Multiple sequence alignment - TraesCS4A01G173200

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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 TraesCS4A01G173200 chr4A 100.000 3650 0 0 1 3650 440256161 440252512 0.000000e+00 6741.0
1 TraesCS4A01G173200 chr4A 96.128 1033 38 2 2619 3650 684869412 684870443 0.000000e+00 1685.0
2 TraesCS4A01G173200 chr4A 89.252 214 22 1 1 213 454779600 454779813 2.160000e-67 267.0
3 TraesCS4A01G173200 chr3A 93.528 2395 113 14 230 2617 10289962 10292321 0.000000e+00 3526.0
4 TraesCS4A01G173200 chr4B 93.813 1988 98 11 633 2617 191787977 191789942 0.000000e+00 2966.0
5 TraesCS4A01G173200 chr4B 90.090 222 21 1 403 624 191715032 191715252 1.660000e-73 287.0
6 TraesCS4A01G173200 chr4D 94.063 1954 81 7 668 2617 127927843 127929765 0.000000e+00 2933.0
7 TraesCS4A01G173200 chr4D 95.656 1036 41 4 2619 3650 52452801 52453836 0.000000e+00 1661.0
8 TraesCS4A01G173200 chr4D 95.652 1035 41 4 2619 3650 381423150 381424183 0.000000e+00 1659.0
9 TraesCS4A01G173200 chr4D 91.031 446 26 11 212 655 127927127 127927560 1.130000e-164 590.0
10 TraesCS4A01G173200 chr4D 79.602 402 71 8 293 693 458156947 458156556 9.980000e-71 278.0
11 TraesCS4A01G173200 chr1D 96.609 1032 35 0 2619 3650 234905812 234904781 0.000000e+00 1712.0
12 TraesCS4A01G173200 chr1D 96.415 1032 36 1 2619 3650 146641764 146642794 0.000000e+00 1700.0
13 TraesCS4A01G173200 chr1D 92.857 56 4 0 428 483 246680724 246680669 8.400000e-12 82.4
14 TraesCS4A01G173200 chr2D 96.128 1033 38 2 2619 3650 325727790 325728821 0.000000e+00 1685.0
15 TraesCS4A01G173200 chr2D 87.793 213 15 8 11 213 625245900 625246111 4.710000e-59 239.0
16 TraesCS4A01G173200 chr1A 95.934 1033 40 2 2619 3650 76767732 76768763 0.000000e+00 1674.0
17 TraesCS4A01G173200 chr1A 89.401 217 21 2 1 216 540179209 540178994 4.640000e-69 272.0
18 TraesCS4A01G173200 chr1A 86.957 207 23 3 9 213 108908390 108908594 2.830000e-56 230.0
19 TraesCS4A01G173200 chr6D 95.833 1032 36 3 2619 3650 55635724 55636748 0.000000e+00 1661.0
20 TraesCS4A01G173200 chr6D 95.455 1034 44 3 2619 3650 41402203 41401171 0.000000e+00 1646.0
21 TraesCS4A01G173200 chr6D 89.756 205 17 4 11 213 61351950 61351748 3.620000e-65 259.0
22 TraesCS4A01G173200 chr7B 75.587 1364 249 48 1259 2604 86165885 86164588 6.750000e-167 597.0
23 TraesCS4A01G173200 chr7D 74.797 1357 263 45 1259 2604 124504982 124503694 4.150000e-149 538.0
24 TraesCS4A01G173200 chr7D 83.333 96 15 1 397 491 209515128 209515223 1.810000e-13 87.9
25 TraesCS4A01G173200 chr7A 74.726 1369 249 48 1259 2604 126919188 126917894 4.180000e-144 521.0
26 TraesCS4A01G173200 chr6A 87.324 213 24 3 1 211 196825177 196825388 1.310000e-59 241.0
27 TraesCS4A01G173200 chr6B 86.385 213 24 4 1 213 311147519 311147312 1.020000e-55 228.0
28 TraesCS4A01G173200 chr5A 85.849 212 25 5 7 216 674370327 674370119 1.710000e-53 220.0
29 TraesCS4A01G173200 chr3B 85.185 216 28 4 1 214 763214870 763214657 6.140000e-53 219.0
30 TraesCS4A01G173200 chrUn 76.329 414 75 14 293 701 397660239 397660634 2.220000e-47 200.0
31 TraesCS4A01G173200 chr1B 76.329 414 75 14 293 701 98429050 98429445 2.220000e-47 200.0


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 TraesCS4A01G173200 chr4A 440252512 440256161 3649 True 6741.0 6741 100.000 1 3650 1 chr4A.!!$R1 3649
1 TraesCS4A01G173200 chr4A 684869412 684870443 1031 False 1685.0 1685 96.128 2619 3650 1 chr4A.!!$F2 1031
2 TraesCS4A01G173200 chr3A 10289962 10292321 2359 False 3526.0 3526 93.528 230 2617 1 chr3A.!!$F1 2387
3 TraesCS4A01G173200 chr4B 191787977 191789942 1965 False 2966.0 2966 93.813 633 2617 1 chr4B.!!$F2 1984
4 TraesCS4A01G173200 chr4D 127927127 127929765 2638 False 1761.5 2933 92.547 212 2617 2 chr4D.!!$F3 2405
5 TraesCS4A01G173200 chr4D 52452801 52453836 1035 False 1661.0 1661 95.656 2619 3650 1 chr4D.!!$F1 1031
6 TraesCS4A01G173200 chr4D 381423150 381424183 1033 False 1659.0 1659 95.652 2619 3650 1 chr4D.!!$F2 1031
7 TraesCS4A01G173200 chr1D 234904781 234905812 1031 True 1712.0 1712 96.609 2619 3650 1 chr1D.!!$R1 1031
8 TraesCS4A01G173200 chr1D 146641764 146642794 1030 False 1700.0 1700 96.415 2619 3650 1 chr1D.!!$F1 1031
9 TraesCS4A01G173200 chr2D 325727790 325728821 1031 False 1685.0 1685 96.128 2619 3650 1 chr2D.!!$F1 1031
10 TraesCS4A01G173200 chr1A 76767732 76768763 1031 False 1674.0 1674 95.934 2619 3650 1 chr1A.!!$F1 1031
11 TraesCS4A01G173200 chr6D 55635724 55636748 1024 False 1661.0 1661 95.833 2619 3650 1 chr6D.!!$F1 1031
12 TraesCS4A01G173200 chr6D 41401171 41402203 1032 True 1646.0 1646 95.455 2619 3650 1 chr6D.!!$R1 1031
13 TraesCS4A01G173200 chr7B 86164588 86165885 1297 True 597.0 597 75.587 1259 2604 1 chr7B.!!$R1 1345
14 TraesCS4A01G173200 chr7D 124503694 124504982 1288 True 538.0 538 74.797 1259 2604 1 chr7D.!!$R1 1345
15 TraesCS4A01G173200 chr7A 126917894 126919188 1294 True 521.0 521 74.726 1259 2604 1 chr7A.!!$R1 1345

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
732 1007 1.538047 GGTCAATGCTCCAGCTTTCA 58.462 50.0 0.00 0.0 42.66 2.69 F
1248 1530 0.109723 CCCCCGACTTGGAAGACAAA 59.890 55.0 0.00 0.0 42.00 2.83 F
1551 1833 0.179026 TCCTATACGCGCTCCTCACT 60.179 55.0 5.73 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2197 0.105964 TTGTCGGACTTGACCACCAG 59.894 55.000 9.88 0.0 38.11 4.00 R
2617 2959 0.451783 GGCTCAAATCGAACCGCAAT 59.548 50.000 0.00 0.0 0.00 3.56 R
2766 3110 3.255642 TGGCTGCCTTTGTAATTCACTTC 59.744 43.478 21.03 0.0 0.00 3.01 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
26 27 9.003658 TGATAATTCTGAGAACCAAAGAGAAAC 57.996 33.333 0.00 0.00 0.00 2.78
27 28 8.924511 ATAATTCTGAGAACCAAAGAGAAACA 57.075 30.769 0.00 0.00 0.00 2.83
28 29 6.625873 ATTCTGAGAACCAAAGAGAAACAC 57.374 37.500 0.00 0.00 0.00 3.32
29 30 5.097742 TCTGAGAACCAAAGAGAAACACA 57.902 39.130 0.00 0.00 0.00 3.72
30 31 5.496556 TCTGAGAACCAAAGAGAAACACAA 58.503 37.500 0.00 0.00 0.00 3.33
31 32 5.943416 TCTGAGAACCAAAGAGAAACACAAA 59.057 36.000 0.00 0.00 0.00 2.83
32 33 6.094048 TCTGAGAACCAAAGAGAAACACAAAG 59.906 38.462 0.00 0.00 0.00 2.77
33 34 5.943416 TGAGAACCAAAGAGAAACACAAAGA 59.057 36.000 0.00 0.00 0.00 2.52
34 35 6.094048 TGAGAACCAAAGAGAAACACAAAGAG 59.906 38.462 0.00 0.00 0.00 2.85
35 36 5.358160 AGAACCAAAGAGAAACACAAAGAGG 59.642 40.000 0.00 0.00 0.00 3.69
36 37 3.381590 ACCAAAGAGAAACACAAAGAGGC 59.618 43.478 0.00 0.00 0.00 4.70
37 38 3.633986 CCAAAGAGAAACACAAAGAGGCT 59.366 43.478 0.00 0.00 0.00 4.58
38 39 4.098501 CCAAAGAGAAACACAAAGAGGCTT 59.901 41.667 0.00 0.00 0.00 4.35
39 40 5.394553 CCAAAGAGAAACACAAAGAGGCTTT 60.395 40.000 0.00 0.00 0.00 3.51
40 41 5.506686 AAGAGAAACACAAAGAGGCTTTC 57.493 39.130 0.00 0.00 0.00 2.62
41 42 4.526970 AGAGAAACACAAAGAGGCTTTCA 58.473 39.130 0.00 0.00 0.00 2.69
42 43 4.578105 AGAGAAACACAAAGAGGCTTTCAG 59.422 41.667 0.00 0.00 0.00 3.02
43 44 4.526970 AGAAACACAAAGAGGCTTTCAGA 58.473 39.130 0.00 0.00 0.00 3.27
44 45 4.578105 AGAAACACAAAGAGGCTTTCAGAG 59.422 41.667 0.00 0.00 0.00 3.35
45 46 2.856222 ACACAAAGAGGCTTTCAGAGG 58.144 47.619 0.00 0.00 0.00 3.69
52 53 3.584947 GGCTTTCAGAGGCTGGATT 57.415 52.632 0.00 0.00 46.86 3.01
53 54 2.717639 GGCTTTCAGAGGCTGGATTA 57.282 50.000 0.00 0.00 46.86 1.75
54 55 2.293170 GGCTTTCAGAGGCTGGATTAC 58.707 52.381 0.00 0.00 46.86 1.89
55 56 2.356125 GGCTTTCAGAGGCTGGATTACA 60.356 50.000 0.00 0.00 46.86 2.41
95 96 9.736414 AATTTATCATGGACATTCCTAGAGATG 57.264 33.333 0.00 0.00 37.46 2.90
96 97 5.758790 ATCATGGACATTCCTAGAGATGG 57.241 43.478 9.26 0.00 37.46 3.51
97 98 4.560739 TCATGGACATTCCTAGAGATGGT 58.439 43.478 9.26 0.00 37.46 3.55
98 99 5.715921 TCATGGACATTCCTAGAGATGGTA 58.284 41.667 9.26 0.00 37.46 3.25
99 100 6.326161 TCATGGACATTCCTAGAGATGGTAT 58.674 40.000 9.26 0.62 37.46 2.73
100 101 7.478721 TCATGGACATTCCTAGAGATGGTATA 58.521 38.462 9.26 0.00 37.46 1.47
101 102 7.617329 TCATGGACATTCCTAGAGATGGTATAG 59.383 40.741 9.26 0.00 37.46 1.31
102 103 6.864421 TGGACATTCCTAGAGATGGTATAGT 58.136 40.000 9.26 0.00 37.46 2.12
103 104 7.306013 TGGACATTCCTAGAGATGGTATAGTT 58.694 38.462 9.26 0.00 37.46 2.24
104 105 7.789831 TGGACATTCCTAGAGATGGTATAGTTT 59.210 37.037 9.26 0.00 37.46 2.66
105 106 9.310449 GGACATTCCTAGAGATGGTATAGTTTA 57.690 37.037 9.26 0.00 32.53 2.01
110 111 9.535170 TTCCTAGAGATGGTATAGTTTAGATGG 57.465 37.037 0.00 0.00 0.00 3.51
111 112 7.616150 TCCTAGAGATGGTATAGTTTAGATGGC 59.384 40.741 0.00 0.00 0.00 4.40
112 113 6.613153 AGAGATGGTATAGTTTAGATGGCC 57.387 41.667 0.00 0.00 0.00 5.36
113 114 6.326970 AGAGATGGTATAGTTTAGATGGCCT 58.673 40.000 3.32 0.00 0.00 5.19
114 115 6.212388 AGAGATGGTATAGTTTAGATGGCCTG 59.788 42.308 3.32 0.00 0.00 4.85
115 116 6.084738 AGATGGTATAGTTTAGATGGCCTGA 58.915 40.000 3.32 0.00 0.00 3.86
116 117 6.732862 AGATGGTATAGTTTAGATGGCCTGAT 59.267 38.462 3.32 0.00 0.00 2.90
117 118 6.763715 TGGTATAGTTTAGATGGCCTGATT 57.236 37.500 3.32 0.00 0.00 2.57
118 119 7.865530 TGGTATAGTTTAGATGGCCTGATTA 57.134 36.000 3.32 0.00 0.00 1.75
119 120 8.449423 TGGTATAGTTTAGATGGCCTGATTAT 57.551 34.615 3.32 0.00 0.00 1.28
120 121 8.890472 TGGTATAGTTTAGATGGCCTGATTATT 58.110 33.333 3.32 0.00 0.00 1.40
121 122 9.740710 GGTATAGTTTAGATGGCCTGATTATTT 57.259 33.333 3.32 0.00 0.00 1.40
151 152 9.772282 CTTTTATTTTGTTGTACATAACGTTGC 57.228 29.630 11.99 0.00 33.28 4.17
152 153 9.517609 TTTTATTTTGTTGTACATAACGTTGCT 57.482 25.926 11.99 0.00 33.28 3.91
153 154 9.517609 TTTATTTTGTTGTACATAACGTTGCTT 57.482 25.926 11.99 0.00 33.28 3.91
156 157 7.895582 TTTGTTGTACATAACGTTGCTTAAC 57.104 32.000 11.99 9.10 33.28 2.01
157 158 6.847956 TGTTGTACATAACGTTGCTTAACT 57.152 33.333 11.99 0.00 33.28 2.24
158 159 7.249186 TGTTGTACATAACGTTGCTTAACTT 57.751 32.000 11.99 0.00 33.28 2.66
159 160 7.695820 TGTTGTACATAACGTTGCTTAACTTT 58.304 30.769 11.99 0.00 33.28 2.66
160 161 8.182881 TGTTGTACATAACGTTGCTTAACTTTT 58.817 29.630 11.99 0.00 33.28 2.27
161 162 8.466026 GTTGTACATAACGTTGCTTAACTTTTG 58.534 33.333 11.99 0.00 0.00 2.44
162 163 7.917597 TGTACATAACGTTGCTTAACTTTTGA 58.082 30.769 11.99 0.00 0.00 2.69
163 164 8.396390 TGTACATAACGTTGCTTAACTTTTGAA 58.604 29.630 11.99 0.00 0.00 2.69
164 165 9.389570 GTACATAACGTTGCTTAACTTTTGAAT 57.610 29.630 11.99 0.00 0.00 2.57
165 166 8.280909 ACATAACGTTGCTTAACTTTTGAATG 57.719 30.769 11.99 3.78 0.00 2.67
166 167 8.132362 ACATAACGTTGCTTAACTTTTGAATGA 58.868 29.630 11.99 0.00 0.00 2.57
167 168 8.963130 CATAACGTTGCTTAACTTTTGAATGAA 58.037 29.630 11.99 0.00 0.00 2.57
168 169 7.820044 AACGTTGCTTAACTTTTGAATGAAA 57.180 28.000 0.00 0.00 0.00 2.69
169 170 7.820044 ACGTTGCTTAACTTTTGAATGAAAA 57.180 28.000 0.00 0.00 32.44 2.29
170 171 8.419076 ACGTTGCTTAACTTTTGAATGAAAAT 57.581 26.923 0.00 0.00 32.98 1.82
171 172 8.878769 ACGTTGCTTAACTTTTGAATGAAAATT 58.121 25.926 0.00 0.00 32.98 1.82
175 176 8.973378 TGCTTAACTTTTGAATGAAAATTACCG 58.027 29.630 0.00 0.00 32.98 4.02
176 177 8.974408 GCTTAACTTTTGAATGAAAATTACCGT 58.026 29.630 0.00 0.00 32.98 4.83
181 182 9.673454 ACTTTTGAATGAAAATTACCGTAGAAC 57.327 29.630 0.00 0.00 32.98 3.01
182 183 8.716619 TTTTGAATGAAAATTACCGTAGAACG 57.283 30.769 0.00 0.00 42.11 3.95
183 184 7.655236 TTGAATGAAAATTACCGTAGAACGA 57.345 32.000 0.15 0.00 46.05 3.85
184 185 7.837202 TGAATGAAAATTACCGTAGAACGAT 57.163 32.000 0.15 0.00 46.05 3.73
185 186 8.259049 TGAATGAAAATTACCGTAGAACGATT 57.741 30.769 0.15 0.00 46.05 3.34
186 187 8.172484 TGAATGAAAATTACCGTAGAACGATTG 58.828 33.333 0.15 0.00 46.05 2.67
187 188 7.605410 ATGAAAATTACCGTAGAACGATTGT 57.395 32.000 0.15 0.00 46.05 2.71
188 189 7.424227 TGAAAATTACCGTAGAACGATTGTT 57.576 32.000 0.00 0.00 46.05 2.83
200 201 4.985044 AACGATTGTTCTACGGTCTTTG 57.015 40.909 0.00 0.00 30.83 2.77
201 202 3.323243 ACGATTGTTCTACGGTCTTTGG 58.677 45.455 0.00 0.00 0.00 3.28
202 203 3.243975 ACGATTGTTCTACGGTCTTTGGT 60.244 43.478 0.00 0.00 0.00 3.67
203 204 3.744426 CGATTGTTCTACGGTCTTTGGTT 59.256 43.478 0.00 0.00 0.00 3.67
204 205 4.143179 CGATTGTTCTACGGTCTTTGGTTC 60.143 45.833 0.00 0.00 0.00 3.62
205 206 3.823281 TGTTCTACGGTCTTTGGTTCA 57.177 42.857 0.00 0.00 0.00 3.18
206 207 4.139859 TGTTCTACGGTCTTTGGTTCAA 57.860 40.909 0.00 0.00 0.00 2.69
207 208 4.515361 TGTTCTACGGTCTTTGGTTCAAA 58.485 39.130 0.00 0.00 0.00 2.69
208 209 4.942483 TGTTCTACGGTCTTTGGTTCAAAA 59.058 37.500 0.00 0.00 32.75 2.44
209 210 5.415077 TGTTCTACGGTCTTTGGTTCAAAAA 59.585 36.000 0.00 0.00 32.75 1.94
326 327 7.759489 ATATATTGTTGCGGGTGTTGATATT 57.241 32.000 0.00 0.00 0.00 1.28
337 338 4.020662 GGGTGTTGATATTTTTGAAGGCCA 60.021 41.667 5.01 0.00 0.00 5.36
338 339 5.338300 GGGTGTTGATATTTTTGAAGGCCAT 60.338 40.000 5.01 0.00 0.00 4.40
339 340 5.812127 GGTGTTGATATTTTTGAAGGCCATC 59.188 40.000 5.01 2.09 0.00 3.51
340 341 6.397272 GTGTTGATATTTTTGAAGGCCATCA 58.603 36.000 6.57 6.57 0.00 3.07
341 342 6.311200 GTGTTGATATTTTTGAAGGCCATCAC 59.689 38.462 10.89 0.00 0.00 3.06
342 343 6.014755 TGTTGATATTTTTGAAGGCCATCACA 60.015 34.615 10.89 0.35 0.00 3.58
373 374 9.273137 TCTTTAAGGATAGAAGATGGTCTCTTT 57.727 33.333 0.00 0.00 44.42 2.52
396 397 5.661458 TCTTTTCTCCGTCTGGAATGATAC 58.339 41.667 0.00 0.00 45.87 2.24
471 472 7.967854 TGAACTAAGAAGAACAACACAACAATG 59.032 33.333 0.00 0.00 0.00 2.82
475 476 3.883830 AGAACAACACAACAATGGCAA 57.116 38.095 0.00 0.00 0.00 4.52
482 483 5.163774 ACAACACAACAATGGCAAAATGAAC 60.164 36.000 0.00 0.00 0.00 3.18
497 498 2.194201 TGAACCGTTTTCCCTCATCC 57.806 50.000 0.00 0.00 0.00 3.51
516 517 9.035607 CCTCATCCGTTATACATATCTTTATGC 57.964 37.037 0.00 0.00 39.09 3.14
565 567 3.118738 ACCCCATCGAACAAGTATCAGAC 60.119 47.826 0.00 0.00 0.00 3.51
576 578 2.562296 AGTATCAGACCCCACACCAAT 58.438 47.619 0.00 0.00 0.00 3.16
585 587 6.792473 TCAGACCCCACACCAATAGATATATT 59.208 38.462 0.00 0.00 0.00 1.28
732 1007 1.538047 GGTCAATGCTCCAGCTTTCA 58.462 50.000 0.00 0.00 42.66 2.69
737 1012 1.985473 ATGCTCCAGCTTTCACACAA 58.015 45.000 0.00 0.00 42.66 3.33
776 1051 6.971602 TGGAGTAGTAATTAGCTCGATCTTG 58.028 40.000 0.00 0.00 0.00 3.02
777 1052 6.546403 TGGAGTAGTAATTAGCTCGATCTTGT 59.454 38.462 0.00 0.00 0.00 3.16
924 1201 8.340618 AGTAATTTTGCCCTATATGTATGCAG 57.659 34.615 0.00 0.00 32.88 4.41
1006 1288 5.000012 AGTTGTGATCGAGTAGATGGAAC 58.000 43.478 0.00 0.00 40.26 3.62
1044 1326 3.124686 GCGGAGGCGAGAGAGAAT 58.875 61.111 0.00 0.00 0.00 2.40
1045 1327 2.332277 GCGGAGGCGAGAGAGAATA 58.668 57.895 0.00 0.00 0.00 1.75
1046 1328 0.669077 GCGGAGGCGAGAGAGAATAA 59.331 55.000 0.00 0.00 0.00 1.40
1106 1388 0.602638 TTCTTGCTGGTCGCGTTGAT 60.603 50.000 5.77 0.00 43.27 2.57
1118 1400 2.482374 GTTGATGCACCTGCTCGC 59.518 61.111 0.00 0.00 42.66 5.03
1137 1419 3.003173 CTGGCCTCCCACTTCGGA 61.003 66.667 3.32 0.00 35.79 4.55
1233 1515 2.285743 AACCAGCTCCTCTCCCCC 60.286 66.667 0.00 0.00 0.00 5.40
1248 1530 0.109723 CCCCCGACTTGGAAGACAAA 59.890 55.000 0.00 0.00 42.00 2.83
1336 1618 1.704082 CCCTACCTGGTGGAGAGGA 59.296 63.158 12.27 0.00 40.24 3.71
1344 1626 1.758514 GGTGGAGAGGATGAGGCGA 60.759 63.158 0.00 0.00 0.00 5.54
1473 1755 5.574443 CGATCGTCATCATACATGCAAGTAT 59.426 40.000 8.75 8.75 35.14 2.12
1551 1833 0.179026 TCCTATACGCGCTCCTCACT 60.179 55.000 5.73 0.00 0.00 3.41
1557 1839 4.803426 GCGCTCCTCACTGACCGG 62.803 72.222 0.00 0.00 0.00 5.28
1578 1860 1.760086 CCTCCTCGTCCATGAGCCT 60.760 63.158 0.00 0.00 34.56 4.58
1581 1863 2.060383 CCTCGTCCATGAGCCTCCA 61.060 63.158 0.00 0.00 34.56 3.86
1815 2127 2.287668 CGTGTTTCTTCTCACCGAGAGT 60.288 50.000 5.03 0.00 44.98 3.24
1885 2197 2.143122 TGATCAACAAGTTCGACTGGC 58.857 47.619 0.00 0.00 0.00 4.85
2007 2319 0.620556 ACCATCTTGGCAGGTACCTG 59.379 55.000 33.74 33.74 42.67 4.00
2037 2349 2.861974 AACCGGGTGTGGGGGATT 60.862 61.111 6.32 0.00 0.00 3.01
2208 2550 4.947147 GCCACCAGCGAACCACCA 62.947 66.667 0.00 0.00 0.00 4.17
2239 2581 4.282195 AGGCGAAGAAGAAGAAGAAGAAGA 59.718 41.667 0.00 0.00 0.00 2.87
2240 2582 4.991687 GGCGAAGAAGAAGAAGAAGAAGAA 59.008 41.667 0.00 0.00 0.00 2.52
2241 2583 5.120053 GGCGAAGAAGAAGAAGAAGAAGAAG 59.880 44.000 0.00 0.00 0.00 2.85
2439 2781 1.930251 TCTACCTGCTGAGCTTCTGT 58.070 50.000 5.83 0.00 0.00 3.41
2444 2786 1.146637 CTGCTGAGCTTCTGTGACAC 58.853 55.000 5.83 0.00 0.00 3.67
2468 2810 3.387947 GACGACGGGGTGGTCCAT 61.388 66.667 0.00 0.00 35.72 3.41
2479 2821 0.322322 GTGGTCCATGTTCGGGTACA 59.678 55.000 0.00 0.00 0.00 2.90
2504 2846 4.529731 GGGGCTGGCTGGGATTCC 62.530 72.222 0.00 0.00 0.00 3.01
2555 2897 3.771160 GATGAGGGCCGACGTGGT 61.771 66.667 0.00 0.00 41.21 4.16
2617 2959 2.316867 CCGTCATTGCTCACGTGCA 61.317 57.895 11.67 2.98 41.65 4.57
2677 3020 3.512329 AGTCATGCATTGCCTTGAAATGA 59.488 39.130 6.12 4.68 37.22 2.57
2700 3043 0.403655 TGCCATTGGTGCAGGAAGTA 59.596 50.000 4.26 0.00 34.05 2.24
2766 3110 6.496571 CCTAGATCTAGGTAGTTGTGTTTCG 58.503 44.000 32.80 9.02 45.93 3.46
2832 3176 4.094887 CGCACTGTATGGCAACTAATTTCT 59.905 41.667 0.00 0.00 37.61 2.52
2904 3248 0.385029 TGTGAACACACAATGGCTGC 59.615 50.000 3.39 0.00 40.83 5.25
3000 3345 9.710900 GACTTGTGATATATGAACATACATGGA 57.289 33.333 0.00 0.00 0.00 3.41
3064 3412 2.224744 ACATGCTGTGTGGTGGATGTTA 60.225 45.455 0.00 0.00 41.27 2.41
3153 3502 8.461222 TGTGAAGATATGGCAACTCATTTTTAG 58.539 33.333 0.00 0.00 37.61 1.85
3192 3541 5.293324 TCAGTCGCCACATTATATGTTTGTC 59.707 40.000 0.00 0.00 42.70 3.18
3207 3556 5.621197 TGTTTGTCCATTGTAGTATGTGC 57.379 39.130 0.00 0.00 0.00 4.57
3343 3696 0.550914 TGGACAATCATAGGGGGTGC 59.449 55.000 0.00 0.00 0.00 5.01
3473 3828 9.654663 GATCTAGGTAGTTGTATTTCAAAGTGT 57.345 33.333 0.00 0.00 37.81 3.55
3536 3891 2.310538 GGATGGCAACTAATTCCCTGG 58.689 52.381 0.00 0.00 37.61 4.45
3543 3898 4.566907 GGCAACTAATTCCCTGGTCAACTA 60.567 45.833 0.00 0.00 0.00 2.24
3546 3901 4.781934 ACTAATTCCCTGGTCAACTATGC 58.218 43.478 0.00 0.00 0.00 3.14
3558 3913 1.538047 AACTATGCCAGTTGCCACAG 58.462 50.000 0.30 0.00 46.01 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.003658 GTTTCTCTTTGGTTCTCAGAATTATCA 57.996 33.333 0.00 0.00 0.00 2.15
1 2 9.003658 TGTTTCTCTTTGGTTCTCAGAATTATC 57.996 33.333 0.00 0.00 0.00 1.75
2 3 8.787852 GTGTTTCTCTTTGGTTCTCAGAATTAT 58.212 33.333 0.00 0.00 0.00 1.28
3 4 7.773224 TGTGTTTCTCTTTGGTTCTCAGAATTA 59.227 33.333 0.00 0.00 0.00 1.40
4 5 6.603201 TGTGTTTCTCTTTGGTTCTCAGAATT 59.397 34.615 0.00 0.00 0.00 2.17
5 6 6.122277 TGTGTTTCTCTTTGGTTCTCAGAAT 58.878 36.000 0.00 0.00 0.00 2.40
6 7 5.496556 TGTGTTTCTCTTTGGTTCTCAGAA 58.503 37.500 0.00 0.00 0.00 3.02
7 8 5.097742 TGTGTTTCTCTTTGGTTCTCAGA 57.902 39.130 0.00 0.00 0.00 3.27
8 9 5.818136 TTGTGTTTCTCTTTGGTTCTCAG 57.182 39.130 0.00 0.00 0.00 3.35
9 10 5.943416 TCTTTGTGTTTCTCTTTGGTTCTCA 59.057 36.000 0.00 0.00 0.00 3.27
10 11 6.436843 TCTTTGTGTTTCTCTTTGGTTCTC 57.563 37.500 0.00 0.00 0.00 2.87
11 12 5.358160 CCTCTTTGTGTTTCTCTTTGGTTCT 59.642 40.000 0.00 0.00 0.00 3.01
12 13 5.582550 CCTCTTTGTGTTTCTCTTTGGTTC 58.417 41.667 0.00 0.00 0.00 3.62
13 14 4.142160 GCCTCTTTGTGTTTCTCTTTGGTT 60.142 41.667 0.00 0.00 0.00 3.67
14 15 3.381590 GCCTCTTTGTGTTTCTCTTTGGT 59.618 43.478 0.00 0.00 0.00 3.67
15 16 3.633986 AGCCTCTTTGTGTTTCTCTTTGG 59.366 43.478 0.00 0.00 0.00 3.28
16 17 4.907879 AGCCTCTTTGTGTTTCTCTTTG 57.092 40.909 0.00 0.00 0.00 2.77
17 18 5.418840 TGAAAGCCTCTTTGTGTTTCTCTTT 59.581 36.000 0.00 0.00 0.00 2.52
18 19 4.949856 TGAAAGCCTCTTTGTGTTTCTCTT 59.050 37.500 0.00 0.00 0.00 2.85
19 20 4.526970 TGAAAGCCTCTTTGTGTTTCTCT 58.473 39.130 0.00 0.00 0.00 3.10
20 21 4.576463 TCTGAAAGCCTCTTTGTGTTTCTC 59.424 41.667 0.00 0.00 0.00 2.87
21 22 4.526970 TCTGAAAGCCTCTTTGTGTTTCT 58.473 39.130 0.00 0.00 0.00 2.52
22 23 4.261363 CCTCTGAAAGCCTCTTTGTGTTTC 60.261 45.833 0.00 0.00 0.00 2.78
23 24 3.633986 CCTCTGAAAGCCTCTTTGTGTTT 59.366 43.478 0.00 0.00 0.00 2.83
24 25 3.217626 CCTCTGAAAGCCTCTTTGTGTT 58.782 45.455 0.00 0.00 0.00 3.32
25 26 2.856222 CCTCTGAAAGCCTCTTTGTGT 58.144 47.619 0.00 0.00 0.00 3.72
26 27 1.538950 GCCTCTGAAAGCCTCTTTGTG 59.461 52.381 0.00 0.00 0.00 3.33
27 28 1.423161 AGCCTCTGAAAGCCTCTTTGT 59.577 47.619 0.00 0.00 0.00 2.83
28 29 1.811359 CAGCCTCTGAAAGCCTCTTTG 59.189 52.381 0.00 0.00 32.44 2.77
29 30 1.271817 CCAGCCTCTGAAAGCCTCTTT 60.272 52.381 0.00 0.00 32.44 2.52
30 31 0.327591 CCAGCCTCTGAAAGCCTCTT 59.672 55.000 0.00 0.00 32.44 2.85
31 32 0.546267 TCCAGCCTCTGAAAGCCTCT 60.546 55.000 0.00 0.00 32.44 3.69
32 33 0.545646 ATCCAGCCTCTGAAAGCCTC 59.454 55.000 0.00 0.00 32.44 4.70
33 34 0.998145 AATCCAGCCTCTGAAAGCCT 59.002 50.000 0.00 0.00 32.44 4.58
34 35 2.293170 GTAATCCAGCCTCTGAAAGCC 58.707 52.381 0.00 0.00 32.44 4.35
35 36 2.941720 CTGTAATCCAGCCTCTGAAAGC 59.058 50.000 0.00 0.00 33.59 3.51
36 37 4.478206 TCTGTAATCCAGCCTCTGAAAG 57.522 45.455 0.00 0.00 41.25 2.62
37 38 6.349300 GTTATCTGTAATCCAGCCTCTGAAA 58.651 40.000 0.00 0.00 41.25 2.69
38 39 5.163301 GGTTATCTGTAATCCAGCCTCTGAA 60.163 44.000 0.00 0.00 41.25 3.02
39 40 4.345257 GGTTATCTGTAATCCAGCCTCTGA 59.655 45.833 0.00 0.00 41.25 3.27
40 41 4.346418 AGGTTATCTGTAATCCAGCCTCTG 59.654 45.833 0.00 0.00 41.25 3.35
41 42 4.561752 AGGTTATCTGTAATCCAGCCTCT 58.438 43.478 0.00 0.00 41.25 3.69
42 43 4.965200 AGGTTATCTGTAATCCAGCCTC 57.035 45.455 0.00 0.00 41.25 4.70
43 44 5.468658 ACTAGGTTATCTGTAATCCAGCCT 58.531 41.667 0.00 0.00 41.25 4.58
44 45 5.810080 ACTAGGTTATCTGTAATCCAGCC 57.190 43.478 0.00 0.00 41.25 4.85
45 46 9.780186 ATTAAACTAGGTTATCTGTAATCCAGC 57.220 33.333 0.00 0.00 41.25 4.85
69 70 9.736414 CATCTCTAGGAATGTCCATGATAAATT 57.264 33.333 0.00 0.00 39.61 1.82
70 71 8.327271 CCATCTCTAGGAATGTCCATGATAAAT 58.673 37.037 0.00 0.00 39.61 1.40
71 72 7.293299 ACCATCTCTAGGAATGTCCATGATAAA 59.707 37.037 0.00 0.00 39.61 1.40
72 73 6.789457 ACCATCTCTAGGAATGTCCATGATAA 59.211 38.462 0.00 0.00 39.61 1.75
73 74 6.326161 ACCATCTCTAGGAATGTCCATGATA 58.674 40.000 0.00 0.00 39.61 2.15
74 75 5.161135 ACCATCTCTAGGAATGTCCATGAT 58.839 41.667 0.00 0.00 39.61 2.45
75 76 4.560739 ACCATCTCTAGGAATGTCCATGA 58.439 43.478 0.00 0.00 39.61 3.07
76 77 4.970860 ACCATCTCTAGGAATGTCCATG 57.029 45.455 0.00 0.00 39.61 3.66
77 78 7.483018 ACTATACCATCTCTAGGAATGTCCAT 58.517 38.462 0.00 0.00 39.61 3.41
78 79 6.864421 ACTATACCATCTCTAGGAATGTCCA 58.136 40.000 0.00 0.00 39.61 4.02
79 80 7.784470 AACTATACCATCTCTAGGAATGTCC 57.216 40.000 0.00 0.00 36.58 4.02
84 85 9.535170 CCATCTAAACTATACCATCTCTAGGAA 57.465 37.037 0.00 0.00 0.00 3.36
85 86 7.616150 GCCATCTAAACTATACCATCTCTAGGA 59.384 40.741 0.00 0.00 0.00 2.94
86 87 7.147811 GGCCATCTAAACTATACCATCTCTAGG 60.148 44.444 0.00 0.00 0.00 3.02
87 88 7.617723 AGGCCATCTAAACTATACCATCTCTAG 59.382 40.741 5.01 0.00 0.00 2.43
88 89 7.397476 CAGGCCATCTAAACTATACCATCTCTA 59.603 40.741 5.01 0.00 0.00 2.43
89 90 6.212388 CAGGCCATCTAAACTATACCATCTCT 59.788 42.308 5.01 0.00 0.00 3.10
90 91 6.211584 TCAGGCCATCTAAACTATACCATCTC 59.788 42.308 5.01 0.00 0.00 2.75
91 92 6.084738 TCAGGCCATCTAAACTATACCATCT 58.915 40.000 5.01 0.00 0.00 2.90
92 93 6.360370 TCAGGCCATCTAAACTATACCATC 57.640 41.667 5.01 0.00 0.00 3.51
93 94 6.959606 ATCAGGCCATCTAAACTATACCAT 57.040 37.500 5.01 0.00 0.00 3.55
94 95 6.763715 AATCAGGCCATCTAAACTATACCA 57.236 37.500 5.01 0.00 0.00 3.25
95 96 9.740710 AAATAATCAGGCCATCTAAACTATACC 57.259 33.333 5.01 0.00 0.00 2.73
125 126 9.772282 GCAACGTTATGTACAACAAAATAAAAG 57.228 29.630 0.00 0.00 0.00 2.27
126 127 9.517609 AGCAACGTTATGTACAACAAAATAAAA 57.482 25.926 0.00 0.00 0.00 1.52
127 128 9.517609 AAGCAACGTTATGTACAACAAAATAAA 57.482 25.926 0.00 0.00 0.00 1.40
130 131 8.960075 GTTAAGCAACGTTATGTACAACAAAAT 58.040 29.630 0.00 0.00 0.00 1.82
131 132 8.182881 AGTTAAGCAACGTTATGTACAACAAAA 58.817 29.630 0.00 0.00 39.78 2.44
132 133 7.695820 AGTTAAGCAACGTTATGTACAACAAA 58.304 30.769 0.00 0.00 39.78 2.83
133 134 7.249186 AGTTAAGCAACGTTATGTACAACAA 57.751 32.000 0.00 0.00 39.78 2.83
134 135 6.847956 AGTTAAGCAACGTTATGTACAACA 57.152 33.333 0.00 0.00 39.78 3.33
135 136 8.466026 CAAAAGTTAAGCAACGTTATGTACAAC 58.534 33.333 0.00 1.26 39.78 3.32
136 137 8.396390 TCAAAAGTTAAGCAACGTTATGTACAA 58.604 29.630 0.00 0.00 39.78 2.41
137 138 7.917597 TCAAAAGTTAAGCAACGTTATGTACA 58.082 30.769 0.00 0.00 39.78 2.90
138 139 8.770850 TTCAAAAGTTAAGCAACGTTATGTAC 57.229 30.769 0.00 0.00 39.78 2.90
139 140 9.388346 CATTCAAAAGTTAAGCAACGTTATGTA 57.612 29.630 0.00 0.00 39.78 2.29
140 141 8.132362 TCATTCAAAAGTTAAGCAACGTTATGT 58.868 29.630 0.00 0.00 39.78 2.29
141 142 8.500837 TCATTCAAAAGTTAAGCAACGTTATG 57.499 30.769 0.00 0.00 39.78 1.90
142 143 9.522804 TTTCATTCAAAAGTTAAGCAACGTTAT 57.477 25.926 0.00 0.00 39.78 1.89
143 144 8.912787 TTTCATTCAAAAGTTAAGCAACGTTA 57.087 26.923 0.00 0.00 39.78 3.18
144 145 7.820044 TTTCATTCAAAAGTTAAGCAACGTT 57.180 28.000 0.00 0.00 39.78 3.99
145 146 7.820044 TTTTCATTCAAAAGTTAAGCAACGT 57.180 28.000 0.00 0.00 39.78 3.99
149 150 8.973378 CGGTAATTTTCATTCAAAAGTTAAGCA 58.027 29.630 0.00 0.00 37.40 3.91
150 151 8.974408 ACGGTAATTTTCATTCAAAAGTTAAGC 58.026 29.630 0.00 0.00 37.40 3.09
155 156 9.673454 GTTCTACGGTAATTTTCATTCAAAAGT 57.327 29.630 0.00 0.00 37.40 2.66
156 157 8.837059 CGTTCTACGGTAATTTTCATTCAAAAG 58.163 33.333 0.00 0.00 36.30 2.27
157 158 8.557864 TCGTTCTACGGTAATTTTCATTCAAAA 58.442 29.630 0.00 0.00 42.81 2.44
158 159 8.085720 TCGTTCTACGGTAATTTTCATTCAAA 57.914 30.769 0.00 0.00 42.81 2.69
159 160 7.655236 TCGTTCTACGGTAATTTTCATTCAA 57.345 32.000 0.00 0.00 42.81 2.69
160 161 7.837202 ATCGTTCTACGGTAATTTTCATTCA 57.163 32.000 0.00 0.00 42.81 2.57
161 162 8.173130 ACAATCGTTCTACGGTAATTTTCATTC 58.827 33.333 0.00 0.00 42.81 2.67
162 163 8.036273 ACAATCGTTCTACGGTAATTTTCATT 57.964 30.769 0.00 0.00 42.81 2.57
163 164 7.605410 ACAATCGTTCTACGGTAATTTTCAT 57.395 32.000 0.00 0.00 42.81 2.57
164 165 7.424227 AACAATCGTTCTACGGTAATTTTCA 57.576 32.000 0.00 0.00 42.81 2.69
165 166 7.927913 GAACAATCGTTCTACGGTAATTTTC 57.072 36.000 0.00 0.00 46.72 2.29
179 180 3.744426 CCAAAGACCGTAGAACAATCGTT 59.256 43.478 0.00 0.00 38.33 3.85
180 181 3.243975 ACCAAAGACCGTAGAACAATCGT 60.244 43.478 0.00 0.00 0.00 3.73
181 182 3.323243 ACCAAAGACCGTAGAACAATCG 58.677 45.455 0.00 0.00 0.00 3.34
182 183 4.753107 TGAACCAAAGACCGTAGAACAATC 59.247 41.667 0.00 0.00 0.00 2.67
183 184 4.710324 TGAACCAAAGACCGTAGAACAAT 58.290 39.130 0.00 0.00 0.00 2.71
184 185 4.139859 TGAACCAAAGACCGTAGAACAA 57.860 40.909 0.00 0.00 0.00 2.83
185 186 3.823281 TGAACCAAAGACCGTAGAACA 57.177 42.857 0.00 0.00 0.00 3.18
186 187 5.488645 TTTTGAACCAAAGACCGTAGAAC 57.511 39.130 0.00 0.00 34.72 3.01
243 244 9.755804 TTATCAGATTTGCTAAGTCACATCTAG 57.244 33.333 0.00 0.00 33.22 2.43
270 271 7.595130 GCAAATCTGTCGAAGAGGTTTATTTTT 59.405 33.333 4.13 0.00 38.67 1.94
276 277 3.251004 GTGCAAATCTGTCGAAGAGGTTT 59.749 43.478 0.00 0.00 38.67 3.27
282 283 3.624326 TTTGGTGCAAATCTGTCGAAG 57.376 42.857 0.00 0.00 0.00 3.79
326 327 4.773674 AGATTGATGTGATGGCCTTCAAAA 59.226 37.500 21.99 14.07 32.07 2.44
340 341 9.790344 CCATCTTCTATCCTTAAAGATTGATGT 57.210 33.333 9.56 0.01 37.59 3.06
341 342 9.790344 ACCATCTTCTATCCTTAAAGATTGATG 57.210 33.333 0.03 3.14 37.59 3.07
373 374 4.826274 ATCATTCCAGACGGAGAAAAGA 57.174 40.909 0.00 0.00 44.10 2.52
471 472 2.139917 GGGAAAACGGTTCATTTTGCC 58.860 47.619 5.21 5.21 46.14 4.52
475 476 3.509967 GGATGAGGGAAAACGGTTCATTT 59.490 43.478 0.00 0.00 0.00 2.32
482 483 2.389962 TAACGGATGAGGGAAAACGG 57.610 50.000 0.00 0.00 0.00 4.44
516 517 6.532657 GCTTAACAATGGGAAACATGATTGAG 59.467 38.462 0.00 0.00 40.44 3.02
521 522 4.075682 TCGCTTAACAATGGGAAACATGA 58.924 39.130 0.00 0.00 40.44 3.07
529 530 0.322997 TGGGGTCGCTTAACAATGGG 60.323 55.000 0.00 0.00 0.00 4.00
565 567 6.778821 TGACAATATATCTATTGGTGTGGGG 58.221 40.000 13.59 0.00 45.69 4.96
585 587 5.872070 TGTAATGCGTTCTTACATCATGACA 59.128 36.000 0.00 0.00 34.90 3.58
594 596 5.585500 TTCTGTGTGTAATGCGTTCTTAC 57.415 39.130 0.00 0.00 0.00 2.34
732 1007 4.043561 TCCAACAATATACCCACCTTGTGT 59.956 41.667 0.00 0.00 32.47 3.72
737 1012 5.286221 ACTACTCCAACAATATACCCACCT 58.714 41.667 0.00 0.00 0.00 4.00
751 1026 7.068348 ACAAGATCGAGCTAATTACTACTCCAA 59.932 37.037 2.34 0.00 0.00 3.53
776 1051 3.698040 TCTGACCCTCCGAGTTATTACAC 59.302 47.826 0.00 0.00 0.00 2.90
777 1052 3.698040 GTCTGACCCTCCGAGTTATTACA 59.302 47.826 0.00 0.00 0.00 2.41
823 1098 3.306156 GGAACGTAACTGCTTTCCTCTCT 60.306 47.826 0.00 0.00 34.93 3.10
824 1099 2.994578 GGAACGTAACTGCTTTCCTCTC 59.005 50.000 0.00 0.00 34.93 3.20
924 1201 0.316841 GAGGCGAGAGACATCATCCC 59.683 60.000 0.00 0.00 46.78 3.85
1006 1288 1.010574 GTCGACCTCGCAGATCTCG 60.011 63.158 3.51 0.00 39.60 4.04
1044 1326 2.822255 GCTGCATCCCGGCGTTTA 60.822 61.111 6.01 0.00 35.83 2.01
1216 1498 2.285743 GGGGGAGAGGAGCTGGTT 60.286 66.667 0.00 0.00 0.00 3.67
1220 1502 2.937285 AAGTCGGGGGAGAGGAGCT 61.937 63.158 0.00 0.00 0.00 4.09
1233 1515 3.364964 CCGGATTTTTGTCTTCCAAGTCG 60.365 47.826 0.00 0.00 33.75 4.18
1336 1618 1.399744 TTGGCCTCGTATCGCCTCAT 61.400 55.000 3.32 0.00 45.90 2.90
1344 1626 2.234913 GACGGTGGTTGGCCTCGTAT 62.235 60.000 3.32 0.00 42.06 3.06
1446 1728 1.995484 CATGTATGATGACGATCGCCC 59.005 52.381 16.60 8.14 0.00 6.13
1473 1755 1.458486 GGTTGGGATCCACACCACA 59.542 57.895 21.61 4.59 35.92 4.17
1500 1782 2.046023 CTGAGCATCCGGTTGCCA 60.046 61.111 29.42 24.31 43.83 4.92
1551 1833 3.933048 GACGAGGAGGACCCGGTCA 62.933 68.421 19.43 0.00 40.61 4.02
1557 1839 2.022240 GCTCATGGACGAGGAGGACC 62.022 65.000 1.28 0.00 32.80 4.46
1578 1860 2.041762 AGGCCCTGCATCTCTGGA 59.958 61.111 0.00 0.00 35.98 3.86
1682 1964 1.271982 TGACGTAGCTCTCCTTGGAGT 60.272 52.381 15.44 0.62 35.89 3.85
1885 2197 0.105964 TTGTCGGACTTGACCACCAG 59.894 55.000 9.88 0.00 38.11 4.00
1928 2240 2.972505 GGCGGTACATGGGCATCG 60.973 66.667 0.00 0.00 0.00 3.84
2037 2349 1.142870 CCCTCAAAGAACCTGTCCACA 59.857 52.381 0.00 0.00 0.00 4.17
2208 2550 3.934391 CTTCTTCGCCTCCGCCGTT 62.934 63.158 0.00 0.00 0.00 4.44
2239 2581 2.048127 GACTGCGACGGCCTTCTT 60.048 61.111 7.75 0.00 38.85 2.52
2240 2582 4.070552 GGACTGCGACGGCCTTCT 62.071 66.667 7.75 0.00 38.85 2.85
2241 2583 4.070552 AGGACTGCGACGGCCTTC 62.071 66.667 0.00 0.00 38.85 3.46
2327 2669 1.896660 GACACCACCATGTTGCCGT 60.897 57.895 0.00 0.00 31.24 5.68
2332 2674 1.896660 GCACCGACACCACCATGTT 60.897 57.895 0.00 0.00 31.24 2.71
2335 2677 2.281484 GTGCACCGACACCACCAT 60.281 61.111 5.22 0.00 34.35 3.55
2439 2781 1.081708 CGTCGTCACCATCGTGTCA 60.082 57.895 0.00 0.00 41.09 3.58
2444 2786 3.755628 ACCCCGTCGTCACCATCG 61.756 66.667 0.00 0.00 0.00 3.84
2468 2810 2.507547 GCGCGATGTACCCGAACA 60.508 61.111 12.10 0.00 0.00 3.18
2504 2846 3.945434 GCATCAGCATCCACGGCG 61.945 66.667 4.80 4.80 41.58 6.46
2570 2912 2.226315 ATGCAGGGCTCCACAGACA 61.226 57.895 0.00 0.00 0.00 3.41
2617 2959 0.451783 GGCTCAAATCGAACCGCAAT 59.548 50.000 0.00 0.00 0.00 3.56
2700 3043 8.049721 TCAAACCCTGAAATTAACCAACAAAAT 58.950 29.630 0.00 0.00 0.00 1.82
2766 3110 3.255642 TGGCTGCCTTTGTAATTCACTTC 59.744 43.478 21.03 0.00 0.00 3.01
3064 3412 6.369615 GCAGGACAATTCAAAAAGTGCATAAT 59.630 34.615 0.00 0.00 33.83 1.28
3173 3522 4.891627 TGGACAAACATATAATGTGGCG 57.108 40.909 0.00 0.00 44.07 5.69
3192 3541 3.297134 AAGGGGCACATACTACAATGG 57.703 47.619 0.00 0.00 0.00 3.16
3207 3556 7.201609 GCAAAAGAAACTAGAAACAAAAAGGGG 60.202 37.037 0.00 0.00 0.00 4.79
3343 3696 7.426410 AGACAGTACATAACTATGAACATCCG 58.574 38.462 3.73 0.00 35.76 4.18
3546 3901 4.380867 GGAAAACATATCTGTGGCAACTGG 60.381 45.833 0.00 0.00 35.22 4.00
3558 3913 3.115554 GTTGCCGCATGGAAAACATATC 58.884 45.455 0.00 0.00 37.84 1.63


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

AutoCloner maintained by Alex Coulton.