Multiple sequence alignment - TraesCS3B01G338000

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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 TraesCS3B01G338000 chr3B 100.000 3980 0 0 1 3980 544560204 544556225 0.000000e+00 7350.0
1 TraesCS3B01G338000 chr3B 96.875 32 0 1 2007 2038 811790267 811790297 7.000000e-03 52.8
2 TraesCS3B01G338000 chr3A 87.450 1984 158 46 2035 3980 532845214 532847144 0.000000e+00 2200.0
3 TraesCS3B01G338000 chr3A 89.722 1294 72 30 738 1989 532843932 532845206 0.000000e+00 1596.0
4 TraesCS3B01G338000 chr3A 82.699 289 18 13 158 430 532843048 532843320 1.110000e-55 228.0
5 TraesCS3B01G338000 chr3A 94.366 142 7 1 1 141 532842581 532842722 2.410000e-52 217.0
6 TraesCS3B01G338000 chr3D 89.017 1302 63 34 741 1992 418238656 418237385 0.000000e+00 1539.0
7 TraesCS3B01G338000 chr3D 86.183 1158 62 29 2035 3119 418237380 418236248 0.000000e+00 1162.0
8 TraesCS3B01G338000 chr3D 95.292 701 28 3 3285 3980 418235887 418235187 0.000000e+00 1107.0
9 TraesCS3B01G338000 chr3D 83.770 610 56 19 158 739 418239279 418238685 4.530000e-149 538.0
10 TraesCS3B01G338000 chr3D 92.361 144 10 1 1 143 418239761 418239618 1.880000e-48 204.0
11 TraesCS3B01G338000 chr3D 92.254 142 7 3 3107 3245 418236026 418235886 8.720000e-47 198.0
12 TraesCS3B01G338000 chr3D 94.681 94 4 1 337 429 23068008 23067915 1.150000e-30 145.0
13 TraesCS3B01G338000 chr3D 96.970 33 0 1 2011 2043 113456571 113456540 2.000000e-03 54.7
14 TraesCS3B01G338000 chr2B 84.165 461 44 16 1546 1989 726686006 726686454 1.710000e-113 420.0
15 TraesCS3B01G338000 chr6D 97.753 89 2 0 341 429 114190320 114190408 1.920000e-33 154.0
16 TraesCS3B01G338000 chr1D 94.681 94 5 0 337 430 423607310 423607403 3.210000e-31 147.0
17 TraesCS3B01G338000 chr1D 96.591 88 2 1 336 423 423916626 423916712 1.150000e-30 145.0
18 TraesCS3B01G338000 chr1D 100.000 29 0 0 2011 2039 459859690 459859662 2.000000e-03 54.7
19 TraesCS3B01G338000 chr1D 100.000 29 0 0 2011 2039 480550995 480550967 2.000000e-03 54.7
20 TraesCS3B01G338000 chr1B 97.619 84 2 0 341 424 572913838 572913921 1.150000e-30 145.0
21 TraesCS3B01G338000 chr2D 90.741 108 5 5 342 448 584839593 584839490 5.360000e-29 139.0
22 TraesCS3B01G338000 chr2D 100.000 30 0 0 2011 2040 367592343 367592372 5.560000e-04 56.5
23 TraesCS3B01G338000 chr1A 92.708 96 6 1 340 435 477696940 477696846 1.930000e-28 137.0
24 TraesCS3B01G338000 chr2A 100.000 30 0 0 2011 2040 103132985 103133014 5.560000e-04 56.5
25 TraesCS3B01G338000 chr7B 100.000 29 0 0 2011 2039 612300155 612300183 2.000000e-03 54.7
26 TraesCS3B01G338000 chr5D 100.000 29 0 0 2011 2039 413056201 413056173 2.000000e-03 54.7
27 TraesCS3B01G338000 chr4B 96.970 33 0 1 2007 2039 429357428 429357397 2.000000e-03 54.7


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 TraesCS3B01G338000 chr3B 544556225 544560204 3979 True 7350.000000 7350 100.000000 1 3980 1 chr3B.!!$R1 3979
1 TraesCS3B01G338000 chr3A 532842581 532847144 4563 False 1060.250000 2200 88.559250 1 3980 4 chr3A.!!$F1 3979
2 TraesCS3B01G338000 chr3D 418235187 418239761 4574 True 791.333333 1539 89.812833 1 3980 6 chr3D.!!$R3 3979

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
520 891 0.324923 ACATACTCCTACCCGTGCCA 60.325 55.0 0.0 0.0 0.00 4.92 F
1495 2332 0.096976 GGTGACGCCATTTGTGATCG 59.903 55.0 0.0 0.0 37.17 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 3192 0.257039 TGGAGTACCGTCTAGGGGAC 59.743 60.0 7.63 0.3 46.96 4.46 R
3138 4393 0.257039 AGCTGCTCCAGGGGTTTATG 59.743 55.0 0.00 0.0 31.21 1.90 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
45 47 9.146586 TGCTAATGATTTGCCTTAATAAATCCT 57.853 29.630 8.98 5.43 40.73 3.24
71 73 4.537936 ACAAAGAAGAAAAGCGACACTC 57.462 40.909 0.00 0.00 0.00 3.51
143 145 7.094549 CCACATTTTAAAACATACTCCCTTCGA 60.095 37.037 1.97 0.00 0.00 3.71
144 146 8.458843 CACATTTTAAAACATACTCCCTTCGAT 58.541 33.333 1.97 0.00 0.00 3.59
145 147 8.674607 ACATTTTAAAACATACTCCCTTCGATC 58.325 33.333 1.97 0.00 0.00 3.69
147 149 4.837093 AAAACATACTCCCTTCGATCCA 57.163 40.909 0.00 0.00 0.00 3.41
149 151 6.494666 AAAACATACTCCCTTCGATCCATA 57.505 37.500 0.00 0.00 0.00 2.74
151 153 6.688073 AACATACTCCCTTCGATCCATAAT 57.312 37.500 0.00 0.00 0.00 1.28
152 154 7.792364 AACATACTCCCTTCGATCCATAATA 57.208 36.000 0.00 0.00 0.00 0.98
153 155 7.411486 ACATACTCCCTTCGATCCATAATAG 57.589 40.000 0.00 0.00 0.00 1.73
154 156 6.381420 ACATACTCCCTTCGATCCATAATAGG 59.619 42.308 0.00 0.00 0.00 2.57
155 157 4.097418 ACTCCCTTCGATCCATAATAGGG 58.903 47.826 8.06 8.06 43.01 3.53
156 158 3.450904 TCCCTTCGATCCATAATAGGGG 58.549 50.000 13.34 0.00 42.13 4.79
216 544 6.093909 AGCAAAAAGACAAATTCAGGTTTTGG 59.906 34.615 0.00 3.07 38.18 3.28
218 546 5.948742 AAAGACAAATTCAGGTTTTGGGA 57.051 34.783 0.00 0.00 38.18 4.37
221 549 6.499106 AGACAAATTCAGGTTTTGGGAAAT 57.501 33.333 0.00 0.00 38.18 2.17
222 550 6.899089 AGACAAATTCAGGTTTTGGGAAATT 58.101 32.000 0.00 0.00 38.18 1.82
223 551 7.345691 AGACAAATTCAGGTTTTGGGAAATTT 58.654 30.769 0.00 0.00 38.18 1.82
224 552 7.833682 AGACAAATTCAGGTTTTGGGAAATTTT 59.166 29.630 0.00 0.00 38.18 1.82
225 553 8.359875 ACAAATTCAGGTTTTGGGAAATTTTT 57.640 26.923 0.00 0.00 38.18 1.94
226 554 9.467796 ACAAATTCAGGTTTTGGGAAATTTTTA 57.532 25.926 0.00 0.00 38.18 1.52
229 557 9.859152 AATTCAGGTTTTGGGAAATTTTTATGA 57.141 25.926 0.00 0.00 0.00 2.15
230 558 8.900983 TTCAGGTTTTGGGAAATTTTTATGAG 57.099 30.769 0.00 0.00 0.00 2.90
231 559 7.449247 TCAGGTTTTGGGAAATTTTTATGAGG 58.551 34.615 0.00 0.00 0.00 3.86
232 560 7.291182 TCAGGTTTTGGGAAATTTTTATGAGGA 59.709 33.333 0.00 0.00 0.00 3.71
233 561 7.936301 CAGGTTTTGGGAAATTTTTATGAGGAA 59.064 33.333 0.00 0.00 0.00 3.36
234 562 8.156820 AGGTTTTGGGAAATTTTTATGAGGAAG 58.843 33.333 0.00 0.00 0.00 3.46
235 563 7.936847 GGTTTTGGGAAATTTTTATGAGGAAGT 59.063 33.333 0.00 0.00 0.00 3.01
236 564 8.988934 GTTTTGGGAAATTTTTATGAGGAAGTC 58.011 33.333 0.00 0.00 0.00 3.01
263 591 3.851128 GAGTACCCGGGCTCCAGC 61.851 72.222 24.08 4.28 41.14 4.85
280 608 2.896801 GCGTATGGCCCAATGAGCG 61.897 63.158 0.00 0.00 34.80 5.03
304 632 3.822192 CCACATCGACCGAGCGGA 61.822 66.667 16.83 0.00 38.96 5.54
434 793 6.671614 ACTACAACGACTGAATTGTTCAAA 57.328 33.333 0.00 0.00 39.67 2.69
447 806 7.269435 GAATTGTTCAAATCGTCAATTCCAG 57.731 36.000 14.55 0.00 44.51 3.86
448 807 6.573664 ATTGTTCAAATCGTCAATTCCAGA 57.426 33.333 0.00 0.00 0.00 3.86
449 808 5.356882 TGTTCAAATCGTCAATTCCAGAC 57.643 39.130 0.00 0.00 0.00 3.51
450 809 4.819088 TGTTCAAATCGTCAATTCCAGACA 59.181 37.500 0.00 0.00 35.77 3.41
451 810 5.147162 GTTCAAATCGTCAATTCCAGACAC 58.853 41.667 0.00 0.00 35.77 3.67
453 812 4.690748 TCAAATCGTCAATTCCAGACACTC 59.309 41.667 0.00 0.00 35.77 3.51
467 838 9.995003 ATTCCAGACACTCTATAGAAATCAATC 57.005 33.333 3.57 0.00 0.00 2.67
482 853 6.314896 AGAAATCAATCTCTAACTCGGCTTTG 59.685 38.462 0.00 0.00 0.00 2.77
487 858 1.993370 CTCTAACTCGGCTTTGGTTCG 59.007 52.381 0.00 0.00 0.00 3.95
505 876 5.651576 TGGTTCGGTGTACTGTACATACATA 59.348 40.000 22.21 8.24 41.34 2.29
508 879 6.609237 TCGGTGTACTGTACATACATACTC 57.391 41.667 22.21 7.93 41.34 2.59
511 882 6.707608 CGGTGTACTGTACATACATACTCCTA 59.292 42.308 22.21 0.00 41.34 2.94
512 883 7.307632 CGGTGTACTGTACATACATACTCCTAC 60.308 44.444 22.21 5.98 41.34 3.18
513 884 7.040823 GGTGTACTGTACATACATACTCCTACC 60.041 44.444 22.21 10.85 41.34 3.18
514 885 7.000472 TGTACTGTACATACATACTCCTACCC 59.000 42.308 16.26 0.00 35.36 3.69
515 886 5.068636 ACTGTACATACATACTCCTACCCG 58.931 45.833 0.00 0.00 35.36 5.28
516 887 5.052693 TGTACATACATACTCCTACCCGT 57.947 43.478 0.00 0.00 0.00 5.28
517 888 4.823442 TGTACATACATACTCCTACCCGTG 59.177 45.833 0.00 0.00 0.00 4.94
518 889 2.626743 ACATACATACTCCTACCCGTGC 59.373 50.000 0.00 0.00 0.00 5.34
519 890 1.696063 TACATACTCCTACCCGTGCC 58.304 55.000 0.00 0.00 0.00 5.01
520 891 0.324923 ACATACTCCTACCCGTGCCA 60.325 55.000 0.00 0.00 0.00 4.92
521 892 1.048601 CATACTCCTACCCGTGCCAT 58.951 55.000 0.00 0.00 0.00 4.40
522 893 1.048601 ATACTCCTACCCGTGCCATG 58.951 55.000 0.00 0.00 0.00 3.66
523 894 1.682451 TACTCCTACCCGTGCCATGC 61.682 60.000 0.00 0.00 0.00 4.06
524 895 3.757248 CTCCTACCCGTGCCATGCC 62.757 68.421 0.00 0.00 0.00 4.40
525 896 3.797353 CCTACCCGTGCCATGCCT 61.797 66.667 0.00 0.00 0.00 4.75
526 897 2.514592 CTACCCGTGCCATGCCTG 60.515 66.667 0.00 0.00 0.00 4.85
527 898 3.326578 TACCCGTGCCATGCCTGT 61.327 61.111 0.00 0.00 0.00 4.00
553 924 4.341783 GGGACCAGCTGCAGCAGT 62.342 66.667 38.24 32.89 45.16 4.40
560 931 2.031616 GCTGCAGCAGTGTCTCCA 59.968 61.111 33.36 0.00 41.59 3.86
650 1021 3.110178 GTCGTCGGTGCCTTTCGG 61.110 66.667 0.00 0.00 0.00 4.30
727 1113 5.650543 GGAAATACTAAACGTACGGGAAGA 58.349 41.667 21.06 0.15 0.00 2.87
748 1578 8.462811 GGAAGATATGATATCTAGCTGTTTCGA 58.537 37.037 14.86 0.00 0.00 3.71
823 1653 1.659335 GACGGAACTCGACGTGCAA 60.659 57.895 3.34 0.00 44.24 4.08
826 1656 0.732880 CGGAACTCGACGTGCAAGAT 60.733 55.000 6.65 0.00 42.43 2.40
843 1675 4.326817 GCAAGATGCATATTCAAACGCAAA 59.673 37.500 2.96 0.00 44.26 3.68
844 1676 5.499652 GCAAGATGCATATTCAAACGCAAAG 60.500 40.000 2.96 0.00 44.26 2.77
952 1784 4.094684 CGCTTCGGATCTCACCAC 57.905 61.111 0.00 0.00 0.00 4.16
953 1785 1.519455 CGCTTCGGATCTCACCACC 60.519 63.158 0.00 0.00 0.00 4.61
954 1786 1.596934 GCTTCGGATCTCACCACCA 59.403 57.895 0.00 0.00 0.00 4.17
955 1787 0.741221 GCTTCGGATCTCACCACCAC 60.741 60.000 0.00 0.00 0.00 4.16
956 1788 0.898320 CTTCGGATCTCACCACCACT 59.102 55.000 0.00 0.00 0.00 4.00
986 1823 1.745489 GTCCGGCACTCCATTCCAC 60.745 63.158 0.00 0.00 0.00 4.02
997 1834 2.610859 ATTCCACCCCCAGTCGCT 60.611 61.111 0.00 0.00 0.00 4.93
1011 1848 2.101185 CGCTCGATGACGCAGACT 59.899 61.111 0.00 0.00 39.58 3.24
1015 1852 2.278206 CGATGACGCAGACTCCCG 60.278 66.667 0.00 0.00 0.00 5.14
1325 2162 1.412387 GAAGACAACGTACGTGACCC 58.588 55.000 23.57 11.52 0.00 4.46
1403 2240 2.755650 TGGTCTTCTTCTTCTTGTCGC 58.244 47.619 0.00 0.00 0.00 5.19
1493 2330 1.541147 CAAGGTGACGCCATTTGTGAT 59.459 47.619 7.99 0.00 40.61 3.06
1494 2331 1.453155 AGGTGACGCCATTTGTGATC 58.547 50.000 7.99 0.00 40.61 2.92
1495 2332 0.096976 GGTGACGCCATTTGTGATCG 59.903 55.000 0.00 0.00 37.17 3.69
1516 2366 2.231745 CTGCGATCACACGGCTGTTG 62.232 60.000 0.00 0.00 0.00 3.33
1518 2368 1.492873 CGATCACACGGCTGTTGTG 59.507 57.895 17.20 17.20 42.99 3.33
1544 2397 5.117592 TCGCGTTTACTACTAACTTTTCTGC 59.882 40.000 5.77 0.00 0.00 4.26
1545 2398 5.303485 GCGTTTACTACTAACTTTTCTGCG 58.697 41.667 0.00 0.00 0.00 5.18
1548 2401 7.381839 CGTTTACTACTAACTTTTCTGCGATC 58.618 38.462 0.00 0.00 0.00 3.69
1549 2402 7.061441 CGTTTACTACTAACTTTTCTGCGATCA 59.939 37.037 0.00 0.00 0.00 2.92
1688 2574 3.119459 GCTCTGTAACCGAAGATCAGTGA 60.119 47.826 0.00 0.00 0.00 3.41
1689 2575 4.416620 CTCTGTAACCGAAGATCAGTGAC 58.583 47.826 0.00 0.00 0.00 3.67
1690 2576 3.824443 TCTGTAACCGAAGATCAGTGACA 59.176 43.478 0.00 0.00 0.00 3.58
1691 2577 4.082733 TCTGTAACCGAAGATCAGTGACAG 60.083 45.833 12.93 12.93 42.24 3.51
1692 2578 3.572682 TGTAACCGAAGATCAGTGACAGT 59.427 43.478 0.00 0.00 0.00 3.55
1693 2579 2.732412 ACCGAAGATCAGTGACAGTG 57.268 50.000 3.70 3.70 0.00 3.66
1694 2580 1.964223 ACCGAAGATCAGTGACAGTGT 59.036 47.619 10.07 0.00 0.00 3.55
1695 2581 3.154710 ACCGAAGATCAGTGACAGTGTA 58.845 45.455 10.07 0.00 0.00 2.90
1696 2582 3.764434 ACCGAAGATCAGTGACAGTGTAT 59.236 43.478 10.07 3.06 0.00 2.29
1697 2583 4.108336 CCGAAGATCAGTGACAGTGTATG 58.892 47.826 10.07 0.00 0.00 2.39
1729 2625 6.749139 TGCTAGTATTAGTCATGATGTGTCC 58.251 40.000 0.00 0.00 0.00 4.02
1766 2662 2.229062 GGAGACAGTCGACATCAGAACA 59.771 50.000 19.50 0.00 0.00 3.18
1769 2665 3.256879 AGACAGTCGACATCAGAACATGT 59.743 43.478 19.50 9.66 39.84 3.21
1775 2671 2.347755 CGACATCAGAACATGTGAGCAG 59.652 50.000 0.00 0.00 37.11 4.24
1812 2708 7.479579 AGCAAGTTCCTGGAGAGGTATATATA 58.520 38.462 0.00 0.00 40.76 0.86
1814 2710 7.178628 GCAAGTTCCTGGAGAGGTATATATACA 59.821 40.741 21.56 2.49 40.76 2.29
1816 2712 9.482175 AAGTTCCTGGAGAGGTATATATACATC 57.518 37.037 23.70 23.70 42.56 3.06
1817 2713 8.624670 AGTTCCTGGAGAGGTATATATACATCA 58.375 37.037 29.45 15.26 44.11 3.07
1845 2741 0.250513 GCTCTCCCTCGTGGACAATT 59.749 55.000 4.76 0.00 38.61 2.32
1880 2776 2.415090 GCTCATTGTGTTCCATCTGTGC 60.415 50.000 0.00 0.00 0.00 4.57
1881 2777 2.161855 TCATTGTGTTCCATCTGTGCC 58.838 47.619 0.00 0.00 0.00 5.01
1882 2778 1.203052 CATTGTGTTCCATCTGTGCCC 59.797 52.381 0.00 0.00 0.00 5.36
1884 2780 0.405198 TGTGTTCCATCTGTGCCCAT 59.595 50.000 0.00 0.00 0.00 4.00
1890 2798 1.524002 CATCTGTGCCCATCGACCT 59.476 57.895 0.00 0.00 0.00 3.85
1942 2850 2.352422 GCTCCTGCATCCACCACA 59.648 61.111 0.00 0.00 39.41 4.17
2003 2911 1.435105 GGTACGCTACCTCCGTTCC 59.565 63.158 6.87 0.00 45.52 3.62
2004 2912 1.315257 GGTACGCTACCTCCGTTCCA 61.315 60.000 5.00 0.00 45.52 3.53
2005 2913 0.527565 GTACGCTACCTCCGTTCCAA 59.472 55.000 0.00 0.00 39.88 3.53
2006 2914 1.067635 GTACGCTACCTCCGTTCCAAA 60.068 52.381 0.00 0.00 39.88 3.28
2007 2915 0.393820 ACGCTACCTCCGTTCCAAAA 59.606 50.000 0.00 0.00 34.96 2.44
2008 2916 1.002773 ACGCTACCTCCGTTCCAAAAT 59.997 47.619 0.00 0.00 34.96 1.82
2009 2917 2.234414 ACGCTACCTCCGTTCCAAAATA 59.766 45.455 0.00 0.00 34.96 1.40
2010 2918 2.606272 CGCTACCTCCGTTCCAAAATAC 59.394 50.000 0.00 0.00 0.00 1.89
2011 2919 3.602483 GCTACCTCCGTTCCAAAATACA 58.398 45.455 0.00 0.00 0.00 2.29
2012 2920 4.196971 GCTACCTCCGTTCCAAAATACAT 58.803 43.478 0.00 0.00 0.00 2.29
2013 2921 4.272748 GCTACCTCCGTTCCAAAATACATC 59.727 45.833 0.00 0.00 0.00 3.06
2014 2922 4.569719 ACCTCCGTTCCAAAATACATCT 57.430 40.909 0.00 0.00 0.00 2.90
2015 2923 5.687166 ACCTCCGTTCCAAAATACATCTA 57.313 39.130 0.00 0.00 0.00 1.98
2016 2924 6.248569 ACCTCCGTTCCAAAATACATCTAT 57.751 37.500 0.00 0.00 0.00 1.98
2017 2925 6.659824 ACCTCCGTTCCAAAATACATCTATT 58.340 36.000 0.00 0.00 0.00 1.73
2018 2926 7.116736 ACCTCCGTTCCAAAATACATCTATTT 58.883 34.615 0.00 0.00 34.54 1.40
2019 2927 7.614192 ACCTCCGTTCCAAAATACATCTATTTT 59.386 33.333 0.00 0.00 41.40 1.82
2030 2938 7.568199 AATACATCTATTTTGAAACGGAGGG 57.432 36.000 0.00 0.00 0.00 4.30
2031 2939 5.174037 ACATCTATTTTGAAACGGAGGGA 57.826 39.130 0.00 0.00 0.00 4.20
2032 2940 5.186198 ACATCTATTTTGAAACGGAGGGAG 58.814 41.667 0.00 0.00 0.00 4.30
2033 2941 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
2037 2945 4.426736 TTTTGAAACGGAGGGAGTAGTT 57.573 40.909 0.00 0.00 0.00 2.24
2054 2962 6.812160 GGAGTAGTTACGATCAACAACATTCT 59.188 38.462 0.00 0.00 0.00 2.40
2090 2998 1.570813 CAGTGAAGCACAACGACAGA 58.429 50.000 0.00 0.00 36.74 3.41
2091 2999 1.524355 CAGTGAAGCACAACGACAGAG 59.476 52.381 0.00 0.00 36.74 3.35
2101 3009 3.243877 CACAACGACAGAGTTCTGAACAG 59.756 47.826 21.50 13.18 46.59 3.16
2102 3010 2.141535 ACGACAGAGTTCTGAACAGC 57.858 50.000 21.50 13.06 46.59 4.40
2103 3011 1.683917 ACGACAGAGTTCTGAACAGCT 59.316 47.619 21.50 14.93 46.59 4.24
2104 3012 2.885266 ACGACAGAGTTCTGAACAGCTA 59.115 45.455 21.50 0.00 46.59 3.32
2105 3013 3.508012 ACGACAGAGTTCTGAACAGCTAT 59.492 43.478 21.50 8.39 46.59 2.97
2106 3014 4.700692 ACGACAGAGTTCTGAACAGCTATA 59.299 41.667 21.50 0.00 46.59 1.31
2107 3015 5.031578 CGACAGAGTTCTGAACAGCTATAC 58.968 45.833 21.50 11.25 46.59 1.47
2108 3016 4.987832 ACAGAGTTCTGAACAGCTATACG 58.012 43.478 21.50 9.25 46.59 3.06
2109 3017 4.142359 ACAGAGTTCTGAACAGCTATACGG 60.142 45.833 21.50 8.95 46.59 4.02
2110 3018 4.017808 AGAGTTCTGAACAGCTATACGGT 58.982 43.478 21.50 0.00 0.00 4.83
2111 3019 5.066117 CAGAGTTCTGAACAGCTATACGGTA 59.934 44.000 21.50 0.00 46.59 4.02
2117 3025 5.296283 TCTGAACAGCTATACGGTACTTCTC 59.704 44.000 0.00 0.00 0.00 2.87
2191 3099 4.552365 ATGACCCCGCGCCTCATG 62.552 66.667 0.00 0.00 0.00 3.07
2431 3339 1.377202 GTCCTCTGCGGCCAATTCA 60.377 57.895 2.24 0.00 0.00 2.57
2466 3379 3.075884 ACTCAGTCTCAGGTACTCGAAC 58.924 50.000 0.00 0.00 34.60 3.95
2478 3391 7.753531 CAGGTACTCGAACGAACGTTCTTCT 62.754 48.000 28.36 16.75 44.72 2.85
2502 3415 2.727123 TTTGTTCCAGGAGTTCAGCA 57.273 45.000 0.00 0.00 0.00 4.41
2503 3416 2.957402 TTGTTCCAGGAGTTCAGCAT 57.043 45.000 0.00 0.00 0.00 3.79
2504 3417 2.957402 TGTTCCAGGAGTTCAGCATT 57.043 45.000 0.00 0.00 0.00 3.56
2505 3418 2.783135 TGTTCCAGGAGTTCAGCATTC 58.217 47.619 0.00 0.00 0.00 2.67
2542 3472 6.306199 TGGAGATTGTTCTTCATTTTCTCCA 58.694 36.000 13.28 13.28 44.84 3.86
2544 3474 6.207417 GGAGATTGTTCTTCATTTTCTCCACA 59.793 38.462 10.41 0.00 41.51 4.17
2545 3475 6.974965 AGATTGTTCTTCATTTTCTCCACAC 58.025 36.000 0.00 0.00 0.00 3.82
2551 3483 7.040478 TGTTCTTCATTTTCTCCACACATAAGG 60.040 37.037 0.00 0.00 0.00 2.69
2560 3492 3.395639 TCCACACATAAGGACGTTGTTC 58.604 45.455 0.00 0.00 0.00 3.18
2565 3497 4.750098 ACACATAAGGACGTTGTTCTTCTG 59.250 41.667 0.00 0.00 32.99 3.02
2566 3498 4.152402 CACATAAGGACGTTGTTCTTCTGG 59.848 45.833 7.88 0.00 31.94 3.86
2567 3499 2.256117 AAGGACGTTGTTCTTCTGGG 57.744 50.000 0.00 0.00 0.00 4.45
2588 3524 3.067074 TTTTTCAGGACGCACGACA 57.933 47.368 0.00 0.00 0.00 4.35
2630 3566 0.034337 TCCGTCAAGCAAGGTACCAC 59.966 55.000 15.94 2.82 0.00 4.16
2644 3589 0.904649 TACCACTCGGTACCTCTCGA 59.095 55.000 10.90 0.79 46.71 4.04
2692 3665 3.431415 GGCAACAACTTATTTCCCTCCT 58.569 45.455 0.00 0.00 0.00 3.69
2693 3666 3.444034 GGCAACAACTTATTTCCCTCCTC 59.556 47.826 0.00 0.00 0.00 3.71
2694 3667 4.336280 GCAACAACTTATTTCCCTCCTCT 58.664 43.478 0.00 0.00 0.00 3.69
2695 3668 4.396478 GCAACAACTTATTTCCCTCCTCTC 59.604 45.833 0.00 0.00 0.00 3.20
2696 3669 5.804771 GCAACAACTTATTTCCCTCCTCTCT 60.805 44.000 0.00 0.00 0.00 3.10
2697 3670 6.241645 CAACAACTTATTTCCCTCCTCTCTT 58.758 40.000 0.00 0.00 0.00 2.85
2698 3671 6.455690 ACAACTTATTTCCCTCCTCTCTTT 57.544 37.500 0.00 0.00 0.00 2.52
2699 3672 6.853490 ACAACTTATTTCCCTCCTCTCTTTT 58.147 36.000 0.00 0.00 0.00 2.27
2733 3706 4.056125 CGCAGGAGCCGTCTGTCA 62.056 66.667 0.00 0.00 37.52 3.58
2775 3748 0.674581 TCGCCAACATCAAGGAGCTG 60.675 55.000 0.00 0.00 0.00 4.24
2862 3847 4.655762 TTCGGATACAGATCTTGAGGTG 57.344 45.455 0.00 0.00 32.15 4.00
2958 3952 2.402564 CTCCTCTCATTTCAGGGCCTA 58.597 52.381 5.28 0.00 0.00 3.93
3041 4061 2.143008 TGCAATGCAGCAAGTGAAAG 57.857 45.000 2.72 0.00 42.46 2.62
3134 4389 1.000233 TACGAAGAACTGCACGCGTC 61.000 55.000 9.86 5.12 33.69 5.19
3138 4393 0.027586 AAGAACTGCACGCGTCAAAC 59.972 50.000 9.86 0.00 0.00 2.93
3139 4394 1.087202 AGAACTGCACGCGTCAAACA 61.087 50.000 9.86 4.53 0.00 2.83
3140 4395 0.041312 GAACTGCACGCGTCAAACAT 60.041 50.000 9.86 0.00 0.00 2.71
3141 4396 1.193650 GAACTGCACGCGTCAAACATA 59.806 47.619 9.86 0.00 0.00 2.29
3144 4399 1.969256 CTGCACGCGTCAAACATAAAC 59.031 47.619 9.86 0.00 0.00 2.01
3145 4400 1.323791 GCACGCGTCAAACATAAACC 58.676 50.000 9.86 0.00 0.00 3.27
3160 4415 1.846712 AAACCCCTGGAGCAGCTCTC 61.847 60.000 21.99 12.48 41.15 3.20
3173 4428 1.446966 GCTCTCCTGCGTTCCAGAC 60.447 63.158 0.00 0.00 44.64 3.51
3246 4503 2.888212 TGGAAAACAGATCAAAGGGGG 58.112 47.619 0.00 0.00 0.00 5.40
3247 4504 2.178984 TGGAAAACAGATCAAAGGGGGT 59.821 45.455 0.00 0.00 0.00 4.95
3248 4505 2.826128 GGAAAACAGATCAAAGGGGGTC 59.174 50.000 0.00 0.00 0.00 4.46
3249 4506 3.496331 GAAAACAGATCAAAGGGGGTCA 58.504 45.455 0.00 0.00 0.00 4.02
3250 4507 3.833559 AAACAGATCAAAGGGGGTCAT 57.166 42.857 0.00 0.00 0.00 3.06
3251 4508 2.814805 ACAGATCAAAGGGGGTCATG 57.185 50.000 0.00 0.00 0.00 3.07
3252 4509 1.995542 ACAGATCAAAGGGGGTCATGT 59.004 47.619 0.00 0.00 0.00 3.21
3253 4510 2.291153 ACAGATCAAAGGGGGTCATGTG 60.291 50.000 0.00 0.00 0.00 3.21
3254 4511 1.106285 GATCAAAGGGGGTCATGTGC 58.894 55.000 0.00 0.00 0.00 4.57
3278 4535 4.389992 GTCACACATGGTAGTGATCACAAG 59.610 45.833 27.02 11.99 45.46 3.16
3283 4540 3.769739 TGGTAGTGATCACAAGCAGTT 57.230 42.857 27.02 7.64 0.00 3.16
3284 4541 3.402110 TGGTAGTGATCACAAGCAGTTG 58.598 45.455 27.02 0.00 39.82 3.16
3339 4602 7.121315 AGGGTTTACTTGCAATGATAAGAGAAC 59.879 37.037 0.00 0.00 0.00 3.01
3382 4645 6.097915 TCTGAAAGTCAAGAAGAATACCGT 57.902 37.500 0.00 0.00 33.76 4.83
3413 4683 6.400579 TTCAGAGTCGTAAGTCGTAACTAG 57.599 41.667 0.00 0.00 40.80 2.57
3487 4757 0.952280 TCTCAGTGTCAGTGGTCGAC 59.048 55.000 7.13 7.13 0.00 4.20
3626 4896 5.310409 ACTTCTGGATTATGTACATGGGG 57.690 43.478 18.81 3.23 0.00 4.96
3681 4951 7.902920 AGTTTTACTCGGGGAGTATATGTAA 57.097 36.000 6.34 0.00 43.45 2.41
3725 4996 4.646492 GGATGATGTTTTTGTAGATGGGCT 59.354 41.667 0.00 0.00 0.00 5.19
3758 5029 3.070734 TGCATCTGCTATTCTTCTCCTCC 59.929 47.826 3.53 0.00 42.66 4.30
3940 5211 6.809869 TCAGAGTCATCGATGTGATATTTGT 58.190 36.000 24.09 0.91 34.83 2.83
3958 5229 8.737168 ATATTTGTCACATAGTTACATGCTGT 57.263 30.769 0.00 0.00 0.00 4.40
3959 5230 6.480524 TTTGTCACATAGTTACATGCTGTC 57.519 37.500 0.00 0.00 0.00 3.51
3963 5234 4.929211 TCACATAGTTACATGCTGTCACAC 59.071 41.667 0.00 0.00 27.41 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 6.759827 AGTGTCGCTTTTCTTCTTTGTTAGTA 59.240 34.615 0.00 0.00 0.00 1.82
58 60 0.850856 AACGTCGAGTGTCGCTTTTC 59.149 50.000 0.00 0.00 40.21 2.29
90 92 3.565307 AGCAAAGGAGAAATCACCACAA 58.435 40.909 0.00 0.00 0.00 3.33
228 556 5.068067 GGTACTCCTTATGTGAGACTTCCTC 59.932 48.000 0.00 0.00 42.30 3.71
229 557 4.957327 GGTACTCCTTATGTGAGACTTCCT 59.043 45.833 0.00 0.00 33.95 3.36
230 558 4.099727 GGGTACTCCTTATGTGAGACTTCC 59.900 50.000 0.00 0.00 33.95 3.46
231 559 4.202030 CGGGTACTCCTTATGTGAGACTTC 60.202 50.000 0.00 0.00 33.95 3.01
232 560 3.700038 CGGGTACTCCTTATGTGAGACTT 59.300 47.826 0.00 0.00 33.95 3.01
233 561 3.288964 CGGGTACTCCTTATGTGAGACT 58.711 50.000 0.00 0.00 33.95 3.24
234 562 2.361438 CCGGGTACTCCTTATGTGAGAC 59.639 54.545 0.00 0.00 33.95 3.36
235 563 2.662866 CCGGGTACTCCTTATGTGAGA 58.337 52.381 0.00 0.00 33.95 3.27
236 564 1.687123 CCCGGGTACTCCTTATGTGAG 59.313 57.143 14.18 0.00 35.92 3.51
261 589 1.526917 GCTCATTGGGCCATACGCT 60.527 57.895 7.26 0.00 37.74 5.07
263 591 0.603707 ATCGCTCATTGGGCCATACG 60.604 55.000 7.26 7.46 0.00 3.06
280 608 1.592669 CGGTCGATGTGGGCTCATC 60.593 63.158 0.00 11.20 40.29 2.92
312 663 1.207089 TGGCGAGTTCCTTGTATCCAG 59.793 52.381 0.00 0.00 0.00 3.86
434 793 5.860941 ATAGAGTGTCTGGAATTGACGAT 57.139 39.130 0.00 0.00 37.26 3.73
453 812 8.519526 AGCCGAGTTAGAGATTGATTTCTATAG 58.480 37.037 0.00 0.00 0.00 1.31
467 838 1.993370 CGAACCAAAGCCGAGTTAGAG 59.007 52.381 0.00 0.00 0.00 2.43
472 843 1.597027 CACCGAACCAAAGCCGAGT 60.597 57.895 0.00 0.00 0.00 4.18
476 847 0.872388 CAGTACACCGAACCAAAGCC 59.128 55.000 0.00 0.00 0.00 4.35
482 853 4.439305 TGTATGTACAGTACACCGAACC 57.561 45.455 15.89 1.69 42.23 3.62
487 858 6.956202 AGGAGTATGTATGTACAGTACACC 57.044 41.667 15.89 9.68 42.23 4.16
505 876 3.031417 GCATGGCACGGGTAGGAGT 62.031 63.158 0.00 0.00 0.00 3.85
508 879 3.797353 AGGCATGGCACGGGTAGG 61.797 66.667 22.64 0.00 0.00 3.18
511 882 4.284550 AACAGGCATGGCACGGGT 62.285 61.111 22.64 10.75 0.00 5.28
512 883 3.751246 CAACAGGCATGGCACGGG 61.751 66.667 22.64 10.10 0.00 5.28
513 884 4.424566 GCAACAGGCATGGCACGG 62.425 66.667 22.64 12.63 43.97 4.94
515 886 3.304721 TGGCAACAGGCATGGCAC 61.305 61.111 22.64 4.96 46.85 5.01
526 897 2.564721 GCTGGTCCCAACTGGCAAC 61.565 63.158 0.00 0.00 0.00 4.17
527 898 2.203480 GCTGGTCCCAACTGGCAA 60.203 61.111 0.00 0.00 0.00 4.52
560 931 1.829533 GTCCGGGCATGCCATTCAT 60.830 57.895 36.56 0.00 37.98 2.57
650 1021 0.528684 GATGTACTGCTGGTCGCTCC 60.529 60.000 0.00 0.00 40.11 4.70
727 1113 7.397476 TCCCTTCGAAACAGCTAGATATCATAT 59.603 37.037 5.32 0.00 0.00 1.78
748 1578 4.533815 GGGGAAGATACGAAAAATCCCTT 58.466 43.478 16.03 0.00 44.81 3.95
823 1653 4.107622 GCTTTGCGTTTGAATATGCATCT 58.892 39.130 0.19 0.00 39.60 2.90
951 1783 1.751349 GACGTGGTGGTGGTAGTGGT 61.751 60.000 0.00 0.00 0.00 4.16
952 1784 1.005394 GACGTGGTGGTGGTAGTGG 60.005 63.158 0.00 0.00 0.00 4.00
953 1785 1.005394 GGACGTGGTGGTGGTAGTG 60.005 63.158 0.00 0.00 0.00 2.74
954 1786 2.567497 CGGACGTGGTGGTGGTAGT 61.567 63.158 0.00 0.00 0.00 2.73
955 1787 2.260434 CGGACGTGGTGGTGGTAG 59.740 66.667 0.00 0.00 0.00 3.18
956 1788 3.304721 CCGGACGTGGTGGTGGTA 61.305 66.667 0.00 0.00 0.00 3.25
986 1823 3.147595 TCATCGAGCGACTGGGGG 61.148 66.667 0.00 0.00 0.00 5.40
997 1834 2.761195 CGGGAGTCTGCGTCATCGA 61.761 63.158 0.00 0.00 39.71 3.59
1308 2145 1.662044 GGGGTCACGTACGTTGTCT 59.338 57.895 20.23 0.00 0.00 3.41
1403 2240 1.471676 CCTTCACCAGCTTAGCCTACG 60.472 57.143 0.00 0.00 0.00 3.51
1495 2332 2.125912 AGCCGTGTGATCGCAGAC 60.126 61.111 9.75 2.05 42.51 3.51
1516 2366 3.496155 AGTTAGTAGTAAACGCGAGCAC 58.504 45.455 15.93 6.89 32.00 4.40
1518 2368 5.344396 AGAAAAGTTAGTAGTAAACGCGAGC 59.656 40.000 15.93 0.00 32.00 5.03
1544 2397 0.671472 TCCAGCTGCAAGTGTGATCG 60.671 55.000 8.66 0.00 35.30 3.69
1545 2398 1.085091 CTCCAGCTGCAAGTGTGATC 58.915 55.000 8.66 0.00 35.30 2.92
1548 2401 0.533531 TGTCTCCAGCTGCAAGTGTG 60.534 55.000 8.66 0.00 35.30 3.82
1549 2402 0.399454 ATGTCTCCAGCTGCAAGTGT 59.601 50.000 8.66 0.00 35.30 3.55
1666 2552 3.119459 TCACTGATCTTCGGTTACAGAGC 60.119 47.826 0.00 0.00 32.75 4.09
1729 2625 2.164219 GTCTCCTGACTCTGCAGAGAAG 59.836 54.545 42.76 34.85 44.74 2.85
1754 2650 2.340337 TGCTCACATGTTCTGATGTCG 58.660 47.619 0.00 0.00 34.18 4.35
1766 2662 2.125912 GCGACCGACTGCTCACAT 60.126 61.111 0.00 0.00 0.00 3.21
1769 2665 3.158537 TTTGGCGACCGACTGCTCA 62.159 57.895 0.00 0.00 0.00 4.26
1775 2671 1.782028 AACTTGCTTTGGCGACCGAC 61.782 55.000 0.00 0.00 42.25 4.79
1812 2708 2.104451 GGGAGAGCAGTGATCATGATGT 59.896 50.000 14.30 0.00 0.00 3.06
1814 2710 2.633967 GAGGGAGAGCAGTGATCATGAT 59.366 50.000 8.25 8.25 0.00 2.45
1816 2712 1.269673 CGAGGGAGAGCAGTGATCATG 60.270 57.143 11.60 0.00 0.00 3.07
1817 2713 1.039068 CGAGGGAGAGCAGTGATCAT 58.961 55.000 11.60 0.00 0.00 2.45
1845 2741 4.874396 CACAATGAGCTGCTAGAGATGAAA 59.126 41.667 0.15 0.00 0.00 2.69
1880 2776 2.762459 TTCGGGGAGGTCGATGGG 60.762 66.667 0.00 0.00 36.49 4.00
1881 2777 1.756950 TCTTCGGGGAGGTCGATGG 60.757 63.158 0.00 0.00 36.49 3.51
1882 2778 1.437986 GTCTTCGGGGAGGTCGATG 59.562 63.158 0.00 0.00 36.49 3.84
1884 2780 2.749044 CGTCTTCGGGGAGGTCGA 60.749 66.667 0.00 0.00 34.62 4.20
1942 2850 2.772691 GGAAGATCCGTCGGCTCGT 61.773 63.158 6.34 4.56 0.00 4.18
1989 2897 1.734163 ATTTTGGAACGGAGGTAGCG 58.266 50.000 0.00 0.00 0.00 4.26
1992 2900 5.687166 AGATGTATTTTGGAACGGAGGTA 57.313 39.130 0.00 0.00 0.00 3.08
1993 2901 4.569719 AGATGTATTTTGGAACGGAGGT 57.430 40.909 0.00 0.00 0.00 3.85
1994 2902 7.568199 AAATAGATGTATTTTGGAACGGAGG 57.432 36.000 2.10 0.00 35.66 4.30
2004 2912 8.466798 CCCTCCGTTTCAAAATAGATGTATTTT 58.533 33.333 13.35 13.35 45.75 1.82
2005 2913 7.832187 TCCCTCCGTTTCAAAATAGATGTATTT 59.168 33.333 2.10 2.10 40.04 1.40
2006 2914 7.343357 TCCCTCCGTTTCAAAATAGATGTATT 58.657 34.615 0.00 0.00 0.00 1.89
2007 2915 6.895782 TCCCTCCGTTTCAAAATAGATGTAT 58.104 36.000 0.00 0.00 0.00 2.29
2008 2916 6.070424 ACTCCCTCCGTTTCAAAATAGATGTA 60.070 38.462 0.00 0.00 0.00 2.29
2009 2917 5.174037 TCCCTCCGTTTCAAAATAGATGT 57.826 39.130 0.00 0.00 0.00 3.06
2010 2918 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
2011 2919 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
2012 2920 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
2013 2921 5.731591 ACTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
2014 2922 5.750352 ACTACTCCCTCCGTTTCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
2015 2923 4.635699 ACTACTCCCTCCGTTTCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
2016 2924 4.426736 AACTACTCCCTCCGTTTCAAAA 57.573 40.909 0.00 0.00 0.00 2.44
2017 2925 4.559300 CGTAACTACTCCCTCCGTTTCAAA 60.559 45.833 0.00 0.00 0.00 2.69
2018 2926 3.057315 CGTAACTACTCCCTCCGTTTCAA 60.057 47.826 0.00 0.00 0.00 2.69
2019 2927 2.489329 CGTAACTACTCCCTCCGTTTCA 59.511 50.000 0.00 0.00 0.00 2.69
2020 2928 2.749621 TCGTAACTACTCCCTCCGTTTC 59.250 50.000 0.00 0.00 0.00 2.78
2021 2929 2.795329 TCGTAACTACTCCCTCCGTTT 58.205 47.619 0.00 0.00 0.00 3.60
2022 2930 2.496899 TCGTAACTACTCCCTCCGTT 57.503 50.000 0.00 0.00 0.00 4.44
2023 2931 2.092753 TGATCGTAACTACTCCCTCCGT 60.093 50.000 0.00 0.00 0.00 4.69
2024 2932 2.569059 TGATCGTAACTACTCCCTCCG 58.431 52.381 0.00 0.00 0.00 4.63
2025 2933 3.698040 TGTTGATCGTAACTACTCCCTCC 59.302 47.826 0.00 0.00 0.00 4.30
2026 2934 4.978083 TGTTGATCGTAACTACTCCCTC 57.022 45.455 0.00 0.00 0.00 4.30
2027 2935 4.525487 TGTTGTTGATCGTAACTACTCCCT 59.475 41.667 10.32 0.00 37.26 4.20
2028 2936 4.813027 TGTTGTTGATCGTAACTACTCCC 58.187 43.478 10.32 0.00 37.26 4.30
2029 2937 6.812160 AGAATGTTGTTGATCGTAACTACTCC 59.188 38.462 10.32 2.84 37.26 3.85
2030 2938 7.813852 AGAATGTTGTTGATCGTAACTACTC 57.186 36.000 10.32 3.44 37.26 2.59
2031 2939 8.521176 AGTAGAATGTTGTTGATCGTAACTACT 58.479 33.333 10.32 0.00 37.26 2.57
2032 2940 8.684973 AGTAGAATGTTGTTGATCGTAACTAC 57.315 34.615 0.00 0.00 37.00 2.73
2059 2967 7.254421 CGTTGTGCTTCACTGCAGATAATATTA 60.254 37.037 23.35 0.00 44.20 0.98
2060 2968 6.457392 CGTTGTGCTTCACTGCAGATAATATT 60.457 38.462 23.35 0.00 44.20 1.28
2062 2970 4.329801 CGTTGTGCTTCACTGCAGATAATA 59.670 41.667 23.35 3.61 44.20 0.98
2063 2971 3.125829 CGTTGTGCTTCACTGCAGATAAT 59.874 43.478 23.35 0.00 44.20 1.28
2064 2972 2.480037 CGTTGTGCTTCACTGCAGATAA 59.520 45.455 23.35 12.71 44.20 1.75
2076 2984 2.159099 TCAGAACTCTGTCGTTGTGCTT 60.159 45.455 6.61 0.00 44.12 3.91
2090 2998 4.948621 AGTACCGTATAGCTGTTCAGAACT 59.051 41.667 14.51 0.00 0.00 3.01
2091 2999 5.246145 AGTACCGTATAGCTGTTCAGAAC 57.754 43.478 6.32 6.32 0.00 3.01
2101 3009 5.035443 CACACAAGAGAAGTACCGTATAGC 58.965 45.833 0.00 0.00 0.00 2.97
2102 3010 5.035443 GCACACAAGAGAAGTACCGTATAG 58.965 45.833 0.00 0.00 0.00 1.31
2103 3011 4.460034 TGCACACAAGAGAAGTACCGTATA 59.540 41.667 0.00 0.00 0.00 1.47
2104 3012 3.257375 TGCACACAAGAGAAGTACCGTAT 59.743 43.478 0.00 0.00 0.00 3.06
2105 3013 2.624364 TGCACACAAGAGAAGTACCGTA 59.376 45.455 0.00 0.00 0.00 4.02
2106 3014 1.411246 TGCACACAAGAGAAGTACCGT 59.589 47.619 0.00 0.00 0.00 4.83
2107 3015 1.792949 GTGCACACAAGAGAAGTACCG 59.207 52.381 13.17 0.00 0.00 4.02
2108 3016 1.792949 CGTGCACACAAGAGAAGTACC 59.207 52.381 18.64 0.00 0.00 3.34
2109 3017 2.470821 ACGTGCACACAAGAGAAGTAC 58.529 47.619 18.64 0.00 0.00 2.73
2110 3018 2.863740 CAACGTGCACACAAGAGAAGTA 59.136 45.455 18.64 0.00 0.00 2.24
2111 3019 1.665679 CAACGTGCACACAAGAGAAGT 59.334 47.619 18.64 0.00 0.00 3.01
2117 3025 0.726827 ACTGTCAACGTGCACACAAG 59.273 50.000 18.64 9.61 0.00 3.16
2201 3109 3.760035 GGACCTCTGCTTCGGCGA 61.760 66.667 4.99 4.99 45.37 5.54
2284 3192 0.257039 TGGAGTACCGTCTAGGGGAC 59.743 60.000 7.63 0.30 46.96 4.46
2486 3399 2.746362 CTGAATGCTGAACTCCTGGAAC 59.254 50.000 0.00 0.00 0.00 3.62
2487 3400 2.877300 GCTGAATGCTGAACTCCTGGAA 60.877 50.000 0.00 0.00 38.95 3.53
2489 3402 1.093159 GCTGAATGCTGAACTCCTGG 58.907 55.000 0.00 0.00 38.95 4.45
2501 3414 2.864946 CTCCAGATGAACGAGCTGAATG 59.135 50.000 0.00 0.00 40.87 2.67
2502 3415 2.762887 TCTCCAGATGAACGAGCTGAAT 59.237 45.455 0.00 0.00 40.87 2.57
2503 3416 2.171003 TCTCCAGATGAACGAGCTGAA 58.829 47.619 0.00 0.00 40.87 3.02
2504 3417 1.839424 TCTCCAGATGAACGAGCTGA 58.161 50.000 0.00 0.00 40.87 4.26
2505 3418 2.864946 CAATCTCCAGATGAACGAGCTG 59.135 50.000 0.00 0.00 37.87 4.24
2511 3441 6.998968 ATGAAGAACAATCTCCAGATGAAC 57.001 37.500 0.00 0.00 33.77 3.18
2542 3472 4.750098 CAGAAGAACAACGTCCTTATGTGT 59.250 41.667 0.00 0.00 0.00 3.72
2544 3474 4.315803 CCAGAAGAACAACGTCCTTATGT 58.684 43.478 0.00 0.00 29.87 2.29
2545 3475 3.684788 CCCAGAAGAACAACGTCCTTATG 59.315 47.826 0.00 0.00 0.00 1.90
2551 3483 1.963172 AACCCCAGAAGAACAACGTC 58.037 50.000 0.00 0.00 0.00 4.34
2579 3515 1.202417 CCATCTATCCTTGTCGTGCGT 60.202 52.381 0.00 0.00 0.00 5.24
2588 3524 4.043596 AGAACTCCTTGCCATCTATCCTT 58.956 43.478 0.00 0.00 0.00 3.36
2630 3566 3.505464 AACAAATCGAGAGGTACCGAG 57.495 47.619 6.18 0.00 38.25 4.63
2708 3681 2.899339 GGCTCCTGCGGATGAAGC 60.899 66.667 0.00 0.00 40.82 3.86
2733 3706 3.058224 GGAAAGCAGCAAACTGTTCGTAT 60.058 43.478 0.00 0.00 46.30 3.06
2775 3748 1.648467 GGGATTGCCTGTGAGCGTTC 61.648 60.000 0.00 0.00 34.65 3.95
2862 3847 3.875134 GCACCACCACACCAATATAGTAC 59.125 47.826 0.00 0.00 0.00 2.73
2958 3952 2.266055 GTGAGGCTGCGGCTAAGT 59.734 61.111 18.85 0.00 38.98 2.24
2967 3961 0.859232 GTGTGTGTTACGTGAGGCTG 59.141 55.000 0.00 0.00 0.00 4.85
3041 4061 5.295431 TCTGCATACAAAGTGCACATAAC 57.705 39.130 21.04 0.28 46.76 1.89
3075 4095 8.900511 TGATTATTCTTTTCTTTTGCGATGAG 57.099 30.769 0.00 0.00 0.00 2.90
3134 4389 2.493278 CTGCTCCAGGGGTTTATGTTTG 59.507 50.000 0.00 0.00 0.00 2.93
3138 4393 0.257039 AGCTGCTCCAGGGGTTTATG 59.743 55.000 0.00 0.00 31.21 1.90
3139 4394 0.548510 GAGCTGCTCCAGGGGTTTAT 59.451 55.000 18.80 0.00 31.21 1.40
3140 4395 0.547712 AGAGCTGCTCCAGGGGTTTA 60.548 55.000 25.09 0.00 31.21 2.01
3141 4396 1.846712 GAGAGCTGCTCCAGGGGTTT 61.847 60.000 25.09 4.73 37.69 3.27
3251 4508 2.930887 ATCACTACCATGTGTGACGCAC 60.931 50.000 12.29 12.29 44.52 5.34
3252 4509 0.676736 TCACTACCATGTGTGACGCA 59.323 50.000 0.00 0.00 38.15 5.24
3253 4510 1.927174 GATCACTACCATGTGTGACGC 59.073 52.381 13.23 0.00 44.52 5.19
3254 4511 2.923655 GTGATCACTACCATGTGTGACG 59.076 50.000 18.83 0.00 44.52 4.35
3295 4558 1.069022 CCTGTTCAATCTTGGTGCGTG 60.069 52.381 0.00 0.00 0.00 5.34
3296 4559 1.238439 CCTGTTCAATCTTGGTGCGT 58.762 50.000 0.00 0.00 0.00 5.24
3339 4602 5.869344 TCAGAATCTGAATTGTAGTGGTTCG 59.131 40.000 10.99 0.00 37.57 3.95
3374 4637 5.411781 ACTCTGAATGTGAAGACGGTATTC 58.588 41.667 8.50 8.50 0.00 1.75
3382 4645 5.617087 CGACTTACGACTCTGAATGTGAAGA 60.617 44.000 0.00 0.00 45.77 2.87
3413 4683 3.428589 GGTTGAAATCTGGCATCTGCTTC 60.429 47.826 1.70 0.00 41.70 3.86
3681 4951 5.815581 TCCTGCCTTACAGTCACATAAAAT 58.184 37.500 0.00 0.00 45.68 1.82
3725 4996 1.663379 GCAGATGCAAGCTCATGGCA 61.663 55.000 0.00 5.04 41.58 4.92
3758 5029 3.018149 ACGCTAACTAAGAGGGAGTGAG 58.982 50.000 0.00 0.00 0.00 3.51
3951 5222 3.044235 TCCTACTTGTGTGACAGCATG 57.956 47.619 0.00 0.00 46.00 4.06
3952 5223 3.769739 TTCCTACTTGTGTGACAGCAT 57.230 42.857 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.