Multiple sequence alignment - TraesCS6D01G351100

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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 TraesCS6D01G351100 chr6D 100.000 3062 0 0 1 3062 448484536 448487597 0.000000e+00 5655.0
1 TraesCS6D01G351100 chr6D 93.660 2145 95 7 367 2510 448060056 448057952 0.000000e+00 3169.0
2 TraesCS6D01G351100 chr6D 86.406 1177 134 13 962 2119 448429029 448430198 0.000000e+00 1264.0
3 TraesCS6D01G351100 chr6D 94.221 571 13 2 2511 3062 427867404 427866835 0.000000e+00 854.0
4 TraesCS6D01G351100 chr6D 98.693 306 4 0 2511 2816 57832587 57832892 7.470000e-151 544.0
5 TraesCS6D01G351100 chr6D 81.223 687 118 8 1376 2055 448159824 448159142 7.470000e-151 544.0
6 TraesCS6D01G351100 chr6D 82.840 169 23 5 2124 2290 448430279 448430443 2.460000e-31 147.0
7 TraesCS6D01G351100 chr6B 90.011 1752 99 22 805 2510 678931672 678929951 0.000000e+00 2196.0
8 TraesCS6D01G351100 chr6B 86.457 1174 139 8 962 2119 679285003 679286172 0.000000e+00 1269.0
9 TraesCS6D01G351100 chr6B 86.406 1177 140 8 962 2122 679330399 679329227 0.000000e+00 1269.0
10 TraesCS6D01G351100 chr6B 78.539 1095 188 35 984 2055 679278129 679279199 0.000000e+00 676.0
11 TraesCS6D01G351100 chr6B 94.860 214 9 1 624 837 678932178 678931967 1.760000e-87 333.0
12 TraesCS6D01G351100 chr6B 83.575 207 31 1 1036 1239 678741343 678741137 1.120000e-44 191.0
13 TraesCS6D01G351100 chr6B 86.713 143 17 2 379 520 583282474 583282615 1.140000e-34 158.0
14 TraesCS6D01G351100 chr6B 83.230 161 21 5 2132 2290 679286264 679286420 3.180000e-30 143.0
15 TraesCS6D01G351100 chr6B 83.230 161 21 5 2132 2290 679329138 679328982 3.180000e-30 143.0
16 TraesCS6D01G351100 chr6B 85.345 116 13 2 241 355 469709383 469709495 1.930000e-22 117.0
17 TraesCS6D01G351100 chr6B 84.426 122 12 3 108 223 430553425 430553545 2.500000e-21 113.0
18 TraesCS6D01G351100 chr6A 85.714 1106 135 12 962 2050 594516410 594515311 0.000000e+00 1146.0
19 TraesCS6D01G351100 chr6A 80.000 1095 173 34 984 2055 594520666 594519595 0.000000e+00 767.0
20 TraesCS6D01G351100 chr6A 78.182 1155 208 25 947 2077 594530353 594529219 0.000000e+00 697.0
21 TraesCS6D01G351100 chr6A 87.619 105 9 2 247 351 557557907 557557807 5.360000e-23 119.0
22 TraesCS6D01G351100 chr6A 82.927 123 17 3 234 355 599827807 599827926 1.160000e-19 108.0
23 TraesCS6D01G351100 chr6A 93.617 47 2 1 394 439 536219000 536218954 5.480000e-08 69.4
24 TraesCS6D01G351100 chr1D 95.447 571 7 1 2511 3062 479811444 479812014 0.000000e+00 893.0
25 TraesCS6D01G351100 chr1D 95.271 571 8 1 2511 3062 442326385 442325815 0.000000e+00 887.0
26 TraesCS6D01G351100 chr1D 94.755 572 11 8 2510 3062 241469089 241469660 0.000000e+00 872.0
27 TraesCS6D01G351100 chr1D 91.979 561 19 15 2511 3062 415413057 415412514 0.000000e+00 763.0
28 TraesCS6D01G351100 chr1D 90.625 96 7 1 522 617 32225323 32225416 3.210000e-25 126.0
29 TraesCS6D01G351100 chr1D 82.418 91 8 4 152 237 236040322 236040409 4.240000e-09 73.1
30 TraesCS6D01G351100 chr2D 94.406 572 13 1 2510 3062 555170868 555171439 0.000000e+00 861.0
31 TraesCS6D01G351100 chr2D 87.778 90 10 1 423 512 574349358 574349446 1.500000e-18 104.0
32 TraesCS6D01G351100 chr2D 83.529 85 9 1 158 237 53679718 53679802 1.180000e-09 75.0
33 TraesCS6D01G351100 chrUn 94.241 573 14 3 2509 3062 29137721 29137149 0.000000e+00 857.0
34 TraesCS6D01G351100 chrUn 98.693 306 4 0 2511 2816 29129084 29129389 7.470000e-151 544.0
35 TraesCS6D01G351100 chrUn 85.938 128 16 2 368 493 12291090 12291217 5.330000e-28 135.0
36 TraesCS6D01G351100 chrUn 80.153 131 18 6 522 652 42214083 42214205 1.170000e-14 91.6
37 TraesCS6D01G351100 chr4D 94.056 572 14 2 2510 3062 374048998 374048428 0.000000e+00 850.0
38 TraesCS6D01G351100 chr3D 93.583 561 22 11 2511 3062 550460691 550461246 0.000000e+00 824.0
39 TraesCS6D01G351100 chr3D 82.099 162 24 2 368 524 168185809 168185648 1.920000e-27 134.0
40 TraesCS6D01G351100 chr3D 84.848 132 14 3 106 231 268103869 268103738 8.910000e-26 128.0
41 TraesCS6D01G351100 chr3D 83.206 131 18 2 522 652 612876363 612876237 1.930000e-22 117.0
42 TraesCS6D01G351100 chr3D 86.667 105 8 4 249 352 579047302 579047401 8.970000e-21 111.0
43 TraesCS6D01G351100 chr5D 92.692 561 27 11 2511 3062 502188893 502189448 0.000000e+00 797.0
44 TraesCS6D01G351100 chr5D 90.909 561 24 16 2511 3062 351809315 351809857 0.000000e+00 728.0
45 TraesCS6D01G351100 chr7D 92.513 561 28 11 2511 3062 514672446 514671891 0.000000e+00 791.0
46 TraesCS6D01G351100 chr7D 82.927 164 19 8 368 524 207600854 207601015 4.120000e-29 139.0
47 TraesCS6D01G351100 chr7D 84.545 110 12 3 247 355 497318704 497318809 1.500000e-18 104.0
48 TraesCS6D01G351100 chr2B 87.612 557 46 17 2511 3062 17505377 17505915 2.590000e-175 625.0
49 TraesCS6D01G351100 chr2B 84.733 131 16 2 522 652 593683167 593683293 8.910000e-26 128.0
50 TraesCS6D01G351100 chr2B 83.582 134 18 2 522 655 118067307 118067178 4.150000e-24 122.0
51 TraesCS6D01G351100 chr2B 83.333 138 17 3 91 222 551252515 551252378 4.150000e-24 122.0
52 TraesCS6D01G351100 chr2B 81.379 145 17 8 522 662 161696222 161696360 3.230000e-20 110.0
53 TraesCS6D01G351100 chr1B 88.971 136 7 4 107 235 82315126 82314992 8.790000e-36 161.0
54 TraesCS6D01G351100 chr7B 86.923 130 12 2 99 223 606358756 606358627 1.140000e-29 141.0
55 TraesCS6D01G351100 chr7B 80.952 147 17 9 102 240 263288321 263288178 4.180000e-19 106.0
56 TraesCS6D01G351100 chr2A 83.660 153 13 6 89 229 112224137 112224289 1.920000e-27 134.0
57 TraesCS6D01G351100 chr2A 81.290 155 26 3 367 520 205256461 205256613 4.150000e-24 122.0
58 TraesCS6D01G351100 chr7A 83.688 141 19 2 522 662 34972439 34972303 2.480000e-26 130.0
59 TraesCS6D01G351100 chr7A 84.252 127 14 3 110 231 648679255 648679380 5.360000e-23 119.0
60 TraesCS6D01G351100 chr7A 85.981 107 10 3 247 352 63409507 63409609 3.230000e-20 110.0
61 TraesCS6D01G351100 chr7A 100.000 28 0 0 485 512 265008372 265008345 6.000000e-03 52.8
62 TraesCS6D01G351100 chr4A 86.777 121 11 2 108 223 374365170 374365050 2.480000e-26 130.0
63 TraesCS6D01G351100 chr4A 85.246 122 12 4 248 366 696725813 696725931 1.490000e-23 121.0
64 TraesCS6D01G351100 chr3B 82.979 141 19 3 522 662 687075862 687075727 4.150000e-24 122.0
65 TraesCS6D01G351100 chr3B 85.088 114 15 2 419 530 22430204 22430091 6.940000e-22 115.0
66 TraesCS6D01G351100 chr3B 78.082 146 30 2 368 512 761641007 761641151 1.170000e-14 91.6
67 TraesCS6D01G351100 chr5B 83.740 123 12 6 247 366 35428598 35428481 3.230000e-20 110.0
68 TraesCS6D01G351100 chr5B 85.455 110 11 3 247 355 633769853 633769958 3.230000e-20 110.0
69 TraesCS6D01G351100 chr3A 82.955 88 12 3 368 453 745576879 745576793 3.270000e-10 76.8


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 TraesCS6D01G351100 chr6D 448484536 448487597 3061 False 5655.0 5655 100.0000 1 3062 1 chr6D.!!$F2 3061
1 TraesCS6D01G351100 chr6D 448057952 448060056 2104 True 3169.0 3169 93.6600 367 2510 1 chr6D.!!$R2 2143
2 TraesCS6D01G351100 chr6D 427866835 427867404 569 True 854.0 854 94.2210 2511 3062 1 chr6D.!!$R1 551
3 TraesCS6D01G351100 chr6D 448429029 448430443 1414 False 705.5 1264 84.6230 962 2290 2 chr6D.!!$F3 1328
4 TraesCS6D01G351100 chr6D 448159142 448159824 682 True 544.0 544 81.2230 1376 2055 1 chr6D.!!$R3 679
5 TraesCS6D01G351100 chr6B 678929951 678932178 2227 True 1264.5 2196 92.4355 624 2510 2 chr6B.!!$R2 1886
6 TraesCS6D01G351100 chr6B 679285003 679286420 1417 False 706.0 1269 84.8435 962 2290 2 chr6B.!!$F5 1328
7 TraesCS6D01G351100 chr6B 679328982 679330399 1417 True 706.0 1269 84.8180 962 2290 2 chr6B.!!$R3 1328
8 TraesCS6D01G351100 chr6B 679278129 679279199 1070 False 676.0 676 78.5390 984 2055 1 chr6B.!!$F4 1071
9 TraesCS6D01G351100 chr6A 594515311 594520666 5355 True 956.5 1146 82.8570 962 2055 2 chr6A.!!$R4 1093
10 TraesCS6D01G351100 chr6A 594529219 594530353 1134 True 697.0 697 78.1820 947 2077 1 chr6A.!!$R3 1130
11 TraesCS6D01G351100 chr1D 479811444 479812014 570 False 893.0 893 95.4470 2511 3062 1 chr1D.!!$F4 551
12 TraesCS6D01G351100 chr1D 442325815 442326385 570 True 887.0 887 95.2710 2511 3062 1 chr1D.!!$R2 551
13 TraesCS6D01G351100 chr1D 241469089 241469660 571 False 872.0 872 94.7550 2510 3062 1 chr1D.!!$F3 552
14 TraesCS6D01G351100 chr1D 415412514 415413057 543 True 763.0 763 91.9790 2511 3062 1 chr1D.!!$R1 551
15 TraesCS6D01G351100 chr2D 555170868 555171439 571 False 861.0 861 94.4060 2510 3062 1 chr2D.!!$F2 552
16 TraesCS6D01G351100 chrUn 29137149 29137721 572 True 857.0 857 94.2410 2509 3062 1 chrUn.!!$R1 553
17 TraesCS6D01G351100 chr4D 374048428 374048998 570 True 850.0 850 94.0560 2510 3062 1 chr4D.!!$R1 552
18 TraesCS6D01G351100 chr3D 550460691 550461246 555 False 824.0 824 93.5830 2511 3062 1 chr3D.!!$F1 551
19 TraesCS6D01G351100 chr5D 502188893 502189448 555 False 797.0 797 92.6920 2511 3062 1 chr5D.!!$F2 551
20 TraesCS6D01G351100 chr5D 351809315 351809857 542 False 728.0 728 90.9090 2511 3062 1 chr5D.!!$F1 551
21 TraesCS6D01G351100 chr7D 514671891 514672446 555 True 791.0 791 92.5130 2511 3062 1 chr7D.!!$R1 551
22 TraesCS6D01G351100 chr2B 17505377 17505915 538 False 625.0 625 87.6120 2511 3062 1 chr2B.!!$F1 551

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
199 200 0.248661 CATACTGTGACGCCCGAGAG 60.249 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 5471 0.037605 CTTCCCGGTTAGTTCGCACT 60.038 55.0 0.0 0.0 36.99 4.4 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.136695 CTGAGCTAGCTCTGTTGGAGG 59.863 57.143 37.42 17.29 43.12 4.30
31 32 3.686916 GCTCTGTTGGAGGTAGTCTTT 57.313 47.619 0.00 0.00 42.08 2.52
33 34 3.866449 GCTCTGTTGGAGGTAGTCTTTGG 60.866 52.174 0.00 0.00 42.08 3.28
35 36 1.073284 TGTTGGAGGTAGTCTTTGGCC 59.927 52.381 0.00 0.00 0.00 5.36
36 37 1.351350 GTTGGAGGTAGTCTTTGGCCT 59.649 52.381 3.32 0.00 0.00 5.19
39 40 1.574263 GAGGTAGTCTTTGGCCTCCT 58.426 55.000 3.32 0.00 41.08 3.69
40 41 1.909986 GAGGTAGTCTTTGGCCTCCTT 59.090 52.381 3.32 0.00 41.08 3.36
41 42 2.306219 GAGGTAGTCTTTGGCCTCCTTT 59.694 50.000 3.32 0.00 41.08 3.11
42 43 2.306219 AGGTAGTCTTTGGCCTCCTTTC 59.694 50.000 3.32 0.00 0.00 2.62
43 44 2.306219 GGTAGTCTTTGGCCTCCTTTCT 59.694 50.000 3.32 0.00 0.00 2.52
44 45 2.575805 AGTCTTTGGCCTCCTTTCTG 57.424 50.000 3.32 0.00 0.00 3.02
45 46 1.074566 AGTCTTTGGCCTCCTTTCTGG 59.925 52.381 3.32 0.00 37.10 3.86
50 51 2.044551 GCCTCCTTTCTGGGCCTG 60.045 66.667 4.53 4.06 39.96 4.85
52 53 1.925455 CCTCCTTTCTGGGCCTGGA 60.925 63.158 10.79 0.00 36.20 3.86
55 56 0.549902 TCCTTTCTGGGCCTGGATCA 60.550 55.000 10.79 0.00 36.20 2.92
56 57 0.394899 CCTTTCTGGGCCTGGATCAC 60.395 60.000 10.79 0.00 0.00 3.06
57 58 0.745845 CTTTCTGGGCCTGGATCACG 60.746 60.000 10.79 0.00 0.00 4.35
58 59 2.196997 TTTCTGGGCCTGGATCACGG 62.197 60.000 10.79 0.00 0.00 4.94
59 60 3.402681 CTGGGCCTGGATCACGGT 61.403 66.667 4.53 0.00 0.00 4.83
60 61 3.391665 CTGGGCCTGGATCACGGTC 62.392 68.421 4.53 0.00 0.00 4.79
61 62 4.530857 GGGCCTGGATCACGGTCG 62.531 72.222 0.84 0.00 0.00 4.79
64 65 4.530857 CCTGGATCACGGTCGGCC 62.531 72.222 0.00 0.00 0.00 6.13
83 84 2.853731 CGGAAGGCTACAGTAGTCAG 57.146 55.000 14.74 0.00 31.34 3.51
85 86 2.952978 CGGAAGGCTACAGTAGTCAGAT 59.047 50.000 14.74 0.12 31.34 2.90
87 88 4.211920 GGAAGGCTACAGTAGTCAGATCT 58.788 47.826 14.74 0.00 31.34 2.75
88 89 5.378332 GGAAGGCTACAGTAGTCAGATCTA 58.622 45.833 14.74 0.00 31.34 1.98
89 90 5.828859 GGAAGGCTACAGTAGTCAGATCTAA 59.171 44.000 14.74 0.00 31.34 2.10
90 91 6.016610 GGAAGGCTACAGTAGTCAGATCTAAG 60.017 46.154 14.74 0.00 31.34 2.18
91 92 5.381757 AGGCTACAGTAGTCAGATCTAAGG 58.618 45.833 14.74 0.00 31.34 2.69
92 93 5.132985 AGGCTACAGTAGTCAGATCTAAGGA 59.867 44.000 14.74 0.00 31.34 3.36
94 95 6.072175 GGCTACAGTAGTCAGATCTAAGGATG 60.072 46.154 7.36 0.00 31.46 3.51
95 96 6.488683 GCTACAGTAGTCAGATCTAAGGATGT 59.511 42.308 9.42 0.00 31.46 3.06
96 97 6.707440 ACAGTAGTCAGATCTAAGGATGTG 57.293 41.667 0.00 0.00 42.43 3.21
98 99 4.586841 AGTAGTCAGATCTAAGGATGTGCC 59.413 45.833 0.00 0.00 41.31 5.01
99 100 2.363680 AGTCAGATCTAAGGATGTGCCG 59.636 50.000 0.00 0.00 41.31 5.69
100 101 2.362397 GTCAGATCTAAGGATGTGCCGA 59.638 50.000 0.00 0.00 41.31 5.54
102 103 1.689273 AGATCTAAGGATGTGCCGACC 59.311 52.381 0.00 0.00 43.43 4.79
103 104 0.759346 ATCTAAGGATGTGCCGACCC 59.241 55.000 0.00 0.00 43.43 4.46
104 105 1.146263 CTAAGGATGTGCCGACCCC 59.854 63.158 0.00 0.00 43.43 4.95
105 106 1.613928 TAAGGATGTGCCGACCCCA 60.614 57.895 0.00 0.00 43.43 4.96
106 107 1.202099 TAAGGATGTGCCGACCCCAA 61.202 55.000 0.00 0.00 43.43 4.12
107 108 2.034999 GGATGTGCCGACCCCAAA 59.965 61.111 0.00 0.00 0.00 3.28
108 109 1.379843 GGATGTGCCGACCCCAAAT 60.380 57.895 0.00 0.00 0.00 2.32
109 110 0.970427 GGATGTGCCGACCCCAAATT 60.970 55.000 0.00 0.00 0.00 1.82
110 111 1.683629 GGATGTGCCGACCCCAAATTA 60.684 52.381 0.00 0.00 0.00 1.40
111 112 1.676006 GATGTGCCGACCCCAAATTAG 59.324 52.381 0.00 0.00 0.00 1.73
112 113 0.402504 TGTGCCGACCCCAAATTAGT 59.597 50.000 0.00 0.00 0.00 2.24
113 114 1.629353 TGTGCCGACCCCAAATTAGTA 59.371 47.619 0.00 0.00 0.00 1.82
114 115 2.011947 GTGCCGACCCCAAATTAGTAC 58.988 52.381 0.00 0.00 0.00 2.73
116 117 1.748244 GCCGACCCCAAATTAGTACCC 60.748 57.143 0.00 0.00 0.00 3.69
117 118 1.841919 CCGACCCCAAATTAGTACCCT 59.158 52.381 0.00 0.00 0.00 4.34
118 119 2.240414 CCGACCCCAAATTAGTACCCTT 59.760 50.000 0.00 0.00 0.00 3.95
119 120 3.538591 CGACCCCAAATTAGTACCCTTC 58.461 50.000 0.00 0.00 0.00 3.46
120 121 3.538591 GACCCCAAATTAGTACCCTTCG 58.461 50.000 0.00 0.00 0.00 3.79
121 122 2.914941 ACCCCAAATTAGTACCCTTCGT 59.085 45.455 0.00 0.00 0.00 3.85
122 123 3.331591 ACCCCAAATTAGTACCCTTCGTT 59.668 43.478 0.00 0.00 0.00 3.85
123 124 4.202599 ACCCCAAATTAGTACCCTTCGTTT 60.203 41.667 0.00 0.00 0.00 3.60
124 125 5.014018 ACCCCAAATTAGTACCCTTCGTTTA 59.986 40.000 0.00 0.00 0.00 2.01
125 126 6.124340 CCCCAAATTAGTACCCTTCGTTTAT 58.876 40.000 0.00 0.00 0.00 1.40
126 127 7.092489 ACCCCAAATTAGTACCCTTCGTTTATA 60.092 37.037 0.00 0.00 0.00 0.98
128 129 9.346005 CCCAAATTAGTACCCTTCGTTTATATT 57.654 33.333 0.00 0.00 0.00 1.28
181 182 8.942338 ACGTATTATTACATGAGAAGAAAGCA 57.058 30.769 0.00 0.00 0.00 3.91
182 183 9.547753 ACGTATTATTACATGAGAAGAAAGCAT 57.452 29.630 0.00 0.00 0.00 3.79
187 188 9.890629 TTATTACATGAGAAGAAAGCATACTGT 57.109 29.630 0.00 0.00 0.00 3.55
190 191 5.641209 ACATGAGAAGAAAGCATACTGTGAC 59.359 40.000 0.00 0.00 0.00 3.67
191 192 4.237724 TGAGAAGAAAGCATACTGTGACG 58.762 43.478 0.00 0.00 0.00 4.35
192 193 2.996621 AGAAGAAAGCATACTGTGACGC 59.003 45.455 0.00 0.00 0.00 5.19
194 195 0.727398 GAAAGCATACTGTGACGCCC 59.273 55.000 0.00 0.00 0.00 6.13
195 196 1.019278 AAAGCATACTGTGACGCCCG 61.019 55.000 0.00 0.00 0.00 6.13
196 197 1.884075 AAGCATACTGTGACGCCCGA 61.884 55.000 0.00 0.00 0.00 5.14
197 198 1.878522 GCATACTGTGACGCCCGAG 60.879 63.158 0.00 0.00 0.00 4.63
198 199 1.807226 CATACTGTGACGCCCGAGA 59.193 57.895 0.00 0.00 0.00 4.04
199 200 0.248661 CATACTGTGACGCCCGAGAG 60.249 60.000 0.00 0.00 0.00 3.20
201 202 1.303799 TACTGTGACGCCCGAGAGAC 61.304 60.000 0.00 0.00 0.00 3.36
202 203 2.282251 TGTGACGCCCGAGAGACT 60.282 61.111 0.00 0.00 0.00 3.24
203 204 2.259875 CTGTGACGCCCGAGAGACTC 62.260 65.000 0.00 0.00 0.00 3.36
204 205 2.033602 TGACGCCCGAGAGACTCA 59.966 61.111 5.02 0.00 0.00 3.41
205 206 1.602605 TGACGCCCGAGAGACTCAA 60.603 57.895 5.02 0.00 0.00 3.02
206 207 1.153997 GACGCCCGAGAGACTCAAC 60.154 63.158 5.02 0.00 0.00 3.18
208 209 2.579738 GCCCGAGAGACTCAACCC 59.420 66.667 5.02 0.00 0.00 4.11
209 210 2.885861 CCCGAGAGACTCAACCCG 59.114 66.667 5.02 2.79 0.00 5.28
210 211 1.977544 CCCGAGAGACTCAACCCGT 60.978 63.158 5.02 0.00 0.00 5.28
213 214 1.867919 CGAGAGACTCAACCCGTGCT 61.868 60.000 5.02 0.00 0.00 4.40
214 215 0.318762 GAGAGACTCAACCCGTGCTT 59.681 55.000 5.02 0.00 0.00 3.91
215 216 0.759346 AGAGACTCAACCCGTGCTTT 59.241 50.000 5.02 0.00 0.00 3.51
216 217 1.968493 AGAGACTCAACCCGTGCTTTA 59.032 47.619 5.02 0.00 0.00 1.85
217 218 2.567615 AGAGACTCAACCCGTGCTTTAT 59.432 45.455 5.02 0.00 0.00 1.40
218 219 3.008049 AGAGACTCAACCCGTGCTTTATT 59.992 43.478 5.02 0.00 0.00 1.40
219 220 4.222145 AGAGACTCAACCCGTGCTTTATTA 59.778 41.667 5.02 0.00 0.00 0.98
220 221 5.099042 AGACTCAACCCGTGCTTTATTAT 57.901 39.130 0.00 0.00 0.00 1.28
221 222 5.497474 AGACTCAACCCGTGCTTTATTATT 58.503 37.500 0.00 0.00 0.00 1.40
222 223 6.646267 AGACTCAACCCGTGCTTTATTATTA 58.354 36.000 0.00 0.00 0.00 0.98
225 226 5.127491 TCAACCCGTGCTTTATTATTAGGG 58.873 41.667 0.00 0.00 43.03 3.53
226 227 5.104444 TCAACCCGTGCTTTATTATTAGGGA 60.104 40.000 4.00 0.00 39.95 4.20
227 228 5.376756 ACCCGTGCTTTATTATTAGGGAA 57.623 39.130 4.00 0.00 39.95 3.97
228 229 5.757988 ACCCGTGCTTTATTATTAGGGAAA 58.242 37.500 4.00 0.00 39.95 3.13
229 230 5.826208 ACCCGTGCTTTATTATTAGGGAAAG 59.174 40.000 4.00 0.00 39.95 2.62
230 231 6.059484 CCCGTGCTTTATTATTAGGGAAAGA 58.941 40.000 0.00 0.00 39.95 2.52
232 233 7.881232 CCCGTGCTTTATTATTAGGGAAAGATA 59.119 37.037 0.00 0.00 39.95 1.98
246 247 7.489239 AGGGAAAGATATATAGTTCCTCAGC 57.511 40.000 19.31 8.65 39.63 4.26
247 248 7.252678 AGGGAAAGATATATAGTTCCTCAGCT 58.747 38.462 19.31 10.13 39.63 4.24
248 249 7.737149 AGGGAAAGATATATAGTTCCTCAGCTT 59.263 37.037 19.31 0.40 39.63 3.74
250 251 9.785982 GGAAAGATATATAGTTCCTCAGCTTTT 57.214 33.333 15.29 0.00 37.21 2.27
260 261 5.046304 AGTTCCTCAGCTTTTATAGTCTGCA 60.046 40.000 0.00 0.00 31.88 4.41
262 263 6.731292 TCCTCAGCTTTTATAGTCTGCATA 57.269 37.500 0.00 0.00 31.88 3.14
263 264 7.308450 TCCTCAGCTTTTATAGTCTGCATAT 57.692 36.000 0.00 0.00 31.88 1.78
264 265 8.422577 TCCTCAGCTTTTATAGTCTGCATATA 57.577 34.615 0.00 0.00 31.88 0.86
265 266 8.870116 TCCTCAGCTTTTATAGTCTGCATATAA 58.130 33.333 0.00 0.00 31.88 0.98
266 267 9.664332 CCTCAGCTTTTATAGTCTGCATATAAT 57.336 33.333 0.00 0.00 31.88 1.28
290 291 6.966435 ATTTTGTCAAAGTCAAACCTTGTG 57.034 33.333 0.00 0.00 35.05 3.33
291 292 5.713792 TTTGTCAAAGTCAAACCTTGTGA 57.286 34.783 0.00 0.00 31.17 3.58
292 293 5.713792 TTGTCAAAGTCAAACCTTGTGAA 57.286 34.783 0.00 0.00 0.00 3.18
293 294 5.713792 TGTCAAAGTCAAACCTTGTGAAA 57.286 34.783 0.00 0.00 0.00 2.69
294 295 6.279513 TGTCAAAGTCAAACCTTGTGAAAT 57.720 33.333 0.00 0.00 0.00 2.17
296 297 7.158021 TGTCAAAGTCAAACCTTGTGAAATTT 58.842 30.769 0.00 0.00 0.00 1.82
297 298 7.117523 TGTCAAAGTCAAACCTTGTGAAATTTG 59.882 33.333 0.00 0.00 36.36 2.32
299 300 4.441792 AGTCAAACCTTGTGAAATTTGCC 58.558 39.130 0.00 0.00 33.09 4.52
300 301 4.162131 AGTCAAACCTTGTGAAATTTGCCT 59.838 37.500 0.00 0.00 33.09 4.75
301 302 5.362430 AGTCAAACCTTGTGAAATTTGCCTA 59.638 36.000 0.00 0.00 33.09 3.93
302 303 6.045955 GTCAAACCTTGTGAAATTTGCCTAA 58.954 36.000 0.00 0.00 33.09 2.69
303 304 6.705825 GTCAAACCTTGTGAAATTTGCCTAAT 59.294 34.615 0.00 0.00 33.09 1.73
304 305 7.870445 GTCAAACCTTGTGAAATTTGCCTAATA 59.130 33.333 0.00 0.00 33.09 0.98
305 306 8.424918 TCAAACCTTGTGAAATTTGCCTAATAA 58.575 29.630 0.00 0.00 33.09 1.40
306 307 8.495148 CAAACCTTGTGAAATTTGCCTAATAAC 58.505 33.333 0.00 0.00 0.00 1.89
307 308 7.539034 ACCTTGTGAAATTTGCCTAATAACT 57.461 32.000 0.00 0.00 0.00 2.24
308 309 7.962441 ACCTTGTGAAATTTGCCTAATAACTT 58.038 30.769 0.00 0.00 0.00 2.66
309 310 8.428852 ACCTTGTGAAATTTGCCTAATAACTTT 58.571 29.630 0.00 0.00 0.00 2.66
310 311 9.921637 CCTTGTGAAATTTGCCTAATAACTTTA 57.078 29.630 0.00 0.00 0.00 1.85
509 511 9.316730 ACAAATCTTATACGCGGAGTAAAAATA 57.683 29.630 12.47 0.00 39.04 1.40
519 521 5.685511 CGCGGAGTAAAAATAAATGAATGGG 59.314 40.000 0.00 0.00 0.00 4.00
535 537 5.445069 TGAATGGGGTATCAAAGTACATGG 58.555 41.667 0.00 0.00 0.00 3.66
698 700 6.072563 GCCTAAAAACACGTTTGGGTTATCTA 60.073 38.462 2.58 0.00 40.34 1.98
1428 4761 3.995048 CCAAGAACCTAAAGAACGACTCC 59.005 47.826 0.00 0.00 0.00 3.85
1474 4807 3.707458 TCCATGGTTACCGCGCCA 61.707 61.111 12.58 2.29 39.33 5.69
1777 5125 1.768275 TGCACAAGGAAGAGGAAGACA 59.232 47.619 0.00 0.00 0.00 3.41
1833 5181 2.361104 GACATGGGGCGGCTGAAA 60.361 61.111 9.56 0.00 0.00 2.69
2102 5451 3.868077 GTGGTAATGAGCTAGCTGTCTTG 59.132 47.826 24.99 0.00 0.00 3.02
2122 5471 1.438651 GACTCGGTACATTGCTGCAA 58.561 50.000 18.43 18.43 0.00 4.08
2126 5554 0.454957 CGGTACATTGCTGCAAGTGC 60.455 55.000 20.72 18.84 42.50 4.40
2231 5665 8.988934 GGTTTATTGTCATCAGATATTTCGCTA 58.011 33.333 0.00 0.00 0.00 4.26
2258 5695 7.953005 TTTAGCATCAATCTTCCATGGTTTA 57.047 32.000 12.58 0.00 30.99 2.01
2281 5718 2.706339 ATGTCATGGCTTCAGGTCTC 57.294 50.000 0.00 0.00 0.00 3.36
2363 5800 6.036735 TGTTATTATCACTTAGTTCTTGCGCC 59.963 38.462 4.18 0.00 0.00 6.53
2551 5988 2.967201 CCATAATTGGGGCATCACATGT 59.033 45.455 0.00 0.00 39.56 3.21
2826 6287 1.153939 CTCACTCGCTCGAACCCTG 60.154 63.158 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.189752 CCTCCAACAGAGCTAGCTCA 58.810 55.000 38.86 20.87 44.99 4.26
6 7 2.291930 ACTACCTCCAACAGAGCTAGCT 60.292 50.000 19.45 19.45 41.74 3.32
7 8 2.100087 GACTACCTCCAACAGAGCTAGC 59.900 54.545 6.62 6.62 41.74 3.42
8 9 3.626930 AGACTACCTCCAACAGAGCTAG 58.373 50.000 0.00 0.00 41.74 3.42
9 10 3.741245 AGACTACCTCCAACAGAGCTA 57.259 47.619 0.00 0.00 41.74 3.32
11 12 3.330267 CAAAGACTACCTCCAACAGAGC 58.670 50.000 0.00 0.00 41.74 4.09
12 13 3.866449 GCCAAAGACTACCTCCAACAGAG 60.866 52.174 0.00 0.00 42.83 3.35
13 14 2.038557 GCCAAAGACTACCTCCAACAGA 59.961 50.000 0.00 0.00 0.00 3.41
14 15 2.427506 GCCAAAGACTACCTCCAACAG 58.572 52.381 0.00 0.00 0.00 3.16
15 16 1.073284 GGCCAAAGACTACCTCCAACA 59.927 52.381 0.00 0.00 0.00 3.33
16 17 1.351350 AGGCCAAAGACTACCTCCAAC 59.649 52.381 5.01 0.00 0.00 3.77
17 18 1.628846 GAGGCCAAAGACTACCTCCAA 59.371 52.381 5.01 0.00 42.44 3.53
21 22 2.046280 AAGGAGGCCAAAGACTACCT 57.954 50.000 5.01 0.00 34.43 3.08
23 24 3.339141 CAGAAAGGAGGCCAAAGACTAC 58.661 50.000 5.01 0.00 0.00 2.73
24 25 2.305927 CCAGAAAGGAGGCCAAAGACTA 59.694 50.000 5.01 0.00 41.22 2.59
25 26 1.074566 CCAGAAAGGAGGCCAAAGACT 59.925 52.381 5.01 0.00 41.22 3.24
26 27 1.539157 CCAGAAAGGAGGCCAAAGAC 58.461 55.000 5.01 0.00 41.22 3.01
27 28 0.405585 CCCAGAAAGGAGGCCAAAGA 59.594 55.000 5.01 0.00 41.22 2.52
29 30 1.228862 GCCCAGAAAGGAGGCCAAA 60.229 57.895 5.01 0.00 41.00 3.28
30 31 2.440599 GCCCAGAAAGGAGGCCAA 59.559 61.111 5.01 0.00 41.00 4.52
33 34 2.044551 CAGGCCCAGAAAGGAGGC 60.045 66.667 0.00 0.00 46.37 4.70
35 36 0.182299 GATCCAGGCCCAGAAAGGAG 59.818 60.000 0.00 0.00 41.22 3.69
36 37 0.549902 TGATCCAGGCCCAGAAAGGA 60.550 55.000 0.00 0.00 41.22 3.36
38 39 0.745845 CGTGATCCAGGCCCAGAAAG 60.746 60.000 0.00 0.00 0.00 2.62
39 40 1.299648 CGTGATCCAGGCCCAGAAA 59.700 57.895 0.00 0.00 0.00 2.52
40 41 2.669133 CCGTGATCCAGGCCCAGAA 61.669 63.158 0.00 0.00 0.00 3.02
41 42 3.083349 CCGTGATCCAGGCCCAGA 61.083 66.667 0.00 0.00 0.00 3.86
42 43 3.391665 GACCGTGATCCAGGCCCAG 62.392 68.421 0.00 0.00 0.00 4.45
43 44 3.399181 GACCGTGATCCAGGCCCA 61.399 66.667 0.00 0.00 0.00 5.36
44 45 4.530857 CGACCGTGATCCAGGCCC 62.531 72.222 0.00 0.00 0.00 5.80
45 46 4.530857 CCGACCGTGATCCAGGCC 62.531 72.222 0.00 0.00 0.00 5.19
47 48 4.530857 GGCCGACCGTGATCCAGG 62.531 72.222 0.00 2.36 0.00 4.45
63 64 1.405821 CTGACTACTGTAGCCTTCCGG 59.594 57.143 14.55 0.00 0.00 5.14
64 65 2.366533 TCTGACTACTGTAGCCTTCCG 58.633 52.381 14.55 2.53 0.00 4.30
66 67 6.016610 CCTTAGATCTGACTACTGTAGCCTTC 60.017 46.154 14.55 5.94 0.00 3.46
67 68 5.830991 CCTTAGATCTGACTACTGTAGCCTT 59.169 44.000 14.55 0.00 0.00 4.35
69 70 5.378332 TCCTTAGATCTGACTACTGTAGCC 58.622 45.833 14.55 4.40 0.00 3.93
70 71 6.488683 ACATCCTTAGATCTGACTACTGTAGC 59.511 42.308 14.55 8.25 0.00 3.58
71 72 7.521423 GCACATCCTTAGATCTGACTACTGTAG 60.521 44.444 13.13 13.13 0.00 2.74
72 73 6.263392 GCACATCCTTAGATCTGACTACTGTA 59.737 42.308 5.18 0.00 0.00 2.74
73 74 5.068460 GCACATCCTTAGATCTGACTACTGT 59.932 44.000 5.18 0.00 0.00 3.55
74 75 5.508825 GGCACATCCTTAGATCTGACTACTG 60.509 48.000 5.18 0.00 0.00 2.74
75 76 4.586841 GGCACATCCTTAGATCTGACTACT 59.413 45.833 5.18 0.00 0.00 2.57
77 78 3.570125 CGGCACATCCTTAGATCTGACTA 59.430 47.826 5.18 0.00 24.63 2.59
78 79 2.363680 CGGCACATCCTTAGATCTGACT 59.636 50.000 5.18 0.00 24.63 3.41
79 80 2.362397 TCGGCACATCCTTAGATCTGAC 59.638 50.000 5.18 0.00 0.00 3.51
80 81 2.362397 GTCGGCACATCCTTAGATCTGA 59.638 50.000 5.18 0.00 0.00 3.27
81 82 2.546795 GGTCGGCACATCCTTAGATCTG 60.547 54.545 5.18 0.00 0.00 2.90
82 83 1.689273 GGTCGGCACATCCTTAGATCT 59.311 52.381 0.00 0.00 0.00 2.75
83 84 1.270358 GGGTCGGCACATCCTTAGATC 60.270 57.143 0.00 0.00 0.00 2.75
85 86 1.335132 GGGGTCGGCACATCCTTAGA 61.335 60.000 0.00 0.00 0.00 2.10
87 88 1.202099 TTGGGGTCGGCACATCCTTA 61.202 55.000 0.00 0.00 0.00 2.69
88 89 2.075355 TTTGGGGTCGGCACATCCTT 62.075 55.000 0.00 0.00 0.00 3.36
89 90 1.863155 ATTTGGGGTCGGCACATCCT 61.863 55.000 0.00 0.00 0.00 3.24
90 91 0.970427 AATTTGGGGTCGGCACATCC 60.970 55.000 0.00 0.00 0.00 3.51
91 92 1.676006 CTAATTTGGGGTCGGCACATC 59.324 52.381 0.00 0.00 0.00 3.06
92 93 1.005450 ACTAATTTGGGGTCGGCACAT 59.995 47.619 0.00 0.00 0.00 3.21
94 95 2.011947 GTACTAATTTGGGGTCGGCAC 58.988 52.381 0.00 0.00 0.00 5.01
95 96 1.065272 GGTACTAATTTGGGGTCGGCA 60.065 52.381 0.00 0.00 0.00 5.69
96 97 1.671979 GGTACTAATTTGGGGTCGGC 58.328 55.000 0.00 0.00 0.00 5.54
98 99 3.538591 GAAGGGTACTAATTTGGGGTCG 58.461 50.000 0.00 0.00 0.00 4.79
99 100 3.054875 ACGAAGGGTACTAATTTGGGGTC 60.055 47.826 0.00 0.00 0.00 4.46
100 101 2.914941 ACGAAGGGTACTAATTTGGGGT 59.085 45.455 0.00 0.00 0.00 4.95
102 103 8.913487 ATATAAACGAAGGGTACTAATTTGGG 57.087 34.615 0.00 0.00 0.00 4.12
155 156 9.378551 TGCTTTCTTCTCATGTAATAATACGTT 57.621 29.630 0.00 0.00 34.60 3.99
156 157 8.942338 TGCTTTCTTCTCATGTAATAATACGT 57.058 30.769 0.00 0.00 34.60 3.57
163 164 8.043113 TCACAGTATGCTTTCTTCTCATGTAAT 58.957 33.333 0.00 0.00 42.53 1.89
164 165 7.331934 GTCACAGTATGCTTTCTTCTCATGTAA 59.668 37.037 0.00 0.00 42.53 2.41
166 167 5.641209 GTCACAGTATGCTTTCTTCTCATGT 59.359 40.000 0.00 0.00 42.53 3.21
167 168 5.220359 CGTCACAGTATGCTTTCTTCTCATG 60.220 44.000 0.00 0.00 42.53 3.07
168 169 4.867047 CGTCACAGTATGCTTTCTTCTCAT 59.133 41.667 0.00 0.00 42.53 2.90
169 170 4.237724 CGTCACAGTATGCTTTCTTCTCA 58.762 43.478 0.00 0.00 42.53 3.27
171 172 2.996621 GCGTCACAGTATGCTTTCTTCT 59.003 45.455 0.00 0.00 42.53 2.85
172 173 2.094417 GGCGTCACAGTATGCTTTCTTC 59.906 50.000 0.00 0.00 42.53 2.87
173 174 2.076863 GGCGTCACAGTATGCTTTCTT 58.923 47.619 0.00 0.00 42.53 2.52
175 176 0.727398 GGGCGTCACAGTATGCTTTC 59.273 55.000 0.00 0.00 42.53 2.62
176 177 1.019278 CGGGCGTCACAGTATGCTTT 61.019 55.000 0.00 0.00 42.53 3.51
177 178 1.447838 CGGGCGTCACAGTATGCTT 60.448 57.895 0.00 0.00 42.53 3.91
178 179 2.184322 CGGGCGTCACAGTATGCT 59.816 61.111 0.00 0.00 42.53 3.79
179 180 1.878522 CTCGGGCGTCACAGTATGC 60.879 63.158 0.00 0.00 42.53 3.14
180 181 0.248661 CTCTCGGGCGTCACAGTATG 60.249 60.000 0.00 0.00 46.00 2.39
181 182 0.393944 TCTCTCGGGCGTCACAGTAT 60.394 55.000 0.00 0.00 0.00 2.12
182 183 1.002990 TCTCTCGGGCGTCACAGTA 60.003 57.895 0.00 0.00 0.00 2.74
183 184 2.282251 TCTCTCGGGCGTCACAGT 60.282 61.111 0.00 0.00 0.00 3.55
184 185 2.179517 GTCTCTCGGGCGTCACAG 59.820 66.667 0.00 0.00 0.00 3.66
185 186 2.282251 AGTCTCTCGGGCGTCACA 60.282 61.111 0.00 0.00 0.00 3.58
186 187 1.863662 TTGAGTCTCTCGGGCGTCAC 61.864 60.000 0.65 0.00 32.35 3.67
187 188 1.602605 TTGAGTCTCTCGGGCGTCA 60.603 57.895 0.65 0.00 32.35 4.35
190 191 2.182030 GGTTGAGTCTCTCGGGCG 59.818 66.667 0.65 0.00 32.35 6.13
191 192 2.579738 GGGTTGAGTCTCTCGGGC 59.420 66.667 0.65 0.00 32.35 6.13
192 193 1.977544 ACGGGTTGAGTCTCTCGGG 60.978 63.158 11.47 0.00 32.35 5.14
194 195 1.444553 GCACGGGTTGAGTCTCTCG 60.445 63.158 0.65 6.62 32.35 4.04
195 196 0.318762 AAGCACGGGTTGAGTCTCTC 59.681 55.000 0.65 0.00 0.00 3.20
196 197 0.759346 AAAGCACGGGTTGAGTCTCT 59.241 50.000 0.65 0.00 0.00 3.10
197 198 2.450609 TAAAGCACGGGTTGAGTCTC 57.549 50.000 0.00 0.00 0.00 3.36
198 199 3.418684 AATAAAGCACGGGTTGAGTCT 57.581 42.857 0.00 0.00 0.00 3.24
199 200 5.813080 AATAATAAAGCACGGGTTGAGTC 57.187 39.130 0.00 0.00 0.00 3.36
201 202 5.238650 CCCTAATAATAAAGCACGGGTTGAG 59.761 44.000 0.00 0.00 0.00 3.02
202 203 5.104444 TCCCTAATAATAAAGCACGGGTTGA 60.104 40.000 0.00 0.00 0.00 3.18
203 204 5.127491 TCCCTAATAATAAAGCACGGGTTG 58.873 41.667 0.00 0.00 0.00 3.77
204 205 5.376756 TCCCTAATAATAAAGCACGGGTT 57.623 39.130 0.00 0.00 0.00 4.11
205 206 5.376756 TTCCCTAATAATAAAGCACGGGT 57.623 39.130 0.00 0.00 0.00 5.28
206 207 6.059484 TCTTTCCCTAATAATAAAGCACGGG 58.941 40.000 0.00 0.00 0.00 5.28
220 221 9.036980 GCTGAGGAACTATATATCTTTCCCTAA 57.963 37.037 16.55 6.73 41.55 2.69
221 222 8.402683 AGCTGAGGAACTATATATCTTTCCCTA 58.597 37.037 16.55 8.92 41.55 3.53
222 223 7.252678 AGCTGAGGAACTATATATCTTTCCCT 58.747 38.462 16.55 7.23 41.55 4.20
234 235 7.147655 TGCAGACTATAAAAGCTGAGGAACTAT 60.148 37.037 0.00 0.00 41.55 2.12
235 236 6.154534 TGCAGACTATAAAAGCTGAGGAACTA 59.845 38.462 0.00 0.00 41.55 2.24
237 238 5.178797 TGCAGACTATAAAAGCTGAGGAAC 58.821 41.667 0.00 0.00 33.64 3.62
238 239 5.420725 TGCAGACTATAAAAGCTGAGGAA 57.579 39.130 0.00 0.00 33.64 3.36
264 265 9.097257 CACAAGGTTTGACTTTGACAAAATATT 57.903 29.630 9.49 0.00 37.36 1.28
265 266 8.474025 TCACAAGGTTTGACTTTGACAAAATAT 58.526 29.630 9.49 0.00 37.36 1.28
266 267 7.831753 TCACAAGGTTTGACTTTGACAAAATA 58.168 30.769 9.49 0.00 37.36 1.40
267 268 6.696411 TCACAAGGTTTGACTTTGACAAAAT 58.304 32.000 9.49 0.00 37.36 1.82
268 269 6.090483 TCACAAGGTTTGACTTTGACAAAA 57.910 33.333 9.49 0.00 37.36 2.44
269 270 5.713792 TCACAAGGTTTGACTTTGACAAA 57.286 34.783 9.49 0.00 37.36 2.83
270 271 5.713792 TTCACAAGGTTTGACTTTGACAA 57.286 34.783 9.49 0.00 37.36 3.18
271 272 5.713792 TTTCACAAGGTTTGACTTTGACA 57.286 34.783 9.49 0.00 37.36 3.58
274 275 6.250089 GCAAATTTCACAAGGTTTGACTTTG 58.750 36.000 1.95 1.95 40.51 2.77
277 278 4.162131 AGGCAAATTTCACAAGGTTTGACT 59.838 37.500 0.00 0.00 43.21 3.41
279 280 4.751767 AGGCAAATTTCACAAGGTTTGA 57.248 36.364 0.00 0.00 34.38 2.69
281 282 8.428852 AGTTATTAGGCAAATTTCACAAGGTTT 58.571 29.630 0.00 0.00 0.00 3.27
283 284 7.539034 AGTTATTAGGCAAATTTCACAAGGT 57.461 32.000 0.00 0.00 0.00 3.50
284 285 8.831715 AAAGTTATTAGGCAAATTTCACAAGG 57.168 30.769 0.00 0.00 0.00 3.61
477 479 6.102006 TCCGCGTATAAGATTTGTTTGAAG 57.898 37.500 4.92 0.00 0.00 3.02
488 490 9.531942 TCATTTATTTTTACTCCGCGTATAAGA 57.468 29.630 4.92 0.00 0.00 2.10
495 497 5.685511 CCCATTCATTTATTTTTACTCCGCG 59.314 40.000 0.00 0.00 0.00 6.46
509 511 7.069826 CCATGTACTTTGATACCCCATTCATTT 59.930 37.037 0.00 0.00 0.00 2.32
516 518 5.192722 TCAATCCATGTACTTTGATACCCCA 59.807 40.000 0.00 0.00 0.00 4.96
519 521 7.624360 TGTTCAATCCATGTACTTTGATACC 57.376 36.000 0.00 0.00 31.17 2.73
549 551 8.830580 CAAGACAATTATGACGACTCCATTTAT 58.169 33.333 0.00 0.00 0.00 1.40
550 552 7.201609 GCAAGACAATTATGACGACTCCATTTA 60.202 37.037 0.00 0.00 0.00 1.40
558 560 5.912396 TGTTTTGCAAGACAATTATGACGAC 59.088 36.000 19.53 0.00 38.31 4.34
698 700 7.050970 TCGTGCTTATCCATGAGTTAGTTAT 57.949 36.000 0.00 0.00 0.00 1.89
868 1198 2.431057 GGAGGAACGGAGCAAGAAGATA 59.569 50.000 0.00 0.00 0.00 1.98
951 1287 0.171455 CGCGGCTCTCATAGGGATAC 59.829 60.000 0.00 0.00 0.00 2.24
1300 4611 4.394712 CCTCAGCCGCCCGACTTT 62.395 66.667 0.00 0.00 0.00 2.66
1521 4866 1.743252 GGTCTCAAGGAGCTTGCGG 60.743 63.158 0.00 0.00 40.84 5.69
1522 4867 2.097038 CGGTCTCAAGGAGCTTGCG 61.097 63.158 0.00 0.00 40.84 4.85
1777 5125 1.453379 GCAGATGCTGGCAGGTGAT 60.453 57.895 17.64 0.00 38.21 3.06
1833 5181 4.029520 ACAGCTTCTCCTCACATATCAGT 58.970 43.478 0.00 0.00 0.00 3.41
2102 5451 0.391130 TGCAGCAATGTACCGAGTCC 60.391 55.000 0.00 0.00 0.00 3.85
2122 5471 0.037605 CTTCCCGGTTAGTTCGCACT 60.038 55.000 0.00 0.00 36.99 4.40
2126 5554 0.320073 TGCACTTCCCGGTTAGTTCG 60.320 55.000 0.00 0.00 0.00 3.95
2231 5665 5.954150 ACCATGGAAGATTGATGCTAAAACT 59.046 36.000 21.47 0.00 0.00 2.66
2258 5695 3.053842 AGACCTGAAGCCATGACATTCAT 60.054 43.478 0.00 0.00 37.65 2.57
2281 5718 2.728318 CCGACGCAATATCTGATGACAG 59.272 50.000 0.00 0.00 44.66 3.51
2391 5828 8.239314 ACAGAATAATGTGAAACTACTTGCATG 58.761 33.333 0.00 0.00 38.04 4.06
2489 5926 3.091545 CCAACTAACATCAACATGCCCT 58.908 45.455 0.00 0.00 32.57 5.19
2551 5988 5.601583 TTAGCAATCGTGGTACCAATCTA 57.398 39.130 18.31 8.75 37.45 1.98
2826 6287 3.825833 CTCGCCGACGCCATAGACC 62.826 68.421 0.00 0.00 39.84 3.85


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

AutoCloner maintained by Alex Coulton.