Multiple sequence alignment - TraesCS4A01G121200

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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 TraesCS4A01G121200 chr4A 100.000 3825 0 0 720 4544 149646304 149650128 0.000000e+00 7064.0
1 TraesCS4A01G121200 chr4A 100.000 334 0 0 1 334 149645585 149645918 6.460000e-173 617.0
2 TraesCS4A01G121200 chr4A 77.778 234 42 9 3288 3512 29087119 29086887 7.930000e-28 135.0
3 TraesCS4A01G121200 chr4A 91.489 47 3 1 4389 4434 149649921 149649967 3.800000e-06 63.9
4 TraesCS4A01G121200 chr4A 91.489 47 3 1 4337 4383 149649973 149650018 3.800000e-06 63.9
5 TraesCS4A01G121200 chr4D 90.321 2118 118 25 720 2804 322860599 322858536 0.000000e+00 2695.0
6 TraesCS4A01G121200 chr4D 95.624 1668 52 7 2878 4544 322858489 322856842 0.000000e+00 2656.0
7 TraesCS4A01G121200 chr4D 92.806 278 18 1 1 278 322860917 322860642 7.080000e-108 401.0
8 TraesCS4A01G121200 chr4D 93.617 47 2 1 4337 4383 322856994 322856949 8.160000e-08 69.4
9 TraesCS4A01G121200 chr4B 96.820 1195 27 5 3357 4544 398233313 398234503 0.000000e+00 1986.0
10 TraesCS4A01G121200 chr4B 95.745 47 1 1 4337 4383 398234349 398234394 1.750000e-09 75.0
11 TraesCS4A01G121200 chr2A 84.225 374 47 10 3637 4004 719283710 719283343 2.010000e-93 353.0
12 TraesCS4A01G121200 chr6D 88.889 54 6 0 3442 3495 411804702 411804755 2.930000e-07 67.6
13 TraesCS4A01G121200 chr5D 88.462 52 5 1 1 51 486230558 486230609 1.360000e-05 62.1


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 TraesCS4A01G121200 chr4A 149645585 149650128 4543 False 1952.20 7064 95.7445 1 4544 4 chr4A.!!$F1 4543
1 TraesCS4A01G121200 chr4D 322856842 322860917 4075 True 1455.35 2695 93.0920 1 4544 4 chr4D.!!$R1 4543
2 TraesCS4A01G121200 chr4B 398233313 398234503 1190 False 1030.50 1986 96.2825 3357 4544 2 chr4B.!!$F1 1187

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
969 977 1.754380 TTACCAGTCTGCCACACGCT 61.754 55.0 0.00 0.00 38.78 5.07 F
1681 1710 0.035458 CTCCACGGAAGCTTCAGGTT 59.965 55.0 26.86 7.63 38.61 3.50 F
1690 1719 0.035458 AGCTTCAGGTTCAGTTCCCG 59.965 55.0 0.00 0.00 0.00 5.14 F
1762 1791 0.036010 CGATTCCTCTGCACAAGGGT 60.036 55.0 9.91 1.03 34.46 4.34 F
2607 2640 0.322816 ATGCAAGGACACTGCGGATT 60.323 50.0 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2631 2664 0.106519 CATTCGCCCCCTTCCATCTT 60.107 55.000 0.0 0.0 0.00 2.40 R
2694 2727 0.183492 TCAGCACTCACCCAGCTTTT 59.817 50.000 0.0 0.0 36.26 2.27 R
3309 3348 0.317854 GCTTCGCCACTTGTTCCAAC 60.318 55.000 0.0 0.0 0.00 3.77 R
3321 3360 1.131315 GGAGTCTTCATTTGCTTCGCC 59.869 52.381 0.0 0.0 0.00 5.54 R
4462 4510 0.976641 TCGCAAATCACTCCTCCAGT 59.023 50.000 0.0 0.0 34.67 4.00 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
31 32 2.190578 GGGTTCCATGGAGCTCGG 59.809 66.667 25.62 3.50 0.00 4.63
59 60 2.883828 CGCCCCACTCAGTGAAGGT 61.884 63.158 6.30 0.00 35.23 3.50
91 92 7.020827 TGGAAGTGGAGTTTCTTATCTCAAT 57.979 36.000 0.00 0.00 32.93 2.57
97 98 8.547173 AGTGGAGTTTCTTATCTCAATCTCAAT 58.453 33.333 0.00 0.00 32.93 2.57
101 102 7.994194 AGTTTCTTATCTCAATCTCAATTGCC 58.006 34.615 0.00 0.00 41.76 4.52
121 122 4.017958 TGCCCCTGGATGAACTGTAAATTA 60.018 41.667 0.00 0.00 0.00 1.40
122 123 4.953579 GCCCCTGGATGAACTGTAAATTAA 59.046 41.667 0.00 0.00 0.00 1.40
156 157 9.649024 CATAATTTTGTTGTGGCAAACTTTAAG 57.351 29.630 11.78 0.00 37.98 1.85
158 159 3.810310 TGTTGTGGCAAACTTTAAGGG 57.190 42.857 11.78 0.00 0.00 3.95
220 221 2.286772 CGGTGCAAGGTGTTACTTTCAC 60.287 50.000 0.00 0.00 41.71 3.18
222 223 3.243068 GGTGCAAGGTGTTACTTTCACAG 60.243 47.826 10.02 0.00 43.38 3.66
316 317 9.823647 TTCTGATTTACTGTTCATAAGAGGATC 57.176 33.333 0.00 0.00 0.00 3.36
317 318 8.981659 TCTGATTTACTGTTCATAAGAGGATCA 58.018 33.333 0.00 0.00 37.82 2.92
318 319 9.775854 CTGATTTACTGTTCATAAGAGGATCAT 57.224 33.333 0.00 0.00 37.82 2.45
322 323 9.958180 TTTACTGTTCATAAGAGGATCATTTGA 57.042 29.630 0.00 0.00 37.82 2.69
323 324 9.605275 TTACTGTTCATAAGAGGATCATTTGAG 57.395 33.333 0.00 0.00 37.82 3.02
324 325 6.541641 ACTGTTCATAAGAGGATCATTTGAGC 59.458 38.462 0.00 0.00 37.82 4.26
325 326 6.656902 TGTTCATAAGAGGATCATTTGAGCT 58.343 36.000 0.00 0.00 37.82 4.09
326 327 7.114754 TGTTCATAAGAGGATCATTTGAGCTT 58.885 34.615 0.00 0.00 37.82 3.74
327 328 7.066645 TGTTCATAAGAGGATCATTTGAGCTTG 59.933 37.037 0.00 0.00 37.82 4.01
328 329 6.892485 TCATAAGAGGATCATTTGAGCTTGA 58.108 36.000 0.00 0.00 37.82 3.02
329 330 6.990939 TCATAAGAGGATCATTTGAGCTTGAG 59.009 38.462 0.00 0.00 37.82 3.02
330 331 5.432680 AAGAGGATCATTTGAGCTTGAGA 57.567 39.130 0.00 0.00 37.82 3.27
331 332 5.633655 AGAGGATCATTTGAGCTTGAGAT 57.366 39.130 0.00 0.00 37.82 2.75
332 333 6.003859 AGAGGATCATTTGAGCTTGAGATT 57.996 37.500 0.00 0.00 37.82 2.40
333 334 7.134362 AGAGGATCATTTGAGCTTGAGATTA 57.866 36.000 0.00 0.00 37.82 1.75
775 776 3.007398 AGGAGTACTTGCCTCTGTTCTTG 59.993 47.826 0.00 0.00 0.00 3.02
924 932 2.099098 CGTCCTTGTGTTTTTGCCTTCT 59.901 45.455 0.00 0.00 0.00 2.85
936 944 4.468689 CCTTCTTCCCGGGTCGCC 62.469 72.222 22.86 0.00 0.00 5.54
938 946 3.952628 CTTCTTCCCGGGTCGCCAC 62.953 68.421 22.86 0.00 0.00 5.01
969 977 1.754380 TTACCAGTCTGCCACACGCT 61.754 55.000 0.00 0.00 38.78 5.07
1080 1088 1.753649 CTCATCTCCTTCGCTTCCTCA 59.246 52.381 0.00 0.00 0.00 3.86
1113 1121 3.031013 CTCCTTCCTCTTCTCCCTCTTC 58.969 54.545 0.00 0.00 0.00 2.87
1239 1259 1.379527 GAGCGGAGGTGTTTATTGGG 58.620 55.000 0.00 0.00 39.88 4.12
1268 1288 1.075970 GGGCCTTGGGGGAAGATTC 60.076 63.158 0.84 0.00 37.23 2.52
1272 1292 1.609783 CTTGGGGGAAGATTCGGCT 59.390 57.895 0.00 0.00 32.82 5.52
1309 1329 4.645921 GGCGTGCTGGTGGTTTGC 62.646 66.667 0.00 0.00 0.00 3.68
1331 1351 3.521796 GGGCTCGGCAATGAAGGC 61.522 66.667 0.00 0.00 0.00 4.35
1394 1414 1.375523 GTGGTGCGGTTTCGGAGAT 60.376 57.895 0.00 0.00 37.41 2.75
1395 1415 1.375396 TGGTGCGGTTTCGGAGATG 60.375 57.895 0.00 0.00 37.41 2.90
1445 1465 1.203994 TCTCCGAGGTTTGGATTCGAC 59.796 52.381 0.00 0.00 36.49 4.20
1463 1483 1.552792 GACAGTGGAGGAGAAAGGAGG 59.447 57.143 0.00 0.00 0.00 4.30
1469 1489 1.066787 GGAGGAGAAAGGAGGTGTTCG 60.067 57.143 0.00 0.00 0.00 3.95
1471 1491 1.619332 AGGAGAAAGGAGGTGTTCGAC 59.381 52.381 0.00 0.00 0.00 4.20
1472 1492 1.337917 GGAGAAAGGAGGTGTTCGACC 60.338 57.143 0.00 0.00 46.58 4.79
1479 1499 3.144285 GGTGTTCGACCAGGTGGA 58.856 61.111 0.00 0.00 45.34 4.02
1480 1500 1.004918 GGTGTTCGACCAGGTGGAG 60.005 63.158 0.00 0.00 45.34 3.86
1481 1501 1.469335 GGTGTTCGACCAGGTGGAGA 61.469 60.000 0.00 0.00 45.34 3.71
1482 1502 0.319641 GTGTTCGACCAGGTGGAGAC 60.320 60.000 0.00 3.51 38.94 3.36
1483 1503 0.757561 TGTTCGACCAGGTGGAGACA 60.758 55.000 0.00 6.19 38.94 3.41
1484 1504 0.038159 GTTCGACCAGGTGGAGACAG 60.038 60.000 0.00 0.00 44.46 3.51
1550 1579 1.467035 CGAAGGCAAGAAAGCTGATGC 60.467 52.381 0.00 0.00 38.06 3.91
1573 1602 1.089920 CTCGGCAAGGAGGTCAAATG 58.910 55.000 0.00 0.00 0.00 2.32
1577 1606 2.369394 GGCAAGGAGGTCAAATGTAGG 58.631 52.381 0.00 0.00 0.00 3.18
1594 1623 3.204418 GCAATGCTTCTGCCTCCC 58.796 61.111 0.00 0.00 38.71 4.30
1595 1624 1.679977 GCAATGCTTCTGCCTCCCA 60.680 57.895 0.00 0.00 38.71 4.37
1596 1625 1.941999 GCAATGCTTCTGCCTCCCAC 61.942 60.000 0.00 0.00 38.71 4.61
1597 1626 1.377725 AATGCTTCTGCCTCCCACG 60.378 57.895 0.00 0.00 38.71 4.94
1598 1627 2.826777 AATGCTTCTGCCTCCCACGG 62.827 60.000 0.00 0.00 38.71 4.94
1628 1657 2.072298 AGCTGCGTCAGTTGAGAAATC 58.928 47.619 8.32 0.00 33.43 2.17
1629 1658 1.129437 GCTGCGTCAGTTGAGAAATCC 59.871 52.381 8.32 0.00 33.43 3.01
1638 1667 4.402474 TCAGTTGAGAAATCCGATAGAGCA 59.598 41.667 0.00 0.00 39.76 4.26
1642 1671 4.122776 TGAGAAATCCGATAGAGCAAAGC 58.877 43.478 0.00 0.00 39.76 3.51
1644 1673 3.135530 AGAAATCCGATAGAGCAAAGCCT 59.864 43.478 0.00 0.00 39.76 4.58
1645 1674 2.540265 ATCCGATAGAGCAAAGCCTG 57.460 50.000 0.00 0.00 39.76 4.85
1667 1696 2.666619 CGCAAGCTGTCAATTTCTCCAC 60.667 50.000 0.00 0.00 0.00 4.02
1681 1710 0.035458 CTCCACGGAAGCTTCAGGTT 59.965 55.000 26.86 7.63 38.61 3.50
1689 1718 2.278332 AAGCTTCAGGTTCAGTTCCC 57.722 50.000 0.00 0.00 0.00 3.97
1690 1719 0.035458 AGCTTCAGGTTCAGTTCCCG 59.965 55.000 0.00 0.00 0.00 5.14
1691 1720 0.250338 GCTTCAGGTTCAGTTCCCGT 60.250 55.000 0.00 0.00 0.00 5.28
1692 1721 1.001633 GCTTCAGGTTCAGTTCCCGTA 59.998 52.381 0.00 0.00 0.00 4.02
1693 1722 2.931320 GCTTCAGGTTCAGTTCCCGTAG 60.931 54.545 0.00 0.00 0.00 3.51
1694 1723 0.606604 TCAGGTTCAGTTCCCGTAGC 59.393 55.000 0.00 0.00 0.00 3.58
1710 1739 2.114488 TAGCGGGGACAAAAGGCGAA 62.114 55.000 0.00 0.00 0.00 4.70
1711 1740 2.340328 GCGGGGACAAAAGGCGAAT 61.340 57.895 0.00 0.00 0.00 3.34
1712 1741 1.800681 CGGGGACAAAAGGCGAATC 59.199 57.895 0.00 0.00 0.00 2.52
1713 1742 1.654023 CGGGGACAAAAGGCGAATCC 61.654 60.000 0.00 0.00 0.00 3.01
1714 1743 2.189833 GGGACAAAAGGCGAATCCC 58.810 57.895 0.00 0.00 42.30 3.85
1715 1744 0.323451 GGGACAAAAGGCGAATCCCT 60.323 55.000 0.13 0.00 44.94 4.20
1716 1745 0.811281 GGACAAAAGGCGAATCCCTG 59.189 55.000 0.00 0.00 34.80 4.45
1717 1746 0.171231 GACAAAAGGCGAATCCCTGC 59.829 55.000 0.00 0.00 34.80 4.85
1718 1747 0.539438 ACAAAAGGCGAATCCCTGCA 60.539 50.000 0.00 0.00 34.80 4.41
1742 1771 2.418083 GCCATGCCGGAGAAAAGGG 61.418 63.158 5.05 0.00 36.56 3.95
1754 1783 0.735471 GAAAAGGGCGATTCCTCTGC 59.265 55.000 0.00 0.00 35.80 4.26
1762 1791 0.036010 CGATTCCTCTGCACAAGGGT 60.036 55.000 9.91 1.03 34.46 4.34
1770 1799 1.630369 TCTGCACAAGGGTCTTATGCT 59.370 47.619 11.41 0.00 37.20 3.79
1781 1810 1.086696 TCTTATGCTTCGCAACAGGC 58.913 50.000 0.00 0.00 43.62 4.85
1805 1834 1.812571 CCAGTGGGAAATCTCAAACCG 59.187 52.381 0.00 0.00 35.59 4.44
1817 1849 3.275143 TCTCAAACCGTTCAGCAAAGAA 58.725 40.909 0.00 0.00 0.00 2.52
1848 1880 2.105766 GAAGCTCCAGCCAATCCAAAT 58.894 47.619 0.00 0.00 43.38 2.32
1850 1882 2.659428 AGCTCCAGCCAATCCAAATAC 58.341 47.619 0.00 0.00 43.38 1.89
1851 1883 2.243221 AGCTCCAGCCAATCCAAATACT 59.757 45.455 0.00 0.00 43.38 2.12
1857 1889 4.037208 CCAGCCAATCCAAATACTAAGCAG 59.963 45.833 0.00 0.00 0.00 4.24
1883 1915 2.496899 AATGTGATTCAGGAAGCGGT 57.503 45.000 0.00 0.00 0.00 5.68
1894 1926 2.224314 CAGGAAGCGGTTCAGAGAAAAC 59.776 50.000 26.94 8.55 33.93 2.43
1895 1927 2.104963 AGGAAGCGGTTCAGAGAAAACT 59.895 45.455 26.94 10.62 33.93 2.66
1922 1954 1.879884 CGAGAAGCAGCATAGCGCA 60.880 57.895 11.47 0.00 46.13 6.09
1938 1970 3.562869 GCAGTGCGATGTTTACGAC 57.437 52.632 0.00 0.00 0.00 4.34
1944 1976 1.749609 GCGATGTTTACGACGGGAGC 61.750 60.000 0.00 0.00 0.00 4.70
1965 1997 1.476891 TGGGTGTTCGATGAGAGCTAC 59.523 52.381 0.00 0.00 0.00 3.58
1985 2017 1.398390 CCCACTCTACGCAAGCAATTC 59.602 52.381 0.00 0.00 45.62 2.17
2034 2066 3.558505 CTGTGAAGCAAATGGAAGAACG 58.441 45.455 0.00 0.00 0.00 3.95
2098 2130 4.807303 GCAATATCCCTAGGTGCTGCATTA 60.807 45.833 5.27 1.03 32.43 1.90
2099 2131 5.503927 CAATATCCCTAGGTGCTGCATTAT 58.496 41.667 5.27 0.00 0.00 1.28
2100 2132 5.786121 ATATCCCTAGGTGCTGCATTATT 57.214 39.130 5.27 0.00 0.00 1.40
2101 2133 6.891306 ATATCCCTAGGTGCTGCATTATTA 57.109 37.500 5.27 0.00 0.00 0.98
2102 2134 5.786121 ATCCCTAGGTGCTGCATTATTAT 57.214 39.130 5.27 0.00 0.00 1.28
2103 2135 6.891306 ATCCCTAGGTGCTGCATTATTATA 57.109 37.500 5.27 0.00 0.00 0.98
2104 2136 6.049955 TCCCTAGGTGCTGCATTATTATAC 57.950 41.667 5.27 0.00 0.00 1.47
2105 2137 5.546110 TCCCTAGGTGCTGCATTATTATACA 59.454 40.000 5.27 0.00 0.00 2.29
2106 2138 6.043822 TCCCTAGGTGCTGCATTATTATACAA 59.956 38.462 5.27 0.00 0.00 2.41
2107 2139 6.886459 CCCTAGGTGCTGCATTATTATACAAT 59.114 38.462 5.27 0.00 0.00 2.71
2108 2140 7.394359 CCCTAGGTGCTGCATTATTATACAATT 59.606 37.037 5.27 0.00 0.00 2.32
2109 2141 9.448438 CCTAGGTGCTGCATTATTATACAATTA 57.552 33.333 5.27 0.00 0.00 1.40
2139 2171 0.703488 TCCCCAGTTTCATGGATGCA 59.297 50.000 0.00 0.00 43.57 3.96
2162 2195 7.408839 CAAGACTTTGCGTTTGAAATTTTTG 57.591 32.000 0.00 0.00 0.00 2.44
2163 2196 5.559227 AGACTTTGCGTTTGAAATTTTTGC 58.441 33.333 0.00 0.00 0.00 3.68
2164 2197 5.121454 AGACTTTGCGTTTGAAATTTTTGCA 59.879 32.000 0.00 0.00 0.00 4.08
2171 2204 6.904011 TGCGTTTGAAATTTTTGCATTTACTG 59.096 30.769 0.00 0.00 0.00 2.74
2172 2205 7.122550 GCGTTTGAAATTTTTGCATTTACTGA 58.877 30.769 0.00 0.00 0.00 3.41
2184 2217 5.070001 TGCATTTACTGACTTAAGCTTGGT 58.930 37.500 9.86 7.94 0.00 3.67
2185 2218 6.234920 TGCATTTACTGACTTAAGCTTGGTA 58.765 36.000 9.86 0.32 0.00 3.25
2191 2224 9.817809 TTTACTGACTTAAGCTTGGTATATGAG 57.182 33.333 9.86 0.00 0.00 2.90
2223 2256 2.951642 TCTGCTAACTTTGCTTGCTGTT 59.048 40.909 0.00 0.32 0.00 3.16
2254 2287 4.400567 AGGTTTGATGCTAGGAAAATGCTC 59.599 41.667 0.00 0.00 0.00 4.26
2266 2299 2.044832 AAATGCTCGAGATGCTGCGC 62.045 55.000 18.75 0.00 0.00 6.09
2311 2344 3.265995 GGGACTCCCTTAACAGGAATCAA 59.734 47.826 6.90 0.00 44.19 2.57
2356 2389 0.972883 GAGAAGCAGTGTCAGACCCT 59.027 55.000 0.00 0.00 0.00 4.34
2446 2479 6.097696 TCCTGGTTCGTATGTCATGAATCTTA 59.902 38.462 0.00 0.00 34.77 2.10
2553 2586 4.335416 AGTACCATGTCACCCATTTCTTG 58.665 43.478 0.00 0.00 0.00 3.02
2571 2604 1.236616 TGGTGCATGAAGGCAAGTCG 61.237 55.000 0.00 0.00 46.93 4.18
2607 2640 0.322816 ATGCAAGGACACTGCGGATT 60.323 50.000 0.00 0.00 0.00 3.01
2619 2652 2.061773 CTGCGGATTGATACCATCGAC 58.938 52.381 0.00 0.00 0.00 4.20
2631 2664 2.437895 ATCGACCGGAGCTCGTCA 60.438 61.111 9.46 8.63 37.11 4.35
2646 2679 1.452108 GTCAAGATGGAAGGGGGCG 60.452 63.158 0.00 0.00 0.00 6.13
2694 2727 5.418524 CCATTGGTGGTCTCATCATAAAACA 59.581 40.000 0.00 0.00 40.83 2.83
2708 2741 4.892934 TCATAAAACAAAAGCTGGGTGAGT 59.107 37.500 0.00 0.00 0.00 3.41
2717 2750 0.743701 GCTGGGTGAGTGCTGATGAG 60.744 60.000 0.00 0.00 0.00 2.90
2736 2769 6.942005 TGATGAGCTCAGAAAAGAATTAACCA 59.058 34.615 22.96 0.00 0.00 3.67
2772 2805 2.862541 AGTTAGTTTGCATGACAGGCA 58.137 42.857 11.36 11.36 40.00 4.75
2788 2821 4.839121 ACAGGCATTTTATCTGGTTACGA 58.161 39.130 0.00 0.00 33.19 3.43
2790 2823 6.588204 ACAGGCATTTTATCTGGTTACGATA 58.412 36.000 0.00 0.00 33.19 2.92
2791 2824 7.051623 ACAGGCATTTTATCTGGTTACGATAA 58.948 34.615 0.00 0.00 32.98 1.75
2792 2825 7.719633 ACAGGCATTTTATCTGGTTACGATAAT 59.280 33.333 0.00 0.00 34.40 1.28
2793 2826 8.567948 CAGGCATTTTATCTGGTTACGATAATT 58.432 33.333 0.00 0.00 34.40 1.40
2794 2827 9.131791 AGGCATTTTATCTGGTTACGATAATTT 57.868 29.630 0.00 0.00 34.40 1.82
2814 2847 9.971922 ATAATTTAGATTTGTAAATGAGCTGCC 57.028 29.630 0.00 0.00 33.71 4.85
2815 2848 6.832520 TTTAGATTTGTAAATGAGCTGCCA 57.167 33.333 0.00 0.00 0.00 4.92
2816 2849 4.708726 AGATTTGTAAATGAGCTGCCAC 57.291 40.909 0.00 0.00 0.00 5.01
2817 2850 4.338879 AGATTTGTAAATGAGCTGCCACT 58.661 39.130 0.00 0.00 0.00 4.00
2818 2851 3.921119 TTTGTAAATGAGCTGCCACTG 57.079 42.857 0.00 0.00 0.00 3.66
2819 2852 2.566833 TGTAAATGAGCTGCCACTGT 57.433 45.000 0.00 0.00 0.00 3.55
2820 2853 2.426522 TGTAAATGAGCTGCCACTGTC 58.573 47.619 0.00 0.00 0.00 3.51
2821 2854 2.038952 TGTAAATGAGCTGCCACTGTCT 59.961 45.455 0.00 0.00 0.00 3.41
2822 2855 3.260632 TGTAAATGAGCTGCCACTGTCTA 59.739 43.478 0.00 0.00 0.00 2.59
2828 2861 2.675348 GAGCTGCCACTGTCTATGTTTC 59.325 50.000 0.00 0.00 0.00 2.78
2833 2866 3.932710 TGCCACTGTCTATGTTTCGATTC 59.067 43.478 0.00 0.00 0.00 2.52
2834 2867 4.184629 GCCACTGTCTATGTTTCGATTCT 58.815 43.478 0.00 0.00 0.00 2.40
2836 2869 5.446473 GCCACTGTCTATGTTTCGATTCTTG 60.446 44.000 0.00 0.00 0.00 3.02
2842 2875 8.262715 TGTCTATGTTTCGATTCTTGCAAATA 57.737 30.769 0.00 0.00 0.00 1.40
2844 2877 9.722056 GTCTATGTTTCGATTCTTGCAAATATT 57.278 29.630 0.00 0.00 0.00 1.28
2848 2881 8.275015 TGTTTCGATTCTTGCAAATATTAGGA 57.725 30.769 0.00 0.00 0.00 2.94
2849 2882 8.181573 TGTTTCGATTCTTGCAAATATTAGGAC 58.818 33.333 0.00 0.00 0.00 3.85
2850 2883 8.398665 GTTTCGATTCTTGCAAATATTAGGACT 58.601 33.333 0.00 0.00 0.00 3.85
2851 2884 8.506168 TTCGATTCTTGCAAATATTAGGACTT 57.494 30.769 0.00 0.00 0.00 3.01
2853 2886 6.634436 CGATTCTTGCAAATATTAGGACTTGC 59.366 38.462 0.00 1.40 43.52 4.01
2858 2891 5.500234 TGCAAATATTAGGACTTGCAGAGT 58.500 37.500 6.21 1.82 46.76 3.24
2859 2892 6.649155 TGCAAATATTAGGACTTGCAGAGTA 58.351 36.000 6.21 0.00 46.76 2.59
2861 2894 7.609918 TGCAAATATTAGGACTTGCAGAGTAAA 59.390 33.333 6.21 0.00 46.76 2.01
2863 2896 9.941664 CAAATATTAGGACTTGCAGAGTAAATG 57.058 33.333 2.17 0.00 39.19 2.32
2864 2897 7.736447 ATATTAGGACTTGCAGAGTAAATGC 57.264 36.000 2.17 0.00 44.11 3.56
2866 2899 3.604582 AGGACTTGCAGAGTAAATGCTC 58.395 45.455 0.00 0.00 44.17 4.26
2868 2901 4.467795 AGGACTTGCAGAGTAAATGCTCTA 59.532 41.667 0.54 0.00 43.37 2.43
2869 2902 5.046304 AGGACTTGCAGAGTAAATGCTCTAA 60.046 40.000 0.54 0.00 43.37 2.10
2871 2904 6.042638 ACTTGCAGAGTAAATGCTCTAAGA 57.957 37.500 14.22 0.01 43.37 2.10
2872 2905 6.105333 ACTTGCAGAGTAAATGCTCTAAGAG 58.895 40.000 14.22 9.05 43.37 2.85
2873 2906 5.667539 TGCAGAGTAAATGCTCTAAGAGT 57.332 39.130 0.54 0.00 43.37 3.24
2876 2915 5.689961 GCAGAGTAAATGCTCTAAGAGTAGC 59.310 44.000 0.54 0.00 43.37 3.58
2887 2926 4.424626 TCTAAGAGTAGCATGTTTCTGCG 58.575 43.478 0.00 0.00 46.86 5.18
2892 2931 1.398390 GTAGCATGTTTCTGCGAAGGG 59.602 52.381 0.00 0.00 46.86 3.95
2894 2933 1.508088 CATGTTTCTGCGAAGGGGC 59.492 57.895 0.00 0.00 0.00 5.80
2951 2990 6.598753 GCATTTGCTTGCAGATTGAATTAT 57.401 33.333 0.00 0.00 42.31 1.28
3041 3080 2.186903 GCATCATGGGTCGACCGT 59.813 61.111 27.68 16.41 44.64 4.83
3047 3086 1.551430 TCATGGGTCGACCGTTACATT 59.449 47.619 27.68 7.84 44.64 2.71
3053 3092 2.417651 GGTCGACCGTTACATTGATCCA 60.418 50.000 20.85 0.00 0.00 3.41
3083 3122 2.483876 CAAGTGTTCTTCCGAAGCTCA 58.516 47.619 3.00 2.67 0.00 4.26
3139 3178 7.394077 TGATCTGAGCTTTTCAATTCCAATACA 59.606 33.333 0.00 0.00 34.81 2.29
3142 3181 5.077134 AGCTTTTCAATTCCAATACAGGC 57.923 39.130 0.00 0.00 0.00 4.85
3234 3273 2.124278 GGCGGGGAGTGGAATTCC 60.124 66.667 18.17 18.17 42.98 3.01
3279 3318 2.672961 TGCCTCTTAATGACACTCGG 57.327 50.000 0.00 0.00 0.00 4.63
3309 3348 0.811219 TGCCCGAGAGAAATGCGATG 60.811 55.000 0.00 0.00 0.00 3.84
3349 3388 4.999950 AGCAAATGAAGACTCCTGTAACAG 59.000 41.667 0.00 0.00 0.00 3.16
3554 3594 6.183360 GGTTTTACAAGTTAGTGACTGGCTTT 60.183 38.462 0.00 0.00 39.00 3.51
3562 3602 3.515602 AGTGACTGGCTTTCCATCTTT 57.484 42.857 0.00 0.00 42.51 2.52
3698 3738 4.215399 GCTGGTAATGTGTCAAGCAAGTTA 59.785 41.667 0.00 0.00 0.00 2.24
3758 3798 8.989980 GCACAATACAACTAAGAGAGTTTAAGT 58.010 33.333 0.00 0.00 46.79 2.24
3784 3824 7.696453 TCGCGAATAAAATTCATCTTTTCCTTC 59.304 33.333 6.20 0.00 31.15 3.46
3805 3845 6.599638 CCTTCCCTACCAAAAGATAAGACTTG 59.400 42.308 0.00 0.00 0.00 3.16
3885 3925 6.738453 GCAACTCCAGTTTGAAAACCATGTAT 60.738 38.462 2.34 0.00 39.71 2.29
3934 3978 7.044771 GCATGTTCACACACAATTATGTTATCG 60.045 37.037 0.00 0.00 37.82 2.92
4000 4044 5.391629 GCTTGGTACTTGGGACTTTATTTCG 60.392 44.000 0.00 0.00 0.00 3.46
4067 4111 7.016268 TCCCTTGTATAATGAACTGGGATAGAC 59.984 40.741 0.00 0.00 36.29 2.59
4073 4117 3.328382 TGAACTGGGATAGACGTTTGG 57.672 47.619 0.00 0.00 0.00 3.28
4075 4119 2.762535 ACTGGGATAGACGTTTGGTG 57.237 50.000 0.00 0.00 0.00 4.17
4076 4120 2.253610 ACTGGGATAGACGTTTGGTGA 58.746 47.619 0.00 0.00 0.00 4.02
4077 4121 2.635915 ACTGGGATAGACGTTTGGTGAA 59.364 45.455 0.00 0.00 0.00 3.18
4111 4158 6.425210 AGTTTACAGCAGCCTATATCATCA 57.575 37.500 0.00 0.00 0.00 3.07
4432 4480 3.125146 GCATGAAGCGACATTGTCTTACA 59.875 43.478 14.54 9.45 0.00 2.41
4462 4510 1.075374 ACCTTTGCATAGCAGTTGGGA 59.925 47.619 0.00 0.00 40.61 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.602237 GAGCTCCATGGAACCCGAA 59.398 57.895 17.00 0.00 0.00 4.30
14 15 2.190578 CCGAGCTCCATGGAACCC 59.809 66.667 17.00 0.36 0.00 4.11
17 18 1.596934 GTCACCGAGCTCCATGGAA 59.403 57.895 17.00 0.00 0.00 3.53
26 27 2.251371 GCGTTTTGGTCACCGAGC 59.749 61.111 0.00 0.00 0.00 5.03
31 32 1.792118 GAGTGGGGCGTTTTGGTCAC 61.792 60.000 0.00 0.00 0.00 3.67
59 60 5.385198 AGAAACTCCACTTCCAATTGCTAA 58.615 37.500 0.00 0.00 0.00 3.09
91 92 1.297968 TCATCCAGGGGCAATTGAGA 58.702 50.000 10.34 0.00 0.00 3.27
97 98 1.367346 TACAGTTCATCCAGGGGCAA 58.633 50.000 0.00 0.00 0.00 4.52
128 129 8.723942 AAAGTTTGCCACAACAAAATTATGTA 57.276 26.923 3.52 0.00 44.39 2.29
132 133 7.281100 CCCTTAAAGTTTGCCACAACAAAATTA 59.719 33.333 0.00 0.00 44.39 1.40
156 157 5.699097 TTTGCTTGTACTACAAACATCCC 57.301 39.130 5.98 0.00 37.69 3.85
183 184 3.695556 TGCACCGATGTGATTTCATGATT 59.304 39.130 0.00 0.00 45.76 2.57
220 221 2.730715 GCAAATGCATGCAAAATGCCTG 60.731 45.455 30.21 18.91 45.70 4.85
222 223 1.902840 GCAAATGCATGCAAAATGCC 58.097 45.000 30.21 19.10 45.70 4.40
237 238 7.820648 TGGCAAACTTTAAGAAAAATTGCAAA 58.179 26.923 1.71 7.31 43.01 3.68
291 292 8.981659 TGATCCTCTTATGAACAGTAAATCAGA 58.018 33.333 0.00 0.00 0.00 3.27
292 293 9.775854 ATGATCCTCTTATGAACAGTAAATCAG 57.224 33.333 0.00 0.00 0.00 2.90
297 298 9.605275 CTCAAATGATCCTCTTATGAACAGTAA 57.395 33.333 0.00 0.00 0.00 2.24
300 301 6.766944 AGCTCAAATGATCCTCTTATGAACAG 59.233 38.462 0.00 0.00 0.00 3.16
301 302 6.656902 AGCTCAAATGATCCTCTTATGAACA 58.343 36.000 0.00 0.00 0.00 3.18
302 303 7.281774 TCAAGCTCAAATGATCCTCTTATGAAC 59.718 37.037 0.00 0.00 0.00 3.18
303 304 7.341030 TCAAGCTCAAATGATCCTCTTATGAA 58.659 34.615 0.00 0.00 0.00 2.57
304 305 6.892485 TCAAGCTCAAATGATCCTCTTATGA 58.108 36.000 0.00 0.00 0.00 2.15
305 306 6.990939 TCTCAAGCTCAAATGATCCTCTTATG 59.009 38.462 0.00 0.00 0.00 1.90
308 309 5.432680 TCTCAAGCTCAAATGATCCTCTT 57.567 39.130 0.00 0.00 0.00 2.85
309 310 5.633655 ATCTCAAGCTCAAATGATCCTCT 57.366 39.130 0.00 0.00 0.00 3.69
731 732 4.744795 ACTCTAGCCTTTCGTTGATCAT 57.255 40.909 0.00 0.00 0.00 2.45
775 776 8.932791 TCTTTTCTTTCGGTATATGTGAAGAAC 58.067 33.333 0.00 0.00 0.00 3.01
838 845 4.163458 TGGAGTAAGTGGAGTGACTTTTGT 59.837 41.667 0.00 0.00 37.38 2.83
840 847 4.163458 TGTGGAGTAAGTGGAGTGACTTTT 59.837 41.667 0.00 0.00 37.38 2.27
899 906 0.249280 CAAAAACACAAGGACGGGGC 60.249 55.000 0.00 0.00 0.00 5.80
904 911 3.801114 AGAAGGCAAAAACACAAGGAC 57.199 42.857 0.00 0.00 0.00 3.85
936 944 0.745128 TGGTAATAAAGGCGGCGGTG 60.745 55.000 9.78 0.00 0.00 4.94
938 946 0.463116 ACTGGTAATAAAGGCGGCGG 60.463 55.000 9.78 0.00 0.00 6.13
969 977 4.047059 GTTGTCGGCGAGGTCGGA 62.047 66.667 11.20 0.00 40.23 4.55
1080 1088 1.943860 AGGAAGGAGAAGAGGAGGGAT 59.056 52.381 0.00 0.00 0.00 3.85
1135 1143 3.090532 GGCGAAGGGGAGGTGGAT 61.091 66.667 0.00 0.00 0.00 3.41
1229 1249 1.304952 CCTCCGCCCCCAATAAACA 59.695 57.895 0.00 0.00 0.00 2.83
1268 1288 3.775654 GGTCTCCCTCCACAGCCG 61.776 72.222 0.00 0.00 0.00 5.52
1272 1292 4.631740 TGGCGGTCTCCCTCCACA 62.632 66.667 0.00 0.00 40.78 4.17
1331 1351 1.153289 CCAGGACCGGCTTCATCAG 60.153 63.158 0.00 0.00 0.00 2.90
1344 1364 2.069775 TCAAAAATCCCACCTCCAGGA 58.930 47.619 0.00 0.00 38.94 3.86
1346 1366 3.006859 GGTTTCAAAAATCCCACCTCCAG 59.993 47.826 0.00 0.00 0.00 3.86
1378 1398 2.750888 GCATCTCCGAAACCGCACC 61.751 63.158 0.00 0.00 0.00 5.01
1413 1433 3.441241 TCGGAGAGAATAGCCTCCC 57.559 57.895 0.00 0.00 44.66 4.30
1445 1465 1.277557 CACCTCCTTTCTCCTCCACTG 59.722 57.143 0.00 0.00 0.00 3.66
1463 1483 0.319641 GTCTCCACCTGGTCGAACAC 60.320 60.000 0.00 0.00 36.34 3.32
1469 1489 2.219325 CTCGCTGTCTCCACCTGGTC 62.219 65.000 0.00 0.00 36.34 4.02
1471 1491 1.536073 TTCTCGCTGTCTCCACCTGG 61.536 60.000 0.00 0.00 0.00 4.45
1472 1492 0.108898 CTTCTCGCTGTCTCCACCTG 60.109 60.000 0.00 0.00 0.00 4.00
1473 1493 1.882989 GCTTCTCGCTGTCTCCACCT 61.883 60.000 0.00 0.00 35.14 4.00
1474 1494 1.446966 GCTTCTCGCTGTCTCCACC 60.447 63.158 0.00 0.00 35.14 4.61
1475 1495 4.177229 GCTTCTCGCTGTCTCCAC 57.823 61.111 0.00 0.00 35.14 4.02
1484 1504 1.086634 ATCTTTCGCCAGCTTCTCGC 61.087 55.000 0.00 0.00 39.57 5.03
1485 1505 1.325943 GAATCTTTCGCCAGCTTCTCG 59.674 52.381 0.00 0.00 0.00 4.04
1506 1526 0.466739 AGTTGGGTTTCACCGGAACC 60.467 55.000 9.46 12.28 39.83 3.62
1510 1530 1.149627 TGGAGTTGGGTTTCACCGG 59.850 57.895 0.00 0.00 39.83 5.28
1512 1532 1.170290 CGGTGGAGTTGGGTTTCACC 61.170 60.000 0.00 0.00 43.06 4.02
1514 1534 0.547075 TTCGGTGGAGTTGGGTTTCA 59.453 50.000 0.00 0.00 0.00 2.69
1528 1548 0.108585 TCAGCTTTCTTGCCTTCGGT 59.891 50.000 0.00 0.00 0.00 4.69
1535 1555 0.179179 GACGGCATCAGCTTTCTTGC 60.179 55.000 0.00 0.00 41.70 4.01
1537 1557 1.731720 GAGACGGCATCAGCTTTCTT 58.268 50.000 0.00 0.00 41.70 2.52
1551 1580 2.154798 TTGACCTCCTTGCCGAGACG 62.155 60.000 0.00 0.00 30.97 4.18
1558 1587 1.745653 GCCTACATTTGACCTCCTTGC 59.254 52.381 0.00 0.00 0.00 4.01
1561 1590 3.624777 CATTGCCTACATTTGACCTCCT 58.375 45.455 0.00 0.00 0.00 3.69
1562 1591 2.099756 GCATTGCCTACATTTGACCTCC 59.900 50.000 0.00 0.00 0.00 4.30
1563 1592 3.019564 AGCATTGCCTACATTTGACCTC 58.980 45.455 4.70 0.00 0.00 3.85
1577 1606 1.679977 TGGGAGGCAGAAGCATTGC 60.680 57.895 0.00 0.00 44.61 3.56
1601 1630 4.790962 CTGACGCAGCTGCCCCAT 62.791 66.667 32.07 15.72 37.91 4.00
1605 1634 2.666190 TCAACTGACGCAGCTGCC 60.666 61.111 32.07 19.77 37.91 4.85
1620 1649 4.122776 GCTTTGCTCTATCGGATTTCTCA 58.877 43.478 0.00 0.00 0.00 3.27
1638 1667 2.908940 ACAGCTTGCGCAGGCTTT 60.909 55.556 40.27 32.84 41.20 3.51
1642 1671 0.038892 AAATTGACAGCTTGCGCAGG 60.039 50.000 16.21 16.21 39.10 4.85
1644 1673 0.953727 AGAAATTGACAGCTTGCGCA 59.046 45.000 5.66 5.66 39.10 6.09
1645 1674 1.611043 GAGAAATTGACAGCTTGCGC 58.389 50.000 0.00 0.00 0.00 6.09
1647 1676 2.666619 CGTGGAGAAATTGACAGCTTGC 60.667 50.000 0.00 0.00 0.00 4.01
1656 1685 2.813754 TGAAGCTTCCGTGGAGAAATTG 59.186 45.455 23.42 0.00 0.00 2.32
1662 1691 0.035458 AACCTGAAGCTTCCGTGGAG 59.965 55.000 26.53 16.83 0.00 3.86
1667 1696 1.801178 GAACTGAACCTGAAGCTTCCG 59.199 52.381 23.42 16.98 0.00 4.30
1689 1718 2.396157 GCCTTTTGTCCCCGCTACG 61.396 63.158 0.00 0.00 0.00 3.51
1690 1719 2.396157 CGCCTTTTGTCCCCGCTAC 61.396 63.158 0.00 0.00 0.00 3.58
1691 1720 2.046700 CGCCTTTTGTCCCCGCTA 60.047 61.111 0.00 0.00 0.00 4.26
1692 1721 2.764637 ATTCGCCTTTTGTCCCCGCT 62.765 55.000 0.00 0.00 0.00 5.52
1693 1722 2.266376 GATTCGCCTTTTGTCCCCGC 62.266 60.000 0.00 0.00 0.00 6.13
1694 1723 1.654023 GGATTCGCCTTTTGTCCCCG 61.654 60.000 0.00 0.00 0.00 5.73
1729 1758 1.715862 GAATCGCCCTTTTCTCCGGC 61.716 60.000 0.00 0.00 39.41 6.13
1731 1760 0.107654 AGGAATCGCCCTTTTCTCCG 60.108 55.000 0.00 0.00 37.37 4.63
1742 1771 1.372087 CCCTTGTGCAGAGGAATCGC 61.372 60.000 15.94 0.00 36.33 4.58
1781 1810 1.452108 GAGATTTCCCACTGGCCCG 60.452 63.158 0.00 0.00 0.00 6.13
1788 1817 2.882137 TGAACGGTTTGAGATTTCCCAC 59.118 45.455 0.00 0.00 0.00 4.61
1792 1821 3.896648 TGCTGAACGGTTTGAGATTTC 57.103 42.857 0.00 0.00 0.00 2.17
1805 1834 3.627577 TCCTGAGTTGTTCTTTGCTGAAC 59.372 43.478 9.67 9.67 44.60 3.18
1857 1889 4.023365 GCTTCCTGAATCACATTAGCATCC 60.023 45.833 0.00 0.00 0.00 3.51
1866 1898 1.071542 TGAACCGCTTCCTGAATCACA 59.928 47.619 0.00 0.00 0.00 3.58
1883 1915 3.253188 CGCCAAATCCAGTTTTCTCTGAA 59.747 43.478 0.00 0.00 37.61 3.02
1894 1926 0.731417 CTGCTTCTCGCCAAATCCAG 59.269 55.000 0.00 0.00 38.05 3.86
1895 1927 1.308069 GCTGCTTCTCGCCAAATCCA 61.308 55.000 0.00 0.00 38.05 3.41
1922 1954 0.734942 CCCGTCGTAAACATCGCACT 60.735 55.000 0.00 0.00 0.00 4.40
1938 1970 3.019003 ATCGAACACCCAGCTCCCG 62.019 63.158 0.00 0.00 0.00 5.14
1944 1976 0.534412 AGCTCTCATCGAACACCCAG 59.466 55.000 0.00 0.00 0.00 4.45
1965 1997 1.398390 GAATTGCTTGCGTAGAGTGGG 59.602 52.381 0.00 0.00 0.00 4.61
1985 2017 0.390603 TTGGTCTACGAATGGGCACG 60.391 55.000 0.00 0.00 0.00 5.34
2034 2066 5.414765 CCTCCACTTGGTATACTTTTGTTCC 59.585 44.000 2.25 0.00 36.34 3.62
2111 2143 9.532494 CATCCATGAAACTGGGGAAATATAATA 57.468 33.333 0.00 0.00 36.89 0.98
2112 2144 7.038799 GCATCCATGAAACTGGGGAAATATAAT 60.039 37.037 0.00 0.00 36.89 1.28
2116 2148 3.960102 GCATCCATGAAACTGGGGAAATA 59.040 43.478 0.00 0.00 36.89 1.40
2125 2157 5.130292 CAAAGTCTTGCATCCATGAAACT 57.870 39.130 0.00 0.00 0.00 2.66
2139 2171 6.020984 GCAAAAATTTCAAACGCAAAGTCTT 58.979 32.000 0.00 0.00 0.00 3.01
2148 2181 8.327429 AGTCAGTAAATGCAAAAATTTCAAACG 58.673 29.630 0.00 0.00 32.16 3.60
2161 2194 5.070001 ACCAAGCTTAAGTCAGTAAATGCA 58.930 37.500 0.00 0.00 0.00 3.96
2162 2195 5.629079 ACCAAGCTTAAGTCAGTAAATGC 57.371 39.130 0.00 0.00 0.00 3.56
2171 2204 7.736447 ATTGCTCATATACCAAGCTTAAGTC 57.264 36.000 0.00 0.00 36.96 3.01
2172 2205 8.408601 CAAATTGCTCATATACCAAGCTTAAGT 58.591 33.333 0.00 2.20 36.96 2.24
2177 2210 4.038402 GCCAAATTGCTCATATACCAAGCT 59.962 41.667 0.00 0.00 36.96 3.74
2184 2217 5.074804 AGCAGATGCCAAATTGCTCATATA 58.925 37.500 0.14 0.00 42.89 0.86
2185 2218 3.895656 AGCAGATGCCAAATTGCTCATAT 59.104 39.130 0.14 0.00 42.89 1.78
2191 2224 3.515330 AGTTAGCAGATGCCAAATTGC 57.485 42.857 0.14 0.00 43.38 3.56
2223 2256 8.415950 TTTCCTAGCATCAAACCTGAATTTTA 57.584 30.769 0.00 0.00 34.49 1.52
2266 2299 1.683790 CGAACACTAGCCGCTTTCCG 61.684 60.000 0.00 0.00 0.00 4.30
2278 2311 2.584391 GGAGTCCCCTGCGAACACT 61.584 63.158 0.00 0.00 0.00 3.55
2356 2389 1.818060 CGGGTTTCATGAATCCTTGCA 59.182 47.619 27.04 2.94 32.22 4.08
2553 2586 0.955428 TCGACTTGCCTTCATGCACC 60.955 55.000 0.00 0.00 41.88 5.01
2571 2604 1.800286 GCATGCTTTTGGCCGATTCTC 60.800 52.381 11.37 0.00 40.92 2.87
2588 2621 0.322816 AATCCGCAGTGTCCTTGCAT 60.323 50.000 0.00 0.00 41.59 3.96
2607 2640 0.467474 AGCTCCGGTCGATGGTATCA 60.467 55.000 0.00 0.00 0.00 2.15
2619 2652 1.227089 CCATCTTGACGAGCTCCGG 60.227 63.158 8.47 0.00 43.93 5.14
2631 2664 0.106519 CATTCGCCCCCTTCCATCTT 60.107 55.000 0.00 0.00 0.00 2.40
2646 2679 5.572896 GGCAGTATTAAACACAAGCACATTC 59.427 40.000 0.00 0.00 0.00 2.67
2694 2727 0.183492 TCAGCACTCACCCAGCTTTT 59.817 50.000 0.00 0.00 36.26 2.27
2717 2750 6.319141 ACAGTGGTTAATTCTTTTCTGAGC 57.681 37.500 0.00 0.00 0.00 4.26
2788 2821 9.971922 GGCAGCTCATTTACAAATCTAAATTAT 57.028 29.630 0.00 0.00 0.00 1.28
2790 2823 7.761249 GTGGCAGCTCATTTACAAATCTAAATT 59.239 33.333 0.00 0.00 0.00 1.82
2791 2824 7.123247 AGTGGCAGCTCATTTACAAATCTAAAT 59.877 33.333 0.00 0.00 0.00 1.40
2792 2825 6.434028 AGTGGCAGCTCATTTACAAATCTAAA 59.566 34.615 0.00 0.00 0.00 1.85
2793 2826 5.945784 AGTGGCAGCTCATTTACAAATCTAA 59.054 36.000 0.00 0.00 0.00 2.10
2794 2827 5.355071 CAGTGGCAGCTCATTTACAAATCTA 59.645 40.000 0.00 0.00 0.00 1.98
2795 2828 4.157289 CAGTGGCAGCTCATTTACAAATCT 59.843 41.667 0.00 0.00 0.00 2.40
2796 2829 4.082571 ACAGTGGCAGCTCATTTACAAATC 60.083 41.667 0.00 0.00 0.00 2.17
2797 2830 3.828451 ACAGTGGCAGCTCATTTACAAAT 59.172 39.130 0.00 0.00 0.00 2.32
2798 2831 3.221771 ACAGTGGCAGCTCATTTACAAA 58.778 40.909 0.00 0.00 0.00 2.83
2799 2832 2.813754 GACAGTGGCAGCTCATTTACAA 59.186 45.455 0.00 0.00 0.00 2.41
2800 2833 2.038952 AGACAGTGGCAGCTCATTTACA 59.961 45.455 0.00 0.00 0.00 2.41
2801 2834 2.704572 AGACAGTGGCAGCTCATTTAC 58.295 47.619 0.00 0.00 0.00 2.01
2802 2835 4.080919 ACATAGACAGTGGCAGCTCATTTA 60.081 41.667 0.00 0.00 0.00 1.40
2803 2836 3.276857 CATAGACAGTGGCAGCTCATTT 58.723 45.455 0.00 0.00 0.00 2.32
2804 2837 2.238144 ACATAGACAGTGGCAGCTCATT 59.762 45.455 0.00 0.00 0.00 2.57
2805 2838 1.836166 ACATAGACAGTGGCAGCTCAT 59.164 47.619 0.00 0.00 0.00 2.90
2806 2839 1.269958 ACATAGACAGTGGCAGCTCA 58.730 50.000 0.00 0.00 0.00 4.26
2807 2840 2.393271 AACATAGACAGTGGCAGCTC 57.607 50.000 0.00 0.00 0.00 4.09
2808 2841 2.704572 GAAACATAGACAGTGGCAGCT 58.295 47.619 0.00 0.00 0.00 4.24
2809 2842 1.394917 CGAAACATAGACAGTGGCAGC 59.605 52.381 0.00 0.00 0.00 5.25
2810 2843 2.959516 TCGAAACATAGACAGTGGCAG 58.040 47.619 0.00 0.00 0.00 4.85
2811 2844 3.610040 ATCGAAACATAGACAGTGGCA 57.390 42.857 0.00 0.00 0.00 4.92
2812 2845 4.184629 AGAATCGAAACATAGACAGTGGC 58.815 43.478 0.00 0.00 0.00 5.01
2813 2846 5.446473 GCAAGAATCGAAACATAGACAGTGG 60.446 44.000 0.00 0.00 0.00 4.00
2814 2847 5.120674 TGCAAGAATCGAAACATAGACAGTG 59.879 40.000 0.00 0.00 0.00 3.66
2815 2848 5.237815 TGCAAGAATCGAAACATAGACAGT 58.762 37.500 0.00 0.00 0.00 3.55
2816 2849 5.784750 TGCAAGAATCGAAACATAGACAG 57.215 39.130 0.00 0.00 0.00 3.51
2817 2850 6.552859 TTTGCAAGAATCGAAACATAGACA 57.447 33.333 0.00 0.00 0.00 3.41
2818 2851 9.722056 AATATTTGCAAGAATCGAAACATAGAC 57.278 29.630 0.00 0.00 0.00 2.59
2822 2855 8.902806 TCCTAATATTTGCAAGAATCGAAACAT 58.097 29.630 0.00 0.00 0.00 2.71
2828 2861 6.634436 GCAAGTCCTAATATTTGCAAGAATCG 59.366 38.462 0.00 0.00 43.93 3.34
2836 2869 7.553881 TTACTCTGCAAGTCCTAATATTTGC 57.446 36.000 5.04 0.00 44.56 3.68
2842 2875 5.749462 AGCATTTACTCTGCAAGTCCTAAT 58.251 37.500 5.04 3.04 42.15 1.73
2844 2877 4.467795 AGAGCATTTACTCTGCAAGTCCTA 59.532 41.667 5.04 0.00 45.36 2.94
2846 2879 3.604582 AGAGCATTTACTCTGCAAGTCC 58.395 45.455 5.04 0.00 45.36 3.85
2847 2880 6.102663 TCTTAGAGCATTTACTCTGCAAGTC 58.897 40.000 4.35 0.00 46.50 3.01
2848 2881 6.042638 TCTTAGAGCATTTACTCTGCAAGT 57.957 37.500 4.35 6.74 46.50 3.16
2849 2882 6.105333 ACTCTTAGAGCATTTACTCTGCAAG 58.895 40.000 9.44 1.80 46.50 4.01
2850 2883 6.042638 ACTCTTAGAGCATTTACTCTGCAA 57.957 37.500 9.44 0.00 46.50 4.08
2851 2884 5.667539 ACTCTTAGAGCATTTACTCTGCA 57.332 39.130 9.44 0.00 46.50 4.41
2853 2886 6.800543 TGCTACTCTTAGAGCATTTACTCTG 58.199 40.000 9.44 0.00 46.50 3.35
2863 2896 4.269844 GCAGAAACATGCTACTCTTAGAGC 59.730 45.833 9.44 0.00 43.07 4.09
2864 2897 4.502282 CGCAGAAACATGCTACTCTTAGAG 59.498 45.833 7.82 7.82 44.24 2.43
2866 2899 4.424626 TCGCAGAAACATGCTACTCTTAG 58.575 43.478 0.00 0.00 44.24 2.18
2868 2901 3.319137 TCGCAGAAACATGCTACTCTT 57.681 42.857 0.00 0.00 44.24 2.85
2869 2902 3.257393 CTTCGCAGAAACATGCTACTCT 58.743 45.455 0.00 0.00 45.90 3.24
2871 2904 2.350522 CCTTCGCAGAAACATGCTACT 58.649 47.619 0.00 0.00 45.90 2.57
2872 2905 1.398390 CCCTTCGCAGAAACATGCTAC 59.602 52.381 0.00 0.00 45.90 3.58
2873 2906 1.678728 CCCCTTCGCAGAAACATGCTA 60.679 52.381 0.00 0.00 45.90 3.49
2876 2915 1.508088 GCCCCTTCGCAGAAACATG 59.492 57.895 0.00 0.00 45.90 3.21
2887 2926 1.815817 ATGTTGGTTTGCGCCCCTTC 61.816 55.000 4.18 0.90 0.00 3.46
2892 2931 4.269844 CCATAAATTATGTTGGTTTGCGCC 59.730 41.667 4.18 0.00 34.36 6.53
2894 2933 5.655488 TCCCATAAATTATGTTGGTTTGCG 58.345 37.500 11.55 0.00 34.36 4.85
2951 2990 5.888982 GGACAGTATCCCCTTCTTGATAA 57.111 43.478 0.00 0.00 42.46 1.75
3041 3080 3.120130 GCGTTTTCCGTGGATCAATGTAA 60.120 43.478 0.00 0.00 39.32 2.41
3047 3086 0.871722 CTTGCGTTTTCCGTGGATCA 59.128 50.000 0.00 0.00 39.32 2.92
3053 3092 1.375551 AGAACACTTGCGTTTTCCGT 58.624 45.000 0.00 0.00 39.32 4.69
3056 3095 2.372350 CGGAAGAACACTTGCGTTTTC 58.628 47.619 13.78 0.00 45.45 2.29
3083 3122 1.673767 ACCTGAAGTGTGATGGGGAT 58.326 50.000 0.00 0.00 0.00 3.85
3154 3193 3.619487 GCTTATTGGGGATTGCAGCAAAA 60.619 43.478 12.97 1.35 0.00 2.44
3166 3205 3.260380 TGACCATGTTTTGCTTATTGGGG 59.740 43.478 0.00 0.00 0.00 4.96
3309 3348 0.317854 GCTTCGCCACTTGTTCCAAC 60.318 55.000 0.00 0.00 0.00 3.77
3321 3360 1.131315 GGAGTCTTCATTTGCTTCGCC 59.869 52.381 0.00 0.00 0.00 5.54
3349 3388 7.770897 ACCAGATAGATTGGTAATGTTCAGAAC 59.229 37.037 6.32 6.32 46.80 3.01
3375 3414 1.722034 GGTGGCCATCTATCCTGAGA 58.278 55.000 9.72 0.00 0.00 3.27
3554 3594 6.659242 GGACAAGAGGACATTTTAAAGATGGA 59.341 38.462 12.13 0.00 0.00 3.41
3562 3602 3.330701 AGCTGGGACAAGAGGACATTTTA 59.669 43.478 0.00 0.00 38.70 1.52
3698 3738 7.070198 TGGCAAATGTTTCAGAATCCATATCAT 59.930 33.333 0.00 0.00 0.00 2.45
3758 3798 7.083875 AGGAAAAGATGAATTTTATTCGCGA 57.916 32.000 3.71 3.71 32.62 5.87
3784 3824 9.765795 CTATACAAGTCTTATCTTTTGGTAGGG 57.234 37.037 0.00 0.00 0.00 3.53
3885 3925 5.784177 CTTGCCTGTACTCTTGAGAACTTA 58.216 41.667 4.49 0.00 0.00 2.24
4067 4111 3.848272 ATTGCCATACTTCACCAAACG 57.152 42.857 0.00 0.00 0.00 3.60
4073 4117 6.093495 TGCTGTAAACTATTGCCATACTTCAC 59.907 38.462 0.00 0.00 0.00 3.18
4075 4119 6.677781 TGCTGTAAACTATTGCCATACTTC 57.322 37.500 0.00 0.00 0.00 3.01
4076 4120 5.066505 GCTGCTGTAAACTATTGCCATACTT 59.933 40.000 0.00 0.00 0.00 2.24
4077 4121 4.576463 GCTGCTGTAAACTATTGCCATACT 59.424 41.667 0.00 0.00 0.00 2.12
4339 4386 4.385825 TGCTTTGTCTTCACCGTAATCTT 58.614 39.130 0.00 0.00 0.00 2.40
4426 4474 5.300539 TGCAAAGGTAAGCATTGTTGTAAGA 59.699 36.000 0.00 0.00 35.51 2.10
4427 4475 5.527951 TGCAAAGGTAAGCATTGTTGTAAG 58.472 37.500 0.00 0.00 35.51 2.34
4428 4476 5.521906 TGCAAAGGTAAGCATTGTTGTAA 57.478 34.783 0.00 0.00 35.51 2.41
4462 4510 0.976641 TCGCAAATCACTCCTCCAGT 59.023 50.000 0.00 0.00 34.67 4.00


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

AutoCloner maintained by Alex Coulton.