Multiple sequence alignment - TraesCS6A01G399900

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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 TraesCS6A01G399900 chr6A 100.000 2493 0 0 504 2996 609427775 609425283 0.000000e+00 4604.0
1 TraesCS6A01G399900 chr6A 88.089 1654 191 4 507 2158 609403299 609401650 0.000000e+00 1958.0
2 TraesCS6A01G399900 chr6A 100.000 206 0 0 1 206 609428278 609428073 6.060000e-102 381.0
3 TraesCS6A01G399900 chr6D 96.289 1967 70 3 504 2469 462614920 462612956 0.000000e+00 3225.0
4 TraesCS6A01G399900 chr6D 88.659 1596 174 4 521 2116 462555548 462553960 0.000000e+00 1938.0
5 TraesCS6A01G399900 chr6D 99.020 102 0 1 2466 2567 389248212 389248312 6.600000e-42 182.0
6 TraesCS6A01G399900 chr6D 99.020 102 0 1 2466 2567 389253007 389253107 6.600000e-42 182.0
7 TraesCS6A01G399900 chr6D 87.234 141 2 4 66 206 462615453 462615329 2.410000e-31 147.0
8 TraesCS6A01G399900 chr6D 100.000 44 0 0 2659 2702 431398326 431398369 6.880000e-12 82.4
9 TraesCS6A01G399900 chr6B 97.703 1654 38 0 504 2157 705316522 705314869 0.000000e+00 2844.0
10 TraesCS6A01G399900 chr6B 87.500 1360 164 3 710 2066 705182947 705181591 0.000000e+00 1565.0
11 TraesCS6A01G399900 chr6B 96.687 332 7 1 2142 2469 705314718 705314387 1.570000e-152 549.0
12 TraesCS6A01G399900 chr6B 98.942 189 2 0 2808 2996 705314118 705313930 3.700000e-89 339.0
13 TraesCS6A01G399900 chr6B 93.151 219 13 2 507 724 705183844 705183627 1.340000e-83 320.0
14 TraesCS6A01G399900 chr6B 98.230 113 2 0 2703 2815 705314388 705314276 6.550000e-47 198.0
15 TraesCS6A01G399900 chr6B 85.816 141 2 4 66 206 705316702 705316580 1.870000e-27 134.0
16 TraesCS6A01G399900 chrUn 97.183 426 12 0 842 1267 476451864 476451439 0.000000e+00 721.0
17 TraesCS6A01G399900 chrUn 99.020 102 0 1 2466 2567 397078467 397078367 6.600000e-42 182.0
18 TraesCS6A01G399900 chrUn 99.020 102 0 1 2466 2567 424751318 424751218 6.600000e-42 182.0
19 TraesCS6A01G399900 chrUn 99.020 102 0 1 2466 2567 455551729 455551829 6.600000e-42 182.0
20 TraesCS6A01G399900 chrUn 99.000 100 1 0 2559 2658 381153044 381153143 2.370000e-41 180.0
21 TraesCS6A01G399900 chrUn 100.000 44 0 0 2659 2702 453774763 453774806 6.880000e-12 82.4
22 TraesCS6A01G399900 chrUn 100.000 44 0 0 2659 2702 463113994 463113951 6.880000e-12 82.4
23 TraesCS6A01G399900 chrUn 100.000 44 0 0 2659 2702 465624453 465624410 6.880000e-12 82.4
24 TraesCS6A01G399900 chr3D 87.002 577 67 4 507 1079 144479052 144478480 0.000000e+00 643.0
25 TraesCS6A01G399900 chr3D 99.020 102 0 1 2466 2567 48688857 48688757 6.600000e-42 182.0
26 TraesCS6A01G399900 chr4D 99.020 102 0 1 2466 2567 207361943 207361843 6.600000e-42 182.0
27 TraesCS6A01G399900 chr1D 99.020 102 0 1 2466 2567 51918418 51918318 6.600000e-42 182.0
28 TraesCS6A01G399900 chr1D 99.020 102 0 1 2466 2567 79823771 79823871 6.600000e-42 182.0
29 TraesCS6A01G399900 chr1D 98.000 100 2 0 2559 2658 51869829 51869928 1.100000e-39 174.0
30 TraesCS6A01G399900 chr1D 100.000 44 0 0 2659 2702 16963866 16963823 6.880000e-12 82.4
31 TraesCS6A01G399900 chr1D 100.000 44 0 0 2659 2702 254487997 254488040 6.880000e-12 82.4
32 TraesCS6A01G399900 chr7D 99.000 100 1 0 2559 2658 231541582 231541681 2.370000e-41 180.0
33 TraesCS6A01G399900 chr7D 99.000 100 1 0 2559 2658 231596710 231596611 2.370000e-41 180.0
34 TraesCS6A01G399900 chr2B 99.000 100 1 0 2559 2658 800864273 800864372 2.370000e-41 180.0
35 TraesCS6A01G399900 chr2A 99.000 100 1 0 2559 2658 393116661 393116760 2.370000e-41 180.0
36 TraesCS6A01G399900 chr5D 98.980 98 1 0 2561 2658 503293987 503293890 3.070000e-40 176.0
37 TraesCS6A01G399900 chr5D 100.000 44 0 0 2659 2702 6209384 6209341 6.880000e-12 82.4
38 TraesCS6A01G399900 chr5A 98.980 98 1 0 2561 2658 257663601 257663504 3.070000e-40 176.0
39 TraesCS6A01G399900 chr1B 98.000 100 2 0 2559 2658 633709810 633709711 1.100000e-39 174.0
40 TraesCS6A01G399900 chr7A 87.156 109 7 2 2839 2940 519793 519685 1.890000e-22 117.0
41 TraesCS6A01G399900 chr7A 81.034 116 22 0 651 766 495536861 495536976 3.180000e-15 93.5
42 TraesCS6A01G399900 chr3B 88.636 88 5 3 2851 2933 817040766 817040853 5.280000e-18 102.0
43 TraesCS6A01G399900 chr1A 100.000 44 0 0 2659 2702 256027863 256027820 6.880000e-12 82.4
44 TraesCS6A01G399900 chr1A 100.000 44 0 0 2659 2702 297947789 297947746 6.880000e-12 82.4
45 TraesCS6A01G399900 chr3A 97.436 39 1 0 2767 2805 739762022 739762060 1.930000e-07 67.6


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 TraesCS6A01G399900 chr6A 609425283 609428278 2995 True 2492.5 4604 100.0000 1 2996 2 chr6A.!!$R2 2995
1 TraesCS6A01G399900 chr6A 609401650 609403299 1649 True 1958.0 1958 88.0890 507 2158 1 chr6A.!!$R1 1651
2 TraesCS6A01G399900 chr6D 462553960 462555548 1588 True 1938.0 1938 88.6590 521 2116 1 chr6D.!!$R1 1595
3 TraesCS6A01G399900 chr6D 462612956 462615453 2497 True 1686.0 3225 91.7615 66 2469 2 chr6D.!!$R2 2403
4 TraesCS6A01G399900 chr6B 705181591 705183844 2253 True 942.5 1565 90.3255 507 2066 2 chr6B.!!$R1 1559
5 TraesCS6A01G399900 chr6B 705313930 705316702 2772 True 812.8 2844 95.4756 66 2996 5 chr6B.!!$R2 2930
6 TraesCS6A01G399900 chr3D 144478480 144479052 572 True 643.0 643 87.0020 507 1079 1 chr3D.!!$R2 572

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
25 26 0.107643 TTCACGGGAGCAACACATGA 59.892 50.0 0.00 0.0 0.00 3.07 F
1029 1840 0.457337 GCCCTTACGACACGTACCTG 60.457 60.0 3.52 0.0 42.13 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2779 0.099436 GTATGCGCTTCTTGCAAGGG 59.901 55.0 25.73 18.76 46.87 3.95 R
2506 3493 0.031817 AATGAGGGGCAAGGGGATTG 60.032 55.0 0.00 0.00 42.20 2.67 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
20 21 4.473643 CCTTTCACGGGAGCAACA 57.526 55.556 0.00 0.00 0.00 3.33
21 22 1.949257 CCTTTCACGGGAGCAACAC 59.051 57.895 0.00 0.00 0.00 3.32
22 23 0.817634 CCTTTCACGGGAGCAACACA 60.818 55.000 0.00 0.00 0.00 3.72
23 24 1.238439 CTTTCACGGGAGCAACACAT 58.762 50.000 0.00 0.00 0.00 3.21
24 25 0.950836 TTTCACGGGAGCAACACATG 59.049 50.000 0.00 0.00 0.00 3.21
25 26 0.107643 TTCACGGGAGCAACACATGA 59.892 50.000 0.00 0.00 0.00 3.07
26 27 0.602638 TCACGGGAGCAACACATGAC 60.603 55.000 0.00 0.00 0.00 3.06
27 28 0.603707 CACGGGAGCAACACATGACT 60.604 55.000 0.00 0.00 0.00 3.41
28 29 0.603707 ACGGGAGCAACACATGACTG 60.604 55.000 0.00 0.00 0.00 3.51
29 30 1.878775 GGGAGCAACACATGACTGC 59.121 57.895 0.00 4.97 36.29 4.40
30 31 0.890542 GGGAGCAACACATGACTGCA 60.891 55.000 16.69 0.00 38.58 4.41
31 32 0.520404 GGAGCAACACATGACTGCAG 59.480 55.000 13.48 13.48 38.58 4.41
32 33 1.233019 GAGCAACACATGACTGCAGT 58.767 50.000 21.88 21.88 38.58 4.40
33 34 1.605710 GAGCAACACATGACTGCAGTT 59.394 47.619 22.65 2.27 38.58 3.16
34 35 1.605710 AGCAACACATGACTGCAGTTC 59.394 47.619 22.65 14.43 38.58 3.01
35 36 1.334556 GCAACACATGACTGCAGTTCA 59.665 47.619 22.65 19.50 36.09 3.18
36 37 2.223548 GCAACACATGACTGCAGTTCAA 60.224 45.455 22.65 10.54 36.09 2.69
37 38 3.624900 CAACACATGACTGCAGTTCAAG 58.375 45.455 22.65 18.01 0.00 3.02
38 39 2.923121 ACACATGACTGCAGTTCAAGT 58.077 42.857 22.65 18.62 0.00 3.16
39 40 2.615447 ACACATGACTGCAGTTCAAGTG 59.385 45.455 30.75 30.75 0.00 3.16
40 41 2.874086 CACATGACTGCAGTTCAAGTGA 59.126 45.455 29.87 11.28 0.00 3.41
41 42 3.313249 CACATGACTGCAGTTCAAGTGAA 59.687 43.478 29.87 11.43 0.00 3.18
42 43 3.947196 ACATGACTGCAGTTCAAGTGAAA 59.053 39.130 22.65 0.00 35.58 2.69
43 44 4.581824 ACATGACTGCAGTTCAAGTGAAAT 59.418 37.500 22.65 1.14 35.58 2.17
44 45 5.068198 ACATGACTGCAGTTCAAGTGAAATT 59.932 36.000 22.65 0.45 35.58 1.82
45 46 4.923893 TGACTGCAGTTCAAGTGAAATTG 58.076 39.130 22.65 0.00 35.58 2.32
46 47 3.709987 ACTGCAGTTCAAGTGAAATTGC 58.290 40.909 15.25 18.06 42.40 3.56
47 48 3.130869 ACTGCAGTTCAAGTGAAATTGCA 59.869 39.130 15.25 22.67 45.84 4.08
48 49 4.114073 CTGCAGTTCAAGTGAAATTGCAA 58.886 39.130 23.53 0.00 46.51 4.08
49 50 4.114073 TGCAGTTCAAGTGAAATTGCAAG 58.886 39.130 22.26 2.95 45.46 4.01
50 51 4.142204 TGCAGTTCAAGTGAAATTGCAAGA 60.142 37.500 22.26 8.24 45.46 3.02
51 52 4.986659 GCAGTTCAAGTGAAATTGCAAGAT 59.013 37.500 19.18 0.00 42.02 2.40
52 53 5.464389 GCAGTTCAAGTGAAATTGCAAGATT 59.536 36.000 19.18 2.27 42.02 2.40
53 54 6.018507 GCAGTTCAAGTGAAATTGCAAGATTT 60.019 34.615 19.18 0.87 42.02 2.17
54 55 7.466320 GCAGTTCAAGTGAAATTGCAAGATTTT 60.466 33.333 19.18 0.04 42.02 1.82
55 56 8.060090 CAGTTCAAGTGAAATTGCAAGATTTTC 58.940 33.333 14.37 14.37 35.58 2.29
56 57 7.225341 AGTTCAAGTGAAATTGCAAGATTTTCC 59.775 33.333 17.21 10.83 35.58 3.13
57 58 5.990996 TCAAGTGAAATTGCAAGATTTTCCC 59.009 36.000 17.21 9.13 29.75 3.97
58 59 5.549742 AGTGAAATTGCAAGATTTTCCCA 57.450 34.783 17.21 2.63 29.75 4.37
59 60 5.927819 AGTGAAATTGCAAGATTTTCCCAA 58.072 33.333 17.21 1.54 29.75 4.12
60 61 5.759763 AGTGAAATTGCAAGATTTTCCCAAC 59.240 36.000 17.21 11.07 29.75 3.77
61 62 5.759763 GTGAAATTGCAAGATTTTCCCAACT 59.240 36.000 17.21 0.00 29.75 3.16
62 63 6.260714 GTGAAATTGCAAGATTTTCCCAACTT 59.739 34.615 17.21 0.00 29.75 2.66
63 64 6.827762 TGAAATTGCAAGATTTTCCCAACTTT 59.172 30.769 17.21 4.09 29.75 2.66
64 65 6.622833 AATTGCAAGATTTTCCCAACTTTG 57.377 33.333 4.94 0.00 0.00 2.77
78 79 5.188751 TCCCAACTTTGAACCAATCACTTTT 59.811 36.000 0.00 0.00 37.92 2.27
114 115 1.795162 GCAATAGCACGCCATGTTGTC 60.795 52.381 0.00 0.00 41.58 3.18
128 129 4.646040 CCATGTTGTCATCTCTCTCTCTCT 59.354 45.833 0.00 0.00 31.15 3.10
131 132 5.185454 TGTTGTCATCTCTCTCTCTCTCTC 58.815 45.833 0.00 0.00 0.00 3.20
132 133 5.045651 TGTTGTCATCTCTCTCTCTCTCTCT 60.046 44.000 0.00 0.00 0.00 3.10
133 134 5.282055 TGTCATCTCTCTCTCTCTCTCTC 57.718 47.826 0.00 0.00 0.00 3.20
134 135 4.964897 TGTCATCTCTCTCTCTCTCTCTCT 59.035 45.833 0.00 0.00 0.00 3.10
135 136 5.069648 TGTCATCTCTCTCTCTCTCTCTCTC 59.930 48.000 0.00 0.00 0.00 3.20
136 137 5.304101 GTCATCTCTCTCTCTCTCTCTCTCT 59.696 48.000 0.00 0.00 0.00 3.10
137 138 5.538053 TCATCTCTCTCTCTCTCTCTCTCTC 59.462 48.000 0.00 0.00 0.00 3.20
138 139 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
139 140 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
140 141 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
141 142 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
142 143 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
143 144 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
144 145 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
145 146 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
146 147 3.386078 TCTCTCTCTCTCTCTCTCTCTGC 59.614 52.174 0.00 0.00 0.00 4.26
588 700 6.766467 ACCGGTTCATATCCTTCTTGATAAAC 59.234 38.462 0.00 0.00 31.34 2.01
840 1651 2.166459 CTCCAATACCTTGTCGCTCTCA 59.834 50.000 0.00 0.00 0.00 3.27
884 1695 3.502211 ACCAATTCTACCAACTGCTTTCG 59.498 43.478 0.00 0.00 0.00 3.46
934 1745 9.513906 TTTTTCATGACCTTGATAGTGTATTGA 57.486 29.630 0.00 0.00 0.00 2.57
1009 1820 3.857854 GTGAGCGCATGCCTCGTG 61.858 66.667 22.87 8.11 44.31 4.35
1029 1840 0.457337 GCCCTTACGACACGTACCTG 60.457 60.000 3.52 0.00 42.13 4.00
1114 1925 7.888021 TGCTACAAGAAAATATTCCTCCTTTCA 59.112 33.333 0.00 0.00 36.12 2.69
1210 2021 9.167311 ACAATGATAGAGTTAAATCACACTTCC 57.833 33.333 5.62 0.00 35.06 3.46
1215 2026 8.794335 ATAGAGTTAAATCACACTTCCCTTTC 57.206 34.615 5.62 0.00 0.00 2.62
1245 2056 3.192212 GTCTGAAAGGGGAAAGCATTCAG 59.808 47.826 3.82 7.34 45.18 3.02
1260 2074 3.675228 GCATTCAGAAAACTGAGCATGGG 60.675 47.826 0.00 0.00 34.56 4.00
1461 2275 0.461961 GCTTGTCGCTGGAGGAGTAT 59.538 55.000 0.00 0.00 35.14 2.12
1965 2779 1.804748 GTTTCGGAACATGTGGTCTCC 59.195 52.381 0.38 0.98 35.79 3.71
2043 2857 3.008330 AGTTGAGATGACAATGAGCTGC 58.992 45.455 0.00 0.00 32.36 5.25
2161 3143 8.297470 AGCCATGCAAAGAAGATTAATTTCTA 57.703 30.769 11.05 1.01 33.92 2.10
2191 3177 1.339920 TGAGCACACCATGTACCATGG 60.340 52.381 19.19 19.19 44.54 3.66
2466 3453 8.964150 GGTAATGACAACAAATACAAAGTGTTC 58.036 33.333 0.00 0.00 33.27 3.18
2467 3454 9.509855 GTAATGACAACAAATACAAAGTGTTCA 57.490 29.630 0.00 0.00 33.27 3.18
2468 3455 8.994429 AATGACAACAAATACAAAGTGTTCAA 57.006 26.923 0.00 0.00 33.27 2.69
2469 3456 8.994429 ATGACAACAAATACAAAGTGTTCAAA 57.006 26.923 0.00 0.00 33.27 2.69
2470 3457 8.994429 TGACAACAAATACAAAGTGTTCAAAT 57.006 26.923 0.00 0.00 33.27 2.32
2471 3458 9.081997 TGACAACAAATACAAAGTGTTCAAATC 57.918 29.630 0.00 0.00 33.27 2.17
2472 3459 8.994429 ACAACAAATACAAAGTGTTCAAATCA 57.006 26.923 0.00 0.00 33.27 2.57
2473 3460 8.868916 ACAACAAATACAAAGTGTTCAAATCAC 58.131 29.630 0.00 0.00 33.27 3.06
2474 3461 7.678194 ACAAATACAAAGTGTTCAAATCACG 57.322 32.000 0.00 0.00 40.28 4.35
2475 3462 7.254852 ACAAATACAAAGTGTTCAAATCACGT 58.745 30.769 0.00 0.00 40.28 4.49
2476 3463 7.431084 ACAAATACAAAGTGTTCAAATCACGTC 59.569 33.333 0.00 0.00 40.28 4.34
2477 3464 6.861065 ATACAAAGTGTTCAAATCACGTCT 57.139 33.333 0.00 0.00 40.28 4.18
2478 3465 5.560966 ACAAAGTGTTCAAATCACGTCTT 57.439 34.783 0.00 0.00 40.28 3.01
2479 3466 6.671614 ACAAAGTGTTCAAATCACGTCTTA 57.328 33.333 0.00 0.00 40.28 2.10
2480 3467 7.259290 ACAAAGTGTTCAAATCACGTCTTAT 57.741 32.000 0.00 0.00 40.28 1.73
2481 3468 8.373048 ACAAAGTGTTCAAATCACGTCTTATA 57.627 30.769 0.00 0.00 40.28 0.98
2482 3469 8.832521 ACAAAGTGTTCAAATCACGTCTTATAA 58.167 29.630 0.00 0.00 40.28 0.98
2483 3470 9.825972 CAAAGTGTTCAAATCACGTCTTATAAT 57.174 29.630 0.00 0.00 40.28 1.28
2510 3497 8.655651 AGAAGAAATCTTTCTCGGTATCAATC 57.344 34.615 5.69 0.00 46.22 2.67
2511 3498 7.713073 AGAAGAAATCTTTCTCGGTATCAATCC 59.287 37.037 5.69 0.00 46.22 3.01
2512 3499 6.292150 AGAAATCTTTCTCGGTATCAATCCC 58.708 40.000 0.00 0.00 43.72 3.85
2513 3500 4.625607 ATCTTTCTCGGTATCAATCCCC 57.374 45.455 0.00 0.00 0.00 4.81
2514 3501 3.654273 TCTTTCTCGGTATCAATCCCCT 58.346 45.455 0.00 0.00 0.00 4.79
2515 3502 4.037927 TCTTTCTCGGTATCAATCCCCTT 58.962 43.478 0.00 0.00 0.00 3.95
2516 3503 3.838244 TTCTCGGTATCAATCCCCTTG 57.162 47.619 0.00 0.00 36.09 3.61
2517 3504 1.416401 TCTCGGTATCAATCCCCTTGC 59.584 52.381 0.00 0.00 34.66 4.01
2518 3505 0.472471 TCGGTATCAATCCCCTTGCC 59.528 55.000 0.00 0.00 34.66 4.52
2519 3506 0.537371 CGGTATCAATCCCCTTGCCC 60.537 60.000 0.00 0.00 34.66 5.36
2520 3507 0.178961 GGTATCAATCCCCTTGCCCC 60.179 60.000 0.00 0.00 34.66 5.80
2521 3508 0.853530 GTATCAATCCCCTTGCCCCT 59.146 55.000 0.00 0.00 34.66 4.79
2522 3509 1.149101 TATCAATCCCCTTGCCCCTC 58.851 55.000 0.00 0.00 34.66 4.30
2523 3510 0.925720 ATCAATCCCCTTGCCCCTCA 60.926 55.000 0.00 0.00 34.66 3.86
2524 3511 0.925720 TCAATCCCCTTGCCCCTCAT 60.926 55.000 0.00 0.00 34.66 2.90
2525 3512 0.031817 CAATCCCCTTGCCCCTCATT 60.032 55.000 0.00 0.00 0.00 2.57
2526 3513 0.262876 AATCCCCTTGCCCCTCATTC 59.737 55.000 0.00 0.00 0.00 2.67
2527 3514 0.628668 ATCCCCTTGCCCCTCATTCT 60.629 55.000 0.00 0.00 0.00 2.40
2528 3515 0.850883 TCCCCTTGCCCCTCATTCTT 60.851 55.000 0.00 0.00 0.00 2.52
2529 3516 0.041684 CCCCTTGCCCCTCATTCTTT 59.958 55.000 0.00 0.00 0.00 2.52
2530 3517 1.188863 CCCTTGCCCCTCATTCTTTG 58.811 55.000 0.00 0.00 0.00 2.77
2531 3518 1.272648 CCCTTGCCCCTCATTCTTTGA 60.273 52.381 0.00 0.00 0.00 2.69
2552 3539 5.423015 TGAGAATCAGAAGGATCCTTTTCG 58.577 41.667 27.68 18.14 42.56 3.46
2553 3540 5.187772 TGAGAATCAGAAGGATCCTTTTCGA 59.812 40.000 27.68 22.24 42.56 3.71
2554 3541 5.669477 AGAATCAGAAGGATCCTTTTCGAG 58.331 41.667 27.68 15.31 36.26 4.04
2555 3542 5.188751 AGAATCAGAAGGATCCTTTTCGAGT 59.811 40.000 27.68 21.28 36.26 4.18
2556 3543 4.891992 TCAGAAGGATCCTTTTCGAGTT 57.108 40.909 27.68 2.88 36.26 3.01
2557 3544 5.228945 TCAGAAGGATCCTTTTCGAGTTT 57.771 39.130 27.68 2.05 36.26 2.66
2558 3545 5.238583 TCAGAAGGATCCTTTTCGAGTTTC 58.761 41.667 27.68 11.96 36.26 2.78
2559 3546 4.393371 CAGAAGGATCCTTTTCGAGTTTCC 59.607 45.833 27.68 10.99 36.26 3.13
2560 3547 4.041691 AGAAGGATCCTTTTCGAGTTTCCA 59.958 41.667 27.68 0.00 36.26 3.53
2561 3548 3.944087 AGGATCCTTTTCGAGTTTCCAG 58.056 45.455 9.02 0.00 30.59 3.86
2562 3549 3.328050 AGGATCCTTTTCGAGTTTCCAGT 59.672 43.478 9.02 0.00 30.59 4.00
2563 3550 4.072839 GGATCCTTTTCGAGTTTCCAGTT 58.927 43.478 3.84 0.00 0.00 3.16
2564 3551 4.519350 GGATCCTTTTCGAGTTTCCAGTTT 59.481 41.667 3.84 0.00 0.00 2.66
2565 3552 5.334957 GGATCCTTTTCGAGTTTCCAGTTTC 60.335 44.000 3.84 0.00 0.00 2.78
2566 3553 4.777463 TCCTTTTCGAGTTTCCAGTTTCT 58.223 39.130 0.00 0.00 0.00 2.52
2567 3554 4.574828 TCCTTTTCGAGTTTCCAGTTTCTG 59.425 41.667 0.00 0.00 0.00 3.02
2589 3576 4.244326 TCCAGAGCGGAGTAGAGC 57.756 61.111 0.00 0.00 39.64 4.09
2590 3577 1.303282 TCCAGAGCGGAGTAGAGCA 59.697 57.895 0.00 0.00 39.64 4.26
2591 3578 0.749818 TCCAGAGCGGAGTAGAGCAG 60.750 60.000 0.00 0.00 39.64 4.24
2592 3579 1.034838 CCAGAGCGGAGTAGAGCAGT 61.035 60.000 0.00 0.00 36.56 4.40
2593 3580 0.814457 CAGAGCGGAGTAGAGCAGTT 59.186 55.000 0.00 0.00 35.48 3.16
2594 3581 1.203523 CAGAGCGGAGTAGAGCAGTTT 59.796 52.381 0.00 0.00 35.48 2.66
2595 3582 1.203523 AGAGCGGAGTAGAGCAGTTTG 59.796 52.381 0.00 0.00 35.48 2.93
2596 3583 0.247736 AGCGGAGTAGAGCAGTTTGG 59.752 55.000 0.00 0.00 35.48 3.28
2597 3584 0.037232 GCGGAGTAGAGCAGTTTGGT 60.037 55.000 0.00 0.00 0.00 3.67
2598 3585 1.203994 GCGGAGTAGAGCAGTTTGGTA 59.796 52.381 0.00 0.00 0.00 3.25
2599 3586 2.735762 GCGGAGTAGAGCAGTTTGGTAG 60.736 54.545 0.00 0.00 0.00 3.18
2600 3587 2.735762 CGGAGTAGAGCAGTTTGGTAGC 60.736 54.545 0.00 0.00 0.00 3.58
2601 3588 2.498078 GGAGTAGAGCAGTTTGGTAGCT 59.502 50.000 0.00 0.00 42.17 3.32
2605 3592 3.217242 AGCAGTTTGGTAGCTCACG 57.783 52.632 0.00 0.00 32.05 4.35
2606 3593 0.679505 AGCAGTTTGGTAGCTCACGA 59.320 50.000 0.00 0.00 32.05 4.35
2607 3594 1.071605 GCAGTTTGGTAGCTCACGAG 58.928 55.000 0.00 0.00 0.00 4.18
2608 3595 1.714794 CAGTTTGGTAGCTCACGAGG 58.285 55.000 0.00 0.00 0.00 4.63
2609 3596 0.037232 AGTTTGGTAGCTCACGAGGC 60.037 55.000 0.00 0.00 0.00 4.70
2610 3597 0.037232 GTTTGGTAGCTCACGAGGCT 60.037 55.000 0.00 0.00 43.02 4.58
2611 3598 0.246635 TTTGGTAGCTCACGAGGCTC 59.753 55.000 3.87 3.87 40.74 4.70
2612 3599 1.605058 TTGGTAGCTCACGAGGCTCC 61.605 60.000 9.32 0.00 40.74 4.70
2613 3600 1.755008 GGTAGCTCACGAGGCTCCT 60.755 63.158 9.32 2.05 40.74 3.69
2614 3601 0.465824 GGTAGCTCACGAGGCTCCTA 60.466 60.000 9.32 1.00 40.74 2.94
2615 3602 1.390565 GTAGCTCACGAGGCTCCTAA 58.609 55.000 9.32 0.00 40.74 2.69
2616 3603 1.065851 GTAGCTCACGAGGCTCCTAAC 59.934 57.143 9.32 0.00 40.74 2.34
2617 3604 1.142097 GCTCACGAGGCTCCTAACC 59.858 63.158 9.32 0.00 0.00 2.85
2618 3605 1.324005 GCTCACGAGGCTCCTAACCT 61.324 60.000 9.32 0.00 41.41 3.50
2619 3606 1.187087 CTCACGAGGCTCCTAACCTT 58.813 55.000 9.32 0.00 37.77 3.50
2620 3607 0.895530 TCACGAGGCTCCTAACCTTG 59.104 55.000 9.32 0.00 43.44 3.61
2621 3608 0.895530 CACGAGGCTCCTAACCTTGA 59.104 55.000 9.32 0.00 40.69 3.02
2622 3609 1.134965 CACGAGGCTCCTAACCTTGAG 60.135 57.143 9.32 0.00 40.69 3.02
2623 3610 0.461961 CGAGGCTCCTAACCTTGAGG 59.538 60.000 9.32 0.00 40.69 3.86
2633 3620 4.695560 CCTTGAGGTCACGGGTTC 57.304 61.111 0.00 0.00 32.20 3.62
2634 3621 1.374252 CCTTGAGGTCACGGGTTCG 60.374 63.158 0.00 0.00 43.02 3.95
2635 3622 1.663739 CTTGAGGTCACGGGTTCGA 59.336 57.895 0.00 0.00 40.11 3.71
2636 3623 0.246635 CTTGAGGTCACGGGTTCGAT 59.753 55.000 0.00 0.00 40.11 3.59
2637 3624 0.682852 TTGAGGTCACGGGTTCGATT 59.317 50.000 0.00 0.00 40.11 3.34
2638 3625 0.245539 TGAGGTCACGGGTTCGATTC 59.754 55.000 0.00 0.00 40.11 2.52
2639 3626 0.459759 GAGGTCACGGGTTCGATTCC 60.460 60.000 0.00 0.00 40.11 3.01
2640 3627 1.449070 GGTCACGGGTTCGATTCCC 60.449 63.158 14.08 14.08 41.41 3.97
2645 3632 4.829588 GGGTTCGATTCCCGTCTC 57.170 61.111 9.87 0.00 39.75 3.36
2646 3633 1.143401 GGGTTCGATTCCCGTCTCC 59.857 63.158 9.87 0.00 39.75 3.71
2647 3634 1.226888 GGTTCGATTCCCGTCTCCG 60.227 63.158 0.00 0.00 39.75 4.63
2648 3635 1.877165 GTTCGATTCCCGTCTCCGC 60.877 63.158 0.00 0.00 39.75 5.54
2649 3636 2.344981 TTCGATTCCCGTCTCCGCA 61.345 57.895 0.00 0.00 39.75 5.69
2650 3637 2.552585 TTCGATTCCCGTCTCCGCAC 62.553 60.000 0.00 0.00 39.75 5.34
2651 3638 2.893398 GATTCCCGTCTCCGCACT 59.107 61.111 0.00 0.00 0.00 4.40
2652 3639 1.218316 GATTCCCGTCTCCGCACTT 59.782 57.895 0.00 0.00 0.00 3.16
2653 3640 0.458669 GATTCCCGTCTCCGCACTTA 59.541 55.000 0.00 0.00 0.00 2.24
2654 3641 0.460311 ATTCCCGTCTCCGCACTTAG 59.540 55.000 0.00 0.00 0.00 2.18
2655 3642 2.202756 CCCGTCTCCGCACTTAGC 60.203 66.667 0.00 0.00 40.87 3.09
2656 3643 2.571757 CCGTCTCCGCACTTAGCA 59.428 61.111 0.00 0.00 46.13 3.49
2657 3644 1.517257 CCGTCTCCGCACTTAGCAG 60.517 63.158 0.00 0.00 46.13 4.24
2658 3645 1.506718 CGTCTCCGCACTTAGCAGA 59.493 57.895 0.00 0.00 46.13 4.26
2659 3646 0.109272 CGTCTCCGCACTTAGCAGAA 60.109 55.000 0.00 0.00 46.13 3.02
2660 3647 1.634702 GTCTCCGCACTTAGCAGAAG 58.365 55.000 0.00 0.00 46.13 2.85
2661 3648 0.532573 TCTCCGCACTTAGCAGAAGG 59.467 55.000 3.72 0.00 46.13 3.46
2662 3649 0.532573 CTCCGCACTTAGCAGAAGGA 59.467 55.000 3.72 0.00 46.13 3.36
2663 3650 1.137872 CTCCGCACTTAGCAGAAGGAT 59.862 52.381 3.72 0.00 46.13 3.24
2664 3651 1.555075 TCCGCACTTAGCAGAAGGATT 59.445 47.619 3.72 0.00 46.13 3.01
2665 3652 2.027192 TCCGCACTTAGCAGAAGGATTT 60.027 45.455 3.72 0.00 46.13 2.17
2666 3653 2.749621 CCGCACTTAGCAGAAGGATTTT 59.250 45.455 3.72 0.00 46.13 1.82
2667 3654 3.181506 CCGCACTTAGCAGAAGGATTTTC 60.182 47.826 3.72 0.00 46.13 2.29
2668 3655 3.436704 CGCACTTAGCAGAAGGATTTTCA 59.563 43.478 3.72 0.00 46.13 2.69
2669 3656 4.436584 CGCACTTAGCAGAAGGATTTTCAG 60.437 45.833 3.72 0.00 46.13 3.02
2670 3657 4.142513 GCACTTAGCAGAAGGATTTTCAGG 60.143 45.833 3.72 0.00 44.79 3.86
2671 3658 5.248640 CACTTAGCAGAAGGATTTTCAGGA 58.751 41.667 3.72 0.00 0.00 3.86
2672 3659 5.884792 CACTTAGCAGAAGGATTTTCAGGAT 59.115 40.000 3.72 0.00 0.00 3.24
2673 3660 7.050377 CACTTAGCAGAAGGATTTTCAGGATA 58.950 38.462 3.72 0.00 0.00 2.59
2674 3661 7.011857 CACTTAGCAGAAGGATTTTCAGGATAC 59.988 40.741 3.72 0.00 0.00 2.24
2699 3686 6.740944 TCCTTCGTGGAATAAGATATTGGA 57.259 37.500 0.00 0.00 42.94 3.53
2700 3687 7.316393 TCCTTCGTGGAATAAGATATTGGAT 57.684 36.000 0.00 0.00 42.94 3.41
2701 3688 7.386851 TCCTTCGTGGAATAAGATATTGGATC 58.613 38.462 0.00 0.00 42.94 3.36
2722 3709 4.801221 CCGCTCGCGCAAAAGCTC 62.801 66.667 20.01 0.00 36.35 4.09
2765 3752 1.196354 CTTTCTTCACTGGAGCAAGCG 59.804 52.381 0.00 0.00 0.00 4.68
2911 4063 6.533730 ACTACAAGTCATTTGAATGGAGTGA 58.466 36.000 10.23 0.00 36.52 3.41
2948 4100 0.325016 TCAGCTCTCTCATGGCAGGA 60.325 55.000 0.46 0.46 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.817634 TGTGTTGCTCCCGTGAAAGG 60.818 55.000 0.00 0.00 0.00 3.11
4 5 1.069022 CATGTGTTGCTCCCGTGAAAG 60.069 52.381 0.00 0.00 0.00 2.62
5 6 0.950836 CATGTGTTGCTCCCGTGAAA 59.049 50.000 0.00 0.00 0.00 2.69
6 7 0.107643 TCATGTGTTGCTCCCGTGAA 59.892 50.000 0.00 0.00 0.00 3.18
7 8 0.602638 GTCATGTGTTGCTCCCGTGA 60.603 55.000 0.00 0.00 0.00 4.35
8 9 0.603707 AGTCATGTGTTGCTCCCGTG 60.604 55.000 0.00 0.00 0.00 4.94
9 10 0.603707 CAGTCATGTGTTGCTCCCGT 60.604 55.000 0.00 0.00 0.00 5.28
10 11 1.915614 GCAGTCATGTGTTGCTCCCG 61.916 60.000 10.22 0.00 35.05 5.14
11 12 0.890542 TGCAGTCATGTGTTGCTCCC 60.891 55.000 15.83 0.00 38.60 4.30
12 13 0.520404 CTGCAGTCATGTGTTGCTCC 59.480 55.000 5.25 0.00 38.60 4.70
13 14 1.233019 ACTGCAGTCATGTGTTGCTC 58.767 50.000 15.25 0.00 38.60 4.26
14 15 1.605710 GAACTGCAGTCATGTGTTGCT 59.394 47.619 21.95 0.00 38.60 3.91
15 16 1.334556 TGAACTGCAGTCATGTGTTGC 59.665 47.619 21.95 10.47 38.30 4.17
16 17 3.065786 ACTTGAACTGCAGTCATGTGTTG 59.934 43.478 21.95 7.81 0.00 3.33
17 18 3.065786 CACTTGAACTGCAGTCATGTGTT 59.934 43.478 30.71 16.46 35.88 3.32
18 19 2.615447 CACTTGAACTGCAGTCATGTGT 59.385 45.455 30.71 21.29 35.88 3.72
19 20 2.874086 TCACTTGAACTGCAGTCATGTG 59.126 45.455 31.81 31.81 39.40 3.21
20 21 3.198409 TCACTTGAACTGCAGTCATGT 57.802 42.857 21.95 21.51 0.00 3.21
21 22 4.556942 TTTCACTTGAACTGCAGTCATG 57.443 40.909 21.95 20.94 33.13 3.07
22 23 5.526115 CAATTTCACTTGAACTGCAGTCAT 58.474 37.500 21.95 5.00 33.13 3.06
23 24 4.734402 GCAATTTCACTTGAACTGCAGTCA 60.734 41.667 21.95 16.54 40.30 3.41
24 25 3.732721 GCAATTTCACTTGAACTGCAGTC 59.267 43.478 21.95 14.06 40.30 3.51
25 26 3.130869 TGCAATTTCACTTGAACTGCAGT 59.869 39.130 15.25 15.25 42.94 4.40
26 27 3.708890 TGCAATTTCACTTGAACTGCAG 58.291 40.909 13.48 13.48 42.94 4.41
27 28 3.797451 TGCAATTTCACTTGAACTGCA 57.203 38.095 17.87 17.87 44.30 4.41
28 29 4.362279 TCTTGCAATTTCACTTGAACTGC 58.638 39.130 14.36 14.36 40.66 4.40
29 30 7.473027 AAATCTTGCAATTTCACTTGAACTG 57.527 32.000 0.00 0.00 33.13 3.16
30 31 7.225341 GGAAAATCTTGCAATTTCACTTGAACT 59.775 33.333 20.10 0.00 35.32 3.01
31 32 7.347448 GGAAAATCTTGCAATTTCACTTGAAC 58.653 34.615 20.10 3.58 35.32 3.18
32 33 6.482973 GGGAAAATCTTGCAATTTCACTTGAA 59.517 34.615 20.10 0.00 34.43 2.69
33 34 5.990996 GGGAAAATCTTGCAATTTCACTTGA 59.009 36.000 20.10 5.08 34.43 3.02
34 35 5.759273 TGGGAAAATCTTGCAATTTCACTTG 59.241 36.000 21.01 0.64 37.37 3.16
35 36 5.927819 TGGGAAAATCTTGCAATTTCACTT 58.072 33.333 21.01 3.83 37.37 3.16
36 37 5.549742 TGGGAAAATCTTGCAATTTCACT 57.450 34.783 21.01 0.00 37.37 3.41
37 38 5.759763 AGTTGGGAAAATCTTGCAATTTCAC 59.240 36.000 20.10 18.16 37.07 3.18
38 39 5.927819 AGTTGGGAAAATCTTGCAATTTCA 58.072 33.333 20.10 4.51 35.32 2.69
39 40 6.866010 AAGTTGGGAAAATCTTGCAATTTC 57.134 33.333 13.30 13.30 33.38 2.17
40 41 6.827762 TCAAAGTTGGGAAAATCTTGCAATTT 59.172 30.769 0.00 0.00 0.00 1.82
41 42 6.355747 TCAAAGTTGGGAAAATCTTGCAATT 58.644 32.000 0.00 0.00 0.00 2.32
42 43 5.927819 TCAAAGTTGGGAAAATCTTGCAAT 58.072 33.333 0.00 0.00 0.00 3.56
43 44 5.350504 TCAAAGTTGGGAAAATCTTGCAA 57.649 34.783 0.00 0.00 0.00 4.08
44 45 5.115480 GTTCAAAGTTGGGAAAATCTTGCA 58.885 37.500 0.00 0.00 0.00 4.08
45 46 4.511454 GGTTCAAAGTTGGGAAAATCTTGC 59.489 41.667 0.00 0.00 0.00 4.01
46 47 5.669477 TGGTTCAAAGTTGGGAAAATCTTG 58.331 37.500 0.00 0.00 0.00 3.02
47 48 5.948742 TGGTTCAAAGTTGGGAAAATCTT 57.051 34.783 0.00 0.00 0.00 2.40
48 49 5.948742 TTGGTTCAAAGTTGGGAAAATCT 57.051 34.783 0.00 0.00 0.00 2.40
49 50 6.202762 GTGATTGGTTCAAAGTTGGGAAAATC 59.797 38.462 7.42 7.42 35.70 2.17
50 51 6.054941 GTGATTGGTTCAAAGTTGGGAAAAT 58.945 36.000 0.00 0.00 35.70 1.82
51 52 5.188751 AGTGATTGGTTCAAAGTTGGGAAAA 59.811 36.000 0.00 0.00 35.70 2.29
52 53 4.714308 AGTGATTGGTTCAAAGTTGGGAAA 59.286 37.500 0.00 0.00 35.70 3.13
53 54 4.285863 AGTGATTGGTTCAAAGTTGGGAA 58.714 39.130 0.00 0.00 35.70 3.97
54 55 3.909732 AGTGATTGGTTCAAAGTTGGGA 58.090 40.909 0.00 0.00 35.70 4.37
55 56 4.670896 AAGTGATTGGTTCAAAGTTGGG 57.329 40.909 0.00 0.00 35.70 4.12
56 57 7.264947 ACTAAAAGTGATTGGTTCAAAGTTGG 58.735 34.615 0.00 0.00 35.70 3.77
57 58 8.190784 AGACTAAAAGTGATTGGTTCAAAGTTG 58.809 33.333 0.00 0.00 35.70 3.16
58 59 8.293699 AGACTAAAAGTGATTGGTTCAAAGTT 57.706 30.769 0.00 0.00 35.70 2.66
59 60 7.881775 AGACTAAAAGTGATTGGTTCAAAGT 57.118 32.000 0.00 0.00 35.70 2.66
60 61 9.237846 GAAAGACTAAAAGTGATTGGTTCAAAG 57.762 33.333 0.00 0.00 35.70 2.77
61 62 8.744652 TGAAAGACTAAAAGTGATTGGTTCAAA 58.255 29.630 0.00 0.00 35.70 2.69
62 63 8.188139 GTGAAAGACTAAAAGTGATTGGTTCAA 58.812 33.333 0.00 0.00 35.70 2.69
63 64 7.201785 GGTGAAAGACTAAAAGTGATTGGTTCA 60.202 37.037 0.00 0.00 0.00 3.18
64 65 7.139392 GGTGAAAGACTAAAAGTGATTGGTTC 58.861 38.462 0.00 0.00 0.00 3.62
78 79 5.186992 TGCTATTGCTACTGGTGAAAGACTA 59.813 40.000 0.00 0.00 40.48 2.59
114 115 5.539574 AGAGAGAGAGAGAGAGAGAGAGATG 59.460 48.000 0.00 0.00 0.00 2.90
128 129 2.171237 CAGGCAGAGAGAGAGAGAGAGA 59.829 54.545 0.00 0.00 0.00 3.10
131 132 2.092753 AGACAGGCAGAGAGAGAGAGAG 60.093 54.545 0.00 0.00 0.00 3.20
132 133 1.915489 AGACAGGCAGAGAGAGAGAGA 59.085 52.381 0.00 0.00 0.00 3.10
133 134 2.092753 AGAGACAGGCAGAGAGAGAGAG 60.093 54.545 0.00 0.00 0.00 3.20
134 135 1.915489 AGAGACAGGCAGAGAGAGAGA 59.085 52.381 0.00 0.00 0.00 3.10
135 136 2.425143 AGAGACAGGCAGAGAGAGAG 57.575 55.000 0.00 0.00 0.00 3.20
136 137 2.897271 AAGAGACAGGCAGAGAGAGA 57.103 50.000 0.00 0.00 0.00 3.10
137 138 3.959535 AAAAGAGACAGGCAGAGAGAG 57.040 47.619 0.00 0.00 0.00 3.20
138 139 3.900601 AGAAAAAGAGACAGGCAGAGAGA 59.099 43.478 0.00 0.00 0.00 3.10
139 140 4.244862 GAGAAAAAGAGACAGGCAGAGAG 58.755 47.826 0.00 0.00 0.00 3.20
140 141 3.643320 TGAGAAAAAGAGACAGGCAGAGA 59.357 43.478 0.00 0.00 0.00 3.10
141 142 4.000331 TGAGAAAAAGAGACAGGCAGAG 58.000 45.455 0.00 0.00 0.00 3.35
142 143 4.130118 GTTGAGAAAAAGAGACAGGCAGA 58.870 43.478 0.00 0.00 0.00 4.26
143 144 3.251972 GGTTGAGAAAAAGAGACAGGCAG 59.748 47.826 0.00 0.00 0.00 4.85
144 145 3.214328 GGTTGAGAAAAAGAGACAGGCA 58.786 45.455 0.00 0.00 0.00 4.75
145 146 3.214328 TGGTTGAGAAAAAGAGACAGGC 58.786 45.455 0.00 0.00 0.00 4.85
146 147 5.048434 GGATTGGTTGAGAAAAAGAGACAGG 60.048 44.000 0.00 0.00 0.00 4.00
840 1651 8.579850 TGGTATGAAAGCACTTGATAGAATTT 57.420 30.769 0.00 0.00 0.00 1.82
884 1695 3.508793 TGTAGTAGTGCTCCTTGTGGTAC 59.491 47.826 0.00 0.00 34.23 3.34
1009 1820 1.153765 GGTACGTGTCGTAAGGGCC 60.154 63.158 0.00 0.00 43.95 5.80
1029 1840 5.049680 ACCAAACATGAAGTTGTCGATGTAC 60.050 40.000 0.00 0.00 41.19 2.90
1092 1903 7.394641 GGAGTGAAAGGAGGAATATTTTCTTGT 59.605 37.037 0.00 0.00 32.28 3.16
1114 1925 3.261897 ATGATCGGAAGAACAGTTGGAGT 59.738 43.478 0.00 0.00 46.25 3.85
1215 2026 1.089920 CCCCTTTCAGACGCAAGATG 58.910 55.000 0.00 0.00 43.62 2.90
1260 2074 1.821136 CTCCCAGTTGGAATGAAAGCC 59.179 52.381 0.00 0.00 44.57 4.35
1284 2098 7.118496 TGAAGTAAATTCAACCACAACCAAT 57.882 32.000 0.00 0.00 45.00 3.16
1965 2779 0.099436 GTATGCGCTTCTTGCAAGGG 59.901 55.000 25.73 18.76 46.87 3.95
2161 3143 1.419762 TGGTGTGCTCATACAGGTTGT 59.580 47.619 0.00 0.00 0.00 3.32
2191 3177 2.989166 GTGCCAATAAGAGCTTGCAAAC 59.011 45.455 0.00 0.00 0.00 2.93
2484 3471 9.103861 GATTGATACCGAGAAAGATTTCTTCTT 57.896 33.333 9.11 0.00 46.84 2.52
2485 3472 7.713073 GGATTGATACCGAGAAAGATTTCTTCT 59.287 37.037 9.11 0.00 46.84 2.85
2486 3473 7.041712 GGGATTGATACCGAGAAAGATTTCTTC 60.042 40.741 9.11 3.72 46.84 2.87
2487 3474 6.768381 GGGATTGATACCGAGAAAGATTTCTT 59.232 38.462 9.11 0.00 46.84 2.52
2489 3476 5.470437 GGGGATTGATACCGAGAAAGATTTC 59.530 44.000 0.00 0.00 37.45 2.17
2490 3477 5.132816 AGGGGATTGATACCGAGAAAGATTT 59.867 40.000 0.00 0.00 0.00 2.17
2491 3478 4.660771 AGGGGATTGATACCGAGAAAGATT 59.339 41.667 0.00 0.00 0.00 2.40
2492 3479 4.235372 AGGGGATTGATACCGAGAAAGAT 58.765 43.478 0.00 0.00 0.00 2.40
2493 3480 3.654273 AGGGGATTGATACCGAGAAAGA 58.346 45.455 0.00 0.00 0.00 2.52
2494 3481 4.130118 CAAGGGGATTGATACCGAGAAAG 58.870 47.826 0.00 0.00 41.83 2.62
2495 3482 3.684413 GCAAGGGGATTGATACCGAGAAA 60.684 47.826 0.00 0.00 41.83 2.52
2496 3483 2.158813 GCAAGGGGATTGATACCGAGAA 60.159 50.000 0.00 0.00 41.83 2.87
2497 3484 1.416401 GCAAGGGGATTGATACCGAGA 59.584 52.381 0.00 0.00 41.83 4.04
2498 3485 1.543429 GGCAAGGGGATTGATACCGAG 60.543 57.143 0.00 0.00 41.83 4.63
2499 3486 0.472471 GGCAAGGGGATTGATACCGA 59.528 55.000 0.00 0.00 41.83 4.69
2500 3487 0.537371 GGGCAAGGGGATTGATACCG 60.537 60.000 0.00 0.00 41.83 4.02
2501 3488 0.178961 GGGGCAAGGGGATTGATACC 60.179 60.000 0.00 0.00 41.83 2.73
2502 3489 0.853530 AGGGGCAAGGGGATTGATAC 59.146 55.000 0.00 0.00 41.83 2.24
2503 3490 1.149101 GAGGGGCAAGGGGATTGATA 58.851 55.000 0.00 0.00 41.83 2.15
2504 3491 0.925720 TGAGGGGCAAGGGGATTGAT 60.926 55.000 0.00 0.00 41.83 2.57
2505 3492 0.925720 ATGAGGGGCAAGGGGATTGA 60.926 55.000 0.00 0.00 41.83 2.57
2506 3493 0.031817 AATGAGGGGCAAGGGGATTG 60.032 55.000 0.00 0.00 42.20 2.67
2507 3494 0.262876 GAATGAGGGGCAAGGGGATT 59.737 55.000 0.00 0.00 0.00 3.01
2508 3495 0.628668 AGAATGAGGGGCAAGGGGAT 60.629 55.000 0.00 0.00 0.00 3.85
2509 3496 0.850883 AAGAATGAGGGGCAAGGGGA 60.851 55.000 0.00 0.00 0.00 4.81
2510 3497 0.041684 AAAGAATGAGGGGCAAGGGG 59.958 55.000 0.00 0.00 0.00 4.79
2511 3498 1.188863 CAAAGAATGAGGGGCAAGGG 58.811 55.000 0.00 0.00 0.00 3.95
2512 3499 2.220653 TCAAAGAATGAGGGGCAAGG 57.779 50.000 0.00 0.00 33.04 3.61
2519 3506 7.227116 GATCCTTCTGATTCTCAAAGAATGAGG 59.773 40.741 13.72 11.35 44.41 3.86
2520 3507 7.227116 GGATCCTTCTGATTCTCAAAGAATGAG 59.773 40.741 3.84 8.14 44.41 2.90
2521 3508 7.052873 GGATCCTTCTGATTCTCAAAGAATGA 58.947 38.462 3.84 0.00 44.41 2.57
2522 3509 7.055378 AGGATCCTTCTGATTCTCAAAGAATG 58.945 38.462 9.02 0.00 44.41 2.67
2523 3510 7.210618 AGGATCCTTCTGATTCTCAAAGAAT 57.789 36.000 9.02 1.92 46.84 2.40
2524 3511 6.633325 AGGATCCTTCTGATTCTCAAAGAA 57.367 37.500 9.02 0.00 33.73 2.52
2525 3512 6.633325 AAGGATCCTTCTGATTCTCAAAGA 57.367 37.500 21.89 0.00 38.45 2.52
2526 3513 7.413877 CGAAAAGGATCCTTCTGATTCTCAAAG 60.414 40.741 27.20 9.97 38.45 2.77
2527 3514 6.372659 CGAAAAGGATCCTTCTGATTCTCAAA 59.627 38.462 27.20 0.00 38.45 2.69
2528 3515 5.877012 CGAAAAGGATCCTTCTGATTCTCAA 59.123 40.000 27.20 0.00 38.45 3.02
2529 3516 5.187772 TCGAAAAGGATCCTTCTGATTCTCA 59.812 40.000 27.20 12.66 38.45 3.27
2530 3517 5.665459 TCGAAAAGGATCCTTCTGATTCTC 58.335 41.667 27.20 13.16 38.45 2.87
2531 3518 5.188751 ACTCGAAAAGGATCCTTCTGATTCT 59.811 40.000 27.20 7.13 41.42 2.40
2532 3519 5.423886 ACTCGAAAAGGATCCTTCTGATTC 58.576 41.667 27.20 23.01 34.84 2.52
2533 3520 5.428184 ACTCGAAAAGGATCCTTCTGATT 57.572 39.130 27.20 17.36 34.84 2.57
2534 3521 5.428184 AACTCGAAAAGGATCCTTCTGAT 57.572 39.130 27.20 13.74 34.84 2.90
2535 3522 4.891992 AACTCGAAAAGGATCCTTCTGA 57.108 40.909 27.20 21.38 34.84 3.27
2536 3523 4.393371 GGAAACTCGAAAAGGATCCTTCTG 59.607 45.833 27.20 18.60 34.84 3.02
2537 3524 4.041691 TGGAAACTCGAAAAGGATCCTTCT 59.958 41.667 27.20 14.65 35.77 2.85
2538 3525 4.324267 TGGAAACTCGAAAAGGATCCTTC 58.676 43.478 27.20 15.03 35.77 3.46
2539 3526 4.202472 ACTGGAAACTCGAAAAGGATCCTT 60.202 41.667 21.89 21.89 35.77 3.36
2540 3527 3.328050 ACTGGAAACTCGAAAAGGATCCT 59.672 43.478 9.02 9.02 35.77 3.24
2541 3528 3.676093 ACTGGAAACTCGAAAAGGATCC 58.324 45.455 2.48 2.48 35.48 3.36
2542 3529 5.470437 AGAAACTGGAAACTCGAAAAGGATC 59.530 40.000 0.00 0.00 0.00 3.36
2543 3530 5.239525 CAGAAACTGGAAACTCGAAAAGGAT 59.760 40.000 0.00 0.00 0.00 3.24
2544 3531 4.574828 CAGAAACTGGAAACTCGAAAAGGA 59.425 41.667 0.00 0.00 0.00 3.36
2545 3532 4.848757 CAGAAACTGGAAACTCGAAAAGG 58.151 43.478 0.00 0.00 0.00 3.11
2573 3560 1.034838 ACTGCTCTACTCCGCTCTGG 61.035 60.000 0.00 0.00 40.09 3.86
2574 3561 0.814457 AACTGCTCTACTCCGCTCTG 59.186 55.000 0.00 0.00 0.00 3.35
2575 3562 1.203523 CAAACTGCTCTACTCCGCTCT 59.796 52.381 0.00 0.00 0.00 4.09
2576 3563 1.634702 CAAACTGCTCTACTCCGCTC 58.365 55.000 0.00 0.00 0.00 5.03
2577 3564 0.247736 CCAAACTGCTCTACTCCGCT 59.752 55.000 0.00 0.00 0.00 5.52
2578 3565 0.037232 ACCAAACTGCTCTACTCCGC 60.037 55.000 0.00 0.00 0.00 5.54
2579 3566 2.735762 GCTACCAAACTGCTCTACTCCG 60.736 54.545 0.00 0.00 0.00 4.63
2580 3567 2.498078 AGCTACCAAACTGCTCTACTCC 59.502 50.000 0.00 0.00 30.41 3.85
2581 3568 3.776340 GAGCTACCAAACTGCTCTACTC 58.224 50.000 6.92 0.00 46.69 2.59
2582 3569 3.878160 GAGCTACCAAACTGCTCTACT 57.122 47.619 6.92 0.00 46.69 2.57
2587 3574 0.679505 TCGTGAGCTACCAAACTGCT 59.320 50.000 0.00 0.00 40.02 4.24
2588 3575 1.071605 CTCGTGAGCTACCAAACTGC 58.928 55.000 0.00 0.00 0.00 4.40
2589 3576 1.714794 CCTCGTGAGCTACCAAACTG 58.285 55.000 0.00 0.00 0.00 3.16
2590 3577 0.037232 GCCTCGTGAGCTACCAAACT 60.037 55.000 0.00 0.00 0.00 2.66
2591 3578 0.037232 AGCCTCGTGAGCTACCAAAC 60.037 55.000 0.00 0.00 39.29 2.93
2592 3579 0.246635 GAGCCTCGTGAGCTACCAAA 59.753 55.000 0.00 0.00 41.75 3.28
2593 3580 1.605058 GGAGCCTCGTGAGCTACCAA 61.605 60.000 0.00 0.00 41.75 3.67
2594 3581 2.052690 GGAGCCTCGTGAGCTACCA 61.053 63.158 0.00 0.00 41.75 3.25
2595 3582 0.465824 TAGGAGCCTCGTGAGCTACC 60.466 60.000 0.00 7.16 42.62 3.18
2596 3583 1.065851 GTTAGGAGCCTCGTGAGCTAC 59.934 57.143 0.00 2.96 41.75 3.58
2597 3584 1.390565 GTTAGGAGCCTCGTGAGCTA 58.609 55.000 0.00 0.00 41.75 3.32
2598 3585 1.324005 GGTTAGGAGCCTCGTGAGCT 61.324 60.000 0.00 0.00 45.23 4.09
2599 3586 1.142097 GGTTAGGAGCCTCGTGAGC 59.858 63.158 0.00 0.00 0.00 4.26
2600 3587 1.134965 CAAGGTTAGGAGCCTCGTGAG 60.135 57.143 0.00 0.00 34.81 3.51
2601 3588 0.895530 CAAGGTTAGGAGCCTCGTGA 59.104 55.000 0.00 0.00 34.81 4.35
2602 3589 0.895530 TCAAGGTTAGGAGCCTCGTG 59.104 55.000 0.00 0.00 34.81 4.35
2603 3590 1.187087 CTCAAGGTTAGGAGCCTCGT 58.813 55.000 0.00 0.00 34.81 4.18
2604 3591 0.461961 CCTCAAGGTTAGGAGCCTCG 59.538 60.000 0.00 0.00 36.08 4.63
2616 3603 1.374252 CGAACCCGTGACCTCAAGG 60.374 63.158 0.55 0.55 43.72 3.61
2617 3604 0.246635 ATCGAACCCGTGACCTCAAG 59.753 55.000 0.00 0.00 37.05 3.02
2618 3605 0.682852 AATCGAACCCGTGACCTCAA 59.317 50.000 0.00 0.00 37.05 3.02
2619 3606 0.245539 GAATCGAACCCGTGACCTCA 59.754 55.000 0.00 0.00 37.05 3.86
2620 3607 0.459759 GGAATCGAACCCGTGACCTC 60.460 60.000 0.00 0.00 37.05 3.85
2621 3608 1.595357 GGAATCGAACCCGTGACCT 59.405 57.895 0.00 0.00 37.05 3.85
2622 3609 1.449070 GGGAATCGAACCCGTGACC 60.449 63.158 13.87 0.00 37.85 4.02
2623 3610 4.196965 GGGAATCGAACCCGTGAC 57.803 61.111 13.87 0.00 37.85 3.67
2628 3615 1.143401 GGAGACGGGAATCGAACCC 59.857 63.158 17.69 17.69 42.43 4.11
2629 3616 4.829588 GGAGACGGGAATCGAACC 57.170 61.111 0.00 0.00 42.43 3.62
2646 3633 3.436704 TGAAAATCCTTCTGCTAAGTGCG 59.563 43.478 0.00 0.00 46.63 5.34
2647 3634 4.142513 CCTGAAAATCCTTCTGCTAAGTGC 60.143 45.833 0.00 0.00 43.25 4.40
2648 3635 5.248640 TCCTGAAAATCCTTCTGCTAAGTG 58.751 41.667 0.00 0.00 0.00 3.16
2649 3636 5.505181 TCCTGAAAATCCTTCTGCTAAGT 57.495 39.130 0.00 0.00 0.00 2.24
2650 3637 7.278875 AGTATCCTGAAAATCCTTCTGCTAAG 58.721 38.462 0.00 0.00 0.00 2.18
2651 3638 7.200434 AGTATCCTGAAAATCCTTCTGCTAA 57.800 36.000 0.00 0.00 0.00 3.09
2652 3639 6.814954 AGTATCCTGAAAATCCTTCTGCTA 57.185 37.500 0.00 0.00 0.00 3.49
2653 3640 5.707066 AGTATCCTGAAAATCCTTCTGCT 57.293 39.130 0.00 0.00 0.00 4.24
2654 3641 5.298026 GGAAGTATCCTGAAAATCCTTCTGC 59.702 44.000 0.00 0.00 42.93 4.26
2655 3642 6.934048 GGAAGTATCCTGAAAATCCTTCTG 57.066 41.667 0.00 0.00 42.93 3.02
2677 3664 7.161404 TGATCCAATATCTTATTCCACGAAGG 58.839 38.462 0.00 0.00 39.47 3.46
2678 3665 8.499162 GTTGATCCAATATCTTATTCCACGAAG 58.501 37.037 0.00 0.00 0.00 3.79
2679 3666 7.444183 GGTTGATCCAATATCTTATTCCACGAA 59.556 37.037 0.00 0.00 35.97 3.85
2680 3667 6.934645 GGTTGATCCAATATCTTATTCCACGA 59.065 38.462 0.00 0.00 35.97 4.35
2681 3668 6.149474 GGGTTGATCCAATATCTTATTCCACG 59.851 42.308 0.00 0.00 38.11 4.94
2682 3669 6.149474 CGGGTTGATCCAATATCTTATTCCAC 59.851 42.308 0.00 0.00 38.11 4.02
2683 3670 6.237901 CGGGTTGATCCAATATCTTATTCCA 58.762 40.000 0.00 0.00 38.11 3.53
2684 3671 5.123979 GCGGGTTGATCCAATATCTTATTCC 59.876 44.000 0.00 0.00 38.11 3.01
2685 3672 5.940470 AGCGGGTTGATCCAATATCTTATTC 59.060 40.000 0.00 0.00 38.11 1.75
2686 3673 5.880901 AGCGGGTTGATCCAATATCTTATT 58.119 37.500 0.00 0.00 38.11 1.40
2687 3674 5.491982 GAGCGGGTTGATCCAATATCTTAT 58.508 41.667 0.00 0.00 38.11 1.73
2688 3675 4.560716 CGAGCGGGTTGATCCAATATCTTA 60.561 45.833 0.00 0.00 38.11 2.10
2689 3676 3.744660 GAGCGGGTTGATCCAATATCTT 58.255 45.455 0.00 0.00 38.11 2.40
2690 3677 2.289072 CGAGCGGGTTGATCCAATATCT 60.289 50.000 0.00 0.00 38.11 1.98
2691 3678 2.069273 CGAGCGGGTTGATCCAATATC 58.931 52.381 0.00 0.00 38.11 1.63
2692 3679 1.878102 GCGAGCGGGTTGATCCAATAT 60.878 52.381 0.00 0.00 38.11 1.28
2693 3680 0.531974 GCGAGCGGGTTGATCCAATA 60.532 55.000 0.00 0.00 38.11 1.90
2694 3681 1.819632 GCGAGCGGGTTGATCCAAT 60.820 57.895 0.00 0.00 38.11 3.16
2695 3682 2.435938 GCGAGCGGGTTGATCCAA 60.436 61.111 0.00 0.00 38.11 3.53
2696 3683 4.812476 CGCGAGCGGGTTGATCCA 62.812 66.667 9.90 0.00 38.11 3.41
2722 3709 6.574350 AGGAAATGAGTACTCTATTTGGTCG 58.426 40.000 25.06 0.00 0.00 4.79
2765 3752 0.543277 TCCATCTCCATGCCTGTGTC 59.457 55.000 0.00 0.00 0.00 3.67
2911 4063 5.186198 AGCTGACTGTTGAACAACTTTACT 58.814 37.500 16.70 6.14 41.67 2.24
2948 4100 9.523168 GTAGTATGATTTAGACCTCTGATACCT 57.477 37.037 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.