Multiple sequence alignment - TraesCS2A01G582900

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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 TraesCS2A01G582900 chr2A 100.000 6385 0 0 1 6385 775073290 775066906 0.000000e+00 11791.0
1 TraesCS2A01G582900 chr2A 93.868 636 31 6 5572 6204 77280932 77281562 0.000000e+00 952.0
2 TraesCS2A01G582900 chr2A 95.652 184 6 1 6204 6385 77319895 77320078 1.740000e-75 294.0
3 TraesCS2A01G582900 chr2A 86.614 254 31 3 6 258 717249817 717249566 1.750000e-70 278.0
4 TraesCS2A01G582900 chr2A 85.490 255 32 4 6 258 13139932 13140183 1.770000e-65 261.0
5 TraesCS2A01G582900 chr2A 84.825 257 34 4 9 264 770919418 770919670 2.950000e-63 254.0
6 TraesCS2A01G582900 chr2A 84.436 257 33 6 6 258 674496334 674496081 4.940000e-61 246.0
7 TraesCS2A01G582900 chr2A 80.531 113 22 0 584 696 63590922 63591034 3.170000e-13 87.9
8 TraesCS2A01G582900 chr2D 96.161 1641 53 6 2839 4475 649777178 649778812 0.000000e+00 2673.0
9 TraesCS2A01G582900 chr2D 95.438 1074 25 9 4505 5573 649778878 649779932 0.000000e+00 1690.0
10 TraesCS2A01G582900 chr2D 96.246 879 25 4 1979 2850 649764375 649765252 0.000000e+00 1434.0
11 TraesCS2A01G582900 chr2D 90.120 668 45 6 857 1514 649762105 649762761 0.000000e+00 848.0
12 TraesCS2A01G582900 chr2D 88.698 699 41 13 135 809 649757821 649758505 0.000000e+00 819.0
13 TraesCS2A01G582900 chr2D 95.876 485 14 1 1504 1988 649763403 649763881 0.000000e+00 780.0
14 TraesCS2A01G582900 chr2D 77.515 169 29 7 523 690 588968055 588968215 6.820000e-15 93.5
15 TraesCS2A01G582900 chr2D 86.567 67 9 0 624 690 445024665 445024731 2.470000e-09 75.0
16 TraesCS2A01G582900 chr2B 94.974 1134 41 3 4441 5573 785770735 785771853 0.000000e+00 1764.0
17 TraesCS2A01G582900 chr2B 87.183 827 64 18 8 809 785755963 785756772 0.000000e+00 902.0
18 TraesCS2A01G582900 chr2B 86.940 268 24 7 4462 4729 12902505 12902249 2.250000e-74 291.0
19 TraesCS2A01G582900 chr2B 86.220 254 31 3 6 257 136434459 136434208 8.160000e-69 272.0
20 TraesCS2A01G582900 chr2B 79.433 141 27 2 551 690 704288649 704288788 1.470000e-16 99.0
21 TraesCS2A01G582900 chr7A 96.810 815 23 3 5572 6385 702245891 702245079 0.000000e+00 1358.0
22 TraesCS2A01G582900 chr7A 91.489 94 7 1 3689 3782 50004312 50004220 1.870000e-25 128.0
23 TraesCS2A01G582900 chrUn 89.362 329 22 6 6057 6385 62171203 62171518 9.970000e-108 401.0
24 TraesCS2A01G582900 chrUn 89.362 329 22 6 6057 6385 293738066 293737751 9.970000e-108 401.0
25 TraesCS2A01G582900 chrUn 87.417 151 15 3 3776 3923 86350547 86350398 3.060000e-38 171.0
26 TraesCS2A01G582900 chr4B 90.244 246 23 1 6081 6326 64084449 64084205 2.870000e-83 320.0
27 TraesCS2A01G582900 chr4B 77.953 127 28 0 537 663 44082169 44082043 5.310000e-11 80.5
28 TraesCS2A01G582900 chr6B 89.837 246 24 1 6081 6326 716581003 716580759 1.340000e-81 315.0
29 TraesCS2A01G582900 chr6B 92.958 142 5 3 5902 6039 84674515 84674655 1.090000e-47 202.0
30 TraesCS2A01G582900 chr6B 92.222 90 7 0 3687 3776 452529826 452529737 1.870000e-25 128.0
31 TraesCS2A01G582900 chr6B 77.241 145 26 5 547 690 438956852 438956714 1.910000e-10 78.7
32 TraesCS2A01G582900 chr3A 79.123 479 69 14 2691 3139 609474540 609475017 1.040000e-77 302.0
33 TraesCS2A01G582900 chr3A 84.314 153 19 4 3775 3922 657308170 657308018 1.860000e-30 145.0
34 TraesCS2A01G582900 chr3A 93.478 92 5 1 3685 3776 168842600 168842510 1.120000e-27 135.0
35 TraesCS2A01G582900 chr3B 87.313 268 23 6 4462 4729 74507545 74507801 4.840000e-76 296.0
36 TraesCS2A01G582900 chr3B 86.940 268 25 6 4462 4729 39227436 39227179 6.260000e-75 292.0
37 TraesCS2A01G582900 chr3B 86.617 269 24 8 4462 4729 296853729 296853986 2.910000e-73 287.0
38 TraesCS2A01G582900 chr3B 79.075 454 62 16 2691 3113 620183473 620183924 1.360000e-71 281.0
39 TraesCS2A01G582900 chr3B 86.395 147 17 3 3776 3919 542728473 542728619 2.380000e-34 158.0
40 TraesCS2A01G582900 chr3B 94.253 87 3 1 3692 3776 368605427 368605341 1.440000e-26 132.0
41 TraesCS2A01G582900 chr3B 97.368 38 1 0 5792 5829 61088265 61088302 1.490000e-06 65.8
42 TraesCS2A01G582900 chr5B 86.194 268 26 7 4462 4729 546017962 546018218 4.870000e-71 279.0
43 TraesCS2A01G582900 chr5B 86.722 241 31 1 7 246 605317147 605317387 3.800000e-67 267.0
44 TraesCS2A01G582900 chr5D 85.448 268 28 8 4462 4729 392359087 392359343 1.060000e-67 268.0
45 TraesCS2A01G582900 chr5D 81.443 97 18 0 602 698 538689551 538689647 5.310000e-11 80.5
46 TraesCS2A01G582900 chr7D 84.825 257 33 5 3 258 555537009 555537260 2.950000e-63 254.0
47 TraesCS2A01G582900 chr1D 84.436 257 34 4 3 257 6407277 6407529 1.370000e-61 248.0
48 TraesCS2A01G582900 chr4D 90.476 189 11 2 6197 6385 436888090 436887909 6.400000e-60 243.0
49 TraesCS2A01G582900 chr4D 76.323 359 44 16 2774 3094 477537517 477537162 3.080000e-33 154.0
50 TraesCS2A01G582900 chr4D 92.683 82 5 1 6105 6186 436888261 436888181 4.040000e-22 117.0
51 TraesCS2A01G582900 chr4D 93.548 62 4 0 6057 6118 436888337 436888276 6.820000e-15 93.5
52 TraesCS2A01G582900 chr1B 80.682 264 42 8 3428 3687 198484975 198485233 5.050000e-46 196.0
53 TraesCS2A01G582900 chr1B 86.301 146 18 2 3776 3919 198485237 198485382 2.380000e-34 158.0
54 TraesCS2A01G582900 chr7B 86.928 153 17 2 3776 3925 11566432 11566280 1.100000e-37 169.0
55 TraesCS2A01G582900 chr7B 87.681 138 11 4 5902 6039 28946179 28946048 8.570000e-34 156.0
56 TraesCS2A01G582900 chr5A 87.143 140 16 2 3776 3913 540034534 540034673 2.380000e-34 158.0
57 TraesCS2A01G582900 chr5A 82.386 176 30 1 524 699 340162830 340163004 1.110000e-32 152.0
58 TraesCS2A01G582900 chr5A 93.478 92 6 0 3691 3782 549199813 549199722 3.100000e-28 137.0
59 TraesCS2A01G582900 chr6A 85.417 144 18 3 3781 3922 536585201 536585059 5.160000e-31 147.0
60 TraesCS2A01G582900 chr6A 85.816 141 17 3 3781 3919 574842240 574842379 5.160000e-31 147.0
61 TraesCS2A01G582900 chr4A 83.803 142 20 3 2955 3094 684420541 684420401 1.440000e-26 132.0
62 TraesCS2A01G582900 chr3D 95.122 82 4 0 3695 3776 599385816 599385735 5.200000e-26 130.0
63 TraesCS2A01G582900 chr3D 90.909 88 7 1 4642 4729 124640005 124640091 4.040000e-22 117.0
64 TraesCS2A01G582900 chr1A 91.209 91 8 0 3688 3778 57407823 57407733 2.420000e-24 124.0
65 TraesCS2A01G582900 chr1A 92.941 85 5 1 3692 3776 564307705 564307622 8.690000e-24 122.0


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 TraesCS2A01G582900 chr2A 775066906 775073290 6384 True 11791.00 11791 100.0000 1 6385 1 chr2A.!!$R3 6384
1 TraesCS2A01G582900 chr2A 77280932 77281562 630 False 952.00 952 93.8680 5572 6204 1 chr2A.!!$F3 632
2 TraesCS2A01G582900 chr2D 649777178 649779932 2754 False 2181.50 2673 95.7995 2839 5573 2 chr2D.!!$F4 2734
3 TraesCS2A01G582900 chr2D 649757821 649765252 7431 False 970.25 1434 92.7350 135 2850 4 chr2D.!!$F3 2715
4 TraesCS2A01G582900 chr2B 785770735 785771853 1118 False 1764.00 1764 94.9740 4441 5573 1 chr2B.!!$F3 1132
5 TraesCS2A01G582900 chr2B 785755963 785756772 809 False 902.00 902 87.1830 8 809 1 chr2B.!!$F2 801
6 TraesCS2A01G582900 chr7A 702245079 702245891 812 True 1358.00 1358 96.8100 5572 6385 1 chr7A.!!$R2 813

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
754 778 0.106819 ACCCGACTACCGTATGAGCT 60.107 55.000 0.00 0.00 36.31 4.09 F
2109 6865 0.320374 TCACTGGTAACGCCTCTTGG 59.680 55.000 0.00 0.00 42.51 3.61 F
2369 7129 1.077357 TGTTTGCGACCCAACACCT 60.077 52.632 0.00 0.00 31.97 4.00 F
3786 8548 1.204231 GGAGGGAGTACACGTTTCCTC 59.796 57.143 3.95 3.95 39.84 3.71 F
4241 9004 1.079256 TCTGTAGGGTGGAGCTGCT 59.921 57.895 6.82 0.00 0.00 4.24 F
5037 9837 0.389817 CAATCTGTCGCCGGAAGTGA 60.390 55.000 5.05 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 6903 0.031111 TTGGAGAGTCGGGGATGGAT 60.031 55.000 0.00 0.00 0.00 3.41 R
3874 8636 0.250597 GGGTGGGCTCAAAGTTACGT 60.251 55.000 0.00 0.00 0.00 3.57 R
3943 8706 1.578215 AACCTGCCTGGCTGATGGAT 61.578 55.000 25.04 11.32 40.22 3.41 R
4908 9708 0.942410 GTAACGAGTCTGCCGCACAA 60.942 55.000 0.00 0.00 0.00 3.33 R
5044 9844 1.002868 AACAGCCGCTTCAGCTCAT 60.003 52.632 0.00 0.00 38.95 2.90 R
6340 11148 5.750547 TGCAATTGAAACTTGAAAATACGCA 59.249 32.000 10.34 0.00 0.00 5.24 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
37 38 7.623268 AAATGTGCGAACATTTCTTAAACTC 57.377 32.000 25.84 0.00 44.25 3.01
51 52 5.305585 TCTTAAACTCCACGAATTCTTGCT 58.694 37.500 6.42 0.00 0.00 3.91
86 87 1.068333 CAGCCCAAATTCTTGTCCGTG 60.068 52.381 0.00 0.00 0.00 4.94
88 89 1.200020 GCCCAAATTCTTGTCCGTGAG 59.800 52.381 0.00 0.00 0.00 3.51
96 97 1.813178 TCTTGTCCGTGAGAGTAGCAG 59.187 52.381 0.00 0.00 0.00 4.24
97 98 1.813178 CTTGTCCGTGAGAGTAGCAGA 59.187 52.381 0.00 0.00 0.00 4.26
104 105 4.278669 TCCGTGAGAGTAGCAGATTATTCC 59.721 45.833 0.00 0.00 0.00 3.01
106 107 4.023963 CGTGAGAGTAGCAGATTATTCCGA 60.024 45.833 0.00 0.00 0.00 4.55
111 112 4.079970 AGTAGCAGATTATTCCGATCGGA 58.920 43.478 32.59 32.59 43.52 4.55
125 126 5.535333 TCCGATCGGAATTGTAGTATTTCC 58.465 41.667 33.96 0.00 42.05 3.13
177 179 4.168101 AGACCAGGATTACAAGTTCAGGA 58.832 43.478 0.00 0.00 0.00 3.86
199 201 5.519927 GGATGCCAATTTTCGGTATTCAAAG 59.480 40.000 0.00 0.00 0.00 2.77
241 243 8.470002 AGCTTTTGTCTACAACTTCAAGATTTT 58.530 29.630 8.48 0.00 35.28 1.82
292 294 1.174783 ACCTACGTACTGTGAGGCTG 58.825 55.000 0.00 0.00 31.81 4.85
298 300 0.603707 GTACTGTGAGGCTGCTTGCA 60.604 55.000 0.00 0.00 45.15 4.08
430 432 5.604565 TGGATATAAGATGTCAGTGTGCAG 58.395 41.667 0.00 0.00 0.00 4.41
435 437 0.516001 GATGTCAGTGTGCAGTGCTG 59.484 55.000 17.60 6.19 0.00 4.41
436 438 0.179037 ATGTCAGTGTGCAGTGCTGT 60.179 50.000 17.60 0.00 0.00 4.40
437 439 1.091197 TGTCAGTGTGCAGTGCTGTG 61.091 55.000 17.60 8.30 0.00 3.66
474 476 5.749032 GCATATACAGGGTTAAGGGCATCTT 60.749 44.000 0.00 0.00 39.40 2.40
480 482 3.011708 AGGGTTAAGGGCATCTTCAATGT 59.988 43.478 0.00 0.00 36.93 2.71
488 490 2.450476 GCATCTTCAATGTTGACCCCT 58.550 47.619 0.00 0.00 36.83 4.79
497 499 5.886609 TCAATGTTGACCCCTCTAAAATGA 58.113 37.500 0.00 0.00 31.01 2.57
499 501 6.780031 TCAATGTTGACCCCTCTAAAATGAAA 59.220 34.615 0.00 0.00 31.01 2.69
508 510 5.007332 CCCCTCTAAAATGAAAACGGTATCG 59.993 44.000 0.00 0.00 43.02 2.92
527 529 4.388499 TCCGCGGACAAAGGGAGC 62.388 66.667 27.28 0.00 0.00 4.70
558 560 0.442310 CCATGCCCGCGTATATTTCG 59.558 55.000 4.92 0.00 0.00 3.46
579 581 9.672086 ATTTCGAAACGAATTTCAACAAATCTA 57.328 25.926 13.81 0.00 45.28 1.98
618 620 7.243604 AGCCAGATGATTTTCATTTAAACCA 57.756 32.000 0.00 0.00 37.20 3.67
673 675 5.828299 TTAAACAAAAGTGACCAGACCTG 57.172 39.130 0.00 0.00 0.00 4.00
697 699 5.873146 ACCTAGTCTAAATCTAAGGTGGC 57.127 43.478 0.00 0.00 0.00 5.01
704 728 3.983044 AAATCTAAGGTGGCGTTCTCT 57.017 42.857 0.00 0.00 0.00 3.10
735 759 2.841044 GGGACGGGCGGGATCTTA 60.841 66.667 0.00 0.00 0.00 2.10
754 778 0.106819 ACCCGACTACCGTATGAGCT 60.107 55.000 0.00 0.00 36.31 4.09
760 784 1.140452 ACTACCGTATGAGCTCCGAGA 59.860 52.381 12.15 0.00 0.00 4.04
809 833 7.535258 CGGAAAAATAAGACATGAGACACAAAG 59.465 37.037 0.00 0.00 0.00 2.77
810 834 7.809806 GGAAAAATAAGACATGAGACACAAAGG 59.190 37.037 0.00 0.00 0.00 3.11
811 835 8.463930 AAAAATAAGACATGAGACACAAAGGA 57.536 30.769 0.00 0.00 0.00 3.36
812 836 7.440523 AAATAAGACATGAGACACAAAGGAC 57.559 36.000 0.00 0.00 0.00 3.85
813 837 4.696479 AAGACATGAGACACAAAGGACT 57.304 40.909 0.00 0.00 0.00 3.85
831 4423 7.698836 AAGGACTCACGAAATTCAAAATTTG 57.301 32.000 0.00 0.00 0.00 2.32
844 4436 2.490993 AAATTTGGGAAGCCGCAGCG 62.491 55.000 8.18 8.18 46.67 5.18
856 4448 3.491652 GCAGCGGGCGAGACTTTC 61.492 66.667 0.00 0.00 0.00 2.62
857 4449 2.048222 CAGCGGGCGAGACTTTCA 60.048 61.111 0.00 0.00 0.00 2.69
858 4450 2.097038 CAGCGGGCGAGACTTTCAG 61.097 63.158 0.00 0.00 0.00 3.02
859 4451 3.491652 GCGGGCGAGACTTTCAGC 61.492 66.667 0.00 0.00 0.00 4.26
860 4452 3.181967 CGGGCGAGACTTTCAGCG 61.182 66.667 0.00 0.00 0.00 5.18
861 4453 2.815647 GGGCGAGACTTTCAGCGG 60.816 66.667 0.00 0.00 0.00 5.52
862 4454 2.815647 GGCGAGACTTTCAGCGGG 60.816 66.667 0.00 0.00 0.00 6.13
942 4534 2.616893 CCCATTCCCCCACCCTCA 60.617 66.667 0.00 0.00 0.00 3.86
943 4535 2.683475 CCATTCCCCCACCCTCAC 59.317 66.667 0.00 0.00 0.00 3.51
944 4536 2.683475 CATTCCCCCACCCTCACC 59.317 66.667 0.00 0.00 0.00 4.02
945 4537 1.930656 CATTCCCCCACCCTCACCT 60.931 63.158 0.00 0.00 0.00 4.00
946 4538 1.151361 ATTCCCCCACCCTCACCTT 60.151 57.895 0.00 0.00 0.00 3.50
947 4539 1.214992 ATTCCCCCACCCTCACCTTC 61.215 60.000 0.00 0.00 0.00 3.46
960 4552 2.612115 CCTTCCCTCCCAGCACCT 60.612 66.667 0.00 0.00 0.00 4.00
1017 4609 1.064946 GATGACCTCACGGCTCTCG 59.935 63.158 0.00 0.00 45.88 4.04
1072 4671 3.485431 GCTCCGACGACGACGAGA 61.485 66.667 20.63 14.18 42.66 4.04
1113 4712 2.203029 GCCGAGTTCCCCGAATCC 60.203 66.667 0.00 0.00 0.00 3.01
1120 4719 1.987855 TTCCCCGAATCCACGCTCT 60.988 57.895 0.00 0.00 0.00 4.09
1128 4727 0.670546 AATCCACGCTCTCACGGTTG 60.671 55.000 0.00 0.00 37.37 3.77
1135 4734 1.007271 CTCTCACGGTTGTCGCTGT 60.007 57.895 0.00 0.00 43.89 4.40
1231 4830 0.391793 GAGGAAGAAGGGCAAGGACG 60.392 60.000 0.00 0.00 0.00 4.79
1236 4835 2.032681 AAGGGCAAGGACGACAGC 59.967 61.111 0.00 0.00 0.00 4.40
1237 4836 3.883744 AAGGGCAAGGACGACAGCG 62.884 63.158 0.00 0.00 44.79 5.18
1238 4837 4.373116 GGGCAAGGACGACAGCGA 62.373 66.667 0.00 0.00 41.64 4.93
1254 4853 1.132029 CGACGACGATGACGACTGT 59.868 57.895 0.00 0.00 42.66 3.55
1317 4916 4.722700 GCCAAGGCGAGGGCTTCA 62.723 66.667 9.41 0.00 45.21 3.02
1409 5010 7.308830 CCCTTCTTCCACTTTCTCTTTACAATG 60.309 40.741 0.00 0.00 0.00 2.82
1446 5047 7.077605 CCGCCAGTTACATAATTCATTACATG 58.922 38.462 0.00 0.00 0.00 3.21
1448 5049 7.587392 CGCCAGTTACATAATTCATTACATGTG 59.413 37.037 9.11 0.00 0.00 3.21
1449 5050 8.620416 GCCAGTTACATAATTCATTACATGTGA 58.380 33.333 9.11 0.00 0.00 3.58
1456 5057 9.935682 ACATAATTCATTACATGTGAAATCGTC 57.064 29.630 9.11 0.00 38.89 4.20
1460 5061 7.848223 TTCATTACATGTGAAATCGTCTCAT 57.152 32.000 9.11 0.00 40.33 2.90
1487 5088 1.312815 AAGCCAAGTCTCACAACTGC 58.687 50.000 0.00 0.00 0.00 4.40
1491 5092 1.808945 CCAAGTCTCACAACTGCCATC 59.191 52.381 0.00 0.00 0.00 3.51
1497 5098 1.228831 CACAACTGCCATCCCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
1560 5813 4.263639 ACAGGACCCATGCCATATATTCAG 60.264 45.833 0.00 0.00 0.00 3.02
1625 5878 4.853924 TTTCCTGAAACAAAGCTCCATC 57.146 40.909 0.00 0.00 0.00 3.51
1639 5892 6.959639 AAGCTCCATCAAGTCTGTTTTTAA 57.040 33.333 0.00 0.00 0.00 1.52
1685 5938 2.032178 GGCAGTTGTGTGTGAAGAACTC 59.968 50.000 0.00 0.00 31.74 3.01
1710 5963 7.596248 TCAAGATTCTTAAACAAAAGCAGCATC 59.404 33.333 0.00 0.00 0.00 3.91
1785 6038 3.787001 CTTCTGGGTCGCCCTCCC 61.787 72.222 14.76 7.07 45.70 4.30
1786 6039 4.332543 TTCTGGGTCGCCCTCCCT 62.333 66.667 14.76 0.00 45.70 4.20
1787 6040 4.779733 TCTGGGTCGCCCTCCCTC 62.780 72.222 14.76 0.00 45.70 4.30
1788 6041 4.787280 CTGGGTCGCCCTCCCTCT 62.787 72.222 14.76 0.00 45.70 3.69
1789 6042 4.779733 TGGGTCGCCCTCCCTCTC 62.780 72.222 14.76 0.00 45.70 3.20
1790 6043 4.467107 GGGTCGCCCTCCCTCTCT 62.467 72.222 7.58 0.00 41.34 3.10
1822 6075 5.589192 AGCTTCCTGTATACGTACATGAAC 58.411 41.667 0.00 0.36 39.18 3.18
1949 6202 7.099764 CCTTAGTGCATTCTTCTTCAGTTAGA 58.900 38.462 0.00 0.00 0.00 2.10
1952 6205 4.092091 GTGCATTCTTCTTCAGTTAGACGG 59.908 45.833 0.00 0.00 0.00 4.79
1956 6209 6.456181 GCATTCTTCTTCAGTTAGACGGATTG 60.456 42.308 0.00 0.00 0.00 2.67
2109 6865 0.320374 TCACTGGTAACGCCTCTTGG 59.680 55.000 0.00 0.00 42.51 3.61
2133 6889 3.522750 AGCCAGGGATCAGATGATAATCC 59.477 47.826 0.00 0.00 38.60 3.01
2139 6895 4.782156 GGGATCAGATGATAATCCTGTCCT 59.218 45.833 0.00 0.00 39.18 3.85
2146 6902 7.732140 TCAGATGATAATCCTGTCCTATGTTCT 59.268 37.037 0.00 0.00 0.00 3.01
2147 6903 9.029368 CAGATGATAATCCTGTCCTATGTTCTA 57.971 37.037 0.00 0.00 0.00 2.10
2183 6939 3.887716 CTCCAAATCATGCCCTTCCTTAG 59.112 47.826 0.00 0.00 0.00 2.18
2184 6940 3.527253 TCCAAATCATGCCCTTCCTTAGA 59.473 43.478 0.00 0.00 0.00 2.10
2186 6942 4.280174 CCAAATCATGCCCTTCCTTAGATG 59.720 45.833 0.00 0.00 0.00 2.90
2187 6943 4.803329 AATCATGCCCTTCCTTAGATGT 57.197 40.909 0.00 0.00 0.00 3.06
2198 6958 5.770162 CCTTCCTTAGATGTTGGACACTTTT 59.230 40.000 0.00 0.00 0.00 2.27
2204 6964 8.143835 CCTTAGATGTTGGACACTTTTTGAAAT 58.856 33.333 0.00 0.00 0.00 2.17
2205 6965 8.870160 TTAGATGTTGGACACTTTTTGAAATG 57.130 30.769 0.00 0.00 0.00 2.32
2206 6966 5.754890 AGATGTTGGACACTTTTTGAAATGC 59.245 36.000 0.00 0.00 0.00 3.56
2207 6967 5.083533 TGTTGGACACTTTTTGAAATGCT 57.916 34.783 0.00 0.00 0.00 3.79
2209 6969 4.320608 TGGACACTTTTTGAAATGCTCC 57.679 40.909 0.00 0.00 0.00 4.70
2210 6970 3.243367 TGGACACTTTTTGAAATGCTCCG 60.243 43.478 0.00 0.00 0.00 4.63
2211 6971 2.726241 GACACTTTTTGAAATGCTCCGC 59.274 45.455 0.00 0.00 0.00 5.54
2212 6972 2.362077 ACACTTTTTGAAATGCTCCGCT 59.638 40.909 0.00 0.00 0.00 5.52
2246 7006 3.902881 TCCATTGTTTGGTGTTGCTTT 57.097 38.095 0.00 0.00 46.52 3.51
2272 7032 1.202952 TGTTGTTCCATGGGTGGTACC 60.203 52.381 13.02 4.43 43.11 3.34
2344 7104 7.009179 TCACATTGTGAGAAAGGAATCTAGT 57.991 36.000 15.41 0.00 37.67 2.57
2369 7129 1.077357 TGTTTGCGACCCAACACCT 60.077 52.632 0.00 0.00 31.97 4.00
2376 7136 1.754380 CGACCCAACACCTCTGTCCA 61.754 60.000 0.00 0.00 0.00 4.02
2571 7333 7.221970 CGCACAACATACTTTTGATTCAAATG 58.778 34.615 18.43 18.43 33.19 2.32
2627 7389 5.413523 ACCGTTCAACTTGTAACAAGAAAGT 59.586 36.000 0.00 0.59 35.70 2.66
2668 7430 8.986847 CATAGATTTGGATCATGTCTAACTGTC 58.013 37.037 0.00 0.00 34.60 3.51
2751 7513 6.040247 CGTGGTAGCATTTCTGTATCAGTTA 58.960 40.000 0.00 0.00 32.61 2.24
2831 7593 3.375299 GTCATCTATGTGTTGACTTGCCC 59.625 47.826 0.00 0.00 40.44 5.36
2850 7612 2.600731 CCTTCAGCACTACTTCTCACG 58.399 52.381 0.00 0.00 0.00 4.35
2852 7614 3.190744 CCTTCAGCACTACTTCTCACGTA 59.809 47.826 0.00 0.00 0.00 3.57
2858 7620 2.341760 CACTACTTCTCACGTAAAGCGC 59.658 50.000 0.00 0.00 46.11 5.92
2977 7739 6.384258 TGTTTTTGAAATGCAGTGCTACTA 57.616 33.333 17.60 0.00 0.00 1.82
3026 7788 4.034285 CAAGTATTGGGGTCAAGGTCTT 57.966 45.455 0.00 0.00 43.94 3.01
3118 7880 4.015764 TGCAAAACTATGCCAGCATCTTA 58.984 39.130 8.71 0.00 45.83 2.10
3169 7931 4.465512 CAACCGACGCATGGCAGC 62.466 66.667 0.00 0.00 0.00 5.25
3249 8011 4.924625 AGTTTCTCTCTGTACTCTGCCTA 58.075 43.478 0.00 0.00 0.00 3.93
3250 8012 5.515106 AGTTTCTCTCTGTACTCTGCCTAT 58.485 41.667 0.00 0.00 0.00 2.57
3276 8038 5.663456 TCTTGCTTTCTTTGATGCTTGTTT 58.337 33.333 0.00 0.00 0.00 2.83
3278 8040 6.919662 TCTTGCTTTCTTTGATGCTTGTTTAG 59.080 34.615 0.00 0.00 0.00 1.85
3312 8074 4.332543 CAGTGTGCTACTCTGTTGTCAAAA 59.667 41.667 9.02 0.00 37.60 2.44
3321 8083 4.876107 ACTCTGTTGTCAAAAGTCAATCGT 59.124 37.500 2.62 0.00 0.00 3.73
3381 8143 8.463456 AAACCATTTGTTTCTTGCAAAATTTG 57.537 26.923 0.00 0.57 43.74 2.32
3412 8174 8.682128 TCTTCAAAACATTAAATACCGCATTC 57.318 30.769 0.00 0.00 0.00 2.67
3427 8189 3.393800 CGCATTCTTCCAGTAGTATGGG 58.606 50.000 0.00 0.00 41.01 4.00
3451 8213 9.305925 GGGAAATTATGAGCTTATTTGAACAAG 57.694 33.333 0.00 0.00 0.00 3.16
3489 8251 3.245586 TGGCTATTGTGGGGAACAGATTT 60.246 43.478 0.00 0.00 40.74 2.17
3749 8511 7.479070 CAAGCTATGCTAGTTTGTAAAAACG 57.521 36.000 2.83 0.00 40.67 3.60
3751 8513 6.828672 AGCTATGCTAGTTTGTAAAAACGTC 58.171 36.000 2.83 0.00 36.99 4.34
3786 8548 1.204231 GGAGGGAGTACACGTTTCCTC 59.796 57.143 3.95 3.95 39.84 3.71
3801 8563 5.482878 ACGTTTCCTCTAGTAATCTGGGAAA 59.517 40.000 0.00 0.00 36.66 3.13
3874 8636 2.341846 AGGGCGTTCAGTTTTCTCAA 57.658 45.000 0.00 0.00 0.00 3.02
3892 8655 1.265905 CAACGTAACTTTGAGCCCACC 59.734 52.381 0.00 0.00 0.00 4.61
3913 8676 6.665248 CCACCCTCCATTTTCTTTCTAGATTT 59.335 38.462 0.00 0.00 0.00 2.17
3957 8720 1.134907 CAACAAATCCATCAGCCAGGC 60.135 52.381 1.84 1.84 0.00 4.85
4030 8793 2.144730 GCTCTTCTATCATGCTGGCAG 58.855 52.381 10.94 10.94 0.00 4.85
4101 8864 5.243060 TCCGGTCATCGATATGTGAAATAGT 59.757 40.000 0.00 0.00 42.43 2.12
4137 8900 7.989170 TCTTGATTCATCAGTAATGTATGCACT 59.011 33.333 0.00 0.00 38.19 4.40
4142 8905 7.833285 TCATCAGTAATGTATGCACTACCTA 57.167 36.000 0.00 0.00 36.68 3.08
4143 8906 8.245195 TCATCAGTAATGTATGCACTACCTAA 57.755 34.615 0.00 0.00 36.68 2.69
4144 8907 8.700973 TCATCAGTAATGTATGCACTACCTAAA 58.299 33.333 0.00 0.00 36.68 1.85
4162 8925 4.947388 CCTAAAAATGGCCTGCAACTACTA 59.053 41.667 3.32 0.00 0.00 1.82
4241 9004 1.079256 TCTGTAGGGTGGAGCTGCT 59.921 57.895 6.82 0.00 0.00 4.24
4340 9103 8.708742 TCATTGTTCTGAAATACAGTTTCTACG 58.291 33.333 0.00 0.00 45.86 3.51
4371 9134 3.192633 GTGCAGGTATTTTACAACAGGGG 59.807 47.826 0.00 0.00 0.00 4.79
4453 9216 2.356125 GGCTGTGGAGTTGTACCATCAT 60.356 50.000 0.00 0.00 39.69 2.45
4492 9255 1.609208 AATGATAACCTGATGCGGCC 58.391 50.000 0.00 0.00 0.00 6.13
4528 9327 8.080363 AGTTAAAACTGGACCTATTCTCCTAG 57.920 38.462 0.00 0.00 37.98 3.02
4649 9449 8.826765 CCTGTAATGTAATAGGATCCTATGGTT 58.173 37.037 30.84 23.07 39.03 3.67
4713 9513 2.158475 TGATTTCAGGACACTGCCCTTT 60.158 45.455 0.00 0.00 44.54 3.11
4735 9535 4.531854 TGTTTCTGATTTGAGGAACACCA 58.468 39.130 0.00 0.00 36.66 4.17
4890 9690 8.454106 CACTTTATGATTCTGATCGACCTTTTT 58.546 33.333 0.00 0.00 34.91 1.94
4908 9708 5.047092 CCTTTTTATTTGGACATGCAGGAGT 60.047 40.000 4.84 0.00 0.00 3.85
5037 9837 0.389817 CAATCTGTCGCCGGAAGTGA 60.390 55.000 5.05 0.00 0.00 3.41
5176 9976 4.699522 GCGCGAGGGGTTGAAGGT 62.700 66.667 12.10 0.00 0.00 3.50
5422 10222 9.254133 CGTTTCTTTACTGAGATGATGACATAT 57.746 33.333 0.00 0.00 36.82 1.78
5454 10259 7.201956 GGATCATCTTTGTGTCTGTACCTATCT 60.202 40.741 0.00 0.00 0.00 1.98
5624 10429 4.591498 ACCTATGGTCAATGCCGTTAGATA 59.409 41.667 0.00 0.00 0.00 1.98
5719 10524 2.894387 CTTGCTCTAGGCCTGCGC 60.894 66.667 17.99 15.42 40.92 6.09
5770 10576 2.923655 CACACGCCTCTATGTTACTGTG 59.076 50.000 0.00 0.00 0.00 3.66
5796 10602 6.346359 GCAACATCTGAAGCAATCTGTTTTTC 60.346 38.462 0.00 0.00 0.00 2.29
5862 10669 1.335810 CCACAGATCGCATCCATTTGG 59.664 52.381 0.00 0.00 0.00 3.28
6075 10882 5.211973 AGCTTATGTCAGGTGAGAGGAATA 58.788 41.667 0.00 0.00 0.00 1.75
6157 10965 7.873719 TTTGGAAAAAGAGATGTAGACACAA 57.126 32.000 0.00 0.00 38.42 3.33
6299 11107 6.878389 ACAAAATTGAAGGAAAAAGAGTTGCA 59.122 30.769 0.00 0.00 0.00 4.08
6310 11118 8.951243 AGGAAAAAGAGTTGCAGAAATATCTAC 58.049 33.333 0.00 0.00 33.50 2.59
6311 11119 8.730680 GGAAAAAGAGTTGCAGAAATATCTACA 58.269 33.333 0.00 0.00 33.50 2.74
6346 11154 4.452890 GCACGAATTATCTTGTGCGTAT 57.547 40.909 0.06 0.00 46.80 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.613358 AGCAAGAATTCGTGGAGTTTAAG 57.387 39.130 20.66 0.00 0.00 1.85
37 38 6.146184 CACTATACCATAGCAAGAATTCGTGG 59.854 42.308 20.66 14.51 0.00 4.94
51 52 1.358152 GGCTGGCCCACTATACCATA 58.642 55.000 0.00 0.00 31.79 2.74
71 72 4.092091 GCTACTCTCACGGACAAGAATTTG 59.908 45.833 0.00 0.00 40.24 2.32
86 87 5.328691 CGATCGGAATAATCTGCTACTCTC 58.671 45.833 7.38 0.00 31.55 3.20
88 89 4.156190 TCCGATCGGAATAATCTGCTACTC 59.844 45.833 33.96 0.00 42.05 2.59
104 105 5.983720 ACTGGAAATACTACAATTCCGATCG 59.016 40.000 8.51 8.51 44.48 3.69
106 107 6.538742 CACACTGGAAATACTACAATTCCGAT 59.461 38.462 0.00 0.00 44.48 4.18
111 112 8.512138 GTTTAGCACACTGGAAATACTACAATT 58.488 33.333 0.00 0.00 0.00 2.32
160 162 3.266772 TGGCATCCTGAACTTGTAATCCT 59.733 43.478 0.00 0.00 0.00 3.24
177 179 6.036577 ACTTTGAATACCGAAAATTGGCAT 57.963 33.333 0.00 0.00 0.00 4.40
199 201 8.084684 AGACAAAAGCTAAATCAAATCCTGAAC 58.915 33.333 0.00 0.00 37.67 3.18
258 260 2.723273 GTAGGTAGGCCATGCAAAAGT 58.277 47.619 5.01 0.00 37.19 2.66
259 261 1.670811 CGTAGGTAGGCCATGCAAAAG 59.329 52.381 5.01 0.00 37.19 2.27
262 264 1.137479 GTACGTAGGTAGGCCATGCAA 59.863 52.381 5.01 0.00 37.19 4.08
292 294 0.740868 TGAGCGTCACCTATGCAAGC 60.741 55.000 0.00 0.00 43.05 4.01
298 300 2.289072 GGTATGCATGAGCGTCACCTAT 60.289 50.000 10.16 0.00 46.23 2.57
430 432 0.661187 CCATGTTCGCAACACAGCAC 60.661 55.000 4.23 0.00 45.50 4.40
435 437 0.808125 TATGCCCATGTTCGCAACAC 59.192 50.000 3.78 0.00 45.50 3.32
436 438 1.761449 ATATGCCCATGTTCGCAACA 58.239 45.000 3.78 4.56 46.94 3.33
437 439 2.616376 TGTATATGCCCATGTTCGCAAC 59.384 45.455 3.78 0.00 38.75 4.17
474 476 5.886609 TCATTTTAGAGGGGTCAACATTGA 58.113 37.500 0.00 0.00 34.20 2.57
480 482 4.521256 CCGTTTTCATTTTAGAGGGGTCAA 59.479 41.667 0.00 0.00 0.00 3.18
488 490 5.581874 GGACCGATACCGTTTTCATTTTAGA 59.418 40.000 0.00 0.00 0.00 2.10
508 510 3.952628 CTCCCTTTGTCCGCGGACC 62.953 68.421 45.59 31.25 43.97 4.46
521 523 2.285368 TTGGATGGTCGGCTCCCT 60.285 61.111 0.00 0.00 0.00 4.20
527 529 2.120909 GGCATGGTTGGATGGTCGG 61.121 63.158 0.00 0.00 0.00 4.79
579 581 7.350744 TCATCTGGCTTGCATGTAATTTATT 57.649 32.000 0.00 0.00 0.00 1.40
595 597 7.903995 TTGGTTTAAATGAAAATCATCTGGC 57.096 32.000 0.00 0.00 35.76 4.85
644 646 9.959749 GTCTGGTCACTTTTGTTTAATGAAATA 57.040 29.630 0.00 0.00 0.00 1.40
645 647 7.926018 GGTCTGGTCACTTTTGTTTAATGAAAT 59.074 33.333 0.00 0.00 0.00 2.17
646 648 7.123547 AGGTCTGGTCACTTTTGTTTAATGAAA 59.876 33.333 0.00 0.00 0.00 2.69
647 649 6.605594 AGGTCTGGTCACTTTTGTTTAATGAA 59.394 34.615 0.00 0.00 0.00 2.57
648 650 6.039270 CAGGTCTGGTCACTTTTGTTTAATGA 59.961 38.462 0.00 0.00 0.00 2.57
662 664 2.110188 AGACTAGGTTCAGGTCTGGTCA 59.890 50.000 8.96 0.00 41.82 4.02
666 668 6.783708 AGATTTAGACTAGGTTCAGGTCTG 57.216 41.667 0.00 0.00 40.08 3.51
673 675 6.282167 GCCACCTTAGATTTAGACTAGGTTC 58.718 44.000 0.00 0.00 0.00 3.62
697 699 1.079127 ATGGGCACGGAAGAGAACG 60.079 57.895 0.00 0.00 0.00 3.95
731 755 3.470709 CTCATACGGTAGTCGGGTAAGA 58.529 50.000 0.00 0.00 44.45 2.10
735 759 0.106819 AGCTCATACGGTAGTCGGGT 60.107 55.000 0.00 0.00 44.45 5.28
740 764 1.140452 TCTCGGAGCTCATACGGTAGT 59.860 52.381 17.19 0.00 0.00 2.73
743 767 1.025812 CTTCTCGGAGCTCATACGGT 58.974 55.000 17.19 0.00 0.00 4.83
754 778 1.289066 CGCACCTTCACTTCTCGGA 59.711 57.895 0.00 0.00 0.00 4.55
760 784 2.665185 GCGACCGCACCTTCACTT 60.665 61.111 9.73 0.00 41.49 3.16
783 807 6.480524 TGTGTCTCATGTCTTATTTTTCCG 57.519 37.500 0.00 0.00 0.00 4.30
788 812 7.227156 AGTCCTTTGTGTCTCATGTCTTATTT 58.773 34.615 0.00 0.00 0.00 1.40
790 814 6.014242 TGAGTCCTTTGTGTCTCATGTCTTAT 60.014 38.462 0.00 0.00 32.95 1.73
793 817 3.643320 TGAGTCCTTTGTGTCTCATGTCT 59.357 43.478 0.00 0.00 32.95 3.41
809 833 5.405269 CCCAAATTTTGAATTTCGTGAGTCC 59.595 40.000 10.72 0.00 0.00 3.85
810 834 6.212955 TCCCAAATTTTGAATTTCGTGAGTC 58.787 36.000 10.72 0.00 0.00 3.36
811 835 6.155475 TCCCAAATTTTGAATTTCGTGAGT 57.845 33.333 10.72 0.00 0.00 3.41
812 836 6.346838 GCTTCCCAAATTTTGAATTTCGTGAG 60.347 38.462 10.72 0.00 0.00 3.51
813 837 5.465056 GCTTCCCAAATTTTGAATTTCGTGA 59.535 36.000 10.72 0.00 0.00 4.35
844 4436 2.815647 CCGCTGAAAGTCTCGCCC 60.816 66.667 0.00 0.00 35.30 6.13
848 4440 2.436824 GGGCCCGCTGAAAGTCTC 60.437 66.667 5.69 0.00 35.30 3.36
849 4441 3.249189 TGGGCCCGCTGAAAGTCT 61.249 61.111 19.37 0.00 35.30 3.24
850 4442 3.056328 GTGGGCCCGCTGAAAGTC 61.056 66.667 28.79 0.23 35.30 3.01
851 4443 4.660938 GGTGGGCCCGCTGAAAGT 62.661 66.667 33.66 0.00 35.30 2.66
852 4444 4.659172 TGGTGGGCCCGCTGAAAG 62.659 66.667 33.66 0.00 35.15 2.62
853 4445 4.211330 TTGGTGGGCCCGCTGAAA 62.211 61.111 33.66 22.10 35.15 2.69
854 4446 4.659172 CTTGGTGGGCCCGCTGAA 62.659 66.667 33.66 23.99 35.15 3.02
877 4469 2.111384 TGGAGTGGAGACCAGCTATTC 58.889 52.381 0.00 0.00 32.34 1.75
919 4511 4.750695 TGGGGGAATGGGGAGCGA 62.751 66.667 0.00 0.00 0.00 4.93
942 4534 2.936032 GGTGCTGGGAGGGAAGGT 60.936 66.667 0.00 0.00 0.00 3.50
943 4535 2.612115 AGGTGCTGGGAGGGAAGG 60.612 66.667 0.00 0.00 0.00 3.46
944 4536 1.492133 TTGAGGTGCTGGGAGGGAAG 61.492 60.000 0.00 0.00 0.00 3.46
945 4537 1.463214 TTGAGGTGCTGGGAGGGAA 60.463 57.895 0.00 0.00 0.00 3.97
946 4538 1.920325 CTTGAGGTGCTGGGAGGGA 60.920 63.158 0.00 0.00 0.00 4.20
947 4539 2.673523 CTTGAGGTGCTGGGAGGG 59.326 66.667 0.00 0.00 0.00 4.30
1102 4701 1.956629 GAGAGCGTGGATTCGGGGAA 61.957 60.000 0.00 0.00 0.00 3.97
1104 4703 2.107141 GAGAGCGTGGATTCGGGG 59.893 66.667 0.00 0.00 0.00 5.73
1113 4712 2.365068 CGACAACCGTGAGAGCGTG 61.365 63.158 0.00 0.00 0.00 5.34
1120 4719 1.885388 CCAACAGCGACAACCGTGA 60.885 57.895 0.00 0.00 41.15 4.35
1128 4727 2.281484 TGAAGCCCCAACAGCGAC 60.281 61.111 0.00 0.00 34.64 5.19
1209 4808 1.746991 CTTGCCCTTCTTCCTCCGC 60.747 63.158 0.00 0.00 0.00 5.54
1231 4830 2.209076 CGTCATCGTCGTCGCTGTC 61.209 63.158 5.86 0.18 35.19 3.51
1236 4835 1.120714 CACAGTCGTCATCGTCGTCG 61.121 60.000 0.00 0.00 38.33 5.12
1237 4836 0.110328 ACACAGTCGTCATCGTCGTC 60.110 55.000 0.00 0.00 38.33 4.20
1238 4837 0.385598 CACACAGTCGTCATCGTCGT 60.386 55.000 0.00 0.00 38.33 4.34
1254 4853 3.228017 TCGCCGTCCAGAACCACA 61.228 61.111 0.00 0.00 0.00 4.17
1409 5010 1.883926 AACTGGCGGTTAATGGAACAC 59.116 47.619 10.62 0.00 40.09 3.32
1446 5047 4.871993 AGCAATCATGAGACGATTTCAC 57.128 40.909 0.09 0.00 30.65 3.18
1448 5049 5.438972 GCTTAGCAATCATGAGACGATTTC 58.561 41.667 0.09 0.00 30.65 2.17
1449 5050 4.274459 GGCTTAGCAATCATGAGACGATTT 59.726 41.667 6.53 0.00 30.65 2.17
1451 5052 3.181462 TGGCTTAGCAATCATGAGACGAT 60.181 43.478 6.53 0.00 0.00 3.73
1455 5056 4.080695 AGACTTGGCTTAGCAATCATGAGA 60.081 41.667 6.53 0.00 0.00 3.27
1456 5057 4.197750 AGACTTGGCTTAGCAATCATGAG 58.802 43.478 6.53 0.00 0.00 2.90
1457 5058 4.194640 GAGACTTGGCTTAGCAATCATGA 58.805 43.478 6.53 0.00 0.00 3.07
1458 5059 3.943381 TGAGACTTGGCTTAGCAATCATG 59.057 43.478 6.53 0.16 0.00 3.07
1460 5061 3.244526 TGTGAGACTTGGCTTAGCAATCA 60.245 43.478 6.53 0.00 0.00 2.57
1461 5062 3.338249 TGTGAGACTTGGCTTAGCAATC 58.662 45.455 6.53 0.00 0.00 2.67
1462 5063 3.423539 TGTGAGACTTGGCTTAGCAAT 57.576 42.857 6.53 0.00 0.00 3.56
1463 5064 2.878406 GTTGTGAGACTTGGCTTAGCAA 59.122 45.455 6.53 0.00 0.00 3.91
1464 5065 2.104792 AGTTGTGAGACTTGGCTTAGCA 59.895 45.455 6.53 0.00 0.00 3.49
1487 5088 1.050421 GGAGCCAAATTGGGGGATGG 61.050 60.000 14.59 0.00 38.19 3.51
1491 5092 0.325484 TCATGGAGCCAAATTGGGGG 60.325 55.000 14.59 0.00 38.19 5.40
1497 5098 5.698104 TGATATCTGTTCATGGAGCCAAAT 58.302 37.500 3.98 0.00 0.00 2.32
1560 5813 4.207841 GCTTTTGATGTTGCAAGACTGAAC 59.792 41.667 0.00 0.00 0.00 3.18
1625 5878 4.728608 GTGTCGCACTTAAAAACAGACTTG 59.271 41.667 3.20 0.00 0.00 3.16
1639 5892 1.230635 GGATGCAACTGTGTCGCACT 61.231 55.000 10.54 0.00 38.73 4.40
1685 5938 7.410087 CGATGCTGCTTTTGTTTAAGAATCTTG 60.410 37.037 5.64 0.00 0.00 3.02
1822 6075 6.773976 TTTGGCCCTCTCTTAACAAATATG 57.226 37.500 0.00 0.00 0.00 1.78
1828 6081 9.739276 CATATATAATTTGGCCCTCTCTTAACA 57.261 33.333 0.00 0.00 0.00 2.41
1927 6180 6.093404 CGTCTAACTGAAGAAGAATGCACTA 58.907 40.000 0.00 0.00 0.00 2.74
1929 6182 4.092091 CCGTCTAACTGAAGAAGAATGCAC 59.908 45.833 0.00 0.00 0.00 4.57
1949 6202 3.253432 GGCTTTCTTGAAGAACAATCCGT 59.747 43.478 7.21 0.00 37.57 4.69
1952 6205 4.452455 TCTCGGCTTTCTTGAAGAACAATC 59.548 41.667 7.21 0.00 37.57 2.67
1956 6209 2.739379 CCTCTCGGCTTTCTTGAAGAAC 59.261 50.000 7.21 0.00 37.57 3.01
2109 6865 5.396213 GGATTATCATCTGATCCCTGGCTAC 60.396 48.000 0.00 0.00 34.61 3.58
2133 6889 4.223923 GGGGATGGATAGAACATAGGACAG 59.776 50.000 0.00 0.00 0.00 3.51
2139 6895 4.087182 GAGTCGGGGATGGATAGAACATA 58.913 47.826 0.00 0.00 0.00 2.29
2146 6902 0.857675 TGGAGAGTCGGGGATGGATA 59.142 55.000 0.00 0.00 0.00 2.59
2147 6903 0.031111 TTGGAGAGTCGGGGATGGAT 60.031 55.000 0.00 0.00 0.00 3.41
2183 6939 5.754890 AGCATTTCAAAAAGTGTCCAACATC 59.245 36.000 0.00 0.00 0.00 3.06
2184 6940 5.673514 AGCATTTCAAAAAGTGTCCAACAT 58.326 33.333 0.00 0.00 0.00 2.71
2186 6942 4.507756 GGAGCATTTCAAAAAGTGTCCAAC 59.492 41.667 0.00 0.00 30.18 3.77
2187 6943 4.692228 GGAGCATTTCAAAAAGTGTCCAA 58.308 39.130 0.00 0.00 30.18 3.53
2206 6966 4.158579 TGGAAGCTCATATGTATAGCGGAG 59.841 45.833 1.90 0.00 41.19 4.63
2207 6967 4.086457 TGGAAGCTCATATGTATAGCGGA 58.914 43.478 1.90 0.00 41.19 5.54
2209 6969 5.871524 ACAATGGAAGCTCATATGTATAGCG 59.128 40.000 1.90 0.00 41.19 4.26
2210 6970 7.678947 AACAATGGAAGCTCATATGTATAGC 57.321 36.000 6.75 6.75 36.48 2.97
2272 7032 2.031420 CACTGACCTGTGACAAAGCATG 60.031 50.000 1.43 0.00 40.12 4.06
2300 7060 6.582636 TGTGATAATTGGTGATCCTAGACAC 58.417 40.000 0.00 0.00 36.44 3.67
2301 7061 6.806668 TGTGATAATTGGTGATCCTAGACA 57.193 37.500 0.00 0.00 34.23 3.41
2303 7063 7.716560 CACAATGTGATAATTGGTGATCCTAGA 59.283 37.037 7.78 0.00 41.06 2.43
2344 7104 3.578272 GGTCGCAAACACGGTGCA 61.578 61.111 8.30 0.00 42.33 4.57
2369 7129 3.431346 GCAATGAGCATAGACTGGACAGA 60.431 47.826 6.29 0.00 44.79 3.41
2376 7136 3.687551 ATGCAAGGCAATGAGCATAGACT 60.688 43.478 0.00 0.00 45.09 3.24
2523 7285 3.815809 CAGTGAACAGGGGACACTTAAA 58.184 45.455 0.00 0.00 41.93 1.52
2627 7389 8.719596 TCCAAATCTATGTACTTAAATAGGCCA 58.280 33.333 5.01 0.00 0.00 5.36
2668 7430 6.038050 GCTCCTCCTTATCTCTGTTCAATTTG 59.962 42.308 0.00 0.00 0.00 2.32
2831 7593 3.290308 ACGTGAGAAGTAGTGCTGAAG 57.710 47.619 0.00 0.00 0.00 3.02
2850 7612 1.369625 ACCATGCTACAGCGCTTTAC 58.630 50.000 7.50 1.55 45.83 2.01
2852 7614 2.009774 CTTACCATGCTACAGCGCTTT 58.990 47.619 7.50 3.33 45.83 3.51
2858 7620 4.935205 TGCTTGTTACTTACCATGCTACAG 59.065 41.667 0.00 0.00 0.00 2.74
2961 7723 7.166473 GCATACAAAATAGTAGCACTGCATTTC 59.834 37.037 3.30 0.00 30.53 2.17
2977 7739 3.696051 AGCTGGAACATCGCATACAAAAT 59.304 39.130 0.00 0.00 38.20 1.82
3017 7779 7.949690 ATGATCATCATTCAAAAGACCTTGA 57.050 32.000 1.18 0.00 32.13 3.02
3026 7788 7.107639 AGCATGACAATGATCATCATTCAAA 57.892 32.000 10.13 0.00 43.03 2.69
3103 7865 3.930336 TCGGAATAAGATGCTGGCATAG 58.070 45.455 8.11 0.00 36.70 2.23
3105 7867 2.369860 TCTCGGAATAAGATGCTGGCAT 59.630 45.455 7.86 7.86 39.69 4.40
3118 7880 2.571653 TCATCCAGGTGTTTCTCGGAAT 59.428 45.455 0.00 0.00 0.00 3.01
3178 7940 4.444081 CCTCGGAGGTCCTCGGGT 62.444 72.222 22.54 0.00 32.74 5.28
3204 7966 3.702045 AGACAGAGAAGAAATCTACCGGG 59.298 47.826 6.32 0.00 38.96 5.73
3249 8011 6.764560 ACAAGCATCAAAGAAAGCAAGAAAAT 59.235 30.769 0.00 0.00 0.00 1.82
3250 8012 6.108015 ACAAGCATCAAAGAAAGCAAGAAAA 58.892 32.000 0.00 0.00 0.00 2.29
3312 8074 5.938125 ACCTACAGCAAATAAACGATTGACT 59.062 36.000 0.00 0.00 0.00 3.41
3321 8083 7.399634 ACCTAGCTAAACCTACAGCAAATAAA 58.600 34.615 0.00 0.00 40.36 1.40
3409 8171 9.799106 CATAATTTCCCATACTACTGGAAGAAT 57.201 33.333 0.00 0.00 39.22 2.40
3412 8174 7.389053 GCTCATAATTTCCCATACTACTGGAAG 59.611 40.741 0.00 0.00 39.22 3.46
3451 8213 9.160496 CACAATAGCCATTATCTCCTAATTCTC 57.840 37.037 0.00 0.00 0.00 2.87
3681 8443 5.456763 GGGACGGAGGGAGTAGTAATTACTA 60.457 48.000 19.30 19.30 42.69 1.82
3695 8457 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3749 8511 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3751 8513 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3859 8621 5.385396 AGTTACGTTGAGAAAACTGAACG 57.615 39.130 16.96 16.96 45.15 3.95
3874 8636 0.250597 GGGTGGGCTCAAAGTTACGT 60.251 55.000 0.00 0.00 0.00 3.57
3892 8655 6.153340 TGGCAAATCTAGAAAGAAAATGGAGG 59.847 38.462 0.00 0.00 34.73 4.30
3943 8706 1.578215 AACCTGCCTGGCTGATGGAT 61.578 55.000 25.04 11.32 40.22 3.41
3957 8720 3.550656 GTTCTCCACGCGAACCTG 58.449 61.111 15.93 0.00 35.81 4.00
3966 8729 2.756760 TGTGATACGGTAGGTTCTCCAC 59.243 50.000 0.00 0.00 35.89 4.02
4030 8793 3.257393 CTCACCTCTGATAGCACAACAC 58.743 50.000 0.00 0.00 0.00 3.32
4101 8864 5.713389 ACTGATGAATCAAGAATTTGAGGCA 59.287 36.000 0.00 0.00 45.89 4.75
4137 8900 3.773560 AGTTGCAGGCCATTTTTAGGTA 58.226 40.909 5.01 0.00 0.00 3.08
4142 8905 5.067805 GCTATAGTAGTTGCAGGCCATTTTT 59.932 40.000 5.01 0.00 0.00 1.94
4143 8906 4.580580 GCTATAGTAGTTGCAGGCCATTTT 59.419 41.667 5.01 0.00 0.00 1.82
4144 8907 4.137543 GCTATAGTAGTTGCAGGCCATTT 58.862 43.478 5.01 0.00 0.00 2.32
4162 8925 4.005650 CCAGAACTGTGTGATGTTGCTAT 58.994 43.478 1.18 0.00 0.00 2.97
4241 9004 3.107601 AGCCAATTACTGCTAGACTCCA 58.892 45.455 0.00 0.00 35.69 3.86
4355 9118 4.082408 GCCTGTTCCCCTGTTGTAAAATAC 60.082 45.833 0.00 0.00 0.00 1.89
4358 9121 2.312390 GCCTGTTCCCCTGTTGTAAAA 58.688 47.619 0.00 0.00 0.00 1.52
4364 9127 1.774217 TCTGGCCTGTTCCCCTGTT 60.774 57.895 3.32 0.00 0.00 3.16
4476 9239 0.179045 ACTGGCCGCATCAGGTTATC 60.179 55.000 0.00 0.00 36.62 1.75
4492 9255 5.467063 GTCCAGTTTTAACTTGAGGAGACTG 59.533 44.000 1.61 0.00 37.89 3.51
4528 9327 1.297664 CACAGGAGATGCAGCTAAGC 58.702 55.000 3.45 0.00 0.00 3.09
4577 9376 6.048684 TGGGGGAAGACCTTATATCCATACTA 59.951 42.308 0.00 0.00 40.03 1.82
4649 9449 4.518590 CAGAAACCAATACCACATCACACA 59.481 41.667 0.00 0.00 0.00 3.72
4713 9513 4.531854 TGGTGTTCCTCAAATCAGAAACA 58.468 39.130 0.00 0.00 34.23 2.83
4735 9535 4.210331 AGTTTGGCTTCACTTCAGACAAT 58.790 39.130 0.00 0.00 39.11 2.71
4816 9616 1.471684 ACATAACCCTGACGTCGAGAC 59.528 52.381 11.62 0.00 0.00 3.36
4890 9690 3.758023 CACAACTCCTGCATGTCCAAATA 59.242 43.478 0.00 0.00 0.00 1.40
4908 9708 0.942410 GTAACGAGTCTGCCGCACAA 60.942 55.000 0.00 0.00 0.00 3.33
5037 9837 1.539065 CCGCTTCAGCTCATATCCGTT 60.539 52.381 0.00 0.00 39.32 4.44
5044 9844 1.002868 AACAGCCGCTTCAGCTCAT 60.003 52.632 0.00 0.00 38.95 2.90
5422 10222 5.005740 CAGACACAAAGATGATCCCTTTCA 58.994 41.667 7.09 0.00 32.04 2.69
5598 10403 1.308998 CGGCATTGACCATAGGTTCC 58.691 55.000 0.00 0.00 35.25 3.62
5624 10429 7.503566 CCAAATCCACATGAAGACCATTACTAT 59.496 37.037 0.00 0.00 31.94 2.12
5770 10576 2.490903 ACAGATTGCTTCAGATGTTGCC 59.509 45.455 0.00 0.00 0.00 4.52
5777 10583 9.896645 ATAGATAGAAAAACAGATTGCTTCAGA 57.103 29.630 0.00 0.00 0.00 3.27
5892 10699 6.109156 TCACACATGTAGTAACCTGAATGT 57.891 37.500 0.00 0.00 31.75 2.71
6157 10965 8.015658 GCTGAACAGATAAATTTTCGTAGTTGT 58.984 33.333 5.97 0.00 0.00 3.32
6340 11148 5.750547 TGCAATTGAAACTTGAAAATACGCA 59.249 32.000 10.34 0.00 0.00 5.24
6346 11154 7.966246 ATGCTATGCAATTGAAACTTGAAAA 57.034 28.000 10.34 0.00 43.62 2.29


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

AutoCloner maintained by Alex Coulton.