Multiple sequence alignment - TraesCS1B01G007300

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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 TraesCS1B01G007300 chr1B 100.000 4738 0 0 1 4738 4142679 4147416 0.000000e+00 8750.0
1 TraesCS1B01G007300 chr1B 90.076 2761 202 32 1194 3909 4519876 4517143 0.000000e+00 3515.0
2 TraesCS1B01G007300 chr1B 94.201 2190 116 4 2549 4738 4541140 4538962 0.000000e+00 3330.0
3 TraesCS1B01G007300 chr1B 88.980 2686 227 33 1278 3909 4109364 4112034 0.000000e+00 3256.0
4 TraesCS1B01G007300 chr1B 82.759 783 81 35 1257 2006 538505114 538505875 0.000000e+00 649.0
5 TraesCS1B01G007300 chr1B 90.979 388 23 6 48 434 4108082 4108458 3.270000e-141 512.0
6 TraesCS1B01G007300 chr1B 78.698 676 68 27 3906 4548 4595668 4595036 9.620000e-102 381.0
7 TraesCS1B01G007300 chr1B 83.251 406 42 12 420 804 4108680 4109080 2.710000e-92 350.0
8 TraesCS1B01G007300 chr1B 81.776 428 51 14 3907 4309 4798182 4797757 2.730000e-87 333.0
9 TraesCS1B01G007300 chr1B 79.091 550 65 25 1117 1648 46691135 46691652 2.730000e-87 333.0
10 TraesCS1B01G007300 chr1B 82.776 389 39 13 3927 4288 4112105 4112492 5.910000e-84 322.0
11 TraesCS1B01G007300 chr1B 90.233 215 13 6 4449 4663 4951962 4951756 1.680000e-69 274.0
12 TraesCS1B01G007300 chr1B 79.286 420 63 13 419 830 46690477 46690880 6.040000e-69 272.0
13 TraesCS1B01G007300 chr1B 80.211 379 40 17 1193 1548 4542983 4542617 7.870000e-63 252.0
14 TraesCS1B01G007300 chr1B 76.957 447 54 23 3950 4364 4933069 4932640 4.800000e-50 209.0
15 TraesCS1B01G007300 chr1B 86.070 201 15 6 1123 1321 4955319 4955130 2.240000e-48 204.0
16 TraesCS1B01G007300 chr1B 84.422 199 15 8 1460 1643 4597991 4597794 1.050000e-41 182.0
17 TraesCS1B01G007300 chr1B 89.916 119 11 1 4 121 4107981 4108099 8.210000e-33 152.0
18 TraesCS1B01G007300 chr1B 83.523 176 13 7 1193 1359 46691700 46691868 2.950000e-32 150.0
19 TraesCS1B01G007300 chr1B 77.778 261 28 18 898 1155 4109131 4109364 2.970000e-27 134.0
20 TraesCS1B01G007300 chr1B 77.381 252 18 24 1249 1482 4109862 4110092 3.880000e-21 113.0
21 TraesCS1B01G007300 chr1B 83.871 124 5 7 1365 1482 4519199 4519085 2.330000e-18 104.0
22 TraesCS1B01G007300 chr1B 93.220 59 4 0 4346 4404 4516594 4516536 2.350000e-13 87.9
23 TraesCS1B01G007300 chr3D 92.509 2256 150 9 1665 3909 560025277 560023030 0.000000e+00 3212.0
24 TraesCS1B01G007300 chr3D 82.239 518 41 21 3906 4392 560022981 560022484 2.660000e-107 399.0
25 TraesCS1B01G007300 chr3D 80.316 569 52 36 1111 1648 560025867 560025328 4.480000e-100 375.0
26 TraesCS1B01G007300 chr3D 77.647 255 23 22 1249 1485 560025206 560024968 1.790000e-24 124.0
27 TraesCS1B01G007300 chr3D 81.443 97 7 4 992 1088 560025992 560025907 8.510000e-08 69.4
28 TraesCS1B01G007300 chr6B 86.673 2266 240 38 1666 3909 120595809 120593584 0.000000e+00 2455.0
29 TraesCS1B01G007300 chr6B 84.058 276 34 5 3907 4181 120131007 120130741 1.690000e-64 257.0
30 TraesCS1B01G007300 chr6B 83.920 199 21 5 4211 4408 120130677 120130489 3.770000e-41 180.0
31 TraesCS1B01G007300 chr6B 78.648 281 28 13 440 699 120350125 120349856 1.770000e-34 158.0
32 TraesCS1B01G007300 chr6B 88.732 71 4 1 760 830 120318324 120318258 3.040000e-12 84.2
33 TraesCS1B01G007300 chr6B 80.165 121 15 4 1528 1648 120355104 120354993 1.090000e-11 82.4
34 TraesCS1B01G007300 chr5D 88.721 1986 189 24 1945 3910 57819423 57821393 0.000000e+00 2394.0
35 TraesCS1B01G007300 chr5D 82.623 305 37 9 445 736 57818284 57818585 6.080000e-64 255.0
36 TraesCS1B01G007300 chr5D 87.383 214 23 2 4196 4405 57821810 57822023 4.740000e-60 243.0
37 TraesCS1B01G007300 chr5D 79.920 249 20 16 1238 1467 57819161 57819398 6.350000e-34 156.0
38 TraesCS1B01G007300 chr5D 80.749 187 20 8 1471 1648 57819471 57819650 1.070000e-26 132.0
39 TraesCS1B01G007300 chr5B 88.496 1982 193 23 1949 3910 60826097 60824131 0.000000e+00 2364.0
40 TraesCS1B01G007300 chr5B 82.873 543 46 22 3906 4410 60824083 60823550 1.210000e-120 444.0
41 TraesCS1B01G007300 chr5B 82.353 187 18 7 1471 1648 60826053 60825873 1.060000e-31 148.0
42 TraesCS1B01G007300 chr5B 88.235 119 10 3 4526 4644 60823496 60823382 6.390000e-29 139.0
43 TraesCS1B01G007300 chr5B 88.750 80 2 3 897 974 60826705 60826631 1.820000e-14 91.6
44 TraesCS1B01G007300 chr5B 100.000 29 0 0 4659 4687 60823380 60823352 2.000000e-03 54.7
45 TraesCS1B01G007300 chr1A 93.770 1557 96 1 2353 3909 3013317 3014872 0.000000e+00 2337.0
46 TraesCS1B01G007300 chr1A 89.612 1829 156 24 2108 3909 2943274 2945095 0.000000e+00 2294.0
47 TraesCS1B01G007300 chr1A 86.193 746 46 24 4019 4738 3015085 3015799 0.000000e+00 754.0
48 TraesCS1B01G007300 chr1A 82.746 284 34 6 3906 4181 2945144 2945420 6.130000e-59 239.0
49 TraesCS1B01G007300 chr1A 77.366 486 50 29 1194 1648 32545241 32545697 2.850000e-57 233.0
50 TraesCS1B01G007300 chr1A 81.333 225 38 2 4188 4408 3520939 3520715 3.770000e-41 180.0
51 TraesCS1B01G007300 chr1A 81.624 234 26 10 1342 1569 2949520 2949742 1.350000e-40 178.0
52 TraesCS1B01G007300 chr1D 88.895 1783 177 10 2141 3907 49764438 49766215 0.000000e+00 2176.0
53 TraesCS1B01G007300 chr1D 95.000 60 3 0 4346 4405 33988075 33988134 1.400000e-15 95.3
54 TraesCS1B01G007300 chr2B 82.798 779 76 31 1257 2006 741895653 741896402 1.110000e-180 643.0
55 TraesCS1B01G007300 chr6A 80.791 531 61 20 3907 4410 613495530 613496046 1.240000e-100 377.0
56 TraesCS1B01G007300 chr6A 77.612 402 40 25 1166 1548 613492719 613493089 1.040000e-46 198.0
57 TraesCS1B01G007300 chr6A 81.053 190 17 10 4497 4684 64063662 64063490 2.970000e-27 134.0
58 TraesCS1B01G007300 chr6A 88.172 93 10 1 430 521 64176240 64176148 5.010000e-20 110.0
59 TraesCS1B01G007300 chr6D 80.488 533 62 20 3907 4408 53142933 53142412 2.080000e-98 370.0
60 TraesCS1B01G007300 chr6D 78.117 393 29 20 440 810 51072980 51073337 3.740000e-46 196.0
61 TraesCS1B01G007300 chr6D 77.608 393 32 22 440 810 51347762 51348120 2.250000e-43 187.0
62 TraesCS1B01G007300 chr3B 92.549 255 19 0 1673 1927 318290232 318290486 2.690000e-97 366.0
63 TraesCS1B01G007300 chr3B 87.387 111 5 2 1673 1775 762525964 762525855 8.330000e-23 119.0
64 TraesCS1B01G007300 chrUn 93.868 212 7 5 4522 4731 318171397 318171604 9.900000e-82 315.0
65 TraesCS1B01G007300 chrUn 81.624 234 26 10 1342 1569 325465861 325466083 1.350000e-40 178.0
66 TraesCS1B01G007300 chrUn 85.185 108 7 4 1193 1291 325465747 325465854 8.390000e-18 102.0
67 TraesCS1B01G007300 chr4A 80.573 314 24 13 1193 1494 666694322 666694034 1.730000e-49 207.0
68 TraesCS1B01G007300 chr4A 86.170 94 9 2 2058 2148 578290593 578290685 1.090000e-16 99.0
69 TraesCS1B01G007300 chr5A 85.567 97 10 2 2058 2151 72758606 72758511 1.090000e-16 99.0
70 TraesCS1B01G007300 chr3A 85.106 94 10 2 2058 2148 475549282 475549190 5.050000e-15 93.5


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 TraesCS1B01G007300 chr1B 4142679 4147416 4737 False 8750.000000 8750 100.000000 1 4738 1 chr1B.!!$F1 4737
1 TraesCS1B01G007300 chr1B 4538962 4542983 4021 True 1791.000000 3330 87.206000 1193 4738 2 chr1B.!!$R4 3545
2 TraesCS1B01G007300 chr1B 4516536 4519876 3340 True 1235.633333 3515 89.055667 1194 4404 3 chr1B.!!$R3 3210
3 TraesCS1B01G007300 chr1B 4107981 4112492 4511 False 691.285714 3256 84.437286 4 4288 7 chr1B.!!$F3 4284
4 TraesCS1B01G007300 chr1B 538505114 538505875 761 False 649.000000 649 82.759000 1257 2006 1 chr1B.!!$F2 749
5 TraesCS1B01G007300 chr1B 4595036 4597991 2955 True 281.500000 381 81.560000 1460 4548 2 chr1B.!!$R5 3088
6 TraesCS1B01G007300 chr1B 46690477 46691868 1391 False 251.666667 333 80.633333 419 1648 3 chr1B.!!$F4 1229
7 TraesCS1B01G007300 chr1B 4951756 4955319 3563 True 239.000000 274 88.151500 1123 4663 2 chr1B.!!$R6 3540
8 TraesCS1B01G007300 chr3D 560022484 560025992 3508 True 835.880000 3212 82.830800 992 4392 5 chr3D.!!$R1 3400
9 TraesCS1B01G007300 chr6B 120593584 120595809 2225 True 2455.000000 2455 86.673000 1666 3909 1 chr6B.!!$R4 2243
10 TraesCS1B01G007300 chr6B 120130489 120131007 518 True 218.500000 257 83.989000 3907 4408 2 chr6B.!!$R5 501
11 TraesCS1B01G007300 chr5D 57818284 57822023 3739 False 636.000000 2394 83.879200 445 4405 5 chr5D.!!$F1 3960
12 TraesCS1B01G007300 chr5B 60823352 60826705 3353 True 540.216667 2364 88.451167 897 4687 6 chr5B.!!$R1 3790
13 TraesCS1B01G007300 chr1A 3013317 3015799 2482 False 1545.500000 2337 89.981500 2353 4738 2 chr1A.!!$F4 2385
14 TraesCS1B01G007300 chr1A 2943274 2945420 2146 False 1266.500000 2294 86.179000 2108 4181 2 chr1A.!!$F3 2073
15 TraesCS1B01G007300 chr1D 49764438 49766215 1777 False 2176.000000 2176 88.895000 2141 3907 1 chr1D.!!$F2 1766
16 TraesCS1B01G007300 chr2B 741895653 741896402 749 False 643.000000 643 82.798000 1257 2006 1 chr2B.!!$F1 749
17 TraesCS1B01G007300 chr6A 613492719 613496046 3327 False 287.500000 377 79.201500 1166 4410 2 chr6A.!!$F1 3244
18 TraesCS1B01G007300 chr6D 53142412 53142933 521 True 370.000000 370 80.488000 3907 4408 1 chr6D.!!$R1 501

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
833 1205 0.039618 GGGAAGCCCATGTGAGGAAA 59.960 55.0 0.00 0.0 44.65 3.13 F
1095 1576 0.034863 GAGTGACCCCTCTCGAGTCT 60.035 60.0 13.13 0.0 0.00 3.24 F
1654 2349 0.107703 TAAATCTCCCTGCGTGCCTG 60.108 55.0 0.00 0.0 0.00 4.85 F
3374 5150 0.179124 CTCTAGCCCTCAACTGTCGC 60.179 60.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 2992 0.247460 TGATGAGTTCACAGGGAGCG 59.753 55.0 0.00 0.0 0.00 5.03 R
1961 3222 0.249868 CTGCAAGAAGACCCACGTGA 60.250 55.0 19.30 0.0 34.07 4.35 R
3468 5244 0.110486 ACACGAATTGGGCAGGACTT 59.890 50.0 0.00 0.0 0.00 3.01 R
4192 6187 0.812549 TAGTGCCACGCGAACATAGA 59.187 50.0 15.93 0.0 0.00 1.98 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
26 27 6.822667 TCTAATTGAATCAAAGAAGCAGCA 57.177 33.333 0.00 0.00 0.00 4.41
33 34 0.949397 CAAAGAAGCAGCAGCACTCA 59.051 50.000 3.17 0.00 45.49 3.41
34 35 0.950116 AAAGAAGCAGCAGCACTCAC 59.050 50.000 3.17 0.00 45.49 3.51
42 43 2.900106 GCAGCACTCACCCCTCCTT 61.900 63.158 0.00 0.00 0.00 3.36
45 46 2.266055 CACTCACCCCTCCTTCGC 59.734 66.667 0.00 0.00 0.00 4.70
113 114 3.056536 GCTATTATGGATGAGGTCGAGCA 60.057 47.826 18.15 0.79 0.00 4.26
213 270 0.657368 CTGTGTTTCACGAAAGCCGC 60.657 55.000 0.00 0.00 43.32 6.53
230 287 0.301687 CGCTAGTAGGCATTTGTGCG 59.698 55.000 0.00 0.00 36.41 5.34
240 297 3.119029 AGGCATTTGTGCGCTAATGAAAT 60.119 39.130 30.03 15.94 39.18 2.17
246 303 6.630676 TTTGTGCGCTAATGAAATCAAATC 57.369 33.333 9.73 0.00 0.00 2.17
247 304 4.671377 TGTGCGCTAATGAAATCAAATCC 58.329 39.130 9.73 0.00 0.00 3.01
284 341 5.297569 ACACCTATTTTCCTCCTCTATGC 57.702 43.478 0.00 0.00 0.00 3.14
285 342 4.202264 ACACCTATTTTCCTCCTCTATGCG 60.202 45.833 0.00 0.00 0.00 4.73
286 343 4.039245 CACCTATTTTCCTCCTCTATGCGA 59.961 45.833 0.00 0.00 0.00 5.10
287 344 4.841246 ACCTATTTTCCTCCTCTATGCGAT 59.159 41.667 0.00 0.00 0.00 4.58
288 345 6.017192 ACCTATTTTCCTCCTCTATGCGATA 58.983 40.000 0.00 0.00 0.00 2.92
289 346 6.071278 ACCTATTTTCCTCCTCTATGCGATAC 60.071 42.308 0.00 0.00 0.00 2.24
290 347 5.808366 ATTTTCCTCCTCTATGCGATACA 57.192 39.130 0.00 0.00 0.00 2.29
291 348 5.808366 TTTTCCTCCTCTATGCGATACAT 57.192 39.130 0.00 0.00 43.18 2.29
292 349 4.790765 TTCCTCCTCTATGCGATACATG 57.209 45.455 0.00 0.00 40.06 3.21
301 358 5.237815 TCTATGCGATACATGGGTCATTTC 58.762 41.667 0.00 0.00 40.06 2.17
308 365 2.596346 ACATGGGTCATTTCAGCAACA 58.404 42.857 0.00 0.00 0.00 3.33
330 387 1.342082 CGAGTTGTGGCGGAGTAACG 61.342 60.000 0.00 0.00 0.00 3.18
335 392 2.171725 GTGGCGGAGTAACGATGGC 61.172 63.158 0.00 0.00 35.47 4.40
549 852 5.987777 TTTGCAACATGTGAAGATTTTGG 57.012 34.783 0.00 0.00 0.00 3.28
659 973 7.633193 TGGACATATTTTACAACGCCTTAAT 57.367 32.000 0.00 0.00 0.00 1.40
660 974 8.057536 TGGACATATTTTACAACGCCTTAATT 57.942 30.769 0.00 0.00 0.00 1.40
813 1185 2.231380 AGCCATTCCGGGTGTTCCT 61.231 57.895 0.00 0.00 46.40 3.36
814 1186 2.046285 GCCATTCCGGGTGTTCCTG 61.046 63.158 0.00 0.00 39.70 3.86
820 1192 2.359975 CGGGTGTTCCTGGGAAGC 60.360 66.667 1.88 0.00 36.50 3.86
821 1193 2.035783 GGGTGTTCCTGGGAAGCC 59.964 66.667 1.88 8.06 34.49 4.35
831 1203 3.415186 GGGAAGCCCATGTGAGGA 58.585 61.111 0.00 0.00 44.65 3.71
832 1204 1.691219 GGGAAGCCCATGTGAGGAA 59.309 57.895 0.00 0.00 44.65 3.36
833 1205 0.039618 GGGAAGCCCATGTGAGGAAA 59.960 55.000 0.00 0.00 44.65 3.13
834 1206 1.549950 GGGAAGCCCATGTGAGGAAAA 60.550 52.381 0.00 0.00 44.65 2.29
835 1207 2.247358 GGAAGCCCATGTGAGGAAAAA 58.753 47.619 0.00 0.00 0.00 1.94
853 1225 2.798976 AAAAGCTCGCAATGCAAAGA 57.201 40.000 5.91 0.00 0.00 2.52
854 1226 2.798976 AAAGCTCGCAATGCAAAGAA 57.201 40.000 5.91 0.00 0.00 2.52
855 1227 3.308438 AAAGCTCGCAATGCAAAGAAT 57.692 38.095 5.91 0.00 0.00 2.40
856 1228 2.273370 AGCTCGCAATGCAAAGAATG 57.727 45.000 5.91 0.00 0.00 2.67
857 1229 1.542915 AGCTCGCAATGCAAAGAATGT 59.457 42.857 5.91 0.00 0.00 2.71
858 1230 2.029649 AGCTCGCAATGCAAAGAATGTT 60.030 40.909 5.91 0.00 0.00 2.71
859 1231 2.733026 GCTCGCAATGCAAAGAATGTTT 59.267 40.909 5.91 0.00 0.00 2.83
860 1232 3.181537 GCTCGCAATGCAAAGAATGTTTC 60.182 43.478 5.91 0.00 0.00 2.78
880 1252 2.825836 GGAAGCCCATGTGAGCGG 60.826 66.667 0.00 0.00 0.00 5.52
881 1253 2.825836 GAAGCCCATGTGAGCGGG 60.826 66.667 0.00 0.00 46.15 6.13
960 1416 2.903079 GAATCAAAGAAGCGGCGGCG 62.903 60.000 28.70 28.70 46.35 6.46
974 1430 3.223589 GGCGCTCTCCTCTCCTCC 61.224 72.222 7.64 0.00 0.00 4.30
975 1431 3.591835 GCGCTCTCCTCTCCTCCG 61.592 72.222 0.00 0.00 0.00 4.63
977 1433 3.223589 GCTCTCCTCTCCTCCGCC 61.224 72.222 0.00 0.00 0.00 6.13
978 1434 2.600731 CTCTCCTCTCCTCCGCCT 59.399 66.667 0.00 0.00 0.00 5.52
979 1435 1.528309 CTCTCCTCTCCTCCGCCTC 60.528 68.421 0.00 0.00 0.00 4.70
980 1436 2.904866 CTCCTCTCCTCCGCCTCG 60.905 72.222 0.00 0.00 0.00 4.63
1026 1507 2.598394 TCTCCCGGTCGGTCGTTT 60.598 61.111 8.67 0.00 0.00 3.60
1027 1508 2.126189 CTCCCGGTCGGTCGTTTC 60.126 66.667 8.67 0.00 0.00 2.78
1028 1509 3.637926 CTCCCGGTCGGTCGTTTCC 62.638 68.421 8.67 0.00 0.00 3.13
1029 1510 4.747529 CCCGGTCGGTCGTTTCCC 62.748 72.222 8.67 0.00 0.00 3.97
1030 1511 4.747529 CCGGTCGGTCGTTTCCCC 62.748 72.222 0.55 0.00 0.00 4.81
1031 1512 3.688159 CGGTCGGTCGTTTCCCCT 61.688 66.667 0.00 0.00 0.00 4.79
1053 1534 0.604511 CAAGGAAGGTACCGCCGTTT 60.605 55.000 17.72 7.95 43.70 3.60
1056 1537 0.518636 GGAAGGTACCGCCGTTTTTC 59.481 55.000 6.18 2.72 43.70 2.29
1057 1538 0.164432 GAAGGTACCGCCGTTTTTCG 59.836 55.000 6.18 0.00 43.70 3.46
1058 1539 0.249826 AAGGTACCGCCGTTTTTCGA 60.250 50.000 6.18 0.00 43.70 3.71
1074 1555 0.658368 TCGATTCGCTTCTCCTCTCG 59.342 55.000 0.00 0.00 0.00 4.04
1079 1560 0.321741 TCGCTTCTCCTCTCGTGAGT 60.322 55.000 13.09 0.00 38.61 3.41
1088 1569 0.322997 CTCTCGTGAGTGACCCCTCT 60.323 60.000 6.33 0.00 35.67 3.69
1090 1571 1.649390 CTCGTGAGTGACCCCTCTCG 61.649 65.000 6.37 6.37 45.14 4.04
1091 1572 1.674651 CGTGAGTGACCCCTCTCGA 60.675 63.158 6.78 0.00 46.09 4.04
1092 1573 1.649390 CGTGAGTGACCCCTCTCGAG 61.649 65.000 5.93 5.93 46.09 4.04
1095 1576 0.034863 GAGTGACCCCTCTCGAGTCT 60.035 60.000 13.13 0.00 0.00 3.24
1097 1578 0.528470 GTGACCCCTCTCGAGTCTTG 59.472 60.000 13.13 2.92 0.00 3.02
1119 1641 1.373590 ATGTACATGGCCGCCGTTTC 61.374 55.000 7.78 0.00 0.00 2.78
1127 1649 2.098233 GCCGCCGTTTCTCGATTCA 61.098 57.895 0.00 0.00 42.86 2.57
1129 1651 1.693083 CCGCCGTTTCTCGATTCACC 61.693 60.000 0.00 0.00 42.86 4.02
1164 1690 3.850508 GGAAACCAAACCGGCAGT 58.149 55.556 0.00 0.00 39.03 4.40
1165 1691 3.024431 GGAAACCAAACCGGCAGTA 57.976 52.632 0.00 0.00 39.03 2.74
1166 1692 0.879090 GGAAACCAAACCGGCAGTAG 59.121 55.000 0.00 0.00 39.03 2.57
1167 1693 0.879090 GAAACCAAACCGGCAGTAGG 59.121 55.000 0.00 0.00 39.03 3.18
1168 1694 0.475044 AAACCAAACCGGCAGTAGGA 59.525 50.000 0.00 0.00 39.03 2.94
1181 1707 5.241949 CCGGCAGTAGGAGTATATATCATCC 59.758 48.000 7.70 7.70 0.00 3.51
1182 1708 5.241949 CGGCAGTAGGAGTATATATCATCCC 59.758 48.000 10.97 0.56 31.86 3.85
1183 1709 5.540719 GGCAGTAGGAGTATATATCATCCCC 59.459 48.000 10.97 3.75 31.86 4.81
1184 1710 5.241949 GCAGTAGGAGTATATATCATCCCCG 59.758 48.000 10.97 2.03 31.86 5.73
1185 1711 6.366340 CAGTAGGAGTATATATCATCCCCGT 58.634 44.000 10.97 0.00 31.86 5.28
1236 1780 4.079096 AGCCATTCTCCTAGGTACAGTAGT 60.079 45.833 9.08 0.00 0.00 2.73
1329 1956 2.289072 CCCTGTGAACTCAACTCATCGT 60.289 50.000 0.00 0.00 0.00 3.73
1335 1962 2.071688 ACTCAACTCATCGTCTGTGC 57.928 50.000 0.00 0.00 0.00 4.57
1338 1965 1.067565 TCAACTCATCGTCTGTGCCTC 60.068 52.381 0.00 0.00 0.00 4.70
1371 2005 9.367160 TGATTGATTTCCCTACTTTCTTTCTTT 57.633 29.630 0.00 0.00 0.00 2.52
1391 2025 1.351017 TCTTGCCCAACCAAGACCTAG 59.649 52.381 0.81 0.00 44.49 3.02
1394 2028 1.073284 TGCCCAACCAAGACCTAGAAC 59.927 52.381 0.00 0.00 0.00 3.01
1406 2040 8.114743 ACCAAGACCTAGAACTACACTACTAAT 58.885 37.037 0.00 0.00 0.00 1.73
1439 2073 8.945758 CATATATGCTCTGCTTTTCATGTTAC 57.054 34.615 0.00 0.00 0.00 2.50
1440 2074 8.781196 CATATATGCTCTGCTTTTCATGTTACT 58.219 33.333 0.00 0.00 0.00 2.24
1441 2075 4.754372 TGCTCTGCTTTTCATGTTACTG 57.246 40.909 0.00 0.00 0.00 2.74
1442 2076 4.136796 TGCTCTGCTTTTCATGTTACTGT 58.863 39.130 0.00 0.00 0.00 3.55
1443 2077 4.580167 TGCTCTGCTTTTCATGTTACTGTT 59.420 37.500 0.00 0.00 0.00 3.16
1444 2078 5.762711 TGCTCTGCTTTTCATGTTACTGTTA 59.237 36.000 0.00 0.00 0.00 2.41
1445 2079 6.262049 TGCTCTGCTTTTCATGTTACTGTTAA 59.738 34.615 0.00 0.00 0.00 2.01
1446 2080 7.040478 TGCTCTGCTTTTCATGTTACTGTTAAT 60.040 33.333 0.00 0.00 0.00 1.40
1447 2081 7.809806 GCTCTGCTTTTCATGTTACTGTTAATT 59.190 33.333 0.00 0.00 0.00 1.40
1450 2084 9.559958 CTGCTTTTCATGTTACTGTTAATTAGG 57.440 33.333 0.00 0.00 0.00 2.69
1451 2085 9.073475 TGCTTTTCATGTTACTGTTAATTAGGT 57.927 29.630 0.00 0.00 0.00 3.08
1452 2086 9.341899 GCTTTTCATGTTACTGTTAATTAGGTG 57.658 33.333 0.00 0.00 0.00 4.00
1453 2087 9.341899 CTTTTCATGTTACTGTTAATTAGGTGC 57.658 33.333 0.00 0.00 0.00 5.01
1454 2088 6.995511 TCATGTTACTGTTAATTAGGTGCC 57.004 37.500 0.00 0.00 0.00 5.01
1455 2089 6.717289 TCATGTTACTGTTAATTAGGTGCCT 58.283 36.000 0.00 0.00 0.00 4.75
1456 2090 6.821665 TCATGTTACTGTTAATTAGGTGCCTC 59.178 38.462 0.00 0.00 0.00 4.70
1457 2091 5.493809 TGTTACTGTTAATTAGGTGCCTCC 58.506 41.667 0.00 0.00 0.00 4.30
1458 2092 5.013287 TGTTACTGTTAATTAGGTGCCTCCA 59.987 40.000 0.00 0.00 39.02 3.86
1482 2162 7.318141 CAAATAAGTTGGTTCAGATTCAGCAT 58.682 34.615 0.00 0.00 33.18 3.79
1501 2181 7.587629 TCAGCATGTTTCTTTGTATTCTCTTG 58.412 34.615 0.00 0.00 37.40 3.02
1532 2215 2.795231 ATTCAGGCTCTGCTTGCTAA 57.205 45.000 0.00 0.00 35.58 3.09
1533 2216 1.813513 TTCAGGCTCTGCTTGCTAAC 58.186 50.000 0.00 0.00 35.58 2.34
1548 2235 7.287061 TGCTTGCTAACTAATTATGGTGGTAT 58.713 34.615 0.00 0.00 0.00 2.73
1574 2265 3.947834 AGTTTTATGATGTGGCCTGTAGC 59.052 43.478 3.32 0.00 42.60 3.58
1575 2266 3.643199 TTTATGATGTGGCCTGTAGCA 57.357 42.857 3.32 0.00 46.50 3.49
1608 2299 6.539649 TTTCTTTCTAACAATCCAGACACG 57.460 37.500 0.00 0.00 0.00 4.49
1621 2312 1.480954 CAGACACGGGTAAGGTGCTAT 59.519 52.381 0.00 0.00 38.98 2.97
1625 2316 3.573110 GACACGGGTAAGGTGCTATCTAT 59.427 47.826 0.00 0.00 38.98 1.98
1648 2343 9.360093 CTATCTACTTTAATAAATCTCCCTGCG 57.640 37.037 0.00 0.00 0.00 5.18
1650 2345 6.984474 TCTACTTTAATAAATCTCCCTGCGTG 59.016 38.462 0.00 0.00 0.00 5.34
1651 2346 4.335594 ACTTTAATAAATCTCCCTGCGTGC 59.664 41.667 0.00 0.00 0.00 5.34
1652 2347 1.680338 AATAAATCTCCCTGCGTGCC 58.320 50.000 0.00 0.00 0.00 5.01
1653 2348 0.839946 ATAAATCTCCCTGCGTGCCT 59.160 50.000 0.00 0.00 0.00 4.75
1654 2349 0.107703 TAAATCTCCCTGCGTGCCTG 60.108 55.000 0.00 0.00 0.00 4.85
1655 2350 2.826777 AAATCTCCCTGCGTGCCTGG 62.827 60.000 0.00 0.00 0.00 4.45
1657 2352 4.335647 CTCCCTGCGTGCCTGGTT 62.336 66.667 0.00 0.00 0.00 3.67
1658 2353 4.641645 TCCCTGCGTGCCTGGTTG 62.642 66.667 0.00 0.00 0.00 3.77
1662 2357 4.947147 TGCGTGCCTGGTTGGACC 62.947 66.667 0.00 0.00 39.22 4.46
1663 2358 4.643387 GCGTGCCTGGTTGGACCT 62.643 66.667 0.00 0.00 39.58 3.85
1666 2361 0.250553 CGTGCCTGGTTGGACCTAAA 60.251 55.000 0.00 0.00 39.58 1.85
1667 2362 1.534729 GTGCCTGGTTGGACCTAAAG 58.465 55.000 0.00 0.00 39.58 1.85
1668 2363 1.145571 TGCCTGGTTGGACCTAAAGT 58.854 50.000 0.00 0.00 39.58 2.66
1669 2364 1.497286 TGCCTGGTTGGACCTAAAGTT 59.503 47.619 0.00 0.00 39.58 2.66
1684 2846 8.724229 GGACCTAAAGTTCGTAATGTTGTAAAT 58.276 33.333 0.00 0.00 0.00 1.40
1725 2898 8.560374 ACTACTTAGAAAGTAAGCTTTTTGCAG 58.440 33.333 3.20 0.00 44.25 4.41
1775 2954 7.065803 TGCAGCAAATACCAGTATTTCTAGTTC 59.934 37.037 11.86 2.84 42.11 3.01
1796 2975 5.839262 TCAACATATATTCGATTGGCGTC 57.161 39.130 0.00 0.00 41.80 5.19
1816 2995 6.534079 GGCGTCATCTATTAATAATAACCGCT 59.466 38.462 19.19 0.00 0.00 5.52
1832 3016 0.247460 CGCTCCCTGTGAACTCATCA 59.753 55.000 0.00 0.00 35.05 3.07
1839 3023 0.678950 TGTGAACTCATCAGCCGTGA 59.321 50.000 0.00 0.00 39.19 4.35
1849 3033 3.127376 TCATCAGCCGTGACAAAATGATG 59.873 43.478 11.93 11.93 43.32 3.07
1895 3083 6.256757 CAGGCAAGAGCTACAAGTACTAATTC 59.743 42.308 0.00 0.00 41.70 2.17
1904 3097 7.611855 AGCTACAAGTACTAATTCCAATTTGCT 59.388 33.333 0.00 0.00 0.00 3.91
1908 3101 5.965922 AGTACTAATTCCAATTTGCTTGCC 58.034 37.500 0.00 0.00 33.20 4.52
2008 3350 3.811722 TGCGTCAAATCTAGCTTGTTG 57.188 42.857 0.00 0.00 0.00 3.33
2027 3377 8.899771 GCTTGTTGCTTTATATTCCCTTAGTTA 58.100 33.333 0.00 0.00 38.95 2.24
2154 3523 8.594881 ACAGATAATGTGCTAGCTATGTTAAC 57.405 34.615 17.23 4.14 41.91 2.01
2200 3576 4.823790 AACAAGTTTTGGACGGATACAC 57.176 40.909 0.00 0.00 34.12 2.90
2341 3744 4.011023 TCCGTTGTTTTCTGAACCTTGAA 58.989 39.130 0.00 0.00 0.00 2.69
2349 3753 8.870160 TGTTTTCTGAACCTTGAAATGTATTG 57.130 30.769 0.00 0.00 33.04 1.90
2375 3792 6.150976 CCTGATTGGTACAGCTAAATTGTTCA 59.849 38.462 0.00 0.00 42.39 3.18
2446 3863 5.248248 TCACCAGGACAAGTGATCTCAATTA 59.752 40.000 0.00 0.00 38.07 1.40
2574 3991 1.304134 GCCCGGTTCCCAAATCTGT 60.304 57.895 0.00 0.00 0.00 3.41
2585 4002 3.075882 TCCCAAATCTGTGGAAAGTGGAT 59.924 43.478 0.00 0.00 41.65 3.41
2597 4014 5.927115 GTGGAAAGTGGATATCGATTACTCC 59.073 44.000 1.71 8.72 0.00 3.85
2604 4021 3.368116 GGATATCGATTACTCCGGTTGGG 60.368 52.174 1.71 0.00 35.24 4.12
2664 4081 5.991328 TCTTGTGTTTTCATCTCACTGTC 57.009 39.130 0.00 0.00 33.82 3.51
2670 4087 2.215942 TTCATCTCACTGTCCCTCGA 57.784 50.000 0.00 0.00 0.00 4.04
2765 4533 1.423584 TGGTGTCTCTCAGGCTGAAA 58.576 50.000 19.29 4.12 0.00 2.69
2897 4666 2.375509 GGAATACCTTGGTAGGGATGGG 59.624 54.545 5.71 0.00 44.97 4.00
2912 4681 2.125350 GGGTCGCTGGAAGAGCTG 60.125 66.667 0.00 0.00 46.64 4.24
3011 4781 3.480470 TGAGTTTGAGAGCAAAAGAGGG 58.520 45.455 0.00 0.00 44.91 4.30
3019 4789 4.102210 TGAGAGCAAAAGAGGGAGATATGG 59.898 45.833 0.00 0.00 0.00 2.74
3020 4790 3.145286 GAGCAAAAGAGGGAGATATGGC 58.855 50.000 0.00 0.00 0.00 4.40
3068 4844 4.824479 TGACTCCTTGTATGATGCTCAA 57.176 40.909 0.00 0.00 0.00 3.02
3095 4871 6.552629 CATGGATATGTATGATTTCTGCTGC 58.447 40.000 0.00 0.00 0.00 5.25
3098 4874 5.409520 GGATATGTATGATTTCTGCTGCGAA 59.590 40.000 0.00 0.00 0.00 4.70
3374 5150 0.179124 CTCTAGCCCTCAACTGTCGC 60.179 60.000 0.00 0.00 0.00 5.19
3406 5182 6.040278 CAGATGATAGACCTCAGCTTTACAGA 59.960 42.308 0.00 0.00 39.76 3.41
3468 5244 3.330701 AGAGGGTTTTCTGGTGCTCATTA 59.669 43.478 0.00 0.00 0.00 1.90
3505 5281 1.400142 TGTTCTTGTGCTCAACAACGG 59.600 47.619 12.79 0.00 43.96 4.44
3514 5290 1.597937 GCTCAACAACGGCAACTTCTG 60.598 52.381 0.00 0.00 0.00 3.02
3703 5479 3.079578 CTGAACTGGAACATGCACAGAT 58.920 45.455 16.03 6.62 38.20 2.90
3707 5483 4.019792 ACTGGAACATGCACAGATGTTA 57.980 40.909 16.03 0.00 44.78 2.41
4192 6187 5.239087 CCTTGTTTTATTGTGCAAATGCCTT 59.761 36.000 2.46 0.00 41.18 4.35
4730 6940 1.136141 GTTGCATCAGTTCAGCTCGTG 60.136 52.381 0.00 0.00 0.00 4.35
4733 6943 0.742281 CATCAGTTCAGCTCGTGGGG 60.742 60.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.750963 GCTGCTTCTTTGATTCAATTAGAAGG 59.249 38.462 26.89 18.49 38.10 3.46
4 5 5.515626 GCTGCTGCTTCTTTGATTCAATTAG 59.484 40.000 8.53 0.00 36.03 1.73
6 7 4.243270 GCTGCTGCTTCTTTGATTCAATT 58.757 39.130 8.53 0.00 36.03 2.32
7 8 3.257375 TGCTGCTGCTTCTTTGATTCAAT 59.743 39.130 17.00 0.00 40.48 2.57
9 10 2.030540 GTGCTGCTGCTTCTTTGATTCA 60.031 45.455 17.00 0.00 40.48 2.57
26 27 2.286523 CGAAGGAGGGGTGAGTGCT 61.287 63.158 0.00 0.00 0.00 4.40
68 69 3.000727 GCGATAGGGAATTAATGGACCG 58.999 50.000 0.00 0.00 0.00 4.79
82 83 5.268118 TCATCCATAATAGCTGCGATAGG 57.732 43.478 0.00 0.00 0.00 2.57
113 114 0.602905 GTCAGCTGTTAACCGCCACT 60.603 55.000 17.18 0.00 0.00 4.00
124 125 1.968017 CACCAATGGCGTCAGCTGT 60.968 57.895 14.67 0.00 44.37 4.40
125 126 1.672030 TCACCAATGGCGTCAGCTG 60.672 57.895 7.63 7.63 44.37 4.24
189 246 3.311596 GGCTTTCGTGAAACACAGTTAGT 59.688 43.478 0.00 0.00 35.74 2.24
230 287 9.860898 AACAGTTAAGGATTTGATTTCATTAGC 57.139 29.630 0.00 0.00 0.00 3.09
276 333 2.562738 TGACCCATGTATCGCATAGAGG 59.437 50.000 0.00 0.00 35.74 3.69
284 341 3.205338 TGCTGAAATGACCCATGTATCG 58.795 45.455 0.00 0.00 0.00 2.92
285 342 4.398988 TGTTGCTGAAATGACCCATGTATC 59.601 41.667 0.00 0.00 0.00 2.24
286 343 4.158394 GTGTTGCTGAAATGACCCATGTAT 59.842 41.667 0.00 0.00 0.00 2.29
287 344 3.505680 GTGTTGCTGAAATGACCCATGTA 59.494 43.478 0.00 0.00 0.00 2.29
288 345 2.297033 GTGTTGCTGAAATGACCCATGT 59.703 45.455 0.00 0.00 0.00 3.21
289 346 2.296752 TGTGTTGCTGAAATGACCCATG 59.703 45.455 0.00 0.00 0.00 3.66
290 347 2.297033 GTGTGTTGCTGAAATGACCCAT 59.703 45.455 0.00 0.00 0.00 4.00
291 348 1.680735 GTGTGTTGCTGAAATGACCCA 59.319 47.619 0.00 0.00 0.00 4.51
292 349 1.334960 CGTGTGTTGCTGAAATGACCC 60.335 52.381 0.00 0.00 0.00 4.46
308 365 1.457823 TACTCCGCCACAACTCGTGT 61.458 55.000 0.00 0.00 44.78 4.49
531 831 4.984161 GTGACCCAAAATCTTCACATGTTG 59.016 41.667 0.00 0.00 38.60 3.33
532 832 4.648762 TGTGACCCAAAATCTTCACATGTT 59.351 37.500 0.00 0.00 42.61 2.71
542 845 4.582701 TGTTCATGTGTGACCCAAAATC 57.417 40.909 0.00 0.00 33.11 2.17
549 852 5.399301 CGAAAAGAAATGTTCATGTGTGACC 59.601 40.000 0.00 0.00 33.11 4.02
611 925 7.433131 CCATGTCCACGAAAAGAAATTATCATG 59.567 37.037 0.00 0.00 0.00 3.07
616 930 5.765677 TGTCCATGTCCACGAAAAGAAATTA 59.234 36.000 0.00 0.00 0.00 1.40
619 933 3.546724 TGTCCATGTCCACGAAAAGAAA 58.453 40.909 0.00 0.00 0.00 2.52
622 936 5.818136 AATATGTCCATGTCCACGAAAAG 57.182 39.130 0.00 0.00 0.00 2.27
755 1127 0.035439 TTCGGCCTTCCAGACCATTC 60.035 55.000 0.00 0.00 0.00 2.67
758 1130 0.404040 ATTTTCGGCCTTCCAGACCA 59.596 50.000 0.00 0.00 0.00 4.02
764 1136 0.377203 CGCACTATTTTCGGCCTTCC 59.623 55.000 0.00 0.00 0.00 3.46
772 1144 1.296649 GCCGACGCGCACTATTTTC 60.297 57.895 5.73 0.00 0.00 2.29
814 1186 0.039618 TTTCCTCACATGGGCTTCCC 59.960 55.000 0.00 0.00 45.71 3.97
833 1205 3.096489 TCTTTGCATTGCGAGCTTTTT 57.904 38.095 3.84 0.00 0.00 1.94
834 1206 2.798976 TCTTTGCATTGCGAGCTTTT 57.201 40.000 3.84 0.00 0.00 2.27
835 1207 2.798976 TTCTTTGCATTGCGAGCTTT 57.201 40.000 3.84 0.00 0.00 3.51
836 1208 2.029649 ACATTCTTTGCATTGCGAGCTT 60.030 40.909 3.84 0.00 0.00 3.74
837 1209 1.542915 ACATTCTTTGCATTGCGAGCT 59.457 42.857 3.84 0.00 0.00 4.09
838 1210 1.986698 ACATTCTTTGCATTGCGAGC 58.013 45.000 3.84 0.00 0.00 5.03
839 1211 4.089493 CAGAAACATTCTTTGCATTGCGAG 59.911 41.667 3.84 4.92 38.11 5.03
840 1212 3.982701 CAGAAACATTCTTTGCATTGCGA 59.017 39.130 3.84 0.00 38.11 5.10
841 1213 3.122278 CCAGAAACATTCTTTGCATTGCG 59.878 43.478 3.84 0.00 38.11 4.85
842 1214 3.434299 CCCAGAAACATTCTTTGCATTGC 59.566 43.478 0.46 0.46 38.11 3.56
843 1215 4.885413 TCCCAGAAACATTCTTTGCATTG 58.115 39.130 0.00 0.00 38.11 2.82
844 1216 5.544650 CTTCCCAGAAACATTCTTTGCATT 58.455 37.500 0.00 0.00 38.11 3.56
845 1217 4.562143 GCTTCCCAGAAACATTCTTTGCAT 60.562 41.667 0.00 0.00 38.11 3.96
846 1218 3.243839 GCTTCCCAGAAACATTCTTTGCA 60.244 43.478 0.00 0.00 38.11 4.08
847 1219 3.320626 GCTTCCCAGAAACATTCTTTGC 58.679 45.455 0.00 0.00 38.11 3.68
848 1220 3.306294 GGGCTTCCCAGAAACATTCTTTG 60.306 47.826 0.00 0.00 44.65 2.77
849 1221 2.899900 GGGCTTCCCAGAAACATTCTTT 59.100 45.455 0.00 0.00 44.65 2.52
850 1222 2.529632 GGGCTTCCCAGAAACATTCTT 58.470 47.619 0.00 0.00 44.65 2.52
851 1223 2.222227 GGGCTTCCCAGAAACATTCT 57.778 50.000 0.00 0.00 44.65 2.40
880 1252 4.436998 CGTGAGCGGAGGACCACC 62.437 72.222 0.00 0.00 35.59 4.61
881 1253 3.343788 CTCGTGAGCGGAGGACCAC 62.344 68.421 0.00 0.00 38.89 4.16
895 1286 1.823610 GTAAACCCTAGCCAGTCTCGT 59.176 52.381 0.00 0.00 0.00 4.18
960 1416 3.223589 GGCGGAGGAGAGGAGAGC 61.224 72.222 0.00 0.00 0.00 4.09
1026 1507 1.652947 GTACCTTCCTTGACAGGGGA 58.347 55.000 3.41 0.00 41.25 4.81
1027 1508 0.618981 GGTACCTTCCTTGACAGGGG 59.381 60.000 4.06 0.00 41.25 4.79
1028 1509 0.249398 CGGTACCTTCCTTGACAGGG 59.751 60.000 10.90 0.00 41.25 4.45
1029 1510 0.391263 GCGGTACCTTCCTTGACAGG 60.391 60.000 10.90 0.00 42.50 4.00
1030 1511 0.391263 GGCGGTACCTTCCTTGACAG 60.391 60.000 10.90 0.00 34.51 3.51
1031 1512 1.675219 GGCGGTACCTTCCTTGACA 59.325 57.895 10.90 0.00 34.51 3.58
1053 1534 2.478031 CGAGAGGAGAAGCGAATCGAAA 60.478 50.000 6.91 0.00 0.00 3.46
1056 1537 0.378962 ACGAGAGGAGAAGCGAATCG 59.621 55.000 0.00 0.00 35.00 3.34
1057 1538 1.402259 TCACGAGAGGAGAAGCGAATC 59.598 52.381 0.00 0.00 0.00 2.52
1058 1539 1.403679 CTCACGAGAGGAGAAGCGAAT 59.596 52.381 1.41 0.00 38.26 3.34
1074 1555 0.609681 ACTCGAGAGGGGTCACTCAC 60.610 60.000 21.68 0.00 39.97 3.51
1079 1560 0.404426 TCAAGACTCGAGAGGGGTCA 59.596 55.000 21.68 0.00 36.96 4.02
1088 1569 3.676049 GCCATGTACATGTCAAGACTCGA 60.676 47.826 29.25 0.00 37.11 4.04
1090 1571 2.939103 GGCCATGTACATGTCAAGACTC 59.061 50.000 29.25 4.25 37.11 3.36
1091 1572 2.677902 CGGCCATGTACATGTCAAGACT 60.678 50.000 29.25 0.00 37.11 3.24
1092 1573 1.665679 CGGCCATGTACATGTCAAGAC 59.334 52.381 29.25 17.70 37.11 3.01
1095 1576 1.029408 GGCGGCCATGTACATGTCAA 61.029 55.000 29.25 0.00 37.11 3.18
1097 1578 2.534019 CGGCGGCCATGTACATGTC 61.534 63.158 29.25 20.12 37.11 3.06
1119 1641 4.991056 TCAAGAACAAGAAGGTGAATCGAG 59.009 41.667 0.00 0.00 0.00 4.04
1127 1649 2.158608 CCCCTGTCAAGAACAAGAAGGT 60.159 50.000 0.00 0.00 37.45 3.50
1129 1651 3.492102 TCCCCTGTCAAGAACAAGAAG 57.508 47.619 0.00 0.00 37.45 2.85
1161 1687 6.366340 ACGGGGATGATATATACTCCTACTG 58.634 44.000 11.12 5.40 0.00 2.74
1164 1690 6.586015 TGACGGGGATGATATATACTCCTA 57.414 41.667 11.12 0.00 0.00 2.94
1165 1691 5.467668 TGACGGGGATGATATATACTCCT 57.532 43.478 11.12 0.00 0.00 3.69
1166 1692 7.834881 TTATGACGGGGATGATATATACTCC 57.165 40.000 4.97 4.97 0.00 3.85
1167 1693 8.692710 TGTTTATGACGGGGATGATATATACTC 58.307 37.037 0.00 0.00 0.00 2.59
1168 1694 8.603898 TGTTTATGACGGGGATGATATATACT 57.396 34.615 0.00 0.00 0.00 2.12
1181 1707 8.508875 ACATTAACTAAGTTTGTTTATGACGGG 58.491 33.333 25.31 8.25 36.90 5.28
1182 1708 9.887406 AACATTAACTAAGTTTGTTTATGACGG 57.113 29.630 25.31 8.52 36.90 4.79
1236 1780 5.251182 ACCCTAGGCAAAAAGCTTACTTA 57.749 39.130 2.05 0.00 44.79 2.24
1282 1829 8.983724 GCCAATCTAATATCTGTTCAACTAGAC 58.016 37.037 0.00 0.00 0.00 2.59
1329 1956 1.825090 ATCATTTTGCGAGGCACAGA 58.175 45.000 0.00 0.00 38.71 3.41
1335 1962 4.114794 GGGAAATCAATCATTTTGCGAGG 58.885 43.478 0.00 0.00 34.60 4.63
1338 1965 5.894807 AGTAGGGAAATCAATCATTTTGCG 58.105 37.500 0.00 0.00 34.60 4.85
1371 2005 1.351017 CTAGGTCTTGGTTGGGCAAGA 59.649 52.381 0.00 0.00 35.34 3.02
1438 2072 4.650972 TTGGAGGCACCTAATTAACAGT 57.349 40.909 1.84 0.00 39.86 3.55
1439 2073 7.339466 ACTTATTTGGAGGCACCTAATTAACAG 59.661 37.037 14.67 9.25 42.31 3.16
1440 2074 7.179269 ACTTATTTGGAGGCACCTAATTAACA 58.821 34.615 14.67 0.00 42.31 2.41
1441 2075 7.640597 ACTTATTTGGAGGCACCTAATTAAC 57.359 36.000 14.67 0.00 42.31 2.01
1442 2076 8.062065 CAACTTATTTGGAGGCACCTAATTAA 57.938 34.615 14.67 7.53 42.31 1.40
1443 2077 7.639113 CAACTTATTTGGAGGCACCTAATTA 57.361 36.000 14.67 6.36 42.31 1.40
1444 2078 6.530019 CAACTTATTTGGAGGCACCTAATT 57.470 37.500 14.67 0.00 42.31 1.40
1457 2091 6.680810 TGCTGAATCTGAACCAACTTATTTG 58.319 36.000 0.00 0.00 34.63 2.32
1458 2092 6.899393 TGCTGAATCTGAACCAACTTATTT 57.101 33.333 0.00 0.00 0.00 1.40
1482 2162 8.974060 ACTAACCAAGAGAATACAAAGAAACA 57.026 30.769 0.00 0.00 0.00 2.83
1501 2181 5.008118 GCAGAGCCTGAATAATGAACTAACC 59.992 44.000 6.40 0.00 32.44 2.85
1548 2235 6.909550 ACAGGCCACATCATAAAACTAAAA 57.090 33.333 5.01 0.00 0.00 1.52
1553 2240 3.694072 TGCTACAGGCCACATCATAAAAC 59.306 43.478 5.01 0.00 40.92 2.43
1557 2244 2.705127 TGATGCTACAGGCCACATCATA 59.295 45.455 16.57 1.85 42.86 2.15
1584 2275 6.017440 CCGTGTCTGGATTGTTAGAAAGAAAA 60.017 38.462 0.00 0.00 0.00 2.29
1590 2281 2.635915 ACCCGTGTCTGGATTGTTAGAA 59.364 45.455 0.00 0.00 0.00 2.10
1591 2282 2.253610 ACCCGTGTCTGGATTGTTAGA 58.746 47.619 0.00 0.00 0.00 2.10
1592 2283 2.762535 ACCCGTGTCTGGATTGTTAG 57.237 50.000 0.00 0.00 0.00 2.34
1601 2292 0.892755 TAGCACCTTACCCGTGTCTG 59.107 55.000 0.00 0.00 33.61 3.51
1605 2296 3.827302 AGATAGATAGCACCTTACCCGTG 59.173 47.826 0.00 0.00 0.00 4.94
1608 2299 7.541916 AAAGTAGATAGATAGCACCTTACCC 57.458 40.000 0.00 0.00 0.00 3.69
1625 2316 6.984474 CACGCAGGGAGATTTATTAAAGTAGA 59.016 38.462 0.00 0.00 0.00 2.59
1643 2338 4.641645 TCCAACCAGGCACGCAGG 62.642 66.667 0.00 0.00 37.29 4.85
1644 2339 3.357079 GTCCAACCAGGCACGCAG 61.357 66.667 0.00 0.00 37.29 5.18
1648 2343 1.202891 ACTTTAGGTCCAACCAGGCAC 60.203 52.381 0.00 0.00 41.95 5.01
1650 2345 2.160205 GAACTTTAGGTCCAACCAGGC 58.840 52.381 0.00 0.00 41.95 4.85
1651 2346 2.224450 ACGAACTTTAGGTCCAACCAGG 60.224 50.000 0.00 0.00 41.95 4.45
1652 2347 3.121738 ACGAACTTTAGGTCCAACCAG 57.878 47.619 0.00 0.00 41.95 4.00
1653 2348 4.686191 TTACGAACTTTAGGTCCAACCA 57.314 40.909 0.00 0.00 41.95 3.67
1654 2349 4.999311 ACATTACGAACTTTAGGTCCAACC 59.001 41.667 0.00 0.00 38.99 3.77
1655 2350 6.017687 ACAACATTACGAACTTTAGGTCCAAC 60.018 38.462 0.00 0.00 0.00 3.77
1656 2351 6.056884 ACAACATTACGAACTTTAGGTCCAA 58.943 36.000 0.00 0.00 0.00 3.53
1657 2352 5.613329 ACAACATTACGAACTTTAGGTCCA 58.387 37.500 0.00 0.00 0.00 4.02
1658 2353 7.656707 TTACAACATTACGAACTTTAGGTCC 57.343 36.000 0.00 0.00 0.00 4.46
1667 2362 9.274065 GGAGAATGAATTTACAACATTACGAAC 57.726 33.333 0.00 0.00 34.94 3.95
1668 2363 9.226606 AGGAGAATGAATTTACAACATTACGAA 57.773 29.630 0.00 0.00 34.94 3.85
1669 2364 8.786826 AGGAGAATGAATTTACAACATTACGA 57.213 30.769 0.00 0.00 34.94 3.43
1684 2846 9.986157 TTTCTAAGTAGTACCTAGGAGAATGAA 57.014 33.333 17.98 5.18 0.00 2.57
1685 2847 9.629878 CTTTCTAAGTAGTACCTAGGAGAATGA 57.370 37.037 17.98 0.00 0.00 2.57
1725 2898 2.287909 CCTAGGCAAGTACTCGATCAGC 60.288 54.545 0.00 0.00 0.00 4.26
1775 2954 5.590104 TGACGCCAATCGAATATATGTTG 57.410 39.130 0.00 0.00 41.67 3.33
1786 2965 9.901724 GTTATTATTAATAGATGACGCCAATCG 57.098 33.333 0.00 0.00 45.38 3.34
1796 2975 8.041323 ACAGGGAGCGGTTATTATTAATAGATG 58.959 37.037 0.00 0.00 0.00 2.90
1813 2992 0.247460 TGATGAGTTCACAGGGAGCG 59.753 55.000 0.00 0.00 0.00 5.03
1816 2995 0.615331 GGCTGATGAGTTCACAGGGA 59.385 55.000 0.00 0.00 33.00 4.20
1832 3016 2.744202 GAGACATCATTTTGTCACGGCT 59.256 45.455 7.28 0.00 46.81 5.52
1839 3023 5.163281 AGAGAGCAGAGACATCATTTTGT 57.837 39.130 0.00 0.00 0.00 2.83
1849 3033 2.345876 GGCAAGAAAGAGAGCAGAGAC 58.654 52.381 0.00 0.00 0.00 3.36
1851 3035 1.002888 TGGGCAAGAAAGAGAGCAGAG 59.997 52.381 0.00 0.00 0.00 3.35
1853 3037 1.451067 CTGGGCAAGAAAGAGAGCAG 58.549 55.000 0.00 0.00 0.00 4.24
1855 3039 1.311651 GCCTGGGCAAGAAAGAGAGC 61.312 60.000 6.75 0.00 41.49 4.09
1895 3083 0.397564 AACCAGGGCAAGCAAATTGG 59.602 50.000 0.00 0.00 39.47 3.16
1904 3097 3.571590 AGTAACATGAAAACCAGGGCAA 58.428 40.909 0.00 0.00 0.00 4.52
1908 3101 8.458843 CACCTAATTAGTAACATGAAAACCAGG 58.541 37.037 11.50 0.00 0.00 4.45
1961 3222 0.249868 CTGCAAGAAGACCCACGTGA 60.250 55.000 19.30 0.00 34.07 4.35
2019 3365 9.262358 GGCTGAGTAATGAACTAATAACTAAGG 57.738 37.037 0.00 0.00 39.07 2.69
2027 3377 5.363939 GCAGAGGCTGAGTAATGAACTAAT 58.636 41.667 0.00 0.00 36.22 1.73
2028 3378 4.759782 GCAGAGGCTGAGTAATGAACTAA 58.240 43.478 0.00 0.00 36.22 2.24
2029 3379 4.392921 GCAGAGGCTGAGTAATGAACTA 57.607 45.455 0.00 0.00 36.22 2.24
2137 3499 6.538742 GGAGATTTGTTAACATAGCTAGCACA 59.461 38.462 18.83 7.63 0.00 4.57
2149 3518 6.012658 TCACAAGCATGGAGATTTGTTAAC 57.987 37.500 0.00 0.00 31.84 2.01
2154 3523 5.159209 GTTCTTCACAAGCATGGAGATTTG 58.841 41.667 0.00 0.00 0.00 2.32
2341 3744 4.339247 GCTGTACCAATCAGGCAATACATT 59.661 41.667 0.00 0.00 43.14 2.71
2349 3753 4.399303 ACAATTTAGCTGTACCAATCAGGC 59.601 41.667 0.00 0.00 43.14 4.85
2375 3792 0.398664 CCTCCGGTAGGTCCTCCATT 60.399 60.000 0.00 0.00 40.94 3.16
2397 3814 4.313282 CTGTTGAGAATCTCTGTCAGCAA 58.687 43.478 11.92 0.00 32.00 3.91
2446 3863 3.565307 TGCTTTGACACAAGGGAAAGAT 58.435 40.909 0.00 0.00 0.00 2.40
2542 3959 2.404789 GGGCGCACAATGATGTCG 59.595 61.111 10.83 0.00 37.82 4.35
2574 3991 5.278808 CGGAGTAATCGATATCCACTTTCCA 60.279 44.000 18.90 0.00 0.00 3.53
2585 4002 2.669781 ACCCAACCGGAGTAATCGATA 58.330 47.619 9.46 0.00 34.64 2.92
2604 4021 2.290323 ACTGCTTTCCATGTCCAGGTAC 60.290 50.000 0.00 0.00 0.00 3.34
2664 4081 1.202580 GGTGAGGTCAATCATCGAGGG 60.203 57.143 0.00 0.00 0.00 4.30
2670 4087 4.851639 AGCTTAAGGTGAGGTCAATCAT 57.148 40.909 6.33 0.00 0.00 2.45
2765 4533 6.834168 ATCGAAGTTATTTTTGGTGTGGAT 57.166 33.333 0.00 0.00 0.00 3.41
2912 4681 6.374333 TGATACCTTTGCAATTCTTCACTACC 59.626 38.462 0.00 0.00 0.00 3.18
3011 4781 4.565236 CCTGGATCAAGAAGGCCATATCTC 60.565 50.000 5.01 0.00 0.00 2.75
3019 4789 2.295885 CATCACCTGGATCAAGAAGGC 58.704 52.381 0.00 0.00 32.57 4.35
3020 4790 3.641434 ACATCACCTGGATCAAGAAGG 57.359 47.619 0.00 0.00 32.57 3.46
3068 4844 6.946583 AGCAGAAATCATACATATCCATGCTT 59.053 34.615 0.00 0.00 35.75 3.91
3095 4871 6.640907 CCAACCTTAAATCCTTCAAACTTTCG 59.359 38.462 0.00 0.00 0.00 3.46
3098 4874 5.508994 CGCCAACCTTAAATCCTTCAAACTT 60.509 40.000 0.00 0.00 0.00 2.66
3374 5150 5.211174 TGAGGTCTATCATCTGAAGCATG 57.789 43.478 0.00 0.00 0.00 4.06
3468 5244 0.110486 ACACGAATTGGGCAGGACTT 59.890 50.000 0.00 0.00 0.00 3.01
3505 5281 1.728971 CCTCGTCATCACAGAAGTTGC 59.271 52.381 0.00 0.00 0.00 4.17
3514 5290 1.202580 CCTTCATCCCCTCGTCATCAC 60.203 57.143 0.00 0.00 0.00 3.06
3703 5479 5.010719 ACTCGATGACCAAAGACTCTTAACA 59.989 40.000 0.00 0.00 0.00 2.41
3707 5483 3.829601 AGACTCGATGACCAAAGACTCTT 59.170 43.478 0.00 0.00 0.00 2.85
4192 6187 0.812549 TAGTGCCACGCGAACATAGA 59.187 50.000 15.93 0.00 0.00 1.98
4259 6310 2.436417 ACAAGCATGTCGCCTTTGTAT 58.564 42.857 0.00 0.00 44.04 2.29
4690 6896 5.107065 GCAACGAGCTGTCTTGTTACTAAAT 60.107 40.000 0.00 0.00 43.35 1.40


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

AutoCloner maintained by Alex Coulton.