Multiple sequence alignment - TraesCS1A01G303600

Loading Multiple Alignment...

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 TraesCS1A01G303600 chr1A 100.000 2621 0 0 1 2621 497193770 497191150 0.000000e+00 4841.0
1 TraesCS1A01G303600 chr1A 97.196 107 3 0 2402 2508 252774238 252774132 5.760000e-42 182.0
2 TraesCS1A01G303600 chr1A 86.408 103 14 0 2408 2510 24325440 24325542 2.130000e-21 113.0
3 TraesCS1A01G303600 chr1B 91.433 1856 75 30 456 2249 538165879 538164046 0.000000e+00 2470.0
4 TraesCS1A01G303600 chr1D 90.228 1883 75 39 602 2384 400956964 400955091 0.000000e+00 2357.0
5 TraesCS1A01G303600 chr1D 86.127 519 47 17 90 595 400957508 400957002 1.070000e-148 536.0
6 TraesCS1A01G303600 chr1D 89.922 129 13 0 2386 2514 475488175 475488047 1.610000e-37 167.0
7 TraesCS1A01G303600 chr3D 91.150 113 10 0 2402 2514 301993266 301993154 1.260000e-33 154.0
8 TraesCS1A01G303600 chr3D 81.416 113 19 2 2402 2514 48800465 48800355 9.990000e-15 91.6
9 TraesCS1A01G303600 chr6A 89.423 104 11 0 2406 2509 603364278 603364175 5.890000e-27 132.0
10 TraesCS1A01G303600 chr3A 84.404 109 16 1 2402 2510 41614365 41614472 3.570000e-19 106.0
11 TraesCS1A01G303600 chr6B 84.314 102 16 0 2408 2509 551962895 551962794 1.660000e-17 100.0
12 TraesCS1A01G303600 chr3B 81.513 119 18 4 2402 2519 616891595 616891710 7.720000e-16 95.3
13 TraesCS1A01G303600 chr4D 84.884 86 13 0 1085 1170 102534312 102534227 1.290000e-13 87.9
14 TraesCS1A01G303600 chr4B 82.759 87 15 0 1085 1171 147066773 147066687 7.780000e-11 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G303600 chr1A 497191150 497193770 2620 True 4841.0 4841 100.0000 1 2621 1 chr1A.!!$R2 2620
1 TraesCS1A01G303600 chr1B 538164046 538165879 1833 True 2470.0 2470 91.4330 456 2249 1 chr1B.!!$R1 1793
2 TraesCS1A01G303600 chr1D 400955091 400957508 2417 True 1446.5 2357 88.1775 90 2384 2 chr1D.!!$R2 2294

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
228 250 0.034059 CCCTATGATGCGACACCTCC 59.966 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2071 0.03831 GAAGGGCCTTTGGTGCTAGT 59.962 55.0 21.92 0.0 0.0 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.879197 CCAAAGCCTTCTTCCATTTTCT 57.121 40.909 0.00 0.00 0.00 2.52
22 23 4.563061 CCAAAGCCTTCTTCCATTTTCTG 58.437 43.478 0.00 0.00 0.00 3.02
38 39 7.967890 CATTTTCTGGAAAATTAGCCTTTGT 57.032 32.000 15.86 0.00 45.67 2.83
39 40 8.021955 CATTTTCTGGAAAATTAGCCTTTGTC 57.978 34.615 15.86 0.00 45.67 3.18
40 41 5.722021 TTCTGGAAAATTAGCCTTTGTCC 57.278 39.130 0.00 0.00 0.00 4.02
41 42 4.735369 TCTGGAAAATTAGCCTTTGTCCA 58.265 39.130 3.50 3.50 0.00 4.02
42 43 5.144100 TCTGGAAAATTAGCCTTTGTCCAA 58.856 37.500 4.78 0.00 0.00 3.53
43 44 5.600484 TCTGGAAAATTAGCCTTTGTCCAAA 59.400 36.000 4.78 0.00 0.00 3.28
44 45 5.852827 TGGAAAATTAGCCTTTGTCCAAAG 58.147 37.500 11.89 11.89 45.47 2.77
45 46 4.690748 GGAAAATTAGCCTTTGTCCAAAGC 59.309 41.667 13.13 9.30 44.76 3.51
46 47 4.953940 AAATTAGCCTTTGTCCAAAGCA 57.046 36.364 13.13 0.00 44.76 3.91
47 48 4.953940 AATTAGCCTTTGTCCAAAGCAA 57.046 36.364 13.13 7.79 44.76 3.91
48 49 4.525912 ATTAGCCTTTGTCCAAAGCAAG 57.474 40.909 13.13 3.00 44.76 4.01
49 50 2.071778 AGCCTTTGTCCAAAGCAAGA 57.928 45.000 13.13 0.00 44.76 3.02
50 51 1.959282 AGCCTTTGTCCAAAGCAAGAG 59.041 47.619 13.13 2.38 44.76 2.85
51 52 1.683385 GCCTTTGTCCAAAGCAAGAGT 59.317 47.619 13.13 0.00 44.76 3.24
52 53 2.101415 GCCTTTGTCCAAAGCAAGAGTT 59.899 45.455 13.13 0.00 44.76 3.01
53 54 3.796844 GCCTTTGTCCAAAGCAAGAGTTC 60.797 47.826 13.13 0.00 44.76 3.01
54 55 3.633986 CCTTTGTCCAAAGCAAGAGTTCT 59.366 43.478 13.13 0.00 44.76 3.01
55 56 4.498682 CCTTTGTCCAAAGCAAGAGTTCTG 60.499 45.833 13.13 0.00 44.76 3.02
56 57 3.281727 TGTCCAAAGCAAGAGTTCTGT 57.718 42.857 0.00 0.00 0.00 3.41
57 58 3.620488 TGTCCAAAGCAAGAGTTCTGTT 58.380 40.909 0.00 0.00 0.00 3.16
58 59 3.378112 TGTCCAAAGCAAGAGTTCTGTTG 59.622 43.478 5.51 5.51 0.00 3.33
65 66 4.298744 GCAAGAGTTCTGTTGCTTTTCT 57.701 40.909 21.70 0.00 44.68 2.52
66 67 4.676546 GCAAGAGTTCTGTTGCTTTTCTT 58.323 39.130 21.70 0.00 44.68 2.52
67 68 5.105063 GCAAGAGTTCTGTTGCTTTTCTTT 58.895 37.500 21.70 0.00 44.68 2.52
68 69 5.230936 GCAAGAGTTCTGTTGCTTTTCTTTC 59.769 40.000 21.70 0.00 44.68 2.62
69 70 6.558909 CAAGAGTTCTGTTGCTTTTCTTTCT 58.441 36.000 0.00 0.00 0.00 2.52
70 71 7.679638 GCAAGAGTTCTGTTGCTTTTCTTTCTA 60.680 37.037 21.70 0.00 44.68 2.10
71 72 7.489574 AGAGTTCTGTTGCTTTTCTTTCTAG 57.510 36.000 0.00 0.00 0.00 2.43
72 73 7.275920 AGAGTTCTGTTGCTTTTCTTTCTAGA 58.724 34.615 0.00 0.00 0.00 2.43
73 74 7.770897 AGAGTTCTGTTGCTTTTCTTTCTAGAA 59.229 33.333 0.00 0.00 38.61 2.10
74 75 8.281212 AGTTCTGTTGCTTTTCTTTCTAGAAA 57.719 30.769 16.85 16.85 46.07 2.52
128 129 8.747538 AAAAAGAGGTTGAAACACAGTAGTAT 57.252 30.769 0.00 0.00 0.00 2.12
140 141 9.922305 GAAACACAGTAGTATAAGATTTGATGC 57.078 33.333 0.00 0.00 0.00 3.91
156 157 4.806640 TGATGCTGTTCTACTCACATGA 57.193 40.909 0.00 0.00 0.00 3.07
185 186 2.032799 TCGTTTTCTCGCAAACATGCTT 59.967 40.909 0.00 0.00 36.58 3.91
195 197 5.105752 TCGCAAACATGCTTAAAACTGTTT 58.894 33.333 0.00 0.00 41.22 2.83
216 238 1.048601 GTGGATCGAAGGCCCTATGA 58.951 55.000 0.00 0.00 0.00 2.15
219 241 1.677217 GGATCGAAGGCCCTATGATGC 60.677 57.143 0.00 0.00 0.00 3.91
224 246 0.179045 AAGGCCCTATGATGCGACAC 60.179 55.000 0.00 0.00 0.00 3.67
225 247 1.598130 GGCCCTATGATGCGACACC 60.598 63.158 0.00 0.00 0.00 4.16
226 248 1.447643 GCCCTATGATGCGACACCT 59.552 57.895 0.00 0.00 0.00 4.00
227 249 0.601311 GCCCTATGATGCGACACCTC 60.601 60.000 0.00 0.00 0.00 3.85
228 250 0.034059 CCCTATGATGCGACACCTCC 59.966 60.000 0.00 0.00 0.00 4.30
229 251 1.043816 CCTATGATGCGACACCTCCT 58.956 55.000 0.00 0.00 0.00 3.69
230 252 1.000283 CCTATGATGCGACACCTCCTC 60.000 57.143 0.00 0.00 0.00 3.71
231 253 1.000283 CTATGATGCGACACCTCCTCC 60.000 57.143 0.00 0.00 0.00 4.30
232 254 0.689080 ATGATGCGACACCTCCTCCT 60.689 55.000 0.00 0.00 0.00 3.69
240 262 2.192263 GACACCTCCTCCTCCTCATTT 58.808 52.381 0.00 0.00 0.00 2.32
260 282 5.843673 TTTGTCGCATCTCTATCTTCTCT 57.156 39.130 0.00 0.00 0.00 3.10
264 286 5.358160 TGTCGCATCTCTATCTTCTCTTTCA 59.642 40.000 0.00 0.00 0.00 2.69
269 291 7.274033 CGCATCTCTATCTTCTCTTTCATCATC 59.726 40.741 0.00 0.00 0.00 2.92
287 309 2.971598 CGCACAATCTCCACCCCCT 61.972 63.158 0.00 0.00 0.00 4.79
289 311 0.681243 GCACAATCTCCACCCCCTTC 60.681 60.000 0.00 0.00 0.00 3.46
292 314 1.616628 AATCTCCACCCCCTTCGCT 60.617 57.895 0.00 0.00 0.00 4.93
308 330 2.985456 CTGGCACCACTCCTCCTC 59.015 66.667 0.00 0.00 0.00 3.71
313 335 1.893919 GCACCACTCCTCCTCTGTCC 61.894 65.000 0.00 0.00 0.00 4.02
329 351 2.107141 CCCCGTCATCGCTTCTCC 59.893 66.667 0.00 0.00 35.54 3.71
356 378 6.080406 CACTTCCTTTAACTTTCTCGCAATC 58.920 40.000 0.00 0.00 0.00 2.67
392 414 3.550678 GCGAATTAGCACACACTACCTAC 59.449 47.826 5.59 0.00 37.05 3.18
407 429 8.709646 CACACTACCTACAATGACTAGAAAAAC 58.290 37.037 0.00 0.00 0.00 2.43
409 431 7.063074 CACTACCTACAATGACTAGAAAAACCG 59.937 40.741 0.00 0.00 0.00 4.44
433 455 7.042791 CCGCAAGAAAACAAACATAATTTCAGT 60.043 33.333 0.00 0.00 43.02 3.41
447 469 9.043548 ACATAATTTCAGTACCACTTACCTACT 57.956 33.333 0.00 0.00 0.00 2.57
476 498 4.491676 GTGCGACCATTCTAAGTCTAACA 58.508 43.478 0.00 0.00 0.00 2.41
587 609 3.506067 CCACTAAAAATCTCACCCCACAC 59.494 47.826 0.00 0.00 0.00 3.82
595 617 4.657814 ATCTCACCCCACACTAATTTGT 57.342 40.909 0.00 0.00 0.00 2.83
596 618 4.447138 TCTCACCCCACACTAATTTGTT 57.553 40.909 0.00 0.00 0.00 2.83
597 619 4.394729 TCTCACCCCACACTAATTTGTTC 58.605 43.478 0.00 0.00 0.00 3.18
599 621 2.227865 CACCCCACACTAATTTGTTCCG 59.772 50.000 0.00 0.00 0.00 4.30
600 622 2.106857 ACCCCACACTAATTTGTTCCGA 59.893 45.455 0.00 0.00 0.00 4.55
601 623 3.150767 CCCCACACTAATTTGTTCCGAA 58.849 45.455 0.00 0.00 0.00 4.30
602 624 3.190535 CCCCACACTAATTTGTTCCGAAG 59.809 47.826 0.00 0.00 0.00 3.79
626 681 3.486383 AGTCACAAGTAACCCACCAATG 58.514 45.455 0.00 0.00 0.00 2.82
627 682 2.556622 GTCACAAGTAACCCACCAATGG 59.443 50.000 0.00 0.00 46.81 3.16
662 717 1.815003 CAAAGTGTGGCCCTCTGATTC 59.185 52.381 0.00 0.00 0.00 2.52
704 759 7.173907 CACAAGTGACTCACTAATCTTGGATTT 59.826 37.037 12.22 0.00 44.62 2.17
731 786 1.561076 AGTGGCATGGCACTATCAAGA 59.439 47.619 43.43 9.59 0.00 3.02
735 790 3.216800 GGCATGGCACTATCAAGAATCA 58.783 45.455 15.47 0.00 0.00 2.57
738 793 4.577693 GCATGGCACTATCAAGAATCAAGA 59.422 41.667 0.00 0.00 0.00 3.02
786 841 2.557059 TACACGTGAGCGCCATGAGG 62.557 60.000 25.01 14.82 42.83 3.86
880 935 2.932855 TACCACCGTGACCAAATCAA 57.067 45.000 0.00 0.00 39.72 2.57
893 948 4.886579 ACCAAATCAAACAAGCTCCATTC 58.113 39.130 0.00 0.00 0.00 2.67
922 977 0.613853 TCGTCTCCACCGATCCCTTT 60.614 55.000 0.00 0.00 0.00 3.11
927 982 1.139058 CTCCACCGATCCCTTTGGTAG 59.861 57.143 0.00 0.00 40.46 3.18
990 1078 7.833786 TCCTCGATCTATCTAGTCTAGTCTTC 58.166 42.308 6.77 0.00 0.00 2.87
1021 1109 3.047877 CGAAGGTGCACCCGAACC 61.048 66.667 32.29 15.20 38.74 3.62
1630 1727 2.103143 CCTCGTAGCGCCACTGAG 59.897 66.667 16.26 16.26 0.00 3.35
1638 1735 2.262915 CGCCACTGAGACTGGGTC 59.737 66.667 0.00 0.00 0.00 4.46
1649 1746 4.148825 CTGGGTCGCCTCCTTCGG 62.149 72.222 0.00 0.00 0.00 4.30
1662 1767 1.298859 CCTTCGGTTTGCCTCCTTCG 61.299 60.000 0.00 0.00 0.00 3.79
1684 1789 0.682292 TTCCGAAATTGTTTGGGCCC 59.318 50.000 17.59 17.59 38.69 5.80
1708 1813 1.975363 GCAGAACAGCTCCGATGTGC 61.975 60.000 0.00 0.00 0.00 4.57
1824 1930 9.308318 GTGTATGGTTTTGTTCATTTTTACTGT 57.692 29.630 0.00 0.00 0.00 3.55
1944 2070 5.048507 GTCTACGTTCTCTCCAACTTTTGT 58.951 41.667 0.00 0.00 0.00 2.83
1945 2071 6.183360 TGTCTACGTTCTCTCCAACTTTTGTA 60.183 38.462 0.00 0.00 0.00 2.41
1946 2072 6.143598 GTCTACGTTCTCTCCAACTTTTGTAC 59.856 42.308 0.00 0.00 0.00 2.90
1947 2073 5.019785 ACGTTCTCTCCAACTTTTGTACT 57.980 39.130 0.00 0.00 0.00 2.73
1961 2087 0.326927 TGTACTAGCACCAAAGGCCC 59.673 55.000 0.00 0.00 0.00 5.80
2011 2138 6.201806 CGATGTAGAATCTGAAATCTGAACCC 59.798 42.308 0.00 0.00 0.00 4.11
2076 2228 3.358076 CTTCCTCGGTCGACCAGCC 62.358 68.421 32.80 7.61 35.14 4.85
2095 2247 2.584694 GCGCTCACTCCAGCTAGC 60.585 66.667 6.62 6.62 37.25 3.42
2098 2250 1.593787 GCTCACTCCAGCTAGCACA 59.406 57.895 18.83 0.00 36.38 4.57
2102 2254 2.095461 TCACTCCAGCTAGCACAGTAG 58.905 52.381 18.83 9.04 0.00 2.57
2137 2292 0.377203 GATCCGCGTTGAATTCCCAC 59.623 55.000 4.92 0.00 0.00 4.61
2215 2370 3.057174 CCATAGGCCAGTAAGATCGACTC 60.057 52.174 5.01 0.00 0.00 3.36
2224 2379 5.117745 CCAGTAAGATCGACTCGCATTATTG 59.882 44.000 0.73 0.90 0.00 1.90
2228 2384 6.422776 AAGATCGACTCGCATTATTGTTTT 57.577 33.333 0.00 0.00 0.00 2.43
2230 2386 6.478588 AGATCGACTCGCATTATTGTTTTTC 58.521 36.000 0.00 0.00 0.00 2.29
2249 2405 6.907206 TTTTCTGAAACAAGGCAAAAGATG 57.093 33.333 1.58 0.00 0.00 2.90
2280 2436 6.536224 CCAGCAATGAAAAATATTTCCTGTCC 59.464 38.462 0.10 0.00 43.54 4.02
2306 2462 5.528870 AGAAAACTTATTTGAAACCAGCCG 58.471 37.500 0.00 0.00 0.00 5.52
2322 2478 1.165270 GCCGTGGCTACAAAATGACT 58.835 50.000 2.98 0.00 38.26 3.41
2387 2545 7.897575 AATGAAGATTGAAGATACTATCGCC 57.102 36.000 0.00 0.00 0.00 5.54
2388 2546 5.784177 TGAAGATTGAAGATACTATCGCCC 58.216 41.667 0.00 0.00 0.00 6.13
2389 2547 5.540337 TGAAGATTGAAGATACTATCGCCCT 59.460 40.000 0.00 0.00 0.00 5.19
2390 2548 5.398603 AGATTGAAGATACTATCGCCCTG 57.601 43.478 0.00 0.00 0.00 4.45
2391 2549 4.835615 AGATTGAAGATACTATCGCCCTGT 59.164 41.667 0.00 0.00 0.00 4.00
2392 2550 5.305644 AGATTGAAGATACTATCGCCCTGTT 59.694 40.000 0.00 0.00 0.00 3.16
2393 2551 5.353394 TTGAAGATACTATCGCCCTGTTT 57.647 39.130 0.00 0.00 0.00 2.83
2394 2552 4.693283 TGAAGATACTATCGCCCTGTTTG 58.307 43.478 0.00 0.00 0.00 2.93
2395 2553 3.753294 AGATACTATCGCCCTGTTTGG 57.247 47.619 0.00 0.00 0.00 3.28
2396 2554 3.305720 AGATACTATCGCCCTGTTTGGA 58.694 45.455 0.00 0.00 38.35 3.53
2397 2555 3.709653 AGATACTATCGCCCTGTTTGGAA 59.290 43.478 0.00 0.00 38.35 3.53
2398 2556 4.348168 AGATACTATCGCCCTGTTTGGAAT 59.652 41.667 0.00 0.00 38.35 3.01
2399 2557 2.919228 ACTATCGCCCTGTTTGGAATC 58.081 47.619 0.00 0.00 38.35 2.52
2400 2558 2.222027 CTATCGCCCTGTTTGGAATCC 58.778 52.381 0.00 0.00 38.35 3.01
2401 2559 0.395724 ATCGCCCTGTTTGGAATCCC 60.396 55.000 0.00 0.00 38.35 3.85
2402 2560 1.000896 CGCCCTGTTTGGAATCCCT 60.001 57.895 0.00 0.00 38.35 4.20
2403 2561 1.032114 CGCCCTGTTTGGAATCCCTC 61.032 60.000 0.00 0.00 38.35 4.30
2404 2562 0.684479 GCCCTGTTTGGAATCCCTCC 60.684 60.000 0.00 0.00 45.64 4.30
2411 2569 2.506472 GGAATCCCTCCGTGGAGC 59.494 66.667 10.53 0.00 40.69 4.70
2412 2570 2.066999 GGAATCCCTCCGTGGAGCT 61.067 63.158 10.53 0.00 40.69 4.09
2413 2571 1.144936 GAATCCCTCCGTGGAGCTG 59.855 63.158 10.53 4.08 40.69 4.24
2414 2572 1.613630 AATCCCTCCGTGGAGCTGT 60.614 57.895 10.53 0.00 40.69 4.40
2415 2573 0.325296 AATCCCTCCGTGGAGCTGTA 60.325 55.000 10.53 0.00 40.69 2.74
2416 2574 0.757188 ATCCCTCCGTGGAGCTGTAG 60.757 60.000 10.53 0.00 40.69 2.74
2417 2575 1.379977 CCCTCCGTGGAGCTGTAGA 60.380 63.158 10.53 0.00 40.69 2.59
2418 2576 1.388065 CCCTCCGTGGAGCTGTAGAG 61.388 65.000 10.53 0.00 40.69 2.43
2419 2577 1.435515 CTCCGTGGAGCTGTAGAGC 59.564 63.158 3.08 3.08 46.64 4.09
2430 2588 2.010497 GCTGTAGAGCTGGGTTTTAGC 58.990 52.381 4.27 0.00 42.52 3.09
2431 2589 2.633488 CTGTAGAGCTGGGTTTTAGCC 58.367 52.381 0.00 0.00 42.07 3.93
2432 2590 1.982226 TGTAGAGCTGGGTTTTAGCCA 59.018 47.619 0.00 0.00 44.64 4.75
2433 2591 2.290071 TGTAGAGCTGGGTTTTAGCCAC 60.290 50.000 0.00 0.00 41.50 5.01
2434 2592 1.068121 AGAGCTGGGTTTTAGCCACT 58.932 50.000 0.00 0.00 41.50 4.00
2435 2593 1.003696 AGAGCTGGGTTTTAGCCACTC 59.996 52.381 14.24 14.24 41.50 3.51
2436 2594 0.038310 AGCTGGGTTTTAGCCACTCC 59.962 55.000 0.00 0.00 41.50 3.85
2437 2595 0.038310 GCTGGGTTTTAGCCACTCCT 59.962 55.000 0.00 0.00 41.50 3.69
2438 2596 1.547901 GCTGGGTTTTAGCCACTCCTT 60.548 52.381 0.00 0.00 41.50 3.36
2439 2597 2.290705 GCTGGGTTTTAGCCACTCCTTA 60.291 50.000 0.00 0.00 41.50 2.69
2440 2598 3.812882 GCTGGGTTTTAGCCACTCCTTAA 60.813 47.826 0.00 0.00 41.50 1.85
2441 2599 4.403734 CTGGGTTTTAGCCACTCCTTAAA 58.596 43.478 0.00 0.00 41.50 1.52
2442 2600 4.805744 TGGGTTTTAGCCACTCCTTAAAA 58.194 39.130 0.00 0.00 41.50 1.52
2443 2601 5.209659 TGGGTTTTAGCCACTCCTTAAAAA 58.790 37.500 0.00 0.00 41.50 1.94
2444 2602 5.841783 TGGGTTTTAGCCACTCCTTAAAAAT 59.158 36.000 0.00 0.00 41.50 1.82
2445 2603 6.327887 TGGGTTTTAGCCACTCCTTAAAAATT 59.672 34.615 0.00 0.00 41.50 1.82
2446 2604 7.509659 TGGGTTTTAGCCACTCCTTAAAAATTA 59.490 33.333 0.00 0.00 41.50 1.40
2447 2605 8.033038 GGGTTTTAGCCACTCCTTAAAAATTAG 58.967 37.037 0.00 0.00 35.40 1.73
2448 2606 7.544566 GGTTTTAGCCACTCCTTAAAAATTAGC 59.455 37.037 0.00 0.00 0.00 3.09
2449 2607 8.304596 GTTTTAGCCACTCCTTAAAAATTAGCT 58.695 33.333 0.00 0.00 0.00 3.32
2450 2608 5.904362 AGCCACTCCTTAAAAATTAGCTG 57.096 39.130 0.00 0.00 0.00 4.24
2451 2609 4.706962 AGCCACTCCTTAAAAATTAGCTGG 59.293 41.667 0.00 0.00 0.00 4.85
2452 2610 4.705023 GCCACTCCTTAAAAATTAGCTGGA 59.295 41.667 0.00 0.00 0.00 3.86
2453 2611 5.163612 GCCACTCCTTAAAAATTAGCTGGAG 60.164 44.000 8.90 8.90 43.56 3.86
2454 2612 6.180472 CCACTCCTTAAAAATTAGCTGGAGA 58.820 40.000 15.64 0.00 41.31 3.71
2455 2613 6.094186 CCACTCCTTAAAAATTAGCTGGAGAC 59.906 42.308 15.64 0.00 41.31 3.36
2456 2614 6.881602 CACTCCTTAAAAATTAGCTGGAGACT 59.118 38.462 15.64 0.00 41.31 3.24
2457 2615 6.881602 ACTCCTTAAAAATTAGCTGGAGACTG 59.118 38.462 15.64 0.00 41.31 3.51
2458 2616 6.180472 TCCTTAAAAATTAGCTGGAGACTGG 58.820 40.000 0.00 0.00 0.00 4.00
2459 2617 5.946377 CCTTAAAAATTAGCTGGAGACTGGT 59.054 40.000 0.00 0.00 42.88 4.00
2460 2618 6.094186 CCTTAAAAATTAGCTGGAGACTGGTC 59.906 42.308 0.00 0.00 40.64 4.02
2461 2619 3.636153 AAATTAGCTGGAGACTGGTCC 57.364 47.619 0.00 0.00 40.64 4.46
2462 2620 1.115467 ATTAGCTGGAGACTGGTCCG 58.885 55.000 0.00 0.00 39.81 4.79
2463 2621 1.605058 TTAGCTGGAGACTGGTCCGC 61.605 60.000 0.00 0.00 39.81 5.54
2464 2622 2.500815 TAGCTGGAGACTGGTCCGCT 62.501 60.000 15.92 15.92 43.88 5.52
2465 2623 2.888863 CTGGAGACTGGTCCGCTC 59.111 66.667 0.00 0.00 39.81 5.03
2466 2624 2.680352 TGGAGACTGGTCCGCTCC 60.680 66.667 15.05 15.05 46.60 4.70
2467 2625 3.827898 GGAGACTGGTCCGCTCCG 61.828 72.222 8.89 0.00 38.88 4.63
2480 2638 2.989639 CTCCGGGAGCATTGTCCA 59.010 61.111 11.83 0.00 38.52 4.02
2481 2639 1.153289 CTCCGGGAGCATTGTCCAG 60.153 63.158 11.83 4.01 38.52 3.86
2482 2640 2.124570 CCGGGAGCATTGTCCAGG 60.125 66.667 0.00 8.99 44.35 4.45
2483 2641 2.124570 CGGGAGCATTGTCCAGGG 60.125 66.667 7.34 0.00 38.52 4.45
2484 2642 2.669133 CGGGAGCATTGTCCAGGGA 61.669 63.158 7.34 0.00 38.52 4.20
2485 2643 1.225704 GGGAGCATTGTCCAGGGAG 59.774 63.158 7.34 0.00 38.52 4.30
2486 2644 1.452833 GGAGCATTGTCCAGGGAGC 60.453 63.158 0.00 0.00 36.51 4.70
2487 2645 1.817099 GAGCATTGTCCAGGGAGCG 60.817 63.158 0.00 0.00 0.00 5.03
2488 2646 2.825836 GCATTGTCCAGGGAGCGG 60.826 66.667 0.00 0.00 0.00 5.52
2489 2647 2.989639 CATTGTCCAGGGAGCGGA 59.010 61.111 0.00 0.00 0.00 5.54
2490 2648 1.153289 CATTGTCCAGGGAGCGGAG 60.153 63.158 0.00 0.00 31.65 4.63
2491 2649 1.306141 ATTGTCCAGGGAGCGGAGA 60.306 57.895 0.00 0.00 31.65 3.71
2492 2650 1.333636 ATTGTCCAGGGAGCGGAGAG 61.334 60.000 0.00 0.00 31.65 3.20
2493 2651 3.151022 GTCCAGGGAGCGGAGAGG 61.151 72.222 0.00 0.00 31.65 3.69
2494 2652 3.347590 TCCAGGGAGCGGAGAGGA 61.348 66.667 0.00 0.00 0.00 3.71
2495 2653 2.837291 CCAGGGAGCGGAGAGGAG 60.837 72.222 0.00 0.00 0.00 3.69
2496 2654 3.535962 CAGGGAGCGGAGAGGAGC 61.536 72.222 0.00 0.00 0.00 4.70
2497 2655 4.851214 AGGGAGCGGAGAGGAGCC 62.851 72.222 0.00 0.00 0.00 4.70
2504 2662 4.856607 GGAGAGGAGCCGAACGCG 62.857 72.222 3.53 3.53 44.76 6.01
2518 2676 3.961182 CGAACGCGGCCTATATATATGT 58.039 45.455 12.47 0.00 0.00 2.29
2519 2677 5.099484 CGAACGCGGCCTATATATATGTA 57.901 43.478 12.47 0.00 0.00 2.29
2520 2678 5.696822 CGAACGCGGCCTATATATATGTAT 58.303 41.667 12.47 0.00 0.00 2.29
2521 2679 5.567915 CGAACGCGGCCTATATATATGTATG 59.432 44.000 12.47 0.00 0.00 2.39
2522 2680 5.386958 ACGCGGCCTATATATATGTATGG 57.613 43.478 12.47 0.00 0.00 2.74
2523 2681 5.074804 ACGCGGCCTATATATATGTATGGA 58.925 41.667 12.47 0.00 0.00 3.41
2524 2682 5.715279 ACGCGGCCTATATATATGTATGGAT 59.285 40.000 12.47 0.00 0.00 3.41
2525 2683 6.210784 ACGCGGCCTATATATATGTATGGATT 59.789 38.462 12.47 0.00 0.00 3.01
2526 2684 7.395206 ACGCGGCCTATATATATGTATGGATTA 59.605 37.037 12.47 0.00 0.00 1.75
2527 2685 8.414003 CGCGGCCTATATATATGTATGGATTAT 58.586 37.037 0.00 0.00 0.00 1.28
2570 2728 6.595772 CTGTAAGATAACAGCCTCACAATC 57.404 41.667 0.00 0.00 40.40 2.67
2571 2729 6.048732 TGTAAGATAACAGCCTCACAATCA 57.951 37.500 0.00 0.00 0.00 2.57
2572 2730 6.472016 TGTAAGATAACAGCCTCACAATCAA 58.528 36.000 0.00 0.00 0.00 2.57
2573 2731 6.595326 TGTAAGATAACAGCCTCACAATCAAG 59.405 38.462 0.00 0.00 0.00 3.02
2574 2732 5.171339 AGATAACAGCCTCACAATCAAGT 57.829 39.130 0.00 0.00 0.00 3.16
2575 2733 6.299805 AGATAACAGCCTCACAATCAAGTA 57.700 37.500 0.00 0.00 0.00 2.24
2576 2734 6.893583 AGATAACAGCCTCACAATCAAGTAT 58.106 36.000 0.00 0.00 0.00 2.12
2577 2735 7.341805 AGATAACAGCCTCACAATCAAGTATT 58.658 34.615 0.00 0.00 0.00 1.89
2578 2736 8.486210 AGATAACAGCCTCACAATCAAGTATTA 58.514 33.333 0.00 0.00 0.00 0.98
2579 2737 9.109393 GATAACAGCCTCACAATCAAGTATTAA 57.891 33.333 0.00 0.00 0.00 1.40
2580 2738 7.759489 AACAGCCTCACAATCAAGTATTAAA 57.241 32.000 0.00 0.00 0.00 1.52
2581 2739 7.759489 ACAGCCTCACAATCAAGTATTAAAA 57.241 32.000 0.00 0.00 0.00 1.52
2582 2740 8.353423 ACAGCCTCACAATCAAGTATTAAAAT 57.647 30.769 0.00 0.00 0.00 1.82
2583 2741 9.461312 ACAGCCTCACAATCAAGTATTAAAATA 57.539 29.630 0.00 0.00 0.00 1.40
2603 2761 8.617290 AAAATATCAAACGGAGTACAAGAAGT 57.383 30.769 0.00 0.00 45.00 3.01
2604 2762 7.596749 AATATCAAACGGAGTACAAGAAGTG 57.403 36.000 0.00 0.00 45.00 3.16
2605 2763 4.395959 TCAAACGGAGTACAAGAAGTGT 57.604 40.909 0.00 0.00 45.00 3.55
2606 2764 4.365723 TCAAACGGAGTACAAGAAGTGTC 58.634 43.478 0.00 0.00 45.00 3.67
2607 2765 3.382048 AACGGAGTACAAGAAGTGTCC 57.618 47.619 0.00 0.00 45.00 4.02
2608 2766 1.978542 CGGAGTACAAGAAGTGTCCG 58.021 55.000 0.00 0.00 45.66 4.79
2609 2767 1.711206 GGAGTACAAGAAGTGTCCGC 58.289 55.000 0.00 0.00 41.98 5.54
2610 2768 1.000506 GGAGTACAAGAAGTGTCCGCA 59.999 52.381 0.00 0.00 41.98 5.69
2611 2769 2.353803 GGAGTACAAGAAGTGTCCGCAT 60.354 50.000 0.00 0.00 41.98 4.73
2612 2770 2.668457 GAGTACAAGAAGTGTCCGCATG 59.332 50.000 0.00 0.00 41.98 4.06
2613 2771 2.037251 AGTACAAGAAGTGTCCGCATGT 59.963 45.455 0.00 0.00 41.98 3.21
2614 2772 2.831685 ACAAGAAGTGTCCGCATGTA 57.168 45.000 0.00 0.00 34.38 2.29
2615 2773 2.413837 ACAAGAAGTGTCCGCATGTAC 58.586 47.619 0.00 0.00 34.38 2.90
2616 2774 2.224185 ACAAGAAGTGTCCGCATGTACA 60.224 45.455 0.00 0.00 34.38 2.90
2617 2775 2.805671 CAAGAAGTGTCCGCATGTACAA 59.194 45.455 0.00 0.00 0.00 2.41
2618 2776 3.120321 AGAAGTGTCCGCATGTACAAA 57.880 42.857 0.00 0.00 0.00 2.83
2619 2777 2.806244 AGAAGTGTCCGCATGTACAAAC 59.194 45.455 0.00 0.00 0.00 2.93
2620 2778 2.248280 AGTGTCCGCATGTACAAACA 57.752 45.000 0.00 0.00 40.69 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.563061 CAGAAAATGGAAGAAGGCTTTGG 58.437 43.478 0.00 0.00 33.61 3.28
14 15 7.118245 GGACAAAGGCTAATTTTCCAGAAAATG 59.882 37.037 16.83 8.43 46.76 2.32
16 17 6.098982 TGGACAAAGGCTAATTTTCCAGAAAA 59.901 34.615 7.94 7.94 43.48 2.29
17 18 5.600484 TGGACAAAGGCTAATTTTCCAGAAA 59.400 36.000 3.27 0.00 31.57 2.52
18 19 5.144100 TGGACAAAGGCTAATTTTCCAGAA 58.856 37.500 3.27 0.00 31.57 3.02
19 20 4.735369 TGGACAAAGGCTAATTTTCCAGA 58.265 39.130 3.27 0.00 31.57 3.86
20 21 5.467035 TTGGACAAAGGCTAATTTTCCAG 57.533 39.130 6.85 0.00 34.18 3.86
21 22 5.741673 GCTTTGGACAAAGGCTAATTTTCCA 60.742 40.000 22.14 3.27 45.85 3.53
22 23 4.690748 GCTTTGGACAAAGGCTAATTTTCC 59.309 41.667 22.14 0.00 45.85 3.13
23 24 5.296748 TGCTTTGGACAAAGGCTAATTTTC 58.703 37.500 22.14 6.62 45.85 2.29
24 25 5.289083 TGCTTTGGACAAAGGCTAATTTT 57.711 34.783 22.14 0.00 45.85 1.82
25 26 4.953940 TGCTTTGGACAAAGGCTAATTT 57.046 36.364 22.14 0.00 45.85 1.82
26 27 4.588528 TCTTGCTTTGGACAAAGGCTAATT 59.411 37.500 22.14 0.00 45.85 1.40
27 28 4.151883 TCTTGCTTTGGACAAAGGCTAAT 58.848 39.130 22.14 0.00 45.85 1.73
28 29 3.561143 TCTTGCTTTGGACAAAGGCTAA 58.439 40.909 22.14 11.99 45.85 3.09
29 30 3.149196 CTCTTGCTTTGGACAAAGGCTA 58.851 45.455 22.14 12.38 45.85 3.93
30 31 1.959282 CTCTTGCTTTGGACAAAGGCT 59.041 47.619 22.14 0.00 45.85 4.58
31 32 1.683385 ACTCTTGCTTTGGACAAAGGC 59.317 47.619 22.14 15.75 45.85 4.35
32 33 3.633986 AGAACTCTTGCTTTGGACAAAGG 59.366 43.478 22.14 10.45 45.85 3.11
34 35 4.016444 ACAGAACTCTTGCTTTGGACAAA 58.984 39.130 0.00 0.00 0.00 2.83
35 36 3.620488 ACAGAACTCTTGCTTTGGACAA 58.380 40.909 0.00 0.00 0.00 3.18
36 37 3.281727 ACAGAACTCTTGCTTTGGACA 57.718 42.857 0.00 0.00 0.00 4.02
37 38 3.793465 GCAACAGAACTCTTGCTTTGGAC 60.793 47.826 7.37 0.00 39.79 4.02
38 39 2.358898 GCAACAGAACTCTTGCTTTGGA 59.641 45.455 7.37 0.00 39.79 3.53
39 40 2.735823 GCAACAGAACTCTTGCTTTGG 58.264 47.619 7.37 0.00 39.79 3.28
44 45 4.298744 AGAAAAGCAACAGAACTCTTGC 57.701 40.909 6.68 6.68 42.67 4.01
45 46 6.558909 AGAAAGAAAAGCAACAGAACTCTTG 58.441 36.000 0.00 0.00 0.00 3.02
46 47 6.765915 AGAAAGAAAAGCAACAGAACTCTT 57.234 33.333 0.00 0.00 0.00 2.85
47 48 7.275920 TCTAGAAAGAAAAGCAACAGAACTCT 58.724 34.615 0.00 0.00 0.00 3.24
48 49 7.484035 TCTAGAAAGAAAAGCAACAGAACTC 57.516 36.000 0.00 0.00 0.00 3.01
49 50 7.865706 TTCTAGAAAGAAAAGCAACAGAACT 57.134 32.000 1.68 0.00 38.81 3.01
107 108 8.418597 TCTTATACTACTGTGTTTCAACCTCT 57.581 34.615 0.00 0.00 0.00 3.69
108 109 9.654663 AATCTTATACTACTGTGTTTCAACCTC 57.345 33.333 0.00 0.00 0.00 3.85
120 121 9.539825 AGAACAGCATCAAATCTTATACTACTG 57.460 33.333 0.00 0.00 0.00 2.74
128 129 7.386059 TGTGAGTAGAACAGCATCAAATCTTA 58.614 34.615 0.00 0.00 0.00 2.10
137 138 4.541973 TGTCATGTGAGTAGAACAGCAT 57.458 40.909 0.00 0.00 0.00 3.79
140 141 7.531871 CGAAAATTTGTCATGTGAGTAGAACAG 59.468 37.037 0.00 0.00 0.00 3.16
148 149 7.356719 CGAGAAAACGAAAATTTGTCATGTGAG 60.357 37.037 0.00 0.00 31.53 3.51
156 157 5.346281 TGTTTGCGAGAAAACGAAAATTTGT 59.654 32.000 0.00 0.00 41.74 2.83
185 186 4.517453 CCTTCGATCCACCAAACAGTTTTA 59.483 41.667 0.00 0.00 0.00 1.52
195 197 0.399949 ATAGGGCCTTCGATCCACCA 60.400 55.000 13.45 0.00 0.00 4.17
216 238 2.060980 GGAGGAGGAGGTGTCGCAT 61.061 63.158 0.00 0.00 0.00 4.73
219 241 0.396417 ATGAGGAGGAGGAGGTGTCG 60.396 60.000 0.00 0.00 0.00 4.35
224 246 1.137872 CGACAAATGAGGAGGAGGAGG 59.862 57.143 0.00 0.00 0.00 4.30
225 247 1.472376 GCGACAAATGAGGAGGAGGAG 60.472 57.143 0.00 0.00 0.00 3.69
226 248 0.537188 GCGACAAATGAGGAGGAGGA 59.463 55.000 0.00 0.00 0.00 3.71
227 249 0.250234 TGCGACAAATGAGGAGGAGG 59.750 55.000 0.00 0.00 0.00 4.30
228 250 2.158986 AGATGCGACAAATGAGGAGGAG 60.159 50.000 0.00 0.00 0.00 3.69
229 251 1.833630 AGATGCGACAAATGAGGAGGA 59.166 47.619 0.00 0.00 0.00 3.71
230 252 2.158986 AGAGATGCGACAAATGAGGAGG 60.159 50.000 0.00 0.00 0.00 4.30
231 253 3.176552 AGAGATGCGACAAATGAGGAG 57.823 47.619 0.00 0.00 0.00 3.69
232 254 4.586421 AGATAGAGATGCGACAAATGAGGA 59.414 41.667 0.00 0.00 0.00 3.71
240 262 5.358160 TGAAAGAGAAGATAGAGATGCGACA 59.642 40.000 0.00 0.00 0.00 4.35
260 282 3.374988 GTGGAGATTGTGCGATGATGAAA 59.625 43.478 0.00 0.00 0.00 2.69
264 286 1.475751 GGGTGGAGATTGTGCGATGAT 60.476 52.381 0.00 0.00 0.00 2.45
269 291 2.438434 GGGGGTGGAGATTGTGCG 60.438 66.667 0.00 0.00 0.00 5.34
287 309 3.240134 GAGGAGTGGTGCCAGCGAA 62.240 63.158 0.00 0.00 0.00 4.70
289 311 4.767255 GGAGGAGTGGTGCCAGCG 62.767 72.222 0.00 0.00 0.00 5.18
292 314 1.915266 CAGAGGAGGAGTGGTGCCA 60.915 63.158 0.00 0.00 0.00 4.92
308 330 1.519455 GAAGCGATGACGGGGACAG 60.519 63.158 0.00 0.00 40.15 3.51
313 335 2.278857 CGGAGAAGCGATGACGGG 60.279 66.667 0.00 0.00 40.15 5.28
329 351 3.120649 CGAGAAAGTTAAAGGAAGTGGCG 60.121 47.826 0.00 0.00 0.00 5.69
377 399 3.578716 AGTCATTGTAGGTAGTGTGTGCT 59.421 43.478 0.00 0.00 0.00 4.40
392 414 5.356882 TCTTGCGGTTTTTCTAGTCATTG 57.643 39.130 0.00 0.00 0.00 2.82
407 429 7.042791 ACTGAAATTATGTTTGTTTTCTTGCGG 60.043 33.333 0.00 0.00 0.00 5.69
433 455 3.523564 ACCGGACTAGTAGGTAAGTGGTA 59.476 47.826 17.99 0.00 36.34 3.25
447 469 0.968901 AGAATGGTCGCACCGGACTA 60.969 55.000 9.46 0.00 42.58 2.59
524 546 0.608130 TCTCAAGTGCGGCAGTACAT 59.392 50.000 11.30 0.00 35.31 2.29
572 594 5.393866 ACAAATTAGTGTGGGGTGAGATTT 58.606 37.500 0.00 0.00 0.00 2.17
573 595 4.998051 ACAAATTAGTGTGGGGTGAGATT 58.002 39.130 0.00 0.00 0.00 2.40
574 596 4.657814 ACAAATTAGTGTGGGGTGAGAT 57.342 40.909 0.00 0.00 0.00 2.75
587 609 6.954944 TGTGACTTTCTTCGGAACAAATTAG 58.045 36.000 0.00 0.00 33.18 1.73
595 617 4.812626 GGTTACTTGTGACTTTCTTCGGAA 59.187 41.667 0.00 0.00 0.00 4.30
596 618 4.374399 GGTTACTTGTGACTTTCTTCGGA 58.626 43.478 0.00 0.00 0.00 4.55
597 619 3.497262 GGGTTACTTGTGACTTTCTTCGG 59.503 47.826 0.00 0.00 0.00 4.30
599 621 4.275196 GGTGGGTTACTTGTGACTTTCTTC 59.725 45.833 0.00 0.00 0.00 2.87
600 622 4.204799 GGTGGGTTACTTGTGACTTTCTT 58.795 43.478 0.00 0.00 0.00 2.52
601 623 3.201266 TGGTGGGTTACTTGTGACTTTCT 59.799 43.478 0.00 0.00 0.00 2.52
602 624 3.547746 TGGTGGGTTACTTGTGACTTTC 58.452 45.455 0.00 0.00 0.00 2.62
662 717 1.428448 TGTGACTTTTCGCATCCTCG 58.572 50.000 0.00 0.00 37.33 4.63
731 786 7.337942 GGGATGACATTAACAACTCTCTTGATT 59.662 37.037 0.00 0.00 0.00 2.57
735 790 5.251700 AGGGGATGACATTAACAACTCTCTT 59.748 40.000 0.00 0.00 0.00 2.85
738 793 4.848357 CAGGGGATGACATTAACAACTCT 58.152 43.478 0.00 0.00 0.00 3.24
786 841 3.064324 GTGGGCAGGGTGATGTGC 61.064 66.667 0.00 0.00 39.08 4.57
880 935 6.259608 CGAAGAATAGATGAATGGAGCTTGTT 59.740 38.462 0.00 0.00 0.00 2.83
893 948 3.315470 TCGGTGGAGACGAAGAATAGATG 59.685 47.826 0.00 0.00 37.42 2.90
922 977 1.374947 GCTGCTGGTTGGTCTACCA 59.625 57.895 0.00 0.00 45.73 3.25
947 1002 4.154347 GCAGGGAGAGGTGAGCCG 62.154 72.222 0.00 0.00 40.50 5.52
990 1078 2.672651 TTCGCCATGGCCACACTG 60.673 61.111 30.79 15.66 37.98 3.66
1071 1159 2.430921 GTCAGTGTCACCGGCTCG 60.431 66.667 0.00 0.00 0.00 5.03
1284 1372 4.144703 GTCTCCTCGCCGGGGAAC 62.145 72.222 22.77 13.65 46.19 3.62
1630 1727 2.579738 GAAGGAGGCGACCCAGTC 59.420 66.667 0.00 0.00 0.00 3.51
1649 1746 1.130561 CGGAAATCGAAGGAGGCAAAC 59.869 52.381 0.00 0.00 42.43 2.93
1662 1767 3.000041 GGCCCAAACAATTTCGGAAATC 59.000 45.455 15.78 1.88 0.00 2.17
1671 1776 1.250840 GCTCTCGGGCCCAAACAATT 61.251 55.000 24.92 0.00 0.00 2.32
1853 1959 9.444600 GAGTAATACAGTTTCATCCCACTTTAA 57.555 33.333 0.00 0.00 0.00 1.52
1855 1961 6.884836 GGAGTAATACAGTTTCATCCCACTTT 59.115 38.462 0.00 0.00 0.00 2.66
1858 1964 5.990668 AGGAGTAATACAGTTTCATCCCAC 58.009 41.667 0.00 0.00 0.00 4.61
1859 1965 7.931015 ATAGGAGTAATACAGTTTCATCCCA 57.069 36.000 0.00 0.00 0.00 4.37
1944 2070 1.280998 GAAGGGCCTTTGGTGCTAGTA 59.719 52.381 21.92 0.00 0.00 1.82
1945 2071 0.038310 GAAGGGCCTTTGGTGCTAGT 59.962 55.000 21.92 0.00 0.00 2.57
1946 2072 0.329596 AGAAGGGCCTTTGGTGCTAG 59.670 55.000 21.92 0.00 0.00 3.42
1947 2073 0.328258 GAGAAGGGCCTTTGGTGCTA 59.672 55.000 21.92 0.00 0.00 3.49
1961 2087 7.525759 GGAGAATTTCAGCTAACTTTGAGAAG 58.474 38.462 0.00 0.00 38.87 2.85
2011 2138 1.666888 GGCCTCTTTGACACGCAATTG 60.667 52.381 0.00 0.00 36.15 2.32
2076 2228 1.226916 CTAGCTGGAGTGAGCGCTG 60.227 63.158 18.48 0.00 44.24 5.18
2095 2247 2.278857 CCGGCGCTAGCTACTGTG 60.279 66.667 13.93 0.00 44.37 3.66
2215 2370 7.282916 CCTTGTTTCAGAAAAACAATAATGCG 58.717 34.615 14.39 4.54 45.56 4.73
2224 2379 6.720012 TCTTTTGCCTTGTTTCAGAAAAAC 57.280 33.333 0.00 0.00 0.00 2.43
2228 2384 5.350633 CACATCTTTTGCCTTGTTTCAGAA 58.649 37.500 0.00 0.00 0.00 3.02
2230 2386 3.492011 GCACATCTTTTGCCTTGTTTCAG 59.508 43.478 0.00 0.00 33.58 3.02
2249 2405 6.402442 GAAATATTTTTCATTGCTGGTGGCAC 60.402 38.462 9.70 9.70 44.26 5.01
2264 2420 9.147732 AGTTTTCTCTGGACAGGAAATATTTTT 57.852 29.630 1.43 0.00 32.10 1.94
2266 2422 8.712228 AAGTTTTCTCTGGACAGGAAATATTT 57.288 30.769 0.00 0.00 32.10 1.40
2280 2436 6.642540 GGCTGGTTTCAAATAAGTTTTCTCTG 59.357 38.462 0.00 0.00 0.00 3.35
2306 2462 3.317993 ACCAACAGTCATTTTGTAGCCAC 59.682 43.478 0.00 0.00 0.00 5.01
2322 2478 6.981559 GGTAAAATAAGTTTGCTTGACCAACA 59.018 34.615 0.00 0.00 36.22 3.33
2367 2525 5.305644 ACAGGGCGATAGTATCTTCAATCTT 59.694 40.000 8.49 0.00 39.35 2.40
2380 2538 2.222027 GGATTCCAAACAGGGCGATAG 58.778 52.381 0.00 0.00 38.24 2.08
2384 2542 1.000896 AGGGATTCCAAACAGGGCG 60.001 57.895 4.80 0.00 38.24 6.13
2385 2543 0.684479 GGAGGGATTCCAAACAGGGC 60.684 60.000 4.80 0.00 46.01 5.19
2386 2544 3.596362 GGAGGGATTCCAAACAGGG 57.404 57.895 4.80 0.00 46.01 4.45
2394 2552 2.066999 AGCTCCACGGAGGGATTCC 61.067 63.158 14.86 0.00 42.19 3.01
2395 2553 1.144936 CAGCTCCACGGAGGGATTC 59.855 63.158 14.86 0.00 42.19 2.52
2396 2554 0.325296 TACAGCTCCACGGAGGGATT 60.325 55.000 14.86 0.00 42.19 3.01
2397 2555 0.757188 CTACAGCTCCACGGAGGGAT 60.757 60.000 14.86 0.00 42.19 3.85
2398 2556 1.379977 CTACAGCTCCACGGAGGGA 60.380 63.158 14.86 0.00 42.19 4.20
2399 2557 1.379977 TCTACAGCTCCACGGAGGG 60.380 63.158 14.86 0.00 42.19 4.30
2400 2558 2.010582 GCTCTACAGCTCCACGGAGG 62.011 65.000 14.86 1.77 43.09 4.30
2401 2559 1.435515 GCTCTACAGCTCCACGGAG 59.564 63.158 8.84 8.84 43.09 4.63
2402 2560 3.604629 GCTCTACAGCTCCACGGA 58.395 61.111 0.00 0.00 43.09 4.69
2411 2569 2.027192 TGGCTAAAACCCAGCTCTACAG 60.027 50.000 0.00 0.00 39.09 2.74
2412 2570 1.982226 TGGCTAAAACCCAGCTCTACA 59.018 47.619 0.00 0.00 39.09 2.74
2413 2571 2.027100 AGTGGCTAAAACCCAGCTCTAC 60.027 50.000 0.00 0.00 39.09 2.59
2414 2572 2.236395 GAGTGGCTAAAACCCAGCTCTA 59.764 50.000 0.00 0.00 39.09 2.43
2415 2573 1.003696 GAGTGGCTAAAACCCAGCTCT 59.996 52.381 0.00 0.00 39.09 4.09
2416 2574 1.454201 GAGTGGCTAAAACCCAGCTC 58.546 55.000 0.00 0.00 39.09 4.09
2417 2575 0.038310 GGAGTGGCTAAAACCCAGCT 59.962 55.000 0.00 0.00 39.09 4.24
2418 2576 0.038310 AGGAGTGGCTAAAACCCAGC 59.962 55.000 0.00 0.00 38.35 4.85
2419 2577 2.586648 AAGGAGTGGCTAAAACCCAG 57.413 50.000 0.00 0.00 31.89 4.45
2420 2578 4.456662 TTTAAGGAGTGGCTAAAACCCA 57.543 40.909 0.00 0.00 0.00 4.51
2421 2579 5.794726 TTTTTAAGGAGTGGCTAAAACCC 57.205 39.130 0.00 0.00 0.00 4.11
2422 2580 7.544566 GCTAATTTTTAAGGAGTGGCTAAAACC 59.455 37.037 0.00 0.00 0.00 3.27
2423 2581 8.304596 AGCTAATTTTTAAGGAGTGGCTAAAAC 58.695 33.333 0.00 0.00 0.00 2.43
2424 2582 8.303876 CAGCTAATTTTTAAGGAGTGGCTAAAA 58.696 33.333 0.00 0.00 0.00 1.52
2425 2583 7.093945 CCAGCTAATTTTTAAGGAGTGGCTAAA 60.094 37.037 0.00 0.00 0.00 1.85
2426 2584 6.377146 CCAGCTAATTTTTAAGGAGTGGCTAA 59.623 38.462 0.00 0.00 0.00 3.09
2427 2585 5.885912 CCAGCTAATTTTTAAGGAGTGGCTA 59.114 40.000 0.00 0.00 0.00 3.93
2428 2586 4.706962 CCAGCTAATTTTTAAGGAGTGGCT 59.293 41.667 0.00 0.00 0.00 4.75
2429 2587 4.705023 TCCAGCTAATTTTTAAGGAGTGGC 59.295 41.667 0.00 0.00 0.00 5.01
2430 2588 6.094186 GTCTCCAGCTAATTTTTAAGGAGTGG 59.906 42.308 9.91 0.00 41.40 4.00
2431 2589 6.881602 AGTCTCCAGCTAATTTTTAAGGAGTG 59.118 38.462 9.91 0.00 41.40 3.51
2432 2590 6.881602 CAGTCTCCAGCTAATTTTTAAGGAGT 59.118 38.462 9.91 0.00 41.40 3.85
2433 2591 6.317391 CCAGTCTCCAGCTAATTTTTAAGGAG 59.683 42.308 4.90 4.90 41.88 3.69
2434 2592 6.180472 CCAGTCTCCAGCTAATTTTTAAGGA 58.820 40.000 0.00 0.00 0.00 3.36
2435 2593 5.946377 ACCAGTCTCCAGCTAATTTTTAAGG 59.054 40.000 0.00 0.00 0.00 2.69
2436 2594 6.094186 GGACCAGTCTCCAGCTAATTTTTAAG 59.906 42.308 0.00 0.00 0.00 1.85
2437 2595 5.944007 GGACCAGTCTCCAGCTAATTTTTAA 59.056 40.000 0.00 0.00 0.00 1.52
2438 2596 5.497474 GGACCAGTCTCCAGCTAATTTTTA 58.503 41.667 0.00 0.00 0.00 1.52
2439 2597 4.336280 GGACCAGTCTCCAGCTAATTTTT 58.664 43.478 0.00 0.00 0.00 1.94
2440 2598 3.619979 CGGACCAGTCTCCAGCTAATTTT 60.620 47.826 0.00 0.00 0.00 1.82
2441 2599 2.093447 CGGACCAGTCTCCAGCTAATTT 60.093 50.000 0.00 0.00 0.00 1.82
2442 2600 1.482593 CGGACCAGTCTCCAGCTAATT 59.517 52.381 0.00 0.00 0.00 1.40
2443 2601 1.115467 CGGACCAGTCTCCAGCTAAT 58.885 55.000 0.00 0.00 0.00 1.73
2444 2602 1.605058 GCGGACCAGTCTCCAGCTAA 61.605 60.000 0.00 0.00 31.26 3.09
2445 2603 2.052690 GCGGACCAGTCTCCAGCTA 61.053 63.158 0.00 0.00 31.26 3.32
2446 2604 3.386237 GCGGACCAGTCTCCAGCT 61.386 66.667 0.00 0.00 31.26 4.24
2447 2605 3.363844 GAGCGGACCAGTCTCCAGC 62.364 68.421 0.00 0.00 32.96 4.85
2448 2606 2.716017 GGAGCGGACCAGTCTCCAG 61.716 68.421 15.77 0.00 44.38 3.86
2449 2607 2.680352 GGAGCGGACCAGTCTCCA 60.680 66.667 15.77 0.00 44.38 3.86
2450 2608 3.827898 CGGAGCGGACCAGTCTCC 61.828 72.222 12.25 12.25 42.19 3.71
2463 2621 1.153289 CTGGACAATGCTCCCGGAG 60.153 63.158 10.41 10.41 0.00 4.63
2464 2622 2.669133 CCTGGACAATGCTCCCGGA 61.669 63.158 0.73 0.00 36.94 5.14
2465 2623 2.124570 CCTGGACAATGCTCCCGG 60.125 66.667 0.00 0.00 0.00 5.73
2466 2624 2.124570 CCCTGGACAATGCTCCCG 60.125 66.667 0.00 0.00 0.00 5.14
2467 2625 1.225704 CTCCCTGGACAATGCTCCC 59.774 63.158 0.00 0.00 0.00 4.30
2468 2626 1.452833 GCTCCCTGGACAATGCTCC 60.453 63.158 0.00 0.00 0.00 4.70
2469 2627 1.817099 CGCTCCCTGGACAATGCTC 60.817 63.158 0.00 0.00 0.00 4.26
2470 2628 2.270205 CGCTCCCTGGACAATGCT 59.730 61.111 0.00 0.00 0.00 3.79
2471 2629 2.825836 CCGCTCCCTGGACAATGC 60.826 66.667 0.00 0.00 0.00 3.56
2472 2630 1.153289 CTCCGCTCCCTGGACAATG 60.153 63.158 0.00 0.00 0.00 2.82
2473 2631 1.306141 TCTCCGCTCCCTGGACAAT 60.306 57.895 0.00 0.00 0.00 2.71
2474 2632 1.984570 CTCTCCGCTCCCTGGACAA 60.985 63.158 0.00 0.00 0.00 3.18
2475 2633 2.363018 CTCTCCGCTCCCTGGACA 60.363 66.667 0.00 0.00 0.00 4.02
2476 2634 3.151022 CCTCTCCGCTCCCTGGAC 61.151 72.222 0.00 0.00 0.00 4.02
2477 2635 3.347590 TCCTCTCCGCTCCCTGGA 61.348 66.667 0.00 0.00 0.00 3.86
2478 2636 2.837291 CTCCTCTCCGCTCCCTGG 60.837 72.222 0.00 0.00 0.00 4.45
2479 2637 3.535962 GCTCCTCTCCGCTCCCTG 61.536 72.222 0.00 0.00 0.00 4.45
2480 2638 4.851214 GGCTCCTCTCCGCTCCCT 62.851 72.222 0.00 0.00 0.00 4.20
2483 2641 3.141488 TTCGGCTCCTCTCCGCTC 61.141 66.667 0.00 0.00 46.05 5.03
2484 2642 3.453679 GTTCGGCTCCTCTCCGCT 61.454 66.667 0.00 0.00 46.05 5.52
2485 2643 4.856607 CGTTCGGCTCCTCTCCGC 62.857 72.222 0.00 0.00 46.05 5.54
2487 2645 4.856607 CGCGTTCGGCTCCTCTCC 62.857 72.222 0.00 0.00 40.44 3.71
2497 2655 3.961182 ACATATATATAGGCCGCGTTCG 58.039 45.455 4.92 0.00 0.00 3.95
2498 2656 5.862323 CCATACATATATATAGGCCGCGTTC 59.138 44.000 4.92 0.00 0.00 3.95
2499 2657 5.537295 TCCATACATATATATAGGCCGCGTT 59.463 40.000 4.92 0.00 0.00 4.84
2500 2658 5.074804 TCCATACATATATATAGGCCGCGT 58.925 41.667 4.92 0.00 0.00 6.01
2501 2659 5.638596 TCCATACATATATATAGGCCGCG 57.361 43.478 0.00 0.00 0.00 6.46
2535 2693 9.582431 GCTGTTATCTTACAGTATACAGTCAAA 57.418 33.333 3.93 0.00 45.76 2.69
2536 2694 8.195436 GGCTGTTATCTTACAGTATACAGTCAA 58.805 37.037 3.93 0.00 45.76 3.18
2537 2695 7.560262 AGGCTGTTATCTTACAGTATACAGTCA 59.440 37.037 3.93 0.00 45.76 3.41
2538 2696 7.942990 AGGCTGTTATCTTACAGTATACAGTC 58.057 38.462 3.93 0.00 45.76 3.51
2539 2697 7.560262 TGAGGCTGTTATCTTACAGTATACAGT 59.440 37.037 5.50 5.86 45.76 3.55
2540 2698 7.863375 GTGAGGCTGTTATCTTACAGTATACAG 59.137 40.741 5.50 0.00 45.76 2.74
2541 2699 7.340999 TGTGAGGCTGTTATCTTACAGTATACA 59.659 37.037 5.50 4.27 45.76 2.29
2542 2700 7.713750 TGTGAGGCTGTTATCTTACAGTATAC 58.286 38.462 0.00 0.00 45.76 1.47
2543 2701 7.891498 TGTGAGGCTGTTATCTTACAGTATA 57.109 36.000 0.00 0.00 45.76 1.47
2544 2702 6.791867 TGTGAGGCTGTTATCTTACAGTAT 57.208 37.500 0.00 0.00 45.76 2.12
2545 2703 6.599356 TTGTGAGGCTGTTATCTTACAGTA 57.401 37.500 0.00 0.00 45.76 2.74
2546 2704 5.483685 TTGTGAGGCTGTTATCTTACAGT 57.516 39.130 0.00 0.00 45.76 3.55
2547 2705 6.108687 TGATTGTGAGGCTGTTATCTTACAG 58.891 40.000 0.00 0.00 46.55 2.74
2548 2706 6.048732 TGATTGTGAGGCTGTTATCTTACA 57.951 37.500 0.00 0.00 0.00 2.41
2549 2707 6.595716 ACTTGATTGTGAGGCTGTTATCTTAC 59.404 38.462 0.00 0.00 0.00 2.34
2550 2708 6.711277 ACTTGATTGTGAGGCTGTTATCTTA 58.289 36.000 0.00 0.00 0.00 2.10
2551 2709 5.564550 ACTTGATTGTGAGGCTGTTATCTT 58.435 37.500 0.00 0.00 0.00 2.40
2552 2710 5.171339 ACTTGATTGTGAGGCTGTTATCT 57.829 39.130 0.00 0.00 0.00 1.98
2553 2711 7.559590 AATACTTGATTGTGAGGCTGTTATC 57.440 36.000 0.00 0.00 0.00 1.75
2554 2712 9.461312 TTTAATACTTGATTGTGAGGCTGTTAT 57.539 29.630 0.00 0.00 0.00 1.89
2555 2713 8.856153 TTTAATACTTGATTGTGAGGCTGTTA 57.144 30.769 0.00 0.00 0.00 2.41
2556 2714 7.759489 TTTAATACTTGATTGTGAGGCTGTT 57.241 32.000 0.00 0.00 0.00 3.16
2557 2715 7.759489 TTTTAATACTTGATTGTGAGGCTGT 57.241 32.000 0.00 0.00 0.00 4.40
2577 2735 9.715121 ACTTCTTGTACTCCGTTTGATATTTTA 57.285 29.630 0.00 0.00 0.00 1.52
2578 2736 8.504005 CACTTCTTGTACTCCGTTTGATATTTT 58.496 33.333 0.00 0.00 0.00 1.82
2579 2737 7.660208 ACACTTCTTGTACTCCGTTTGATATTT 59.340 33.333 0.00 0.00 36.32 1.40
2580 2738 7.159372 ACACTTCTTGTACTCCGTTTGATATT 58.841 34.615 0.00 0.00 36.32 1.28
2581 2739 6.698380 ACACTTCTTGTACTCCGTTTGATAT 58.302 36.000 0.00 0.00 36.32 1.63
2582 2740 6.092955 ACACTTCTTGTACTCCGTTTGATA 57.907 37.500 0.00 0.00 36.32 2.15
2583 2741 4.957296 ACACTTCTTGTACTCCGTTTGAT 58.043 39.130 0.00 0.00 36.32 2.57
2584 2742 4.365723 GACACTTCTTGTACTCCGTTTGA 58.634 43.478 0.00 0.00 39.17 2.69
2585 2743 3.493503 GGACACTTCTTGTACTCCGTTTG 59.506 47.826 0.00 0.00 39.17 2.93
2586 2744 3.725490 GGACACTTCTTGTACTCCGTTT 58.275 45.455 0.00 0.00 39.17 3.60
2587 2745 2.288030 CGGACACTTCTTGTACTCCGTT 60.288 50.000 7.54 0.00 40.52 4.44
2588 2746 1.268899 CGGACACTTCTTGTACTCCGT 59.731 52.381 7.54 0.00 40.52 4.69
2589 2747 1.978542 CGGACACTTCTTGTACTCCG 58.021 55.000 2.09 2.09 39.17 4.63
2590 2748 1.000506 TGCGGACACTTCTTGTACTCC 59.999 52.381 0.00 0.00 39.17 3.85
2591 2749 2.433868 TGCGGACACTTCTTGTACTC 57.566 50.000 0.00 0.00 39.17 2.59
2592 2750 2.037251 ACATGCGGACACTTCTTGTACT 59.963 45.455 0.00 0.00 39.17 2.73
2593 2751 2.413837 ACATGCGGACACTTCTTGTAC 58.586 47.619 0.00 0.00 39.17 2.90
2594 2752 2.831685 ACATGCGGACACTTCTTGTA 57.168 45.000 0.00 0.00 39.17 2.41
2595 2753 2.224185 TGTACATGCGGACACTTCTTGT 60.224 45.455 0.00 0.00 43.10 3.16
2596 2754 2.412870 TGTACATGCGGACACTTCTTG 58.587 47.619 0.00 0.00 0.00 3.02
2597 2755 2.831685 TGTACATGCGGACACTTCTT 57.168 45.000 0.00 0.00 0.00 2.52
2598 2756 2.806244 GTTTGTACATGCGGACACTTCT 59.194 45.455 0.00 0.00 0.00 2.85
2599 2757 2.546368 TGTTTGTACATGCGGACACTTC 59.454 45.455 0.00 0.00 0.00 3.01
2600 2758 2.566913 TGTTTGTACATGCGGACACTT 58.433 42.857 0.00 0.00 0.00 3.16
2601 2759 2.248280 TGTTTGTACATGCGGACACT 57.752 45.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.