Multiple sequence alignment - TraesCS1D01G206000

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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 TraesCS1D01G206000 chr1D 100.000 5674 0 0 1 5674 291787959 291793632 0.000000e+00 10479.0
1 TraesCS1D01G206000 chr1D 93.857 2051 100 16 1702 3745 291089662 291087631 0.000000e+00 3066.0
2 TraesCS1D01G206000 chr1D 89.893 1029 49 23 3875 4876 291087611 291086611 0.000000e+00 1273.0
3 TraesCS1D01G206000 chr1B 97.120 2326 47 8 1672 3994 392729030 392731338 0.000000e+00 3906.0
4 TraesCS1D01G206000 chr1B 92.935 736 38 10 4081 4815 392731338 392732060 0.000000e+00 1059.0
5 TraesCS1D01G206000 chr1B 94.799 596 29 1 819 1414 392721541 392722134 0.000000e+00 928.0
6 TraesCS1D01G206000 chr1B 88.275 742 55 20 4948 5673 392736537 392737262 0.000000e+00 859.0
7 TraesCS1D01G206000 chr1B 86.563 387 31 10 4569 4946 392736124 392736498 1.900000e-109 407.0
8 TraesCS1D01G206000 chr1B 92.179 179 12 1 1 179 392720557 392720733 9.440000e-63 252.0
9 TraesCS1D01G206000 chr1B 95.484 155 6 1 4417 4571 392735890 392736043 4.390000e-61 246.0
10 TraesCS1D01G206000 chr1B 89.781 137 4 5 4817 4946 392734717 392734850 3.520000e-37 167.0
11 TraesCS1D01G206000 chr1A 94.683 2257 93 9 1746 3995 363693200 363695436 0.000000e+00 3478.0
12 TraesCS1D01G206000 chr1A 93.878 2058 111 6 1756 3812 363426937 363424894 0.000000e+00 3088.0
13 TraesCS1D01G206000 chr1A 87.979 1123 86 27 4083 5172 363695437 363696543 0.000000e+00 1280.0
14 TraesCS1D01G206000 chr1A 91.807 830 30 9 614 1415 363690271 363691090 0.000000e+00 1122.0
15 TraesCS1D01G206000 chr1A 90.781 640 38 13 4248 4867 363424260 363423622 0.000000e+00 835.0
16 TraesCS1D01G206000 chr1A 87.699 439 34 8 5240 5671 363697954 363698379 1.420000e-135 494.0
17 TraesCS1D01G206000 chr1A 92.553 282 7 3 1452 1729 363692710 363692981 5.330000e-105 392.0
18 TraesCS1D01G206000 chr1A 94.175 206 7 2 3789 3994 363424714 363424514 5.520000e-80 309.0
19 TraesCS1D01G206000 chr1A 93.413 167 11 0 4083 4249 363424509 363424343 1.220000e-61 248.0
20 TraesCS1D01G206000 chr2D 84.388 237 21 5 1454 1690 18206530 18206750 9.570000e-53 219.0
21 TraesCS1D01G206000 chr2D 82.278 237 26 9 1452 1686 378360071 378360293 2.090000e-44 191.0
22 TraesCS1D01G206000 chr3B 85.000 220 17 7 1467 1686 654346266 654346063 5.760000e-50 209.0
23 TraesCS1D01G206000 chr3B 83.475 236 22 8 1452 1686 654355676 654355457 2.680000e-48 204.0
24 TraesCS1D01G206000 chr3A 85.238 210 17 3 1462 1671 46168418 46168223 2.680000e-48 204.0
25 TraesCS1D01G206000 chr3A 94.792 96 4 1 3999 4093 43293382 43293477 1.270000e-31 148.0
26 TraesCS1D01G206000 chr3A 92.157 51 2 2 3673 3722 252529758 252529807 2.840000e-08 71.3
27 TraesCS1D01G206000 chr3A 92.857 42 3 0 1407 1448 604327328 604327369 1.710000e-05 62.1
28 TraesCS1D01G206000 chr3D 89.024 164 12 2 1523 1686 495320565 495320408 1.250000e-46 198.0
29 TraesCS1D01G206000 chr3D 88.060 67 4 4 1454 1518 466817850 466817914 6.100000e-10 76.8
30 TraesCS1D01G206000 chr6A 81.897 232 27 6 1452 1682 412366482 412366265 1.260000e-41 182.0
31 TraesCS1D01G206000 chr6A 94.059 101 2 4 3986 4084 405449814 405449912 3.540000e-32 150.0
32 TraesCS1D01G206000 chr6A 93.878 98 6 0 3990 4087 548412694 548412791 1.270000e-31 148.0
33 TraesCS1D01G206000 chr6A 89.231 65 5 2 1455 1519 115348598 115348660 4.710000e-11 80.5
34 TraesCS1D01G206000 chr2A 87.037 162 15 5 1522 1682 744446469 744446313 1.620000e-40 178.0
35 TraesCS1D01G206000 chr2A 93.939 99 5 1 3991 4088 69386048 69385950 1.270000e-31 148.0
36 TraesCS1D01G206000 chr2A 78.771 179 24 8 1455 1631 751235854 751235688 2.160000e-19 108.0
37 TraesCS1D01G206000 chr2B 97.753 89 2 0 3996 4084 511275882 511275970 2.740000e-33 154.0
38 TraesCS1D01G206000 chr5D 93.939 99 6 0 3990 4088 458893836 458893934 3.540000e-32 150.0
39 TraesCS1D01G206000 chr5B 94.792 96 5 0 3993 4088 454649328 454649423 3.540000e-32 150.0
40 TraesCS1D01G206000 chr4A 91.667 108 7 2 3989 4095 640807564 640807670 1.270000e-31 148.0
41 TraesCS1D01G206000 chr6D 88.732 71 6 2 1452 1521 303623300 303623369 1.010000e-12 86.1
42 TraesCS1D01G206000 chr7D 93.182 44 2 1 1455 1498 614354413 614354455 4.750000e-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 TraesCS1D01G206000 chr1D 291787959 291793632 5673 False 10479.000000 10479 100.00000 1 5674 1 chr1D.!!$F1 5673
1 TraesCS1D01G206000 chr1D 291086611 291089662 3051 True 2169.500000 3066 91.87500 1702 4876 2 chr1D.!!$R1 3174
2 TraesCS1D01G206000 chr1B 392729030 392737262 8232 False 1107.333333 3906 91.69300 1672 5673 6 chr1B.!!$F2 4001
3 TraesCS1D01G206000 chr1B 392720557 392722134 1577 False 590.000000 928 93.48900 1 1414 2 chr1B.!!$F1 1413
4 TraesCS1D01G206000 chr1A 363690271 363698379 8108 False 1353.200000 3478 90.94420 614 5671 5 chr1A.!!$F1 5057
5 TraesCS1D01G206000 chr1A 363423622 363426937 3315 True 1120.000000 3088 93.06175 1756 4867 4 chr1A.!!$R1 3111

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
483 589 0.173481 TTCGGGATCGTCAAGCTCTG 59.827 55.0 0.00 0.0 37.69 3.35 F
489 595 0.176680 ATCGTCAAGCTCTGCGGAAT 59.823 50.0 0.00 0.0 0.00 3.01 F
493 599 0.179111 TCAAGCTCTGCGGAATACGG 60.179 55.0 0.00 0.0 44.51 4.02 F
531 637 0.250989 TTTGGCGACTCCCGGAAAAT 60.251 50.0 0.73 0.0 39.04 1.82 F
1518 3451 0.380378 GCGCGAGGATGGCAAATTTA 59.620 50.0 12.10 0.0 41.24 1.40 F
1593 3529 0.803380 GGTGAATTTGCCATGCTCGC 60.803 55.0 0.00 0.0 0.00 5.03 F
2338 4479 1.112916 TGCTGAAGTGACCCGAGACA 61.113 55.0 0.00 0.0 0.00 3.41 F
3074 5219 0.034089 AGGAGCCTTAACACCATGGC 60.034 55.0 13.04 0.0 45.21 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1767 0.532115 AAATTTGCCATCCTCGTGCC 59.468 50.000 0.00 0.00 0.00 5.01 R
1571 3507 0.544833 AGCATGGCAAATTCACCCCA 60.545 50.000 0.00 0.00 0.00 4.96 R
1593 3529 2.019984 GAGGATGGCAAGTTTAGCTGG 58.980 52.381 0.00 0.00 0.00 4.85 R
1647 3583 4.467082 ACATCAGATTTTTAGGCATGGCAA 59.533 37.500 22.64 10.74 0.00 4.52 R
3031 5176 2.760385 GAGAGCCTACCCCACGCT 60.760 66.667 0.00 0.00 34.97 5.07 R
3062 5207 3.355378 CTCTCCAATGCCATGGTGTTAA 58.645 45.455 14.67 0.36 41.46 2.01 R
3997 6350 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73 R
4771 11522 0.693622 TACACGCCCTCCAATTCCAA 59.306 50.000 0.00 0.00 0.00 3.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 8.652810 ACAGAATATTTATGGAAAATTGCAGC 57.347 30.769 6.57 0.00 30.13 5.25
70 71 8.480501 ACAGAATATTTATGGAAAATTGCAGCT 58.519 29.630 0.00 0.00 30.13 4.24
88 89 4.502950 GCAGCTTTCATATCTCTAGCACCT 60.503 45.833 0.00 0.00 34.37 4.00
89 90 5.279206 GCAGCTTTCATATCTCTAGCACCTA 60.279 44.000 0.00 0.00 34.37 3.08
122 123 5.120674 GCAACTGGTTTAAATTTGGCTGATC 59.879 40.000 0.00 0.00 0.00 2.92
127 128 5.242838 TGGTTTAAATTTGGCTGATCGTCTT 59.757 36.000 0.00 0.00 0.00 3.01
132 133 5.712152 AATTTGGCTGATCGTCTTCTTTT 57.288 34.783 0.00 0.00 0.00 2.27
139 140 5.447010 GGCTGATCGTCTTCTTTTCATTCTG 60.447 44.000 0.00 0.00 0.00 3.02
141 142 5.793817 TGATCGTCTTCTTTTCATTCTGGA 58.206 37.500 0.00 0.00 0.00 3.86
179 180 5.738619 TGCTAAGTTGGTCTCATCAGTTA 57.261 39.130 0.00 0.00 0.00 2.24
180 181 6.109156 TGCTAAGTTGGTCTCATCAGTTAA 57.891 37.500 0.00 0.00 0.00 2.01
181 182 5.932303 TGCTAAGTTGGTCTCATCAGTTAAC 59.068 40.000 0.00 0.00 0.00 2.01
190 237 6.826231 TGGTCTCATCAGTTAACAAGTTTGAA 59.174 34.615 8.61 0.00 0.00 2.69
196 243 9.658475 TCATCAGTTAACAAGTTTGAATTTACG 57.342 29.630 8.61 0.00 0.00 3.18
206 253 5.556915 AGTTTGAATTTACGTGGAGATCCA 58.443 37.500 0.00 0.00 45.30 3.41
279 329 3.444034 AGACGTGCAATAACTAGAGCAGA 59.556 43.478 0.00 0.00 37.72 4.26
293 343 2.961721 CAGAGTGTGTGTGCGCGT 60.962 61.111 8.43 0.00 0.00 6.01
296 346 1.947146 GAGTGTGTGTGCGCGTGTA 60.947 57.895 8.43 0.00 0.00 2.90
313 363 6.291955 GCGCGTGTATTGTGTTGTATATTAGT 60.292 38.462 8.43 0.00 0.00 2.24
315 365 8.908678 CGCGTGTATTGTGTTGTATATTAGTAT 58.091 33.333 0.00 0.00 0.00 2.12
361 413 5.221165 GCGCACCAATATACCCAAAGTAAAT 60.221 40.000 0.30 0.00 33.70 1.40
371 423 2.286418 CCCAAAGTAAATGCGAGCGATC 60.286 50.000 0.00 0.00 0.00 3.69
377 429 2.203800 AAATGCGAGCGATCGAGTTA 57.796 45.000 29.29 9.74 34.64 2.24
380 446 0.317854 TGCGAGCGATCGAGTTATGG 60.318 55.000 29.29 0.00 34.64 2.74
408 512 1.607178 CCAATGAAGCTGCCCACCA 60.607 57.895 0.00 0.00 0.00 4.17
409 513 0.974010 CCAATGAAGCTGCCCACCAT 60.974 55.000 0.00 0.00 0.00 3.55
421 525 1.868469 CCCACCATTGTGCAAAACAG 58.132 50.000 0.00 0.00 40.74 3.16
428 532 0.610174 TTGTGCAAAACAGGCCACAA 59.390 45.000 5.01 0.35 40.74 3.33
433 537 1.118838 CAAAACAGGCCACAAGGGAA 58.881 50.000 5.01 0.00 40.01 3.97
438 542 0.610232 CAGGCCACAAGGGAAAGGAG 60.610 60.000 5.01 0.00 40.01 3.69
440 544 1.460699 GCCACAAGGGAAAGGAGGT 59.539 57.895 0.00 0.00 40.01 3.85
441 545 0.895559 GCCACAAGGGAAAGGAGGTG 60.896 60.000 0.00 0.00 40.01 4.00
455 561 7.421382 GGGAAAGGAGGTGATATCTTTGGATTA 60.421 40.741 3.98 0.00 33.71 1.75
456 562 7.998964 GGAAAGGAGGTGATATCTTTGGATTAA 59.001 37.037 3.98 0.00 33.71 1.40
457 563 8.986929 AAAGGAGGTGATATCTTTGGATTAAG 57.013 34.615 3.98 0.00 33.71 1.85
458 564 7.084268 AGGAGGTGATATCTTTGGATTAAGG 57.916 40.000 3.98 0.00 33.71 2.69
459 565 5.707764 GGAGGTGATATCTTTGGATTAAGGC 59.292 44.000 3.98 0.00 33.71 4.35
460 566 5.635120 AGGTGATATCTTTGGATTAAGGCC 58.365 41.667 3.98 0.00 33.71 5.19
461 567 4.767409 GGTGATATCTTTGGATTAAGGCCC 59.233 45.833 0.00 0.00 33.71 5.80
462 568 5.458215 GGTGATATCTTTGGATTAAGGCCCT 60.458 44.000 0.00 0.00 33.71 5.19
463 569 5.707764 GTGATATCTTTGGATTAAGGCCCTC 59.292 44.000 0.00 0.00 33.71 4.30
464 570 5.612688 TGATATCTTTGGATTAAGGCCCTCT 59.387 40.000 0.00 0.00 33.71 3.69
465 571 4.888626 ATCTTTGGATTAAGGCCCTCTT 57.111 40.909 0.00 0.00 39.40 2.85
466 572 4.236527 TCTTTGGATTAAGGCCCTCTTC 57.763 45.455 0.00 0.00 36.93 2.87
467 573 2.710096 TTGGATTAAGGCCCTCTTCG 57.290 50.000 0.00 0.00 36.93 3.79
468 574 0.837272 TGGATTAAGGCCCTCTTCGG 59.163 55.000 0.00 0.00 36.93 4.30
478 584 3.650409 CCTCTTCGGGATCGTCAAG 57.350 57.895 0.00 0.00 37.69 3.02
479 585 0.528684 CCTCTTCGGGATCGTCAAGC 60.529 60.000 0.00 0.00 37.69 4.01
480 586 0.457851 CTCTTCGGGATCGTCAAGCT 59.542 55.000 0.00 0.00 37.69 3.74
481 587 0.456221 TCTTCGGGATCGTCAAGCTC 59.544 55.000 0.00 0.00 37.69 4.09
482 588 0.457851 CTTCGGGATCGTCAAGCTCT 59.542 55.000 0.00 0.00 37.69 4.09
483 589 0.173481 TTCGGGATCGTCAAGCTCTG 59.827 55.000 0.00 0.00 37.69 3.35
484 590 1.880340 CGGGATCGTCAAGCTCTGC 60.880 63.158 0.00 0.00 0.00 4.26
485 591 1.880340 GGGATCGTCAAGCTCTGCG 60.880 63.158 0.00 0.00 0.00 5.18
486 592 1.880340 GGATCGTCAAGCTCTGCGG 60.880 63.158 0.00 0.00 0.00 5.69
487 593 1.139734 GATCGTCAAGCTCTGCGGA 59.860 57.895 0.00 0.00 0.00 5.54
488 594 0.458543 GATCGTCAAGCTCTGCGGAA 60.459 55.000 0.00 0.00 0.00 4.30
489 595 0.176680 ATCGTCAAGCTCTGCGGAAT 59.823 50.000 0.00 0.00 0.00 3.01
490 596 0.815095 TCGTCAAGCTCTGCGGAATA 59.185 50.000 0.00 0.00 0.00 1.75
491 597 0.924090 CGTCAAGCTCTGCGGAATAC 59.076 55.000 0.00 0.00 0.00 1.89
493 599 0.179111 TCAAGCTCTGCGGAATACGG 60.179 55.000 0.00 0.00 44.51 4.02
494 600 1.144057 AAGCTCTGCGGAATACGGG 59.856 57.895 0.00 0.00 44.51 5.28
495 601 2.280186 GCTCTGCGGAATACGGGG 60.280 66.667 0.00 0.00 44.51 5.73
496 602 2.421739 CTCTGCGGAATACGGGGG 59.578 66.667 0.00 0.00 44.51 5.40
497 603 3.809374 CTCTGCGGAATACGGGGGC 62.809 68.421 0.00 0.00 44.51 5.80
501 607 4.597215 CGGAATACGGGGGCGGAC 62.597 72.222 0.00 0.00 39.42 4.79
502 608 3.472726 GGAATACGGGGGCGGACA 61.473 66.667 0.00 0.00 0.00 4.02
503 609 2.108362 GAATACGGGGGCGGACAG 59.892 66.667 0.00 0.00 0.00 3.51
504 610 3.456105 GAATACGGGGGCGGACAGG 62.456 68.421 0.00 0.00 0.00 4.00
515 621 3.365265 GGACAGGGCGCCACTTTG 61.365 66.667 30.85 21.60 0.00 2.77
516 622 3.365265 GACAGGGCGCCACTTTGG 61.365 66.667 30.85 13.19 41.55 3.28
525 631 2.742372 CCACTTTGGCGACTCCCG 60.742 66.667 0.00 0.00 42.21 5.14
526 632 2.742372 CACTTTGGCGACTCCCGG 60.742 66.667 0.00 0.00 39.04 5.73
527 633 2.920912 ACTTTGGCGACTCCCGGA 60.921 61.111 0.73 0.00 39.04 5.14
528 634 2.345991 CTTTGGCGACTCCCGGAA 59.654 61.111 0.73 0.00 39.04 4.30
529 635 1.302192 CTTTGGCGACTCCCGGAAA 60.302 57.895 0.73 0.00 39.04 3.13
530 636 0.887387 CTTTGGCGACTCCCGGAAAA 60.887 55.000 0.73 0.00 39.04 2.29
531 637 0.250989 TTTGGCGACTCCCGGAAAAT 60.251 50.000 0.73 0.00 39.04 1.82
532 638 0.614294 TTGGCGACTCCCGGAAAATA 59.386 50.000 0.73 0.00 39.04 1.40
533 639 0.834612 TGGCGACTCCCGGAAAATAT 59.165 50.000 0.73 0.00 39.04 1.28
534 640 1.226746 GGCGACTCCCGGAAAATATG 58.773 55.000 0.73 0.00 39.04 1.78
535 641 1.202604 GGCGACTCCCGGAAAATATGA 60.203 52.381 0.73 0.00 39.04 2.15
536 642 2.550208 GGCGACTCCCGGAAAATATGAT 60.550 50.000 0.73 0.00 39.04 2.45
537 643 2.480419 GCGACTCCCGGAAAATATGATG 59.520 50.000 0.73 0.00 39.04 3.07
538 644 2.480419 CGACTCCCGGAAAATATGATGC 59.520 50.000 0.73 0.00 33.91 3.91
539 645 2.480419 GACTCCCGGAAAATATGATGCG 59.520 50.000 0.73 0.00 0.00 4.73
542 648 1.604604 CCGGAAAATATGATGCGGGT 58.395 50.000 11.64 0.00 45.47 5.28
543 649 1.535462 CCGGAAAATATGATGCGGGTC 59.465 52.381 11.64 0.00 45.47 4.46
544 650 1.194547 CGGAAAATATGATGCGGGTCG 59.805 52.381 0.00 0.00 0.00 4.79
565 671 4.116328 CGCTCCACCGCTCGAGAA 62.116 66.667 18.75 0.00 0.00 2.87
566 672 2.202676 GCTCCACCGCTCGAGAAG 60.203 66.667 18.75 8.72 0.00 2.85
590 696 4.056125 TGCGGTGTCGGAGAGCTG 62.056 66.667 0.00 0.00 36.95 4.24
592 698 4.803426 CGGTGTCGGAGAGCTGCC 62.803 72.222 0.00 0.00 36.95 4.85
648 754 5.178797 ACTGTATTGAGCTTCGCTGTAATT 58.821 37.500 0.00 0.00 39.88 1.40
702 809 5.073965 TCCCCCTGTTTGAGTAACATAAAGT 59.926 40.000 0.00 0.00 45.31 2.66
909 1258 3.136123 CTGCCGCCTTGACCCATG 61.136 66.667 0.00 0.00 0.00 3.66
1004 1353 0.394216 CCCTGTGCCGAATCAATGGA 60.394 55.000 0.00 0.00 0.00 3.41
1065 1414 3.151022 CCTCCTCCTCGTCTGGCC 61.151 72.222 0.00 0.00 0.00 5.36
1217 1566 4.141287 CCCTCTACTGAATCTCGAGTGAT 58.859 47.826 13.13 0.00 0.00 3.06
1296 1645 2.951642 TGCTTTCTGACAAGGGTTTCTG 59.048 45.455 0.00 0.00 0.00 3.02
1358 1707 1.886886 TTTACCAGGGTTTCGAGCAC 58.113 50.000 0.00 0.00 0.00 4.40
1418 1767 8.783833 AGCTCAAATAGGTGCTATATATGTTG 57.216 34.615 0.00 0.00 33.68 3.33
1419 1768 7.826252 AGCTCAAATAGGTGCTATATATGTTGG 59.174 37.037 0.00 0.00 33.68 3.77
1420 1769 7.414540 GCTCAAATAGGTGCTATATATGTTGGC 60.415 40.741 0.00 0.00 0.00 4.52
1421 1770 7.457561 TCAAATAGGTGCTATATATGTTGGCA 58.542 34.615 0.00 0.00 0.00 4.92
1425 1774 4.910746 GTGCTATATATGTTGGCACGAG 57.089 45.455 11.37 0.00 42.53 4.18
1426 1775 3.679980 GTGCTATATATGTTGGCACGAGG 59.320 47.826 11.37 0.00 42.53 4.63
1427 1776 3.576550 TGCTATATATGTTGGCACGAGGA 59.423 43.478 0.00 0.00 0.00 3.71
1428 1777 4.222810 TGCTATATATGTTGGCACGAGGAT 59.777 41.667 0.00 0.00 0.00 3.24
1429 1778 4.568359 GCTATATATGTTGGCACGAGGATG 59.432 45.833 0.00 0.00 0.00 3.51
1430 1779 2.260844 ATATGTTGGCACGAGGATGG 57.739 50.000 0.00 0.00 0.00 3.51
1435 1784 3.924507 GGCACGAGGATGGCAAAT 58.075 55.556 0.00 0.00 44.34 2.32
1438 1787 1.748493 GGCACGAGGATGGCAAATTTA 59.252 47.619 0.00 0.00 44.34 1.40
1439 1788 2.223572 GGCACGAGGATGGCAAATTTAG 60.224 50.000 0.00 0.00 44.34 1.85
1440 1789 2.423538 GCACGAGGATGGCAAATTTAGT 59.576 45.455 0.00 0.00 0.00 2.24
1442 1791 4.618227 GCACGAGGATGGCAAATTTAGTTT 60.618 41.667 0.00 0.00 0.00 2.66
1491 3424 5.844301 ATCAAACGTTTTTCATGGCAATC 57.156 34.783 11.66 0.00 0.00 2.67
1516 3449 2.774799 GGCGCGAGGATGGCAAATT 61.775 57.895 12.10 0.00 41.24 1.82
1517 3450 1.139520 GCGCGAGGATGGCAAATTT 59.860 52.632 12.10 0.00 41.24 1.82
1518 3451 0.380378 GCGCGAGGATGGCAAATTTA 59.620 50.000 12.10 0.00 41.24 1.40
1519 3452 1.597937 GCGCGAGGATGGCAAATTTAG 60.598 52.381 12.10 0.00 41.24 1.85
1520 3453 1.670811 CGCGAGGATGGCAAATTTAGT 59.329 47.619 0.00 0.00 41.24 2.24
1521 3454 2.286418 CGCGAGGATGGCAAATTTAGTC 60.286 50.000 0.00 0.00 41.24 2.59
1522 3455 2.682856 GCGAGGATGGCAAATTTAGTCA 59.317 45.455 0.00 0.00 40.68 3.41
1523 3456 3.128589 GCGAGGATGGCAAATTTAGTCAA 59.871 43.478 0.00 0.00 40.68 3.18
1524 3457 4.380444 GCGAGGATGGCAAATTTAGTCAAA 60.380 41.667 0.00 0.00 40.68 2.69
1525 3458 5.679638 GCGAGGATGGCAAATTTAGTCAAAT 60.680 40.000 0.00 0.00 40.68 2.32
1593 3529 0.803380 GGTGAATTTGCCATGCTCGC 60.803 55.000 0.00 0.00 0.00 5.03
1647 3583 3.634568 TGCCATGAAAAACGTTCGATT 57.365 38.095 0.00 0.00 0.00 3.34
1866 4005 7.416154 AATCATTTGCAATCTGTTTCAGTTG 57.584 32.000 0.00 0.00 32.61 3.16
2006 4145 6.974622 TGAAAATGAAGAAAGTGAAACAGAGC 59.025 34.615 0.00 0.00 41.43 4.09
2012 4151 7.047891 TGAAGAAAGTGAAACAGAGCTAGAAA 58.952 34.615 0.00 0.00 41.43 2.52
2013 4152 7.552687 TGAAGAAAGTGAAACAGAGCTAGAAAA 59.447 33.333 0.00 0.00 41.43 2.29
2071 4210 2.479837 TGCTGACCGTAAGAAACAGTG 58.520 47.619 0.00 0.00 43.02 3.66
2146 4285 8.303876 GGTTTGTGCTCTTTCCTTATAAATTCA 58.696 33.333 0.00 0.00 0.00 2.57
2233 4372 9.134734 GTTTTGTGTTTGATGAAAGTAAAGACA 57.865 29.630 0.00 0.00 36.29 3.41
2293 4432 7.045416 TGAACACTTCAACTTTACAGCTAAGA 58.955 34.615 1.70 0.00 36.59 2.10
2338 4479 1.112916 TGCTGAAGTGACCCGAGACA 61.113 55.000 0.00 0.00 0.00 3.41
2453 4594 5.805728 AGTAGTGCTATATAATGGGTTGCC 58.194 41.667 0.00 0.00 0.00 4.52
2765 4908 3.552875 TCCTAGATCTGTCACCTTACCG 58.447 50.000 5.18 0.00 0.00 4.02
2862 5005 6.603201 CCTTACATAACATTGAATCCCTGTGT 59.397 38.462 0.00 0.00 0.00 3.72
3031 5176 1.562942 TCGGTCCTCAAGCTCCTACTA 59.437 52.381 0.00 0.00 0.00 1.82
3062 5207 2.416680 GCTCTCAAATGAAGGAGCCT 57.583 50.000 11.58 0.00 43.51 4.58
3074 5219 0.034089 AGGAGCCTTAACACCATGGC 60.034 55.000 13.04 0.00 45.21 4.40
3373 5518 1.548719 CACGTGTCTCAAGTATCCCCA 59.451 52.381 7.58 0.00 0.00 4.96
3391 5536 2.224113 CCCAAGCTGCAAAGAACACAAT 60.224 45.455 1.02 0.00 0.00 2.71
3392 5537 3.460103 CCAAGCTGCAAAGAACACAATT 58.540 40.909 1.02 0.00 0.00 2.32
3393 5538 4.501229 CCCAAGCTGCAAAGAACACAATTA 60.501 41.667 1.02 0.00 0.00 1.40
3394 5539 4.682860 CCAAGCTGCAAAGAACACAATTAG 59.317 41.667 1.02 0.00 0.00 1.73
3395 5540 5.507817 CCAAGCTGCAAAGAACACAATTAGA 60.508 40.000 1.02 0.00 0.00 2.10
3396 5541 5.772825 AGCTGCAAAGAACACAATTAGAA 57.227 34.783 1.02 0.00 0.00 2.10
3397 5542 6.147864 AGCTGCAAAGAACACAATTAGAAA 57.852 33.333 1.02 0.00 0.00 2.52
3398 5543 6.752168 AGCTGCAAAGAACACAATTAGAAAT 58.248 32.000 1.02 0.00 0.00 2.17
3426 5571 4.689612 TTGGAGTCTAGGTGCCAATATC 57.310 45.455 6.91 0.00 35.61 1.63
3436 5581 2.912956 GGTGCCAATATCCCCTCTGATA 59.087 50.000 0.00 0.00 0.00 2.15
3731 5882 0.756442 AAATCATGGCCGGGGATGTG 60.756 55.000 2.18 0.00 0.00 3.21
3851 6204 1.021390 CAGCTGGTGAAACGGGCTAG 61.021 60.000 5.57 0.00 41.86 3.42
3852 6205 2.399356 GCTGGTGAAACGGGCTAGC 61.399 63.158 6.04 6.04 38.12 3.42
3853 6206 1.296715 CTGGTGAAACGGGCTAGCT 59.703 57.895 15.72 0.00 38.12 3.32
3854 6207 0.535335 CTGGTGAAACGGGCTAGCTA 59.465 55.000 15.72 0.00 38.12 3.32
3884 6237 6.070710 AGGACTCCAGTTCTAGTTAACATTCC 60.071 42.308 8.61 0.00 30.53 3.01
3994 6347 8.715088 GCGTGTTCTCTTACTTTTAGGAAATAA 58.285 33.333 0.00 0.00 0.00 1.40
4015 6368 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
4025 6378 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
4034 6387 7.804129 CGTCCCAAAATATAAGAACGTTTTTGA 59.196 33.333 13.87 2.81 38.79 2.69
4066 6419 8.995220 TGCTAGTGTCAAAAACGTTCTTATATT 58.005 29.630 0.00 0.00 0.00 1.28
4067 6420 9.821662 GCTAGTGTCAAAAACGTTCTTATATTT 57.178 29.630 0.00 0.00 0.00 1.40
4105 6461 4.647564 ATATGCATTGGGAAGTCTAGGG 57.352 45.455 3.54 0.00 0.00 3.53
4150 6506 8.571461 AAGCATCCACCATACAATATATGAAG 57.429 34.615 0.00 0.00 0.00 3.02
4191 6548 7.235080 CGAGATAAGCAAGAGCAATCAATATG 58.765 38.462 0.00 0.00 45.49 1.78
4279 6720 9.189723 CACACAGTAGTTATGATGATGTAGATG 57.810 37.037 0.00 0.00 0.00 2.90
4717 7165 4.689705 GCCATAAAGAATGTCTGATGGGGA 60.690 45.833 15.91 0.00 35.41 4.81
4723 7171 1.275666 ATGTCTGATGGGGACGTTGA 58.724 50.000 0.00 0.00 36.58 3.18
4774 11525 2.723124 GTGGTGCCACACTTATTTGG 57.277 50.000 15.81 0.00 45.53 3.28
4775 11526 2.235016 GTGGTGCCACACTTATTTGGA 58.765 47.619 15.81 0.00 45.53 3.53
4776 11527 2.625790 GTGGTGCCACACTTATTTGGAA 59.374 45.455 15.81 0.00 45.53 3.53
4908 11684 5.700722 CAGCATATGCAACCATTCATACT 57.299 39.130 28.62 0.81 45.16 2.12
4909 11685 6.806388 CAGCATATGCAACCATTCATACTA 57.194 37.500 28.62 0.00 45.16 1.82
4946 11722 3.389656 TCTTGTGGTGGTATTCTGTGACA 59.610 43.478 0.00 0.00 0.00 3.58
4957 11770 5.414454 GGTATTCTGTGACAACCAGCAATTA 59.586 40.000 0.00 0.00 0.00 1.40
5016 11829 7.895975 TGAATCACATTCAGAGTTGTCTTAG 57.104 36.000 0.00 0.00 43.84 2.18
5017 11830 6.875726 TGAATCACATTCAGAGTTGTCTTAGG 59.124 38.462 0.00 0.00 43.84 2.69
5018 11831 6.611613 ATCACATTCAGAGTTGTCTTAGGA 57.388 37.500 0.00 0.00 0.00 2.94
5019 11832 6.419484 TCACATTCAGAGTTGTCTTAGGAA 57.581 37.500 0.00 0.00 0.00 3.36
5020 11833 6.459066 TCACATTCAGAGTTGTCTTAGGAAG 58.541 40.000 0.00 0.00 0.00 3.46
5021 11834 6.042093 TCACATTCAGAGTTGTCTTAGGAAGT 59.958 38.462 0.00 0.00 0.00 3.01
5022 11835 7.232737 TCACATTCAGAGTTGTCTTAGGAAGTA 59.767 37.037 0.00 0.00 0.00 2.24
5023 11836 8.037758 CACATTCAGAGTTGTCTTAGGAAGTAT 58.962 37.037 0.00 0.00 0.00 2.12
5028 11847 9.393512 TCAGAGTTGTCTTAGGAAGTATAGTAC 57.606 37.037 0.00 0.00 0.00 2.73
5088 11907 2.467826 GCACCAGCGCCTTCTCATC 61.468 63.158 2.29 0.00 0.00 2.92
5089 11908 1.220206 CACCAGCGCCTTCTCATCT 59.780 57.895 2.29 0.00 0.00 2.90
5105 11924 0.620556 ATCTGGCGGTTCTTCCACAT 59.379 50.000 0.00 0.00 35.57 3.21
5106 11925 0.400213 TCTGGCGGTTCTTCCACATT 59.600 50.000 0.00 0.00 35.57 2.71
5107 11926 1.202879 TCTGGCGGTTCTTCCACATTT 60.203 47.619 0.00 0.00 35.57 2.32
5108 11927 2.039216 TCTGGCGGTTCTTCCACATTTA 59.961 45.455 0.00 0.00 35.57 1.40
5124 11943 7.040494 TCCACATTTATGTATGCAAACCAATG 58.960 34.615 0.00 0.00 39.39 2.82
5132 11951 2.758497 GCAAACCAATGCATCAGCC 58.242 52.632 0.00 0.00 45.70 4.85
5149 11968 4.005650 TCAGCCTGACATCAACAAAGATC 58.994 43.478 0.00 0.00 0.00 2.75
5150 11969 3.754850 CAGCCTGACATCAACAAAGATCA 59.245 43.478 0.00 0.00 0.00 2.92
5222 12052 8.742777 TCTACTTTTATTGTTAGCCTTCTCGTA 58.257 33.333 0.00 0.00 0.00 3.43
5230 12060 5.790593 TGTTAGCCTTCTCGTAACAAGATT 58.209 37.500 0.00 0.00 34.50 2.40
5232 12062 6.708949 TGTTAGCCTTCTCGTAACAAGATTTT 59.291 34.615 0.00 0.00 34.50 1.82
5249 13411 9.093458 ACAAGATTTTTGAAACTAGATCCCATT 57.907 29.630 0.00 0.00 0.00 3.16
5370 13535 6.220726 AGTTGTCACTTTTTAATTGTGCCT 57.779 33.333 0.00 0.00 0.00 4.75
5450 13615 7.994425 TTTTAATTCTGTCTGAGTTGGCATA 57.006 32.000 0.00 0.00 0.00 3.14
5553 13723 1.268488 GCAAACATGCTCGTGTGTTGA 60.268 47.619 14.98 0.00 38.47 3.18
5558 13728 4.305989 ACATGCTCGTGTGTTGAAAAAT 57.694 36.364 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.480501 AGCTGCAATTTTCCATAAATATTCTGT 58.519 29.630 1.02 0.00 0.00 3.41
67 68 8.694540 CATATAGGTGCTAGAGATATGAAAGCT 58.305 37.037 0.00 0.00 33.98 3.74
73 74 9.258826 GCAATTCATATAGGTGCTAGAGATATG 57.741 37.037 0.00 0.00 33.60 1.78
122 123 3.999663 AGCTCCAGAATGAAAAGAAGACG 59.000 43.478 0.00 0.00 39.69 4.18
127 128 9.685276 TCAAAATATAGCTCCAGAATGAAAAGA 57.315 29.630 0.00 0.00 39.69 2.52
132 133 9.716531 CATACTCAAAATATAGCTCCAGAATGA 57.283 33.333 0.00 0.00 39.69 2.57
139 140 9.495572 AACTTAGCATACTCAAAATATAGCTCC 57.504 33.333 0.00 0.00 32.70 4.70
141 142 9.277783 CCAACTTAGCATACTCAAAATATAGCT 57.722 33.333 0.00 0.00 35.06 3.32
152 153 5.907207 TGATGAGACCAACTTAGCATACTC 58.093 41.667 0.00 0.00 0.00 2.59
157 158 4.623932 AACTGATGAGACCAACTTAGCA 57.376 40.909 0.00 0.00 0.00 3.49
179 180 6.687081 TCTCCACGTAAATTCAAACTTGTT 57.313 33.333 0.00 0.00 0.00 2.83
180 181 6.072673 GGATCTCCACGTAAATTCAAACTTGT 60.073 38.462 0.00 0.00 35.64 3.16
181 182 6.072728 TGGATCTCCACGTAAATTCAAACTTG 60.073 38.462 0.00 0.00 42.01 3.16
245 295 9.162764 AGTTATTGCACGTCTAAATGACTTAAT 57.837 29.630 6.17 0.00 43.25 1.40
248 298 8.033038 TCTAGTTATTGCACGTCTAAATGACTT 58.967 33.333 13.55 3.63 43.25 3.01
261 311 4.328440 CACACTCTGCTCTAGTTATTGCAC 59.672 45.833 0.00 0.00 0.00 4.57
262 312 4.021104 ACACACTCTGCTCTAGTTATTGCA 60.021 41.667 0.00 0.00 0.00 4.08
279 329 0.878523 AATACACGCGCACACACACT 60.879 50.000 5.73 0.00 0.00 3.55
315 365 7.224753 TGCGCTGGTTTTTCATGTTTTATTTTA 59.775 29.630 9.73 0.00 0.00 1.52
316 366 6.037610 TGCGCTGGTTTTTCATGTTTTATTTT 59.962 30.769 9.73 0.00 0.00 1.82
317 367 5.525378 TGCGCTGGTTTTTCATGTTTTATTT 59.475 32.000 9.73 0.00 0.00 1.40
318 368 5.050431 GTGCGCTGGTTTTTCATGTTTTATT 60.050 36.000 9.73 0.00 0.00 1.40
319 369 4.447389 GTGCGCTGGTTTTTCATGTTTTAT 59.553 37.500 9.73 0.00 0.00 1.40
323 374 1.537990 GGTGCGCTGGTTTTTCATGTT 60.538 47.619 9.73 0.00 0.00 2.71
334 385 0.179032 TGGGTATATTGGTGCGCTGG 60.179 55.000 9.73 0.00 0.00 4.85
361 413 0.317854 CCATAACTCGATCGCTCGCA 60.318 55.000 11.09 0.00 44.65 5.10
371 423 3.861840 TGGCTTCTCTTTCCATAACTCG 58.138 45.455 0.00 0.00 0.00 4.18
377 429 3.446516 GCTTCATTGGCTTCTCTTTCCAT 59.553 43.478 0.00 0.00 0.00 3.41
380 446 3.672781 GCAGCTTCATTGGCTTCTCTTTC 60.673 47.826 0.00 0.00 38.03 2.62
408 512 0.829333 TGTGGCCTGTTTTGCACAAT 59.171 45.000 3.32 0.00 33.87 2.71
409 513 0.610174 TTGTGGCCTGTTTTGCACAA 59.390 45.000 3.32 0.00 33.87 3.33
421 525 1.304464 CCTCCTTTCCCTTGTGGCC 60.304 63.158 0.00 0.00 0.00 5.36
428 532 4.166919 CCAAAGATATCACCTCCTTTCCCT 59.833 45.833 5.32 0.00 0.00 4.20
433 537 7.521669 CCTTAATCCAAAGATATCACCTCCTT 58.478 38.462 5.32 0.00 30.42 3.36
438 542 4.767409 GGGCCTTAATCCAAAGATATCACC 59.233 45.833 0.84 0.00 30.42 4.02
440 544 5.612688 AGAGGGCCTTAATCCAAAGATATCA 59.387 40.000 7.89 0.00 30.42 2.15
441 545 6.133253 AGAGGGCCTTAATCCAAAGATATC 57.867 41.667 7.89 0.00 30.42 1.63
460 566 0.528684 GCTTGACGATCCCGAAGAGG 60.529 60.000 0.00 0.00 39.50 3.69
461 567 0.457851 AGCTTGACGATCCCGAAGAG 59.542 55.000 0.00 0.00 39.50 2.85
462 568 0.456221 GAGCTTGACGATCCCGAAGA 59.544 55.000 0.00 0.00 39.50 2.87
463 569 0.457851 AGAGCTTGACGATCCCGAAG 59.542 55.000 0.00 0.00 39.50 3.79
464 570 0.173481 CAGAGCTTGACGATCCCGAA 59.827 55.000 0.00 0.00 39.50 4.30
465 571 1.809869 CAGAGCTTGACGATCCCGA 59.190 57.895 0.00 0.00 39.50 5.14
466 572 1.880340 GCAGAGCTTGACGATCCCG 60.880 63.158 0.00 0.00 42.50 5.14
467 573 1.880340 CGCAGAGCTTGACGATCCC 60.880 63.158 0.00 0.00 0.00 3.85
468 574 1.880340 CCGCAGAGCTTGACGATCC 60.880 63.158 4.96 0.00 0.00 3.36
469 575 0.458543 TTCCGCAGAGCTTGACGATC 60.459 55.000 4.96 0.00 0.00 3.69
470 576 0.176680 ATTCCGCAGAGCTTGACGAT 59.823 50.000 4.96 0.00 0.00 3.73
471 577 0.815095 TATTCCGCAGAGCTTGACGA 59.185 50.000 4.96 0.00 0.00 4.20
472 578 0.924090 GTATTCCGCAGAGCTTGACG 59.076 55.000 0.00 0.00 0.00 4.35
473 579 0.924090 CGTATTCCGCAGAGCTTGAC 59.076 55.000 0.00 0.00 0.00 3.18
474 580 0.179111 CCGTATTCCGCAGAGCTTGA 60.179 55.000 0.00 0.00 34.38 3.02
475 581 1.154205 CCCGTATTCCGCAGAGCTTG 61.154 60.000 0.00 0.00 34.38 4.01
476 582 1.144057 CCCGTATTCCGCAGAGCTT 59.856 57.895 0.00 0.00 34.38 3.74
477 583 2.797278 CCCCGTATTCCGCAGAGCT 61.797 63.158 0.00 0.00 34.38 4.09
478 584 2.280186 CCCCGTATTCCGCAGAGC 60.280 66.667 0.00 0.00 34.38 4.09
479 585 2.421739 CCCCCGTATTCCGCAGAG 59.578 66.667 0.00 0.00 34.38 3.35
480 586 3.857038 GCCCCCGTATTCCGCAGA 61.857 66.667 0.00 0.00 34.38 4.26
484 590 4.597215 GTCCGCCCCCGTATTCCG 62.597 72.222 0.00 0.00 0.00 4.30
485 591 3.456105 CTGTCCGCCCCCGTATTCC 62.456 68.421 0.00 0.00 0.00 3.01
486 592 2.108362 CTGTCCGCCCCCGTATTC 59.892 66.667 0.00 0.00 0.00 1.75
487 593 3.476419 CCTGTCCGCCCCCGTATT 61.476 66.667 0.00 0.00 0.00 1.89
498 604 3.365265 CAAAGTGGCGCCCTGTCC 61.365 66.667 26.77 6.51 0.00 4.02
499 605 3.365265 CCAAAGTGGCGCCCTGTC 61.365 66.667 26.77 11.91 0.00 3.51
508 614 2.742372 CGGGAGTCGCCAAAGTGG 60.742 66.667 0.98 0.00 41.55 4.00
509 615 2.725203 TTCCGGGAGTCGCCAAAGTG 62.725 60.000 0.00 0.00 38.95 3.16
510 616 2.047213 TTTCCGGGAGTCGCCAAAGT 62.047 55.000 0.00 0.00 38.95 2.66
511 617 0.887387 TTTTCCGGGAGTCGCCAAAG 60.887 55.000 0.00 0.00 38.95 2.77
512 618 0.250989 ATTTTCCGGGAGTCGCCAAA 60.251 50.000 0.00 0.00 38.95 3.28
513 619 0.614294 TATTTTCCGGGAGTCGCCAA 59.386 50.000 0.00 0.00 38.95 4.52
514 620 0.834612 ATATTTTCCGGGAGTCGCCA 59.165 50.000 0.00 0.00 38.95 5.69
515 621 1.202604 TCATATTTTCCGGGAGTCGCC 60.203 52.381 0.00 0.00 37.59 5.54
516 622 2.234300 TCATATTTTCCGGGAGTCGC 57.766 50.000 0.00 0.00 37.59 5.19
517 623 2.480419 GCATCATATTTTCCGGGAGTCG 59.520 50.000 0.00 0.00 38.88 4.18
518 624 2.480419 CGCATCATATTTTCCGGGAGTC 59.520 50.000 0.00 0.00 0.00 3.36
519 625 2.494059 CGCATCATATTTTCCGGGAGT 58.506 47.619 0.00 0.00 0.00 3.85
520 626 1.806542 CCGCATCATATTTTCCGGGAG 59.193 52.381 0.00 0.00 32.58 4.30
521 627 1.890876 CCGCATCATATTTTCCGGGA 58.109 50.000 0.00 0.00 32.58 5.14
523 629 1.535462 GACCCGCATCATATTTTCCGG 59.465 52.381 0.00 0.00 35.74 5.14
524 630 1.194547 CGACCCGCATCATATTTTCCG 59.805 52.381 0.00 0.00 0.00 4.30
525 631 2.969443 CGACCCGCATCATATTTTCC 57.031 50.000 0.00 0.00 0.00 3.13
548 654 4.116328 TTCTCGAGCGGTGGAGCG 62.116 66.667 20.24 4.42 43.00 5.03
549 655 2.202676 CTTCTCGAGCGGTGGAGC 60.203 66.667 20.24 0.00 37.41 4.70
550 656 2.202676 GCTTCTCGAGCGGTGGAG 60.203 66.667 19.17 19.17 42.46 3.86
558 664 2.581953 GCAGCTCCGCTTCTCGAG 60.582 66.667 5.93 5.93 41.67 4.04
559 665 4.482684 CGCAGCTCCGCTTCTCGA 62.483 66.667 0.00 0.00 41.67 4.04
561 667 4.443266 ACCGCAGCTCCGCTTCTC 62.443 66.667 0.00 0.00 36.40 2.87
562 668 4.749310 CACCGCAGCTCCGCTTCT 62.749 66.667 0.00 0.00 36.40 2.85
568 674 4.803426 CTCCGACACCGCAGCTCC 62.803 72.222 0.00 0.00 0.00 4.70
569 675 3.691744 CTCTCCGACACCGCAGCTC 62.692 68.421 0.00 0.00 0.00 4.09
570 676 3.753434 CTCTCCGACACCGCAGCT 61.753 66.667 0.00 0.00 0.00 4.24
572 678 3.753434 AGCTCTCCGACACCGCAG 61.753 66.667 0.00 0.00 0.00 5.18
573 679 4.056125 CAGCTCTCCGACACCGCA 62.056 66.667 0.00 0.00 0.00 5.69
575 681 4.803426 GGCAGCTCTCCGACACCG 62.803 72.222 0.00 0.00 0.00 4.94
582 688 2.125350 CCTGTTCGGCAGCTCTCC 60.125 66.667 0.00 0.00 43.71 3.71
591 697 3.248602 GCATGTAATTAGAGCCTGTTCGG 59.751 47.826 0.00 0.00 0.00 4.30
592 698 4.122776 AGCATGTAATTAGAGCCTGTTCG 58.877 43.478 0.00 0.00 0.00 3.95
593 699 6.017852 GGTTAGCATGTAATTAGAGCCTGTTC 60.018 42.308 0.00 0.00 0.00 3.18
594 700 5.823045 GGTTAGCATGTAATTAGAGCCTGTT 59.177 40.000 0.00 0.00 0.00 3.16
595 701 5.131142 AGGTTAGCATGTAATTAGAGCCTGT 59.869 40.000 0.00 0.00 0.00 4.00
596 702 5.615289 AGGTTAGCATGTAATTAGAGCCTG 58.385 41.667 0.00 0.00 0.00 4.85
597 703 5.896073 AGGTTAGCATGTAATTAGAGCCT 57.104 39.130 0.00 0.00 0.00 4.58
702 809 0.179032 TGAACTTGGCTCGGCAAGAA 60.179 50.000 31.58 17.59 33.06 2.52
991 1340 0.742990 TGACGGTCCATTGATTCGGC 60.743 55.000 5.55 0.00 0.00 5.54
1004 1353 1.595993 CTGACCAGGACGATGACGGT 61.596 60.000 0.00 0.00 44.46 4.83
1065 1414 3.005540 GCAATGCGTTGGAAGGGGG 62.006 63.158 19.93 0.00 35.83 5.40
1217 1566 2.769663 AGTCTTGGTTGTGGTGTCACTA 59.230 45.455 2.35 0.00 43.94 2.74
1263 1612 6.552859 TGTCAGAAAGCACGAATTATGAAA 57.447 33.333 0.00 0.00 29.54 2.69
1275 1624 2.951642 CAGAAACCCTTGTCAGAAAGCA 59.048 45.455 0.00 0.00 0.00 3.91
1358 1707 2.154462 ACTCCAATGAAAAGCGACCAG 58.846 47.619 0.00 0.00 0.00 4.00
1415 1764 1.523154 TTTGCCATCCTCGTGCCAAC 61.523 55.000 0.00 0.00 0.00 3.77
1416 1765 0.611618 ATTTGCCATCCTCGTGCCAA 60.612 50.000 0.00 0.00 0.00 4.52
1418 1767 0.532115 AAATTTGCCATCCTCGTGCC 59.468 50.000 0.00 0.00 0.00 5.01
1419 1768 2.423538 ACTAAATTTGCCATCCTCGTGC 59.576 45.455 0.00 0.00 0.00 5.34
1420 1769 4.701956 AACTAAATTTGCCATCCTCGTG 57.298 40.909 0.00 0.00 0.00 4.35
1421 1770 5.059404 CAAACTAAATTTGCCATCCTCGT 57.941 39.130 0.00 0.00 41.30 4.18
1439 1788 9.810231 CCATGTGTAAAATCTAAATTTGCAAAC 57.190 29.630 15.41 0.00 34.83 2.93
1440 1789 8.502387 GCCATGTGTAAAATCTAAATTTGCAAA 58.498 29.630 15.44 15.44 34.83 3.68
1442 1791 7.157347 TGCCATGTGTAAAATCTAAATTTGCA 58.843 30.769 0.00 0.00 35.27 4.08
1443 1792 7.593875 TGCCATGTGTAAAATCTAAATTTGC 57.406 32.000 0.00 0.00 35.27 3.68
1446 1795 9.941325 TGATTTGCCATGTGTAAAATCTAAATT 57.059 25.926 15.06 0.00 32.09 1.82
1447 1796 9.941325 TTGATTTGCCATGTGTAAAATCTAAAT 57.059 25.926 15.06 0.00 32.09 1.40
1448 1797 9.770097 TTTGATTTGCCATGTGTAAAATCTAAA 57.230 25.926 15.06 12.10 32.09 1.85
1449 1798 9.202273 GTTTGATTTGCCATGTGTAAAATCTAA 57.798 29.630 15.06 12.44 32.09 2.10
1453 1802 5.988561 ACGTTTGATTTGCCATGTGTAAAAT 59.011 32.000 0.00 0.00 32.09 1.82
1491 3424 1.224069 CCATCCTCGCGCCAACATAG 61.224 60.000 0.00 0.00 0.00 2.23
1522 3455 2.799978 GCCGTGCTTGCAAACTAAATTT 59.200 40.909 0.00 0.00 0.00 1.82
1523 3456 2.223923 TGCCGTGCTTGCAAACTAAATT 60.224 40.909 0.00 0.00 35.40 1.82
1524 3457 1.339610 TGCCGTGCTTGCAAACTAAAT 59.660 42.857 0.00 0.00 35.40 1.40
1525 3458 0.741326 TGCCGTGCTTGCAAACTAAA 59.259 45.000 0.00 0.00 35.40 1.85
1566 3499 1.337118 GGCAAATTCACCCCAGTTCA 58.663 50.000 0.00 0.00 0.00 3.18
1571 3507 0.544833 AGCATGGCAAATTCACCCCA 60.545 50.000 0.00 0.00 0.00 4.96
1593 3529 2.019984 GAGGATGGCAAGTTTAGCTGG 58.980 52.381 0.00 0.00 0.00 4.85
1647 3583 4.467082 ACATCAGATTTTTAGGCATGGCAA 59.533 37.500 22.64 10.74 0.00 4.52
1781 3919 7.518370 GCACCCTATTGATAAACGAGTACAATG 60.518 40.741 0.00 0.00 33.99 2.82
1866 4005 6.144563 CACATCATCGTCACTACCATCATTAC 59.855 42.308 0.00 0.00 0.00 1.89
2146 4285 8.398665 GGAAATGTGCTCGAAATAAAGAGTTAT 58.601 33.333 0.00 0.00 36.88 1.89
2338 4479 7.257722 CAAAGAACATTACACAGTTGTCCTTT 58.742 34.615 0.00 0.00 37.15 3.11
2765 4908 7.606456 TCCTGACTAGATATGAAAACAACAACC 59.394 37.037 0.00 0.00 0.00 3.77
2889 5032 5.795441 GGCAAGACTCAATTCGAATACAAAC 59.205 40.000 11.83 4.01 0.00 2.93
3031 5176 2.760385 GAGAGCCTACCCCACGCT 60.760 66.667 0.00 0.00 34.97 5.07
3062 5207 3.355378 CTCTCCAATGCCATGGTGTTAA 58.645 45.455 14.67 0.36 41.46 2.01
3074 5219 4.261489 GCCAAGACATAATGCTCTCCAATG 60.261 45.833 0.00 0.00 0.00 2.82
3373 5518 5.772825 TCTAATTGTGTTCTTTGCAGCTT 57.227 34.783 0.00 0.00 0.00 3.74
3393 5538 7.554476 GCACCTAGACTCCAATTCTAAATTTCT 59.446 37.037 0.00 0.00 0.00 2.52
3394 5539 7.201741 GGCACCTAGACTCCAATTCTAAATTTC 60.202 40.741 0.00 0.00 0.00 2.17
3395 5540 6.603599 GGCACCTAGACTCCAATTCTAAATTT 59.396 38.462 0.00 0.00 0.00 1.82
3396 5541 6.122964 GGCACCTAGACTCCAATTCTAAATT 58.877 40.000 0.00 0.00 0.00 1.82
3397 5542 5.191722 TGGCACCTAGACTCCAATTCTAAAT 59.808 40.000 0.00 0.00 0.00 1.40
3398 5543 4.534500 TGGCACCTAGACTCCAATTCTAAA 59.466 41.667 0.00 0.00 0.00 1.85
3436 5581 8.239314 CAGATTGCGCACCAGATATTTATAATT 58.761 33.333 11.12 0.00 0.00 1.40
3454 5599 4.285292 GCTTTGATTATGGACAGATTGCG 58.715 43.478 0.00 0.00 0.00 4.85
3731 5882 1.069049 GCCATCTCTCTGCTCCTCTTC 59.931 57.143 0.00 0.00 0.00 2.87
3851 6204 4.479786 AGAACTGGAGTCCTGATTTAGC 57.520 45.455 21.84 0.00 0.00 3.09
3852 6205 6.783708 ACTAGAACTGGAGTCCTGATTTAG 57.216 41.667 21.84 18.92 0.00 1.85
3853 6206 8.529476 GTTAACTAGAACTGGAGTCCTGATTTA 58.471 37.037 21.84 9.28 0.00 1.40
3854 6207 7.016268 TGTTAACTAGAACTGGAGTCCTGATTT 59.984 37.037 21.84 8.62 0.00 2.17
3884 6237 4.158025 ACTCTGTGTTCTCCACTATTACCG 59.842 45.833 0.00 0.00 44.81 4.02
3994 6347 1.572415 TGGGACGGAGGGAGTACTATT 59.428 52.381 0.00 0.00 0.00 1.73
3995 6348 1.229131 TGGGACGGAGGGAGTACTAT 58.771 55.000 0.00 0.00 0.00 2.12
3996 6349 1.002069 TTGGGACGGAGGGAGTACTA 58.998 55.000 0.00 0.00 0.00 1.82
3997 6350 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
3998 6351 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
3999 6352 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4000 6353 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4040 6393 6.854496 ATAAGAACGTTTTTGACACTAGCA 57.146 33.333 13.87 0.00 0.00 3.49
4041 6394 9.821662 AAATATAAGAACGTTTTTGACACTAGC 57.178 29.630 13.87 0.00 0.00 3.42
4047 6400 8.908678 GTCCCAAAATATAAGAACGTTTTTGAC 58.091 33.333 13.87 5.89 38.79 3.18
4049 6402 7.061326 CCGTCCCAAAATATAAGAACGTTTTTG 59.939 37.037 13.87 12.16 37.14 2.44
4057 6410 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
4066 6419 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
4067 6420 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
4105 6461 6.488817 TGCTTAGGTTTTCGAACTGTAAAAC 58.511 36.000 0.00 8.27 42.28 2.43
4150 6506 7.489435 TGCTTATCTCGCTAAATACATAGCATC 59.511 37.037 7.06 0.00 46.94 3.91
4191 6548 7.383102 TGAAATGAGAATAGCCAGAGAAAAC 57.617 36.000 0.00 0.00 0.00 2.43
4655 7103 3.493002 CCTCTCAATCAGAGTCATCCTGC 60.493 52.174 0.00 0.00 46.85 4.85
4717 7165 6.925211 TGAGAATACAGAAGAAGATCAACGT 58.075 36.000 0.00 0.00 0.00 3.99
4771 11522 0.693622 TACACGCCCTCCAATTCCAA 59.306 50.000 0.00 0.00 0.00 3.53
4772 11523 0.916086 ATACACGCCCTCCAATTCCA 59.084 50.000 0.00 0.00 0.00 3.53
4773 11524 2.922740 TATACACGCCCTCCAATTCC 57.077 50.000 0.00 0.00 0.00 3.01
4774 11525 4.387862 CGTATTATACACGCCCTCCAATTC 59.612 45.833 3.16 0.00 31.94 2.17
4775 11526 4.202284 ACGTATTATACACGCCCTCCAATT 60.202 41.667 3.16 0.00 43.10 2.32
4776 11527 3.322828 ACGTATTATACACGCCCTCCAAT 59.677 43.478 3.16 0.00 43.10 3.16
4907 11683 6.105333 CCACAAGACAAGAGAAAGGATCTAG 58.895 44.000 0.00 0.00 38.96 2.43
4908 11684 5.544176 ACCACAAGACAAGAGAAAGGATCTA 59.456 40.000 0.00 0.00 38.96 1.98
4909 11685 4.349342 ACCACAAGACAAGAGAAAGGATCT 59.651 41.667 0.00 0.00 42.61 2.75
4993 11806 7.099764 TCCTAAGACAACTCTGAATGTGATTC 58.900 38.462 0.99 0.00 39.70 2.52
5124 11943 1.456296 TGTTGATGTCAGGCTGATGC 58.544 50.000 21.84 13.17 38.76 3.91
5132 11951 9.903682 AATTAAAGTGATCTTTGTTGATGTCAG 57.096 29.630 0.00 0.00 42.86 3.51
5197 12027 7.829378 ACGAGAAGGCTAACAATAAAAGTAG 57.171 36.000 0.00 0.00 0.00 2.57
5222 12052 8.477419 TGGGATCTAGTTTCAAAAATCTTGTT 57.523 30.769 0.00 0.00 0.00 2.83
5232 12062 9.308000 ACATGTTAAAATGGGATCTAGTTTCAA 57.692 29.630 10.41 0.00 31.46 2.69
5272 13434 6.345298 TCATAATCTGGCAACTATCAACGAA 58.655 36.000 0.00 0.00 37.61 3.85
5274 13436 5.755375 ACTCATAATCTGGCAACTATCAACG 59.245 40.000 0.00 0.00 37.61 4.10
5355 13520 4.448732 GGCAACTCAGGCACAATTAAAAAG 59.551 41.667 0.00 0.00 0.00 2.27
5367 13532 5.237048 TGAAATAAAAATGGCAACTCAGGC 58.763 37.500 0.00 0.00 37.61 4.85
5558 13728 8.170730 TCAAGTATGAGGCTAGGAGATGTAATA 58.829 37.037 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.