Multiple sequence alignment - TraesCS1D01G240000

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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 TraesCS1D01G240000 chr1D 100.000 3963 0 0 981 4943 329735126 329731164 0.000000e+00 7319.0
1 TraesCS1D01G240000 chr1D 100.000 618 0 0 1 618 329736106 329735489 0.000000e+00 1142.0
2 TraesCS1D01G240000 chr1A 92.459 2652 127 32 981 3585 426891905 426889280 0.000000e+00 3722.0
3 TraesCS1D01G240000 chr1A 91.806 720 39 6 4224 4943 426888649 426887950 0.000000e+00 985.0
4 TraesCS1D01G240000 chr1A 84.665 626 67 12 1 613 426892563 426891954 9.160000e-167 597.0
5 TraesCS1D01G240000 chr1A 91.367 417 15 8 3837 4240 426889079 426888671 7.230000e-153 551.0
6 TraesCS1D01G240000 chr1A 92.593 81 5 1 3741 3820 426889225 426889145 1.120000e-21 115.0
7 TraesCS1D01G240000 chr1B 95.351 1355 52 8 2076 3428 444690613 444689268 0.000000e+00 2143.0
8 TraesCS1D01G240000 chr1B 92.289 1219 62 11 3741 4943 444689073 444687871 0.000000e+00 1701.0
9 TraesCS1D01G240000 chr1B 88.077 520 41 14 981 1489 444691296 444690787 9.160000e-167 597.0
10 TraesCS1D01G240000 chr1B 85.741 526 42 11 94 613 444691844 444691346 4.380000e-145 525.0
11 TraesCS1D01G240000 chr1B 94.845 194 6 2 3475 3664 444689265 444689072 2.890000e-77 300.0
12 TraesCS1D01G240000 chr1B 92.857 56 4 0 2 57 444710905 444710850 1.140000e-11 82.4
13 TraesCS1D01G240000 chr3B 85.553 443 39 11 2715 3134 179384038 179384478 1.630000e-119 440.0
14 TraesCS1D01G240000 chr3B 88.764 89 5 3 3663 3748 828548738 828548652 2.430000e-18 104.0
15 TraesCS1D01G240000 chr3A 84.910 444 41 10 2715 3134 521357356 521356915 4.570000e-115 425.0
16 TraesCS1D01G240000 chr5D 83.105 438 45 18 2724 3134 62093688 62093253 6.040000e-99 372.0
17 TraesCS1D01G240000 chr5D 95.522 67 3 0 3068 3134 32757957 32758023 1.880000e-19 108.0
18 TraesCS1D01G240000 chr5D 89.157 83 9 0 3660 3742 61045887 61045805 2.430000e-18 104.0
19 TraesCS1D01G240000 chr5D 89.286 84 6 2 3660 3743 370941368 370941288 8.750000e-18 102.0
20 TraesCS1D01G240000 chr5D 85.507 69 10 0 98 166 382501652 382501720 6.860000e-09 73.1
21 TraesCS1D01G240000 chr4A 81.081 296 28 11 2864 3134 177596976 177596684 1.390000e-50 211.0
22 TraesCS1D01G240000 chr4A 86.508 126 11 3 1380 1501 634050533 634050410 3.100000e-27 134.0
23 TraesCS1D01G240000 chr4A 79.612 103 21 0 94 196 112730342 112730240 1.910000e-09 75.0
24 TraesCS1D01G240000 chr7D 91.860 86 3 2 3658 3742 177987445 177987527 3.130000e-22 117.0
25 TraesCS1D01G240000 chr7D 90.805 87 4 3 3660 3742 617804788 617804874 4.040000e-21 113.0
26 TraesCS1D01G240000 chr7D 84.112 107 6 7 3646 3743 38011281 38011385 5.270000e-15 93.5
27 TraesCS1D01G240000 chr4D 85.849 106 11 4 1400 1501 160049893 160049788 5.230000e-20 110.0
28 TraesCS1D01G240000 chr3D 89.412 85 4 2 3663 3742 411724429 411724345 8.750000e-18 102.0
29 TraesCS1D01G240000 chr3D 88.372 86 7 1 3660 3742 112712761 112712676 3.150000e-17 100.0
30 TraesCS1D01G240000 chr3D 79.675 123 12 9 3622 3742 110398500 110398389 5.310000e-10 76.8
31 TraesCS1D01G240000 chr2D 89.412 85 3 3 3663 3742 138762765 138762682 8.750000e-18 102.0
32 TraesCS1D01G240000 chr5A 86.585 82 9 1 1547 1626 568914102 568914183 6.820000e-14 89.8
33 TraesCS1D01G240000 chr5A 88.333 60 5 1 1561 1618 518787034 518786975 2.470000e-08 71.3
34 TraesCS1D01G240000 chr2B 76.301 173 37 3 58 228 769053901 769054071 6.820000e-14 89.8
35 TraesCS1D01G240000 chr2B 87.500 72 9 0 1547 1618 761956906 761956977 3.170000e-12 84.2
36 TraesCS1D01G240000 chr6B 85.366 82 10 1 1547 1626 626253641 626253722 3.170000e-12 84.2
37 TraesCS1D01G240000 chr6B 85.135 74 9 1 1547 1618 647772144 647772217 1.910000e-09 75.0
38 TraesCS1D01G240000 chr7A 90.196 51 5 0 1561 1611 271152145 271152095 3.190000e-07 67.6
39 TraesCS1D01G240000 chr5B 83.562 73 10 1 1548 1618 699302242 699302170 3.190000e-07 67.6


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 TraesCS1D01G240000 chr1D 329731164 329736106 4942 True 4230.5 7319 100.0000 1 4943 2 chr1D.!!$R1 4942
1 TraesCS1D01G240000 chr1A 426887950 426892563 4613 True 1194.0 3722 90.5780 1 4943 5 chr1A.!!$R1 4942
2 TraesCS1D01G240000 chr1B 444687871 444691844 3973 True 1053.2 2143 91.2606 94 4943 5 chr1B.!!$R2 4849

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
439 456 0.589229 CCACGAGACGTATGCGAGAC 60.589 60.0 11.07 1.0 38.32 3.36 F
521 538 0.887387 ATCCGTCGTTGGTTGGTTGG 60.887 55.0 0.00 0.0 0.00 3.77 F
523 540 0.887387 CCGTCGTTGGTTGGTTGGAT 60.887 55.0 0.00 0.0 0.00 3.41 F
1747 1789 0.623723 TTGGTGGTGGGAGATTAGCC 59.376 55.0 0.00 0.0 0.00 3.93 F
3677 3781 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.0 0.00 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1524 1.275291 TCCAAGTTCCGAGTGGACATC 59.725 52.381 0.00 0.0 46.45 3.06 R
1723 1765 1.423794 ATCTCCCACCACCAACGGTT 61.424 55.000 0.00 0.0 37.07 4.44 R
1750 1792 1.508632 CACCGACGGTTCAAACAGAT 58.491 50.000 19.02 0.0 31.02 2.90 R
3725 3829 0.264955 ACATACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.0 0.00 4.00 R
4780 4993 0.105964 ACGTTCCAGCACTACAAGCA 59.894 50.000 0.00 0.0 0.00 3.91 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
42 43 0.608130 TGTGTGCTAGCCAACGAGAT 59.392 50.000 13.29 0.00 0.00 2.75
44 45 2.076863 GTGTGCTAGCCAACGAGATTT 58.923 47.619 13.29 0.00 0.00 2.17
48 49 3.058224 GTGCTAGCCAACGAGATTTTGTT 60.058 43.478 13.29 0.00 0.00 2.83
63 64 7.020914 AGATTTTGTTTCAGACACTTCAGAC 57.979 36.000 0.00 0.00 38.18 3.51
66 67 2.429250 TGTTTCAGACACTTCAGACCGA 59.571 45.455 0.00 0.00 32.00 4.69
81 82 5.739959 TCAGACCGATTCAATGGTTCAATA 58.260 37.500 0.00 0.00 38.99 1.90
89 90 3.792401 TCAATGGTTCAATAGCGACGAT 58.208 40.909 0.00 0.00 0.00 3.73
92 93 1.663643 TGGTTCAATAGCGACGATTGC 59.336 47.619 0.00 0.00 34.82 3.56
96 105 1.227263 AATAGCGACGATTGCGGCT 60.227 52.632 0.00 4.01 45.51 5.52
132 141 2.542020 TGTGCATGAAGACTTTCCGA 57.458 45.000 0.00 0.00 32.09 4.55
140 149 5.050499 GCATGAAGACTTTCCGACTATCATG 60.050 44.000 0.00 7.79 43.45 3.07
143 152 5.363868 TGAAGACTTTCCGACTATCATGGAT 59.636 40.000 0.00 0.00 32.09 3.41
145 154 6.582677 AGACTTTCCGACTATCATGGATAG 57.417 41.667 10.83 10.83 45.21 2.08
161 170 2.587522 GATAGGGTCAAAATGGCTCCC 58.412 52.381 0.00 0.00 38.50 4.30
175 184 1.153647 CTCCCGTAGCGATGCAACA 60.154 57.895 0.00 0.00 0.00 3.33
192 201 4.908687 AACAGTGGCGCGTCAGCA 62.909 61.111 16.68 0.00 45.49 4.41
199 208 3.922893 GCGCGTCAGCAGCTCATC 61.923 66.667 8.43 0.00 45.49 2.92
206 215 0.967380 TCAGCAGCTCATCCTGACGA 60.967 55.000 0.00 0.00 34.77 4.20
211 220 1.931841 CAGCTCATCCTGACGACAATG 59.068 52.381 0.00 0.00 34.77 2.82
217 226 0.762418 TCCTGACGACAATGGTGGTT 59.238 50.000 0.00 0.00 35.99 3.67
283 292 6.572314 GCACTGCATTTCTTACCAACCTTTAT 60.572 38.462 0.00 0.00 0.00 1.40
286 295 9.255029 ACTGCATTTCTTACCAACCTTTATAAT 57.745 29.630 0.00 0.00 0.00 1.28
432 449 1.000521 TGGGACCCACGAGACGTAT 60.001 57.895 9.95 0.00 38.32 3.06
439 456 0.589229 CCACGAGACGTATGCGAGAC 60.589 60.000 11.07 1.00 38.32 3.36
455 472 1.300697 GACAAGTCGTGGCCTCGTT 60.301 57.895 25.10 11.73 0.00 3.85
517 534 1.785321 CGAATCCGTCGTTGGTTGG 59.215 57.895 0.00 0.00 45.09 3.77
518 535 0.947180 CGAATCCGTCGTTGGTTGGT 60.947 55.000 0.00 0.00 45.09 3.67
520 537 0.948678 AATCCGTCGTTGGTTGGTTG 59.051 50.000 0.00 0.00 0.00 3.77
521 538 0.887387 ATCCGTCGTTGGTTGGTTGG 60.887 55.000 0.00 0.00 0.00 3.77
522 539 1.524165 CCGTCGTTGGTTGGTTGGA 60.524 57.895 0.00 0.00 0.00 3.53
523 540 0.887387 CCGTCGTTGGTTGGTTGGAT 60.887 55.000 0.00 0.00 0.00 3.41
524 541 0.948678 CGTCGTTGGTTGGTTGGATT 59.051 50.000 0.00 0.00 0.00 3.01
525 542 1.069500 CGTCGTTGGTTGGTTGGATTC 60.069 52.381 0.00 0.00 0.00 2.52
526 543 2.227194 GTCGTTGGTTGGTTGGATTCT 58.773 47.619 0.00 0.00 0.00 2.40
527 544 2.225727 GTCGTTGGTTGGTTGGATTCTC 59.774 50.000 0.00 0.00 0.00 2.87
528 545 2.105821 TCGTTGGTTGGTTGGATTCTCT 59.894 45.455 0.00 0.00 0.00 3.10
529 546 2.884639 CGTTGGTTGGTTGGATTCTCTT 59.115 45.455 0.00 0.00 0.00 2.85
530 547 3.317993 CGTTGGTTGGTTGGATTCTCTTT 59.682 43.478 0.00 0.00 0.00 2.52
531 548 4.556699 CGTTGGTTGGTTGGATTCTCTTTC 60.557 45.833 0.00 0.00 0.00 2.62
535 552 5.073428 GGTTGGTTGGATTCTCTTTCTCTT 58.927 41.667 0.00 0.00 0.00 2.85
537 554 6.294231 GGTTGGTTGGATTCTCTTTCTCTTTC 60.294 42.308 0.00 0.00 0.00 2.62
1169 1197 4.996434 GCTGTGGTGTCCTGCGCT 62.996 66.667 9.73 0.00 0.00 5.92
1175 1203 1.153745 GGTGTCCTGCGCTGTAGAG 60.154 63.158 9.73 0.00 0.00 2.43
1201 1229 4.532834 GGGTTAATTGGTTCTAGGATGCA 58.467 43.478 0.00 0.00 0.00 3.96
1273 1301 2.095969 TCGTTATTGCAAAGCTTCGTGG 60.096 45.455 1.71 0.00 0.00 4.94
1322 1350 3.932710 GACTAGCCGTGATTGTTGAATCA 59.067 43.478 0.00 0.00 44.73 2.57
1358 1386 5.007234 CCACGTTTGTTCAGTTAGTTGATGA 59.993 40.000 0.00 0.00 0.00 2.92
1359 1387 6.293407 CCACGTTTGTTCAGTTAGTTGATGAT 60.293 38.462 0.00 0.00 0.00 2.45
1360 1388 6.574832 CACGTTTGTTCAGTTAGTTGATGATG 59.425 38.462 0.00 0.00 0.00 3.07
1371 1399 9.888878 CAGTTAGTTGATGATGCCATTATTTAG 57.111 33.333 0.00 0.00 32.09 1.85
1413 1446 4.261801 CCAAGTTCGGATGTTGGATACTT 58.738 43.478 11.63 0.00 43.01 2.24
1414 1447 4.094887 CCAAGTTCGGATGTTGGATACTTG 59.905 45.833 11.63 9.54 43.01 3.16
1440 1473 7.775561 GGATTCCCATTTTGTCTCTTGTAGTAT 59.224 37.037 0.00 0.00 0.00 2.12
1443 1476 5.523916 CCCATTTTGTCTCTTGTAGTATCGG 59.476 44.000 0.00 0.00 0.00 4.18
1452 1485 5.416013 TCTCTTGTAGTATCGGATGCTATGG 59.584 44.000 17.03 11.02 30.25 2.74
1453 1486 5.321927 TCTTGTAGTATCGGATGCTATGGA 58.678 41.667 17.03 12.67 30.25 3.41
1458 1492 6.873605 TGTAGTATCGGATGCTATGGATTTTG 59.126 38.462 17.03 0.00 30.25 2.44
1471 1505 6.914757 GCTATGGATTTTGCTAAAGTCATCAC 59.085 38.462 12.14 5.65 0.00 3.06
1476 1510 7.611467 TGGATTTTGCTAAAGTCATCACATAGT 59.389 33.333 0.00 0.00 0.00 2.12
1510 1544 1.275291 GATGTCCACTCGGAACTTGGA 59.725 52.381 0.00 0.00 45.20 3.53
1521 1555 3.751175 TCGGAACTTGGACATGTTCATTC 59.249 43.478 23.68 9.66 43.29 2.67
1559 1593 5.586643 TGTTTATGTAGTGTTCACAAGCACA 59.413 36.000 5.74 4.48 38.02 4.57
1567 1601 3.608073 GTGTTCACAAGCACAAACTGTTC 59.392 43.478 0.00 0.00 35.81 3.18
1569 1603 4.233789 GTTCACAAGCACAAACTGTTCAA 58.766 39.130 0.00 0.00 0.00 2.69
1574 1608 6.039159 TCACAAGCACAAACTGTTCAATCATA 59.961 34.615 0.00 0.00 0.00 2.15
1746 1788 1.751437 GTTGGTGGTGGGAGATTAGC 58.249 55.000 0.00 0.00 0.00 3.09
1747 1789 0.623723 TTGGTGGTGGGAGATTAGCC 59.376 55.000 0.00 0.00 0.00 3.93
1748 1790 1.146263 GGTGGTGGGAGATTAGCCG 59.854 63.158 0.00 0.00 0.00 5.52
1750 1792 1.117150 GTGGTGGGAGATTAGCCGTA 58.883 55.000 0.00 0.00 0.00 4.02
1765 1807 1.392510 GCCGTATCTGTTTGAACCGTC 59.607 52.381 0.00 0.00 0.00 4.79
1788 1830 1.737236 TGCTTTGGCGTGACATGTATC 59.263 47.619 0.00 0.00 42.25 2.24
1795 1837 2.418746 GGCGTGACATGTATCCTCAGTT 60.419 50.000 0.00 0.00 0.00 3.16
1814 1856 8.783093 CCTCAGTTAGTTGATGTGATTTTGTAA 58.217 33.333 0.00 0.00 0.00 2.41
1828 1870 6.968904 GTGATTTTGTAATGACAGTAGCATGG 59.031 38.462 0.00 0.00 36.76 3.66
1849 1891 6.798315 TGGATTTACCAAATTGCAATGTTG 57.202 33.333 13.82 17.35 46.75 3.33
1850 1892 5.704515 TGGATTTACCAAATTGCAATGTTGG 59.295 36.000 30.82 30.82 46.75 3.77
1851 1893 5.936956 GGATTTACCAAATTGCAATGTTGGA 59.063 36.000 34.90 23.78 43.82 3.53
1859 1901 0.825410 TGCAATGTTGGATGCCCATC 59.175 50.000 0.00 0.00 43.12 3.51
1869 1911 1.040646 GATGCCCATCTGGTCTCGTA 58.959 55.000 1.11 0.00 35.04 3.43
1872 1914 2.239400 TGCCCATCTGGTCTCGTATAG 58.761 52.381 0.00 0.00 36.04 1.31
1924 1969 5.350091 GGTTAACTGAGCTCTGAAATGTCTC 59.650 44.000 25.49 8.03 0.00 3.36
1929 1974 3.575687 TGAGCTCTGAAATGTCTCACTCA 59.424 43.478 16.19 0.00 0.00 3.41
1945 1991 6.150140 GTCTCACTCAGAATTTATGCCTGTTT 59.850 38.462 0.00 0.00 30.72 2.83
1946 1992 6.149973 TCTCACTCAGAATTTATGCCTGTTTG 59.850 38.462 0.00 0.00 0.00 2.93
1954 2000 2.414058 TATGCCTGTTTGCAAACACG 57.586 45.000 35.10 30.65 45.84 4.49
1971 2017 6.090898 GCAAACACGAACTGTCTAAGTCATAT 59.909 38.462 0.00 0.00 38.56 1.78
1975 2021 9.871238 AACACGAACTGTCTAAGTCATATATTT 57.129 29.630 0.00 0.00 38.56 1.40
2019 2078 4.870021 ATATGCTTTCTGTTCCCCTTCT 57.130 40.909 0.00 0.00 0.00 2.85
2022 2081 3.955471 TGCTTTCTGTTCCCCTTCTATG 58.045 45.455 0.00 0.00 0.00 2.23
2028 2087 3.907474 TCTGTTCCCCTTCTATGTTCACA 59.093 43.478 0.00 0.00 0.00 3.58
2359 2419 4.694509 ACTTGCACAGCTTCTCTTGATAAG 59.305 41.667 0.00 0.00 0.00 1.73
2508 2568 7.039504 CCTTCTGGTTGCCTTATATAATGCATT 60.040 37.037 21.36 17.56 36.85 3.56
2539 2599 3.202906 TGTGTGGTTAGTGTTTCTGCTC 58.797 45.455 0.00 0.00 0.00 4.26
2653 2714 6.569179 ATGTATTGTGAACTTGTGGTAACC 57.431 37.500 0.00 0.00 0.00 2.85
2761 2822 7.855904 GCATATTGCTTGCGTAACTATTTACTT 59.144 33.333 2.01 0.00 40.96 2.24
2814 2875 7.117667 GTGACAAACCAAATATTTGATTCCACC 59.882 37.037 26.32 11.73 40.55 4.61
2860 2921 4.018050 AGGTTCTTGATATTTGTGGCTCCT 60.018 41.667 0.00 0.00 0.00 3.69
2861 2922 5.191722 AGGTTCTTGATATTTGTGGCTCCTA 59.808 40.000 0.00 0.00 0.00 2.94
2862 2923 5.885912 GGTTCTTGATATTTGTGGCTCCTAA 59.114 40.000 0.00 0.00 0.00 2.69
2908 2972 8.836413 CAGGCTCGAAAATAATTTTCCTACATA 58.164 33.333 0.00 0.00 44.73 2.29
2959 3023 4.635473 TCACCCTCCCTCTCATTAATCTT 58.365 43.478 0.00 0.00 0.00 2.40
2965 3029 3.457380 TCCCTCTCATTAATCTTGCAGCT 59.543 43.478 0.00 0.00 0.00 4.24
2966 3030 3.564644 CCCTCTCATTAATCTTGCAGCTG 59.435 47.826 10.11 10.11 0.00 4.24
2967 3031 4.197750 CCTCTCATTAATCTTGCAGCTGT 58.802 43.478 16.64 0.00 0.00 4.40
2968 3032 4.639310 CCTCTCATTAATCTTGCAGCTGTT 59.361 41.667 16.64 3.51 0.00 3.16
2995 3059 2.262572 ACAATCGATTTTTCTGCGGC 57.737 45.000 8.21 0.00 0.00 6.53
3091 3178 2.413796 TCAACTGTTGTGTCACGTGTTC 59.586 45.455 19.12 10.68 0.00 3.18
3237 3325 4.871822 AGCCTAATTCCCAAGTAGCATTT 58.128 39.130 0.00 0.00 0.00 2.32
3280 3368 9.581289 AGTTAGACATACTTATCTATGTGAGCT 57.419 33.333 0.00 0.00 37.45 4.09
3283 3371 8.926092 AGACATACTTATCTATGTGAGCTACA 57.074 34.615 0.00 0.00 44.87 2.74
3284 3372 9.008965 AGACATACTTATCTATGTGAGCTACAG 57.991 37.037 0.00 0.00 43.80 2.74
3585 3675 9.975218 AGAGGATAAAATTGCTAAAGGTAAGAA 57.025 29.630 0.00 0.00 0.00 2.52
3662 3766 6.043243 TGTTCCTCAATCCTCAGTAGAAAACT 59.957 38.462 0.00 0.00 39.81 2.66
3663 3767 7.234782 TGTTCCTCAATCCTCAGTAGAAAACTA 59.765 37.037 0.00 0.00 35.76 2.24
3664 3768 7.171630 TCCTCAATCCTCAGTAGAAAACTAC 57.828 40.000 0.00 0.00 35.76 2.73
3665 3769 6.954684 TCCTCAATCCTCAGTAGAAAACTACT 59.045 38.462 0.00 0.00 40.45 2.57
3666 3770 7.122948 TCCTCAATCCTCAGTAGAAAACTACTC 59.877 40.741 6.90 0.00 38.01 2.59
3667 3771 7.171630 TCAATCCTCAGTAGAAAACTACTCC 57.828 40.000 6.90 0.00 38.01 3.85
3668 3772 6.154706 TCAATCCTCAGTAGAAAACTACTCCC 59.845 42.308 6.90 0.00 38.01 4.30
3669 3773 5.272405 TCCTCAGTAGAAAACTACTCCCT 57.728 43.478 6.90 0.00 38.01 4.20
3670 3774 5.262804 TCCTCAGTAGAAAACTACTCCCTC 58.737 45.833 6.90 0.00 38.01 4.30
3671 3775 4.403113 CCTCAGTAGAAAACTACTCCCTCC 59.597 50.000 6.90 0.00 38.01 4.30
3672 3776 4.015084 TCAGTAGAAAACTACTCCCTCCG 58.985 47.826 6.90 0.00 38.01 4.63
3673 3777 3.762823 CAGTAGAAAACTACTCCCTCCGT 59.237 47.826 6.90 0.00 38.01 4.69
3674 3778 4.015764 AGTAGAAAACTACTCCCTCCGTC 58.984 47.826 0.00 0.00 35.43 4.79
3675 3779 2.177734 AGAAAACTACTCCCTCCGTCC 58.822 52.381 0.00 0.00 0.00 4.79
3676 3780 1.206610 GAAAACTACTCCCTCCGTCCC 59.793 57.143 0.00 0.00 0.00 4.46
3677 3781 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
3678 3782 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3679 3783 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3680 3784 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3681 3785 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3682 3786 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3683 3787 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3684 3788 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3685 3789 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3686 3790 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3687 3791 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3688 3792 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3689 3793 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
3690 3794 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
3691 3795 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
3692 3796 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
3693 3797 4.625742 CCGTCCCATAATATAAGAGCGTTG 59.374 45.833 0.00 0.00 0.00 4.10
3694 3798 5.466819 CGTCCCATAATATAAGAGCGTTGA 58.533 41.667 0.00 0.00 0.00 3.18
3695 3799 5.573282 CGTCCCATAATATAAGAGCGTTGAG 59.427 44.000 0.00 0.00 0.00 3.02
3705 3809 2.093983 GCGTTGAGCGTTGTAGCG 59.906 61.111 0.00 0.00 43.66 4.26
3706 3810 2.654912 GCGTTGAGCGTTGTAGCGT 61.655 57.895 0.00 0.00 43.66 5.07
3707 3811 1.339235 GCGTTGAGCGTTGTAGCGTA 61.339 55.000 0.00 0.00 43.66 4.42
3708 3812 1.054574 CGTTGAGCGTTGTAGCGTAA 58.945 50.000 0.00 0.00 43.00 3.18
3709 3813 1.452773 CGTTGAGCGTTGTAGCGTAAA 59.547 47.619 0.00 0.00 43.00 2.01
3710 3814 2.097299 CGTTGAGCGTTGTAGCGTAAAA 60.097 45.455 0.00 0.00 43.00 1.52
3711 3815 3.602038 CGTTGAGCGTTGTAGCGTAAAAA 60.602 43.478 0.00 0.00 43.00 1.94
3733 3837 8.446599 AAAAACACTCTTATATTATGGGACGG 57.553 34.615 0.00 0.00 0.00 4.79
3734 3838 6.989155 AACACTCTTATATTATGGGACGGA 57.011 37.500 0.00 0.00 0.00 4.69
3735 3839 6.591750 ACACTCTTATATTATGGGACGGAG 57.408 41.667 0.00 0.00 0.00 4.63
3736 3840 5.480772 ACACTCTTATATTATGGGACGGAGG 59.519 44.000 0.00 0.00 0.00 4.30
3737 3841 5.024118 ACTCTTATATTATGGGACGGAGGG 58.976 45.833 0.00 0.00 0.00 4.30
3738 3842 5.222484 ACTCTTATATTATGGGACGGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
3739 3843 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4143 4312 6.473455 GCTGAATACACCAATAAATGAACTGC 59.527 38.462 0.00 0.00 0.00 4.40
4146 4315 6.849085 ATACACCAATAAATGAACTGCCAA 57.151 33.333 0.00 0.00 0.00 4.52
4165 4334 4.220602 GCCAAGGGTCTTATTTCACAACAT 59.779 41.667 0.00 0.00 0.00 2.71
4187 4357 7.095910 ACATCAACACTTCACTCTCTAGATTG 58.904 38.462 0.00 0.00 0.00 2.67
4188 4358 6.656632 TCAACACTTCACTCTCTAGATTGT 57.343 37.500 0.00 0.00 0.00 2.71
4189 4359 7.761038 TCAACACTTCACTCTCTAGATTGTA 57.239 36.000 0.00 0.00 0.00 2.41
4190 4360 7.594714 TCAACACTTCACTCTCTAGATTGTAC 58.405 38.462 0.00 0.00 0.00 2.90
4191 4361 7.448777 TCAACACTTCACTCTCTAGATTGTACT 59.551 37.037 0.00 0.00 0.00 2.73
4192 4362 7.768807 ACACTTCACTCTCTAGATTGTACTT 57.231 36.000 0.00 0.00 0.00 2.24
4208 4378 4.684877 TGTACTTGTACACACGACAATGT 58.315 39.130 9.28 0.00 36.27 2.71
4218 4388 2.866156 ACACGACAATGTCACTCTGTTG 59.134 45.455 14.24 0.00 32.09 3.33
4247 4455 6.453396 CGAACGGTCTAAGTAGCAAACAATAC 60.453 42.308 0.00 0.00 0.00 1.89
4249 4457 4.259690 CGGTCTAAGTAGCAAACAATACGC 60.260 45.833 0.00 0.00 0.00 4.42
4284 4492 2.242926 CTCCGAGCTTGGATGATCCTA 58.757 52.381 23.49 4.03 37.46 2.94
4411 4619 7.020827 TGTATTCCTCCTTGACTTTCTTCAT 57.979 36.000 0.00 0.00 0.00 2.57
4451 4659 1.439644 GATCGCTCTGGTCAGGGAC 59.560 63.158 1.43 0.00 38.11 4.46
4574 4786 6.228258 ACTTTTGAGTATTACCTCTGCGAAA 58.772 36.000 0.00 0.00 32.50 3.46
4583 4795 0.649475 CCTCTGCGAAATGCTTCTCG 59.351 55.000 0.00 0.00 46.63 4.04
4622 4834 2.574212 GCGGTTTTCAGCATCGCG 60.574 61.111 0.00 0.00 40.56 5.87
4682 4894 2.483583 TTGCGGCGCATAAAAATAGG 57.516 45.000 36.69 0.00 38.76 2.57
4687 4899 3.606153 GCGGCGCATAAAAATAGGTACTG 60.606 47.826 29.21 0.00 41.52 2.74
4692 4904 6.259387 GGCGCATAAAAATAGGTACTGTAGTT 59.741 38.462 10.83 0.00 41.52 2.24
4693 4905 7.342942 GCGCATAAAAATAGGTACTGTAGTTC 58.657 38.462 0.30 0.00 41.52 3.01
4694 4906 7.010738 GCGCATAAAAATAGGTACTGTAGTTCA 59.989 37.037 0.30 0.00 41.52 3.18
4710 4923 7.094377 ACTGTAGTTCATTTTTGTGTGTTCAGT 60.094 33.333 0.00 0.00 0.00 3.41
4712 4925 7.753132 TGTAGTTCATTTTTGTGTGTTCAGTTC 59.247 33.333 0.00 0.00 0.00 3.01
4743 4956 2.223386 TGTAGAAAAATAATGGCGCCGC 60.223 45.455 23.90 0.00 0.00 6.53
4838 5051 1.953231 CTCCTGGAGCTGACGATGCA 61.953 60.000 11.42 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.981859 TGGCGAGAAATCCTAACCTC 57.018 50.000 0.00 0.00 0.00 3.85
11 12 1.089920 AGCACACATGGCGAGAAATC 58.910 50.000 0.00 0.00 36.08 2.17
12 13 2.283298 CTAGCACACATGGCGAGAAAT 58.717 47.619 0.00 0.00 36.27 2.17
42 43 4.094294 CGGTCTGAAGTGTCTGAAACAAAA 59.906 41.667 0.02 0.00 40.31 2.44
44 45 3.118920 TCGGTCTGAAGTGTCTGAAACAA 60.119 43.478 0.02 0.00 40.31 2.83
48 49 3.320826 TGAATCGGTCTGAAGTGTCTGAA 59.679 43.478 0.00 0.00 33.95 3.02
63 64 3.559655 TCGCTATTGAACCATTGAATCGG 59.440 43.478 0.00 0.00 0.00 4.18
66 67 4.188462 TCGTCGCTATTGAACCATTGAAT 58.812 39.130 0.00 0.00 0.00 2.57
81 82 4.135153 AGAGCCGCAATCGTCGCT 62.135 61.111 0.00 0.00 36.25 4.93
89 90 1.596934 CTAAGGACCAGAGCCGCAA 59.403 57.895 0.00 0.00 0.00 4.85
92 93 2.022240 GCTCCTAAGGACCAGAGCCG 62.022 65.000 12.42 0.00 44.76 5.52
96 105 1.833630 CACATGCTCCTAAGGACCAGA 59.166 52.381 0.00 0.00 0.00 3.86
132 141 6.546484 CCATTTTGACCCTATCCATGATAGT 58.454 40.000 9.57 0.00 40.05 2.12
140 149 2.587522 GGAGCCATTTTGACCCTATCC 58.412 52.381 0.00 0.00 0.00 2.59
143 152 0.254747 CGGGAGCCATTTTGACCCTA 59.745 55.000 0.00 0.00 38.51 3.53
145 154 0.034863 TACGGGAGCCATTTTGACCC 60.035 55.000 0.00 0.00 37.42 4.46
161 170 0.790207 ACTGTTGTTGCATCGCTACG 59.210 50.000 0.00 0.00 37.12 3.51
166 175 1.440850 CGCCACTGTTGTTGCATCG 60.441 57.895 0.00 0.00 34.89 3.84
168 177 2.336088 GCGCCACTGTTGTTGCAT 59.664 55.556 0.00 0.00 34.89 3.96
169 178 4.249020 CGCGCCACTGTTGTTGCA 62.249 61.111 0.00 0.00 34.89 4.08
175 184 4.908687 TGCTGACGCGCCACTGTT 62.909 61.111 5.73 0.00 39.65 3.16
199 208 0.874390 CAACCACCATTGTCGTCAGG 59.126 55.000 0.00 0.00 0.00 3.86
206 215 1.791103 CGCCGAACAACCACCATTGT 61.791 55.000 0.00 0.00 44.76 2.71
211 220 3.656045 CACCGCCGAACAACCACC 61.656 66.667 0.00 0.00 0.00 4.61
217 226 4.063967 ATCGAGCACCGCCGAACA 62.064 61.111 0.00 0.00 35.66 3.18
249 258 4.546829 AGAAATGCAGTGCAATCCAAAT 57.453 36.364 23.90 0.00 43.62 2.32
260 269 8.644374 TTATAAAGGTTGGTAAGAAATGCAGT 57.356 30.769 0.00 0.00 0.00 4.40
286 295 9.739276 AAATGTTTTTCTATGGACACAGATCTA 57.261 29.630 0.00 0.00 0.00 1.98
398 415 3.254903 GGTCCCACGTTTTAAGCAAATCT 59.745 43.478 0.00 0.00 0.00 2.40
402 419 1.320507 GGGTCCCACGTTTTAAGCAA 58.679 50.000 1.78 0.00 0.00 3.91
432 449 2.355837 GCCACGACTTGTCTCGCA 60.356 61.111 0.00 0.00 37.15 5.10
439 456 2.317609 CCAACGAGGCCACGACTTG 61.318 63.158 29.67 21.70 37.03 3.16
455 472 1.067915 GGATTTGCGTTTGCTTAGCCA 60.068 47.619 0.29 0.00 43.34 4.75
517 534 6.593770 GGAGAGAAAGAGAAAGAGAATCCAAC 59.406 42.308 0.00 0.00 33.66 3.77
518 535 6.500049 AGGAGAGAAAGAGAAAGAGAATCCAA 59.500 38.462 0.00 0.00 33.66 3.53
520 537 6.381133 AGAGGAGAGAAAGAGAAAGAGAATCC 59.619 42.308 0.00 0.00 33.66 3.01
521 538 7.410120 AGAGGAGAGAAAGAGAAAGAGAATC 57.590 40.000 0.00 0.00 0.00 2.52
522 539 6.381133 GGAGAGGAGAGAAAGAGAAAGAGAAT 59.619 42.308 0.00 0.00 0.00 2.40
523 540 5.714806 GGAGAGGAGAGAAAGAGAAAGAGAA 59.285 44.000 0.00 0.00 0.00 2.87
524 541 5.015178 AGGAGAGGAGAGAAAGAGAAAGAGA 59.985 44.000 0.00 0.00 0.00 3.10
525 542 5.126061 CAGGAGAGGAGAGAAAGAGAAAGAG 59.874 48.000 0.00 0.00 0.00 2.85
526 543 5.016173 CAGGAGAGGAGAGAAAGAGAAAGA 58.984 45.833 0.00 0.00 0.00 2.52
527 544 4.160252 CCAGGAGAGGAGAGAAAGAGAAAG 59.840 50.000 0.00 0.00 0.00 2.62
528 545 4.093011 CCAGGAGAGGAGAGAAAGAGAAA 58.907 47.826 0.00 0.00 0.00 2.52
529 546 3.707316 CCAGGAGAGGAGAGAAAGAGAA 58.293 50.000 0.00 0.00 0.00 2.87
530 547 2.622977 GCCAGGAGAGGAGAGAAAGAGA 60.623 54.545 0.00 0.00 0.00 3.10
531 548 1.756538 GCCAGGAGAGGAGAGAAAGAG 59.243 57.143 0.00 0.00 0.00 2.85
535 552 1.002274 GGGCCAGGAGAGGAGAGAA 59.998 63.158 4.39 0.00 0.00 2.87
537 554 0.189574 TATGGGCCAGGAGAGGAGAG 59.810 60.000 13.78 0.00 0.00 3.20
1181 1209 4.495844 GCGTGCATCCTAGAACCAATTAAC 60.496 45.833 0.00 0.00 0.00 2.01
1182 1210 3.625764 GCGTGCATCCTAGAACCAATTAA 59.374 43.478 0.00 0.00 0.00 1.40
1337 1365 5.565259 GCATCATCAACTAACTGAACAAACG 59.435 40.000 0.00 0.00 0.00 3.60
1398 1431 3.815401 GGAATCCAAGTATCCAACATCCG 59.185 47.826 0.00 0.00 33.30 4.18
1414 1447 5.946377 ACTACAAGAGACAAAATGGGAATCC 59.054 40.000 0.00 0.00 0.00 3.01
1440 1473 3.213206 AGCAAAATCCATAGCATCCGA 57.787 42.857 0.00 0.00 0.00 4.55
1443 1476 7.031226 TGACTTTAGCAAAATCCATAGCATC 57.969 36.000 0.00 0.00 0.00 3.91
1458 1492 8.596380 GTGAGTTAACTATGTGATGACTTTAGC 58.404 37.037 8.42 0.00 0.00 3.09
1476 1510 6.183360 CGAGTGGACATCTCATAGTGAGTTAA 60.183 42.308 6.83 0.00 44.58 2.01
1490 1524 1.275291 TCCAAGTTCCGAGTGGACATC 59.725 52.381 0.00 0.00 46.45 3.06
1510 1544 7.064609 CAGATAACAGTAACCGAATGAACATGT 59.935 37.037 0.00 0.00 0.00 3.21
1521 1555 8.804743 CACTACATAAACAGATAACAGTAACCG 58.195 37.037 0.00 0.00 0.00 4.44
1567 1601 8.867112 AAGCAACAGCAAAGAATATATGATTG 57.133 30.769 0.00 0.00 0.00 2.67
1569 1603 9.309516 CAAAAGCAACAGCAAAGAATATATGAT 57.690 29.630 0.00 0.00 0.00 2.45
1574 1608 6.985645 TGAACAAAAGCAACAGCAAAGAATAT 59.014 30.769 0.00 0.00 0.00 1.28
1582 1616 4.916983 ATACTGAACAAAAGCAACAGCA 57.083 36.364 0.00 0.00 32.67 4.41
1723 1765 1.423794 ATCTCCCACCACCAACGGTT 61.424 55.000 0.00 0.00 37.07 4.44
1746 1788 1.652124 CGACGGTTCAAACAGATACGG 59.348 52.381 0.00 0.00 32.21 4.02
1747 1789 1.652124 CCGACGGTTCAAACAGATACG 59.348 52.381 5.48 0.00 33.58 3.06
1748 1790 2.410730 CACCGACGGTTCAAACAGATAC 59.589 50.000 19.02 0.00 31.02 2.24
1750 1792 1.508632 CACCGACGGTTCAAACAGAT 58.491 50.000 19.02 0.00 31.02 2.90
1765 1807 2.616330 ATGTCACGCCAAAGCACCG 61.616 57.895 0.00 0.00 39.83 4.94
1777 1819 6.631016 TCAACTAACTGAGGATACATGTCAC 58.369 40.000 0.00 0.00 41.41 3.67
1788 1830 7.206981 ACAAAATCACATCAACTAACTGAGG 57.793 36.000 0.00 0.00 33.38 3.86
1795 1837 9.283768 ACTGTCATTACAAAATCACATCAACTA 57.716 29.630 0.00 0.00 34.49 2.24
1814 1856 5.372343 TGGTAAATCCATGCTACTGTCAT 57.628 39.130 0.00 0.00 41.93 3.06
1820 1862 5.659463 TGCAATTTGGTAAATCCATGCTAC 58.341 37.500 10.74 0.00 45.06 3.58
1828 1870 7.465989 CATCCAACATTGCAATTTGGTAAATC 58.534 34.615 30.84 0.00 40.68 2.17
1840 1882 4.535287 TGGGCATCCAACATTGCA 57.465 50.000 0.00 0.00 40.73 4.08
1859 1901 6.621316 AAGACATGTACTATACGAGACCAG 57.379 41.667 0.00 0.00 0.00 4.00
1892 1934 6.577103 TCAGAGCTCAGTTAACCATCTAATG 58.423 40.000 17.77 0.00 0.00 1.90
1893 1935 6.798427 TCAGAGCTCAGTTAACCATCTAAT 57.202 37.500 17.77 0.00 0.00 1.73
1894 1936 6.605471 TTCAGAGCTCAGTTAACCATCTAA 57.395 37.500 17.77 0.00 0.00 2.10
1908 1953 4.082300 TCTGAGTGAGACATTTCAGAGCTC 60.082 45.833 5.27 5.27 40.65 4.09
1924 1969 4.860907 GCAAACAGGCATAAATTCTGAGTG 59.139 41.667 0.00 0.00 33.19 3.51
1929 1974 5.609423 TGTTTGCAAACAGGCATAAATTCT 58.391 33.333 35.10 0.00 43.45 2.40
1945 1991 3.527533 ACTTAGACAGTTCGTGTTTGCA 58.472 40.909 0.00 0.00 40.56 4.08
1946 1992 3.554324 TGACTTAGACAGTTCGTGTTTGC 59.446 43.478 0.00 0.00 40.56 3.68
2046 2105 5.363101 TCTGCTTGCTCATCGAAGATATTT 58.637 37.500 0.00 0.00 45.12 1.40
2254 2314 9.528489 AATAGGTTGCAAGGAGTAAATTTTCTA 57.472 29.630 0.00 0.00 0.00 2.10
2359 2419 4.269523 TGCAGTGGGCTGGTGGTC 62.270 66.667 0.00 0.00 45.15 4.02
2508 2568 5.680619 ACACTAACCACACATCAAGAAAGA 58.319 37.500 0.00 0.00 0.00 2.52
2539 2599 9.341899 CAGTGAAATATTTCTTTCCCTTTTACG 57.658 33.333 24.77 7.28 38.02 3.18
2626 2687 4.700213 ACCACAAGTTCACAATACATAGCC 59.300 41.667 0.00 0.00 0.00 3.93
2630 2691 5.475564 GGGTTACCACAAGTTCACAATACAT 59.524 40.000 2.98 0.00 36.50 2.29
2653 2714 7.537715 TGTTACACAAGCAAATAAGATGATGG 58.462 34.615 0.00 0.00 0.00 3.51
2690 2751 4.402155 CCCAGCAAACCAGCATAGAAATAA 59.598 41.667 0.00 0.00 36.85 1.40
2761 2822 3.070878 TCATCCAGCACAGAAACAGTACA 59.929 43.478 0.00 0.00 0.00 2.90
2814 2875 6.475402 CCTTTACTTTAGTTGCACAAACCTTG 59.525 38.462 0.00 0.00 39.85 3.61
2908 2972 2.684881 GACGATTTCTTGGATGGTGCAT 59.315 45.455 0.00 0.00 0.00 3.96
2968 3032 7.344441 CGCAGAAAAATCGATTGTATATCACA 58.656 34.615 12.25 0.00 34.51 3.58
2995 3059 7.387122 CCACATATCAATTGTCTATCAGTCCTG 59.613 40.741 5.13 0.00 0.00 3.86
3065 3130 3.063452 ACGTGACACAACAGTTGAATGAC 59.937 43.478 20.56 9.44 0.00 3.06
3152 3239 1.875963 GCAACAAGCATAGCCACGT 59.124 52.632 0.00 0.00 44.79 4.49
3237 3325 2.264005 ACTAACATGTCCGGCACAAA 57.736 45.000 0.00 0.00 38.97 2.83
3278 3366 7.820872 TCCCAAGTTTAAAGTGTATACTGTAGC 59.179 37.037 4.17 0.00 37.19 3.58
3281 3369 9.662947 GTATCCCAAGTTTAAAGTGTATACTGT 57.337 33.333 4.17 0.00 37.19 3.55
3282 3370 9.661563 TGTATCCCAAGTTTAAAGTGTATACTG 57.338 33.333 4.17 0.00 37.19 2.74
3430 3519 4.981674 ACGGTTGAAAAACATATGCACTTG 59.018 37.500 1.58 0.00 27.66 3.16
3500 3590 4.105697 TGGTTGAATCTACAAGAAAGGGGT 59.894 41.667 0.00 0.00 0.00 4.95
3592 3696 6.542370 CCAATGGATCGTAGAAAAGTATGGTT 59.458 38.462 0.00 0.00 43.58 3.67
3635 3739 7.733773 TTTCTACTGAGGATTGAGGAACATA 57.266 36.000 0.00 0.00 0.00 2.29
3662 3766 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3663 3767 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3664 3768 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3665 3769 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
3666 3770 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
3667 3771 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
3668 3772 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
3669 3773 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
3670 3774 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
3671 3775 5.466819 TCAACGCTCTTATATTATGGGACG 58.533 41.667 0.00 0.00 0.00 4.79
3672 3776 5.348997 GCTCAACGCTCTTATATTATGGGAC 59.651 44.000 0.00 0.00 35.14 4.46
3673 3777 5.479306 GCTCAACGCTCTTATATTATGGGA 58.521 41.667 0.00 0.00 35.14 4.37
3674 3778 4.327357 CGCTCAACGCTCTTATATTATGGG 59.673 45.833 0.00 0.00 36.13 4.00
3675 3779 5.441700 CGCTCAACGCTCTTATATTATGG 57.558 43.478 0.00 0.00 36.13 2.74
3690 3794 3.508648 TTTTACGCTACAACGCTCAAC 57.491 42.857 0.00 0.00 36.19 3.18
3708 3812 8.269317 TCCGTCCCATAATATAAGAGTGTTTTT 58.731 33.333 0.00 0.00 0.00 1.94
3709 3813 7.798071 TCCGTCCCATAATATAAGAGTGTTTT 58.202 34.615 0.00 0.00 0.00 2.43
3710 3814 7.369551 TCCGTCCCATAATATAAGAGTGTTT 57.630 36.000 0.00 0.00 0.00 2.83
3711 3815 6.014499 CCTCCGTCCCATAATATAAGAGTGTT 60.014 42.308 0.00 0.00 0.00 3.32
3712 3816 5.480772 CCTCCGTCCCATAATATAAGAGTGT 59.519 44.000 0.00 0.00 0.00 3.55
3713 3817 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
3714 3818 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
3715 3819 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3716 3820 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3717 3821 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3718 3822 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3719 3823 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3720 3824 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3721 3825 4.202749 ACATACTCCCTCCGTCCCATAATA 60.203 45.833 0.00 0.00 0.00 0.98
3722 3826 3.173965 CATACTCCCTCCGTCCCATAAT 58.826 50.000 0.00 0.00 0.00 1.28
3723 3827 2.090943 ACATACTCCCTCCGTCCCATAA 60.091 50.000 0.00 0.00 0.00 1.90
3724 3828 1.502039 ACATACTCCCTCCGTCCCATA 59.498 52.381 0.00 0.00 0.00 2.74
3725 3829 0.264955 ACATACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
3726 3830 0.686441 CACATACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
3727 3831 0.396695 TCACATACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
3728 3832 1.705873 ATCACATACTCCCTCCGTCC 58.294 55.000 0.00 0.00 0.00 4.79
3729 3833 5.470047 AATTATCACATACTCCCTCCGTC 57.530 43.478 0.00 0.00 0.00 4.79
3730 3834 5.888982 AAATTATCACATACTCCCTCCGT 57.111 39.130 0.00 0.00 0.00 4.69
3731 3835 8.314751 AGATAAAATTATCACATACTCCCTCCG 58.685 37.037 13.94 0.00 41.52 4.63
3732 3836 9.442047 CAGATAAAATTATCACATACTCCCTCC 57.558 37.037 13.94 0.00 41.52 4.30
4080 4246 4.250464 TGGTACTTCCATCACGATTTGAC 58.750 43.478 0.00 0.00 41.93 3.18
4143 4312 5.476599 TGATGTTGTGAAATAAGACCCTTGG 59.523 40.000 0.00 0.00 0.00 3.61
4146 4315 6.016276 GTGTTGATGTTGTGAAATAAGACCCT 60.016 38.462 0.00 0.00 0.00 4.34
4165 4334 6.656632 ACAATCTAGAGAGTGAAGTGTTGA 57.343 37.500 13.53 0.00 42.16 3.18
4187 4357 4.741185 TGACATTGTCGTGTGTACAAGTAC 59.259 41.667 11.97 3.47 40.00 2.73
4188 4358 4.741185 GTGACATTGTCGTGTGTACAAGTA 59.259 41.667 11.97 0.00 40.00 2.24
4189 4359 3.554324 GTGACATTGTCGTGTGTACAAGT 59.446 43.478 11.97 0.00 40.00 3.16
4190 4360 3.802139 AGTGACATTGTCGTGTGTACAAG 59.198 43.478 11.97 0.00 40.00 3.16
4191 4361 3.787785 AGTGACATTGTCGTGTGTACAA 58.212 40.909 11.97 0.00 40.85 2.41
4192 4362 3.067601 AGAGTGACATTGTCGTGTGTACA 59.932 43.478 11.97 0.00 34.95 2.90
4208 4378 1.067846 CCGTTCGATCCAACAGAGTGA 60.068 52.381 4.06 0.00 0.00 3.41
4218 4388 2.357009 TGCTACTTAGACCGTTCGATCC 59.643 50.000 0.00 0.00 0.00 3.36
4247 4455 0.379669 GAGGATGCAGTTCAATGGCG 59.620 55.000 0.00 0.00 0.00 5.69
4249 4457 1.019673 CGGAGGATGCAGTTCAATGG 58.980 55.000 0.00 0.00 0.00 3.16
4355 4563 1.372623 GACGACGGTGACCAAGGAC 60.373 63.158 1.11 0.00 0.00 3.85
4574 4786 1.227380 GACATCGCCCGAGAAGCAT 60.227 57.895 0.00 0.00 0.00 3.79
4583 4795 4.408821 TGGTGCCTGACATCGCCC 62.409 66.667 5.35 1.86 28.88 6.13
4607 4819 1.019278 TCTCCGCGATGCTGAAAACC 61.019 55.000 8.23 0.00 0.00 3.27
4622 4834 0.737715 ATCGCAACGACAAGCTCTCC 60.738 55.000 0.00 0.00 39.18 3.71
4682 4894 8.178964 TGAACACACAAAAATGAACTACAGTAC 58.821 33.333 0.00 0.00 0.00 2.73
4687 4899 7.968405 AGAACTGAACACACAAAAATGAACTAC 59.032 33.333 0.00 0.00 0.00 2.73
4692 4904 8.600449 AAAAAGAACTGAACACACAAAAATGA 57.400 26.923 0.00 0.00 0.00 2.57
4743 4956 3.487711 CCATCGACGAGGTCTACTTTCTG 60.488 52.174 8.86 0.00 0.00 3.02
4779 4992 0.792640 CGTTCCAGCACTACAAGCAG 59.207 55.000 0.00 0.00 0.00 4.24
4780 4993 0.105964 ACGTTCCAGCACTACAAGCA 59.894 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.