Multiple sequence alignment - TraesCS3B01G227400

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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 TraesCS3B01G227400 chr3B 100.000 4722 0 0 1 4722 323322780 323327501 0.000000e+00 8720
1 TraesCS3B01G227400 chr7B 90.734 2698 213 20 2034 4720 155299583 155302254 0.000000e+00 3563
2 TraesCS3B01G227400 chr7B 87.400 1754 195 21 2986 4722 297410151 297408407 0.000000e+00 1991
3 TraesCS3B01G227400 chr7B 91.196 761 61 4 2616 3371 154812717 154813476 0.000000e+00 1029
4 TraesCS3B01G227400 chr7B 88.528 462 30 10 2035 2495 154812268 154812707 5.380000e-149 538
5 TraesCS3B01G227400 chr2A 93.136 1690 104 7 3042 4722 461017787 461019473 0.000000e+00 2468
6 TraesCS3B01G227400 chr2A 89.989 1778 141 17 2965 4722 12356496 12354736 0.000000e+00 2263
7 TraesCS3B01G227400 chr2A 89.365 1796 178 7 2936 4722 503466883 503468674 0.000000e+00 2246
8 TraesCS3B01G227400 chr2A 88.746 1715 177 10 3020 4722 604137620 604135910 0.000000e+00 2084
9 TraesCS3B01G227400 chr2A 90.371 997 82 8 2033 3018 461016812 461017805 0.000000e+00 1297
10 TraesCS3B01G227400 chr2A 92.578 256 12 5 2033 2282 12357361 12357107 1.250000e-95 361
11 TraesCS3B01G227400 chr2A 84.711 242 23 13 1780 2019 316894255 316894484 3.680000e-56 230
12 TraesCS3B01G227400 chr2A 81.273 267 33 16 1771 2033 404695184 404694931 2.880000e-47 200
13 TraesCS3B01G227400 chr5A 89.013 1793 185 6 2939 4722 650294681 650292892 0.000000e+00 2209
14 TraesCS3B01G227400 chr5A 89.155 1715 171 9 3020 4722 329235987 329234276 0.000000e+00 2122
15 TraesCS3B01G227400 chr5A 81.369 263 33 14 1775 2033 253638969 253638719 2.880000e-47 200
16 TraesCS3B01G227400 chr7A 88.792 1713 178 8 3020 4722 693187371 693189079 0.000000e+00 2087
17 TraesCS3B01G227400 chr7D 88.040 1714 185 12 3020 4722 353915965 353917669 0.000000e+00 2012
18 TraesCS3B01G227400 chr7D 90.090 444 37 6 2032 2474 426215592 426215155 1.910000e-158 569
19 TraesCS3B01G227400 chr7D 86.824 296 30 6 2586 2877 426215159 426214869 5.890000e-84 322
20 TraesCS3B01G227400 chr3D 95.691 1114 45 3 364 1475 260334280 260335392 0.000000e+00 1788
21 TraesCS3B01G227400 chr3D 93.939 396 20 2 1634 2028 260336213 260336605 3.150000e-166 595
22 TraesCS3B01G227400 chr3D 94.118 306 15 3 1 304 260333976 260334280 3.330000e-126 462
23 TraesCS3B01G227400 chr3D 88.281 128 9 1 2489 2616 484195271 484195150 1.060000e-31 148
24 TraesCS3B01G227400 chr3A 94.808 1117 47 4 398 1504 355274124 355273009 0.000000e+00 1731
25 TraesCS3B01G227400 chr3A 91.166 1132 76 12 2033 3160 65407573 65406462 0.000000e+00 1515
26 TraesCS3B01G227400 chr3A 93.822 518 22 3 404 911 355274639 355274122 0.000000e+00 771
27 TraesCS3B01G227400 chr3A 93.811 307 16 3 1 305 355275251 355274946 4.310000e-125 459
28 TraesCS3B01G227400 chr3A 95.067 223 8 1 1636 1858 355273011 355272792 9.730000e-92 348
29 TraesCS3B01G227400 chr3A 83.721 258 26 14 1780 2033 322820171 322819926 3.680000e-56 230
30 TraesCS3B01G227400 chr3A 81.413 269 31 16 1764 2028 318645353 318645100 8.010000e-48 202
31 TraesCS3B01G227400 chrUn 90.222 450 35 8 2028 2474 402808142 402808585 3.170000e-161 579
32 TraesCS3B01G227400 chrUn 87.838 296 26 7 2586 2877 402808581 402808870 5.850000e-89 339
33 TraesCS3B01G227400 chrUn 83.922 255 28 12 1776 2028 144416044 144416287 1.020000e-56 231
34 TraesCS3B01G227400 chrUn 84.064 251 27 12 1780 2028 144426946 144427185 3.680000e-56 230
35 TraesCS3B01G227400 chrUn 83.658 257 28 13 1780 2033 396179345 396179100 3.680000e-56 230
36 TraesCS3B01G227400 chrUn 82.609 253 27 14 1769 2019 118169867 118170104 1.720000e-49 207
37 TraesCS3B01G227400 chrUn 81.679 262 30 15 1779 2034 143318018 143317769 8.010000e-48 202
38 TraesCS3B01G227400 chrUn 80.952 273 34 16 1766 2033 240137213 240136954 2.880000e-47 200
39 TraesCS3B01G227400 chrUn 80.882 272 34 15 1766 2033 158793171 158792914 1.040000e-46 198
40 TraesCS3B01G227400 chr5D 89.933 447 35 6 2033 2474 256742870 256742429 6.860000e-158 568
41 TraesCS3B01G227400 chr5D 88.176 296 29 4 2586 2877 256742433 256742140 9.730000e-92 348
42 TraesCS3B01G227400 chr5D 90.086 232 22 1 2778 3008 397834405 397834174 2.760000e-77 300
43 TraesCS3B01G227400 chr2D 95.755 212 8 1 2034 2245 271527477 271527267 1.630000e-89 340
44 TraesCS3B01G227400 chr2D 92.140 229 17 1 2778 3005 416392907 416393135 5.890000e-84 322
45 TraesCS3B01G227400 chr2D 89.224 232 24 1 2778 3008 120543794 120543563 5.980000e-74 289
46 TraesCS3B01G227400 chr1D 90.777 206 18 1 2778 2982 37904948 37904743 1.670000e-69 274
47 TraesCS3B01G227400 chr1A 84.921 252 24 13 1779 2028 508660967 508661206 4.720000e-60 243
48 TraesCS3B01G227400 chr1A 85.356 239 22 12 1792 2028 214510038 214509811 7.900000e-58 235
49 TraesCS3B01G227400 chr1A 84.462 251 25 13 1780 2028 508664732 508664970 7.900000e-58 235
50 TraesCS3B01G227400 chr2B 82.072 251 31 13 1780 2028 350668355 350668117 8.010000e-48 202
51 TraesCS3B01G227400 chr5B 92.188 128 10 0 2489 2616 180041905 180041778 1.040000e-41 182


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 TraesCS3B01G227400 chr3B 323322780 323327501 4721 False 8720.000000 8720 100.000000 1 4722 1 chr3B.!!$F1 4721
1 TraesCS3B01G227400 chr7B 155299583 155302254 2671 False 3563.000000 3563 90.734000 2034 4720 1 chr7B.!!$F1 2686
2 TraesCS3B01G227400 chr7B 297408407 297410151 1744 True 1991.000000 1991 87.400000 2986 4722 1 chr7B.!!$R1 1736
3 TraesCS3B01G227400 chr7B 154812268 154813476 1208 False 783.500000 1029 89.862000 2035 3371 2 chr7B.!!$F2 1336
4 TraesCS3B01G227400 chr2A 503466883 503468674 1791 False 2246.000000 2246 89.365000 2936 4722 1 chr2A.!!$F2 1786
5 TraesCS3B01G227400 chr2A 604135910 604137620 1710 True 2084.000000 2084 88.746000 3020 4722 1 chr2A.!!$R2 1702
6 TraesCS3B01G227400 chr2A 461016812 461019473 2661 False 1882.500000 2468 91.753500 2033 4722 2 chr2A.!!$F3 2689
7 TraesCS3B01G227400 chr2A 12354736 12357361 2625 True 1312.000000 2263 91.283500 2033 4722 2 chr2A.!!$R3 2689
8 TraesCS3B01G227400 chr5A 650292892 650294681 1789 True 2209.000000 2209 89.013000 2939 4722 1 chr5A.!!$R3 1783
9 TraesCS3B01G227400 chr5A 329234276 329235987 1711 True 2122.000000 2122 89.155000 3020 4722 1 chr5A.!!$R2 1702
10 TraesCS3B01G227400 chr7A 693187371 693189079 1708 False 2087.000000 2087 88.792000 3020 4722 1 chr7A.!!$F1 1702
11 TraesCS3B01G227400 chr7D 353915965 353917669 1704 False 2012.000000 2012 88.040000 3020 4722 1 chr7D.!!$F1 1702
12 TraesCS3B01G227400 chr7D 426214869 426215592 723 True 445.500000 569 88.457000 2032 2877 2 chr7D.!!$R1 845
13 TraesCS3B01G227400 chr3D 260333976 260336605 2629 False 948.333333 1788 94.582667 1 2028 3 chr3D.!!$F1 2027
14 TraesCS3B01G227400 chr3A 65406462 65407573 1111 True 1515.000000 1515 91.166000 2033 3160 1 chr3A.!!$R1 1127
15 TraesCS3B01G227400 chr3A 355272792 355275251 2459 True 827.250000 1731 94.377000 1 1858 4 chr3A.!!$R4 1857
16 TraesCS3B01G227400 chrUn 402808142 402808870 728 False 459.000000 579 89.030000 2028 2877 2 chrUn.!!$F4 849
17 TraesCS3B01G227400 chr5D 256742140 256742870 730 True 458.000000 568 89.054500 2033 2877 2 chr5D.!!$R2 844
18 TraesCS3B01G227400 chr1A 508660967 508664970 4003 False 239.000000 243 84.691500 1779 2028 2 chr1A.!!$F1 249

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
927 1669 0.038890 GGCAAGGGAAGGAGCTCTTT 59.961 55.0 11.38 11.38 35.50 2.52 F
2884 4729 0.246635 GTGCAGTCGTCCTGTATGGT 59.753 55.0 0.00 0.00 43.55 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2913 4759 0.037303 ACCGTCTGGAGAGAACGGTA 59.963 55.0 16.36 0.0 45.87 4.02 R
4423 8886 0.167470 CAATGCACAAGCCGTCTCAG 59.833 55.0 0.00 0.0 41.13 3.35 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
80 82 5.560722 TCCGATTATAGCTGGGAATGAAA 57.439 39.130 0.00 0.00 0.00 2.69
118 120 7.391148 TGTTTTCTAGATAAAAGATGGTGCC 57.609 36.000 0.00 0.00 0.00 5.01
120 122 7.669722 TGTTTTCTAGATAAAAGATGGTGCCTT 59.330 33.333 0.00 0.00 0.00 4.35
179 182 0.874390 GCTGTTTCTCATTGACGGCA 59.126 50.000 0.00 0.00 43.42 5.69
198 201 2.930887 GCAGTGGTCGCAAGTTATGAGA 60.931 50.000 0.00 0.00 35.31 3.27
228 231 5.566469 TGAGGTAATTTGTGAAGGGTTAGG 58.434 41.667 0.00 0.00 0.00 2.69
271 274 5.105554 TGTTGTCAAATTTGGTGCTACTTGT 60.106 36.000 17.90 0.00 0.00 3.16
276 279 5.705441 TCAAATTTGGTGCTACTTGTAGGAG 59.295 40.000 17.90 0.00 0.00 3.69
305 308 6.251471 AGATCTGGAACTGAAACATTTGGAT 58.749 36.000 0.00 0.00 40.32 3.41
306 309 6.723052 AGATCTGGAACTGAAACATTTGGATT 59.277 34.615 0.00 0.00 40.32 3.01
307 310 6.088016 TCTGGAACTGAAACATTTGGATTG 57.912 37.500 0.00 0.00 32.07 2.67
308 311 4.630111 TGGAACTGAAACATTTGGATTGC 58.370 39.130 0.00 0.00 0.00 3.56
309 312 3.674753 GGAACTGAAACATTTGGATTGCG 59.325 43.478 0.00 0.00 0.00 4.85
310 313 2.676076 ACTGAAACATTTGGATTGCGC 58.324 42.857 0.00 0.00 0.00 6.09
311 314 1.650153 CTGAAACATTTGGATTGCGCG 59.350 47.619 0.00 0.00 0.00 6.86
312 315 0.366534 GAAACATTTGGATTGCGCGC 59.633 50.000 27.26 27.26 0.00 6.86
313 316 1.343510 AAACATTTGGATTGCGCGCG 61.344 50.000 28.44 28.44 0.00 6.86
314 317 2.950710 CATTTGGATTGCGCGCGG 60.951 61.111 33.06 13.66 0.00 6.46
315 318 4.191950 ATTTGGATTGCGCGCGGG 62.192 61.111 33.06 20.05 0.00 6.13
377 380 1.795768 GTGCAGTTCGGTCTGATTGA 58.204 50.000 10.89 0.00 37.61 2.57
384 387 3.007940 AGTTCGGTCTGATTGATGGTTCA 59.992 43.478 0.00 0.00 0.00 3.18
433 1165 2.110011 ACTTGTTCTGTGGGCCCTAAAT 59.890 45.455 25.70 0.00 0.00 1.40
461 1193 0.251742 CCTGGCCCTGTCCATTTTGA 60.252 55.000 0.00 0.00 35.22 2.69
470 1202 3.221771 CTGTCCATTTTGACCCAGAACA 58.778 45.455 0.00 0.00 34.25 3.18
494 1226 0.465278 GGGCATTTGAGAGGAGGAGC 60.465 60.000 0.00 0.00 0.00 4.70
631 1364 1.077212 CCCTGCCTTCACTGATGGG 60.077 63.158 11.89 4.19 0.00 4.00
634 1367 0.325933 CTGCCTTCACTGATGGGTCA 59.674 55.000 11.89 3.11 0.00 4.02
641 1374 2.195727 TCACTGATGGGTCATAGGCAA 58.804 47.619 0.00 0.00 32.98 4.52
678 1412 1.418637 TCCTTGCTACCCTCAACGTTT 59.581 47.619 0.00 0.00 0.00 3.60
685 1419 0.256464 ACCCTCAACGTTTTGGTCCA 59.744 50.000 0.00 0.00 33.06 4.02
691 1425 4.457603 CCTCAACGTTTTGGTCCATATTCA 59.542 41.667 0.00 0.00 33.06 2.57
704 1438 2.434336 CCATATTCAGGACGAGGGAACA 59.566 50.000 0.00 0.00 0.00 3.18
724 1458 7.220030 GGAACATAAGATTAGATCCAGAGCAA 58.780 38.462 0.00 0.00 0.00 3.91
819 1561 4.043310 TGAGGTTGGTGGAGAAAGATTGAT 59.957 41.667 0.00 0.00 0.00 2.57
829 1571 2.173356 AGAAAGATTGATGCCGGATGGA 59.827 45.455 5.05 0.00 37.49 3.41
872 1614 0.375106 GTAAAGCTGATGAGGTGCGC 59.625 55.000 0.00 0.00 0.00 6.09
927 1669 0.038890 GGCAAGGGAAGGAGCTCTTT 59.961 55.000 11.38 11.38 35.50 2.52
942 1684 4.411013 AGCTCTTTAGGAGGCACATTTTT 58.589 39.130 0.00 0.00 42.08 1.94
1035 1777 0.322456 AGAAGCTATGGCGGCAACAA 60.322 50.000 18.31 3.57 44.37 2.83
1102 1844 1.036707 GCCTGCTAGATCGTCTCCTT 58.963 55.000 0.00 0.00 0.00 3.36
1105 1847 2.690497 CCTGCTAGATCGTCTCCTTTGA 59.310 50.000 0.00 0.00 0.00 2.69
1121 1863 7.389053 GTCTCCTTTGACACAGAGTAAATCATT 59.611 37.037 0.00 0.00 36.97 2.57
1126 1868 7.977789 TTGACACAGAGTAAATCATTTGCTA 57.022 32.000 0.03 0.00 35.68 3.49
1127 1869 8.565896 TTGACACAGAGTAAATCATTTGCTAT 57.434 30.769 0.03 0.00 35.68 2.97
1275 2017 0.392336 TGCAACATCCACCCTTTTGC 59.608 50.000 0.00 0.00 42.37 3.68
1279 2021 0.402504 ACATCCACCCTTTTGCGGTA 59.597 50.000 0.00 0.00 30.42 4.02
1307 2049 1.143889 TGTGGTCTTGGCCATTGTGTA 59.856 47.619 6.09 0.00 41.08 2.90
1313 2055 3.189287 GTCTTGGCCATTGTGTAGACAAG 59.811 47.826 22.52 7.15 45.29 3.16
1323 2065 1.344763 GTGTAGACAAGTGCCCAGACT 59.655 52.381 0.00 0.00 0.00 3.24
1418 2160 2.609459 GTGGCATCTGATGTTTAGACCG 59.391 50.000 18.19 0.00 0.00 4.79
1479 2221 4.225042 AGGGTGATGTTAATAGCACACAGA 59.775 41.667 22.40 0.00 42.57 3.41
1487 2229 9.265901 GATGTTAATAGCACACAGATAGAACAT 57.734 33.333 0.00 0.00 39.41 2.71
1501 2243 7.121759 ACAGATAGAACATGAATTTGGGTCTTG 59.878 37.037 0.00 0.00 0.00 3.02
1502 2244 6.604795 AGATAGAACATGAATTTGGGTCTTGG 59.395 38.462 0.00 0.00 0.00 3.61
1504 2246 1.901833 ACATGAATTTGGGTCTTGGGC 59.098 47.619 0.00 0.00 0.00 5.36
1505 2247 2.181975 CATGAATTTGGGTCTTGGGCT 58.818 47.619 0.00 0.00 0.00 5.19
1506 2248 3.245586 ACATGAATTTGGGTCTTGGGCTA 60.246 43.478 0.00 0.00 0.00 3.93
1507 2249 3.534357 TGAATTTGGGTCTTGGGCTAA 57.466 42.857 0.00 0.00 0.00 3.09
1508 2250 3.850752 TGAATTTGGGTCTTGGGCTAAA 58.149 40.909 0.00 0.00 0.00 1.85
1509 2251 4.227197 TGAATTTGGGTCTTGGGCTAAAA 58.773 39.130 0.00 0.00 0.00 1.52
1510 2252 4.039852 TGAATTTGGGTCTTGGGCTAAAAC 59.960 41.667 0.00 0.00 0.00 2.43
1511 2253 2.003937 TTGGGTCTTGGGCTAAAACC 57.996 50.000 0.00 0.00 0.00 3.27
1512 2254 0.250989 TGGGTCTTGGGCTAAAACCG 60.251 55.000 0.00 0.00 0.00 4.44
1513 2255 0.251033 GGGTCTTGGGCTAAAACCGT 60.251 55.000 0.00 0.00 0.00 4.83
1514 2256 1.612676 GGTCTTGGGCTAAAACCGTT 58.387 50.000 0.00 0.00 0.00 4.44
1515 2257 1.268625 GGTCTTGGGCTAAAACCGTTG 59.731 52.381 0.00 0.00 0.00 4.10
1516 2258 1.268625 GTCTTGGGCTAAAACCGTTGG 59.731 52.381 0.00 0.00 0.00 3.77
1517 2259 1.133730 TCTTGGGCTAAAACCGTTGGT 60.134 47.619 0.00 0.00 37.65 3.67
1518 2260 2.106166 TCTTGGGCTAAAACCGTTGGTA 59.894 45.455 0.00 0.00 33.12 3.25
1519 2261 2.883122 TGGGCTAAAACCGTTGGTAT 57.117 45.000 0.00 0.00 33.12 2.73
1520 2262 2.438411 TGGGCTAAAACCGTTGGTATG 58.562 47.619 0.00 0.00 33.12 2.39
1521 2263 2.040012 TGGGCTAAAACCGTTGGTATGA 59.960 45.455 0.00 0.00 33.12 2.15
1522 2264 3.083293 GGGCTAAAACCGTTGGTATGAA 58.917 45.455 0.00 0.00 33.12 2.57
1523 2265 3.506844 GGGCTAAAACCGTTGGTATGAAA 59.493 43.478 0.00 0.00 33.12 2.69
1524 2266 4.158949 GGGCTAAAACCGTTGGTATGAAAT 59.841 41.667 0.00 0.00 33.12 2.17
1525 2267 5.099575 GGCTAAAACCGTTGGTATGAAATG 58.900 41.667 0.00 0.00 33.12 2.32
1526 2268 5.099575 GCTAAAACCGTTGGTATGAAATGG 58.900 41.667 0.00 0.00 39.25 3.16
1527 2269 5.106078 GCTAAAACCGTTGGTATGAAATGGA 60.106 40.000 1.53 0.00 37.18 3.41
1528 2270 5.385509 AAAACCGTTGGTATGAAATGGAG 57.614 39.130 1.53 0.00 37.18 3.86
1529 2271 3.992943 ACCGTTGGTATGAAATGGAGA 57.007 42.857 1.53 0.00 37.18 3.71
1530 2272 4.503714 ACCGTTGGTATGAAATGGAGAT 57.496 40.909 1.53 0.00 37.18 2.75
1531 2273 4.855340 ACCGTTGGTATGAAATGGAGATT 58.145 39.130 1.53 0.00 37.18 2.40
1532 2274 4.881850 ACCGTTGGTATGAAATGGAGATTC 59.118 41.667 1.53 0.00 37.18 2.52
1533 2275 5.126067 CCGTTGGTATGAAATGGAGATTCT 58.874 41.667 0.00 0.00 36.00 2.40
1534 2276 6.126883 ACCGTTGGTATGAAATGGAGATTCTA 60.127 38.462 1.53 0.00 37.18 2.10
1535 2277 6.936900 CCGTTGGTATGAAATGGAGATTCTAT 59.063 38.462 0.00 0.00 36.00 1.98
1536 2278 7.095060 CCGTTGGTATGAAATGGAGATTCTATG 60.095 40.741 0.00 0.00 36.00 2.23
1537 2279 7.571983 CGTTGGTATGAAATGGAGATTCTATGC 60.572 40.741 0.00 0.00 0.00 3.14
1538 2280 6.240894 TGGTATGAAATGGAGATTCTATGCC 58.759 40.000 0.00 0.00 0.00 4.40
1539 2281 6.183361 TGGTATGAAATGGAGATTCTATGCCA 60.183 38.462 0.00 0.00 32.97 4.92
1540 2282 6.716628 GGTATGAAATGGAGATTCTATGCCAA 59.283 38.462 0.00 0.00 33.51 4.52
1541 2283 6.896021 ATGAAATGGAGATTCTATGCCAAG 57.104 37.500 0.00 0.00 33.51 3.61
1542 2284 4.581824 TGAAATGGAGATTCTATGCCAAGC 59.418 41.667 0.00 0.00 33.51 4.01
1543 2285 4.450305 AATGGAGATTCTATGCCAAGCT 57.550 40.909 0.00 0.00 33.51 3.74
1544 2286 5.573380 AATGGAGATTCTATGCCAAGCTA 57.427 39.130 0.00 0.00 33.51 3.32
1545 2287 4.613925 TGGAGATTCTATGCCAAGCTAG 57.386 45.455 0.00 0.00 0.00 3.42
1546 2288 3.244353 TGGAGATTCTATGCCAAGCTAGC 60.244 47.826 6.62 6.62 0.00 3.42
1547 2289 3.007831 GGAGATTCTATGCCAAGCTAGCT 59.992 47.826 12.68 12.68 0.00 3.32
1548 2290 4.504689 GGAGATTCTATGCCAAGCTAGCTT 60.505 45.833 24.42 24.42 36.60 3.74
1549 2291 4.640364 AGATTCTATGCCAAGCTAGCTTC 58.360 43.478 27.08 17.15 33.42 3.86
1550 2292 3.912496 TTCTATGCCAAGCTAGCTTCA 57.088 42.857 27.08 22.07 33.42 3.02
1551 2293 3.465742 TCTATGCCAAGCTAGCTTCAG 57.534 47.619 27.08 21.01 33.42 3.02
1552 2294 3.033909 TCTATGCCAAGCTAGCTTCAGA 58.966 45.455 27.08 18.21 33.42 3.27
1553 2295 2.328819 ATGCCAAGCTAGCTTCAGAG 57.671 50.000 27.08 15.47 33.42 3.35
1554 2296 1.269958 TGCCAAGCTAGCTTCAGAGA 58.730 50.000 27.08 9.09 33.42 3.10
1555 2297 1.066573 TGCCAAGCTAGCTTCAGAGAC 60.067 52.381 27.08 9.30 33.42 3.36
1556 2298 1.742071 GCCAAGCTAGCTTCAGAGACC 60.742 57.143 27.08 7.11 33.42 3.85
1557 2299 1.470632 CCAAGCTAGCTTCAGAGACCG 60.471 57.143 27.08 12.96 33.42 4.79
1558 2300 1.474478 CAAGCTAGCTTCAGAGACCGA 59.526 52.381 27.08 0.00 33.42 4.69
1559 2301 1.840737 AGCTAGCTTCAGAGACCGAA 58.159 50.000 12.68 0.00 0.00 4.30
1560 2302 2.383855 AGCTAGCTTCAGAGACCGAAT 58.616 47.619 12.68 0.00 0.00 3.34
1561 2303 2.763448 AGCTAGCTTCAGAGACCGAATT 59.237 45.455 12.68 0.00 0.00 2.17
1562 2304 3.196685 AGCTAGCTTCAGAGACCGAATTT 59.803 43.478 12.68 0.00 0.00 1.82
1563 2305 4.402793 AGCTAGCTTCAGAGACCGAATTTA 59.597 41.667 12.68 0.00 0.00 1.40
1564 2306 5.069781 AGCTAGCTTCAGAGACCGAATTTAT 59.930 40.000 12.68 0.00 0.00 1.40
1565 2307 5.755861 GCTAGCTTCAGAGACCGAATTTATT 59.244 40.000 7.70 0.00 0.00 1.40
1566 2308 6.292596 GCTAGCTTCAGAGACCGAATTTATTG 60.293 42.308 7.70 0.00 0.00 1.90
1567 2309 5.491982 AGCTTCAGAGACCGAATTTATTGT 58.508 37.500 0.00 0.00 0.00 2.71
1568 2310 5.352569 AGCTTCAGAGACCGAATTTATTGTG 59.647 40.000 0.00 0.00 0.00 3.33
1569 2311 5.351465 GCTTCAGAGACCGAATTTATTGTGA 59.649 40.000 0.00 0.00 0.00 3.58
1570 2312 6.456181 GCTTCAGAGACCGAATTTATTGTGAG 60.456 42.308 0.00 0.00 0.00 3.51
1571 2313 6.280855 TCAGAGACCGAATTTATTGTGAGA 57.719 37.500 0.00 0.00 0.00 3.27
1572 2314 6.878317 TCAGAGACCGAATTTATTGTGAGAT 58.122 36.000 0.00 0.00 0.00 2.75
1573 2315 7.331026 TCAGAGACCGAATTTATTGTGAGATT 58.669 34.615 0.00 0.00 0.00 2.40
1574 2316 7.824289 TCAGAGACCGAATTTATTGTGAGATTT 59.176 33.333 0.00 0.00 0.00 2.17
1575 2317 8.119226 CAGAGACCGAATTTATTGTGAGATTTC 58.881 37.037 0.00 0.00 0.00 2.17
1576 2318 7.281100 AGAGACCGAATTTATTGTGAGATTTCC 59.719 37.037 0.00 0.00 0.00 3.13
1577 2319 7.112779 AGACCGAATTTATTGTGAGATTTCCT 58.887 34.615 0.00 0.00 0.00 3.36
1578 2320 8.265055 AGACCGAATTTATTGTGAGATTTCCTA 58.735 33.333 0.00 0.00 0.00 2.94
1579 2321 8.438676 ACCGAATTTATTGTGAGATTTCCTAG 57.561 34.615 0.00 0.00 0.00 3.02
1580 2322 8.047310 ACCGAATTTATTGTGAGATTTCCTAGT 58.953 33.333 0.00 0.00 0.00 2.57
1581 2323 8.338259 CCGAATTTATTGTGAGATTTCCTAGTG 58.662 37.037 0.00 0.00 0.00 2.74
1582 2324 7.852945 CGAATTTATTGTGAGATTTCCTAGTGC 59.147 37.037 0.00 0.00 0.00 4.40
1583 2325 8.814038 AATTTATTGTGAGATTTCCTAGTGCT 57.186 30.769 0.00 0.00 0.00 4.40
1584 2326 7.849804 TTTATTGTGAGATTTCCTAGTGCTC 57.150 36.000 0.00 0.00 0.00 4.26
1585 2327 4.890158 TTGTGAGATTTCCTAGTGCTCA 57.110 40.909 0.00 0.00 33.58 4.26
1586 2328 5.426689 TTGTGAGATTTCCTAGTGCTCAT 57.573 39.130 0.00 0.00 37.84 2.90
1587 2329 5.016051 TGTGAGATTTCCTAGTGCTCATC 57.984 43.478 0.00 0.00 37.84 2.92
1588 2330 4.713814 TGTGAGATTTCCTAGTGCTCATCT 59.286 41.667 0.00 0.00 37.84 2.90
1589 2331 5.893824 TGTGAGATTTCCTAGTGCTCATCTA 59.106 40.000 0.00 0.00 37.84 1.98
1590 2332 6.552725 TGTGAGATTTCCTAGTGCTCATCTAT 59.447 38.462 0.00 0.00 37.84 1.98
1591 2333 6.867816 GTGAGATTTCCTAGTGCTCATCTATG 59.132 42.308 0.00 0.00 37.84 2.23
1592 2334 6.014755 TGAGATTTCCTAGTGCTCATCTATGG 60.015 42.308 0.00 0.00 31.24 2.74
1593 2335 6.080682 AGATTTCCTAGTGCTCATCTATGGA 58.919 40.000 0.00 0.00 0.00 3.41
1594 2336 6.730038 AGATTTCCTAGTGCTCATCTATGGAT 59.270 38.462 0.00 0.00 0.00 3.41
1609 2351 5.624159 TCTATGGATGATTGCCTACTTTGG 58.376 41.667 0.00 0.00 0.00 3.28
1624 2366 7.391148 CCTACTTTGGCAAGCTCTTTATAAA 57.609 36.000 0.00 0.00 32.57 1.40
1625 2367 7.826690 CCTACTTTGGCAAGCTCTTTATAAAA 58.173 34.615 0.00 0.00 32.57 1.52
1626 2368 8.303876 CCTACTTTGGCAAGCTCTTTATAAAAA 58.696 33.333 0.00 0.00 32.57 1.94
1627 2369 7.946655 ACTTTGGCAAGCTCTTTATAAAAAC 57.053 32.000 0.00 0.00 32.57 2.43
1628 2370 7.496747 ACTTTGGCAAGCTCTTTATAAAAACA 58.503 30.769 0.00 0.00 32.57 2.83
1629 2371 7.653311 ACTTTGGCAAGCTCTTTATAAAAACAG 59.347 33.333 0.00 0.00 32.57 3.16
1630 2372 6.648879 TGGCAAGCTCTTTATAAAAACAGT 57.351 33.333 0.00 0.00 0.00 3.55
1631 2373 7.753309 TGGCAAGCTCTTTATAAAAACAGTA 57.247 32.000 0.00 0.00 0.00 2.74
1632 2374 8.172352 TGGCAAGCTCTTTATAAAAACAGTAA 57.828 30.769 0.00 0.00 0.00 2.24
1638 3042 9.363401 AGCTCTTTATAAAAACAGTAAAAGGGT 57.637 29.630 0.00 0.00 29.20 4.34
1662 3066 4.976540 ACTGTCTTTAGGGTAACTGCTT 57.023 40.909 0.00 0.00 0.00 3.91
1704 3108 9.693739 TTGCTTTGGATATGAATAGTTTAAGGA 57.306 29.630 0.00 0.00 0.00 3.36
1764 3168 3.145551 GCCTGGCCCATGCTTCTG 61.146 66.667 7.66 0.00 37.74 3.02
1766 3170 1.000521 CCTGGCCCATGCTTCTGAA 60.001 57.895 0.00 0.00 37.74 3.02
1825 3229 7.720442 TCATTCGATGATAATCACACTCTTCT 58.280 34.615 0.00 0.00 33.59 2.85
1913 3317 2.747446 TCGCTAAGCAAATTTCCTGGAC 59.253 45.455 0.00 0.00 0.00 4.02
1917 3321 3.369546 AAGCAAATTTCCTGGACGTTG 57.630 42.857 0.00 2.37 0.00 4.10
1949 3353 1.701847 AGAAGCATGGTCAACCTGACT 59.298 47.619 0.00 0.00 46.19 3.41
1964 3368 5.419155 CAACCTGACTATGAAGGTCTAGTCA 59.581 44.000 10.88 10.88 46.29 3.41
1965 3369 4.951094 ACCTGACTATGAAGGTCTAGTCAC 59.049 45.833 8.02 0.00 45.42 3.67
2193 3602 7.302948 TCCTAACATGGTATTAGAGCCTTAGA 58.697 38.462 0.00 0.00 32.31 2.10
2215 3630 1.226435 TTTTTCGCACGCGCAACTT 60.226 47.368 5.73 0.00 38.40 2.66
2266 3681 4.021925 GCTGCCTTCTCCCACCGT 62.022 66.667 0.00 0.00 0.00 4.83
2267 3682 2.656069 GCTGCCTTCTCCCACCGTA 61.656 63.158 0.00 0.00 0.00 4.02
2282 3701 1.500844 CGTACGTCGCTGTCTTCCT 59.499 57.895 7.22 0.00 0.00 3.36
2302 3721 3.364441 TGGATGTGTTGCGCCTGC 61.364 61.111 4.18 0.00 43.20 4.85
2350 3769 4.436998 GGTGGCTCGCTGCGTACT 62.437 66.667 22.48 0.00 44.05 2.73
2453 3885 1.395045 CGGCTCCACTCCATCTGCTA 61.395 60.000 0.00 0.00 0.00 3.49
2465 3897 3.459227 TCCATCTGCTAATTGGTCATCCA 59.541 43.478 0.00 0.00 42.66 3.41
2582 4017 0.466189 CTGTTGTTGCTCAGGGGTGT 60.466 55.000 0.00 0.00 0.00 4.16
2640 4087 2.783135 GACTGCCTTTGGTCTGAATCA 58.217 47.619 0.00 0.00 0.00 2.57
2732 4335 2.097825 GGATTGGTCATCTGCTGCTTT 58.902 47.619 0.00 0.00 31.67 3.51
2884 4729 0.246635 GTGCAGTCGTCCTGTATGGT 59.753 55.000 0.00 0.00 43.55 3.55
2895 4740 2.026729 TCCTGTATGGTGATTTCCGCAA 60.027 45.455 0.00 0.00 37.07 4.85
2905 4751 2.195922 GATTTCCGCAAATGTGATGGC 58.804 47.619 0.00 0.00 31.94 4.40
2913 4759 2.358898 GCAAATGTGATGGCCGTTCTAT 59.641 45.455 0.00 0.00 0.00 1.98
3040 4889 2.372504 TGGTAAATGTCGTTCTTCCCCA 59.627 45.455 0.00 0.00 0.00 4.96
3087 4978 3.118775 TGTGCTGGTACATATGACTCCAC 60.119 47.826 10.38 8.90 38.20 4.02
3125 5016 2.991540 GCCTTCCCTTGGCGCTTT 60.992 61.111 7.64 0.00 41.03 3.51
3150 5041 0.170339 TGTCTACATGCGGACTCGTG 59.830 55.000 16.18 0.00 38.89 4.35
3214 5105 3.710722 CCTCTGGCGGCTTCCACT 61.711 66.667 11.43 0.00 31.74 4.00
3278 5178 5.417580 CCTACTTCAGCTCTCTACTTCACTT 59.582 44.000 0.00 0.00 0.00 3.16
3284 5184 4.157656 CAGCTCTCTACTTCACTTAGCAGT 59.842 45.833 0.00 0.00 0.00 4.40
3518 5427 6.100859 ACATCTCCATGGATTCTTGATACTGT 59.899 38.462 16.63 7.30 33.82 3.55
3569 5479 2.673368 CACCTTGTCTTCTATTCGTGCC 59.327 50.000 0.00 0.00 0.00 5.01
3570 5480 2.301870 ACCTTGTCTTCTATTCGTGCCA 59.698 45.455 0.00 0.00 0.00 4.92
3682 5592 3.340928 CTGATGTTGCTCATGTTCCTCA 58.659 45.455 0.00 0.00 36.83 3.86
3735 5645 1.116308 TGTTGACTCTGGTTGTCGGA 58.884 50.000 0.00 0.00 37.26 4.55
3838 5763 1.599576 GGTCTCTGGGAGCTTGACC 59.400 63.158 0.00 0.00 40.05 4.02
3877 5802 2.893398 CTACCACCGCCAGTCTCC 59.107 66.667 0.00 0.00 0.00 3.71
3986 5911 1.745489 GACGCGGCCTTCTTGGATT 60.745 57.895 12.47 0.00 38.35 3.01
3992 5917 1.676014 CGGCCTTCTTGGATTCGTCTT 60.676 52.381 0.00 0.00 38.35 3.01
3994 5919 2.010497 GCCTTCTTGGATTCGTCTTCC 58.990 52.381 0.00 0.00 38.35 3.46
4018 5943 3.060602 GGTGTGTCTTTAGACTGTCAGC 58.939 50.000 10.88 11.84 44.99 4.26
4260 6420 1.608055 CTGCCATGGTTCACACTCAA 58.392 50.000 14.67 0.00 0.00 3.02
4294 6455 1.157870 CGGGTGTTTCGTGCTGACTT 61.158 55.000 0.00 0.00 0.00 3.01
4362 8563 2.564947 CAGGGTACTCTTGCTCAGTTCT 59.435 50.000 0.00 0.00 0.00 3.01
4363 8564 2.829120 AGGGTACTCTTGCTCAGTTCTC 59.171 50.000 0.00 0.00 0.00 2.87
4364 8565 2.829120 GGGTACTCTTGCTCAGTTCTCT 59.171 50.000 0.00 0.00 0.00 3.10
4423 8886 0.955428 TGCAAGCATCGTCACCTTCC 60.955 55.000 0.00 0.00 0.00 3.46
4439 8902 2.031012 CCTGAGACGGCTTGTGCA 59.969 61.111 0.00 0.00 41.91 4.57
4467 8930 2.427245 GCAGCCTCTCTTCCGCCTA 61.427 63.158 0.00 0.00 0.00 3.93
4486 8949 4.729856 CTTTTGGGCTGCGGCTGC 62.730 66.667 21.78 21.78 43.20 5.25
4549 9014 0.032615 TGCAGGGTGGTGTTCCTTTT 60.033 50.000 0.00 0.00 34.23 2.27
4553 9018 1.569072 AGGGTGGTGTTCCTTTTGAGT 59.431 47.619 0.00 0.00 34.23 3.41
4587 9052 1.022735 TCTCCTGATTACTCGACGCC 58.977 55.000 0.00 0.00 0.00 5.68
4637 9102 2.047655 TAGCCCCTTGTGAACGCG 60.048 61.111 3.53 3.53 0.00 6.01
4684 9149 5.067936 TGAGTGTGTCTTCTTAGGCTATAGC 59.932 44.000 16.78 16.78 41.14 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.138320 GTCGATGATGGATGCGAATGT 58.862 47.619 0.00 0.00 34.29 2.71
69 70 5.093849 AGAATGGCAAATTTCATTCCCAG 57.906 39.130 20.66 0.00 46.09 4.45
107 109 4.384056 CATCTCGATAAGGCACCATCTTT 58.616 43.478 0.00 0.00 0.00 2.52
118 120 3.543680 ACACCCAACCATCTCGATAAG 57.456 47.619 0.00 0.00 0.00 1.73
120 122 3.770388 TGTAACACCCAACCATCTCGATA 59.230 43.478 0.00 0.00 0.00 2.92
179 182 3.678056 TTCTCATAACTTGCGACCACT 57.322 42.857 0.00 0.00 0.00 4.00
203 206 6.663523 CCTAACCCTTCACAAATTACCTCATT 59.336 38.462 0.00 0.00 0.00 2.57
228 231 1.117150 ATGGCATGGAAAGCATGTCC 58.883 50.000 0.00 0.00 45.37 4.02
271 274 6.281190 TCAGTTCCAGATCTTATCCTCCTA 57.719 41.667 0.00 0.00 0.00 2.94
276 279 7.872113 AATGTTTCAGTTCCAGATCTTATCC 57.128 36.000 0.00 0.00 0.00 2.59
349 352 2.666190 GAACTGCACGCCAGAGCA 60.666 61.111 10.29 0.00 44.64 4.26
350 353 3.782244 CGAACTGCACGCCAGAGC 61.782 66.667 10.29 1.83 44.64 4.09
351 354 3.114616 CCGAACTGCACGCCAGAG 61.115 66.667 10.29 2.37 44.64 3.35
352 355 3.858868 GACCGAACTGCACGCCAGA 62.859 63.158 10.29 0.00 44.64 3.86
354 357 3.923864 AGACCGAACTGCACGCCA 61.924 61.111 0.00 0.00 0.00 5.69
355 358 3.414700 CAGACCGAACTGCACGCC 61.415 66.667 0.00 0.00 0.00 5.68
356 359 1.291877 AATCAGACCGAACTGCACGC 61.292 55.000 4.39 0.00 37.75 5.34
357 360 0.439985 CAATCAGACCGAACTGCACG 59.560 55.000 4.39 0.00 37.75 5.34
358 361 1.795768 TCAATCAGACCGAACTGCAC 58.204 50.000 4.39 0.00 37.75 4.57
359 362 2.349590 CATCAATCAGACCGAACTGCA 58.650 47.619 4.39 0.00 37.75 4.41
360 363 1.667724 CCATCAATCAGACCGAACTGC 59.332 52.381 4.39 0.00 37.75 4.40
361 364 2.977914 ACCATCAATCAGACCGAACTG 58.022 47.619 0.00 0.00 39.02 3.16
362 365 3.007940 TGAACCATCAATCAGACCGAACT 59.992 43.478 0.00 0.00 30.99 3.01
363 366 3.334691 TGAACCATCAATCAGACCGAAC 58.665 45.455 0.00 0.00 30.99 3.95
377 380 2.551413 AAGCCCTGCCCTGAACCAT 61.551 57.895 0.00 0.00 0.00 3.55
433 1165 2.642807 GGACAGGGCCAGGCTTATTATA 59.357 50.000 12.43 0.00 0.00 0.98
470 1202 3.102204 CCTCCTCTCAAATGCCCAAAAT 58.898 45.455 0.00 0.00 0.00 1.82
494 1226 5.221661 ACAAAGACTACTCCACAAACCCTAG 60.222 44.000 0.00 0.00 0.00 3.02
614 1347 0.393537 GACCCATCAGTGAAGGCAGG 60.394 60.000 8.97 2.70 0.00 4.85
624 1357 1.202855 CCCTTGCCTATGACCCATCAG 60.203 57.143 0.00 0.00 38.57 2.90
631 1364 1.471676 CGACAGACCCTTGCCTATGAC 60.472 57.143 0.00 0.00 0.00 3.06
634 1367 1.689273 GATCGACAGACCCTTGCCTAT 59.311 52.381 0.00 0.00 0.00 2.57
641 1374 0.106419 GGAGGAGATCGACAGACCCT 60.106 60.000 0.00 0.00 0.00 4.34
685 1419 5.839063 TCTTATGTTCCCTCGTCCTGAATAT 59.161 40.000 0.00 0.00 0.00 1.28
691 1425 5.455872 TCTAATCTTATGTTCCCTCGTCCT 58.544 41.667 0.00 0.00 0.00 3.85
704 1438 5.244851 TCGCTTGCTCTGGATCTAATCTTAT 59.755 40.000 0.00 0.00 0.00 1.73
724 1458 4.098807 GTCCTTTATTCCTCTCTTCTCGCT 59.901 45.833 0.00 0.00 0.00 4.93
819 1561 2.192979 GCATTCCTCCATCCGGCA 59.807 61.111 0.00 0.00 0.00 5.69
829 1571 2.076622 CTCGATCCGACGGCATTCCT 62.077 60.000 9.66 0.00 0.00 3.36
872 1614 3.864686 CGCGACAATTCCAGGCGG 61.865 66.667 0.00 0.00 42.86 6.13
885 1627 2.573869 CTCTTCCTCCTTGCGCGA 59.426 61.111 12.10 0.00 0.00 5.87
942 1684 0.253044 GCCCTCATCTTGGTAGCACA 59.747 55.000 0.00 0.00 0.00 4.57
948 1690 1.792757 TTGCCAGCCCTCATCTTGGT 61.793 55.000 0.00 0.00 0.00 3.67
951 1693 1.210204 TCCTTGCCAGCCCTCATCTT 61.210 55.000 0.00 0.00 0.00 2.40
1035 1777 6.262496 CAGCAATAGATTCTGACATGGATGTT 59.738 38.462 0.00 0.00 41.95 2.71
1067 1809 2.439104 GGCAGCTGGGGGAGACTAG 61.439 68.421 17.12 0.00 0.00 2.57
1102 1844 6.882610 AGCAAATGATTTACTCTGTGTCAA 57.117 33.333 0.00 0.00 0.00 3.18
1105 1847 6.183360 GCCATAGCAAATGATTTACTCTGTGT 60.183 38.462 0.00 0.00 39.53 3.72
1121 1863 1.445942 GCCCGACTAGCCATAGCAA 59.554 57.895 0.00 0.00 43.56 3.91
1275 2017 2.677836 CAAGACCACAACCATCATACCG 59.322 50.000 0.00 0.00 0.00 4.02
1279 2021 1.549203 GCCAAGACCACAACCATCAT 58.451 50.000 0.00 0.00 0.00 2.45
1307 2049 1.131638 TTCAGTCTGGGCACTTGTCT 58.868 50.000 0.00 0.00 0.00 3.41
1313 2055 1.338020 CAAGGTTTTCAGTCTGGGCAC 59.662 52.381 0.00 0.00 0.00 5.01
1323 2065 1.478654 GGCAGACTCCCAAGGTTTTCA 60.479 52.381 0.00 0.00 0.00 2.69
1418 2160 3.382546 AGGTCTAATGCAATTGGTCATGC 59.617 43.478 7.72 0.00 42.86 4.06
1479 2221 5.658190 CCCAAGACCCAAATTCATGTTCTAT 59.342 40.000 0.00 0.00 0.00 1.98
1487 2229 3.534357 TTAGCCCAAGACCCAAATTCA 57.466 42.857 0.00 0.00 0.00 2.57
1501 2243 2.713877 TCATACCAACGGTTTTAGCCC 58.286 47.619 0.00 0.00 37.09 5.19
1502 2244 4.769859 TTTCATACCAACGGTTTTAGCC 57.230 40.909 0.00 0.00 37.09 3.93
1504 2246 6.373216 TCTCCATTTCATACCAACGGTTTTAG 59.627 38.462 0.00 0.00 37.09 1.85
1505 2247 6.239396 TCTCCATTTCATACCAACGGTTTTA 58.761 36.000 0.00 0.00 37.09 1.52
1506 2248 5.074115 TCTCCATTTCATACCAACGGTTTT 58.926 37.500 0.00 0.00 37.09 2.43
1507 2249 4.658063 TCTCCATTTCATACCAACGGTTT 58.342 39.130 0.00 0.00 37.09 3.27
1508 2250 4.295141 TCTCCATTTCATACCAACGGTT 57.705 40.909 0.00 0.00 37.09 4.44
1509 2251 3.992943 TCTCCATTTCATACCAACGGT 57.007 42.857 0.00 0.00 40.16 4.83
1510 2252 5.126067 AGAATCTCCATTTCATACCAACGG 58.874 41.667 0.00 0.00 0.00 4.44
1511 2253 7.571983 GCATAGAATCTCCATTTCATACCAACG 60.572 40.741 0.00 0.00 0.00 4.10
1512 2254 7.308830 GGCATAGAATCTCCATTTCATACCAAC 60.309 40.741 0.00 0.00 0.00 3.77
1513 2255 6.716628 GGCATAGAATCTCCATTTCATACCAA 59.283 38.462 0.00 0.00 0.00 3.67
1514 2256 6.183361 TGGCATAGAATCTCCATTTCATACCA 60.183 38.462 0.00 0.00 0.00 3.25
1515 2257 6.240894 TGGCATAGAATCTCCATTTCATACC 58.759 40.000 0.00 0.00 0.00 2.73
1516 2258 7.574592 GCTTGGCATAGAATCTCCATTTCATAC 60.575 40.741 0.00 0.00 0.00 2.39
1517 2259 6.432162 GCTTGGCATAGAATCTCCATTTCATA 59.568 38.462 0.00 0.00 0.00 2.15
1518 2260 5.243283 GCTTGGCATAGAATCTCCATTTCAT 59.757 40.000 0.00 0.00 0.00 2.57
1519 2261 4.581824 GCTTGGCATAGAATCTCCATTTCA 59.418 41.667 0.00 0.00 0.00 2.69
1520 2262 4.826183 AGCTTGGCATAGAATCTCCATTTC 59.174 41.667 0.00 0.00 0.00 2.17
1521 2263 4.801164 AGCTTGGCATAGAATCTCCATTT 58.199 39.130 0.00 0.00 0.00 2.32
1522 2264 4.450305 AGCTTGGCATAGAATCTCCATT 57.550 40.909 0.00 0.00 0.00 3.16
1523 2265 4.565236 GCTAGCTTGGCATAGAATCTCCAT 60.565 45.833 7.70 0.00 0.00 3.41
1524 2266 3.244353 GCTAGCTTGGCATAGAATCTCCA 60.244 47.826 7.70 0.00 0.00 3.86
1525 2267 3.007831 AGCTAGCTTGGCATAGAATCTCC 59.992 47.826 12.68 0.00 0.00 3.71
1526 2268 4.270245 AGCTAGCTTGGCATAGAATCTC 57.730 45.455 12.68 0.00 0.00 2.75
1527 2269 4.102210 TGAAGCTAGCTTGGCATAGAATCT 59.898 41.667 33.91 5.48 36.26 2.40
1528 2270 4.384056 TGAAGCTAGCTTGGCATAGAATC 58.616 43.478 33.91 15.84 36.26 2.52
1529 2271 4.102210 TCTGAAGCTAGCTTGGCATAGAAT 59.898 41.667 33.91 6.30 36.26 2.40
1530 2272 3.452264 TCTGAAGCTAGCTTGGCATAGAA 59.548 43.478 33.91 9.85 36.26 2.10
1531 2273 3.033909 TCTGAAGCTAGCTTGGCATAGA 58.966 45.455 33.91 22.52 36.26 1.98
1532 2274 3.069300 TCTCTGAAGCTAGCTTGGCATAG 59.931 47.826 33.91 24.40 36.26 2.23
1533 2275 3.033909 TCTCTGAAGCTAGCTTGGCATA 58.966 45.455 33.91 17.25 36.26 3.14
1534 2276 1.836166 TCTCTGAAGCTAGCTTGGCAT 59.164 47.619 33.91 10.50 36.26 4.40
1535 2277 1.066573 GTCTCTGAAGCTAGCTTGGCA 60.067 52.381 33.91 23.71 36.26 4.92
1536 2278 1.650825 GTCTCTGAAGCTAGCTTGGC 58.349 55.000 33.91 20.46 36.26 4.52
1537 2279 1.470632 CGGTCTCTGAAGCTAGCTTGG 60.471 57.143 33.91 23.84 36.26 3.61
1538 2280 1.474478 TCGGTCTCTGAAGCTAGCTTG 59.526 52.381 33.91 20.28 36.26 4.01
1539 2281 1.840737 TCGGTCTCTGAAGCTAGCTT 58.159 50.000 29.71 29.71 39.23 3.74
1540 2282 1.840737 TTCGGTCTCTGAAGCTAGCT 58.159 50.000 12.68 12.68 0.00 3.32
1541 2283 2.880963 ATTCGGTCTCTGAAGCTAGC 57.119 50.000 6.62 6.62 0.00 3.42
1542 2284 6.758886 ACAATAAATTCGGTCTCTGAAGCTAG 59.241 38.462 0.00 0.00 0.00 3.42
1543 2285 6.535150 CACAATAAATTCGGTCTCTGAAGCTA 59.465 38.462 0.00 0.00 0.00 3.32
1544 2286 5.352569 CACAATAAATTCGGTCTCTGAAGCT 59.647 40.000 0.00 0.00 0.00 3.74
1545 2287 5.351465 TCACAATAAATTCGGTCTCTGAAGC 59.649 40.000 0.00 0.00 0.00 3.86
1546 2288 6.813649 TCTCACAATAAATTCGGTCTCTGAAG 59.186 38.462 0.00 0.00 0.00 3.02
1547 2289 6.697395 TCTCACAATAAATTCGGTCTCTGAA 58.303 36.000 0.00 0.00 0.00 3.02
1548 2290 6.280855 TCTCACAATAAATTCGGTCTCTGA 57.719 37.500 0.00 0.00 0.00 3.27
1549 2291 7.545362 AATCTCACAATAAATTCGGTCTCTG 57.455 36.000 0.00 0.00 0.00 3.35
1550 2292 7.281100 GGAAATCTCACAATAAATTCGGTCTCT 59.719 37.037 0.00 0.00 0.00 3.10
1551 2293 7.281100 AGGAAATCTCACAATAAATTCGGTCTC 59.719 37.037 0.00 0.00 0.00 3.36
1552 2294 7.112779 AGGAAATCTCACAATAAATTCGGTCT 58.887 34.615 0.00 0.00 0.00 3.85
1553 2295 7.321745 AGGAAATCTCACAATAAATTCGGTC 57.678 36.000 0.00 0.00 0.00 4.79
1554 2296 8.047310 ACTAGGAAATCTCACAATAAATTCGGT 58.953 33.333 0.00 0.00 0.00 4.69
1555 2297 8.338259 CACTAGGAAATCTCACAATAAATTCGG 58.662 37.037 0.00 0.00 0.00 4.30
1556 2298 7.852945 GCACTAGGAAATCTCACAATAAATTCG 59.147 37.037 0.00 0.00 0.00 3.34
1557 2299 8.897752 AGCACTAGGAAATCTCACAATAAATTC 58.102 33.333 0.00 0.00 0.00 2.17
1558 2300 8.814038 AGCACTAGGAAATCTCACAATAAATT 57.186 30.769 0.00 0.00 0.00 1.82
1559 2301 8.049117 TGAGCACTAGGAAATCTCACAATAAAT 58.951 33.333 0.00 0.00 0.00 1.40
1560 2302 7.394016 TGAGCACTAGGAAATCTCACAATAAA 58.606 34.615 0.00 0.00 0.00 1.40
1561 2303 6.946340 TGAGCACTAGGAAATCTCACAATAA 58.054 36.000 0.00 0.00 0.00 1.40
1562 2304 6.544928 TGAGCACTAGGAAATCTCACAATA 57.455 37.500 0.00 0.00 0.00 1.90
1563 2305 5.426689 TGAGCACTAGGAAATCTCACAAT 57.573 39.130 0.00 0.00 0.00 2.71
1564 2306 4.890158 TGAGCACTAGGAAATCTCACAA 57.110 40.909 0.00 0.00 0.00 3.33
1565 2307 4.713814 AGATGAGCACTAGGAAATCTCACA 59.286 41.667 0.00 0.00 36.72 3.58
1566 2308 5.275067 AGATGAGCACTAGGAAATCTCAC 57.725 43.478 0.00 0.00 36.72 3.51
1567 2309 6.014755 CCATAGATGAGCACTAGGAAATCTCA 60.015 42.308 0.00 0.00 38.05 3.27
1568 2310 6.210385 TCCATAGATGAGCACTAGGAAATCTC 59.790 42.308 0.00 0.00 0.00 2.75
1569 2311 6.080682 TCCATAGATGAGCACTAGGAAATCT 58.919 40.000 0.00 0.00 0.00 2.40
1570 2312 6.352016 TCCATAGATGAGCACTAGGAAATC 57.648 41.667 0.00 0.00 0.00 2.17
1571 2313 6.949117 ATCCATAGATGAGCACTAGGAAAT 57.051 37.500 0.00 0.00 0.00 2.17
1585 2327 6.243900 CCAAAGTAGGCAATCATCCATAGAT 58.756 40.000 0.00 0.00 0.00 1.98
1586 2328 5.624159 CCAAAGTAGGCAATCATCCATAGA 58.376 41.667 0.00 0.00 0.00 1.98
1587 2329 5.954296 CCAAAGTAGGCAATCATCCATAG 57.046 43.478 0.00 0.00 0.00 2.23
1600 2342 7.391148 TTTATAAAGAGCTTGCCAAAGTAGG 57.609 36.000 0.00 0.00 35.69 3.18
1601 2343 9.129209 GTTTTTATAAAGAGCTTGCCAAAGTAG 57.871 33.333 0.00 0.00 35.69 2.57
1602 2344 8.634444 TGTTTTTATAAAGAGCTTGCCAAAGTA 58.366 29.630 0.00 0.00 35.69 2.24
1603 2345 7.496747 TGTTTTTATAAAGAGCTTGCCAAAGT 58.503 30.769 0.00 0.00 35.69 2.66
1604 2346 7.653311 ACTGTTTTTATAAAGAGCTTGCCAAAG 59.347 33.333 3.23 0.00 37.98 2.77
1605 2347 7.496747 ACTGTTTTTATAAAGAGCTTGCCAAA 58.503 30.769 3.23 0.00 37.98 3.28
1606 2348 7.049799 ACTGTTTTTATAAAGAGCTTGCCAA 57.950 32.000 3.23 0.00 37.98 4.52
1607 2349 6.648879 ACTGTTTTTATAAAGAGCTTGCCA 57.351 33.333 3.23 0.00 37.98 4.92
1608 2350 9.471084 TTTTACTGTTTTTATAAAGAGCTTGCC 57.529 29.630 3.23 0.00 37.98 4.52
1612 2354 9.363401 ACCCTTTTACTGTTTTTATAAAGAGCT 57.637 29.630 3.23 0.00 37.98 4.09
1627 2369 7.174426 CCCTAAAGACAGTTTACCCTTTTACTG 59.826 40.741 0.00 0.00 42.75 2.74
1628 2370 7.147248 ACCCTAAAGACAGTTTACCCTTTTACT 60.147 37.037 0.00 0.00 32.00 2.24
1629 2371 7.000472 ACCCTAAAGACAGTTTACCCTTTTAC 59.000 38.462 0.00 0.00 32.00 2.01
1630 2372 7.152942 ACCCTAAAGACAGTTTACCCTTTTA 57.847 36.000 0.00 0.00 32.00 1.52
1631 2373 6.022107 ACCCTAAAGACAGTTTACCCTTTT 57.978 37.500 0.00 0.00 32.00 2.27
1632 2374 5.658198 ACCCTAAAGACAGTTTACCCTTT 57.342 39.130 0.00 0.00 33.87 3.11
1638 3042 6.429521 AGCAGTTACCCTAAAGACAGTTTA 57.570 37.500 0.00 0.00 0.00 2.01
1702 3106 2.893489 ACCCTCACAGAAGCAAAAATCC 59.107 45.455 0.00 0.00 0.00 3.01
1703 3107 5.473504 TCTTACCCTCACAGAAGCAAAAATC 59.526 40.000 0.00 0.00 0.00 2.17
1704 3108 5.385198 TCTTACCCTCACAGAAGCAAAAAT 58.615 37.500 0.00 0.00 0.00 1.82
1714 3118 3.012518 CAGCCAATTCTTACCCTCACAG 58.987 50.000 0.00 0.00 0.00 3.66
1764 3168 1.457346 CATCACCAGCTCCCAGTTTC 58.543 55.000 0.00 0.00 0.00 2.78
1766 3170 1.687612 CCATCACCAGCTCCCAGTT 59.312 57.895 0.00 0.00 0.00 3.16
1825 3229 0.672401 GTCGTTCTCCGCCCAAATCA 60.672 55.000 0.00 0.00 36.19 2.57
1917 3321 3.619054 GCTTCTAGCATCGTCGGC 58.381 61.111 0.00 0.00 41.89 5.54
1949 3353 5.949952 TGCTTGTAGTGACTAGACCTTCATA 59.050 40.000 0.00 0.00 30.81 2.15
1951 3355 4.149598 TGCTTGTAGTGACTAGACCTTCA 58.850 43.478 0.00 0.00 30.81 3.02
1964 3368 5.067674 TGCTTGTTCTTTGATTGCTTGTAGT 59.932 36.000 0.00 0.00 0.00 2.73
1965 3369 5.522456 TGCTTGTTCTTTGATTGCTTGTAG 58.478 37.500 0.00 0.00 0.00 2.74
2266 3681 0.952497 ACGAGGAAGACAGCGACGTA 60.952 55.000 0.00 0.00 0.00 3.57
2267 3682 2.259439 ACGAGGAAGACAGCGACGT 61.259 57.895 0.00 0.00 0.00 4.34
2282 3701 3.047280 GGCGCAACACATCCACGA 61.047 61.111 10.83 0.00 0.00 4.35
2302 3721 1.805945 GCAGAGGCGTTGACCTACG 60.806 63.158 0.00 0.00 41.32 3.51
2303 3722 0.108138 ATGCAGAGGCGTTGACCTAC 60.108 55.000 0.00 0.00 45.35 3.18
2371 3801 1.132436 CCACGTGCTTGTGTATGCG 59.868 57.895 10.91 0.00 38.20 4.73
2416 3848 1.067916 GCACAAAGCACTTGGGTGG 59.932 57.895 13.90 0.00 40.91 4.61
2512 3947 0.447801 CCCAAATCGTGAAGGAAGCG 59.552 55.000 0.00 0.00 0.00 4.68
2576 4011 0.949105 CACACGAGCAGTTACACCCC 60.949 60.000 0.00 0.00 0.00 4.95
2582 4017 0.667487 GAGCAGCACACGAGCAGTTA 60.667 55.000 0.00 0.00 36.85 2.24
2640 4087 2.100879 AAAGAGGACGAGGCAACGCT 62.101 55.000 0.00 0.00 46.39 5.07
2884 4729 2.417107 GCCATCACATTTGCGGAAATCA 60.417 45.455 12.36 0.00 28.65 2.57
2895 4740 3.740115 GGTATAGAACGGCCATCACATT 58.260 45.455 2.24 0.00 0.00 2.71
2905 4751 2.947652 TGGAGAGAACGGTATAGAACGG 59.052 50.000 0.00 0.00 34.70 4.44
2913 4759 0.037303 ACCGTCTGGAGAGAACGGTA 59.963 55.000 16.36 0.00 45.87 4.02
3125 5016 0.320050 TCCGCATGTAGACAAGCACA 59.680 50.000 10.18 0.00 40.24 4.57
3150 5041 2.359975 CAAAGGCCGGTGGAGGAC 60.360 66.667 1.90 0.00 40.48 3.85
3278 5178 3.130516 CGAAGTCCCACAATCTACTGCTA 59.869 47.826 0.00 0.00 0.00 3.49
3284 5184 2.232941 GACCACGAAGTCCCACAATCTA 59.767 50.000 0.00 0.00 41.61 1.98
3518 5427 5.540911 TCATGACGCATATGAAAGATGCTA 58.459 37.500 6.97 0.00 46.16 3.49
3534 5444 3.273434 ACAAGGTGGATGAATCATGACG 58.727 45.455 0.00 0.00 0.00 4.35
3535 5445 4.521146 AGACAAGGTGGATGAATCATGAC 58.479 43.478 0.00 0.00 0.00 3.06
3569 5479 5.114780 AGAACATGAACAGGAGAATCGATG 58.885 41.667 0.00 0.00 34.37 3.84
3570 5480 5.350504 AGAACATGAACAGGAGAATCGAT 57.649 39.130 0.00 0.00 34.37 3.59
3682 5592 2.887151 AAGGAGCTGCATGGTAAGTT 57.113 45.000 8.35 0.00 0.00 2.66
3735 5645 8.592809 AGAACAAGAGTCAAAGTCTAGAATGAT 58.407 33.333 0.00 0.00 0.00 2.45
3838 5763 2.269241 GGAGGGAAGGTGAAGCCG 59.731 66.667 0.00 0.00 43.70 5.52
3880 5805 1.339151 GGTAGACAAGGCAACAGAGGG 60.339 57.143 0.00 0.00 41.41 4.30
3992 5917 2.806608 GTCTAAAGACACACCACGGA 57.193 50.000 5.24 0.00 44.18 4.69
4173 6279 5.509716 AATATATCCACGTGTGTCGAGAA 57.490 39.130 15.65 0.00 42.86 2.87
4260 6420 2.433239 ACACCCGAATAGGCGTAAGAAT 59.567 45.455 0.00 0.00 39.21 2.40
4362 8563 2.015456 TGAGCACCAGGAGAAGAAGA 57.985 50.000 0.00 0.00 0.00 2.87
4363 8564 2.630158 CATGAGCACCAGGAGAAGAAG 58.370 52.381 0.00 0.00 0.00 2.85
4364 8565 1.339438 GCATGAGCACCAGGAGAAGAA 60.339 52.381 0.00 0.00 41.58 2.52
4423 8886 0.167470 CAATGCACAAGCCGTCTCAG 59.833 55.000 0.00 0.00 41.13 3.35
4439 8902 3.579534 AGAGAGGCTGCAATCATCAAT 57.420 42.857 0.50 0.00 0.00 2.57
4467 8930 2.521708 AGCCGCAGCCCAAAAGTT 60.522 55.556 0.00 0.00 41.25 2.66
4480 8943 2.032528 TGGAAGTGAAGGCAGCCG 59.967 61.111 5.55 0.00 0.00 5.52
4486 8949 5.922053 TGATGAGATATGTGGAAGTGAAGG 58.078 41.667 0.00 0.00 0.00 3.46
4549 9014 6.813649 CAGGAGAACGATCAAAAAGATACTCA 59.186 38.462 0.00 0.00 37.00 3.41
4553 9018 9.314321 GTAATCAGGAGAACGATCAAAAAGATA 57.686 33.333 0.00 0.00 37.00 1.98
4587 9052 4.213059 AGCAAACACAACCAAACAAACAAG 59.787 37.500 0.00 0.00 0.00 3.16
4637 9102 3.257933 CTGAGCGGACAGTTTGGC 58.742 61.111 0.00 0.00 33.73 4.52
4684 9149 1.670087 CGGTAGCCCTTATGCTCATCG 60.670 57.143 0.00 0.00 41.68 3.84


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

AutoCloner maintained by Alex Coulton.