Multiple sequence alignment - TraesCS4D01G005800

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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 TraesCS4D01G005800 chr4D 100.000 3225 0 0 1 3225 3302016 3305240 0.000000e+00 5956.0
1 TraesCS4D01G005800 chr4D 97.727 44 1 0 1652 1695 3303623 3303666 3.450000e-10 76.8
2 TraesCS4D01G005800 chr4D 97.727 44 1 0 1608 1651 3303667 3303710 3.450000e-10 76.8
3 TraesCS4D01G005800 chr3D 99.402 2173 10 1 548 2720 548543649 548541480 0.000000e+00 3938.0
4 TraesCS4D01G005800 chr3D 94.348 230 12 1 2493 2722 559476654 559476882 5.120000e-93 351.0
5 TraesCS4D01G005800 chr3D 97.727 44 1 0 1608 1651 548542548 548542505 3.450000e-10 76.8
6 TraesCS4D01G005800 chr3D 97.727 44 1 0 1652 1695 548542592 548542549 3.450000e-10 76.8
7 TraesCS4D01G005800 chr7A 96.722 1495 45 3 1217 2711 480987805 480989295 0.000000e+00 2486.0
8 TraesCS4D01G005800 chr7A 94.856 661 32 2 1708 2368 536711940 536712598 0.000000e+00 1031.0
9 TraesCS4D01G005800 chr7A 94.251 661 36 2 1708 2368 608673111 608673769 0.000000e+00 1009.0
10 TraesCS4D01G005800 chr7A 88.857 691 41 6 547 1203 480985031 480985719 0.000000e+00 817.0
11 TraesCS4D01G005800 chr7A 86.916 428 32 14 780 1195 536709250 536709665 2.930000e-125 459.0
12 TraesCS4D01G005800 chr7A 98.016 252 4 1 1217 1467 608672871 608673122 1.370000e-118 436.0
13 TraesCS4D01G005800 chr7A 97.222 252 6 1 1217 1467 536711700 536711951 2.970000e-115 425.0
14 TraesCS4D01G005800 chr7A 93.773 273 15 2 2096 2368 649156509 649156239 2.990000e-110 409.0
15 TraesCS4D01G005800 chr7A 97.727 44 1 0 1652 1695 480988194 480988237 3.450000e-10 76.8
16 TraesCS4D01G005800 chr7A 97.727 44 1 0 1608 1651 480988238 480988281 3.450000e-10 76.8
17 TraesCS4D01G005800 chr6A 92.794 1013 53 10 1713 2721 8396986 8397982 0.000000e+00 1448.0
18 TraesCS4D01G005800 chr6A 85.879 694 28 19 545 1195 8395391 8396057 0.000000e+00 675.0
19 TraesCS4D01G005800 chr1A 94.809 655 32 2 1714 2368 576629777 576629125 0.000000e+00 1020.0
20 TraesCS4D01G005800 chr1A 86.636 434 28 10 780 1195 576632479 576632058 1.360000e-123 453.0
21 TraesCS4D01G005800 chr1A 96.825 252 7 1 1217 1467 576630023 576629772 1.380000e-113 420.0
22 TraesCS4D01G005800 chr3A 98.584 565 8 0 1217 1781 38027737 38027173 0.000000e+00 1000.0
23 TraesCS4D01G005800 chr3A 89.884 692 37 6 544 1203 38030511 38029821 0.000000e+00 859.0
24 TraesCS4D01G005800 chr3A 94.655 449 22 2 1920 2368 594624366 594624812 0.000000e+00 695.0
25 TraesCS4D01G005800 chr3A 83.058 242 17 7 780 1009 369078231 369078460 7.060000e-47 198.0
26 TraesCS4D01G005800 chr3A 97.727 44 1 0 1608 1651 38027302 38027259 3.450000e-10 76.8
27 TraesCS4D01G005800 chr3A 97.727 44 1 0 1652 1695 38027346 38027303 3.450000e-10 76.8
28 TraesCS4D01G005800 chr4A 93.192 661 37 3 1708 2368 725277056 725277708 0.000000e+00 965.0
29 TraesCS4D01G005800 chr4A 88.571 420 24 7 788 1195 725275244 725275651 3.740000e-134 488.0
30 TraesCS4D01G005800 chr4A 95.802 262 11 0 2964 3225 602189754 602189493 1.070000e-114 424.0
31 TraesCS4D01G005800 chr4A 99.471 189 1 0 1279 1467 725276879 725277067 8.570000e-91 344.0
32 TraesCS4D01G005800 chr4A 85.627 327 41 5 38 358 602192572 602192246 3.990000e-89 339.0
33 TraesCS4D01G005800 chr4A 86.996 223 13 7 2714 2921 602189973 602189752 1.500000e-58 237.0
34 TraesCS4D01G005800 chr5A 97.642 212 5 0 2500 2711 645390585 645390796 6.580000e-97 364.0
35 TraesCS4D01G005800 chr5A 81.500 400 56 8 1808 2207 537994874 537995255 2.420000e-81 313.0
36 TraesCS4D01G005800 chr7D 94.043 235 13 1 2493 2726 1526349 1526115 3.960000e-94 355.0
37 TraesCS4D01G005800 chr7D 94.258 209 11 1 548 756 599464744 599464537 5.190000e-83 318.0
38 TraesCS4D01G005800 chr7D 93.810 210 12 1 547 756 584038110 584038318 6.720000e-82 315.0
39 TraesCS4D01G005800 chr2D 94.737 228 11 1 2493 2720 204265564 204265790 1.420000e-93 353.0
40 TraesCS4D01G005800 chr2D 94.258 209 11 1 548 756 462487106 462486899 5.190000e-83 318.0
41 TraesCS4D01G005800 chr1D 94.298 228 13 0 2493 2720 37432674 37432447 1.840000e-92 350.0
42 TraesCS4D01G005800 chr5D 93.939 231 13 1 2493 2723 486229268 486229497 6.620000e-92 348.0
43 TraesCS4D01G005800 chr5D 94.286 210 11 1 547 756 486229018 486229226 1.440000e-83 320.0
44 TraesCS4D01G005800 chr5D 94.258 209 11 1 548 756 424910347 424910140 5.190000e-83 318.0
45 TraesCS4D01G005800 chrUn 83.081 396 47 7 1813 2207 75400411 75400035 3.080000e-90 342.0
46 TraesCS4D01G005800 chr7B 95.500 200 9 0 557 756 705810909 705810710 1.440000e-83 320.0
47 TraesCS4D01G005800 chr7B 86.996 223 21 5 1217 1437 728283615 728283831 8.940000e-61 244.0
48 TraesCS4D01G005800 chr4B 86.996 223 21 5 1217 1437 415769701 415769485 8.940000e-61 244.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G005800 chr4D 3302016 3305240 3224 False 2036.533333 5956 98.484667 1 3225 3 chr4D.!!$F1 3224
1 TraesCS4D01G005800 chr3D 548541480 548543649 2169 True 1363.866667 3938 98.285333 548 2720 3 chr3D.!!$R1 2172
2 TraesCS4D01G005800 chr7A 480985031 480989295 4264 False 864.150000 2486 95.258250 547 2711 4 chr7A.!!$F1 2164
3 TraesCS4D01G005800 chr7A 608672871 608673769 898 False 722.500000 1009 96.133500 1217 2368 2 chr7A.!!$F3 1151
4 TraesCS4D01G005800 chr7A 536709250 536712598 3348 False 638.333333 1031 92.998000 780 2368 3 chr7A.!!$F2 1588
5 TraesCS4D01G005800 chr6A 8395391 8397982 2591 False 1061.500000 1448 89.336500 545 2721 2 chr6A.!!$F1 2176
6 TraesCS4D01G005800 chr1A 576629125 576632479 3354 True 631.000000 1020 92.756667 780 2368 3 chr1A.!!$R1 1588
7 TraesCS4D01G005800 chr3A 38027173 38030511 3338 True 503.150000 1000 95.980500 544 1781 4 chr3A.!!$R1 1237
8 TraesCS4D01G005800 chr4A 725275244 725277708 2464 False 599.000000 965 93.744667 788 2368 3 chr4A.!!$F1 1580
9 TraesCS4D01G005800 chr4A 602189493 602192572 3079 True 333.333333 424 89.475000 38 3225 3 chr4A.!!$R1 3187

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
475 482 0.251474 ATTTGCTTGAGGCCAGCTCA 60.251 50.0 14.14 1.98 40.92 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2721 6390 5.525484 TCCTCTAGTTTGCATTAGGTAGGA 58.475 41.667 0.0 0.0 0.0 2.94 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
35 36 9.807649 AAGGACATATATTGATTTCTTTGTTGC 57.192 29.630 0.00 0.00 0.00 4.17
36 37 8.970020 AGGACATATATTGATTTCTTTGTTGCA 58.030 29.630 0.00 0.00 0.00 4.08
60 61 8.511321 GCAATTGATTATATATGACGTTGGGAA 58.489 33.333 10.34 0.00 0.00 3.97
68 69 0.400213 TGACGTTGGGAAGGCTTGAT 59.600 50.000 3.46 0.00 0.00 2.57
89 90 1.078759 AAGCGATCGAGCGAACAAGG 61.079 55.000 29.29 0.00 43.00 3.61
127 128 9.240159 GCTAGATCTTTCTTTGTAAGTAGTAGC 57.760 37.037 0.00 0.00 33.17 3.58
134 135 7.591006 TTCTTTGTAAGTAGTAGCGAATTGG 57.409 36.000 0.00 0.00 0.00 3.16
144 145 1.033746 AGCGAATTGGTGATGGCCTG 61.034 55.000 3.32 0.00 0.00 4.85
149 150 2.369983 ATTGGTGATGGCCTGGTATG 57.630 50.000 3.32 0.00 0.00 2.39
156 157 2.107031 TGATGGCCTGGTATGATTGAGG 59.893 50.000 3.32 0.00 0.00 3.86
163 164 3.070734 CCTGGTATGATTGAGGTGAGAGG 59.929 52.174 0.00 0.00 0.00 3.69
166 167 4.406972 TGGTATGATTGAGGTGAGAGGAAG 59.593 45.833 0.00 0.00 0.00 3.46
180 181 5.122396 GTGAGAGGAAGCGATTAATGTTGTT 59.878 40.000 0.00 0.00 0.00 2.83
191 192 6.237542 GCGATTAATGTTGTTAATGTGGCTTG 60.238 38.462 0.00 0.00 0.00 4.01
206 207 3.072944 TGGCTTGCAAAATAAATGTGCC 58.927 40.909 12.27 12.27 37.48 5.01
213 214 6.400579 TGCAAAATAAATGTGCCATTAACG 57.599 33.333 1.52 0.00 37.48 3.18
216 217 6.735957 GCAAAATAAATGTGCCATTAACGTTG 59.264 34.615 11.99 0.00 31.94 4.10
219 220 7.954788 AATAAATGTGCCATTAACGTTGTTT 57.045 28.000 11.99 0.00 0.00 2.83
220 221 5.898630 AAATGTGCCATTAACGTTGTTTC 57.101 34.783 11.99 0.00 0.00 2.78
221 222 4.846779 ATGTGCCATTAACGTTGTTTCT 57.153 36.364 11.99 0.00 0.00 2.52
222 223 5.950758 ATGTGCCATTAACGTTGTTTCTA 57.049 34.783 11.99 0.00 0.00 2.10
224 225 5.753744 TGTGCCATTAACGTTGTTTCTAAG 58.246 37.500 11.99 0.00 0.00 2.18
231 233 7.586300 CCATTAACGTTGTTTCTAAGTCAGTTG 59.414 37.037 11.99 0.00 0.00 3.16
238 240 8.477709 CGTTGTTTCTAAGTCAGTTGTAGTTAG 58.522 37.037 0.00 0.00 0.00 2.34
247 249 7.916914 AGTCAGTTGTAGTTAGTGTTGTTTT 57.083 32.000 0.00 0.00 0.00 2.43
251 253 8.447833 TCAGTTGTAGTTAGTGTTGTTTTCAAG 58.552 33.333 0.00 0.00 40.74 3.02
254 256 7.311364 TGTAGTTAGTGTTGTTTTCAAGTCC 57.689 36.000 0.00 0.00 40.74 3.85
297 300 9.680315 TTGTTTTAAGTATTTTCGGTAATGTGG 57.320 29.630 0.00 0.00 0.00 4.17
304 307 7.215085 AGTATTTTCGGTAATGTGGAGGATAC 58.785 38.462 0.00 0.00 0.00 2.24
308 311 4.219919 TCGGTAATGTGGAGGATACATCA 58.780 43.478 0.00 0.00 37.77 3.07
316 319 4.284490 TGTGGAGGATACATCATTAGAGCC 59.716 45.833 0.00 0.00 41.41 4.70
317 320 4.284490 GTGGAGGATACATCATTAGAGCCA 59.716 45.833 0.00 0.00 41.41 4.75
320 323 5.188555 GGAGGATACATCATTAGAGCCATGA 59.811 44.000 0.00 0.00 41.41 3.07
329 332 3.845781 TTAGAGCCATGAGGGACATTC 57.154 47.619 0.00 0.00 40.01 2.67
330 333 0.467384 AGAGCCATGAGGGACATTCG 59.533 55.000 0.00 0.00 40.01 3.34
331 334 0.533755 GAGCCATGAGGGACATTCGG 60.534 60.000 0.00 0.00 40.01 4.30
333 336 0.468226 GCCATGAGGGACATTCGGTA 59.532 55.000 0.00 0.00 40.01 4.02
336 339 3.141398 CCATGAGGGACATTCGGTAATG 58.859 50.000 0.00 0.00 46.66 1.90
351 358 5.250200 TCGGTAATGTGGTTGAATAGCTTT 58.750 37.500 0.00 0.00 0.00 3.51
354 361 6.183360 CGGTAATGTGGTTGAATAGCTTTGAT 60.183 38.462 0.00 0.00 0.00 2.57
358 365 8.523915 AATGTGGTTGAATAGCTTTGATCATA 57.476 30.769 0.00 0.00 0.00 2.15
360 367 7.933396 TGTGGTTGAATAGCTTTGATCATATG 58.067 34.615 0.00 0.00 0.00 1.78
361 368 7.013559 TGTGGTTGAATAGCTTTGATCATATGG 59.986 37.037 2.13 0.00 0.00 2.74
363 370 7.946219 TGGTTGAATAGCTTTGATCATATGGAT 59.054 33.333 2.13 0.00 39.53 3.41
364 371 8.800332 GGTTGAATAGCTTTGATCATATGGATT 58.200 33.333 2.13 0.00 36.00 3.01
366 373 9.577222 TTGAATAGCTTTGATCATATGGATTCA 57.423 29.630 14.21 14.21 36.00 2.57
370 377 6.124340 AGCTTTGATCATATGGATTCACACA 58.876 36.000 2.13 0.00 36.00 3.72
371 378 6.604396 AGCTTTGATCATATGGATTCACACAA 59.396 34.615 2.13 0.00 36.00 3.33
372 379 7.123098 AGCTTTGATCATATGGATTCACACAAA 59.877 33.333 2.13 0.00 36.00 2.83
373 380 7.924412 GCTTTGATCATATGGATTCACACAAAT 59.076 33.333 2.13 0.00 36.00 2.32
382 389 6.839124 TGGATTCACACAAATAATCTTGCT 57.161 33.333 0.00 0.00 31.66 3.91
383 390 7.230849 TGGATTCACACAAATAATCTTGCTT 57.769 32.000 0.00 0.00 31.66 3.91
384 391 7.669427 TGGATTCACACAAATAATCTTGCTTT 58.331 30.769 0.00 0.00 31.66 3.51
385 392 8.149647 TGGATTCACACAAATAATCTTGCTTTT 58.850 29.630 0.00 0.00 31.66 2.27
386 393 9.638239 GGATTCACACAAATAATCTTGCTTTTA 57.362 29.630 0.00 0.00 31.66 1.52
410 417 7.873699 ATAGGTATTGGTAGTAGATTGGCTT 57.126 36.000 0.00 0.00 0.00 4.35
412 419 7.304497 AGGTATTGGTAGTAGATTGGCTTAG 57.696 40.000 0.00 0.00 0.00 2.18
413 420 5.932883 GGTATTGGTAGTAGATTGGCTTAGC 59.067 44.000 0.00 0.00 0.00 3.09
414 421 5.896073 ATTGGTAGTAGATTGGCTTAGCT 57.104 39.130 3.59 0.00 0.00 3.32
415 422 5.693769 TTGGTAGTAGATTGGCTTAGCTT 57.306 39.130 3.59 0.00 0.00 3.74
416 423 5.693769 TGGTAGTAGATTGGCTTAGCTTT 57.306 39.130 3.59 0.00 0.00 3.51
417 424 6.062258 TGGTAGTAGATTGGCTTAGCTTTT 57.938 37.500 3.59 0.00 0.00 2.27
419 426 6.113411 GGTAGTAGATTGGCTTAGCTTTTGA 58.887 40.000 3.59 0.00 0.00 2.69
420 427 6.598064 GGTAGTAGATTGGCTTAGCTTTTGAA 59.402 38.462 3.59 0.00 0.00 2.69
421 428 7.120726 GGTAGTAGATTGGCTTAGCTTTTGAAA 59.879 37.037 3.59 0.00 0.00 2.69
422 429 7.709149 AGTAGATTGGCTTAGCTTTTGAAAT 57.291 32.000 3.59 0.00 0.00 2.17
423 430 8.127150 AGTAGATTGGCTTAGCTTTTGAAATT 57.873 30.769 3.59 0.00 0.00 1.82
424 431 8.246871 AGTAGATTGGCTTAGCTTTTGAAATTC 58.753 33.333 3.59 0.00 0.00 2.17
425 432 6.401394 AGATTGGCTTAGCTTTTGAAATTCC 58.599 36.000 3.59 0.00 0.00 3.01
426 433 5.806654 TTGGCTTAGCTTTTGAAATTCCT 57.193 34.783 3.59 0.00 0.00 3.36
427 434 5.806654 TGGCTTAGCTTTTGAAATTCCTT 57.193 34.783 3.59 0.00 0.00 3.36
428 435 5.783111 TGGCTTAGCTTTTGAAATTCCTTC 58.217 37.500 3.59 0.00 34.31 3.46
430 437 5.335661 GGCTTAGCTTTTGAAATTCCTTCGA 60.336 40.000 3.59 0.00 36.78 3.71
432 439 4.147219 AGCTTTTGAAATTCCTTCGACG 57.853 40.909 0.00 0.00 36.78 5.12
433 440 3.564225 AGCTTTTGAAATTCCTTCGACGT 59.436 39.130 0.00 0.00 36.78 4.34
434 441 4.753107 AGCTTTTGAAATTCCTTCGACGTA 59.247 37.500 0.00 0.00 36.78 3.57
435 442 5.080068 GCTTTTGAAATTCCTTCGACGTAG 58.920 41.667 0.00 0.00 36.78 3.51
436 443 5.333875 GCTTTTGAAATTCCTTCGACGTAGT 60.334 40.000 0.68 0.00 36.78 2.73
438 445 4.247267 TGAAATTCCTTCGACGTAGTGT 57.753 40.909 0.68 0.00 36.50 3.55
439 446 4.624015 TGAAATTCCTTCGACGTAGTGTT 58.376 39.130 0.68 0.00 36.50 3.32
440 447 5.051816 TGAAATTCCTTCGACGTAGTGTTT 58.948 37.500 0.68 0.00 36.50 2.83
441 448 5.176223 TGAAATTCCTTCGACGTAGTGTTTC 59.824 40.000 12.31 12.31 36.50 2.78
442 449 7.175916 TGAAATTCCTTCGACGTAGTGTTTCA 61.176 38.462 15.39 15.39 36.50 2.69
443 450 9.092757 TGAAATTCCTTCGACGTAGTGTTTCAC 62.093 40.741 15.39 0.00 36.50 3.18
453 460 6.110543 ACGTAGTGTTTCACAAAGGTAAAC 57.889 37.500 0.00 0.00 42.51 2.01
454 461 5.065090 ACGTAGTGTTTCACAAAGGTAAACC 59.935 40.000 0.00 0.00 42.51 3.27
455 462 5.064962 CGTAGTGTTTCACAAAGGTAAACCA 59.935 40.000 1.26 0.00 36.74 3.67
456 463 5.986501 AGTGTTTCACAAAGGTAAACCAA 57.013 34.783 1.26 0.00 36.74 3.67
457 464 6.538945 AGTGTTTCACAAAGGTAAACCAAT 57.461 33.333 1.26 0.00 36.74 3.16
458 465 6.941857 AGTGTTTCACAAAGGTAAACCAATT 58.058 32.000 1.26 0.00 36.74 2.32
459 466 7.390823 AGTGTTTCACAAAGGTAAACCAATTT 58.609 30.769 1.26 0.00 36.74 1.82
460 467 7.333174 AGTGTTTCACAAAGGTAAACCAATTTG 59.667 33.333 10.66 10.66 37.26 2.32
462 469 5.606348 TCACAAAGGTAAACCAATTTGCT 57.394 34.783 11.69 1.02 35.67 3.91
463 470 5.983540 TCACAAAGGTAAACCAATTTGCTT 58.016 33.333 11.69 0.00 35.67 3.91
464 471 5.814705 TCACAAAGGTAAACCAATTTGCTTG 59.185 36.000 11.69 6.17 35.67 4.01
465 472 5.814705 CACAAAGGTAAACCAATTTGCTTGA 59.185 36.000 11.69 0.00 35.67 3.02
466 473 6.018832 CACAAAGGTAAACCAATTTGCTTGAG 60.019 38.462 11.69 0.00 35.67 3.02
467 474 4.871933 AGGTAAACCAATTTGCTTGAGG 57.128 40.909 1.26 0.00 36.97 3.86
468 475 3.006859 AGGTAAACCAATTTGCTTGAGGC 59.993 43.478 1.26 0.00 36.97 4.70
469 476 2.549064 AAACCAATTTGCTTGAGGCC 57.451 45.000 0.00 0.00 40.92 5.19
470 477 1.422531 AACCAATTTGCTTGAGGCCA 58.577 45.000 5.01 0.00 40.92 5.36
473 480 0.606604 CAATTTGCTTGAGGCCAGCT 59.393 50.000 14.14 0.00 40.92 4.24
475 482 0.251474 ATTTGCTTGAGGCCAGCTCA 60.251 50.000 14.14 1.98 40.92 4.26
476 483 1.174712 TTTGCTTGAGGCCAGCTCAC 61.175 55.000 14.14 0.00 40.92 3.51
478 485 2.045536 CTTGAGGCCAGCTCACCC 60.046 66.667 5.01 0.00 0.00 4.61
479 486 2.853542 TTGAGGCCAGCTCACCCA 60.854 61.111 5.01 0.00 0.00 4.51
480 487 2.416107 CTTGAGGCCAGCTCACCCAA 62.416 60.000 5.01 2.61 0.00 4.12
482 489 3.177884 AGGCCAGCTCACCCAACA 61.178 61.111 5.01 0.00 0.00 3.33
483 490 2.203480 GGCCAGCTCACCCAACAA 60.203 61.111 0.00 0.00 0.00 2.83
485 492 1.187567 GGCCAGCTCACCCAACAAAT 61.188 55.000 0.00 0.00 0.00 2.32
487 494 1.619654 CCAGCTCACCCAACAAATGA 58.380 50.000 0.00 0.00 0.00 2.57
488 495 2.173519 CCAGCTCACCCAACAAATGAT 58.826 47.619 0.00 0.00 0.00 2.45
489 496 2.165030 CCAGCTCACCCAACAAATGATC 59.835 50.000 0.00 0.00 0.00 2.92
491 498 3.446161 CAGCTCACCCAACAAATGATCAT 59.554 43.478 1.18 1.18 0.00 2.45
492 499 4.641541 CAGCTCACCCAACAAATGATCATA 59.358 41.667 9.04 0.00 0.00 2.15
493 500 5.301045 CAGCTCACCCAACAAATGATCATAT 59.699 40.000 9.04 0.00 0.00 1.78
494 501 5.301045 AGCTCACCCAACAAATGATCATATG 59.699 40.000 9.04 6.23 0.00 1.78
495 502 5.518848 TCACCCAACAAATGATCATATGC 57.481 39.130 9.04 0.00 0.00 3.14
496 503 4.954826 TCACCCAACAAATGATCATATGCA 59.045 37.500 9.04 0.00 0.00 3.96
497 504 5.068067 TCACCCAACAAATGATCATATGCAG 59.932 40.000 9.04 0.00 0.00 4.41
498 505 5.068067 CACCCAACAAATGATCATATGCAGA 59.932 40.000 9.04 0.00 0.00 4.26
499 506 5.301045 ACCCAACAAATGATCATATGCAGAG 59.699 40.000 9.04 0.00 0.00 3.35
500 507 5.278808 CCCAACAAATGATCATATGCAGAGG 60.279 44.000 9.04 5.70 0.00 3.69
501 508 5.533528 CCAACAAATGATCATATGCAGAGGA 59.466 40.000 9.04 0.00 0.00 3.71
502 509 6.040054 CCAACAAATGATCATATGCAGAGGAA 59.960 38.462 9.04 0.00 0.00 3.36
503 510 7.417003 CCAACAAATGATCATATGCAGAGGAAA 60.417 37.037 9.04 0.00 0.00 3.13
504 511 7.834881 ACAAATGATCATATGCAGAGGAAAT 57.165 32.000 9.04 0.00 0.00 2.17
505 512 8.246430 ACAAATGATCATATGCAGAGGAAATT 57.754 30.769 9.04 0.69 0.00 1.82
506 513 8.701895 ACAAATGATCATATGCAGAGGAAATTT 58.298 29.630 9.04 6.95 0.00 1.82
508 515 8.473358 AATGATCATATGCAGAGGAAATTTGA 57.527 30.769 9.04 0.00 0.00 2.69
510 517 6.489022 TGATCATATGCAGAGGAAATTTGAGG 59.511 38.462 0.00 0.00 0.00 3.86
511 518 4.581824 TCATATGCAGAGGAAATTTGAGGC 59.418 41.667 0.00 0.00 0.00 4.70
512 519 2.291209 TGCAGAGGAAATTTGAGGCA 57.709 45.000 0.00 0.00 0.00 4.75
513 520 2.596346 TGCAGAGGAAATTTGAGGCAA 58.404 42.857 0.00 0.00 0.00 4.52
514 521 2.559668 TGCAGAGGAAATTTGAGGCAAG 59.440 45.455 0.00 0.00 0.00 4.01
515 522 2.560105 GCAGAGGAAATTTGAGGCAAGT 59.440 45.455 0.00 0.00 0.00 3.16
516 523 3.366781 GCAGAGGAAATTTGAGGCAAGTC 60.367 47.826 0.00 0.00 0.00 3.01
517 524 3.822735 CAGAGGAAATTTGAGGCAAGTCA 59.177 43.478 0.00 0.00 0.00 3.41
518 525 4.077822 AGAGGAAATTTGAGGCAAGTCAG 58.922 43.478 0.00 0.00 0.00 3.51
519 526 3.823304 GAGGAAATTTGAGGCAAGTCAGT 59.177 43.478 0.00 0.00 0.00 3.41
520 527 4.985538 AGGAAATTTGAGGCAAGTCAGTA 58.014 39.130 0.00 0.00 0.00 2.74
521 528 4.762251 AGGAAATTTGAGGCAAGTCAGTAC 59.238 41.667 0.00 0.00 0.00 2.73
522 529 4.518970 GGAAATTTGAGGCAAGTCAGTACA 59.481 41.667 0.00 0.00 0.00 2.90
523 530 5.335191 GGAAATTTGAGGCAAGTCAGTACAG 60.335 44.000 0.00 0.00 0.00 2.74
524 531 4.623932 ATTTGAGGCAAGTCAGTACAGA 57.376 40.909 0.00 0.00 0.00 3.41
525 532 4.623932 TTTGAGGCAAGTCAGTACAGAT 57.376 40.909 0.00 0.00 0.00 2.90
526 533 3.599730 TGAGGCAAGTCAGTACAGATG 57.400 47.619 0.00 0.00 0.00 2.90
527 534 2.275318 GAGGCAAGTCAGTACAGATGC 58.725 52.381 5.53 5.53 33.64 3.91
528 535 1.065854 AGGCAAGTCAGTACAGATGCC 60.066 52.381 19.84 19.84 45.29 4.40
529 536 1.065854 GGCAAGTCAGTACAGATGCCT 60.066 52.381 20.05 0.00 43.36 4.75
530 537 2.616510 GGCAAGTCAGTACAGATGCCTT 60.617 50.000 20.05 5.10 43.36 4.35
531 538 3.369471 GGCAAGTCAGTACAGATGCCTTA 60.369 47.826 20.05 0.00 43.36 2.69
532 539 4.446371 GCAAGTCAGTACAGATGCCTTAT 58.554 43.478 3.19 0.00 0.00 1.73
533 540 4.878397 GCAAGTCAGTACAGATGCCTTATT 59.122 41.667 3.19 0.00 0.00 1.40
534 541 5.007136 GCAAGTCAGTACAGATGCCTTATTC 59.993 44.000 3.19 0.00 0.00 1.75
535 542 6.344500 CAAGTCAGTACAGATGCCTTATTCT 58.656 40.000 0.00 0.00 0.00 2.40
536 543 6.552445 AGTCAGTACAGATGCCTTATTCTT 57.448 37.500 0.00 0.00 0.00 2.52
537 544 6.344500 AGTCAGTACAGATGCCTTATTCTTG 58.656 40.000 0.00 0.00 0.00 3.02
538 545 6.070538 AGTCAGTACAGATGCCTTATTCTTGT 60.071 38.462 0.00 0.00 0.00 3.16
539 546 6.036517 GTCAGTACAGATGCCTTATTCTTGTG 59.963 42.308 0.00 0.00 0.00 3.33
540 547 5.877012 CAGTACAGATGCCTTATTCTTGTGT 59.123 40.000 0.00 0.00 0.00 3.72
541 548 6.036517 CAGTACAGATGCCTTATTCTTGTGTC 59.963 42.308 0.00 0.00 0.00 3.67
542 549 4.265073 ACAGATGCCTTATTCTTGTGTCC 58.735 43.478 0.00 0.00 0.00 4.02
991 1466 3.898123 GACTCCATCCTATTCCTAGCACA 59.102 47.826 0.00 0.00 0.00 4.57
2385 6054 8.847196 GGTTGTTGAAGAGACTTACCTTAAAAT 58.153 33.333 0.00 0.00 0.00 1.82
2733 6402 2.973694 TCGTTGGTCCTACCTAATGC 57.026 50.000 0.00 0.00 39.58 3.56
2734 6403 2.181125 TCGTTGGTCCTACCTAATGCA 58.819 47.619 0.00 0.00 39.58 3.96
2735 6404 2.568062 TCGTTGGTCCTACCTAATGCAA 59.432 45.455 0.00 0.00 39.58 4.08
2736 6405 3.008157 TCGTTGGTCCTACCTAATGCAAA 59.992 43.478 0.00 0.00 39.58 3.68
2737 6406 3.126343 CGTTGGTCCTACCTAATGCAAAC 59.874 47.826 0.00 0.00 39.58 2.93
2738 6407 4.332828 GTTGGTCCTACCTAATGCAAACT 58.667 43.478 0.00 0.00 39.58 2.66
2739 6408 5.493809 GTTGGTCCTACCTAATGCAAACTA 58.506 41.667 0.00 0.00 39.58 2.24
2740 6409 5.353394 TGGTCCTACCTAATGCAAACTAG 57.647 43.478 0.00 0.00 39.58 2.57
2741 6410 5.027460 TGGTCCTACCTAATGCAAACTAGA 58.973 41.667 0.00 0.00 39.58 2.43
2742 6411 5.128827 TGGTCCTACCTAATGCAAACTAGAG 59.871 44.000 0.00 0.00 39.58 2.43
2743 6412 5.453480 GGTCCTACCTAATGCAAACTAGAGG 60.453 48.000 0.00 0.00 34.73 3.69
2744 6413 5.363005 GTCCTACCTAATGCAAACTAGAGGA 59.637 44.000 0.00 0.00 0.00 3.71
2745 6414 5.962031 TCCTACCTAATGCAAACTAGAGGAA 59.038 40.000 0.00 0.00 0.00 3.36
2746 6415 6.615726 TCCTACCTAATGCAAACTAGAGGAAT 59.384 38.462 0.00 0.00 0.00 3.01
2787 6456 8.418681 GCGAGTAATCATAAATCTAGACGAAAC 58.581 37.037 0.00 0.00 0.00 2.78
2799 6468 3.512033 AGACGAAACAGAGTATCCAGC 57.488 47.619 0.00 0.00 33.66 4.85
2816 6485 2.165167 CAGCAAATGGAAGAAGAGCCA 58.835 47.619 0.00 0.00 38.78 4.75
2865 6548 2.290916 AGGTAGTATGAGCACGACGATG 59.709 50.000 0.00 0.00 0.00 3.84
2918 6601 7.408123 CAAGCAGATCAATCATCAAACTAGAC 58.592 38.462 0.00 0.00 33.29 2.59
2919 6602 6.647229 AGCAGATCAATCATCAAACTAGACA 58.353 36.000 0.00 0.00 33.29 3.41
2920 6603 6.538021 AGCAGATCAATCATCAAACTAGACAC 59.462 38.462 0.00 0.00 33.29 3.67
2921 6604 6.314648 GCAGATCAATCATCAAACTAGACACA 59.685 38.462 0.00 0.00 33.29 3.72
2922 6605 7.675870 GCAGATCAATCATCAAACTAGACACAC 60.676 40.741 0.00 0.00 33.29 3.82
2923 6606 7.548427 CAGATCAATCATCAAACTAGACACACT 59.452 37.037 0.00 0.00 33.29 3.55
2924 6607 8.753133 AGATCAATCATCAAACTAGACACACTA 58.247 33.333 0.00 0.00 33.29 2.74
2947 6630 9.836076 ACTAGAAATAAAACTTGAATTAACGGC 57.164 29.630 0.00 0.00 0.00 5.68
2948 6631 7.790861 AGAAATAAAACTTGAATTAACGGCG 57.209 32.000 4.80 4.80 0.00 6.46
2949 6632 7.586747 AGAAATAAAACTTGAATTAACGGCGA 58.413 30.769 16.62 0.00 0.00 5.54
2950 6633 8.077386 AGAAATAAAACTTGAATTAACGGCGAA 58.923 29.630 16.62 0.00 0.00 4.70
2951 6634 7.557036 AATAAAACTTGAATTAACGGCGAAC 57.443 32.000 16.62 0.00 0.00 3.95
2961 6644 4.420143 CGGCGAACGGAATCAGAT 57.580 55.556 0.00 0.00 39.42 2.90
2962 6645 1.927210 CGGCGAACGGAATCAGATG 59.073 57.895 0.00 0.00 39.42 2.90
3083 6766 4.052229 CCAGACGAGGACGCGGTT 62.052 66.667 12.47 0.00 43.96 4.44
3106 6789 0.179234 TTCGATATTTGGCGGCTCCA 59.821 50.000 11.43 0.00 44.85 3.86
3117 6800 2.266055 GGCTCCAGTTCACCCTCG 59.734 66.667 0.00 0.00 0.00 4.63
3174 6857 5.505819 CGTCTCGATAACTCTAATGGCTTCA 60.506 44.000 0.00 0.00 0.00 3.02
3182 6865 1.077787 TAATGGCTTCACCGGCAGG 60.078 57.895 0.00 0.00 43.02 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.807649 GCAACAAAGAAATCAATATATGTCCTT 57.192 29.630 0.00 0.00 0.00 3.36
10 11 8.970020 TGCAACAAAGAAATCAATATATGTCCT 58.030 29.630 0.00 0.00 0.00 3.85
11 12 9.585099 TTGCAACAAAGAAATCAATATATGTCC 57.415 29.630 0.00 0.00 0.00 4.02
30 31 9.662545 CAACGTCATATATAATCAATTGCAACA 57.337 29.630 0.00 0.00 0.00 3.33
31 32 9.117145 CCAACGTCATATATAATCAATTGCAAC 57.883 33.333 0.00 0.00 0.00 4.17
32 33 8.296000 CCCAACGTCATATATAATCAATTGCAA 58.704 33.333 0.00 0.00 0.00 4.08
33 34 7.663493 TCCCAACGTCATATATAATCAATTGCA 59.337 33.333 0.00 0.00 0.00 4.08
34 35 8.039603 TCCCAACGTCATATATAATCAATTGC 57.960 34.615 0.00 0.00 0.00 3.56
36 37 9.231297 CCTTCCCAACGTCATATATAATCAATT 57.769 33.333 0.00 0.00 0.00 2.32
41 42 6.374417 AGCCTTCCCAACGTCATATATAAT 57.626 37.500 0.00 0.00 0.00 1.28
44 45 4.102524 TCAAGCCTTCCCAACGTCATATAT 59.897 41.667 0.00 0.00 0.00 0.86
51 52 0.400213 TCATCAAGCCTTCCCAACGT 59.600 50.000 0.00 0.00 0.00 3.99
52 53 1.470098 CTTCATCAAGCCTTCCCAACG 59.530 52.381 0.00 0.00 0.00 4.10
68 69 0.388006 TTGTTCGCTCGATCGCTTCA 60.388 50.000 11.09 0.43 0.00 3.02
127 128 0.680921 ACCAGGCCATCACCAATTCG 60.681 55.000 5.01 0.00 0.00 3.34
134 135 3.144506 CTCAATCATACCAGGCCATCAC 58.855 50.000 5.01 0.00 0.00 3.06
144 145 4.742138 GCTTCCTCTCACCTCAATCATACC 60.742 50.000 0.00 0.00 0.00 2.73
149 150 1.478510 TCGCTTCCTCTCACCTCAATC 59.521 52.381 0.00 0.00 0.00 2.67
156 157 4.631813 ACAACATTAATCGCTTCCTCTCAC 59.368 41.667 0.00 0.00 0.00 3.51
163 164 6.020678 GCCACATTAACAACATTAATCGCTTC 60.021 38.462 0.00 0.00 0.00 3.86
166 167 5.339990 AGCCACATTAACAACATTAATCGC 58.660 37.500 0.00 0.00 0.00 4.58
180 181 6.128336 GCACATTTATTTTGCAAGCCACATTA 60.128 34.615 0.00 0.00 36.22 1.90
206 207 8.120465 ACAACTGACTTAGAAACAACGTTAATG 58.880 33.333 0.00 0.00 0.00 1.90
213 214 9.310716 ACTAACTACAACTGACTTAGAAACAAC 57.689 33.333 0.00 0.00 0.00 3.32
216 217 8.868635 ACACTAACTACAACTGACTTAGAAAC 57.131 34.615 0.00 0.00 0.00 2.78
219 220 8.004087 ACAACACTAACTACAACTGACTTAGA 57.996 34.615 0.00 0.00 0.00 2.10
220 221 8.644318 AACAACACTAACTACAACTGACTTAG 57.356 34.615 0.00 0.00 0.00 2.18
221 222 9.439500 AAAACAACACTAACTACAACTGACTTA 57.561 29.630 0.00 0.00 0.00 2.24
222 223 7.916914 AAACAACACTAACTACAACTGACTT 57.083 32.000 0.00 0.00 0.00 3.01
224 225 7.745015 TGAAAACAACACTAACTACAACTGAC 58.255 34.615 0.00 0.00 0.00 3.51
231 233 7.311364 TGGACTTGAAAACAACACTAACTAC 57.689 36.000 0.00 0.00 0.00 2.73
238 240 7.820044 TTGTAATTGGACTTGAAAACAACAC 57.180 32.000 0.00 0.00 0.00 3.32
278 281 6.057321 TCCTCCACATTACCGAAAATACTT 57.943 37.500 0.00 0.00 0.00 2.24
282 285 5.996644 TGTATCCTCCACATTACCGAAAAT 58.003 37.500 0.00 0.00 0.00 1.82
291 294 6.471146 GCTCTAATGATGTATCCTCCACATT 58.529 40.000 0.00 0.00 36.76 2.71
297 300 6.291648 TCATGGCTCTAATGATGTATCCTC 57.708 41.667 0.00 0.00 0.00 3.71
304 307 3.072038 TGTCCCTCATGGCTCTAATGATG 59.928 47.826 0.00 0.00 33.69 3.07
308 311 3.244353 CGAATGTCCCTCATGGCTCTAAT 60.244 47.826 0.00 0.00 36.81 1.73
329 332 5.123186 TCAAAGCTATTCAACCACATTACCG 59.877 40.000 0.00 0.00 0.00 4.02
330 333 6.509418 TCAAAGCTATTCAACCACATTACC 57.491 37.500 0.00 0.00 0.00 2.85
331 334 7.761409 TGATCAAAGCTATTCAACCACATTAC 58.239 34.615 0.00 0.00 0.00 1.89
333 336 6.839124 TGATCAAAGCTATTCAACCACATT 57.161 33.333 0.00 0.00 0.00 2.71
336 339 7.229306 TCCATATGATCAAAGCTATTCAACCAC 59.771 37.037 3.65 0.00 0.00 4.16
340 343 9.577222 TGAATCCATATGATCAAAGCTATTCAA 57.423 29.630 17.07 7.19 31.61 2.69
343 346 8.790718 GTGTGAATCCATATGATCAAAGCTATT 58.209 33.333 3.65 0.00 31.61 1.73
358 365 7.414222 AGCAAGATTATTTGTGTGAATCCAT 57.586 32.000 0.00 0.00 31.21 3.41
360 367 8.538409 AAAAGCAAGATTATTTGTGTGAATCC 57.462 30.769 0.00 0.00 31.21 3.01
383 390 9.388672 AGCCAATCTACTACCAATACCTATAAA 57.611 33.333 0.00 0.00 0.00 1.40
384 391 8.967779 AGCCAATCTACTACCAATACCTATAA 57.032 34.615 0.00 0.00 0.00 0.98
385 392 8.967779 AAGCCAATCTACTACCAATACCTATA 57.032 34.615 0.00 0.00 0.00 1.31
386 393 7.873699 AAGCCAATCTACTACCAATACCTAT 57.126 36.000 0.00 0.00 0.00 2.57
387 394 7.039223 GCTAAGCCAATCTACTACCAATACCTA 60.039 40.741 0.00 0.00 0.00 3.08
388 395 6.239629 GCTAAGCCAATCTACTACCAATACCT 60.240 42.308 0.00 0.00 0.00 3.08
389 396 5.932883 GCTAAGCCAATCTACTACCAATACC 59.067 44.000 0.00 0.00 0.00 2.73
390 397 6.760291 AGCTAAGCCAATCTACTACCAATAC 58.240 40.000 0.00 0.00 0.00 1.89
391 398 6.996180 AGCTAAGCCAATCTACTACCAATA 57.004 37.500 0.00 0.00 0.00 1.90
392 399 5.896073 AGCTAAGCCAATCTACTACCAAT 57.104 39.130 0.00 0.00 0.00 3.16
395 402 6.113411 TCAAAAGCTAAGCCAATCTACTACC 58.887 40.000 0.00 0.00 0.00 3.18
396 403 7.611213 TTCAAAAGCTAAGCCAATCTACTAC 57.389 36.000 0.00 0.00 0.00 2.73
397 404 8.807948 ATTTCAAAAGCTAAGCCAATCTACTA 57.192 30.769 0.00 0.00 0.00 1.82
398 405 7.709149 ATTTCAAAAGCTAAGCCAATCTACT 57.291 32.000 0.00 0.00 0.00 2.57
400 407 7.397192 AGGAATTTCAAAAGCTAAGCCAATCTA 59.603 33.333 0.00 0.00 0.00 1.98
401 408 6.212187 AGGAATTTCAAAAGCTAAGCCAATCT 59.788 34.615 0.00 0.00 0.00 2.40
402 409 6.401394 AGGAATTTCAAAAGCTAAGCCAATC 58.599 36.000 0.00 0.00 0.00 2.67
403 410 6.364568 AGGAATTTCAAAAGCTAAGCCAAT 57.635 33.333 0.00 0.00 0.00 3.16
404 411 5.806654 AGGAATTTCAAAAGCTAAGCCAA 57.193 34.783 0.00 0.00 0.00 4.52
405 412 5.564651 CGAAGGAATTTCAAAAGCTAAGCCA 60.565 40.000 0.00 0.00 35.43 4.75
406 413 4.859245 CGAAGGAATTTCAAAAGCTAAGCC 59.141 41.667 0.00 0.00 35.43 4.35
410 417 4.753107 ACGTCGAAGGAATTTCAAAAGCTA 59.247 37.500 0.00 0.00 35.43 3.32
412 419 3.885358 ACGTCGAAGGAATTTCAAAAGC 58.115 40.909 0.00 0.00 35.43 3.51
413 420 6.071463 CACTACGTCGAAGGAATTTCAAAAG 58.929 40.000 0.00 0.00 35.43 2.27
414 421 5.524646 ACACTACGTCGAAGGAATTTCAAAA 59.475 36.000 0.00 0.00 35.43 2.44
415 422 5.051816 ACACTACGTCGAAGGAATTTCAAA 58.948 37.500 0.00 0.00 35.43 2.69
416 423 4.624015 ACACTACGTCGAAGGAATTTCAA 58.376 39.130 0.00 0.00 35.43 2.69
417 424 4.247267 ACACTACGTCGAAGGAATTTCA 57.753 40.909 0.00 0.00 35.43 2.69
419 426 5.050567 GTGAAACACTACGTCGAAGGAATTT 60.051 40.000 0.00 0.00 36.32 1.82
420 427 4.446719 GTGAAACACTACGTCGAAGGAATT 59.553 41.667 0.00 0.00 36.32 2.17
421 428 3.985925 GTGAAACACTACGTCGAAGGAAT 59.014 43.478 0.00 0.00 36.32 3.01
422 429 3.181488 TGTGAAACACTACGTCGAAGGAA 60.181 43.478 0.00 0.00 45.67 3.36
423 430 2.358582 TGTGAAACACTACGTCGAAGGA 59.641 45.455 0.00 0.00 45.67 3.36
424 431 2.734670 TGTGAAACACTACGTCGAAGG 58.265 47.619 0.00 0.00 45.67 3.46
430 437 7.295955 TGGTTTACCTTTGTGAAACACTACGT 61.296 38.462 0.00 0.00 41.82 3.57
432 439 6.439675 TGGTTTACCTTTGTGAAACACTAC 57.560 37.500 0.00 0.00 41.82 2.73
433 440 7.648039 ATTGGTTTACCTTTGTGAAACACTA 57.352 32.000 0.00 0.00 41.82 2.74
434 441 5.986501 TTGGTTTACCTTTGTGAAACACT 57.013 34.783 0.00 0.00 41.82 3.55
435 442 7.460296 CAAATTGGTTTACCTTTGTGAAACAC 58.540 34.615 0.00 0.00 41.82 3.32
436 443 6.092807 GCAAATTGGTTTACCTTTGTGAAACA 59.907 34.615 12.47 0.00 40.79 2.83
438 445 6.410540 AGCAAATTGGTTTACCTTTGTGAAA 58.589 32.000 12.47 0.00 35.09 2.69
439 446 5.983540 AGCAAATTGGTTTACCTTTGTGAA 58.016 33.333 12.47 0.00 35.09 3.18
440 447 5.606348 AGCAAATTGGTTTACCTTTGTGA 57.394 34.783 12.47 0.00 35.09 3.58
441 448 5.814705 TCAAGCAAATTGGTTTACCTTTGTG 59.185 36.000 7.77 0.00 35.69 3.33
442 449 5.983540 TCAAGCAAATTGGTTTACCTTTGT 58.016 33.333 7.77 1.75 35.69 2.83
443 450 5.466393 CCTCAAGCAAATTGGTTTACCTTTG 59.534 40.000 7.77 8.50 35.69 2.77
447 454 3.325870 GCCTCAAGCAAATTGGTTTACC 58.674 45.455 7.77 0.00 42.97 2.85
449 456 2.968574 TGGCCTCAAGCAAATTGGTTTA 59.031 40.909 7.77 0.00 46.50 2.01
450 457 1.767681 TGGCCTCAAGCAAATTGGTTT 59.232 42.857 7.77 0.00 46.50 3.27
451 458 1.345415 CTGGCCTCAAGCAAATTGGTT 59.655 47.619 3.32 4.40 46.50 3.67
452 459 0.971386 CTGGCCTCAAGCAAATTGGT 59.029 50.000 3.32 0.00 46.50 3.67
453 460 0.390735 GCTGGCCTCAAGCAAATTGG 60.391 55.000 3.32 0.00 46.50 3.16
454 461 0.606604 AGCTGGCCTCAAGCAAATTG 59.393 50.000 15.36 0.00 46.50 2.32
455 462 0.893447 GAGCTGGCCTCAAGCAAATT 59.107 50.000 15.36 0.00 46.50 1.82
456 463 2.576298 GAGCTGGCCTCAAGCAAAT 58.424 52.632 15.36 0.00 46.50 2.32
457 464 4.085876 GAGCTGGCCTCAAGCAAA 57.914 55.556 15.36 0.00 46.50 3.68
464 471 2.360475 GTTGGGTGAGCTGGCCTC 60.360 66.667 3.32 0.00 41.15 4.70
465 472 2.296945 TTTGTTGGGTGAGCTGGCCT 62.297 55.000 3.32 0.00 0.00 5.19
466 473 1.187567 ATTTGTTGGGTGAGCTGGCC 61.188 55.000 0.00 0.00 0.00 5.36
467 474 0.037975 CATTTGTTGGGTGAGCTGGC 60.038 55.000 0.00 0.00 0.00 4.85
468 475 1.619654 TCATTTGTTGGGTGAGCTGG 58.380 50.000 0.00 0.00 0.00 4.85
469 476 2.821378 TGATCATTTGTTGGGTGAGCTG 59.179 45.455 0.00 0.00 0.00 4.24
470 477 3.159213 TGATCATTTGTTGGGTGAGCT 57.841 42.857 0.00 0.00 0.00 4.09
473 480 4.954826 TGCATATGATCATTTGTTGGGTGA 59.045 37.500 22.18 0.00 0.00 4.02
475 482 5.202765 TCTGCATATGATCATTTGTTGGGT 58.797 37.500 22.18 0.00 0.00 4.51
476 483 5.278808 CCTCTGCATATGATCATTTGTTGGG 60.279 44.000 22.18 16.03 0.00 4.12
478 485 6.628919 TCCTCTGCATATGATCATTTGTTG 57.371 37.500 22.18 16.28 0.00 3.33
479 486 7.649533 TTTCCTCTGCATATGATCATTTGTT 57.350 32.000 22.18 0.00 0.00 2.83
480 487 7.834881 ATTTCCTCTGCATATGATCATTTGT 57.165 32.000 22.18 5.33 0.00 2.83
482 489 8.920174 TCAAATTTCCTCTGCATATGATCATTT 58.080 29.630 14.65 2.68 0.00 2.32
483 490 8.473358 TCAAATTTCCTCTGCATATGATCATT 57.527 30.769 14.65 0.00 0.00 2.57
485 492 6.489022 CCTCAAATTTCCTCTGCATATGATCA 59.511 38.462 6.97 0.00 0.00 2.92
487 494 5.243283 GCCTCAAATTTCCTCTGCATATGAT 59.757 40.000 6.97 0.00 0.00 2.45
488 495 4.581824 GCCTCAAATTTCCTCTGCATATGA 59.418 41.667 6.97 0.00 0.00 2.15
489 496 4.340097 TGCCTCAAATTTCCTCTGCATATG 59.660 41.667 0.00 0.00 0.00 1.78
491 498 3.966979 TGCCTCAAATTTCCTCTGCATA 58.033 40.909 0.00 0.00 0.00 3.14
492 499 2.811410 TGCCTCAAATTTCCTCTGCAT 58.189 42.857 0.00 0.00 0.00 3.96
493 500 2.291209 TGCCTCAAATTTCCTCTGCA 57.709 45.000 0.00 0.00 0.00 4.41
494 501 2.560105 ACTTGCCTCAAATTTCCTCTGC 59.440 45.455 0.00 0.00 0.00 4.26
495 502 3.822735 TGACTTGCCTCAAATTTCCTCTG 59.177 43.478 0.00 0.00 0.00 3.35
496 503 4.077822 CTGACTTGCCTCAAATTTCCTCT 58.922 43.478 0.00 0.00 0.00 3.69
497 504 3.823304 ACTGACTTGCCTCAAATTTCCTC 59.177 43.478 0.00 0.00 0.00 3.71
498 505 3.837355 ACTGACTTGCCTCAAATTTCCT 58.163 40.909 0.00 0.00 0.00 3.36
499 506 4.518970 TGTACTGACTTGCCTCAAATTTCC 59.481 41.667 0.00 0.00 0.00 3.13
500 507 5.470098 TCTGTACTGACTTGCCTCAAATTTC 59.530 40.000 0.00 0.00 0.00 2.17
501 508 5.376625 TCTGTACTGACTTGCCTCAAATTT 58.623 37.500 0.00 0.00 0.00 1.82
502 509 4.973168 TCTGTACTGACTTGCCTCAAATT 58.027 39.130 0.00 0.00 0.00 1.82
503 510 4.623932 TCTGTACTGACTTGCCTCAAAT 57.376 40.909 0.00 0.00 0.00 2.32
504 511 4.318332 CATCTGTACTGACTTGCCTCAAA 58.682 43.478 4.39 0.00 0.00 2.69
505 512 3.866066 GCATCTGTACTGACTTGCCTCAA 60.866 47.826 14.22 0.00 0.00 3.02
506 513 2.354103 GCATCTGTACTGACTTGCCTCA 60.354 50.000 14.22 0.00 0.00 3.86
508 515 1.065854 GGCATCTGTACTGACTTGCCT 60.066 52.381 27.39 3.52 40.59 4.75
510 517 2.393271 AGGCATCTGTACTGACTTGC 57.607 50.000 16.00 16.00 0.00 4.01
511 518 6.344500 AGAATAAGGCATCTGTACTGACTTG 58.656 40.000 11.06 5.67 41.99 3.16
512 519 6.552445 AGAATAAGGCATCTGTACTGACTT 57.448 37.500 4.39 5.80 44.18 3.01
513 520 6.070538 ACAAGAATAAGGCATCTGTACTGACT 60.071 38.462 4.39 0.00 31.69 3.41
514 521 6.036517 CACAAGAATAAGGCATCTGTACTGAC 59.963 42.308 4.39 0.00 0.00 3.51
515 522 6.108687 CACAAGAATAAGGCATCTGTACTGA 58.891 40.000 4.80 4.80 0.00 3.41
516 523 5.877012 ACACAAGAATAAGGCATCTGTACTG 59.123 40.000 0.00 0.00 0.00 2.74
517 524 6.054860 ACACAAGAATAAGGCATCTGTACT 57.945 37.500 0.00 0.00 0.00 2.73
518 525 5.294552 GGACACAAGAATAAGGCATCTGTAC 59.705 44.000 0.00 0.00 0.00 2.90
519 526 5.189736 AGGACACAAGAATAAGGCATCTGTA 59.810 40.000 0.00 0.00 0.00 2.74
520 527 4.018960 AGGACACAAGAATAAGGCATCTGT 60.019 41.667 0.00 0.00 0.00 3.41
521 528 4.521146 AGGACACAAGAATAAGGCATCTG 58.479 43.478 0.00 0.00 0.00 2.90
522 529 4.851639 AGGACACAAGAATAAGGCATCT 57.148 40.909 0.00 0.00 0.00 2.90
523 530 4.816925 GGTAGGACACAAGAATAAGGCATC 59.183 45.833 0.00 0.00 0.00 3.91
524 531 4.385310 GGGTAGGACACAAGAATAAGGCAT 60.385 45.833 0.00 0.00 0.00 4.40
525 532 3.054655 GGGTAGGACACAAGAATAAGGCA 60.055 47.826 0.00 0.00 0.00 4.75
526 533 3.054655 TGGGTAGGACACAAGAATAAGGC 60.055 47.826 0.00 0.00 0.00 4.35
527 534 4.837093 TGGGTAGGACACAAGAATAAGG 57.163 45.455 0.00 0.00 0.00 2.69
528 535 4.630069 CGTTGGGTAGGACACAAGAATAAG 59.370 45.833 0.00 0.00 42.98 1.73
529 536 4.283978 TCGTTGGGTAGGACACAAGAATAA 59.716 41.667 0.00 0.00 42.98 1.40
530 537 3.833650 TCGTTGGGTAGGACACAAGAATA 59.166 43.478 0.00 0.00 42.98 1.75
531 538 2.635915 TCGTTGGGTAGGACACAAGAAT 59.364 45.455 0.00 0.00 42.98 2.40
532 539 2.040939 TCGTTGGGTAGGACACAAGAA 58.959 47.619 0.00 0.00 42.98 2.52
533 540 1.707106 TCGTTGGGTAGGACACAAGA 58.293 50.000 0.00 0.00 42.98 3.02
534 541 2.536761 TTCGTTGGGTAGGACACAAG 57.463 50.000 0.00 0.00 42.98 3.16
535 542 3.278668 TTTTCGTTGGGTAGGACACAA 57.721 42.857 0.00 0.00 39.55 3.33
536 543 3.278668 TTTTTCGTTGGGTAGGACACA 57.721 42.857 0.00 0.00 0.00 3.72
991 1466 2.264794 GGTTGACATCGCCCGTCT 59.735 61.111 0.00 0.00 34.37 4.18
2721 6390 5.525484 TCCTCTAGTTTGCATTAGGTAGGA 58.475 41.667 0.00 0.00 0.00 2.94
2722 6391 5.871396 TCCTCTAGTTTGCATTAGGTAGG 57.129 43.478 0.00 0.00 0.00 3.18
2730 6399 8.624776 GCTTGTTAATATTCCTCTAGTTTGCAT 58.375 33.333 0.00 0.00 0.00 3.96
2731 6400 7.609918 TGCTTGTTAATATTCCTCTAGTTTGCA 59.390 33.333 0.00 0.00 0.00 4.08
2732 6401 7.985476 TGCTTGTTAATATTCCTCTAGTTTGC 58.015 34.615 0.00 0.00 0.00 3.68
2736 6405 8.624776 GCAAATGCTTGTTAATATTCCTCTAGT 58.375 33.333 0.00 0.00 38.21 2.57
2737 6406 7.800380 CGCAAATGCTTGTTAATATTCCTCTAG 59.200 37.037 3.63 0.00 39.32 2.43
2738 6407 7.497579 TCGCAAATGCTTGTTAATATTCCTCTA 59.502 33.333 3.63 0.00 39.32 2.43
2739 6408 6.318648 TCGCAAATGCTTGTTAATATTCCTCT 59.681 34.615 3.63 0.00 39.32 3.69
2740 6409 6.494842 TCGCAAATGCTTGTTAATATTCCTC 58.505 36.000 3.63 0.00 39.32 3.71
2741 6410 6.095440 ACTCGCAAATGCTTGTTAATATTCCT 59.905 34.615 3.63 0.00 39.32 3.36
2742 6411 6.265577 ACTCGCAAATGCTTGTTAATATTCC 58.734 36.000 3.63 0.00 39.32 3.01
2743 6412 8.835467 TTACTCGCAAATGCTTGTTAATATTC 57.165 30.769 3.63 0.00 39.32 1.75
2744 6413 9.450807 GATTACTCGCAAATGCTTGTTAATATT 57.549 29.630 3.63 0.00 39.32 1.28
2745 6414 8.620416 TGATTACTCGCAAATGCTTGTTAATAT 58.380 29.630 3.63 0.00 39.32 1.28
2746 6415 7.980062 TGATTACTCGCAAATGCTTGTTAATA 58.020 30.769 3.63 0.00 39.32 0.98
2778 6447 4.014406 TGCTGGATACTCTGTTTCGTCTA 58.986 43.478 0.00 0.00 37.61 2.59
2805 6474 9.521503 GGAACAATAAATAAATGGCTCTTCTTC 57.478 33.333 0.00 0.00 0.00 2.87
2841 6510 2.159421 CGTCGTGCTCATACTACCTTGT 60.159 50.000 0.00 0.00 0.00 3.16
2842 6511 2.096980 TCGTCGTGCTCATACTACCTTG 59.903 50.000 0.00 0.00 0.00 3.61
2843 6512 2.362736 TCGTCGTGCTCATACTACCTT 58.637 47.619 0.00 0.00 0.00 3.50
2844 6513 2.034104 TCGTCGTGCTCATACTACCT 57.966 50.000 0.00 0.00 0.00 3.08
2921 6604 9.836076 GCCGTTAATTCAAGTTTTATTTCTAGT 57.164 29.630 0.00 0.00 0.00 2.57
2922 6605 8.995906 CGCCGTTAATTCAAGTTTTATTTCTAG 58.004 33.333 0.00 0.00 0.00 2.43
2923 6606 8.719648 TCGCCGTTAATTCAAGTTTTATTTCTA 58.280 29.630 0.00 0.00 0.00 2.10
2924 6607 7.586747 TCGCCGTTAATTCAAGTTTTATTTCT 58.413 30.769 0.00 0.00 0.00 2.52
2925 6608 7.784790 TCGCCGTTAATTCAAGTTTTATTTC 57.215 32.000 0.00 0.00 0.00 2.17
2926 6609 7.149096 CGTTCGCCGTTAATTCAAGTTTTATTT 60.149 33.333 0.00 0.00 0.00 1.40
2927 6610 6.303733 CGTTCGCCGTTAATTCAAGTTTTATT 59.696 34.615 0.00 0.00 0.00 1.40
2928 6611 5.791480 CGTTCGCCGTTAATTCAAGTTTTAT 59.209 36.000 0.00 0.00 0.00 1.40
2929 6612 5.138788 CGTTCGCCGTTAATTCAAGTTTTA 58.861 37.500 0.00 0.00 0.00 1.52
2930 6613 3.969981 CGTTCGCCGTTAATTCAAGTTTT 59.030 39.130 0.00 0.00 0.00 2.43
2931 6614 3.547601 CGTTCGCCGTTAATTCAAGTTT 58.452 40.909 0.00 0.00 0.00 2.66
2932 6615 2.096119 CCGTTCGCCGTTAATTCAAGTT 60.096 45.455 0.00 0.00 33.66 2.66
2933 6616 1.461897 CCGTTCGCCGTTAATTCAAGT 59.538 47.619 0.00 0.00 33.66 3.16
2934 6617 1.727880 TCCGTTCGCCGTTAATTCAAG 59.272 47.619 0.00 0.00 33.66 3.02
2935 6618 1.793258 TCCGTTCGCCGTTAATTCAA 58.207 45.000 0.00 0.00 33.66 2.69
2936 6619 1.793258 TTCCGTTCGCCGTTAATTCA 58.207 45.000 0.00 0.00 33.66 2.57
2937 6620 2.349275 TGATTCCGTTCGCCGTTAATTC 59.651 45.455 0.00 0.00 33.66 2.17
2938 6621 2.348660 TGATTCCGTTCGCCGTTAATT 58.651 42.857 0.00 0.00 33.66 1.40
2939 6622 1.931172 CTGATTCCGTTCGCCGTTAAT 59.069 47.619 0.00 0.00 33.66 1.40
2940 6623 1.067706 TCTGATTCCGTTCGCCGTTAA 60.068 47.619 0.00 0.00 33.66 2.01
2941 6624 0.527113 TCTGATTCCGTTCGCCGTTA 59.473 50.000 0.00 0.00 33.66 3.18
2942 6625 0.108329 ATCTGATTCCGTTCGCCGTT 60.108 50.000 0.00 0.00 33.66 4.44
2943 6626 0.806102 CATCTGATTCCGTTCGCCGT 60.806 55.000 0.00 0.00 33.66 5.68
2944 6627 1.927210 CATCTGATTCCGTTCGCCG 59.073 57.895 0.00 0.00 0.00 6.46
2945 6628 1.089481 TGCATCTGATTCCGTTCGCC 61.089 55.000 0.00 0.00 0.00 5.54
2946 6629 0.026803 GTGCATCTGATTCCGTTCGC 59.973 55.000 0.00 0.00 0.00 4.70
2947 6630 1.590238 GAGTGCATCTGATTCCGTTCG 59.410 52.381 0.00 0.00 0.00 3.95
2948 6631 1.590238 CGAGTGCATCTGATTCCGTTC 59.410 52.381 0.00 0.00 0.00 3.95
2949 6632 1.645034 CGAGTGCATCTGATTCCGTT 58.355 50.000 0.00 0.00 0.00 4.44
2950 6633 0.807667 GCGAGTGCATCTGATTCCGT 60.808 55.000 0.00 0.00 42.15 4.69
2951 6634 1.930100 GCGAGTGCATCTGATTCCG 59.070 57.895 0.00 0.00 42.15 4.30
2962 6645 9.931210 AATAAACTAAGTAAATAATGCGAGTGC 57.069 29.630 0.00 0.00 43.20 4.40
3033 6716 4.891727 CCGCCAATCGTCTCCCGG 62.892 72.222 0.00 0.00 37.11 5.73
3055 6738 2.507102 CGTCTGGTGCTACGCTGG 60.507 66.667 0.00 0.00 31.66 4.85
3074 6757 5.220340 CCAAATATCGAATATAACCGCGTCC 60.220 44.000 4.92 0.00 0.00 4.79
3083 6766 4.081365 TGGAGCCGCCAAATATCGAATATA 60.081 41.667 0.00 0.00 45.87 0.86
3106 6789 0.694444 ATATGGGCCGAGGGTGAACT 60.694 55.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.