Multiple sequence alignment - TraesCS1B01G039700

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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 TraesCS1B01G039700 chr1B 100.000 3827 0 0 1 3827 19076664 19072838 0.000000e+00 7068.0
1 TraesCS1B01G039700 chr1B 89.651 2754 256 17 762 3491 18118342 18115594 0.000000e+00 3480.0
2 TraesCS1B01G039700 chr1B 89.486 2083 201 16 763 2836 18868005 18870078 0.000000e+00 2617.0
3 TraesCS1B01G039700 chr1B 88.837 2141 216 14 828 2961 539872559 539870435 0.000000e+00 2608.0
4 TraesCS1B01G039700 chr1B 87.140 2224 255 25 756 2964 17896263 17894056 0.000000e+00 2494.0
5 TraesCS1B01G039700 chr1B 87.729 2127 230 24 893 3006 18093358 18091250 0.000000e+00 2453.0
6 TraesCS1B01G039700 chr1B 90.528 1763 113 23 1767 3491 17965661 17963915 0.000000e+00 2281.0
7 TraesCS1B01G039700 chr1B 87.319 276 28 5 3555 3827 18115374 18115103 3.710000e-80 309.0
8 TraesCS1B01G039700 chr1B 85.811 296 30 8 3534 3827 17963697 17963412 1.730000e-78 303.0
9 TraesCS1B01G039700 chr1B 80.758 343 39 14 3489 3827 18112969 18112650 3.820000e-60 243.0
10 TraesCS1B01G039700 chr1B 91.111 180 10 1 585 758 17966282 17966103 4.940000e-59 239.0
11 TraesCS1B01G039700 chr1B 76.555 418 50 19 3032 3415 18113466 18113063 6.530000e-43 185.0
12 TraesCS1B01G039700 chr1B 85.143 175 22 4 3654 3827 18870730 18870901 3.930000e-40 176.0
13 TraesCS1B01G039700 chr1B 80.500 200 35 3 820 1017 133119222 133119419 2.380000e-32 150.0
14 TraesCS1B01G039700 chr1B 78.981 157 19 10 3298 3454 18686214 18686356 1.130000e-15 95.3
15 TraesCS1B01G039700 chr1B 78.808 151 18 10 3304 3454 18090939 18090803 5.270000e-14 89.8
16 TraesCS1B01G039700 chr1B 78.808 151 18 10 3304 3454 18362886 18362750 5.270000e-14 89.8
17 TraesCS1B01G039700 chr1B 97.959 49 1 0 3443 3491 18113058 18113010 6.810000e-13 86.1
18 TraesCS1B01G039700 chr1D 88.922 2699 249 22 758 3416 13262739 13265427 0.000000e+00 3282.0
19 TraesCS1B01G039700 chr1D 86.125 2746 309 37 761 3450 12551680 12548951 0.000000e+00 2894.0
20 TraesCS1B01G039700 chr1A 90.762 2100 185 7 758 2854 14577870 14579963 0.000000e+00 2795.0
21 TraesCS1B01G039700 chr1A 90.583 2092 190 6 758 2846 14585209 14587296 0.000000e+00 2765.0
22 TraesCS1B01G039700 chr2B 88.554 2193 228 19 761 2941 95097167 95094986 0.000000e+00 2638.0
23 TraesCS1B01G039700 chr2B 78.808 151 18 10 3304 3454 95094583 95094447 5.270000e-14 89.8
24 TraesCS1B01G039700 chr3D 76.471 357 59 19 1 346 4008736 4009078 1.830000e-38 171.0
25 TraesCS1B01G039700 chr3D 75.862 261 40 15 95 346 423860867 423861113 1.120000e-20 111.0
26 TraesCS1B01G039700 chr3A 75.429 350 58 15 1 346 595757987 595758312 1.110000e-30 145.0
27 TraesCS1B01G039700 chr3A 72.822 287 52 23 73 339 597823757 597823477 1.470000e-09 75.0
28 TraesCS1B01G039700 chr5D 80.124 161 23 6 128 280 43396956 43397115 1.120000e-20 111.0
29 TraesCS1B01G039700 chr5D 84.507 71 7 4 133 202 528123907 528123974 2.470000e-07 67.6
30 TraesCS1B01G039700 chr6A 81.119 143 21 5 206 346 536577817 536577955 4.040000e-20 110.0
31 TraesCS1B01G039700 chr5B 73.481 362 62 24 1 344 331315142 331314797 5.230000e-19 106.0
32 TraesCS1B01G039700 chr5B 76.712 146 24 8 40 178 540259270 540259128 5.300000e-09 73.1
33 TraesCS1B01G039700 chr4D 78.676 136 23 6 217 351 70996889 70996759 6.810000e-13 86.1
34 TraesCS1B01G039700 chr3B 84.722 72 7 4 137 206 616896953 616896884 6.860000e-08 69.4
35 TraesCS1B01G039700 chr7D 85.294 68 5 4 131 195 88145113 88145048 8.870000e-07 65.8
36 TraesCS1B01G039700 chr7D 75.796 157 20 15 40 187 307666944 307666797 3.190000e-06 63.9
37 TraesCS1B01G039700 chr4A 85.075 67 7 3 137 202 693210430 693210366 8.870000e-07 65.8
38 TraesCS1B01G039700 chr2D 84.058 69 7 4 137 203 622338923 622338989 3.190000e-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 TraesCS1B01G039700 chr1B 19072838 19076664 3826 True 7068.00 7068 100.0000 1 3827 1 chr1B.!!$R3 3826
1 TraesCS1B01G039700 chr1B 539870435 539872559 2124 True 2608.00 2608 88.8370 828 2961 1 chr1B.!!$R4 2133
2 TraesCS1B01G039700 chr1B 17894056 17896263 2207 True 2494.00 2494 87.1400 756 2964 1 chr1B.!!$R1 2208
3 TraesCS1B01G039700 chr1B 18868005 18870901 2896 False 1396.50 2617 87.3145 763 3827 2 chr1B.!!$F3 3064
4 TraesCS1B01G039700 chr1B 18090803 18093358 2555 True 1271.40 2453 83.2685 893 3454 2 chr1B.!!$R6 2561
5 TraesCS1B01G039700 chr1B 17963412 17966282 2870 True 941.00 2281 89.1500 585 3827 3 chr1B.!!$R5 3242
6 TraesCS1B01G039700 chr1B 18112650 18118342 5692 True 860.62 3480 86.4484 762 3827 5 chr1B.!!$R7 3065
7 TraesCS1B01G039700 chr1D 13262739 13265427 2688 False 3282.00 3282 88.9220 758 3416 1 chr1D.!!$F1 2658
8 TraesCS1B01G039700 chr1D 12548951 12551680 2729 True 2894.00 2894 86.1250 761 3450 1 chr1D.!!$R1 2689
9 TraesCS1B01G039700 chr1A 14577870 14579963 2093 False 2795.00 2795 90.7620 758 2854 1 chr1A.!!$F1 2096
10 TraesCS1B01G039700 chr1A 14585209 14587296 2087 False 2765.00 2765 90.5830 758 2846 1 chr1A.!!$F2 2088
11 TraesCS1B01G039700 chr2B 95094447 95097167 2720 True 1363.90 2638 83.6810 761 3454 2 chr2B.!!$R1 2693

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
613 614 0.251653 TCCAGAGTTCACGGCCTACT 60.252 55.000 0.00 0.0 0.00 2.57 F
642 643 0.769873 CCATGCCTGGCTTCTCCTAT 59.230 55.000 21.03 0.0 35.23 2.57 F
826 998 1.599518 CCAACGGCTTGCACCTACA 60.600 57.895 0.00 0.0 0.00 2.74 F
1923 2095 1.353022 TGCACGGAAGGAAGGGTAATT 59.647 47.619 0.00 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1810 0.102120 CATCTGGACTCACTCCTCGC 59.898 60.000 0.00 0.0 40.26 5.03 R
1923 2095 0.673985 CGAGGATATCCCGTGCTTCA 59.326 55.000 18.56 0.0 40.87 3.02 R
1951 2123 1.696336 AGGCCTCATACCTATGTGCAG 59.304 52.381 0.00 0.0 35.10 4.41 R
3108 3374 1.228552 GGTGGGAGAAGCAAAGGCA 60.229 57.895 0.00 0.0 44.61 4.75 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 9.665719 TGAATGACTAAGCTATTTTGTATGTCA 57.334 29.630 0.00 0.00 36.55 3.58
36 37 9.922305 GAATGACTAAGCTATTTTGTATGTCAC 57.078 33.333 0.00 0.00 35.26 3.67
37 38 7.520119 TGACTAAGCTATTTTGTATGTCACG 57.480 36.000 0.00 0.00 0.00 4.35
38 39 6.533723 TGACTAAGCTATTTTGTATGTCACGG 59.466 38.462 0.00 0.00 0.00 4.94
39 40 6.636705 ACTAAGCTATTTTGTATGTCACGGA 58.363 36.000 0.00 0.00 0.00 4.69
40 41 5.796350 AAGCTATTTTGTATGTCACGGAC 57.204 39.130 0.00 0.00 0.00 4.79
41 42 4.827692 AGCTATTTTGTATGTCACGGACA 58.172 39.130 8.81 8.81 46.90 4.02
42 43 4.870426 AGCTATTTTGTATGTCACGGACAG 59.130 41.667 11.50 0.00 46.04 3.51
43 44 4.630069 GCTATTTTGTATGTCACGGACAGT 59.370 41.667 11.50 4.46 46.04 3.55
44 45 5.121768 GCTATTTTGTATGTCACGGACAGTT 59.878 40.000 11.50 0.69 46.04 3.16
45 46 6.348213 GCTATTTTGTATGTCACGGACAGTTT 60.348 38.462 11.50 0.10 46.04 2.66
46 47 5.821516 TTTTGTATGTCACGGACAGTTTT 57.178 34.783 11.50 0.00 46.04 2.43
47 48 5.821516 TTTGTATGTCACGGACAGTTTTT 57.178 34.783 11.50 0.00 46.04 1.94
93 94 9.153721 TCAATTCATGAACATTTTTGAATAGGC 57.846 29.630 11.07 0.00 37.72 3.93
94 95 8.937884 CAATTCATGAACATTTTTGAATAGGCA 58.062 29.630 11.07 0.00 37.72 4.75
95 96 9.504708 AATTCATGAACATTTTTGAATAGGCAA 57.495 25.926 11.07 0.00 37.72 4.52
96 97 8.899427 TTCATGAACATTTTTGAATAGGCAAA 57.101 26.923 3.38 0.00 36.08 3.68
97 98 8.899427 TCATGAACATTTTTGAATAGGCAAAA 57.101 26.923 0.00 0.00 43.69 2.44
98 99 9.504708 TCATGAACATTTTTGAATAGGCAAAAT 57.495 25.926 0.00 0.00 44.45 1.82
210 211 8.604640 AAATTGTGAATATTGTTGCATGAACA 57.395 26.923 0.00 1.54 43.11 3.18
225 226 9.674208 GTTGCATGAACAATTTTAAATATCACG 57.326 29.630 0.00 0.00 34.35 4.35
226 227 9.631452 TTGCATGAACAATTTTAAATATCACGA 57.369 25.926 0.00 0.00 0.00 4.35
227 228 9.631452 TGCATGAACAATTTTAAATATCACGAA 57.369 25.926 0.00 0.00 0.00 3.85
228 229 9.885743 GCATGAACAATTTTAAATATCACGAAC 57.114 29.630 0.00 0.00 0.00 3.95
247 248 5.822584 GAACATTTTCGGAATCCACAAAC 57.177 39.130 0.00 0.00 0.00 2.93
248 249 4.927978 ACATTTTCGGAATCCACAAACA 57.072 36.364 0.00 0.00 0.00 2.83
249 250 5.467035 ACATTTTCGGAATCCACAAACAT 57.533 34.783 0.00 0.00 0.00 2.71
250 251 5.852827 ACATTTTCGGAATCCACAAACATT 58.147 33.333 0.00 0.00 0.00 2.71
251 252 6.287525 ACATTTTCGGAATCCACAAACATTT 58.712 32.000 0.00 0.00 0.00 2.32
252 253 7.437748 ACATTTTCGGAATCCACAAACATTTA 58.562 30.769 0.00 0.00 0.00 1.40
253 254 8.093927 ACATTTTCGGAATCCACAAACATTTAT 58.906 29.630 0.00 0.00 0.00 1.40
254 255 8.594687 CATTTTCGGAATCCACAAACATTTATC 58.405 33.333 0.00 0.00 0.00 1.75
255 256 6.825944 TTCGGAATCCACAAACATTTATCA 57.174 33.333 0.00 0.00 0.00 2.15
256 257 6.825944 TCGGAATCCACAAACATTTATCAA 57.174 33.333 0.00 0.00 0.00 2.57
257 258 7.403312 TCGGAATCCACAAACATTTATCAAT 57.597 32.000 0.00 0.00 0.00 2.57
258 259 7.835822 TCGGAATCCACAAACATTTATCAATT 58.164 30.769 0.00 0.00 0.00 2.32
259 260 8.310382 TCGGAATCCACAAACATTTATCAATTT 58.690 29.630 0.00 0.00 0.00 1.82
260 261 8.934825 CGGAATCCACAAACATTTATCAATTTT 58.065 29.630 0.00 0.00 0.00 1.82
360 361 8.934973 AAAAACGAAGACGAAATTAGAATCAG 57.065 30.769 0.00 0.00 42.66 2.90
361 362 5.704217 ACGAAGACGAAATTAGAATCAGC 57.296 39.130 0.00 0.00 42.66 4.26
362 363 5.168569 ACGAAGACGAAATTAGAATCAGCA 58.831 37.500 0.00 0.00 42.66 4.41
363 364 5.637810 ACGAAGACGAAATTAGAATCAGCAA 59.362 36.000 0.00 0.00 42.66 3.91
364 365 6.147164 ACGAAGACGAAATTAGAATCAGCAAA 59.853 34.615 0.00 0.00 42.66 3.68
365 366 7.148407 ACGAAGACGAAATTAGAATCAGCAAAT 60.148 33.333 0.00 0.00 42.66 2.32
366 367 8.328146 CGAAGACGAAATTAGAATCAGCAAATA 58.672 33.333 0.00 0.00 42.66 1.40
411 412 8.993424 AGAACCAATAACCACTTGATATAGTCT 58.007 33.333 0.00 0.00 0.00 3.24
412 413 9.614792 GAACCAATAACCACTTGATATAGTCTT 57.385 33.333 0.00 0.00 0.00 3.01
413 414 9.614792 AACCAATAACCACTTGATATAGTCTTC 57.385 33.333 0.00 0.00 0.00 2.87
414 415 8.768397 ACCAATAACCACTTGATATAGTCTTCA 58.232 33.333 0.00 0.00 0.00 3.02
415 416 9.046296 CCAATAACCACTTGATATAGTCTTCAC 57.954 37.037 0.00 0.00 0.00 3.18
416 417 9.046296 CAATAACCACTTGATATAGTCTTCACC 57.954 37.037 0.00 0.00 0.00 4.02
417 418 6.875972 AACCACTTGATATAGTCTTCACCT 57.124 37.500 0.00 0.00 0.00 4.00
418 419 7.973048 AACCACTTGATATAGTCTTCACCTA 57.027 36.000 0.00 0.00 0.00 3.08
419 420 7.589958 ACCACTTGATATAGTCTTCACCTAG 57.410 40.000 0.00 0.00 0.00 3.02
420 421 7.126733 ACCACTTGATATAGTCTTCACCTAGT 58.873 38.462 0.00 0.00 0.00 2.57
421 422 8.280084 ACCACTTGATATAGTCTTCACCTAGTA 58.720 37.037 0.00 0.00 0.00 1.82
422 423 8.569641 CCACTTGATATAGTCTTCACCTAGTAC 58.430 40.741 0.00 0.00 0.00 2.73
423 424 9.121658 CACTTGATATAGTCTTCACCTAGTACA 57.878 37.037 0.00 0.00 0.00 2.90
424 425 9.869667 ACTTGATATAGTCTTCACCTAGTACAT 57.130 33.333 0.00 0.00 0.00 2.29
431 432 6.583562 AGTCTTCACCTAGTACATTTATGGC 58.416 40.000 0.00 0.00 0.00 4.40
432 433 6.384305 AGTCTTCACCTAGTACATTTATGGCT 59.616 38.462 0.00 0.00 0.00 4.75
433 434 7.048512 GTCTTCACCTAGTACATTTATGGCTT 58.951 38.462 0.00 0.00 0.00 4.35
434 435 7.224949 GTCTTCACCTAGTACATTTATGGCTTC 59.775 40.741 0.00 0.00 0.00 3.86
435 436 5.925509 TCACCTAGTACATTTATGGCTTCC 58.074 41.667 0.00 0.00 0.00 3.46
436 437 5.063880 CACCTAGTACATTTATGGCTTCCC 58.936 45.833 0.00 0.00 0.00 3.97
437 438 4.202326 ACCTAGTACATTTATGGCTTCCCG 60.202 45.833 0.00 0.00 0.00 5.14
438 439 3.208747 AGTACATTTATGGCTTCCCGG 57.791 47.619 0.00 0.00 0.00 5.73
439 440 2.508300 AGTACATTTATGGCTTCCCGGT 59.492 45.455 0.00 0.00 0.00 5.28
440 441 3.712733 AGTACATTTATGGCTTCCCGGTA 59.287 43.478 0.00 0.00 0.00 4.02
441 442 2.927028 ACATTTATGGCTTCCCGGTAC 58.073 47.619 0.00 0.00 0.00 3.34
442 443 2.508300 ACATTTATGGCTTCCCGGTACT 59.492 45.455 0.00 0.00 0.00 2.73
443 444 3.712733 ACATTTATGGCTTCCCGGTACTA 59.287 43.478 0.00 0.00 0.00 1.82
444 445 3.825143 TTTATGGCTTCCCGGTACTAC 57.175 47.619 0.00 0.00 0.00 2.73
445 446 2.457813 TATGGCTTCCCGGTACTACA 57.542 50.000 0.00 0.00 0.00 2.74
446 447 1.802553 ATGGCTTCCCGGTACTACAT 58.197 50.000 0.00 0.00 0.00 2.29
447 448 1.575419 TGGCTTCCCGGTACTACATT 58.425 50.000 0.00 0.00 0.00 2.71
448 449 1.910671 TGGCTTCCCGGTACTACATTT 59.089 47.619 0.00 0.00 0.00 2.32
449 450 2.093341 TGGCTTCCCGGTACTACATTTC 60.093 50.000 0.00 0.00 0.00 2.17
450 451 2.169978 GGCTTCCCGGTACTACATTTCT 59.830 50.000 0.00 0.00 0.00 2.52
451 452 3.370209 GGCTTCCCGGTACTACATTTCTT 60.370 47.826 0.00 0.00 0.00 2.52
452 453 3.621715 GCTTCCCGGTACTACATTTCTTG 59.378 47.826 0.00 0.00 0.00 3.02
453 454 3.899052 TCCCGGTACTACATTTCTTGG 57.101 47.619 0.00 0.00 0.00 3.61
454 455 2.502538 TCCCGGTACTACATTTCTTGGG 59.497 50.000 0.00 0.00 35.40 4.12
455 456 2.285977 CCGGTACTACATTTCTTGGGC 58.714 52.381 0.00 0.00 0.00 5.36
456 457 2.093128 CCGGTACTACATTTCTTGGGCT 60.093 50.000 0.00 0.00 0.00 5.19
457 458 3.606687 CGGTACTACATTTCTTGGGCTT 58.393 45.455 0.00 0.00 0.00 4.35
458 459 3.374058 CGGTACTACATTTCTTGGGCTTG 59.626 47.826 0.00 0.00 0.00 4.01
459 460 3.128764 GGTACTACATTTCTTGGGCTTGC 59.871 47.826 0.00 0.00 0.00 4.01
460 461 3.160679 ACTACATTTCTTGGGCTTGCT 57.839 42.857 0.00 0.00 0.00 3.91
461 462 4.301072 ACTACATTTCTTGGGCTTGCTA 57.699 40.909 0.00 0.00 0.00 3.49
462 463 4.265073 ACTACATTTCTTGGGCTTGCTAG 58.735 43.478 0.00 0.00 0.00 3.42
463 464 3.160679 ACATTTCTTGGGCTTGCTAGT 57.839 42.857 0.00 0.00 0.00 2.57
464 465 4.301072 ACATTTCTTGGGCTTGCTAGTA 57.699 40.909 0.00 0.00 0.00 1.82
465 466 4.662278 ACATTTCTTGGGCTTGCTAGTAA 58.338 39.130 0.00 0.00 0.00 2.24
466 467 5.076873 ACATTTCTTGGGCTTGCTAGTAAA 58.923 37.500 0.00 0.00 0.00 2.01
467 468 5.716703 ACATTTCTTGGGCTTGCTAGTAAAT 59.283 36.000 0.00 0.00 0.00 1.40
468 469 6.211384 ACATTTCTTGGGCTTGCTAGTAAATT 59.789 34.615 0.00 0.00 0.00 1.82
469 470 6.664428 TTTCTTGGGCTTGCTAGTAAATTT 57.336 33.333 0.00 0.00 0.00 1.82
470 471 7.768807 TTTCTTGGGCTTGCTAGTAAATTTA 57.231 32.000 0.00 0.00 0.00 1.40
471 472 7.954666 TTCTTGGGCTTGCTAGTAAATTTAT 57.045 32.000 0.31 0.00 0.00 1.40
472 473 7.954666 TCTTGGGCTTGCTAGTAAATTTATT 57.045 32.000 0.31 0.00 0.00 1.40
473 474 8.361169 TCTTGGGCTTGCTAGTAAATTTATTT 57.639 30.769 0.31 0.00 0.00 1.40
474 475 8.811994 TCTTGGGCTTGCTAGTAAATTTATTTT 58.188 29.630 0.31 0.00 0.00 1.82
475 476 8.996024 TTGGGCTTGCTAGTAAATTTATTTTC 57.004 30.769 0.31 0.00 0.00 2.29
476 477 8.361169 TGGGCTTGCTAGTAAATTTATTTTCT 57.639 30.769 0.31 0.00 33.07 2.52
477 478 8.811994 TGGGCTTGCTAGTAAATTTATTTTCTT 58.188 29.630 0.31 0.00 31.31 2.52
478 479 9.087424 GGGCTTGCTAGTAAATTTATTTTCTTG 57.913 33.333 0.31 0.00 31.31 3.02
479 480 9.087424 GGCTTGCTAGTAAATTTATTTTCTTGG 57.913 33.333 0.31 0.00 31.31 3.61
480 481 9.639601 GCTTGCTAGTAAATTTATTTTCTTGGT 57.360 29.630 0.31 0.00 31.31 3.67
560 561 8.904834 AGTAGTATGTGATATGAATATCCGGAC 58.095 37.037 6.12 0.00 38.66 4.79
561 562 7.962995 AGTATGTGATATGAATATCCGGACT 57.037 36.000 6.12 0.00 38.66 3.85
563 564 8.904834 AGTATGTGATATGAATATCCGGACTAC 58.095 37.037 6.12 0.00 38.66 2.73
564 565 7.962995 ATGTGATATGAATATCCGGACTACT 57.037 36.000 6.12 0.00 38.66 2.57
566 567 8.507524 TGTGATATGAATATCCGGACTACTAG 57.492 38.462 6.12 0.00 38.66 2.57
567 568 8.326529 TGTGATATGAATATCCGGACTACTAGA 58.673 37.037 6.12 0.00 38.66 2.43
568 569 8.614346 GTGATATGAATATCCGGACTACTAGAC 58.386 40.741 6.12 0.00 38.66 2.59
569 570 8.549731 TGATATGAATATCCGGACTACTAGACT 58.450 37.037 6.12 0.00 38.66 3.24
571 572 9.835389 ATATGAATATCCGGACTACTAGACTAC 57.165 37.037 6.12 0.00 0.00 2.73
572 573 7.071069 TGAATATCCGGACTACTAGACTACA 57.929 40.000 6.12 0.00 0.00 2.74
573 574 6.933521 TGAATATCCGGACTACTAGACTACAC 59.066 42.308 6.12 0.00 0.00 2.90
574 575 6.684897 ATATCCGGACTACTAGACTACACT 57.315 41.667 6.12 0.00 0.00 3.55
575 576 7.789202 ATATCCGGACTACTAGACTACACTA 57.211 40.000 6.12 0.00 0.00 2.74
576 577 5.269505 TCCGGACTACTAGACTACACTAC 57.730 47.826 0.00 0.00 0.00 2.73
577 578 4.711846 TCCGGACTACTAGACTACACTACA 59.288 45.833 0.00 0.00 0.00 2.74
578 579 5.365025 TCCGGACTACTAGACTACACTACAT 59.635 44.000 0.00 0.00 0.00 2.29
579 580 5.695816 CCGGACTACTAGACTACACTACATC 59.304 48.000 0.00 0.00 0.00 3.06
580 581 5.695816 CGGACTACTAGACTACACTACATCC 59.304 48.000 0.00 0.00 0.00 3.51
581 582 5.997129 GGACTACTAGACTACACTACATCCC 59.003 48.000 0.00 0.00 0.00 3.85
582 583 5.939447 ACTACTAGACTACACTACATCCCC 58.061 45.833 0.00 0.00 0.00 4.81
583 584 4.875578 ACTAGACTACACTACATCCCCA 57.124 45.455 0.00 0.00 0.00 4.96
591 592 1.825474 CACTACATCCCCACTCGTCTT 59.175 52.381 0.00 0.00 0.00 3.01
603 604 1.271102 ACTCGTCTTGCTCCAGAGTTC 59.729 52.381 0.00 0.00 38.86 3.01
607 608 0.318441 TCTTGCTCCAGAGTTCACGG 59.682 55.000 0.00 0.00 0.00 4.94
613 614 0.251653 TCCAGAGTTCACGGCCTACT 60.252 55.000 0.00 0.00 0.00 2.57
641 642 1.348008 CCCATGCCTGGCTTCTCCTA 61.348 60.000 21.03 0.00 41.64 2.94
642 643 0.769873 CCATGCCTGGCTTCTCCTAT 59.230 55.000 21.03 0.00 35.23 2.57
715 722 4.680237 CCTCGCAACCCTCACGCA 62.680 66.667 0.00 0.00 0.00 5.24
791 963 2.839098 CATATCCCAAGGCGCCCT 59.161 61.111 26.15 7.54 33.87 5.19
807 979 2.048222 CTCCGACGTGTGGCACAT 60.048 61.111 24.95 8.79 44.52 3.21
826 998 1.599518 CCAACGGCTTGCACCTACA 60.600 57.895 0.00 0.00 0.00 2.74
888 1060 2.048127 GCACTCGCCTTCTTCGGT 60.048 61.111 0.00 0.00 0.00 4.69
993 1165 3.117171 GCTCTGGACGTGCTGCTG 61.117 66.667 8.99 5.62 0.00 4.41
1021 1193 4.383861 CTGAGCTCGGCTGCACCA 62.384 66.667 10.21 0.00 39.88 4.17
1312 1484 2.617274 GCGGTCAGGGTGCTGAAAC 61.617 63.158 0.00 0.00 34.88 2.78
1408 1580 2.292845 AGAAGCAAAGAAGCTGCAGAAC 59.707 45.455 20.43 7.52 45.89 3.01
1640 1812 8.261908 GCTTATATTTAAAGAAATGCACAAGCG 58.738 33.333 0.00 0.00 46.23 4.68
1923 2095 1.353022 TGCACGGAAGGAAGGGTAATT 59.647 47.619 0.00 0.00 0.00 1.40
1951 2123 2.672478 CGGGATATCCTCGACTTGATGC 60.672 54.545 21.18 0.00 35.95 3.91
1995 2167 9.627123 CCTGATGTTCCCATCTTTAATTTACTA 57.373 33.333 4.51 0.00 46.38 1.82
2020 2192 1.286260 GGATACTGCCTAGTCCGCG 59.714 63.158 0.00 0.00 38.36 6.46
2249 2421 0.381801 CGAACTGTTGCTGCAAAGGT 59.618 50.000 17.80 14.70 0.00 3.50
2867 3059 6.695278 TGAAATTTAACTTCTTTCACTTGCCG 59.305 34.615 0.00 0.00 34.80 5.69
2883 3086 1.904771 CCGTGGGTCCATCTGCTTA 59.095 57.895 0.00 0.00 0.00 3.09
2934 3137 8.622948 AAATAGGAAGTCAGTTTAGAACAAGG 57.377 34.615 0.00 0.00 0.00 3.61
3011 3271 3.897505 ACTAGGCCTGCAAAAACTCAAAT 59.102 39.130 17.99 0.00 0.00 2.32
3025 3285 3.871485 ACTCAAATAGAAGGAGCAGCAG 58.129 45.455 0.00 0.00 31.88 4.24
3108 3374 0.531200 GTAGTGGCTGGCGTCTAAGT 59.469 55.000 7.31 0.00 0.00 2.24
3121 3387 2.413453 CGTCTAAGTGCCTTTGCTTCTC 59.587 50.000 0.00 0.00 38.71 2.87
3237 3506 4.825422 CCAGATACGCATGGTCAGATTAT 58.175 43.478 0.00 0.00 0.00 1.28
3307 3625 1.303155 GCTTGTCCCTGCTGAAGCT 60.303 57.895 3.61 0.00 42.66 3.74
3352 3670 4.087907 ACAGGGTACTAGAGAGGTGTTTC 58.912 47.826 0.00 0.00 0.00 2.78
3441 3759 4.552355 CAGCATGCAAAAGTCTGAATCAA 58.448 39.130 21.98 0.00 0.00 2.57
3446 3764 7.705325 AGCATGCAAAAGTCTGAATCAAATATC 59.295 33.333 21.98 0.00 0.00 1.63
3506 3863 6.985059 AGACCTTCTGTAACTGTTAGTGTTTC 59.015 38.462 0.00 0.00 0.00 2.78
3518 3875 5.968254 TGTTAGTGTTTCGTATATGCTGGA 58.032 37.500 0.00 0.00 0.00 3.86
3519 3876 6.040247 TGTTAGTGTTTCGTATATGCTGGAG 58.960 40.000 0.00 0.00 0.00 3.86
3523 3880 4.034048 GTGTTTCGTATATGCTGGAGTTGG 59.966 45.833 0.00 0.00 0.00 3.77
3528 3885 6.904463 TCGTATATGCTGGAGTTGGTTATA 57.096 37.500 0.00 0.00 0.00 0.98
3529 3886 6.684686 TCGTATATGCTGGAGTTGGTTATAC 58.315 40.000 0.00 0.00 0.00 1.47
3530 3887 6.265876 TCGTATATGCTGGAGTTGGTTATACA 59.734 38.462 0.00 0.00 0.00 2.29
3531 3888 7.039293 TCGTATATGCTGGAGTTGGTTATACAT 60.039 37.037 0.00 0.00 0.00 2.29
3546 4062 6.159046 TGGTTATACATGTTAGTTTAGGGCCT 59.841 38.462 12.58 12.58 0.00 5.19
3547 4063 7.058525 GGTTATACATGTTAGTTTAGGGCCTT 58.941 38.462 13.45 0.00 0.00 4.35
3549 4065 4.382386 ACATGTTAGTTTAGGGCCTTGT 57.618 40.909 13.45 3.11 0.00 3.16
3555 4071 3.322191 AGTTTAGGGCCTTGTTCCAAA 57.678 42.857 13.45 1.23 0.00 3.28
3558 4074 5.399113 AGTTTAGGGCCTTGTTCCAAATTA 58.601 37.500 13.45 0.00 0.00 1.40
3565 4083 6.271159 AGGGCCTTGTTCCAAATTATTTGTTA 59.729 34.615 15.40 2.07 38.98 2.41
3581 4099 2.903798 TGTTATGATCGATGCAGCACA 58.096 42.857 0.54 5.41 0.00 4.57
3588 4106 1.237533 TCGATGCAGCACAATGTTGT 58.762 45.000 1.53 0.00 43.36 3.32
3712 4265 6.620877 TGTTCAGAGGTAATATGGTTCTGT 57.379 37.500 0.00 0.00 37.23 3.41
3732 4286 4.562082 TGTCCGTAATTTCATCGACTGTT 58.438 39.130 0.00 0.00 0.00 3.16
3746 4300 3.745975 TCGACTGTTAGCATGTTCCTTTG 59.254 43.478 0.00 0.00 0.00 2.77
3754 4308 7.946207 TGTTAGCATGTTCCTTTGTTATTCAA 58.054 30.769 0.00 0.00 0.00 2.69
3762 4316 7.816640 TGTTCCTTTGTTATTCAATACTCTGC 58.183 34.615 0.00 0.00 35.84 4.26
3818 4372 8.931385 ATAGTATGTTTGATGCATTTTGAACC 57.069 30.769 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.665719 TGACATACAAAATAGCTTAGTCATTCA 57.334 29.630 0.00 0.00 0.00 2.57
10 11 9.922305 GTGACATACAAAATAGCTTAGTCATTC 57.078 33.333 0.00 0.00 36.12 2.67
11 12 8.604035 CGTGACATACAAAATAGCTTAGTCATT 58.396 33.333 0.00 0.00 36.12 2.57
12 13 7.224753 CCGTGACATACAAAATAGCTTAGTCAT 59.775 37.037 0.00 0.00 36.12 3.06
13 14 6.533723 CCGTGACATACAAAATAGCTTAGTCA 59.466 38.462 0.00 0.00 0.00 3.41
14 15 6.755141 TCCGTGACATACAAAATAGCTTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
15 16 6.534079 GTCCGTGACATACAAAATAGCTTAGT 59.466 38.462 0.00 0.00 32.09 2.24
16 17 6.533723 TGTCCGTGACATACAAAATAGCTTAG 59.466 38.462 0.00 0.00 37.67 2.18
17 18 6.399743 TGTCCGTGACATACAAAATAGCTTA 58.600 36.000 0.00 0.00 37.67 3.09
18 19 5.242434 TGTCCGTGACATACAAAATAGCTT 58.758 37.500 0.00 0.00 37.67 3.74
19 20 4.827692 TGTCCGTGACATACAAAATAGCT 58.172 39.130 3.02 0.00 37.67 3.32
20 21 4.630069 ACTGTCCGTGACATACAAAATAGC 59.370 41.667 7.11 0.00 41.94 2.97
21 22 6.721571 AACTGTCCGTGACATACAAAATAG 57.278 37.500 7.11 0.00 41.94 1.73
22 23 7.499321 AAAACTGTCCGTGACATACAAAATA 57.501 32.000 7.11 0.00 41.94 1.40
23 24 6.385649 AAAACTGTCCGTGACATACAAAAT 57.614 33.333 7.11 0.00 41.94 1.82
24 25 5.821516 AAAACTGTCCGTGACATACAAAA 57.178 34.783 7.11 0.00 41.94 2.44
25 26 5.821516 AAAAACTGTCCGTGACATACAAA 57.178 34.783 7.11 0.00 41.94 2.83
67 68 9.153721 GCCTATTCAAAAATGTTCATGAATTGA 57.846 29.630 12.12 13.57 41.40 2.57
68 69 8.937884 TGCCTATTCAAAAATGTTCATGAATTG 58.062 29.630 12.12 11.45 41.40 2.32
69 70 9.504708 TTGCCTATTCAAAAATGTTCATGAATT 57.495 25.926 12.12 0.00 41.40 2.17
70 71 9.504708 TTTGCCTATTCAAAAATGTTCATGAAT 57.495 25.926 12.12 5.34 43.08 2.57
71 72 8.899427 TTTGCCTATTCAAAAATGTTCATGAA 57.101 26.923 3.38 3.38 36.35 2.57
72 73 8.899427 TTTTGCCTATTCAAAAATGTTCATGA 57.101 26.923 0.00 0.00 41.37 3.07
184 185 9.053840 TGTTCATGCAACAATATTCACAATTTT 57.946 25.926 7.87 0.00 42.35 1.82
185 186 8.604640 TGTTCATGCAACAATATTCACAATTT 57.395 26.923 7.87 0.00 42.35 1.82
199 200 9.674208 CGTGATATTTAAAATTGTTCATGCAAC 57.326 29.630 0.00 0.00 35.28 4.17
200 201 9.631452 TCGTGATATTTAAAATTGTTCATGCAA 57.369 25.926 0.00 0.00 0.00 4.08
201 202 9.631452 TTCGTGATATTTAAAATTGTTCATGCA 57.369 25.926 0.00 0.00 0.00 3.96
202 203 9.885743 GTTCGTGATATTTAAAATTGTTCATGC 57.114 29.630 0.00 0.00 0.00 4.06
225 226 5.285651 TGTTTGTGGATTCCGAAAATGTTC 58.714 37.500 0.00 0.00 0.00 3.18
226 227 5.269505 TGTTTGTGGATTCCGAAAATGTT 57.730 34.783 0.00 0.00 0.00 2.71
227 228 4.927978 TGTTTGTGGATTCCGAAAATGT 57.072 36.364 0.00 0.00 0.00 2.71
228 229 6.783892 AAATGTTTGTGGATTCCGAAAATG 57.216 33.333 0.00 0.00 0.00 2.32
229 230 8.310382 TGATAAATGTTTGTGGATTCCGAAAAT 58.690 29.630 0.00 0.00 0.00 1.82
230 231 7.661968 TGATAAATGTTTGTGGATTCCGAAAA 58.338 30.769 0.00 0.00 0.00 2.29
231 232 7.220741 TGATAAATGTTTGTGGATTCCGAAA 57.779 32.000 0.00 0.00 0.00 3.46
232 233 6.825944 TGATAAATGTTTGTGGATTCCGAA 57.174 33.333 0.00 0.00 0.00 4.30
233 234 6.825944 TTGATAAATGTTTGTGGATTCCGA 57.174 33.333 0.00 0.00 0.00 4.55
234 235 8.477984 AAATTGATAAATGTTTGTGGATTCCG 57.522 30.769 0.00 0.00 0.00 4.30
335 336 7.534239 GCTGATTCTAATTTCGTCTTCGTTTTT 59.466 33.333 0.00 0.00 38.33 1.94
336 337 7.015877 GCTGATTCTAATTTCGTCTTCGTTTT 58.984 34.615 0.00 0.00 38.33 2.43
337 338 6.147164 TGCTGATTCTAATTTCGTCTTCGTTT 59.853 34.615 0.00 0.00 38.33 3.60
338 339 5.637810 TGCTGATTCTAATTTCGTCTTCGTT 59.362 36.000 0.00 0.00 38.33 3.85
339 340 5.168569 TGCTGATTCTAATTTCGTCTTCGT 58.831 37.500 0.00 0.00 38.33 3.85
340 341 5.702622 TGCTGATTCTAATTTCGTCTTCG 57.297 39.130 0.00 0.00 38.55 3.79
385 386 8.993424 AGACTATATCAAGTGGTTATTGGTTCT 58.007 33.333 0.00 0.00 0.00 3.01
386 387 9.614792 AAGACTATATCAAGTGGTTATTGGTTC 57.385 33.333 0.00 0.00 0.00 3.62
387 388 9.614792 GAAGACTATATCAAGTGGTTATTGGTT 57.385 33.333 0.00 0.00 0.00 3.67
388 389 8.768397 TGAAGACTATATCAAGTGGTTATTGGT 58.232 33.333 0.00 0.00 0.00 3.67
389 390 9.046296 GTGAAGACTATATCAAGTGGTTATTGG 57.954 37.037 0.00 0.00 0.00 3.16
390 391 9.046296 GGTGAAGACTATATCAAGTGGTTATTG 57.954 37.037 0.00 0.00 0.00 1.90
391 392 8.993424 AGGTGAAGACTATATCAAGTGGTTATT 58.007 33.333 0.00 0.00 0.00 1.40
392 393 8.554490 AGGTGAAGACTATATCAAGTGGTTAT 57.446 34.615 0.00 0.00 0.00 1.89
393 394 7.973048 AGGTGAAGACTATATCAAGTGGTTA 57.027 36.000 0.00 0.00 0.00 2.85
394 395 6.875972 AGGTGAAGACTATATCAAGTGGTT 57.124 37.500 0.00 0.00 0.00 3.67
395 396 7.126733 ACTAGGTGAAGACTATATCAAGTGGT 58.873 38.462 0.00 0.00 0.00 4.16
396 397 7.589958 ACTAGGTGAAGACTATATCAAGTGG 57.410 40.000 0.00 0.00 0.00 4.00
397 398 9.121658 TGTACTAGGTGAAGACTATATCAAGTG 57.878 37.037 0.00 0.00 0.00 3.16
398 399 9.869667 ATGTACTAGGTGAAGACTATATCAAGT 57.130 33.333 0.00 0.00 0.00 3.16
405 406 8.368668 GCCATAAATGTACTAGGTGAAGACTAT 58.631 37.037 0.00 0.00 0.00 2.12
406 407 7.563924 AGCCATAAATGTACTAGGTGAAGACTA 59.436 37.037 0.00 0.00 0.00 2.59
407 408 6.384305 AGCCATAAATGTACTAGGTGAAGACT 59.616 38.462 0.00 0.00 0.00 3.24
408 409 6.583562 AGCCATAAATGTACTAGGTGAAGAC 58.416 40.000 0.00 0.00 0.00 3.01
409 410 6.808321 AGCCATAAATGTACTAGGTGAAGA 57.192 37.500 0.00 0.00 0.00 2.87
410 411 6.483640 GGAAGCCATAAATGTACTAGGTGAAG 59.516 42.308 0.00 0.00 0.00 3.02
411 412 6.354130 GGAAGCCATAAATGTACTAGGTGAA 58.646 40.000 0.00 0.00 0.00 3.18
412 413 5.163237 GGGAAGCCATAAATGTACTAGGTGA 60.163 44.000 0.00 0.00 0.00 4.02
413 414 5.063880 GGGAAGCCATAAATGTACTAGGTG 58.936 45.833 0.00 0.00 0.00 4.00
414 415 4.202326 CGGGAAGCCATAAATGTACTAGGT 60.202 45.833 0.00 0.00 0.00 3.08
415 416 4.315803 CGGGAAGCCATAAATGTACTAGG 58.684 47.826 0.00 0.00 0.00 3.02
416 417 4.202326 ACCGGGAAGCCATAAATGTACTAG 60.202 45.833 6.32 0.00 0.00 2.57
417 418 3.712733 ACCGGGAAGCCATAAATGTACTA 59.287 43.478 6.32 0.00 0.00 1.82
418 419 2.508300 ACCGGGAAGCCATAAATGTACT 59.492 45.455 6.32 0.00 0.00 2.73
419 420 2.927028 ACCGGGAAGCCATAAATGTAC 58.073 47.619 6.32 0.00 0.00 2.90
420 421 3.712733 AGTACCGGGAAGCCATAAATGTA 59.287 43.478 6.32 0.00 0.00 2.29
421 422 2.508300 AGTACCGGGAAGCCATAAATGT 59.492 45.455 6.32 0.00 0.00 2.71
422 423 3.208747 AGTACCGGGAAGCCATAAATG 57.791 47.619 6.32 0.00 0.00 2.32
423 424 3.712733 TGTAGTACCGGGAAGCCATAAAT 59.287 43.478 6.32 0.00 0.00 1.40
424 425 3.106054 TGTAGTACCGGGAAGCCATAAA 58.894 45.455 6.32 0.00 0.00 1.40
425 426 2.749600 TGTAGTACCGGGAAGCCATAA 58.250 47.619 6.32 0.00 0.00 1.90
426 427 2.457813 TGTAGTACCGGGAAGCCATA 57.542 50.000 6.32 0.00 0.00 2.74
427 428 1.802553 ATGTAGTACCGGGAAGCCAT 58.197 50.000 6.32 0.00 0.00 4.40
428 429 1.575419 AATGTAGTACCGGGAAGCCA 58.425 50.000 6.32 0.00 0.00 4.75
429 430 2.169978 AGAAATGTAGTACCGGGAAGCC 59.830 50.000 6.32 0.00 0.00 4.35
430 431 3.538634 AGAAATGTAGTACCGGGAAGC 57.461 47.619 6.32 0.00 0.00 3.86
431 432 4.189231 CCAAGAAATGTAGTACCGGGAAG 58.811 47.826 6.32 0.00 0.00 3.46
432 433 3.054948 CCCAAGAAATGTAGTACCGGGAA 60.055 47.826 6.32 0.00 32.60 3.97
433 434 2.502538 CCCAAGAAATGTAGTACCGGGA 59.497 50.000 6.32 0.00 32.60 5.14
434 435 2.914059 CCCAAGAAATGTAGTACCGGG 58.086 52.381 6.32 0.00 0.00 5.73
435 436 2.093128 AGCCCAAGAAATGTAGTACCGG 60.093 50.000 0.00 0.00 0.00 5.28
436 437 3.261981 AGCCCAAGAAATGTAGTACCG 57.738 47.619 0.00 0.00 0.00 4.02
437 438 3.128764 GCAAGCCCAAGAAATGTAGTACC 59.871 47.826 0.00 0.00 0.00 3.34
438 439 4.010349 AGCAAGCCCAAGAAATGTAGTAC 58.990 43.478 0.00 0.00 0.00 2.73
439 440 4.301072 AGCAAGCCCAAGAAATGTAGTA 57.699 40.909 0.00 0.00 0.00 1.82
440 441 3.160679 AGCAAGCCCAAGAAATGTAGT 57.839 42.857 0.00 0.00 0.00 2.73
441 442 4.265073 ACTAGCAAGCCCAAGAAATGTAG 58.735 43.478 0.00 0.00 0.00 2.74
442 443 4.301072 ACTAGCAAGCCCAAGAAATGTA 57.699 40.909 0.00 0.00 0.00 2.29
443 444 3.160679 ACTAGCAAGCCCAAGAAATGT 57.839 42.857 0.00 0.00 0.00 2.71
444 445 5.643379 TTTACTAGCAAGCCCAAGAAATG 57.357 39.130 0.00 0.00 0.00 2.32
445 446 6.857437 AATTTACTAGCAAGCCCAAGAAAT 57.143 33.333 0.00 0.00 0.00 2.17
446 447 6.664428 AAATTTACTAGCAAGCCCAAGAAA 57.336 33.333 0.00 0.00 0.00 2.52
447 448 7.954666 ATAAATTTACTAGCAAGCCCAAGAA 57.045 32.000 0.00 0.00 0.00 2.52
448 449 7.954666 AATAAATTTACTAGCAAGCCCAAGA 57.045 32.000 0.00 0.00 0.00 3.02
449 450 9.087424 GAAAATAAATTTACTAGCAAGCCCAAG 57.913 33.333 0.00 0.00 0.00 3.61
450 451 8.811994 AGAAAATAAATTTACTAGCAAGCCCAA 58.188 29.630 0.00 0.00 0.00 4.12
451 452 8.361169 AGAAAATAAATTTACTAGCAAGCCCA 57.639 30.769 0.00 0.00 0.00 5.36
452 453 9.087424 CAAGAAAATAAATTTACTAGCAAGCCC 57.913 33.333 0.00 0.00 0.00 5.19
453 454 9.087424 CCAAGAAAATAAATTTACTAGCAAGCC 57.913 33.333 0.00 0.00 0.00 4.35
454 455 9.639601 ACCAAGAAAATAAATTTACTAGCAAGC 57.360 29.630 0.00 0.00 0.00 4.01
534 535 8.904834 GTCCGGATATTCATATCACATACTACT 58.095 37.037 7.81 0.00 40.67 2.57
535 536 8.904834 AGTCCGGATATTCATATCACATACTAC 58.095 37.037 7.81 0.00 40.67 2.73
537 538 7.962995 AGTCCGGATATTCATATCACATACT 57.037 36.000 7.81 0.00 40.67 2.12
538 539 8.904834 AGTAGTCCGGATATTCATATCACATAC 58.095 37.037 7.81 0.00 40.67 2.39
540 541 7.962995 AGTAGTCCGGATATTCATATCACAT 57.037 36.000 7.81 0.00 40.67 3.21
541 542 8.326529 TCTAGTAGTCCGGATATTCATATCACA 58.673 37.037 7.81 0.00 40.67 3.58
542 543 8.614346 GTCTAGTAGTCCGGATATTCATATCAC 58.386 40.741 7.81 0.00 40.67 3.06
543 544 8.549731 AGTCTAGTAGTCCGGATATTCATATCA 58.450 37.037 7.81 0.00 40.67 2.15
544 545 8.967664 AGTCTAGTAGTCCGGATATTCATATC 57.032 38.462 7.81 0.00 38.70 1.63
545 546 9.835389 GTAGTCTAGTAGTCCGGATATTCATAT 57.165 37.037 7.81 0.00 0.00 1.78
546 547 8.819845 TGTAGTCTAGTAGTCCGGATATTCATA 58.180 37.037 7.81 0.00 0.00 2.15
547 548 7.607223 GTGTAGTCTAGTAGTCCGGATATTCAT 59.393 40.741 7.81 0.00 0.00 2.57
548 549 6.933521 GTGTAGTCTAGTAGTCCGGATATTCA 59.066 42.308 7.81 0.00 0.00 2.57
549 550 7.160726 AGTGTAGTCTAGTAGTCCGGATATTC 58.839 42.308 7.81 0.00 0.00 1.75
550 551 7.077050 AGTGTAGTCTAGTAGTCCGGATATT 57.923 40.000 7.81 0.00 0.00 1.28
551 552 6.684897 AGTGTAGTCTAGTAGTCCGGATAT 57.315 41.667 7.81 1.63 0.00 1.63
552 553 6.551227 TGTAGTGTAGTCTAGTAGTCCGGATA 59.449 42.308 7.81 0.00 0.00 2.59
553 554 5.365025 TGTAGTGTAGTCTAGTAGTCCGGAT 59.635 44.000 7.81 0.00 0.00 4.18
554 555 4.711846 TGTAGTGTAGTCTAGTAGTCCGGA 59.288 45.833 0.00 0.00 0.00 5.14
555 556 5.016051 TGTAGTGTAGTCTAGTAGTCCGG 57.984 47.826 0.00 0.00 0.00 5.14
556 557 5.695816 GGATGTAGTGTAGTCTAGTAGTCCG 59.304 48.000 0.00 0.00 0.00 4.79
557 558 5.997129 GGGATGTAGTGTAGTCTAGTAGTCC 59.003 48.000 0.00 0.00 0.00 3.85
558 559 5.997129 GGGGATGTAGTGTAGTCTAGTAGTC 59.003 48.000 0.00 0.00 0.00 2.59
559 560 5.431073 TGGGGATGTAGTGTAGTCTAGTAGT 59.569 44.000 0.00 0.00 0.00 2.73
560 561 5.764192 GTGGGGATGTAGTGTAGTCTAGTAG 59.236 48.000 0.00 0.00 0.00 2.57
561 562 5.431073 AGTGGGGATGTAGTGTAGTCTAGTA 59.569 44.000 0.00 0.00 0.00 1.82
562 563 4.230041 AGTGGGGATGTAGTGTAGTCTAGT 59.770 45.833 0.00 0.00 0.00 2.57
563 564 4.794334 AGTGGGGATGTAGTGTAGTCTAG 58.206 47.826 0.00 0.00 0.00 2.43
564 565 4.685302 CGAGTGGGGATGTAGTGTAGTCTA 60.685 50.000 0.00 0.00 0.00 2.59
565 566 3.633418 GAGTGGGGATGTAGTGTAGTCT 58.367 50.000 0.00 0.00 0.00 3.24
566 567 2.358267 CGAGTGGGGATGTAGTGTAGTC 59.642 54.545 0.00 0.00 0.00 2.59
567 568 2.291411 ACGAGTGGGGATGTAGTGTAGT 60.291 50.000 0.00 0.00 0.00 2.73
568 569 2.358267 GACGAGTGGGGATGTAGTGTAG 59.642 54.545 0.00 0.00 0.00 2.74
569 570 2.025605 AGACGAGTGGGGATGTAGTGTA 60.026 50.000 0.00 0.00 0.00 2.90
570 571 1.183549 GACGAGTGGGGATGTAGTGT 58.816 55.000 0.00 0.00 0.00 3.55
571 572 1.475403 AGACGAGTGGGGATGTAGTG 58.525 55.000 0.00 0.00 0.00 2.74
572 573 1.825474 CAAGACGAGTGGGGATGTAGT 59.175 52.381 0.00 0.00 0.00 2.73
573 574 1.471676 GCAAGACGAGTGGGGATGTAG 60.472 57.143 0.00 0.00 0.00 2.74
574 575 0.535335 GCAAGACGAGTGGGGATGTA 59.465 55.000 0.00 0.00 0.00 2.29
575 576 1.194781 AGCAAGACGAGTGGGGATGT 61.195 55.000 0.00 0.00 0.00 3.06
576 577 0.460987 GAGCAAGACGAGTGGGGATG 60.461 60.000 0.00 0.00 0.00 3.51
577 578 1.617947 GGAGCAAGACGAGTGGGGAT 61.618 60.000 0.00 0.00 0.00 3.85
578 579 2.283529 GGAGCAAGACGAGTGGGGA 61.284 63.158 0.00 0.00 0.00 4.81
579 580 2.266055 GGAGCAAGACGAGTGGGG 59.734 66.667 0.00 0.00 0.00 4.96
580 581 1.079543 CTGGAGCAAGACGAGTGGG 60.080 63.158 0.00 0.00 0.00 4.61
581 582 0.108898 CTCTGGAGCAAGACGAGTGG 60.109 60.000 0.00 0.00 0.00 4.00
582 583 0.600557 ACTCTGGAGCAAGACGAGTG 59.399 55.000 0.00 0.00 33.99 3.51
583 584 1.271102 GAACTCTGGAGCAAGACGAGT 59.729 52.381 0.00 0.00 36.58 4.18
591 592 2.343758 GCCGTGAACTCTGGAGCA 59.656 61.111 0.00 0.00 0.00 4.26
603 604 1.079127 CCTTGGTGAGTAGGCCGTG 60.079 63.158 0.00 0.00 0.00 4.94
641 642 3.864686 GCGACATTGACGCGGCAT 61.865 61.111 19.26 0.00 46.05 4.40
791 963 2.048597 GATGTGCCACACGTCGGA 60.049 61.111 0.00 0.00 39.96 4.55
807 979 1.302192 GTAGGTGCAAGCCGTTGGA 60.302 57.895 0.00 0.00 33.87 3.53
816 988 0.983467 TGAGGATGCTGTAGGTGCAA 59.017 50.000 0.00 0.00 44.01 4.08
873 1045 2.197643 GACGACCGAAGAAGGCGAGT 62.198 60.000 0.00 0.00 35.71 4.18
906 1078 1.536073 CGACTTGGTCTGCCTCCAGA 61.536 60.000 0.00 0.00 45.54 3.86
1312 1484 7.155328 GGTATGATACCCTTACTTGTCATCTG 58.845 42.308 10.58 0.00 43.18 2.90
1408 1580 2.827322 TCATGGCCATGGAGTCAAAAAG 59.173 45.455 38.81 14.56 39.24 2.27
1521 1693 4.940046 AGAATACAGTCTGTTGCCATTGAG 59.060 41.667 11.54 0.00 0.00 3.02
1638 1810 0.102120 CATCTGGACTCACTCCTCGC 59.898 60.000 0.00 0.00 40.26 5.03
1640 1812 3.626930 ACTACATCTGGACTCACTCCTC 58.373 50.000 0.00 0.00 40.26 3.71
1923 2095 0.673985 CGAGGATATCCCGTGCTTCA 59.326 55.000 18.56 0.00 40.87 3.02
1951 2123 1.696336 AGGCCTCATACCTATGTGCAG 59.304 52.381 0.00 0.00 35.10 4.41
1995 2167 2.628657 GACTAGGCAGTATCCACCGATT 59.371 50.000 0.00 0.00 34.21 3.34
2020 2192 4.789012 TTTTTGTTGCATCCTCCATCTC 57.211 40.909 0.00 0.00 0.00 2.75
2249 2421 8.733458 CAGATTCAACCATCTCATTAAACTTCA 58.267 33.333 0.00 0.00 30.50 3.02
2545 2717 2.260844 TTGTCAGCTTCTTCCACTGG 57.739 50.000 0.00 0.00 32.19 4.00
2867 3059 1.555075 TGTCTAAGCAGATGGACCCAC 59.445 52.381 0.00 0.00 32.09 4.61
2950 3153 4.690748 GTGCTGCAACTGAATTGTACTCTA 59.309 41.667 2.77 0.00 40.77 2.43
3000 3244 5.536161 TGCTGCTCCTTCTATTTGAGTTTTT 59.464 36.000 0.00 0.00 0.00 1.94
3078 3341 4.875713 CCACTACATGCCCCGCCC 62.876 72.222 0.00 0.00 0.00 6.13
3108 3374 1.228552 GGTGGGAGAAGCAAAGGCA 60.229 57.895 0.00 0.00 44.61 4.75
3506 3863 6.452242 TGTATAACCAACTCCAGCATATACG 58.548 40.000 0.00 0.00 30.90 3.06
3518 3875 7.555195 GCCCTAAACTAACATGTATAACCAACT 59.445 37.037 0.00 0.00 0.00 3.16
3519 3876 7.201758 GGCCCTAAACTAACATGTATAACCAAC 60.202 40.741 0.00 0.00 0.00 3.77
3523 3880 7.555195 ACAAGGCCCTAAACTAACATGTATAAC 59.445 37.037 0.00 0.00 0.00 1.89
3528 3885 4.382386 ACAAGGCCCTAAACTAACATGT 57.618 40.909 0.00 0.00 0.00 3.21
3529 3886 4.157840 GGAACAAGGCCCTAAACTAACATG 59.842 45.833 0.00 0.00 0.00 3.21
3530 3887 4.202631 TGGAACAAGGCCCTAAACTAACAT 60.203 41.667 0.00 0.00 31.92 2.71
3531 3888 3.138653 TGGAACAAGGCCCTAAACTAACA 59.861 43.478 0.00 0.00 31.92 2.41
3549 4065 9.462174 GCATCGATCATAACAAATAATTTGGAA 57.538 29.630 0.00 0.00 44.81 3.53
3555 4071 7.080099 GTGCTGCATCGATCATAACAAATAAT 58.920 34.615 5.27 0.00 0.00 1.28
3558 4074 4.336153 TGTGCTGCATCGATCATAACAAAT 59.664 37.500 5.27 0.00 0.00 2.32
3565 4083 2.294979 ACATTGTGCTGCATCGATCAT 58.705 42.857 5.27 0.00 0.00 2.45
3581 4099 6.126568 AGTTACAGCGTTAAACACAACATT 57.873 33.333 0.71 0.00 0.00 2.71
3588 4106 3.207778 AGCCAAGTTACAGCGTTAAACA 58.792 40.909 0.71 0.00 0.00 2.83
3596 4114 6.106673 TGATCTAGTTAAGCCAAGTTACAGC 58.893 40.000 0.00 0.00 0.00 4.40
3679 4232 9.987272 CATATTACCTCTGAACATTGATCTGTA 57.013 33.333 0.00 0.00 0.00 2.74
3712 4265 4.802039 GCTAACAGTCGATGAAATTACGGA 59.198 41.667 0.00 0.00 0.00 4.69
3732 4286 9.461312 AGTATTGAATAACAAAGGAACATGCTA 57.539 29.630 0.00 0.00 42.03 3.49
3746 4300 8.113062 GCGATGATATGCAGAGTATTGAATAAC 58.887 37.037 0.00 0.00 0.00 1.89
3762 4316 9.696917 TTATTATAGGCATACTGCGATGATATG 57.303 33.333 0.00 0.00 46.21 1.78
3770 4324 9.847706 CTATATCCTTATTATAGGCATACTGCG 57.152 37.037 0.00 0.00 46.21 5.18
3795 4349 6.996509 AGGTTCAAAATGCATCAAACATACT 58.003 32.000 0.00 0.00 0.00 2.12
3796 4350 7.092716 AGAGGTTCAAAATGCATCAAACATAC 58.907 34.615 0.00 0.00 0.00 2.39
3797 4351 7.177216 AGAGAGGTTCAAAATGCATCAAACATA 59.823 33.333 0.00 0.00 0.00 2.29
3801 4355 5.302568 ACAGAGAGGTTCAAAATGCATCAAA 59.697 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.