Multiple sequence alignment - TraesCS5A01G241800

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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 TraesCS5A01G241800 chr5A 100.000 7190 0 0 1 7190 457431227 457438416 0.000000e+00 13278.0
1 TraesCS5A01G241800 chr5A 81.220 1853 321 22 4538 6372 705844083 705842240 0.000000e+00 1469.0
2 TraesCS5A01G241800 chr5A 96.864 287 8 1 3528 3814 457434024 457434309 5.050000e-131 479.0
3 TraesCS5A01G241800 chr5A 96.864 287 8 1 2798 3083 457434754 457435040 5.050000e-131 479.0
4 TraesCS5A01G241800 chr5A 100.000 35 0 0 3105 3139 457433990 457434024 1.670000e-06 65.8
5 TraesCS5A01G241800 chr5A 100.000 35 0 0 2764 2798 457434331 457434365 1.670000e-06 65.8
6 TraesCS5A01G241800 chr5A 97.368 38 0 1 2617 2654 457433812 457433848 6.020000e-06 63.9
7 TraesCS5A01G241800 chr5A 97.368 38 0 1 2586 2622 457433843 457433880 6.020000e-06 63.9
8 TraesCS5A01G241800 chr5D 97.801 2956 64 1 4210 7164 355203253 355206208 0.000000e+00 5097.0
9 TraesCS5A01G241800 chr5D 97.903 2003 38 3 623 2622 355199476 355201477 0.000000e+00 3463.0
10 TraesCS5A01G241800 chr5D 95.431 985 25 12 3233 4213 355202014 355202982 0.000000e+00 1552.0
11 TraesCS5A01G241800 chr5D 96.907 582 13 4 2617 3198 355201441 355202017 0.000000e+00 970.0
12 TraesCS5A01G241800 chr5D 96.703 455 13 2 1 454 355199039 355199492 0.000000e+00 756.0
13 TraesCS5A01G241800 chr5D 96.864 287 8 1 2798 3083 355202309 355202595 5.050000e-131 479.0
14 TraesCS5A01G241800 chr5D 96.167 287 9 2 3528 3814 355201618 355201902 1.090000e-127 468.0
15 TraesCS5A01G241800 chr5D 97.143 35 1 0 3105 3139 355201584 355201618 7.790000e-05 60.2
16 TraesCS5A01G241800 chr5D 100.000 30 0 0 7161 7190 355206264 355206293 1.000000e-03 56.5
17 TraesCS5A01G241800 chr5B 96.149 2908 88 8 4263 7169 419998121 420001005 0.000000e+00 4728.0
18 TraesCS5A01G241800 chr5B 94.868 1520 37 17 1119 2622 419996007 419997501 0.000000e+00 2337.0
19 TraesCS5A01G241800 chr5B 95.935 369 15 0 623 991 419995640 419996008 3.710000e-167 599.0
20 TraesCS5A01G241800 chr5B 93.750 272 13 3 185 454 419995387 419995656 8.690000e-109 405.0
21 TraesCS5A01G241800 chr5B 97.283 184 3 2 458 640 428847337 428847155 1.950000e-80 311.0
22 TraesCS5A01G241800 chr5B 92.254 142 5 4 2617 2758 419997465 419997600 5.690000e-46 196.0
23 TraesCS5A01G241800 chr5B 92.143 140 7 2 1 136 419995248 419995387 2.050000e-45 195.0
24 TraesCS5A01G241800 chr6A 83.882 1731 259 15 4474 6194 572136849 572138569 0.000000e+00 1633.0
25 TraesCS5A01G241800 chr6A 78.648 1124 168 46 958 2049 572134784 572135867 0.000000e+00 680.0
26 TraesCS5A01G241800 chr6A 79.070 301 45 12 1102 1389 158907243 158907538 2.650000e-44 191.0
27 TraesCS5A01G241800 chr6D 83.430 1732 262 18 4474 6194 427483497 427485214 0.000000e+00 1585.0
28 TraesCS5A01G241800 chr6D 76.798 1474 236 60 628 2049 427481030 427482449 0.000000e+00 730.0
29 TraesCS5A01G241800 chr4B 81.789 1845 317 14 4539 6372 625975191 625977027 0.000000e+00 1528.0
30 TraesCS5A01G241800 chr4B 81.112 1853 323 22 4538 6372 665877098 665875255 0.000000e+00 1458.0
31 TraesCS5A01G241800 chr4B 100.000 171 0 0 452 622 598406478 598406308 4.190000e-82 316.0
32 TraesCS5A01G241800 chr4B 75.931 349 58 21 2218 2551 665557791 665558128 9.660000e-34 156.0
33 TraesCS5A01G241800 chrUn 80.947 1921 331 30 4474 6372 108321654 108323561 0.000000e+00 1487.0
34 TraesCS5A01G241800 chr3D 80.736 1604 278 28 4540 6135 561172311 561173891 0.000000e+00 1221.0
35 TraesCS5A01G241800 chr6B 76.178 1486 238 71 624 2049 643261931 643263360 0.000000e+00 676.0
36 TraesCS5A01G241800 chr6B 100.000 172 0 0 454 625 314575910 314576081 1.160000e-82 318.0
37 TraesCS5A01G241800 chr6B 98.864 176 2 0 447 622 490650679 490650504 1.510000e-81 315.0
38 TraesCS5A01G241800 chr6B 98.870 177 1 1 452 627 602840930 602841106 1.510000e-81 315.0
39 TraesCS5A01G241800 chr6B 77.133 293 51 11 1109 1389 212629282 212628994 9.660000e-34 156.0
40 TraesCS5A01G241800 chr7A 77.701 722 103 30 3124 3828 663948878 663949558 8.750000e-104 388.0
41 TraesCS5A01G241800 chr1B 84.066 364 57 1 3329 3691 264350415 264350052 4.130000e-92 350.0
42 TraesCS5A01G241800 chr1B 95.960 198 5 3 444 641 449828202 449828396 1.160000e-82 318.0
43 TraesCS5A01G241800 chr2B 99.435 177 0 1 452 628 244915772 244915597 3.240000e-83 320.0
44 TraesCS5A01G241800 chr7B 100.000 172 0 0 454 625 611525479 611525308 1.160000e-82 318.0
45 TraesCS5A01G241800 chr7B 78.654 520 71 16 3327 3831 633677329 633676835 7.010000e-80 309.0
46 TraesCS5A01G241800 chr7B 93.596 203 10 3 450 650 59060054 59059853 4.220000e-77 300.0
47 TraesCS5A01G241800 chr4A 92.754 69 5 0 2690 2758 63822316 63822248 4.590000e-17 100.0


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 TraesCS5A01G241800 chr5A 457431227 457438416 7189 False 13278.000000 13278 100.000000 1 7190 1 chr5A.!!$F1 7189
1 TraesCS5A01G241800 chr5A 705842240 705844083 1843 True 1469.000000 1469 81.220000 4538 6372 1 chr5A.!!$R1 1834
2 TraesCS5A01G241800 chr5A 457433812 457435040 1228 False 202.900000 479 98.077333 2586 3814 6 chr5A.!!$F2 1228
3 TraesCS5A01G241800 chr5D 355199039 355206293 7254 False 1433.522222 5097 97.213222 1 7190 9 chr5D.!!$F1 7189
4 TraesCS5A01G241800 chr5B 419995248 420001005 5757 False 1410.000000 4728 94.183167 1 7169 6 chr5B.!!$F1 7168
5 TraesCS5A01G241800 chr6A 572134784 572138569 3785 False 1156.500000 1633 81.265000 958 6194 2 chr6A.!!$F2 5236
6 TraesCS5A01G241800 chr6D 427481030 427485214 4184 False 1157.500000 1585 80.114000 628 6194 2 chr6D.!!$F1 5566
7 TraesCS5A01G241800 chr4B 625975191 625977027 1836 False 1528.000000 1528 81.789000 4539 6372 1 chr4B.!!$F1 1833
8 TraesCS5A01G241800 chr4B 665875255 665877098 1843 True 1458.000000 1458 81.112000 4538 6372 1 chr4B.!!$R2 1834
9 TraesCS5A01G241800 chrUn 108321654 108323561 1907 False 1487.000000 1487 80.947000 4474 6372 1 chrUn.!!$F1 1898
10 TraesCS5A01G241800 chr3D 561172311 561173891 1580 False 1221.000000 1221 80.736000 4540 6135 1 chr3D.!!$F1 1595
11 TraesCS5A01G241800 chr6B 643261931 643263360 1429 False 676.000000 676 76.178000 624 2049 1 chr6B.!!$F3 1425
12 TraesCS5A01G241800 chr7A 663948878 663949558 680 False 388.000000 388 77.701000 3124 3828 1 chr7A.!!$F1 704

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
556 561 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.0 8.73 0.00 40.08 4.58 F
562 567 0.392193 AATGCAGAGAGGCTGGTTCG 60.392 55.0 0.00 0.00 45.03 3.95 F
598 603 0.606673 GCACAAGTGGGGAGGACTTC 60.607 60.0 2.00 0.00 31.05 3.01 F
599 604 0.764890 CACAAGTGGGGAGGACTTCA 59.235 55.0 0.00 0.00 31.05 3.02 F
600 605 0.765510 ACAAGTGGGGAGGACTTCAC 59.234 55.0 0.00 0.00 31.05 3.18 F
1841 1898 0.986527 TGCAGACACTGGGTGATGAT 59.013 50.0 4.62 0.00 36.96 2.45 F
3855 4198 0.397941 TTCTGGAGCTCCACACTTGG 59.602 55.0 32.00 20.25 45.56 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1928 0.178992 CAACACTCTGGGGGAAGCAA 60.179 55.000 0.00 0.00 0.00 3.91 R
2510 2654 5.011586 ACTAGTCTGGTACCTGAAGTTCTC 58.988 45.833 21.76 9.44 0.00 2.87 R
2699 2847 9.030452 GGGACATAACCAATGGCATAAATAATA 57.970 33.333 0.00 0.00 46.56 0.98 R
3855 4198 4.974645 TGGATATATGGGACCTTGTGTC 57.025 45.455 0.00 0.00 43.67 3.67 R
3856 4199 5.725551 TTTGGATATATGGGACCTTGTGT 57.274 39.130 0.00 0.00 0.00 3.72 R
3885 4237 0.108585 TCTCTTGGTGTTGTCCTGCC 59.891 55.000 0.00 0.00 0.00 4.85 R
6700 7388 0.531974 GCAACACACTCCCTTCGACA 60.532 55.000 0.00 0.00 0.00 4.35 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
137 142 1.416480 CGGGAGGAGGATAAACCCCC 61.416 65.000 0.00 0.00 40.05 5.40
323 328 1.000060 GCTGTGCTGATTTTGCCTTCA 60.000 47.619 0.00 0.00 0.00 3.02
330 335 4.992319 TGCTGATTTTGCCTTCATTTTCAG 59.008 37.500 0.00 0.00 34.04 3.02
337 342 1.401539 GCCTTCATTTTCAGTCGTGCC 60.402 52.381 0.00 0.00 0.00 5.01
446 451 6.260377 GTTTTAGTTTGTGTTACACTGGTCC 58.740 40.000 16.79 0.82 35.11 4.46
447 452 3.637911 AGTTTGTGTTACACTGGTCCA 57.362 42.857 16.79 0.00 35.11 4.02
448 453 3.275999 AGTTTGTGTTACACTGGTCCAC 58.724 45.455 16.79 4.54 35.11 4.02
449 454 2.335316 TTGTGTTACACTGGTCCACC 57.665 50.000 16.79 0.00 35.11 4.61
450 455 0.470766 TGTGTTACACTGGTCCACCC 59.529 55.000 16.79 0.00 35.11 4.61
451 456 0.470766 GTGTTACACTGGTCCACCCA 59.529 55.000 8.41 0.00 42.51 4.51
452 457 1.073284 GTGTTACACTGGTCCACCCAT 59.927 52.381 8.41 0.00 44.15 4.00
453 458 2.303600 GTGTTACACTGGTCCACCCATA 59.696 50.000 8.41 0.00 44.15 2.74
454 459 2.980379 TGTTACACTGGTCCACCCATAA 59.020 45.455 0.00 0.00 44.15 1.90
455 460 3.394940 TGTTACACTGGTCCACCCATAAA 59.605 43.478 0.00 0.00 44.15 1.40
456 461 4.141228 TGTTACACTGGTCCACCCATAAAA 60.141 41.667 0.00 0.00 44.15 1.52
457 462 3.603965 ACACTGGTCCACCCATAAAAA 57.396 42.857 0.00 0.00 44.15 1.94
458 463 3.496331 ACACTGGTCCACCCATAAAAAG 58.504 45.455 0.00 0.00 44.15 2.27
459 464 2.825532 CACTGGTCCACCCATAAAAAGG 59.174 50.000 0.00 0.00 44.15 3.11
460 465 2.719705 ACTGGTCCACCCATAAAAAGGA 59.280 45.455 0.00 0.00 44.15 3.36
461 466 3.089284 CTGGTCCACCCATAAAAAGGAC 58.911 50.000 0.00 0.00 44.15 3.85
464 469 4.028993 GTCCACCCATAAAAAGGACAGA 57.971 45.455 0.00 0.00 46.15 3.41
465 470 3.756963 GTCCACCCATAAAAAGGACAGAC 59.243 47.826 0.00 0.00 46.15 3.51
466 471 3.089284 CCACCCATAAAAAGGACAGACC 58.911 50.000 0.00 0.00 39.35 3.85
467 472 3.089284 CACCCATAAAAAGGACAGACCC 58.911 50.000 0.00 0.00 40.05 4.46
468 473 2.719705 ACCCATAAAAAGGACAGACCCA 59.280 45.455 0.00 0.00 40.05 4.51
469 474 3.245264 ACCCATAAAAAGGACAGACCCAG 60.245 47.826 0.00 0.00 40.05 4.45
470 475 3.245264 CCCATAAAAAGGACAGACCCAGT 60.245 47.826 0.00 0.00 40.05 4.00
471 476 3.758554 CCATAAAAAGGACAGACCCAGTG 59.241 47.826 0.00 0.00 40.05 3.66
472 477 1.692411 AAAAAGGACAGACCCAGTGC 58.308 50.000 0.00 0.00 40.05 4.40
473 478 0.550914 AAAAGGACAGACCCAGTGCA 59.449 50.000 0.00 0.00 40.05 4.57
474 479 0.773644 AAAGGACAGACCCAGTGCAT 59.226 50.000 0.00 0.00 40.05 3.96
475 480 1.656587 AAGGACAGACCCAGTGCATA 58.343 50.000 0.00 0.00 40.05 3.14
476 481 1.198713 AGGACAGACCCAGTGCATAG 58.801 55.000 0.00 0.00 40.05 2.23
477 482 1.195115 GGACAGACCCAGTGCATAGA 58.805 55.000 0.00 0.00 0.00 1.98
478 483 1.555075 GGACAGACCCAGTGCATAGAA 59.445 52.381 0.00 0.00 0.00 2.10
479 484 2.419297 GGACAGACCCAGTGCATAGAAG 60.419 54.545 0.00 0.00 0.00 2.85
480 485 1.065854 ACAGACCCAGTGCATAGAAGC 60.066 52.381 0.00 0.00 0.00 3.86
481 486 1.209019 CAGACCCAGTGCATAGAAGCT 59.791 52.381 0.00 0.00 34.99 3.74
482 487 1.484240 AGACCCAGTGCATAGAAGCTC 59.516 52.381 0.00 0.00 34.99 4.09
483 488 0.543749 ACCCAGTGCATAGAAGCTCC 59.456 55.000 0.00 0.00 34.99 4.70
484 489 0.179034 CCCAGTGCATAGAAGCTCCC 60.179 60.000 0.00 0.00 34.99 4.30
485 490 0.543277 CCAGTGCATAGAAGCTCCCA 59.457 55.000 0.00 0.00 34.99 4.37
486 491 1.661341 CAGTGCATAGAAGCTCCCAC 58.339 55.000 0.00 0.00 34.99 4.61
487 492 1.065926 CAGTGCATAGAAGCTCCCACA 60.066 52.381 0.00 0.00 34.99 4.17
488 493 1.065854 AGTGCATAGAAGCTCCCACAC 60.066 52.381 0.00 0.00 34.99 3.82
489 494 0.983467 TGCATAGAAGCTCCCACACA 59.017 50.000 0.00 0.00 34.99 3.72
490 495 1.350684 TGCATAGAAGCTCCCACACAA 59.649 47.619 0.00 0.00 34.99 3.33
491 496 2.012673 GCATAGAAGCTCCCACACAAG 58.987 52.381 0.00 0.00 0.00 3.16
492 497 2.636830 CATAGAAGCTCCCACACAAGG 58.363 52.381 0.00 0.00 0.00 3.61
493 498 1.729586 TAGAAGCTCCCACACAAGGT 58.270 50.000 0.00 0.00 0.00 3.50
501 506 4.481195 CACACAAGGTGGGGTCTG 57.519 61.111 1.07 0.00 44.04 3.51
502 507 1.228245 CACACAAGGTGGGGTCTGG 60.228 63.158 1.07 0.00 44.04 3.86
503 508 2.436109 CACAAGGTGGGGTCTGGG 59.564 66.667 0.00 0.00 0.00 4.45
504 509 2.858974 ACAAGGTGGGGTCTGGGG 60.859 66.667 0.00 0.00 0.00 4.96
505 510 2.531685 CAAGGTGGGGTCTGGGGA 60.532 66.667 0.00 0.00 0.00 4.81
506 511 2.204151 AAGGTGGGGTCTGGGGAG 60.204 66.667 0.00 0.00 0.00 4.30
507 512 3.891432 AAGGTGGGGTCTGGGGAGG 62.891 68.421 0.00 0.00 0.00 4.30
509 514 4.348495 GTGGGGTCTGGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
510 515 3.300962 TGGGGTCTGGGGAGGGAT 61.301 66.667 0.00 0.00 0.00 3.85
511 516 2.044620 GGGGTCTGGGGAGGGATT 59.955 66.667 0.00 0.00 0.00 3.01
512 517 1.320512 GGGGTCTGGGGAGGGATTA 59.679 63.158 0.00 0.00 0.00 1.75
513 518 0.103876 GGGGTCTGGGGAGGGATTAT 60.104 60.000 0.00 0.00 0.00 1.28
514 519 1.153565 GGGGTCTGGGGAGGGATTATA 59.846 57.143 0.00 0.00 0.00 0.98
515 520 2.552367 GGGTCTGGGGAGGGATTATAG 58.448 57.143 0.00 0.00 0.00 1.31
516 521 2.552367 GGTCTGGGGAGGGATTATAGG 58.448 57.143 0.00 0.00 0.00 2.57
517 522 2.113777 GGTCTGGGGAGGGATTATAGGA 59.886 54.545 0.00 0.00 0.00 2.94
518 523 3.441054 GGTCTGGGGAGGGATTATAGGAA 60.441 52.174 0.00 0.00 0.00 3.36
519 524 3.583526 GTCTGGGGAGGGATTATAGGAAC 59.416 52.174 0.00 0.00 0.00 3.62
520 525 2.913617 CTGGGGAGGGATTATAGGAACC 59.086 54.545 0.00 0.00 0.00 3.62
521 526 2.531463 TGGGGAGGGATTATAGGAACCT 59.469 50.000 0.00 0.00 0.00 3.50
522 527 3.741438 TGGGGAGGGATTATAGGAACCTA 59.259 47.826 2.93 2.93 0.00 3.08
523 528 4.202901 TGGGGAGGGATTATAGGAACCTAG 60.203 50.000 6.72 0.00 31.45 3.02
524 529 4.202912 GGGGAGGGATTATAGGAACCTAGT 60.203 50.000 6.72 0.00 31.45 2.57
525 530 5.024785 GGGAGGGATTATAGGAACCTAGTC 58.975 50.000 6.72 4.93 31.45 2.59
526 531 5.222589 GGGAGGGATTATAGGAACCTAGTCT 60.223 48.000 6.72 0.00 31.45 3.24
527 532 6.324544 GGAGGGATTATAGGAACCTAGTCTT 58.675 44.000 6.72 0.00 31.45 3.01
528 533 7.477008 GGAGGGATTATAGGAACCTAGTCTTA 58.523 42.308 6.72 0.00 31.45 2.10
529 534 7.396907 GGAGGGATTATAGGAACCTAGTCTTAC 59.603 44.444 6.72 0.00 31.45 2.34
530 535 7.247500 AGGGATTATAGGAACCTAGTCTTACC 58.753 42.308 6.72 4.95 31.45 2.85
531 536 6.440010 GGGATTATAGGAACCTAGTCTTACCC 59.560 46.154 6.72 9.62 31.45 3.69
532 537 6.440010 GGATTATAGGAACCTAGTCTTACCCC 59.560 46.154 6.72 0.00 31.45 4.95
533 538 6.618836 TTATAGGAACCTAGTCTTACCCCT 57.381 41.667 6.72 0.00 31.45 4.79
534 539 3.117552 AGGAACCTAGTCTTACCCCTG 57.882 52.381 0.00 0.00 0.00 4.45
535 540 1.485480 GGAACCTAGTCTTACCCCTGC 59.515 57.143 0.00 0.00 0.00 4.85
536 541 2.185387 GAACCTAGTCTTACCCCTGCA 58.815 52.381 0.00 0.00 0.00 4.41
537 542 2.337359 ACCTAGTCTTACCCCTGCAA 57.663 50.000 0.00 0.00 0.00 4.08
538 543 2.627933 ACCTAGTCTTACCCCTGCAAA 58.372 47.619 0.00 0.00 0.00 3.68
539 544 2.572104 ACCTAGTCTTACCCCTGCAAAG 59.428 50.000 0.00 0.00 0.00 2.77
540 545 2.572104 CCTAGTCTTACCCCTGCAAAGT 59.428 50.000 0.00 0.00 0.00 2.66
541 546 2.568623 AGTCTTACCCCTGCAAAGTG 57.431 50.000 0.00 0.00 0.00 3.16
542 547 0.881796 GTCTTACCCCTGCAAAGTGC 59.118 55.000 0.00 0.00 45.29 4.40
553 558 1.978542 GCAAAGTGCAATGCAGAGAG 58.021 50.000 8.73 0.33 44.26 3.20
554 559 1.402456 GCAAAGTGCAATGCAGAGAGG 60.402 52.381 8.73 0.00 44.26 3.69
555 560 0.886563 AAAGTGCAATGCAGAGAGGC 59.113 50.000 8.73 0.00 40.08 4.70
556 561 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.000 8.73 0.00 40.08 4.58
558 563 1.378119 TGCAATGCAGAGAGGCTGG 60.378 57.895 2.72 0.00 45.03 4.85
559 564 1.378250 GCAATGCAGAGAGGCTGGT 60.378 57.895 0.00 0.00 45.03 4.00
560 565 0.964358 GCAATGCAGAGAGGCTGGTT 60.964 55.000 0.00 0.00 45.03 3.67
561 566 1.093159 CAATGCAGAGAGGCTGGTTC 58.907 55.000 0.00 0.00 45.03 3.62
562 567 0.392193 AATGCAGAGAGGCTGGTTCG 60.392 55.000 0.00 0.00 45.03 3.95
563 568 1.260538 ATGCAGAGAGGCTGGTTCGA 61.261 55.000 0.00 0.00 45.03 3.71
564 569 1.293498 GCAGAGAGGCTGGTTCGAA 59.707 57.895 0.00 0.00 45.03 3.71
565 570 1.016653 GCAGAGAGGCTGGTTCGAAC 61.017 60.000 20.14 20.14 45.03 3.95
574 579 3.479979 GGTTCGAACCCAGGACCT 58.520 61.111 33.02 0.00 43.43 3.85
575 580 1.295746 GGTTCGAACCCAGGACCTC 59.704 63.158 33.02 7.79 43.43 3.85
576 581 1.192803 GGTTCGAACCCAGGACCTCT 61.193 60.000 33.02 0.00 43.43 3.69
577 582 0.685660 GTTCGAACCCAGGACCTCTT 59.314 55.000 17.68 0.00 0.00 2.85
578 583 0.685097 TTCGAACCCAGGACCTCTTG 59.315 55.000 0.00 0.00 0.00 3.02
579 584 1.192146 TCGAACCCAGGACCTCTTGG 61.192 60.000 0.00 0.00 42.20 3.61
580 585 1.002011 GAACCCAGGACCTCTTGGC 60.002 63.158 0.00 0.00 41.31 4.52
581 586 1.774217 AACCCAGGACCTCTTGGCA 60.774 57.895 0.00 0.00 41.31 4.92
582 587 2.069165 AACCCAGGACCTCTTGGCAC 62.069 60.000 0.00 0.00 41.31 5.01
583 588 2.528818 CCCAGGACCTCTTGGCACA 61.529 63.158 0.00 0.00 41.31 4.57
594 599 2.449518 TGGCACAAGTGGGGAGGA 60.450 61.111 2.00 0.00 31.92 3.71
595 600 2.034221 GGCACAAGTGGGGAGGAC 59.966 66.667 2.00 0.00 0.00 3.85
596 601 2.529744 GGCACAAGTGGGGAGGACT 61.530 63.158 2.00 0.00 0.00 3.85
597 602 1.456287 GCACAAGTGGGGAGGACTT 59.544 57.895 2.00 0.00 33.82 3.01
598 603 0.606673 GCACAAGTGGGGAGGACTTC 60.607 60.000 2.00 0.00 31.05 3.01
599 604 0.764890 CACAAGTGGGGAGGACTTCA 59.235 55.000 0.00 0.00 31.05 3.02
600 605 0.765510 ACAAGTGGGGAGGACTTCAC 59.234 55.000 0.00 0.00 31.05 3.18
606 611 1.003233 GGGAGGACTTCACCACTGC 60.003 63.158 0.00 0.00 0.00 4.40
607 612 1.374758 GGAGGACTTCACCACTGCG 60.375 63.158 0.00 0.00 0.00 5.18
608 613 2.029844 GAGGACTTCACCACTGCGC 61.030 63.158 0.00 0.00 0.00 6.09
609 614 3.050275 GGACTTCACCACTGCGCC 61.050 66.667 4.18 0.00 0.00 6.53
610 615 2.280797 GACTTCACCACTGCGCCA 60.281 61.111 4.18 0.00 0.00 5.69
611 616 2.281070 ACTTCACCACTGCGCCAG 60.281 61.111 4.18 4.99 37.52 4.85
612 617 3.052082 CTTCACCACTGCGCCAGG 61.052 66.667 4.18 6.64 35.51 4.45
625 630 4.729918 CCAGGCCTGCCCTCACAC 62.730 72.222 28.39 0.00 44.09 3.82
671 676 5.489792 TTCTTACTTCTCTGGCACTTCAT 57.510 39.130 0.00 0.00 0.00 2.57
722 727 6.842163 ACCGCAAAGTATCTTTGTTTATCAG 58.158 36.000 18.94 7.11 0.00 2.90
908 923 5.705400 AGTTCCCAGAGAAATTTTCTTCCA 58.295 37.500 12.73 0.00 40.87 3.53
1097 1125 5.755409 TTGGTGTGATCTAGCCTTTTAGA 57.245 39.130 0.00 0.00 34.38 2.10
1119 1147 7.150783 AGACTCTAGAATTGAATTTGGTTGC 57.849 36.000 0.00 0.00 0.00 4.17
1813 1870 9.816354 GGCAAGAATTATATGTTACAATTGGTT 57.184 29.630 10.83 0.00 0.00 3.67
1841 1898 0.986527 TGCAGACACTGGGTGATGAT 59.013 50.000 4.62 0.00 36.96 2.45
1871 1928 3.118738 CGGGTAATTGCTCTACTTCTGGT 60.119 47.826 0.00 0.00 0.00 4.00
2072 2210 6.778834 TGATGTGAAATCTTTGCCATATGT 57.221 33.333 1.24 0.00 0.00 2.29
2076 2214 7.643569 TGTGAAATCTTTGCCATATGTATGT 57.356 32.000 1.24 0.00 31.82 2.29
2090 2228 4.743057 ATGTATGTGTTGAGCAGCTCTA 57.257 40.909 23.15 13.39 0.00 2.43
2199 2337 7.472334 AACCTTCAGAGATGCAAATTTACAT 57.528 32.000 3.46 3.46 0.00 2.29
2200 2338 6.860080 ACCTTCAGAGATGCAAATTTACATG 58.140 36.000 8.66 0.00 0.00 3.21
2464 2604 9.274065 GCCTTAAAACTTAAATGACATAGTTCG 57.726 33.333 3.18 0.00 30.92 3.95
2510 2654 8.393366 CACTTACACAAAATCATATCACCTGAG 58.607 37.037 0.00 0.00 0.00 3.35
3853 4196 1.980765 TCATTCTGGAGCTCCACACTT 59.019 47.619 32.00 13.62 42.01 3.16
3855 4198 0.397941 TTCTGGAGCTCCACACTTGG 59.602 55.000 32.00 20.25 45.56 3.61
3878 4230 5.690865 GACACAAGGTCCCATATATCCAAA 58.309 41.667 0.00 0.00 40.83 3.28
3879 4231 6.279813 ACACAAGGTCCCATATATCCAAAT 57.720 37.500 0.00 0.00 0.00 2.32
3880 4232 7.401060 ACACAAGGTCCCATATATCCAAATA 57.599 36.000 0.00 0.00 0.00 1.40
3881 4233 8.000171 ACACAAGGTCCCATATATCCAAATAT 58.000 34.615 0.00 0.00 32.72 1.28
3882 4234 8.456124 ACACAAGGTCCCATATATCCAAATATT 58.544 33.333 0.00 0.00 30.59 1.28
3883 4235 8.960591 CACAAGGTCCCATATATCCAAATATTC 58.039 37.037 0.00 0.00 30.59 1.75
3884 4236 8.677871 ACAAGGTCCCATATATCCAAATATTCA 58.322 33.333 0.00 0.00 30.59 2.57
3885 4237 9.182214 CAAGGTCCCATATATCCAAATATTCAG 57.818 37.037 0.00 0.00 30.59 3.02
3886 4238 7.876371 AGGTCCCATATATCCAAATATTCAGG 58.124 38.462 0.00 0.00 30.59 3.86
3887 4239 6.547510 GGTCCCATATATCCAAATATTCAGGC 59.452 42.308 2.73 0.00 30.59 4.85
3888 4240 7.118723 GTCCCATATATCCAAATATTCAGGCA 58.881 38.462 2.73 0.00 30.59 4.75
3889 4241 7.284034 GTCCCATATATCCAAATATTCAGGCAG 59.716 40.741 2.73 0.00 30.59 4.85
3890 4242 6.548622 CCCATATATCCAAATATTCAGGCAGG 59.451 42.308 2.73 0.00 30.59 4.85
3891 4243 7.348815 CCATATATCCAAATATTCAGGCAGGA 58.651 38.462 2.73 0.00 30.59 3.86
3892 4244 7.284034 CCATATATCCAAATATTCAGGCAGGAC 59.716 40.741 2.73 0.00 30.59 3.85
3893 4245 4.524802 ATCCAAATATTCAGGCAGGACA 57.475 40.909 2.73 0.00 0.00 4.02
3894 4246 4.314522 TCCAAATATTCAGGCAGGACAA 57.685 40.909 2.73 0.00 0.00 3.18
3895 4247 4.016444 TCCAAATATTCAGGCAGGACAAC 58.984 43.478 2.73 0.00 0.00 3.32
3896 4248 3.763360 CCAAATATTCAGGCAGGACAACA 59.237 43.478 0.00 0.00 0.00 3.33
3897 4249 4.380867 CCAAATATTCAGGCAGGACAACAC 60.381 45.833 0.00 0.00 0.00 3.32
3898 4250 2.489938 TATTCAGGCAGGACAACACC 57.510 50.000 0.00 0.00 0.00 4.16
3899 4251 0.478072 ATTCAGGCAGGACAACACCA 59.522 50.000 0.00 0.00 0.00 4.17
3900 4252 0.257328 TTCAGGCAGGACAACACCAA 59.743 50.000 0.00 0.00 0.00 3.67
3943 4295 2.409870 CCAGCAATTCCCGGTCAGC 61.410 63.158 0.00 0.00 0.00 4.26
3964 4316 2.076863 GCATCTTGAACTGTACGGCTT 58.923 47.619 0.23 0.00 0.00 4.35
4021 4373 4.095185 GTGTTACGGCCATTTATGCTACAA 59.905 41.667 2.24 0.00 0.00 2.41
4470 5137 5.920840 GGAGCTTTCCAAAGAAATGTGTTAC 59.079 40.000 3.11 0.00 41.12 2.50
4984 5662 4.834496 TCTCTTTTGGTTTGATGCAAGGAT 59.166 37.500 0.00 0.00 0.00 3.24
5081 5759 3.424703 TGATGGAAGGGAGCAAGAAAAG 58.575 45.455 0.00 0.00 0.00 2.27
5170 5848 1.640149 TGCCTCTCCCAAATCCAATGA 59.360 47.619 0.00 0.00 0.00 2.57
5481 6159 1.142688 AGTGGTGGCCTTCTTGGGAT 61.143 55.000 3.32 0.00 36.00 3.85
5988 6666 7.420002 GCACATTAATTGAGATTGCTGATGTA 58.580 34.615 0.00 0.00 0.00 2.29
6141 6819 4.708726 GCAATCTGCTTTGTTCTACCAT 57.291 40.909 0.00 0.00 40.96 3.55
6232 6918 9.976511 AATGTTTTATCATTCCATGCTTATCTG 57.023 29.630 0.00 0.00 33.43 2.90
6253 6939 4.641396 TGTAGGAACCACAACTTCATCTG 58.359 43.478 0.00 0.00 0.00 2.90
6313 7001 7.239166 TCTGAGAAACATCGCATTATTCTTC 57.761 36.000 0.00 0.00 30.89 2.87
6316 7004 6.595326 TGAGAAACATCGCATTATTCTTCAGT 59.405 34.615 0.00 0.00 30.89 3.41
6421 7109 8.837389 GTTTTCAGTTTCTAATCTTGTACAGGT 58.163 33.333 4.75 0.00 0.00 4.00
6513 7201 7.769044 TGGAAGCTATTGTTGAACCTACTAATC 59.231 37.037 0.00 0.00 0.00 1.75
6558 7246 5.302059 GCCCACTAGACAAGTAGACATGATA 59.698 44.000 0.00 0.00 35.76 2.15
6580 7268 1.964608 CTGGAATCCGAGCTGCTGGA 61.965 60.000 18.60 18.60 38.95 3.86
6584 7272 2.215191 ATCCGAGCTGCTGGATTCA 58.785 52.632 20.69 4.52 42.31 2.57
6589 7277 1.329906 CGAGCTGCTGGATTCATGAAC 59.670 52.381 11.07 4.95 0.00 3.18
6591 7279 0.248377 GCTGCTGGATTCATGAACGC 60.248 55.000 11.07 11.45 0.00 4.84
6600 7288 2.414058 TTCATGAACGCGTTTGCATT 57.586 40.000 27.32 1.13 42.97 3.56
6606 7294 1.452145 AACGCGTTTGCATTGGAGGT 61.452 50.000 20.79 0.00 42.97 3.85
6667 7355 1.300971 CTGCCATGTTGGGTGACTCG 61.301 60.000 0.00 0.00 38.19 4.18
6675 7363 4.452733 GGGTGACTCGCTTCCCCG 62.453 72.222 0.00 0.00 34.32 5.73
6737 7425 1.565288 TGCCTGGATCAATCACCATCA 59.435 47.619 0.00 0.00 35.54 3.07
6818 7506 6.925610 TGTCAATTGATACTTGATAGGTGC 57.074 37.500 12.12 0.00 35.26 5.01
6855 7543 8.665685 GTGTATAGTTTGTTTTGATCCTAGTGG 58.334 37.037 0.00 0.00 0.00 4.00
6861 7549 7.176690 AGTTTGTTTTGATCCTAGTGGTATTGG 59.823 37.037 0.00 0.00 34.23 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.875514 CCATTCATGACCTATGTGCCG 59.124 52.381 0.00 0.00 38.01 5.69
16 17 3.213206 TCCATTCATGACCTATGTGCC 57.787 47.619 0.00 0.00 38.01 5.01
137 142 2.189594 TGTGAATTCACCAGAGGCTG 57.810 50.000 30.66 0.00 45.88 4.85
181 186 1.611592 GCATTCAGTTTGTGCTGCGC 61.612 55.000 6.19 6.19 36.49 6.09
262 267 6.939163 GGTCCAGAATGCATCAAGTATAAGAT 59.061 38.462 0.00 0.00 31.97 2.40
330 335 2.143122 TGAAACAAGATCAGGCACGAC 58.857 47.619 0.00 0.00 0.00 4.34
337 342 7.294676 TGAACGACATATGAAACAAGATCAG 57.705 36.000 10.38 0.00 0.00 2.90
417 422 7.254863 CCAGTGTAACACAAACTAAAACCGTAT 60.255 37.037 0.00 0.00 41.43 3.06
446 451 3.089284 GGGTCTGTCCTTTTTATGGGTG 58.911 50.000 0.00 0.00 36.25 4.61
447 452 2.719705 TGGGTCTGTCCTTTTTATGGGT 59.280 45.455 0.00 0.00 36.25 4.51
448 453 3.245264 ACTGGGTCTGTCCTTTTTATGGG 60.245 47.826 0.00 0.00 36.25 4.00
449 454 3.758554 CACTGGGTCTGTCCTTTTTATGG 59.241 47.826 0.00 0.00 36.25 2.74
450 455 3.191371 GCACTGGGTCTGTCCTTTTTATG 59.809 47.826 0.00 0.00 36.25 1.90
451 456 3.181434 TGCACTGGGTCTGTCCTTTTTAT 60.181 43.478 0.00 0.00 36.25 1.40
452 457 2.173782 TGCACTGGGTCTGTCCTTTTTA 59.826 45.455 0.00 0.00 36.25 1.52
453 458 1.064017 TGCACTGGGTCTGTCCTTTTT 60.064 47.619 0.00 0.00 36.25 1.94
454 459 0.550914 TGCACTGGGTCTGTCCTTTT 59.449 50.000 0.00 0.00 36.25 2.27
455 460 0.773644 ATGCACTGGGTCTGTCCTTT 59.226 50.000 0.00 0.00 36.25 3.11
456 461 1.556911 CTATGCACTGGGTCTGTCCTT 59.443 52.381 0.00 0.00 36.25 3.36
457 462 1.198713 CTATGCACTGGGTCTGTCCT 58.801 55.000 0.00 0.00 36.25 3.85
458 463 1.195115 TCTATGCACTGGGTCTGTCC 58.805 55.000 0.00 0.00 0.00 4.02
459 464 2.898705 CTTCTATGCACTGGGTCTGTC 58.101 52.381 0.00 0.00 0.00 3.51
460 465 1.065854 GCTTCTATGCACTGGGTCTGT 60.066 52.381 0.00 0.00 0.00 3.41
461 466 1.209019 AGCTTCTATGCACTGGGTCTG 59.791 52.381 0.00 0.00 34.99 3.51
462 467 1.484240 GAGCTTCTATGCACTGGGTCT 59.516 52.381 0.00 0.00 34.99 3.85
463 468 1.474143 GGAGCTTCTATGCACTGGGTC 60.474 57.143 0.00 0.00 34.99 4.46
464 469 0.543749 GGAGCTTCTATGCACTGGGT 59.456 55.000 0.00 0.00 34.99 4.51
465 470 0.179034 GGGAGCTTCTATGCACTGGG 60.179 60.000 0.00 0.00 34.99 4.45
466 471 0.543277 TGGGAGCTTCTATGCACTGG 59.457 55.000 0.00 0.00 34.99 4.00
467 472 1.065926 TGTGGGAGCTTCTATGCACTG 60.066 52.381 0.00 0.00 34.99 3.66
468 473 1.065854 GTGTGGGAGCTTCTATGCACT 60.066 52.381 0.00 0.00 34.99 4.40
469 474 1.339055 TGTGTGGGAGCTTCTATGCAC 60.339 52.381 0.00 0.00 34.99 4.57
470 475 0.983467 TGTGTGGGAGCTTCTATGCA 59.017 50.000 0.00 0.00 34.99 3.96
471 476 2.012673 CTTGTGTGGGAGCTTCTATGC 58.987 52.381 0.00 0.00 0.00 3.14
472 477 2.026822 ACCTTGTGTGGGAGCTTCTATG 60.027 50.000 0.00 0.00 0.00 2.23
473 478 2.026822 CACCTTGTGTGGGAGCTTCTAT 60.027 50.000 0.00 0.00 41.52 1.98
474 479 1.347707 CACCTTGTGTGGGAGCTTCTA 59.652 52.381 0.00 0.00 41.52 2.10
475 480 0.109342 CACCTTGTGTGGGAGCTTCT 59.891 55.000 0.00 0.00 41.52 2.85
476 481 2.633860 CACCTTGTGTGGGAGCTTC 58.366 57.895 0.00 0.00 41.52 3.86
477 482 4.907457 CACCTTGTGTGGGAGCTT 57.093 55.556 0.00 0.00 41.52 3.74
484 489 1.228245 CCAGACCCCACCTTGTGTG 60.228 63.158 0.00 0.00 45.01 3.82
485 490 2.460853 CCCAGACCCCACCTTGTGT 61.461 63.158 0.00 0.00 0.00 3.72
486 491 2.436109 CCCAGACCCCACCTTGTG 59.564 66.667 0.00 0.00 0.00 3.33
487 492 2.858974 CCCCAGACCCCACCTTGT 60.859 66.667 0.00 0.00 0.00 3.16
488 493 2.531685 TCCCCAGACCCCACCTTG 60.532 66.667 0.00 0.00 0.00 3.61
489 494 2.204151 CTCCCCAGACCCCACCTT 60.204 66.667 0.00 0.00 0.00 3.50
490 495 4.354943 CCTCCCCAGACCCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
492 497 3.660092 ATCCCTCCCCAGACCCCAC 62.660 68.421 0.00 0.00 0.00 4.61
493 498 1.542093 TAATCCCTCCCCAGACCCCA 61.542 60.000 0.00 0.00 0.00 4.96
494 499 0.103876 ATAATCCCTCCCCAGACCCC 60.104 60.000 0.00 0.00 0.00 4.95
495 500 2.552367 CTATAATCCCTCCCCAGACCC 58.448 57.143 0.00 0.00 0.00 4.46
496 501 2.113777 TCCTATAATCCCTCCCCAGACC 59.886 54.545 0.00 0.00 0.00 3.85
497 502 3.562108 TCCTATAATCCCTCCCCAGAC 57.438 52.381 0.00 0.00 0.00 3.51
498 503 3.441054 GGTTCCTATAATCCCTCCCCAGA 60.441 52.174 0.00 0.00 0.00 3.86
499 504 2.913617 GGTTCCTATAATCCCTCCCCAG 59.086 54.545 0.00 0.00 0.00 4.45
500 505 2.531463 AGGTTCCTATAATCCCTCCCCA 59.469 50.000 0.00 0.00 0.00 4.96
501 506 3.293215 AGGTTCCTATAATCCCTCCCC 57.707 52.381 0.00 0.00 0.00 4.81
502 507 5.024785 GACTAGGTTCCTATAATCCCTCCC 58.975 50.000 0.00 0.00 0.00 4.30
503 508 5.906254 AGACTAGGTTCCTATAATCCCTCC 58.094 45.833 0.00 0.00 0.00 4.30
504 509 7.396907 GGTAAGACTAGGTTCCTATAATCCCTC 59.603 44.444 0.00 0.00 0.00 4.30
505 510 7.247500 GGTAAGACTAGGTTCCTATAATCCCT 58.753 42.308 0.00 0.00 0.00 4.20
506 511 6.440010 GGGTAAGACTAGGTTCCTATAATCCC 59.560 46.154 0.00 4.36 0.00 3.85
507 512 6.440010 GGGGTAAGACTAGGTTCCTATAATCC 59.560 46.154 0.00 0.00 0.00 3.01
508 513 7.178805 CAGGGGTAAGACTAGGTTCCTATAATC 59.821 44.444 0.00 0.00 0.00 1.75
509 514 7.017531 CAGGGGTAAGACTAGGTTCCTATAAT 58.982 42.308 0.00 0.00 0.00 1.28
510 515 6.379579 CAGGGGTAAGACTAGGTTCCTATAA 58.620 44.000 0.00 0.00 0.00 0.98
511 516 5.694949 GCAGGGGTAAGACTAGGTTCCTATA 60.695 48.000 0.00 0.00 0.00 1.31
512 517 4.817286 CAGGGGTAAGACTAGGTTCCTAT 58.183 47.826 0.00 0.00 0.00 2.57
513 518 3.629282 GCAGGGGTAAGACTAGGTTCCTA 60.629 52.174 0.00 0.00 0.00 2.94
514 519 2.893153 GCAGGGGTAAGACTAGGTTCCT 60.893 54.545 0.00 0.00 0.00 3.36
515 520 1.485480 GCAGGGGTAAGACTAGGTTCC 59.515 57.143 0.00 0.00 0.00 3.62
516 521 2.185387 TGCAGGGGTAAGACTAGGTTC 58.815 52.381 0.00 0.00 0.00 3.62
517 522 2.337359 TGCAGGGGTAAGACTAGGTT 57.663 50.000 0.00 0.00 0.00 3.50
518 523 2.337359 TTGCAGGGGTAAGACTAGGT 57.663 50.000 0.00 0.00 0.00 3.08
519 524 2.572104 ACTTTGCAGGGGTAAGACTAGG 59.428 50.000 2.16 0.00 0.00 3.02
520 525 3.600388 CACTTTGCAGGGGTAAGACTAG 58.400 50.000 2.16 0.00 0.00 2.57
521 526 2.290071 GCACTTTGCAGGGGTAAGACTA 60.290 50.000 2.16 0.00 44.26 2.59
522 527 1.545651 GCACTTTGCAGGGGTAAGACT 60.546 52.381 2.16 0.00 44.26 3.24
523 528 0.881796 GCACTTTGCAGGGGTAAGAC 59.118 55.000 2.16 0.00 44.26 3.01
524 529 3.339547 GCACTTTGCAGGGGTAAGA 57.660 52.632 2.16 0.00 44.26 2.10
534 539 1.402456 CCTCTCTGCATTGCACTTTGC 60.402 52.381 7.38 8.20 45.29 3.68
535 540 1.402456 GCCTCTCTGCATTGCACTTTG 60.402 52.381 7.38 0.00 33.79 2.77
536 541 0.886563 GCCTCTCTGCATTGCACTTT 59.113 50.000 7.38 0.00 33.79 2.66
537 542 0.037877 AGCCTCTCTGCATTGCACTT 59.962 50.000 7.38 0.00 33.79 3.16
538 543 0.677098 CAGCCTCTCTGCATTGCACT 60.677 55.000 7.38 0.00 35.78 4.40
539 544 1.654954 CCAGCCTCTCTGCATTGCAC 61.655 60.000 7.38 0.00 41.50 4.57
540 545 1.378119 CCAGCCTCTCTGCATTGCA 60.378 57.895 11.50 11.50 41.50 4.08
541 546 0.964358 AACCAGCCTCTCTGCATTGC 60.964 55.000 0.46 0.46 41.50 3.56
542 547 1.093159 GAACCAGCCTCTCTGCATTG 58.907 55.000 0.00 0.00 41.50 2.82
543 548 0.392193 CGAACCAGCCTCTCTGCATT 60.392 55.000 0.00 0.00 41.50 3.56
544 549 1.220206 CGAACCAGCCTCTCTGCAT 59.780 57.895 0.00 0.00 41.50 3.96
545 550 1.471829 TTCGAACCAGCCTCTCTGCA 61.472 55.000 0.00 0.00 41.50 4.41
546 551 1.016653 GTTCGAACCAGCCTCTCTGC 61.017 60.000 17.68 0.00 41.50 4.26
547 552 3.129792 GTTCGAACCAGCCTCTCTG 57.870 57.895 17.68 0.00 42.49 3.35
558 563 0.685660 AAGAGGTCCTGGGTTCGAAC 59.314 55.000 20.14 20.14 0.00 3.95
559 564 0.685097 CAAGAGGTCCTGGGTTCGAA 59.315 55.000 0.00 0.00 0.00 3.71
560 565 1.192146 CCAAGAGGTCCTGGGTTCGA 61.192 60.000 0.00 0.00 30.82 3.71
561 566 1.296715 CCAAGAGGTCCTGGGTTCG 59.703 63.158 0.00 0.00 30.82 3.95
562 567 1.002011 GCCAAGAGGTCCTGGGTTC 60.002 63.158 0.00 0.00 38.32 3.62
563 568 1.774217 TGCCAAGAGGTCCTGGGTT 60.774 57.895 0.00 0.00 38.32 4.11
564 569 2.121963 TGCCAAGAGGTCCTGGGT 60.122 61.111 0.00 0.00 38.32 4.51
565 570 2.067932 TTGTGCCAAGAGGTCCTGGG 62.068 60.000 0.00 0.00 39.14 4.45
566 571 0.607489 CTTGTGCCAAGAGGTCCTGG 60.607 60.000 0.00 0.00 37.19 4.45
567 572 0.109342 ACTTGTGCCAAGAGGTCCTG 59.891 55.000 18.22 0.00 37.19 3.86
568 573 0.109342 CACTTGTGCCAAGAGGTCCT 59.891 55.000 18.22 0.00 37.19 3.85
569 574 0.890996 CCACTTGTGCCAAGAGGTCC 60.891 60.000 18.22 0.00 37.19 4.46
570 575 0.890996 CCCACTTGTGCCAAGAGGTC 60.891 60.000 21.11 0.00 37.19 3.85
571 576 1.151450 CCCACTTGTGCCAAGAGGT 59.849 57.895 21.11 2.99 37.19 3.85
572 577 1.604593 CCCCACTTGTGCCAAGAGG 60.605 63.158 18.22 18.17 38.23 3.69
573 578 0.607489 CTCCCCACTTGTGCCAAGAG 60.607 60.000 18.22 11.85 0.00 2.85
574 579 1.455849 CTCCCCACTTGTGCCAAGA 59.544 57.895 18.22 0.00 0.00 3.02
575 580 1.604593 CCTCCCCACTTGTGCCAAG 60.605 63.158 11.87 11.87 0.00 3.61
576 581 2.081787 TCCTCCCCACTTGTGCCAA 61.082 57.895 0.00 0.00 0.00 4.52
577 582 2.449518 TCCTCCCCACTTGTGCCA 60.450 61.111 0.00 0.00 0.00 4.92
578 583 2.034221 GTCCTCCCCACTTGTGCC 59.966 66.667 0.00 0.00 0.00 5.01
579 584 0.606673 GAAGTCCTCCCCACTTGTGC 60.607 60.000 0.00 0.00 34.10 4.57
580 585 0.764890 TGAAGTCCTCCCCACTTGTG 59.235 55.000 0.00 0.00 34.10 3.33
581 586 0.765510 GTGAAGTCCTCCCCACTTGT 59.234 55.000 0.00 0.00 34.10 3.16
582 587 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.000 0.00 0.00 34.10 3.16
583 588 0.401395 TGGTGAAGTCCTCCCCACTT 60.401 55.000 0.00 0.00 36.77 3.16
584 589 1.128188 GTGGTGAAGTCCTCCCCACT 61.128 60.000 0.00 0.00 41.83 4.00
585 590 1.128188 AGTGGTGAAGTCCTCCCCAC 61.128 60.000 0.00 0.00 44.69 4.61
586 591 1.127567 CAGTGGTGAAGTCCTCCCCA 61.128 60.000 0.00 0.00 0.00 4.96
587 592 1.679898 CAGTGGTGAAGTCCTCCCC 59.320 63.158 0.00 0.00 0.00 4.81
588 593 1.003233 GCAGTGGTGAAGTCCTCCC 60.003 63.158 0.00 0.00 0.00 4.30
589 594 1.374758 CGCAGTGGTGAAGTCCTCC 60.375 63.158 0.00 0.00 0.00 4.30
590 595 2.029844 GCGCAGTGGTGAAGTCCTC 61.030 63.158 0.30 0.00 0.00 3.71
591 596 2.031163 GCGCAGTGGTGAAGTCCT 59.969 61.111 0.30 0.00 0.00 3.85
592 597 3.050275 GGCGCAGTGGTGAAGTCC 61.050 66.667 10.83 0.00 0.00 3.85
593 598 2.280797 TGGCGCAGTGGTGAAGTC 60.281 61.111 10.83 0.00 0.00 3.01
594 599 2.281070 CTGGCGCAGTGGTGAAGT 60.281 61.111 10.83 0.00 0.00 3.01
595 600 3.052082 CCTGGCGCAGTGGTGAAG 61.052 66.667 10.83 0.00 0.00 3.02
608 613 4.729918 GTGTGAGGGCAGGCCTGG 62.730 72.222 33.46 15.81 36.10 4.45
609 614 3.644606 AGTGTGAGGGCAGGCCTG 61.645 66.667 29.34 29.34 36.10 4.85
610 615 3.644606 CAGTGTGAGGGCAGGCCT 61.645 66.667 17.36 17.36 36.10 5.19
611 616 4.729918 CCAGTGTGAGGGCAGGCC 62.730 72.222 4.33 4.33 0.00 5.19
612 617 3.909086 GACCAGTGTGAGGGCAGGC 62.909 68.421 0.00 0.00 33.02 4.85
613 618 2.348998 GACCAGTGTGAGGGCAGG 59.651 66.667 0.00 0.00 33.02 4.85
614 619 2.348998 GGACCAGTGTGAGGGCAG 59.651 66.667 0.00 0.00 35.15 4.85
615 620 2.447572 TGGACCAGTGTGAGGGCA 60.448 61.111 0.00 0.00 35.15 5.36
616 621 2.032681 GTGGACCAGTGTGAGGGC 59.967 66.667 0.00 0.00 0.00 5.19
617 622 2.750350 GGTGGACCAGTGTGAGGG 59.250 66.667 0.00 0.00 35.64 4.30
618 623 2.146724 TGGGTGGACCAGTGTGAGG 61.147 63.158 0.00 0.00 46.80 3.86
619 624 3.562250 TGGGTGGACCAGTGTGAG 58.438 61.111 0.00 0.00 46.80 3.51
722 727 1.806758 GGCGGTGCATGCATCAAAC 60.807 57.895 29.40 17.80 0.00 2.93
785 792 2.705127 ACAGGTTTGCCCATTTTGTCAT 59.295 40.909 0.00 0.00 34.66 3.06
908 923 6.268847 ACTTAAGAGTGAACATTCAGAGGTCT 59.731 38.462 10.09 0.00 37.98 3.85
1097 1125 5.619981 GCGCAACCAAATTCAATTCTAGAGT 60.620 40.000 0.30 0.00 0.00 3.24
1119 1147 6.516478 TTGAAATCTCTATCGAAATCAGCG 57.484 37.500 0.00 0.00 0.00 5.18
1156 1189 0.530431 GTGCCACAAGCCCAAAACAG 60.530 55.000 0.00 0.00 42.71 3.16
1701 1758 4.623932 TGTGAGAAGTAGTTCCAGCAAT 57.376 40.909 6.68 0.00 32.48 3.56
1813 1870 2.289631 CCCAGTGTCTGCAGTTCACATA 60.290 50.000 30.10 6.31 34.94 2.29
1841 1898 2.699768 GCAATTACCCGCTGCAGCA 61.700 57.895 36.03 18.59 42.21 4.41
1871 1928 0.178992 CAACACTCTGGGGGAAGCAA 60.179 55.000 0.00 0.00 0.00 3.91
2072 2210 7.054491 TCATAATAGAGCTGCTCAACACATA 57.946 36.000 29.49 13.54 32.06 2.29
2076 2214 7.278135 AGAAATCATAATAGAGCTGCTCAACA 58.722 34.615 29.49 15.44 32.06 3.33
2090 2228 8.854117 GCACCCATTAAGAAGAGAAATCATAAT 58.146 33.333 0.00 0.00 0.00 1.28
2464 2604 9.871299 GTAAGTGAAAGTCAAAAGAAGAATCTC 57.129 33.333 0.00 0.00 33.77 2.75
2510 2654 5.011586 ACTAGTCTGGTACCTGAAGTTCTC 58.988 45.833 21.76 9.44 0.00 2.87
2699 2847 9.030452 GGGACATAACCAATGGCATAAATAATA 57.970 33.333 0.00 0.00 46.56 0.98
3855 4198 4.974645 TGGATATATGGGACCTTGTGTC 57.025 45.455 0.00 0.00 43.67 3.67
3856 4199 5.725551 TTTGGATATATGGGACCTTGTGT 57.274 39.130 0.00 0.00 0.00 3.72
3878 4230 2.308570 TGGTGTTGTCCTGCCTGAATAT 59.691 45.455 0.00 0.00 0.00 1.28
3879 4231 1.702401 TGGTGTTGTCCTGCCTGAATA 59.298 47.619 0.00 0.00 0.00 1.75
3880 4232 0.478072 TGGTGTTGTCCTGCCTGAAT 59.522 50.000 0.00 0.00 0.00 2.57
3881 4233 0.257328 TTGGTGTTGTCCTGCCTGAA 59.743 50.000 0.00 0.00 0.00 3.02
3882 4234 0.179020 CTTGGTGTTGTCCTGCCTGA 60.179 55.000 0.00 0.00 0.00 3.86
3883 4235 0.179020 TCTTGGTGTTGTCCTGCCTG 60.179 55.000 0.00 0.00 0.00 4.85
3884 4236 0.109342 CTCTTGGTGTTGTCCTGCCT 59.891 55.000 0.00 0.00 0.00 4.75
3885 4237 0.108585 TCTCTTGGTGTTGTCCTGCC 59.891 55.000 0.00 0.00 0.00 4.85
3886 4238 1.202698 ACTCTCTTGGTGTTGTCCTGC 60.203 52.381 0.00 0.00 0.00 4.85
3887 4239 2.487934 CACTCTCTTGGTGTTGTCCTG 58.512 52.381 0.00 0.00 0.00 3.86
3888 4240 1.202698 GCACTCTCTTGGTGTTGTCCT 60.203 52.381 0.00 0.00 37.07 3.85
3889 4241 1.230324 GCACTCTCTTGGTGTTGTCC 58.770 55.000 0.00 0.00 37.07 4.02
3890 4242 1.230324 GGCACTCTCTTGGTGTTGTC 58.770 55.000 0.00 0.00 37.07 3.18
3891 4243 0.179018 GGGCACTCTCTTGGTGTTGT 60.179 55.000 0.00 0.00 37.07 3.32
3892 4244 0.109342 AGGGCACTCTCTTGGTGTTG 59.891 55.000 0.00 0.00 37.07 3.33
3893 4245 0.109342 CAGGGCACTCTCTTGGTGTT 59.891 55.000 0.00 0.00 37.07 3.32
3894 4246 1.056700 ACAGGGCACTCTCTTGGTGT 61.057 55.000 0.00 0.00 37.07 4.16
3895 4247 0.976641 TACAGGGCACTCTCTTGGTG 59.023 55.000 0.00 0.00 37.70 4.17
3896 4248 1.556911 CATACAGGGCACTCTCTTGGT 59.443 52.381 0.00 0.00 0.00 3.67
3897 4249 1.556911 ACATACAGGGCACTCTCTTGG 59.443 52.381 0.00 0.00 0.00 3.61
3898 4250 2.499289 AGACATACAGGGCACTCTCTTG 59.501 50.000 0.00 0.00 0.00 3.02
3899 4251 2.826488 AGACATACAGGGCACTCTCTT 58.174 47.619 0.00 0.00 0.00 2.85
3900 4252 2.499289 CAAGACATACAGGGCACTCTCT 59.501 50.000 0.00 0.00 0.00 3.10
3937 4289 0.445436 CAGTTCAAGATGCGCTGACC 59.555 55.000 9.73 0.00 0.00 4.02
3943 4295 0.370273 GCCGTACAGTTCAAGATGCG 59.630 55.000 0.00 0.00 0.00 4.73
4470 5137 9.011095 ACAGCTAATCAATGATCAGGAAATATG 57.989 33.333 0.09 2.37 0.00 1.78
4953 5631 5.576447 TCAAACCAAAAGAGAGAAACCAC 57.424 39.130 0.00 0.00 0.00 4.16
4970 5648 3.940209 TCCAACATCCTTGCATCAAAC 57.060 42.857 0.00 0.00 0.00 2.93
4984 5662 7.445121 TGCCAAATTATACACAAATTCCAACA 58.555 30.769 0.00 0.00 0.00 3.33
5081 5759 2.280186 CTCCATACCGCTTCCGCC 60.280 66.667 0.00 0.00 0.00 6.13
5170 5848 7.671398 CCTATCATTAGGCAGGTTAAATCCAAT 59.329 37.037 0.00 0.00 38.75 3.16
5481 6159 2.224523 ACAATTGAGTTGCCTTCTCGGA 60.225 45.455 13.59 0.00 41.69 4.55
5988 6666 8.821894 GCAATTCTATCGTCAGTAAGAGATTTT 58.178 33.333 0.00 0.00 0.00 1.82
6099 6777 2.989639 CCCTCCAAGCCATCACGA 59.010 61.111 0.00 0.00 0.00 4.35
6141 6819 4.183865 CAGCATCCACGATTCTGAAGTAA 58.816 43.478 0.00 0.00 35.84 2.24
6220 6906 4.130118 GTGGTTCCTACAGATAAGCATGG 58.870 47.826 0.00 0.00 33.67 3.66
6232 6918 4.452455 CACAGATGAAGTTGTGGTTCCTAC 59.548 45.833 0.00 0.00 40.69 3.18
6253 6939 5.802064 TCACATCAACTCAACGTTTAACAC 58.198 37.500 0.00 0.00 32.27 3.32
6421 7109 8.030913 AGGAGGAAAACTGAACTTACTTTCTA 57.969 34.615 0.00 0.00 0.00 2.10
6513 7201 3.734902 GCAAAGTTTCCACTGTTGACCTG 60.735 47.826 0.00 0.00 31.60 4.00
6558 7246 0.975040 AGCAGCTCGGATTCCAGAGT 60.975 55.000 19.05 8.80 36.88 3.24
6580 7268 2.634982 ATGCAAACGCGTTCATGAAT 57.365 40.000 26.77 17.82 0.00 2.57
6584 7272 0.595588 TCCAATGCAAACGCGTTCAT 59.404 45.000 26.77 21.44 36.47 2.57
6589 7277 1.442520 CACCTCCAATGCAAACGCG 60.443 57.895 3.53 3.53 0.00 6.01
6591 7279 4.557942 GCACCTCCAATGCAAACG 57.442 55.556 0.00 0.00 42.88 3.60
6600 7288 3.889525 ATCCCCCACTGCACCTCCA 62.890 63.158 0.00 0.00 0.00 3.86
6606 7294 0.918983 CCTCTAAATCCCCCACTGCA 59.081 55.000 0.00 0.00 0.00 4.41
6675 7363 0.890683 CAGGATTTGCTTCCACCCAC 59.109 55.000 4.16 0.00 38.32 4.61
6700 7388 0.531974 GCAACACACTCCCTTCGACA 60.532 55.000 0.00 0.00 0.00 4.35
6737 7425 6.209391 AGCAAGCAGAACAAACCTAACATAAT 59.791 34.615 0.00 0.00 0.00 1.28
6818 7506 6.636562 ACAAACTATACACCGAGGATAGAG 57.363 41.667 12.34 0.00 0.00 2.43
6828 7516 8.665685 CACTAGGATCAAAACAAACTATACACC 58.334 37.037 0.00 0.00 0.00 4.16
6855 7543 7.773690 ACCTATCAAGTATCAACCAACCAATAC 59.226 37.037 0.00 0.00 0.00 1.89
6858 7546 5.943416 CACCTATCAAGTATCAACCAACCAA 59.057 40.000 0.00 0.00 0.00 3.67
6861 7549 7.448748 AAACACCTATCAAGTATCAACCAAC 57.551 36.000 0.00 0.00 0.00 3.77
7122 7810 9.829507 ATAAGAAAAATGACTAGACATCCAGAG 57.170 33.333 8.16 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.