Multiple sequence alignment - TraesCS7A01G144100

Loading Multiple Alignment...

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 TraesCS7A01G144100 chr7A 100.000 8850 0 0 1 8850 94913805 94922654 0.000000e+00 16343.0
1 TraesCS7A01G144100 chr7A 92.840 810 50 7 1 804 142488955 142489762 0.000000e+00 1168.0
2 TraesCS7A01G144100 chr3A 98.955 5359 56 0 2222 7580 35054602 35059960 0.000000e+00 9587.0
3 TraesCS7A01G144100 chr3A 93.284 804 49 3 1 804 56961055 56961853 0.000000e+00 1181.0
4 TraesCS7A01G144100 chr3A 92.725 811 51 7 1 806 402503067 402503874 0.000000e+00 1164.0
5 TraesCS7A01G144100 chr3B 98.731 5360 63 5 2222 7580 169248892 169243537 0.000000e+00 9516.0
6 TraesCS7A01G144100 chr3B 93.023 43 3 0 8067 8109 520610334 520610292 7.420000e-06 63.9
7 TraesCS7A01G144100 chr6A 98.585 5371 74 2 2214 7584 70157905 70163273 0.000000e+00 9496.0
8 TraesCS7A01G144100 chr6A 92.822 808 53 2 1 804 279676674 279677480 0.000000e+00 1166.0
9 TraesCS7A01G144100 chr5A 98.656 5359 71 1 2222 7580 26152141 26146784 0.000000e+00 9496.0
10 TraesCS7A01G144100 chr2B 98.563 5360 77 0 2221 7580 71346762 71341403 0.000000e+00 9472.0
11 TraesCS7A01G144100 chr2B 95.542 5361 234 3 2222 7580 659787081 659781724 0.000000e+00 8571.0
12 TraesCS7A01G144100 chr2B 89.432 1145 99 7 2654 3785 775409704 775408569 0.000000e+00 1424.0
13 TraesCS7A01G144100 chr2B 85.564 381 39 2 2801 3172 755933979 755933606 1.390000e-102 385.0
14 TraesCS7A01G144100 chr2B 88.562 306 35 0 2370 2675 775409954 775409649 1.090000e-98 372.0
15 TraesCS7A01G144100 chr2B 87.117 326 37 5 2221 2542 44441656 44441332 1.820000e-96 364.0
16 TraesCS7A01G144100 chr2B 85.163 337 33 7 2222 2542 334701299 334701634 6.620000e-86 329.0
17 TraesCS7A01G144100 chr2B 92.670 191 12 1 8660 8850 774840439 774840627 3.150000e-69 274.0
18 TraesCS7A01G144100 chr2B 91.667 192 13 2 8659 8850 744311796 744311608 6.810000e-66 263.0
19 TraesCS7A01G144100 chr2B 97.122 139 4 0 2220 2358 71341541 71341403 1.490000e-57 235.0
20 TraesCS7A01G144100 chr1B 96.742 5371 162 9 2221 7580 310939248 310933880 0.000000e+00 8937.0
21 TraesCS7A01G144100 chr1B 80.429 1211 204 22 1007 2207 580537620 580538807 0.000000e+00 893.0
22 TraesCS7A01G144100 chr1B 77.714 1216 213 40 1013 2216 589225975 589224806 0.000000e+00 691.0
23 TraesCS7A01G144100 chr4A 95.821 5360 222 2 2222 7580 347518905 347513547 0.000000e+00 8656.0
24 TraesCS7A01G144100 chr6B 95.856 5309 219 1 2222 7529 12737446 12732138 0.000000e+00 8584.0
25 TraesCS7A01G144100 chr7D 91.273 1398 82 16 828 2221 92762309 92763670 0.000000e+00 1869.0
26 TraesCS7A01G144100 chr7D 86.375 389 35 11 7581 7952 92763666 92764053 8.270000e-110 409.0
27 TraesCS7A01G144100 chr7B 92.791 1304 60 12 922 2221 45177042 45175769 0.000000e+00 1857.0
28 TraesCS7A01G144100 chr7B 89.615 260 21 5 7581 7837 45175773 45175517 8.570000e-85 326.0
29 TraesCS7A01G144100 chr7B 82.799 343 29 9 804 1128 45186231 45185901 6.770000e-71 279.0
30 TraesCS7A01G144100 chr5B 93.210 810 49 6 1 806 276223879 276224686 0.000000e+00 1186.0
31 TraesCS7A01G144100 chr5B 85.577 312 30 5 2213 2509 145482801 145483112 6.670000e-81 313.0
32 TraesCS7A01G144100 chr3D 93.300 806 50 4 1 804 607268681 607267878 0.000000e+00 1186.0
33 TraesCS7A01G144100 chr1A 92.980 812 51 5 1 808 343619365 343620174 0.000000e+00 1179.0
34 TraesCS7A01G144100 chr1A 77.562 1132 199 39 1097 2216 533155812 533154724 4.510000e-177 632.0
35 TraesCS7A01G144100 chr6D 93.078 809 48 6 2 808 143497951 143498753 0.000000e+00 1177.0
36 TraesCS7A01G144100 chr6D 95.556 45 1 1 8064 8107 424178730 424178774 4.430000e-08 71.3
37 TraesCS7A01G144100 chr5D 92.848 811 46 8 1 805 8704044 8703240 0.000000e+00 1166.0
38 TraesCS7A01G144100 chr5D 92.149 777 46 10 8062 8835 482796046 482796810 0.000000e+00 1083.0
39 TraesCS7A01G144100 chr5D 93.117 247 15 2 8604 8850 388861281 388861525 2.350000e-95 361.0
40 TraesCS7A01G144100 chr2A 93.434 792 43 7 8062 8848 59243072 59243859 0.000000e+00 1166.0
41 TraesCS7A01G144100 chr2A 74.792 960 171 52 1285 2215 179348013 179348930 5.050000e-97 366.0
42 TraesCS7A01G144100 chr2A 73.762 949 184 48 1277 2214 722061915 722061021 6.670000e-81 313.0
43 TraesCS7A01G144100 chr1D 80.181 1216 204 31 1007 2207 429025191 429026384 0.000000e+00 876.0
44 TraesCS7A01G144100 chr1D 79.577 1229 209 31 1007 2214 429491959 429493166 0.000000e+00 841.0
45 TraesCS7A01G144100 chr1D 77.539 1211 206 44 1013 2207 435926716 435927876 0.000000e+00 669.0
46 TraesCS7A01G144100 chr2D 91.146 192 15 1 8659 8850 631308312 631308501 8.810000e-65 259.0
47 TraesCS7A01G144100 chrUn 81.172 239 28 14 8376 8604 41497262 41497031 9.130000e-40 176.0


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 TraesCS7A01G144100 chr7A 94913805 94922654 8849 False 16343.0 16343 100.000 1 8850 1 chr7A.!!$F1 8849
1 TraesCS7A01G144100 chr7A 142488955 142489762 807 False 1168.0 1168 92.840 1 804 1 chr7A.!!$F2 803
2 TraesCS7A01G144100 chr3A 35054602 35059960 5358 False 9587.0 9587 98.955 2222 7580 1 chr3A.!!$F1 5358
3 TraesCS7A01G144100 chr3A 56961055 56961853 798 False 1181.0 1181 93.284 1 804 1 chr3A.!!$F2 803
4 TraesCS7A01G144100 chr3A 402503067 402503874 807 False 1164.0 1164 92.725 1 806 1 chr3A.!!$F3 805
5 TraesCS7A01G144100 chr3B 169243537 169248892 5355 True 9516.0 9516 98.731 2222 7580 1 chr3B.!!$R1 5358
6 TraesCS7A01G144100 chr6A 70157905 70163273 5368 False 9496.0 9496 98.585 2214 7584 1 chr6A.!!$F1 5370
7 TraesCS7A01G144100 chr6A 279676674 279677480 806 False 1166.0 1166 92.822 1 804 1 chr6A.!!$F2 803
8 TraesCS7A01G144100 chr5A 26146784 26152141 5357 True 9496.0 9496 98.656 2222 7580 1 chr5A.!!$R1 5358
9 TraesCS7A01G144100 chr2B 71341403 71346762 5359 True 9472.0 9472 98.563 2221 7580 1 chr2B.!!$R2 5359
10 TraesCS7A01G144100 chr2B 659781724 659787081 5357 True 8571.0 8571 95.542 2222 7580 1 chr2B.!!$R4 5358
11 TraesCS7A01G144100 chr2B 775408569 775409954 1385 True 898.0 1424 88.997 2370 3785 2 chr2B.!!$R7 1415
12 TraesCS7A01G144100 chr1B 310933880 310939248 5368 True 8937.0 8937 96.742 2221 7580 1 chr1B.!!$R1 5359
13 TraesCS7A01G144100 chr1B 580537620 580538807 1187 False 893.0 893 80.429 1007 2207 1 chr1B.!!$F1 1200
14 TraesCS7A01G144100 chr1B 589224806 589225975 1169 True 691.0 691 77.714 1013 2216 1 chr1B.!!$R2 1203
15 TraesCS7A01G144100 chr4A 347513547 347518905 5358 True 8656.0 8656 95.821 2222 7580 1 chr4A.!!$R1 5358
16 TraesCS7A01G144100 chr6B 12732138 12737446 5308 True 8584.0 8584 95.856 2222 7529 1 chr6B.!!$R1 5307
17 TraesCS7A01G144100 chr7D 92762309 92764053 1744 False 1139.0 1869 88.824 828 7952 2 chr7D.!!$F1 7124
18 TraesCS7A01G144100 chr7B 45175517 45177042 1525 True 1091.5 1857 91.203 922 7837 2 chr7B.!!$R2 6915
19 TraesCS7A01G144100 chr5B 276223879 276224686 807 False 1186.0 1186 93.210 1 806 1 chr5B.!!$F2 805
20 TraesCS7A01G144100 chr3D 607267878 607268681 803 True 1186.0 1186 93.300 1 804 1 chr3D.!!$R1 803
21 TraesCS7A01G144100 chr1A 343619365 343620174 809 False 1179.0 1179 92.980 1 808 1 chr1A.!!$F1 807
22 TraesCS7A01G144100 chr1A 533154724 533155812 1088 True 632.0 632 77.562 1097 2216 1 chr1A.!!$R1 1119
23 TraesCS7A01G144100 chr6D 143497951 143498753 802 False 1177.0 1177 93.078 2 808 1 chr6D.!!$F1 806
24 TraesCS7A01G144100 chr5D 8703240 8704044 804 True 1166.0 1166 92.848 1 805 1 chr5D.!!$R1 804
25 TraesCS7A01G144100 chr5D 482796046 482796810 764 False 1083.0 1083 92.149 8062 8835 1 chr5D.!!$F2 773
26 TraesCS7A01G144100 chr2A 59243072 59243859 787 False 1166.0 1166 93.434 8062 8848 1 chr2A.!!$F1 786
27 TraesCS7A01G144100 chr2A 179348013 179348930 917 False 366.0 366 74.792 1285 2215 1 chr2A.!!$F2 930
28 TraesCS7A01G144100 chr2A 722061021 722061915 894 True 313.0 313 73.762 1277 2214 1 chr2A.!!$R1 937
29 TraesCS7A01G144100 chr1D 429025191 429026384 1193 False 876.0 876 80.181 1007 2207 1 chr1D.!!$F1 1200
30 TraesCS7A01G144100 chr1D 429491959 429493166 1207 False 841.0 841 79.577 1007 2214 1 chr1D.!!$F2 1207
31 TraesCS7A01G144100 chr1D 435926716 435927876 1160 False 669.0 669 77.539 1013 2207 1 chr1D.!!$F3 1194

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
849 878 0.038618 TTCGTGATGGTCAGACGTGG 60.039 55.000 0.00 0.00 34.69 4.94 F
1497 1551 0.108019 ACGTGGAGGGGAGTTTGAAC 59.892 55.000 0.00 0.00 0.00 3.18 F
1612 1669 0.685097 ACGCATGGTTCCTGTACACT 59.315 50.000 0.00 0.00 0.00 3.55 F
2035 2115 1.542547 GGCTTCCTGGACAAGACGAAA 60.543 52.381 0.00 0.00 0.00 3.46 F
2965 3061 0.818445 CTGGTGCATCTGCTGGATCC 60.818 60.000 4.20 4.20 42.66 3.36 F
3233 3329 0.461548 GATCCAGTCATCGCTCACCA 59.538 55.000 0.00 0.00 0.00 4.17 F
4027 4126 3.074412 ACTTTCCATGCAAGAACCGTAG 58.926 45.455 9.29 1.08 0.00 3.51 F
5504 5609 2.596851 GCACCAGCTCTTCCCAGGA 61.597 63.158 0.00 0.00 37.91 3.86 F
5530 5635 2.846532 CCTGGGCCTCAAGGTGTT 59.153 61.111 4.53 0.00 37.57 3.32 F
6900 7006 6.252015 GTGAAGCGTATTCTTCGTTATGTACA 59.748 38.462 0.00 0.00 44.01 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1918 0.539051 CTCCCGAAGCAGAGGAACAT 59.461 55.000 0.00 0.00 0.00 2.71 R
2729 2816 0.677842 GACAATCCGTACGGGGCTAT 59.322 55.000 32.80 16.94 36.01 2.97 R
2965 3061 1.139058 GTGTAGTAGGCCATGTGGGAG 59.861 57.143 5.01 0.00 40.01 4.30 R
3233 3329 1.852626 CCAAGGAGGACACCCCCTT 60.853 63.158 0.00 0.00 41.10 3.95 R
4358 4458 1.315257 GGATGACCAAGCCGTGCATT 61.315 55.000 0.00 0.00 35.97 3.56 R
4569 4669 9.325198 TGACATAATAATTATGACCACTCACAC 57.675 33.333 0.00 0.00 44.52 3.82 R
5359 5464 0.616111 ACGGCTCCTCCTGTTCATCT 60.616 55.000 0.00 0.00 0.00 2.90 R
6900 7006 0.914644 ACCATATGCTGCAGTGAGGT 59.085 50.000 16.64 13.27 0.00 3.85 R
7230 7336 4.319477 GCTTTGTTCGAGCATGAAACACTA 60.319 41.667 1.75 0.00 39.89 2.74 R
7951 8095 0.250234 ACGAGGATCCATGTGTGTGG 59.750 55.000 15.82 0.00 40.76 4.17 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
379 382 8.656849 ACTTATAATTTATAGCGCAAGATTCGG 58.343 33.333 11.47 0.00 43.02 4.30
486 490 7.325660 ACACATGCATACCTCTGAAAAATAG 57.674 36.000 0.00 0.00 0.00 1.73
541 547 0.881796 TGAGAGAAAGCGAGCGAGAA 59.118 50.000 0.00 0.00 0.00 2.87
574 603 0.930726 GAGAGGGAGGAGAGAGGGAA 59.069 60.000 0.00 0.00 0.00 3.97
587 616 0.458260 GAGGGAAAGAGAGACGCCTC 59.542 60.000 0.00 0.00 39.72 4.70
642 671 0.107410 TTTGTGTGAACACCGAGGCT 60.107 50.000 10.92 0.00 45.88 4.58
722 751 9.487442 ACAAAAATAAAGAAGATGGGCCTATTA 57.513 29.630 1.86 0.00 0.00 0.98
738 767 5.221722 GGCCTATTATGGTCTTGAGTGATGA 60.222 44.000 0.00 0.00 0.00 2.92
740 769 6.593382 GCCTATTATGGTCTTGAGTGATGATC 59.407 42.308 0.00 0.00 0.00 2.92
793 822 1.134487 CGTTGCAACGTATGGGCTG 59.866 57.895 37.16 11.84 46.63 4.85
808 837 6.404293 CGTATGGGCTGTTTTGCTAGTTAATT 60.404 38.462 0.00 0.00 0.00 1.40
809 838 5.385509 TGGGCTGTTTTGCTAGTTAATTC 57.614 39.130 0.00 0.00 0.00 2.17
810 839 4.830046 TGGGCTGTTTTGCTAGTTAATTCA 59.170 37.500 0.00 0.00 0.00 2.57
811 840 5.303078 TGGGCTGTTTTGCTAGTTAATTCAA 59.697 36.000 0.00 0.00 0.00 2.69
812 841 5.633601 GGGCTGTTTTGCTAGTTAATTCAAC 59.366 40.000 0.00 0.00 37.41 3.18
813 842 6.212955 GGCTGTTTTGCTAGTTAATTCAACA 58.787 36.000 0.00 0.00 39.81 3.33
814 843 6.363357 GGCTGTTTTGCTAGTTAATTCAACAG 59.637 38.462 14.20 14.20 41.77 3.16
815 844 7.325599 CTGTTTTGCTAGTTAATTCAACAGC 57.674 36.000 0.00 0.00 39.81 4.40
816 845 7.038154 TGTTTTGCTAGTTAATTCAACAGCT 57.962 32.000 0.00 0.00 39.74 4.24
817 846 8.160521 TGTTTTGCTAGTTAATTCAACAGCTA 57.839 30.769 0.00 9.79 39.74 3.32
818 847 8.073768 TGTTTTGCTAGTTAATTCAACAGCTAC 58.926 33.333 0.00 12.34 39.74 3.58
819 848 7.737972 TTTGCTAGTTAATTCAACAGCTACA 57.262 32.000 0.00 0.00 39.74 2.74
820 849 6.968131 TGCTAGTTAATTCAACAGCTACAG 57.032 37.500 0.00 0.00 39.74 2.74
821 850 5.351465 TGCTAGTTAATTCAACAGCTACAGC 59.649 40.000 0.00 0.00 39.74 4.40
822 851 5.351465 GCTAGTTAATTCAACAGCTACAGCA 59.649 40.000 3.70 0.00 39.81 4.41
823 852 5.869753 AGTTAATTCAACAGCTACAGCAG 57.130 39.130 3.70 0.00 39.81 4.24
824 853 4.154918 AGTTAATTCAACAGCTACAGCAGC 59.845 41.667 3.70 0.00 41.79 5.25
825 854 6.261463 AGTTAATTCAACAGCTACAGCAGCA 61.261 40.000 3.70 0.00 43.89 4.41
826 855 7.521377 AGTTAATTCAACAGCTACAGCAGCAT 61.521 38.462 3.70 0.00 43.89 3.79
843 872 2.941064 AGCATTGATTCGTGATGGTCAG 59.059 45.455 0.00 0.00 0.00 3.51
849 878 0.038618 TTCGTGATGGTCAGACGTGG 60.039 55.000 0.00 0.00 34.69 4.94
850 879 0.891904 TCGTGATGGTCAGACGTGGA 60.892 55.000 0.00 0.00 34.69 4.02
856 885 3.055167 TGATGGTCAGACGTGGAAATCAT 60.055 43.478 0.00 0.00 0.00 2.45
880 909 0.729140 CCATTCGTTCGTTTGCTGCC 60.729 55.000 0.00 0.00 0.00 4.85
892 921 2.202703 GCTGCCGTACCTACCACG 60.203 66.667 0.00 0.00 39.10 4.94
893 922 2.998279 GCTGCCGTACCTACCACGT 61.998 63.158 0.00 0.00 37.71 4.49
894 923 1.138247 CTGCCGTACCTACCACGTC 59.862 63.158 0.00 0.00 37.71 4.34
895 924 2.275547 CTGCCGTACCTACCACGTCC 62.276 65.000 0.00 0.00 37.71 4.79
896 925 2.342650 GCCGTACCTACCACGTCCA 61.343 63.158 0.00 0.00 37.71 4.02
899 928 1.205417 CCGTACCTACCACGTCCAAAT 59.795 52.381 0.00 0.00 37.71 2.32
900 929 2.264813 CGTACCTACCACGTCCAAATG 58.735 52.381 0.00 0.00 34.74 2.32
901 930 2.353011 CGTACCTACCACGTCCAAATGT 60.353 50.000 0.00 0.00 34.74 2.71
902 931 2.178912 ACCTACCACGTCCAAATGTG 57.821 50.000 0.00 0.00 41.30 3.21
903 932 1.418637 ACCTACCACGTCCAAATGTGT 59.581 47.619 0.00 0.00 40.23 3.72
904 933 2.633967 ACCTACCACGTCCAAATGTGTA 59.366 45.455 0.00 0.00 40.23 2.90
905 934 3.262405 ACCTACCACGTCCAAATGTGTAT 59.738 43.478 0.00 0.00 40.23 2.29
906 935 4.467082 ACCTACCACGTCCAAATGTGTATA 59.533 41.667 0.00 0.00 40.23 1.47
907 936 5.129815 ACCTACCACGTCCAAATGTGTATAT 59.870 40.000 0.00 0.00 40.23 0.86
908 937 6.053005 CCTACCACGTCCAAATGTGTATATT 58.947 40.000 0.00 0.00 40.23 1.28
909 938 6.540914 CCTACCACGTCCAAATGTGTATATTT 59.459 38.462 0.00 0.00 40.23 1.40
910 939 6.189677 ACCACGTCCAAATGTGTATATTTG 57.810 37.500 7.00 7.00 44.01 2.32
911 940 5.708230 ACCACGTCCAAATGTGTATATTTGT 59.292 36.000 11.45 0.00 43.28 2.83
912 941 6.879993 ACCACGTCCAAATGTGTATATTTGTA 59.120 34.615 11.45 0.00 43.28 2.41
913 942 7.554835 ACCACGTCCAAATGTGTATATTTGTAT 59.445 33.333 11.45 0.00 43.28 2.29
914 943 9.047371 CCACGTCCAAATGTGTATATTTGTATA 57.953 33.333 11.45 0.00 43.28 1.47
933 962 6.604171 TGTATAGATCCACTGATGCCATTTT 58.396 36.000 0.00 0.00 0.00 1.82
936 965 7.756395 ATAGATCCACTGATGCCATTTTTAG 57.244 36.000 0.00 0.00 0.00 1.85
938 967 5.591877 AGATCCACTGATGCCATTTTTAGTC 59.408 40.000 0.00 0.00 0.00 2.59
939 968 4.661222 TCCACTGATGCCATTTTTAGTCA 58.339 39.130 0.00 0.00 0.00 3.41
940 969 5.263599 TCCACTGATGCCATTTTTAGTCAT 58.736 37.500 0.00 0.00 0.00 3.06
941 970 5.357878 TCCACTGATGCCATTTTTAGTCATC 59.642 40.000 0.00 0.00 35.40 2.92
945 978 6.127814 ACTGATGCCATTTTTAGTCATCACTG 60.128 38.462 0.00 0.00 38.70 3.66
978 1011 2.162008 GTCGACGAAGAAAGAGTAGCCT 59.838 50.000 0.00 0.00 0.00 4.58
983 1016 2.094494 CGAAGAAAGAGTAGCCTGCAGA 60.094 50.000 17.39 0.00 0.00 4.26
984 1017 3.258228 GAAGAAAGAGTAGCCTGCAGAC 58.742 50.000 17.39 2.52 0.00 3.51
985 1018 2.251818 AGAAAGAGTAGCCTGCAGACA 58.748 47.619 17.39 0.00 0.00 3.41
992 1025 1.801178 GTAGCCTGCAGACAAGAACAC 59.199 52.381 17.39 0.00 0.00 3.32
993 1026 0.471617 AGCCTGCAGACAAGAACACT 59.528 50.000 17.39 0.00 0.00 3.55
1032 1065 1.384989 CGACCATCGTCCTACTGCCT 61.385 60.000 0.00 0.00 35.40 4.75
1094 1127 2.410469 GCGGATGCTCCAATGCAC 59.590 61.111 0.00 0.00 46.33 4.57
1176 1212 3.179265 GACATCGCCGACCACGTG 61.179 66.667 9.08 9.08 37.88 4.49
1257 1293 4.065281 CTCCCGACCGACCACACC 62.065 72.222 0.00 0.00 0.00 4.16
1489 1543 3.975591 AGGACGACGTGGAGGGGA 61.976 66.667 4.58 0.00 0.00 4.81
1490 1544 3.450115 GGACGACGTGGAGGGGAG 61.450 72.222 4.58 0.00 0.00 4.30
1491 1545 2.675772 GACGACGTGGAGGGGAGT 60.676 66.667 4.58 0.00 0.00 3.85
1492 1546 2.203596 ACGACGTGGAGGGGAGTT 60.204 61.111 3.97 0.00 0.00 3.01
1493 1547 1.813728 GACGACGTGGAGGGGAGTTT 61.814 60.000 4.58 0.00 0.00 2.66
1496 1550 0.395312 GACGTGGAGGGGAGTTTGAA 59.605 55.000 0.00 0.00 0.00 2.69
1497 1551 0.108019 ACGTGGAGGGGAGTTTGAAC 59.892 55.000 0.00 0.00 0.00 3.18
1612 1669 0.685097 ACGCATGGTTCCTGTACACT 59.315 50.000 0.00 0.00 0.00 3.55
1660 1717 3.112075 ATCGTCAACACGGCAGCG 61.112 61.111 0.00 0.00 46.70 5.18
1932 2012 4.394712 CGGCCACCGCTTCCTCTT 62.395 66.667 2.24 0.00 41.17 2.85
2035 2115 1.542547 GGCTTCCTGGACAAGACGAAA 60.543 52.381 0.00 0.00 0.00 3.46
2167 2247 4.089239 TTCGGCGTGCCCATGCTA 62.089 61.111 6.85 0.00 42.72 3.49
2373 2460 7.392113 TGTGTTTAACATGGTATCAACCCTAAG 59.608 37.037 0.00 0.00 38.34 2.18
2395 2482 1.668419 GTCCAATGTATTCCGCTGCT 58.332 50.000 0.00 0.00 0.00 4.24
2400 2487 2.511600 GTATTCCGCTGCTGCCGT 60.512 61.111 10.24 0.00 35.36 5.68
2745 2832 2.055299 CCATAGCCCCGTACGGATT 58.945 57.895 35.41 20.88 37.50 3.01
2965 3061 0.818445 CTGGTGCATCTGCTGGATCC 60.818 60.000 4.20 4.20 42.66 3.36
3233 3329 0.461548 GATCCAGTCATCGCTCACCA 59.538 55.000 0.00 0.00 0.00 4.17
3632 3728 4.041917 CTGCCAATGTTGCCGCGT 62.042 61.111 4.92 0.00 0.00 6.01
4027 4126 3.074412 ACTTTCCATGCAAGAACCGTAG 58.926 45.455 9.29 1.08 0.00 3.51
5504 5609 2.596851 GCACCAGCTCTTCCCAGGA 61.597 63.158 0.00 0.00 37.91 3.86
5530 5635 2.846532 CCTGGGCCTCAAGGTGTT 59.153 61.111 4.53 0.00 37.57 3.32
6900 7006 6.252015 GTGAAGCGTATTCTTCGTTATGTACA 59.748 38.462 0.00 0.00 44.01 2.90
7230 7336 8.335484 TGGAGCTACATATCTCTCATCTAATCT 58.665 37.037 0.00 0.00 0.00 2.40
7246 7352 6.451064 TCTAATCTAGTGTTTCATGCTCGA 57.549 37.500 0.00 0.00 0.00 4.04
7438 7544 4.968719 TCAGGGCATAGTTAAGATTGAGGA 59.031 41.667 0.00 0.00 0.00 3.71
7504 7610 8.905850 TCTTGTATATTGTATCGTACACCTTGA 58.094 33.333 0.00 0.00 38.63 3.02
7639 7747 2.277120 CGCGGGAACTACGTCGAG 60.277 66.667 0.00 0.00 34.54 4.04
7837 7954 0.185901 TGCCCAAAAGAGGAAGCACT 59.814 50.000 0.00 0.00 0.00 4.40
7838 7955 0.884514 GCCCAAAAGAGGAAGCACTC 59.115 55.000 0.00 0.00 37.77 3.51
7839 7956 1.819305 GCCCAAAAGAGGAAGCACTCA 60.819 52.381 5.98 0.00 39.97 3.41
7840 7957 1.882623 CCCAAAAGAGGAAGCACTCAC 59.117 52.381 5.98 0.00 39.97 3.51
7841 7958 2.575532 CCAAAAGAGGAAGCACTCACA 58.424 47.619 5.98 0.00 39.97 3.58
7842 7959 2.291741 CCAAAAGAGGAAGCACTCACAC 59.708 50.000 5.98 0.00 39.97 3.82
7843 7960 2.262423 AAAGAGGAAGCACTCACACC 57.738 50.000 5.98 0.00 39.97 4.16
7844 7961 1.131638 AAGAGGAAGCACTCACACCA 58.868 50.000 5.98 0.00 39.97 4.17
7845 7962 0.394565 AGAGGAAGCACTCACACCAC 59.605 55.000 5.98 0.00 39.97 4.16
7846 7963 0.946221 GAGGAAGCACTCACACCACG 60.946 60.000 0.00 0.00 37.44 4.94
7847 7964 1.227556 GGAAGCACTCACACCACGT 60.228 57.895 0.00 0.00 0.00 4.49
7865 7982 3.329743 CGTGAACGTAGTCGGATATGT 57.670 47.619 0.00 0.00 45.00 2.29
7866 7983 3.033873 CGTGAACGTAGTCGGATATGTG 58.966 50.000 0.00 0.00 45.00 3.21
7867 7984 2.787680 GTGAACGTAGTCGGATATGTGC 59.212 50.000 0.00 0.00 45.00 4.57
7869 7986 3.129813 TGAACGTAGTCGGATATGTGCTT 59.870 43.478 0.00 0.00 45.00 3.91
7870 7987 3.795623 ACGTAGTCGGATATGTGCTTT 57.204 42.857 0.00 0.00 29.74 3.51
7901 8045 4.438744 GGGAATAAATTCACCGCAGTTCTG 60.439 45.833 5.15 0.00 38.53 3.02
7908 8052 1.152963 ACCGCAGTTCTGGCTGTTT 60.153 52.632 1.97 0.00 38.65 2.83
7937 8081 9.540538 TTCATTTCTATTCTGTTTGGGGAATAA 57.459 29.630 0.00 0.00 35.07 1.40
7943 8087 9.713684 TCTATTCTGTTTGGGGAATAAATTCAT 57.286 29.630 5.15 0.00 38.53 2.57
7946 8090 6.184068 TCTGTTTGGGGAATAAATTCATCGA 58.816 36.000 5.15 0.00 38.53 3.59
7947 8091 6.318648 TCTGTTTGGGGAATAAATTCATCGAG 59.681 38.462 5.15 0.00 38.53 4.04
7948 8092 5.949354 TGTTTGGGGAATAAATTCATCGAGT 59.051 36.000 5.15 0.00 38.53 4.18
7949 8093 6.127758 TGTTTGGGGAATAAATTCATCGAGTG 60.128 38.462 5.15 0.00 38.53 3.51
7950 8094 5.110814 TGGGGAATAAATTCATCGAGTGT 57.889 39.130 5.15 0.00 38.53 3.55
7951 8095 5.123227 TGGGGAATAAATTCATCGAGTGTC 58.877 41.667 5.15 0.00 38.53 3.67
7953 8097 5.123227 GGGAATAAATTCATCGAGTGTCCA 58.877 41.667 5.15 0.00 38.53 4.02
7954 8098 5.007724 GGGAATAAATTCATCGAGTGTCCAC 59.992 44.000 5.15 0.00 38.53 4.02
7955 8099 5.584649 GGAATAAATTCATCGAGTGTCCACA 59.415 40.000 5.15 0.00 38.53 4.17
7956 8100 6.422776 AATAAATTCATCGAGTGTCCACAC 57.577 37.500 1.28 1.28 46.77 3.82
7957 8101 6.092122 GAATAAATTCATCGAGTGTCCACACA 59.908 38.462 12.31 0.00 41.44 3.72
7958 8102 7.883839 GAATAAATTCATCGAGTGTCCACACAC 60.884 40.741 12.31 5.00 43.28 3.82
7969 8113 0.536724 TCCACACACATGGATCCTCG 59.463 55.000 14.23 6.37 44.14 4.63
7970 8114 0.250234 CCACACACATGGATCCTCGT 59.750 55.000 14.23 7.07 43.02 4.18
7971 8115 1.645034 CACACACATGGATCCTCGTC 58.355 55.000 14.23 0.00 0.00 4.20
7972 8116 0.537188 ACACACATGGATCCTCGTCC 59.463 55.000 14.23 0.00 38.81 4.79
7987 8131 2.442189 CGTCCAACGAATTCTGCATC 57.558 50.000 3.52 0.00 46.05 3.91
7988 8132 2.002586 CGTCCAACGAATTCTGCATCT 58.997 47.619 3.52 0.00 46.05 2.90
7989 8133 3.186909 CGTCCAACGAATTCTGCATCTA 58.813 45.455 3.52 0.00 46.05 1.98
7990 8134 3.804325 CGTCCAACGAATTCTGCATCTAT 59.196 43.478 3.52 0.00 46.05 1.98
7991 8135 4.084849 CGTCCAACGAATTCTGCATCTATC 60.085 45.833 3.52 0.00 46.05 2.08
7992 8136 5.053145 GTCCAACGAATTCTGCATCTATCT 58.947 41.667 3.52 0.00 0.00 1.98
7993 8137 5.525378 GTCCAACGAATTCTGCATCTATCTT 59.475 40.000 3.52 0.00 0.00 2.40
7994 8138 6.701841 GTCCAACGAATTCTGCATCTATCTTA 59.298 38.462 3.52 0.00 0.00 2.10
7995 8139 6.925718 TCCAACGAATTCTGCATCTATCTTAG 59.074 38.462 3.52 0.00 0.00 2.18
7996 8140 6.347240 CCAACGAATTCTGCATCTATCTTAGC 60.347 42.308 3.52 0.00 0.00 3.09
7997 8141 4.920340 ACGAATTCTGCATCTATCTTAGCG 59.080 41.667 3.52 0.00 0.00 4.26
7998 8142 4.920340 CGAATTCTGCATCTATCTTAGCGT 59.080 41.667 3.52 0.00 0.00 5.07
7999 8143 5.164109 CGAATTCTGCATCTATCTTAGCGTG 60.164 44.000 3.52 0.00 0.00 5.34
8000 8144 4.655762 TTCTGCATCTATCTTAGCGTGT 57.344 40.909 0.00 0.00 0.00 4.49
8001 8145 4.655762 TCTGCATCTATCTTAGCGTGTT 57.344 40.909 0.00 0.00 0.00 3.32
8002 8146 5.011090 TCTGCATCTATCTTAGCGTGTTT 57.989 39.130 0.00 0.00 0.00 2.83
8003 8147 5.419542 TCTGCATCTATCTTAGCGTGTTTT 58.580 37.500 0.00 0.00 0.00 2.43
8004 8148 6.569780 TCTGCATCTATCTTAGCGTGTTTTA 58.430 36.000 0.00 0.00 0.00 1.52
8005 8149 7.210174 TCTGCATCTATCTTAGCGTGTTTTAT 58.790 34.615 0.00 0.00 0.00 1.40
8006 8150 7.382488 TCTGCATCTATCTTAGCGTGTTTTATC 59.618 37.037 0.00 0.00 0.00 1.75
8007 8151 6.983890 TGCATCTATCTTAGCGTGTTTTATCA 59.016 34.615 0.00 0.00 0.00 2.15
8008 8152 7.494298 TGCATCTATCTTAGCGTGTTTTATCAA 59.506 33.333 0.00 0.00 0.00 2.57
8009 8153 8.499162 GCATCTATCTTAGCGTGTTTTATCAAT 58.501 33.333 0.00 0.00 0.00 2.57
8019 8163 8.810652 AGCGTGTTTTATCAATTTTTATGTGT 57.189 26.923 0.00 0.00 0.00 3.72
8020 8164 8.911662 AGCGTGTTTTATCAATTTTTATGTGTC 58.088 29.630 0.00 0.00 0.00 3.67
8021 8165 8.695284 GCGTGTTTTATCAATTTTTATGTGTCA 58.305 29.630 0.00 0.00 0.00 3.58
8022 8166 9.987901 CGTGTTTTATCAATTTTTATGTGTCAC 57.012 29.630 0.00 0.00 0.00 3.67
8023 8167 9.987901 GTGTTTTATCAATTTTTATGTGTCACG 57.012 29.630 0.00 0.00 0.00 4.35
8024 8168 9.737427 TGTTTTATCAATTTTTATGTGTCACGT 57.263 25.926 2.65 2.65 0.00 4.49
8030 8174 9.959749 ATCAATTTTTATGTGTCACGTAAAACT 57.040 25.926 29.94 24.78 44.51 2.66
8034 8178 8.770850 TTTTTATGTGTCACGTAAAACTAAGC 57.229 30.769 29.94 0.00 44.51 3.09
8035 8179 7.718272 TTTATGTGTCACGTAAAACTAAGCT 57.282 32.000 22.45 0.00 36.83 3.74
8036 8180 5.591643 ATGTGTCACGTAAAACTAAGCTG 57.408 39.130 0.00 0.00 0.00 4.24
8037 8181 3.805422 TGTGTCACGTAAAACTAAGCTGG 59.195 43.478 0.00 0.00 0.00 4.85
8038 8182 3.805971 GTGTCACGTAAAACTAAGCTGGT 59.194 43.478 0.00 0.00 0.00 4.00
8039 8183 4.984161 GTGTCACGTAAAACTAAGCTGGTA 59.016 41.667 0.00 0.00 0.00 3.25
8040 8184 5.636543 GTGTCACGTAAAACTAAGCTGGTAT 59.363 40.000 0.00 0.00 0.00 2.73
8041 8185 5.636121 TGTCACGTAAAACTAAGCTGGTATG 59.364 40.000 0.00 0.00 0.00 2.39
8042 8186 5.636543 GTCACGTAAAACTAAGCTGGTATGT 59.363 40.000 0.00 0.00 0.00 2.29
8043 8187 5.636121 TCACGTAAAACTAAGCTGGTATGTG 59.364 40.000 0.00 0.00 32.32 3.21
8044 8188 4.933400 ACGTAAAACTAAGCTGGTATGTGG 59.067 41.667 0.00 0.00 0.00 4.17
8045 8189 4.331717 CGTAAAACTAAGCTGGTATGTGGG 59.668 45.833 0.00 0.00 0.00 4.61
8046 8190 2.420058 AACTAAGCTGGTATGTGGGC 57.580 50.000 0.00 0.00 0.00 5.36
8047 8191 1.285280 ACTAAGCTGGTATGTGGGCA 58.715 50.000 0.00 0.00 0.00 5.36
8048 8192 1.846439 ACTAAGCTGGTATGTGGGCAT 59.154 47.619 0.00 0.00 39.03 4.40
8049 8193 2.242196 ACTAAGCTGGTATGTGGGCATT 59.758 45.455 0.00 0.00 36.58 3.56
8050 8194 2.236489 AAGCTGGTATGTGGGCATTT 57.764 45.000 0.00 0.00 36.58 2.32
8051 8195 3.380471 AAGCTGGTATGTGGGCATTTA 57.620 42.857 0.00 0.00 36.58 1.40
8052 8196 3.600448 AGCTGGTATGTGGGCATTTAT 57.400 42.857 0.00 0.00 36.58 1.40
8053 8197 3.914771 AGCTGGTATGTGGGCATTTATT 58.085 40.909 0.00 0.00 36.58 1.40
8054 8198 3.891366 AGCTGGTATGTGGGCATTTATTC 59.109 43.478 0.00 0.00 36.58 1.75
8055 8199 3.304659 GCTGGTATGTGGGCATTTATTCG 60.305 47.826 0.00 0.00 36.58 3.34
8056 8200 4.133820 CTGGTATGTGGGCATTTATTCGA 58.866 43.478 0.00 0.00 36.58 3.71
8057 8201 4.724399 TGGTATGTGGGCATTTATTCGAT 58.276 39.130 0.00 0.00 36.58 3.59
8058 8202 5.136828 TGGTATGTGGGCATTTATTCGATT 58.863 37.500 0.00 0.00 36.58 3.34
8059 8203 5.009510 TGGTATGTGGGCATTTATTCGATTG 59.990 40.000 0.00 0.00 36.58 2.67
8060 8204 5.240623 GGTATGTGGGCATTTATTCGATTGA 59.759 40.000 0.00 0.00 36.58 2.57
8070 8214 8.816144 GGCATTTATTCGATTGAAATTGCTAAA 58.184 29.630 15.96 9.92 37.71 1.85
8142 8288 5.559770 TGGATCTGTTTGCTGTAATTCTCA 58.440 37.500 0.00 0.00 0.00 3.27
8145 8291 5.300969 TCTGTTTGCTGTAATTCTCATGC 57.699 39.130 0.00 0.00 0.00 4.06
8190 8336 1.507713 CGTTGTCGCTCGTTGCATG 60.508 57.895 0.00 0.00 43.06 4.06
8198 8344 2.435234 TCGTTGCATGGCCCGTAC 60.435 61.111 0.00 0.00 0.00 3.67
8407 8556 2.945456 AGTCTGTCTGTGTGTCCACTA 58.055 47.619 0.00 0.00 42.34 2.74
8739 8890 2.748209 ATTCCCCGGACCCTTATTTG 57.252 50.000 0.73 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
395 399 0.884514 TTTGCAATTTGGATCGCCGA 59.115 45.000 0.00 0.00 36.79 5.54
455 459 7.124573 TCAGAGGTATGCATGTGTAGTTATT 57.875 36.000 10.16 0.00 0.00 1.40
486 490 1.007387 CTGTTGTTTTCCCCTGCGC 60.007 57.895 0.00 0.00 0.00 6.09
541 547 0.933700 CCTCTCCCTCTCTCCCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
574 603 1.859302 AATCCTGAGGCGTCTCTCTT 58.141 50.000 19.37 3.52 40.58 2.85
587 616 7.389803 TGTGTGTTGAATATGGTTAATCCTG 57.610 36.000 0.00 0.00 37.07 3.86
642 671 2.043752 TCACCCTCACCGGCGATA 60.044 61.111 9.30 0.00 0.00 2.92
722 751 4.081476 TCAACGATCATCACTCAAGACCAT 60.081 41.667 0.00 0.00 0.00 3.55
738 767 2.987149 CACACGCTCTTAACTCAACGAT 59.013 45.455 0.00 0.00 0.00 3.73
740 769 2.124903 ACACACGCTCTTAACTCAACG 58.875 47.619 0.00 0.00 0.00 4.10
785 814 6.661377 TGAATTAACTAGCAAAACAGCCCATA 59.339 34.615 0.00 0.00 34.23 2.74
793 822 8.073768 TGTAGCTGTTGAATTAACTAGCAAAAC 58.926 33.333 0.00 8.76 41.61 2.43
815 844 2.931969 TCACGAATCAATGCTGCTGTAG 59.068 45.455 0.00 0.00 0.00 2.74
816 845 2.971307 TCACGAATCAATGCTGCTGTA 58.029 42.857 0.00 0.00 0.00 2.74
817 846 1.812235 TCACGAATCAATGCTGCTGT 58.188 45.000 0.00 0.00 0.00 4.40
818 847 2.540973 CCATCACGAATCAATGCTGCTG 60.541 50.000 0.00 0.00 0.00 4.41
819 848 1.674441 CCATCACGAATCAATGCTGCT 59.326 47.619 0.00 0.00 0.00 4.24
820 849 1.402968 ACCATCACGAATCAATGCTGC 59.597 47.619 0.00 0.00 0.00 5.25
821 850 2.679336 TGACCATCACGAATCAATGCTG 59.321 45.455 0.00 0.00 0.00 4.41
822 851 2.941064 CTGACCATCACGAATCAATGCT 59.059 45.455 0.00 0.00 0.00 3.79
823 852 2.938451 TCTGACCATCACGAATCAATGC 59.062 45.455 0.00 0.00 0.00 3.56
824 853 3.000623 CGTCTGACCATCACGAATCAATG 59.999 47.826 1.55 0.00 35.49 2.82
825 854 3.190079 CGTCTGACCATCACGAATCAAT 58.810 45.455 1.55 0.00 35.49 2.57
826 855 2.029380 ACGTCTGACCATCACGAATCAA 60.029 45.455 1.55 0.00 37.00 2.57
843 872 3.536956 TGGTCCTATGATTTCCACGTC 57.463 47.619 0.00 0.00 0.00 4.34
849 878 4.809426 ACGAACGAATGGTCCTATGATTTC 59.191 41.667 0.14 0.00 0.00 2.17
850 879 4.766375 ACGAACGAATGGTCCTATGATTT 58.234 39.130 0.14 0.00 0.00 2.17
856 885 2.070783 GCAAACGAACGAATGGTCCTA 58.929 47.619 0.14 0.00 0.00 2.94
880 909 2.264813 CATTTGGACGTGGTAGGTACG 58.735 52.381 0.00 0.00 46.31 3.67
901 930 9.875691 GCATCAGTGGATCTATACAAATATACA 57.124 33.333 0.00 0.00 0.00 2.29
902 931 9.319143 GGCATCAGTGGATCTATACAAATATAC 57.681 37.037 0.00 0.00 0.00 1.47
903 932 9.045745 TGGCATCAGTGGATCTATACAAATATA 57.954 33.333 0.00 0.00 0.00 0.86
904 933 7.921304 TGGCATCAGTGGATCTATACAAATAT 58.079 34.615 0.00 0.00 0.00 1.28
905 934 7.315066 TGGCATCAGTGGATCTATACAAATA 57.685 36.000 0.00 0.00 0.00 1.40
906 935 6.191657 TGGCATCAGTGGATCTATACAAAT 57.808 37.500 0.00 0.00 0.00 2.32
907 936 5.628797 TGGCATCAGTGGATCTATACAAA 57.371 39.130 0.00 0.00 0.00 2.83
908 937 5.830799 ATGGCATCAGTGGATCTATACAA 57.169 39.130 0.00 0.00 0.00 2.41
909 938 5.830799 AATGGCATCAGTGGATCTATACA 57.169 39.130 0.00 0.00 0.00 2.29
910 939 7.516198 AAAAATGGCATCAGTGGATCTATAC 57.484 36.000 0.00 0.00 0.00 1.47
911 940 8.439971 ACTAAAAATGGCATCAGTGGATCTATA 58.560 33.333 0.00 0.00 0.00 1.31
912 941 7.293073 ACTAAAAATGGCATCAGTGGATCTAT 58.707 34.615 0.00 0.00 0.00 1.98
913 942 6.662755 ACTAAAAATGGCATCAGTGGATCTA 58.337 36.000 0.00 0.00 0.00 1.98
914 943 5.513233 ACTAAAAATGGCATCAGTGGATCT 58.487 37.500 0.00 0.00 0.00 2.75
915 944 5.357878 TGACTAAAAATGGCATCAGTGGATC 59.642 40.000 0.00 0.00 0.00 3.36
916 945 5.263599 TGACTAAAAATGGCATCAGTGGAT 58.736 37.500 0.00 0.00 0.00 3.41
917 946 4.661222 TGACTAAAAATGGCATCAGTGGA 58.339 39.130 0.00 0.00 0.00 4.02
918 947 5.125900 TGATGACTAAAAATGGCATCAGTGG 59.874 40.000 8.03 0.00 40.05 4.00
919 948 6.032094 GTGATGACTAAAAATGGCATCAGTG 58.968 40.000 11.92 0.00 43.99 3.66
920 949 5.948162 AGTGATGACTAAAAATGGCATCAGT 59.052 36.000 11.92 12.25 43.99 3.41
953 986 3.712091 ACTCTTTCTTCGTCGACTGTT 57.288 42.857 14.70 0.00 0.00 3.16
954 987 3.365164 GCTACTCTTTCTTCGTCGACTGT 60.365 47.826 14.70 1.50 0.00 3.55
957 990 2.162008 AGGCTACTCTTTCTTCGTCGAC 59.838 50.000 5.18 5.18 0.00 4.20
978 1011 2.036475 GGAGAGAGTGTTCTTGTCTGCA 59.964 50.000 0.00 0.00 32.53 4.41
983 1016 2.289945 GCCATGGAGAGAGTGTTCTTGT 60.290 50.000 18.40 0.00 32.53 3.16
984 1017 2.289882 TGCCATGGAGAGAGTGTTCTTG 60.290 50.000 18.40 0.00 32.53 3.02
985 1018 1.980765 TGCCATGGAGAGAGTGTTCTT 59.019 47.619 18.40 0.00 32.53 2.52
992 1025 1.471684 GTTTTGCTGCCATGGAGAGAG 59.528 52.381 18.40 6.03 0.00 3.20
993 1026 1.538047 GTTTTGCTGCCATGGAGAGA 58.462 50.000 18.40 0.00 0.00 3.10
1257 1293 3.471244 GATCCACTCCTCGACGCCG 62.471 68.421 0.00 0.00 37.07 6.46
1412 1454 4.787999 CGGAGGTGAAGTAGACGC 57.212 61.111 0.00 0.00 0.00 5.19
1479 1521 0.396811 AGTTCAAACTCCCCTCCACG 59.603 55.000 0.00 0.00 32.86 4.94
1489 1543 0.307760 CGCGCCTTCAAGTTCAAACT 59.692 50.000 0.00 0.00 42.04 2.66
1490 1544 0.660300 CCGCGCCTTCAAGTTCAAAC 60.660 55.000 0.00 0.00 0.00 2.93
1491 1545 1.098712 ACCGCGCCTTCAAGTTCAAA 61.099 50.000 0.00 0.00 0.00 2.69
1492 1546 1.525077 ACCGCGCCTTCAAGTTCAA 60.525 52.632 0.00 0.00 0.00 2.69
1493 1547 2.110213 ACCGCGCCTTCAAGTTCA 59.890 55.556 0.00 0.00 0.00 3.18
1496 1550 3.936203 TCCACCGCGCCTTCAAGT 61.936 61.111 0.00 0.00 0.00 3.16
1497 1551 3.423154 GTCCACCGCGCCTTCAAG 61.423 66.667 0.00 0.00 0.00 3.02
1612 1669 1.971505 CTTCCATGTAGCGCCTCCCA 61.972 60.000 2.29 0.00 0.00 4.37
1838 1918 0.539051 CTCCCGAAGCAGAGGAACAT 59.461 55.000 0.00 0.00 0.00 2.71
2035 2115 2.608988 CACACCAGCCCTCTCCCT 60.609 66.667 0.00 0.00 0.00 4.20
2400 2487 4.141965 ATGTGGATGCGGTCGCGA 62.142 61.111 3.71 3.71 45.51 5.87
2729 2816 0.677842 GACAATCCGTACGGGGCTAT 59.322 55.000 32.80 16.94 36.01 2.97
2965 3061 1.139058 GTGTAGTAGGCCATGTGGGAG 59.861 57.143 5.01 0.00 40.01 4.30
3233 3329 1.852626 CCAAGGAGGACACCCCCTT 60.853 63.158 0.00 0.00 41.10 3.95
3932 4031 2.689658 TGGGTCGATGGAATAGGATGT 58.310 47.619 0.00 0.00 0.00 3.06
4027 4126 2.286294 GTGAATCTGATCATGTCCACGC 59.714 50.000 0.00 0.00 0.00 5.34
4358 4458 1.315257 GGATGACCAAGCCGTGCATT 61.315 55.000 0.00 0.00 35.97 3.56
4569 4669 9.325198 TGACATAATAATTATGACCACTCACAC 57.675 33.333 0.00 0.00 44.52 3.82
5359 5464 0.616111 ACGGCTCCTCCTGTTCATCT 60.616 55.000 0.00 0.00 0.00 2.90
5504 5609 3.099170 AGGCCCAGGCGATTCCAT 61.099 61.111 0.00 0.00 43.06 3.41
5987 6092 2.297698 TTAACACCAGAGACCGGAGA 57.702 50.000 9.46 0.00 0.00 3.71
6900 7006 0.914644 ACCATATGCTGCAGTGAGGT 59.085 50.000 16.64 13.27 0.00 3.85
7230 7336 4.319477 GCTTTGTTCGAGCATGAAACACTA 60.319 41.667 1.75 0.00 39.89 2.74
7246 7352 7.661437 TGATAGTCAACTTCTATGTGCTTTGTT 59.339 33.333 0.00 0.00 0.00 2.83
7511 7617 9.368416 GGGTGTGGCTATCTCATATATATAAGA 57.632 37.037 0.00 0.00 0.00 2.10
7696 7804 2.440430 TTCTCCCTCGCCTCCTCG 60.440 66.667 0.00 0.00 0.00 4.63
7698 7806 2.042435 CCTTCTCCCTCGCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
7753 7867 1.371558 GTGGGAAGAACCGCTCTGT 59.628 57.895 0.00 0.00 40.11 3.41
7845 7962 3.033873 CACATATCCGACTACGTTCACG 58.966 50.000 0.00 0.00 46.33 4.35
7846 7963 2.787680 GCACATATCCGACTACGTTCAC 59.212 50.000 0.00 0.00 37.88 3.18
7847 7964 2.686405 AGCACATATCCGACTACGTTCA 59.314 45.455 0.00 0.00 37.88 3.18
7848 7965 3.351020 AGCACATATCCGACTACGTTC 57.649 47.619 0.00 0.00 37.88 3.95
7849 7966 3.795623 AAGCACATATCCGACTACGTT 57.204 42.857 0.00 0.00 37.88 3.99
7850 7967 3.795623 AAAGCACATATCCGACTACGT 57.204 42.857 0.00 0.00 37.88 3.57
7862 7979 1.422531 TCCCCAAAGCAAAAGCACAT 58.577 45.000 0.00 0.00 0.00 3.21
7863 7980 1.198713 TTCCCCAAAGCAAAAGCACA 58.801 45.000 0.00 0.00 0.00 4.57
7864 7981 2.549064 ATTCCCCAAAGCAAAAGCAC 57.451 45.000 0.00 0.00 0.00 4.40
7865 7982 4.696479 TTTATTCCCCAAAGCAAAAGCA 57.304 36.364 0.00 0.00 0.00 3.91
7866 7983 5.704978 TGAATTTATTCCCCAAAGCAAAAGC 59.295 36.000 0.32 0.00 35.97 3.51
7867 7984 6.149308 GGTGAATTTATTCCCCAAAGCAAAAG 59.851 38.462 0.00 0.00 34.87 2.27
7869 7986 5.555966 GGTGAATTTATTCCCCAAAGCAAA 58.444 37.500 0.00 0.00 34.87 3.68
7870 7987 4.322349 CGGTGAATTTATTCCCCAAAGCAA 60.322 41.667 5.11 0.00 34.48 3.91
7877 8021 2.375146 ACTGCGGTGAATTTATTCCCC 58.625 47.619 0.00 0.00 35.97 4.81
7894 8038 4.843220 ATGAAAGAAACAGCCAGAACTG 57.157 40.909 0.00 0.00 43.59 3.16
7901 8045 7.597386 ACAGAATAGAAATGAAAGAAACAGCC 58.403 34.615 0.00 0.00 0.00 4.85
7908 8052 7.237982 TCCCCAAACAGAATAGAAATGAAAGA 58.762 34.615 0.00 0.00 0.00 2.52
7937 8081 3.401033 TGTGTGGACACTCGATGAATT 57.599 42.857 11.09 0.00 46.55 2.17
7951 8095 0.250234 ACGAGGATCCATGTGTGTGG 59.750 55.000 15.82 0.00 40.76 4.17
7953 8097 0.537188 GGACGAGGATCCATGTGTGT 59.463 55.000 15.82 2.35 38.77 3.72
7954 8098 0.536724 TGGACGAGGATCCATGTGTG 59.463 55.000 15.82 0.00 44.14 3.82
7955 8099 2.990977 TGGACGAGGATCCATGTGT 58.009 52.632 15.82 6.20 44.14 3.72
7960 8104 4.426971 TCGTTGGACGAGGATCCA 57.573 55.556 15.82 0.00 46.73 3.41
7968 8112 2.002586 AGATGCAGAATTCGTTGGACG 58.997 47.619 0.00 0.00 44.19 4.79
7969 8113 5.053145 AGATAGATGCAGAATTCGTTGGAC 58.947 41.667 0.00 0.00 0.00 4.02
7970 8114 5.282055 AGATAGATGCAGAATTCGTTGGA 57.718 39.130 0.00 0.00 0.00 3.53
7971 8115 5.998454 AAGATAGATGCAGAATTCGTTGG 57.002 39.130 0.00 0.00 0.00 3.77
7972 8116 6.588552 GCTAAGATAGATGCAGAATTCGTTG 58.411 40.000 0.00 0.00 0.00 4.10
7973 8117 5.403766 CGCTAAGATAGATGCAGAATTCGTT 59.596 40.000 0.00 0.00 0.00 3.85
7974 8118 4.920340 CGCTAAGATAGATGCAGAATTCGT 59.080 41.667 0.00 0.00 0.00 3.85
7975 8119 4.920340 ACGCTAAGATAGATGCAGAATTCG 59.080 41.667 0.00 0.00 0.00 3.34
7976 8120 5.694006 ACACGCTAAGATAGATGCAGAATTC 59.306 40.000 0.00 0.00 0.00 2.17
7977 8121 5.605534 ACACGCTAAGATAGATGCAGAATT 58.394 37.500 0.00 0.00 0.00 2.17
7978 8122 5.207110 ACACGCTAAGATAGATGCAGAAT 57.793 39.130 0.00 0.00 0.00 2.40
7979 8123 4.655762 ACACGCTAAGATAGATGCAGAA 57.344 40.909 0.00 0.00 0.00 3.02
7980 8124 4.655762 AACACGCTAAGATAGATGCAGA 57.344 40.909 0.00 0.00 0.00 4.26
7981 8125 5.725110 AAAACACGCTAAGATAGATGCAG 57.275 39.130 0.00 0.00 0.00 4.41
7982 8126 6.983890 TGATAAAACACGCTAAGATAGATGCA 59.016 34.615 0.00 0.00 0.00 3.96
7983 8127 7.408132 TGATAAAACACGCTAAGATAGATGC 57.592 36.000 0.00 0.00 0.00 3.91
7993 8137 9.900710 ACACATAAAAATTGATAAAACACGCTA 57.099 25.926 0.00 0.00 0.00 4.26
7994 8138 8.810652 ACACATAAAAATTGATAAAACACGCT 57.189 26.923 0.00 0.00 0.00 5.07
7995 8139 8.695284 TGACACATAAAAATTGATAAAACACGC 58.305 29.630 0.00 0.00 0.00 5.34
7996 8140 9.987901 GTGACACATAAAAATTGATAAAACACG 57.012 29.630 0.00 0.00 0.00 4.49
7997 8141 9.987901 CGTGACACATAAAAATTGATAAAACAC 57.012 29.630 6.37 0.00 0.00 3.32
7998 8142 9.737427 ACGTGACACATAAAAATTGATAAAACA 57.263 25.926 6.37 0.00 0.00 2.83
8004 8148 9.959749 AGTTTTACGTGACACATAAAAATTGAT 57.040 25.926 18.22 3.64 31.47 2.57
8008 8152 9.389570 GCTTAGTTTTACGTGACACATAAAAAT 57.610 29.630 19.52 19.52 31.47 1.82
8009 8153 8.614346 AGCTTAGTTTTACGTGACACATAAAAA 58.386 29.630 18.22 11.71 31.47 1.94
8010 8154 8.065407 CAGCTTAGTTTTACGTGACACATAAAA 58.935 33.333 13.91 13.91 0.00 1.52
8011 8155 7.307514 CCAGCTTAGTTTTACGTGACACATAAA 60.308 37.037 6.37 4.49 0.00 1.40
8012 8156 6.146510 CCAGCTTAGTTTTACGTGACACATAA 59.853 38.462 6.37 0.00 0.00 1.90
8013 8157 5.636121 CCAGCTTAGTTTTACGTGACACATA 59.364 40.000 6.37 0.00 0.00 2.29
8014 8158 4.451096 CCAGCTTAGTTTTACGTGACACAT 59.549 41.667 6.37 0.00 0.00 3.21
8015 8159 3.805422 CCAGCTTAGTTTTACGTGACACA 59.195 43.478 6.37 0.00 0.00 3.72
8016 8160 3.805971 ACCAGCTTAGTTTTACGTGACAC 59.194 43.478 0.00 0.00 0.00 3.67
8017 8161 4.062677 ACCAGCTTAGTTTTACGTGACA 57.937 40.909 0.00 0.00 0.00 3.58
8018 8162 5.636543 ACATACCAGCTTAGTTTTACGTGAC 59.363 40.000 0.00 0.00 0.00 3.67
8019 8163 5.636121 CACATACCAGCTTAGTTTTACGTGA 59.364 40.000 0.00 0.00 0.00 4.35
8020 8164 5.163893 CCACATACCAGCTTAGTTTTACGTG 60.164 44.000 0.00 0.00 0.00 4.49
8021 8165 4.933400 CCACATACCAGCTTAGTTTTACGT 59.067 41.667 0.00 0.00 0.00 3.57
8022 8166 4.331717 CCCACATACCAGCTTAGTTTTACG 59.668 45.833 0.00 0.00 0.00 3.18
8023 8167 4.095932 GCCCACATACCAGCTTAGTTTTAC 59.904 45.833 0.00 0.00 0.00 2.01
8024 8168 4.263550 TGCCCACATACCAGCTTAGTTTTA 60.264 41.667 0.00 0.00 0.00 1.52
8025 8169 3.089284 GCCCACATACCAGCTTAGTTTT 58.911 45.455 0.00 0.00 0.00 2.43
8026 8170 2.041081 TGCCCACATACCAGCTTAGTTT 59.959 45.455 0.00 0.00 0.00 2.66
8027 8171 1.633432 TGCCCACATACCAGCTTAGTT 59.367 47.619 0.00 0.00 0.00 2.24
8028 8172 1.285280 TGCCCACATACCAGCTTAGT 58.715 50.000 0.00 0.00 0.00 2.24
8029 8173 2.645838 ATGCCCACATACCAGCTTAG 57.354 50.000 0.00 0.00 33.67 2.18
8030 8174 3.380471 AAATGCCCACATACCAGCTTA 57.620 42.857 0.00 0.00 34.62 3.09
8031 8175 2.236489 AAATGCCCACATACCAGCTT 57.764 45.000 0.00 0.00 34.62 3.74
8032 8176 3.600448 ATAAATGCCCACATACCAGCT 57.400 42.857 0.00 0.00 34.62 4.24
8033 8177 3.304659 CGAATAAATGCCCACATACCAGC 60.305 47.826 0.00 0.00 34.62 4.85
8034 8178 4.133820 TCGAATAAATGCCCACATACCAG 58.866 43.478 0.00 0.00 34.62 4.00
8035 8179 4.157849 TCGAATAAATGCCCACATACCA 57.842 40.909 0.00 0.00 34.62 3.25
8036 8180 5.240623 TCAATCGAATAAATGCCCACATACC 59.759 40.000 0.00 0.00 34.62 2.73
8037 8181 6.312399 TCAATCGAATAAATGCCCACATAC 57.688 37.500 0.00 0.00 34.62 2.39
8038 8182 6.951062 TTCAATCGAATAAATGCCCACATA 57.049 33.333 0.00 0.00 34.62 2.29
8039 8183 5.850557 TTCAATCGAATAAATGCCCACAT 57.149 34.783 0.00 0.00 38.49 3.21
8040 8184 5.651387 TTTCAATCGAATAAATGCCCACA 57.349 34.783 0.00 0.00 0.00 4.17
8041 8185 6.509997 GCAATTTCAATCGAATAAATGCCCAC 60.510 38.462 0.00 0.00 0.00 4.61
8042 8186 5.523188 GCAATTTCAATCGAATAAATGCCCA 59.477 36.000 0.00 0.00 0.00 5.36
8043 8187 5.754890 AGCAATTTCAATCGAATAAATGCCC 59.245 36.000 0.00 0.00 0.00 5.36
8044 8188 6.833342 AGCAATTTCAATCGAATAAATGCC 57.167 33.333 0.00 0.00 0.00 4.40
8051 8195 9.241317 GATGTGATTTAGCAATTTCAATCGAAT 57.759 29.630 0.00 0.00 0.00 3.34
8052 8196 8.461222 AGATGTGATTTAGCAATTTCAATCGAA 58.539 29.630 0.00 0.00 0.00 3.71
8053 8197 7.988737 AGATGTGATTTAGCAATTTCAATCGA 58.011 30.769 0.00 0.00 0.00 3.59
8054 8198 9.378597 CTAGATGTGATTTAGCAATTTCAATCG 57.621 33.333 0.00 0.00 0.00 3.34
8092 8236 8.267620 TGATTAGGGATTTAGATGTGACATCT 57.732 34.615 28.69 28.69 0.00 2.90
8107 8251 5.537674 GCAAACAGATCCAATGATTAGGGAT 59.462 40.000 0.00 0.00 43.92 3.85
8113 8257 6.839124 TTACAGCAAACAGATCCAATGATT 57.161 33.333 0.00 0.00 0.00 2.57
8114 8258 7.341256 AGAATTACAGCAAACAGATCCAATGAT 59.659 33.333 0.00 0.00 0.00 2.45
8115 8259 6.660521 AGAATTACAGCAAACAGATCCAATGA 59.339 34.615 0.00 0.00 0.00 2.57
8142 8288 8.246180 ACAAAATACGAGATCAGAATTTTGCAT 58.754 29.630 22.23 10.91 45.09 3.96
8145 8291 9.398170 ACAACAAAATACGAGATCAGAATTTTG 57.602 29.630 21.45 21.45 45.94 2.44
8298 8446 2.138320 CACGAACATCTGAAGCACACT 58.862 47.619 0.00 0.00 0.00 3.55
8362 8510 2.884087 AAGGGACGCGCACACGATAG 62.884 60.000 5.73 0.00 43.93 2.08
8407 8556 5.137551 TCGAAAAAGGAAAAGAATGGTCCT 58.862 37.500 0.00 0.00 43.86 3.85
8416 8566 7.306807 GGAAAATGAAGCTCGAAAAAGGAAAAG 60.307 37.037 0.00 0.00 0.00 2.27
8558 8708 2.257286 GACAAACATGCATCGGCGCT 62.257 55.000 7.64 0.00 45.35 5.92
8700 8851 7.502226 GGGGAATTTGATGATAGACATGTAACA 59.498 37.037 0.00 0.00 39.56 2.41
8739 8890 4.026407 GTGCTAATATTGAACGCGAAACC 58.974 43.478 15.93 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.