Multiple sequence alignment - TraesCS3B01G009700

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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 TraesCS3B01G009700 chr3B 100.000 2628 0 0 1 2628 4554994 4557621 0.000000e+00 4854
1 TraesCS3B01G009700 chr3D 91.355 1955 152 13 681 2628 2308338 2310282 0.000000e+00 2658
2 TraesCS3B01G009700 chr3D 86.719 512 64 3 82 592 2307565 2308073 1.370000e-157 566
3 TraesCS3B01G009700 chr3A 90.032 622 49 8 939 1555 1712351 1711738 0.000000e+00 793
4 TraesCS3B01G009700 chr3A 85.561 187 19 7 885 1065 1713078 1712894 3.450000e-44 189


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 TraesCS3B01G009700 chr3B 4554994 4557621 2627 False 4854 4854 100.0000 1 2628 1 chr3B.!!$F1 2627
1 TraesCS3B01G009700 chr3D 2307565 2310282 2717 False 1612 2658 89.0370 82 2628 2 chr3D.!!$F1 2546
2 TraesCS3B01G009700 chr3A 1711738 1713078 1340 True 491 793 87.7965 885 1555 2 chr3A.!!$R1 670

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
77 78 0.032678 ATCAGGGCTCGCTGATAACG 59.967 55.0 22.61 0.0 38.4 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2777 0.105658 CGAAGGAGGGGATGGTAGGA 60.106 60.0 0.0 0.0 0.0 2.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.736531 GGCCCAAAGCACCAACTG 59.263 61.111 0.00 0.00 46.50 3.16
18 19 2.133641 GGCCCAAAGCACCAACTGT 61.134 57.895 0.00 0.00 46.50 3.55
27 28 4.519610 ACCAACTGTGAATGGGCC 57.480 55.556 0.00 0.00 41.17 5.80
28 29 1.853428 ACCAACTGTGAATGGGCCT 59.147 52.632 4.53 0.00 41.17 5.19
29 30 1.072266 ACCAACTGTGAATGGGCCTA 58.928 50.000 4.53 0.00 41.17 3.93
30 31 1.427368 ACCAACTGTGAATGGGCCTAA 59.573 47.619 4.53 0.00 41.17 2.69
31 32 2.158385 ACCAACTGTGAATGGGCCTAAA 60.158 45.455 4.53 0.00 41.17 1.85
32 33 2.896685 CCAACTGTGAATGGGCCTAAAA 59.103 45.455 4.53 0.00 32.87 1.52
33 34 3.306019 CCAACTGTGAATGGGCCTAAAAC 60.306 47.826 4.53 0.00 32.87 2.43
34 35 3.237268 ACTGTGAATGGGCCTAAAACA 57.763 42.857 4.53 1.99 0.00 2.83
35 36 2.890945 ACTGTGAATGGGCCTAAAACAC 59.109 45.455 4.53 9.55 0.00 3.32
36 37 2.231235 CTGTGAATGGGCCTAAAACACC 59.769 50.000 4.53 0.00 0.00 4.16
37 38 2.243810 GTGAATGGGCCTAAAACACCA 58.756 47.619 4.53 0.00 37.41 4.17
38 39 2.831526 GTGAATGGGCCTAAAACACCAT 59.168 45.455 4.53 0.00 45.18 3.55
39 40 2.830923 TGAATGGGCCTAAAACACCATG 59.169 45.455 4.53 0.00 42.60 3.66
40 41 1.864669 ATGGGCCTAAAACACCATGG 58.135 50.000 11.19 11.19 41.88 3.66
41 42 0.252012 TGGGCCTAAAACACCATGGG 60.252 55.000 18.09 7.72 0.00 4.00
42 43 1.613317 GGGCCTAAAACACCATGGGC 61.613 60.000 18.09 6.75 41.79 5.36
43 44 1.897423 GCCTAAAACACCATGGGCC 59.103 57.895 18.09 0.00 34.19 5.80
44 45 1.613317 GCCTAAAACACCATGGGCCC 61.613 60.000 17.59 17.59 34.19 5.80
45 46 0.975556 CCTAAAACACCATGGGCCCC 60.976 60.000 22.27 0.85 0.00 5.80
46 47 0.041090 CTAAAACACCATGGGCCCCT 59.959 55.000 22.27 6.51 0.00 4.79
47 48 1.286553 CTAAAACACCATGGGCCCCTA 59.713 52.381 22.27 0.09 0.00 3.53
48 49 0.489567 AAAACACCATGGGCCCCTAA 59.510 50.000 22.27 0.00 0.00 2.69
49 50 0.489567 AAACACCATGGGCCCCTAAA 59.510 50.000 22.27 0.00 0.00 1.85
50 51 0.041090 AACACCATGGGCCCCTAAAG 59.959 55.000 22.27 9.36 0.00 1.85
51 52 1.076044 CACCATGGGCCCCTAAAGG 60.076 63.158 22.27 16.06 0.00 3.11
64 65 2.110578 CCTAAAGGGCCAAAATCAGGG 58.889 52.381 6.18 0.00 0.00 4.45
69 70 2.491621 GCCAAAATCAGGGCTCGC 59.508 61.111 0.00 0.00 46.74 5.03
70 71 2.048603 GCCAAAATCAGGGCTCGCT 61.049 57.895 0.00 0.00 46.74 4.93
71 72 1.805254 CCAAAATCAGGGCTCGCTG 59.195 57.895 7.53 7.53 0.00 5.18
72 73 0.677731 CCAAAATCAGGGCTCGCTGA 60.678 55.000 17.07 17.07 0.00 4.26
73 74 1.386533 CAAAATCAGGGCTCGCTGAT 58.613 50.000 19.61 19.61 41.53 2.90
74 75 2.564771 CAAAATCAGGGCTCGCTGATA 58.435 47.619 23.69 4.28 39.15 2.15
75 76 2.945008 CAAAATCAGGGCTCGCTGATAA 59.055 45.455 23.69 3.66 39.15 1.75
76 77 2.246719 AATCAGGGCTCGCTGATAAC 57.753 50.000 23.69 0.00 39.15 1.89
77 78 0.032678 ATCAGGGCTCGCTGATAACG 59.967 55.000 22.61 0.00 38.40 3.18
78 79 1.592669 CAGGGCTCGCTGATAACGG 60.593 63.158 8.06 0.00 0.00 4.44
79 80 2.967615 GGGCTCGCTGATAACGGC 60.968 66.667 0.00 0.00 44.17 5.68
80 81 2.107141 GGCTCGCTGATAACGGCT 59.893 61.111 2.04 0.00 45.30 5.52
83 84 1.605712 GGCTCGCTGATAACGGCTAAT 60.606 52.381 2.04 0.00 45.30 1.73
90 91 3.815401 GCTGATAACGGCTAATCACCATT 59.185 43.478 0.00 0.00 44.22 3.16
98 99 0.381801 CTAATCACCATTGGCCGCAC 59.618 55.000 1.54 0.00 0.00 5.34
117 118 1.176527 CACTGGCCGATTGTGGAAAT 58.823 50.000 0.00 0.00 0.00 2.17
120 121 0.251564 TGGCCGATTGTGGAAATGGT 60.252 50.000 0.00 0.00 0.00 3.55
177 178 0.598065 AAATCAGAAGCAACACGGGC 59.402 50.000 0.00 0.00 0.00 6.13
178 179 1.244019 AATCAGAAGCAACACGGGCC 61.244 55.000 0.00 0.00 0.00 5.80
184 185 1.788067 AAGCAACACGGGCCGTTAAC 61.788 55.000 32.12 18.91 38.32 2.01
199 200 1.461897 GTTAACGGGTCGAATGGTGTG 59.538 52.381 0.00 0.00 0.00 3.82
221 222 4.524714 TGACGGATCAAAAATAGCCCAAAA 59.475 37.500 0.00 0.00 0.00 2.44
230 231 0.887933 ATAGCCCAAAAGCAACACGG 59.112 50.000 0.00 0.00 34.23 4.94
233 234 2.498056 CCCAAAAGCAACACGGGCT 61.498 57.895 0.00 0.00 45.15 5.19
252 253 2.159517 GCTGTTAATGGACTCAAAGCCG 60.160 50.000 0.00 0.00 0.00 5.52
256 257 5.250200 TGTTAATGGACTCAAAGCCGTAAT 58.750 37.500 0.00 0.00 0.00 1.89
276 277 4.183771 GCCAAAAATGGCGCGAAT 57.816 50.000 12.10 0.00 45.79 3.34
278 279 1.013524 GCCAAAAATGGCGCGAATGT 61.014 50.000 12.10 0.00 45.79 2.71
288 289 0.096976 GCGCGAATGTAACACATGCT 59.903 50.000 12.10 0.00 37.97 3.79
293 294 4.667922 CGCGAATGTAACACATGCTGTTAA 60.668 41.667 17.02 10.98 45.16 2.01
299 300 6.641169 TGTAACACATGCTGTTAAATGGAA 57.359 33.333 17.02 0.44 45.16 3.53
318 319 2.192861 CAAAAGGCACGAGTGGGCA 61.193 57.895 5.32 0.00 0.00 5.36
319 320 1.454847 AAAAGGCACGAGTGGGCAA 60.455 52.632 5.32 0.00 0.00 4.52
344 345 0.673644 ATGCCCTAGACGCAACACAC 60.674 55.000 8.31 0.00 40.22 3.82
347 349 1.736645 CCTAGACGCAACACACCGG 60.737 63.158 0.00 0.00 0.00 5.28
355 357 0.802494 GCAACACACCGGTAATGGAG 59.198 55.000 19.33 12.94 0.00 3.86
357 359 0.398696 AACACACCGGTAATGGAGCA 59.601 50.000 19.33 0.00 0.00 4.26
373 375 1.737735 GCAAAAGGTGCGAATGCCC 60.738 57.895 0.00 0.00 45.10 5.36
375 377 0.033228 CAAAAGGTGCGAATGCCCAA 59.967 50.000 0.00 0.00 41.78 4.12
384 386 0.596082 CGAATGCCCAAAAACGGTCT 59.404 50.000 0.00 0.00 0.00 3.85
390 392 1.616159 CCCAAAAACGGTCTGGACAT 58.384 50.000 3.11 0.00 31.38 3.06
396 398 5.413213 CCAAAAACGGTCTGGACATAACATA 59.587 40.000 3.10 0.00 31.38 2.29
399 401 5.871396 AACGGTCTGGACATAACATAGAT 57.129 39.130 3.10 0.00 0.00 1.98
403 405 7.229308 ACGGTCTGGACATAACATAGATAGTA 58.771 38.462 3.10 0.00 0.00 1.82
423 425 3.694043 AAATGGGCCAAAATACACCAC 57.306 42.857 11.89 0.00 33.42 4.16
425 427 0.896019 TGGGCCAAAATACACCACGG 60.896 55.000 2.13 0.00 0.00 4.94
427 429 0.609681 GGCCAAAATACACCACGGGA 60.610 55.000 0.00 0.00 0.00 5.14
432 434 3.142951 CAAAATACACCACGGGACAGAA 58.857 45.455 0.00 0.00 0.00 3.02
451 453 0.179032 AATGGCCAAGACACACGACA 60.179 50.000 10.96 0.00 0.00 4.35
453 455 1.069090 GGCCAAGACACACGACAGA 59.931 57.895 0.00 0.00 0.00 3.41
455 457 0.249489 GCCAAGACACACGACAGACT 60.249 55.000 0.00 0.00 0.00 3.24
465 467 2.367567 ACACGACAGACTGTAAATGGGT 59.632 45.455 8.41 3.47 0.00 4.51
467 469 1.732259 CGACAGACTGTAAATGGGTGC 59.268 52.381 8.41 0.00 0.00 5.01
478 480 5.971763 TGTAAATGGGTGCAAATATTCCAC 58.028 37.500 9.55 9.55 0.00 4.02
532 534 5.104374 GTCTTAAACGGATCGGAATACACA 58.896 41.667 7.35 0.00 0.00 3.72
541 543 2.432444 TCGGAATACACAAAAGGCCTG 58.568 47.619 5.69 0.00 0.00 4.85
546 548 5.170748 GGAATACACAAAAGGCCTGAAATG 58.829 41.667 5.69 5.84 0.00 2.32
562 564 0.251564 AATGGCCCGGAAACATCACA 60.252 50.000 0.73 0.00 0.00 3.58
563 565 0.033208 ATGGCCCGGAAACATCACAT 60.033 50.000 0.73 0.00 0.00 3.21
564 566 0.251564 TGGCCCGGAAACATCACATT 60.252 50.000 0.73 0.00 0.00 2.71
567 569 1.818674 GCCCGGAAACATCACATTCTT 59.181 47.619 0.73 0.00 0.00 2.52
577 579 5.343307 ACATCACATTCTTTAATTGGCCC 57.657 39.130 0.00 0.00 0.00 5.80
578 580 4.776837 ACATCACATTCTTTAATTGGCCCA 59.223 37.500 0.00 0.00 0.00 5.36
585 587 7.605691 CACATTCTTTAATTGGCCCAAAATACA 59.394 33.333 0.00 0.00 0.00 2.29
595 597 3.988379 CCCAAAATACATCATGGGTCG 57.012 47.619 1.45 0.00 46.13 4.79
596 598 3.287222 CCCAAAATACATCATGGGTCGT 58.713 45.455 1.45 0.00 46.13 4.34
597 599 4.456535 CCCAAAATACATCATGGGTCGTA 58.543 43.478 1.45 0.00 46.13 3.43
598 600 4.884744 CCCAAAATACATCATGGGTCGTAA 59.115 41.667 1.45 0.00 46.13 3.18
599 601 5.358442 CCCAAAATACATCATGGGTCGTAAA 59.642 40.000 1.45 0.00 46.13 2.01
600 602 6.127591 CCCAAAATACATCATGGGTCGTAAAA 60.128 38.462 1.45 0.00 46.13 1.52
601 603 6.972328 CCAAAATACATCATGGGTCGTAAAAG 59.028 38.462 0.00 0.00 0.00 2.27
602 604 6.693315 AAATACATCATGGGTCGTAAAAGG 57.307 37.500 0.00 0.00 0.00 3.11
603 605 3.713826 ACATCATGGGTCGTAAAAGGT 57.286 42.857 0.00 0.00 0.00 3.50
604 606 3.606687 ACATCATGGGTCGTAAAAGGTC 58.393 45.455 0.00 0.00 0.00 3.85
605 607 2.773993 TCATGGGTCGTAAAAGGTCC 57.226 50.000 0.00 0.00 0.00 4.46
606 608 1.066716 TCATGGGTCGTAAAAGGTCCG 60.067 52.381 0.00 0.00 0.00 4.79
607 609 0.978907 ATGGGTCGTAAAAGGTCCGT 59.021 50.000 0.00 0.00 0.00 4.69
608 610 0.033781 TGGGTCGTAAAAGGTCCGTG 59.966 55.000 0.00 0.00 0.00 4.94
609 611 0.318120 GGGTCGTAAAAGGTCCGTGA 59.682 55.000 0.00 0.00 0.00 4.35
610 612 1.270252 GGGTCGTAAAAGGTCCGTGAA 60.270 52.381 0.00 0.00 0.00 3.18
611 613 2.064014 GGTCGTAAAAGGTCCGTGAAG 58.936 52.381 0.00 0.00 0.00 3.02
612 614 1.458445 GTCGTAAAAGGTCCGTGAAGC 59.542 52.381 0.00 0.00 0.00 3.86
613 615 1.068895 TCGTAAAAGGTCCGTGAAGCA 59.931 47.619 0.00 0.00 0.00 3.91
614 616 1.459592 CGTAAAAGGTCCGTGAAGCAG 59.540 52.381 0.00 0.00 0.00 4.24
615 617 1.197036 GTAAAAGGTCCGTGAAGCAGC 59.803 52.381 0.00 0.00 0.00 5.25
616 618 0.465460 AAAAGGTCCGTGAAGCAGCA 60.465 50.000 0.00 0.00 0.00 4.41
617 619 0.250901 AAAGGTCCGTGAAGCAGCAT 60.251 50.000 0.00 0.00 0.00 3.79
618 620 0.957395 AAGGTCCGTGAAGCAGCATG 60.957 55.000 0.00 0.00 40.87 4.06
619 621 2.401766 GGTCCGTGAAGCAGCATGG 61.402 63.158 10.01 10.01 44.60 3.66
620 622 2.046023 TCCGTGAAGCAGCATGGG 60.046 61.111 14.74 5.29 43.64 4.00
629 631 0.828762 AGCAGCATGGGCAGTGAAAA 60.829 50.000 0.00 0.00 44.61 2.29
650 652 1.347320 CTCGAAAGCAAGTACCGGTC 58.653 55.000 12.40 2.55 0.00 4.79
655 657 3.242804 CGAAAGCAAGTACCGGTCAAAAA 60.243 43.478 12.40 0.00 0.00 1.94
713 919 1.014352 GTGAATCCATGCGGTGTACC 58.986 55.000 0.00 0.00 0.00 3.34
803 1009 9.256477 CATTCAGTGCATATTGATTTATTGCTT 57.744 29.630 0.00 0.00 0.00 3.91
806 1012 8.252417 TCAGTGCATATTGATTTATTGCTTGTT 58.748 29.630 0.00 0.00 0.00 2.83
847 1053 8.031864 ACAAACAATCAATGGACGCATTAATTA 58.968 29.630 0.00 0.00 0.00 1.40
888 1094 6.280855 TGCAGTGCTCTATAACTAGAAACA 57.719 37.500 17.60 0.00 33.59 2.83
913 1119 9.749490 CAATCAATGACAGCATTAATTGAAAAC 57.251 29.630 8.20 0.00 46.33 2.43
927 1133 5.850557 ATTGAAAACATATCCCATTCGCA 57.149 34.783 0.00 0.00 0.00 5.10
950 1160 0.881118 GATTGTCCTTGCTTTGGCGA 59.119 50.000 0.00 0.00 42.25 5.54
977 1187 1.307866 TAGAAAGCCCCCTCCCCAG 60.308 63.158 0.00 0.00 0.00 4.45
999 1210 7.829211 CCCAGACAATATTCTAAACAGGAAAGA 59.171 37.037 0.00 0.00 0.00 2.52
1077 1961 5.630069 GCCCCTTCTGATCATTCTACTTTCA 60.630 44.000 0.00 0.00 0.00 2.69
1105 1989 7.014134 CCATTCATAAACCTACAACATATGCCA 59.986 37.037 1.58 0.00 0.00 4.92
1184 2068 9.585099 TTTGTTCTTACAATTTGCATCATATCC 57.415 29.630 0.00 0.00 43.43 2.59
1194 2078 4.458256 TGCATCATATCCCCATTGAACT 57.542 40.909 0.00 0.00 0.00 3.01
1354 2238 2.097104 CGGCGTACAATTGTATAAGGCG 60.097 50.000 31.41 31.41 40.93 5.52
1358 2242 3.121463 CGTACAATTGTATAAGGCGCGAG 60.121 47.826 20.72 0.00 32.54 5.03
1376 2260 3.886123 CGAGAACCCCCAAGTGAATAAT 58.114 45.455 0.00 0.00 0.00 1.28
1409 2293 3.196469 TGATTTCTGATGCTCTTCGTCCT 59.804 43.478 0.00 0.00 0.00 3.85
1430 2314 2.342650 GGCGGACAATGGCATGTGT 61.343 57.895 0.00 7.86 32.57 3.72
1454 2338 3.305950 GCAACCATGTGCTTTTGGTGATA 60.306 43.478 5.91 0.00 45.44 2.15
1562 2446 8.684386 TTGATCAATAAAGTCTTTGGTGTGTA 57.316 30.769 3.38 0.00 0.00 2.90
1576 2460 3.146066 GGTGTGTATGCACTTTTCTCCA 58.854 45.455 15.25 0.00 45.44 3.86
1591 2475 9.695526 CACTTTTCTCCATTTCATTTCATACAA 57.304 29.630 0.00 0.00 0.00 2.41
1709 2593 7.738847 ACATCAAATCAAAACCAAAGGAAGAT 58.261 30.769 0.00 0.00 0.00 2.40
1711 2595 6.446318 TCAAATCAAAACCAAAGGAAGATCG 58.554 36.000 0.00 0.00 0.00 3.69
1712 2596 3.915437 TCAAAACCAAAGGAAGATCGC 57.085 42.857 0.00 0.00 0.00 4.58
1713 2597 3.218453 TCAAAACCAAAGGAAGATCGCA 58.782 40.909 0.00 0.00 0.00 5.10
1714 2598 3.253188 TCAAAACCAAAGGAAGATCGCAG 59.747 43.478 0.00 0.00 0.00 5.18
1762 2646 2.326428 TGGGCCTGACTATAGGTAAGC 58.674 52.381 4.53 1.86 40.11 3.09
1821 2705 6.212888 ACCATTGGATTAGCTTCAACAATC 57.787 37.500 10.37 0.00 0.00 2.67
1831 2715 9.427127 GATTAGCTTCAACAATCGTTATTCTTC 57.573 33.333 0.00 0.00 32.75 2.87
1855 2739 6.214412 TCCATCTTTCTCTAGCTTTCTTCCTT 59.786 38.462 0.00 0.00 0.00 3.36
1869 2753 4.785511 TCTTCCTTCTCGAATCGTTCTT 57.214 40.909 1.52 0.00 0.00 2.52
1874 2758 3.440228 CTTCTCGAATCGTTCTTCCTCC 58.560 50.000 1.52 0.00 0.00 4.30
1875 2759 2.443416 TCTCGAATCGTTCTTCCTCCA 58.557 47.619 1.52 0.00 0.00 3.86
1876 2760 2.163815 TCTCGAATCGTTCTTCCTCCAC 59.836 50.000 1.52 0.00 0.00 4.02
1884 2768 0.034896 TTCTTCCTCCACTGTTCGCC 59.965 55.000 0.00 0.00 0.00 5.54
1889 2773 2.599281 TCCACTGTTCGCCTCCGA 60.599 61.111 0.00 0.00 42.66 4.55
1893 2777 0.600255 CACTGTTCGCCTCCGAGTTT 60.600 55.000 0.00 0.00 45.35 2.66
1906 2790 1.497161 CGAGTTTCCTACCATCCCCT 58.503 55.000 0.00 0.00 0.00 4.79
1913 2797 0.105658 CCTACCATCCCCTCCTTCGA 60.106 60.000 0.00 0.00 0.00 3.71
1923 2807 2.158505 CCCCTCCTTCGAGTGGTCTATA 60.159 54.545 6.46 0.00 33.93 1.31
1927 2811 5.283314 CCTCCTTCGAGTGGTCTATAGACC 61.283 54.167 35.75 35.75 46.96 3.85
1952 2836 9.590451 CCTGAATGTGATTTTTATTGCTTATGT 57.410 29.630 0.00 0.00 0.00 2.29
1966 2850 5.351233 TGCTTATGTTGTTCTTTGTACCG 57.649 39.130 0.00 0.00 0.00 4.02
1985 2869 8.129496 TGTACCGCCTTGATAGATAATGAATA 57.871 34.615 0.00 0.00 0.00 1.75
1986 2870 8.758829 TGTACCGCCTTGATAGATAATGAATAT 58.241 33.333 0.00 0.00 0.00 1.28
2053 2939 2.876550 GTTCGTTAAGGTGAACTGGCTT 59.123 45.455 7.55 0.00 40.94 4.35
2071 2957 4.037446 TGGCTTAACAAGTTGTTAGCTTGG 59.963 41.667 28.92 19.44 42.93 3.61
2086 2974 1.256812 CTTGGCCCACCCTTGTAAAG 58.743 55.000 0.00 0.00 45.69 1.85
2105 2993 8.462143 TGTAAAGACTGATATCGACAAAAGTC 57.538 34.615 9.52 9.52 35.39 3.01
2106 2994 6.969828 AAAGACTGATATCGACAAAAGTCC 57.030 37.500 12.59 0.22 35.70 3.85
2108 2996 4.398358 AGACTGATATCGACAAAAGTCCGA 59.602 41.667 12.59 0.00 35.70 4.55
2121 3009 2.029838 AGTCCGATTGTCATGGAAGC 57.970 50.000 0.00 0.00 32.60 3.86
2122 3010 1.017387 GTCCGATTGTCATGGAAGCC 58.983 55.000 0.00 0.00 32.60 4.35
2183 3071 6.908870 TCTTTGGAATCAACATAGTCATCG 57.091 37.500 0.00 0.00 31.78 3.84
2189 3077 6.267699 TGGAATCAACATAGTCATCGTATCCT 59.732 38.462 0.00 0.00 0.00 3.24
2217 3105 1.399440 CCACACGCCAAGAGAATGATG 59.601 52.381 0.00 0.00 0.00 3.07
2234 3122 7.337167 AGAATGATGAGTAACTTGAAGATGCT 58.663 34.615 0.00 0.00 0.00 3.79
2237 3125 6.233434 TGATGAGTAACTTGAAGATGCTTGT 58.767 36.000 0.00 0.00 0.00 3.16
2239 3127 6.304356 TGAGTAACTTGAAGATGCTTGTTG 57.696 37.500 0.00 0.00 0.00 3.33
2264 3152 9.921637 TGTCTGCATTATAAATCATCGTATACA 57.078 29.630 3.32 0.00 0.00 2.29
2275 3163 4.583426 TCATCGTATACAAAATTGCGCAC 58.417 39.130 11.12 0.00 0.00 5.34
2276 3164 3.392769 TCGTATACAAAATTGCGCACC 57.607 42.857 11.12 0.00 0.00 5.01
2287 3176 1.333177 TTGCGCACCCCAAACTAAAT 58.667 45.000 11.12 0.00 0.00 1.40
2291 3180 3.511934 TGCGCACCCCAAACTAAATAAAT 59.488 39.130 5.66 0.00 0.00 1.40
2354 3243 7.753309 AGGTACACTTGCATAATAAAACACA 57.247 32.000 0.00 0.00 0.00 3.72
2355 3244 7.590279 AGGTACACTTGCATAATAAAACACAC 58.410 34.615 0.00 0.00 0.00 3.82
2356 3245 7.229707 AGGTACACTTGCATAATAAAACACACA 59.770 33.333 0.00 0.00 0.00 3.72
2360 3249 7.925483 ACACTTGCATAATAAAACACACACATT 59.075 29.630 0.00 0.00 0.00 2.71
2362 3251 7.925483 ACTTGCATAATAAAACACACACATTGT 59.075 29.630 0.00 0.00 39.97 2.71
2432 3322 4.551702 TTAAAGTGAGCATCTACAGCCA 57.448 40.909 0.00 0.00 34.92 4.75
2450 3340 1.615883 CCAGACCACTCATATCCTCCG 59.384 57.143 0.00 0.00 0.00 4.63
2454 3344 1.837439 ACCACTCATATCCTCCGCAAA 59.163 47.619 0.00 0.00 0.00 3.68
2460 3350 0.249322 ATATCCTCCGCAAACGTCCG 60.249 55.000 0.00 0.00 37.70 4.79
2482 3372 0.606401 CGGACAGCCTGGTCATTGTT 60.606 55.000 0.00 0.00 39.59 2.83
2483 3373 1.168714 GGACAGCCTGGTCATTGTTC 58.831 55.000 0.00 0.00 39.59 3.18
2485 3375 0.108585 ACAGCCTGGTCATTGTTCGT 59.891 50.000 0.00 0.00 0.00 3.85
2486 3376 1.346395 ACAGCCTGGTCATTGTTCGTA 59.654 47.619 0.00 0.00 0.00 3.43
2487 3377 1.732259 CAGCCTGGTCATTGTTCGTAC 59.268 52.381 0.00 0.00 0.00 3.67
2488 3378 1.346395 AGCCTGGTCATTGTTCGTACA 59.654 47.619 0.00 0.00 0.00 2.90
2489 3379 1.732259 GCCTGGTCATTGTTCGTACAG 59.268 52.381 0.00 0.00 35.28 2.74
2491 3381 2.028476 CCTGGTCATTGTTCGTACAGGA 60.028 50.000 0.00 0.00 45.14 3.86
2495 3385 3.512680 GTCATTGTTCGTACAGGAGAGG 58.487 50.000 0.00 0.00 35.28 3.69
2503 3393 2.307980 TCGTACAGGAGAGGGAGAAGAA 59.692 50.000 0.00 0.00 0.00 2.52
2555 3445 0.875908 CCATATGTCCGTGCTGTCCG 60.876 60.000 1.24 0.00 0.00 4.79
2572 3462 2.948979 GTCCGCAAATCACCATATCCAA 59.051 45.455 0.00 0.00 0.00 3.53
2583 3473 6.889595 TCACCATATCCAAGGCATATATGA 57.110 37.500 17.10 0.00 36.22 2.15
2594 3484 6.927936 CCAAGGCATATATGAGAAGGATATCG 59.072 42.308 17.10 0.00 0.00 2.92
2615 3505 2.593026 GGATTTTTCTGGGTGTGTCCA 58.407 47.619 0.00 0.00 38.11 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.133641 ACAGTTGGTGCTTTGGGCC 61.134 57.895 0.00 0.00 40.92 5.80
1 2 1.067916 CACAGTTGGTGCTTTGGGC 59.932 57.895 0.00 0.00 41.36 5.36
10 11 1.072266 TAGGCCCATTCACAGTTGGT 58.928 50.000 0.00 0.00 0.00 3.67
11 12 2.214376 TTAGGCCCATTCACAGTTGG 57.786 50.000 0.00 0.00 0.00 3.77
12 13 3.320541 TGTTTTAGGCCCATTCACAGTTG 59.679 43.478 0.00 0.00 0.00 3.16
13 14 3.320826 GTGTTTTAGGCCCATTCACAGTT 59.679 43.478 0.00 0.00 0.00 3.16
14 15 2.890945 GTGTTTTAGGCCCATTCACAGT 59.109 45.455 0.00 0.00 0.00 3.55
15 16 2.231235 GGTGTTTTAGGCCCATTCACAG 59.769 50.000 0.00 0.00 0.00 3.66
16 17 2.243810 GGTGTTTTAGGCCCATTCACA 58.756 47.619 0.00 0.00 0.00 3.58
17 18 2.243810 TGGTGTTTTAGGCCCATTCAC 58.756 47.619 0.00 3.00 0.00 3.18
18 19 2.685106 TGGTGTTTTAGGCCCATTCA 57.315 45.000 0.00 0.00 0.00 2.57
19 20 2.168313 CCATGGTGTTTTAGGCCCATTC 59.832 50.000 2.57 0.00 35.53 2.67
20 21 2.187100 CCATGGTGTTTTAGGCCCATT 58.813 47.619 2.57 0.00 35.53 3.16
21 22 1.622173 CCCATGGTGTTTTAGGCCCAT 60.622 52.381 11.73 0.00 38.20 4.00
22 23 0.252012 CCCATGGTGTTTTAGGCCCA 60.252 55.000 11.73 0.00 0.00 5.36
23 24 1.613317 GCCCATGGTGTTTTAGGCCC 61.613 60.000 11.73 0.00 34.23 5.80
24 25 1.897423 GCCCATGGTGTTTTAGGCC 59.103 57.895 11.73 0.00 34.23 5.19
25 26 1.613317 GGGCCCATGGTGTTTTAGGC 61.613 60.000 19.95 5.44 39.73 3.93
26 27 0.975556 GGGGCCCATGGTGTTTTAGG 60.976 60.000 26.86 0.00 0.00 2.69
27 28 0.041090 AGGGGCCCATGGTGTTTTAG 59.959 55.000 27.72 0.00 0.00 1.85
28 29 1.383963 TAGGGGCCCATGGTGTTTTA 58.616 50.000 27.72 1.09 0.00 1.52
29 30 0.489567 TTAGGGGCCCATGGTGTTTT 59.510 50.000 27.72 2.27 0.00 2.43
30 31 0.489567 TTTAGGGGCCCATGGTGTTT 59.510 50.000 27.72 3.14 0.00 2.83
31 32 0.041090 CTTTAGGGGCCCATGGTGTT 59.959 55.000 27.72 4.03 0.00 3.32
32 33 1.697297 CTTTAGGGGCCCATGGTGT 59.303 57.895 27.72 4.91 0.00 4.16
33 34 1.076044 CCTTTAGGGGCCCATGGTG 60.076 63.158 27.72 10.75 0.00 4.17
34 35 3.438822 CCTTTAGGGGCCCATGGT 58.561 61.111 27.72 6.26 0.00 3.55
44 45 2.110578 CCCTGATTTTGGCCCTTTAGG 58.889 52.381 0.00 0.18 39.47 2.69
45 46 1.482182 GCCCTGATTTTGGCCCTTTAG 59.518 52.381 0.00 0.00 41.97 1.85
46 47 1.567357 GCCCTGATTTTGGCCCTTTA 58.433 50.000 0.00 0.00 41.97 1.85
47 48 2.376063 GCCCTGATTTTGGCCCTTT 58.624 52.632 0.00 0.00 41.97 3.11
48 49 4.135293 GCCCTGATTTTGGCCCTT 57.865 55.556 0.00 0.00 41.97 3.95
53 54 0.677731 TCAGCGAGCCCTGATTTTGG 60.678 55.000 0.00 0.00 36.96 3.28
54 55 2.858622 TCAGCGAGCCCTGATTTTG 58.141 52.632 0.00 0.00 36.96 2.44
59 60 1.437573 CGTTATCAGCGAGCCCTGA 59.562 57.895 2.33 2.33 45.16 3.86
60 61 1.592669 CCGTTATCAGCGAGCCCTG 60.593 63.158 0.00 0.00 0.00 4.45
61 62 2.815308 CCGTTATCAGCGAGCCCT 59.185 61.111 0.00 0.00 0.00 5.19
62 63 2.083835 TAGCCGTTATCAGCGAGCCC 62.084 60.000 0.00 0.00 0.00 5.19
63 64 0.249322 TTAGCCGTTATCAGCGAGCC 60.249 55.000 0.00 0.00 0.00 4.70
64 65 1.721926 GATTAGCCGTTATCAGCGAGC 59.278 52.381 0.00 0.00 0.00 5.03
65 66 2.726760 GTGATTAGCCGTTATCAGCGAG 59.273 50.000 0.00 0.00 31.81 5.03
66 67 2.545113 GGTGATTAGCCGTTATCAGCGA 60.545 50.000 0.00 0.00 38.86 4.93
67 68 1.792949 GGTGATTAGCCGTTATCAGCG 59.207 52.381 0.00 0.00 38.86 5.18
68 69 2.833794 TGGTGATTAGCCGTTATCAGC 58.166 47.619 0.00 0.00 45.07 4.26
69 70 4.214119 CCAATGGTGATTAGCCGTTATCAG 59.786 45.833 0.00 0.00 33.80 2.90
70 71 4.133820 CCAATGGTGATTAGCCGTTATCA 58.866 43.478 0.00 0.00 33.80 2.15
71 72 3.058224 GCCAATGGTGATTAGCCGTTATC 60.058 47.826 0.00 0.00 33.80 1.75
72 73 2.884639 GCCAATGGTGATTAGCCGTTAT 59.115 45.455 0.00 0.00 33.80 1.89
73 74 2.294074 GCCAATGGTGATTAGCCGTTA 58.706 47.619 0.00 0.00 33.80 3.18
74 75 1.102978 GCCAATGGTGATTAGCCGTT 58.897 50.000 0.00 0.00 35.76 4.44
75 76 0.751643 GGCCAATGGTGATTAGCCGT 60.752 55.000 0.00 0.00 36.74 5.68
76 77 2.032981 GGCCAATGGTGATTAGCCG 58.967 57.895 0.00 0.00 36.74 5.52
77 78 2.032981 CGGCCAATGGTGATTAGCC 58.967 57.895 2.24 0.00 41.54 3.93
78 79 1.360192 GCGGCCAATGGTGATTAGC 59.640 57.895 2.24 0.00 0.00 3.09
79 80 0.381801 GTGCGGCCAATGGTGATTAG 59.618 55.000 2.24 0.00 0.00 1.73
80 81 0.322906 TGTGCGGCCAATGGTGATTA 60.323 50.000 2.24 0.00 0.00 1.75
83 84 2.983030 GTGTGCGGCCAATGGTGA 60.983 61.111 2.24 0.00 0.00 4.02
98 99 1.135315 CATTTCCACAATCGGCCAGTG 60.135 52.381 2.24 5.57 0.00 3.66
120 121 4.160814 CCCGTTATATATTCGGTCCATGGA 59.839 45.833 11.44 11.44 42.30 3.41
125 126 4.789012 TGACCCGTTATATATTCGGTCC 57.211 45.455 20.03 14.23 42.30 4.46
148 149 4.789012 TGCTTCTGATTTTGGTCCATTC 57.211 40.909 0.00 0.00 0.00 2.67
156 157 2.664916 CCCGTGTTGCTTCTGATTTTG 58.335 47.619 0.00 0.00 0.00 2.44
157 158 1.000274 GCCCGTGTTGCTTCTGATTTT 60.000 47.619 0.00 0.00 0.00 1.82
178 179 0.717224 CACCATTCGACCCGTTAACG 59.283 55.000 20.99 20.99 39.44 3.18
184 185 2.092291 CGTCACACCATTCGACCCG 61.092 63.158 0.00 0.00 0.00 5.28
187 188 1.278238 GATCCGTCACACCATTCGAC 58.722 55.000 0.00 0.00 0.00 4.20
188 189 0.892063 TGATCCGTCACACCATTCGA 59.108 50.000 0.00 0.00 0.00 3.71
193 194 3.438781 GCTATTTTTGATCCGTCACACCA 59.561 43.478 0.00 0.00 33.11 4.17
199 200 4.712122 TTTGGGCTATTTTTGATCCGTC 57.288 40.909 0.00 0.00 0.00 4.79
230 231 2.164422 GGCTTTGAGTCCATTAACAGCC 59.836 50.000 0.00 0.00 0.00 4.85
233 234 3.134574 ACGGCTTTGAGTCCATTAACA 57.865 42.857 0.00 0.00 0.00 2.41
288 289 4.098044 TCGTGCCTTTTGTTCCATTTAACA 59.902 37.500 0.00 0.00 37.58 2.41
293 294 2.034558 CACTCGTGCCTTTTGTTCCATT 59.965 45.455 0.00 0.00 0.00 3.16
299 300 2.193536 GCCCACTCGTGCCTTTTGT 61.194 57.895 0.00 0.00 0.00 2.83
308 309 1.537990 GCATTTTTGTTGCCCACTCGT 60.538 47.619 0.00 0.00 33.95 4.18
318 319 2.235016 TGCGTCTAGGGCATTTTTGTT 58.765 42.857 5.44 0.00 35.04 2.83
319 320 1.904287 TGCGTCTAGGGCATTTTTGT 58.096 45.000 5.44 0.00 35.04 2.83
344 345 1.472480 CACCTTTTGCTCCATTACCGG 59.528 52.381 0.00 0.00 0.00 5.28
357 359 0.755686 TTTGGGCATTCGCACCTTTT 59.244 45.000 0.00 0.00 42.78 2.27
365 367 0.596082 AGACCGTTTTTGGGCATTCG 59.404 50.000 0.00 0.00 40.67 3.34
369 371 1.104577 GTCCAGACCGTTTTTGGGCA 61.105 55.000 0.00 0.00 40.67 5.36
371 373 1.616159 ATGTCCAGACCGTTTTTGGG 58.384 50.000 0.00 0.00 32.76 4.12
373 375 4.822036 TGTTATGTCCAGACCGTTTTTG 57.178 40.909 0.00 0.00 0.00 2.44
375 377 6.045072 TCTATGTTATGTCCAGACCGTTTT 57.955 37.500 0.00 0.00 0.00 2.43
384 386 8.100791 GCCCATTTACTATCTATGTTATGTCCA 58.899 37.037 0.00 0.00 0.00 4.02
390 392 9.875708 ATTTTGGCCCATTTACTATCTATGTTA 57.124 29.630 0.00 0.00 0.00 2.41
396 398 6.549736 GGTGTATTTTGGCCCATTTACTATCT 59.450 38.462 0.00 0.00 0.00 1.98
399 401 5.419471 GTGGTGTATTTTGGCCCATTTACTA 59.581 40.000 0.00 0.00 0.00 1.82
403 405 2.028567 CGTGGTGTATTTTGGCCCATTT 60.029 45.455 0.00 0.00 0.00 2.32
423 425 0.322456 TCTTGGCCATTTCTGTCCCG 60.322 55.000 6.09 0.00 0.00 5.14
425 427 1.541588 GTGTCTTGGCCATTTCTGTCC 59.458 52.381 6.09 0.00 0.00 4.02
427 429 1.956477 GTGTGTCTTGGCCATTTCTGT 59.044 47.619 6.09 0.00 0.00 3.41
432 434 0.179032 TGTCGTGTGTCTTGGCCATT 60.179 50.000 6.09 0.00 0.00 3.16
451 453 6.096846 GGAATATTTGCACCCATTTACAGTCT 59.903 38.462 0.00 0.00 0.00 3.24
453 455 5.719085 TGGAATATTTGCACCCATTTACAGT 59.281 36.000 0.00 0.00 0.00 3.55
455 457 5.971763 GTGGAATATTTGCACCCATTTACA 58.028 37.500 0.93 0.00 45.00 2.41
465 467 1.339247 ACGTCCCGTGGAATATTTGCA 60.339 47.619 0.00 0.00 39.18 4.08
467 469 5.548706 TTTTACGTCCCGTGGAATATTTG 57.451 39.130 0.00 0.00 41.39 2.32
478 480 4.492409 GCCGTTAATACTTTTTACGTCCCG 60.492 45.833 0.00 0.00 0.00 5.14
491 493 4.332428 AGACCCATAGTGCCGTTAATAC 57.668 45.455 0.00 0.00 0.00 1.89
495 497 4.506758 GTTTAAGACCCATAGTGCCGTTA 58.493 43.478 0.00 0.00 0.00 3.18
500 502 3.255969 TCCGTTTAAGACCCATAGTGC 57.744 47.619 0.00 0.00 0.00 4.40
541 543 1.135112 GTGATGTTTCCGGGCCATTTC 60.135 52.381 4.39 0.00 0.00 2.17
546 548 0.455815 GAATGTGATGTTTCCGGGCC 59.544 55.000 0.00 0.00 0.00 5.80
562 564 8.547173 TGATGTATTTTGGGCCAATTAAAGAAT 58.453 29.630 21.65 17.14 0.00 2.40
563 565 7.911651 TGATGTATTTTGGGCCAATTAAAGAA 58.088 30.769 21.65 10.65 0.00 2.52
564 566 7.487822 TGATGTATTTTGGGCCAATTAAAGA 57.512 32.000 21.65 6.07 0.00 2.52
567 569 6.409005 CCCATGATGTATTTTGGGCCAATTAA 60.409 38.462 21.65 13.06 42.23 1.40
577 579 6.972328 CCTTTTACGACCCATGATGTATTTTG 59.028 38.462 0.00 0.00 0.00 2.44
578 580 6.661805 ACCTTTTACGACCCATGATGTATTTT 59.338 34.615 0.00 0.00 0.00 1.82
585 587 2.419574 CGGACCTTTTACGACCCATGAT 60.420 50.000 0.00 0.00 0.00 2.45
592 594 1.458445 GCTTCACGGACCTTTTACGAC 59.542 52.381 0.00 0.00 0.00 4.34
593 595 1.068895 TGCTTCACGGACCTTTTACGA 59.931 47.619 0.00 0.00 0.00 3.43
594 596 1.459592 CTGCTTCACGGACCTTTTACG 59.540 52.381 0.00 0.00 0.00 3.18
595 597 1.197036 GCTGCTTCACGGACCTTTTAC 59.803 52.381 0.00 0.00 0.00 2.01
596 598 1.202710 TGCTGCTTCACGGACCTTTTA 60.203 47.619 0.00 0.00 0.00 1.52
597 599 0.465460 TGCTGCTTCACGGACCTTTT 60.465 50.000 0.00 0.00 0.00 2.27
598 600 0.250901 ATGCTGCTTCACGGACCTTT 60.251 50.000 0.00 0.00 0.00 3.11
599 601 0.957395 CATGCTGCTTCACGGACCTT 60.957 55.000 0.00 0.00 0.00 3.50
600 602 1.376424 CATGCTGCTTCACGGACCT 60.376 57.895 0.00 0.00 0.00 3.85
601 603 2.401766 CCATGCTGCTTCACGGACC 61.402 63.158 0.00 0.00 0.00 4.46
602 604 2.401766 CCCATGCTGCTTCACGGAC 61.402 63.158 0.00 0.00 0.00 4.79
603 605 2.046023 CCCATGCTGCTTCACGGA 60.046 61.111 0.00 0.00 0.00 4.69
604 606 3.818787 GCCCATGCTGCTTCACGG 61.819 66.667 0.00 0.00 33.53 4.94
605 607 3.047718 CTGCCCATGCTGCTTCACG 62.048 63.158 0.00 0.00 38.71 4.35
606 608 1.975407 ACTGCCCATGCTGCTTCAC 60.975 57.895 0.00 0.00 39.83 3.18
607 609 1.974875 CACTGCCCATGCTGCTTCA 60.975 57.895 0.00 0.00 39.83 3.02
608 610 1.246056 TTCACTGCCCATGCTGCTTC 61.246 55.000 0.00 0.00 39.83 3.86
609 611 0.828762 TTTCACTGCCCATGCTGCTT 60.829 50.000 0.00 0.00 39.83 3.91
610 612 0.828762 TTTTCACTGCCCATGCTGCT 60.829 50.000 0.00 0.00 39.83 4.24
611 613 0.389426 CTTTTCACTGCCCATGCTGC 60.389 55.000 0.00 0.00 39.83 5.25
612 614 0.389426 GCTTTTCACTGCCCATGCTG 60.389 55.000 0.00 0.00 41.75 4.41
613 615 0.541296 AGCTTTTCACTGCCCATGCT 60.541 50.000 0.00 0.00 38.71 3.79
614 616 0.108945 GAGCTTTTCACTGCCCATGC 60.109 55.000 0.00 0.00 38.26 4.06
615 617 0.169672 CGAGCTTTTCACTGCCCATG 59.830 55.000 0.00 0.00 0.00 3.66
616 618 0.036732 TCGAGCTTTTCACTGCCCAT 59.963 50.000 0.00 0.00 0.00 4.00
617 619 0.179032 TTCGAGCTTTTCACTGCCCA 60.179 50.000 0.00 0.00 0.00 5.36
618 620 0.951558 TTTCGAGCTTTTCACTGCCC 59.048 50.000 0.00 0.00 0.00 5.36
619 621 1.664302 GCTTTCGAGCTTTTCACTGCC 60.664 52.381 0.00 0.00 0.00 4.85
620 622 1.002468 TGCTTTCGAGCTTTTCACTGC 60.002 47.619 0.00 0.00 35.49 4.40
629 631 0.389948 CCGGTACTTGCTTTCGAGCT 60.390 55.000 0.00 0.00 35.49 4.09
663 665 6.273825 CACATAGTACATACTTTCGAGCCTT 58.726 40.000 0.00 0.00 37.73 4.35
666 668 5.828747 TCCACATAGTACATACTTTCGAGC 58.171 41.667 0.00 0.00 37.73 5.03
668 670 7.031372 GTGTTCCACATAGTACATACTTTCGA 58.969 38.462 0.00 0.00 34.71 3.71
670 672 6.810182 ACGTGTTCCACATAGTACATACTTTC 59.190 38.462 0.00 0.00 34.46 2.62
671 673 6.588756 CACGTGTTCCACATAGTACATACTTT 59.411 38.462 7.58 0.00 34.46 2.66
673 675 5.416639 TCACGTGTTCCACATAGTACATACT 59.583 40.000 16.51 0.00 35.86 2.12
675 677 5.900865 TCACGTGTTCCACATAGTACATA 57.099 39.130 16.51 0.00 33.40 2.29
676 678 4.794278 TCACGTGTTCCACATAGTACAT 57.206 40.909 16.51 0.00 33.40 2.29
677 679 4.587584 TTCACGTGTTCCACATAGTACA 57.412 40.909 16.51 0.00 33.40 2.90
678 680 4.565564 GGATTCACGTGTTCCACATAGTAC 59.434 45.833 25.41 0.00 33.40 2.73
679 681 4.221041 TGGATTCACGTGTTCCACATAGTA 59.779 41.667 27.68 12.03 34.65 1.82
775 981 9.681692 GCAATAAATCAATATGCACTGAATGTA 57.318 29.630 0.00 0.00 0.00 2.29
813 1019 7.201316 GCGTCCATTGATTGTTTGTGTATTTAC 60.201 37.037 0.00 0.00 0.00 2.01
820 1026 3.010624 TGCGTCCATTGATTGTTTGTG 57.989 42.857 0.00 0.00 0.00 3.33
847 1053 8.873144 AGCACTGCATTAATGGGATATATTTTT 58.127 29.630 17.02 0.00 0.00 1.94
888 1094 9.491675 TGTTTTCAATTAATGCTGTCATTGATT 57.508 25.926 7.32 7.75 44.60 2.57
896 1102 8.076910 TGGGATATGTTTTCAATTAATGCTGT 57.923 30.769 0.00 0.00 0.00 4.40
898 1104 9.768662 GAATGGGATATGTTTTCAATTAATGCT 57.231 29.630 0.00 0.00 0.00 3.79
913 1119 5.775686 ACAATCAATTGCGAATGGGATATG 58.224 37.500 0.00 0.00 41.38 1.78
927 1133 3.667360 GCCAAAGCAAGGACAATCAATT 58.333 40.909 0.00 0.00 39.53 2.32
950 1160 5.095097 GGAGGGGGCTTTCTAGTTATAGAT 58.905 45.833 0.00 0.00 37.86 1.98
1077 1961 8.413229 GCATATGTTGTAGGTTTATGAATGGTT 58.587 33.333 4.29 0.00 0.00 3.67
1251 2135 9.944079 TGGAAATTATGGGTTATTTCTTGGATA 57.056 29.630 0.00 0.00 39.53 2.59
1354 2238 0.322546 ATTCACTTGGGGGTTCTCGC 60.323 55.000 0.00 0.00 0.00 5.03
1358 2242 5.238650 CGTGATATTATTCACTTGGGGGTTC 59.761 44.000 3.41 0.00 43.10 3.62
1376 2260 6.108687 AGCATCAGAAATCAAGAACGTGATA 58.891 36.000 3.98 0.00 37.25 2.15
1382 2266 5.121454 ACGAAGAGCATCAGAAATCAAGAAC 59.879 40.000 0.00 0.00 37.82 3.01
1409 2293 1.152984 CATGCCATTGTCCGCCCTA 60.153 57.895 0.00 0.00 0.00 3.53
1430 2314 1.950828 CCAAAAGCACATGGTTGCAA 58.049 45.000 10.57 0.00 45.62 4.08
1562 2446 6.761312 TGAAATGAAATGGAGAAAAGTGCAT 58.239 32.000 0.00 0.00 0.00 3.96
1602 2486 6.381420 TGAGAAAGTAATTTGGTTGTTTGGGA 59.619 34.615 0.00 0.00 0.00 4.37
1616 2500 7.067496 TCAGTCTCCTGTTTGAGAAAGTAAT 57.933 36.000 0.00 0.00 42.75 1.89
1617 2501 6.479972 TCAGTCTCCTGTTTGAGAAAGTAA 57.520 37.500 0.00 0.00 42.75 2.24
1661 2545 9.920946 ATGTACAATATTGGATTAGAACAACCT 57.079 29.630 19.37 0.00 0.00 3.50
1679 2563 8.428063 TCCTTTGGTTTTGATTTGATGTACAAT 58.572 29.630 0.00 0.00 38.36 2.71
1690 2574 4.280677 TGCGATCTTCCTTTGGTTTTGATT 59.719 37.500 0.00 0.00 0.00 2.57
1712 2596 6.699575 ATAGTTAACCTTTTAGCATGCCTG 57.300 37.500 15.66 0.00 0.00 4.85
1713 2597 7.718334 AAATAGTTAACCTTTTAGCATGCCT 57.282 32.000 15.66 4.37 0.00 4.75
1714 2598 8.683615 ACTAAATAGTTAACCTTTTAGCATGCC 58.316 33.333 24.21 0.00 35.87 4.40
1802 2686 5.957842 AACGATTGTTGAAGCTAATCCAA 57.042 34.783 0.00 0.00 36.81 3.53
1804 2688 7.920738 AGAATAACGATTGTTGAAGCTAATCC 58.079 34.615 8.70 0.00 39.12 3.01
1806 2690 8.398665 GGAAGAATAACGATTGTTGAAGCTAAT 58.601 33.333 8.70 0.00 39.12 1.73
1821 2705 7.206687 AGCTAGAGAAAGATGGAAGAATAACG 58.793 38.462 0.00 0.00 0.00 3.18
1831 2715 5.988287 AGGAAGAAAGCTAGAGAAAGATGG 58.012 41.667 0.00 0.00 0.00 3.51
1855 2739 2.163815 GTGGAGGAAGAACGATTCGAGA 59.836 50.000 13.95 0.00 34.02 4.04
1869 2753 2.283529 GGAGGCGAACAGTGGAGGA 61.284 63.158 0.00 0.00 0.00 3.71
1874 2758 0.600255 AAACTCGGAGGCGAACAGTG 60.600 55.000 10.23 0.00 0.00 3.66
1875 2759 0.319641 GAAACTCGGAGGCGAACAGT 60.320 55.000 10.23 0.00 0.00 3.55
1876 2760 1.014564 GGAAACTCGGAGGCGAACAG 61.015 60.000 10.23 0.00 0.00 3.16
1884 2768 1.413077 GGGATGGTAGGAAACTCGGAG 59.587 57.143 2.83 2.83 43.67 4.63
1893 2777 0.105658 CGAAGGAGGGGATGGTAGGA 60.106 60.000 0.00 0.00 0.00 2.94
1923 2807 7.472334 AGCAATAAAAATCACATTCAGGTCT 57.528 32.000 0.00 0.00 0.00 3.85
1952 2836 2.920524 TCAAGGCGGTACAAAGAACAA 58.079 42.857 0.00 0.00 0.00 2.83
2035 2921 3.810941 TGTTAAGCCAGTTCACCTTAACG 59.189 43.478 14.18 0.00 46.92 3.18
2036 2922 5.298527 ACTTGTTAAGCCAGTTCACCTTAAC 59.701 40.000 12.92 12.92 45.44 2.01
2053 2939 2.888414 GGGCCAAGCTAACAACTTGTTA 59.112 45.455 4.39 12.75 42.41 2.41
2071 2957 1.073284 TCAGTCTTTACAAGGGTGGGC 59.927 52.381 0.00 0.00 0.00 5.36
2097 2985 3.750371 TCCATGACAATCGGACTTTTGT 58.250 40.909 0.00 0.00 38.71 2.83
2101 2989 2.359900 GCTTCCATGACAATCGGACTT 58.640 47.619 0.00 0.00 0.00 3.01
2105 2993 1.439353 CCGGCTTCCATGACAATCGG 61.439 60.000 0.00 0.00 0.00 4.18
2106 2994 0.744414 ACCGGCTTCCATGACAATCG 60.744 55.000 0.00 0.00 0.00 3.34
2108 2996 0.327924 TCACCGGCTTCCATGACAAT 59.672 50.000 0.00 0.00 0.00 2.71
2121 3009 1.672881 GATTGAGCAAATCCTCACCGG 59.327 52.381 0.00 0.00 41.28 5.28
2183 3071 2.799917 GCGTGTGGACAGATGAGGATAC 60.800 54.545 0.00 0.00 0.00 2.24
2189 3077 0.320683 CTTGGCGTGTGGACAGATGA 60.321 55.000 0.00 0.00 32.99 2.92
2217 3105 6.203723 AGACAACAAGCATCTTCAAGTTACTC 59.796 38.462 0.00 0.00 0.00 2.59
2234 3122 7.984391 ACGATGATTTATAATGCAGACAACAA 58.016 30.769 0.00 0.00 0.00 2.83
2264 3152 0.467804 AGTTTGGGGTGCGCAATTTT 59.532 45.000 14.00 0.00 36.27 1.82
2275 3163 9.421399 ACCTTCTATCATTTATTTAGTTTGGGG 57.579 33.333 0.00 0.00 0.00 4.96
2335 3224 7.872163 ATGTGTGTGTTTTATTATGCAAGTG 57.128 32.000 0.00 0.00 0.00 3.16
2411 3301 4.222810 TCTGGCTGTAGATGCTCACTTTAA 59.777 41.667 0.00 0.00 0.00 1.52
2429 3319 1.346068 GGAGGATATGAGTGGTCTGGC 59.654 57.143 0.00 0.00 0.00 4.85
2432 3322 1.333177 GCGGAGGATATGAGTGGTCT 58.667 55.000 0.00 0.00 0.00 3.85
2460 3350 2.185310 AATGACCAGGCTGTCCGTCC 62.185 60.000 14.43 0.31 37.47 4.79
2462 3352 1.003355 CAATGACCAGGCTGTCCGT 60.003 57.895 14.43 3.98 37.47 4.69
2472 3362 2.894765 TCTCCTGTACGAACAATGACCA 59.105 45.455 0.00 0.00 34.49 4.02
2474 3364 3.512680 CCTCTCCTGTACGAACAATGAC 58.487 50.000 0.00 0.00 34.49 3.06
2482 3372 1.914108 TCTTCTCCCTCTCCTGTACGA 59.086 52.381 0.00 0.00 0.00 3.43
2483 3373 2.421751 TCTTCTCCCTCTCCTGTACG 57.578 55.000 0.00 0.00 0.00 3.67
2503 3393 1.119684 GTCCAGTTGGGTGGCTTTTT 58.880 50.000 0.00 0.00 37.53 1.94
2507 3397 3.580319 GGGTCCAGTTGGGTGGCT 61.580 66.667 0.00 0.00 37.53 4.75
2510 3400 3.182263 TGGGGGTCCAGTTGGGTG 61.182 66.667 0.00 0.00 38.32 4.61
2511 3401 3.182996 GTGGGGGTCCAGTTGGGT 61.183 66.667 0.00 0.00 45.05 4.51
2512 3402 2.858974 AGTGGGGGTCCAGTTGGG 60.859 66.667 0.00 0.00 43.96 4.12
2555 3445 2.694628 TGCCTTGGATATGGTGATTTGC 59.305 45.455 0.00 0.00 0.00 3.68
2572 3462 5.541868 CCCGATATCCTTCTCATATATGCCT 59.458 44.000 7.92 0.00 0.00 4.75
2583 3473 5.456763 CCCAGAAAAATCCCGATATCCTTCT 60.457 44.000 0.00 0.00 0.00 2.85
2594 3484 1.893137 GGACACACCCAGAAAAATCCC 59.107 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.