Multiple sequence alignment - TraesCS1A01G273900

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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 TraesCS1A01G273900 chr1A 100.000 3892 0 0 1 3892 467260927 467257036 0.000000e+00 7188.0
1 TraesCS1A01G273900 chr1A 84.141 227 15 13 355 572 468593267 468593053 2.370000e-47 200.0
2 TraesCS1A01G273900 chr1D 87.743 2366 162 59 142 2421 368323412 368321089 0.000000e+00 2645.0
3 TraesCS1A01G273900 chr1D 84.522 1486 147 47 1000 2413 369903966 369902492 0.000000e+00 1393.0
4 TraesCS1A01G273900 chr1D 94.522 785 43 0 3108 3892 368320047 368319263 0.000000e+00 1212.0
5 TraesCS1A01G273900 chr1D 90.816 392 19 3 2712 3086 368320652 368320261 3.470000e-140 508.0
6 TraesCS1A01G273900 chr1D 83.425 543 27 23 437 959 369904538 369904039 2.760000e-121 446.0
7 TraesCS1A01G273900 chr1D 88.796 357 31 5 48 395 369904900 369904544 2.780000e-116 429.0
8 TraesCS1A01G273900 chr1D 91.815 281 21 2 1 279 368332822 368332542 1.310000e-104 390.0
9 TraesCS1A01G273900 chr1D 85.757 337 29 5 2712 3029 369899721 369899385 4.820000e-89 339.0
10 TraesCS1A01G273900 chr1D 86.061 330 18 13 2415 2716 368321053 368320724 2.900000e-86 329.0
11 TraesCS1A01G273900 chr1D 94.891 137 7 0 2583 2719 369899926 369899790 8.470000e-52 215.0
12 TraesCS1A01G273900 chr1D 86.131 137 14 5 2435 2566 369902427 369902291 4.050000e-30 143.0
13 TraesCS1A01G273900 chr1D 96.386 83 1 1 3028 3110 369899303 369899223 6.780000e-28 135.0
14 TraesCS1A01G273900 chr1D 87.778 90 10 1 48 137 368325498 368325410 1.910000e-18 104.0
15 TraesCS1A01G273900 chr1B 85.079 1461 132 35 1000 2408 492358033 492356607 0.000000e+00 1411.0
16 TraesCS1A01G273900 chr1B 93.152 774 50 1 3122 3892 492335840 492335067 0.000000e+00 1133.0
17 TraesCS1A01G273900 chr1B 86.382 984 74 27 54 1002 492359028 492358070 0.000000e+00 1020.0
18 TraesCS1A01G273900 chr1B 90.263 380 23 9 2712 3086 492356153 492355783 5.850000e-133 484.0
19 TraesCS1A01G273900 chr1B 83.654 312 21 14 2435 2716 492356536 492356225 2.310000e-67 267.0
20 TraesCS1A01G273900 chr1B 100.000 28 0 0 3083 3110 492355650 492355623 7.000000e-03 52.8
21 TraesCS1A01G273900 chr3A 93.119 218 15 0 996 1213 627275630 627275847 1.740000e-83 320.0
22 TraesCS1A01G273900 chr3A 83.256 215 31 1 999 1213 107618000 107617791 3.970000e-45 193.0
23 TraesCS1A01G273900 chr3A 91.667 96 8 0 2432 2527 627277292 627277387 2.440000e-27 134.0
24 TraesCS1A01G273900 chr3A 95.062 81 4 0 1290 1370 627275942 627276022 1.140000e-25 128.0
25 TraesCS1A01G273900 chr3A 87.143 70 9 0 1527 1596 627276288 627276357 3.220000e-11 80.5
26 TraesCS1A01G273900 chr3D 92.308 221 16 1 994 1213 484345579 484345799 2.920000e-81 313.0
27 TraesCS1A01G273900 chr3D 91.667 96 8 0 2432 2527 484347293 484347388 2.440000e-27 134.0
28 TraesCS1A01G273900 chr3D 93.827 81 5 0 1290 1370 484345906 484345986 5.280000e-24 122.0
29 TraesCS1A01G273900 chr3D 88.571 70 8 0 1527 1596 484346249 484346318 6.930000e-13 86.1
30 TraesCS1A01G273900 chr3D 100.000 33 0 0 3053 3085 67062388 67062420 1.170000e-05 62.1
31 TraesCS1A01G273900 chr3B 91.441 222 18 1 993 1213 647177881 647178102 1.760000e-78 303.0
32 TraesCS1A01G273900 chr3B 93.182 88 5 1 1290 1377 647178235 647178321 1.140000e-25 128.0
33 TraesCS1A01G273900 chr3B 88.571 70 8 0 1527 1596 647178615 647178684 6.930000e-13 86.1
34 TraesCS1A01G273900 chr3B 96.970 33 1 0 3055 3087 39451088 39451120 5.430000e-04 56.5
35 TraesCS1A01G273900 chr5D 83.721 215 29 2 999 1213 10495640 10495432 8.530000e-47 198.0
36 TraesCS1A01G273900 chr5D 83.721 215 30 1 999 1213 511490989 511490780 8.530000e-47 198.0
37 TraesCS1A01G273900 chr6D 82.517 143 20 1 1074 1216 443355408 443355545 1.900000e-23 121.0
38 TraesCS1A01G273900 chr6D 94.643 56 3 0 1537 1592 468860022 468859967 1.930000e-13 87.9
39 TraesCS1A01G273900 chr6D 97.059 34 1 0 3051 3084 15700687 15700720 1.510000e-04 58.4
40 TraesCS1A01G273900 chr4D 100.000 31 0 0 3056 3086 213840193 213840223 1.510000e-04 58.4
41 TraesCS1A01G273900 chr7D 96.875 32 1 0 3056 3087 75800907 75800876 2.000000e-03 54.7
42 TraesCS1A01G273900 chr5B 100.000 29 0 0 3056 3084 98664859 98664887 2.000000e-03 54.7


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 TraesCS1A01G273900 chr1A 467257036 467260927 3891 True 7188.000000 7188 100.000000 1 3892 1 chr1A.!!$R1 3891
1 TraesCS1A01G273900 chr1D 368319263 368325498 6235 True 959.600000 2645 89.384000 48 3892 5 chr1D.!!$R2 3844
2 TraesCS1A01G273900 chr1D 369899223 369904900 5677 True 442.857143 1393 88.558286 48 3110 7 chr1D.!!$R3 3062
3 TraesCS1A01G273900 chr1B 492335067 492335840 773 True 1133.000000 1133 93.152000 3122 3892 1 chr1B.!!$R1 770
4 TraesCS1A01G273900 chr1B 492355623 492359028 3405 True 646.960000 1411 89.075600 54 3110 5 chr1B.!!$R2 3056

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
624 2643 0.037326 GCACAGGATCAGGTCGAACA 60.037 55.0 1.87 0.0 0.0 3.18 F
2517 4790 0.250770 AGAGCCCCAACGGAAAACTC 60.251 55.0 0.00 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2538 4811 0.178955 TGGGGACACCACGAACTAGA 60.179 55.0 0.0 0.0 46.80 2.43 R
3631 8772 0.461548 GGTGGACGATGATCTGCTCA 59.538 55.0 0.0 0.0 38.53 4.26 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
46 47 9.699703 TTTGTAACTGTAAATTTTTGCTATCCC 57.300 29.630 0.00 0.00 0.00 3.85
52 53 6.731467 TGTAAATTTTTGCTATCCCCTCTCT 58.269 36.000 0.00 0.00 0.00 3.10
74 75 9.942850 TCTCTTGTATCTGTATGTTCAAATTCA 57.057 29.630 0.00 0.00 0.00 2.57
110 111 0.888736 TGTGCATCCAAACAGGTCGG 60.889 55.000 0.00 0.00 39.02 4.79
111 112 0.605319 GTGCATCCAAACAGGTCGGA 60.605 55.000 0.00 0.00 39.02 4.55
139 140 7.092079 TGGCAACTTGAGTCATTTGATATTTG 58.908 34.615 15.81 3.47 37.61 2.32
174 2168 1.178276 ACAGTCGGCCAAACAACAAA 58.822 45.000 2.24 0.00 0.00 2.83
176 2170 2.192624 CAGTCGGCCAAACAACAAAAG 58.807 47.619 2.24 0.00 0.00 2.27
201 2196 5.694006 TGGAACCGTAGCAATTTCAATTTTG 59.306 36.000 0.00 0.00 0.00 2.44
202 2197 5.120053 GGAACCGTAGCAATTTCAATTTTGG 59.880 40.000 0.00 0.00 0.00 3.28
235 2231 1.818642 ACTGGAATCTGCACTTGAGC 58.181 50.000 0.00 0.00 0.00 4.26
252 2248 2.008329 GAGCTCTGCAGACCAATTCAG 58.992 52.381 13.74 1.19 0.00 3.02
254 2250 1.736681 GCTCTGCAGACCAATTCAGTC 59.263 52.381 13.74 0.00 34.31 3.51
273 2269 2.032528 CTGCAACCAAGCGGAGGA 59.967 61.111 0.00 0.00 43.63 3.71
274 2270 1.600636 CTGCAACCAAGCGGAGGAA 60.601 57.895 0.00 0.00 43.63 3.36
293 2291 4.023707 AGGAACTCAGATTTTCTGCAAACG 60.024 41.667 0.00 0.00 43.95 3.60
320 2318 6.845302 TGTTGCTGAAAGTTGATCATGATAC 58.155 36.000 8.54 4.23 35.30 2.24
416 2424 3.447944 GTCCTGAGTACCTAGGAAACAGG 59.552 52.174 26.70 26.70 44.25 4.00
476 2489 1.348036 GGCCAAGGCTATCTATCCGTT 59.652 52.381 11.40 0.00 41.60 4.44
477 2490 2.613223 GGCCAAGGCTATCTATCCGTTC 60.613 54.545 11.40 0.00 41.60 3.95
478 2491 2.927014 GCCAAGGCTATCTATCCGTTCG 60.927 54.545 3.29 0.00 38.26 3.95
479 2492 2.296471 CCAAGGCTATCTATCCGTTCGT 59.704 50.000 0.00 0.00 0.00 3.85
545 2558 2.095617 CGAATGCAACATGCTTGACAGA 60.096 45.455 6.60 0.00 45.31 3.41
552 2565 3.069079 ACATGCTTGACAGAGATGCTT 57.931 42.857 6.60 0.00 0.00 3.91
572 2585 5.127682 TGCTTGAGCCTTTTTCTTCTTCTTT 59.872 36.000 0.00 0.00 41.18 2.52
573 2586 6.321181 TGCTTGAGCCTTTTTCTTCTTCTTTA 59.679 34.615 0.00 0.00 41.18 1.85
589 2608 9.838339 CTTCTTCTTTATTATTAGCCTCTCCAA 57.162 33.333 0.00 0.00 0.00 3.53
599 2618 3.127425 AGCCTCTCCAAGTAAACACAC 57.873 47.619 0.00 0.00 0.00 3.82
601 2620 2.413837 CCTCTCCAAGTAAACACACGG 58.586 52.381 0.00 0.00 0.00 4.94
622 2641 0.532573 GAGCACAGGATCAGGTCGAA 59.467 55.000 0.00 0.00 0.00 3.71
623 2642 0.247736 AGCACAGGATCAGGTCGAAC 59.752 55.000 0.00 0.00 0.00 3.95
624 2643 0.037326 GCACAGGATCAGGTCGAACA 60.037 55.000 1.87 0.00 0.00 3.18
625 2644 1.406069 GCACAGGATCAGGTCGAACAT 60.406 52.381 1.87 0.00 0.00 2.71
627 2646 3.448686 CACAGGATCAGGTCGAACATAC 58.551 50.000 1.87 0.00 0.00 2.39
672 2702 9.162764 CGGGAGGAAATTATACATTTATACTGG 57.837 37.037 0.00 0.00 0.00 4.00
845 2901 3.330720 CCTCCCACCGGCTTCCTT 61.331 66.667 0.00 0.00 0.00 3.36
846 2902 2.269241 CTCCCACCGGCTTCCTTC 59.731 66.667 0.00 0.00 0.00 3.46
847 2903 3.327404 TCCCACCGGCTTCCTTCC 61.327 66.667 0.00 0.00 0.00 3.46
858 2914 1.943340 GCTTCCTTCCGCCTATTTCAG 59.057 52.381 0.00 0.00 0.00 3.02
865 2921 1.682451 CCGCCTATTTCAGTCCCCGA 61.682 60.000 0.00 0.00 0.00 5.14
867 2923 1.120530 GCCTATTTCAGTCCCCGAGA 58.879 55.000 0.00 0.00 0.00 4.04
915 2971 3.012959 TCCCTCTCCCATCTCTAACAACT 59.987 47.826 0.00 0.00 0.00 3.16
955 3035 1.517694 TTTGTATCCGTCGCTCGCC 60.518 57.895 0.00 0.00 38.35 5.54
979 3059 1.357334 CGACCGAGAAGAGCTAGCC 59.643 63.158 12.13 2.81 0.00 3.93
980 3060 1.098712 CGACCGAGAAGAGCTAGCCT 61.099 60.000 12.13 5.44 0.00 4.58
981 3061 1.810794 CGACCGAGAAGAGCTAGCCTA 60.811 57.143 12.13 0.00 0.00 3.93
982 3062 1.877443 GACCGAGAAGAGCTAGCCTAG 59.123 57.143 12.13 1.41 0.00 3.02
1213 3333 3.365265 CCAACGTCCAGGCAAGCC 61.365 66.667 2.02 2.02 0.00 4.35
1219 3339 1.304381 GTCCAGGCAAGCCATCCAA 60.304 57.895 14.40 0.00 38.92 3.53
1221 3341 2.718073 CCAGGCAAGCCATCCAAGC 61.718 63.158 14.40 0.00 38.92 4.01
1242 3385 2.506472 CTAGCCCCTTTCCTCGCC 59.494 66.667 0.00 0.00 0.00 5.54
1281 3424 2.431942 GCGTTGACGGACGTGGAT 60.432 61.111 0.53 0.00 44.50 3.41
1283 3426 1.081041 CGTTGACGGACGTGGATGA 60.081 57.895 0.53 0.00 38.19 2.92
1378 3526 2.461110 CCGCACCGTAATGCACTCC 61.461 63.158 0.00 0.00 46.47 3.85
1398 3546 4.219115 TCCTCTCACTCTTCAGTTTCAGT 58.781 43.478 0.00 0.00 0.00 3.41
1421 3569 8.298140 CAGTAGATATCTTCCCGGTAAAGTAAG 58.702 40.741 11.25 1.85 0.00 2.34
1592 3743 4.222847 GGCGTCTCCATCGGGACC 62.223 72.222 0.00 0.00 38.64 4.46
1596 3747 1.170919 CGTCTCCATCGGGACCGTAT 61.171 60.000 10.90 0.56 38.64 3.06
1597 3748 0.314302 GTCTCCATCGGGACCGTATG 59.686 60.000 10.90 12.14 38.64 2.39
1645 3799 2.952245 CTGCTGCCTGTTGACTGC 59.048 61.111 0.00 0.00 0.00 4.40
1665 3819 3.311322 TGCTTCAGTACACCGTTCAAAAG 59.689 43.478 0.00 0.00 0.00 2.27
1675 3830 0.845768 CGTTCAAAAGCAAAGGCACG 59.154 50.000 0.00 0.00 44.61 5.34
1676 3831 1.797348 CGTTCAAAAGCAAAGGCACGT 60.797 47.619 0.00 0.00 44.61 4.49
1677 3832 1.852280 GTTCAAAAGCAAAGGCACGTC 59.148 47.619 0.00 0.00 44.61 4.34
1678 3833 0.383949 TCAAAAGCAAAGGCACGTCC 59.616 50.000 0.00 0.00 44.61 4.79
1679 3834 0.597377 CAAAAGCAAAGGCACGTCCC 60.597 55.000 0.00 0.00 44.61 4.46
1683 3838 2.281208 CAAAGGCACGTCCCCGAA 60.281 61.111 0.00 0.00 37.88 4.30
1695 3860 3.119352 ACGTCCCCGAATTACTTACTGTC 60.119 47.826 0.00 0.00 37.88 3.51
1706 3871 6.716934 ATTACTTACTGTCATCTGATCGGT 57.283 37.500 0.42 0.00 0.00 4.69
1714 3882 3.190874 GTCATCTGATCGGTGTTTCTCC 58.809 50.000 0.42 0.00 0.00 3.71
1762 3930 2.325583 TCAAAGACAAGGACAACGCT 57.674 45.000 0.00 0.00 0.00 5.07
1768 3936 2.229302 AGACAAGGACAACGCTACTCTC 59.771 50.000 0.00 0.00 0.00 3.20
1774 3942 1.671845 GACAACGCTACTCTCGAGGAT 59.328 52.381 13.56 3.45 0.00 3.24
1777 3945 2.612672 CAACGCTACTCTCGAGGATGTA 59.387 50.000 13.56 12.13 0.00 2.29
1793 3961 0.542467 TGTACTGCAACCCGGGACTA 60.542 55.000 32.02 9.50 34.50 2.59
1801 3969 2.944094 GCAACCCGGGACTAACATGATT 60.944 50.000 32.02 3.07 0.00 2.57
1804 3972 1.134098 CCCGGGACTAACATGATTGCT 60.134 52.381 18.48 0.00 0.00 3.91
1828 3996 1.417890 GGCTACTGCATGTATGGGAGT 59.582 52.381 0.00 0.00 41.91 3.85
1843 4011 1.940613 GGGAGTTCATGCACGGTAATC 59.059 52.381 0.00 0.00 0.00 1.75
1845 4013 2.351726 GGAGTTCATGCACGGTAATCAC 59.648 50.000 0.00 0.00 0.00 3.06
1846 4014 3.000041 GAGTTCATGCACGGTAATCACA 59.000 45.455 0.00 0.00 0.00 3.58
1847 4015 2.742053 AGTTCATGCACGGTAATCACAC 59.258 45.455 0.00 0.00 0.00 3.82
1848 4016 1.732941 TCATGCACGGTAATCACACC 58.267 50.000 0.00 0.00 35.04 4.16
1853 4021 1.196911 CACGGTAATCACACCCCCTA 58.803 55.000 0.00 0.00 34.90 3.53
1856 4024 2.848071 ACGGTAATCACACCCCCTAATT 59.152 45.455 0.00 0.00 34.90 1.40
1858 4026 4.474287 ACGGTAATCACACCCCCTAATTAA 59.526 41.667 0.00 0.00 34.90 1.40
1859 4027 5.044993 ACGGTAATCACACCCCCTAATTAAA 60.045 40.000 0.00 0.00 34.90 1.52
1860 4028 5.887035 CGGTAATCACACCCCCTAATTAAAA 59.113 40.000 0.00 0.00 34.90 1.52
1861 4029 6.038936 CGGTAATCACACCCCCTAATTAAAAG 59.961 42.308 0.00 0.00 34.90 2.27
1862 4030 6.893554 GGTAATCACACCCCCTAATTAAAAGT 59.106 38.462 0.00 0.00 31.91 2.66
1864 4032 7.865530 AATCACACCCCCTAATTAAAAGTTT 57.134 32.000 0.00 0.00 0.00 2.66
1889 4058 7.416154 TTTTCACTTCCACTACTTTACATCG 57.584 36.000 0.00 0.00 0.00 3.84
1890 4059 5.970317 TCACTTCCACTACTTTACATCGA 57.030 39.130 0.00 0.00 0.00 3.59
1891 4060 6.525578 TCACTTCCACTACTTTACATCGAT 57.474 37.500 0.00 0.00 0.00 3.59
1903 4072 9.967346 CTACTTTACATCGATTCTTCATCCTAA 57.033 33.333 0.00 0.00 0.00 2.69
1909 4078 8.147642 ACATCGATTCTTCATCCTAAATTGAC 57.852 34.615 0.00 0.00 0.00 3.18
1910 4079 7.989741 ACATCGATTCTTCATCCTAAATTGACT 59.010 33.333 0.00 0.00 0.00 3.41
1919 4088 5.877012 TCATCCTAAATTGACTGCTGTTCTC 59.123 40.000 0.00 0.00 0.00 2.87
1920 4089 5.227569 TCCTAAATTGACTGCTGTTCTCA 57.772 39.130 0.00 0.00 0.00 3.27
1921 4090 4.997395 TCCTAAATTGACTGCTGTTCTCAC 59.003 41.667 0.00 0.00 0.00 3.51
1922 4091 4.154918 CCTAAATTGACTGCTGTTCTCACC 59.845 45.833 0.00 0.00 0.00 4.02
1923 4092 1.800805 ATTGACTGCTGTTCTCACCG 58.199 50.000 0.00 0.00 0.00 4.94
1925 4094 0.969149 TGACTGCTGTTCTCACCGAT 59.031 50.000 0.00 0.00 0.00 4.18
1926 4095 1.337167 TGACTGCTGTTCTCACCGATG 60.337 52.381 0.00 0.00 0.00 3.84
1933 4102 1.086634 GTTCTCACCGATGGCAGCTC 61.087 60.000 0.00 0.00 0.00 4.09
2002 4171 3.297736 CCTCGGGGAGTTCATACTAACT 58.702 50.000 0.00 0.00 42.36 2.24
2284 4501 0.596082 GCCAACATTGCAGGTACGTT 59.404 50.000 0.00 0.00 0.00 3.99
2451 4724 6.494893 TTTAGTATGGTTGCTGATGTTCAC 57.505 37.500 0.00 0.00 0.00 3.18
2490 4763 0.865769 GCATATTTCTGTACCCCGCG 59.134 55.000 0.00 0.00 0.00 6.46
2514 4787 0.476771 AGAAGAGCCCCAACGGAAAA 59.523 50.000 0.00 0.00 0.00 2.29
2517 4790 0.250770 AGAGCCCCAACGGAAAACTC 60.251 55.000 0.00 0.00 0.00 3.01
2551 4832 1.401148 CGGACACTCTAGTTCGTGGTG 60.401 57.143 11.97 0.00 35.79 4.17
2566 4847 1.212935 GTGGTGTCCCCAGCTGATTAT 59.787 52.381 17.39 0.00 46.45 1.28
2567 4848 1.490490 TGGTGTCCCCAGCTGATTATC 59.510 52.381 17.39 2.18 38.72 1.75
2569 4850 1.490490 GTGTCCCCAGCTGATTATCCA 59.510 52.381 17.39 0.83 0.00 3.41
2573 4854 4.603171 TGTCCCCAGCTGATTATCCATATT 59.397 41.667 17.39 0.00 0.00 1.28
2574 4855 4.946157 GTCCCCAGCTGATTATCCATATTG 59.054 45.833 17.39 0.00 0.00 1.90
2578 7208 6.005823 CCCAGCTGATTATCCATATTGACAA 58.994 40.000 17.39 0.00 0.00 3.18
2581 7211 7.308408 CCAGCTGATTATCCATATTGACAAGTG 60.308 40.741 17.39 0.00 0.00 3.16
2625 7255 1.810755 GTTTTCCCCATGTCGTTCCTC 59.189 52.381 0.00 0.00 0.00 3.71
2726 7432 4.096984 AGAGCAGCACTTTATGTTATTGCC 59.903 41.667 0.00 0.00 33.48 4.52
2797 7503 2.307686 AGGCCCTTGAAATCGTTCCTTA 59.692 45.455 0.00 0.00 32.28 2.69
2861 7567 5.347093 CGATGATGTGGAGGAGATTAAATCG 59.653 44.000 0.00 0.00 0.00 3.34
2894 7600 3.838271 TCGAGCACCGCCTGATCC 61.838 66.667 0.00 0.00 38.37 3.36
2906 7612 1.202428 GCCTGATCCGAGTACCTGAAC 60.202 57.143 0.00 0.00 0.00 3.18
2937 7644 1.510623 GTTCTGCATCGCGTTGCTG 60.511 57.895 34.25 32.69 43.18 4.41
2944 7651 1.595609 CATCGCGTTGCTGAAAGAAC 58.404 50.000 5.77 0.00 34.07 3.01
2959 7684 6.913132 GCTGAAAGAACAAAGTTAAACTCCTC 59.087 38.462 0.00 0.00 34.07 3.71
3003 7730 1.869767 GATCATTGTCATGGCCTCGAC 59.130 52.381 15.78 15.78 0.00 4.20
3113 8251 2.747446 CACACCCCCTTACTTTTCATCG 59.253 50.000 0.00 0.00 0.00 3.84
3120 8258 5.527582 CCCCCTTACTTTTCATCGTTATCAG 59.472 44.000 0.00 0.00 0.00 2.90
3134 8272 9.731819 TCATCGTTATCAGTAATAAGAGTTCAC 57.268 33.333 0.00 0.00 30.39 3.18
3137 8275 8.188799 TCGTTATCAGTAATAAGAGTTCACTGG 58.811 37.037 0.00 0.00 37.72 4.00
3160 8298 7.424803 TGGTCTTGTAATTCATCACAGTTTTG 58.575 34.615 0.00 0.00 0.00 2.44
3182 8320 1.593196 TTCAGAGCAAGGAAACCACG 58.407 50.000 0.00 0.00 0.00 4.94
3183 8321 0.250295 TCAGAGCAAGGAAACCACGG 60.250 55.000 0.00 0.00 0.00 4.94
3216 8354 3.021695 CCTCATGCATTCAGACACCAAT 58.978 45.455 0.00 0.00 0.00 3.16
3251 8389 3.621715 GGGACTGGACAAAACGATCATAC 59.378 47.826 0.00 0.00 0.00 2.39
3304 8442 8.172484 GTCAAATTAAACAGAACCAAAACAACC 58.828 33.333 0.00 0.00 0.00 3.77
3317 8455 0.182775 AACAACCACCACCAGGACTC 59.817 55.000 0.00 0.00 38.69 3.36
3336 8474 3.190744 ACTCACTGATCAAGCAAATGCAG 59.809 43.478 8.28 0.00 45.16 4.41
3338 8476 1.822990 ACTGATCAAGCAAATGCAGGG 59.177 47.619 8.28 0.00 45.16 4.45
3359 8497 0.035725 CAGGCTCATCTCAACAGGCA 60.036 55.000 0.00 0.00 35.19 4.75
3553 8694 3.739300 CGTACCTCTTGTTTCGTGATGTT 59.261 43.478 0.00 0.00 0.00 2.71
3554 8695 4.376008 CGTACCTCTTGTTTCGTGATGTTG 60.376 45.833 0.00 0.00 0.00 3.33
3631 8772 4.790962 CGCAGAGGCCTGGTGCAT 62.791 66.667 28.14 0.00 43.89 3.96
3632 8773 3.138798 GCAGAGGCCTGGTGCATG 61.139 66.667 25.51 10.12 43.89 4.06
3647 8788 1.146637 GCATGAGCAGATCATCGTCC 58.853 55.000 0.00 0.00 46.01 4.79
3701 8842 2.941333 CAGCCAACACACGAGCTG 59.059 61.111 0.00 0.00 45.92 4.24
3703 8844 0.599991 CAGCCAACACACGAGCTGTA 60.600 55.000 0.00 0.00 46.00 2.74
3710 8851 1.749634 ACACACGAGCTGTAGGATACC 59.250 52.381 0.00 0.00 42.12 2.73
3744 8885 1.566018 CTTTGGTTCCACGGCGTCTC 61.566 60.000 10.85 0.23 0.00 3.36
3791 8932 2.124695 CAGAACGGGCTAAGGGGC 60.125 66.667 0.00 0.00 40.05 5.80
3796 8937 4.315941 CGGGCTAAGGGGCGGATC 62.316 72.222 0.00 0.00 42.03 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.699703 GGGATAGCAAAAATTTACAGTTACAAA 57.300 29.630 0.00 0.00 0.00 2.83
21 22 8.308207 GGGGATAGCAAAAATTTACAGTTACAA 58.692 33.333 0.00 0.00 0.00 2.41
22 23 7.672239 AGGGGATAGCAAAAATTTACAGTTACA 59.328 33.333 0.00 0.00 0.00 2.41
23 24 8.063200 AGGGGATAGCAAAAATTTACAGTTAC 57.937 34.615 0.00 0.00 0.00 2.50
24 25 8.113462 AGAGGGGATAGCAAAAATTTACAGTTA 58.887 33.333 0.00 0.00 0.00 2.24
25 26 6.954102 AGAGGGGATAGCAAAAATTTACAGTT 59.046 34.615 0.00 0.00 0.00 3.16
26 27 6.494059 AGAGGGGATAGCAAAAATTTACAGT 58.506 36.000 0.00 0.00 0.00 3.55
27 28 6.830838 AGAGAGGGGATAGCAAAAATTTACAG 59.169 38.462 0.00 0.00 0.00 2.74
28 29 6.731467 AGAGAGGGGATAGCAAAAATTTACA 58.269 36.000 0.00 0.00 0.00 2.41
29 30 7.122799 ACAAGAGAGGGGATAGCAAAAATTTAC 59.877 37.037 0.00 0.00 0.00 2.01
30 31 7.182060 ACAAGAGAGGGGATAGCAAAAATTTA 58.818 34.615 0.00 0.00 0.00 1.40
31 32 6.019108 ACAAGAGAGGGGATAGCAAAAATTT 58.981 36.000 0.00 0.00 0.00 1.82
32 33 5.583932 ACAAGAGAGGGGATAGCAAAAATT 58.416 37.500 0.00 0.00 0.00 1.82
33 34 5.198602 ACAAGAGAGGGGATAGCAAAAAT 57.801 39.130 0.00 0.00 0.00 1.82
34 35 4.657814 ACAAGAGAGGGGATAGCAAAAA 57.342 40.909 0.00 0.00 0.00 1.94
35 36 5.667626 AGATACAAGAGAGGGGATAGCAAAA 59.332 40.000 0.00 0.00 0.00 2.44
36 37 5.070981 CAGATACAAGAGAGGGGATAGCAAA 59.929 44.000 0.00 0.00 0.00 3.68
37 38 4.590647 CAGATACAAGAGAGGGGATAGCAA 59.409 45.833 0.00 0.00 0.00 3.91
38 39 4.155709 CAGATACAAGAGAGGGGATAGCA 58.844 47.826 0.00 0.00 0.00 3.49
39 40 4.156477 ACAGATACAAGAGAGGGGATAGC 58.844 47.826 0.00 0.00 0.00 2.97
40 41 6.951198 ACATACAGATACAAGAGAGGGGATAG 59.049 42.308 0.00 0.00 0.00 2.08
41 42 6.864421 ACATACAGATACAAGAGAGGGGATA 58.136 40.000 0.00 0.00 0.00 2.59
42 43 5.721225 ACATACAGATACAAGAGAGGGGAT 58.279 41.667 0.00 0.00 0.00 3.85
43 44 5.144159 ACATACAGATACAAGAGAGGGGA 57.856 43.478 0.00 0.00 0.00 4.81
44 45 5.363868 TGAACATACAGATACAAGAGAGGGG 59.636 44.000 0.00 0.00 0.00 4.79
45 46 6.471233 TGAACATACAGATACAAGAGAGGG 57.529 41.667 0.00 0.00 0.00 4.30
46 47 8.954950 ATTTGAACATACAGATACAAGAGAGG 57.045 34.615 0.00 0.00 0.00 3.69
52 53 9.942850 TCTCTGAATTTGAACATACAGATACAA 57.057 29.630 0.00 0.00 34.64 2.41
74 75 4.914983 TGCACATGATTCCTTTCTTCTCT 58.085 39.130 0.00 0.00 0.00 3.10
110 111 5.531634 TCAAATGACTCAAGTTGCCAATTC 58.468 37.500 0.00 0.00 0.00 2.17
111 112 5.534207 TCAAATGACTCAAGTTGCCAATT 57.466 34.783 0.00 0.00 0.00 2.32
139 140 1.269936 ACTGTTGGAAATGCTTGCTGC 60.270 47.619 0.00 0.00 43.25 5.25
174 2168 3.482436 TGAAATTGCTACGGTTCCACTT 58.518 40.909 0.00 0.00 0.00 3.16
176 2170 3.907894 TTGAAATTGCTACGGTTCCAC 57.092 42.857 0.00 0.00 0.00 4.02
201 2196 1.762957 TCCAGTTCATCTCCGGAATCC 59.237 52.381 5.23 0.00 0.00 3.01
202 2197 3.543680 TTCCAGTTCATCTCCGGAATC 57.456 47.619 5.23 0.00 30.87 2.52
235 2231 2.354259 GGACTGAATTGGTCTGCAGAG 58.646 52.381 18.89 5.13 34.47 3.35
252 2248 3.365265 CCGCTTGGTTGCAGGGAC 61.365 66.667 0.00 0.00 0.00 4.46
254 2250 3.058160 CTCCGCTTGGTTGCAGGG 61.058 66.667 0.00 0.00 0.00 4.45
273 2269 6.845392 ACAAACGTTTGCAGAAAATCTGAGTT 60.845 34.615 34.70 11.58 45.88 3.01
274 2270 5.393027 ACAAACGTTTGCAGAAAATCTGAGT 60.393 36.000 34.70 12.19 45.88 3.41
293 2291 5.978919 TCATGATCAACTTTCAGCAACAAAC 59.021 36.000 0.00 0.00 0.00 2.93
320 2318 1.414181 AGGAGTAGCCATCATCAACCG 59.586 52.381 0.00 0.00 40.02 4.44
416 2424 1.400846 CACTTGAGCTGATGTCATGGC 59.599 52.381 0.00 0.00 0.00 4.40
476 2489 4.890088 AGTGGCATTAAAGTAGACAACGA 58.110 39.130 0.00 0.00 0.00 3.85
477 2490 5.408604 AGAAGTGGCATTAAAGTAGACAACG 59.591 40.000 0.00 0.00 0.00 4.10
478 2491 6.803154 AGAAGTGGCATTAAAGTAGACAAC 57.197 37.500 0.00 0.00 0.00 3.32
479 2492 7.284489 ACAAAGAAGTGGCATTAAAGTAGACAA 59.716 33.333 0.00 0.00 0.00 3.18
545 2558 4.405548 AGAAGAAAAAGGCTCAAGCATCT 58.594 39.130 4.13 0.00 44.36 2.90
572 2585 8.764558 TGTGTTTACTTGGAGAGGCTAATAATA 58.235 33.333 0.00 0.00 0.00 0.98
573 2586 7.553044 GTGTGTTTACTTGGAGAGGCTAATAAT 59.447 37.037 0.00 0.00 0.00 1.28
578 2597 3.305813 CGTGTGTTTACTTGGAGAGGCTA 60.306 47.826 0.00 0.00 0.00 3.93
580 2599 1.798813 CGTGTGTTTACTTGGAGAGGC 59.201 52.381 0.00 0.00 0.00 4.70
581 2600 2.413837 CCGTGTGTTTACTTGGAGAGG 58.586 52.381 0.00 0.00 0.00 3.69
586 2605 1.519408 CTCCCCGTGTGTTTACTTGG 58.481 55.000 0.00 0.00 0.00 3.61
589 2608 0.250166 GTGCTCCCCGTGTGTTTACT 60.250 55.000 0.00 0.00 0.00 2.24
599 2618 2.503061 CTGATCCTGTGCTCCCCG 59.497 66.667 0.00 0.00 0.00 5.73
601 2620 1.524482 GACCTGATCCTGTGCTCCC 59.476 63.158 0.00 0.00 0.00 4.30
622 2641 2.223112 CGCCGTTCGTACTACTGTATGT 60.223 50.000 0.00 0.00 37.08 2.29
623 2642 2.369600 CGCCGTTCGTACTACTGTATG 58.630 52.381 0.00 0.00 37.09 2.39
624 2643 2.744787 CGCCGTTCGTACTACTGTAT 57.255 50.000 0.00 0.00 0.00 2.29
665 2695 9.163894 ACACTACTAGGTGATAGTACCAGTATA 57.836 37.037 6.18 0.00 43.17 1.47
666 2696 8.043429 ACACTACTAGGTGATAGTACCAGTAT 57.957 38.462 6.18 0.00 43.17 2.12
669 2699 5.466058 CGACACTACTAGGTGATAGTACCAG 59.534 48.000 6.18 0.00 43.17 4.00
670 2700 5.104776 ACGACACTACTAGGTGATAGTACCA 60.105 44.000 6.18 0.00 43.17 3.25
671 2701 5.236047 CACGACACTACTAGGTGATAGTACC 59.764 48.000 6.18 0.00 43.17 3.34
672 2702 5.236047 CCACGACACTACTAGGTGATAGTAC 59.764 48.000 6.18 0.00 43.17 2.73
673 2703 5.104776 ACCACGACACTACTAGGTGATAGTA 60.105 44.000 6.18 0.00 43.17 1.82
674 2704 4.197750 CCACGACACTACTAGGTGATAGT 58.802 47.826 6.18 0.00 46.70 2.12
675 2705 4.197750 ACCACGACACTACTAGGTGATAG 58.802 47.826 6.18 0.00 40.13 2.08
676 2706 4.194640 GACCACGACACTACTAGGTGATA 58.805 47.826 6.18 0.00 40.13 2.15
677 2707 3.015327 GACCACGACACTACTAGGTGAT 58.985 50.000 6.18 0.00 40.13 3.06
678 2708 2.224597 TGACCACGACACTACTAGGTGA 60.225 50.000 6.18 0.00 40.13 4.02
679 2709 2.156917 TGACCACGACACTACTAGGTG 58.843 52.381 0.00 0.00 42.34 4.00
680 2710 2.574006 TGACCACGACACTACTAGGT 57.426 50.000 0.00 0.00 0.00 3.08
681 2711 3.928727 TTTGACCACGACACTACTAGG 57.071 47.619 0.00 0.00 0.00 3.02
682 2712 4.174009 CCATTTGACCACGACACTACTAG 58.826 47.826 0.00 0.00 0.00 2.57
683 2713 3.056393 CCCATTTGACCACGACACTACTA 60.056 47.826 0.00 0.00 0.00 1.82
765 2812 1.269569 CGTAGCGTGGATATGCTTGGA 60.270 52.381 0.00 0.00 46.84 3.53
815 2867 4.778143 GGAGGCGTGCCGGATGTT 62.778 66.667 5.05 0.00 41.95 2.71
844 2900 0.544697 GGGGACTGAAATAGGCGGAA 59.455 55.000 0.00 0.00 34.11 4.30
845 2901 1.682451 CGGGGACTGAAATAGGCGGA 61.682 60.000 0.00 0.00 34.11 5.54
846 2902 1.227556 CGGGGACTGAAATAGGCGG 60.228 63.158 0.00 0.00 34.11 6.13
847 2903 0.249489 CTCGGGGACTGAAATAGGCG 60.249 60.000 0.00 0.00 46.55 5.52
955 3035 2.749044 TCTTCTCGGTCGTCGGGG 60.749 66.667 0.00 0.00 40.39 5.73
1213 3333 2.517919 GGCTAGGGGGCTTGGATG 59.482 66.667 0.00 0.00 37.53 3.51
1219 3339 2.696504 GAAAGGGGCTAGGGGGCT 60.697 66.667 0.00 0.00 40.65 5.19
1221 3341 2.044620 AGGAAAGGGGCTAGGGGG 59.955 66.667 0.00 0.00 0.00 5.40
1242 3385 2.236690 CGCGCAGAGATTGAAAACAAG 58.763 47.619 8.75 0.00 0.00 3.16
1272 3415 0.102120 CTGCTCTCTCATCCACGTCC 59.898 60.000 0.00 0.00 0.00 4.79
1279 3422 1.120795 CCTCCCCCTGCTCTCTCATC 61.121 65.000 0.00 0.00 0.00 2.92
1281 3424 2.235602 CTCCTCCCCCTGCTCTCTCA 62.236 65.000 0.00 0.00 0.00 3.27
1283 3426 2.695597 CTCCTCCCCCTGCTCTCT 59.304 66.667 0.00 0.00 0.00 3.10
1378 3526 6.567687 TCTACTGAAACTGAAGAGTGAGAG 57.432 41.667 0.00 0.00 30.61 3.20
1398 3546 9.425248 TTTCTTACTTTACCGGGAAGATATCTA 57.575 33.333 22.11 5.32 0.00 1.98
1466 3617 2.971430 TCTCTTCAGACACGAGAACG 57.029 50.000 0.00 0.00 45.75 3.95
1469 3620 2.490991 TCGTTCTCTTCAGACACGAGA 58.509 47.619 0.00 0.00 37.31 4.04
1592 3743 2.287909 GCAGAGTAAGAGGAGCCATACG 60.288 54.545 0.00 0.00 0.00 3.06
1596 3747 1.827969 GAAGCAGAGTAAGAGGAGCCA 59.172 52.381 0.00 0.00 0.00 4.75
1597 3748 2.100749 GAGAAGCAGAGTAAGAGGAGCC 59.899 54.545 0.00 0.00 0.00 4.70
1645 3799 3.311322 TGCTTTTGAACGGTGTACTGAAG 59.689 43.478 0.00 0.00 0.00 3.02
1675 3830 4.460948 TGACAGTAAGTAATTCGGGGAC 57.539 45.455 0.00 0.00 0.00 4.46
1676 3831 4.960469 AGATGACAGTAAGTAATTCGGGGA 59.040 41.667 0.00 0.00 0.00 4.81
1677 3832 5.050490 CAGATGACAGTAAGTAATTCGGGG 58.950 45.833 0.00 0.00 0.00 5.73
1678 3833 5.902681 TCAGATGACAGTAAGTAATTCGGG 58.097 41.667 0.00 0.00 0.00 5.14
1679 3834 6.360947 CGATCAGATGACAGTAAGTAATTCGG 59.639 42.308 0.00 0.00 0.00 4.30
1683 3838 6.096987 ACACCGATCAGATGACAGTAAGTAAT 59.903 38.462 0.00 0.00 0.00 1.89
1706 3871 5.619309 CGAAGATCTACAGAACGGAGAAACA 60.619 44.000 0.00 0.00 0.00 2.83
1714 3882 3.891324 GATCCCGAAGATCTACAGAACG 58.109 50.000 0.00 0.00 46.85 3.95
1762 3930 3.277142 TGCAGTACATCCTCGAGAGTA 57.723 47.619 15.71 10.84 0.00 2.59
1768 3936 0.806102 CGGGTTGCAGTACATCCTCG 60.806 60.000 0.00 0.00 38.11 4.63
1774 3942 0.542467 TAGTCCCGGGTTGCAGTACA 60.542 55.000 22.86 0.00 0.00 2.90
1777 3945 1.373812 GTTAGTCCCGGGTTGCAGT 59.626 57.895 22.86 6.41 0.00 4.40
1804 3972 1.475571 CCATACATGCAGTAGCCAGCA 60.476 52.381 0.00 0.00 45.92 4.41
1822 3990 0.687920 TTACCGTGCATGAACTCCCA 59.312 50.000 7.72 0.00 0.00 4.37
1828 3996 2.080693 GGTGTGATTACCGTGCATGAA 58.919 47.619 7.72 0.00 0.00 2.57
1864 4032 7.711772 TCGATGTAAAGTAGTGGAAGTGAAAAA 59.288 33.333 0.00 0.00 0.00 1.94
1877 4045 9.967346 TTAGGATGAAGAATCGATGTAAAGTAG 57.033 33.333 0.00 0.00 35.99 2.57
1886 4055 7.041508 GCAGTCAATTTAGGATGAAGAATCGAT 60.042 37.037 0.00 0.00 35.99 3.59
1887 4056 6.258727 GCAGTCAATTTAGGATGAAGAATCGA 59.741 38.462 0.00 0.00 35.99 3.59
1889 4058 7.066766 ACAGCAGTCAATTTAGGATGAAGAATC 59.933 37.037 0.00 0.00 34.19 2.52
1890 4059 6.888632 ACAGCAGTCAATTTAGGATGAAGAAT 59.111 34.615 0.00 0.00 0.00 2.40
1891 4060 6.240894 ACAGCAGTCAATTTAGGATGAAGAA 58.759 36.000 0.00 0.00 0.00 2.52
1903 4072 2.146342 CGGTGAGAACAGCAGTCAATT 58.854 47.619 0.00 0.00 43.66 2.32
1907 4076 1.354040 CATCGGTGAGAACAGCAGTC 58.646 55.000 0.00 0.00 43.66 3.51
1909 4078 1.364626 GCCATCGGTGAGAACAGCAG 61.365 60.000 0.00 0.00 43.66 4.24
1910 4079 1.375908 GCCATCGGTGAGAACAGCA 60.376 57.895 0.00 0.00 43.66 4.41
1919 4088 3.190849 CACGAGCTGCCATCGGTG 61.191 66.667 14.49 7.54 44.36 4.94
1920 4089 1.884075 TAACACGAGCTGCCATCGGT 61.884 55.000 14.49 7.61 44.36 4.69
1921 4090 0.739462 TTAACACGAGCTGCCATCGG 60.739 55.000 14.49 7.09 44.36 4.18
1922 4091 0.647410 CTTAACACGAGCTGCCATCG 59.353 55.000 9.39 9.39 45.54 3.84
1923 4092 0.375106 GCTTAACACGAGCTGCCATC 59.625 55.000 0.00 0.00 37.18 3.51
1925 4094 1.070615 TGCTTAACACGAGCTGCCA 59.929 52.632 0.00 0.00 40.75 4.92
1926 4095 1.497722 GTGCTTAACACGAGCTGCC 59.502 57.895 0.00 0.00 40.07 4.85
1963 4132 3.055819 CGAGGGAAGGATCAAGAGTGAAA 60.056 47.826 0.00 0.00 37.30 2.69
1999 4168 5.838521 ACAAACCTTTATGTTGGGATGAGTT 59.161 36.000 0.00 0.00 0.00 3.01
2002 4171 5.389520 TCACAAACCTTTATGTTGGGATGA 58.610 37.500 0.00 0.00 0.00 2.92
2193 4381 5.576774 TGAAATGAGATGTACTGCGTACTTG 59.423 40.000 16.13 0.00 39.49 3.16
2284 4501 1.704628 TGGGGAAACTTGCATCTCTCA 59.295 47.619 0.00 0.00 0.00 3.27
2490 4763 0.955919 CGTTGGGGCTCTTCTTGTCC 60.956 60.000 0.00 0.00 0.00 4.02
2526 4799 1.828832 GAACTAGAGTGTCCGCATCG 58.171 55.000 0.00 0.00 0.00 3.84
2532 4805 1.612463 ACACCACGAACTAGAGTGTCC 59.388 52.381 0.00 0.00 37.05 4.02
2535 4808 1.067776 GGGACACCACGAACTAGAGTG 60.068 57.143 0.00 3.80 38.05 3.51
2536 4809 1.254954 GGGACACCACGAACTAGAGT 58.745 55.000 0.00 0.00 36.50 3.24
2537 4810 0.531200 GGGGACACCACGAACTAGAG 59.469 60.000 0.00 0.00 39.85 2.43
2538 4811 0.178955 TGGGGACACCACGAACTAGA 60.179 55.000 0.00 0.00 46.80 2.43
2540 4813 1.823169 GCTGGGGACACCACGAACTA 61.823 60.000 0.00 0.00 46.80 2.24
2541 4814 3.148084 CTGGGGACACCACGAACT 58.852 61.111 0.00 0.00 46.80 3.01
2542 4815 2.668550 GCTGGGGACACCACGAAC 60.669 66.667 0.00 0.00 46.80 3.95
2551 4832 4.851639 ATATGGATAATCAGCTGGGGAC 57.148 45.455 15.13 2.26 0.00 4.46
2566 4847 7.888021 ACTGAAAATACCACTTGTCAATATGGA 59.112 33.333 18.49 6.75 36.04 3.41
2567 4848 7.970061 CACTGAAAATACCACTTGTCAATATGG 59.030 37.037 12.44 12.44 38.26 2.74
2569 4850 8.635765 ACACTGAAAATACCACTTGTCAATAT 57.364 30.769 0.00 0.00 0.00 1.28
2573 4854 6.038161 CAGAACACTGAAAATACCACTTGTCA 59.962 38.462 0.00 0.00 33.94 3.58
2574 4855 6.038271 ACAGAACACTGAAAATACCACTTGTC 59.962 38.462 0.00 0.00 35.80 3.18
2578 7208 5.694910 CGTACAGAACACTGAAAATACCACT 59.305 40.000 0.00 0.00 35.80 4.00
2581 7211 5.347907 CCTCGTACAGAACACTGAAAATACC 59.652 44.000 0.00 0.00 35.80 2.73
2625 7255 2.515523 CCTCCGGCTTGCTCCATG 60.516 66.667 0.00 0.00 0.00 3.66
2699 7329 2.354259 ACATAAAGTGCTGCTCTGAGC 58.646 47.619 22.38 22.38 42.82 4.26
2700 7330 6.484540 CAATAACATAAAGTGCTGCTCTGAG 58.515 40.000 4.83 0.00 0.00 3.35
2726 7432 1.075542 TTACAGCACGCCAAAGATCG 58.924 50.000 0.00 0.00 0.00 3.69
2771 7477 0.109132 CGATTTCAAGGGCCTGCAAC 60.109 55.000 6.92 0.00 0.00 4.17
2797 7503 3.571590 GGAGACCTCTGGTGTATCTCAT 58.428 50.000 0.00 0.00 35.25 2.90
2861 7567 1.868251 CGACTCCGAAGCGTACAGC 60.868 63.158 0.00 0.00 41.97 4.40
2894 7600 3.918591 GTGTATGTGTGTTCAGGTACTCG 59.081 47.826 0.00 0.00 34.60 4.18
2906 7612 4.655027 GATGCAGAACATGTGTATGTGTG 58.345 43.478 0.00 0.00 46.54 3.82
2937 7644 7.067129 ACCTGAGGAGTTTAACTTTGTTCTTTC 59.933 37.037 4.99 0.00 0.00 2.62
2944 7651 6.289064 ACACTACCTGAGGAGTTTAACTTTG 58.711 40.000 4.99 0.00 0.00 2.77
2959 7684 5.977635 TCAGAATCACCATAACACTACCTG 58.022 41.667 0.00 0.00 0.00 4.00
3113 8251 9.303537 GACCAGTGAACTCTTATTACTGATAAC 57.696 37.037 0.00 0.00 40.80 1.89
3120 8258 9.654663 ATTACAAGACCAGTGAACTCTTATTAC 57.345 33.333 0.00 0.00 0.00 1.89
3134 8272 6.808008 AACTGTGATGAATTACAAGACCAG 57.192 37.500 0.00 0.00 0.00 4.00
3137 8275 6.917477 TGCAAAACTGTGATGAATTACAAGAC 59.083 34.615 0.00 0.00 0.00 3.01
3160 8298 1.888512 TGGTTTCCTTGCTCTGAATGC 59.111 47.619 0.00 0.00 0.00 3.56
3182 8320 1.670967 GCATGAGGCTTCTGTTTTGCC 60.671 52.381 0.00 0.00 46.42 4.52
3183 8321 1.000060 TGCATGAGGCTTCTGTTTTGC 60.000 47.619 0.00 0.06 45.15 3.68
3216 8354 4.412858 TGTCCAGTCCCCTTACAAACTTAA 59.587 41.667 0.00 0.00 0.00 1.85
3251 8389 2.740055 GTGCCGTGCTCTCCTGTG 60.740 66.667 0.00 0.00 0.00 3.66
3304 8442 0.979665 ATCAGTGAGTCCTGGTGGTG 59.020 55.000 0.00 0.00 33.14 4.17
3317 8455 2.416836 CCCTGCATTTGCTTGATCAGTG 60.417 50.000 3.94 0.00 42.66 3.66
3336 8474 1.452833 GTTGAGATGAGCCTGGCCC 60.453 63.158 16.57 3.45 0.00 5.80
3338 8476 0.747283 CCTGTTGAGATGAGCCTGGC 60.747 60.000 11.65 11.65 0.00 4.85
3359 8497 1.238439 CATTCAACTTGACGGCCACT 58.762 50.000 2.24 0.00 0.00 4.00
3553 8694 0.536724 CGTGGTGGAGATGGACATCA 59.463 55.000 14.16 0.00 40.22 3.07
3554 8695 0.537188 ACGTGGTGGAGATGGACATC 59.463 55.000 4.15 4.15 38.09 3.06
3604 8745 1.812922 GCCTCTGCGATGTCTGTGG 60.813 63.158 0.00 0.00 0.00 4.17
3631 8772 0.461548 GGTGGACGATGATCTGCTCA 59.538 55.000 0.00 0.00 38.53 4.26
3632 8773 0.461548 TGGTGGACGATGATCTGCTC 59.538 55.000 0.00 0.00 0.00 4.26
3647 8788 2.056577 GAAGACCGAAAGTACGTGGTG 58.943 52.381 0.00 0.00 34.12 4.17
3674 8815 3.606846 CGTGTGTTGGCTGTTGTTATGAG 60.607 47.826 0.00 0.00 0.00 2.90
3701 8842 3.967987 ACTTCATGGGTCTGGTATCCTAC 59.032 47.826 0.00 0.00 0.00 3.18
3703 8844 3.136641 ACTTCATGGGTCTGGTATCCT 57.863 47.619 0.00 0.00 0.00 3.24
3710 8851 3.490348 ACCAAAGAACTTCATGGGTCTG 58.510 45.455 14.72 0.00 37.26 3.51
3744 8885 1.202806 TGACTGCTCCACTCCCAAAAG 60.203 52.381 0.00 0.00 0.00 2.27
3791 8932 0.803768 CTGAGACGTTGCTGGATCCG 60.804 60.000 7.39 3.14 0.00 4.18
3796 8937 3.114616 CCGCTGAGACGTTGCTGG 61.115 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.