2D.!!$R2 1686
2 TraesCS2D01G449500 chr2A 699640632 699643730 3098 True 1007.0 1753 91.983667 1 2789 3 chr2A.!!$R2 2788
3 TraesCS2D01G449500 chr2A 699605067 699606175 1108 True 640.5 970 86.355500 847 2011 2 chr2A.!!$R1 1164
4 TraesCS2D01G449500 chr2B 668170824 668172098 1274 True 1430.0 1430 87.336000 775 2031 1 chr2B.!!$R3 1256
5 TraesCS2D01G449500 chr2B 668051258 668052701 1443 True 926.5 1555 88.740000 855 2563 2 chr2B.!!$R4 1708
6 TraesCS2D01G449500 chr2B 668165043 668165681 638 True 725.0 725 87.673000 2164 2789 1 chr2B.!!$R2 625

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
671 1217 0.183492 TGCAGCCCACTTTCTGTTCT 59.817 50.0 0.0 0.0 33.09 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 2894 1.176527 CCATTCATTTCTGGCGGTGT 58.823 50.0 0.0 0.0 0.0 4.16 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
19 20 2.550830 ATCAATATGGCCACGGAGAC 57.449 50.000 8.16 0.00 0.00 3.36
34 35 3.235195 CGGAGACTGTACTCACGAAAAG 58.765 50.000 0.00 0.00 38.51 2.27
59 60 2.945668 GGTTGACATAGGTCTTCCATGC 59.054 50.000 9.22 0.00 44.61 4.06
63 64 5.830799 TGACATAGGTCTTCCATGCATAT 57.169 39.130 9.22 0.00 44.61 1.78
74 75 3.664107 TCCATGCATATAAGTTCGCCTC 58.336 45.455 0.00 0.00 0.00 4.70
95 96 1.391485 CGTGTGAGAAAGCTTGATCGG 59.609 52.381 0.00 0.00 0.00 4.18
133 134 1.956629 AACGTCCAGGATGTAGGCCG 61.957 60.000 15.17 3.22 30.95 6.13
156 157 2.892425 GGAACGGAGCCAGCATCG 60.892 66.667 0.00 0.00 0.00 3.84
171 172 1.833049 ATCGGAGTAGGCGAAGGGG 60.833 63.158 0.00 0.00 0.00 4.79
178 179 0.250597 GTAGGCGAAGGGGTTGTTGT 60.251 55.000 0.00 0.00 0.00 3.32
182 183 0.240945 GCGAAGGGGTTGTTGTGATG 59.759 55.000 0.00 0.00 0.00 3.07
188 189 1.203001 GGGGTTGTTGTGATGGGAGAA 60.203 52.381 0.00 0.00 0.00 2.87
189 190 2.162681 GGGTTGTTGTGATGGGAGAAG 58.837 52.381 0.00 0.00 0.00 2.85
190 191 2.162681 GGTTGTTGTGATGGGAGAAGG 58.837 52.381 0.00 0.00 0.00 3.46
211 212 1.097547 GGAGTTGGACATGATGGCGG 61.098 60.000 0.00 0.00 0.00 6.13
294 313 1.394963 GGAGGGAAGTAGGGGTGGA 59.605 63.158 0.00 0.00 0.00 4.02
317 336 2.342650 CGGCTGTTGTGGGGGATTG 61.343 63.158 0.00 0.00 0.00 2.67
336 355 2.064581 GGAGGGTGGGTGTAGCGAT 61.065 63.158 0.00 0.00 0.00 4.58
338 357 2.189521 GGGTGGGTGTAGCGATGG 59.810 66.667 0.00 0.00 0.00 3.51
339 358 2.513897 GGTGGGTGTAGCGATGGC 60.514 66.667 0.00 0.00 40.37 4.40
340 359 2.267642 GTGGGTGTAGCGATGGCA 59.732 61.111 1.50 0.00 43.41 4.92
341 360 1.376683 GTGGGTGTAGCGATGGCAA 60.377 57.895 1.50 0.00 43.41 4.52
350 369 1.776662 AGCGATGGCAACTAGGTAGA 58.223 50.000 1.50 0.00 43.41 2.59
362 381 1.532604 TAGGTAGATGCGGCATCGGG 61.533 60.000 30.88 0.00 44.67 5.14
363 382 2.357517 GTAGATGCGGCATCGGGG 60.358 66.667 30.88 0.00 44.67 5.73
383 402 1.470165 CGGCTAGGGTTAGGGTAGGC 61.470 65.000 0.00 0.00 36.30 3.93
386 405 1.691801 GCTAGGGTTAGGGTAGGCAGT 60.692 57.143 0.00 0.00 0.00 4.40
391 410 2.363975 TTAGGGTAGGCAGTGGCGG 61.364 63.158 11.51 0.00 42.47 6.13
392 411 3.612115 TAGGGTAGGCAGTGGCGGT 62.612 63.158 11.51 0.00 42.47 5.68
394 413 3.702048 GGTAGGCAGTGGCGGTGA 61.702 66.667 11.51 0.00 42.47 4.02
441 460 1.008571 AGGGTTTAGAGAGGGAGGACC 59.991 57.143 0.00 0.00 40.67 4.46
451 470 2.117051 GAGGGAGGACCGAAATAAGGT 58.883 52.381 0.00 0.00 46.96 3.50
476 495 5.989168 TGATACCATGTAAAGAATAGGTGCG 59.011 40.000 0.00 0.00 0.00 5.34
506 525 6.038603 ACGATATATTCATTGGGTGCATATGC 59.961 38.462 21.09 21.09 42.50 3.14
531 1075 7.764443 GCACATACATATAGGTACAATAGGTGG 59.236 40.741 12.42 8.51 0.00 4.61
532 1076 8.812972 CACATACATATAGGTACAATAGGTGGT 58.187 37.037 12.42 8.94 0.00 4.16
560 1104 6.342111 GTCCTCAACTATACAAGAAAGGAGG 58.658 44.000 0.00 0.00 34.00 4.30
616 1160 6.981762 ATACATCTCAACAAGAGCAAAGAG 57.018 37.500 0.00 0.00 44.35 2.85
626 1170 5.625150 ACAAGAGCAAAGAGGTATTGAGTT 58.375 37.500 8.40 0.00 46.80 3.01
642 1186 1.276421 GAGTTCAAGACCAGGCTAGCA 59.724 52.381 18.24 0.00 0.00 3.49
643 1187 1.912043 AGTTCAAGACCAGGCTAGCAT 59.088 47.619 18.24 6.55 0.00 3.79
658 1202 4.925646 GGCTAGCATAATTAAATTGCAGCC 59.074 41.667 22.67 22.67 44.87 4.85
661 1205 4.696455 AGCATAATTAAATTGCAGCCCAC 58.304 39.130 11.15 0.00 38.84 4.61
666 1212 5.488262 AATTAAATTGCAGCCCACTTTCT 57.512 34.783 0.00 0.00 30.20 2.52
671 1217 0.183492 TGCAGCCCACTTTCTGTTCT 59.817 50.000 0.00 0.00 33.09 3.01
683 1229 4.452455 ACTTTCTGTTCTCGTTTAGGCATG 59.548 41.667 0.00 0.00 0.00 4.06
686 1232 3.509967 TCTGTTCTCGTTTAGGCATGAGA 59.490 43.478 0.00 0.00 37.09 3.27
688 1234 4.245660 TGTTCTCGTTTAGGCATGAGAAG 58.754 43.478 7.90 0.00 45.44 2.85
689 1235 4.021456 TGTTCTCGTTTAGGCATGAGAAGA 60.021 41.667 7.90 5.04 45.44 2.87
698 1244 1.662629 GGCATGAGAAGATCACACGTG 59.337 52.381 15.48 15.48 41.91 4.49
700 1246 2.602211 GCATGAGAAGATCACACGTGAG 59.398 50.000 25.01 15.63 43.61 3.51
702 1248 3.839051 TGAGAAGATCACACGTGAGAG 57.161 47.619 25.01 11.69 43.61 3.20
705 1251 2.163412 AGAAGATCACACGTGAGAGAGC 59.837 50.000 25.01 18.46 43.61 4.09
706 1252 1.832883 AGATCACACGTGAGAGAGCT 58.167 50.000 25.01 20.33 43.61 4.09
707 1253 2.992593 AGATCACACGTGAGAGAGCTA 58.007 47.619 25.01 0.00 43.61 3.32
708 1254 3.348119 AGATCACACGTGAGAGAGCTAA 58.652 45.455 25.01 0.00 43.61 3.09
711 1268 5.767665 AGATCACACGTGAGAGAGCTAATAT 59.232 40.000 25.01 0.59 43.61 1.28
760 1458 7.962934 TTATTGTATTGACTAAAACATGCGC 57.037 32.000 0.00 0.00 0.00 6.09
768 1466 4.994852 TGACTAAAACATGCGCTTCTACTT 59.005 37.500 9.73 0.00 0.00 2.24
769 1467 5.107104 TGACTAAAACATGCGCTTCTACTTG 60.107 40.000 9.73 0.00 0.00 3.16
822 1545 0.303493 AATGCATAAAGTACGCCGCG 59.697 50.000 12.14 12.14 0.00 6.46
824 1547 1.143373 TGCATAAAGTACGCCGCGAG 61.143 55.000 21.79 3.30 0.00 5.03
1815 2582 3.770263 CGGAGCCGATTTACCGATATA 57.230 47.619 2.00 0.00 46.94 0.86
1817 2584 4.487948 CGGAGCCGATTTACCGATATAAA 58.512 43.478 2.00 0.00 46.94 1.40
1820 2593 6.921857 CGGAGCCGATTTACCGATATAAATAT 59.078 38.462 2.00 0.00 46.94 1.28
1823 2596 8.433421 AGCCGATTTACCGATATAAATATTGG 57.567 34.615 12.86 12.86 45.83 3.16
1824 2597 7.497909 AGCCGATTTACCGATATAAATATTGGG 59.502 37.037 17.11 9.27 45.03 4.12
1828 2601 7.599630 TTTACCGATATAAATATTGGGCGTC 57.400 36.000 17.11 0.00 45.03 5.19
1893 2675 7.628234 AGAAATCTACTGAAATGTGAGTCCAT 58.372 34.615 0.00 0.00 0.00 3.41
2011 2811 5.389778 TGATTCAATGGAATGAACGTTTCG 58.610 37.500 0.46 0.00 43.69 3.46
2012 2812 4.822036 TTCAATGGAATGAACGTTTCGT 57.178 36.364 0.46 0.00 43.97 3.85
2031 2831 7.749126 CGTTTCGTTTTTCCAAGCTTATCTATT 59.251 33.333 0.00 0.00 0.00 1.73
2032 2832 9.406828 GTTTCGTTTTTCCAAGCTTATCTATTT 57.593 29.630 0.00 0.00 0.00 1.40
2033 2833 9.974980 TTTCGTTTTTCCAAGCTTATCTATTTT 57.025 25.926 0.00 0.00 0.00 1.82
2034 2834 9.974980 TTCGTTTTTCCAAGCTTATCTATTTTT 57.025 25.926 0.00 0.00 0.00 1.94
2041 2841 9.693739 TTCCAAGCTTATCTATTTTTATCACCA 57.306 29.630 0.00 0.00 0.00 4.17
2042 2842 9.342308 TCCAAGCTTATCTATTTTTATCACCAG 57.658 33.333 0.00 0.00 0.00 4.00
2043 2843 9.342308 CCAAGCTTATCTATTTTTATCACCAGA 57.658 33.333 0.00 0.00 0.00 3.86
2056 2856 8.810652 TTTTATCACCAGAAAGGAATTTTTCG 57.189 30.769 0.00 0.00 40.99 3.46
2057 2857 7.753309 TTATCACCAGAAAGGAATTTTTCGA 57.247 32.000 0.00 0.00 40.99 3.71
2058 2858 6.648879 ATCACCAGAAAGGAATTTTTCGAA 57.351 33.333 0.00 0.00 40.99 3.71
2059 2859 6.458232 TCACCAGAAAGGAATTTTTCGAAA 57.542 33.333 6.47 6.47 40.99 3.46
2060 2860 6.868622 TCACCAGAAAGGAATTTTTCGAAAA 58.131 32.000 19.08 19.08 40.99 2.29
2061 2861 7.324178 TCACCAGAAAGGAATTTTTCGAAAAA 58.676 30.769 31.74 31.74 40.99 1.94
2062 2862 7.491048 TCACCAGAAAGGAATTTTTCGAAAAAG 59.509 33.333 32.39 20.40 39.42 2.27
2063 2863 6.761242 ACCAGAAAGGAATTTTTCGAAAAAGG 59.239 34.615 32.39 26.44 39.42 3.11
2064 2864 6.983890 CCAGAAAGGAATTTTTCGAAAAAGGA 59.016 34.615 32.39 16.87 39.42 3.36
2065 2865 7.042725 CCAGAAAGGAATTTTTCGAAAAAGGAC 60.043 37.037 32.39 24.88 39.42 3.85
2066 2866 6.695713 AGAAAGGAATTTTTCGAAAAAGGACG 59.304 34.615 32.39 0.00 40.78 4.79
2067 2867 4.295870 AGGAATTTTTCGAAAAAGGACGC 58.704 39.130 32.39 21.15 40.78 5.19
2068 2868 4.037565 AGGAATTTTTCGAAAAAGGACGCT 59.962 37.500 32.39 21.65 40.78 5.07
2069 2869 4.743151 GGAATTTTTCGAAAAAGGACGCTT 59.257 37.500 32.39 23.29 40.78 4.68
2070 2870 5.233476 GGAATTTTTCGAAAAAGGACGCTTT 59.767 36.000 32.39 22.71 40.78 3.51
2071 2871 6.418523 GGAATTTTTCGAAAAAGGACGCTTTA 59.581 34.615 32.39 13.01 40.78 1.85
2072 2872 7.115805 GGAATTTTTCGAAAAAGGACGCTTTAT 59.884 33.333 32.39 15.08 40.78 1.40
2073 2873 9.120422 GAATTTTTCGAAAAAGGACGCTTTATA 57.880 29.630 32.39 12.38 40.78 0.98
2074 2874 9.465985 AATTTTTCGAAAAAGGACGCTTTATAA 57.534 25.926 32.39 12.00 40.78 0.98
2075 2875 7.840981 TTTTCGAAAAAGGACGCTTTATAAC 57.159 32.000 20.56 0.00 0.00 1.89
2076 2876 6.790285 TTCGAAAAAGGACGCTTTATAACT 57.210 33.333 0.00 0.00 0.00 2.24
2077 2877 6.160664 TCGAAAAAGGACGCTTTATAACTG 57.839 37.500 0.00 0.00 0.00 3.16
2078 2878 5.927689 TCGAAAAAGGACGCTTTATAACTGA 59.072 36.000 0.00 0.00 0.00 3.41
2079 2879 6.424509 TCGAAAAAGGACGCTTTATAACTGAA 59.575 34.615 0.00 0.00 0.00 3.02
2080 2880 7.041916 TCGAAAAAGGACGCTTTATAACTGAAA 60.042 33.333 0.00 0.00 0.00 2.69
2081 2881 7.588488 CGAAAAAGGACGCTTTATAACTGAAAA 59.412 33.333 0.00 0.00 0.00 2.29
2082 2882 9.406828 GAAAAAGGACGCTTTATAACTGAAAAT 57.593 29.630 0.00 0.00 0.00 1.82
2083 2883 8.742554 AAAAGGACGCTTTATAACTGAAAATG 57.257 30.769 0.00 0.00 0.00 2.32
2084 2884 7.448748 AAGGACGCTTTATAACTGAAAATGT 57.551 32.000 0.00 0.00 0.00 2.71
2085 2885 8.556213 AAGGACGCTTTATAACTGAAAATGTA 57.444 30.769 0.00 0.00 0.00 2.29
2086 2886 8.732746 AGGACGCTTTATAACTGAAAATGTAT 57.267 30.769 0.00 0.00 0.00 2.29
2087 2887 9.826574 AGGACGCTTTATAACTGAAAATGTATA 57.173 29.630 0.00 0.00 0.00 1.47
2090 2890 9.931210 ACGCTTTATAACTGAAAATGTATAAGC 57.069 29.630 0.00 0.00 0.00 3.09
2091 2891 9.929722 CGCTTTATAACTGAAAATGTATAAGCA 57.070 29.630 0.00 0.00 0.00 3.91
2099 2899 7.693952 ACTGAAAATGTATAAGCATTACACCG 58.306 34.615 0.00 0.00 38.03 4.94
2100 2900 6.491394 TGAAAATGTATAAGCATTACACCGC 58.509 36.000 0.00 0.00 38.03 5.68
2101 2901 5.432885 AAATGTATAAGCATTACACCGCC 57.567 39.130 0.00 0.00 38.03 6.13
2102 2902 3.545366 TGTATAAGCATTACACCGCCA 57.455 42.857 0.00 0.00 30.46 5.69
2103 2903 3.462982 TGTATAAGCATTACACCGCCAG 58.537 45.455 0.00 0.00 30.46 4.85
2104 2904 3.133183 TGTATAAGCATTACACCGCCAGA 59.867 43.478 0.00 0.00 30.46 3.86
2105 2905 2.772077 TAAGCATTACACCGCCAGAA 57.228 45.000 0.00 0.00 0.00 3.02
2106 2906 1.904287 AAGCATTACACCGCCAGAAA 58.096 45.000 0.00 0.00 0.00 2.52
2107 2907 2.128771 AGCATTACACCGCCAGAAAT 57.871 45.000 0.00 0.00 0.00 2.17
2108 2908 1.745087 AGCATTACACCGCCAGAAATG 59.255 47.619 0.00 0.00 0.00 2.32
2109 2909 1.742831 GCATTACACCGCCAGAAATGA 59.257 47.619 0.00 0.00 30.77 2.57
2110 2910 2.163412 GCATTACACCGCCAGAAATGAA 59.837 45.455 0.00 0.00 30.77 2.57
2111 2911 3.181487 GCATTACACCGCCAGAAATGAAT 60.181 43.478 0.00 0.00 30.77 2.57
2112 2912 4.353737 CATTACACCGCCAGAAATGAATG 58.646 43.478 0.00 0.00 30.77 2.67
2113 2913 1.176527 ACACCGCCAGAAATGAATGG 58.823 50.000 0.00 0.00 39.73 3.16
2123 2923 6.136541 CCAGAAATGAATGGCCTAACTTAC 57.863 41.667 3.32 0.00 0.00 2.34
2124 2924 5.067805 CCAGAAATGAATGGCCTAACTTACC 59.932 44.000 3.32 0.00 0.00 2.85
2125 2925 5.652014 CAGAAATGAATGGCCTAACTTACCA 59.348 40.000 3.32 0.00 37.99 3.25
2126 2926 5.652452 AGAAATGAATGGCCTAACTTACCAC 59.348 40.000 3.32 0.00 35.99 4.16
2127 2927 4.862641 ATGAATGGCCTAACTTACCACT 57.137 40.909 3.32 0.00 35.99 4.00
2128 2928 3.950397 TGAATGGCCTAACTTACCACTG 58.050 45.455 3.32 0.00 35.99 3.66
2129 2929 3.585289 TGAATGGCCTAACTTACCACTGA 59.415 43.478 3.32 0.00 35.99 3.41
2130 2930 3.914426 ATGGCCTAACTTACCACTGAG 57.086 47.619 3.32 0.00 35.99 3.35
2131 2931 2.616524 TGGCCTAACTTACCACTGAGT 58.383 47.619 3.32 0.00 0.00 3.41
2132 2932 3.781808 TGGCCTAACTTACCACTGAGTA 58.218 45.455 3.32 0.00 0.00 2.59
2133 2933 3.767673 TGGCCTAACTTACCACTGAGTAG 59.232 47.826 3.32 0.00 0.00 2.57
2134 2934 3.132467 GGCCTAACTTACCACTGAGTAGG 59.868 52.174 0.00 0.00 0.00 3.18
2135 2935 3.768215 GCCTAACTTACCACTGAGTAGGT 59.232 47.826 10.67 10.67 41.89 3.08
2136 2936 4.381718 GCCTAACTTACCACTGAGTAGGTG 60.382 50.000 14.30 4.32 38.87 4.00
2137 2937 3.679824 AACTTACCACTGAGTAGGTGC 57.320 47.619 14.30 0.00 38.87 5.01
2138 2938 1.900486 ACTTACCACTGAGTAGGTGCC 59.100 52.381 14.30 0.00 38.87 5.01
2139 2939 2.180276 CTTACCACTGAGTAGGTGCCT 58.820 52.381 14.30 0.00 38.87 4.75
2140 2940 2.320681 TACCACTGAGTAGGTGCCTT 57.679 50.000 14.30 0.00 38.87 4.35
2141 2941 1.435256 ACCACTGAGTAGGTGCCTTT 58.565 50.000 6.02 0.00 36.60 3.11
2142 2942 1.774856 ACCACTGAGTAGGTGCCTTTT 59.225 47.619 6.02 0.00 36.60 2.27
2143 2943 2.174854 ACCACTGAGTAGGTGCCTTTTT 59.825 45.455 6.02 0.00 36.60 1.94
2144 2944 2.814336 CCACTGAGTAGGTGCCTTTTTC 59.186 50.000 0.00 0.00 33.78 2.29
2145 2945 3.496870 CCACTGAGTAGGTGCCTTTTTCT 60.497 47.826 0.00 0.00 33.78 2.52
2146 2946 4.137543 CACTGAGTAGGTGCCTTTTTCTT 58.862 43.478 0.00 0.00 0.00 2.52
2147 2947 4.580580 CACTGAGTAGGTGCCTTTTTCTTT 59.419 41.667 0.00 0.00 0.00 2.52
2148 2948 5.067805 CACTGAGTAGGTGCCTTTTTCTTTT 59.932 40.000 0.00 0.00 0.00 2.27
2149 2949 5.299531 ACTGAGTAGGTGCCTTTTTCTTTTC 59.700 40.000 0.00 0.00 0.00 2.29
2150 2950 4.583073 TGAGTAGGTGCCTTTTTCTTTTCC 59.417 41.667 0.00 0.00 0.00 3.13
2151 2951 4.804597 AGTAGGTGCCTTTTTCTTTTCCT 58.195 39.130 0.00 0.00 0.00 3.36
2152 2952 5.208890 AGTAGGTGCCTTTTTCTTTTCCTT 58.791 37.500 0.00 0.00 0.00 3.36
2153 2953 4.672587 AGGTGCCTTTTTCTTTTCCTTC 57.327 40.909 0.00 0.00 0.00 3.46
2154 2954 4.290093 AGGTGCCTTTTTCTTTTCCTTCT 58.710 39.130 0.00 0.00 0.00 2.85
2155 2955 5.454966 AGGTGCCTTTTTCTTTTCCTTCTA 58.545 37.500 0.00 0.00 0.00 2.10
2156 2956 5.897250 AGGTGCCTTTTTCTTTTCCTTCTAA 59.103 36.000 0.00 0.00 0.00 2.10
2157 2957 6.382859 AGGTGCCTTTTTCTTTTCCTTCTAAA 59.617 34.615 0.00 0.00 0.00 1.85
2158 2958 6.479001 GGTGCCTTTTTCTTTTCCTTCTAAAC 59.521 38.462 0.00 0.00 0.00 2.01
2159 2959 7.265673 GTGCCTTTTTCTTTTCCTTCTAAACT 58.734 34.615 0.00 0.00 0.00 2.66
2160 2960 8.410912 GTGCCTTTTTCTTTTCCTTCTAAACTA 58.589 33.333 0.00 0.00 0.00 2.24
2161 2961 8.630037 TGCCTTTTTCTTTTCCTTCTAAACTAG 58.370 33.333 0.00 0.00 0.00 2.57
2162 2962 7.595502 GCCTTTTTCTTTTCCTTCTAAACTAGC 59.404 37.037 0.00 0.00 0.00 3.42
2163 2963 8.851145 CCTTTTTCTTTTCCTTCTAAACTAGCT 58.149 33.333 0.00 0.00 0.00 3.32
2164 2964 9.670719 CTTTTTCTTTTCCTTCTAAACTAGCTG 57.329 33.333 0.00 0.00 0.00 4.24
2165 2965 6.803154 TTCTTTTCCTTCTAAACTAGCTGC 57.197 37.500 0.00 0.00 0.00 5.25
2166 2966 6.115448 TCTTTTCCTTCTAAACTAGCTGCT 57.885 37.500 7.57 7.57 0.00 4.24
2167 2967 6.166982 TCTTTTCCTTCTAAACTAGCTGCTC 58.833 40.000 4.91 0.00 0.00 4.26
2168 2968 5.746990 TTTCCTTCTAAACTAGCTGCTCT 57.253 39.130 4.91 0.00 0.00 4.09
2169 2969 4.993029 TCCTTCTAAACTAGCTGCTCTC 57.007 45.455 4.91 0.00 0.00 3.20
2170 2970 4.344978 TCCTTCTAAACTAGCTGCTCTCA 58.655 43.478 4.91 0.00 0.00 3.27
2179 2979 1.473258 AGCTGCTCTCACTCTACCAG 58.527 55.000 0.00 0.00 0.00 4.00
2182 2982 2.416701 GCTGCTCTCACTCTACCAGTTC 60.417 54.545 0.00 0.00 30.26 3.01
2183 2983 2.822561 CTGCTCTCACTCTACCAGTTCA 59.177 50.000 0.00 0.00 30.26 3.18
2217 3024 9.125026 CTTTCACTTCCATTTATATAAGCAGGT 57.875 33.333 0.00 0.00 0.00 4.00
2293 3100 8.762645 TCAAGTAGATAATGTGATGACTTCCTT 58.237 33.333 0.00 0.00 0.00 3.36
2316 3123 8.936864 CCTTAAACTTTGTATTGATCGTCTTCT 58.063 33.333 0.00 0.00 0.00 2.85
2367 3175 5.646577 ACTTCGTGCCTATGATACCTATC 57.353 43.478 0.00 0.00 0.00 2.08
2608 3441 4.154918 CCCTTTGCAAAGATCACTCACTAC 59.845 45.833 35.25 0.00 38.28 2.73
2610 3443 5.334414 CCTTTGCAAAGATCACTCACTACAC 60.334 44.000 35.25 0.00 38.28 2.90
2633 3466 1.837439 TCAGGTGTTGACAAGTGGAGT 59.163 47.619 0.00 0.00 0.00 3.85
2711 3545 2.066262 CTAATCGTGCGTCCAAACACT 58.934 47.619 0.00 0.00 34.58 3.55
2723 3557 4.202010 CGTCCAAACACTGAACCATTTTCT 60.202 41.667 0.00 0.00 0.00 2.52
2740 3574 8.917088 ACCATTTTCTTCTTTGAATTTCTCTCA 58.083 29.630 0.00 0.00 0.00 3.27
2765 3599 4.789784 GAGATCTTCGAAACTAGATCCCG 58.210 47.826 17.33 0.00 45.05 5.14
2782 3616 2.004733 CCCGAGTTAATGGGTTTCGAC 58.995 52.381 0.00 0.00 40.76 4.20
2786 3620 3.060363 CGAGTTAATGGGTTTCGACGAAG 59.940 47.826 10.61 0.00 33.38 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.299297 ACCTCCCTTTTCGTGAGTACAG 59.701 50.000 0.00 0.00 0.00 2.74
34 35 2.170817 GGAAGACCTATGTCAACCTCCC 59.829 54.545 0.81 0.00 44.33 4.30
40 41 3.998913 TGCATGGAAGACCTATGTCAA 57.001 42.857 0.81 0.00 44.33 3.18
59 60 2.794910 CACACGGAGGCGAACTTATATG 59.205 50.000 0.00 0.00 0.00 1.78
63 64 0.242825 CTCACACGGAGGCGAACTTA 59.757 55.000 0.00 0.00 40.13 2.24
74 75 1.391485 CGATCAAGCTTTCTCACACGG 59.609 52.381 0.00 0.00 0.00 4.94
95 96 3.286669 CGATCTTCGGTCGCGTTC 58.713 61.111 5.77 0.09 36.00 3.95
113 114 0.179081 GGCCTACATCCTGGACGTTC 60.179 60.000 0.00 0.00 0.00 3.95
133 134 3.920093 CTGGCTCCGTTCCCAACCC 62.920 68.421 0.00 0.00 0.00 4.11
149 150 0.596083 CTTCGCCTACTCCGATGCTG 60.596 60.000 0.00 0.00 34.35 4.41
156 157 1.221021 CAACCCCTTCGCCTACTCC 59.779 63.158 0.00 0.00 0.00 3.85
171 172 3.077359 CTCCTTCTCCCATCACAACAAC 58.923 50.000 0.00 0.00 0.00 3.32
178 179 2.191400 CAACTCCTCCTTCTCCCATCA 58.809 52.381 0.00 0.00 0.00 3.07
182 183 0.906066 GTCCAACTCCTCCTTCTCCC 59.094 60.000 0.00 0.00 0.00 4.30
188 189 1.842562 CCATCATGTCCAACTCCTCCT 59.157 52.381 0.00 0.00 0.00 3.69
189 190 1.748591 GCCATCATGTCCAACTCCTCC 60.749 57.143 0.00 0.00 0.00 4.30
190 191 1.673168 GCCATCATGTCCAACTCCTC 58.327 55.000 0.00 0.00 0.00 3.71
211 212 1.451387 CCACCATCTACCCAACCGC 60.451 63.158 0.00 0.00 0.00 5.68
275 294 1.693103 CCACCCCTACTTCCCTCCC 60.693 68.421 0.00 0.00 0.00 4.30
305 324 2.245379 CCCTCCCAATCCCCCACAA 61.245 63.158 0.00 0.00 0.00 3.33
317 336 3.782443 CGCTACACCCACCCTCCC 61.782 72.222 0.00 0.00 0.00 4.30
336 355 0.464036 CCGCATCTACCTAGTTGCCA 59.536 55.000 8.98 0.00 42.92 4.92
338 357 0.179084 TGCCGCATCTACCTAGTTGC 60.179 55.000 5.60 5.60 42.61 4.17
339 358 2.408050 GATGCCGCATCTACCTAGTTG 58.592 52.381 23.55 0.00 37.82 3.16
340 359 1.000163 CGATGCCGCATCTACCTAGTT 60.000 52.381 26.73 0.00 38.59 2.24
341 360 0.598562 CGATGCCGCATCTACCTAGT 59.401 55.000 26.73 0.00 38.59 2.57
362 381 1.458209 TACCCTAACCCTAGCCGCC 60.458 63.158 0.00 0.00 0.00 6.13
363 382 1.470165 CCTACCCTAACCCTAGCCGC 61.470 65.000 0.00 0.00 0.00 6.53
383 402 1.949847 CTCCCTAGTCACCGCCACTG 61.950 65.000 0.00 0.00 0.00 3.66
386 405 3.075005 GCTCCCTAGTCACCGCCA 61.075 66.667 0.00 0.00 0.00 5.69
391 410 0.811616 CGCCATTGCTCCCTAGTCAC 60.812 60.000 0.00 0.00 34.43 3.67
392 411 0.975556 TCGCCATTGCTCCCTAGTCA 60.976 55.000 0.00 0.00 34.43 3.41
394 413 1.522569 GTCGCCATTGCTCCCTAGT 59.477 57.895 0.00 0.00 34.43 2.57
414 433 1.409427 CCTCTCTAAACCCTAGCCACG 59.591 57.143 0.00 0.00 0.00 4.94
424 443 2.140839 TCGGTCCTCCCTCTCTAAAC 57.859 55.000 0.00 0.00 0.00 2.01
441 460 9.104965 TCTTTACATGGTATCAACCTTATTTCG 57.895 33.333 0.00 0.00 46.91 3.46
451 470 6.481976 CGCACCTATTCTTTACATGGTATCAA 59.518 38.462 0.00 0.00 0.00 2.57
464 483 1.816835 TCGTGAGTCGCACCTATTCTT 59.183 47.619 4.28 0.00 44.85 2.52
476 495 5.120830 GCACCCAATGAATATATCGTGAGTC 59.879 44.000 0.00 0.00 0.00 3.36
506 525 8.812972 ACCACCTATTGTACCTATATGTATGTG 58.187 37.037 0.00 0.00 0.00 3.21
508 527 9.031537 TGACCACCTATTGTACCTATATGTATG 57.968 37.037 0.00 0.00 0.00 2.39
509 528 9.032624 GTGACCACCTATTGTACCTATATGTAT 57.967 37.037 0.00 0.00 0.00 2.29
510 529 7.175467 CGTGACCACCTATTGTACCTATATGTA 59.825 40.741 0.00 0.00 0.00 2.29
511 530 6.015688 CGTGACCACCTATTGTACCTATATGT 60.016 42.308 0.00 0.00 0.00 2.29
512 531 6.015688 ACGTGACCACCTATTGTACCTATATG 60.016 42.308 0.00 0.00 0.00 1.78
531 1075 5.306532 TCTTGTATAGTTGAGGACGTGAC 57.693 43.478 0.00 0.00 0.00 3.67
532 1076 5.970317 TTCTTGTATAGTTGAGGACGTGA 57.030 39.130 0.00 0.00 0.00 4.35
587 1131 9.665719 TTTGCTCTTGTTGAGATGTATATAACA 57.334 29.630 0.00 0.00 45.39 2.41
590 1134 9.755804 CTCTTTGCTCTTGTTGAGATGTATATA 57.244 33.333 0.00 0.00 45.39 0.86
596 1140 4.070716 ACCTCTTTGCTCTTGTTGAGATG 58.929 43.478 0.00 0.00 45.39 2.90
611 1155 6.187727 TGGTCTTGAACTCAATACCTCTTT 57.812 37.500 21.10 0.00 46.86 2.52
616 1160 3.010420 GCCTGGTCTTGAACTCAATACC 58.990 50.000 16.30 16.30 46.90 2.73
622 1166 1.276421 TGCTAGCCTGGTCTTGAACTC 59.724 52.381 13.29 0.00 0.00 3.01
626 1170 4.778213 AATTATGCTAGCCTGGTCTTGA 57.222 40.909 13.29 0.00 0.00 3.02
634 1178 5.776744 GCTGCAATTTAATTATGCTAGCCT 58.223 37.500 13.29 4.74 40.66 4.58
636 1180 4.925646 GGGCTGCAATTTAATTATGCTAGC 59.074 41.667 8.10 8.10 40.36 3.42
642 1186 7.043565 CAGAAAGTGGGCTGCAATTTAATTAT 58.956 34.615 0.50 0.00 0.00 1.28
643 1187 6.014669 ACAGAAAGTGGGCTGCAATTTAATTA 60.015 34.615 0.50 0.00 35.57 1.40
658 1202 3.186613 GCCTAAACGAGAACAGAAAGTGG 59.813 47.826 0.00 0.00 0.00 4.00
661 1205 4.690748 TCATGCCTAAACGAGAACAGAAAG 59.309 41.667 0.00 0.00 0.00 2.62
666 1212 3.953712 TCTCATGCCTAAACGAGAACA 57.046 42.857 0.00 0.00 31.73 3.18
671 1217 4.081697 TGTGATCTTCTCATGCCTAAACGA 60.082 41.667 0.00 0.00 35.97 3.85
683 1229 3.730662 GCTCTCTCACGTGTGATCTTCTC 60.731 52.174 19.62 4.32 39.13 2.87
686 1232 2.166829 AGCTCTCTCACGTGTGATCTT 58.833 47.619 19.62 4.85 39.13 2.40
688 1234 3.766676 TTAGCTCTCTCACGTGTGATC 57.233 47.619 19.62 12.13 39.13 2.92
689 1235 6.398234 AATATTAGCTCTCTCACGTGTGAT 57.602 37.500 19.62 8.48 39.13 3.06
707 1253 9.927081 AACCAATCTGATGAAAGAGGTAATATT 57.073 29.630 0.00 0.00 0.00 1.28
708 1254 9.927081 AAACCAATCTGATGAAAGAGGTAATAT 57.073 29.630 0.00 0.00 0.00 1.28
711 1268 8.477419 AAAAACCAATCTGATGAAAGAGGTAA 57.523 30.769 0.00 0.00 0.00 2.85
738 1295 6.194796 AGCGCATGTTTTAGTCAATACAAT 57.805 33.333 11.47 0.00 30.81 2.71
739 1296 5.621197 AGCGCATGTTTTAGTCAATACAA 57.379 34.783 11.47 0.00 30.81 2.41
741 1298 5.869350 AGAAGCGCATGTTTTAGTCAATAC 58.131 37.500 11.47 0.00 0.00 1.89
742 1299 6.816640 AGTAGAAGCGCATGTTTTAGTCAATA 59.183 34.615 11.47 0.00 0.00 1.90
743 1300 5.643777 AGTAGAAGCGCATGTTTTAGTCAAT 59.356 36.000 11.47 0.00 0.00 2.57
744 1301 4.994852 AGTAGAAGCGCATGTTTTAGTCAA 59.005 37.500 11.47 0.00 0.00 3.18
746 1303 5.107065 ACAAGTAGAAGCGCATGTTTTAGTC 60.107 40.000 11.47 0.00 0.00 2.59
757 1455 0.164647 CAGCACACAAGTAGAAGCGC 59.835 55.000 0.00 0.00 0.00 5.92
759 1457 2.872245 TGTTCAGCACACAAGTAGAAGC 59.128 45.455 0.00 0.00 0.00 3.86
760 1458 3.059325 GCTGTTCAGCACACAAGTAGAAG 60.059 47.826 18.26 0.00 34.41 2.85
768 1466 0.109153 AGATGGCTGTTCAGCACACA 59.891 50.000 23.23 13.96 36.33 3.72
769 1467 1.198637 GAAGATGGCTGTTCAGCACAC 59.801 52.381 23.23 14.02 36.33 3.82
814 1537 1.517694 GATCAAACCTCGCGGCGTA 60.518 57.895 22.90 8.25 0.00 4.42
822 1545 1.696832 GCTGACGCGGATCAAACCTC 61.697 60.000 12.47 0.00 0.00 3.85
824 1547 1.369091 ATGCTGACGCGGATCAAACC 61.369 55.000 12.47 0.00 39.65 3.27
825 1548 0.447801 AATGCTGACGCGGATCAAAC 59.552 50.000 12.47 1.78 39.65 2.93
826 1549 0.447406 CAATGCTGACGCGGATCAAA 59.553 50.000 12.47 0.00 39.65 2.69
831 1558 2.436469 ATGCAATGCTGACGCGGA 60.436 55.556 12.47 0.00 39.65 5.54
836 1563 1.063649 CGGCTGATGCAATGCTGAC 59.936 57.895 6.82 0.00 41.91 3.51
837 1564 1.078285 TCGGCTGATGCAATGCTGA 60.078 52.632 6.82 13.93 41.91 4.26
878 1614 0.036732 TGCGGGCATCTTCTTCAAGT 59.963 50.000 0.00 0.00 0.00 3.16
1659 2424 1.525535 GCCTGCGATCATCTGCCTT 60.526 57.895 0.00 0.00 0.00 4.35
1813 2580 6.713450 ACGGAAAATAGACGCCCAATATTTAT 59.287 34.615 0.00 0.00 30.82 1.40
1815 2582 4.885325 ACGGAAAATAGACGCCCAATATTT 59.115 37.500 0.00 0.00 32.00 1.40
1817 2584 4.081322 ACGGAAAATAGACGCCCAATAT 57.919 40.909 0.00 0.00 0.00 1.28
1820 2593 2.234414 ACTACGGAAAATAGACGCCCAA 59.766 45.455 0.00 0.00 0.00 4.12
1823 2596 2.606272 CCAACTACGGAAAATAGACGCC 59.394 50.000 0.00 0.00 0.00 5.68
1824 2597 3.514645 TCCAACTACGGAAAATAGACGC 58.485 45.455 0.00 0.00 29.93 5.19
1828 2601 8.488651 AAGTACAATCCAACTACGGAAAATAG 57.511 34.615 0.00 0.00 38.95 1.73
2031 2831 8.634444 TCGAAAAATTCCTTTCTGGTGATAAAA 58.366 29.630 2.11 0.00 33.86 1.52
2032 2832 8.172352 TCGAAAAATTCCTTTCTGGTGATAAA 57.828 30.769 2.11 0.00 33.86 1.40
2033 2833 7.753309 TCGAAAAATTCCTTTCTGGTGATAA 57.247 32.000 2.11 0.00 33.86 1.75
2034 2834 7.753309 TTCGAAAAATTCCTTTCTGGTGATA 57.247 32.000 0.00 0.00 33.86 2.15
2035 2835 6.648879 TTCGAAAAATTCCTTTCTGGTGAT 57.351 33.333 0.00 0.00 33.86 3.06
2036 2836 6.458232 TTTCGAAAAATTCCTTTCTGGTGA 57.542 33.333 8.44 0.00 33.86 4.02
2037 2837 7.254421 CCTTTTTCGAAAAATTCCTTTCTGGTG 60.254 37.037 30.37 16.51 37.27 4.17
2038 2838 6.761242 CCTTTTTCGAAAAATTCCTTTCTGGT 59.239 34.615 30.37 0.00 37.27 4.00
2039 2839 6.983890 TCCTTTTTCGAAAAATTCCTTTCTGG 59.016 34.615 30.37 23.97 37.27 3.86
2040 2840 7.305993 CGTCCTTTTTCGAAAAATTCCTTTCTG 60.306 37.037 30.37 17.69 37.27 3.02
2041 2841 6.695713 CGTCCTTTTTCGAAAAATTCCTTTCT 59.304 34.615 30.37 0.00 37.27 2.52
2042 2842 6.561533 GCGTCCTTTTTCGAAAAATTCCTTTC 60.562 38.462 30.37 17.19 37.27 2.62
2043 2843 5.233476 GCGTCCTTTTTCGAAAAATTCCTTT 59.767 36.000 30.37 0.00 37.27 3.11
2044 2844 4.743151 GCGTCCTTTTTCGAAAAATTCCTT 59.257 37.500 30.37 0.00 37.27 3.36
2045 2845 4.037565 AGCGTCCTTTTTCGAAAAATTCCT 59.962 37.500 30.37 20.07 37.27 3.36
2046 2846 4.295870 AGCGTCCTTTTTCGAAAAATTCC 58.704 39.130 30.37 20.39 37.27 3.01
2047 2847 5.883328 AAGCGTCCTTTTTCGAAAAATTC 57.117 34.783 30.37 21.98 37.27 2.17
2048 2848 7.940178 ATAAAGCGTCCTTTTTCGAAAAATT 57.060 28.000 30.37 22.46 41.37 1.82
2049 2849 8.908678 GTTATAAAGCGTCCTTTTTCGAAAAAT 58.091 29.630 30.37 18.16 41.37 1.82
2050 2850 8.130469 AGTTATAAAGCGTCCTTTTTCGAAAAA 58.870 29.630 28.86 28.86 41.37 1.94
2051 2851 7.588488 CAGTTATAAAGCGTCCTTTTTCGAAAA 59.412 33.333 19.08 19.08 41.37 2.29
2052 2852 7.041916 TCAGTTATAAAGCGTCCTTTTTCGAAA 60.042 33.333 6.47 6.47 41.37 3.46
2053 2853 6.424509 TCAGTTATAAAGCGTCCTTTTTCGAA 59.575 34.615 0.00 0.00 41.37 3.71
2054 2854 5.927689 TCAGTTATAAAGCGTCCTTTTTCGA 59.072 36.000 0.00 0.00 41.37 3.71
2055 2855 6.160664 TCAGTTATAAAGCGTCCTTTTTCG 57.839 37.500 0.00 0.00 41.37 3.46
2056 2856 8.791355 TTTTCAGTTATAAAGCGTCCTTTTTC 57.209 30.769 0.00 0.00 41.37 2.29
2057 2857 9.191995 CATTTTCAGTTATAAAGCGTCCTTTTT 57.808 29.630 0.00 0.00 41.37 1.94
2058 2858 8.357402 ACATTTTCAGTTATAAAGCGTCCTTTT 58.643 29.630 0.00 0.00 41.37 2.27
2059 2859 7.882179 ACATTTTCAGTTATAAAGCGTCCTTT 58.118 30.769 0.00 0.00 43.43 3.11
2060 2860 7.448748 ACATTTTCAGTTATAAAGCGTCCTT 57.551 32.000 0.00 0.00 0.00 3.36
2061 2861 8.732746 ATACATTTTCAGTTATAAAGCGTCCT 57.267 30.769 0.00 0.00 0.00 3.85
2064 2864 9.931210 GCTTATACATTTTCAGTTATAAAGCGT 57.069 29.630 0.00 0.00 0.00 5.07
2065 2865 9.929722 TGCTTATACATTTTCAGTTATAAAGCG 57.070 29.630 0.00 0.00 0.00 4.68
2073 2873 8.181573 CGGTGTAATGCTTATACATTTTCAGTT 58.818 33.333 0.00 0.00 40.64 3.16
2074 2874 7.678690 GCGGTGTAATGCTTATACATTTTCAGT 60.679 37.037 0.00 0.00 40.64 3.41
2075 2875 6.632834 GCGGTGTAATGCTTATACATTTTCAG 59.367 38.462 0.00 0.00 40.64 3.02
2076 2876 6.459024 GGCGGTGTAATGCTTATACATTTTCA 60.459 38.462 0.00 0.00 40.64 2.69
2077 2877 5.912955 GGCGGTGTAATGCTTATACATTTTC 59.087 40.000 0.00 0.00 40.64 2.29
2078 2878 5.358442 TGGCGGTGTAATGCTTATACATTTT 59.642 36.000 0.00 0.00 40.64 1.82
2079 2879 4.884744 TGGCGGTGTAATGCTTATACATTT 59.115 37.500 0.00 0.00 40.64 2.32
2080 2880 4.456535 TGGCGGTGTAATGCTTATACATT 58.543 39.130 0.00 0.00 42.73 2.71
2081 2881 4.065088 CTGGCGGTGTAATGCTTATACAT 58.935 43.478 1.25 0.00 35.84 2.29
2082 2882 3.133183 TCTGGCGGTGTAATGCTTATACA 59.867 43.478 0.00 0.00 0.00 2.29
2083 2883 3.724374 TCTGGCGGTGTAATGCTTATAC 58.276 45.455 0.00 0.00 0.00 1.47
2084 2884 4.409718 TTCTGGCGGTGTAATGCTTATA 57.590 40.909 0.00 0.00 0.00 0.98
2085 2885 3.275617 TTCTGGCGGTGTAATGCTTAT 57.724 42.857 0.00 0.00 0.00 1.73
2086 2886 2.772077 TTCTGGCGGTGTAATGCTTA 57.228 45.000 0.00 0.00 0.00 3.09
2087 2887 1.904287 TTTCTGGCGGTGTAATGCTT 58.096 45.000 0.00 0.00 0.00 3.91
2088 2888 1.745087 CATTTCTGGCGGTGTAATGCT 59.255 47.619 0.00 0.00 0.00 3.79
2089 2889 1.742831 TCATTTCTGGCGGTGTAATGC 59.257 47.619 11.19 0.00 0.00 3.56
2090 2890 4.353737 CATTCATTTCTGGCGGTGTAATG 58.646 43.478 10.30 10.30 0.00 1.90
2091 2891 3.381272 CCATTCATTTCTGGCGGTGTAAT 59.619 43.478 0.00 0.00 0.00 1.89
2092 2892 2.752354 CCATTCATTTCTGGCGGTGTAA 59.248 45.455 0.00 0.00 0.00 2.41
2093 2893 2.364632 CCATTCATTTCTGGCGGTGTA 58.635 47.619 0.00 0.00 0.00 2.90
2094 2894 1.176527 CCATTCATTTCTGGCGGTGT 58.823 50.000 0.00 0.00 0.00 4.16
2100 2900 5.067805 GGTAAGTTAGGCCATTCATTTCTGG 59.932 44.000 5.01 0.00 35.53 3.86
2101 2901 5.652014 TGGTAAGTTAGGCCATTCATTTCTG 59.348 40.000 5.01 0.00 0.00 3.02
2102 2902 5.652452 GTGGTAAGTTAGGCCATTCATTTCT 59.348 40.000 5.01 0.00 34.52 2.52
2103 2903 5.652452 AGTGGTAAGTTAGGCCATTCATTTC 59.348 40.000 5.01 0.00 34.52 2.17
2104 2904 5.418840 CAGTGGTAAGTTAGGCCATTCATTT 59.581 40.000 5.01 0.00 34.52 2.32
2105 2905 4.949856 CAGTGGTAAGTTAGGCCATTCATT 59.050 41.667 5.01 0.00 34.52 2.57
2106 2906 4.227300 TCAGTGGTAAGTTAGGCCATTCAT 59.773 41.667 5.01 0.00 34.52 2.57
2107 2907 3.585289 TCAGTGGTAAGTTAGGCCATTCA 59.415 43.478 5.01 0.00 34.52 2.57
2108 2908 4.192317 CTCAGTGGTAAGTTAGGCCATTC 58.808 47.826 5.01 0.00 34.52 2.67
2109 2909 3.587506 ACTCAGTGGTAAGTTAGGCCATT 59.412 43.478 5.01 0.00 34.52 3.16
2110 2910 3.182152 ACTCAGTGGTAAGTTAGGCCAT 58.818 45.455 5.01 0.00 34.52 4.40
2111 2911 2.616524 ACTCAGTGGTAAGTTAGGCCA 58.383 47.619 5.01 0.00 0.00 5.36
2112 2912 3.132467 CCTACTCAGTGGTAAGTTAGGCC 59.868 52.174 0.00 0.00 0.00 5.19
2113 2913 3.768215 ACCTACTCAGTGGTAAGTTAGGC 59.232 47.826 0.00 0.00 34.36 3.93
2114 2914 4.381718 GCACCTACTCAGTGGTAAGTTAGG 60.382 50.000 0.00 0.00 35.71 2.69
2115 2915 4.381718 GGCACCTACTCAGTGGTAAGTTAG 60.382 50.000 0.00 0.00 35.71 2.34
2116 2916 3.512724 GGCACCTACTCAGTGGTAAGTTA 59.487 47.826 0.00 0.00 35.71 2.24
2117 2917 2.302157 GGCACCTACTCAGTGGTAAGTT 59.698 50.000 0.00 0.00 35.71 2.66
2118 2918 1.900486 GGCACCTACTCAGTGGTAAGT 59.100 52.381 0.00 0.00 35.71 2.24
2119 2919 2.180276 AGGCACCTACTCAGTGGTAAG 58.820 52.381 0.00 0.00 35.71 2.34
2120 2920 2.320681 AGGCACCTACTCAGTGGTAA 57.679 50.000 0.00 0.00 35.71 2.85
2121 2921 2.320681 AAGGCACCTACTCAGTGGTA 57.679 50.000 0.00 0.00 35.71 3.25
2122 2922 1.435256 AAAGGCACCTACTCAGTGGT 58.565 50.000 0.00 0.00 35.71 4.16
2123 2923 2.568623 AAAAGGCACCTACTCAGTGG 57.431 50.000 0.00 0.00 35.71 4.00
2124 2924 3.744660 AGAAAAAGGCACCTACTCAGTG 58.255 45.455 0.00 0.00 38.30 3.66
2125 2925 4.439253 AAGAAAAAGGCACCTACTCAGT 57.561 40.909 0.00 0.00 0.00 3.41
2126 2926 5.278512 GGAAAAGAAAAAGGCACCTACTCAG 60.279 44.000 0.00 0.00 0.00 3.35
2127 2927 4.583073 GGAAAAGAAAAAGGCACCTACTCA 59.417 41.667 0.00 0.00 0.00 3.41
2128 2928 4.827835 AGGAAAAGAAAAAGGCACCTACTC 59.172 41.667 0.00 0.00 0.00 2.59
2129 2929 4.804597 AGGAAAAGAAAAAGGCACCTACT 58.195 39.130 0.00 0.00 0.00 2.57
2130 2930 5.302059 AGAAGGAAAAGAAAAAGGCACCTAC 59.698 40.000 0.00 0.00 0.00 3.18
2131 2931 5.454966 AGAAGGAAAAGAAAAAGGCACCTA 58.545 37.500 0.00 0.00 0.00 3.08
2132 2932 4.290093 AGAAGGAAAAGAAAAAGGCACCT 58.710 39.130 0.00 0.00 0.00 4.00
2133 2933 4.672587 AGAAGGAAAAGAAAAAGGCACC 57.327 40.909 0.00 0.00 0.00 5.01
2134 2934 7.265673 AGTTTAGAAGGAAAAGAAAAAGGCAC 58.734 34.615 0.00 0.00 0.00 5.01
2135 2935 7.418337 AGTTTAGAAGGAAAAGAAAAAGGCA 57.582 32.000 0.00 0.00 0.00 4.75
2136 2936 7.595502 GCTAGTTTAGAAGGAAAAGAAAAAGGC 59.404 37.037 0.00 0.00 0.00 4.35
2137 2937 8.851145 AGCTAGTTTAGAAGGAAAAGAAAAAGG 58.149 33.333 0.00 0.00 0.00 3.11
2138 2938 9.670719 CAGCTAGTTTAGAAGGAAAAGAAAAAG 57.329 33.333 0.00 0.00 0.00 2.27
2139 2939 8.135529 GCAGCTAGTTTAGAAGGAAAAGAAAAA 58.864 33.333 0.00 0.00 0.00 1.94
2140 2940 7.502561 AGCAGCTAGTTTAGAAGGAAAAGAAAA 59.497 33.333 0.00 0.00 0.00 2.29
2141 2941 6.998673 AGCAGCTAGTTTAGAAGGAAAAGAAA 59.001 34.615 0.00 0.00 0.00 2.52
2142 2942 6.534634 AGCAGCTAGTTTAGAAGGAAAAGAA 58.465 36.000 0.00 0.00 0.00 2.52
2143 2943 6.014156 AGAGCAGCTAGTTTAGAAGGAAAAGA 60.014 38.462 0.00 0.00 0.00 2.52
2144 2944 6.169800 AGAGCAGCTAGTTTAGAAGGAAAAG 58.830 40.000 0.00 0.00 0.00 2.27
2145 2945 6.115448 AGAGCAGCTAGTTTAGAAGGAAAA 57.885 37.500 0.00 0.00 0.00 2.29
2146 2946 5.246203 TGAGAGCAGCTAGTTTAGAAGGAAA 59.754 40.000 0.00 0.00 0.00 3.13
2147 2947 4.772624 TGAGAGCAGCTAGTTTAGAAGGAA 59.227 41.667 0.00 0.00 0.00 3.36
2148 2948 4.158764 GTGAGAGCAGCTAGTTTAGAAGGA 59.841 45.833 0.00 0.00 0.00 3.36
2149 2949 4.159506 AGTGAGAGCAGCTAGTTTAGAAGG 59.840 45.833 0.00 0.00 0.00 3.46
2150 2950 5.125417 AGAGTGAGAGCAGCTAGTTTAGAAG 59.875 44.000 0.00 0.00 0.00 2.85
2151 2951 5.013547 AGAGTGAGAGCAGCTAGTTTAGAA 58.986 41.667 0.00 0.00 0.00 2.10
2152 2952 4.594970 AGAGTGAGAGCAGCTAGTTTAGA 58.405 43.478 0.00 0.00 0.00 2.10
2153 2953 4.981806 AGAGTGAGAGCAGCTAGTTTAG 57.018 45.455 0.00 0.00 0.00 1.85
2154 2954 4.641094 GGTAGAGTGAGAGCAGCTAGTTTA 59.359 45.833 0.00 0.00 0.00 2.01
2155 2955 3.445805 GGTAGAGTGAGAGCAGCTAGTTT 59.554 47.826 0.00 0.00 0.00 2.66
2156 2956 3.020984 GGTAGAGTGAGAGCAGCTAGTT 58.979 50.000 0.00 0.00 0.00 2.24
2157 2957 2.025793 TGGTAGAGTGAGAGCAGCTAGT 60.026 50.000 0.00 0.00 0.00 2.57
2158 2958 2.618241 CTGGTAGAGTGAGAGCAGCTAG 59.382 54.545 0.00 0.00 34.69 3.42
2159 2959 2.025793 ACTGGTAGAGTGAGAGCAGCTA 60.026 50.000 0.00 0.00 43.43 3.32
2160 2960 1.272425 ACTGGTAGAGTGAGAGCAGCT 60.272 52.381 0.00 0.00 43.43 4.24
2161 2961 1.181786 ACTGGTAGAGTGAGAGCAGC 58.818 55.000 1.23 0.00 43.43 5.25
2162 2962 2.822561 TGAACTGGTAGAGTGAGAGCAG 59.177 50.000 0.00 0.00 44.80 4.24
2163 2963 2.876581 TGAACTGGTAGAGTGAGAGCA 58.123 47.619 0.00 0.00 34.02 4.26
2164 2964 4.642885 AGTATGAACTGGTAGAGTGAGAGC 59.357 45.833 0.00 0.00 34.02 4.09
2227 3034 7.057264 TGGATCCAACGGATAATACAAATCAA 58.943 34.615 13.46 0.00 43.27 2.57
2228 3035 6.596621 TGGATCCAACGGATAATACAAATCA 58.403 36.000 13.46 0.00 43.27 2.57
2229 3036 7.504924 TTGGATCCAACGGATAATACAAATC 57.495 36.000 23.63 0.00 43.27 2.17
2230 3037 7.889873 TTTGGATCCAACGGATAATACAAAT 57.110 32.000 27.04 0.00 43.27 2.32
2276 3083 9.349713 ACAAAGTTTAAGGAAGTCATCACATTA 57.650 29.630 0.00 0.00 0.00 1.90
2281 3088 9.567776 TCAATACAAAGTTTAAGGAAGTCATCA 57.432 29.630 0.00 0.00 0.00 3.07
2342 3150 5.455056 AGGTATCATAGGCACGAAGTAAG 57.545 43.478 0.00 0.00 41.61 2.34
2608 3441 2.868583 CACTTGTCAACACCTGAGAGTG 59.131 50.000 0.48 0.48 40.37 3.51
2610 3443 2.103094 TCCACTTGTCAACACCTGAGAG 59.897 50.000 0.00 0.00 33.60 3.20
2633 3466 8.506168 AAAAGAGAGAAAACTCACATGTTGTA 57.494 30.769 0.00 0.00 39.14 2.41
2711 3545 9.533253 GAGAAATTCAAAGAAGAAAATGGTTCA 57.467 29.630 0.00 0.00 0.00 3.18
2765 3599 4.240096 TCTTCGTCGAAACCCATTAACTC 58.760 43.478 9.30 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.