Multiple sequence alignment - TraesCS5A01G099300

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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 TraesCS5A01G099300 chr5A 100.000 6231 0 0 1547 7777 141888808 141882578 0.000000e+00 11507.0
1 TraesCS5A01G099300 chr5A 100.000 1144 0 0 1 1144 141890354 141889211 0.000000e+00 2113.0
2 TraesCS5A01G099300 chr5A 77.540 187 37 5 5061 5246 327732371 327732189 2.970000e-19 108.0
3 TraesCS5A01G099300 chr5B 93.523 3227 127 37 1547 4743 139357141 139353967 0.000000e+00 4726.0
4 TraesCS5A01G099300 chr5B 87.005 1539 121 35 6098 7601 139353844 139352350 0.000000e+00 1661.0
5 TraesCS5A01G099300 chr5B 85.290 775 92 17 1 756 139358408 139357637 0.000000e+00 780.0
6 TraesCS5A01G099300 chr5B 94.054 370 18 1 775 1144 139357552 139357187 6.820000e-155 558.0
7 TraesCS5A01G099300 chr5B 88.995 209 11 6 7581 7777 139351768 139351560 1.680000e-61 248.0
8 TraesCS5A01G099300 chr5B 79.205 327 49 14 4745 5062 685581263 685580947 7.910000e-50 209.0
9 TraesCS5A01G099300 chr5B 92.537 67 5 0 6034 6100 139353977 139353911 6.420000e-16 97.1
10 TraesCS5A01G099300 chr5B 94.595 37 2 0 4757 4793 437617970 437617934 3.030000e-04 58.4
11 TraesCS5A01G099300 chr5D 96.987 2655 49 11 1790 4434 126580229 126577596 0.000000e+00 4431.0
12 TraesCS5A01G099300 chr5D 95.506 1847 57 11 5935 7777 126575761 126573937 0.000000e+00 2928.0
13 TraesCS5A01G099300 chr5D 95.101 1490 58 4 4432 5908 126577482 126575995 0.000000e+00 2333.0
14 TraesCS5A01G099300 chr5D 85.386 609 75 9 1 599 126672711 126672107 3.080000e-173 619.0
15 TraesCS5A01G099300 chr5D 98.929 280 3 0 865 1144 126580749 126580470 1.160000e-137 501.0
16 TraesCS5A01G099300 chr5D 97.990 199 4 0 1547 1745 126580425 126580227 5.780000e-91 346.0
17 TraesCS5A01G099300 chr5D 82.597 385 49 12 420 789 80369546 80369927 2.710000e-84 324.0
18 TraesCS5A01G099300 chr5D 77.184 206 42 4 5057 5262 495223257 495223057 1.770000e-21 115.0
19 TraesCS5A01G099300 chr5D 82.667 75 9 4 125 197 16229545 16229473 6.510000e-06 63.9
20 TraesCS5A01G099300 chr7D 77.252 1099 169 43 4745 5774 89289187 89288101 3.150000e-158 569.0
21 TraesCS5A01G099300 chr7D 82.008 239 37 3 5061 5296 72952613 72952378 1.710000e-46 198.0
22 TraesCS5A01G099300 chr6A 80.564 638 84 23 4789 5393 346593794 346593164 9.200000e-124 455.0
23 TraesCS5A01G099300 chr6A 81.690 71 11 2 4959 5027 549642822 549642752 3.030000e-04 58.4
24 TraesCS5A01G099300 chr6D 80.935 535 63 26 4789 5290 249957836 249958364 3.400000e-103 387.0
25 TraesCS5A01G099300 chr1D 83.668 398 42 13 409 791 223723547 223723158 3.450000e-93 353.0
26 TraesCS5A01G099300 chr3D 83.377 385 46 12 420 788 582021340 582020958 2.690000e-89 340.0
27 TraesCS5A01G099300 chr3D 81.491 389 48 16 419 788 546621792 546622175 1.640000e-76 298.0
28 TraesCS5A01G099300 chr4A 83.871 372 42 14 420 776 26986181 26986549 9.670000e-89 339.0
29 TraesCS5A01G099300 chr4B 82.474 388 52 10 420 793 671670325 671670710 7.530000e-85 326.0
30 TraesCS5A01G099300 chr4B 72.575 536 100 33 4748 5245 665956115 665955589 1.760000e-26 132.0
31 TraesCS5A01G099300 chr4B 76.733 202 41 5 5061 5262 461183611 461183806 2.970000e-19 108.0
32 TraesCS5A01G099300 chr1B 82.412 398 47 13 409 791 323260139 323259750 7.530000e-85 326.0
33 TraesCS5A01G099300 chr1B 100.000 30 0 0 4757 4786 659136575 659136546 1.000000e-03 56.5
34 TraesCS5A01G099300 chr1A 82.005 389 41 17 415 788 68457199 68456825 3.530000e-78 303.0
35 TraesCS5A01G099300 chr1A 78.495 186 33 5 5073 5257 492055518 492055339 1.770000e-21 115.0
36 TraesCS5A01G099300 chr6B 84.500 200 26 5 4857 5053 337846331 337846528 7.960000e-45 193.0
37 TraesCS5A01G099300 chr2D 86.842 114 15 0 131 244 63929568 63929455 2.280000e-25 128.0
38 TraesCS5A01G099300 chr3A 91.111 45 3 1 4756 4799 566889233 566889189 8.430000e-05 60.2
39 TraesCS5A01G099300 chr7B 94.595 37 2 0 4757 4793 610204473 610204437 3.030000e-04 58.4
40 TraesCS5A01G099300 chr7A 89.362 47 4 1 4747 4793 579495270 579495225 3.030000e-04 58.4
41 TraesCS5A01G099300 chr2B 94.595 37 2 0 4757 4793 769011100 769011064 3.030000e-04 58.4


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 TraesCS5A01G099300 chr5A 141882578 141890354 7776 True 6810.000000 11507 100.0000 1 7777 2 chr5A.!!$R2 7776
1 TraesCS5A01G099300 chr5B 139351560 139358408 6848 True 1345.016667 4726 90.2340 1 7777 6 chr5B.!!$R3 7776
2 TraesCS5A01G099300 chr5D 126573937 126580749 6812 True 2107.800000 4431 96.9026 865 7777 5 chr5D.!!$R4 6912
3 TraesCS5A01G099300 chr5D 126672107 126672711 604 True 619.000000 619 85.3860 1 599 1 chr5D.!!$R2 598
4 TraesCS5A01G099300 chr7D 89288101 89289187 1086 True 569.000000 569 77.2520 4745 5774 1 chr7D.!!$R2 1029
5 TraesCS5A01G099300 chr6A 346593164 346593794 630 True 455.000000 455 80.5640 4789 5393 1 chr6A.!!$R1 604
6 TraesCS5A01G099300 chr6D 249957836 249958364 528 False 387.000000 387 80.9350 4789 5290 1 chr6D.!!$F1 501

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
765 785 0.100325 TGCAAAATATTCCGGCAGCG 59.900 50.000 0.00 0.00 0.00 5.18 F
766 786 0.380378 GCAAAATATTCCGGCAGCGA 59.620 50.000 0.00 0.00 0.00 4.93 F
1770 1897 0.033504 GTTGCTCGTCCTGGAAGTGA 59.966 55.000 14.46 5.34 0.00 3.41 F
2110 2238 0.251608 GGGGTGGGTTTATGCTGTGT 60.252 55.000 0.00 0.00 0.00 3.72 F
2113 2241 1.271926 GGTGGGTTTATGCTGTGTCCT 60.272 52.381 0.00 0.00 0.00 3.85 F
2187 2315 3.784701 TCCTCAGTCATTTAGAGCGTC 57.215 47.619 0.00 0.00 0.00 5.19 F
4079 4228 0.531974 TGCACACCCGTGAAGTCTTC 60.532 55.000 5.58 5.58 46.80 2.87 F
4940 5225 0.548510 GCCCCTAACAAGAGAGGCAT 59.451 55.000 0.00 0.00 40.20 4.40 F
5630 5994 0.179018 GTAGCCGATGCCAGGGAATT 60.179 55.000 0.00 0.00 38.69 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1878 0.033504 TCACTTCCAGGACGAGCAAC 59.966 55.000 0.00 0.0 0.0 4.17 R
2181 2309 0.318275 CAATAGGCTCTCGGACGCTC 60.318 60.000 0.00 0.0 0.0 5.03 R
3001 3130 5.631929 CGGTCATATAGTGCAGCGTTTATAA 59.368 40.000 0.00 0.0 0.0 0.98 R
3789 3926 2.945668 GAGACAAACACTGCTTGAAGGT 59.054 45.455 0.00 0.0 0.0 3.50 R
4079 4228 3.744942 GTGTGCTGCTGTATGGATATCAG 59.255 47.826 4.83 0.0 0.0 2.90 R
4240 4389 5.006386 GGTGAAGATGGTGATCAAGAAAGT 58.994 41.667 0.00 0.0 0.0 2.66 R
4955 5240 0.240945 GCTTTGGTGATGTTGGACGG 59.759 55.000 0.00 0.0 0.0 4.79 R
6191 6844 1.523758 GACTTGCGAACAGGGAACAT 58.476 50.000 0.00 0.0 0.0 2.71 R
7500 8184 2.167693 TGGTGAGCTATACCACTTTCCG 59.832 50.000 16.24 0.0 43.0 4.30 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 2.029828 AGTCCTACACAGAGTGCTTTCG 60.030 50.000 0.00 0.00 36.98 3.46
30 31 1.939934 CACAGAGTGCTTTCGTTCCAA 59.060 47.619 0.00 0.00 0.00 3.53
31 32 2.354510 CACAGAGTGCTTTCGTTCCAAA 59.645 45.455 0.00 0.00 0.00 3.28
43 44 8.573035 TGCTTTCGTTCCAAAAAGACTTATTAT 58.427 29.630 0.00 0.00 35.02 1.28
80 81 9.722056 CTAATTGCTTATGAAATCTTACACACC 57.278 33.333 0.00 0.00 0.00 4.16
111 117 0.698818 GAAGGTGGGAAGGATGGTGT 59.301 55.000 0.00 0.00 0.00 4.16
120 126 2.582052 GAAGGATGGTGTGTGGTGAAA 58.418 47.619 0.00 0.00 0.00 2.69
123 129 2.708861 AGGATGGTGTGTGGTGAAACTA 59.291 45.455 0.00 0.00 36.74 2.24
156 162 4.145052 AGGCATATGACATAGTCGAGTGA 58.855 43.478 12.11 0.00 34.95 3.41
197 203 3.749665 TTTGAAGCTGGGTTTTCATGG 57.250 42.857 0.00 0.00 33.68 3.66
201 207 1.212751 GCTGGGTTTTCATGGCGAC 59.787 57.895 0.00 0.00 0.00 5.19
205 211 0.893727 GGGTTTTCATGGCGACTGGT 60.894 55.000 0.00 0.00 0.00 4.00
211 217 2.198827 TCATGGCGACTGGTTTCATT 57.801 45.000 0.00 0.00 0.00 2.57
241 247 1.531149 CTTGTGTGTCATCGGTGGAAC 59.469 52.381 0.00 0.00 0.00 3.62
243 249 1.071542 TGTGTGTCATCGGTGGAACAT 59.928 47.619 7.47 0.00 44.52 2.71
246 252 3.749088 GTGTGTCATCGGTGGAACATAAA 59.251 43.478 7.47 0.00 44.52 1.40
249 255 4.000325 TGTCATCGGTGGAACATAAAGTG 59.000 43.478 0.00 0.00 44.52 3.16
284 290 5.063180 TCGAAAACTATCACGCCTTCTAA 57.937 39.130 0.00 0.00 0.00 2.10
287 293 6.424509 TCGAAAACTATCACGCCTTCTAAAAA 59.575 34.615 0.00 0.00 0.00 1.94
289 295 7.506328 AAAACTATCACGCCTTCTAAAAAGT 57.494 32.000 0.00 0.00 0.00 2.66
292 298 7.506328 ACTATCACGCCTTCTAAAAAGTTTT 57.494 32.000 0.00 0.00 0.00 2.43
297 303 7.932335 TCACGCCTTCTAAAAAGTTTTGATAA 58.068 30.769 0.61 0.00 0.00 1.75
322 328 9.717942 AAGGTGACTCTTTATAATCATATCTGC 57.282 33.333 0.00 0.00 42.68 4.26
352 358 5.790593 TGTGTATGGAAGGACTTACAACTC 58.209 41.667 0.37 3.74 36.91 3.01
405 411 5.587844 CCAATGGAGATGATCTCTTTTCGTT 59.412 40.000 20.73 9.60 42.95 3.85
424 430 6.887376 TCGTTGCAAGAACACTATATCTTC 57.113 37.500 0.00 0.00 33.73 2.87
473 482 8.796475 ACTATTTCTTTCAACATGCAAGTATGT 58.204 29.630 0.00 0.00 42.82 2.29
476 485 6.822667 TCTTTCAACATGCAAGTATGTCAT 57.177 33.333 4.29 0.00 40.24 3.06
512 521 2.037144 GCATGAGAAAATGCCCATCCT 58.963 47.619 0.00 0.00 45.93 3.24
532 541 7.233553 CCATCCTACTACCATATGTCTCTCAAA 59.766 40.741 1.24 0.00 0.00 2.69
550 559 6.339730 TCTCAAAATGCAAACATGTCACTTT 58.660 32.000 0.00 0.00 36.36 2.66
558 567 7.160547 TGCAAACATGTCACTTTATCATGAT 57.839 32.000 13.81 13.81 40.64 2.45
564 573 7.868775 ACATGTCACTTTATCATGATATGCAC 58.131 34.615 16.06 11.37 44.09 4.57
592 602 6.540438 AAAGATCCATCTCAATGTGCAAAT 57.460 33.333 0.00 0.00 35.76 2.32
761 781 8.755696 TGAAATATATTGCAAAATATTCCGGC 57.244 30.769 1.71 0.00 29.96 6.13
763 783 8.761575 AAATATATTGCAAAATATTCCGGCAG 57.238 30.769 1.71 0.00 35.68 4.85
764 784 2.292103 TTGCAAAATATTCCGGCAGC 57.708 45.000 0.00 0.00 35.68 5.25
765 785 0.100325 TGCAAAATATTCCGGCAGCG 59.900 50.000 0.00 0.00 0.00 5.18
766 786 0.380378 GCAAAATATTCCGGCAGCGA 59.620 50.000 0.00 0.00 0.00 4.93
767 787 1.859998 GCAAAATATTCCGGCAGCGAC 60.860 52.381 0.00 0.00 0.00 5.19
768 788 0.655733 AAAATATTCCGGCAGCGACG 59.344 50.000 0.00 0.00 0.00 5.12
769 789 0.461339 AAATATTCCGGCAGCGACGT 60.461 50.000 0.00 0.00 28.54 4.34
770 790 0.386476 AATATTCCGGCAGCGACGTA 59.614 50.000 0.00 0.00 28.54 3.57
780 866 1.451927 AGCGACGTACGGGGTATCA 60.452 57.895 21.06 0.00 42.83 2.15
782 868 0.874390 GCGACGTACGGGGTATCATA 59.126 55.000 21.06 0.00 42.83 2.15
795 881 5.621555 CGGGGTATCATATAGTTGAAGACGG 60.622 48.000 0.00 0.00 0.00 4.79
797 883 5.337330 GGGTATCATATAGTTGAAGACGGGG 60.337 48.000 0.00 0.00 0.00 5.73
802 888 2.221906 TAGTTGAAGACGGGGCTCGC 62.222 60.000 6.72 0.00 43.89 5.03
845 931 3.373226 TTCCAGGGAAGACGGACG 58.627 61.111 0.00 0.00 0.00 4.79
859 945 3.066621 AGACGGACGTGTAAACAGTAACA 59.933 43.478 0.53 0.00 0.00 2.41
860 946 3.981211 ACGGACGTGTAAACAGTAACAT 58.019 40.909 0.00 0.00 0.00 2.71
861 947 4.370917 ACGGACGTGTAAACAGTAACATT 58.629 39.130 0.00 0.00 0.00 2.71
862 948 5.527951 ACGGACGTGTAAACAGTAACATTA 58.472 37.500 0.00 0.00 0.00 1.90
863 949 6.158598 ACGGACGTGTAAACAGTAACATTAT 58.841 36.000 0.00 0.00 0.00 1.28
890 976 2.047939 AGGCGGGTTTACGTTCCG 60.048 61.111 12.71 12.71 45.84 4.30
957 1043 3.372025 GCCATCCCATCCTAGAAACAAGT 60.372 47.826 0.00 0.00 0.00 3.16
1745 1872 9.793252 GTGGTCGAGTAAAAATTACAGTAGATA 57.207 33.333 3.37 0.00 0.00 1.98
1746 1873 9.793252 TGGTCGAGTAAAAATTACAGTAGATAC 57.207 33.333 3.37 0.00 0.00 2.24
1758 1885 9.464714 AATTACAGTAGATACTTATGTTGCTCG 57.535 33.333 0.00 0.00 33.46 5.03
1759 1886 6.452494 ACAGTAGATACTTATGTTGCTCGT 57.548 37.500 0.00 0.00 33.46 4.18
1760 1887 6.496571 ACAGTAGATACTTATGTTGCTCGTC 58.503 40.000 0.00 0.00 33.46 4.20
1761 1888 5.915758 CAGTAGATACTTATGTTGCTCGTCC 59.084 44.000 0.00 0.00 33.46 4.79
1762 1889 5.828859 AGTAGATACTTATGTTGCTCGTCCT 59.171 40.000 0.00 0.00 31.13 3.85
1763 1890 4.938080 AGATACTTATGTTGCTCGTCCTG 58.062 43.478 0.00 0.00 0.00 3.86
1764 1891 2.386661 ACTTATGTTGCTCGTCCTGG 57.613 50.000 0.00 0.00 0.00 4.45
1765 1892 1.899814 ACTTATGTTGCTCGTCCTGGA 59.100 47.619 0.00 0.00 0.00 3.86
1766 1893 2.301870 ACTTATGTTGCTCGTCCTGGAA 59.698 45.455 0.00 0.00 0.00 3.53
1767 1894 2.672961 TATGTTGCTCGTCCTGGAAG 57.327 50.000 0.00 0.00 0.00 3.46
1768 1895 0.687354 ATGTTGCTCGTCCTGGAAGT 59.313 50.000 9.46 0.00 0.00 3.01
1769 1896 0.249868 TGTTGCTCGTCCTGGAAGTG 60.250 55.000 9.46 8.28 0.00 3.16
1770 1897 0.033504 GTTGCTCGTCCTGGAAGTGA 59.966 55.000 14.46 5.34 0.00 3.41
1771 1898 0.756294 TTGCTCGTCCTGGAAGTGAA 59.244 50.000 14.46 2.30 0.00 3.18
1772 1899 0.976641 TGCTCGTCCTGGAAGTGAAT 59.023 50.000 14.46 0.00 0.00 2.57
1773 1900 1.347707 TGCTCGTCCTGGAAGTGAATT 59.652 47.619 14.46 0.00 0.00 2.17
1774 1901 1.734465 GCTCGTCCTGGAAGTGAATTG 59.266 52.381 14.46 0.00 0.00 2.32
1775 1902 2.872038 GCTCGTCCTGGAAGTGAATTGT 60.872 50.000 14.46 0.00 0.00 2.71
1776 1903 2.738846 CTCGTCCTGGAAGTGAATTGTG 59.261 50.000 9.46 0.00 0.00 3.33
1777 1904 2.367241 TCGTCCTGGAAGTGAATTGTGA 59.633 45.455 9.46 0.00 0.00 3.58
1778 1905 3.007940 TCGTCCTGGAAGTGAATTGTGAT 59.992 43.478 9.46 0.00 0.00 3.06
1779 1906 3.753272 CGTCCTGGAAGTGAATTGTGATT 59.247 43.478 0.00 0.00 0.00 2.57
1780 1907 4.216257 CGTCCTGGAAGTGAATTGTGATTT 59.784 41.667 0.00 0.00 0.00 2.17
1781 1908 5.411361 CGTCCTGGAAGTGAATTGTGATTTA 59.589 40.000 0.00 0.00 0.00 1.40
1782 1909 6.402550 CGTCCTGGAAGTGAATTGTGATTTAG 60.403 42.308 0.00 0.00 0.00 1.85
1783 1910 6.655003 GTCCTGGAAGTGAATTGTGATTTAGA 59.345 38.462 0.00 0.00 0.00 2.10
1784 1911 7.337942 GTCCTGGAAGTGAATTGTGATTTAGAT 59.662 37.037 0.00 0.00 0.00 1.98
1785 1912 7.337689 TCCTGGAAGTGAATTGTGATTTAGATG 59.662 37.037 0.00 0.00 0.00 2.90
1786 1913 6.855836 TGGAAGTGAATTGTGATTTAGATGC 58.144 36.000 0.00 0.00 0.00 3.91
1787 1914 6.433716 TGGAAGTGAATTGTGATTTAGATGCA 59.566 34.615 0.00 0.00 0.00 3.96
1788 1915 6.971184 GGAAGTGAATTGTGATTTAGATGCAG 59.029 38.462 0.00 0.00 0.00 4.41
1789 1916 6.446781 AGTGAATTGTGATTTAGATGCAGG 57.553 37.500 0.00 0.00 0.00 4.85
1790 1917 6.182627 AGTGAATTGTGATTTAGATGCAGGA 58.817 36.000 0.00 0.00 0.00 3.86
1791 1918 6.832384 AGTGAATTGTGATTTAGATGCAGGAT 59.168 34.615 0.00 0.00 0.00 3.24
1792 1919 7.013083 AGTGAATTGTGATTTAGATGCAGGATC 59.987 37.037 0.00 0.00 0.00 3.36
1793 1920 7.013083 GTGAATTGTGATTTAGATGCAGGATCT 59.987 37.037 9.69 9.69 44.24 2.75
1863 1990 8.890718 TCCGAGATAGGTATTCATATTAGTTCG 58.109 37.037 0.00 0.00 0.00 3.95
1877 2004 2.474410 AGTTCGGAAGTTCATCCACC 57.526 50.000 5.01 0.00 39.61 4.61
1902 2029 7.374272 CGATGAGACTATAACTGGATCAACAT 58.626 38.462 0.00 0.00 0.00 2.71
1966 2094 9.469807 TGCGATAAACACTTAAATTTGACATTT 57.530 25.926 0.00 0.00 0.00 2.32
2068 2196 4.091945 CCAATCACTCGCCACATTATATCG 59.908 45.833 0.00 0.00 0.00 2.92
2110 2238 0.251608 GGGGTGGGTTTATGCTGTGT 60.252 55.000 0.00 0.00 0.00 3.72
2113 2241 1.271926 GGTGGGTTTATGCTGTGTCCT 60.272 52.381 0.00 0.00 0.00 3.85
2181 2309 4.406972 TCTGGTGGATCCTCAGTCATTTAG 59.593 45.833 24.73 7.73 37.07 1.85
2187 2315 3.784701 TCCTCAGTCATTTAGAGCGTC 57.215 47.619 0.00 0.00 0.00 5.19
2338 2466 9.868277 TGTTCTTTGTTGTTTCATTCTTTACAT 57.132 25.926 0.00 0.00 0.00 2.29
2750 2879 4.399303 GTGCTATGCCTTTTGGTGAGTAAT 59.601 41.667 0.00 0.00 42.99 1.89
2764 2893 5.828328 TGGTGAGTAATCGAGTATCATGTCT 59.172 40.000 0.00 0.00 33.17 3.41
3001 3130 4.619679 ACTCTCTTTTCTAGCCTGGAGAT 58.380 43.478 0.00 0.00 30.93 2.75
3422 3551 6.519382 TCGAAGAAGAGTTGCATCATATGAT 58.481 36.000 12.62 12.62 34.56 2.45
3634 3763 7.924947 TGAAGATAGTGATTGTGAGCAAGATAG 59.075 37.037 0.00 0.00 38.10 2.08
3791 3928 9.705290 ATAATGTTGTTGGAATTTGTTAAGACC 57.295 29.630 0.00 0.00 0.00 3.85
3795 3932 7.093727 TGTTGTTGGAATTTGTTAAGACCTTCA 60.094 33.333 0.00 0.00 0.00 3.02
3796 3933 7.411486 TGTTGGAATTTGTTAAGACCTTCAA 57.589 32.000 0.00 0.00 0.00 2.69
3797 3934 7.488322 TGTTGGAATTTGTTAAGACCTTCAAG 58.512 34.615 0.00 0.00 0.00 3.02
3798 3935 6.084326 TGGAATTTGTTAAGACCTTCAAGC 57.916 37.500 0.00 0.00 0.00 4.01
3799 3936 5.596361 TGGAATTTGTTAAGACCTTCAAGCA 59.404 36.000 0.00 0.00 0.00 3.91
3800 3937 6.152379 GGAATTTGTTAAGACCTTCAAGCAG 58.848 40.000 0.00 0.00 0.00 4.24
3801 3938 6.239036 GGAATTTGTTAAGACCTTCAAGCAGT 60.239 38.462 0.00 0.00 0.00 4.40
3802 3939 5.499139 TTTGTTAAGACCTTCAAGCAGTG 57.501 39.130 0.00 0.00 0.00 3.66
3803 3940 4.150897 TGTTAAGACCTTCAAGCAGTGT 57.849 40.909 0.00 0.00 0.00 3.55
3804 3941 4.523083 TGTTAAGACCTTCAAGCAGTGTT 58.477 39.130 0.00 0.00 0.00 3.32
3805 3942 4.947388 TGTTAAGACCTTCAAGCAGTGTTT 59.053 37.500 0.00 0.00 0.00 2.83
3806 3943 5.163663 TGTTAAGACCTTCAAGCAGTGTTTG 60.164 40.000 13.08 13.08 0.00 2.93
3854 3991 9.824216 ATGAGATCATTGGGAAGAATCATATTT 57.176 29.630 0.00 0.00 31.37 1.40
3880 4017 4.020307 TCACTGTATTTCTGACATGCCTGA 60.020 41.667 0.00 0.00 0.00 3.86
3991 4133 9.661563 ATTTTGCATGACATTCTGTTATTCATT 57.338 25.926 0.00 0.00 0.00 2.57
3992 4134 8.692110 TTTGCATGACATTCTGTTATTCATTC 57.308 30.769 0.00 0.00 0.00 2.67
4079 4228 0.531974 TGCACACCCGTGAAGTCTTC 60.532 55.000 5.58 5.58 46.80 2.87
4240 4389 6.001460 CCAAGATCTGTAAGTTACCCACAAA 58.999 40.000 10.51 0.00 33.76 2.83
4295 4444 7.038941 AGTCAAGTAGCTTAGTGTTGTTATCCT 60.039 37.037 0.00 0.00 0.00 3.24
4322 4471 1.679977 GCCCTCATGCCAGCTCAAA 60.680 57.895 0.00 0.00 0.00 2.69
4367 4518 8.879759 TCAGAAATTTTAACTCGATATCCACAC 58.120 33.333 0.00 0.00 0.00 3.82
4522 4789 6.959639 TTTTCTCCTTGTTGTAGCATTTCT 57.040 33.333 0.00 0.00 0.00 2.52
4602 4869 7.224297 ACGATATTCTGCAGGTAACCATTTAT 58.776 34.615 15.13 0.00 37.17 1.40
4651 4918 4.142609 TCAATGCAGGTGACTTATCTCC 57.857 45.455 0.00 0.00 40.21 3.71
4660 4931 1.133450 TGACTTATCTCCTCCCCTCCG 60.133 57.143 0.00 0.00 0.00 4.63
4668 4939 2.269241 CTCCCCTCCGACTTTGGC 59.731 66.667 0.00 0.00 0.00 4.52
4728 5010 9.761504 TTTTCTCAACATTTCAATAATTGCTCA 57.238 25.926 0.00 0.00 0.00 4.26
4828 5113 4.774726 CAGATAGGGGTACATCACATAGCT 59.225 45.833 0.00 0.00 32.55 3.32
4841 5126 4.910195 TCACATAGCTTGAACACAAGGAT 58.090 39.130 11.09 0.00 40.65 3.24
4926 5211 0.624254 GCTAAACCCACTAAGCCCCT 59.376 55.000 0.00 0.00 0.00 4.79
4940 5225 0.548510 GCCCCTAACAAGAGAGGCAT 59.451 55.000 0.00 0.00 40.20 4.40
4947 5232 3.914426 AACAAGAGAGGCATACCGAAT 57.086 42.857 0.00 0.00 42.76 3.34
4982 5268 2.880443 ACATCACCAAAGCCAACATCT 58.120 42.857 0.00 0.00 0.00 2.90
5082 5400 1.153086 GCGGAGATGAAGGCCATGT 60.153 57.895 5.01 0.00 35.17 3.21
5201 5519 3.302347 CTCATAGCCGCCGGATCCC 62.302 68.421 7.68 0.00 0.00 3.85
5465 5797 1.883544 CGACGAGCCGAGAGAGCTA 60.884 63.158 1.50 0.00 41.75 3.32
5511 5860 1.374190 CAGAGGACACTGGCAAGCT 59.626 57.895 0.00 0.00 34.64 3.74
5515 5864 2.391389 GGACACTGGCAAGCTACGC 61.391 63.158 0.00 0.00 0.00 4.42
5520 5869 2.668212 TGGCAAGCTACGCACACC 60.668 61.111 9.99 0.00 0.00 4.16
5630 5994 0.179018 GTAGCCGATGCCAGGGAATT 60.179 55.000 0.00 0.00 38.69 2.17
5652 6016 0.953960 CCACCGTAGCCTCAACAACC 60.954 60.000 0.00 0.00 0.00 3.77
5660 6024 2.184167 CCTCAACAACCGCCACGTT 61.184 57.895 0.00 0.00 0.00 3.99
5666 6030 4.250305 AACCGCCACGTTGGAGCT 62.250 61.111 8.04 0.00 40.96 4.09
5834 6211 1.070786 TGAACTTCCAGGCCGTGAC 59.929 57.895 0.00 0.00 0.00 3.67
5908 6285 0.972883 GATTGGATCTCGGGGAGGAG 59.027 60.000 0.00 0.00 35.32 3.69
5909 6286 0.472734 ATTGGATCTCGGGGAGGAGG 60.473 60.000 0.00 0.00 34.74 4.30
5910 6287 2.203714 GGATCTCGGGGAGGAGGG 60.204 72.222 0.00 0.00 34.74 4.30
5911 6288 2.203714 GATCTCGGGGAGGAGGGG 60.204 72.222 0.00 0.00 34.74 4.79
5912 6289 3.837213 GATCTCGGGGAGGAGGGGG 62.837 73.684 0.00 0.00 34.74 5.40
5931 6308 4.910585 CTACCCGCCGCCACCATC 62.911 72.222 0.00 0.00 0.00 3.51
6082 6666 0.319083 CAGTGCATGCATGGGTTTGT 59.681 50.000 25.64 0.00 0.00 2.83
6191 6844 8.384607 TGTTGCACACACTATTAATAAAGTCA 57.615 30.769 0.00 0.00 0.00 3.41
6225 6878 2.287547 GCAAGTCGCCTGAAACAATTCA 60.288 45.455 0.00 0.00 43.05 2.57
6464 7136 1.229658 CCACTTCCTCCCTGGGACT 60.230 63.158 12.53 0.00 34.78 3.85
6465 7137 1.557269 CCACTTCCTCCCTGGGACTG 61.557 65.000 12.53 6.24 34.78 3.51
6466 7138 0.838122 CACTTCCTCCCTGGGACTGT 60.838 60.000 12.53 5.39 34.78 3.55
6467 7139 0.838122 ACTTCCTCCCTGGGACTGTG 60.838 60.000 12.53 1.51 34.78 3.66
6468 7140 1.538876 TTCCTCCCTGGGACTGTGG 60.539 63.158 12.53 11.99 34.78 4.17
6469 7141 3.011517 CCTCCCTGGGACTGTGGG 61.012 72.222 12.53 7.51 42.20 4.61
6470 7142 2.122729 CTCCCTGGGACTGTGGGA 59.877 66.667 12.53 3.84 46.78 4.37
6471 7143 2.203938 TCCCTGGGACTGTGGGAC 60.204 66.667 12.53 0.00 44.37 4.46
6472 7144 2.529136 CCCTGGGACTGTGGGACA 60.529 66.667 7.01 0.00 43.47 4.02
6473 7145 1.925455 CCCTGGGACTGTGGGACAT 60.925 63.158 7.01 0.00 44.52 3.06
6474 7146 1.500783 CCCTGGGACTGTGGGACATT 61.501 60.000 7.01 0.00 44.52 2.71
6475 7147 1.285280 CCTGGGACTGTGGGACATTA 58.715 55.000 0.00 0.00 44.52 1.90
6476 7148 1.846439 CCTGGGACTGTGGGACATTAT 59.154 52.381 0.00 0.00 44.52 1.28
6477 7149 2.158755 CCTGGGACTGTGGGACATTATC 60.159 54.545 0.00 0.00 44.52 1.75
6482 7154 4.640647 GGGACTGTGGGACATTATCTTTTC 59.359 45.833 0.00 0.00 44.52 2.29
6783 7456 7.608308 TTGCCAAAAGAATTATAATTGCCAC 57.392 32.000 15.39 1.34 0.00 5.01
6964 7641 2.462456 TTCATGGCTCTATGCGATCC 57.538 50.000 0.00 0.00 44.05 3.36
7252 7935 5.650703 TCGAGACACTAATCTGTTGGTCATA 59.349 40.000 0.00 0.00 0.00 2.15
7449 8133 3.433306 TTAAGAAGGGTGACATGGGTG 57.567 47.619 0.00 0.00 0.00 4.61
7464 8148 4.892934 ACATGGGTGTCTTTCTAAAAGCAA 59.107 37.500 0.00 0.00 31.41 3.91
7471 8155 7.039993 GGGTGTCTTTCTAAAAGCAATTTCCTA 60.040 37.037 0.00 0.00 32.27 2.94
7473 8157 9.346725 GTGTCTTTCTAAAAGCAATTTCCTATG 57.653 33.333 0.00 0.00 32.27 2.23
7607 8291 5.699143 AGATTTCCTCTATGGTTCCCAATG 58.301 41.667 0.00 0.00 36.95 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.035684 GTCTTTTTGGAACGAAAGCACTC 58.964 43.478 0.00 0.00 35.18 3.51
75 76 5.124457 CCACCTTCTTCTGATTAATGGTGTG 59.876 44.000 13.34 4.88 41.27 3.82
80 81 5.591877 CCTTCCCACCTTCTTCTGATTAATG 59.408 44.000 0.00 0.00 0.00 1.90
111 117 6.992123 CCTTATGCATATCTAGTTTCACCACA 59.008 38.462 7.36 0.00 0.00 4.17
138 144 6.701145 AACACTCACTCGACTATGTCATAT 57.299 37.500 0.00 0.00 32.09 1.78
156 162 2.590821 AGCATTGCTTCCAGAAACACT 58.409 42.857 5.03 0.00 33.89 3.55
177 183 2.224257 GCCATGAAAACCCAGCTTCAAA 60.224 45.455 0.00 0.00 35.31 2.69
197 203 5.739161 GTCATAATCAAATGAAACCAGTCGC 59.261 40.000 0.00 0.00 37.61 5.19
201 207 8.084073 ACACAAGTCATAATCAAATGAAACCAG 58.916 33.333 0.00 0.00 37.61 4.00
205 211 8.628280 TGACACACAAGTCATAATCAAATGAAA 58.372 29.630 0.00 0.00 43.18 2.69
264 270 7.582352 ACTTTTTAGAAGGCGTGATAGTTTTC 58.418 34.615 0.00 0.00 0.00 2.29
265 271 7.506328 ACTTTTTAGAAGGCGTGATAGTTTT 57.494 32.000 0.00 0.00 0.00 2.43
275 281 7.326063 CACCTTATCAAAACTTTTTAGAAGGCG 59.674 37.037 16.65 8.00 36.69 5.52
297 303 9.099071 AGCAGATATGATTATAAAGAGTCACCT 57.901 33.333 0.00 0.00 0.00 4.00
311 317 7.174426 CCATACACAACATGAGCAGATATGATT 59.826 37.037 0.00 0.00 0.00 2.57
321 327 3.375299 GTCCTTCCATACACAACATGAGC 59.625 47.826 0.00 0.00 0.00 4.26
322 328 4.836825 AGTCCTTCCATACACAACATGAG 58.163 43.478 0.00 0.00 0.00 2.90
329 335 5.542635 AGAGTTGTAAGTCCTTCCATACACA 59.457 40.000 0.00 0.00 0.00 3.72
373 379 5.963092 AGATCATCTCCATTGGTCTCTCTA 58.037 41.667 1.86 0.00 28.23 2.43
378 384 5.972327 AAAGAGATCATCTCCATTGGTCT 57.028 39.130 11.33 0.00 44.42 3.85
382 388 6.484540 CAACGAAAAGAGATCATCTCCATTG 58.515 40.000 11.33 4.61 44.42 2.82
383 389 5.065731 GCAACGAAAAGAGATCATCTCCATT 59.934 40.000 11.33 6.64 44.42 3.16
439 445 7.605449 CATGTTGAAAGAAATAGTTGATGGGT 58.395 34.615 0.00 0.00 0.00 4.51
445 452 7.935338 ACTTGCATGTTGAAAGAAATAGTTG 57.065 32.000 0.00 0.00 34.90 3.16
473 482 8.087750 TCTCATGCATGTTGTACGATAATATGA 58.912 33.333 25.43 0.58 30.90 2.15
476 485 8.655651 TTTCTCATGCATGTTGTACGATAATA 57.344 30.769 25.43 1.25 0.00 0.98
505 514 5.584913 AGAGACATATGGTAGTAGGATGGG 58.415 45.833 7.80 0.00 0.00 4.00
509 518 8.642432 CATTTTGAGAGACATATGGTAGTAGGA 58.358 37.037 7.80 0.00 0.00 2.94
512 521 7.791029 TGCATTTTGAGAGACATATGGTAGTA 58.209 34.615 7.80 0.00 0.00 1.82
532 541 7.604549 TCATGATAAAGTGACATGTTTGCATT 58.395 30.769 0.00 0.00 41.14 3.56
572 581 8.102800 TGTATATTTGCACATTGAGATGGATC 57.897 34.615 0.00 0.00 37.60 3.36
573 582 8.520351 CATGTATATTTGCACATTGAGATGGAT 58.480 33.333 0.00 0.00 37.60 3.41
574 583 7.720515 TCATGTATATTTGCACATTGAGATGGA 59.279 33.333 0.00 0.00 37.60 3.41
737 757 8.755696 TGCCGGAATATTTTGCAATATATTTC 57.244 30.769 25.99 23.92 34.91 2.17
738 758 7.331687 GCTGCCGGAATATTTTGCAATATATTT 59.668 33.333 25.99 15.43 34.91 1.40
744 764 2.799207 CGCTGCCGGAATATTTTGCAAT 60.799 45.455 5.05 0.00 0.00 3.56
760 780 2.995881 GATACCCCGTACGTCGCTGC 62.996 65.000 15.21 0.00 38.35 5.25
761 781 1.009222 GATACCCCGTACGTCGCTG 60.009 63.158 15.21 0.00 38.35 5.18
763 783 0.874390 TATGATACCCCGTACGTCGC 59.126 55.000 15.21 0.00 38.35 5.19
764 784 3.935203 ACTATATGATACCCCGTACGTCG 59.065 47.826 15.21 5.89 39.52 5.12
765 785 5.412594 TCAACTATATGATACCCCGTACGTC 59.587 44.000 15.21 5.18 0.00 4.34
766 786 5.316167 TCAACTATATGATACCCCGTACGT 58.684 41.667 15.21 0.00 0.00 3.57
767 787 5.885230 TCAACTATATGATACCCCGTACG 57.115 43.478 8.69 8.69 0.00 3.67
768 788 7.311408 GTCTTCAACTATATGATACCCCGTAC 58.689 42.308 0.00 0.00 0.00 3.67
769 789 6.149973 CGTCTTCAACTATATGATACCCCGTA 59.850 42.308 0.00 0.00 0.00 4.02
770 790 5.048224 CGTCTTCAACTATATGATACCCCGT 60.048 44.000 0.00 0.00 0.00 5.28
773 859 5.337330 CCCCGTCTTCAACTATATGATACCC 60.337 48.000 0.00 0.00 0.00 3.69
780 866 2.296471 CGAGCCCCGTCTTCAACTATAT 59.704 50.000 0.00 0.00 0.00 0.86
782 868 0.460311 CGAGCCCCGTCTTCAACTAT 59.540 55.000 0.00 0.00 0.00 2.12
795 881 4.742201 TTCAGCTGTCGCGAGCCC 62.742 66.667 10.24 0.00 40.08 5.19
797 883 1.136872 CTAGTTCAGCTGTCGCGAGC 61.137 60.000 10.24 11.33 42.32 5.03
802 888 4.017380 ACGTATTCTAGTTCAGCTGTCG 57.983 45.455 14.67 6.79 0.00 4.35
807 893 6.810182 TGGAAGTTTACGTATTCTAGTTCAGC 59.190 38.462 0.00 0.00 0.00 4.26
808 894 7.488471 CCTGGAAGTTTACGTATTCTAGTTCAG 59.512 40.741 15.40 9.93 31.67 3.02
810 896 6.755607 CCCTGGAAGTTTACGTATTCTAGTTC 59.244 42.308 15.40 10.89 31.67 3.01
845 931 7.906527 CCGGCTTAATAATGTTACTGTTTACAC 59.093 37.037 0.00 0.00 0.00 2.90
890 976 2.164017 GGAAGACGACAGGAAGAGTACC 59.836 54.545 0.00 0.00 0.00 3.34
957 1043 4.314440 GTGGCTGTGGACTCGGCA 62.314 66.667 7.40 0.00 41.03 5.69
1745 1872 1.899814 TCCAGGACGAGCAACATAAGT 59.100 47.619 0.00 0.00 0.00 2.24
1746 1873 2.672961 TCCAGGACGAGCAACATAAG 57.327 50.000 0.00 0.00 0.00 1.73
1747 1874 2.301870 ACTTCCAGGACGAGCAACATAA 59.698 45.455 0.00 0.00 0.00 1.90
1748 1875 1.899814 ACTTCCAGGACGAGCAACATA 59.100 47.619 0.00 0.00 0.00 2.29
1749 1876 0.687354 ACTTCCAGGACGAGCAACAT 59.313 50.000 0.00 0.00 0.00 2.71
1750 1877 0.249868 CACTTCCAGGACGAGCAACA 60.250 55.000 0.00 0.00 0.00 3.33
1751 1878 0.033504 TCACTTCCAGGACGAGCAAC 59.966 55.000 0.00 0.00 0.00 4.17
1752 1879 0.756294 TTCACTTCCAGGACGAGCAA 59.244 50.000 0.00 0.00 0.00 3.91
1753 1880 0.976641 ATTCACTTCCAGGACGAGCA 59.023 50.000 0.00 0.00 0.00 4.26
1754 1881 1.734465 CAATTCACTTCCAGGACGAGC 59.266 52.381 0.00 0.00 0.00 5.03
1755 1882 2.738846 CACAATTCACTTCCAGGACGAG 59.261 50.000 0.00 0.00 0.00 4.18
1756 1883 2.367241 TCACAATTCACTTCCAGGACGA 59.633 45.455 0.00 0.00 0.00 4.20
1757 1884 2.766313 TCACAATTCACTTCCAGGACG 58.234 47.619 0.00 0.00 0.00 4.79
1758 1885 5.712152 AAATCACAATTCACTTCCAGGAC 57.288 39.130 0.00 0.00 0.00 3.85
1759 1886 6.778821 TCTAAATCACAATTCACTTCCAGGA 58.221 36.000 0.00 0.00 0.00 3.86
1760 1887 7.478322 CATCTAAATCACAATTCACTTCCAGG 58.522 38.462 0.00 0.00 0.00 4.45
1761 1888 6.971184 GCATCTAAATCACAATTCACTTCCAG 59.029 38.462 0.00 0.00 0.00 3.86
1762 1889 6.433716 TGCATCTAAATCACAATTCACTTCCA 59.566 34.615 0.00 0.00 0.00 3.53
1763 1890 6.855836 TGCATCTAAATCACAATTCACTTCC 58.144 36.000 0.00 0.00 0.00 3.46
1764 1891 6.971184 CCTGCATCTAAATCACAATTCACTTC 59.029 38.462 0.00 0.00 0.00 3.01
1765 1892 6.660521 TCCTGCATCTAAATCACAATTCACTT 59.339 34.615 0.00 0.00 0.00 3.16
1766 1893 6.182627 TCCTGCATCTAAATCACAATTCACT 58.817 36.000 0.00 0.00 0.00 3.41
1767 1894 6.441093 TCCTGCATCTAAATCACAATTCAC 57.559 37.500 0.00 0.00 0.00 3.18
1768 1895 7.058525 AGATCCTGCATCTAAATCACAATTCA 58.941 34.615 0.00 0.00 40.41 2.57
1769 1896 7.507733 AGATCCTGCATCTAAATCACAATTC 57.492 36.000 0.00 0.00 40.41 2.17
1770 1897 7.893124 AAGATCCTGCATCTAAATCACAATT 57.107 32.000 0.00 0.00 41.47 2.32
1771 1898 7.893124 AAAGATCCTGCATCTAAATCACAAT 57.107 32.000 0.00 0.00 41.47 2.71
1772 1899 8.049117 AGTAAAGATCCTGCATCTAAATCACAA 58.951 33.333 0.00 0.00 41.47 3.33
1773 1900 7.568349 AGTAAAGATCCTGCATCTAAATCACA 58.432 34.615 0.00 0.00 41.47 3.58
1774 1901 8.443953 AAGTAAAGATCCTGCATCTAAATCAC 57.556 34.615 0.00 0.00 41.47 3.06
1775 1902 9.770097 CTAAGTAAAGATCCTGCATCTAAATCA 57.230 33.333 0.00 0.00 41.47 2.57
1776 1903 8.716909 GCTAAGTAAAGATCCTGCATCTAAATC 58.283 37.037 0.00 0.00 41.47 2.17
1777 1904 8.213679 TGCTAAGTAAAGATCCTGCATCTAAAT 58.786 33.333 0.00 0.00 41.47 1.40
1778 1905 7.564793 TGCTAAGTAAAGATCCTGCATCTAAA 58.435 34.615 0.00 0.00 41.47 1.85
1779 1906 7.124573 TGCTAAGTAAAGATCCTGCATCTAA 57.875 36.000 0.00 0.00 41.47 2.10
1780 1907 6.731292 TGCTAAGTAAAGATCCTGCATCTA 57.269 37.500 0.00 0.00 41.47 1.98
1781 1908 5.620738 TGCTAAGTAAAGATCCTGCATCT 57.379 39.130 0.00 0.00 44.56 2.90
1782 1909 6.666417 CATTGCTAAGTAAAGATCCTGCATC 58.334 40.000 0.00 0.00 0.00 3.91
1783 1910 5.009410 GCATTGCTAAGTAAAGATCCTGCAT 59.991 40.000 0.16 0.00 0.00 3.96
1784 1911 4.336433 GCATTGCTAAGTAAAGATCCTGCA 59.664 41.667 0.16 0.00 0.00 4.41
1785 1912 4.261363 GGCATTGCTAAGTAAAGATCCTGC 60.261 45.833 8.82 0.00 0.00 4.85
1786 1913 5.008415 CAGGCATTGCTAAGTAAAGATCCTG 59.992 44.000 8.82 0.00 0.00 3.86
1787 1914 5.128919 CAGGCATTGCTAAGTAAAGATCCT 58.871 41.667 8.82 0.00 0.00 3.24
1788 1915 4.884164 ACAGGCATTGCTAAGTAAAGATCC 59.116 41.667 8.82 0.00 0.00 3.36
1789 1916 6.442513 AACAGGCATTGCTAAGTAAAGATC 57.557 37.500 8.82 0.00 0.00 2.75
1790 1917 6.660949 AGAAACAGGCATTGCTAAGTAAAGAT 59.339 34.615 8.82 0.00 0.00 2.40
1791 1918 6.003950 AGAAACAGGCATTGCTAAGTAAAGA 58.996 36.000 8.82 0.00 0.00 2.52
1792 1919 6.259550 AGAAACAGGCATTGCTAAGTAAAG 57.740 37.500 8.82 0.00 0.00 1.85
1793 1920 6.490040 AGAAGAAACAGGCATTGCTAAGTAAA 59.510 34.615 8.82 0.00 0.00 2.01
1877 2004 6.739112 TGTTGATCCAGTTATAGTCTCATCG 58.261 40.000 0.00 0.00 0.00 3.84
1902 2029 9.271828 CATAAGCTATGAACATACCACAACATA 57.728 33.333 0.00 0.00 38.45 2.29
1934 2061 8.563949 CAAATTTAAGTGTTTATCGCAACTACG 58.436 33.333 0.00 0.00 0.00 3.51
1935 2062 9.601971 TCAAATTTAAGTGTTTATCGCAACTAC 57.398 29.630 0.00 0.00 0.00 2.73
1936 2063 9.601971 GTCAAATTTAAGTGTTTATCGCAACTA 57.398 29.630 0.00 0.00 0.00 2.24
1937 2064 8.132362 TGTCAAATTTAAGTGTTTATCGCAACT 58.868 29.630 0.00 0.00 0.00 3.16
2068 2196 5.225642 CCTTCCTCTTTGTCAATTTGAAGC 58.774 41.667 0.00 0.00 0.00 3.86
2110 2238 4.500887 CCACGTTTCTGAAGAACTACAGGA 60.501 45.833 0.00 0.00 35.20 3.86
2113 2241 4.659111 TCCACGTTTCTGAAGAACTACA 57.341 40.909 0.00 0.00 33.13 2.74
2181 2309 0.318275 CAATAGGCTCTCGGACGCTC 60.318 60.000 0.00 0.00 0.00 5.03
2187 2315 3.118592 AGGTCTTTTCAATAGGCTCTCGG 60.119 47.826 0.00 0.00 0.00 4.63
2338 2466 4.547671 TGAGTTGAAAATGGGGTTGGTAA 58.452 39.130 0.00 0.00 0.00 2.85
2341 2469 5.937975 ATATGAGTTGAAAATGGGGTTGG 57.062 39.130 0.00 0.00 0.00 3.77
3001 3130 5.631929 CGGTCATATAGTGCAGCGTTTATAA 59.368 40.000 0.00 0.00 0.00 0.98
3789 3926 2.945668 GAGACAAACACTGCTTGAAGGT 59.054 45.455 0.00 0.00 0.00 3.50
3791 3928 4.274214 TCATGAGACAAACACTGCTTGAAG 59.726 41.667 0.00 0.00 0.00 3.02
3795 3932 4.139786 ACATCATGAGACAAACACTGCTT 58.860 39.130 0.09 0.00 0.00 3.91
3796 3933 3.748083 ACATCATGAGACAAACACTGCT 58.252 40.909 0.09 0.00 0.00 4.24
3797 3934 4.494350 AACATCATGAGACAAACACTGC 57.506 40.909 0.09 0.00 0.00 4.40
3798 3935 8.908678 CAAAATAACATCATGAGACAAACACTG 58.091 33.333 0.09 0.00 0.00 3.66
3799 3936 8.849168 TCAAAATAACATCATGAGACAAACACT 58.151 29.630 0.09 0.00 0.00 3.55
3800 3937 9.462174 TTCAAAATAACATCATGAGACAAACAC 57.538 29.630 0.09 0.00 0.00 3.32
3854 3991 4.002982 GCATGTCAGAAATACAGTGACCA 58.997 43.478 0.00 0.00 39.96 4.02
3880 4017 7.984617 GCTGAGAAAGTAATATGAAGAAGAGGT 59.015 37.037 0.00 0.00 0.00 3.85
3991 4133 6.214615 TCTCTGAACCCAGGTACAAATATTGA 59.785 38.462 0.00 0.00 40.76 2.57
3992 4134 6.414732 TCTCTGAACCCAGGTACAAATATTG 58.585 40.000 0.00 0.00 40.76 1.90
4079 4228 3.744942 GTGTGCTGCTGTATGGATATCAG 59.255 47.826 4.83 0.00 0.00 2.90
4240 4389 5.006386 GGTGAAGATGGTGATCAAGAAAGT 58.994 41.667 0.00 0.00 0.00 2.66
4295 4444 1.985473 GGCATGAGGGCATCAACATA 58.015 50.000 5.73 0.00 42.53 2.29
4367 4518 8.020819 ACAACATAAGAACACGGACAAAATATG 58.979 33.333 0.00 0.00 0.00 1.78
4602 4869 0.401738 CTGGGGCTTTGACAGAAGGA 59.598 55.000 0.00 0.00 34.21 3.36
4651 4918 2.245438 GAGCCAAAGTCGGAGGGGAG 62.245 65.000 0.00 0.00 0.00 4.30
4652 4919 2.203938 AGCCAAAGTCGGAGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
4660 4931 7.486232 GCATTGACTATTTAAAGAGCCAAAGTC 59.514 37.037 14.25 3.77 0.00 3.01
4668 4939 9.897744 TTTTCAGTGCATTGACTATTTAAAGAG 57.102 29.630 11.95 8.29 0.00 2.85
4828 5113 1.960417 TCACGCATCCTTGTGTTCAA 58.040 45.000 0.00 0.00 43.99 2.69
4841 5126 2.983030 GGGTGCCATGTTCACGCA 60.983 61.111 20.12 8.15 43.93 5.24
4926 5211 4.499188 CGATTCGGTATGCCTCTCTTGTTA 60.499 45.833 0.00 0.00 0.00 2.41
4947 5232 3.545124 ATGTTGGACGGCTTGCCGA 62.545 57.895 35.96 16.15 36.94 5.54
4955 5240 0.240945 GCTTTGGTGATGTTGGACGG 59.759 55.000 0.00 0.00 0.00 4.79
4982 5268 3.986006 GTCGCTCACGGTGTCCCA 61.986 66.667 8.17 0.00 40.63 4.37
5067 5385 1.869767 CGCTAACATGGCCTTCATCTC 59.130 52.381 3.32 0.00 32.92 2.75
5082 5400 2.678786 TCCTTCTTGGAGGCGCTAA 58.321 52.632 7.64 0.00 40.56 3.09
5201 5519 2.102084 TGGCTTCCTCATCTCAGATTCG 59.898 50.000 0.00 0.00 0.00 3.34
5413 5745 2.045536 GGCCCTGGCAACTCAGAG 60.046 66.667 10.86 0.00 44.11 3.35
5465 5797 1.608717 CCAGTAGCTGCGTCCCTTCT 61.609 60.000 0.00 0.00 0.00 2.85
5511 5860 2.256158 CGTTCTCCGGTGTGCGTA 59.744 61.111 0.00 0.00 0.00 4.42
5515 5864 2.738521 CCTGCGTTCTCCGGTGTG 60.739 66.667 0.00 0.00 36.94 3.82
5520 5869 1.949847 ATCTGGACCTGCGTTCTCCG 61.950 60.000 0.00 0.00 40.40 4.63
5597 5961 1.226030 GGCTACCTTTGACAACGCGT 61.226 55.000 5.58 5.58 0.00 6.01
5630 5994 1.116536 TGTTGAGGCTACGGTGGTCA 61.117 55.000 0.00 0.00 0.00 4.02
5713 6077 3.706373 GGGCCTGCCTCGTGAAGA 61.706 66.667 8.29 0.00 36.10 2.87
5784 6161 4.715130 CCTCCCTCCCCGTGGACA 62.715 72.222 0.00 0.00 35.03 4.02
5914 6291 4.910585 GATGGTGGCGGCGGGTAG 62.911 72.222 9.78 0.00 0.00 3.18
5922 6299 4.489771 GTCCCTGGGATGGTGGCG 62.490 72.222 20.40 0.00 32.73 5.69
5923 6300 4.129148 GGTCCCTGGGATGGTGGC 62.129 72.222 20.40 4.32 32.73 5.01
5924 6301 3.797353 CGGTCCCTGGGATGGTGG 61.797 72.222 20.40 2.98 32.73 4.61
5925 6302 3.797353 CCGGTCCCTGGGATGGTG 61.797 72.222 20.40 8.94 32.73 4.17
5928 6305 4.181010 CTGCCGGTCCCTGGGATG 62.181 72.222 20.40 14.45 32.73 3.51
6020 6604 1.625818 ACAATTCTGAGGTTCTCGCCT 59.374 47.619 0.00 0.00 42.53 5.52
6124 6777 7.234187 TCGCATCAGATCAAAATACTTGTAC 57.766 36.000 0.00 0.00 0.00 2.90
6191 6844 1.523758 GACTTGCGAACAGGGAACAT 58.476 50.000 0.00 0.00 0.00 2.71
6241 6894 2.764737 CCATCATGGGCTCAGGGCT 61.765 63.158 0.00 0.00 41.46 5.19
6340 7007 3.589542 CCACCCCCACCCACACAT 61.590 66.667 0.00 0.00 0.00 3.21
6464 7136 6.484288 ACAGATGAAAAGATAATGTCCCACA 58.516 36.000 0.00 0.00 0.00 4.17
6465 7137 8.506168 TTACAGATGAAAAGATAATGTCCCAC 57.494 34.615 0.00 0.00 0.00 4.61
6466 7138 8.956426 GTTTACAGATGAAAAGATAATGTCCCA 58.044 33.333 0.00 0.00 0.00 4.37
6467 7139 9.178758 AGTTTACAGATGAAAAGATAATGTCCC 57.821 33.333 0.00 0.00 0.00 4.46
6473 7145 8.999431 GGTGTGAGTTTACAGATGAAAAGATAA 58.001 33.333 0.00 0.00 0.00 1.75
6474 7146 8.375506 AGGTGTGAGTTTACAGATGAAAAGATA 58.624 33.333 0.00 0.00 0.00 1.98
6475 7147 7.227156 AGGTGTGAGTTTACAGATGAAAAGAT 58.773 34.615 0.00 0.00 0.00 2.40
6476 7148 6.591935 AGGTGTGAGTTTACAGATGAAAAGA 58.408 36.000 0.00 0.00 0.00 2.52
6477 7149 6.867662 AGGTGTGAGTTTACAGATGAAAAG 57.132 37.500 0.00 0.00 0.00 2.27
6783 7456 2.743752 CGTGCCTGGCGATGAACAG 61.744 63.158 14.98 0.00 34.54 3.16
6964 7641 3.196685 AGAAGAGAAGACCAAGGATTCGG 59.803 47.826 0.00 0.00 0.00 4.30
7087 7769 2.811317 GGCACGTCTCCAGCTTCG 60.811 66.667 0.00 0.00 0.00 3.79
7214 7897 4.523173 AGTGTCTCGATTCACTGAACCTAA 59.477 41.667 17.68 0.00 42.30 2.69
7326 8010 8.425703 TCAATATTCGTGATTAGGACCATGTTA 58.574 33.333 0.00 0.00 0.00 2.41
7327 8011 7.279615 TCAATATTCGTGATTAGGACCATGTT 58.720 34.615 0.00 0.00 0.00 2.71
7449 8133 9.561270 GACATAGGAAATTGCTTTTAGAAAGAC 57.439 33.333 4.69 0.00 0.00 3.01
7500 8184 2.167693 TGGTGAGCTATACCACTTTCCG 59.832 50.000 16.24 0.00 43.00 4.30
7555 8239 4.409574 TGTAGGGTACAGAAACTGGAAACA 59.590 41.667 0.00 0.00 35.51 2.83
7738 9033 6.420638 TCTAGTACAGTACCATGCAGACTAA 58.579 40.000 7.13 0.00 0.00 2.24
7746 9041 6.538742 CCAAACCATTCTAGTACAGTACCATG 59.461 42.308 7.13 5.24 0.00 3.66
7749 9044 6.290294 TCCAAACCATTCTAGTACAGTACC 57.710 41.667 7.13 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.