Multiple sequence alignment - TraesCS5B01G101200

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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 TraesCS5B01G101200 chr5B 100.000 4882 0 0 812 5693 134133174 134128293 0.000000e+00 9016.0
1 TraesCS5B01G101200 chr5B 100.000 386 0 0 1 386 134133985 134133600 0.000000e+00 713.0
2 TraesCS5B01G101200 chr5B 88.485 165 10 4 4316 4472 369483907 369484070 2.090000e-44 191.0
3 TraesCS5B01G101200 chr5B 95.238 63 2 1 5154 5215 626068754 626068692 1.310000e-16 99.0
4 TraesCS5B01G101200 chr5B 91.429 70 4 2 5154 5221 18077030 18077099 1.690000e-15 95.3
5 TraesCS5B01G101200 chr5B 87.342 79 9 1 5154 5231 711837020 711837098 7.860000e-14 89.8
6 TraesCS5B01G101200 chr5A 93.743 2797 96 29 1377 4164 132099141 132096415 0.000000e+00 4122.0
7 TraesCS5B01G101200 chr5A 95.279 932 33 6 4238 5161 132095965 132095037 0.000000e+00 1467.0
8 TraesCS5B01G101200 chr5A 90.653 674 20 10 812 1467 132099785 132099137 0.000000e+00 856.0
9 TraesCS5B01G101200 chr5A 92.202 436 30 2 5261 5693 132095025 132094591 1.050000e-171 614.0
10 TraesCS5B01G101200 chr5A 93.548 124 3 2 5575 5693 132969125 132969248 4.530000e-41 180.0
11 TraesCS5B01G101200 chr5A 96.053 76 3 0 4165 4240 132096326 132096251 2.150000e-24 124.0
12 TraesCS5B01G101200 chr5D 94.148 2529 89 29 812 3310 121086254 121083755 0.000000e+00 3795.0
13 TraesCS5B01G101200 chr5D 95.266 866 24 4 3302 4164 121078675 121077824 0.000000e+00 1356.0
14 TraesCS5B01G101200 chr5D 96.000 725 20 5 4450 5166 121077290 121076567 0.000000e+00 1170.0
15 TraesCS5B01G101200 chr5D 92.213 488 36 1 5208 5693 121076575 121076088 0.000000e+00 689.0
16 TraesCS5B01G101200 chr5D 95.775 284 12 0 4165 4448 121077735 121077452 5.200000e-125 459.0
17 TraesCS5B01G101200 chr5D 86.885 305 36 2 82 386 121086679 121086379 7.070000e-89 339.0
18 TraesCS5B01G101200 chr5D 91.667 120 6 1 5575 5690 121294243 121294362 4.560000e-36 163.0
19 TraesCS5B01G101200 chr1A 89.839 620 49 9 4559 5167 78337975 78337359 0.000000e+00 784.0
20 TraesCS5B01G101200 chr1A 83.978 362 28 9 5332 5689 78337257 78336922 2.560000e-83 320.0
21 TraesCS5B01G101200 chr1A 93.407 91 2 4 4385 4471 460331984 460331894 1.290000e-26 132.0
22 TraesCS5B01G101200 chr1A 100.000 29 0 0 101 129 590006715 590006687 3.000000e-03 54.7
23 TraesCS5B01G101200 chr1D 90.196 561 38 11 4616 5167 84568780 84568228 0.000000e+00 715.0
24 TraesCS5B01G101200 chr1D 87.398 246 28 2 5447 5689 84567137 84566892 4.340000e-71 279.0
25 TraesCS5B01G101200 chr1D 89.474 133 8 2 4340 4472 3432944 3433070 4.560000e-36 163.0
26 TraesCS5B01G101200 chr1D 100.000 31 0 0 4483 4513 84568811 84568781 2.220000e-04 58.4
27 TraesCS5B01G101200 chr7A 94.969 159 7 1 4313 4471 105168566 105168409 1.220000e-61 248.0
28 TraesCS5B01G101200 chr3D 92.025 163 10 3 4310 4471 606485941 606486101 5.740000e-55 226.0
29 TraesCS5B01G101200 chr2D 86.986 146 16 3 4327 4471 568729085 568729228 1.640000e-35 161.0
30 TraesCS5B01G101200 chr2D 92.537 67 4 1 5154 5219 89213131 89213197 1.690000e-15 95.3
31 TraesCS5B01G101200 chr7D 88.550 131 13 2 4336 4466 10510555 10510683 2.120000e-34 158.0
32 TraesCS5B01G101200 chr2B 83.929 112 11 7 4313 4421 3942308 3942415 3.630000e-17 100.0
33 TraesCS5B01G101200 chr2B 96.667 60 1 1 5154 5212 763632534 763632475 1.310000e-16 99.0
34 TraesCS5B01G101200 chr2B 86.275 51 7 0 2259 2309 788093599 788093649 7.970000e-04 56.5
35 TraesCS5B01G101200 chr6B 95.238 63 2 1 5154 5215 68120771 68120833 1.310000e-16 99.0
36 TraesCS5B01G101200 chr3A 95.238 63 2 1 5154 5215 430795015 430795077 1.310000e-16 99.0
37 TraesCS5B01G101200 chr1B 93.939 66 3 1 5154 5218 613039515 613039450 1.310000e-16 99.0
38 TraesCS5B01G101200 chr4B 91.429 70 4 2 5153 5221 57245767 57245699 1.690000e-15 95.3


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 TraesCS5B01G101200 chr5B 134128293 134133985 5692 True 4864.5 9016 100.000000 1 5693 2 chr5B.!!$R2 5692
1 TraesCS5B01G101200 chr5A 132094591 132099785 5194 True 1436.6 4122 93.586000 812 5693 5 chr5A.!!$R1 4881
2 TraesCS5B01G101200 chr5D 121083755 121086679 2924 True 2067.0 3795 90.516500 82 3310 2 chr5D.!!$R2 3228
3 TraesCS5B01G101200 chr5D 121076088 121078675 2587 True 918.5 1356 94.813500 3302 5693 4 chr5D.!!$R1 2391
4 TraesCS5B01G101200 chr1A 78336922 78337975 1053 True 552.0 784 86.908500 4559 5689 2 chr1A.!!$R3 1130
5 TraesCS5B01G101200 chr1D 84566892 84568811 1919 True 350.8 715 92.531333 4483 5689 3 chr1D.!!$R1 1206

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
45 46 0.676736 CCCATCGACTAAGAGGCTCC 59.323 60.0 11.71 0.00 0.00 4.70 F
251 252 0.815615 CATCCCTACGGCAAGCCTTC 60.816 60.0 9.73 0.00 0.00 3.46 F
2053 2183 0.180406 GGGGCGATTTGCTCTTCCTA 59.820 55.0 0.00 0.00 46.29 2.94 F
2142 2272 0.108585 TTCGCTCCTTTGCTTGGTCT 59.891 50.0 0.00 0.00 0.00 3.85 F
2900 3031 2.015736 ATGCAGGTGAGCTCTAAACG 57.984 50.0 16.19 0.89 34.99 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1956 0.107703 CGCCAGCACCCTGAAGATTA 60.108 55.0 0.00 0.0 41.77 1.75 R
2142 2272 1.098712 AACAAGAGCGCCACGGAAAA 61.099 50.0 2.29 0.0 0.00 2.29 R
3864 4001 0.251297 TCCAACATGCCCCAGTGAAG 60.251 55.0 0.00 0.0 0.00 3.02 R
3914 4052 5.408299 GTGACTGTTGTAATGCACATGTCTA 59.592 40.0 0.00 0.0 36.90 2.59 R
4802 5484 0.983378 AGGGATGGGGCTGACACTAC 60.983 60.0 0.00 0.0 0.00 2.73 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
24 25 6.711277 TGTTTAGCTTCCATACTTGAGATGT 58.289 36.000 0.00 0.00 0.00 3.06
25 26 7.847096 TGTTTAGCTTCCATACTTGAGATGTA 58.153 34.615 0.00 0.00 0.00 2.29
26 27 7.764443 TGTTTAGCTTCCATACTTGAGATGTAC 59.236 37.037 0.00 0.00 0.00 2.90
27 28 5.283457 AGCTTCCATACTTGAGATGTACC 57.717 43.478 0.00 0.00 0.00 3.34
28 29 4.101741 AGCTTCCATACTTGAGATGTACCC 59.898 45.833 0.00 0.00 0.00 3.69
29 30 4.141711 GCTTCCATACTTGAGATGTACCCA 60.142 45.833 0.00 0.00 0.00 4.51
30 31 5.455326 GCTTCCATACTTGAGATGTACCCAT 60.455 44.000 0.00 0.00 0.00 4.00
31 32 5.808366 TCCATACTTGAGATGTACCCATC 57.192 43.478 0.00 0.00 46.56 3.51
41 42 4.506886 GATGTACCCATCGACTAAGAGG 57.493 50.000 0.00 0.00 38.28 3.69
42 43 2.029623 TGTACCCATCGACTAAGAGGC 58.970 52.381 0.00 0.00 0.00 4.70
43 44 2.308690 GTACCCATCGACTAAGAGGCT 58.691 52.381 0.00 0.00 0.00 4.58
44 45 1.404843 ACCCATCGACTAAGAGGCTC 58.595 55.000 6.34 6.34 0.00 4.70
45 46 0.676736 CCCATCGACTAAGAGGCTCC 59.323 60.000 11.71 0.00 0.00 4.70
46 47 1.698506 CCATCGACTAAGAGGCTCCT 58.301 55.000 11.71 0.00 0.00 3.69
47 48 1.339610 CCATCGACTAAGAGGCTCCTG 59.660 57.143 11.71 4.16 0.00 3.86
48 49 2.028130 CATCGACTAAGAGGCTCCTGT 58.972 52.381 11.71 7.62 0.00 4.00
49 50 1.464734 TCGACTAAGAGGCTCCTGTG 58.535 55.000 11.71 1.89 0.00 3.66
50 51 1.004394 TCGACTAAGAGGCTCCTGTGA 59.996 52.381 11.71 0.00 0.00 3.58
51 52 2.028130 CGACTAAGAGGCTCCTGTGAT 58.972 52.381 11.71 0.00 0.00 3.06
52 53 2.223688 CGACTAAGAGGCTCCTGTGATG 60.224 54.545 11.71 0.00 0.00 3.07
53 54 3.027412 GACTAAGAGGCTCCTGTGATGA 58.973 50.000 11.71 0.00 0.00 2.92
54 55 3.640967 GACTAAGAGGCTCCTGTGATGAT 59.359 47.826 11.71 0.00 0.00 2.45
55 56 4.036518 ACTAAGAGGCTCCTGTGATGATT 58.963 43.478 11.71 0.00 0.00 2.57
56 57 4.472833 ACTAAGAGGCTCCTGTGATGATTT 59.527 41.667 11.71 0.00 0.00 2.17
57 58 4.313020 AAGAGGCTCCTGTGATGATTTT 57.687 40.909 11.71 0.00 0.00 1.82
58 59 3.618351 AGAGGCTCCTGTGATGATTTTG 58.382 45.455 11.71 0.00 0.00 2.44
59 60 3.009916 AGAGGCTCCTGTGATGATTTTGT 59.990 43.478 11.71 0.00 0.00 2.83
60 61 3.350833 AGGCTCCTGTGATGATTTTGTC 58.649 45.455 0.00 0.00 0.00 3.18
61 62 3.084039 GGCTCCTGTGATGATTTTGTCA 58.916 45.455 0.00 0.00 42.06 3.58
62 63 3.507233 GGCTCCTGTGATGATTTTGTCAA 59.493 43.478 0.00 0.00 40.97 3.18
63 64 4.159135 GGCTCCTGTGATGATTTTGTCAAT 59.841 41.667 0.00 0.00 40.97 2.57
64 65 5.337009 GGCTCCTGTGATGATTTTGTCAATT 60.337 40.000 0.00 0.00 40.97 2.32
65 66 6.161381 GCTCCTGTGATGATTTTGTCAATTT 58.839 36.000 0.00 0.00 40.97 1.82
66 67 6.647895 GCTCCTGTGATGATTTTGTCAATTTT 59.352 34.615 0.00 0.00 40.97 1.82
67 68 7.814107 GCTCCTGTGATGATTTTGTCAATTTTA 59.186 33.333 0.00 0.00 40.97 1.52
68 69 9.132521 CTCCTGTGATGATTTTGTCAATTTTAC 57.867 33.333 0.00 0.00 40.97 2.01
69 70 7.807433 TCCTGTGATGATTTTGTCAATTTTACG 59.193 33.333 0.00 0.00 40.97 3.18
70 71 7.807433 CCTGTGATGATTTTGTCAATTTTACGA 59.193 33.333 0.00 0.00 40.97 3.43
71 72 9.345517 CTGTGATGATTTTGTCAATTTTACGAT 57.654 29.630 0.00 0.00 40.97 3.73
72 73 9.127006 TGTGATGATTTTGTCAATTTTACGATG 57.873 29.630 0.00 0.00 40.97 3.84
73 74 9.128107 GTGATGATTTTGTCAATTTTACGATGT 57.872 29.630 0.00 0.00 40.97 3.06
74 75 9.689976 TGATGATTTTGTCAATTTTACGATGTT 57.310 25.926 0.00 0.00 40.97 2.71
75 76 9.941991 GATGATTTTGTCAATTTTACGATGTTG 57.058 29.630 0.00 0.00 40.97 3.33
76 77 8.864069 TGATTTTGTCAATTTTACGATGTTGT 57.136 26.923 0.00 0.00 32.78 3.32
77 78 8.750416 TGATTTTGTCAATTTTACGATGTTGTG 58.250 29.630 0.00 0.00 32.78 3.33
78 79 8.641499 ATTTTGTCAATTTTACGATGTTGTGT 57.359 26.923 0.00 0.00 0.00 3.72
79 80 7.672351 TTTGTCAATTTTACGATGTTGTGTC 57.328 32.000 0.00 0.00 0.00 3.67
80 81 6.364945 TGTCAATTTTACGATGTTGTGTCA 57.635 33.333 0.00 0.00 0.00 3.58
86 87 1.788258 ACGATGTTGTGTCAGCTCAG 58.212 50.000 0.00 0.00 0.00 3.35
88 89 1.458445 CGATGTTGTGTCAGCTCAGTG 59.542 52.381 0.00 0.00 0.00 3.66
93 94 1.402787 TGTGTCAGCTCAGTGTCTCA 58.597 50.000 0.00 0.00 0.00 3.27
99 100 4.099419 TGTCAGCTCAGTGTCTCAAAAGTA 59.901 41.667 0.00 0.00 0.00 2.24
107 108 7.575909 GCTCAGTGTCTCAAAAGTACTCATAGA 60.576 40.741 0.00 0.00 0.00 1.98
109 110 8.638873 TCAGTGTCTCAAAAGTACTCATAGAAA 58.361 33.333 0.00 0.00 0.00 2.52
117 118 8.822805 TCAAAAGTACTCATAGAAATAGGGTGT 58.177 33.333 0.00 0.00 0.00 4.16
118 119 8.883731 CAAAAGTACTCATAGAAATAGGGTGTG 58.116 37.037 0.00 0.00 0.00 3.82
137 138 1.153529 CATGCGTGCGGGGTAAGTA 60.154 57.895 0.00 0.00 0.00 2.24
151 152 4.927425 GGGGTAAGTATATGTGCGTGTATG 59.073 45.833 0.00 0.00 0.00 2.39
152 153 5.279106 GGGGTAAGTATATGTGCGTGTATGA 60.279 44.000 0.00 0.00 0.00 2.15
159 160 3.733443 ATGTGCGTGTATGAGAGCATA 57.267 42.857 0.00 0.00 41.88 3.14
162 163 3.181476 TGTGCGTGTATGAGAGCATATGT 60.181 43.478 4.29 0.00 41.88 2.29
220 221 7.416154 TCGTCTATTTTAAAAGGTGTGTGAG 57.584 36.000 6.79 0.00 0.00 3.51
226 227 1.680338 AAAAGGTGTGTGAGGTCAGC 58.320 50.000 0.00 0.00 0.00 4.26
241 242 1.121407 TCAGCATCCCCATCCCTACG 61.121 60.000 0.00 0.00 0.00 3.51
251 252 0.815615 CATCCCTACGGCAAGCCTTC 60.816 60.000 9.73 0.00 0.00 3.46
252 253 2.311688 ATCCCTACGGCAAGCCTTCG 62.312 60.000 9.73 0.00 0.00 3.79
265 266 1.607148 AGCCTTCGGTTGCAAGTTTAC 59.393 47.619 0.00 0.00 0.00 2.01
273 274 4.816786 GGTTGCAAGTTTACCGAGTTTA 57.183 40.909 0.00 0.00 0.00 2.01
293 294 6.925165 AGTTTAAATGTGCTTTCTGTTCATGG 59.075 34.615 0.00 0.00 0.00 3.66
329 330 8.506168 TGAACTTCTGTCATTCTAAAGTTTGT 57.494 30.769 0.00 0.00 39.55 2.83
330 331 8.397906 TGAACTTCTGTCATTCTAAAGTTTGTG 58.602 33.333 0.00 0.00 39.55 3.33
829 830 2.001269 AAGGATTGGGGCCTAGCGT 61.001 57.895 0.84 0.00 33.76 5.07
860 869 1.985895 TCCACCTTCCTTCCTTCTTCC 59.014 52.381 0.00 0.00 0.00 3.46
902 911 2.963654 TAGGCCCCTTCCTTTACTCT 57.036 50.000 0.00 0.00 37.66 3.24
929 938 2.279069 ACTCTGCCACCGACTCCTG 61.279 63.158 0.00 0.00 0.00 3.86
935 944 2.681778 CACCGACTCCTGCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
936 945 2.363147 ACCGACTCCTGCCTCCTC 60.363 66.667 0.00 0.00 0.00 3.71
937 946 2.043450 CCGACTCCTGCCTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
938 947 1.684049 CCGACTCCTGCCTCCTCTT 60.684 63.158 0.00 0.00 0.00 2.85
939 948 1.671901 CCGACTCCTGCCTCCTCTTC 61.672 65.000 0.00 0.00 0.00 2.87
940 949 1.671901 CGACTCCTGCCTCCTCTTCC 61.672 65.000 0.00 0.00 0.00 3.46
962 971 2.946650 CCCCTTCCCCACCACCAT 60.947 66.667 0.00 0.00 0.00 3.55
1132 1144 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1251 1273 1.200020 CTTTGCTTGGTCCGATTGGTC 59.800 52.381 0.00 0.00 36.30 4.02
1270 1296 1.805539 CATTGCTTCGTCTCGCGGA 60.806 57.895 6.13 0.00 41.72 5.54
1421 1533 2.030363 TGGTTATTGTTTTGCTCGCCAG 60.030 45.455 0.00 0.00 0.00 4.85
1435 1547 0.960364 CGCCAGGGCCGCATAATTAT 60.960 55.000 4.42 0.00 37.98 1.28
1443 1555 1.201812 GCCGCATAATTATCGTGCTCG 60.202 52.381 0.81 0.81 36.74 5.03
1475 1587 0.962356 CCAACTCACCATGGTCCTGC 60.962 60.000 16.53 0.00 31.84 4.85
1483 1595 2.424601 CACCATGGTCCTGCAGTAATTG 59.575 50.000 16.53 3.63 0.00 2.32
1581 1693 7.892778 TGTTTGTAACAAGCGATACAAGATA 57.107 32.000 0.00 0.00 40.27 1.98
1585 1697 8.812147 TTGTAACAAGCGATACAAGATATAGG 57.188 34.615 0.00 0.00 35.98 2.57
1606 1718 2.029290 GGTTAGTTCGTGCTTGAGAGGA 60.029 50.000 0.00 0.00 0.00 3.71
1611 1723 2.154854 TCGTGCTTGAGAGGAAACTG 57.845 50.000 0.00 0.00 44.43 3.16
1617 1729 2.675348 GCTTGAGAGGAAACTGAATCCG 59.325 50.000 0.00 0.00 44.43 4.18
1621 1733 1.065854 AGAGGAAACTGAATCCGCCAG 60.066 52.381 0.00 0.00 44.43 4.85
1689 1801 2.031683 CACAAGTTGAGTTGGTTCGTCC 59.968 50.000 10.54 0.00 0.00 4.79
1694 1806 4.504858 AGTTGAGTTGGTTCGTCCATATC 58.495 43.478 3.33 5.57 46.60 1.63
1700 1813 3.007979 TGGTTCGTCCATATCGAATCG 57.992 47.619 0.00 0.00 46.95 3.34
1706 1819 2.671070 CGTCCATATCGAATCGCCATGA 60.671 50.000 14.77 0.00 0.00 3.07
1709 1822 2.669924 CCATATCGAATCGCCATGACTG 59.330 50.000 14.77 0.07 0.00 3.51
1711 1824 4.485163 CATATCGAATCGCCATGACTGTA 58.515 43.478 9.63 0.00 0.00 2.74
1712 1825 2.951457 TCGAATCGCCATGACTGTAA 57.049 45.000 0.00 0.00 0.00 2.41
1713 1826 3.239587 TCGAATCGCCATGACTGTAAA 57.760 42.857 0.00 0.00 0.00 2.01
1714 1827 3.792401 TCGAATCGCCATGACTGTAAAT 58.208 40.909 0.00 0.00 0.00 1.40
1715 1828 4.188462 TCGAATCGCCATGACTGTAAATT 58.812 39.130 0.00 0.00 0.00 1.82
1716 1829 4.270084 TCGAATCGCCATGACTGTAAATTC 59.730 41.667 0.00 0.00 0.00 2.17
1717 1830 4.271049 CGAATCGCCATGACTGTAAATTCT 59.729 41.667 0.00 0.00 0.00 2.40
1718 1831 5.490139 AATCGCCATGACTGTAAATTCTG 57.510 39.130 0.00 0.00 0.00 3.02
1719 1832 4.200838 TCGCCATGACTGTAAATTCTGA 57.799 40.909 0.00 0.00 0.00 3.27
1720 1833 4.769688 TCGCCATGACTGTAAATTCTGAT 58.230 39.130 0.00 0.00 0.00 2.90
1721 1834 5.185454 TCGCCATGACTGTAAATTCTGATT 58.815 37.500 0.00 0.00 0.00 2.57
1722 1835 6.345298 TCGCCATGACTGTAAATTCTGATTA 58.655 36.000 0.00 0.00 0.00 1.75
1723 1836 6.479990 TCGCCATGACTGTAAATTCTGATTAG 59.520 38.462 0.00 0.00 0.00 1.73
1724 1837 6.258727 CGCCATGACTGTAAATTCTGATTAGT 59.741 38.462 0.00 0.00 0.00 2.24
1725 1838 7.201644 CGCCATGACTGTAAATTCTGATTAGTT 60.202 37.037 0.00 0.00 0.00 2.24
1726 1839 8.462016 GCCATGACTGTAAATTCTGATTAGTTT 58.538 33.333 0.00 0.00 0.00 2.66
1761 1884 8.846211 TGATCTTAATTTCGTCCATTTAATCCC 58.154 33.333 0.00 0.00 0.00 3.85
1782 1908 4.323104 CCCTTTGGACTTGTTTGGTTGAAA 60.323 41.667 0.00 0.00 0.00 2.69
1812 1938 3.002051 CGATAAGTCGTCGTGTGACATTG 60.002 47.826 0.00 0.00 45.80 2.82
1830 1956 7.975616 GTGACATTGCAATGACTGGTAAAATAT 59.024 33.333 38.99 16.69 39.67 1.28
2053 2183 0.180406 GGGGCGATTTGCTCTTCCTA 59.820 55.000 0.00 0.00 46.29 2.94
2054 2184 1.587547 GGGCGATTTGCTCTTCCTAG 58.412 55.000 0.00 0.00 42.52 3.02
2058 2188 1.486726 CGATTTGCTCTTCCTAGGGGT 59.513 52.381 9.46 0.00 0.00 4.95
2098 2228 3.140814 GCCCCATCTTTCCGTGGC 61.141 66.667 0.00 0.00 34.08 5.01
2142 2272 0.108585 TTCGCTCCTTTGCTTGGTCT 59.891 50.000 0.00 0.00 0.00 3.85
2179 2309 7.255277 GCTCTTGTTGGAGTTTAAACATCTTCT 60.255 37.037 20.06 0.00 36.26 2.85
2332 2462 2.549329 CCCTTTGAAAAATGGCAACTGC 59.451 45.455 0.00 0.00 41.14 4.40
2762 2893 8.905850 TGTGATGTATGCAAGTTTTATGATGAT 58.094 29.630 0.00 0.00 0.00 2.45
2791 2922 7.113404 CGTATGTCTCAATTTTGTTTTCTGTGG 59.887 37.037 0.00 0.00 0.00 4.17
2900 3031 2.015736 ATGCAGGTGAGCTCTAAACG 57.984 50.000 16.19 0.89 34.99 3.60
2910 3041 5.285651 GTGAGCTCTAAACGCTATCTTCAT 58.714 41.667 16.19 0.00 37.96 2.57
3046 3177 4.974368 TTGTGTTAACTGTTGTTCCAGG 57.026 40.909 7.22 0.00 37.59 4.45
3200 3331 6.032094 GCAATGGATCATGCCTTAATAATCG 58.968 40.000 6.19 0.00 0.00 3.34
3391 3523 6.432162 GGTACATATGATGTGCAGGATGAATT 59.568 38.462 10.38 0.00 46.01 2.17
3392 3524 6.570672 ACATATGATGTGCAGGATGAATTC 57.429 37.500 10.38 0.00 43.01 2.17
3393 3525 6.304624 ACATATGATGTGCAGGATGAATTCT 58.695 36.000 10.38 0.00 43.01 2.40
3394 3526 6.776116 ACATATGATGTGCAGGATGAATTCTT 59.224 34.615 10.38 0.00 43.01 2.52
3395 3527 4.976224 TGATGTGCAGGATGAATTCTTG 57.024 40.909 7.05 1.78 39.69 3.02
3615 3747 6.906659 AGTGAAATTTTCTGTGCAGTATCTG 58.093 36.000 10.33 0.00 34.12 2.90
3712 3845 8.340757 TGGTGGACCATAATAAGTAAATCCTTT 58.659 33.333 0.00 0.00 42.01 3.11
3755 3888 8.147244 AGATATATGTGTACCCAGTTATTCCC 57.853 38.462 0.00 0.00 0.00 3.97
3781 3918 5.934935 TTTTTAACCTCTCCGATGTTGTC 57.065 39.130 0.00 0.00 0.00 3.18
3864 4001 3.037431 AGACAGCTCTTGACATGACAC 57.963 47.619 0.00 0.00 0.00 3.67
3898 4035 5.822519 GCATGTTGGATCAAGAGGTATAACA 59.177 40.000 0.00 0.00 0.00 2.41
3934 4072 8.746922 AATTTTAGACATGTGCATTACAACAG 57.253 30.769 1.15 0.00 43.77 3.16
4174 4400 4.501400 GGTTTGTGCTAGTTTTTCTGCCAT 60.501 41.667 0.00 0.00 0.00 4.40
4212 4438 8.416329 ACAAATTAGCTTTCTCACAGAAAATGT 58.584 29.630 0.00 0.00 42.95 2.71
4440 4954 9.661187 GATACATGTGAATCAGAAAAATGCTAG 57.339 33.333 9.11 0.00 0.00 3.42
4745 5427 1.276138 TGTATCACCTGGTCTGTGCAG 59.724 52.381 0.00 0.00 33.71 4.41
4846 5528 1.062587 CTTCGCCGCTTTACCATTCTG 59.937 52.381 0.00 0.00 0.00 3.02
4962 5649 3.774766 AGCACCATTACTCTGTATCACCA 59.225 43.478 0.00 0.00 0.00 4.17
5060 5750 0.321122 CTGCTGTTGTCAGGTCCCTC 60.321 60.000 0.00 0.00 41.57 4.30
5167 5857 7.540474 TTCATCACTCTTCTAGTACAAACCT 57.460 36.000 0.00 0.00 35.76 3.50
5169 5859 7.963532 TCATCACTCTTCTAGTACAAACCTTT 58.036 34.615 0.00 0.00 35.76 3.11
5170 5860 8.429641 TCATCACTCTTCTAGTACAAACCTTTT 58.570 33.333 0.00 0.00 35.76 2.27
5172 5862 8.433421 TCACTCTTCTAGTACAAACCTTTTTG 57.567 34.615 0.00 0.00 41.49 2.44
5185 5875 7.551035 CAAACCTTTTTGTCCATTTTGATGA 57.449 32.000 0.00 0.00 37.85 2.92
5186 5876 7.408910 CAAACCTTTTTGTCCATTTTGATGAC 58.591 34.615 0.00 0.00 37.85 3.06
5187 5877 6.232581 ACCTTTTTGTCCATTTTGATGACA 57.767 33.333 0.00 0.00 0.00 3.58
5188 5878 6.648192 ACCTTTTTGTCCATTTTGATGACAA 58.352 32.000 0.00 0.00 34.47 3.18
5189 5879 6.762661 ACCTTTTTGTCCATTTTGATGACAAG 59.237 34.615 0.00 0.00 37.13 3.16
5190 5880 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
5191 5881 7.925483 CCTTTTTGTCCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.13 2.24
5192 5882 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
5193 5883 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
5194 5884 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
5195 5885 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
5196 5886 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
5197 5887 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
5198 5888 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
5199 5889 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
5200 5890 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
5201 5891 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
5202 5892 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
5203 5893 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
5204 5894 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
5205 5895 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5206 5896 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5207 5897 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
5208 5898 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
5209 5899 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
5210 5900 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
5211 5901 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
5212 5902 0.251297 TTTCGGACGGAGGGAGTACA 60.251 55.000 0.00 0.00 0.00 2.90
5213 5903 0.251297 TTCGGACGGAGGGAGTACAA 60.251 55.000 0.00 0.00 0.00 2.41
5214 5904 0.251297 TCGGACGGAGGGAGTACAAA 60.251 55.000 0.00 0.00 0.00 2.83
5215 5905 0.108945 CGGACGGAGGGAGTACAAAC 60.109 60.000 0.00 0.00 0.00 2.93
5219 5909 1.553704 ACGGAGGGAGTACAAACCATC 59.446 52.381 8.99 8.99 36.43 3.51
5239 5929 2.231964 TCGTCAGTTGGCTAAACCGTAT 59.768 45.455 0.00 0.00 43.94 3.06
5274 5964 3.072915 TGGTATGCATCCTGTATTCCCAG 59.927 47.826 0.19 0.00 30.92 4.45
5288 5978 2.693762 CCCAGTGCCATGCTTGTCG 61.694 63.158 0.00 0.00 0.00 4.35
5294 5984 1.522258 GTGCCATGCTTGTCGTTTTTG 59.478 47.619 0.00 0.00 0.00 2.44
5295 5985 1.139163 GCCATGCTTGTCGTTTTTGG 58.861 50.000 0.00 0.00 0.00 3.28
5297 5987 2.820330 CCATGCTTGTCGTTTTTGGTT 58.180 42.857 0.00 0.00 0.00 3.67
5320 6010 0.317770 CGCGACAACAAAAGCCATGT 60.318 50.000 0.00 0.00 0.00 3.21
5323 6013 3.574614 GCGACAACAAAAGCCATGTATT 58.425 40.909 0.00 0.00 0.00 1.89
5386 7002 6.394345 AAATAGGGTTCTCTCAAGGTGAAT 57.606 37.500 0.00 0.00 31.43 2.57
5450 7066 4.164221 ACACAGCTATTACCAGTAGGCATT 59.836 41.667 0.00 0.00 39.06 3.56
5564 7182 1.162698 CTGATGGGACTGCACACTTG 58.837 55.000 0.00 0.00 0.00 3.16
5610 7231 5.766174 TGTTGTTAGGGTTTCAGGTAATCAC 59.234 40.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.224949 GGTACATCTCAAGTATGGAAGCTAAAC 59.775 40.741 0.00 0.00 0.00 2.01
2 3 7.272978 GGTACATCTCAAGTATGGAAGCTAAA 58.727 38.462 0.00 0.00 0.00 1.85
3 4 6.183360 GGGTACATCTCAAGTATGGAAGCTAA 60.183 42.308 0.00 0.00 0.00 3.09
4 5 5.304614 GGGTACATCTCAAGTATGGAAGCTA 59.695 44.000 0.00 0.00 0.00 3.32
5 6 4.101741 GGGTACATCTCAAGTATGGAAGCT 59.898 45.833 0.00 0.00 0.00 3.74
6 7 4.141711 TGGGTACATCTCAAGTATGGAAGC 60.142 45.833 0.00 0.00 0.00 3.86
7 8 5.614324 TGGGTACATCTCAAGTATGGAAG 57.386 43.478 0.00 0.00 0.00 3.46
21 22 2.628657 GCCTCTTAGTCGATGGGTACAT 59.371 50.000 0.00 0.00 40.85 2.29
22 23 2.029623 GCCTCTTAGTCGATGGGTACA 58.970 52.381 0.00 0.00 0.00 2.90
23 24 2.293955 GAGCCTCTTAGTCGATGGGTAC 59.706 54.545 0.00 0.00 0.00 3.34
24 25 2.584236 GAGCCTCTTAGTCGATGGGTA 58.416 52.381 0.00 0.00 0.00 3.69
25 26 1.404843 GAGCCTCTTAGTCGATGGGT 58.595 55.000 0.00 0.00 0.00 4.51
26 27 0.676736 GGAGCCTCTTAGTCGATGGG 59.323 60.000 0.00 0.00 0.00 4.00
27 28 1.339610 CAGGAGCCTCTTAGTCGATGG 59.660 57.143 0.00 0.00 0.00 3.51
28 29 2.028130 ACAGGAGCCTCTTAGTCGATG 58.972 52.381 0.00 0.00 0.00 3.84
29 30 2.028130 CACAGGAGCCTCTTAGTCGAT 58.972 52.381 0.00 0.00 0.00 3.59
30 31 1.004394 TCACAGGAGCCTCTTAGTCGA 59.996 52.381 0.00 0.00 0.00 4.20
31 32 1.464734 TCACAGGAGCCTCTTAGTCG 58.535 55.000 0.00 0.00 0.00 4.18
32 33 3.027412 TCATCACAGGAGCCTCTTAGTC 58.973 50.000 0.00 0.00 0.00 2.59
33 34 3.107402 TCATCACAGGAGCCTCTTAGT 57.893 47.619 0.00 0.00 0.00 2.24
34 35 4.686191 AATCATCACAGGAGCCTCTTAG 57.314 45.455 0.00 0.00 0.00 2.18
35 36 5.188434 CAAAATCATCACAGGAGCCTCTTA 58.812 41.667 0.00 0.00 0.00 2.10
36 37 4.015084 CAAAATCATCACAGGAGCCTCTT 58.985 43.478 0.00 0.00 0.00 2.85
37 38 3.009916 ACAAAATCATCACAGGAGCCTCT 59.990 43.478 0.00 0.00 0.00 3.69
38 39 3.350833 ACAAAATCATCACAGGAGCCTC 58.649 45.455 0.00 0.00 0.00 4.70
39 40 3.245016 TGACAAAATCATCACAGGAGCCT 60.245 43.478 0.00 0.00 29.99 4.58
40 41 3.084039 TGACAAAATCATCACAGGAGCC 58.916 45.455 0.00 0.00 29.99 4.70
41 42 4.771590 TTGACAAAATCATCACAGGAGC 57.228 40.909 0.00 0.00 37.11 4.70
42 43 9.132521 GTAAAATTGACAAAATCATCACAGGAG 57.867 33.333 0.00 0.00 37.11 3.69
43 44 7.807433 CGTAAAATTGACAAAATCATCACAGGA 59.193 33.333 0.00 0.00 37.11 3.86
44 45 7.807433 TCGTAAAATTGACAAAATCATCACAGG 59.193 33.333 0.00 0.00 37.11 4.00
45 46 8.726650 TCGTAAAATTGACAAAATCATCACAG 57.273 30.769 0.00 0.00 37.11 3.66
46 47 9.127006 CATCGTAAAATTGACAAAATCATCACA 57.873 29.630 0.00 0.00 37.11 3.58
47 48 9.128107 ACATCGTAAAATTGACAAAATCATCAC 57.872 29.630 0.00 0.00 37.11 3.06
48 49 9.689976 AACATCGTAAAATTGACAAAATCATCA 57.310 25.926 0.00 0.00 37.11 3.07
49 50 9.941991 CAACATCGTAAAATTGACAAAATCATC 57.058 29.630 0.00 0.00 37.11 2.92
50 51 9.474920 ACAACATCGTAAAATTGACAAAATCAT 57.525 25.926 0.00 0.00 37.11 2.45
51 52 8.750416 CACAACATCGTAAAATTGACAAAATCA 58.250 29.630 0.00 0.00 34.65 2.57
52 53 8.751335 ACACAACATCGTAAAATTGACAAAATC 58.249 29.630 0.00 0.00 0.00 2.17
53 54 8.641499 ACACAACATCGTAAAATTGACAAAAT 57.359 26.923 0.00 0.00 0.00 1.82
54 55 7.755373 TGACACAACATCGTAAAATTGACAAAA 59.245 29.630 0.00 0.00 0.00 2.44
55 56 7.251281 TGACACAACATCGTAAAATTGACAAA 58.749 30.769 0.00 0.00 0.00 2.83
56 57 6.786207 TGACACAACATCGTAAAATTGACAA 58.214 32.000 0.00 0.00 0.00 3.18
57 58 6.364945 TGACACAACATCGTAAAATTGACA 57.635 33.333 0.00 0.00 0.00 3.58
58 59 5.339611 GCTGACACAACATCGTAAAATTGAC 59.660 40.000 0.00 0.00 0.00 3.18
59 60 5.238432 AGCTGACACAACATCGTAAAATTGA 59.762 36.000 0.00 0.00 0.00 2.57
60 61 5.451908 AGCTGACACAACATCGTAAAATTG 58.548 37.500 0.00 0.00 0.00 2.32
61 62 5.238432 TGAGCTGACACAACATCGTAAAATT 59.762 36.000 0.00 0.00 0.00 1.82
62 63 4.754618 TGAGCTGACACAACATCGTAAAAT 59.245 37.500 0.00 0.00 0.00 1.82
63 64 4.123506 TGAGCTGACACAACATCGTAAAA 58.876 39.130 0.00 0.00 0.00 1.52
64 65 3.723260 TGAGCTGACACAACATCGTAAA 58.277 40.909 0.00 0.00 0.00 2.01
65 66 3.243737 ACTGAGCTGACACAACATCGTAA 60.244 43.478 0.00 0.00 0.00 3.18
66 67 2.296190 ACTGAGCTGACACAACATCGTA 59.704 45.455 0.00 0.00 0.00 3.43
67 68 1.069204 ACTGAGCTGACACAACATCGT 59.931 47.619 0.00 0.00 0.00 3.73
68 69 1.458445 CACTGAGCTGACACAACATCG 59.542 52.381 0.00 0.00 0.00 3.84
69 70 2.478134 GACACTGAGCTGACACAACATC 59.522 50.000 0.00 0.00 0.00 3.06
70 71 2.103771 AGACACTGAGCTGACACAACAT 59.896 45.455 0.00 0.00 0.00 2.71
71 72 1.482182 AGACACTGAGCTGACACAACA 59.518 47.619 0.00 0.00 0.00 3.33
72 73 2.131183 GAGACACTGAGCTGACACAAC 58.869 52.381 0.00 0.00 0.00 3.32
73 74 1.756538 TGAGACACTGAGCTGACACAA 59.243 47.619 0.00 0.00 0.00 3.33
74 75 1.402787 TGAGACACTGAGCTGACACA 58.597 50.000 0.00 0.00 0.00 3.72
75 76 2.515926 TTGAGACACTGAGCTGACAC 57.484 50.000 0.00 0.00 0.00 3.67
76 77 3.118629 ACTTTTGAGACACTGAGCTGACA 60.119 43.478 0.00 0.00 0.00 3.58
77 78 3.462021 ACTTTTGAGACACTGAGCTGAC 58.538 45.455 0.00 0.00 0.00 3.51
78 79 3.827008 ACTTTTGAGACACTGAGCTGA 57.173 42.857 0.00 0.00 0.00 4.26
79 80 4.626042 AGTACTTTTGAGACACTGAGCTG 58.374 43.478 0.00 0.00 0.00 4.24
80 81 4.342378 TGAGTACTTTTGAGACACTGAGCT 59.658 41.667 0.00 0.00 0.00 4.09
88 89 9.535878 CCCTATTTCTATGAGTACTTTTGAGAC 57.464 37.037 0.00 0.00 0.00 3.36
93 94 7.553044 GCACACCCTATTTCTATGAGTACTTTT 59.447 37.037 0.00 0.00 0.00 2.27
99 100 5.371526 CATGCACACCCTATTTCTATGAGT 58.628 41.667 0.00 0.00 0.00 3.41
107 108 0.810648 CACGCATGCACACCCTATTT 59.189 50.000 19.57 0.00 0.00 1.40
109 110 4.223800 CACGCATGCACACCCTAT 57.776 55.556 19.57 0.00 0.00 2.57
134 135 4.278419 TGCTCTCATACACGCACATATACT 59.722 41.667 0.00 0.00 0.00 2.12
137 138 3.733443 TGCTCTCATACACGCACATAT 57.267 42.857 0.00 0.00 0.00 1.78
151 152 6.045318 ACACAGTACAATCACATATGCTCTC 58.955 40.000 1.58 0.00 0.00 3.20
152 153 5.982356 ACACAGTACAATCACATATGCTCT 58.018 37.500 1.58 0.00 0.00 4.09
162 163 9.225436 TGCATATCTTTTAACACAGTACAATCA 57.775 29.630 0.00 0.00 0.00 2.57
200 201 7.504924 TGACCTCACACACCTTTTAAAATAG 57.495 36.000 0.09 0.00 0.00 1.73
201 202 6.016610 GCTGACCTCACACACCTTTTAAAATA 60.017 38.462 0.09 0.00 0.00 1.40
207 208 1.064758 TGCTGACCTCACACACCTTTT 60.065 47.619 0.00 0.00 0.00 2.27
211 212 0.674895 GGATGCTGACCTCACACACC 60.675 60.000 0.00 0.00 0.00 4.16
220 221 0.768221 TAGGGATGGGGATGCTGACC 60.768 60.000 0.00 0.00 0.00 4.02
252 253 3.703286 AAACTCGGTAAACTTGCAACC 57.297 42.857 0.00 0.00 0.00 3.77
256 257 5.116528 GCACATTTAAACTCGGTAAACTTGC 59.883 40.000 0.00 0.00 30.49 4.01
265 266 5.108385 ACAGAAAGCACATTTAAACTCGG 57.892 39.130 0.00 0.00 0.00 4.63
273 274 4.586001 ACTCCATGAACAGAAAGCACATTT 59.414 37.500 0.00 0.00 0.00 2.32
860 869 0.654472 GTCAAAATGGCGCGCGATAG 60.654 55.000 37.18 20.28 0.00 2.08
902 911 1.270625 CGGTGGCAGAGTGGTAGAAAA 60.271 52.381 0.00 0.00 0.00 2.29
929 938 2.379459 GGGAAGGGGAAGAGGAGGC 61.379 68.421 0.00 0.00 0.00 4.70
935 944 1.230182 GGGAAGGGGAAGGGGAAGA 60.230 63.158 0.00 0.00 0.00 2.87
936 945 2.317378 GGGGAAGGGGAAGGGGAAG 61.317 68.421 0.00 0.00 0.00 3.46
937 946 2.204401 GGGGAAGGGGAAGGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
938 947 3.558124 TGGGGAAGGGGAAGGGGA 61.558 66.667 0.00 0.00 0.00 4.81
939 948 3.347590 GTGGGGAAGGGGAAGGGG 61.348 72.222 0.00 0.00 0.00 4.79
940 949 3.347590 GGTGGGGAAGGGGAAGGG 61.348 72.222 0.00 0.00 0.00 3.95
1106 1118 3.036959 GGAGGGGAGGGGAGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
1197 1209 1.741770 GCAGACGCCACGGAAAGAT 60.742 57.895 0.00 0.00 0.00 2.40
1270 1296 2.768527 ACCAGAGATGGATCACGATGTT 59.231 45.455 0.31 0.00 0.00 2.71
1312 1338 1.958205 GATCTTGCATCTCCGCCGG 60.958 63.158 0.00 0.00 0.00 6.13
1399 1511 2.287909 TGGCGAGCAAAACAATAACCAC 60.288 45.455 0.00 0.00 0.00 4.16
1400 1512 1.957177 TGGCGAGCAAAACAATAACCA 59.043 42.857 0.00 0.00 0.00 3.67
1401 1513 2.595386 CTGGCGAGCAAAACAATAACC 58.405 47.619 0.00 0.00 0.00 2.85
1421 1533 0.168128 GCACGATAATTATGCGGCCC 59.832 55.000 1.78 0.00 0.00 5.80
1435 1547 1.811645 TTCCACATGGACGAGCACGA 61.812 55.000 11.40 0.00 45.39 4.35
1443 1555 2.293399 GTGAGTTGGTTTCCACATGGAC 59.707 50.000 0.00 0.00 45.39 4.02
1470 1582 0.403655 TGGTGCCAATTACTGCAGGA 59.596 50.000 19.93 6.60 38.34 3.86
1472 1584 1.538047 AGTGGTGCCAATTACTGCAG 58.462 50.000 13.48 13.48 38.34 4.41
1572 1684 7.232941 AGCACGAACTAACCCTATATCTTGTAT 59.767 37.037 0.00 0.00 0.00 2.29
1575 1687 5.844004 AGCACGAACTAACCCTATATCTTG 58.156 41.667 0.00 0.00 0.00 3.02
1581 1693 3.767673 TCTCAAGCACGAACTAACCCTAT 59.232 43.478 0.00 0.00 0.00 2.57
1585 1697 2.029290 TCCTCTCAAGCACGAACTAACC 60.029 50.000 0.00 0.00 0.00 2.85
1606 1718 2.162681 CCTTTCTGGCGGATTCAGTTT 58.837 47.619 0.00 0.00 34.15 2.66
1621 1733 1.963464 TACGGACGATGGGGCCTTTC 61.963 60.000 0.84 0.00 0.00 2.62
1689 1801 3.320626 ACAGTCATGGCGATTCGATATG 58.679 45.455 10.88 12.53 0.00 1.78
1694 1806 4.271049 AGAATTTACAGTCATGGCGATTCG 59.729 41.667 0.62 0.62 32.10 3.34
1700 1813 7.559590 ACTAATCAGAATTTACAGTCATGGC 57.440 36.000 0.00 0.00 0.00 4.40
1725 1838 9.458374 GGACGAAATTAAGATCAAAAGTTCAAA 57.542 29.630 15.78 0.00 31.09 2.69
1726 1839 8.625651 TGGACGAAATTAAGATCAAAAGTTCAA 58.374 29.630 15.78 1.97 31.09 2.69
1727 1840 8.160521 TGGACGAAATTAAGATCAAAAGTTCA 57.839 30.769 15.78 4.62 31.09 3.18
1728 1841 9.626045 AATGGACGAAATTAAGATCAAAAGTTC 57.374 29.630 9.09 9.09 0.00 3.01
1761 1884 6.983474 AATTTCAACCAAACAAGTCCAAAG 57.017 33.333 0.00 0.00 0.00 2.77
1830 1956 0.107703 CGCCAGCACCCTGAAGATTA 60.108 55.000 0.00 0.00 41.77 1.75
1895 2021 6.866248 ACAAGTTCCCATTTTGCTAATTTACG 59.134 34.615 0.00 0.00 0.00 3.18
1985 2115 5.185249 GTCTTCCCCCTTGGTTTAATTCTTC 59.815 44.000 0.00 0.00 34.77 2.87
1994 2124 2.434774 GCGTCTTCCCCCTTGGTT 59.565 61.111 0.00 0.00 34.77 3.67
2053 2183 4.165372 ACACGGAACAAATATGATACCCCT 59.835 41.667 0.00 0.00 0.00 4.79
2054 2184 4.457466 ACACGGAACAAATATGATACCCC 58.543 43.478 0.00 0.00 0.00 4.95
2058 2188 7.255312 GGGCAATTACACGGAACAAATATGATA 60.255 37.037 0.00 0.00 0.00 2.15
2098 2228 1.487231 CCAAGAAACGCGTCAGACG 59.513 57.895 19.10 19.10 45.88 4.18
2142 2272 1.098712 AACAAGAGCGCCACGGAAAA 61.099 50.000 2.29 0.00 0.00 2.29
2332 2462 6.238049 GCTCTATGCAAACTGTCAACATCTAG 60.238 42.308 0.00 0.00 42.31 2.43
2402 2532 4.012374 CCTACAGTGAAGACAATGCCATT 58.988 43.478 0.00 0.00 44.47 3.16
2632 2763 3.384467 TGACATCCTGCGAGACATGATTA 59.616 43.478 0.00 0.00 31.95 1.75
2645 2776 7.558161 TTAGTTTGAGCATAATGACATCCTG 57.442 36.000 0.00 0.00 0.00 3.86
2762 2893 7.855409 CAGAAAACAAAATTGAGACATACGTCA 59.145 33.333 0.00 0.00 45.23 4.35
2791 2922 7.970061 TGATACGAACCACACTAAGTACATAAC 59.030 37.037 0.00 0.00 0.00 1.89
3200 3331 4.935808 AGATTATCGTCAACTGTTTCCCAC 59.064 41.667 0.00 0.00 0.00 4.61
3342 3473 6.036300 CCGTCGGCAGATTTAAAATACAAGTA 59.964 38.462 0.00 0.00 0.00 2.24
3350 3481 3.661944 TGTACCGTCGGCAGATTTAAAA 58.338 40.909 12.28 0.00 0.00 1.52
3431 3563 9.914834 ACCCTATTTATTGCAGAACAAATAGTA 57.085 29.630 19.27 2.05 42.86 1.82
3550 3682 6.554334 TCCAATAAGTGAAACAGTACAAGC 57.446 37.500 0.00 0.00 41.43 4.01
3615 3747 9.750125 ACTCTTGTTCCTTTTAATGAATCAAAC 57.250 29.630 0.00 0.00 0.00 2.93
3706 3839 6.068010 TCCATGTTAACACAAGTGAAAGGAT 58.932 36.000 11.22 0.00 36.16 3.24
3712 3845 9.546428 CATATATCTCCATGTTAACACAAGTGA 57.454 33.333 11.22 9.12 36.16 3.41
3719 3852 8.372459 GGGTACACATATATCTCCATGTTAACA 58.628 37.037 11.41 11.41 33.12 2.41
3781 3918 6.687105 GCCAATAAATAGTTACAACAGAAGCG 59.313 38.462 0.00 0.00 0.00 4.68
3864 4001 0.251297 TCCAACATGCCCCAGTGAAG 60.251 55.000 0.00 0.00 0.00 3.02
3912 4050 6.484977 TGACTGTTGTAATGCACATGTCTAAA 59.515 34.615 0.00 0.00 36.90 1.85
3914 4052 5.408299 GTGACTGTTGTAATGCACATGTCTA 59.592 40.000 0.00 0.00 36.90 2.59
4011 4149 5.713025 TCATTATTGAAGCAAGCTCCAAAC 58.287 37.500 0.00 0.00 0.00 2.93
4353 4867 9.962783 AATCCGTATAGTAGTCTACATTGAAAC 57.037 33.333 12.54 1.51 0.00 2.78
4440 4954 8.624776 CCCTCTGTTCCAAAATATAAGATGTTC 58.375 37.037 0.00 0.00 0.00 3.18
4455 5129 5.070001 CACAAAAATACTCCCTCTGTTCCA 58.930 41.667 0.00 0.00 0.00 3.53
4745 5427 1.134946 GTGTATGGTTCTGGCATTGGC 59.865 52.381 2.73 2.73 40.13 4.52
4802 5484 0.983378 AGGGATGGGGCTGACACTAC 60.983 60.000 0.00 0.00 0.00 2.73
4846 5528 6.446781 TCAAGAGATGAATTGAATCTTGGC 57.553 37.500 17.24 2.09 44.40 4.52
4962 5649 2.803956 CATATGCTGGGCTTCATCCAT 58.196 47.619 0.00 0.00 33.29 3.41
5167 5857 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
5169 5859 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
5170 5860 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
5172 5862 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
5173 5863 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
5174 5864 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
5175 5865 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
5176 5866 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
5177 5867 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
5178 5868 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
5179 5869 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
5180 5870 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
5181 5871 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
5182 5872 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
5183 5873 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
5184 5874 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5185 5875 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5186 5876 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5187 5877 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
5188 5878 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
5189 5879 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
5190 5880 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
5191 5881 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
5192 5882 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
5193 5883 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
5194 5884 0.251297 TTGTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
5195 5885 0.251297 TTTGTACTCCCTCCGTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
5196 5886 0.108945 GTTTGTACTCCCTCCGTCCG 60.109 60.000 0.00 0.00 0.00 4.79
5197 5887 0.248565 GGTTTGTACTCCCTCCGTCC 59.751 60.000 0.00 0.00 0.00 4.79
5198 5888 0.971386 TGGTTTGTACTCCCTCCGTC 59.029 55.000 0.00 0.00 0.00 4.79
5199 5889 1.553704 GATGGTTTGTACTCCCTCCGT 59.446 52.381 0.00 0.00 0.00 4.69
5200 5890 1.470979 CGATGGTTTGTACTCCCTCCG 60.471 57.143 0.00 0.00 0.00 4.63
5201 5891 1.553704 ACGATGGTTTGTACTCCCTCC 59.446 52.381 0.00 0.00 0.00 4.30
5202 5892 2.232941 TGACGATGGTTTGTACTCCCTC 59.767 50.000 0.00 0.00 0.00 4.30
5203 5893 2.233922 CTGACGATGGTTTGTACTCCCT 59.766 50.000 0.00 0.00 0.00 4.20
5204 5894 2.028385 ACTGACGATGGTTTGTACTCCC 60.028 50.000 0.00 0.00 0.00 4.30
5205 5895 3.314541 ACTGACGATGGTTTGTACTCC 57.685 47.619 0.00 0.00 0.00 3.85
5206 5896 3.432252 CCAACTGACGATGGTTTGTACTC 59.568 47.826 0.00 0.00 31.84 2.59
5207 5897 3.399330 CCAACTGACGATGGTTTGTACT 58.601 45.455 0.00 0.00 31.84 2.73
5208 5898 2.095919 GCCAACTGACGATGGTTTGTAC 60.096 50.000 0.00 0.00 39.00 2.90
5209 5899 2.147958 GCCAACTGACGATGGTTTGTA 58.852 47.619 0.00 0.00 39.00 2.41
5210 5900 0.951558 GCCAACTGACGATGGTTTGT 59.048 50.000 0.00 0.00 39.00 2.83
5211 5901 1.238439 AGCCAACTGACGATGGTTTG 58.762 50.000 0.00 0.00 39.00 2.93
5212 5902 2.851263 TAGCCAACTGACGATGGTTT 57.149 45.000 0.00 0.00 39.00 3.27
5213 5903 2.812011 GTTTAGCCAACTGACGATGGTT 59.188 45.455 0.00 0.00 39.00 3.67
5214 5904 2.423577 GTTTAGCCAACTGACGATGGT 58.576 47.619 0.00 0.00 39.00 3.55
5215 5905 1.737793 GGTTTAGCCAACTGACGATGG 59.262 52.381 0.00 0.00 39.80 3.51
5219 5909 2.068837 TACGGTTTAGCCAACTGACG 57.931 50.000 11.33 2.98 43.78 4.35
5239 5929 2.304470 TGCATACCAGTTGCAGGTAAGA 59.696 45.455 7.36 0.00 44.73 2.10
5274 5964 1.522258 CAAAAACGACAAGCATGGCAC 59.478 47.619 0.00 0.00 32.33 5.01
5288 5978 0.658897 TGTCGCGGAGAACCAAAAAC 59.341 50.000 6.13 0.00 35.59 2.43
5294 5984 0.658897 TTTTGTTGTCGCGGAGAACC 59.341 50.000 6.13 0.00 35.38 3.62
5295 5985 1.920272 GCTTTTGTTGTCGCGGAGAAC 60.920 52.381 6.13 8.85 36.54 3.01
5297 5987 1.503818 GGCTTTTGTTGTCGCGGAGA 61.504 55.000 6.13 0.00 0.00 3.71
5320 6010 5.975988 ATTCCAACCTAAGGAGAGCAATA 57.024 39.130 0.00 0.00 36.33 1.90
5323 6013 4.657814 AAATTCCAACCTAAGGAGAGCA 57.342 40.909 0.00 0.00 36.33 4.26
5357 6060 6.122277 CCTTGAGAGAACCCTATTTTGCATA 58.878 40.000 0.00 0.00 0.00 3.14
5386 7002 2.367241 TCGTCACCCTTTCATCTTCACA 59.633 45.455 0.00 0.00 0.00 3.58
5450 7066 5.530915 CAGTTTTGGACATGGACAGAAACTA 59.469 40.000 19.12 0.00 34.99 2.24
5537 7155 3.072184 GTGCAGTCCCATCAGATCCTAAT 59.928 47.826 0.00 0.00 0.00 1.73
5564 7182 5.532406 ACAACCAATATCATCCATGTGTAGC 59.468 40.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.