Multiple sequence alignment - TraesCS5A01G216400

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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 TraesCS5A01G216400 chr5A 100.000 3690 0 0 1 3690 433235256 433231567 0.000000e+00 6815.0
1 TraesCS5A01G216400 chr5A 94.118 119 7 0 481 599 1300338 1300456 8.140000e-42 182.0
2 TraesCS5A01G216400 chr5D 92.593 1485 68 22 921 2376 332429221 332427750 0.000000e+00 2095.0
3 TraesCS5A01G216400 chr5D 90.632 427 28 5 2602 3020 332410264 332409842 1.160000e-154 556.0
4 TraesCS5A01G216400 chr5D 92.749 331 12 2 600 925 332432276 332431953 5.580000e-128 468.0
5 TraesCS5A01G216400 chr5D 97.260 219 5 1 2368 2585 332410468 332410250 1.620000e-98 370.0
6 TraesCS5A01G216400 chr5D 98.137 161 3 0 323 483 332432442 332432282 7.800000e-72 281.0
7 TraesCS5A01G216400 chr5D 76.349 241 27 14 3 242 332432792 332432581 6.520000e-18 102.0
8 TraesCS5A01G216400 chr5D 85.135 74 7 1 169 242 332432592 332432523 5.110000e-09 73.1
9 TraesCS5A01G216400 chr5B 92.292 1492 72 15 924 2381 388312479 388310997 0.000000e+00 2078.0
10 TraesCS5A01G216400 chr5B 87.217 618 76 2 3074 3690 671131796 671132411 0.000000e+00 701.0
11 TraesCS5A01G216400 chr5B 92.806 278 9 5 213 482 388314092 388313818 3.450000e-105 392.0
12 TraesCS5A01G216400 chr5B 89.520 229 9 3 2369 2585 388310116 388309891 3.630000e-70 276.0
13 TraesCS5A01G216400 chr5B 93.373 166 6 5 752 916 388313628 388313467 1.320000e-59 241.0
14 TraesCS5A01G216400 chr5B 91.391 151 6 4 600 750 388313811 388313668 2.250000e-47 200.0
15 TraesCS5A01G216400 chr5B 85.135 74 7 1 169 242 388314044 388313975 5.110000e-09 73.1
16 TraesCS5A01G216400 chr1A 96.446 619 22 0 3072 3690 558596420 558597038 0.000000e+00 1022.0
17 TraesCS5A01G216400 chr1B 89.127 607 65 1 3071 3677 32753117 32753722 0.000000e+00 754.0
18 TraesCS5A01G216400 chr1B 83.683 619 94 7 3072 3686 666642472 666641857 8.890000e-161 577.0
19 TraesCS5A01G216400 chr2A 88.704 602 67 1 3084 3685 207925035 207924435 0.000000e+00 734.0
20 TraesCS5A01G216400 chr7B 85.761 618 87 1 3074 3690 744722027 744721410 0.000000e+00 652.0
21 TraesCS5A01G216400 chr2D 85.572 603 81 6 3071 3670 633556263 633555664 8.700000e-176 627.0
22 TraesCS5A01G216400 chr2B 84.715 615 92 2 3072 3686 91026575 91025963 6.770000e-172 614.0
23 TraesCS5A01G216400 chr4A 84.168 619 88 9 3072 3686 741791411 741790799 3.170000e-165 592.0
24 TraesCS5A01G216400 chr4A 92.500 120 8 1 481 599 203256349 203256468 1.760000e-38 171.0
25 TraesCS5A01G216400 chr4A 92.500 120 8 1 481 599 707659519 707659638 1.760000e-38 171.0
26 TraesCS5A01G216400 chr7A 94.118 119 7 0 481 599 544260219 544260101 8.140000e-42 182.0
27 TraesCS5A01G216400 chr6B 92.500 120 8 1 481 599 29755218 29755099 1.760000e-38 171.0
28 TraesCS5A01G216400 chr6A 92.500 120 8 1 481 599 423274286 423274405 1.760000e-38 171.0
29 TraesCS5A01G216400 chr4D 92.500 120 8 1 481 599 289405111 289405230 1.760000e-38 171.0
30 TraesCS5A01G216400 chr3D 92.500 120 8 1 481 599 148770030 148770149 1.760000e-38 171.0
31 TraesCS5A01G216400 chr1D 92.500 120 8 1 481 599 426274191 426274310 1.760000e-38 171.0


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 TraesCS5A01G216400 chr5A 433231567 433235256 3689 True 6815.00 6815 100.000000 1 3690 1 chr5A.!!$R1 3689
1 TraesCS5A01G216400 chr5D 332427750 332432792 5042 True 603.82 2095 88.992600 3 2376 5 chr5D.!!$R2 2373
2 TraesCS5A01G216400 chr5D 332409842 332410468 626 True 463.00 556 93.946000 2368 3020 2 chr5D.!!$R1 652
3 TraesCS5A01G216400 chr5B 671131796 671132411 615 False 701.00 701 87.217000 3074 3690 1 chr5B.!!$F1 616
4 TraesCS5A01G216400 chr5B 388309891 388314092 4201 True 543.35 2078 90.752833 169 2585 6 chr5B.!!$R1 2416
5 TraesCS5A01G216400 chr1A 558596420 558597038 618 False 1022.00 1022 96.446000 3072 3690 1 chr1A.!!$F1 618
6 TraesCS5A01G216400 chr1B 32753117 32753722 605 False 754.00 754 89.127000 3071 3677 1 chr1B.!!$F1 606
7 TraesCS5A01G216400 chr1B 666641857 666642472 615 True 577.00 577 83.683000 3072 3686 1 chr1B.!!$R1 614
8 TraesCS5A01G216400 chr2A 207924435 207925035 600 True 734.00 734 88.704000 3084 3685 1 chr2A.!!$R1 601
9 TraesCS5A01G216400 chr7B 744721410 744722027 617 True 652.00 652 85.761000 3074 3690 1 chr7B.!!$R1 616
10 TraesCS5A01G216400 chr2D 633555664 633556263 599 True 627.00 627 85.572000 3071 3670 1 chr2D.!!$R1 599
11 TraesCS5A01G216400 chr2B 91025963 91026575 612 True 614.00 614 84.715000 3072 3686 1 chr2B.!!$R1 614
12 TraesCS5A01G216400 chr4A 741790799 741791411 612 True 592.00 592 84.168000 3072 3686 1 chr4A.!!$R1 614

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
496 589 0.115745 ACCTACTCCCTCCGTCCAAA 59.884 55.0 0.0 0.0 0.0 3.28 F
1016 4138 0.833834 ACCCTCACCTCTCACCACTG 60.834 60.0 0.0 0.0 0.0 3.66 F
2326 5488 0.915364 AGAGGGAGCAGCCTAAAAGG 59.085 55.0 0.0 0.0 38.8 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 4986 0.398522 TCACCCTCACCTCGCCATAT 60.399 55.000 0.00 0.0 0.00 1.78 R
2593 6665 0.030235 GTGGACAAAAGGTTCCACGC 59.970 55.000 5.06 0.0 42.39 5.34 R
3248 7322 1.058903 GCGAGATGCGTTTTCCGAC 59.941 57.895 0.00 0.0 43.41 4.79 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
17 18 4.466133 TTTGTACAGGCCACCACG 57.534 55.556 5.01 0.00 0.00 4.94
18 19 1.228003 TTTGTACAGGCCACCACGG 60.228 57.895 5.01 0.00 38.11 4.94
27 28 0.965363 GGCCACCACGGATGTCATTT 60.965 55.000 0.00 0.00 36.56 2.32
38 39 4.582656 ACGGATGTCATTTCAAGGTCAAAA 59.417 37.500 0.00 0.00 0.00 2.44
41 42 6.089820 CGGATGTCATTTCAAGGTCAAAATTG 59.910 38.462 0.00 0.00 0.00 2.32
45 46 5.702209 GTCATTTCAAGGTCAAAATTGGCAT 59.298 36.000 0.00 0.00 33.59 4.40
47 48 3.042871 TCAAGGTCAAAATTGGCATGC 57.957 42.857 9.90 9.90 33.59 4.06
50 51 1.972795 AGGTCAAAATTGGCATGCTGT 59.027 42.857 18.92 0.55 33.59 4.40
56 57 5.119125 GTCAAAATTGGCATGCTGTTAGAAC 59.881 40.000 18.92 4.20 31.86 3.01
62 63 2.925563 GGCATGCTGTTAGAACATTTGC 59.074 45.455 18.92 12.39 38.41 3.68
76 77 4.978083 ACATTTGCTGATGTTCATCCTC 57.022 40.909 9.83 3.29 36.92 3.71
77 78 4.338012 ACATTTGCTGATGTTCATCCTCA 58.662 39.130 9.83 5.48 36.92 3.86
82 83 5.988310 TGCTGATGTTCATCCTCAATTTT 57.012 34.783 9.83 0.00 0.00 1.82
83 84 6.349243 TGCTGATGTTCATCCTCAATTTTT 57.651 33.333 9.83 0.00 0.00 1.94
145 147 5.749596 CTGTTCATACAGGTGTGTTTGAA 57.250 39.130 7.15 7.15 46.26 2.69
151 153 0.944386 CAGGTGTGTTTGAACTCGGG 59.056 55.000 0.00 0.00 0.00 5.14
152 154 0.834612 AGGTGTGTTTGAACTCGGGA 59.165 50.000 0.00 0.00 0.00 5.14
153 155 1.202651 AGGTGTGTTTGAACTCGGGAG 60.203 52.381 0.00 0.00 0.00 4.30
154 156 0.586802 GTGTGTTTGAACTCGGGAGC 59.413 55.000 0.00 0.00 0.00 4.70
155 157 0.179234 TGTGTTTGAACTCGGGAGCA 59.821 50.000 0.00 0.00 0.00 4.26
156 158 0.868406 GTGTTTGAACTCGGGAGCAG 59.132 55.000 0.00 0.00 0.00 4.24
157 159 0.756294 TGTTTGAACTCGGGAGCAGA 59.244 50.000 0.00 0.00 0.00 4.26
158 160 1.347707 TGTTTGAACTCGGGAGCAGAT 59.652 47.619 0.00 0.00 0.00 2.90
159 161 2.565391 TGTTTGAACTCGGGAGCAGATA 59.435 45.455 0.00 0.00 0.00 1.98
160 162 3.007506 TGTTTGAACTCGGGAGCAGATAA 59.992 43.478 0.00 0.00 0.00 1.75
161 163 4.192317 GTTTGAACTCGGGAGCAGATAAT 58.808 43.478 0.00 0.00 0.00 1.28
162 164 3.459232 TGAACTCGGGAGCAGATAATG 57.541 47.619 0.00 0.00 0.00 1.90
174 176 1.875514 CAGATAATGCATGTCCACGGG 59.124 52.381 0.00 0.00 0.00 5.28
175 177 1.490490 AGATAATGCATGTCCACGGGT 59.510 47.619 0.00 0.00 0.00 5.28
176 178 2.092429 AGATAATGCATGTCCACGGGTT 60.092 45.455 0.00 0.00 0.00 4.11
177 179 3.135712 AGATAATGCATGTCCACGGGTTA 59.864 43.478 0.00 0.00 0.00 2.85
178 180 1.750193 AATGCATGTCCACGGGTTAG 58.250 50.000 0.00 0.00 0.00 2.34
179 181 0.618458 ATGCATGTCCACGGGTTAGT 59.382 50.000 0.00 0.00 0.00 2.24
180 182 0.321210 TGCATGTCCACGGGTTAGTG 60.321 55.000 0.00 0.00 41.53 2.74
196 198 3.065306 TGGTTACTCCCACCGCTG 58.935 61.111 0.00 0.00 37.07 5.18
251 253 4.915667 GCCCACAGATTAGTTTTTCGTTTC 59.084 41.667 0.00 0.00 0.00 2.78
266 268 1.676006 CGTTTCAGAAAAGCCCACAGT 59.324 47.619 0.00 0.00 0.00 3.55
268 270 3.447742 GTTTCAGAAAAGCCCACAGTTG 58.552 45.455 0.00 0.00 0.00 3.16
269 271 2.435372 TCAGAAAAGCCCACAGTTGT 57.565 45.000 0.00 0.00 0.00 3.32
274 284 1.692411 AAAGCCCACAGTTGTTCCTC 58.308 50.000 0.00 0.00 0.00 3.71
287 297 1.090052 GTTCCTCCCGCTACATGTGC 61.090 60.000 9.11 9.29 0.00 4.57
291 301 1.539065 CCTCCCGCTACATGTGCTAAG 60.539 57.143 9.11 0.00 0.00 2.18
309 319 9.890629 TGTGCTAAGTCATGAATAGAAAATACT 57.109 29.630 16.99 0.00 0.00 2.12
378 471 2.872858 GTTCGGGTTCTTCCTATCATGC 59.127 50.000 0.00 0.00 36.25 4.06
427 520 4.706962 CCACTTTGGGGAGAAAATTCTAGG 59.293 45.833 0.00 0.00 33.64 3.02
479 572 0.942410 TACTCGAGTTGCAACGCACC 60.942 55.000 28.85 16.30 38.71 5.01
483 576 0.944311 CGAGTTGCAACGCACCTACT 60.944 55.000 28.85 8.58 38.71 2.57
484 577 0.790814 GAGTTGCAACGCACCTACTC 59.209 55.000 25.82 11.36 38.71 2.59
485 578 0.602905 AGTTGCAACGCACCTACTCC 60.603 55.000 23.21 0.00 38.71 3.85
486 579 1.302192 TTGCAACGCACCTACTCCC 60.302 57.895 0.00 0.00 38.71 4.30
487 580 1.764571 TTGCAACGCACCTACTCCCT 61.765 55.000 0.00 0.00 38.71 4.20
488 581 1.448013 GCAACGCACCTACTCCCTC 60.448 63.158 0.00 0.00 0.00 4.30
489 582 1.218316 CAACGCACCTACTCCCTCC 59.782 63.158 0.00 0.00 0.00 4.30
490 583 2.348888 AACGCACCTACTCCCTCCG 61.349 63.158 0.00 0.00 0.00 4.63
491 584 2.754658 CGCACCTACTCCCTCCGT 60.755 66.667 0.00 0.00 0.00 4.69
492 585 2.772691 CGCACCTACTCCCTCCGTC 61.773 68.421 0.00 0.00 0.00 4.79
493 586 2.424733 GCACCTACTCCCTCCGTCC 61.425 68.421 0.00 0.00 0.00 4.79
494 587 1.000019 CACCTACTCCCTCCGTCCA 60.000 63.158 0.00 0.00 0.00 4.02
495 588 0.613853 CACCTACTCCCTCCGTCCAA 60.614 60.000 0.00 0.00 0.00 3.53
496 589 0.115745 ACCTACTCCCTCCGTCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
497 590 1.272807 CCTACTCCCTCCGTCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
498 591 1.838077 CCTACTCCCTCCGTCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
499 592 2.238898 CCTACTCCCTCCGTCCAAAATT 59.761 50.000 0.00 0.00 0.00 1.82
500 593 2.491675 ACTCCCTCCGTCCAAAATTC 57.508 50.000 0.00 0.00 0.00 2.17
501 594 1.985895 ACTCCCTCCGTCCAAAATTCT 59.014 47.619 0.00 0.00 0.00 2.40
502 595 2.375509 ACTCCCTCCGTCCAAAATTCTT 59.624 45.455 0.00 0.00 0.00 2.52
503 596 2.749621 CTCCCTCCGTCCAAAATTCTTG 59.250 50.000 0.00 0.00 0.00 3.02
504 597 1.202348 CCCTCCGTCCAAAATTCTTGC 59.798 52.381 0.00 0.00 0.00 4.01
505 598 1.202348 CCTCCGTCCAAAATTCTTGCC 59.798 52.381 0.00 0.00 0.00 4.52
506 599 2.162681 CTCCGTCCAAAATTCTTGCCT 58.837 47.619 0.00 0.00 0.00 4.75
507 600 2.558359 CTCCGTCCAAAATTCTTGCCTT 59.442 45.455 0.00 0.00 0.00 4.35
508 601 3.756434 CTCCGTCCAAAATTCTTGCCTTA 59.244 43.478 0.00 0.00 0.00 2.69
509 602 4.340617 TCCGTCCAAAATTCTTGCCTTAT 58.659 39.130 0.00 0.00 0.00 1.73
510 603 5.502079 TCCGTCCAAAATTCTTGCCTTATA 58.498 37.500 0.00 0.00 0.00 0.98
511 604 6.126409 TCCGTCCAAAATTCTTGCCTTATAT 58.874 36.000 0.00 0.00 0.00 0.86
512 605 6.605594 TCCGTCCAAAATTCTTGCCTTATATT 59.394 34.615 0.00 0.00 0.00 1.28
513 606 7.123547 TCCGTCCAAAATTCTTGCCTTATATTT 59.876 33.333 0.00 0.00 0.00 1.40
514 607 7.222611 CCGTCCAAAATTCTTGCCTTATATTTG 59.777 37.037 0.00 0.00 0.00 2.32
515 608 7.254084 CGTCCAAAATTCTTGCCTTATATTTGC 60.254 37.037 0.00 0.00 0.00 3.68
516 609 7.011389 GTCCAAAATTCTTGCCTTATATTTGCC 59.989 37.037 0.00 0.00 0.00 4.52
517 610 7.049754 CCAAAATTCTTGCCTTATATTTGCCT 58.950 34.615 0.00 0.00 0.00 4.75
518 611 8.203485 CCAAAATTCTTGCCTTATATTTGCCTA 58.797 33.333 0.00 0.00 0.00 3.93
519 612 9.598517 CAAAATTCTTGCCTTATATTTGCCTAA 57.401 29.630 0.00 0.00 0.00 2.69
524 617 8.094798 TCTTGCCTTATATTTGCCTAAATACG 57.905 34.615 0.00 0.00 40.51 3.06
525 618 7.934665 TCTTGCCTTATATTTGCCTAAATACGA 59.065 33.333 0.00 0.00 40.51 3.43
526 619 8.453238 TTGCCTTATATTTGCCTAAATACGAA 57.547 30.769 0.00 0.00 40.51 3.85
527 620 8.630054 TGCCTTATATTTGCCTAAATACGAAT 57.370 30.769 0.00 0.00 40.51 3.34
528 621 8.511321 TGCCTTATATTTGCCTAAATACGAATG 58.489 33.333 0.00 0.00 40.51 2.67
529 622 8.512138 GCCTTATATTTGCCTAAATACGAATGT 58.488 33.333 0.00 0.00 40.51 2.71
537 630 9.944663 TTTGCCTAAATACGAATGTATCAAATC 57.055 29.630 0.00 0.00 40.42 2.17
538 631 8.669946 TGCCTAAATACGAATGTATCAAATCA 57.330 30.769 0.00 0.00 40.42 2.57
539 632 8.556194 TGCCTAAATACGAATGTATCAAATCAC 58.444 33.333 0.00 0.00 40.42 3.06
540 633 7.740346 GCCTAAATACGAATGTATCAAATCACG 59.260 37.037 0.00 0.00 40.42 4.35
541 634 8.761497 CCTAAATACGAATGTATCAAATCACGT 58.239 33.333 0.00 0.00 40.42 4.49
544 637 9.834628 AAATACGAATGTATCAAATCACGTTTT 57.165 25.926 0.00 0.00 40.42 2.43
547 640 8.025243 ACGAATGTATCAAATCACGTTTTAGT 57.975 30.769 0.00 0.00 0.00 2.24
548 641 9.142515 ACGAATGTATCAAATCACGTTTTAGTA 57.857 29.630 0.00 0.00 0.00 1.82
597 690 8.587952 AATCTAAAACAAGAATTTTGGAACGG 57.412 30.769 1.89 0.00 40.87 4.44
598 691 7.336161 TCTAAAACAAGAATTTTGGAACGGA 57.664 32.000 0.00 0.00 36.47 4.69
679 772 1.000607 GCAGTGGTTCTGACGAGTGTA 60.001 52.381 0.00 0.00 46.27 2.90
680 773 2.352814 GCAGTGGTTCTGACGAGTGTAT 60.353 50.000 0.00 0.00 46.27 2.29
681 774 3.861131 GCAGTGGTTCTGACGAGTGTATT 60.861 47.826 0.00 0.00 46.27 1.89
682 775 4.307432 CAGTGGTTCTGACGAGTGTATTT 58.693 43.478 0.00 0.00 46.27 1.40
683 776 4.750098 CAGTGGTTCTGACGAGTGTATTTT 59.250 41.667 0.00 0.00 46.27 1.82
684 777 5.924254 CAGTGGTTCTGACGAGTGTATTTTA 59.076 40.000 0.00 0.00 46.27 1.52
685 778 5.924825 AGTGGTTCTGACGAGTGTATTTTAC 59.075 40.000 0.00 0.00 0.00 2.01
690 783 7.811713 GGTTCTGACGAGTGTATTTTACTAACT 59.188 37.037 0.00 0.00 0.00 2.24
750 843 9.849166 GTATTTTACTAGCTCTATCCATCAGTC 57.151 37.037 0.00 0.00 0.00 3.51
992 4112 5.721232 CGTCTTTATATACCCATCACTCCC 58.279 45.833 0.00 0.00 0.00 4.30
1016 4138 0.833834 ACCCTCACCTCTCACCACTG 60.834 60.000 0.00 0.00 0.00 3.66
1081 4209 1.138568 ATGCTTCCCAGGATCCAGAG 58.861 55.000 15.82 3.03 0.00 3.35
1092 4220 3.388676 CAGGATCCAGAGAAGCATCTTCT 59.611 47.826 15.82 8.66 35.54 2.85
1154 4282 6.844829 TGATGATCACCATGGAGATAACATT 58.155 36.000 22.77 2.95 35.17 2.71
1337 4477 1.480212 TTTCTGGCAGCTTCTCGGGA 61.480 55.000 10.34 0.00 0.00 5.14
1345 4485 2.498726 CTTCTCGGGAGCCTGCTC 59.501 66.667 10.68 10.68 42.04 4.26
1402 4542 6.908870 CGTGTACATGTACAGGTACTACTA 57.091 41.667 36.53 22.24 45.61 1.82
1431 4572 2.005451 GTGCAAGCTCGTGATCTGAAT 58.995 47.619 0.00 0.00 0.00 2.57
1445 4586 4.635765 TGATCTGAATTTCTTAACCGCTGG 59.364 41.667 0.00 0.00 0.00 4.85
1510 4651 3.126831 GGTGCATGACTGATACTAGTGC 58.873 50.000 5.39 0.00 0.00 4.40
1633 4774 4.803426 CGAGGTCTGGCTCACCGC 62.803 72.222 0.49 0.33 39.13 5.68
1730 4872 6.825721 AGCCTAGCCTGATTATGCATAATAAC 59.174 38.462 27.71 18.28 33.53 1.89
1743 4885 3.546020 GCATAATAACGCATGCACGAACT 60.546 43.478 19.57 0.00 45.51 3.01
1757 4899 3.492383 GCACGAACTATGACATCCATGAG 59.508 47.826 0.00 0.00 36.71 2.90
1760 4902 3.739810 CGAACTATGACATCCATGAGCAG 59.260 47.826 0.00 0.00 36.71 4.24
1785 4927 4.342092 TCGATCAAGAACCTATGATGCTGA 59.658 41.667 0.00 0.00 36.45 4.26
1822 4973 5.063880 AGTAATCGAGGGGCAAATCAATAC 58.936 41.667 0.00 0.00 0.00 1.89
1879 5038 9.941325 GAGAATCTTGAGATGGTATGAATATGT 57.059 33.333 0.00 0.00 34.49 2.29
1952 5112 5.981174 TCAGATCTGTAGTCATGATGCAAA 58.019 37.500 21.92 0.00 0.00 3.68
2010 5170 4.508124 GTGCACATCCGGTTAATTCTAGAG 59.492 45.833 13.17 0.00 0.00 2.43
2013 5173 4.344102 CACATCCGGTTAATTCTAGAGGGA 59.656 45.833 0.00 0.00 0.00 4.20
2062 5223 2.288763 ACACGAAAATTTGGTGGGATGC 60.289 45.455 21.48 0.00 42.74 3.91
2128 5290 5.411669 GGTGTAATCCTGAACACAAGTTAGG 59.588 44.000 7.78 0.00 46.22 2.69
2136 5298 1.774639 ACACAAGTTAGGCGTACGTG 58.225 50.000 17.90 7.67 0.00 4.49
2183 5345 3.689569 GCCAAGAGGAAGCAAGGGATAAT 60.690 47.826 0.00 0.00 36.89 1.28
2184 5346 4.446311 GCCAAGAGGAAGCAAGGGATAATA 60.446 45.833 0.00 0.00 36.89 0.98
2185 5347 5.694995 CCAAGAGGAAGCAAGGGATAATAA 58.305 41.667 0.00 0.00 36.89 1.40
2326 5488 0.915364 AGAGGGAGCAGCCTAAAAGG 59.085 55.000 0.00 0.00 38.80 3.11
2585 6657 6.468543 GTCTCTTATCCTTTTGTCCACTCTT 58.531 40.000 0.00 0.00 0.00 2.85
2586 6658 6.937465 GTCTCTTATCCTTTTGTCCACTCTTT 59.063 38.462 0.00 0.00 0.00 2.52
2588 6660 7.998964 TCTCTTATCCTTTTGTCCACTCTTTTT 59.001 33.333 0.00 0.00 0.00 1.94
2608 6680 3.320673 TTTTTGCGTGGAACCTTTTGT 57.679 38.095 0.00 0.00 0.00 2.83
2609 6681 2.570442 TTTGCGTGGAACCTTTTGTC 57.430 45.000 0.00 0.00 0.00 3.18
2610 6682 0.741915 TTGCGTGGAACCTTTTGTCC 59.258 50.000 0.00 0.00 0.00 4.02
2611 6683 0.394488 TGCGTGGAACCTTTTGTCCA 60.394 50.000 0.00 0.00 0.00 4.02
2612 6684 0.030235 GCGTGGAACCTTTTGTCCAC 59.970 55.000 11.93 11.93 46.56 4.02
2615 6687 2.932261 GTGGAACCTTTTGTCCACTCT 58.068 47.619 14.20 0.00 46.53 3.24
2616 6688 2.879026 GTGGAACCTTTTGTCCACTCTC 59.121 50.000 14.20 0.00 46.53 3.20
2623 6695 6.287589 ACCTTTTGTCCACTCTCATACTAG 57.712 41.667 0.00 0.00 0.00 2.57
2635 6707 6.970043 CACTCTCATACTAGTACTGCTTTCAC 59.030 42.308 4.31 0.00 0.00 3.18
2667 6740 1.682323 GCCCCTCCACGTTAACAAAAA 59.318 47.619 6.39 0.00 0.00 1.94
2682 6755 7.062371 CGTTAACAAAAACAACTTCCATGACAA 59.938 33.333 6.39 0.00 0.00 3.18
2707 6780 5.831702 AAGAACGACCGTATCTGTTATCT 57.168 39.130 0.00 0.00 0.00 1.98
2713 6786 5.125097 ACGACCGTATCTGTTATCTGTTTCT 59.875 40.000 0.00 0.00 0.00 2.52
2740 6813 9.144747 GTAGTGCTGTATGAATAATATCCAGTG 57.855 37.037 0.00 0.00 0.00 3.66
2790 6863 7.947890 TCTGGGTAGGTTTCTTAATGTTTTCAT 59.052 33.333 0.00 0.00 43.05 2.57
2811 6884 2.225467 GCTTTCTTCTGCTGTTGGAGT 58.775 47.619 0.00 0.00 33.13 3.85
2812 6885 2.031333 GCTTTCTTCTGCTGTTGGAGTG 60.031 50.000 0.00 0.00 33.13 3.51
2815 6888 3.777106 TCTTCTGCTGTTGGAGTGAAT 57.223 42.857 0.00 0.00 33.13 2.57
2817 6890 5.227569 TCTTCTGCTGTTGGAGTGAATAA 57.772 39.130 0.00 0.00 33.13 1.40
2819 6892 6.946340 TCTTCTGCTGTTGGAGTGAATAATA 58.054 36.000 0.00 0.00 33.13 0.98
2820 6893 7.568349 TCTTCTGCTGTTGGAGTGAATAATAT 58.432 34.615 0.00 0.00 33.13 1.28
2821 6894 7.712639 TCTTCTGCTGTTGGAGTGAATAATATC 59.287 37.037 0.00 0.00 33.13 1.63
2822 6895 7.129457 TCTGCTGTTGGAGTGAATAATATCT 57.871 36.000 0.00 0.00 33.13 1.98
2823 6896 6.988580 TCTGCTGTTGGAGTGAATAATATCTG 59.011 38.462 0.00 0.00 33.13 2.90
2824 6897 6.057533 TGCTGTTGGAGTGAATAATATCTGG 58.942 40.000 0.00 0.00 0.00 3.86
2831 6904 8.742125 TGGAGTGAATAATATCTGGGTAGATT 57.258 34.615 0.00 0.00 40.79 2.40
2850 6923 0.038251 TCAGTGCGCCAGTGTCTAAG 60.038 55.000 4.18 0.00 36.33 2.18
2851 6924 0.319900 CAGTGCGCCAGTGTCTAAGT 60.320 55.000 4.18 0.00 30.89 2.24
2861 6934 4.093998 GCCAGTGTCTAAGTGAATCACATG 59.906 45.833 16.38 5.18 36.74 3.21
2868 6941 7.959651 GTGTCTAAGTGAATCACATGTTCAATC 59.040 37.037 16.38 0.00 37.34 2.67
2911 6984 5.015817 TGGAGGAAAGGGAAGCCTTATTTTA 59.984 40.000 0.00 0.00 30.70 1.52
2912 6985 6.136857 GGAGGAAAGGGAAGCCTTATTTTAT 58.863 40.000 0.00 0.00 30.70 1.40
2937 7010 6.690194 AGCATGTTTTCTACCAATCATCTC 57.310 37.500 0.00 0.00 0.00 2.75
2948 7021 2.614057 CCAATCATCTCGTAAAGCCACC 59.386 50.000 0.00 0.00 0.00 4.61
3016 7089 5.662456 GACAGTCTATTAAACCAGTCTCCC 58.338 45.833 0.00 0.00 0.00 4.30
3020 7093 7.147707 ACAGTCTATTAAACCAGTCTCCCATAC 60.148 40.741 0.00 0.00 0.00 2.39
3021 7094 6.040616 AGTCTATTAAACCAGTCTCCCATACG 59.959 42.308 0.00 0.00 0.00 3.06
3022 7095 3.899052 TTAAACCAGTCTCCCATACGG 57.101 47.619 0.00 0.00 0.00 4.02
3023 7096 0.252197 AAACCAGTCTCCCATACGGC 59.748 55.000 0.00 0.00 0.00 5.68
3024 7097 0.617820 AACCAGTCTCCCATACGGCT 60.618 55.000 0.00 0.00 0.00 5.52
3025 7098 1.043673 ACCAGTCTCCCATACGGCTC 61.044 60.000 0.00 0.00 0.00 4.70
3026 7099 1.043116 CCAGTCTCCCATACGGCTCA 61.043 60.000 0.00 0.00 0.00 4.26
3027 7100 0.387202 CAGTCTCCCATACGGCTCAG 59.613 60.000 0.00 0.00 0.00 3.35
3028 7101 1.068250 GTCTCCCATACGGCTCAGC 59.932 63.158 0.00 0.00 0.00 4.26
3029 7102 2.134287 TCTCCCATACGGCTCAGCC 61.134 63.158 5.22 5.22 46.75 4.85
3042 7115 1.964552 CTCAGCCTGAGCCCATTAAG 58.035 55.000 9.13 0.00 37.72 1.85
3043 7116 0.107017 TCAGCCTGAGCCCATTAAGC 60.107 55.000 0.00 0.00 41.25 3.09
3044 7117 1.105759 CAGCCTGAGCCCATTAAGCC 61.106 60.000 0.00 0.00 41.25 4.35
3045 7118 2.189499 GCCTGAGCCCATTAAGCCG 61.189 63.158 0.00 0.00 0.00 5.52
3046 7119 2.189499 CCTGAGCCCATTAAGCCGC 61.189 63.158 0.00 0.00 0.00 6.53
3047 7120 2.124320 TGAGCCCATTAAGCCGCC 60.124 61.111 0.00 0.00 0.00 6.13
3048 7121 3.279875 GAGCCCATTAAGCCGCCG 61.280 66.667 0.00 0.00 0.00 6.46
3049 7122 4.875713 AGCCCATTAAGCCGCCGG 62.876 66.667 0.00 0.00 0.00 6.13
3051 7124 2.900337 CCCATTAAGCCGCCGGTC 60.900 66.667 4.45 0.00 0.00 4.79
3052 7125 2.900337 CCATTAAGCCGCCGGTCC 60.900 66.667 4.45 0.00 0.00 4.46
3053 7126 2.189521 CATTAAGCCGCCGGTCCT 59.810 61.111 4.45 0.00 0.00 3.85
3054 7127 1.451387 CATTAAGCCGCCGGTCCTT 60.451 57.895 4.45 2.81 0.00 3.36
3055 7128 1.153229 ATTAAGCCGCCGGTCCTTC 60.153 57.895 4.45 0.00 0.00 3.46
3056 7129 1.623542 ATTAAGCCGCCGGTCCTTCT 61.624 55.000 4.45 0.00 0.00 2.85
3057 7130 0.971959 TTAAGCCGCCGGTCCTTCTA 60.972 55.000 4.45 0.00 0.00 2.10
3058 7131 0.757935 TAAGCCGCCGGTCCTTCTAT 60.758 55.000 4.45 0.00 0.00 1.98
3059 7132 0.757935 AAGCCGCCGGTCCTTCTATA 60.758 55.000 4.45 0.00 0.00 1.31
3060 7133 1.179814 AGCCGCCGGTCCTTCTATAG 61.180 60.000 4.45 0.00 0.00 1.31
3061 7134 1.965219 CCGCCGGTCCTTCTATAGG 59.035 63.158 1.90 0.00 46.27 2.57
3062 7135 1.533469 CCGCCGGTCCTTCTATAGGG 61.533 65.000 1.90 0.00 44.86 3.53
3063 7136 0.538977 CGCCGGTCCTTCTATAGGGA 60.539 60.000 1.90 0.00 44.86 4.20
3150 7223 1.191535 TCCGGACTCTACCACCAATG 58.808 55.000 0.00 0.00 0.00 2.82
3163 7236 2.756042 CCAATGCCGATCCTCCCCA 61.756 63.158 0.00 0.00 0.00 4.96
3175 7248 1.132657 TCCTCCCCAACTTGGTACTCA 60.133 52.381 7.06 0.00 35.17 3.41
3199 7272 3.165875 CTGATTAAGGGGATAGCCTCGA 58.834 50.000 0.00 0.00 40.72 4.04
3248 7322 0.966179 GTTGCTAGGGTTTTGGTGGG 59.034 55.000 0.00 0.00 0.00 4.61
3271 7346 1.470979 GGAAAACGCATCTCGCTAGGA 60.471 52.381 0.00 0.00 43.23 2.94
3525 7600 2.683572 TCGCCTGGAGCCTAGCAA 60.684 61.111 0.00 0.00 38.78 3.91
3598 7673 4.453480 ACTGTTTGGGAGATTGGAAGAA 57.547 40.909 0.00 0.00 0.00 2.52
3600 7675 4.104738 ACTGTTTGGGAGATTGGAAGAAGA 59.895 41.667 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.485294 ATCCGTGGTGGCCTGTACAA 61.485 55.000 3.32 0.00 37.80 2.41
12 13 2.224769 ACCTTGAAATGACATCCGTGGT 60.225 45.455 0.00 0.00 0.00 4.16
17 18 6.369615 CCAATTTTGACCTTGAAATGACATCC 59.630 38.462 0.00 0.00 0.00 3.51
18 19 6.128472 GCCAATTTTGACCTTGAAATGACATC 60.128 38.462 0.00 0.00 0.00 3.06
27 28 2.633967 AGCATGCCAATTTTGACCTTGA 59.366 40.909 15.66 0.00 0.00 3.02
38 39 5.172934 CAAATGTTCTAACAGCATGCCAAT 58.827 37.500 15.66 2.73 43.04 3.16
41 42 2.925563 GCAAATGTTCTAACAGCATGCC 59.074 45.455 15.66 0.00 43.04 4.40
45 46 4.520111 ACATCAGCAAATGTTCTAACAGCA 59.480 37.500 1.62 0.00 43.04 4.41
56 57 4.976224 TGAGGATGAACATCAGCAAATG 57.024 40.909 15.22 0.00 39.54 2.32
130 132 2.484065 CCCGAGTTCAAACACACCTGTA 60.484 50.000 0.00 0.00 0.00 2.74
133 135 0.834612 TCCCGAGTTCAAACACACCT 59.165 50.000 0.00 0.00 0.00 4.00
134 136 1.226746 CTCCCGAGTTCAAACACACC 58.773 55.000 0.00 0.00 0.00 4.16
135 137 0.586802 GCTCCCGAGTTCAAACACAC 59.413 55.000 0.00 0.00 0.00 3.82
139 141 2.100605 ATCTGCTCCCGAGTTCAAAC 57.899 50.000 0.00 0.00 0.00 2.93
154 156 1.875514 CCCGTGGACATGCATTATCTG 59.124 52.381 0.00 0.00 0.00 2.90
155 157 1.490490 ACCCGTGGACATGCATTATCT 59.510 47.619 0.00 0.00 0.00 1.98
156 158 1.967319 ACCCGTGGACATGCATTATC 58.033 50.000 0.00 0.00 0.00 1.75
157 159 2.435372 AACCCGTGGACATGCATTAT 57.565 45.000 0.00 0.00 0.00 1.28
158 160 2.237643 ACTAACCCGTGGACATGCATTA 59.762 45.455 0.00 0.00 0.00 1.90
159 161 1.004277 ACTAACCCGTGGACATGCATT 59.996 47.619 0.00 0.00 0.00 3.56
160 162 0.618458 ACTAACCCGTGGACATGCAT 59.382 50.000 0.00 0.00 0.00 3.96
161 163 0.321210 CACTAACCCGTGGACATGCA 60.321 55.000 0.00 0.00 0.00 3.96
162 164 2.466867 CACTAACCCGTGGACATGC 58.533 57.895 0.00 0.00 0.00 4.06
169 171 1.066645 GGGAGTAACCACTAACCCGTG 60.067 57.143 0.00 0.00 41.20 4.94
170 172 1.269958 GGGAGTAACCACTAACCCGT 58.730 55.000 0.00 0.00 41.20 5.28
171 173 1.269012 TGGGAGTAACCACTAACCCG 58.731 55.000 0.00 0.00 40.33 5.28
179 181 3.065306 CAGCGGTGGGAGTAACCA 58.935 61.111 6.74 0.00 41.20 3.67
180 182 2.436115 GCAGCGGTGGGAGTAACC 60.436 66.667 17.54 0.00 38.08 2.85
185 187 3.129502 CACATGCAGCGGTGGGAG 61.130 66.667 17.54 0.00 0.00 4.30
251 253 2.223805 GGAACAACTGTGGGCTTTTCTG 60.224 50.000 0.00 0.00 0.00 3.02
266 268 0.981183 ACATGTAGCGGGAGGAACAA 59.019 50.000 0.00 0.00 0.00 2.83
268 270 1.090052 GCACATGTAGCGGGAGGAAC 61.090 60.000 0.00 0.00 0.00 3.62
269 271 1.220749 GCACATGTAGCGGGAGGAA 59.779 57.895 0.00 0.00 0.00 3.36
274 284 1.134818 TGACTTAGCACATGTAGCGGG 60.135 52.381 0.00 3.86 37.01 6.13
291 301 7.715249 TGTGGGCTAGTATTTTCTATTCATGAC 59.285 37.037 0.00 0.00 0.00 3.06
310 320 9.780186 GATTTAATAACTACTAATCTGTGGGCT 57.220 33.333 0.00 0.00 0.00 5.19
378 471 3.612479 GCATTTGCTTTCCTACACACAGG 60.612 47.826 0.00 0.00 38.21 4.00
427 520 2.097304 TGCCATCATTGTCACGCATAAC 59.903 45.455 0.00 0.00 0.00 1.89
479 572 3.197983 AGAATTTTGGACGGAGGGAGTAG 59.802 47.826 0.00 0.00 0.00 2.57
483 576 2.790433 CAAGAATTTTGGACGGAGGGA 58.210 47.619 0.00 0.00 0.00 4.20
484 577 1.202348 GCAAGAATTTTGGACGGAGGG 59.798 52.381 0.00 0.00 0.00 4.30
485 578 1.202348 GGCAAGAATTTTGGACGGAGG 59.798 52.381 0.00 0.00 0.00 4.30
486 579 2.162681 AGGCAAGAATTTTGGACGGAG 58.837 47.619 0.00 0.00 0.00 4.63
487 580 2.286365 AGGCAAGAATTTTGGACGGA 57.714 45.000 0.00 0.00 0.00 4.69
488 581 4.718940 ATAAGGCAAGAATTTTGGACGG 57.281 40.909 0.00 0.00 0.00 4.79
489 582 7.254084 GCAAATATAAGGCAAGAATTTTGGACG 60.254 37.037 0.00 0.00 0.00 4.79
490 583 7.011389 GGCAAATATAAGGCAAGAATTTTGGAC 59.989 37.037 0.00 0.00 0.00 4.02
491 584 7.047271 GGCAAATATAAGGCAAGAATTTTGGA 58.953 34.615 0.00 0.00 0.00 3.53
492 585 7.049754 AGGCAAATATAAGGCAAGAATTTTGG 58.950 34.615 4.13 0.00 0.00 3.28
493 586 9.598517 TTAGGCAAATATAAGGCAAGAATTTTG 57.401 29.630 4.13 0.00 0.00 2.44
498 591 8.564574 CGTATTTAGGCAAATATAAGGCAAGAA 58.435 33.333 4.13 0.00 38.54 2.52
499 592 7.934665 TCGTATTTAGGCAAATATAAGGCAAGA 59.065 33.333 4.13 0.00 38.54 3.02
500 593 8.094798 TCGTATTTAGGCAAATATAAGGCAAG 57.905 34.615 4.13 0.00 38.54 4.01
501 594 8.453238 TTCGTATTTAGGCAAATATAAGGCAA 57.547 30.769 4.13 0.00 38.54 4.52
502 595 8.511321 CATTCGTATTTAGGCAAATATAAGGCA 58.489 33.333 4.13 0.00 38.54 4.75
503 596 8.512138 ACATTCGTATTTAGGCAAATATAAGGC 58.488 33.333 5.74 0.00 38.54 4.35
511 604 9.944663 GATTTGATACATTCGTATTTAGGCAAA 57.055 29.630 0.00 0.00 38.48 3.68
512 605 9.114952 TGATTTGATACATTCGTATTTAGGCAA 57.885 29.630 0.00 0.00 38.48 4.52
513 606 8.556194 GTGATTTGATACATTCGTATTTAGGCA 58.444 33.333 0.00 0.00 38.48 4.75
514 607 7.740346 CGTGATTTGATACATTCGTATTTAGGC 59.260 37.037 0.00 0.00 38.48 3.93
515 608 8.761497 ACGTGATTTGATACATTCGTATTTAGG 58.239 33.333 0.00 0.00 38.48 2.69
518 611 9.834628 AAAACGTGATTTGATACATTCGTATTT 57.165 25.926 0.00 0.00 38.48 1.40
521 614 9.142515 ACTAAAACGTGATTTGATACATTCGTA 57.857 29.630 0.00 0.00 0.00 3.43
522 615 8.025243 ACTAAAACGTGATTTGATACATTCGT 57.975 30.769 0.00 0.00 0.00 3.85
571 664 9.685828 CCGTTCCAAAATTCTTGTTTTAGATTA 57.314 29.630 0.00 0.00 30.56 1.75
572 665 8.417884 TCCGTTCCAAAATTCTTGTTTTAGATT 58.582 29.630 0.00 0.00 30.56 2.40
573 666 7.947282 TCCGTTCCAAAATTCTTGTTTTAGAT 58.053 30.769 0.00 0.00 30.56 1.98
574 667 7.336161 TCCGTTCCAAAATTCTTGTTTTAGA 57.664 32.000 0.00 0.00 30.56 2.10
575 668 8.587952 AATCCGTTCCAAAATTCTTGTTTTAG 57.412 30.769 0.00 0.00 30.56 1.85
577 670 9.203421 GATAATCCGTTCCAAAATTCTTGTTTT 57.797 29.630 0.00 0.00 0.00 2.43
578 671 8.585018 AGATAATCCGTTCCAAAATTCTTGTTT 58.415 29.630 0.00 0.00 0.00 2.83
579 672 8.028938 CAGATAATCCGTTCCAAAATTCTTGTT 58.971 33.333 0.00 0.00 0.00 2.83
580 673 7.538575 CAGATAATCCGTTCCAAAATTCTTGT 58.461 34.615 0.00 0.00 0.00 3.16
581 674 6.473455 GCAGATAATCCGTTCCAAAATTCTTG 59.527 38.462 0.00 0.00 0.00 3.02
582 675 6.378280 AGCAGATAATCCGTTCCAAAATTCTT 59.622 34.615 0.00 0.00 0.00 2.52
583 676 5.888161 AGCAGATAATCCGTTCCAAAATTCT 59.112 36.000 0.00 0.00 0.00 2.40
584 677 6.136541 AGCAGATAATCCGTTCCAAAATTC 57.863 37.500 0.00 0.00 0.00 2.17
585 678 6.152661 TGAAGCAGATAATCCGTTCCAAAATT 59.847 34.615 0.00 0.00 0.00 1.82
586 679 5.652014 TGAAGCAGATAATCCGTTCCAAAAT 59.348 36.000 0.00 0.00 0.00 1.82
587 680 5.007034 TGAAGCAGATAATCCGTTCCAAAA 58.993 37.500 0.00 0.00 0.00 2.44
588 681 4.584874 TGAAGCAGATAATCCGTTCCAAA 58.415 39.130 0.00 0.00 0.00 3.28
589 682 4.214986 TGAAGCAGATAATCCGTTCCAA 57.785 40.909 0.00 0.00 0.00 3.53
590 683 3.904800 TGAAGCAGATAATCCGTTCCA 57.095 42.857 0.00 0.00 0.00 3.53
591 684 3.561725 CCTTGAAGCAGATAATCCGTTCC 59.438 47.826 0.00 0.00 0.00 3.62
592 685 3.561725 CCCTTGAAGCAGATAATCCGTTC 59.438 47.826 0.00 0.00 0.00 3.95
593 686 3.545703 CCCTTGAAGCAGATAATCCGTT 58.454 45.455 0.00 0.00 0.00 4.44
594 687 2.158755 CCCCTTGAAGCAGATAATCCGT 60.159 50.000 0.00 0.00 0.00 4.69
595 688 2.498167 CCCCTTGAAGCAGATAATCCG 58.502 52.381 0.00 0.00 0.00 4.18
596 689 2.443255 TCCCCCTTGAAGCAGATAATCC 59.557 50.000 0.00 0.00 0.00 3.01
597 690 3.137360 AGTCCCCCTTGAAGCAGATAATC 59.863 47.826 0.00 0.00 0.00 1.75
598 691 3.126453 AGTCCCCCTTGAAGCAGATAAT 58.874 45.455 0.00 0.00 0.00 1.28
633 726 4.062991 ACAACAAGTGTAGATTCGAACCC 58.937 43.478 0.00 0.00 39.29 4.11
662 755 5.924825 AGTAAAATACACTCGTCAGAACCAC 59.075 40.000 0.00 0.00 0.00 4.16
679 772 9.331282 GGTGATCAGAGCATAAGTTAGTAAAAT 57.669 33.333 0.00 0.00 0.00 1.82
680 773 7.769044 GGGTGATCAGAGCATAAGTTAGTAAAA 59.231 37.037 0.00 0.00 0.00 1.52
681 774 7.093068 TGGGTGATCAGAGCATAAGTTAGTAAA 60.093 37.037 0.00 0.00 0.00 2.01
682 775 6.382859 TGGGTGATCAGAGCATAAGTTAGTAA 59.617 38.462 0.00 0.00 0.00 2.24
683 776 5.897250 TGGGTGATCAGAGCATAAGTTAGTA 59.103 40.000 0.00 0.00 0.00 1.82
684 777 4.716784 TGGGTGATCAGAGCATAAGTTAGT 59.283 41.667 0.00 0.00 0.00 2.24
685 778 5.282055 TGGGTGATCAGAGCATAAGTTAG 57.718 43.478 0.00 0.00 0.00 2.34
690 783 3.495629 GCAGATGGGTGATCAGAGCATAA 60.496 47.826 0.00 0.00 32.86 1.90
692 785 1.202782 GCAGATGGGTGATCAGAGCAT 60.203 52.381 0.00 0.00 32.86 3.79
742 835 7.219154 GCGATCGATAAATAACTAGACTGATGG 59.781 40.741 21.57 0.00 0.00 3.51
750 843 6.305877 GTGGTGAGCGATCGATAAATAACTAG 59.694 42.308 21.57 0.00 0.00 2.57
992 4112 1.079256 TGAGAGGTGAGGGTGGAGG 59.921 63.158 0.00 0.00 0.00 4.30
1081 4209 2.894126 TCCCCGAGATAGAAGATGCTTC 59.106 50.000 0.00 0.00 0.00 3.86
1092 4220 1.542175 CACCCTCCTCCCCGAGATA 59.458 63.158 0.00 0.00 30.97 1.98
1154 4282 2.741985 CGCCGCTGGATGTCAACA 60.742 61.111 0.00 0.00 0.00 3.33
1402 4542 1.374758 GAGCTTGCACGTAGGCTGT 60.375 57.895 0.00 0.00 35.01 4.40
1431 4572 0.608035 CAGCCCCAGCGGTTAAGAAA 60.608 55.000 0.00 0.00 46.67 2.52
1460 4601 1.218047 CCACGAAGCCTTCCGATCA 59.782 57.895 0.00 0.00 0.00 2.92
1491 4632 3.448660 ACAGCACTAGTATCAGTCATGCA 59.551 43.478 0.00 0.00 0.00 3.96
1510 4651 2.113774 TCACCCCTGCAAGCACAG 59.886 61.111 0.00 0.00 37.42 3.66
1730 4872 0.998669 TGTCATAGTTCGTGCATGCG 59.001 50.000 14.09 0.00 0.00 4.73
1743 4885 3.828451 TCGATCTGCTCATGGATGTCATA 59.172 43.478 0.00 0.00 34.12 2.15
1757 4899 4.876125 TCATAGGTTCTTGATCGATCTGC 58.124 43.478 25.02 10.80 0.00 4.26
1760 4902 5.348179 CAGCATCATAGGTTCTTGATCGATC 59.652 44.000 18.72 18.72 30.24 3.69
1785 4927 8.953313 CCCCTCGATTACTTGTAATTAACTTTT 58.047 33.333 7.35 0.00 0.00 2.27
1822 4973 2.347150 TCGCCATATATGCAAATACGCG 59.653 45.455 18.34 18.34 35.95 6.01
1835 4986 0.398522 TCACCCTCACCTCGCCATAT 60.399 55.000 0.00 0.00 0.00 1.78
1879 5038 2.231478 CCCTGCTTCAACGTCTCTCTAA 59.769 50.000 0.00 0.00 0.00 2.10
1926 5086 4.749099 GCATCATGACTACAGATCTGAACC 59.251 45.833 29.27 14.33 0.00 3.62
1952 5112 3.019564 GCCAGGAGCAGATTACATTTGT 58.980 45.455 0.00 0.00 42.97 2.83
2062 5223 5.352293 TCACAAATACAGTATCTTGCAGCAG 59.648 40.000 0.00 0.00 0.00 4.24
2128 5290 1.654105 CACCTTGAGATTCACGTACGC 59.346 52.381 16.72 0.00 0.00 4.42
2136 5298 6.992063 TCAAATTCTAGCACCTTGAGATTC 57.008 37.500 0.00 0.00 0.00 2.52
2326 5488 2.052782 ATAAATGAACCGGTCCCTGC 57.947 50.000 8.04 0.00 0.00 4.85
2588 6660 3.254892 GACAAAAGGTTCCACGCAAAAA 58.745 40.909 0.00 0.00 0.00 1.94
2590 6662 1.135333 GGACAAAAGGTTCCACGCAAA 59.865 47.619 0.00 0.00 0.00 3.68
2591 6663 0.741915 GGACAAAAGGTTCCACGCAA 59.258 50.000 0.00 0.00 0.00 4.85
2592 6664 0.394488 TGGACAAAAGGTTCCACGCA 60.394 50.000 0.00 0.00 0.00 5.24
2593 6665 0.030235 GTGGACAAAAGGTTCCACGC 59.970 55.000 5.06 0.00 42.39 5.34
2596 6668 2.507886 TGAGAGTGGACAAAAGGTTCCA 59.492 45.455 0.00 0.00 0.00 3.53
2597 6669 3.208747 TGAGAGTGGACAAAAGGTTCC 57.791 47.619 0.00 0.00 0.00 3.62
2598 6670 5.552178 AGTATGAGAGTGGACAAAAGGTTC 58.448 41.667 0.00 0.00 0.00 3.62
2599 6671 5.568620 AGTATGAGAGTGGACAAAAGGTT 57.431 39.130 0.00 0.00 0.00 3.50
2600 6672 5.780793 ACTAGTATGAGAGTGGACAAAAGGT 59.219 40.000 0.00 0.00 0.00 3.50
2601 6673 6.287589 ACTAGTATGAGAGTGGACAAAAGG 57.712 41.667 0.00 0.00 0.00 3.11
2602 6674 7.971168 CAGTACTAGTATGAGAGTGGACAAAAG 59.029 40.741 5.75 0.00 0.00 2.27
2603 6675 7.577046 GCAGTACTAGTATGAGAGTGGACAAAA 60.577 40.741 5.75 0.00 0.00 2.44
2604 6676 6.127703 GCAGTACTAGTATGAGAGTGGACAAA 60.128 42.308 5.75 0.00 0.00 2.83
2605 6677 5.357314 GCAGTACTAGTATGAGAGTGGACAA 59.643 44.000 5.75 0.00 0.00 3.18
2606 6678 4.882427 GCAGTACTAGTATGAGAGTGGACA 59.118 45.833 5.75 0.00 0.00 4.02
2607 6679 5.127491 AGCAGTACTAGTATGAGAGTGGAC 58.873 45.833 5.75 0.00 0.00 4.02
2608 6680 5.375283 AGCAGTACTAGTATGAGAGTGGA 57.625 43.478 5.75 0.00 0.00 4.02
2609 6681 6.095580 TGAAAGCAGTACTAGTATGAGAGTGG 59.904 42.308 5.75 0.00 0.00 4.00
2610 6682 6.970043 GTGAAAGCAGTACTAGTATGAGAGTG 59.030 42.308 5.75 0.00 0.00 3.51
2611 6683 6.183360 CGTGAAAGCAGTACTAGTATGAGAGT 60.183 42.308 5.75 0.00 0.00 3.24
2612 6684 6.195868 CGTGAAAGCAGTACTAGTATGAGAG 58.804 44.000 5.75 0.00 0.00 3.20
2613 6685 5.066117 CCGTGAAAGCAGTACTAGTATGAGA 59.934 44.000 5.75 0.00 0.00 3.27
2614 6686 5.274718 CCGTGAAAGCAGTACTAGTATGAG 58.725 45.833 5.75 0.66 0.00 2.90
2615 6687 4.097437 CCCGTGAAAGCAGTACTAGTATGA 59.903 45.833 5.75 0.00 0.00 2.15
2616 6688 4.360563 CCCGTGAAAGCAGTACTAGTATG 58.639 47.826 5.75 6.88 0.00 2.39
2623 6695 1.069227 CAAAGCCCGTGAAAGCAGTAC 60.069 52.381 0.00 0.00 0.00 2.73
2648 6720 2.688958 TGTTTTTGTTAACGTGGAGGGG 59.311 45.455 0.26 0.00 0.00 4.79
2649 6721 4.106909 GTTGTTTTTGTTAACGTGGAGGG 58.893 43.478 0.26 0.00 0.00 4.30
2652 6724 5.048224 TGGAAGTTGTTTTTGTTAACGTGGA 60.048 36.000 0.26 0.00 0.00 4.02
2653 6725 5.162075 TGGAAGTTGTTTTTGTTAACGTGG 58.838 37.500 0.26 0.00 0.00 4.94
2655 6727 6.528774 GTCATGGAAGTTGTTTTTGTTAACGT 59.471 34.615 0.26 0.00 0.00 3.99
2656 6728 6.528423 TGTCATGGAAGTTGTTTTTGTTAACG 59.472 34.615 0.26 0.00 0.00 3.18
2682 6755 7.063074 CAGATAACAGATACGGTCGTTCTTTTT 59.937 37.037 0.16 3.91 0.00 1.94
2713 6786 8.870116 ACTGGATATTATTCATACAGCACTACA 58.130 33.333 0.00 0.00 37.80 2.74
2750 6823 7.931015 ACCTACCCAGATATTATTCACTCAA 57.069 36.000 0.00 0.00 0.00 3.02
2790 6863 2.224606 CTCCAACAGCAGAAGAAAGCA 58.775 47.619 0.00 0.00 0.00 3.91
2811 6884 8.097038 GCACTGAATCTACCCAGATATTATTCA 58.903 37.037 0.00 0.00 40.81 2.57
2812 6885 7.276658 CGCACTGAATCTACCCAGATATTATTC 59.723 40.741 0.00 0.00 40.81 1.75
2815 6888 5.566826 GCGCACTGAATCTACCCAGATATTA 60.567 44.000 0.30 0.00 40.81 0.98
2817 6890 3.306364 GCGCACTGAATCTACCCAGATAT 60.306 47.826 0.30 0.00 40.81 1.63
2819 6892 1.202580 GCGCACTGAATCTACCCAGAT 60.203 52.381 0.30 0.00 43.67 2.90
2820 6893 0.175760 GCGCACTGAATCTACCCAGA 59.824 55.000 0.30 0.00 34.65 3.86
2821 6894 0.811616 GGCGCACTGAATCTACCCAG 60.812 60.000 10.83 0.00 36.53 4.45
2822 6895 1.220749 GGCGCACTGAATCTACCCA 59.779 57.895 10.83 0.00 0.00 4.51
2823 6896 0.811616 CTGGCGCACTGAATCTACCC 60.812 60.000 10.83 0.00 0.00 3.69
2824 6897 0.108138 ACTGGCGCACTGAATCTACC 60.108 55.000 10.83 0.00 0.00 3.18
2831 6904 0.038251 CTTAGACACTGGCGCACTGA 60.038 55.000 10.83 0.00 0.00 3.41
2850 6923 4.701651 TCCCTGATTGAACATGTGATTCAC 59.298 41.667 9.93 9.93 35.82 3.18
2851 6924 4.701651 GTCCCTGATTGAACATGTGATTCA 59.298 41.667 0.00 0.00 34.27 2.57
2861 6934 4.830826 AAAAAGACGTCCCTGATTGAAC 57.169 40.909 13.01 0.00 0.00 3.18
2911 6984 8.757982 AGATGATTGGTAGAAAACATGCTTAT 57.242 30.769 0.00 0.00 0.00 1.73
2912 6985 7.011389 CGAGATGATTGGTAGAAAACATGCTTA 59.989 37.037 0.00 0.00 0.00 3.09
2926 6999 3.270877 GTGGCTTTACGAGATGATTGGT 58.729 45.455 0.00 0.00 0.00 3.67
2937 7010 2.030363 TGCTGAAAATGGTGGCTTTACG 60.030 45.455 0.00 0.00 0.00 3.18
2948 7021 7.259882 TGCTTAACATCCTTATGCTGAAAATG 58.740 34.615 0.00 0.00 36.50 2.32
3023 7096 1.964552 CTTAATGGGCTCAGGCTGAG 58.035 55.000 34.76 34.76 46.90 3.35
3024 7097 0.107017 GCTTAATGGGCTCAGGCTGA 60.107 55.000 17.68 17.68 38.73 4.26
3025 7098 1.105759 GGCTTAATGGGCTCAGGCTG 61.106 60.000 8.58 8.58 38.73 4.85
3026 7099 1.228510 GGCTTAATGGGCTCAGGCT 59.771 57.895 0.00 0.00 38.73 4.58
3027 7100 2.189499 CGGCTTAATGGGCTCAGGC 61.189 63.158 0.00 0.00 37.82 4.85
3028 7101 2.189499 GCGGCTTAATGGGCTCAGG 61.189 63.158 0.00 0.00 0.00 3.86
3029 7102 2.189499 GGCGGCTTAATGGGCTCAG 61.189 63.158 0.00 0.00 0.00 3.35
3030 7103 2.124320 GGCGGCTTAATGGGCTCA 60.124 61.111 0.00 0.00 0.00 4.26
3031 7104 3.279875 CGGCGGCTTAATGGGCTC 61.280 66.667 7.61 0.00 0.00 4.70
3032 7105 4.875713 CCGGCGGCTTAATGGGCT 62.876 66.667 15.42 0.00 0.00 5.19
3034 7107 2.900337 GACCGGCGGCTTAATGGG 60.900 66.667 28.71 1.56 0.00 4.00
3035 7108 2.886730 AAGGACCGGCGGCTTAATGG 62.887 60.000 28.71 2.39 0.00 3.16
3036 7109 1.436983 GAAGGACCGGCGGCTTAATG 61.437 60.000 28.71 0.00 0.00 1.90
3037 7110 1.153229 GAAGGACCGGCGGCTTAAT 60.153 57.895 28.71 5.55 0.00 1.40
3038 7111 0.971959 TAGAAGGACCGGCGGCTTAA 60.972 55.000 28.71 10.87 0.00 1.85
3039 7112 0.757935 ATAGAAGGACCGGCGGCTTA 60.758 55.000 28.71 8.51 0.00 3.09
3040 7113 0.757935 TATAGAAGGACCGGCGGCTT 60.758 55.000 28.71 22.09 0.00 4.35
3041 7114 1.152610 TATAGAAGGACCGGCGGCT 60.153 57.895 28.71 17.12 0.00 5.52
3042 7115 1.289380 CTATAGAAGGACCGGCGGC 59.711 63.158 28.71 18.78 0.00 6.53
3061 7134 0.106894 CGCCAGGGGAAGATTAGTCC 59.893 60.000 0.00 0.00 0.00 3.85
3062 7135 0.106894 CCGCCAGGGGAAGATTAGTC 59.893 60.000 4.70 0.00 0.00 2.59
3063 7136 1.984288 GCCGCCAGGGGAAGATTAGT 61.984 60.000 4.70 0.00 38.20 2.24
3064 7137 1.227973 GCCGCCAGGGGAAGATTAG 60.228 63.158 4.70 0.00 38.20 1.73
3065 7138 1.692749 AGCCGCCAGGGGAAGATTA 60.693 57.895 4.70 0.00 38.20 1.75
3066 7139 3.017581 AGCCGCCAGGGGAAGATT 61.018 61.111 4.70 0.00 38.20 2.40
3067 7140 3.483869 GAGCCGCCAGGGGAAGAT 61.484 66.667 4.70 0.00 38.20 2.40
3150 7223 1.452108 CAAGTTGGGGAGGATCGGC 60.452 63.158 0.00 0.00 34.37 5.54
3163 7236 5.491982 CTTAATCAGCCTGAGTACCAAGTT 58.508 41.667 0.58 0.00 0.00 2.66
3175 7248 1.988846 GGCTATCCCCTTAATCAGCCT 59.011 52.381 3.21 0.00 44.15 4.58
3199 7272 1.349067 GACCAAGGCCGGGTAGATAT 58.651 55.000 20.43 0.00 39.19 1.63
3248 7322 1.058903 GCGAGATGCGTTTTCCGAC 59.941 57.895 0.00 0.00 43.41 4.79
3271 7346 1.546323 CCGATCCTGCCATAGCCAAAT 60.546 52.381 0.00 0.00 38.69 2.32
3525 7600 6.266786 CCTAATGGTTTGAAAGTTACACCCTT 59.733 38.462 0.00 0.00 0.00 3.95
3598 7673 2.444895 GCCCCTCCTCCGTGATCT 60.445 66.667 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.