Multiple sequence alignment - TraesCS7B01G444200

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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 TraesCS7B01G444200 chr7B 100.000 6254 0 0 1 6254 708677304 708671051 0.000000e+00 11550
1 TraesCS7B01G444200 chr7B 90.412 1116 92 10 1963 3072 652439025 652437919 0.000000e+00 1454
2 TraesCS7B01G444200 chr7B 92.438 1005 71 3 1963 2964 656302399 656303401 0.000000e+00 1430
3 TraesCS7B01G444200 chr7B 89.893 1118 98 11 1963 3074 652973819 652972711 0.000000e+00 1424
4 TraesCS7B01G444200 chr7B 87.204 1055 93 19 749 1802 652061227 652060214 0.000000e+00 1162
5 TraesCS7B01G444200 chr7B 89.532 898 71 13 908 1802 652174914 652174037 0.000000e+00 1116
6 TraesCS7B01G444200 chr7B 89.557 881 77 8 1 871 652402716 652401841 0.000000e+00 1103
7 TraesCS7B01G444200 chr7B 89.330 881 80 9 1 871 652440952 652440076 0.000000e+00 1094
8 TraesCS7B01G444200 chr7B 86.173 1027 115 17 4796 5814 652167156 652166149 0.000000e+00 1085
9 TraesCS7B01G444200 chr7B 89.951 816 71 9 1 808 722090936 722090124 0.000000e+00 1042
10 TraesCS7B01G444200 chr7B 89.693 815 72 10 1 808 656300417 656301226 0.000000e+00 1029
11 TraesCS7B01G444200 chr7B 87.545 827 75 9 5439 6253 722087252 722086442 0.000000e+00 931
12 TraesCS7B01G444200 chr7B 88.974 653 60 8 4796 5440 651872360 651871712 0.000000e+00 797
13 TraesCS7B01G444200 chr7B 82.016 1012 108 43 4796 5744 656303975 656304975 0.000000e+00 793
14 TraesCS7B01G444200 chr7B 88.636 484 43 3 5734 6215 656314943 656315416 4.200000e-161 579
15 TraesCS7B01G444200 chr7B 91.000 400 24 4 5827 6224 652166171 652165782 4.290000e-146 529
16 TraesCS7B01G444200 chr7B 82.903 620 75 16 5439 6033 652970712 652970099 4.290000e-146 529
17 TraesCS7B01G444200 chr7B 88.053 452 37 1 3392 3826 652972710 652972259 2.580000e-143 520
18 TraesCS7B01G444200 chr7B 87.611 452 39 8 3392 3826 652399740 652399289 5.590000e-140 508
19 TraesCS7B01G444200 chr7B 90.339 383 25 4 5874 6254 651871433 651871061 5.630000e-135 492
20 TraesCS7B01G444200 chr7B 86.292 445 44 1 3399 3826 652437927 652437483 9.490000e-128 468
21 TraesCS7B01G444200 chr7B 89.542 306 23 3 1503 1802 656301982 656302284 4.580000e-101 379
22 TraesCS7B01G444200 chr7B 95.276 127 6 0 6098 6224 652970099 652969973 1.060000e-47 202
23 TraesCS7B01G444200 chr7B 89.286 140 13 2 3846 3984 652053515 652053377 2.320000e-39 174
24 TraesCS7B01G444200 chr2D 89.947 2278 154 29 4023 6254 107822280 107820032 0.000000e+00 2868
25 TraesCS7B01G444200 chr2D 93.418 1504 89 7 1963 3461 107837248 107835750 0.000000e+00 2220
26 TraesCS7B01G444200 chr2D 90.583 977 81 5 907 1881 107838199 107837232 0.000000e+00 1284
27 TraesCS7B01G444200 chr2D 91.409 873 50 9 1 871 107839054 107838205 0.000000e+00 1173
28 TraesCS7B01G444200 chr2D 84.010 763 90 23 4003 4752 290733463 290734206 0.000000e+00 704
29 TraesCS7B01G444200 chr2D 88.760 516 39 8 3490 3987 107835276 107834762 1.150000e-171 614
30 TraesCS7B01G444200 chr2D 81.466 723 103 25 4049 4752 579062659 579061949 1.180000e-156 564
31 TraesCS7B01G444200 chr2D 91.216 148 13 0 3392 3539 337373238 337373091 1.060000e-47 202
32 TraesCS7B01G444200 chr7D 88.277 1817 137 30 1 1802 584276385 584278140 0.000000e+00 2106
33 TraesCS7B01G444200 chr7D 91.079 1121 76 15 1963 3074 582678811 582677706 0.000000e+00 1495
34 TraesCS7B01G444200 chr7D 90.974 1119 78 15 1963 3074 582601596 582600494 0.000000e+00 1485
35 TraesCS7B01G444200 chr7D 90.152 1117 96 10 1963 3074 584592803 584591696 0.000000e+00 1441
36 TraesCS7B01G444200 chr7D 91.774 1009 77 4 1963 2967 586119954 586120960 0.000000e+00 1399
37 TraesCS7B01G444200 chr7D 90.778 900 70 10 907 1802 582679728 582678838 0.000000e+00 1190
38 TraesCS7B01G444200 chr7D 90.757 898 72 9 907 1802 582602957 582602069 0.000000e+00 1188
39 TraesCS7B01G444200 chr7D 90.046 874 74 9 5 871 584218477 584217610 0.000000e+00 1120
40 TraesCS7B01G444200 chr7D 89.659 880 79 7 1 871 584604460 584603584 0.000000e+00 1110
41 TraesCS7B01G444200 chr7D 85.849 848 70 18 5439 6253 584213543 584212713 0.000000e+00 856
42 TraesCS7B01G444200 chr7D 89.922 645 52 7 907 1544 584603582 584602944 0.000000e+00 819
43 TraesCS7B01G444200 chr7D 86.225 755 88 13 4011 4752 4790587 4789836 0.000000e+00 804
44 TraesCS7B01G444200 chr7D 86.412 655 76 10 4796 5440 584214226 584213575 0.000000e+00 704
45 TraesCS7B01G444200 chr7D 91.423 513 42 1 1290 1802 583034547 583034037 0.000000e+00 702
46 TraesCS7B01G444200 chr7D 84.094 635 67 13 5439 6045 584589744 584589116 3.250000e-162 582
47 TraesCS7B01G444200 chr7D 91.343 335 29 0 3492 3826 582600074 582599740 5.710000e-125 459
48 TraesCS7B01G444200 chr7D 91.045 335 30 0 3492 3826 582677286 582676952 2.660000e-123 453
49 TraesCS7B01G444200 chr7D 87.658 316 37 2 3074 3389 500979270 500978957 3.560000e-97 366
50 TraesCS7B01G444200 chr7D 87.342 316 40 0 3074 3389 277745558 277745243 4.610000e-96 363
51 TraesCS7B01G444200 chr7D 89.954 219 22 0 3544 3762 586114682 586114900 3.690000e-72 283
52 TraesCS7B01G444200 chr7D 92.994 157 11 0 6098 6254 584589131 584588975 4.880000e-56 230
53 TraesCS7B01G444200 chr7D 88.189 127 15 0 3861 3987 584279887 584280013 1.090000e-32 152
54 TraesCS7B01G444200 chr7A 89.833 1495 114 21 1 1480 708496261 708494790 0.000000e+00 1884
55 TraesCS7B01G444200 chr7A 87.483 1438 133 15 3358 4754 708469285 708467854 0.000000e+00 1615
56 TraesCS7B01G444200 chr7A 90.617 1119 90 11 1963 3074 674682039 674680929 0.000000e+00 1471
57 TraesCS7B01G444200 chr7A 90.423 898 68 12 907 1802 674683073 674682192 0.000000e+00 1166
58 TraesCS7B01G444200 chr7A 90.455 880 74 6 1 871 675870535 675871413 0.000000e+00 1151
59 TraesCS7B01G444200 chr7A 89.440 928 69 19 301 1226 675907782 675908682 0.000000e+00 1144
60 TraesCS7B01G444200 chr7A 88.427 890 96 6 4796 5680 675875414 675876301 0.000000e+00 1066
61 TraesCS7B01G444200 chr7A 88.427 890 96 6 4796 5680 675913289 675914176 0.000000e+00 1066
62 TraesCS7B01G444200 chr7A 87.289 653 69 10 4796 5438 677446664 677447312 0.000000e+00 734
63 TraesCS7B01G444200 chr7A 87.156 654 71 10 4796 5440 677616622 677617271 0.000000e+00 730
64 TraesCS7B01G444200 chr7A 88.153 574 48 9 5650 6215 677001274 677001835 0.000000e+00 665
65 TraesCS7B01G444200 chr7A 88.200 500 48 7 2861 3358 708487188 708486698 2.510000e-163 586
66 TraesCS7B01G444200 chr7A 88.636 484 43 3 5719 6200 675876297 675876770 4.200000e-161 579
67 TraesCS7B01G444200 chr7A 88.636 484 43 3 5719 6200 675914172 675914645 4.200000e-161 579
68 TraesCS7B01G444200 chr7A 88.983 354 25 6 5284 5632 708467520 708467176 5.790000e-115 425
69 TraesCS7B01G444200 chr7A 88.131 337 32 4 1562 1890 708490561 708490225 1.630000e-105 394
70 TraesCS7B01G444200 chr7A 86.897 290 26 4 3542 3826 677616110 677616392 1.310000e-81 315
71 TraesCS7B01G444200 chr7A 90.123 243 12 3 5975 6215 677449557 677449789 7.880000e-79 305
72 TraesCS7B01G444200 chr7A 86.166 253 21 5 907 1158 677440288 677440527 1.730000e-65 261
73 TraesCS7B01G444200 chr7A 88.816 152 16 1 3392 3543 297033991 297033841 1.070000e-42 185
74 TraesCS7B01G444200 chr7A 87.179 156 20 0 3393 3548 209158528 209158373 1.790000e-40 178
75 TraesCS7B01G444200 chr7A 88.652 141 16 0 3847 3987 675875207 675875347 8.340000e-39 172
76 TraesCS7B01G444200 chr7A 88.652 141 16 0 3847 3987 675913082 675913222 8.340000e-39 172
77 TraesCS7B01G444200 chr7A 90.435 115 8 2 2961 3074 444756543 444756655 1.400000e-31 148
78 TraesCS7B01G444200 chrUn 87.929 729 83 4 4955 5680 308863195 308863921 0.000000e+00 854
79 TraesCS7B01G444200 chrUn 88.636 484 43 3 5719 6200 308863917 308864390 4.200000e-161 579
80 TraesCS7B01G444200 chr4B 86.093 755 84 18 4011 4752 181428181 181428927 0.000000e+00 793
81 TraesCS7B01G444200 chr3D 85.770 766 80 17 4008 4752 355734213 355734970 0.000000e+00 784
82 TraesCS7B01G444200 chr3D 88.125 160 16 2 3389 3545 542914309 542914468 2.980000e-43 187
83 TraesCS7B01G444200 chr5B 84.882 721 92 14 4013 4729 657135495 657136202 0.000000e+00 712
84 TraesCS7B01G444200 chr5B 86.068 323 45 0 3067 3389 520251347 520251669 1.290000e-91 348
85 TraesCS7B01G444200 chr5A 87.346 569 63 7 4008 4568 241189089 241189656 1.470000e-180 643
86 TraesCS7B01G444200 chr5A 85.801 331 47 0 3059 3389 4762225 4762555 9.970000e-93 351
87 TraesCS7B01G444200 chr5A 87.975 158 19 0 3389 3546 454709278 454709435 2.980000e-43 187
88 TraesCS7B01G444200 chr1B 80.986 710 116 15 4057 4752 419392454 419391750 4.260000e-151 545
89 TraesCS7B01G444200 chr1B 87.662 154 19 0 3392 3545 488941031 488941184 4.980000e-41 180
90 TraesCS7B01G444200 chr6A 80.833 720 106 28 4049 4750 566447504 566446799 2.570000e-148 536
91 TraesCS7B01G444200 chr2A 79.420 758 125 23 4011 4746 591577492 591576744 2.010000e-139 507
92 TraesCS7B01G444200 chr2A 87.025 316 41 0 3074 3389 715997456 715997141 2.140000e-94 357
93 TraesCS7B01G444200 chr2B 87.188 320 39 2 3070 3389 476094808 476094491 4.610000e-96 363
94 TraesCS7B01G444200 chr6D 86.435 317 42 1 3074 3389 386785582 386785266 4.640000e-91 346
95 TraesCS7B01G444200 chr5D 92.857 154 11 0 3392 3545 59922186 59922033 2.270000e-54 224
96 TraesCS7B01G444200 chr5D 88.816 152 13 1 3389 3540 451008009 451008156 3.850000e-42 183


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 TraesCS7B01G444200 chr7B 708671051 708677304 6253 True 11550.000000 11550 100.000000 1 6254 1 chr7B.!!$R4 6253
1 TraesCS7B01G444200 chr7B 652060214 652061227 1013 True 1162.000000 1162 87.204000 749 1802 1 chr7B.!!$R2 1053
2 TraesCS7B01G444200 chr7B 652174037 652174914 877 True 1116.000000 1116 89.532000 908 1802 1 chr7B.!!$R3 894
3 TraesCS7B01G444200 chr7B 652437483 652440952 3469 True 1005.333333 1454 88.678000 1 3826 3 chr7B.!!$R8 3825
4 TraesCS7B01G444200 chr7B 722086442 722090936 4494 True 986.500000 1042 88.748000 1 6253 2 chr7B.!!$R10 6252
5 TraesCS7B01G444200 chr7B 656300417 656304975 4558 False 907.750000 1430 88.422250 1 5744 4 chr7B.!!$F2 5743
6 TraesCS7B01G444200 chr7B 652165782 652167156 1374 True 807.000000 1085 88.586500 4796 6224 2 chr7B.!!$R6 1428
7 TraesCS7B01G444200 chr7B 652399289 652402716 3427 True 805.500000 1103 88.584000 1 3826 2 chr7B.!!$R7 3825
8 TraesCS7B01G444200 chr7B 652969973 652973819 3846 True 668.750000 1424 89.031250 1963 6224 4 chr7B.!!$R9 4261
9 TraesCS7B01G444200 chr7B 651871061 651872360 1299 True 644.500000 797 89.656500 4796 6254 2 chr7B.!!$R5 1458
10 TraesCS7B01G444200 chr2D 107820032 107822280 2248 True 2868.000000 2868 89.947000 4023 6254 1 chr2D.!!$R1 2231
11 TraesCS7B01G444200 chr2D 107834762 107839054 4292 True 1322.750000 2220 91.042500 1 3987 4 chr2D.!!$R4 3986
12 TraesCS7B01G444200 chr2D 290733463 290734206 743 False 704.000000 704 84.010000 4003 4752 1 chr2D.!!$F1 749
13 TraesCS7B01G444200 chr2D 579061949 579062659 710 True 564.000000 564 81.466000 4049 4752 1 chr2D.!!$R3 703
14 TraesCS7B01G444200 chr7D 586119954 586120960 1006 False 1399.000000 1399 91.774000 1963 2967 1 chr7D.!!$F2 1004
15 TraesCS7B01G444200 chr7D 584276385 584280013 3628 False 1129.000000 2106 88.233000 1 3987 2 chr7D.!!$F3 3986
16 TraesCS7B01G444200 chr7D 582676952 582679728 2776 True 1046.000000 1495 90.967333 907 3826 3 chr7D.!!$R6 2919
17 TraesCS7B01G444200 chr7D 582599740 582602957 3217 True 1044.000000 1485 91.024667 907 3826 3 chr7D.!!$R5 2919
18 TraesCS7B01G444200 chr7D 584602944 584604460 1516 True 964.500000 1110 89.790500 1 1544 2 chr7D.!!$R9 1543
19 TraesCS7B01G444200 chr7D 584212713 584218477 5764 True 893.333333 1120 87.435667 5 6253 3 chr7D.!!$R7 6248
20 TraesCS7B01G444200 chr7D 4789836 4790587 751 True 804.000000 804 86.225000 4011 4752 1 chr7D.!!$R1 741
21 TraesCS7B01G444200 chr7D 584588975 584592803 3828 True 751.000000 1441 89.080000 1963 6254 3 chr7D.!!$R8 4291
22 TraesCS7B01G444200 chr7D 583034037 583034547 510 True 702.000000 702 91.423000 1290 1802 1 chr7D.!!$R4 512
23 TraesCS7B01G444200 chr7A 708494790 708496261 1471 True 1884.000000 1884 89.833000 1 1480 1 chr7A.!!$R3 1479
24 TraesCS7B01G444200 chr7A 674680929 674683073 2144 True 1318.500000 1471 90.520000 907 3074 2 chr7A.!!$R4 2167
25 TraesCS7B01G444200 chr7A 675907782 675908682 900 False 1144.000000 1144 89.440000 301 1226 1 chr7A.!!$F2 925
26 TraesCS7B01G444200 chr7A 708467176 708469285 2109 True 1020.000000 1615 88.233000 3358 5632 2 chr7A.!!$R5 2274
27 TraesCS7B01G444200 chr7A 675870535 675876770 6235 False 742.000000 1151 89.042500 1 6200 4 chr7A.!!$F5 6199
28 TraesCS7B01G444200 chr7A 677001274 677001835 561 False 665.000000 665 88.153000 5650 6215 1 chr7A.!!$F3 565
29 TraesCS7B01G444200 chr7A 675913082 675914645 1563 False 605.666667 1066 88.571667 3847 6200 3 chr7A.!!$F6 2353
30 TraesCS7B01G444200 chr7A 677616110 677617271 1161 False 522.500000 730 87.026500 3542 5440 2 chr7A.!!$F8 1898
31 TraesCS7B01G444200 chr7A 677446664 677449789 3125 False 519.500000 734 88.706000 4796 6215 2 chr7A.!!$F7 1419
32 TraesCS7B01G444200 chr7A 708486698 708490561 3863 True 490.000000 586 88.165500 1562 3358 2 chr7A.!!$R6 1796
33 TraesCS7B01G444200 chrUn 308863195 308864390 1195 False 716.500000 854 88.282500 4955 6200 2 chrUn.!!$F1 1245
34 TraesCS7B01G444200 chr4B 181428181 181428927 746 False 793.000000 793 86.093000 4011 4752 1 chr4B.!!$F1 741
35 TraesCS7B01G444200 chr3D 355734213 355734970 757 False 784.000000 784 85.770000 4008 4752 1 chr3D.!!$F1 744
36 TraesCS7B01G444200 chr5B 657135495 657136202 707 False 712.000000 712 84.882000 4013 4729 1 chr5B.!!$F2 716
37 TraesCS7B01G444200 chr5A 241189089 241189656 567 False 643.000000 643 87.346000 4008 4568 1 chr5A.!!$F2 560
38 TraesCS7B01G444200 chr1B 419391750 419392454 704 True 545.000000 545 80.986000 4057 4752 1 chr1B.!!$R1 695
39 TraesCS7B01G444200 chr6A 566446799 566447504 705 True 536.000000 536 80.833000 4049 4750 1 chr6A.!!$R1 701
40 TraesCS7B01G444200 chr2A 591576744 591577492 748 True 507.000000 507 79.420000 4011 4746 1 chr2A.!!$R1 735

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
708 742 0.179097 GACCTGGTCCTCGAATGCTC 60.179 60.0 16.14 0.00 0.00 4.26 F
875 1060 0.246635 ACACACTAGGCATGTCGGAC 59.753 55.0 0.00 0.00 0.00 4.79 F
882 1067 0.247736 AGGCATGTCGGACTTCTCAC 59.752 55.0 9.88 0.00 0.00 3.51 F
1404 1642 1.498865 CTGGCGCTTGTGACGACTTT 61.499 55.0 7.64 0.00 39.98 2.66 F
2380 6110 0.544357 ACGTCTGGACCTCCCATTCA 60.544 55.0 0.00 0.00 45.57 2.57 F
2634 7595 0.725784 CTTGAATTGCGTCACCGTGC 60.726 55.0 0.00 0.00 36.15 5.34 F
3646 9997 0.038744 AATCCAAGAGCCCACAGTGG 59.961 55.0 13.35 13.35 37.25 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2198 0.793861 TTAAGCTAACTTGGCACGCG 59.206 50.0 3.53 3.53 36.57 6.01 R
1927 2414 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.00 0.00 3.72 R
1937 2424 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.00 0.00 3.72 R
2953 8529 1.165270 CGACCAGCCTAAAACCCAAG 58.835 55.0 0.00 0.00 0.00 3.61 R
3573 9906 0.034089 AGGAACTGCCAGGCCATAAC 60.034 55.0 9.64 0.00 37.18 1.89 R
3996 10456 0.038892 ACGACCGGATGTACACACAC 60.039 55.0 9.46 0.00 37.54 3.82 R
5640 12951 0.386100 CGATGGAGTATGCCTCGACG 60.386 60.0 0.00 0.00 41.46 5.12 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
172 177 9.594478 AATTTGGTTAAACTTTGAGTAGTTTGG 57.406 29.630 10.98 0.00 45.36 3.28
251 270 1.153489 CATGCTAGCCGTGCTCACT 60.153 57.895 13.29 0.00 40.44 3.41
255 274 1.000145 GCTAGCCGTGCTCACTAAAC 59.000 55.000 2.29 0.00 40.44 2.01
262 281 2.596452 CGTGCTCACTAAACACTCGAT 58.404 47.619 0.00 0.00 32.07 3.59
273 292 5.807520 ACTAAACACTCGATGCATGTAAGAG 59.192 40.000 2.46 10.02 35.28 2.85
332 351 5.569355 TCATTAGTCCAAGCTCATCCAAAA 58.431 37.500 0.00 0.00 0.00 2.44
379 398 1.964223 ACTCCGTGAGAGAAGAAAGCA 59.036 47.619 7.76 0.00 46.50 3.91
445 467 0.753479 TTGAGAGCCCGGTTGCAAAA 60.753 50.000 0.00 0.00 0.00 2.44
448 470 1.000843 GAGAGCCCGGTTGCAAAAATT 59.999 47.619 0.00 0.00 0.00 1.82
561 588 3.293311 AATGCAGCAGTGTGATTTGAC 57.707 42.857 0.00 0.00 0.00 3.18
658 689 3.028850 ACTTGGGCGTACTAAGCTATGA 58.971 45.455 5.53 0.00 41.00 2.15
708 742 0.179097 GACCTGGTCCTCGAATGCTC 60.179 60.000 16.14 0.00 0.00 4.26
783 817 6.963049 ATACAAACATGTTTACGGACTCTC 57.037 37.500 22.87 0.00 0.00 3.20
817 1002 6.295719 TGGAAAACACTAGGAGAATAGGAC 57.704 41.667 0.00 0.00 0.00 3.85
872 1057 1.337728 TGGAACACACTAGGCATGTCG 60.338 52.381 0.00 0.00 0.00 4.35
873 1058 1.359848 GAACACACTAGGCATGTCGG 58.640 55.000 0.00 0.00 0.00 4.79
875 1060 0.246635 ACACACTAGGCATGTCGGAC 59.753 55.000 0.00 0.00 0.00 4.79
876 1061 0.532573 CACACTAGGCATGTCGGACT 59.467 55.000 9.88 0.00 0.00 3.85
878 1063 1.204941 ACACTAGGCATGTCGGACTTC 59.795 52.381 9.88 0.00 0.00 3.01
880 1065 1.751924 ACTAGGCATGTCGGACTTCTC 59.248 52.381 9.88 0.00 0.00 2.87
881 1066 1.751351 CTAGGCATGTCGGACTTCTCA 59.249 52.381 9.88 0.00 0.00 3.27
882 1067 0.247736 AGGCATGTCGGACTTCTCAC 59.752 55.000 9.88 0.00 0.00 3.51
885 1070 2.480416 GGCATGTCGGACTTCTCACTAG 60.480 54.545 9.88 0.00 0.00 2.57
887 1072 3.119459 GCATGTCGGACTTCTCACTAGAA 60.119 47.826 9.88 0.00 39.47 2.10
899 1084 6.885952 TTCTCACTAGAAGAATAGGATCGG 57.114 41.667 0.00 0.00 36.80 4.18
901 1086 6.234920 TCTCACTAGAAGAATAGGATCGGAG 58.765 44.000 0.00 0.00 0.00 4.63
903 1088 6.602278 TCACTAGAAGAATAGGATCGGAGAA 58.398 40.000 0.00 0.00 43.58 2.87
904 1089 7.235079 TCACTAGAAGAATAGGATCGGAGAAT 58.765 38.462 0.00 0.00 43.58 2.40
905 1090 7.392113 TCACTAGAAGAATAGGATCGGAGAATC 59.608 40.741 0.00 0.00 43.58 2.52
945 1148 3.576982 TCACTCGATAGTCCACCAAACTT 59.423 43.478 0.00 0.00 31.97 2.66
1025 1236 4.646572 ACGCCTTCAGAAAAGAATCTCTT 58.353 39.130 0.00 0.00 38.59 2.85
1124 1335 4.568072 TTGGCTGTATCTTTCCTAGCAA 57.432 40.909 0.00 0.00 36.15 3.91
1367 1605 3.895998 TGCAATCATGTATGCCAACCTA 58.104 40.909 18.29 1.49 41.87 3.08
1404 1642 1.498865 CTGGCGCTTGTGACGACTTT 61.499 55.000 7.64 0.00 39.98 2.66
1450 1688 5.216648 GCTCCTATGAGATTGTTACTCGTC 58.783 45.833 0.00 0.00 41.42 4.20
1467 1705 1.959985 CGTCCTAGCACTCTGATCCAT 59.040 52.381 0.00 0.00 0.00 3.41
1497 1735 2.659063 CGATCCTCCCAGTGTGGCA 61.659 63.158 0.00 0.00 35.79 4.92
1654 2088 9.835389 AGAGAAAGAAAGAAGATCATAAGGATG 57.165 33.333 0.00 0.00 36.00 3.51
1672 2106 1.555967 TGGATTACAAAAGGGCAGCC 58.444 50.000 1.26 1.26 0.00 4.85
1757 2194 6.534793 GGATTTTTGTTCTTGAAAACTGCTCA 59.465 34.615 0.00 0.00 0.00 4.26
1761 2198 4.732784 TGTTCTTGAAAACTGCTCAACAC 58.267 39.130 0.00 0.00 0.00 3.32
1803 2240 7.656707 AAAATCCATTCATTACTTGTGTTGC 57.343 32.000 0.00 0.00 0.00 4.17
1827 2302 5.989551 ACAAATGAAATTGTTGGACTTGC 57.010 34.783 0.00 0.00 40.52 4.01
1841 2316 5.713792 TGGACTTGCGGATCAAAATAAAA 57.286 34.783 0.00 0.00 33.65 1.52
1863 2350 6.867662 AATTGACTTTTCTCGAGAACACAT 57.132 33.333 27.03 13.04 33.13 3.21
1865 2352 8.553459 AATTGACTTTTCTCGAGAACACATAT 57.447 30.769 27.03 13.25 33.13 1.78
1866 2353 9.653287 AATTGACTTTTCTCGAGAACACATATA 57.347 29.630 27.03 8.36 33.13 0.86
1867 2354 8.462143 TTGACTTTTCTCGAGAACACATATAC 57.538 34.615 27.03 13.04 33.13 1.47
1868 2355 7.599171 TGACTTTTCTCGAGAACACATATACA 58.401 34.615 27.03 15.11 33.13 2.29
1869 2356 8.251026 TGACTTTTCTCGAGAACACATATACAT 58.749 33.333 27.03 1.91 33.13 2.29
1870 2357 9.731819 GACTTTTCTCGAGAACACATATACATA 57.268 33.333 27.03 5.53 33.13 2.29
1871 2358 9.517609 ACTTTTCTCGAGAACACATATACATAC 57.482 33.333 27.03 0.00 33.13 2.39
1872 2359 9.516314 CTTTTCTCGAGAACACATATACATACA 57.484 33.333 27.03 4.87 33.13 2.29
1876 2363 9.280174 TCTCGAGAACACATATACATACATACA 57.720 33.333 14.01 0.00 0.00 2.29
1920 2407 9.088987 ACATCCATACATACATACATACAGACA 57.911 33.333 0.00 0.00 0.00 3.41
1940 2427 7.844482 CAGACATATATATGTGTGTGTGTGTG 58.156 38.462 30.94 14.76 46.68 3.82
1941 2428 7.492344 CAGACATATATATGTGTGTGTGTGTGT 59.508 37.037 30.94 9.77 46.68 3.72
1942 2429 7.492344 AGACATATATATGTGTGTGTGTGTGTG 59.508 37.037 28.82 0.75 46.20 3.82
1943 2430 7.102993 ACATATATATGTGTGTGTGTGTGTGT 58.897 34.615 24.39 0.00 44.66 3.72
1944 2431 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
1945 2432 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
1946 2433 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1947 2434 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1948 2435 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1949 2436 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1950 2437 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1951 2438 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1952 2439 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1953 2440 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1954 2441 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1955 2442 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1956 2443 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1957 2444 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1958 2445 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1959 2446 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1960 2447 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1961 2448 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2008 5728 1.979855 TTGTCCCACCAACATGTCAG 58.020 50.000 0.00 0.00 0.00 3.51
2175 5895 9.669353 GCATCGATGTGATACAAATTTTAGAAT 57.331 29.630 25.47 0.00 34.83 2.40
2354 6081 9.923143 ATTGTTTGCCTAAACTTAAGGTTATTC 57.077 29.630 13.29 8.74 45.06 1.75
2358 6085 8.845413 TTGCCTAAACTTAAGGTTATTCGTAA 57.155 30.769 13.29 7.32 37.12 3.18
2380 6110 0.544357 ACGTCTGGACCTCCCATTCA 60.544 55.000 0.00 0.00 45.57 2.57
2468 6205 1.676006 CAAGTTGTTGGGACAGTCACC 59.324 52.381 0.00 0.62 42.39 4.02
2491 6228 5.340277 CCTCCACATGGGCATTATATATGGT 60.340 44.000 0.00 0.00 36.21 3.55
2634 7595 0.725784 CTTGAATTGCGTCACCGTGC 60.726 55.000 0.00 0.00 36.15 5.34
2679 7640 9.066892 GGTAATTGATTTGTAGATATCTTGCCA 57.933 33.333 11.25 3.08 0.00 4.92
2704 7665 6.490381 ACTCACACTAGTCACTAATTCACTGA 59.510 38.462 0.00 0.00 0.00 3.41
2746 8310 6.127591 TGCTCCTATTAGTCTCAGTTTCACTC 60.128 42.308 0.00 0.00 0.00 3.51
2872 8444 9.210426 CGTAACATTTAGATTGCATGTTCTAAC 57.790 33.333 11.64 2.61 40.71 2.34
3001 8578 8.990163 TGGAGTATCATAAGCGGTATCATATA 57.010 34.615 0.00 0.00 36.25 0.86
3120 8697 7.593875 CTTAGATGAGGTGCTAAGCATATTC 57.406 40.000 0.00 0.00 41.91 1.75
3192 8769 7.402862 TGTAGCTAAGCTTCCTTCCTTTAATT 58.597 34.615 0.00 0.00 40.44 1.40
3260 8837 4.929819 AAACGTTTTGCCTAGGTTCATT 57.070 36.364 11.31 0.00 0.00 2.57
3390 8968 4.883354 GCATTGGGAGGGGCCTCG 62.883 72.222 0.84 0.00 43.59 4.63
3573 9906 4.107622 GCATCCTGACAATTTTTGGATCG 58.892 43.478 0.00 0.00 35.57 3.69
3579 9912 6.035843 CCTGACAATTTTTGGATCGTTATGG 58.964 40.000 0.00 0.00 34.12 2.74
3585 9918 0.465460 TTGGATCGTTATGGCCTGGC 60.465 55.000 11.05 11.05 0.00 4.85
3609 9960 0.179073 CCTTACTGGGAGTGATGCCG 60.179 60.000 0.00 0.00 0.00 5.69
3646 9997 0.038744 AATCCAAGAGCCCACAGTGG 59.961 55.000 13.35 13.35 37.25 4.00
3712 10063 4.767255 CAGAGCCCAGGCACCGAC 62.767 72.222 12.03 0.00 44.88 4.79
3788 10141 3.406595 GATTCGGCCCCTCCACCAG 62.407 68.421 0.00 0.00 34.01 4.00
3814 10167 3.622060 TTTGGCTCCGCAGTAGGCC 62.622 63.158 0.00 0.00 38.53 5.19
3859 10319 4.643387 GCTCGTTGGTGGTGGGCT 62.643 66.667 0.00 0.00 0.00 5.19
3919 10379 3.429141 CAGCAGTCGGCCAGCTTG 61.429 66.667 2.24 0.00 46.50 4.01
3943 10403 4.850386 AGTTGGAAAACACTAGGGGATAGT 59.150 41.667 0.00 0.00 46.04 2.12
3993 10453 1.140852 ACACTAGGCATGTGTGTGTGT 59.859 47.619 13.31 10.00 45.57 3.72
3995 10455 3.007940 ACACTAGGCATGTGTGTGTGTAT 59.992 43.478 13.31 0.00 45.57 2.29
3996 10456 3.371898 CACTAGGCATGTGTGTGTGTATG 59.628 47.826 0.00 0.00 0.00 2.39
3997 10457 2.566833 AGGCATGTGTGTGTGTATGT 57.433 45.000 0.00 0.00 0.00 2.29
3998 10458 2.153645 AGGCATGTGTGTGTGTATGTG 58.846 47.619 0.00 0.00 0.00 3.21
3999 10459 1.879380 GGCATGTGTGTGTGTATGTGT 59.121 47.619 0.00 0.00 0.00 3.72
4000 10460 2.350676 GGCATGTGTGTGTGTATGTGTG 60.351 50.000 0.00 0.00 0.00 3.82
4001 10461 2.290367 GCATGTGTGTGTGTATGTGTGT 59.710 45.455 0.00 0.00 0.00 3.72
4002 10462 3.849281 GCATGTGTGTGTGTATGTGTGTG 60.849 47.826 0.00 0.00 0.00 3.82
4004 10464 4.124851 TGTGTGTGTGTATGTGTGTGTA 57.875 40.909 0.00 0.00 0.00 2.90
4005 10465 3.866327 TGTGTGTGTGTATGTGTGTGTAC 59.134 43.478 0.00 0.00 0.00 2.90
4006 10466 3.866327 GTGTGTGTGTATGTGTGTGTACA 59.134 43.478 0.00 0.00 34.63 2.90
4009 10469 4.151689 GTGTGTGTATGTGTGTGTACATCC 59.848 45.833 0.00 0.00 41.31 3.51
4155 10619 4.829872 AATCAACCCGTGGTCTGTATTA 57.170 40.909 0.00 0.00 33.12 0.98
4431 10996 1.480205 GGCGATCCGAATTGCAAATG 58.520 50.000 1.71 0.00 43.18 2.32
4454 11020 5.067936 TGAACACACATTAAAACCCGATTGT 59.932 36.000 0.00 0.00 0.00 2.71
4729 11332 6.830838 AGATCATGTGTTATTTTTCTCTCCCC 59.169 38.462 0.00 0.00 0.00 4.81
4754 11357 1.202770 ACGGGCTCTTTTGCTAGTGTT 60.203 47.619 0.00 0.00 0.00 3.32
4762 11392 5.120986 GCTCTTTTGCTAGTGTTAGACTTCC 59.879 44.000 0.00 0.00 35.96 3.46
4775 11406 5.652452 TGTTAGACTTCCTCTCATCGATCAA 59.348 40.000 0.00 0.00 0.00 2.57
4776 11407 6.322456 TGTTAGACTTCCTCTCATCGATCAAT 59.678 38.462 0.00 0.00 0.00 2.57
4778 11409 5.139727 AGACTTCCTCTCATCGATCAATCT 58.860 41.667 0.00 0.00 0.00 2.40
4780 11411 5.139727 ACTTCCTCTCATCGATCAATCTCT 58.860 41.667 0.00 0.00 0.00 3.10
4792 11423 2.621338 TCAATCTCTAACCTGCTTGCG 58.379 47.619 0.00 0.00 0.00 4.85
4855 11499 3.502595 GGCGCCTTTAGGAAAGAATATCC 59.497 47.826 22.15 0.00 41.02 2.59
4863 11509 2.104963 AGGAAAGAATATCCGGAGCCAC 59.895 50.000 11.34 1.61 42.03 5.01
5078 11737 4.926238 GCATGTGCTAGTATGTCCACTATC 59.074 45.833 0.00 0.00 38.21 2.08
5116 11775 1.737735 CACGAGCCGAGTCAATGCA 60.738 57.895 0.00 0.00 0.00 3.96
5117 11776 1.005037 ACGAGCCGAGTCAATGCAA 60.005 52.632 0.00 0.00 0.00 4.08
5129 11788 3.866379 AATGCAAGCACCCGAGCCA 62.866 57.895 0.00 0.00 34.23 4.75
5206 11865 4.183865 TGATGAAAGCTCTGATAACGTGG 58.816 43.478 0.00 0.00 0.00 4.94
5279 11939 0.110238 ATGTTGTTGTTGCTAGCGCG 60.110 50.000 10.77 0.00 39.65 6.86
5280 11940 1.278637 GTTGTTGTTGCTAGCGCGT 59.721 52.632 10.77 0.00 39.65 6.01
5306 12244 3.558033 ACAGCCATGATGCAATGATACA 58.442 40.909 0.00 0.00 0.00 2.29
5382 12576 8.818622 TGTAATACTGTAATACACACTCTCCT 57.181 34.615 10.82 0.00 32.33 3.69
5383 12577 9.910267 TGTAATACTGTAATACACACTCTCCTA 57.090 33.333 10.82 0.00 32.33 2.94
5453 12710 4.385825 TGTTTTACTGCCTGATCGTTTCT 58.614 39.130 0.00 0.00 0.00 2.52
5488 12745 4.441792 TGTCATCAAGTCCCGATGTAATG 58.558 43.478 0.00 0.00 40.92 1.90
5637 12948 2.360600 CCAAACCCATCGCCGGAA 60.361 61.111 5.05 0.00 0.00 4.30
5640 12951 1.453197 AAACCCATCGCCGGAATCC 60.453 57.895 5.05 0.00 0.00 3.01
5661 12972 1.106944 TCGAGGCATACTCCATCGCA 61.107 55.000 0.00 0.00 43.57 5.10
5681 12998 0.451299 CCATAGATCGTCGTCTCGCG 60.451 60.000 0.00 0.00 43.01 5.87
5693 13070 0.459585 GTCTCGCGAAACCCATAGCA 60.460 55.000 11.33 0.00 0.00 3.49
5732 13113 0.669077 GTCCATCTCGTGCGTCCTAT 59.331 55.000 0.00 0.00 0.00 2.57
5788 13169 3.887621 ACACACATCGCCTACATAACT 57.112 42.857 0.00 0.00 0.00 2.24
5825 13206 1.748403 GAGCAGATCCCGGCATACA 59.252 57.895 0.00 0.00 35.90 2.29
5971 13390 2.224281 GGCCTCATGTAATCGGATCACA 60.224 50.000 0.00 0.00 0.00 3.58
5972 13391 3.557898 GGCCTCATGTAATCGGATCACAT 60.558 47.826 0.72 0.72 33.22 3.21
6029 15095 0.096976 CGAACCGCGATGCTTTCAAT 59.903 50.000 8.23 0.00 44.57 2.57
6063 15131 9.923143 CCTAATAAATCATACCACGACTTCATA 57.077 33.333 0.00 0.00 0.00 2.15
6090 15158 6.530019 AAATTAATCTTTCCCAACGCTCAT 57.470 33.333 0.00 0.00 0.00 2.90
6091 15159 4.963276 TTAATCTTTCCCAACGCTCATG 57.037 40.909 0.00 0.00 0.00 3.07
6092 15160 1.098050 ATCTTTCCCAACGCTCATGC 58.902 50.000 0.00 0.00 0.00 4.06
6093 15161 0.960364 TCTTTCCCAACGCTCATGCC 60.960 55.000 0.00 0.00 35.36 4.40
6094 15162 0.962356 CTTTCCCAACGCTCATGCCT 60.962 55.000 0.00 0.00 35.36 4.75
6095 15163 1.243342 TTTCCCAACGCTCATGCCTG 61.243 55.000 0.00 0.00 35.36 4.85
6096 15164 3.136123 CCCAACGCTCATGCCTGG 61.136 66.667 0.00 0.00 38.02 4.45
6248 15316 2.898729 TGCTTGAGATAGCACTAGGC 57.101 50.000 0.00 0.00 45.72 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 159 7.415877 GGTCAAAGCCAAACTACTCAAAGTTTA 60.416 37.037 1.96 0.00 45.59 2.01
172 177 3.370672 CGCCCATAAAATTTGGTCAAAGC 59.629 43.478 0.00 0.00 33.32 3.51
211 226 0.848942 GCATGCGTGATCAGTACTCG 59.151 55.000 10.93 0.00 0.00 4.18
251 270 5.961272 TCTCTTACATGCATCGAGTGTTTA 58.039 37.500 0.00 0.00 0.00 2.01
255 274 3.739810 CCATCTCTTACATGCATCGAGTG 59.260 47.826 0.00 0.00 0.00 3.51
262 281 4.712051 ATTAGGCCATCTCTTACATGCA 57.288 40.909 5.01 0.00 0.00 3.96
273 292 5.872070 GTGATTAGCTGAGTATTAGGCCATC 59.128 44.000 5.01 0.00 0.00 3.51
332 351 0.109723 TTCTTGTGCGTAAGGCCCTT 59.890 50.000 0.00 0.00 42.61 3.95
445 467 3.947834 GCCTACTGCTGGTTGTATGAATT 59.052 43.478 0.00 0.00 36.87 2.17
448 470 2.691409 GCCTACTGCTGGTTGTATGA 57.309 50.000 0.00 0.00 36.87 2.15
561 588 2.424601 ACTCATTTCCACCGCATGAATG 59.575 45.455 0.00 0.00 0.00 2.67
658 689 2.906389 TGTGGACTGAAGGACAAGCTAT 59.094 45.455 0.00 0.00 0.00 2.97
698 732 8.385858 CCACATTATATATTGTGAGCATTCGAG 58.614 37.037 27.65 11.98 44.74 4.04
758 792 7.274033 CGAGAGTCCGTAAACATGTTTGTATTA 59.726 37.037 29.72 10.09 34.06 0.98
783 817 2.097466 AGTGTTTTCCAACAGAAGCACG 59.903 45.455 0.00 0.00 43.83 5.34
817 1002 3.070018 GCATGAACATAGGATTCTCCGG 58.930 50.000 0.00 0.00 42.75 5.14
876 1061 6.602278 TCCGATCCTATTCTTCTAGTGAGAA 58.398 40.000 11.75 11.75 39.47 2.87
878 1063 6.234920 TCTCCGATCCTATTCTTCTAGTGAG 58.765 44.000 0.00 0.00 0.00 3.51
880 1065 6.885952 TTCTCCGATCCTATTCTTCTAGTG 57.114 41.667 0.00 0.00 0.00 2.74
881 1066 7.235079 TGATTCTCCGATCCTATTCTTCTAGT 58.765 38.462 0.00 0.00 0.00 2.57
882 1067 7.695480 TGATTCTCCGATCCTATTCTTCTAG 57.305 40.000 0.00 0.00 0.00 2.43
893 1078 5.980116 CCGACAATATATGATTCTCCGATCC 59.020 44.000 0.00 0.00 0.00 3.36
894 1079 6.693545 GTCCGACAATATATGATTCTCCGATC 59.306 42.308 0.00 0.00 0.00 3.69
895 1080 6.378564 AGTCCGACAATATATGATTCTCCGAT 59.621 38.462 0.40 0.00 0.00 4.18
896 1081 5.710567 AGTCCGACAATATATGATTCTCCGA 59.289 40.000 0.40 0.00 0.00 4.55
897 1082 5.955488 AGTCCGACAATATATGATTCTCCG 58.045 41.667 0.40 0.00 0.00 4.63
898 1083 7.607250 AGAAGTCCGACAATATATGATTCTCC 58.393 38.462 0.40 0.00 0.00 3.71
899 1084 8.300286 TGAGAAGTCCGACAATATATGATTCTC 58.700 37.037 11.59 11.59 39.41 2.87
901 1086 8.085296 AGTGAGAAGTCCGACAATATATGATTC 58.915 37.037 0.40 0.00 0.00 2.52
903 1088 7.531857 AGTGAGAAGTCCGACAATATATGAT 57.468 36.000 0.40 0.00 0.00 2.45
904 1089 6.293462 CGAGTGAGAAGTCCGACAATATATGA 60.293 42.308 0.40 0.00 0.00 2.15
905 1090 5.853810 CGAGTGAGAAGTCCGACAATATATG 59.146 44.000 0.40 0.00 0.00 1.78
945 1148 5.300752 AGTTGAAGAAAAGAATGAGCGAGA 58.699 37.500 0.00 0.00 0.00 4.04
992 1199 0.323302 TGAAGGCGTCATTGGCTGTA 59.677 50.000 0.00 0.00 45.07 2.74
996 1207 0.881118 TTTCTGAAGGCGTCATTGGC 59.119 50.000 3.00 0.00 35.07 4.52
1025 1236 5.499313 TGACAATTAGGAGCATGATCACAA 58.501 37.500 13.85 6.13 0.00 3.33
1064 1275 4.805719 ACTCTTCATACATGTGCACATACG 59.194 41.667 30.92 21.77 34.26 3.06
1124 1335 8.716909 CCAATTTAACGCCAAAATGAATTAAGT 58.283 29.630 0.29 0.00 0.00 2.24
1201 1422 8.114290 CGATGCAAGAACGTGTTTATAATTAGT 58.886 33.333 0.00 0.00 0.00 2.24
1212 1433 1.954146 ACGCGATGCAAGAACGTGT 60.954 52.632 15.93 15.33 43.90 4.49
1266 1487 1.179814 AGAGTATCCGATGGACGCCC 61.180 60.000 0.00 0.00 41.07 6.13
1367 1605 2.170397 CCAGAAAAGGTGTTGGGCTTTT 59.830 45.455 0.00 0.00 0.00 2.27
1404 1642 6.042093 AGCAGTAGGAATAGCAGTAGCATTTA 59.958 38.462 0.00 0.00 45.49 1.40
1450 1688 4.040095 TCATGAATGGATCAGAGTGCTAGG 59.960 45.833 0.00 0.00 42.53 3.02
1467 1705 2.564771 GGAGGATCGTTGCATCATGAA 58.435 47.619 0.00 0.00 34.37 2.57
1558 1974 6.675413 ACCCTTCCTGTTTATTAAAAACCC 57.325 37.500 9.35 0.00 0.00 4.11
1559 1975 8.090214 GGTAACCCTTCCTGTTTATTAAAAACC 58.910 37.037 9.35 0.00 0.00 3.27
1560 1976 8.640651 TGGTAACCCTTCCTGTTTATTAAAAAC 58.359 33.333 0.00 6.41 0.00 2.43
1654 2088 1.478105 CTGGCTGCCCTTTTGTAATCC 59.522 52.381 17.53 0.00 0.00 3.01
1757 2194 1.938861 CTAACTTGGCACGCGTGTT 59.061 52.632 36.80 25.44 0.00 3.32
1761 2198 0.793861 TTAAGCTAACTTGGCACGCG 59.206 50.000 3.53 3.53 36.57 6.01
1802 2239 6.346838 GCAAGTCCAACAATTTCATTTGTAGC 60.347 38.462 0.00 0.00 38.85 3.58
1803 2240 6.129115 CGCAAGTCCAACAATTTCATTTGTAG 60.129 38.462 0.00 0.00 38.85 2.74
1841 2316 9.088512 GTATATGTGTTCTCGAGAAAAGTCAAT 57.911 33.333 28.58 18.63 35.58 2.57
1894 2381 9.088987 TGTCTGTATGTATGTATGTATGGATGT 57.911 33.333 0.00 0.00 0.00 3.06
1910 2397 9.696917 CACACACACATATATATGTCTGTATGT 57.303 33.333 26.56 22.15 41.68 2.29
1911 2398 9.696917 ACACACACACATATATATGTCTGTATG 57.303 33.333 27.30 27.30 41.68 2.39
1912 2399 9.696917 CACACACACACATATATATGTCTGTAT 57.303 33.333 26.56 18.38 41.68 2.29
1913 2400 8.691797 ACACACACACACATATATATGTCTGTA 58.308 33.333 26.56 0.00 41.68 2.74
1914 2401 7.492344 CACACACACACACATATATATGTCTGT 59.508 37.037 23.44 23.44 43.47 3.41
1915 2402 7.492344 ACACACACACACACATATATATGTCTG 59.508 37.037 22.81 22.59 44.57 3.51
1916 2403 7.492344 CACACACACACACACATATATATGTCT 59.508 37.037 22.81 11.12 44.57 3.41
1917 2404 7.277760 ACACACACACACACACATATATATGTC 59.722 37.037 22.81 0.00 44.57 3.06
1919 2406 7.064490 ACACACACACACACACACATATATATG 59.936 37.037 19.21 19.21 39.55 1.78
1920 2407 7.064490 CACACACACACACACACACATATATAT 59.936 37.037 0.00 0.00 0.00 0.86
1921 2408 6.367422 CACACACACACACACACACATATATA 59.633 38.462 0.00 0.00 0.00 0.86
1922 2409 5.179182 CACACACACACACACACACATATAT 59.821 40.000 0.00 0.00 0.00 0.86
1923 2410 4.509600 CACACACACACACACACACATATA 59.490 41.667 0.00 0.00 0.00 0.86
1924 2411 3.312146 CACACACACACACACACACATAT 59.688 43.478 0.00 0.00 0.00 1.78
1925 2412 2.675348 CACACACACACACACACACATA 59.325 45.455 0.00 0.00 0.00 2.29
1926 2413 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
1927 2414 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1928 2415 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1929 2416 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1930 2417 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1931 2418 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1932 2419 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1933 2420 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1934 2421 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1935 2422 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1936 2423 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1937 2424 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1938 2425 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1939 2426 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1940 2427 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1941 2428 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1942 2429 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1943 2430 2.070028 GTACACACACACACACACACA 58.930 47.619 0.00 0.00 0.00 3.72
1944 2431 2.070028 TGTACACACACACACACACAC 58.930 47.619 0.00 0.00 0.00 3.82
1945 2432 2.457366 TGTACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
1959 2446 1.673400 GTGTGTGCATTGGTGTGTACA 59.327 47.619 0.00 0.00 41.41 2.90
1960 2447 1.001815 GGTGTGTGCATTGGTGTGTAC 60.002 52.381 0.00 0.00 35.59 2.90
1961 2448 1.133945 AGGTGTGTGCATTGGTGTGTA 60.134 47.619 0.00 0.00 0.00 2.90
1975 5695 3.374058 GTGGGACAAATCGAATAGGTGTG 59.626 47.826 0.00 0.00 44.16 3.82
2008 5728 3.920412 GCTTTCATCGTCAAAAATCCACC 59.080 43.478 0.00 0.00 0.00 4.61
2175 5895 6.691255 ACTAACACCATTGTAGGGTTCTAA 57.309 37.500 0.00 0.00 36.19 2.10
2183 5903 9.464714 GATACAGTGATACTAACACCATTGTAG 57.535 37.037 0.00 0.00 38.82 2.74
2354 6081 2.223665 GGGAGGTCCAGACGTATTTACG 60.224 54.545 8.49 8.49 45.93 3.18
2358 6085 3.703804 TGGGAGGTCCAGACGTATT 57.296 52.632 0.00 0.00 41.46 1.89
2380 6110 1.768684 ATCAACCACTCAGGCACCGT 61.769 55.000 0.00 0.00 43.14 4.83
2468 6205 5.591472 CACCATATATAATGCCCATGTGGAG 59.409 44.000 0.00 0.00 35.26 3.86
2491 6228 4.285775 TGTTTCTCACATCACCATCTACCA 59.714 41.667 0.00 0.00 0.00 3.25
2634 7595 9.231297 CAATTACCAACCAGGGTATCTATATTG 57.769 37.037 0.00 0.00 42.75 1.90
2679 7640 6.490381 TCAGTGAATTAGTGACTAGTGTGAGT 59.510 38.462 0.00 0.00 33.82 3.41
2872 8444 9.646427 GAAAGGTCTATTATCTAGTATTGCCAG 57.354 37.037 0.00 0.00 0.00 4.85
2953 8529 1.165270 CGACCAGCCTAAAACCCAAG 58.835 55.000 0.00 0.00 0.00 3.61
2960 8536 2.835764 ACTCCATTACGACCAGCCTAAA 59.164 45.455 0.00 0.00 0.00 1.85
3001 8578 4.985538 TCCAAAAAGTCTAGTTGGCATCT 58.014 39.130 3.23 3.23 41.38 2.90
3087 8664 1.556911 ACCTCATCTAAGCACCAGTGG 59.443 52.381 7.91 7.91 0.00 4.00
3091 8668 1.279496 AGCACCTCATCTAAGCACCA 58.721 50.000 0.00 0.00 0.00 4.17
3120 8697 7.661968 TGAGGAGTATAGTTGCTAAGCTATTG 58.338 38.462 0.00 0.00 0.00 1.90
3192 8769 9.008965 TGCATGAAGAACTTTAGTTGCTAAATA 57.991 29.630 0.00 0.00 38.56 1.40
3232 8809 6.394025 ACCTAGGCAAAACGTTTAAATGAA 57.606 33.333 15.03 0.00 0.00 2.57
3233 8810 6.039493 TGAACCTAGGCAAAACGTTTAAATGA 59.961 34.615 15.03 0.00 0.00 2.57
3242 8819 3.502211 AGTGAATGAACCTAGGCAAAACG 59.498 43.478 9.30 0.00 0.00 3.60
3284 8862 4.167892 AGGAGAGAGATGAGTATGGTGACT 59.832 45.833 0.00 0.00 0.00 3.41
3368 8946 2.054453 GCCCCTCCCAATGCTTCAC 61.054 63.158 0.00 0.00 0.00 3.18
3371 8949 2.948924 AGGCCCCTCCCAATGCTT 60.949 61.111 0.00 0.00 34.51 3.91
3513 9846 5.451798 GGTCGTAACGGGGAGTATCATTTAA 60.452 44.000 0.00 0.00 36.25 1.52
3573 9906 0.034089 AGGAACTGCCAGGCCATAAC 60.034 55.000 9.64 0.00 37.18 1.89
3599 9936 1.726791 CGGTAATATGCGGCATCACTC 59.273 52.381 20.34 8.89 0.00 3.51
3646 9997 0.531974 TCCACCTGACAGTGAAACGC 60.532 55.000 0.00 0.00 45.86 4.84
3712 10063 0.813610 TGAAGGCACCACACTGTTCG 60.814 55.000 0.00 0.00 0.00 3.95
3814 10167 1.004628 TGAGGATCCCATTGTGGTGTG 59.995 52.381 8.55 0.00 35.17 3.82
3904 10364 3.123620 CTCAAGCTGGCCGACTGC 61.124 66.667 0.00 0.00 43.63 4.40
3919 10379 3.782656 TCCCCTAGTGTTTTCCAACTC 57.217 47.619 0.00 0.00 33.58 3.01
3943 10403 7.817478 CCACCGTAGAAGCATAAACATATGATA 59.183 37.037 10.38 2.63 0.00 2.15
3988 10448 3.366724 CGGATGTACACACACATACACAC 59.633 47.826 0.00 0.00 39.38 3.82
3990 10450 2.927477 CCGGATGTACACACACATACAC 59.073 50.000 0.00 0.00 39.38 2.90
3993 10453 2.159352 CGACCGGATGTACACACACATA 60.159 50.000 9.46 0.00 39.25 2.29
3995 10455 0.038983 CGACCGGATGTACACACACA 60.039 55.000 9.46 0.00 37.54 3.72
3996 10456 0.038892 ACGACCGGATGTACACACAC 60.039 55.000 9.46 0.00 37.54 3.82
3997 10457 0.241749 GACGACCGGATGTACACACA 59.758 55.000 9.46 0.00 39.52 3.72
3998 10458 0.457337 GGACGACCGGATGTACACAC 60.457 60.000 9.46 0.00 0.00 3.82
3999 10459 0.894642 TGGACGACCGGATGTACACA 60.895 55.000 9.46 3.48 39.42 3.72
4000 10460 0.458669 ATGGACGACCGGATGTACAC 59.541 55.000 16.17 5.60 39.42 2.90
4001 10461 0.742505 GATGGACGACCGGATGTACA 59.257 55.000 9.46 13.84 39.42 2.90
4002 10462 0.742505 TGATGGACGACCGGATGTAC 59.257 55.000 9.46 7.37 39.42 2.90
4004 10464 1.254975 TGTGATGGACGACCGGATGT 61.255 55.000 9.46 5.56 39.42 3.06
4005 10465 0.104855 ATGTGATGGACGACCGGATG 59.895 55.000 9.46 1.33 39.42 3.51
4006 10466 0.389391 GATGTGATGGACGACCGGAT 59.611 55.000 9.46 0.00 39.42 4.18
4009 10469 2.010145 AAAGATGTGATGGACGACCG 57.990 50.000 0.00 0.00 39.42 4.79
4118 10582 6.488683 CGGGTTGATTAATATAAAAGGCAGGA 59.511 38.462 0.00 0.00 0.00 3.86
4387 10952 6.183360 CGCTGGTATGAAAGAAAAATGGATCT 60.183 38.462 0.00 0.00 0.00 2.75
4431 10996 5.401079 CACAATCGGGTTTTAATGTGTGTTC 59.599 40.000 0.00 0.00 34.85 3.18
4454 11020 8.378172 AGTGTTATCGATGTTTTCTTTTCTCA 57.622 30.769 8.54 0.00 0.00 3.27
4534 11104 4.064491 GCACGCACACTCGCTCAC 62.064 66.667 0.00 0.00 0.00 3.51
4608 11206 1.209019 CAATGGTAGCCTCAGTGCTCT 59.791 52.381 0.00 0.00 41.68 4.09
4707 11306 5.886609 TGGGGAGAGAAAAATAACACATGA 58.113 37.500 0.00 0.00 0.00 3.07
4729 11332 1.444895 GCAAAAGAGCCCGTGCATG 60.445 57.895 0.00 0.00 41.13 4.06
4754 11357 6.303054 AGATTGATCGATGAGAGGAAGTCTA 58.697 40.000 0.54 0.00 34.71 2.59
4762 11392 6.380995 CAGGTTAGAGATTGATCGATGAGAG 58.619 44.000 0.54 0.00 0.00 3.20
4863 11509 2.726760 GCTACGATGACAATTAGGAGCG 59.273 50.000 0.00 0.00 0.00 5.03
4949 11604 1.910671 ACCAGCCAATTCAATGCCAAT 59.089 42.857 0.00 0.00 0.00 3.16
5034 11693 4.159506 TGCAAGAATGTGGTTAATTAGCCC 59.840 41.667 15.03 7.67 0.00 5.19
5116 11775 0.618458 TAATTCTGGCTCGGGTGCTT 59.382 50.000 0.00 0.00 0.00 3.91
5117 11776 0.839946 ATAATTCTGGCTCGGGTGCT 59.160 50.000 0.00 0.00 0.00 4.40
5129 11788 5.360591 CAAAGCACGGTCCTCTATAATTCT 58.639 41.667 0.00 0.00 0.00 2.40
5130 11789 4.511826 CCAAAGCACGGTCCTCTATAATTC 59.488 45.833 0.00 0.00 0.00 2.17
5206 11865 2.040544 CACAGTCACAATCGCCCCC 61.041 63.158 0.00 0.00 0.00 5.40
5279 11939 1.869774 TGCATCATGGCTGTATCGAC 58.130 50.000 0.00 0.00 34.04 4.20
5280 11940 2.618442 TTGCATCATGGCTGTATCGA 57.382 45.000 0.00 0.00 34.04 3.59
5338 12276 1.345715 ATAAGAGCCGGGAAGGGGTG 61.346 60.000 2.18 0.00 41.48 4.61
5402 12599 7.865820 TCATATCTCAAAAGAATCTCACCCTT 58.134 34.615 0.00 0.00 34.49 3.95
5453 12710 7.103641 GGACTTGATGACAACTAACAGGATAA 58.896 38.462 0.00 0.00 32.27 1.75
5637 12948 0.467474 TGGAGTATGCCTCGACGGAT 60.467 55.000 5.24 0.00 41.46 4.18
5640 12951 0.386100 CGATGGAGTATGCCTCGACG 60.386 60.000 0.00 0.00 41.46 5.12
5661 12972 0.587285 GCGAGACGACGATCTATGGT 59.413 55.000 0.00 0.00 35.09 3.55
5681 12998 3.117888 TGAGGAGGAATGCTATGGGTTTC 60.118 47.826 0.00 0.00 0.00 2.78
5693 13070 1.265454 GGACACCGGTGAGGAGGAAT 61.265 60.000 40.21 16.10 45.00 3.01
5732 13113 2.184322 GCGCCTGTGCTGTAGCTA 59.816 61.111 0.00 0.00 42.66 3.32
5772 13153 4.481368 TTCCAAGTTATGTAGGCGATGT 57.519 40.909 0.00 0.00 0.00 3.06
5788 13169 1.346395 TCCAGCGACTTAGCTTTCCAA 59.654 47.619 0.00 0.00 46.80 3.53
5825 13206 6.014669 ACTCTCATTCAGTGACTTAGCTTTCT 60.015 38.462 0.00 0.00 32.22 2.52
5918 13334 2.170012 TCCAACGGCCTCTATTACCT 57.830 50.000 0.00 0.00 0.00 3.08
5956 13375 4.988540 CGTTACCATGTGATCCGATTACAT 59.011 41.667 11.94 11.94 39.71 2.29
6029 15095 9.161629 CGTGGTATGATTTATTAGGCATGATTA 57.838 33.333 0.00 0.00 0.00 1.75
6063 15131 6.935167 AGCGTTGGGAAAGATTAATTTTGAT 58.065 32.000 0.00 0.00 0.00 2.57
6091 15159 1.678635 TTATGTGCAGGCACCAGGC 60.679 57.895 20.60 0.00 45.63 4.85
6092 15160 0.608856 TGTTATGTGCAGGCACCAGG 60.609 55.000 20.60 0.00 45.63 4.45
6093 15161 1.246649 TTGTTATGTGCAGGCACCAG 58.753 50.000 20.60 0.00 45.63 4.00
6094 15162 1.818060 GATTGTTATGTGCAGGCACCA 59.182 47.619 20.60 9.15 45.63 4.17
6095 15163 2.094675 AGATTGTTATGTGCAGGCACC 58.905 47.619 20.60 6.69 45.63 5.01
6096 15164 3.057315 ACAAGATTGTTATGTGCAGGCAC 60.057 43.478 17.11 17.11 41.94 5.01


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

AutoCloner maintained by Alex Coulton.