Multiple sequence alignment - TraesCS3B01G148600

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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 TraesCS3B01G148600 chr3B 100.000 4270 0 0 1 4270 139835505 139831236 0.000000e+00 7886.0
1 TraesCS3B01G148600 chr3B 78.813 1095 144 42 2329 3401 139779147 139778119 0.000000e+00 656.0
2 TraesCS3B01G148600 chr3B 77.347 1161 172 60 1158 2268 139780391 139779272 1.700000e-168 603.0
3 TraesCS3B01G148600 chr3B 80.000 130 17 4 393 522 139781104 139780984 2.120000e-13 87.9
4 TraesCS3B01G148600 chr3B 100.000 31 0 0 319 349 139835159 139835129 1.660000e-04 58.4
5 TraesCS3B01G148600 chr3B 100.000 31 0 0 347 377 139835187 139835157 1.660000e-04 58.4
6 TraesCS3B01G148600 chr3A 88.145 4285 268 91 100 4270 106679809 106675651 0.000000e+00 4878.0
7 TraesCS3B01G148600 chr3A 93.995 766 41 2 3137 3897 106674680 106673915 0.000000e+00 1155.0
8 TraesCS3B01G148600 chr3A 78.403 1102 144 46 2329 3409 106661981 106660953 7.790000e-177 630.0
9 TraesCS3B01G148600 chr3A 89.933 447 36 7 3592 4035 106673478 106673038 6.200000e-158 568.0
10 TraesCS3B01G148600 chr3A 79.510 776 110 29 1067 1816 106663278 106662526 1.370000e-139 507.0
11 TraesCS3B01G148600 chr3A 91.327 196 17 0 2052 2247 106662290 106662095 7.040000e-68 268.0
12 TraesCS3B01G148600 chr3D 90.681 2468 127 44 863 3284 90381885 90379475 0.000000e+00 3188.0
13 TraesCS3B01G148600 chr3D 79.317 1112 149 44 2329 3409 90373826 90372765 0.000000e+00 704.0
14 TraesCS3B01G148600 chr3D 88.514 592 19 8 234 819 90382718 90382170 0.000000e+00 671.0
15 TraesCS3B01G148600 chr3D 84.626 696 52 20 3261 3953 90379471 90378828 3.600000e-180 641.0
16 TraesCS3B01G148600 chr3D 76.048 1169 174 68 1154 2268 90375064 90373948 1.060000e-140 510.0
17 TraesCS3B01G148600 chr3D 86.726 226 21 8 3 222 90391355 90391577 4.270000e-60 243.0
18 TraesCS3B01G148600 chr3D 85.455 55 8 0 393 447 90375773 90375719 1.660000e-04 58.4
19 TraesCS3B01G148600 chr7D 76.940 464 74 17 3822 4269 562645558 562645112 2.570000e-57 233.0
20 TraesCS3B01G148600 chr5A 90.854 164 15 0 2052 2215 311157734 311157571 2.000000e-53 220.0
21 TraesCS3B01G148600 chr4B 77.031 357 53 20 2339 2672 20366576 20366226 1.220000e-40 178.0
22 TraesCS3B01G148600 chr4B 73.301 412 88 15 2059 2455 20360638 20361042 9.630000e-27 132.0
23 TraesCS3B01G148600 chr4D 72.540 630 126 35 2059 2672 10834667 10835265 1.230000e-35 161.0
24 TraesCS3B01G148600 chr6D 83.636 165 23 4 3626 3786 143476621 143476457 7.400000e-33 152.0
25 TraesCS3B01G148600 chr6D 79.703 202 35 6 3627 3824 181729736 181729537 1.600000e-29 141.0
26 TraesCS3B01G148600 chr4A 82.286 175 31 0 2059 2233 592530375 592530549 7.400000e-33 152.0
27 TraesCS3B01G148600 chr4A 82.286 175 31 0 2059 2233 592816719 592816893 7.400000e-33 152.0
28 TraesCS3B01G148600 chr4A 82.286 175 31 0 2059 2233 593096932 593097106 7.400000e-33 152.0
29 TraesCS3B01G148600 chr6A 83.636 165 22 5 3626 3786 234170883 234170720 2.660000e-32 150.0
30 TraesCS3B01G148600 chr1B 83.030 165 24 4 3626 3786 449252302 449252138 3.440000e-31 147.0
31 TraesCS3B01G148600 chr2D 79.897 194 36 3 3628 3818 589535632 589535439 5.760000e-29 139.0
32 TraesCS3B01G148600 chr1D 79.208 202 37 5 3627 3824 481698014 481697814 7.450000e-28 135.0


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 TraesCS3B01G148600 chr3B 139831236 139835505 4269 True 2667.600000 7886 100.000000 1 4270 3 chr3B.!!$R2 4269
1 TraesCS3B01G148600 chr3B 139778119 139781104 2985 True 448.966667 656 78.720000 393 3401 3 chr3B.!!$R1 3008
2 TraesCS3B01G148600 chr3A 106673038 106679809 6771 True 2200.333333 4878 90.691000 100 4270 3 chr3A.!!$R2 4170
3 TraesCS3B01G148600 chr3A 106660953 106663278 2325 True 468.333333 630 83.080000 1067 3409 3 chr3A.!!$R1 2342
4 TraesCS3B01G148600 chr3D 90372765 90382718 9953 True 962.066667 3188 84.106833 234 3953 6 chr3D.!!$R1 3719

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
626 700 0.460987 GCAGCTGTGCGAGATAACCT 60.461 55.0 16.64 0.0 40.71 3.50 F
1948 2383 0.178068 ACACACGCAACACCTCTTCT 59.822 50.0 0.00 0.0 0.00 2.85 F
3204 3802 0.106268 TGCTCCACCAAAAGCCAAGA 60.106 50.0 0.00 0.0 37.73 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 2845 0.110238 GCACTCGTCCAACGTACGTA 60.110 55.000 23.12 2.73 43.14 3.57 R
3253 3851 0.322546 GGATCAACGGCCCAAGAACT 60.323 55.000 0.00 0.00 0.00 3.01 R
4152 4955 1.199097 CTTTGTCAATTTAGGCGCCGT 59.801 47.619 23.20 12.38 0.00 5.68 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
23 24 6.024552 TGAATTTGAGGTTTGTAGCATTCC 57.975 37.500 0.00 0.00 0.00 3.01
24 25 5.047377 TGAATTTGAGGTTTGTAGCATTCCC 60.047 40.000 0.00 0.00 0.00 3.97
25 26 3.806949 TTGAGGTTTGTAGCATTCCCT 57.193 42.857 0.00 0.00 0.00 4.20
26 27 4.919774 TTGAGGTTTGTAGCATTCCCTA 57.080 40.909 0.00 0.00 0.00 3.53
27 28 4.919774 TGAGGTTTGTAGCATTCCCTAA 57.080 40.909 0.00 0.00 0.00 2.69
28 29 5.249780 TGAGGTTTGTAGCATTCCCTAAA 57.750 39.130 0.00 0.00 0.00 1.85
29 30 5.826643 TGAGGTTTGTAGCATTCCCTAAAT 58.173 37.500 0.00 0.00 0.00 1.40
30 31 5.885912 TGAGGTTTGTAGCATTCCCTAAATC 59.114 40.000 0.00 0.00 0.00 2.17
31 32 5.826643 AGGTTTGTAGCATTCCCTAAATCA 58.173 37.500 0.00 0.00 0.00 2.57
32 33 6.435164 AGGTTTGTAGCATTCCCTAAATCAT 58.565 36.000 0.00 0.00 0.00 2.45
33 34 6.547510 AGGTTTGTAGCATTCCCTAAATCATC 59.452 38.462 0.00 0.00 0.00 2.92
34 35 6.321181 GGTTTGTAGCATTCCCTAAATCATCA 59.679 38.462 0.00 0.00 0.00 3.07
35 36 7.147915 GGTTTGTAGCATTCCCTAAATCATCAA 60.148 37.037 0.00 0.00 0.00 2.57
36 37 6.942532 TGTAGCATTCCCTAAATCATCAAC 57.057 37.500 0.00 0.00 0.00 3.18
37 38 6.662755 TGTAGCATTCCCTAAATCATCAACT 58.337 36.000 0.00 0.00 0.00 3.16
38 39 7.118723 TGTAGCATTCCCTAAATCATCAACTT 58.881 34.615 0.00 0.00 0.00 2.66
39 40 6.461110 AGCATTCCCTAAATCATCAACTTG 57.539 37.500 0.00 0.00 0.00 3.16
40 41 6.189859 AGCATTCCCTAAATCATCAACTTGA 58.810 36.000 0.00 0.00 0.00 3.02
41 42 6.320672 AGCATTCCCTAAATCATCAACTTGAG 59.679 38.462 0.00 0.00 0.00 3.02
42 43 6.096001 GCATTCCCTAAATCATCAACTTGAGT 59.904 38.462 0.00 0.00 0.00 3.41
43 44 7.283127 GCATTCCCTAAATCATCAACTTGAGTA 59.717 37.037 0.00 0.00 0.00 2.59
44 45 9.347240 CATTCCCTAAATCATCAACTTGAGTAT 57.653 33.333 0.00 0.00 0.00 2.12
45 46 8.737168 TTCCCTAAATCATCAACTTGAGTATG 57.263 34.615 0.00 0.00 0.00 2.39
46 47 7.861629 TCCCTAAATCATCAACTTGAGTATGT 58.138 34.615 0.00 0.00 0.00 2.29
47 48 8.328758 TCCCTAAATCATCAACTTGAGTATGTT 58.671 33.333 0.00 0.00 0.00 2.71
48 49 8.960591 CCCTAAATCATCAACTTGAGTATGTTT 58.039 33.333 0.00 0.00 0.00 2.83
49 50 9.994432 CCTAAATCATCAACTTGAGTATGTTTC 57.006 33.333 0.00 0.00 0.00 2.78
52 53 9.903682 AAATCATCAACTTGAGTATGTTTCTTG 57.096 29.630 0.00 0.00 0.00 3.02
53 54 8.627208 ATCATCAACTTGAGTATGTTTCTTGT 57.373 30.769 0.00 0.00 0.00 3.16
54 55 8.450578 TCATCAACTTGAGTATGTTTCTTGTT 57.549 30.769 0.00 0.00 0.00 2.83
55 56 8.344831 TCATCAACTTGAGTATGTTTCTTGTTG 58.655 33.333 0.00 0.00 33.82 3.33
56 57 7.857734 TCAACTTGAGTATGTTTCTTGTTGA 57.142 32.000 0.00 0.00 36.35 3.18
57 58 8.450578 TCAACTTGAGTATGTTTCTTGTTGAT 57.549 30.769 0.00 0.00 35.18 2.57
58 59 8.344831 TCAACTTGAGTATGTTTCTTGTTGATG 58.655 33.333 0.00 0.00 35.18 3.07
59 60 6.672147 ACTTGAGTATGTTTCTTGTTGATGC 58.328 36.000 0.00 0.00 0.00 3.91
60 61 6.262944 ACTTGAGTATGTTTCTTGTTGATGCA 59.737 34.615 0.00 0.00 0.00 3.96
61 62 6.822667 TGAGTATGTTTCTTGTTGATGCAT 57.177 33.333 0.00 0.00 0.00 3.96
62 63 6.845302 TGAGTATGTTTCTTGTTGATGCATC 58.155 36.000 20.14 20.14 0.00 3.91
63 64 6.430616 TGAGTATGTTTCTTGTTGATGCATCA 59.569 34.615 25.42 25.42 34.44 3.07
64 65 7.040548 TGAGTATGTTTCTTGTTGATGCATCAA 60.041 33.333 33.08 33.08 43.94 2.57
81 82 4.751060 CATCAAATGCAGTTGCCAATACT 58.249 39.130 21.53 0.00 41.18 2.12
82 83 4.870123 TCAAATGCAGTTGCCAATACTT 57.130 36.364 21.53 0.00 41.18 2.24
83 84 4.808558 TCAAATGCAGTTGCCAATACTTC 58.191 39.130 21.53 0.00 41.18 3.01
84 85 4.523943 TCAAATGCAGTTGCCAATACTTCT 59.476 37.500 21.53 0.00 41.18 2.85
85 86 4.708726 AATGCAGTTGCCAATACTTCTC 57.291 40.909 1.06 0.00 41.18 2.87
86 87 2.436417 TGCAGTTGCCAATACTTCTCC 58.564 47.619 1.06 0.00 41.18 3.71
87 88 2.040278 TGCAGTTGCCAATACTTCTCCT 59.960 45.455 1.06 0.00 41.18 3.69
88 89 3.084786 GCAGTTGCCAATACTTCTCCTT 58.915 45.455 0.00 0.00 34.31 3.36
89 90 3.507622 GCAGTTGCCAATACTTCTCCTTT 59.492 43.478 0.00 0.00 34.31 3.11
90 91 4.616835 GCAGTTGCCAATACTTCTCCTTTG 60.617 45.833 0.00 0.00 34.31 2.77
91 92 3.507622 AGTTGCCAATACTTCTCCTTTGC 59.492 43.478 0.00 0.00 0.00 3.68
92 93 3.439857 TGCCAATACTTCTCCTTTGCT 57.560 42.857 0.00 0.00 0.00 3.91
93 94 3.766545 TGCCAATACTTCTCCTTTGCTT 58.233 40.909 0.00 0.00 0.00 3.91
94 95 4.151883 TGCCAATACTTCTCCTTTGCTTT 58.848 39.130 0.00 0.00 0.00 3.51
95 96 4.022068 TGCCAATACTTCTCCTTTGCTTTG 60.022 41.667 0.00 0.00 0.00 2.77
96 97 4.488879 CCAATACTTCTCCTTTGCTTTGC 58.511 43.478 0.00 0.00 0.00 3.68
97 98 4.219288 CCAATACTTCTCCTTTGCTTTGCT 59.781 41.667 0.00 0.00 0.00 3.91
98 99 5.397326 CAATACTTCTCCTTTGCTTTGCTC 58.603 41.667 0.00 0.00 0.00 4.26
114 115 1.555075 TGCTCTGAAATTAGCTCCGGT 59.445 47.619 0.00 0.00 39.53 5.28
127 128 9.710818 AAATTAGCTCCGGTAGATAATAGGATA 57.289 33.333 18.43 0.00 44.17 2.59
138 139 9.685828 GGTAGATAATAGGATAATTCATCTCGC 57.314 37.037 0.00 0.00 33.78 5.03
185 187 5.917541 AATCATTAAACGATACGCCGATT 57.082 34.783 0.00 0.00 0.00 3.34
186 188 5.917541 ATCATTAAACGATACGCCGATTT 57.082 34.783 0.00 0.00 0.00 2.17
188 190 6.109320 TCATTAAACGATACGCCGATTTTT 57.891 33.333 0.00 0.00 0.00 1.94
226 228 5.730550 AGTAGGACAATATTTTCGCTGACA 58.269 37.500 0.00 0.00 0.00 3.58
227 229 6.349300 AGTAGGACAATATTTTCGCTGACAT 58.651 36.000 0.00 0.00 0.00 3.06
240 242 2.668250 GCTGACATACACACACACGTA 58.332 47.619 0.00 0.00 0.00 3.57
398 428 5.874810 ACGTTTAGATGCTGCAAGATCTTAA 59.125 36.000 7.86 2.72 34.33 1.85
524 554 1.403814 TCCTCTGTATCTTGCTCCCG 58.596 55.000 0.00 0.00 0.00 5.14
626 700 0.460987 GCAGCTGTGCGAGATAACCT 60.461 55.000 16.64 0.00 40.71 3.50
686 760 0.893727 CCAAACCGGGAAAGGACAGG 60.894 60.000 6.32 0.00 34.73 4.00
713 787 1.455773 ATCTCCTGCACCGATCCGA 60.456 57.895 0.00 0.00 0.00 4.55
714 788 1.739338 ATCTCCTGCACCGATCCGAC 61.739 60.000 0.00 0.00 0.00 4.79
715 789 3.432051 CTCCTGCACCGATCCGACC 62.432 68.421 0.00 0.00 0.00 4.79
716 790 3.461773 CCTGCACCGATCCGACCT 61.462 66.667 0.00 0.00 0.00 3.85
717 791 2.125326 CCTGCACCGATCCGACCTA 61.125 63.158 0.00 0.00 0.00 3.08
718 792 1.360551 CTGCACCGATCCGACCTAG 59.639 63.158 0.00 0.00 0.00 3.02
723 797 1.200252 CACCGATCCGACCTAGCTATG 59.800 57.143 0.00 0.00 0.00 2.23
725 799 1.740585 CCGATCCGACCTAGCTATGAG 59.259 57.143 2.75 0.00 0.00 2.90
800 874 4.624024 GCACTATTACTGCTACGACAAACA 59.376 41.667 0.00 0.00 0.00 2.83
820 895 8.992073 ACAAACAAAGATATTTGGCTTCAATTC 58.008 29.630 16.65 0.00 39.61 2.17
825 900 4.823989 AGATATTTGGCTTCAATTCTCCCG 59.176 41.667 0.00 0.00 0.00 5.14
829 904 2.368439 TGGCTTCAATTCTCCCGATTG 58.632 47.619 0.00 0.00 0.00 2.67
897 1223 2.168326 ATTGATGCACACACGACTGA 57.832 45.000 0.00 0.00 0.00 3.41
943 1296 0.764369 TACTAGCATCCCCAGCCAGG 60.764 60.000 0.00 0.00 37.03 4.45
952 1305 1.078848 CCCAGCCAGGTCTTCTTCG 60.079 63.158 0.00 0.00 34.66 3.79
989 1342 1.134965 GCTGATCGTAGTGGCAGAGTT 60.135 52.381 0.00 0.00 0.00 3.01
1085 1450 7.550597 TCCTTCTCATCATCTATATGTTGCT 57.449 36.000 0.00 0.00 34.24 3.91
1198 1564 1.217244 GGTATCGGCCACAGTTCGT 59.783 57.895 2.24 0.00 0.00 3.85
1339 1708 4.835615 AGCCTCGACCTACATATGATTCTT 59.164 41.667 10.38 0.00 0.00 2.52
1340 1709 5.047660 AGCCTCGACCTACATATGATTCTTC 60.048 44.000 10.38 0.00 0.00 2.87
1366 1740 1.134907 CATGCTTCTTGGTCATTGCCC 60.135 52.381 0.00 0.00 0.00 5.36
1371 1745 0.327924 TCTTGGTCATTGCCCGTCAT 59.672 50.000 0.00 0.00 0.00 3.06
1549 1929 1.300971 CCTGCAAGTCACCCATCACG 61.301 60.000 0.00 0.00 0.00 4.35
1561 1941 1.134401 CCCATCACGATGCAGGTAACT 60.134 52.381 1.28 0.00 41.47 2.24
1605 1998 5.927689 ACGATCTGACCGTACTCTTATCTAG 59.072 44.000 0.00 0.00 38.61 2.43
1607 2000 7.089538 CGATCTGACCGTACTCTTATCTAGTA 58.910 42.308 0.00 0.00 0.00 1.82
1608 2001 7.760794 CGATCTGACCGTACTCTTATCTAGTAT 59.239 40.741 0.00 0.00 32.34 2.12
1638 2040 7.082602 CAGTATAATCGCCGACAGTATAAACT 58.917 38.462 0.00 0.00 35.91 2.66
1860 2279 7.741027 TGCTTCTTCAATCCATCTTCATATC 57.259 36.000 0.00 0.00 0.00 1.63
1864 2291 7.741027 TCTTCAATCCATCTTCATATCTTGC 57.259 36.000 0.00 0.00 0.00 4.01
1870 2297 3.567164 CCATCTTCATATCTTGCCCACAC 59.433 47.826 0.00 0.00 0.00 3.82
1948 2383 0.178068 ACACACGCAACACCTCTTCT 59.822 50.000 0.00 0.00 0.00 2.85
1950 2385 1.792949 CACACGCAACACCTCTTCTAC 59.207 52.381 0.00 0.00 0.00 2.59
1979 2432 5.861787 CGAACCAAAAATACCCATTTCAGTC 59.138 40.000 0.00 0.00 33.09 3.51
2049 2505 4.490743 GTGCATGTAATTGTAACCAACCC 58.509 43.478 0.00 0.00 32.26 4.11
2050 2506 4.021894 GTGCATGTAATTGTAACCAACCCA 60.022 41.667 0.00 0.00 32.26 4.51
2255 2711 1.769026 CGTCTCCTCTTCCTCCATCA 58.231 55.000 0.00 0.00 0.00 3.07
2275 2731 0.893447 AGTCCGGTACAGTAACAGCC 59.107 55.000 0.00 0.00 0.00 4.85
2277 2733 0.251922 TCCGGTACAGTAACAGCCCT 60.252 55.000 0.00 0.00 0.00 5.19
2279 2735 1.674817 CCGGTACAGTAACAGCCCTTG 60.675 57.143 0.00 0.00 0.00 3.61
2280 2736 1.274167 CGGTACAGTAACAGCCCTTGA 59.726 52.381 0.00 0.00 0.00 3.02
2319 2840 5.563475 GCTTCATGTGTGTTTGCAATACTCT 60.563 40.000 0.00 0.00 0.00 3.24
2320 2841 6.348458 GCTTCATGTGTGTTTGCAATACTCTA 60.348 38.462 0.00 0.00 0.00 2.43
2322 2843 6.898041 TCATGTGTGTTTGCAATACTCTAAC 58.102 36.000 0.00 0.00 0.00 2.34
2323 2844 6.484977 TCATGTGTGTTTGCAATACTCTAACA 59.515 34.615 0.00 4.11 0.00 2.41
2324 2845 6.875948 TGTGTGTTTGCAATACTCTAACAT 57.124 33.333 0.00 0.00 32.10 2.71
2327 2877 6.953743 GTGTGTTTGCAATACTCTAACATACG 59.046 38.462 0.00 0.00 33.41 3.06
2331 2881 7.008538 TGTTTGCAATACTCTAACATACGTACG 59.991 37.037 15.01 15.01 0.00 3.67
2356 2910 1.002430 ACGAGTGCAGGTGATGATTGT 59.998 47.619 0.00 0.00 0.00 2.71
2434 2990 2.746142 CGGTCATGGCATCAGGTACAAT 60.746 50.000 0.00 0.00 0.00 2.71
2435 2991 2.620115 GGTCATGGCATCAGGTACAATG 59.380 50.000 0.00 0.00 0.00 2.82
2440 3002 1.818060 GGCATCAGGTACAATGCACAA 59.182 47.619 21.36 0.00 46.80 3.33
2495 3064 5.448654 AGTGCATAAGGGCTGATGAATTTA 58.551 37.500 0.00 0.00 34.04 1.40
2496 3065 5.893255 AGTGCATAAGGGCTGATGAATTTAA 59.107 36.000 0.00 0.00 34.04 1.52
2497 3066 6.552350 AGTGCATAAGGGCTGATGAATTTAAT 59.448 34.615 0.00 0.00 34.04 1.40
2498 3067 7.070322 AGTGCATAAGGGCTGATGAATTTAATT 59.930 33.333 0.00 0.00 34.04 1.40
2499 3068 7.712205 GTGCATAAGGGCTGATGAATTTAATTT 59.288 33.333 0.00 0.00 34.04 1.82
2632 3211 7.203255 AGTATCCAACTGCAACTTCTTTAAC 57.797 36.000 0.00 0.00 36.93 2.01
2659 3238 3.600388 GAACGGTGTCAGGATCAAATCT 58.400 45.455 0.00 0.00 0.00 2.40
2728 3307 0.179023 TGTGTGTGCCTTGCATCAGA 60.179 50.000 0.00 0.00 41.91 3.27
2818 3403 9.690913 ATTCCCCTGATAACATATATGATGTTG 57.309 33.333 19.63 3.82 41.73 3.33
2830 3418 3.806625 ATGATGTTGTAAATGCAGGGC 57.193 42.857 0.00 0.00 0.00 5.19
2917 3505 3.442625 TCGACATCGACCAGTTCTATTGT 59.557 43.478 0.00 0.00 44.22 2.71
2920 3508 3.513912 ACATCGACCAGTTCTATTGTCCA 59.486 43.478 0.00 0.00 0.00 4.02
3204 3802 0.106268 TGCTCCACCAAAAGCCAAGA 60.106 50.000 0.00 0.00 37.73 3.02
3253 3851 0.395586 AAGGTGAAGCCACAAGTGCA 60.396 50.000 0.00 0.00 44.93 4.57
3274 3872 2.813226 TTCTTGGGCCGTTGATCCCG 62.813 60.000 0.00 0.00 45.60 5.14
3284 3909 1.673033 CGTTGATCCCGAGTGCTCTTT 60.673 52.381 0.00 0.00 0.00 2.52
3436 4061 6.129273 CGACTACACATACACACAAGTTGTAC 60.129 42.308 8.49 0.00 35.67 2.90
3469 4094 7.647715 AGCACAATGTATGTTGTTCAAAGTTAC 59.352 33.333 0.00 0.00 41.46 2.50
3520 4145 0.842030 TGGACATGCCTGAAGACCCT 60.842 55.000 0.00 0.00 37.63 4.34
3543 4168 5.848286 ATAGCTCCACCAATCATATTGGA 57.152 39.130 22.29 3.46 42.06 3.53
3554 4179 9.110502 CACCAATCATATTGGATAGATCATCTG 57.889 37.037 22.29 5.28 42.06 2.90
3654 4283 3.981211 CTTGTACAATGCAAGGTGCTTT 58.019 40.909 9.13 0.00 45.31 3.51
3676 4305 9.397280 GCTTTGGAAGTACCTAGAGAAATAAAT 57.603 33.333 0.00 0.00 39.86 1.40
3718 4349 8.035394 CACCGTGCTTATATGTAAAGGATAGAT 58.965 37.037 6.52 0.00 0.00 1.98
3721 4352 9.077674 CGTGCTTATATGTAAAGGATAGATGAC 57.922 37.037 0.00 0.00 0.00 3.06
3745 4376 5.517322 AATTAGGTACCGCTTCTGTAGAG 57.483 43.478 6.18 0.00 0.00 2.43
3863 4494 5.853572 TCCCCTAAAAAGCTAAAGAGGAA 57.146 39.130 6.29 0.00 0.00 3.36
3901 4534 2.754946 TCCTTAACCTGCACCTAACG 57.245 50.000 0.00 0.00 0.00 3.18
3911 4544 1.065273 CACCTAACGACCGATCCCG 59.935 63.158 0.00 0.00 0.00 5.14
3915 4548 1.405105 CCTAACGACCGATCCCGTAAA 59.595 52.381 0.00 0.00 38.13 2.01
3937 4570 9.827411 GTAAAAGCTTTAGAGGAGTAACAATTG 57.173 33.333 13.10 3.24 0.00 2.32
3948 4581 3.421844 AGTAACAATTGTCCTCCTTGGC 58.578 45.455 12.39 0.00 35.26 4.52
4036 4839 2.757124 CCCTACCCACCCTGCATCC 61.757 68.421 0.00 0.00 0.00 3.51
4067 4870 2.202756 GTCGCCCTACTTGCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
4070 4873 2.420568 CGCCCTACTTGCCTCGGTA 61.421 63.158 0.00 0.00 0.00 4.02
4148 4951 1.202256 CGATTCGGTCGGTTCTCATCA 60.202 52.381 0.00 0.00 46.47 3.07
4150 4953 0.245539 TTCGGTCGGTTCTCATCACC 59.754 55.000 0.00 0.00 0.00 4.02
4170 4973 0.800012 GACGGCGCCTAAATTGACAA 59.200 50.000 26.68 0.00 0.00 3.18
4172 4975 1.199097 ACGGCGCCTAAATTGACAAAG 59.801 47.619 26.68 6.20 0.00 2.77
4181 4984 1.904287 AATTGACAAAGCTACGGCCA 58.096 45.000 2.24 0.00 39.73 5.36
4266 5070 0.034756 CGAACCACACATCCACCTCA 59.965 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.047377 GGGAATGCTACAAACCTCAAATTCA 60.047 40.000 0.00 0.00 0.00 2.57
1 2 5.185828 AGGGAATGCTACAAACCTCAAATTC 59.814 40.000 0.00 0.00 0.00 2.17
2 3 5.086621 AGGGAATGCTACAAACCTCAAATT 58.913 37.500 0.00 0.00 0.00 1.82
3 4 4.677182 AGGGAATGCTACAAACCTCAAAT 58.323 39.130 0.00 0.00 0.00 2.32
5 6 3.806949 AGGGAATGCTACAAACCTCAA 57.193 42.857 0.00 0.00 0.00 3.02
6 7 4.919774 TTAGGGAATGCTACAAACCTCA 57.080 40.909 0.00 0.00 0.00 3.86
7 8 5.885912 TGATTTAGGGAATGCTACAAACCTC 59.114 40.000 0.00 0.00 0.00 3.85
8 9 5.826643 TGATTTAGGGAATGCTACAAACCT 58.173 37.500 0.00 0.00 0.00 3.50
9 10 6.321181 TGATGATTTAGGGAATGCTACAAACC 59.679 38.462 0.00 0.00 0.00 3.27
10 11 7.333528 TGATGATTTAGGGAATGCTACAAAC 57.666 36.000 0.00 0.00 0.00 2.93
11 12 7.615365 AGTTGATGATTTAGGGAATGCTACAAA 59.385 33.333 0.00 0.00 0.00 2.83
12 13 7.118723 AGTTGATGATTTAGGGAATGCTACAA 58.881 34.615 0.00 0.00 0.00 2.41
13 14 6.662755 AGTTGATGATTTAGGGAATGCTACA 58.337 36.000 0.00 0.00 0.00 2.74
15 16 7.345691 TCAAGTTGATGATTTAGGGAATGCTA 58.654 34.615 0.08 0.00 0.00 3.49
16 17 6.189859 TCAAGTTGATGATTTAGGGAATGCT 58.810 36.000 0.08 0.00 0.00 3.79
17 18 6.096001 ACTCAAGTTGATGATTTAGGGAATGC 59.904 38.462 5.91 0.00 0.00 3.56
18 19 7.636150 ACTCAAGTTGATGATTTAGGGAATG 57.364 36.000 5.91 0.00 0.00 2.67
19 20 9.347240 CATACTCAAGTTGATGATTTAGGGAAT 57.653 33.333 5.91 0.00 0.00 3.01
20 21 8.328758 ACATACTCAAGTTGATGATTTAGGGAA 58.671 33.333 5.91 0.00 0.00 3.97
21 22 7.861629 ACATACTCAAGTTGATGATTTAGGGA 58.138 34.615 5.91 0.00 0.00 4.20
22 23 8.511604 AACATACTCAAGTTGATGATTTAGGG 57.488 34.615 5.91 0.00 0.00 3.53
23 24 9.994432 GAAACATACTCAAGTTGATGATTTAGG 57.006 33.333 5.91 0.00 0.00 2.69
26 27 9.903682 CAAGAAACATACTCAAGTTGATGATTT 57.096 29.630 5.91 5.82 0.00 2.17
27 28 9.071276 ACAAGAAACATACTCAAGTTGATGATT 57.929 29.630 5.91 3.23 0.00 2.57
28 29 8.627208 ACAAGAAACATACTCAAGTTGATGAT 57.373 30.769 5.91 0.00 0.00 2.45
29 30 8.344831 CAACAAGAAACATACTCAAGTTGATGA 58.655 33.333 5.91 0.00 36.78 2.92
30 31 8.344831 TCAACAAGAAACATACTCAAGTTGATG 58.655 33.333 5.91 4.72 38.21 3.07
31 32 8.450578 TCAACAAGAAACATACTCAAGTTGAT 57.549 30.769 5.91 0.00 38.21 2.57
32 33 7.857734 TCAACAAGAAACATACTCAAGTTGA 57.142 32.000 5.25 5.25 40.06 3.18
33 34 7.113965 GCATCAACAAGAAACATACTCAAGTTG 59.886 37.037 0.00 0.00 36.19 3.16
34 35 7.141363 GCATCAACAAGAAACATACTCAAGTT 58.859 34.615 0.00 0.00 0.00 2.66
35 36 6.262944 TGCATCAACAAGAAACATACTCAAGT 59.737 34.615 0.00 0.00 0.00 3.16
36 37 6.671190 TGCATCAACAAGAAACATACTCAAG 58.329 36.000 0.00 0.00 0.00 3.02
37 38 6.631971 TGCATCAACAAGAAACATACTCAA 57.368 33.333 0.00 0.00 0.00 3.02
38 39 6.430616 TGATGCATCAACAAGAAACATACTCA 59.569 34.615 26.87 0.00 33.08 3.41
39 40 6.845302 TGATGCATCAACAAGAAACATACTC 58.155 36.000 26.87 0.00 33.08 2.59
40 41 6.822667 TGATGCATCAACAAGAAACATACT 57.177 33.333 26.87 0.00 33.08 2.12
41 42 7.872163 TTTGATGCATCAACAAGAAACATAC 57.128 32.000 35.75 2.88 45.63 2.39
42 43 8.468720 CATTTGATGCATCAACAAGAAACATA 57.531 30.769 35.75 20.43 45.63 2.29
43 44 7.359262 CATTTGATGCATCAACAAGAAACAT 57.641 32.000 35.75 22.83 45.63 2.71
44 45 6.772770 CATTTGATGCATCAACAAGAAACA 57.227 33.333 35.75 21.74 45.63 2.83
59 60 4.751060 AGTATTGGCAACTGCATTTGATG 58.249 39.130 19.89 0.00 44.36 3.07
60 61 5.186409 AGAAGTATTGGCAACTGCATTTGAT 59.814 36.000 19.89 7.66 44.36 2.57
61 62 4.523943 AGAAGTATTGGCAACTGCATTTGA 59.476 37.500 19.89 0.21 44.36 2.69
62 63 4.813027 AGAAGTATTGGCAACTGCATTTG 58.187 39.130 12.16 12.16 44.36 2.32
63 64 4.082026 GGAGAAGTATTGGCAACTGCATTT 60.082 41.667 0.00 0.00 44.36 2.32
64 65 3.445096 GGAGAAGTATTGGCAACTGCATT 59.555 43.478 0.00 0.00 44.36 3.56
65 66 3.019564 GGAGAAGTATTGGCAACTGCAT 58.980 45.455 0.00 0.00 44.36 3.96
66 67 2.040278 AGGAGAAGTATTGGCAACTGCA 59.960 45.455 0.00 0.00 44.36 4.41
67 68 2.716217 AGGAGAAGTATTGGCAACTGC 58.284 47.619 0.00 0.00 41.14 4.40
68 69 4.616835 GCAAAGGAGAAGTATTGGCAACTG 60.617 45.833 0.00 0.00 37.61 3.16
69 70 3.507622 GCAAAGGAGAAGTATTGGCAACT 59.492 43.478 0.00 0.00 37.61 3.16
70 71 3.507622 AGCAAAGGAGAAGTATTGGCAAC 59.492 43.478 0.00 0.00 0.00 4.17
71 72 3.766545 AGCAAAGGAGAAGTATTGGCAA 58.233 40.909 0.68 0.68 0.00 4.52
72 73 3.439857 AGCAAAGGAGAAGTATTGGCA 57.560 42.857 0.00 0.00 0.00 4.92
73 74 4.488879 CAAAGCAAAGGAGAAGTATTGGC 58.511 43.478 0.00 0.00 0.00 4.52
74 75 4.219288 AGCAAAGCAAAGGAGAAGTATTGG 59.781 41.667 0.00 0.00 0.00 3.16
75 76 5.182760 AGAGCAAAGCAAAGGAGAAGTATTG 59.817 40.000 0.00 0.00 0.00 1.90
76 77 5.182760 CAGAGCAAAGCAAAGGAGAAGTATT 59.817 40.000 0.00 0.00 0.00 1.89
77 78 4.699257 CAGAGCAAAGCAAAGGAGAAGTAT 59.301 41.667 0.00 0.00 0.00 2.12
78 79 4.067896 CAGAGCAAAGCAAAGGAGAAGTA 58.932 43.478 0.00 0.00 0.00 2.24
79 80 2.883386 CAGAGCAAAGCAAAGGAGAAGT 59.117 45.455 0.00 0.00 0.00 3.01
80 81 3.144506 TCAGAGCAAAGCAAAGGAGAAG 58.855 45.455 0.00 0.00 0.00 2.85
81 82 3.213206 TCAGAGCAAAGCAAAGGAGAA 57.787 42.857 0.00 0.00 0.00 2.87
82 83 2.936919 TCAGAGCAAAGCAAAGGAGA 57.063 45.000 0.00 0.00 0.00 3.71
83 84 3.996150 TTTCAGAGCAAAGCAAAGGAG 57.004 42.857 0.00 0.00 0.00 3.69
84 85 4.942761 AATTTCAGAGCAAAGCAAAGGA 57.057 36.364 0.00 0.00 0.00 3.36
85 86 4.624452 GCTAATTTCAGAGCAAAGCAAAGG 59.376 41.667 0.00 0.00 38.62 3.11
86 87 5.467705 AGCTAATTTCAGAGCAAAGCAAAG 58.532 37.500 1.03 0.00 41.36 2.77
87 88 5.458041 AGCTAATTTCAGAGCAAAGCAAA 57.542 34.783 1.03 0.00 41.36 3.68
88 89 4.082571 GGAGCTAATTTCAGAGCAAAGCAA 60.083 41.667 1.03 0.00 41.36 3.91
89 90 3.441572 GGAGCTAATTTCAGAGCAAAGCA 59.558 43.478 1.03 0.00 41.36 3.91
90 91 3.486542 CGGAGCTAATTTCAGAGCAAAGC 60.487 47.826 1.03 0.00 41.36 3.51
91 92 3.064545 CCGGAGCTAATTTCAGAGCAAAG 59.935 47.826 0.00 0.00 41.36 2.77
92 93 3.009723 CCGGAGCTAATTTCAGAGCAAA 58.990 45.455 0.00 0.00 41.36 3.68
93 94 2.027192 ACCGGAGCTAATTTCAGAGCAA 60.027 45.455 9.46 0.00 41.36 3.91
94 95 1.555075 ACCGGAGCTAATTTCAGAGCA 59.445 47.619 9.46 0.00 41.36 4.26
95 96 2.317530 ACCGGAGCTAATTTCAGAGC 57.682 50.000 9.46 0.00 39.08 4.09
96 97 4.920640 TCTACCGGAGCTAATTTCAGAG 57.079 45.455 9.46 0.00 0.00 3.35
97 98 6.971726 TTATCTACCGGAGCTAATTTCAGA 57.028 37.500 9.46 0.00 0.00 3.27
98 99 7.976734 CCTATTATCTACCGGAGCTAATTTCAG 59.023 40.741 9.46 4.16 30.76 3.02
154 155 9.302773 GCGTATCGTTTAATGATTTATCTGAAC 57.697 33.333 4.91 0.00 0.00 3.18
199 201 8.662141 GTCAGCGAAAATATTGTCCTACTTTTA 58.338 33.333 0.00 0.00 0.00 1.52
207 209 6.183360 TGTGTATGTCAGCGAAAATATTGTCC 60.183 38.462 0.00 0.00 0.00 4.02
212 214 5.641636 TGTGTGTGTATGTCAGCGAAAATAT 59.358 36.000 0.00 0.00 0.00 1.28
226 228 2.823924 TGGCTTACGTGTGTGTGTAT 57.176 45.000 0.00 0.00 0.00 2.29
227 229 2.036089 TGATGGCTTACGTGTGTGTGTA 59.964 45.455 0.00 0.00 0.00 2.90
240 242 2.125512 GGCGAGTCGTGATGGCTT 60.126 61.111 15.08 0.00 0.00 4.35
337 367 4.851010 TCAGAATATCGCGTACATTCGAA 58.149 39.130 5.77 0.00 38.28 3.71
530 560 6.723977 TGGCTTGATTAAAGGGTGAATTTACT 59.276 34.615 0.00 0.00 36.30 2.24
626 700 1.321805 CGAGCCCCAAAATGCCATGA 61.322 55.000 0.00 0.00 0.00 3.07
713 787 7.141758 TGGAATTCATTTCTCATAGCTAGGT 57.858 36.000 7.93 0.00 34.56 3.08
714 788 7.500227 TGTTGGAATTCATTTCTCATAGCTAGG 59.500 37.037 7.93 0.00 34.56 3.02
715 789 8.341173 GTGTTGGAATTCATTTCTCATAGCTAG 58.659 37.037 7.93 0.00 34.56 3.42
716 790 7.011389 CGTGTTGGAATTCATTTCTCATAGCTA 59.989 37.037 7.93 0.00 34.56 3.32
717 791 6.183360 CGTGTTGGAATTCATTTCTCATAGCT 60.183 38.462 7.93 0.00 34.56 3.32
718 792 5.967674 CGTGTTGGAATTCATTTCTCATAGC 59.032 40.000 7.93 0.00 34.56 2.97
723 797 5.862924 TCTCGTGTTGGAATTCATTTCTC 57.137 39.130 7.93 0.00 34.56 2.87
725 799 6.428385 AGATCTCGTGTTGGAATTCATTTC 57.572 37.500 7.93 0.00 0.00 2.17
779 853 7.149973 TCTTTGTTTGTCGTAGCAGTAATAGT 58.850 34.615 0.00 0.00 0.00 2.12
780 854 7.576750 TCTTTGTTTGTCGTAGCAGTAATAG 57.423 36.000 0.00 0.00 0.00 1.73
781 855 9.811995 ATATCTTTGTTTGTCGTAGCAGTAATA 57.188 29.630 0.00 0.00 0.00 0.98
800 874 6.183360 CGGGAGAATTGAAGCCAAATATCTTT 60.183 38.462 0.00 0.00 35.67 2.52
820 895 2.315781 TAGCAGCAGCCAATCGGGAG 62.316 60.000 0.00 0.00 43.56 4.30
859 939 0.862701 TTTATACACGCGCGAGACGG 60.863 55.000 39.36 20.98 43.93 4.79
897 1223 5.451847 TCGTAGTCGTACTGATGATGCAGT 61.452 45.833 0.00 0.00 42.55 4.40
952 1305 0.249238 AGCAGCTGAATCGATCGGTC 60.249 55.000 20.43 13.46 36.73 4.79
989 1342 2.769893 CGCATACCATGATGATCACCA 58.230 47.619 0.00 0.00 0.00 4.17
1085 1450 1.274167 AGATCCGTACGTCAGGCAAAA 59.726 47.619 15.21 0.00 0.00 2.44
1284 1650 5.599242 TGTTATACCTTGGTATCATCCGTCA 59.401 40.000 14.83 4.33 0.00 4.35
1339 1708 0.111061 ACCAAGAAGCATGCAGGTGA 59.889 50.000 21.98 0.00 0.00 4.02
1340 1709 0.524862 GACCAAGAAGCATGCAGGTG 59.475 55.000 21.98 11.70 0.00 4.00
1388 1762 0.749049 CGGAGGATGCAGATGAGTGA 59.251 55.000 0.00 0.00 0.00 3.41
1488 1868 0.401738 CAGCAAGAAGGTCCTTCCCA 59.598 55.000 25.31 0.00 40.98 4.37
1489 1869 0.962855 GCAGCAAGAAGGTCCTTCCC 60.963 60.000 25.31 15.14 40.98 3.97
1561 1941 1.167851 CGGTAGACGGTCAGGTGTTA 58.832 55.000 11.27 0.00 39.42 2.41
1573 1953 0.304098 CGGTCAGATCGTCGGTAGAC 59.696 60.000 0.00 2.75 43.72 2.59
1605 1998 7.065216 TGTCGGCGATTATACTGTACTATAC 57.935 40.000 14.79 0.00 0.00 1.47
1607 2000 5.704515 ACTGTCGGCGATTATACTGTACTAT 59.295 40.000 14.79 0.00 0.00 2.12
1608 2001 5.059161 ACTGTCGGCGATTATACTGTACTA 58.941 41.667 14.79 0.00 0.00 1.82
1638 2040 2.036414 AGAGACGCTCCAGCCTCA 59.964 61.111 7.36 0.00 37.91 3.86
1860 2279 1.735386 CTGATCAGAGTGTGGGCAAG 58.265 55.000 18.34 0.00 0.00 4.01
1864 2291 0.743701 GCAGCTGATCAGAGTGTGGG 60.744 60.000 27.04 7.47 0.00 4.61
1870 2297 1.049855 AGAGGGGCAGCTGATCAGAG 61.050 60.000 27.04 17.74 0.00 3.35
1948 2383 3.083293 GGTATTTTTGGTTCGGCAGGTA 58.917 45.455 0.00 0.00 0.00 3.08
1950 2385 1.203758 GGGTATTTTTGGTTCGGCAGG 59.796 52.381 0.00 0.00 0.00 4.85
2017 2473 5.894807 ACAATTACATGCACCTGAATTAGC 58.105 37.500 0.00 0.00 0.00 3.09
2050 2506 0.681733 ACGAGAATGACACCAGCTGT 59.318 50.000 13.81 0.00 34.96 4.40
2194 2650 0.899253 TGGTGATCCCGTCCGTGTTA 60.899 55.000 0.00 0.00 35.15 2.41
2255 2711 1.274447 GGCTGTTACTGTACCGGACTT 59.726 52.381 9.46 0.00 0.00 3.01
2275 2731 7.494211 TGAAGCAATGGATTTTATCATCAAGG 58.506 34.615 0.00 0.00 0.00 3.61
2277 2733 8.479689 ACATGAAGCAATGGATTTTATCATCAA 58.520 29.630 0.00 0.00 31.46 2.57
2279 2735 7.924412 ACACATGAAGCAATGGATTTTATCATC 59.076 33.333 0.00 0.00 31.46 2.92
2280 2736 7.709182 CACACATGAAGCAATGGATTTTATCAT 59.291 33.333 0.00 0.00 31.46 2.45
2319 2840 3.435327 ACTCGTCCAACGTACGTATGTTA 59.565 43.478 27.90 14.44 43.14 2.41
2320 2841 2.226437 ACTCGTCCAACGTACGTATGTT 59.774 45.455 24.14 24.14 43.14 2.71
2322 2843 2.171567 CACTCGTCCAACGTACGTATG 58.828 52.381 23.12 19.84 43.14 2.39
2323 2844 1.466360 GCACTCGTCCAACGTACGTAT 60.466 52.381 23.12 9.26 43.14 3.06
2324 2845 0.110238 GCACTCGTCCAACGTACGTA 60.110 55.000 23.12 2.73 43.14 3.57
2327 2877 1.007336 CCTGCACTCGTCCAACGTAC 61.007 60.000 0.00 0.00 43.14 3.67
2331 2881 0.320771 ATCACCTGCACTCGTCCAAC 60.321 55.000 0.00 0.00 0.00 3.77
2356 2910 4.626604 GTGGTTTCCGTTATAATCGACACA 59.373 41.667 8.43 0.00 0.00 3.72
2524 3093 5.228945 ACAAGAAAGAAGCTGCTTAGGTA 57.771 39.130 15.95 0.00 0.00 3.08
2632 3211 2.014554 CCTGACACCGTTCGTCGTG 61.015 63.158 0.00 0.00 36.11 4.35
2659 3238 1.133945 TGCTTCAGTGTTACCTGCCAA 60.134 47.619 0.00 0.00 32.32 4.52
2699 3278 2.580661 GCACACACATGCACAACAC 58.419 52.632 0.00 0.00 45.39 3.32
2818 3403 2.283472 CTTGCCCGCCCTGCATTTAC 62.283 60.000 0.00 0.00 38.76 2.01
2830 3418 4.107051 CTCGCTTTGCCTTGCCCG 62.107 66.667 0.00 0.00 0.00 6.13
3204 3802 2.532843 GCTCCCATGGGCATTCATAAT 58.467 47.619 27.41 0.00 34.68 1.28
3235 3833 0.820891 CTGCACTTGTGGCTTCACCT 60.821 55.000 2.81 0.00 40.53 4.00
3253 3851 0.322546 GGATCAACGGCCCAAGAACT 60.323 55.000 0.00 0.00 0.00 3.01
3274 3872 4.558538 ATGTTCACAACAAAGAGCACTC 57.441 40.909 0.00 0.00 45.86 3.51
3284 3909 3.563808 GTCCAAGCACTATGTTCACAACA 59.436 43.478 0.00 0.00 46.94 3.33
3436 4061 3.409851 ACATACATTGTGCTTGATGCG 57.590 42.857 0.00 0.00 46.63 4.73
3469 4094 5.605534 AGATCAATAAGAGTTGGACATCCG 58.394 41.667 0.00 0.00 39.43 4.18
3520 4145 6.950860 TCCAATATGATTGGTGGAGCTATA 57.049 37.500 15.98 0.00 40.40 1.31
3654 4283 9.268282 ACTGATTTATTTCTCTAGGTACTTCCA 57.732 33.333 0.00 0.00 41.75 3.53
3676 4305 3.013921 ACGGTGCTTCAAGAAAAACTGA 58.986 40.909 9.22 0.00 0.00 3.41
3718 4349 4.708421 ACAGAAGCGGTACCTAATTAGTCA 59.292 41.667 10.90 0.00 0.00 3.41
3721 4352 6.485984 TCTCTACAGAAGCGGTACCTAATTAG 59.514 42.308 10.90 5.43 0.00 1.73
3788 4419 4.890158 TGCAAGGTGTTTAGAGAGATGA 57.110 40.909 0.00 0.00 0.00 2.92
3799 4430 3.197265 GCTTTGAACAATGCAAGGTGTT 58.803 40.909 16.60 12.12 40.61 3.32
3884 4517 2.344025 GGTCGTTAGGTGCAGGTTAAG 58.656 52.381 0.00 0.00 0.00 1.85
3885 4518 1.337074 CGGTCGTTAGGTGCAGGTTAA 60.337 52.381 0.00 0.00 0.00 2.01
3901 4534 2.019948 AAGCTTTTACGGGATCGGTC 57.980 50.000 0.00 0.00 41.39 4.79
3911 4544 9.827411 CAATTGTTACTCCTCTAAAGCTTTTAC 57.173 33.333 18.47 0.00 0.00 2.01
3915 4548 6.655425 GGACAATTGTTACTCCTCTAAAGCTT 59.345 38.462 13.36 0.00 0.00 3.74
3937 4570 4.785453 CTGGCGGCCAAGGAGGAC 62.785 72.222 23.94 0.00 44.64 3.85
3948 4581 5.154932 CGAGTATATTTAAGAGTCTGGCGG 58.845 45.833 0.00 0.00 0.00 6.13
4015 4818 4.426313 GCAGGGTGGGTAGGGTGC 62.426 72.222 0.00 0.00 0.00 5.01
4022 4825 2.618185 ATGGGATGCAGGGTGGGT 60.618 61.111 0.00 0.00 0.00 4.51
4070 4873 2.515901 GGTGGCTTGTGGTGGACT 59.484 61.111 0.00 0.00 0.00 3.85
4095 4898 4.221422 GCGGCGGGTGCTATGAGA 62.221 66.667 9.78 0.00 42.25 3.27
4119 4922 2.038329 ACCGAATCGAGGTGGGGA 59.962 61.111 3.36 0.00 41.10 4.81
4148 4951 2.104253 CAATTTAGGCGCCGTCGGT 61.104 57.895 23.20 5.39 35.95 4.69
4150 4953 1.347221 GTCAATTTAGGCGCCGTCG 59.653 57.895 23.20 7.91 39.07 5.12
4152 4955 1.199097 CTTTGTCAATTTAGGCGCCGT 59.801 47.619 23.20 12.38 0.00 5.68
4223 5027 2.456577 CCCGTCAAATCCCTCCAAAAT 58.543 47.619 0.00 0.00 0.00 1.82
4248 5052 1.880027 GTTGAGGTGGATGTGTGGTTC 59.120 52.381 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.