Multiple sequence alignment - TraesCS1A01G216000

Loading Multiple Alignment...

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 TraesCS1A01G216000 chr1A 100.000 2840 0 0 1 2840 382097850 382100689 0.000000e+00 5245
1 TraesCS1A01G216000 chr1A 93.597 1671 72 21 907 2569 462342251 462343894 0.000000e+00 2460
2 TraesCS1A01G216000 chr1A 88.914 451 41 7 2394 2840 462343845 462344290 5.350000e-152 547
3 TraesCS1A01G216000 chr1A 79.351 770 106 29 196 931 329177837 329178587 2.540000e-135 492
4 TraesCS1A01G216000 chr1A 80.921 608 65 37 239 824 34158515 34159093 1.560000e-117 433
5 TraesCS1A01G216000 chr1D 93.450 1939 94 16 907 2840 327011836 327013746 0.000000e+00 2846
6 TraesCS1A01G216000 chr1D 79.444 647 89 24 196 828 327011098 327011714 4.380000e-113 418
7 TraesCS1A01G216000 chr6B 97.411 1622 38 3 199 1819 673014745 673016363 0.000000e+00 2760
8 TraesCS1A01G216000 chr6B 96.963 428 11 2 2413 2840 673016361 673016786 0.000000e+00 717
9 TraesCS1A01G216000 chr6B 78.886 772 96 42 198 928 59735569 59734824 7.170000e-126 460
10 TraesCS1A01G216000 chr6B 97.500 200 4 1 1 200 207834521 207834323 9.740000e-90 340
11 TraesCS1A01G216000 chr6B 96.465 198 7 0 1 198 685081432 685081235 7.590000e-86 327
12 TraesCS1A01G216000 chr6B 94.634 205 11 0 1 205 701623510 701623306 4.570000e-83 318
13 TraesCS1A01G216000 chr5A 93.413 1670 74 21 907 2569 354272990 354274630 0.000000e+00 2442
14 TraesCS1A01G216000 chr5A 87.838 444 44 8 2401 2840 354274588 354275025 1.950000e-141 512
15 TraesCS1A01G216000 chr5A 79.036 768 108 29 198 931 705599704 705598956 7.120000e-131 477
16 TraesCS1A01G216000 chr2A 89.214 1947 163 25 935 2840 572843153 572845093 0.000000e+00 2388
17 TraesCS1A01G216000 chr2A 89.870 1619 138 20 935 2542 779782478 779784081 0.000000e+00 2058
18 TraesCS1A01G216000 chr2A 89.568 1620 143 20 935 2542 779738970 779740575 0.000000e+00 2032
19 TraesCS1A01G216000 chr2A 85.504 476 53 12 2076 2542 779701828 779702296 1.530000e-132 483
20 TraesCS1A01G216000 chr6D 94.300 1421 76 4 1091 2506 208551764 208550344 0.000000e+00 2170
21 TraesCS1A01G216000 chr6D 91.026 390 34 1 2451 2840 208550441 208550053 2.510000e-145 525
22 TraesCS1A01G216000 chr4B 90.098 1636 141 19 935 2561 97891313 97889690 0.000000e+00 2104
23 TraesCS1A01G216000 chr4B 89.492 590 59 1 2254 2840 11609021 11609610 0.000000e+00 743
24 TraesCS1A01G216000 chr4B 96.939 196 6 0 1 196 274383376 274383571 2.110000e-86 329
25 TraesCS1A01G216000 chr4B 94.554 202 10 1 1 202 468248413 468248213 7.640000e-81 311
26 TraesCS1A01G216000 chr5D 94.901 608 22 4 236 838 182935894 182936497 0.000000e+00 942
27 TraesCS1A01G216000 chr5D 80.680 647 83 26 195 828 47009325 47009942 5.540000e-127 464
28 TraesCS1A01G216000 chr2D 94.831 445 16 4 397 838 407209787 407209347 0.000000e+00 688
29 TraesCS1A01G216000 chr4D 90.930 441 37 3 2401 2840 349959022 349959460 8.760000e-165 590
30 TraesCS1A01G216000 chr4D 87.330 442 52 4 2401 2840 79009167 79009606 1.170000e-138 503
31 TraesCS1A01G216000 chr5B 90.745 443 38 3 2399 2840 524502376 524502816 3.150000e-164 588
32 TraesCS1A01G216000 chr5B 79.064 769 113 36 195 931 710172594 710173346 4.250000e-133 484
33 TraesCS1A01G216000 chr7D 78.967 794 104 34 196 953 3671948 3671182 1.530000e-132 483
34 TraesCS1A01G216000 chr6A 78.995 776 101 35 195 931 569693987 569694739 9.210000e-130 473
35 TraesCS1A01G216000 chr3A 80.614 619 85 20 193 798 469829896 469829300 2.010000e-121 446
36 TraesCS1A01G216000 chr7B 99.505 202 1 0 1 202 358413898 358413697 4.470000e-98 368
37 TraesCS1A01G216000 chr7B 99.485 194 1 0 1 194 223664908 223664715 1.250000e-93 353
38 TraesCS1A01G216000 chr7B 95.980 199 8 0 1 199 683924460 683924658 9.810000e-85 324
39 TraesCS1A01G216000 chr3B 96.392 194 7 0 3 196 512936756 512936563 1.270000e-83 320


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 TraesCS1A01G216000 chr1A 382097850 382100689 2839 False 5245.0 5245 100.0000 1 2840 1 chr1A.!!$F3 2839
1 TraesCS1A01G216000 chr1A 462342251 462344290 2039 False 1503.5 2460 91.2555 907 2840 2 chr1A.!!$F4 1933
2 TraesCS1A01G216000 chr1A 329177837 329178587 750 False 492.0 492 79.3510 196 931 1 chr1A.!!$F2 735
3 TraesCS1A01G216000 chr1A 34158515 34159093 578 False 433.0 433 80.9210 239 824 1 chr1A.!!$F1 585
4 TraesCS1A01G216000 chr1D 327011098 327013746 2648 False 1632.0 2846 86.4470 196 2840 2 chr1D.!!$F1 2644
5 TraesCS1A01G216000 chr6B 673014745 673016786 2041 False 1738.5 2760 97.1870 199 2840 2 chr6B.!!$F1 2641
6 TraesCS1A01G216000 chr6B 59734824 59735569 745 True 460.0 460 78.8860 198 928 1 chr6B.!!$R1 730
7 TraesCS1A01G216000 chr5A 354272990 354275025 2035 False 1477.0 2442 90.6255 907 2840 2 chr5A.!!$F1 1933
8 TraesCS1A01G216000 chr5A 705598956 705599704 748 True 477.0 477 79.0360 198 931 1 chr5A.!!$R1 733
9 TraesCS1A01G216000 chr2A 572843153 572845093 1940 False 2388.0 2388 89.2140 935 2840 1 chr2A.!!$F1 1905
10 TraesCS1A01G216000 chr2A 779782478 779784081 1603 False 2058.0 2058 89.8700 935 2542 1 chr2A.!!$F4 1607
11 TraesCS1A01G216000 chr2A 779738970 779740575 1605 False 2032.0 2032 89.5680 935 2542 1 chr2A.!!$F3 1607
12 TraesCS1A01G216000 chr6D 208550053 208551764 1711 True 1347.5 2170 92.6630 1091 2840 2 chr6D.!!$R1 1749
13 TraesCS1A01G216000 chr4B 97889690 97891313 1623 True 2104.0 2104 90.0980 935 2561 1 chr4B.!!$R1 1626
14 TraesCS1A01G216000 chr4B 11609021 11609610 589 False 743.0 743 89.4920 2254 2840 1 chr4B.!!$F1 586
15 TraesCS1A01G216000 chr5D 182935894 182936497 603 False 942.0 942 94.9010 236 838 1 chr5D.!!$F2 602
16 TraesCS1A01G216000 chr5D 47009325 47009942 617 False 464.0 464 80.6800 195 828 1 chr5D.!!$F1 633
17 TraesCS1A01G216000 chr5B 710172594 710173346 752 False 484.0 484 79.0640 195 931 1 chr5B.!!$F2 736
18 TraesCS1A01G216000 chr7D 3671182 3671948 766 True 483.0 483 78.9670 196 953 1 chr7D.!!$R1 757
19 TraesCS1A01G216000 chr6A 569693987 569694739 752 False 473.0 473 78.9950 195 931 1 chr6A.!!$F1 736
20 TraesCS1A01G216000 chr3A 469829300 469829896 596 True 446.0 446 80.6140 193 798 1 chr3A.!!$R1 605

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
61 62 0.034337 ATGCAGGCTGCCAAACAAAG 59.966 50.0 34.58 2.5 44.23 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 1998 0.034574 ACAGCATACCCCGCATCAAA 60.035 50.0 0.0 0.0 0.0 2.69 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
32 33 7.724128 TCGAAATTCGAAATTGTTCATCATG 57.276 32.000 16.25 0.00 46.90 3.07
33 34 7.304735 TCGAAATTCGAAATTGTTCATCATGT 58.695 30.769 16.25 0.00 46.90 3.21
34 35 7.481483 TCGAAATTCGAAATTGTTCATCATGTC 59.519 33.333 16.25 0.00 46.90 3.06
35 36 7.482743 CGAAATTCGAAATTGTTCATCATGTCT 59.517 33.333 10.18 0.00 43.74 3.41
36 37 9.773328 GAAATTCGAAATTGTTCATCATGTCTA 57.227 29.630 2.53 0.00 32.89 2.59
39 40 8.948853 TTCGAAATTGTTCATCATGTCTAAAC 57.051 30.769 0.00 0.00 32.89 2.01
40 41 8.093659 TCGAAATTGTTCATCATGTCTAAACA 57.906 30.769 0.00 0.00 35.01 2.83
41 42 8.015087 TCGAAATTGTTCATCATGTCTAAACAC 58.985 33.333 0.00 0.00 33.98 3.32
42 43 7.802720 CGAAATTGTTCATCATGTCTAAACACA 59.197 33.333 0.00 0.00 33.98 3.72
43 44 9.630098 GAAATTGTTCATCATGTCTAAACACAT 57.370 29.630 0.00 0.00 34.29 3.21
49 50 3.141002 CATGTCTAAACACATGCAGGC 57.859 47.619 0.00 0.00 45.43 4.85
50 51 2.566833 TGTCTAAACACATGCAGGCT 57.433 45.000 0.00 0.00 0.00 4.58
51 52 2.153645 TGTCTAAACACATGCAGGCTG 58.846 47.619 10.94 10.94 0.00 4.85
52 53 1.135575 GTCTAAACACATGCAGGCTGC 60.136 52.381 31.91 31.91 45.29 5.25
53 54 0.171903 CTAAACACATGCAGGCTGCC 59.828 55.000 34.58 18.22 44.23 4.85
54 55 0.539207 TAAACACATGCAGGCTGCCA 60.539 50.000 34.58 23.02 44.23 4.92
55 56 1.401318 AAACACATGCAGGCTGCCAA 61.401 50.000 34.58 19.32 44.23 4.52
56 57 1.401318 AACACATGCAGGCTGCCAAA 61.401 50.000 34.58 18.54 44.23 3.28
57 58 1.373748 CACATGCAGGCTGCCAAAC 60.374 57.895 34.58 9.58 44.23 2.93
58 59 1.833492 ACATGCAGGCTGCCAAACA 60.833 52.632 34.58 17.76 44.23 2.83
59 60 1.368209 CATGCAGGCTGCCAAACAA 59.632 52.632 34.58 16.98 44.23 2.83
60 61 0.249953 CATGCAGGCTGCCAAACAAA 60.250 50.000 34.58 16.22 44.23 2.83
61 62 0.034337 ATGCAGGCTGCCAAACAAAG 59.966 50.000 34.58 2.50 44.23 2.77
62 63 1.329171 TGCAGGCTGCCAAACAAAGT 61.329 50.000 34.58 0.00 44.23 2.66
63 64 0.598419 GCAGGCTGCCAAACAAAGTC 60.598 55.000 28.87 0.00 37.42 3.01
64 65 1.035139 CAGGCTGCCAAACAAAGTCT 58.965 50.000 22.65 0.00 0.00 3.24
65 66 1.000938 CAGGCTGCCAAACAAAGTCTC 60.001 52.381 22.65 0.00 0.00 3.36
66 67 1.032014 GGCTGCCAAACAAAGTCTCA 58.968 50.000 15.17 0.00 0.00 3.27
67 68 1.408702 GGCTGCCAAACAAAGTCTCAA 59.591 47.619 15.17 0.00 0.00 3.02
68 69 2.463876 GCTGCCAAACAAAGTCTCAAC 58.536 47.619 0.00 0.00 0.00 3.18
69 70 2.099756 GCTGCCAAACAAAGTCTCAACT 59.900 45.455 0.00 0.00 37.32 3.16
70 71 3.793465 GCTGCCAAACAAAGTCTCAACTC 60.793 47.826 0.00 0.00 33.48 3.01
71 72 3.351740 TGCCAAACAAAGTCTCAACTCA 58.648 40.909 0.00 0.00 33.48 3.41
72 73 3.378112 TGCCAAACAAAGTCTCAACTCAG 59.622 43.478 0.00 0.00 33.48 3.35
73 74 3.793465 GCCAAACAAAGTCTCAACTCAGC 60.793 47.826 0.00 0.00 33.48 4.26
74 75 3.378112 CCAAACAAAGTCTCAACTCAGCA 59.622 43.478 0.00 0.00 33.48 4.41
75 76 4.037208 CCAAACAAAGTCTCAACTCAGCAT 59.963 41.667 0.00 0.00 33.48 3.79
76 77 4.825546 AACAAAGTCTCAACTCAGCATG 57.174 40.909 0.00 0.00 33.48 4.06
77 78 3.813443 ACAAAGTCTCAACTCAGCATGT 58.187 40.909 0.00 0.00 37.40 3.21
78 79 3.812053 ACAAAGTCTCAACTCAGCATGTC 59.188 43.478 0.00 0.00 37.40 3.06
79 80 4.063689 CAAAGTCTCAACTCAGCATGTCT 58.936 43.478 0.00 0.00 37.40 3.41
80 81 3.591196 AGTCTCAACTCAGCATGTCTC 57.409 47.619 0.00 0.00 37.40 3.36
81 82 2.896044 AGTCTCAACTCAGCATGTCTCA 59.104 45.455 0.00 0.00 37.40 3.27
82 83 3.056678 AGTCTCAACTCAGCATGTCTCAG 60.057 47.826 0.00 0.00 37.40 3.35
83 84 2.001159 CTCAACTCAGCATGTCTCAGC 58.999 52.381 0.00 0.00 37.40 4.26
84 85 0.720027 CAACTCAGCATGTCTCAGCG 59.280 55.000 0.00 0.00 37.40 5.18
85 86 1.018226 AACTCAGCATGTCTCAGCGC 61.018 55.000 0.00 0.00 37.40 5.92
86 87 1.447314 CTCAGCATGTCTCAGCGCA 60.447 57.895 11.47 0.00 37.40 6.09
87 88 0.810426 CTCAGCATGTCTCAGCGCAT 60.810 55.000 11.47 0.00 37.40 4.73
88 89 0.461135 TCAGCATGTCTCAGCGCATA 59.539 50.000 11.47 0.00 37.40 3.14
89 90 0.580578 CAGCATGTCTCAGCGCATAC 59.419 55.000 11.47 1.96 35.48 2.39
90 91 0.176449 AGCATGTCTCAGCGCATACA 59.824 50.000 11.47 8.45 35.48 2.29
91 92 1.202615 AGCATGTCTCAGCGCATACAT 60.203 47.619 11.47 10.56 35.48 2.29
92 93 1.194098 GCATGTCTCAGCGCATACATC 59.806 52.381 11.47 4.56 30.32 3.06
93 94 1.454653 CATGTCTCAGCGCATACATCG 59.545 52.381 11.47 5.12 30.32 3.84
100 101 3.408755 CGCATACATCGCTGCCAA 58.591 55.556 0.00 0.00 34.89 4.52
101 102 1.720894 CGCATACATCGCTGCCAAA 59.279 52.632 0.00 0.00 34.89 3.28
102 103 0.589729 CGCATACATCGCTGCCAAAC 60.590 55.000 0.00 0.00 34.89 2.93
103 104 0.451383 GCATACATCGCTGCCAAACA 59.549 50.000 0.00 0.00 32.15 2.83
104 105 1.135431 GCATACATCGCTGCCAAACAA 60.135 47.619 0.00 0.00 32.15 2.83
105 106 2.518949 CATACATCGCTGCCAAACAAC 58.481 47.619 0.00 0.00 0.00 3.32
106 107 1.598882 TACATCGCTGCCAAACAACA 58.401 45.000 0.00 0.00 0.00 3.33
107 108 0.743688 ACATCGCTGCCAAACAACAA 59.256 45.000 0.00 0.00 0.00 2.83
108 109 1.130955 CATCGCTGCCAAACAACAAC 58.869 50.000 0.00 0.00 0.00 3.32
109 110 0.743688 ATCGCTGCCAAACAACAACA 59.256 45.000 0.00 0.00 0.00 3.33
110 111 0.528017 TCGCTGCCAAACAACAACAA 59.472 45.000 0.00 0.00 0.00 2.83
111 112 0.644843 CGCTGCCAAACAACAACAAC 59.355 50.000 0.00 0.00 0.00 3.32
112 113 1.735369 CGCTGCCAAACAACAACAACT 60.735 47.619 0.00 0.00 0.00 3.16
113 114 1.660104 GCTGCCAAACAACAACAACTG 59.340 47.619 0.00 0.00 0.00 3.16
114 115 1.660104 CTGCCAAACAACAACAACTGC 59.340 47.619 0.00 0.00 0.00 4.40
115 116 1.001293 TGCCAAACAACAACAACTGCA 59.999 42.857 0.00 0.00 0.00 4.41
116 117 2.278854 GCCAAACAACAACAACTGCAT 58.721 42.857 0.00 0.00 0.00 3.96
117 118 2.030701 GCCAAACAACAACAACTGCATG 59.969 45.455 0.00 0.00 0.00 4.06
118 119 2.608546 CCAAACAACAACAACTGCATGG 59.391 45.455 0.00 0.00 0.00 3.66
119 120 3.519579 CAAACAACAACAACTGCATGGA 58.480 40.909 0.00 0.00 0.00 3.41
120 121 2.869233 ACAACAACAACTGCATGGAC 57.131 45.000 0.00 0.00 0.00 4.02
121 122 2.378038 ACAACAACAACTGCATGGACT 58.622 42.857 0.00 0.00 0.00 3.85
122 123 2.358898 ACAACAACAACTGCATGGACTC 59.641 45.455 0.00 0.00 0.00 3.36
123 124 2.346766 ACAACAACTGCATGGACTCA 57.653 45.000 0.00 0.00 0.00 3.41
124 125 2.224606 ACAACAACTGCATGGACTCAG 58.775 47.619 0.00 0.00 36.45 3.35
125 126 1.068748 CAACAACTGCATGGACTCAGC 60.069 52.381 0.00 0.00 33.80 4.26
126 127 0.109153 ACAACTGCATGGACTCAGCA 59.891 50.000 0.00 0.00 36.72 4.41
127 128 1.271762 ACAACTGCATGGACTCAGCAT 60.272 47.619 0.00 0.00 37.68 3.79
128 129 1.132453 CAACTGCATGGACTCAGCATG 59.868 52.381 0.00 0.00 37.68 4.06
129 130 0.327259 ACTGCATGGACTCAGCATGT 59.673 50.000 0.00 0.00 37.68 3.21
130 131 1.015109 CTGCATGGACTCAGCATGTC 58.985 55.000 0.00 0.00 37.68 3.06
131 132 0.616891 TGCATGGACTCAGCATGTCT 59.383 50.000 0.00 0.00 37.40 3.41
132 133 1.832998 TGCATGGACTCAGCATGTCTA 59.167 47.619 0.00 0.00 37.40 2.59
133 134 2.208431 GCATGGACTCAGCATGTCTAC 58.792 52.381 0.00 0.00 37.40 2.59
134 135 2.419159 GCATGGACTCAGCATGTCTACA 60.419 50.000 0.00 0.00 37.40 2.74
135 136 3.193263 CATGGACTCAGCATGTCTACAC 58.807 50.000 0.00 0.00 37.40 2.90
136 137 2.529632 TGGACTCAGCATGTCTACACT 58.470 47.619 0.00 0.00 37.40 3.55
137 138 2.899900 TGGACTCAGCATGTCTACACTT 59.100 45.455 0.00 0.00 37.40 3.16
138 139 4.086457 TGGACTCAGCATGTCTACACTTA 58.914 43.478 0.00 0.00 37.40 2.24
139 140 4.158579 TGGACTCAGCATGTCTACACTTAG 59.841 45.833 0.00 0.00 37.40 2.18
140 141 4.109050 GACTCAGCATGTCTACACTTAGC 58.891 47.826 0.00 0.00 37.40 3.09
141 142 3.511540 ACTCAGCATGTCTACACTTAGCA 59.488 43.478 0.00 0.00 37.40 3.49
142 143 4.161189 ACTCAGCATGTCTACACTTAGCAT 59.839 41.667 0.00 0.00 37.40 3.79
143 144 4.436332 TCAGCATGTCTACACTTAGCATG 58.564 43.478 0.00 0.00 39.89 4.06
144 145 4.081476 TCAGCATGTCTACACTTAGCATGT 60.081 41.667 0.00 0.00 39.52 3.21
145 146 5.127031 TCAGCATGTCTACACTTAGCATGTA 59.873 40.000 0.00 0.00 39.52 2.29
146 147 5.987953 CAGCATGTCTACACTTAGCATGTAT 59.012 40.000 0.00 0.00 39.52 2.29
147 148 5.987953 AGCATGTCTACACTTAGCATGTATG 59.012 40.000 0.00 0.00 39.52 2.39
148 149 5.985530 GCATGTCTACACTTAGCATGTATGA 59.014 40.000 0.00 0.00 39.52 2.15
149 150 6.145209 GCATGTCTACACTTAGCATGTATGAG 59.855 42.308 0.00 0.00 39.52 2.90
150 151 7.428826 CATGTCTACACTTAGCATGTATGAGA 58.571 38.462 0.00 0.00 36.32 3.27
151 152 7.032377 TGTCTACACTTAGCATGTATGAGAG 57.968 40.000 0.00 0.00 32.24 3.20
152 153 6.039829 TGTCTACACTTAGCATGTATGAGAGG 59.960 42.308 0.00 0.00 32.24 3.69
153 154 6.263392 GTCTACACTTAGCATGTATGAGAGGA 59.737 42.308 0.00 0.00 32.24 3.71
154 155 5.528043 ACACTTAGCATGTATGAGAGGAG 57.472 43.478 0.00 0.00 0.00 3.69
155 156 5.204292 ACACTTAGCATGTATGAGAGGAGA 58.796 41.667 0.00 0.00 0.00 3.71
156 157 5.658634 ACACTTAGCATGTATGAGAGGAGAA 59.341 40.000 0.00 0.00 0.00 2.87
157 158 5.982516 CACTTAGCATGTATGAGAGGAGAAC 59.017 44.000 0.00 0.00 0.00 3.01
158 159 5.658634 ACTTAGCATGTATGAGAGGAGAACA 59.341 40.000 0.00 0.00 0.00 3.18
159 160 6.155221 ACTTAGCATGTATGAGAGGAGAACAA 59.845 38.462 0.00 0.00 0.00 2.83
160 161 4.764172 AGCATGTATGAGAGGAGAACAAC 58.236 43.478 0.00 0.00 0.00 3.32
161 162 4.469227 AGCATGTATGAGAGGAGAACAACT 59.531 41.667 0.00 0.00 0.00 3.16
162 163 5.658634 AGCATGTATGAGAGGAGAACAACTA 59.341 40.000 0.00 0.00 0.00 2.24
163 164 5.982516 GCATGTATGAGAGGAGAACAACTAG 59.017 44.000 0.00 0.00 0.00 2.57
164 165 6.511416 CATGTATGAGAGGAGAACAACTAGG 58.489 44.000 0.00 0.00 0.00 3.02
165 166 4.402793 TGTATGAGAGGAGAACAACTAGGC 59.597 45.833 0.00 0.00 0.00 3.93
166 167 3.176924 TGAGAGGAGAACAACTAGGCT 57.823 47.619 0.00 0.00 0.00 4.58
167 168 4.317530 TGAGAGGAGAACAACTAGGCTA 57.682 45.455 0.00 0.00 0.00 3.93
168 169 4.274147 TGAGAGGAGAACAACTAGGCTAG 58.726 47.826 19.83 19.83 0.00 3.42
169 170 3.634910 GAGAGGAGAACAACTAGGCTAGG 59.365 52.174 24.57 10.93 0.00 3.02
170 171 3.011934 AGAGGAGAACAACTAGGCTAGGT 59.988 47.826 24.57 16.82 0.00 3.08
171 172 3.367321 AGGAGAACAACTAGGCTAGGTC 58.633 50.000 24.57 15.30 0.00 3.85
172 173 2.431419 GGAGAACAACTAGGCTAGGTCC 59.569 54.545 24.57 12.00 0.00 4.46
173 174 3.097614 GAGAACAACTAGGCTAGGTCCA 58.902 50.000 24.57 0.00 0.00 4.02
174 175 3.707102 GAGAACAACTAGGCTAGGTCCAT 59.293 47.826 24.57 7.20 0.00 3.41
175 176 3.452627 AGAACAACTAGGCTAGGTCCATG 59.547 47.826 24.57 16.19 0.00 3.66
176 177 1.486726 ACAACTAGGCTAGGTCCATGC 59.513 52.381 24.57 0.00 0.00 4.06
177 178 1.486310 CAACTAGGCTAGGTCCATGCA 59.514 52.381 24.57 0.00 0.00 3.96
178 179 2.105477 CAACTAGGCTAGGTCCATGCAT 59.895 50.000 24.57 0.00 0.00 3.96
179 180 1.696336 ACTAGGCTAGGTCCATGCATG 59.304 52.381 24.57 20.19 0.00 4.06
180 181 0.397941 TAGGCTAGGTCCATGCATGC 59.602 55.000 21.69 11.82 0.00 4.06
181 182 1.150081 GGCTAGGTCCATGCATGCT 59.850 57.895 21.69 14.98 0.00 3.79
182 183 0.397941 GGCTAGGTCCATGCATGCTA 59.602 55.000 21.69 15.30 0.00 3.49
183 184 1.517242 GCTAGGTCCATGCATGCTAC 58.483 55.000 21.69 19.26 0.00 3.58
184 185 1.879796 GCTAGGTCCATGCATGCTACC 60.880 57.143 28.92 28.92 34.41 3.18
185 186 1.417517 CTAGGTCCATGCATGCTACCA 59.582 52.381 33.49 23.73 35.78 3.25
186 187 0.625316 AGGTCCATGCATGCTACCAA 59.375 50.000 33.49 11.94 35.78 3.67
187 188 1.005805 AGGTCCATGCATGCTACCAAA 59.994 47.619 33.49 10.57 35.78 3.28
188 189 1.134946 GGTCCATGCATGCTACCAAAC 59.865 52.381 30.16 16.16 34.39 2.93
189 190 1.818060 GTCCATGCATGCTACCAAACA 59.182 47.619 21.69 0.00 0.00 2.83
190 191 1.818060 TCCATGCATGCTACCAAACAC 59.182 47.619 21.69 0.00 0.00 3.32
191 192 1.545136 CCATGCATGCTACCAAACACA 59.455 47.619 21.69 0.00 0.00 3.72
192 193 2.598589 CATGCATGCTACCAAACACAC 58.401 47.619 20.33 0.00 0.00 3.82
193 194 0.958091 TGCATGCTACCAAACACACC 59.042 50.000 20.33 0.00 0.00 4.16
584 605 1.018148 CATCTCACGCTACCTCGTCT 58.982 55.000 0.00 0.00 41.21 4.18
722 743 1.378762 CGCCCCTTTCTTCCCTTCA 59.621 57.895 0.00 0.00 0.00 3.02
781 803 3.710722 CTGCCTCGGCTCCCAACT 61.711 66.667 9.65 0.00 42.51 3.16
798 826 2.278332 ACTTTGAACAGGGAAGAGCC 57.722 50.000 0.00 0.00 0.00 4.70
1086 1183 7.607607 GGATTGTATGCTTACATGATGGTCATA 59.392 37.037 12.73 0.00 38.12 2.15
1284 1381 8.579850 AGAGAAATTTGTTGTTGGATAGCATA 57.420 30.769 0.00 0.00 0.00 3.14
1323 1420 6.041979 AGGAACAAGTTGCCATGTTTCTTTAT 59.958 34.615 1.81 0.00 41.52 1.40
1369 1466 4.985538 AGGACACTACAACCTATCTTCG 57.014 45.455 0.00 0.00 31.78 3.79
1449 1547 5.009510 GGAGTTGAGAGATGAGATGATTCGA 59.990 44.000 0.00 0.00 0.00 3.71
1618 1717 3.718434 TGGAGCAATAGATGGGACTCATT 59.282 43.478 0.00 0.00 35.97 2.57
1899 1998 8.090831 GCTTGTTCATAGGAAAATTCTTCCTTT 58.909 33.333 20.08 13.26 46.21 3.11
1935 2034 0.821711 TGTGAGGCCGGGTTTTCTTG 60.822 55.000 2.18 0.00 0.00 3.02
1985 2084 4.030913 TGAAAGAGTATGGTCGAGGGAAT 58.969 43.478 0.00 0.00 0.00 3.01
2381 2481 4.713553 TGATGTGTGACTTGGTGTTGTAT 58.286 39.130 0.00 0.00 0.00 2.29
2382 2482 5.129634 TGATGTGTGACTTGGTGTTGTATT 58.870 37.500 0.00 0.00 0.00 1.89
2383 2483 5.592282 TGATGTGTGACTTGGTGTTGTATTT 59.408 36.000 0.00 0.00 0.00 1.40
2430 2837 5.714333 TGCTGGAATTCATTTTTAGGTGCTA 59.286 36.000 7.93 0.00 0.00 3.49
2433 2840 7.391148 TGGAATTCATTTTTAGGTGCTAGAC 57.609 36.000 7.93 0.00 0.00 2.59
2449 2856 4.647853 TGCTAGACCGTCATTTATAGGTGT 59.352 41.667 0.40 0.00 37.07 4.16
2456 2863 5.588648 ACCGTCATTTATAGGTGTTGGAATG 59.411 40.000 0.00 0.00 35.36 2.67
2474 2881 4.462483 GGAATGTCATTTTTAGGTGCTGGA 59.538 41.667 0.00 0.00 0.00 3.86
2477 2884 5.643379 TGTCATTTTTAGGTGCTGGAATC 57.357 39.130 0.00 0.00 0.00 2.52
2514 2921 6.072008 TGCTGAAATACATTTTTGAGCTGCTA 60.072 34.615 0.15 0.00 32.55 3.49
2577 3087 5.880332 GCTGGGATGTGTTATTAACTTCTGA 59.120 40.000 7.99 0.00 0.00 3.27
2674 3184 0.107214 TCATGAATTGGACTCCGCCC 60.107 55.000 0.00 0.00 0.00 6.13
2832 3342 4.847198 ACTCAAGTGCACAATCATATCCA 58.153 39.130 21.04 0.00 0.00 3.41
2835 3345 4.637091 TCAAGTGCACAATCATATCCACAG 59.363 41.667 21.04 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.482743 AGACATGATGAACAATTTCGAATTTCG 59.517 33.333 12.54 12.54 42.10 3.46
10 11 8.679288 AGACATGATGAACAATTTCGAATTTC 57.321 30.769 0.00 0.75 34.04 2.17
13 14 9.559958 GTTTAGACATGATGAACAATTTCGAAT 57.440 29.630 0.00 0.00 34.04 3.34
14 15 8.563732 TGTTTAGACATGATGAACAATTTCGAA 58.436 29.630 0.00 0.00 34.04 3.71
15 16 8.015087 GTGTTTAGACATGATGAACAATTTCGA 58.985 33.333 0.00 0.00 38.23 3.71
16 17 7.802720 TGTGTTTAGACATGATGAACAATTTCG 59.197 33.333 0.00 0.00 38.23 3.46
17 18 9.630098 ATGTGTTTAGACATGATGAACAATTTC 57.370 29.630 0.00 0.00 38.23 2.17
30 31 2.751259 CAGCCTGCATGTGTTTAGACAT 59.249 45.455 0.00 0.00 38.23 3.06
31 32 2.153645 CAGCCTGCATGTGTTTAGACA 58.846 47.619 0.00 0.00 0.00 3.41
32 33 1.135575 GCAGCCTGCATGTGTTTAGAC 60.136 52.381 12.82 0.00 44.26 2.59
33 34 1.167851 GCAGCCTGCATGTGTTTAGA 58.832 50.000 12.82 0.00 44.26 2.10
34 35 3.708195 GCAGCCTGCATGTGTTTAG 57.292 52.632 12.82 0.00 44.26 1.85
44 45 0.598419 GACTTTGTTTGGCAGCCTGC 60.598 55.000 14.15 8.55 44.08 4.85
45 46 1.000938 GAGACTTTGTTTGGCAGCCTG 60.001 52.381 14.15 0.00 0.00 4.85
46 47 1.322442 GAGACTTTGTTTGGCAGCCT 58.678 50.000 14.15 0.00 0.00 4.58
47 48 1.032014 TGAGACTTTGTTTGGCAGCC 58.968 50.000 3.66 3.66 0.00 4.85
48 49 2.099756 AGTTGAGACTTTGTTTGGCAGC 59.900 45.455 0.00 0.00 29.87 5.25
49 50 3.378112 TGAGTTGAGACTTTGTTTGGCAG 59.622 43.478 0.00 0.00 35.88 4.85
50 51 3.351740 TGAGTTGAGACTTTGTTTGGCA 58.648 40.909 0.00 0.00 35.88 4.92
51 52 3.793465 GCTGAGTTGAGACTTTGTTTGGC 60.793 47.826 0.00 0.00 35.88 4.52
52 53 3.378112 TGCTGAGTTGAGACTTTGTTTGG 59.622 43.478 0.00 0.00 35.88 3.28
53 54 4.621068 TGCTGAGTTGAGACTTTGTTTG 57.379 40.909 0.00 0.00 35.88 2.93
54 55 4.641989 ACATGCTGAGTTGAGACTTTGTTT 59.358 37.500 0.00 0.00 35.88 2.83
55 56 4.202441 ACATGCTGAGTTGAGACTTTGTT 58.798 39.130 0.00 0.00 35.88 2.83
56 57 3.812053 GACATGCTGAGTTGAGACTTTGT 59.188 43.478 0.00 0.00 35.88 2.83
57 58 4.063689 AGACATGCTGAGTTGAGACTTTG 58.936 43.478 0.00 0.00 35.88 2.77
58 59 4.202295 TGAGACATGCTGAGTTGAGACTTT 60.202 41.667 0.00 0.00 35.88 2.66
59 60 3.323115 TGAGACATGCTGAGTTGAGACTT 59.677 43.478 0.00 0.00 35.88 3.01
60 61 2.896044 TGAGACATGCTGAGTTGAGACT 59.104 45.455 0.00 0.00 39.32 3.24
61 62 3.252400 CTGAGACATGCTGAGTTGAGAC 58.748 50.000 0.00 0.00 0.00 3.36
62 63 2.353505 GCTGAGACATGCTGAGTTGAGA 60.354 50.000 0.00 0.00 29.65 3.27
63 64 2.001159 GCTGAGACATGCTGAGTTGAG 58.999 52.381 0.00 0.00 29.65 3.02
64 65 1.670967 CGCTGAGACATGCTGAGTTGA 60.671 52.381 0.00 0.00 29.65 3.18
65 66 0.720027 CGCTGAGACATGCTGAGTTG 59.280 55.000 0.00 0.00 29.65 3.16
66 67 1.018226 GCGCTGAGACATGCTGAGTT 61.018 55.000 0.00 0.00 29.65 3.01
67 68 1.447489 GCGCTGAGACATGCTGAGT 60.447 57.895 0.00 0.00 29.65 3.41
68 69 0.810426 ATGCGCTGAGACATGCTGAG 60.810 55.000 9.73 0.00 0.00 3.35
69 70 0.461135 TATGCGCTGAGACATGCTGA 59.539 50.000 9.73 0.00 0.00 4.26
70 71 0.580578 GTATGCGCTGAGACATGCTG 59.419 55.000 9.73 0.00 0.00 4.41
71 72 0.176449 TGTATGCGCTGAGACATGCT 59.824 50.000 9.73 0.00 31.11 3.79
72 73 1.194098 GATGTATGCGCTGAGACATGC 59.806 52.381 12.11 0.00 32.75 4.06
73 74 1.454653 CGATGTATGCGCTGAGACATG 59.545 52.381 12.11 0.00 32.75 3.21
74 75 1.775869 CGATGTATGCGCTGAGACAT 58.224 50.000 9.73 8.48 35.26 3.06
75 76 3.256620 CGATGTATGCGCTGAGACA 57.743 52.632 9.73 2.73 0.00 3.41
83 84 0.589729 GTTTGGCAGCGATGTATGCG 60.590 55.000 1.22 0.00 43.49 4.73
84 85 0.451383 TGTTTGGCAGCGATGTATGC 59.549 50.000 1.22 0.00 41.80 3.14
85 86 2.095314 TGTTGTTTGGCAGCGATGTATG 60.095 45.455 1.22 0.00 0.00 2.39
86 87 2.158559 TGTTGTTTGGCAGCGATGTAT 58.841 42.857 1.22 0.00 0.00 2.29
87 88 1.598882 TGTTGTTTGGCAGCGATGTA 58.401 45.000 1.22 0.00 0.00 2.29
88 89 0.743688 TTGTTGTTTGGCAGCGATGT 59.256 45.000 1.22 0.00 0.00 3.06
89 90 1.130955 GTTGTTGTTTGGCAGCGATG 58.869 50.000 0.00 0.00 0.00 3.84
90 91 0.743688 TGTTGTTGTTTGGCAGCGAT 59.256 45.000 0.00 0.00 0.00 4.58
91 92 0.528017 TTGTTGTTGTTTGGCAGCGA 59.472 45.000 0.00 0.00 0.00 4.93
92 93 0.644843 GTTGTTGTTGTTTGGCAGCG 59.355 50.000 0.00 0.00 0.00 5.18
93 94 1.660104 CAGTTGTTGTTGTTTGGCAGC 59.340 47.619 0.00 0.00 0.00 5.25
94 95 1.660104 GCAGTTGTTGTTGTTTGGCAG 59.340 47.619 0.00 0.00 0.00 4.85
95 96 1.001293 TGCAGTTGTTGTTGTTTGGCA 59.999 42.857 0.00 0.00 0.00 4.92
96 97 1.719600 TGCAGTTGTTGTTGTTTGGC 58.280 45.000 0.00 0.00 0.00 4.52
97 98 2.608546 CCATGCAGTTGTTGTTGTTTGG 59.391 45.455 0.00 0.00 0.00 3.28
98 99 3.306703 GTCCATGCAGTTGTTGTTGTTTG 59.693 43.478 0.00 0.00 0.00 2.93
99 100 3.195396 AGTCCATGCAGTTGTTGTTGTTT 59.805 39.130 0.00 0.00 0.00 2.83
100 101 2.760092 AGTCCATGCAGTTGTTGTTGTT 59.240 40.909 0.00 0.00 0.00 2.83
101 102 2.358898 GAGTCCATGCAGTTGTTGTTGT 59.641 45.455 0.00 0.00 0.00 3.32
102 103 2.358582 TGAGTCCATGCAGTTGTTGTTG 59.641 45.455 0.00 0.00 0.00 3.33
103 104 2.620115 CTGAGTCCATGCAGTTGTTGTT 59.380 45.455 0.00 0.00 0.00 2.83
104 105 2.224606 CTGAGTCCATGCAGTTGTTGT 58.775 47.619 0.00 0.00 0.00 3.32
105 106 1.068748 GCTGAGTCCATGCAGTTGTTG 60.069 52.381 0.00 0.00 34.66 3.33
106 107 1.242076 GCTGAGTCCATGCAGTTGTT 58.758 50.000 0.00 0.00 34.66 2.83
107 108 0.109153 TGCTGAGTCCATGCAGTTGT 59.891 50.000 0.00 0.00 34.66 3.32
108 109 1.132453 CATGCTGAGTCCATGCAGTTG 59.868 52.381 0.00 0.00 40.18 3.16
109 110 1.271762 ACATGCTGAGTCCATGCAGTT 60.272 47.619 8.73 0.00 42.89 3.16
110 111 0.327259 ACATGCTGAGTCCATGCAGT 59.673 50.000 8.73 4.95 42.89 4.40
111 112 1.015109 GACATGCTGAGTCCATGCAG 58.985 55.000 8.73 0.00 42.89 4.41
112 113 0.616891 AGACATGCTGAGTCCATGCA 59.383 50.000 8.73 7.05 42.89 3.96
113 114 2.208431 GTAGACATGCTGAGTCCATGC 58.792 52.381 8.73 1.97 42.89 4.06
114 115 3.118847 AGTGTAGACATGCTGAGTCCATG 60.119 47.826 7.58 7.58 44.28 3.66
115 116 3.102972 AGTGTAGACATGCTGAGTCCAT 58.897 45.455 0.00 0.00 36.68 3.41
116 117 2.529632 AGTGTAGACATGCTGAGTCCA 58.470 47.619 0.00 0.00 36.68 4.02
117 118 3.601443 AAGTGTAGACATGCTGAGTCC 57.399 47.619 0.00 0.00 36.68 3.85
118 119 4.109050 GCTAAGTGTAGACATGCTGAGTC 58.891 47.826 0.00 0.00 36.26 3.36
119 120 3.511540 TGCTAAGTGTAGACATGCTGAGT 59.488 43.478 0.00 0.00 0.00 3.41
120 121 4.115401 TGCTAAGTGTAGACATGCTGAG 57.885 45.455 0.00 0.00 0.00 3.35
121 122 4.081476 ACATGCTAAGTGTAGACATGCTGA 60.081 41.667 13.37 0.00 41.09 4.26
122 123 4.186926 ACATGCTAAGTGTAGACATGCTG 58.813 43.478 13.37 0.00 41.09 4.41
123 124 4.478206 ACATGCTAAGTGTAGACATGCT 57.522 40.909 13.37 0.00 41.09 3.79
124 125 5.985530 TCATACATGCTAAGTGTAGACATGC 59.014 40.000 13.37 0.00 41.09 4.06
125 126 7.428826 TCTCATACATGCTAAGTGTAGACATG 58.571 38.462 0.00 12.52 42.00 3.21
126 127 7.255766 CCTCTCATACATGCTAAGTGTAGACAT 60.256 40.741 0.00 0.00 35.69 3.06
127 128 6.039829 CCTCTCATACATGCTAAGTGTAGACA 59.960 42.308 0.00 0.00 35.69 3.41
128 129 6.263392 TCCTCTCATACATGCTAAGTGTAGAC 59.737 42.308 0.00 0.00 35.69 2.59
129 130 6.365520 TCCTCTCATACATGCTAAGTGTAGA 58.634 40.000 0.00 0.00 35.69 2.59
130 131 6.488344 TCTCCTCTCATACATGCTAAGTGTAG 59.512 42.308 0.00 0.00 35.69 2.74
131 132 6.365520 TCTCCTCTCATACATGCTAAGTGTA 58.634 40.000 0.00 0.00 36.58 2.90
132 133 5.204292 TCTCCTCTCATACATGCTAAGTGT 58.796 41.667 0.00 0.00 0.00 3.55
133 134 5.781210 TCTCCTCTCATACATGCTAAGTG 57.219 43.478 0.00 0.00 0.00 3.16
134 135 5.658634 TGTTCTCCTCTCATACATGCTAAGT 59.341 40.000 0.00 0.00 0.00 2.24
135 136 6.154203 TGTTCTCCTCTCATACATGCTAAG 57.846 41.667 0.00 0.00 0.00 2.18
136 137 6.155221 AGTTGTTCTCCTCTCATACATGCTAA 59.845 38.462 0.00 0.00 0.00 3.09
137 138 5.658634 AGTTGTTCTCCTCTCATACATGCTA 59.341 40.000 0.00 0.00 0.00 3.49
138 139 4.469227 AGTTGTTCTCCTCTCATACATGCT 59.531 41.667 0.00 0.00 0.00 3.79
139 140 4.764172 AGTTGTTCTCCTCTCATACATGC 58.236 43.478 0.00 0.00 0.00 4.06
140 141 6.511416 CCTAGTTGTTCTCCTCTCATACATG 58.489 44.000 0.00 0.00 0.00 3.21
141 142 5.069781 GCCTAGTTGTTCTCCTCTCATACAT 59.930 44.000 0.00 0.00 0.00 2.29
142 143 4.402793 GCCTAGTTGTTCTCCTCTCATACA 59.597 45.833 0.00 0.00 0.00 2.29
143 144 4.647399 AGCCTAGTTGTTCTCCTCTCATAC 59.353 45.833 0.00 0.00 0.00 2.39
144 145 4.873010 AGCCTAGTTGTTCTCCTCTCATA 58.127 43.478 0.00 0.00 0.00 2.15
145 146 3.718723 AGCCTAGTTGTTCTCCTCTCAT 58.281 45.455 0.00 0.00 0.00 2.90
146 147 3.176924 AGCCTAGTTGTTCTCCTCTCA 57.823 47.619 0.00 0.00 0.00 3.27
147 148 3.634910 CCTAGCCTAGTTGTTCTCCTCTC 59.365 52.174 0.00 0.00 0.00 3.20
148 149 3.011934 ACCTAGCCTAGTTGTTCTCCTCT 59.988 47.826 0.00 0.00 0.00 3.69
149 150 3.367321 ACCTAGCCTAGTTGTTCTCCTC 58.633 50.000 0.00 0.00 0.00 3.71
150 151 3.367321 GACCTAGCCTAGTTGTTCTCCT 58.633 50.000 0.00 0.00 0.00 3.69
151 152 2.431419 GGACCTAGCCTAGTTGTTCTCC 59.569 54.545 0.00 0.00 0.00 3.71
152 153 3.097614 TGGACCTAGCCTAGTTGTTCTC 58.902 50.000 0.00 0.00 0.00 2.87
153 154 3.185880 TGGACCTAGCCTAGTTGTTCT 57.814 47.619 0.00 0.00 0.00 3.01
154 155 3.798202 CATGGACCTAGCCTAGTTGTTC 58.202 50.000 0.00 0.00 0.00 3.18
155 156 2.092914 GCATGGACCTAGCCTAGTTGTT 60.093 50.000 0.00 0.00 0.00 2.83
156 157 1.486726 GCATGGACCTAGCCTAGTTGT 59.513 52.381 0.00 0.00 0.00 3.32
157 158 1.486310 TGCATGGACCTAGCCTAGTTG 59.514 52.381 0.00 0.00 0.00 3.16
158 159 1.879575 TGCATGGACCTAGCCTAGTT 58.120 50.000 0.00 0.00 0.00 2.24
159 160 1.696336 CATGCATGGACCTAGCCTAGT 59.304 52.381 19.40 0.00 0.00 2.57
160 161 1.610102 GCATGCATGGACCTAGCCTAG 60.610 57.143 27.34 0.00 0.00 3.02
161 162 0.397941 GCATGCATGGACCTAGCCTA 59.602 55.000 27.34 0.00 0.00 3.93
162 163 1.150081 GCATGCATGGACCTAGCCT 59.850 57.895 27.34 0.00 0.00 4.58
163 164 0.397941 TAGCATGCATGGACCTAGCC 59.602 55.000 27.34 8.57 0.00 3.93
164 165 1.517242 GTAGCATGCATGGACCTAGC 58.483 55.000 27.34 11.62 0.00 3.42
165 166 1.417517 TGGTAGCATGCATGGACCTAG 59.582 52.381 27.34 0.91 0.00 3.02
166 167 1.506025 TGGTAGCATGCATGGACCTA 58.494 50.000 27.34 16.92 0.00 3.08
167 168 0.625316 TTGGTAGCATGCATGGACCT 59.375 50.000 27.34 17.91 0.00 3.85
168 169 1.134946 GTTTGGTAGCATGCATGGACC 59.865 52.381 27.34 20.05 0.00 4.46
169 170 1.818060 TGTTTGGTAGCATGCATGGAC 59.182 47.619 27.34 12.23 0.00 4.02
170 171 1.818060 GTGTTTGGTAGCATGCATGGA 59.182 47.619 27.34 0.00 0.00 3.41
171 172 1.545136 TGTGTTTGGTAGCATGCATGG 59.455 47.619 27.34 10.03 0.00 3.66
172 173 2.598589 GTGTGTTTGGTAGCATGCATG 58.401 47.619 22.70 22.70 0.00 4.06
173 174 1.545582 GGTGTGTTTGGTAGCATGCAT 59.454 47.619 21.98 7.68 0.00 3.96
174 175 0.958091 GGTGTGTTTGGTAGCATGCA 59.042 50.000 21.98 2.77 0.00 3.96
175 176 0.243636 GGGTGTGTTTGGTAGCATGC 59.756 55.000 10.51 10.51 0.00 4.06
176 177 1.909700 AGGGTGTGTTTGGTAGCATG 58.090 50.000 0.00 0.00 0.00 4.06
177 178 2.675658 AAGGGTGTGTTTGGTAGCAT 57.324 45.000 0.00 0.00 0.00 3.79
178 179 2.224670 CCTAAGGGTGTGTTTGGTAGCA 60.225 50.000 0.00 0.00 0.00 3.49
179 180 2.433436 CCTAAGGGTGTGTTTGGTAGC 58.567 52.381 0.00 0.00 0.00 3.58
180 181 3.067684 CCCTAAGGGTGTGTTTGGTAG 57.932 52.381 0.00 0.00 38.25 3.18
193 194 2.433436 GCTACCAAACACACCCTAAGG 58.567 52.381 0.00 0.00 40.04 2.69
417 419 2.922950 CGGGTTGGTCGTTCGAGGA 61.923 63.158 0.00 0.00 0.00 3.71
565 586 1.018148 AGACGAGGTAGCGTGAGATG 58.982 55.000 0.00 0.00 45.72 2.90
722 743 2.364448 GAGAGGAGGAAGGCGGGT 60.364 66.667 0.00 0.00 0.00 5.28
798 826 1.003839 TACAGCAACAAGGGCTCGG 60.004 57.895 0.00 0.00 40.23 4.63
799 827 0.602638 TGTACAGCAACAAGGGCTCG 60.603 55.000 0.00 0.00 40.23 5.03
800 828 1.160137 CTGTACAGCAACAAGGGCTC 58.840 55.000 10.54 0.00 40.23 4.70
801 829 0.764890 TCTGTACAGCAACAAGGGCT 59.235 50.000 18.45 0.00 43.77 5.19
802 830 1.160137 CTCTGTACAGCAACAAGGGC 58.840 55.000 18.45 0.00 0.00 5.19
1086 1183 7.121315 GGTGTTTGTTGCCTAGATCTTCTAAAT 59.879 37.037 0.00 0.00 0.00 1.40
1323 1420 3.181427 ACCTTTGGTTATGGCCAACTACA 60.181 43.478 10.96 4.21 46.98 2.74
1449 1547 1.384191 GCAATGGTTGGAGGGAGGT 59.616 57.895 0.00 0.00 0.00 3.85
1618 1717 2.949177 TTTGGGACTCTAGCAAGCAA 57.051 45.000 0.00 0.00 0.00 3.91
1780 1879 1.211457 CAACCCATCTTCCCTCTCCAG 59.789 57.143 0.00 0.00 0.00 3.86
1899 1998 0.034574 ACAGCATACCCCGCATCAAA 60.035 50.000 0.00 0.00 0.00 2.69
1985 2084 4.410099 ACTCTTTGGCATTTTGAGGATGA 58.590 39.130 0.00 0.00 0.00 2.92
2334 2434 5.049398 TGTTTTACAACACCAAGACACAC 57.951 39.130 0.00 0.00 38.03 3.82
2430 2837 4.468510 TCCAACACCTATAAATGACGGTCT 59.531 41.667 9.88 0.00 0.00 3.85
2433 2840 5.588648 ACATTCCAACACCTATAAATGACGG 59.411 40.000 0.00 0.00 0.00 4.79
2442 2849 7.673926 ACCTAAAAATGACATTCCAACACCTAT 59.326 33.333 0.05 0.00 0.00 2.57
2449 2856 5.279406 CCAGCACCTAAAAATGACATTCCAA 60.279 40.000 0.05 0.00 0.00 3.53
2456 2863 5.183904 ACAGATTCCAGCACCTAAAAATGAC 59.816 40.000 0.00 0.00 0.00 3.06
2674 3184 3.490800 TTCAACATCATTGCCGACATG 57.509 42.857 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.