Multiple sequence alignment - TraesCS2D01G134100

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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 TraesCS2D01G134100 chr2D 100.000 4259 0 0 1 4259 79054033 79049775 0.000000e+00 7866.0
1 TraesCS2D01G134100 chr2D 98.889 90 1 0 2942 3031 412382603 412382514 1.230000e-35 161.0
2 TraesCS2D01G134100 chr2D 100.000 29 0 0 2 30 160195475 160195503 2.000000e-03 54.7
3 TraesCS2D01G134100 chr2D 100.000 29 0 0 2 30 260370071 260370043 2.000000e-03 54.7
4 TraesCS2D01G134100 chr2D 90.698 43 1 3 64 106 524045789 524045828 2.000000e-03 54.7
5 TraesCS2D01G134100 chr2D 94.444 36 1 1 2 36 609638911 609638946 2.000000e-03 54.7
6 TraesCS2D01G134100 chr2A 91.983 2133 82 40 842 2944 79311120 79309047 0.000000e+00 2909.0
7 TraesCS2D01G134100 chr2A 95.366 820 38 0 3025 3844 79309049 79308230 0.000000e+00 1304.0
8 TraesCS2D01G134100 chr2A 97.674 172 4 0 4086 4257 79307869 79307698 3.220000e-76 296.0
9 TraesCS2D01G134100 chr2A 90.476 147 10 3 260 406 79311949 79311807 1.560000e-44 191.0
10 TraesCS2D01G134100 chr2A 91.781 73 5 1 88 160 79313595 79313524 2.710000e-17 100.0
11 TraesCS2D01G134100 chr2A 87.931 58 2 5 51 107 611763505 611763558 3.560000e-06 63.9
12 TraesCS2D01G134100 chr2A 100.000 30 0 0 188 217 79313049 79313020 5.950000e-04 56.5
13 TraesCS2D01G134100 chr2B 88.708 2391 111 71 637 2944 122715930 122713616 0.000000e+00 2772.0
14 TraesCS2D01G134100 chr2B 93.014 1045 54 12 3025 4068 122713618 122712592 0.000000e+00 1507.0
15 TraesCS2D01G134100 chr2B 98.837 172 2 0 4086 4257 122712448 122712277 1.490000e-79 307.0
16 TraesCS2D01G134100 chr6A 96.907 97 1 2 2942 3036 558041266 558041362 1.230000e-35 161.0
17 TraesCS2D01G134100 chr1A 96.809 94 3 0 2942 3035 345300414 345300321 1.590000e-34 158.0
18 TraesCS2D01G134100 chr1A 100.000 45 0 0 3934 3978 549055193 549055237 2.730000e-12 84.2
19 TraesCS2D01G134100 chr1A 97.778 45 0 1 3934 3978 16555416 16555459 4.570000e-10 76.8
20 TraesCS2D01G134100 chr1A 100.000 29 0 0 2 30 232340403 232340375 2.000000e-03 54.7
21 TraesCS2D01G134100 chr1A 100.000 29 0 0 2 30 592144770 592144742 2.000000e-03 54.7
22 TraesCS2D01G134100 chr7B 95.876 97 3 1 2932 3028 93439160 93439065 5.700000e-34 156.0
23 TraesCS2D01G134100 chr6D 96.809 94 1 1 2942 3035 441898296 441898387 5.700000e-34 156.0
24 TraesCS2D01G134100 chr5B 94.898 98 4 1 2933 3030 432174794 432174698 7.380000e-33 152.0
25 TraesCS2D01G134100 chr5B 100.000 31 0 0 78 108 605337239 605337269 1.650000e-04 58.4
26 TraesCS2D01G134100 chr5B 100.000 29 0 0 2 30 339290288 339290316 2.000000e-03 54.7
27 TraesCS2D01G134100 chr5B 100.000 29 0 0 2 30 681819392 681819364 2.000000e-03 54.7
28 TraesCS2D01G134100 chr3A 93.204 103 5 2 2936 3036 391475382 391475484 2.650000e-32 150.0
29 TraesCS2D01G134100 chr3A 92.381 105 6 2 2927 3029 549639208 549639104 9.540000e-32 148.0
30 TraesCS2D01G134100 chr3A 95.652 46 1 1 3929 3974 597967829 597967873 5.910000e-09 73.1
31 TraesCS2D01G134100 chr3A 90.196 51 5 0 3121 3171 102621161 102621211 2.750000e-07 67.6
32 TraesCS2D01G134100 chr6B 91.667 108 6 3 2932 3039 349967641 349967745 3.430000e-31 147.0
33 TraesCS2D01G134100 chr6B 91.071 56 1 2 3929 3981 463199284 463199230 5.910000e-09 73.1
34 TraesCS2D01G134100 chr6B 86.441 59 8 0 3116 3174 271826958 271826900 9.880000e-07 65.8
35 TraesCS2D01G134100 chr1B 98.000 50 0 1 3929 3978 660597107 660597059 7.590000e-13 86.1
36 TraesCS2D01G134100 chr1B 88.235 51 2 3 58 107 626136335 626136288 1.650000e-04 58.4
37 TraesCS2D01G134100 chr4B 96.000 50 1 1 3929 3978 495284349 495284301 3.530000e-11 80.5
38 TraesCS2D01G134100 chr4B 100.000 29 0 0 2 30 671812039 671812067 2.000000e-03 54.7
39 TraesCS2D01G134100 chr3D 94.118 51 3 0 3121 3171 86338661 86338711 1.270000e-10 78.7
40 TraesCS2D01G134100 chr3D 91.071 56 0 2 3929 3980 36571459 36571513 2.120000e-08 71.3
41 TraesCS2D01G134100 chr4D 92.453 53 3 1 3929 3981 132038760 132038709 1.640000e-09 75.0
42 TraesCS2D01G134100 chr4D 91.837 49 2 2 59 107 28475016 28474970 2.750000e-07 67.6
43 TraesCS2D01G134100 chr7A 91.071 56 1 2 3929 3981 397767029 397766975 5.910000e-09 73.1
44 TraesCS2D01G134100 chr5A 100.000 30 0 0 1 30 679871167 679871138 5.950000e-04 56.5
45 TraesCS2D01G134100 chr5D 100.000 29 0 0 2 30 360916294 360916266 2.000000e-03 54.7
46 TraesCS2D01G134100 chr4A 100.000 29 0 0 78 106 570999293 570999265 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 TraesCS2D01G134100 chr2D 79049775 79054033 4258 True 7866.000000 7866 100.000000 1 4259 1 chr2D.!!$R1 4258
1 TraesCS2D01G134100 chr2A 79307698 79313595 5897 True 809.416667 2909 94.546667 88 4257 6 chr2A.!!$R1 4169
2 TraesCS2D01G134100 chr2B 122712277 122715930 3653 True 1528.666667 2772 93.519667 637 4257 3 chr2B.!!$R1 3620

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
234 1726 0.250793 AATCCGACGGCCATGTTACA 59.749 50.0 9.66 0.0 0.0 2.41 F
236 1728 0.461163 TCCGACGGCCATGTTACATG 60.461 55.0 17.60 17.6 0.0 3.21 F
1353 3151 0.579156 GCATCTTCGGTCTGATTCGC 59.421 55.0 0.00 0.0 0.0 4.70 F
2349 4219 0.375106 GCCAATACGCAGAGAAGCAC 59.625 55.0 0.00 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 3981 0.254747 CCCTTCTAAATGTGGCCGGA 59.745 55.0 5.05 0.00 0.00 5.14 R
2224 4094 4.180377 TGGACATACTCCTAGTAGGGTG 57.820 50.0 16.44 11.66 36.85 4.61 R
2427 4297 1.129058 ACCTCGGTTCAGACCTTGTT 58.871 50.0 0.00 0.00 44.20 2.83 R
3423 5295 0.595095 CTTCAGCTGGACCTTTGTGC 59.405 55.0 15.13 0.00 0.00 4.57 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
23 24 6.526566 CAAGTGTCTCAACCTTAGTACAAC 57.473 41.667 0.00 0.00 0.00 3.32
24 25 6.281405 CAAGTGTCTCAACCTTAGTACAACT 58.719 40.000 0.00 0.00 0.00 3.16
25 26 6.481434 AGTGTCTCAACCTTAGTACAACTT 57.519 37.500 0.00 0.00 0.00 2.66
26 27 6.885922 AGTGTCTCAACCTTAGTACAACTTT 58.114 36.000 0.00 0.00 0.00 2.66
27 28 8.015185 AGTGTCTCAACCTTAGTACAACTTTA 57.985 34.615 0.00 0.00 0.00 1.85
28 29 8.648693 AGTGTCTCAACCTTAGTACAACTTTAT 58.351 33.333 0.00 0.00 0.00 1.40
29 30 9.918630 GTGTCTCAACCTTAGTACAACTTTATA 57.081 33.333 0.00 0.00 0.00 0.98
99 100 7.602517 AAGAGACATTTATTTTGAGACGGAG 57.397 36.000 0.00 0.00 0.00 4.63
101 102 6.049955 AGACATTTATTTTGAGACGGAGGA 57.950 37.500 0.00 0.00 0.00 3.71
111 112 6.540438 TTTGAGACGGAGGAAGTATTGTAT 57.460 37.500 0.00 0.00 0.00 2.29
114 115 7.273320 TGAGACGGAGGAAGTATTGTATTAG 57.727 40.000 0.00 0.00 0.00 1.73
145 146 4.373156 ACATATCCTAAACCTGATGGGC 57.627 45.455 0.00 0.00 39.10 5.36
156 157 2.578021 ACCTGATGGGCAGTCAATTACT 59.422 45.455 0.00 0.00 43.33 2.24
179 187 3.509659 GGCCTTGCCGGTCAATAC 58.490 61.111 1.90 3.22 39.62 1.89
181 189 1.743995 GCCTTGCCGGTCAATACGT 60.744 57.895 1.90 0.00 33.57 3.57
183 191 1.808891 GCCTTGCCGGTCAATACGTAT 60.809 52.381 1.90 1.14 33.57 3.06
184 192 2.546373 GCCTTGCCGGTCAATACGTATA 60.546 50.000 8.83 0.00 33.57 1.47
185 193 3.314553 CCTTGCCGGTCAATACGTATAG 58.685 50.000 8.83 0.00 33.57 1.31
186 194 2.427232 TGCCGGTCAATACGTATAGC 57.573 50.000 8.83 2.97 0.00 2.97
234 1726 0.250793 AATCCGACGGCCATGTTACA 59.749 50.000 9.66 0.00 0.00 2.41
236 1728 0.461163 TCCGACGGCCATGTTACATG 60.461 55.000 17.60 17.60 0.00 3.21
239 1731 1.202020 CGACGGCCATGTTACATGTTG 60.202 52.381 21.84 13.87 0.00 3.33
240 1732 2.080693 GACGGCCATGTTACATGTTGA 58.919 47.619 21.84 0.00 0.00 3.18
241 1733 1.810151 ACGGCCATGTTACATGTTGAC 59.190 47.619 21.84 10.39 0.00 3.18
242 1734 2.083774 CGGCCATGTTACATGTTGACT 58.916 47.619 21.84 0.00 0.00 3.41
243 1735 2.487762 CGGCCATGTTACATGTTGACTT 59.512 45.455 21.84 0.00 0.00 3.01
244 1736 3.057596 CGGCCATGTTACATGTTGACTTT 60.058 43.478 21.84 0.00 0.00 2.66
245 1737 4.558496 CGGCCATGTTACATGTTGACTTTT 60.558 41.667 21.84 0.00 0.00 2.27
246 1738 5.296748 GGCCATGTTACATGTTGACTTTTT 58.703 37.500 21.84 0.00 0.00 1.94
271 1763 1.831106 TGCAGGGAGATCATGTTACGT 59.169 47.619 0.00 0.00 0.00 3.57
272 1764 3.028130 TGCAGGGAGATCATGTTACGTA 58.972 45.455 0.00 0.00 0.00 3.57
278 1770 5.598830 AGGGAGATCATGTTACGTATTGACT 59.401 40.000 0.00 1.80 0.00 3.41
287 1779 8.410912 TCATGTTACGTATTGACTTGCTACTAT 58.589 33.333 0.00 0.00 0.00 2.12
353 1845 2.436646 CCATCCCCTCGTGCACAC 60.437 66.667 18.64 0.00 0.00 3.82
354 1846 2.436646 CATCCCCTCGTGCACACC 60.437 66.667 18.64 0.00 0.00 4.16
405 1897 0.963355 AGAGTCCACAGAGGCGAGAC 60.963 60.000 0.00 0.00 37.29 3.36
406 1898 2.179517 GTCCACAGAGGCGAGACG 59.820 66.667 0.00 0.00 37.29 4.18
407 1899 2.033602 TCCACAGAGGCGAGACGA 59.966 61.111 0.00 0.00 37.29 4.20
408 1900 2.041115 TCCACAGAGGCGAGACGAG 61.041 63.158 0.00 0.00 37.29 4.18
409 1901 2.336478 CCACAGAGGCGAGACGAGT 61.336 63.158 0.00 0.00 0.00 4.18
410 1902 1.135731 CACAGAGGCGAGACGAGTC 59.864 63.158 0.00 0.00 0.00 3.36
411 1903 1.302591 ACAGAGGCGAGACGAGTCA 60.303 57.895 5.99 0.00 0.00 3.41
412 1904 1.135731 CAGAGGCGAGACGAGTCAC 59.864 63.158 5.99 0.00 0.00 3.67
413 1905 2.098680 GAGGCGAGACGAGTCACG 59.901 66.667 16.45 16.45 44.44 4.35
615 2123 1.303091 CCCGCCCCGAAACTTAACAG 61.303 60.000 0.00 0.00 0.00 3.16
623 2131 1.193874 CGAAACTTAACAGACCCGCAC 59.806 52.381 0.00 0.00 0.00 5.34
624 2132 2.215196 GAAACTTAACAGACCCGCACA 58.785 47.619 0.00 0.00 0.00 4.57
625 2133 1.878953 AACTTAACAGACCCGCACAG 58.121 50.000 0.00 0.00 0.00 3.66
626 2134 0.602905 ACTTAACAGACCCGCACAGC 60.603 55.000 0.00 0.00 0.00 4.40
627 2135 1.298859 CTTAACAGACCCGCACAGCC 61.299 60.000 0.00 0.00 0.00 4.85
628 2136 2.046009 TTAACAGACCCGCACAGCCA 62.046 55.000 0.00 0.00 0.00 4.75
629 2137 2.725203 TAACAGACCCGCACAGCCAC 62.725 60.000 0.00 0.00 0.00 5.01
630 2138 4.624364 CAGACCCGCACAGCCACA 62.624 66.667 0.00 0.00 0.00 4.17
631 2139 4.626081 AGACCCGCACAGCCACAC 62.626 66.667 0.00 0.00 0.00 3.82
676 2184 1.537562 CCAACCGACCTAATACCGAGC 60.538 57.143 0.00 0.00 0.00 5.03
677 2185 1.135527 CAACCGACCTAATACCGAGCA 59.864 52.381 0.00 0.00 0.00 4.26
678 2186 1.030457 ACCGACCTAATACCGAGCAG 58.970 55.000 0.00 0.00 0.00 4.24
1221 3019 1.271840 ACATGGCCTACGACACCCAT 61.272 55.000 3.32 0.00 38.56 4.00
1352 3150 1.590238 GTGCATCTTCGGTCTGATTCG 59.410 52.381 0.00 0.00 0.00 3.34
1353 3151 0.579156 GCATCTTCGGTCTGATTCGC 59.421 55.000 0.00 0.00 0.00 4.70
1381 3181 4.040376 GCCGCTCAATTCATTCATTCTTC 58.960 43.478 0.00 0.00 0.00 2.87
1395 3195 3.750652 TCATTCTTCGTGCACATTGCTTA 59.249 39.130 18.64 0.00 45.31 3.09
1396 3196 4.395854 TCATTCTTCGTGCACATTGCTTAT 59.604 37.500 18.64 0.00 45.31 1.73
1397 3197 5.584251 TCATTCTTCGTGCACATTGCTTATA 59.416 36.000 18.64 0.00 45.31 0.98
1603 3411 3.136260 AGCAAAGATTTTTGAGGGGCAAA 59.864 39.130 12.62 0.00 45.21 3.68
1604 3412 3.250762 GCAAAGATTTTTGAGGGGCAAAC 59.749 43.478 12.62 0.00 45.64 2.93
1672 3480 5.998454 ATTGCTCGGTGATTGAAATCTAG 57.002 39.130 4.76 0.00 36.39 2.43
1712 3543 8.783093 CCAAGTTTTCACAATAGTTACTGATGA 58.217 33.333 0.00 0.00 0.00 2.92
1743 3574 6.765403 TGGTACTCCCAATGTGTATATTAGC 58.235 40.000 0.00 0.00 41.50 3.09
1928 3789 0.851469 ATCTGAATCCTGGGCAGCAT 59.149 50.000 0.00 0.00 0.00 3.79
2044 3911 4.099573 CCAAGGTGTATATATAGGAGGCCG 59.900 50.000 0.00 0.00 0.00 6.13
2058 3925 0.743345 AGGCCGCGTTAACAATCTCC 60.743 55.000 4.92 0.03 0.00 3.71
2059 3926 0.743345 GGCCGCGTTAACAATCTCCT 60.743 55.000 4.92 0.00 0.00 3.69
2084 3954 9.159364 CTCTCTGTATTTCATTTCACTGATCAA 57.841 33.333 0.00 0.00 0.00 2.57
2111 3981 1.135094 ATCCCGATGTGCCTCAGAAT 58.865 50.000 0.00 0.00 0.00 2.40
2219 4089 5.993441 TCTATAGCTACACATACACGCTACA 59.007 40.000 0.00 0.00 36.18 2.74
2220 4090 3.146618 AGCTACACATACACGCTACAC 57.853 47.619 0.00 0.00 0.00 2.90
2221 4091 2.490509 AGCTACACATACACGCTACACA 59.509 45.455 0.00 0.00 0.00 3.72
2222 4092 3.130516 AGCTACACATACACGCTACACAT 59.869 43.478 0.00 0.00 0.00 3.21
2224 4094 4.440103 GCTACACATACACGCTACACATAC 59.560 45.833 0.00 0.00 0.00 2.39
2225 4095 4.443913 ACACATACACGCTACACATACA 57.556 40.909 0.00 0.00 0.00 2.29
2226 4096 4.171005 ACACATACACGCTACACATACAC 58.829 43.478 0.00 0.00 0.00 2.90
2227 4097 3.550275 CACATACACGCTACACATACACC 59.450 47.826 0.00 0.00 0.00 4.16
2228 4098 2.945447 TACACGCTACACATACACCC 57.055 50.000 0.00 0.00 0.00 4.61
2229 4099 1.263356 ACACGCTACACATACACCCT 58.737 50.000 0.00 0.00 0.00 4.34
2230 4100 2.449464 ACACGCTACACATACACCCTA 58.551 47.619 0.00 0.00 0.00 3.53
2231 4101 2.165030 ACACGCTACACATACACCCTAC 59.835 50.000 0.00 0.00 0.00 3.18
2232 4102 2.426024 CACGCTACACATACACCCTACT 59.574 50.000 0.00 0.00 0.00 2.57
2233 4103 3.628942 CACGCTACACATACACCCTACTA 59.371 47.826 0.00 0.00 0.00 1.82
2234 4104 3.881688 ACGCTACACATACACCCTACTAG 59.118 47.826 0.00 0.00 0.00 2.57
2235 4105 3.252701 CGCTACACATACACCCTACTAGG 59.747 52.174 0.00 0.00 34.30 3.02
2236 4106 4.467769 GCTACACATACACCCTACTAGGA 58.532 47.826 3.36 0.00 37.67 2.94
2237 4107 4.519730 GCTACACATACACCCTACTAGGAG 59.480 50.000 3.36 0.00 37.67 3.69
2238 4108 4.604784 ACACATACACCCTACTAGGAGT 57.395 45.455 3.36 4.79 37.67 3.85
2239 4109 5.722172 ACACATACACCCTACTAGGAGTA 57.278 43.478 3.36 6.74 37.67 2.59
2240 4110 6.277064 ACACATACACCCTACTAGGAGTAT 57.723 41.667 3.36 8.56 37.67 2.12
2309 4179 3.010250 GGGAACATCCTTGGGAAGTAAGT 59.990 47.826 0.00 0.00 32.11 2.24
2349 4219 0.375106 GCCAATACGCAGAGAAGCAC 59.625 55.000 0.00 0.00 0.00 4.40
2384 4254 1.153369 CCATGGCGAGGTACCTGTG 60.153 63.158 22.10 12.92 0.00 3.66
2387 4257 3.702048 GGCGAGGTACCTGTGCCA 61.702 66.667 34.53 0.00 41.30 4.92
2393 4263 2.223829 CGAGGTACCTGTGCCAGATTAG 60.224 54.545 22.10 0.00 37.85 1.73
2394 4264 3.031736 GAGGTACCTGTGCCAGATTAGA 58.968 50.000 22.10 0.00 37.85 2.10
2400 4270 2.355513 CCTGTGCCAGATTAGAGTTGCT 60.356 50.000 4.00 0.00 32.44 3.91
2409 4279 4.809958 CAGATTAGAGTTGCTGTGAGGATG 59.190 45.833 0.00 0.00 0.00 3.51
2412 4282 1.364626 GAGTTGCTGTGAGGATGGCG 61.365 60.000 0.00 0.00 0.00 5.69
2426 4296 0.976641 ATGGCGTGGTCGATGGATAT 59.023 50.000 0.00 0.00 39.71 1.63
2427 4297 1.623163 TGGCGTGGTCGATGGATATA 58.377 50.000 0.00 0.00 39.71 0.86
2437 4307 5.221441 TGGTCGATGGATATAACAAGGTCTG 60.221 44.000 0.00 0.00 0.00 3.51
2440 4310 6.421202 GTCGATGGATATAACAAGGTCTGAAC 59.579 42.308 0.00 0.00 0.00 3.18
2441 4311 5.696724 CGATGGATATAACAAGGTCTGAACC 59.303 44.000 0.00 0.00 46.87 3.62
2452 4323 2.376109 GGTCTGAACCGAGGTGATAGA 58.624 52.381 0.00 0.00 35.36 1.98
2469 4340 5.991606 GTGATAGAAAGCACATACCATAGCA 59.008 40.000 0.00 0.00 41.73 3.49
2558 4429 5.685511 ACATCAACAAATGACAAAACGTAGC 59.314 36.000 0.00 0.00 41.93 3.58
2920 4792 4.164796 TGGAATGGAAGAGCATAGTGTCAT 59.835 41.667 0.00 0.00 0.00 3.06
2944 4816 7.295322 TGCAGTAGAGCATTCTATTGATACT 57.705 36.000 8.99 0.00 42.92 2.12
2945 4817 7.730084 TGCAGTAGAGCATTCTATTGATACTT 58.270 34.615 8.99 0.00 42.92 2.24
2946 4818 7.869937 TGCAGTAGAGCATTCTATTGATACTTC 59.130 37.037 8.99 0.00 42.92 3.01
2947 4819 7.330700 GCAGTAGAGCATTCTATTGATACTTCC 59.669 40.741 8.99 0.00 42.92 3.46
2948 4820 8.584157 CAGTAGAGCATTCTATTGATACTTCCT 58.416 37.037 0.68 0.00 42.92 3.36
2949 4821 8.802267 AGTAGAGCATTCTATTGATACTTCCTC 58.198 37.037 0.00 0.00 38.17 3.71
2950 4822 7.003402 AGAGCATTCTATTGATACTTCCTCC 57.997 40.000 0.00 0.00 0.00 4.30
2951 4823 5.788450 AGCATTCTATTGATACTTCCTCCG 58.212 41.667 0.00 0.00 0.00 4.63
2952 4824 5.305644 AGCATTCTATTGATACTTCCTCCGT 59.694 40.000 0.00 0.00 0.00 4.69
2953 4825 6.493802 AGCATTCTATTGATACTTCCTCCGTA 59.506 38.462 0.00 0.00 0.00 4.02
2954 4826 7.015292 AGCATTCTATTGATACTTCCTCCGTAA 59.985 37.037 0.00 0.00 0.00 3.18
2955 4827 7.656137 GCATTCTATTGATACTTCCTCCGTAAA 59.344 37.037 0.00 0.00 0.00 2.01
2956 4828 8.979574 CATTCTATTGATACTTCCTCCGTAAAC 58.020 37.037 0.00 0.00 0.00 2.01
2957 4829 7.893124 TCTATTGATACTTCCTCCGTAAACT 57.107 36.000 0.00 0.00 0.00 2.66
2958 4830 8.985315 TCTATTGATACTTCCTCCGTAAACTA 57.015 34.615 0.00 0.00 0.00 2.24
2959 4831 9.412460 TCTATTGATACTTCCTCCGTAAACTAA 57.588 33.333 0.00 0.00 0.00 2.24
2968 4840 8.358895 ACTTCCTCCGTAAACTAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
2969 4841 6.906659 TCCTCCGTAAACTAATATAAGAGCG 58.093 40.000 0.00 0.00 0.00 5.03
2970 4842 6.488006 TCCTCCGTAAACTAATATAAGAGCGT 59.512 38.462 0.00 0.00 0.00 5.07
2971 4843 7.013655 TCCTCCGTAAACTAATATAAGAGCGTT 59.986 37.037 0.00 0.00 0.00 4.84
2972 4844 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2973 4845 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2974 4846 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2975 4847 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3020 4892 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
3021 4893 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
3022 4894 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
3023 4895 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
3024 4896 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
3106 4978 6.359617 CGGACAATGTCAATGTTGTTTAAGAC 59.640 38.462 15.86 0.00 38.57 3.01
3141 5013 3.804325 CAGTGCTAGATACATCCGTTTGG 59.196 47.826 0.00 0.00 0.00 3.28
3186 5058 6.042666 GGAGGAAGTAATAAAGAGGCTCTGAT 59.957 42.308 19.53 11.94 0.00 2.90
3314 5186 1.635487 CAAATTGGGAGGACAGGAGGA 59.365 52.381 0.00 0.00 0.00 3.71
3423 5295 2.319844 ACCAGGGAAAAGGCTGAAAAG 58.680 47.619 0.00 0.00 0.00 2.27
3626 5498 4.558538 ACAGTCAATGTCTTGAAAGCAC 57.441 40.909 0.00 0.00 42.85 4.40
3755 5628 8.619546 GCTGACATAAATAAGAGAAAGCAAGAT 58.380 33.333 0.00 0.00 0.00 2.40
3825 5698 4.673441 ACATGTCTGTTTAGCTAGCTACG 58.327 43.478 24.09 12.50 28.70 3.51
3872 5828 0.769873 AGATGGCCTCTGCTTATGGG 59.230 55.000 3.32 0.00 37.74 4.00
3945 5901 7.540474 TGTACTATCCAGAAATAGATGACCC 57.460 40.000 0.00 0.00 34.08 4.46
3947 5903 7.567250 TGTACTATCCAGAAATAGATGACCCAA 59.433 37.037 0.00 0.00 34.08 4.12
3948 5904 6.831976 ACTATCCAGAAATAGATGACCCAAC 58.168 40.000 0.00 0.00 34.08 3.77
3949 5905 5.983333 ATCCAGAAATAGATGACCCAACT 57.017 39.130 0.00 0.00 0.00 3.16
3952 5908 5.945784 TCCAGAAATAGATGACCCAACTTTG 59.054 40.000 0.00 0.00 0.00 2.77
3953 5909 5.711976 CCAGAAATAGATGACCCAACTTTGT 59.288 40.000 0.00 0.00 0.00 2.83
3954 5910 6.884295 CCAGAAATAGATGACCCAACTTTGTA 59.116 38.462 0.00 0.00 0.00 2.41
3955 5911 7.148239 CCAGAAATAGATGACCCAACTTTGTAC 60.148 40.741 0.00 0.00 0.00 2.90
3956 5912 7.607991 CAGAAATAGATGACCCAACTTTGTACT 59.392 37.037 0.00 0.00 0.00 2.73
3958 5914 9.444600 GAAATAGATGACCCAACTTTGTACTAA 57.555 33.333 0.00 0.00 0.00 2.24
3959 5915 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
3960 5916 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
3961 5917 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
3962 5918 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
3963 5919 6.687081 TGACCCAACTTTGTACTAACTTTG 57.313 37.500 0.00 0.00 0.00 2.77
3964 5920 5.591067 TGACCCAACTTTGTACTAACTTTGG 59.409 40.000 14.15 14.15 33.25 3.28
3965 5921 5.757988 ACCCAACTTTGTACTAACTTTGGA 58.242 37.500 19.22 0.00 35.07 3.53
3966 5922 6.189133 ACCCAACTTTGTACTAACTTTGGAA 58.811 36.000 19.22 0.00 35.07 3.53
3967 5923 6.095860 ACCCAACTTTGTACTAACTTTGGAAC 59.904 38.462 19.22 0.00 35.07 3.62
3968 5924 6.196571 CCAACTTTGTACTAACTTTGGAACG 58.803 40.000 15.25 0.00 35.07 3.95
3969 5925 5.996669 ACTTTGTACTAACTTTGGAACGG 57.003 39.130 0.00 0.00 0.00 4.44
3970 5926 5.673514 ACTTTGTACTAACTTTGGAACGGA 58.326 37.500 0.00 0.00 0.00 4.69
3971 5927 5.756833 ACTTTGTACTAACTTTGGAACGGAG 59.243 40.000 0.00 0.00 0.00 4.63
3972 5928 4.261578 TGTACTAACTTTGGAACGGAGG 57.738 45.455 0.00 0.00 0.00 4.30
3973 5929 2.853235 ACTAACTTTGGAACGGAGGG 57.147 50.000 0.00 0.00 0.00 4.30
3974 5930 2.332117 ACTAACTTTGGAACGGAGGGA 58.668 47.619 0.00 0.00 0.00 4.20
3975 5931 2.302157 ACTAACTTTGGAACGGAGGGAG 59.698 50.000 0.00 0.00 0.00 4.30
4077 6065 6.349300 ACTGTTTACATATCAAGCAGGGTAG 58.651 40.000 12.35 0.00 38.21 3.18
4248 6331 6.554334 TTAGACAAACAACATAAGCCAGTC 57.446 37.500 0.00 0.00 0.00 3.51
4257 6340 3.450904 ACATAAGCCAGTCCAGAAGGTA 58.549 45.455 0.00 0.00 35.89 3.08
4258 6341 3.452627 ACATAAGCCAGTCCAGAAGGTAG 59.547 47.826 0.00 0.00 35.89 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.281405 AGTTGTACTAAGGTTGAGACACTTG 58.719 40.000 0.00 0.00 0.00 3.16
1 2 6.481434 AGTTGTACTAAGGTTGAGACACTT 57.519 37.500 0.00 0.00 0.00 3.16
2 3 6.481434 AAGTTGTACTAAGGTTGAGACACT 57.519 37.500 0.00 0.00 0.00 3.55
3 4 8.828688 ATAAAGTTGTACTAAGGTTGAGACAC 57.171 34.615 0.00 0.00 0.00 3.67
71 72 9.922305 CCGTCTCAAAATAAATGTCTCTTAATC 57.078 33.333 0.00 0.00 0.00 1.75
72 73 9.667107 TCCGTCTCAAAATAAATGTCTCTTAAT 57.333 29.630 0.00 0.00 0.00 1.40
73 74 9.151471 CTCCGTCTCAAAATAAATGTCTCTTAA 57.849 33.333 0.00 0.00 0.00 1.85
74 75 7.764443 CCTCCGTCTCAAAATAAATGTCTCTTA 59.236 37.037 0.00 0.00 0.00 2.10
75 76 6.595716 CCTCCGTCTCAAAATAAATGTCTCTT 59.404 38.462 0.00 0.00 0.00 2.85
76 77 6.070767 TCCTCCGTCTCAAAATAAATGTCTCT 60.071 38.462 0.00 0.00 0.00 3.10
77 78 6.106673 TCCTCCGTCTCAAAATAAATGTCTC 58.893 40.000 0.00 0.00 0.00 3.36
78 79 6.049955 TCCTCCGTCTCAAAATAAATGTCT 57.950 37.500 0.00 0.00 0.00 3.41
79 80 6.371825 ACTTCCTCCGTCTCAAAATAAATGTC 59.628 38.462 0.00 0.00 0.00 3.06
80 81 6.238648 ACTTCCTCCGTCTCAAAATAAATGT 58.761 36.000 0.00 0.00 0.00 2.71
81 82 6.743575 ACTTCCTCCGTCTCAAAATAAATG 57.256 37.500 0.00 0.00 0.00 2.32
82 83 8.893727 CAATACTTCCTCCGTCTCAAAATAAAT 58.106 33.333 0.00 0.00 0.00 1.40
83 84 7.881232 ACAATACTTCCTCCGTCTCAAAATAAA 59.119 33.333 0.00 0.00 0.00 1.40
84 85 7.391620 ACAATACTTCCTCCGTCTCAAAATAA 58.608 34.615 0.00 0.00 0.00 1.40
85 86 6.942976 ACAATACTTCCTCCGTCTCAAAATA 58.057 36.000 0.00 0.00 0.00 1.40
86 87 5.805728 ACAATACTTCCTCCGTCTCAAAAT 58.194 37.500 0.00 0.00 0.00 1.82
99 100 5.442391 TGGTTGGGCTAATACAATACTTCC 58.558 41.667 0.00 0.00 0.00 3.46
101 102 6.722129 TGTTTGGTTGGGCTAATACAATACTT 59.278 34.615 4.95 0.00 0.00 2.24
111 112 4.601406 AGGATATGTTTGGTTGGGCTAA 57.399 40.909 0.00 0.00 0.00 3.09
114 115 4.142026 GGTTTAGGATATGTTTGGTTGGGC 60.142 45.833 0.00 0.00 0.00 5.36
173 181 1.621814 GGGGCTGGCTATACGTATTGA 59.378 52.381 19.19 0.00 0.00 2.57
176 184 1.203137 TCAGGGGCTGGCTATACGTAT 60.203 52.381 13.54 13.54 31.51 3.06
177 185 0.186630 TCAGGGGCTGGCTATACGTA 59.813 55.000 0.00 0.00 31.51 3.57
178 186 0.471971 ATCAGGGGCTGGCTATACGT 60.472 55.000 0.00 0.00 31.51 3.57
179 187 0.247736 GATCAGGGGCTGGCTATACG 59.752 60.000 0.00 0.00 31.51 3.06
181 189 2.292521 CCTAGATCAGGGGCTGGCTATA 60.293 54.545 0.00 0.00 41.26 1.31
183 191 0.178921 CCTAGATCAGGGGCTGGCTA 60.179 60.000 0.00 0.00 41.26 3.93
184 192 1.461075 CCTAGATCAGGGGCTGGCT 60.461 63.158 0.00 0.00 41.26 4.75
185 193 3.155750 CCTAGATCAGGGGCTGGC 58.844 66.667 0.00 0.00 41.26 4.85
186 194 3.155750 GCCTAGATCAGGGGCTGG 58.844 66.667 13.85 0.00 45.66 4.85
247 1739 4.155826 CGTAACATGATCTCCCTGCAAAAA 59.844 41.667 0.00 0.00 0.00 1.94
248 1740 3.689161 CGTAACATGATCTCCCTGCAAAA 59.311 43.478 0.00 0.00 0.00 2.44
249 1741 3.270027 CGTAACATGATCTCCCTGCAAA 58.730 45.455 0.00 0.00 0.00 3.68
250 1742 2.236146 ACGTAACATGATCTCCCTGCAA 59.764 45.455 0.00 0.00 0.00 4.08
251 1743 1.831106 ACGTAACATGATCTCCCTGCA 59.169 47.619 0.00 0.00 0.00 4.41
252 1744 2.604046 ACGTAACATGATCTCCCTGC 57.396 50.000 0.00 0.00 0.00 4.85
253 1745 5.692204 GTCAATACGTAACATGATCTCCCTG 59.308 44.000 0.00 0.00 0.00 4.45
254 1746 5.598830 AGTCAATACGTAACATGATCTCCCT 59.401 40.000 0.00 0.00 0.00 4.20
255 1747 5.844004 AGTCAATACGTAACATGATCTCCC 58.156 41.667 0.00 0.00 0.00 4.30
256 1748 6.292381 GCAAGTCAATACGTAACATGATCTCC 60.292 42.308 0.00 0.00 0.00 3.71
257 1749 6.477033 AGCAAGTCAATACGTAACATGATCTC 59.523 38.462 0.00 0.00 0.00 2.75
258 1750 6.341316 AGCAAGTCAATACGTAACATGATCT 58.659 36.000 0.00 3.26 0.00 2.75
287 1779 3.038788 TGAGATCAACTTGCTTGCGTA 57.961 42.857 0.00 0.00 0.00 4.42
329 1821 2.111878 CGAGGGGATGGTGGATGC 59.888 66.667 0.00 0.00 0.00 3.91
353 1845 2.202492 CGAGGCTTCGTGAGACGG 60.202 66.667 10.50 0.00 42.81 4.79
385 1877 0.678366 TCTCGCCTCTGTGGACTCTC 60.678 60.000 0.00 0.00 38.35 3.20
386 1878 0.963355 GTCTCGCCTCTGTGGACTCT 60.963 60.000 0.00 0.00 38.35 3.24
387 1879 1.509004 GTCTCGCCTCTGTGGACTC 59.491 63.158 0.00 0.00 38.35 3.36
388 1880 2.336478 CGTCTCGCCTCTGTGGACT 61.336 63.158 0.00 0.00 38.35 3.85
389 1881 2.179517 CGTCTCGCCTCTGTGGAC 59.820 66.667 0.00 0.00 38.35 4.02
390 1882 2.033602 TCGTCTCGCCTCTGTGGA 59.966 61.111 0.00 0.00 38.35 4.02
391 1883 2.259875 GACTCGTCTCGCCTCTGTGG 62.260 65.000 0.00 0.00 39.35 4.17
477 1969 3.040763 GATCTGGAGGCGCGATGC 61.041 66.667 12.10 2.63 45.38 3.91
478 1970 2.356793 GGATCTGGAGGCGCGATG 60.357 66.667 12.10 0.00 0.00 3.84
479 1971 2.522923 AGGATCTGGAGGCGCGAT 60.523 61.111 12.10 0.00 0.00 4.58
480 1972 3.219928 GAGGATCTGGAGGCGCGA 61.220 66.667 12.10 0.00 0.00 5.87
481 1973 4.292178 GGAGGATCTGGAGGCGCG 62.292 72.222 0.00 0.00 33.73 6.86
482 1974 4.292178 CGGAGGATCTGGAGGCGC 62.292 72.222 0.00 0.00 38.01 6.53
599 2091 1.162698 GGTCTGTTAAGTTTCGGGGC 58.837 55.000 0.00 0.00 0.00 5.80
600 2092 1.817357 GGGTCTGTTAAGTTTCGGGG 58.183 55.000 0.00 0.00 0.00 5.73
605 2113 2.218603 CTGTGCGGGTCTGTTAAGTTT 58.781 47.619 0.00 0.00 0.00 2.66
724 2232 3.036959 GGAGGAGGAGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
727 2235 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1396 3196 9.739276 AGAAATGTCAATCTTCCATTTGTACTA 57.261 29.630 0.00 0.00 38.53 1.82
1397 3197 8.641498 AGAAATGTCAATCTTCCATTTGTACT 57.359 30.769 0.00 0.00 38.53 2.73
1591 3399 0.457851 CAACACGTTTGCCCCTCAAA 59.542 50.000 0.00 0.00 42.01 2.69
1603 3411 2.736343 TTCGATCGTCGGCAACACGT 62.736 55.000 15.94 0.00 40.88 4.49
1604 3412 1.998550 CTTCGATCGTCGGCAACACG 61.999 60.000 15.94 0.00 40.88 4.49
1630 3438 2.118313 TCAGCACCATCAATCACCTG 57.882 50.000 0.00 0.00 0.00 4.00
1740 3571 6.015772 TGTTGATATGGTCGTATGCTAAGCTA 60.016 38.462 0.00 0.00 0.00 3.32
1741 3572 5.221441 TGTTGATATGGTCGTATGCTAAGCT 60.221 40.000 0.00 0.00 0.00 3.74
1743 3574 7.171508 ACATTGTTGATATGGTCGTATGCTAAG 59.828 37.037 0.00 0.00 0.00 2.18
1795 3626 7.538678 CCTGTTTTAATCAGCAGTGTAACAATC 59.461 37.037 0.00 0.00 41.43 2.67
1928 3789 4.413189 TGGATTGATGAATGGCCTAGAAGA 59.587 41.667 3.32 0.00 0.00 2.87
2044 3911 3.851098 ACAGAGAGGAGATTGTTAACGC 58.149 45.455 0.26 0.00 0.00 4.84
2058 3925 8.713737 TGATCAGTGAAATGAAATACAGAGAG 57.286 34.615 0.00 0.00 31.76 3.20
2059 3926 9.506018 TTTGATCAGTGAAATGAAATACAGAGA 57.494 29.630 0.00 0.00 31.76 3.10
2084 3954 4.102524 TGAGGCACATCGGGATTAATACTT 59.897 41.667 0.00 0.00 0.00 2.24
2111 3981 0.254747 CCCTTCTAAATGTGGCCGGA 59.745 55.000 5.05 0.00 0.00 5.14
2214 4084 4.467769 TCCTAGTAGGGTGTATGTGTAGC 58.532 47.826 16.44 0.00 35.59 3.58
2221 4091 5.374753 TGGACATACTCCTAGTAGGGTGTAT 59.625 44.000 16.44 18.97 42.91 2.29
2222 4092 4.728350 TGGACATACTCCTAGTAGGGTGTA 59.272 45.833 16.44 17.76 36.85 2.90
2224 4094 4.180377 TGGACATACTCCTAGTAGGGTG 57.820 50.000 16.44 11.66 36.85 4.61
2225 4095 4.419200 TCATGGACATACTCCTAGTAGGGT 59.581 45.833 16.44 14.45 36.85 4.34
2226 4096 4.767928 GTCATGGACATACTCCTAGTAGGG 59.232 50.000 16.44 9.43 36.85 3.53
2227 4097 5.636123 AGTCATGGACATACTCCTAGTAGG 58.364 45.833 10.24 10.24 40.26 3.18
2228 4098 7.681679 TCTAGTCATGGACATACTCCTAGTAG 58.318 42.308 0.00 0.00 40.26 2.57
2229 4099 7.628501 TCTAGTCATGGACATACTCCTAGTA 57.371 40.000 0.00 0.00 40.26 1.82
2230 4100 6.517013 TCTAGTCATGGACATACTCCTAGT 57.483 41.667 0.00 0.00 40.26 2.57
2231 4101 8.544622 TCTATCTAGTCATGGACATACTCCTAG 58.455 40.741 0.00 0.00 40.26 3.02
2232 4102 8.450780 TCTATCTAGTCATGGACATACTCCTA 57.549 38.462 0.00 0.00 40.26 2.94
2233 4103 7.336475 TCTATCTAGTCATGGACATACTCCT 57.664 40.000 0.00 0.00 40.26 3.69
2234 4104 6.601613 CCTCTATCTAGTCATGGACATACTCC 59.398 46.154 0.00 0.00 39.97 3.85
2235 4105 6.094881 GCCTCTATCTAGTCATGGACATACTC 59.905 46.154 0.00 0.00 34.60 2.59
2236 4106 5.949354 GCCTCTATCTAGTCATGGACATACT 59.051 44.000 0.00 0.00 34.60 2.12
2237 4107 5.949354 AGCCTCTATCTAGTCATGGACATAC 59.051 44.000 0.00 0.00 34.60 2.39
2238 4108 6.012069 AGAGCCTCTATCTAGTCATGGACATA 60.012 42.308 0.00 0.00 34.60 2.29
2239 4109 5.009436 AGCCTCTATCTAGTCATGGACAT 57.991 43.478 0.00 0.00 34.60 3.06
2240 4110 4.105537 AGAGCCTCTATCTAGTCATGGACA 59.894 45.833 0.00 0.00 34.60 4.02
2241 4111 4.662278 AGAGCCTCTATCTAGTCATGGAC 58.338 47.826 0.00 0.00 0.00 4.02
2255 4125 2.829120 GTGAGGACAAGTTAGAGCCTCT 59.171 50.000 0.00 0.00 44.23 3.69
2384 4254 2.935201 CTCACAGCAACTCTAATCTGGC 59.065 50.000 0.00 0.00 0.00 4.85
2387 4257 4.141756 CCATCCTCACAGCAACTCTAATCT 60.142 45.833 0.00 0.00 0.00 2.40
2393 4263 1.364626 CGCCATCCTCACAGCAACTC 61.365 60.000 0.00 0.00 0.00 3.01
2394 4264 1.376424 CGCCATCCTCACAGCAACT 60.376 57.895 0.00 0.00 0.00 3.16
2400 4270 2.662596 GACCACGCCATCCTCACA 59.337 61.111 0.00 0.00 0.00 3.58
2409 4279 2.288579 TGTTATATCCATCGACCACGCC 60.289 50.000 0.00 0.00 39.58 5.68
2412 4282 4.957296 ACCTTGTTATATCCATCGACCAC 58.043 43.478 0.00 0.00 0.00 4.16
2426 4296 2.036733 CACCTCGGTTCAGACCTTGTTA 59.963 50.000 0.00 0.00 44.20 2.41
2427 4297 1.129058 ACCTCGGTTCAGACCTTGTT 58.871 50.000 0.00 0.00 44.20 2.83
2437 4307 2.930682 GTGCTTTCTATCACCTCGGTTC 59.069 50.000 0.00 0.00 0.00 3.62
2440 4310 2.672961 TGTGCTTTCTATCACCTCGG 57.327 50.000 0.00 0.00 32.51 4.63
2441 4311 4.051922 GGTATGTGCTTTCTATCACCTCG 58.948 47.826 0.00 0.00 32.51 4.63
2452 4323 3.209410 GCTCTGCTATGGTATGTGCTTT 58.791 45.455 0.00 0.00 0.00 3.51
2529 4400 9.737427 ACGTTTTGTCATTTGTTGATGTAATTA 57.263 25.926 0.00 0.00 36.54 1.40
2548 4419 7.027760 TCATCTAGTTCTACTGCTACGTTTTG 58.972 38.462 0.00 0.00 0.00 2.44
2558 4429 7.543868 CACTTCAGGTTTCATCTAGTTCTACTG 59.456 40.741 0.00 0.00 0.00 2.74
2775 4647 3.507162 AACATCTGGACATGTGTTGGA 57.493 42.857 1.15 0.00 37.07 3.53
2830 4702 7.255590 CCTGACTGTTCTGAATTGTAAAATGGT 60.256 37.037 0.00 0.00 0.00 3.55
2943 4815 7.537991 CGCTCTTATATTAGTTTACGGAGGAAG 59.462 40.741 0.00 0.00 0.00 3.46
2944 4816 7.013655 ACGCTCTTATATTAGTTTACGGAGGAA 59.986 37.037 0.00 0.00 0.00 3.36
2945 4817 6.488006 ACGCTCTTATATTAGTTTACGGAGGA 59.512 38.462 0.00 0.00 0.00 3.71
2946 4818 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2947 4819 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2948 4820 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2949 4821 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2994 4866 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2995 4867 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2996 4868 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2997 4869 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2998 4870 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3007 4879 9.498176 GAAAATTGTACTCCCTCTGTAAACTAA 57.502 33.333 0.00 0.00 0.00 2.24
3008 4880 8.653191 TGAAAATTGTACTCCCTCTGTAAACTA 58.347 33.333 0.00 0.00 0.00 2.24
3009 4881 7.514721 TGAAAATTGTACTCCCTCTGTAAACT 58.485 34.615 0.00 0.00 0.00 2.66
3010 4882 7.739498 TGAAAATTGTACTCCCTCTGTAAAC 57.261 36.000 0.00 0.00 0.00 2.01
3011 4883 8.934023 AATGAAAATTGTACTCCCTCTGTAAA 57.066 30.769 0.00 0.00 0.00 2.01
3013 4885 9.613428 CATAATGAAAATTGTACTCCCTCTGTA 57.387 33.333 0.00 0.00 0.00 2.74
3014 4886 7.067494 GCATAATGAAAATTGTACTCCCTCTGT 59.933 37.037 0.00 0.00 0.00 3.41
3015 4887 7.284034 AGCATAATGAAAATTGTACTCCCTCTG 59.716 37.037 0.00 0.00 0.00 3.35
3016 4888 7.349598 AGCATAATGAAAATTGTACTCCCTCT 58.650 34.615 0.00 0.00 0.00 3.69
3017 4889 7.573968 AGCATAATGAAAATTGTACTCCCTC 57.426 36.000 0.00 0.00 0.00 4.30
3018 4890 7.961326 AAGCATAATGAAAATTGTACTCCCT 57.039 32.000 0.00 0.00 0.00 4.20
3019 4891 8.250332 TGAAAGCATAATGAAAATTGTACTCCC 58.750 33.333 0.00 0.00 0.00 4.30
3020 4892 9.294030 CTGAAAGCATAATGAAAATTGTACTCC 57.706 33.333 0.00 0.00 0.00 3.85
3021 4893 9.846248 ACTGAAAGCATAATGAAAATTGTACTC 57.154 29.630 0.00 0.00 37.60 2.59
3025 4897 9.768662 AGAAACTGAAAGCATAATGAAAATTGT 57.231 25.926 0.00 0.00 37.60 2.71
3076 4948 1.806542 ACATTGACATTGTCCGACAGC 59.193 47.619 14.05 0.00 0.00 4.40
3106 4978 5.282055 TCTAGCACTGAAATGGGAGTATG 57.718 43.478 0.00 0.00 0.00 2.39
3314 5186 2.434702 CGGAGCTTTATCCTGGTAGGTT 59.565 50.000 0.00 0.00 37.20 3.50
3423 5295 0.595095 CTTCAGCTGGACCTTTGTGC 59.405 55.000 15.13 0.00 0.00 4.57
3465 5337 4.475028 TGTAAAAATCGCATTGCTCTGTG 58.525 39.130 7.12 0.00 0.00 3.66
3626 5498 4.606961 ACGTTTACTTGCACCAAATTCAG 58.393 39.130 0.00 0.00 0.00 3.02
3641 5513 7.948278 ATGGATCAGCTTCTAATACGTTTAC 57.052 36.000 0.00 0.00 0.00 2.01
3761 5634 7.675161 TCCATGTTCTTAGATCTGATTACCA 57.325 36.000 5.18 0.00 0.00 3.25
3825 5698 2.283145 ATAATCAGTCCTGGGCATGC 57.717 50.000 9.90 9.90 0.00 4.06
3867 5823 6.125589 TGCTCAACATAGATTATGCCCATA 57.874 37.500 0.00 0.00 39.79 2.74
3872 5828 6.909357 GTGACTTTGCTCAACATAGATTATGC 59.091 38.462 0.00 0.00 39.79 3.14
3929 5885 5.711976 ACAAAGTTGGGTCATCTATTTCTGG 59.288 40.000 0.00 0.00 0.00 3.86
3930 5886 6.824305 ACAAAGTTGGGTCATCTATTTCTG 57.176 37.500 0.00 0.00 0.00 3.02
3931 5887 7.690256 AGTACAAAGTTGGGTCATCTATTTCT 58.310 34.615 0.00 0.00 0.00 2.52
3932 5888 7.923414 AGTACAAAGTTGGGTCATCTATTTC 57.077 36.000 0.00 0.00 0.00 2.17
3933 5889 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
3934 5890 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
3935 5891 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
3936 5892 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
3937 5893 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
3938 5894 7.360361 CAAAGTTAGTACAAAGTTGGGTCATC 58.640 38.462 0.00 0.00 0.00 2.92
3940 5896 5.591067 CCAAAGTTAGTACAAAGTTGGGTCA 59.409 40.000 0.00 0.00 30.84 4.02
3941 5897 5.824097 TCCAAAGTTAGTACAAAGTTGGGTC 59.176 40.000 12.57 0.00 35.25 4.46
3942 5898 5.757988 TCCAAAGTTAGTACAAAGTTGGGT 58.242 37.500 12.57 0.00 35.25 4.51
3943 5899 6.500910 GTTCCAAAGTTAGTACAAAGTTGGG 58.499 40.000 12.57 0.00 35.09 4.12
3944 5900 6.196571 CGTTCCAAAGTTAGTACAAAGTTGG 58.803 40.000 0.00 2.51 0.00 3.77
3945 5901 6.037391 TCCGTTCCAAAGTTAGTACAAAGTTG 59.963 38.462 0.00 0.00 0.00 3.16
3947 5903 5.673514 TCCGTTCCAAAGTTAGTACAAAGT 58.326 37.500 0.00 0.00 0.00 2.66
3948 5904 5.178809 CCTCCGTTCCAAAGTTAGTACAAAG 59.821 44.000 0.00 0.00 0.00 2.77
3949 5905 5.058490 CCTCCGTTCCAAAGTTAGTACAAA 58.942 41.667 0.00 0.00 0.00 2.83
3952 5908 3.259123 TCCCTCCGTTCCAAAGTTAGTAC 59.741 47.826 0.00 0.00 0.00 2.73
3953 5909 3.509442 TCCCTCCGTTCCAAAGTTAGTA 58.491 45.455 0.00 0.00 0.00 1.82
3954 5910 2.302157 CTCCCTCCGTTCCAAAGTTAGT 59.698 50.000 0.00 0.00 0.00 2.24
3955 5911 2.302157 ACTCCCTCCGTTCCAAAGTTAG 59.698 50.000 0.00 0.00 0.00 2.34
3956 5912 2.332117 ACTCCCTCCGTTCCAAAGTTA 58.668 47.619 0.00 0.00 0.00 2.24
3958 5914 1.622312 GTACTCCCTCCGTTCCAAAGT 59.378 52.381 0.00 0.00 0.00 2.66
3959 5915 1.621814 TGTACTCCCTCCGTTCCAAAG 59.378 52.381 0.00 0.00 0.00 2.77
3960 5916 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
3961 5917 1.719529 TTGTACTCCCTCCGTTCCAA 58.280 50.000 0.00 0.00 0.00 3.53
3962 5918 1.946984 ATTGTACTCCCTCCGTTCCA 58.053 50.000 0.00 0.00 0.00 3.53
3963 5919 2.235402 TCAATTGTACTCCCTCCGTTCC 59.765 50.000 5.13 0.00 0.00 3.62
3964 5920 3.604875 TCAATTGTACTCCCTCCGTTC 57.395 47.619 5.13 0.00 0.00 3.95
3965 5921 4.360951 TTTCAATTGTACTCCCTCCGTT 57.639 40.909 5.13 0.00 0.00 4.44
3966 5922 4.360951 TTTTCAATTGTACTCCCTCCGT 57.639 40.909 5.13 0.00 0.00 4.69
3967 5923 6.183360 GGTTATTTTCAATTGTACTCCCTCCG 60.183 42.308 5.13 0.00 0.00 4.63
3968 5924 6.661805 TGGTTATTTTCAATTGTACTCCCTCC 59.338 38.462 5.13 2.32 0.00 4.30
3969 5925 7.696992 TGGTTATTTTCAATTGTACTCCCTC 57.303 36.000 5.13 0.00 0.00 4.30
3970 5926 7.507616 TGTTGGTTATTTTCAATTGTACTCCCT 59.492 33.333 5.13 0.00 0.00 4.20
3971 5927 7.662897 TGTTGGTTATTTTCAATTGTACTCCC 58.337 34.615 5.13 0.00 0.00 4.30
3972 5928 8.573035 TCTGTTGGTTATTTTCAATTGTACTCC 58.427 33.333 5.13 1.87 0.00 3.85


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

AutoCloner maintained by Alex Coulton.