Multiple sequence alignment - TraesCS4D01G016300

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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 TraesCS4D01G016300 chr4D 100.000 2777 0 0 1 2777 7410916 7413692 0.000000e+00 5129.0
1 TraesCS4D01G016300 chr4D 86.364 88 12 0 44 131 503564369 503564456 2.280000e-16 97.1
2 TraesCS4D01G016300 chr4B 88.982 1189 91 18 1356 2527 13280527 13281692 0.000000e+00 1434.0
3 TraesCS4D01G016300 chr4B 85.275 944 73 40 453 1355 13279491 13280409 0.000000e+00 913.0
4 TraesCS4D01G016300 chr4B 85.920 348 35 5 2176 2520 385036599 385036935 2.630000e-95 359.0
5 TraesCS4D01G016300 chr4B 90.955 199 15 3 134 329 13278591 13278789 5.900000e-67 265.0
6 TraesCS4D01G016300 chr4A 90.890 933 46 12 1544 2459 596218141 596219051 0.000000e+00 1216.0
7 TraesCS4D01G016300 chr4A 96.416 279 8 2 2459 2737 596219141 596219417 2.520000e-125 459.0
8 TraesCS4D01G016300 chr4A 88.312 231 11 7 615 836 596217633 596217856 2.120000e-66 263.0
9 TraesCS4D01G016300 chr4A 94.737 57 3 0 77 133 582438983 582438927 3.810000e-14 89.8
10 TraesCS4D01G016300 chr2B 86.842 342 31 5 2182 2520 269029608 269029278 1.210000e-98 370.0
11 TraesCS4D01G016300 chr2B 85.920 348 35 5 2176 2520 391899367 391899703 2.630000e-95 359.0
12 TraesCS4D01G016300 chr2B 85.039 254 35 3 2526 2777 108229283 108229031 3.550000e-64 255.0
13 TraesCS4D01G016300 chr2B 86.316 190 25 1 2527 2716 495923694 495923882 3.630000e-49 206.0
14 TraesCS4D01G016300 chr7B 85.965 342 31 7 2182 2520 263415012 263414685 1.580000e-92 350.0
15 TraesCS4D01G016300 chr7B 85.673 342 35 5 2182 2520 552984302 552983972 5.690000e-92 348.0
16 TraesCS4D01G016300 chr2A 85.057 348 38 5 2176 2520 435371182 435371518 2.650000e-90 342.0
17 TraesCS4D01G016300 chr5B 90.777 206 15 4 2182 2386 18377090 18376888 3.520000e-69 272.0
18 TraesCS4D01G016300 chr5B 84.861 251 35 3 2526 2774 642363863 642364112 1.650000e-62 250.0
19 TraesCS4D01G016300 chr6D 89.362 94 10 0 42 135 457640635 457640728 4.860000e-23 119.0
20 TraesCS4D01G016300 chrUn 88.095 84 9 1 50 132 126990304 126990221 6.330000e-17 99.0
21 TraesCS4D01G016300 chr3B 93.939 66 3 1 67 131 796512030 796511965 6.330000e-17 99.0
22 TraesCS4D01G016300 chr7A 95.833 48 2 0 2669 2716 91620034 91620081 8.250000e-11 78.7
23 TraesCS4D01G016300 chr2D 80.198 101 16 4 41 141 112917465 112917561 3.840000e-09 73.1
24 TraesCS4D01G016300 chr3D 80.435 92 12 4 34 125 471581870 471581785 6.420000e-07 65.8
25 TraesCS4D01G016300 chr6B 95.000 40 2 0 87 126 126806129 126806168 2.310000e-06 63.9
26 TraesCS4D01G016300 chr5D 93.023 43 3 0 95 137 234820485 234820443 2.310000e-06 63.9


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 TraesCS4D01G016300 chr4D 7410916 7413692 2776 False 5129.000000 5129 100.000000 1 2777 1 chr4D.!!$F1 2776
1 TraesCS4D01G016300 chr4B 13278591 13281692 3101 False 870.666667 1434 88.404000 134 2527 3 chr4B.!!$F2 2393
2 TraesCS4D01G016300 chr4A 596217633 596219417 1784 False 646.000000 1216 91.872667 615 2737 3 chr4A.!!$F1 2122

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
559 1158 0.030235 GGCCGGGAATATTTGAACGC 59.97 55.0 2.18 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 3055 0.106015 AAGCAGAACAAGCACCCCTT 60.106 50.0 0.0 0.0 0.0 3.95 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.832248 AGTTTCAGTCAAGTGACAGAACA 58.168 39.130 16.16 7.64 45.79 3.18
23 24 5.431765 AGTTTCAGTCAAGTGACAGAACAT 58.568 37.500 16.16 7.52 45.79 2.71
24 25 6.582636 AGTTTCAGTCAAGTGACAGAACATA 58.417 36.000 16.16 2.98 45.79 2.29
25 26 7.220030 AGTTTCAGTCAAGTGACAGAACATAT 58.780 34.615 16.16 3.60 45.79 1.78
26 27 8.367911 AGTTTCAGTCAAGTGACAGAACATATA 58.632 33.333 16.16 2.38 45.79 0.86
27 28 8.988934 GTTTCAGTCAAGTGACAGAACATATAA 58.011 33.333 16.16 1.78 45.79 0.98
28 29 9.554395 TTTCAGTCAAGTGACAGAACATATAAA 57.446 29.630 16.16 1.19 45.79 1.40
32 33 8.534333 GTCAAGTGACAGAACATATAAACAGA 57.466 34.615 6.57 0.00 44.18 3.41
33 34 8.988934 GTCAAGTGACAGAACATATAAACAGAA 58.011 33.333 6.57 0.00 44.18 3.02
34 35 9.554395 TCAAGTGACAGAACATATAAACAGAAA 57.446 29.630 0.00 0.00 0.00 2.52
51 52 8.726650 AAACAGAAAAAGACAAAATTTTGCAC 57.273 26.923 26.94 20.90 41.79 4.57
52 53 7.432350 ACAGAAAAAGACAAAATTTTGCACA 57.568 28.000 26.94 0.00 41.79 4.57
53 54 7.520686 ACAGAAAAAGACAAAATTTTGCACAG 58.479 30.769 26.94 7.18 41.79 3.66
54 55 7.387397 ACAGAAAAAGACAAAATTTTGCACAGA 59.613 29.630 26.94 0.00 41.79 3.41
55 56 8.392612 CAGAAAAAGACAAAATTTTGCACAGAT 58.607 29.630 26.94 12.34 41.79 2.90
56 57 8.606602 AGAAAAAGACAAAATTTTGCACAGATC 58.393 29.630 26.94 18.73 41.79 2.75
57 58 8.496707 AAAAAGACAAAATTTTGCACAGATCT 57.503 26.923 26.94 18.64 41.79 2.75
58 59 7.704789 AAAGACAAAATTTTGCACAGATCTC 57.295 32.000 26.94 15.72 41.79 2.75
59 60 5.776744 AGACAAAATTTTGCACAGATCTCC 58.223 37.500 26.94 6.96 41.79 3.71
60 61 5.302568 AGACAAAATTTTGCACAGATCTCCA 59.697 36.000 26.94 0.00 41.79 3.86
61 62 6.014840 AGACAAAATTTTGCACAGATCTCCAT 60.015 34.615 26.94 6.23 41.79 3.41
62 63 7.177216 AGACAAAATTTTGCACAGATCTCCATA 59.823 33.333 26.94 0.00 41.79 2.74
63 64 7.844009 ACAAAATTTTGCACAGATCTCCATAT 58.156 30.769 26.94 2.76 41.79 1.78
64 65 8.970020 ACAAAATTTTGCACAGATCTCCATATA 58.030 29.630 26.94 0.00 41.79 0.86
65 66 9.806203 CAAAATTTTGCACAGATCTCCATATAA 57.194 29.630 17.48 0.00 0.00 0.98
67 68 8.985315 AATTTTGCACAGATCTCCATATAAGA 57.015 30.769 0.00 0.00 0.00 2.10
68 69 9.584008 AATTTTGCACAGATCTCCATATAAGAT 57.416 29.630 0.00 0.53 36.19 2.40
71 72 9.881649 TTTGCACAGATCTCCATATAAGATATC 57.118 33.333 0.00 0.00 33.64 1.63
72 73 8.599624 TGCACAGATCTCCATATAAGATATCA 57.400 34.615 5.32 0.00 33.64 2.15
73 74 9.210228 TGCACAGATCTCCATATAAGATATCAT 57.790 33.333 5.32 0.00 33.64 2.45
74 75 9.478768 GCACAGATCTCCATATAAGATATCATG 57.521 37.037 5.32 0.00 33.64 3.07
90 91 7.366513 AGATATCATGAATATAGCATCGACCG 58.633 38.462 5.32 0.00 30.37 4.79
91 92 5.582689 ATCATGAATATAGCATCGACCGA 57.417 39.130 0.00 0.00 0.00 4.69
92 93 4.986622 TCATGAATATAGCATCGACCGAG 58.013 43.478 0.00 0.00 0.00 4.63
93 94 4.700213 TCATGAATATAGCATCGACCGAGA 59.300 41.667 0.00 0.00 0.00 4.04
94 95 4.421033 TGAATATAGCATCGACCGAGAC 57.579 45.455 0.00 0.00 0.00 3.36
95 96 4.072839 TGAATATAGCATCGACCGAGACT 58.927 43.478 0.00 0.76 0.00 3.24
96 97 4.519350 TGAATATAGCATCGACCGAGACTT 59.481 41.667 0.00 0.00 0.00 3.01
97 98 5.009710 TGAATATAGCATCGACCGAGACTTT 59.990 40.000 0.00 0.00 0.00 2.66
98 99 2.561733 TAGCATCGACCGAGACTTTG 57.438 50.000 0.00 0.00 0.00 2.77
99 100 0.603569 AGCATCGACCGAGACTTTGT 59.396 50.000 0.00 0.00 0.00 2.83
100 101 1.000955 AGCATCGACCGAGACTTTGTT 59.999 47.619 0.00 0.00 0.00 2.83
101 102 2.230508 AGCATCGACCGAGACTTTGTTA 59.769 45.455 0.00 0.00 0.00 2.41
102 103 2.991190 GCATCGACCGAGACTTTGTTAA 59.009 45.455 0.00 0.00 0.00 2.01
103 104 3.060895 GCATCGACCGAGACTTTGTTAAG 59.939 47.826 0.00 0.00 37.40 1.85
115 116 5.517322 ACTTTGTTAAGTCTCAGTCGACT 57.483 39.130 13.58 13.58 45.73 4.18
116 117 5.282510 ACTTTGTTAAGTCTCAGTCGACTG 58.717 41.667 34.76 34.76 43.14 3.51
117 118 5.067413 ACTTTGTTAAGTCTCAGTCGACTGA 59.933 40.000 38.24 38.24 44.30 3.41
131 132 6.210078 CAGTCGACTGAGATTTAGTAATCCC 58.790 44.000 36.73 0.00 46.59 3.85
132 133 5.008811 AGTCGACTGAGATTTAGTAATCCCG 59.991 44.000 19.30 0.00 40.91 5.14
166 167 2.676748 TGGAAAGACACCTTTGGCAAT 58.323 42.857 0.00 0.00 42.30 3.56
180 181 1.281867 TGGCAATGGTAGAACCTCCAG 59.718 52.381 0.00 0.00 39.58 3.86
185 186 2.661176 TGGTAGAACCTCCAGGGAAT 57.339 50.000 0.00 0.00 39.58 3.01
196 197 1.368203 TCCAGGGAATAGGAGGGTTCA 59.632 52.381 0.00 0.00 0.00 3.18
197 198 2.205342 CCAGGGAATAGGAGGGTTCAA 58.795 52.381 0.00 0.00 0.00 2.69
213 215 7.766738 GGAGGGTTCAACAAAATTAAAGTGAAA 59.233 33.333 0.00 0.00 0.00 2.69
283 286 5.185828 GGGGCAAAATTAGATGAGTTTCTGT 59.814 40.000 0.00 0.00 0.00 3.41
305 308 5.477984 TGTCCAATTCAAATTTCAGAGGAGG 59.522 40.000 0.00 0.00 0.00 4.30
315 318 1.001641 CAGAGGAGGCCAAACCCTG 60.002 63.158 5.01 10.82 40.58 4.45
328 331 3.818210 CCAAACCCTGGCCAAATTAAAAC 59.182 43.478 7.01 0.00 38.76 2.43
329 332 3.394674 AACCCTGGCCAAATTAAAACG 57.605 42.857 7.01 0.00 0.00 3.60
330 333 1.621317 ACCCTGGCCAAATTAAAACGG 59.379 47.619 7.01 0.00 0.00 4.44
331 334 1.674519 CCCTGGCCAAATTAAAACGGC 60.675 52.381 7.01 4.28 44.10 5.68
332 335 1.001406 CCTGGCCAAATTAAAACGGCA 59.999 47.619 7.01 3.79 46.75 5.69
333 336 2.354604 CCTGGCCAAATTAAAACGGCAT 60.355 45.455 7.01 0.00 46.75 4.40
334 337 3.333804 CTGGCCAAATTAAAACGGCATT 58.666 40.909 7.01 0.00 46.75 3.56
337 340 3.120373 GGCCAAATTAAAACGGCATTGTG 60.120 43.478 12.74 0.00 46.75 3.33
338 341 3.666638 GCCAAATTAAAACGGCATTGTGC 60.667 43.478 7.35 0.00 44.25 4.57
354 357 6.620678 GCATTGTGCCTAATTTTACTGAGAA 58.379 36.000 0.00 0.00 37.42 2.87
356 359 5.880054 TGTGCCTAATTTTACTGAGAAGC 57.120 39.130 0.00 0.00 0.00 3.86
357 360 5.312895 TGTGCCTAATTTTACTGAGAAGCA 58.687 37.500 0.00 0.00 0.00 3.91
358 361 5.181245 TGTGCCTAATTTTACTGAGAAGCAC 59.819 40.000 0.00 0.00 45.29 4.40
361 364 5.643777 GCCTAATTTTACTGAGAAGCACTGA 59.356 40.000 0.00 0.00 0.00 3.41
362 365 6.317391 GCCTAATTTTACTGAGAAGCACTGAT 59.683 38.462 0.00 0.00 0.00 2.90
363 366 7.466590 GCCTAATTTTACTGAGAAGCACTGATC 60.467 40.741 0.00 0.00 0.00 2.92
364 367 7.768120 CCTAATTTTACTGAGAAGCACTGATCT 59.232 37.037 0.00 0.00 0.00 2.75
365 368 7.608308 AATTTTACTGAGAAGCACTGATCTC 57.392 36.000 0.00 5.67 41.95 2.75
367 370 5.574891 TTACTGAGAAGCACTGATCTCTC 57.425 43.478 11.45 0.00 42.07 3.20
369 372 3.193267 ACTGAGAAGCACTGATCTCTCAC 59.807 47.826 6.11 0.00 42.07 3.51
370 373 3.429492 TGAGAAGCACTGATCTCTCACT 58.571 45.455 6.11 0.00 42.07 3.41
371 374 3.831333 TGAGAAGCACTGATCTCTCACTT 59.169 43.478 6.11 0.00 42.07 3.16
372 375 4.175516 GAGAAGCACTGATCTCTCACTTG 58.824 47.826 0.00 0.00 39.18 3.16
373 376 3.055963 AGAAGCACTGATCTCTCACTTGG 60.056 47.826 0.00 0.00 0.00 3.61
374 377 2.255406 AGCACTGATCTCTCACTTGGT 58.745 47.619 0.00 0.00 0.00 3.67
375 378 2.636893 AGCACTGATCTCTCACTTGGTT 59.363 45.455 0.00 0.00 0.00 3.67
376 379 3.834813 AGCACTGATCTCTCACTTGGTTA 59.165 43.478 0.00 0.00 0.00 2.85
377 380 4.284490 AGCACTGATCTCTCACTTGGTTAA 59.716 41.667 0.00 0.00 0.00 2.01
378 381 4.997395 GCACTGATCTCTCACTTGGTTAAA 59.003 41.667 0.00 0.00 0.00 1.52
379 382 5.470098 GCACTGATCTCTCACTTGGTTAAAA 59.530 40.000 0.00 0.00 0.00 1.52
380 383 6.566753 GCACTGATCTCTCACTTGGTTAAAAC 60.567 42.308 0.00 0.00 0.00 2.43
398 986 7.063308 GGTTAAAACCGAGTATGATTACGACAA 59.937 37.037 0.00 0.00 39.66 3.18
399 987 6.642683 AAAACCGAGTATGATTACGACAAG 57.357 37.500 0.00 0.00 33.32 3.16
401 989 6.441093 AACCGAGTATGATTACGACAAGTA 57.559 37.500 0.00 0.00 33.32 2.24
405 993 5.846994 CGAGTATGATTACGACAAGTAGAGC 59.153 44.000 0.00 0.00 36.56 4.09
410 998 0.961857 TACGACAAGTAGAGCCCGCA 60.962 55.000 0.00 0.00 0.00 5.69
419 1007 2.040009 TAGAGCCCGCATGTAAGCCC 62.040 60.000 0.00 0.00 0.00 5.19
422 1010 2.589540 CCCGCATGTAAGCCCTGA 59.410 61.111 0.00 0.00 0.00 3.86
423 1011 1.819632 CCCGCATGTAAGCCCTGAC 60.820 63.158 0.00 0.00 0.00 3.51
424 1012 2.173669 CCGCATGTAAGCCCTGACG 61.174 63.158 0.00 0.00 0.00 4.35
425 1013 2.813179 CGCATGTAAGCCCTGACGC 61.813 63.158 0.00 0.00 0.00 5.19
426 1014 2.813179 GCATGTAAGCCCTGACGCG 61.813 63.158 3.53 3.53 0.00 6.01
427 1015 2.173669 CATGTAAGCCCTGACGCGG 61.174 63.158 12.47 0.00 0.00 6.46
437 1025 3.982424 CTGACGCGGCGCAAATGTC 62.982 63.158 32.61 27.82 0.00 3.06
439 1027 4.383602 ACGCGGCGCAAATGTCAC 62.384 61.111 32.61 0.00 0.00 3.67
442 1030 2.480555 CGGCGCAAATGTCACCTC 59.519 61.111 10.83 0.00 0.00 3.85
443 1031 2.324330 CGGCGCAAATGTCACCTCA 61.324 57.895 10.83 0.00 0.00 3.86
448 1036 2.653890 CGCAAATGTCACCTCAGTTTG 58.346 47.619 0.00 0.00 33.98 2.93
450 1038 3.489059 CGCAAATGTCACCTCAGTTTGTT 60.489 43.478 0.00 0.00 33.53 2.83
451 1039 4.044426 GCAAATGTCACCTCAGTTTGTTC 58.956 43.478 0.00 0.00 33.53 3.18
456 1044 3.195661 GTCACCTCAGTTTGTTCGACTT 58.804 45.455 0.00 0.00 0.00 3.01
457 1045 3.621715 GTCACCTCAGTTTGTTCGACTTT 59.378 43.478 0.00 0.00 0.00 2.66
462 1050 4.094294 CCTCAGTTTGTTCGACTTTTGTGA 59.906 41.667 0.00 0.00 0.00 3.58
464 1052 4.452795 TCAGTTTGTTCGACTTTTGTGACA 59.547 37.500 0.00 0.00 0.00 3.58
471 1059 3.993547 TCGACTTTTGTGACAACGTTTC 58.006 40.909 0.00 0.60 0.00 2.78
476 1064 6.388259 ACTTTTGTGACAACGTTTCAAATG 57.612 33.333 0.00 12.04 32.97 2.32
483 1071 5.746245 GTGACAACGTTTCAAATGGATTCAA 59.254 36.000 0.00 0.00 0.00 2.69
491 1079 5.726980 TTCAAATGGATTCAAGGGTTCAG 57.273 39.130 0.00 0.00 0.00 3.02
492 1080 4.088634 TCAAATGGATTCAAGGGTTCAGG 58.911 43.478 0.00 0.00 0.00 3.86
493 1081 3.833559 AATGGATTCAAGGGTTCAGGT 57.166 42.857 0.00 0.00 0.00 4.00
494 1082 3.833559 ATGGATTCAAGGGTTCAGGTT 57.166 42.857 0.00 0.00 0.00 3.50
495 1083 3.154827 TGGATTCAAGGGTTCAGGTTC 57.845 47.619 0.00 0.00 0.00 3.62
496 1084 2.445145 TGGATTCAAGGGTTCAGGTTCA 59.555 45.455 0.00 0.00 0.00 3.18
497 1085 3.084786 GGATTCAAGGGTTCAGGTTCAG 58.915 50.000 0.00 0.00 0.00 3.02
498 1086 3.498661 GGATTCAAGGGTTCAGGTTCAGT 60.499 47.826 0.00 0.00 0.00 3.41
499 1087 2.638480 TCAAGGGTTCAGGTTCAGTG 57.362 50.000 0.00 0.00 0.00 3.66
500 1088 2.123589 TCAAGGGTTCAGGTTCAGTGA 58.876 47.619 0.00 0.00 0.00 3.41
501 1089 2.158813 TCAAGGGTTCAGGTTCAGTGAC 60.159 50.000 0.00 0.00 0.00 3.67
506 1094 0.031585 TTCAGGTTCAGTGACGACGG 59.968 55.000 0.00 0.00 0.00 4.79
510 1098 1.563173 GTTCAGTGACGACGGTTGC 59.437 57.895 0.00 0.00 0.00 4.17
524 1112 4.319190 CGACGGTTGCAGTTCTTATGAAAA 60.319 41.667 0.00 0.00 33.52 2.29
529 1120 7.593644 ACGGTTGCAGTTCTTATGAAAATTTAC 59.406 33.333 0.00 0.00 33.52 2.01
534 1125 9.809096 TGCAGTTCTTATGAAAATTTACAACAA 57.191 25.926 0.00 0.00 33.52 2.83
542 1133 7.671495 ATGAAAATTTACAACAAATCTGGGC 57.329 32.000 0.00 0.00 0.00 5.36
544 1135 3.866883 ATTTACAACAAATCTGGGCCG 57.133 42.857 0.00 0.00 0.00 6.13
545 1136 1.540267 TTACAACAAATCTGGGCCGG 58.460 50.000 5.83 5.83 0.00 6.13
559 1158 0.030235 GGCCGGGAATATTTGAACGC 59.970 55.000 2.18 0.00 0.00 4.84
565 1164 4.124238 CGGGAATATTTGAACGCTTAGGA 58.876 43.478 0.00 0.00 0.00 2.94
566 1165 4.211374 CGGGAATATTTGAACGCTTAGGAG 59.789 45.833 0.00 0.00 0.00 3.69
601 1200 2.590282 TGGGTACTTAGTTTTGCCCC 57.410 50.000 10.01 0.00 35.39 5.80
602 1201 1.781529 TGGGTACTTAGTTTTGCCCCA 59.218 47.619 10.01 0.00 38.31 4.96
603 1202 2.165167 GGGTACTTAGTTTTGCCCCAC 58.835 52.381 0.00 0.00 0.00 4.61
606 1205 2.445682 ACTTAGTTTTGCCCCACACA 57.554 45.000 0.00 0.00 0.00 3.72
613 1212 1.599606 TTTGCCCCACACACACACAC 61.600 55.000 0.00 0.00 0.00 3.82
652 1259 4.529109 ACTCTGTAGAGGCTCTGTTTTC 57.471 45.455 26.95 11.78 46.13 2.29
654 1261 2.891580 TCTGTAGAGGCTCTGTTTTCGT 59.108 45.455 26.95 0.16 0.00 3.85
668 1275 4.717629 TCGTTCACCAGGCGAGCG 62.718 66.667 7.37 7.37 38.30 5.03
714 1321 1.303317 ACCAACCATCCAAGCCGAC 60.303 57.895 0.00 0.00 0.00 4.79
756 1363 3.400599 AAAGCGGCCCGGTAGGATG 62.401 63.158 8.88 0.00 41.02 3.51
771 1378 1.064946 GATGGACCTCTCGCAGTCG 59.935 63.158 0.00 0.00 33.66 4.18
899 1552 2.287608 CGAGCTTTTCCCAACAGTTTCC 60.288 50.000 0.00 0.00 0.00 3.13
933 1590 2.066999 GCCTCCATCGTCTTCCCCT 61.067 63.158 0.00 0.00 0.00 4.79
953 1611 3.457234 CTCGTCGAATCAATCCAATCCA 58.543 45.455 0.00 0.00 0.00 3.41
954 1612 3.194861 TCGTCGAATCAATCCAATCCAC 58.805 45.455 0.00 0.00 0.00 4.02
955 1613 2.287915 CGTCGAATCAATCCAATCCACC 59.712 50.000 0.00 0.00 0.00 4.61
961 1619 1.284785 TCAATCCAATCCACCCCAGTC 59.715 52.381 0.00 0.00 0.00 3.51
964 1622 0.774096 TCCAATCCACCCCAGTCCAA 60.774 55.000 0.00 0.00 0.00 3.53
986 1644 2.586838 TCCATTCCATTCCATTCCACCT 59.413 45.455 0.00 0.00 0.00 4.00
994 1652 5.130477 TCCATTCCATTCCACCTAGAACTAC 59.870 44.000 0.00 0.00 0.00 2.73
996 1654 3.028850 TCCATTCCACCTAGAACTACCG 58.971 50.000 0.00 0.00 0.00 4.02
998 1656 3.181478 CCATTCCACCTAGAACTACCGAC 60.181 52.174 0.00 0.00 0.00 4.79
1206 1882 1.566298 CCTTCTTCCAGTCCCAGGGG 61.566 65.000 5.33 0.92 0.00 4.79
1363 2159 9.790389 CTTCTTTCACCACTACTATACTACAAG 57.210 37.037 0.00 0.00 0.00 3.16
1365 2161 9.524496 TCTTTCACCACTACTATACTACAAGAA 57.476 33.333 0.00 0.00 0.00 2.52
1368 2164 8.640063 TCACCACTACTATACTACAAGAAACA 57.360 34.615 0.00 0.00 0.00 2.83
1383 2179 9.594478 CTACAAGAAACAATTTACAGGGTTTTT 57.406 29.630 0.00 0.00 33.92 1.94
1385 2181 9.373603 ACAAGAAACAATTTACAGGGTTTTTAC 57.626 29.630 0.00 0.00 33.92 2.01
1391 2187 6.543100 ACAATTTACAGGGTTTTTACTGACGA 59.457 34.615 0.00 0.00 38.09 4.20
1395 2191 5.900865 ACAGGGTTTTTACTGACGAAAAA 57.099 34.783 0.00 0.00 38.09 1.94
1396 2192 6.459670 ACAGGGTTTTTACTGACGAAAAAT 57.540 33.333 0.00 0.00 37.89 1.82
1397 2193 6.270064 ACAGGGTTTTTACTGACGAAAAATG 58.730 36.000 0.00 0.00 37.89 2.32
1406 2204 7.665561 TTACTGACGAAAAATGTGATGATGA 57.334 32.000 0.00 0.00 0.00 2.92
1422 2220 3.284617 TGATGATGCAGATGTCTTTGGG 58.715 45.455 0.00 0.00 0.00 4.12
1449 2247 3.052082 TCGACGGACGACTCCACC 61.052 66.667 0.00 0.00 46.45 4.61
1450 2248 4.112341 CGACGGACGACTCCACCC 62.112 72.222 0.00 0.00 45.77 4.61
1524 2322 4.527583 GCCGAGCCTGAGCCAGAG 62.528 72.222 4.00 0.00 41.25 3.35
1525 2323 4.527583 CCGAGCCTGAGCCAGAGC 62.528 72.222 4.00 5.88 41.25 4.09
1526 2324 3.767806 CGAGCCTGAGCCAGAGCA 61.768 66.667 13.69 0.00 43.56 4.26
1542 2340 2.174107 CATGCAGCCACAACGTCG 59.826 61.111 0.00 0.00 0.00 5.12
1578 2376 2.435059 GGTGCGACTGAAGCTCCC 60.435 66.667 0.00 0.00 41.05 4.30
1744 2542 1.004560 ACCGTGCTCATCAGTGTGG 60.005 57.895 0.00 0.00 0.00 4.17
1797 2598 0.250727 CCCCCATAGCCATTACCGTG 60.251 60.000 0.00 0.00 0.00 4.94
1806 2607 0.321210 CCATTACCGTGACACCAGCA 60.321 55.000 0.00 0.00 0.00 4.41
1823 2624 3.498397 CCAGCAAATGTATCGATGTACCC 59.502 47.826 8.54 0.00 0.00 3.69
1828 2629 4.778534 AATGTATCGATGTACCCTACGG 57.221 45.455 8.54 0.00 0.00 4.02
1829 2630 1.881973 TGTATCGATGTACCCTACGGC 59.118 52.381 8.54 0.00 0.00 5.68
1876 2680 2.877786 TGTTACACCATGTTGCAGTGAG 59.122 45.455 9.75 0.00 35.47 3.51
1976 2780 4.156556 ACAATGGAATCAGACAATGTTCCG 59.843 41.667 0.00 0.00 39.77 4.30
1977 2781 2.710377 TGGAATCAGACAATGTTCCGG 58.290 47.619 0.00 0.00 39.77 5.14
1978 2782 1.401905 GGAATCAGACAATGTTCCGGC 59.598 52.381 0.00 0.00 32.85 6.13
1979 2783 2.083774 GAATCAGACAATGTTCCGGCA 58.916 47.619 0.00 0.00 0.00 5.69
1980 2784 1.742761 ATCAGACAATGTTCCGGCAG 58.257 50.000 0.00 0.00 0.00 4.85
1982 2786 0.321564 CAGACAATGTTCCGGCAGGA 60.322 55.000 0.00 0.00 46.75 3.86
2018 2822 3.696045 TGCCATAATTCCCCAATATCCG 58.304 45.455 0.00 0.00 0.00 4.18
2086 2891 1.409064 CGGATGAAGTAGCCTAGCACA 59.591 52.381 0.00 0.00 30.73 4.57
2238 3055 2.103094 CTGAAATACGAGGCTGGGATCA 59.897 50.000 0.51 0.00 0.00 2.92
2261 3078 0.312102 GGTGCTTGTTCTGCTTGTCC 59.688 55.000 0.00 0.00 0.00 4.02
2344 3161 4.854291 CACAACAGCGACTGTAAAACAAAA 59.146 37.500 11.92 0.00 44.62 2.44
2346 3163 5.741982 ACAACAGCGACTGTAAAACAAAATC 59.258 36.000 11.92 0.00 44.62 2.17
2348 3165 3.906008 CAGCGACTGTAAAACAAAATCGG 59.094 43.478 0.00 0.00 32.21 4.18
2385 3202 2.738743 ACGGATGAGGCCATGAAAAAT 58.261 42.857 5.01 0.00 32.09 1.82
2444 3261 5.103290 TCCAAAACTAACTCGAAACATGC 57.897 39.130 0.00 0.00 0.00 4.06
2570 3480 1.068753 CTATGCCTCTCCACAGCGG 59.931 63.158 0.00 0.00 0.00 5.52
2578 3488 3.682292 CTCCACAGCGGTTAGGCCC 62.682 68.421 0.00 0.00 35.57 5.80
2596 3506 1.298667 CTCCCACCCGTCCGATTTT 59.701 57.895 0.00 0.00 0.00 1.82
2629 3539 2.396608 CCTGGATCACCTCTGTCATCT 58.603 52.381 0.00 0.00 37.04 2.90
2651 3561 2.340328 CCTGCCCCACTTTTACCGC 61.340 63.158 0.00 0.00 0.00 5.68
2716 3626 1.002366 CTTCGGCGATTTCCTGTGAG 58.998 55.000 11.76 0.00 0.00 3.51
2717 3627 1.019278 TTCGGCGATTTCCTGTGAGC 61.019 55.000 11.76 0.00 0.00 4.26
2729 3639 0.179048 CTGTGAGCTGGACCAACACA 60.179 55.000 20.18 20.18 38.78 3.72
2730 3640 0.473755 TGTGAGCTGGACCAACACAT 59.526 50.000 18.58 0.00 36.72 3.21
2731 3641 1.133823 TGTGAGCTGGACCAACACATT 60.134 47.619 18.58 0.00 36.72 2.71
2733 3643 1.142667 TGAGCTGGACCAACACATTGA 59.857 47.619 0.00 0.00 38.15 2.57
2734 3644 1.808945 GAGCTGGACCAACACATTGAG 59.191 52.381 0.00 0.00 38.15 3.02
2735 3645 0.242017 GCTGGACCAACACATTGAGC 59.758 55.000 0.00 0.00 38.15 4.26
2736 3646 0.883833 CTGGACCAACACATTGAGCC 59.116 55.000 0.00 0.00 38.15 4.70
2737 3647 0.184692 TGGACCAACACATTGAGCCA 59.815 50.000 0.00 0.00 38.15 4.75
2738 3648 0.883833 GGACCAACACATTGAGCCAG 59.116 55.000 0.00 0.00 38.15 4.85
2739 3649 0.883833 GACCAACACATTGAGCCAGG 59.116 55.000 0.00 0.00 38.15 4.45
2740 3650 0.540365 ACCAACACATTGAGCCAGGG 60.540 55.000 0.00 0.00 38.15 4.45
2741 3651 0.540365 CCAACACATTGAGCCAGGGT 60.540 55.000 0.00 0.00 38.15 4.34
2742 3652 1.271871 CCAACACATTGAGCCAGGGTA 60.272 52.381 0.00 0.00 38.15 3.69
2743 3653 2.513753 CAACACATTGAGCCAGGGTAA 58.486 47.619 0.00 0.00 38.15 2.85
2744 3654 2.200373 ACACATTGAGCCAGGGTAAC 57.800 50.000 0.00 0.00 0.00 2.50
2745 3655 1.705186 ACACATTGAGCCAGGGTAACT 59.295 47.619 0.00 0.00 0.00 2.24
2746 3656 2.910319 ACACATTGAGCCAGGGTAACTA 59.090 45.455 0.00 0.00 0.00 2.24
2747 3657 3.270877 CACATTGAGCCAGGGTAACTAC 58.729 50.000 0.00 0.00 0.00 2.73
2748 3658 2.093658 ACATTGAGCCAGGGTAACTACG 60.094 50.000 0.00 0.00 0.00 3.51
2749 3659 1.636148 TTGAGCCAGGGTAACTACGT 58.364 50.000 0.00 0.00 0.00 3.57
2750 3660 0.892755 TGAGCCAGGGTAACTACGTG 59.107 55.000 0.00 0.00 0.00 4.49
2751 3661 0.459759 GAGCCAGGGTAACTACGTGC 60.460 60.000 0.00 0.00 0.00 5.34
2752 3662 1.808390 GCCAGGGTAACTACGTGCG 60.808 63.158 0.00 0.00 0.00 5.34
2753 3663 1.808390 CCAGGGTAACTACGTGCGC 60.808 63.158 0.00 0.00 0.00 6.09
2754 3664 2.156446 CAGGGTAACTACGTGCGCG 61.156 63.158 19.78 19.78 44.93 6.86
2755 3665 2.179018 GGGTAACTACGTGCGCGA 59.821 61.111 28.73 9.16 42.00 5.87
2756 3666 1.444212 GGGTAACTACGTGCGCGAA 60.444 57.895 28.73 0.00 42.00 4.70
2757 3667 1.677353 GGGTAACTACGTGCGCGAAC 61.677 60.000 28.73 9.55 42.00 3.95
2758 3668 1.677353 GGTAACTACGTGCGCGAACC 61.677 60.000 28.73 19.32 42.00 3.62
2759 3669 1.444212 TAACTACGTGCGCGAACCC 60.444 57.895 28.73 0.00 42.00 4.11
2760 3670 2.139888 TAACTACGTGCGCGAACCCA 62.140 55.000 28.73 5.27 42.00 4.51
2761 3671 3.179265 CTACGTGCGCGAACCCAG 61.179 66.667 28.73 4.89 42.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.147704 TGTTTATATGTTCTGTCACTTGACTGA 58.852 33.333 13.26 13.26 46.52 3.41
5 6 8.310406 TGTTTATATGTTCTGTCACTTGACTG 57.690 34.615 10.63 9.97 44.99 3.51
6 7 8.367911 TCTGTTTATATGTTCTGTCACTTGACT 58.632 33.333 10.63 0.00 44.99 3.41
7 8 8.534333 TCTGTTTATATGTTCTGTCACTTGAC 57.466 34.615 2.19 2.19 44.97 3.18
8 9 9.554395 TTTCTGTTTATATGTTCTGTCACTTGA 57.446 29.630 0.00 0.00 0.00 3.02
25 26 9.818796 GTGCAAAATTTTGTCTTTTTCTGTTTA 57.181 25.926 27.13 2.49 40.24 2.01
26 27 8.348507 TGTGCAAAATTTTGTCTTTTTCTGTTT 58.651 25.926 27.13 0.00 40.24 2.83
27 28 7.869800 TGTGCAAAATTTTGTCTTTTTCTGTT 58.130 26.923 27.13 0.00 40.24 3.16
28 29 7.387397 TCTGTGCAAAATTTTGTCTTTTTCTGT 59.613 29.630 27.13 0.00 40.24 3.41
29 30 7.741198 TCTGTGCAAAATTTTGTCTTTTTCTG 58.259 30.769 27.13 14.84 40.24 3.02
30 31 7.903995 TCTGTGCAAAATTTTGTCTTTTTCT 57.096 28.000 27.13 0.00 40.24 2.52
31 32 8.606602 AGATCTGTGCAAAATTTTGTCTTTTTC 58.393 29.630 27.13 18.34 40.24 2.29
32 33 8.496707 AGATCTGTGCAAAATTTTGTCTTTTT 57.503 26.923 27.13 12.26 40.24 1.94
33 34 7.225341 GGAGATCTGTGCAAAATTTTGTCTTTT 59.775 33.333 27.13 11.83 40.24 2.27
34 35 6.703165 GGAGATCTGTGCAAAATTTTGTCTTT 59.297 34.615 27.13 11.37 40.24 2.52
35 36 6.183360 TGGAGATCTGTGCAAAATTTTGTCTT 60.183 34.615 27.13 10.48 40.24 3.01
36 37 5.302568 TGGAGATCTGTGCAAAATTTTGTCT 59.697 36.000 27.13 20.98 40.24 3.41
37 38 5.531634 TGGAGATCTGTGCAAAATTTTGTC 58.468 37.500 27.13 20.36 40.24 3.18
38 39 5.534207 TGGAGATCTGTGCAAAATTTTGT 57.466 34.783 27.13 10.37 40.24 2.83
39 40 9.806203 TTATATGGAGATCTGTGCAAAATTTTG 57.194 29.630 23.74 23.74 41.03 2.44
41 42 9.412460 TCTTATATGGAGATCTGTGCAAAATTT 57.588 29.630 0.00 0.00 0.00 1.82
42 43 8.985315 TCTTATATGGAGATCTGTGCAAAATT 57.015 30.769 0.00 0.00 0.00 1.82
45 46 9.881649 GATATCTTATATGGAGATCTGTGCAAA 57.118 33.333 0.00 0.00 35.56 3.68
46 47 9.039165 TGATATCTTATATGGAGATCTGTGCAA 57.961 33.333 0.00 0.00 35.56 4.08
47 48 8.599624 TGATATCTTATATGGAGATCTGTGCA 57.400 34.615 0.00 0.00 35.56 4.57
48 49 9.478768 CATGATATCTTATATGGAGATCTGTGC 57.521 37.037 0.00 0.00 35.56 4.57
64 65 7.864882 CGGTCGATGCTATATTCATGATATCTT 59.135 37.037 3.98 0.00 33.09 2.40
65 66 7.229506 TCGGTCGATGCTATATTCATGATATCT 59.770 37.037 3.98 0.00 33.09 1.98
66 67 7.363431 TCGGTCGATGCTATATTCATGATATC 58.637 38.462 0.00 0.00 33.09 1.63
67 68 7.229506 TCTCGGTCGATGCTATATTCATGATAT 59.770 37.037 0.00 0.00 35.19 1.63
68 69 6.542370 TCTCGGTCGATGCTATATTCATGATA 59.458 38.462 0.00 0.00 0.00 2.15
69 70 5.358160 TCTCGGTCGATGCTATATTCATGAT 59.642 40.000 0.00 0.00 0.00 2.45
70 71 4.700213 TCTCGGTCGATGCTATATTCATGA 59.300 41.667 0.00 0.00 0.00 3.07
71 72 4.795795 GTCTCGGTCGATGCTATATTCATG 59.204 45.833 0.00 0.00 0.00 3.07
72 73 4.702612 AGTCTCGGTCGATGCTATATTCAT 59.297 41.667 0.00 0.00 0.00 2.57
73 74 4.072839 AGTCTCGGTCGATGCTATATTCA 58.927 43.478 0.00 0.00 0.00 2.57
74 75 4.688511 AGTCTCGGTCGATGCTATATTC 57.311 45.455 0.00 0.00 0.00 1.75
75 76 5.221263 ACAAAGTCTCGGTCGATGCTATATT 60.221 40.000 0.00 0.00 0.00 1.28
76 77 4.278669 ACAAAGTCTCGGTCGATGCTATAT 59.721 41.667 0.00 0.00 0.00 0.86
77 78 3.630769 ACAAAGTCTCGGTCGATGCTATA 59.369 43.478 0.00 0.00 0.00 1.31
78 79 2.427453 ACAAAGTCTCGGTCGATGCTAT 59.573 45.455 0.00 0.00 0.00 2.97
79 80 1.816835 ACAAAGTCTCGGTCGATGCTA 59.183 47.619 0.00 0.00 0.00 3.49
80 81 0.603569 ACAAAGTCTCGGTCGATGCT 59.396 50.000 0.00 0.00 0.00 3.79
81 82 1.429463 AACAAAGTCTCGGTCGATGC 58.571 50.000 0.00 0.00 0.00 3.91
82 83 4.235360 ACTTAACAAAGTCTCGGTCGATG 58.765 43.478 0.00 0.00 0.00 3.84
83 84 4.483311 GACTTAACAAAGTCTCGGTCGAT 58.517 43.478 10.31 0.00 44.32 3.59
84 85 3.893720 GACTTAACAAAGTCTCGGTCGA 58.106 45.455 10.31 0.00 44.32 4.20
107 108 6.210078 GGGATTACTAAATCTCAGTCGACTG 58.790 44.000 34.76 34.76 41.55 3.51
108 109 5.008811 CGGGATTACTAAATCTCAGTCGACT 59.991 44.000 13.58 13.58 41.95 4.18
109 110 5.008415 TCGGGATTACTAAATCTCAGTCGAC 59.992 44.000 7.70 7.70 41.95 4.20
110 111 5.128205 TCGGGATTACTAAATCTCAGTCGA 58.872 41.667 0.00 0.00 41.95 4.20
111 112 5.434352 TCGGGATTACTAAATCTCAGTCG 57.566 43.478 0.00 0.00 41.95 4.18
122 123 9.938280 CCATCTGTTTTTATATCGGGATTACTA 57.062 33.333 0.00 0.00 0.00 1.82
123 124 8.656806 TCCATCTGTTTTTATATCGGGATTACT 58.343 33.333 0.00 0.00 0.00 2.24
124 125 8.842358 TCCATCTGTTTTTATATCGGGATTAC 57.158 34.615 0.00 0.00 0.00 1.89
125 126 9.854668 TTTCCATCTGTTTTTATATCGGGATTA 57.145 29.630 0.00 0.00 0.00 1.75
126 127 8.760980 TTTCCATCTGTTTTTATATCGGGATT 57.239 30.769 0.00 0.00 0.00 3.01
127 128 8.217799 TCTTTCCATCTGTTTTTATATCGGGAT 58.782 33.333 0.00 0.00 0.00 3.85
128 129 7.497909 GTCTTTCCATCTGTTTTTATATCGGGA 59.502 37.037 0.00 0.00 0.00 5.14
129 130 7.282224 TGTCTTTCCATCTGTTTTTATATCGGG 59.718 37.037 0.00 0.00 0.00 5.14
130 131 8.122952 GTGTCTTTCCATCTGTTTTTATATCGG 58.877 37.037 0.00 0.00 0.00 4.18
131 132 8.122952 GGTGTCTTTCCATCTGTTTTTATATCG 58.877 37.037 0.00 0.00 0.00 2.92
132 133 9.178758 AGGTGTCTTTCCATCTGTTTTTATATC 57.821 33.333 0.00 0.00 0.00 1.63
166 167 2.661176 ATTCCCTGGAGGTTCTACCA 57.339 50.000 0.00 0.00 41.95 3.25
180 181 3.732048 TTGTTGAACCCTCCTATTCCC 57.268 47.619 0.00 0.00 0.00 3.97
185 186 7.780745 TCACTTTAATTTTGTTGAACCCTCCTA 59.219 33.333 0.00 0.00 0.00 2.94
213 215 4.281688 CAGATTCAGGTTCCACCAATTTGT 59.718 41.667 0.00 0.00 41.95 2.83
220 222 3.425162 AGTTCAGATTCAGGTTCCACC 57.575 47.619 0.00 0.00 38.99 4.61
221 223 4.020128 ACCTAGTTCAGATTCAGGTTCCAC 60.020 45.833 0.00 0.00 36.16 4.02
222 224 4.168101 ACCTAGTTCAGATTCAGGTTCCA 58.832 43.478 0.00 0.00 36.16 3.53
223 225 4.828072 ACCTAGTTCAGATTCAGGTTCC 57.172 45.455 0.00 0.00 36.16 3.62
283 286 4.463891 GCCTCCTCTGAAATTTGAATTGGA 59.536 41.667 0.00 0.00 0.00 3.53
317 320 4.064137 GCACAATGCCGTTTTAATTTGG 57.936 40.909 0.00 0.00 37.42 3.28
330 333 6.194796 TCTCAGTAAAATTAGGCACAATGC 57.805 37.500 0.00 0.00 44.08 3.56
331 334 6.749118 GCTTCTCAGTAAAATTAGGCACAATG 59.251 38.462 0.00 0.00 0.00 2.82
332 335 6.434028 TGCTTCTCAGTAAAATTAGGCACAAT 59.566 34.615 0.00 0.00 0.00 2.71
333 336 5.767665 TGCTTCTCAGTAAAATTAGGCACAA 59.232 36.000 0.00 0.00 0.00 3.33
334 337 5.181245 GTGCTTCTCAGTAAAATTAGGCACA 59.819 40.000 0.00 0.00 43.55 4.57
337 340 5.643777 TCAGTGCTTCTCAGTAAAATTAGGC 59.356 40.000 0.00 0.00 0.00 3.93
338 341 7.768120 AGATCAGTGCTTCTCAGTAAAATTAGG 59.232 37.037 0.00 0.00 0.00 2.69
339 342 8.715191 AGATCAGTGCTTCTCAGTAAAATTAG 57.285 34.615 0.00 0.00 0.00 1.73
340 343 8.535335 AGAGATCAGTGCTTCTCAGTAAAATTA 58.465 33.333 19.12 0.00 40.69 1.40
341 344 7.393216 AGAGATCAGTGCTTCTCAGTAAAATT 58.607 34.615 19.12 0.83 40.69 1.82
342 345 6.945218 AGAGATCAGTGCTTCTCAGTAAAAT 58.055 36.000 19.12 1.36 40.69 1.82
343 346 6.015095 TGAGAGATCAGTGCTTCTCAGTAAAA 60.015 38.462 19.12 0.36 40.69 1.52
344 347 5.478332 TGAGAGATCAGTGCTTCTCAGTAAA 59.522 40.000 19.12 3.80 40.69 2.01
345 348 5.012893 TGAGAGATCAGTGCTTCTCAGTAA 58.987 41.667 19.12 5.05 40.69 2.24
346 349 4.397730 GTGAGAGATCAGTGCTTCTCAGTA 59.602 45.833 19.12 7.31 40.69 2.74
347 350 3.193267 GTGAGAGATCAGTGCTTCTCAGT 59.807 47.826 19.12 5.49 40.69 3.41
348 351 3.444742 AGTGAGAGATCAGTGCTTCTCAG 59.555 47.826 19.12 0.00 40.69 3.35
350 353 4.175516 CAAGTGAGAGATCAGTGCTTCTC 58.824 47.826 12.53 12.53 38.93 2.87
351 354 3.055963 CCAAGTGAGAGATCAGTGCTTCT 60.056 47.826 0.00 0.00 0.00 2.85
354 357 2.255406 ACCAAGTGAGAGATCAGTGCT 58.745 47.619 0.00 0.00 0.00 4.40
356 359 6.892691 GTTTTAACCAAGTGAGAGATCAGTG 58.107 40.000 0.00 0.00 0.00 3.66
361 364 5.221661 ACTCGGTTTTAACCAAGTGAGAGAT 60.222 40.000 16.29 3.17 44.37 2.75
362 365 4.100498 ACTCGGTTTTAACCAAGTGAGAGA 59.900 41.667 16.29 2.78 44.37 3.10
363 366 4.377897 ACTCGGTTTTAACCAAGTGAGAG 58.622 43.478 16.29 12.76 44.37 3.20
364 367 4.411256 ACTCGGTTTTAACCAAGTGAGA 57.589 40.909 16.29 3.89 44.37 3.27
365 368 5.929992 TCATACTCGGTTTTAACCAAGTGAG 59.070 40.000 14.07 12.22 45.54 3.51
367 370 6.737254 ATCATACTCGGTTTTAACCAAGTG 57.263 37.500 14.07 0.75 45.54 3.16
372 375 6.531240 TGTCGTAATCATACTCGGTTTTAACC 59.469 38.462 1.42 1.42 45.76 2.85
373 376 7.510428 TGTCGTAATCATACTCGGTTTTAAC 57.490 36.000 0.00 0.00 0.00 2.01
374 377 7.814107 ACTTGTCGTAATCATACTCGGTTTTAA 59.186 33.333 0.00 0.00 0.00 1.52
375 378 7.315142 ACTTGTCGTAATCATACTCGGTTTTA 58.685 34.615 0.00 0.00 0.00 1.52
376 379 6.161381 ACTTGTCGTAATCATACTCGGTTTT 58.839 36.000 0.00 0.00 0.00 2.43
377 380 5.717119 ACTTGTCGTAATCATACTCGGTTT 58.283 37.500 0.00 0.00 0.00 3.27
378 381 5.320549 ACTTGTCGTAATCATACTCGGTT 57.679 39.130 0.00 0.00 0.00 4.44
379 382 4.978083 ACTTGTCGTAATCATACTCGGT 57.022 40.909 0.00 0.00 0.00 4.69
380 383 6.296365 TCTACTTGTCGTAATCATACTCGG 57.704 41.667 0.00 0.00 0.00 4.63
381 384 5.846994 GCTCTACTTGTCGTAATCATACTCG 59.153 44.000 0.00 0.00 0.00 4.18
385 973 4.023450 CGGGCTCTACTTGTCGTAATCATA 60.023 45.833 0.00 0.00 0.00 2.15
387 975 2.098607 CGGGCTCTACTTGTCGTAATCA 59.901 50.000 0.00 0.00 0.00 2.57
393 981 1.141881 ATGCGGGCTCTACTTGTCG 59.858 57.895 0.00 0.00 0.00 4.35
398 986 0.105039 GCTTACATGCGGGCTCTACT 59.895 55.000 0.00 0.00 0.00 2.57
399 987 0.880718 GGCTTACATGCGGGCTCTAC 60.881 60.000 0.00 0.00 0.00 2.59
401 989 2.190578 GGCTTACATGCGGGCTCT 59.809 61.111 0.00 0.00 0.00 4.09
405 993 1.819632 GTCAGGGCTTACATGCGGG 60.820 63.158 0.00 0.00 0.00 6.13
410 998 2.186903 CCGCGTCAGGGCTTACAT 59.813 61.111 4.92 0.00 0.00 2.29
419 1007 3.982424 GACATTTGCGCCGCGTCAG 62.982 63.158 15.34 4.35 0.00 3.51
422 1010 4.383602 GTGACATTTGCGCCGCGT 62.384 61.111 15.34 0.00 0.00 6.01
424 1012 3.667429 GAGGTGACATTTGCGCCGC 62.667 63.158 4.18 0.00 40.77 6.53
425 1013 2.244436 CTGAGGTGACATTTGCGCCG 62.244 60.000 4.18 0.00 40.77 6.46
426 1014 1.237285 ACTGAGGTGACATTTGCGCC 61.237 55.000 4.18 0.00 36.17 6.53
427 1015 0.593128 AACTGAGGTGACATTTGCGC 59.407 50.000 0.00 0.00 0.00 6.09
428 1016 2.033299 ACAAACTGAGGTGACATTTGCG 59.967 45.455 0.00 0.00 34.34 4.85
429 1017 3.715628 ACAAACTGAGGTGACATTTGC 57.284 42.857 0.00 0.00 34.34 3.68
430 1018 4.035091 TCGAACAAACTGAGGTGACATTTG 59.965 41.667 0.00 0.00 36.54 2.32
433 1021 3.131396 GTCGAACAAACTGAGGTGACAT 58.869 45.455 0.00 0.00 0.00 3.06
437 1025 4.142687 ACAAAAGTCGAACAAACTGAGGTG 60.143 41.667 0.00 0.00 0.00 4.00
439 1027 4.094294 TCACAAAAGTCGAACAAACTGAGG 59.906 41.667 0.00 0.00 0.00 3.86
442 1030 4.717991 TGTCACAAAAGTCGAACAAACTG 58.282 39.130 0.00 0.00 0.00 3.16
443 1031 5.151389 GTTGTCACAAAAGTCGAACAAACT 58.849 37.500 0.00 0.00 0.00 2.66
448 1036 3.378959 ACGTTGTCACAAAAGTCGAAC 57.621 42.857 5.37 0.00 0.00 3.95
450 1038 3.432592 TGAAACGTTGTCACAAAAGTCGA 59.567 39.130 0.00 0.00 0.00 4.20
451 1039 3.738399 TGAAACGTTGTCACAAAAGTCG 58.262 40.909 0.00 0.00 0.00 4.18
456 1044 5.060662 TCCATTTGAAACGTTGTCACAAA 57.939 34.783 18.12 18.12 35.49 2.83
457 1045 4.703645 TCCATTTGAAACGTTGTCACAA 57.296 36.364 0.00 4.06 0.00 3.33
462 1050 5.288804 CCTTGAATCCATTTGAAACGTTGT 58.711 37.500 0.00 0.00 0.00 3.32
464 1052 4.343814 ACCCTTGAATCCATTTGAAACGTT 59.656 37.500 0.00 0.00 0.00 3.99
471 1059 3.834231 ACCTGAACCCTTGAATCCATTTG 59.166 43.478 0.00 0.00 0.00 2.32
476 1064 3.084786 CTGAACCTGAACCCTTGAATCC 58.915 50.000 0.00 0.00 0.00 3.01
483 1071 0.393077 CGTCACTGAACCTGAACCCT 59.607 55.000 0.00 0.00 0.00 4.34
491 1079 1.828331 GCAACCGTCGTCACTGAACC 61.828 60.000 0.00 0.00 0.00 3.62
492 1080 1.149361 TGCAACCGTCGTCACTGAAC 61.149 55.000 0.00 0.00 0.00 3.18
493 1081 0.874175 CTGCAACCGTCGTCACTGAA 60.874 55.000 0.00 0.00 0.00 3.02
494 1082 1.299850 CTGCAACCGTCGTCACTGA 60.300 57.895 0.00 0.00 0.00 3.41
495 1083 1.151777 AACTGCAACCGTCGTCACTG 61.152 55.000 0.00 0.00 0.00 3.66
496 1084 0.874607 GAACTGCAACCGTCGTCACT 60.875 55.000 0.00 0.00 0.00 3.41
497 1085 0.874607 AGAACTGCAACCGTCGTCAC 60.875 55.000 0.00 0.00 0.00 3.67
498 1086 0.179094 AAGAACTGCAACCGTCGTCA 60.179 50.000 0.00 0.00 0.00 4.35
499 1087 1.774639 TAAGAACTGCAACCGTCGTC 58.225 50.000 0.00 0.00 0.00 4.20
500 1088 2.066262 CATAAGAACTGCAACCGTCGT 58.934 47.619 0.00 0.00 0.00 4.34
501 1089 2.333926 TCATAAGAACTGCAACCGTCG 58.666 47.619 0.00 0.00 0.00 5.12
524 1112 2.495669 CCGGCCCAGATTTGTTGTAAAT 59.504 45.455 0.00 0.00 0.00 1.40
529 1120 0.897863 TTCCCGGCCCAGATTTGTTG 60.898 55.000 0.00 0.00 0.00 3.33
534 1125 2.176798 TCAAATATTCCCGGCCCAGATT 59.823 45.455 0.00 0.00 0.00 2.40
542 1133 3.250040 CCTAAGCGTTCAAATATTCCCGG 59.750 47.826 0.00 0.00 0.00 5.73
544 1135 5.365619 TCTCCTAAGCGTTCAAATATTCCC 58.634 41.667 0.00 0.00 0.00 3.97
545 1136 5.467063 CCTCTCCTAAGCGTTCAAATATTCC 59.533 44.000 0.00 0.00 0.00 3.01
559 1158 2.073101 GGGCCCCACCTCTCCTAAG 61.073 68.421 12.23 0.00 39.10 2.18
581 1180 2.380590 TGGGGCAAAACTAAGTACCCAT 59.619 45.455 0.00 0.00 41.48 4.00
591 1190 0.613292 TGTGTGTGTGGGGCAAAACT 60.613 50.000 0.00 0.00 0.00 2.66
634 1233 3.305398 ACGAAAACAGAGCCTCTACAG 57.695 47.619 0.00 0.00 0.00 2.74
635 1234 3.069016 TGAACGAAAACAGAGCCTCTACA 59.931 43.478 0.00 0.00 0.00 2.74
636 1235 3.429207 GTGAACGAAAACAGAGCCTCTAC 59.571 47.826 0.00 0.00 0.00 2.59
668 1275 2.517875 ATTGCCTCCCATGCTCGC 60.518 61.111 0.00 0.00 0.00 5.03
669 1276 2.249535 CGATTGCCTCCCATGCTCG 61.250 63.158 0.00 0.00 0.00 5.03
670 1277 1.895707 CCGATTGCCTCCCATGCTC 60.896 63.158 0.00 0.00 0.00 4.26
671 1278 2.194056 CCGATTGCCTCCCATGCT 59.806 61.111 0.00 0.00 0.00 3.79
672 1279 2.908940 CCCGATTGCCTCCCATGC 60.909 66.667 0.00 0.00 0.00 4.06
673 1280 1.076777 AACCCGATTGCCTCCCATG 60.077 57.895 0.00 0.00 0.00 3.66
677 1284 3.140814 GCCAACCCGATTGCCTCC 61.141 66.667 0.00 0.00 36.93 4.30
694 1301 2.398554 CGGCTTGGATGGTTGGTCG 61.399 63.158 0.00 0.00 0.00 4.79
828 1437 4.101448 CTAACTGCTGCCCGGGCT 62.101 66.667 43.34 26.37 42.51 5.19
899 1552 1.890510 GGCGGCAGGGTTTATACGG 60.891 63.158 3.07 0.00 0.00 4.02
933 1590 3.194861 GTGGATTGGATTGATTCGACGA 58.805 45.455 0.00 0.00 0.00 4.20
953 1611 0.631212 GGAATGGATTGGACTGGGGT 59.369 55.000 0.00 0.00 0.00 4.95
954 1612 0.630673 TGGAATGGATTGGACTGGGG 59.369 55.000 0.00 0.00 0.00 4.96
955 1613 2.761786 ATGGAATGGATTGGACTGGG 57.238 50.000 0.00 0.00 0.00 4.45
961 1619 3.968649 TGGAATGGAATGGAATGGATTGG 59.031 43.478 0.00 0.00 0.00 3.16
964 1622 3.208234 AGGTGGAATGGAATGGAATGGAT 59.792 43.478 0.00 0.00 0.00 3.41
986 1644 1.945394 GAGCCATCGTCGGTAGTTCTA 59.055 52.381 0.00 0.00 0.00 2.10
1068 1726 0.506080 GCATCGTCATCGTCATCTGC 59.494 55.000 0.00 0.00 38.33 4.26
1108 1784 4.767255 GCACGGGGACAGGCTGAG 62.767 72.222 23.66 9.08 0.00 3.35
1245 1921 4.194720 CCGAGGACGAGGCCGAAG 62.195 72.222 0.00 0.00 42.66 3.79
1326 2002 0.836400 TGAAAGAAGGGAGGCGAGGT 60.836 55.000 0.00 0.00 0.00 3.85
1328 2004 0.391793 GGTGAAAGAAGGGAGGCGAG 60.392 60.000 0.00 0.00 0.00 5.03
1331 2009 0.402121 AGTGGTGAAAGAAGGGAGGC 59.598 55.000 0.00 0.00 0.00 4.70
1363 2159 9.027129 GTCAGTAAAAACCCTGTAAATTGTTTC 57.973 33.333 0.00 0.00 31.01 2.78
1365 2161 7.067251 TCGTCAGTAAAAACCCTGTAAATTGTT 59.933 33.333 0.00 0.00 0.00 2.83
1368 2164 7.571080 TTCGTCAGTAAAAACCCTGTAAATT 57.429 32.000 0.00 0.00 0.00 1.82
1372 2168 6.998968 TTTTTCGTCAGTAAAAACCCTGTA 57.001 33.333 0.00 0.00 32.40 2.74
1379 2175 9.179552 CATCATCACATTTTTCGTCAGTAAAAA 57.820 29.630 0.00 0.00 39.41 1.94
1383 2179 7.677041 GCATCATCATCACATTTTTCGTCAGTA 60.677 37.037 0.00 0.00 0.00 2.74
1385 2181 5.454554 GCATCATCATCACATTTTTCGTCAG 59.545 40.000 0.00 0.00 0.00 3.51
1391 2187 6.873997 ACATCTGCATCATCATCACATTTTT 58.126 32.000 0.00 0.00 0.00 1.94
1395 2191 4.974399 AGACATCTGCATCATCATCACAT 58.026 39.130 0.00 0.00 0.00 3.21
1396 2192 4.417426 AGACATCTGCATCATCATCACA 57.583 40.909 0.00 0.00 0.00 3.58
1397 2193 5.505819 CCAAAGACATCTGCATCATCATCAC 60.506 44.000 0.00 0.00 0.00 3.06
1406 2204 1.033746 CGCCCCAAAGACATCTGCAT 61.034 55.000 0.00 0.00 0.00 3.96
1453 2251 4.362476 GGCCTTTGCGGTTGGCTG 62.362 66.667 0.00 0.00 45.45 4.85
1521 2319 2.330372 CGTTGTGGCTGCATGCTCT 61.330 57.895 20.33 0.00 42.39 4.09
1522 2320 2.177531 CGTTGTGGCTGCATGCTC 59.822 61.111 20.33 10.52 42.39 4.26
1523 2321 2.595463 ACGTTGTGGCTGCATGCT 60.595 55.556 20.33 0.00 42.39 3.79
1524 2322 2.126734 GACGTTGTGGCTGCATGC 60.127 61.111 11.82 11.82 41.94 4.06
1525 2323 2.174107 CGACGTTGTGGCTGCATG 59.826 61.111 0.50 0.00 0.00 4.06
1526 2324 2.030412 TCGACGTTGTGGCTGCAT 59.970 55.556 0.50 0.00 0.00 3.96
1539 2337 4.517703 CTCTCCGGCGTCGTCGAC 62.518 72.222 22.65 15.51 42.36 4.20
1797 2598 3.623060 ACATCGATACATTTGCTGGTGTC 59.377 43.478 0.00 0.00 0.00 3.67
1823 2624 0.933509 GAATCTACACCGCGCCGTAG 60.934 60.000 20.84 20.84 37.12 3.51
1828 2629 2.526120 GCCTGAATCTACACCGCGC 61.526 63.158 0.00 0.00 0.00 6.86
1829 2630 1.883084 GGCCTGAATCTACACCGCG 60.883 63.158 0.00 0.00 0.00 6.46
1876 2680 6.223138 TCGAACACATGAACTGTAACATTC 57.777 37.500 0.00 0.00 35.91 2.67
1977 2781 3.798202 CAGGTAGGTGTTATTCTCCTGC 58.202 50.000 0.00 0.00 39.91 4.85
1978 2782 3.432326 GGCAGGTAGGTGTTATTCTCCTG 60.432 52.174 0.00 0.00 39.91 3.86
1979 2783 2.772515 GGCAGGTAGGTGTTATTCTCCT 59.227 50.000 0.00 0.00 42.01 3.69
1980 2784 2.504175 TGGCAGGTAGGTGTTATTCTCC 59.496 50.000 0.00 0.00 0.00 3.71
1982 2786 5.968676 TTATGGCAGGTAGGTGTTATTCT 57.031 39.130 0.00 0.00 0.00 2.40
1984 2788 6.068670 GGAATTATGGCAGGTAGGTGTTATT 58.931 40.000 0.00 0.00 0.00 1.40
1990 2794 1.780919 GGGGAATTATGGCAGGTAGGT 59.219 52.381 0.00 0.00 0.00 3.08
2018 2822 4.320608 TCTTTTCACCATTTCCTTGTGC 57.679 40.909 0.00 0.00 0.00 4.57
2086 2891 8.540388 ACATATTAACTGTAGACTGGTGACATT 58.460 33.333 0.00 0.00 41.51 2.71
2238 3055 0.106015 AAGCAGAACAAGCACCCCTT 60.106 50.000 0.00 0.00 0.00 3.95
2261 3078 3.189287 GGACTTATGCTGGTTGAGTTGTG 59.811 47.826 0.00 0.00 0.00 3.33
2344 3161 4.630069 CGTTAGTGACATTTTCTTCCCGAT 59.370 41.667 0.00 0.00 0.00 4.18
2346 3163 3.124636 CCGTTAGTGACATTTTCTTCCCG 59.875 47.826 0.00 0.00 0.00 5.14
2348 3165 5.642063 TCATCCGTTAGTGACATTTTCTTCC 59.358 40.000 0.00 0.00 0.00 3.46
2385 3202 9.722184 TGGATTTTGAATGAATTTTATCAAGCA 57.278 25.926 0.00 0.00 33.71 3.91
2427 3244 4.134563 ACCTTGCATGTTTCGAGTTAGTT 58.865 39.130 0.00 0.00 0.00 2.24
2547 3457 1.365633 GTGGAGAGGCATAGCTCGG 59.634 63.158 0.00 0.00 31.95 4.63
2570 3480 3.793888 CGGGTGGGAGGGCCTAAC 61.794 72.222 5.73 5.38 0.00 2.34
2578 3488 0.538118 TAAAATCGGACGGGTGGGAG 59.462 55.000 0.00 0.00 0.00 4.30
2596 3506 1.072806 GATCCAGGCCATGCATGTCTA 59.927 52.381 24.58 8.67 38.76 2.59
2629 3539 0.699981 GTAAAAGTGGGGCAGGGGTA 59.300 55.000 0.00 0.00 0.00 3.69
2651 3561 1.417372 TACGTTTGGTAGCCGTTTCG 58.583 50.000 0.00 0.00 36.12 3.46
2716 3626 0.242017 GCTCAATGTGTTGGTCCAGC 59.758 55.000 0.00 0.00 35.99 4.85
2717 3627 0.883833 GGCTCAATGTGTTGGTCCAG 59.116 55.000 0.00 0.00 35.99 3.86
2729 3639 2.093658 CACGTAGTTACCCTGGCTCAAT 60.094 50.000 0.00 0.00 41.61 2.57
2730 3640 1.274167 CACGTAGTTACCCTGGCTCAA 59.726 52.381 0.00 0.00 41.61 3.02
2731 3641 0.892755 CACGTAGTTACCCTGGCTCA 59.107 55.000 0.00 0.00 41.61 4.26
2733 3643 1.595357 GCACGTAGTTACCCTGGCT 59.405 57.895 0.00 0.00 41.61 4.75
2734 3644 1.808390 CGCACGTAGTTACCCTGGC 60.808 63.158 0.00 0.00 41.61 4.85
2735 3645 1.808390 GCGCACGTAGTTACCCTGG 60.808 63.158 0.30 0.00 41.61 4.45
2736 3646 2.156446 CGCGCACGTAGTTACCCTG 61.156 63.158 8.75 0.00 41.61 4.45
2737 3647 1.865788 TTCGCGCACGTAGTTACCCT 61.866 55.000 8.75 0.00 41.61 4.34
2738 3648 1.444212 TTCGCGCACGTAGTTACCC 60.444 57.895 8.75 0.00 41.61 3.69
2739 3649 1.677353 GGTTCGCGCACGTAGTTACC 61.677 60.000 8.75 0.00 41.61 2.85
2740 3650 1.677353 GGGTTCGCGCACGTAGTTAC 61.677 60.000 8.75 0.00 41.61 2.50
2741 3651 1.444212 GGGTTCGCGCACGTAGTTA 60.444 57.895 8.75 0.00 41.61 2.24
2742 3652 2.735857 GGGTTCGCGCACGTAGTT 60.736 61.111 8.75 0.00 41.61 2.24
2744 3654 3.179265 CTGGGTTCGCGCACGTAG 61.179 66.667 8.75 0.00 41.18 3.51


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

AutoCloner maintained by Alex Coulton.