Multiple sequence alignment - TraesCS5D01G034700

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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 TraesCS5D01G034700 chr5D 100.000 9084 0 0 1 9084 33708782 33699699 0.000000e+00 16776.0
1 TraesCS5D01G034700 chr5D 84.404 327 35 8 2407 2733 497146268 497145958 3.190000e-79 307.0
2 TraesCS5D01G034700 chr5D 83.792 327 37 7 2407 2733 497235038 497234728 6.900000e-76 296.0
3 TraesCS5D01G034700 chr5D 83.333 330 39 7 2404 2733 497456622 497456935 3.210000e-74 291.0
4 TraesCS5D01G034700 chr5D 97.546 163 4 0 512 674 127452142 127451980 6.950000e-71 279.0
5 TraesCS5D01G034700 chr5D 95.000 180 6 3 512 691 293426833 293427009 6.950000e-71 279.0
6 TraesCS5D01G034700 chr5D 93.333 45 3 0 3926 3970 543347336 543347380 5.890000e-07 67.6
7 TraesCS5D01G034700 chr5A 96.694 8107 161 39 669 8711 22279833 22271770 0.000000e+00 13387.0
8 TraesCS5D01G034700 chr5A 95.946 148 6 0 8937 9084 22269957 22269810 3.280000e-59 241.0
9 TraesCS5D01G034700 chr5A 87.958 191 15 5 8713 8903 22271732 22271550 1.540000e-52 219.0
10 TraesCS5D01G034700 chr5B 94.821 4151 129 29 790 4875 24924843 24920714 0.000000e+00 6396.0
11 TraesCS5D01G034700 chr5B 95.198 3769 109 21 4908 8658 24920713 24916999 0.000000e+00 5891.0
12 TraesCS5D01G034700 chr5B 89.416 1011 40 14 2911 3882 79771846 79770864 0.000000e+00 1212.0
13 TraesCS5D01G034700 chr5B 95.088 509 18 5 2911 3416 473797786 473797282 0.000000e+00 795.0
14 TraesCS5D01G034700 chr5B 91.813 171 13 1 8713 8883 24916453 24916284 4.240000e-58 237.0
15 TraesCS5D01G034700 chr5B 94.194 155 4 2 8934 9084 24915840 24915687 1.970000e-56 231.0
16 TraesCS5D01G034700 chr5B 91.753 97 7 1 710 806 24924948 24924853 5.720000e-27 134.0
17 TraesCS5D01G034700 chr2B 89.802 1010 37 14 2911 3882 467488508 467489489 0.000000e+00 1234.0
18 TraesCS5D01G034700 chr6B 89.713 1011 37 15 2911 3882 481038801 481039783 0.000000e+00 1229.0
19 TraesCS5D01G034700 chr6B 89.604 1010 39 14 2911 3882 123888826 123887845 0.000000e+00 1223.0
20 TraesCS5D01G034700 chr6B 92.342 666 26 3 2911 3552 218966168 218965504 0.000000e+00 924.0
21 TraesCS5D01G034700 chr6B 83.133 83 7 4 3894 3969 350831935 350831853 1.640000e-07 69.4
22 TraesCS5D01G034700 chr7B 89.604 1010 39 14 2911 3882 513731616 513730635 0.000000e+00 1223.0
23 TraesCS5D01G034700 chr7B 100.000 28 0 0 3957 3984 516814283 516814256 1.600000e-02 52.8
24 TraesCS5D01G034700 chr1A 89.604 1010 39 14 2911 3882 278156591 278157572 0.000000e+00 1223.0
25 TraesCS5D01G034700 chr1A 88.953 344 34 4 163 505 536670336 536670676 1.090000e-113 422.0
26 TraesCS5D01G034700 chr3B 89.406 1010 40 15 2911 3882 792619829 792618849 0.000000e+00 1210.0
27 TraesCS5D01G034700 chr7D 87.154 506 52 7 1 505 530556623 530557116 6.160000e-156 562.0
28 TraesCS5D01G034700 chr7D 93.623 345 21 1 159 503 602783059 602782716 1.750000e-141 514.0
29 TraesCS5D01G034700 chr7D 98.160 163 3 0 512 674 363554708 363554546 1.490000e-72 285.0
30 TraesCS5D01G034700 chr7D 97.546 163 4 0 512 674 224070725 224070887 6.950000e-71 279.0
31 TraesCS5D01G034700 chr7D 96.988 166 5 0 512 677 461573035 461572870 6.950000e-71 279.0
32 TraesCS5D01G034700 chr7D 96.933 163 5 0 512 674 121683292 121683130 3.230000e-69 274.0
33 TraesCS5D01G034700 chr7D 94.444 162 8 1 1 161 602783327 602783166 1.960000e-61 248.0
34 TraesCS5D01G034700 chr7D 83.529 85 5 4 3894 3969 628666073 628665989 4.550000e-08 71.3
35 TraesCS5D01G034700 chrUn 86.355 557 25 11 3350 3882 410374700 410374171 2.210000e-155 560.0
36 TraesCS5D01G034700 chrUn 91.139 158 14 0 1 158 185728648 185728805 1.990000e-51 215.0
37 TraesCS5D01G034700 chr4A 94.587 351 18 1 159 508 606505243 606505593 8.020000e-150 542.0
38 TraesCS5D01G034700 chr4A 96.296 162 5 1 1 161 606504975 606505136 1.940000e-66 265.0
39 TraesCS5D01G034700 chr4A 75.969 258 45 13 428 677 441762165 441762413 5.760000e-22 117.0
40 TraesCS5D01G034700 chr3A 93.696 349 19 2 159 505 621921327 621921674 3.760000e-143 520.0
41 TraesCS5D01G034700 chr3A 89.943 348 31 3 159 504 590370977 590371322 6.470000e-121 446.0
42 TraesCS5D01G034700 chr3A 96.296 162 5 1 1 161 590370709 590370870 1.940000e-66 265.0
43 TraesCS5D01G034700 chr3A 92.994 157 10 1 6 161 621921064 621921220 2.550000e-55 228.0
44 TraesCS5D01G034700 chr3A 87.179 78 8 2 3894 3970 365354962 365355038 4.520000e-13 87.9
45 TraesCS5D01G034700 chr3A 82.759 87 5 7 3894 3971 550510612 550510697 1.640000e-07 69.4
46 TraesCS5D01G034700 chr3A 97.436 39 1 0 3931 3969 434843977 434843939 5.890000e-07 67.6
47 TraesCS5D01G034700 chr2A 89.685 349 32 4 159 506 754020608 754020263 8.370000e-120 442.0
48 TraesCS5D01G034700 chr6D 89.826 344 34 1 164 506 71360166 71360509 3.010000e-119 440.0
49 TraesCS5D01G034700 chr6D 83.486 327 48 5 2410 2733 438551472 438551149 5.330000e-77 300.0
50 TraesCS5D01G034700 chr6D 93.038 158 11 0 1 158 328837917 328837760 1.970000e-56 231.0
51 TraesCS5D01G034700 chr6D 91.772 158 13 0 1 158 71359893 71360050 4.270000e-53 220.0
52 TraesCS5D01G034700 chr3D 88.251 366 39 3 2407 2772 129679076 129678715 1.400000e-117 435.0
53 TraesCS5D01G034700 chr3D 89.244 344 35 2 164 505 327463223 327463566 6.520000e-116 429.0
54 TraesCS5D01G034700 chr3D 93.038 158 11 0 1 158 327462950 327463107 1.970000e-56 231.0
55 TraesCS5D01G034700 chr3D 81.000 100 19 0 5108 5207 559647203 559647104 7.560000e-11 80.5
56 TraesCS5D01G034700 chr2D 87.772 368 40 4 2404 2771 42697024 42697386 8.430000e-115 425.0
57 TraesCS5D01G034700 chr2D 85.714 364 30 5 2829 3191 602417603 602417945 1.860000e-96 364.0
58 TraesCS5D01G034700 chr2D 84.242 330 36 7 2404 2733 80982375 80982688 3.190000e-79 307.0
59 TraesCS5D01G034700 chr2D 97.605 167 3 1 512 678 475083656 475083491 1.490000e-72 285.0
60 TraesCS5D01G034700 chr7A 96.386 166 6 0 512 677 61888701 61888866 3.230000e-69 274.0
61 TraesCS5D01G034700 chr7A 93.038 158 11 0 1 158 8218169 8218012 1.970000e-56 231.0
62 TraesCS5D01G034700 chr4D 96.933 163 5 0 512 674 468208644 468208806 3.230000e-69 274.0
63 TraesCS5D01G034700 chr4D 100.000 28 0 0 3950 3977 398568012 398567985 1.600000e-02 52.8
64 TraesCS5D01G034700 chr4B 100.000 28 0 0 3950 3977 491119038 491119011 1.600000e-02 52.8


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 TraesCS5D01G034700 chr5D 33699699 33708782 9083 True 16776.000000 16776 100.000000 1 9084 1 chr5D.!!$R1 9083
1 TraesCS5D01G034700 chr5A 22269810 22279833 10023 True 4615.666667 13387 93.532667 669 9084 3 chr5A.!!$R1 8415
2 TraesCS5D01G034700 chr5B 24915687 24924948 9261 True 2577.800000 6396 93.555800 710 9084 5 chr5B.!!$R3 8374
3 TraesCS5D01G034700 chr5B 79770864 79771846 982 True 1212.000000 1212 89.416000 2911 3882 1 chr5B.!!$R1 971
4 TraesCS5D01G034700 chr5B 473797282 473797786 504 True 795.000000 795 95.088000 2911 3416 1 chr5B.!!$R2 505
5 TraesCS5D01G034700 chr2B 467488508 467489489 981 False 1234.000000 1234 89.802000 2911 3882 1 chr2B.!!$F1 971
6 TraesCS5D01G034700 chr6B 481038801 481039783 982 False 1229.000000 1229 89.713000 2911 3882 1 chr6B.!!$F1 971
7 TraesCS5D01G034700 chr6B 123887845 123888826 981 True 1223.000000 1223 89.604000 2911 3882 1 chr6B.!!$R1 971
8 TraesCS5D01G034700 chr6B 218965504 218966168 664 True 924.000000 924 92.342000 2911 3552 1 chr6B.!!$R2 641
9 TraesCS5D01G034700 chr7B 513730635 513731616 981 True 1223.000000 1223 89.604000 2911 3882 1 chr7B.!!$R1 971
10 TraesCS5D01G034700 chr1A 278156591 278157572 981 False 1223.000000 1223 89.604000 2911 3882 1 chr1A.!!$F1 971
11 TraesCS5D01G034700 chr3B 792618849 792619829 980 True 1210.000000 1210 89.406000 2911 3882 1 chr3B.!!$R1 971
12 TraesCS5D01G034700 chr7D 602782716 602783327 611 True 381.000000 514 94.033500 1 503 2 chr7D.!!$R5 502
13 TraesCS5D01G034700 chrUn 410374171 410374700 529 True 560.000000 560 86.355000 3350 3882 1 chrUn.!!$R1 532
14 TraesCS5D01G034700 chr4A 606504975 606505593 618 False 403.500000 542 95.441500 1 508 2 chr4A.!!$F2 507
15 TraesCS5D01G034700 chr3A 621921064 621921674 610 False 374.000000 520 93.345000 6 505 2 chr3A.!!$F4 499
16 TraesCS5D01G034700 chr3A 590370709 590371322 613 False 355.500000 446 93.119500 1 504 2 chr3A.!!$F3 503
17 TraesCS5D01G034700 chr6D 71359893 71360509 616 False 330.000000 440 90.799000 1 506 2 chr6D.!!$F1 505
18 TraesCS5D01G034700 chr3D 327462950 327463566 616 False 330.000000 429 91.141000 1 505 2 chr3D.!!$F1 504

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
526 645 0.033306 GGAGTACTCCCTCCGTTCCT 60.033 60.000 28.87 0.0 43.94 3.36 F
1471 1645 1.190643 AGACTCTGCCTCTACTTGCC 58.809 55.000 0.00 0.0 0.00 4.52 F
2222 2406 1.066286 GCTCTGTCTCCAGCATGTCTT 60.066 52.381 0.00 0.0 38.66 3.01 F
3607 3836 2.028567 GCTTATAGCCCGCATCTTCTCT 60.029 50.000 0.00 0.0 34.48 3.10 F
3882 4120 2.968675 ACGAAGTATACACCAGGTTGC 58.031 47.619 5.50 0.0 41.94 4.17 F
5054 5295 0.889994 GTGGATTGTTGGCTGATGCA 59.110 50.000 0.00 0.0 41.91 3.96 F
5099 5340 2.359975 CCCAGGCCCTGTTTCGAC 60.360 66.667 10.47 0.0 0.00 4.20 F
5100 5341 2.742372 CCAGGCCCTGTTTCGACG 60.742 66.667 10.47 0.0 0.00 5.12 F
6947 7192 3.321682 TCAAATAACTGGCAAAAGCAGCT 59.678 39.130 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1723 0.527385 TACGTAATAACCCGCGCACC 60.527 55.000 8.75 0.00 0.00 5.01 R
2449 2637 2.751259 ACTTGCTGCATGGTGTAATGAG 59.249 45.455 18.21 5.00 0.00 2.90 R
3778 4016 0.465705 GGCTCAATCCAGATCGGTCA 59.534 55.000 0.00 0.00 35.57 4.02 R
4848 5088 2.045045 GCCAGGCACCACATAGCA 60.045 61.111 6.55 0.00 0.00 3.49 R
5797 6039 2.095567 GCACTGGTATCACAGCTGTTTG 60.096 50.000 18.94 7.39 42.21 2.93 R
6539 6784 1.512926 CACCTTCACTGTCTTTCGGG 58.487 55.000 0.00 0.00 0.00 5.14 R
6967 7212 3.065925 CAGCATCGGAGCTCATATCGATA 59.934 47.826 20.40 7.75 44.54 2.92 R
7196 7441 2.012673 CTCAGGAAGCGAATCCAAAGG 58.987 52.381 9.28 0.00 42.27 3.11 R
9041 11657 0.034059 CGGAGCACTGAGTTGTCCTT 59.966 55.000 8.05 0.00 0.00 3.36 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
276 394 1.867919 GCGTCGATCTCATCCCCGAT 61.868 60.000 0.00 0.00 33.47 4.18
297 415 2.944557 CATCGCACCGTCGACGAG 60.945 66.667 37.65 28.33 41.62 4.18
338 456 2.755103 GGGCCGATGAGAAATGAAAACT 59.245 45.455 0.00 0.00 0.00 2.66
382 500 2.742372 CGACGGGCAGGTTTCAGG 60.742 66.667 0.00 0.00 0.00 3.86
466 585 7.147983 TGCAAGTTTTTGTATGAAACTGTACCT 60.148 33.333 3.31 0.00 44.24 3.08
525 644 2.502633 GGAGTACTCCCTCCGTTCC 58.497 63.158 28.87 3.41 43.94 3.62
526 645 0.033306 GGAGTACTCCCTCCGTTCCT 60.033 60.000 28.87 0.00 43.94 3.36
527 646 1.213926 GGAGTACTCCCTCCGTTCCTA 59.786 57.143 28.87 0.00 43.94 2.94
528 647 2.357569 GGAGTACTCCCTCCGTTCCTAA 60.358 54.545 28.87 0.00 43.94 2.69
529 648 3.359950 GAGTACTCCCTCCGTTCCTAAA 58.640 50.000 12.13 0.00 0.00 1.85
530 649 3.959449 GAGTACTCCCTCCGTTCCTAAAT 59.041 47.826 12.13 0.00 0.00 1.40
531 650 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
532 651 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
533 652 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
534 653 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
535 654 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
536 655 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
537 656 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
538 657 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
539 658 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
540 659 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
541 660 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
542 661 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
573 692 5.171147 CACTAGGTGGACTACATACGAAG 57.829 47.826 0.00 0.00 0.00 3.79
574 693 3.631227 ACTAGGTGGACTACATACGAAGC 59.369 47.826 0.00 0.00 0.00 3.86
575 694 2.453521 AGGTGGACTACATACGAAGCA 58.546 47.619 0.00 0.00 0.00 3.91
576 695 2.829720 AGGTGGACTACATACGAAGCAA 59.170 45.455 0.00 0.00 0.00 3.91
577 696 3.259876 AGGTGGACTACATACGAAGCAAA 59.740 43.478 0.00 0.00 0.00 3.68
578 697 4.081087 AGGTGGACTACATACGAAGCAAAT 60.081 41.667 0.00 0.00 0.00 2.32
579 698 4.634443 GGTGGACTACATACGAAGCAAATT 59.366 41.667 0.00 0.00 0.00 1.82
580 699 5.447279 GGTGGACTACATACGAAGCAAATTG 60.447 44.000 0.00 0.00 0.00 2.32
581 700 5.350365 GTGGACTACATACGAAGCAAATTGA 59.650 40.000 0.00 0.00 0.00 2.57
582 701 5.935206 TGGACTACATACGAAGCAAATTGAA 59.065 36.000 0.00 0.00 0.00 2.69
583 702 6.597672 TGGACTACATACGAAGCAAATTGAAT 59.402 34.615 0.00 0.00 0.00 2.57
584 703 6.907212 GGACTACATACGAAGCAAATTGAATG 59.093 38.462 0.00 0.00 0.00 2.67
585 704 7.201609 GGACTACATACGAAGCAAATTGAATGA 60.202 37.037 0.00 0.00 0.00 2.57
586 705 8.039603 ACTACATACGAAGCAAATTGAATGAA 57.960 30.769 0.00 0.00 0.00 2.57
587 706 8.677300 ACTACATACGAAGCAAATTGAATGAAT 58.323 29.630 0.00 0.00 0.00 2.57
588 707 7.975866 ACATACGAAGCAAATTGAATGAATC 57.024 32.000 0.00 0.00 0.00 2.52
589 708 7.765307 ACATACGAAGCAAATTGAATGAATCT 58.235 30.769 0.00 0.00 0.00 2.40
590 709 8.892723 ACATACGAAGCAAATTGAATGAATCTA 58.107 29.630 0.00 0.00 0.00 1.98
591 710 9.162793 CATACGAAGCAAATTGAATGAATCTAC 57.837 33.333 0.00 0.00 0.00 2.59
592 711 7.144722 ACGAAGCAAATTGAATGAATCTACA 57.855 32.000 0.00 0.00 0.00 2.74
593 712 7.023575 ACGAAGCAAATTGAATGAATCTACAC 58.976 34.615 0.00 0.00 0.00 2.90
594 713 7.094634 ACGAAGCAAATTGAATGAATCTACACT 60.095 33.333 0.00 0.00 0.00 3.55
595 714 7.752239 CGAAGCAAATTGAATGAATCTACACTT 59.248 33.333 0.00 0.00 0.00 3.16
624 743 7.582667 TCCATCTATATACATCCGTATGTGG 57.417 40.000 3.56 0.00 45.99 4.17
625 744 7.123383 TCCATCTATATACATCCGTATGTGGT 58.877 38.462 3.56 0.00 45.99 4.16
626 745 7.618117 TCCATCTATATACATCCGTATGTGGTT 59.382 37.037 3.56 0.00 45.99 3.67
627 746 7.921214 CCATCTATATACATCCGTATGTGGTTC 59.079 40.741 3.56 0.00 45.99 3.62
628 747 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
629 748 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
630 749 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
631 750 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
632 751 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
633 752 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
634 753 3.812156 TCCGTATGTGGTTCATAGTGG 57.188 47.619 0.00 0.00 39.36 4.00
635 754 3.367321 TCCGTATGTGGTTCATAGTGGA 58.633 45.455 0.00 0.00 39.94 4.02
636 755 3.770388 TCCGTATGTGGTTCATAGTGGAA 59.230 43.478 0.00 0.00 39.60 3.53
637 756 4.407621 TCCGTATGTGGTTCATAGTGGAAT 59.592 41.667 0.00 0.00 39.60 3.01
638 757 4.750098 CCGTATGTGGTTCATAGTGGAATC 59.250 45.833 0.00 0.00 39.36 2.52
639 758 5.453339 CCGTATGTGGTTCATAGTGGAATCT 60.453 44.000 0.00 0.00 39.36 2.40
640 759 5.692204 CGTATGTGGTTCATAGTGGAATCTC 59.308 44.000 0.00 0.00 39.36 2.75
641 760 5.965033 ATGTGGTTCATAGTGGAATCTCT 57.035 39.130 0.00 0.00 34.67 3.10
642 761 7.255486 CGTATGTGGTTCATAGTGGAATCTCTA 60.255 40.741 0.00 0.00 39.36 2.43
643 762 6.222038 TGTGGTTCATAGTGGAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
644 763 5.719563 TGTGGTTCATAGTGGAATCTCTACA 59.280 40.000 0.00 0.00 29.47 2.74
645 764 6.212589 TGTGGTTCATAGTGGAATCTCTACAA 59.787 38.462 0.00 0.00 29.47 2.41
646 765 7.103641 GTGGTTCATAGTGGAATCTCTACAAA 58.896 38.462 0.00 0.00 29.47 2.83
647 766 7.278868 GTGGTTCATAGTGGAATCTCTACAAAG 59.721 40.741 0.00 0.00 29.47 2.77
648 767 7.180229 TGGTTCATAGTGGAATCTCTACAAAGA 59.820 37.037 0.00 0.00 29.47 2.52
649 768 7.492994 GGTTCATAGTGGAATCTCTACAAAGAC 59.507 40.741 0.00 0.00 29.47 3.01
650 769 7.962995 TCATAGTGGAATCTCTACAAAGACT 57.037 36.000 0.00 0.00 29.47 3.24
651 770 8.367660 TCATAGTGGAATCTCTACAAAGACTT 57.632 34.615 0.00 0.00 29.47 3.01
652 771 9.475620 TCATAGTGGAATCTCTACAAAGACTTA 57.524 33.333 0.00 0.00 29.47 2.24
736 861 4.670227 AAACGATAAGAAAGACAGCAGC 57.330 40.909 0.00 0.00 0.00 5.25
743 868 3.909086 AAAGACAGCAGCCGAGGCC 62.909 63.158 10.95 0.00 43.17 5.19
859 1010 3.804873 CGTAAATAGCAGCCTTCTCCTTC 59.195 47.826 0.00 0.00 0.00 3.46
961 1124 2.435938 GTCTCCAAATCCGCCGCA 60.436 61.111 0.00 0.00 0.00 5.69
1454 1628 1.679139 CACCTGGTGAGCACAAAAGA 58.321 50.000 22.33 0.00 35.23 2.52
1471 1645 1.190643 AGACTCTGCCTCTACTTGCC 58.809 55.000 0.00 0.00 0.00 4.52
1512 1686 8.155510 CGGATCATGGATTGGATGAATAGATAT 58.844 37.037 0.00 0.00 33.59 1.63
1548 1722 2.977580 TGCCTAGATTCTGATCATGCCT 59.022 45.455 0.00 0.00 34.60 4.75
1549 1723 3.244457 TGCCTAGATTCTGATCATGCCTG 60.244 47.826 0.00 0.00 34.60 4.85
1569 1743 1.276415 GTGCGCGGGTTATTACGTAA 58.724 50.000 11.02 11.02 0.00 3.18
1752 1931 4.020485 GGGAGTTAGAGAACCAAGCTTGTA 60.020 45.833 24.35 6.89 36.08 2.41
2037 2216 5.694231 TTAGTGACACGCTTACTAACTGA 57.306 39.130 0.00 0.00 33.36 3.41
2038 2217 4.579454 AGTGACACGCTTACTAACTGAA 57.421 40.909 0.00 0.00 0.00 3.02
2222 2406 1.066286 GCTCTGTCTCCAGCATGTCTT 60.066 52.381 0.00 0.00 38.66 3.01
2226 2410 3.071457 TCTGTCTCCAGCATGTCTTGAAA 59.929 43.478 0.00 0.00 38.66 2.69
2300 2485 5.920840 TGTCGTTTCATCTCTAGTTTGTCTG 59.079 40.000 0.00 0.00 0.00 3.51
2302 2487 4.201532 CGTTTCATCTCTAGTTTGTCTGCG 60.202 45.833 0.00 0.00 0.00 5.18
2449 2637 7.094334 CCCACTTTAAACTATTCTGAGGGAAAC 60.094 40.741 0.00 0.00 37.49 2.78
2494 2682 5.026121 TCAGACCAAGAGATCTGGTATTGT 58.974 41.667 0.00 0.00 42.25 2.71
2554 2742 6.823286 TGGATGGGAAGTGAGATTACATAA 57.177 37.500 0.00 0.00 0.00 1.90
2737 2925 3.876320 GGCATTCTGATTCTCTCAAGTCC 59.124 47.826 0.00 0.00 32.14 3.85
2813 3001 5.401531 AATGCTTAGAGTTTCGGTCACTA 57.598 39.130 0.00 0.00 0.00 2.74
2919 3107 4.273318 AGAAAGGTTTCTCAGCAGTGTTT 58.727 39.130 0.00 0.00 43.72 2.83
3278 3484 7.999679 TCTCGATCAAATTTGCCATTCTATTT 58.000 30.769 13.54 0.00 0.00 1.40
3547 3776 7.551617 GTGCACATGGGTAGTAAGTAACTAATT 59.448 37.037 13.17 0.00 42.37 1.40
3607 3836 2.028567 GCTTATAGCCCGCATCTTCTCT 60.029 50.000 0.00 0.00 34.48 3.10
3665 3894 4.082571 AGTGCTAGCCTGTTTATTTGCAAG 60.083 41.667 13.29 0.00 0.00 4.01
3738 3973 9.630098 AAGCATGTTTAGCATTGTATATATTGC 57.370 29.630 7.94 7.94 35.19 3.56
3778 4016 8.223378 TCCCTCCATAATATCAAAGATGATGT 57.777 34.615 1.69 0.00 45.82 3.06
3779 4017 8.105197 TCCCTCCATAATATCAAAGATGATGTG 58.895 37.037 1.69 0.00 45.82 3.21
3882 4120 2.968675 ACGAAGTATACACCAGGTTGC 58.031 47.619 5.50 0.00 41.94 4.17
3909 4147 4.080243 TCCTAGTTACTCCCTCTGTCTCAG 60.080 50.000 0.00 0.00 0.00 3.35
4705 4945 3.305950 GCATGGTTGGCAATGTGTTAAGA 60.306 43.478 1.92 0.00 0.00 2.10
4848 5088 3.826729 GGTCTAGTTTGGTTTGCATCCTT 59.173 43.478 9.35 0.00 0.00 3.36
4882 5122 4.421554 CCTGGAGCCTCCCTGGGA 62.422 72.222 16.13 16.13 40.45 4.37
4994 5235 3.196685 GTCAGATTCTAGTTGCCTGGACT 59.803 47.826 0.00 0.00 0.00 3.85
5044 5285 2.607499 TCCATTTGCAGGTGGATTGTT 58.393 42.857 15.78 0.00 39.51 2.83
5054 5295 0.889994 GTGGATTGTTGGCTGATGCA 59.110 50.000 0.00 0.00 41.91 3.96
5099 5340 2.359975 CCCAGGCCCTGTTTCGAC 60.360 66.667 10.47 0.00 0.00 4.20
5100 5341 2.742372 CCAGGCCCTGTTTCGACG 60.742 66.667 10.47 0.00 0.00 5.12
5569 5811 7.342581 TGATACATGCCAGGTTAGTTTTATGA 58.657 34.615 0.00 0.00 0.00 2.15
5797 6039 3.578688 GCAAGTCAAATCATCAACACCC 58.421 45.455 0.00 0.00 0.00 4.61
6023 6265 3.644966 ATGAATGTGGGTAATGGTCGT 57.355 42.857 0.00 0.00 0.00 4.34
6359 6603 4.593206 CCTCCTGGTTGCTGAGGTATTATA 59.407 45.833 0.00 0.00 40.66 0.98
6360 6604 5.249393 CCTCCTGGTTGCTGAGGTATTATAT 59.751 44.000 0.00 0.00 40.66 0.86
6361 6605 6.240002 CCTCCTGGTTGCTGAGGTATTATATT 60.240 42.308 0.00 0.00 40.66 1.28
6362 6606 7.149202 TCCTGGTTGCTGAGGTATTATATTT 57.851 36.000 0.00 0.00 0.00 1.40
6430 6675 9.199982 CCTGCATGCTTCCTTAATATATTTTTG 57.800 33.333 20.33 0.00 0.00 2.44
6539 6784 7.360438 GGAGATAAATTGGTTGCATATCGACTC 60.360 40.741 0.00 0.00 0.00 3.36
6743 6988 6.716934 TTTCAGATAGAGCCTTCTTACGAT 57.283 37.500 0.00 0.00 34.79 3.73
6787 7032 3.536570 GTCCTCCATCTCTAGTTTTGGC 58.463 50.000 0.00 0.00 0.00 4.52
6947 7192 3.321682 TCAAATAACTGGCAAAAGCAGCT 59.678 39.130 0.00 0.00 0.00 4.24
6967 7212 5.411977 CAGCTCTGTGAATGAAACTTCAGAT 59.588 40.000 0.00 0.00 41.08 2.90
7196 7441 5.163713 GGTCTCAAGCAATACAACCTTGATC 60.164 44.000 3.16 0.00 42.65 2.92
7228 7473 3.555168 CGCTTCCTGAGGTTTACAAGACT 60.555 47.826 0.00 0.00 0.00 3.24
7765 8015 1.574702 CGTTCTTTTCCCCGCTGACC 61.575 60.000 0.00 0.00 0.00 4.02
7771 8021 0.106419 TTTCCCCGCTGACCTGTTTT 60.106 50.000 0.00 0.00 0.00 2.43
7810 8060 0.955919 AGCCCGCTAAGCAAACACTC 60.956 55.000 0.00 0.00 0.00 3.51
7811 8061 1.923227 GCCCGCTAAGCAAACACTCC 61.923 60.000 0.00 0.00 0.00 3.85
7812 8062 0.605319 CCCGCTAAGCAAACACTCCA 60.605 55.000 0.00 0.00 0.00 3.86
7813 8063 1.453155 CCGCTAAGCAAACACTCCAT 58.547 50.000 0.00 0.00 0.00 3.41
7814 8064 2.627945 CCGCTAAGCAAACACTCCATA 58.372 47.619 0.00 0.00 0.00 2.74
7815 8065 3.206150 CCGCTAAGCAAACACTCCATAT 58.794 45.455 0.00 0.00 0.00 1.78
7816 8066 3.002656 CCGCTAAGCAAACACTCCATATG 59.997 47.826 0.00 0.00 0.00 1.78
7817 8067 3.623060 CGCTAAGCAAACACTCCATATGT 59.377 43.478 1.24 0.00 0.00 2.29
7818 8068 4.494690 CGCTAAGCAAACACTCCATATGTG 60.495 45.833 1.24 0.00 40.87 3.21
7819 8069 3.855689 AAGCAAACACTCCATATGTGC 57.144 42.857 1.24 3.13 38.86 4.57
7820 8070 2.794103 AGCAAACACTCCATATGTGCA 58.206 42.857 12.91 0.00 38.86 4.57
7821 8071 3.156293 AGCAAACACTCCATATGTGCAA 58.844 40.909 12.91 0.00 38.86 4.08
7822 8072 3.192001 AGCAAACACTCCATATGTGCAAG 59.808 43.478 12.91 3.45 38.86 4.01
7823 8073 3.057315 GCAAACACTCCATATGTGCAAGT 60.057 43.478 1.24 0.00 38.86 3.16
8090 8340 0.325933 TGATGACTTGTGAGCCTGGG 59.674 55.000 0.00 0.00 0.00 4.45
8235 8486 0.107654 GGAACCGACATGGAAGGGAG 60.108 60.000 0.00 0.00 42.00 4.30
8373 8624 4.150451 GCGTTTGAAACCCATGATTTTCTG 59.850 41.667 15.75 7.85 33.61 3.02
8380 8631 2.418368 CCATGATTTTCTGGGGTCGA 57.582 50.000 0.00 0.00 0.00 4.20
8381 8632 2.292267 CCATGATTTTCTGGGGTCGAG 58.708 52.381 0.00 0.00 0.00 4.04
8382 8633 2.092968 CCATGATTTTCTGGGGTCGAGA 60.093 50.000 0.00 0.00 0.00 4.04
8385 8636 4.301072 TGATTTTCTGGGGTCGAGAAAT 57.699 40.909 6.06 0.00 38.81 2.17
8403 8656 9.101325 TCGAGAAATGGGGTAGATAATTTATCT 57.899 33.333 19.92 19.92 46.67 1.98
8404 8657 9.372369 CGAGAAATGGGGTAGATAATTTATCTC 57.628 37.037 19.69 12.44 44.09 2.75
8427 8688 2.973694 TATACCGCTGTTGTTCCCTC 57.026 50.000 0.00 0.00 0.00 4.30
8472 8733 5.945784 TGTGAACTCCTGCTGCTAATATTTT 59.054 36.000 0.00 0.00 0.00 1.82
8510 8771 6.724893 TTATATACAGCTGCAACCTGAGTA 57.275 37.500 15.27 11.21 34.47 2.59
8511 8772 2.743636 TACAGCTGCAACCTGAGTAC 57.256 50.000 15.27 0.00 34.47 2.73
8524 8786 2.724690 CCTGAGTACAGTTTTGTCGTCG 59.275 50.000 0.00 0.00 42.05 5.12
8546 8808 4.060205 GTTGTTGGGACTCGCTAGTAAAA 58.940 43.478 0.00 0.00 35.56 1.52
8616 8878 3.502211 CGGTTCTGTTTGCCTCAATAACT 59.498 43.478 0.00 0.00 0.00 2.24
8622 8884 2.979813 GTTTGCCTCAATAACTTGCACG 59.020 45.455 0.00 0.00 32.11 5.34
8629 8891 1.241315 AATAACTTGCACGCGGCCTT 61.241 50.000 12.47 5.43 43.89 4.35
8684 9401 1.379044 GGTCACCAAGCCATCCAGG 60.379 63.158 0.00 0.00 41.84 4.45
8712 9429 2.164422 GCTAAGTCCATTGAACTTGCCC 59.836 50.000 0.00 0.00 37.52 5.36
8713 9430 1.247567 AAGTCCATTGAACTTGCCCG 58.752 50.000 0.00 0.00 35.68 6.13
8714 9431 0.400213 AGTCCATTGAACTTGCCCGA 59.600 50.000 0.00 0.00 0.00 5.14
8715 9432 0.521735 GTCCATTGAACTTGCCCGAC 59.478 55.000 0.00 0.00 0.00 4.79
8764 9517 1.688197 CATGGTGTCCAAAGTTGCCTT 59.312 47.619 0.00 0.00 36.95 4.35
8767 9520 0.389025 GTGTCCAAAGTTGCCTTGGG 59.611 55.000 1.95 0.00 42.49 4.12
8817 9570 1.942776 TCTTGCTCTCAGGATGGACA 58.057 50.000 0.00 0.00 36.16 4.02
8821 9574 1.339438 TGCTCTCAGGATGGACAAAGC 60.339 52.381 0.00 0.00 36.16 3.51
8863 9616 0.321564 CTGAATTGGACTGGGCGACA 60.322 55.000 0.00 0.00 0.00 4.35
8879 9632 1.609208 GACACACAATGGTTGGCTCT 58.391 50.000 0.00 0.00 34.12 4.09
8883 9636 0.251297 CACAATGGTTGGCTCTGGGA 60.251 55.000 0.00 0.00 34.12 4.37
8919 9718 2.092212 CCCAGCCATCATTTGAGGTAGT 60.092 50.000 0.00 0.00 0.00 2.73
8920 9719 3.209410 CCAGCCATCATTTGAGGTAGTC 58.791 50.000 0.00 0.00 0.00 2.59
8924 9723 3.678806 GCCATCATTTGAGGTAGTCGACA 60.679 47.826 19.50 0.48 0.00 4.35
8926 9725 4.494484 CATCATTTGAGGTAGTCGACACA 58.506 43.478 19.50 1.48 0.00 3.72
8927 9726 3.909430 TCATTTGAGGTAGTCGACACAC 58.091 45.455 19.50 14.56 0.00 3.82
8928 9727 3.319689 TCATTTGAGGTAGTCGACACACA 59.680 43.478 19.50 13.61 0.00 3.72
8929 9728 3.804786 TTTGAGGTAGTCGACACACAA 57.195 42.857 19.50 17.67 0.00 3.33
8930 9729 4.330944 TTTGAGGTAGTCGACACACAAT 57.669 40.909 19.50 7.55 0.00 2.71
8931 9730 3.297830 TGAGGTAGTCGACACACAATG 57.702 47.619 19.50 0.00 0.00 2.82
9041 11657 1.377202 GCAGATTTGGCGTCCTGGA 60.377 57.895 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.576078 TGGGTGTGATGTTCAGAGTTT 57.424 42.857 0.00 0.00 0.00 2.66
118 119 3.334691 GCCTGCTTGTCATTGTGTACTA 58.665 45.455 0.00 0.00 0.00 1.82
136 137 2.588620 TGTTTTGTGGTATTTCCGCCT 58.411 42.857 0.00 0.00 45.41 5.52
276 394 3.366915 TCGACGGTGCGATGGTCA 61.367 61.111 0.00 0.00 35.01 4.02
297 415 2.226674 CCTTTCGCCTTTCTGTTTCTCC 59.773 50.000 0.00 0.00 0.00 3.71
338 456 2.027073 GCACGCACCGATCACTTCA 61.027 57.895 0.00 0.00 0.00 3.02
382 500 5.266242 CGGAACAAGCTGATACAAATTAGC 58.734 41.667 0.00 0.00 43.33 3.09
466 585 5.553290 TTAATACATAAACTTGCAGCGCA 57.447 34.783 11.47 0.00 36.47 6.09
508 627 2.725221 TAGGAACGGAGGGAGTACTC 57.275 55.000 14.87 14.87 36.76 2.59
509 628 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
510 629 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
511 630 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
512 631 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
513 632 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
514 633 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
515 634 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
516 635 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
551 670 4.497674 GCTTCGTATGTAGTCCACCTAGTG 60.498 50.000 0.00 0.00 0.00 2.74
552 671 3.631227 GCTTCGTATGTAGTCCACCTAGT 59.369 47.826 0.00 0.00 0.00 2.57
553 672 3.630769 TGCTTCGTATGTAGTCCACCTAG 59.369 47.826 0.00 0.00 0.00 3.02
554 673 3.623703 TGCTTCGTATGTAGTCCACCTA 58.376 45.455 0.00 0.00 0.00 3.08
555 674 2.453521 TGCTTCGTATGTAGTCCACCT 58.546 47.619 0.00 0.00 0.00 4.00
556 675 2.953466 TGCTTCGTATGTAGTCCACC 57.047 50.000 0.00 0.00 0.00 4.61
557 676 5.350365 TCAATTTGCTTCGTATGTAGTCCAC 59.650 40.000 0.00 0.00 0.00 4.02
558 677 5.483811 TCAATTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
559 678 6.417191 TTCAATTTGCTTCGTATGTAGTCC 57.583 37.500 0.00 0.00 0.00 3.85
560 679 7.684670 TCATTCAATTTGCTTCGTATGTAGTC 58.315 34.615 0.00 0.00 0.00 2.59
561 680 7.609760 TCATTCAATTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
562 681 9.162793 GATTCATTCAATTTGCTTCGTATGTAG 57.837 33.333 0.00 0.00 0.00 2.74
563 682 8.892723 AGATTCATTCAATTTGCTTCGTATGTA 58.107 29.630 0.00 0.00 0.00 2.29
564 683 7.765307 AGATTCATTCAATTTGCTTCGTATGT 58.235 30.769 0.00 0.00 0.00 2.29
565 684 9.162793 GTAGATTCATTCAATTTGCTTCGTATG 57.837 33.333 0.00 0.00 0.00 2.39
566 685 8.892723 TGTAGATTCATTCAATTTGCTTCGTAT 58.107 29.630 0.00 0.00 0.00 3.06
567 686 8.175069 GTGTAGATTCATTCAATTTGCTTCGTA 58.825 33.333 0.00 0.00 0.00 3.43
568 687 7.023575 GTGTAGATTCATTCAATTTGCTTCGT 58.976 34.615 0.00 0.00 0.00 3.85
569 688 7.246311 AGTGTAGATTCATTCAATTTGCTTCG 58.754 34.615 0.00 0.00 0.00 3.79
570 689 8.976986 AAGTGTAGATTCATTCAATTTGCTTC 57.023 30.769 0.00 0.00 0.00 3.86
598 717 8.642432 CCACATACGGATGTATATAGATGGATT 58.358 37.037 14.23 0.00 44.82 3.01
599 718 7.785028 ACCACATACGGATGTATATAGATGGAT 59.215 37.037 14.23 0.00 44.82 3.41
600 719 7.123383 ACCACATACGGATGTATATAGATGGA 58.877 38.462 14.23 0.00 44.82 3.41
601 720 7.348080 ACCACATACGGATGTATATAGATGG 57.652 40.000 14.23 10.43 44.82 3.51
602 721 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
603 722 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
604 723 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
605 724 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
606 725 9.470399 ACTATGAACCACATACGGATGTATATA 57.530 33.333 14.23 7.10 44.82 0.86
607 726 8.251026 CACTATGAACCACATACGGATGTATAT 58.749 37.037 14.23 1.68 44.82 0.86
608 727 7.309560 CCACTATGAACCACATACGGATGTATA 60.310 40.741 14.23 6.48 44.82 1.47
609 728 6.455647 CACTATGAACCACATACGGATGTAT 58.544 40.000 14.23 5.54 44.82 2.29
610 729 5.221362 CCACTATGAACCACATACGGATGTA 60.221 44.000 14.23 0.00 44.82 2.29
612 731 4.058124 CCACTATGAACCACATACGGATG 58.942 47.826 5.94 5.94 40.07 3.51
613 732 3.964688 TCCACTATGAACCACATACGGAT 59.035 43.478 0.00 0.00 40.07 4.18
614 733 3.367321 TCCACTATGAACCACATACGGA 58.633 45.455 0.00 0.00 40.07 4.69
615 734 3.812156 TCCACTATGAACCACATACGG 57.188 47.619 0.00 0.00 40.07 4.02
616 735 5.601662 AGATTCCACTATGAACCACATACG 58.398 41.667 0.00 0.00 40.07 3.06
617 736 6.821388 AGAGATTCCACTATGAACCACATAC 58.179 40.000 0.00 0.00 40.07 2.39
618 737 7.563556 TGTAGAGATTCCACTATGAACCACATA 59.436 37.037 0.00 0.00 40.07 2.29
619 738 5.965033 AGAGATTCCACTATGAACCACAT 57.035 39.130 0.00 0.00 42.39 3.21
620 739 5.719563 TGTAGAGATTCCACTATGAACCACA 59.280 40.000 0.00 0.00 0.00 4.17
621 740 6.222038 TGTAGAGATTCCACTATGAACCAC 57.778 41.667 0.00 0.00 0.00 4.16
622 741 6.867519 TTGTAGAGATTCCACTATGAACCA 57.132 37.500 0.00 0.00 0.00 3.67
623 742 7.492994 GTCTTTGTAGAGATTCCACTATGAACC 59.507 40.741 0.00 0.00 0.00 3.62
624 743 8.254508 AGTCTTTGTAGAGATTCCACTATGAAC 58.745 37.037 0.00 0.00 0.00 3.18
625 744 8.367660 AGTCTTTGTAGAGATTCCACTATGAA 57.632 34.615 0.00 0.00 0.00 2.57
626 745 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
642 761 9.379791 CTTCCGTTCCTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
643 762 8.827677 CCTTCCGTTCCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
644 763 8.765517 TCCTTCCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
645 764 8.315220 TCCTTCCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
646 765 7.564292 ACTCCTTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
647 766 7.724287 ACTCCTTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
648 767 7.672122 ACTCCTTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
649 768 8.636213 TGTACTCCTTCCGTTCCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
650 769 8.537728 TGTACTCCTTCCGTTCCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
651 770 8.716674 ATGTACTCCTTCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
652 771 7.613551 ATGTACTCCTTCCGTTCCTAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
653 772 7.255730 GCTATGTACTCCTTCCGTTCCTAAATA 60.256 40.741 0.00 0.00 0.00 1.40
654 773 5.952347 ATGTACTCCTTCCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
655 774 5.163478 GCTATGTACTCCTTCCGTTCCTAAA 60.163 44.000 0.00 0.00 0.00 1.85
656 775 4.340381 GCTATGTACTCCTTCCGTTCCTAA 59.660 45.833 0.00 0.00 0.00 2.69
657 776 3.887716 GCTATGTACTCCTTCCGTTCCTA 59.112 47.826 0.00 0.00 0.00 2.94
658 777 2.694109 GCTATGTACTCCTTCCGTTCCT 59.306 50.000 0.00 0.00 0.00 3.36
659 778 2.429610 TGCTATGTACTCCTTCCGTTCC 59.570 50.000 0.00 0.00 0.00 3.62
660 779 3.795623 TGCTATGTACTCCTTCCGTTC 57.204 47.619 0.00 0.00 0.00 3.95
661 780 4.546829 TTTGCTATGTACTCCTTCCGTT 57.453 40.909 0.00 0.00 0.00 4.44
662 781 4.546829 TTTTGCTATGTACTCCTTCCGT 57.453 40.909 0.00 0.00 0.00 4.69
663 782 6.128007 ACAAATTTTGCTATGTACTCCTTCCG 60.128 38.462 9.04 0.00 0.00 4.30
664 783 7.158099 ACAAATTTTGCTATGTACTCCTTCC 57.842 36.000 9.04 0.00 0.00 3.46
665 784 9.774742 CTTACAAATTTTGCTATGTACTCCTTC 57.225 33.333 9.04 0.00 0.00 3.46
666 785 9.515226 TCTTACAAATTTTGCTATGTACTCCTT 57.485 29.630 9.04 0.00 0.00 3.36
667 786 9.515226 TTCTTACAAATTTTGCTATGTACTCCT 57.485 29.630 9.04 0.00 0.00 3.69
719 843 2.863137 CTCGGCTGCTGTCTTTCTTATC 59.137 50.000 8.55 0.00 0.00 1.75
720 844 2.419297 CCTCGGCTGCTGTCTTTCTTAT 60.419 50.000 8.55 0.00 0.00 1.73
726 851 4.400961 GGCCTCGGCTGCTGTCTT 62.401 66.667 8.55 0.00 41.60 3.01
799 924 7.349645 GTCACTTGACCAGAGATGGAATCGA 62.350 48.000 0.31 0.00 42.99 3.59
806 957 3.949842 TGAGTCACTTGACCAGAGATG 57.050 47.619 5.73 0.00 45.85 2.90
859 1010 0.460987 GTGGAGAAGACGATGCCCTG 60.461 60.000 0.00 0.00 0.00 4.45
1321 1495 4.699522 AGGGTGAAGGCGGCGTTC 62.700 66.667 24.20 24.20 0.00 3.95
1454 1628 1.608717 CGGGCAAGTAGAGGCAGAGT 61.609 60.000 0.00 0.00 0.00 3.24
1512 1686 8.159447 AGAATCTAGGCATTACAAATGCATCTA 58.841 33.333 22.16 14.97 46.21 1.98
1513 1687 7.002879 AGAATCTAGGCATTACAAATGCATCT 58.997 34.615 22.16 14.70 46.21 2.90
1548 1722 1.810441 CGTAATAACCCGCGCACCA 60.810 57.895 8.75 0.00 0.00 4.17
1549 1723 0.527385 TACGTAATAACCCGCGCACC 60.527 55.000 8.75 0.00 0.00 5.01
1569 1743 4.277515 ACTAATACCATGCATCATCGCT 57.722 40.909 0.00 0.00 0.00 4.93
1724 1902 5.309806 AGCTTGGTTCTCTAACTCCCTTTAA 59.690 40.000 0.00 0.00 35.81 1.52
1752 1931 4.709886 GGTGCCATTTTAGAAACATAGGGT 59.290 41.667 0.00 0.00 0.00 4.34
1841 2020 2.742856 CGCATTCATTCTACCAGCAGGA 60.743 50.000 0.35 0.00 38.69 3.86
2114 2296 1.627550 GACGCCAAAGAACTCTCCGC 61.628 60.000 0.00 0.00 0.00 5.54
2449 2637 2.751259 ACTTGCTGCATGGTGTAATGAG 59.249 45.455 18.21 5.00 0.00 2.90
2494 2682 7.896383 AGGAATAAATGCAACAGGCTAAATA 57.104 32.000 0.00 0.00 45.15 1.40
2813 3001 3.007614 ACCGTTAGTGCATTTGTACCTCT 59.992 43.478 0.00 0.00 0.00 3.69
3278 3484 8.978874 TCTTATGCAAGAAATTAAGCATAGGA 57.021 30.769 12.17 12.17 46.72 2.94
3438 3667 5.878116 AGAAACCAGCAATATAGCGTTACAA 59.122 36.000 0.00 0.00 40.15 2.41
3607 3836 4.154195 GCGAGGTTAGATTTCAAAAGCTCA 59.846 41.667 17.48 0.00 44.18 4.26
3778 4016 0.465705 GGCTCAATCCAGATCGGTCA 59.534 55.000 0.00 0.00 35.57 4.02
3779 4017 0.465705 TGGCTCAATCCAGATCGGTC 59.534 55.000 0.00 0.00 35.57 4.79
3882 4120 3.301274 CAGAGGGAGTAACTAGGAAGGG 58.699 54.545 0.00 0.00 0.00 3.95
3909 4147 6.483687 ACACTGTCAAAAACGTCTTACATTC 58.516 36.000 0.00 0.00 0.00 2.67
4705 4945 7.119262 CGTGAAAATGGAAGTAGGATTAAGTGT 59.881 37.037 0.00 0.00 0.00 3.55
4848 5088 2.045045 GCCAGGCACCACATAGCA 60.045 61.111 6.55 0.00 0.00 3.49
4882 5122 3.434309 ACCAAACAAATAGCAGGCAGAT 58.566 40.909 0.00 0.00 0.00 2.90
5054 5295 9.298250 CTGGTAGGTAGTATACACATAACTGAT 57.702 37.037 5.50 0.00 45.43 2.90
5100 5341 2.124942 GCCTGGACTAGCACCTGC 60.125 66.667 0.00 6.90 42.49 4.85
5569 5811 6.870971 ACAAAAATCAAGAAAATGCATGCT 57.129 29.167 20.33 0.00 0.00 3.79
5659 5901 6.594159 ACCAGTAATTTCTTAACTCATCCACG 59.406 38.462 0.00 0.00 0.00 4.94
5691 5933 6.183360 CCGTAAGTATGGGAGGAATCTAACAA 60.183 42.308 0.00 0.00 0.00 2.83
5797 6039 2.095567 GCACTGGTATCACAGCTGTTTG 60.096 50.000 18.94 7.39 42.21 2.93
6359 6603 7.596494 CACAAGAATGATATGCGGGAATAAAT 58.404 34.615 0.00 0.00 0.00 1.40
6360 6604 6.514870 GCACAAGAATGATATGCGGGAATAAA 60.515 38.462 0.00 0.00 0.00 1.40
6361 6605 5.048782 GCACAAGAATGATATGCGGGAATAA 60.049 40.000 0.00 0.00 0.00 1.40
6362 6606 4.455533 GCACAAGAATGATATGCGGGAATA 59.544 41.667 0.00 0.00 0.00 1.75
6539 6784 1.512926 CACCTTCACTGTCTTTCGGG 58.487 55.000 0.00 0.00 0.00 5.14
6743 6988 8.050930 GGACCTGTACATAAAAGGGAGATTTTA 58.949 37.037 0.00 0.00 38.59 1.52
6787 7032 5.776744 CCAAAATTCTTCCAAGACTTCCTG 58.223 41.667 0.00 0.00 34.13 3.86
6947 7192 7.547227 TCGATATCTGAAGTTTCATTCACAGA 58.453 34.615 0.34 0.00 36.46 3.41
6967 7212 3.065925 CAGCATCGGAGCTCATATCGATA 59.934 47.826 20.40 7.75 44.54 2.92
7196 7441 2.012673 CTCAGGAAGCGAATCCAAAGG 58.987 52.381 9.28 0.00 42.27 3.11
7228 7473 2.171659 TGGTCTCCTTGTAAACAGCACA 59.828 45.455 0.00 0.00 0.00 4.57
7405 7650 4.326826 TCTATGTTTTTCCTCCAGCAGTG 58.673 43.478 0.00 0.00 0.00 3.66
7461 7706 0.777446 AACCTGGGCAATACCTGTGT 59.223 50.000 0.00 0.00 39.10 3.72
7771 8021 4.336433 GGCTAAGCACATGCAGAGAATAAA 59.664 41.667 6.64 0.00 45.16 1.40
7819 8069 3.069289 TGACTAAGCACATGCAGACTTG 58.931 45.455 6.64 0.00 45.16 3.16
7820 8070 3.332919 CTGACTAAGCACATGCAGACTT 58.667 45.455 6.64 0.00 45.16 3.01
7821 8071 2.969990 CTGACTAAGCACATGCAGACT 58.030 47.619 6.64 0.00 45.16 3.24
8090 8340 7.596248 CCAATTAACCAATCAGCTATACAATGC 59.404 37.037 0.00 0.00 0.00 3.56
8181 8432 2.286125 CGCACAACAAAATGTCAGTCGA 60.286 45.455 0.00 0.00 0.00 4.20
8182 8433 2.036217 CGCACAACAAAATGTCAGTCG 58.964 47.619 0.00 0.00 0.00 4.18
8183 8434 2.384382 CCGCACAACAAAATGTCAGTC 58.616 47.619 0.00 0.00 0.00 3.51
8373 8624 0.468648 CTACCCCATTTCTCGACCCC 59.531 60.000 0.00 0.00 0.00 4.95
8377 8628 9.101325 AGATAAATTATCTACCCCATTTCTCGA 57.899 33.333 13.39 0.00 43.44 4.04
8378 8629 9.372369 GAGATAAATTATCTACCCCATTTCTCG 57.628 37.037 14.82 0.00 45.16 4.04
8403 8656 4.591498 AGGGAACAACAGCGGTATATATGA 59.409 41.667 0.00 0.00 0.00 2.15
8404 8657 4.894784 AGGGAACAACAGCGGTATATATG 58.105 43.478 0.00 0.00 0.00 1.78
8472 8733 8.144478 AGCTGTATATAAATTCTTTCTCGAGCA 58.856 33.333 7.81 0.00 0.00 4.26
8510 8771 2.159626 CCAACAACGACGACAAAACTGT 60.160 45.455 0.00 0.00 0.00 3.55
8511 8772 2.436670 CCAACAACGACGACAAAACTG 58.563 47.619 0.00 0.00 0.00 3.16
8524 8786 3.308438 TTACTAGCGAGTCCCAACAAC 57.692 47.619 1.52 0.00 37.10 3.32
8546 8808 1.134946 GCACAAACAGAACTGCCAACT 59.865 47.619 1.46 0.00 0.00 3.16
8616 8878 3.972276 GGAAAAGGCCGCGTGCAA 61.972 61.111 18.87 0.00 43.89 4.08
8622 8884 2.751837 CTCCCAGGAAAAGGCCGC 60.752 66.667 0.00 0.00 0.00 6.53
8629 8891 1.304282 GCTGATGCCTCCCAGGAAA 59.696 57.895 0.00 0.00 37.67 3.13
8677 9394 1.142465 ACTTAGCCATGAGCCTGGATG 59.858 52.381 0.00 0.00 45.47 3.51
8690 9407 2.164422 GGCAAGTTCAATGGACTTAGCC 59.836 50.000 22.63 22.63 40.51 3.93
8764 9517 1.826054 CTGTCAAACCAACGGCCCA 60.826 57.895 0.00 0.00 0.00 5.36
8767 9520 0.594796 CTTGCTGTCAAACCAACGGC 60.595 55.000 0.19 0.19 46.90 5.68
8769 9522 0.929824 CGCTTGCTGTCAAACCAACG 60.930 55.000 0.00 0.00 0.00 4.10
8770 9523 0.100503 ACGCTTGCTGTCAAACCAAC 59.899 50.000 0.00 0.00 0.00 3.77
8771 9524 0.100325 CACGCTTGCTGTCAAACCAA 59.900 50.000 0.00 0.00 0.00 3.67
8772 9525 1.726865 CACGCTTGCTGTCAAACCA 59.273 52.632 0.00 0.00 0.00 3.67
8793 9546 4.033009 TCCATCCTGAGAGCAAGATGTTA 58.967 43.478 0.00 0.00 40.02 2.41
8815 9568 0.109873 CGACCTACTCGACGCTTTGT 60.110 55.000 0.00 0.00 46.14 2.83
8817 9570 1.239968 ACCGACCTACTCGACGCTTT 61.240 55.000 0.00 0.00 46.14 3.51
8821 9574 2.099831 GCACCGACCTACTCGACG 59.900 66.667 0.00 0.00 46.14 5.12
8863 9616 0.540365 CCCAGAGCCAACCATTGTGT 60.540 55.000 0.00 0.00 0.00 3.72
8926 9725 1.269448 GCGATTGGTTCCACACATTGT 59.731 47.619 0.00 0.00 0.00 2.71
8927 9726 1.402720 GGCGATTGGTTCCACACATTG 60.403 52.381 0.00 0.00 0.00 2.82
8928 9727 0.887933 GGCGATTGGTTCCACACATT 59.112 50.000 0.00 0.00 0.00 2.71
8929 9728 0.251121 TGGCGATTGGTTCCACACAT 60.251 50.000 0.00 0.00 0.00 3.21
8930 9729 0.251121 ATGGCGATTGGTTCCACACA 60.251 50.000 0.00 0.00 31.94 3.72
8931 9730 0.451783 GATGGCGATTGGTTCCACAC 59.548 55.000 0.00 0.00 31.94 3.82
8932 9731 0.679640 GGATGGCGATTGGTTCCACA 60.680 55.000 0.00 0.00 31.94 4.17
9041 11657 0.034059 CGGAGCACTGAGTTGTCCTT 59.966 55.000 8.05 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.