Multiple sequence alignment - TraesCS5D01G411200

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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 TraesCS5D01G411200 chr5D 100.000 3366 0 0 1 3366 474541904 474545269 0.000000e+00 6216.0
1 TraesCS5D01G411200 chr5D 93.738 1086 21 8 630 1677 423748938 423750014 0.000000e+00 1585.0
2 TraesCS5D01G411200 chr5D 97.463 749 16 1 2618 3366 125660187 125660932 0.000000e+00 1275.0
3 TraesCS5D01G411200 chr5D 92.165 919 45 14 2460 3366 78756519 78757422 0.000000e+00 1273.0
4 TraesCS5D01G411200 chr1D 97.035 1990 24 3 630 2584 481961642 481959653 0.000000e+00 3315.0
5 TraesCS5D01G411200 chr1D 97.707 785 18 0 2582 3366 481959399 481958615 0.000000e+00 1351.0
6 TraesCS5D01G411200 chr7D 96.834 1990 27 4 630 2584 135862941 135864929 0.000000e+00 3293.0
7 TraesCS5D01G411200 chr7D 96.268 1983 39 14 630 2584 508795049 508797024 0.000000e+00 3219.0
8 TraesCS5D01G411200 chr7D 94.638 1175 23 7 630 1769 41467226 41466057 0.000000e+00 1784.0
9 TraesCS5D01G411200 chr7D 95.065 851 27 4 630 1467 574241587 574240739 0.000000e+00 1325.0
10 TraesCS5D01G411200 chr7D 97.893 712 12 1 2655 3366 65817146 65817854 0.000000e+00 1229.0
11 TraesCS5D01G411200 chr7D 96.053 608 20 3 2582 3187 135865038 135865643 0.000000e+00 987.0
12 TraesCS5D01G411200 chr7D 86.216 798 67 22 2597 3366 154004387 154005169 0.000000e+00 824.0
13 TraesCS5D01G411200 chr7B 94.761 1985 69 15 629 2584 719469220 719467242 0.000000e+00 3057.0
14 TraesCS5D01G411200 chr2B 93.333 1995 83 14 630 2586 794527294 794529276 0.000000e+00 2902.0
15 TraesCS5D01G411200 chr3A 96.850 1111 34 1 1475 2584 699771153 699772263 0.000000e+00 1857.0
16 TraesCS5D01G411200 chr3A 96.220 1111 40 2 1475 2584 713796581 713797690 0.000000e+00 1818.0
17 TraesCS5D01G411200 chr3A 95.950 1111 44 1 1475 2584 725986678 725987788 0.000000e+00 1801.0
18 TraesCS5D01G411200 chr3A 93.190 279 13 1 3088 3366 725989042 725989314 4.040000e-109 405.0
19 TraesCS5D01G411200 chr2A 96.310 1111 40 1 1475 2584 753952483 753953593 0.000000e+00 1823.0
20 TraesCS5D01G411200 chr2A 95.682 741 31 1 2625 3365 139968946 139968207 0.000000e+00 1190.0
21 TraesCS5D01G411200 chr5A 96.290 1105 40 1 1481 2584 9493865 9492761 0.000000e+00 1812.0
22 TraesCS5D01G411200 chr6A 96.040 1111 43 1 1475 2584 369655743 369656853 0.000000e+00 1807.0
23 TraesCS5D01G411200 chr7A 95.860 1111 44 2 1475 2584 107350392 107351501 0.000000e+00 1796.0
24 TraesCS5D01G411200 chr3D 98.433 766 12 0 1780 2545 152703997 152704762 0.000000e+00 1349.0
25 TraesCS5D01G411200 chr3D 94.737 855 30 5 626 1467 182084690 182085542 0.000000e+00 1315.0
26 TraesCS5D01G411200 chr3D 97.753 712 13 1 2655 3366 152705361 152706069 0.000000e+00 1223.0
27 TraesCS5D01G411200 chr3D 97.612 712 14 1 2655 3366 182087021 182087729 0.000000e+00 1218.0
28 TraesCS5D01G411200 chr3D 97.472 712 15 1 2655 3366 356975932 356975224 0.000000e+00 1212.0
29 TraesCS5D01G411200 chr3D 83.333 216 24 9 2460 2669 152704724 152704933 4.430000e-44 189.0
30 TraesCS5D01G411200 chr3D 100.000 31 0 0 2618 2648 152705301 152705331 1.300000e-04 58.4
31 TraesCS5D01G411200 chr5B 92.609 460 17 6 22 464 581217839 581218298 0.000000e+00 645.0
32 TraesCS5D01G411200 chr5B 97.024 168 5 0 460 627 581218961 581219128 1.980000e-72 283.0


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 TraesCS5D01G411200 chr5D 474541904 474545269 3365 False 6216.00 6216 100.00000 1 3366 1 chr5D.!!$F4 3365
1 TraesCS5D01G411200 chr5D 423748938 423750014 1076 False 1585.00 1585 93.73800 630 1677 1 chr5D.!!$F3 1047
2 TraesCS5D01G411200 chr5D 125660187 125660932 745 False 1275.00 1275 97.46300 2618 3366 1 chr5D.!!$F2 748
3 TraesCS5D01G411200 chr5D 78756519 78757422 903 False 1273.00 1273 92.16500 2460 3366 1 chr5D.!!$F1 906
4 TraesCS5D01G411200 chr1D 481958615 481961642 3027 True 2333.00 3315 97.37100 630 3366 2 chr1D.!!$R1 2736
5 TraesCS5D01G411200 chr7D 508795049 508797024 1975 False 3219.00 3219 96.26800 630 2584 1 chr7D.!!$F3 1954
6 TraesCS5D01G411200 chr7D 135862941 135865643 2702 False 2140.00 3293 96.44350 630 3187 2 chr7D.!!$F4 2557
7 TraesCS5D01G411200 chr7D 41466057 41467226 1169 True 1784.00 1784 94.63800 630 1769 1 chr7D.!!$R1 1139
8 TraesCS5D01G411200 chr7D 574240739 574241587 848 True 1325.00 1325 95.06500 630 1467 1 chr7D.!!$R2 837
9 TraesCS5D01G411200 chr7D 65817146 65817854 708 False 1229.00 1229 97.89300 2655 3366 1 chr7D.!!$F1 711
10 TraesCS5D01G411200 chr7D 154004387 154005169 782 False 824.00 824 86.21600 2597 3366 1 chr7D.!!$F2 769
11 TraesCS5D01G411200 chr7B 719467242 719469220 1978 True 3057.00 3057 94.76100 629 2584 1 chr7B.!!$R1 1955
12 TraesCS5D01G411200 chr2B 794527294 794529276 1982 False 2902.00 2902 93.33300 630 2586 1 chr2B.!!$F1 1956
13 TraesCS5D01G411200 chr3A 699771153 699772263 1110 False 1857.00 1857 96.85000 1475 2584 1 chr3A.!!$F1 1109
14 TraesCS5D01G411200 chr3A 713796581 713797690 1109 False 1818.00 1818 96.22000 1475 2584 1 chr3A.!!$F2 1109
15 TraesCS5D01G411200 chr3A 725986678 725989314 2636 False 1103.00 1801 94.57000 1475 3366 2 chr3A.!!$F3 1891
16 TraesCS5D01G411200 chr2A 753952483 753953593 1110 False 1823.00 1823 96.31000 1475 2584 1 chr2A.!!$F1 1109
17 TraesCS5D01G411200 chr2A 139968207 139968946 739 True 1190.00 1190 95.68200 2625 3365 1 chr2A.!!$R1 740
18 TraesCS5D01G411200 chr5A 9492761 9493865 1104 True 1812.00 1812 96.29000 1481 2584 1 chr5A.!!$R1 1103
19 TraesCS5D01G411200 chr6A 369655743 369656853 1110 False 1807.00 1807 96.04000 1475 2584 1 chr6A.!!$F1 1109
20 TraesCS5D01G411200 chr7A 107350392 107351501 1109 False 1796.00 1796 95.86000 1475 2584 1 chr7A.!!$F1 1109
21 TraesCS5D01G411200 chr3D 182084690 182087729 3039 False 1266.50 1315 96.17450 626 3366 2 chr3D.!!$F2 2740
22 TraesCS5D01G411200 chr3D 356975224 356975932 708 True 1212.00 1212 97.47200 2655 3366 1 chr3D.!!$R1 711
23 TraesCS5D01G411200 chr3D 152703997 152706069 2072 False 704.85 1349 94.87975 1780 3366 4 chr3D.!!$F1 1586
24 TraesCS5D01G411200 chr5B 581217839 581219128 1289 False 464.00 645 94.81650 22 627 2 chr5B.!!$F1 605

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
569 587 0.034337 TCCCCTTCGTACACTTGTGC 59.966 55.0 0.1 0.00 0.00 4.57 F
582 600 0.099968 CTTGTGCCATTCTCGCATGG 59.900 55.0 0.0 4.24 46.04 3.66 F
619 637 0.179234 TGCGGAGTTGGAACTGAACA 59.821 50.0 0.0 0.00 39.88 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2616 2.138320 TGCTTCTGCTTGAACTCTTCG 58.862 47.619 0.0 0.0 40.48 3.79 R
2281 2853 2.625639 AGATCACCCACCAGAAACTCT 58.374 47.619 0.0 0.0 0.00 3.24 R
2686 4225 9.739276 ATGAGAACTTTTATGGTTGAGAACATA 57.261 29.630 0.0 0.0 0.00 2.29 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
18 19 3.458872 CACGAGGGATTAGCAAGCA 57.541 52.632 0.00 0.00 0.00 3.91
19 20 1.009829 CACGAGGGATTAGCAAGCAC 58.990 55.000 0.00 0.00 0.00 4.40
20 21 0.460284 ACGAGGGATTAGCAAGCACG 60.460 55.000 0.00 0.00 0.00 5.34
23 24 2.709475 GGATTAGCAAGCACGCGG 59.291 61.111 12.47 0.00 36.85 6.46
52 53 3.633525 GCATGATTAGTTTGGCATCCTCA 59.366 43.478 0.00 0.00 0.00 3.86
59 60 6.553953 TTAGTTTGGCATCCTCAGTATACA 57.446 37.500 5.50 0.00 0.00 2.29
98 104 1.487482 CATGCATGGGAGTACGTACG 58.513 55.000 19.40 15.01 0.00 3.67
107 113 2.159028 GGGAGTACGTACGGACTAGAGT 60.159 54.545 32.23 11.32 39.83 3.24
116 122 0.240145 CGGACTAGAGTGTCAACGCA 59.760 55.000 0.00 0.00 38.61 5.24
133 139 1.990060 CACCCCATCTCCGGTGTCT 60.990 63.158 0.00 0.00 43.84 3.41
154 168 1.218316 CCTCCTGGCACGGTAGAAC 59.782 63.158 0.00 0.00 0.00 3.01
160 174 2.267961 GCACGGTAGAACCCCCAG 59.732 66.667 0.00 0.00 33.75 4.45
186 200 1.002403 TCCCGGCCTTCCATCTACA 59.998 57.895 0.00 0.00 0.00 2.74
188 202 1.132977 TCCCGGCCTTCCATCTACATA 60.133 52.381 0.00 0.00 0.00 2.29
261 279 3.996888 GGCAATAGCGCGCCGTAC 61.997 66.667 30.33 13.97 43.41 3.67
271 289 1.436336 GCGCCGTACAGTGTAGGAT 59.564 57.895 21.62 0.00 0.00 3.24
348 366 3.496884 GTGGTGCTGATCTGTCGTTTTTA 59.503 43.478 1.27 0.00 0.00 1.52
455 473 3.504520 ACCAAGTTGTCGTGAAACTTTGT 59.495 39.130 1.45 9.38 43.60 2.83
460 478 4.214545 AGTTGTCGTGAAACTTTGTGACAA 59.785 37.500 0.00 0.00 42.21 3.18
495 513 9.006215 GTACTAATAAATCCACAAACAATTCGC 57.994 33.333 0.00 0.00 0.00 4.70
496 514 7.826690 ACTAATAAATCCACAAACAATTCGCT 58.173 30.769 0.00 0.00 0.00 4.93
497 515 7.968405 ACTAATAAATCCACAAACAATTCGCTC 59.032 33.333 0.00 0.00 0.00 5.03
498 516 4.853924 AAATCCACAAACAATTCGCTCT 57.146 36.364 0.00 0.00 0.00 4.09
499 517 4.425577 AATCCACAAACAATTCGCTCTC 57.574 40.909 0.00 0.00 0.00 3.20
500 518 2.844946 TCCACAAACAATTCGCTCTCA 58.155 42.857 0.00 0.00 0.00 3.27
501 519 2.807967 TCCACAAACAATTCGCTCTCAG 59.192 45.455 0.00 0.00 0.00 3.35
502 520 2.807967 CCACAAACAATTCGCTCTCAGA 59.192 45.455 0.00 0.00 0.00 3.27
503 521 3.250762 CCACAAACAATTCGCTCTCAGAA 59.749 43.478 0.00 0.00 0.00 3.02
504 522 4.461405 CACAAACAATTCGCTCTCAGAAG 58.539 43.478 0.00 0.00 0.00 2.85
505 523 4.024556 CACAAACAATTCGCTCTCAGAAGT 60.025 41.667 0.00 0.00 0.00 3.01
506 524 4.212214 ACAAACAATTCGCTCTCAGAAGTC 59.788 41.667 0.00 0.00 0.00 3.01
507 525 3.667497 ACAATTCGCTCTCAGAAGTCA 57.333 42.857 0.00 0.00 0.00 3.41
508 526 3.583806 ACAATTCGCTCTCAGAAGTCAG 58.416 45.455 0.00 0.00 0.00 3.51
509 527 3.256879 ACAATTCGCTCTCAGAAGTCAGA 59.743 43.478 0.00 0.00 0.00 3.27
510 528 4.240888 CAATTCGCTCTCAGAAGTCAGAA 58.759 43.478 0.00 0.00 0.00 3.02
511 529 4.527509 ATTCGCTCTCAGAAGTCAGAAA 57.472 40.909 0.00 0.00 0.00 2.52
512 530 4.322080 TTCGCTCTCAGAAGTCAGAAAA 57.678 40.909 0.00 0.00 0.00 2.29
513 531 3.906998 TCGCTCTCAGAAGTCAGAAAAG 58.093 45.455 0.00 0.00 0.00 2.27
514 532 2.992543 CGCTCTCAGAAGTCAGAAAAGG 59.007 50.000 0.00 0.00 0.00 3.11
515 533 2.741517 GCTCTCAGAAGTCAGAAAAGGC 59.258 50.000 0.00 0.00 0.00 4.35
516 534 2.992543 CTCTCAGAAGTCAGAAAAGGCG 59.007 50.000 0.00 0.00 0.00 5.52
517 535 2.072298 CTCAGAAGTCAGAAAAGGCGG 58.928 52.381 0.00 0.00 0.00 6.13
518 536 1.416401 TCAGAAGTCAGAAAAGGCGGT 59.584 47.619 0.00 0.00 0.00 5.68
519 537 2.631062 TCAGAAGTCAGAAAAGGCGGTA 59.369 45.455 0.00 0.00 0.00 4.02
520 538 3.070446 TCAGAAGTCAGAAAAGGCGGTAA 59.930 43.478 0.00 0.00 0.00 2.85
521 539 3.813166 CAGAAGTCAGAAAAGGCGGTAAA 59.187 43.478 0.00 0.00 0.00 2.01
522 540 3.813724 AGAAGTCAGAAAAGGCGGTAAAC 59.186 43.478 0.00 0.00 0.00 2.01
523 541 2.501261 AGTCAGAAAAGGCGGTAAACC 58.499 47.619 0.00 0.00 0.00 3.27
524 542 2.105993 AGTCAGAAAAGGCGGTAAACCT 59.894 45.455 0.00 0.00 40.02 3.50
525 543 3.325716 AGTCAGAAAAGGCGGTAAACCTA 59.674 43.478 0.00 0.00 36.14 3.08
526 544 4.019591 AGTCAGAAAAGGCGGTAAACCTAT 60.020 41.667 0.00 0.00 36.14 2.57
527 545 4.331992 GTCAGAAAAGGCGGTAAACCTATC 59.668 45.833 0.00 0.00 36.14 2.08
528 546 4.224370 TCAGAAAAGGCGGTAAACCTATCT 59.776 41.667 0.00 0.00 36.14 1.98
529 547 4.941873 CAGAAAAGGCGGTAAACCTATCTT 59.058 41.667 0.00 0.00 36.14 2.40
530 548 5.064834 CAGAAAAGGCGGTAAACCTATCTTC 59.935 44.000 0.00 0.00 36.14 2.87
531 549 4.563140 AAAGGCGGTAAACCTATCTTCA 57.437 40.909 0.00 0.00 36.14 3.02
532 550 3.538634 AGGCGGTAAACCTATCTTCAC 57.461 47.619 0.00 0.00 35.10 3.18
533 551 3.105283 AGGCGGTAAACCTATCTTCACT 58.895 45.455 0.00 0.00 35.10 3.41
534 552 3.518303 AGGCGGTAAACCTATCTTCACTT 59.482 43.478 0.00 0.00 35.10 3.16
535 553 4.019591 AGGCGGTAAACCTATCTTCACTTT 60.020 41.667 0.00 0.00 35.10 2.66
536 554 4.331992 GGCGGTAAACCTATCTTCACTTTC 59.668 45.833 0.00 0.00 0.00 2.62
537 555 4.933400 GCGGTAAACCTATCTTCACTTTCA 59.067 41.667 0.00 0.00 0.00 2.69
538 556 5.063564 GCGGTAAACCTATCTTCACTTTCAG 59.936 44.000 0.00 0.00 0.00 3.02
539 557 6.395629 CGGTAAACCTATCTTCACTTTCAGA 58.604 40.000 0.00 0.00 0.00 3.27
540 558 6.872020 CGGTAAACCTATCTTCACTTTCAGAA 59.128 38.462 0.00 0.00 0.00 3.02
541 559 7.386848 CGGTAAACCTATCTTCACTTTCAGAAA 59.613 37.037 0.00 0.00 0.00 2.52
542 560 8.504815 GGTAAACCTATCTTCACTTTCAGAAAC 58.495 37.037 0.00 0.00 0.00 2.78
543 561 7.511959 AAACCTATCTTCACTTTCAGAAACC 57.488 36.000 0.00 0.00 0.00 3.27
544 562 6.187727 ACCTATCTTCACTTTCAGAAACCA 57.812 37.500 0.00 0.00 0.00 3.67
545 563 6.784031 ACCTATCTTCACTTTCAGAAACCAT 58.216 36.000 0.00 0.00 0.00 3.55
546 564 7.918076 ACCTATCTTCACTTTCAGAAACCATA 58.082 34.615 0.00 0.00 0.00 2.74
547 565 8.383175 ACCTATCTTCACTTTCAGAAACCATAA 58.617 33.333 0.00 0.00 0.00 1.90
548 566 8.669243 CCTATCTTCACTTTCAGAAACCATAAC 58.331 37.037 0.00 0.00 0.00 1.89
549 567 9.442047 CTATCTTCACTTTCAGAAACCATAACT 57.558 33.333 0.00 0.00 0.00 2.24
550 568 8.697507 ATCTTCACTTTCAGAAACCATAACTT 57.302 30.769 0.00 0.00 0.00 2.66
551 569 8.154649 TCTTCACTTTCAGAAACCATAACTTC 57.845 34.615 0.00 0.00 0.00 3.01
552 570 6.877611 TCACTTTCAGAAACCATAACTTCC 57.122 37.500 0.00 0.00 0.00 3.46
553 571 5.768164 TCACTTTCAGAAACCATAACTTCCC 59.232 40.000 0.00 0.00 0.00 3.97
554 572 5.048013 CACTTTCAGAAACCATAACTTCCCC 60.048 44.000 0.00 0.00 0.00 4.81
555 573 5.162980 ACTTTCAGAAACCATAACTTCCCCT 60.163 40.000 0.00 0.00 0.00 4.79
556 574 5.333566 TTCAGAAACCATAACTTCCCCTT 57.666 39.130 0.00 0.00 0.00 3.95
557 575 4.918588 TCAGAAACCATAACTTCCCCTTC 58.081 43.478 0.00 0.00 0.00 3.46
558 576 3.689649 CAGAAACCATAACTTCCCCTTCG 59.310 47.826 0.00 0.00 0.00 3.79
559 577 3.329814 AGAAACCATAACTTCCCCTTCGT 59.670 43.478 0.00 0.00 0.00 3.85
560 578 4.533311 AGAAACCATAACTTCCCCTTCGTA 59.467 41.667 0.00 0.00 0.00 3.43
561 579 3.900966 ACCATAACTTCCCCTTCGTAC 57.099 47.619 0.00 0.00 0.00 3.67
562 580 3.175594 ACCATAACTTCCCCTTCGTACA 58.824 45.455 0.00 0.00 0.00 2.90
563 581 3.055602 ACCATAACTTCCCCTTCGTACAC 60.056 47.826 0.00 0.00 0.00 2.90
564 582 3.197116 CCATAACTTCCCCTTCGTACACT 59.803 47.826 0.00 0.00 0.00 3.55
565 583 4.323257 CCATAACTTCCCCTTCGTACACTT 60.323 45.833 0.00 0.00 0.00 3.16
566 584 2.833631 ACTTCCCCTTCGTACACTTG 57.166 50.000 0.00 0.00 0.00 3.16
567 585 2.044758 ACTTCCCCTTCGTACACTTGT 58.955 47.619 0.00 0.00 0.00 3.16
568 586 2.224209 ACTTCCCCTTCGTACACTTGTG 60.224 50.000 0.00 0.00 0.00 3.33
569 587 0.034337 TCCCCTTCGTACACTTGTGC 59.966 55.000 0.10 0.00 0.00 4.57
570 588 0.953960 CCCCTTCGTACACTTGTGCC 60.954 60.000 0.10 0.00 0.00 5.01
571 589 0.250124 CCCTTCGTACACTTGTGCCA 60.250 55.000 0.10 0.00 0.00 4.92
572 590 1.610624 CCCTTCGTACACTTGTGCCAT 60.611 52.381 0.10 0.00 0.00 4.40
573 591 2.151202 CCTTCGTACACTTGTGCCATT 58.849 47.619 0.10 0.00 0.00 3.16
574 592 2.159627 CCTTCGTACACTTGTGCCATTC 59.840 50.000 0.10 0.00 0.00 2.67
575 593 2.831685 TCGTACACTTGTGCCATTCT 57.168 45.000 0.10 0.00 0.00 2.40
576 594 2.683968 TCGTACACTTGTGCCATTCTC 58.316 47.619 0.10 0.00 0.00 2.87
577 595 1.390123 CGTACACTTGTGCCATTCTCG 59.610 52.381 0.10 0.00 0.00 4.04
578 596 1.128692 GTACACTTGTGCCATTCTCGC 59.871 52.381 0.10 0.00 0.00 5.03
579 597 0.534877 ACACTTGTGCCATTCTCGCA 60.535 50.000 0.10 0.00 0.00 5.10
580 598 0.806868 CACTTGTGCCATTCTCGCAT 59.193 50.000 0.00 0.00 38.76 4.73
581 599 0.806868 ACTTGTGCCATTCTCGCATG 59.193 50.000 0.00 0.00 38.76 4.06
582 600 0.099968 CTTGTGCCATTCTCGCATGG 59.900 55.000 0.00 4.24 46.04 3.66
583 601 1.314534 TTGTGCCATTCTCGCATGGG 61.315 55.000 2.76 2.76 43.76 4.00
584 602 2.124193 TGCCATTCTCGCATGGGG 60.124 61.111 10.21 1.00 43.76 4.96
585 603 2.192979 GCCATTCTCGCATGGGGA 59.807 61.111 10.21 3.50 43.76 4.81
586 604 1.453745 GCCATTCTCGCATGGGGAA 60.454 57.895 10.21 12.12 43.76 3.97
587 605 1.450531 GCCATTCTCGCATGGGGAAG 61.451 60.000 10.21 0.91 43.76 3.46
588 606 0.820891 CCATTCTCGCATGGGGAAGG 60.821 60.000 10.21 12.82 40.29 3.46
589 607 1.152881 ATTCTCGCATGGGGAAGGC 60.153 57.895 10.21 0.00 0.00 4.35
590 608 2.631012 ATTCTCGCATGGGGAAGGCC 62.631 60.000 10.21 0.00 29.52 5.19
591 609 3.801997 CTCGCATGGGGAAGGCCT 61.802 66.667 10.21 0.00 29.52 5.19
592 610 3.338250 TCGCATGGGGAAGGCCTT 61.338 61.111 20.65 20.65 29.52 4.35
593 611 2.362889 CGCATGGGGAAGGCCTTT 60.363 61.111 21.54 2.85 29.52 3.11
594 612 2.418083 CGCATGGGGAAGGCCTTTC 61.418 63.158 21.54 18.88 34.93 2.62
595 613 1.000866 GCATGGGGAAGGCCTTTCT 59.999 57.895 23.45 0.30 36.03 2.52
596 614 1.325476 GCATGGGGAAGGCCTTTCTG 61.325 60.000 23.45 14.78 36.03 3.02
597 615 1.000866 ATGGGGAAGGCCTTTCTGC 59.999 57.895 23.45 8.57 36.03 4.26
605 623 2.672996 GCCTTTCTGCCTTGCGGA 60.673 61.111 0.00 0.00 42.66 5.54
606 624 2.694760 GCCTTTCTGCCTTGCGGAG 61.695 63.158 0.00 0.00 45.12 4.63
607 625 1.302832 CCTTTCTGCCTTGCGGAGT 60.303 57.895 0.00 0.00 45.12 3.85
608 626 0.890996 CCTTTCTGCCTTGCGGAGTT 60.891 55.000 0.00 0.00 45.12 3.01
609 627 0.239347 CTTTCTGCCTTGCGGAGTTG 59.761 55.000 0.00 0.00 45.12 3.16
610 628 1.172180 TTTCTGCCTTGCGGAGTTGG 61.172 55.000 0.00 0.00 45.12 3.77
611 629 2.032528 CTGCCTTGCGGAGTTGGA 59.967 61.111 0.00 0.00 37.02 3.53
612 630 1.600636 CTGCCTTGCGGAGTTGGAA 60.601 57.895 0.00 0.00 37.02 3.53
613 631 1.856265 CTGCCTTGCGGAGTTGGAAC 61.856 60.000 0.00 0.00 37.02 3.62
614 632 1.600916 GCCTTGCGGAGTTGGAACT 60.601 57.895 0.00 0.00 43.16 3.01
615 633 1.856265 GCCTTGCGGAGTTGGAACTG 61.856 60.000 0.00 0.00 39.88 3.16
616 634 0.250295 CCTTGCGGAGTTGGAACTGA 60.250 55.000 0.00 0.00 39.88 3.41
617 635 1.593196 CTTGCGGAGTTGGAACTGAA 58.407 50.000 0.00 0.00 39.88 3.02
618 636 1.264288 CTTGCGGAGTTGGAACTGAAC 59.736 52.381 0.00 0.00 39.88 3.18
619 637 0.179234 TGCGGAGTTGGAACTGAACA 59.821 50.000 0.00 0.00 39.88 3.18
620 638 1.202758 TGCGGAGTTGGAACTGAACAT 60.203 47.619 0.00 0.00 39.88 2.71
621 639 1.464997 GCGGAGTTGGAACTGAACATC 59.535 52.381 0.00 0.00 39.88 3.06
622 640 2.766313 CGGAGTTGGAACTGAACATCA 58.234 47.619 0.00 0.00 39.88 3.07
623 641 2.480419 CGGAGTTGGAACTGAACATCAC 59.520 50.000 0.00 0.00 39.88 3.06
624 642 2.480419 GGAGTTGGAACTGAACATCACG 59.520 50.000 0.00 0.00 39.88 4.35
639 657 0.249699 TCACGCGGTGAGTGAATTGT 60.250 50.000 12.47 0.00 44.56 2.71
707 725 1.066430 TCTAGCGCGTCCCAAAAATCT 60.066 47.619 8.43 0.00 0.00 2.40
911 932 0.250945 ACTCCACTCGCTCACTCTCA 60.251 55.000 0.00 0.00 0.00 3.27
1381 1404 3.134442 ACGAGGGTTTGTGTTAGTGGTAA 59.866 43.478 0.00 0.00 0.00 2.85
1628 2038 2.937591 ACAGTGATTTTGCAAGCATCG 58.062 42.857 13.29 5.07 29.10 3.84
2005 2577 3.274288 GGTTGAGGATGTCACCAAGATC 58.726 50.000 0.00 0.00 33.71 2.75
2269 2841 0.617820 GGGACTGGCTGGTAGAGGAA 60.618 60.000 0.00 0.00 0.00 3.36
2281 2853 5.337652 GCTGGTAGAGGAAAAGAAGAAGCTA 60.338 44.000 0.00 0.00 0.00 3.32
2804 5068 3.366121 CAGTTCACACATAGCAGTTCTCG 59.634 47.826 0.00 0.00 0.00 4.04
2923 5187 0.177604 CTCATCCTGGTGCTCTGGAC 59.822 60.000 8.01 0.00 44.59 4.02
3153 5426 0.324943 GGCAGGACCAGTAGAAGCAA 59.675 55.000 0.00 0.00 38.86 3.91
3161 5434 4.127171 GACCAGTAGAAGCAACAGTTGAA 58.873 43.478 17.99 0.00 0.00 2.69
3313 5640 3.709653 TGGTAGTGAGTTCTGGTTGTCTT 59.290 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.009829 GTGCTTGCTAATCCCTCGTG 58.990 55.000 0.00 0.00 0.00 4.35
1 2 0.460284 CGTGCTTGCTAATCCCTCGT 60.460 55.000 0.00 0.00 0.00 4.18
2 3 1.766143 GCGTGCTTGCTAATCCCTCG 61.766 60.000 0.00 0.00 0.00 4.63
3 4 1.766143 CGCGTGCTTGCTAATCCCTC 61.766 60.000 0.00 0.00 0.00 4.30
4 5 1.815421 CGCGTGCTTGCTAATCCCT 60.815 57.895 0.00 0.00 0.00 4.20
5 6 2.709475 CGCGTGCTTGCTAATCCC 59.291 61.111 0.00 0.00 0.00 3.85
6 7 2.709475 CCGCGTGCTTGCTAATCC 59.291 61.111 4.92 0.00 0.00 3.01
7 8 2.023320 GCCGCGTGCTTGCTAATC 59.977 61.111 4.92 0.00 36.87 1.75
8 9 3.508840 GGCCGCGTGCTTGCTAAT 61.509 61.111 17.07 0.00 40.92 1.73
13 14 3.576356 CATAGGGCCGCGTGCTTG 61.576 66.667 17.07 8.14 40.92 4.01
17 18 3.653009 CATGCATAGGGCCGCGTG 61.653 66.667 4.92 9.27 43.89 5.34
18 19 2.680974 AATCATGCATAGGGCCGCGT 62.681 55.000 4.92 0.00 43.89 6.01
19 20 0.673333 TAATCATGCATAGGGCCGCG 60.673 55.000 0.00 0.00 43.89 6.46
20 21 1.089920 CTAATCATGCATAGGGCCGC 58.910 55.000 0.00 0.00 43.89 6.53
23 24 3.305608 GCCAAACTAATCATGCATAGGGC 60.306 47.826 0.00 0.00 45.13 5.19
31 32 4.885907 ACTGAGGATGCCAAACTAATCATG 59.114 41.667 0.00 0.00 0.00 3.07
52 53 2.548707 CCGGTCTGCATGCATGTATACT 60.549 50.000 26.79 0.00 0.00 2.12
59 60 3.942377 TTGGCCGGTCTGCATGCAT 62.942 57.895 22.97 0.00 0.00 3.96
98 104 1.669211 GGTGCGTTGACACTCTAGTCC 60.669 57.143 0.00 0.00 40.52 3.85
107 113 1.003839 GAGATGGGGTGCGTTGACA 60.004 57.895 0.00 0.00 0.00 3.58
116 122 1.686110 GAGACACCGGAGATGGGGT 60.686 63.158 9.46 0.00 36.87 4.95
133 139 1.379977 CTACCGTGCCAGGAGGAGA 60.380 63.158 1.23 0.00 36.89 3.71
175 189 5.520632 CACGTACCAGTATGTAGATGGAAG 58.479 45.833 2.45 0.00 37.54 3.46
186 200 1.890625 TTGGCCGCACGTACCAGTAT 61.891 55.000 0.00 0.00 34.28 2.12
188 202 2.741486 ATTTGGCCGCACGTACCAGT 62.741 55.000 0.00 0.00 34.28 4.00
260 278 0.759436 CCGGCCCTATCCTACACTGT 60.759 60.000 0.00 0.00 0.00 3.55
261 279 1.472662 CCCGGCCCTATCCTACACTG 61.473 65.000 0.00 0.00 0.00 3.66
348 366 3.197333 CAGACAGAGGGAACATCACAGAT 59.803 47.826 0.00 0.00 0.00 2.90
469 487 9.006215 GCGAATTGTTTGTGGATTTATTAGTAC 57.994 33.333 0.00 0.00 0.00 2.73
470 488 8.952278 AGCGAATTGTTTGTGGATTTATTAGTA 58.048 29.630 0.00 0.00 0.00 1.82
472 490 8.184192 AGAGCGAATTGTTTGTGGATTTATTAG 58.816 33.333 0.00 0.00 0.00 1.73
473 491 8.050778 AGAGCGAATTGTTTGTGGATTTATTA 57.949 30.769 0.00 0.00 0.00 0.98
474 492 6.924111 AGAGCGAATTGTTTGTGGATTTATT 58.076 32.000 0.00 0.00 0.00 1.40
475 493 6.150976 TGAGAGCGAATTGTTTGTGGATTTAT 59.849 34.615 0.00 0.00 0.00 1.40
476 494 5.471797 TGAGAGCGAATTGTTTGTGGATTTA 59.528 36.000 0.00 0.00 0.00 1.40
477 495 4.278170 TGAGAGCGAATTGTTTGTGGATTT 59.722 37.500 0.00 0.00 0.00 2.17
478 496 3.820467 TGAGAGCGAATTGTTTGTGGATT 59.180 39.130 0.00 0.00 0.00 3.01
479 497 3.411446 TGAGAGCGAATTGTTTGTGGAT 58.589 40.909 0.00 0.00 0.00 3.41
480 498 2.807967 CTGAGAGCGAATTGTTTGTGGA 59.192 45.455 0.00 0.00 0.00 4.02
481 499 2.807967 TCTGAGAGCGAATTGTTTGTGG 59.192 45.455 0.00 0.00 0.00 4.17
482 500 4.024556 ACTTCTGAGAGCGAATTGTTTGTG 60.025 41.667 0.00 0.00 0.00 3.33
483 501 4.130118 ACTTCTGAGAGCGAATTGTTTGT 58.870 39.130 0.00 0.00 0.00 2.83
484 502 4.212004 TGACTTCTGAGAGCGAATTGTTTG 59.788 41.667 0.00 0.00 0.00 2.93
485 503 4.380531 TGACTTCTGAGAGCGAATTGTTT 58.619 39.130 0.00 0.00 0.00 2.83
486 504 3.993081 CTGACTTCTGAGAGCGAATTGTT 59.007 43.478 0.00 0.00 0.00 2.83
487 505 3.256879 TCTGACTTCTGAGAGCGAATTGT 59.743 43.478 0.00 0.00 0.00 2.71
488 506 3.842820 TCTGACTTCTGAGAGCGAATTG 58.157 45.455 0.00 0.00 0.00 2.32
489 507 4.527509 TTCTGACTTCTGAGAGCGAATT 57.472 40.909 0.00 0.00 0.00 2.17
490 508 4.527509 TTTCTGACTTCTGAGAGCGAAT 57.472 40.909 0.00 0.00 0.00 3.34
491 509 4.302455 CTTTTCTGACTTCTGAGAGCGAA 58.698 43.478 0.00 0.00 0.00 4.70
492 510 3.305676 CCTTTTCTGACTTCTGAGAGCGA 60.306 47.826 0.00 0.00 0.00 4.93
493 511 2.992543 CCTTTTCTGACTTCTGAGAGCG 59.007 50.000 0.00 0.00 0.00 5.03
494 512 2.741517 GCCTTTTCTGACTTCTGAGAGC 59.258 50.000 0.00 0.00 0.00 4.09
495 513 2.992543 CGCCTTTTCTGACTTCTGAGAG 59.007 50.000 0.00 0.00 0.00 3.20
496 514 2.289072 CCGCCTTTTCTGACTTCTGAGA 60.289 50.000 0.00 0.00 0.00 3.27
497 515 2.072298 CCGCCTTTTCTGACTTCTGAG 58.928 52.381 0.00 0.00 0.00 3.35
498 516 1.416401 ACCGCCTTTTCTGACTTCTGA 59.584 47.619 0.00 0.00 0.00 3.27
499 517 1.884235 ACCGCCTTTTCTGACTTCTG 58.116 50.000 0.00 0.00 0.00 3.02
500 518 3.764237 TTACCGCCTTTTCTGACTTCT 57.236 42.857 0.00 0.00 0.00 2.85
501 519 3.058432 GGTTTACCGCCTTTTCTGACTTC 60.058 47.826 0.00 0.00 0.00 3.01
502 520 2.882761 GGTTTACCGCCTTTTCTGACTT 59.117 45.455 0.00 0.00 0.00 3.01
503 521 2.105993 AGGTTTACCGCCTTTTCTGACT 59.894 45.455 0.00 0.00 42.08 3.41
504 522 2.501261 AGGTTTACCGCCTTTTCTGAC 58.499 47.619 0.00 0.00 42.08 3.51
505 523 2.943036 AGGTTTACCGCCTTTTCTGA 57.057 45.000 0.00 0.00 42.08 3.27
506 524 4.514401 AGATAGGTTTACCGCCTTTTCTG 58.486 43.478 0.00 0.00 42.08 3.02
507 525 4.838904 AGATAGGTTTACCGCCTTTTCT 57.161 40.909 0.00 0.00 42.08 2.52
508 526 4.939439 TGAAGATAGGTTTACCGCCTTTTC 59.061 41.667 0.00 0.00 42.08 2.29
509 527 4.698780 GTGAAGATAGGTTTACCGCCTTTT 59.301 41.667 0.00 0.00 42.08 2.27
510 528 4.019591 AGTGAAGATAGGTTTACCGCCTTT 60.020 41.667 0.00 0.00 42.08 3.11
511 529 3.518303 AGTGAAGATAGGTTTACCGCCTT 59.482 43.478 0.00 0.00 42.08 4.35
512 530 3.105283 AGTGAAGATAGGTTTACCGCCT 58.895 45.455 0.00 0.00 42.08 5.52
513 531 3.538634 AGTGAAGATAGGTTTACCGCC 57.461 47.619 0.00 0.00 42.08 6.13
514 532 4.933400 TGAAAGTGAAGATAGGTTTACCGC 59.067 41.667 0.00 0.00 42.08 5.68
515 533 6.395629 TCTGAAAGTGAAGATAGGTTTACCG 58.604 40.000 0.00 0.00 36.66 4.02
516 534 8.504815 GTTTCTGAAAGTGAAGATAGGTTTACC 58.495 37.037 2.48 0.00 33.76 2.85
517 535 8.504815 GGTTTCTGAAAGTGAAGATAGGTTTAC 58.495 37.037 2.48 0.00 33.76 2.01
518 536 8.215050 TGGTTTCTGAAAGTGAAGATAGGTTTA 58.785 33.333 2.48 0.00 33.76 2.01
519 537 7.060421 TGGTTTCTGAAAGTGAAGATAGGTTT 58.940 34.615 2.48 0.00 33.76 3.27
520 538 6.601332 TGGTTTCTGAAAGTGAAGATAGGTT 58.399 36.000 2.48 0.00 33.76 3.50
521 539 6.187727 TGGTTTCTGAAAGTGAAGATAGGT 57.812 37.500 2.48 0.00 33.76 3.08
522 540 8.669243 GTTATGGTTTCTGAAAGTGAAGATAGG 58.331 37.037 2.48 0.00 33.76 2.57
523 541 9.442047 AGTTATGGTTTCTGAAAGTGAAGATAG 57.558 33.333 2.48 0.00 33.76 2.08
524 542 9.793259 AAGTTATGGTTTCTGAAAGTGAAGATA 57.207 29.630 2.48 0.00 33.76 1.98
525 543 8.697507 AAGTTATGGTTTCTGAAAGTGAAGAT 57.302 30.769 2.48 0.00 33.76 2.40
526 544 7.228706 GGAAGTTATGGTTTCTGAAAGTGAAGA 59.771 37.037 2.48 0.00 33.76 2.87
527 545 7.363431 GGAAGTTATGGTTTCTGAAAGTGAAG 58.637 38.462 2.48 0.00 33.76 3.02
528 546 6.264518 GGGAAGTTATGGTTTCTGAAAGTGAA 59.735 38.462 2.48 0.00 33.76 3.18
529 547 5.768164 GGGAAGTTATGGTTTCTGAAAGTGA 59.232 40.000 2.48 0.00 33.76 3.41
530 548 5.048013 GGGGAAGTTATGGTTTCTGAAAGTG 60.048 44.000 2.48 0.00 33.76 3.16
531 549 5.077564 GGGGAAGTTATGGTTTCTGAAAGT 58.922 41.667 2.48 0.00 33.76 2.66
532 550 5.325239 AGGGGAAGTTATGGTTTCTGAAAG 58.675 41.667 2.48 0.00 0.00 2.62
533 551 5.333566 AGGGGAAGTTATGGTTTCTGAAA 57.666 39.130 0.00 0.00 0.00 2.69
534 552 5.321927 GAAGGGGAAGTTATGGTTTCTGAA 58.678 41.667 0.00 0.00 0.00 3.02
535 553 4.564821 CGAAGGGGAAGTTATGGTTTCTGA 60.565 45.833 0.00 0.00 0.00 3.27
536 554 3.689649 CGAAGGGGAAGTTATGGTTTCTG 59.310 47.826 0.00 0.00 0.00 3.02
537 555 3.329814 ACGAAGGGGAAGTTATGGTTTCT 59.670 43.478 0.00 0.00 0.00 2.52
538 556 3.682696 ACGAAGGGGAAGTTATGGTTTC 58.317 45.455 0.00 0.00 0.00 2.78
539 557 3.801307 ACGAAGGGGAAGTTATGGTTT 57.199 42.857 0.00 0.00 0.00 3.27
540 558 3.583966 TGTACGAAGGGGAAGTTATGGTT 59.416 43.478 0.00 0.00 0.00 3.67
541 559 3.055602 GTGTACGAAGGGGAAGTTATGGT 60.056 47.826 0.00 0.00 0.00 3.55
542 560 3.197116 AGTGTACGAAGGGGAAGTTATGG 59.803 47.826 0.00 0.00 0.00 2.74
543 561 4.467198 AGTGTACGAAGGGGAAGTTATG 57.533 45.455 0.00 0.00 0.00 1.90
544 562 4.285260 ACAAGTGTACGAAGGGGAAGTTAT 59.715 41.667 0.00 0.00 0.00 1.89
545 563 3.642848 ACAAGTGTACGAAGGGGAAGTTA 59.357 43.478 0.00 0.00 0.00 2.24
546 564 2.436911 ACAAGTGTACGAAGGGGAAGTT 59.563 45.455 0.00 0.00 0.00 2.66
547 565 2.044758 ACAAGTGTACGAAGGGGAAGT 58.955 47.619 0.00 0.00 0.00 3.01
548 566 2.413837 CACAAGTGTACGAAGGGGAAG 58.586 52.381 0.00 0.00 0.00 3.46
549 567 1.541670 GCACAAGTGTACGAAGGGGAA 60.542 52.381 1.79 0.00 0.00 3.97
550 568 0.034337 GCACAAGTGTACGAAGGGGA 59.966 55.000 1.79 0.00 0.00 4.81
551 569 0.953960 GGCACAAGTGTACGAAGGGG 60.954 60.000 1.79 0.00 0.00 4.79
552 570 0.250124 TGGCACAAGTGTACGAAGGG 60.250 55.000 1.79 0.00 31.92 3.95
553 571 3.299050 TGGCACAAGTGTACGAAGG 57.701 52.632 1.79 0.00 31.92 3.46
558 576 3.440646 TGCGAGAATGGCACAAGTGTAC 61.441 50.000 1.79 0.00 44.48 2.90
559 577 1.270571 TGCGAGAATGGCACAAGTGTA 60.271 47.619 1.79 0.00 44.48 2.90
560 578 0.534877 TGCGAGAATGGCACAAGTGT 60.535 50.000 1.79 0.00 44.48 3.55
561 579 2.246841 TGCGAGAATGGCACAAGTG 58.753 52.632 0.00 0.00 44.48 3.16
562 580 4.798433 TGCGAGAATGGCACAAGT 57.202 50.000 0.00 0.00 44.48 3.16
568 586 1.450531 CTTCCCCATGCGAGAATGGC 61.451 60.000 4.51 0.00 45.03 4.40
569 587 0.820891 CCTTCCCCATGCGAGAATGG 60.821 60.000 3.01 3.01 45.82 3.16
570 588 1.450531 GCCTTCCCCATGCGAGAATG 61.451 60.000 0.00 0.00 0.00 2.67
571 589 1.152881 GCCTTCCCCATGCGAGAAT 60.153 57.895 0.00 0.00 0.00 2.40
572 590 2.272146 GCCTTCCCCATGCGAGAA 59.728 61.111 0.00 0.00 0.00 2.87
573 591 3.797353 GGCCTTCCCCATGCGAGA 61.797 66.667 0.00 0.00 0.00 4.04
574 592 2.843912 AAAGGCCTTCCCCATGCGAG 62.844 60.000 20.79 0.00 0.00 5.03
575 593 2.837031 GAAAGGCCTTCCCCATGCGA 62.837 60.000 20.79 0.00 0.00 5.10
576 594 2.362889 AAAGGCCTTCCCCATGCG 60.363 61.111 20.79 0.00 0.00 4.73
577 595 1.000866 AGAAAGGCCTTCCCCATGC 59.999 57.895 20.79 0.00 34.21 4.06
578 596 1.325476 GCAGAAAGGCCTTCCCCATG 61.325 60.000 20.79 13.82 34.21 3.66
579 597 1.000866 GCAGAAAGGCCTTCCCCAT 59.999 57.895 20.79 1.36 34.21 4.00
580 598 2.440599 GCAGAAAGGCCTTCCCCA 59.559 61.111 20.79 0.00 34.21 4.96
598 616 1.264288 GTTCAGTTCCAACTCCGCAAG 59.736 52.381 0.00 0.00 37.08 4.01
599 617 1.305201 GTTCAGTTCCAACTCCGCAA 58.695 50.000 0.00 0.00 37.08 4.85
600 618 0.179234 TGTTCAGTTCCAACTCCGCA 59.821 50.000 0.00 0.00 37.08 5.69
601 619 1.464997 GATGTTCAGTTCCAACTCCGC 59.535 52.381 0.00 0.00 37.08 5.54
602 620 2.480419 GTGATGTTCAGTTCCAACTCCG 59.520 50.000 0.00 0.00 37.08 4.63
603 621 2.480419 CGTGATGTTCAGTTCCAACTCC 59.520 50.000 0.00 0.00 37.08 3.85
604 622 2.096218 GCGTGATGTTCAGTTCCAACTC 60.096 50.000 0.00 0.00 37.08 3.01
605 623 1.873591 GCGTGATGTTCAGTTCCAACT 59.126 47.619 0.00 0.00 40.60 3.16
606 624 1.398451 CGCGTGATGTTCAGTTCCAAC 60.398 52.381 0.00 0.00 0.00 3.77
607 625 0.865111 CGCGTGATGTTCAGTTCCAA 59.135 50.000 0.00 0.00 0.00 3.53
608 626 0.948623 CCGCGTGATGTTCAGTTCCA 60.949 55.000 4.92 0.00 0.00 3.53
609 627 0.949105 ACCGCGTGATGTTCAGTTCC 60.949 55.000 4.92 0.00 0.00 3.62
610 628 0.163788 CACCGCGTGATGTTCAGTTC 59.836 55.000 4.92 0.00 35.23 3.01
611 629 0.249699 TCACCGCGTGATGTTCAGTT 60.250 50.000 4.92 0.00 37.67 3.16
612 630 0.667487 CTCACCGCGTGATGTTCAGT 60.667 55.000 4.92 0.00 41.94 3.41
613 631 0.667487 ACTCACCGCGTGATGTTCAG 60.667 55.000 4.92 0.00 41.94 3.02
614 632 0.943835 CACTCACCGCGTGATGTTCA 60.944 55.000 4.92 0.00 41.94 3.18
615 633 0.666274 TCACTCACCGCGTGATGTTC 60.666 55.000 4.92 0.00 41.94 3.18
616 634 0.249699 TTCACTCACCGCGTGATGTT 60.250 50.000 4.92 0.00 41.94 2.71
617 635 0.037326 ATTCACTCACCGCGTGATGT 60.037 50.000 4.92 6.65 41.94 3.06
618 636 1.078709 AATTCACTCACCGCGTGATG 58.921 50.000 4.92 9.34 41.94 3.07
619 637 1.078709 CAATTCACTCACCGCGTGAT 58.921 50.000 4.92 0.00 41.94 3.06
620 638 0.249699 ACAATTCACTCACCGCGTGA 60.250 50.000 4.92 8.28 40.50 4.35
621 639 1.424403 TACAATTCACTCACCGCGTG 58.576 50.000 4.92 3.64 34.45 5.34
622 640 2.157834 TTACAATTCACTCACCGCGT 57.842 45.000 4.92 0.00 0.00 6.01
623 641 3.529634 TTTTACAATTCACTCACCGCG 57.470 42.857 0.00 0.00 0.00 6.46
660 678 2.093341 GGTGGCAATTGGATGCTTCAAT 60.093 45.455 7.72 0.00 45.68 2.57
911 932 1.075374 AGAGCAGAGGAGTGAGAGTGT 59.925 52.381 0.00 0.00 0.00 3.55
1381 1404 7.121759 AGCAATTACAACAATCTGCAGACTAAT 59.878 33.333 20.97 9.99 32.21 1.73
2005 2577 3.760151 TGTTCTGATCTGCCCAATCAAAG 59.240 43.478 0.00 0.00 32.96 2.77
2044 2616 2.138320 TGCTTCTGCTTGAACTCTTCG 58.862 47.619 0.00 0.00 40.48 3.79
2269 2841 5.994668 CACCAGAAACTCTAGCTTCTTCTTT 59.005 40.000 0.00 0.00 28.83 2.52
2281 2853 2.625639 AGATCACCCACCAGAAACTCT 58.374 47.619 0.00 0.00 0.00 3.24
2686 4225 9.739276 ATGAGAACTTTTATGGTTGAGAACATA 57.261 29.630 0.00 0.00 0.00 2.29
2902 5166 1.270414 CCAGAGCACCAGGATGAGGT 61.270 60.000 0.00 0.00 39.69 3.85
2923 5187 4.162509 CAGTAGGGTCTAAAAGGAAGAGGG 59.837 50.000 0.00 0.00 0.00 4.30
3153 5426 3.117131 ACCAGGGGAAGAAATTCAACTGT 60.117 43.478 0.00 0.00 0.00 3.55
3161 5434 4.103311 GCTACATCTACCAGGGGAAGAAAT 59.897 45.833 0.00 0.00 0.00 2.17
3313 5640 3.199727 TGGGCTATGATGTGTGCTTTCTA 59.800 43.478 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.