Multiple sequence alignment - TraesCS4A01G454600

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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 TraesCS4A01G454600 chr4A 100.000 3539 0 0 1 3539 718754130 718750592 0.000000e+00 6536.0
1 TraesCS4A01G454600 chr4A 94.000 150 9 0 1 150 30181733 30181882 9.880000e-56 228.0
2 TraesCS4A01G454600 chr4A 73.305 472 99 16 1333 1780 717050921 717050453 7.920000e-32 148.0
3 TraesCS4A01G454600 chr4A 100.000 28 0 0 424 451 452634769 452634742 6.000000e-03 52.8
4 TraesCS4A01G454600 chr7D 88.969 2484 173 39 317 2735 16121033 16118586 0.000000e+00 2976.0
5 TraesCS4A01G454600 chr7D 96.026 151 5 1 1 151 23185789 23185938 9.810000e-61 244.0
6 TraesCS4A01G454600 chr7D 86.857 175 21 2 1596 1768 582031182 582031008 1.000000e-45 195.0
7 TraesCS4A01G454600 chr7D 100.000 39 0 0 278 316 16121104 16121066 4.900000e-09 73.1
8 TraesCS4A01G454600 chr3D 88.866 2479 183 35 317 2735 584758290 584760735 0.000000e+00 2963.0
9 TraesCS4A01G454600 chr3D 88.049 820 66 18 2733 3539 62333293 62332493 0.000000e+00 942.0
10 TraesCS4A01G454600 chr3D 87.868 816 71 15 2734 3539 56291419 56290622 0.000000e+00 933.0
11 TraesCS4A01G454600 chr3D 87.868 816 71 14 2734 3539 56306622 56305825 0.000000e+00 933.0
12 TraesCS4A01G454600 chr3D 87.760 817 71 16 2734 3539 56289781 56288983 0.000000e+00 928.0
13 TraesCS4A01G454600 chr3D 87.638 817 70 17 2734 3539 56278518 56277722 0.000000e+00 920.0
14 TraesCS4A01G454600 chr3D 86.994 815 81 14 2734 3539 56280156 56279358 0.000000e+00 894.0
15 TraesCS4A01G454600 chr3D 91.304 552 37 4 2989 3539 443317573 443317032 0.000000e+00 743.0
16 TraesCS4A01G454600 chr3D 100.000 39 0 0 278 316 584732766 584732804 4.900000e-09 73.1
17 TraesCS4A01G454600 chr7A 90.637 2136 131 22 320 2431 14920375 14918285 0.000000e+00 2772.0
18 TraesCS4A01G454600 chr7A 75.227 771 156 19 1329 2070 618677792 618678556 2.040000e-87 333.0
19 TraesCS4A01G454600 chr7A 83.420 193 32 0 1329 1521 619022980 619023172 2.810000e-41 180.0
20 TraesCS4A01G454600 chr7A 97.059 68 1 1 250 316 14920478 14920411 2.890000e-21 113.0
21 TraesCS4A01G454600 chr7B 89.969 1944 109 33 499 2402 711443145 711441248 0.000000e+00 2431.0
22 TraesCS4A01G454600 chr7B 75.486 771 149 26 1329 2067 580133993 580134755 1.220000e-89 340.0
23 TraesCS4A01G454600 chr7B 75.323 774 151 23 1329 2070 580135127 580135892 5.660000e-88 335.0
24 TraesCS4A01G454600 chr7B 82.581 310 23 15 2446 2735 711441239 711440941 9.810000e-61 244.0
25 TraesCS4A01G454600 chr7B 95.745 47 2 0 270 316 711443611 711443565 3.790000e-10 76.8
26 TraesCS4A01G454600 chr7B 86.111 72 2 2 317 388 711443528 711443465 1.760000e-08 71.3
27 TraesCS4A01G454600 chr5B 94.840 814 34 1 2734 3539 414974495 414973682 0.000000e+00 1264.0
28 TraesCS4A01G454600 chr6B 94.505 819 31 5 2734 3539 134966010 134966827 0.000000e+00 1251.0
29 TraesCS4A01G454600 chr6B 100.000 28 0 0 424 451 47414657 47414630 6.000000e-03 52.8
30 TraesCS4A01G454600 chr2D 87.654 810 72 9 2734 3539 7985333 7984548 0.000000e+00 917.0
31 TraesCS4A01G454600 chr2D 93.506 154 10 0 1 154 61334186 61334033 2.750000e-56 230.0
32 TraesCS4A01G454600 chr2D 79.812 213 35 7 2734 2943 589263157 589262950 7.920000e-32 148.0
33 TraesCS4A01G454600 chr4D 85.820 811 91 17 2734 3539 483450584 483451375 0.000000e+00 839.0
34 TraesCS4A01G454600 chr4D 88.764 178 19 1 1596 1772 318927920 318928097 2.140000e-52 217.0
35 TraesCS4A01G454600 chr4B 98.013 151 3 0 1 151 608491221 608491071 2.710000e-66 263.0
36 TraesCS4A01G454600 chr6A 96.000 150 5 1 1 150 611451888 611451740 3.530000e-60 243.0
37 TraesCS4A01G454600 chr2A 95.973 149 6 0 1 149 203895033 203894885 3.530000e-60 243.0
38 TraesCS4A01G454600 chr6D 95.364 151 5 2 1 151 318357172 318357320 4.570000e-59 239.0
39 TraesCS4A01G454600 chr2B 94.667 150 7 1 1 150 202009678 202009530 7.640000e-57 231.0
40 TraesCS4A01G454600 chr5D 93.464 153 9 1 1 152 407763409 407763561 3.550000e-55 226.0
41 TraesCS4A01G454600 chr3B 100.000 28 0 0 424 451 126544416 126544443 6.000000e-03 52.8
42 TraesCS4A01G454600 chr1B 100.000 28 0 0 424 451 271186768 271186741 6.000000e-03 52.8


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 TraesCS4A01G454600 chr4A 718750592 718754130 3538 True 6536.000 6536 100.0000 1 3539 1 chr4A.!!$R3 3538
1 TraesCS4A01G454600 chr7D 16118586 16121104 2518 True 1524.550 2976 94.4845 278 2735 2 chr7D.!!$R2 2457
2 TraesCS4A01G454600 chr3D 584758290 584760735 2445 False 2963.000 2963 88.8660 317 2735 1 chr3D.!!$F2 2418
3 TraesCS4A01G454600 chr3D 62332493 62333293 800 True 942.000 942 88.0490 2733 3539 1 chr3D.!!$R2 806
4 TraesCS4A01G454600 chr3D 56305825 56306622 797 True 933.000 933 87.8680 2734 3539 1 chr3D.!!$R1 805
5 TraesCS4A01G454600 chr3D 56288983 56291419 2436 True 930.500 933 87.8140 2734 3539 2 chr3D.!!$R5 805
6 TraesCS4A01G454600 chr3D 56277722 56280156 2434 True 907.000 920 87.3160 2734 3539 2 chr3D.!!$R4 805
7 TraesCS4A01G454600 chr3D 443317032 443317573 541 True 743.000 743 91.3040 2989 3539 1 chr3D.!!$R3 550
8 TraesCS4A01G454600 chr7A 14918285 14920478 2193 True 1442.500 2772 93.8480 250 2431 2 chr7A.!!$R1 2181
9 TraesCS4A01G454600 chr7A 618677792 618678556 764 False 333.000 333 75.2270 1329 2070 1 chr7A.!!$F1 741
10 TraesCS4A01G454600 chr7B 711440941 711443611 2670 True 705.775 2431 88.6015 270 2735 4 chr7B.!!$R1 2465
11 TraesCS4A01G454600 chr7B 580133993 580135892 1899 False 337.500 340 75.4045 1329 2070 2 chr7B.!!$F1 741
12 TraesCS4A01G454600 chr5B 414973682 414974495 813 True 1264.000 1264 94.8400 2734 3539 1 chr5B.!!$R1 805
13 TraesCS4A01G454600 chr6B 134966010 134966827 817 False 1251.000 1251 94.5050 2734 3539 1 chr6B.!!$F1 805
14 TraesCS4A01G454600 chr2D 7984548 7985333 785 True 917.000 917 87.6540 2734 3539 1 chr2D.!!$R1 805
15 TraesCS4A01G454600 chr4D 483450584 483451375 791 False 839.000 839 85.8200 2734 3539 1 chr4D.!!$F2 805

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
172 173 0.031043 ACAACACGCTACGCACACTA 59.969 50.0 0.0 0.0 0.00 2.74 F
236 237 0.462047 CCCGCTAGACGCATCCTTTT 60.462 55.0 0.0 0.0 41.76 2.27 F
322 360 0.821711 CAACGGAAAGCCTCAACCCA 60.822 55.0 0.0 0.0 0.00 4.51 F
1461 2909 0.033228 ATCTCATCTGCTGCTACCGC 59.967 55.0 0.0 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1321 0.178970 GGGGCTCTGCATGATGGAAT 60.179 55.0 0.00 0.0 0.0 3.01 R
1461 2909 0.443869 CGACAACAAGGCAATCTCCG 59.556 55.0 0.00 0.0 0.0 4.63 R
1609 3072 0.527565 CTTCCAACGGGCCAATCAAG 59.472 55.0 4.39 0.0 0.0 3.02 R
2545 4071 0.108585 GAGATCGGGGCCAAATAGCA 59.891 55.0 4.39 0.0 0.0 3.49 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
22 23 2.332063 CCAATGAGGTGGCGAATACT 57.668 50.000 0.00 0.00 0.00 2.12
23 24 3.469008 CCAATGAGGTGGCGAATACTA 57.531 47.619 0.00 0.00 0.00 1.82
24 25 4.008074 CCAATGAGGTGGCGAATACTAT 57.992 45.455 0.00 0.00 0.00 2.12
25 26 5.147330 CCAATGAGGTGGCGAATACTATA 57.853 43.478 0.00 0.00 0.00 1.31
26 27 5.171476 CCAATGAGGTGGCGAATACTATAG 58.829 45.833 0.00 0.00 0.00 1.31
27 28 3.936372 TGAGGTGGCGAATACTATAGC 57.064 47.619 0.00 0.00 0.00 2.97
28 29 3.227614 TGAGGTGGCGAATACTATAGCA 58.772 45.455 0.00 0.00 0.00 3.49
29 30 3.639561 TGAGGTGGCGAATACTATAGCAA 59.360 43.478 0.00 0.00 0.00 3.91
30 31 4.100344 TGAGGTGGCGAATACTATAGCAAA 59.900 41.667 0.00 0.00 0.00 3.68
31 32 5.031066 AGGTGGCGAATACTATAGCAAAA 57.969 39.130 0.00 0.00 0.00 2.44
32 33 5.621193 AGGTGGCGAATACTATAGCAAAAT 58.379 37.500 0.00 0.00 0.00 1.82
33 34 5.701290 AGGTGGCGAATACTATAGCAAAATC 59.299 40.000 0.00 0.00 0.00 2.17
34 35 5.701290 GGTGGCGAATACTATAGCAAAATCT 59.299 40.000 0.00 0.00 0.00 2.40
35 36 6.347725 GGTGGCGAATACTATAGCAAAATCTG 60.348 42.308 0.00 0.00 0.00 2.90
49 50 5.382618 CAAAATCTGCTTTTAGCTCCAGT 57.617 39.130 0.00 0.00 42.97 4.00
50 51 6.500684 CAAAATCTGCTTTTAGCTCCAGTA 57.499 37.500 0.00 0.00 42.97 2.74
51 52 6.317857 CAAAATCTGCTTTTAGCTCCAGTAC 58.682 40.000 0.00 0.00 42.97 2.73
52 53 3.611766 TCTGCTTTTAGCTCCAGTACC 57.388 47.619 0.00 0.00 42.97 3.34
53 54 3.173965 TCTGCTTTTAGCTCCAGTACCT 58.826 45.455 0.00 0.00 42.97 3.08
54 55 3.195825 TCTGCTTTTAGCTCCAGTACCTC 59.804 47.826 0.00 0.00 42.97 3.85
55 56 3.173965 TGCTTTTAGCTCCAGTACCTCT 58.826 45.455 0.00 0.00 42.97 3.69
56 57 3.583086 TGCTTTTAGCTCCAGTACCTCTT 59.417 43.478 0.00 0.00 42.97 2.85
57 58 3.935828 GCTTTTAGCTCCAGTACCTCTTG 59.064 47.826 0.00 0.00 38.45 3.02
58 59 4.563786 GCTTTTAGCTCCAGTACCTCTTGT 60.564 45.833 0.00 0.00 38.45 3.16
59 60 4.537135 TTTAGCTCCAGTACCTCTTGTG 57.463 45.455 0.00 0.00 0.00 3.33
60 61 2.016905 AGCTCCAGTACCTCTTGTGT 57.983 50.000 0.00 0.00 0.00 3.72
61 62 2.330216 AGCTCCAGTACCTCTTGTGTT 58.670 47.619 0.00 0.00 0.00 3.32
62 63 2.706190 AGCTCCAGTACCTCTTGTGTTT 59.294 45.455 0.00 0.00 0.00 2.83
63 64 2.808543 GCTCCAGTACCTCTTGTGTTTG 59.191 50.000 0.00 0.00 0.00 2.93
64 65 3.403038 CTCCAGTACCTCTTGTGTTTGG 58.597 50.000 0.00 0.00 0.00 3.28
65 66 2.105821 TCCAGTACCTCTTGTGTTTGGG 59.894 50.000 0.00 0.00 0.00 4.12
66 67 2.105821 CCAGTACCTCTTGTGTTTGGGA 59.894 50.000 0.00 0.00 0.00 4.37
67 68 3.244911 CCAGTACCTCTTGTGTTTGGGAT 60.245 47.826 0.00 0.00 0.00 3.85
68 69 3.753272 CAGTACCTCTTGTGTTTGGGATG 59.247 47.826 0.00 0.00 0.00 3.51
69 70 1.620822 ACCTCTTGTGTTTGGGATGC 58.379 50.000 0.00 0.00 0.00 3.91
70 71 1.145738 ACCTCTTGTGTTTGGGATGCT 59.854 47.619 0.00 0.00 0.00 3.79
71 72 2.375174 ACCTCTTGTGTTTGGGATGCTA 59.625 45.455 0.00 0.00 0.00 3.49
72 73 3.010584 ACCTCTTGTGTTTGGGATGCTAT 59.989 43.478 0.00 0.00 0.00 2.97
73 74 3.629398 CCTCTTGTGTTTGGGATGCTATC 59.371 47.826 0.00 0.00 0.00 2.08
87 88 6.809630 GGATGCTATCCCTGACTTTATTTC 57.190 41.667 4.36 0.00 43.88 2.17
88 89 6.538263 GGATGCTATCCCTGACTTTATTTCT 58.462 40.000 4.36 0.00 43.88 2.52
89 90 7.001073 GGATGCTATCCCTGACTTTATTTCTT 58.999 38.462 4.36 0.00 43.88 2.52
90 91 7.174080 GGATGCTATCCCTGACTTTATTTCTTC 59.826 40.741 4.36 0.00 43.88 2.87
91 92 7.200434 TGCTATCCCTGACTTTATTTCTTCT 57.800 36.000 0.00 0.00 0.00 2.85
92 93 7.633789 TGCTATCCCTGACTTTATTTCTTCTT 58.366 34.615 0.00 0.00 0.00 2.52
93 94 7.770897 TGCTATCCCTGACTTTATTTCTTCTTC 59.229 37.037 0.00 0.00 0.00 2.87
94 95 7.227711 GCTATCCCTGACTTTATTTCTTCTTCC 59.772 40.741 0.00 0.00 0.00 3.46
95 96 5.816682 TCCCTGACTTTATTTCTTCTTCCC 58.183 41.667 0.00 0.00 0.00 3.97
96 97 5.551977 TCCCTGACTTTATTTCTTCTTCCCT 59.448 40.000 0.00 0.00 0.00 4.20
97 98 6.045577 TCCCTGACTTTATTTCTTCTTCCCTT 59.954 38.462 0.00 0.00 0.00 3.95
98 99 6.151817 CCCTGACTTTATTTCTTCTTCCCTTG 59.848 42.308 0.00 0.00 0.00 3.61
99 100 6.717084 CCTGACTTTATTTCTTCTTCCCTTGT 59.283 38.462 0.00 0.00 0.00 3.16
100 101 7.883311 CCTGACTTTATTTCTTCTTCCCTTGTA 59.117 37.037 0.00 0.00 0.00 2.41
101 102 9.284968 CTGACTTTATTTCTTCTTCCCTTGTAA 57.715 33.333 0.00 0.00 0.00 2.41
102 103 9.635404 TGACTTTATTTCTTCTTCCCTTGTAAA 57.365 29.630 0.00 0.00 0.00 2.01
103 104 9.894783 GACTTTATTTCTTCTTCCCTTGTAAAC 57.105 33.333 0.00 0.00 0.00 2.01
104 105 8.565416 ACTTTATTTCTTCTTCCCTTGTAAACG 58.435 33.333 0.00 0.00 0.00 3.60
105 106 8.680039 TTTATTTCTTCTTCCCTTGTAAACGA 57.320 30.769 0.00 0.00 0.00 3.85
106 107 8.857694 TTATTTCTTCTTCCCTTGTAAACGAT 57.142 30.769 0.00 0.00 0.00 3.73
107 108 6.796705 TTTCTTCTTCCCTTGTAAACGATC 57.203 37.500 0.00 0.00 0.00 3.69
108 109 5.740290 TCTTCTTCCCTTGTAAACGATCT 57.260 39.130 0.00 0.00 0.00 2.75
109 110 6.110411 TCTTCTTCCCTTGTAAACGATCTT 57.890 37.500 0.00 0.00 0.00 2.40
110 111 6.531021 TCTTCTTCCCTTGTAAACGATCTTT 58.469 36.000 0.00 0.00 0.00 2.52
111 112 6.649557 TCTTCTTCCCTTGTAAACGATCTTTC 59.350 38.462 0.00 0.00 0.00 2.62
112 113 5.243207 TCTTCCCTTGTAAACGATCTTTCC 58.757 41.667 0.00 0.00 0.00 3.13
113 114 4.903045 TCCCTTGTAAACGATCTTTCCT 57.097 40.909 0.00 0.00 0.00 3.36
114 115 5.237236 TCCCTTGTAAACGATCTTTCCTT 57.763 39.130 0.00 0.00 0.00 3.36
115 116 5.627135 TCCCTTGTAAACGATCTTTCCTTT 58.373 37.500 0.00 0.00 0.00 3.11
116 117 6.771573 TCCCTTGTAAACGATCTTTCCTTTA 58.228 36.000 0.00 0.00 0.00 1.85
117 118 7.399634 TCCCTTGTAAACGATCTTTCCTTTAT 58.600 34.615 0.00 0.00 0.00 1.40
118 119 7.886446 TCCCTTGTAAACGATCTTTCCTTTATT 59.114 33.333 0.00 0.00 0.00 1.40
119 120 8.520351 CCCTTGTAAACGATCTTTCCTTTATTT 58.480 33.333 0.00 0.00 0.00 1.40
120 121 9.341899 CCTTGTAAACGATCTTTCCTTTATTTG 57.658 33.333 0.00 0.00 0.00 2.32
123 124 8.726988 TGTAAACGATCTTTCCTTTATTTGAGG 58.273 33.333 0.00 0.00 35.53 3.86
124 125 7.996098 AAACGATCTTTCCTTTATTTGAGGA 57.004 32.000 0.00 0.00 41.46 3.71
167 168 3.881780 AAAATAACAACACGCTACGCA 57.118 38.095 0.00 0.00 0.00 5.24
168 169 2.867456 AATAACAACACGCTACGCAC 57.133 45.000 0.00 0.00 0.00 5.34
169 170 1.785768 ATAACAACACGCTACGCACA 58.214 45.000 0.00 0.00 0.00 4.57
170 171 0.854062 TAACAACACGCTACGCACAC 59.146 50.000 0.00 0.00 0.00 3.82
171 172 0.808453 AACAACACGCTACGCACACT 60.808 50.000 0.00 0.00 0.00 3.55
172 173 0.031043 ACAACACGCTACGCACACTA 59.969 50.000 0.00 0.00 0.00 2.74
173 174 1.336517 ACAACACGCTACGCACACTAT 60.337 47.619 0.00 0.00 0.00 2.12
174 175 1.724623 CAACACGCTACGCACACTATT 59.275 47.619 0.00 0.00 0.00 1.73
175 176 2.074547 ACACGCTACGCACACTATTT 57.925 45.000 0.00 0.00 0.00 1.40
176 177 1.724623 ACACGCTACGCACACTATTTG 59.275 47.619 0.00 0.00 0.00 2.32
177 178 1.060553 CACGCTACGCACACTATTTGG 59.939 52.381 0.00 0.00 0.00 3.28
178 179 1.337447 ACGCTACGCACACTATTTGGT 60.337 47.619 0.00 0.00 0.00 3.67
179 180 2.094597 ACGCTACGCACACTATTTGGTA 60.095 45.455 0.00 0.00 0.00 3.25
180 181 2.924926 CGCTACGCACACTATTTGGTAA 59.075 45.455 0.00 0.00 0.00 2.85
181 182 3.368539 CGCTACGCACACTATTTGGTAAA 59.631 43.478 0.00 0.00 0.00 2.01
182 183 4.143073 CGCTACGCACACTATTTGGTAAAA 60.143 41.667 0.00 0.00 0.00 1.52
183 184 5.615106 CGCTACGCACACTATTTGGTAAAAA 60.615 40.000 0.00 0.00 0.00 1.94
233 234 3.917760 GCCCGCTAGACGCATCCT 61.918 66.667 0.00 0.00 41.76 3.24
234 235 2.815308 CCCGCTAGACGCATCCTT 59.185 61.111 0.00 0.00 41.76 3.36
235 236 1.144057 CCCGCTAGACGCATCCTTT 59.856 57.895 0.00 0.00 41.76 3.11
236 237 0.462047 CCCGCTAGACGCATCCTTTT 60.462 55.000 0.00 0.00 41.76 2.27
237 238 1.369625 CCGCTAGACGCATCCTTTTT 58.630 50.000 0.00 0.00 41.76 1.94
322 360 0.821711 CAACGGAAAGCCTCAACCCA 60.822 55.000 0.00 0.00 0.00 4.51
430 468 2.507944 GCGACAGCCCATCCTGAT 59.492 61.111 0.00 0.00 36.67 2.90
431 469 1.596477 GCGACAGCCCATCCTGATC 60.596 63.158 0.00 0.00 36.67 2.92
432 470 1.070445 CGACAGCCCATCCTGATCC 59.930 63.158 0.00 0.00 36.67 3.36
433 471 1.070445 GACAGCCCATCCTGATCCG 59.930 63.158 0.00 0.00 36.67 4.18
436 474 3.564218 GCCCATCCTGATCCGCCT 61.564 66.667 0.00 0.00 0.00 5.52
497 768 2.094182 GTGCTCATTCTCTCCCGTACAA 60.094 50.000 0.00 0.00 0.00 2.41
502 773 5.447818 GCTCATTCTCTCCCGTACAAATTTG 60.448 44.000 16.67 16.67 0.00 2.32
545 820 3.061295 GTCATGCATATGCCTACGAATCG 59.939 47.826 24.54 0.00 41.18 3.34
549 824 3.243737 TGCATATGCCTACGAATCGTCTT 60.244 43.478 24.54 0.00 39.85 3.01
580 855 2.273449 GCTGGATCTGTGGGTGGG 59.727 66.667 0.00 0.00 0.00 4.61
582 857 3.338250 TGGATCTGTGGGTGGGCC 61.338 66.667 0.00 0.00 0.00 5.80
613 908 5.945144 ATGGATTTTCCTCAGAAATTGGG 57.055 39.130 0.00 0.00 41.55 4.12
681 985 5.872617 TCACGGTCTAAATAATTGTCACCTG 59.127 40.000 0.00 0.00 0.00 4.00
705 1009 9.774742 CTGTTTTAGCCTCATGTTCTTATAAAC 57.225 33.333 0.00 0.00 0.00 2.01
706 1010 9.290988 TGTTTTAGCCTCATGTTCTTATAAACA 57.709 29.630 0.00 0.00 42.92 2.83
707 1011 9.774742 GTTTTAGCCTCATGTTCTTATAAACAG 57.225 33.333 0.00 0.00 42.09 3.16
708 1012 9.733556 TTTTAGCCTCATGTTCTTATAAACAGA 57.266 29.630 0.00 0.00 42.09 3.41
709 1013 9.733556 TTTAGCCTCATGTTCTTATAAACAGAA 57.266 29.630 0.00 0.00 42.09 3.02
724 1028 3.818961 ACAGAATGATGTGCTTCGTTG 57.181 42.857 0.00 0.00 39.69 4.10
725 1029 2.485426 ACAGAATGATGTGCTTCGTTGG 59.515 45.455 0.00 0.00 39.69 3.77
755 1059 6.785488 TTACTGTTGTGAGACATTTGCTAG 57.215 37.500 0.00 0.00 0.00 3.42
801 1105 2.992124 TGAACGGTCTGAACTTTGGA 57.008 45.000 0.33 0.00 0.00 3.53
822 1131 3.577649 ATCCACAAGAGTGTAGTCGTG 57.422 47.619 1.85 1.85 44.39 4.35
1003 1317 5.929992 CCTGAATTTGTTTTGTGATGCAGAT 59.070 36.000 0.00 0.00 28.34 2.90
1006 1320 8.296799 TGAATTTGTTTTGTGATGCAGATAAC 57.703 30.769 0.00 0.00 0.00 1.89
1007 1321 7.924947 TGAATTTGTTTTGTGATGCAGATAACA 59.075 29.630 0.00 0.00 0.00 2.41
1009 1323 8.836268 ATTTGTTTTGTGATGCAGATAACATT 57.164 26.923 0.00 0.00 30.56 2.71
1033 1347 3.341202 ATGCAGAGCCCCAGCAGAC 62.341 63.158 0.00 0.00 42.14 3.51
1041 1355 1.757306 CCCCAGCAGACTGTCAGTT 59.243 57.895 7.00 0.00 42.81 3.16
1054 1368 6.199908 CAGACTGTCAGTTGTTTCTACTTCAG 59.800 42.308 7.00 0.00 34.25 3.02
1057 1371 6.535508 ACTGTCAGTTGTTTCTACTTCAGTTC 59.464 38.462 0.00 0.00 36.09 3.01
1060 1374 4.270084 CAGTTGTTTCTACTTCAGTTCGCA 59.730 41.667 0.00 0.00 0.00 5.10
1073 1387 1.341209 AGTTCGCACTGATGTGTCTGA 59.659 47.619 0.00 0.00 45.44 3.27
1075 1389 1.783284 TCGCACTGATGTGTCTGAAC 58.217 50.000 0.00 0.00 45.44 3.18
1129 1443 1.527034 TCACTCCATTGTTGCTCTGC 58.473 50.000 0.00 0.00 0.00 4.26
1242 1556 3.879892 GCACATTAATCCCACCTCTTCTC 59.120 47.826 0.00 0.00 0.00 2.87
1273 1587 2.408565 CTGGCCCTATCCAAGGTTCTA 58.591 52.381 0.00 0.00 44.90 2.10
1285 1599 3.841255 CCAAGGTTCTACTCTTCCTTCCT 59.159 47.826 0.00 0.00 38.09 3.36
1461 2909 0.033228 ATCTCATCTGCTGCTACCGC 59.967 55.000 0.00 0.00 0.00 5.68
1470 2918 2.202878 TGCTACCGCGGAGATTGC 60.203 61.111 35.90 25.30 39.65 3.56
1568 3031 4.158579 CACTCTCACTGCTCCACTTACATA 59.841 45.833 0.00 0.00 0.00 2.29
1584 3047 6.481313 CACTTACATATCCCAACTCACATCTG 59.519 42.308 0.00 0.00 0.00 2.90
1609 3072 0.034670 AAGCACTCAATCCTCCCTGC 60.035 55.000 0.00 0.00 0.00 4.85
1632 3095 0.039618 ATTGGCCCGTTGGAAGTGAT 59.960 50.000 0.00 0.00 0.00 3.06
1644 3107 2.305927 TGGAAGTGATTCTTGGGAGGAC 59.694 50.000 0.00 0.00 36.40 3.85
1725 3188 1.874129 TGGACCACGGTATGAGGATT 58.126 50.000 0.00 0.00 31.87 3.01
2024 3496 4.247380 GGAGCGATGGGGAGGCAG 62.247 72.222 0.00 0.00 0.00 4.85
2056 3528 1.749063 TGTACTACGCCCATCACTCTG 59.251 52.381 0.00 0.00 0.00 3.35
2124 3596 4.019174 CAACTAGCCATCCCAACTTCAAT 58.981 43.478 0.00 0.00 0.00 2.57
2129 3601 1.901159 CCATCCCAACTTCAATTGGCA 59.099 47.619 5.42 0.00 46.77 4.92
2195 3667 0.759346 ATGTTCTACTCCGATGGCCC 59.241 55.000 0.00 0.00 0.00 5.80
2205 3677 1.449423 CGATGGCCCGTGATTGTGA 60.449 57.895 0.00 0.00 0.00 3.58
2211 3683 1.594194 GCCCGTGATTGTGATGGCAA 61.594 55.000 0.00 0.00 38.73 4.52
2230 3725 9.248291 GATGGCAAACACCACTATATTTATTTG 57.752 33.333 0.00 0.00 44.17 2.32
2242 3737 8.072567 CACTATATTTATTTGTCTTGCTGCTCC 58.927 37.037 0.00 0.00 0.00 4.70
2262 3757 5.151632 TCCAGAAGTTCGTTTTCTTTTCG 57.848 39.130 0.00 0.00 32.75 3.46
2335 3842 6.418101 TGTTTATTCTTCTAGGCAGAGCATT 58.582 36.000 0.00 0.00 30.73 3.56
2336 3843 7.564793 TGTTTATTCTTCTAGGCAGAGCATTA 58.435 34.615 0.00 0.00 30.73 1.90
2348 3855 3.509659 GCATTAGGCAACCCGACC 58.490 61.111 0.00 0.00 43.97 4.79
2377 3885 8.585189 ACATTTTGCTTGAATCTCTTTTTCTC 57.415 30.769 0.00 0.00 0.00 2.87
2379 3887 8.913656 CATTTTGCTTGAATCTCTTTTTCTCTC 58.086 33.333 0.00 0.00 0.00 3.20
2443 3951 4.092116 AGCTGTCTAGAAAGCAAGGTTT 57.908 40.909 31.86 11.44 42.06 3.27
2444 3952 4.464947 AGCTGTCTAGAAAGCAAGGTTTT 58.535 39.130 31.86 10.75 42.06 2.43
2445 3953 4.889995 AGCTGTCTAGAAAGCAAGGTTTTT 59.110 37.500 31.86 10.05 42.06 1.94
2476 3984 8.698210 TCCTTCAGTAAGTACTTTGTGTTCTTA 58.302 33.333 14.49 0.00 37.45 2.10
2491 3999 7.727578 TGTGTTCTTATACTGATAGGGACAA 57.272 36.000 0.00 0.00 35.49 3.18
2517 4043 2.048603 GGGTGCAGAGTTCCCATGC 61.049 63.158 4.47 0.00 40.79 4.06
2542 4068 7.547370 GCGGAGTAGCATCATAGATTAAAATCT 59.453 37.037 9.97 9.97 41.67 2.40
2557 4083 2.371658 AATCTCCTGCTATTTGGCCC 57.628 50.000 0.00 0.00 0.00 5.80
2588 4114 1.795286 CTAATCGCGGCTGAGAAATCC 59.205 52.381 6.13 0.00 0.00 3.01
2591 4117 1.142748 CGCGGCTGAGAAATCCTCT 59.857 57.895 0.00 0.00 42.44 3.69
2616 4142 4.994852 GTGAGTTGCCAGTAGTACAAATCA 59.005 41.667 10.09 10.09 43.59 2.57
2660 4188 0.469917 GGGATCGCTCCATTCCTTCA 59.530 55.000 7.74 0.00 44.08 3.02
2667 4196 2.486191 CGCTCCATTCCTTCATTAGCCT 60.486 50.000 0.00 0.00 0.00 4.58
2670 4199 4.140536 CTCCATTCCTTCATTAGCCTTCC 58.859 47.826 0.00 0.00 0.00 3.46
2683 4212 1.077169 AGCCTTCCCGGGAAAATTCTT 59.923 47.619 34.78 15.45 33.34 2.52
2685 4214 3.093814 GCCTTCCCGGGAAAATTCTTTA 58.906 45.455 34.78 11.51 33.34 1.85
2746 4275 2.683916 TCCATCAGGGACGAAGCTT 58.316 52.632 0.00 0.00 42.15 3.74
2801 4350 4.991056 ACAATAGCACCGATATTAGCAGTG 59.009 41.667 0.00 0.00 0.00 3.66
2808 4357 5.861725 CACCGATATTAGCAGTGCAATATG 58.138 41.667 24.79 17.87 29.58 1.78
2809 4358 4.937620 ACCGATATTAGCAGTGCAATATGG 59.062 41.667 24.79 24.30 29.58 2.74
2810 4359 5.178061 CCGATATTAGCAGTGCAATATGGA 58.822 41.667 25.62 10.74 29.42 3.41
2811 4360 5.819379 CCGATATTAGCAGTGCAATATGGAT 59.181 40.000 25.62 13.52 29.42 3.41
2812 4361 6.986231 CCGATATTAGCAGTGCAATATGGATA 59.014 38.462 25.62 13.22 29.42 2.59
2813 4362 7.495606 CCGATATTAGCAGTGCAATATGGATAA 59.504 37.037 25.62 13.87 29.42 1.75
2814 4363 8.331022 CGATATTAGCAGTGCAATATGGATAAC 58.669 37.037 24.79 14.66 29.42 1.89
2815 4364 9.166173 GATATTAGCAGTGCAATATGGATAACA 57.834 33.333 24.79 4.41 29.58 2.41
2816 4365 9.690913 ATATTAGCAGTGCAATATGGATAACAT 57.309 29.630 19.20 0.00 43.68 2.71
2817 4366 7.822161 TTAGCAGTGCAATATGGATAACATT 57.178 32.000 19.20 0.00 41.03 2.71
2818 4367 6.720112 AGCAGTGCAATATGGATAACATTT 57.280 33.333 19.20 0.00 41.03 2.32
2819 4368 6.742109 AGCAGTGCAATATGGATAACATTTC 58.258 36.000 19.20 0.00 41.03 2.17
2820 4369 6.321945 AGCAGTGCAATATGGATAACATTTCA 59.678 34.615 19.20 0.00 41.03 2.69
2821 4370 6.418819 GCAGTGCAATATGGATAACATTTCAC 59.581 38.462 11.09 0.00 41.03 3.18
2822 4371 6.634035 CAGTGCAATATGGATAACATTTCACG 59.366 38.462 0.00 0.00 41.03 4.35
2945 4547 5.428253 ACCACTTGTTCGCATATTCAGTAT 58.572 37.500 0.00 0.00 0.00 2.12
3228 6481 3.448686 GGTATCACTCATGAACTGGTCG 58.551 50.000 0.00 0.00 38.69 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.332063 AGTATTCGCCACCTCATTGG 57.668 50.000 0.00 0.00 42.93 3.16
4 5 4.627467 GCTATAGTATTCGCCACCTCATTG 59.373 45.833 0.84 0.00 0.00 2.82
5 6 4.283467 TGCTATAGTATTCGCCACCTCATT 59.717 41.667 0.84 0.00 0.00 2.57
6 7 3.832490 TGCTATAGTATTCGCCACCTCAT 59.168 43.478 0.84 0.00 0.00 2.90
7 8 3.227614 TGCTATAGTATTCGCCACCTCA 58.772 45.455 0.84 0.00 0.00 3.86
8 9 3.936372 TGCTATAGTATTCGCCACCTC 57.064 47.619 0.84 0.00 0.00 3.85
9 10 4.682778 TTTGCTATAGTATTCGCCACCT 57.317 40.909 0.84 0.00 0.00 4.00
10 11 5.701290 AGATTTTGCTATAGTATTCGCCACC 59.299 40.000 0.84 0.00 0.00 4.61
11 12 6.593978 CAGATTTTGCTATAGTATTCGCCAC 58.406 40.000 0.84 0.00 0.00 5.01
12 13 6.785488 CAGATTTTGCTATAGTATTCGCCA 57.215 37.500 0.84 0.00 0.00 5.69
27 28 5.382618 ACTGGAGCTAAAAGCAGATTTTG 57.617 39.130 6.65 0.00 45.56 2.44
28 29 5.416013 GGTACTGGAGCTAAAAGCAGATTTT 59.584 40.000 1.31 1.31 45.56 1.82
29 30 4.944317 GGTACTGGAGCTAAAAGCAGATTT 59.056 41.667 1.22 0.00 45.56 2.17
30 31 4.226168 AGGTACTGGAGCTAAAAGCAGATT 59.774 41.667 1.22 0.00 40.56 2.40
31 32 3.777522 AGGTACTGGAGCTAAAAGCAGAT 59.222 43.478 1.22 0.00 40.56 2.90
32 33 3.173965 AGGTACTGGAGCTAAAAGCAGA 58.826 45.455 1.22 0.00 40.56 4.26
33 34 3.196685 AGAGGTACTGGAGCTAAAAGCAG 59.803 47.826 1.22 0.00 41.98 4.24
34 35 3.173965 AGAGGTACTGGAGCTAAAAGCA 58.826 45.455 1.22 0.00 41.98 3.91
35 36 3.897141 AGAGGTACTGGAGCTAAAAGC 57.103 47.619 0.00 0.00 41.55 3.51
36 37 4.932200 CACAAGAGGTACTGGAGCTAAAAG 59.068 45.833 0.00 0.00 41.55 2.27
37 38 4.347000 ACACAAGAGGTACTGGAGCTAAAA 59.653 41.667 0.00 0.00 41.55 1.52
38 39 3.901844 ACACAAGAGGTACTGGAGCTAAA 59.098 43.478 0.00 0.00 41.55 1.85
39 40 3.507411 ACACAAGAGGTACTGGAGCTAA 58.493 45.455 0.00 0.00 41.55 3.09
40 41 3.170991 ACACAAGAGGTACTGGAGCTA 57.829 47.619 0.00 0.00 41.55 3.32
41 42 2.016905 ACACAAGAGGTACTGGAGCT 57.983 50.000 0.00 0.00 41.55 4.09
42 43 2.808543 CAAACACAAGAGGTACTGGAGC 59.191 50.000 0.00 0.00 41.55 4.70
43 44 3.403038 CCAAACACAAGAGGTACTGGAG 58.597 50.000 0.00 0.00 41.55 3.86
44 45 2.105821 CCCAAACACAAGAGGTACTGGA 59.894 50.000 0.00 0.00 41.55 3.86
45 46 2.105821 TCCCAAACACAAGAGGTACTGG 59.894 50.000 0.00 0.00 41.55 4.00
46 47 3.485463 TCCCAAACACAAGAGGTACTG 57.515 47.619 0.00 0.00 41.55 2.74
48 49 2.488153 GCATCCCAAACACAAGAGGTAC 59.512 50.000 0.00 0.00 0.00 3.34
49 50 2.375174 AGCATCCCAAACACAAGAGGTA 59.625 45.455 0.00 0.00 0.00 3.08
50 51 1.145738 AGCATCCCAAACACAAGAGGT 59.854 47.619 0.00 0.00 0.00 3.85
51 52 1.915141 AGCATCCCAAACACAAGAGG 58.085 50.000 0.00 0.00 0.00 3.69
52 53 3.629398 GGATAGCATCCCAAACACAAGAG 59.371 47.826 4.36 0.00 43.88 2.85
53 54 3.620488 GGATAGCATCCCAAACACAAGA 58.380 45.455 4.36 0.00 43.88 3.02
65 66 7.936301 AGAAGAAATAAAGTCAGGGATAGCATC 59.064 37.037 0.00 0.00 0.00 3.91
66 67 7.810260 AGAAGAAATAAAGTCAGGGATAGCAT 58.190 34.615 0.00 0.00 0.00 3.79
67 68 7.200434 AGAAGAAATAAAGTCAGGGATAGCA 57.800 36.000 0.00 0.00 0.00 3.49
68 69 7.227711 GGAAGAAGAAATAAAGTCAGGGATAGC 59.772 40.741 0.00 0.00 0.00 2.97
69 70 7.717436 GGGAAGAAGAAATAAAGTCAGGGATAG 59.283 40.741 0.00 0.00 0.00 2.08
70 71 7.406151 AGGGAAGAAGAAATAAAGTCAGGGATA 59.594 37.037 0.00 0.00 0.00 2.59
71 72 6.218522 AGGGAAGAAGAAATAAAGTCAGGGAT 59.781 38.462 0.00 0.00 0.00 3.85
72 73 5.551977 AGGGAAGAAGAAATAAAGTCAGGGA 59.448 40.000 0.00 0.00 0.00 4.20
73 74 5.821097 AGGGAAGAAGAAATAAAGTCAGGG 58.179 41.667 0.00 0.00 0.00 4.45
74 75 6.717084 ACAAGGGAAGAAGAAATAAAGTCAGG 59.283 38.462 0.00 0.00 0.00 3.86
75 76 7.751768 ACAAGGGAAGAAGAAATAAAGTCAG 57.248 36.000 0.00 0.00 0.00 3.51
76 77 9.635404 TTTACAAGGGAAGAAGAAATAAAGTCA 57.365 29.630 0.00 0.00 0.00 3.41
77 78 9.894783 GTTTACAAGGGAAGAAGAAATAAAGTC 57.105 33.333 0.00 0.00 0.00 3.01
78 79 8.565416 CGTTTACAAGGGAAGAAGAAATAAAGT 58.435 33.333 0.00 0.00 0.00 2.66
79 80 8.780249 TCGTTTACAAGGGAAGAAGAAATAAAG 58.220 33.333 0.00 0.00 0.00 1.85
80 81 8.680039 TCGTTTACAAGGGAAGAAGAAATAAA 57.320 30.769 0.00 0.00 0.00 1.40
81 82 8.857694 ATCGTTTACAAGGGAAGAAGAAATAA 57.142 30.769 0.00 0.00 0.00 1.40
82 83 8.319146 AGATCGTTTACAAGGGAAGAAGAAATA 58.681 33.333 0.00 0.00 0.00 1.40
83 84 7.168905 AGATCGTTTACAAGGGAAGAAGAAAT 58.831 34.615 0.00 0.00 0.00 2.17
84 85 6.531021 AGATCGTTTACAAGGGAAGAAGAAA 58.469 36.000 0.00 0.00 0.00 2.52
85 86 6.110411 AGATCGTTTACAAGGGAAGAAGAA 57.890 37.500 0.00 0.00 0.00 2.52
86 87 5.740290 AGATCGTTTACAAGGGAAGAAGA 57.260 39.130 0.00 0.00 0.00 2.87
87 88 6.128254 GGAAAGATCGTTTACAAGGGAAGAAG 60.128 42.308 0.00 0.00 0.00 2.85
88 89 5.704053 GGAAAGATCGTTTACAAGGGAAGAA 59.296 40.000 0.00 0.00 0.00 2.52
89 90 5.012768 AGGAAAGATCGTTTACAAGGGAAGA 59.987 40.000 0.00 0.00 0.00 2.87
90 91 5.246307 AGGAAAGATCGTTTACAAGGGAAG 58.754 41.667 0.00 0.00 0.00 3.46
91 92 5.237236 AGGAAAGATCGTTTACAAGGGAA 57.763 39.130 0.00 0.00 0.00 3.97
92 93 4.903045 AGGAAAGATCGTTTACAAGGGA 57.097 40.909 0.00 0.00 0.00 4.20
93 94 5.959618 AAAGGAAAGATCGTTTACAAGGG 57.040 39.130 0.00 0.00 40.74 3.95
94 95 9.341899 CAAATAAAGGAAAGATCGTTTACAAGG 57.658 33.333 6.02 0.00 44.25 3.61
97 98 8.726988 CCTCAAATAAAGGAAAGATCGTTTACA 58.273 33.333 6.02 0.00 44.25 2.41
98 99 8.943002 TCCTCAAATAAAGGAAAGATCGTTTAC 58.057 33.333 6.02 0.00 44.25 2.01
100 101 7.996098 TCCTCAAATAAAGGAAAGATCGTTT 57.004 32.000 0.00 2.62 43.79 3.60
276 278 0.105760 ACTTGGGTTTGCATGGGTCA 60.106 50.000 0.00 0.00 0.00 4.02
358 396 1.565305 CTCGATCGCTTCCAGAAAGG 58.435 55.000 11.09 0.00 35.37 3.11
359 397 0.926846 GCTCGATCGCTTCCAGAAAG 59.073 55.000 11.09 0.00 38.08 2.62
360 398 0.460284 GGCTCGATCGCTTCCAGAAA 60.460 55.000 11.09 0.00 0.00 2.52
361 399 1.141881 GGCTCGATCGCTTCCAGAA 59.858 57.895 11.09 0.00 0.00 3.02
362 400 2.052104 TGGCTCGATCGCTTCCAGA 61.052 57.895 11.09 0.00 0.00 3.86
363 401 1.880340 GTGGCTCGATCGCTTCCAG 60.880 63.158 18.53 9.19 0.00 3.86
364 402 2.184322 GTGGCTCGATCGCTTCCA 59.816 61.111 11.09 13.85 0.00 3.53
497 768 7.202029 CCCCATATAGATGAAACAAGGCAAATT 60.202 37.037 0.00 0.00 34.73 1.82
502 773 4.729868 ACCCCATATAGATGAAACAAGGC 58.270 43.478 0.00 0.00 34.73 4.35
545 820 2.437343 CGCGAGCCGAGTTCAAGAC 61.437 63.158 0.00 0.00 40.02 3.01
572 847 0.034863 TTCTAATTCGGCCCACCCAC 60.035 55.000 0.00 0.00 0.00 4.61
580 855 5.299279 TGAGGAAAATCCATTCTAATTCGGC 59.701 40.000 0.00 0.00 39.61 5.54
582 857 7.792374 TCTGAGGAAAATCCATTCTAATTCG 57.208 36.000 0.00 0.00 39.61 3.34
613 908 8.169977 TGTTTATAAGATCATTTCATGGAGCC 57.830 34.615 0.00 0.00 0.00 4.70
664 964 8.739972 AGGCTAAAACAGGTGACAATTATTTAG 58.260 33.333 0.00 0.00 34.09 1.85
681 985 9.774742 CTGTTTATAAGAACATGAGGCTAAAAC 57.225 33.333 0.00 2.88 38.71 2.43
687 991 8.213518 TCATTCTGTTTATAAGAACATGAGGC 57.786 34.615 0.00 0.00 38.71 4.70
705 1009 2.743664 TCCAACGAAGCACATCATTCTG 59.256 45.455 0.00 0.00 0.00 3.02
706 1010 3.057969 TCCAACGAAGCACATCATTCT 57.942 42.857 0.00 0.00 0.00 2.40
707 1011 3.751621 CTTCCAACGAAGCACATCATTC 58.248 45.455 0.00 0.00 39.21 2.67
708 1012 3.837213 CTTCCAACGAAGCACATCATT 57.163 42.857 0.00 0.00 39.21 2.57
724 1028 4.873827 TGTCTCACAACAGTAAACACTTCC 59.126 41.667 0.00 0.00 0.00 3.46
725 1029 6.604735 ATGTCTCACAACAGTAAACACTTC 57.395 37.500 0.00 0.00 31.50 3.01
732 1036 6.423905 GTCTAGCAAATGTCTCACAACAGTAA 59.576 38.462 0.00 0.00 31.50 2.24
877 1187 8.293027 TGGATATTTCCTCAGGATCCTAAAAT 57.707 34.615 15.67 18.18 43.07 1.82
878 1188 7.705912 TGGATATTTCCTCAGGATCCTAAAA 57.294 36.000 15.67 12.77 43.07 1.52
879 1189 7.895144 ATGGATATTTCCTCAGGATCCTAAA 57.105 36.000 15.67 11.92 43.07 1.85
885 1195 7.159201 AGAACAATGGATATTTCCTCAGGAT 57.841 36.000 0.00 0.00 43.07 3.24
886 1196 6.581388 AGAACAATGGATATTTCCTCAGGA 57.419 37.500 3.72 0.00 43.07 3.86
989 1303 6.587206 TGGAATGTTATCTGCATCACAAAA 57.413 33.333 0.00 0.00 0.00 2.44
991 1305 5.887035 TGATGGAATGTTATCTGCATCACAA 59.113 36.000 2.60 0.00 29.03 3.33
1003 1317 3.216800 GGCTCTGCATGATGGAATGTTA 58.783 45.455 0.00 0.00 0.00 2.41
1006 1320 0.959553 GGGCTCTGCATGATGGAATG 59.040 55.000 0.00 0.00 0.00 2.67
1007 1321 0.178970 GGGGCTCTGCATGATGGAAT 60.179 55.000 0.00 0.00 0.00 3.01
1009 1323 1.991339 CTGGGGCTCTGCATGATGGA 61.991 60.000 0.00 0.00 0.00 3.41
1033 1347 6.291849 CGAACTGAAGTAGAAACAACTGACAG 60.292 42.308 0.00 0.00 37.77 3.51
1041 1355 3.802139 CAGTGCGAACTGAAGTAGAAACA 59.198 43.478 19.55 0.00 39.99 2.83
1060 1374 4.345257 ACCTTGTAGTTCAGACACATCAGT 59.655 41.667 0.00 0.00 0.00 3.41
1064 1378 4.389374 CCAACCTTGTAGTTCAGACACAT 58.611 43.478 0.00 0.00 0.00 3.21
1073 1387 0.696501 ATCGGCCCAACCTTGTAGTT 59.303 50.000 0.00 0.00 35.61 2.24
1075 1389 0.541863 AGATCGGCCCAACCTTGTAG 59.458 55.000 0.00 0.00 35.61 2.74
1301 1615 6.936900 TCGAGAATTGAAAGGAACAGAAGAAT 59.063 34.615 0.00 0.00 0.00 2.40
1461 2909 0.443869 CGACAACAAGGCAATCTCCG 59.556 55.000 0.00 0.00 0.00 4.63
1470 2918 2.032030 GGTGAACACATCGACAACAAGG 60.032 50.000 7.25 0.00 0.00 3.61
1542 3005 2.125753 GGAGCAGTGAGAGTGCCG 60.126 66.667 0.00 0.00 45.41 5.69
1568 3031 2.040813 ACAAGCAGATGTGAGTTGGGAT 59.959 45.455 9.34 0.00 30.82 3.85
1609 3072 0.527565 CTTCCAACGGGCCAATCAAG 59.472 55.000 4.39 0.00 0.00 3.02
1657 3120 6.550854 TGCACGATCTGATATATCCATCCATA 59.449 38.462 10.25 0.00 0.00 2.74
1725 3188 0.690762 GGGCCAACCTCAGAGTGTAA 59.309 55.000 4.39 0.00 35.85 2.41
2022 3494 3.428870 CGTAGTACAAGTTGTTGCTCCTG 59.571 47.826 14.90 3.59 37.14 3.86
2024 3496 2.157085 GCGTAGTACAAGTTGTTGCTCC 59.843 50.000 14.90 3.61 37.14 4.70
2056 3528 3.426568 GTGCACGCTCCAAGGCTC 61.427 66.667 0.00 0.00 0.00 4.70
2129 3601 2.795329 CTGTGGGCACAAACCTCTTAT 58.205 47.619 0.00 0.00 41.33 1.73
2165 3637 1.404391 AGTAGAACATGCTCGGGTACG 59.596 52.381 0.00 0.00 42.74 3.67
2195 3667 2.318578 GTGTTTGCCATCACAATCACG 58.681 47.619 0.00 0.00 39.26 4.35
2205 3677 8.757877 ACAAATAAATATAGTGGTGTTTGCCAT 58.242 29.630 0.00 0.00 41.08 4.40
2211 3683 9.243105 AGCAAGACAAATAAATATAGTGGTGTT 57.757 29.630 0.00 0.00 0.00 3.32
2230 3725 1.803555 GAACTTCTGGAGCAGCAAGAC 59.196 52.381 0.00 0.00 0.00 3.01
2242 3737 7.162062 CACTTACGAAAAGAAAACGAACTTCTG 59.838 37.037 8.84 0.00 33.40 3.02
2262 3757 2.606275 GCCTAGCATCGGCACTTAC 58.394 57.895 6.11 0.00 46.77 2.34
2288 3795 3.923017 ATAAATCCAATAGCTTGCCGC 57.077 42.857 0.00 0.00 39.57 6.53
2289 3796 6.042143 ACAAAATAAATCCAATAGCTTGCCG 58.958 36.000 0.00 0.00 0.00 5.69
2335 3842 2.120940 TCCAGGTCGGGTTGCCTA 59.879 61.111 0.00 0.00 33.07 3.93
2336 3843 3.637273 GTCCAGGTCGGGTTGCCT 61.637 66.667 0.00 0.00 35.04 4.75
2344 3851 1.879380 TCAAGCAAAATGTCCAGGTCG 59.121 47.619 0.00 0.00 0.00 4.79
2348 3855 5.640189 AGAGATTCAAGCAAAATGTCCAG 57.360 39.130 0.00 0.00 29.14 3.86
2377 3885 5.062308 GTGTCTCTTATTACAAGCCAACGAG 59.938 44.000 0.00 0.00 0.00 4.18
2379 3887 4.201589 CGTGTCTCTTATTACAAGCCAACG 60.202 45.833 0.00 0.00 0.00 4.10
2451 3959 7.787725 AAGAACACAAAGTACTTACTGAAGG 57.212 36.000 8.92 3.32 36.95 3.46
2476 3984 5.371526 CACTGCATTTGTCCCTATCAGTAT 58.628 41.667 0.00 0.00 32.73 2.12
2517 4043 8.994429 AGATTTTAATCTATGATGCTACTCCG 57.006 34.615 3.20 0.00 43.66 4.63
2542 4068 1.352622 ATCGGGGCCAAATAGCAGGA 61.353 55.000 4.39 0.00 0.00 3.86
2545 4071 0.108585 GAGATCGGGGCCAAATAGCA 59.891 55.000 4.39 0.00 0.00 3.49
2557 4083 1.444553 GCGATTAGCGGGAGATCGG 60.445 63.158 7.03 0.00 42.03 4.18
2591 4117 2.232399 TGTACTACTGGCAACTCACGA 58.768 47.619 0.00 0.00 37.61 4.35
2594 4120 4.994852 GTGATTTGTACTACTGGCAACTCA 59.005 41.667 0.00 0.00 32.18 3.41
2597 4123 3.124636 CCGTGATTTGTACTACTGGCAAC 59.875 47.826 0.00 0.00 0.00 4.17
2600 4126 2.093869 TCCCGTGATTTGTACTACTGGC 60.094 50.000 0.00 0.00 0.00 4.85
2616 4142 1.188219 ATAGCGGCATGATCTCCCGT 61.188 55.000 16.58 9.03 43.70 5.28
2642 4170 2.557920 ATGAAGGAATGGAGCGATCC 57.442 50.000 14.17 14.17 0.00 3.36
2660 4188 3.052869 AGAATTTTCCCGGGAAGGCTAAT 60.053 43.478 33.64 26.47 39.21 1.73
2667 4196 3.083293 CGGTAAAGAATTTTCCCGGGAA 58.917 45.455 32.53 32.53 41.87 3.97
2670 4199 2.089201 AGCGGTAAAGAATTTTCCCGG 58.911 47.619 0.00 0.00 45.58 5.73
2683 4212 2.162008 GGGCAAAACGATTTAGCGGTAA 59.838 45.455 2.26 2.26 35.12 2.85
2685 4214 0.524414 GGGCAAAACGATTTAGCGGT 59.476 50.000 0.00 0.00 35.12 5.68
2694 4223 0.873054 TAAAATCGCGGGCAAAACGA 59.127 45.000 6.13 0.00 40.53 3.85
2801 4350 4.917415 GCCGTGAAATGTTATCCATATTGC 59.083 41.667 0.00 0.00 31.97 3.56
2802 4351 6.070897 TGCCGTGAAATGTTATCCATATTG 57.929 37.500 0.00 0.00 31.97 1.90
2803 4352 6.707440 TTGCCGTGAAATGTTATCCATATT 57.293 33.333 0.00 0.00 31.97 1.28
2804 4353 6.899393 ATTGCCGTGAAATGTTATCCATAT 57.101 33.333 0.00 0.00 31.97 1.78
2805 4354 7.994425 ATATTGCCGTGAAATGTTATCCATA 57.006 32.000 0.00 0.00 31.97 2.74
2806 4355 6.899393 ATATTGCCGTGAAATGTTATCCAT 57.101 33.333 0.00 0.00 34.36 3.41
2807 4356 7.809546 TTATATTGCCGTGAAATGTTATCCA 57.190 32.000 0.00 0.00 0.00 3.41
2808 4357 8.564574 TCTTTATATTGCCGTGAAATGTTATCC 58.435 33.333 0.00 0.00 0.00 2.59
2809 4358 9.599322 CTCTTTATATTGCCGTGAAATGTTATC 57.401 33.333 0.00 0.00 0.00 1.75
2810 4359 9.120538 ACTCTTTATATTGCCGTGAAATGTTAT 57.879 29.630 0.00 0.00 0.00 1.89
2811 4360 8.394877 CACTCTTTATATTGCCGTGAAATGTTA 58.605 33.333 0.00 0.00 0.00 2.41
2812 4361 7.120579 TCACTCTTTATATTGCCGTGAAATGTT 59.879 33.333 0.00 0.00 0.00 2.71
2813 4362 6.597672 TCACTCTTTATATTGCCGTGAAATGT 59.402 34.615 0.00 0.00 0.00 2.71
2814 4363 7.015226 TCACTCTTTATATTGCCGTGAAATG 57.985 36.000 0.00 0.00 0.00 2.32
2815 4364 7.624360 TTCACTCTTTATATTGCCGTGAAAT 57.376 32.000 0.00 0.00 37.08 2.17
2816 4365 7.441890 TTTCACTCTTTATATTGCCGTGAAA 57.558 32.000 9.73 9.73 43.43 2.69
2817 4366 7.441890 TTTTCACTCTTTATATTGCCGTGAA 57.558 32.000 0.00 0.00 37.91 3.18
2818 4367 7.624360 ATTTTCACTCTTTATATTGCCGTGA 57.376 32.000 0.00 0.00 0.00 4.35
2819 4368 9.385902 CATATTTTCACTCTTTATATTGCCGTG 57.614 33.333 0.00 0.00 0.00 4.94
2820 4369 8.076178 GCATATTTTCACTCTTTATATTGCCGT 58.924 33.333 0.00 0.00 0.00 5.68
2821 4370 8.075574 TGCATATTTTCACTCTTTATATTGCCG 58.924 33.333 0.00 0.00 0.00 5.69
2822 4371 9.748708 TTGCATATTTTCACTCTTTATATTGCC 57.251 29.630 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.