Multiple sequence alignment - TraesCS5A01G166700

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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 TraesCS5A01G166700 chr5A 100.000 2730 0 0 1 2730 355769560 355772289 0.000000e+00 5042.0
1 TraesCS5A01G166700 chr5A 87.379 103 11 1 1241 1341 698988187 698988085 1.720000e-22 117.0
2 TraesCS5A01G166700 chr2D 87.678 1826 109 27 467 2200 584837569 584835768 0.000000e+00 2019.0
3 TraesCS5A01G166700 chr2D 92.258 155 12 0 834 988 584837358 584837204 1.270000e-53 220.0
4 TraesCS5A01G166700 chr7A 86.507 1801 144 39 319 2052 109760564 109758796 0.000000e+00 1888.0
5 TraesCS5A01G166700 chr7A 95.017 301 14 1 1 301 357463413 357463712 3.180000e-129 472.0
6 TraesCS5A01G166700 chr6D 87.952 1079 73 15 316 1344 118741352 118742423 0.000000e+00 1219.0
7 TraesCS5A01G166700 chr6D 89.942 865 43 16 1342 2200 118742454 118743280 0.000000e+00 1075.0
8 TraesCS5A01G166700 chr6D 92.683 41 3 0 1489 1529 118742561 118742601 2.940000e-05 60.2
9 TraesCS5A01G166700 chr7B 91.055 872 61 4 1342 2196 61273773 61274644 0.000000e+00 1162.0
10 TraesCS5A01G166700 chr7B 90.000 880 57 10 1345 2200 400625769 400624897 0.000000e+00 1109.0
11 TraesCS5A01G166700 chr7B 85.316 1076 101 24 316 1344 61272679 61273744 0.000000e+00 1059.0
12 TraesCS5A01G166700 chr7B 84.405 840 84 15 319 1140 400626664 400625854 0.000000e+00 782.0
13 TraesCS5A01G166700 chr7B 89.792 529 51 3 2202 2730 538771077 538771602 0.000000e+00 675.0
14 TraesCS5A01G166700 chr7B 87.380 523 63 3 2202 2724 538765208 538765727 5.030000e-167 597.0
15 TraesCS5A01G166700 chr5B 90.732 874 51 9 1351 2200 395676491 395675624 0.000000e+00 1138.0
16 TraesCS5A01G166700 chr5B 83.697 871 87 26 305 1140 395677475 395676625 0.000000e+00 771.0
17 TraesCS5A01G166700 chr3B 90.046 874 50 4 1342 2199 795282865 795282013 0.000000e+00 1098.0
18 TraesCS5A01G166700 chr3B 86.040 745 75 10 434 1161 582974177 582973445 0.000000e+00 773.0
19 TraesCS5A01G166700 chr3B 83.601 622 58 23 319 922 795283555 795282960 6.650000e-151 544.0
20 TraesCS5A01G166700 chr3B 92.120 368 25 2 1836 2200 829566186 829566552 1.450000e-142 516.0
21 TraesCS5A01G166700 chr3B 87.266 267 24 3 305 570 582974434 582974177 2.060000e-76 296.0
22 TraesCS5A01G166700 chr3B 93.617 188 9 2 1159 1344 582973419 582973233 7.450000e-71 278.0
23 TraesCS5A01G166700 chr3B 95.122 41 2 0 1489 1529 795282758 795282718 6.310000e-07 65.8
24 TraesCS5A01G166700 chr1B 89.510 877 62 9 1342 2194 635780559 635781429 0.000000e+00 1083.0
25 TraesCS5A01G166700 chr1B 85.182 1073 102 18 319 1344 113801270 113800208 0.000000e+00 1048.0
26 TraesCS5A01G166700 chr1B 88.961 462 35 3 1756 2201 113799821 113799360 8.540000e-155 556.0
27 TraesCS5A01G166700 chr1B 93.352 361 23 1 1342 1701 113800179 113799819 1.440000e-147 532.0
28 TraesCS5A01G166700 chr1B 83.277 592 62 13 316 888 635779838 635780411 6.740000e-141 510.0
29 TraesCS5A01G166700 chr1B 88.350 103 10 1 1241 1341 218989255 218989357 3.690000e-24 122.0
30 TraesCS5A01G166700 chr1B 97.917 48 1 0 1093 1140 635780415 635780462 1.740000e-12 84.2
31 TraesCS5A01G166700 chr4B 88.474 642 54 7 1576 2199 493801786 493801147 0.000000e+00 758.0
32 TraesCS5A01G166700 chr4B 89.247 186 19 1 1159 1344 493854249 493854065 5.880000e-57 231.0
33 TraesCS5A01G166700 chr2B 88.710 558 32 6 1659 2200 600997230 600996688 0.000000e+00 652.0
34 TraesCS5A01G166700 chr2B 87.573 515 60 2 2214 2725 472809058 472809571 6.510000e-166 593.0
35 TraesCS5A01G166700 chr2B 87.184 515 62 2 2214 2725 739671788 739672301 1.410000e-162 582.0
36 TraesCS5A01G166700 chr2B 91.391 302 21 5 5 301 70740600 70740901 2.530000e-110 409.0
37 TraesCS5A01G166700 chr2B 90.040 251 24 1 319 569 600997472 600997223 9.430000e-85 324.0
38 TraesCS5A01G166700 chr2A 87.406 532 64 3 2199 2729 656180709 656180180 2.320000e-170 608.0
39 TraesCS5A01G166700 chr2A 86.857 525 59 5 2214 2730 753328519 753329041 1.820000e-161 579.0
40 TraesCS5A01G166700 chr4D 87.097 527 58 8 2208 2730 339190957 339191477 3.030000e-164 588.0
41 TraesCS5A01G166700 chr4D 86.717 527 60 8 2208 2730 488613817 488614337 6.560000e-161 577.0
42 TraesCS5A01G166700 chr1D 87.097 527 57 9 2208 2730 368310981 368310462 1.090000e-163 586.0
43 TraesCS5A01G166700 chr3A 95.608 296 12 1 6 301 66617536 66617830 8.850000e-130 473.0
44 TraesCS5A01G166700 chr3A 95.221 272 11 2 4 274 593789268 593788998 1.940000e-116 429.0
45 TraesCS5A01G166700 chr3D 93.355 301 15 5 6 301 321992356 321992056 8.970000e-120 440.0
46 TraesCS5A01G166700 chr3D 91.946 298 19 5 9 301 321992404 321992107 1.960000e-111 412.0
47 TraesCS5A01G166700 chr3D 92.150 293 18 5 14 301 321992450 321992158 2.530000e-110 409.0
48 TraesCS5A01G166700 chr4A 91.722 302 20 5 5 301 523718244 523717943 5.440000e-112 414.0
49 TraesCS5A01G166700 chr4A 91.391 302 21 5 5 301 523718193 523717892 2.530000e-110 409.0


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 TraesCS5A01G166700 chr5A 355769560 355772289 2729 False 5042.000000 5042 100.000000 1 2730 1 chr5A.!!$F1 2729
1 TraesCS5A01G166700 chr2D 584835768 584837569 1801 True 1119.500000 2019 89.968000 467 2200 2 chr2D.!!$R1 1733
2 TraesCS5A01G166700 chr7A 109758796 109760564 1768 True 1888.000000 1888 86.507000 319 2052 1 chr7A.!!$R1 1733
3 TraesCS5A01G166700 chr6D 118741352 118743280 1928 False 784.733333 1219 90.192333 316 2200 3 chr6D.!!$F1 1884
4 TraesCS5A01G166700 chr7B 61272679 61274644 1965 False 1110.500000 1162 88.185500 316 2196 2 chr7B.!!$F3 1880
5 TraesCS5A01G166700 chr7B 400624897 400626664 1767 True 945.500000 1109 87.202500 319 2200 2 chr7B.!!$R1 1881
6 TraesCS5A01G166700 chr7B 538771077 538771602 525 False 675.000000 675 89.792000 2202 2730 1 chr7B.!!$F2 528
7 TraesCS5A01G166700 chr7B 538765208 538765727 519 False 597.000000 597 87.380000 2202 2724 1 chr7B.!!$F1 522
8 TraesCS5A01G166700 chr5B 395675624 395677475 1851 True 954.500000 1138 87.214500 305 2200 2 chr5B.!!$R1 1895
9 TraesCS5A01G166700 chr3B 795282013 795283555 1542 True 569.266667 1098 89.589667 319 2199 3 chr3B.!!$R2 1880
10 TraesCS5A01G166700 chr3B 582973233 582974434 1201 True 449.000000 773 88.974333 305 1344 3 chr3B.!!$R1 1039
11 TraesCS5A01G166700 chr1B 113799360 113801270 1910 True 712.000000 1048 89.165000 319 2201 3 chr1B.!!$R1 1882
12 TraesCS5A01G166700 chr1B 635779838 635781429 1591 False 559.066667 1083 90.234667 316 2194 3 chr1B.!!$F2 1878
13 TraesCS5A01G166700 chr4B 493801147 493801786 639 True 758.000000 758 88.474000 1576 2199 1 chr4B.!!$R1 623
14 TraesCS5A01G166700 chr2B 472809058 472809571 513 False 593.000000 593 87.573000 2214 2725 1 chr2B.!!$F2 511
15 TraesCS5A01G166700 chr2B 739671788 739672301 513 False 582.000000 582 87.184000 2214 2725 1 chr2B.!!$F3 511
16 TraesCS5A01G166700 chr2B 600996688 600997472 784 True 488.000000 652 89.375000 319 2200 2 chr2B.!!$R1 1881
17 TraesCS5A01G166700 chr2A 656180180 656180709 529 True 608.000000 608 87.406000 2199 2729 1 chr2A.!!$R1 530
18 TraesCS5A01G166700 chr2A 753328519 753329041 522 False 579.000000 579 86.857000 2214 2730 1 chr2A.!!$F1 516
19 TraesCS5A01G166700 chr4D 339190957 339191477 520 False 588.000000 588 87.097000 2208 2730 1 chr4D.!!$F1 522
20 TraesCS5A01G166700 chr4D 488613817 488614337 520 False 577.000000 577 86.717000 2208 2730 1 chr4D.!!$F2 522
21 TraesCS5A01G166700 chr1D 368310462 368310981 519 True 586.000000 586 87.097000 2208 2730 1 chr1D.!!$R1 522

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
588 726 0.323302 TACGGCTGCCAATTCACTCA 59.677 50.0 20.29 0.00 0.0 3.41 F
692 853 0.463204 ATGAGATGTGAGCCGGTGAG 59.537 55.0 1.90 0.00 0.0 3.51 F
813 1022 0.596577 GCTCCACTATCCGCGACATA 59.403 55.0 8.23 2.24 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1836 0.031857 CTAGCATGCGAGGAGAGTGG 59.968 60.0 19.08 0.0 0.00 4.00 R
1655 1980 0.110486 TGGACCTTGTGCTTTCCCTC 59.890 55.0 0.00 0.0 0.00 4.30 R
2494 2862 0.179029 ATTTATAGCCCGCCGCAGTT 60.179 50.0 0.00 0.0 41.38 3.16 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 3.900966 AGTCGGATTACCAAGGTAACC 57.099 47.619 13.55 14.48 42.44 2.85
21 22 3.175594 AGTCGGATTACCAAGGTAACCA 58.824 45.455 13.55 6.36 42.44 3.67
22 23 3.197116 AGTCGGATTACCAAGGTAACCAG 59.803 47.826 13.55 5.56 42.44 4.00
23 24 3.196254 GTCGGATTACCAAGGTAACCAGA 59.804 47.826 13.55 7.88 42.44 3.86
24 25 3.449737 TCGGATTACCAAGGTAACCAGAG 59.550 47.826 13.55 5.05 42.44 3.35
25 26 3.197116 CGGATTACCAAGGTAACCAGAGT 59.803 47.826 13.55 0.00 42.44 3.24
26 27 4.323257 CGGATTACCAAGGTAACCAGAGTT 60.323 45.833 13.55 0.00 42.44 3.01
27 28 4.941873 GGATTACCAAGGTAACCAGAGTTG 59.058 45.833 13.55 0.00 42.44 3.16
28 29 5.514310 GGATTACCAAGGTAACCAGAGTTGT 60.514 44.000 13.55 0.00 42.44 3.32
29 30 3.208747 ACCAAGGTAACCAGAGTTGTG 57.791 47.619 0.00 0.00 36.68 3.33
30 31 1.880027 CCAAGGTAACCAGAGTTGTGC 59.120 52.381 0.00 0.00 36.68 4.57
31 32 2.487265 CCAAGGTAACCAGAGTTGTGCT 60.487 50.000 0.00 0.00 36.68 4.40
32 33 2.808543 CAAGGTAACCAGAGTTGTGCTC 59.191 50.000 0.00 0.00 40.63 4.26
45 46 4.455606 AGTTGTGCTCTTATAAGATGGGC 58.544 43.478 15.47 15.21 33.93 5.36
46 47 4.164988 AGTTGTGCTCTTATAAGATGGGCT 59.835 41.667 15.47 7.02 33.93 5.19
47 48 4.778213 TGTGCTCTTATAAGATGGGCTT 57.222 40.909 15.47 0.00 40.68 4.35
48 49 4.708177 TGTGCTCTTATAAGATGGGCTTC 58.292 43.478 15.47 12.42 38.05 3.86
49 50 4.164030 TGTGCTCTTATAAGATGGGCTTCA 59.836 41.667 15.47 14.32 38.05 3.02
50 51 5.163163 TGTGCTCTTATAAGATGGGCTTCAT 60.163 40.000 15.47 0.00 38.05 2.57
51 52 6.043127 TGTGCTCTTATAAGATGGGCTTCATA 59.957 38.462 15.47 0.00 38.05 2.15
52 53 6.593382 GTGCTCTTATAAGATGGGCTTCATAG 59.407 42.308 15.47 1.23 38.05 2.23
53 54 5.584251 GCTCTTATAAGATGGGCTTCATAGC 59.416 44.000 15.47 7.30 39.43 2.97
63 64 2.543777 GCTTCATAGCCGGATTACCA 57.456 50.000 5.05 0.00 41.74 3.25
64 65 2.846193 GCTTCATAGCCGGATTACCAA 58.154 47.619 5.05 0.00 41.74 3.67
65 66 2.808543 GCTTCATAGCCGGATTACCAAG 59.191 50.000 5.05 0.35 41.74 3.61
66 67 3.403038 CTTCATAGCCGGATTACCAAGG 58.597 50.000 5.05 0.00 35.59 3.61
67 68 2.404559 TCATAGCCGGATTACCAAGGT 58.595 47.619 5.05 0.00 35.59 3.50
68 69 3.578978 TCATAGCCGGATTACCAAGGTA 58.421 45.455 5.05 0.00 35.59 3.08
69 70 3.968649 TCATAGCCGGATTACCAAGGTAA 59.031 43.478 5.05 13.63 43.56 2.85
70 71 2.704464 AGCCGGATTACCAAGGTAAC 57.296 50.000 13.55 8.07 42.44 2.50
71 72 1.910671 AGCCGGATTACCAAGGTAACA 59.089 47.619 13.55 0.00 42.44 2.41
72 73 2.093128 AGCCGGATTACCAAGGTAACAG 60.093 50.000 13.55 8.14 42.44 3.16
73 74 2.093341 GCCGGATTACCAAGGTAACAGA 60.093 50.000 13.55 0.00 42.44 3.41
74 75 3.793559 CCGGATTACCAAGGTAACAGAG 58.206 50.000 13.55 6.31 42.44 3.35
75 76 3.197116 CCGGATTACCAAGGTAACAGAGT 59.803 47.826 13.55 0.00 42.44 3.24
76 77 4.323257 CCGGATTACCAAGGTAACAGAGTT 60.323 45.833 13.55 0.00 42.44 3.01
77 78 4.630069 CGGATTACCAAGGTAACAGAGTTG 59.370 45.833 13.55 0.00 42.44 3.16
78 79 5.557866 GGATTACCAAGGTAACAGAGTTGT 58.442 41.667 13.55 0.00 42.44 3.32
79 80 5.411669 GGATTACCAAGGTAACAGAGTTGTG 59.588 44.000 13.55 0.00 42.44 3.33
80 81 2.572290 ACCAAGGTAACAGAGTTGTGC 58.428 47.619 0.00 0.00 37.67 4.57
81 82 2.172717 ACCAAGGTAACAGAGTTGTGCT 59.827 45.455 0.00 0.00 37.67 4.40
82 83 3.389983 ACCAAGGTAACAGAGTTGTGCTA 59.610 43.478 0.00 0.00 37.67 3.49
83 84 4.041691 ACCAAGGTAACAGAGTTGTGCTAT 59.958 41.667 0.00 0.00 37.67 2.97
84 85 5.003804 CCAAGGTAACAGAGTTGTGCTATT 58.996 41.667 0.00 0.00 37.67 1.73
85 86 6.170506 CCAAGGTAACAGAGTTGTGCTATTA 58.829 40.000 0.00 0.00 37.67 0.98
86 87 6.823689 CCAAGGTAACAGAGTTGTGCTATTAT 59.176 38.462 0.00 0.00 37.67 1.28
87 88 7.985184 CCAAGGTAACAGAGTTGTGCTATTATA 59.015 37.037 0.00 0.00 37.67 0.98
88 89 9.378551 CAAGGTAACAGAGTTGTGCTATTATAA 57.621 33.333 0.00 0.00 37.67 0.98
94 95 9.507329 AACAGAGTTGTGCTATTATAATATGGG 57.493 33.333 5.64 0.00 37.67 4.00
95 96 7.607991 ACAGAGTTGTGCTATTATAATATGGGC 59.392 37.037 5.64 6.89 35.83 5.36
96 97 7.826252 CAGAGTTGTGCTATTATAATATGGGCT 59.174 37.037 5.64 1.23 0.00 5.19
97 98 8.386264 AGAGTTGTGCTATTATAATATGGGCTT 58.614 33.333 5.64 0.00 0.00 4.35
98 99 8.340618 AGTTGTGCTATTATAATATGGGCTTG 57.659 34.615 5.64 0.00 0.00 4.01
99 100 8.163408 AGTTGTGCTATTATAATATGGGCTTGA 58.837 33.333 5.64 0.00 0.00 3.02
100 101 8.960591 GTTGTGCTATTATAATATGGGCTTGAT 58.039 33.333 5.64 0.00 0.00 2.57
102 103 9.836864 TGTGCTATTATAATATGGGCTTGATAG 57.163 33.333 5.64 0.00 0.00 2.08
113 114 2.543777 GCTTGATAGCCGGATTACCA 57.456 50.000 5.05 0.00 41.74 3.25
114 115 2.846193 GCTTGATAGCCGGATTACCAA 58.154 47.619 5.05 3.08 41.74 3.67
115 116 2.808543 GCTTGATAGCCGGATTACCAAG 59.191 50.000 18.14 18.14 41.74 3.61
116 117 3.403038 CTTGATAGCCGGATTACCAAGG 58.597 50.000 5.05 0.00 35.59 3.61
117 118 2.404559 TGATAGCCGGATTACCAAGGT 58.595 47.619 5.05 0.00 35.59 3.50
118 119 3.578978 TGATAGCCGGATTACCAAGGTA 58.421 45.455 5.05 0.00 35.59 3.08
119 120 3.968649 TGATAGCCGGATTACCAAGGTAA 59.031 43.478 5.05 13.63 43.56 2.85
120 121 2.704464 AGCCGGATTACCAAGGTAAC 57.296 50.000 13.55 8.07 42.44 2.50
121 122 1.910671 AGCCGGATTACCAAGGTAACA 59.089 47.619 13.55 0.00 42.44 2.41
122 123 2.093128 AGCCGGATTACCAAGGTAACAG 60.093 50.000 13.55 8.14 42.44 3.16
123 124 2.093341 GCCGGATTACCAAGGTAACAGA 60.093 50.000 13.55 0.00 42.44 3.41
124 125 3.793559 CCGGATTACCAAGGTAACAGAG 58.206 50.000 13.55 6.31 42.44 3.35
125 126 3.195661 CGGATTACCAAGGTAACAGAGC 58.804 50.000 13.55 0.00 42.44 4.09
126 127 3.118738 CGGATTACCAAGGTAACAGAGCT 60.119 47.826 13.55 0.00 42.44 4.09
127 128 4.192317 GGATTACCAAGGTAACAGAGCTG 58.808 47.826 13.55 0.00 42.44 4.24
128 129 4.323562 GGATTACCAAGGTAACAGAGCTGT 60.324 45.833 13.55 0.00 42.44 4.40
129 130 2.550830 ACCAAGGTAACAGAGCTGTG 57.449 50.000 9.74 9.74 44.13 3.66
130 131 1.160137 CCAAGGTAACAGAGCTGTGC 58.840 55.000 11.42 0.00 44.13 4.57
131 132 1.271054 CCAAGGTAACAGAGCTGTGCT 60.271 52.381 11.42 0.46 44.13 4.40
132 133 7.756778 TTACCAAGGTAACAGAGCTGTGCTC 62.757 48.000 11.42 11.19 44.13 4.26
144 145 4.348863 AGCTGTGCTCTTATAAGATGGG 57.651 45.455 15.47 5.82 30.62 4.00
145 146 2.810852 GCTGTGCTCTTATAAGATGGGC 59.189 50.000 15.47 15.21 33.93 5.36
146 147 3.495806 GCTGTGCTCTTATAAGATGGGCT 60.496 47.826 15.47 0.00 33.93 5.19
147 148 4.712476 CTGTGCTCTTATAAGATGGGCTT 58.288 43.478 15.47 0.00 40.68 4.35
148 149 4.454678 TGTGCTCTTATAAGATGGGCTTG 58.545 43.478 15.47 3.76 37.42 4.01
149 150 4.164030 TGTGCTCTTATAAGATGGGCTTGA 59.836 41.667 15.47 0.00 37.42 3.02
150 151 5.163163 TGTGCTCTTATAAGATGGGCTTGAT 60.163 40.000 15.47 0.00 37.42 2.57
151 152 6.043127 TGTGCTCTTATAAGATGGGCTTGATA 59.957 38.462 15.47 0.00 37.42 2.15
152 153 6.593382 GTGCTCTTATAAGATGGGCTTGATAG 59.407 42.308 15.47 1.23 37.42 2.08
153 154 5.584251 GCTCTTATAAGATGGGCTTGATAGC 59.416 44.000 15.47 7.30 39.43 2.97
163 164 2.543777 GCTTGATAGCCGGATTACCA 57.456 50.000 5.05 0.00 41.74 3.25
164 165 2.846193 GCTTGATAGCCGGATTACCAA 58.154 47.619 5.05 3.08 41.74 3.67
165 166 2.808543 GCTTGATAGCCGGATTACCAAG 59.191 50.000 18.14 18.14 41.74 3.61
166 167 3.403038 CTTGATAGCCGGATTACCAAGG 58.597 50.000 5.05 0.00 35.59 3.61
167 168 2.404559 TGATAGCCGGATTACCAAGGT 58.595 47.619 5.05 0.00 35.59 3.50
168 169 3.578978 TGATAGCCGGATTACCAAGGTA 58.421 45.455 5.05 0.00 35.59 3.08
169 170 3.968649 TGATAGCCGGATTACCAAGGTAA 59.031 43.478 5.05 13.63 43.56 2.85
170 171 2.704464 AGCCGGATTACCAAGGTAAC 57.296 50.000 13.55 8.07 42.44 2.50
171 172 1.910671 AGCCGGATTACCAAGGTAACA 59.089 47.619 13.55 0.00 42.44 2.41
172 173 2.093128 AGCCGGATTACCAAGGTAACAG 60.093 50.000 13.55 8.14 42.44 3.16
173 174 2.093341 GCCGGATTACCAAGGTAACAGA 60.093 50.000 13.55 0.00 42.44 3.41
174 175 3.793559 CCGGATTACCAAGGTAACAGAG 58.206 50.000 13.55 6.31 42.44 3.35
175 176 3.197116 CCGGATTACCAAGGTAACAGAGT 59.803 47.826 13.55 0.00 42.44 3.24
176 177 4.323257 CCGGATTACCAAGGTAACAGAGTT 60.323 45.833 13.55 0.00 42.44 3.01
177 178 4.630069 CGGATTACCAAGGTAACAGAGTTG 59.370 45.833 13.55 0.00 42.44 3.16
178 179 5.557866 GGATTACCAAGGTAACAGAGTTGT 58.442 41.667 13.55 0.00 42.44 3.32
179 180 5.411669 GGATTACCAAGGTAACAGAGTTGTG 59.588 44.000 13.55 0.00 42.44 3.33
180 181 2.572290 ACCAAGGTAACAGAGTTGTGC 58.428 47.619 0.00 0.00 37.67 4.57
181 182 2.172717 ACCAAGGTAACAGAGTTGTGCT 59.827 45.455 0.00 0.00 37.67 4.40
182 183 2.808543 CCAAGGTAACAGAGTTGTGCTC 59.191 50.000 0.00 0.00 44.45 4.26
183 184 8.096482 TTACCAAGGTAACAGAGTTGTGCTCT 62.096 42.308 7.59 0.00 43.52 4.09
184 185 9.477405 TTACCAAGGTAACAGAGTTGTGCTCTT 62.477 40.741 7.59 0.00 41.96 2.85
195 196 6.487689 GAGTTGTGCTCTTATAATATGGGC 57.512 41.667 0.00 0.00 40.98 5.36
196 197 6.192970 AGTTGTGCTCTTATAATATGGGCT 57.807 37.500 0.00 0.00 31.17 5.19
197 198 6.605119 AGTTGTGCTCTTATAATATGGGCTT 58.395 36.000 0.00 0.00 31.17 4.35
198 199 6.488006 AGTTGTGCTCTTATAATATGGGCTTG 59.512 38.462 0.00 0.00 31.17 4.01
199 200 6.186420 TGTGCTCTTATAATATGGGCTTGA 57.814 37.500 0.00 0.00 31.17 3.02
200 201 6.782986 TGTGCTCTTATAATATGGGCTTGAT 58.217 36.000 0.00 0.00 31.17 2.57
201 202 7.917003 TGTGCTCTTATAATATGGGCTTGATA 58.083 34.615 0.00 0.00 31.17 2.15
202 203 8.043113 TGTGCTCTTATAATATGGGCTTGATAG 58.957 37.037 0.00 0.00 31.17 2.08
213 214 2.543777 GCTTGATAGCCGGATTACCA 57.456 50.000 5.05 0.00 41.74 3.25
214 215 2.846193 GCTTGATAGCCGGATTACCAA 58.154 47.619 5.05 3.08 41.74 3.67
215 216 2.808543 GCTTGATAGCCGGATTACCAAG 59.191 50.000 18.14 18.14 41.74 3.61
216 217 3.403038 CTTGATAGCCGGATTACCAAGG 58.597 50.000 5.05 0.00 35.59 3.61
217 218 2.404559 TGATAGCCGGATTACCAAGGT 58.595 47.619 5.05 0.00 35.59 3.50
218 219 3.578978 TGATAGCCGGATTACCAAGGTA 58.421 45.455 5.05 0.00 35.59 3.08
219 220 3.968649 TGATAGCCGGATTACCAAGGTAA 59.031 43.478 5.05 13.63 43.56 2.85
220 221 2.704464 AGCCGGATTACCAAGGTAAC 57.296 50.000 13.55 8.07 42.44 2.50
221 222 1.910671 AGCCGGATTACCAAGGTAACA 59.089 47.619 13.55 0.00 42.44 2.41
222 223 2.093128 AGCCGGATTACCAAGGTAACAG 60.093 50.000 13.55 8.14 42.44 3.16
223 224 2.093341 GCCGGATTACCAAGGTAACAGA 60.093 50.000 13.55 0.00 42.44 3.41
224 225 3.793559 CCGGATTACCAAGGTAACAGAG 58.206 50.000 13.55 6.31 42.44 3.35
225 226 3.195661 CGGATTACCAAGGTAACAGAGC 58.804 50.000 13.55 0.00 42.44 4.09
226 227 3.118738 CGGATTACCAAGGTAACAGAGCT 60.119 47.826 13.55 0.00 42.44 4.09
227 228 4.192317 GGATTACCAAGGTAACAGAGCTG 58.808 47.826 13.55 0.00 42.44 4.24
228 229 4.323562 GGATTACCAAGGTAACAGAGCTGT 60.324 45.833 13.55 0.00 42.44 4.40
229 230 2.550830 ACCAAGGTAACAGAGCTGTG 57.449 50.000 9.74 9.74 44.13 3.66
230 231 1.160137 CCAAGGTAACAGAGCTGTGC 58.840 55.000 11.42 0.00 44.13 4.57
231 232 1.271054 CCAAGGTAACAGAGCTGTGCT 60.271 52.381 11.42 0.46 44.13 4.40
232 233 7.756778 TTACCAAGGTAACAGAGCTGTGCTC 62.757 48.000 11.42 11.19 44.13 4.26
245 246 4.583871 AGCTGTGCTCTTATAATATGGGC 58.416 43.478 0.00 0.00 30.62 5.36
246 247 4.288105 AGCTGTGCTCTTATAATATGGGCT 59.712 41.667 0.00 0.00 30.62 5.19
247 248 5.006386 GCTGTGCTCTTATAATATGGGCTT 58.994 41.667 0.00 0.00 31.17 4.35
248 249 5.106396 GCTGTGCTCTTATAATATGGGCTTG 60.106 44.000 0.00 0.00 31.17 4.01
249 250 6.186420 TGTGCTCTTATAATATGGGCTTGA 57.814 37.500 0.00 0.00 31.17 3.02
250 251 6.782986 TGTGCTCTTATAATATGGGCTTGAT 58.217 36.000 0.00 0.00 31.17 2.57
251 252 7.917003 TGTGCTCTTATAATATGGGCTTGATA 58.083 34.615 0.00 0.00 31.17 2.15
252 253 8.043113 TGTGCTCTTATAATATGGGCTTGATAG 58.957 37.037 0.00 0.00 31.17 2.08
263 264 2.543777 GCTTGATAGCCGGATTACCA 57.456 50.000 5.05 0.00 41.74 3.25
264 265 2.846193 GCTTGATAGCCGGATTACCAA 58.154 47.619 5.05 3.08 41.74 3.67
265 266 2.808543 GCTTGATAGCCGGATTACCAAG 59.191 50.000 18.14 18.14 41.74 3.61
266 267 3.403038 CTTGATAGCCGGATTACCAAGG 58.597 50.000 5.05 0.00 35.59 3.61
267 268 2.404559 TGATAGCCGGATTACCAAGGT 58.595 47.619 5.05 0.00 35.59 3.50
268 269 3.578978 TGATAGCCGGATTACCAAGGTA 58.421 45.455 5.05 0.00 35.59 3.08
269 270 3.968649 TGATAGCCGGATTACCAAGGTAA 59.031 43.478 5.05 13.63 43.56 2.85
270 271 2.704464 AGCCGGATTACCAAGGTAAC 57.296 50.000 13.55 8.07 42.44 2.50
271 272 1.910671 AGCCGGATTACCAAGGTAACA 59.089 47.619 13.55 0.00 42.44 2.41
272 273 2.093128 AGCCGGATTACCAAGGTAACAG 60.093 50.000 13.55 8.14 42.44 3.16
273 274 2.093341 GCCGGATTACCAAGGTAACAGA 60.093 50.000 13.55 0.00 42.44 3.41
274 275 3.793559 CCGGATTACCAAGGTAACAGAG 58.206 50.000 13.55 6.31 42.44 3.35
275 276 3.197116 CCGGATTACCAAGGTAACAGAGT 59.803 47.826 13.55 0.00 42.44 3.24
276 277 4.323257 CCGGATTACCAAGGTAACAGAGTT 60.323 45.833 13.55 0.00 42.44 3.01
277 278 4.630069 CGGATTACCAAGGTAACAGAGTTG 59.370 45.833 13.55 0.00 42.44 3.16
278 279 5.557866 GGATTACCAAGGTAACAGAGTTGT 58.442 41.667 13.55 0.00 42.44 3.32
279 280 5.411669 GGATTACCAAGGTAACAGAGTTGTG 59.588 44.000 13.55 0.00 42.44 3.33
280 281 2.572290 ACCAAGGTAACAGAGTTGTGC 58.428 47.619 0.00 0.00 37.67 4.57
281 282 2.172717 ACCAAGGTAACAGAGTTGTGCT 59.827 45.455 0.00 0.00 37.67 4.40
282 283 2.808543 CCAAGGTAACAGAGTTGTGCTC 59.191 50.000 0.00 0.00 44.45 4.26
283 284 8.096482 TTACCAAGGTAACAGAGTTGTGCTCT 62.096 42.308 7.59 0.00 43.52 4.09
284 285 9.477405 TTACCAAGGTAACAGAGTTGTGCTCTT 62.477 40.741 7.59 0.00 41.96 2.85
295 296 6.487689 GAGTTGTGCTCTTATAATATGGGC 57.512 41.667 0.00 0.00 40.98 5.36
296 297 6.192970 AGTTGTGCTCTTATAATATGGGCT 57.807 37.500 0.00 0.00 31.17 5.19
297 298 6.605119 AGTTGTGCTCTTATAATATGGGCTT 58.395 36.000 0.00 0.00 31.17 4.35
298 299 6.488006 AGTTGTGCTCTTATAATATGGGCTTG 59.512 38.462 0.00 0.00 31.17 4.01
299 300 6.186420 TGTGCTCTTATAATATGGGCTTGA 57.814 37.500 0.00 0.00 31.17 3.02
300 301 6.782986 TGTGCTCTTATAATATGGGCTTGAT 58.217 36.000 0.00 0.00 31.17 2.57
301 302 7.233632 TGTGCTCTTATAATATGGGCTTGATT 58.766 34.615 0.00 0.00 31.17 2.57
302 303 7.391554 TGTGCTCTTATAATATGGGCTTGATTC 59.608 37.037 0.00 0.00 31.17 2.52
303 304 7.391554 GTGCTCTTATAATATGGGCTTGATTCA 59.608 37.037 0.00 0.00 31.17 2.57
334 335 5.506649 GCATAAAAACCGAAGACTGAAACCA 60.507 40.000 0.00 0.00 0.00 3.67
337 338 5.592104 AAAACCGAAGACTGAAACCAAAT 57.408 34.783 0.00 0.00 0.00 2.32
379 381 4.950205 AAGACCGAACTAGAAAAGACCA 57.050 40.909 0.00 0.00 0.00 4.02
429 431 7.550906 AGAAGACCAAATTAGTTATGCTCTGAC 59.449 37.037 0.00 0.00 0.00 3.51
445 447 1.202582 CTGACCGGTCCTACTGTCTTG 59.797 57.143 31.19 5.22 0.00 3.02
450 452 1.746220 CGGTCCTACTGTCTTGAGGAG 59.254 57.143 0.00 0.00 40.07 3.69
487 489 1.134340 ACCGAATAGCCCATACGCAAA 60.134 47.619 0.00 0.00 0.00 3.68
488 490 1.531149 CCGAATAGCCCATACGCAAAG 59.469 52.381 0.00 0.00 0.00 2.77
489 491 1.069906 CGAATAGCCCATACGCAAAGC 60.070 52.381 0.00 0.00 0.00 3.51
570 708 4.122046 CTCATGATTCACAGGAACGCATA 58.878 43.478 0.00 0.00 38.83 3.14
575 713 1.447838 CACAGGAACGCATACGGCT 60.448 57.895 0.00 0.00 46.04 5.52
588 726 0.323302 TACGGCTGCCAATTCACTCA 59.677 50.000 20.29 0.00 0.00 3.41
628 775 1.760875 CTAGGAACCCTAGCCGCCA 60.761 63.158 7.06 0.00 45.64 5.69
630 777 2.808761 TAGGAACCCTAGCCGCCACA 62.809 60.000 0.00 0.00 34.61 4.17
631 778 2.436115 GAACCCTAGCCGCCACAC 60.436 66.667 0.00 0.00 0.00 3.82
632 779 4.388499 AACCCTAGCCGCCACACG 62.388 66.667 0.00 0.00 43.15 4.49
692 853 0.463204 ATGAGATGTGAGCCGGTGAG 59.537 55.000 1.90 0.00 0.00 3.51
704 865 4.778143 GGTGAGGACCGCCGCATT 62.778 66.667 0.00 0.00 45.93 3.56
739 900 1.123077 CCCCTGACCGATGAAGATCA 58.877 55.000 0.00 0.00 0.00 2.92
802 1011 3.129502 CCGTCCGTCGCTCCACTA 61.130 66.667 0.00 0.00 38.35 2.74
813 1022 0.596577 GCTCCACTATCCGCGACATA 59.403 55.000 8.23 2.24 0.00 2.29
912 1121 3.083997 GCCCCGACCAGTGGAGAT 61.084 66.667 18.40 0.00 0.00 2.75
1004 1213 2.663188 GCTCCGCGCCCTAATGAG 60.663 66.667 0.00 0.49 0.00 2.90
1061 1270 1.270358 ACCCGTCTTCTTCAACTCTGC 60.270 52.381 0.00 0.00 0.00 4.26
1065 1274 1.724082 GTCTTCTTCAACTCTGCTCGC 59.276 52.381 0.00 0.00 0.00 5.03
1091 1300 1.335882 GCCGCCTACTACCCTCCTTT 61.336 60.000 0.00 0.00 0.00 3.11
1145 1354 7.593273 GCATCTACTTCATGTCTCTATGTACAC 59.407 40.741 0.00 0.00 0.00 2.90
1330 1569 7.733402 ATCATTGCCAAATTGTATTATTGCC 57.267 32.000 0.00 0.00 0.00 4.52
1449 1763 8.875803 TGAAAACTGTACTAGGTAATTATTGCG 58.124 33.333 0.00 0.00 0.00 4.85
1452 1766 7.998753 ACTGTACTAGGTAATTATTGCGTTC 57.001 36.000 0.00 0.00 0.00 3.95
1477 1792 2.364632 TCAACCAAACACACTCCACTG 58.635 47.619 0.00 0.00 0.00 3.66
1520 1836 1.308998 CCAAACACACTCCACTCCAC 58.691 55.000 0.00 0.00 0.00 4.02
1545 1862 2.961741 TCTCCTCGCATGCTAGAAATCT 59.038 45.455 20.10 0.00 0.00 2.40
1645 1970 5.041940 GCAGAGATGATTGAAGAATTTGGC 58.958 41.667 0.00 0.00 0.00 4.52
1648 1973 5.826737 AGAGATGATTGAAGAATTTGGCGAT 59.173 36.000 0.00 0.00 0.00 4.58
1655 1980 3.694072 TGAAGAATTTGGCGATAAGGTGG 59.306 43.478 0.00 0.00 0.00 4.61
1703 2028 7.384660 GTGGTGCTGAAATTGATTTGTTTGATA 59.615 33.333 0.00 0.00 0.00 2.15
1786 2113 5.832221 TCCAATATTCCATGGGTTGTTGTA 58.168 37.500 13.02 0.00 37.31 2.41
1863 2203 8.997960 GTCAAATGTAAATGTTGTTGCTTTTTG 58.002 29.630 0.00 0.00 0.00 2.44
2038 2381 8.856153 TGAGTTGTAGCAATTAATTTGGTCTA 57.144 30.769 0.00 0.00 44.64 2.59
2187 2551 4.356289 CGAACAAACCAAAAAGACCGAAT 58.644 39.130 0.00 0.00 0.00 3.34
2232 2596 5.319140 CGGATTTTAAACCGGAATCCTTT 57.681 39.130 22.66 10.35 44.20 3.11
2294 2660 3.620488 CCAATAAAGCAGTAGCCTCCAA 58.380 45.455 0.00 0.00 43.56 3.53
2298 2664 0.674895 AAGCAGTAGCCTCCAAAGCG 60.675 55.000 0.00 0.00 43.56 4.68
2310 2676 1.014352 CCAAAGCGGGGTTATCTTCG 58.986 55.000 0.00 0.00 0.00 3.79
2386 2753 0.252197 GTCATTGTAGCCCCCGAGTT 59.748 55.000 0.00 0.00 0.00 3.01
2457 2825 6.747414 AGCAGAAGGTATATGTCATTGGTA 57.253 37.500 0.00 0.00 0.00 3.25
2477 2845 5.050431 TGGTATTGATAACGCGATGTGAATG 60.050 40.000 15.93 0.00 0.00 2.67
2494 2862 4.941263 GTGAATGCACATAAGGTTGAGGTA 59.059 41.667 0.00 0.00 44.51 3.08
2530 2898 2.175878 AATGATCCTGTATGAGCCGC 57.824 50.000 0.00 0.00 0.00 6.53
2575 2943 4.718940 CTTCCAACTGGTTGTTTGAAGT 57.281 40.909 15.87 0.00 45.59 3.01
2613 2983 4.632037 GCAACTTGTGCGCATGAA 57.368 50.000 15.91 9.16 45.10 2.57
2709 3090 3.692257 AGCTGTGACTTGCTCATACTT 57.308 42.857 0.00 0.00 33.90 2.24
2716 3097 8.616076 GCTGTGACTTGCTCATACTTAATAAAT 58.384 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.710324 CACAACTCTGGTTACCTTGGTAA 58.290 43.478 8.07 8.07 33.88 2.85
8 9 3.495453 GCACAACTCTGGTTACCTTGGTA 60.495 47.826 2.07 0.00 33.88 3.25
9 10 2.748465 GCACAACTCTGGTTACCTTGGT 60.748 50.000 2.07 0.00 33.88 3.67
10 11 1.880027 GCACAACTCTGGTTACCTTGG 59.120 52.381 2.07 0.00 33.88 3.61
11 12 2.808543 GAGCACAACTCTGGTTACCTTG 59.191 50.000 2.07 1.09 42.62 3.61
12 13 3.127425 GAGCACAACTCTGGTTACCTT 57.873 47.619 2.07 0.00 42.62 3.50
13 14 2.841442 GAGCACAACTCTGGTTACCT 57.159 50.000 2.07 0.00 42.62 3.08
21 22 9.218760 AAGCCCATCTTATAAGAGCACAACTCT 62.219 40.741 19.51 6.67 45.11 3.24
22 23 4.513318 GCCCATCTTATAAGAGCACAACTC 59.487 45.833 19.51 1.71 46.66 3.01
23 24 4.164988 AGCCCATCTTATAAGAGCACAACT 59.835 41.667 19.51 9.67 38.66 3.16
24 25 4.455606 AGCCCATCTTATAAGAGCACAAC 58.544 43.478 19.51 7.81 38.66 3.32
25 26 4.778213 AGCCCATCTTATAAGAGCACAA 57.222 40.909 19.51 0.00 38.66 3.33
26 27 4.164030 TGAAGCCCATCTTATAAGAGCACA 59.836 41.667 19.51 16.54 38.66 4.57
27 28 4.708177 TGAAGCCCATCTTATAAGAGCAC 58.292 43.478 19.51 14.71 38.66 4.40
28 29 5.573380 ATGAAGCCCATCTTATAAGAGCA 57.427 39.130 19.51 9.46 38.66 4.26
29 30 5.584251 GCTATGAAGCCCATCTTATAAGAGC 59.416 44.000 19.51 16.72 43.40 4.09
45 46 3.181454 ACCTTGGTAATCCGGCTATGAAG 60.181 47.826 0.00 0.00 36.30 3.02
46 47 2.775384 ACCTTGGTAATCCGGCTATGAA 59.225 45.455 0.00 0.00 36.30 2.57
47 48 2.404559 ACCTTGGTAATCCGGCTATGA 58.595 47.619 0.00 0.00 36.30 2.15
48 49 2.930826 ACCTTGGTAATCCGGCTATG 57.069 50.000 0.00 0.00 36.30 2.23
49 50 3.712733 TGTTACCTTGGTAATCCGGCTAT 59.287 43.478 14.41 0.00 36.30 2.97
50 51 3.106054 TGTTACCTTGGTAATCCGGCTA 58.894 45.455 14.41 0.00 36.30 3.93
51 52 1.910671 TGTTACCTTGGTAATCCGGCT 59.089 47.619 14.41 0.00 36.30 5.52
52 53 2.093341 TCTGTTACCTTGGTAATCCGGC 60.093 50.000 14.41 3.50 36.30 6.13
53 54 3.197116 ACTCTGTTACCTTGGTAATCCGG 59.803 47.826 14.41 0.00 36.30 5.14
54 55 4.467198 ACTCTGTTACCTTGGTAATCCG 57.533 45.455 14.41 7.24 36.30 4.18
55 56 5.411669 CACAACTCTGTTACCTTGGTAATCC 59.588 44.000 14.41 4.76 31.64 3.01
56 57 5.106673 GCACAACTCTGTTACCTTGGTAATC 60.107 44.000 14.41 9.40 31.64 1.75
57 58 4.760204 GCACAACTCTGTTACCTTGGTAAT 59.240 41.667 14.41 0.00 31.64 1.89
58 59 4.131596 GCACAACTCTGTTACCTTGGTAA 58.868 43.478 8.07 8.07 31.64 2.85
59 60 3.389983 AGCACAACTCTGTTACCTTGGTA 59.610 43.478 0.00 0.00 31.64 3.25
60 61 2.172717 AGCACAACTCTGTTACCTTGGT 59.827 45.455 0.00 0.00 31.64 3.67
61 62 2.851195 AGCACAACTCTGTTACCTTGG 58.149 47.619 0.00 0.00 31.64 3.61
62 63 7.849804 ATAATAGCACAACTCTGTTACCTTG 57.150 36.000 0.00 0.00 31.64 3.61
68 69 9.507329 CCCATATTATAATAGCACAACTCTGTT 57.493 33.333 10.79 0.00 31.64 3.16
69 70 7.607991 GCCCATATTATAATAGCACAACTCTGT 59.392 37.037 10.79 0.00 35.63 3.41
70 71 7.826252 AGCCCATATTATAATAGCACAACTCTG 59.174 37.037 10.79 1.73 0.00 3.35
71 72 7.922382 AGCCCATATTATAATAGCACAACTCT 58.078 34.615 10.79 0.00 0.00 3.24
72 73 8.454106 CAAGCCCATATTATAATAGCACAACTC 58.546 37.037 10.79 0.00 0.00 3.01
73 74 8.163408 TCAAGCCCATATTATAATAGCACAACT 58.837 33.333 10.79 1.79 0.00 3.16
74 75 8.335532 TCAAGCCCATATTATAATAGCACAAC 57.664 34.615 10.79 0.00 0.00 3.32
76 77 9.836864 CTATCAAGCCCATATTATAATAGCACA 57.163 33.333 10.79 0.00 0.00 4.57
77 78 8.778358 GCTATCAAGCCCATATTATAATAGCAC 58.222 37.037 10.79 1.59 43.40 4.40
78 79 8.908786 GCTATCAAGCCCATATTATAATAGCA 57.091 34.615 10.79 0.00 43.40 3.49
95 96 3.181454 ACCTTGGTAATCCGGCTATCAAG 60.181 47.826 21.09 21.09 37.28 3.02
96 97 2.775384 ACCTTGGTAATCCGGCTATCAA 59.225 45.455 0.00 2.59 36.30 2.57
97 98 2.404559 ACCTTGGTAATCCGGCTATCA 58.595 47.619 0.00 0.00 36.30 2.15
98 99 4.202284 TGTTACCTTGGTAATCCGGCTATC 60.202 45.833 14.41 0.00 36.30 2.08
99 100 3.712733 TGTTACCTTGGTAATCCGGCTAT 59.287 43.478 14.41 0.00 36.30 2.97
100 101 3.106054 TGTTACCTTGGTAATCCGGCTA 58.894 45.455 14.41 0.00 36.30 3.93
101 102 1.910671 TGTTACCTTGGTAATCCGGCT 59.089 47.619 14.41 0.00 36.30 5.52
102 103 2.093341 TCTGTTACCTTGGTAATCCGGC 60.093 50.000 14.41 3.50 36.30 6.13
103 104 3.793559 CTCTGTTACCTTGGTAATCCGG 58.206 50.000 14.41 0.00 36.30 5.14
104 105 3.118738 AGCTCTGTTACCTTGGTAATCCG 60.119 47.826 14.41 7.24 36.30 4.18
105 106 4.192317 CAGCTCTGTTACCTTGGTAATCC 58.808 47.826 14.41 4.76 0.00 3.01
106 107 4.631813 CACAGCTCTGTTACCTTGGTAATC 59.368 45.833 14.41 9.40 42.83 1.75
107 108 4.579869 CACAGCTCTGTTACCTTGGTAAT 58.420 43.478 14.41 0.00 42.83 1.89
108 109 3.805807 GCACAGCTCTGTTACCTTGGTAA 60.806 47.826 8.07 8.07 42.83 2.85
109 110 2.289444 GCACAGCTCTGTTACCTTGGTA 60.289 50.000 0.00 0.00 42.83 3.25
110 111 1.543429 GCACAGCTCTGTTACCTTGGT 60.543 52.381 0.00 0.00 42.83 3.67
111 112 1.160137 GCACAGCTCTGTTACCTTGG 58.840 55.000 0.00 0.00 42.83 3.61
112 113 2.175878 AGCACAGCTCTGTTACCTTG 57.824 50.000 0.00 0.00 42.83 3.61
122 123 8.860737 AAGCCCATCTTATAAGAGCACAGCTC 62.861 46.154 19.51 10.88 43.57 4.09
123 124 3.495806 GCCCATCTTATAAGAGCACAGCT 60.496 47.826 19.51 0.00 43.88 4.24
124 125 2.810852 GCCCATCTTATAAGAGCACAGC 59.189 50.000 19.51 13.49 38.66 4.40
125 126 4.348863 AGCCCATCTTATAAGAGCACAG 57.651 45.455 19.51 8.39 38.66 3.66
126 127 4.164030 TCAAGCCCATCTTATAAGAGCACA 59.836 41.667 19.51 4.58 38.66 4.57
127 128 4.708177 TCAAGCCCATCTTATAAGAGCAC 58.292 43.478 19.51 9.64 38.66 4.40
128 129 5.573380 ATCAAGCCCATCTTATAAGAGCA 57.427 39.130 19.51 4.27 38.66 4.26
129 130 5.584251 GCTATCAAGCCCATCTTATAAGAGC 59.416 44.000 19.51 16.72 43.40 4.09
145 146 3.181454 ACCTTGGTAATCCGGCTATCAAG 60.181 47.826 21.09 21.09 37.28 3.02
146 147 2.775384 ACCTTGGTAATCCGGCTATCAA 59.225 45.455 0.00 2.59 36.30 2.57
147 148 2.404559 ACCTTGGTAATCCGGCTATCA 58.595 47.619 0.00 0.00 36.30 2.15
148 149 4.202284 TGTTACCTTGGTAATCCGGCTATC 60.202 45.833 14.41 0.00 36.30 2.08
149 150 3.712733 TGTTACCTTGGTAATCCGGCTAT 59.287 43.478 14.41 0.00 36.30 2.97
150 151 3.106054 TGTTACCTTGGTAATCCGGCTA 58.894 45.455 14.41 0.00 36.30 3.93
151 152 1.910671 TGTTACCTTGGTAATCCGGCT 59.089 47.619 14.41 0.00 36.30 5.52
152 153 2.093341 TCTGTTACCTTGGTAATCCGGC 60.093 50.000 14.41 3.50 36.30 6.13
153 154 3.197116 ACTCTGTTACCTTGGTAATCCGG 59.803 47.826 14.41 0.00 36.30 5.14
154 155 4.467198 ACTCTGTTACCTTGGTAATCCG 57.533 45.455 14.41 7.24 36.30 4.18
155 156 5.411669 CACAACTCTGTTACCTTGGTAATCC 59.588 44.000 14.41 4.76 31.64 3.01
156 157 5.106673 GCACAACTCTGTTACCTTGGTAATC 60.107 44.000 14.41 9.40 31.64 1.75
157 158 4.760204 GCACAACTCTGTTACCTTGGTAAT 59.240 41.667 14.41 0.00 31.64 1.89
158 159 4.131596 GCACAACTCTGTTACCTTGGTAA 58.868 43.478 8.07 8.07 31.64 2.85
159 160 3.389983 AGCACAACTCTGTTACCTTGGTA 59.610 43.478 0.00 0.00 31.64 3.25
160 161 2.172717 AGCACAACTCTGTTACCTTGGT 59.827 45.455 0.00 0.00 31.64 3.67
161 162 2.808543 GAGCACAACTCTGTTACCTTGG 59.191 50.000 0.00 0.00 42.62 3.61
172 173 6.234177 AGCCCATATTATAAGAGCACAACTC 58.766 40.000 0.00 0.00 46.66 3.01
173 174 6.192970 AGCCCATATTATAAGAGCACAACT 57.807 37.500 0.00 0.00 0.00 3.16
174 175 6.486657 TCAAGCCCATATTATAAGAGCACAAC 59.513 38.462 0.00 0.00 0.00 3.32
175 176 6.600388 TCAAGCCCATATTATAAGAGCACAA 58.400 36.000 0.00 0.00 0.00 3.33
176 177 6.186420 TCAAGCCCATATTATAAGAGCACA 57.814 37.500 0.00 0.00 0.00 4.57
177 178 7.011857 GCTATCAAGCCCATATTATAAGAGCAC 59.988 40.741 0.00 0.00 43.40 4.40
178 179 7.050377 GCTATCAAGCCCATATTATAAGAGCA 58.950 38.462 0.00 0.00 43.40 4.26
179 180 7.489574 GCTATCAAGCCCATATTATAAGAGC 57.510 40.000 0.00 0.00 43.40 4.09
195 196 3.181454 ACCTTGGTAATCCGGCTATCAAG 60.181 47.826 21.09 21.09 37.28 3.02
196 197 2.775384 ACCTTGGTAATCCGGCTATCAA 59.225 45.455 0.00 2.59 36.30 2.57
197 198 2.404559 ACCTTGGTAATCCGGCTATCA 58.595 47.619 0.00 0.00 36.30 2.15
198 199 4.202284 TGTTACCTTGGTAATCCGGCTATC 60.202 45.833 14.41 0.00 36.30 2.08
199 200 3.712733 TGTTACCTTGGTAATCCGGCTAT 59.287 43.478 14.41 0.00 36.30 2.97
200 201 3.106054 TGTTACCTTGGTAATCCGGCTA 58.894 45.455 14.41 0.00 36.30 3.93
201 202 1.910671 TGTTACCTTGGTAATCCGGCT 59.089 47.619 14.41 0.00 36.30 5.52
202 203 2.093341 TCTGTTACCTTGGTAATCCGGC 60.093 50.000 14.41 3.50 36.30 6.13
203 204 3.793559 CTCTGTTACCTTGGTAATCCGG 58.206 50.000 14.41 0.00 36.30 5.14
204 205 3.118738 AGCTCTGTTACCTTGGTAATCCG 60.119 47.826 14.41 7.24 36.30 4.18
205 206 4.192317 CAGCTCTGTTACCTTGGTAATCC 58.808 47.826 14.41 4.76 0.00 3.01
206 207 4.631813 CACAGCTCTGTTACCTTGGTAATC 59.368 45.833 14.41 9.40 42.83 1.75
207 208 4.579869 CACAGCTCTGTTACCTTGGTAAT 58.420 43.478 14.41 0.00 42.83 1.89
208 209 3.805807 GCACAGCTCTGTTACCTTGGTAA 60.806 47.826 8.07 8.07 42.83 2.85
209 210 2.289444 GCACAGCTCTGTTACCTTGGTA 60.289 50.000 0.00 0.00 42.83 3.25
210 211 1.543429 GCACAGCTCTGTTACCTTGGT 60.543 52.381 0.00 0.00 42.83 3.67
211 212 1.160137 GCACAGCTCTGTTACCTTGG 58.840 55.000 0.00 0.00 42.83 3.61
212 213 2.175878 AGCACAGCTCTGTTACCTTG 57.824 50.000 0.00 0.00 42.83 3.61
223 224 4.288105 AGCCCATATTATAAGAGCACAGCT 59.712 41.667 0.00 0.00 43.88 4.24
224 225 4.583871 AGCCCATATTATAAGAGCACAGC 58.416 43.478 0.00 0.00 0.00 4.40
225 226 6.233434 TCAAGCCCATATTATAAGAGCACAG 58.767 40.000 0.00 0.00 0.00 3.66
226 227 6.186420 TCAAGCCCATATTATAAGAGCACA 57.814 37.500 0.00 0.00 0.00 4.57
227 228 7.011857 GCTATCAAGCCCATATTATAAGAGCAC 59.988 40.741 0.00 0.00 43.40 4.40
228 229 7.050377 GCTATCAAGCCCATATTATAAGAGCA 58.950 38.462 0.00 0.00 43.40 4.26
229 230 7.489574 GCTATCAAGCCCATATTATAAGAGC 57.510 40.000 0.00 0.00 43.40 4.09
245 246 3.181454 ACCTTGGTAATCCGGCTATCAAG 60.181 47.826 21.09 21.09 37.28 3.02
246 247 2.775384 ACCTTGGTAATCCGGCTATCAA 59.225 45.455 0.00 2.59 36.30 2.57
247 248 2.404559 ACCTTGGTAATCCGGCTATCA 58.595 47.619 0.00 0.00 36.30 2.15
248 249 4.202284 TGTTACCTTGGTAATCCGGCTATC 60.202 45.833 14.41 0.00 36.30 2.08
249 250 3.712733 TGTTACCTTGGTAATCCGGCTAT 59.287 43.478 14.41 0.00 36.30 2.97
250 251 3.106054 TGTTACCTTGGTAATCCGGCTA 58.894 45.455 14.41 0.00 36.30 3.93
251 252 1.910671 TGTTACCTTGGTAATCCGGCT 59.089 47.619 14.41 0.00 36.30 5.52
252 253 2.093341 TCTGTTACCTTGGTAATCCGGC 60.093 50.000 14.41 3.50 36.30 6.13
253 254 3.197116 ACTCTGTTACCTTGGTAATCCGG 59.803 47.826 14.41 0.00 36.30 5.14
254 255 4.467198 ACTCTGTTACCTTGGTAATCCG 57.533 45.455 14.41 7.24 36.30 4.18
255 256 5.411669 CACAACTCTGTTACCTTGGTAATCC 59.588 44.000 14.41 4.76 31.64 3.01
256 257 5.106673 GCACAACTCTGTTACCTTGGTAATC 60.107 44.000 14.41 9.40 31.64 1.75
257 258 4.760204 GCACAACTCTGTTACCTTGGTAAT 59.240 41.667 14.41 0.00 31.64 1.89
258 259 4.131596 GCACAACTCTGTTACCTTGGTAA 58.868 43.478 8.07 8.07 31.64 2.85
259 260 3.389983 AGCACAACTCTGTTACCTTGGTA 59.610 43.478 0.00 0.00 31.64 3.25
260 261 2.172717 AGCACAACTCTGTTACCTTGGT 59.827 45.455 0.00 0.00 31.64 3.67
261 262 2.808543 GAGCACAACTCTGTTACCTTGG 59.191 50.000 0.00 0.00 42.62 3.61
272 273 6.234177 AGCCCATATTATAAGAGCACAACTC 58.766 40.000 0.00 0.00 46.66 3.01
273 274 6.192970 AGCCCATATTATAAGAGCACAACT 57.807 37.500 0.00 0.00 0.00 3.16
274 275 6.486657 TCAAGCCCATATTATAAGAGCACAAC 59.513 38.462 0.00 0.00 0.00 3.32
275 276 6.600388 TCAAGCCCATATTATAAGAGCACAA 58.400 36.000 0.00 0.00 0.00 3.33
276 277 6.186420 TCAAGCCCATATTATAAGAGCACA 57.814 37.500 0.00 0.00 0.00 4.57
277 278 7.391554 TGAATCAAGCCCATATTATAAGAGCAC 59.608 37.037 0.00 0.00 0.00 4.40
278 279 7.391554 GTGAATCAAGCCCATATTATAAGAGCA 59.608 37.037 0.00 0.00 0.00 4.26
279 280 7.148171 GGTGAATCAAGCCCATATTATAAGAGC 60.148 40.741 0.00 0.00 0.00 4.09
280 281 7.337942 GGGTGAATCAAGCCCATATTATAAGAG 59.662 40.741 4.23 0.00 41.93 2.85
281 282 7.018550 AGGGTGAATCAAGCCCATATTATAAGA 59.981 37.037 11.01 0.00 44.69 2.10
282 283 7.121759 CAGGGTGAATCAAGCCCATATTATAAG 59.878 40.741 11.01 0.00 44.69 1.73
283 284 6.947733 CAGGGTGAATCAAGCCCATATTATAA 59.052 38.462 11.01 0.00 44.69 0.98
284 285 6.484288 CAGGGTGAATCAAGCCCATATTATA 58.516 40.000 11.01 0.00 44.69 0.98
285 286 5.327732 CAGGGTGAATCAAGCCCATATTAT 58.672 41.667 11.01 0.00 44.69 1.28
286 287 4.447616 CCAGGGTGAATCAAGCCCATATTA 60.448 45.833 11.01 0.00 44.69 0.98
287 288 3.569491 CAGGGTGAATCAAGCCCATATT 58.431 45.455 11.01 0.00 44.69 1.28
288 289 2.158415 CCAGGGTGAATCAAGCCCATAT 60.158 50.000 11.01 0.00 44.69 1.78
289 290 1.215173 CCAGGGTGAATCAAGCCCATA 59.785 52.381 11.01 0.00 44.69 2.74
290 291 0.032813 CCAGGGTGAATCAAGCCCAT 60.033 55.000 11.01 0.00 44.69 4.00
291 292 1.383799 CCAGGGTGAATCAAGCCCA 59.616 57.895 11.01 0.00 44.69 5.36
292 293 1.380380 CCCAGGGTGAATCAAGCCC 60.380 63.158 0.00 0.92 42.64 5.19
293 294 2.054453 GCCCAGGGTGAATCAAGCC 61.054 63.158 7.55 0.00 38.03 4.35
294 295 0.685458 ATGCCCAGGGTGAATCAAGC 60.685 55.000 7.55 0.00 0.00 4.01
295 296 2.734755 TATGCCCAGGGTGAATCAAG 57.265 50.000 7.55 0.00 0.00 3.02
296 297 3.464720 TTTATGCCCAGGGTGAATCAA 57.535 42.857 7.55 0.00 0.00 2.57
297 298 3.464720 TTTTATGCCCAGGGTGAATCA 57.535 42.857 7.55 0.00 0.00 2.57
298 299 3.118775 GGTTTTTATGCCCAGGGTGAATC 60.119 47.826 7.55 0.00 0.00 2.52
299 300 2.837591 GGTTTTTATGCCCAGGGTGAAT 59.162 45.455 7.55 1.40 0.00 2.57
300 301 2.252714 GGTTTTTATGCCCAGGGTGAA 58.747 47.619 7.55 0.00 0.00 3.18
301 302 1.888826 CGGTTTTTATGCCCAGGGTGA 60.889 52.381 7.55 0.00 0.00 4.02
302 303 0.530288 CGGTTTTTATGCCCAGGGTG 59.470 55.000 7.55 0.00 0.00 4.61
303 304 0.406361 TCGGTTTTTATGCCCAGGGT 59.594 50.000 7.55 0.00 0.00 4.34
334 335 2.354403 CGGGTTTGGTCTCGGTCTATTT 60.354 50.000 0.00 0.00 0.00 1.40
337 338 0.251297 TCGGGTTTGGTCTCGGTCTA 60.251 55.000 0.00 0.00 0.00 2.59
379 381 9.715121 TCTATTTGTGTAGACCGTATTTTCTTT 57.285 29.630 0.00 0.00 0.00 2.52
411 413 5.099042 ACCGGTCAGAGCATAACTAATTT 57.901 39.130 0.00 0.00 0.00 1.82
423 425 1.096416 GACAGTAGGACCGGTCAGAG 58.904 60.000 34.40 20.63 0.00 3.35
429 431 0.818296 CCTCAAGACAGTAGGACCGG 59.182 60.000 0.00 0.00 31.64 5.28
445 447 5.066764 GGTCTATATGGTCTATTCGCTCCTC 59.933 48.000 0.00 0.00 0.00 3.71
450 452 4.959596 TCGGTCTATATGGTCTATTCGC 57.040 45.455 0.00 0.00 0.00 4.70
570 708 1.073025 TGAGTGAATTGGCAGCCGT 59.927 52.632 7.03 0.00 0.00 5.68
575 713 3.084039 GAGGAATGTGAGTGAATTGGCA 58.916 45.455 0.00 0.00 0.00 4.92
588 726 4.352298 AGTGGGAGAGAAAAAGAGGAATGT 59.648 41.667 0.00 0.00 0.00 2.71
692 853 3.195698 GTCTCAATGCGGCGGTCC 61.196 66.667 9.78 0.00 0.00 4.46
728 889 1.958205 GGGGCGCTGATCTTCATCG 60.958 63.158 7.64 0.00 38.82 3.84
790 999 2.353607 GCGGATAGTGGAGCGACG 60.354 66.667 0.00 0.00 0.00 5.12
802 1011 2.335369 GACGGCTATGTCGCGGAT 59.665 61.111 6.13 0.88 32.11 4.18
856 1065 3.460672 TTCATCGATCAGGGGCGCC 62.461 63.158 21.18 21.18 0.00 6.53
999 1208 2.089980 GCAGATGCTGAACCACTCATT 58.910 47.619 0.00 0.00 38.21 2.57
1004 1213 0.801251 GACTGCAGATGCTGAACCAC 59.199 55.000 23.35 1.82 41.71 4.16
1074 1283 4.344390 AGAAATAAAGGAGGGTAGTAGGCG 59.656 45.833 0.00 0.00 0.00 5.52
1082 1291 4.384208 CGATGTGGAGAAATAAAGGAGGGT 60.384 45.833 0.00 0.00 0.00 4.34
1091 1300 2.168313 TCAGCTGCGATGTGGAGAAATA 59.832 45.455 9.47 0.00 38.54 1.40
1145 1354 4.037208 GCTAACATTGGGAATCACAGATGG 59.963 45.833 10.68 0.00 0.00 3.51
1313 1552 6.774354 GCAGATGGCAATAATACAATTTGG 57.226 37.500 0.78 0.00 43.97 3.28
1330 1569 6.696583 CAGATTCGGCTATATTAGAGCAGATG 59.303 42.308 12.75 6.18 42.48 2.90
1441 1755 3.687212 TGGTTGATGACGAACGCAATAAT 59.313 39.130 0.00 0.00 0.00 1.28
1443 1757 2.689646 TGGTTGATGACGAACGCAATA 58.310 42.857 0.00 0.00 0.00 1.90
1449 1763 3.064820 AGTGTGTTTGGTTGATGACGAAC 59.935 43.478 0.00 0.00 0.00 3.95
1452 1766 2.032030 GGAGTGTGTTTGGTTGATGACG 60.032 50.000 0.00 0.00 0.00 4.35
1477 1792 4.005650 TGATGACAAATGGAGAGTTCTGC 58.994 43.478 0.00 0.00 34.66 4.26
1520 1836 0.031857 CTAGCATGCGAGGAGAGTGG 59.968 60.000 19.08 0.00 0.00 4.00
1545 1862 5.312895 TGCTAGTTCATAGAAAAGTTGGCA 58.687 37.500 0.00 0.00 32.76 4.92
1645 1970 1.209504 TGCTTTCCCTCCACCTTATCG 59.790 52.381 0.00 0.00 0.00 2.92
1648 1973 1.440618 TGTGCTTTCCCTCCACCTTA 58.559 50.000 0.00 0.00 0.00 2.69
1655 1980 0.110486 TGGACCTTGTGCTTTCCCTC 59.890 55.000 0.00 0.00 0.00 4.30
1786 2113 6.058183 ACACAAAGTAAGAAGATCACAAGCT 58.942 36.000 0.00 0.00 0.00 3.74
1994 2337 7.093156 ACAACTCAGATTCATGATACTTCCAGA 60.093 37.037 0.00 0.00 0.00 3.86
2057 2400 4.240096 GGTCTTCGGTCTTTACAATTCGA 58.760 43.478 0.00 0.00 0.00 3.71
2130 2494 6.197364 TCGGTCTTCTAAGAATTCAGTCTC 57.803 41.667 8.44 0.00 36.68 3.36
2254 2619 3.806380 TGGCGAATATTTAAAGGCCGTA 58.194 40.909 0.00 0.00 43.36 4.02
2294 2660 4.534401 GCGAAGATAACCCCGCTT 57.466 55.556 0.00 0.00 43.75 4.68
2298 2664 0.831307 AGTGGAGCGAAGATAACCCC 59.169 55.000 0.00 0.00 0.00 4.95
2386 2753 5.477291 AGACAACTCCTCGAGTCATCTTAAA 59.523 40.000 12.31 0.00 42.59 1.52
2448 2816 5.050363 ACATCGCGTTATCAATACCAATGAC 60.050 40.000 5.77 0.00 0.00 3.06
2457 2825 3.312146 TGCATTCACATCGCGTTATCAAT 59.688 39.130 5.77 0.00 0.00 2.57
2477 2845 3.127030 GCAGTTACCTCAACCTTATGTGC 59.873 47.826 0.00 0.00 37.93 4.57
2482 2850 1.338389 GCCGCAGTTACCTCAACCTTA 60.338 52.381 0.00 0.00 37.93 2.69
2494 2862 0.179029 ATTTATAGCCCGCCGCAGTT 60.179 50.000 0.00 0.00 41.38 3.16
2506 2874 5.521735 GCGGCTCATACAGGATCATTTATAG 59.478 44.000 0.00 0.00 0.00 1.31
2530 2898 2.034879 ATTGGCCGAGTTGCTGACG 61.035 57.895 0.00 0.00 0.00 4.35
2575 2943 5.632118 TGCCACCACTATAGTTTGGTTAAA 58.368 37.500 22.99 10.39 44.06 1.52
2612 2982 0.527565 GCGTTGGATGGCTCAATGTT 59.472 50.000 0.00 0.00 34.58 2.71
2613 2983 0.608856 TGCGTTGGATGGCTCAATGT 60.609 50.000 0.00 0.00 34.58 2.71
2634 3004 2.291465 GCAAATTATCATCAGCTGCCGA 59.709 45.455 9.47 8.17 0.00 5.54


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

AutoCloner maintained by Alex Coulton.