Multiple sequence alignment - TraesCS6B01G162600

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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 TraesCS6B01G162600 chr6B 100.000 4758 0 0 1 4758 169107188 169111945 0.000000e+00 8787.0
1 TraesCS6B01G162600 chr6A 90.713 3435 171 53 687 4059 106798001 106801349 0.000000e+00 4440.0
2 TraesCS6B01G162600 chr6A 93.517 617 31 5 4088 4696 106801456 106802071 0.000000e+00 909.0
3 TraesCS6B01G162600 chr6A 97.500 40 1 0 4719 4758 106802187 106802226 8.540000e-08 69.4
4 TraesCS6B01G162600 chr6D 90.353 1586 101 13 987 2537 88774923 88776491 0.000000e+00 2034.0
5 TraesCS6B01G162600 chr6D 92.466 876 46 3 2550 3407 88776580 88777453 0.000000e+00 1234.0
6 TraesCS6B01G162600 chr6D 88.241 961 76 15 1087 2038 5762632 5761700 0.000000e+00 1114.0
7 TraesCS6B01G162600 chr6D 94.781 594 25 2 3471 4059 88777711 88778303 0.000000e+00 920.0
8 TraesCS6B01G162600 chr6D 90.794 630 25 9 4088 4696 88778410 88779027 0.000000e+00 811.0
9 TraesCS6B01G162600 chr6D 85.915 355 27 9 630 983 88774545 88774877 1.630000e-94 357.0
10 TraesCS6B01G162600 chr7D 82.876 1495 200 37 1000 2447 185131309 185132794 0.000000e+00 1291.0
11 TraesCS6B01G162600 chr7D 85.870 552 70 5 3245 3793 185134115 185134661 8.880000e-162 580.0
12 TraesCS6B01G162600 chr7A 82.277 1546 199 44 1000 2489 192663131 192664657 0.000000e+00 1267.0
13 TraesCS6B01G162600 chr7A 83.480 569 70 11 3245 3804 192665616 192666169 4.250000e-140 508.0
14 TraesCS6B01G162600 chr7A 77.907 172 25 9 2593 2752 192664841 192665011 1.410000e-15 95.3
15 TraesCS6B01G162600 chr7B 82.138 1534 215 37 1000 2489 327268215 327269733 0.000000e+00 1260.0
16 TraesCS6B01G162600 chr7B 85.790 563 72 5 3245 3804 327270685 327271242 1.470000e-164 590.0
17 TraesCS6B01G162600 chr7B 81.455 426 53 16 2596 2999 327269923 327270344 4.590000e-85 326.0
18 TraesCS6B01G162600 chr5D 81.942 515 90 2 5 516 281518432 281517918 2.630000e-117 433.0
19 TraesCS6B01G162600 chr5D 80.971 515 82 6 5 516 53901499 53902000 1.240000e-105 394.0
20 TraesCS6B01G162600 chr5D 94.595 37 1 1 4689 4725 474548796 474548831 6.650000e-04 56.5
21 TraesCS6B01G162600 chr2B 84.670 424 32 15 1084 1506 103894203 103894594 4.460000e-105 392.0
22 TraesCS6B01G162600 chr2B 84.196 367 25 15 1087 1452 755624908 755624574 4.590000e-85 326.0
23 TraesCS6B01G162600 chr3B 85.088 114 15 1 522 635 550497586 550497475 1.080000e-21 115.0


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 TraesCS6B01G162600 chr6B 169107188 169111945 4757 False 8787.000000 8787 100.000000 1 4758 1 chr6B.!!$F1 4757
1 TraesCS6B01G162600 chr6A 106798001 106802226 4225 False 1806.133333 4440 93.910000 687 4758 3 chr6A.!!$F1 4071
2 TraesCS6B01G162600 chr6D 5761700 5762632 932 True 1114.000000 1114 88.241000 1087 2038 1 chr6D.!!$R1 951
3 TraesCS6B01G162600 chr6D 88774545 88779027 4482 False 1071.200000 2034 90.861800 630 4696 5 chr6D.!!$F1 4066
4 TraesCS6B01G162600 chr7D 185131309 185134661 3352 False 935.500000 1291 84.373000 1000 3793 2 chr7D.!!$F1 2793
5 TraesCS6B01G162600 chr7A 192663131 192666169 3038 False 623.433333 1267 81.221333 1000 3804 3 chr7A.!!$F1 2804
6 TraesCS6B01G162600 chr7B 327268215 327271242 3027 False 725.333333 1260 83.127667 1000 3804 3 chr7B.!!$F1 2804
7 TraesCS6B01G162600 chr5D 281517918 281518432 514 True 433.000000 433 81.942000 5 516 1 chr5D.!!$R1 511
8 TraesCS6B01G162600 chr5D 53901499 53902000 501 False 394.000000 394 80.971000 5 516 1 chr5D.!!$F1 511

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
562 566 0.039165 GTTTGGCCAAAAGAGCGAGG 60.039 55.0 31.92 0.00 31.33 4.63 F
563 567 0.467290 TTTGGCCAAAAGAGCGAGGT 60.467 50.0 28.57 0.00 0.00 3.85 F
564 568 0.467290 TTGGCCAAAAGAGCGAGGTT 60.467 50.0 17.98 0.00 0.00 3.50 F
566 570 0.889186 GGCCAAAAGAGCGAGGTTGA 60.889 55.0 0.00 0.00 0.00 3.18 F
567 571 0.951558 GCCAAAAGAGCGAGGTTGAA 59.048 50.0 0.00 0.00 0.00 2.69 F
1049 1104 1.021390 CACTTCTCTCCGCCGCAATT 61.021 55.0 0.00 0.00 0.00 2.32 F
1774 1860 1.747325 ATGGGTGTTGGTGCTGCAAC 61.747 55.0 11.52 11.52 0.00 4.17 F
2859 3222 0.251634 CCTGTGAGGAGAAAGGAGGC 59.748 60.0 0.00 0.00 37.67 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1473 0.250038 AGCGAAAGAAGACAGCAGCA 60.250 50.000 0.00 0.00 0.00 4.41 R
1472 1549 0.690762 GCCGGCTTCTAATCCCCATA 59.309 55.000 22.15 0.00 0.00 2.74 R
1614 1698 0.954452 CTTTGACAGGGCCAGACAAC 59.046 55.000 12.80 0.00 0.00 3.32 R
1774 1860 1.004044 AGCCCCTGATTCAACACTCAG 59.996 52.381 0.00 0.00 38.88 3.35 R
2128 2250 1.098050 CTGCAGGATAACAAGCCCAC 58.902 55.000 5.57 0.00 0.00 4.61 R
2831 3194 0.900421 CTCCTCACAGGCACATGAGA 59.100 55.000 12.60 0.00 43.69 3.27 R
3219 3726 0.036765 GTGTGCCCACTATGTTCCGA 60.037 55.000 0.00 0.00 38.61 4.55 R
4685 5818 0.456482 TTGCTTCGCAAATGCATCCG 60.456 50.000 0.00 3.72 45.96 4.18 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
36 37 1.134699 CAAGGGCTCGTTGCTAGATCA 60.135 52.381 0.00 0.00 42.39 2.92
39 40 1.202580 GGGCTCGTTGCTAGATCACAT 60.203 52.381 0.00 0.00 42.39 3.21
41 42 2.286294 GGCTCGTTGCTAGATCACATTG 59.714 50.000 0.00 0.00 42.39 2.82
48 49 6.992123 TCGTTGCTAGATCACATTGGAATAAT 59.008 34.615 0.00 0.00 0.00 1.28
72 73 5.568392 AGATTTCAGACATCTTTTGAGCCT 58.432 37.500 0.00 0.00 0.00 4.58
75 76 7.667219 AGATTTCAGACATCTTTTGAGCCTTTA 59.333 33.333 0.00 0.00 0.00 1.85
86 87 4.736126 TTGAGCCTTTATGACAGATCGA 57.264 40.909 0.00 0.00 0.00 3.59
96 97 1.203928 GACAGATCGAGCATTCACCG 58.796 55.000 2.38 0.00 0.00 4.94
98 99 1.227380 AGATCGAGCATTCACCGCC 60.227 57.895 2.38 0.00 0.00 6.13
114 115 1.164411 CGCCAACTGGAATGTGCTTA 58.836 50.000 0.00 0.00 37.39 3.09
118 119 4.176271 GCCAACTGGAATGTGCTTATTTC 58.824 43.478 0.00 0.00 37.39 2.17
126 127 8.275040 ACTGGAATGTGCTTATTTCCTAGTATT 58.725 33.333 0.00 0.00 0.00 1.89
149 150 2.107950 TTCAAGGGCACAATACCTCG 57.892 50.000 0.00 0.00 35.64 4.63
150 151 0.981183 TCAAGGGCACAATACCTCGT 59.019 50.000 0.00 0.00 35.64 4.18
151 152 1.349688 TCAAGGGCACAATACCTCGTT 59.650 47.619 0.00 0.00 35.64 3.85
154 155 1.903860 AGGGCACAATACCTCGTTACA 59.096 47.619 0.00 0.00 28.88 2.41
158 159 3.061322 GCACAATACCTCGTTACACACA 58.939 45.455 0.00 0.00 0.00 3.72
162 163 4.059511 CAATACCTCGTTACACACACCAA 58.940 43.478 0.00 0.00 0.00 3.67
191 193 3.091545 TCTGAATTTTCATGGGACCTGC 58.908 45.455 0.00 0.00 36.46 4.85
203 205 0.538287 GGACCTGCAGCTTCCAAACT 60.538 55.000 21.93 0.00 0.00 2.66
239 241 1.200020 GGTTGCATGGCACTAGTTGAC 59.800 52.381 0.00 0.00 38.71 3.18
242 244 1.156736 GCATGGCACTAGTTGACGTT 58.843 50.000 0.00 0.00 34.92 3.99
248 250 5.648178 TGGCACTAGTTGACGTTAGATTA 57.352 39.130 0.00 0.00 34.92 1.75
252 254 5.041940 CACTAGTTGACGTTAGATTAGCCC 58.958 45.833 0.00 0.00 0.00 5.19
253 255 3.160777 AGTTGACGTTAGATTAGCCCG 57.839 47.619 0.00 0.00 0.00 6.13
264 266 3.305720 AGATTAGCCCGTGATTGTCCTA 58.694 45.455 0.00 0.00 0.00 2.94
272 274 4.202182 GCCCGTGATTGTCCTATGTACTTA 60.202 45.833 0.00 0.00 0.00 2.24
289 291 3.470709 ACTTATGCGTCCATTCCTCATG 58.529 45.455 0.00 0.00 32.85 3.07
301 303 4.525996 CATTCCTCATGGTATGTTGTCCA 58.474 43.478 0.00 0.00 36.67 4.02
311 313 5.136828 TGGTATGTTGTCCACACAGAAAAT 58.863 37.500 0.00 0.00 38.61 1.82
313 315 6.205853 TGGTATGTTGTCCACACAGAAAATAC 59.794 38.462 0.00 0.00 38.61 1.89
320 322 4.526650 GTCCACACAGAAAATACCCCATTT 59.473 41.667 0.00 0.00 38.54 2.32
324 326 4.531732 ACACAGAAAATACCCCATTTGCAT 59.468 37.500 0.00 0.00 36.93 3.96
328 330 6.171921 CAGAAAATACCCCATTTGCATTGAA 58.828 36.000 0.00 0.00 36.93 2.69
329 331 6.092533 CAGAAAATACCCCATTTGCATTGAAC 59.907 38.462 0.00 0.00 36.93 3.18
338 340 0.751452 TTGCATTGAACTGCCAAGCA 59.249 45.000 0.00 0.00 41.58 3.91
344 346 4.092383 GCATTGAACTGCCAAGCAATAAAG 59.908 41.667 0.00 0.00 38.41 1.85
347 349 3.058293 TGAACTGCCAAGCAATAAAGTCG 60.058 43.478 0.00 0.00 38.41 4.18
349 351 2.884639 ACTGCCAAGCAATAAAGTCGTT 59.115 40.909 0.00 0.00 38.41 3.85
350 352 3.236816 CTGCCAAGCAATAAAGTCGTTG 58.763 45.455 0.00 0.00 38.41 4.10
353 355 4.202060 TGCCAAGCAATAAAGTCGTTGAAA 60.202 37.500 0.00 0.00 34.76 2.69
359 361 4.475944 CAATAAAGTCGTTGAAAGCCTGG 58.524 43.478 0.00 0.00 0.00 4.45
368 370 4.217550 TCGTTGAAAGCCTGGAAATTAAGG 59.782 41.667 0.00 0.00 36.58 2.69
371 373 3.076785 TGAAAGCCTGGAAATTAAGGGGA 59.923 43.478 0.00 0.00 33.87 4.81
379 381 5.159273 TGGAAATTAAGGGGAATTTGCAC 57.841 39.130 10.54 0.00 46.07 4.57
391 393 3.602483 GAATTTGCACAATCCTTGCCAT 58.398 40.909 0.00 0.00 39.39 4.40
392 394 2.747396 TTTGCACAATCCTTGCCATC 57.253 45.000 0.00 0.00 39.39 3.51
393 395 1.630223 TTGCACAATCCTTGCCATCA 58.370 45.000 0.00 0.00 39.39 3.07
394 396 1.630223 TGCACAATCCTTGCCATCAA 58.370 45.000 0.00 0.00 39.39 2.57
397 399 2.673043 GCACAATCCTTGCCATCAACAG 60.673 50.000 0.00 0.00 33.58 3.16
398 400 2.094390 CACAATCCTTGCCATCAACAGG 60.094 50.000 0.00 0.00 0.00 4.00
401 403 0.482446 TCCTTGCCATCAACAGGGTT 59.518 50.000 0.00 0.00 35.82 4.11
402 404 1.707989 TCCTTGCCATCAACAGGGTTA 59.292 47.619 0.00 0.00 35.82 2.85
403 405 2.094675 CCTTGCCATCAACAGGGTTAG 58.905 52.381 0.00 0.00 30.00 2.34
406 408 3.071874 TGCCATCAACAGGGTTAGAAG 57.928 47.619 0.00 0.00 0.00 2.85
407 409 2.375174 TGCCATCAACAGGGTTAGAAGT 59.625 45.455 0.00 0.00 0.00 3.01
410 412 4.816925 GCCATCAACAGGGTTAGAAGTATC 59.183 45.833 0.00 0.00 0.00 2.24
411 413 5.629133 GCCATCAACAGGGTTAGAAGTATCA 60.629 44.000 0.00 0.00 0.00 2.15
423 427 7.363880 GGGTTAGAAGTATCACTGATCAGTTCA 60.364 40.741 25.84 15.49 40.20 3.18
443 447 1.757682 TCATCCCATTTGCCCGTAAC 58.242 50.000 0.00 0.00 0.00 2.50
444 448 1.004862 TCATCCCATTTGCCCGTAACA 59.995 47.619 0.00 0.00 0.00 2.41
450 454 2.643551 CATTTGCCCGTAACAGGATCT 58.356 47.619 0.00 0.00 0.00 2.75
462 466 8.582437 CCCGTAACAGGATCTATAAGTTCATAA 58.418 37.037 0.00 0.00 0.00 1.90
489 493 1.883926 GTTAGCAATGTGTTTCCCCGT 59.116 47.619 0.00 0.00 0.00 5.28
497 501 0.602905 GTGTTTCCCCGTGGAGTCAG 60.603 60.000 0.00 0.00 43.07 3.51
498 502 1.671379 GTTTCCCCGTGGAGTCAGC 60.671 63.158 0.00 0.00 43.07 4.26
507 511 1.517242 GTGGAGTCAGCACTTTCCTG 58.483 55.000 0.00 0.00 30.63 3.86
509 513 1.202687 TGGAGTCAGCACTTTCCTGTG 60.203 52.381 0.00 0.00 40.62 3.66
516 520 0.957888 GCACTTTCCTGTGAGGGCTC 60.958 60.000 0.00 0.00 39.21 4.70
517 521 0.671781 CACTTTCCTGTGAGGGCTCG 60.672 60.000 0.00 0.00 40.12 5.03
518 522 1.078848 CTTTCCTGTGAGGGCTCGG 60.079 63.158 0.00 0.00 35.59 4.63
519 523 2.527951 CTTTCCTGTGAGGGCTCGGG 62.528 65.000 0.00 0.00 35.59 5.14
522 526 2.363795 CTGTGAGGGCTCGGGGTA 60.364 66.667 0.00 0.00 0.00 3.69
523 527 1.762460 CTGTGAGGGCTCGGGGTAT 60.762 63.158 0.00 0.00 0.00 2.73
524 528 0.469331 CTGTGAGGGCTCGGGGTATA 60.469 60.000 0.00 0.00 0.00 1.47
525 529 0.190069 TGTGAGGGCTCGGGGTATAT 59.810 55.000 0.00 0.00 0.00 0.86
526 530 0.608640 GTGAGGGCTCGGGGTATATG 59.391 60.000 0.00 0.00 0.00 1.78
527 531 0.485543 TGAGGGCTCGGGGTATATGA 59.514 55.000 0.00 0.00 0.00 2.15
528 532 1.078823 TGAGGGCTCGGGGTATATGAT 59.921 52.381 0.00 0.00 0.00 2.45
529 533 1.757699 GAGGGCTCGGGGTATATGATC 59.242 57.143 0.00 0.00 0.00 2.92
530 534 1.078823 AGGGCTCGGGGTATATGATCA 59.921 52.381 0.00 0.00 0.00 2.92
531 535 2.119495 GGGCTCGGGGTATATGATCAT 58.881 52.381 13.81 13.81 0.00 2.45
532 536 2.505819 GGGCTCGGGGTATATGATCATT 59.494 50.000 14.65 4.68 0.00 2.57
533 537 3.432326 GGGCTCGGGGTATATGATCATTC 60.432 52.174 14.65 5.21 0.00 2.67
534 538 3.452627 GGCTCGGGGTATATGATCATTCT 59.547 47.826 14.65 4.65 0.00 2.40
535 539 4.442192 GGCTCGGGGTATATGATCATTCTC 60.442 50.000 14.65 5.15 0.00 2.87
536 540 4.442192 GCTCGGGGTATATGATCATTCTCC 60.442 50.000 14.65 12.77 0.00 3.71
537 541 4.683643 TCGGGGTATATGATCATTCTCCA 58.316 43.478 14.65 0.00 0.00 3.86
538 542 5.090845 TCGGGGTATATGATCATTCTCCAA 58.909 41.667 14.65 0.00 0.00 3.53
539 543 5.046591 TCGGGGTATATGATCATTCTCCAAC 60.047 44.000 14.65 9.23 0.00 3.77
540 544 5.279960 CGGGGTATATGATCATTCTCCAACA 60.280 44.000 14.65 0.00 0.00 3.33
541 545 6.577039 CGGGGTATATGATCATTCTCCAACAT 60.577 42.308 14.65 0.99 0.00 2.71
542 546 7.177878 GGGGTATATGATCATTCTCCAACATT 58.822 38.462 14.65 0.00 0.00 2.71
543 547 7.121759 GGGGTATATGATCATTCTCCAACATTG 59.878 40.741 14.65 0.00 0.00 2.82
544 548 7.667219 GGGTATATGATCATTCTCCAACATTGT 59.333 37.037 14.65 0.00 0.00 2.71
545 549 9.071276 GGTATATGATCATTCTCCAACATTGTT 57.929 33.333 14.65 0.00 0.00 2.83
548 552 6.028146 TGATCATTCTCCAACATTGTTTGG 57.972 37.500 0.00 5.61 46.64 3.28
549 553 4.255833 TCATTCTCCAACATTGTTTGGC 57.744 40.909 0.00 0.00 45.12 4.52
550 554 3.006752 TCATTCTCCAACATTGTTTGGCC 59.993 43.478 0.00 0.00 45.12 5.36
551 555 2.079170 TCTCCAACATTGTTTGGCCA 57.921 45.000 0.00 0.00 45.12 5.36
552 556 2.392662 TCTCCAACATTGTTTGGCCAA 58.607 42.857 16.05 16.05 45.12 4.52
553 557 2.768527 TCTCCAACATTGTTTGGCCAAA 59.231 40.909 27.13 27.13 45.12 3.28
554 558 3.198635 TCTCCAACATTGTTTGGCCAAAA 59.801 39.130 31.92 18.54 45.12 2.44
555 559 3.539604 TCCAACATTGTTTGGCCAAAAG 58.460 40.909 31.92 22.32 45.12 2.27
556 560 3.198635 TCCAACATTGTTTGGCCAAAAGA 59.801 39.130 31.92 22.51 45.12 2.52
557 561 3.560896 CCAACATTGTTTGGCCAAAAGAG 59.439 43.478 31.92 22.32 39.78 2.85
558 562 2.837498 ACATTGTTTGGCCAAAAGAGC 58.163 42.857 31.92 19.63 31.33 4.09
559 563 1.794116 CATTGTTTGGCCAAAAGAGCG 59.206 47.619 31.92 15.64 31.33 5.03
560 564 1.107114 TTGTTTGGCCAAAAGAGCGA 58.893 45.000 31.92 16.49 31.33 4.93
561 565 0.667993 TGTTTGGCCAAAAGAGCGAG 59.332 50.000 31.92 0.00 31.33 5.03
562 566 0.039165 GTTTGGCCAAAAGAGCGAGG 60.039 55.000 31.92 0.00 31.33 4.63
563 567 0.467290 TTTGGCCAAAAGAGCGAGGT 60.467 50.000 28.57 0.00 0.00 3.85
564 568 0.467290 TTGGCCAAAAGAGCGAGGTT 60.467 50.000 17.98 0.00 0.00 3.50
565 569 1.172180 TGGCCAAAAGAGCGAGGTTG 61.172 55.000 0.61 0.00 0.00 3.77
566 570 0.889186 GGCCAAAAGAGCGAGGTTGA 60.889 55.000 0.00 0.00 0.00 3.18
567 571 0.951558 GCCAAAAGAGCGAGGTTGAA 59.048 50.000 0.00 0.00 0.00 2.69
568 572 1.336755 GCCAAAAGAGCGAGGTTGAAA 59.663 47.619 0.00 0.00 0.00 2.69
569 573 2.605580 GCCAAAAGAGCGAGGTTGAAAG 60.606 50.000 0.00 0.00 0.00 2.62
570 574 2.878406 CCAAAAGAGCGAGGTTGAAAGA 59.122 45.455 0.00 0.00 0.00 2.52
571 575 3.315191 CCAAAAGAGCGAGGTTGAAAGAA 59.685 43.478 0.00 0.00 0.00 2.52
572 576 4.022849 CCAAAAGAGCGAGGTTGAAAGAAT 60.023 41.667 0.00 0.00 0.00 2.40
573 577 5.181245 CCAAAAGAGCGAGGTTGAAAGAATA 59.819 40.000 0.00 0.00 0.00 1.75
574 578 6.127897 CCAAAAGAGCGAGGTTGAAAGAATAT 60.128 38.462 0.00 0.00 0.00 1.28
575 579 7.065803 CCAAAAGAGCGAGGTTGAAAGAATATA 59.934 37.037 0.00 0.00 0.00 0.86
576 580 8.450964 CAAAAGAGCGAGGTTGAAAGAATATAA 58.549 33.333 0.00 0.00 0.00 0.98
577 581 8.561738 AAAGAGCGAGGTTGAAAGAATATAAA 57.438 30.769 0.00 0.00 0.00 1.40
578 582 8.738645 AAGAGCGAGGTTGAAAGAATATAAAT 57.261 30.769 0.00 0.00 0.00 1.40
579 583 8.371770 AGAGCGAGGTTGAAAGAATATAAATC 57.628 34.615 0.00 0.00 0.00 2.17
580 584 8.207545 AGAGCGAGGTTGAAAGAATATAAATCT 58.792 33.333 0.00 0.00 0.00 2.40
581 585 8.738645 AGCGAGGTTGAAAGAATATAAATCTT 57.261 30.769 0.00 0.00 38.75 2.40
582 586 9.178758 AGCGAGGTTGAAAGAATATAAATCTTT 57.821 29.630 13.71 13.71 46.81 2.52
583 587 9.226345 GCGAGGTTGAAAGAATATAAATCTTTG 57.774 33.333 17.06 6.50 44.81 2.77
590 594 9.540538 TGAAAGAATATAAATCTTTGAACCCCA 57.459 29.630 17.06 8.40 44.81 4.96
594 598 9.588096 AGAATATAAATCTTTGAACCCCATACC 57.412 33.333 0.00 0.00 0.00 2.73
595 599 9.362151 GAATATAAATCTTTGAACCCCATACCA 57.638 33.333 0.00 0.00 0.00 3.25
596 600 8.706322 ATATAAATCTTTGAACCCCATACCAC 57.294 34.615 0.00 0.00 0.00 4.16
597 601 2.891191 TCTTTGAACCCCATACCACC 57.109 50.000 0.00 0.00 0.00 4.61
598 602 2.066592 TCTTTGAACCCCATACCACCA 58.933 47.619 0.00 0.00 0.00 4.17
599 603 2.652348 TCTTTGAACCCCATACCACCAT 59.348 45.455 0.00 0.00 0.00 3.55
600 604 2.818751 TTGAACCCCATACCACCATC 57.181 50.000 0.00 0.00 0.00 3.51
601 605 1.675007 TGAACCCCATACCACCATCA 58.325 50.000 0.00 0.00 0.00 3.07
602 606 1.283613 TGAACCCCATACCACCATCAC 59.716 52.381 0.00 0.00 0.00 3.06
603 607 1.283613 GAACCCCATACCACCATCACA 59.716 52.381 0.00 0.00 0.00 3.58
604 608 1.607225 ACCCCATACCACCATCACAT 58.393 50.000 0.00 0.00 0.00 3.21
605 609 1.929494 ACCCCATACCACCATCACATT 59.071 47.619 0.00 0.00 0.00 2.71
606 610 2.314549 ACCCCATACCACCATCACATTT 59.685 45.455 0.00 0.00 0.00 2.32
607 611 3.245948 ACCCCATACCACCATCACATTTT 60.246 43.478 0.00 0.00 0.00 1.82
608 612 3.132646 CCCCATACCACCATCACATTTTG 59.867 47.826 0.00 0.00 0.00 2.44
609 613 3.132646 CCCATACCACCATCACATTTTGG 59.867 47.826 0.00 0.00 39.02 3.28
610 614 4.022603 CCATACCACCATCACATTTTGGA 58.977 43.478 0.00 0.00 36.79 3.53
611 615 4.465660 CCATACCACCATCACATTTTGGAA 59.534 41.667 0.00 0.00 36.79 3.53
612 616 5.129155 CCATACCACCATCACATTTTGGAAT 59.871 40.000 0.00 0.00 36.79 3.01
613 617 6.323482 CCATACCACCATCACATTTTGGAATA 59.677 38.462 0.00 0.00 36.79 1.75
614 618 5.659440 ACCACCATCACATTTTGGAATAC 57.341 39.130 0.00 0.00 36.79 1.89
615 619 5.083122 ACCACCATCACATTTTGGAATACA 58.917 37.500 0.00 0.00 36.79 2.29
616 620 5.541868 ACCACCATCACATTTTGGAATACAA 59.458 36.000 0.00 0.00 36.79 2.41
617 621 6.042552 ACCACCATCACATTTTGGAATACAAA 59.957 34.615 0.00 0.00 46.82 2.83
633 637 5.836024 ATACAAAGTTTCCACCAGGAGTA 57.164 39.130 0.00 0.00 46.74 2.59
636 640 4.079958 ACAAAGTTTCCACCAGGAGTAACT 60.080 41.667 0.00 0.00 46.74 2.24
637 641 4.790718 AAGTTTCCACCAGGAGTAACTT 57.209 40.909 10.90 10.90 44.44 2.66
656 660 8.827677 AGTAACTTTACTGTTAAACTTGCTCAG 58.172 33.333 0.70 0.00 42.13 3.35
662 666 5.193679 ACTGTTAAACTTGCTCAGAGGTTT 58.806 37.500 0.00 4.26 36.19 3.27
665 669 7.338449 ACTGTTAAACTTGCTCAGAGGTTTAAA 59.662 33.333 17.81 11.25 42.08 1.52
666 670 7.477494 TGTTAAACTTGCTCAGAGGTTTAAAC 58.523 34.615 17.81 9.98 42.08 2.01
668 672 6.524101 AAACTTGCTCAGAGGTTTAAACAA 57.476 33.333 19.57 2.54 31.34 2.83
669 673 5.757850 ACTTGCTCAGAGGTTTAAACAAG 57.242 39.130 19.57 13.30 39.26 3.16
670 674 4.580580 ACTTGCTCAGAGGTTTAAACAAGG 59.419 41.667 19.57 6.46 38.02 3.61
869 873 2.273449 CGAGCCCAGCCTCCAATT 59.727 61.111 0.00 0.00 0.00 2.32
1049 1104 1.021390 CACTTCTCTCCGCCGCAATT 61.021 55.000 0.00 0.00 0.00 2.32
1062 1117 1.984026 GCAATTCCACCCCACCCTG 60.984 63.158 0.00 0.00 0.00 4.45
1386 1463 7.864108 TTATTCATTCCACTGTTGATAGGTG 57.136 36.000 0.00 0.00 0.00 4.00
1387 1464 3.609853 TCATTCCACTGTTGATAGGTGC 58.390 45.455 0.00 0.00 0.00 5.01
1388 1465 3.008923 TCATTCCACTGTTGATAGGTGCA 59.991 43.478 0.00 0.00 0.00 4.57
1389 1466 3.719268 TTCCACTGTTGATAGGTGCAT 57.281 42.857 0.00 0.00 0.00 3.96
1390 1467 4.835284 TTCCACTGTTGATAGGTGCATA 57.165 40.909 0.00 0.00 0.00 3.14
1396 1473 5.761726 CACTGTTGATAGGTGCATACATGAT 59.238 40.000 0.00 0.00 0.00 2.45
1412 1489 3.439476 ACATGATGCTGCTGTCTTCTTTC 59.561 43.478 0.00 0.00 0.00 2.62
1472 1549 5.608437 TGCCAATAGTCATCTCCTCCTTAAT 59.392 40.000 0.00 0.00 0.00 1.40
1528 1605 5.362556 AAAGTCTGATCAAATGGTTCACG 57.637 39.130 0.00 0.00 0.00 4.35
1553 1631 7.970061 CGTGGCATATATAGCTTTTATGCATTT 59.030 33.333 24.52 0.00 46.36 2.32
1614 1698 4.143305 GCTACTGTTTTACTGCTCTTCACG 60.143 45.833 0.00 0.00 0.00 4.35
1774 1860 1.747325 ATGGGTGTTGGTGCTGCAAC 61.747 55.000 11.52 11.52 0.00 4.17
1819 1910 8.751302 TTCAACATCATTGTCATTGAAATGAG 57.249 30.769 19.49 15.74 45.38 2.90
1843 1934 6.666417 GCAATAGCTTCATATTCCAGAACAG 58.334 40.000 0.00 0.00 37.91 3.16
1847 1940 6.998968 AGCTTCATATTCCAGAACAGAAAG 57.001 37.500 0.00 0.00 0.00 2.62
1866 1961 9.409918 ACAGAAAGTCAGTATATCTTAGTGCTA 57.590 33.333 0.00 0.00 0.00 3.49
1926 2022 1.818642 AGAGATTGCAAGCTGTGACC 58.181 50.000 24.07 7.12 0.00 4.02
1963 2063 8.340443 ACATCTATCAATCATCGAACAACAATG 58.660 33.333 0.00 0.00 0.00 2.82
1998 2101 6.913673 TCGTTTTAATACTTCAGTTTTGGTGC 59.086 34.615 0.00 0.00 0.00 5.01
2013 2116 7.278868 CAGTTTTGGTGCTGTTGGTAAATTTAA 59.721 33.333 0.00 0.00 0.00 1.52
2044 2165 6.899393 TTCCTTGCATATATTGGTCCATTC 57.101 37.500 0.00 0.00 0.00 2.67
2053 2174 9.066892 GCATATATTGGTCCATTCTAGTTTTGA 57.933 33.333 0.00 0.00 0.00 2.69
2060 2181 6.371548 TGGTCCATTCTAGTTTTGAATCTTCG 59.628 38.462 0.00 0.00 32.47 3.79
2083 2204 7.992008 TCGTTGGAACTTGAAAGATTAAAAGT 58.008 30.769 0.00 0.00 34.40 2.66
2128 2250 6.401394 TGACTGAGGACATTCTTACATTCAG 58.599 40.000 0.00 0.00 37.43 3.02
2139 2261 5.235850 TCTTACATTCAGTGGGCTTGTTA 57.764 39.130 0.00 0.00 0.00 2.41
2394 2541 6.908825 TCTGCGCAATTGTAAGTATCTTTTT 58.091 32.000 13.05 0.00 0.00 1.94
2475 2622 4.263905 ACCTCATAGCTTTGGATTGGAACA 60.264 41.667 4.23 0.00 0.00 3.18
2491 2638 6.662865 TTGGAACATGACAACATTACCATT 57.337 33.333 0.00 0.00 39.30 3.16
2649 2977 6.472686 ACCAAGCAAATTAAAACCAGTACA 57.527 33.333 0.00 0.00 0.00 2.90
2710 3055 6.189859 TGAAATATCACTTCAGGAAGGCAAT 58.810 36.000 13.19 6.25 42.53 3.56
2764 3109 7.864108 TTACATGATGTCTAATTTCACCCAG 57.136 36.000 0.00 0.00 0.00 4.45
2809 3172 5.656416 AGAATAGAGGTGGAAGAGTCAAGAG 59.344 44.000 0.00 0.00 0.00 2.85
2842 3205 3.623703 TGTTGCATAATCTCATGTGCCT 58.376 40.909 1.74 0.00 36.79 4.75
2843 3206 3.379057 TGTTGCATAATCTCATGTGCCTG 59.621 43.478 1.74 0.00 36.79 4.85
2859 3222 0.251634 CCTGTGAGGAGAAAGGAGGC 59.748 60.000 0.00 0.00 37.67 4.70
2959 3322 9.942850 AACAAAATACAAGATTATTTGGGAAGG 57.057 29.630 0.00 0.00 32.95 3.46
3027 3503 2.046283 TGTGATTGTCGACGTGAGAC 57.954 50.000 11.62 12.36 38.98 3.36
3123 3602 4.277476 TGTTCCTCAATTCACACTTGGTT 58.723 39.130 0.00 0.00 0.00 3.67
3201 3695 6.206634 CCCACTTGTCATAACTTAACACACAT 59.793 38.462 0.00 0.00 0.00 3.21
3202 3696 7.389330 CCCACTTGTCATAACTTAACACACATA 59.611 37.037 0.00 0.00 0.00 2.29
3211 3718 9.741168 CATAACTTAACACACATACTTCTTTCG 57.259 33.333 0.00 0.00 0.00 3.46
3219 3726 4.202223 ACACATACTTCTTTCGACACCACT 60.202 41.667 0.00 0.00 0.00 4.00
3223 3730 1.000607 CTTCTTTCGACACCACTCGGA 60.001 52.381 0.00 0.00 34.27 4.55
3230 3737 1.201647 CGACACCACTCGGAACATAGT 59.798 52.381 0.00 0.00 35.59 2.12
3402 4221 9.511272 TGTCTACTCAACACTATTAGACAGTAA 57.489 33.333 5.80 0.00 42.25 2.24
3414 4233 3.207044 AGACAGTAAGATTGGAGGGGT 57.793 47.619 0.00 0.00 0.00 4.95
3415 4234 2.840651 AGACAGTAAGATTGGAGGGGTG 59.159 50.000 0.00 0.00 0.00 4.61
3416 4235 1.916181 ACAGTAAGATTGGAGGGGTGG 59.084 52.381 0.00 0.00 0.00 4.61
3418 4237 0.551396 GTAAGATTGGAGGGGTGGGG 59.449 60.000 0.00 0.00 0.00 4.96
3420 4239 1.509548 AAGATTGGAGGGGTGGGGTG 61.510 60.000 0.00 0.00 0.00 4.61
3421 4240 2.946650 ATTGGAGGGGTGGGGTGG 60.947 66.667 0.00 0.00 0.00 4.61
3445 4264 6.157471 GGGGTGGGAGTATCTTCTTTAACTTA 59.843 42.308 0.00 0.00 33.73 2.24
3502 4515 1.447140 GACGTACATTCTGGCGGCA 60.447 57.895 12.58 12.58 30.43 5.69
3728 4749 3.547567 CCTTCACTGAGGCTTCCAG 57.452 57.895 1.90 1.90 37.64 3.86
3748 4769 0.899717 GATGGCTGGGGAAAGCAACA 60.900 55.000 0.00 0.00 45.43 3.33
3800 4821 7.667043 ACTAATTTGTAGTTGAAGATTCGCA 57.333 32.000 0.00 0.00 0.00 5.10
3807 4828 1.812571 GTTGAAGATTCGCACCCATGT 59.187 47.619 0.00 0.00 0.00 3.21
3861 4882 5.640147 TCCTGGTAGATGATTGTGGTTTTT 58.360 37.500 0.00 0.00 0.00 1.94
3878 4899 5.808030 TGGTTTTTCCGACAAGATTTTTGTC 59.192 36.000 9.44 9.44 43.85 3.18
3906 4927 3.243168 CGATTCTACATTGGTGGCATTGG 60.243 47.826 0.00 0.00 0.00 3.16
3953 4979 2.769663 ACTTGTCGAGTATATTGCCCCA 59.230 45.455 0.00 0.00 36.65 4.96
3954 4980 3.391296 ACTTGTCGAGTATATTGCCCCAT 59.609 43.478 0.00 0.00 36.65 4.00
3974 5000 6.294508 CCCCATTCACGTCTTTCATTTAAACT 60.295 38.462 0.00 0.00 0.00 2.66
4165 5272 1.435577 GTACGATTGGTTTCTGCCGT 58.564 50.000 0.00 0.00 0.00 5.68
4204 5330 9.401058 CCACTTTCTTGAGATATTTACCATCTT 57.599 33.333 0.00 0.00 32.86 2.40
4213 5339 9.113838 TGAGATATTTACCATCTTCTTTGAAGC 57.886 33.333 2.71 0.00 32.86 3.86
4429 5557 5.455056 TTATTAAAAGCGGAGGCAAACAA 57.545 34.783 0.00 0.00 43.41 2.83
4475 5603 2.479275 GGTCGCAACCAGAAAGTAGTTC 59.521 50.000 0.00 0.00 45.68 3.01
4522 5650 3.074412 AGATAAACAGCGGAACACAAGG 58.926 45.455 0.00 0.00 0.00 3.61
4532 5665 3.518590 CGGAACACAAGGTACTACCATC 58.481 50.000 8.01 0.00 41.95 3.51
4538 5671 4.468868 ACACAAGGTACTACCATCTAACCC 59.531 45.833 8.01 0.00 41.95 4.11
4608 5741 1.667191 GATGATCGAGCAGCCGCAT 60.667 57.895 7.89 0.00 42.27 4.73
4685 5818 1.893137 CAAAAGCTCCTACCAAACCCC 59.107 52.381 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.542915 CCTTGCACAAGATTGGGACTG 59.457 52.381 11.94 0.00 40.79 3.51
1 2 1.548582 CCCTTGCACAAGATTGGGACT 60.549 52.381 11.94 0.00 40.79 3.85
2 3 0.890683 CCCTTGCACAAGATTGGGAC 59.109 55.000 11.94 0.00 40.79 4.46
3 4 0.899717 GCCCTTGCACAAGATTGGGA 60.900 55.000 11.94 0.00 40.79 4.37
11 12 2.844451 GCAACGAGCCCTTGCACAA 61.844 57.895 3.08 0.00 43.04 3.33
12 13 2.390306 TAGCAACGAGCCCTTGCACA 62.390 55.000 9.92 0.00 45.48 4.57
48 49 6.715280 AGGCTCAAAAGATGTCTGAAATCTA 58.285 36.000 10.69 0.00 33.17 1.98
53 54 6.942005 TCATAAAGGCTCAAAAGATGTCTGAA 59.058 34.615 0.00 0.00 0.00 3.02
56 57 6.240894 TGTCATAAAGGCTCAAAAGATGTCT 58.759 36.000 0.00 0.00 0.00 3.41
59 60 6.748333 TCTGTCATAAAGGCTCAAAAGATG 57.252 37.500 0.00 0.00 0.00 2.90
65 66 4.686972 CTCGATCTGTCATAAAGGCTCAA 58.313 43.478 0.00 0.00 0.00 3.02
66 67 3.491619 GCTCGATCTGTCATAAAGGCTCA 60.492 47.826 0.00 0.00 0.00 4.26
68 69 2.432146 TGCTCGATCTGTCATAAAGGCT 59.568 45.455 0.00 0.00 0.00 4.58
69 70 2.826428 TGCTCGATCTGTCATAAAGGC 58.174 47.619 0.00 0.00 0.00 4.35
72 73 4.811024 GGTGAATGCTCGATCTGTCATAAA 59.189 41.667 0.00 0.00 0.00 1.40
75 76 2.800985 CGGTGAATGCTCGATCTGTCAT 60.801 50.000 0.00 0.00 0.00 3.06
86 87 1.973281 CCAGTTGGCGGTGAATGCT 60.973 57.895 0.00 0.00 0.00 3.79
96 97 3.874392 AATAAGCACATTCCAGTTGGC 57.126 42.857 0.00 0.00 34.44 4.52
98 99 5.649782 AGGAAATAAGCACATTCCAGTTG 57.350 39.130 11.55 0.00 44.08 3.16
114 115 7.068716 GTGCCCTTGAAATCAATACTAGGAAAT 59.931 37.037 0.00 0.00 35.02 2.17
118 119 5.192927 TGTGCCCTTGAAATCAATACTAGG 58.807 41.667 0.00 0.00 35.02 3.02
126 127 4.016444 GAGGTATTGTGCCCTTGAAATCA 58.984 43.478 0.00 0.00 0.00 2.57
174 175 1.551883 GCTGCAGGTCCCATGAAAATT 59.448 47.619 17.12 0.00 0.00 1.82
181 182 1.792757 TTGGAAGCTGCAGGTCCCAT 61.793 55.000 25.30 6.06 0.00 4.00
191 193 4.589216 TTGGAATCAAGTTTGGAAGCTG 57.411 40.909 0.00 0.00 0.00 4.24
203 205 4.151121 TGCAACCAGAGATTTGGAATCAA 58.849 39.130 0.00 0.00 40.87 2.57
239 241 3.454375 ACAATCACGGGCTAATCTAACG 58.546 45.455 0.00 0.00 0.00 3.18
242 244 3.305720 AGGACAATCACGGGCTAATCTA 58.694 45.455 0.00 0.00 0.00 1.98
248 250 1.204146 ACATAGGACAATCACGGGCT 58.796 50.000 0.00 0.00 0.00 5.19
252 254 5.117135 CGCATAAGTACATAGGACAATCACG 59.883 44.000 0.00 0.00 0.00 4.35
253 255 5.983720 ACGCATAAGTACATAGGACAATCAC 59.016 40.000 0.00 0.00 0.00 3.06
264 266 4.100963 TGAGGAATGGACGCATAAGTACAT 59.899 41.667 0.00 0.00 46.95 2.29
289 291 5.705609 ATTTTCTGTGTGGACAACATACC 57.294 39.130 0.00 0.00 41.97 2.73
295 297 3.117474 TGGGGTATTTTCTGTGTGGACAA 60.117 43.478 0.00 0.00 0.00 3.18
301 303 3.900601 TGCAAATGGGGTATTTTCTGTGT 59.099 39.130 0.00 0.00 36.87 3.72
311 313 2.233431 GCAGTTCAATGCAAATGGGGTA 59.767 45.455 0.00 0.00 45.77 3.69
313 315 1.729284 GCAGTTCAATGCAAATGGGG 58.271 50.000 0.00 0.00 45.77 4.96
324 326 4.556501 CGACTTTATTGCTTGGCAGTTCAA 60.557 41.667 0.00 0.00 40.61 2.69
328 330 2.504367 ACGACTTTATTGCTTGGCAGT 58.496 42.857 0.00 0.00 40.61 4.40
329 331 3.058293 TCAACGACTTTATTGCTTGGCAG 60.058 43.478 0.00 0.00 40.61 4.85
338 340 4.394729 TCCAGGCTTTCAACGACTTTATT 58.605 39.130 0.00 0.00 0.00 1.40
344 346 3.643159 AATTTCCAGGCTTTCAACGAC 57.357 42.857 0.00 0.00 0.00 4.34
347 349 4.322725 CCCCTTAATTTCCAGGCTTTCAAC 60.323 45.833 0.00 0.00 0.00 3.18
349 351 3.076785 TCCCCTTAATTTCCAGGCTTTCA 59.923 43.478 0.00 0.00 0.00 2.69
350 352 3.708451 TCCCCTTAATTTCCAGGCTTTC 58.292 45.455 0.00 0.00 0.00 2.62
353 355 4.352658 AATTCCCCTTAATTTCCAGGCT 57.647 40.909 0.00 0.00 0.00 4.58
359 361 6.316140 GGATTGTGCAAATTCCCCTTAATTTC 59.684 38.462 6.55 0.00 37.03 2.17
391 393 5.778241 TCAGTGATACTTCTAACCCTGTTGA 59.222 40.000 0.00 0.00 0.00 3.18
392 394 6.037786 TCAGTGATACTTCTAACCCTGTTG 57.962 41.667 0.00 0.00 0.00 3.33
393 395 6.440647 TGATCAGTGATACTTCTAACCCTGTT 59.559 38.462 5.38 0.00 0.00 3.16
394 396 5.958380 TGATCAGTGATACTTCTAACCCTGT 59.042 40.000 5.38 0.00 0.00 4.00
397 399 6.472686 ACTGATCAGTGATACTTCTAACCC 57.527 41.667 27.37 0.00 40.75 4.11
398 400 7.548097 TGAACTGATCAGTGATACTTCTAACC 58.452 38.462 28.52 0.97 41.58 2.85
401 403 8.525290 TGATGAACTGATCAGTGATACTTCTA 57.475 34.615 28.52 11.88 42.53 2.10
402 404 7.415592 TGATGAACTGATCAGTGATACTTCT 57.584 36.000 28.52 10.60 42.53 2.85
403 405 7.384660 GGATGATGAACTGATCAGTGATACTTC 59.615 40.741 28.52 20.14 42.53 3.01
406 408 5.931146 GGGATGATGAACTGATCAGTGATAC 59.069 44.000 28.52 19.25 42.53 2.24
407 409 5.603813 TGGGATGATGAACTGATCAGTGATA 59.396 40.000 28.52 17.47 42.53 2.15
410 412 4.146745 TGGGATGATGAACTGATCAGTG 57.853 45.455 28.52 4.63 42.53 3.66
411 413 5.384145 AATGGGATGATGAACTGATCAGT 57.616 39.130 22.89 22.89 42.53 3.41
423 427 2.306847 GTTACGGGCAAATGGGATGAT 58.693 47.619 0.00 0.00 0.00 2.45
462 466 5.815222 GGGAAACACATTGCTAACAAAAGTT 59.185 36.000 0.00 0.00 39.77 2.66
473 477 1.175983 TCCACGGGGAAACACATTGC 61.176 55.000 2.24 0.00 41.32 3.56
476 480 0.036306 GACTCCACGGGGAAACACAT 59.964 55.000 8.34 0.00 44.38 3.21
477 481 1.338890 TGACTCCACGGGGAAACACA 61.339 55.000 8.34 2.55 44.38 3.72
489 493 1.131638 ACAGGAAAGTGCTGACTCCA 58.868 50.000 3.61 0.00 38.14 3.86
497 501 0.957888 GAGCCCTCACAGGAAAGTGC 60.958 60.000 0.00 0.00 37.67 4.40
498 502 0.671781 CGAGCCCTCACAGGAAAGTG 60.672 60.000 0.00 0.00 37.67 3.16
507 511 0.608640 CATATACCCCGAGCCCTCAC 59.391 60.000 0.00 0.00 0.00 3.51
509 513 1.757699 GATCATATACCCCGAGCCCTC 59.242 57.143 0.00 0.00 0.00 4.30
516 520 5.178797 GTTGGAGAATGATCATATACCCCG 58.821 45.833 9.04 0.00 0.00 5.73
517 521 6.126863 TGTTGGAGAATGATCATATACCCC 57.873 41.667 9.04 7.04 0.00 4.95
518 522 7.667219 ACAATGTTGGAGAATGATCATATACCC 59.333 37.037 9.04 8.72 0.00 3.69
519 523 8.627208 ACAATGTTGGAGAATGATCATATACC 57.373 34.615 9.04 12.37 0.00 2.73
536 540 3.002553 GCTCTTTTGGCCAAACAATGTTG 59.997 43.478 30.43 15.99 0.00 3.33
537 541 3.205338 GCTCTTTTGGCCAAACAATGTT 58.795 40.909 30.43 0.00 0.00 2.71
538 542 2.802774 CGCTCTTTTGGCCAAACAATGT 60.803 45.455 30.43 0.00 0.00 2.71
539 543 1.794116 CGCTCTTTTGGCCAAACAATG 59.206 47.619 30.43 19.84 0.00 2.82
540 544 1.686052 TCGCTCTTTTGGCCAAACAAT 59.314 42.857 30.43 0.00 0.00 2.71
541 545 1.066908 CTCGCTCTTTTGGCCAAACAA 59.933 47.619 30.43 19.26 0.00 2.83
542 546 0.667993 CTCGCTCTTTTGGCCAAACA 59.332 50.000 30.43 18.35 0.00 2.83
543 547 0.039165 CCTCGCTCTTTTGGCCAAAC 60.039 55.000 30.43 17.48 0.00 2.93
544 548 0.467290 ACCTCGCTCTTTTGGCCAAA 60.467 50.000 27.13 27.13 0.00 3.28
545 549 0.467290 AACCTCGCTCTTTTGGCCAA 60.467 50.000 16.05 16.05 0.00 4.52
546 550 1.150536 AACCTCGCTCTTTTGGCCA 59.849 52.632 0.00 0.00 0.00 5.36
547 551 0.889186 TCAACCTCGCTCTTTTGGCC 60.889 55.000 0.00 0.00 0.00 5.36
548 552 0.951558 TTCAACCTCGCTCTTTTGGC 59.048 50.000 0.00 0.00 0.00 4.52
549 553 2.878406 TCTTTCAACCTCGCTCTTTTGG 59.122 45.455 0.00 0.00 0.00 3.28
550 554 4.552166 TTCTTTCAACCTCGCTCTTTTG 57.448 40.909 0.00 0.00 0.00 2.44
551 555 8.561738 TTATATTCTTTCAACCTCGCTCTTTT 57.438 30.769 0.00 0.00 0.00 2.27
552 556 8.561738 TTTATATTCTTTCAACCTCGCTCTTT 57.438 30.769 0.00 0.00 0.00 2.52
553 557 8.738645 ATTTATATTCTTTCAACCTCGCTCTT 57.261 30.769 0.00 0.00 0.00 2.85
554 558 8.207545 AGATTTATATTCTTTCAACCTCGCTCT 58.792 33.333 0.00 0.00 0.00 4.09
555 559 8.371770 AGATTTATATTCTTTCAACCTCGCTC 57.628 34.615 0.00 0.00 0.00 5.03
556 560 8.738645 AAGATTTATATTCTTTCAACCTCGCT 57.261 30.769 0.00 0.00 29.12 4.93
557 561 9.226345 CAAAGATTTATATTCTTTCAACCTCGC 57.774 33.333 7.77 0.00 40.53 5.03
564 568 9.540538 TGGGGTTCAAAGATTTATATTCTTTCA 57.459 29.630 7.77 0.00 40.53 2.69
568 572 9.588096 GGTATGGGGTTCAAAGATTTATATTCT 57.412 33.333 0.00 0.00 0.00 2.40
569 573 9.362151 TGGTATGGGGTTCAAAGATTTATATTC 57.638 33.333 0.00 0.00 0.00 1.75
570 574 9.143155 GTGGTATGGGGTTCAAAGATTTATATT 57.857 33.333 0.00 0.00 0.00 1.28
571 575 7.728532 GGTGGTATGGGGTTCAAAGATTTATAT 59.271 37.037 0.00 0.00 0.00 0.86
572 576 7.064229 GGTGGTATGGGGTTCAAAGATTTATA 58.936 38.462 0.00 0.00 0.00 0.98
573 577 5.897250 GGTGGTATGGGGTTCAAAGATTTAT 59.103 40.000 0.00 0.00 0.00 1.40
574 578 5.222358 TGGTGGTATGGGGTTCAAAGATTTA 60.222 40.000 0.00 0.00 0.00 1.40
575 579 4.093743 GGTGGTATGGGGTTCAAAGATTT 58.906 43.478 0.00 0.00 0.00 2.17
576 580 3.076785 TGGTGGTATGGGGTTCAAAGATT 59.923 43.478 0.00 0.00 0.00 2.40
577 581 2.652348 TGGTGGTATGGGGTTCAAAGAT 59.348 45.455 0.00 0.00 0.00 2.40
578 582 2.066592 TGGTGGTATGGGGTTCAAAGA 58.933 47.619 0.00 0.00 0.00 2.52
579 583 2.595750 TGGTGGTATGGGGTTCAAAG 57.404 50.000 0.00 0.00 0.00 2.77
580 584 2.380249 TGATGGTGGTATGGGGTTCAAA 59.620 45.455 0.00 0.00 0.00 2.69
581 585 1.996291 TGATGGTGGTATGGGGTTCAA 59.004 47.619 0.00 0.00 0.00 2.69
582 586 1.283613 GTGATGGTGGTATGGGGTTCA 59.716 52.381 0.00 0.00 0.00 3.18
583 587 1.283613 TGTGATGGTGGTATGGGGTTC 59.716 52.381 0.00 0.00 0.00 3.62
584 588 1.377690 TGTGATGGTGGTATGGGGTT 58.622 50.000 0.00 0.00 0.00 4.11
585 589 1.607225 ATGTGATGGTGGTATGGGGT 58.393 50.000 0.00 0.00 0.00 4.95
586 590 2.754012 AATGTGATGGTGGTATGGGG 57.246 50.000 0.00 0.00 0.00 4.96
587 591 3.132646 CCAAAATGTGATGGTGGTATGGG 59.867 47.826 0.00 0.00 31.84 4.00
588 592 4.022603 TCCAAAATGTGATGGTGGTATGG 58.977 43.478 0.00 0.00 37.94 2.74
589 593 5.657826 TTCCAAAATGTGATGGTGGTATG 57.342 39.130 0.00 0.00 37.94 2.39
590 594 6.894654 TGTATTCCAAAATGTGATGGTGGTAT 59.105 34.615 0.00 0.00 37.94 2.73
591 595 6.249192 TGTATTCCAAAATGTGATGGTGGTA 58.751 36.000 0.00 0.00 37.94 3.25
592 596 5.083122 TGTATTCCAAAATGTGATGGTGGT 58.917 37.500 0.00 0.00 37.94 4.16
593 597 5.657826 TGTATTCCAAAATGTGATGGTGG 57.342 39.130 0.00 0.00 37.94 4.61
594 598 7.153985 ACTTTGTATTCCAAAATGTGATGGTG 58.846 34.615 0.00 0.00 42.31 4.17
595 599 7.301868 ACTTTGTATTCCAAAATGTGATGGT 57.698 32.000 0.00 0.00 42.31 3.55
596 600 8.606040 AAACTTTGTATTCCAAAATGTGATGG 57.394 30.769 0.00 0.00 42.31 3.51
597 601 8.711457 GGAAACTTTGTATTCCAAAATGTGATG 58.289 33.333 0.00 0.00 42.31 3.07
598 602 8.831715 GGAAACTTTGTATTCCAAAATGTGAT 57.168 30.769 0.00 0.00 42.31 3.06
608 612 4.403734 TCCTGGTGGAAACTTTGTATTCC 58.596 43.478 0.00 0.00 44.38 3.01
609 613 5.070685 ACTCCTGGTGGAAACTTTGTATTC 58.929 41.667 0.33 0.00 42.66 1.75
610 614 5.061721 ACTCCTGGTGGAAACTTTGTATT 57.938 39.130 0.33 0.00 42.66 1.89
611 615 4.724279 ACTCCTGGTGGAAACTTTGTAT 57.276 40.909 0.33 0.00 42.66 2.29
612 616 5.131475 AGTTACTCCTGGTGGAAACTTTGTA 59.869 40.000 10.94 0.00 39.23 2.41
613 617 4.079958 AGTTACTCCTGGTGGAAACTTTGT 60.080 41.667 10.94 0.00 39.23 2.83
614 618 4.461198 AGTTACTCCTGGTGGAAACTTTG 58.539 43.478 10.94 0.00 39.23 2.77
615 619 4.790718 AGTTACTCCTGGTGGAAACTTT 57.209 40.909 10.94 0.00 39.23 2.66
616 620 4.790718 AAGTTACTCCTGGTGGAAACTT 57.209 40.909 18.11 18.11 43.32 2.66
617 621 4.790718 AAAGTTACTCCTGGTGGAAACT 57.209 40.909 10.94 10.94 42.24 2.66
618 622 5.469084 CAGTAAAGTTACTCCTGGTGGAAAC 59.531 44.000 0.62 2.16 41.82 2.78
619 623 5.131475 ACAGTAAAGTTACTCCTGGTGGAAA 59.869 40.000 0.62 0.00 41.82 3.13
620 624 4.657039 ACAGTAAAGTTACTCCTGGTGGAA 59.343 41.667 0.62 0.00 41.82 3.53
621 625 4.228824 ACAGTAAAGTTACTCCTGGTGGA 58.771 43.478 0.62 0.00 41.82 4.02
622 626 4.618920 ACAGTAAAGTTACTCCTGGTGG 57.381 45.455 0.62 0.00 41.82 4.61
623 627 7.713942 AGTTTAACAGTAAAGTTACTCCTGGTG 59.286 37.037 0.62 0.00 41.82 4.17
624 628 7.799081 AGTTTAACAGTAAAGTTACTCCTGGT 58.201 34.615 0.62 6.91 41.82 4.00
625 629 8.557029 CAAGTTTAACAGTAAAGTTACTCCTGG 58.443 37.037 0.62 0.00 41.82 4.45
626 630 8.068380 GCAAGTTTAACAGTAAAGTTACTCCTG 58.932 37.037 0.62 5.49 41.82 3.86
627 631 7.991460 AGCAAGTTTAACAGTAAAGTTACTCCT 59.009 33.333 0.62 0.00 41.82 3.69
628 632 8.151141 AGCAAGTTTAACAGTAAAGTTACTCC 57.849 34.615 0.62 0.00 41.82 3.85
633 637 7.012421 CCTCTGAGCAAGTTTAACAGTAAAGTT 59.988 37.037 0.00 0.00 41.52 2.66
636 640 6.354130 ACCTCTGAGCAAGTTTAACAGTAAA 58.646 36.000 0.00 0.00 0.00 2.01
637 641 5.925509 ACCTCTGAGCAAGTTTAACAGTAA 58.074 37.500 0.00 0.00 0.00 2.24
670 674 4.002982 TGTATGCTCACTGGTCATTTGAC 58.997 43.478 1.99 1.99 44.04 3.18
680 684 2.086869 CCTGGGTTTGTATGCTCACTG 58.913 52.381 0.00 0.00 0.00 3.66
802 806 5.138276 AGAAGATACGGCCACTACTGATTA 58.862 41.667 2.24 0.00 0.00 1.75
803 807 3.961408 AGAAGATACGGCCACTACTGATT 59.039 43.478 2.24 0.00 0.00 2.57
804 808 3.567397 AGAAGATACGGCCACTACTGAT 58.433 45.455 2.24 0.00 0.00 2.90
805 809 3.014304 AGAAGATACGGCCACTACTGA 57.986 47.619 2.24 0.00 0.00 3.41
806 810 3.491104 GGAAGAAGATACGGCCACTACTG 60.491 52.174 2.24 0.00 0.00 2.74
807 811 2.694109 GGAAGAAGATACGGCCACTACT 59.306 50.000 2.24 0.00 0.00 2.57
808 812 2.694109 AGGAAGAAGATACGGCCACTAC 59.306 50.000 2.24 0.00 0.00 2.73
809 813 2.957006 GAGGAAGAAGATACGGCCACTA 59.043 50.000 2.24 0.00 0.00 2.74
810 814 1.757699 GAGGAAGAAGATACGGCCACT 59.242 52.381 2.24 0.00 0.00 4.00
939 944 2.440599 CCAGGGTTGAGGGTTGGG 59.559 66.667 0.00 0.00 0.00 4.12
1122 1177 2.184579 GGGTTTCGAGCTCGGAGG 59.815 66.667 33.98 8.20 40.29 4.30
1282 1337 1.757682 CTGAGGAAGTAGGCGAGACT 58.242 55.000 0.00 0.00 0.00 3.24
1387 1464 4.127907 AGAAGACAGCAGCATCATGTATG 58.872 43.478 0.00 0.00 38.74 2.39
1388 1465 4.418973 AGAAGACAGCAGCATCATGTAT 57.581 40.909 0.00 0.00 0.00 2.29
1389 1466 3.900966 AGAAGACAGCAGCATCATGTA 57.099 42.857 0.00 0.00 0.00 2.29
1390 1467 2.783609 AGAAGACAGCAGCATCATGT 57.216 45.000 0.00 0.00 0.00 3.21
1396 1473 0.250038 AGCGAAAGAAGACAGCAGCA 60.250 50.000 0.00 0.00 0.00 4.41
1412 1489 3.545624 GCTGAAGTAATTCTGCATCAGCG 60.546 47.826 24.15 0.00 46.83 5.18
1472 1549 0.690762 GCCGGCTTCTAATCCCCATA 59.309 55.000 22.15 0.00 0.00 2.74
1614 1698 0.954452 CTTTGACAGGGCCAGACAAC 59.046 55.000 12.80 0.00 0.00 3.32
1774 1860 1.004044 AGCCCCTGATTCAACACTCAG 59.996 52.381 0.00 0.00 38.88 3.35
1819 1910 6.484643 TCTGTTCTGGAATATGAAGCTATTGC 59.515 38.462 0.00 0.00 40.05 3.56
1926 2022 8.833231 ATGATTGATAGATGTTAACCCTTACG 57.167 34.615 2.48 0.00 0.00 3.18
1975 2078 7.704899 ACAGCACCAAAACTGAAGTATTAAAAC 59.295 33.333 0.00 0.00 37.35 2.43
2013 2116 8.366359 ACCAATATATGCAAGGAAAAGAAAGT 57.634 30.769 0.00 0.00 0.00 2.66
2044 2165 7.190920 AGTTCCAACGAAGATTCAAAACTAG 57.809 36.000 0.00 0.00 0.00 2.57
2053 2174 6.884280 ATCTTTCAAGTTCCAACGAAGATT 57.116 33.333 0.00 0.00 31.64 2.40
2083 2204 7.657354 CAGTCATAACGAATGGATGAAGGATTA 59.343 37.037 0.00 0.00 36.05 1.75
2086 2207 5.128663 TCAGTCATAACGAATGGATGAAGGA 59.871 40.000 0.00 0.00 40.18 3.36
2094 2215 4.123497 TGTCCTCAGTCATAACGAATGG 57.877 45.455 0.00 0.00 40.18 3.16
2128 2250 1.098050 CTGCAGGATAACAAGCCCAC 58.902 55.000 5.57 0.00 0.00 4.61
2322 2469 4.078922 TCTCCAACCTGATGATAGAGGAGT 60.079 45.833 0.00 0.00 41.56 3.85
2440 2587 6.932356 AAGCTATGAGGTTCATGTGTAATG 57.068 37.500 1.94 0.00 37.70 1.90
2547 2754 8.942338 AACGAATACAGAGATTTGCAACTATA 57.058 30.769 0.00 0.00 0.00 1.31
2570 2860 9.099454 CCATTTATCTAAGAGGTGTACAAGAAC 57.901 37.037 0.00 0.00 0.00 3.01
2624 2952 8.184304 TGTACTGGTTTTAATTTGCTTGGTAT 57.816 30.769 0.00 0.00 0.00 2.73
2710 3055 1.804151 GAAACACGAGCTGGCAATGTA 59.196 47.619 0.00 0.00 0.00 2.29
2721 3066 8.761497 TCATGTAAAGTTAAGAAGAAACACGAG 58.239 33.333 0.00 0.00 0.00 4.18
2764 3109 5.844004 TCTCCTATTATGAGGAAGTTTCGC 58.156 41.667 0.00 0.00 45.20 4.70
2809 3172 7.041576 TGAGATTATGCAACAGCATCTATTGTC 60.042 37.037 6.19 4.74 45.46 3.18
2823 3186 3.379057 CACAGGCACATGAGATTATGCAA 59.621 43.478 0.00 0.00 39.92 4.08
2831 3194 0.900421 CTCCTCACAGGCACATGAGA 59.100 55.000 12.60 0.00 43.69 3.27
2842 3205 0.979665 CTGCCTCCTTTCTCCTCACA 59.020 55.000 0.00 0.00 0.00 3.58
2843 3206 0.980423 ACTGCCTCCTTTCTCCTCAC 59.020 55.000 0.00 0.00 0.00 3.51
2978 3419 9.185680 GGCAAGGATTTAGTTCCTAAGAAAATA 57.814 33.333 0.00 0.00 45.63 1.40
3040 3518 3.580022 TCTGCTTCTTGATCAAGTCAGGA 59.420 43.478 30.72 26.53 40.75 3.86
3123 3602 1.344065 TAGCCCGTCTTTCAGGAACA 58.656 50.000 0.00 0.00 0.00 3.18
3201 3695 2.030540 CCGAGTGGTGTCGAAAGAAGTA 60.031 50.000 0.00 0.00 45.01 2.24
3202 3696 1.269621 CCGAGTGGTGTCGAAAGAAGT 60.270 52.381 0.00 0.00 45.01 3.01
3211 3718 2.607187 CACTATGTTCCGAGTGGTGTC 58.393 52.381 0.00 0.00 39.55 3.67
3219 3726 0.036765 GTGTGCCCACTATGTTCCGA 60.037 55.000 0.00 0.00 38.61 4.55
3223 3730 0.685097 ACTCGTGTGCCCACTATGTT 59.315 50.000 0.00 0.00 39.55 2.71
3230 3737 4.927782 GCACCACTCGTGTGCCCA 62.928 66.667 12.06 0.00 44.97 5.36
3402 4221 1.930656 CACCCCACCCCTCCAATCT 60.931 63.158 0.00 0.00 0.00 2.40
3414 4233 2.850851 GATACTCCCACCCCACCCCA 62.851 65.000 0.00 0.00 0.00 4.96
3415 4234 2.043941 ATACTCCCACCCCACCCC 59.956 66.667 0.00 0.00 0.00 4.95
3416 4235 0.623617 AAGATACTCCCACCCCACCC 60.624 60.000 0.00 0.00 0.00 4.61
3418 4237 1.880941 AGAAGATACTCCCACCCCAC 58.119 55.000 0.00 0.00 0.00 4.61
3420 4239 4.473922 AGTTAAAGAAGATACTCCCACCCC 59.526 45.833 0.00 0.00 0.00 4.95
3421 4240 5.695424 AGTTAAAGAAGATACTCCCACCC 57.305 43.478 0.00 0.00 0.00 4.61
3445 4264 9.832445 ATGTTAACGGTTATCTGAAATGAGTAT 57.168 29.630 0.73 0.00 0.00 2.12
3502 4515 1.512926 GAATCGTGTTCACACCAGCT 58.487 50.000 4.48 0.00 43.66 4.24
3728 4749 1.305213 TTGCTTTCCCCAGCCATCC 60.305 57.895 0.00 0.00 39.25 3.51
3748 4769 6.014156 GGTGGCATTCTACCTATCAACTAGAT 60.014 42.308 0.00 0.00 40.86 1.98
3797 4818 1.529226 TTACAAAGGACATGGGTGCG 58.471 50.000 0.00 0.00 40.77 5.34
3800 4821 5.133221 GCTCATATTACAAAGGACATGGGT 58.867 41.667 0.00 0.00 0.00 4.51
3807 4828 7.148086 GGACAACAATGCTCATATTACAAAGGA 60.148 37.037 0.00 0.00 0.00 3.36
3878 4899 3.303329 CCACCAATGTAGAATCGCAATCG 60.303 47.826 0.00 0.00 0.00 3.34
3880 4901 2.358898 GCCACCAATGTAGAATCGCAAT 59.641 45.455 0.00 0.00 0.00 3.56
3891 4912 0.542467 TCAGCCAATGCCACCAATGT 60.542 50.000 0.00 0.00 38.69 2.71
3906 4927 3.575630 TCTACAACACTTGTCGATCAGC 58.424 45.455 0.00 0.00 44.12 4.26
4067 5111 7.088905 AGCTAGAATGCAGAAAATCAAACTTG 58.911 34.615 0.00 0.00 34.99 3.16
4204 5330 4.592485 AAGAGTTCGAGAGCTTCAAAGA 57.408 40.909 0.00 0.00 0.00 2.52
4212 5338 7.123160 ACAATAAGAAAAAGAGTTCGAGAGC 57.877 36.000 0.00 0.00 32.50 4.09
4213 5339 9.937175 AAAACAATAAGAAAAAGAGTTCGAGAG 57.063 29.630 0.00 0.00 32.50 3.20
4373 5501 3.081804 GGGTCGACCACTTTGATTCAAT 58.918 45.455 34.40 0.00 39.85 2.57
4390 5518 2.429235 TAAAAGTTGGGGCGGGGGTC 62.429 60.000 0.00 0.00 0.00 4.46
4391 5519 1.806690 ATAAAAGTTGGGGCGGGGGT 61.807 55.000 0.00 0.00 0.00 4.95
4418 5546 3.427503 CGATGGTTACATTGTTTGCCTCC 60.428 47.826 0.00 0.00 37.47 4.30
4429 5557 3.674997 AGCTGTTGAACGATGGTTACAT 58.325 40.909 0.00 0.00 40.85 2.29
4475 5603 5.640357 TGTTAAGTTGTAATAAGTCCGCCAG 59.360 40.000 0.00 0.00 0.00 4.85
4522 5650 7.496920 GGTGTTTAATGGGTTAGATGGTAGTAC 59.503 40.741 0.00 0.00 0.00 2.73
4532 5665 5.385509 CCAGTTGGTGTTTAATGGGTTAG 57.614 43.478 0.00 0.00 0.00 2.34
4608 5741 2.679059 GCTACTCTGCTCCTCAAATGCA 60.679 50.000 0.00 0.00 35.30 3.96
4685 5818 0.456482 TTGCTTCGCAAATGCATCCG 60.456 50.000 0.00 3.72 45.96 4.18


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

AutoCloner maintained by Alex Coulton.