Multiple sequence alignment - TraesCS6A01G074300

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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 TraesCS6A01G074300 chr6A 100.000 8954 0 0 1 8954 42330606 42339559 0.000000e+00 16536.0
1 TraesCS6A01G074300 chr6A 98.834 5058 55 1 3901 8954 42621852 42626909 0.000000e+00 9010.0
2 TraesCS6A01G074300 chr6A 99.220 3461 27 0 1 3461 42584490 42587950 0.000000e+00 6242.0
3 TraesCS6A01G074300 chr6A 99.220 3461 27 0 1 3461 42618173 42621633 0.000000e+00 6242.0
4 TraesCS6A01G074300 chr6A 99.422 3114 18 0 3661 6774 42560869 42563982 0.000000e+00 5651.0
5 TraesCS6A01G074300 chr6A 99.609 2045 8 0 1417 3461 42554768 42556812 0.000000e+00 3733.0
6 TraesCS6A01G074300 chr6A 99.649 1995 7 0 245 2239 42557298 42559292 0.000000e+00 3646.0
7 TraesCS6A01G074300 chr6A 99.319 1910 13 0 3645 5554 42587943 42589852 0.000000e+00 3456.0
8 TraesCS6A01G074300 chr6A 98.147 1727 32 0 7228 8954 42489874 42491600 0.000000e+00 3013.0
9 TraesCS6A01G074300 chr6A 97.973 1727 35 0 7228 8954 42295791 42297517 0.000000e+00 2996.0
10 TraesCS6A01G074300 chr6A 95.632 1076 20 4 3 1078 42294746 42295794 0.000000e+00 1701.0
11 TraesCS6A01G074300 chr6A 95.265 1077 23 4 3 1078 42488828 42489877 0.000000e+00 1681.0
12 TraesCS6A01G074300 chr6A 99.776 893 2 0 1 893 42553255 42554147 0.000000e+00 1639.0
13 TraesCS6A01G074300 chr6A 99.553 895 4 0 7232 8126 42563980 42564874 0.000000e+00 1631.0
14 TraesCS6A01G074300 chr6A 98.640 662 6 1 1 659 42363608 42364269 0.000000e+00 1170.0
15 TraesCS6A01G074300 chr6A 97.378 534 14 0 8421 8954 42648566 42649099 0.000000e+00 909.0
16 TraesCS6A01G074300 chr6A 99.793 483 1 0 3645 4127 42556805 42557287 0.000000e+00 887.0
17 TraesCS6A01G074300 chr6A 98.191 387 6 1 1079 1464 42624801 42625187 0.000000e+00 675.0
18 TraesCS6A01G074300 chr6A 96.382 387 9 2 6850 7232 42331684 42332069 4.560000e-177 632.0
19 TraesCS6A01G074300 chr6A 96.373 386 9 3 6851 7232 42558133 42558517 1.640000e-176 630.0
20 TraesCS6A01G074300 chr6A 95.855 386 11 2 6851 7232 42619252 42619636 3.550000e-173 619.0
21 TraesCS6A01G074300 chr6A 98.810 336 4 0 8619 8954 42592010 42592345 4.630000e-167 599.0
22 TraesCS6A01G074300 chr6A 99.355 155 1 0 1 155 42582523 42582677 1.900000e-71 281.0
23 TraesCS6A01G074300 chr6A 97.674 43 0 1 8427 8468 42648496 42648538 1.250000e-08 73.1
24 TraesCS6A01G074300 chr6A 100.000 28 0 0 5275 5302 42623155 42623182 1.600000e-02 52.8
25 TraesCS6A01G074300 chrUn 97.269 2380 59 4 1080 3458 244955887 244958261 0.000000e+00 4030.0
26 TraesCS6A01G074300 chrUn 100.000 1523 0 0 1417 2939 392301834 392300312 0.000000e+00 2813.0
27 TraesCS6A01G074300 chrUn 98.986 1479 15 0 794 2272 396143947 396145425 0.000000e+00 2649.0
28 TraesCS6A01G074300 chrUn 99.306 1441 10 0 7514 8954 323449632 323448192 0.000000e+00 2606.0
29 TraesCS6A01G074300 chrUn 99.102 1114 10 0 5556 6669 437835657 437834544 0.000000e+00 2002.0
30 TraesCS6A01G074300 chrUn 93.438 1280 66 7 7230 8503 105229761 105228494 0.000000e+00 1882.0
31 TraesCS6A01G074300 chrUn 97.547 897 22 0 3645 4541 244958257 244959153 0.000000e+00 1535.0
32 TraesCS6A01G074300 chrUn 99.033 827 8 0 8128 8954 447403737 447402911 0.000000e+00 1483.0
33 TraesCS6A01G074300 chrUn 99.733 750 2 0 7232 7981 397515053 397514304 0.000000e+00 1375.0
34 TraesCS6A01G074300 chrUn 99.583 720 3 0 6058 6777 397515767 397515048 0.000000e+00 1314.0
35 TraesCS6A01G074300 chrUn 99.065 428 4 0 557 984 476453551 476453978 0.000000e+00 769.0
36 TraesCS6A01G074300 chrUn 87.237 666 42 17 427 1078 105230396 105229760 0.000000e+00 719.0
37 TraesCS6A01G074300 chrUn 95.822 383 13 3 6851 7232 244955887 244956267 4.590000e-172 616.0
38 TraesCS6A01G074300 chrUn 86.937 444 36 11 1 430 105241769 105241334 6.290000e-131 479.0
39 TraesCS6A01G074300 chrUn 99.355 155 1 0 1 155 331979153 331979307 1.900000e-71 281.0
40 TraesCS6A01G074300 chr4A 97.269 2380 59 4 1080 3458 676196704 676199078 0.000000e+00 4030.0
41 TraesCS6A01G074300 chr4A 96.203 1659 62 1 5571 7228 676200097 676201755 0.000000e+00 2713.0
42 TraesCS6A01G074300 chr4A 97.771 1032 23 0 3645 4676 676199074 676200105 0.000000e+00 1779.0
43 TraesCS6A01G074300 chr4A 95.062 162 7 1 3462 3623 715240308 715240148 4.150000e-63 254.0
44 TraesCS6A01G074300 chr7D 96.349 2383 78 6 1080 3461 39738201 39735827 0.000000e+00 3910.0
45 TraesCS6A01G074300 chr7D 95.539 1659 67 5 5571 7227 39734813 39733160 0.000000e+00 2647.0
46 TraesCS6A01G074300 chr7D 97.967 1033 17 2 3645 4676 39735834 39734805 0.000000e+00 1788.0
47 TraesCS6A01G074300 chr7D 90.226 266 24 2 5302 5567 632159710 632159973 6.650000e-91 346.0
48 TraesCS6A01G074300 chr7D 95.109 184 9 0 3461 3644 610417461 610417278 3.160000e-74 291.0
49 TraesCS6A01G074300 chr2D 95.487 1662 63 6 5571 7227 83052564 83050910 0.000000e+00 2643.0
50 TraesCS6A01G074300 chr2D 97.870 1033 21 1 3645 4676 83053588 83052556 0.000000e+00 1784.0
51 TraesCS6A01G074300 chr2D 96.631 1039 35 0 2423 3461 83054619 83053581 0.000000e+00 1725.0
52 TraesCS6A01G074300 chr2D 81.409 823 133 13 5578 6383 18378050 18377231 0.000000e+00 654.0
53 TraesCS6A01G074300 chr2D 94.083 169 10 0 3476 3644 640045087 640045255 3.210000e-64 257.0
54 TraesCS6A01G074300 chr7A 90.306 1991 160 12 1137 3125 7875930 7873971 0.000000e+00 2577.0
55 TraesCS6A01G074300 chr7A 97.536 893 18 2 4677 5568 48954665 48953776 0.000000e+00 1524.0
56 TraesCS6A01G074300 chr7A 94.100 983 58 0 5571 6553 629814676 629815658 0.000000e+00 1495.0
57 TraesCS6A01G074300 chr7A 91.076 818 38 14 2641 3458 629804696 629805478 0.000000e+00 1074.0
58 TraesCS6A01G074300 chr7A 96.451 648 23 0 4029 4676 629814037 629814684 0.000000e+00 1070.0
59 TraesCS6A01G074300 chr7A 84.205 1032 129 24 6213 7222 7873184 7872165 0.000000e+00 972.0
60 TraesCS6A01G074300 chr7A 86.168 535 74 0 3655 4189 7873710 7873176 6.030000e-161 579.0
61 TraesCS6A01G074300 chr7A 92.098 367 23 2 6600 6960 629815658 629816024 6.200000e-141 512.0
62 TraesCS6A01G074300 chr7A 100.000 28 0 0 5275 5302 48954140 48954113 1.600000e-02 52.8
63 TraesCS6A01G074300 chr6B 92.830 1297 65 12 7228 8503 76793986 76795275 0.000000e+00 1855.0
64 TraesCS6A01G074300 chr6B 87.719 399 34 7 692 1078 76793594 76793989 1.370000e-122 451.0
65 TraesCS6A01G074300 chr6B 90.037 271 22 3 5301 5568 501849092 501848824 6.650000e-91 346.0
66 TraesCS6A01G074300 chr6B 94.536 183 9 1 3462 3644 33462219 33462400 1.900000e-71 281.0
67 TraesCS6A01G074300 chr6B 82.313 294 19 13 399 691 76780160 76780421 3.250000e-54 224.0
68 TraesCS6A01G074300 chr5A 97.200 893 25 0 4676 5568 607393575 607392683 0.000000e+00 1511.0
69 TraesCS6A01G074300 chr5A 96.861 892 28 0 4677 5568 670832942 670832051 0.000000e+00 1493.0
70 TraesCS6A01G074300 chr5A 100.000 28 0 0 5275 5302 670832415 670832388 1.600000e-02 52.8
71 TraesCS6A01G074300 chr3D 95.143 453 20 2 8502 8954 169376846 169377296 0.000000e+00 713.0
72 TraesCS6A01G074300 chr5B 87.542 602 57 13 4677 5269 527594509 527595101 0.000000e+00 680.0
73 TraesCS6A01G074300 chr5D 86.689 601 58 17 4677 5269 385892438 385893024 0.000000e+00 647.0
74 TraesCS6A01G074300 chr1D 96.561 378 12 1 6851 7227 13058411 13058034 7.630000e-175 625.0
75 TraesCS6A01G074300 chr1D 85.974 606 57 18 4677 5272 411294601 411294014 2.750000e-174 623.0
76 TraesCS6A01G074300 chr1D 92.664 259 17 2 5310 5568 411282701 411282445 1.100000e-98 372.0
77 TraesCS6A01G074300 chr1D 79.835 243 29 8 1 235 17156260 17156490 9.310000e-35 159.0
78 TraesCS6A01G074300 chr7B 79.399 699 81 32 4892 5566 745138779 745139438 1.380000e-117 435.0
79 TraesCS6A01G074300 chr7B 91.979 187 13 2 3462 3647 690701578 690701393 2.480000e-65 261.0
80 TraesCS6A01G074300 chr3A 96.216 185 6 1 3460 3644 701862440 701862623 1.460000e-77 302.0
81 TraesCS6A01G074300 chr3A 80.620 129 15 5 3512 3640 699545618 699545736 3.440000e-14 91.6
82 TraesCS6A01G074300 chr2B 92.513 187 12 2 3465 3650 51800969 51800784 5.330000e-67 267.0
83 TraesCS6A01G074300 chr6D 90.860 186 14 3 3460 3644 18932560 18932743 6.940000e-61 246.0
84 TraesCS6A01G074300 chr3B 90.164 183 18 0 3462 3644 47773821 47774003 1.160000e-58 239.0


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 TraesCS6A01G074300 chr6A 42330606 42339559 8953 False 16536.000000 16536 100.000000 1 8954 1 chr6A.!!$F1 8953
1 TraesCS6A01G074300 chr6A 42618173 42626909 8736 False 3319.760000 9010 98.420000 1 8954 5 chr6A.!!$F8 8953
2 TraesCS6A01G074300 chr6A 42582523 42592345 9822 False 2644.500000 6242 99.176000 1 8954 4 chr6A.!!$F7 8953
3 TraesCS6A01G074300 chr6A 42553255 42564874 11619 False 2545.285714 5651 99.167857 1 8126 7 chr6A.!!$F6 8125
4 TraesCS6A01G074300 chr6A 42294746 42297517 2771 False 2348.500000 2996 96.802500 3 8954 2 chr6A.!!$F4 8951
5 TraesCS6A01G074300 chr6A 42488828 42491600 2772 False 2347.000000 3013 96.706000 3 8954 2 chr6A.!!$F5 8951
6 TraesCS6A01G074300 chr6A 42363608 42364269 661 False 1170.000000 1170 98.640000 1 659 1 chr6A.!!$F3 658
7 TraesCS6A01G074300 chr6A 42648496 42649099 603 False 491.050000 909 97.526000 8421 8954 2 chr6A.!!$F9 533
8 TraesCS6A01G074300 chrUn 392300312 392301834 1522 True 2813.000000 2813 100.000000 1417 2939 1 chrUn.!!$R3 1522
9 TraesCS6A01G074300 chrUn 396143947 396145425 1478 False 2649.000000 2649 98.986000 794 2272 1 chrUn.!!$F2 1478
10 TraesCS6A01G074300 chrUn 323448192 323449632 1440 True 2606.000000 2606 99.306000 7514 8954 1 chrUn.!!$R2 1440
11 TraesCS6A01G074300 chrUn 244955887 244959153 3266 False 2060.333333 4030 96.879333 1080 7232 3 chrUn.!!$F4 6152
12 TraesCS6A01G074300 chrUn 437834544 437835657 1113 True 2002.000000 2002 99.102000 5556 6669 1 chrUn.!!$R4 1113
13 TraesCS6A01G074300 chrUn 447402911 447403737 826 True 1483.000000 1483 99.033000 8128 8954 1 chrUn.!!$R5 826
14 TraesCS6A01G074300 chrUn 397514304 397515767 1463 True 1344.500000 1375 99.658000 6058 7981 2 chrUn.!!$R7 1923
15 TraesCS6A01G074300 chrUn 105228494 105230396 1902 True 1300.500000 1882 90.337500 427 8503 2 chrUn.!!$R6 8076
16 TraesCS6A01G074300 chr4A 676196704 676201755 5051 False 2840.666667 4030 97.081000 1080 7228 3 chr4A.!!$F1 6148
17 TraesCS6A01G074300 chr7D 39733160 39738201 5041 True 2781.666667 3910 96.618333 1080 7227 3 chr7D.!!$R2 6147
18 TraesCS6A01G074300 chr2D 83050910 83054619 3709 True 2050.666667 2643 96.662667 2423 7227 3 chr2D.!!$R2 4804
19 TraesCS6A01G074300 chr2D 18377231 18378050 819 True 654.000000 654 81.409000 5578 6383 1 chr2D.!!$R1 805
20 TraesCS6A01G074300 chr7A 7872165 7875930 3765 True 1376.000000 2577 86.893000 1137 7222 3 chr7A.!!$R1 6085
21 TraesCS6A01G074300 chr7A 629804696 629805478 782 False 1074.000000 1074 91.076000 2641 3458 1 chr7A.!!$F1 817
22 TraesCS6A01G074300 chr7A 629814037 629816024 1987 False 1025.666667 1495 94.216333 4029 6960 3 chr7A.!!$F2 2931
23 TraesCS6A01G074300 chr7A 48953776 48954665 889 True 788.400000 1524 98.768000 4677 5568 2 chr7A.!!$R2 891
24 TraesCS6A01G074300 chr6B 76793594 76795275 1681 False 1153.000000 1855 90.274500 692 8503 2 chr6B.!!$F3 7811
25 TraesCS6A01G074300 chr5A 607392683 607393575 892 True 1511.000000 1511 97.200000 4676 5568 1 chr5A.!!$R1 892
26 TraesCS6A01G074300 chr5A 670832051 670832942 891 True 772.900000 1493 98.430500 4677 5568 2 chr5A.!!$R2 891
27 TraesCS6A01G074300 chr5B 527594509 527595101 592 False 680.000000 680 87.542000 4677 5269 1 chr5B.!!$F1 592
28 TraesCS6A01G074300 chr5D 385892438 385893024 586 False 647.000000 647 86.689000 4677 5269 1 chr5D.!!$F1 592
29 TraesCS6A01G074300 chr1D 411294014 411294601 587 True 623.000000 623 85.974000 4677 5272 1 chr1D.!!$R3 595
30 TraesCS6A01G074300 chr7B 745138779 745139438 659 False 435.000000 435 79.399000 4892 5566 1 chr7B.!!$F1 674

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
3457 5543 0.921256 ATAGGCCTTGGCACCTTCCT 60.921 55.000 12.58 1.66 37.50 3.36 F
3460 5546 0.033109 GGCCTTGGCACCTTCCTTAT 60.033 55.000 14.04 0.00 0.00 1.73 F
3513 5599 0.171231 GCCGGACCTCTTTCAAATGC 59.829 55.000 5.05 0.00 0.00 3.56 F
3619 5705 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.000 22.98 22.98 45.83 4.70 F
5990 12188 1.070786 GCCGTGAGTTTGTCCTCCA 59.929 57.895 0.00 0.00 0.00 3.86 F
6900 13123 2.159503 TCTCTCTCATGAAGAACGCGAC 60.160 50.000 15.93 6.52 32.23 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5999 12197 3.570212 AAGCCGAAGCCACCCACT 61.570 61.111 0.00 0.0 41.25 4.00 R
6888 13107 0.303493 GCAAACAGTCGCGTTCTTCA 59.697 50.000 5.77 0.0 0.00 3.02 R
6900 13123 1.044725 GTTGAACGCATCGCAAACAG 58.955 50.000 0.00 0.0 0.00 3.16 R
7032 13255 2.590092 GGCCACACCCTAGCGATT 59.410 61.111 0.00 0.0 0.00 3.34 R
7470 13697 1.377202 GGATGGTGGCAGCGAGAAA 60.377 57.895 12.58 0.0 0.00 2.52 R
7981 14223 4.384647 GCTGTCTGGTCTTATTCCCTGAAT 60.385 45.833 0.00 0.0 36.20 2.57 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
3457 5543 0.921256 ATAGGCCTTGGCACCTTCCT 60.921 55.000 12.58 1.66 37.50 3.36
3458 5544 1.140134 TAGGCCTTGGCACCTTCCTT 61.140 55.000 12.58 0.00 37.50 3.36
3459 5545 1.140134 AGGCCTTGGCACCTTCCTTA 61.140 55.000 14.04 0.00 29.74 2.69
3460 5546 0.033109 GGCCTTGGCACCTTCCTTAT 60.033 55.000 14.04 0.00 0.00 1.73
3461 5547 1.393603 GCCTTGGCACCTTCCTTATC 58.606 55.000 6.79 0.00 0.00 1.75
3462 5548 1.340991 GCCTTGGCACCTTCCTTATCA 60.341 52.381 6.79 0.00 0.00 2.15
3463 5549 2.883888 GCCTTGGCACCTTCCTTATCAA 60.884 50.000 6.79 0.00 0.00 2.57
3464 5550 3.430453 CCTTGGCACCTTCCTTATCAAA 58.570 45.455 0.00 0.00 0.00 2.69
3465 5551 3.445096 CCTTGGCACCTTCCTTATCAAAG 59.555 47.826 0.00 0.00 0.00 2.77
3466 5552 3.806949 TGGCACCTTCCTTATCAAAGT 57.193 42.857 0.00 0.00 0.00 2.66
3467 5553 4.112634 TGGCACCTTCCTTATCAAAGTT 57.887 40.909 0.00 0.00 0.00 2.66
3468 5554 4.479158 TGGCACCTTCCTTATCAAAGTTT 58.521 39.130 0.00 0.00 0.00 2.66
3469 5555 4.898861 TGGCACCTTCCTTATCAAAGTTTT 59.101 37.500 0.00 0.00 0.00 2.43
3470 5556 6.071984 TGGCACCTTCCTTATCAAAGTTTTA 58.928 36.000 0.00 0.00 0.00 1.52
3471 5557 6.551601 TGGCACCTTCCTTATCAAAGTTTTAA 59.448 34.615 0.00 0.00 0.00 1.52
3472 5558 7.070074 TGGCACCTTCCTTATCAAAGTTTTAAA 59.930 33.333 0.00 0.00 0.00 1.52
3473 5559 8.094548 GGCACCTTCCTTATCAAAGTTTTAAAT 58.905 33.333 0.00 0.00 0.00 1.40
3477 5563 9.503427 CCTTCCTTATCAAAGTTTTAAATAGCG 57.497 33.333 0.00 0.00 0.00 4.26
3478 5564 8.905103 TTCCTTATCAAAGTTTTAAATAGCGC 57.095 30.769 0.00 0.00 0.00 5.92
3479 5565 7.184106 TCCTTATCAAAGTTTTAAATAGCGCG 58.816 34.615 0.00 0.00 0.00 6.86
3480 5566 6.075572 CCTTATCAAAGTTTTAAATAGCGCGC 60.076 38.462 26.66 26.66 0.00 6.86
3481 5567 4.413495 TCAAAGTTTTAAATAGCGCGCT 57.587 36.364 38.01 38.01 0.00 5.92
3482 5568 5.533533 TCAAAGTTTTAAATAGCGCGCTA 57.466 34.783 39.72 39.72 0.00 4.26
3483 5569 5.929278 TCAAAGTTTTAAATAGCGCGCTAA 58.071 33.333 40.90 26.03 31.73 3.09
3484 5570 6.019152 TCAAAGTTTTAAATAGCGCGCTAAG 58.981 36.000 40.90 16.07 31.73 2.18
3485 5571 3.936661 AGTTTTAAATAGCGCGCTAAGC 58.063 40.909 40.90 27.92 43.95 3.09
3496 5582 3.958748 GCTAAGCATCCTAGCGCC 58.041 61.111 2.29 0.00 40.15 6.53
3497 5583 2.024319 GCTAAGCATCCTAGCGCCG 61.024 63.158 2.29 0.00 40.15 6.46
3498 5584 1.373497 CTAAGCATCCTAGCGCCGG 60.373 63.158 2.29 5.15 40.15 6.13
3499 5585 1.806461 CTAAGCATCCTAGCGCCGGA 61.806 60.000 17.19 17.19 40.15 5.14
3500 5586 2.083835 TAAGCATCCTAGCGCCGGAC 62.084 60.000 17.21 6.96 40.15 4.79
3501 5587 4.971125 GCATCCTAGCGCCGGACC 62.971 72.222 17.21 8.68 32.41 4.46
3502 5588 3.227276 CATCCTAGCGCCGGACCT 61.227 66.667 17.21 1.80 32.41 3.85
3503 5589 2.913060 ATCCTAGCGCCGGACCTC 60.913 66.667 17.21 0.00 32.41 3.85
3504 5590 3.438615 ATCCTAGCGCCGGACCTCT 62.439 63.158 17.21 0.17 32.41 3.69
3505 5591 2.930777 ATCCTAGCGCCGGACCTCTT 62.931 60.000 17.21 0.00 32.41 2.85
3506 5592 2.722201 CCTAGCGCCGGACCTCTTT 61.722 63.158 5.05 0.00 0.00 2.52
3507 5593 1.227002 CTAGCGCCGGACCTCTTTC 60.227 63.158 5.05 0.00 0.00 2.62
3508 5594 1.945354 CTAGCGCCGGACCTCTTTCA 61.945 60.000 5.05 0.00 0.00 2.69
3509 5595 1.537814 TAGCGCCGGACCTCTTTCAA 61.538 55.000 5.05 0.00 0.00 2.69
3510 5596 1.964373 GCGCCGGACCTCTTTCAAA 60.964 57.895 5.05 0.00 0.00 2.69
3511 5597 1.305930 GCGCCGGACCTCTTTCAAAT 61.306 55.000 5.05 0.00 0.00 2.32
3512 5598 0.447801 CGCCGGACCTCTTTCAAATG 59.552 55.000 5.05 0.00 0.00 2.32
3513 5599 0.171231 GCCGGACCTCTTTCAAATGC 59.829 55.000 5.05 0.00 0.00 3.56
3514 5600 1.826385 CCGGACCTCTTTCAAATGCT 58.174 50.000 0.00 0.00 0.00 3.79
3515 5601 2.939640 GCCGGACCTCTTTCAAATGCTA 60.940 50.000 5.05 0.00 0.00 3.49
3516 5602 3.545703 CCGGACCTCTTTCAAATGCTAT 58.454 45.455 0.00 0.00 0.00 2.97
3517 5603 4.703897 CCGGACCTCTTTCAAATGCTATA 58.296 43.478 0.00 0.00 0.00 1.31
3518 5604 4.752101 CCGGACCTCTTTCAAATGCTATAG 59.248 45.833 0.00 0.00 0.00 1.31
3519 5605 4.212214 CGGACCTCTTTCAAATGCTATAGC 59.788 45.833 18.18 18.18 42.50 2.97
3520 5606 4.212214 GGACCTCTTTCAAATGCTATAGCG 59.788 45.833 19.55 5.67 45.83 4.26
3521 5607 4.130118 ACCTCTTTCAAATGCTATAGCGG 58.870 43.478 19.55 12.34 45.83 5.52
3522 5608 4.141711 ACCTCTTTCAAATGCTATAGCGGA 60.142 41.667 19.55 11.38 45.83 5.54
3523 5609 4.450419 CCTCTTTCAAATGCTATAGCGGAG 59.550 45.833 19.55 14.00 45.83 4.63
3548 5634 8.822105 GCTATAGCGCGCTATTTAAAATATTT 57.178 30.769 46.76 27.75 39.65 1.40
3549 5635 8.725046 GCTATAGCGCGCTATTTAAAATATTTG 58.275 33.333 46.76 26.68 39.65 2.32
3550 5636 9.755064 CTATAGCGCGCTATTTAAAATATTTGT 57.245 29.630 46.76 27.18 39.65 2.83
3552 5638 7.376530 AGCGCGCTATTTAAAATATTTGTTC 57.623 32.000 35.79 0.00 0.00 3.18
3553 5639 6.970043 AGCGCGCTATTTAAAATATTTGTTCA 59.030 30.769 35.79 0.00 0.00 3.18
3554 5640 7.647715 AGCGCGCTATTTAAAATATTTGTTCAT 59.352 29.630 35.79 0.00 0.00 2.57
3555 5641 8.265998 GCGCGCTATTTAAAATATTTGTTCATT 58.734 29.630 26.67 0.00 0.00 2.57
3566 5652 8.970859 AAATATTTGTTCATTTGTTTGGACCA 57.029 26.923 0.00 0.00 0.00 4.02
3567 5653 8.970859 AATATTTGTTCATTTGTTTGGACCAA 57.029 26.923 1.69 1.69 0.00 3.67
3568 5654 8.970859 ATATTTGTTCATTTGTTTGGACCAAA 57.029 26.923 15.89 15.89 36.34 3.28
3569 5655 7.693969 ATTTGTTCATTTGTTTGGACCAAAA 57.306 28.000 21.20 6.76 35.03 2.44
3570 5656 7.693969 TTTGTTCATTTGTTTGGACCAAAAT 57.306 28.000 21.20 8.88 35.03 1.82
3571 5657 6.917217 TGTTCATTTGTTTGGACCAAAATC 57.083 33.333 21.20 10.59 35.03 2.17
3572 5658 6.648192 TGTTCATTTGTTTGGACCAAAATCT 58.352 32.000 21.20 4.22 35.03 2.40
3573 5659 6.760770 TGTTCATTTGTTTGGACCAAAATCTC 59.239 34.615 21.20 9.53 35.03 2.75
3574 5660 6.729690 TCATTTGTTTGGACCAAAATCTCT 57.270 33.333 21.20 3.20 35.03 3.10
3575 5661 7.123355 TCATTTGTTTGGACCAAAATCTCTT 57.877 32.000 21.20 2.35 35.03 2.85
3576 5662 8.243961 TCATTTGTTTGGACCAAAATCTCTTA 57.756 30.769 21.20 2.53 35.03 2.10
3577 5663 8.359642 TCATTTGTTTGGACCAAAATCTCTTAG 58.640 33.333 21.20 7.24 35.03 2.18
3578 5664 5.705609 TGTTTGGACCAAAATCTCTTAGC 57.294 39.130 21.20 6.37 35.03 3.09
3579 5665 4.215399 TGTTTGGACCAAAATCTCTTAGCG 59.785 41.667 21.20 0.00 35.03 4.26
3580 5666 2.356135 TGGACCAAAATCTCTTAGCGC 58.644 47.619 0.00 0.00 0.00 5.92
3581 5667 2.290008 TGGACCAAAATCTCTTAGCGCA 60.290 45.455 11.47 0.00 0.00 6.09
3582 5668 2.747446 GGACCAAAATCTCTTAGCGCAA 59.253 45.455 11.47 0.50 0.00 4.85
3583 5669 3.181506 GGACCAAAATCTCTTAGCGCAAG 60.182 47.826 11.47 11.67 35.38 4.01
3584 5670 3.674997 ACCAAAATCTCTTAGCGCAAGA 58.325 40.909 11.47 15.40 41.10 3.02
3585 5671 3.437049 ACCAAAATCTCTTAGCGCAAGAC 59.563 43.478 11.47 0.00 38.39 3.01
3587 5673 2.656560 AATCTCTTAGCGCAAGACGT 57.343 45.000 11.47 0.00 46.11 4.34
3588 5674 2.656560 ATCTCTTAGCGCAAGACGTT 57.343 45.000 11.47 4.13 46.11 3.99
3589 5675 2.433868 TCTCTTAGCGCAAGACGTTT 57.566 45.000 11.47 0.00 46.11 3.60
3590 5676 2.750948 TCTCTTAGCGCAAGACGTTTT 58.249 42.857 11.47 0.00 46.11 2.43
3591 5677 2.475111 TCTCTTAGCGCAAGACGTTTTG 59.525 45.455 14.13 14.13 46.11 2.44
3592 5678 2.206750 TCTTAGCGCAAGACGTTTTGT 58.793 42.857 18.80 3.52 46.11 2.83
3593 5679 3.382855 TCTTAGCGCAAGACGTTTTGTA 58.617 40.909 18.80 2.60 46.11 2.41
3594 5680 3.803231 TCTTAGCGCAAGACGTTTTGTAA 59.197 39.130 18.80 9.62 46.11 2.41
3595 5681 4.270566 TCTTAGCGCAAGACGTTTTGTAAA 59.729 37.500 18.80 8.33 46.11 2.01
3596 5682 2.711885 AGCGCAAGACGTTTTGTAAAC 58.288 42.857 18.80 7.36 46.11 2.01
3597 5683 1.441725 GCGCAAGACGTTTTGTAAACG 59.558 47.619 18.80 19.53 46.11 3.60
3598 5684 1.441725 CGCAAGACGTTTTGTAAACGC 59.558 47.619 20.66 14.55 46.58 4.84
3599 5685 2.711885 GCAAGACGTTTTGTAAACGCT 58.288 42.857 20.66 16.11 46.58 5.07
3600 5686 3.602038 CGCAAGACGTTTTGTAAACGCTA 60.602 43.478 20.66 0.00 46.58 4.26
3601 5687 4.460505 GCAAGACGTTTTGTAAACGCTAT 58.539 39.130 20.66 5.52 46.58 2.97
3602 5688 5.610975 GCAAGACGTTTTGTAAACGCTATA 58.389 37.500 20.66 0.00 46.58 1.31
3603 5689 5.726679 GCAAGACGTTTTGTAAACGCTATAG 59.273 40.000 20.66 13.62 46.58 1.31
3604 5690 5.446031 AGACGTTTTGTAAACGCTATAGC 57.554 39.130 20.66 15.09 46.58 2.97
3618 5704 3.326733 CTATAGCGTGCTATAGCGGAG 57.673 52.381 27.04 13.65 46.26 4.63
3619 5705 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.000 22.98 22.98 45.83 4.70
3639 5725 4.406001 GCTATAGCGGGCTATTTGAAAC 57.594 45.455 17.49 0.05 39.65 2.78
3640 5726 3.813166 GCTATAGCGGGCTATTTGAAACA 59.187 43.478 17.49 0.00 39.65 2.83
3641 5727 4.083802 GCTATAGCGGGCTATTTGAAACAG 60.084 45.833 17.49 8.76 39.65 3.16
3642 5728 2.200373 AGCGGGCTATTTGAAACAGT 57.800 45.000 0.00 0.00 0.00 3.55
3643 5729 1.812571 AGCGGGCTATTTGAAACAGTG 59.187 47.619 0.00 0.00 0.00 3.66
4550 10685 1.469940 CGTCCCTCTTGGTCGAAGATG 60.470 57.143 0.00 0.00 46.85 2.90
5990 12188 1.070786 GCCGTGAGTTTGTCCTCCA 59.929 57.895 0.00 0.00 0.00 3.86
6888 13107 5.649395 CAGTTCTCTGAACTCTCTCTCTCAT 59.351 44.000 9.67 0.00 43.76 2.90
6900 13123 2.159503 TCTCTCTCATGAAGAACGCGAC 60.160 50.000 15.93 6.52 32.23 5.19
6945 13168 2.630098 GCAGCCTCTTCCCTTTTTCTTT 59.370 45.455 0.00 0.00 0.00 2.52
7032 13255 2.687200 CCATCCCACGTCCTCCCA 60.687 66.667 0.00 0.00 0.00 4.37
7470 13697 2.383245 CTGCACGACCCAAGGTGAGT 62.383 60.000 0.00 0.00 35.25 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 2211 9.703892 CTCCATAATAGATCTGATCTTTTTCGT 57.296 33.333 23.98 10.18 40.76 3.85
1078 3073 4.469227 AGAGAACTGATCCTGCAACTACAT 59.531 41.667 0.00 0.00 0.00 2.29
3457 5543 6.548171 AGCGCGCTATTTAAAACTTTGATAA 58.452 32.000 35.79 0.00 0.00 1.75
3458 5544 6.114221 AGCGCGCTATTTAAAACTTTGATA 57.886 33.333 35.79 0.00 0.00 2.15
3459 5545 4.981794 AGCGCGCTATTTAAAACTTTGAT 58.018 34.783 35.79 0.63 0.00 2.57
3460 5546 4.413495 AGCGCGCTATTTAAAACTTTGA 57.587 36.364 35.79 0.00 0.00 2.69
3461 5547 5.275280 GCTTAGCGCGCTATTTAAAACTTTG 60.275 40.000 38.51 15.49 0.00 2.77
3462 5548 4.791676 GCTTAGCGCGCTATTTAAAACTTT 59.208 37.500 38.51 13.72 0.00 2.66
3463 5549 4.142773 TGCTTAGCGCGCTATTTAAAACTT 60.143 37.500 38.51 13.94 43.27 2.66
3464 5550 3.372822 TGCTTAGCGCGCTATTTAAAACT 59.627 39.130 38.51 14.50 43.27 2.66
3465 5551 3.676540 TGCTTAGCGCGCTATTTAAAAC 58.323 40.909 38.51 22.00 43.27 2.43
3466 5552 4.523813 GATGCTTAGCGCGCTATTTAAAA 58.476 39.130 38.51 24.43 43.27 1.52
3467 5553 3.059188 GGATGCTTAGCGCGCTATTTAAA 60.059 43.478 38.51 25.16 43.27 1.52
3468 5554 2.478894 GGATGCTTAGCGCGCTATTTAA 59.521 45.455 38.51 25.53 43.27 1.52
3469 5555 2.066262 GGATGCTTAGCGCGCTATTTA 58.934 47.619 38.51 26.65 43.27 1.40
3470 5556 0.868406 GGATGCTTAGCGCGCTATTT 59.132 50.000 38.51 23.54 43.27 1.40
3471 5557 0.034059 AGGATGCTTAGCGCGCTATT 59.966 50.000 38.51 23.88 43.27 1.73
3472 5558 0.888619 TAGGATGCTTAGCGCGCTAT 59.111 50.000 38.51 26.50 43.27 2.97
3473 5559 0.241213 CTAGGATGCTTAGCGCGCTA 59.759 55.000 35.48 35.48 43.27 4.26
3474 5560 1.006805 CTAGGATGCTTAGCGCGCT 60.007 57.895 38.01 38.01 43.27 5.92
3475 5561 2.662522 GCTAGGATGCTTAGCGCGC 61.663 63.158 26.66 26.66 43.27 6.86
3476 5562 3.543548 GCTAGGATGCTTAGCGCG 58.456 61.111 0.00 0.00 43.27 6.86
3479 5565 2.024319 CGGCGCTAGGATGCTTAGC 61.024 63.158 7.64 0.00 40.05 3.09
3480 5566 1.373497 CCGGCGCTAGGATGCTTAG 60.373 63.158 15.65 0.00 0.00 2.18
3481 5567 1.830847 TCCGGCGCTAGGATGCTTA 60.831 57.895 18.57 0.00 31.86 3.09
3482 5568 3.154473 TCCGGCGCTAGGATGCTT 61.154 61.111 18.57 0.00 31.86 3.91
3483 5569 3.917760 GTCCGGCGCTAGGATGCT 61.918 66.667 23.55 0.00 40.30 3.79
3484 5570 4.971125 GGTCCGGCGCTAGGATGC 62.971 72.222 23.55 13.99 40.30 3.91
3485 5571 3.214250 GAGGTCCGGCGCTAGGATG 62.214 68.421 23.55 1.65 40.30 3.51
3486 5572 2.913060 GAGGTCCGGCGCTAGGAT 60.913 66.667 23.55 12.05 40.30 3.24
3487 5573 3.657038 AAGAGGTCCGGCGCTAGGA 62.657 63.158 18.57 18.57 34.99 2.94
3488 5574 2.630592 GAAAGAGGTCCGGCGCTAGG 62.631 65.000 7.64 12.03 0.00 3.02
3489 5575 1.227002 GAAAGAGGTCCGGCGCTAG 60.227 63.158 7.64 1.17 0.00 3.42
3490 5576 1.537814 TTGAAAGAGGTCCGGCGCTA 61.538 55.000 7.64 0.00 0.00 4.26
3491 5577 2.391724 TTTGAAAGAGGTCCGGCGCT 62.392 55.000 7.64 0.00 0.00 5.92
3492 5578 1.305930 ATTTGAAAGAGGTCCGGCGC 61.306 55.000 0.00 0.00 0.00 6.53
3493 5579 0.447801 CATTTGAAAGAGGTCCGGCG 59.552 55.000 0.00 0.00 0.00 6.46
3494 5580 0.171231 GCATTTGAAAGAGGTCCGGC 59.829 55.000 0.00 0.00 0.00 6.13
3495 5581 1.826385 AGCATTTGAAAGAGGTCCGG 58.174 50.000 0.00 0.00 0.00 5.14
3496 5582 4.212214 GCTATAGCATTTGAAAGAGGTCCG 59.788 45.833 20.01 0.00 41.59 4.79
3497 5583 4.212214 CGCTATAGCATTTGAAAGAGGTCC 59.788 45.833 23.99 0.00 42.21 4.46
3498 5584 4.212214 CCGCTATAGCATTTGAAAGAGGTC 59.788 45.833 23.99 0.00 42.21 3.85
3499 5585 4.130118 CCGCTATAGCATTTGAAAGAGGT 58.870 43.478 23.99 0.00 42.21 3.85
3500 5586 4.380531 TCCGCTATAGCATTTGAAAGAGG 58.619 43.478 23.99 12.60 42.21 3.69
3501 5587 4.084118 GCTCCGCTATAGCATTTGAAAGAG 60.084 45.833 23.99 15.02 42.21 2.85
3502 5588 3.809832 GCTCCGCTATAGCATTTGAAAGA 59.190 43.478 23.99 6.55 42.21 2.52
3503 5589 3.812053 AGCTCCGCTATAGCATTTGAAAG 59.188 43.478 23.99 10.53 42.62 2.62
3504 5590 3.808728 AGCTCCGCTATAGCATTTGAAA 58.191 40.909 23.99 0.81 42.62 2.69
3505 5591 3.475566 AGCTCCGCTATAGCATTTGAA 57.524 42.857 23.99 2.13 42.62 2.69
3516 5602 2.868196 CGCGCTATAGCTCCGCTA 59.132 61.111 21.98 0.00 45.55 4.26
3519 5605 0.179161 AATAGCGCGCTATAGCTCCG 60.179 55.000 43.81 22.32 43.44 4.63
3520 5606 1.997669 AAATAGCGCGCTATAGCTCC 58.002 50.000 43.81 10.26 43.44 4.70
3521 5607 5.511088 TTTTAAATAGCGCGCTATAGCTC 57.489 39.130 43.81 13.77 43.44 4.09
3522 5608 7.772332 ATATTTTAAATAGCGCGCTATAGCT 57.228 32.000 43.81 33.17 46.53 3.32
3523 5609 8.725046 CAAATATTTTAAATAGCGCGCTATAGC 58.275 33.333 43.81 15.09 38.20 2.97
3524 5610 9.755064 ACAAATATTTTAAATAGCGCGCTATAG 57.245 29.630 43.81 25.10 38.20 1.31
3526 5612 9.113876 GAACAAATATTTTAAATAGCGCGCTAT 57.886 29.630 40.32 40.32 40.63 2.97
3527 5613 8.123575 TGAACAAATATTTTAAATAGCGCGCTA 58.876 29.630 39.72 39.72 0.00 4.26
3528 5614 6.970043 TGAACAAATATTTTAAATAGCGCGCT 59.030 30.769 38.01 38.01 0.00 5.92
3529 5615 7.144007 TGAACAAATATTTTAAATAGCGCGC 57.856 32.000 26.66 26.66 0.00 6.86
3540 5626 9.401058 TGGTCCAAACAAATGAACAAATATTTT 57.599 25.926 0.00 0.00 0.00 1.82
3541 5627 8.970859 TGGTCCAAACAAATGAACAAATATTT 57.029 26.923 0.00 0.00 0.00 1.40
3542 5628 8.970859 TTGGTCCAAACAAATGAACAAATATT 57.029 26.923 0.40 0.00 33.06 1.28
3543 5629 8.970859 TTTGGTCCAAACAAATGAACAAATAT 57.029 26.923 13.26 0.00 39.91 1.28
3544 5630 8.792830 TTTTGGTCCAAACAAATGAACAAATA 57.207 26.923 16.88 0.00 43.12 1.40
3545 5631 7.693969 TTTTGGTCCAAACAAATGAACAAAT 57.306 28.000 16.88 0.00 43.12 2.32
3546 5632 7.609532 AGATTTTGGTCCAAACAAATGAACAAA 59.390 29.630 16.88 0.00 42.26 2.83
3547 5633 7.108847 AGATTTTGGTCCAAACAAATGAACAA 58.891 30.769 16.88 0.00 37.62 2.83
3548 5634 6.648192 AGATTTTGGTCCAAACAAATGAACA 58.352 32.000 16.88 0.00 37.62 3.18
3549 5635 6.986231 AGAGATTTTGGTCCAAACAAATGAAC 59.014 34.615 16.88 0.45 37.62 3.18
3550 5636 7.123355 AGAGATTTTGGTCCAAACAAATGAA 57.877 32.000 16.88 0.74 37.62 2.57
3551 5637 6.729690 AGAGATTTTGGTCCAAACAAATGA 57.270 33.333 16.88 1.50 37.62 2.57
3552 5638 7.116805 GCTAAGAGATTTTGGTCCAAACAAATG 59.883 37.037 16.88 4.42 37.62 2.32
3553 5639 7.154656 GCTAAGAGATTTTGGTCCAAACAAAT 58.845 34.615 16.88 8.07 37.62 2.32
3554 5640 6.512297 GCTAAGAGATTTTGGTCCAAACAAA 58.488 36.000 16.88 3.03 32.79 2.83
3555 5641 5.278266 CGCTAAGAGATTTTGGTCCAAACAA 60.278 40.000 16.88 3.80 32.79 2.83
3556 5642 4.215399 CGCTAAGAGATTTTGGTCCAAACA 59.785 41.667 16.88 8.80 32.79 2.83
3557 5643 4.723248 CGCTAAGAGATTTTGGTCCAAAC 58.277 43.478 16.88 6.69 32.79 2.93
3558 5644 3.190535 GCGCTAAGAGATTTTGGTCCAAA 59.809 43.478 13.26 13.26 0.00 3.28
3559 5645 2.747446 GCGCTAAGAGATTTTGGTCCAA 59.253 45.455 0.00 0.00 0.00 3.53
3560 5646 2.290008 TGCGCTAAGAGATTTTGGTCCA 60.290 45.455 9.73 0.00 0.00 4.02
3561 5647 2.356135 TGCGCTAAGAGATTTTGGTCC 58.644 47.619 9.73 0.00 0.00 4.46
3562 5648 3.684788 TCTTGCGCTAAGAGATTTTGGTC 59.315 43.478 9.73 0.00 40.43 4.02
3563 5649 3.437049 GTCTTGCGCTAAGAGATTTTGGT 59.563 43.478 18.44 0.00 45.71 3.67
3564 5650 3.484229 CGTCTTGCGCTAAGAGATTTTGG 60.484 47.826 18.44 3.89 45.71 3.28
3565 5651 3.123621 ACGTCTTGCGCTAAGAGATTTTG 59.876 43.478 18.44 9.68 45.71 2.44
3566 5652 3.326747 ACGTCTTGCGCTAAGAGATTTT 58.673 40.909 18.44 3.75 45.71 1.82
3567 5653 2.960819 ACGTCTTGCGCTAAGAGATTT 58.039 42.857 18.44 5.09 45.71 2.17
3568 5654 2.656560 ACGTCTTGCGCTAAGAGATT 57.343 45.000 18.44 6.97 45.71 2.40
3569 5655 2.656560 AACGTCTTGCGCTAAGAGAT 57.343 45.000 18.44 9.80 45.71 2.75
3570 5656 2.433868 AAACGTCTTGCGCTAAGAGA 57.566 45.000 18.44 9.99 45.71 3.10
3571 5657 2.221055 ACAAAACGTCTTGCGCTAAGAG 59.779 45.455 18.44 15.07 45.71 2.85
3572 5658 2.206750 ACAAAACGTCTTGCGCTAAGA 58.793 42.857 9.73 13.31 46.11 2.10
3573 5659 2.663279 ACAAAACGTCTTGCGCTAAG 57.337 45.000 9.73 11.02 46.11 2.18
3574 5660 4.273274 GTTTACAAAACGTCTTGCGCTAA 58.727 39.130 9.73 0.00 46.11 3.09
3575 5661 3.602038 CGTTTACAAAACGTCTTGCGCTA 60.602 43.478 9.73 0.00 46.11 4.26
3576 5662 2.711885 GTTTACAAAACGTCTTGCGCT 58.288 42.857 9.73 0.00 46.11 5.92
3577 5663 1.441725 CGTTTACAAAACGTCTTGCGC 59.558 47.619 14.91 0.00 46.11 6.09
3578 5664 1.441725 GCGTTTACAAAACGTCTTGCG 59.558 47.619 21.64 0.00 44.69 4.85
3579 5665 2.711885 AGCGTTTACAAAACGTCTTGC 58.288 42.857 21.64 8.45 44.69 4.01
3580 5666 5.726679 GCTATAGCGTTTACAAAACGTCTTG 59.273 40.000 21.64 0.00 44.69 3.02
3581 5667 5.850931 GCTATAGCGTTTACAAAACGTCTT 58.149 37.500 21.64 12.66 44.69 3.01
3582 5668 5.446031 GCTATAGCGTTTACAAAACGTCT 57.554 39.130 21.64 19.85 44.69 4.18
3599 5685 1.400846 GCTCCGCTATAGCACGCTATA 59.599 52.381 23.99 15.99 42.21 1.31
3600 5686 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.000 23.99 15.45 42.21 2.97
3601 5687 0.889638 AGCTCCGCTATAGCACGCTA 60.890 55.000 23.99 0.39 42.62 4.26
3602 5688 0.889638 TAGCTCCGCTATAGCACGCT 60.890 55.000 25.78 25.78 42.62 5.07
3603 5689 1.579932 TAGCTCCGCTATAGCACGC 59.420 57.895 23.99 20.26 42.62 5.34
3611 5697 2.341101 GCCCGCTATAGCTCCGCTA 61.341 63.158 21.98 0.00 45.55 4.26
3612 5698 2.766306 TAGCCCGCTATAGCTCCGCT 62.766 60.000 24.41 24.41 43.41 5.52
3613 5699 1.668101 ATAGCCCGCTATAGCTCCGC 61.668 60.000 21.98 18.46 40.56 5.54
3614 5700 0.818296 AATAGCCCGCTATAGCTCCG 59.182 55.000 21.98 10.15 40.56 4.63
3615 5701 2.233922 TCAAATAGCCCGCTATAGCTCC 59.766 50.000 21.98 10.06 40.56 4.70
3616 5702 3.594603 TCAAATAGCCCGCTATAGCTC 57.405 47.619 21.98 11.04 40.56 4.09
3617 5703 4.065789 GTTTCAAATAGCCCGCTATAGCT 58.934 43.478 21.98 6.31 43.20 3.32
3618 5704 3.813166 TGTTTCAAATAGCCCGCTATAGC 59.187 43.478 15.09 15.09 38.20 2.97
3619 5705 5.050091 CACTGTTTCAAATAGCCCGCTATAG 60.050 44.000 9.56 6.26 38.20 1.31
3620 5706 4.814234 CACTGTTTCAAATAGCCCGCTATA 59.186 41.667 9.56 0.00 38.20 1.31
3621 5707 3.627577 CACTGTTTCAAATAGCCCGCTAT 59.372 43.478 3.31 3.31 40.63 2.97
3622 5708 3.006940 CACTGTTTCAAATAGCCCGCTA 58.993 45.455 0.00 0.00 0.00 4.26
3623 5709 1.812571 CACTGTTTCAAATAGCCCGCT 59.187 47.619 0.00 0.00 0.00 5.52
3624 5710 1.539827 ACACTGTTTCAAATAGCCCGC 59.460 47.619 0.00 0.00 0.00 6.13
3625 5711 3.365969 GGAACACTGTTTCAAATAGCCCG 60.366 47.826 0.00 0.00 0.00 6.13
3626 5712 3.826729 AGGAACACTGTTTCAAATAGCCC 59.173 43.478 2.94 0.00 0.00 5.19
3627 5713 5.453567 AAGGAACACTGTTTCAAATAGCC 57.546 39.130 2.94 0.00 0.00 3.93
3628 5714 9.937175 GATATAAGGAACACTGTTTCAAATAGC 57.063 33.333 2.94 0.00 0.00 2.97
3630 5716 9.403583 GGGATATAAGGAACACTGTTTCAAATA 57.596 33.333 2.94 1.03 0.00 1.40
3631 5717 7.893302 TGGGATATAAGGAACACTGTTTCAAAT 59.107 33.333 2.94 0.00 0.00 2.32
3632 5718 7.235079 TGGGATATAAGGAACACTGTTTCAAA 58.765 34.615 2.94 0.00 0.00 2.69
3633 5719 6.785076 TGGGATATAAGGAACACTGTTTCAA 58.215 36.000 2.94 0.00 0.00 2.69
3634 5720 6.381498 TGGGATATAAGGAACACTGTTTCA 57.619 37.500 2.94 0.00 0.00 2.69
3635 5721 7.054124 TGATGGGATATAAGGAACACTGTTTC 58.946 38.462 0.00 0.00 0.00 2.78
3636 5722 6.969043 TGATGGGATATAAGGAACACTGTTT 58.031 36.000 0.00 0.00 0.00 2.83
3637 5723 6.575244 TGATGGGATATAAGGAACACTGTT 57.425 37.500 0.00 0.00 0.00 3.16
3638 5724 6.329986 TCATGATGGGATATAAGGAACACTGT 59.670 38.462 0.00 0.00 0.00 3.55
3639 5725 6.652481 GTCATGATGGGATATAAGGAACACTG 59.348 42.308 0.00 0.00 0.00 3.66
3640 5726 6.519043 CGTCATGATGGGATATAAGGAACACT 60.519 42.308 7.06 0.00 0.00 3.55
3641 5727 5.639506 CGTCATGATGGGATATAAGGAACAC 59.360 44.000 7.06 0.00 0.00 3.32
3642 5728 5.793817 CGTCATGATGGGATATAAGGAACA 58.206 41.667 7.06 0.00 0.00 3.18
3643 5729 4.631813 GCGTCATGATGGGATATAAGGAAC 59.368 45.833 16.59 0.00 0.00 3.62
5999 12197 3.570212 AAGCCGAAGCCACCCACT 61.570 61.111 0.00 0.00 41.25 4.00
6888 13107 0.303493 GCAAACAGTCGCGTTCTTCA 59.697 50.000 5.77 0.00 0.00 3.02
6900 13123 1.044725 GTTGAACGCATCGCAAACAG 58.955 50.000 0.00 0.00 0.00 3.16
6945 13168 6.542005 TGTTCTGAAGCACTTGACTGAATAAA 59.458 34.615 0.00 0.00 0.00 1.40
7032 13255 2.590092 GGCCACACCCTAGCGATT 59.410 61.111 0.00 0.00 0.00 3.34
7470 13697 1.377202 GGATGGTGGCAGCGAGAAA 60.377 57.895 12.58 0.00 0.00 2.52
7981 14223 4.384647 GCTGTCTGGTCTTATTCCCTGAAT 60.385 45.833 0.00 0.00 36.20 2.57
8779 15029 6.080682 TCCTCTCCTAGATTTGATATGTGCT 58.919 40.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.