Multiple sequence alignment - TraesCS7D01G217300

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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 TraesCS7D01G217300 chr7D 100.000 3646 0 0 1 3646 177875607 177879252 0.000000e+00 6734.0
1 TraesCS7D01G217300 chr7D 86.639 479 37 12 3122 3587 395971070 395970606 4.200000e-139 505.0
2 TraesCS7D01G217300 chr7A 94.384 2208 86 10 581 2754 181695448 181697651 0.000000e+00 3356.0
3 TraesCS7D01G217300 chr7A 90.355 394 19 12 3 394 181695084 181695460 1.950000e-137 499.0
4 TraesCS7D01G217300 chr7A 97.765 179 3 1 396 573 158648151 158647973 1.270000e-79 307.0
5 TraesCS7D01G217300 chr7B 94.298 1666 51 9 1355 3017 143810451 143812075 0.000000e+00 2510.0
6 TraesCS7D01G217300 chr7B 94.148 769 27 4 607 1359 143807868 143808634 0.000000e+00 1155.0
7 TraesCS7D01G217300 chr7B 94.097 288 12 3 99 385 143807592 143807875 2.010000e-117 433.0
8 TraesCS7D01G217300 chr7B 95.000 180 9 0 394 573 402820543 402820722 2.140000e-72 283.0
9 TraesCS7D01G217300 chr7B 94.488 127 6 1 1 126 143807443 143807569 1.030000e-45 195.0
10 TraesCS7D01G217300 chr2A 84.324 925 117 19 1001 1920 682635589 682634688 0.000000e+00 880.0
11 TraesCS7D01G217300 chr2A 80.896 937 155 12 1002 1920 21275570 21274640 0.000000e+00 717.0
12 TraesCS7D01G217300 chr2A 86.470 643 62 10 1969 2598 682634579 682633949 0.000000e+00 682.0
13 TraesCS7D01G217300 chr2A 83.648 636 102 2 1990 2624 21274452 21273818 6.740000e-167 597.0
14 TraesCS7D01G217300 chr2A 83.630 617 92 4 1990 2598 9388819 9389434 4.080000e-159 571.0
15 TraesCS7D01G217300 chr2A 83.468 617 93 4 1990 2598 9841595 9842210 1.900000e-157 566.0
16 TraesCS7D01G217300 chr2A 81.426 673 115 8 1098 1768 9838779 9839443 3.200000e-150 542.0
17 TraesCS7D01G217300 chr2A 88.636 88 10 0 1065 1152 9137622 9137535 1.380000e-19 108.0
18 TraesCS7D01G217300 chr2B 76.407 1564 294 52 1072 2598 4473065 4471540 0.000000e+00 774.0
19 TraesCS7D01G217300 chr2B 97.753 178 2 1 396 573 474892214 474892039 4.570000e-79 305.0
20 TraesCS7D01G217300 chr2B 76.791 349 73 5 1072 1419 7643188 7643529 4.810000e-44 189.0
21 TraesCS7D01G217300 chr2D 80.711 928 173 4 993 1920 9884589 9883668 0.000000e+00 717.0
22 TraesCS7D01G217300 chr2D 87.751 449 37 10 3122 3560 488224741 488225181 3.250000e-140 508.0
23 TraesCS7D01G217300 chr2D 77.778 351 66 9 1072 1419 3084632 3084291 4.770000e-49 206.0
24 TraesCS7D01G217300 chr2D 95.122 41 2 0 1644 1684 19637072 19637112 8.450000e-07 65.8
25 TraesCS7D01G217300 chr3A 79.676 925 137 28 1000 1909 46584089 46583201 1.440000e-173 619.0
26 TraesCS7D01G217300 chr3A 86.221 479 43 10 3100 3568 440610328 440610793 7.030000e-137 497.0
27 TraesCS7D01G217300 chr3A 85.924 476 41 11 3122 3587 617007209 617006750 5.470000e-133 484.0
28 TraesCS7D01G217300 chr5A 87.047 579 28 14 3100 3646 472912503 472911940 8.660000e-171 610.0
29 TraesCS7D01G217300 chr5A 88.063 444 39 12 3122 3562 43392246 43391814 6.980000e-142 514.0
30 TraesCS7D01G217300 chr5A 87.204 422 44 9 3122 3538 415160815 415161231 4.260000e-129 472.0
31 TraesCS7D01G217300 chr5A 97.253 182 4 1 392 573 312255817 312255637 1.270000e-79 307.0
32 TraesCS7D01G217300 chr5A 100.000 33 0 0 3100 3132 415160774 415160806 1.090000e-05 62.1
33 TraesCS7D01G217300 chr3D 87.164 483 46 13 3100 3573 6515452 6514977 5.360000e-148 534.0
34 TraesCS7D01G217300 chr3D 96.023 176 7 0 398 573 374393444 374393619 1.660000e-73 287.0
35 TraesCS7D01G217300 chr1B 87.225 454 46 10 3122 3569 369229697 369229250 1.170000e-139 507.0
36 TraesCS7D01G217300 chr1B 100.000 33 0 0 3100 3132 369229738 369229706 1.090000e-05 62.1
37 TraesCS7D01G217300 chr6D 85.954 477 36 15 3122 3587 75024854 75024398 7.080000e-132 481.0
38 TraesCS7D01G217300 chr6D 100.000 33 0 0 3100 3132 75024895 75024863 1.090000e-05 62.1
39 TraesCS7D01G217300 chr6B 87.500 408 38 6 3140 3537 135412160 135412564 3.320000e-125 459.0
40 TraesCS7D01G217300 chr6B 97.714 175 3 1 399 573 438406041 438405868 2.130000e-77 300.0
41 TraesCS7D01G217300 chr6B 96.067 178 6 1 396 573 229137191 229137367 4.610000e-74 289.0
42 TraesCS7D01G217300 chr4D 98.876 178 2 0 396 573 365176340 365176163 5.880000e-83 318.0
43 TraesCS7D01G217300 chr1A 97.207 179 3 2 396 573 292177147 292176970 5.920000e-78 302.0
44 TraesCS7D01G217300 chr5B 97.468 79 2 0 3122 3200 230884254 230884332 6.350000e-28 135.0
45 TraesCS7D01G217300 chr1D 97.222 36 1 0 3095 3130 397392168 397392203 1.090000e-05 62.1


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 TraesCS7D01G217300 chr7D 177875607 177879252 3645 False 6734.00 6734 100.00000 1 3646 1 chr7D.!!$F1 3645
1 TraesCS7D01G217300 chr7A 181695084 181697651 2567 False 1927.50 3356 92.36950 3 2754 2 chr7A.!!$F1 2751
2 TraesCS7D01G217300 chr7B 143807443 143812075 4632 False 1073.25 2510 94.25775 1 3017 4 chr7B.!!$F2 3016
3 TraesCS7D01G217300 chr2A 682633949 682635589 1640 True 781.00 880 85.39700 1001 2598 2 chr2A.!!$R3 1597
4 TraesCS7D01G217300 chr2A 21273818 21275570 1752 True 657.00 717 82.27200 1002 2624 2 chr2A.!!$R2 1622
5 TraesCS7D01G217300 chr2A 9388819 9389434 615 False 571.00 571 83.63000 1990 2598 1 chr2A.!!$F1 608
6 TraesCS7D01G217300 chr2A 9838779 9842210 3431 False 554.00 566 82.44700 1098 2598 2 chr2A.!!$F2 1500
7 TraesCS7D01G217300 chr2B 4471540 4473065 1525 True 774.00 774 76.40700 1072 2598 1 chr2B.!!$R1 1526
8 TraesCS7D01G217300 chr2D 9883668 9884589 921 True 717.00 717 80.71100 993 1920 1 chr2D.!!$R2 927
9 TraesCS7D01G217300 chr3A 46583201 46584089 888 True 619.00 619 79.67600 1000 1909 1 chr3A.!!$R1 909
10 TraesCS7D01G217300 chr5A 472911940 472912503 563 True 610.00 610 87.04700 3100 3646 1 chr5A.!!$R3 546

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
469 523 0.108804 TTTTAGAGTCGAGGCCAGCG 60.109 55.000 5.01 8.88 0.00 5.18 F
487 541 0.174845 CGGCCGAGTTACAATCCTCA 59.825 55.000 24.07 0.00 0.00 3.86 F
503 557 0.179137 CTCACTCTCGCGGCATTACA 60.179 55.000 6.13 0.00 0.00 2.41 F
504 558 0.459899 TCACTCTCGCGGCATTACAT 59.540 50.000 6.13 0.00 0.00 2.29 F
526 580 1.066502 ACACAAATATTTTGCCCCGGC 60.067 47.619 0.00 0.00 42.35 6.13 F
2384 6272 1.000607 GTGAGCGTGGAGTACAACTCA 60.001 52.381 9.15 5.42 46.79 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 3742 0.456628 GGTCCTCGTTGTCTCTAGCC 59.543 60.000 0.00 0.00 0.00 3.93 R
2031 5904 0.925558 TCTGCCATGGCCCATTCTAA 59.074 50.000 33.44 11.64 41.09 2.10 R
2339 6215 1.908483 GAACCTCTCCGGCCTGAAT 59.092 57.895 0.00 0.00 35.61 2.57 R
2384 6272 3.925630 CTCCATGTGCGGCCCTTGT 62.926 63.158 0.00 0.00 0.00 3.16 R
2632 6527 9.219603 CTGTGAATAATTTCTAGGACAGTTCAA 57.780 33.333 0.00 0.00 31.99 2.69 R
3288 7192 2.811431 TGTGCTGTAGAAAATCGGTTGG 59.189 45.455 0.00 0.00 0.00 3.77 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
61 62 3.365265 GTTCAGCCCCCGCACAAG 61.365 66.667 0.00 0.00 37.52 3.16
168 220 0.311165 CCCACCAGTCGCTATAGACG 59.689 60.000 3.21 7.07 45.26 4.18
172 224 1.306148 CCAGTCGCTATAGACGTGGA 58.694 55.000 3.21 0.00 45.26 4.02
173 225 1.002684 CCAGTCGCTATAGACGTGGAC 60.003 57.143 3.21 2.54 45.26 4.02
174 226 0.935898 AGTCGCTATAGACGTGGACG 59.064 55.000 3.21 0.00 45.26 4.79
175 227 0.656786 GTCGCTATAGACGTGGACGC 60.657 60.000 3.21 0.00 44.43 5.19
215 268 2.783135 TCGGACGGTTACTAGTCTGTT 58.217 47.619 0.00 0.00 42.62 3.16
216 269 2.485426 TCGGACGGTTACTAGTCTGTTG 59.515 50.000 0.00 0.00 42.62 3.33
217 270 2.227388 CGGACGGTTACTAGTCTGTTGT 59.773 50.000 0.00 0.00 38.55 3.32
394 448 1.162698 CAGTGCACCAACTCCATCTG 58.837 55.000 14.63 0.00 0.00 2.90
395 449 0.767375 AGTGCACCAACTCCATCTGT 59.233 50.000 14.63 0.00 0.00 3.41
396 450 1.143684 AGTGCACCAACTCCATCTGTT 59.856 47.619 14.63 0.00 0.00 3.16
397 451 1.956477 GTGCACCAACTCCATCTGTTT 59.044 47.619 5.22 0.00 0.00 2.83
398 452 2.362077 GTGCACCAACTCCATCTGTTTT 59.638 45.455 5.22 0.00 0.00 2.43
399 453 3.030291 TGCACCAACTCCATCTGTTTTT 58.970 40.909 0.00 0.00 0.00 1.94
425 479 6.415798 TTTAAAACAAGGCAAAAGACTTGC 57.584 33.333 10.80 0.78 46.03 4.01
435 489 5.678132 GCAAAAGACTTGCCATTTTCATT 57.322 34.783 0.00 0.00 39.38 2.57
436 490 5.445845 GCAAAAGACTTGCCATTTTCATTG 58.554 37.500 0.00 0.00 39.38 2.82
437 491 5.236911 GCAAAAGACTTGCCATTTTCATTGA 59.763 36.000 0.00 0.00 39.38 2.57
438 492 6.238429 GCAAAAGACTTGCCATTTTCATTGAA 60.238 34.615 0.00 0.00 39.38 2.69
439 493 7.520937 GCAAAAGACTTGCCATTTTCATTGAAT 60.521 33.333 0.00 0.00 39.38 2.57
440 494 8.991026 CAAAAGACTTGCCATTTTCATTGAATA 58.009 29.630 0.00 0.00 0.00 1.75
441 495 9.558396 AAAAGACTTGCCATTTTCATTGAATAA 57.442 25.926 0.00 0.00 0.00 1.40
442 496 8.767478 AAGACTTGCCATTTTCATTGAATAAG 57.233 30.769 0.00 2.37 0.00 1.73
443 497 8.125978 AGACTTGCCATTTTCATTGAATAAGA 57.874 30.769 0.00 0.00 0.00 2.10
444 498 8.587608 AGACTTGCCATTTTCATTGAATAAGAA 58.412 29.630 0.00 0.00 0.00 2.52
445 499 8.767478 ACTTGCCATTTTCATTGAATAAGAAG 57.233 30.769 0.00 1.97 0.00 2.85
446 500 8.587608 ACTTGCCATTTTCATTGAATAAGAAGA 58.412 29.630 0.00 0.00 0.00 2.87
447 501 9.426837 CTTGCCATTTTCATTGAATAAGAAGAA 57.573 29.630 0.00 0.00 0.00 2.52
448 502 8.991243 TGCCATTTTCATTGAATAAGAAGAAG 57.009 30.769 0.00 0.00 0.00 2.85
449 503 8.036575 TGCCATTTTCATTGAATAAGAAGAAGG 58.963 33.333 0.00 0.00 0.00 3.46
450 504 8.037166 GCCATTTTCATTGAATAAGAAGAAGGT 58.963 33.333 0.00 0.00 0.00 3.50
451 505 9.933723 CCATTTTCATTGAATAAGAAGAAGGTT 57.066 29.630 0.00 0.00 0.00 3.50
460 514 8.758633 TGAATAAGAAGAAGGTTTTAGAGTCG 57.241 34.615 0.00 0.00 0.00 4.18
461 515 8.582437 TGAATAAGAAGAAGGTTTTAGAGTCGA 58.418 33.333 0.00 0.00 0.00 4.20
462 516 8.989653 AATAAGAAGAAGGTTTTAGAGTCGAG 57.010 34.615 0.00 0.00 0.00 4.04
463 517 5.394224 AGAAGAAGGTTTTAGAGTCGAGG 57.606 43.478 0.00 0.00 0.00 4.63
464 518 3.596310 AGAAGGTTTTAGAGTCGAGGC 57.404 47.619 0.00 0.00 0.00 4.70
465 519 2.234168 AGAAGGTTTTAGAGTCGAGGCC 59.766 50.000 0.00 0.00 0.00 5.19
466 520 1.640917 AGGTTTTAGAGTCGAGGCCA 58.359 50.000 5.01 0.00 0.00 5.36
467 521 1.550976 AGGTTTTAGAGTCGAGGCCAG 59.449 52.381 5.01 0.00 0.00 4.85
468 522 1.360820 GTTTTAGAGTCGAGGCCAGC 58.639 55.000 5.01 0.00 0.00 4.85
469 523 0.108804 TTTTAGAGTCGAGGCCAGCG 60.109 55.000 5.01 8.88 0.00 5.18
470 524 1.945354 TTTAGAGTCGAGGCCAGCGG 61.945 60.000 16.53 0.00 0.00 5.52
480 534 4.752879 GCCAGCGGCCGAGTTACA 62.753 66.667 33.48 0.00 44.06 2.41
481 535 2.047655 CCAGCGGCCGAGTTACAA 60.048 61.111 33.48 0.00 0.00 2.41
482 536 1.449601 CCAGCGGCCGAGTTACAAT 60.450 57.895 33.48 0.00 0.00 2.71
483 537 1.429148 CCAGCGGCCGAGTTACAATC 61.429 60.000 33.48 7.54 0.00 2.67
484 538 1.153429 AGCGGCCGAGTTACAATCC 60.153 57.895 33.48 6.65 0.00 3.01
485 539 1.153429 GCGGCCGAGTTACAATCCT 60.153 57.895 33.48 0.00 0.00 3.24
486 540 1.152383 GCGGCCGAGTTACAATCCTC 61.152 60.000 33.48 1.16 0.00 3.71
487 541 0.174845 CGGCCGAGTTACAATCCTCA 59.825 55.000 24.07 0.00 0.00 3.86
488 542 1.653151 GGCCGAGTTACAATCCTCAC 58.347 55.000 0.00 0.00 0.00 3.51
489 543 1.207329 GGCCGAGTTACAATCCTCACT 59.793 52.381 0.00 0.00 0.00 3.41
490 544 2.541556 GCCGAGTTACAATCCTCACTC 58.458 52.381 0.00 0.00 33.61 3.51
491 545 2.166664 GCCGAGTTACAATCCTCACTCT 59.833 50.000 0.00 0.00 34.62 3.24
492 546 3.735514 GCCGAGTTACAATCCTCACTCTC 60.736 52.174 0.00 0.00 34.62 3.20
493 547 3.487711 CCGAGTTACAATCCTCACTCTCG 60.488 52.174 0.00 0.00 41.68 4.04
494 548 3.440228 GAGTTACAATCCTCACTCTCGC 58.560 50.000 0.00 0.00 34.07 5.03
495 549 2.159366 AGTTACAATCCTCACTCTCGCG 60.159 50.000 0.00 0.00 0.00 5.87
496 550 0.738975 TACAATCCTCACTCTCGCGG 59.261 55.000 6.13 0.00 0.00 6.46
497 551 1.880340 CAATCCTCACTCTCGCGGC 60.880 63.158 6.13 0.00 0.00 6.53
498 552 2.351244 AATCCTCACTCTCGCGGCA 61.351 57.895 6.13 0.00 0.00 5.69
499 553 1.680522 AATCCTCACTCTCGCGGCAT 61.681 55.000 6.13 0.00 0.00 4.40
500 554 1.680522 ATCCTCACTCTCGCGGCATT 61.681 55.000 6.13 0.00 0.00 3.56
501 555 1.035385 TCCTCACTCTCGCGGCATTA 61.035 55.000 6.13 0.00 0.00 1.90
502 556 0.872021 CCTCACTCTCGCGGCATTAC 60.872 60.000 6.13 0.00 0.00 1.89
503 557 0.179137 CTCACTCTCGCGGCATTACA 60.179 55.000 6.13 0.00 0.00 2.41
504 558 0.459899 TCACTCTCGCGGCATTACAT 59.540 50.000 6.13 0.00 0.00 2.29
505 559 1.134818 TCACTCTCGCGGCATTACATT 60.135 47.619 6.13 0.00 0.00 2.71
506 560 2.100087 TCACTCTCGCGGCATTACATTA 59.900 45.455 6.13 0.00 0.00 1.90
507 561 2.218759 CACTCTCGCGGCATTACATTAC 59.781 50.000 6.13 0.00 0.00 1.89
508 562 2.159156 ACTCTCGCGGCATTACATTACA 60.159 45.455 6.13 0.00 0.00 2.41
509 563 2.198406 TCTCGCGGCATTACATTACAC 58.802 47.619 6.13 0.00 0.00 2.90
510 564 1.930503 CTCGCGGCATTACATTACACA 59.069 47.619 6.13 0.00 0.00 3.72
511 565 2.347731 TCGCGGCATTACATTACACAA 58.652 42.857 6.13 0.00 0.00 3.33
512 566 2.742589 TCGCGGCATTACATTACACAAA 59.257 40.909 6.13 0.00 0.00 2.83
513 567 3.375610 TCGCGGCATTACATTACACAAAT 59.624 39.130 6.13 0.00 0.00 2.32
514 568 4.571176 TCGCGGCATTACATTACACAAATA 59.429 37.500 6.13 0.00 0.00 1.40
515 569 5.237561 TCGCGGCATTACATTACACAAATAT 59.762 36.000 6.13 0.00 0.00 1.28
516 570 5.912396 CGCGGCATTACATTACACAAATATT 59.088 36.000 0.00 0.00 0.00 1.28
517 571 6.416455 CGCGGCATTACATTACACAAATATTT 59.584 34.615 0.00 0.00 0.00 1.40
518 572 7.043722 CGCGGCATTACATTACACAAATATTTT 60.044 33.333 0.00 0.00 0.00 1.82
519 573 8.055402 GCGGCATTACATTACACAAATATTTTG 58.945 33.333 0.00 3.77 0.00 2.44
520 574 8.055402 CGGCATTACATTACACAAATATTTTGC 58.945 33.333 0.00 1.59 0.00 3.68
521 575 8.334632 GGCATTACATTACACAAATATTTTGCC 58.665 33.333 13.42 13.42 34.96 4.52
522 576 8.334632 GCATTACATTACACAAATATTTTGCCC 58.665 33.333 0.00 0.00 0.00 5.36
523 577 8.825745 CATTACATTACACAAATATTTTGCCCC 58.174 33.333 0.00 0.00 0.00 5.80
524 578 5.415221 ACATTACACAAATATTTTGCCCCG 58.585 37.500 0.00 0.00 0.00 5.73
525 579 4.457834 TTACACAAATATTTTGCCCCGG 57.542 40.909 0.00 0.00 0.00 5.73
526 580 1.066502 ACACAAATATTTTGCCCCGGC 60.067 47.619 0.00 0.00 42.35 6.13
542 596 3.434319 GCACGGCACCACCATGAG 61.434 66.667 0.00 0.00 31.42 2.90
543 597 2.747460 CACGGCACCACCATGAGG 60.747 66.667 0.00 0.00 31.42 3.86
544 598 4.722700 ACGGCACCACCATGAGGC 62.723 66.667 0.00 0.00 39.03 4.70
545 599 4.415150 CGGCACCACCATGAGGCT 62.415 66.667 0.00 0.00 39.03 4.58
546 600 2.036256 GGCACCACCATGAGGCTT 59.964 61.111 0.00 0.00 39.06 4.35
547 601 2.048603 GGCACCACCATGAGGCTTC 61.049 63.158 0.00 0.00 39.06 3.86
548 602 2.048603 GCACCACCATGAGGCTTCC 61.049 63.158 0.00 0.00 39.06 3.46
549 603 1.687612 CACCACCATGAGGCTTCCT 59.312 57.895 0.00 0.00 39.06 3.36
560 614 3.252974 GAGGCTTCCTCTTTGATTCGA 57.747 47.619 5.65 0.00 46.41 3.71
561 615 3.194062 GAGGCTTCCTCTTTGATTCGAG 58.806 50.000 5.65 0.00 46.41 4.04
562 616 1.668237 GGCTTCCTCTTTGATTCGAGC 59.332 52.381 0.00 0.00 0.00 5.03
563 617 2.350522 GCTTCCTCTTTGATTCGAGCA 58.649 47.619 0.00 0.00 0.00 4.26
564 618 2.744202 GCTTCCTCTTTGATTCGAGCAA 59.256 45.455 0.00 0.00 0.00 3.91
565 619 3.425492 GCTTCCTCTTTGATTCGAGCAAC 60.425 47.826 2.70 0.00 0.00 4.17
566 620 3.401033 TCCTCTTTGATTCGAGCAACA 57.599 42.857 2.70 0.00 0.00 3.33
567 621 3.738982 TCCTCTTTGATTCGAGCAACAA 58.261 40.909 2.70 0.00 0.00 2.83
568 622 3.748048 TCCTCTTTGATTCGAGCAACAAG 59.252 43.478 2.70 4.04 0.00 3.16
569 623 3.486584 CTCTTTGATTCGAGCAACAAGC 58.513 45.455 2.70 0.00 46.19 4.01
578 632 4.085302 GCAACAAGCACAACGCAA 57.915 50.000 0.00 0.00 46.13 4.85
579 633 2.592212 GCAACAAGCACAACGCAAT 58.408 47.368 0.00 0.00 46.13 3.56
580 634 1.764851 GCAACAAGCACAACGCAATA 58.235 45.000 0.00 0.00 46.13 1.90
581 635 1.451651 GCAACAAGCACAACGCAATAC 59.548 47.619 0.00 0.00 46.13 1.89
582 636 2.050691 CAACAAGCACAACGCAATACC 58.949 47.619 0.00 0.00 46.13 2.73
583 637 1.313772 ACAAGCACAACGCAATACCA 58.686 45.000 0.00 0.00 46.13 3.25
584 638 1.678627 ACAAGCACAACGCAATACCAA 59.321 42.857 0.00 0.00 46.13 3.67
585 639 2.050691 CAAGCACAACGCAATACCAAC 58.949 47.619 0.00 0.00 46.13 3.77
586 640 1.604604 AGCACAACGCAATACCAACT 58.395 45.000 0.00 0.00 46.13 3.16
587 641 1.535462 AGCACAACGCAATACCAACTC 59.465 47.619 0.00 0.00 46.13 3.01
588 642 1.401018 GCACAACGCAATACCAACTCC 60.401 52.381 0.00 0.00 41.79 3.85
589 643 1.876799 CACAACGCAATACCAACTCCA 59.123 47.619 0.00 0.00 0.00 3.86
590 644 2.487762 CACAACGCAATACCAACTCCAT 59.512 45.455 0.00 0.00 0.00 3.41
591 645 2.747446 ACAACGCAATACCAACTCCATC 59.253 45.455 0.00 0.00 0.00 3.51
592 646 3.009723 CAACGCAATACCAACTCCATCT 58.990 45.455 0.00 0.00 0.00 2.90
593 647 2.632377 ACGCAATACCAACTCCATCTG 58.368 47.619 0.00 0.00 0.00 2.90
721 791 4.097589 ACGGTTACAAGTCTGATAGTAGGC 59.902 45.833 0.00 0.00 0.00 3.93
760 830 2.214376 TGGATTGTTTAGCCCCAGTG 57.786 50.000 0.00 0.00 0.00 3.66
771 841 2.551912 CCCCAGTGCGTTTGTGGTC 61.552 63.158 0.00 0.00 0.00 4.02
904 981 3.117701 AGCTCCATCTACAGTCTAGAGCA 60.118 47.826 11.26 0.00 45.93 4.26
959 1039 2.037847 AGCACCTGATTTGGCCCC 59.962 61.111 0.00 0.00 0.00 5.80
1023 1104 1.134371 GCCTTAGCCACGATTCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
1344 1440 4.005472 GGCATCATCTTCGCGCCG 62.005 66.667 0.00 0.00 32.14 6.46
1800 3742 1.850377 CTTCTGATGCTCCTGCTACG 58.150 55.000 0.00 0.00 40.48 3.51
1857 5592 1.228245 GCTGGGCAAGGAAGACACA 60.228 57.895 0.00 0.00 0.00 3.72
1941 5687 7.435068 TTCACTAATTTGCAACCTTCTCTAC 57.565 36.000 0.00 0.00 0.00 2.59
1942 5688 5.938125 TCACTAATTTGCAACCTTCTCTACC 59.062 40.000 0.00 0.00 0.00 3.18
1947 5693 2.536066 TGCAACCTTCTCTACCTAGCA 58.464 47.619 0.00 0.00 0.00 3.49
1951 5697 4.446371 CAACCTTCTCTACCTAGCATTGG 58.554 47.826 0.00 0.00 0.00 3.16
1954 5700 4.162509 ACCTTCTCTACCTAGCATTGGTTC 59.837 45.833 0.00 0.00 38.88 3.62
1955 5708 4.162320 CCTTCTCTACCTAGCATTGGTTCA 59.838 45.833 0.00 0.00 38.88 3.18
2057 5930 2.401766 GGCCATGGCAGAACTCGTG 61.402 63.158 36.56 0.00 44.11 4.35
2135 6011 2.046988 CGCAGCTCCACCATCACA 60.047 61.111 0.00 0.00 0.00 3.58
2147 6023 1.642037 CCATCACAAGCGCAGACCTG 61.642 60.000 11.47 0.64 0.00 4.00
2384 6272 1.000607 GTGAGCGTGGAGTACAACTCA 60.001 52.381 9.15 5.42 46.79 3.41
2632 6527 0.966920 CTACAAGACCAGACCACCGT 59.033 55.000 0.00 0.00 0.00 4.83
2843 6739 2.514458 AATTTGGCTCCATTCGAGGT 57.486 45.000 0.00 0.00 39.22 3.85
2993 6889 6.046593 TGACTAATCGTTGTTTTGACTCAGT 58.953 36.000 0.00 0.00 0.00 3.41
3025 6921 4.320910 GCTGAAGCCTGTTACCCC 57.679 61.111 0.00 0.00 34.31 4.95
3026 6922 1.685820 GCTGAAGCCTGTTACCCCT 59.314 57.895 0.00 0.00 34.31 4.79
3027 6923 0.038310 GCTGAAGCCTGTTACCCCTT 59.962 55.000 0.00 0.00 34.31 3.95
3028 6924 1.547901 GCTGAAGCCTGTTACCCCTTT 60.548 52.381 0.00 0.00 34.31 3.11
3029 6925 2.290705 GCTGAAGCCTGTTACCCCTTTA 60.291 50.000 0.00 0.00 34.31 1.85
3030 6926 3.610911 CTGAAGCCTGTTACCCCTTTAG 58.389 50.000 0.00 0.00 0.00 1.85
3031 6927 2.983898 TGAAGCCTGTTACCCCTTTAGT 59.016 45.455 0.00 0.00 0.00 2.24
3032 6928 3.008704 TGAAGCCTGTTACCCCTTTAGTC 59.991 47.826 0.00 0.00 0.00 2.59
3033 6929 2.627933 AGCCTGTTACCCCTTTAGTCA 58.372 47.619 0.00 0.00 0.00 3.41
3034 6930 2.572104 AGCCTGTTACCCCTTTAGTCAG 59.428 50.000 0.00 0.00 0.00 3.51
3035 6931 2.940083 GCCTGTTACCCCTTTAGTCAGC 60.940 54.545 0.00 0.00 0.00 4.26
3036 6932 2.572104 CCTGTTACCCCTTTAGTCAGCT 59.428 50.000 0.00 0.00 0.00 4.24
3037 6933 3.773119 CCTGTTACCCCTTTAGTCAGCTA 59.227 47.826 0.00 0.00 0.00 3.32
3038 6934 4.382793 CCTGTTACCCCTTTAGTCAGCTAC 60.383 50.000 0.00 0.00 0.00 3.58
3039 6935 3.516700 TGTTACCCCTTTAGTCAGCTACC 59.483 47.826 0.00 0.00 0.00 3.18
3040 6936 1.581223 ACCCCTTTAGTCAGCTACCC 58.419 55.000 0.00 0.00 0.00 3.69
3041 6937 1.080666 ACCCCTTTAGTCAGCTACCCT 59.919 52.381 0.00 0.00 0.00 4.34
3042 6938 1.763545 CCCCTTTAGTCAGCTACCCTC 59.236 57.143 0.00 0.00 0.00 4.30
3043 6939 2.627217 CCCCTTTAGTCAGCTACCCTCT 60.627 54.545 0.00 0.00 0.00 3.69
3044 6940 2.696187 CCCTTTAGTCAGCTACCCTCTC 59.304 54.545 0.00 0.00 0.00 3.20
3045 6941 3.366396 CCTTTAGTCAGCTACCCTCTCA 58.634 50.000 0.00 0.00 0.00 3.27
3046 6942 3.131400 CCTTTAGTCAGCTACCCTCTCAC 59.869 52.174 0.00 0.00 0.00 3.51
3047 6943 3.741245 TTAGTCAGCTACCCTCTCACT 57.259 47.619 0.00 0.00 0.00 3.41
3048 6944 4.857130 TTAGTCAGCTACCCTCTCACTA 57.143 45.455 0.00 0.00 0.00 2.74
3049 6945 3.290948 AGTCAGCTACCCTCTCACTAG 57.709 52.381 0.00 0.00 0.00 2.57
3050 6946 1.679153 GTCAGCTACCCTCTCACTAGC 59.321 57.143 0.00 0.00 34.27 3.42
3051 6947 1.036707 CAGCTACCCTCTCACTAGCC 58.963 60.000 0.00 0.00 34.55 3.93
3052 6948 0.930726 AGCTACCCTCTCACTAGCCT 59.069 55.000 0.00 0.00 34.55 4.58
3053 6949 2.136863 AGCTACCCTCTCACTAGCCTA 58.863 52.381 0.00 0.00 34.55 3.93
3054 6950 2.719705 AGCTACCCTCTCACTAGCCTAT 59.280 50.000 0.00 0.00 34.55 2.57
3055 6951 2.823154 GCTACCCTCTCACTAGCCTATG 59.177 54.545 0.00 0.00 0.00 2.23
3056 6952 2.390225 ACCCTCTCACTAGCCTATGG 57.610 55.000 0.00 0.00 0.00 2.74
3057 6953 1.860240 ACCCTCTCACTAGCCTATGGA 59.140 52.381 0.00 0.00 0.00 3.41
3058 6954 2.158385 ACCCTCTCACTAGCCTATGGAG 60.158 54.545 0.00 0.00 0.00 3.86
3059 6955 1.892474 CCTCTCACTAGCCTATGGAGC 59.108 57.143 0.00 0.00 0.00 4.70
3060 6956 2.490718 CCTCTCACTAGCCTATGGAGCT 60.491 54.545 0.00 0.00 44.49 4.09
3061 6957 3.230134 CTCTCACTAGCCTATGGAGCTT 58.770 50.000 0.00 0.00 41.83 3.74
3062 6958 3.640967 CTCTCACTAGCCTATGGAGCTTT 59.359 47.826 0.00 0.00 41.83 3.51
3063 6959 4.033709 TCTCACTAGCCTATGGAGCTTTT 58.966 43.478 0.00 0.00 41.83 2.27
3064 6960 4.471386 TCTCACTAGCCTATGGAGCTTTTT 59.529 41.667 0.00 0.00 41.83 1.94
3088 6984 7.437713 TTTTTGAGAATCTCTAGCCTATGGA 57.562 36.000 11.92 0.00 34.92 3.41
3089 6985 6.662865 TTTGAGAATCTCTAGCCTATGGAG 57.337 41.667 11.92 0.00 37.85 3.86
3090 6986 4.085733 TGAGAATCTCTAGCCTATGGAGC 58.914 47.826 11.92 0.00 36.49 4.70
3091 6987 4.202663 TGAGAATCTCTAGCCTATGGAGCT 60.203 45.833 11.92 0.00 39.36 4.09
3092 6988 4.088634 AGAATCTCTAGCCTATGGAGCTG 58.911 47.826 0.00 0.00 41.71 4.24
3093 6989 3.824001 ATCTCTAGCCTATGGAGCTGA 57.176 47.619 0.00 0.00 41.71 4.26
3094 6990 2.870175 TCTCTAGCCTATGGAGCTGAC 58.130 52.381 0.00 0.00 41.71 3.51
3095 6991 1.892474 CTCTAGCCTATGGAGCTGACC 59.108 57.143 0.00 0.00 41.71 4.02
3096 6992 0.972883 CTAGCCTATGGAGCTGACCC 59.027 60.000 0.00 0.00 41.71 4.46
3097 6993 0.264657 TAGCCTATGGAGCTGACCCA 59.735 55.000 0.00 0.00 41.71 4.51
3098 6994 1.147153 GCCTATGGAGCTGACCCAC 59.853 63.158 0.00 0.00 36.36 4.61
3228 7132 2.882777 AGCACGCTCGATCGCTTG 60.883 61.111 11.09 3.65 32.88 4.01
3229 7133 3.181967 GCACGCTCGATCGCTTGT 61.182 61.111 11.09 5.15 32.39 3.16
3230 7134 2.730672 GCACGCTCGATCGCTTGTT 61.731 57.895 11.09 0.00 32.39 2.83
3231 7135 1.781555 CACGCTCGATCGCTTGTTT 59.218 52.632 11.09 0.00 0.00 2.83
3306 7210 4.499037 AAACCAACCGATTTTCTACAGC 57.501 40.909 0.00 0.00 0.00 4.40
3320 7224 5.483685 TTCTACAGCACATACTCTGGTTT 57.516 39.130 0.00 0.00 34.76 3.27
3421 7346 8.296799 TCATCAAATTTGGAAAAAGTTCATCG 57.703 30.769 17.90 0.00 35.25 3.84
3455 7380 8.940768 AAAAAGTTCATCGGATTTGAGAAAAA 57.059 26.923 0.00 0.00 0.00 1.94
3456 7381 8.579682 AAAAGTTCATCGGATTTGAGAAAAAG 57.420 30.769 0.00 0.00 0.00 2.27
3458 7383 7.277174 AGTTCATCGGATTTGAGAAAAAGTT 57.723 32.000 0.00 0.00 0.00 2.66
3459 7384 7.363431 AGTTCATCGGATTTGAGAAAAAGTTC 58.637 34.615 0.00 0.00 0.00 3.01
3460 7385 6.875948 TCATCGGATTTGAGAAAAAGTTCA 57.124 33.333 0.00 0.00 36.09 3.18
3461 7386 7.452880 TCATCGGATTTGAGAAAAAGTTCAT 57.547 32.000 0.00 0.00 36.09 2.57
3462 7387 7.530010 TCATCGGATTTGAGAAAAAGTTCATC 58.470 34.615 0.00 0.00 36.09 2.92
3465 7390 6.203915 TCGGATTTGAGAAAAAGTTCATCGAA 59.796 34.615 0.00 0.00 36.09 3.71
3468 7393 8.239998 GGATTTGAGAAAAAGTTCATCGAATCT 58.760 33.333 17.23 0.00 39.02 2.40
3469 7394 8.961294 ATTTGAGAAAAAGTTCATCGAATCTG 57.039 30.769 0.00 0.00 36.09 2.90
3470 7395 6.486253 TGAGAAAAAGTTCATCGAATCTGG 57.514 37.500 0.00 0.00 36.09 3.86
3517 7442 6.588348 AAAAGTTCGCCAGATTTGAAAAAG 57.412 33.333 0.00 0.00 0.00 2.27
3532 7459 9.787532 GATTTGAAAAAGGTTCATCGATTATGA 57.212 29.630 0.00 0.00 43.03 2.15
3579 7506 8.485976 AACAAAAAGTTCATCAATTTTTCCGA 57.514 26.923 0.00 0.00 34.74 4.55
3580 7507 8.485976 ACAAAAAGTTCATCAATTTTTCCGAA 57.514 26.923 0.00 0.00 34.73 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 4.233005 GCTGCTGAAGACAAATCCTTTTC 58.767 43.478 0.00 0.00 0.00 2.29
168 220 1.089920 TTACTCTCTACGGCGTCCAC 58.910 55.000 19.21 0.00 0.00 4.02
172 224 2.709213 AGTCTTTACTCTCTACGGCGT 58.291 47.619 19.64 19.64 0.00 5.68
173 225 5.421212 AATAGTCTTTACTCTCTACGGCG 57.579 43.478 4.80 4.80 37.15 6.46
174 226 5.442402 CGAATAGTCTTTACTCTCTACGGC 58.558 45.833 0.00 0.00 37.15 5.68
175 227 5.757320 TCCGAATAGTCTTTACTCTCTACGG 59.243 44.000 0.00 0.00 37.15 4.02
215 268 2.550606 GCATTTTCGTCCTACCAACACA 59.449 45.455 0.00 0.00 0.00 3.72
216 269 2.550606 TGCATTTTCGTCCTACCAACAC 59.449 45.455 0.00 0.00 0.00 3.32
217 270 2.852449 TGCATTTTCGTCCTACCAACA 58.148 42.857 0.00 0.00 0.00 3.33
400 454 7.301789 GCAAGTCTTTTGCCTTGTTTTAAAAA 58.698 30.769 1.31 0.00 40.13 1.94
401 455 6.836953 GCAAGTCTTTTGCCTTGTTTTAAAA 58.163 32.000 0.00 0.00 40.13 1.52
402 456 6.415798 GCAAGTCTTTTGCCTTGTTTTAAA 57.584 33.333 0.54 0.00 40.13 1.52
413 467 5.236911 TCAATGAAAATGGCAAGTCTTTTGC 59.763 36.000 1.54 3.39 44.22 3.68
414 468 6.847956 TCAATGAAAATGGCAAGTCTTTTG 57.152 33.333 1.54 4.22 0.00 2.44
415 469 9.558396 TTATTCAATGAAAATGGCAAGTCTTTT 57.442 25.926 0.00 0.00 0.00 2.27
416 470 9.211485 CTTATTCAATGAAAATGGCAAGTCTTT 57.789 29.630 0.00 0.00 0.00 2.52
417 471 8.587608 TCTTATTCAATGAAAATGGCAAGTCTT 58.412 29.630 0.00 0.00 0.00 3.01
418 472 8.125978 TCTTATTCAATGAAAATGGCAAGTCT 57.874 30.769 0.00 0.00 0.00 3.24
419 473 8.761575 TTCTTATTCAATGAAAATGGCAAGTC 57.238 30.769 0.00 0.00 0.00 3.01
420 474 8.587608 TCTTCTTATTCAATGAAAATGGCAAGT 58.412 29.630 0.00 0.00 0.00 3.16
421 475 8.991243 TCTTCTTATTCAATGAAAATGGCAAG 57.009 30.769 0.00 0.00 0.00 4.01
422 476 9.426837 CTTCTTCTTATTCAATGAAAATGGCAA 57.573 29.630 0.00 0.00 0.00 4.52
423 477 8.036575 CCTTCTTCTTATTCAATGAAAATGGCA 58.963 33.333 0.00 0.00 0.00 4.92
424 478 8.037166 ACCTTCTTCTTATTCAATGAAAATGGC 58.963 33.333 0.00 0.00 0.00 4.40
425 479 9.933723 AACCTTCTTCTTATTCAATGAAAATGG 57.066 29.630 0.00 0.00 0.00 3.16
434 488 9.204570 CGACTCTAAAACCTTCTTCTTATTCAA 57.795 33.333 0.00 0.00 0.00 2.69
435 489 8.582437 TCGACTCTAAAACCTTCTTCTTATTCA 58.418 33.333 0.00 0.00 0.00 2.57
436 490 8.983307 TCGACTCTAAAACCTTCTTCTTATTC 57.017 34.615 0.00 0.00 0.00 1.75
437 491 8.035984 CCTCGACTCTAAAACCTTCTTCTTATT 58.964 37.037 0.00 0.00 0.00 1.40
438 492 7.548967 CCTCGACTCTAAAACCTTCTTCTTAT 58.451 38.462 0.00 0.00 0.00 1.73
439 493 6.571925 GCCTCGACTCTAAAACCTTCTTCTTA 60.572 42.308 0.00 0.00 0.00 2.10
440 494 5.785243 CCTCGACTCTAAAACCTTCTTCTT 58.215 41.667 0.00 0.00 0.00 2.52
441 495 4.322123 GCCTCGACTCTAAAACCTTCTTCT 60.322 45.833 0.00 0.00 0.00 2.85
442 496 3.927758 GCCTCGACTCTAAAACCTTCTTC 59.072 47.826 0.00 0.00 0.00 2.87
443 497 3.306849 GGCCTCGACTCTAAAACCTTCTT 60.307 47.826 0.00 0.00 0.00 2.52
444 498 2.234168 GGCCTCGACTCTAAAACCTTCT 59.766 50.000 0.00 0.00 0.00 2.85
445 499 2.028385 TGGCCTCGACTCTAAAACCTTC 60.028 50.000 3.32 0.00 0.00 3.46
446 500 1.975680 TGGCCTCGACTCTAAAACCTT 59.024 47.619 3.32 0.00 0.00 3.50
447 501 1.550976 CTGGCCTCGACTCTAAAACCT 59.449 52.381 3.32 0.00 0.00 3.50
448 502 2.007547 GCTGGCCTCGACTCTAAAACC 61.008 57.143 3.32 0.00 0.00 3.27
449 503 1.360820 GCTGGCCTCGACTCTAAAAC 58.639 55.000 3.32 0.00 0.00 2.43
450 504 0.108804 CGCTGGCCTCGACTCTAAAA 60.109 55.000 3.32 0.00 0.00 1.52
451 505 1.511305 CGCTGGCCTCGACTCTAAA 59.489 57.895 3.32 0.00 0.00 1.85
452 506 2.415608 CCGCTGGCCTCGACTCTAA 61.416 63.158 17.46 0.00 0.00 2.10
453 507 2.829003 CCGCTGGCCTCGACTCTA 60.829 66.667 17.46 0.00 0.00 2.43
464 518 1.429148 GATTGTAACTCGGCCGCTGG 61.429 60.000 23.51 15.48 0.00 4.85
465 519 1.429148 GGATTGTAACTCGGCCGCTG 61.429 60.000 23.51 18.32 0.00 5.18
466 520 1.153429 GGATTGTAACTCGGCCGCT 60.153 57.895 23.51 10.07 0.00 5.52
467 521 1.152383 GAGGATTGTAACTCGGCCGC 61.152 60.000 23.51 6.50 0.00 6.53
468 522 0.174845 TGAGGATTGTAACTCGGCCG 59.825 55.000 22.12 22.12 36.53 6.13
469 523 1.207329 AGTGAGGATTGTAACTCGGCC 59.793 52.381 0.00 0.00 36.53 6.13
470 524 2.166664 AGAGTGAGGATTGTAACTCGGC 59.833 50.000 0.00 0.00 43.06 5.54
471 525 3.487711 CGAGAGTGAGGATTGTAACTCGG 60.488 52.174 0.00 0.00 43.06 4.63
472 526 3.686128 CGAGAGTGAGGATTGTAACTCG 58.314 50.000 0.00 0.00 43.06 4.18
473 527 3.440228 GCGAGAGTGAGGATTGTAACTC 58.560 50.000 0.00 0.00 39.47 3.01
474 528 2.159366 CGCGAGAGTGAGGATTGTAACT 60.159 50.000 0.00 0.00 46.66 2.24
475 529 2.186076 CGCGAGAGTGAGGATTGTAAC 58.814 52.381 0.00 0.00 46.66 2.50
476 530 1.134367 CCGCGAGAGTGAGGATTGTAA 59.866 52.381 8.23 0.00 46.66 2.41
477 531 0.738975 CCGCGAGAGTGAGGATTGTA 59.261 55.000 8.23 0.00 46.66 2.41
478 532 1.513158 CCGCGAGAGTGAGGATTGT 59.487 57.895 8.23 0.00 46.66 2.71
479 533 1.880340 GCCGCGAGAGTGAGGATTG 60.880 63.158 8.23 0.00 46.66 2.67
480 534 1.680522 ATGCCGCGAGAGTGAGGATT 61.681 55.000 8.23 0.00 46.66 3.01
481 535 1.680522 AATGCCGCGAGAGTGAGGAT 61.681 55.000 8.23 0.00 46.66 3.24
482 536 1.035385 TAATGCCGCGAGAGTGAGGA 61.035 55.000 8.23 0.00 46.66 3.71
483 537 0.872021 GTAATGCCGCGAGAGTGAGG 60.872 60.000 8.23 0.00 46.66 3.86
484 538 0.179137 TGTAATGCCGCGAGAGTGAG 60.179 55.000 8.23 0.00 46.66 3.51
485 539 0.459899 ATGTAATGCCGCGAGAGTGA 59.540 50.000 8.23 0.00 46.66 3.41
486 540 1.290203 AATGTAATGCCGCGAGAGTG 58.710 50.000 8.23 0.00 42.41 3.51
487 541 2.159156 TGTAATGTAATGCCGCGAGAGT 60.159 45.455 8.23 0.00 0.00 3.24
488 542 2.218759 GTGTAATGTAATGCCGCGAGAG 59.781 50.000 8.23 0.00 0.00 3.20
489 543 2.198406 GTGTAATGTAATGCCGCGAGA 58.802 47.619 8.23 0.00 0.00 4.04
490 544 1.930503 TGTGTAATGTAATGCCGCGAG 59.069 47.619 8.23 0.00 0.00 5.03
491 545 2.011540 TGTGTAATGTAATGCCGCGA 57.988 45.000 8.23 0.00 0.00 5.87
492 546 2.815657 TTGTGTAATGTAATGCCGCG 57.184 45.000 0.00 0.00 0.00 6.46
493 547 7.692908 AAATATTTGTGTAATGTAATGCCGC 57.307 32.000 0.00 0.00 0.00 6.53
494 548 8.055402 GCAAAATATTTGTGTAATGTAATGCCG 58.945 33.333 0.39 0.00 30.05 5.69
495 549 8.334632 GGCAAAATATTTGTGTAATGTAATGCC 58.665 33.333 13.42 13.42 39.58 4.40
496 550 8.334632 GGGCAAAATATTTGTGTAATGTAATGC 58.665 33.333 0.39 3.29 32.82 3.56
497 551 8.825745 GGGGCAAAATATTTGTGTAATGTAATG 58.174 33.333 0.39 0.00 0.00 1.90
498 552 7.708752 CGGGGCAAAATATTTGTGTAATGTAAT 59.291 33.333 0.39 0.00 0.00 1.89
499 553 7.036220 CGGGGCAAAATATTTGTGTAATGTAA 58.964 34.615 0.39 0.00 0.00 2.41
500 554 6.405953 CCGGGGCAAAATATTTGTGTAATGTA 60.406 38.462 0.39 0.00 0.00 2.29
501 555 5.415221 CGGGGCAAAATATTTGTGTAATGT 58.585 37.500 0.39 0.00 0.00 2.71
502 556 4.808364 CCGGGGCAAAATATTTGTGTAATG 59.192 41.667 0.39 0.00 0.00 1.90
503 557 4.682050 GCCGGGGCAAAATATTTGTGTAAT 60.682 41.667 2.18 0.00 41.49 1.89
504 558 3.368531 GCCGGGGCAAAATATTTGTGTAA 60.369 43.478 2.18 0.00 41.49 2.41
505 559 2.166664 GCCGGGGCAAAATATTTGTGTA 59.833 45.455 2.18 0.00 41.49 2.90
506 560 1.066502 GCCGGGGCAAAATATTTGTGT 60.067 47.619 2.18 0.00 41.49 3.72
507 561 1.650825 GCCGGGGCAAAATATTTGTG 58.349 50.000 2.18 4.09 41.49 3.33
527 581 4.722700 GCCTCATGGTGGTGCCGT 62.723 66.667 7.35 0.00 41.21 5.68
528 582 3.925630 AAGCCTCATGGTGGTGCCG 62.926 63.158 7.35 0.00 41.21 5.69
529 583 2.036256 AAGCCTCATGGTGGTGCC 59.964 61.111 7.35 0.00 35.27 5.01
530 584 2.048603 GGAAGCCTCATGGTGGTGC 61.049 63.158 7.35 0.00 35.27 5.01
531 585 1.687612 AGGAAGCCTCATGGTGGTG 59.312 57.895 7.35 0.00 35.27 4.17
532 586 4.257890 AGGAAGCCTCATGGTGGT 57.742 55.556 7.35 0.00 35.27 4.16
541 595 2.679349 GCTCGAATCAAAGAGGAAGCCT 60.679 50.000 0.00 0.00 36.03 4.58
542 596 1.668237 GCTCGAATCAAAGAGGAAGCC 59.332 52.381 0.00 0.00 35.19 4.35
543 597 2.350522 TGCTCGAATCAAAGAGGAAGC 58.649 47.619 0.00 0.00 35.19 3.86
544 598 3.748048 TGTTGCTCGAATCAAAGAGGAAG 59.252 43.478 0.00 0.00 43.58 3.46
545 599 3.738982 TGTTGCTCGAATCAAAGAGGAA 58.261 40.909 1.86 0.00 41.38 3.36
546 600 3.401033 TGTTGCTCGAATCAAAGAGGA 57.599 42.857 1.86 0.00 35.19 3.71
547 601 3.669023 GCTTGTTGCTCGAATCAAAGAGG 60.669 47.826 1.86 0.00 38.95 3.69
548 602 3.058708 TGCTTGTTGCTCGAATCAAAGAG 60.059 43.478 1.86 4.70 43.37 2.85
549 603 2.877786 TGCTTGTTGCTCGAATCAAAGA 59.122 40.909 1.86 0.00 43.37 2.52
550 604 2.975851 GTGCTTGTTGCTCGAATCAAAG 59.024 45.455 1.86 0.00 43.37 2.77
551 605 2.357323 TGTGCTTGTTGCTCGAATCAAA 59.643 40.909 1.86 0.00 43.37 2.69
552 606 1.946081 TGTGCTTGTTGCTCGAATCAA 59.054 42.857 0.00 0.00 43.37 2.57
553 607 1.592064 TGTGCTTGTTGCTCGAATCA 58.408 45.000 0.00 0.00 43.37 2.57
554 608 2.310577 GTTGTGCTTGTTGCTCGAATC 58.689 47.619 0.00 0.00 43.37 2.52
555 609 1.334059 CGTTGTGCTTGTTGCTCGAAT 60.334 47.619 0.00 0.00 43.37 3.34
556 610 0.027455 CGTTGTGCTTGTTGCTCGAA 59.973 50.000 0.00 0.00 43.37 3.71
557 611 1.641140 CGTTGTGCTTGTTGCTCGA 59.359 52.632 0.00 0.00 43.37 4.04
558 612 2.005537 GCGTTGTGCTTGTTGCTCG 61.006 57.895 0.00 0.00 43.37 5.03
559 613 0.525242 TTGCGTTGTGCTTGTTGCTC 60.525 50.000 0.00 0.00 46.63 4.26
560 614 0.102844 ATTGCGTTGTGCTTGTTGCT 59.897 45.000 0.00 0.00 46.63 3.91
561 615 1.451651 GTATTGCGTTGTGCTTGTTGC 59.548 47.619 0.00 0.00 46.63 4.17
562 616 2.050691 GGTATTGCGTTGTGCTTGTTG 58.949 47.619 0.00 0.00 46.63 3.33
563 617 1.678627 TGGTATTGCGTTGTGCTTGTT 59.321 42.857 0.00 0.00 46.63 2.83
564 618 1.313772 TGGTATTGCGTTGTGCTTGT 58.686 45.000 0.00 0.00 46.63 3.16
565 619 2.050691 GTTGGTATTGCGTTGTGCTTG 58.949 47.619 0.00 0.00 46.63 4.01
566 620 1.953686 AGTTGGTATTGCGTTGTGCTT 59.046 42.857 0.00 0.00 46.63 3.91
567 621 1.535462 GAGTTGGTATTGCGTTGTGCT 59.465 47.619 0.00 0.00 46.63 4.40
568 622 1.401018 GGAGTTGGTATTGCGTTGTGC 60.401 52.381 0.00 0.00 46.70 4.57
569 623 1.876799 TGGAGTTGGTATTGCGTTGTG 59.123 47.619 0.00 0.00 0.00 3.33
570 624 2.264005 TGGAGTTGGTATTGCGTTGT 57.736 45.000 0.00 0.00 0.00 3.32
571 625 3.009723 AGATGGAGTTGGTATTGCGTTG 58.990 45.455 0.00 0.00 0.00 4.10
572 626 3.009723 CAGATGGAGTTGGTATTGCGTT 58.990 45.455 0.00 0.00 0.00 4.84
573 627 2.632377 CAGATGGAGTTGGTATTGCGT 58.368 47.619 0.00 0.00 0.00 5.24
574 628 1.331756 GCAGATGGAGTTGGTATTGCG 59.668 52.381 0.00 0.00 0.00 4.85
575 629 2.357009 CTGCAGATGGAGTTGGTATTGC 59.643 50.000 8.42 0.00 0.00 3.56
576 630 3.614092 ACTGCAGATGGAGTTGGTATTG 58.386 45.455 23.35 0.00 44.54 1.90
585 639 3.883830 AGTGTAGAACTGCAGATGGAG 57.116 47.619 23.35 0.00 37.88 3.86
586 640 5.891551 TGTATAGTGTAGAACTGCAGATGGA 59.108 40.000 23.35 0.00 40.26 3.41
587 641 5.980116 GTGTATAGTGTAGAACTGCAGATGG 59.020 44.000 23.35 0.00 40.26 3.51
588 642 5.980116 GGTGTATAGTGTAGAACTGCAGATG 59.020 44.000 23.35 0.00 40.26 2.90
589 643 5.656859 TGGTGTATAGTGTAGAACTGCAGAT 59.343 40.000 23.35 9.01 40.26 2.90
590 644 5.014202 TGGTGTATAGTGTAGAACTGCAGA 58.986 41.667 23.35 0.00 40.26 4.26
591 645 5.324784 TGGTGTATAGTGTAGAACTGCAG 57.675 43.478 13.48 13.48 40.26 4.41
592 646 5.932619 ATGGTGTATAGTGTAGAACTGCA 57.067 39.130 0.00 0.00 40.26 4.41
593 647 6.700520 GGTTATGGTGTATAGTGTAGAACTGC 59.299 42.308 0.00 0.00 40.26 4.40
721 791 1.999048 ACATGTGCATGCATTTTCGG 58.001 45.000 25.64 12.69 42.39 4.30
760 830 3.889196 TGTAGAAATGACCACAAACGC 57.111 42.857 0.00 0.00 0.00 4.84
771 841 4.747108 GGACGTCCAGATCATGTAGAAATG 59.253 45.833 29.75 0.00 35.64 2.32
854 924 0.522705 GCAGACAAGTCATGCATGCG 60.523 55.000 22.25 12.00 39.75 4.73
904 981 9.031360 CGTGCTGAACTGTTATATTTATAGTGT 57.969 33.333 0.00 0.00 0.00 3.55
933 1013 3.618351 CAAATCAGGTGCTCTCTCCAAT 58.382 45.455 0.00 0.00 0.00 3.16
959 1039 1.202533 CCATGGCGACTTAGTGGTAGG 60.203 57.143 0.00 0.00 0.00 3.18
988 1069 3.682718 GCTAAGGCCATCAAGCAGAGTTA 60.683 47.826 5.01 0.00 35.05 2.24
1023 1104 4.222145 AGAACCTGCCTCAGAATAAACGTA 59.778 41.667 0.00 0.00 32.44 3.57
1207 1303 0.881118 GACACAATGACGTTGGGCAT 59.119 50.000 9.64 0.00 45.43 4.40
1800 3742 0.456628 GGTCCTCGTTGTCTCTAGCC 59.543 60.000 0.00 0.00 0.00 3.93
1857 5592 1.614413 GACGTGAGAGGGAAACTGAGT 59.386 52.381 0.00 0.00 0.00 3.41
1947 5693 7.414222 AATTATTCTGTGAGCATGAACCAAT 57.586 32.000 0.00 0.00 0.00 3.16
1951 5697 6.094719 TGCAAATTATTCTGTGAGCATGAAC 58.905 36.000 0.00 0.00 0.00 3.18
1954 5700 5.865013 TGTTGCAAATTATTCTGTGAGCATG 59.135 36.000 0.00 0.00 0.00 4.06
1955 5708 5.865552 GTGTTGCAAATTATTCTGTGAGCAT 59.134 36.000 0.00 0.00 0.00 3.79
2031 5904 0.925558 TCTGCCATGGCCCATTCTAA 59.074 50.000 33.44 11.64 41.09 2.10
2147 6023 3.406595 AAGATAGTGCAGGCCGGCC 62.407 63.158 39.29 39.29 0.00 6.13
2339 6215 1.908483 GAACCTCTCCGGCCTGAAT 59.092 57.895 0.00 0.00 35.61 2.57
2384 6272 3.925630 CTCCATGTGCGGCCCTTGT 62.926 63.158 0.00 0.00 0.00 3.16
2632 6527 9.219603 CTGTGAATAATTTCTAGGACAGTTCAA 57.780 33.333 0.00 0.00 31.99 2.69
2790 6686 9.528018 GTCAAAGGAAAATTAACAATTCTGACA 57.472 29.630 0.00 0.00 0.00 3.58
2791 6687 9.750125 AGTCAAAGGAAAATTAACAATTCTGAC 57.250 29.630 0.00 0.00 0.00 3.51
2792 6688 9.748708 CAGTCAAAGGAAAATTAACAATTCTGA 57.251 29.630 0.00 0.00 0.00 3.27
2793 6689 9.748708 TCAGTCAAAGGAAAATTAACAATTCTG 57.251 29.630 0.00 0.00 0.00 3.02
2823 6719 3.644966 ACCTCGAATGGAGCCAAATTA 57.355 42.857 0.00 0.00 41.71 1.40
2854 6750 7.891561 ACTTACATATAGCCAAAGTGCAAAAA 58.108 30.769 0.00 0.00 0.00 1.94
3017 6913 3.516700 GGTAGCTGACTAAAGGGGTAACA 59.483 47.826 0.00 0.00 39.74 2.41
3018 6914 3.118482 GGGTAGCTGACTAAAGGGGTAAC 60.118 52.174 0.00 0.00 0.00 2.50
3019 6915 3.109928 GGGTAGCTGACTAAAGGGGTAA 58.890 50.000 0.00 0.00 0.00 2.85
3020 6916 2.316982 AGGGTAGCTGACTAAAGGGGTA 59.683 50.000 0.00 0.00 0.00 3.69
3021 6917 1.080666 AGGGTAGCTGACTAAAGGGGT 59.919 52.381 0.00 0.00 0.00 4.95
3022 6918 1.763545 GAGGGTAGCTGACTAAAGGGG 59.236 57.143 0.00 0.00 0.00 4.79
3023 6919 2.696187 GAGAGGGTAGCTGACTAAAGGG 59.304 54.545 0.00 0.00 0.00 3.95
3024 6920 3.131400 GTGAGAGGGTAGCTGACTAAAGG 59.869 52.174 0.00 0.00 0.00 3.11
3025 6921 4.020543 AGTGAGAGGGTAGCTGACTAAAG 58.979 47.826 0.00 0.00 27.86 1.85
3026 6922 4.048970 AGTGAGAGGGTAGCTGACTAAA 57.951 45.455 0.00 0.00 27.86 1.85
3027 6923 3.741245 AGTGAGAGGGTAGCTGACTAA 57.259 47.619 0.00 0.00 27.86 2.24
3028 6924 3.433882 GCTAGTGAGAGGGTAGCTGACTA 60.434 52.174 0.00 0.00 36.93 2.59
3029 6925 2.685522 GCTAGTGAGAGGGTAGCTGACT 60.686 54.545 0.00 0.00 36.93 3.41
3030 6926 1.679153 GCTAGTGAGAGGGTAGCTGAC 59.321 57.143 0.00 0.00 36.93 3.51
3031 6927 1.410365 GGCTAGTGAGAGGGTAGCTGA 60.410 57.143 0.00 0.00 39.36 4.26
3032 6928 1.036707 GGCTAGTGAGAGGGTAGCTG 58.963 60.000 0.00 0.00 39.36 4.24
3033 6929 0.930726 AGGCTAGTGAGAGGGTAGCT 59.069 55.000 0.00 0.00 39.36 3.32
3034 6930 2.660670 TAGGCTAGTGAGAGGGTAGC 57.339 55.000 0.00 0.00 38.79 3.58
3035 6931 3.074687 TCCATAGGCTAGTGAGAGGGTAG 59.925 52.174 0.00 0.00 0.00 3.18
3036 6932 3.061369 TCCATAGGCTAGTGAGAGGGTA 58.939 50.000 0.00 0.00 0.00 3.69
3037 6933 1.860240 TCCATAGGCTAGTGAGAGGGT 59.140 52.381 0.00 0.00 0.00 4.34
3038 6934 2.524306 CTCCATAGGCTAGTGAGAGGG 58.476 57.143 14.69 0.00 0.00 4.30
3039 6935 1.892474 GCTCCATAGGCTAGTGAGAGG 59.108 57.143 21.02 7.96 0.00 3.69
3040 6936 2.875296 AGCTCCATAGGCTAGTGAGAG 58.125 52.381 21.02 14.51 38.36 3.20
3041 6937 3.320610 AAGCTCCATAGGCTAGTGAGA 57.679 47.619 21.02 6.40 39.30 3.27
3042 6938 4.414337 AAAAGCTCCATAGGCTAGTGAG 57.586 45.455 15.26 15.26 39.30 3.51
3043 6939 4.844349 AAAAAGCTCCATAGGCTAGTGA 57.156 40.909 0.00 0.00 39.30 3.41
3064 6960 7.437713 TCCATAGGCTAGAGATTCTCAAAAA 57.562 36.000 15.83 0.00 32.06 1.94
3065 6961 6.463614 GCTCCATAGGCTAGAGATTCTCAAAA 60.464 42.308 15.83 0.52 32.06 2.44
3066 6962 5.011533 GCTCCATAGGCTAGAGATTCTCAAA 59.988 44.000 15.83 2.90 32.06 2.69
3067 6963 4.526262 GCTCCATAGGCTAGAGATTCTCAA 59.474 45.833 15.83 0.00 32.06 3.02
3068 6964 4.085733 GCTCCATAGGCTAGAGATTCTCA 58.914 47.826 15.83 1.71 32.06 3.27
3069 6965 4.158394 CAGCTCCATAGGCTAGAGATTCTC 59.842 50.000 13.36 5.49 38.03 2.87
3070 6966 4.088634 CAGCTCCATAGGCTAGAGATTCT 58.911 47.826 13.36 4.56 38.03 2.40
3071 6967 4.082245 GTCAGCTCCATAGGCTAGAGATTC 60.082 50.000 13.36 1.70 38.03 2.52
3072 6968 3.831911 GTCAGCTCCATAGGCTAGAGATT 59.168 47.826 13.36 0.37 38.03 2.40
3073 6969 3.430453 GTCAGCTCCATAGGCTAGAGAT 58.570 50.000 13.36 5.52 38.03 2.75
3074 6970 2.489985 GGTCAGCTCCATAGGCTAGAGA 60.490 54.545 13.36 5.71 38.03 3.10
3075 6971 1.892474 GGTCAGCTCCATAGGCTAGAG 59.108 57.143 0.00 3.41 38.03 2.43
3076 6972 1.481428 GGGTCAGCTCCATAGGCTAGA 60.481 57.143 0.00 0.00 38.03 2.43
3077 6973 0.972883 GGGTCAGCTCCATAGGCTAG 59.027 60.000 0.00 0.00 38.03 3.42
3078 6974 0.264657 TGGGTCAGCTCCATAGGCTA 59.735 55.000 0.00 0.00 38.03 3.93
3079 6975 1.003442 TGGGTCAGCTCCATAGGCT 59.997 57.895 0.00 0.00 41.07 4.58
3080 6976 1.147153 GTGGGTCAGCTCCATAGGC 59.853 63.158 0.00 0.00 36.58 3.93
3081 6977 1.043116 TCGTGGGTCAGCTCCATAGG 61.043 60.000 0.00 0.00 36.58 2.57
3082 6978 0.387202 CTCGTGGGTCAGCTCCATAG 59.613 60.000 0.00 0.00 36.58 2.23
3083 6979 0.033503 TCTCGTGGGTCAGCTCCATA 60.034 55.000 0.00 0.00 36.58 2.74
3084 6980 1.305297 TCTCGTGGGTCAGCTCCAT 60.305 57.895 0.00 0.00 36.58 3.41
3085 6981 1.979155 CTCTCGTGGGTCAGCTCCA 60.979 63.158 0.00 0.00 0.00 3.86
3086 6982 2.888863 CTCTCGTGGGTCAGCTCC 59.111 66.667 0.00 0.00 0.00 4.70
3087 6983 2.183046 GCTCTCGTGGGTCAGCTC 59.817 66.667 0.00 0.00 0.00 4.09
3088 6984 2.283532 AGCTCTCGTGGGTCAGCT 60.284 61.111 0.00 0.00 37.40 4.24
3089 6985 2.183046 GAGCTCTCGTGGGTCAGC 59.817 66.667 6.43 0.00 0.00 4.26
3090 6986 1.662438 GAGGAGCTCTCGTGGGTCAG 61.662 65.000 14.64 0.00 33.45 3.51
3091 6987 1.679305 GAGGAGCTCTCGTGGGTCA 60.679 63.158 14.64 0.00 33.45 4.02
3092 6988 3.202467 GAGGAGCTCTCGTGGGTC 58.798 66.667 14.64 0.00 32.18 4.46
3288 7192 2.811431 TGTGCTGTAGAAAATCGGTTGG 59.189 45.455 0.00 0.00 0.00 3.77
3293 7197 5.233050 CCAGAGTATGTGCTGTAGAAAATCG 59.767 44.000 0.00 0.00 0.00 3.34
3295 7199 6.054860 ACCAGAGTATGTGCTGTAGAAAAT 57.945 37.500 0.00 0.00 0.00 1.82
3306 7210 8.630037 ACTTTTTCCTAAAAACCAGAGTATGTG 58.370 33.333 0.00 0.00 35.57 3.21
3450 7375 8.574196 TTTTTCCAGATTCGATGAACTTTTTC 57.426 30.769 0.00 0.00 0.00 2.29
3537 7464 9.160496 ACTTTTTGTTTACAAATTCAATGAGCA 57.840 25.926 8.70 0.00 44.30 4.26
3621 7548 4.316205 TCTTTCGCCTTTTCTTTTTCCC 57.684 40.909 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.