Multiple sequence alignment - TraesCS5B01G329600

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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 TraesCS5B01G329600 chr5B 100.000 3761 0 0 1 3761 513646077 513649837 0.000000e+00 6946.0
1 TraesCS5B01G329600 chr5B 94.220 1903 100 5 869 2761 513711315 513713217 0.000000e+00 2896.0
2 TraesCS5B01G329600 chr5B 84.915 1770 250 14 1006 2760 137112736 137110969 0.000000e+00 1773.0
3 TraesCS5B01G329600 chr5B 83.603 433 58 8 3244 3663 490613465 490613033 9.790000e-106 394.0
4 TraesCS5B01G329600 chr5B 93.443 183 10 2 671 853 513710596 513710776 1.720000e-68 270.0
5 TraesCS5B01G329600 chr5B 94.928 138 7 0 2762 2899 662945332 662945195 2.270000e-52 217.0
6 TraesCS5B01G329600 chr5B 92.754 138 10 0 2762 2899 573410933 573410796 2.290000e-47 200.0
7 TraesCS5B01G329600 chr5D 94.697 2093 93 2 669 2761 424596594 424598668 0.000000e+00 3234.0
8 TraesCS5B01G329600 chr5D 91.034 145 11 2 506 648 384072358 384072214 1.070000e-45 195.0
9 TraesCS5B01G329600 chr5D 81.395 258 30 11 2982 3229 424598849 424599098 1.070000e-45 195.0
10 TraesCS5B01G329600 chr5D 88.272 162 16 3 506 664 439583277 439583438 1.380000e-44 191.0
11 TraesCS5B01G329600 chr5D 90.909 88 6 1 2898 2983 424598699 424598786 2.370000e-22 117.0
12 TraesCS5B01G329600 chr5A 92.275 1864 129 10 911 2761 538348951 538350812 0.000000e+00 2630.0
13 TraesCS5B01G329600 chr5A 85.367 1770 241 15 1006 2760 138430586 138428820 0.000000e+00 1818.0
14 TraesCS5B01G329600 chr5A 84.777 381 26 7 1 368 538348223 538348584 1.660000e-93 353.0
15 TraesCS5B01G329600 chr5A 77.289 568 71 18 3228 3758 17595179 17595725 7.950000e-72 281.0
16 TraesCS5B01G329600 chr5A 86.923 260 14 6 671 911 538348640 538348898 1.330000e-69 274.0
17 TraesCS5B01G329600 chr5A 82.941 340 23 9 2898 3218 538350843 538351166 1.330000e-69 274.0
18 TraesCS5B01G329600 chr7D 81.802 1720 269 26 1064 2760 531977411 531975713 0.000000e+00 1402.0
19 TraesCS5B01G329600 chr7D 81.239 1727 305 11 1010 2719 193935002 193936726 0.000000e+00 1376.0
20 TraesCS5B01G329600 chr7D 80.688 1714 302 23 1054 2745 84422143 84420437 0.000000e+00 1304.0
21 TraesCS5B01G329600 chr7D 87.425 167 19 2 500 664 638470480 638470646 1.380000e-44 191.0
22 TraesCS5B01G329600 chr7B 81.702 1716 276 22 1064 2760 572507610 572505914 0.000000e+00 1395.0
23 TraesCS5B01G329600 chr7B 80.736 1713 305 19 1054 2746 34168283 34169990 0.000000e+00 1312.0
24 TraesCS5B01G329600 chr7B 91.304 138 12 0 2762 2899 13843033 13842896 4.960000e-44 189.0
25 TraesCS5B01G329600 chr1D 81.390 1741 295 25 1021 2742 344676225 344674495 0.000000e+00 1393.0
26 TraesCS5B01G329600 chr1D 80.844 1707 290 27 1032 2718 344284142 344285831 0.000000e+00 1306.0
27 TraesCS5B01G329600 chr1D 87.654 81 10 0 375 455 203751573 203751653 1.110000e-15 95.3
28 TraesCS5B01G329600 chr1A 81.254 1707 283 27 1032 2718 443870082 443871771 0.000000e+00 1345.0
29 TraesCS5B01G329600 chr1A 80.482 1742 289 35 1021 2742 444421750 444420040 0.000000e+00 1286.0
30 TraesCS5B01G329600 chr1A 88.235 85 10 0 369 453 577571273 577571357 6.650000e-18 102.0
31 TraesCS5B01G329600 chr1A 90.411 73 7 0 384 456 570160199 570160127 3.090000e-16 97.1
32 TraesCS5B01G329600 chr7A 80.418 1052 182 19 1688 2721 612532264 612531219 0.000000e+00 780.0
33 TraesCS5B01G329600 chr7A 88.421 95 8 2 365 456 94450109 94450203 1.100000e-20 111.0
34 TraesCS5B01G329600 chr2A 85.792 549 63 9 3225 3761 222593346 222592801 5.450000e-158 568.0
35 TraesCS5B01G329600 chr3B 85.558 547 64 10 3227 3761 597469081 597468538 3.280000e-155 558.0
36 TraesCS5B01G329600 chr3B 87.952 166 18 2 505 668 428703659 428703824 1.070000e-45 195.0
37 TraesCS5B01G329600 chr3B 90.441 136 13 0 2761 2896 611133438 611133573 2.980000e-41 180.0
38 TraesCS5B01G329600 chr3B 87.500 88 9 2 373 459 656575020 656574934 2.390000e-17 100.0
39 TraesCS5B01G329600 chr3D 85.223 494 60 7 3265 3746 110180134 110180626 2.610000e-136 496.0
40 TraesCS5B01G329600 chr3D 88.415 164 16 3 503 664 498263637 498263799 1.070000e-45 195.0
41 TraesCS5B01G329600 chr3D 87.654 162 18 2 503 662 473421000 473420839 1.780000e-43 187.0
42 TraesCS5B01G329600 chr3D 86.207 174 19 5 497 667 108920502 108920331 2.310000e-42 183.0
43 TraesCS5B01G329600 chr4A 86.301 219 22 3 3435 3645 594529643 594529425 8.120000e-57 231.0
44 TraesCS5B01G329600 chr4A 92.647 136 10 0 2761 2896 660691200 660691335 2.960000e-46 196.0
45 TraesCS5B01G329600 chr2B 87.059 170 17 4 506 670 769078004 769078173 1.780000e-43 187.0
46 TraesCS5B01G329600 chr6A 86.747 166 18 2 506 667 97802688 97802523 8.300000e-42 182.0
47 TraesCS5B01G329600 chr3A 90.698 86 8 0 368 453 431819805 431819720 8.540000e-22 115.0


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 TraesCS5B01G329600 chr5B 513646077 513649837 3760 False 6946.00 6946 100.000000 1 3761 1 chr5B.!!$F1 3760
1 TraesCS5B01G329600 chr5B 137110969 137112736 1767 True 1773.00 1773 84.915000 1006 2760 1 chr5B.!!$R1 1754
2 TraesCS5B01G329600 chr5B 513710596 513713217 2621 False 1583.00 2896 93.831500 671 2761 2 chr5B.!!$F2 2090
3 TraesCS5B01G329600 chr5D 424596594 424599098 2504 False 1182.00 3234 89.000333 669 3229 3 chr5D.!!$F2 2560
4 TraesCS5B01G329600 chr5A 138428820 138430586 1766 True 1818.00 1818 85.367000 1006 2760 1 chr5A.!!$R1 1754
5 TraesCS5B01G329600 chr5A 538348223 538351166 2943 False 882.75 2630 86.729000 1 3218 4 chr5A.!!$F2 3217
6 TraesCS5B01G329600 chr5A 17595179 17595725 546 False 281.00 281 77.289000 3228 3758 1 chr5A.!!$F1 530
7 TraesCS5B01G329600 chr7D 531975713 531977411 1698 True 1402.00 1402 81.802000 1064 2760 1 chr7D.!!$R2 1696
8 TraesCS5B01G329600 chr7D 193935002 193936726 1724 False 1376.00 1376 81.239000 1010 2719 1 chr7D.!!$F1 1709
9 TraesCS5B01G329600 chr7D 84420437 84422143 1706 True 1304.00 1304 80.688000 1054 2745 1 chr7D.!!$R1 1691
10 TraesCS5B01G329600 chr7B 572505914 572507610 1696 True 1395.00 1395 81.702000 1064 2760 1 chr7B.!!$R2 1696
11 TraesCS5B01G329600 chr7B 34168283 34169990 1707 False 1312.00 1312 80.736000 1054 2746 1 chr7B.!!$F1 1692
12 TraesCS5B01G329600 chr1D 344674495 344676225 1730 True 1393.00 1393 81.390000 1021 2742 1 chr1D.!!$R1 1721
13 TraesCS5B01G329600 chr1D 344284142 344285831 1689 False 1306.00 1306 80.844000 1032 2718 1 chr1D.!!$F2 1686
14 TraesCS5B01G329600 chr1A 443870082 443871771 1689 False 1345.00 1345 81.254000 1032 2718 1 chr1A.!!$F1 1686
15 TraesCS5B01G329600 chr1A 444420040 444421750 1710 True 1286.00 1286 80.482000 1021 2742 1 chr1A.!!$R1 1721
16 TraesCS5B01G329600 chr7A 612531219 612532264 1045 True 780.00 780 80.418000 1688 2721 1 chr7A.!!$R1 1033
17 TraesCS5B01G329600 chr2A 222592801 222593346 545 True 568.00 568 85.792000 3225 3761 1 chr2A.!!$R1 536
18 TraesCS5B01G329600 chr3B 597468538 597469081 543 True 558.00 558 85.558000 3227 3761 1 chr3B.!!$R1 534

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
352 366 0.541863 CCAGTAACCTGAAGCCGGAT 59.458 55.000 5.05 0.0 41.50 4.18 F
354 368 0.541863 AGTAACCTGAAGCCGGATGG 59.458 55.000 5.05 0.0 38.77 3.51 F
1695 2326 1.064946 CCTCGGCGTCATCTCTCAC 59.935 63.158 6.85 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 2457 1.204146 GTAGATCACCTTGCCCTGGA 58.796 55.000 0.00 0.0 0.00 3.86 R
2334 2986 1.360911 GATCGAGTCCTCCGGCTTC 59.639 63.158 0.00 0.0 0.00 3.86 R
3229 3971 0.108945 CTACGTTCCGAACAGGTCCC 60.109 60.000 11.74 0.0 41.99 4.46 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
71 73 6.406370 AGGGATTTGTTAATTTAAAGCTGGC 58.594 36.000 0.00 0.00 0.00 4.85
74 76 8.204160 GGGATTTGTTAATTTAAAGCTGGCTAT 58.796 33.333 0.00 0.00 0.00 2.97
126 129 3.573538 CCAGATGGATGAAAAACCACACA 59.426 43.478 0.00 0.00 39.06 3.72
129 132 5.636121 CAGATGGATGAAAAACCACACAATG 59.364 40.000 0.00 0.00 39.06 2.82
130 133 3.726607 TGGATGAAAAACCACACAATGC 58.273 40.909 0.00 0.00 0.00 3.56
144 147 5.055144 CACACAATGCTGCTATCATAGAGT 58.945 41.667 0.00 0.00 0.00 3.24
146 149 6.703165 CACACAATGCTGCTATCATAGAGTTA 59.297 38.462 0.00 0.00 0.00 2.24
189 194 1.341482 TGACTTGCAACCACCCAGAAA 60.341 47.619 0.00 0.00 0.00 2.52
190 195 1.754226 GACTTGCAACCACCCAGAAAA 59.246 47.619 0.00 0.00 0.00 2.29
191 196 1.756538 ACTTGCAACCACCCAGAAAAG 59.243 47.619 0.00 0.00 0.00 2.27
192 197 2.031120 CTTGCAACCACCCAGAAAAGA 58.969 47.619 0.00 0.00 0.00 2.52
193 198 1.398692 TGCAACCACCCAGAAAAGAC 58.601 50.000 0.00 0.00 0.00 3.01
194 199 1.341482 TGCAACCACCCAGAAAAGACA 60.341 47.619 0.00 0.00 0.00 3.41
195 200 1.338020 GCAACCACCCAGAAAAGACAG 59.662 52.381 0.00 0.00 0.00 3.51
196 201 1.956477 CAACCACCCAGAAAAGACAGG 59.044 52.381 0.00 0.00 0.00 4.00
197 202 1.518367 ACCACCCAGAAAAGACAGGA 58.482 50.000 0.00 0.00 0.00 3.86
198 203 2.065799 ACCACCCAGAAAAGACAGGAT 58.934 47.619 0.00 0.00 0.00 3.24
199 204 2.224867 ACCACCCAGAAAAGACAGGATG 60.225 50.000 0.00 0.00 46.00 3.51
228 233 6.687081 AAAAAGACAAGATAACGTTGGTGA 57.313 33.333 11.99 0.00 0.00 4.02
248 253 3.531262 ACGAAGTTTTTGGCGATACAC 57.469 42.857 0.00 0.00 37.78 2.90
249 254 3.135994 ACGAAGTTTTTGGCGATACACT 58.864 40.909 0.00 0.00 37.78 3.55
254 261 6.347079 CGAAGTTTTTGGCGATACACTCTTTA 60.347 38.462 0.00 0.00 0.00 1.85
299 313 5.070770 TGGAATTTTGTGGCATACATGTC 57.929 39.130 0.00 0.00 39.48 3.06
315 329 9.304731 GCATACATGTCATTTTGATGTTGTAAT 57.695 29.630 0.00 0.00 28.85 1.89
340 354 3.697619 ACTGTTAAGGGCTCCAGTAAC 57.302 47.619 0.00 2.33 36.44 2.50
343 357 2.304761 TGTTAAGGGCTCCAGTAACCTG 59.695 50.000 11.69 0.00 38.50 4.00
351 365 0.543410 TCCAGTAACCTGAAGCCGGA 60.543 55.000 5.05 0.00 41.50 5.14
352 366 0.541863 CCAGTAACCTGAAGCCGGAT 59.458 55.000 5.05 0.00 41.50 4.18
354 368 0.541863 AGTAACCTGAAGCCGGATGG 59.458 55.000 5.05 0.00 38.77 3.51
395 409 9.862149 ACTCCCTCCGTATCAAAATATAAAAAT 57.138 29.630 0.00 0.00 0.00 1.82
447 461 8.480643 AACGTTTTTATATTCTGAGACAGAGG 57.519 34.615 0.00 0.00 41.75 3.69
448 462 7.837863 ACGTTTTTATATTCTGAGACAGAGGA 58.162 34.615 0.00 0.00 41.75 3.71
449 463 8.311836 ACGTTTTTATATTCTGAGACAGAGGAA 58.688 33.333 0.00 0.00 41.75 3.36
450 464 8.812329 CGTTTTTATATTCTGAGACAGAGGAAG 58.188 37.037 0.00 0.00 41.75 3.46
451 465 9.660180 GTTTTTATATTCTGAGACAGAGGAAGT 57.340 33.333 0.00 0.00 41.75 3.01
482 496 7.391148 TTTCCCAGCTAGATGTATGAAAAAC 57.609 36.000 7.31 0.00 0.00 2.43
488 502 6.149308 CAGCTAGATGTATGAAAAACCACACA 59.851 38.462 0.00 0.00 0.00 3.72
491 505 8.028938 GCTAGATGTATGAAAAACCACACAATT 58.971 33.333 0.00 0.00 0.00 2.32
494 508 8.855110 AGATGTATGAAAAACCACACAATTACA 58.145 29.630 0.00 0.00 0.00 2.41
503 517 6.952773 AACCACACAATTACACTAACACAT 57.047 33.333 0.00 0.00 0.00 3.21
505 519 8.630054 AACCACACAATTACACTAACACATAT 57.370 30.769 0.00 0.00 0.00 1.78
506 520 9.727859 AACCACACAATTACACTAACACATATA 57.272 29.630 0.00 0.00 0.00 0.86
507 521 9.158233 ACCACACAATTACACTAACACATATAC 57.842 33.333 0.00 0.00 0.00 1.47
508 522 9.378551 CCACACAATTACACTAACACATATACT 57.621 33.333 0.00 0.00 0.00 2.12
510 524 9.595823 ACACAATTACACTAACACATATACTCC 57.404 33.333 0.00 0.00 0.00 3.85
511 525 9.042008 CACAATTACACTAACACATATACTCCC 57.958 37.037 0.00 0.00 0.00 4.30
512 526 8.989131 ACAATTACACTAACACATATACTCCCT 58.011 33.333 0.00 0.00 0.00 4.20
513 527 9.477484 CAATTACACTAACACATATACTCCCTC 57.523 37.037 0.00 0.00 0.00 4.30
514 528 8.777578 ATTACACTAACACATATACTCCCTCA 57.222 34.615 0.00 0.00 0.00 3.86
515 529 6.716934 ACACTAACACATATACTCCCTCAG 57.283 41.667 0.00 0.00 0.00 3.35
516 530 6.195700 ACACTAACACATATACTCCCTCAGT 58.804 40.000 0.00 0.00 39.41 3.41
517 531 6.668283 ACACTAACACATATACTCCCTCAGTT 59.332 38.462 0.00 0.00 36.43 3.16
518 532 7.147880 ACACTAACACATATACTCCCTCAGTTC 60.148 40.741 0.00 0.00 36.43 3.01
519 533 7.068839 CACTAACACATATACTCCCTCAGTTCT 59.931 40.741 0.00 0.00 36.43 3.01
520 534 6.875972 AACACATATACTCCCTCAGTTCTT 57.124 37.500 0.00 0.00 36.43 2.52
521 535 7.973048 AACACATATACTCCCTCAGTTCTTA 57.027 36.000 0.00 0.00 36.43 2.10
522 536 7.973048 ACACATATACTCCCTCAGTTCTTAA 57.027 36.000 0.00 0.00 36.43 1.85
523 537 8.375493 ACACATATACTCCCTCAGTTCTTAAA 57.625 34.615 0.00 0.00 36.43 1.52
524 538 8.993424 ACACATATACTCCCTCAGTTCTTAAAT 58.007 33.333 0.00 0.00 36.43 1.40
532 546 9.495382 ACTCCCTCAGTTCTTAAATATAAGTCT 57.505 33.333 0.00 0.00 39.65 3.24
533 547 9.974980 CTCCCTCAGTTCTTAAATATAAGTCTC 57.025 37.037 0.00 0.00 39.65 3.36
534 548 9.716556 TCCCTCAGTTCTTAAATATAAGTCTCT 57.283 33.333 0.00 0.00 39.65 3.10
575 589 9.871238 ATAGACTACATACGAAACAAAATGAGT 57.129 29.630 0.00 0.00 0.00 3.41
576 590 8.018677 AGACTACATACGAAACAAAATGAGTG 57.981 34.615 0.00 0.00 0.00 3.51
577 591 7.117812 AGACTACATACGAAACAAAATGAGTGG 59.882 37.037 0.00 0.00 0.00 4.00
578 592 6.932400 ACTACATACGAAACAAAATGAGTGGA 59.068 34.615 0.00 0.00 0.00 4.02
579 593 5.997385 ACATACGAAACAAAATGAGTGGAC 58.003 37.500 0.00 0.00 0.00 4.02
580 594 3.982576 ACGAAACAAAATGAGTGGACC 57.017 42.857 0.00 0.00 0.00 4.46
581 595 3.551846 ACGAAACAAAATGAGTGGACCT 58.448 40.909 0.00 0.00 0.00 3.85
582 596 4.710324 ACGAAACAAAATGAGTGGACCTA 58.290 39.130 0.00 0.00 0.00 3.08
583 597 5.313712 ACGAAACAAAATGAGTGGACCTAT 58.686 37.500 0.00 0.00 0.00 2.57
584 598 6.469410 ACGAAACAAAATGAGTGGACCTATA 58.531 36.000 0.00 0.00 0.00 1.31
585 599 6.370718 ACGAAACAAAATGAGTGGACCTATAC 59.629 38.462 0.00 0.00 0.00 1.47
586 600 6.594159 CGAAACAAAATGAGTGGACCTATACT 59.406 38.462 0.00 0.00 0.00 2.12
587 601 7.201530 CGAAACAAAATGAGTGGACCTATACTC 60.202 40.741 3.93 3.93 42.77 2.59
588 602 6.875972 ACAAAATGAGTGGACCTATACTCT 57.124 37.500 10.81 0.00 42.86 3.24
589 603 7.973048 ACAAAATGAGTGGACCTATACTCTA 57.027 36.000 10.81 0.49 42.86 2.43
590 604 8.375493 ACAAAATGAGTGGACCTATACTCTAA 57.625 34.615 10.81 0.00 42.86 2.10
591 605 8.822805 ACAAAATGAGTGGACCTATACTCTAAA 58.177 33.333 10.81 0.00 42.86 1.85
592 606 9.667107 CAAAATGAGTGGACCTATACTCTAAAA 57.333 33.333 10.81 0.00 42.86 1.52
593 607 9.892130 AAAATGAGTGGACCTATACTCTAAAAG 57.108 33.333 10.81 0.00 42.86 2.27
594 608 7.604657 ATGAGTGGACCTATACTCTAAAAGG 57.395 40.000 10.81 0.00 42.86 3.11
595 609 5.363005 TGAGTGGACCTATACTCTAAAAGGC 59.637 44.000 10.81 0.00 42.86 4.35
596 610 4.341520 AGTGGACCTATACTCTAAAAGGCG 59.658 45.833 0.00 0.00 31.98 5.52
597 611 4.099113 GTGGACCTATACTCTAAAAGGCGT 59.901 45.833 0.00 0.00 31.98 5.68
598 612 4.340381 TGGACCTATACTCTAAAAGGCGTC 59.660 45.833 0.00 0.00 31.98 5.19
599 613 4.583907 GGACCTATACTCTAAAAGGCGTCT 59.416 45.833 0.00 0.00 31.98 4.18
600 614 5.767168 GGACCTATACTCTAAAAGGCGTCTA 59.233 44.000 0.00 0.00 31.98 2.59
601 615 6.433716 GGACCTATACTCTAAAAGGCGTCTAT 59.566 42.308 0.00 0.00 31.98 1.98
602 616 7.609532 GGACCTATACTCTAAAAGGCGTCTATA 59.390 40.741 0.00 0.00 31.98 1.31
603 617 9.176460 GACCTATACTCTAAAAGGCGTCTATAT 57.824 37.037 0.00 0.00 31.98 0.86
609 623 7.828712 ACTCTAAAAGGCGTCTATATACATCC 58.171 38.462 0.00 0.00 0.00 3.51
610 624 7.450634 ACTCTAAAAGGCGTCTATATACATCCA 59.549 37.037 0.00 0.00 0.00 3.41
611 625 8.185506 TCTAAAAGGCGTCTATATACATCCAA 57.814 34.615 0.00 0.00 0.00 3.53
612 626 8.644216 TCTAAAAGGCGTCTATATACATCCAAA 58.356 33.333 0.00 0.00 0.00 3.28
613 627 9.436957 CTAAAAGGCGTCTATATACATCCAAAT 57.563 33.333 0.00 0.00 0.00 2.32
615 629 9.959721 AAAAGGCGTCTATATACATCCAAATAT 57.040 29.630 0.00 0.00 0.00 1.28
618 632 9.422681 AGGCGTCTATATACATCCAAATATAGT 57.577 33.333 0.00 0.00 38.75 2.12
697 711 5.379732 AACGTTTTGTTCCTTTGAGTTCA 57.620 34.783 0.00 0.00 35.27 3.18
764 778 5.880901 AGGATAACCTTGTTGACAATGTCT 58.119 37.500 14.97 0.00 45.36 3.41
765 779 6.306987 AGGATAACCTTGTTGACAATGTCTT 58.693 36.000 14.97 1.26 45.36 3.01
766 780 6.777580 AGGATAACCTTGTTGACAATGTCTTT 59.222 34.615 14.97 0.00 45.36 2.52
767 781 7.287696 AGGATAACCTTGTTGACAATGTCTTTT 59.712 33.333 14.97 0.00 45.36 2.27
768 782 8.573035 GGATAACCTTGTTGACAATGTCTTTTA 58.427 33.333 14.97 2.59 34.41 1.52
769 783 9.612620 GATAACCTTGTTGACAATGTCTTTTAG 57.387 33.333 14.97 6.98 34.41 1.85
770 784 5.831997 ACCTTGTTGACAATGTCTTTTAGC 58.168 37.500 14.97 0.00 35.02 3.09
771 785 5.221244 ACCTTGTTGACAATGTCTTTTAGCC 60.221 40.000 14.97 0.00 35.02 3.93
772 786 5.221224 CCTTGTTGACAATGTCTTTTAGCCA 60.221 40.000 14.97 0.00 35.02 4.75
773 787 6.403866 TTGTTGACAATGTCTTTTAGCCAT 57.596 33.333 14.97 0.00 33.15 4.40
774 788 7.309133 CCTTGTTGACAATGTCTTTTAGCCATA 60.309 37.037 14.97 0.00 35.02 2.74
775 789 6.908825 TGTTGACAATGTCTTTTAGCCATAC 58.091 36.000 14.97 0.00 33.15 2.39
776 790 6.488344 TGTTGACAATGTCTTTTAGCCATACA 59.512 34.615 14.97 1.49 33.15 2.29
777 791 7.013750 TGTTGACAATGTCTTTTAGCCATACAA 59.986 33.333 14.97 0.00 33.15 2.41
778 792 7.144722 TGACAATGTCTTTTAGCCATACAAG 57.855 36.000 14.97 0.00 33.15 3.16
779 793 5.954335 ACAATGTCTTTTAGCCATACAAGC 58.046 37.500 0.00 0.00 0.00 4.01
780 794 5.105756 ACAATGTCTTTTAGCCATACAAGCC 60.106 40.000 0.00 0.00 0.00 4.35
781 795 3.006940 TGTCTTTTAGCCATACAAGCCG 58.993 45.455 0.00 0.00 0.00 5.52
859 1247 2.512301 GCGCACAGCTAGCTTCTCG 61.512 63.158 16.46 18.21 44.04 4.04
860 1248 1.137614 CGCACAGCTAGCTTCTCGA 59.862 57.895 16.46 0.00 0.00 4.04
924 1550 1.349688 AGGTTTACCATGCCGTGAGAA 59.650 47.619 1.13 0.00 38.89 2.87
956 1583 2.839975 CCTACTTAAGGCCTAGCTTGC 58.160 52.381 5.16 0.00 38.97 4.01
1651 2280 3.782443 CTGGCCACCCGGACCTAC 61.782 72.222 0.00 0.00 41.25 3.18
1653 2282 3.782443 GGCCACCCGGACCTACAG 61.782 72.222 0.73 0.00 31.82 2.74
1695 2326 1.064946 CCTCGGCGTCATCTCTCAC 59.935 63.158 6.85 0.00 0.00 3.51
1764 2395 2.126965 CGCGACGACTCGGACTTT 60.127 61.111 0.00 0.00 40.53 2.66
2181 2833 3.260884 TCCGAGGCTTCTTCAACTACAAT 59.739 43.478 0.00 0.00 0.00 2.71
2310 2962 1.269621 GGCGTGCTCCTACGATATGTT 60.270 52.381 2.14 0.00 46.46 2.71
2321 2973 5.010314 TCCTACGATATGTTAAGGCGTCATT 59.990 40.000 0.00 0.00 36.51 2.57
2373 3025 5.006153 TCGGTGTCGACATCATCTTTTAT 57.994 39.130 27.32 0.00 40.88 1.40
2457 3109 1.758319 CGTTGCATAAGTACGGCGGG 61.758 60.000 13.24 0.00 0.00 6.13
2482 3134 3.771160 ACTGGGGTAAGAGCCGCG 61.771 66.667 0.00 0.00 43.50 6.46
2550 3202 7.792364 TGAGTTTCTTAGGGTGAAAGATAGA 57.208 36.000 0.00 0.00 34.58 1.98
2666 3318 1.615392 AGGACTTTGCATTTGCTCCAC 59.385 47.619 10.18 0.00 42.66 4.02
2700 3352 0.250513 CTCCGGAGCAAGGCTACTTT 59.749 55.000 20.67 0.00 39.88 2.66
2761 3413 8.656849 TCTGCTCGTTCTTCAAGAATTATTAAC 58.343 33.333 2.39 0.00 36.50 2.01
2762 3414 8.317891 TGCTCGTTCTTCAAGAATTATTAACA 57.682 30.769 2.39 0.00 36.50 2.41
2763 3415 8.443160 TGCTCGTTCTTCAAGAATTATTAACAG 58.557 33.333 2.39 0.00 36.50 3.16
2766 3418 8.717821 TCGTTCTTCAAGAATTATTAACAGTGG 58.282 33.333 2.39 0.00 36.50 4.00
2768 3420 7.072177 TCTTCAAGAATTATTAACAGTGGCG 57.928 36.000 0.00 0.00 0.00 5.69
2769 3421 5.811399 TCAAGAATTATTAACAGTGGCGG 57.189 39.130 0.00 0.00 0.00 6.13
2771 3423 5.584649 TCAAGAATTATTAACAGTGGCGGAG 59.415 40.000 0.00 0.00 0.00 4.63
2787 3439 2.464865 CGGAGCTAGAACCAGATTTCG 58.535 52.381 0.00 0.00 0.00 3.46
2788 3440 2.205911 GGAGCTAGAACCAGATTTCGC 58.794 52.381 0.00 0.00 0.00 4.70
2789 3441 2.205911 GAGCTAGAACCAGATTTCGCC 58.794 52.381 0.00 0.00 0.00 5.54
2790 3442 1.834263 AGCTAGAACCAGATTTCGCCT 59.166 47.619 0.00 0.00 0.00 5.52
2791 3443 1.936547 GCTAGAACCAGATTTCGCCTG 59.063 52.381 0.00 0.00 0.00 4.85
2795 3447 2.830370 CCAGATTTCGCCTGGGGC 60.830 66.667 5.77 0.00 45.66 5.80
2804 3456 4.809070 GCCTGGGGCTAAGCTATG 57.191 61.111 0.80 0.00 46.69 2.23
2805 3457 1.839894 GCCTGGGGCTAAGCTATGT 59.160 57.895 0.80 0.00 46.69 2.29
2806 3458 0.536006 GCCTGGGGCTAAGCTATGTG 60.536 60.000 0.80 0.00 46.69 3.21
2807 3459 1.131638 CCTGGGGCTAAGCTATGTGA 58.868 55.000 0.00 0.00 0.00 3.58
2808 3460 1.071385 CCTGGGGCTAAGCTATGTGAG 59.929 57.143 0.00 0.00 0.00 3.51
2809 3461 1.765314 CTGGGGCTAAGCTATGTGAGT 59.235 52.381 0.00 0.00 0.00 3.41
2810 3462 1.486310 TGGGGCTAAGCTATGTGAGTG 59.514 52.381 0.00 0.00 0.00 3.51
2811 3463 1.762957 GGGGCTAAGCTATGTGAGTGA 59.237 52.381 0.00 0.00 0.00 3.41
2812 3464 2.170607 GGGGCTAAGCTATGTGAGTGAA 59.829 50.000 0.00 0.00 0.00 3.18
2813 3465 3.370527 GGGGCTAAGCTATGTGAGTGAAA 60.371 47.826 0.00 0.00 0.00 2.69
2814 3466 4.261801 GGGCTAAGCTATGTGAGTGAAAA 58.738 43.478 0.00 0.00 0.00 2.29
2815 3467 4.700213 GGGCTAAGCTATGTGAGTGAAAAA 59.300 41.667 0.00 0.00 0.00 1.94
2816 3468 5.392057 GGGCTAAGCTATGTGAGTGAAAAAC 60.392 44.000 0.00 0.00 0.00 2.43
2817 3469 5.412904 GGCTAAGCTATGTGAGTGAAAAACT 59.587 40.000 0.00 0.00 43.85 2.66
2818 3470 6.072452 GGCTAAGCTATGTGAGTGAAAAACTT 60.072 38.462 0.00 0.00 40.07 2.66
2819 3471 7.363431 GCTAAGCTATGTGAGTGAAAAACTTT 58.637 34.615 0.00 0.00 40.07 2.66
2820 3472 7.862873 GCTAAGCTATGTGAGTGAAAAACTTTT 59.137 33.333 0.00 0.00 40.07 2.27
2821 3473 9.736023 CTAAGCTATGTGAGTGAAAAACTTTTT 57.264 29.630 0.00 0.00 40.07 1.94
2873 3525 9.930158 AATTATAAGGGAATTTGTTACTAGGCA 57.070 29.630 0.00 0.00 0.00 4.75
2875 3527 7.823745 ATAAGGGAATTTGTTACTAGGCATG 57.176 36.000 0.00 0.00 0.00 4.06
2876 3528 4.536765 AGGGAATTTGTTACTAGGCATGG 58.463 43.478 0.00 0.00 0.00 3.66
2877 3529 3.636764 GGGAATTTGTTACTAGGCATGGG 59.363 47.826 0.00 0.00 0.00 4.00
2878 3530 3.636764 GGAATTTGTTACTAGGCATGGGG 59.363 47.826 0.00 0.00 0.00 4.96
2879 3531 2.137810 TTTGTTACTAGGCATGGGGC 57.862 50.000 0.00 0.00 43.74 5.80
2942 3595 6.435430 TTGTCGGACCTGAAAATAATGATG 57.565 37.500 5.55 0.00 0.00 3.07
2945 3598 5.584649 GTCGGACCTGAAAATAATGATGTGA 59.415 40.000 0.00 0.00 0.00 3.58
2955 3608 9.153721 TGAAAATAATGATGTGATTTTCCTTGC 57.846 29.630 13.76 0.00 43.89 4.01
2970 3623 9.303537 GATTTTCCTTGCTATATACGAGGATAC 57.696 37.037 16.09 8.80 45.29 2.24
3102 3825 1.305802 ACACCGAGCCATCCACCTA 60.306 57.895 0.00 0.00 0.00 3.08
3111 3834 0.535102 CCATCCACCTATCCAACGGC 60.535 60.000 0.00 0.00 0.00 5.68
3141 3881 6.643360 TGTTTTGATGCAGATCTTTCAATGTG 59.357 34.615 11.38 0.00 0.00 3.21
3143 3883 6.578163 TTGATGCAGATCTTTCAATGTGAA 57.422 33.333 0.00 0.00 34.03 3.18
3153 3893 8.746530 AGATCTTTCAATGTGAAAATGCAGTAT 58.253 29.630 5.06 0.00 44.69 2.12
3164 3904 7.782168 TGTGAAAATGCAGTATATTTCCCCATA 59.218 33.333 0.00 0.00 32.21 2.74
3165 3905 8.637986 GTGAAAATGCAGTATATTTCCCCATAA 58.362 33.333 0.00 0.00 32.21 1.90
3194 3936 7.661437 GTGTATGGGATCAGTTTATTGCAGATA 59.339 37.037 0.00 0.00 0.00 1.98
3283 4025 7.112779 ACAGAGGAATAGAAAAATGTGTAGGG 58.887 38.462 0.00 0.00 0.00 3.53
3284 4026 7.112779 CAGAGGAATAGAAAAATGTGTAGGGT 58.887 38.462 0.00 0.00 0.00 4.34
3285 4027 7.066284 CAGAGGAATAGAAAAATGTGTAGGGTG 59.934 40.741 0.00 0.00 0.00 4.61
3286 4028 6.187682 AGGAATAGAAAAATGTGTAGGGTGG 58.812 40.000 0.00 0.00 0.00 4.61
3287 4029 6.011981 AGGAATAGAAAAATGTGTAGGGTGGA 60.012 38.462 0.00 0.00 0.00 4.02
3290 4032 2.215942 AAAATGTGTAGGGTGGAGGC 57.784 50.000 0.00 0.00 0.00 4.70
3291 4033 0.331616 AAATGTGTAGGGTGGAGGCC 59.668 55.000 0.00 0.00 0.00 5.19
3295 4038 3.090532 GTAGGGTGGAGGCCAGGG 61.091 72.222 5.01 0.00 32.34 4.45
3310 4053 1.242076 CAGGGCAGAGTGAAAACCTG 58.758 55.000 0.00 0.00 39.45 4.00
3319 4062 0.032540 GTGAAAACCTGCAGGCTTGG 59.967 55.000 33.06 10.36 39.32 3.61
3364 4107 2.032681 AGCTTGGGACGCAGGAAC 59.967 61.111 5.77 0.00 0.00 3.62
3366 4109 2.429930 CTTGGGACGCAGGAACCA 59.570 61.111 0.00 0.00 0.00 3.67
3406 4152 4.197498 GCGCTTACGGCCGGACTA 62.197 66.667 31.76 10.38 40.57 2.59
3452 4199 1.269166 GTGCGACTAGGTGAATCGTG 58.731 55.000 0.00 0.00 38.13 4.35
3464 4211 3.370978 GGTGAATCGTGGTTACATGTGAG 59.629 47.826 9.11 0.00 35.12 3.51
3471 4218 4.099419 TCGTGGTTACATGTGAGCATAGAT 59.901 41.667 23.08 0.00 35.12 1.98
3510 4264 2.198827 TTAGCAACACAGGTCCATGG 57.801 50.000 4.97 4.97 0.00 3.66
3536 4290 3.930848 GTCCATGTAAACAAGGTCTACCG 59.069 47.826 4.44 0.00 42.08 4.02
3539 4293 3.688694 TGTAAACAAGGTCTACCGCAT 57.311 42.857 0.00 0.00 42.08 4.73
3542 4317 4.822896 TGTAAACAAGGTCTACCGCATTTT 59.177 37.500 0.00 0.00 42.08 1.82
3563 4342 4.771590 TTTGAGTCATGTCAAATCCAGC 57.228 40.909 7.25 0.00 40.68 4.85
3633 4415 0.174845 CGGATGCTTCAGTTCCCGTA 59.825 55.000 1.64 0.00 33.02 4.02
3646 4428 0.250381 TCCCGTAAAAAGCGCAGGAA 60.250 50.000 11.47 0.00 0.00 3.36
3670 4452 3.942115 AGAAGCCTTTTCTTAGGAATCGC 59.058 43.478 0.00 0.00 37.50 4.58
3691 4473 4.532834 GCCTGGGATATTTCCTTTGTACA 58.467 43.478 1.99 0.00 42.20 2.90
3692 4474 5.140454 GCCTGGGATATTTCCTTTGTACAT 58.860 41.667 0.00 0.00 42.20 2.29
3700 4482 7.441458 GGATATTTCCTTTGTACATAACGCTCT 59.559 37.037 0.00 0.00 39.14 4.09
3746 4528 0.526211 GAAACCTCCACAATTCCCGC 59.474 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 6.976934 AACAAATCCCTTAACAGTTGACAT 57.023 33.333 0.00 0.00 0.00 3.06
114 117 2.825205 AGCAGCATTGTGTGGTTTTTC 58.175 42.857 0.00 0.00 36.12 2.29
115 118 2.985957 AGCAGCATTGTGTGGTTTTT 57.014 40.000 0.00 0.00 36.12 1.94
144 147 6.836242 AGGCTCCCAAATCAAACAAAAATAA 58.164 32.000 0.00 0.00 0.00 1.40
146 149 5.308976 AGGCTCCCAAATCAAACAAAAAT 57.691 34.783 0.00 0.00 0.00 1.82
152 157 2.893489 AGTCAAGGCTCCCAAATCAAAC 59.107 45.455 0.00 0.00 0.00 2.93
158 163 0.106268 TGCAAGTCAAGGCTCCCAAA 60.106 50.000 0.00 0.00 0.00 3.28
163 168 0.312102 GTGGTTGCAAGTCAAGGCTC 59.688 55.000 0.00 0.00 34.91 4.70
164 169 1.109323 GGTGGTTGCAAGTCAAGGCT 61.109 55.000 0.00 0.00 34.91 4.58
205 210 6.492254 GTCACCAACGTTATCTTGTCTTTTT 58.508 36.000 0.00 0.00 0.00 1.94
206 211 5.277154 CGTCACCAACGTTATCTTGTCTTTT 60.277 40.000 0.00 0.00 46.42 2.27
207 212 4.210537 CGTCACCAACGTTATCTTGTCTTT 59.789 41.667 0.00 0.00 46.42 2.52
228 233 3.135994 AGTGTATCGCCAAAAACTTCGT 58.864 40.909 0.00 0.00 0.00 3.85
282 296 6.519382 TCAAAATGACATGTATGCCACAAAA 58.481 32.000 0.00 0.00 41.55 2.44
315 329 1.771854 TGGAGCCCTTAACAGTTGACA 59.228 47.619 0.00 0.00 0.00 3.58
340 354 1.895707 GCATCCATCCGGCTTCAGG 60.896 63.158 0.00 0.00 0.00 3.86
343 357 1.152881 AAGGCATCCATCCGGCTTC 60.153 57.895 0.00 0.00 43.88 3.86
369 383 9.862149 ATTTTTATATTTTGATACGGAGGGAGT 57.138 29.630 0.00 0.00 0.00 3.85
421 435 8.936864 CCTCTGTCTCAGAATATAAAAACGTTT 58.063 33.333 7.96 7.96 40.18 3.60
422 436 8.311836 TCCTCTGTCTCAGAATATAAAAACGTT 58.688 33.333 0.00 0.00 40.18 3.99
423 437 7.837863 TCCTCTGTCTCAGAATATAAAAACGT 58.162 34.615 1.22 0.00 40.18 3.99
424 438 8.703604 TTCCTCTGTCTCAGAATATAAAAACG 57.296 34.615 1.22 0.00 40.18 3.60
425 439 9.660180 ACTTCCTCTGTCTCAGAATATAAAAAC 57.340 33.333 1.22 0.00 40.18 2.43
462 476 5.647658 TGTGGTTTTTCATACATCTAGCTGG 59.352 40.000 0.00 0.00 0.00 4.85
473 487 9.953697 GTTAGTGTAATTGTGTGGTTTTTCATA 57.046 29.630 0.00 0.00 0.00 2.15
482 496 9.378551 AGTATATGTGTTAGTGTAATTGTGTGG 57.621 33.333 0.00 0.00 0.00 4.17
488 502 9.209048 TGAGGGAGTATATGTGTTAGTGTAATT 57.791 33.333 0.00 0.00 0.00 1.40
491 505 7.351952 ACTGAGGGAGTATATGTGTTAGTGTA 58.648 38.462 0.00 0.00 30.86 2.90
494 508 7.126733 AGAACTGAGGGAGTATATGTGTTAGT 58.873 38.462 0.00 0.00 33.09 2.24
506 520 9.495382 AGACTTATATTTAAGAACTGAGGGAGT 57.505 33.333 9.58 0.00 38.56 3.85
507 521 9.974980 GAGACTTATATTTAAGAACTGAGGGAG 57.025 37.037 9.58 0.00 38.56 4.30
508 522 9.716556 AGAGACTTATATTTAAGAACTGAGGGA 57.283 33.333 9.58 0.00 38.56 4.20
549 563 9.871238 ACTCATTTTGTTTCGTATGTAGTCTAT 57.129 29.630 0.00 0.00 0.00 1.98
550 564 9.135843 CACTCATTTTGTTTCGTATGTAGTCTA 57.864 33.333 0.00 0.00 0.00 2.59
551 565 7.117812 CCACTCATTTTGTTTCGTATGTAGTCT 59.882 37.037 0.00 0.00 0.00 3.24
552 566 7.117236 TCCACTCATTTTGTTTCGTATGTAGTC 59.883 37.037 0.00 0.00 0.00 2.59
553 567 6.932400 TCCACTCATTTTGTTTCGTATGTAGT 59.068 34.615 0.00 0.00 0.00 2.73
554 568 7.234384 GTCCACTCATTTTGTTTCGTATGTAG 58.766 38.462 0.00 0.00 0.00 2.74
555 569 6.148150 GGTCCACTCATTTTGTTTCGTATGTA 59.852 38.462 0.00 0.00 0.00 2.29
556 570 5.048991 GGTCCACTCATTTTGTTTCGTATGT 60.049 40.000 0.00 0.00 0.00 2.29
557 571 5.181245 AGGTCCACTCATTTTGTTTCGTATG 59.819 40.000 0.00 0.00 0.00 2.39
558 572 5.313712 AGGTCCACTCATTTTGTTTCGTAT 58.686 37.500 0.00 0.00 0.00 3.06
559 573 4.710324 AGGTCCACTCATTTTGTTTCGTA 58.290 39.130 0.00 0.00 0.00 3.43
560 574 3.551846 AGGTCCACTCATTTTGTTTCGT 58.448 40.909 0.00 0.00 0.00 3.85
561 575 5.880054 ATAGGTCCACTCATTTTGTTTCG 57.120 39.130 0.00 0.00 0.00 3.46
562 576 7.824779 AGAGTATAGGTCCACTCATTTTGTTTC 59.175 37.037 9.80 0.00 42.99 2.78
563 577 7.690256 AGAGTATAGGTCCACTCATTTTGTTT 58.310 34.615 9.80 0.00 42.99 2.83
564 578 7.259088 AGAGTATAGGTCCACTCATTTTGTT 57.741 36.000 9.80 0.00 42.99 2.83
565 579 6.875972 AGAGTATAGGTCCACTCATTTTGT 57.124 37.500 9.80 0.00 42.99 2.83
566 580 9.667107 TTTTAGAGTATAGGTCCACTCATTTTG 57.333 33.333 9.80 0.00 42.99 2.44
567 581 9.892130 CTTTTAGAGTATAGGTCCACTCATTTT 57.108 33.333 9.80 0.00 42.99 1.82
568 582 8.487028 CCTTTTAGAGTATAGGTCCACTCATTT 58.513 37.037 9.80 0.00 42.99 2.32
569 583 7.419172 GCCTTTTAGAGTATAGGTCCACTCATT 60.419 40.741 9.80 0.00 42.99 2.57
570 584 6.042208 GCCTTTTAGAGTATAGGTCCACTCAT 59.958 42.308 9.80 0.08 42.99 2.90
571 585 5.363005 GCCTTTTAGAGTATAGGTCCACTCA 59.637 44.000 9.80 0.00 42.99 3.41
572 586 5.507650 CGCCTTTTAGAGTATAGGTCCACTC 60.508 48.000 0.44 0.44 41.25 3.51
573 587 4.341520 CGCCTTTTAGAGTATAGGTCCACT 59.658 45.833 0.00 0.00 0.00 4.00
574 588 4.099113 ACGCCTTTTAGAGTATAGGTCCAC 59.901 45.833 0.00 0.00 0.00 4.02
575 589 4.284178 ACGCCTTTTAGAGTATAGGTCCA 58.716 43.478 0.00 0.00 0.00 4.02
576 590 4.583907 AGACGCCTTTTAGAGTATAGGTCC 59.416 45.833 0.00 0.00 0.00 4.46
577 591 5.771153 AGACGCCTTTTAGAGTATAGGTC 57.229 43.478 0.00 0.00 0.00 3.85
583 597 8.954350 GGATGTATATAGACGCCTTTTAGAGTA 58.046 37.037 2.86 0.00 0.00 2.59
584 598 7.450634 TGGATGTATATAGACGCCTTTTAGAGT 59.549 37.037 9.68 0.00 0.00 3.24
585 599 7.827701 TGGATGTATATAGACGCCTTTTAGAG 58.172 38.462 9.68 0.00 0.00 2.43
586 600 7.770366 TGGATGTATATAGACGCCTTTTAGA 57.230 36.000 9.68 0.00 0.00 2.10
587 601 8.827177 TTTGGATGTATATAGACGCCTTTTAG 57.173 34.615 9.68 0.00 0.00 1.85
589 603 9.959721 ATATTTGGATGTATATAGACGCCTTTT 57.040 29.630 9.68 0.12 0.00 2.27
592 606 9.422681 ACTATATTTGGATGTATATAGACGCCT 57.577 33.333 13.30 0.00 38.63 5.52
647 661 9.462606 AGTCAATTATTCCCTTCGTTTCTAAAT 57.537 29.630 0.00 0.00 0.00 1.40
648 662 8.857694 AGTCAATTATTCCCTTCGTTTCTAAA 57.142 30.769 0.00 0.00 0.00 1.85
649 663 9.947433 TTAGTCAATTATTCCCTTCGTTTCTAA 57.053 29.630 0.00 0.00 0.00 2.10
650 664 9.947433 TTTAGTCAATTATTCCCTTCGTTTCTA 57.053 29.630 0.00 0.00 0.00 2.10
651 665 8.727910 GTTTAGTCAATTATTCCCTTCGTTTCT 58.272 33.333 0.00 0.00 0.00 2.52
652 666 7.691050 CGTTTAGTCAATTATTCCCTTCGTTTC 59.309 37.037 0.00 0.00 0.00 2.78
653 667 7.173735 ACGTTTAGTCAATTATTCCCTTCGTTT 59.826 33.333 0.00 0.00 0.00 3.60
654 668 6.652062 ACGTTTAGTCAATTATTCCCTTCGTT 59.348 34.615 0.00 0.00 0.00 3.85
655 669 6.168389 ACGTTTAGTCAATTATTCCCTTCGT 58.832 36.000 0.00 0.00 0.00 3.85
656 670 6.657836 ACGTTTAGTCAATTATTCCCTTCG 57.342 37.500 0.00 0.00 0.00 3.79
657 671 9.124807 CAAAACGTTTAGTCAATTATTCCCTTC 57.875 33.333 15.03 0.00 0.00 3.46
658 672 8.635328 ACAAAACGTTTAGTCAATTATTCCCTT 58.365 29.630 15.03 0.00 0.00 3.95
659 673 8.173542 ACAAAACGTTTAGTCAATTATTCCCT 57.826 30.769 15.03 0.00 0.00 4.20
660 674 8.806177 AACAAAACGTTTAGTCAATTATTCCC 57.194 30.769 15.03 0.00 32.35 3.97
661 675 8.908678 GGAACAAAACGTTTAGTCAATTATTCC 58.091 33.333 15.03 7.40 38.19 3.01
662 676 9.673454 AGGAACAAAACGTTTAGTCAATTATTC 57.327 29.630 15.03 1.62 38.19 1.75
665 679 9.291664 CAAAGGAACAAAACGTTTAGTCAATTA 57.708 29.630 15.03 0.00 38.19 1.40
666 680 8.030106 TCAAAGGAACAAAACGTTTAGTCAATT 58.970 29.630 15.03 7.85 38.19 2.32
667 681 7.540299 TCAAAGGAACAAAACGTTTAGTCAAT 58.460 30.769 15.03 0.00 38.19 2.57
697 711 0.396974 TGGTTGCAGGTCAAGGCTTT 60.397 50.000 0.00 0.00 34.91 3.51
763 777 4.434713 AAACGGCTTGTATGGCTAAAAG 57.565 40.909 0.00 0.00 0.00 2.27
764 778 4.142556 GCTAAACGGCTTGTATGGCTAAAA 60.143 41.667 0.00 0.00 0.00 1.52
765 779 3.375922 GCTAAACGGCTTGTATGGCTAAA 59.624 43.478 0.00 0.00 0.00 1.85
766 780 2.940410 GCTAAACGGCTTGTATGGCTAA 59.060 45.455 0.00 0.00 0.00 3.09
767 781 2.557317 GCTAAACGGCTTGTATGGCTA 58.443 47.619 0.00 0.00 0.00 3.93
768 782 1.379527 GCTAAACGGCTTGTATGGCT 58.620 50.000 0.00 0.00 0.00 4.75
769 783 0.380733 GGCTAAACGGCTTGTATGGC 59.619 55.000 0.00 0.00 34.85 4.40
770 784 1.021968 GGGCTAAACGGCTTGTATGG 58.978 55.000 0.00 0.00 38.46 2.74
771 785 2.038387 AGGGCTAAACGGCTTGTATG 57.962 50.000 0.00 0.00 38.46 2.39
772 786 2.801077 AAGGGCTAAACGGCTTGTAT 57.199 45.000 0.00 0.00 38.46 2.29
773 787 2.833338 TCTAAGGGCTAAACGGCTTGTA 59.167 45.455 0.00 0.00 38.46 2.41
774 788 1.626825 TCTAAGGGCTAAACGGCTTGT 59.373 47.619 0.00 0.00 38.46 3.16
775 789 2.396590 TCTAAGGGCTAAACGGCTTG 57.603 50.000 0.00 0.00 38.46 4.01
776 790 3.079578 GTTTCTAAGGGCTAAACGGCTT 58.920 45.455 0.00 0.00 38.46 4.35
777 791 2.039348 TGTTTCTAAGGGCTAAACGGCT 59.961 45.455 0.00 0.00 36.19 5.52
778 792 2.161012 GTGTTTCTAAGGGCTAAACGGC 59.839 50.000 0.00 0.00 36.19 5.68
779 793 3.404899 TGTGTTTCTAAGGGCTAAACGG 58.595 45.455 0.00 0.00 36.19 4.44
780 794 3.120304 GCTGTGTTTCTAAGGGCTAAACG 60.120 47.826 0.00 0.00 36.19 3.60
781 795 4.072839 AGCTGTGTTTCTAAGGGCTAAAC 58.927 43.478 0.00 0.00 34.45 2.01
974 1601 3.009363 TCTCTTGATGATTGGTTGCCTGA 59.991 43.478 0.00 0.00 0.00 3.86
1104 1732 2.347490 GTGCACATCACCGGGTCT 59.653 61.111 13.17 0.00 39.79 3.85
1650 2279 4.070552 GAGACCTTCGCCGCCTGT 62.071 66.667 0.00 0.00 0.00 4.00
1651 2280 4.821589 GGAGACCTTCGCCGCCTG 62.822 72.222 0.00 0.00 0.00 4.85
1695 2326 2.046988 TGCATGGCCAGAGTCACG 60.047 61.111 13.05 0.00 0.00 4.35
1764 2395 2.752358 CTGGCCACCTGCTCTTGA 59.248 61.111 0.00 0.00 40.92 3.02
1826 2457 1.204146 GTAGATCACCTTGCCCTGGA 58.796 55.000 0.00 0.00 0.00 3.86
2181 2833 2.272146 GGGATGCTGAAGCCGGAA 59.728 61.111 5.05 0.00 41.18 4.30
2208 2860 2.633657 GCTATGAATGCCGGTGCG 59.366 61.111 1.90 0.00 41.78 5.34
2334 2986 1.360911 GATCGAGTCCTCCGGCTTC 59.639 63.158 0.00 0.00 0.00 3.86
2403 3055 1.377202 GTCCACCACATCGGCATGT 60.377 57.895 0.00 0.00 44.72 3.21
2666 3318 1.224069 CGGAGCACAGTGTGAGTTGG 61.224 60.000 27.37 7.35 35.23 3.77
2700 3352 1.531365 CACCTTTCCTGGCCTGCAA 60.531 57.895 3.32 0.00 0.00 4.08
2761 3413 1.153549 GGTTCTAGCTCCGCCACTG 60.154 63.158 0.00 0.00 0.00 3.66
2762 3414 1.608717 CTGGTTCTAGCTCCGCCACT 61.609 60.000 0.00 0.00 0.00 4.00
2763 3415 1.153549 CTGGTTCTAGCTCCGCCAC 60.154 63.158 0.00 0.00 0.00 5.01
2766 3418 2.205911 GAAATCTGGTTCTAGCTCCGC 58.794 52.381 0.00 0.00 0.00 5.54
2768 3420 2.205911 GCGAAATCTGGTTCTAGCTCC 58.794 52.381 0.00 0.00 0.00 4.70
2769 3421 2.159028 AGGCGAAATCTGGTTCTAGCTC 60.159 50.000 0.00 0.00 0.00 4.09
2771 3423 1.936547 CAGGCGAAATCTGGTTCTAGC 59.063 52.381 0.00 0.00 0.00 3.42
2772 3424 2.555199 CCAGGCGAAATCTGGTTCTAG 58.445 52.381 2.21 0.00 44.97 2.43
2774 3426 3.558674 CCAGGCGAAATCTGGTTCT 57.441 52.632 2.21 0.00 44.97 3.01
2788 3440 1.071385 CTCACATAGCTTAGCCCCAGG 59.929 57.143 0.00 0.00 0.00 4.45
2789 3441 1.765314 ACTCACATAGCTTAGCCCCAG 59.235 52.381 0.00 0.00 0.00 4.45
2790 3442 1.486310 CACTCACATAGCTTAGCCCCA 59.514 52.381 0.00 0.00 0.00 4.96
2791 3443 1.762957 TCACTCACATAGCTTAGCCCC 59.237 52.381 0.00 0.00 0.00 5.80
2792 3444 3.543680 TTCACTCACATAGCTTAGCCC 57.456 47.619 0.00 0.00 0.00 5.19
2793 3445 5.412904 AGTTTTTCACTCACATAGCTTAGCC 59.587 40.000 0.00 0.00 0.00 3.93
2794 3446 6.487689 AGTTTTTCACTCACATAGCTTAGC 57.512 37.500 0.00 0.00 0.00 3.09
2795 3447 9.736023 AAAAAGTTTTTCACTCACATAGCTTAG 57.264 29.630 7.79 0.00 32.94 2.18
2847 3499 9.930158 TGCCTAGTAACAAATTCCCTTATAATT 57.070 29.630 0.00 0.00 0.00 1.40
2849 3501 9.349713 CATGCCTAGTAACAAATTCCCTTATAA 57.650 33.333 0.00 0.00 0.00 0.98
2850 3502 7.942341 CCATGCCTAGTAACAAATTCCCTTATA 59.058 37.037 0.00 0.00 0.00 0.98
2851 3503 6.777580 CCATGCCTAGTAACAAATTCCCTTAT 59.222 38.462 0.00 0.00 0.00 1.73
2852 3504 6.126409 CCATGCCTAGTAACAAATTCCCTTA 58.874 40.000 0.00 0.00 0.00 2.69
2853 3505 4.956075 CCATGCCTAGTAACAAATTCCCTT 59.044 41.667 0.00 0.00 0.00 3.95
2854 3506 4.536765 CCATGCCTAGTAACAAATTCCCT 58.463 43.478 0.00 0.00 0.00 4.20
2855 3507 3.636764 CCCATGCCTAGTAACAAATTCCC 59.363 47.826 0.00 0.00 0.00 3.97
2856 3508 3.636764 CCCCATGCCTAGTAACAAATTCC 59.363 47.826 0.00 0.00 0.00 3.01
2857 3509 3.068165 GCCCCATGCCTAGTAACAAATTC 59.932 47.826 0.00 0.00 0.00 2.17
2858 3510 3.031013 GCCCCATGCCTAGTAACAAATT 58.969 45.455 0.00 0.00 0.00 1.82
2859 3511 2.244769 AGCCCCATGCCTAGTAACAAAT 59.755 45.455 0.00 0.00 42.71 2.32
2860 3512 1.638589 AGCCCCATGCCTAGTAACAAA 59.361 47.619 0.00 0.00 42.71 2.83
2861 3513 1.295020 AGCCCCATGCCTAGTAACAA 58.705 50.000 0.00 0.00 42.71 2.83
2862 3514 2.184088 TAGCCCCATGCCTAGTAACA 57.816 50.000 0.00 0.00 42.71 2.41
2863 3515 3.369576 GCTATAGCCCCATGCCTAGTAAC 60.370 52.174 14.13 0.00 42.71 2.50
2864 3516 2.838202 GCTATAGCCCCATGCCTAGTAA 59.162 50.000 14.13 0.00 42.71 2.24
2865 3517 2.467880 GCTATAGCCCCATGCCTAGTA 58.532 52.381 14.13 0.00 42.71 1.82
2866 3518 1.280457 GCTATAGCCCCATGCCTAGT 58.720 55.000 14.13 0.00 42.71 2.57
2885 3537 4.729918 GTGGTGAGGCAGCTGGGG 62.730 72.222 17.12 0.00 32.61 4.96
2888 3540 4.694233 AGCGTGGTGAGGCAGCTG 62.694 66.667 10.11 10.11 36.73 4.24
2889 3541 4.385405 GAGCGTGGTGAGGCAGCT 62.385 66.667 0.00 0.00 41.29 4.24
2891 3543 2.738213 AAAGGAGCGTGGTGAGGCAG 62.738 60.000 0.00 0.00 35.31 4.85
2892 3544 2.731691 GAAAGGAGCGTGGTGAGGCA 62.732 60.000 0.00 0.00 35.31 4.75
2893 3545 2.032681 AAAGGAGCGTGGTGAGGC 59.967 61.111 0.00 0.00 0.00 4.70
2894 3546 0.671781 CAGAAAGGAGCGTGGTGAGG 60.672 60.000 0.00 0.00 0.00 3.86
2895 3547 0.671781 CCAGAAAGGAGCGTGGTGAG 60.672 60.000 0.00 0.00 41.22 3.51
2896 3548 1.371183 CCAGAAAGGAGCGTGGTGA 59.629 57.895 0.00 0.00 41.22 4.02
2942 3595 7.152645 TCCTCGTATATAGCAAGGAAAATCAC 58.847 38.462 5.57 0.00 33.27 3.06
2945 3598 8.812972 TGTATCCTCGTATATAGCAAGGAAAAT 58.187 33.333 10.29 0.82 39.47 1.82
3039 3762 8.134895 TGACAAACAAGGAACTAAAACATCATC 58.865 33.333 0.00 0.00 38.49 2.92
3054 3777 7.891561 TCCCAAAGTATAATTGACAAACAAGG 58.108 34.615 0.00 0.00 42.02 3.61
3102 3825 2.890311 TCAAAACATTCAGCCGTTGGAT 59.110 40.909 0.00 0.00 0.00 3.41
3111 3834 7.088272 TGAAAGATCTGCATCAAAACATTCAG 58.912 34.615 0.00 0.00 0.00 3.02
3143 3883 9.212593 ACTTTTATGGGGAAATATACTGCATTT 57.787 29.630 0.00 0.00 0.00 2.32
3164 3904 7.178274 TGCAATAAACTGATCCCATACACTTTT 59.822 33.333 0.00 0.00 0.00 2.27
3165 3905 6.663093 TGCAATAAACTGATCCCATACACTTT 59.337 34.615 0.00 0.00 0.00 2.66
3229 3971 0.108945 CTACGTTCCGAACAGGTCCC 60.109 60.000 11.74 0.00 41.99 4.46
3230 3972 0.108945 CCTACGTTCCGAACAGGTCC 60.109 60.000 11.74 0.00 41.99 4.46
3231 3973 0.600057 ACCTACGTTCCGAACAGGTC 59.400 55.000 14.68 0.00 41.99 3.85
3232 3974 0.316204 CACCTACGTTCCGAACAGGT 59.684 55.000 14.68 14.68 41.99 4.00
3283 4025 4.106925 CTCTGCCCTGGCCTCCAC 62.107 72.222 3.32 0.00 41.09 4.02
3284 4026 4.664267 ACTCTGCCCTGGCCTCCA 62.664 66.667 3.32 0.00 41.09 3.86
3285 4027 4.106925 CACTCTGCCCTGGCCTCC 62.107 72.222 3.32 0.00 41.09 4.30
3286 4028 2.129555 TTTCACTCTGCCCTGGCCTC 62.130 60.000 3.32 0.00 41.09 4.70
3287 4029 1.719063 TTTTCACTCTGCCCTGGCCT 61.719 55.000 3.32 0.00 41.09 5.19
3290 4032 0.111253 AGGTTTTCACTCTGCCCTGG 59.889 55.000 0.00 0.00 0.00 4.45
3291 4033 1.242076 CAGGTTTTCACTCTGCCCTG 58.758 55.000 0.00 0.00 34.10 4.45
3298 4041 1.000938 CAAGCCTGCAGGTTTTCACTC 60.001 52.381 30.06 12.98 36.44 3.51
3310 4053 0.323725 TCCTCCAATTCCAAGCCTGC 60.324 55.000 0.00 0.00 0.00 4.85
3347 4090 2.032681 GTTCCTGCGTCCCAAGCT 59.967 61.111 0.00 0.00 35.28 3.74
3351 4094 1.534476 TACTGGTTCCTGCGTCCCA 60.534 57.895 0.00 0.00 0.00 4.37
3354 4097 0.737715 CAGCTACTGGTTCCTGCGTC 60.738 60.000 0.00 0.00 0.00 5.19
3364 4107 4.720046 TCTATCTCCTGTACAGCTACTGG 58.280 47.826 17.86 3.69 41.34 4.00
3366 4109 5.242838 GCATTCTATCTCCTGTACAGCTACT 59.757 44.000 17.86 4.61 0.00 2.57
3433 4179 1.269166 CACGATTCACCTAGTCGCAC 58.731 55.000 0.00 0.00 38.85 5.34
3452 4199 5.359756 TGTGATCTATGCTCACATGTAACC 58.640 41.667 0.00 0.00 45.97 2.85
3471 4218 2.281414 CGGTGGTGGTGCATGTGA 60.281 61.111 0.00 0.00 0.00 3.58
3510 4264 4.589908 AGACCTTGTTTACATGGACCATC 58.410 43.478 18.47 7.95 42.04 3.51
3542 4317 4.022935 GTGCTGGATTTGACATGACTCAAA 60.023 41.667 12.36 12.36 42.83 2.69
3544 4319 3.076621 GTGCTGGATTTGACATGACTCA 58.923 45.455 0.00 0.00 0.00 3.41
3548 4323 2.306805 AGGAGTGCTGGATTTGACATGA 59.693 45.455 0.00 0.00 0.00 3.07
3563 4342 1.893808 AAACTGGCGTGCAGGAGTG 60.894 57.895 11.29 1.15 0.00 3.51
3594 4376 0.521291 CGGGAAGCTCATTTTTCGCA 59.479 50.000 0.00 0.00 36.41 5.10
3620 4402 2.664698 GCGCTTTTTACGGGAACTGAAG 60.665 50.000 0.00 0.00 38.67 3.02
3633 4415 2.473816 GCTTCTTTTCCTGCGCTTTTT 58.526 42.857 9.73 0.00 0.00 1.94
3646 4428 5.106118 GCGATTCCTAAGAAAAGGCTTCTTT 60.106 40.000 6.76 0.00 42.04 2.52
3658 4440 2.103153 ATCCCAGGCGATTCCTAAGA 57.897 50.000 0.00 0.00 45.52 2.10
3676 4458 8.732746 AAGAGCGTTATGTACAAAGGAAATAT 57.267 30.769 0.00 0.00 0.00 1.28
3678 4460 8.556213 TTAAGAGCGTTATGTACAAAGGAAAT 57.444 30.769 0.00 0.00 0.00 2.17
3713 4495 0.673985 GGTTTCTTTTTCTGCGGGCT 59.326 50.000 0.00 0.00 0.00 5.19
3714 4496 0.673985 AGGTTTCTTTTTCTGCGGGC 59.326 50.000 0.00 0.00 0.00 6.13
3722 4504 4.202212 CGGGAATTGTGGAGGTTTCTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
3726 4508 1.886655 GCGGGAATTGTGGAGGTTTCT 60.887 52.381 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.