Multiple sequence alignment - TraesCS6D01G153400

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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 TraesCS6D01G153400 chr6D 100.000 5945 0 0 1 5945 127373824 127379768 0.000000e+00 10979
1 TraesCS6D01G153400 chr6B 93.155 2761 100 33 3247 5945 226393607 226396340 0.000000e+00 3969
2 TraesCS6D01G153400 chr6B 91.265 2736 161 50 454 3165 226390893 226393574 0.000000e+00 3657
3 TraesCS6D01G153400 chr6B 82.203 236 41 1 176 411 226390585 226390819 1.010000e-47 202
4 TraesCS6D01G153400 chr6B 95.294 85 4 0 3158 3242 137385852 137385768 1.040000e-27 135
5 TraesCS6D01G153400 chr6B 92.941 85 6 0 3158 3242 552501494 552501410 2.250000e-24 124
6 TraesCS6D01G153400 chr6B 92.941 85 6 0 3158 3242 632187380 632187296 2.250000e-24 124
7 TraesCS6D01G153400 chr6A 92.177 2301 116 27 93 2357 150987871 150985599 0.000000e+00 3193
8 TraesCS6D01G153400 chr6A 95.476 1923 62 10 2908 4809 150984950 150983032 0.000000e+00 3046
9 TraesCS6D01G153400 chr6A 89.252 1163 50 25 4840 5945 150983032 150981888 0.000000e+00 1386
10 TraesCS6D01G153400 chr6A 92.527 562 11 10 2356 2914 150985503 150984970 0.000000e+00 776
11 TraesCS6D01G153400 chr6A 90.323 93 9 0 3151 3243 391627237 391627145 8.090000e-24 122
12 TraesCS6D01G153400 chr7D 74.564 401 88 10 5550 5943 515236276 515236669 4.770000e-36 163
13 TraesCS6D01G153400 chr7D 74.010 404 85 13 5550 5943 515220070 515220463 4.800000e-31 147
14 TraesCS6D01G153400 chr7D 73.762 404 86 13 5550 5943 514093770 514093377 2.230000e-29 141
15 TraesCS6D01G153400 chr7B 74.752 404 82 13 5550 5943 544882580 544882187 4.770000e-36 163
16 TraesCS6D01G153400 chr7A 73.945 403 87 11 5550 5943 587519894 587519501 4.800000e-31 147
17 TraesCS6D01G153400 chr7A 73.945 403 87 11 5550 5943 588739013 588739406 4.800000e-31 147
18 TraesCS6D01G153400 chr7A 73.449 403 87 13 5551 5943 586692281 586692673 3.740000e-27 134
19 TraesCS6D01G153400 chr7A 92.135 89 7 0 3154 3242 84745732 84745820 6.250000e-25 126
20 TraesCS6D01G153400 chr4B 94.318 88 5 0 3159 3246 92663231 92663318 1.040000e-27 135
21 TraesCS6D01G153400 chr3D 92.135 89 7 0 3157 3245 5400427 5400339 6.250000e-25 126
22 TraesCS6D01G153400 chr2B 92.135 89 7 0 3154 3242 3463084 3462996 6.250000e-25 126


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 TraesCS6D01G153400 chr6D 127373824 127379768 5944 False 10979.000000 10979 100.000000 1 5945 1 chr6D.!!$F1 5944
1 TraesCS6D01G153400 chr6B 226390585 226396340 5755 False 2609.333333 3969 88.874333 176 5945 3 chr6B.!!$F1 5769
2 TraesCS6D01G153400 chr6A 150981888 150987871 5983 True 2100.250000 3193 92.358000 93 5945 4 chr6A.!!$R2 5852

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
955 1013 0.108424 CCTCCGAGCAAACCAGAGAG 60.108 60.000 0.0 0.0 0.0 3.20 F
1246 1304 0.033011 ACTCGTCCTGCCCATCTACT 60.033 55.000 0.0 0.0 0.0 2.57 F
1664 1741 0.391130 TGTTCAGCCCGTAGTGATGC 60.391 55.000 0.0 0.0 0.0 3.91 F
2284 2369 1.083401 CGCGTGAACTGTGTGCTTC 60.083 57.895 0.0 0.0 0.0 3.86 F
4147 4362 0.950555 AGAGCAAAGCGACGCATCAA 60.951 50.000 23.7 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2514 2697 0.033920 ACGACTGAACAGCATGCAGA 59.966 50.000 21.98 0.0 42.53 4.26 R
2723 2906 8.918202 TCAGACAGGACACTAAAATAAACATT 57.082 30.769 0.00 0.0 0.00 2.71 R
3652 3865 8.527567 AAGAGAAGAATTGAACTAGAAACGAG 57.472 34.615 0.00 0.0 0.00 4.18 R
4192 4407 0.605083 AAAACGTACTCCCTCCGTCC 59.395 55.000 0.00 0.0 32.95 4.79 R
5492 5796 1.588403 CTCGCATGCCTCTGACTCG 60.588 63.158 13.15 0.0 0.00 4.18 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
22 23 4.450053 ACAATGAGAAGATCAAGCTAGCC 58.550 43.478 12.13 0.00 42.53 3.93
23 24 4.080695 ACAATGAGAAGATCAAGCTAGCCA 60.081 41.667 12.13 0.00 42.53 4.75
24 25 4.767578 ATGAGAAGATCAAGCTAGCCAA 57.232 40.909 12.13 0.00 42.53 4.52
25 26 4.558226 TGAGAAGATCAAGCTAGCCAAA 57.442 40.909 12.13 0.00 34.02 3.28
26 27 5.108187 TGAGAAGATCAAGCTAGCCAAAT 57.892 39.130 12.13 1.70 34.02 2.32
27 28 5.121811 TGAGAAGATCAAGCTAGCCAAATC 58.878 41.667 12.13 11.49 34.02 2.17
28 29 4.125703 AGAAGATCAAGCTAGCCAAATCG 58.874 43.478 12.13 0.00 0.00 3.34
29 30 3.550437 AGATCAAGCTAGCCAAATCGT 57.450 42.857 12.13 0.08 0.00 3.73
30 31 3.878778 AGATCAAGCTAGCCAAATCGTT 58.121 40.909 12.13 0.00 0.00 3.85
31 32 3.624861 AGATCAAGCTAGCCAAATCGTTG 59.375 43.478 12.13 7.68 34.25 4.10
32 33 1.468520 TCAAGCTAGCCAAATCGTTGC 59.531 47.619 12.13 0.00 33.01 4.17
33 34 1.470098 CAAGCTAGCCAAATCGTTGCT 59.530 47.619 12.13 0.00 33.01 3.91
34 35 2.677836 CAAGCTAGCCAAATCGTTGCTA 59.322 45.455 12.13 0.00 33.01 3.49
35 36 2.280628 AGCTAGCCAAATCGTTGCTAC 58.719 47.619 12.13 0.00 33.01 3.58
36 37 2.093447 AGCTAGCCAAATCGTTGCTACT 60.093 45.455 12.13 0.00 33.01 2.57
37 38 2.678336 GCTAGCCAAATCGTTGCTACTT 59.322 45.455 2.29 0.00 33.01 2.24
38 39 3.127030 GCTAGCCAAATCGTTGCTACTTT 59.873 43.478 2.29 0.00 33.01 2.66
39 40 3.831715 AGCCAAATCGTTGCTACTTTC 57.168 42.857 0.00 0.00 33.01 2.62
40 41 2.488153 AGCCAAATCGTTGCTACTTTCC 59.512 45.455 0.00 0.00 33.01 3.13
41 42 2.227865 GCCAAATCGTTGCTACTTTCCA 59.772 45.455 0.00 0.00 33.01 3.53
42 43 3.305064 GCCAAATCGTTGCTACTTTCCAA 60.305 43.478 0.00 0.00 33.01 3.53
43 44 4.618227 GCCAAATCGTTGCTACTTTCCAAT 60.618 41.667 0.00 0.00 33.01 3.16
44 45 5.095490 CCAAATCGTTGCTACTTTCCAATC 58.905 41.667 0.00 0.00 33.01 2.67
45 46 4.965119 AATCGTTGCTACTTTCCAATCC 57.035 40.909 0.00 0.00 0.00 3.01
46 47 3.410631 TCGTTGCTACTTTCCAATCCA 57.589 42.857 0.00 0.00 0.00 3.41
47 48 3.334691 TCGTTGCTACTTTCCAATCCAG 58.665 45.455 0.00 0.00 0.00 3.86
48 49 2.159517 CGTTGCTACTTTCCAATCCAGC 60.160 50.000 0.00 0.00 0.00 4.85
49 50 2.128771 TGCTACTTTCCAATCCAGCC 57.871 50.000 0.00 0.00 0.00 4.85
50 51 1.017387 GCTACTTTCCAATCCAGCCG 58.983 55.000 0.00 0.00 0.00 5.52
51 52 1.406887 GCTACTTTCCAATCCAGCCGA 60.407 52.381 0.00 0.00 0.00 5.54
52 53 2.555199 CTACTTTCCAATCCAGCCGAG 58.445 52.381 0.00 0.00 0.00 4.63
53 54 0.984230 ACTTTCCAATCCAGCCGAGA 59.016 50.000 0.00 0.00 0.00 4.04
54 55 1.561542 ACTTTCCAATCCAGCCGAGAT 59.438 47.619 0.00 0.00 0.00 2.75
55 56 2.771943 ACTTTCCAATCCAGCCGAGATA 59.228 45.455 0.00 0.00 0.00 1.98
56 57 3.181461 ACTTTCCAATCCAGCCGAGATAG 60.181 47.826 0.00 0.00 0.00 2.08
57 58 2.381752 TCCAATCCAGCCGAGATAGA 57.618 50.000 0.00 0.00 0.00 1.98
58 59 2.894731 TCCAATCCAGCCGAGATAGAT 58.105 47.619 0.00 0.00 0.00 1.98
59 60 2.828520 TCCAATCCAGCCGAGATAGATC 59.171 50.000 0.00 0.00 0.00 2.75
60 61 2.564504 CCAATCCAGCCGAGATAGATCA 59.435 50.000 0.00 0.00 0.00 2.92
61 62 3.583806 CAATCCAGCCGAGATAGATCAC 58.416 50.000 0.00 0.00 0.00 3.06
62 63 2.364972 TCCAGCCGAGATAGATCACA 57.635 50.000 0.00 0.00 0.00 3.58
63 64 2.666317 TCCAGCCGAGATAGATCACAA 58.334 47.619 0.00 0.00 0.00 3.33
64 65 2.625314 TCCAGCCGAGATAGATCACAAG 59.375 50.000 0.00 0.00 0.00 3.16
65 66 2.402305 CAGCCGAGATAGATCACAAGC 58.598 52.381 0.00 0.00 0.00 4.01
66 67 1.342819 AGCCGAGATAGATCACAAGCC 59.657 52.381 0.00 0.00 0.00 4.35
67 68 1.606737 GCCGAGATAGATCACAAGCCC 60.607 57.143 0.00 0.00 0.00 5.19
68 69 1.688735 CCGAGATAGATCACAAGCCCA 59.311 52.381 0.00 0.00 0.00 5.36
69 70 2.546795 CCGAGATAGATCACAAGCCCAC 60.547 54.545 0.00 0.00 0.00 4.61
70 71 2.363680 CGAGATAGATCACAAGCCCACT 59.636 50.000 0.00 0.00 0.00 4.00
71 72 3.181471 CGAGATAGATCACAAGCCCACTT 60.181 47.826 0.00 0.00 36.19 3.16
72 73 4.681781 CGAGATAGATCACAAGCCCACTTT 60.682 45.833 0.00 0.00 32.29 2.66
73 74 4.775236 AGATAGATCACAAGCCCACTTTC 58.225 43.478 0.00 0.00 32.29 2.62
74 75 2.957402 AGATCACAAGCCCACTTTCA 57.043 45.000 0.00 0.00 32.29 2.69
75 76 3.228188 AGATCACAAGCCCACTTTCAA 57.772 42.857 0.00 0.00 32.29 2.69
76 77 3.152341 AGATCACAAGCCCACTTTCAAG 58.848 45.455 0.00 0.00 32.29 3.02
77 78 2.727123 TCACAAGCCCACTTTCAAGA 57.273 45.000 0.00 0.00 32.29 3.02
78 79 2.297701 TCACAAGCCCACTTTCAAGAC 58.702 47.619 0.00 0.00 32.29 3.01
79 80 2.023673 CACAAGCCCACTTTCAAGACA 58.976 47.619 0.00 0.00 32.29 3.41
80 81 2.426738 CACAAGCCCACTTTCAAGACAA 59.573 45.455 0.00 0.00 32.29 3.18
81 82 3.068590 CACAAGCCCACTTTCAAGACAAT 59.931 43.478 0.00 0.00 32.29 2.71
82 83 3.706086 ACAAGCCCACTTTCAAGACAATT 59.294 39.130 0.00 0.00 32.29 2.32
83 84 4.892934 ACAAGCCCACTTTCAAGACAATTA 59.107 37.500 0.00 0.00 32.29 1.40
84 85 5.362430 ACAAGCCCACTTTCAAGACAATTAA 59.638 36.000 0.00 0.00 32.29 1.40
85 86 6.041979 ACAAGCCCACTTTCAAGACAATTAAT 59.958 34.615 0.00 0.00 32.29 1.40
86 87 6.029346 AGCCCACTTTCAAGACAATTAATG 57.971 37.500 0.00 0.00 0.00 1.90
87 88 6.041979 AAGCCCACTTTCAAGACAATTAATGT 59.958 34.615 0.00 0.00 37.74 2.71
88 89 6.719370 AGCCCACTTTCAAGACAATTAATGTA 59.281 34.615 0.00 0.00 44.12 2.29
89 90 7.397192 AGCCCACTTTCAAGACAATTAATGTAT 59.603 33.333 0.00 0.00 44.12 2.29
90 91 7.489113 GCCCACTTTCAAGACAATTAATGTATG 59.511 37.037 0.00 0.00 44.12 2.39
91 92 7.975616 CCCACTTTCAAGACAATTAATGTATGG 59.024 37.037 0.00 0.00 44.12 2.74
148 149 1.613437 CGTTTTTCAAGAGGCATGGGT 59.387 47.619 0.00 0.00 0.00 4.51
153 154 0.325933 TCAAGAGGCATGGGTCTGTG 59.674 55.000 0.00 0.00 0.00 3.66
171 172 3.843304 GCTAGCGGAGGCAGTCTA 58.157 61.111 0.00 0.00 43.41 2.59
181 182 1.079336 GGCAGTCTAACGGTGGACC 60.079 63.158 13.94 0.00 35.92 4.46
272 273 2.798680 CTAGATGCACACGTCCTGTAC 58.201 52.381 0.00 0.00 31.66 2.90
283 284 1.684734 TCCTGTACGAAGGAGGCCC 60.685 63.158 0.00 0.00 41.60 5.80
340 341 6.495181 TGAAAGCATAAATCCACCTTACCAAA 59.505 34.615 0.00 0.00 0.00 3.28
359 360 4.258543 CAAATTAGCCTCGGACCAAACTA 58.741 43.478 0.00 0.00 0.00 2.24
365 366 1.139058 CCTCGGACCAAACTATGAGGG 59.861 57.143 2.27 0.00 39.42 4.30
559 599 2.379005 TGCAGGCCGAGATCGATATAT 58.621 47.619 0.00 0.00 43.02 0.86
582 622 3.458189 ACGATTCATGAGATCCGGTTTC 58.542 45.455 0.00 0.00 0.00 2.78
583 623 2.472861 CGATTCATGAGATCCGGTTTCG 59.527 50.000 0.00 0.00 0.00 3.46
589 629 2.995283 TGAGATCCGGTTTCGAGACTA 58.005 47.619 0.00 0.00 39.00 2.59
592 641 4.755629 TGAGATCCGGTTTCGAGACTATAG 59.244 45.833 0.00 0.00 39.00 1.31
596 645 2.601741 CCGGTTTCGAGACTATAGACGC 60.602 54.545 6.78 0.88 39.00 5.19
597 646 2.601741 CGGTTTCGAGACTATAGACGCC 60.602 54.545 6.78 5.57 39.00 5.68
600 649 3.472283 TTCGAGACTATAGACGCCTCT 57.528 47.619 6.78 0.00 0.00 3.69
632 681 3.510360 TGACAACTCTACTAGGGTTGCTC 59.490 47.826 23.56 19.58 42.55 4.26
642 691 3.444388 ACTAGGGTTGCTCTTAAGAGACG 59.556 47.826 32.16 10.90 44.74 4.18
652 701 4.740934 GCTCTTAAGAGACGGGCAACATAT 60.741 45.833 32.16 0.00 44.74 1.78
690 739 3.934068 ACAATCGGTGTCTTTTATCCGT 58.066 40.909 0.00 0.00 42.95 4.69
691 740 5.075858 ACAATCGGTGTCTTTTATCCGTA 57.924 39.130 0.00 0.00 42.95 4.02
834 892 1.285950 CGAGAAGGACACGTCAGCA 59.714 57.895 0.00 0.00 0.00 4.41
939 997 2.750888 CGGCTTTTACTGCGCCCTC 61.751 63.158 4.18 0.00 40.70 4.30
951 1009 2.747855 GCCCTCCGAGCAAACCAG 60.748 66.667 0.00 0.00 0.00 4.00
952 1010 3.068881 CCCTCCGAGCAAACCAGA 58.931 61.111 0.00 0.00 0.00 3.86
953 1011 1.078848 CCCTCCGAGCAAACCAGAG 60.079 63.158 0.00 0.00 0.00 3.35
954 1012 1.544825 CCCTCCGAGCAAACCAGAGA 61.545 60.000 0.00 0.00 0.00 3.10
955 1013 0.108424 CCTCCGAGCAAACCAGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
956 1014 0.108424 CTCCGAGCAAACCAGAGAGG 60.108 60.000 0.00 0.00 45.67 3.69
957 1015 0.541998 TCCGAGCAAACCAGAGAGGA 60.542 55.000 0.00 0.00 41.22 3.71
958 1016 0.108424 CCGAGCAAACCAGAGAGGAG 60.108 60.000 0.00 0.00 41.22 3.69
959 1017 0.108424 CGAGCAAACCAGAGAGGAGG 60.108 60.000 0.00 0.00 41.22 4.30
963 1021 1.338579 GCAAACCAGAGAGGAGGACAG 60.339 57.143 0.00 0.00 41.22 3.51
988 1046 3.243892 GACGCGCGCAAGAGAGAG 61.244 66.667 32.58 14.51 39.71 3.20
990 1048 3.243892 CGCGCGCAAGAGAGAGAC 61.244 66.667 32.61 0.00 39.71 3.36
991 1049 2.126307 GCGCGCAAGAGAGAGACA 60.126 61.111 29.10 0.00 40.82 3.41
992 1050 2.440569 GCGCGCAAGAGAGAGACAC 61.441 63.158 29.10 0.00 40.82 3.67
993 1051 1.211449 CGCGCAAGAGAGAGACACT 59.789 57.895 8.75 0.00 40.82 3.55
994 1052 0.448197 CGCGCAAGAGAGAGACACTA 59.552 55.000 8.75 0.00 40.82 2.74
1232 1290 0.830444 TGCTTCCACCAGGTACTCGT 60.830 55.000 0.00 0.00 34.60 4.18
1246 1304 0.033011 ACTCGTCCTGCCCATCTACT 60.033 55.000 0.00 0.00 0.00 2.57
1311 1369 6.088883 GCTTAGAGTAGAGCGAGCATAATTTC 59.911 42.308 0.00 0.00 0.00 2.17
1312 1370 4.877282 AGAGTAGAGCGAGCATAATTTCC 58.123 43.478 0.00 0.00 0.00 3.13
1362 1420 6.098124 TCGATTGAATGCTTGGGGAATTAATT 59.902 34.615 0.00 0.00 0.00 1.40
1403 1461 3.461946 GTGACTAGCACTTTGTGATGC 57.538 47.619 9.26 0.00 44.27 3.91
1404 1462 2.807967 GTGACTAGCACTTTGTGATGCA 59.192 45.455 9.26 0.00 44.59 3.96
1405 1463 3.069289 TGACTAGCACTTTGTGATGCAG 58.931 45.455 1.52 0.00 44.59 4.41
1655 1732 1.934589 TAATCGTGATGTTCAGCCCG 58.065 50.000 0.00 0.00 0.00 6.13
1664 1741 0.391130 TGTTCAGCCCGTAGTGATGC 60.391 55.000 0.00 0.00 0.00 3.91
1776 1859 3.866651 TGGTCATGTTGGTTTTTGTTGG 58.133 40.909 0.00 0.00 0.00 3.77
1782 1865 7.875554 GGTCATGTTGGTTTTTGTTGGTTATAT 59.124 33.333 0.00 0.00 0.00 0.86
1806 1889 2.905075 TCTGGTTTATCATGGCACGAG 58.095 47.619 0.00 0.00 0.00 4.18
1987 2072 9.479549 TTCTGGAGAAGCAAAGGAATATTTTAT 57.520 29.630 0.00 0.00 0.00 1.40
2146 2231 2.029838 ACTGTGGATTCATCTTCCGC 57.970 50.000 0.00 0.00 42.83 5.54
2207 2292 1.425066 TCTTTGACCATGCCCTGTCTT 59.575 47.619 2.22 0.00 32.67 3.01
2228 2313 6.021626 GTCTTGATACAACTCGACGTTATGAC 60.022 42.308 0.00 0.00 33.63 3.06
2240 2325 4.499399 CGACGTTATGACCAAGTATGTCAG 59.501 45.833 0.00 0.00 45.20 3.51
2242 2327 6.032956 ACGTTATGACCAAGTATGTCAGAA 57.967 37.500 0.00 0.00 45.20 3.02
2284 2369 1.083401 CGCGTGAACTGTGTGCTTC 60.083 57.895 0.00 0.00 0.00 3.86
2302 2387 6.716628 TGTGCTTCTATGTTCTCCAGAAAATT 59.283 34.615 0.00 0.00 34.12 1.82
2385 2568 4.979335 AGCCTGGCTAATAAGAAGATTCC 58.021 43.478 21.98 0.00 36.99 3.01
2408 2591 5.334879 CCTTTTTATGGTCATATGGCTACGC 60.335 44.000 7.36 0.00 0.00 4.42
2413 2596 3.616219 TGGTCATATGGCTACGCTTTTT 58.384 40.909 7.36 0.00 0.00 1.94
2420 2603 3.485947 TGGCTACGCTTTTTGCTTATG 57.514 42.857 0.00 0.00 40.11 1.90
2929 3141 3.805207 GTGTGTTACACTGGAACCTCTT 58.195 45.455 16.79 0.00 45.27 2.85
3152 3364 7.609760 TGTCGACACATCTTTGCTAATTAAT 57.390 32.000 15.76 0.00 0.00 1.40
3287 3499 4.946784 AACCTTGATTCACTAATGTCGC 57.053 40.909 0.00 0.00 0.00 5.19
3652 3865 6.416750 GTGTAATGTTTGTTTTCTACTGGTGC 59.583 38.462 0.00 0.00 0.00 5.01
3756 3970 9.281371 AGAAGTACACTTTTCCCTAAATAACAC 57.719 33.333 0.00 0.00 36.11 3.32
4062 4277 2.996621 CCTCGTTGTTTTGTTTTTGCCA 59.003 40.909 0.00 0.00 0.00 4.92
4093 4308 7.884257 TGTTGAAGTCAATCTGATTATTGCAA 58.116 30.769 0.00 0.00 38.24 4.08
4094 4309 8.358895 TGTTGAAGTCAATCTGATTATTGCAAA 58.641 29.630 1.71 0.00 38.24 3.68
4095 4310 9.195411 GTTGAAGTCAATCTGATTATTGCAAAA 57.805 29.630 1.71 0.00 38.24 2.44
4096 4311 9.761504 TTGAAGTCAATCTGATTATTGCAAAAA 57.238 25.926 1.71 0.00 36.89 1.94
4137 4352 3.515630 GATTAAGCCCAAAGAGCAAAGC 58.484 45.455 0.00 0.00 0.00 3.51
4140 4355 1.081175 GCCCAAAGAGCAAAGCGAC 60.081 57.895 0.00 0.00 0.00 5.19
4147 4362 0.950555 AGAGCAAAGCGACGCATCAA 60.951 50.000 23.70 0.00 0.00 2.57
4191 4406 7.584108 TCAAACATATGTAAGCACTCTGTTTG 58.416 34.615 9.21 15.45 43.56 2.93
4192 4407 6.500684 AACATATGTAAGCACTCTGTTTGG 57.499 37.500 9.21 0.00 0.00 3.28
4193 4408 4.943705 ACATATGTAAGCACTCTGTTTGGG 59.056 41.667 6.56 0.00 0.00 4.12
4194 4409 3.788227 ATGTAAGCACTCTGTTTGGGA 57.212 42.857 0.00 0.00 0.00 4.37
4195 4410 2.846193 TGTAAGCACTCTGTTTGGGAC 58.154 47.619 0.00 0.00 0.00 4.46
4196 4411 1.798813 GTAAGCACTCTGTTTGGGACG 59.201 52.381 0.00 0.00 0.00 4.79
4197 4412 0.535102 AAGCACTCTGTTTGGGACGG 60.535 55.000 0.00 0.00 35.87 4.79
4198 4413 1.070786 GCACTCTGTTTGGGACGGA 59.929 57.895 0.00 0.00 41.36 4.69
4201 4416 3.478780 TCTGTTTGGGACGGAGGG 58.521 61.111 0.00 0.00 38.74 4.30
4202 4417 1.152204 TCTGTTTGGGACGGAGGGA 60.152 57.895 0.00 0.00 38.74 4.20
4203 4418 1.192146 TCTGTTTGGGACGGAGGGAG 61.192 60.000 0.00 0.00 38.74 4.30
4249 4482 4.314961 TCAATCCATGGTGCATACGTATC 58.685 43.478 12.58 1.78 0.00 2.24
4296 4529 7.068962 TGGTCTTCTCCGTGTGTATATTCATAA 59.931 37.037 0.00 0.00 0.00 1.90
4336 4569 9.844257 TTTGTTACCAAAATCTCATTCCATTTT 57.156 25.926 0.00 0.00 37.62 1.82
4382 4615 0.831711 ATGCCCGAAGTGCCCTTTTT 60.832 50.000 0.00 0.00 0.00 1.94
4383 4616 1.289066 GCCCGAAGTGCCCTTTTTC 59.711 57.895 0.00 0.00 0.00 2.29
4386 4619 1.318576 CCGAAGTGCCCTTTTTCACT 58.681 50.000 0.00 0.00 44.64 3.41
4390 4623 2.341846 AGTGCCCTTTTTCACTTCGA 57.658 45.000 0.00 0.00 40.32 3.71
4417 4651 4.796110 AACCCATGCATACTCCTGTAAT 57.204 40.909 0.00 0.00 31.80 1.89
4420 4654 4.202398 ACCCATGCATACTCCTGTAATCTG 60.202 45.833 0.00 0.00 31.80 2.90
4425 4659 7.498900 CCATGCATACTCCTGTAATCTGTTTTA 59.501 37.037 0.00 0.00 31.80 1.52
4465 4699 3.006672 GCAACTAGCACACCACACT 57.993 52.632 0.00 0.00 44.79 3.55
4755 4989 2.684881 CTGTTGCAAGGTTCAGTGAACT 59.315 45.455 29.89 16.42 41.70 3.01
4756 4990 3.876914 CTGTTGCAAGGTTCAGTGAACTA 59.123 43.478 29.89 12.69 41.70 2.24
4809 5043 7.241376 ACATTATCGGTCTTGAAAATTTCGAC 58.759 34.615 0.97 3.62 0.00 4.20
4810 5044 6.788684 TTATCGGTCTTGAAAATTTCGACA 57.211 33.333 13.13 0.00 0.00 4.35
4955 5189 0.745845 CTTCCATGAGCCAAGACGGG 60.746 60.000 0.00 0.00 34.06 5.28
5030 5264 4.568072 TGTATCTTGAAGGGCTTAGCAA 57.432 40.909 6.53 0.00 0.00 3.91
5034 5268 1.135721 CTTGAAGGGCTTAGCAATGGC 59.864 52.381 6.53 0.00 41.61 4.40
5094 5343 8.771766 CCTAGTGATGATGTGATAACTTGATTG 58.228 37.037 0.00 0.00 0.00 2.67
5099 5348 9.176460 TGATGATGTGATAACTTGATTGCTTTA 57.824 29.630 0.00 0.00 0.00 1.85
5100 5349 9.661187 GATGATGTGATAACTTGATTGCTTTAG 57.339 33.333 0.00 0.00 0.00 1.85
5101 5350 8.565896 TGATGTGATAACTTGATTGCTTTAGT 57.434 30.769 0.00 0.00 0.00 2.24
5103 5352 7.060600 TGTGATAACTTGATTGCTTTAGTCG 57.939 36.000 0.00 0.00 0.00 4.18
5105 5354 6.092259 GTGATAACTTGATTGCTTTAGTCGGT 59.908 38.462 0.00 0.00 0.00 4.69
5137 5402 5.700846 GATGATATCGTGATTCTACCGTGT 58.299 41.667 1.08 0.00 0.00 4.49
5158 5423 6.033966 GTGTGTCATTTCGTTTTCTTCCTTT 58.966 36.000 0.00 0.00 0.00 3.11
5228 5493 6.043411 CCGAAGTAAATTTTGTTGGGTTTCA 58.957 36.000 0.00 0.00 0.00 2.69
5266 5533 2.464865 CAGACGCTAGGTAGATTGTGC 58.535 52.381 0.00 0.00 0.00 4.57
5317 5607 1.830477 TGCATGGGCCAATTCTTAACC 59.170 47.619 11.89 0.00 40.13 2.85
5344 5634 4.176271 TCAGACACTTGCTATCATTGACG 58.824 43.478 0.00 0.00 0.00 4.35
5352 5642 5.581085 ACTTGCTATCATTGACGAGTTAACC 59.419 40.000 0.88 0.00 0.00 2.85
5382 5675 6.148811 GCTGCTTACACCAGTTGATTTAAGTA 59.851 38.462 0.00 0.00 32.93 2.24
5383 5676 7.308348 GCTGCTTACACCAGTTGATTTAAGTAA 60.308 37.037 0.00 0.00 32.93 2.24
5384 5677 8.453238 TGCTTACACCAGTTGATTTAAGTAAA 57.547 30.769 0.00 0.00 0.00 2.01
5420 5716 7.305474 ACAAACGTATGATAGGAAGCAAAAAG 58.695 34.615 0.00 0.00 0.00 2.27
5421 5717 7.174253 ACAAACGTATGATAGGAAGCAAAAAGA 59.826 33.333 0.00 0.00 0.00 2.52
5425 5721 8.573035 ACGTATGATAGGAAGCAAAAAGAAAAA 58.427 29.630 0.00 0.00 0.00 1.94
5426 5722 8.850452 CGTATGATAGGAAGCAAAAAGAAAAAC 58.150 33.333 0.00 0.00 0.00 2.43
5429 5725 9.612066 ATGATAGGAAGCAAAAAGAAAAACAAA 57.388 25.926 0.00 0.00 0.00 2.83
5477 5777 4.832823 ACAAAAGAAAGAATGAATCCGGGT 59.167 37.500 0.00 0.00 0.00 5.28
5574 5878 0.240945 CGGCCATGGTCTTGTTGTTC 59.759 55.000 15.80 0.00 0.00 3.18
5796 6100 1.553704 GGGTAGGAGACGTTGTCCATT 59.446 52.381 17.55 3.53 36.43 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.080695 TGGCTAGCTTGATCTTCTCATTGT 60.081 41.667 15.72 0.00 32.72 2.71
1 2 4.449131 TGGCTAGCTTGATCTTCTCATTG 58.551 43.478 15.72 0.00 32.72 2.82
2 3 4.767578 TGGCTAGCTTGATCTTCTCATT 57.232 40.909 15.72 0.00 32.72 2.57
3 4 4.767578 TTGGCTAGCTTGATCTTCTCAT 57.232 40.909 15.72 0.00 32.72 2.90
4 5 4.558226 TTTGGCTAGCTTGATCTTCTCA 57.442 40.909 15.72 0.00 0.00 3.27
5 6 4.210955 CGATTTGGCTAGCTTGATCTTCTC 59.789 45.833 15.72 0.00 0.00 2.87
8 9 3.878778 ACGATTTGGCTAGCTTGATCTT 58.121 40.909 15.72 6.34 0.00 2.40
9 10 3.550437 ACGATTTGGCTAGCTTGATCT 57.450 42.857 15.72 3.58 0.00 2.75
10 11 3.790123 GCAACGATTTGGCTAGCTTGATC 60.790 47.826 15.72 13.36 32.81 2.92
11 12 2.098117 GCAACGATTTGGCTAGCTTGAT 59.902 45.455 15.72 5.84 32.81 2.57
12 13 1.468520 GCAACGATTTGGCTAGCTTGA 59.531 47.619 15.72 0.57 32.81 3.02
13 14 1.470098 AGCAACGATTTGGCTAGCTTG 59.530 47.619 15.72 10.26 32.81 4.01
14 15 1.826385 AGCAACGATTTGGCTAGCTT 58.174 45.000 15.72 0.00 32.81 3.74
15 16 2.093447 AGTAGCAACGATTTGGCTAGCT 60.093 45.455 15.72 0.00 32.81 3.32
16 17 2.280628 AGTAGCAACGATTTGGCTAGC 58.719 47.619 6.04 6.04 32.81 3.42
17 18 4.201822 GGAAAGTAGCAACGATTTGGCTAG 60.202 45.833 0.00 0.00 32.81 3.42
18 19 3.687698 GGAAAGTAGCAACGATTTGGCTA 59.312 43.478 0.00 0.00 32.81 3.93
19 20 2.488153 GGAAAGTAGCAACGATTTGGCT 59.512 45.455 0.00 0.00 32.81 4.75
20 21 2.227865 TGGAAAGTAGCAACGATTTGGC 59.772 45.455 0.00 0.00 32.81 4.52
21 22 4.497473 TTGGAAAGTAGCAACGATTTGG 57.503 40.909 0.00 0.00 32.81 3.28
22 23 5.095490 GGATTGGAAAGTAGCAACGATTTG 58.905 41.667 0.00 0.00 35.62 2.32
23 24 4.764823 TGGATTGGAAAGTAGCAACGATTT 59.235 37.500 0.00 0.00 0.00 2.17
24 25 4.331968 TGGATTGGAAAGTAGCAACGATT 58.668 39.130 0.00 0.00 0.00 3.34
25 26 3.941483 CTGGATTGGAAAGTAGCAACGAT 59.059 43.478 0.00 0.00 0.00 3.73
26 27 3.334691 CTGGATTGGAAAGTAGCAACGA 58.665 45.455 0.00 0.00 0.00 3.85
27 28 2.159517 GCTGGATTGGAAAGTAGCAACG 60.160 50.000 0.00 0.00 32.45 4.10
28 29 2.164422 GGCTGGATTGGAAAGTAGCAAC 59.836 50.000 0.00 0.00 33.40 4.17
29 30 2.446435 GGCTGGATTGGAAAGTAGCAA 58.554 47.619 0.00 0.00 33.40 3.91
30 31 1.678728 CGGCTGGATTGGAAAGTAGCA 60.679 52.381 0.00 0.00 33.40 3.49
31 32 1.017387 CGGCTGGATTGGAAAGTAGC 58.983 55.000 0.00 0.00 31.71 3.58
32 33 2.168521 TCTCGGCTGGATTGGAAAGTAG 59.831 50.000 0.00 0.00 0.00 2.57
33 34 2.184533 TCTCGGCTGGATTGGAAAGTA 58.815 47.619 0.00 0.00 0.00 2.24
34 35 0.984230 TCTCGGCTGGATTGGAAAGT 59.016 50.000 0.00 0.00 0.00 2.66
35 36 2.338577 ATCTCGGCTGGATTGGAAAG 57.661 50.000 0.00 0.00 0.00 2.62
36 37 3.038280 TCTATCTCGGCTGGATTGGAAA 58.962 45.455 0.00 0.00 0.00 3.13
37 38 2.677914 TCTATCTCGGCTGGATTGGAA 58.322 47.619 0.00 0.00 0.00 3.53
38 39 2.381752 TCTATCTCGGCTGGATTGGA 57.618 50.000 0.00 0.00 0.00 3.53
39 40 2.564504 TGATCTATCTCGGCTGGATTGG 59.435 50.000 0.00 0.00 0.00 3.16
40 41 3.006217 TGTGATCTATCTCGGCTGGATTG 59.994 47.826 0.00 0.00 0.00 2.67
41 42 3.234353 TGTGATCTATCTCGGCTGGATT 58.766 45.455 0.00 0.00 0.00 3.01
42 43 2.881734 TGTGATCTATCTCGGCTGGAT 58.118 47.619 0.00 0.00 0.00 3.41
43 44 2.364972 TGTGATCTATCTCGGCTGGA 57.635 50.000 0.00 0.00 0.00 3.86
44 45 2.865670 GCTTGTGATCTATCTCGGCTGG 60.866 54.545 0.00 0.00 0.00 4.85
45 46 2.402305 GCTTGTGATCTATCTCGGCTG 58.598 52.381 0.00 0.00 0.00 4.85
46 47 1.342819 GGCTTGTGATCTATCTCGGCT 59.657 52.381 0.00 0.00 0.00 5.52
47 48 1.606737 GGGCTTGTGATCTATCTCGGC 60.607 57.143 0.00 0.00 0.00 5.54
48 49 1.688735 TGGGCTTGTGATCTATCTCGG 59.311 52.381 0.00 0.00 0.00 4.63
49 50 2.363680 AGTGGGCTTGTGATCTATCTCG 59.636 50.000 0.00 0.00 0.00 4.04
50 51 4.414337 AAGTGGGCTTGTGATCTATCTC 57.586 45.455 0.00 0.00 32.92 2.75
51 52 4.225942 TGAAAGTGGGCTTGTGATCTATCT 59.774 41.667 0.00 0.00 34.71 1.98
52 53 4.517285 TGAAAGTGGGCTTGTGATCTATC 58.483 43.478 0.00 0.00 34.71 2.08
53 54 4.574674 TGAAAGTGGGCTTGTGATCTAT 57.425 40.909 0.00 0.00 34.71 1.98
54 55 4.041567 TCTTGAAAGTGGGCTTGTGATCTA 59.958 41.667 0.00 0.00 34.71 1.98
55 56 2.957402 TGAAAGTGGGCTTGTGATCT 57.043 45.000 0.00 0.00 34.71 2.75
56 57 3.057946 GTCTTGAAAGTGGGCTTGTGATC 60.058 47.826 0.00 0.00 34.71 2.92
57 58 2.887152 GTCTTGAAAGTGGGCTTGTGAT 59.113 45.455 0.00 0.00 34.71 3.06
58 59 2.297701 GTCTTGAAAGTGGGCTTGTGA 58.702 47.619 0.00 0.00 34.71 3.58
59 60 2.023673 TGTCTTGAAAGTGGGCTTGTG 58.976 47.619 0.00 0.00 34.71 3.33
60 61 2.435372 TGTCTTGAAAGTGGGCTTGT 57.565 45.000 0.00 0.00 34.71 3.16
61 62 4.326504 AATTGTCTTGAAAGTGGGCTTG 57.673 40.909 0.00 0.00 34.71 4.01
62 63 6.041979 ACATTAATTGTCTTGAAAGTGGGCTT 59.958 34.615 0.00 0.00 30.89 4.35
63 64 5.539955 ACATTAATTGTCTTGAAAGTGGGCT 59.460 36.000 0.00 0.00 30.89 5.19
64 65 5.783111 ACATTAATTGTCTTGAAAGTGGGC 58.217 37.500 0.00 0.00 30.89 5.36
65 66 7.975616 CCATACATTAATTGTCTTGAAAGTGGG 59.024 37.037 0.00 0.00 39.87 4.61
66 67 7.975616 CCCATACATTAATTGTCTTGAAAGTGG 59.024 37.037 0.00 0.00 39.87 4.00
67 68 8.522830 ACCCATACATTAATTGTCTTGAAAGTG 58.477 33.333 0.00 0.00 39.87 3.16
68 69 8.650143 ACCCATACATTAATTGTCTTGAAAGT 57.350 30.769 0.00 0.00 39.87 2.66
69 70 8.739039 TGACCCATACATTAATTGTCTTGAAAG 58.261 33.333 0.00 0.00 39.87 2.62
70 71 8.642935 TGACCCATACATTAATTGTCTTGAAA 57.357 30.769 0.00 0.00 39.87 2.69
71 72 7.888021 ACTGACCCATACATTAATTGTCTTGAA 59.112 33.333 0.00 0.00 39.87 2.69
72 73 7.402054 ACTGACCCATACATTAATTGTCTTGA 58.598 34.615 0.00 0.00 39.87 3.02
73 74 7.630242 ACTGACCCATACATTAATTGTCTTG 57.370 36.000 0.00 0.00 39.87 3.02
74 75 9.920946 AATACTGACCCATACATTAATTGTCTT 57.079 29.630 0.00 0.00 39.87 3.01
75 76 9.342308 CAATACTGACCCATACATTAATTGTCT 57.658 33.333 0.00 0.00 39.87 3.41
76 77 8.567948 CCAATACTGACCCATACATTAATTGTC 58.432 37.037 0.00 0.00 39.87 3.18
77 78 8.278639 TCCAATACTGACCCATACATTAATTGT 58.721 33.333 0.00 0.00 42.62 2.71
78 79 8.690203 TCCAATACTGACCCATACATTAATTG 57.310 34.615 0.00 0.00 0.00 2.32
79 80 8.502738 ACTCCAATACTGACCCATACATTAATT 58.497 33.333 0.00 0.00 0.00 1.40
80 81 8.045720 ACTCCAATACTGACCCATACATTAAT 57.954 34.615 0.00 0.00 0.00 1.40
81 82 7.446106 ACTCCAATACTGACCCATACATTAA 57.554 36.000 0.00 0.00 0.00 1.40
82 83 7.347222 AGAACTCCAATACTGACCCATACATTA 59.653 37.037 0.00 0.00 0.00 1.90
83 84 5.975988 ACTCCAATACTGACCCATACATT 57.024 39.130 0.00 0.00 0.00 2.71
84 85 5.667626 AGAACTCCAATACTGACCCATACAT 59.332 40.000 0.00 0.00 0.00 2.29
85 86 5.030147 AGAACTCCAATACTGACCCATACA 58.970 41.667 0.00 0.00 0.00 2.29
86 87 5.615925 AGAACTCCAATACTGACCCATAC 57.384 43.478 0.00 0.00 0.00 2.39
87 88 5.964477 AGAAGAACTCCAATACTGACCCATA 59.036 40.000 0.00 0.00 0.00 2.74
88 89 4.785376 AGAAGAACTCCAATACTGACCCAT 59.215 41.667 0.00 0.00 0.00 4.00
89 90 4.168101 AGAAGAACTCCAATACTGACCCA 58.832 43.478 0.00 0.00 0.00 4.51
90 91 4.678309 CGAGAAGAACTCCAATACTGACCC 60.678 50.000 0.00 0.00 42.18 4.46
91 92 4.425520 CGAGAAGAACTCCAATACTGACC 58.574 47.826 0.00 0.00 42.18 4.02
148 149 3.461773 GCCTCCGCTAGCCACAGA 61.462 66.667 9.66 0.11 0.00 3.41
153 154 1.392710 TTAGACTGCCTCCGCTAGCC 61.393 60.000 9.66 0.00 35.36 3.93
166 167 0.974383 CCTTGGTCCACCGTTAGACT 59.026 55.000 0.00 0.00 39.43 3.24
171 172 2.526046 CCTCCCTTGGTCCACCGTT 61.526 63.158 0.00 0.00 39.43 4.44
272 273 3.854669 AGATGCGGGCCTCCTTCG 61.855 66.667 0.84 0.00 0.00 3.79
296 297 6.345250 GCTTTCACGTGAATTCAAACATTCAG 60.345 38.462 30.10 19.79 42.58 3.02
340 341 3.709653 TCATAGTTTGGTCCGAGGCTAAT 59.290 43.478 0.00 0.00 0.00 1.73
359 360 6.098695 CCAATTGTCAATATGGTTTCCCTCAT 59.901 38.462 4.43 0.00 0.00 2.90
365 366 8.253113 AGTTGATCCAATTGTCAATATGGTTTC 58.747 33.333 12.92 16.75 36.79 2.78
535 575 0.032130 TCGATCTCGGCCTGCATAAC 59.968 55.000 0.00 0.00 40.29 1.89
559 599 2.031870 ACCGGATCTCATGAATCGTCA 58.968 47.619 9.46 0.00 38.41 4.35
582 622 4.510711 TGTTTAGAGGCGTCTATAGTCTCG 59.489 45.833 16.39 5.22 35.12 4.04
583 623 5.759273 TCTGTTTAGAGGCGTCTATAGTCTC 59.241 44.000 16.39 2.01 35.12 3.36
589 629 6.490381 TGTCATATCTGTTTAGAGGCGTCTAT 59.510 38.462 16.39 4.84 35.12 1.98
592 641 4.933330 TGTCATATCTGTTTAGAGGCGTC 58.067 43.478 0.00 0.00 36.14 5.19
596 645 8.908903 AGTAGAGTTGTCATATCTGTTTAGAGG 58.091 37.037 0.00 0.00 36.14 3.69
600 649 9.132923 CCCTAGTAGAGTTGTCATATCTGTTTA 57.867 37.037 0.00 0.00 0.00 2.01
632 681 8.251026 TGATATATATGTTGCCCGTCTCTTAAG 58.749 37.037 0.00 0.00 0.00 1.85
642 691 2.607635 CGCCGTGATATATATGTTGCCC 59.392 50.000 0.00 0.00 0.00 5.36
652 701 4.612033 CGATTGTCTACACGCCGTGATATA 60.612 45.833 25.94 4.99 36.96 0.86
685 734 8.606602 GGTTCGTTTGATTAAATACTTACGGAT 58.393 33.333 0.00 0.00 0.00 4.18
686 735 7.601886 TGGTTCGTTTGATTAAATACTTACGGA 59.398 33.333 0.00 0.00 0.00 4.69
687 736 7.741198 TGGTTCGTTTGATTAAATACTTACGG 58.259 34.615 0.00 0.00 0.00 4.02
701 759 3.937814 AGAGCATGTATGGTTCGTTTGA 58.062 40.909 0.00 0.00 38.85 2.69
919 977 2.175811 GGCGCAGTAAAAGCCGTG 59.824 61.111 10.83 0.00 41.53 4.94
939 997 0.108424 CTCCTCTCTGGTTTGCTCGG 60.108 60.000 0.00 0.00 37.07 4.63
949 1007 0.817013 GTGCTCTGTCCTCCTCTCTG 59.183 60.000 0.00 0.00 0.00 3.35
951 1009 0.530288 GTGTGCTCTGTCCTCCTCTC 59.470 60.000 0.00 0.00 0.00 3.20
952 1010 1.247419 CGTGTGCTCTGTCCTCCTCT 61.247 60.000 0.00 0.00 0.00 3.69
953 1011 1.214062 CGTGTGCTCTGTCCTCCTC 59.786 63.158 0.00 0.00 0.00 3.71
954 1012 1.228583 TCGTGTGCTCTGTCCTCCT 60.229 57.895 0.00 0.00 0.00 3.69
955 1013 1.080434 GTCGTGTGCTCTGTCCTCC 60.080 63.158 0.00 0.00 0.00 4.30
956 1014 1.442857 CGTCGTGTGCTCTGTCCTC 60.443 63.158 0.00 0.00 0.00 3.71
957 1015 2.645567 CGTCGTGTGCTCTGTCCT 59.354 61.111 0.00 0.00 0.00 3.85
958 1016 3.106407 GCGTCGTGTGCTCTGTCC 61.106 66.667 0.00 0.00 0.00 4.02
959 1017 3.461982 CGCGTCGTGTGCTCTGTC 61.462 66.667 0.00 0.00 0.00 3.51
983 1041 1.478510 CCATTGCCGTAGTGTCTCTCT 59.521 52.381 0.00 0.00 0.00 3.10
984 1042 1.927895 CCATTGCCGTAGTGTCTCTC 58.072 55.000 0.00 0.00 0.00 3.20
986 1044 1.421410 CGCCATTGCCGTAGTGTCTC 61.421 60.000 0.00 0.00 0.00 3.36
987 1045 1.447838 CGCCATTGCCGTAGTGTCT 60.448 57.895 0.00 0.00 0.00 3.41
988 1046 2.461110 CCGCCATTGCCGTAGTGTC 61.461 63.158 0.00 0.00 0.00 3.67
990 1048 2.125310 TCCGCCATTGCCGTAGTG 60.125 61.111 0.00 0.00 0.00 2.74
991 1049 2.186903 CTCCGCCATTGCCGTAGT 59.813 61.111 0.00 0.00 0.00 2.73
992 1050 2.588877 CCTCCGCCATTGCCGTAG 60.589 66.667 0.00 0.00 0.00 3.51
993 1051 4.169696 CCCTCCGCCATTGCCGTA 62.170 66.667 0.00 0.00 0.00 4.02
1232 1290 0.833287 GAGCAAGTAGATGGGCAGGA 59.167 55.000 0.00 0.00 0.00 3.86
1311 1369 1.538512 CAGCAATCAGTTGGACTGTGG 59.461 52.381 7.85 1.34 46.03 4.17
1312 1370 2.983402 CAGCAATCAGTTGGACTGTG 57.017 50.000 7.85 1.96 46.03 3.66
1328 1386 0.659417 CATTCAATCGATGCGCCAGC 60.659 55.000 4.18 0.00 45.41 4.85
1337 1395 2.505650 TTCCCCAAGCATTCAATCGA 57.494 45.000 0.00 0.00 0.00 3.59
1362 1420 2.902705 ACTACAACTTCGGCAACTCA 57.097 45.000 0.00 0.00 0.00 3.41
1397 1455 5.411361 TCACCAACTACAATTACTGCATCAC 59.589 40.000 0.00 0.00 0.00 3.06
1401 1459 6.488344 TCAAATCACCAACTACAATTACTGCA 59.512 34.615 0.00 0.00 0.00 4.41
1402 1460 6.908825 TCAAATCACCAACTACAATTACTGC 58.091 36.000 0.00 0.00 0.00 4.40
1429 1489 7.257722 GCACAGCAGTAATTAATTAACCACAT 58.742 34.615 9.48 0.00 0.00 3.21
1612 1672 1.959226 CACAACGCCGTGCTTACCT 60.959 57.895 0.00 0.00 0.00 3.08
1664 1741 7.630026 TCAGCAGCATAATTAAACACGATAAG 58.370 34.615 0.00 0.00 0.00 1.73
1745 1826 6.723298 AACCAACATGACCAAATTAGAACA 57.277 33.333 0.00 0.00 0.00 3.18
1776 1859 9.013229 TGCCATGATAAACCAGATGAATATAAC 57.987 33.333 0.00 0.00 0.00 1.89
1782 1865 3.627123 CGTGCCATGATAAACCAGATGAA 59.373 43.478 0.00 0.00 0.00 2.57
1806 1889 2.858745 TCAGGGTCTTTGCACTTTACC 58.141 47.619 0.00 0.00 0.00 2.85
2024 2109 4.685169 AGGTTGAAACATAACATCAGCG 57.315 40.909 0.00 0.00 0.00 5.18
2146 2231 1.179174 TGACTGGAGTCTGTGGTCCG 61.179 60.000 8.24 0.00 44.99 4.79
2207 2292 4.156373 TGGTCATAACGTCGAGTTGTATCA 59.844 41.667 0.00 1.38 44.01 2.15
2228 2313 5.471456 AGCTCAAGTTTTCTGACATACTTGG 59.529 40.000 18.09 12.91 44.63 3.61
2240 2325 6.743575 TTCTATGCCTAAGCTCAAGTTTTC 57.256 37.500 0.00 0.00 40.80 2.29
2242 2327 6.690194 CATTCTATGCCTAAGCTCAAGTTT 57.310 37.500 0.00 0.00 40.80 2.66
2284 2369 9.329913 CACGTTTTAATTTTCTGGAGAACATAG 57.670 33.333 0.00 0.00 33.13 2.23
2302 2387 5.391523 GCATTGTCCATAGAAGCACGTTTTA 60.392 40.000 0.00 0.00 0.00 1.52
2420 2603 7.605410 TTGTGTATGCTTAGCTTTAGGTAAC 57.395 36.000 5.60 0.00 34.68 2.50
2457 2640 8.600625 CCATGAAATTTGAGCAAATGACTATTG 58.399 33.333 9.02 4.00 40.57 1.90
2462 2645 5.240121 ACCCATGAAATTTGAGCAAATGAC 58.760 37.500 9.02 7.25 40.57 3.06
2514 2697 0.033920 ACGACTGAACAGCATGCAGA 59.966 50.000 21.98 0.00 42.53 4.26
2723 2906 8.918202 TCAGACAGGACACTAAAATAAACATT 57.082 30.769 0.00 0.00 0.00 2.71
3652 3865 8.527567 AAGAGAAGAATTGAACTAGAAACGAG 57.472 34.615 0.00 0.00 0.00 4.18
4096 4311 2.699846 TCCAAGCCTTGCACAGATTTTT 59.300 40.909 0.00 0.00 0.00 1.94
4097 4312 2.318908 TCCAAGCCTTGCACAGATTTT 58.681 42.857 0.00 0.00 0.00 1.82
4098 4313 1.999648 TCCAAGCCTTGCACAGATTT 58.000 45.000 0.00 0.00 0.00 2.17
4099 4314 2.226962 ATCCAAGCCTTGCACAGATT 57.773 45.000 0.00 0.00 0.00 2.40
4100 4315 2.226962 AATCCAAGCCTTGCACAGAT 57.773 45.000 0.00 0.00 0.00 2.90
4137 4352 2.592796 TTGTGACAATTGATGCGTCG 57.407 45.000 13.59 0.00 32.17 5.12
4191 4406 1.253593 AAACGTACTCCCTCCGTCCC 61.254 60.000 0.00 0.00 32.95 4.46
4192 4407 0.605083 AAAACGTACTCCCTCCGTCC 59.395 55.000 0.00 0.00 32.95 4.79
4193 4408 3.575965 TTAAAACGTACTCCCTCCGTC 57.424 47.619 0.00 0.00 32.95 4.79
4194 4409 4.541973 AATTAAAACGTACTCCCTCCGT 57.458 40.909 0.00 0.00 36.17 4.69
4195 4410 5.894807 TCTAATTAAAACGTACTCCCTCCG 58.105 41.667 0.00 0.00 0.00 4.63
4196 4411 6.279123 CCTCTAATTAAAACGTACTCCCTCC 58.721 44.000 0.00 0.00 0.00 4.30
4197 4412 5.752472 GCCTCTAATTAAAACGTACTCCCTC 59.248 44.000 0.00 0.00 0.00 4.30
4198 4413 5.188359 TGCCTCTAATTAAAACGTACTCCCT 59.812 40.000 0.00 0.00 0.00 4.20
4199 4414 5.422145 TGCCTCTAATTAAAACGTACTCCC 58.578 41.667 0.00 0.00 0.00 4.30
4200 4415 8.652810 TTATGCCTCTAATTAAAACGTACTCC 57.347 34.615 0.00 0.00 0.00 3.85
4249 4482 7.768120 AGACCAGCAGATTGAGTAAGAAATAAG 59.232 37.037 0.00 0.00 0.00 1.73
4382 4615 3.595173 CATGGGTTACACATCGAAGTGA 58.405 45.455 26.09 8.13 42.05 3.41
4383 4616 2.095853 GCATGGGTTACACATCGAAGTG 59.904 50.000 18.59 18.59 44.93 3.16
4386 4619 2.481289 TGCATGGGTTACACATCGAA 57.519 45.000 0.00 0.00 0.00 3.71
4390 4623 3.459598 AGGAGTATGCATGGGTTACACAT 59.540 43.478 10.16 0.00 0.00 3.21
4438 4672 2.021584 TGCTAGTTGCTGCGTCACG 61.022 57.895 0.00 0.00 43.37 4.35
4465 4699 3.943381 GTCTCAGATTGCATCCATTCACA 59.057 43.478 0.00 0.00 0.00 3.58
4755 4989 9.981114 GATGGAAAAGAAAAGAAAAAGGACATA 57.019 29.630 0.00 0.00 0.00 2.29
4756 4990 7.653311 CGATGGAAAAGAAAAGAAAAAGGACAT 59.347 33.333 0.00 0.00 0.00 3.06
4837 5071 8.042515 TCAAGATCACACATCATGTCATCTTTA 58.957 33.333 11.28 4.41 40.64 1.85
4846 5080 3.630312 TGCCATCAAGATCACACATCATG 59.370 43.478 0.00 0.00 0.00 3.07
4955 5189 4.494091 TCCAAGAACTGAAGATCATCCC 57.506 45.455 0.00 0.00 0.00 3.85
5030 5264 8.581578 CCCAATTTTATTACTATTTACCGCCAT 58.418 33.333 0.00 0.00 0.00 4.40
5069 5318 8.281194 GCAATCAAGTTATCACATCATCACTAG 58.719 37.037 0.00 0.00 0.00 2.57
5070 5319 7.989170 AGCAATCAAGTTATCACATCATCACTA 59.011 33.333 0.00 0.00 0.00 2.74
5071 5320 6.827251 AGCAATCAAGTTATCACATCATCACT 59.173 34.615 0.00 0.00 0.00 3.41
5072 5321 7.024340 AGCAATCAAGTTATCACATCATCAC 57.976 36.000 0.00 0.00 0.00 3.06
5073 5322 7.634671 AAGCAATCAAGTTATCACATCATCA 57.365 32.000 0.00 0.00 0.00 3.07
5074 5323 9.661187 CTAAAGCAATCAAGTTATCACATCATC 57.339 33.333 0.00 0.00 0.00 2.92
5075 5324 9.182214 ACTAAAGCAATCAAGTTATCACATCAT 57.818 29.630 0.00 0.00 0.00 2.45
5094 5343 2.421424 TCGAGGAAGTACCGACTAAAGC 59.579 50.000 0.00 0.00 44.74 3.51
5099 5348 2.414994 TCATCGAGGAAGTACCGACT 57.585 50.000 0.00 0.00 44.74 4.18
5100 5349 4.972201 GATATCATCGAGGAAGTACCGAC 58.028 47.826 2.91 0.00 44.74 4.79
5158 5423 1.593196 CGGTGTTGCAGAGGAGAAAA 58.407 50.000 0.00 0.00 0.00 2.29
5228 5493 2.323580 GCGTTGCTCTTGCTCAGCT 61.324 57.895 0.00 0.00 40.48 4.24
5266 5533 4.323553 GTGATAGTTAGCTACCACCCAG 57.676 50.000 0.00 0.00 36.03 4.45
5317 5607 7.484007 GTCAATGATAGCAAGTGTCTGATTTTG 59.516 37.037 0.00 0.00 0.00 2.44
5344 5634 1.797025 AAGCAGCTGACGGTTAACTC 58.203 50.000 20.43 0.00 0.00 3.01
5352 5642 4.673403 TGGTGTAAGCAGCTGACG 57.327 55.556 20.43 0.00 40.88 4.35
5384 5677 9.458374 CCTATCATACGTTTGTTTTCAGTTTTT 57.542 29.630 5.89 0.00 0.00 1.94
5492 5796 1.588403 CTCGCATGCCTCTGACTCG 60.588 63.158 13.15 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.