Multiple sequence alignment - TraesCS4D01G261700

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 TraesCS4D01G261700 chr4D 100.000 3685 0 0 1 3685 432764091 432760407 0.000000e+00 6806
1 TraesCS4D01G261700 chr4A 88.496 904 47 18 1 873 34042828 34041951 0.000000e+00 1040
2 TraesCS4D01G261700 chr4A 87.368 760 48 13 2939 3685 34039447 34038723 0.000000e+00 828
3 TraesCS4D01G261700 chr4A 93.608 485 25 5 2222 2703 34040195 34039714 0.000000e+00 719
4 TraesCS4D01G261700 chr4A 87.241 580 33 22 911 1481 34041946 34041399 1.120000e-174 623
5 TraesCS4D01G261700 chr4A 87.773 458 45 7 1465 1918 34041383 34040933 3.260000e-145 525
6 TraesCS4D01G261700 chr4A 87.970 266 22 5 1916 2179 34040645 34040388 4.620000e-79 305
7 TraesCS4D01G261700 chr4A 93.122 189 12 1 2747 2934 34039716 34039528 3.620000e-70 276
8 TraesCS4D01G261700 chr4B 87.623 711 63 11 2994 3685 530499451 530500155 0.000000e+00 802
9 TraesCS4D01G261700 chr4B 84.946 465 56 10 1338 1796 530476975 530477431 3.350000e-125 459
10 TraesCS4D01G261700 chr4B 93.197 294 20 0 2328 2621 530498757 530499050 2.030000e-117 433
11 TraesCS4D01G261700 chr4B 90.493 284 18 4 615 891 530476210 530476491 2.090000e-97 366


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 TraesCS4D01G261700 chr4D 432760407 432764091 3684 True 6806.000000 6806 100.000000 1 3685 1 chr4D.!!$R1 3684
1 TraesCS4D01G261700 chr4A 34038723 34042828 4105 True 616.571429 1040 89.368286 1 3685 7 chr4A.!!$R1 3684
2 TraesCS4D01G261700 chr4B 530498757 530500155 1398 False 617.500000 802 90.410000 2328 3685 2 chr4B.!!$F2 1357
3 TraesCS4D01G261700 chr4B 530476210 530477431 1221 False 412.500000 459 87.719500 615 1796 2 chr4B.!!$F1 1181

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
84 85 0.032678 ATTCCTAGTCATGCCTCGCG 59.967 55.0 0.0 0.0 0.0 5.87 F
1693 1871 0.037326 GCATCCGTCTGTGACCTCAA 60.037 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2433 0.183731 GGCTTCTATTGAGGGGGTGG 59.816 60.0 0.00 0.00 0.00 4.61 R
3066 3828 0.095245 CATCGTTGCCATGTCGACAC 59.905 55.0 22.71 9.19 36.46 3.67 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
28 29 1.978542 AGCGTTATGTCTCGTGTGTC 58.021 50.000 0.00 0.00 0.00 3.67
43 44 5.399858 TCGTGTGTCTTCTGTAAATAGCTC 58.600 41.667 0.00 0.00 0.00 4.09
70 71 9.907229 ATTTCTTTCGGTTCTCTTATAATTCCT 57.093 29.630 0.00 0.00 0.00 3.36
84 85 0.032678 ATTCCTAGTCATGCCTCGCG 59.967 55.000 0.00 0.00 0.00 5.87
99 100 2.055838 CTCGCGTTTTACACTGCTGTA 58.944 47.619 5.77 0.00 0.00 2.74
106 107 6.455113 CGCGTTTTACACTGCTGTATTTAGAT 60.455 38.462 0.00 0.00 32.70 1.98
156 160 2.297701 GTTGCTTCTTCAGGTGGTGAA 58.702 47.619 0.00 0.00 43.26 3.18
227 231 5.477984 CACTGGTTACCACTTACCACTAGTA 59.522 44.000 0.00 0.00 39.44 1.82
229 233 4.463891 TGGTTACCACTTACCACTAGTAGC 59.536 45.833 0.00 0.00 39.44 3.58
234 238 3.944015 CCACTTACCACTAGTAGCTACGT 59.056 47.826 17.99 11.72 30.92 3.57
238 242 7.201767 CCACTTACCACTAGTAGCTACGTAATT 60.202 40.741 17.99 10.81 30.92 1.40
240 244 5.511234 ACCACTAGTAGCTACGTAATTGG 57.489 43.478 17.99 19.99 0.00 3.16
241 245 4.202090 ACCACTAGTAGCTACGTAATTGGC 60.202 45.833 22.01 0.00 0.00 4.52
243 247 4.738740 CACTAGTAGCTACGTAATTGGCAC 59.261 45.833 17.99 4.01 0.00 5.01
244 248 2.805845 AGTAGCTACGTAATTGGCACG 58.194 47.619 17.99 0.00 44.80 5.34
245 249 1.856597 GTAGCTACGTAATTGGCACGG 59.143 52.381 8.40 0.00 43.59 4.94
246 250 0.533491 AGCTACGTAATTGGCACGGA 59.467 50.000 7.22 0.00 43.59 4.69
247 251 1.066716 AGCTACGTAATTGGCACGGAA 60.067 47.619 7.22 0.00 43.59 4.30
263 267 0.733150 GGAATGGCAACTAACGAGGC 59.267 55.000 0.00 0.00 37.61 4.70
292 296 3.207778 TGTCAAAAGTTGGTAGGTTCGG 58.792 45.455 0.00 0.00 0.00 4.30
315 322 5.407084 GGTTTGAACTCTCTAAGCTTGACTC 59.593 44.000 9.86 0.00 33.66 3.36
335 342 4.020573 ACTCAAGGACGATCCACATTACAA 60.021 41.667 6.78 0.00 39.61 2.41
344 351 2.088423 TCCACATTACAATGCCGTTCC 58.912 47.619 1.84 0.00 40.04 3.62
346 353 2.091541 CACATTACAATGCCGTTCCCT 58.908 47.619 1.84 0.00 40.04 4.20
347 354 2.091541 ACATTACAATGCCGTTCCCTG 58.908 47.619 1.84 0.00 40.04 4.45
420 427 4.478206 TGCCACCAAAAACTTGAATTGA 57.522 36.364 0.00 0.00 0.00 2.57
425 432 5.452356 CCACCAAAAACTTGAATTGAGCTCT 60.452 40.000 16.19 0.00 0.00 4.09
427 434 7.373493 CACCAAAAACTTGAATTGAGCTCTAT 58.627 34.615 16.19 10.36 0.00 1.98
428 435 7.869429 CACCAAAAACTTGAATTGAGCTCTATT 59.131 33.333 21.07 21.07 0.00 1.73
477 503 6.310941 TCTTGAAGGGAACATTTGGATGTAA 58.689 36.000 0.00 0.00 45.58 2.41
527 553 2.501723 TCCCTGGTGCTGAAAGATACTC 59.498 50.000 0.00 0.00 34.07 2.59
539 565 2.898729 AGATACTCGGACCAATGCTG 57.101 50.000 0.00 0.00 0.00 4.41
540 566 1.202580 AGATACTCGGACCAATGCTGC 60.203 52.381 0.00 0.00 0.00 5.25
658 687 0.438445 CGACGAGAACCACGTACGTA 59.562 55.000 22.34 0.00 43.97 3.57
729 758 1.596934 GATGGTGGAAGCGACAGGA 59.403 57.895 0.00 0.00 36.92 3.86
806 841 3.391355 GCTTGCGCGTAACGGTAT 58.609 55.556 5.23 0.00 43.93 2.73
817 852 0.747644 TAACGGTATGAGGCGTCGGA 60.748 55.000 1.39 0.00 0.00 4.55
884 919 4.570663 CACCCGATCGCGACCTCC 62.571 72.222 12.93 0.00 40.82 4.30
904 939 4.992511 CCCGCCCCGAAACAACGA 62.993 66.667 0.00 0.00 35.09 3.85
905 940 3.419759 CCGCCCCGAAACAACGAG 61.420 66.667 0.00 0.00 35.09 4.18
906 941 4.084888 CGCCCCGAAACAACGAGC 62.085 66.667 0.00 0.00 35.09 5.03
909 944 1.890041 CCCCGAAACAACGAGCACA 60.890 57.895 0.00 0.00 35.09 4.57
974 1083 2.487762 TCAAAAACCTCATTAGCCGCTG 59.512 45.455 2.16 0.00 0.00 5.18
1027 1155 0.517316 GCTTCCGAATCGTTGCAAGT 59.483 50.000 0.00 0.00 0.00 3.16
1045 1173 0.652592 GTTCCATCGATCAGTTGCCG 59.347 55.000 0.00 0.00 0.00 5.69
1048 1176 0.249447 CCATCGATCAGTTGCCGCTA 60.249 55.000 0.00 0.00 0.00 4.26
1061 1189 3.264897 CGCTACAGACATGCCGGC 61.265 66.667 22.73 22.73 0.00 6.13
1147 1278 2.975536 CGGCCTCGTCCAAGGTAA 59.024 61.111 0.00 0.00 38.79 2.85
1215 1352 2.859273 ATCGGGAGAAGCGGCACAAG 62.859 60.000 1.45 0.00 45.37 3.16
1216 1353 2.347490 GGGAGAAGCGGCACAAGA 59.653 61.111 1.45 0.00 0.00 3.02
1246 1383 2.880879 CGTGTGATGAGTCGGCGG 60.881 66.667 7.21 0.00 0.00 6.13
1251 1388 4.796231 GATGAGTCGGCGGCGTGT 62.796 66.667 31.06 19.17 0.00 4.49
1343 1480 0.790814 CTCCCTGCTTCGTTTCGTTC 59.209 55.000 0.00 0.00 0.00 3.95
1348 1485 0.578211 TGCTTCGTTTCGTTCCGTTC 59.422 50.000 0.00 0.00 0.00 3.95
1400 1538 7.742767 TGATCTGTGAACTCCATGATATGAAT 58.257 34.615 0.00 0.00 0.00 2.57
1451 1596 5.233902 TGTGAATTTTCAATTTTGAGCACGG 59.766 36.000 0.00 0.00 39.21 4.94
1547 1725 2.158505 CCATGATGAAGAATGGGGAGCT 60.159 50.000 0.00 0.00 39.82 4.09
1639 1817 3.445096 CCTGTAATTTTGAGCAAGAGGGG 59.555 47.826 0.00 0.00 0.00 4.79
1682 1860 2.677836 TGCTTTCTACAATGCATCCGTC 59.322 45.455 0.00 0.00 37.66 4.79
1689 1867 0.729116 CAATGCATCCGTCTGTGACC 59.271 55.000 0.00 0.00 0.00 4.02
1690 1868 0.615331 AATGCATCCGTCTGTGACCT 59.385 50.000 0.00 0.00 0.00 3.85
1693 1871 0.037326 GCATCCGTCTGTGACCTCAA 60.037 55.000 0.00 0.00 0.00 3.02
1696 1874 1.185618 TCCGTCTGTGACCTCAAGGG 61.186 60.000 0.29 0.00 40.27 3.95
1733 1911 1.961793 TGTCCAAGTCAAACGGAAGG 58.038 50.000 0.00 0.00 0.00 3.46
1784 1962 2.427410 GTCGCAAACGCCAAGCAG 60.427 61.111 0.00 0.00 39.84 4.24
1798 1976 4.558496 CGCCAAGCAGATTCAAAAGGTAAA 60.558 41.667 0.00 0.00 0.00 2.01
1818 1996 9.418045 AGGTAAATTTTGTTTATGGTGAATTCG 57.582 29.630 0.00 0.00 0.00 3.34
1826 2004 7.372451 TGTTTATGGTGAATTCGAAAGGTAG 57.628 36.000 0.00 0.00 0.00 3.18
1828 2006 7.827236 TGTTTATGGTGAATTCGAAAGGTAGAT 59.173 33.333 0.00 0.00 0.00 1.98
1841 2019 8.570096 TCGAAAGGTAGATTGAATATTGTACG 57.430 34.615 0.00 0.00 0.00 3.67
1842 2020 7.168637 TCGAAAGGTAGATTGAATATTGTACGC 59.831 37.037 0.00 0.00 0.00 4.42
1845 2023 7.715265 AGGTAGATTGAATATTGTACGCAAG 57.285 36.000 0.00 0.00 38.10 4.01
1865 2043 8.481132 CGCAAGTTTATCTAGTTTATCATTGC 57.519 34.615 0.00 0.00 35.89 3.56
1866 2044 8.338259 CGCAAGTTTATCTAGTTTATCATTGCT 58.662 33.333 0.00 0.00 36.80 3.91
1932 2400 6.694411 GCCAATCATAAAATGTTACAGCAGAG 59.306 38.462 0.00 0.00 0.00 3.35
1933 2401 7.198390 CCAATCATAAAATGTTACAGCAGAGG 58.802 38.462 0.00 0.00 0.00 3.69
1944 2412 1.696336 ACAGCAGAGGAGCTTCTTTCA 59.304 47.619 0.00 0.00 43.70 2.69
1965 2433 7.903995 TTCAAAATAAAATGAAGCCATGTCC 57.096 32.000 0.00 0.00 32.14 4.02
1971 2439 2.043953 GAAGCCATGTCCCACCCC 60.044 66.667 0.00 0.00 0.00 4.95
1979 2447 1.143684 CATGTCCCACCCCCTCAATAG 59.856 57.143 0.00 0.00 0.00 1.73
1996 2464 2.200373 TAGAAGCCCAACAAGCCTTC 57.800 50.000 0.00 0.00 0.00 3.46
2055 2523 5.468072 GTGCTTTCAGAGTTTCAGATTCTGA 59.532 40.000 12.38 12.38 43.98 3.27
2068 2536 5.367302 TCAGATTCTGAACAATGTGACACA 58.633 37.500 13.96 11.41 37.57 3.72
2082 2656 1.202521 TGACACACTGACACTCGCATT 60.203 47.619 0.00 0.00 0.00 3.56
2096 2670 6.084925 ACACTCGCATTAGTATTAGTATCGC 58.915 40.000 0.00 0.00 0.00 4.58
2113 2687 6.613233 AGTATCGCACTGTAATATAGTCAGC 58.387 40.000 0.00 0.00 35.62 4.26
2114 2688 3.885358 TCGCACTGTAATATAGTCAGCG 58.115 45.455 13.05 13.05 40.06 5.18
2116 2690 3.643763 GCACTGTAATATAGTCAGCGCT 58.356 45.455 2.64 2.64 35.33 5.92
2117 2691 4.051922 GCACTGTAATATAGTCAGCGCTT 58.948 43.478 7.50 0.00 35.33 4.68
2118 2692 4.084849 GCACTGTAATATAGTCAGCGCTTG 60.085 45.833 7.50 3.43 35.33 4.01
2119 2693 4.051922 ACTGTAATATAGTCAGCGCTTGC 58.948 43.478 7.50 2.91 39.58 4.01
2134 2710 4.533222 GCGCTTGCTTTAAAGAAGTACAA 58.467 39.130 19.48 11.33 35.07 2.41
2142 2718 8.682128 TGCTTTAAAGAAGTACAAAACTGTTG 57.318 30.769 19.48 0.00 38.88 3.33
2155 2731 5.106157 ACAAAACTGTTGGAACTGTTCTCAG 60.106 40.000 24.02 24.02 46.08 3.35
2167 2743 2.414481 CTGTTCTCAGACCGAATGCTTG 59.586 50.000 0.00 0.00 43.76 4.01
2171 2747 4.471904 TCTCAGACCGAATGCTTGTAAT 57.528 40.909 0.00 0.00 0.00 1.89
2172 2748 5.592104 TCTCAGACCGAATGCTTGTAATA 57.408 39.130 0.00 0.00 0.00 0.98
2195 2774 4.202121 ACGAACACCACCACTATATGCTAG 60.202 45.833 0.00 0.00 0.00 3.42
2201 2780 6.610020 ACACCACCACTATATGCTAGACTTAA 59.390 38.462 0.00 0.00 0.00 1.85
2213 2792 9.757227 ATATGCTAGACTTAACATTTCTCAGAC 57.243 33.333 0.00 0.00 0.00 3.51
2214 2793 6.398918 TGCTAGACTTAACATTTCTCAGACC 58.601 40.000 0.00 0.00 0.00 3.85
2217 2796 6.097915 AGACTTAACATTTCTCAGACCGAA 57.902 37.500 0.00 0.00 0.00 4.30
2218 2797 6.702329 AGACTTAACATTTCTCAGACCGAAT 58.298 36.000 0.00 0.00 0.00 3.34
2219 2798 6.591834 AGACTTAACATTTCTCAGACCGAATG 59.408 38.462 0.00 0.00 0.00 2.67
2220 2799 5.122396 ACTTAACATTTCTCAGACCGAATGC 59.878 40.000 0.00 0.00 0.00 3.56
2222 2801 3.679389 ACATTTCTCAGACCGAATGCTT 58.321 40.909 0.00 0.00 0.00 3.91
2223 2802 4.074970 ACATTTCTCAGACCGAATGCTTT 58.925 39.130 0.00 0.00 0.00 3.51
2224 2803 4.083110 ACATTTCTCAGACCGAATGCTTTG 60.083 41.667 0.00 0.00 0.00 2.77
2225 2804 3.401033 TTCTCAGACCGAATGCTTTGA 57.599 42.857 0.00 0.00 0.00 2.69
2226 2805 3.401033 TCTCAGACCGAATGCTTTGAA 57.599 42.857 0.00 0.00 0.00 2.69
2228 2807 3.498397 TCTCAGACCGAATGCTTTGAAAC 59.502 43.478 0.00 0.00 0.00 2.78
2229 2808 2.552315 TCAGACCGAATGCTTTGAAACC 59.448 45.455 0.00 0.00 0.00 3.27
2230 2809 2.554032 CAGACCGAATGCTTTGAAACCT 59.446 45.455 0.00 0.00 0.00 3.50
2231 2810 2.554032 AGACCGAATGCTTTGAAACCTG 59.446 45.455 0.00 0.00 0.00 4.00
2240 2854 5.235850 TGCTTTGAAACCTGTAGTATCCA 57.764 39.130 0.00 0.00 0.00 3.41
2242 2856 5.647658 TGCTTTGAAACCTGTAGTATCCATG 59.352 40.000 0.00 0.00 0.00 3.66
2243 2857 5.449177 GCTTTGAAACCTGTAGTATCCATGC 60.449 44.000 0.00 0.00 0.00 4.06
2244 2858 4.835284 TGAAACCTGTAGTATCCATGCA 57.165 40.909 0.00 0.00 0.00 3.96
2266 2880 4.741676 CAGCAAAACAGATTCAGTGGTTTC 59.258 41.667 0.00 0.00 32.36 2.78
2282 2896 3.003897 TGGTTTCCTTCGAACAAAATCGG 59.996 43.478 0.00 0.00 42.92 4.18
2290 2904 1.253100 GAACAAAATCGGCCCTTGGA 58.747 50.000 0.00 0.00 0.00 3.53
2307 2921 2.942804 TGGATTTCACAACTTCTGGCA 58.057 42.857 0.00 0.00 0.00 4.92
2308 2922 2.886523 TGGATTTCACAACTTCTGGCAG 59.113 45.455 8.58 8.58 0.00 4.85
2309 2923 2.887152 GGATTTCACAACTTCTGGCAGT 59.113 45.455 15.27 0.00 0.00 4.40
2310 2924 4.072131 GGATTTCACAACTTCTGGCAGTA 58.928 43.478 15.27 3.63 0.00 2.74
2312 2926 3.552132 TTCACAACTTCTGGCAGTACA 57.448 42.857 15.27 0.00 0.00 2.90
2422 3036 1.377987 GGCCCATCACAAACGGCTA 60.378 57.895 0.00 0.00 41.35 3.93
2552 3166 3.214123 CAGGTCGCCGGGATCGTA 61.214 66.667 2.18 0.00 33.95 3.43
2592 3206 3.149196 TGCTTCAGGTTTGATCAGGTTC 58.851 45.455 0.00 0.00 32.27 3.62
2633 3247 1.066908 GAGGAGAACATGAGAGCCGAG 59.933 57.143 0.00 0.00 0.00 4.63
2643 3257 4.586421 ACATGAGAGCCGAGATAAGATTGA 59.414 41.667 0.00 0.00 0.00 2.57
2645 3259 3.005261 TGAGAGCCGAGATAAGATTGAGC 59.995 47.826 0.00 0.00 0.00 4.26
2648 3262 2.961741 AGCCGAGATAAGATTGAGCTCA 59.038 45.455 13.74 13.74 0.00 4.26
2650 3264 3.491619 GCCGAGATAAGATTGAGCTCACA 60.492 47.826 18.03 8.50 0.00 3.58
2653 3267 4.496507 CGAGATAAGATTGAGCTCACACGA 60.497 45.833 18.03 1.16 0.00 4.35
2692 3306 1.104630 AGCGAGGTGTAGTTAGCCTC 58.895 55.000 0.00 0.00 43.88 4.70
2707 3321 0.038801 GCCTCTGAAACTTGCCTTGC 60.039 55.000 0.00 0.00 0.00 4.01
2708 3322 1.613836 CCTCTGAAACTTGCCTTGCT 58.386 50.000 0.00 0.00 0.00 3.91
2715 3329 2.774439 AACTTGCCTTGCTTTGTACG 57.226 45.000 0.00 0.00 0.00 3.67
2716 3330 1.675552 ACTTGCCTTGCTTTGTACGT 58.324 45.000 0.00 0.00 0.00 3.57
2717 3331 2.841215 ACTTGCCTTGCTTTGTACGTA 58.159 42.857 0.00 0.00 0.00 3.57
2718 3332 3.408634 ACTTGCCTTGCTTTGTACGTAT 58.591 40.909 0.00 0.00 0.00 3.06
2719 3333 3.188460 ACTTGCCTTGCTTTGTACGTATG 59.812 43.478 0.00 0.00 0.00 2.39
2720 3334 3.046968 TGCCTTGCTTTGTACGTATGA 57.953 42.857 0.00 0.00 0.00 2.15
2722 3336 4.760878 TGCCTTGCTTTGTACGTATGATA 58.239 39.130 0.00 0.00 0.00 2.15
2723 3337 4.569162 TGCCTTGCTTTGTACGTATGATAC 59.431 41.667 0.00 0.00 0.00 2.24
2792 3408 0.760189 ACATGGCAGTTGGTTTGGCT 60.760 50.000 0.00 0.00 41.29 4.75
2806 3425 0.532417 TTGGCTGTGCATTTTGTGGC 60.532 50.000 0.00 0.00 0.00 5.01
2835 3454 3.005472 GGTGTCAGCTCACTTGTAGTGTA 59.995 47.826 5.61 0.00 46.03 2.90
2836 3455 3.982058 GTGTCAGCTCACTTGTAGTGTAC 59.018 47.826 6.71 0.00 46.03 2.90
2845 3464 6.250104 GCTCACTTGTAGTGTACGTACATTAC 59.750 42.308 35.82 35.82 46.03 1.89
2854 3473 6.980593 AGTGTACGTACATTACAGGTTGTAA 58.019 36.000 29.58 4.33 45.63 2.41
2889 3512 0.537143 GGTGCATGGTCAAGGTGTGA 60.537 55.000 0.00 0.00 0.00 3.58
2936 3635 6.731292 AGCATCTATATTGTGGAGTGTGTA 57.269 37.500 0.00 0.00 0.00 2.90
2937 3636 6.516718 AGCATCTATATTGTGGAGTGTGTAC 58.483 40.000 0.00 0.00 0.00 2.90
2962 3661 6.647212 TTTCTGACTATTTGCACTCGTATG 57.353 37.500 0.00 0.00 0.00 2.39
2964 3663 6.445357 TCTGACTATTTGCACTCGTATGTA 57.555 37.500 0.00 0.00 0.00 2.29
2966 3665 8.161699 TCTGACTATTTGCACTCGTATGTATA 57.838 34.615 0.00 0.00 0.00 1.47
2975 3690 8.880878 TTGCACTCGTATGTATATACAAACAT 57.119 30.769 19.11 6.85 39.29 2.71
2991 3724 5.401550 ACAAACATTGCTGACAATTATCCG 58.598 37.500 0.00 0.00 44.21 4.18
3045 3807 3.270027 AGCGTATGAGCTTATTGTTGCA 58.730 40.909 0.00 0.00 46.80 4.08
3046 3808 3.879295 AGCGTATGAGCTTATTGTTGCAT 59.121 39.130 0.00 0.00 46.80 3.96
3047 3809 3.970610 GCGTATGAGCTTATTGTTGCATG 59.029 43.478 0.00 0.00 0.00 4.06
3048 3810 4.496341 GCGTATGAGCTTATTGTTGCATGT 60.496 41.667 0.00 0.00 0.00 3.21
3049 3811 4.965762 CGTATGAGCTTATTGTTGCATGTG 59.034 41.667 0.00 0.00 0.00 3.21
3050 3812 5.220643 CGTATGAGCTTATTGTTGCATGTGA 60.221 40.000 0.00 0.00 0.00 3.58
3051 3813 4.690184 TGAGCTTATTGTTGCATGTGAG 57.310 40.909 0.00 0.00 0.00 3.51
3052 3814 3.441222 TGAGCTTATTGTTGCATGTGAGG 59.559 43.478 0.00 0.00 0.00 3.86
3053 3815 3.689347 AGCTTATTGTTGCATGTGAGGA 58.311 40.909 0.00 0.00 0.00 3.71
3054 3816 4.081406 AGCTTATTGTTGCATGTGAGGAA 58.919 39.130 0.00 0.00 0.00 3.36
3055 3817 4.708421 AGCTTATTGTTGCATGTGAGGAAT 59.292 37.500 0.00 0.00 0.00 3.01
3056 3818 5.887598 AGCTTATTGTTGCATGTGAGGAATA 59.112 36.000 0.00 0.00 0.00 1.75
3057 3819 5.973565 GCTTATTGTTGCATGTGAGGAATAC 59.026 40.000 0.00 0.00 0.00 1.89
3058 3820 4.621068 ATTGTTGCATGTGAGGAATACG 57.379 40.909 0.00 0.00 0.00 3.06
3059 3821 2.355197 TGTTGCATGTGAGGAATACGG 58.645 47.619 0.00 0.00 0.00 4.02
3060 3822 2.027653 TGTTGCATGTGAGGAATACGGA 60.028 45.455 0.00 0.00 0.00 4.69
3061 3823 2.602257 TGCATGTGAGGAATACGGAG 57.398 50.000 0.00 0.00 0.00 4.63
3063 3825 2.205074 GCATGTGAGGAATACGGAGTG 58.795 52.381 0.00 0.00 45.73 3.51
3064 3826 2.826428 CATGTGAGGAATACGGAGTGG 58.174 52.381 0.00 0.00 45.73 4.00
3065 3827 1.933021 TGTGAGGAATACGGAGTGGT 58.067 50.000 0.00 0.00 45.73 4.16
3066 3828 1.548719 TGTGAGGAATACGGAGTGGTG 59.451 52.381 0.00 0.00 45.73 4.17
3067 3829 1.549170 GTGAGGAATACGGAGTGGTGT 59.451 52.381 0.00 0.00 45.73 4.16
3208 3978 4.184649 AGAAAGTTCCACCACCTTTCAT 57.815 40.909 12.33 0.00 44.06 2.57
3209 3979 4.145052 AGAAAGTTCCACCACCTTTCATC 58.855 43.478 12.33 0.00 44.06 2.92
3210 3980 2.586648 AGTTCCACCACCTTTCATCC 57.413 50.000 0.00 0.00 0.00 3.51
3211 3981 1.780309 AGTTCCACCACCTTTCATCCA 59.220 47.619 0.00 0.00 0.00 3.41
3364 4142 5.185056 CACATAACCCCTTTCTTTAACCCTG 59.815 44.000 0.00 0.00 0.00 4.45
3382 4163 1.377333 GCACTTGGGGGCACTACTC 60.377 63.158 0.00 0.00 0.00 2.59
3455 4236 2.421739 GCGGCATCCTCGGTATGT 59.578 61.111 0.00 0.00 0.00 2.29
3531 4313 3.393970 CTCTTCGGGGCAGCCAGA 61.394 66.667 15.19 9.42 0.00 3.86
3542 4324 1.300971 GCAGCCAGATCAGCGAACAA 61.301 55.000 0.00 0.00 34.64 2.83
3554 4336 0.674895 GCGAACAAGAGCCCATGTCT 60.675 55.000 0.00 0.00 0.00 3.41
3562 4344 1.701847 AGAGCCCATGTCTTTGACACT 59.298 47.619 2.31 0.00 45.65 3.55
3563 4345 1.808945 GAGCCCATGTCTTTGACACTG 59.191 52.381 2.31 3.61 45.65 3.66
3564 4346 0.242017 GCCCATGTCTTTGACACTGC 59.758 55.000 2.31 3.00 45.65 4.40
3566 4348 1.955778 CCCATGTCTTTGACACTGCAA 59.044 47.619 2.31 0.00 45.65 4.08
3567 4349 2.287788 CCCATGTCTTTGACACTGCAAC 60.288 50.000 2.31 0.00 45.65 4.17
3570 4352 1.064758 TGTCTTTGACACTGCAACCCT 60.065 47.619 0.00 0.00 37.67 4.34
3589 4371 1.135915 CTAGAGGAGCGCTTGTGTGAT 59.864 52.381 13.26 0.00 0.00 3.06
3630 4412 1.459592 CGAAGTCCACAAAGCTAACGG 59.540 52.381 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.547532 ACAGAAGACACACGAGACATAAC 58.452 43.478 0.00 0.00 0.00 1.89
28 29 8.119226 CCGAAAGAAATGAGCTATTTACAGAAG 58.881 37.037 0.00 0.00 39.06 2.85
43 44 9.937175 GGAATTATAAGAGAACCGAAAGAAATG 57.063 33.333 0.00 0.00 0.00 2.32
70 71 2.264813 GTAAAACGCGAGGCATGACTA 58.735 47.619 15.93 0.00 0.00 2.59
84 85 9.974750 GAGAATCTAAATACAGCAGTGTAAAAC 57.025 33.333 0.00 0.00 42.54 2.43
106 107 7.652105 GCATGATACGGTCAGTTAATAAGAGAA 59.348 37.037 0.00 0.00 40.92 2.87
227 231 0.533491 TCCGTGCCAATTACGTAGCT 59.467 50.000 6.17 0.00 39.76 3.32
229 233 2.286833 CCATTCCGTGCCAATTACGTAG 59.713 50.000 0.00 0.00 39.76 3.51
234 238 1.203523 GTTGCCATTCCGTGCCAATTA 59.796 47.619 0.00 0.00 0.00 1.40
238 242 0.250945 TTAGTTGCCATTCCGTGCCA 60.251 50.000 0.00 0.00 0.00 4.92
240 244 0.179200 CGTTAGTTGCCATTCCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
241 245 1.393539 CTCGTTAGTTGCCATTCCGTG 59.606 52.381 0.00 0.00 0.00 4.94
243 247 1.006832 CCTCGTTAGTTGCCATTCCG 58.993 55.000 0.00 0.00 0.00 4.30
244 248 0.733150 GCCTCGTTAGTTGCCATTCC 59.267 55.000 0.00 0.00 0.00 3.01
245 249 0.373716 CGCCTCGTTAGTTGCCATTC 59.626 55.000 0.00 0.00 0.00 2.67
246 250 1.644786 GCGCCTCGTTAGTTGCCATT 61.645 55.000 0.00 0.00 0.00 3.16
247 251 2.106683 GCGCCTCGTTAGTTGCCAT 61.107 57.895 0.00 0.00 0.00 4.40
263 267 3.249917 ACCAACTTTTGACAAAACTGCG 58.750 40.909 9.30 3.04 0.00 5.18
292 296 5.986135 TGAGTCAAGCTTAGAGAGTTCAAAC 59.014 40.000 0.00 0.00 0.00 2.93
315 322 4.496341 GCATTGTAATGTGGATCGTCCTTG 60.496 45.833 6.48 0.00 38.65 3.61
356 363 0.677098 ACAGAAGCAGCAGCAGGATG 60.677 55.000 3.17 0.00 45.49 3.51
361 368 1.601759 GGGAACAGAAGCAGCAGCA 60.602 57.895 3.17 0.00 45.49 4.41
420 427 8.095792 CAGGATTCATGTTAGATCAATAGAGCT 58.904 37.037 0.00 0.00 44.06 4.09
425 432 7.072328 TGGACCAGGATTCATGTTAGATCAATA 59.928 37.037 0.00 0.00 0.00 1.90
427 434 5.191522 TGGACCAGGATTCATGTTAGATCAA 59.808 40.000 0.00 0.00 0.00 2.57
428 435 4.721274 TGGACCAGGATTCATGTTAGATCA 59.279 41.667 0.00 0.00 0.00 2.92
442 468 1.635487 CCCTTCAAGAATGGACCAGGA 59.365 52.381 0.00 0.00 0.00 3.86
477 503 4.038271 TGCTCCAAGAGGATGAACAATT 57.962 40.909 0.00 0.00 44.70 2.32
527 553 3.818787 GGCAGCAGCATTGGTCCG 61.819 66.667 2.65 0.00 44.61 4.79
540 566 1.973281 AACACAAGGATGCGGGCAG 60.973 57.895 0.00 0.00 0.00 4.85
601 627 7.389053 GGCTTCTTCTACTCAAATCAAAGAGAA 59.611 37.037 0.00 0.00 35.83 2.87
602 628 6.876257 GGCTTCTTCTACTCAAATCAAAGAGA 59.124 38.462 0.00 0.00 35.83 3.10
608 634 4.537135 ACGGCTTCTTCTACTCAAATCA 57.463 40.909 0.00 0.00 0.00 2.57
609 635 4.691216 ACAACGGCTTCTTCTACTCAAATC 59.309 41.667 0.00 0.00 0.00 2.17
610 636 4.642429 ACAACGGCTTCTTCTACTCAAAT 58.358 39.130 0.00 0.00 0.00 2.32
611 637 4.056050 GACAACGGCTTCTTCTACTCAAA 58.944 43.478 0.00 0.00 0.00 2.69
612 638 3.650139 GACAACGGCTTCTTCTACTCAA 58.350 45.455 0.00 0.00 0.00 3.02
613 639 2.351447 CGACAACGGCTTCTTCTACTCA 60.351 50.000 0.00 0.00 35.72 3.41
729 758 2.365237 GTAGCCGGACCTCCCCTT 60.365 66.667 5.05 0.00 0.00 3.95
817 852 2.919328 GGTGGCTTTGGCTTGGCT 60.919 61.111 0.00 0.00 38.73 4.75
891 926 1.440938 TTGTGCTCGTTGTTTCGGGG 61.441 55.000 0.00 0.00 0.00 5.73
892 927 0.378962 TTTGTGCTCGTTGTTTCGGG 59.621 50.000 0.00 0.00 0.00 5.14
893 928 1.063469 AGTTTGTGCTCGTTGTTTCGG 59.937 47.619 0.00 0.00 0.00 4.30
895 930 2.716398 GGAGTTTGTGCTCGTTGTTTC 58.284 47.619 0.00 0.00 36.41 2.78
896 931 1.063469 CGGAGTTTGTGCTCGTTGTTT 59.937 47.619 0.00 0.00 36.41 2.83
897 932 0.655733 CGGAGTTTGTGCTCGTTGTT 59.344 50.000 0.00 0.00 36.41 2.83
898 933 0.461339 ACGGAGTTTGTGCTCGTTGT 60.461 50.000 0.00 0.00 37.78 3.32
899 934 0.042188 CACGGAGTTTGTGCTCGTTG 60.042 55.000 0.00 0.00 41.61 4.10
900 935 1.157870 CCACGGAGTTTGTGCTCGTT 61.158 55.000 0.00 0.00 41.61 3.85
901 936 1.594293 CCACGGAGTTTGTGCTCGT 60.594 57.895 0.00 0.00 41.61 4.18
902 937 2.954753 GCCACGGAGTTTGTGCTCG 61.955 63.158 0.00 0.00 41.61 5.03
903 938 2.617274 GGCCACGGAGTTTGTGCTC 61.617 63.158 0.00 0.00 41.61 4.26
904 939 2.594592 GGCCACGGAGTTTGTGCT 60.595 61.111 0.00 0.00 41.61 4.40
905 940 4.025401 CGGCCACGGAGTTTGTGC 62.025 66.667 2.24 0.00 41.61 4.57
906 941 4.025401 GCGGCCACGGAGTTTGTG 62.025 66.667 2.24 0.00 41.61 3.33
909 944 3.518419 TTACGCGGCCACGGAGTTT 62.518 57.895 18.84 0.00 41.61 2.66
932 967 1.741770 CGAGTGGCGAAAGGAAGGG 60.742 63.158 0.00 0.00 44.57 3.95
935 970 1.223187 GAAACGAGTGGCGAAAGGAA 58.777 50.000 0.00 0.00 44.57 3.36
974 1083 1.446966 GACGCAGACCTGAAGAGCC 60.447 63.158 0.47 0.00 0.00 4.70
1027 1155 1.089481 GCGGCAACTGATCGATGGAA 61.089 55.000 0.54 0.00 0.00 3.53
1045 1173 2.897350 GGCCGGCATGTCTGTAGC 60.897 66.667 30.85 1.84 0.00 3.58
1048 1176 4.760047 GACGGCCGGCATGTCTGT 62.760 66.667 32.14 19.58 0.00 3.41
1137 1268 3.206964 GGCTCTTGCTATTACCTTGGAC 58.793 50.000 0.00 0.00 39.59 4.02
1147 1278 1.821332 GCGCCTTGGCTCTTGCTAT 60.821 57.895 10.12 0.00 39.59 2.97
1167 1298 1.215655 CTTTCGCCTTCCTATCGCCG 61.216 60.000 0.00 0.00 0.00 6.46
1170 1301 1.202417 TCTGCTTTCGCCTTCCTATCG 60.202 52.381 0.00 0.00 34.43 2.92
1171 1308 2.478831 CTCTGCTTTCGCCTTCCTATC 58.521 52.381 0.00 0.00 34.43 2.08
1172 1309 1.139853 CCTCTGCTTTCGCCTTCCTAT 59.860 52.381 0.00 0.00 34.43 2.57
1175 1312 1.021920 GTCCTCTGCTTTCGCCTTCC 61.022 60.000 0.00 0.00 34.43 3.46
1176 1313 1.355066 CGTCCTCTGCTTTCGCCTTC 61.355 60.000 0.00 0.00 34.43 3.46
1194 1331 4.207281 TGCCGCTTCTCCCGATCG 62.207 66.667 8.51 8.51 0.00 3.69
1343 1480 0.249398 CTAGGGAACAGTGGGAACGG 59.751 60.000 0.00 0.00 0.00 4.44
1348 1485 1.196012 GGACTCTAGGGAACAGTGGG 58.804 60.000 0.00 0.00 0.00 4.61
1400 1538 7.388224 TGCTTGTGATAACCGACAAAGTATTAA 59.612 33.333 0.00 0.00 31.83 1.40
1403 1541 5.242434 TGCTTGTGATAACCGACAAAGTAT 58.758 37.500 0.00 0.00 31.83 2.12
1404 1542 4.633175 TGCTTGTGATAACCGACAAAGTA 58.367 39.130 0.00 0.00 31.83 2.24
1405 1543 3.472652 TGCTTGTGATAACCGACAAAGT 58.527 40.909 0.00 0.00 31.83 2.66
1406 1544 4.083324 ACATGCTTGTGATAACCGACAAAG 60.083 41.667 4.14 0.00 33.85 2.77
1471 1616 6.493189 TGGTACCATGCATCAGAACTTATA 57.507 37.500 11.60 0.00 0.00 0.98
1472 1617 5.372343 TGGTACCATGCATCAGAACTTAT 57.628 39.130 11.60 0.00 0.00 1.73
1473 1618 4.835284 TGGTACCATGCATCAGAACTTA 57.165 40.909 11.60 0.00 0.00 2.24
1475 1620 3.200605 TGATGGTACCATGCATCAGAACT 59.799 43.478 32.07 3.75 36.70 3.01
1476 1621 3.313526 GTGATGGTACCATGCATCAGAAC 59.686 47.826 32.07 14.08 36.70 3.01
1557 1735 2.484264 GCTCAAACAGCTTACGGTCATT 59.516 45.455 0.00 0.00 45.83 2.57
1639 1817 4.443978 TCAATCATCTCCCTGAATTCCC 57.556 45.455 2.27 0.00 0.00 3.97
1643 1821 4.726035 AGCATCAATCATCTCCCTGAAT 57.274 40.909 0.00 0.00 0.00 2.57
1682 1860 0.397941 TCTTGCCCTTGAGGTCACAG 59.602 55.000 0.00 0.00 38.26 3.66
1689 1867 4.335416 TGGTTTATCTTCTTGCCCTTGAG 58.665 43.478 0.00 0.00 0.00 3.02
1690 1868 4.202567 ACTGGTTTATCTTCTTGCCCTTGA 60.203 41.667 0.00 0.00 0.00 3.02
1693 1871 4.082125 CAACTGGTTTATCTTCTTGCCCT 58.918 43.478 0.00 0.00 0.00 5.19
1696 1874 4.518970 TGGACAACTGGTTTATCTTCTTGC 59.481 41.667 0.00 0.00 0.00 4.01
1798 1976 8.147704 ACCTTTCGAATTCACCATAAACAAAAT 58.852 29.630 6.22 0.00 0.00 1.82
1818 1996 8.138365 TGCGTACAATATTCAATCTACCTTTC 57.862 34.615 0.00 0.00 0.00 2.62
1821 1999 7.272978 ACTTGCGTACAATATTCAATCTACCT 58.727 34.615 0.00 0.00 34.61 3.08
1884 2062 7.453126 TGGCTGGAGGAATGAAAAAGTAAATTA 59.547 33.333 0.00 0.00 0.00 1.40
1886 2064 5.779771 TGGCTGGAGGAATGAAAAAGTAAAT 59.220 36.000 0.00 0.00 0.00 1.40
1888 2066 4.735369 TGGCTGGAGGAATGAAAAAGTAA 58.265 39.130 0.00 0.00 0.00 2.24
1890 2068 3.243359 TGGCTGGAGGAATGAAAAAGT 57.757 42.857 0.00 0.00 0.00 2.66
1891 2069 4.221262 TGATTGGCTGGAGGAATGAAAAAG 59.779 41.667 0.00 0.00 0.00 2.27
1892 2070 4.158786 TGATTGGCTGGAGGAATGAAAAA 58.841 39.130 0.00 0.00 0.00 1.94
1907 2085 6.563422 TCTGCTGTAACATTTTATGATTGGC 58.437 36.000 0.00 0.00 0.00 4.52
1944 2412 6.172630 GTGGGACATGGCTTCATTTTATTTT 58.827 36.000 0.00 0.00 44.52 1.82
1965 2433 0.183731 GGCTTCTATTGAGGGGGTGG 59.816 60.000 0.00 0.00 0.00 4.61
1971 2439 2.424956 GCTTGTTGGGCTTCTATTGAGG 59.575 50.000 0.00 0.00 0.00 3.86
1996 2464 3.119388 CCATATGGCCCATAGCAAATTCG 60.119 47.826 9.29 0.00 46.50 3.34
2021 2489 5.483685 ACTCTGAAAGCACACAAGGTATA 57.516 39.130 0.00 0.00 0.00 1.47
2055 2523 3.609853 AGTGTCAGTGTGTCACATTGTT 58.390 40.909 23.19 9.10 38.55 2.83
2068 2536 6.452494 ACTAATACTAATGCGAGTGTCAGT 57.548 37.500 0.00 0.00 0.00 3.41
2096 2670 4.084849 GCAAGCGCTGACTATATTACAGTG 60.085 45.833 12.58 0.19 42.60 3.66
2112 2686 4.141855 TGTACTTCTTTAAAGCAAGCGC 57.858 40.909 19.03 0.00 38.99 5.92
2113 2687 6.691388 AGTTTTGTACTTCTTTAAAGCAAGCG 59.309 34.615 19.03 7.14 31.29 4.68
2114 2688 7.488150 ACAGTTTTGTACTTCTTTAAAGCAAGC 59.512 33.333 19.03 11.07 35.25 4.01
2116 2690 9.134734 CAACAGTTTTGTACTTCTTTAAAGCAA 57.865 29.630 10.51 5.81 36.23 3.91
2117 2691 7.757624 CCAACAGTTTTGTACTTCTTTAAAGCA 59.242 33.333 10.51 0.00 36.23 3.91
2118 2692 7.971722 TCCAACAGTTTTGTACTTCTTTAAAGC 59.028 33.333 10.51 0.00 36.23 3.51
2119 2693 9.849166 TTCCAACAGTTTTGTACTTCTTTAAAG 57.151 29.630 9.04 9.04 36.23 1.85
2120 2694 9.628746 GTTCCAACAGTTTTGTACTTCTTTAAA 57.371 29.630 0.00 0.00 36.23 1.52
2121 2695 9.016438 AGTTCCAACAGTTTTGTACTTCTTTAA 57.984 29.630 0.00 0.00 36.23 1.52
2123 2697 7.039993 ACAGTTCCAACAGTTTTGTACTTCTTT 60.040 33.333 0.00 0.00 36.23 2.52
2124 2698 6.433093 ACAGTTCCAACAGTTTTGTACTTCTT 59.567 34.615 0.00 0.00 36.23 2.52
2134 2710 4.636206 GTCTGAGAACAGTTCCAACAGTTT 59.364 41.667 21.52 1.34 43.81 2.66
2142 2718 2.814280 TTCGGTCTGAGAACAGTTCC 57.186 50.000 9.85 2.55 43.81 3.62
2155 2731 4.327898 TGTTCGTATTACAAGCATTCGGTC 59.672 41.667 0.00 0.00 0.00 4.79
2167 2743 6.145048 GCATATAGTGGTGGTGTTCGTATTAC 59.855 42.308 0.00 0.00 0.00 1.89
2171 2747 3.702548 AGCATATAGTGGTGGTGTTCGTA 59.297 43.478 0.00 0.00 37.12 3.43
2172 2748 2.500098 AGCATATAGTGGTGGTGTTCGT 59.500 45.455 0.00 0.00 37.12 3.85
2195 2774 6.673316 GCATTCGGTCTGAGAAATGTTAAGTC 60.673 42.308 7.08 0.00 0.00 3.01
2201 2780 3.340814 AGCATTCGGTCTGAGAAATGT 57.659 42.857 7.08 0.00 0.00 2.71
2209 2788 2.554032 AGGTTTCAAAGCATTCGGTCTG 59.446 45.455 1.44 0.00 0.00 3.51
2210 2789 2.554032 CAGGTTTCAAAGCATTCGGTCT 59.446 45.455 1.44 0.00 0.00 3.85
2211 2790 2.293399 ACAGGTTTCAAAGCATTCGGTC 59.707 45.455 1.44 0.00 0.00 4.79
2212 2791 2.306847 ACAGGTTTCAAAGCATTCGGT 58.693 42.857 1.44 0.00 0.00 4.69
2213 2792 3.502211 ACTACAGGTTTCAAAGCATTCGG 59.498 43.478 1.44 0.00 0.00 4.30
2214 2793 4.749245 ACTACAGGTTTCAAAGCATTCG 57.251 40.909 1.44 0.00 0.00 3.34
2217 2796 5.815581 TGGATACTACAGGTTTCAAAGCAT 58.184 37.500 1.44 0.00 37.61 3.79
2218 2797 5.235850 TGGATACTACAGGTTTCAAAGCA 57.764 39.130 1.44 0.00 37.61 3.91
2219 2798 5.449177 GCATGGATACTACAGGTTTCAAAGC 60.449 44.000 0.00 0.00 37.61 3.51
2220 2799 5.647658 TGCATGGATACTACAGGTTTCAAAG 59.352 40.000 0.00 0.00 37.61 2.77
2222 2801 5.172687 TGCATGGATACTACAGGTTTCAA 57.827 39.130 0.00 0.00 37.61 2.69
2223 2802 4.769688 CTGCATGGATACTACAGGTTTCA 58.230 43.478 0.00 0.00 37.61 2.69
2224 2803 3.561725 GCTGCATGGATACTACAGGTTTC 59.438 47.826 0.00 0.00 33.75 2.78
2225 2804 3.054434 TGCTGCATGGATACTACAGGTTT 60.054 43.478 0.00 0.00 33.75 3.27
2226 2805 2.505407 TGCTGCATGGATACTACAGGTT 59.495 45.455 0.00 0.00 33.75 3.50
2228 2807 2.916702 TGCTGCATGGATACTACAGG 57.083 50.000 0.00 0.00 33.75 4.00
2229 2808 4.395854 TGTTTTGCTGCATGGATACTACAG 59.604 41.667 1.84 0.00 35.46 2.74
2230 2809 4.331108 TGTTTTGCTGCATGGATACTACA 58.669 39.130 1.84 0.00 37.61 2.74
2231 2810 4.635765 TCTGTTTTGCTGCATGGATACTAC 59.364 41.667 1.84 0.00 37.61 2.73
2240 2854 3.305813 CCACTGAATCTGTTTTGCTGCAT 60.306 43.478 1.84 0.00 0.00 3.96
2242 2856 2.035066 ACCACTGAATCTGTTTTGCTGC 59.965 45.455 0.00 0.00 0.00 5.25
2243 2857 3.996150 ACCACTGAATCTGTTTTGCTG 57.004 42.857 0.00 0.00 0.00 4.41
2244 2858 4.202151 GGAAACCACTGAATCTGTTTTGCT 60.202 41.667 0.00 0.00 31.51 3.91
2266 2880 0.170339 GGGCCGATTTTGTTCGAAGG 59.830 55.000 0.00 0.00 41.62 3.46
2282 2896 2.893489 AGAAGTTGTGAAATCCAAGGGC 59.107 45.455 0.00 0.00 0.00 5.19
2290 2904 4.460263 TGTACTGCCAGAAGTTGTGAAAT 58.540 39.130 0.00 0.00 0.00 2.17
2592 3206 4.809496 ATCCTTGGGCTGGCTGCG 62.809 66.667 10.35 0.00 44.05 5.18
2608 3222 1.411977 CTCTCATGTTCTCCTCGGCAT 59.588 52.381 0.00 0.00 0.00 4.40
2633 3247 5.750547 TGAATCGTGTGAGCTCAATCTTATC 59.249 40.000 20.19 13.52 0.00 1.75
2643 3257 1.550327 TCCTCTGAATCGTGTGAGCT 58.450 50.000 0.00 0.00 0.00 4.09
2645 3259 4.111198 CTGAATCCTCTGAATCGTGTGAG 58.889 47.826 0.00 0.00 0.00 3.51
2648 3262 4.019858 TCTCTGAATCCTCTGAATCGTGT 58.980 43.478 0.00 0.00 0.00 4.49
2650 3264 4.892345 TGATCTCTGAATCCTCTGAATCGT 59.108 41.667 0.00 0.00 0.00 3.73
2653 3267 4.262121 CGCTGATCTCTGAATCCTCTGAAT 60.262 45.833 0.00 0.00 0.00 2.57
2692 3306 3.169355 ACAAAGCAAGGCAAGTTTCAG 57.831 42.857 0.00 0.00 0.00 3.02
2722 3336 7.438459 GCACACCTATACAAGATAAAGAATCGT 59.562 37.037 0.00 0.00 39.79 3.73
2723 3337 7.653713 AGCACACCTATACAAGATAAAGAATCG 59.346 37.037 0.00 0.00 39.79 3.34
2724 3338 8.894768 AGCACACCTATACAAGATAAAGAATC 57.105 34.615 0.00 0.00 34.52 2.52
2725 3339 8.486210 TGAGCACACCTATACAAGATAAAGAAT 58.514 33.333 0.00 0.00 0.00 2.40
2726 3340 7.847096 TGAGCACACCTATACAAGATAAAGAA 58.153 34.615 0.00 0.00 0.00 2.52
2727 3341 7.418337 TGAGCACACCTATACAAGATAAAGA 57.582 36.000 0.00 0.00 0.00 2.52
2728 3342 8.147058 AGATGAGCACACCTATACAAGATAAAG 58.853 37.037 0.00 0.00 0.00 1.85
2729 3343 8.023021 AGATGAGCACACCTATACAAGATAAA 57.977 34.615 0.00 0.00 0.00 1.40
2730 3344 7.603180 AGATGAGCACACCTATACAAGATAA 57.397 36.000 0.00 0.00 0.00 1.75
2731 3345 7.069950 ACAAGATGAGCACACCTATACAAGATA 59.930 37.037 0.00 0.00 0.00 1.98
2732 3346 6.126940 ACAAGATGAGCACACCTATACAAGAT 60.127 38.462 0.00 0.00 0.00 2.40
2733 3347 5.187772 ACAAGATGAGCACACCTATACAAGA 59.812 40.000 0.00 0.00 0.00 3.02
2734 3348 5.292834 CACAAGATGAGCACACCTATACAAG 59.707 44.000 0.00 0.00 0.00 3.16
2735 3349 5.178061 CACAAGATGAGCACACCTATACAA 58.822 41.667 0.00 0.00 0.00 2.41
2736 3350 4.222810 ACACAAGATGAGCACACCTATACA 59.777 41.667 0.00 0.00 0.00 2.29
2737 3351 4.759782 ACACAAGATGAGCACACCTATAC 58.240 43.478 0.00 0.00 0.00 1.47
2738 3352 5.420725 AACACAAGATGAGCACACCTATA 57.579 39.130 0.00 0.00 0.00 1.31
2792 3408 0.248825 GTCACGCCACAAAATGCACA 60.249 50.000 0.00 0.00 0.00 4.57
2854 3473 2.503356 TGCACCCTGTTTCACCATTTTT 59.497 40.909 0.00 0.00 0.00 1.94
2889 3512 8.445493 GCTTTACATGCAATTAAGAAAGCAAAT 58.555 29.630 18.78 0.00 44.15 2.32
2920 3543 7.387948 GTCAGAAAAGTACACACTCCACAATAT 59.612 37.037 0.00 0.00 32.29 1.28
2936 3635 5.057149 ACGAGTGCAAATAGTCAGAAAAGT 58.943 37.500 0.00 0.00 0.00 2.66
2937 3636 5.597813 ACGAGTGCAAATAGTCAGAAAAG 57.402 39.130 0.00 0.00 0.00 2.27
2966 3665 7.148086 ACGGATAATTGTCAGCAATGTTTGTAT 60.148 33.333 4.48 0.00 43.89 2.29
2975 3690 5.697473 TGAAAACGGATAATTGTCAGCAA 57.303 34.783 4.48 0.00 39.16 3.91
2991 3724 6.310467 GGAGTCAAAAGAACAACCTTGAAAAC 59.690 38.462 0.00 0.00 30.03 2.43
3045 3807 2.168521 CACCACTCCGTATTCCTCACAT 59.831 50.000 0.00 0.00 0.00 3.21
3046 3808 1.548719 CACCACTCCGTATTCCTCACA 59.451 52.381 0.00 0.00 0.00 3.58
3047 3809 1.549170 ACACCACTCCGTATTCCTCAC 59.451 52.381 0.00 0.00 0.00 3.51
3048 3810 1.548719 CACACCACTCCGTATTCCTCA 59.451 52.381 0.00 0.00 0.00 3.86
3049 3811 1.549170 ACACACCACTCCGTATTCCTC 59.451 52.381 0.00 0.00 0.00 3.71
3050 3812 1.549170 GACACACCACTCCGTATTCCT 59.451 52.381 0.00 0.00 0.00 3.36
3051 3813 1.734707 CGACACACCACTCCGTATTCC 60.735 57.143 0.00 0.00 0.00 3.01
3052 3814 1.200716 TCGACACACCACTCCGTATTC 59.799 52.381 0.00 0.00 0.00 1.75
3053 3815 1.068055 GTCGACACACCACTCCGTATT 60.068 52.381 11.55 0.00 0.00 1.89
3054 3816 0.524862 GTCGACACACCACTCCGTAT 59.475 55.000 11.55 0.00 0.00 3.06
3055 3817 0.818852 TGTCGACACACCACTCCGTA 60.819 55.000 15.76 0.00 0.00 4.02
3056 3818 1.461091 ATGTCGACACACCACTCCGT 61.461 55.000 22.71 0.00 34.48 4.69
3057 3819 1.008875 CATGTCGACACACCACTCCG 61.009 60.000 22.71 0.00 34.48 4.63
3058 3820 0.670546 CCATGTCGACACACCACTCC 60.671 60.000 22.71 0.00 34.48 3.85
3059 3821 1.291877 GCCATGTCGACACACCACTC 61.292 60.000 22.71 2.33 34.48 3.51
3060 3822 1.301716 GCCATGTCGACACACCACT 60.302 57.895 22.71 0.00 34.48 4.00
3061 3823 1.163420 TTGCCATGTCGACACACCAC 61.163 55.000 22.71 9.52 34.48 4.16
3062 3824 1.147153 TTGCCATGTCGACACACCA 59.853 52.632 22.71 14.58 34.48 4.17
3063 3825 1.574428 GTTGCCATGTCGACACACC 59.426 57.895 22.71 12.03 34.48 4.16
3064 3826 1.204062 CGTTGCCATGTCGACACAC 59.796 57.895 22.71 13.62 34.48 3.82
3065 3827 0.320334 ATCGTTGCCATGTCGACACA 60.320 50.000 22.71 12.07 36.46 3.72
3066 3828 0.095245 CATCGTTGCCATGTCGACAC 59.905 55.000 22.71 9.19 36.46 3.67
3067 3829 1.634757 GCATCGTTGCCATGTCGACA 61.635 55.000 22.48 22.48 43.38 4.35
3152 3922 1.068541 GCTTGTTTGTTTAGGGGCTCG 60.069 52.381 0.00 0.00 0.00 5.03
3208 3978 3.657398 ACAGCTTGATGAATGGATGGA 57.343 42.857 0.00 0.00 0.00 3.41
3209 3979 3.446161 ACAACAGCTTGATGAATGGATGG 59.554 43.478 0.00 0.00 0.00 3.51
3210 3980 4.713824 ACAACAGCTTGATGAATGGATG 57.286 40.909 0.00 0.00 0.00 3.51
3211 3981 6.839124 TTAACAACAGCTTGATGAATGGAT 57.161 33.333 0.00 0.00 0.00 3.41
3364 4142 1.377333 GAGTAGTGCCCCCAAGTGC 60.377 63.158 0.00 0.00 0.00 4.40
3531 4313 0.254178 ATGGGCTCTTGTTCGCTGAT 59.746 50.000 0.00 0.00 0.00 2.90
3537 4319 3.057946 GTCAAAGACATGGGCTCTTGTTC 60.058 47.826 6.56 0.83 32.36 3.18
3542 4324 1.701847 AGTGTCAAAGACATGGGCTCT 59.298 47.619 2.90 0.00 44.63 4.09
3554 4336 2.224523 CCTCTAGGGTTGCAGTGTCAAA 60.225 50.000 2.22 0.00 0.00 2.69
3562 4344 3.019003 GCGCTCCTCTAGGGTTGCA 62.019 63.158 0.00 0.00 40.25 4.08
3563 4345 2.202946 GCGCTCCTCTAGGGTTGC 60.203 66.667 0.00 0.00 40.25 4.17
3564 4346 0.460987 CAAGCGCTCCTCTAGGGTTG 60.461 60.000 12.06 0.00 40.25 3.77
3566 4348 1.305381 ACAAGCGCTCCTCTAGGGT 60.305 57.895 12.06 0.00 40.25 4.34
3567 4349 1.142748 CACAAGCGCTCCTCTAGGG 59.857 63.158 12.06 0.00 41.05 3.53
3570 4352 1.135139 GATCACACAAGCGCTCCTCTA 59.865 52.381 12.06 0.00 0.00 2.43
3610 4392 1.459592 CCGTTAGCTTTGTGGACTTCG 59.540 52.381 0.00 0.00 0.00 3.79
3630 4412 7.008901 GCCTCATTAACGCTAATTAAACAAACC 59.991 37.037 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.