Multiple sequence alignment - TraesCS3B01G171000

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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 TraesCS3B01G171000 chr3B 100.000 5180 0 0 1 5180 171815230 171810051 0.000000e+00 9566.0
1 TraesCS3B01G171000 chr3B 100.000 2556 0 0 5372 7927 171809859 171807304 0.000000e+00 4721.0
2 TraesCS3B01G171000 chr3B 83.869 1494 157 48 749 2202 171799857 171798408 0.000000e+00 1347.0
3 TraesCS3B01G171000 chr3B 87.352 759 82 9 6487 7244 171796918 171796173 0.000000e+00 857.0
4 TraesCS3B01G171000 chr3B 96.063 508 20 0 7420 7927 173023424 173022917 0.000000e+00 828.0
5 TraesCS3B01G171000 chr3B 96.071 509 18 2 7421 7927 259252751 259253259 0.000000e+00 828.0
6 TraesCS3B01G171000 chr3B 95.898 512 17 2 7420 7927 259265427 259265938 0.000000e+00 826.0
7 TraesCS3B01G171000 chr3B 82.293 689 65 27 5656 6309 171797776 171797110 1.950000e-150 544.0
8 TraesCS3B01G171000 chr3B 87.106 349 38 5 4598 4943 23953756 23953412 9.650000e-104 388.0
9 TraesCS3B01G171000 chr3B 80.982 163 20 7 4511 4662 385185390 385185552 1.400000e-22 119.0
10 TraesCS3B01G171000 chr3B 84.615 104 14 2 7305 7407 171709917 171709815 1.410000e-17 102.0
11 TraesCS3B01G171000 chr3B 97.727 44 1 0 4885 4928 3818377 3818334 8.530000e-10 76.8
12 TraesCS3B01G171000 chr3B 97.674 43 1 0 4886 4928 4717708 4717666 3.070000e-09 75.0
13 TraesCS3B01G171000 chr3D 94.400 3339 111 32 746 4042 119424764 119421460 0.000000e+00 5060.0
14 TraesCS3B01G171000 chr3D 94.055 2069 73 9 5375 7421 119419881 119417841 0.000000e+00 3094.0
15 TraesCS3B01G171000 chr3D 95.496 977 41 3 4161 5137 119421201 119420228 0.000000e+00 1557.0
16 TraesCS3B01G171000 chr3D 82.887 1455 159 38 746 2156 119411549 119410141 0.000000e+00 1225.0
17 TraesCS3B01G171000 chr3D 83.241 907 88 38 2594 3458 378910127 378911011 0.000000e+00 774.0
18 TraesCS3B01G171000 chr3D 84.561 706 79 17 6420 7116 119408686 119408002 0.000000e+00 673.0
19 TraesCS3B01G171000 chr3D 80.202 495 64 22 4108 4573 80258610 80258121 2.740000e-89 340.0
20 TraesCS3B01G171000 chr3D 81.167 377 46 15 4163 4521 565799979 565800348 6.060000e-71 279.0
21 TraesCS3B01G171000 chr3A 90.053 2091 117 39 2874 4894 126162298 126160229 0.000000e+00 2625.0
22 TraesCS3B01G171000 chr3A 94.264 1290 59 8 5829 7111 126158573 126157292 0.000000e+00 1958.0
23 TraesCS3B01G171000 chr3A 91.433 1179 66 8 746 1918 126164202 126163053 0.000000e+00 1585.0
24 TraesCS3B01G171000 chr3A 82.824 1572 150 54 746 2241 126123504 126121977 0.000000e+00 1297.0
25 TraesCS3B01G171000 chr3A 96.408 696 19 4 1917 2611 126162986 126162296 0.000000e+00 1142.0
26 TraesCS3B01G171000 chr3A 86.629 703 66 17 6420 7116 126120259 126119579 0.000000e+00 752.0
27 TraesCS3B01G171000 chr3A 90.713 463 22 3 5375 5816 126159902 126159440 1.470000e-166 597.0
28 TraesCS3B01G171000 chr3A 80.625 640 64 23 4337 4943 513898717 513898105 2.630000e-119 440.0
29 TraesCS3B01G171000 chr3A 79.589 681 68 31 5656 6309 126121403 126120767 9.510000e-114 422.0
30 TraesCS3B01G171000 chr3A 73.045 486 116 15 53 530 65967091 65966613 2.960000e-34 158.0
31 TraesCS3B01G171000 chr3A 89.535 86 9 0 7322 7407 126036455 126036370 8.410000e-20 110.0
32 TraesCS3B01G171000 chr3A 96.078 51 1 1 2852 2901 126107774 126107824 1.830000e-11 82.4
33 TraesCS3B01G171000 chr3A 82.857 70 6 6 2879 2944 700283290 700283223 3.090000e-04 58.4
34 TraesCS3B01G171000 chr4B 89.956 687 64 4 1 686 481582684 481582002 0.000000e+00 881.0
35 TraesCS3B01G171000 chr4B 82.123 179 18 8 4509 4676 514609058 514609233 2.980000e-29 141.0
36 TraesCS3B01G171000 chr4B 87.037 54 5 1 4660 4713 600518912 600518963 8.590000e-05 60.2
37 TraesCS3B01G171000 chr5B 89.083 687 72 3 1 686 665571140 665570456 0.000000e+00 850.0
38 TraesCS3B01G171000 chr5B 96.457 508 16 2 7421 7927 466399124 466398618 0.000000e+00 837.0
39 TraesCS3B01G171000 chr5B 96.101 513 19 1 7416 7927 451491048 451491560 0.000000e+00 835.0
40 TraesCS3B01G171000 chr5B 96.071 509 19 1 7420 7927 21505578 21505070 0.000000e+00 828.0
41 TraesCS3B01G171000 chr5B 79.641 167 31 3 7128 7291 679766462 679766296 5.030000e-22 117.0
42 TraesCS3B01G171000 chr5B 79.394 165 32 2 7128 7290 261347222 261347058 1.810000e-21 115.0
43 TraesCS3B01G171000 chr5B 79.641 167 27 6 7125 7287 554818268 554818431 6.500000e-21 113.0
44 TraesCS3B01G171000 chr5B 83.333 90 8 6 2843 2926 278042380 278042468 8.530000e-10 76.8
45 TraesCS3B01G171000 chr6B 95.898 512 19 2 7417 7927 366518803 366518293 0.000000e+00 828.0
46 TraesCS3B01G171000 chr6B 79.279 444 52 18 4163 4570 6884853 6885292 2.820000e-69 274.0
47 TraesCS3B01G171000 chr6B 79.882 169 29 5 7128 7292 655298517 655298684 1.400000e-22 119.0
48 TraesCS3B01G171000 chr6B 87.097 93 12 0 2481 2573 27118259 27118351 1.090000e-18 106.0
49 TraesCS3B01G171000 chrUn 96.063 508 18 2 7421 7927 31773509 31774015 0.000000e+00 826.0
50 TraesCS3B01G171000 chrUn 88.889 54 4 1 4660 4713 37062141 37062090 1.850000e-06 65.8
51 TraesCS3B01G171000 chr7B 95.890 511 19 2 7419 7927 699950061 699949551 0.000000e+00 826.0
52 TraesCS3B01G171000 chr7B 89.412 85 9 0 2487 2571 505750276 505750360 3.020000e-19 108.0
53 TraesCS3B01G171000 chr1B 88.529 680 76 2 1 680 18866674 18867351 0.000000e+00 822.0
54 TraesCS3B01G171000 chr1B 83.569 566 71 14 4509 5064 411984285 411984838 1.970000e-140 510.0
55 TraesCS3B01G171000 chr1B 82.169 415 53 15 4163 4573 640063164 640062767 3.540000e-88 337.0
56 TraesCS3B01G171000 chr1B 79.215 433 51 19 4163 4570 520347009 520347427 1.700000e-66 265.0
57 TraesCS3B01G171000 chr5A 86.944 674 83 5 1 672 367618174 367617504 0.000000e+00 752.0
58 TraesCS3B01G171000 chr5A 86.047 86 12 0 2486 2571 676585397 676585482 8.470000e-15 93.5
59 TraesCS3B01G171000 chr5A 82.474 97 17 0 3558 3654 485411627 485411723 1.420000e-12 86.1
60 TraesCS3B01G171000 chr1D 82.995 788 82 23 4180 4922 434363883 434364663 0.000000e+00 665.0
61 TraesCS3B01G171000 chr1D 100.000 33 0 0 714 746 319525405 319525373 2.390000e-05 62.1
62 TraesCS3B01G171000 chr4A 79.540 435 61 16 4163 4573 718818722 718818292 1.300000e-72 285.0
63 TraesCS3B01G171000 chr4A 83.133 83 11 3 2852 2932 627755412 627755331 1.100000e-08 73.1
64 TraesCS3B01G171000 chr6A 80.368 326 46 14 4163 4481 76961184 76961498 1.720000e-56 231.0
65 TraesCS3B01G171000 chr6A 80.392 153 26 4 7138 7287 21523123 21522972 6.500000e-21 113.0
66 TraesCS3B01G171000 chr2B 83.333 162 23 2 4757 4915 693155712 693155552 6.410000e-31 147.0
67 TraesCS3B01G171000 chr2B 83.007 153 22 4 7138 7287 794586025 794585874 1.390000e-27 135.0
68 TraesCS3B01G171000 chr2B 84.615 91 13 1 2482 2571 32057918 32058008 1.100000e-13 89.8
69 TraesCS3B01G171000 chr2B 97.297 37 1 0 710 746 219624826 219624862 6.640000e-06 63.9
70 TraesCS3B01G171000 chr2A 80.392 153 26 4 7138 7287 593911155 593911306 6.500000e-21 113.0
71 TraesCS3B01G171000 chr2A 91.379 58 3 2 2851 2907 723996686 723996630 2.370000e-10 78.7
72 TraesCS3B01G171000 chr2A 97.297 37 1 0 710 746 177997193 177997229 6.640000e-06 63.9
73 TraesCS3B01G171000 chr2A 100.000 33 0 0 714 746 390323141 390323109 2.390000e-05 62.1
74 TraesCS3B01G171000 chr2A 75.352 142 25 10 3124 3261 263430199 263430064 8.590000e-05 60.2
75 TraesCS3B01G171000 chr6D 88.298 94 9 2 2478 2571 105560457 105560548 2.340000e-20 111.0
76 TraesCS3B01G171000 chr2D 84.884 86 5 6 2852 2929 637863946 637864031 6.590000e-11 80.5
77 TraesCS3B01G171000 chr2D 83.158 95 6 9 2858 2945 13612445 13612354 2.370000e-10 78.7
78 TraesCS3B01G171000 chr7A 86.301 73 9 1 2504 2576 421732094 421732023 2.370000e-10 78.7
79 TraesCS3B01G171000 chr7A 100.000 33 0 0 714 746 236375812 236375844 2.390000e-05 62.1
80 TraesCS3B01G171000 chr4D 100.000 33 0 0 714 746 105236729 105236761 2.390000e-05 62.1


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 TraesCS3B01G171000 chr3B 171807304 171815230 7926 True 7143.500000 9566 100.000000 1 7927 2 chr3B.!!$R7 7926
1 TraesCS3B01G171000 chr3B 171796173 171799857 3684 True 916.000000 1347 84.504667 749 7244 3 chr3B.!!$R6 6495
2 TraesCS3B01G171000 chr3B 173022917 173023424 507 True 828.000000 828 96.063000 7420 7927 1 chr3B.!!$R5 507
3 TraesCS3B01G171000 chr3B 259252751 259253259 508 False 828.000000 828 96.071000 7421 7927 1 chr3B.!!$F1 506
4 TraesCS3B01G171000 chr3B 259265427 259265938 511 False 826.000000 826 95.898000 7420 7927 1 chr3B.!!$F2 507
5 TraesCS3B01G171000 chr3D 119417841 119424764 6923 True 3237.000000 5060 94.650333 746 7421 3 chr3D.!!$R3 6675
6 TraesCS3B01G171000 chr3D 119408002 119411549 3547 True 949.000000 1225 83.724000 746 7116 2 chr3D.!!$R2 6370
7 TraesCS3B01G171000 chr3D 378910127 378911011 884 False 774.000000 774 83.241000 2594 3458 1 chr3D.!!$F1 864
8 TraesCS3B01G171000 chr3A 126157292 126164202 6910 True 1581.400000 2625 92.574200 746 7111 5 chr3A.!!$R6 6365
9 TraesCS3B01G171000 chr3A 126119579 126123504 3925 True 823.666667 1297 83.014000 746 7116 3 chr3A.!!$R5 6370
10 TraesCS3B01G171000 chr3A 513898105 513898717 612 True 440.000000 440 80.625000 4337 4943 1 chr3A.!!$R3 606
11 TraesCS3B01G171000 chr4B 481582002 481582684 682 True 881.000000 881 89.956000 1 686 1 chr4B.!!$R1 685
12 TraesCS3B01G171000 chr5B 665570456 665571140 684 True 850.000000 850 89.083000 1 686 1 chr5B.!!$R4 685
13 TraesCS3B01G171000 chr5B 466398618 466399124 506 True 837.000000 837 96.457000 7421 7927 1 chr5B.!!$R3 506
14 TraesCS3B01G171000 chr5B 451491048 451491560 512 False 835.000000 835 96.101000 7416 7927 1 chr5B.!!$F2 511
15 TraesCS3B01G171000 chr5B 21505070 21505578 508 True 828.000000 828 96.071000 7420 7927 1 chr5B.!!$R1 507
16 TraesCS3B01G171000 chr6B 366518293 366518803 510 True 828.000000 828 95.898000 7417 7927 1 chr6B.!!$R1 510
17 TraesCS3B01G171000 chrUn 31773509 31774015 506 False 826.000000 826 96.063000 7421 7927 1 chrUn.!!$F1 506
18 TraesCS3B01G171000 chr7B 699949551 699950061 510 True 826.000000 826 95.890000 7419 7927 1 chr7B.!!$R1 508
19 TraesCS3B01G171000 chr1B 18866674 18867351 677 False 822.000000 822 88.529000 1 680 1 chr1B.!!$F1 679
20 TraesCS3B01G171000 chr1B 411984285 411984838 553 False 510.000000 510 83.569000 4509 5064 1 chr1B.!!$F2 555
21 TraesCS3B01G171000 chr5A 367617504 367618174 670 True 752.000000 752 86.944000 1 672 1 chr5A.!!$R1 671
22 TraesCS3B01G171000 chr1D 434363883 434364663 780 False 665.000000 665 82.995000 4180 4922 1 chr1D.!!$F1 742

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
694 698 0.034477 TTTTCGGGGAAGCCTCCATC 60.034 55.000 3.19 0.00 44.51 3.51 F
978 1015 0.043053 CGTCGCATTACTGGCATTCG 60.043 55.000 0.00 0.00 0.00 3.34 F
1908 2004 0.984230 ACGAAAGAAGGGGATCAGCA 59.016 50.000 0.00 0.00 0.00 4.41 F
2456 2703 1.382522 GTGTGTATGACCCTGCATGG 58.617 55.000 6.46 6.46 0.00 3.66 F
4030 4646 0.323360 AAAAAGGGCGATGCTAGGCA 60.323 50.000 0.00 0.00 44.86 4.75 F
4394 5198 0.249031 CTGTCGTCACTGCACTGTCA 60.249 55.000 0.00 0.00 0.00 3.58 F
5132 5976 1.672356 GATGGTGGTGCACGAGCTT 60.672 57.895 27.48 22.44 42.74 3.74 F
5789 6768 0.625849 CACCTGAGTGGGCCCTTATT 59.374 55.000 25.70 5.36 40.55 1.40 F
5790 6769 0.919710 ACCTGAGTGGGCCCTTATTC 59.080 55.000 25.70 15.14 41.11 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1696 0.174845 TACCATAGGCGTGTGCTCAC 59.825 55.000 8.86 8.86 42.25 3.51 R
2016 2191 2.704572 ACAGAAGCTTGCATGACCTAC 58.295 47.619 2.10 0.00 0.00 3.18 R
3876 4492 1.476488 GGTTCCGGCACATAAGCAAAT 59.524 47.619 6.56 0.00 35.83 2.32 R
4376 5180 0.389025 ATGACAGTGCAGTGACGACA 59.611 50.000 28.02 19.43 0.00 4.35 R
5789 6768 0.178068 GATTAACGCCTGGGAGCAGA 59.822 55.000 0.00 0.00 0.00 4.26 R
5790 6769 0.179000 AGATTAACGCCTGGGAGCAG 59.821 55.000 0.00 0.00 0.00 4.24 R
6624 8935 0.507358 CGACATGATGATCTGCTGCG 59.493 55.000 0.00 0.00 0.00 5.18 R
6648 8959 1.211743 GCTGTTTGTTGGCTTCTTGC 58.788 50.000 0.00 0.00 41.94 4.01 R
7147 9466 1.335496 GGTGTAAAAGCGCTGGAAACA 59.665 47.619 12.58 10.97 39.59 2.83 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
102 103 0.731514 CAATCTGCTTTGCCACTGCG 60.732 55.000 0.00 0.00 41.78 5.18
143 144 2.108075 TGAGATTGAAGGGCAAGTTGGA 59.892 45.455 4.75 0.00 40.42 3.53
183 186 8.986477 ACTGCAACTTATCAAATTGTAATTCC 57.014 30.769 0.00 0.00 0.00 3.01
234 237 2.993220 CAGTATGACTGCGTGTTTGCTA 59.007 45.455 0.00 0.00 39.62 3.49
243 246 2.097304 TGCGTGTTTGCTAATATGCCAG 59.903 45.455 16.53 0.00 36.78 4.85
264 267 2.202878 CTACCATCCCACACGCGG 60.203 66.667 12.47 1.27 0.00 6.46
396 399 1.157870 GGATATGGAACGTGTGGCGG 61.158 60.000 0.00 0.00 46.52 6.13
405 408 2.025418 CGTGTGGCGGTGTAGAACC 61.025 63.158 0.00 0.00 46.60 3.62
445 448 1.131771 CGTCGGTTCATCATCATCGG 58.868 55.000 0.00 0.00 0.00 4.18
459 462 1.340889 TCATCGGCATCATCGATCACA 59.659 47.619 0.00 0.00 44.30 3.58
492 495 1.006043 TCCTCTTCCGTCAGATCCAGT 59.994 52.381 0.00 0.00 0.00 4.00
493 496 1.407258 CCTCTTCCGTCAGATCCAGTC 59.593 57.143 0.00 0.00 0.00 3.51
495 498 3.546724 CTCTTCCGTCAGATCCAGTCTA 58.453 50.000 0.00 0.00 34.69 2.59
558 561 0.459411 GAGCGTCTGCCTTCTCCTTC 60.459 60.000 0.00 0.00 44.31 3.46
564 567 1.845627 CTGCCTTCTCCTTCCCAGCA 61.846 60.000 0.00 0.00 0.00 4.41
573 576 3.234630 CTTCCCAGCACCGGACGAA 62.235 63.158 9.46 0.00 0.00 3.85
584 587 2.893398 GGACGAAGCCATCTCGGT 59.107 61.111 0.00 0.00 36.97 4.69
591 594 1.548357 AAGCCATCTCGGTGCTGTCT 61.548 55.000 0.00 0.00 35.08 3.41
655 659 0.532196 CCTCGAAACCCTAATCGCCC 60.532 60.000 0.00 0.00 38.87 6.13
656 660 0.464452 CTCGAAACCCTAATCGCCCT 59.536 55.000 0.00 0.00 38.87 5.19
657 661 0.462789 TCGAAACCCTAATCGCCCTC 59.537 55.000 0.00 0.00 38.87 4.30
658 662 0.464452 CGAAACCCTAATCGCCCTCT 59.536 55.000 0.00 0.00 31.71 3.69
659 663 1.538419 CGAAACCCTAATCGCCCTCTC 60.538 57.143 0.00 0.00 31.71 3.20
660 664 1.485066 GAAACCCTAATCGCCCTCTCA 59.515 52.381 0.00 0.00 0.00 3.27
662 666 0.760945 ACCCTAATCGCCCTCTCAGG 60.761 60.000 0.00 0.00 34.30 3.86
663 667 0.470080 CCCTAATCGCCCTCTCAGGA 60.470 60.000 0.00 0.00 37.67 3.86
686 690 3.079578 GTTTCCTAGGTTTTCGGGGAAG 58.920 50.000 9.08 0.00 37.37 3.46
687 691 0.616891 TCCTAGGTTTTCGGGGAAGC 59.383 55.000 9.08 0.00 0.00 3.86
688 692 0.393944 CCTAGGTTTTCGGGGAAGCC 60.394 60.000 0.00 0.00 0.00 4.35
689 693 0.618981 CTAGGTTTTCGGGGAAGCCT 59.381 55.000 0.56 0.56 34.76 4.58
690 694 0.616891 TAGGTTTTCGGGGAAGCCTC 59.383 55.000 0.00 0.00 33.39 4.70
691 695 1.677966 GGTTTTCGGGGAAGCCTCC 60.678 63.158 0.00 0.00 41.59 4.30
692 696 1.074248 GTTTTCGGGGAAGCCTCCA 59.926 57.895 3.19 0.00 44.51 3.86
693 697 0.323451 GTTTTCGGGGAAGCCTCCAT 60.323 55.000 3.19 0.00 44.51 3.41
694 698 0.034477 TTTTCGGGGAAGCCTCCATC 60.034 55.000 3.19 0.00 44.51 3.51
695 699 1.921869 TTTCGGGGAAGCCTCCATCC 61.922 60.000 3.19 0.00 44.51 3.51
696 700 3.089874 CGGGGAAGCCTCCATCCA 61.090 66.667 3.19 0.00 44.51 3.41
697 701 2.597903 GGGGAAGCCTCCATCCAC 59.402 66.667 3.19 0.00 44.51 4.02
698 702 2.003548 GGGGAAGCCTCCATCCACT 61.004 63.158 3.19 0.00 44.51 4.00
699 703 1.575447 GGGGAAGCCTCCATCCACTT 61.575 60.000 3.19 0.00 44.51 3.16
700 704 1.213296 GGGAAGCCTCCATCCACTTA 58.787 55.000 3.19 0.00 44.51 2.24
701 705 1.141858 GGGAAGCCTCCATCCACTTAG 59.858 57.143 3.19 0.00 44.51 2.18
702 706 1.840635 GGAAGCCTCCATCCACTTAGT 59.159 52.381 0.00 0.00 41.96 2.24
703 707 2.239907 GGAAGCCTCCATCCACTTAGTT 59.760 50.000 0.00 0.00 41.96 2.24
704 708 3.454812 GGAAGCCTCCATCCACTTAGTTA 59.545 47.826 0.00 0.00 41.96 2.24
705 709 4.443598 GGAAGCCTCCATCCACTTAGTTAG 60.444 50.000 0.00 0.00 41.96 2.34
706 710 2.436173 AGCCTCCATCCACTTAGTTAGC 59.564 50.000 0.00 0.00 0.00 3.09
707 711 2.436173 GCCTCCATCCACTTAGTTAGCT 59.564 50.000 0.00 0.00 0.00 3.32
708 712 3.641906 GCCTCCATCCACTTAGTTAGCTA 59.358 47.826 0.00 0.00 0.00 3.32
709 713 4.101119 GCCTCCATCCACTTAGTTAGCTAA 59.899 45.833 0.86 0.86 35.98 3.09
710 714 5.396436 GCCTCCATCCACTTAGTTAGCTAAA 60.396 44.000 7.99 0.00 36.82 1.85
711 715 6.650120 CCTCCATCCACTTAGTTAGCTAAAA 58.350 40.000 7.99 0.00 36.82 1.52
712 716 7.110155 CCTCCATCCACTTAGTTAGCTAAAAA 58.890 38.462 7.99 5.13 36.82 1.94
739 743 7.687941 TGTTCTTTTCTGAATCAATAGTCCC 57.312 36.000 0.00 0.00 0.00 4.46
740 744 7.230747 TGTTCTTTTCTGAATCAATAGTCCCA 58.769 34.615 0.00 0.00 0.00 4.37
741 745 7.174946 TGTTCTTTTCTGAATCAATAGTCCCAC 59.825 37.037 0.00 0.00 0.00 4.61
742 746 6.180472 TCTTTTCTGAATCAATAGTCCCACC 58.820 40.000 0.00 0.00 0.00 4.61
743 747 5.779241 TTTCTGAATCAATAGTCCCACCT 57.221 39.130 0.00 0.00 0.00 4.00
744 748 5.359194 TTCTGAATCAATAGTCCCACCTC 57.641 43.478 0.00 0.00 0.00 3.85
758 762 2.417586 CCCACCTCGGAAATACGAAAAC 59.582 50.000 0.00 0.00 42.98 2.43
767 771 4.609708 CGGAAATACGAAAACTTGGAAACG 59.390 41.667 0.00 0.00 35.47 3.60
774 778 5.463286 ACGAAAACTTGGAAACGAAAAAGT 58.537 33.333 0.00 0.00 34.40 2.66
834 849 8.463930 TTTATCAAATATTTCCCGAGCAGATT 57.536 30.769 0.00 0.00 0.00 2.40
870 898 5.986135 CCAGCGCAGAATTAACTACTAGAAT 59.014 40.000 11.47 0.00 0.00 2.40
941 969 2.137425 TATACCTCCACATCGCGGCG 62.137 60.000 17.70 17.70 0.00 6.46
978 1015 0.043053 CGTCGCATTACTGGCATTCG 60.043 55.000 0.00 0.00 0.00 3.34
1452 1517 2.239654 GTGGAGGGTGATCATTGAGGAA 59.760 50.000 0.00 0.00 0.00 3.36
1551 1616 2.571757 CTCGCCGTGCTGGTTCTA 59.428 61.111 0.00 0.00 41.21 2.10
1610 1675 2.353607 CGTGATCTACCGCGGCTC 60.354 66.667 28.58 17.34 36.51 4.70
1700 1767 3.904965 TCACCCAACAGTAACACCATCTA 59.095 43.478 0.00 0.00 0.00 1.98
1712 1780 8.824781 CAGTAACACCATCTAAGAATTCAGATG 58.175 37.037 21.01 21.01 45.11 2.90
1737 1810 7.967854 TGTATGTTCTGTTTTGTTTCAGTTCTG 59.032 33.333 0.00 0.00 33.89 3.02
1817 1894 9.956720 GTATGATCTCTTGTTTATTTGGATTGG 57.043 33.333 0.00 0.00 0.00 3.16
1908 2004 0.984230 ACGAAAGAAGGGGATCAGCA 59.016 50.000 0.00 0.00 0.00 4.41
1996 2171 2.356069 GGTAGCTATTGTTTGGCTCTGC 59.644 50.000 0.00 0.00 37.50 4.26
2000 2175 1.806542 CTATTGTTTGGCTCTGCGTGT 59.193 47.619 0.00 0.00 0.00 4.49
2016 2191 4.854399 TGCGTGTACCTTTTGAATTGAAG 58.146 39.130 0.00 0.00 0.00 3.02
2150 2381 5.875359 CCCACACTTCTCCTAATTAACAGTC 59.125 44.000 0.00 0.00 0.00 3.51
2224 2471 6.305693 ACTTGTTCTAGCTGTGATTTGTTC 57.694 37.500 0.00 0.00 0.00 3.18
2254 2501 2.734276 AAAGTGTGCAACGGTTTTGT 57.266 40.000 0.00 0.00 42.39 2.83
2305 2552 3.252215 CCGTCAGTCAATTTTTGTAGCCA 59.748 43.478 0.00 0.00 0.00 4.75
2456 2703 1.382522 GTGTGTATGACCCTGCATGG 58.617 55.000 6.46 6.46 0.00 3.66
2467 2714 3.817647 GACCCTGCATGGATGATTACTTC 59.182 47.826 15.66 0.00 38.35 3.01
2473 2720 4.343814 TGCATGGATGATTACTTCTCCGTA 59.656 41.667 0.00 0.00 0.00 4.02
2679 2933 5.049129 TGTGAGAGCGACTCTACATGATATG 60.049 44.000 0.00 0.00 41.35 1.78
2680 2934 4.083057 TGAGAGCGACTCTACATGATATGC 60.083 45.833 0.00 0.00 41.35 3.14
2720 2974 6.318144 ACATTTGAGAGATGCTTAATCACCAG 59.682 38.462 0.00 0.00 37.81 4.00
3070 3622 3.015934 TGCTGATGATGTGTGTTTTGC 57.984 42.857 0.00 0.00 0.00 3.68
3142 3694 9.415544 GATTGAGAAAATTGCACTATTTTGACT 57.584 29.630 12.65 5.88 37.72 3.41
3263 3820 8.867097 GGTAATACCATCCACTAACTCATTCTA 58.133 37.037 4.24 0.00 38.42 2.10
3596 4158 7.907389 ACTGATAAGGATAAAGTGACTGACAA 58.093 34.615 0.00 0.00 0.00 3.18
3648 4210 7.885922 TGTGCTAATGTTTCTACCTCCATTTTA 59.114 33.333 0.00 0.00 0.00 1.52
3926 4542 4.917415 GCAGTTTACAATCGCTGTTTGATT 59.083 37.500 6.42 0.00 39.64 2.57
3954 4570 2.051334 TAATTAGCAATGGCCGCAGT 57.949 45.000 0.00 0.00 42.56 4.40
4030 4646 0.323360 AAAAAGGGCGATGCTAGGCA 60.323 50.000 0.00 0.00 44.86 4.75
4052 4668 4.988598 CACGCCGACCCAGCTGTT 62.989 66.667 13.81 0.00 0.00 3.16
4053 4669 4.681978 ACGCCGACCCAGCTGTTC 62.682 66.667 13.81 7.72 0.00 3.18
4096 4729 2.311688 GATGTACCCAGCCCCAGTCG 62.312 65.000 0.00 0.00 0.00 4.18
4105 4738 1.142748 GCCCCAGTCGTCTGATCTG 59.857 63.158 11.41 0.00 43.76 2.90
4108 4741 1.142748 CCAGTCGTCTGATCTGCCC 59.857 63.158 11.41 0.00 43.76 5.36
4151 4810 2.621338 TCATCTTCTTCTTTCGCGCAT 58.379 42.857 8.75 0.00 0.00 4.73
4156 4815 2.739704 CTTCTTTCGCGCATGCCGA 61.740 57.895 22.05 22.05 40.02 5.54
4157 4816 2.886512 CTTCTTTCGCGCATGCCGAC 62.887 60.000 24.55 9.80 40.02 4.79
4158 4817 3.490759 CTTTCGCGCATGCCGACT 61.491 61.111 24.55 0.00 40.02 4.18
4166 4956 2.665000 CATGCCGACTGTCCCTGT 59.335 61.111 1.55 0.00 0.00 4.00
4278 5081 2.005960 GCAGCATCCGTACTCGTCCT 62.006 60.000 0.00 0.00 35.01 3.85
4290 5093 4.367023 CGTCCTTCGGTCCGGCAA 62.367 66.667 12.29 0.00 35.71 4.52
4295 5098 1.004918 CTTCGGTCCGGCAAGAAGT 60.005 57.895 12.29 0.00 36.34 3.01
4394 5198 0.249031 CTGTCGTCACTGCACTGTCA 60.249 55.000 0.00 0.00 0.00 3.58
4476 5281 5.829924 AGCTTTTTCTCTCATTGGTTGAAGA 59.170 36.000 0.00 0.00 32.78 2.87
4723 5562 2.904866 GGTGCCGTGGTTGAAGCA 60.905 61.111 0.00 0.00 0.00 3.91
4974 5818 4.030452 GGTGGTTGCAGCAGCGTC 62.030 66.667 2.05 0.00 46.23 5.19
5024 5868 2.202610 CGCATCGCTTCTGGTCGA 60.203 61.111 0.00 0.00 39.17 4.20
5092 5936 4.778143 GGTCAAGGCGACGGGCAT 62.778 66.667 0.00 0.00 46.42 4.40
5132 5976 1.672356 GATGGTGGTGCACGAGCTT 60.672 57.895 27.48 22.44 42.74 3.74
5137 5981 3.730761 GGTGCACGAGCTTGCTGG 61.731 66.667 11.45 0.81 43.41 4.85
5160 6004 4.049640 GGCCGGTGCATCGCAAAA 62.050 61.111 15.51 0.00 41.47 2.44
5161 6005 2.504681 GCCGGTGCATCGCAAAAG 60.505 61.111 15.51 0.16 41.47 2.27
5162 6006 2.179018 CCGGTGCATCGCAAAAGG 59.821 61.111 15.51 0.00 41.47 3.11
5163 6007 2.504681 CGGTGCATCGCAAAAGGC 60.505 61.111 6.36 0.00 41.47 4.35
5172 6016 4.056125 GCAAAAGGCGTGAGGGGC 62.056 66.667 0.00 0.00 0.00 5.80
5173 6017 3.737172 CAAAAGGCGTGAGGGGCG 61.737 66.667 0.00 0.00 37.59 6.13
5174 6018 4.265056 AAAAGGCGTGAGGGGCGT 62.265 61.111 0.00 0.00 37.59 5.68
5644 6617 6.684131 GCAAAAATCAAAGAAAAAGTGACTGC 59.316 34.615 0.00 0.00 0.00 4.40
5737 6716 6.832900 TGTATGGGTATGAAAGATGCAATTGA 59.167 34.615 10.34 0.00 0.00 2.57
5742 6721 6.459298 GGGTATGAAAGATGCAATTGAGTCTG 60.459 42.308 10.34 0.00 0.00 3.51
5789 6768 0.625849 CACCTGAGTGGGCCCTTATT 59.374 55.000 25.70 5.36 40.55 1.40
5790 6769 0.919710 ACCTGAGTGGGCCCTTATTC 59.080 55.000 25.70 15.14 41.11 1.75
6196 8041 3.564225 CCTCCTCACGCTTTTTGTAAGTT 59.436 43.478 0.00 0.00 0.00 2.66
6434 8730 9.356433 CATGTGTTTAATTTCTAACATGCATGA 57.644 29.630 32.75 10.86 39.07 3.07
6618 8929 4.110036 TCATCGAGAAAAGATTGAGCGA 57.890 40.909 0.00 0.00 0.00 4.93
6646 8957 2.817901 CAGCAGATCATCATGTCGTCA 58.182 47.619 0.00 0.00 0.00 4.35
6648 8959 2.133553 GCAGATCATCATGTCGTCAGG 58.866 52.381 0.00 0.00 0.00 3.86
6801 9113 3.555966 ACCAGAGTTTTCCCTCAACTTG 58.444 45.455 0.00 0.00 34.49 3.16
6848 9160 4.220572 GCTCGTAGTCGGTCTTATCATTC 58.779 47.826 0.00 0.00 37.69 2.67
6872 9184 6.922957 TCTGCAATTGTGGTATGAAAACTTTC 59.077 34.615 7.40 0.00 37.69 2.62
6928 9244 9.528018 TTTGGAATAAGTTTGTTGTGATTTCTC 57.472 29.630 0.00 0.00 0.00 2.87
6929 9245 8.463930 TGGAATAAGTTTGTTGTGATTTCTCT 57.536 30.769 0.00 0.00 0.00 3.10
6954 9270 8.985315 TTGTAGCTATTTCAAGATGGATCATT 57.015 30.769 0.00 0.00 0.00 2.57
7077 9396 3.392616 GAGCATTGAGAGAGGGGGATTTA 59.607 47.826 0.00 0.00 0.00 1.40
7133 9452 5.708697 ACCAGTACATGTTTACTTTAAGGCC 59.291 40.000 2.30 0.00 29.30 5.19
7136 9455 7.107542 CAGTACATGTTTACTTTAAGGCCCTA 58.892 38.462 2.30 0.00 29.30 3.53
7147 9466 4.513406 TTAAGGCCCTAATTGGATCGTT 57.487 40.909 0.00 0.00 38.35 3.85
7212 9531 2.354821 GGTCGTTTTGTTTCTCAGCTGT 59.645 45.455 14.67 0.00 0.00 4.40
7226 9545 2.488937 TCAGCTGTAAATCACGTACGGA 59.511 45.455 21.06 14.09 30.62 4.69
7285 9605 2.051334 TACATTGATTCCAAGCGGGG 57.949 50.000 0.00 0.00 35.48 5.73
7293 9613 1.198759 TTCCAAGCGGGGCTAAGAGT 61.199 55.000 0.00 0.00 38.25 3.24
7341 9661 9.628746 AAATTTGTCGTTTTAACTTGTTGTAGT 57.371 25.926 0.00 0.00 0.00 2.73
7432 9752 2.925724 TGGTTGGTTGAAAGATCGTGT 58.074 42.857 0.00 0.00 0.00 4.49
7468 9791 2.686405 GGGGGTGAATAGGCGTTTTAAG 59.314 50.000 0.00 0.00 0.00 1.85
7499 9822 3.445096 GGTAGAGGCTTGAACAAATGCAT 59.555 43.478 0.00 0.00 0.00 3.96
7718 10042 3.056393 ACGATGTATCCCGAAGTTCACAA 60.056 43.478 3.32 0.00 0.00 3.33
7840 10164 3.627395 AGATGCCGTGATTCCACTAAA 57.373 42.857 0.00 0.00 41.06 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 0.539669 GCAGTTGTGGGCTAGGGTTT 60.540 55.000 0.00 0.00 0.00 3.27
183 186 1.640069 CGACTGCATGAAGCCATCG 59.360 57.895 0.00 0.00 44.83 3.84
216 219 5.277297 GCATATTAGCAAACACGCAGTCATA 60.277 40.000 0.00 0.00 41.61 2.15
243 246 2.595655 GTGTGGGATGGTAGCCCC 59.404 66.667 0.00 0.00 45.40 5.80
249 252 4.388499 GACCGCGTGTGGGATGGT 62.388 66.667 4.92 0.00 35.14 3.55
264 267 1.129809 CACCAAACGTGATCGCGAC 59.870 57.895 33.43 6.32 46.20 5.19
348 351 1.986575 GCAATGCTCTTCGTCCTGCC 61.987 60.000 0.00 0.00 0.00 4.85
396 399 1.078637 GGCGGGGAAGGTTCTACAC 60.079 63.158 0.00 0.00 0.00 2.90
405 408 3.636231 TGGTCACTGGCGGGGAAG 61.636 66.667 0.00 0.00 0.00 3.46
445 448 0.234106 CCGCTTGTGATCGATGATGC 59.766 55.000 0.54 0.00 0.00 3.91
492 495 1.152525 GGAGGAGGCGATGGGTAGA 60.153 63.158 0.00 0.00 0.00 2.59
493 496 1.457643 TGGAGGAGGCGATGGGTAG 60.458 63.158 0.00 0.00 0.00 3.18
495 498 2.765807 CTGGAGGAGGCGATGGGT 60.766 66.667 0.00 0.00 0.00 4.51
538 541 1.893919 AAGGAGAAGGCAGACGCTCC 61.894 60.000 9.62 9.62 42.37 4.70
540 543 1.594310 GAAGGAGAAGGCAGACGCT 59.406 57.895 0.00 0.00 38.60 5.07
544 547 1.557269 GCTGGGAAGGAGAAGGCAGA 61.557 60.000 0.00 0.00 0.00 4.26
564 567 2.893398 GAGATGGCTTCGTCCGGT 59.107 61.111 0.00 0.00 0.00 5.28
573 576 2.581354 GACAGCACCGAGATGGCT 59.419 61.111 0.00 0.00 39.06 4.75
584 587 3.838271 GGCGGATCGGAGACAGCA 61.838 66.667 4.16 0.00 42.51 4.41
629 632 4.202284 CGATTAGGGTTTCGAGGGGAAATA 60.202 45.833 0.00 0.00 45.80 1.40
630 633 3.433173 CGATTAGGGTTTCGAGGGGAAAT 60.433 47.826 0.00 0.00 45.80 2.17
662 666 2.617276 CCCCGAAAACCTAGGAAACCTC 60.617 54.545 17.98 3.57 34.61 3.85
663 667 1.353358 CCCCGAAAACCTAGGAAACCT 59.647 52.381 17.98 0.00 37.71 3.50
665 669 2.865119 TCCCCGAAAACCTAGGAAAC 57.135 50.000 17.98 2.96 0.00 2.78
666 670 2.553685 GCTTCCCCGAAAACCTAGGAAA 60.554 50.000 17.98 0.00 36.22 3.13
686 690 2.436173 AGCTAACTAAGTGGATGGAGGC 59.564 50.000 0.00 0.00 0.00 4.70
687 691 5.871396 TTAGCTAACTAAGTGGATGGAGG 57.129 43.478 0.86 0.00 33.35 4.30
713 717 8.743714 GGGACTATTGATTCAGAAAAGAACATT 58.256 33.333 0.00 0.00 0.00 2.71
714 718 7.890127 TGGGACTATTGATTCAGAAAAGAACAT 59.110 33.333 0.00 0.00 0.00 2.71
715 719 7.174946 GTGGGACTATTGATTCAGAAAAGAACA 59.825 37.037 0.00 0.00 0.00 3.18
716 720 7.362142 GGTGGGACTATTGATTCAGAAAAGAAC 60.362 40.741 0.00 0.00 0.00 3.01
717 721 6.659242 GGTGGGACTATTGATTCAGAAAAGAA 59.341 38.462 0.00 0.00 0.00 2.52
718 722 6.012508 AGGTGGGACTATTGATTCAGAAAAGA 60.013 38.462 0.00 0.00 0.00 2.52
719 723 6.183347 AGGTGGGACTATTGATTCAGAAAAG 58.817 40.000 0.00 0.00 0.00 2.27
720 724 6.139679 AGGTGGGACTATTGATTCAGAAAA 57.860 37.500 0.00 0.00 0.00 2.29
721 725 5.626809 CGAGGTGGGACTATTGATTCAGAAA 60.627 44.000 0.00 0.00 0.00 2.52
722 726 4.141937 CGAGGTGGGACTATTGATTCAGAA 60.142 45.833 0.00 0.00 0.00 3.02
723 727 3.384789 CGAGGTGGGACTATTGATTCAGA 59.615 47.826 0.00 0.00 0.00 3.27
724 728 3.493350 CCGAGGTGGGACTATTGATTCAG 60.493 52.174 0.00 0.00 0.00 3.02
725 729 2.434336 CCGAGGTGGGACTATTGATTCA 59.566 50.000 0.00 0.00 0.00 2.57
726 730 2.698797 TCCGAGGTGGGACTATTGATTC 59.301 50.000 0.00 0.00 38.76 2.52
727 731 2.759355 TCCGAGGTGGGACTATTGATT 58.241 47.619 0.00 0.00 38.76 2.57
728 732 2.471815 TCCGAGGTGGGACTATTGAT 57.528 50.000 0.00 0.00 38.76 2.57
729 733 2.241281 TTCCGAGGTGGGACTATTGA 57.759 50.000 0.00 0.00 38.76 2.57
730 734 3.560636 ATTTCCGAGGTGGGACTATTG 57.439 47.619 0.00 0.00 38.76 1.90
731 735 3.069158 CGTATTTCCGAGGTGGGACTATT 59.931 47.826 0.00 0.00 38.76 1.73
732 736 2.626743 CGTATTTCCGAGGTGGGACTAT 59.373 50.000 0.00 0.00 38.76 2.12
733 737 2.026641 CGTATTTCCGAGGTGGGACTA 58.973 52.381 0.00 0.00 38.76 2.59
734 738 0.822164 CGTATTTCCGAGGTGGGACT 59.178 55.000 0.00 0.00 38.76 3.85
735 739 0.819582 TCGTATTTCCGAGGTGGGAC 59.180 55.000 0.00 0.00 38.76 4.46
736 740 1.559368 TTCGTATTTCCGAGGTGGGA 58.441 50.000 0.00 0.00 38.23 4.37
737 741 2.389962 TTTCGTATTTCCGAGGTGGG 57.610 50.000 0.00 0.00 38.23 4.61
738 742 3.332034 AGTTTTCGTATTTCCGAGGTGG 58.668 45.455 0.00 0.00 38.23 4.61
739 743 4.378046 CCAAGTTTTCGTATTTCCGAGGTG 60.378 45.833 0.00 0.00 38.23 4.00
740 744 3.749609 CCAAGTTTTCGTATTTCCGAGGT 59.250 43.478 0.00 0.00 38.23 3.85
741 745 3.998341 TCCAAGTTTTCGTATTTCCGAGG 59.002 43.478 0.00 0.00 38.23 4.63
742 746 5.600908 TTCCAAGTTTTCGTATTTCCGAG 57.399 39.130 0.00 0.00 38.23 4.63
743 747 5.558653 CGTTTCCAAGTTTTCGTATTTCCGA 60.559 40.000 0.00 0.00 34.52 4.55
744 748 4.609708 CGTTTCCAAGTTTTCGTATTTCCG 59.390 41.667 0.00 0.00 0.00 4.30
758 762 5.154222 GCCTATCACTTTTTCGTTTCCAAG 58.846 41.667 0.00 0.00 0.00 3.61
767 771 3.344515 AGGGAACGCCTATCACTTTTTC 58.655 45.455 0.00 0.00 0.00 2.29
774 778 1.271856 TCACAAGGGAACGCCTATCA 58.728 50.000 0.00 0.00 0.00 2.15
813 818 5.436175 TGAATCTGCTCGGGAAATATTTGA 58.564 37.500 5.17 0.00 0.00 2.69
823 828 1.363744 GTTCACTGAATCTGCTCGGG 58.636 55.000 0.00 0.00 0.00 5.14
870 898 9.826574 ATAGAGTAGTTGCCAATTTTAATCGTA 57.173 29.630 0.00 0.00 0.00 3.43
941 969 0.391263 CGCTGTAGAACTTGGGACCC 60.391 60.000 2.45 2.45 0.00 4.46
978 1015 3.934579 TGTGTGTATCACTCACATGATGC 59.065 43.478 0.00 0.00 44.54 3.91
1037 1088 1.256812 AGCCCCTCAAATTTCAACCG 58.743 50.000 0.00 0.00 0.00 4.44
1415 1480 4.760047 ACCAGCCCACGATGTCGC 62.760 66.667 1.77 0.00 44.43 5.19
1424 1489 3.889525 ATCACCCTCCACCAGCCCA 62.890 63.158 0.00 0.00 0.00 5.36
1452 1517 3.936203 TCCACCACGCGGAAAGCT 61.936 61.111 12.47 0.00 45.59 3.74
1533 1598 2.890847 CTAGAACCAGCACGGCGAGG 62.891 65.000 16.62 12.35 39.03 4.63
1551 1616 1.088306 CGAGCACGAAGTAGTCCTCT 58.912 55.000 0.00 0.00 41.61 3.69
1631 1696 0.174845 TACCATAGGCGTGTGCTCAC 59.825 55.000 8.86 8.86 42.25 3.51
1632 1697 0.899019 TTACCATAGGCGTGTGCTCA 59.101 50.000 0.00 0.00 42.25 4.26
1700 1767 9.903682 CAAAACAGAACATACATCTGAATTCTT 57.096 29.630 7.05 0.00 45.74 2.52
1712 1780 7.044052 GCAGAACTGAAACAAAACAGAACATAC 60.044 37.037 5.97 0.00 37.54 2.39
1817 1894 6.276091 AGGAAATCTTGCAAAACTCTTTGAC 58.724 36.000 0.00 0.00 44.03 3.18
1974 2149 3.609853 CAGAGCCAAACAATAGCTACCA 58.390 45.455 0.00 0.00 36.87 3.25
1996 2171 6.204108 ACCTACTTCAATTCAAAAGGTACACG 59.796 38.462 0.00 0.00 34.18 4.49
2000 2175 7.094377 GCATGACCTACTTCAATTCAAAAGGTA 60.094 37.037 0.00 0.00 36.04 3.08
2016 2191 2.704572 ACAGAAGCTTGCATGACCTAC 58.295 47.619 2.10 0.00 0.00 3.18
2224 2471 4.552767 CGTTGCACACTTTACTTTCTGGAG 60.553 45.833 0.00 0.00 0.00 3.86
2254 2501 4.497291 AATTCAGGTGCCCGACTAATAA 57.503 40.909 0.00 0.00 0.00 1.40
2451 2698 3.733337 ACGGAGAAGTAATCATCCATGC 58.267 45.455 0.00 0.00 0.00 4.06
2494 2741 9.594478 TTTGAACGCTCTTATATTTCTGTATGA 57.406 29.630 0.00 0.00 0.00 2.15
2679 2933 4.622313 TCAAATGTTGAAGATGAATTGCGC 59.378 37.500 0.00 0.00 36.59 6.09
2680 2934 6.088173 TCTCAAATGTTGAAGATGAATTGCG 58.912 36.000 0.00 0.00 39.58 4.85
3273 3830 8.316640 ACAGTGCAACAAATTTTGAAAGTTTA 57.683 26.923 15.81 0.00 41.43 2.01
3876 4492 1.476488 GGTTCCGGCACATAAGCAAAT 59.524 47.619 6.56 0.00 35.83 2.32
3926 4542 6.256757 GCGGCCATTGCTAATTAAAATGTTTA 59.743 34.615 2.24 0.00 37.74 2.01
4081 4714 2.682494 GACGACTGGGGCTGGGTA 60.682 66.667 0.00 0.00 0.00 3.69
4115 4748 2.234908 AGATGAAGAAGTCAACGAGGGG 59.765 50.000 0.00 0.00 40.50 4.79
4119 4778 6.090483 AGAAGAAGATGAAGAAGTCAACGA 57.910 37.500 0.00 0.00 40.50 3.85
4156 4815 4.008933 GCCAGCGACAGGGACAGT 62.009 66.667 0.00 0.00 0.00 3.55
4157 4816 4.767255 GGCCAGCGACAGGGACAG 62.767 72.222 0.00 0.00 30.28 3.51
4253 5056 1.447140 GTACGGATGCTGCAACGGA 60.447 57.895 26.03 19.19 0.00 4.69
4258 5061 1.138883 GACGAGTACGGATGCTGCA 59.861 57.895 4.13 4.13 44.46 4.41
4278 5081 1.005394 GACTTCTTGCCGGACCGAA 60.005 57.895 17.49 0.97 0.00 4.30
4290 5093 2.809861 TACGAGGGGCGACGACTTCT 62.810 60.000 0.00 0.00 44.57 2.85
4371 5175 3.601685 TGCAGTGACGACAGCGGA 61.602 61.111 0.00 0.00 43.17 5.54
4376 5180 0.389025 ATGACAGTGCAGTGACGACA 59.611 50.000 28.02 19.43 0.00 4.35
4394 5198 4.742201 AAGCTGCGTCGGCGACAT 62.742 61.111 35.62 15.45 44.10 3.06
4884 5728 2.924640 CTGCCTCCTGCCATGGAT 59.075 61.111 18.40 0.00 40.16 3.41
4997 5841 1.163420 AAGCGATGCGACCAACAACA 61.163 50.000 0.00 0.00 0.00 3.33
5091 5935 1.077501 CCCTTGTCGCCATGGACAT 60.078 57.895 18.40 0.00 45.62 3.06
5092 5936 2.350895 CCCTTGTCGCCATGGACA 59.649 61.111 18.40 9.34 44.74 4.02
5144 5988 2.504681 CTTTTGCGATGCACCGGC 60.505 61.111 0.82 0.00 38.71 6.13
5155 5999 4.056125 GCCCCTCACGCCTTTTGC 62.056 66.667 0.00 0.00 0.00 3.68
5156 6000 3.737172 CGCCCCTCACGCCTTTTG 61.737 66.667 0.00 0.00 0.00 2.44
5157 6001 4.265056 ACGCCCCTCACGCCTTTT 62.265 61.111 0.00 0.00 0.00 2.27
5371 6215 2.509336 CGTCCGATCCCTGTGCAC 60.509 66.667 10.75 10.75 0.00 4.57
5372 6216 4.451150 GCGTCCGATCCCTGTGCA 62.451 66.667 0.00 0.00 0.00 4.57
5373 6217 4.451150 TGCGTCCGATCCCTGTGC 62.451 66.667 0.00 0.00 0.00 4.57
5574 6529 3.574396 TCAGATATACTTTGGGAGCCTCG 59.426 47.826 0.00 0.00 0.00 4.63
5701 6679 6.216801 TCATACCCATACACTGTACTGAAC 57.783 41.667 6.77 0.00 0.00 3.18
5737 6716 4.559862 ATTTTAGCTAGTGGTGCAGACT 57.440 40.909 3.86 3.86 0.00 3.24
5742 6721 9.902196 TTTAAACTAAATTTTAGCTAGTGGTGC 57.098 29.630 14.67 0.00 0.00 5.01
5789 6768 0.178068 GATTAACGCCTGGGAGCAGA 59.822 55.000 0.00 0.00 0.00 4.26
5790 6769 0.179000 AGATTAACGCCTGGGAGCAG 59.821 55.000 0.00 0.00 0.00 4.24
6008 7846 7.298507 ACATTAATCATGTGCAATTTTCTGC 57.701 32.000 0.00 0.00 45.12 4.26
6105 7948 3.704512 CATTTTGTGGCTGCGCATATAA 58.295 40.909 12.24 2.31 0.00 0.98
6236 8099 8.558973 AACCAAAGAAAAGATGATGAGAGTAG 57.441 34.615 0.00 0.00 0.00 2.57
6351 8217 6.916387 ACTAAGACACACACATATATACGTGC 59.084 38.462 8.80 0.00 36.57 5.34
6425 8687 4.435425 GTGTGCCATTTTATCATGCATGT 58.565 39.130 25.43 15.34 0.00 3.21
6434 8730 4.862641 AGTAGGAGGTGTGCCATTTTAT 57.137 40.909 0.00 0.00 37.19 1.40
6569 8880 2.649034 GTCGCCTGGAGTGACGAA 59.351 61.111 0.00 0.00 45.52 3.85
6618 8929 0.596083 GATGATCTGCTGCGCGTACT 60.596 55.000 8.43 0.00 0.00 2.73
6624 8935 0.507358 CGACATGATGATCTGCTGCG 59.493 55.000 0.00 0.00 0.00 5.18
6625 8936 1.526041 GACGACATGATGATCTGCTGC 59.474 52.381 0.00 0.00 0.00 5.25
6627 8938 2.223994 CCTGACGACATGATGATCTGCT 60.224 50.000 0.00 0.00 0.00 4.24
6648 8959 1.211743 GCTGTTTGTTGGCTTCTTGC 58.788 50.000 0.00 0.00 41.94 4.01
6788 9100 5.996644 TCACTTCTTACAAGTTGAGGGAAA 58.003 37.500 10.54 0.00 0.00 3.13
6801 9113 7.095649 GCATGGAAAACCAAAATCACTTCTTAC 60.096 37.037 0.00 0.00 0.00 2.34
6848 9160 6.925165 AGAAAGTTTTCATACCACAATTGCAG 59.075 34.615 5.05 0.00 39.61 4.41
6872 9184 6.493116 CCTTAGCAATCATTAAGACAGCAAG 58.507 40.000 0.00 0.00 33.21 4.01
6928 9244 8.618702 ATGATCCATCTTGAAATAGCTACAAG 57.381 34.615 13.73 13.73 41.27 3.16
6929 9245 8.843262 CAATGATCCATCTTGAAATAGCTACAA 58.157 33.333 0.00 0.00 0.00 2.41
7035 9352 9.584008 AATGCTCAAGATATATCAGTCCAAAAT 57.416 29.630 15.08 0.00 0.00 1.82
7077 9396 8.810990 ACTCTAGCTCTGTAACTATGTAACTT 57.189 34.615 0.00 0.00 0.00 2.66
7133 9452 4.438744 GCTGGAAACAACGATCCAATTAGG 60.439 45.833 0.00 0.00 44.77 2.69
7136 9455 3.575965 GCTGGAAACAACGATCCAATT 57.424 42.857 0.00 0.00 44.77 2.32
7147 9466 1.335496 GGTGTAAAAGCGCTGGAAACA 59.665 47.619 12.58 10.97 39.59 2.83
7285 9605 9.593134 TTCTCAGATAGAAAATCAACTCTTAGC 57.407 33.333 0.00 0.00 41.35 3.09
7317 9637 9.068008 CAACTACAACAAGTTAAAACGACAAAT 57.932 29.630 0.00 0.00 37.61 2.32
7341 9661 7.066163 CAGTGCTCAAGATATACCAATCAACAA 59.934 37.037 0.00 0.00 0.00 2.83
7432 9752 4.945645 CCCCCTCTAGGCGACATA 57.054 61.111 0.00 0.00 0.00 2.29
7468 9791 8.677148 TTGTTCAAGCCTCTACCATAATTATC 57.323 34.615 0.00 0.00 0.00 1.75
7718 10042 3.051081 GGAGATTAGCATCCGCAAGAT 57.949 47.619 0.00 0.00 42.27 2.40


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

AutoCloner maintained by Alex Coulton.