Multiple sequence alignment - TraesCS6B01G113400

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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 TraesCS6B01G113400 chr6B 100.000 4321 0 0 1 4321 95818131 95822451 0.000000e+00 7980.0
1 TraesCS6B01G113400 chr6B 82.905 1556 205 30 937 2452 62001218 62002752 0.000000e+00 1343.0
2 TraesCS6B01G113400 chr6B 88.004 892 95 2 1020 1908 95722926 95723808 0.000000e+00 1044.0
3 TraesCS6B01G113400 chr6B 81.978 1082 113 34 1913 2952 95755895 95756936 0.000000e+00 843.0
4 TraesCS6B01G113400 chr6B 100.000 449 0 0 4674 5122 95822804 95823252 0.000000e+00 830.0
5 TraesCS6B01G113400 chr6B 79.061 277 39 10 3148 3419 62003245 62003507 6.820000e-39 172.0
6 TraesCS6B01G113400 chr6D 94.885 1994 96 5 863 2852 41545468 41543477 0.000000e+00 3112.0
7 TraesCS6B01G113400 chr6D 83.575 2003 239 44 1020 2952 28683579 28681597 0.000000e+00 1794.0
8 TraesCS6B01G113400 chr6D 89.209 1075 109 4 1020 2089 41596462 41595390 0.000000e+00 1336.0
9 TraesCS6B01G113400 chr6D 88.348 781 50 10 3147 3908 41543429 41542671 0.000000e+00 900.0
10 TraesCS6B01G113400 chr6D 82.412 904 110 29 2087 2952 41583082 41582190 0.000000e+00 743.0
11 TraesCS6B01G113400 chr6D 93.348 451 25 3 4674 5122 41541922 41541475 0.000000e+00 662.0
12 TraesCS6B01G113400 chr6D 93.766 385 20 2 3912 4292 41542341 41541957 4.450000e-160 575.0
13 TraesCS6B01G113400 chr6D 76.900 329 46 16 3329 3630 28681191 28680866 5.310000e-35 159.0
14 TraesCS6B01G113400 chr6D 96.552 58 2 0 2895 2952 41543477 41543420 4.220000e-16 97.1
15 TraesCS6B01G113400 chr6D 95.238 42 2 0 3110 3151 19352424 19352383 3.310000e-07 67.6
16 TraesCS6B01G113400 chr6D 100.000 35 0 0 4171 4205 28680328 28680294 1.190000e-06 65.8
17 TraesCS6B01G113400 chr6A 93.702 1810 73 10 861 2662 52039201 52037425 0.000000e+00 2673.0
18 TraesCS6B01G113400 chr6A 90.007 1521 125 15 858 2361 52118905 52117395 0.000000e+00 1941.0
19 TraesCS6B01G113400 chr6A 83.651 1994 253 38 1020 2952 33967125 33969106 0.000000e+00 1808.0
20 TraesCS6B01G113400 chr6A 89.252 735 46 5 3147 3863 52037193 52036474 0.000000e+00 889.0
21 TraesCS6B01G113400 chr6A 93.939 396 24 0 440 835 60158942 60158547 2.640000e-167 599.0
22 TraesCS6B01G113400 chr6A 92.248 387 23 3 3912 4292 52036467 52036082 4.510000e-150 542.0
23 TraesCS6B01G113400 chr6A 91.901 284 19 3 4674 4956 52036047 52035767 1.340000e-105 394.0
24 TraesCS6B01G113400 chr6A 94.048 252 14 1 2701 2952 52037434 52037184 1.040000e-101 381.0
25 TraesCS6B01G113400 chr6A 94.531 128 6 1 4996 5122 52035766 52035639 4.050000e-46 196.0
26 TraesCS6B01G113400 chr6A 80.905 199 34 4 2952 3148 46302351 46302547 2.470000e-33 154.0
27 TraesCS6B01G113400 chr6A 94.872 39 2 0 4164 4202 33970273 33970311 1.540000e-05 62.1
28 TraesCS6B01G113400 chr7A 90.940 872 41 17 1 835 130299993 130300863 0.000000e+00 1138.0
29 TraesCS6B01G113400 chr7A 90.226 798 36 21 1 758 170896546 170897341 0.000000e+00 1003.0
30 TraesCS6B01G113400 chr5A 91.014 868 40 17 1 831 426267328 426266462 0.000000e+00 1136.0
31 TraesCS6B01G113400 chrUn 90.559 858 44 24 1 824 49013984 49014838 0.000000e+00 1101.0
32 TraesCS6B01G113400 chrUn 88.377 869 61 9 1 831 259680611 259681477 0.000000e+00 1009.0
33 TraesCS6B01G113400 chrUn 88.377 869 61 9 1 831 359784687 359785553 0.000000e+00 1009.0
34 TraesCS6B01G113400 chrUn 79.227 207 29 14 2949 3148 263441532 263441333 1.160000e-26 132.0
35 TraesCS6B01G113400 chrUn 78.605 215 33 12 2945 3152 136329385 136329593 4.160000e-26 130.0
36 TraesCS6B01G113400 chrUn 97.959 49 0 1 3101 3148 379883102 379883054 3.290000e-12 84.2
37 TraesCS6B01G113400 chrUn 97.959 49 0 1 3101 3148 466515864 466515912 3.290000e-12 84.2
38 TraesCS6B01G113400 chrUn 97.297 37 1 0 3112 3148 312869480 312869444 4.280000e-06 63.9
39 TraesCS6B01G113400 chrUn 97.297 37 1 0 3112 3148 312874349 312874385 4.280000e-06 63.9
40 TraesCS6B01G113400 chrUn 97.297 37 1 0 3112 3148 340781264 340781228 4.280000e-06 63.9
41 TraesCS6B01G113400 chr3A 89.643 869 52 17 1 831 738658661 738659529 0.000000e+00 1072.0
42 TraesCS6B01G113400 chr3A 93.893 393 24 0 440 832 181139082 181139474 1.230000e-165 593.0
43 TraesCS6B01G113400 chr1A 89.192 842 64 15 1 835 53995245 53994424 0.000000e+00 1026.0
44 TraesCS6B01G113400 chr1A 89.111 799 44 11 1 758 441796288 441795492 0.000000e+00 953.0
45 TraesCS6B01G113400 chr1A 75.758 198 39 9 2956 3148 4159480 4159287 1.960000e-14 91.6
46 TraesCS6B01G113400 chr7B 90.602 798 31 21 1 758 37080688 37081481 0.000000e+00 1018.0
47 TraesCS6B01G113400 chr7B 93.434 198 12 1 2952 3148 613197072 613196875 5.020000e-75 292.0
48 TraesCS6B01G113400 chr7B 88.832 197 18 4 2954 3150 469795007 469795199 6.630000e-59 239.0
49 TraesCS6B01G113400 chr3B 94.279 402 22 1 440 840 807502058 807502459 9.430000e-172 614.0
50 TraesCS6B01G113400 chr3B 94.264 401 20 2 440 840 100830186 100829789 1.220000e-170 610.0
51 TraesCS6B01G113400 chr3B 95.065 385 18 1 440 824 437812717 437812334 5.670000e-169 604.0
52 TraesCS6B01G113400 chr3B 94.545 165 6 3 2966 3129 752079738 752079900 8.510000e-63 252.0
53 TraesCS6B01G113400 chr4A 93.451 397 26 0 440 836 520123529 520123925 1.590000e-164 590.0
54 TraesCS6B01G113400 chr4A 92.453 212 13 2 2952 3163 657941068 657940860 3.000000e-77 300.0
55 TraesCS6B01G113400 chr4A 91.981 212 14 2 2952 3163 657980528 657980320 1.390000e-75 294.0
56 TraesCS6B01G113400 chr2D 75.109 1149 229 40 1037 2155 586571385 586572506 7.710000e-133 484.0
57 TraesCS6B01G113400 chr2D 81.281 203 27 10 2952 3148 414964743 414964940 2.470000e-33 154.0
58 TraesCS6B01G113400 chr2D 84.516 155 24 0 1037 1191 586748743 586748897 2.470000e-33 154.0
59 TraesCS6B01G113400 chr4D 74.314 1129 240 33 1041 2153 73993518 73992424 2.830000e-117 433.0
60 TraesCS6B01G113400 chr4D 77.340 203 28 13 2949 3148 456060353 456060540 2.520000e-18 104.0
61 TraesCS6B01G113400 chr4B 73.608 1167 255 38 1013 2155 106049399 106048262 2.870000e-107 399.0
62 TraesCS6B01G113400 chr4B 92.784 194 14 0 2955 3148 87432075 87431882 1.090000e-71 281.0
63 TraesCS6B01G113400 chr4B 92.347 196 14 1 2954 3148 507235562 507235367 1.400000e-70 278.0
64 TraesCS6B01G113400 chr4B 77.451 204 35 8 2953 3148 120250389 120250589 1.510000e-20 111.0
65 TraesCS6B01G113400 chr4B 87.805 82 7 3 3069 3148 20732129 20732209 5.460000e-15 93.5
66 TraesCS6B01G113400 chr5B 95.960 198 5 3 2953 3148 690688165 690687969 8.280000e-83 318.0
67 TraesCS6B01G113400 chr5B 77.833 203 33 12 2953 3148 589464154 589463957 1.170000e-21 115.0
68 TraesCS6B01G113400 chr5B 81.600 125 22 1 1065 1188 685443756 685443880 9.070000e-18 102.0
69 TraesCS6B01G113400 chr5B 75.691 181 40 4 1015 1191 685422907 685422727 2.540000e-13 87.9
70 TraesCS6B01G113400 chr1B 95.431 197 7 2 2953 3148 680159032 680158837 3.850000e-81 313.0
71 TraesCS6B01G113400 chr1B 94.444 198 9 2 2952 3148 59058219 59058023 2.320000e-78 303.0
72 TraesCS6B01G113400 chr7D 81.188 202 27 10 2952 3148 537208963 537209158 8.880000e-33 152.0
73 TraesCS6B01G113400 chr5D 75.862 203 40 9 2951 3148 550558668 550558470 1.520000e-15 95.3
74 TraesCS6B01G113400 chr2A 81.720 93 13 3 2321 2411 721519140 721519230 1.980000e-09 75.0
75 TraesCS6B01G113400 chr1D 95.745 47 1 1 3103 3148 48024446 48024400 1.980000e-09 75.0


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 TraesCS6B01G113400 chr6B 95818131 95823252 5121 False 4405.000000 7980 100.000000 1 5122 2 chr6B.!!$F4 5121
1 TraesCS6B01G113400 chr6B 95722926 95723808 882 False 1044.000000 1044 88.004000 1020 1908 1 chr6B.!!$F1 888
2 TraesCS6B01G113400 chr6B 95755895 95756936 1041 False 843.000000 843 81.978000 1913 2952 1 chr6B.!!$F2 1039
3 TraesCS6B01G113400 chr6B 62001218 62003507 2289 False 757.500000 1343 80.983000 937 3419 2 chr6B.!!$F3 2482
4 TraesCS6B01G113400 chr6D 41595390 41596462 1072 True 1336.000000 1336 89.209000 1020 2089 1 chr6D.!!$R3 1069
5 TraesCS6B01G113400 chr6D 41541475 41545468 3993 True 1069.220000 3112 93.379800 863 5122 5 chr6D.!!$R5 4259
6 TraesCS6B01G113400 chr6D 41582190 41583082 892 True 743.000000 743 82.412000 2087 2952 1 chr6D.!!$R2 865
7 TraesCS6B01G113400 chr6D 28680294 28683579 3285 True 672.933333 1794 86.825000 1020 4205 3 chr6D.!!$R4 3185
8 TraesCS6B01G113400 chr6A 52117395 52118905 1510 True 1941.000000 1941 90.007000 858 2361 1 chr6A.!!$R1 1503
9 TraesCS6B01G113400 chr6A 33967125 33970311 3186 False 935.050000 1808 89.261500 1020 4202 2 chr6A.!!$F2 3182
10 TraesCS6B01G113400 chr6A 52035639 52039201 3562 True 845.833333 2673 92.613667 861 5122 6 chr6A.!!$R3 4261
11 TraesCS6B01G113400 chr7A 130299993 130300863 870 False 1138.000000 1138 90.940000 1 835 1 chr7A.!!$F1 834
12 TraesCS6B01G113400 chr7A 170896546 170897341 795 False 1003.000000 1003 90.226000 1 758 1 chr7A.!!$F2 757
13 TraesCS6B01G113400 chr5A 426266462 426267328 866 True 1136.000000 1136 91.014000 1 831 1 chr5A.!!$R1 830
14 TraesCS6B01G113400 chrUn 49013984 49014838 854 False 1101.000000 1101 90.559000 1 824 1 chrUn.!!$F1 823
15 TraesCS6B01G113400 chrUn 259680611 259681477 866 False 1009.000000 1009 88.377000 1 831 1 chrUn.!!$F3 830
16 TraesCS6B01G113400 chrUn 359784687 359785553 866 False 1009.000000 1009 88.377000 1 831 1 chrUn.!!$F5 830
17 TraesCS6B01G113400 chr3A 738658661 738659529 868 False 1072.000000 1072 89.643000 1 831 1 chr3A.!!$F2 830
18 TraesCS6B01G113400 chr1A 53994424 53995245 821 True 1026.000000 1026 89.192000 1 835 1 chr1A.!!$R2 834
19 TraesCS6B01G113400 chr1A 441795492 441796288 796 True 953.000000 953 89.111000 1 758 1 chr1A.!!$R3 757
20 TraesCS6B01G113400 chr7B 37080688 37081481 793 False 1018.000000 1018 90.602000 1 758 1 chr7B.!!$F1 757
21 TraesCS6B01G113400 chr2D 586571385 586572506 1121 False 484.000000 484 75.109000 1037 2155 1 chr2D.!!$F2 1118
22 TraesCS6B01G113400 chr4D 73992424 73993518 1094 True 433.000000 433 74.314000 1041 2153 1 chr4D.!!$R1 1112
23 TraesCS6B01G113400 chr4B 106048262 106049399 1137 True 399.000000 399 73.608000 1013 2155 1 chr4B.!!$R2 1142

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
80 82 0.889994 TGTGTGCATTTGCCATCTCC 59.110 50.000 0.00 0.00 41.18 3.71 F
963 1013 1.065418 TCCTCGCTTCTTCCCATTTCC 60.065 52.381 0.00 0.00 0.00 3.13 F
1047 1109 0.100682 CGGTCAACCTCATCGACGAT 59.899 55.000 4.05 4.05 0.00 3.73 F
1539 1613 0.163788 CAACTGATGGCAACGACGAC 59.836 55.000 0.00 0.00 42.51 4.34 F
3017 3241 0.253327 AAAACTGATCGAGGAGGGCC 59.747 55.000 0.00 0.00 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1028 1087 0.100682 ATCGTCGATGAGGTTGACCG 59.899 55.000 13.65 0.00 42.08 4.79 R
2957 3181 1.530323 TAACTTTTTCCTGGCTCCGC 58.470 50.000 0.00 0.00 0.00 5.54 R
2998 3222 0.253327 GGCCCTCCTCGATCAGTTTT 59.747 55.000 0.00 0.00 0.00 2.43 R
3141 3365 0.390860 AGTCTGACAGTGACAGTGGC 59.609 55.000 19.68 12.22 36.94 5.01 R
4964 5913 1.346395 TCGTTGTACTGGATGCCTTGT 59.654 47.619 0.00 0.00 0.00 3.16 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
65 67 3.706055 CACAAGGGCTAGTGTGTGT 57.294 52.632 3.62 0.00 40.22 3.72
80 82 0.889994 TGTGTGCATTTGCCATCTCC 59.110 50.000 0.00 0.00 41.18 3.71
84 86 2.492773 GCATTTGCCATCTCCCCCG 61.493 63.158 0.00 0.00 34.31 5.73
234 244 2.032071 GGGTACACGGCAACTGCT 59.968 61.111 1.06 0.00 41.70 4.24
360 370 2.736890 CGTGCACGTAAGCAGATGA 58.263 52.632 30.50 0.00 46.69 2.92
433 444 4.727475 GCAACTCTTTCAACTGCCTAATC 58.273 43.478 0.00 0.00 0.00 1.75
436 447 6.606768 CAACTCTTTCAACTGCCTAATCTTC 58.393 40.000 0.00 0.00 0.00 2.87
437 448 5.869579 ACTCTTTCAACTGCCTAATCTTCA 58.130 37.500 0.00 0.00 0.00 3.02
562 605 3.985279 CAGTTAAACGAACATGGACGAGA 59.015 43.478 17.79 3.05 40.86 4.04
782 828 8.158132 TGTTCCTCTTATACACCACACAAAATA 58.842 33.333 0.00 0.00 0.00 1.40
824 870 1.507562 CACACGTGTGGCACTTATCA 58.492 50.000 35.65 0.00 42.10 2.15
826 872 1.070134 ACACGTGTGGCACTTATCAGT 59.930 47.619 22.71 7.14 34.19 3.41
849 895 9.769093 CAGTGTCCTAAATTATTAAAAGAACCG 57.231 33.333 0.00 0.00 0.00 4.44
850 896 9.511272 AGTGTCCTAAATTATTAAAAGAACCGT 57.489 29.630 0.00 0.00 0.00 4.83
963 1013 1.065418 TCCTCGCTTCTTCCCATTTCC 60.065 52.381 0.00 0.00 0.00 3.13
969 1019 2.633488 CTTCTTCCCATTTCCTCCGAC 58.367 52.381 0.00 0.00 0.00 4.79
1047 1109 0.100682 CGGTCAACCTCATCGACGAT 59.899 55.000 4.05 4.05 0.00 3.73
1062 1124 3.242268 CGATGTCGTCGCAGAGATT 57.758 52.632 0.67 0.00 44.33 2.40
1101 1163 2.665603 GAGCCCGAGCACCTCTTT 59.334 61.111 0.00 0.00 43.56 2.52
1105 1167 2.262915 CCGAGCACCTCTTTCGCT 59.737 61.111 0.00 0.00 39.12 4.93
1211 1276 3.003173 CCTCGGCCTCCTCCACAA 61.003 66.667 0.00 0.00 0.00 3.33
1431 1505 0.459585 CCAATCCGGACATCGACGTT 60.460 55.000 6.12 0.00 42.43 3.99
1452 1526 2.829914 ATCTACACCGCCGCCGTA 60.830 61.111 0.00 0.00 0.00 4.02
1521 1595 2.338620 CGTGTCGTCTTCCTGGCA 59.661 61.111 0.00 0.00 0.00 4.92
1529 1603 1.457346 GTCTTCCTGGCAACTGATGG 58.543 55.000 0.00 0.00 37.83 3.51
1539 1613 0.163788 CAACTGATGGCAACGACGAC 59.836 55.000 0.00 0.00 42.51 4.34
1577 1651 1.544691 GTACTCATCGGTCACAGGTGT 59.455 52.381 0.00 0.00 0.00 4.16
1607 1681 1.802960 GCCGGTATCTCTCGACGATAA 59.197 52.381 1.90 0.00 0.00 1.75
1910 2029 1.003696 GTCAAGGAAGGTGAAGGGAGG 59.996 57.143 0.00 0.00 0.00 4.30
1964 2083 2.024177 TGGAGAAAATCATGCCCATGGA 60.024 45.455 15.22 0.00 39.24 3.41
2040 2159 4.202111 TGTGTCATCTTCGTCAGAACAGAA 60.202 41.667 0.00 0.00 34.16 3.02
2089 2208 1.608283 CCGGACTGGTGAAGAAGGTTC 60.608 57.143 0.00 0.00 0.00 3.62
2154 2286 5.981494 TCTACACTCCTGGTATGGTACTA 57.019 43.478 0.00 0.00 0.00 1.82
2194 2326 6.088824 CAGCTTCCATAAGTTTGCTTAGTTG 58.911 40.000 0.00 0.00 40.17 3.16
2232 2366 9.944663 TTTGTGAACAATTAGTCAATCAGTTAC 57.055 29.630 0.00 0.00 35.55 2.50
2273 2421 8.454570 AATATTTGTTAGTTTGTATACCCGGG 57.545 34.615 22.25 22.25 0.00 5.73
2403 2560 5.353111 TGATATGCATTGGTTGAATTGCTG 58.647 37.500 3.54 0.00 0.00 4.41
2517 2711 4.345257 TCTCAAGCTCAGTCTTGTAACCTT 59.655 41.667 8.21 0.00 42.90 3.50
2588 2796 3.503748 AGTTGGCTATGAGTTTTCTGCAC 59.496 43.478 0.00 0.00 0.00 4.57
2619 2829 4.080413 TCTCAGATCATGGCATTGTTACCA 60.080 41.667 0.00 0.00 41.06 3.25
2654 2865 3.450457 ACCTGATCTCTTAGTCTGCCTTG 59.550 47.826 0.00 0.00 0.00 3.61
2674 2888 7.826744 TGCCTTGGTTGTTTTCTTTTAGATTTT 59.173 29.630 0.00 0.00 0.00 1.82
2747 2963 7.381408 GTGCAGGTCAATATGATCAATTTCATG 59.619 37.037 0.00 6.28 36.97 3.07
2810 3033 8.607459 CATGTCAGTCATATTTCTGTTACTTCC 58.393 37.037 4.49 0.00 34.67 3.46
2867 3091 8.445275 AGAATAGTGTGTAGTCTATCTGTCTG 57.555 38.462 0.00 0.00 0.00 3.51
2872 3096 5.746245 GTGTGTAGTCTATCTGTCTGCATTC 59.254 44.000 0.00 0.00 30.95 2.67
2883 3107 2.827322 TGTCTGCATTCCCTTTTCATGG 59.173 45.455 0.00 0.00 0.00 3.66
2943 3167 1.754803 CCGGGATGTCAAGTAGCAGTA 59.245 52.381 0.00 0.00 0.00 2.74
2944 3168 2.365617 CCGGGATGTCAAGTAGCAGTAT 59.634 50.000 0.00 0.00 0.00 2.12
2945 3169 3.553096 CCGGGATGTCAAGTAGCAGTATC 60.553 52.174 0.00 0.00 0.00 2.24
2946 3170 3.068165 CGGGATGTCAAGTAGCAGTATCA 59.932 47.826 0.00 0.00 0.00 2.15
2947 3171 4.372656 GGGATGTCAAGTAGCAGTATCAC 58.627 47.826 0.00 0.00 0.00 3.06
2948 3172 4.100189 GGGATGTCAAGTAGCAGTATCACT 59.900 45.833 0.00 0.00 0.00 3.41
2963 3187 4.008933 ACTGTCCAGTGGCGGAGC 62.009 66.667 16.43 1.24 44.47 4.70
2979 3203 3.343617 CGGAGCCAGGAAAAAGTTATCA 58.656 45.455 0.00 0.00 0.00 2.15
2980 3204 3.375299 CGGAGCCAGGAAAAAGTTATCAG 59.625 47.826 0.00 0.00 0.00 2.90
2981 3205 3.696548 GGAGCCAGGAAAAAGTTATCAGG 59.303 47.826 0.00 0.00 0.00 3.86
2982 3206 3.696548 GAGCCAGGAAAAAGTTATCAGGG 59.303 47.826 0.00 0.00 0.00 4.45
2983 3207 3.333680 AGCCAGGAAAAAGTTATCAGGGA 59.666 43.478 0.00 0.00 0.00 4.20
2984 3208 3.696548 GCCAGGAAAAAGTTATCAGGGAG 59.303 47.826 0.00 0.00 0.00 4.30
2985 3209 4.273318 CCAGGAAAAAGTTATCAGGGAGG 58.727 47.826 0.00 0.00 0.00 4.30
2986 3210 3.696548 CAGGAAAAAGTTATCAGGGAGGC 59.303 47.826 0.00 0.00 0.00 4.70
2987 3211 3.024547 GGAAAAAGTTATCAGGGAGGCC 58.975 50.000 0.00 0.00 0.00 5.19
2988 3212 2.420058 AAAAGTTATCAGGGAGGCCG 57.580 50.000 0.00 0.00 0.00 6.13
2989 3213 0.546598 AAAGTTATCAGGGAGGCCGG 59.453 55.000 0.00 0.00 0.00 6.13
2990 3214 1.345715 AAGTTATCAGGGAGGCCGGG 61.346 60.000 2.18 0.00 0.00 5.73
2991 3215 2.070650 GTTATCAGGGAGGCCGGGT 61.071 63.158 2.18 0.00 0.00 5.28
2992 3216 2.070039 TTATCAGGGAGGCCGGGTG 61.070 63.158 2.18 0.00 0.00 4.61
2993 3217 2.539277 TTATCAGGGAGGCCGGGTGA 62.539 60.000 2.18 0.00 0.00 4.02
2994 3218 2.326529 TATCAGGGAGGCCGGGTGAT 62.327 60.000 2.18 14.70 0.00 3.06
2995 3219 4.181010 CAGGGAGGCCGGGTGATG 62.181 72.222 2.18 0.00 0.00 3.07
2998 3222 3.161450 GGAGGCCGGGTGATGCTA 61.161 66.667 2.18 0.00 0.00 3.49
2999 3223 2.742116 GGAGGCCGGGTGATGCTAA 61.742 63.158 2.18 0.00 0.00 3.09
3000 3224 1.223487 GAGGCCGGGTGATGCTAAA 59.777 57.895 2.18 0.00 0.00 1.85
3001 3225 0.393808 GAGGCCGGGTGATGCTAAAA 60.394 55.000 2.18 0.00 0.00 1.52
3002 3226 0.679960 AGGCCGGGTGATGCTAAAAC 60.680 55.000 2.18 0.00 0.00 2.43
3003 3227 0.679960 GGCCGGGTGATGCTAAAACT 60.680 55.000 2.18 0.00 0.00 2.66
3004 3228 0.451783 GCCGGGTGATGCTAAAACTG 59.548 55.000 2.18 0.00 0.00 3.16
3005 3229 1.948611 GCCGGGTGATGCTAAAACTGA 60.949 52.381 2.18 0.00 0.00 3.41
3006 3230 2.643551 CCGGGTGATGCTAAAACTGAT 58.356 47.619 0.00 0.00 0.00 2.90
3007 3231 2.614057 CCGGGTGATGCTAAAACTGATC 59.386 50.000 0.00 0.00 0.00 2.92
3008 3232 2.285220 CGGGTGATGCTAAAACTGATCG 59.715 50.000 0.00 0.00 0.00 3.69
3009 3233 3.531538 GGGTGATGCTAAAACTGATCGA 58.468 45.455 0.00 0.00 0.00 3.59
3010 3234 3.557595 GGGTGATGCTAAAACTGATCGAG 59.442 47.826 0.00 0.00 0.00 4.04
3011 3235 3.557595 GGTGATGCTAAAACTGATCGAGG 59.442 47.826 0.00 0.00 0.00 4.63
3012 3236 4.433615 GTGATGCTAAAACTGATCGAGGA 58.566 43.478 0.00 0.00 0.00 3.71
3013 3237 4.505922 GTGATGCTAAAACTGATCGAGGAG 59.494 45.833 0.00 0.00 0.00 3.69
3014 3238 3.526931 TGCTAAAACTGATCGAGGAGG 57.473 47.619 0.00 0.00 0.00 4.30
3015 3239 2.168521 TGCTAAAACTGATCGAGGAGGG 59.831 50.000 0.00 0.00 0.00 4.30
3016 3240 2.827652 CTAAAACTGATCGAGGAGGGC 58.172 52.381 0.00 0.00 0.00 5.19
3017 3241 0.253327 AAAACTGATCGAGGAGGGCC 59.747 55.000 0.00 0.00 0.00 5.80
3018 3242 0.909610 AAACTGATCGAGGAGGGCCA 60.910 55.000 6.18 0.00 36.29 5.36
3019 3243 0.909610 AACTGATCGAGGAGGGCCAA 60.910 55.000 6.18 0.00 36.29 4.52
3020 3244 0.909610 ACTGATCGAGGAGGGCCAAA 60.910 55.000 6.18 0.00 36.29 3.28
3021 3245 0.471617 CTGATCGAGGAGGGCCAAAT 59.528 55.000 6.18 0.00 36.29 2.32
3022 3246 0.469917 TGATCGAGGAGGGCCAAATC 59.530 55.000 6.18 0.00 36.29 2.17
3023 3247 0.761802 GATCGAGGAGGGCCAAATCT 59.238 55.000 6.18 0.00 36.29 2.40
3024 3248 1.141858 GATCGAGGAGGGCCAAATCTT 59.858 52.381 6.18 0.00 36.29 2.40
3025 3249 1.874129 TCGAGGAGGGCCAAATCTTA 58.126 50.000 6.18 0.00 36.29 2.10
3026 3250 1.762957 TCGAGGAGGGCCAAATCTTAG 59.237 52.381 6.18 0.00 36.29 2.18
3027 3251 1.762957 CGAGGAGGGCCAAATCTTAGA 59.237 52.381 6.18 0.00 36.29 2.10
3028 3252 2.170607 CGAGGAGGGCCAAATCTTAGAA 59.829 50.000 6.18 0.00 36.29 2.10
3029 3253 3.370527 CGAGGAGGGCCAAATCTTAGAAA 60.371 47.826 6.18 0.00 36.29 2.52
3030 3254 4.600062 GAGGAGGGCCAAATCTTAGAAAA 58.400 43.478 6.18 0.00 36.29 2.29
3031 3255 5.010708 AGGAGGGCCAAATCTTAGAAAAA 57.989 39.130 6.18 0.00 36.29 1.94
3032 3256 5.593786 AGGAGGGCCAAATCTTAGAAAAAT 58.406 37.500 6.18 0.00 36.29 1.82
3033 3257 5.423290 AGGAGGGCCAAATCTTAGAAAAATG 59.577 40.000 6.18 0.00 36.29 2.32
3034 3258 5.422012 GGAGGGCCAAATCTTAGAAAAATGA 59.578 40.000 6.18 0.00 0.00 2.57
3035 3259 6.406288 GGAGGGCCAAATCTTAGAAAAATGAG 60.406 42.308 6.18 0.00 0.00 2.90
3036 3260 6.019108 AGGGCCAAATCTTAGAAAAATGAGT 58.981 36.000 6.18 0.00 0.00 3.41
3037 3261 6.498303 AGGGCCAAATCTTAGAAAAATGAGTT 59.502 34.615 6.18 0.00 0.00 3.01
3038 3262 7.016563 AGGGCCAAATCTTAGAAAAATGAGTTT 59.983 33.333 6.18 0.00 0.00 2.66
3039 3263 7.661437 GGGCCAAATCTTAGAAAAATGAGTTTT 59.339 33.333 4.39 0.00 42.28 2.43
3055 3279 9.995003 AAATGAGTTTTTAGCATCAAATAACCA 57.005 25.926 0.00 0.00 0.00 3.67
3056 3280 9.643693 AATGAGTTTTTAGCATCAAATAACCAG 57.356 29.630 0.00 0.00 0.00 4.00
3057 3281 8.177119 TGAGTTTTTAGCATCAAATAACCAGT 57.823 30.769 0.00 0.00 0.00 4.00
3058 3282 9.290988 TGAGTTTTTAGCATCAAATAACCAGTA 57.709 29.630 0.00 0.00 0.00 2.74
3101 3325 9.264719 AGAAAAATTAGCTTGAAATCCTGTTTG 57.735 29.630 0.00 0.00 0.00 2.93
3102 3326 8.962884 AAAAATTAGCTTGAAATCCTGTTTGT 57.037 26.923 0.00 0.00 0.00 2.83
3103 3327 8.962884 AAAATTAGCTTGAAATCCTGTTTGTT 57.037 26.923 0.00 0.00 0.00 2.83
3105 3329 9.696917 AAATTAGCTTGAAATCCTGTTTGTTAG 57.303 29.630 0.00 0.00 0.00 2.34
3106 3330 5.712152 AGCTTGAAATCCTGTTTGTTAGG 57.288 39.130 0.00 0.00 36.63 2.69
3107 3331 4.524328 AGCTTGAAATCCTGTTTGTTAGGG 59.476 41.667 0.00 0.00 35.96 3.53
3108 3332 4.321974 GCTTGAAATCCTGTTTGTTAGGGG 60.322 45.833 0.00 0.00 35.96 4.79
3109 3333 3.773560 TGAAATCCTGTTTGTTAGGGGG 58.226 45.455 0.00 0.00 35.96 5.40
3214 3675 3.307674 TGTCACAATTTGATTTCGCAGC 58.692 40.909 2.79 0.00 36.32 5.25
3220 3681 7.431960 GTCACAATTTGATTTCGCAGCAATATA 59.568 33.333 2.79 0.00 36.32 0.86
3226 3687 9.701098 ATTTGATTTCGCAGCAATATATTCATT 57.299 25.926 0.00 0.00 0.00 2.57
3311 3789 4.216042 TGTGTCAAGGTTATGCTGTCATTG 59.784 41.667 0.00 0.00 34.22 2.82
3492 4013 5.640357 TGTGCGTAGTTGTATTAAAGAAGGG 59.360 40.000 0.00 0.00 0.00 3.95
3495 4016 7.065443 GTGCGTAGTTGTATTAAAGAAGGGATT 59.935 37.037 0.00 0.00 0.00 3.01
3532 4053 5.073428 AGGAAAGCTAAAAAGAGAAGGGTG 58.927 41.667 0.00 0.00 0.00 4.61
3549 4070 2.158608 GGGTGGAGTATGGGAATGGAAG 60.159 54.545 0.00 0.00 0.00 3.46
3556 4077 4.808042 AGTATGGGAATGGAAGGGAAATG 58.192 43.478 0.00 0.00 0.00 2.32
3617 4138 5.011738 ACAGTCCATACCGAGAGAAAGAAAA 59.988 40.000 0.00 0.00 0.00 2.29
3717 4284 7.251994 TCTTTACTGCGTTTATGTGTTTGTTT 58.748 30.769 0.00 0.00 0.00 2.83
3718 4285 6.798207 TTACTGCGTTTATGTGTTTGTTTG 57.202 33.333 0.00 0.00 0.00 2.93
3719 4286 4.109050 ACTGCGTTTATGTGTTTGTTTGG 58.891 39.130 0.00 0.00 0.00 3.28
3720 4287 4.109050 CTGCGTTTATGTGTTTGTTTGGT 58.891 39.130 0.00 0.00 0.00 3.67
3721 4288 4.106197 TGCGTTTATGTGTTTGTTTGGTC 58.894 39.130 0.00 0.00 0.00 4.02
3722 4289 4.142359 TGCGTTTATGTGTTTGTTTGGTCT 60.142 37.500 0.00 0.00 0.00 3.85
3723 4290 4.206200 GCGTTTATGTGTTTGTTTGGTCTG 59.794 41.667 0.00 0.00 0.00 3.51
3724 4291 5.336744 CGTTTATGTGTTTGTTTGGTCTGT 58.663 37.500 0.00 0.00 0.00 3.41
3725 4292 5.802956 CGTTTATGTGTTTGTTTGGTCTGTT 59.197 36.000 0.00 0.00 0.00 3.16
3752 4319 5.984627 TCTGTTTGTCAACAATGTCATACG 58.015 37.500 0.00 0.00 42.53 3.06
3830 4400 6.071334 TGCTAGTAGTGCAAACTGAGAATACT 60.071 38.462 12.15 0.00 37.51 2.12
3831 4401 7.122204 TGCTAGTAGTGCAAACTGAGAATACTA 59.878 37.037 12.15 0.00 37.51 1.82
3832 4402 8.138712 GCTAGTAGTGCAAACTGAGAATACTAT 58.861 37.037 12.15 0.00 0.00 2.12
3835 4405 9.804758 AGTAGTGCAAACTGAGAATACTATTAC 57.195 33.333 2.28 0.00 0.00 1.89
3933 4831 0.104487 ATGCATCCAGAGCTGTCGAG 59.896 55.000 0.00 0.00 0.00 4.04
3965 4867 6.992063 ATTATGTTGCTACTTTGTCTCAGG 57.008 37.500 0.00 0.00 0.00 3.86
4031 4945 9.616634 GTGTATATCAAATCATGCTGTAAATGG 57.383 33.333 0.00 0.00 0.00 3.16
4162 5076 2.046700 GGCGAATTGGACGTCCCA 60.047 61.111 31.19 21.93 44.93 4.37
4211 5158 4.564406 GGCTTCCTGAAGTCTTGATGAAGA 60.564 45.833 17.13 0.00 39.78 2.87
4244 5192 7.170828 GCTGTCAAATCCTTTTATTTTCCGTTT 59.829 33.333 0.00 0.00 0.00 3.60
4264 5212 5.924254 CGTTTAGTTGTATTCTCTGGTGACA 59.076 40.000 0.00 0.00 39.59 3.58
4284 5232 5.014123 TGACAGGTAGACCCAAAATTCATCT 59.986 40.000 0.00 0.00 36.42 2.90
4292 5240 5.126707 AGACCCAAAATTCATCTGAATCAGC 59.873 40.000 5.18 0.00 43.41 4.26
4293 5241 5.021458 ACCCAAAATTCATCTGAATCAGCT 58.979 37.500 5.18 0.00 43.41 4.24
4294 5242 6.189859 ACCCAAAATTCATCTGAATCAGCTA 58.810 36.000 5.18 0.00 43.41 3.32
4295 5243 6.320672 ACCCAAAATTCATCTGAATCAGCTAG 59.679 38.462 5.18 0.00 43.41 3.42
4296 5244 6.320672 CCCAAAATTCATCTGAATCAGCTAGT 59.679 38.462 5.18 0.00 43.41 2.57
4297 5245 7.194278 CCAAAATTCATCTGAATCAGCTAGTG 58.806 38.462 5.18 2.38 43.41 2.74
4313 5261 5.649602 GCTAGTGCTGCTTTCATAGTAAG 57.350 43.478 0.00 0.00 36.03 2.34
4314 5262 5.352284 GCTAGTGCTGCTTTCATAGTAAGA 58.648 41.667 0.00 0.00 36.03 2.10
4315 5263 5.812642 GCTAGTGCTGCTTTCATAGTAAGAA 59.187 40.000 0.00 0.00 36.03 2.52
4316 5264 6.019156 GCTAGTGCTGCTTTCATAGTAAGAAG 60.019 42.308 0.00 0.00 36.03 2.85
4318 5266 6.467677 AGTGCTGCTTTCATAGTAAGAAGAA 58.532 36.000 0.00 0.00 30.99 2.52
4319 5267 6.936900 AGTGCTGCTTTCATAGTAAGAAGAAA 59.063 34.615 0.00 0.00 30.99 2.52
4744 5692 9.814899 ACTCAGAGATTGTATTTCAGTCTAATG 57.185 33.333 3.79 0.00 41.96 1.90
4749 5697 5.794687 TTGTATTTCAGTCTAATGTGCCG 57.205 39.130 0.00 0.00 0.00 5.69
4804 5752 2.363680 TGCTTCACTGAGCTAGGCTATC 59.636 50.000 0.00 0.00 43.11 2.08
4825 5773 3.387699 TCATGTGGAGTCTCTTGTCAACA 59.612 43.478 0.00 0.00 0.00 3.33
4830 5778 4.271291 GTGGAGTCTCTTGTCAACAACTTC 59.729 45.833 0.00 0.00 0.00 3.01
4831 5779 4.162320 TGGAGTCTCTTGTCAACAACTTCT 59.838 41.667 0.00 0.00 0.00 2.85
4848 5796 6.381133 ACAACTTCTTTTCCATTTTGTCCTCT 59.619 34.615 0.00 0.00 0.00 3.69
4968 5917 8.950210 TGCTCATATTTTTCCTTTCTAGACAAG 58.050 33.333 0.00 0.00 0.00 3.16
4975 5925 3.181329 TCCTTTCTAGACAAGGCATCCA 58.819 45.455 20.35 7.76 40.77 3.41
4982 5932 3.059352 AGACAAGGCATCCAGTACAAC 57.941 47.619 0.00 0.00 0.00 3.32
4992 5942 3.380479 TCCAGTACAACGAACTCTTGG 57.620 47.619 0.00 0.00 0.00 3.61
4998 5948 3.859411 ACAACGAACTCTTGGCAAAAA 57.141 38.095 0.00 0.00 0.00 1.94
5000 5950 4.754322 ACAACGAACTCTTGGCAAAAATT 58.246 34.783 0.00 0.00 0.00 1.82
5001 5951 5.175127 ACAACGAACTCTTGGCAAAAATTT 58.825 33.333 0.00 0.00 0.00 1.82
5048 5998 6.234177 ACTCTAATATCAGCAAATAGGTGGC 58.766 40.000 0.00 0.00 45.66 5.01
5096 6046 6.311735 ACATACTCCCTTTGGTTGTAAATGT 58.688 36.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.430423 GCGAACTGCTGAACGCCG 62.430 66.667 20.32 8.37 44.27 6.46
35 37 1.298563 CCTTGTGTGTGCGTGCAAG 60.299 57.895 0.00 0.00 38.33 4.01
65 67 1.381599 GGGGGAGATGGCAAATGCA 60.382 57.895 7.80 0.00 44.36 3.96
84 86 1.737008 GGAGAGGAAACGGACGTGC 60.737 63.158 0.00 0.00 0.00 5.34
94 96 1.779061 GCTTGGGTGTGGGAGAGGAA 61.779 60.000 0.00 0.00 0.00 3.36
234 244 2.804697 TCTGCTTACGTGCACACTAA 57.195 45.000 18.64 10.38 38.12 2.24
360 370 4.469657 TGCCATGTAAAAGGAAGAGTTGT 58.530 39.130 0.00 0.00 0.00 3.32
431 442 9.979578 GTCTGATCTAATGTAGTTGATGAAGAT 57.020 33.333 0.00 0.00 0.00 2.40
433 444 8.200120 TGGTCTGATCTAATGTAGTTGATGAAG 58.800 37.037 0.00 0.00 0.00 3.02
562 605 0.037303 CAGTTGCCATGGTCCAGACT 59.963 55.000 14.67 7.60 0.00 3.24
629 674 2.590092 GCCCGTATGTCAGGCCTT 59.410 61.111 0.00 0.00 41.00 4.35
680 725 1.620798 CCTCCTGATCCCTCTCACACA 60.621 57.143 0.00 0.00 0.00 3.72
720 766 3.490078 CGTGTGGGCAAAACAAGTAATGT 60.490 43.478 0.00 0.00 46.82 2.71
787 833 3.459063 GGCGTTAGGGAGTCCGCT 61.459 66.667 2.26 4.26 45.11 5.52
824 870 9.511272 ACGGTTCTTTTAATAATTTAGGACACT 57.489 29.630 0.00 0.00 0.00 3.55
860 906 3.109847 TGGCTCGCCAGTTCTTTTT 57.890 47.368 6.52 0.00 41.89 1.94
861 907 4.898607 TGGCTCGCCAGTTCTTTT 57.101 50.000 6.52 0.00 41.89 2.27
906 952 0.111639 GGCCTACTTGGTTGGGTTCA 59.888 55.000 0.00 0.00 38.35 3.18
963 1013 3.253838 TTTGGGTGGGGGTCGGAG 61.254 66.667 0.00 0.00 0.00 4.63
969 1019 4.631740 GTGGGGTTTGGGTGGGGG 62.632 72.222 0.00 0.00 0.00 5.40
1028 1087 0.100682 ATCGTCGATGAGGTTGACCG 59.899 55.000 13.65 0.00 42.08 4.79
1047 1109 0.452184 GGAGAATCTCTGCGACGACA 59.548 55.000 10.38 0.00 33.73 4.35
1105 1167 4.069232 CTTGCAGACGAGGGCGGA 62.069 66.667 0.00 0.00 43.17 5.54
1431 1505 1.663739 GGCGGCGGTGTAGATCATA 59.336 57.895 9.78 0.00 0.00 2.15
1506 1580 0.249868 CAGTTGCCAGGAAGACGACA 60.250 55.000 0.00 0.00 0.00 4.35
1521 1595 1.282248 CGTCGTCGTTGCCATCAGTT 61.282 55.000 0.00 0.00 0.00 3.16
1539 1613 2.050351 ACACTCGCCTTGACGACG 60.050 61.111 0.00 0.00 37.09 5.12
1577 1651 3.365291 GATACCGGCGCACTCCACA 62.365 63.158 10.83 0.00 0.00 4.17
1607 1681 0.464373 CCGGGCATAGCATTCACAGT 60.464 55.000 0.00 0.00 0.00 3.55
1674 1757 2.028337 GCTACTCGCCTAGGCTGC 59.972 66.667 30.55 20.85 39.32 5.25
1910 2029 4.380444 CCATGCACTGTACCCATTTTGTAC 60.380 45.833 0.00 0.00 39.19 2.90
1964 2083 1.693606 CATTGCCTTTGAGGGGTTTGT 59.306 47.619 0.00 0.00 35.37 2.83
2040 2159 1.754803 TCGATCGTGAATAAGCCACCT 59.245 47.619 15.94 0.00 0.00 4.00
2089 2208 3.721087 AAAGTAGACCCCAGGTTCATG 57.279 47.619 0.00 0.00 35.25 3.07
2154 2286 5.774690 TGGAAGCTGTAAAATGAAGGACAAT 59.225 36.000 0.00 0.00 0.00 2.71
2194 2326 2.420722 TGTTCACAAACGAGAACCAACC 59.579 45.455 0.00 0.00 42.57 3.77
2403 2560 5.756195 TTGACAAGGCTGTATGCATATTC 57.244 39.130 10.16 0.00 45.15 1.75
2517 2711 4.693566 GCTATGTGCTAGTGGTGTTTACAA 59.306 41.667 0.00 0.00 38.95 2.41
2588 2796 3.006217 TGCCATGATCTGAGAAGATACCG 59.994 47.826 0.00 0.00 0.00 4.02
2654 2865 8.942338 AGTGGAAAATCTAAAAGAAAACAACC 57.058 30.769 0.00 0.00 0.00 3.77
2747 2963 8.416329 ACCCAACTTTTCAATATTATGATCAGC 58.584 33.333 0.09 0.00 0.00 4.26
2775 2992 8.043113 AGAAATATGACTGACATGCTAAACAGA 58.957 33.333 2.89 0.00 39.77 3.41
2872 3096 9.768662 CCTGATATAAAAATTCCATGAAAAGGG 57.231 33.333 0.00 0.00 0.00 3.95
2883 3107 9.573133 CCAACACTGAACCTGATATAAAAATTC 57.427 33.333 0.00 0.00 0.00 2.17
2946 3170 4.008933 GCTCCGCCACTGGACAGT 62.009 66.667 0.00 0.00 43.61 3.55
2957 3181 1.530323 TAACTTTTTCCTGGCTCCGC 58.470 50.000 0.00 0.00 0.00 5.54
2958 3182 3.343617 TGATAACTTTTTCCTGGCTCCG 58.656 45.455 0.00 0.00 0.00 4.63
2959 3183 3.696548 CCTGATAACTTTTTCCTGGCTCC 59.303 47.826 0.00 0.00 0.00 4.70
2960 3184 3.696548 CCCTGATAACTTTTTCCTGGCTC 59.303 47.826 0.00 0.00 0.00 4.70
2961 3185 3.333680 TCCCTGATAACTTTTTCCTGGCT 59.666 43.478 0.00 0.00 0.00 4.75
2962 3186 3.696548 CTCCCTGATAACTTTTTCCTGGC 59.303 47.826 0.00 0.00 0.00 4.85
2963 3187 4.273318 CCTCCCTGATAACTTTTTCCTGG 58.727 47.826 0.00 0.00 0.00 4.45
2964 3188 3.696548 GCCTCCCTGATAACTTTTTCCTG 59.303 47.826 0.00 0.00 0.00 3.86
2965 3189 3.309193 GGCCTCCCTGATAACTTTTTCCT 60.309 47.826 0.00 0.00 0.00 3.36
2966 3190 3.024547 GGCCTCCCTGATAACTTTTTCC 58.975 50.000 0.00 0.00 0.00 3.13
2967 3191 2.683362 CGGCCTCCCTGATAACTTTTTC 59.317 50.000 0.00 0.00 0.00 2.29
2968 3192 2.620627 CCGGCCTCCCTGATAACTTTTT 60.621 50.000 0.00 0.00 0.00 1.94
2969 3193 1.064685 CCGGCCTCCCTGATAACTTTT 60.065 52.381 0.00 0.00 0.00 2.27
2970 3194 0.546598 CCGGCCTCCCTGATAACTTT 59.453 55.000 0.00 0.00 0.00 2.66
2971 3195 1.345715 CCCGGCCTCCCTGATAACTT 61.346 60.000 0.00 0.00 0.00 2.66
2972 3196 1.766461 CCCGGCCTCCCTGATAACT 60.766 63.158 0.00 0.00 0.00 2.24
2973 3197 2.070650 ACCCGGCCTCCCTGATAAC 61.071 63.158 0.00 0.00 0.00 1.89
2974 3198 2.070039 CACCCGGCCTCCCTGATAA 61.070 63.158 0.00 0.00 0.00 1.75
2975 3199 2.326529 ATCACCCGGCCTCCCTGATA 62.327 60.000 0.00 0.00 0.00 2.15
2976 3200 3.721172 ATCACCCGGCCTCCCTGAT 62.721 63.158 0.00 0.00 0.00 2.90
2977 3201 4.414956 ATCACCCGGCCTCCCTGA 62.415 66.667 0.00 0.00 0.00 3.86
2978 3202 4.181010 CATCACCCGGCCTCCCTG 62.181 72.222 0.00 0.00 0.00 4.45
2981 3205 2.265467 TTTAGCATCACCCGGCCTCC 62.265 60.000 0.00 0.00 0.00 4.30
2982 3206 0.393808 TTTTAGCATCACCCGGCCTC 60.394 55.000 0.00 0.00 0.00 4.70
2983 3207 0.679960 GTTTTAGCATCACCCGGCCT 60.680 55.000 0.00 0.00 0.00 5.19
2984 3208 0.679960 AGTTTTAGCATCACCCGGCC 60.680 55.000 0.00 0.00 0.00 6.13
2985 3209 0.451783 CAGTTTTAGCATCACCCGGC 59.548 55.000 0.00 0.00 0.00 6.13
2986 3210 2.107950 TCAGTTTTAGCATCACCCGG 57.892 50.000 0.00 0.00 0.00 5.73
2987 3211 2.285220 CGATCAGTTTTAGCATCACCCG 59.715 50.000 0.00 0.00 0.00 5.28
2988 3212 3.531538 TCGATCAGTTTTAGCATCACCC 58.468 45.455 0.00 0.00 0.00 4.61
2989 3213 3.557595 CCTCGATCAGTTTTAGCATCACC 59.442 47.826 0.00 0.00 0.00 4.02
2990 3214 4.433615 TCCTCGATCAGTTTTAGCATCAC 58.566 43.478 0.00 0.00 0.00 3.06
2991 3215 4.442052 CCTCCTCGATCAGTTTTAGCATCA 60.442 45.833 0.00 0.00 0.00 3.07
2992 3216 4.054671 CCTCCTCGATCAGTTTTAGCATC 58.945 47.826 0.00 0.00 0.00 3.91
2993 3217 3.181461 CCCTCCTCGATCAGTTTTAGCAT 60.181 47.826 0.00 0.00 0.00 3.79
2994 3218 2.168521 CCCTCCTCGATCAGTTTTAGCA 59.831 50.000 0.00 0.00 0.00 3.49
2995 3219 2.827652 CCCTCCTCGATCAGTTTTAGC 58.172 52.381 0.00 0.00 0.00 3.09
2996 3220 2.483889 GGCCCTCCTCGATCAGTTTTAG 60.484 54.545 0.00 0.00 0.00 1.85
2997 3221 1.485066 GGCCCTCCTCGATCAGTTTTA 59.515 52.381 0.00 0.00 0.00 1.52
2998 3222 0.253327 GGCCCTCCTCGATCAGTTTT 59.747 55.000 0.00 0.00 0.00 2.43
2999 3223 0.909610 TGGCCCTCCTCGATCAGTTT 60.910 55.000 0.00 0.00 0.00 2.66
3000 3224 0.909610 TTGGCCCTCCTCGATCAGTT 60.910 55.000 0.00 0.00 0.00 3.16
3001 3225 0.909610 TTTGGCCCTCCTCGATCAGT 60.910 55.000 0.00 0.00 0.00 3.41
3002 3226 0.471617 ATTTGGCCCTCCTCGATCAG 59.528 55.000 0.00 0.00 0.00 2.90
3003 3227 0.469917 GATTTGGCCCTCCTCGATCA 59.530 55.000 0.00 0.00 0.00 2.92
3004 3228 0.761802 AGATTTGGCCCTCCTCGATC 59.238 55.000 0.00 0.00 0.00 3.69
3005 3229 1.216990 AAGATTTGGCCCTCCTCGAT 58.783 50.000 0.00 0.00 0.00 3.59
3006 3230 1.762957 CTAAGATTTGGCCCTCCTCGA 59.237 52.381 0.00 0.00 0.00 4.04
3007 3231 1.762957 TCTAAGATTTGGCCCTCCTCG 59.237 52.381 0.00 0.00 0.00 4.63
3008 3232 3.933861 TTCTAAGATTTGGCCCTCCTC 57.066 47.619 0.00 0.00 0.00 3.71
3009 3233 4.675063 TTTTCTAAGATTTGGCCCTCCT 57.325 40.909 0.00 0.00 0.00 3.69
3010 3234 5.422012 TCATTTTTCTAAGATTTGGCCCTCC 59.578 40.000 0.00 0.00 0.00 4.30
3011 3235 6.153510 ACTCATTTTTCTAAGATTTGGCCCTC 59.846 38.462 0.00 0.00 0.00 4.30
3012 3236 6.019108 ACTCATTTTTCTAAGATTTGGCCCT 58.981 36.000 0.00 0.00 0.00 5.19
3013 3237 6.286240 ACTCATTTTTCTAAGATTTGGCCC 57.714 37.500 0.00 0.00 0.00 5.80
3014 3238 8.607441 AAAACTCATTTTTCTAAGATTTGGCC 57.393 30.769 0.00 0.00 34.19 5.36
3029 3253 9.995003 TGGTTATTTGATGCTAAAAACTCATTT 57.005 25.926 0.00 0.00 0.00 2.32
3030 3254 9.643693 CTGGTTATTTGATGCTAAAAACTCATT 57.356 29.630 0.00 0.00 0.00 2.57
3031 3255 8.806146 ACTGGTTATTTGATGCTAAAAACTCAT 58.194 29.630 0.00 0.00 0.00 2.90
3032 3256 8.177119 ACTGGTTATTTGATGCTAAAAACTCA 57.823 30.769 0.00 0.00 0.00 3.41
3075 3299 9.264719 CAAACAGGATTTCAAGCTAATTTTTCT 57.735 29.630 0.00 0.00 0.00 2.52
3076 3300 9.045223 ACAAACAGGATTTCAAGCTAATTTTTC 57.955 29.630 0.00 0.00 0.00 2.29
3077 3301 8.962884 ACAAACAGGATTTCAAGCTAATTTTT 57.037 26.923 0.00 0.00 0.00 1.94
3078 3302 8.962884 AACAAACAGGATTTCAAGCTAATTTT 57.037 26.923 0.00 0.00 0.00 1.82
3079 3303 9.696917 CTAACAAACAGGATTTCAAGCTAATTT 57.303 29.630 0.00 0.00 0.00 1.82
3080 3304 8.306761 CCTAACAAACAGGATTTCAAGCTAATT 58.693 33.333 0.00 0.00 34.91 1.40
3081 3305 7.093771 CCCTAACAAACAGGATTTCAAGCTAAT 60.094 37.037 0.00 0.00 34.91 1.73
3082 3306 6.208599 CCCTAACAAACAGGATTTCAAGCTAA 59.791 38.462 0.00 0.00 34.91 3.09
3083 3307 5.710099 CCCTAACAAACAGGATTTCAAGCTA 59.290 40.000 0.00 0.00 34.91 3.32
3084 3308 4.524328 CCCTAACAAACAGGATTTCAAGCT 59.476 41.667 0.00 0.00 34.91 3.74
3085 3309 4.321974 CCCCTAACAAACAGGATTTCAAGC 60.322 45.833 0.00 0.00 34.91 4.01
3086 3310 4.220602 CCCCCTAACAAACAGGATTTCAAG 59.779 45.833 0.00 0.00 34.91 3.02
3087 3311 4.156477 CCCCCTAACAAACAGGATTTCAA 58.844 43.478 0.00 0.00 34.91 2.69
3088 3312 3.773560 CCCCCTAACAAACAGGATTTCA 58.226 45.455 0.00 0.00 34.91 2.69
3135 3359 1.373497 CAGTGACAGTGGCGGAGAC 60.373 63.158 2.02 0.00 0.00 3.36
3136 3360 1.806461 GACAGTGACAGTGGCGGAGA 61.806 60.000 14.70 0.00 0.00 3.71
3137 3361 1.373497 GACAGTGACAGTGGCGGAG 60.373 63.158 14.70 0.00 0.00 4.63
3138 3362 2.087462 CTGACAGTGACAGTGGCGGA 62.087 60.000 18.88 0.00 34.79 5.54
3139 3363 1.665916 CTGACAGTGACAGTGGCGG 60.666 63.158 10.62 10.62 0.00 6.13
3140 3364 0.941463 GTCTGACAGTGACAGTGGCG 60.941 60.000 19.68 8.18 36.81 5.69
3141 3365 0.390860 AGTCTGACAGTGACAGTGGC 59.609 55.000 19.68 12.22 36.94 5.01
3142 3366 2.898729 AAGTCTGACAGTGACAGTGG 57.101 50.000 19.68 0.00 36.94 4.00
3143 3367 4.201851 CCAAAAAGTCTGACAGTGACAGTG 60.202 45.833 19.68 8.80 36.94 3.66
3144 3368 3.941483 CCAAAAAGTCTGACAGTGACAGT 59.059 43.478 19.68 1.68 36.94 3.55
3145 3369 4.034510 GTCCAAAAAGTCTGACAGTGACAG 59.965 45.833 15.36 15.36 36.94 3.51
3146 3370 3.938963 GTCCAAAAAGTCTGACAGTGACA 59.061 43.478 10.88 0.00 36.94 3.58
3193 3418 3.243334 TGCTGCGAAATCAAATTGTGACA 60.243 39.130 0.00 0.00 39.72 3.58
3250 3712 7.603651 TCTTATCTGACTTCAACCTGTTAGAC 58.396 38.462 0.00 0.00 32.91 2.59
3311 3789 1.000938 CACAGAGGTGCCTTTTTGCTC 60.001 52.381 0.00 0.00 38.37 4.26
3467 3978 6.148150 CCCTTCTTTAATACAACTACGCACAA 59.852 38.462 0.00 0.00 0.00 3.33
3470 3981 6.040209 TCCCTTCTTTAATACAACTACGCA 57.960 37.500 0.00 0.00 0.00 5.24
3492 4013 8.000780 AGCTTTCCTTGTATGGACATTTAATC 57.999 34.615 0.00 0.00 35.58 1.75
3495 4016 8.871629 TTTAGCTTTCCTTGTATGGACATTTA 57.128 30.769 0.00 0.00 35.58 1.40
3532 4053 2.418669 TCCCTTCCATTCCCATACTCC 58.581 52.381 0.00 0.00 0.00 3.85
3549 4070 2.358322 TCCCTATTTCGGCATTTCCC 57.642 50.000 0.00 0.00 0.00 3.97
3556 4077 7.039313 AGAATAATGTTTTCCCTATTTCGGC 57.961 36.000 0.00 0.00 0.00 5.54
3617 4138 4.870426 CCAGCACGAGTTTGTAGTCATTAT 59.130 41.667 0.00 0.00 0.00 1.28
3717 4284 4.075682 TGACAAACAGAACAAACAGACCA 58.924 39.130 0.00 0.00 0.00 4.02
3718 4285 4.695217 TGACAAACAGAACAAACAGACC 57.305 40.909 0.00 0.00 0.00 3.85
3719 4286 5.457140 TGTTGACAAACAGAACAAACAGAC 58.543 37.500 0.00 0.00 41.41 3.51
3720 4287 5.697473 TGTTGACAAACAGAACAAACAGA 57.303 34.783 0.00 0.00 41.41 3.41
3721 4288 6.365789 ACATTGTTGACAAACAGAACAAACAG 59.634 34.615 0.10 0.00 46.66 3.16
3722 4289 6.219473 ACATTGTTGACAAACAGAACAAACA 58.781 32.000 0.10 0.00 46.66 2.83
3723 4290 6.364706 TGACATTGTTGACAAACAGAACAAAC 59.635 34.615 0.10 0.00 46.66 2.93
3724 4291 6.450545 TGACATTGTTGACAAACAGAACAAA 58.549 32.000 0.10 0.00 46.66 2.83
3725 4292 6.018589 TGACATTGTTGACAAACAGAACAA 57.981 33.333 0.10 0.00 46.66 2.83
3780 4349 3.624861 CACAAATGGACTGGCTACATCTC 59.375 47.826 0.00 0.00 0.00 2.75
3830 4400 4.601406 AGGTTTCCCATGCCAAGTAATA 57.399 40.909 0.00 0.00 0.00 0.98
3831 4401 3.473113 AGGTTTCCCATGCCAAGTAAT 57.527 42.857 0.00 0.00 0.00 1.89
3832 4402 2.990740 AGGTTTCCCATGCCAAGTAA 57.009 45.000 0.00 0.00 0.00 2.24
3833 4403 2.916934 AGTAGGTTTCCCATGCCAAGTA 59.083 45.455 0.00 0.00 0.00 2.24
3834 4404 1.710809 AGTAGGTTTCCCATGCCAAGT 59.289 47.619 0.00 0.00 0.00 3.16
3835 4405 2.290896 TGAGTAGGTTTCCCATGCCAAG 60.291 50.000 0.00 0.00 0.00 3.61
3863 4433 7.064016 GTCCATAACAAGTCAAATCTCAGAGAC 59.936 40.741 0.91 0.00 0.00 3.36
3865 4435 7.102346 AGTCCATAACAAGTCAAATCTCAGAG 58.898 38.462 0.00 0.00 0.00 3.35
3909 4807 3.059120 CGACAGCTCTGGATGCATATTTG 60.059 47.826 0.00 0.00 31.14 2.32
3920 4818 3.724508 ATACAATCTCGACAGCTCTGG 57.275 47.619 1.66 0.00 34.19 3.86
4020 4929 4.374689 TCCCAACTTACCATTTACAGCA 57.625 40.909 0.00 0.00 0.00 4.41
4031 4945 5.523438 TCAAAACCAACATCCCAACTTAC 57.477 39.130 0.00 0.00 0.00 2.34
4162 5076 4.217118 CAGCAGCAGAATTAAGGTCAGTTT 59.783 41.667 0.00 0.00 0.00 2.66
4211 5158 4.026356 AAAGGATTTGACAGCAGTAGCT 57.974 40.909 0.00 0.00 45.87 3.32
4244 5192 5.084519 ACCTGTCACCAGAGAATACAACTA 58.915 41.667 0.00 0.00 41.50 2.24
4264 5212 5.779241 TCAGATGAATTTTGGGTCTACCT 57.221 39.130 0.00 0.00 41.11 3.08
4292 5240 7.261325 TCTTCTTACTATGAAAGCAGCACTAG 58.739 38.462 0.00 0.00 0.00 2.57
4293 5241 7.170393 TCTTCTTACTATGAAAGCAGCACTA 57.830 36.000 0.00 0.00 0.00 2.74
4294 5242 6.042638 TCTTCTTACTATGAAAGCAGCACT 57.957 37.500 0.00 0.00 0.00 4.40
4295 5243 6.727824 TTCTTCTTACTATGAAAGCAGCAC 57.272 37.500 0.00 0.00 0.00 4.40
4296 5244 7.133891 GTTTCTTCTTACTATGAAAGCAGCA 57.866 36.000 0.00 0.00 0.00 4.41
4676 5624 3.181465 ACTCAGACGAAAACATCCACAGT 60.181 43.478 0.00 0.00 0.00 3.55
4744 5692 3.505680 TGAATATGAAATATGCCCGGCAC 59.494 43.478 16.16 1.58 43.04 5.01
4749 5697 4.768968 AGCCACTGAATATGAAATATGCCC 59.231 41.667 0.00 0.00 38.94 5.36
4804 5752 3.732212 TGTTGACAAGAGACTCCACATG 58.268 45.455 0.00 0.00 0.00 3.21
4825 5773 6.683861 GCAGAGGACAAAATGGAAAAGAAGTT 60.684 38.462 0.00 0.00 0.00 2.66
4830 5778 4.861102 AGCAGAGGACAAAATGGAAAAG 57.139 40.909 0.00 0.00 0.00 2.27
4831 5779 5.363580 AGAAAGCAGAGGACAAAATGGAAAA 59.636 36.000 0.00 0.00 0.00 2.29
4848 5796 3.290710 AGCAAGAACTGGAAAGAAAGCA 58.709 40.909 0.00 0.00 0.00 3.91
4964 5913 1.346395 TCGTTGTACTGGATGCCTTGT 59.654 47.619 0.00 0.00 0.00 3.16
4968 5917 2.000447 GAGTTCGTTGTACTGGATGCC 59.000 52.381 0.00 0.00 0.00 4.40
4975 5925 2.902705 TGCCAAGAGTTCGTTGTACT 57.097 45.000 0.00 0.00 0.00 2.73
5001 5951 9.634163 GAGTTTTTCTTTGTCTGGTCTTAAAAA 57.366 29.630 0.00 0.00 0.00 1.94
5012 5962 9.507329 TGCTGATATTAGAGTTTTTCTTTGTCT 57.493 29.630 0.00 0.00 37.36 3.41


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

AutoCloner maintained by Alex Coulton.