Multiple sequence alignment - TraesCS2D01G111700

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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 TraesCS2D01G111700 chr2D 100.000 3206 0 0 900 4105 62034572 62031367 0.000000e+00 5921.0
1 TraesCS2D01G111700 chr2D 100.000 487 0 0 1 487 62035471 62034985 0.000000e+00 900.0
2 TraesCS2D01G111700 chr2D 100.000 196 0 0 4441 4636 62031031 62030836 3.410000e-96 363.0
3 TraesCS2D01G111700 chr2D 87.708 301 26 5 1741 2038 165661848 165662140 1.600000e-89 340.0
4 TraesCS2D01G111700 chr2D 78.974 195 39 1 31 225 477275236 477275044 1.050000e-26 132.0
5 TraesCS2D01G111700 chr2A 89.128 1067 58 17 2050 3114 62370730 62369720 0.000000e+00 1275.0
6 TraesCS2D01G111700 chr2A 91.730 786 45 9 900 1673 62371827 62371050 0.000000e+00 1074.0
7 TraesCS2D01G111700 chr2A 85.989 935 52 35 3203 4105 62369723 62368836 0.000000e+00 928.0
8 TraesCS2D01G111700 chr2A 91.242 491 33 7 1 487 62372421 62371937 0.000000e+00 660.0
9 TraesCS2D01G111700 chr2B 84.521 1221 117 33 2038 3243 97396128 97394965 0.000000e+00 1142.0
10 TraesCS2D01G111700 chr2B 93.836 730 37 4 3319 4040 97394796 97394067 0.000000e+00 1092.0
11 TraesCS2D01G111700 chr2B 89.873 790 50 15 900 1673 97397247 97396472 0.000000e+00 989.0
12 TraesCS2D01G111700 chr2B 91.878 197 7 4 4441 4636 97393985 97393797 2.750000e-67 267.0
13 TraesCS2D01G111700 chr2B 94.505 91 3 1 399 487 97397462 97397372 6.250000e-29 139.0
14 TraesCS2D01G111700 chr2B 100.000 38 0 0 4068 4105 97394066 97394029 2.310000e-08 71.3
15 TraesCS2D01G111700 chr3B 86.635 419 33 13 939 1357 80351142 80351537 4.260000e-120 442.0
16 TraesCS2D01G111700 chr3B 78.414 454 51 30 1070 1502 729710686 729710259 7.700000e-63 252.0
17 TraesCS2D01G111700 chr3B 83.505 291 25 14 1070 1355 350050154 350050426 2.770000e-62 250.0
18 TraesCS2D01G111700 chr1A 87.948 307 25 6 1737 2040 29638895 29639192 7.380000e-93 351.0
19 TraesCS2D01G111700 chr1A 78.097 452 57 30 1070 1502 26548101 26547673 9.960000e-62 248.0
20 TraesCS2D01G111700 chr5A 88.119 303 25 5 1741 2040 685424355 685424061 2.650000e-92 350.0
21 TraesCS2D01G111700 chr5A 87.459 303 25 6 1741 2040 460168325 460168617 2.070000e-88 337.0
22 TraesCS2D01G111700 chr4A 88.119 303 25 5 1741 2040 741933450 741933156 2.650000e-92 350.0
23 TraesCS2D01G111700 chr6B 87.789 303 26 5 1741 2040 666647933 666648227 1.230000e-90 344.0
24 TraesCS2D01G111700 chr6B 84.138 290 25 12 1070 1355 553748456 553748728 1.280000e-65 261.0
25 TraesCS2D01G111700 chr5B 87.789 303 26 5 1741 2040 653177822 653178116 1.230000e-90 344.0
26 TraesCS2D01G111700 chr5B 84.590 305 35 8 1737 2038 163655843 163655548 4.540000e-75 292.0
27 TraesCS2D01G111700 chr5B 84.083 289 27 14 1070 1355 711381015 711381287 1.280000e-65 261.0
28 TraesCS2D01G111700 chr5D 87.708 301 26 5 1741 2038 437730567 437730275 1.600000e-89 340.0
29 TraesCS2D01G111700 chr5D 79.424 243 41 6 32 271 455809805 455810041 3.710000e-36 163.0
30 TraesCS2D01G111700 chr5D 78.166 229 44 5 1 225 298865118 298865344 1.740000e-29 141.0
31 TraesCS2D01G111700 chr3A 86.441 236 23 8 1070 1303 622458915 622459143 2.770000e-62 250.0
32 TraesCS2D01G111700 chr3D 81.183 186 32 3 32 217 579896173 579895991 3.740000e-31 147.0
33 TraesCS2D01G111700 chr1B 79.695 197 38 2 30 225 323322863 323322668 1.740000e-29 141.0
34 TraesCS2D01G111700 chr4D 79.592 196 35 4 32 225 13309434 13309626 8.090000e-28 135.0
35 TraesCS2D01G111700 chr7A 77.021 235 47 6 33 266 193612711 193612939 1.350000e-25 128.0
36 TraesCS2D01G111700 chr7A 79.082 196 33 5 32 224 546267235 546267425 1.350000e-25 128.0


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 TraesCS2D01G111700 chr2D 62030836 62035471 4635 True 2394.666667 5921 100.00000 1 4636 3 chr2D.!!$R2 4635
1 TraesCS2D01G111700 chr2A 62368836 62372421 3585 True 984.250000 1275 89.52225 1 4105 4 chr2A.!!$R1 4104
2 TraesCS2D01G111700 chr2B 97393797 97397462 3665 True 616.716667 1142 92.43550 399 4636 6 chr2B.!!$R1 4237

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
128 129 0.610232 GGGCACTTGCATGGAGACTT 60.610 55.0 3.15 0.0 44.36 3.01 F
1304 1309 0.037232 GTCCGTTTCCTCTGTCTGGG 60.037 60.0 0.00 0.0 0.00 4.45 F
1699 1719 0.029267 AATGAGGGGAGGATGGAGCT 60.029 55.0 0.00 0.0 0.00 4.09 F
1712 1732 0.107703 TGGAGCTGGCTTTATCGGTG 60.108 55.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1700 0.029267 AGCTCCATCCTCCCCTCATT 60.029 55.000 0.00 0.00 0.00 2.57 R
2670 2754 0.610687 GGCTGCTTAGTGGACTCAGT 59.389 55.000 0.00 0.00 0.00 3.41 R
3587 3823 1.014564 CCGACGGAAGGAACTGCTTC 61.015 60.000 8.64 2.57 40.86 3.86 R
3695 3931 4.446719 GCCAGATTGTTTTTGCTCAGAAAG 59.553 41.667 0.00 0.00 0.00 2.62 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
60 61 4.383552 GGTGTCAGGTGCTTCAGATCTATT 60.384 45.833 0.00 0.00 0.00 1.73
64 65 6.054295 GTCAGGTGCTTCAGATCTATTCAAT 58.946 40.000 0.00 0.00 0.00 2.57
65 66 6.018098 GTCAGGTGCTTCAGATCTATTCAATG 60.018 42.308 0.00 0.00 0.00 2.82
80 81 2.552031 TCAATGGTTCAACAACGACGA 58.448 42.857 0.00 0.00 32.68 4.20
91 92 1.662122 ACAACGACGACCACAAACTTC 59.338 47.619 0.00 0.00 0.00 3.01
93 94 1.567504 ACGACGACCACAAACTTCAG 58.432 50.000 0.00 0.00 0.00 3.02
97 98 0.817634 CGACCACAAACTTCAGGGCA 60.818 55.000 0.00 0.00 0.00 5.36
98 99 1.620822 GACCACAAACTTCAGGGCAT 58.379 50.000 0.00 0.00 0.00 4.40
99 100 1.541588 GACCACAAACTTCAGGGCATC 59.458 52.381 0.00 0.00 0.00 3.91
115 116 1.003051 ATCGGTCCTTAGGGGCACT 59.997 57.895 0.00 0.00 39.39 4.40
118 119 1.378646 GGTCCTTAGGGGCACTTGC 60.379 63.158 0.00 0.00 39.39 4.01
128 129 0.610232 GGGCACTTGCATGGAGACTT 60.610 55.000 3.15 0.00 44.36 3.01
131 132 1.200948 GCACTTGCATGGAGACTTTCC 59.799 52.381 4.44 0.00 42.96 3.13
167 168 2.187946 CAAGCTGGCTCCGGTAGG 59.812 66.667 0.00 0.00 39.46 3.18
223 224 1.876714 CGGCGGTAGTGGTCATTCG 60.877 63.158 0.00 0.00 0.00 3.34
225 226 2.171725 GCGGTAGTGGTCATTCGGC 61.172 63.158 0.00 0.00 0.00 5.54
229 230 1.641577 GTAGTGGTCATTCGGCAGAC 58.358 55.000 0.00 0.00 0.00 3.51
230 231 1.204941 GTAGTGGTCATTCGGCAGACT 59.795 52.381 0.00 0.00 35.18 3.24
231 232 1.557099 AGTGGTCATTCGGCAGACTA 58.443 50.000 0.00 0.00 35.18 2.59
232 233 1.478510 AGTGGTCATTCGGCAGACTAG 59.521 52.381 0.00 0.00 35.18 2.57
245 246 2.298729 GCAGACTAGCTGGGGATCTAAG 59.701 54.545 13.68 0.00 45.03 2.18
255 256 4.644685 GCTGGGGATCTAAGTGCAATTTTA 59.355 41.667 4.05 0.00 0.00 1.52
256 257 5.302823 GCTGGGGATCTAAGTGCAATTTTAT 59.697 40.000 4.05 0.00 0.00 1.40
258 259 7.014230 GCTGGGGATCTAAGTGCAATTTTATTA 59.986 37.037 4.05 0.00 0.00 0.98
259 260 9.082313 CTGGGGATCTAAGTGCAATTTTATTAT 57.918 33.333 4.05 0.00 0.00 1.28
260 261 8.859090 TGGGGATCTAAGTGCAATTTTATTATG 58.141 33.333 4.05 0.00 0.00 1.90
271 273 6.593382 TGCAATTTTATTATGTTTGAGGTGCC 59.407 34.615 0.00 0.00 0.00 5.01
293 295 9.712305 GTGCCTTTAGCTCTTATAATAGATTCA 57.288 33.333 2.20 0.00 44.23 2.57
362 365 3.135225 TGAATTTGGACGAACGATGTGT 58.865 40.909 0.14 0.00 0.00 3.72
380 383 1.142667 TGTCATCAGCAACCACAGGAA 59.857 47.619 0.00 0.00 0.00 3.36
381 384 1.808945 GTCATCAGCAACCACAGGAAG 59.191 52.381 0.00 0.00 0.00 3.46
989 992 3.057245 GCAGAAGCTTTCGAATCCCTTTT 60.057 43.478 0.00 0.00 37.91 2.27
1144 1149 2.280524 TCGTTCCTTGCCGTGTGG 60.281 61.111 0.00 0.00 38.77 4.17
1304 1309 0.037232 GTCCGTTTCCTCTGTCTGGG 60.037 60.000 0.00 0.00 0.00 4.45
1305 1310 0.178944 TCCGTTTCCTCTGTCTGGGA 60.179 55.000 0.00 0.00 0.00 4.37
1306 1311 0.037232 CCGTTTCCTCTGTCTGGGAC 60.037 60.000 0.00 0.00 0.00 4.46
1307 1312 0.969894 CGTTTCCTCTGTCTGGGACT 59.030 55.000 0.00 0.00 33.15 3.85
1308 1313 1.067495 CGTTTCCTCTGTCTGGGACTC 60.067 57.143 0.00 0.00 33.15 3.36
1309 1314 2.252714 GTTTCCTCTGTCTGGGACTCT 58.747 52.381 0.00 0.00 33.15 3.24
1321 1326 1.920835 GGACTCTGGGGGAACTGCT 60.921 63.158 0.00 0.00 0.00 4.24
1325 1330 0.984230 CTCTGGGGGAACTGCTTGTA 59.016 55.000 0.00 0.00 0.00 2.41
1341 1346 6.707161 ACTGCTTGTAAATTGTGCATTTCAAT 59.293 30.769 0.00 0.00 36.43 2.57
1350 1355 2.892215 TGTGCATTTCAATCTGCCTTGA 59.108 40.909 0.00 0.00 37.59 3.02
1426 1432 8.355913 TGATGCATGAACTGTGTGTTAATTTTA 58.644 29.630 2.46 0.00 39.30 1.52
1427 1433 9.357652 GATGCATGAACTGTGTGTTAATTTTAT 57.642 29.630 2.46 0.00 39.30 1.40
1429 1435 7.536964 TGCATGAACTGTGTGTTAATTTTATCG 59.463 33.333 0.00 0.00 39.30 2.92
1431 1437 7.499321 TGAACTGTGTGTTAATTTTATCGGT 57.501 32.000 0.00 0.00 39.30 4.69
1446 1452 2.536761 TCGGTCAAGTTGAAATCGGT 57.463 45.000 7.25 0.00 0.00 4.69
1451 1457 4.212636 CGGTCAAGTTGAAATCGGTTTAGT 59.787 41.667 7.25 0.00 0.00 2.24
1468 1474 0.333993 AGTTCCCATCAGCAATGCCT 59.666 50.000 0.00 0.00 33.71 4.75
1474 1480 1.179152 CATCAGCAATGCCTGTGGAA 58.821 50.000 0.00 0.00 34.47 3.53
1479 1485 1.274167 AGCAATGCCTGTGGAATTGTG 59.726 47.619 16.20 0.00 34.48 3.33
1520 1530 2.742372 GGGTAGCTGTGGTGTGCG 60.742 66.667 0.00 0.00 0.00 5.34
1522 1532 2.357517 GTAGCTGTGGTGTGCGCT 60.358 61.111 9.73 0.00 36.56 5.92
1523 1533 2.048222 TAGCTGTGGTGTGCGCTC 60.048 61.111 9.73 5.51 34.14 5.03
1524 1534 3.914605 TAGCTGTGGTGTGCGCTCG 62.915 63.158 9.73 0.00 34.14 5.03
1571 1582 7.858382 CGAGTATTCAATTCTGGAGTAGTGTAG 59.142 40.741 0.00 0.00 0.00 2.74
1583 1602 2.093447 AGTAGTGTAGCACAAGGATGGC 60.093 50.000 2.01 0.00 36.74 4.40
1611 1631 5.006153 TCGTAGGACAAGATGTGGTTATG 57.994 43.478 0.00 0.00 0.00 1.90
1612 1632 4.464951 TCGTAGGACAAGATGTGGTTATGT 59.535 41.667 0.00 0.00 0.00 2.29
1613 1633 5.653330 TCGTAGGACAAGATGTGGTTATGTA 59.347 40.000 0.00 0.00 0.00 2.29
1614 1634 6.322969 TCGTAGGACAAGATGTGGTTATGTAT 59.677 38.462 0.00 0.00 0.00 2.29
1622 1642 7.987458 ACAAGATGTGGTTATGTATAGGTTGAG 59.013 37.037 0.00 0.00 0.00 3.02
1624 1644 5.685520 TGTGGTTATGTATAGGTTGAGCA 57.314 39.130 0.00 0.00 0.00 4.26
1673 1693 2.026262 TCTTTCCCTGTAATCAGTGGCC 60.026 50.000 0.00 0.00 39.82 5.36
1675 1695 0.548926 TCCCTGTAATCAGTGGCCCA 60.549 55.000 0.00 0.00 39.82 5.36
1676 1696 0.331278 CCCTGTAATCAGTGGCCCAA 59.669 55.000 0.00 0.00 39.82 4.12
1678 1698 1.463674 CTGTAATCAGTGGCCCAACC 58.536 55.000 0.00 0.00 36.97 3.77
1679 1699 1.271871 CTGTAATCAGTGGCCCAACCA 60.272 52.381 0.00 0.00 38.30 3.67
1687 1707 3.712287 GGCCCAACCAAATGAGGG 58.288 61.111 0.00 0.00 44.37 4.30
1688 1708 1.989508 GGCCCAACCAAATGAGGGG 60.990 63.158 0.00 0.00 41.75 4.79
1689 1709 1.078347 GCCCAACCAAATGAGGGGA 59.922 57.895 0.00 0.00 41.49 4.81
1690 1710 0.972471 GCCCAACCAAATGAGGGGAG 60.972 60.000 0.00 0.00 41.49 4.30
1691 1711 0.324645 CCCAACCAAATGAGGGGAGG 60.325 60.000 0.00 0.00 41.49 4.30
1692 1712 0.704076 CCAACCAAATGAGGGGAGGA 59.296 55.000 0.00 0.00 0.00 3.71
1693 1713 1.288932 CCAACCAAATGAGGGGAGGAT 59.711 52.381 0.00 0.00 0.00 3.24
1694 1714 2.381911 CAACCAAATGAGGGGAGGATG 58.618 52.381 0.00 0.00 0.00 3.51
1695 1715 0.929244 ACCAAATGAGGGGAGGATGG 59.071 55.000 0.00 0.00 0.00 3.51
1696 1716 1.225373 CCAAATGAGGGGAGGATGGA 58.775 55.000 0.00 0.00 0.00 3.41
1697 1717 1.144503 CCAAATGAGGGGAGGATGGAG 59.855 57.143 0.00 0.00 0.00 3.86
1698 1718 0.849417 AAATGAGGGGAGGATGGAGC 59.151 55.000 0.00 0.00 0.00 4.70
1699 1719 0.029267 AATGAGGGGAGGATGGAGCT 60.029 55.000 0.00 0.00 0.00 4.09
1700 1720 0.767446 ATGAGGGGAGGATGGAGCTG 60.767 60.000 0.00 0.00 0.00 4.24
1701 1721 2.040043 AGGGGAGGATGGAGCTGG 60.040 66.667 0.00 0.00 0.00 4.85
1702 1722 3.883549 GGGGAGGATGGAGCTGGC 61.884 72.222 0.00 0.00 0.00 4.85
1703 1723 2.771762 GGGAGGATGGAGCTGGCT 60.772 66.667 0.00 0.00 0.00 4.75
1704 1724 2.381941 GGGAGGATGGAGCTGGCTT 61.382 63.158 0.00 0.00 0.00 4.35
1705 1725 1.611965 GGAGGATGGAGCTGGCTTT 59.388 57.895 0.00 0.00 0.00 3.51
1706 1726 0.839946 GGAGGATGGAGCTGGCTTTA 59.160 55.000 0.00 0.00 0.00 1.85
1707 1727 1.423161 GGAGGATGGAGCTGGCTTTAT 59.577 52.381 0.00 0.00 0.00 1.40
1708 1728 2.551938 GGAGGATGGAGCTGGCTTTATC 60.552 54.545 0.00 4.38 0.00 1.75
1709 1729 1.071385 AGGATGGAGCTGGCTTTATCG 59.929 52.381 0.00 0.00 0.00 2.92
1710 1730 1.517242 GATGGAGCTGGCTTTATCGG 58.483 55.000 0.00 0.00 0.00 4.18
1711 1731 0.839946 ATGGAGCTGGCTTTATCGGT 59.160 50.000 0.00 0.00 0.00 4.69
1712 1732 0.107703 TGGAGCTGGCTTTATCGGTG 60.108 55.000 0.00 0.00 0.00 4.94
1713 1733 0.178068 GGAGCTGGCTTTATCGGTGA 59.822 55.000 0.00 0.00 0.00 4.02
1714 1734 1.202698 GGAGCTGGCTTTATCGGTGAT 60.203 52.381 0.00 0.00 0.00 3.06
1715 1735 2.139118 GAGCTGGCTTTATCGGTGATC 58.861 52.381 0.00 0.00 0.00 2.92
1716 1736 1.202698 AGCTGGCTTTATCGGTGATCC 60.203 52.381 0.00 0.00 0.00 3.36
1717 1737 1.202698 GCTGGCTTTATCGGTGATCCT 60.203 52.381 0.00 0.00 0.00 3.24
1718 1738 2.760374 CTGGCTTTATCGGTGATCCTC 58.240 52.381 0.00 0.00 0.00 3.71
1719 1739 2.366916 CTGGCTTTATCGGTGATCCTCT 59.633 50.000 0.00 0.00 0.00 3.69
1720 1740 2.103094 TGGCTTTATCGGTGATCCTCTG 59.897 50.000 0.00 0.00 0.00 3.35
1721 1741 2.365617 GGCTTTATCGGTGATCCTCTGA 59.634 50.000 0.00 0.00 0.00 3.27
1722 1742 3.385577 GCTTTATCGGTGATCCTCTGAC 58.614 50.000 0.00 0.00 0.00 3.51
1723 1743 3.633235 CTTTATCGGTGATCCTCTGACG 58.367 50.000 0.00 0.00 0.00 4.35
1724 1744 2.632987 TATCGGTGATCCTCTGACGA 57.367 50.000 0.00 0.00 34.70 4.20
1725 1745 1.313772 ATCGGTGATCCTCTGACGAG 58.686 55.000 0.00 0.00 37.01 4.18
1726 1746 0.252197 TCGGTGATCCTCTGACGAGA 59.748 55.000 0.00 0.00 39.74 4.04
1727 1747 0.660488 CGGTGATCCTCTGACGAGAG 59.340 60.000 0.00 0.00 44.94 3.20
1743 1763 3.694566 ACGAGAGTTTTTGCTTTCAAGGT 59.305 39.130 0.00 0.00 46.40 3.50
1768 1788 0.108207 ATGCCTAGACAGAGCATGGC 59.892 55.000 3.01 0.00 45.20 4.40
1774 1794 2.675519 GACAGAGCATGGCTTCTCG 58.324 57.895 0.00 0.00 39.88 4.04
1790 1810 4.627467 GCTTCTCGATCAAGTTTCTTGCTA 59.373 41.667 4.82 0.00 0.00 3.49
1792 1812 4.495422 TCTCGATCAAGTTTCTTGCTACC 58.505 43.478 4.82 0.00 0.00 3.18
1881 1909 9.205719 CTATCTCCAAACTGATAATGATGTGAG 57.794 37.037 0.00 0.00 0.00 3.51
1936 1964 3.077359 AGAGGCATAAACAGTGCAGTTC 58.923 45.455 0.00 0.00 44.25 3.01
1941 1969 5.355350 AGGCATAAACAGTGCAGTTCTAATC 59.645 40.000 0.00 0.00 44.25 1.75
1946 1974 3.589988 ACAGTGCAGTTCTAATCTTCCG 58.410 45.455 0.00 0.00 0.00 4.30
1951 1979 5.597182 AGTGCAGTTCTAATCTTCCGGTATA 59.403 40.000 0.00 0.00 0.00 1.47
1982 2011 7.128109 TGGGTAATAATGTCATGGAAGTCCTTA 59.872 37.037 0.00 0.00 36.82 2.69
1983 2012 7.444487 GGGTAATAATGTCATGGAAGTCCTTAC 59.556 40.741 0.00 0.00 36.82 2.34
1996 2026 8.651589 TGGAAGTCCTTACTATACTCATATGG 57.348 38.462 2.13 0.00 33.75 2.74
2000 2030 7.536625 AGTCCTTACTATACTCATATGGGTGT 58.463 38.462 18.87 14.36 32.84 4.16
2017 2047 5.898174 TGGGTGTTTAGTATACTCACATCG 58.102 41.667 19.31 0.00 0.00 3.84
2018 2048 5.653330 TGGGTGTTTAGTATACTCACATCGA 59.347 40.000 19.31 13.92 0.00 3.59
2048 2113 5.037385 CACGGTGTCAGTTATACTCATGAG 58.963 45.833 21.37 21.37 0.00 2.90
2117 2193 2.084546 AGAAATAGTTTCCTGTGGCGC 58.915 47.619 0.00 0.00 40.54 6.53
2158 2234 2.282555 CACATTTCTCGTGATAGCACCG 59.717 50.000 5.36 1.07 42.09 4.94
2164 2240 1.402259 CTCGTGATAGCACCGTTCTCT 59.598 52.381 5.36 0.00 42.09 3.10
2172 2248 3.746045 AGCACCGTTCTCTTCAGTTTA 57.254 42.857 0.00 0.00 0.00 2.01
2213 2289 6.604171 TCACTAGGTCGTTATATGTAGGGAA 58.396 40.000 0.00 0.00 0.00 3.97
2396 2475 7.147828 GGAGATGATTTTCTTTTTAAGGAGGGG 60.148 40.741 0.00 0.00 0.00 4.79
2400 2479 6.431852 TGATTTTCTTTTTAAGGAGGGGTACG 59.568 38.462 0.00 0.00 0.00 3.67
2401 2480 3.339253 TCTTTTTAAGGAGGGGTACGC 57.661 47.619 0.29 0.29 43.76 4.42
2423 2502 6.256539 ACGCTCAGTGATCAATGTTATTACAG 59.743 38.462 21.49 11.38 37.77 2.74
2460 2544 0.738975 TGATAGGCAGGTCGAAGTCG 59.261 55.000 0.00 0.00 41.45 4.18
2504 2588 0.995024 ACTGCCTCCTGCCTAATTGT 59.005 50.000 0.00 0.00 40.16 2.71
2620 2704 7.601886 TCTTCAGCAGTAGATTGAAAAAGAGAG 59.398 37.037 0.00 0.00 31.11 3.20
2634 2718 4.950205 AAAGAGAGAGAACAACCGGTAA 57.050 40.909 8.00 0.00 0.00 2.85
2670 2754 3.074857 AGGGCCCAAGATTACCTGATA 57.925 47.619 27.56 0.00 0.00 2.15
2704 2788 1.419387 GCAGCCACATAGATCCCTCTT 59.581 52.381 0.00 0.00 32.66 2.85
2705 2789 2.549778 GCAGCCACATAGATCCCTCTTC 60.550 54.545 0.00 0.00 32.66 2.87
2706 2790 2.971330 CAGCCACATAGATCCCTCTTCT 59.029 50.000 0.00 0.00 32.66 2.85
2707 2791 4.155709 CAGCCACATAGATCCCTCTTCTA 58.844 47.826 0.00 0.00 32.66 2.10
2709 2793 5.070981 CAGCCACATAGATCCCTCTTCTAAA 59.929 44.000 0.00 0.00 32.66 1.85
2710 2794 5.071115 AGCCACATAGATCCCTCTTCTAAAC 59.929 44.000 0.00 0.00 32.66 2.01
2744 2828 2.485426 GCATTCTGCTTCAACTGCACTA 59.515 45.455 0.00 0.00 40.96 2.74
2747 2831 4.600692 TTCTGCTTCAACTGCACTAGTA 57.399 40.909 0.00 0.00 39.18 1.82
2805 2890 6.977502 CCAGTTAGTCTCTTATCATGACACAG 59.022 42.308 0.00 0.00 33.56 3.66
2919 3004 9.039870 CATCTGAATTAGTATGGTTCTGACTTC 57.960 37.037 0.00 0.00 34.26 3.01
2960 3047 2.432510 TGGATTTTCGTTTTGCCCTTGT 59.567 40.909 0.00 0.00 0.00 3.16
2963 3050 2.570442 TTTCGTTTTGCCCTTGTGAC 57.430 45.000 0.00 0.00 0.00 3.67
2967 3054 1.047801 GTTTTGCCCTTGTGACCCAT 58.952 50.000 0.00 0.00 0.00 4.00
2987 3074 3.074675 TCTCGTGGAAGAGAGTTAGCT 57.925 47.619 0.00 0.00 41.86 3.32
2988 3075 2.750166 TCTCGTGGAAGAGAGTTAGCTG 59.250 50.000 0.00 0.00 41.86 4.24
2989 3076 1.202582 TCGTGGAAGAGAGTTAGCTGC 59.797 52.381 0.00 0.00 0.00 5.25
2990 3077 1.634702 GTGGAAGAGAGTTAGCTGCG 58.365 55.000 0.00 0.00 0.00 5.18
2991 3078 0.108615 TGGAAGAGAGTTAGCTGCGC 60.109 55.000 0.00 0.00 0.00 6.09
3037 3129 7.360361 ACTTTTCAGACCTTTTATTAACGCTG 58.640 34.615 0.00 0.00 0.00 5.18
3059 3151 3.533606 AGGTTCCTGTGATCTCATTCG 57.466 47.619 0.00 0.00 0.00 3.34
3096 3188 6.231211 ACCTACTTGTATTGTTCTTGACTGG 58.769 40.000 0.00 0.00 0.00 4.00
3120 3212 5.755861 GTCTTATAGATGTCCTGCCACTTTC 59.244 44.000 0.00 0.00 0.00 2.62
3121 3213 2.672961 TAGATGTCCTGCCACTTTCG 57.327 50.000 0.00 0.00 0.00 3.46
3154 3246 3.698040 AGGCAATATTCTGGTTTGCTCAG 59.302 43.478 6.80 0.00 43.98 3.35
3174 3266 3.053077 AGCAGGGTAATATGTTGGGCTA 58.947 45.455 0.00 0.00 0.00 3.93
3178 3270 4.218417 CAGGGTAATATGTTGGGCTATTGC 59.782 45.833 0.00 0.00 38.76 3.56
3189 3281 0.378610 GGCTATTGCGCAGTCCTTTC 59.621 55.000 9.34 0.00 40.82 2.62
3190 3282 1.086696 GCTATTGCGCAGTCCTTTCA 58.913 50.000 9.34 0.00 0.00 2.69
3199 3292 1.528129 CAGTCCTTTCAGGCACTTCC 58.472 55.000 0.00 0.00 34.60 3.46
3293 3386 9.474920 TGATTTCATTCAATTTGTTTGTCTACC 57.525 29.630 0.00 0.00 36.65 3.18
3317 3410 3.372566 CCTTGTTATCCCTGGTGGCATTA 60.373 47.826 0.00 0.00 0.00 1.90
3353 3588 2.695359 TCTTATCAACGTCCTTGTGCC 58.305 47.619 0.00 0.00 0.00 5.01
3354 3589 2.037902 TCTTATCAACGTCCTTGTGCCA 59.962 45.455 0.00 0.00 0.00 4.92
3355 3590 2.779755 TATCAACGTCCTTGTGCCAT 57.220 45.000 0.00 0.00 0.00 4.40
3356 3591 1.909700 ATCAACGTCCTTGTGCCATT 58.090 45.000 0.00 0.00 0.00 3.16
3357 3592 1.686355 TCAACGTCCTTGTGCCATTT 58.314 45.000 0.00 0.00 0.00 2.32
3358 3593 2.028130 TCAACGTCCTTGTGCCATTTT 58.972 42.857 0.00 0.00 0.00 1.82
3359 3594 2.428890 TCAACGTCCTTGTGCCATTTTT 59.571 40.909 0.00 0.00 0.00 1.94
3384 3619 3.708403 TCAAACAGAGTGCATCTCCAT 57.292 42.857 11.24 0.29 43.71 3.41
3385 3620 4.025040 TCAAACAGAGTGCATCTCCATT 57.975 40.909 11.24 5.28 43.71 3.16
3386 3621 4.005650 TCAAACAGAGTGCATCTCCATTC 58.994 43.478 11.24 0.00 43.71 2.67
3457 3692 6.548441 TGTTTTGGCTGTACACATACTTAC 57.452 37.500 0.00 0.00 32.00 2.34
3459 3694 6.425721 TGTTTTGGCTGTACACATACTTACTC 59.574 38.462 0.00 0.00 32.00 2.59
3491 3727 1.289160 TCTACCTTGGCAGGCTTCAT 58.711 50.000 0.00 0.00 45.56 2.57
3560 3796 3.639094 AGTACTATGATCACCAGTCAGGC 59.361 47.826 13.63 5.49 43.14 4.85
3587 3823 3.423123 GGTCAAAAGTTCACGACTATGCG 60.423 47.826 0.00 0.00 37.72 4.73
3695 3931 7.041780 AGCTGATATGGAATTCGTTGATGTTAC 60.042 37.037 0.00 0.00 0.00 2.50
3705 3941 4.627058 TCGTTGATGTTACTTTCTGAGCA 58.373 39.130 0.00 0.00 0.00 4.26
3706 3942 5.053811 TCGTTGATGTTACTTTCTGAGCAA 58.946 37.500 0.00 0.00 0.00 3.91
3831 4069 6.098552 TCCGTGGTGATGGAAATATGTACTTA 59.901 38.462 0.00 0.00 34.00 2.24
3959 4218 9.606631 AAGCTTATGGAGTGTCTTATTTCTAAG 57.393 33.333 0.00 0.00 36.46 2.18
4045 4305 1.988293 TTGAGGGCGTTTTGATGGAA 58.012 45.000 0.00 0.00 0.00 3.53
4052 4322 1.336240 GCGTTTTGATGGAAAGCAGCT 60.336 47.619 0.00 0.00 0.00 4.24
4060 4330 2.113860 TGGAAAGCAGCTGGTCATAC 57.886 50.000 20.46 12.65 0.00 2.39
4470 4740 5.337894 GCTTAGCTGCTGATATCTATTCCCA 60.338 44.000 13.43 0.00 0.00 4.37
4480 4750 6.499436 TGATATCTATTCCCACTCCGGATAA 58.501 40.000 3.57 0.00 36.56 1.75
4503 4773 1.310933 TACCTCTTGGAGACGCGGAC 61.311 60.000 12.47 3.93 37.04 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.956477 GCACCTGACACCAAATCTTGT 59.044 47.619 0.00 0.00 0.00 3.16
30 31 2.664402 AGCACCTGACACCAAATCTT 57.336 45.000 0.00 0.00 0.00 2.40
60 61 2.285756 GTCGTCGTTGTTGAACCATTGA 59.714 45.455 0.00 0.00 0.00 2.57
64 65 0.108281 TGGTCGTCGTTGTTGAACCA 60.108 50.000 0.00 0.00 0.00 3.67
65 66 0.302589 GTGGTCGTCGTTGTTGAACC 59.697 55.000 0.00 0.00 0.00 3.62
80 81 1.620822 GATGCCCTGAAGTTTGTGGT 58.379 50.000 0.00 0.00 0.00 4.16
91 92 1.447643 CCTAAGGACCGATGCCCTG 59.552 63.158 0.00 0.00 32.12 4.45
93 94 2.819284 CCCCTAAGGACCGATGCCC 61.819 68.421 0.00 0.00 38.24 5.36
97 98 0.620700 AAGTGCCCCTAAGGACCGAT 60.621 55.000 0.00 0.00 38.24 4.18
98 99 1.229400 AAGTGCCCCTAAGGACCGA 60.229 57.895 0.00 0.00 38.24 4.69
99 100 1.078426 CAAGTGCCCCTAAGGACCG 60.078 63.158 0.00 0.00 38.24 4.79
115 116 1.347707 AGTCGGAAAGTCTCCATGCAA 59.652 47.619 0.00 0.00 45.74 4.08
118 119 3.664107 TGAAAGTCGGAAAGTCTCCATG 58.336 45.455 0.00 0.00 45.74 3.66
128 129 2.036733 ACCTTGTCGATGAAAGTCGGAA 59.963 45.455 0.00 0.00 41.74 4.30
131 132 2.672714 TGACCTTGTCGATGAAAGTCG 58.327 47.619 0.00 0.00 42.74 4.18
136 137 2.416747 CAGCTTGACCTTGTCGATGAA 58.583 47.619 0.00 0.00 34.95 2.57
188 189 0.596083 CCGCTAGAATGAGCTGACGG 60.596 60.000 0.00 0.00 40.51 4.79
223 224 0.762461 AGATCCCCAGCTAGTCTGCC 60.762 60.000 8.23 0.00 41.50 4.85
225 226 3.320541 CACTTAGATCCCCAGCTAGTCTG 59.679 52.174 7.07 7.07 42.49 3.51
229 230 2.042464 TGCACTTAGATCCCCAGCTAG 58.958 52.381 0.00 0.00 0.00 3.42
230 231 2.174685 TGCACTTAGATCCCCAGCTA 57.825 50.000 0.00 0.00 0.00 3.32
231 232 1.289160 TTGCACTTAGATCCCCAGCT 58.711 50.000 0.00 0.00 0.00 4.24
232 233 2.355010 ATTGCACTTAGATCCCCAGC 57.645 50.000 0.00 0.00 0.00 4.85
235 236 8.860088 ACATAATAAAATTGCACTTAGATCCCC 58.140 33.333 0.00 0.00 0.00 4.81
245 246 7.412891 GGCACCTCAAACATAATAAAATTGCAC 60.413 37.037 0.00 0.00 0.00 4.57
255 256 5.264395 AGCTAAAGGCACCTCAAACATAAT 58.736 37.500 0.00 0.00 44.79 1.28
256 257 4.662278 AGCTAAAGGCACCTCAAACATAA 58.338 39.130 0.00 0.00 44.79 1.90
258 259 3.084786 GAGCTAAAGGCACCTCAAACAT 58.915 45.455 0.00 0.00 44.79 2.71
259 260 2.106511 AGAGCTAAAGGCACCTCAAACA 59.893 45.455 0.00 0.00 44.79 2.83
260 261 2.784347 AGAGCTAAAGGCACCTCAAAC 58.216 47.619 0.00 0.00 44.79 2.93
351 354 1.349234 TGCTGATGACACATCGTTCG 58.651 50.000 7.14 0.00 0.00 3.95
362 365 1.271543 CCTTCCTGTGGTTGCTGATGA 60.272 52.381 0.00 0.00 0.00 2.92
380 383 1.767692 GGGAATGGTGTGTGTCCCT 59.232 57.895 0.12 0.00 45.50 4.20
381 384 4.415783 GGGAATGGTGTGTGTCCC 57.584 61.111 0.00 0.00 42.98 4.46
989 992 4.794648 CCGCCATTCCTTCCGCCA 62.795 66.667 0.00 0.00 0.00 5.69
1124 1129 2.355363 CACGGCAAGGAACGACGA 60.355 61.111 0.00 0.00 0.00 4.20
1144 1149 6.982724 GGGGATCAGATTCAATTCAATTCAAC 59.017 38.462 0.00 0.00 0.00 3.18
1252 1257 0.445436 GCTTGACGCTGGTCTTCATG 59.555 55.000 0.00 0.00 43.79 3.07
1304 1309 0.322008 CAAGCAGTTCCCCCAGAGTC 60.322 60.000 0.00 0.00 0.00 3.36
1305 1310 1.062488 ACAAGCAGTTCCCCCAGAGT 61.062 55.000 0.00 0.00 0.00 3.24
1306 1311 0.984230 TACAAGCAGTTCCCCCAGAG 59.016 55.000 0.00 0.00 0.00 3.35
1307 1312 1.440618 TTACAAGCAGTTCCCCCAGA 58.559 50.000 0.00 0.00 0.00 3.86
1308 1313 2.286365 TTTACAAGCAGTTCCCCCAG 57.714 50.000 0.00 0.00 0.00 4.45
1309 1314 2.896685 CAATTTACAAGCAGTTCCCCCA 59.103 45.455 0.00 0.00 0.00 4.96
1321 1326 6.147492 GGCAGATTGAAATGCACAATTTACAA 59.853 34.615 7.83 2.03 44.37 2.41
1325 1330 4.901868 AGGCAGATTGAAATGCACAATTT 58.098 34.783 7.83 0.00 44.37 1.82
1341 1346 3.326006 ACTCAGAAGACAATCAAGGCAGA 59.674 43.478 0.00 0.00 0.00 4.26
1350 1355 9.512588 ACATAGAAATTCAACTCAGAAGACAAT 57.487 29.630 0.00 0.00 0.00 2.71
1426 1432 3.053831 ACCGATTTCAACTTGACCGAT 57.946 42.857 8.26 0.00 0.00 4.18
1427 1433 2.536761 ACCGATTTCAACTTGACCGA 57.463 45.000 8.26 0.00 0.00 4.69
1429 1435 5.684550 ACTAAACCGATTTCAACTTGACC 57.315 39.130 0.00 0.00 0.00 4.02
1431 1437 5.239963 GGGAACTAAACCGATTTCAACTTGA 59.760 40.000 0.00 0.00 0.00 3.02
1446 1452 2.760092 GGCATTGCTGATGGGAACTAAA 59.240 45.455 8.82 0.00 36.21 1.85
1451 1457 0.040058 ACAGGCATTGCTGATGGGAA 59.960 50.000 8.82 0.00 36.21 3.97
1468 1474 1.753649 CACCACAACCACAATTCCACA 59.246 47.619 0.00 0.00 0.00 4.17
1474 1480 1.497286 AGTACCCACCACAACCACAAT 59.503 47.619 0.00 0.00 0.00 2.71
1479 1485 0.250597 GTCCAGTACCCACCACAACC 60.251 60.000 0.00 0.00 0.00 3.77
1544 1555 5.980116 CACTACTCCAGAATTGAATACTCGG 59.020 44.000 0.00 0.00 0.00 4.63
1571 1582 1.268896 CGATTCATGCCATCCTTGTGC 60.269 52.381 0.00 0.00 0.00 4.57
1583 1602 4.509230 CCACATCTTGTCCTACGATTCATG 59.491 45.833 0.00 0.00 0.00 3.07
1611 1631 4.697514 TCTGCATTCTGCTCAACCTATAC 58.302 43.478 0.34 0.00 45.31 1.47
1612 1632 5.357742 TTCTGCATTCTGCTCAACCTATA 57.642 39.130 0.34 0.00 45.31 1.31
1613 1633 3.920231 TCTGCATTCTGCTCAACCTAT 57.080 42.857 0.34 0.00 45.31 2.57
1614 1634 3.701205 TTCTGCATTCTGCTCAACCTA 57.299 42.857 0.34 0.00 45.31 3.08
1622 1642 4.805192 TGTTTCTTTGTTTCTGCATTCTGC 59.195 37.500 0.00 0.00 45.29 4.26
1624 1644 9.768662 AATTATGTTTCTTTGTTTCTGCATTCT 57.231 25.926 0.00 0.00 0.00 2.40
1673 1693 0.704076 TCCTCCCCTCATTTGGTTGG 59.296 55.000 0.00 0.00 0.00 3.77
1675 1695 1.288932 CCATCCTCCCCTCATTTGGTT 59.711 52.381 0.00 0.00 0.00 3.67
1676 1696 0.929244 CCATCCTCCCCTCATTTGGT 59.071 55.000 0.00 0.00 0.00 3.67
1678 1698 1.478288 GCTCCATCCTCCCCTCATTTG 60.478 57.143 0.00 0.00 0.00 2.32
1679 1699 0.849417 GCTCCATCCTCCCCTCATTT 59.151 55.000 0.00 0.00 0.00 2.32
1680 1700 0.029267 AGCTCCATCCTCCCCTCATT 60.029 55.000 0.00 0.00 0.00 2.57
1681 1701 0.767446 CAGCTCCATCCTCCCCTCAT 60.767 60.000 0.00 0.00 0.00 2.90
1682 1702 1.383664 CAGCTCCATCCTCCCCTCA 60.384 63.158 0.00 0.00 0.00 3.86
1683 1703 2.146061 CCAGCTCCATCCTCCCCTC 61.146 68.421 0.00 0.00 0.00 4.30
1684 1704 2.040043 CCAGCTCCATCCTCCCCT 60.040 66.667 0.00 0.00 0.00 4.79
1685 1705 3.883549 GCCAGCTCCATCCTCCCC 61.884 72.222 0.00 0.00 0.00 4.81
1686 1706 1.931007 AAAGCCAGCTCCATCCTCCC 61.931 60.000 0.00 0.00 0.00 4.30
1687 1707 0.839946 TAAAGCCAGCTCCATCCTCC 59.160 55.000 0.00 0.00 0.00 4.30
1688 1708 2.777094 GATAAAGCCAGCTCCATCCTC 58.223 52.381 0.00 0.00 0.00 3.71
1689 1709 1.071385 CGATAAAGCCAGCTCCATCCT 59.929 52.381 0.00 0.00 0.00 3.24
1690 1710 1.517242 CGATAAAGCCAGCTCCATCC 58.483 55.000 0.00 0.00 0.00 3.51
1691 1711 1.202698 ACCGATAAAGCCAGCTCCATC 60.203 52.381 0.00 0.00 0.00 3.51
1692 1712 0.839946 ACCGATAAAGCCAGCTCCAT 59.160 50.000 0.00 0.00 0.00 3.41
1693 1713 0.107703 CACCGATAAAGCCAGCTCCA 60.108 55.000 0.00 0.00 0.00 3.86
1694 1714 0.178068 TCACCGATAAAGCCAGCTCC 59.822 55.000 0.00 0.00 0.00 4.70
1695 1715 2.139118 GATCACCGATAAAGCCAGCTC 58.861 52.381 0.00 0.00 0.00 4.09
1696 1716 1.202698 GGATCACCGATAAAGCCAGCT 60.203 52.381 0.00 0.00 0.00 4.24
1697 1717 1.202698 AGGATCACCGATAAAGCCAGC 60.203 52.381 0.00 0.00 41.83 4.85
1698 1718 2.366916 AGAGGATCACCGATAAAGCCAG 59.633 50.000 0.00 0.00 41.83 4.85
1699 1719 2.103094 CAGAGGATCACCGATAAAGCCA 59.897 50.000 0.00 0.00 41.83 4.75
1700 1720 2.365617 TCAGAGGATCACCGATAAAGCC 59.634 50.000 0.00 0.00 41.83 4.35
1701 1721 3.385577 GTCAGAGGATCACCGATAAAGC 58.614 50.000 0.00 0.00 41.83 3.51
1702 1722 3.315470 TCGTCAGAGGATCACCGATAAAG 59.685 47.826 0.00 0.00 41.83 1.85
1703 1723 3.284617 TCGTCAGAGGATCACCGATAAA 58.715 45.455 0.00 0.00 41.83 1.40
1704 1724 2.879026 CTCGTCAGAGGATCACCGATAA 59.121 50.000 0.00 0.00 40.75 1.75
1705 1725 2.104281 TCTCGTCAGAGGATCACCGATA 59.896 50.000 0.00 0.00 44.47 2.92
1706 1726 1.134068 TCTCGTCAGAGGATCACCGAT 60.134 52.381 0.00 0.00 44.47 4.18
1707 1727 0.252197 TCTCGTCAGAGGATCACCGA 59.748 55.000 0.00 0.00 44.47 4.69
1708 1728 0.660488 CTCTCGTCAGAGGATCACCG 59.340 60.000 0.00 0.00 42.49 4.94
1715 1735 9.770038 CTTGAAAGCAAAAACTCTCGTCAGAGG 62.770 44.444 6.14 0.00 41.12 3.69
1716 1736 6.995971 CTTGAAAGCAAAAACTCTCGTCAGAG 60.996 42.308 0.00 0.00 41.85 3.35
1717 1737 4.188462 TGAAAGCAAAAACTCTCGTCAGA 58.812 39.130 0.00 0.00 0.00 3.27
1718 1738 4.536364 TGAAAGCAAAAACTCTCGTCAG 57.464 40.909 0.00 0.00 0.00 3.51
1719 1739 4.201910 CCTTGAAAGCAAAAACTCTCGTCA 60.202 41.667 0.00 0.00 32.73 4.35
1720 1740 4.201920 ACCTTGAAAGCAAAAACTCTCGTC 60.202 41.667 0.00 0.00 32.73 4.20
1721 1741 3.694566 ACCTTGAAAGCAAAAACTCTCGT 59.305 39.130 0.00 0.00 32.73 4.18
1722 1742 4.037690 CACCTTGAAAGCAAAAACTCTCG 58.962 43.478 0.00 0.00 32.73 4.04
1723 1743 4.998788 ACACCTTGAAAGCAAAAACTCTC 58.001 39.130 0.00 0.00 32.73 3.20
1724 1744 6.715347 ATACACCTTGAAAGCAAAAACTCT 57.285 33.333 0.00 0.00 32.73 3.24
1725 1745 8.915654 CATAATACACCTTGAAAGCAAAAACTC 58.084 33.333 0.00 0.00 32.73 3.01
1726 1746 7.384932 GCATAATACACCTTGAAAGCAAAAACT 59.615 33.333 0.00 0.00 32.73 2.66
1727 1747 7.360017 GGCATAATACACCTTGAAAGCAAAAAC 60.360 37.037 0.00 0.00 32.73 2.43
1728 1748 6.648725 GGCATAATACACCTTGAAAGCAAAAA 59.351 34.615 0.00 0.00 32.73 1.94
1729 1749 6.014669 AGGCATAATACACCTTGAAAGCAAAA 60.015 34.615 0.00 0.00 32.73 2.44
1730 1750 5.480073 AGGCATAATACACCTTGAAAGCAAA 59.520 36.000 0.00 0.00 32.73 3.68
1731 1751 5.016173 AGGCATAATACACCTTGAAAGCAA 58.984 37.500 0.00 0.00 0.00 3.91
1732 1752 4.599041 AGGCATAATACACCTTGAAAGCA 58.401 39.130 0.00 0.00 0.00 3.91
1733 1753 6.017852 GTCTAGGCATAATACACCTTGAAAGC 60.018 42.308 0.00 0.00 37.14 3.51
1734 1754 7.047891 TGTCTAGGCATAATACACCTTGAAAG 58.952 38.462 0.00 0.00 37.14 2.62
1735 1755 6.953101 TGTCTAGGCATAATACACCTTGAAA 58.047 36.000 0.00 0.00 37.14 2.69
1736 1756 6.382859 TCTGTCTAGGCATAATACACCTTGAA 59.617 38.462 0.00 0.00 37.14 2.69
1737 1757 5.897250 TCTGTCTAGGCATAATACACCTTGA 59.103 40.000 0.00 0.00 34.92 3.02
1738 1758 6.161855 TCTGTCTAGGCATAATACACCTTG 57.838 41.667 0.00 0.00 34.92 3.61
1739 1759 5.221541 GCTCTGTCTAGGCATAATACACCTT 60.222 44.000 0.00 0.00 34.92 3.50
1743 1763 5.279657 CCATGCTCTGTCTAGGCATAATACA 60.280 44.000 0.00 0.00 43.62 2.29
1768 1788 5.062809 GGTAGCAAGAAACTTGATCGAGAAG 59.937 44.000 17.27 3.33 0.00 2.85
1774 1794 4.072131 TGTGGGTAGCAAGAAACTTGATC 58.928 43.478 14.44 3.95 0.00 2.92
1841 1862 9.851686 AGTTTGGAGATAGTATTGCATCAATAA 57.148 29.630 1.31 0.00 37.94 1.40
1846 1867 7.976135 ATCAGTTTGGAGATAGTATTGCATC 57.024 36.000 0.00 0.00 0.00 3.91
1853 1874 9.987272 CACATCATTATCAGTTTGGAGATAGTA 57.013 33.333 0.00 0.00 0.00 1.82
1855 1876 9.205719 CTCACATCATTATCAGTTTGGAGATAG 57.794 37.037 0.00 0.00 0.00 2.08
1860 1881 7.819644 CAAACTCACATCATTATCAGTTTGGA 58.180 34.615 12.49 0.00 43.46 3.53
1881 1909 2.747989 GCAGCTACCTCCCTTAACAAAC 59.252 50.000 0.00 0.00 0.00 2.93
1936 1964 7.005709 ACCCAAAGATATACCGGAAGATTAG 57.994 40.000 9.46 0.00 0.00 1.73
1941 1969 9.162764 CATTATTACCCAAAGATATACCGGAAG 57.837 37.037 9.46 0.00 0.00 3.46
1951 1979 8.061304 ACTTCCATGACATTATTACCCAAAGAT 58.939 33.333 0.00 0.00 0.00 2.40
1996 2026 6.183360 ACCTCGATGTGAGTATACTAAACACC 60.183 42.308 18.43 11.22 43.64 4.16
2000 2030 7.989170 TGTAGACCTCGATGTGAGTATACTAAA 59.011 37.037 5.09 0.00 43.64 1.85
2017 2047 1.245732 ACTGACACCGTGTAGACCTC 58.754 55.000 3.58 0.00 0.00 3.85
2018 2048 1.700955 AACTGACACCGTGTAGACCT 58.299 50.000 3.58 0.00 0.00 3.85
2048 2113 2.101750 GGTTGACTAGCTAGAGCCCTTC 59.898 54.545 27.45 13.13 43.38 3.46
2231 2308 7.725844 TGCCACTCTGACATCTAGAAAGATATA 59.274 37.037 0.00 0.00 40.65 0.86
2244 2321 2.089980 GCAGAATTGCCACTCTGACAT 58.910 47.619 0.00 0.00 44.74 3.06
2282 2359 6.948886 TGAGGGATAGTAGAGATTATGTGTCC 59.051 42.308 0.00 0.00 0.00 4.02
2348 2426 5.133322 TCCTAGAGGTAGGGTAAATTCTCGA 59.867 44.000 0.00 0.00 45.65 4.04
2396 2475 6.589830 AATAACATTGATCACTGAGCGTAC 57.410 37.500 18.94 0.00 0.00 3.67
2400 2479 7.493971 AGACTGTAATAACATTGATCACTGAGC 59.506 37.037 18.94 4.00 34.37 4.26
2401 2480 8.939201 AGACTGTAATAACATTGATCACTGAG 57.061 34.615 18.94 7.02 34.37 3.35
2423 2502 8.526978 TGCCTATCAGATCAGATAACATAAGAC 58.473 37.037 8.92 0.00 30.59 3.01
2440 2524 1.268794 CGACTTCGACCTGCCTATCAG 60.269 57.143 0.00 0.00 43.02 2.90
2441 2525 0.738975 CGACTTCGACCTGCCTATCA 59.261 55.000 0.00 0.00 43.02 2.15
2442 2526 1.022735 TCGACTTCGACCTGCCTATC 58.977 55.000 0.00 0.00 44.22 2.08
2443 2527 3.186345 TCGACTTCGACCTGCCTAT 57.814 52.632 0.00 0.00 44.22 2.57
2444 2528 4.728409 TCGACTTCGACCTGCCTA 57.272 55.556 0.00 0.00 44.22 3.93
2493 2577 4.264253 TCATCACCAGAACAATTAGGCAG 58.736 43.478 0.00 0.00 0.00 4.85
2596 2680 7.445121 TCTCTCTTTTTCAATCTACTGCTGAA 58.555 34.615 0.00 0.00 0.00 3.02
2620 2704 4.514066 ACAGATTGTTTACCGGTTGTTCTC 59.486 41.667 15.04 3.39 0.00 2.87
2670 2754 0.610687 GGCTGCTTAGTGGACTCAGT 59.389 55.000 0.00 0.00 0.00 3.41
2704 2788 8.514594 CAGAATGCCTGACTTATTTTGTTTAGA 58.485 33.333 0.00 0.00 45.78 2.10
2705 2789 8.679288 CAGAATGCCTGACTTATTTTGTTTAG 57.321 34.615 0.00 0.00 45.78 1.85
2744 2828 4.161565 TGTCACAGTGGAAGTTTCTGTACT 59.838 41.667 0.00 0.00 39.89 2.73
2747 2831 3.197766 TCTGTCACAGTGGAAGTTTCTGT 59.802 43.478 4.28 0.00 42.14 3.41
2805 2890 6.705863 ATATTCATTCTGCCAAGGAAGTTC 57.294 37.500 0.00 0.00 0.00 3.01
2850 2935 3.652057 AGCTGGCTGGCTTAAGATAAA 57.348 42.857 6.67 0.00 39.86 1.40
2851 2936 4.982241 ATAGCTGGCTGGCTTAAGATAA 57.018 40.909 6.67 0.00 42.97 1.75
2852 2937 5.087323 ACTATAGCTGGCTGGCTTAAGATA 58.913 41.667 6.67 0.00 42.97 1.98
2853 2938 3.906846 ACTATAGCTGGCTGGCTTAAGAT 59.093 43.478 6.67 0.00 42.97 2.40
2919 3004 1.209019 AGAGGTGCTCAAGCCTACATG 59.791 52.381 0.00 0.00 41.18 3.21
2967 3054 2.750166 CAGCTAACTCTCTTCCACGAGA 59.250 50.000 0.00 0.00 37.69 4.04
3037 3129 4.363999 CGAATGAGATCACAGGAACCTAC 58.636 47.826 0.00 0.00 0.00 3.18
3096 3188 4.946478 AGTGGCAGGACATCTATAAGAC 57.054 45.455 0.00 0.00 0.00 3.01
3120 3212 7.657761 ACCAGAATATTGCCTCTATTTTAGTCG 59.342 37.037 0.00 0.00 0.00 4.18
3121 3213 8.910351 ACCAGAATATTGCCTCTATTTTAGTC 57.090 34.615 0.00 0.00 0.00 2.59
3154 3246 2.364972 AGCCCAACATATTACCCTGC 57.635 50.000 0.00 0.00 0.00 4.85
3199 3292 8.979534 AGTAGGAACCTAAAGGATTAACAGTAG 58.020 37.037 2.23 0.00 38.94 2.57
3293 3386 1.408822 GCCACCAGGGATAACAAGGAG 60.409 57.143 0.00 0.00 40.01 3.69
3331 3539 3.689649 GGCACAAGGACGTTGATAAGATT 59.310 43.478 14.50 0.00 38.60 2.40
3356 3591 4.427096 TGCACTCTGTTTGAACGAAAAA 57.573 36.364 0.00 0.00 0.00 1.94
3357 3592 4.335315 AGATGCACTCTGTTTGAACGAAAA 59.665 37.500 0.00 0.00 31.12 2.29
3358 3593 3.876914 AGATGCACTCTGTTTGAACGAAA 59.123 39.130 0.00 0.00 31.12 3.46
3359 3594 3.466836 AGATGCACTCTGTTTGAACGAA 58.533 40.909 0.00 0.00 31.12 3.85
3360 3595 3.059884 GAGATGCACTCTGTTTGAACGA 58.940 45.455 8.50 0.00 41.94 3.85
3361 3596 2.158449 GGAGATGCACTCTGTTTGAACG 59.842 50.000 13.59 0.00 44.37 3.95
3362 3597 3.141398 TGGAGATGCACTCTGTTTGAAC 58.859 45.455 13.59 0.00 44.37 3.18
3363 3598 3.490439 TGGAGATGCACTCTGTTTGAA 57.510 42.857 13.59 0.00 44.37 2.69
3364 3599 3.708403 ATGGAGATGCACTCTGTTTGA 57.292 42.857 13.59 0.00 44.37 2.69
3365 3600 4.008330 AGAATGGAGATGCACTCTGTTTG 58.992 43.478 13.59 0.00 44.37 2.93
3366 3601 4.298103 AGAATGGAGATGCACTCTGTTT 57.702 40.909 13.59 7.16 44.37 2.83
3367 3602 3.996921 AGAATGGAGATGCACTCTGTT 57.003 42.857 13.59 9.72 44.37 3.16
3368 3603 3.996921 AAGAATGGAGATGCACTCTGT 57.003 42.857 13.59 3.50 44.37 3.41
3369 3604 5.021033 ACTAAGAATGGAGATGCACTCTG 57.979 43.478 13.59 0.00 44.37 3.35
3370 3605 5.690464 AACTAAGAATGGAGATGCACTCT 57.310 39.130 13.59 7.17 44.37 3.24
3371 3606 5.448360 GCAAACTAAGAATGGAGATGCACTC 60.448 44.000 7.52 7.52 44.24 3.51
3372 3607 4.397417 GCAAACTAAGAATGGAGATGCACT 59.603 41.667 0.00 0.00 32.82 4.40
3373 3608 4.156556 TGCAAACTAAGAATGGAGATGCAC 59.843 41.667 0.00 0.00 35.61 4.57
3374 3609 4.334552 TGCAAACTAAGAATGGAGATGCA 58.665 39.130 0.00 0.00 37.01 3.96
3375 3610 4.970662 TGCAAACTAAGAATGGAGATGC 57.029 40.909 0.00 0.00 33.03 3.91
3376 3611 6.860080 ACAATGCAAACTAAGAATGGAGATG 58.140 36.000 0.00 0.00 0.00 2.90
3384 3619 7.918562 GGTCAAGTAAACAATGCAAACTAAGAA 59.081 33.333 0.00 0.00 0.00 2.52
3385 3620 7.284489 AGGTCAAGTAAACAATGCAAACTAAGA 59.716 33.333 0.00 0.00 0.00 2.10
3386 3621 7.425606 AGGTCAAGTAAACAATGCAAACTAAG 58.574 34.615 0.00 0.00 0.00 2.18
3457 3692 7.554118 TGCCAAGGTAGAAGAATCAAATAAGAG 59.446 37.037 0.00 0.00 0.00 2.85
3459 3694 7.201767 CCTGCCAAGGTAGAAGAATCAAATAAG 60.202 40.741 5.73 0.00 38.96 1.73
3491 3727 4.664267 AGGGTGAGGGCCTGAGCA 62.664 66.667 23.38 6.94 42.56 4.26
3560 3796 2.544267 GTCGTGAACTTTTGACCCTGAG 59.456 50.000 0.00 0.00 0.00 3.35
3587 3823 1.014564 CCGACGGAAGGAACTGCTTC 61.015 60.000 8.64 2.57 40.86 3.86
3684 3920 4.990543 TGCTCAGAAAGTAACATCAACG 57.009 40.909 0.00 0.00 0.00 4.10
3695 3931 4.446719 GCCAGATTGTTTTTGCTCAGAAAG 59.553 41.667 0.00 0.00 0.00 2.62
3705 3941 6.440436 GCATTTGAAATGCCAGATTGTTTTT 58.560 32.000 27.65 0.00 39.01 1.94
3706 3942 6.004408 GCATTTGAAATGCCAGATTGTTTT 57.996 33.333 27.65 0.00 39.01 2.43
3831 4069 2.224426 TGCACGGTTCAGGAAAGTACAT 60.224 45.455 0.00 0.00 0.00 2.29
3894 4147 2.095461 AGCTTCTGCATACTCGTCTGA 58.905 47.619 0.00 0.00 42.74 3.27
3948 4207 7.058005 GCTTATTGTCGCGTCTTAGAAATAAG 58.942 38.462 19.20 19.20 38.36 1.73
3959 4218 2.896289 CATCATGCTTATTGTCGCGTC 58.104 47.619 5.77 0.00 0.00 5.19
4045 4305 2.182827 TCAGAGTATGACCAGCTGCTT 58.817 47.619 8.66 0.00 31.12 3.91
4052 4322 6.010850 ACAAGTAGACTTCAGAGTATGACCA 58.989 40.000 0.00 0.00 37.77 4.02
4060 4330 9.921637 AAGAGATTAAACAAGTAGACTTCAGAG 57.078 33.333 0.00 0.00 33.11 3.35
4470 4740 1.858246 AGAGGTACCCTTATCCGGAGT 59.142 52.381 11.34 4.15 31.76 3.85
4480 4750 0.971447 GCGTCTCCAAGAGGTACCCT 60.971 60.000 8.74 2.33 36.03 4.34
4497 4767 1.083015 CAGAAACCAAACGTCCGCG 60.083 57.895 0.00 0.00 44.93 6.46
4503 4773 7.222224 GGTATAGATACACTCAGAAACCAAACG 59.778 40.741 2.28 0.00 34.98 3.60
4594 4865 4.531854 TCACAAGTCCAATGAAAGGTCAA 58.468 39.130 0.00 0.00 37.30 3.18
4595 4866 4.163441 TCACAAGTCCAATGAAAGGTCA 57.837 40.909 0.00 0.00 38.41 4.02


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

AutoCloner maintained by Alex Coulton.