Multiple sequence alignment - TraesCS6D01G359200

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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 TraesCS6D01G359200 chr6D 100.000 5090 0 0 1 5090 451774853 451769764 0.000000e+00 9400.0
1 TraesCS6D01G359200 chr6A 94.441 3508 159 21 733 4227 597689666 597686182 0.000000e+00 5365.0
2 TraesCS6D01G359200 chr6A 81.845 336 40 12 83 405 597690278 597689951 3.910000e-66 263.0
3 TraesCS6D01G359200 chr6A 90.000 80 5 2 566 643 597689867 597689789 3.240000e-17 100.0
4 TraesCS6D01G359200 chr6B 88.596 2771 197 68 215 2929 686183043 686180336 0.000000e+00 3256.0
5 TraesCS6D01G359200 chr6B 95.693 1184 40 8 2942 4118 686180265 686179086 0.000000e+00 1893.0
6 TraesCS6D01G359200 chr6B 91.848 871 52 15 4235 5089 259073194 259072327 0.000000e+00 1197.0
7 TraesCS6D01G359200 chr6B 95.000 40 1 1 2793 2832 155759146 155759108 1.530000e-05 62.1
8 TraesCS6D01G359200 chr4D 96.185 865 22 5 4235 5090 313885087 313884225 0.000000e+00 1404.0
9 TraesCS6D01G359200 chr4D 96.185 865 19 6 4235 5090 355818480 355817621 0.000000e+00 1402.0
10 TraesCS6D01G359200 chr2D 95.954 865 21 5 4235 5090 568249078 568248219 0.000000e+00 1391.0
11 TraesCS6D01G359200 chr7A 95.944 863 24 5 4237 5090 211723895 211723035 0.000000e+00 1389.0
12 TraesCS6D01G359200 chr7A 91.954 870 53 9 4235 5089 547149930 547149063 0.000000e+00 1203.0
13 TraesCS6D01G359200 chr7B 95.829 863 26 4 4237 5090 697093248 697092387 0.000000e+00 1386.0
14 TraesCS6D01G359200 chr7B 91.724 870 55 14 4235 5089 124130194 124131061 0.000000e+00 1192.0
15 TraesCS6D01G359200 chr3A 95.497 866 29 4 4234 5090 33139894 33140758 0.000000e+00 1375.0
16 TraesCS6D01G359200 chr5A 84.286 70 9 2 2758 2826 591992484 591992416 3.290000e-07 67.6
17 TraesCS6D01G359200 chr1D 83.117 77 9 4 2752 2826 463550148 463550222 3.290000e-07 67.6


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 TraesCS6D01G359200 chr6D 451769764 451774853 5089 True 9400.000000 9400 100.0000 1 5090 1 chr6D.!!$R1 5089
1 TraesCS6D01G359200 chr6A 597686182 597690278 4096 True 1909.333333 5365 88.7620 83 4227 3 chr6A.!!$R1 4144
2 TraesCS6D01G359200 chr6B 686179086 686183043 3957 True 2574.500000 3256 92.1445 215 4118 2 chr6B.!!$R3 3903
3 TraesCS6D01G359200 chr6B 259072327 259073194 867 True 1197.000000 1197 91.8480 4235 5089 1 chr6B.!!$R2 854
4 TraesCS6D01G359200 chr4D 313884225 313885087 862 True 1404.000000 1404 96.1850 4235 5090 1 chr4D.!!$R1 855
5 TraesCS6D01G359200 chr4D 355817621 355818480 859 True 1402.000000 1402 96.1850 4235 5090 1 chr4D.!!$R2 855
6 TraesCS6D01G359200 chr2D 568248219 568249078 859 True 1391.000000 1391 95.9540 4235 5090 1 chr2D.!!$R1 855
7 TraesCS6D01G359200 chr7A 211723035 211723895 860 True 1389.000000 1389 95.9440 4237 5090 1 chr7A.!!$R1 853
8 TraesCS6D01G359200 chr7A 547149063 547149930 867 True 1203.000000 1203 91.9540 4235 5089 1 chr7A.!!$R2 854
9 TraesCS6D01G359200 chr7B 697092387 697093248 861 True 1386.000000 1386 95.8290 4237 5090 1 chr7B.!!$R1 853
10 TraesCS6D01G359200 chr7B 124130194 124131061 867 False 1192.000000 1192 91.7240 4235 5089 1 chr7B.!!$F1 854
11 TraesCS6D01G359200 chr3A 33139894 33140758 864 False 1375.000000 1375 95.4970 4234 5090 1 chr3A.!!$F1 856

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
437 468 0.033503 TCTCTATGTGGCCGACCTGA 60.034 55.0 0.00 0.00 36.63 3.86 F
632 685 0.036388 CTAGCGTTCTTGCTGGGGAA 60.036 55.0 0.00 0.00 46.70 3.97 F
634 687 0.251341 AGCGTTCTTGCTGGGGAATT 60.251 50.0 0.00 0.00 45.28 2.17 F
788 888 0.597118 GCTGAGCTCCTACTGCATCG 60.597 60.0 12.15 0.00 0.00 3.84 F
1989 2110 0.681564 TGGACTTCCTCTCGAGCTCC 60.682 60.0 7.81 5.03 36.82 4.70 F
3471 3659 0.248661 CCATCTCACTCTACACGCCG 60.249 60.0 0.00 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 2467 1.070786 GGTGGTGCGGAACTTCTCA 59.929 57.895 0.00 0.00 0.0 3.27 R
2608 2729 1.079127 CCTTGACCTTGCCGTCGAT 60.079 57.895 0.00 0.00 35.4 3.59 R
2651 2772 2.622011 GCGGTTTGGTTGATGGCGA 61.622 57.895 0.00 0.00 0.0 5.54 R
2656 2777 1.674322 CGAGGGCGGTTTGGTTGAT 60.674 57.895 0.00 0.00 0.0 2.57 R
3474 3662 1.444553 CTTGGTGACCTCGACGAGC 60.445 63.158 19.55 7.41 0.0 5.03 R
4655 4862 1.461127 GTTGTGTCCGAGCAAGATGAC 59.539 52.381 0.00 0.00 0.0 3.06 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
19 20 1.243902 GTGCGAAATTTGAGGGACCA 58.756 50.000 0.00 0.00 0.00 4.02
20 21 1.611491 GTGCGAAATTTGAGGGACCAA 59.389 47.619 0.00 0.00 0.00 3.67
21 22 2.035321 GTGCGAAATTTGAGGGACCAAA 59.965 45.455 0.00 0.00 39.93 3.28
22 23 2.695666 TGCGAAATTTGAGGGACCAAAA 59.304 40.909 0.00 0.00 39.20 2.44
23 24 3.243704 TGCGAAATTTGAGGGACCAAAAG 60.244 43.478 0.00 0.00 39.20 2.27
24 25 3.317150 CGAAATTTGAGGGACCAAAAGC 58.683 45.455 0.00 0.00 39.20 3.51
25 26 3.243704 CGAAATTTGAGGGACCAAAAGCA 60.244 43.478 0.00 0.00 39.20 3.91
26 27 3.751479 AATTTGAGGGACCAAAAGCAC 57.249 42.857 0.00 0.00 39.20 4.40
27 28 2.151502 TTTGAGGGACCAAAAGCACA 57.848 45.000 0.00 0.00 33.56 4.57
28 29 1.398692 TTGAGGGACCAAAAGCACAC 58.601 50.000 0.00 0.00 0.00 3.82
29 30 0.550914 TGAGGGACCAAAAGCACACT 59.449 50.000 0.00 0.00 0.00 3.55
30 31 1.771854 TGAGGGACCAAAAGCACACTA 59.228 47.619 0.00 0.00 0.00 2.74
31 32 2.224523 TGAGGGACCAAAAGCACACTAG 60.225 50.000 0.00 0.00 0.00 2.57
32 33 1.774856 AGGGACCAAAAGCACACTAGT 59.225 47.619 0.00 0.00 0.00 2.57
33 34 2.152016 GGGACCAAAAGCACACTAGTC 58.848 52.381 0.00 0.00 0.00 2.59
34 35 2.224548 GGGACCAAAAGCACACTAGTCT 60.225 50.000 0.00 0.00 0.00 3.24
35 36 3.067833 GGACCAAAAGCACACTAGTCTC 58.932 50.000 0.00 0.00 0.00 3.36
36 37 3.244249 GGACCAAAAGCACACTAGTCTCT 60.244 47.826 0.00 0.00 0.00 3.10
37 38 3.991121 GACCAAAAGCACACTAGTCTCTC 59.009 47.826 0.00 0.00 0.00 3.20
38 39 3.388024 ACCAAAAGCACACTAGTCTCTCA 59.612 43.478 0.00 0.00 0.00 3.27
39 40 4.040952 ACCAAAAGCACACTAGTCTCTCAT 59.959 41.667 0.00 0.00 0.00 2.90
40 41 4.999950 CCAAAAGCACACTAGTCTCTCATT 59.000 41.667 0.00 0.00 0.00 2.57
41 42 5.471456 CCAAAAGCACACTAGTCTCTCATTT 59.529 40.000 0.00 0.00 0.00 2.32
42 43 6.016777 CCAAAAGCACACTAGTCTCTCATTTT 60.017 38.462 0.00 0.00 0.00 1.82
43 44 7.420800 CAAAAGCACACTAGTCTCTCATTTTT 58.579 34.615 0.00 0.00 0.00 1.94
88 89 6.471233 TGAGTAAATCATCTCAGTACCTGG 57.529 41.667 0.00 0.00 36.04 4.45
92 93 2.940514 TCATCTCAGTACCTGGGGAA 57.059 50.000 0.00 0.00 31.91 3.97
95 96 2.715763 TCTCAGTACCTGGGGAAGTT 57.284 50.000 0.00 0.00 31.91 2.66
98 99 3.326880 TCTCAGTACCTGGGGAAGTTTTC 59.673 47.826 0.00 0.00 31.91 2.29
103 104 2.666317 ACCTGGGGAAGTTTTCACTTG 58.334 47.619 0.00 0.00 43.79 3.16
114 115 0.388659 TTTCACTTGCCATGGTGCAC 59.611 50.000 14.67 8.80 41.88 4.57
115 116 1.794151 TTCACTTGCCATGGTGCACG 61.794 55.000 14.67 6.25 41.88 5.34
116 117 2.203337 ACTTGCCATGGTGCACGT 60.203 55.556 14.67 6.93 41.88 4.49
117 118 1.072332 ACTTGCCATGGTGCACGTA 59.928 52.632 14.67 2.43 41.33 3.57
118 119 1.234615 ACTTGCCATGGTGCACGTAC 61.235 55.000 14.67 0.00 41.33 3.67
119 120 2.239341 CTTGCCATGGTGCACGTACG 62.239 60.000 15.01 15.01 41.88 3.67
134 135 1.390123 CGTACGTGCTTGGAATGACAG 59.610 52.381 7.22 0.00 0.00 3.51
144 149 4.636206 GCTTGGAATGACAGGGTAACTTAG 59.364 45.833 0.00 0.00 0.00 2.18
146 151 4.172807 TGGAATGACAGGGTAACTTAGGT 58.827 43.478 0.00 0.00 0.00 3.08
176 181 3.334078 CATGCTTTTCCGTCCATGC 57.666 52.632 0.00 0.00 0.00 4.06
177 182 0.527113 CATGCTTTTCCGTCCATGCA 59.473 50.000 0.00 0.00 34.88 3.96
178 183 1.135527 CATGCTTTTCCGTCCATGCAT 59.864 47.619 0.00 0.00 41.08 3.96
179 184 0.527113 TGCTTTTCCGTCCATGCATG 59.473 50.000 20.19 20.19 0.00 4.06
180 185 0.803380 GCTTTTCCGTCCATGCATGC 60.803 55.000 21.69 11.82 0.00 4.06
181 186 0.527113 CTTTTCCGTCCATGCATGCA 59.473 50.000 25.04 25.04 0.00 3.96
182 187 1.135527 CTTTTCCGTCCATGCATGCAT 59.864 47.619 27.46 27.46 37.08 3.96
190 195 1.067416 CATGCATGCATGTGAGGGC 59.933 57.895 40.30 12.66 46.20 5.19
196 201 2.031674 ATGCATGTGAGGGCGATCGA 62.032 55.000 21.57 0.00 0.00 3.59
266 293 1.076850 TCGTGATGCATGCCCCAAT 60.077 52.632 16.68 0.71 0.00 3.16
287 314 2.850404 CGTTCGCGTTGCTTGCTA 59.150 55.556 5.77 0.00 35.57 3.49
288 315 1.225475 CGTTCGCGTTGCTTGCTAG 60.225 57.895 5.77 0.00 35.57 3.42
365 396 2.969262 ACCCTAGCTTAGATCCTCAAGC 59.031 50.000 13.68 13.68 46.03 4.01
405 436 7.323049 TGATCACAAACTAGAGTAGACTAGC 57.677 40.000 0.00 0.00 42.29 3.42
406 437 7.113437 TGATCACAAACTAGAGTAGACTAGCT 58.887 38.462 0.00 0.00 42.29 3.32
407 438 8.265764 TGATCACAAACTAGAGTAGACTAGCTA 58.734 37.037 0.00 0.00 42.29 3.32
408 439 8.671384 ATCACAAACTAGAGTAGACTAGCTAG 57.329 38.462 19.44 19.44 42.29 3.42
409 440 7.622713 TCACAAACTAGAGTAGACTAGCTAGT 58.377 38.462 26.35 26.35 43.82 2.57
420 451 4.957684 GACTAGCTAGTCCTCTCTCTCT 57.042 50.000 34.56 7.17 45.33 3.10
421 452 4.884247 GACTAGCTAGTCCTCTCTCTCTC 58.116 52.174 34.56 12.66 45.33 3.20
422 453 4.557705 ACTAGCTAGTCCTCTCTCTCTCT 58.442 47.826 20.95 0.00 0.00 3.10
423 454 5.712752 ACTAGCTAGTCCTCTCTCTCTCTA 58.287 45.833 20.95 0.00 0.00 2.43
424 455 6.323737 ACTAGCTAGTCCTCTCTCTCTCTAT 58.676 44.000 20.95 0.00 0.00 1.98
425 456 5.489792 AGCTAGTCCTCTCTCTCTCTATG 57.510 47.826 0.00 0.00 0.00 2.23
427 458 4.997395 GCTAGTCCTCTCTCTCTCTATGTG 59.003 50.000 0.00 0.00 0.00 3.21
429 460 2.884639 GTCCTCTCTCTCTCTATGTGGC 59.115 54.545 0.00 0.00 0.00 5.01
430 461 2.158534 TCCTCTCTCTCTCTATGTGGCC 60.159 54.545 0.00 0.00 0.00 5.36
431 462 1.879380 CTCTCTCTCTCTATGTGGCCG 59.121 57.143 0.00 0.00 0.00 6.13
433 464 1.606668 CTCTCTCTCTATGTGGCCGAC 59.393 57.143 0.00 0.00 0.00 4.79
434 465 0.671251 CTCTCTCTATGTGGCCGACC 59.329 60.000 0.00 0.00 0.00 4.79
435 466 0.259065 TCTCTCTATGTGGCCGACCT 59.741 55.000 0.00 0.00 36.63 3.85
437 468 0.033503 TCTCTATGTGGCCGACCTGA 60.034 55.000 0.00 0.00 36.63 3.86
438 469 0.824109 CTCTATGTGGCCGACCTGAA 59.176 55.000 0.00 0.00 36.63 3.02
439 470 0.535335 TCTATGTGGCCGACCTGAAC 59.465 55.000 0.00 0.00 36.63 3.18
440 471 0.537188 CTATGTGGCCGACCTGAACT 59.463 55.000 0.00 0.00 36.63 3.01
442 473 2.432628 GTGGCCGACCTGAACTCG 60.433 66.667 0.00 0.00 36.63 4.18
444 475 1.982395 TGGCCGACCTGAACTCGAT 60.982 57.895 0.00 0.00 36.63 3.59
445 476 1.227002 GGCCGACCTGAACTCGATC 60.227 63.158 0.00 0.00 32.65 3.69
446 477 1.586564 GCCGACCTGAACTCGATCG 60.587 63.158 9.36 9.36 32.65 3.69
447 478 1.801332 CCGACCTGAACTCGATCGT 59.199 57.895 15.94 0.00 32.65 3.73
448 479 0.523546 CCGACCTGAACTCGATCGTG 60.524 60.000 15.94 15.53 32.65 4.35
450 481 1.395954 CGACCTGAACTCGATCGTGTA 59.604 52.381 21.77 7.80 32.65 2.90
451 482 2.031807 CGACCTGAACTCGATCGTGTAT 59.968 50.000 21.77 12.60 32.65 2.29
452 483 3.619729 GACCTGAACTCGATCGTGTATC 58.380 50.000 21.77 19.25 0.00 2.24
453 484 3.280295 ACCTGAACTCGATCGTGTATCT 58.720 45.455 21.77 7.89 31.87 1.98
454 485 3.695060 ACCTGAACTCGATCGTGTATCTT 59.305 43.478 21.77 7.53 31.87 2.40
455 486 4.880120 ACCTGAACTCGATCGTGTATCTTA 59.120 41.667 21.77 4.35 31.87 2.10
456 487 5.206299 CCTGAACTCGATCGTGTATCTTAC 58.794 45.833 21.77 10.50 31.87 2.34
457 488 5.165911 TGAACTCGATCGTGTATCTTACC 57.834 43.478 21.77 7.36 31.87 2.85
464 495 5.105635 TCGATCGTGTATCTTACCACCTTTT 60.106 40.000 15.94 0.00 31.87 2.27
473 504 5.093849 TCTTACCACCTTTTATCCTTCCG 57.906 43.478 0.00 0.00 0.00 4.30
495 526 4.681483 CGATCTTTGTTTCTTCCTTTTGCC 59.319 41.667 0.00 0.00 0.00 4.52
499 530 5.874261 TCTTTGTTTCTTCCTTTTGCCTTTG 59.126 36.000 0.00 0.00 0.00 2.77
512 563 2.997485 GCCTTTGGCTTCAGTAACTG 57.003 50.000 0.73 0.00 46.69 3.16
513 564 1.068264 GCCTTTGGCTTCAGTAACTGC 60.068 52.381 0.73 0.00 46.69 4.40
514 565 2.508526 CCTTTGGCTTCAGTAACTGCT 58.491 47.619 0.00 0.00 0.00 4.24
515 566 2.227388 CCTTTGGCTTCAGTAACTGCTG 59.773 50.000 0.00 0.00 37.81 4.41
516 567 1.238439 TTGGCTTCAGTAACTGCTGC 58.762 50.000 0.00 0.00 36.49 5.25
517 568 0.397941 TGGCTTCAGTAACTGCTGCT 59.602 50.000 0.00 0.00 36.49 4.24
518 569 0.801251 GGCTTCAGTAACTGCTGCTG 59.199 55.000 4.89 4.89 39.01 4.41
519 570 1.609061 GGCTTCAGTAACTGCTGCTGA 60.609 52.381 13.69 3.71 44.14 4.26
520 571 2.354259 GCTTCAGTAACTGCTGCTGAT 58.646 47.619 13.69 3.98 45.02 2.90
521 572 2.746362 GCTTCAGTAACTGCTGCTGATT 59.254 45.455 13.69 6.57 45.02 2.57
522 573 3.181512 GCTTCAGTAACTGCTGCTGATTC 60.182 47.826 13.69 0.00 45.02 2.52
523 574 3.969287 TCAGTAACTGCTGCTGATTCT 57.031 42.857 13.69 1.98 41.35 2.40
524 575 3.593096 TCAGTAACTGCTGCTGATTCTG 58.407 45.455 13.69 13.81 41.35 3.02
525 576 2.095532 CAGTAACTGCTGCTGATTCTGC 59.904 50.000 13.69 8.46 40.00 4.26
526 577 2.027377 AGTAACTGCTGCTGATTCTGCT 60.027 45.455 13.69 1.50 32.95 4.24
527 578 1.451067 AACTGCTGCTGATTCTGCTC 58.549 50.000 13.69 8.63 32.95 4.26
528 579 0.392729 ACTGCTGCTGATTCTGCTCC 60.393 55.000 13.69 7.73 32.95 4.70
529 580 0.392595 CTGCTGCTGATTCTGCTCCA 60.393 55.000 15.38 11.14 32.95 3.86
530 581 0.392595 TGCTGCTGATTCTGCTCCAG 60.393 55.000 15.38 6.96 32.95 3.86
556 607 2.514205 ACACTGCTGTTTTGGCATTC 57.486 45.000 0.00 0.00 39.07 2.67
558 609 2.223876 ACACTGCTGTTTTGGCATTCTG 60.224 45.455 0.00 0.00 39.07 3.02
560 611 2.694628 ACTGCTGTTTTGGCATTCTGAA 59.305 40.909 0.00 0.00 39.07 3.02
561 612 3.132646 ACTGCTGTTTTGGCATTCTGAAA 59.867 39.130 0.00 0.00 39.07 2.69
563 614 4.511527 TGCTGTTTTGGCATTCTGAAAAA 58.488 34.783 0.00 0.00 34.56 1.94
568 619 6.586344 TGTTTTGGCATTCTGAAAAATACCA 58.414 32.000 0.00 0.00 31.53 3.25
569 620 6.705381 TGTTTTGGCATTCTGAAAAATACCAG 59.295 34.615 0.00 0.00 34.34 4.00
629 682 1.078848 AGCTAGCGTTCTTGCTGGG 60.079 57.895 9.55 0.00 46.76 4.45
630 683 2.109126 GCTAGCGTTCTTGCTGGGG 61.109 63.158 0.00 0.00 46.70 4.96
632 685 0.036388 CTAGCGTTCTTGCTGGGGAA 60.036 55.000 0.00 0.00 46.70 3.97
634 687 0.251341 AGCGTTCTTGCTGGGGAATT 60.251 50.000 0.00 0.00 45.28 2.17
637 690 1.260544 GTTCTTGCTGGGGAATTGCT 58.739 50.000 0.00 0.00 0.00 3.91
638 691 1.203287 GTTCTTGCTGGGGAATTGCTC 59.797 52.381 0.00 0.00 0.00 4.26
639 692 0.700564 TCTTGCTGGGGAATTGCTCT 59.299 50.000 0.00 0.00 0.00 4.09
640 693 0.815734 CTTGCTGGGGAATTGCTCTG 59.184 55.000 0.00 0.00 0.00 3.35
641 694 1.252904 TTGCTGGGGAATTGCTCTGC 61.253 55.000 19.69 19.69 0.00 4.26
658 713 4.274459 GCTCTGCATCCAAGGTAATTAGTG 59.726 45.833 0.00 0.00 0.00 2.74
667 737 4.536765 CAAGGTAATTAGTGCCCATCCTT 58.463 43.478 0.00 0.00 34.89 3.36
670 740 6.530601 AGGTAATTAGTGCCCATCCTTAAT 57.469 37.500 0.00 0.00 30.73 1.40
671 741 6.922540 AGGTAATTAGTGCCCATCCTTAATT 58.077 36.000 0.00 0.00 30.73 1.40
675 748 6.715347 ATTAGTGCCCATCCTTAATTTGTC 57.285 37.500 0.00 0.00 0.00 3.18
687 760 5.300792 TCCTTAATTTGTCGCCTGTTCTTTT 59.699 36.000 0.00 0.00 0.00 2.27
715 788 7.711772 TCTTGGAGAAAACGTAAAACATACAGA 59.288 33.333 0.00 0.00 0.00 3.41
716 789 7.789273 TGGAGAAAACGTAAAACATACAGAA 57.211 32.000 0.00 0.00 0.00 3.02
742 841 9.896645 AGTAGTAGTACTGTAGTATGTTGCTTA 57.103 33.333 13.29 0.00 38.14 3.09
774 874 1.205064 CCGTGTTCGCTTTGCTGAG 59.795 57.895 0.00 0.00 35.54 3.35
788 888 0.597118 GCTGAGCTCCTACTGCATCG 60.597 60.000 12.15 0.00 0.00 3.84
789 889 0.743688 CTGAGCTCCTACTGCATCGT 59.256 55.000 12.15 0.00 0.00 3.73
795 897 4.770795 AGCTCCTACTGCATCGTTTAAAT 58.229 39.130 0.00 0.00 0.00 1.40
803 905 6.500684 ACTGCATCGTTTAAATTCAGATGT 57.499 33.333 18.32 3.60 40.37 3.06
806 908 8.511321 ACTGCATCGTTTAAATTCAGATGTTAA 58.489 29.630 18.32 9.95 40.37 2.01
812 914 7.967854 TCGTTTAAATTCAGATGTTAATGCTGG 59.032 33.333 0.00 0.00 0.00 4.85
816 918 6.630444 AATTCAGATGTTAATGCTGGCTAG 57.370 37.500 0.00 0.00 0.00 3.42
855 963 0.798776 ACGTAGCTTGCATGCTGTTC 59.201 50.000 31.20 20.76 43.87 3.18
874 982 4.745125 TGTTCAAAGTAGCAGAGACTTTCG 59.255 41.667 0.00 0.00 43.59 3.46
921 1029 2.027377 AGTCAGCAGCATAAGTGAAGCT 60.027 45.455 0.00 0.00 39.63 3.74
922 1030 3.196469 AGTCAGCAGCATAAGTGAAGCTA 59.804 43.478 0.00 0.00 36.73 3.32
923 1031 3.308323 GTCAGCAGCATAAGTGAAGCTAC 59.692 47.826 0.00 0.00 36.73 3.58
924 1032 3.196469 TCAGCAGCATAAGTGAAGCTACT 59.804 43.478 0.00 0.00 36.73 2.57
925 1033 4.402474 TCAGCAGCATAAGTGAAGCTACTA 59.598 41.667 0.00 0.00 36.73 1.82
926 1034 4.744137 CAGCAGCATAAGTGAAGCTACTAG 59.256 45.833 0.00 0.00 36.73 2.57
927 1035 4.404073 AGCAGCATAAGTGAAGCTACTAGT 59.596 41.667 0.00 0.00 36.73 2.57
928 1036 4.742659 GCAGCATAAGTGAAGCTACTAGTC 59.257 45.833 0.00 0.00 36.73 2.59
929 1037 5.679894 GCAGCATAAGTGAAGCTACTAGTCA 60.680 44.000 0.00 0.00 36.73 3.41
930 1038 5.976534 CAGCATAAGTGAAGCTACTAGTCAG 59.023 44.000 0.00 0.00 36.73 3.51
931 1039 4.742659 GCATAAGTGAAGCTACTAGTCAGC 59.257 45.833 0.00 7.42 39.41 4.26
951 1059 2.616842 GCCAGTAGCAGAGTAGTCTCTC 59.383 54.545 0.00 0.00 46.84 3.20
952 1060 3.684413 GCCAGTAGCAGAGTAGTCTCTCT 60.684 52.174 0.00 0.90 46.84 3.10
954 1062 4.383661 CCAGTAGCAGAGTAGTCTCTCTCA 60.384 50.000 0.00 0.00 46.84 3.27
955 1063 4.811024 CAGTAGCAGAGTAGTCTCTCTCAG 59.189 50.000 0.00 2.01 46.84 3.35
956 1064 4.469945 AGTAGCAGAGTAGTCTCTCTCAGT 59.530 45.833 0.00 0.00 46.84 3.41
957 1065 5.659525 AGTAGCAGAGTAGTCTCTCTCAGTA 59.340 44.000 0.00 0.00 46.84 2.74
962 1070 6.403049 CAGAGTAGTCTCTCTCAGTACTCAA 58.597 44.000 14.28 0.00 46.84 3.02
963 1071 7.047891 CAGAGTAGTCTCTCTCAGTACTCAAT 58.952 42.308 14.28 0.00 46.84 2.57
965 1073 8.421784 AGAGTAGTCTCTCTCAGTACTCAATAG 58.578 40.741 14.28 0.00 46.84 1.73
968 1076 7.624360 AGTCTCTCTCAGTACTCAATAGTTG 57.376 40.000 0.00 0.00 37.15 3.16
978 1086 9.997482 TCAGTACTCAATAGTTGTTTTTCAAAC 57.003 29.630 0.00 0.00 37.81 2.93
1392 1510 1.150567 GCGAGCTCTACGACGAGGTA 61.151 60.000 12.85 0.00 41.44 3.08
1530 1651 2.978010 AACCACTTCAAGCGGCGG 60.978 61.111 9.78 0.00 0.00 6.13
1740 1861 2.504244 GCCGAGTCCGACTTCGTG 60.504 66.667 1.71 4.21 38.22 4.35
1983 2104 1.216710 GCAGGTGGACTTCCTCTCG 59.783 63.158 0.00 0.00 36.82 4.04
1989 2110 0.681564 TGGACTTCCTCTCGAGCTCC 60.682 60.000 7.81 5.03 36.82 4.70
2211 2332 3.511540 TCATCTTCAAGGACATCGTGACT 59.488 43.478 0.00 0.00 33.76 3.41
2365 2486 1.371558 GAGAAGTTCCGCACCACCT 59.628 57.895 0.00 0.00 0.00 4.00
2397 2518 3.434319 TACCTCGTCGTGTCCGGC 61.434 66.667 0.00 0.00 34.69 6.13
2603 2724 2.705220 CGTCATCGTCGCCGTAGA 59.295 61.111 0.00 0.00 35.01 2.59
2616 2737 4.281946 GTAGACGACATCGACGGC 57.718 61.111 8.54 0.00 43.02 5.68
2631 2752 3.056328 GGCAAGGTCAAGGACGCC 61.056 66.667 0.00 0.00 31.73 5.68
2670 2791 2.261361 GCCATCAACCAAACCGCC 59.739 61.111 0.00 0.00 0.00 6.13
2761 2882 2.830321 CCAAGTAAGTACTCTCCCCGTT 59.170 50.000 0.00 0.00 34.99 4.44
2763 2884 4.492611 CAAGTAAGTACTCTCCCCGTTTC 58.507 47.826 0.00 0.00 34.99 2.78
2787 2912 9.817809 TTCTTTTTACTCGTCATATAAGATGCT 57.182 29.630 0.00 0.00 0.00 3.79
2860 2988 9.950680 ATGAACGCCTACAATATTTAATTGAAG 57.049 29.630 4.82 0.00 33.51 3.02
2862 2990 9.783256 GAACGCCTACAATATTTAATTGAAGTT 57.217 29.630 4.82 3.79 33.51 2.66
2957 3142 7.681939 TTTCCTGTAAACATGGTCATACTTC 57.318 36.000 0.00 0.00 0.00 3.01
2972 3157 8.298854 TGGTCATACTTCATGAAATTTGACTTG 58.701 33.333 27.60 10.82 45.28 3.16
3210 3398 3.414700 GACAGCAAGGTGGACGCG 61.415 66.667 3.53 3.53 0.00 6.01
3432 3620 4.789075 CGCTACGACCCCACCGTG 62.789 72.222 0.00 0.00 40.76 4.94
3471 3659 0.248661 CCATCTCACTCTACACGCCG 60.249 60.000 0.00 0.00 0.00 6.46
3474 3662 4.111016 TCACTCTACACGCCGCGG 62.111 66.667 24.05 24.05 0.00 6.46
3498 3686 2.435059 GAGGTCACCAAGGAGCGC 60.435 66.667 0.00 0.00 40.14 5.92
3810 3998 2.034066 ACCAACCACATGGAGCCG 59.966 61.111 4.53 0.00 43.54 5.52
3813 4001 4.047125 AACCACATGGAGCCGGGG 62.047 66.667 2.18 0.00 38.94 5.73
3843 4031 1.283793 CGCCAAGGACAACAAGCTG 59.716 57.895 0.00 0.00 0.00 4.24
4110 4302 1.134250 GTTCCATGAGCTTCCCTCCTC 60.134 57.143 0.00 0.00 39.98 3.71
4148 4340 0.179094 TAAACTACGGGCTGCATCGG 60.179 55.000 16.44 4.98 0.00 4.18
4167 4359 1.467734 GGATTCGCATGCATCCTCATC 59.532 52.381 23.45 12.35 36.72 2.92
4189 4381 4.827284 TCAGACTCTCCAAATTTGTTTCCC 59.173 41.667 16.73 2.26 0.00 3.97
4220 4412 6.092122 TCGAATGTTTGTATCGATTCTTTGCT 59.908 34.615 1.71 0.00 40.34 3.91
4227 4419 9.214953 GTTTGTATCGATTCTTTGCTAATTCAG 57.785 33.333 1.71 0.00 0.00 3.02
4228 4420 8.492673 TTGTATCGATTCTTTGCTAATTCAGT 57.507 30.769 1.71 0.00 0.00 3.41
4229 4421 9.594478 TTGTATCGATTCTTTGCTAATTCAGTA 57.406 29.630 1.71 0.00 0.00 2.74
4230 4422 9.031360 TGTATCGATTCTTTGCTAATTCAGTAC 57.969 33.333 1.71 0.00 0.00 2.73
4231 4423 6.569228 TCGATTCTTTGCTAATTCAGTACG 57.431 37.500 0.00 0.00 0.00 3.67
4232 4424 5.005394 TCGATTCTTTGCTAATTCAGTACGC 59.995 40.000 0.00 0.00 0.00 4.42
4261 4453 2.814097 CGGACCCAGGACAAAAATGACT 60.814 50.000 0.00 0.00 0.00 3.41
4655 4862 3.604875 TTACTTAAACCAGAGGAGCGG 57.395 47.619 0.00 0.00 0.00 5.52
4755 4962 8.964420 TTTTGGATAAAATTTAGCAAGACTCG 57.036 30.769 3.35 0.00 31.13 4.18
4804 5014 6.855763 ATAATTCATTTGGGCTCAAAGTCA 57.144 33.333 18.23 3.63 44.87 3.41
4997 5211 6.479884 ACTCATCAATGCTTCTCCTTTTACT 58.520 36.000 0.00 0.00 0.00 2.24
5008 5222 8.641541 TGCTTCTCCTTTTACTTTGATCAATTT 58.358 29.630 9.40 1.73 0.00 1.82
5073 5292 7.961326 ATTCCTTGTATTATTGGCAGAACTT 57.039 32.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.243902 TGGTCCCTCAAATTTCGCAC 58.756 50.000 0.00 0.00 0.00 5.34
1 2 1.988293 TTGGTCCCTCAAATTTCGCA 58.012 45.000 0.00 0.00 0.00 5.10
2 3 3.317150 CTTTTGGTCCCTCAAATTTCGC 58.683 45.455 0.00 0.00 36.63 4.70
3 4 3.243704 TGCTTTTGGTCCCTCAAATTTCG 60.244 43.478 0.00 0.00 36.63 3.46
4 5 4.058124 GTGCTTTTGGTCCCTCAAATTTC 58.942 43.478 0.00 0.00 36.63 2.17
5 6 3.454082 TGTGCTTTTGGTCCCTCAAATTT 59.546 39.130 0.00 0.00 36.63 1.82
6 7 3.037549 TGTGCTTTTGGTCCCTCAAATT 58.962 40.909 0.00 0.00 36.63 1.82
7 8 2.365293 GTGTGCTTTTGGTCCCTCAAAT 59.635 45.455 0.00 0.00 36.63 2.32
8 9 1.754226 GTGTGCTTTTGGTCCCTCAAA 59.246 47.619 0.00 0.00 35.15 2.69
10 11 0.550914 AGTGTGCTTTTGGTCCCTCA 59.449 50.000 0.00 0.00 0.00 3.86
11 12 2.224548 ACTAGTGTGCTTTTGGTCCCTC 60.225 50.000 0.00 0.00 0.00 4.30
12 13 1.774856 ACTAGTGTGCTTTTGGTCCCT 59.225 47.619 0.00 0.00 0.00 4.20
13 14 2.152016 GACTAGTGTGCTTTTGGTCCC 58.848 52.381 0.00 0.00 0.00 4.46
14 15 3.067833 GAGACTAGTGTGCTTTTGGTCC 58.932 50.000 0.00 0.00 0.00 4.46
15 16 3.991121 GAGAGACTAGTGTGCTTTTGGTC 59.009 47.826 0.00 0.00 0.00 4.02
16 17 3.388024 TGAGAGACTAGTGTGCTTTTGGT 59.612 43.478 0.00 0.00 0.00 3.67
17 18 3.995199 TGAGAGACTAGTGTGCTTTTGG 58.005 45.455 0.00 0.00 0.00 3.28
18 19 6.551385 AAATGAGAGACTAGTGTGCTTTTG 57.449 37.500 0.00 0.00 0.00 2.44
19 20 7.573968 AAAAATGAGAGACTAGTGTGCTTTT 57.426 32.000 0.00 0.00 0.00 2.27
80 81 3.053826 AGTGAAAACTTCCCCAGGTACT 58.946 45.455 0.00 0.00 43.88 2.73
81 82 3.503800 AGTGAAAACTTCCCCAGGTAC 57.496 47.619 0.00 0.00 0.00 3.34
85 86 1.341209 GGCAAGTGAAAACTTCCCCAG 59.659 52.381 0.00 0.00 0.00 4.45
88 89 2.289010 CCATGGCAAGTGAAAACTTCCC 60.289 50.000 0.00 0.00 0.00 3.97
92 93 1.069049 GCACCATGGCAAGTGAAAACT 59.931 47.619 21.19 0.00 36.01 2.66
95 96 0.388659 GTGCACCATGGCAAGTGAAA 59.611 50.000 21.19 8.44 46.93 2.69
98 99 2.256158 CGTGCACCATGGCAAGTG 59.744 61.111 13.04 14.70 46.93 3.16
103 104 2.740826 ACGTACGTGCACCATGGC 60.741 61.111 22.14 0.00 0.00 4.40
114 115 1.390123 CTGTCATTCCAAGCACGTACG 59.610 52.381 15.01 15.01 0.00 3.67
115 116 1.732259 CCTGTCATTCCAAGCACGTAC 59.268 52.381 0.00 0.00 0.00 3.67
116 117 1.338674 CCCTGTCATTCCAAGCACGTA 60.339 52.381 0.00 0.00 0.00 3.57
117 118 0.606401 CCCTGTCATTCCAAGCACGT 60.606 55.000 0.00 0.00 0.00 4.49
118 119 0.606401 ACCCTGTCATTCCAAGCACG 60.606 55.000 0.00 0.00 0.00 5.34
119 120 2.488153 GTTACCCTGTCATTCCAAGCAC 59.512 50.000 0.00 0.00 0.00 4.40
134 135 3.815809 TGCATGCATACCTAAGTTACCC 58.184 45.455 18.46 0.00 0.00 3.69
161 166 0.803380 GCATGCATGGACGGAAAAGC 60.803 55.000 27.34 5.70 0.00 3.51
176 181 1.838568 CGATCGCCCTCACATGCATG 61.839 60.000 25.09 25.09 0.00 4.06
177 182 1.596203 CGATCGCCCTCACATGCAT 60.596 57.895 0.26 0.00 0.00 3.96
178 183 2.031674 ATCGATCGCCCTCACATGCA 62.032 55.000 11.09 0.00 0.00 3.96
179 184 1.287730 GATCGATCGCCCTCACATGC 61.288 60.000 11.09 0.00 0.00 4.06
180 185 1.005804 CGATCGATCGCCCTCACATG 61.006 60.000 32.34 5.11 43.84 3.21
181 186 1.287191 CGATCGATCGCCCTCACAT 59.713 57.895 32.34 0.00 43.84 3.21
182 187 2.721859 CGATCGATCGCCCTCACA 59.278 61.111 32.34 0.00 43.84 3.58
228 247 0.716108 GGATGAGTGTGACGAAAGCG 59.284 55.000 0.00 0.00 44.79 4.68
284 311 2.356793 ATGCGCGGATCAGCTAGC 60.357 61.111 15.92 6.62 34.40 3.42
287 314 3.218294 ATCGATGCGCGGATCAGCT 62.218 57.895 34.64 18.61 41.33 4.24
288 315 2.724708 GATCGATGCGCGGATCAGC 61.725 63.158 34.64 22.38 41.33 4.26
340 368 2.630580 GAGGATCTAAGCTAGGGTGTGG 59.369 54.545 0.00 0.00 0.00 4.17
345 375 2.301583 GGCTTGAGGATCTAAGCTAGGG 59.698 54.545 20.81 0.00 43.72 3.53
365 396 2.321263 ATCATGCTCTGCGTGGAGGG 62.321 60.000 11.20 0.00 44.68 4.30
405 436 5.551233 CCACATAGAGAGAGAGAGGACTAG 58.449 50.000 0.00 0.00 0.00 2.57
406 437 4.202419 GCCACATAGAGAGAGAGAGGACTA 60.202 50.000 0.00 0.00 0.00 2.59
407 438 3.435026 GCCACATAGAGAGAGAGAGGACT 60.435 52.174 0.00 0.00 0.00 3.85
408 439 2.884639 GCCACATAGAGAGAGAGAGGAC 59.115 54.545 0.00 0.00 0.00 3.85
409 440 2.158534 GGCCACATAGAGAGAGAGAGGA 60.159 54.545 0.00 0.00 0.00 3.71
410 441 2.238521 GGCCACATAGAGAGAGAGAGG 58.761 57.143 0.00 0.00 0.00 3.69
413 444 1.606668 GTCGGCCACATAGAGAGAGAG 59.393 57.143 2.24 0.00 0.00 3.20
414 445 1.681538 GTCGGCCACATAGAGAGAGA 58.318 55.000 2.24 0.00 0.00 3.10
416 447 0.259065 AGGTCGGCCACATAGAGAGA 59.741 55.000 9.71 0.00 37.19 3.10
417 448 0.387202 CAGGTCGGCCACATAGAGAG 59.613 60.000 9.71 0.00 37.19 3.20
418 449 0.033503 TCAGGTCGGCCACATAGAGA 60.034 55.000 9.71 0.00 37.19 3.10
419 450 0.824109 TTCAGGTCGGCCACATAGAG 59.176 55.000 9.71 0.00 37.19 2.43
420 451 0.535335 GTTCAGGTCGGCCACATAGA 59.465 55.000 9.71 0.00 37.19 1.98
421 452 0.537188 AGTTCAGGTCGGCCACATAG 59.463 55.000 9.71 0.00 37.19 2.23
422 453 0.535335 GAGTTCAGGTCGGCCACATA 59.465 55.000 9.71 0.00 37.19 2.29
423 454 1.296715 GAGTTCAGGTCGGCCACAT 59.703 57.895 9.71 0.00 37.19 3.21
424 455 2.741092 GAGTTCAGGTCGGCCACA 59.259 61.111 9.71 0.00 37.19 4.17
425 456 2.227089 ATCGAGTTCAGGTCGGCCAC 62.227 60.000 9.71 0.00 38.02 5.01
427 458 1.227002 GATCGAGTTCAGGTCGGCC 60.227 63.158 0.00 0.00 38.02 6.13
429 460 0.523546 CACGATCGAGTTCAGGTCGG 60.524 60.000 24.34 0.00 38.02 4.79
430 461 0.168348 ACACGATCGAGTTCAGGTCG 59.832 55.000 24.34 1.08 38.84 4.79
431 462 3.312973 AGATACACGATCGAGTTCAGGTC 59.687 47.826 24.34 12.85 39.80 3.85
433 464 3.972950 AGATACACGATCGAGTTCAGG 57.027 47.619 24.34 4.40 39.80 3.86
434 465 5.206299 GGTAAGATACACGATCGAGTTCAG 58.794 45.833 24.34 6.51 39.80 3.02
435 466 4.637091 TGGTAAGATACACGATCGAGTTCA 59.363 41.667 24.34 6.35 39.80 3.18
437 468 4.201990 GGTGGTAAGATACACGATCGAGTT 60.202 45.833 24.34 10.79 39.80 3.01
438 469 3.314635 GGTGGTAAGATACACGATCGAGT 59.685 47.826 24.34 22.76 39.80 4.18
439 470 3.564644 AGGTGGTAAGATACACGATCGAG 59.435 47.826 24.34 17.42 39.80 4.04
440 471 3.548770 AGGTGGTAAGATACACGATCGA 58.451 45.455 24.34 0.00 39.80 3.59
442 473 7.384387 GGATAAAAGGTGGTAAGATACACGATC 59.616 40.741 0.00 0.00 38.46 3.69
444 475 6.381994 AGGATAAAAGGTGGTAAGATACACGA 59.618 38.462 0.00 0.00 38.46 4.35
445 476 6.579865 AGGATAAAAGGTGGTAAGATACACG 58.420 40.000 0.00 0.00 38.46 4.49
446 477 7.498239 GGAAGGATAAAAGGTGGTAAGATACAC 59.502 40.741 0.00 0.00 36.89 2.90
447 478 7.571025 GGAAGGATAAAAGGTGGTAAGATACA 58.429 38.462 0.00 0.00 0.00 2.29
448 479 6.704937 CGGAAGGATAAAAGGTGGTAAGATAC 59.295 42.308 0.00 0.00 0.00 2.24
450 481 5.427481 TCGGAAGGATAAAAGGTGGTAAGAT 59.573 40.000 0.00 0.00 0.00 2.40
451 482 4.778958 TCGGAAGGATAAAAGGTGGTAAGA 59.221 41.667 0.00 0.00 0.00 2.10
452 483 5.093849 TCGGAAGGATAAAAGGTGGTAAG 57.906 43.478 0.00 0.00 0.00 2.34
453 484 5.427481 AGATCGGAAGGATAAAAGGTGGTAA 59.573 40.000 0.00 0.00 34.82 2.85
454 485 4.966805 AGATCGGAAGGATAAAAGGTGGTA 59.033 41.667 0.00 0.00 34.82 3.25
455 486 3.780850 AGATCGGAAGGATAAAAGGTGGT 59.219 43.478 0.00 0.00 34.82 4.16
456 487 4.423625 AGATCGGAAGGATAAAAGGTGG 57.576 45.455 0.00 0.00 34.82 4.61
457 488 5.648092 ACAAAGATCGGAAGGATAAAAGGTG 59.352 40.000 0.00 0.00 34.82 4.00
464 495 6.070194 AGGAAGAAACAAAGATCGGAAGGATA 60.070 38.462 0.00 0.00 34.82 2.59
473 504 5.847304 AGGCAAAAGGAAGAAACAAAGATC 58.153 37.500 0.00 0.00 0.00 2.75
495 526 2.351157 GCAGCAGTTACTGAAGCCAAAG 60.351 50.000 17.40 0.00 40.25 2.77
499 530 0.801251 CAGCAGCAGTTACTGAAGCC 59.199 55.000 17.40 0.00 40.25 4.35
511 562 0.392595 CTGGAGCAGAATCAGCAGCA 60.393 55.000 0.00 0.00 32.44 4.41
512 563 2.395651 CTGGAGCAGAATCAGCAGC 58.604 57.895 0.00 0.00 32.44 5.25
524 575 0.595825 GCAGTGTTGTTTGCTGGAGC 60.596 55.000 0.00 0.00 42.50 4.70
525 576 3.557207 GCAGTGTTGTTTGCTGGAG 57.443 52.632 0.00 0.00 37.35 3.86
530 581 2.094099 CCAAAACAGCAGTGTTGTTTGC 59.906 45.455 30.81 0.00 46.68 3.68
531 582 2.094099 GCCAAAACAGCAGTGTTGTTTG 59.906 45.455 30.81 23.99 46.68 2.93
532 583 2.289320 TGCCAAAACAGCAGTGTTGTTT 60.289 40.909 26.60 26.60 46.68 2.83
533 584 1.274728 TGCCAAAACAGCAGTGTTGTT 59.725 42.857 18.47 18.47 46.68 2.83
534 585 0.894141 TGCCAAAACAGCAGTGTTGT 59.106 45.000 6.82 6.82 46.68 3.32
535 586 2.228138 ATGCCAAAACAGCAGTGTTG 57.772 45.000 5.30 5.30 46.68 3.33
536 587 5.946553 TCAGAATGCCAAAACAGCAGTGTT 61.947 41.667 0.00 0.00 44.90 3.32
537 588 2.034124 AGAATGCCAAAACAGCAGTGT 58.966 42.857 0.00 0.00 44.90 3.55
538 589 2.034939 TCAGAATGCCAAAACAGCAGTG 59.965 45.455 0.00 0.00 44.90 3.66
547 598 6.418057 ACTGGTATTTTTCAGAATGCCAAA 57.582 33.333 8.40 0.00 46.51 3.28
558 609 9.556030 CGAAGGATAAAGAAACTGGTATTTTTC 57.444 33.333 0.00 0.00 32.76 2.29
560 611 7.362660 GGCGAAGGATAAAGAAACTGGTATTTT 60.363 37.037 0.00 0.00 0.00 1.82
561 612 6.095021 GGCGAAGGATAAAGAAACTGGTATTT 59.905 38.462 0.00 0.00 0.00 1.40
563 614 5.123936 GGCGAAGGATAAAGAAACTGGTAT 58.876 41.667 0.00 0.00 0.00 2.73
568 619 3.604875 TCGGCGAAGGATAAAGAAACT 57.395 42.857 7.35 0.00 0.00 2.66
569 620 3.483085 CGTTCGGCGAAGGATAAAGAAAC 60.483 47.826 31.79 12.49 44.77 2.78
578 629 0.179156 GACATACGTTCGGCGAAGGA 60.179 55.000 38.70 25.60 44.77 3.36
627 680 0.396139 TGGATGCAGAGCAATTCCCC 60.396 55.000 8.65 1.57 43.62 4.81
629 682 1.407979 CCTTGGATGCAGAGCAATTCC 59.592 52.381 5.00 5.00 43.62 3.01
630 683 2.097825 ACCTTGGATGCAGAGCAATTC 58.902 47.619 0.00 0.00 43.62 2.17
632 685 3.370840 TTACCTTGGATGCAGAGCAAT 57.629 42.857 0.00 0.00 43.62 3.56
634 687 3.370840 AATTACCTTGGATGCAGAGCA 57.629 42.857 0.00 0.00 44.86 4.26
637 690 4.199310 GCACTAATTACCTTGGATGCAGA 58.801 43.478 0.00 0.00 0.00 4.26
638 691 3.316308 GGCACTAATTACCTTGGATGCAG 59.684 47.826 0.00 0.00 33.48 4.41
639 692 3.287222 GGCACTAATTACCTTGGATGCA 58.713 45.455 0.00 0.00 33.48 3.96
640 693 2.623416 GGGCACTAATTACCTTGGATGC 59.377 50.000 0.00 0.00 0.00 3.91
641 694 3.897239 TGGGCACTAATTACCTTGGATG 58.103 45.455 0.00 0.00 0.00 3.51
658 713 1.067060 GGCGACAAATTAAGGATGGGC 59.933 52.381 0.00 0.00 0.00 5.36
687 760 8.675504 TGTATGTTTTACGTTTTCTCCAAGAAA 58.324 29.630 0.00 0.00 42.00 2.52
690 763 7.857569 TCTGTATGTTTTACGTTTTCTCCAAG 58.142 34.615 0.00 0.00 0.00 3.61
691 764 7.789273 TCTGTATGTTTTACGTTTTCTCCAA 57.211 32.000 0.00 0.00 0.00 3.53
692 765 7.496591 ACTTCTGTATGTTTTACGTTTTCTCCA 59.503 33.333 0.00 0.00 0.00 3.86
693 766 7.858583 ACTTCTGTATGTTTTACGTTTTCTCC 58.141 34.615 0.00 0.00 0.00 3.71
695 768 9.538508 ACTACTTCTGTATGTTTTACGTTTTCT 57.461 29.630 0.00 0.00 0.00 2.52
698 771 9.971922 ACTACTACTTCTGTATGTTTTACGTTT 57.028 29.630 0.00 0.00 0.00 3.60
715 788 8.804912 AGCAACATACTACAGTACTACTACTT 57.195 34.615 0.00 0.00 30.03 2.24
716 789 8.804912 AAGCAACATACTACAGTACTACTACT 57.195 34.615 0.00 0.00 33.01 2.57
726 799 8.598924 CAGACAAGAATAAGCAACATACTACAG 58.401 37.037 0.00 0.00 0.00 2.74
727 800 8.311109 TCAGACAAGAATAAGCAACATACTACA 58.689 33.333 0.00 0.00 0.00 2.74
728 801 8.703604 TCAGACAAGAATAAGCAACATACTAC 57.296 34.615 0.00 0.00 0.00 2.73
742 841 2.930826 ACACGGGTTCAGACAAGAAT 57.069 45.000 0.00 0.00 0.00 2.40
774 874 5.064707 TGAATTTAAACGATGCAGTAGGAGC 59.935 40.000 0.00 0.00 0.00 4.70
788 888 7.761249 AGCCAGCATTAACATCTGAATTTAAAC 59.239 33.333 0.00 0.00 0.00 2.01
789 889 7.839907 AGCCAGCATTAACATCTGAATTTAAA 58.160 30.769 0.00 0.00 0.00 1.52
795 897 5.102953 ACTAGCCAGCATTAACATCTGAA 57.897 39.130 0.00 0.00 0.00 3.02
816 918 4.152402 ACGTACTGTGATGAATTGCTTGAC 59.848 41.667 0.00 0.00 0.00 3.18
833 935 1.066858 ACAGCATGCAAGCTACGTACT 60.067 47.619 21.98 0.00 44.54 2.73
834 936 1.359848 ACAGCATGCAAGCTACGTAC 58.640 50.000 21.98 0.00 44.54 3.67
855 963 3.059884 TGCGAAAGTCTCTGCTACTTTG 58.940 45.455 5.98 1.34 44.94 2.77
898 1006 3.425892 GCTTCACTTATGCTGCTGACTTG 60.426 47.826 0.00 0.00 0.00 3.16
899 1007 2.746362 GCTTCACTTATGCTGCTGACTT 59.254 45.455 0.00 0.00 0.00 3.01
921 1029 3.054287 ACTCTGCTACTGGCTGACTAGTA 60.054 47.826 0.00 0.00 42.53 1.82
922 1030 2.291282 ACTCTGCTACTGGCTGACTAGT 60.291 50.000 0.00 0.00 42.53 2.57
923 1031 2.374184 ACTCTGCTACTGGCTGACTAG 58.626 52.381 0.00 0.00 42.53 2.57
924 1032 2.516227 ACTCTGCTACTGGCTGACTA 57.484 50.000 0.00 0.00 42.53 2.59
925 1033 2.291282 ACTACTCTGCTACTGGCTGACT 60.291 50.000 0.00 0.00 42.53 3.41
926 1034 2.096248 ACTACTCTGCTACTGGCTGAC 58.904 52.381 0.00 0.00 42.53 3.51
927 1035 2.025793 AGACTACTCTGCTACTGGCTGA 60.026 50.000 0.00 0.00 44.59 4.26
928 1036 2.357637 GAGACTACTCTGCTACTGGCTG 59.642 54.545 0.00 0.00 39.78 4.85
929 1037 2.650322 GAGACTACTCTGCTACTGGCT 58.350 52.381 0.00 0.00 39.78 4.75
941 1049 8.086143 ACTATTGAGTACTGAGAGAGACTACT 57.914 38.462 0.00 0.00 32.65 2.57
943 1051 8.322828 ACAACTATTGAGTACTGAGAGAGACTA 58.677 37.037 0.00 0.00 33.58 2.59
950 1058 9.607988 TTGAAAAACAACTATTGAGTACTGAGA 57.392 29.630 0.00 0.00 33.58 3.27
952 1060 9.997482 GTTTGAAAAACAACTATTGAGTACTGA 57.003 29.630 0.00 0.00 38.29 3.41
963 1071 9.112725 GGAACCTACTAGTTTGAAAAACAACTA 57.887 33.333 0.00 0.00 38.29 2.24
1239 1357 2.263852 CTCTGCTTCCAGCGCTGA 59.736 61.111 38.06 21.04 46.26 4.26
1302 1420 2.256764 CTCTCGTGCTCGCACACT 59.743 61.111 20.54 0.00 46.47 3.55
1392 1510 4.379243 CGGCGCTGGAAGGTGAGT 62.379 66.667 8.83 0.00 0.00 3.41
1629 1750 1.369448 GTAGCTCTCGACGATGCGG 60.369 63.158 14.40 0.00 0.00 5.69
1857 1978 1.674651 GAAGTCCTTGCCCCGGAAC 60.675 63.158 0.73 0.00 31.13 3.62
1983 2104 2.185608 GCGAGGAACCAGGAGCTC 59.814 66.667 4.71 4.71 0.00 4.09
1989 2110 3.649277 CTCCGTGGCGAGGAACCAG 62.649 68.421 2.44 0.00 38.04 4.00
2187 2308 2.600420 CACGATGTCCTTGAAGATGACG 59.400 50.000 0.00 0.00 0.00 4.35
2211 2332 4.662961 CACTGCTCGTCCCGCACA 62.663 66.667 0.00 0.00 33.19 4.57
2346 2467 1.070786 GGTGGTGCGGAACTTCTCA 59.929 57.895 0.00 0.00 0.00 3.27
2365 2486 3.766691 GTACGCCTTCCTGCCGGA 61.767 66.667 5.05 0.00 37.60 5.14
2601 2722 1.154016 CTTGCCGTCGATGTCGTCT 60.154 57.895 3.52 0.00 40.80 4.18
2603 2724 2.126071 CCTTGCCGTCGATGTCGT 60.126 61.111 3.52 0.00 40.80 4.34
2608 2729 1.079127 CCTTGACCTTGCCGTCGAT 60.079 57.895 0.00 0.00 35.40 3.59
2651 2772 2.622011 GCGGTTTGGTTGATGGCGA 61.622 57.895 0.00 0.00 0.00 5.54
2656 2777 1.674322 CGAGGGCGGTTTGGTTGAT 60.674 57.895 0.00 0.00 0.00 2.57
2670 2791 2.443016 CTGGGGAGGAGGACGAGG 60.443 72.222 0.00 0.00 0.00 4.63
2761 2882 9.817809 AGCATCTTATATGACGAGTAAAAAGAA 57.182 29.630 0.00 0.00 0.00 2.52
2785 2910 7.908193 TTTTACGAAGTTTGAATTCAGAAGC 57.092 32.000 8.41 0.00 37.78 3.86
2957 3142 9.472361 AAGATTTGTCTCAAGTCAAATTTCATG 57.528 29.630 13.75 0.00 41.40 3.07
2984 3169 6.831664 AAGAGGGAGGTTGATGTGTTATAT 57.168 37.500 0.00 0.00 0.00 0.86
2985 3170 6.443849 AGAAAGAGGGAGGTTGATGTGTTATA 59.556 38.462 0.00 0.00 0.00 0.98
3175 3363 2.040145 TGTCCATGTTGAAGCTGATGGA 59.960 45.455 0.00 0.00 41.69 3.41
3474 3662 1.444553 CTTGGTGACCTCGACGAGC 60.445 63.158 19.55 7.41 0.00 5.03
3843 4031 2.357034 TCGCCCTTGTCGTGCTTC 60.357 61.111 0.00 0.00 0.00 3.86
4110 4302 1.830279 ATGCTATGCAATGGGATCGG 58.170 50.000 0.00 0.00 43.62 4.18
4148 4340 2.148768 TGATGAGGATGCATGCGAATC 58.851 47.619 21.26 21.26 0.00 2.52
4167 4359 4.320494 CGGGAAACAAATTTGGAGAGTCTG 60.320 45.833 21.74 7.75 0.00 3.51
4189 4381 3.365520 TCGATACAAACATTCGACCAACG 59.634 43.478 0.00 0.00 37.01 4.10
4220 4412 0.179094 CCCCTGCGCGTACTGAATTA 60.179 55.000 8.43 0.00 0.00 1.40
4261 4453 1.216930 TGTGATAGAGATGGACCCCGA 59.783 52.381 0.00 0.00 0.00 5.14
4351 4544 7.912056 TCTCTGGTAAGCATATTCATATTGC 57.088 36.000 0.00 0.00 0.00 3.56
4621 4827 8.276252 TGGTTTAAGTAATATTTGTGAGCTCC 57.724 34.615 12.15 3.09 0.00 4.70
4655 4862 1.461127 GTTGTGTCCGAGCAAGATGAC 59.539 52.381 0.00 0.00 0.00 3.06
4755 4962 9.820229 TTTCGTGATTTCAACATAGTATTTGAC 57.180 29.630 7.05 0.00 31.42 3.18
4804 5014 1.824230 TGAACTGCTTGTTTGCTTGGT 59.176 42.857 0.00 0.00 39.30 3.67
5018 5237 3.779183 AGCTGGAGAAGAGATCAATTGGA 59.221 43.478 5.42 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.