Multiple sequence alignment - TraesCS7A01G117200

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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 TraesCS7A01G117200 chr7A 100.000 3452 0 0 1 3452 75357993 75361444 0.000000e+00 6375.0
1 TraesCS7A01G117200 chr7A 86.395 147 12 4 629 773 730308140 730308280 1.660000e-33 154.0
2 TraesCS7A01G117200 chr7A 86.395 147 12 4 629 773 730355145 730355285 1.660000e-33 154.0
3 TraesCS7A01G117200 chr3B 97.325 3028 56 8 432 3452 9888969 9885960 0.000000e+00 5120.0
4 TraesCS7A01G117200 chr6A 97.189 3024 63 5 432 3452 590675825 590672821 0.000000e+00 5094.0
5 TraesCS7A01G117200 chr6A 87.841 403 41 8 1 399 584005160 584005558 1.880000e-127 466.0
6 TraesCS7A01G117200 chr2A 98.228 2426 40 1 1030 3452 698197702 698195277 0.000000e+00 4239.0
7 TraesCS7A01G117200 chr2A 94.944 534 8 4 432 965 698203930 698203416 0.000000e+00 819.0
8 TraesCS7A01G117200 chr2A 92.048 503 36 1 2724 3226 737423434 737422936 0.000000e+00 704.0
9 TraesCS7A01G117200 chr2A 91.525 177 14 1 1564 1739 257014163 257014339 3.440000e-60 243.0
10 TraesCS7A01G117200 chr2A 96.875 32 0 1 965 996 698197730 698197700 6.000000e-03 52.8
11 TraesCS7A01G117200 chr7D 92.318 1510 97 16 838 2333 617831456 617829952 0.000000e+00 2128.0
12 TraesCS7A01G117200 chr7D 91.462 1101 68 8 2362 3452 617829956 617828872 0.000000e+00 1489.0
13 TraesCS7A01G117200 chr7D 90.909 814 56 7 838 1648 386517163 386516365 0.000000e+00 1077.0
14 TraesCS7A01G117200 chr7D 93.712 652 36 5 1683 2333 386516365 386515718 0.000000e+00 972.0
15 TraesCS7A01G117200 chr7D 89.322 487 41 5 2362 2839 386515722 386515238 4.930000e-168 601.0
16 TraesCS7A01G117200 chr6D 92.336 535 37 1 2724 3258 337762314 337762844 0.000000e+00 758.0
17 TraesCS7A01G117200 chr6D 94.531 128 6 1 3323 3449 337762845 337762972 2.720000e-46 196.0
18 TraesCS7A01G117200 chr4D 91.978 536 37 3 2724 3258 499724578 499725108 0.000000e+00 747.0
19 TraesCS7A01G117200 chr4D 91.215 535 41 3 2724 3258 508478467 508478995 0.000000e+00 723.0
20 TraesCS7A01G117200 chr4D 87.781 401 41 8 1 399 456264478 456264084 2.430000e-126 462.0
21 TraesCS7A01G117200 chr4D 86.849 403 41 7 1 399 418395554 418395948 1.140000e-119 440.0
22 TraesCS7A01G117200 chr4D 96.063 127 4 1 3327 3452 508479000 508479126 4.520000e-49 206.0
23 TraesCS7A01G117200 chr2D 91.619 525 40 2 2733 3257 331546292 331545772 0.000000e+00 723.0
24 TraesCS7A01G117200 chr2D 89.912 456 42 3 1290 1742 207480309 207479855 4.960000e-163 584.0
25 TraesCS7A01G117200 chr2D 87.811 402 38 9 1 399 634170312 634169919 8.730000e-126 460.0
26 TraesCS7A01G117200 chr2D 94.574 129 6 1 3325 3452 331545768 331545640 7.560000e-47 198.0
27 TraesCS7A01G117200 chr3A 95.366 410 15 4 1 407 475468832 475469240 0.000000e+00 649.0
28 TraesCS7A01G117200 chr1A 95.122 410 15 4 1 407 470501343 470501750 2.900000e-180 641.0
29 TraesCS7A01G117200 chr3D 88.889 396 36 8 1 394 330210339 330209950 6.700000e-132 481.0
30 TraesCS7A01G117200 chr3D 87.531 401 39 9 1 399 433981781 433982172 1.460000e-123 453.0
31 TraesCS7A01G117200 chr1B 88.060 402 41 7 1 399 598295165 598294768 1.450000e-128 470.0
32 TraesCS7A01G117200 chr5A 94.656 131 6 1 3323 3452 692544815 692544945 5.840000e-48 202.0
33 TraesCS7A01G117200 chr5A 94.656 131 6 1 3323 3452 692551384 692551514 5.840000e-48 202.0
34 TraesCS7A01G117200 chr5D 88.024 167 18 2 1037 1201 238665957 238666123 2.720000e-46 196.0


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 TraesCS7A01G117200 chr7A 75357993 75361444 3451 False 6375.000000 6375 100.000000 1 3452 1 chr7A.!!$F1 3451
1 TraesCS7A01G117200 chr3B 9885960 9888969 3009 True 5120.000000 5120 97.325000 432 3452 1 chr3B.!!$R1 3020
2 TraesCS7A01G117200 chr6A 590672821 590675825 3004 True 5094.000000 5094 97.189000 432 3452 1 chr6A.!!$R1 3020
3 TraesCS7A01G117200 chr2A 698195277 698197730 2453 True 2145.900000 4239 97.551500 965 3452 2 chr2A.!!$R3 2487
4 TraesCS7A01G117200 chr2A 698203416 698203930 514 True 819.000000 819 94.944000 432 965 1 chr2A.!!$R1 533
5 TraesCS7A01G117200 chr7D 617828872 617831456 2584 True 1808.500000 2128 91.890000 838 3452 2 chr7D.!!$R2 2614
6 TraesCS7A01G117200 chr7D 386515238 386517163 1925 True 883.333333 1077 91.314333 838 2839 3 chr7D.!!$R1 2001
7 TraesCS7A01G117200 chr6D 337762314 337762972 658 False 477.000000 758 93.433500 2724 3449 2 chr6D.!!$F1 725
8 TraesCS7A01G117200 chr4D 499724578 499725108 530 False 747.000000 747 91.978000 2724 3258 1 chr4D.!!$F2 534
9 TraesCS7A01G117200 chr4D 508478467 508479126 659 False 464.500000 723 93.639000 2724 3452 2 chr4D.!!$F3 728
10 TraesCS7A01G117200 chr2D 331545640 331546292 652 True 460.500000 723 93.096500 2733 3452 2 chr2D.!!$R3 719

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
101 102 0.179171 CTCGTCGTACGTGAAGGCAT 60.179 55.000 16.05 0.0 43.14 4.40 F
102 103 0.455464 TCGTCGTACGTGAAGGCATG 60.455 55.000 16.05 0.0 43.14 4.06 F
103 104 0.455464 CGTCGTACGTGAAGGCATGA 60.455 55.000 16.05 0.0 36.74 3.07 F
171 172 0.542467 AACAATGCATCAGGTGGGCA 60.542 50.000 0.00 0.0 42.43 5.36 F
173 174 1.063792 ACAATGCATCAGGTGGGCATA 60.064 47.619 0.00 0.0 46.77 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 1896 4.552355 TGCAGAATTGATTCACTTTGCAG 58.448 39.130 15.61 0.0 38.49 4.41 R
1925 1933 6.162777 TGTTAATGCTACCAAGGAAAAATGC 58.837 36.000 0.00 0.0 0.00 3.56 R
2358 2375 7.280652 CCAAACCTGTCAAAATCTGAAATTTGT 59.719 33.333 14.83 0.0 37.68 2.83 R
2388 2405 4.389374 CCCGGTCAAGCATGTTATAGATT 58.611 43.478 0.00 0.0 0.00 2.40 R
3161 3194 2.492484 GTCGACTTTCTCTAGCAAGGGA 59.508 50.000 8.70 0.0 0.00 4.20 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.959516 TGAGTAGTTTGCGTCAGATGG 58.040 47.619 0.00 0.00 0.00 3.51
21 22 2.560981 TGAGTAGTTTGCGTCAGATGGA 59.439 45.455 0.00 0.00 0.00 3.41
22 23 2.924290 GAGTAGTTTGCGTCAGATGGAC 59.076 50.000 0.00 0.00 43.36 4.02
23 24 2.000447 GTAGTTTGCGTCAGATGGACC 59.000 52.381 0.00 0.00 43.95 4.46
24 25 0.396435 AGTTTGCGTCAGATGGACCA 59.604 50.000 0.00 0.00 43.95 4.02
25 26 1.003580 AGTTTGCGTCAGATGGACCAT 59.996 47.619 6.71 6.71 43.95 3.55
26 27 1.131126 GTTTGCGTCAGATGGACCATG 59.869 52.381 12.99 0.00 43.95 3.66
27 28 0.612744 TTGCGTCAGATGGACCATGA 59.387 50.000 12.99 2.10 43.95 3.07
28 29 0.612744 TGCGTCAGATGGACCATGAA 59.387 50.000 12.99 0.00 43.95 2.57
29 30 1.003003 TGCGTCAGATGGACCATGAAA 59.997 47.619 12.99 0.00 43.95 2.69
30 31 2.292267 GCGTCAGATGGACCATGAAAT 58.708 47.619 12.99 0.00 43.95 2.17
31 32 2.289002 GCGTCAGATGGACCATGAAATC 59.711 50.000 12.99 0.00 43.95 2.17
32 33 3.801698 CGTCAGATGGACCATGAAATCT 58.198 45.455 12.99 0.00 43.95 2.40
33 34 4.194640 CGTCAGATGGACCATGAAATCTT 58.805 43.478 12.99 0.00 43.95 2.40
34 35 5.359756 CGTCAGATGGACCATGAAATCTTA 58.640 41.667 12.99 0.00 43.95 2.10
35 36 5.464722 CGTCAGATGGACCATGAAATCTTAG 59.535 44.000 12.99 0.00 43.95 2.18
36 37 6.352516 GTCAGATGGACCATGAAATCTTAGT 58.647 40.000 12.99 0.00 40.83 2.24
37 38 6.825721 GTCAGATGGACCATGAAATCTTAGTT 59.174 38.462 12.99 0.00 40.83 2.24
38 39 6.825213 TCAGATGGACCATGAAATCTTAGTTG 59.175 38.462 12.99 0.00 0.00 3.16
39 40 6.039047 CAGATGGACCATGAAATCTTAGTTGG 59.961 42.308 12.99 0.00 0.00 3.77
40 41 5.512942 TGGACCATGAAATCTTAGTTGGA 57.487 39.130 0.00 0.00 0.00 3.53
41 42 5.253330 TGGACCATGAAATCTTAGTTGGAC 58.747 41.667 0.00 0.00 0.00 4.02
42 43 5.014123 TGGACCATGAAATCTTAGTTGGACT 59.986 40.000 0.00 0.00 0.00 3.85
43 44 5.586643 GGACCATGAAATCTTAGTTGGACTC 59.413 44.000 0.00 0.00 0.00 3.36
44 45 5.501156 ACCATGAAATCTTAGTTGGACTCC 58.499 41.667 0.00 0.00 0.00 3.85
45 46 5.251700 ACCATGAAATCTTAGTTGGACTCCT 59.748 40.000 0.00 0.00 0.00 3.69
46 47 5.819901 CCATGAAATCTTAGTTGGACTCCTC 59.180 44.000 0.00 0.00 0.00 3.71
47 48 6.409704 CATGAAATCTTAGTTGGACTCCTCA 58.590 40.000 0.00 0.00 0.00 3.86
48 49 6.627087 TGAAATCTTAGTTGGACTCCTCAT 57.373 37.500 0.00 0.00 0.00 2.90
49 50 6.409704 TGAAATCTTAGTTGGACTCCTCATG 58.590 40.000 0.00 0.00 0.00 3.07
50 51 3.895232 TCTTAGTTGGACTCCTCATGC 57.105 47.619 0.00 0.00 0.00 4.06
51 52 3.173151 TCTTAGTTGGACTCCTCATGCA 58.827 45.455 0.00 0.00 0.00 3.96
52 53 3.776969 TCTTAGTTGGACTCCTCATGCAT 59.223 43.478 0.00 0.00 0.00 3.96
53 54 4.225942 TCTTAGTTGGACTCCTCATGCATT 59.774 41.667 0.00 0.00 0.00 3.56
54 55 3.446442 AGTTGGACTCCTCATGCATTT 57.554 42.857 0.00 0.00 0.00 2.32
55 56 3.771216 AGTTGGACTCCTCATGCATTTT 58.229 40.909 0.00 0.00 0.00 1.82
56 57 3.508793 AGTTGGACTCCTCATGCATTTTG 59.491 43.478 0.00 0.00 0.00 2.44
57 58 3.438216 TGGACTCCTCATGCATTTTGA 57.562 42.857 0.00 0.00 0.00 2.69
58 59 3.084039 TGGACTCCTCATGCATTTTGAC 58.916 45.455 0.00 0.00 0.00 3.18
59 60 2.096496 GGACTCCTCATGCATTTTGACG 59.904 50.000 0.00 0.00 0.00 4.35
60 61 2.086869 ACTCCTCATGCATTTTGACGG 58.913 47.619 0.00 0.00 0.00 4.79
61 62 1.402968 CTCCTCATGCATTTTGACGGG 59.597 52.381 0.00 0.00 0.00 5.28
62 63 1.004161 TCCTCATGCATTTTGACGGGA 59.996 47.619 0.00 0.00 0.00 5.14
63 64 1.402968 CCTCATGCATTTTGACGGGAG 59.597 52.381 0.00 0.00 0.00 4.30
74 75 4.954118 ACGGGAGTCACTGGGCCA 62.954 66.667 5.85 5.85 40.62 5.36
75 76 3.636231 CGGGAGTCACTGGGCCAA 61.636 66.667 8.04 0.00 0.00 4.52
76 77 2.352805 GGGAGTCACTGGGCCAAG 59.647 66.667 8.04 5.25 0.00 3.61
77 78 2.529744 GGGAGTCACTGGGCCAAGT 61.530 63.158 7.09 7.09 0.00 3.16
83 84 4.320844 ACTGGGCCAAGTGAGACT 57.679 55.556 13.58 0.00 0.00 3.24
84 85 2.062070 ACTGGGCCAAGTGAGACTC 58.938 57.895 13.58 0.00 0.00 3.36
85 86 1.079543 CTGGGCCAAGTGAGACTCG 60.080 63.158 8.04 0.00 0.00 4.18
86 87 1.821061 CTGGGCCAAGTGAGACTCGT 61.821 60.000 8.04 0.00 0.00 4.18
87 88 1.079750 GGGCCAAGTGAGACTCGTC 60.080 63.158 4.39 0.00 0.00 4.20
88 89 1.444553 GGCCAAGTGAGACTCGTCG 60.445 63.158 0.00 0.00 34.09 5.12
89 90 1.286260 GCCAAGTGAGACTCGTCGT 59.714 57.895 0.00 0.00 34.09 4.34
90 91 0.520404 GCCAAGTGAGACTCGTCGTA 59.480 55.000 0.00 0.00 34.09 3.43
91 92 1.728502 GCCAAGTGAGACTCGTCGTAC 60.729 57.143 0.00 0.00 34.09 3.67
92 93 1.463693 CCAAGTGAGACTCGTCGTACG 60.464 57.143 9.53 9.53 44.19 3.67
93 94 1.194098 CAAGTGAGACTCGTCGTACGT 59.806 52.381 16.05 0.00 43.14 3.57
94 95 0.788995 AGTGAGACTCGTCGTACGTG 59.211 55.000 16.05 9.46 43.14 4.49
95 96 0.786581 GTGAGACTCGTCGTACGTGA 59.213 55.000 16.05 13.28 43.14 4.35
96 97 1.193203 GTGAGACTCGTCGTACGTGAA 59.807 52.381 16.05 0.68 43.14 3.18
97 98 1.458445 TGAGACTCGTCGTACGTGAAG 59.542 52.381 16.05 12.67 43.14 3.02
98 99 0.795085 AGACTCGTCGTACGTGAAGG 59.205 55.000 16.05 1.86 43.14 3.46
99 100 0.792356 GACTCGTCGTACGTGAAGGC 60.792 60.000 16.05 9.21 43.14 4.35
100 101 1.208358 CTCGTCGTACGTGAAGGCA 59.792 57.895 16.05 0.00 43.14 4.75
101 102 0.179171 CTCGTCGTACGTGAAGGCAT 60.179 55.000 16.05 0.00 43.14 4.40
102 103 0.455464 TCGTCGTACGTGAAGGCATG 60.455 55.000 16.05 0.00 43.14 4.06
103 104 0.455464 CGTCGTACGTGAAGGCATGA 60.455 55.000 16.05 0.00 36.74 3.07
104 105 0.989890 GTCGTACGTGAAGGCATGAC 59.010 55.000 16.05 0.00 35.02 3.06
105 106 0.599060 TCGTACGTGAAGGCATGACA 59.401 50.000 16.05 0.00 35.02 3.58
106 107 0.992072 CGTACGTGAAGGCATGACAG 59.008 55.000 7.22 0.00 35.02 3.51
107 108 1.402325 CGTACGTGAAGGCATGACAGA 60.402 52.381 7.22 0.00 35.02 3.41
108 109 2.263077 GTACGTGAAGGCATGACAGAG 58.737 52.381 0.00 0.00 35.02 3.35
109 110 0.969149 ACGTGAAGGCATGACAGAGA 59.031 50.000 0.00 0.00 35.02 3.10
110 111 1.344438 ACGTGAAGGCATGACAGAGAA 59.656 47.619 0.00 0.00 35.02 2.87
111 112 2.224281 ACGTGAAGGCATGACAGAGAAA 60.224 45.455 0.00 0.00 35.02 2.52
112 113 2.807967 CGTGAAGGCATGACAGAGAAAA 59.192 45.455 0.00 0.00 32.63 2.29
113 114 3.250762 CGTGAAGGCATGACAGAGAAAAA 59.749 43.478 0.00 0.00 32.63 1.94
114 115 4.612259 CGTGAAGGCATGACAGAGAAAAAG 60.612 45.833 0.00 0.00 32.63 2.27
115 116 4.516698 GTGAAGGCATGACAGAGAAAAAGA 59.483 41.667 0.00 0.00 0.00 2.52
116 117 5.182760 GTGAAGGCATGACAGAGAAAAAGAT 59.817 40.000 0.00 0.00 0.00 2.40
117 118 5.771666 TGAAGGCATGACAGAGAAAAAGATT 59.228 36.000 0.00 0.00 0.00 2.40
118 119 5.893897 AGGCATGACAGAGAAAAAGATTC 57.106 39.130 0.00 0.00 0.00 2.52
119 120 4.704057 AGGCATGACAGAGAAAAAGATTCC 59.296 41.667 0.00 0.00 0.00 3.01
120 121 4.704057 GGCATGACAGAGAAAAAGATTCCT 59.296 41.667 0.00 0.00 0.00 3.36
121 122 5.184671 GGCATGACAGAGAAAAAGATTCCTT 59.815 40.000 0.00 0.00 0.00 3.36
122 123 6.320944 GCATGACAGAGAAAAAGATTCCTTC 58.679 40.000 0.00 0.00 0.00 3.46
123 124 6.624642 GCATGACAGAGAAAAAGATTCCTTCC 60.625 42.308 0.00 0.00 0.00 3.46
124 125 5.940617 TGACAGAGAAAAAGATTCCTTCCA 58.059 37.500 0.00 0.00 0.00 3.53
125 126 6.546484 TGACAGAGAAAAAGATTCCTTCCAT 58.454 36.000 0.00 0.00 0.00 3.41
126 127 7.689299 TGACAGAGAAAAAGATTCCTTCCATA 58.311 34.615 0.00 0.00 0.00 2.74
127 128 8.331740 TGACAGAGAAAAAGATTCCTTCCATAT 58.668 33.333 0.00 0.00 0.00 1.78
128 129 8.744568 ACAGAGAAAAAGATTCCTTCCATATC 57.255 34.615 0.00 0.00 0.00 1.63
129 130 7.777440 ACAGAGAAAAAGATTCCTTCCATATCC 59.223 37.037 0.00 0.00 0.00 2.59
130 131 7.230309 CAGAGAAAAAGATTCCTTCCATATCCC 59.770 40.741 0.00 0.00 0.00 3.85
131 132 7.130129 AGAGAAAAAGATTCCTTCCATATCCCT 59.870 37.037 0.00 0.00 0.00 4.20
132 133 8.350180 AGAAAAAGATTCCTTCCATATCCCTA 57.650 34.615 0.00 0.00 0.00 3.53
133 134 8.791749 AGAAAAAGATTCCTTCCATATCCCTAA 58.208 33.333 0.00 0.00 0.00 2.69
134 135 9.593565 GAAAAAGATTCCTTCCATATCCCTAAT 57.406 33.333 0.00 0.00 0.00 1.73
135 136 9.958125 AAAAAGATTCCTTCCATATCCCTAATT 57.042 29.630 0.00 0.00 0.00 1.40
136 137 9.958125 AAAAGATTCCTTCCATATCCCTAATTT 57.042 29.630 0.00 0.00 0.00 1.82
166 167 9.777297 AAATTAAACTAAAACAATGCATCAGGT 57.223 25.926 0.00 0.00 0.00 4.00
167 168 8.761575 ATTAAACTAAAACAATGCATCAGGTG 57.238 30.769 0.00 0.00 0.00 4.00
168 169 4.789012 ACTAAAACAATGCATCAGGTGG 57.211 40.909 0.00 0.00 0.00 4.61
169 170 3.511146 ACTAAAACAATGCATCAGGTGGG 59.489 43.478 0.00 0.00 0.00 4.61
170 171 0.609662 AAACAATGCATCAGGTGGGC 59.390 50.000 0.00 0.00 0.00 5.36
171 172 0.542467 AACAATGCATCAGGTGGGCA 60.542 50.000 0.00 0.00 42.43 5.36
173 174 1.063792 ACAATGCATCAGGTGGGCATA 60.064 47.619 0.00 0.00 46.77 3.14
174 175 2.244695 CAATGCATCAGGTGGGCATAT 58.755 47.619 0.00 1.05 46.77 1.78
175 176 2.631062 CAATGCATCAGGTGGGCATATT 59.369 45.455 0.00 0.00 46.77 1.28
176 177 2.457813 TGCATCAGGTGGGCATATTT 57.542 45.000 0.00 0.00 31.58 1.40
177 178 2.309613 TGCATCAGGTGGGCATATTTC 58.690 47.619 0.00 0.00 31.58 2.17
178 179 2.309613 GCATCAGGTGGGCATATTTCA 58.690 47.619 0.00 0.00 0.00 2.69
179 180 2.694628 GCATCAGGTGGGCATATTTCAA 59.305 45.455 0.00 0.00 0.00 2.69
180 181 3.132646 GCATCAGGTGGGCATATTTCAAA 59.867 43.478 0.00 0.00 0.00 2.69
181 182 4.382901 GCATCAGGTGGGCATATTTCAAAA 60.383 41.667 0.00 0.00 0.00 2.44
182 183 5.732633 CATCAGGTGGGCATATTTCAAAAA 58.267 37.500 0.00 0.00 0.00 1.94
183 184 6.350906 CATCAGGTGGGCATATTTCAAAAAT 58.649 36.000 0.00 0.00 0.00 1.82
184 185 6.371595 TCAGGTGGGCATATTTCAAAAATT 57.628 33.333 0.00 0.00 0.00 1.82
185 186 6.405538 TCAGGTGGGCATATTTCAAAAATTC 58.594 36.000 0.00 0.00 0.00 2.17
186 187 6.013898 TCAGGTGGGCATATTTCAAAAATTCA 60.014 34.615 0.00 0.00 0.00 2.57
187 188 6.092533 CAGGTGGGCATATTTCAAAAATTCAC 59.907 38.462 0.00 0.00 0.00 3.18
188 189 6.013466 AGGTGGGCATATTTCAAAAATTCACT 60.013 34.615 0.00 0.00 0.00 3.41
189 190 7.180051 AGGTGGGCATATTTCAAAAATTCACTA 59.820 33.333 0.00 0.00 0.00 2.74
190 191 7.821846 GGTGGGCATATTTCAAAAATTCACTAA 59.178 33.333 0.00 0.00 0.00 2.24
191 192 8.872845 GTGGGCATATTTCAAAAATTCACTAAG 58.127 33.333 0.00 0.00 0.00 2.18
192 193 8.592809 TGGGCATATTTCAAAAATTCACTAAGT 58.407 29.630 0.00 0.00 0.00 2.24
193 194 9.435688 GGGCATATTTCAAAAATTCACTAAGTT 57.564 29.630 0.00 0.00 0.00 2.66
238 239 8.785184 AGAACAATTTAGCTATAGTACCTCCT 57.215 34.615 0.84 0.00 0.00 3.69
239 240 9.878737 AGAACAATTTAGCTATAGTACCTCCTA 57.121 33.333 0.84 0.00 0.00 2.94
241 242 9.657728 AACAATTTAGCTATAGTACCTCCTAGT 57.342 33.333 0.84 0.00 0.00 2.57
242 243 9.657728 ACAATTTAGCTATAGTACCTCCTAGTT 57.342 33.333 0.84 0.00 0.00 2.24
281 282 8.631676 AAATCATGTTTTGAAAAATGTTTGCC 57.368 26.923 0.91 0.00 38.03 4.52
282 283 6.998968 TCATGTTTTGAAAAATGTTTGCCT 57.001 29.167 6.54 0.00 35.55 4.75
283 284 7.388460 TCATGTTTTGAAAAATGTTTGCCTT 57.612 28.000 6.54 0.00 35.55 4.35
284 285 7.824672 TCATGTTTTGAAAAATGTTTGCCTTT 58.175 26.923 6.54 0.00 35.55 3.11
285 286 8.302438 TCATGTTTTGAAAAATGTTTGCCTTTT 58.698 25.926 6.54 0.00 35.55 2.27
286 287 8.585436 CATGTTTTGAAAAATGTTTGCCTTTTC 58.415 29.630 0.00 0.00 38.80 2.29
287 288 7.651808 TGTTTTGAAAAATGTTTGCCTTTTCA 58.348 26.923 5.36 5.36 43.65 2.69
353 354 9.528018 ACAAATTCGAAAAATATTCACAACTGT 57.472 25.926 0.00 0.00 0.00 3.55
358 359 9.872757 TTCGAAAAATATTCACAACTGTACTTC 57.127 29.630 0.00 0.00 0.00 3.01
359 360 8.500773 TCGAAAAATATTCACAACTGTACTTCC 58.499 33.333 0.00 0.00 0.00 3.46
360 361 8.504005 CGAAAAATATTCACAACTGTACTTCCT 58.496 33.333 0.00 0.00 0.00 3.36
361 362 9.612620 GAAAAATATTCACAACTGTACTTCCTG 57.387 33.333 0.00 0.00 0.00 3.86
362 363 7.687941 AAATATTCACAACTGTACTTCCTGG 57.312 36.000 0.00 0.00 0.00 4.45
363 364 4.706842 ATTCACAACTGTACTTCCTGGT 57.293 40.909 0.00 0.00 0.00 4.00
364 365 4.497291 TTCACAACTGTACTTCCTGGTT 57.503 40.909 0.00 0.00 0.00 3.67
365 366 4.497291 TCACAACTGTACTTCCTGGTTT 57.503 40.909 0.00 0.00 0.00 3.27
366 367 5.617528 TCACAACTGTACTTCCTGGTTTA 57.382 39.130 0.00 0.00 0.00 2.01
367 368 5.991861 TCACAACTGTACTTCCTGGTTTAA 58.008 37.500 0.00 0.00 0.00 1.52
368 369 6.416415 TCACAACTGTACTTCCTGGTTTAAA 58.584 36.000 0.00 0.00 0.00 1.52
369 370 6.885376 TCACAACTGTACTTCCTGGTTTAAAA 59.115 34.615 0.00 0.00 0.00 1.52
370 371 7.393796 TCACAACTGTACTTCCTGGTTTAAAAA 59.606 33.333 0.00 0.00 0.00 1.94
452 453 8.954950 TGTTATTGGAAATTTTGCAGAAAAGA 57.045 26.923 3.51 0.00 34.53 2.52
564 565 2.700897 AGTATATTCAAGCCGCAGTCCT 59.299 45.455 0.00 0.00 0.00 3.85
565 566 2.717639 ATATTCAAGCCGCAGTCCTT 57.282 45.000 0.00 0.00 0.00 3.36
566 567 2.489938 TATTCAAGCCGCAGTCCTTT 57.510 45.000 0.00 0.00 0.00 3.11
567 568 2.489938 ATTCAAGCCGCAGTCCTTTA 57.510 45.000 0.00 0.00 0.00 1.85
568 569 2.264005 TTCAAGCCGCAGTCCTTTAA 57.736 45.000 0.00 0.00 0.00 1.52
569 570 2.264005 TCAAGCCGCAGTCCTTTAAA 57.736 45.000 0.00 0.00 0.00 1.52
570 571 1.877443 TCAAGCCGCAGTCCTTTAAAC 59.123 47.619 0.00 0.00 0.00 2.01
571 572 1.606668 CAAGCCGCAGTCCTTTAAACA 59.393 47.619 0.00 0.00 0.00 2.83
572 573 2.200373 AGCCGCAGTCCTTTAAACAT 57.800 45.000 0.00 0.00 0.00 2.71
573 574 3.343941 AGCCGCAGTCCTTTAAACATA 57.656 42.857 0.00 0.00 0.00 2.29
574 575 3.007635 AGCCGCAGTCCTTTAAACATAC 58.992 45.455 0.00 0.00 0.00 2.39
575 576 2.745281 GCCGCAGTCCTTTAAACATACA 59.255 45.455 0.00 0.00 0.00 2.29
576 577 3.377172 GCCGCAGTCCTTTAAACATACAT 59.623 43.478 0.00 0.00 0.00 2.29
577 578 4.495844 GCCGCAGTCCTTTAAACATACATC 60.496 45.833 0.00 0.00 0.00 3.06
578 579 4.634004 CCGCAGTCCTTTAAACATACATCA 59.366 41.667 0.00 0.00 0.00 3.07
579 580 5.447279 CCGCAGTCCTTTAAACATACATCAC 60.447 44.000 0.00 0.00 0.00 3.06
580 581 5.447279 CGCAGTCCTTTAAACATACATCACC 60.447 44.000 0.00 0.00 0.00 4.02
581 582 5.163652 GCAGTCCTTTAAACATACATCACCC 60.164 44.000 0.00 0.00 0.00 4.61
582 583 5.943416 CAGTCCTTTAAACATACATCACCCA 59.057 40.000 0.00 0.00 0.00 4.51
590 591 2.135139 CATACATCACCCAACGATCCG 58.865 52.381 0.00 0.00 0.00 4.18
927 928 2.800736 GTTGGATCGGTGCATGGC 59.199 61.111 0.00 0.00 0.00 4.40
1130 1131 3.485463 AATTCCGTCAAGAGGTGTGAA 57.515 42.857 0.00 0.00 0.00 3.18
1154 1155 3.247006 TCGTTTTACTGGATGCTCTCC 57.753 47.619 0.00 0.00 45.19 3.71
1225 1226 7.454380 TCTGTATGGATTTGAAAAAGGACCAAT 59.546 33.333 0.00 0.00 0.00 3.16
1522 1524 2.871022 CTGCACATCATGAGTAAGAGGC 59.129 50.000 0.09 0.00 0.00 4.70
1662 1670 6.874664 TGCGTTATCATCTTTTGTACAGGTTA 59.125 34.615 0.00 0.00 0.00 2.85
1862 1870 5.064707 CCCAACCGATAATGAACAAGTACAG 59.935 44.000 0.00 0.00 0.00 2.74
1888 1896 9.827411 GTTTTATAGATGGTTCAAGTGAAGTTC 57.173 33.333 0.00 0.00 34.27 3.01
1925 1933 2.578786 TCTGCAAGATACCATGCCATG 58.421 47.619 0.00 0.00 38.67 3.66
2327 2344 6.403866 ACCTTTGTTTGTTCATGCTTCATA 57.596 33.333 0.00 0.00 0.00 2.15
2388 2405 3.636300 CAGATTTTGACAGGTTTGGGTCA 59.364 43.478 0.00 0.00 41.93 4.02
2631 2657 3.340034 CCTACGGTTCCAAGCACAATTA 58.660 45.455 0.00 0.00 0.00 1.40
3161 3194 9.401058 CCTCAATAGGTACATCTCTGAATTTTT 57.599 33.333 0.00 0.00 38.19 1.94
3182 3215 2.492484 TCCCTTGCTAGAGAAAGTCGAC 59.508 50.000 7.70 7.70 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.560981 TCCATCTGACGCAAACTACTCA 59.439 45.455 0.00 0.00 0.00 3.41
1 2 2.924290 GTCCATCTGACGCAAACTACTC 59.076 50.000 0.00 0.00 33.49 2.59
2 3 2.353803 GGTCCATCTGACGCAAACTACT 60.354 50.000 0.00 0.00 45.46 2.57
3 4 2.000447 GGTCCATCTGACGCAAACTAC 59.000 52.381 0.00 0.00 45.46 2.73
5 6 0.396435 TGGTCCATCTGACGCAAACT 59.604 50.000 0.00 0.00 45.46 2.66
7 8 1.003003 TCATGGTCCATCTGACGCAAA 59.997 47.619 0.00 0.00 45.46 3.68
8 9 0.612744 TCATGGTCCATCTGACGCAA 59.387 50.000 0.00 0.00 45.46 4.85
9 10 0.612744 TTCATGGTCCATCTGACGCA 59.387 50.000 0.00 0.00 45.46 5.24
10 11 1.737838 TTTCATGGTCCATCTGACGC 58.262 50.000 0.00 0.00 45.46 5.19
11 12 3.801698 AGATTTCATGGTCCATCTGACG 58.198 45.455 0.00 0.00 45.46 4.35
12 13 6.352516 ACTAAGATTTCATGGTCCATCTGAC 58.647 40.000 0.00 0.00 43.67 3.51
13 14 6.566079 ACTAAGATTTCATGGTCCATCTGA 57.434 37.500 0.00 0.00 0.00 3.27
14 15 6.039047 CCAACTAAGATTTCATGGTCCATCTG 59.961 42.308 0.00 0.00 0.00 2.90
15 16 6.069440 TCCAACTAAGATTTCATGGTCCATCT 60.069 38.462 0.00 0.00 0.00 2.90
16 17 6.038714 GTCCAACTAAGATTTCATGGTCCATC 59.961 42.308 0.00 0.00 0.00 3.51
17 18 5.888161 GTCCAACTAAGATTTCATGGTCCAT 59.112 40.000 0.00 0.00 0.00 3.41
18 19 5.014123 AGTCCAACTAAGATTTCATGGTCCA 59.986 40.000 0.00 0.00 0.00 4.02
19 20 5.501156 AGTCCAACTAAGATTTCATGGTCC 58.499 41.667 0.00 0.00 0.00 4.46
20 21 5.586643 GGAGTCCAACTAAGATTTCATGGTC 59.413 44.000 3.60 0.00 0.00 4.02
21 22 5.251700 AGGAGTCCAACTAAGATTTCATGGT 59.748 40.000 12.86 0.00 0.00 3.55
22 23 5.749462 AGGAGTCCAACTAAGATTTCATGG 58.251 41.667 12.86 0.00 0.00 3.66
23 24 6.409704 TGAGGAGTCCAACTAAGATTTCATG 58.590 40.000 12.86 0.00 0.00 3.07
24 25 6.627087 TGAGGAGTCCAACTAAGATTTCAT 57.373 37.500 12.86 0.00 0.00 2.57
25 26 6.409704 CATGAGGAGTCCAACTAAGATTTCA 58.590 40.000 12.86 2.29 0.00 2.69
26 27 5.295540 GCATGAGGAGTCCAACTAAGATTTC 59.704 44.000 12.86 0.00 0.00 2.17
27 28 5.189180 GCATGAGGAGTCCAACTAAGATTT 58.811 41.667 12.86 0.00 0.00 2.17
28 29 4.225942 TGCATGAGGAGTCCAACTAAGATT 59.774 41.667 12.86 0.00 0.00 2.40
29 30 3.776969 TGCATGAGGAGTCCAACTAAGAT 59.223 43.478 12.86 0.00 0.00 2.40
30 31 3.173151 TGCATGAGGAGTCCAACTAAGA 58.827 45.455 12.86 0.00 0.00 2.10
31 32 3.616956 TGCATGAGGAGTCCAACTAAG 57.383 47.619 12.86 0.00 0.00 2.18
32 33 4.574674 AATGCATGAGGAGTCCAACTAA 57.425 40.909 12.86 0.00 0.00 2.24
33 34 4.574674 AAATGCATGAGGAGTCCAACTA 57.425 40.909 12.86 0.00 0.00 2.24
34 35 3.446442 AAATGCATGAGGAGTCCAACT 57.554 42.857 12.86 0.00 0.00 3.16
35 36 3.507233 TCAAAATGCATGAGGAGTCCAAC 59.493 43.478 12.86 5.68 0.00 3.77
36 37 3.507233 GTCAAAATGCATGAGGAGTCCAA 59.493 43.478 12.86 0.00 0.00 3.53
37 38 3.084039 GTCAAAATGCATGAGGAGTCCA 58.916 45.455 12.86 0.00 0.00 4.02
38 39 2.096496 CGTCAAAATGCATGAGGAGTCC 59.904 50.000 0.00 0.00 35.30 3.85
39 40 2.096496 CCGTCAAAATGCATGAGGAGTC 59.904 50.000 0.00 0.00 35.30 3.36
40 41 2.086869 CCGTCAAAATGCATGAGGAGT 58.913 47.619 0.00 0.00 35.30 3.85
41 42 1.402968 CCCGTCAAAATGCATGAGGAG 59.597 52.381 0.00 0.00 35.30 3.69
42 43 1.004161 TCCCGTCAAAATGCATGAGGA 59.996 47.619 0.00 0.00 35.30 3.71
43 44 1.402968 CTCCCGTCAAAATGCATGAGG 59.597 52.381 0.00 0.16 33.60 3.86
44 45 2.086869 ACTCCCGTCAAAATGCATGAG 58.913 47.619 0.00 2.16 0.00 2.90
45 46 2.083774 GACTCCCGTCAAAATGCATGA 58.916 47.619 0.00 0.00 39.98 3.07
46 47 1.811965 TGACTCCCGTCAAAATGCATG 59.188 47.619 0.00 0.00 46.61 4.06
47 48 2.198827 TGACTCCCGTCAAAATGCAT 57.801 45.000 0.00 0.00 46.61 3.96
48 49 3.715871 TGACTCCCGTCAAAATGCA 57.284 47.368 0.00 0.00 46.61 3.96
56 57 4.083862 GGCCCAGTGACTCCCGTC 62.084 72.222 0.00 0.00 40.64 4.79
57 58 4.954118 TGGCCCAGTGACTCCCGT 62.954 66.667 0.00 0.00 0.00 5.28
58 59 3.612247 CTTGGCCCAGTGACTCCCG 62.612 68.421 0.00 0.00 0.00 5.14
59 60 2.352805 CTTGGCCCAGTGACTCCC 59.647 66.667 0.00 0.00 0.00 4.30
60 61 1.302832 CACTTGGCCCAGTGACTCC 60.303 63.158 28.78 0.00 46.29 3.85
61 62 0.321122 CTCACTTGGCCCAGTGACTC 60.321 60.000 30.59 0.00 46.76 3.36
62 63 0.764369 TCTCACTTGGCCCAGTGACT 60.764 55.000 30.59 0.00 46.76 3.41
63 64 0.603975 GTCTCACTTGGCCCAGTGAC 60.604 60.000 30.59 20.76 46.76 3.67
65 66 0.321122 GAGTCTCACTTGGCCCAGTG 60.321 60.000 27.23 27.23 44.96 3.66
66 67 1.821061 CGAGTCTCACTTGGCCCAGT 61.821 60.000 2.99 2.99 0.00 4.00
67 68 1.079543 CGAGTCTCACTTGGCCCAG 60.080 63.158 0.00 0.00 0.00 4.45
68 69 1.816863 GACGAGTCTCACTTGGCCCA 61.817 60.000 0.00 0.00 31.08 5.36
69 70 1.079750 GACGAGTCTCACTTGGCCC 60.080 63.158 0.00 0.00 31.08 5.80
70 71 1.444553 CGACGAGTCTCACTTGGCC 60.445 63.158 0.00 0.00 33.92 5.36
71 72 0.520404 TACGACGAGTCTCACTTGGC 59.480 55.000 0.00 0.00 34.13 4.52
72 73 1.463693 CGTACGACGAGTCTCACTTGG 60.464 57.143 10.44 0.00 46.05 3.61
73 74 1.194098 ACGTACGACGAGTCTCACTTG 59.806 52.381 24.41 0.00 46.05 3.16
74 75 1.194098 CACGTACGACGAGTCTCACTT 59.806 52.381 24.41 0.00 46.05 3.16
75 76 0.788995 CACGTACGACGAGTCTCACT 59.211 55.000 24.41 0.00 46.05 3.41
76 77 0.786581 TCACGTACGACGAGTCTCAC 59.213 55.000 24.41 0.00 46.05 3.51
77 78 1.458445 CTTCACGTACGACGAGTCTCA 59.542 52.381 24.41 1.80 46.05 3.27
78 79 1.201899 CCTTCACGTACGACGAGTCTC 60.202 57.143 24.41 0.00 46.05 3.36
79 80 0.795085 CCTTCACGTACGACGAGTCT 59.205 55.000 24.41 0.00 46.05 3.24
80 81 0.792356 GCCTTCACGTACGACGAGTC 60.792 60.000 24.41 2.07 46.05 3.36
81 82 1.208614 GCCTTCACGTACGACGAGT 59.791 57.895 24.41 0.00 46.05 4.18
82 83 0.179171 ATGCCTTCACGTACGACGAG 60.179 55.000 24.41 14.80 46.05 4.18
83 84 0.455464 CATGCCTTCACGTACGACGA 60.455 55.000 24.41 14.92 46.05 4.20
85 86 0.989890 GTCATGCCTTCACGTACGAC 59.010 55.000 24.41 1.02 0.00 4.34
86 87 0.599060 TGTCATGCCTTCACGTACGA 59.401 50.000 24.41 0.00 0.00 3.43
87 88 0.992072 CTGTCATGCCTTCACGTACG 59.008 55.000 15.01 15.01 0.00 3.67
88 89 2.094700 TCTCTGTCATGCCTTCACGTAC 60.095 50.000 0.00 0.00 0.00 3.67
89 90 2.167662 TCTCTGTCATGCCTTCACGTA 58.832 47.619 0.00 0.00 0.00 3.57
90 91 0.969149 TCTCTGTCATGCCTTCACGT 59.031 50.000 0.00 0.00 0.00 4.49
91 92 2.084610 TTCTCTGTCATGCCTTCACG 57.915 50.000 0.00 0.00 0.00 4.35
92 93 4.516698 TCTTTTTCTCTGTCATGCCTTCAC 59.483 41.667 0.00 0.00 0.00 3.18
93 94 4.717877 TCTTTTTCTCTGTCATGCCTTCA 58.282 39.130 0.00 0.00 0.00 3.02
94 95 5.893897 ATCTTTTTCTCTGTCATGCCTTC 57.106 39.130 0.00 0.00 0.00 3.46
95 96 5.184671 GGAATCTTTTTCTCTGTCATGCCTT 59.815 40.000 0.00 0.00 0.00 4.35
96 97 4.704057 GGAATCTTTTTCTCTGTCATGCCT 59.296 41.667 0.00 0.00 0.00 4.75
97 98 4.704057 AGGAATCTTTTTCTCTGTCATGCC 59.296 41.667 0.00 0.00 0.00 4.40
98 99 5.893897 AGGAATCTTTTTCTCTGTCATGC 57.106 39.130 0.00 0.00 0.00 4.06
99 100 6.432162 TGGAAGGAATCTTTTTCTCTGTCATG 59.568 38.462 0.00 0.00 32.52 3.07
100 101 6.546484 TGGAAGGAATCTTTTTCTCTGTCAT 58.454 36.000 0.00 0.00 32.52 3.06
101 102 5.940617 TGGAAGGAATCTTTTTCTCTGTCA 58.059 37.500 0.00 0.00 32.52 3.58
102 103 8.744568 ATATGGAAGGAATCTTTTTCTCTGTC 57.255 34.615 0.00 0.00 32.52 3.51
103 104 7.777440 GGATATGGAAGGAATCTTTTTCTCTGT 59.223 37.037 0.00 0.00 32.52 3.41
104 105 7.230309 GGGATATGGAAGGAATCTTTTTCTCTG 59.770 40.741 0.00 0.00 32.52 3.35
105 106 7.130129 AGGGATATGGAAGGAATCTTTTTCTCT 59.870 37.037 0.00 0.00 32.52 3.10
106 107 7.293828 AGGGATATGGAAGGAATCTTTTTCTC 58.706 38.462 0.00 0.00 32.52 2.87
107 108 7.231251 AGGGATATGGAAGGAATCTTTTTCT 57.769 36.000 0.00 0.00 32.52 2.52
108 109 8.996651 TTAGGGATATGGAAGGAATCTTTTTC 57.003 34.615 0.00 0.00 32.52 2.29
109 110 9.958125 AATTAGGGATATGGAAGGAATCTTTTT 57.042 29.630 0.00 0.00 32.52 1.94
110 111 9.958125 AAATTAGGGATATGGAAGGAATCTTTT 57.042 29.630 0.00 0.00 32.52 2.27
140 141 9.777297 ACCTGATGCATTGTTTTAGTTTAATTT 57.223 25.926 0.00 0.00 0.00 1.82
141 142 9.206870 CACCTGATGCATTGTTTTAGTTTAATT 57.793 29.630 0.00 0.00 0.00 1.40
142 143 7.818930 CCACCTGATGCATTGTTTTAGTTTAAT 59.181 33.333 0.00 0.00 0.00 1.40
143 144 7.151308 CCACCTGATGCATTGTTTTAGTTTAA 58.849 34.615 0.00 0.00 0.00 1.52
144 145 6.295011 CCCACCTGATGCATTGTTTTAGTTTA 60.295 38.462 0.00 0.00 0.00 2.01
145 146 5.511202 CCCACCTGATGCATTGTTTTAGTTT 60.511 40.000 0.00 0.00 0.00 2.66
146 147 4.021192 CCCACCTGATGCATTGTTTTAGTT 60.021 41.667 0.00 0.00 0.00 2.24
147 148 3.511146 CCCACCTGATGCATTGTTTTAGT 59.489 43.478 0.00 0.00 0.00 2.24
148 149 3.676873 GCCCACCTGATGCATTGTTTTAG 60.677 47.826 0.00 0.00 0.00 1.85
149 150 2.233431 GCCCACCTGATGCATTGTTTTA 59.767 45.455 0.00 0.00 0.00 1.52
150 151 1.002315 GCCCACCTGATGCATTGTTTT 59.998 47.619 0.00 0.00 0.00 2.43
151 152 0.609662 GCCCACCTGATGCATTGTTT 59.390 50.000 0.00 0.00 0.00 2.83
152 153 0.542467 TGCCCACCTGATGCATTGTT 60.542 50.000 0.00 0.00 0.00 2.83
153 154 0.324923 ATGCCCACCTGATGCATTGT 60.325 50.000 0.00 0.00 42.79 2.71
154 155 1.694844 TATGCCCACCTGATGCATTG 58.305 50.000 0.00 0.00 42.79 2.82
155 156 2.688902 ATATGCCCACCTGATGCATT 57.311 45.000 0.00 0.00 42.79 3.56
156 157 2.688902 AATATGCCCACCTGATGCAT 57.311 45.000 0.00 0.00 46.68 3.96
157 158 2.309613 GAAATATGCCCACCTGATGCA 58.690 47.619 0.00 0.00 39.68 3.96
158 159 2.309613 TGAAATATGCCCACCTGATGC 58.690 47.619 0.00 0.00 0.00 3.91
159 160 5.341872 TTTTGAAATATGCCCACCTGATG 57.658 39.130 0.00 0.00 0.00 3.07
160 161 6.564557 ATTTTTGAAATATGCCCACCTGAT 57.435 33.333 0.00 0.00 0.00 2.90
161 162 6.013898 TGAATTTTTGAAATATGCCCACCTGA 60.014 34.615 0.00 0.00 0.00 3.86
162 163 6.092533 GTGAATTTTTGAAATATGCCCACCTG 59.907 38.462 0.00 0.00 0.00 4.00
163 164 6.013466 AGTGAATTTTTGAAATATGCCCACCT 60.013 34.615 0.00 0.00 0.00 4.00
164 165 6.172630 AGTGAATTTTTGAAATATGCCCACC 58.827 36.000 0.00 0.00 0.00 4.61
165 166 8.770438 TTAGTGAATTTTTGAAATATGCCCAC 57.230 30.769 0.00 0.00 0.00 4.61
166 167 8.592809 ACTTAGTGAATTTTTGAAATATGCCCA 58.407 29.630 0.00 0.00 0.00 5.36
167 168 9.435688 AACTTAGTGAATTTTTGAAATATGCCC 57.564 29.630 0.00 0.00 0.00 5.36
212 213 9.878737 AGGAGGTACTATAGCTAAATTGTTCTA 57.121 33.333 0.00 0.00 41.55 2.10
213 214 8.785184 AGGAGGTACTATAGCTAAATTGTTCT 57.215 34.615 0.00 0.00 41.55 3.01
215 216 9.657728 ACTAGGAGGTACTATAGCTAAATTGTT 57.342 33.333 0.00 0.00 41.55 2.83
216 217 9.657728 AACTAGGAGGTACTATAGCTAAATTGT 57.342 33.333 0.00 0.00 41.55 2.71
255 256 9.085250 GGCAAACATTTTTCAAAACATGATTTT 57.915 25.926 0.00 0.00 38.03 1.82
256 257 8.468399 AGGCAAACATTTTTCAAAACATGATTT 58.532 25.926 0.00 0.00 38.03 2.17
257 258 7.998580 AGGCAAACATTTTTCAAAACATGATT 58.001 26.923 0.00 0.00 38.03 2.57
258 259 7.571080 AGGCAAACATTTTTCAAAACATGAT 57.429 28.000 0.00 0.00 38.03 2.45
259 260 6.998968 AGGCAAACATTTTTCAAAACATGA 57.001 29.167 0.00 0.00 35.85 3.07
260 261 8.463456 AAAAGGCAAACATTTTTCAAAACATG 57.537 26.923 0.00 0.00 33.47 3.21
261 262 8.302438 TGAAAAGGCAAACATTTTTCAAAACAT 58.698 25.926 8.63 0.00 43.73 2.71
262 263 7.651808 TGAAAAGGCAAACATTTTTCAAAACA 58.348 26.923 8.63 0.00 43.73 2.83
327 328 9.528018 ACAGTTGTGAATATTTTTCGAATTTGT 57.472 25.926 0.00 0.00 0.00 2.83
332 333 9.872757 GAAGTACAGTTGTGAATATTTTTCGAA 57.127 29.630 0.00 0.00 0.00 3.71
333 334 8.500773 GGAAGTACAGTTGTGAATATTTTTCGA 58.499 33.333 0.00 0.00 0.00 3.71
334 335 8.504005 AGGAAGTACAGTTGTGAATATTTTTCG 58.496 33.333 0.00 0.00 0.00 3.46
335 336 9.612620 CAGGAAGTACAGTTGTGAATATTTTTC 57.387 33.333 0.00 0.00 0.00 2.29
336 337 8.576442 CCAGGAAGTACAGTTGTGAATATTTTT 58.424 33.333 0.00 0.00 0.00 1.94
337 338 7.724061 ACCAGGAAGTACAGTTGTGAATATTTT 59.276 33.333 0.00 0.00 0.00 1.82
338 339 7.231467 ACCAGGAAGTACAGTTGTGAATATTT 58.769 34.615 0.00 0.00 0.00 1.40
339 340 6.779860 ACCAGGAAGTACAGTTGTGAATATT 58.220 36.000 0.00 0.00 0.00 1.28
340 341 6.374417 ACCAGGAAGTACAGTTGTGAATAT 57.626 37.500 0.00 0.00 0.00 1.28
341 342 5.818678 ACCAGGAAGTACAGTTGTGAATA 57.181 39.130 0.00 0.00 0.00 1.75
342 343 4.706842 ACCAGGAAGTACAGTTGTGAAT 57.293 40.909 0.00 0.00 0.00 2.57
343 344 4.497291 AACCAGGAAGTACAGTTGTGAA 57.503 40.909 0.00 0.00 0.00 3.18
344 345 4.497291 AAACCAGGAAGTACAGTTGTGA 57.503 40.909 0.00 0.00 0.00 3.58
345 346 6.687081 TTTAAACCAGGAAGTACAGTTGTG 57.313 37.500 0.00 0.00 0.00 3.33
346 347 7.706100 TTTTTAAACCAGGAAGTACAGTTGT 57.294 32.000 0.00 0.00 0.00 3.32
421 422 9.995003 TCTGCAAAATTTCCAATAACATAGTTT 57.005 25.926 0.00 0.00 0.00 2.66
422 423 9.995003 TTCTGCAAAATTTCCAATAACATAGTT 57.005 25.926 0.00 0.00 0.00 2.24
423 424 9.995003 TTTCTGCAAAATTTCCAATAACATAGT 57.005 25.926 0.00 0.00 0.00 2.12
426 427 9.558396 TCTTTTCTGCAAAATTTCCAATAACAT 57.442 25.926 0.00 0.00 30.91 2.71
427 428 8.825745 GTCTTTTCTGCAAAATTTCCAATAACA 58.174 29.630 0.00 0.00 30.91 2.41
428 429 8.282592 GGTCTTTTCTGCAAAATTTCCAATAAC 58.717 33.333 0.00 0.00 30.91 1.89
429 430 7.443879 GGGTCTTTTCTGCAAAATTTCCAATAA 59.556 33.333 0.00 0.00 30.91 1.40
430 431 6.934083 GGGTCTTTTCTGCAAAATTTCCAATA 59.066 34.615 0.00 0.00 30.91 1.90
452 453 6.408092 GGGTTGAATTTGAAGAAAAAGAGGGT 60.408 38.462 0.00 0.00 0.00 4.34
529 530 9.542462 GCTTGAATATACTAAACTACATGGTCA 57.458 33.333 0.00 0.00 0.00 4.02
564 565 6.094325 GGATCGTTGGGTGATGTATGTTTAAA 59.906 38.462 0.00 0.00 0.00 1.52
565 566 5.587043 GGATCGTTGGGTGATGTATGTTTAA 59.413 40.000 0.00 0.00 0.00 1.52
566 567 5.120399 GGATCGTTGGGTGATGTATGTTTA 58.880 41.667 0.00 0.00 0.00 2.01
567 568 3.945285 GGATCGTTGGGTGATGTATGTTT 59.055 43.478 0.00 0.00 0.00 2.83
568 569 3.541632 GGATCGTTGGGTGATGTATGTT 58.458 45.455 0.00 0.00 0.00 2.71
569 570 2.483013 CGGATCGTTGGGTGATGTATGT 60.483 50.000 0.00 0.00 0.00 2.29
570 571 2.135139 CGGATCGTTGGGTGATGTATG 58.865 52.381 0.00 0.00 0.00 2.39
571 572 1.540363 GCGGATCGTTGGGTGATGTAT 60.540 52.381 0.00 0.00 0.00 2.29
572 573 0.179094 GCGGATCGTTGGGTGATGTA 60.179 55.000 0.00 0.00 0.00 2.29
573 574 1.449601 GCGGATCGTTGGGTGATGT 60.450 57.895 0.00 0.00 0.00 3.06
574 575 0.744414 AAGCGGATCGTTGGGTGATG 60.744 55.000 0.00 0.00 0.00 3.07
575 576 0.462047 GAAGCGGATCGTTGGGTGAT 60.462 55.000 0.00 0.00 0.00 3.06
576 577 1.079405 GAAGCGGATCGTTGGGTGA 60.079 57.895 0.00 0.00 0.00 4.02
577 578 2.106683 GGAAGCGGATCGTTGGGTG 61.107 63.158 0.00 0.00 0.00 4.61
578 579 2.267961 GGAAGCGGATCGTTGGGT 59.732 61.111 0.00 0.00 0.00 4.51
579 580 1.815421 CAGGAAGCGGATCGTTGGG 60.815 63.158 0.00 0.00 0.00 4.12
580 581 0.673644 AACAGGAAGCGGATCGTTGG 60.674 55.000 0.00 0.00 0.00 3.77
581 582 0.721718 GAACAGGAAGCGGATCGTTG 59.278 55.000 0.00 0.00 0.00 4.10
582 583 0.391263 GGAACAGGAAGCGGATCGTT 60.391 55.000 0.00 0.00 0.00 3.85
590 591 3.056328 GCGTGGGGAACAGGAAGC 61.056 66.667 0.00 0.00 37.13 3.86
911 912 2.440065 GGCCATGCACCGATCCAA 60.440 61.111 0.00 0.00 0.00 3.53
948 949 1.528292 CCCTCCCTAGATCTTCGCGG 61.528 65.000 6.13 0.00 0.00 6.46
1130 1131 5.028549 AGAGCATCCAGTAAAACGATGAT 57.971 39.130 0.00 0.00 36.33 2.45
1154 1155 7.650504 ACAAAATGCATATGAAGAAATGATCGG 59.349 33.333 16.80 0.00 0.00 4.18
1522 1524 5.669357 GCCATTTGCAAACATGATTTCTTCG 60.669 40.000 15.41 0.00 40.77 3.79
1662 1670 9.581099 CCACAAAAGTTAACACTTGATAGTTTT 57.419 29.630 20.38 8.12 42.89 2.43
1862 1870 9.827411 GAACTTCACTTGAACCATCTATAAAAC 57.173 33.333 0.00 0.00 0.00 2.43
1888 1896 4.552355 TGCAGAATTGATTCACTTTGCAG 58.448 39.130 15.61 0.00 38.49 4.41
1925 1933 6.162777 TGTTAATGCTACCAAGGAAAAATGC 58.837 36.000 0.00 0.00 0.00 3.56
2358 2375 7.280652 CCAAACCTGTCAAAATCTGAAATTTGT 59.719 33.333 14.83 0.00 37.68 2.83
2388 2405 4.389374 CCCGGTCAAGCATGTTATAGATT 58.611 43.478 0.00 0.00 0.00 2.40
3161 3194 2.492484 GTCGACTTTCTCTAGCAAGGGA 59.508 50.000 8.70 0.00 0.00 4.20
3182 3215 5.493133 TTATAGCTACGGCAAAACAATGG 57.507 39.130 0.00 0.00 41.70 3.16
3251 3284 6.115446 CACTATCCTGGAGCAAAATCAACTA 58.885 40.000 1.52 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.