Multiple sequence alignment - TraesCS5A01G311600

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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 TraesCS5A01G311600 chr5A 100.000 3018 0 0 1 3018 523149954 523146937 0.000000e+00 5574.0
1 TraesCS5A01G311600 chr5A 95.949 1012 23 4 2022 3018 74866427 74865419 0.000000e+00 1626.0
2 TraesCS5A01G311600 chr5A 84.140 744 99 11 1163 1904 522861743 522861017 0.000000e+00 702.0
3 TraesCS5A01G311600 chr5A 78.187 651 103 24 1239 1880 523450133 523450753 2.200000e-101 379.0
4 TraesCS5A01G311600 chr5A 84.438 347 48 3 1252 1592 522883359 522883013 1.340000e-88 337.0
5 TraesCS5A01G311600 chr5A 90.805 87 8 0 499 585 559089021 559089107 1.900000e-22 117.0
6 TraesCS5A01G311600 chr5D 94.617 1356 45 9 647 1995 411226351 411225017 0.000000e+00 2074.0
7 TraesCS5A01G311600 chr5D 82.410 830 119 18 1163 1987 410867021 410866214 0.000000e+00 699.0
8 TraesCS5A01G311600 chr5D 85.303 347 45 4 1247 1592 410444211 410444552 1.330000e-93 353.0
9 TraesCS5A01G311600 chr5D 85.143 350 46 5 1249 1592 411149305 411148956 1.330000e-93 353.0
10 TraesCS5A01G311600 chr5D 84.286 350 49 3 1249 1592 410952929 410952580 1.340000e-88 337.0
11 TraesCS5A01G311600 chr5B 89.908 1407 68 24 647 2024 493696025 493694664 0.000000e+00 1744.0
12 TraesCS5A01G311600 chr5B 82.530 830 117 19 1163 1987 493174582 493173776 0.000000e+00 704.0
13 TraesCS5A01G311600 chr5B 77.649 519 78 26 1 500 493696731 493696232 6.370000e-72 281.0
14 TraesCS5A01G311600 chr7A 91.863 1020 52 9 2024 3018 12983433 12984446 0.000000e+00 1395.0
15 TraesCS5A01G311600 chr7B 91.732 1016 56 10 2024 3018 336385515 336386523 0.000000e+00 1386.0
16 TraesCS5A01G311600 chr7B 87.515 841 81 19 2025 2850 744917469 744916638 0.000000e+00 950.0
17 TraesCS5A01G311600 chr7B 89.759 166 13 2 2551 2716 444169994 444169833 3.050000e-50 209.0
18 TraesCS5A01G311600 chr7B 91.045 134 12 0 2885 3018 744916640 744916507 6.650000e-42 182.0
19 TraesCS5A01G311600 chr3B 85.799 1007 86 14 2024 3018 823097324 823098285 0.000000e+00 1014.0
20 TraesCS5A01G311600 chr3B 92.222 90 6 1 495 584 443802373 443802461 3.160000e-25 126.0
21 TraesCS5A01G311600 chr7D 84.884 1032 109 20 2024 3018 189328592 189327571 0.000000e+00 998.0
22 TraesCS5A01G311600 chr7D 87.500 80 9 1 502 581 300064615 300064537 1.150000e-14 91.6
23 TraesCS5A01G311600 chr3A 83.249 591 79 12 2139 2716 75623331 75623914 2.670000e-145 525.0
24 TraesCS5A01G311600 chr3A 91.566 83 7 0 502 584 215068665 215068583 6.840000e-22 115.0
25 TraesCS5A01G311600 chr3D 80.921 456 45 15 2270 2716 82558630 82559052 3.750000e-84 322.0
26 TraesCS5A01G311600 chr4A 79.873 472 58 23 2492 2941 698360229 698359773 8.120000e-81 311.0
27 TraesCS5A01G311600 chr4A 91.566 83 7 0 504 586 743649237 743649155 6.840000e-22 115.0
28 TraesCS5A01G311600 chr4A 90.123 81 8 0 504 584 518197048 518197128 4.110000e-19 106.0
29 TraesCS5A01G311600 chr2A 90.361 166 12 2 2551 2716 1634726 1634565 6.550000e-52 215.0
30 TraesCS5A01G311600 chr2A 95.238 42 2 0 2031 2072 12344342 12344383 1.940000e-07 67.6
31 TraesCS5A01G311600 chr2B 86.585 82 11 0 502 583 518450004 518449923 1.150000e-14 91.6
32 TraesCS5A01G311600 chr6A 84.615 91 13 1 494 584 610200538 610200627 4.140000e-14 89.8
33 TraesCS5A01G311600 chr2D 85.542 83 12 0 502 584 148843858 148843776 1.490000e-13 87.9


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 TraesCS5A01G311600 chr5A 523146937 523149954 3017 True 5574.0 5574 100.0000 1 3018 1 chr5A.!!$R4 3017
1 TraesCS5A01G311600 chr5A 74865419 74866427 1008 True 1626.0 1626 95.9490 2022 3018 1 chr5A.!!$R1 996
2 TraesCS5A01G311600 chr5A 522861017 522861743 726 True 702.0 702 84.1400 1163 1904 1 chr5A.!!$R2 741
3 TraesCS5A01G311600 chr5A 523450133 523450753 620 False 379.0 379 78.1870 1239 1880 1 chr5A.!!$F1 641
4 TraesCS5A01G311600 chr5D 411225017 411226351 1334 True 2074.0 2074 94.6170 647 1995 1 chr5D.!!$R4 1348
5 TraesCS5A01G311600 chr5D 410866214 410867021 807 True 699.0 699 82.4100 1163 1987 1 chr5D.!!$R1 824
6 TraesCS5A01G311600 chr5B 493694664 493696731 2067 True 1012.5 1744 83.7785 1 2024 2 chr5B.!!$R2 2023
7 TraesCS5A01G311600 chr5B 493173776 493174582 806 True 704.0 704 82.5300 1163 1987 1 chr5B.!!$R1 824
8 TraesCS5A01G311600 chr7A 12983433 12984446 1013 False 1395.0 1395 91.8630 2024 3018 1 chr7A.!!$F1 994
9 TraesCS5A01G311600 chr7B 336385515 336386523 1008 False 1386.0 1386 91.7320 2024 3018 1 chr7B.!!$F1 994
10 TraesCS5A01G311600 chr7B 744916507 744917469 962 True 566.0 950 89.2800 2025 3018 2 chr7B.!!$R2 993
11 TraesCS5A01G311600 chr3B 823097324 823098285 961 False 1014.0 1014 85.7990 2024 3018 1 chr3B.!!$F2 994
12 TraesCS5A01G311600 chr7D 189327571 189328592 1021 True 998.0 998 84.8840 2024 3018 1 chr7D.!!$R1 994
13 TraesCS5A01G311600 chr3A 75623331 75623914 583 False 525.0 525 83.2490 2139 2716 1 chr3A.!!$F1 577

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
190 198 0.101759 CGCCCATTGCCATCTCAAAG 59.898 55.0 0.00 0.0 36.24 2.77 F
475 490 0.466555 TTTGTTTGGTACCCGCTGCT 60.467 50.0 10.07 0.0 0.00 4.24 F
491 506 0.685097 TGCTCTACCCGAAAAGCACT 59.315 50.0 0.00 0.0 39.69 4.40 F
709 813 1.083489 TGCTAAGATGAAAACGCCGG 58.917 50.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2043 0.978907 TAGTTTTGACCCGAGTCCCC 59.021 55.000 0.00 0.0 42.81 4.81 R
1992 2132 1.026182 CATCATGGGTCCACACCGTG 61.026 60.000 0.00 0.0 44.91 4.94 R
2011 2151 3.068165 GTCACTGGCCTTTTATTATGCCC 59.932 47.826 3.32 0.0 43.35 5.36 R
2080 2220 3.559655 CGGCTGTTAATGGATGAATCGAA 59.440 43.478 0.00 0.0 0.00 3.71 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
28 29 8.447053 GGAAAGCACAAAACAAAAATCAAGTTA 58.553 29.630 0.00 0.00 0.00 2.24
63 64 3.007635 ACTTCCGTAAGCATTGGTAAGC 58.992 45.455 0.00 0.00 36.05 3.09
66 67 2.027561 TCCGTAAGCATTGGTAAGCACT 60.028 45.455 0.00 0.00 0.00 4.40
67 68 3.196039 TCCGTAAGCATTGGTAAGCACTA 59.804 43.478 0.00 0.00 0.00 2.74
69 70 4.574828 CCGTAAGCATTGGTAAGCACTAAT 59.425 41.667 0.00 0.00 36.37 1.73
72 73 7.123830 CGTAAGCATTGGTAAGCACTAATTAC 58.876 38.462 0.00 0.00 33.93 1.89
73 74 7.011109 CGTAAGCATTGGTAAGCACTAATTACT 59.989 37.037 0.00 0.00 33.93 2.24
77 81 8.028938 AGCATTGGTAAGCACTAATTACTTTTG 58.971 33.333 0.00 0.00 33.93 2.44
78 82 7.275560 GCATTGGTAAGCACTAATTACTTTTGG 59.724 37.037 0.00 0.00 33.93 3.28
83 87 8.573885 GGTAAGCACTAATTACTTTTGGTTCTT 58.426 33.333 0.00 0.00 34.29 2.52
88 92 9.353999 GCACTAATTACTTTTGGTTCTTATTGG 57.646 33.333 0.00 0.00 0.00 3.16
103 107 7.917505 GGTTCTTATTGGTTGCAAGATCAATAG 59.082 37.037 19.84 16.20 34.75 1.73
108 112 6.441093 TTGGTTGCAAGATCAATAGATGAC 57.559 37.500 0.00 0.00 41.93 3.06
110 114 4.521943 GTTGCAAGATCAATAGATGACGC 58.478 43.478 0.00 0.00 41.93 5.19
113 117 3.186001 GCAAGATCAATAGATGACGCCAG 59.814 47.826 0.00 0.00 41.93 4.85
128 134 2.432510 ACGCCAGTGAAATTTGGGAAAA 59.567 40.909 0.00 0.00 34.96 2.29
129 135 3.059166 CGCCAGTGAAATTTGGGAAAAG 58.941 45.455 0.00 0.00 34.96 2.27
131 137 4.702831 GCCAGTGAAATTTGGGAAAAGAA 58.297 39.130 0.00 0.00 34.96 2.52
133 139 5.409520 GCCAGTGAAATTTGGGAAAAGAATC 59.590 40.000 0.00 0.00 34.96 2.52
137 143 8.553696 CAGTGAAATTTGGGAAAAGAATCAAAG 58.446 33.333 0.00 0.00 33.45 2.77
139 145 8.768019 GTGAAATTTGGGAAAAGAATCAAAGAG 58.232 33.333 0.00 0.00 33.45 2.85
140 146 7.442062 TGAAATTTGGGAAAAGAATCAAAGAGC 59.558 33.333 0.00 0.00 33.45 4.09
141 147 4.503741 TTGGGAAAAGAATCAAAGAGCG 57.496 40.909 0.00 0.00 0.00 5.03
143 149 3.081804 GGGAAAAGAATCAAAGAGCGGA 58.918 45.455 0.00 0.00 0.00 5.54
146 152 5.336770 GGGAAAAGAATCAAAGAGCGGAAAT 60.337 40.000 0.00 0.00 0.00 2.17
148 154 7.312899 GGAAAAGAATCAAAGAGCGGAAATTA 58.687 34.615 0.00 0.00 0.00 1.40
149 155 7.273598 GGAAAAGAATCAAAGAGCGGAAATTAC 59.726 37.037 0.00 0.00 0.00 1.89
150 156 6.817765 AAGAATCAAAGAGCGGAAATTACA 57.182 33.333 0.00 0.00 0.00 2.41
163 171 5.331902 CGGAAATTACACCTATGCTTGTTG 58.668 41.667 0.00 0.00 0.00 3.33
164 172 5.650543 GGAAATTACACCTATGCTTGTTGG 58.349 41.667 0.00 0.00 0.00 3.77
171 179 2.092914 ACCTATGCTTGTTGGCTAGGTC 60.093 50.000 0.00 0.00 39.60 3.85
173 181 1.026718 ATGCTTGTTGGCTAGGTCGC 61.027 55.000 0.00 0.00 0.00 5.19
181 189 2.902343 GCTAGGTCGCCCATTGCC 60.902 66.667 0.00 0.00 36.24 4.52
182 190 2.589540 CTAGGTCGCCCATTGCCA 59.410 61.111 0.00 0.00 36.24 4.92
183 191 1.149174 CTAGGTCGCCCATTGCCAT 59.851 57.895 0.00 0.00 36.24 4.40
187 195 1.451927 GTCGCCCATTGCCATCTCA 60.452 57.895 0.00 0.00 36.24 3.27
189 197 0.323269 TCGCCCATTGCCATCTCAAA 60.323 50.000 0.00 0.00 36.24 2.69
190 198 0.101759 CGCCCATTGCCATCTCAAAG 59.898 55.000 0.00 0.00 36.24 2.77
204 214 0.623194 TCAAAGGGGATGGATGCGAA 59.377 50.000 0.00 0.00 0.00 4.70
206 216 2.034124 CAAAGGGGATGGATGCGAATT 58.966 47.619 0.00 0.00 0.00 2.17
207 217 1.696063 AAGGGGATGGATGCGAATTG 58.304 50.000 0.00 0.00 0.00 2.32
208 218 0.552848 AGGGGATGGATGCGAATTGT 59.447 50.000 0.00 0.00 0.00 2.71
214 224 5.418840 GGGGATGGATGCGAATTGTTTATAT 59.581 40.000 0.00 0.00 0.00 0.86
215 225 6.324819 GGGATGGATGCGAATTGTTTATATG 58.675 40.000 0.00 0.00 0.00 1.78
219 229 8.801715 ATGGATGCGAATTGTTTATATGTTTC 57.198 30.769 0.00 0.00 0.00 2.78
220 230 7.199766 TGGATGCGAATTGTTTATATGTTTCC 58.800 34.615 0.00 0.00 0.00 3.13
225 235 8.065407 TGCGAATTGTTTATATGTTTCCGATAC 58.935 33.333 0.00 0.00 0.00 2.24
242 252 7.461182 TCCGATACAATTTGTTGAAATTCCT 57.539 32.000 7.45 0.00 39.34 3.36
244 254 8.026607 TCCGATACAATTTGTTGAAATTCCTTC 58.973 33.333 7.45 0.00 39.34 3.46
250 260 8.360390 ACAATTTGTTGAAATTCCTTCTACTCC 58.640 33.333 0.00 0.00 39.34 3.85
251 261 6.554334 TTTGTTGAAATTCCTTCTACTCCG 57.446 37.500 0.00 0.00 39.61 4.63
252 262 4.575885 TGTTGAAATTCCTTCTACTCCGG 58.424 43.478 0.00 0.00 39.61 5.14
253 263 4.285003 TGTTGAAATTCCTTCTACTCCGGA 59.715 41.667 2.93 2.93 39.61 5.14
254 264 5.045869 TGTTGAAATTCCTTCTACTCCGGAT 60.046 40.000 3.57 0.00 39.61 4.18
255 265 6.155565 TGTTGAAATTCCTTCTACTCCGGATA 59.844 38.462 3.57 0.00 39.61 2.59
256 266 6.158023 TGAAATTCCTTCTACTCCGGATAC 57.842 41.667 3.57 0.00 34.86 2.24
257 267 5.659525 TGAAATTCCTTCTACTCCGGATACA 59.340 40.000 3.57 0.00 34.86 2.29
258 268 6.155565 TGAAATTCCTTCTACTCCGGATACAA 59.844 38.462 3.57 0.00 34.86 2.41
259 269 5.793030 ATTCCTTCTACTCCGGATACAAG 57.207 43.478 3.57 5.11 0.00 3.16
260 270 3.563223 TCCTTCTACTCCGGATACAAGG 58.437 50.000 18.96 18.96 0.00 3.61
261 271 3.053095 TCCTTCTACTCCGGATACAAGGT 60.053 47.826 21.96 12.42 32.33 3.50
262 272 3.705072 CCTTCTACTCCGGATACAAGGTT 59.295 47.826 3.57 0.00 0.00 3.50
265 275 3.698040 TCTACTCCGGATACAAGGTTGTC 59.302 47.826 3.57 0.00 42.35 3.18
306 316 6.763715 ATATTTACTGATGGGCTAAGTGGA 57.236 37.500 0.00 0.00 0.00 4.02
317 327 2.076863 GCTAAGTGGACCATGACACAC 58.923 52.381 14.60 10.40 39.99 3.82
318 328 2.699954 CTAAGTGGACCATGACACACC 58.300 52.381 14.60 3.33 39.99 4.16
320 330 0.687354 AGTGGACCATGACACACCTC 59.313 55.000 14.60 3.86 39.99 3.85
321 331 0.670546 GTGGACCATGACACACCTCG 60.671 60.000 0.00 0.00 37.54 4.63
322 332 1.741770 GGACCATGACACACCTCGC 60.742 63.158 0.00 0.00 0.00 5.03
323 333 1.741770 GACCATGACACACCTCGCC 60.742 63.158 0.00 0.00 0.00 5.54
335 345 2.210711 CCTCGCCCCTCCAGTATCC 61.211 68.421 0.00 0.00 0.00 2.59
337 347 2.122813 CGCCCCTCCAGTATCCCT 60.123 66.667 0.00 0.00 0.00 4.20
340 350 1.124477 GCCCCTCCAGTATCCCTGAG 61.124 65.000 0.00 0.00 44.49 3.35
344 354 2.035632 CCTCCAGTATCCCTGAGTGAC 58.964 57.143 0.00 0.00 44.49 3.67
358 368 0.886563 AGTGACTGTACCTACACGCC 59.113 55.000 0.00 0.00 38.15 5.68
361 371 1.271762 TGACTGTACCTACACGCCTCT 60.272 52.381 0.00 0.00 31.93 3.69
362 372 1.132643 GACTGTACCTACACGCCTCTG 59.867 57.143 0.00 0.00 31.93 3.35
363 373 1.174783 CTGTACCTACACGCCTCTGT 58.825 55.000 0.00 0.00 31.93 3.41
395 408 3.765511 TGCTTTAGATGATTTGGCAAGCT 59.234 39.130 0.00 0.00 36.84 3.74
397 410 4.565564 GCTTTAGATGATTTGGCAAGCTTG 59.434 41.667 22.44 22.44 33.80 4.01
402 416 1.203038 TGATTTGGCAAGCTTGAGGGA 60.203 47.619 30.39 12.50 0.00 4.20
411 425 2.029838 AGCTTGAGGGACTAATTGCG 57.970 50.000 0.00 0.00 41.55 4.85
413 427 2.084546 GCTTGAGGGACTAATTGCGTT 58.915 47.619 0.00 0.00 41.55 4.84
426 441 7.844653 GGACTAATTGCGTTCGTAATAGAAAAG 59.155 37.037 8.67 5.37 0.00 2.27
435 450 6.518736 CGTTCGTAATAGAAAAGCAAAAGTCC 59.481 38.462 0.00 0.00 0.00 3.85
446 461 7.667219 AGAAAAGCAAAAGTCCTTCATAGATCA 59.333 33.333 0.00 0.00 0.00 2.92
447 462 6.998968 AAGCAAAAGTCCTTCATAGATCAG 57.001 37.500 0.00 0.00 0.00 2.90
449 464 4.578105 GCAAAAGTCCTTCATAGATCAGGG 59.422 45.833 0.00 0.00 0.00 4.45
450 465 5.749462 CAAAAGTCCTTCATAGATCAGGGT 58.251 41.667 0.00 0.00 0.00 4.34
461 476 6.074648 TCATAGATCAGGGTTGGTTTTTGTT 58.925 36.000 0.00 0.00 0.00 2.83
473 488 2.465855 GTTTTTGTTTGGTACCCGCTG 58.534 47.619 10.07 0.00 0.00 5.18
475 490 0.466555 TTTGTTTGGTACCCGCTGCT 60.467 50.000 10.07 0.00 0.00 4.24
476 491 0.887387 TTGTTTGGTACCCGCTGCTC 60.887 55.000 10.07 0.00 0.00 4.26
481 496 2.794028 GGTACCCGCTGCTCTACCC 61.794 68.421 0.00 0.00 0.00 3.69
483 498 3.348554 TACCCGCTGCTCTACCCGA 62.349 63.158 0.00 0.00 0.00 5.14
491 506 0.685097 TGCTCTACCCGAAAAGCACT 59.315 50.000 0.00 0.00 39.69 4.40
496 511 4.142881 GCTCTACCCGAAAAGCACTTAAAG 60.143 45.833 0.00 0.00 34.86 1.85
497 512 4.964593 TCTACCCGAAAAGCACTTAAAGT 58.035 39.130 0.00 0.00 0.00 2.66
499 514 6.523840 TCTACCCGAAAAGCACTTAAAGTTA 58.476 36.000 0.00 0.00 0.00 2.24
500 515 5.684550 ACCCGAAAAGCACTTAAAGTTAG 57.315 39.130 0.00 0.00 0.00 2.34
501 516 5.128205 ACCCGAAAAGCACTTAAAGTTAGT 58.872 37.500 0.00 0.00 0.00 2.24
503 518 5.334646 CCCGAAAAGCACTTAAAGTTAGTCC 60.335 44.000 0.00 0.00 0.00 3.85
506 521 6.347483 CGAAAAGCACTTAAAGTTAGTCCCTC 60.347 42.308 0.00 0.00 0.00 4.30
507 522 4.554960 AGCACTTAAAGTTAGTCCCTCC 57.445 45.455 0.00 0.00 0.00 4.30
508 523 4.168883 AGCACTTAAAGTTAGTCCCTCCT 58.831 43.478 0.00 0.00 0.00 3.69
509 524 4.597940 AGCACTTAAAGTTAGTCCCTCCTT 59.402 41.667 0.00 0.00 0.00 3.36
511 526 6.271624 AGCACTTAAAGTTAGTCCCTCCTTAA 59.728 38.462 0.00 0.00 0.00 1.85
512 527 6.938596 GCACTTAAAGTTAGTCCCTCCTTAAA 59.061 38.462 0.00 0.00 0.00 1.52
513 528 7.094890 GCACTTAAAGTTAGTCCCTCCTTAAAC 60.095 40.741 0.00 0.00 0.00 2.01
515 530 9.384849 ACTTAAAGTTAGTCCCTCCTTAAACTA 57.615 33.333 0.00 0.00 0.00 2.24
525 540 9.848710 AGTCCCTCCTTAAACTAATATAAAAGC 57.151 33.333 0.00 0.00 0.00 3.51
526 541 8.771766 GTCCCTCCTTAAACTAATATAAAAGCG 58.228 37.037 0.00 0.00 0.00 4.68
527 542 8.488668 TCCCTCCTTAAACTAATATAAAAGCGT 58.511 33.333 0.00 0.00 0.00 5.07
578 593 8.644318 ACGCTGTTATATTAGTTTACAGAAGG 57.356 34.615 0.00 0.00 38.74 3.46
580 595 8.969267 CGCTGTTATATTAGTTTACAGAAGGAG 58.031 37.037 0.00 0.00 38.74 3.69
591 695 7.736893 AGTTTACAGAAGGAGTACAACTGATT 58.263 34.615 0.00 0.00 33.53 2.57
610 714 4.815308 TGATTCAAACAAGGCCAAATGTTG 59.185 37.500 18.60 10.56 39.57 3.33
618 722 1.619827 AGGCCAAATGTTGTCACATGG 59.380 47.619 5.01 0.00 43.34 3.66
619 723 1.344114 GGCCAAATGTTGTCACATGGT 59.656 47.619 0.00 0.00 43.34 3.55
621 725 3.367292 GGCCAAATGTTGTCACATGGTAG 60.367 47.826 0.00 0.00 43.34 3.18
623 727 3.507233 CCAAATGTTGTCACATGGTAGCT 59.493 43.478 0.00 0.00 43.34 3.32
624 728 4.699735 CCAAATGTTGTCACATGGTAGCTA 59.300 41.667 0.00 0.00 43.34 3.32
625 729 5.182950 CCAAATGTTGTCACATGGTAGCTAA 59.817 40.000 0.00 0.00 43.34 3.09
626 730 6.294453 CCAAATGTTGTCACATGGTAGCTAAA 60.294 38.462 0.00 0.00 43.34 1.85
627 731 7.315142 CAAATGTTGTCACATGGTAGCTAAAT 58.685 34.615 0.00 0.00 43.34 1.40
628 732 8.458052 CAAATGTTGTCACATGGTAGCTAAATA 58.542 33.333 0.00 0.00 43.34 1.40
629 733 6.978343 TGTTGTCACATGGTAGCTAAATAC 57.022 37.500 0.00 0.00 0.00 1.89
630 734 6.468543 TGTTGTCACATGGTAGCTAAATACA 58.531 36.000 0.00 0.00 0.00 2.29
631 735 6.370442 TGTTGTCACATGGTAGCTAAATACAC 59.630 38.462 0.00 0.00 0.00 2.90
632 736 6.294361 TGTCACATGGTAGCTAAATACACT 57.706 37.500 0.00 0.00 0.00 3.55
633 737 6.707290 TGTCACATGGTAGCTAAATACACTT 58.293 36.000 0.00 0.00 0.00 3.16
634 738 6.816640 TGTCACATGGTAGCTAAATACACTTC 59.183 38.462 0.00 0.00 0.00 3.01
635 739 6.816640 GTCACATGGTAGCTAAATACACTTCA 59.183 38.462 0.00 0.00 0.00 3.02
636 740 6.816640 TCACATGGTAGCTAAATACACTTCAC 59.183 38.462 0.00 0.00 0.00 3.18
637 741 6.037172 CACATGGTAGCTAAATACACTTCACC 59.963 42.308 0.00 0.00 0.00 4.02
638 742 5.748670 TGGTAGCTAAATACACTTCACCA 57.251 39.130 0.00 0.00 0.00 4.17
639 743 5.730550 TGGTAGCTAAATACACTTCACCAG 58.269 41.667 0.00 0.00 0.00 4.00
640 744 4.571176 GGTAGCTAAATACACTTCACCAGC 59.429 45.833 0.00 0.00 0.00 4.85
641 745 4.286297 AGCTAAATACACTTCACCAGCA 57.714 40.909 0.00 0.00 0.00 4.41
642 746 4.651778 AGCTAAATACACTTCACCAGCAA 58.348 39.130 0.00 0.00 0.00 3.91
643 747 5.070001 AGCTAAATACACTTCACCAGCAAA 58.930 37.500 0.00 0.00 0.00 3.68
644 748 5.534654 AGCTAAATACACTTCACCAGCAAAA 59.465 36.000 0.00 0.00 0.00 2.44
645 749 5.629435 GCTAAATACACTTCACCAGCAAAAC 59.371 40.000 0.00 0.00 0.00 2.43
646 750 5.590530 AAATACACTTCACCAGCAAAACA 57.409 34.783 0.00 0.00 0.00 2.83
647 751 5.590530 AATACACTTCACCAGCAAAACAA 57.409 34.783 0.00 0.00 0.00 2.83
648 752 3.951775 ACACTTCACCAGCAAAACAAA 57.048 38.095 0.00 0.00 0.00 2.83
649 753 4.264460 ACACTTCACCAGCAAAACAAAA 57.736 36.364 0.00 0.00 0.00 2.44
650 754 3.993736 ACACTTCACCAGCAAAACAAAAC 59.006 39.130 0.00 0.00 0.00 2.43
651 755 3.060628 CACTTCACCAGCAAAACAAAACG 59.939 43.478 0.00 0.00 0.00 3.60
683 787 4.880886 TTCACATCACAAGAACACACTG 57.119 40.909 0.00 0.00 0.00 3.66
686 790 5.125356 TCACATCACAAGAACACACTGATT 58.875 37.500 0.00 0.00 0.00 2.57
701 805 6.656270 ACACACTGATTTGATGCTAAGATGAA 59.344 34.615 0.00 0.00 0.00 2.57
709 813 1.083489 TGCTAAGATGAAAACGCCGG 58.917 50.000 0.00 0.00 0.00 6.13
732 836 1.440618 TGGGATACACCAACACACCT 58.559 50.000 0.00 0.00 41.20 4.00
807 912 5.562623 CACAAACGCGGTTAAAAAGATACTC 59.437 40.000 10.12 0.00 0.00 2.59
818 923 3.589951 AAAGATACTCCATGCATGCCT 57.410 42.857 21.69 1.31 0.00 4.75
901 1030 1.339824 ACGTCTACACCGAGGAGTCAT 60.340 52.381 0.00 0.00 0.00 3.06
1053 1182 6.137104 TGGTTTACTGAGTACTCCTAGTCT 57.863 41.667 20.11 0.18 0.00 3.24
1054 1183 7.037730 ACTGGTTTACTGAGTACTCCTAGTCTA 60.038 40.741 20.11 7.10 0.00 2.59
1055 1184 7.693132 TGGTTTACTGAGTACTCCTAGTCTAA 58.307 38.462 20.11 11.90 0.00 2.10
1056 1185 8.334734 TGGTTTACTGAGTACTCCTAGTCTAAT 58.665 37.037 20.11 0.00 0.00 1.73
1057 1186 9.844257 GGTTTACTGAGTACTCCTAGTCTAATA 57.156 37.037 20.11 0.17 0.00 0.98
1132 1261 5.246145 ACTAGCCTAGCAAAAGTACGTAG 57.754 43.478 0.00 0.00 0.00 3.51
1134 1263 5.882557 ACTAGCCTAGCAAAAGTACGTAGTA 59.117 40.000 2.72 0.00 45.11 1.82
1914 2043 1.807165 CCACTGATGACACCGAGCG 60.807 63.158 0.00 0.00 0.00 5.03
1938 2071 3.933332 GGACTCGGGTCAAAACTATCTTG 59.067 47.826 18.98 0.00 43.77 3.02
2008 2148 3.055719 GCACGGTGTGGACCCATG 61.056 66.667 10.24 0.00 39.39 3.66
2011 2151 1.026182 CACGGTGTGGACCCATGATG 61.026 60.000 0.00 0.00 39.39 3.07
2033 2173 4.307443 GGCATAATAAAAGGCCAGTGAC 57.693 45.455 5.01 0.00 45.70 3.67
2508 2675 8.871629 TGAAGCAAAATATTACTAGGTTCCAA 57.128 30.769 13.73 1.28 33.84 3.53
2664 2838 2.819608 GCTCCAAGGTTGATTGTAGCAA 59.180 45.455 0.00 0.00 40.66 3.91
2731 2912 1.194781 ACACCTCAGAGGCAACCGAT 61.195 55.000 17.31 0.00 39.63 4.18
2817 2998 2.049063 GACGACGGTTGCAGCTCT 60.049 61.111 0.00 0.00 0.00 4.09
2957 3170 1.229496 TCCACCAGGCCAGCTTCTA 60.229 57.895 5.01 0.00 33.74 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 8.209917 AGTAATTAGTGCTTACCAATGCTTAC 57.790 34.615 0.00 0.00 30.89 2.34
66 67 9.699703 GCAACCAATAAGAACCAAAAGTAATTA 57.300 29.630 0.00 0.00 0.00 1.40
67 68 8.207545 TGCAACCAATAAGAACCAAAAGTAATT 58.792 29.630 0.00 0.00 0.00 1.40
69 70 7.113658 TGCAACCAATAAGAACCAAAAGTAA 57.886 32.000 0.00 0.00 0.00 2.24
72 73 6.279882 TCTTGCAACCAATAAGAACCAAAAG 58.720 36.000 0.00 0.00 0.00 2.27
73 74 6.227298 TCTTGCAACCAATAAGAACCAAAA 57.773 33.333 0.00 0.00 0.00 2.44
77 81 5.643379 TGATCTTGCAACCAATAAGAACC 57.357 39.130 0.00 0.00 34.47 3.62
78 82 8.677300 TCTATTGATCTTGCAACCAATAAGAAC 58.323 33.333 17.58 4.82 34.47 3.01
83 87 7.041848 CGTCATCTATTGATCTTGCAACCAATA 60.042 37.037 16.69 16.69 36.54 1.90
88 92 4.521943 GCGTCATCTATTGATCTTGCAAC 58.478 43.478 0.00 0.00 36.54 4.17
103 107 2.415893 CCCAAATTTCACTGGCGTCATC 60.416 50.000 0.00 0.00 0.00 2.92
108 112 2.810439 TTTCCCAAATTTCACTGGCG 57.190 45.000 0.00 0.00 0.00 5.69
110 114 6.523840 TGATTCTTTTCCCAAATTTCACTGG 58.476 36.000 0.00 0.00 0.00 4.00
113 117 8.661352 TCTTTGATTCTTTTCCCAAATTTCAC 57.339 30.769 0.00 0.00 0.00 3.18
128 134 5.123979 GGTGTAATTTCCGCTCTTTGATTCT 59.876 40.000 0.00 0.00 0.00 2.40
129 135 5.123979 AGGTGTAATTTCCGCTCTTTGATTC 59.876 40.000 0.00 0.00 0.00 2.52
131 137 4.589908 AGGTGTAATTTCCGCTCTTTGAT 58.410 39.130 0.00 0.00 0.00 2.57
133 139 5.730568 GCATAGGTGTAATTTCCGCTCTTTG 60.731 44.000 0.00 0.00 0.00 2.77
137 143 3.467803 AGCATAGGTGTAATTTCCGCTC 58.532 45.455 0.00 0.00 0.00 5.03
139 145 3.377172 ACAAGCATAGGTGTAATTTCCGC 59.623 43.478 0.00 0.00 0.00 5.54
140 146 5.331902 CAACAAGCATAGGTGTAATTTCCG 58.668 41.667 0.00 0.00 0.00 4.30
141 147 5.650543 CCAACAAGCATAGGTGTAATTTCC 58.349 41.667 0.00 0.00 0.00 3.13
143 149 4.772100 AGCCAACAAGCATAGGTGTAATTT 59.228 37.500 0.00 0.00 34.23 1.82
146 152 3.433306 AGCCAACAAGCATAGGTGTAA 57.567 42.857 0.00 0.00 34.23 2.41
148 154 2.356125 CCTAGCCAACAAGCATAGGTGT 60.356 50.000 0.00 0.00 33.00 4.16
149 155 2.292267 CCTAGCCAACAAGCATAGGTG 58.708 52.381 0.00 0.00 33.00 4.00
150 156 1.916181 ACCTAGCCAACAAGCATAGGT 59.084 47.619 8.13 8.13 39.73 3.08
171 179 0.101759 CTTTGAGATGGCAATGGGCG 59.898 55.000 0.00 0.00 46.16 6.13
174 182 1.117150 CCCCTTTGAGATGGCAATGG 58.883 55.000 0.00 0.00 40.73 3.16
176 184 2.674420 CATCCCCTTTGAGATGGCAAT 58.326 47.619 0.00 0.00 36.94 3.56
178 186 3.909587 CATCCCCTTTGAGATGGCA 57.090 52.632 0.00 0.00 36.94 4.92
181 189 2.236766 GCATCCATCCCCTTTGAGATG 58.763 52.381 0.00 0.00 39.69 2.90
182 190 1.202855 CGCATCCATCCCCTTTGAGAT 60.203 52.381 0.00 0.00 0.00 2.75
183 191 0.181114 CGCATCCATCCCCTTTGAGA 59.819 55.000 0.00 0.00 0.00 3.27
187 195 2.034124 CAATTCGCATCCATCCCCTTT 58.966 47.619 0.00 0.00 0.00 3.11
189 197 0.552848 ACAATTCGCATCCATCCCCT 59.447 50.000 0.00 0.00 0.00 4.79
190 198 1.402787 AACAATTCGCATCCATCCCC 58.597 50.000 0.00 0.00 0.00 4.81
214 224 8.879342 AATTTCAACAAATTGTATCGGAAACA 57.121 26.923 0.00 0.00 40.16 2.83
215 225 8.432359 GGAATTTCAACAAATTGTATCGGAAAC 58.568 33.333 0.00 0.00 41.47 2.78
219 229 8.028938 AGAAGGAATTTCAACAAATTGTATCGG 58.971 33.333 0.00 0.00 41.47 4.18
220 230 8.970691 AGAAGGAATTTCAACAAATTGTATCG 57.029 30.769 0.00 0.00 41.47 2.92
225 235 7.538678 CGGAGTAGAAGGAATTTCAACAAATTG 59.461 37.037 0.00 0.00 41.47 2.32
231 241 4.828829 TCCGGAGTAGAAGGAATTTCAAC 58.171 43.478 0.00 0.00 38.31 3.18
233 243 5.659525 TGTATCCGGAGTAGAAGGAATTTCA 59.340 40.000 11.34 0.00 38.31 2.69
242 252 4.091549 ACAACCTTGTATCCGGAGTAGAA 58.908 43.478 11.34 6.79 40.16 2.10
244 254 3.700038 AGACAACCTTGTATCCGGAGTAG 59.300 47.826 11.34 4.11 42.43 2.57
257 267 4.910458 ACTAGCATACCAAGACAACCTT 57.090 40.909 0.00 0.00 34.91 3.50
258 268 6.561519 ATTACTAGCATACCAAGACAACCT 57.438 37.500 0.00 0.00 0.00 3.50
259 269 8.904099 ATAATTACTAGCATACCAAGACAACC 57.096 34.615 0.00 0.00 0.00 3.77
289 299 0.912486 GGTCCACTTAGCCCATCAGT 59.088 55.000 0.00 0.00 0.00 3.41
301 311 0.687354 GAGGTGTGTCATGGTCCACT 59.313 55.000 0.00 0.00 32.76 4.00
303 313 1.671166 CGAGGTGTGTCATGGTCCA 59.329 57.895 0.00 0.00 0.00 4.02
306 316 2.347490 GGCGAGGTGTGTCATGGT 59.653 61.111 0.00 0.00 0.00 3.55
310 320 3.311110 GAGGGGCGAGGTGTGTCA 61.311 66.667 0.00 0.00 0.00 3.58
317 327 2.210711 GGATACTGGAGGGGCGAGG 61.211 68.421 0.00 0.00 0.00 4.63
318 328 2.210711 GGGATACTGGAGGGGCGAG 61.211 68.421 0.00 0.00 0.00 5.03
320 330 2.122813 AGGGATACTGGAGGGGCG 60.123 66.667 0.00 0.00 0.00 6.13
321 331 3.568578 CAGGGATACTGGAGGGGC 58.431 66.667 0.00 0.00 43.70 5.80
335 345 2.161808 CGTGTAGGTACAGTCACTCAGG 59.838 54.545 0.00 0.00 36.78 3.86
337 347 1.538512 GCGTGTAGGTACAGTCACTCA 59.461 52.381 0.00 0.00 36.78 3.41
340 350 0.886563 AGGCGTGTAGGTACAGTCAC 59.113 55.000 0.00 0.00 36.78 3.67
344 354 1.132643 GACAGAGGCGTGTAGGTACAG 59.867 57.143 0.00 0.00 36.78 2.74
358 368 6.287107 TCTAAAGCAAAGAAAACGACAGAG 57.713 37.500 0.00 0.00 0.00 3.35
361 371 6.612247 TCATCTAAAGCAAAGAAAACGACA 57.388 33.333 0.00 0.00 0.00 4.35
362 372 8.420189 CAAATCATCTAAAGCAAAGAAAACGAC 58.580 33.333 0.00 0.00 0.00 4.34
363 373 7.594758 CCAAATCATCTAAAGCAAAGAAAACGA 59.405 33.333 0.00 0.00 0.00 3.85
395 408 2.289195 ACGAACGCAATTAGTCCCTCAA 60.289 45.455 0.00 0.00 0.00 3.02
397 410 2.005971 ACGAACGCAATTAGTCCCTC 57.994 50.000 0.00 0.00 0.00 4.30
402 416 7.148540 TGCTTTTCTATTACGAACGCAATTAGT 60.149 33.333 0.00 0.00 31.05 2.24
411 425 7.582352 AGGACTTTTGCTTTTCTATTACGAAC 58.418 34.615 0.00 0.00 0.00 3.95
413 427 7.442969 TGAAGGACTTTTGCTTTTCTATTACGA 59.557 33.333 0.00 0.00 32.64 3.43
426 441 4.578105 CCCTGATCTATGAAGGACTTTTGC 59.422 45.833 0.00 0.00 32.43 3.68
435 450 6.209391 ACAAAAACCAACCCTGATCTATGAAG 59.791 38.462 0.00 0.00 0.00 3.02
441 456 4.141733 CCAAACAAAAACCAACCCTGATCT 60.142 41.667 0.00 0.00 0.00 2.75
446 461 3.198200 GGTACCAAACAAAAACCAACCCT 59.802 43.478 7.15 0.00 0.00 4.34
447 462 3.533547 GGTACCAAACAAAAACCAACCC 58.466 45.455 7.15 0.00 0.00 4.11
473 488 1.809684 AAGTGCTTTTCGGGTAGAGC 58.190 50.000 0.00 0.00 35.74 4.09
475 490 4.964593 ACTTTAAGTGCTTTTCGGGTAGA 58.035 39.130 0.00 0.00 0.00 2.59
476 491 5.684550 AACTTTAAGTGCTTTTCGGGTAG 57.315 39.130 0.00 0.00 0.00 3.18
481 496 5.469084 AGGGACTAACTTTAAGTGCTTTTCG 59.531 40.000 0.00 0.00 36.02 3.46
483 498 5.768662 GGAGGGACTAACTTTAAGTGCTTTT 59.231 40.000 0.00 0.00 41.55 2.27
500 515 8.771766 CGCTTTTATATTAGTTTAAGGAGGGAC 58.228 37.037 0.00 0.00 0.00 4.46
501 516 8.488668 ACGCTTTTATATTAGTTTAAGGAGGGA 58.511 33.333 0.00 0.00 0.00 4.20
552 567 9.095065 CCTTCTGTAAACTAATATAACAGCGTT 57.905 33.333 0.00 0.02 37.94 4.84
553 568 8.472413 TCCTTCTGTAAACTAATATAACAGCGT 58.528 33.333 0.00 0.00 37.94 5.07
554 569 8.867112 TCCTTCTGTAAACTAATATAACAGCG 57.133 34.615 0.00 0.00 37.94 5.18
555 570 9.819267 ACTCCTTCTGTAAACTAATATAACAGC 57.181 33.333 0.00 0.00 37.94 4.40
563 578 8.867097 TCAGTTGTACTCCTTCTGTAAACTAAT 58.133 33.333 0.00 0.00 0.00 1.73
566 581 6.726490 TCAGTTGTACTCCTTCTGTAAACT 57.274 37.500 0.00 0.00 0.00 2.66
567 582 7.656137 TGAATCAGTTGTACTCCTTCTGTAAAC 59.344 37.037 0.00 0.00 0.00 2.01
569 584 7.297936 TGAATCAGTTGTACTCCTTCTGTAA 57.702 36.000 0.00 0.00 0.00 2.41
570 585 6.911250 TGAATCAGTTGTACTCCTTCTGTA 57.089 37.500 0.00 0.00 0.00 2.74
571 586 5.808366 TGAATCAGTTGTACTCCTTCTGT 57.192 39.130 0.00 0.00 0.00 3.41
572 587 6.483307 TGTTTGAATCAGTTGTACTCCTTCTG 59.517 38.462 0.00 0.00 0.00 3.02
574 589 6.861065 TGTTTGAATCAGTTGTACTCCTTC 57.139 37.500 0.00 0.00 0.00 3.46
576 591 5.765182 CCTTGTTTGAATCAGTTGTACTCCT 59.235 40.000 0.00 0.00 0.00 3.69
577 592 5.562890 GCCTTGTTTGAATCAGTTGTACTCC 60.563 44.000 0.00 0.00 0.00 3.85
578 593 5.452777 GCCTTGTTTGAATCAGTTGTACTC 58.547 41.667 0.00 0.00 0.00 2.59
580 595 4.037446 TGGCCTTGTTTGAATCAGTTGTAC 59.963 41.667 3.32 0.00 0.00 2.90
586 690 4.634199 ACATTTGGCCTTGTTTGAATCAG 58.366 39.130 3.32 0.00 0.00 2.90
591 695 3.196469 TGACAACATTTGGCCTTGTTTGA 59.804 39.130 14.17 2.43 38.13 2.69
610 714 6.816640 TGAAGTGTATTTAGCTACCATGTGAC 59.183 38.462 0.00 0.00 0.00 3.67
618 722 5.175859 TGCTGGTGAAGTGTATTTAGCTAC 58.824 41.667 0.00 0.00 0.00 3.58
619 723 5.414789 TGCTGGTGAAGTGTATTTAGCTA 57.585 39.130 0.00 0.00 0.00 3.32
621 725 5.371115 TTTGCTGGTGAAGTGTATTTAGC 57.629 39.130 0.00 0.00 0.00 3.09
623 727 6.701145 TGTTTTGCTGGTGAAGTGTATTTA 57.299 33.333 0.00 0.00 0.00 1.40
624 728 5.590530 TGTTTTGCTGGTGAAGTGTATTT 57.409 34.783 0.00 0.00 0.00 1.40
625 729 5.590530 TTGTTTTGCTGGTGAAGTGTATT 57.409 34.783 0.00 0.00 0.00 1.89
626 730 5.590530 TTTGTTTTGCTGGTGAAGTGTAT 57.409 34.783 0.00 0.00 0.00 2.29
627 731 5.164954 GTTTTGTTTTGCTGGTGAAGTGTA 58.835 37.500 0.00 0.00 0.00 2.90
628 732 3.951775 TTTGTTTTGCTGGTGAAGTGT 57.048 38.095 0.00 0.00 0.00 3.55
629 733 3.060628 CGTTTTGTTTTGCTGGTGAAGTG 59.939 43.478 0.00 0.00 0.00 3.16
630 734 3.249917 CGTTTTGTTTTGCTGGTGAAGT 58.750 40.909 0.00 0.00 0.00 3.01
631 735 3.249917 ACGTTTTGTTTTGCTGGTGAAG 58.750 40.909 0.00 0.00 0.00 3.02
632 736 3.305398 ACGTTTTGTTTTGCTGGTGAA 57.695 38.095 0.00 0.00 0.00 3.18
633 737 4.436242 TTACGTTTTGTTTTGCTGGTGA 57.564 36.364 0.00 0.00 0.00 4.02
634 738 5.710613 ATTTACGTTTTGTTTTGCTGGTG 57.289 34.783 0.00 0.00 0.00 4.17
635 739 6.253942 GTGTATTTACGTTTTGTTTTGCTGGT 59.746 34.615 0.00 0.00 0.00 4.00
636 740 6.474102 AGTGTATTTACGTTTTGTTTTGCTGG 59.526 34.615 0.00 0.00 0.00 4.85
637 741 7.444558 AGTGTATTTACGTTTTGTTTTGCTG 57.555 32.000 0.00 0.00 0.00 4.41
638 742 8.468720 AAAGTGTATTTACGTTTTGTTTTGCT 57.531 26.923 0.00 0.00 0.00 3.91
639 743 8.373992 TGAAAGTGTATTTACGTTTTGTTTTGC 58.626 29.630 0.00 0.00 0.00 3.68
640 744 9.664826 GTGAAAGTGTATTTACGTTTTGTTTTG 57.335 29.630 0.00 0.00 0.00 2.44
641 745 9.408069 TGTGAAAGTGTATTTACGTTTTGTTTT 57.592 25.926 0.00 0.00 0.00 2.43
642 746 8.967552 TGTGAAAGTGTATTTACGTTTTGTTT 57.032 26.923 0.00 0.00 0.00 2.83
643 747 9.228636 GATGTGAAAGTGTATTTACGTTTTGTT 57.771 29.630 0.00 0.00 0.00 2.83
644 748 8.399425 TGATGTGAAAGTGTATTTACGTTTTGT 58.601 29.630 0.00 0.00 0.00 2.83
645 749 8.678510 GTGATGTGAAAGTGTATTTACGTTTTG 58.321 33.333 0.00 0.00 0.00 2.44
646 750 8.399425 TGTGATGTGAAAGTGTATTTACGTTTT 58.601 29.630 0.00 0.00 0.00 2.43
647 751 7.921787 TGTGATGTGAAAGTGTATTTACGTTT 58.078 30.769 0.00 0.00 0.00 3.60
648 752 7.485418 TGTGATGTGAAAGTGTATTTACGTT 57.515 32.000 0.00 0.00 0.00 3.99
649 753 7.439955 TCTTGTGATGTGAAAGTGTATTTACGT 59.560 33.333 0.00 0.00 0.00 3.57
650 754 7.792925 TCTTGTGATGTGAAAGTGTATTTACG 58.207 34.615 0.00 0.00 0.00 3.18
651 755 9.382244 GTTCTTGTGATGTGAAAGTGTATTTAC 57.618 33.333 0.00 0.00 0.00 2.01
683 787 5.456822 GGCGTTTTCATCTTAGCATCAAATC 59.543 40.000 0.00 0.00 0.00 2.17
686 790 3.181511 CGGCGTTTTCATCTTAGCATCAA 60.182 43.478 0.00 0.00 0.00 2.57
701 805 0.464916 GTATCCCATTCCCGGCGTTT 60.465 55.000 6.01 0.00 0.00 3.60
709 813 2.752903 GTGTGTTGGTGTATCCCATTCC 59.247 50.000 0.00 0.00 33.60 3.01
732 836 3.189702 GTGACGGCCAACTTGCTAATTTA 59.810 43.478 2.24 0.00 0.00 1.40
818 923 0.839277 CCATCACCTCACAGCCCATA 59.161 55.000 0.00 0.00 0.00 2.74
966 1095 0.040425 GTGAAATGCGACGGCTTTGT 60.040 50.000 0.00 0.00 40.82 2.83
1053 1182 4.974645 CCTTGGTGGCTATGACCTATTA 57.025 45.455 0.00 0.00 34.26 0.98
1054 1183 3.864789 CCTTGGTGGCTATGACCTATT 57.135 47.619 0.00 0.00 34.26 1.73
1089 1218 1.153269 GCTGGCTGGAGTAAGGAGC 60.153 63.158 0.00 0.00 0.00 4.70
1132 1261 1.814169 GCAAGCTAGGCGGTGGTAC 60.814 63.158 0.00 0.00 0.00 3.34
1133 1262 1.956629 GAGCAAGCTAGGCGGTGGTA 61.957 60.000 0.00 0.00 36.08 3.25
1134 1263 3.316573 GAGCAAGCTAGGCGGTGGT 62.317 63.158 0.00 0.00 36.08 4.16
1135 1264 2.512515 GAGCAAGCTAGGCGGTGG 60.513 66.667 0.00 0.00 36.08 4.61
1136 1265 2.887568 CGAGCAAGCTAGGCGGTG 60.888 66.667 0.00 0.00 36.08 4.94
1156 1285 3.499737 CGTGTCCATTGCCGCTCC 61.500 66.667 0.00 0.00 0.00 4.70
1179 1308 2.383527 CGAGTTCCAGTTGCGCTCC 61.384 63.158 9.73 0.00 0.00 4.70
1278 1407 1.594331 GCGTCTCCTTGAACTTGGTT 58.406 50.000 0.00 0.00 0.00 3.67
1914 2043 0.978907 TAGTTTTGACCCGAGTCCCC 59.021 55.000 0.00 0.00 42.81 4.81
1922 2055 3.017442 GGAGCCAAGATAGTTTTGACCC 58.983 50.000 0.00 0.00 0.00 4.46
1992 2132 1.026182 CATCATGGGTCCACACCGTG 61.026 60.000 0.00 0.00 44.91 4.94
2005 2145 4.283978 TGGCCTTTTATTATGCCCATCATG 59.716 41.667 3.32 0.00 43.35 3.07
2008 2148 3.897505 ACTGGCCTTTTATTATGCCCATC 59.102 43.478 3.32 0.00 43.35 3.51
2011 2151 3.068165 GTCACTGGCCTTTTATTATGCCC 59.932 47.826 3.32 0.00 43.35 5.36
2080 2220 3.559655 CGGCTGTTAATGGATGAATCGAA 59.440 43.478 0.00 0.00 0.00 3.71
2583 2755 8.624776 GCTCATATTTTTGCTGGAAACTAGTAT 58.375 33.333 0.00 0.00 0.00 2.12
2731 2912 2.358984 GCCGGAACCGTTTAGCCA 60.359 61.111 5.05 0.00 37.81 4.75
2957 3170 1.359117 CGACCACCGATATGCGAGT 59.641 57.895 0.00 0.00 44.57 4.18


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

AutoCloner maintained by Alex Coulton.