Multiple sequence alignment - TraesCS1B01G367200

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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 TraesCS1B01G367200 chr1B 100.000 5975 0 0 1 5975 597804862 597810836 0.000000e+00 11034.0
1 TraesCS1B01G367200 chr1B 99.121 1024 9 0 4952 5975 655769509 655770532 0.000000e+00 1842.0
2 TraesCS1B01G367200 chr1A 92.022 3961 206 55 966 4853 537542052 537538129 0.000000e+00 5463.0
3 TraesCS1B01G367200 chr1A 99.023 1024 10 0 4952 5975 517045164 517046187 0.000000e+00 1836.0
4 TraesCS1B01G367200 chr1A 95.652 69 2 1 870 937 537542108 537542040 6.330000e-20 110.0
5 TraesCS1B01G367200 chr1D 96.385 2794 72 12 2176 4952 440404934 440407715 0.000000e+00 4573.0
6 TraesCS1B01G367200 chr1D 91.939 918 43 9 1241 2127 440404012 440404929 0.000000e+00 1256.0
7 TraesCS1B01G367200 chr1D 85.345 348 34 7 519 855 440403116 440403457 1.590000e-90 344.0
8 TraesCS1B01G367200 chr1D 78.132 471 47 27 29 478 440402685 440403120 1.290000e-61 248.0
9 TraesCS1B01G367200 chr7A 99.219 1024 8 0 4952 5975 281734723 281733700 0.000000e+00 1847.0
10 TraesCS1B01G367200 chr7B 99.026 1027 10 0 4949 5975 457408149 457407123 0.000000e+00 1842.0
11 TraesCS1B01G367200 chr7B 99.120 1023 9 0 4953 5975 468117246 468116224 0.000000e+00 1840.0
12 TraesCS1B01G367200 chr2B 99.119 1022 9 0 4954 5975 495153115 495152094 0.000000e+00 1838.0
13 TraesCS1B01G367200 chr5B 99.023 1024 10 0 4952 5975 48316269 48315246 0.000000e+00 1836.0
14 TraesCS1B01G367200 chr5B 77.823 248 29 9 515 748 491116002 491115767 4.860000e-26 130.0
15 TraesCS1B01G367200 chr4B 99.023 1024 10 0 4952 5975 5372869 5373892 0.000000e+00 1836.0
16 TraesCS1B01G367200 chr4A 98.274 1043 14 3 4937 5975 735616 734574 0.000000e+00 1823.0
17 TraesCS1B01G367200 chr5A 81.330 391 51 9 377 749 579869428 579869814 1.260000e-76 298.0
18 TraesCS1B01G367200 chr5A 80.997 321 36 15 439 745 656051532 656051223 1.300000e-56 231.0
19 TraesCS1B01G367200 chr5A 87.037 108 10 3 639 745 584510847 584510951 1.050000e-22 119.0
20 TraesCS1B01G367200 chr2D 80.846 402 46 20 358 740 37826256 37826645 2.730000e-73 287.0
21 TraesCS1B01G367200 chr3D 83.648 318 34 12 442 746 548716242 548716554 3.530000e-72 283.0
22 TraesCS1B01G367200 chr3D 80.925 346 44 10 417 746 347629241 347628902 2.760000e-63 254.0
23 TraesCS1B01G367200 chr3D 81.191 319 35 9 439 747 5754499 5754802 3.600000e-57 233.0
24 TraesCS1B01G367200 chr2A 83.077 325 33 10 439 745 118665173 118664853 5.900000e-70 276.0
25 TraesCS1B01G367200 chr3A 81.388 317 39 8 446 746 466814170 466813858 2.150000e-59 241.0
26 TraesCS1B01G367200 chr3A 80.938 320 42 15 439 745 644630019 644630332 1.000000e-57 235.0
27 TraesCS1B01G367200 chr3B 81.410 312 40 10 439 747 12097200 12097496 7.740000e-59 239.0
28 TraesCS1B01G367200 chrUn 79.245 371 51 13 386 747 35220860 35220507 1.000000e-57 235.0
29 TraesCS1B01G367200 chrUn 79.112 383 42 24 386 746 309799548 309799182 4.660000e-56 230.0
30 TraesCS1B01G367200 chrUn 78.346 254 29 17 386 626 315208295 315208055 2.250000e-29 141.0
31 TraesCS1B01G367200 chr6D 80.392 306 35 15 448 740 306127054 306126761 6.070000e-50 209.0
32 TraesCS1B01G367200 chr6A 88.406 69 8 0 153 221 94378683 94378615 3.840000e-12 84.2


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 TraesCS1B01G367200 chr1B 597804862 597810836 5974 False 11034.00 11034 100.00000 1 5975 1 chr1B.!!$F1 5974
1 TraesCS1B01G367200 chr1B 655769509 655770532 1023 False 1842.00 1842 99.12100 4952 5975 1 chr1B.!!$F2 1023
2 TraesCS1B01G367200 chr1A 537538129 537542108 3979 True 2786.50 5463 93.83700 870 4853 2 chr1A.!!$R1 3983
3 TraesCS1B01G367200 chr1A 517045164 517046187 1023 False 1836.00 1836 99.02300 4952 5975 1 chr1A.!!$F1 1023
4 TraesCS1B01G367200 chr1D 440402685 440407715 5030 False 1605.25 4573 87.95025 29 4952 4 chr1D.!!$F1 4923
5 TraesCS1B01G367200 chr7A 281733700 281734723 1023 True 1847.00 1847 99.21900 4952 5975 1 chr7A.!!$R1 1023
6 TraesCS1B01G367200 chr7B 457407123 457408149 1026 True 1842.00 1842 99.02600 4949 5975 1 chr7B.!!$R1 1026
7 TraesCS1B01G367200 chr7B 468116224 468117246 1022 True 1840.00 1840 99.12000 4953 5975 1 chr7B.!!$R2 1022
8 TraesCS1B01G367200 chr2B 495152094 495153115 1021 True 1838.00 1838 99.11900 4954 5975 1 chr2B.!!$R1 1021
9 TraesCS1B01G367200 chr5B 48315246 48316269 1023 True 1836.00 1836 99.02300 4952 5975 1 chr5B.!!$R1 1023
10 TraesCS1B01G367200 chr4B 5372869 5373892 1023 False 1836.00 1836 99.02300 4952 5975 1 chr4B.!!$F1 1023
11 TraesCS1B01G367200 chr4A 734574 735616 1042 True 1823.00 1823 98.27400 4937 5975 1 chr4A.!!$R1 1038

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
927 956 0.028770 CAGCGTTGTTTCGAAGCCAA 59.971 50.000 9.65 8.66 0.00 4.52 F
928 957 0.028902 AGCGTTGTTTCGAAGCCAAC 59.971 50.000 22.80 22.80 36.09 3.77 F
1106 1138 0.105401 CCCCCTCCTCTTCCTCCTAC 60.105 65.000 0.00 0.00 0.00 3.18 F
1761 1985 0.385974 GCACATTGACGGCAACTGTC 60.386 55.000 5.42 3.52 36.72 3.51 F
1908 2132 0.828022 TGGTGTTCTACTATGGCGGG 59.172 55.000 0.00 0.00 0.00 6.13 F
2079 2325 0.981183 TTCACGATACCAGTTGGGCT 59.019 50.000 2.79 0.00 42.05 5.19 F
2157 2403 0.984230 TTTCCTTCAGCTCGGTGGAT 59.016 50.000 0.00 0.00 0.00 3.41 F
2183 2429 2.180308 TCTCCCTCCTATCCTTTCCCTC 59.820 54.545 0.00 0.00 0.00 4.30 F
2311 2557 2.457598 AGGCAGTCACTTTCCGAGATA 58.542 47.619 0.00 0.00 0.00 1.98 F
4258 4537 1.511850 CAACACGAATGGAGCTCACA 58.488 50.000 17.19 11.60 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2093 1.000163 AGTGACTGACTAAGCGTGTGG 60.000 52.381 0.00 0.00 30.86 4.17 R
1972 2196 1.205893 GCTCCACAGAGAACAGGGTAG 59.794 57.143 0.00 0.00 43.39 3.18 R
1974 2198 1.821061 CGCTCCACAGAGAACAGGGT 61.821 60.000 0.00 0.00 43.39 4.34 R
3725 3998 0.676151 GCTTGCTAGCTTGCTCCTGT 60.676 55.000 20.64 0.00 44.27 4.00 R
3751 4024 2.371841 ACTGTGTTGGCCATGTCTAGAA 59.628 45.455 6.09 0.00 0.00 2.10 R
3773 4046 5.823861 AAACCCCAATTGCTTCTGTTAAT 57.176 34.783 0.00 0.00 0.00 1.40 R
3891 4169 7.973388 TCGTTCCCATGATCATTAAAATTTCAC 59.027 33.333 5.16 0.00 0.00 3.18 R
4252 4531 1.200948 GCTGAACCCATCTTTGTGAGC 59.799 52.381 0.00 0.00 0.00 4.26 R
4342 4621 0.732880 ACTTGGAGAATCGTGCGACG 60.733 55.000 0.00 2.79 44.19 5.12 R
5213 5499 1.909459 TATTCAGCGCAGGCCTCCAA 61.909 55.000 11.47 0.00 41.24 3.53 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
44 45 2.267961 CGGGTCCTGGTTGCCTAC 59.732 66.667 0.00 0.00 0.00 3.18
49 50 1.601166 GTCCTGGTTGCCTACGTTTT 58.399 50.000 0.00 0.00 0.00 2.43
51 52 3.340928 GTCCTGGTTGCCTACGTTTTAT 58.659 45.455 0.00 0.00 0.00 1.40
54 55 3.374058 CCTGGTTGCCTACGTTTTATGAG 59.626 47.826 0.00 0.00 0.00 2.90
55 56 4.250464 CTGGTTGCCTACGTTTTATGAGA 58.750 43.478 0.00 0.00 0.00 3.27
72 73 2.753452 TGAGAATCAGTCACCTACCGAC 59.247 50.000 0.00 0.00 42.56 4.79
73 74 3.018149 GAGAATCAGTCACCTACCGACT 58.982 50.000 0.00 0.00 44.55 4.18
74 75 3.018149 AGAATCAGTCACCTACCGACTC 58.982 50.000 0.00 0.00 41.80 3.36
75 76 2.810870 ATCAGTCACCTACCGACTCT 57.189 50.000 0.00 0.00 41.80 3.24
76 77 1.822506 TCAGTCACCTACCGACTCTG 58.177 55.000 0.00 0.00 41.80 3.35
83 84 2.231478 CACCTACCGACTCTGACAACAT 59.769 50.000 0.00 0.00 0.00 2.71
105 106 4.478206 TGTTTCAAAGCCAAATGGTCAA 57.522 36.364 0.71 0.00 37.57 3.18
108 109 1.339610 TCAAAGCCAAATGGTCAACCG 59.660 47.619 0.71 0.00 39.43 4.44
111 112 1.372872 GCCAAATGGTCAACCGTGC 60.373 57.895 0.71 0.00 39.43 5.34
112 113 1.288752 CCAAATGGTCAACCGTGCC 59.711 57.895 0.00 0.00 39.43 5.01
137 150 3.924610 GACGTTTAGCATGTCCGAATTC 58.075 45.455 0.00 0.00 35.57 2.17
139 152 4.000988 ACGTTTAGCATGTCCGAATTCTT 58.999 39.130 3.52 0.00 0.00 2.52
140 153 4.142902 ACGTTTAGCATGTCCGAATTCTTG 60.143 41.667 3.52 0.00 0.00 3.02
141 154 4.092821 CGTTTAGCATGTCCGAATTCTTGA 59.907 41.667 3.52 0.00 0.00 3.02
142 155 5.390461 CGTTTAGCATGTCCGAATTCTTGAA 60.390 40.000 3.52 0.00 0.00 2.69
143 156 6.555315 GTTTAGCATGTCCGAATTCTTGAAT 58.445 36.000 3.52 0.00 0.00 2.57
146 159 3.549070 GCATGTCCGAATTCTTGAATTGC 59.451 43.478 12.62 8.60 0.00 3.56
147 160 3.469899 TGTCCGAATTCTTGAATTGCG 57.530 42.857 12.62 13.88 0.00 4.85
148 161 3.070748 TGTCCGAATTCTTGAATTGCGA 58.929 40.909 12.62 5.71 0.00 5.10
150 163 4.155826 TGTCCGAATTCTTGAATTGCGATT 59.844 37.500 12.62 0.00 0.00 3.34
151 164 5.095490 GTCCGAATTCTTGAATTGCGATTT 58.905 37.500 12.62 0.00 0.00 2.17
152 165 6.128145 TGTCCGAATTCTTGAATTGCGATTTA 60.128 34.615 12.62 0.00 0.00 1.40
153 166 6.912591 GTCCGAATTCTTGAATTGCGATTTAT 59.087 34.615 12.62 0.00 0.00 1.40
171 184 7.661859 CGATTTATTTTTGCTTCGTTGCATTA 58.338 30.769 6.00 0.00 42.96 1.90
222 235 2.006888 CGACGTGCATGGATTTAAGGT 58.993 47.619 11.36 0.00 0.00 3.50
228 241 5.047377 ACGTGCATGGATTTAAGGTTTTGAT 60.047 36.000 11.36 0.00 0.00 2.57
232 245 8.196771 GTGCATGGATTTAAGGTTTTGATATGA 58.803 33.333 0.00 0.00 0.00 2.15
260 273 7.665080 GTGTAACTGTCTAGCAAAACTTTTG 57.335 36.000 9.54 9.54 0.00 2.44
265 278 3.888930 TGTCTAGCAAAACTTTTGAGGGG 59.111 43.478 16.90 5.02 0.00 4.79
266 279 2.890945 TCTAGCAAAACTTTTGAGGGGC 59.109 45.455 16.90 2.50 0.00 5.80
267 280 0.758734 AGCAAAACTTTTGAGGGGCC 59.241 50.000 16.90 0.00 0.00 5.80
268 281 0.599991 GCAAAACTTTTGAGGGGCCG 60.600 55.000 16.90 0.00 0.00 6.13
269 282 0.750249 CAAAACTTTTGAGGGGCCGT 59.250 50.000 8.35 0.00 0.00 5.68
270 283 1.037493 AAAACTTTTGAGGGGCCGTC 58.963 50.000 19.10 19.10 0.00 4.79
271 284 0.826256 AAACTTTTGAGGGGCCGTCC 60.826 55.000 22.54 6.28 0.00 4.79
272 285 2.746277 CTTTTGAGGGGCCGTCCG 60.746 66.667 22.54 5.77 36.01 4.79
273 286 4.338710 TTTTGAGGGGCCGTCCGG 62.339 66.667 22.54 0.24 36.01 5.14
285 298 4.980805 GTCCGGCACAGGCAACGA 62.981 66.667 0.00 0.00 43.71 3.85
286 299 4.015406 TCCGGCACAGGCAACGAT 62.015 61.111 0.00 0.00 43.71 3.73
287 300 3.499737 CCGGCACAGGCAACGATC 61.500 66.667 0.00 0.00 43.71 3.69
288 301 3.853330 CGGCACAGGCAACGATCG 61.853 66.667 14.88 14.88 43.71 3.69
291 304 2.476051 CACAGGCAACGATCGTGC 59.524 61.111 23.51 24.39 46.39 5.34
319 332 1.574134 GTCCGTTGACGTTTTGAGGA 58.426 50.000 2.63 0.00 37.74 3.71
323 336 0.584876 GTTGACGTTTTGAGGACCGG 59.415 55.000 0.00 0.00 0.00 5.28
324 337 0.464870 TTGACGTTTTGAGGACCGGA 59.535 50.000 9.46 0.00 0.00 5.14
327 340 2.148768 GACGTTTTGAGGACCGGATTT 58.851 47.619 9.46 0.00 0.00 2.17
328 341 1.877443 ACGTTTTGAGGACCGGATTTG 59.123 47.619 9.46 0.00 0.00 2.32
330 343 1.067846 GTTTTGAGGACCGGATTTGCC 60.068 52.381 9.46 0.67 0.00 4.52
331 344 0.111446 TTTGAGGACCGGATTTGCCA 59.889 50.000 9.46 0.00 35.94 4.92
332 345 0.111446 TTGAGGACCGGATTTGCCAA 59.889 50.000 9.46 1.33 35.94 4.52
344 357 4.202202 CGGATTTGCCAAGCCCAAATATAA 60.202 41.667 0.00 0.00 41.52 0.98
354 367 7.542025 CCAAGCCCAAATATAATTGCTCTATC 58.458 38.462 0.00 0.00 0.00 2.08
356 369 8.457261 CAAGCCCAAATATAATTGCTCTATCTC 58.543 37.037 0.00 0.00 0.00 2.75
373 386 2.602878 TCTCGAGTATGGCGTTTTGAC 58.397 47.619 13.13 0.00 0.00 3.18
375 388 1.068402 TCGAGTATGGCGTTTTGACGA 60.068 47.619 2.79 0.00 34.64 4.20
379 392 0.800012 TATGGCGTTTTGACGAAGGC 59.200 50.000 2.79 0.00 39.11 4.35
383 396 1.203313 CGTTTTGACGAAGGCCGAC 59.797 57.895 0.00 0.00 41.76 4.79
384 397 1.572941 GTTTTGACGAAGGCCGACC 59.427 57.895 0.00 0.00 41.76 4.79
478 496 8.856153 ATGTGAGGTGTATGTGTGTAAAATTA 57.144 30.769 0.00 0.00 0.00 1.40
479 497 8.317891 TGTGAGGTGTATGTGTGTAAAATTAG 57.682 34.615 0.00 0.00 0.00 1.73
480 498 7.389330 TGTGAGGTGTATGTGTGTAAAATTAGG 59.611 37.037 0.00 0.00 0.00 2.69
481 499 7.604927 GTGAGGTGTATGTGTGTAAAATTAGGA 59.395 37.037 0.00 0.00 0.00 2.94
482 500 8.325787 TGAGGTGTATGTGTGTAAAATTAGGAT 58.674 33.333 0.00 0.00 0.00 3.24
483 501 8.506168 AGGTGTATGTGTGTAAAATTAGGATG 57.494 34.615 0.00 0.00 0.00 3.51
484 502 8.325787 AGGTGTATGTGTGTAAAATTAGGATGA 58.674 33.333 0.00 0.00 0.00 2.92
485 503 8.952278 GGTGTATGTGTGTAAAATTAGGATGAA 58.048 33.333 0.00 0.00 0.00 2.57
499 517 9.485206 AAATTAGGATGAAATATGCTGAAATGC 57.515 29.630 0.00 0.00 0.00 3.56
501 519 6.474140 AGGATGAAATATGCTGAAATGCAA 57.526 33.333 0.00 0.00 46.61 4.08
502 520 6.278363 AGGATGAAATATGCTGAAATGCAAC 58.722 36.000 0.00 0.00 46.61 4.17
503 521 5.464389 GGATGAAATATGCTGAAATGCAACC 59.536 40.000 0.00 0.00 46.61 3.77
504 522 5.664294 TGAAATATGCTGAAATGCAACCT 57.336 34.783 0.00 0.00 46.61 3.50
505 523 5.412640 TGAAATATGCTGAAATGCAACCTG 58.587 37.500 0.00 0.00 46.61 4.00
506 524 5.047164 TGAAATATGCTGAAATGCAACCTGT 60.047 36.000 0.00 0.00 46.61 4.00
507 525 6.152492 TGAAATATGCTGAAATGCAACCTGTA 59.848 34.615 0.00 0.00 46.61 2.74
508 526 6.720112 AATATGCTGAAATGCAACCTGTAT 57.280 33.333 0.00 0.00 46.61 2.29
509 527 3.853831 TGCTGAAATGCAACCTGTATG 57.146 42.857 0.00 0.00 40.29 2.39
510 528 3.419943 TGCTGAAATGCAACCTGTATGA 58.580 40.909 0.00 0.00 40.29 2.15
511 529 3.825585 TGCTGAAATGCAACCTGTATGAA 59.174 39.130 0.00 0.00 40.29 2.57
512 530 4.280425 TGCTGAAATGCAACCTGTATGAAA 59.720 37.500 0.00 0.00 40.29 2.69
513 531 5.221402 TGCTGAAATGCAACCTGTATGAAAA 60.221 36.000 0.00 0.00 40.29 2.29
514 532 5.695816 GCTGAAATGCAACCTGTATGAAAAA 59.304 36.000 0.00 0.00 0.00 1.94
515 533 6.128742 GCTGAAATGCAACCTGTATGAAAAAG 60.129 38.462 0.00 0.00 0.00 2.27
516 534 7.048629 TGAAATGCAACCTGTATGAAAAAGA 57.951 32.000 0.00 0.00 0.00 2.52
517 535 7.669427 TGAAATGCAACCTGTATGAAAAAGAT 58.331 30.769 0.00 0.00 0.00 2.40
518 536 8.801299 TGAAATGCAACCTGTATGAAAAAGATA 58.199 29.630 0.00 0.00 0.00 1.98
519 537 9.638239 GAAATGCAACCTGTATGAAAAAGATAA 57.362 29.630 0.00 0.00 0.00 1.75
520 538 9.995003 AAATGCAACCTGTATGAAAAAGATAAA 57.005 25.926 0.00 0.00 0.00 1.40
523 541 9.638239 TGCAACCTGTATGAAAAAGATAAATTC 57.362 29.630 0.00 0.00 0.00 2.17
524 542 9.638239 GCAACCTGTATGAAAAAGATAAATTCA 57.362 29.630 0.00 0.00 37.47 2.57
554 572 8.144478 TCTGGAAGAATAAGTAGTATCATGTGC 58.856 37.037 0.00 0.00 42.31 4.57
569 587 1.616159 TGTGCTAAAAAGCCCCAGAC 58.384 50.000 0.00 0.00 0.00 3.51
596 615 1.336755 GCACAACCCTCGTTTCAATGT 59.663 47.619 0.00 0.00 0.00 2.71
602 621 5.533154 ACAACCCTCGTTTCAATGTATTTCA 59.467 36.000 0.00 0.00 0.00 2.69
604 623 6.436843 ACCCTCGTTTCAATGTATTTCATC 57.563 37.500 0.00 0.00 35.48 2.92
640 659 4.380841 ACTTGTGCATTATGCCTTCATG 57.619 40.909 15.06 14.05 44.23 3.07
727 755 4.459089 GAGGCCTCCACGGTGCTC 62.459 72.222 23.19 0.00 34.25 4.26
749 778 0.602562 CCTCCAAAAGCATTTCCGCA 59.397 50.000 0.00 0.00 37.28 5.69
780 809 2.691409 TTGATGGCTTCTCCCGTAAG 57.309 50.000 1.86 0.00 0.00 2.34
781 810 0.178068 TGATGGCTTCTCCCGTAAGC 59.822 55.000 1.86 0.00 46.90 3.09
782 811 0.466124 GATGGCTTCTCCCGTAAGCT 59.534 55.000 7.65 0.00 46.81 3.74
785 814 1.219393 GCTTCTCCCGTAAGCTGCT 59.781 57.895 0.00 0.00 44.75 4.24
803 832 0.461135 CTGCTCTGCTCTCTCCTTCC 59.539 60.000 0.00 0.00 0.00 3.46
818 847 0.603707 CTTCCAGAAGCAGCGTTCCA 60.604 55.000 0.00 0.00 0.00 3.53
829 858 1.219393 GCGTTCCAAGGAGAGGAGG 59.781 63.158 0.00 0.00 36.33 4.30
920 949 1.083657 CACGGACAGCGTTGTTTCG 60.084 57.895 20.65 20.65 37.76 3.46
924 953 0.384353 GGACAGCGTTGTTTCGAAGC 60.384 55.000 6.30 4.89 37.76 3.86
925 954 0.384353 GACAGCGTTGTTTCGAAGCC 60.384 55.000 6.30 0.00 37.76 4.35
926 955 1.092921 ACAGCGTTGTTTCGAAGCCA 61.093 50.000 9.65 2.58 32.28 4.75
927 956 0.028770 CAGCGTTGTTTCGAAGCCAA 59.971 50.000 9.65 8.66 0.00 4.52
928 957 0.028902 AGCGTTGTTTCGAAGCCAAC 59.971 50.000 22.80 22.80 36.09 3.77
929 958 0.248296 GCGTTGTTTCGAAGCCAACA 60.248 50.000 27.72 16.32 38.65 3.33
930 959 1.462791 CGTTGTTTCGAAGCCAACAC 58.537 50.000 27.72 13.50 38.65 3.32
931 960 1.202087 CGTTGTTTCGAAGCCAACACA 60.202 47.619 27.72 15.46 38.65 3.72
932 961 2.182014 GTTGTTTCGAAGCCAACACAC 58.818 47.619 25.56 13.47 38.61 3.82
933 962 1.454201 TGTTTCGAAGCCAACACACA 58.546 45.000 9.65 0.17 0.00 3.72
934 963 1.131504 TGTTTCGAAGCCAACACACAC 59.868 47.619 9.65 0.00 0.00 3.82
935 964 0.375454 TTTCGAAGCCAACACACACG 59.625 50.000 0.00 0.00 0.00 4.49
936 965 2.042520 TTCGAAGCCAACACACACGC 62.043 55.000 0.00 0.00 0.00 5.34
937 966 2.052237 GAAGCCAACACACACGCG 60.052 61.111 3.53 3.53 0.00 6.01
938 967 2.819552 GAAGCCAACACACACGCGT 61.820 57.895 5.58 5.58 0.00 6.01
939 968 2.317685 GAAGCCAACACACACGCGTT 62.318 55.000 10.22 0.00 0.00 4.84
940 969 1.928706 AAGCCAACACACACGCGTTT 61.929 50.000 10.22 0.00 0.00 3.60
941 970 1.937362 GCCAACACACACGCGTTTC 60.937 57.895 10.22 0.00 0.00 2.78
942 971 1.425825 CCAACACACACGCGTTTCA 59.574 52.632 10.22 0.00 0.00 2.69
943 972 0.179187 CCAACACACACGCGTTTCAA 60.179 50.000 10.22 0.00 0.00 2.69
944 973 1.607713 CAACACACACGCGTTTCAAA 58.392 45.000 10.22 0.00 0.00 2.69
945 974 1.979469 CAACACACACGCGTTTCAAAA 59.021 42.857 10.22 0.00 0.00 2.44
946 975 2.333389 ACACACACGCGTTTCAAAAA 57.667 40.000 10.22 0.00 0.00 1.94
983 1012 1.961277 CCAACACACACGCTCCTCC 60.961 63.158 0.00 0.00 0.00 4.30
990 1019 1.380112 ACACGCTCCTCCCCTACTC 60.380 63.158 0.00 0.00 0.00 2.59
1006 1035 1.299468 CTCGATTTCTCCCGCCTCG 60.299 63.158 0.00 0.00 0.00 4.63
1010 1039 1.153349 ATTTCTCCCGCCTCGCTTC 60.153 57.895 0.00 0.00 0.00 3.86
1015 1044 4.715523 CCCGCCTCGCTTCCCAAA 62.716 66.667 0.00 0.00 0.00 3.28
1016 1045 3.127533 CCGCCTCGCTTCCCAAAG 61.128 66.667 0.00 0.00 35.47 2.77
1037 1069 1.951209 AAATCCCCAAATCCACCACC 58.049 50.000 0.00 0.00 0.00 4.61
1098 1130 4.806339 CCGCCTCCCCCTCCTCTT 62.806 72.222 0.00 0.00 0.00 2.85
1102 1134 1.074850 CCTCCCCCTCCTCTTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
1105 1137 0.254638 TCCCCCTCCTCTTCCTCCTA 60.255 60.000 0.00 0.00 0.00 2.94
1106 1138 0.105401 CCCCCTCCTCTTCCTCCTAC 60.105 65.000 0.00 0.00 0.00 3.18
1107 1139 0.938192 CCCCTCCTCTTCCTCCTACT 59.062 60.000 0.00 0.00 0.00 2.57
1117 1149 2.482333 CCTCCTACTCGCCGTCCTG 61.482 68.421 0.00 0.00 0.00 3.86
1185 1223 3.568853 GCCGAGATAACAGGTAAGCTCTA 59.431 47.826 0.00 0.00 0.00 2.43
1186 1224 4.557097 GCCGAGATAACAGGTAAGCTCTAC 60.557 50.000 0.00 0.00 0.00 2.59
1234 1272 2.420547 CCTAAACCCTAACCCTAACCGC 60.421 54.545 0.00 0.00 0.00 5.68
1471 1685 1.271001 CCGAACCGAAACCCTACCTTT 60.271 52.381 0.00 0.00 0.00 3.11
1472 1686 2.497138 CGAACCGAAACCCTACCTTTT 58.503 47.619 0.00 0.00 0.00 2.27
1473 1687 2.481568 CGAACCGAAACCCTACCTTTTC 59.518 50.000 0.00 0.00 0.00 2.29
1478 1697 4.957954 ACCGAAACCCTACCTTTTCTTTTT 59.042 37.500 0.00 0.00 30.79 1.94
1495 1714 2.929531 TTTTTGTGCTTGCTCGAACA 57.070 40.000 0.00 0.00 0.00 3.18
1641 1860 2.494918 CGCCGGATCCTCGACTTT 59.505 61.111 5.05 0.00 0.00 2.66
1704 1923 1.122019 AGGAAGGTGCGTGGTTCTCT 61.122 55.000 0.00 0.00 0.00 3.10
1712 1932 2.476997 GTGCGTGGTTCTCTTTCTTCTC 59.523 50.000 0.00 0.00 0.00 2.87
1746 1970 3.790152 TTTGCTTGTTGTATGTGCACA 57.210 38.095 24.08 24.08 33.13 4.57
1761 1985 0.385974 GCACATTGACGGCAACTGTC 60.386 55.000 5.42 3.52 36.72 3.51
1784 2008 2.476185 CGCGAGATGTTGATTTGGGAAC 60.476 50.000 0.00 0.00 0.00 3.62
1881 2105 2.172483 CTCTGGCCCACACGCTTAGT 62.172 60.000 0.00 0.00 0.00 2.24
1905 2129 3.195825 AGTCACTGGTGTTCTACTATGGC 59.804 47.826 0.53 0.00 0.00 4.40
1908 2132 0.828022 TGGTGTTCTACTATGGCGGG 59.172 55.000 0.00 0.00 0.00 6.13
1972 2196 4.464597 TCTTTCAGGTAAGCTCTTCCTCTC 59.535 45.833 0.00 0.00 0.00 3.20
1974 2198 4.864483 TCAGGTAAGCTCTTCCTCTCTA 57.136 45.455 0.00 0.00 0.00 2.43
1988 2212 2.757868 CCTCTCTACCCTGTTCTCTGTG 59.242 54.545 0.00 0.00 0.00 3.66
1992 2216 1.205893 CTACCCTGTTCTCTGTGGAGC 59.794 57.143 0.00 0.00 39.31 4.70
2012 2236 4.122776 AGCGCCACTTAATCTGATAACTG 58.877 43.478 2.29 0.00 0.00 3.16
2033 2277 7.009179 ACTGGAGAGTCAGTTTTCATAATGA 57.991 36.000 0.00 0.00 44.74 2.57
2065 2311 8.237949 TGAAGTTCTCTTATTCTCTACTTCACG 58.762 37.037 9.86 0.00 42.73 4.35
2079 2325 0.981183 TTCACGATACCAGTTGGGCT 59.019 50.000 2.79 0.00 42.05 5.19
2117 2363 3.753272 GCATATTCGGCACTATTGGACAT 59.247 43.478 0.00 0.00 0.00 3.06
2157 2403 0.984230 TTTCCTTCAGCTCGGTGGAT 59.016 50.000 0.00 0.00 0.00 3.41
2172 2418 4.542931 TCGGTGGATATTATCTCCCTCCTA 59.457 45.833 3.77 0.00 31.32 2.94
2174 2420 5.536916 CGGTGGATATTATCTCCCTCCTATC 59.463 48.000 3.77 0.00 31.32 2.08
2183 2429 2.180308 TCTCCCTCCTATCCTTTCCCTC 59.820 54.545 0.00 0.00 0.00 4.30
2213 2459 8.641499 TTTGTTTTTCCTGAATGTATTCACAC 57.359 30.769 3.28 0.00 41.51 3.82
2311 2557 2.457598 AGGCAGTCACTTTCCGAGATA 58.542 47.619 0.00 0.00 0.00 1.98
2444 2691 8.729756 CAGTTGTGAGTATTCATTTGACCATTA 58.270 33.333 0.00 0.00 35.39 1.90
2500 2747 6.317893 CACTCTTGGACATCATGATGATTTCA 59.682 38.462 36.37 24.27 41.20 2.69
2501 2748 6.888088 ACTCTTGGACATCATGATGATTTCAA 59.112 34.615 36.37 27.84 41.20 2.69
2560 2807 4.662961 TGTCGGGACTGCTGCGTG 62.663 66.667 0.00 0.00 0.00 5.34
2655 2902 4.877823 TGTCATCTATGGTTCATTGTGCTC 59.122 41.667 0.00 0.00 0.00 4.26
2862 3115 4.530553 TGAGTTCCTGTTGTCTAATAGCCA 59.469 41.667 0.00 0.00 0.00 4.75
2905 3158 9.423061 CCTAGAAAGGGATTGTTAATGTTTTTG 57.577 33.333 0.00 0.00 39.48 2.44
3002 3258 6.701841 TCGAGTTTCATTACTATCATTGCTCC 59.298 38.462 0.00 0.00 0.00 4.70
3021 3277 7.172868 TGCTCCATTGACAATTTGACATAAT 57.827 32.000 2.79 0.00 0.00 1.28
3154 3410 4.465512 GTTGATGCTGGCGTGGCG 62.466 66.667 0.00 0.00 0.00 5.69
3246 3504 3.623510 GGCTGTTTGCTGACTATTCTACC 59.376 47.826 0.00 0.00 42.39 3.18
3247 3505 3.307242 GCTGTTTGCTGACTATTCTACCG 59.693 47.826 0.00 0.00 38.95 4.02
3262 3520 7.776969 ACTATTCTACCGGTTATCACTTCACTA 59.223 37.037 15.04 0.00 0.00 2.74
3365 3623 6.998968 ATCATCAAGACAGTTTCAAGGATC 57.001 37.500 0.00 0.00 0.00 3.36
3378 3636 2.837591 TCAAGGATCGAAGGGATGTCAA 59.162 45.455 0.00 0.00 34.82 3.18
3516 3779 7.296628 ACAGCCTTTTGTTATTCATGGTTTA 57.703 32.000 0.00 0.00 0.00 2.01
3725 3998 2.889512 ACTCAGTGTGGTGGTATCAGA 58.110 47.619 0.00 0.00 0.00 3.27
3773 4046 3.169908 TCTAGACATGGCCAACACAGTA 58.830 45.455 10.96 0.00 0.00 2.74
3795 4068 5.823861 ATTAACAGAAGCAATTGGGGTTT 57.176 34.783 7.72 0.00 0.00 3.27
3891 4169 3.057734 GCGGTAGAAATTGGATACGGAG 58.942 50.000 0.00 0.00 42.51 4.63
4050 4329 4.402474 CAGGTTTGAAAGTGGTCCTTTTCT 59.598 41.667 15.77 0.00 43.47 2.52
4258 4537 1.511850 CAACACGAATGGAGCTCACA 58.488 50.000 17.19 11.60 0.00 3.58
4342 4621 1.923356 TTCAGGTTTGCCATCCTTCC 58.077 50.000 0.00 0.00 37.19 3.46
4349 4628 3.195698 GCCATCCTTCCGTCGCAC 61.196 66.667 0.00 0.00 0.00 5.34
4381 4660 4.960938 AGTTCACTATTGTTGTCTCAGCA 58.039 39.130 0.00 0.00 0.00 4.41
4783 5065 7.309316 GGTTCTACGAAGGATAGGAAAGGATAG 60.309 44.444 0.00 0.00 0.00 2.08
4784 5066 6.246919 TCTACGAAGGATAGGAAAGGATAGG 58.753 44.000 0.00 0.00 0.00 2.57
4785 5067 4.161102 ACGAAGGATAGGAAAGGATAGGG 58.839 47.826 0.00 0.00 0.00 3.53
4786 5068 4.161102 CGAAGGATAGGAAAGGATAGGGT 58.839 47.826 0.00 0.00 0.00 4.34
4787 5069 4.021016 CGAAGGATAGGAAAGGATAGGGTG 60.021 50.000 0.00 0.00 0.00 4.61
4923 5209 1.053424 AGTCTTCCCGTACTGGCAAA 58.947 50.000 0.00 0.00 35.87 3.68
5213 5499 0.745845 CCGCTATGCACTGGAGCTTT 60.746 55.000 9.31 0.00 33.91 3.51
5252 5538 2.079170 TGCCCAAACCATCTCAAACA 57.921 45.000 0.00 0.00 0.00 2.83
5379 5665 0.811616 GCATCTCCGCCACACCTAAG 60.812 60.000 0.00 0.00 0.00 2.18
5531 5817 1.224592 GCCACTTCATCCATCCGGT 59.775 57.895 0.00 0.00 0.00 5.28
5718 6004 7.087895 AGTTCTACTAAGCCTAAACCCTTTT 57.912 36.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.135306 GACCCGGTCTTCTTCTTCTTTTT 58.865 43.478 10.59 0.00 0.00 1.94
11 12 3.496337 GGACCCGGTCTTCTTCTTCTTTT 60.496 47.826 17.27 0.00 32.47 2.27
12 13 2.038689 GGACCCGGTCTTCTTCTTCTTT 59.961 50.000 17.27 0.00 32.47 2.52
13 14 1.624312 GGACCCGGTCTTCTTCTTCTT 59.376 52.381 17.27 0.00 32.47 2.52
14 15 1.203199 AGGACCCGGTCTTCTTCTTCT 60.203 52.381 17.27 0.41 32.47 2.85
15 16 1.066787 CAGGACCCGGTCTTCTTCTTC 60.067 57.143 17.27 0.00 32.47 2.87
16 17 0.977395 CAGGACCCGGTCTTCTTCTT 59.023 55.000 17.27 0.00 32.47 2.52
17 18 0.905337 CCAGGACCCGGTCTTCTTCT 60.905 60.000 17.27 2.59 32.47 2.85
18 19 1.192803 ACCAGGACCCGGTCTTCTTC 61.193 60.000 17.27 0.12 32.47 2.87
19 20 0.767060 AACCAGGACCCGGTCTTCTT 60.767 55.000 17.27 0.84 34.99 2.52
20 21 1.152096 AACCAGGACCCGGTCTTCT 60.152 57.895 17.27 4.07 34.99 2.85
21 22 1.003718 CAACCAGGACCCGGTCTTC 60.004 63.158 17.27 1.62 34.99 2.87
22 23 3.157680 CAACCAGGACCCGGTCTT 58.842 61.111 17.27 6.98 34.99 3.01
23 24 3.637273 GCAACCAGGACCCGGTCT 61.637 66.667 17.27 0.80 34.99 3.85
24 25 4.717313 GGCAACCAGGACCCGGTC 62.717 72.222 9.30 9.30 34.99 4.79
25 26 3.857521 TAGGCAACCAGGACCCGGT 62.858 63.158 0.00 0.00 38.85 5.28
26 27 3.006728 TAGGCAACCAGGACCCGG 61.007 66.667 0.00 0.00 37.17 5.73
27 28 2.267961 GTAGGCAACCAGGACCCG 59.732 66.667 0.00 0.00 37.17 5.28
44 45 6.255887 GGTAGGTGACTGATTCTCATAAAACG 59.744 42.308 0.00 0.00 43.88 3.60
49 50 4.579340 GTCGGTAGGTGACTGATTCTCATA 59.421 45.833 0.00 0.00 45.38 2.15
51 52 2.753452 GTCGGTAGGTGACTGATTCTCA 59.247 50.000 0.00 0.00 45.38 3.27
54 55 3.018149 AGAGTCGGTAGGTGACTGATTC 58.982 50.000 0.00 1.86 46.29 2.52
55 56 2.755655 CAGAGTCGGTAGGTGACTGATT 59.244 50.000 0.00 0.00 46.29 2.57
64 65 3.254060 CAATGTTGTCAGAGTCGGTAGG 58.746 50.000 0.00 0.00 0.00 3.18
66 67 4.330944 AACAATGTTGTCAGAGTCGGTA 57.669 40.909 0.00 0.00 41.31 4.02
67 68 2.910688 ACAATGTTGTCAGAGTCGGT 57.089 45.000 0.00 0.00 36.50 4.69
68 69 3.559655 TGAAACAATGTTGTCAGAGTCGG 59.440 43.478 0.00 0.00 41.31 4.79
70 71 5.456822 GCTTTGAAACAATGTTGTCAGAGTC 59.543 40.000 19.27 13.02 41.31 3.36
72 73 4.741676 GGCTTTGAAACAATGTTGTCAGAG 59.258 41.667 16.58 16.58 41.31 3.35
73 74 4.159321 TGGCTTTGAAACAATGTTGTCAGA 59.841 37.500 0.00 1.15 41.31 3.27
74 75 4.431809 TGGCTTTGAAACAATGTTGTCAG 58.568 39.130 0.00 0.00 41.31 3.51
75 76 4.462508 TGGCTTTGAAACAATGTTGTCA 57.537 36.364 0.00 3.36 41.31 3.58
76 77 5.793026 TTTGGCTTTGAAACAATGTTGTC 57.207 34.783 0.00 0.70 41.31 3.18
83 84 4.478206 TGACCATTTGGCTTTGAAACAA 57.522 36.364 0.00 0.00 39.32 2.83
105 106 2.444700 CTAAACGTCCAGGGCACGGT 62.445 60.000 5.72 0.00 41.73 4.83
108 109 0.676782 ATGCTAAACGTCCAGGGCAC 60.677 55.000 0.00 0.00 32.52 5.01
111 112 1.369625 GACATGCTAAACGTCCAGGG 58.630 55.000 0.00 0.00 0.00 4.45
112 113 1.369625 GGACATGCTAAACGTCCAGG 58.630 55.000 2.98 0.00 46.98 4.45
135 148 8.309163 AGCAAAAATAAATCGCAATTCAAGAA 57.691 26.923 0.00 0.00 0.00 2.52
137 150 7.420485 CGAAGCAAAAATAAATCGCAATTCAAG 59.580 33.333 0.00 0.00 0.00 3.02
139 152 6.364706 ACGAAGCAAAAATAAATCGCAATTCA 59.635 30.769 0.00 0.00 33.88 2.57
140 153 6.751259 ACGAAGCAAAAATAAATCGCAATTC 58.249 32.000 0.00 0.00 33.88 2.17
141 154 6.704512 ACGAAGCAAAAATAAATCGCAATT 57.295 29.167 0.00 0.00 33.88 2.32
142 155 6.524490 CAACGAAGCAAAAATAAATCGCAAT 58.476 32.000 0.00 0.00 33.88 3.56
143 156 5.611412 GCAACGAAGCAAAAATAAATCGCAA 60.611 36.000 0.00 0.00 33.88 4.85
146 159 5.493397 TGCAACGAAGCAAAAATAAATCG 57.507 34.783 4.17 0.00 42.46 3.34
228 241 8.896320 TTTGCTAGACAGTTACACTTTTCATA 57.104 30.769 0.00 0.00 0.00 2.15
232 245 7.625828 AGTTTTGCTAGACAGTTACACTTTT 57.374 32.000 0.00 0.00 0.00 2.27
239 252 6.262273 CCCTCAAAAGTTTTGCTAGACAGTTA 59.738 38.462 21.21 1.90 0.00 2.24
240 253 5.067805 CCCTCAAAAGTTTTGCTAGACAGTT 59.932 40.000 21.21 0.00 0.00 3.16
246 259 2.029020 GGCCCCTCAAAAGTTTTGCTAG 60.029 50.000 21.21 14.70 0.00 3.42
253 266 1.228459 GGACGGCCCCTCAAAAGTT 60.228 57.895 0.00 0.00 0.00 2.66
268 281 4.980805 TCGTTGCCTGTGCCGGAC 62.981 66.667 5.05 0.46 36.33 4.79
269 282 3.950794 GATCGTTGCCTGTGCCGGA 62.951 63.158 5.05 0.00 36.33 5.14
270 283 3.499737 GATCGTTGCCTGTGCCGG 61.500 66.667 0.00 0.00 36.33 6.13
271 284 3.853330 CGATCGTTGCCTGTGCCG 61.853 66.667 7.03 0.00 36.33 5.69
272 285 2.742372 ACGATCGTTGCCTGTGCC 60.742 61.111 16.60 0.00 36.33 5.01
273 286 2.476051 CACGATCGTTGCCTGTGC 59.524 61.111 20.14 0.00 38.26 4.57
274 287 2.476051 GCACGATCGTTGCCTGTG 59.524 61.111 20.14 6.65 0.00 3.66
275 288 2.742372 GGCACGATCGTTGCCTGT 60.742 61.111 34.55 9.76 44.72 4.00
279 292 4.505217 CGCTGGCACGATCGTTGC 62.505 66.667 20.14 23.19 34.06 4.17
280 293 4.505217 GCGCTGGCACGATCGTTG 62.505 66.667 20.14 15.00 39.62 4.10
309 322 1.401018 GCAAATCCGGTCCTCAAAACG 60.401 52.381 0.00 0.00 0.00 3.60
316 329 1.678970 GCTTGGCAAATCCGGTCCT 60.679 57.895 0.00 0.00 37.80 3.85
319 332 2.679996 GGGCTTGGCAAATCCGGT 60.680 61.111 0.00 0.00 37.80 5.28
323 336 6.293571 GCAATTATATTTGGGCTTGGCAAATC 60.294 38.462 0.00 0.00 31.84 2.17
324 337 5.532032 GCAATTATATTTGGGCTTGGCAAAT 59.468 36.000 0.00 0.00 33.68 2.32
327 340 3.710677 AGCAATTATATTTGGGCTTGGCA 59.289 39.130 8.92 0.00 0.00 4.92
328 341 4.039609 AGAGCAATTATATTTGGGCTTGGC 59.960 41.667 8.92 0.00 0.00 4.52
330 343 8.345724 AGATAGAGCAATTATATTTGGGCTTG 57.654 34.615 8.92 0.00 0.00 4.01
331 344 7.335422 CGAGATAGAGCAATTATATTTGGGCTT 59.665 37.037 8.92 0.00 0.00 4.35
332 345 6.820656 CGAGATAGAGCAATTATATTTGGGCT 59.179 38.462 8.92 0.00 0.00 5.19
344 357 3.119673 CGCCATACTCGAGATAGAGCAAT 60.120 47.826 21.68 0.00 41.77 3.56
354 367 1.320555 CGTCAAAACGCCATACTCGAG 59.679 52.381 11.84 11.84 42.82 4.04
356 369 3.850207 CGTCAAAACGCCATACTCG 57.150 52.632 0.00 0.00 42.82 4.18
375 388 4.141824 TGAATTTTTCAAAAGGTCGGCCTT 60.142 37.500 17.56 17.56 45.08 4.35
424 441 9.781834 TTGTTTACTTGTAAGACAATCAGTTTG 57.218 29.630 0.00 0.00 37.48 2.93
426 443 8.621286 CCTTGTTTACTTGTAAGACAATCAGTT 58.379 33.333 14.86 0.00 37.48 3.16
427 444 7.990886 TCCTTGTTTACTTGTAAGACAATCAGT 59.009 33.333 14.86 0.00 37.48 3.41
428 445 8.378172 TCCTTGTTTACTTGTAAGACAATCAG 57.622 34.615 14.86 10.51 37.48 2.90
429 446 8.783093 CATCCTTGTTTACTTGTAAGACAATCA 58.217 33.333 14.86 9.36 37.48 2.57
430 447 8.784043 ACATCCTTGTTTACTTGTAAGACAATC 58.216 33.333 14.86 0.00 32.68 2.67
431 448 8.567948 CACATCCTTGTTTACTTGTAAGACAAT 58.432 33.333 14.86 5.45 33.69 2.71
432 449 7.771361 TCACATCCTTGTTTACTTGTAAGACAA 59.229 33.333 14.28 14.28 33.30 3.18
434 451 7.095187 CCTCACATCCTTGTTTACTTGTAAGAC 60.095 40.741 0.00 0.00 32.34 3.01
436 453 6.710744 ACCTCACATCCTTGTTTACTTGTAAG 59.289 38.462 0.00 0.00 32.34 2.34
478 496 6.278363 GTTGCATTTCAGCATATTTCATCCT 58.722 36.000 0.00 0.00 45.19 3.24
479 497 5.464389 GGTTGCATTTCAGCATATTTCATCC 59.536 40.000 0.00 0.00 45.19 3.51
480 498 6.200286 CAGGTTGCATTTCAGCATATTTCATC 59.800 38.462 0.00 0.00 45.19 2.92
481 499 6.046593 CAGGTTGCATTTCAGCATATTTCAT 58.953 36.000 0.00 0.00 45.19 2.57
482 500 5.047164 ACAGGTTGCATTTCAGCATATTTCA 60.047 36.000 0.00 0.00 45.19 2.69
483 501 5.413499 ACAGGTTGCATTTCAGCATATTTC 58.587 37.500 0.00 0.00 45.19 2.17
484 502 5.410355 ACAGGTTGCATTTCAGCATATTT 57.590 34.783 0.00 0.00 45.19 1.40
485 503 6.321945 TCATACAGGTTGCATTTCAGCATATT 59.678 34.615 0.00 0.00 45.19 1.28
486 504 5.829391 TCATACAGGTTGCATTTCAGCATAT 59.171 36.000 0.00 0.00 45.19 1.78
487 505 5.192176 TCATACAGGTTGCATTTCAGCATA 58.808 37.500 0.00 0.00 45.19 3.14
488 506 4.018490 TCATACAGGTTGCATTTCAGCAT 58.982 39.130 0.00 0.00 45.19 3.79
489 507 3.419943 TCATACAGGTTGCATTTCAGCA 58.580 40.909 0.00 0.00 43.99 4.41
490 508 4.439305 TTCATACAGGTTGCATTTCAGC 57.561 40.909 0.00 0.00 0.00 4.26
491 509 7.147312 TCTTTTTCATACAGGTTGCATTTCAG 58.853 34.615 0.00 0.00 0.00 3.02
492 510 7.048629 TCTTTTTCATACAGGTTGCATTTCA 57.951 32.000 0.00 0.00 0.00 2.69
493 511 9.638239 TTATCTTTTTCATACAGGTTGCATTTC 57.362 29.630 0.00 0.00 0.00 2.17
494 512 9.995003 TTTATCTTTTTCATACAGGTTGCATTT 57.005 25.926 0.00 0.00 0.00 2.32
497 515 9.638239 GAATTTATCTTTTTCATACAGGTTGCA 57.362 29.630 0.00 0.00 0.00 4.08
498 516 9.638239 TGAATTTATCTTTTTCATACAGGTTGC 57.362 29.630 0.00 0.00 0.00 4.17
528 546 8.144478 GCACATGATACTACTTATTCTTCCAGA 58.856 37.037 0.00 0.00 0.00 3.86
537 555 9.057089 GGCTTTTTAGCACATGATACTACTTAT 57.943 33.333 0.00 0.00 36.33 1.73
541 559 5.008712 GGGGCTTTTTAGCACATGATACTAC 59.991 44.000 0.00 0.00 40.62 2.73
549 567 2.171003 GTCTGGGGCTTTTTAGCACAT 58.829 47.619 1.46 0.00 40.62 3.21
602 621 8.101654 TGCACAAGTACGTAAATTTTTAGGAT 57.898 30.769 0.00 0.00 33.88 3.24
604 623 8.736751 AATGCACAAGTACGTAAATTTTTAGG 57.263 30.769 0.00 2.18 35.34 2.69
689 717 8.575589 GGCCTCCAAATGTAAAATTCAAAATTT 58.424 29.630 0.00 0.00 0.00 1.82
690 718 7.944000 AGGCCTCCAAATGTAAAATTCAAAATT 59.056 29.630 0.00 0.00 0.00 1.82
710 738 4.459089 GAGCACCGTGGAGGCCTC 62.459 72.222 25.59 25.59 46.52 4.70
723 751 2.672996 GCTTTTGGAGGCCGAGCA 60.673 61.111 0.00 0.00 33.68 4.26
727 755 0.108662 GGAAATGCTTTTGGAGGCCG 60.109 55.000 1.76 0.00 0.00 6.13
735 763 4.265073 AGAGATAGTGCGGAAATGCTTTT 58.735 39.130 0.00 0.00 35.36 2.27
749 778 6.407979 GGAGAAGCCATCAAAAGAGAGATAGT 60.408 42.308 0.00 0.00 36.34 2.12
780 809 1.519898 GAGAGAGCAGAGCAGCAGC 60.520 63.158 0.00 0.00 42.56 5.25
781 810 1.142314 GGAGAGAGCAGAGCAGCAG 59.858 63.158 0.00 0.00 36.85 4.24
782 811 0.903924 AAGGAGAGAGCAGAGCAGCA 60.904 55.000 0.00 0.00 36.85 4.41
785 814 0.251967 TGGAAGGAGAGAGCAGAGCA 60.252 55.000 0.00 0.00 0.00 4.26
803 832 0.603707 TCCTTGGAACGCTGCTTCTG 60.604 55.000 0.00 0.00 0.00 3.02
818 847 2.041350 TCGTAAGTCACCTCCTCTCCTT 59.959 50.000 0.00 0.00 39.48 3.36
829 858 3.299340 TTGCCTTCTCTCGTAAGTCAC 57.701 47.619 0.00 0.00 39.48 3.67
873 902 3.243401 GGCAAGTCTGTCCGTTGATTTTT 60.243 43.478 0.00 0.00 0.00 1.94
874 903 2.293399 GGCAAGTCTGTCCGTTGATTTT 59.707 45.455 0.00 0.00 0.00 1.82
875 904 1.880027 GGCAAGTCTGTCCGTTGATTT 59.120 47.619 0.00 0.00 0.00 2.17
876 905 1.523758 GGCAAGTCTGTCCGTTGATT 58.476 50.000 0.00 0.00 0.00 2.57
877 906 0.670546 CGGCAAGTCTGTCCGTTGAT 60.671 55.000 5.19 0.00 37.42 2.57
878 907 1.300620 CGGCAAGTCTGTCCGTTGA 60.301 57.895 5.19 0.00 37.42 3.18
879 908 1.300620 TCGGCAAGTCTGTCCGTTG 60.301 57.895 11.41 0.00 40.73 4.10
920 949 2.052237 CGCGTGTGTGTTGGCTTC 60.052 61.111 0.00 0.00 0.00 3.86
927 956 2.333389 TTTTTGAAACGCGTGTGTGT 57.667 40.000 14.98 0.00 41.58 3.72
951 980 9.296400 GCGTGTGTGTTGGAATATTTATTTATT 57.704 29.630 0.00 0.00 0.00 1.40
952 981 8.682710 AGCGTGTGTGTTGGAATATTTATTTAT 58.317 29.630 0.00 0.00 0.00 1.40
953 982 8.046294 AGCGTGTGTGTTGGAATATTTATTTA 57.954 30.769 0.00 0.00 0.00 1.40
954 983 6.919721 AGCGTGTGTGTTGGAATATTTATTT 58.080 32.000 0.00 0.00 0.00 1.40
955 984 6.404293 GGAGCGTGTGTGTTGGAATATTTATT 60.404 38.462 0.00 0.00 0.00 1.40
956 985 5.065988 GGAGCGTGTGTGTTGGAATATTTAT 59.934 40.000 0.00 0.00 0.00 1.40
957 986 4.393680 GGAGCGTGTGTGTTGGAATATTTA 59.606 41.667 0.00 0.00 0.00 1.40
958 987 3.190535 GGAGCGTGTGTGTTGGAATATTT 59.809 43.478 0.00 0.00 0.00 1.40
959 988 2.747446 GGAGCGTGTGTGTTGGAATATT 59.253 45.455 0.00 0.00 0.00 1.28
960 989 2.027192 AGGAGCGTGTGTGTTGGAATAT 60.027 45.455 0.00 0.00 0.00 1.28
961 990 1.346395 AGGAGCGTGTGTGTTGGAATA 59.654 47.619 0.00 0.00 0.00 1.75
962 991 0.108585 AGGAGCGTGTGTGTTGGAAT 59.891 50.000 0.00 0.00 0.00 3.01
963 992 0.531974 GAGGAGCGTGTGTGTTGGAA 60.532 55.000 0.00 0.00 0.00 3.53
964 993 1.069090 GAGGAGCGTGTGTGTTGGA 59.931 57.895 0.00 0.00 0.00 3.53
983 1012 0.032267 GCGGGAGAAATCGAGTAGGG 59.968 60.000 0.00 0.00 0.00 3.53
990 1019 2.907897 AAGCGAGGCGGGAGAAATCG 62.908 60.000 0.00 0.00 36.51 3.34
1006 1035 2.256306 TGGGGATTTTCTTTGGGAAGC 58.744 47.619 0.00 0.00 35.16 3.86
1010 1039 3.586618 TGGATTTGGGGATTTTCTTTGGG 59.413 43.478 0.00 0.00 0.00 4.12
1013 1042 4.041567 GTGGTGGATTTGGGGATTTTCTTT 59.958 41.667 0.00 0.00 0.00 2.52
1014 1043 3.582647 GTGGTGGATTTGGGGATTTTCTT 59.417 43.478 0.00 0.00 0.00 2.52
1015 1044 3.173151 GTGGTGGATTTGGGGATTTTCT 58.827 45.455 0.00 0.00 0.00 2.52
1016 1045 2.236146 GGTGGTGGATTTGGGGATTTTC 59.764 50.000 0.00 0.00 0.00 2.29
1084 1116 1.074850 GAGGAAGAGGAGGGGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
1089 1121 1.477923 CGAGTAGGAGGAAGAGGAGGG 60.478 61.905 0.00 0.00 0.00 4.30
1097 1129 1.751927 GGACGGCGAGTAGGAGGAA 60.752 63.158 16.62 0.00 0.00 3.36
1098 1130 2.124403 GGACGGCGAGTAGGAGGA 60.124 66.667 16.62 0.00 0.00 3.71
1102 1134 3.127352 GAGCAGGACGGCGAGTAGG 62.127 68.421 16.62 0.00 39.27 3.18
1199 1237 1.063190 GTTTAGGGGGATTTGGGGAGG 60.063 57.143 0.00 0.00 0.00 4.30
1201 1239 1.012395 GGTTTAGGGGGATTTGGGGA 58.988 55.000 0.00 0.00 0.00 4.81
1478 1697 2.221169 AGATGTTCGAGCAAGCACAAA 58.779 42.857 5.91 0.00 0.00 2.83
1480 1699 1.432514 GAGATGTTCGAGCAAGCACA 58.567 50.000 5.91 0.00 0.00 4.57
1492 1711 3.012518 CAAGAAATCAGGCCGAGATGTT 58.987 45.455 13.51 10.12 0.00 2.71
1495 1714 1.561542 ACCAAGAAATCAGGCCGAGAT 59.438 47.619 7.80 7.80 0.00 2.75
1625 1844 1.589196 CGAAAGTCGAGGATCCGGC 60.589 63.158 5.98 1.51 43.74 6.13
1694 1913 1.721926 GCGAGAAGAAAGAGAACCACG 59.278 52.381 0.00 0.00 0.00 4.94
1704 1923 1.804151 CCACGGAAATGCGAGAAGAAA 59.196 47.619 0.16 0.00 0.00 2.52
1712 1932 0.318614 AGCAAAACCACGGAAATGCG 60.319 50.000 0.00 0.00 38.74 4.73
1746 1970 1.291877 GCGAGACAGTTGCCGTCAAT 61.292 55.000 0.00 0.00 35.77 2.57
1761 1985 1.328680 CCCAAATCAACATCTCGCGAG 59.671 52.381 30.03 30.03 0.00 5.03
1784 2008 3.129287 AGAGACAAACACAAAAGCACCAG 59.871 43.478 0.00 0.00 0.00 4.00
1869 2093 1.000163 AGTGACTGACTAAGCGTGTGG 60.000 52.381 0.00 0.00 30.86 4.17
1881 2105 4.462834 CCATAGTAGAACACCAGTGACTGA 59.537 45.833 15.33 0.00 32.44 3.41
1905 2129 4.969196 CCGATCGTCATGGCCCCG 62.969 72.222 15.09 0.00 0.00 5.73
1972 2196 1.205893 GCTCCACAGAGAACAGGGTAG 59.794 57.143 0.00 0.00 43.39 3.18
1974 2198 1.821061 CGCTCCACAGAGAACAGGGT 61.821 60.000 0.00 0.00 43.39 4.34
1988 2212 2.246719 ATCAGATTAAGTGGCGCTCC 57.753 50.000 7.64 0.00 0.00 4.70
1992 2216 4.693283 TCCAGTTATCAGATTAAGTGGCG 58.307 43.478 15.27 0.00 45.99 5.69
2012 2236 8.498054 TCAATCATTATGAAAACTGACTCTCC 57.502 34.615 0.00 0.00 0.00 3.71
2065 2311 8.540388 TCTAATTATCATAGCCCAACTGGTATC 58.460 37.037 0.00 0.00 36.04 2.24
2079 2325 9.967346 GCCGAATATGCTACTCTAATTATCATA 57.033 33.333 0.00 0.00 0.00 2.15
2101 2347 4.002906 GGATTATGTCCAATAGTGCCGA 57.997 45.455 0.00 0.00 46.96 5.54
2117 2363 3.689347 AGCACATGTTCTTGCAGGATTA 58.311 40.909 0.00 0.00 41.48 1.75
2157 2403 6.283084 AGGGAAAGGATAGGAGGGAGATAATA 59.717 42.308 0.00 0.00 0.00 0.98
2172 2418 7.379059 AAAAACAAATGAAGAGGGAAAGGAT 57.621 32.000 0.00 0.00 0.00 3.24
2174 2420 5.991606 GGAAAAACAAATGAAGAGGGAAAGG 59.008 40.000 0.00 0.00 0.00 3.11
2311 2557 9.343539 GAGGCAGGTAGTGAGAAATAAAATAAT 57.656 33.333 0.00 0.00 0.00 1.28
2501 2748 3.055530 TGTCATGCCAACCTGTTGTTTTT 60.056 39.130 9.03 0.00 38.85 1.94
2655 2902 9.849166 AATGTAAATGTAGGTGGAAATTAAACG 57.151 29.630 0.00 0.00 0.00 3.60
2704 2951 5.408299 GTCAAAGTCATGGGGCAATTTAAAC 59.592 40.000 0.00 0.00 0.00 2.01
2824 3077 5.689068 CAGGAACTCAAAAAGACAAGCATTC 59.311 40.000 0.00 0.00 34.60 2.67
2862 3115 7.235812 CCTTTCTAGGGCAATATAGTAGAACCT 59.764 40.741 0.00 0.00 37.94 3.50
2989 3245 7.123098 TCAAATTGTCAATGGAGCAATGATAGT 59.877 33.333 0.00 0.00 33.68 2.12
3154 3410 2.857592 TAGCCCACTCGACGAAATAC 57.142 50.000 0.00 0.00 0.00 1.89
3246 3504 3.617263 GCCAGTTAGTGAAGTGATAACCG 59.383 47.826 0.00 0.00 38.12 4.44
3247 3505 4.575885 TGCCAGTTAGTGAAGTGATAACC 58.424 43.478 0.00 0.00 38.12 2.85
3262 3520 3.132646 TCAAAGATGCAAAACTGCCAGTT 59.867 39.130 3.74 3.74 40.80 3.16
3365 3623 4.319046 CGCATAAATCTTGACATCCCTTCG 60.319 45.833 0.00 0.00 0.00 3.79
3378 3636 5.536161 ACCTTGATAAATGGCGCATAAATCT 59.464 36.000 10.83 0.00 0.00 2.40
3470 3733 5.646360 TGTAAGCCTGTAATTAGCAAGTTCC 59.354 40.000 0.00 0.00 0.00 3.62
3516 3779 9.542462 TCTGCTTAGCGATATTACATAGTTTTT 57.458 29.630 0.00 0.00 0.00 1.94
3616 3886 6.902341 ACTGTGTGCTCTTATAACAACAATG 58.098 36.000 0.00 0.00 0.00 2.82
3725 3998 0.676151 GCTTGCTAGCTTGCTCCTGT 60.676 55.000 20.64 0.00 44.27 4.00
3751 4024 2.371841 ACTGTGTTGGCCATGTCTAGAA 59.628 45.455 6.09 0.00 0.00 2.10
3773 4046 5.823861 AAACCCCAATTGCTTCTGTTAAT 57.176 34.783 0.00 0.00 0.00 1.40
3891 4169 7.973388 TCGTTCCCATGATCATTAAAATTTCAC 59.027 33.333 5.16 0.00 0.00 3.18
4252 4531 1.200948 GCTGAACCCATCTTTGTGAGC 59.799 52.381 0.00 0.00 0.00 4.26
4258 4537 2.299326 AGCTTGCTGAACCCATCTTT 57.701 45.000 0.00 0.00 0.00 2.52
4342 4621 0.732880 ACTTGGAGAATCGTGCGACG 60.733 55.000 0.00 2.79 44.19 5.12
4349 4628 6.147821 ACAACAATAGTGAACTTGGAGAATCG 59.852 38.462 0.00 0.00 34.37 3.34
4381 4660 6.659242 CCTGGACAAGTAAAATCAAGTGGTAT 59.341 38.462 0.00 0.00 0.00 2.73
4783 5065 0.811281 GTAACATTCAGCTGCCACCC 59.189 55.000 9.47 0.00 0.00 4.61
4784 5066 0.811281 GGTAACATTCAGCTGCCACC 59.189 55.000 9.47 5.72 0.00 4.61
4785 5067 1.533625 TGGTAACATTCAGCTGCCAC 58.466 50.000 9.47 0.00 46.17 5.01
4831 5113 7.575505 ACTCATAGCTAACCTAACACTAGAGA 58.424 38.462 0.00 0.00 0.00 3.10
4832 5114 7.811117 ACTCATAGCTAACCTAACACTAGAG 57.189 40.000 0.00 0.00 0.00 2.43
4923 5209 5.598830 ACCTAGATAACAATCTGGATCGTGT 59.401 40.000 0.00 0.00 31.70 4.49
5213 5499 1.909459 TATTCAGCGCAGGCCTCCAA 61.909 55.000 11.47 0.00 41.24 3.53
5252 5538 3.181440 TGAGGAGAAGCTTGTCCAACATT 60.181 43.478 36.25 20.54 42.72 2.71
5379 5665 2.774439 AAAGGCGACATGTTCAACAC 57.226 45.000 0.00 0.00 0.00 3.32
5718 6004 3.874383 TGGAGACAAACCTTGGAATCA 57.126 42.857 0.00 0.00 37.44 2.57


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

AutoCloner maintained by Alex Coulton.