Multiple sequence alignment - TraesCS7A01G437500

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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 TraesCS7A01G437500 chr7A 100.000 3216 0 0 1 3216 632187167 632190382 0.000000e+00 5939.0
1 TraesCS7A01G437500 chr7A 87.124 1926 155 48 1 1906 630670773 630672625 0.000000e+00 2097.0
2 TraesCS7A01G437500 chr7A 85.980 1990 152 49 15 1958 631653306 631651398 0.000000e+00 2012.0
3 TraesCS7A01G437500 chr7A 97.719 789 16 2 2015 2801 642324138 642324926 0.000000e+00 1356.0
4 TraesCS7A01G437500 chr7A 97.586 787 16 3 2015 2800 573609232 573610016 0.000000e+00 1345.0
5 TraesCS7A01G437500 chr7A 87.184 1225 87 26 671 1883 632265592 632266758 0.000000e+00 1328.0
6 TraesCS7A01G437500 chr7A 89.192 1064 71 16 823 1886 617551986 617550967 0.000000e+00 1288.0
7 TraesCS7A01G437500 chr7A 95.346 795 21 9 2011 2800 543440970 543441753 0.000000e+00 1249.0
8 TraesCS7A01G437500 chr7A 81.504 811 90 27 5 769 625641577 625642373 2.120000e-171 612.0
9 TraesCS7A01G437500 chr7A 80.419 812 88 29 15 770 625674360 625675156 1.300000e-153 553.0
10 TraesCS7A01G437500 chr7A 91.635 263 13 6 2957 3215 631849184 631848927 3.950000e-94 355.0
11 TraesCS7A01G437500 chr7A 90.000 280 8 6 2957 3216 630672748 630673027 8.540000e-91 344.0
12 TraesCS7A01G437500 chr7A 87.793 213 19 7 2985 3193 617550853 617550644 3.210000e-60 243.0
13 TraesCS7A01G437500 chr7A 81.447 318 28 18 504 791 617552301 617551985 6.940000e-57 231.0
14 TraesCS7A01G437500 chr7A 85.646 209 24 4 682 890 631878026 631877824 6.990000e-52 215.0
15 TraesCS7A01G437500 chr7A 91.538 130 11 0 2802 2931 42121587 42121458 2.550000e-41 180.0
16 TraesCS7A01G437500 chr7D 84.174 1864 154 63 1 1808 530431619 530429841 0.000000e+00 1677.0
17 TraesCS7A01G437500 chr7D 91.233 1095 75 9 726 1808 548560595 548561680 0.000000e+00 1471.0
18 TraesCS7A01G437500 chr7D 88.328 1148 78 22 839 1958 548066914 548065795 0.000000e+00 1327.0
19 TraesCS7A01G437500 chr7D 89.086 1072 56 20 857 1906 548324917 548325949 0.000000e+00 1275.0
20 TraesCS7A01G437500 chr7D 84.884 1032 74 32 827 1807 573969075 573970075 0.000000e+00 966.0
21 TraesCS7A01G437500 chr7D 81.165 807 86 36 15 769 543730820 543731612 3.570000e-164 588.0
22 TraesCS7A01G437500 chr7D 95.000 220 6 2 2957 3175 548326064 548326279 1.100000e-89 340.0
23 TraesCS7A01G437500 chr7D 80.263 380 49 20 407 772 548324523 548324890 2.460000e-66 263.0
24 TraesCS7A01G437500 chr7D 80.702 228 20 13 2965 3191 530429669 530429465 4.300000e-34 156.0
25 TraesCS7A01G437500 chr7D 86.301 146 6 6 2968 3105 548065756 548065617 2.590000e-31 147.0
26 TraesCS7A01G437500 chr7D 96.154 52 2 0 792 843 548324870 548324921 5.720000e-13 86.1
27 TraesCS7A01G437500 chr7B 90.178 1069 76 18 839 1907 591057006 591055967 0.000000e+00 1365.0
28 TraesCS7A01G437500 chr7B 89.880 1087 68 14 827 1909 591566042 591567090 0.000000e+00 1360.0
29 TraesCS7A01G437500 chr7B 90.655 1038 61 17 842 1876 591599776 591600780 0.000000e+00 1347.0
30 TraesCS7A01G437500 chr7B 83.866 1221 95 50 705 1906 569439949 569438812 0.000000e+00 1070.0
31 TraesCS7A01G437500 chr7B 85.215 629 49 22 1 609 591565282 591565886 9.870000e-170 606.0
32 TraesCS7A01G437500 chr7B 83.409 657 48 17 1 609 569440735 569440092 1.300000e-153 553.0
33 TraesCS7A01G437500 chr7B 78.966 832 86 33 1 796 569482495 569481717 4.820000e-133 484.0
34 TraesCS7A01G437500 chr7B 88.235 153 12 4 463 609 591057207 591057055 9.170000e-41 178.0
35 TraesCS7A01G437500 chr7B 82.174 230 17 11 2965 3193 569438702 569438496 3.300000e-40 176.0
36 TraesCS7A01G437500 chr7B 79.681 251 27 10 2957 3193 632799505 632799265 3.320000e-35 159.0
37 TraesCS7A01G437500 chr7B 90.196 102 10 0 671 772 587615111 587615212 2.010000e-27 134.0
38 TraesCS7A01G437500 chr7B 84.459 148 8 5 2962 3107 260131982 260132116 7.240000e-27 132.0
39 TraesCS7A01G437500 chr7B 95.833 72 3 0 3145 3216 569480453 569480382 2.030000e-22 117.0
40 TraesCS7A01G437500 chr7B 98.485 66 1 0 3151 3216 591055736 591055671 2.030000e-22 117.0
41 TraesCS7A01G437500 chr7B 95.000 60 3 0 407 466 591057287 591057228 9.500000e-16 95.3
42 TraesCS7A01G437500 chr3A 97.970 788 12 4 2015 2801 311449089 311448305 0.000000e+00 1363.0
43 TraesCS7A01G437500 chr3A 95.691 789 26 7 2015 2801 131575516 131574734 0.000000e+00 1262.0
44 TraesCS7A01G437500 chrUn 89.852 1084 68 14 830 1909 355335373 355334328 0.000000e+00 1354.0
45 TraesCS7A01G437500 chrUn 89.488 1075 61 16 839 1909 337590886 337589860 0.000000e+00 1312.0
46 TraesCS7A01G437500 chrUn 85.215 629 49 20 1 609 355336136 355335532 9.870000e-170 606.0
47 TraesCS7A01G437500 chrUn 95.890 73 2 1 3145 3216 70734921 70734993 2.030000e-22 117.0
48 TraesCS7A01G437500 chr6A 97.335 788 18 3 2015 2801 401210280 401211065 0.000000e+00 1336.0
49 TraesCS7A01G437500 chr6A 97.208 788 11 2 2015 2801 453909377 453910154 0.000000e+00 1323.0
50 TraesCS7A01G437500 chr2A 97.212 789 18 4 2015 2801 636058001 636058787 0.000000e+00 1332.0
51 TraesCS7A01G437500 chr2A 94.146 205 9 3 2015 2217 636058786 636058583 3.120000e-80 309.0
52 TraesCS7A01G437500 chr2A 92.958 213 11 4 2008 2217 81078234 81078445 1.120000e-79 307.0
53 TraesCS7A01G437500 chr1A 96.835 790 17 7 2015 2801 316715153 316715937 0.000000e+00 1314.0
54 TraesCS7A01G437500 chr6B 81.773 812 86 37 5 769 694680372 694681168 9.800000e-175 623.0
55 TraesCS7A01G437500 chr1D 80.970 825 84 35 5 772 110904567 110905375 1.290000e-163 586.0
56 TraesCS7A01G437500 chr1B 80.563 782 89 40 5 734 169024351 169025121 7.850000e-151 544.0
57 TraesCS7A01G437500 chr1B 84.507 142 6 6 2962 3101 550546655 550546782 3.370000e-25 126.0
58 TraesCS7A01G437500 chr2D 99.237 131 1 0 2802 2932 87595246 87595376 1.490000e-58 237.0
59 TraesCS7A01G437500 chr2D 94.643 56 3 0 1958 2013 87595199 87595254 1.590000e-13 87.9
60 TraesCS7A01G437500 chr5D 99.231 130 1 0 2802 2931 379223510 379223639 5.360000e-58 235.0
61 TraesCS7A01G437500 chr5D 95.556 90 4 0 2802 2891 547426829 547426740 9.300000e-31 145.0
62 TraesCS7A01G437500 chr5D 95.890 73 1 2 3145 3216 86777769 86777698 2.030000e-22 117.0
63 TraesCS7A01G437500 chr5D 92.857 56 4 0 1958 2013 379223463 379223518 7.390000e-12 82.4
64 TraesCS7A01G437500 chr5D 93.878 49 3 0 1961 2009 547426873 547426825 1.240000e-09 75.0
65 TraesCS7A01G437500 chr5A 99.231 130 1 0 2802 2931 619946219 619946090 5.360000e-58 235.0
66 TraesCS7A01G437500 chr5A 92.308 143 11 0 2802 2944 44145102 44144960 1.510000e-48 204.0
67 TraesCS7A01G437500 chr5A 96.429 56 2 0 1958 2013 619946266 619946211 3.420000e-15 93.5
68 TraesCS7A01G437500 chr5A 91.071 56 5 0 1958 2013 44145149 44145094 3.440000e-10 76.8
69 TraesCS7A01G437500 chr4D 96.992 133 4 0 2802 2934 103487568 103487436 1.160000e-54 224.0
70 TraesCS7A01G437500 chr4D 94.643 56 3 0 1958 2013 103487615 103487560 1.590000e-13 87.9
71 TraesCS7A01G437500 chr2B 88.344 163 12 4 304 466 113273320 113273165 4.240000e-44 189.0
72 TraesCS7A01G437500 chr2B 87.730 163 13 4 304 466 678387153 678386998 1.970000e-42 183.0
73 TraesCS7A01G437500 chr2B 85.135 148 7 5 2962 3107 107755924 107755790 1.560000e-28 137.0
74 TraesCS7A01G437500 chr4A 92.683 123 9 0 678 800 141908995 141908873 9.170000e-41 178.0
75 TraesCS7A01G437500 chr3B 84.459 148 7 3 2962 3107 289983988 289984121 7.240000e-27 132.0


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 TraesCS7A01G437500 chr7A 632187167 632190382 3215 False 5939.000000 5939 100.000000 1 3216 1 chr7A.!!$F5 3215
1 TraesCS7A01G437500 chr7A 631651398 631653306 1908 True 2012.000000 2012 85.980000 15 1958 1 chr7A.!!$R2 1943
2 TraesCS7A01G437500 chr7A 642324138 642324926 788 False 1356.000000 1356 97.719000 2015 2801 1 chr7A.!!$F7 786
3 TraesCS7A01G437500 chr7A 573609232 573610016 784 False 1345.000000 1345 97.586000 2015 2800 1 chr7A.!!$F2 785
4 TraesCS7A01G437500 chr7A 632265592 632266758 1166 False 1328.000000 1328 87.184000 671 1883 1 chr7A.!!$F6 1212
5 TraesCS7A01G437500 chr7A 543440970 543441753 783 False 1249.000000 1249 95.346000 2011 2800 1 chr7A.!!$F1 789
6 TraesCS7A01G437500 chr7A 630670773 630673027 2254 False 1220.500000 2097 88.562000 1 3216 2 chr7A.!!$F8 3215
7 TraesCS7A01G437500 chr7A 625641577 625642373 796 False 612.000000 612 81.504000 5 769 1 chr7A.!!$F3 764
8 TraesCS7A01G437500 chr7A 617550644 617552301 1657 True 587.333333 1288 86.144000 504 3193 3 chr7A.!!$R5 2689
9 TraesCS7A01G437500 chr7A 625674360 625675156 796 False 553.000000 553 80.419000 15 770 1 chr7A.!!$F4 755
10 TraesCS7A01G437500 chr7D 548560595 548561680 1085 False 1471.000000 1471 91.233000 726 1808 1 chr7D.!!$F2 1082
11 TraesCS7A01G437500 chr7D 573969075 573970075 1000 False 966.000000 966 84.884000 827 1807 1 chr7D.!!$F3 980
12 TraesCS7A01G437500 chr7D 530429465 530431619 2154 True 916.500000 1677 82.438000 1 3191 2 chr7D.!!$R1 3190
13 TraesCS7A01G437500 chr7D 548065617 548066914 1297 True 737.000000 1327 87.314500 839 3105 2 chr7D.!!$R2 2266
14 TraesCS7A01G437500 chr7D 543730820 543731612 792 False 588.000000 588 81.165000 15 769 1 chr7D.!!$F1 754
15 TraesCS7A01G437500 chr7D 548324523 548326279 1756 False 491.025000 1275 90.125750 407 3175 4 chr7D.!!$F4 2768
16 TraesCS7A01G437500 chr7B 591599776 591600780 1004 False 1347.000000 1347 90.655000 842 1876 1 chr7B.!!$F3 1034
17 TraesCS7A01G437500 chr7B 591565282 591567090 1808 False 983.000000 1360 87.547500 1 1909 2 chr7B.!!$F4 1908
18 TraesCS7A01G437500 chr7B 569438496 569440735 2239 True 599.666667 1070 83.149667 1 3193 3 chr7B.!!$R2 3192
19 TraesCS7A01G437500 chr7B 591055671 591057287 1616 True 438.825000 1365 92.974500 407 3216 4 chr7B.!!$R4 2809
20 TraesCS7A01G437500 chr7B 569480382 569482495 2113 True 300.500000 484 87.399500 1 3216 2 chr7B.!!$R3 3215
21 TraesCS7A01G437500 chr3A 311448305 311449089 784 True 1363.000000 1363 97.970000 2015 2801 1 chr3A.!!$R2 786
22 TraesCS7A01G437500 chr3A 131574734 131575516 782 True 1262.000000 1262 95.691000 2015 2801 1 chr3A.!!$R1 786
23 TraesCS7A01G437500 chrUn 337589860 337590886 1026 True 1312.000000 1312 89.488000 839 1909 1 chrUn.!!$R1 1070
24 TraesCS7A01G437500 chrUn 355334328 355336136 1808 True 980.000000 1354 87.533500 1 1909 2 chrUn.!!$R2 1908
25 TraesCS7A01G437500 chr6A 401210280 401211065 785 False 1336.000000 1336 97.335000 2015 2801 1 chr6A.!!$F1 786
26 TraesCS7A01G437500 chr6A 453909377 453910154 777 False 1323.000000 1323 97.208000 2015 2801 1 chr6A.!!$F2 786
27 TraesCS7A01G437500 chr2A 636058001 636058787 786 False 1332.000000 1332 97.212000 2015 2801 1 chr2A.!!$F2 786
28 TraesCS7A01G437500 chr1A 316715153 316715937 784 False 1314.000000 1314 96.835000 2015 2801 1 chr1A.!!$F1 786
29 TraesCS7A01G437500 chr6B 694680372 694681168 796 False 623.000000 623 81.773000 5 769 1 chr6B.!!$F1 764
30 TraesCS7A01G437500 chr1D 110904567 110905375 808 False 586.000000 586 80.970000 5 772 1 chr1D.!!$F1 767
31 TraesCS7A01G437500 chr1B 169024351 169025121 770 False 544.000000 544 80.563000 5 734 1 chr1B.!!$F1 729

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
262 276 0.541392 TGCATATCTTCACCACGCCT 59.459 50.0 0.0 0.0 0.00 5.52 F
1482 1809 0.320771 CGTCCTCAAGGTCACCAAGG 60.321 60.0 0.0 0.0 36.34 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1965 0.033504 TCTGCCGTCTTCTTGGACAC 59.966 55.0 0.0 0.0 36.12 3.67 R
2868 3328 0.036306 AAAAATCGACTCTGGGCCGT 59.964 50.0 0.0 0.0 0.00 5.68 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
105 106 3.561213 CTCAGCCATGACGCAGCG 61.561 66.667 14.82 14.82 0.00 5.18
262 276 0.541392 TGCATATCTTCACCACGCCT 59.459 50.000 0.00 0.00 0.00 5.52
329 348 4.862092 CGCGCTCGTGCATCCTCT 62.862 66.667 5.56 0.00 39.64 3.69
386 409 1.228894 TCCTCCTCAGTGAACGGCT 60.229 57.895 0.00 0.00 0.00 5.52
527 607 4.254709 TGCCTCACGCAGCAGGTT 62.255 61.111 0.00 0.00 44.64 3.50
775 973 3.672503 GGTGGCCATGGGGTTCCT 61.673 66.667 9.72 0.00 36.17 3.36
776 974 2.313427 GGTGGCCATGGGGTTCCTA 61.313 63.158 9.72 0.00 36.17 2.94
803 1051 4.602259 CTGGTGCGTGACGGTGGT 62.602 66.667 7.25 0.00 0.00 4.16
819 1067 4.028490 GTCATGGGGTGGCCGTGA 62.028 66.667 0.00 0.00 0.00 4.35
820 1068 3.253061 TCATGGGGTGGCCGTGAA 61.253 61.111 0.00 0.00 31.31 3.18
821 1069 2.044053 CATGGGGTGGCCGTGAAT 60.044 61.111 0.00 0.00 0.00 2.57
1080 1392 4.559229 CGATCGCAGGAGCTCGCA 62.559 66.667 7.83 0.00 39.10 5.10
1199 1511 1.185315 CAGACCAATTTTCCCGCCAT 58.815 50.000 0.00 0.00 0.00 4.40
1323 1635 1.022451 GTCTCTCGAGACGCTGAGGT 61.022 60.000 12.08 0.00 46.93 3.85
1337 1652 2.862541 CTGAGGTTGGTTCCATCAACA 58.137 47.619 8.82 0.00 44.38 3.33
1478 1805 1.080705 CGACGTCCTCAAGGTCACC 60.081 63.158 10.58 0.00 41.80 4.02
1479 1806 1.802337 CGACGTCCTCAAGGTCACCA 61.802 60.000 10.58 0.00 41.80 4.17
1480 1807 0.391597 GACGTCCTCAAGGTCACCAA 59.608 55.000 3.51 0.00 41.43 3.67
1482 1809 0.320771 CGTCCTCAAGGTCACCAAGG 60.321 60.000 0.00 0.00 36.34 3.61
1483 1810 1.056660 GTCCTCAAGGTCACCAAGGA 58.943 55.000 8.25 8.25 36.34 3.36
1484 1811 1.056660 TCCTCAAGGTCACCAAGGAC 58.943 55.000 8.25 0.00 37.06 3.85
1485 1812 0.320771 CCTCAAGGTCACCAAGGACG 60.321 60.000 0.00 0.00 38.70 4.79
1486 1813 0.679505 CTCAAGGTCACCAAGGACGA 59.320 55.000 0.00 0.00 38.70 4.20
1487 1814 0.391597 TCAAGGTCACCAAGGACGAC 59.608 55.000 0.00 0.00 38.70 4.34
1585 1942 1.878656 AAGACGAAGCGACCTCCCAG 61.879 60.000 0.00 0.00 0.00 4.45
1586 1943 2.600769 ACGAAGCGACCTCCCAGT 60.601 61.111 0.00 0.00 0.00 4.00
1587 1944 2.182030 CGAAGCGACCTCCCAGTC 59.818 66.667 0.00 0.00 0.00 3.51
1588 1945 2.579738 GAAGCGACCTCCCAGTCC 59.420 66.667 0.00 0.00 32.91 3.85
1589 1946 3.003763 AAGCGACCTCCCAGTCCC 61.004 66.667 0.00 0.00 32.91 4.46
1590 1947 3.846405 AAGCGACCTCCCAGTCCCA 62.846 63.158 0.00 0.00 32.91 4.37
1599 1956 2.406559 CTCCCAGTCCCAAGATCATCT 58.593 52.381 0.00 0.00 0.00 2.90
1608 1965 1.068753 AAGATCATCTGCGAGCCGG 59.931 57.895 0.00 0.00 0.00 6.13
1835 2195 1.001641 GGTGCAGCCAATCAGGAGT 60.002 57.895 4.03 0.00 41.22 3.85
1886 2249 0.392193 CGGTCAGGAAGCAGCTTCAT 60.392 55.000 31.68 24.99 41.77 2.57
1940 2377 7.167136 GGTCACTTTTACGTATATCCTTCTTCG 59.833 40.741 0.00 0.00 0.00 3.79
1959 2396 4.225497 GAAGGCTCGAACATGGGG 57.775 61.111 0.00 0.00 0.00 4.96
1960 2397 1.602237 GAAGGCTCGAACATGGGGA 59.398 57.895 0.00 0.00 0.00 4.81
1961 2398 0.744771 GAAGGCTCGAACATGGGGAC 60.745 60.000 0.00 0.00 0.00 4.46
1962 2399 1.201429 AAGGCTCGAACATGGGGACT 61.201 55.000 0.00 0.00 0.00 3.85
1963 2400 1.153349 GGCTCGAACATGGGGACTC 60.153 63.158 0.00 0.00 0.00 3.36
1964 2401 1.519455 GCTCGAACATGGGGACTCG 60.519 63.158 0.00 0.00 0.00 4.18
1965 2402 1.945354 GCTCGAACATGGGGACTCGA 61.945 60.000 0.00 2.10 37.95 4.04
1966 2403 0.530744 CTCGAACATGGGGACTCGAA 59.469 55.000 0.00 0.00 39.60 3.71
1967 2404 0.530744 TCGAACATGGGGACTCGAAG 59.469 55.000 0.00 0.00 37.38 3.79
1968 2405 0.530744 CGAACATGGGGACTCGAAGA 59.469 55.000 0.00 0.00 33.13 2.87
1969 2406 1.067142 CGAACATGGGGACTCGAAGAA 60.067 52.381 0.00 0.00 34.09 2.52
1970 2407 2.622436 GAACATGGGGACTCGAAGAAG 58.378 52.381 0.00 0.00 34.09 2.85
1971 2408 1.938585 ACATGGGGACTCGAAGAAGA 58.061 50.000 0.00 0.00 34.09 2.87
1972 2409 2.257207 ACATGGGGACTCGAAGAAGAA 58.743 47.619 0.00 0.00 34.09 2.52
1973 2410 2.234908 ACATGGGGACTCGAAGAAGAAG 59.765 50.000 0.00 0.00 34.09 2.85
1974 2411 1.267121 TGGGGACTCGAAGAAGAAGG 58.733 55.000 0.00 0.00 34.09 3.46
1975 2412 0.537653 GGGGACTCGAAGAAGAAGGG 59.462 60.000 0.00 0.00 34.09 3.95
1976 2413 1.268066 GGGACTCGAAGAAGAAGGGT 58.732 55.000 0.00 0.00 34.09 4.34
1977 2414 1.066787 GGGACTCGAAGAAGAAGGGTG 60.067 57.143 0.00 0.00 34.09 4.61
1978 2415 1.619332 GGACTCGAAGAAGAAGGGTGT 59.381 52.381 0.00 0.00 34.09 4.16
1979 2416 2.352912 GGACTCGAAGAAGAAGGGTGTC 60.353 54.545 0.00 0.00 34.09 3.67
1980 2417 2.296471 GACTCGAAGAAGAAGGGTGTCA 59.704 50.000 0.00 0.00 34.09 3.58
1981 2418 2.297597 ACTCGAAGAAGAAGGGTGTCAG 59.702 50.000 0.00 0.00 34.09 3.51
1982 2419 1.618837 TCGAAGAAGAAGGGTGTCAGG 59.381 52.381 0.00 0.00 0.00 3.86
1983 2420 1.618837 CGAAGAAGAAGGGTGTCAGGA 59.381 52.381 0.00 0.00 0.00 3.86
1984 2421 2.353208 CGAAGAAGAAGGGTGTCAGGAG 60.353 54.545 0.00 0.00 0.00 3.69
1985 2422 1.650528 AGAAGAAGGGTGTCAGGAGG 58.349 55.000 0.00 0.00 0.00 4.30
1986 2423 1.150135 AGAAGAAGGGTGTCAGGAGGA 59.850 52.381 0.00 0.00 0.00 3.71
1987 2424 1.978580 GAAGAAGGGTGTCAGGAGGAA 59.021 52.381 0.00 0.00 0.00 3.36
1988 2425 2.118403 AGAAGGGTGTCAGGAGGAAA 57.882 50.000 0.00 0.00 0.00 3.13
1989 2426 2.418669 AGAAGGGTGTCAGGAGGAAAA 58.581 47.619 0.00 0.00 0.00 2.29
1990 2427 2.989571 AGAAGGGTGTCAGGAGGAAAAT 59.010 45.455 0.00 0.00 0.00 1.82
1991 2428 4.175962 AGAAGGGTGTCAGGAGGAAAATA 58.824 43.478 0.00 0.00 0.00 1.40
1992 2429 4.226168 AGAAGGGTGTCAGGAGGAAAATAG 59.774 45.833 0.00 0.00 0.00 1.73
1993 2430 3.532102 AGGGTGTCAGGAGGAAAATAGT 58.468 45.455 0.00 0.00 0.00 2.12
1994 2431 3.916989 AGGGTGTCAGGAGGAAAATAGTT 59.083 43.478 0.00 0.00 0.00 2.24
1995 2432 5.098663 AGGGTGTCAGGAGGAAAATAGTTA 58.901 41.667 0.00 0.00 0.00 2.24
1996 2433 5.189934 AGGGTGTCAGGAGGAAAATAGTTAG 59.810 44.000 0.00 0.00 0.00 2.34
1997 2434 5.045797 GGGTGTCAGGAGGAAAATAGTTAGT 60.046 44.000 0.00 0.00 0.00 2.24
1998 2435 6.155737 GGGTGTCAGGAGGAAAATAGTTAGTA 59.844 42.308 0.00 0.00 0.00 1.82
1999 2436 7.266400 GGTGTCAGGAGGAAAATAGTTAGTAG 58.734 42.308 0.00 0.00 0.00 2.57
2000 2437 6.757478 GTGTCAGGAGGAAAATAGTTAGTAGC 59.243 42.308 0.00 0.00 0.00 3.58
2001 2438 5.978322 GTCAGGAGGAAAATAGTTAGTAGCG 59.022 44.000 0.00 0.00 0.00 4.26
2002 2439 5.068723 TCAGGAGGAAAATAGTTAGTAGCGG 59.931 44.000 0.00 0.00 0.00 5.52
2003 2440 4.344390 AGGAGGAAAATAGTTAGTAGCGGG 59.656 45.833 0.00 0.00 0.00 6.13
2004 2441 4.502777 GGAGGAAAATAGTTAGTAGCGGGG 60.503 50.000 0.00 0.00 0.00 5.73
2005 2442 3.390311 AGGAAAATAGTTAGTAGCGGGGG 59.610 47.826 0.00 0.00 0.00 5.40
2006 2443 3.389002 GGAAAATAGTTAGTAGCGGGGGA 59.611 47.826 0.00 0.00 0.00 4.81
2007 2444 4.375272 GAAAATAGTTAGTAGCGGGGGAC 58.625 47.826 0.00 0.00 0.00 4.46
2008 2445 3.325359 AATAGTTAGTAGCGGGGGACT 57.675 47.619 0.00 0.00 0.00 3.85
2009 2446 2.062971 TAGTTAGTAGCGGGGGACTG 57.937 55.000 0.00 0.00 40.79 3.51
2010 2447 0.686769 AGTTAGTAGCGGGGGACTGG 60.687 60.000 0.00 0.00 37.13 4.00
2011 2448 0.685458 GTTAGTAGCGGGGGACTGGA 60.685 60.000 0.00 0.00 37.13 3.86
2012 2449 0.041535 TTAGTAGCGGGGGACTGGAA 59.958 55.000 0.00 0.00 37.13 3.53
2013 2450 0.041535 TAGTAGCGGGGGACTGGAAA 59.958 55.000 0.00 0.00 37.13 3.13
2142 2580 2.456840 CCTCCCCTCCCCTTGACT 59.543 66.667 0.00 0.00 0.00 3.41
2252 2693 0.321564 TTGCCTCCGGATGAACAGTG 60.322 55.000 11.34 0.00 0.00 3.66
2768 3228 6.930475 TGGAGGTTGTATATTAGACTAGGGT 58.070 40.000 0.00 0.00 0.00 4.34
2801 3261 4.051922 GGGTGTAATATGCACTTCTCTCG 58.948 47.826 9.60 0.00 37.07 4.04
2802 3262 4.051922 GGTGTAATATGCACTTCTCTCGG 58.948 47.826 9.60 0.00 37.07 4.63
2803 3263 4.202121 GGTGTAATATGCACTTCTCTCGGA 60.202 45.833 9.60 0.00 37.07 4.55
2804 3264 4.740695 GTGTAATATGCACTTCTCTCGGAC 59.259 45.833 0.00 0.00 34.30 4.79
2805 3265 4.645136 TGTAATATGCACTTCTCTCGGACT 59.355 41.667 0.00 0.00 0.00 3.85
2806 3266 4.314740 AATATGCACTTCTCTCGGACTC 57.685 45.455 0.00 0.00 0.00 3.36
2807 3267 0.453793 ATGCACTTCTCTCGGACTCG 59.546 55.000 0.00 0.00 37.82 4.18
2808 3268 0.605589 TGCACTTCTCTCGGACTCGA 60.606 55.000 0.00 0.00 43.86 4.04
2809 3269 0.522180 GCACTTCTCTCGGACTCGAA 59.478 55.000 0.00 0.00 45.47 3.71
2810 3270 1.133407 GCACTTCTCTCGGACTCGAAT 59.867 52.381 0.00 0.00 45.47 3.34
2811 3271 2.791567 CACTTCTCTCGGACTCGAATG 58.208 52.381 0.00 0.00 45.47 2.67
2812 3272 1.746220 ACTTCTCTCGGACTCGAATGG 59.254 52.381 0.00 0.00 45.47 3.16
2813 3273 0.456221 TTCTCTCGGACTCGAATGGC 59.544 55.000 0.00 0.00 45.47 4.40
2814 3274 0.679960 TCTCTCGGACTCGAATGGCA 60.680 55.000 0.00 0.00 45.47 4.92
2815 3275 0.173481 CTCTCGGACTCGAATGGCAA 59.827 55.000 0.00 0.00 45.47 4.52
2816 3276 0.824109 TCTCGGACTCGAATGGCAAT 59.176 50.000 0.00 0.00 45.47 3.56
2817 3277 1.207089 TCTCGGACTCGAATGGCAATT 59.793 47.619 0.00 0.00 45.47 2.32
2818 3278 1.328680 CTCGGACTCGAATGGCAATTG 59.671 52.381 0.00 0.00 45.47 2.32
2819 3279 1.086696 CGGACTCGAATGGCAATTGT 58.913 50.000 7.40 0.00 39.00 2.71
2820 3280 1.202065 CGGACTCGAATGGCAATTGTG 60.202 52.381 7.40 0.00 39.00 3.33
2821 3281 4.930592 CGGACTCGAATGGCAATTGTGC 62.931 54.545 7.40 0.00 44.12 4.57
2829 3289 4.874534 GCAATTGTGCGCACAGAT 57.125 50.000 38.37 29.94 41.93 2.90
2830 3290 3.111536 GCAATTGTGCGCACAGATT 57.888 47.368 38.37 32.80 41.93 2.40
2831 3291 0.986992 GCAATTGTGCGCACAGATTC 59.013 50.000 38.37 25.71 41.93 2.52
2832 3292 1.621107 CAATTGTGCGCACAGATTCC 58.379 50.000 38.37 14.05 42.94 3.01
2833 3293 1.068402 CAATTGTGCGCACAGATTCCA 60.068 47.619 38.37 25.72 42.94 3.53
2834 3294 0.523072 ATTGTGCGCACAGATTCCAC 59.477 50.000 38.37 12.51 42.94 4.02
2835 3295 0.534877 TTGTGCGCACAGATTCCACT 60.535 50.000 38.37 0.00 42.94 4.00
2836 3296 0.950555 TGTGCGCACAGATTCCACTC 60.951 55.000 37.86 9.30 36.21 3.51
2837 3297 0.950555 GTGCGCACAGATTCCACTCA 60.951 55.000 34.52 0.00 0.00 3.41
2838 3298 0.671472 TGCGCACAGATTCCACTCAG 60.671 55.000 5.66 0.00 0.00 3.35
2839 3299 0.671781 GCGCACAGATTCCACTCAGT 60.672 55.000 0.30 0.00 0.00 3.41
2840 3300 1.404181 GCGCACAGATTCCACTCAGTA 60.404 52.381 0.30 0.00 0.00 2.74
2841 3301 2.263077 CGCACAGATTCCACTCAGTAC 58.737 52.381 0.00 0.00 0.00 2.73
2842 3302 2.352715 CGCACAGATTCCACTCAGTACA 60.353 50.000 0.00 0.00 0.00 2.90
2843 3303 3.664107 GCACAGATTCCACTCAGTACAA 58.336 45.455 0.00 0.00 0.00 2.41
2844 3304 4.256920 GCACAGATTCCACTCAGTACAAT 58.743 43.478 0.00 0.00 0.00 2.71
2845 3305 4.331168 GCACAGATTCCACTCAGTACAATC 59.669 45.833 0.00 1.09 0.00 2.67
2846 3306 5.728471 CACAGATTCCACTCAGTACAATCT 58.272 41.667 5.03 5.03 34.75 2.40
2848 3308 5.728471 CAGATTCCACTCAGTACAATCTGT 58.272 41.667 20.68 0.00 42.71 3.41
2849 3309 6.867550 CAGATTCCACTCAGTACAATCTGTA 58.132 40.000 20.68 0.00 42.71 2.74
2861 3321 6.233430 GTACAATCTGTACCATGCATGATC 57.767 41.667 28.31 16.57 45.52 2.92
2862 3322 4.139786 ACAATCTGTACCATGCATGATCC 58.860 43.478 28.31 14.30 0.00 3.36
2863 3323 4.139038 CAATCTGTACCATGCATGATCCA 58.861 43.478 28.31 17.80 0.00 3.41
2864 3324 4.652679 ATCTGTACCATGCATGATCCAT 57.347 40.909 28.31 9.97 0.00 3.41
2865 3325 4.011966 TCTGTACCATGCATGATCCATC 57.988 45.455 28.31 11.69 0.00 3.51
2866 3326 3.079578 CTGTACCATGCATGATCCATCC 58.920 50.000 28.31 8.56 0.00 3.51
2867 3327 2.079158 GTACCATGCATGATCCATCCG 58.921 52.381 28.31 10.78 0.00 4.18
2868 3328 0.766752 ACCATGCATGATCCATCCGA 59.233 50.000 28.31 0.00 0.00 4.55
2869 3329 1.162698 CCATGCATGATCCATCCGAC 58.837 55.000 28.31 0.00 0.00 4.79
2870 3330 0.794473 CATGCATGATCCATCCGACG 59.206 55.000 22.59 0.00 0.00 5.12
2871 3331 0.321034 ATGCATGATCCATCCGACGG 60.321 55.000 7.84 7.84 0.00 4.79
2872 3332 2.320587 GCATGATCCATCCGACGGC 61.321 63.158 9.66 0.00 0.00 5.68
2873 3333 1.669115 CATGATCCATCCGACGGCC 60.669 63.158 9.66 0.00 0.00 6.13
2874 3334 2.883828 ATGATCCATCCGACGGCCC 61.884 63.158 9.66 0.00 0.00 5.80
2875 3335 3.546543 GATCCATCCGACGGCCCA 61.547 66.667 9.66 0.00 0.00 5.36
2876 3336 3.521529 GATCCATCCGACGGCCCAG 62.522 68.421 9.66 0.00 0.00 4.45
2877 3337 4.770362 TCCATCCGACGGCCCAGA 62.770 66.667 9.66 0.00 0.00 3.86
2878 3338 4.227134 CCATCCGACGGCCCAGAG 62.227 72.222 9.66 0.00 0.00 3.35
2879 3339 3.461773 CATCCGACGGCCCAGAGT 61.462 66.667 9.66 0.00 0.00 3.24
2880 3340 3.148279 ATCCGACGGCCCAGAGTC 61.148 66.667 9.66 0.00 0.00 3.36
2884 3344 2.893398 GACGGCCCAGAGTCGATT 59.107 61.111 0.00 0.00 0.00 3.34
2885 3345 1.218316 GACGGCCCAGAGTCGATTT 59.782 57.895 0.00 0.00 0.00 2.17
2886 3346 0.391263 GACGGCCCAGAGTCGATTTT 60.391 55.000 0.00 0.00 0.00 1.82
2887 3347 0.036306 ACGGCCCAGAGTCGATTTTT 59.964 50.000 0.00 0.00 0.00 1.94
2888 3348 0.727398 CGGCCCAGAGTCGATTTTTC 59.273 55.000 0.00 0.00 0.00 2.29
2889 3349 1.676014 CGGCCCAGAGTCGATTTTTCT 60.676 52.381 0.00 0.00 0.00 2.52
2890 3350 2.418197 CGGCCCAGAGTCGATTTTTCTA 60.418 50.000 0.00 0.00 0.00 2.10
2891 3351 3.741388 CGGCCCAGAGTCGATTTTTCTAT 60.741 47.826 0.00 0.00 0.00 1.98
2892 3352 4.200092 GGCCCAGAGTCGATTTTTCTATT 58.800 43.478 0.00 0.00 0.00 1.73
2893 3353 4.640647 GGCCCAGAGTCGATTTTTCTATTT 59.359 41.667 0.00 0.00 0.00 1.40
2894 3354 5.125578 GGCCCAGAGTCGATTTTTCTATTTT 59.874 40.000 0.00 0.00 0.00 1.82
2895 3355 6.350194 GGCCCAGAGTCGATTTTTCTATTTTT 60.350 38.462 0.00 0.00 0.00 1.94
2896 3356 6.528072 GCCCAGAGTCGATTTTTCTATTTTTG 59.472 38.462 0.00 0.00 0.00 2.44
2897 3357 6.528072 CCCAGAGTCGATTTTTCTATTTTTGC 59.472 38.462 0.00 0.00 0.00 3.68
2898 3358 7.083858 CCAGAGTCGATTTTTCTATTTTTGCA 58.916 34.615 0.00 0.00 0.00 4.08
2899 3359 7.061094 CCAGAGTCGATTTTTCTATTTTTGCAC 59.939 37.037 0.00 0.00 0.00 4.57
2900 3360 7.061094 CAGAGTCGATTTTTCTATTTTTGCACC 59.939 37.037 0.00 0.00 0.00 5.01
2901 3361 6.981722 AGTCGATTTTTCTATTTTTGCACCT 58.018 32.000 0.00 0.00 0.00 4.00
2902 3362 8.106247 AGTCGATTTTTCTATTTTTGCACCTA 57.894 30.769 0.00 0.00 0.00 3.08
2903 3363 8.237267 AGTCGATTTTTCTATTTTTGCACCTAG 58.763 33.333 0.00 0.00 0.00 3.02
2904 3364 8.234546 GTCGATTTTTCTATTTTTGCACCTAGA 58.765 33.333 0.00 0.00 0.00 2.43
2905 3365 8.234546 TCGATTTTTCTATTTTTGCACCTAGAC 58.765 33.333 0.00 0.00 0.00 2.59
2906 3366 7.484959 CGATTTTTCTATTTTTGCACCTAGACC 59.515 37.037 0.00 0.00 0.00 3.85
2907 3367 7.833285 TTTTTCTATTTTTGCACCTAGACCT 57.167 32.000 0.00 0.00 0.00 3.85
2908 3368 7.448748 TTTTCTATTTTTGCACCTAGACCTC 57.551 36.000 0.00 0.00 0.00 3.85
2909 3369 6.374417 TTCTATTTTTGCACCTAGACCTCT 57.626 37.500 0.00 0.00 0.00 3.69
2910 3370 6.374417 TCTATTTTTGCACCTAGACCTCTT 57.626 37.500 0.00 0.00 0.00 2.85
2911 3371 6.407202 TCTATTTTTGCACCTAGACCTCTTC 58.593 40.000 0.00 0.00 0.00 2.87
2912 3372 4.706842 TTTTTGCACCTAGACCTCTTCT 57.293 40.909 0.00 0.00 38.51 2.85
2913 3373 4.706842 TTTTGCACCTAGACCTCTTCTT 57.293 40.909 0.00 0.00 35.55 2.52
2914 3374 3.963428 TTGCACCTAGACCTCTTCTTC 57.037 47.619 0.00 0.00 35.55 2.87
2915 3375 3.176924 TGCACCTAGACCTCTTCTTCT 57.823 47.619 0.00 0.00 35.55 2.85
2916 3376 4.317530 TGCACCTAGACCTCTTCTTCTA 57.682 45.455 0.00 0.00 35.55 2.10
2917 3377 4.873010 TGCACCTAGACCTCTTCTTCTAT 58.127 43.478 0.00 0.00 35.55 1.98
2918 3378 5.273208 TGCACCTAGACCTCTTCTTCTATT 58.727 41.667 0.00 0.00 35.55 1.73
2919 3379 5.361285 TGCACCTAGACCTCTTCTTCTATTC 59.639 44.000 0.00 0.00 35.55 1.75
2920 3380 5.596772 GCACCTAGACCTCTTCTTCTATTCT 59.403 44.000 0.00 0.00 35.55 2.40
2921 3381 6.773685 GCACCTAGACCTCTTCTTCTATTCTA 59.226 42.308 0.00 0.00 35.55 2.10
2922 3382 7.040686 GCACCTAGACCTCTTCTTCTATTCTAG 60.041 44.444 0.00 0.00 35.55 2.43
2923 3383 7.996644 CACCTAGACCTCTTCTTCTATTCTAGT 59.003 40.741 0.00 0.00 35.55 2.57
2924 3384 8.215736 ACCTAGACCTCTTCTTCTATTCTAGTC 58.784 40.741 0.00 0.00 35.55 2.59
2925 3385 7.386848 CCTAGACCTCTTCTTCTATTCTAGTCG 59.613 44.444 0.00 0.00 35.55 4.18
2926 3386 6.655930 AGACCTCTTCTTCTATTCTAGTCGT 58.344 40.000 0.00 0.00 0.00 4.34
2927 3387 7.114095 AGACCTCTTCTTCTATTCTAGTCGTT 58.886 38.462 0.00 0.00 0.00 3.85
2928 3388 7.281549 AGACCTCTTCTTCTATTCTAGTCGTTC 59.718 40.741 0.00 0.00 0.00 3.95
2929 3389 6.319405 ACCTCTTCTTCTATTCTAGTCGTTCC 59.681 42.308 0.00 0.00 0.00 3.62
2930 3390 6.238814 CCTCTTCTTCTATTCTAGTCGTTCCC 60.239 46.154 0.00 0.00 0.00 3.97
2931 3391 5.593502 TCTTCTTCTATTCTAGTCGTTCCCC 59.406 44.000 0.00 0.00 0.00 4.81
2932 3392 3.881688 TCTTCTATTCTAGTCGTTCCCCG 59.118 47.826 0.00 0.00 38.13 5.73
2933 3393 3.565764 TCTATTCTAGTCGTTCCCCGA 57.434 47.619 0.00 0.00 45.00 5.14
2940 3400 2.046700 TCGTTCCCCGAACATGGC 60.047 61.111 0.00 0.00 44.03 4.40
2941 3401 3.496131 CGTTCCCCGAACATGGCG 61.496 66.667 0.00 0.00 42.05 5.69
2942 3402 2.359478 GTTCCCCGAACATGGCGT 60.359 61.111 0.00 0.00 41.62 5.68
2943 3403 1.078988 GTTCCCCGAACATGGCGTA 60.079 57.895 0.00 0.00 41.62 4.42
2944 3404 1.087771 GTTCCCCGAACATGGCGTAG 61.088 60.000 0.00 0.00 41.62 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 4.827087 CTCCGCTGCGTCATGGCT 62.827 66.667 21.59 0.00 0.00 4.75
136 145 3.474570 CTCCTGGGGAAGCCGGAG 61.475 72.222 5.05 0.00 37.33 4.63
223 232 4.697756 CTCGGGCTGGCCGTTTCA 62.698 66.667 36.53 20.14 36.85 2.69
243 257 0.541392 AGGCGTGGTGAAGATATGCA 59.459 50.000 0.00 0.00 0.00 3.96
339 362 1.890979 GTCATGCGGCAGATCCTGG 60.891 63.158 9.25 0.00 31.21 4.45
399 422 2.970974 GCCACGTTCTGCCTTCTGC 61.971 63.158 0.00 0.00 41.77 4.26
400 423 2.328099 GGCCACGTTCTGCCTTCTG 61.328 63.158 12.14 0.00 44.46 3.02
401 424 2.032681 GGCCACGTTCTGCCTTCT 59.967 61.111 12.14 0.00 44.46 2.85
402 425 3.423154 CGGCCACGTTCTGCCTTC 61.423 66.667 16.07 0.00 45.71 3.46
403 426 3.883744 CTCGGCCACGTTCTGCCTT 62.884 63.158 16.07 0.00 45.71 4.35
404 427 4.379243 CTCGGCCACGTTCTGCCT 62.379 66.667 16.07 0.00 45.71 4.75
628 751 4.641645 TCCACCGCAACCTGCTGG 62.642 66.667 8.29 8.29 42.25 4.85
629 752 3.052082 CTCCACCGCAACCTGCTG 61.052 66.667 0.00 0.00 42.25 4.41
652 775 3.188786 CTACAAGCTGACGCGCCC 61.189 66.667 5.73 0.00 42.32 6.13
796 1044 3.646715 CCACCCCATGACCACCGT 61.647 66.667 0.00 0.00 0.00 4.83
802 1050 2.837031 ATTCACGGCCACCCCATGAC 62.837 60.000 2.24 0.00 0.00 3.06
803 1051 2.611505 ATTCACGGCCACCCCATGA 61.612 57.895 2.24 0.00 0.00 3.07
814 1062 1.086696 CTTGCCCTGTACATTCACGG 58.913 55.000 0.00 0.00 0.00 4.94
815 1063 1.808411 ACTTGCCCTGTACATTCACG 58.192 50.000 0.00 0.00 0.00 4.35
816 1064 4.546570 GAAAACTTGCCCTGTACATTCAC 58.453 43.478 0.00 0.00 0.00 3.18
817 1065 3.252215 CGAAAACTTGCCCTGTACATTCA 59.748 43.478 0.00 0.00 0.00 2.57
818 1066 3.252458 ACGAAAACTTGCCCTGTACATTC 59.748 43.478 0.00 0.00 0.00 2.67
819 1067 3.004315 CACGAAAACTTGCCCTGTACATT 59.996 43.478 0.00 0.00 0.00 2.71
820 1068 2.552315 CACGAAAACTTGCCCTGTACAT 59.448 45.455 0.00 0.00 0.00 2.29
821 1069 1.944024 CACGAAAACTTGCCCTGTACA 59.056 47.619 0.00 0.00 0.00 2.90
866 1114 1.136565 CGATTGAACGGCGGCAAAT 59.863 52.632 18.57 11.29 0.00 2.32
933 1213 3.066814 GGCCGTACTCCAGTCGGT 61.067 66.667 14.84 0.00 45.11 4.69
1323 1635 0.538516 CCCGGTGTTGATGGAACCAA 60.539 55.000 0.00 0.00 33.30 3.67
1467 1788 0.679505 TCGTCCTTGGTGACCTTGAG 59.320 55.000 2.11 0.00 31.35 3.02
1478 1805 3.499737 GGCATGGCGTCGTCCTTG 61.500 66.667 2.41 13.54 35.18 3.61
1482 1809 3.630148 CATCGGCATGGCGTCGTC 61.630 66.667 36.29 0.00 0.00 4.20
1483 1810 3.657448 TTCATCGGCATGGCGTCGT 62.657 57.895 36.29 22.58 0.00 4.34
1484 1811 2.874694 CTTCATCGGCATGGCGTCG 61.875 63.158 36.29 27.98 0.00 5.12
1485 1812 1.089481 TTCTTCATCGGCATGGCGTC 61.089 55.000 36.29 0.00 0.00 5.19
1486 1813 1.078497 TTCTTCATCGGCATGGCGT 60.078 52.632 36.29 22.99 0.00 5.68
1487 1814 1.645455 CTTCTTCATCGGCATGGCG 59.355 57.895 33.54 33.54 0.00 5.69
1555 1912 1.006571 TTCGTCTTCACGTCAGGGC 60.007 57.895 0.00 0.00 46.76 5.19
1585 1942 1.863267 CTCGCAGATGATCTTGGGAC 58.137 55.000 0.00 0.00 33.89 4.46
1586 1943 0.105593 GCTCGCAGATGATCTTGGGA 59.894 55.000 0.00 2.25 33.89 4.37
1587 1944 0.883814 GGCTCGCAGATGATCTTGGG 60.884 60.000 0.00 0.00 33.89 4.12
1588 1945 1.220169 CGGCTCGCAGATGATCTTGG 61.220 60.000 0.00 0.00 33.89 3.61
1589 1946 1.220169 CCGGCTCGCAGATGATCTTG 61.220 60.000 0.00 0.00 33.89 3.02
1590 1947 1.068753 CCGGCTCGCAGATGATCTT 59.931 57.895 0.00 0.00 33.89 2.40
1599 1956 4.680237 CTTGGACACCGGCTCGCA 62.680 66.667 0.00 0.00 0.00 5.10
1608 1965 0.033504 TCTGCCGTCTTCTTGGACAC 59.966 55.000 0.00 0.00 36.12 3.67
1835 2195 1.676635 GACCATGGAGCTGCTGCAA 60.677 57.895 27.28 11.45 42.74 4.08
1940 2377 2.464459 CCCATGTTCGAGCCTTCGC 61.464 63.158 0.00 0.00 46.28 4.70
1946 2383 1.519455 CGAGTCCCCATGTTCGAGC 60.519 63.158 0.00 0.00 35.19 5.03
1958 2395 1.619332 ACACCCTTCTTCTTCGAGTCC 59.381 52.381 0.00 0.00 0.00 3.85
1959 2396 2.296471 TGACACCCTTCTTCTTCGAGTC 59.704 50.000 0.00 0.00 0.00 3.36
1960 2397 2.297597 CTGACACCCTTCTTCTTCGAGT 59.702 50.000 0.00 0.00 0.00 4.18
1961 2398 2.353208 CCTGACACCCTTCTTCTTCGAG 60.353 54.545 0.00 0.00 0.00 4.04
1962 2399 1.618837 CCTGACACCCTTCTTCTTCGA 59.381 52.381 0.00 0.00 0.00 3.71
1963 2400 1.618837 TCCTGACACCCTTCTTCTTCG 59.381 52.381 0.00 0.00 0.00 3.79
1964 2401 2.027653 CCTCCTGACACCCTTCTTCTTC 60.028 54.545 0.00 0.00 0.00 2.87
1965 2402 1.981495 CCTCCTGACACCCTTCTTCTT 59.019 52.381 0.00 0.00 0.00 2.52
1966 2403 1.150135 TCCTCCTGACACCCTTCTTCT 59.850 52.381 0.00 0.00 0.00 2.85
1967 2404 1.645710 TCCTCCTGACACCCTTCTTC 58.354 55.000 0.00 0.00 0.00 2.87
1968 2405 2.118403 TTCCTCCTGACACCCTTCTT 57.882 50.000 0.00 0.00 0.00 2.52
1969 2406 2.118403 TTTCCTCCTGACACCCTTCT 57.882 50.000 0.00 0.00 0.00 2.85
1970 2407 2.951229 TTTTCCTCCTGACACCCTTC 57.049 50.000 0.00 0.00 0.00 3.46
1971 2408 3.916989 ACTATTTTCCTCCTGACACCCTT 59.083 43.478 0.00 0.00 0.00 3.95
1972 2409 3.532102 ACTATTTTCCTCCTGACACCCT 58.468 45.455 0.00 0.00 0.00 4.34
1973 2410 4.302559 AACTATTTTCCTCCTGACACCC 57.697 45.455 0.00 0.00 0.00 4.61
1974 2411 6.051179 ACTAACTATTTTCCTCCTGACACC 57.949 41.667 0.00 0.00 0.00 4.16
1975 2412 6.757478 GCTACTAACTATTTTCCTCCTGACAC 59.243 42.308 0.00 0.00 0.00 3.67
1976 2413 6.405508 CGCTACTAACTATTTTCCTCCTGACA 60.406 42.308 0.00 0.00 0.00 3.58
1977 2414 5.978322 CGCTACTAACTATTTTCCTCCTGAC 59.022 44.000 0.00 0.00 0.00 3.51
1978 2415 5.068723 CCGCTACTAACTATTTTCCTCCTGA 59.931 44.000 0.00 0.00 0.00 3.86
1979 2416 5.290386 CCGCTACTAACTATTTTCCTCCTG 58.710 45.833 0.00 0.00 0.00 3.86
1980 2417 4.344390 CCCGCTACTAACTATTTTCCTCCT 59.656 45.833 0.00 0.00 0.00 3.69
1981 2418 4.502777 CCCCGCTACTAACTATTTTCCTCC 60.503 50.000 0.00 0.00 0.00 4.30
1982 2419 4.502777 CCCCCGCTACTAACTATTTTCCTC 60.503 50.000 0.00 0.00 0.00 3.71
1983 2420 3.390311 CCCCCGCTACTAACTATTTTCCT 59.610 47.826 0.00 0.00 0.00 3.36
1984 2421 3.389002 TCCCCCGCTACTAACTATTTTCC 59.611 47.826 0.00 0.00 0.00 3.13
1985 2422 4.100653 AGTCCCCCGCTACTAACTATTTTC 59.899 45.833 0.00 0.00 0.00 2.29
1986 2423 4.035814 AGTCCCCCGCTACTAACTATTTT 58.964 43.478 0.00 0.00 0.00 1.82
1987 2424 3.387050 CAGTCCCCCGCTACTAACTATTT 59.613 47.826 0.00 0.00 0.00 1.40
1988 2425 2.963782 CAGTCCCCCGCTACTAACTATT 59.036 50.000 0.00 0.00 0.00 1.73
1989 2426 2.595238 CAGTCCCCCGCTACTAACTAT 58.405 52.381 0.00 0.00 0.00 2.12
1990 2427 1.410648 CCAGTCCCCCGCTACTAACTA 60.411 57.143 0.00 0.00 0.00 2.24
1991 2428 0.686769 CCAGTCCCCCGCTACTAACT 60.687 60.000 0.00 0.00 0.00 2.24
1992 2429 0.685458 TCCAGTCCCCCGCTACTAAC 60.685 60.000 0.00 0.00 0.00 2.34
1993 2430 0.041535 TTCCAGTCCCCCGCTACTAA 59.958 55.000 0.00 0.00 0.00 2.24
1994 2431 0.041535 TTTCCAGTCCCCCGCTACTA 59.958 55.000 0.00 0.00 0.00 1.82
1995 2432 0.838987 TTTTCCAGTCCCCCGCTACT 60.839 55.000 0.00 0.00 0.00 2.57
1996 2433 0.392595 CTTTTCCAGTCCCCCGCTAC 60.393 60.000 0.00 0.00 0.00 3.58
1997 2434 0.545787 TCTTTTCCAGTCCCCCGCTA 60.546 55.000 0.00 0.00 0.00 4.26
1998 2435 1.842381 CTCTTTTCCAGTCCCCCGCT 61.842 60.000 0.00 0.00 0.00 5.52
1999 2436 1.377333 CTCTTTTCCAGTCCCCCGC 60.377 63.158 0.00 0.00 0.00 6.13
2000 2437 0.690762 TTCTCTTTTCCAGTCCCCCG 59.309 55.000 0.00 0.00 0.00 5.73
2001 2438 1.705745 ACTTCTCTTTTCCAGTCCCCC 59.294 52.381 0.00 0.00 0.00 5.40
2002 2439 2.784347 CACTTCTCTTTTCCAGTCCCC 58.216 52.381 0.00 0.00 0.00 4.81
2003 2440 2.155279 GCACTTCTCTTTTCCAGTCCC 58.845 52.381 0.00 0.00 0.00 4.46
2004 2441 2.851195 TGCACTTCTCTTTTCCAGTCC 58.149 47.619 0.00 0.00 0.00 3.85
2005 2442 6.749923 AATATGCACTTCTCTTTTCCAGTC 57.250 37.500 0.00 0.00 0.00 3.51
2006 2443 7.119846 GTGTAATATGCACTTCTCTTTTCCAGT 59.880 37.037 0.00 0.00 34.30 4.00
2007 2444 7.414540 GGTGTAATATGCACTTCTCTTTTCCAG 60.415 40.741 9.60 0.00 37.07 3.86
2008 2445 6.374333 GGTGTAATATGCACTTCTCTTTTCCA 59.626 38.462 9.60 0.00 37.07 3.53
2009 2446 6.183360 GGGTGTAATATGCACTTCTCTTTTCC 60.183 42.308 9.60 0.00 37.07 3.13
2010 2447 6.183360 GGGGTGTAATATGCACTTCTCTTTTC 60.183 42.308 9.60 0.00 37.07 2.29
2011 2448 5.652452 GGGGTGTAATATGCACTTCTCTTTT 59.348 40.000 9.60 0.00 37.07 2.27
2012 2449 5.044846 AGGGGTGTAATATGCACTTCTCTTT 60.045 40.000 9.60 0.00 37.07 2.52
2013 2450 4.475016 AGGGGTGTAATATGCACTTCTCTT 59.525 41.667 9.60 0.00 37.07 2.85
2142 2580 1.104630 GTCAAACCCGGTCAAAACCA 58.895 50.000 0.00 0.00 46.86 3.67
2344 2790 5.817784 TGTTTCCAATTTATTACCTCCGGA 58.182 37.500 2.93 2.93 0.00 5.14
2768 3228 5.427157 TGCATATTACACCCCTCAACTCTAA 59.573 40.000 0.00 0.00 0.00 2.10
2801 3261 1.468054 GCACAATTGCCATTCGAGTCC 60.468 52.381 5.05 0.00 43.66 3.85
2802 3262 1.900237 GCACAATTGCCATTCGAGTC 58.100 50.000 5.05 0.00 43.66 3.36
2812 3272 0.986992 GAATCTGTGCGCACAATTGC 59.013 50.000 39.43 25.77 46.21 3.56
2813 3273 1.068402 TGGAATCTGTGCGCACAATTG 60.068 47.619 39.43 29.01 41.33 2.32
2814 3274 1.068333 GTGGAATCTGTGCGCACAATT 60.068 47.619 39.43 35.02 41.33 2.32
2815 3275 0.523072 GTGGAATCTGTGCGCACAAT 59.477 50.000 39.43 30.41 41.33 2.71
2816 3276 0.534877 AGTGGAATCTGTGCGCACAA 60.535 50.000 39.43 29.71 41.33 3.33
2817 3277 0.950555 GAGTGGAATCTGTGCGCACA 60.951 55.000 38.28 38.28 39.32 4.57
2818 3278 0.950555 TGAGTGGAATCTGTGCGCAC 60.951 55.000 33.11 33.11 0.00 5.34
2819 3279 0.671472 CTGAGTGGAATCTGTGCGCA 60.671 55.000 5.66 5.66 0.00 6.09
2820 3280 0.671781 ACTGAGTGGAATCTGTGCGC 60.672 55.000 0.00 0.00 31.05 6.09
2821 3281 2.263077 GTACTGAGTGGAATCTGTGCG 58.737 52.381 0.00 0.00 33.88 5.34
2822 3282 3.319137 TGTACTGAGTGGAATCTGTGC 57.681 47.619 0.00 0.00 35.38 4.57
2823 3283 5.579904 CAGATTGTACTGAGTGGAATCTGTG 59.420 44.000 25.27 12.69 42.41 3.66
2824 3284 5.728471 CAGATTGTACTGAGTGGAATCTGT 58.272 41.667 25.27 7.05 42.41 3.41
2847 3307 2.079158 CGGATGGATCATGCATGGTAC 58.921 52.381 25.97 21.18 31.64 3.34
2848 3308 1.977129 TCGGATGGATCATGCATGGTA 59.023 47.619 25.97 8.77 31.64 3.25
2849 3309 0.766752 TCGGATGGATCATGCATGGT 59.233 50.000 25.97 20.58 31.64 3.55
2850 3310 1.162698 GTCGGATGGATCATGCATGG 58.837 55.000 25.97 7.85 31.64 3.66
2851 3311 0.794473 CGTCGGATGGATCATGCATG 59.206 55.000 21.07 21.07 31.64 4.06
2852 3312 0.321034 CCGTCGGATGGATCATGCAT 60.321 55.000 10.90 0.00 31.64 3.96
2853 3313 1.069596 CCGTCGGATGGATCATGCA 59.930 57.895 10.90 0.00 31.64 3.96
2854 3314 2.320587 GCCGTCGGATGGATCATGC 61.321 63.158 20.37 0.00 0.00 4.06
2855 3315 1.669115 GGCCGTCGGATGGATCATG 60.669 63.158 20.37 0.00 0.00 3.07
2856 3316 2.743718 GGCCGTCGGATGGATCAT 59.256 61.111 20.37 0.00 0.00 2.45
2857 3317 3.546543 GGGCCGTCGGATGGATCA 61.547 66.667 20.37 0.00 0.00 2.92
2858 3318 3.521529 CTGGGCCGTCGGATGGATC 62.522 68.421 20.37 10.74 0.00 3.36
2859 3319 3.550431 CTGGGCCGTCGGATGGAT 61.550 66.667 20.37 0.00 0.00 3.41
2860 3320 4.770362 TCTGGGCCGTCGGATGGA 62.770 66.667 20.37 4.02 0.00 3.41
2861 3321 4.227134 CTCTGGGCCGTCGGATGG 62.227 72.222 17.49 12.04 0.00 3.51
2862 3322 3.432051 GACTCTGGGCCGTCGGATG 62.432 68.421 17.49 1.04 0.00 3.51
2863 3323 3.148279 GACTCTGGGCCGTCGGAT 61.148 66.667 17.49 0.00 0.00 4.18
2867 3327 0.391263 AAAATCGACTCTGGGCCGTC 60.391 55.000 0.00 0.00 0.00 4.79
2868 3328 0.036306 AAAAATCGACTCTGGGCCGT 59.964 50.000 0.00 0.00 0.00 5.68
2869 3329 0.727398 GAAAAATCGACTCTGGGCCG 59.273 55.000 0.00 0.00 0.00 6.13
2870 3330 2.115343 AGAAAAATCGACTCTGGGCC 57.885 50.000 0.00 0.00 0.00 5.80
2871 3331 5.819825 AAATAGAAAAATCGACTCTGGGC 57.180 39.130 0.00 0.00 0.00 5.36
2872 3332 6.528072 GCAAAAATAGAAAAATCGACTCTGGG 59.472 38.462 0.00 0.00 0.00 4.45
2873 3333 7.061094 GTGCAAAAATAGAAAAATCGACTCTGG 59.939 37.037 0.00 0.00 0.00 3.86
2874 3334 7.061094 GGTGCAAAAATAGAAAAATCGACTCTG 59.939 37.037 0.00 0.00 0.00 3.35
2875 3335 7.040409 AGGTGCAAAAATAGAAAAATCGACTCT 60.040 33.333 0.00 0.00 0.00 3.24
2876 3336 7.084486 AGGTGCAAAAATAGAAAAATCGACTC 58.916 34.615 0.00 0.00 0.00 3.36
2877 3337 6.981722 AGGTGCAAAAATAGAAAAATCGACT 58.018 32.000 0.00 0.00 0.00 4.18
2878 3338 8.234546 TCTAGGTGCAAAAATAGAAAAATCGAC 58.765 33.333 0.00 0.00 0.00 4.20
2879 3339 8.234546 GTCTAGGTGCAAAAATAGAAAAATCGA 58.765 33.333 0.00 0.00 0.00 3.59
2880 3340 7.484959 GGTCTAGGTGCAAAAATAGAAAAATCG 59.515 37.037 0.00 0.00 0.00 3.34
2881 3341 8.523658 AGGTCTAGGTGCAAAAATAGAAAAATC 58.476 33.333 0.00 0.00 0.00 2.17
2882 3342 8.422577 AGGTCTAGGTGCAAAAATAGAAAAAT 57.577 30.769 0.00 0.00 0.00 1.82
2883 3343 7.724061 AGAGGTCTAGGTGCAAAAATAGAAAAA 59.276 33.333 0.00 0.00 0.00 1.94
2884 3344 7.231467 AGAGGTCTAGGTGCAAAAATAGAAAA 58.769 34.615 0.00 0.00 0.00 2.29
2885 3345 6.779860 AGAGGTCTAGGTGCAAAAATAGAAA 58.220 36.000 0.00 0.00 0.00 2.52
2886 3346 6.374417 AGAGGTCTAGGTGCAAAAATAGAA 57.626 37.500 0.00 0.00 0.00 2.10
2887 3347 6.213600 AGAAGAGGTCTAGGTGCAAAAATAGA 59.786 38.462 0.00 0.00 33.56 1.98
2888 3348 6.410540 AGAAGAGGTCTAGGTGCAAAAATAG 58.589 40.000 0.00 0.00 33.56 1.73
2889 3349 6.374417 AGAAGAGGTCTAGGTGCAAAAATA 57.626 37.500 0.00 0.00 33.56 1.40
2890 3350 5.248380 AGAAGAGGTCTAGGTGCAAAAAT 57.752 39.130 0.00 0.00 33.56 1.82
2891 3351 4.706842 AGAAGAGGTCTAGGTGCAAAAA 57.293 40.909 0.00 0.00 33.56 1.94
2892 3352 4.348168 AGAAGAAGAGGTCTAGGTGCAAAA 59.652 41.667 0.00 0.00 34.56 2.44
2893 3353 3.904339 AGAAGAAGAGGTCTAGGTGCAAA 59.096 43.478 0.00 0.00 34.56 3.68
2894 3354 3.511477 AGAAGAAGAGGTCTAGGTGCAA 58.489 45.455 0.00 0.00 34.56 4.08
2895 3355 3.176924 AGAAGAAGAGGTCTAGGTGCA 57.823 47.619 0.00 0.00 34.56 4.57
2896 3356 5.596772 AGAATAGAAGAAGAGGTCTAGGTGC 59.403 44.000 0.00 0.00 34.56 5.01
2897 3357 7.996644 ACTAGAATAGAAGAAGAGGTCTAGGTG 59.003 40.741 0.00 0.00 42.77 4.00
2898 3358 8.109560 ACTAGAATAGAAGAAGAGGTCTAGGT 57.890 38.462 0.00 0.00 42.77 3.08
2899 3359 7.386848 CGACTAGAATAGAAGAAGAGGTCTAGG 59.613 44.444 0.00 0.00 42.77 3.02
2900 3360 7.929785 ACGACTAGAATAGAAGAAGAGGTCTAG 59.070 40.741 0.00 0.00 42.77 2.43
2901 3361 7.794041 ACGACTAGAATAGAAGAAGAGGTCTA 58.206 38.462 0.00 0.00 42.77 2.59
2902 3362 6.655930 ACGACTAGAATAGAAGAAGAGGTCT 58.344 40.000 0.00 0.00 42.77 3.85
2903 3363 6.930667 ACGACTAGAATAGAAGAAGAGGTC 57.069 41.667 0.00 0.00 42.77 3.85
2904 3364 6.319405 GGAACGACTAGAATAGAAGAAGAGGT 59.681 42.308 0.00 0.00 42.77 3.85
2905 3365 6.238814 GGGAACGACTAGAATAGAAGAAGAGG 60.239 46.154 0.00 0.00 42.77 3.69
2906 3366 6.238814 GGGGAACGACTAGAATAGAAGAAGAG 60.239 46.154 0.00 0.00 42.77 2.85
2907 3367 5.593502 GGGGAACGACTAGAATAGAAGAAGA 59.406 44.000 0.00 0.00 42.77 2.87
2908 3368 5.834169 GGGGAACGACTAGAATAGAAGAAG 58.166 45.833 0.00 0.00 42.77 2.85
2909 3369 5.848833 GGGGAACGACTAGAATAGAAGAA 57.151 43.478 0.00 0.00 42.77 2.52
2924 3384 2.839043 TACGCCATGTTCGGGGAACG 62.839 60.000 9.02 0.00 44.55 3.95
2925 3385 1.078988 TACGCCATGTTCGGGGAAC 60.079 57.895 9.02 1.65 41.43 3.62
2926 3386 1.219664 CTACGCCATGTTCGGGGAA 59.780 57.895 9.02 0.00 41.43 3.97
2927 3387 2.897207 CTACGCCATGTTCGGGGA 59.103 61.111 9.02 0.00 41.43 4.81
2928 3388 2.895372 GCTACGCCATGTTCGGGG 60.895 66.667 9.02 0.00 44.36 5.73
2929 3389 2.125310 TGCTACGCCATGTTCGGG 60.125 61.111 9.02 0.00 0.00 5.14
2930 3390 0.179121 TACTGCTACGCCATGTTCGG 60.179 55.000 9.02 0.00 0.00 4.30
2931 3391 1.200483 CTACTGCTACGCCATGTTCG 58.800 55.000 3.46 3.46 0.00 3.95
2932 3392 2.295253 ACTACTGCTACGCCATGTTC 57.705 50.000 0.00 0.00 0.00 3.18
2933 3393 2.289444 ACAACTACTGCTACGCCATGTT 60.289 45.455 0.00 0.00 0.00 2.71
2934 3394 1.275291 ACAACTACTGCTACGCCATGT 59.725 47.619 0.00 0.00 0.00 3.21
2935 3395 2.010145 ACAACTACTGCTACGCCATG 57.990 50.000 0.00 0.00 0.00 3.66
2936 3396 3.194968 ACTTACAACTACTGCTACGCCAT 59.805 43.478 0.00 0.00 0.00 4.40
2937 3397 2.559668 ACTTACAACTACTGCTACGCCA 59.440 45.455 0.00 0.00 0.00 5.69
2938 3398 3.227810 ACTTACAACTACTGCTACGCC 57.772 47.619 0.00 0.00 0.00 5.68
2939 3399 3.181533 GCAACTTACAACTACTGCTACGC 60.182 47.826 0.00 0.00 0.00 4.42
2940 3400 4.235360 AGCAACTTACAACTACTGCTACG 58.765 43.478 0.00 0.00 38.32 3.51
2941 3401 4.323868 CGAGCAACTTACAACTACTGCTAC 59.676 45.833 0.00 0.00 40.10 3.58
2942 3402 4.022589 ACGAGCAACTTACAACTACTGCTA 60.023 41.667 0.00 0.00 40.10 3.49
2943 3403 3.243771 ACGAGCAACTTACAACTACTGCT 60.244 43.478 0.00 0.00 42.57 4.24
2944 3404 3.057734 ACGAGCAACTTACAACTACTGC 58.942 45.455 0.00 0.00 0.00 4.40
2945 3405 4.323868 GCTACGAGCAACTTACAACTACTG 59.676 45.833 0.00 0.00 41.89 2.74
2946 3406 4.217983 AGCTACGAGCAACTTACAACTACT 59.782 41.667 9.09 0.00 45.56 2.57
2947 3407 4.483311 AGCTACGAGCAACTTACAACTAC 58.517 43.478 9.09 0.00 45.56 2.73
2948 3408 4.670992 CGAGCTACGAGCAACTTACAACTA 60.671 45.833 9.09 0.00 45.56 2.24
2949 3409 3.576648 GAGCTACGAGCAACTTACAACT 58.423 45.455 9.09 0.00 45.56 3.16
2950 3410 2.341760 CGAGCTACGAGCAACTTACAAC 59.658 50.000 9.09 0.00 45.56 3.32
2951 3411 2.030540 ACGAGCTACGAGCAACTTACAA 60.031 45.455 11.64 0.00 45.56 2.41
2952 3412 1.538512 ACGAGCTACGAGCAACTTACA 59.461 47.619 11.64 0.00 45.56 2.41
2953 3413 2.259505 ACGAGCTACGAGCAACTTAC 57.740 50.000 11.64 0.00 45.56 2.34
2954 3414 3.791122 GCATACGAGCTACGAGCAACTTA 60.791 47.826 11.64 2.79 45.56 2.24
2955 3415 2.798680 CATACGAGCTACGAGCAACTT 58.201 47.619 11.64 1.07 45.56 2.66


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

AutoCloner maintained by Alex Coulton.