Multiple sequence alignment - TraesCS6B01G178200

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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 TraesCS6B01G178200 chr6B 100.000 4353 0 0 1 4353 197735899 197740251 0.000000e+00 8039.0
1 TraesCS6B01G178200 chr6B 96.755 678 22 0 2387 3064 177405388 177406065 0.000000e+00 1131.0
2 TraesCS6B01G178200 chr6B 95.000 680 24 2 2385 3064 690454613 690455282 0.000000e+00 1059.0
3 TraesCS6B01G178200 chr6B 94.017 117 6 1 3450 3565 197739282 197739398 4.470000e-40 176.0
4 TraesCS6B01G178200 chr6B 94.017 117 6 1 3384 3500 197739348 197739463 4.470000e-40 176.0
5 TraesCS6B01G178200 chr6B 96.386 83 3 0 3414 3496 197736141 197736223 2.110000e-28 137.0
6 TraesCS6B01G178200 chr6B 92.771 83 6 0 3480 3562 197736141 197736223 2.130000e-23 121.0
7 TraesCS6B01G178200 chr6B 97.959 49 1 0 3382 3430 197736175 197736223 7.760000e-13 86.1
8 TraesCS6B01G178200 chr6B 92.157 51 1 2 3850 3900 45709479 45709526 7.810000e-08 69.4
9 TraesCS6B01G178200 chrUn 96.550 2203 50 8 185 2385 331036468 331038646 0.000000e+00 3624.0
10 TraesCS6B01G178200 chrUn 95.982 672 12 3 3683 4353 341211800 341212457 0.000000e+00 1077.0
11 TraesCS6B01G178200 chrUn 89.153 673 73 0 2387 3059 336410825 336410153 0.000000e+00 839.0
12 TraesCS6B01G178200 chrUn 97.351 453 10 2 3048 3500 331038632 331039082 0.000000e+00 769.0
13 TraesCS6B01G178200 chrUn 96.983 232 7 0 3450 3681 331038967 331039198 1.470000e-104 390.0
14 TraesCS6B01G178200 chrUn 93.701 127 5 1 185 311 336411558 336411681 2.070000e-43 187.0
15 TraesCS6B01G178200 chrUn 82.386 176 8 6 47 199 336411358 336411533 9.820000e-27 132.0
16 TraesCS6B01G178200 chrUn 90.566 53 4 1 3382 3434 331039031 331039082 7.810000e-08 69.4
17 TraesCS6B01G178200 chr2D 94.183 2080 109 6 309 2382 594188437 594190510 0.000000e+00 3160.0
18 TraesCS6B01G178200 chr2D 88.728 346 22 11 3048 3385 594190499 594190835 1.460000e-109 407.0
19 TraesCS6B01G178200 chr2D 83.806 247 24 11 3850 4087 566757933 566758172 2.040000e-53 220.0
20 TraesCS6B01G178200 chr2D 82.500 240 28 11 3890 4123 566758594 566758825 9.550000e-47 198.0
21 TraesCS6B01G178200 chr2B 94.589 2033 86 13 367 2383 721276646 721278670 0.000000e+00 3123.0
22 TraesCS6B01G178200 chr2B 92.647 680 48 2 2386 3064 296059741 296059063 0.000000e+00 977.0
23 TraesCS6B01G178200 chr2B 91.349 682 56 3 2386 3067 109880313 109880991 0.000000e+00 929.0
24 TraesCS6B01G178200 chr2B 88.529 340 28 3 3048 3384 721278658 721278989 6.780000e-108 401.0
25 TraesCS6B01G178200 chr2B 86.818 220 28 1 3499 3718 754984311 754984529 1.210000e-60 244.0
26 TraesCS6B01G178200 chr2B 92.308 143 11 0 3850 3992 679631779 679631637 2.050000e-48 204.0
27 TraesCS6B01G178200 chr2A 95.174 1347 56 6 1041 2383 728773005 728774346 0.000000e+00 2119.0
28 TraesCS6B01G178200 chr2A 90.947 729 62 4 309 1035 728772330 728773056 0.000000e+00 977.0
29 TraesCS6B01G178200 chr2A 89.937 318 20 3 3072 3385 728774345 728774654 2.440000e-107 399.0
30 TraesCS6B01G178200 chr2A 81.961 255 32 11 3850 4092 706578073 706578325 2.050000e-48 204.0
31 TraesCS6B01G178200 chr4A 92.296 675 52 0 2390 3064 169682407 169683081 0.000000e+00 959.0
32 TraesCS6B01G178200 chr4A 83.239 352 30 14 3850 4176 712214593 712214246 3.290000e-76 296.0
33 TraesCS6B01G178200 chr4A 91.429 140 11 1 3850 3988 712367543 712367682 1.600000e-44 191.0
34 TraesCS6B01G178200 chr5B 92.035 678 53 1 2387 3064 666584538 666585214 0.000000e+00 952.0
35 TraesCS6B01G178200 chr3B 91.765 680 56 0 2385 3064 384335306 384335985 0.000000e+00 946.0
36 TraesCS6B01G178200 chr7B 92.857 644 46 0 2421 3064 14774696 14774053 0.000000e+00 935.0
37 TraesCS6B01G178200 chr4D 83.807 352 28 13 3850 4176 327910223 327909876 1.520000e-79 307.0
38 TraesCS6B01G178200 chr4D 87.879 132 6 3 4223 4353 327909787 327909665 3.510000e-31 147.0
39 TraesCS6B01G178200 chr3D 83.714 350 31 11 3850 4176 432506317 432505971 1.520000e-79 307.0
40 TraesCS6B01G178200 chr7D 90.045 221 18 2 3499 3719 37537153 37536937 2.560000e-72 283.0
41 TraesCS6B01G178200 chr7D 89.450 218 22 1 3499 3716 410891677 410891893 1.540000e-69 274.0
42 TraesCS6B01G178200 chr6A 82.044 362 26 18 3850 4176 528953758 528953401 5.550000e-69 272.0
43 TraesCS6B01G178200 chr5D 91.667 132 8 3 2 132 551015204 551015333 3.460000e-41 180.0


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 TraesCS6B01G178200 chr6B 197735899 197740251 4352 False 8039.0 8039 100.000000 1 4353 1 chr6B.!!$F3 4352
1 TraesCS6B01G178200 chr6B 177405388 177406065 677 False 1131.0 1131 96.755000 2387 3064 1 chr6B.!!$F2 677
2 TraesCS6B01G178200 chr6B 690454613 690455282 669 False 1059.0 1059 95.000000 2385 3064 1 chr6B.!!$F4 679
3 TraesCS6B01G178200 chrUn 331036468 331039198 2730 False 1213.1 3624 95.362500 185 3681 4 chrUn.!!$F2 3496
4 TraesCS6B01G178200 chrUn 341211800 341212457 657 False 1077.0 1077 95.982000 3683 4353 1 chrUn.!!$F1 670
5 TraesCS6B01G178200 chrUn 336410153 336410825 672 True 839.0 839 89.153000 2387 3059 1 chrUn.!!$R1 672
6 TraesCS6B01G178200 chr2D 594188437 594190835 2398 False 1783.5 3160 91.455500 309 3385 2 chr2D.!!$F2 3076
7 TraesCS6B01G178200 chr2D 566757933 566758825 892 False 209.0 220 83.153000 3850 4123 2 chr2D.!!$F1 273
8 TraesCS6B01G178200 chr2B 721276646 721278989 2343 False 1762.0 3123 91.559000 367 3384 2 chr2B.!!$F3 3017
9 TraesCS6B01G178200 chr2B 296059063 296059741 678 True 977.0 977 92.647000 2386 3064 1 chr2B.!!$R1 678
10 TraesCS6B01G178200 chr2B 109880313 109880991 678 False 929.0 929 91.349000 2386 3067 1 chr2B.!!$F1 681
11 TraesCS6B01G178200 chr2A 728772330 728774654 2324 False 1165.0 2119 92.019333 309 3385 3 chr2A.!!$F2 3076
12 TraesCS6B01G178200 chr4A 169682407 169683081 674 False 959.0 959 92.296000 2390 3064 1 chr4A.!!$F1 674
13 TraesCS6B01G178200 chr5B 666584538 666585214 676 False 952.0 952 92.035000 2387 3064 1 chr5B.!!$F1 677
14 TraesCS6B01G178200 chr3B 384335306 384335985 679 False 946.0 946 91.765000 2385 3064 1 chr3B.!!$F1 679
15 TraesCS6B01G178200 chr7B 14774053 14774696 643 True 935.0 935 92.857000 2421 3064 1 chr7B.!!$R1 643
16 TraesCS6B01G178200 chr4D 327909665 327910223 558 True 227.0 307 85.843000 3850 4353 2 chr4D.!!$R1 503

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
160 161 0.036732 TGACCTGAACCATCCTGCAC 59.963 55.000 0.0 0.0 0.00 4.57 F
163 164 0.321564 CCTGAACCATCCTGCACGAA 60.322 55.000 0.0 0.0 0.00 3.85 F
165 166 0.605319 TGAACCATCCTGCACGAACC 60.605 55.000 0.0 0.0 0.00 3.62 F
167 168 0.889186 AACCATCCTGCACGAACCAC 60.889 55.000 0.0 0.0 0.00 4.16 F
277 278 1.004200 GACCCCAATGGACGACGTT 60.004 57.895 0.0 0.0 38.00 3.99 F
1828 1867 0.730840 AGCGTTAAATTGGCTACGGC 59.269 50.000 0.0 0.0 34.75 5.68 F
2498 2540 0.761187 TCAAGCCAACTCTCAGTGCT 59.239 50.000 0.0 0.0 29.91 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1864 0.457443 TGCACACTCTCATCTAGCCG 59.543 55.000 0.00 0.0 0.00 5.52 R
1826 1865 2.275318 GTTGCACACTCTCATCTAGCC 58.725 52.381 0.00 0.0 0.00 3.93 R
1827 1866 2.928757 CTGTTGCACACTCTCATCTAGC 59.071 50.000 0.00 0.0 0.00 3.42 R
1828 1867 4.185467 ACTGTTGCACACTCTCATCTAG 57.815 45.455 0.00 0.0 0.00 2.43 R
1909 1948 4.442706 CACCTGCGGAAGTTGTAGATAAT 58.557 43.478 0.00 0.0 0.00 1.28 R
2793 2835 0.108585 ACATCACGTTCCTTGGTGCT 59.891 50.000 0.00 0.0 34.20 4.40 R
3430 3490 1.740296 CACGTCGTCCATTGGGGTC 60.740 63.158 2.09 0.0 38.11 4.46 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 2.045045 CTGGATTCCAGCGCCCAA 60.045 61.111 19.49 0.00 45.13 4.12
21 22 1.678635 CTGGATTCCAGCGCCCAAA 60.679 57.895 19.49 0.00 45.13 3.28
22 23 1.937546 CTGGATTCCAGCGCCCAAAC 61.938 60.000 19.49 0.00 45.13 2.93
23 24 1.976474 GGATTCCAGCGCCCAAACA 60.976 57.895 2.29 0.00 0.00 2.83
24 25 1.531739 GGATTCCAGCGCCCAAACAA 61.532 55.000 2.29 0.00 0.00 2.83
25 26 0.316841 GATTCCAGCGCCCAAACAAA 59.683 50.000 2.29 0.00 0.00 2.83
26 27 0.755686 ATTCCAGCGCCCAAACAAAA 59.244 45.000 2.29 0.00 0.00 2.44
27 28 0.537188 TTCCAGCGCCCAAACAAAAA 59.463 45.000 2.29 0.00 0.00 1.94
47 48 1.398692 AAAAACGATGCCCACACTGT 58.601 45.000 0.00 0.00 0.00 3.55
48 49 0.951558 AAAACGATGCCCACACTGTC 59.048 50.000 0.00 0.00 0.00 3.51
49 50 1.227999 AAACGATGCCCACACTGTCG 61.228 55.000 0.00 0.00 38.21 4.35
50 51 2.094757 AACGATGCCCACACTGTCGA 62.095 55.000 0.00 0.00 36.28 4.20
51 52 1.153568 CGATGCCCACACTGTCGAT 60.154 57.895 0.00 0.00 34.46 3.59
52 53 0.740868 CGATGCCCACACTGTCGATT 60.741 55.000 0.00 0.00 34.46 3.34
53 54 1.009829 GATGCCCACACTGTCGATTC 58.990 55.000 0.00 0.00 0.00 2.52
54 55 0.392998 ATGCCCACACTGTCGATTCC 60.393 55.000 0.00 0.00 0.00 3.01
55 56 1.745489 GCCCACACTGTCGATTCCC 60.745 63.158 0.00 0.00 0.00 3.97
56 57 1.676968 CCCACACTGTCGATTCCCA 59.323 57.895 0.00 0.00 0.00 4.37
57 58 0.673644 CCCACACTGTCGATTCCCAC 60.674 60.000 0.00 0.00 0.00 4.61
58 59 0.673644 CCACACTGTCGATTCCCACC 60.674 60.000 0.00 0.00 0.00 4.61
59 60 0.321671 CACACTGTCGATTCCCACCT 59.678 55.000 0.00 0.00 0.00 4.00
60 61 0.608640 ACACTGTCGATTCCCACCTC 59.391 55.000 0.00 0.00 0.00 3.85
61 62 0.108138 CACTGTCGATTCCCACCTCC 60.108 60.000 0.00 0.00 0.00 4.30
62 63 1.265454 ACTGTCGATTCCCACCTCCC 61.265 60.000 0.00 0.00 0.00 4.30
63 64 1.229368 TGTCGATTCCCACCTCCCA 60.229 57.895 0.00 0.00 0.00 4.37
64 65 1.221021 GTCGATTCCCACCTCCCAC 59.779 63.158 0.00 0.00 0.00 4.61
65 66 1.080354 TCGATTCCCACCTCCCACT 59.920 57.895 0.00 0.00 0.00 4.00
66 67 0.976073 TCGATTCCCACCTCCCACTC 60.976 60.000 0.00 0.00 0.00 3.51
67 68 1.522569 GATTCCCACCTCCCACTCG 59.477 63.158 0.00 0.00 0.00 4.18
68 69 1.972660 GATTCCCACCTCCCACTCGG 61.973 65.000 0.00 0.00 0.00 4.63
69 70 2.765705 ATTCCCACCTCCCACTCGGT 62.766 60.000 0.00 0.00 0.00 4.69
70 71 3.391382 CCCACCTCCCACTCGGTC 61.391 72.222 0.00 0.00 0.00 4.79
71 72 3.391382 CCACCTCCCACTCGGTCC 61.391 72.222 0.00 0.00 0.00 4.46
72 73 2.603473 CACCTCCCACTCGGTCCA 60.603 66.667 0.00 0.00 0.00 4.02
73 74 1.990060 CACCTCCCACTCGGTCCAT 60.990 63.158 0.00 0.00 0.00 3.41
74 75 1.686110 ACCTCCCACTCGGTCCATC 60.686 63.158 0.00 0.00 0.00 3.51
75 76 1.381872 CCTCCCACTCGGTCCATCT 60.382 63.158 0.00 0.00 0.00 2.90
76 77 0.978146 CCTCCCACTCGGTCCATCTT 60.978 60.000 0.00 0.00 0.00 2.40
77 78 0.176680 CTCCCACTCGGTCCATCTTG 59.823 60.000 0.00 0.00 0.00 3.02
78 79 1.221840 CCCACTCGGTCCATCTTGG 59.778 63.158 0.00 0.00 39.43 3.61
79 80 1.221840 CCACTCGGTCCATCTTGGG 59.778 63.158 0.00 0.00 38.32 4.12
80 81 1.264749 CCACTCGGTCCATCTTGGGA 61.265 60.000 0.00 0.00 38.32 4.37
81 82 0.613260 CACTCGGTCCATCTTGGGAA 59.387 55.000 0.00 0.00 39.05 3.97
82 83 1.003118 CACTCGGTCCATCTTGGGAAA 59.997 52.381 0.00 0.00 39.05 3.13
83 84 1.702957 ACTCGGTCCATCTTGGGAAAA 59.297 47.619 0.00 0.00 39.05 2.29
84 85 2.107552 ACTCGGTCCATCTTGGGAAAAA 59.892 45.455 0.00 0.00 39.05 1.94
85 86 3.245264 ACTCGGTCCATCTTGGGAAAAAT 60.245 43.478 0.00 0.00 39.05 1.82
86 87 3.088532 TCGGTCCATCTTGGGAAAAATG 58.911 45.455 0.00 0.00 39.05 2.32
87 88 2.417243 CGGTCCATCTTGGGAAAAATGC 60.417 50.000 0.00 0.00 39.05 3.56
88 89 2.833943 GGTCCATCTTGGGAAAAATGCT 59.166 45.455 0.00 0.00 39.05 3.79
89 90 3.261643 GGTCCATCTTGGGAAAAATGCTT 59.738 43.478 0.00 0.00 39.05 3.91
90 91 4.466015 GGTCCATCTTGGGAAAAATGCTTA 59.534 41.667 0.00 0.00 39.05 3.09
91 92 5.394553 GGTCCATCTTGGGAAAAATGCTTAG 60.395 44.000 0.00 0.00 39.05 2.18
92 93 5.418840 GTCCATCTTGGGAAAAATGCTTAGA 59.581 40.000 0.00 0.00 39.05 2.10
93 94 6.015918 TCCATCTTGGGAAAAATGCTTAGAA 58.984 36.000 0.00 0.00 38.32 2.10
94 95 6.153340 TCCATCTTGGGAAAAATGCTTAGAAG 59.847 38.462 0.00 0.00 38.32 2.85
95 96 6.153340 CCATCTTGGGAAAAATGCTTAGAAGA 59.847 38.462 0.00 0.00 32.67 2.87
96 97 7.309990 CCATCTTGGGAAAAATGCTTAGAAGAA 60.310 37.037 0.00 0.00 32.67 2.52
97 98 7.595819 TCTTGGGAAAAATGCTTAGAAGAAA 57.404 32.000 0.00 0.00 0.00 2.52
98 99 8.017418 TCTTGGGAAAAATGCTTAGAAGAAAA 57.983 30.769 0.00 0.00 0.00 2.29
99 100 7.926018 TCTTGGGAAAAATGCTTAGAAGAAAAC 59.074 33.333 0.00 0.00 0.00 2.43
100 101 7.360113 TGGGAAAAATGCTTAGAAGAAAACT 57.640 32.000 0.00 0.00 0.00 2.66
101 102 7.433680 TGGGAAAAATGCTTAGAAGAAAACTC 58.566 34.615 0.00 0.00 0.00 3.01
102 103 7.287696 TGGGAAAAATGCTTAGAAGAAAACTCT 59.712 33.333 0.00 0.00 0.00 3.24
103 104 8.793592 GGGAAAAATGCTTAGAAGAAAACTCTA 58.206 33.333 0.00 0.00 0.00 2.43
104 105 9.613957 GGAAAAATGCTTAGAAGAAAACTCTAC 57.386 33.333 0.00 0.00 0.00 2.59
105 106 9.319223 GAAAAATGCTTAGAAGAAAACTCTACG 57.681 33.333 0.00 0.00 0.00 3.51
106 107 8.603242 AAAATGCTTAGAAGAAAACTCTACGA 57.397 30.769 0.00 0.00 0.00 3.43
107 108 8.603242 AAATGCTTAGAAGAAAACTCTACGAA 57.397 30.769 0.00 0.00 0.00 3.85
108 109 8.603242 AATGCTTAGAAGAAAACTCTACGAAA 57.397 30.769 0.00 0.00 0.00 3.46
109 110 8.603242 ATGCTTAGAAGAAAACTCTACGAAAA 57.397 30.769 0.00 0.00 0.00 2.29
110 111 8.428186 TGCTTAGAAGAAAACTCTACGAAAAA 57.572 30.769 0.00 0.00 0.00 1.94
141 142 1.892209 AAAAACCAGCGATTCGTCCT 58.108 45.000 8.03 0.00 0.00 3.85
142 143 1.156736 AAAACCAGCGATTCGTCCTG 58.843 50.000 8.03 7.26 0.00 3.86
143 144 0.320374 AAACCAGCGATTCGTCCTGA 59.680 50.000 13.23 0.00 0.00 3.86
144 145 0.389948 AACCAGCGATTCGTCCTGAC 60.390 55.000 13.23 0.00 0.00 3.51
145 146 1.519455 CCAGCGATTCGTCCTGACC 60.519 63.158 13.23 0.00 0.00 4.02
146 147 1.513158 CAGCGATTCGTCCTGACCT 59.487 57.895 8.03 0.00 0.00 3.85
147 148 0.803768 CAGCGATTCGTCCTGACCTG 60.804 60.000 8.03 0.91 0.00 4.00
148 149 0.965866 AGCGATTCGTCCTGACCTGA 60.966 55.000 8.03 0.00 0.00 3.86
149 150 0.108804 GCGATTCGTCCTGACCTGAA 60.109 55.000 8.03 0.00 0.00 3.02
150 151 1.630148 CGATTCGTCCTGACCTGAAC 58.370 55.000 0.00 0.00 0.00 3.18
151 152 1.736032 CGATTCGTCCTGACCTGAACC 60.736 57.143 0.00 0.00 0.00 3.62
152 153 1.275291 GATTCGTCCTGACCTGAACCA 59.725 52.381 0.00 0.00 0.00 3.67
153 154 1.348064 TTCGTCCTGACCTGAACCAT 58.652 50.000 0.00 0.00 0.00 3.55
154 155 0.895530 TCGTCCTGACCTGAACCATC 59.104 55.000 0.00 0.00 0.00 3.51
155 156 0.108138 CGTCCTGACCTGAACCATCC 60.108 60.000 0.00 0.00 0.00 3.51
156 157 1.280457 GTCCTGACCTGAACCATCCT 58.720 55.000 0.00 0.00 0.00 3.24
157 158 1.065854 GTCCTGACCTGAACCATCCTG 60.066 57.143 0.00 0.00 0.00 3.86
158 159 0.393537 CCTGACCTGAACCATCCTGC 60.394 60.000 0.00 0.00 0.00 4.85
159 160 0.325933 CTGACCTGAACCATCCTGCA 59.674 55.000 0.00 0.00 0.00 4.41
160 161 0.036732 TGACCTGAACCATCCTGCAC 59.963 55.000 0.00 0.00 0.00 4.57
161 162 1.003355 ACCTGAACCATCCTGCACG 60.003 57.895 0.00 0.00 0.00 5.34
162 163 1.296392 CCTGAACCATCCTGCACGA 59.704 57.895 0.00 0.00 0.00 4.35
163 164 0.321564 CCTGAACCATCCTGCACGAA 60.322 55.000 0.00 0.00 0.00 3.85
164 165 0.798776 CTGAACCATCCTGCACGAAC 59.201 55.000 0.00 0.00 0.00 3.95
165 166 0.605319 TGAACCATCCTGCACGAACC 60.605 55.000 0.00 0.00 0.00 3.62
166 167 0.605319 GAACCATCCTGCACGAACCA 60.605 55.000 0.00 0.00 0.00 3.67
167 168 0.889186 AACCATCCTGCACGAACCAC 60.889 55.000 0.00 0.00 0.00 4.16
168 169 2.040544 CCATCCTGCACGAACCACC 61.041 63.158 0.00 0.00 0.00 4.61
169 170 2.047274 ATCCTGCACGAACCACCG 60.047 61.111 0.00 0.00 0.00 4.94
170 171 4.980805 TCCTGCACGAACCACCGC 62.981 66.667 0.00 0.00 0.00 5.68
171 172 4.988598 CCTGCACGAACCACCGCT 62.989 66.667 0.00 0.00 0.00 5.52
172 173 3.414700 CTGCACGAACCACCGCTC 61.415 66.667 0.00 0.00 0.00 5.03
173 174 4.980805 TGCACGAACCACCGCTCC 62.981 66.667 0.00 0.00 0.00 4.70
174 175 4.681978 GCACGAACCACCGCTCCT 62.682 66.667 0.00 0.00 0.00 3.69
175 176 2.432628 CACGAACCACCGCTCCTC 60.433 66.667 0.00 0.00 0.00 3.71
176 177 3.692406 ACGAACCACCGCTCCTCC 61.692 66.667 0.00 0.00 0.00 4.30
177 178 4.452733 CGAACCACCGCTCCTCCC 62.453 72.222 0.00 0.00 0.00 4.30
178 179 4.452733 GAACCACCGCTCCTCCCG 62.453 72.222 0.00 0.00 0.00 5.14
180 181 4.779733 ACCACCGCTCCTCCCGAT 62.780 66.667 0.00 0.00 0.00 4.18
181 182 3.917760 CCACCGCTCCTCCCGATC 61.918 72.222 0.00 0.00 0.00 3.69
182 183 3.917760 CACCGCTCCTCCCGATCC 61.918 72.222 0.00 0.00 0.00 3.36
183 184 4.458829 ACCGCTCCTCCCGATCCA 62.459 66.667 0.00 0.00 0.00 3.41
243 244 2.058595 ATCTCCCCGTCTCCAACCG 61.059 63.158 0.00 0.00 0.00 4.44
273 274 3.395702 CCGGACCCCAATGGACGA 61.396 66.667 0.00 0.00 39.31 4.20
276 277 2.660802 GACCCCAATGGACGACGT 59.339 61.111 0.00 0.00 38.00 4.34
277 278 1.004200 GACCCCAATGGACGACGTT 60.004 57.895 0.00 0.00 38.00 3.99
278 279 1.296056 GACCCCAATGGACGACGTTG 61.296 60.000 0.00 0.00 44.09 4.10
279 280 1.004320 CCCCAATGGACGACGTTGA 60.004 57.895 10.51 0.00 46.77 3.18
748 763 2.029918 GGAAGAGCGGCAGAAAAATTGT 60.030 45.455 1.45 0.00 0.00 2.71
1292 1307 6.053632 TGTCACCACATTGATATTCTCAGT 57.946 37.500 0.00 0.00 34.68 3.41
1369 1387 5.456042 CCCAGTATACTGATGGCACCATTTA 60.456 44.000 30.41 0.00 46.59 1.40
1370 1388 6.061441 CCAGTATACTGATGGCACCATTTAA 58.939 40.000 30.41 0.00 46.59 1.52
1572 1590 7.557719 AGCTATGCATATACCAAGAAAACTGTT 59.442 33.333 6.92 0.00 0.00 3.16
1593 1611 3.486383 TGAGAAGGCTTTTGGTCGAAAT 58.514 40.909 0.00 0.00 0.00 2.17
1659 1677 1.610522 GGAAGTGTTGCTCAAGTGCAT 59.389 47.619 0.00 0.00 42.96 3.96
1809 1848 6.683974 GCTAAAGCTTCAAGATGTATTCCA 57.316 37.500 11.86 0.00 38.21 3.53
1810 1849 6.723282 GCTAAAGCTTCAAGATGTATTCCAG 58.277 40.000 11.86 0.00 38.21 3.86
1811 1850 5.573337 AAAGCTTCAAGATGTATTCCAGC 57.427 39.130 0.00 0.00 0.00 4.85
1812 1851 3.201290 AGCTTCAAGATGTATTCCAGCG 58.799 45.455 0.00 0.00 33.68 5.18
1813 1852 2.939103 GCTTCAAGATGTATTCCAGCGT 59.061 45.455 0.00 0.00 33.68 5.07
1814 1853 3.375299 GCTTCAAGATGTATTCCAGCGTT 59.625 43.478 0.00 0.00 33.68 4.84
1815 1854 4.570772 GCTTCAAGATGTATTCCAGCGTTA 59.429 41.667 0.00 0.00 33.68 3.18
1816 1855 5.064707 GCTTCAAGATGTATTCCAGCGTTAA 59.935 40.000 0.00 0.00 33.68 2.01
1817 1856 6.403200 GCTTCAAGATGTATTCCAGCGTTAAA 60.403 38.462 0.00 0.00 33.68 1.52
1818 1857 7.624360 TTCAAGATGTATTCCAGCGTTAAAT 57.376 32.000 0.00 0.00 33.68 1.40
1819 1858 7.624360 TCAAGATGTATTCCAGCGTTAAATT 57.376 32.000 0.00 0.00 33.68 1.82
1820 1859 7.471721 TCAAGATGTATTCCAGCGTTAAATTG 58.528 34.615 0.00 0.00 33.68 2.32
1821 1860 6.377327 AGATGTATTCCAGCGTTAAATTGG 57.623 37.500 0.00 0.00 33.68 3.16
1822 1861 4.364415 TGTATTCCAGCGTTAAATTGGC 57.636 40.909 0.00 0.00 31.94 4.52
1823 1862 4.013728 TGTATTCCAGCGTTAAATTGGCT 58.986 39.130 0.00 0.00 37.55 4.75
1824 1863 5.186942 TGTATTCCAGCGTTAAATTGGCTA 58.813 37.500 0.00 0.00 34.75 3.93
1825 1864 4.632538 ATTCCAGCGTTAAATTGGCTAC 57.367 40.909 0.00 0.00 34.75 3.58
1826 1865 2.004017 TCCAGCGTTAAATTGGCTACG 58.996 47.619 0.00 0.00 34.75 3.51
1827 1866 1.063469 CCAGCGTTAAATTGGCTACGG 59.937 52.381 0.00 0.00 34.75 4.02
1828 1867 0.730840 AGCGTTAAATTGGCTACGGC 59.269 50.000 0.00 0.00 34.75 5.68
1949 1988 5.739935 GCAGGTGGAAAGATGTGTCATTTTT 60.740 40.000 0.00 0.00 0.00 1.94
2108 2147 3.671702 GCACTCTTGAAAATGCTACTGGC 60.672 47.826 0.00 0.00 42.22 4.85
2382 2424 9.730705 TTTGGCATTAGAATTATCCAGATAGAG 57.269 33.333 0.00 0.00 0.00 2.43
2383 2425 8.670521 TGGCATTAGAATTATCCAGATAGAGA 57.329 34.615 0.00 0.00 0.00 3.10
2498 2540 0.761187 TCAAGCCAACTCTCAGTGCT 59.239 50.000 0.00 0.00 29.91 4.40
2539 2581 1.515519 GCACACTGATGCGCCAATG 60.516 57.895 4.18 0.00 35.50 2.82
2623 2665 3.024547 AGTTCACTCAAGATAGGCGCTA 58.975 45.455 7.64 0.00 0.00 4.26
2669 2711 4.993584 CGAATGCCATAGATCAACTAGCTT 59.006 41.667 0.00 0.00 34.35 3.74
2766 2808 1.201429 ACTCCGCAATGAAGGGGTCT 61.201 55.000 0.00 0.00 36.21 3.85
2779 2821 1.134098 AGGGGTCTGATATGCCAAACG 60.134 52.381 0.00 0.00 0.00 3.60
2807 2849 1.101049 CACCAAGCACCAAGGAACGT 61.101 55.000 0.00 0.00 0.00 3.99
2894 2943 0.179468 TTGATAGTAACCCAGCCCGC 59.821 55.000 0.00 0.00 0.00 6.13
2895 2944 1.070957 GATAGTAACCCAGCCCGCC 59.929 63.158 0.00 0.00 0.00 6.13
2896 2945 1.384082 ATAGTAACCCAGCCCGCCT 60.384 57.895 0.00 0.00 0.00 5.52
2897 2946 1.408453 ATAGTAACCCAGCCCGCCTC 61.408 60.000 0.00 0.00 0.00 4.70
2898 2947 2.808761 TAGTAACCCAGCCCGCCTCA 62.809 60.000 0.00 0.00 0.00 3.86
2899 2948 3.399181 TAACCCAGCCCGCCTCAG 61.399 66.667 0.00 0.00 0.00 3.35
3385 3445 6.748198 TGGTTTACGAAAACTGAACAATTGAC 59.252 34.615 13.59 6.46 43.76 3.18
3386 3446 6.075780 GGTTTACGAAAACTGAACAATTGACG 60.076 38.462 13.59 5.98 43.76 4.35
3387 3447 3.359654 ACGAAAACTGAACAATTGACGC 58.640 40.909 13.59 1.28 0.00 5.19
3388 3448 3.064820 ACGAAAACTGAACAATTGACGCT 59.935 39.130 13.59 0.00 0.00 5.07
3389 3449 3.418619 CGAAAACTGAACAATTGACGCTG 59.581 43.478 13.59 7.27 0.00 5.18
3390 3450 2.405892 AACTGAACAATTGACGCTGC 57.594 45.000 13.59 0.00 0.00 5.25
3391 3451 0.593128 ACTGAACAATTGACGCTGCC 59.407 50.000 13.59 0.00 0.00 4.85
3392 3452 0.453282 CTGAACAATTGACGCTGCCG 60.453 55.000 13.59 0.00 41.14 5.69
3393 3453 1.797537 GAACAATTGACGCTGCCGC 60.798 57.895 13.59 0.00 38.22 6.53
3394 3454 3.267597 AACAATTGACGCTGCCGCC 62.268 57.895 13.59 0.00 38.22 6.13
3395 3455 4.817063 CAATTGACGCTGCCGCCG 62.817 66.667 0.00 0.00 38.22 6.46
3444 3504 3.395702 CCGGACCCCAATGGACGA 61.396 66.667 0.00 0.00 39.31 4.20
3445 3505 2.125269 CGGACCCCAATGGACGAC 60.125 66.667 0.00 0.00 39.31 4.34
3446 3506 2.125269 GGACCCCAATGGACGACG 60.125 66.667 0.00 0.00 38.00 5.12
3447 3507 2.660802 GACCCCAATGGACGACGT 59.339 61.111 0.00 0.00 38.00 4.34
3448 3508 1.740296 GACCCCAATGGACGACGTG 60.740 63.158 4.58 0.00 38.00 4.49
3601 3661 4.884257 TTCTCCGCGCGGCCATAC 62.884 66.667 42.78 0.00 34.68 2.39
3644 3704 1.533219 CCTATCATGGCTGCCACCA 59.467 57.895 25.99 13.96 45.82 4.17
3778 3838 4.611310 TCTGTTATGGTCGACGAACTAG 57.389 45.455 15.00 16.64 0.00 2.57
3782 3842 1.183549 ATGGTCGACGAACTAGCCTT 58.816 50.000 15.00 0.00 0.00 4.35
3785 3845 0.714439 GTCGACGAACTAGCCTTTGC 59.286 55.000 0.00 0.00 37.95 3.68
3842 3902 9.074576 TCAATATTTTCAGTATCGTCTAGGCTA 57.925 33.333 0.00 0.00 0.00 3.93
4143 4267 3.366374 GGCAGGTAGTGTTCTGAATTTGC 60.366 47.826 0.00 0.00 33.11 3.68
4181 4305 8.043710 CCTTTATATGGAGGGCATTCTTAGTAG 58.956 40.741 0.00 0.00 0.00 2.57
4256 4424 1.000506 CTGCTGCCTTTCAAGTTGCAT 59.999 47.619 0.00 0.00 32.53 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.531739 TTGTTTGGGCGCTGGAATCC 61.532 55.000 7.64 0.00 0.00 3.01
7 8 0.755686 TTTTGTTTGGGCGCTGGAAT 59.244 45.000 7.64 0.00 0.00 3.01
8 9 0.537188 TTTTTGTTTGGGCGCTGGAA 59.463 45.000 7.64 0.00 0.00 3.53
9 10 2.202866 TTTTTGTTTGGGCGCTGGA 58.797 47.368 7.64 0.00 0.00 3.86
10 11 4.844420 TTTTTGTTTGGGCGCTGG 57.156 50.000 7.64 0.00 0.00 4.85
28 29 1.336755 GACAGTGTGGGCATCGTTTTT 59.663 47.619 0.00 0.00 0.00 1.94
29 30 0.951558 GACAGTGTGGGCATCGTTTT 59.048 50.000 0.00 0.00 0.00 2.43
30 31 1.227999 CGACAGTGTGGGCATCGTTT 61.228 55.000 0.00 0.00 0.00 3.60
31 32 1.667830 CGACAGTGTGGGCATCGTT 60.668 57.895 0.00 0.00 0.00 3.85
32 33 1.888436 ATCGACAGTGTGGGCATCGT 61.888 55.000 0.00 0.00 34.47 3.73
33 34 0.740868 AATCGACAGTGTGGGCATCG 60.741 55.000 0.00 0.00 0.00 3.84
34 35 1.009829 GAATCGACAGTGTGGGCATC 58.990 55.000 0.00 0.00 0.00 3.91
35 36 0.392998 GGAATCGACAGTGTGGGCAT 60.393 55.000 0.00 0.00 0.00 4.40
36 37 1.003839 GGAATCGACAGTGTGGGCA 60.004 57.895 0.00 0.00 0.00 5.36
37 38 1.745489 GGGAATCGACAGTGTGGGC 60.745 63.158 0.00 0.00 0.00 5.36
38 39 0.673644 GTGGGAATCGACAGTGTGGG 60.674 60.000 0.00 0.00 0.00 4.61
39 40 0.673644 GGTGGGAATCGACAGTGTGG 60.674 60.000 0.00 0.00 0.00 4.17
40 41 0.321671 AGGTGGGAATCGACAGTGTG 59.678 55.000 0.00 0.00 0.00 3.82
41 42 0.608640 GAGGTGGGAATCGACAGTGT 59.391 55.000 0.00 0.00 0.00 3.55
42 43 0.108138 GGAGGTGGGAATCGACAGTG 60.108 60.000 0.00 0.00 0.00 3.66
43 44 1.265454 GGGAGGTGGGAATCGACAGT 61.265 60.000 0.00 0.00 0.00 3.55
44 45 1.264749 TGGGAGGTGGGAATCGACAG 61.265 60.000 0.00 0.00 0.00 3.51
45 46 1.229368 TGGGAGGTGGGAATCGACA 60.229 57.895 0.00 0.00 0.00 4.35
46 47 1.221021 GTGGGAGGTGGGAATCGAC 59.779 63.158 0.00 0.00 0.00 4.20
47 48 0.976073 GAGTGGGAGGTGGGAATCGA 60.976 60.000 0.00 0.00 0.00 3.59
48 49 1.522569 GAGTGGGAGGTGGGAATCG 59.477 63.158 0.00 0.00 0.00 3.34
49 50 1.522569 CGAGTGGGAGGTGGGAATC 59.477 63.158 0.00 0.00 0.00 2.52
50 51 1.995626 CCGAGTGGGAGGTGGGAAT 60.996 63.158 0.00 0.00 38.47 3.01
51 52 2.606519 CCGAGTGGGAGGTGGGAA 60.607 66.667 0.00 0.00 38.47 3.97
52 53 3.899545 GACCGAGTGGGAGGTGGGA 62.900 68.421 0.00 0.00 41.51 4.37
53 54 3.391382 GACCGAGTGGGAGGTGGG 61.391 72.222 0.00 0.00 41.51 4.61
54 55 3.391382 GGACCGAGTGGGAGGTGG 61.391 72.222 0.00 0.00 41.51 4.61
55 56 1.961180 GATGGACCGAGTGGGAGGTG 61.961 65.000 0.00 0.00 41.51 4.00
56 57 1.686110 GATGGACCGAGTGGGAGGT 60.686 63.158 0.00 0.00 44.64 3.85
57 58 0.978146 AAGATGGACCGAGTGGGAGG 60.978 60.000 0.00 0.00 40.75 4.30
58 59 0.176680 CAAGATGGACCGAGTGGGAG 59.823 60.000 0.00 0.00 40.75 4.30
59 60 1.264749 CCAAGATGGACCGAGTGGGA 61.265 60.000 0.00 0.00 40.96 4.37
60 61 1.221840 CCAAGATGGACCGAGTGGG 59.778 63.158 0.00 0.00 40.96 4.61
61 62 1.221840 CCCAAGATGGACCGAGTGG 59.778 63.158 0.00 0.00 40.96 4.00
62 63 0.613260 TTCCCAAGATGGACCGAGTG 59.387 55.000 0.00 0.00 40.96 3.51
63 64 1.358152 TTTCCCAAGATGGACCGAGT 58.642 50.000 0.00 0.00 40.96 4.18
64 65 2.489938 TTTTCCCAAGATGGACCGAG 57.510 50.000 0.00 0.00 40.96 4.63
65 66 2.961531 TTTTTCCCAAGATGGACCGA 57.038 45.000 0.00 0.00 40.96 4.69
66 67 2.417243 GCATTTTTCCCAAGATGGACCG 60.417 50.000 0.00 0.00 40.96 4.79
67 68 2.833943 AGCATTTTTCCCAAGATGGACC 59.166 45.455 0.00 0.00 40.96 4.46
68 69 4.541973 AAGCATTTTTCCCAAGATGGAC 57.458 40.909 0.00 0.00 40.96 4.02
69 70 5.579047 TCTAAGCATTTTTCCCAAGATGGA 58.421 37.500 0.00 0.00 40.96 3.41
70 71 5.920193 TCTAAGCATTTTTCCCAAGATGG 57.080 39.130 0.00 0.00 37.25 3.51
71 72 7.161773 TCTTCTAAGCATTTTTCCCAAGATG 57.838 36.000 0.00 0.00 0.00 2.90
72 73 7.781324 TTCTTCTAAGCATTTTTCCCAAGAT 57.219 32.000 0.00 0.00 0.00 2.40
73 74 7.595819 TTTCTTCTAAGCATTTTTCCCAAGA 57.404 32.000 0.00 0.00 0.00 3.02
74 75 7.928167 AGTTTTCTTCTAAGCATTTTTCCCAAG 59.072 33.333 0.00 0.00 0.00 3.61
75 76 7.791029 AGTTTTCTTCTAAGCATTTTTCCCAA 58.209 30.769 0.00 0.00 0.00 4.12
76 77 7.287696 AGAGTTTTCTTCTAAGCATTTTTCCCA 59.712 33.333 0.00 0.00 0.00 4.37
77 78 7.661968 AGAGTTTTCTTCTAAGCATTTTTCCC 58.338 34.615 0.00 0.00 0.00 3.97
78 79 9.613957 GTAGAGTTTTCTTCTAAGCATTTTTCC 57.386 33.333 0.00 0.00 34.79 3.13
79 80 9.319223 CGTAGAGTTTTCTTCTAAGCATTTTTC 57.681 33.333 0.00 0.00 34.79 2.29
80 81 9.052759 TCGTAGAGTTTTCTTCTAAGCATTTTT 57.947 29.630 0.00 0.00 34.79 1.94
81 82 8.603242 TCGTAGAGTTTTCTTCTAAGCATTTT 57.397 30.769 0.00 0.00 34.79 1.82
82 83 8.603242 TTCGTAGAGTTTTCTTCTAAGCATTT 57.397 30.769 0.00 0.00 38.43 2.32
83 84 8.603242 TTTCGTAGAGTTTTCTTCTAAGCATT 57.397 30.769 0.00 0.00 38.43 3.56
84 85 8.603242 TTTTCGTAGAGTTTTCTTCTAAGCAT 57.397 30.769 0.00 0.00 38.43 3.79
85 86 8.428186 TTTTTCGTAGAGTTTTCTTCTAAGCA 57.572 30.769 0.00 0.00 38.43 3.91
122 123 1.535462 CAGGACGAATCGCTGGTTTTT 59.465 47.619 1.15 0.00 0.00 1.94
123 124 1.156736 CAGGACGAATCGCTGGTTTT 58.843 50.000 1.15 0.00 0.00 2.43
124 125 0.320374 TCAGGACGAATCGCTGGTTT 59.680 50.000 1.15 0.00 0.00 3.27
125 126 0.389948 GTCAGGACGAATCGCTGGTT 60.390 55.000 1.15 0.00 0.00 3.67
126 127 1.215647 GTCAGGACGAATCGCTGGT 59.784 57.895 1.15 0.00 0.00 4.00
127 128 1.519455 GGTCAGGACGAATCGCTGG 60.519 63.158 1.15 0.00 0.00 4.85
128 129 0.803768 CAGGTCAGGACGAATCGCTG 60.804 60.000 1.15 3.07 0.00 5.18
129 130 0.965866 TCAGGTCAGGACGAATCGCT 60.966 55.000 1.15 0.00 0.00 4.93
130 131 0.108804 TTCAGGTCAGGACGAATCGC 60.109 55.000 1.15 0.00 0.00 4.58
131 132 1.630148 GTTCAGGTCAGGACGAATCG 58.370 55.000 0.00 0.00 0.00 3.34
132 133 1.275291 TGGTTCAGGTCAGGACGAATC 59.725 52.381 0.00 0.00 0.00 2.52
133 134 1.348064 TGGTTCAGGTCAGGACGAAT 58.652 50.000 0.00 0.00 0.00 3.34
134 135 1.275291 GATGGTTCAGGTCAGGACGAA 59.725 52.381 0.00 0.00 0.00 3.85
135 136 0.895530 GATGGTTCAGGTCAGGACGA 59.104 55.000 0.00 0.00 0.00 4.20
136 137 0.108138 GGATGGTTCAGGTCAGGACG 60.108 60.000 0.00 0.00 0.00 4.79
137 138 1.065854 CAGGATGGTTCAGGTCAGGAC 60.066 57.143 0.00 0.00 0.00 3.85
138 139 1.279496 CAGGATGGTTCAGGTCAGGA 58.721 55.000 0.00 0.00 0.00 3.86
139 140 0.393537 GCAGGATGGTTCAGGTCAGG 60.394 60.000 0.00 0.00 35.86 3.86
140 141 0.325933 TGCAGGATGGTTCAGGTCAG 59.674 55.000 0.00 0.00 35.86 3.51
141 142 0.036732 GTGCAGGATGGTTCAGGTCA 59.963 55.000 0.00 0.00 35.86 4.02
142 143 1.021390 CGTGCAGGATGGTTCAGGTC 61.021 60.000 0.00 0.00 35.86 3.85
143 144 1.003355 CGTGCAGGATGGTTCAGGT 60.003 57.895 0.00 0.00 35.86 4.00
144 145 0.321564 TTCGTGCAGGATGGTTCAGG 60.322 55.000 10.35 0.00 35.86 3.86
145 146 0.798776 GTTCGTGCAGGATGGTTCAG 59.201 55.000 10.35 0.00 35.86 3.02
146 147 0.605319 GGTTCGTGCAGGATGGTTCA 60.605 55.000 10.35 0.00 35.86 3.18
147 148 0.605319 TGGTTCGTGCAGGATGGTTC 60.605 55.000 10.35 0.00 35.86 3.62
148 149 0.889186 GTGGTTCGTGCAGGATGGTT 60.889 55.000 10.35 0.00 35.86 3.67
149 150 1.302511 GTGGTTCGTGCAGGATGGT 60.303 57.895 10.35 0.00 35.86 3.55
150 151 2.040544 GGTGGTTCGTGCAGGATGG 61.041 63.158 10.35 0.00 35.86 3.51
151 152 2.390599 CGGTGGTTCGTGCAGGATG 61.391 63.158 10.35 0.00 40.87 3.51
152 153 2.047274 CGGTGGTTCGTGCAGGAT 60.047 61.111 10.35 0.00 0.00 3.24
153 154 4.980805 GCGGTGGTTCGTGCAGGA 62.981 66.667 4.68 4.68 0.00 3.86
154 155 4.988598 AGCGGTGGTTCGTGCAGG 62.989 66.667 0.00 0.00 0.00 4.85
155 156 3.414700 GAGCGGTGGTTCGTGCAG 61.415 66.667 0.00 0.00 0.00 4.41
156 157 4.980805 GGAGCGGTGGTTCGTGCA 62.981 66.667 0.00 0.00 0.00 4.57
157 158 4.681978 AGGAGCGGTGGTTCGTGC 62.682 66.667 0.00 0.00 0.00 5.34
158 159 2.432628 GAGGAGCGGTGGTTCGTG 60.433 66.667 0.00 0.00 0.00 4.35
159 160 3.692406 GGAGGAGCGGTGGTTCGT 61.692 66.667 0.00 0.00 0.00 3.85
160 161 4.452733 GGGAGGAGCGGTGGTTCG 62.453 72.222 0.00 0.00 0.00 3.95
161 162 4.452733 CGGGAGGAGCGGTGGTTC 62.453 72.222 0.00 0.00 0.00 3.62
163 164 4.779733 ATCGGGAGGAGCGGTGGT 62.780 66.667 0.00 0.00 0.00 4.16
164 165 3.917760 GATCGGGAGGAGCGGTGG 61.918 72.222 0.00 0.00 0.00 4.61
165 166 3.917760 GGATCGGGAGGAGCGGTG 61.918 72.222 0.00 0.00 0.00 4.94
166 167 4.458829 TGGATCGGGAGGAGCGGT 62.459 66.667 0.00 0.00 0.00 5.68
167 168 3.917760 GTGGATCGGGAGGAGCGG 61.918 72.222 0.00 0.00 0.00 5.52
168 169 2.978298 TAGGTGGATCGGGAGGAGCG 62.978 65.000 0.00 0.00 0.00 5.03
169 170 1.152525 TAGGTGGATCGGGAGGAGC 60.153 63.158 0.00 0.00 0.00 4.70
170 171 0.828343 GGTAGGTGGATCGGGAGGAG 60.828 65.000 0.00 0.00 0.00 3.69
171 172 1.232216 GGTAGGTGGATCGGGAGGA 59.768 63.158 0.00 0.00 0.00 3.71
172 173 1.115930 CAGGTAGGTGGATCGGGAGG 61.116 65.000 0.00 0.00 0.00 4.30
173 174 1.749334 GCAGGTAGGTGGATCGGGAG 61.749 65.000 0.00 0.00 0.00 4.30
174 175 1.760875 GCAGGTAGGTGGATCGGGA 60.761 63.158 0.00 0.00 0.00 5.14
175 176 1.749334 GAGCAGGTAGGTGGATCGGG 61.749 65.000 0.00 0.00 0.00 5.14
176 177 1.742768 GAGCAGGTAGGTGGATCGG 59.257 63.158 0.00 0.00 0.00 4.18
177 178 1.360551 CGAGCAGGTAGGTGGATCG 59.639 63.158 0.00 0.00 0.00 3.69
178 179 1.068250 GCGAGCAGGTAGGTGGATC 59.932 63.158 0.00 0.00 0.00 3.36
179 180 1.381872 AGCGAGCAGGTAGGTGGAT 60.382 57.895 0.00 0.00 0.00 3.41
180 181 2.037367 AGCGAGCAGGTAGGTGGA 59.963 61.111 0.00 0.00 0.00 4.02
181 182 2.496817 GAGCGAGCAGGTAGGTGG 59.503 66.667 0.00 0.00 0.00 4.61
182 183 2.496817 GGAGCGAGCAGGTAGGTG 59.503 66.667 0.00 0.00 0.00 4.00
183 184 2.760385 GGGAGCGAGCAGGTAGGT 60.760 66.667 0.00 0.00 0.00 3.08
426 427 2.271800 GAGATCAAATCGAAGGCACGT 58.728 47.619 0.00 0.00 34.70 4.49
578 589 0.101399 GCTGACCTCGACATCACGAT 59.899 55.000 0.00 0.00 41.39 3.73
748 763 3.674997 GAGTTGACCAATACAGCCTGAA 58.325 45.455 0.00 0.00 0.00 3.02
904 919 2.074579 AGGGCTCCAGTATAGGCTCTA 58.925 52.381 0.00 0.00 39.38 2.43
1091 1106 4.214119 CACAAGCAGCTCTACTTAAAAGCA 59.786 41.667 0.00 0.00 38.51 3.91
1175 1190 6.605471 TCTTCTCACCTAGCATCAACTTTA 57.395 37.500 0.00 0.00 0.00 1.85
1369 1387 7.233757 CCTATACTTACTGCCAAGAGTATCCTT 59.766 40.741 0.00 0.00 36.83 3.36
1370 1388 6.722129 CCTATACTTACTGCCAAGAGTATCCT 59.278 42.308 0.00 0.00 36.83 3.24
1477 1495 4.391830 GTCGTTTGCAAATAGATCAGGACA 59.608 41.667 16.21 0.00 0.00 4.02
1572 1590 2.631160 TTCGACCAAAAGCCTTCTCA 57.369 45.000 0.00 0.00 0.00 3.27
1659 1677 0.887933 GGAATTTCAAAGCAGCCCGA 59.112 50.000 0.00 0.00 0.00 5.14
1802 1820 4.632538 AGCCAATTTAACGCTGGAATAC 57.367 40.909 1.64 0.00 31.38 1.89
1808 1847 1.531058 GCCGTAGCCAATTTAACGCTG 60.531 52.381 0.00 0.00 34.03 5.18
1809 1848 0.730840 GCCGTAGCCAATTTAACGCT 59.269 50.000 0.00 0.00 36.63 5.07
1810 1849 0.730840 AGCCGTAGCCAATTTAACGC 59.269 50.000 0.00 0.00 41.25 4.84
1811 1850 3.450578 TCTAGCCGTAGCCAATTTAACG 58.549 45.455 0.00 0.00 41.25 3.18
1812 1851 5.054477 TCATCTAGCCGTAGCCAATTTAAC 58.946 41.667 0.00 0.00 41.25 2.01
1813 1852 5.069914 TCTCATCTAGCCGTAGCCAATTTAA 59.930 40.000 0.00 0.00 41.25 1.52
1814 1853 4.587262 TCTCATCTAGCCGTAGCCAATTTA 59.413 41.667 0.00 0.00 41.25 1.40
1815 1854 3.388024 TCTCATCTAGCCGTAGCCAATTT 59.612 43.478 0.00 0.00 41.25 1.82
1816 1855 2.965831 TCTCATCTAGCCGTAGCCAATT 59.034 45.455 0.00 0.00 41.25 2.32
1817 1856 2.560542 CTCTCATCTAGCCGTAGCCAAT 59.439 50.000 0.00 0.00 41.25 3.16
1818 1857 1.957177 CTCTCATCTAGCCGTAGCCAA 59.043 52.381 0.00 0.00 41.25 4.52
1819 1858 1.133761 ACTCTCATCTAGCCGTAGCCA 60.134 52.381 0.00 0.00 41.25 4.75
1820 1859 1.268352 CACTCTCATCTAGCCGTAGCC 59.732 57.143 0.00 0.00 41.25 3.93
1821 1860 1.950909 ACACTCTCATCTAGCCGTAGC 59.049 52.381 0.00 0.00 40.32 3.58
1822 1861 2.287308 GCACACTCTCATCTAGCCGTAG 60.287 54.545 0.00 0.00 0.00 3.51
1823 1862 1.676529 GCACACTCTCATCTAGCCGTA 59.323 52.381 0.00 0.00 0.00 4.02
1824 1863 0.457851 GCACACTCTCATCTAGCCGT 59.542 55.000 0.00 0.00 0.00 5.68
1825 1864 0.457443 TGCACACTCTCATCTAGCCG 59.543 55.000 0.00 0.00 0.00 5.52
1826 1865 2.275318 GTTGCACACTCTCATCTAGCC 58.725 52.381 0.00 0.00 0.00 3.93
1827 1866 2.928757 CTGTTGCACACTCTCATCTAGC 59.071 50.000 0.00 0.00 0.00 3.42
1828 1867 4.185467 ACTGTTGCACACTCTCATCTAG 57.815 45.455 0.00 0.00 0.00 2.43
1909 1948 4.442706 CACCTGCGGAAGTTGTAGATAAT 58.557 43.478 0.00 0.00 0.00 1.28
1949 1988 7.831691 TGAACAAATGGATAAAGAGGTTTCA 57.168 32.000 0.00 0.00 0.00 2.69
2108 2147 6.652481 AGACAAAGAGATGGTTGAATGTAGTG 59.348 38.462 0.00 0.00 0.00 2.74
2423 2465 5.302360 GGGCGGATTGTAACACTATGATTA 58.698 41.667 0.00 0.00 0.00 1.75
2498 2540 1.964223 GCCTAGCTAGCACACTGGATA 59.036 52.381 18.83 0.00 0.00 2.59
2536 2578 2.029623 CAGCAGGGAAGCTAATGCATT 58.970 47.619 17.56 17.56 44.54 3.56
2539 2581 1.020437 GTCAGCAGGGAAGCTAATGC 58.980 55.000 4.66 4.66 44.54 3.56
2623 2665 1.609208 GGCAACACCAGATCAGTTGT 58.391 50.000 16.38 3.00 43.31 3.32
2669 2711 3.986996 TCATGGAGATTGACTGCTTGA 57.013 42.857 0.00 0.00 44.21 3.02
2766 2808 2.799126 AACCTCCGTTTGGCATATCA 57.201 45.000 0.00 0.00 34.14 2.15
2793 2835 0.108585 ACATCACGTTCCTTGGTGCT 59.891 50.000 0.00 0.00 34.20 4.40
2807 2849 4.281657 AGGTGTAGCTAGATCACACATCA 58.718 43.478 16.42 0.00 43.44 3.07
2894 2943 0.890996 GTGCTGGAAACCACCTGAGG 60.891 60.000 0.00 0.00 0.00 3.86
2895 2944 0.109342 AGTGCTGGAAACCACCTGAG 59.891 55.000 0.00 0.00 32.48 3.35
2896 2945 0.179020 CAGTGCTGGAAACCACCTGA 60.179 55.000 0.00 0.00 32.48 3.86
2897 2946 0.179020 TCAGTGCTGGAAACCACCTG 60.179 55.000 0.00 0.00 32.48 4.00
2898 2947 0.773644 ATCAGTGCTGGAAACCACCT 59.226 50.000 0.00 0.00 32.48 4.00
2899 2948 1.168714 GATCAGTGCTGGAAACCACC 58.831 55.000 0.00 0.00 32.48 4.61
2900 2949 1.168714 GGATCAGTGCTGGAAACCAC 58.831 55.000 0.00 0.00 0.00 4.16
2917 2966 1.004200 GAAGGAAAACGAGGGCGGA 60.004 57.895 0.00 0.00 43.17 5.54
2946 2995 1.906574 ACTTTGGCGATCCTGGAACTA 59.093 47.619 0.00 0.00 0.00 2.24
3427 3487 3.395702 TCGTCCATTGGGGTCCGG 61.396 66.667 2.09 0.00 38.11 5.14
3428 3488 2.125269 GTCGTCCATTGGGGTCCG 60.125 66.667 2.09 1.14 38.11 4.79
3429 3489 2.125269 CGTCGTCCATTGGGGTCC 60.125 66.667 2.09 0.00 38.11 4.46
3430 3490 1.740296 CACGTCGTCCATTGGGGTC 60.740 63.158 2.09 0.00 38.11 4.46
3431 3491 2.345991 CACGTCGTCCATTGGGGT 59.654 61.111 2.09 0.00 38.11 4.95
3432 3492 2.435938 CCACGTCGTCCATTGGGG 60.436 66.667 2.09 0.00 38.37 4.96
3433 3493 1.740296 GTCCACGTCGTCCATTGGG 60.740 63.158 2.09 0.00 0.00 4.12
3434 3494 2.092291 CGTCCACGTCGTCCATTGG 61.092 63.158 0.00 0.00 34.11 3.16
3435 3495 2.726691 GCGTCCACGTCGTCCATTG 61.727 63.158 0.00 0.00 42.22 2.82
3436 3496 2.431942 GCGTCCACGTCGTCCATT 60.432 61.111 0.00 0.00 42.22 3.16
3437 3497 4.430765 GGCGTCCACGTCGTCCAT 62.431 66.667 0.00 0.00 42.22 3.41
3569 3629 3.470567 GAACGTGACCGCGCTCTG 61.471 66.667 5.56 0.00 37.70 3.35
3644 3704 4.719369 GTCGTTCCTGCCGACGCT 62.719 66.667 0.00 0.00 44.29 5.07
3681 3741 4.471386 AGTATAGCAAATCACCTGTGGAGT 59.529 41.667 0.00 0.00 0.00 3.85
3778 3838 2.006169 GTAGAGAAGCTGAGCAAAGGC 58.994 52.381 7.39 0.00 41.61 4.35
3782 3842 3.791973 GCTAGTAGAGAAGCTGAGCAA 57.208 47.619 7.39 0.00 35.80 3.91
3842 3902 2.836981 CAGGTTGATCTTGACCTCTCCT 59.163 50.000 11.50 0.00 44.28 3.69
3892 3952 7.792364 ATGTAATCCAAGAACGATATCCCTA 57.208 36.000 0.00 0.00 0.00 3.53
4143 4267 6.404293 CCTCCATATAAAGGTTTTGACCAACG 60.404 42.308 0.00 0.00 0.00 4.10
4256 4424 2.553602 ACATCACCTGTAACACGTACGA 59.446 45.455 24.41 0.00 35.91 3.43


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

AutoCloner maintained by Alex Coulton.