Multiple sequence alignment - TraesCS3B01G595200

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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 TraesCS3B01G595200 chr3B 100.000 2659 0 0 949 3607 818277509 818274851 0.000000e+00 4911
1 TraesCS3B01G595200 chr3B 100.000 586 0 0 1 586 818278457 818277872 0.000000e+00 1083
2 TraesCS3B01G595200 chr3D 93.333 2205 92 28 1056 3253 608401150 608403306 0.000000e+00 3206
3 TraesCS3B01G595200 chr3D 91.522 460 23 7 138 586 608400554 608401008 1.420000e-173 619
4 TraesCS3B01G595200 chr3D 91.536 319 24 3 3285 3602 608403306 608403622 1.540000e-118 436
5 TraesCS3B01G595200 chr3A 94.835 2033 79 16 949 2971 740888356 740886340 0.000000e+00 3149
6 TraesCS3B01G595200 chr3A 86.067 1134 91 26 1540 2650 143700522 143699433 0.000000e+00 1157
7 TraesCS3B01G595200 chr3A 85.476 840 81 17 2578 3416 740885630 740884831 0.000000e+00 837
8 TraesCS3B01G595200 chr3A 85.437 618 40 27 3002 3607 740886336 740885757 6.670000e-167 597
9 TraesCS3B01G595200 chr3A 84.477 612 64 16 3007 3607 740884791 740884200 3.120000e-160 575
10 TraesCS3B01G595200 chr3A 78.049 369 29 23 230 586 740888783 740888455 6.150000e-43 185
11 TraesCS3B01G595200 chr4D 86.965 1542 116 39 1125 2650 311190468 311188996 0.000000e+00 1655
12 TraesCS3B01G595200 chr1B 85.983 1541 132 31 1125 2649 532235352 532236824 0.000000e+00 1572
13 TraesCS3B01G595200 chr4A 82.043 1537 155 54 1125 2650 67744978 67743552 0.000000e+00 1197
14 TraesCS3B01G595200 chr6A 83.586 1255 136 37 1126 2364 43118165 43119365 0.000000e+00 1112
15 TraesCS3B01G595200 chr6A 82.709 1255 138 42 1126 2364 43103215 43104406 0.000000e+00 1042
16 TraesCS3B01G595200 chrUn 87.066 835 71 19 1122 1938 325727627 325728442 0.000000e+00 909
17 TraesCS3B01G595200 chrUn 87.139 832 70 19 1125 1938 334361412 334360600 0.000000e+00 909
18 TraesCS3B01G595200 chr2B 87.129 808 71 11 1125 1926 175745678 175746458 0.000000e+00 885
19 TraesCS3B01G595200 chr2B 83.435 821 68 26 1123 1938 368311452 368310695 0.000000e+00 701


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 TraesCS3B01G595200 chr3B 818274851 818278457 3606 True 2997.000000 4911 100.000000 1 3607 2 chr3B.!!$R1 3606
1 TraesCS3B01G595200 chr3D 608400554 608403622 3068 False 1420.333333 3206 92.130333 138 3602 3 chr3D.!!$F1 3464
2 TraesCS3B01G595200 chr3A 143699433 143700522 1089 True 1157.000000 1157 86.067000 1540 2650 1 chr3A.!!$R1 1110
3 TraesCS3B01G595200 chr3A 740884200 740888783 4583 True 1068.600000 3149 85.654800 230 3607 5 chr3A.!!$R2 3377
4 TraesCS3B01G595200 chr4D 311188996 311190468 1472 True 1655.000000 1655 86.965000 1125 2650 1 chr4D.!!$R1 1525
5 TraesCS3B01G595200 chr1B 532235352 532236824 1472 False 1572.000000 1572 85.983000 1125 2649 1 chr1B.!!$F1 1524
6 TraesCS3B01G595200 chr4A 67743552 67744978 1426 True 1197.000000 1197 82.043000 1125 2650 1 chr4A.!!$R1 1525
7 TraesCS3B01G595200 chr6A 43118165 43119365 1200 False 1112.000000 1112 83.586000 1126 2364 1 chr6A.!!$F2 1238
8 TraesCS3B01G595200 chr6A 43103215 43104406 1191 False 1042.000000 1042 82.709000 1126 2364 1 chr6A.!!$F1 1238
9 TraesCS3B01G595200 chrUn 325727627 325728442 815 False 909.000000 909 87.066000 1122 1938 1 chrUn.!!$F1 816
10 TraesCS3B01G595200 chrUn 334360600 334361412 812 True 909.000000 909 87.139000 1125 1938 1 chrUn.!!$R1 813
11 TraesCS3B01G595200 chr2B 175745678 175746458 780 False 885.000000 885 87.129000 1125 1926 1 chr2B.!!$F1 801
12 TraesCS3B01G595200 chr2B 368310695 368311452 757 True 701.000000 701 83.435000 1123 1938 1 chr2B.!!$R1 815

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
108 109 0.036952 CCGAGCCACATGTCTCAAGT 60.037 55.0 13.32 0.0 0.00 3.16 F
111 112 0.399454 AGCCACATGTCTCAAGTGCT 59.601 50.0 0.00 0.0 32.62 4.40 F
226 227 0.466555 CTCCTTCTCCTCGTCCCGAT 60.467 60.0 0.00 0.0 34.61 4.18 F
2066 2131 0.600782 ATGTTTGCTTGCTTTGGGCG 60.601 50.0 0.00 0.0 45.43 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2131 0.171007 CACATTGGTCGAATGGGTGC 59.829 55.000 11.68 0.0 45.20 5.01 R
2216 2290 4.196626 TCTAATGCCGTAATATTCCCCG 57.803 45.455 0.00 0.0 0.00 5.73 R
2230 2305 1.869767 CGGCTCTCCAACATCTAATGC 59.130 52.381 0.00 0.0 0.00 3.56 R
2975 3068 0.249447 CGCATCGGAGCAGGATGTTA 60.249 55.000 11.63 0.0 42.53 2.41 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
18 19 1.227002 GCTACGTCACCTAGCTGGC 60.227 63.158 0.00 0.00 40.22 4.85
19 20 1.668101 GCTACGTCACCTAGCTGGCT 61.668 60.000 0.00 0.00 40.22 4.75
20 21 0.818296 CTACGTCACCTAGCTGGCTT 59.182 55.000 0.00 0.00 40.22 4.35
21 22 1.204941 CTACGTCACCTAGCTGGCTTT 59.795 52.381 0.00 0.00 40.22 3.51
22 23 1.263356 ACGTCACCTAGCTGGCTTTA 58.737 50.000 0.00 0.00 40.22 1.85
23 24 1.831736 ACGTCACCTAGCTGGCTTTAT 59.168 47.619 0.00 0.00 40.22 1.40
24 25 2.159085 ACGTCACCTAGCTGGCTTTATC 60.159 50.000 0.00 0.00 40.22 1.75
25 26 2.101582 CGTCACCTAGCTGGCTTTATCT 59.898 50.000 0.00 0.00 40.22 1.98
26 27 3.723260 GTCACCTAGCTGGCTTTATCTC 58.277 50.000 0.00 0.00 40.22 2.75
27 28 2.700897 TCACCTAGCTGGCTTTATCTCC 59.299 50.000 0.00 0.00 40.22 3.71
28 29 2.435805 CACCTAGCTGGCTTTATCTCCA 59.564 50.000 0.00 0.00 40.22 3.86
29 30 2.436173 ACCTAGCTGGCTTTATCTCCAC 59.564 50.000 0.00 0.00 40.22 4.02
30 31 2.703007 CCTAGCTGGCTTTATCTCCACT 59.297 50.000 0.00 0.00 0.00 4.00
31 32 3.135530 CCTAGCTGGCTTTATCTCCACTT 59.864 47.826 0.00 0.00 0.00 3.16
32 33 3.274095 AGCTGGCTTTATCTCCACTTC 57.726 47.619 0.00 0.00 0.00 3.01
33 34 2.092699 AGCTGGCTTTATCTCCACTTCC 60.093 50.000 0.00 0.00 0.00 3.46
34 35 2.924421 CTGGCTTTATCTCCACTTCCC 58.076 52.381 0.00 0.00 0.00 3.97
35 36 2.507471 CTGGCTTTATCTCCACTTCCCT 59.493 50.000 0.00 0.00 0.00 4.20
36 37 2.919602 TGGCTTTATCTCCACTTCCCTT 59.080 45.455 0.00 0.00 0.00 3.95
37 38 3.282885 GGCTTTATCTCCACTTCCCTTG 58.717 50.000 0.00 0.00 0.00 3.61
38 39 3.308473 GGCTTTATCTCCACTTCCCTTGT 60.308 47.826 0.00 0.00 0.00 3.16
39 40 4.336280 GCTTTATCTCCACTTCCCTTGTT 58.664 43.478 0.00 0.00 0.00 2.83
40 41 4.767409 GCTTTATCTCCACTTCCCTTGTTT 59.233 41.667 0.00 0.00 0.00 2.83
41 42 5.106118 GCTTTATCTCCACTTCCCTTGTTTC 60.106 44.000 0.00 0.00 0.00 2.78
42 43 5.576563 TTATCTCCACTTCCCTTGTTTCA 57.423 39.130 0.00 0.00 0.00 2.69
43 44 4.664688 ATCTCCACTTCCCTTGTTTCAT 57.335 40.909 0.00 0.00 0.00 2.57
44 45 4.021102 TCTCCACTTCCCTTGTTTCATC 57.979 45.455 0.00 0.00 0.00 2.92
45 46 3.394274 TCTCCACTTCCCTTGTTTCATCA 59.606 43.478 0.00 0.00 0.00 3.07
46 47 3.486383 TCCACTTCCCTTGTTTCATCAC 58.514 45.455 0.00 0.00 0.00 3.06
47 48 2.558359 CCACTTCCCTTGTTTCATCACC 59.442 50.000 0.00 0.00 0.00 4.02
48 49 3.490348 CACTTCCCTTGTTTCATCACCT 58.510 45.455 0.00 0.00 0.00 4.00
49 50 3.503748 CACTTCCCTTGTTTCATCACCTC 59.496 47.826 0.00 0.00 0.00 3.85
50 51 2.472695 TCCCTTGTTTCATCACCTCG 57.527 50.000 0.00 0.00 0.00 4.63
51 52 0.804989 CCCTTGTTTCATCACCTCGC 59.195 55.000 0.00 0.00 0.00 5.03
52 53 1.522668 CCTTGTTTCATCACCTCGCA 58.477 50.000 0.00 0.00 0.00 5.10
53 54 2.086869 CCTTGTTTCATCACCTCGCAT 58.913 47.619 0.00 0.00 0.00 4.73
54 55 2.159476 CCTTGTTTCATCACCTCGCATG 60.159 50.000 0.00 0.00 0.00 4.06
55 56 2.183478 TGTTTCATCACCTCGCATGT 57.817 45.000 0.00 0.00 0.00 3.21
56 57 2.076100 TGTTTCATCACCTCGCATGTC 58.924 47.619 0.00 0.00 0.00 3.06
57 58 1.061131 GTTTCATCACCTCGCATGTCG 59.939 52.381 0.00 0.00 40.15 4.35
58 59 0.246360 TTCATCACCTCGCATGTCGT 59.754 50.000 8.91 0.00 39.67 4.34
59 60 0.458370 TCATCACCTCGCATGTCGTG 60.458 55.000 8.91 6.93 39.67 4.35
63 64 3.966215 CCTCGCATGTCGTGGTTT 58.034 55.556 17.06 0.00 44.39 3.27
64 65 2.244000 CCTCGCATGTCGTGGTTTT 58.756 52.632 17.06 0.00 44.39 2.43
65 66 0.110238 CCTCGCATGTCGTGGTTTTG 60.110 55.000 17.06 0.00 44.39 2.44
66 67 0.110238 CTCGCATGTCGTGGTTTTGG 60.110 55.000 8.91 0.00 39.67 3.28
67 68 0.533085 TCGCATGTCGTGGTTTTGGA 60.533 50.000 8.91 0.00 39.67 3.53
68 69 0.385473 CGCATGTCGTGGTTTTGGAC 60.385 55.000 0.00 0.00 0.00 4.02
69 70 0.665835 GCATGTCGTGGTTTTGGACA 59.334 50.000 0.00 0.00 44.00 4.02
71 72 2.668279 GCATGTCGTGGTTTTGGACATC 60.668 50.000 3.12 0.00 45.55 3.06
72 73 1.600023 TGTCGTGGTTTTGGACATCC 58.400 50.000 0.00 0.00 35.89 3.51
73 74 0.515564 GTCGTGGTTTTGGACATCCG 59.484 55.000 0.00 0.00 39.43 4.18
74 75 1.209127 CGTGGTTTTGGACATCCGC 59.791 57.895 0.00 0.00 39.43 5.54
75 76 1.584495 GTGGTTTTGGACATCCGCC 59.416 57.895 0.00 0.00 39.43 6.13
76 77 1.151679 TGGTTTTGGACATCCGCCA 59.848 52.632 0.00 0.00 39.43 5.69
77 78 0.251564 TGGTTTTGGACATCCGCCAT 60.252 50.000 0.00 0.00 39.43 4.40
78 79 0.173255 GGTTTTGGACATCCGCCATG 59.827 55.000 0.00 0.00 39.43 3.66
79 80 0.173255 GTTTTGGACATCCGCCATGG 59.827 55.000 7.63 7.63 39.43 3.66
80 81 0.251564 TTTTGGACATCCGCCATGGT 60.252 50.000 14.67 0.00 39.43 3.55
81 82 0.251564 TTTGGACATCCGCCATGGTT 60.252 50.000 14.67 0.00 39.43 3.67
82 83 0.621082 TTGGACATCCGCCATGGTTA 59.379 50.000 14.67 0.00 39.43 2.85
83 84 0.843309 TGGACATCCGCCATGGTTAT 59.157 50.000 14.67 1.55 39.43 1.89
84 85 1.202758 TGGACATCCGCCATGGTTATC 60.203 52.381 14.67 3.04 39.43 1.75
85 86 1.148310 GACATCCGCCATGGTTATCG 58.852 55.000 14.67 8.10 39.52 2.92
86 87 0.250295 ACATCCGCCATGGTTATCGG 60.250 55.000 19.23 19.23 42.96 4.18
87 88 0.250295 CATCCGCCATGGTTATCGGT 60.250 55.000 22.82 11.36 42.28 4.69
88 89 0.250295 ATCCGCCATGGTTATCGGTG 60.250 55.000 22.82 4.44 42.28 4.94
89 90 2.542907 CCGCCATGGTTATCGGTGC 61.543 63.158 17.58 0.00 37.33 5.01
90 91 2.542907 CGCCATGGTTATCGGTGCC 61.543 63.158 14.67 0.00 0.00 5.01
91 92 2.542907 GCCATGGTTATCGGTGCCG 61.543 63.158 14.67 3.94 41.35 5.69
100 101 4.758251 TCGGTGCCGAGCCACATG 62.758 66.667 9.48 0.00 44.01 3.21
102 103 3.127533 GGTGCCGAGCCACATGTC 61.128 66.667 0.00 0.00 37.46 3.06
103 104 2.046892 GTGCCGAGCCACATGTCT 60.047 61.111 0.00 0.00 35.80 3.41
104 105 2.103042 GTGCCGAGCCACATGTCTC 61.103 63.158 0.00 0.00 35.80 3.36
105 106 2.265739 GCCGAGCCACATGTCTCA 59.734 61.111 13.32 0.00 0.00 3.27
106 107 1.375908 GCCGAGCCACATGTCTCAA 60.376 57.895 13.32 0.00 0.00 3.02
107 108 1.364626 GCCGAGCCACATGTCTCAAG 61.365 60.000 13.32 6.37 0.00 3.02
108 109 0.036952 CCGAGCCACATGTCTCAAGT 60.037 55.000 13.32 0.00 0.00 3.16
109 110 1.073964 CGAGCCACATGTCTCAAGTG 58.926 55.000 13.32 0.00 33.58 3.16
110 111 0.801251 GAGCCACATGTCTCAAGTGC 59.199 55.000 9.16 0.00 32.62 4.40
111 112 0.399454 AGCCACATGTCTCAAGTGCT 59.601 50.000 0.00 0.00 32.62 4.40
112 113 0.801251 GCCACATGTCTCAAGTGCTC 59.199 55.000 0.00 0.00 32.62 4.26
113 114 1.446907 CCACATGTCTCAAGTGCTCC 58.553 55.000 0.00 0.00 32.62 4.70
114 115 1.002888 CCACATGTCTCAAGTGCTCCT 59.997 52.381 0.00 0.00 32.62 3.69
115 116 2.344950 CACATGTCTCAAGTGCTCCTC 58.655 52.381 0.00 0.00 0.00 3.71
116 117 1.277557 ACATGTCTCAAGTGCTCCTCC 59.722 52.381 0.00 0.00 0.00 4.30
117 118 0.908198 ATGTCTCAAGTGCTCCTCCC 59.092 55.000 0.00 0.00 0.00 4.30
118 119 1.216710 GTCTCAAGTGCTCCTCCCG 59.783 63.158 0.00 0.00 0.00 5.14
119 120 1.984570 TCTCAAGTGCTCCTCCCGG 60.985 63.158 0.00 0.00 0.00 5.73
120 121 3.672295 CTCAAGTGCTCCTCCCGGC 62.672 68.421 0.00 0.00 0.00 6.13
121 122 4.020617 CAAGTGCTCCTCCCGGCA 62.021 66.667 0.00 0.00 36.01 5.69
122 123 3.710722 AAGTGCTCCTCCCGGCAG 61.711 66.667 0.00 0.00 39.22 4.85
123 124 4.704103 AGTGCTCCTCCCGGCAGA 62.704 66.667 0.00 0.00 39.22 4.26
124 125 3.706373 GTGCTCCTCCCGGCAGAA 61.706 66.667 0.00 0.00 39.22 3.02
125 126 3.393970 TGCTCCTCCCGGCAGAAG 61.394 66.667 0.00 0.00 34.22 2.85
126 127 4.168291 GCTCCTCCCGGCAGAAGG 62.168 72.222 0.00 0.00 0.00 3.46
136 137 4.162690 GCAGAAGGGCGTCGGGAT 62.163 66.667 0.00 0.00 0.00 3.85
149 150 1.274167 GTCGGGATTACACACCTCACA 59.726 52.381 0.00 0.00 0.00 3.58
159 160 4.689612 ACACACCTCACAATCAACTAGT 57.310 40.909 0.00 0.00 0.00 2.57
163 164 3.007940 CACCTCACAATCAACTAGTCCCA 59.992 47.826 0.00 0.00 0.00 4.37
169 170 1.933021 ATCAACTAGTCCCACGGTGA 58.067 50.000 10.28 0.00 0.00 4.02
195 196 4.301628 CAACCAATGTTCTTCCTTGCTTC 58.698 43.478 0.00 0.00 30.42 3.86
196 197 2.893489 ACCAATGTTCTTCCTTGCTTCC 59.107 45.455 0.00 0.00 0.00 3.46
209 210 1.280457 TGCTTCCCCTCTTTCTCCTC 58.720 55.000 0.00 0.00 0.00 3.71
210 211 0.544223 GCTTCCCCTCTTTCTCCTCC 59.456 60.000 0.00 0.00 0.00 4.30
211 212 1.903955 GCTTCCCCTCTTTCTCCTCCT 60.904 57.143 0.00 0.00 0.00 3.69
217 218 2.292851 CCCTCTTTCTCCTCCTTCTCCT 60.293 54.545 0.00 0.00 0.00 3.69
225 226 1.077644 CTCCTTCTCCTCGTCCCGA 60.078 63.158 0.00 0.00 0.00 5.14
226 227 0.466555 CTCCTTCTCCTCGTCCCGAT 60.467 60.000 0.00 0.00 34.61 4.18
244 245 2.037772 CGATCCCTCCTCCGAATCAAAT 59.962 50.000 0.00 0.00 0.00 2.32
351 354 8.511465 AAACAAACGAAGAATCATCAATCAAG 57.489 30.769 0.00 0.00 0.00 3.02
366 372 9.304731 TCATCAATCAAGTCAAGAAAACAAAAG 57.695 29.630 0.00 0.00 0.00 2.27
411 417 1.375523 GAACGGCGTTGGGACATCT 60.376 57.895 31.90 1.43 39.30 2.90
418 424 1.418342 CGTTGGGACATCTAACGGCG 61.418 60.000 4.80 4.80 42.31 6.46
431 437 3.578272 CGGCGGAGAGGAGACGAG 61.578 72.222 0.00 0.00 42.33 4.18
437 443 1.476110 CGGAGAGGAGACGAGAAGGAT 60.476 57.143 0.00 0.00 0.00 3.24
992 1008 2.338620 GAAAGCCCGCGCCTTTTT 59.661 55.556 19.38 9.36 34.57 1.94
1629 1681 1.961180 GCAAGGAGGCCTTCGAGCTA 61.961 60.000 19.92 0.00 42.67 3.32
2041 2106 4.439057 GGGAGTTATTAGACGCATGTTCA 58.561 43.478 0.00 0.00 0.00 3.18
2066 2131 0.600782 ATGTTTGCTTGCTTTGGGCG 60.601 50.000 0.00 0.00 45.43 6.13
2203 2277 1.301244 GCGATCGCCAGGTGATGAT 60.301 57.895 29.48 2.83 32.57 2.45
2230 2305 1.337447 ACGCATCGGGGAATATTACGG 60.337 52.381 6.78 0.54 0.00 4.02
2278 2359 4.564769 TGTTTGCTTCCGTTTGATGTTTTC 59.435 37.500 0.00 0.00 0.00 2.29
2279 2360 4.647424 TTGCTTCCGTTTGATGTTTTCT 57.353 36.364 0.00 0.00 0.00 2.52
2280 2361 5.759506 TTGCTTCCGTTTGATGTTTTCTA 57.240 34.783 0.00 0.00 0.00 2.10
2406 2492 3.751175 CCTCCAGTTTGCGTATTCAAGAA 59.249 43.478 0.00 0.00 0.00 2.52
2410 2496 4.378459 CCAGTTTGCGTATTCAAGAAGGTC 60.378 45.833 0.00 0.00 0.00 3.85
2440 2526 5.357878 TCCTGTTGCATTTTGGAGTATCATC 59.642 40.000 0.00 0.00 36.25 2.92
2452 2538 4.019411 TGGAGTATCATCCAGCAAGACAAA 60.019 41.667 0.00 0.00 44.56 2.83
2453 2539 4.574013 GGAGTATCATCCAGCAAGACAAAG 59.426 45.833 0.00 0.00 39.34 2.77
2466 2552 6.634436 CAGCAAGACAAAGTTTGTTACTGATC 59.366 38.462 21.70 7.82 45.52 2.92
2491 2577 2.485124 GCAAGCATCTGGATAGTGAGCT 60.485 50.000 0.00 0.00 0.00 4.09
2495 2581 3.069872 AGCATCTGGATAGTGAGCTCTTG 59.930 47.826 16.19 0.00 0.00 3.02
2508 2594 2.555757 GAGCTCTTGAATTGTTGGCAGT 59.444 45.455 6.43 0.00 0.00 4.40
2509 2595 2.295349 AGCTCTTGAATTGTTGGCAGTG 59.705 45.455 0.00 0.00 0.00 3.66
2617 2704 6.355405 CGTAGCAAAGATTCAATAAAGCATCG 59.645 38.462 0.00 0.00 0.00 3.84
2653 2740 9.631257 TTTTCTGCTCTTCAATTGGATATATCA 57.369 29.630 14.60 0.00 0.00 2.15
2654 2741 8.613060 TTCTGCTCTTCAATTGGATATATCAC 57.387 34.615 14.60 4.90 0.00 3.06
2693 2780 4.344968 CACCCTTCCATCCTTGTTTTCTTT 59.655 41.667 0.00 0.00 0.00 2.52
2699 2786 6.405278 TCCATCCTTGTTTTCTTTCTTTCC 57.595 37.500 0.00 0.00 0.00 3.13
2774 2866 3.001330 GTGTGCTCTGTTACTGTTGTCAC 59.999 47.826 0.00 0.00 0.00 3.67
2794 2886 5.408604 GTCACCATCTTTACGTTCTTGTCAT 59.591 40.000 0.00 0.00 0.00 3.06
2795 2887 6.588756 GTCACCATCTTTACGTTCTTGTCATA 59.411 38.462 0.00 0.00 0.00 2.15
2801 2893 8.926710 CATCTTTACGTTCTTGTCATACTTTCT 58.073 33.333 0.00 0.00 0.00 2.52
2803 2895 9.622004 TCTTTACGTTCTTGTCATACTTTCTAG 57.378 33.333 0.00 0.00 0.00 2.43
2851 2943 9.090692 CACCATTTTTGTGAAATATCTTCATCC 57.909 33.333 4.40 0.00 35.74 3.51
2861 2953 6.947733 TGAAATATCTTCATCCAACCTGTTGT 59.052 34.615 9.03 0.00 38.85 3.32
2884 2976 5.712152 TTCCAGAAAAGAAAGATCCAAGC 57.288 39.130 0.00 0.00 0.00 4.01
2892 2984 5.876651 AAGAAAGATCCAAGCACCTTTTT 57.123 34.783 0.00 0.00 0.00 1.94
2971 3064 7.077605 TGTTTCGAGCACTCAATTATTTCTTG 58.922 34.615 0.00 0.00 0.00 3.02
2973 3066 7.433708 TTCGAGCACTCAATTATTTCTTGAA 57.566 32.000 0.00 0.00 32.53 2.69
2974 3067 7.433708 TCGAGCACTCAATTATTTCTTGAAA 57.566 32.000 0.00 0.00 32.53 2.69
2975 3068 8.044060 TCGAGCACTCAATTATTTCTTGAAAT 57.956 30.769 12.42 12.42 32.53 2.17
2976 3069 9.161629 TCGAGCACTCAATTATTTCTTGAAATA 57.838 29.630 10.66 10.66 32.53 1.40
2977 3070 9.773328 CGAGCACTCAATTATTTCTTGAAATAA 57.227 29.630 22.68 22.68 38.52 1.40
2988 3081 6.515272 TTTCTTGAAATAACATCCTGCTCC 57.485 37.500 0.00 0.00 0.00 4.70
2989 3082 4.191544 TCTTGAAATAACATCCTGCTCCG 58.808 43.478 0.00 0.00 0.00 4.63
2990 3083 3.904800 TGAAATAACATCCTGCTCCGA 57.095 42.857 0.00 0.00 0.00 4.55
2991 3084 4.422073 TGAAATAACATCCTGCTCCGAT 57.578 40.909 0.00 0.00 0.00 4.18
2992 3085 4.129380 TGAAATAACATCCTGCTCCGATG 58.871 43.478 6.67 6.67 42.37 3.84
2993 3086 2.175878 ATAACATCCTGCTCCGATGC 57.824 50.000 7.79 0.00 40.70 3.91
2994 3087 0.249447 TAACATCCTGCTCCGATGCG 60.249 55.000 7.79 0.00 40.70 4.73
2995 3088 1.960040 AACATCCTGCTCCGATGCGA 61.960 55.000 7.79 0.00 40.70 5.10
2996 3089 1.005275 CATCCTGCTCCGATGCGAT 60.005 57.895 0.00 0.00 35.36 4.58
2997 3090 1.005275 ATCCTGCTCCGATGCGATG 60.005 57.895 0.00 0.00 35.36 3.84
2998 3091 2.446142 ATCCTGCTCCGATGCGATGG 62.446 60.000 0.00 0.00 35.36 3.51
2999 3092 3.344215 CTGCTCCGATGCGATGGC 61.344 66.667 0.00 0.00 40.52 4.40
3000 3093 3.804153 CTGCTCCGATGCGATGGCT 62.804 63.158 0.15 0.00 40.82 4.75
3020 3113 3.091545 CTGGCTTGTTGATTGTACCCAT 58.908 45.455 0.00 0.00 0.00 4.00
3029 3122 3.684908 TGATTGTACCCATGACCTGTTG 58.315 45.455 0.00 0.00 0.00 3.33
3033 3126 2.224670 TGTACCCATGACCTGTTGGAAC 60.225 50.000 0.00 0.00 34.81 3.62
3034 3127 1.149101 ACCCATGACCTGTTGGAACT 58.851 50.000 0.00 0.00 34.81 3.01
3038 3131 2.488891 CCATGACCTGTTGGAACTTGGA 60.489 50.000 0.00 0.00 38.82 3.53
3039 3132 3.221771 CATGACCTGTTGGAACTTGGAA 58.778 45.455 8.44 0.01 37.04 3.53
3041 3134 2.230660 GACCTGTTGGAACTTGGAAGG 58.769 52.381 8.44 0.00 37.04 3.46
3042 3135 1.569072 ACCTGTTGGAACTTGGAAGGT 59.431 47.619 8.44 0.00 37.04 3.50
3043 3136 2.024369 ACCTGTTGGAACTTGGAAGGTT 60.024 45.455 8.44 0.00 32.70 3.50
3044 3137 3.031013 CCTGTTGGAACTTGGAAGGTTT 58.969 45.455 0.00 0.00 34.57 3.27
3045 3138 4.211920 CCTGTTGGAACTTGGAAGGTTTA 58.788 43.478 0.00 0.00 34.57 2.01
3046 3139 4.037565 CCTGTTGGAACTTGGAAGGTTTAC 59.962 45.833 0.00 0.00 34.57 2.01
3073 3166 2.975851 GCAGCAGAGATTCAACAAAACG 59.024 45.455 0.00 0.00 0.00 3.60
3096 3189 7.467623 ACGTCATTCAAGATATTTTCTGCTTC 58.532 34.615 0.00 0.00 33.93 3.86
3109 3202 2.771089 TCTGCTTCAGCCTACAGTTTG 58.229 47.619 0.00 0.00 41.18 2.93
3110 3203 2.104792 TCTGCTTCAGCCTACAGTTTGT 59.895 45.455 0.00 0.00 41.18 2.83
3189 3292 5.913137 TCTTTTCTTGCTTTCTTCACCAA 57.087 34.783 0.00 0.00 0.00 3.67
3217 3320 6.881602 ACAGGAGGTCATATTTTTCTGTCTTC 59.118 38.462 0.00 0.00 29.51 2.87
3220 3323 7.609532 AGGAGGTCATATTTTTCTGTCTTCTTG 59.390 37.037 0.00 0.00 0.00 3.02
3240 3343 0.947244 AACAAAGCCAACGAGCTGAG 59.053 50.000 0.00 0.00 44.11 3.35
3244 3347 0.601311 AAGCCAACGAGCTGAGTGTC 60.601 55.000 0.00 0.00 44.11 3.67
3350 3455 4.784177 TCTTCATGAAATCTGCTGGCATA 58.216 39.130 9.88 0.00 0.00 3.14
3356 3461 2.875094 AATCTGCTGGCATATCTCCC 57.125 50.000 0.00 0.00 0.00 4.30
3395 3500 7.934120 TCCAAATAACCCTTTTGTTTTATGTGG 59.066 33.333 3.79 3.79 39.35 4.17
3422 3527 1.608055 CTGCACAACCCTCATCACAA 58.392 50.000 0.00 0.00 0.00 3.33
3425 3530 3.758023 CTGCACAACCCTCATCACAATAA 59.242 43.478 0.00 0.00 0.00 1.40
3485 5133 7.944729 AGTCTGCATAACTACAATTCCATTT 57.055 32.000 0.25 0.00 0.00 2.32
3502 5151 8.791327 ATTCCATTTTGGTATCCAATGTTTTC 57.209 30.769 1.97 0.00 43.55 2.29
3507 5156 9.012161 CATTTTGGTATCCAATGTTTTCCAATT 57.988 29.630 1.97 0.00 43.55 2.32
3512 5161 8.317679 TGGTATCCAATGTTTTCCAATTAAAGG 58.682 33.333 0.00 0.00 0.00 3.11
3513 5162 8.536175 GGTATCCAATGTTTTCCAATTAAAGGA 58.464 33.333 0.00 0.00 0.00 3.36
3602 5251 1.573857 TCCTGTCCTAGTCCTGCCATA 59.426 52.381 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.227002 GCCAGCTAGGTGACGTAGC 60.227 63.158 25.00 25.00 42.85 3.58
1 2 0.818296 AAGCCAGCTAGGTGACGTAG 59.182 55.000 23.31 7.89 40.61 3.51
2 3 1.263356 AAAGCCAGCTAGGTGACGTA 58.737 50.000 23.31 0.00 40.61 3.57
3 4 1.263356 TAAAGCCAGCTAGGTGACGT 58.737 50.000 23.31 7.22 40.61 4.34
4 5 2.101582 AGATAAAGCCAGCTAGGTGACG 59.898 50.000 23.31 8.58 40.61 4.35
5 6 3.493524 GGAGATAAAGCCAGCTAGGTGAC 60.494 52.174 23.31 12.13 40.61 3.67
6 7 2.700897 GGAGATAAAGCCAGCTAGGTGA 59.299 50.000 23.31 2.98 40.61 4.02
7 8 2.435805 TGGAGATAAAGCCAGCTAGGTG 59.564 50.000 15.13 15.13 40.61 4.00
8 9 2.436173 GTGGAGATAAAGCCAGCTAGGT 59.564 50.000 0.00 0.00 40.61 3.08
9 10 2.703007 AGTGGAGATAAAGCCAGCTAGG 59.297 50.000 0.00 0.00 41.84 3.02
10 11 4.376146 GAAGTGGAGATAAAGCCAGCTAG 58.624 47.826 0.00 0.00 34.22 3.42
11 12 3.134804 GGAAGTGGAGATAAAGCCAGCTA 59.865 47.826 0.00 0.00 34.22 3.32
12 13 2.092699 GGAAGTGGAGATAAAGCCAGCT 60.093 50.000 0.00 0.00 34.22 4.24
13 14 2.293170 GGAAGTGGAGATAAAGCCAGC 58.707 52.381 0.00 0.00 34.22 4.85
14 15 2.507471 AGGGAAGTGGAGATAAAGCCAG 59.493 50.000 0.00 0.00 34.22 4.85
15 16 2.562296 AGGGAAGTGGAGATAAAGCCA 58.438 47.619 0.00 0.00 0.00 4.75
16 17 3.282885 CAAGGGAAGTGGAGATAAAGCC 58.717 50.000 0.00 0.00 0.00 4.35
17 18 3.956744 ACAAGGGAAGTGGAGATAAAGC 58.043 45.455 0.00 0.00 0.00 3.51
18 19 6.003950 TGAAACAAGGGAAGTGGAGATAAAG 58.996 40.000 0.00 0.00 0.00 1.85
19 20 5.947663 TGAAACAAGGGAAGTGGAGATAAA 58.052 37.500 0.00 0.00 0.00 1.40
20 21 5.576563 TGAAACAAGGGAAGTGGAGATAA 57.423 39.130 0.00 0.00 0.00 1.75
21 22 5.250543 TGATGAAACAAGGGAAGTGGAGATA 59.749 40.000 0.00 0.00 0.00 1.98
22 23 4.043310 TGATGAAACAAGGGAAGTGGAGAT 59.957 41.667 0.00 0.00 0.00 2.75
23 24 3.394274 TGATGAAACAAGGGAAGTGGAGA 59.606 43.478 0.00 0.00 0.00 3.71
24 25 3.503748 GTGATGAAACAAGGGAAGTGGAG 59.496 47.826 0.00 0.00 0.00 3.86
25 26 3.486383 GTGATGAAACAAGGGAAGTGGA 58.514 45.455 0.00 0.00 0.00 4.02
26 27 2.558359 GGTGATGAAACAAGGGAAGTGG 59.442 50.000 0.00 0.00 0.00 4.00
27 28 3.490348 AGGTGATGAAACAAGGGAAGTG 58.510 45.455 0.00 0.00 0.00 3.16
28 29 3.756117 GAGGTGATGAAACAAGGGAAGT 58.244 45.455 0.00 0.00 0.00 3.01
29 30 2.744202 CGAGGTGATGAAACAAGGGAAG 59.256 50.000 0.00 0.00 0.00 3.46
30 31 2.778299 CGAGGTGATGAAACAAGGGAA 58.222 47.619 0.00 0.00 0.00 3.97
31 32 1.610624 GCGAGGTGATGAAACAAGGGA 60.611 52.381 0.00 0.00 0.00 4.20
32 33 0.804989 GCGAGGTGATGAAACAAGGG 59.195 55.000 0.00 0.00 0.00 3.95
33 34 1.522668 TGCGAGGTGATGAAACAAGG 58.477 50.000 0.00 0.00 0.00 3.61
34 35 2.485426 ACATGCGAGGTGATGAAACAAG 59.515 45.455 0.00 0.00 0.00 3.16
35 36 2.483877 GACATGCGAGGTGATGAAACAA 59.516 45.455 0.00 0.00 0.00 2.83
36 37 2.076100 GACATGCGAGGTGATGAAACA 58.924 47.619 0.00 0.00 0.00 2.83
37 38 1.061131 CGACATGCGAGGTGATGAAAC 59.939 52.381 3.85 0.00 44.57 2.78
38 39 1.337728 ACGACATGCGAGGTGATGAAA 60.338 47.619 14.88 0.00 44.57 2.69
39 40 0.246360 ACGACATGCGAGGTGATGAA 59.754 50.000 14.88 0.00 44.57 2.57
40 41 0.458370 CACGACATGCGAGGTGATGA 60.458 55.000 14.88 0.00 44.57 2.92
41 42 1.423721 CCACGACATGCGAGGTGATG 61.424 60.000 14.88 3.46 44.40 3.07
42 43 1.153568 CCACGACATGCGAGGTGAT 60.154 57.895 14.88 0.00 44.40 3.06
43 44 2.261361 CCACGACATGCGAGGTGA 59.739 61.111 14.88 0.00 44.40 4.02
47 48 0.110238 CCAAAACCACGACATGCGAG 60.110 55.000 14.88 7.96 44.57 5.03
48 49 0.533085 TCCAAAACCACGACATGCGA 60.533 50.000 14.88 0.00 44.57 5.10
49 50 4.265436 ATGTCCAAAACCACGACATGCG 62.265 50.000 7.79 7.79 43.74 4.73
50 51 0.665835 TGTCCAAAACCACGACATGC 59.334 50.000 0.00 0.00 31.74 4.06
51 52 2.095263 GGATGTCCAAAACCACGACATG 60.095 50.000 6.65 0.00 45.02 3.21
53 54 1.600023 GGATGTCCAAAACCACGACA 58.400 50.000 0.00 0.00 40.58 4.35
54 55 0.515564 CGGATGTCCAAAACCACGAC 59.484 55.000 0.00 0.00 35.14 4.34
55 56 1.231958 GCGGATGTCCAAAACCACGA 61.232 55.000 0.00 0.00 35.14 4.35
56 57 1.209127 GCGGATGTCCAAAACCACG 59.791 57.895 0.00 0.00 35.14 4.94
57 58 1.175983 TGGCGGATGTCCAAAACCAC 61.176 55.000 0.00 0.00 35.14 4.16
58 59 0.251564 ATGGCGGATGTCCAAAACCA 60.252 50.000 0.00 1.75 37.13 3.67
59 60 0.173255 CATGGCGGATGTCCAAAACC 59.827 55.000 0.00 0.00 37.13 3.27
60 61 0.173255 CCATGGCGGATGTCCAAAAC 59.827 55.000 0.00 0.00 37.13 2.43
61 62 0.251564 ACCATGGCGGATGTCCAAAA 60.252 50.000 13.04 0.00 37.13 2.44
62 63 0.251564 AACCATGGCGGATGTCCAAA 60.252 50.000 13.04 0.00 37.13 3.28
63 64 0.621082 TAACCATGGCGGATGTCCAA 59.379 50.000 13.04 0.00 37.13 3.53
64 65 0.843309 ATAACCATGGCGGATGTCCA 59.157 50.000 13.04 0.00 38.63 4.02
65 66 1.523758 GATAACCATGGCGGATGTCC 58.476 55.000 13.04 0.00 38.63 4.02
66 67 1.148310 CGATAACCATGGCGGATGTC 58.852 55.000 13.04 3.02 38.63 3.06
67 68 0.250295 CCGATAACCATGGCGGATGT 60.250 55.000 20.28 0.00 46.29 3.06
68 69 0.250295 ACCGATAACCATGGCGGATG 60.250 55.000 28.51 10.55 46.29 3.51
69 70 0.250295 CACCGATAACCATGGCGGAT 60.250 55.000 28.51 13.36 46.29 4.18
70 71 1.145156 CACCGATAACCATGGCGGA 59.855 57.895 28.51 9.17 46.29 5.54
72 73 2.542907 GGCACCGATAACCATGGCG 61.543 63.158 13.04 7.12 0.00 5.69
73 74 2.542907 CGGCACCGATAACCATGGC 61.543 63.158 13.04 0.00 42.83 4.40
74 75 1.145156 TCGGCACCGATAACCATGG 59.855 57.895 11.19 11.19 44.01 3.66
75 76 4.846551 TCGGCACCGATAACCATG 57.153 55.556 7.89 0.00 44.01 3.66
83 84 4.758251 CATGTGGCTCGGCACCGA 62.758 66.667 19.08 11.90 46.87 4.69
85 86 3.127533 GACATGTGGCTCGGCACC 61.128 66.667 19.08 2.05 0.00 5.01
86 87 2.046892 AGACATGTGGCTCGGCAC 60.047 61.111 15.72 15.72 0.00 5.01
87 88 2.265739 GAGACATGTGGCTCGGCA 59.734 61.111 1.15 0.00 40.87 5.69
92 93 0.399454 AGCACTTGAGACATGTGGCT 59.601 50.000 1.15 0.00 39.09 4.75
93 94 0.801251 GAGCACTTGAGACATGTGGC 59.199 55.000 1.15 0.00 39.09 5.01
94 95 1.002888 AGGAGCACTTGAGACATGTGG 59.997 52.381 1.15 0.00 39.09 4.17
95 96 2.344950 GAGGAGCACTTGAGACATGTG 58.655 52.381 1.15 11.56 40.80 3.21
96 97 1.277557 GGAGGAGCACTTGAGACATGT 59.722 52.381 0.00 0.00 0.00 3.21
97 98 1.406614 GGGAGGAGCACTTGAGACATG 60.407 57.143 0.00 0.00 0.00 3.21
98 99 0.908198 GGGAGGAGCACTTGAGACAT 59.092 55.000 0.00 0.00 0.00 3.06
99 100 1.536073 CGGGAGGAGCACTTGAGACA 61.536 60.000 0.00 0.00 0.00 3.41
100 101 1.216710 CGGGAGGAGCACTTGAGAC 59.783 63.158 0.00 0.00 0.00 3.36
101 102 3.700109 CGGGAGGAGCACTTGAGA 58.300 61.111 0.00 0.00 0.00 3.27
119 120 2.306255 TAATCCCGACGCCCTTCTGC 62.306 60.000 0.00 0.00 0.00 4.26
120 121 0.529992 GTAATCCCGACGCCCTTCTG 60.530 60.000 0.00 0.00 0.00 3.02
121 122 0.974010 TGTAATCCCGACGCCCTTCT 60.974 55.000 0.00 0.00 0.00 2.85
122 123 0.808847 GTGTAATCCCGACGCCCTTC 60.809 60.000 0.00 0.00 0.00 3.46
123 124 1.219935 GTGTAATCCCGACGCCCTT 59.780 57.895 0.00 0.00 0.00 3.95
124 125 1.985662 TGTGTAATCCCGACGCCCT 60.986 57.895 0.00 0.00 0.00 5.19
125 126 1.812507 GTGTGTAATCCCGACGCCC 60.813 63.158 0.00 0.00 0.00 6.13
126 127 1.812507 GGTGTGTAATCCCGACGCC 60.813 63.158 0.00 0.00 33.34 5.68
127 128 0.804933 GAGGTGTGTAATCCCGACGC 60.805 60.000 0.00 0.00 0.00 5.19
128 129 0.528924 TGAGGTGTGTAATCCCGACG 59.471 55.000 0.00 0.00 0.00 5.12
129 130 1.274167 TGTGAGGTGTGTAATCCCGAC 59.726 52.381 0.00 0.00 0.00 4.79
130 131 1.634960 TGTGAGGTGTGTAATCCCGA 58.365 50.000 0.00 0.00 0.00 5.14
131 132 2.465860 TTGTGAGGTGTGTAATCCCG 57.534 50.000 0.00 0.00 0.00 5.14
132 133 3.950397 TGATTGTGAGGTGTGTAATCCC 58.050 45.455 0.00 0.00 0.00 3.85
133 134 5.003804 AGTTGATTGTGAGGTGTGTAATCC 58.996 41.667 0.00 0.00 0.00 3.01
134 135 6.874134 ACTAGTTGATTGTGAGGTGTGTAATC 59.126 38.462 0.00 0.00 0.00 1.75
135 136 6.769512 ACTAGTTGATTGTGAGGTGTGTAAT 58.230 36.000 0.00 0.00 0.00 1.89
136 137 6.169557 ACTAGTTGATTGTGAGGTGTGTAA 57.830 37.500 0.00 0.00 0.00 2.41
149 150 2.028385 GTCACCGTGGGACTAGTTGATT 60.028 50.000 0.00 0.00 32.54 2.57
159 160 4.612412 GTTGGCGTCACCGTGGGA 62.612 66.667 0.00 0.00 43.94 4.37
163 164 2.112297 ATTGGTTGGCGTCACCGT 59.888 55.556 0.00 0.00 43.94 4.83
169 170 0.958822 GGAAGAACATTGGTTGGCGT 59.041 50.000 0.00 0.00 37.36 5.68
195 196 2.115427 GAGAAGGAGGAGAAAGAGGGG 58.885 57.143 0.00 0.00 0.00 4.79
196 197 2.115427 GGAGAAGGAGGAGAAAGAGGG 58.885 57.143 0.00 0.00 0.00 4.30
225 226 4.092116 GAATTTGATTCGGAGGAGGGAT 57.908 45.455 0.00 0.00 0.00 3.85
226 227 3.560636 GAATTTGATTCGGAGGAGGGA 57.439 47.619 0.00 0.00 0.00 4.20
244 245 2.125326 ATCGGCCGTCTCCATCGAA 61.125 57.895 27.15 0.67 33.53 3.71
329 332 7.300320 TGACTTGATTGATGATTCTTCGTTTG 58.700 34.615 0.00 0.00 0.00 2.93
351 354 5.234972 CCATTCTGCCTTTTGTTTTCTTGAC 59.765 40.000 0.00 0.00 0.00 3.18
411 417 2.110967 CGTCTCCTCTCCGCCGTTA 61.111 63.158 0.00 0.00 0.00 3.18
418 424 1.953686 CATCCTTCTCGTCTCCTCTCC 59.046 57.143 0.00 0.00 0.00 3.71
1056 1072 2.125512 CACCAGTAGGACGGCAGC 60.126 66.667 0.00 0.00 38.69 5.25
1057 1073 1.320344 TAGCACCAGTAGGACGGCAG 61.320 60.000 0.00 0.00 38.69 4.85
1058 1074 1.304630 TAGCACCAGTAGGACGGCA 60.305 57.895 0.00 0.00 38.69 5.69
1293 1321 1.082117 GCACGATGACCGGGTTGTAG 61.082 60.000 6.32 0.00 45.17 2.74
1657 1709 1.378514 CCTGGTGGTACATGTGGCC 60.379 63.158 9.11 11.28 44.52 5.36
2041 2106 3.374678 CCAAAGCAAGCAAACATGTTGTT 59.625 39.130 12.82 3.59 43.41 2.83
2066 2131 0.171007 CACATTGGTCGAATGGGTGC 59.829 55.000 11.68 0.00 45.20 5.01
2216 2290 4.196626 TCTAATGCCGTAATATTCCCCG 57.803 45.455 0.00 0.00 0.00 5.73
2230 2305 1.869767 CGGCTCTCCAACATCTAATGC 59.130 52.381 0.00 0.00 0.00 3.56
2406 2492 1.371558 GCAACAGGAAGACCGACCT 59.628 57.895 0.00 0.00 41.83 3.85
2410 2496 2.607771 CCAAAATGCAACAGGAAGACCG 60.608 50.000 0.00 0.00 41.83 4.79
2440 2526 5.036737 CAGTAACAAACTTTGTCTTGCTGG 58.963 41.667 7.62 0.00 44.59 4.85
2452 2538 4.142816 GCTTGCATCGATCAGTAACAAACT 60.143 41.667 0.00 0.00 39.81 2.66
2453 2539 4.091424 GCTTGCATCGATCAGTAACAAAC 58.909 43.478 0.00 0.00 0.00 2.93
2466 2552 2.479275 CACTATCCAGATGCTTGCATCG 59.521 50.000 24.18 19.28 36.73 3.84
2491 2577 2.294233 GAGCACTGCCAACAATTCAAGA 59.706 45.455 0.00 0.00 0.00 3.02
2495 2581 2.798976 TTGAGCACTGCCAACAATTC 57.201 45.000 0.00 0.00 0.00 2.17
2508 2594 5.009510 TGGAATTCGAAGAAACAATTGAGCA 59.990 36.000 13.59 0.00 45.90 4.26
2509 2595 5.460646 TGGAATTCGAAGAAACAATTGAGC 58.539 37.500 13.59 0.61 45.90 4.26
2617 2704 6.674694 TGAAGAGCAGAAAATATCTTGAGC 57.325 37.500 0.00 0.00 35.73 4.26
2653 2740 3.963428 GGTGACCTTGATCAGTACAGT 57.037 47.619 0.00 0.00 0.00 3.55
2677 2764 6.040842 TGAGGAAAGAAAGAAAACAAGGATGG 59.959 38.462 0.00 0.00 0.00 3.51
2693 2780 4.684724 ACAGTATACCTGGTGAGGAAAGA 58.315 43.478 10.23 0.00 46.06 2.52
2699 2786 5.046591 TGGAAAAGACAGTATACCTGGTGAG 60.047 44.000 10.23 0.00 46.06 3.51
2774 2866 7.596749 AAGTATGACAAGAACGTAAAGATGG 57.403 36.000 0.00 0.00 0.00 3.51
2831 2923 8.306038 CAGGTTGGATGAAGATATTTCACAAAA 58.694 33.333 3.46 0.00 0.00 2.44
2832 2924 7.451255 ACAGGTTGGATGAAGATATTTCACAAA 59.549 33.333 3.46 0.00 0.00 2.83
2851 2943 5.323371 TCTTTTCTGGAAACAACAGGTTG 57.677 39.130 10.45 10.45 45.58 3.77
2854 2946 6.207691 TCTTTCTTTTCTGGAAACAACAGG 57.792 37.500 0.00 0.00 42.06 4.00
2861 2953 5.598005 TGCTTGGATCTTTCTTTTCTGGAAA 59.402 36.000 0.00 0.00 0.00 3.13
2892 2984 5.280945 GCAACTCTGCTTCACATAAAACAA 58.719 37.500 0.00 0.00 45.74 2.83
2943 3035 8.299570 AGAAATAATTGAGTGCTCGAAACAATT 58.700 29.630 0.00 0.00 41.69 2.32
2951 3043 9.773328 TTATTTCAAGAAATAATTGAGTGCTCG 57.227 29.630 18.94 0.00 44.01 5.03
2971 3064 3.058639 GCATCGGAGCAGGATGTTATTTC 60.059 47.826 11.63 0.00 42.53 2.17
2973 3066 2.498167 GCATCGGAGCAGGATGTTATT 58.502 47.619 11.63 0.00 42.53 1.40
2974 3067 1.606480 CGCATCGGAGCAGGATGTTAT 60.606 52.381 11.63 0.00 42.53 1.89
2975 3068 0.249447 CGCATCGGAGCAGGATGTTA 60.249 55.000 11.63 0.00 42.53 2.41
2976 3069 1.522355 CGCATCGGAGCAGGATGTT 60.522 57.895 11.63 0.00 42.53 2.71
2977 3070 1.752358 ATCGCATCGGAGCAGGATGT 61.752 55.000 11.63 0.00 42.53 3.06
2978 3071 1.005275 ATCGCATCGGAGCAGGATG 60.005 57.895 7.15 7.15 43.23 3.51
2979 3072 1.005275 CATCGCATCGGAGCAGGAT 60.005 57.895 1.23 0.00 0.00 3.24
2980 3073 2.418777 CATCGCATCGGAGCAGGA 59.581 61.111 1.23 0.00 0.00 3.86
2981 3074 2.664185 CCATCGCATCGGAGCAGG 60.664 66.667 1.23 0.00 0.00 4.85
2982 3075 3.344215 GCCATCGCATCGGAGCAG 61.344 66.667 1.23 0.00 34.03 4.24
2983 3076 3.853487 AGCCATCGCATCGGAGCA 61.853 61.111 1.23 0.00 37.52 4.26
2984 3077 3.344215 CAGCCATCGCATCGGAGC 61.344 66.667 0.00 0.00 37.52 4.70
2985 3078 2.664185 CCAGCCATCGCATCGGAG 60.664 66.667 0.00 0.00 37.52 4.63
2986 3079 4.916293 GCCAGCCATCGCATCGGA 62.916 66.667 0.00 0.00 37.52 4.55
2987 3080 4.923942 AGCCAGCCATCGCATCGG 62.924 66.667 0.00 0.00 37.52 4.18
2988 3081 2.898840 AAGCCAGCCATCGCATCG 60.899 61.111 0.00 0.00 37.52 3.84
2989 3082 1.660560 AACAAGCCAGCCATCGCATC 61.661 55.000 0.00 0.00 37.52 3.91
2990 3083 1.679977 AACAAGCCAGCCATCGCAT 60.680 52.632 0.00 0.00 37.52 4.73
2991 3084 2.282391 AACAAGCCAGCCATCGCA 60.282 55.556 0.00 0.00 37.52 5.10
2992 3085 1.660560 ATCAACAAGCCAGCCATCGC 61.661 55.000 0.00 0.00 0.00 4.58
2993 3086 0.813184 AATCAACAAGCCAGCCATCG 59.187 50.000 0.00 0.00 0.00 3.84
2994 3087 1.547372 ACAATCAACAAGCCAGCCATC 59.453 47.619 0.00 0.00 0.00 3.51
2995 3088 1.636148 ACAATCAACAAGCCAGCCAT 58.364 45.000 0.00 0.00 0.00 4.40
2996 3089 1.885887 GTACAATCAACAAGCCAGCCA 59.114 47.619 0.00 0.00 0.00 4.75
2997 3090 1.202348 GGTACAATCAACAAGCCAGCC 59.798 52.381 0.00 0.00 0.00 4.85
2998 3091 1.202348 GGGTACAATCAACAAGCCAGC 59.798 52.381 0.00 0.00 0.00 4.85
2999 3092 2.513753 TGGGTACAATCAACAAGCCAG 58.486 47.619 0.00 0.00 34.72 4.85
3000 3093 2.666272 TGGGTACAATCAACAAGCCA 57.334 45.000 0.00 0.00 37.17 4.75
3020 3113 2.422803 CCTTCCAAGTTCCAACAGGTCA 60.423 50.000 0.00 0.00 0.00 4.02
3029 3122 3.826729 AGCATGTAAACCTTCCAAGTTCC 59.173 43.478 0.00 0.00 0.00 3.62
3033 3126 2.557924 TGCAGCATGTAAACCTTCCAAG 59.442 45.455 0.00 0.00 39.31 3.61
3034 3127 2.557924 CTGCAGCATGTAAACCTTCCAA 59.442 45.455 0.00 0.00 39.31 3.53
3073 3166 7.431668 GCTGAAGCAGAAAATATCTTGAATGAC 59.568 37.037 0.00 0.00 41.59 3.06
3144 3247 3.784763 AGGATGAGAAGGTGACCATGATT 59.215 43.478 3.63 0.00 0.00 2.57
3189 3292 5.251700 ACAGAAAAATATGACCTCCTGTCCT 59.748 40.000 0.00 0.00 43.78 3.85
3210 3313 4.354587 GTTGGCTTTGTTCAAGAAGACAG 58.645 43.478 0.00 0.00 41.59 3.51
3217 3320 1.334869 AGCTCGTTGGCTTTGTTCAAG 59.665 47.619 0.00 0.00 39.86 3.02
3220 3323 0.944386 TCAGCTCGTTGGCTTTGTTC 59.056 50.000 0.00 0.00 41.00 3.18
3335 3440 3.080319 GGGAGATATGCCAGCAGATTTC 58.920 50.000 8.77 8.77 30.90 2.17
3350 3455 4.629122 TGGATCTTTCTCTTCTGGGAGAT 58.371 43.478 0.00 0.00 41.29 2.75
3356 3461 7.115414 AGGGTTATTTGGATCTTTCTCTTCTG 58.885 38.462 0.00 0.00 0.00 3.02
3507 5156 7.092623 TGGGCTGTTCATAGAATAACTCCTTTA 60.093 37.037 0.00 0.00 0.00 1.85
3512 5161 6.058183 ACATGGGCTGTTCATAGAATAACTC 58.942 40.000 0.00 0.00 32.90 3.01
3513 5162 6.006275 ACATGGGCTGTTCATAGAATAACT 57.994 37.500 0.00 0.00 32.90 2.24
3528 5177 2.124403 GCAGCAGCTACATGGGCT 60.124 61.111 9.21 9.21 41.07 5.19
3530 5179 1.077930 ACTGCAGCAGCTACATGGG 60.078 57.895 23.05 0.00 42.74 4.00


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

AutoCloner maintained by Alex Coulton.