Multiple sequence alignment - TraesCS2D01G519100

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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 TraesCS2D01G519100 chr2D 100.000 3139 0 0 948 4086 608981190 608978052 0.000000e+00 5797.0
1 TraesCS2D01G519100 chr2D 100.000 616 0 0 1 616 608982137 608981522 0.000000e+00 1138.0
2 TraesCS2D01G519100 chr2D 97.619 42 1 0 19 60 593274276 593274235 5.670000e-09 73.1
3 TraesCS2D01G519100 chr2A 93.935 2193 101 15 1906 4086 740874648 740872476 0.000000e+00 3284.0
4 TraesCS2D01G519100 chr2A 92.727 770 49 7 1041 1805 740875411 740874644 0.000000e+00 1105.0
5 TraesCS2D01G519100 chr2A 96.631 564 17 1 55 616 740876128 740875565 0.000000e+00 935.0
6 TraesCS2D01G519100 chr2A 98.077 52 1 0 975 1026 740875453 740875402 1.560000e-14 91.6
7 TraesCS2D01G519100 chr2A 100.000 43 0 0 19 61 769662155 769662113 3.390000e-11 80.5
8 TraesCS2D01G519100 chr2A 88.136 59 5 1 19 75 48475613 48475555 7.330000e-08 69.4
9 TraesCS2D01G519100 chr2B 94.172 1287 54 11 1906 3182 742893789 742892514 0.000000e+00 1941.0
10 TraesCS2D01G519100 chr2B 92.164 855 61 5 3236 4086 742892515 742891663 0.000000e+00 1203.0
11 TraesCS2D01G519100 chr2B 90.550 836 55 11 975 1805 742894601 742893785 0.000000e+00 1085.0
12 TraesCS2D01G519100 chr2B 96.996 566 13 3 55 616 742895257 742894692 0.000000e+00 948.0
13 TraesCS2D01G519100 chr2B 95.652 46 2 0 7 52 677350273 677350228 1.580000e-09 75.0
14 TraesCS2D01G519100 chr4D 95.370 108 5 0 1803 1910 477738865 477738758 5.430000e-39 172.0
15 TraesCS2D01G519100 chr7B 93.694 111 7 0 1803 1913 683101574 683101464 2.530000e-37 167.0
16 TraesCS2D01G519100 chr3D 89.922 129 11 2 1796 1923 44007323 44007450 9.090000e-37 165.0
17 TraesCS2D01G519100 chr3D 92.793 111 8 0 1800 1910 536331028 536331138 1.180000e-35 161.0
18 TraesCS2D01G519100 chr5D 91.525 118 9 1 1804 1921 365693410 365693294 1.180000e-35 161.0
19 TraesCS2D01G519100 chr5A 91.525 118 9 1 1804 1921 467377559 467377443 1.180000e-35 161.0
20 TraesCS2D01G519100 chr5A 92.105 114 8 1 1804 1917 308093232 308093344 4.230000e-35 159.0
21 TraesCS2D01G519100 chr5A 92.105 114 8 1 1804 1917 308179776 308179888 4.230000e-35 159.0
22 TraesCS2D01G519100 chr4B 89.831 118 10 2 1801 1917 414860742 414860858 2.540000e-32 150.0
23 TraesCS2D01G519100 chr4B 95.556 45 1 1 13 56 37318540 37318496 2.040000e-08 71.3
24 TraesCS2D01G519100 chr4A 97.619 42 1 0 19 60 631219840 631219799 5.670000e-09 73.1
25 TraesCS2D01G519100 chr1D 90.741 54 3 2 19 72 483405149 483405098 2.040000e-08 71.3
26 TraesCS2D01G519100 chr6B 93.478 46 3 0 19 64 705945665 705945710 7.330000e-08 69.4
27 TraesCS2D01G519100 chr5B 89.286 56 5 1 19 74 556628675 556628729 7.330000e-08 69.4


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 TraesCS2D01G519100 chr2D 608978052 608982137 4085 True 3467.50 5797 100.0000 1 4086 2 chr2D.!!$R2 4085
1 TraesCS2D01G519100 chr2A 740872476 740876128 3652 True 1353.90 3284 95.3425 55 4086 4 chr2A.!!$R3 4031
2 TraesCS2D01G519100 chr2B 742891663 742895257 3594 True 1294.25 1941 93.4705 55 4086 4 chr2B.!!$R2 4031

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
984 1059 1.315981 TGCGCCTCTCTAGGTCACTG 61.316 60.0 4.18 0.0 45.64 3.66 F
2400 2504 1.146544 TCAAAGGGGAAGGGGAAGGG 61.147 60.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 2537 0.326264 GGGCGGCTGAGGATGATATT 59.674 55.0 9.56 0.0 0.0 1.28 R
3964 4080 0.320946 TAAGACGTTTTGGGAGGCCG 60.321 55.0 0.83 0.0 0.0 6.13 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
24 25 7.792364 TTTAGGAGATACTTCCTCAAGTTGA 57.208 36.000 5.25 5.25 44.33 3.18
25 26 5.930837 AGGAGATACTTCCTCAAGTTGAG 57.069 43.478 23.58 23.58 44.33 3.02
26 27 5.337788 AGGAGATACTTCCTCAAGTTGAGT 58.662 41.667 27.07 14.67 44.33 3.41
27 28 5.420739 AGGAGATACTTCCTCAAGTTGAGTC 59.579 44.000 27.07 18.05 44.33 3.36
28 29 5.186021 GGAGATACTTCCTCAAGTTGAGTCA 59.814 44.000 27.07 13.53 42.80 3.41
29 30 6.127196 GGAGATACTTCCTCAAGTTGAGTCAT 60.127 42.308 27.07 14.26 42.80 3.06
30 31 6.872920 AGATACTTCCTCAAGTTGAGTCATC 58.127 40.000 27.07 19.99 42.80 2.92
31 32 6.667414 AGATACTTCCTCAAGTTGAGTCATCT 59.333 38.462 27.07 21.39 42.80 2.90
32 33 7.836685 AGATACTTCCTCAAGTTGAGTCATCTA 59.163 37.037 27.07 12.53 42.80 1.98
33 34 6.865834 ACTTCCTCAAGTTGAGTCATCTAT 57.134 37.500 27.07 7.13 42.80 1.98
34 35 7.251321 ACTTCCTCAAGTTGAGTCATCTATT 57.749 36.000 27.07 4.66 42.80 1.73
35 36 7.684529 ACTTCCTCAAGTTGAGTCATCTATTT 58.315 34.615 27.07 3.38 42.80 1.40
36 37 8.160106 ACTTCCTCAAGTTGAGTCATCTATTTT 58.840 33.333 27.07 2.23 42.80 1.82
37 38 7.912056 TCCTCAAGTTGAGTCATCTATTTTG 57.088 36.000 27.07 10.59 42.80 2.44
38 39 6.881065 TCCTCAAGTTGAGTCATCTATTTTGG 59.119 38.462 27.07 11.35 42.80 3.28
39 40 6.881065 CCTCAAGTTGAGTCATCTATTTTGGA 59.119 38.462 27.07 0.00 42.80 3.53
40 41 7.391554 CCTCAAGTTGAGTCATCTATTTTGGAA 59.608 37.037 27.07 0.00 42.80 3.53
41 42 8.099364 TCAAGTTGAGTCATCTATTTTGGAAC 57.901 34.615 0.08 0.00 0.00 3.62
42 43 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
43 44 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
44 45 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
45 46 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
46 47 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
47 48 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
48 49 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
49 50 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
50 51 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
51 52 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
52 53 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
53 54 3.343941 TTTTGGAACGGAGGGAGTATG 57.656 47.619 0.00 0.00 0.00 2.39
158 162 5.728255 CGATCATACATGTTCCGTTTTCTC 58.272 41.667 2.30 0.00 0.00 2.87
341 345 6.410942 AAAGCTTCTTTAATGGCAAGAACT 57.589 33.333 0.00 0.00 35.71 3.01
525 529 5.561725 GCTTGATAAATCATCCGAAGCTTCC 60.562 44.000 20.62 3.48 38.62 3.46
984 1059 1.315981 TGCGCCTCTCTAGGTCACTG 61.316 60.000 4.18 0.00 45.64 3.66
1027 1124 2.746279 TCAGGTGATCTCTCTCTCCC 57.254 55.000 0.00 0.00 30.64 4.30
1028 1125 2.213310 TCAGGTGATCTCTCTCTCCCT 58.787 52.381 0.00 0.00 30.64 4.20
1029 1126 2.174639 TCAGGTGATCTCTCTCTCCCTC 59.825 54.545 0.00 0.00 30.64 4.30
1030 1127 2.175499 CAGGTGATCTCTCTCTCCCTCT 59.825 54.545 0.00 0.00 30.64 3.69
1031 1128 2.443255 AGGTGATCTCTCTCTCCCTCTC 59.557 54.545 0.00 0.00 30.64 3.20
1032 1129 2.443255 GGTGATCTCTCTCTCCCTCTCT 59.557 54.545 0.00 0.00 0.00 3.10
1033 1130 3.496870 GGTGATCTCTCTCTCCCTCTCTC 60.497 56.522 0.00 0.00 0.00 3.20
1034 1131 3.392616 GTGATCTCTCTCTCCCTCTCTCT 59.607 52.174 0.00 0.00 0.00 3.10
1035 1132 3.648067 TGATCTCTCTCTCCCTCTCTCTC 59.352 52.174 0.00 0.00 0.00 3.20
1036 1133 3.421394 TCTCTCTCTCCCTCTCTCTCT 57.579 52.381 0.00 0.00 0.00 3.10
1037 1134 3.309296 TCTCTCTCTCCCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1038 1135 3.051803 TCTCTCTCTCCCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1039 1136 3.309296 TCTCTCTCCCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1040 1137 3.051803 TCTCTCTCCCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1041 1138 3.309296 TCTCTCCCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1042 1139 3.051803 TCTCTCCCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1043 1140 3.309296 TCTCCCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1044 1141 3.051803 TCTCCCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1045 1142 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1046 1143 3.051803 TCCCTCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1047 1144 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
1048 1145 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
1179 1276 6.147985 GGAGAAAAACAAAGTAGGAGCTACAG 59.852 42.308 0.00 0.00 39.22 2.74
1205 1302 7.410485 GTTTCTATCTATGCCTGCAAAAGTAC 58.590 38.462 0.00 0.00 0.00 2.73
1262 1359 2.481185 GTGCATGTTGCTTCCCATTTTG 59.519 45.455 0.00 0.00 45.31 2.44
1329 1426 9.932207 TTCATAAGATTTTTGCATGATTTCTGT 57.068 25.926 0.00 0.00 0.00 3.41
1331 1428 9.967245 CATAAGATTTTTGCATGATTTCTGTTG 57.033 29.630 0.00 0.00 0.00 3.33
1334 1431 6.647895 AGATTTTTGCATGATTTCTGTTGGTC 59.352 34.615 0.00 0.00 0.00 4.02
1335 1432 4.933505 TTTGCATGATTTCTGTTGGTCA 57.066 36.364 0.00 0.00 0.00 4.02
1354 1451 6.578023 TGGTCAGAAATTTGTTTTTAGGGTG 58.422 36.000 0.00 0.00 0.00 4.61
1356 1453 7.070571 TGGTCAGAAATTTGTTTTTAGGGTGAT 59.929 33.333 0.00 0.00 0.00 3.06
1361 1458 7.719193 AGAAATTTGTTTTTAGGGTGATTTGGG 59.281 33.333 0.00 0.00 0.00 4.12
1370 1467 7.916077 TTTAGGGTGATTTGGGTAAAAGAAA 57.084 32.000 0.00 0.00 0.00 2.52
1372 1469 4.591498 AGGGTGATTTGGGTAAAAGAAACC 59.409 41.667 0.00 0.00 36.19 3.27
1396 1493 6.444633 CAGACCATCAATTTCTATGGATTGC 58.555 40.000 15.07 5.00 44.62 3.56
1417 1514 5.587289 TGCTTTCTTACACCACAATTTCAC 58.413 37.500 0.00 0.00 0.00 3.18
1436 1533 6.935240 TTCACAGGATTTCTAAGAAGAGGA 57.065 37.500 0.00 0.00 31.96 3.71
1443 1540 8.267894 CAGGATTTCTAAGAAGAGGATAAACCA 58.732 37.037 0.00 0.00 42.04 3.67
1500 1597 2.214376 TTGTATTTGTGCCTCCCAGG 57.786 50.000 0.00 0.00 38.80 4.45
1523 1620 5.238214 GGCATCTTCTGTCACTTCATATTCC 59.762 44.000 0.00 0.00 0.00 3.01
1524 1621 6.054295 GCATCTTCTGTCACTTCATATTCCT 58.946 40.000 0.00 0.00 0.00 3.36
1525 1622 7.212976 GCATCTTCTGTCACTTCATATTCCTA 58.787 38.462 0.00 0.00 0.00 2.94
1527 1624 9.205719 CATCTTCTGTCACTTCATATTCCTATG 57.794 37.037 0.00 0.00 36.79 2.23
1528 1625 7.730084 TCTTCTGTCACTTCATATTCCTATGG 58.270 38.462 0.00 0.00 36.23 2.74
1553 1653 8.677300 GGAATTACTAGCATCAAATGAGTCAAA 58.323 33.333 0.00 0.00 0.00 2.69
1554 1654 9.713740 GAATTACTAGCATCAAATGAGTCAAAG 57.286 33.333 0.00 0.00 0.00 2.77
1555 1655 8.798859 ATTACTAGCATCAAATGAGTCAAAGT 57.201 30.769 0.00 0.00 0.00 2.66
1589 1689 1.219213 TGGTTTCCCATGGACCAAAGT 59.781 47.619 18.98 0.00 40.31 2.66
1590 1690 2.325484 GGTTTCCCATGGACCAAAGTT 58.675 47.619 15.22 0.00 33.61 2.66
1619 1719 9.460019 TCATGACATCTCAACCATACATTTTTA 57.540 29.630 0.00 0.00 0.00 1.52
1674 1775 7.951806 TCCAAAGATGCCCTTATTATTGATCAT 59.048 33.333 0.00 0.00 34.00 2.45
1716 1817 8.410141 CAGTTTTTGTGTCCCAAAGAACTATTA 58.590 33.333 11.39 0.00 43.63 0.98
1758 1859 2.378038 ACCAAGAACAAAAGCTCAGCA 58.622 42.857 0.00 0.00 0.00 4.41
1800 1901 3.575256 TGCACTGATTTTGAGGCTTCATT 59.425 39.130 0.00 0.00 32.27 2.57
1801 1902 4.766373 TGCACTGATTTTGAGGCTTCATTA 59.234 37.500 0.00 0.00 32.27 1.90
1802 1903 5.106038 TGCACTGATTTTGAGGCTTCATTAG 60.106 40.000 0.00 0.00 32.27 1.73
1803 1904 5.105997 GCACTGATTTTGAGGCTTCATTAGT 60.106 40.000 0.00 0.00 32.27 2.24
1804 1905 6.094048 GCACTGATTTTGAGGCTTCATTAGTA 59.906 38.462 0.00 0.00 32.27 1.82
1805 1906 7.467623 CACTGATTTTGAGGCTTCATTAGTAC 58.532 38.462 0.00 0.00 32.27 2.73
1806 1907 7.335422 CACTGATTTTGAGGCTTCATTAGTACT 59.665 37.037 0.00 0.00 32.27 2.73
1807 1908 7.550906 ACTGATTTTGAGGCTTCATTAGTACTC 59.449 37.037 0.00 0.00 32.27 2.59
1808 1909 6.823689 TGATTTTGAGGCTTCATTAGTACTCC 59.176 38.462 0.00 0.00 32.45 3.85
1809 1910 4.386867 TTGAGGCTTCATTAGTACTCCG 57.613 45.455 0.00 0.00 32.45 4.63
1810 1911 3.362706 TGAGGCTTCATTAGTACTCCGT 58.637 45.455 0.00 0.00 32.45 4.69
1811 1912 3.380637 TGAGGCTTCATTAGTACTCCGTC 59.619 47.826 0.00 0.00 32.45 4.79
1812 1913 2.694109 AGGCTTCATTAGTACTCCGTCC 59.306 50.000 0.00 0.00 0.00 4.79
1813 1914 2.543238 GGCTTCATTAGTACTCCGTCCG 60.543 54.545 0.00 0.00 0.00 4.79
1814 1915 2.098770 GCTTCATTAGTACTCCGTCCGT 59.901 50.000 0.00 0.00 0.00 4.69
1815 1916 3.428589 GCTTCATTAGTACTCCGTCCGTT 60.429 47.826 0.00 0.00 0.00 4.44
1816 1917 4.741342 CTTCATTAGTACTCCGTCCGTTT 58.259 43.478 0.00 0.00 0.00 3.60
1817 1918 4.100707 TCATTAGTACTCCGTCCGTTTG 57.899 45.455 0.00 0.00 0.00 2.93
1818 1919 3.507233 TCATTAGTACTCCGTCCGTTTGT 59.493 43.478 0.00 0.00 0.00 2.83
1819 1920 4.022068 TCATTAGTACTCCGTCCGTTTGTT 60.022 41.667 0.00 0.00 0.00 2.83
1820 1921 2.896745 AGTACTCCGTCCGTTTGTTT 57.103 45.000 0.00 0.00 0.00 2.83
1821 1922 3.183793 AGTACTCCGTCCGTTTGTTTT 57.816 42.857 0.00 0.00 0.00 2.43
1822 1923 3.534554 AGTACTCCGTCCGTTTGTTTTT 58.465 40.909 0.00 0.00 0.00 1.94
1823 1924 4.692228 AGTACTCCGTCCGTTTGTTTTTA 58.308 39.130 0.00 0.00 0.00 1.52
1824 1925 5.299949 AGTACTCCGTCCGTTTGTTTTTAT 58.700 37.500 0.00 0.00 0.00 1.40
1825 1926 6.454795 AGTACTCCGTCCGTTTGTTTTTATA 58.545 36.000 0.00 0.00 0.00 0.98
1826 1927 6.928492 AGTACTCCGTCCGTTTGTTTTTATAA 59.072 34.615 0.00 0.00 0.00 0.98
1827 1928 6.232139 ACTCCGTCCGTTTGTTTTTATAAG 57.768 37.500 0.00 0.00 0.00 1.73
1828 1929 5.990996 ACTCCGTCCGTTTGTTTTTATAAGA 59.009 36.000 0.00 0.00 0.00 2.10
1829 1930 6.073602 ACTCCGTCCGTTTGTTTTTATAAGAC 60.074 38.462 0.00 0.00 0.00 3.01
1830 1931 5.074791 CCGTCCGTTTGTTTTTATAAGACG 58.925 41.667 9.76 9.76 42.98 4.18
1831 1932 5.333263 CCGTCCGTTTGTTTTTATAAGACGT 60.333 40.000 13.55 0.00 42.08 4.34
1832 1933 6.128729 CGTCCGTTTGTTTTTATAAGACGTT 58.871 36.000 8.92 0.00 39.62 3.99
1833 1934 6.628461 CGTCCGTTTGTTTTTATAAGACGTTT 59.372 34.615 8.92 0.00 39.62 3.60
1834 1935 7.149462 CGTCCGTTTGTTTTTATAAGACGTTTC 60.149 37.037 8.92 0.00 39.62 2.78
1835 1936 7.639461 GTCCGTTTGTTTTTATAAGACGTTTCA 59.361 33.333 0.00 0.00 0.00 2.69
1836 1937 7.851963 TCCGTTTGTTTTTATAAGACGTTTCAG 59.148 33.333 0.00 0.00 0.00 3.02
1837 1938 7.851963 CCGTTTGTTTTTATAAGACGTTTCAGA 59.148 33.333 0.00 0.00 0.00 3.27
1838 1939 8.667204 CGTTTGTTTTTATAAGACGTTTCAGAC 58.333 33.333 0.00 0.00 0.00 3.51
1839 1940 9.493206 GTTTGTTTTTATAAGACGTTTCAGACA 57.507 29.630 0.00 0.00 0.00 3.41
1840 1941 9.710979 TTTGTTTTTATAAGACGTTTCAGACAG 57.289 29.630 0.00 0.00 0.00 3.51
1841 1942 7.349711 TGTTTTTATAAGACGTTTCAGACAGC 58.650 34.615 0.00 0.00 0.00 4.40
1842 1943 7.225931 TGTTTTTATAAGACGTTTCAGACAGCT 59.774 33.333 0.00 0.00 0.00 4.24
1843 1944 7.724305 TTTTATAAGACGTTTCAGACAGCTT 57.276 32.000 0.00 0.00 0.00 3.74
1844 1945 6.706055 TTATAAGACGTTTCAGACAGCTTG 57.294 37.500 0.00 0.00 0.00 4.01
1845 1946 2.604046 AGACGTTTCAGACAGCTTGT 57.396 45.000 0.00 0.00 0.00 3.16
1846 1947 2.906354 AGACGTTTCAGACAGCTTGTT 58.094 42.857 0.00 0.00 0.00 2.83
1847 1948 3.270877 AGACGTTTCAGACAGCTTGTTT 58.729 40.909 0.00 0.00 0.00 2.83
1848 1949 3.689649 AGACGTTTCAGACAGCTTGTTTT 59.310 39.130 0.00 0.00 0.00 2.43
1849 1950 3.758300 ACGTTTCAGACAGCTTGTTTTG 58.242 40.909 0.00 0.00 0.00 2.44
1850 1951 3.190535 ACGTTTCAGACAGCTTGTTTTGT 59.809 39.130 0.00 0.00 0.00 2.83
1851 1952 4.393680 ACGTTTCAGACAGCTTGTTTTGTA 59.606 37.500 0.00 0.00 0.00 2.41
1852 1953 4.728608 CGTTTCAGACAGCTTGTTTTGTAC 59.271 41.667 0.00 0.00 0.00 2.90
1853 1954 5.447279 CGTTTCAGACAGCTTGTTTTGTACT 60.447 40.000 0.00 0.00 0.00 2.73
1854 1955 5.484173 TTCAGACAGCTTGTTTTGTACTG 57.516 39.130 0.00 0.00 0.00 2.74
1855 1956 4.513442 TCAGACAGCTTGTTTTGTACTGT 58.487 39.130 0.00 0.00 43.93 3.55
1856 1957 4.941263 TCAGACAGCTTGTTTTGTACTGTT 59.059 37.500 0.00 0.00 41.45 3.16
1857 1958 5.414454 TCAGACAGCTTGTTTTGTACTGTTT 59.586 36.000 0.00 0.00 41.45 2.83
1858 1959 6.072175 TCAGACAGCTTGTTTTGTACTGTTTT 60.072 34.615 0.00 0.00 41.45 2.43
1859 1960 6.033831 CAGACAGCTTGTTTTGTACTGTTTTG 59.966 38.462 0.00 0.00 41.45 2.44
1860 1961 6.019779 ACAGCTTGTTTTGTACTGTTTTGA 57.980 33.333 0.00 0.00 38.38 2.69
1861 1962 6.451393 ACAGCTTGTTTTGTACTGTTTTGAA 58.549 32.000 0.00 0.00 38.38 2.69
1862 1963 6.364976 ACAGCTTGTTTTGTACTGTTTTGAAC 59.635 34.615 0.00 0.00 38.38 3.18
1863 1964 5.571357 AGCTTGTTTTGTACTGTTTTGAACG 59.429 36.000 0.00 0.00 0.00 3.95
1864 1965 5.220135 GCTTGTTTTGTACTGTTTTGAACGG 60.220 40.000 0.00 0.00 43.50 4.44
1874 1975 4.261736 TGTTTTGAACGGTGTCTTAACG 57.738 40.909 0.00 0.00 0.00 3.18
1875 1976 3.683822 TGTTTTGAACGGTGTCTTAACGT 59.316 39.130 0.00 0.00 43.43 3.99
1876 1977 4.201705 TGTTTTGAACGGTGTCTTAACGTC 60.202 41.667 0.00 0.00 40.31 4.34
1877 1978 3.441496 TTGAACGGTGTCTTAACGTCT 57.559 42.857 0.00 0.00 40.31 4.18
1878 1979 4.566545 TTGAACGGTGTCTTAACGTCTA 57.433 40.909 0.00 0.00 40.31 2.59
1879 1980 4.566545 TGAACGGTGTCTTAACGTCTAA 57.433 40.909 0.00 0.00 40.31 2.10
1880 1981 4.930963 TGAACGGTGTCTTAACGTCTAAA 58.069 39.130 0.00 0.00 40.31 1.85
1881 1982 5.347342 TGAACGGTGTCTTAACGTCTAAAA 58.653 37.500 0.00 0.00 40.31 1.52
1882 1983 5.231991 TGAACGGTGTCTTAACGTCTAAAAC 59.768 40.000 0.00 0.00 40.31 2.43
1899 2000 9.019867 CGTCTAAAACGTCTTATAAAAACGAAC 57.980 33.333 20.71 10.74 46.42 3.95
1900 2001 9.848172 GTCTAAAACGTCTTATAAAAACGAACA 57.152 29.630 20.71 7.27 39.59 3.18
1903 2004 8.982925 AAAACGTCTTATAAAAACGAACAGAG 57.017 30.769 20.71 0.00 39.59 3.35
1904 2005 6.701432 ACGTCTTATAAAAACGAACAGAGG 57.299 37.500 20.71 5.58 39.59 3.69
1921 2022 9.852091 CGAACAGAGGTAGTAACTATTTACTTT 57.148 33.333 10.40 0.00 44.77 2.66
2038 2140 3.857052 CCTTCAAGGTGCGTAGAACATA 58.143 45.455 0.00 0.00 0.00 2.29
2042 2144 5.079689 TCAAGGTGCGTAGAACATATGAA 57.920 39.130 10.38 0.00 0.00 2.57
2052 2154 6.146184 GCGTAGAACATATGAATGTACTGCAT 59.854 38.462 10.38 0.00 45.79 3.96
2054 2156 8.551205 CGTAGAACATATGAATGTACTGCATTT 58.449 33.333 10.38 0.00 45.79 2.32
2057 2159 9.618890 AGAACATATGAATGTACTGCATTTACT 57.381 29.630 10.38 0.00 45.79 2.24
2099 2201 5.238214 GCATCTCAGTCACAAAGAAACTCTT 59.762 40.000 0.00 0.00 38.59 2.85
2113 2215 2.855209 ACTCTTCACATGAGCTTGCT 57.145 45.000 0.00 0.00 35.12 3.91
2115 2217 4.277515 ACTCTTCACATGAGCTTGCTAA 57.722 40.909 0.00 0.00 35.12 3.09
2124 2226 4.082571 ACATGAGCTTGCTAAACCAATCAC 60.083 41.667 0.00 0.00 0.00 3.06
2163 2267 9.871238 CTTACTTGCTAGTATAACTTCCAAGAA 57.129 33.333 8.86 11.20 37.32 2.52
2245 2349 1.813753 CATCATCGACGGGCCGTTT 60.814 57.895 34.58 18.29 41.37 3.60
2400 2504 1.146544 TCAAAGGGGAAGGGGAAGGG 61.147 60.000 0.00 0.00 0.00 3.95
2454 2558 1.475169 TATCATCCTCAGCCGCCCAG 61.475 60.000 0.00 0.00 0.00 4.45
2515 2622 1.858739 AACCACCGGCATACCACCAT 61.859 55.000 0.00 0.00 34.57 3.55
2521 2628 1.227102 GGCATACCACCATCAGCCA 59.773 57.895 0.00 0.00 41.63 4.75
2575 2682 4.335647 CCCACCGAGCAGCAACCT 62.336 66.667 0.00 0.00 0.00 3.50
3162 3274 4.334203 TGTGTTTTGCGTGTCTTGATTACT 59.666 37.500 0.00 0.00 0.00 2.24
3163 3275 4.670621 GTGTTTTGCGTGTCTTGATTACTG 59.329 41.667 0.00 0.00 0.00 2.74
3164 3276 4.334203 TGTTTTGCGTGTCTTGATTACTGT 59.666 37.500 0.00 0.00 0.00 3.55
3165 3277 5.524281 TGTTTTGCGTGTCTTGATTACTGTA 59.476 36.000 0.00 0.00 0.00 2.74
3166 3278 5.585500 TTTGCGTGTCTTGATTACTGTAC 57.415 39.130 0.00 0.00 0.00 2.90
3185 3297 4.570369 TGTACCAATGATTCGTGTATGCAG 59.430 41.667 0.00 0.00 0.00 4.41
3211 3323 7.043590 GCTGCTATGCAAGAATCATTTTTGTAG 60.044 37.037 2.81 0.00 38.41 2.74
3212 3324 7.259882 TGCTATGCAAGAATCATTTTTGTAGG 58.740 34.615 2.81 0.00 34.76 3.18
3213 3325 6.698766 GCTATGCAAGAATCATTTTTGTAGGG 59.301 38.462 2.81 0.00 0.00 3.53
3214 3326 5.404466 TGCAAGAATCATTTTTGTAGGGG 57.596 39.130 2.81 0.00 0.00 4.79
3215 3327 4.222588 TGCAAGAATCATTTTTGTAGGGGG 59.777 41.667 2.81 0.00 0.00 5.40
3278 3390 4.969484 TCTCCCATTCACATCAGATCATG 58.031 43.478 0.00 0.00 0.00 3.07
3279 3391 4.072839 CTCCCATTCACATCAGATCATGG 58.927 47.826 0.00 0.00 0.00 3.66
3480 3594 7.173047 GGCAAATAAATGGTGTGTGAGAAATTT 59.827 33.333 0.00 0.00 0.00 1.82
3514 3628 3.370672 TGCAATACAGCAATACGACACTG 59.629 43.478 0.00 0.00 42.46 3.66
3566 3680 4.753233 CCTACATCCTCAACTCTTGACTG 58.247 47.826 0.00 0.00 35.46 3.51
3585 3699 3.067106 CTGTAAACGCTCCTCAACATGT 58.933 45.455 0.00 0.00 0.00 3.21
3627 3742 2.590114 GGTCTGGTTACCCCGTGCT 61.590 63.158 0.00 0.00 35.15 4.40
3682 3797 3.041940 GTGTGCCGAGACCAACCG 61.042 66.667 0.00 0.00 0.00 4.44
3692 3807 2.762745 GAGACCAACCGCTCTTACAAA 58.237 47.619 0.00 0.00 0.00 2.83
3725 3840 4.993584 AGCACATCAACTTTGTCTAGTCTG 59.006 41.667 0.00 0.00 0.00 3.51
3731 3846 5.047847 TCAACTTTGTCTAGTCTGTTTCGG 58.952 41.667 0.00 0.00 0.00 4.30
3733 3848 3.387050 ACTTTGTCTAGTCTGTTTCGGGT 59.613 43.478 0.00 0.00 0.00 5.28
3734 3849 4.586001 ACTTTGTCTAGTCTGTTTCGGGTA 59.414 41.667 0.00 0.00 0.00 3.69
3735 3850 4.510038 TTGTCTAGTCTGTTTCGGGTAC 57.490 45.455 0.00 0.00 0.00 3.34
3815 3930 4.657408 TGTCCTGCCGCAATGCCA 62.657 61.111 0.00 0.00 0.00 4.92
3830 3945 5.737290 CGCAATGCCAAAATACACTTAGTAC 59.263 40.000 0.00 0.00 35.05 2.73
3871 3986 4.431416 AAATCCAACCCAAAAACCTTCC 57.569 40.909 0.00 0.00 0.00 3.46
3876 3991 3.454447 CCAACCCAAAAACCTTCCTCTTT 59.546 43.478 0.00 0.00 0.00 2.52
3914 4029 1.228552 TGGCTTGGCTGAACCCTTC 60.229 57.895 0.00 0.00 37.83 3.46
3933 4049 1.326245 TCGATGCTATTTTTGCCGACG 59.674 47.619 0.00 0.00 0.00 5.12
3936 4052 2.323939 TGCTATTTTTGCCGACGTTG 57.676 45.000 0.00 0.00 0.00 4.10
3937 4053 0.981956 GCTATTTTTGCCGACGTTGC 59.018 50.000 0.00 0.09 0.00 4.17
3964 4080 6.590068 TCTCTGATGGAGAATCAATTTCCTC 58.410 40.000 0.00 0.00 46.85 3.71
4057 4173 0.991146 TGCACCACCATGACAGGTAT 59.009 50.000 0.00 0.00 40.77 2.73
4072 4188 2.436542 CAGGTATGGTCCCGTTATCCAA 59.563 50.000 0.00 0.00 34.80 3.53
4078 4194 1.578583 GTCCCGTTATCCAATGGACG 58.421 55.000 3.09 4.36 42.66 4.79
4079 4195 1.134610 GTCCCGTTATCCAATGGACGT 60.135 52.381 3.09 0.00 42.66 4.34
4080 4196 1.137479 TCCCGTTATCCAATGGACGTC 59.863 52.381 3.09 7.13 42.66 4.34
4081 4197 1.138266 CCCGTTATCCAATGGACGTCT 59.862 52.381 16.46 0.00 42.66 4.18
4082 4198 2.470821 CCGTTATCCAATGGACGTCTC 58.529 52.381 16.46 6.30 42.66 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.792364 TCAACTTGAGGAAGTATCTCCTAAA 57.208 36.000 0.00 0.00 46.33 1.85
1 2 7.411486 CTCAACTTGAGGAAGTATCTCCTAA 57.589 40.000 10.57 0.00 46.33 2.69
16 17 7.095229 CGTTCCAAAATAGATGACTCAACTTGA 60.095 37.037 0.00 0.00 0.00 3.02
17 18 7.017645 CGTTCCAAAATAGATGACTCAACTTG 58.982 38.462 0.00 0.00 0.00 3.16
18 19 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
19 20 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
20 21 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
21 22 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
22 23 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
23 24 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
24 25 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
25 26 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
26 27 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
27 28 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
28 29 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
29 30 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
30 31 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
31 32 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
32 33 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
33 34 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
34 35 2.027561 CACATACTCCCTCCGTTCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
35 36 1.553248 CACATACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
36 37 1.191535 CACATACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
37 38 0.464452 CCACATACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
38 39 0.464452 CCCACATACTCCCTCCGTTC 59.536 60.000 0.00 0.00 0.00 3.95
39 40 0.042131 TCCCACATACTCCCTCCGTT 59.958 55.000 0.00 0.00 0.00 4.44
40 41 0.397254 CTCCCACATACTCCCTCCGT 60.397 60.000 0.00 0.00 0.00 4.69
41 42 1.115930 CCTCCCACATACTCCCTCCG 61.116 65.000 0.00 0.00 0.00 4.63
42 43 0.031010 ACCTCCCACATACTCCCTCC 60.031 60.000 0.00 0.00 0.00 4.30
43 44 1.123928 CACCTCCCACATACTCCCTC 58.876 60.000 0.00 0.00 0.00 4.30
44 45 0.417841 ACACCTCCCACATACTCCCT 59.582 55.000 0.00 0.00 0.00 4.20
45 46 1.286248 AACACCTCCCACATACTCCC 58.714 55.000 0.00 0.00 0.00 4.30
46 47 3.105283 AGTAACACCTCCCACATACTCC 58.895 50.000 0.00 0.00 0.00 3.85
47 48 4.820894 AAGTAACACCTCCCACATACTC 57.179 45.455 0.00 0.00 0.00 2.59
48 49 5.578157 AAAAGTAACACCTCCCACATACT 57.422 39.130 0.00 0.00 0.00 2.12
114 115 3.726607 GCTGTGAAGTATCAGGAGATGG 58.273 50.000 0.00 0.00 35.88 3.51
181 185 2.284150 CGTACATGTCCGCGAATCAAAT 59.716 45.455 8.23 0.00 0.00 2.32
341 345 2.103094 CGAAGTGAGGCCATGGAATCTA 59.897 50.000 18.40 0.66 0.00 1.98
525 529 2.027625 GGTCGTCTGGTTGAAGGCG 61.028 63.158 0.00 0.00 46.52 5.52
947 970 0.633921 CAGGGGAAGAGAGAGGGAGA 59.366 60.000 0.00 0.00 0.00 3.71
948 971 1.048160 GCAGGGGAAGAGAGAGGGAG 61.048 65.000 0.00 0.00 0.00 4.30
949 972 1.002274 GCAGGGGAAGAGAGAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
953 976 3.077556 GGCGCAGGGGAAGAGAGA 61.078 66.667 10.83 0.00 0.00 3.10
984 1059 2.613595 TGTCATGCTGTTGTTGTGAGTC 59.386 45.455 0.00 0.00 0.00 3.36
1025 1122 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
1026 1123 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1027 1124 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1028 1125 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1029 1126 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1030 1127 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1031 1128 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1032 1129 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1033 1130 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1034 1131 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1035 1132 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1036 1133 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1037 1134 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1038 1135 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1039 1136 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1040 1137 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1041 1138 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1042 1139 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1043 1140 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1044 1141 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1045 1142 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1046 1143 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1047 1144 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1048 1145 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1179 1276 5.358160 ACTTTTGCAGGCATAGATAGAAACC 59.642 40.000 9.89 0.00 0.00 3.27
1205 1302 7.372451 TGGGTTTTGAATTACGAGAAGTATG 57.628 36.000 0.00 0.00 34.88 2.39
1262 1359 6.704493 TGTTACCAAGTGAATGACTAAGTCAC 59.296 38.462 0.00 1.43 45.65 3.67
1329 1426 7.044798 CACCCTAAAAACAAATTTCTGACCAA 58.955 34.615 0.00 0.00 0.00 3.67
1331 1428 6.811954 TCACCCTAAAAACAAATTTCTGACC 58.188 36.000 0.00 0.00 0.00 4.02
1334 1431 8.558700 CCAAATCACCCTAAAAACAAATTTCTG 58.441 33.333 0.00 0.00 0.00 3.02
1335 1432 7.719193 CCCAAATCACCCTAAAAACAAATTTCT 59.281 33.333 0.00 0.00 0.00 2.52
1354 1451 5.303333 TGGTCTGGTTTCTTTTACCCAAATC 59.697 40.000 0.00 0.00 34.66 2.17
1356 1453 4.611367 TGGTCTGGTTTCTTTTACCCAAA 58.389 39.130 0.00 0.00 34.66 3.28
1361 1458 8.360390 AGAAATTGATGGTCTGGTTTCTTTTAC 58.640 33.333 0.00 0.00 33.50 2.01
1370 1467 5.715439 TCCATAGAAATTGATGGTCTGGT 57.285 39.130 11.92 0.00 42.82 4.00
1372 1469 6.264744 AGCAATCCATAGAAATTGATGGTCTG 59.735 38.462 11.92 11.17 42.82 3.51
1396 1493 6.039270 TCCTGTGAAATTGTGGTGTAAGAAAG 59.961 38.462 0.00 0.00 0.00 2.62
1417 1514 8.267894 TGGTTTATCCTCTTCTTAGAAATCCTG 58.732 37.037 0.00 0.00 37.07 3.86
1462 1559 9.533831 AAATACAAATTTCCATGAGGTCTAACT 57.466 29.630 0.00 0.00 35.89 2.24
1500 1597 6.054295 AGGAATATGAAGTGACAGAAGATGC 58.946 40.000 0.00 0.00 0.00 3.91
1523 1620 9.499479 ACTCATTTGATGCTAGTAATTCCATAG 57.501 33.333 0.00 0.00 0.00 2.23
1524 1621 9.494271 GACTCATTTGATGCTAGTAATTCCATA 57.506 33.333 0.00 0.00 0.00 2.74
1525 1622 7.994911 TGACTCATTTGATGCTAGTAATTCCAT 59.005 33.333 0.00 0.00 0.00 3.41
1527 1624 7.792374 TGACTCATTTGATGCTAGTAATTCC 57.208 36.000 0.00 0.00 0.00 3.01
1528 1625 9.713740 CTTTGACTCATTTGATGCTAGTAATTC 57.286 33.333 0.00 0.00 0.00 2.17
1589 1689 3.786368 TGGTTGAGATGTCATGACCAA 57.214 42.857 22.85 15.83 39.61 3.67
1590 1690 4.224818 TGTATGGTTGAGATGTCATGACCA 59.775 41.667 22.85 16.38 44.29 4.02
1629 1730 7.394923 TCTTTGGAACTCAGGTTTCTAAAAACA 59.605 33.333 3.71 0.00 45.44 2.83
1674 1775 6.127479 ACAAAAACTGCAATTCCTTCACTACA 60.127 34.615 0.00 0.00 0.00 2.74
1716 1817 8.929260 TGGTTATCTTATGAATGAATGCTCAT 57.071 30.769 0.00 0.00 44.54 2.90
1758 1859 6.888632 AGTGCATACTTTCCAATTTCAGAGAT 59.111 34.615 0.00 0.00 31.66 2.75
1805 1906 6.301861 GTCTTATAAAAACAAACGGACGGAG 58.698 40.000 0.00 0.00 0.00 4.63
1806 1907 5.107530 CGTCTTATAAAAACAAACGGACGGA 60.108 40.000 9.14 0.00 39.80 4.69
1807 1908 5.074791 CGTCTTATAAAAACAAACGGACGG 58.925 41.667 9.14 0.00 39.80 4.79
1808 1909 5.669122 ACGTCTTATAAAAACAAACGGACG 58.331 37.500 13.36 13.36 45.86 4.79
1809 1910 7.639461 TGAAACGTCTTATAAAAACAAACGGAC 59.361 33.333 0.00 0.00 33.26 4.79
1810 1911 7.692088 TGAAACGTCTTATAAAAACAAACGGA 58.308 30.769 0.00 0.00 33.26 4.69
1811 1912 7.851963 TCTGAAACGTCTTATAAAAACAAACGG 59.148 33.333 0.00 0.00 33.26 4.44
1812 1913 8.667204 GTCTGAAACGTCTTATAAAAACAAACG 58.333 33.333 0.00 0.00 35.00 3.60
1813 1914 9.493206 TGTCTGAAACGTCTTATAAAAACAAAC 57.507 29.630 0.00 0.00 0.00 2.93
1814 1915 9.710979 CTGTCTGAAACGTCTTATAAAAACAAA 57.289 29.630 0.00 0.00 0.00 2.83
1815 1916 7.853929 GCTGTCTGAAACGTCTTATAAAAACAA 59.146 33.333 0.00 0.00 0.00 2.83
1816 1917 7.225931 AGCTGTCTGAAACGTCTTATAAAAACA 59.774 33.333 0.00 0.00 0.00 2.83
1817 1918 7.573627 AGCTGTCTGAAACGTCTTATAAAAAC 58.426 34.615 0.00 0.00 0.00 2.43
1818 1919 7.724305 AGCTGTCTGAAACGTCTTATAAAAA 57.276 32.000 0.00 0.00 0.00 1.94
1819 1920 7.225931 ACAAGCTGTCTGAAACGTCTTATAAAA 59.774 33.333 0.00 0.00 0.00 1.52
1820 1921 6.704493 ACAAGCTGTCTGAAACGTCTTATAAA 59.296 34.615 0.00 0.00 0.00 1.40
1821 1922 6.220930 ACAAGCTGTCTGAAACGTCTTATAA 58.779 36.000 0.00 0.00 0.00 0.98
1822 1923 5.779922 ACAAGCTGTCTGAAACGTCTTATA 58.220 37.500 0.00 0.00 0.00 0.98
1823 1924 4.632153 ACAAGCTGTCTGAAACGTCTTAT 58.368 39.130 0.00 0.00 0.00 1.73
1824 1925 4.054780 ACAAGCTGTCTGAAACGTCTTA 57.945 40.909 0.00 0.00 0.00 2.10
1825 1926 2.906354 ACAAGCTGTCTGAAACGTCTT 58.094 42.857 0.00 0.00 0.00 3.01
1826 1927 2.604046 ACAAGCTGTCTGAAACGTCT 57.396 45.000 0.00 0.00 0.00 4.18
1827 1928 3.675467 AAACAAGCTGTCTGAAACGTC 57.325 42.857 0.00 0.00 0.00 4.34
1828 1929 3.190535 ACAAAACAAGCTGTCTGAAACGT 59.809 39.130 0.00 0.00 0.00 3.99
1829 1930 3.758300 ACAAAACAAGCTGTCTGAAACG 58.242 40.909 0.00 0.00 0.00 3.60
1830 1931 5.739161 CAGTACAAAACAAGCTGTCTGAAAC 59.261 40.000 0.00 0.00 0.00 2.78
1831 1932 5.414454 ACAGTACAAAACAAGCTGTCTGAAA 59.586 36.000 0.00 0.00 35.78 2.69
1832 1933 4.941263 ACAGTACAAAACAAGCTGTCTGAA 59.059 37.500 0.00 0.00 35.78 3.02
1833 1934 4.513442 ACAGTACAAAACAAGCTGTCTGA 58.487 39.130 0.00 0.00 35.78 3.27
1834 1935 4.882671 ACAGTACAAAACAAGCTGTCTG 57.117 40.909 0.00 0.00 35.78 3.51
1835 1936 5.897377 AAACAGTACAAAACAAGCTGTCT 57.103 34.783 0.00 0.00 39.19 3.41
1836 1937 6.090129 TCAAAACAGTACAAAACAAGCTGTC 58.910 36.000 0.00 0.00 39.19 3.51
1837 1938 6.019779 TCAAAACAGTACAAAACAAGCTGT 57.980 33.333 0.00 0.00 41.51 4.40
1838 1939 6.452350 CGTTCAAAACAGTACAAAACAAGCTG 60.452 38.462 0.00 0.00 0.00 4.24
1839 1940 5.571357 CGTTCAAAACAGTACAAAACAAGCT 59.429 36.000 0.00 0.00 0.00 3.74
1840 1941 5.220135 CCGTTCAAAACAGTACAAAACAAGC 60.220 40.000 0.00 0.00 0.00 4.01
1841 1942 5.859648 ACCGTTCAAAACAGTACAAAACAAG 59.140 36.000 0.00 0.00 0.00 3.16
1842 1943 5.629849 CACCGTTCAAAACAGTACAAAACAA 59.370 36.000 0.00 0.00 0.00 2.83
1843 1944 5.154932 CACCGTTCAAAACAGTACAAAACA 58.845 37.500 0.00 0.00 0.00 2.83
1844 1945 5.155643 ACACCGTTCAAAACAGTACAAAAC 58.844 37.500 0.00 0.00 0.00 2.43
1845 1946 5.181622 AGACACCGTTCAAAACAGTACAAAA 59.818 36.000 0.00 0.00 0.00 2.44
1846 1947 4.696402 AGACACCGTTCAAAACAGTACAAA 59.304 37.500 0.00 0.00 0.00 2.83
1847 1948 4.255301 AGACACCGTTCAAAACAGTACAA 58.745 39.130 0.00 0.00 0.00 2.41
1848 1949 3.864243 AGACACCGTTCAAAACAGTACA 58.136 40.909 0.00 0.00 0.00 2.90
1849 1950 4.870221 AAGACACCGTTCAAAACAGTAC 57.130 40.909 0.00 0.00 0.00 2.73
1850 1951 5.005586 CGTTAAGACACCGTTCAAAACAGTA 59.994 40.000 0.00 0.00 0.00 2.74
1851 1952 4.201744 CGTTAAGACACCGTTCAAAACAGT 60.202 41.667 0.00 0.00 0.00 3.55
1852 1953 4.201744 ACGTTAAGACACCGTTCAAAACAG 60.202 41.667 0.00 0.00 0.00 3.16
1853 1954 3.683822 ACGTTAAGACACCGTTCAAAACA 59.316 39.130 0.00 0.00 0.00 2.83
1854 1955 4.033243 AGACGTTAAGACACCGTTCAAAAC 59.967 41.667 0.00 0.00 34.51 2.43
1855 1956 4.183101 AGACGTTAAGACACCGTTCAAAA 58.817 39.130 0.00 0.00 34.51 2.44
1856 1957 3.784338 AGACGTTAAGACACCGTTCAAA 58.216 40.909 0.00 0.00 34.51 2.69
1857 1958 3.441496 AGACGTTAAGACACCGTTCAA 57.559 42.857 0.00 0.00 34.51 2.69
1858 1959 4.566545 TTAGACGTTAAGACACCGTTCA 57.433 40.909 0.00 0.00 34.51 3.18
1859 1960 5.608206 CGTTTTAGACGTTAAGACACCGTTC 60.608 44.000 0.00 0.00 46.49 3.95
1860 1961 4.207019 CGTTTTAGACGTTAAGACACCGTT 59.793 41.667 0.00 0.00 46.49 4.44
1861 1962 3.730715 CGTTTTAGACGTTAAGACACCGT 59.269 43.478 0.00 0.00 46.49 4.83
1862 1963 4.283950 CGTTTTAGACGTTAAGACACCG 57.716 45.455 0.00 0.00 46.49 4.94
1874 1975 9.848172 TGTTCGTTTTTATAAGACGTTTTAGAC 57.152 29.630 17.49 11.04 37.95 2.59
1878 1979 8.066000 CCTCTGTTCGTTTTTATAAGACGTTTT 58.934 33.333 17.49 0.00 37.95 2.43
1879 1980 7.225341 ACCTCTGTTCGTTTTTATAAGACGTTT 59.775 33.333 17.49 0.00 37.95 3.60
1880 1981 6.703165 ACCTCTGTTCGTTTTTATAAGACGTT 59.297 34.615 17.49 0.00 37.95 3.99
1881 1982 6.218746 ACCTCTGTTCGTTTTTATAAGACGT 58.781 36.000 17.49 0.00 37.95 4.34
1882 1983 6.701432 ACCTCTGTTCGTTTTTATAAGACG 57.299 37.500 13.97 13.97 38.09 4.18
1883 1984 8.754230 ACTACCTCTGTTCGTTTTTATAAGAC 57.246 34.615 0.00 0.00 0.00 3.01
1890 1991 9.551734 AAATAGTTACTACCTCTGTTCGTTTTT 57.448 29.630 0.00 0.00 0.00 1.94
1892 1993 9.631452 GTAAATAGTTACTACCTCTGTTCGTTT 57.369 33.333 5.84 0.00 37.27 3.60
1893 1994 9.018582 AGTAAATAGTTACTACCTCTGTTCGTT 57.981 33.333 13.65 0.00 46.59 3.85
1894 1995 8.572855 AGTAAATAGTTACTACCTCTGTTCGT 57.427 34.615 13.65 0.00 46.59 3.85
1921 2022 3.535280 TGTGTTGACAGAAGCACAGTA 57.465 42.857 0.00 0.00 37.00 2.74
2056 2158 9.649167 TGAGATGCATGAATGAACATATAGTAG 57.351 33.333 2.46 0.00 0.00 2.57
2057 2159 9.649167 CTGAGATGCATGAATGAACATATAGTA 57.351 33.333 2.46 0.00 0.00 1.82
2058 2160 8.155510 ACTGAGATGCATGAATGAACATATAGT 58.844 33.333 2.46 0.00 0.00 2.12
2069 2171 5.250982 TCTTTGTGACTGAGATGCATGAAT 58.749 37.500 2.46 0.00 0.00 2.57
2099 2201 3.138884 TGGTTTAGCAAGCTCATGTGA 57.861 42.857 0.00 0.00 0.00 3.58
2113 2215 7.484975 AGAAATTTGTGTTCGTGATTGGTTTA 58.515 30.769 0.00 0.00 0.00 2.01
2115 2217 5.901552 AGAAATTTGTGTTCGTGATTGGTT 58.098 33.333 0.00 0.00 0.00 3.67
2124 2226 7.352739 ACTAGCAAGTAAGAAATTTGTGTTCG 58.647 34.615 0.00 0.00 32.84 3.95
2153 2257 7.054124 TCTGTACAAGTCATTTTCTTGGAAGT 58.946 34.615 0.00 0.00 44.29 3.01
2157 2261 7.439157 TGATCTGTACAAGTCATTTTCTTGG 57.561 36.000 0.00 0.00 44.29 3.61
2163 2267 7.038729 TCCTCTCTTGATCTGTACAAGTCATTT 60.039 37.037 9.81 0.00 43.30 2.32
2174 2278 4.582656 CGTCCTAATCCTCTCTTGATCTGT 59.417 45.833 0.00 0.00 0.00 3.41
2245 2349 3.208594 GCATGATAGCTTGTGTGGATCA 58.791 45.455 0.00 0.00 0.00 2.92
2433 2537 0.326264 GGGCGGCTGAGGATGATATT 59.674 55.000 9.56 0.00 0.00 1.28
2454 2558 1.153568 TATGTCTGTGGCTGCTCGC 60.154 57.895 0.00 0.00 38.13 5.03
2468 2575 1.400530 GGCGGCTGAGGGTAGTATGT 61.401 60.000 0.00 0.00 0.00 2.29
2497 2604 2.265467 GATGGTGGTATGCCGGTGGT 62.265 60.000 1.90 0.00 37.67 4.16
2515 2622 2.848679 TGCTCAGTGGGTGGCTGA 60.849 61.111 0.00 0.00 40.28 4.26
2521 2628 3.958860 GGTGGCTGCTCAGTGGGT 61.959 66.667 0.00 0.00 0.00 4.51
2575 2682 3.702048 GGCTGAGGGTGGTACGCA 61.702 66.667 0.00 0.00 43.02 5.24
2578 2685 4.468689 GGCGGCTGAGGGTGGTAC 62.469 72.222 0.00 0.00 0.00 3.34
3133 3240 1.255084 GACACGCAAAACACATGCAAC 59.745 47.619 0.00 0.00 44.01 4.17
3162 3274 4.508662 TGCATACACGAATCATTGGTACA 58.491 39.130 0.00 0.00 0.00 2.90
3163 3275 4.552767 GCTGCATACACGAATCATTGGTAC 60.553 45.833 0.00 0.00 0.00 3.34
3164 3276 3.559655 GCTGCATACACGAATCATTGGTA 59.440 43.478 0.00 0.00 0.00 3.25
3165 3277 2.355756 GCTGCATACACGAATCATTGGT 59.644 45.455 0.00 0.00 0.00 3.67
3166 3278 2.615447 AGCTGCATACACGAATCATTGG 59.385 45.455 1.02 0.00 0.00 3.16
3185 3297 5.579511 ACAAAAATGATTCTTGCATAGCAGC 59.420 36.000 0.00 0.00 40.61 5.25
3215 3327 4.079961 ATGCAAAGCCCCTCCCCC 62.080 66.667 0.00 0.00 0.00 5.40
3216 3328 2.761213 CATGCAAAGCCCCTCCCC 60.761 66.667 0.00 0.00 0.00 4.81
3217 3329 0.688749 ATTCATGCAAAGCCCCTCCC 60.689 55.000 0.00 0.00 0.00 4.30
3220 3332 2.037144 GATGATTCATGCAAAGCCCCT 58.963 47.619 3.32 0.00 0.00 4.79
3278 3390 2.600867 CGATTCTCTCGTCTTTTCAGCC 59.399 50.000 0.00 0.00 42.56 4.85
3279 3391 3.898005 CGATTCTCTCGTCTTTTCAGC 57.102 47.619 0.00 0.00 42.56 4.26
3443 3557 5.931724 ACCATTTATTTGCCAAAGTGCTAAC 59.068 36.000 0.00 0.00 0.00 2.34
3480 3594 6.670077 TGCTGTATTGCATTTAATCGTACA 57.330 33.333 0.00 0.00 38.12 2.90
3501 3615 4.928661 ACAAATCTCAGTGTCGTATTGC 57.071 40.909 0.00 0.00 0.00 3.56
3566 3680 5.796350 AATACATGTTGAGGAGCGTTTAC 57.204 39.130 2.30 0.00 0.00 2.01
3627 3742 4.612412 GGTCCGTTGTCGCACCCA 62.612 66.667 0.00 0.00 41.57 4.51
3679 3794 3.454812 AGATATGGGTTTGTAAGAGCGGT 59.545 43.478 0.00 0.00 0.00 5.68
3682 3797 5.467063 GTGCTAGATATGGGTTTGTAAGAGC 59.533 44.000 0.00 0.00 0.00 4.09
3692 3807 5.636903 AAGTTGATGTGCTAGATATGGGT 57.363 39.130 0.00 0.00 0.00 4.51
3725 3840 1.869132 GTTGACACTGGTACCCGAAAC 59.131 52.381 10.07 5.07 0.00 2.78
3731 3846 1.414919 TGTGGAGTTGACACTGGTACC 59.585 52.381 4.43 4.43 39.52 3.34
3733 3848 3.646162 AGATTGTGGAGTTGACACTGGTA 59.354 43.478 0.00 0.00 39.52 3.25
3734 3849 2.439507 AGATTGTGGAGTTGACACTGGT 59.560 45.455 0.00 0.00 39.52 4.00
3735 3850 3.131709 AGATTGTGGAGTTGACACTGG 57.868 47.619 0.00 0.00 39.52 4.00
3737 3852 4.422073 TGAAGATTGTGGAGTTGACACT 57.578 40.909 0.00 0.00 39.52 3.55
3738 3853 4.756642 TGATGAAGATTGTGGAGTTGACAC 59.243 41.667 0.00 0.00 39.26 3.67
3739 3854 4.756642 GTGATGAAGATTGTGGAGTTGACA 59.243 41.667 0.00 0.00 0.00 3.58
3815 3930 8.079809 GCACATGGTTTGTACTAAGTGTATTTT 58.920 33.333 0.00 0.00 36.57 1.82
3830 3945 3.724508 TTACTTGGTGCACATGGTTTG 57.275 42.857 20.43 3.62 0.00 2.93
3871 3986 2.550830 AGGTAGCACCACACAAAGAG 57.449 50.000 7.86 0.00 41.95 2.85
3876 3991 1.203137 AGGAGTAGGTAGCACCACACA 60.203 52.381 7.86 0.00 41.95 3.72
3914 4029 1.062002 ACGTCGGCAAAAATAGCATCG 59.938 47.619 0.00 0.00 0.00 3.84
3960 4076 2.754375 GTTTTGGGAGGCCGAGGA 59.246 61.111 0.00 0.00 0.00 3.71
3962 4078 2.032071 ACGTTTTGGGAGGCCGAG 59.968 61.111 0.00 0.00 0.00 4.63
3964 4080 0.320946 TAAGACGTTTTGGGAGGCCG 60.321 55.000 0.83 0.00 0.00 6.13
3994 4110 8.685838 ACTAAAGCAACAAATTACTACTTCCA 57.314 30.769 0.00 0.00 0.00 3.53
4005 4121 7.009723 CGGTAACAACAAACTAAAGCAACAAAT 59.990 33.333 0.00 0.00 0.00 2.32
4012 4128 4.219143 AGCGGTAACAACAAACTAAAGC 57.781 40.909 0.00 0.00 0.00 3.51
4018 4134 4.156182 GCATTCTAGCGGTAACAACAAAC 58.844 43.478 0.00 0.00 0.00 2.93
4028 4144 1.078426 GGTGGTGCATTCTAGCGGT 60.078 57.895 0.00 0.00 37.31 5.68
4057 4173 1.210967 GTCCATTGGATAACGGGACCA 59.789 52.381 9.01 0.00 37.51 4.02


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

AutoCloner maintained by Alex Coulton.