Multiple sequence alignment - TraesCS4A01G436000

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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 TraesCS4A01G436000 chr4A 100.000 3326 0 0 1 3326 705765554 705762229 0.000000e+00 6143.0
1 TraesCS4A01G436000 chr4A 90.722 1261 106 3 1080 2329 692394322 692393062 0.000000e+00 1670.0
2 TraesCS4A01G436000 chr4A 90.121 577 46 6 1151 1716 694755703 694756279 0.000000e+00 739.0
3 TraesCS4A01G436000 chr4A 89.810 579 53 2 1751 2323 694756275 694756853 0.000000e+00 737.0
4 TraesCS4A01G436000 chr4A 76.526 426 68 22 2926 3326 664204616 664204198 1.560000e-48 204.0
5 TraesCS4A01G436000 chr4A 77.941 272 42 15 3062 3326 632017141 632017401 1.600000e-33 154.0
6 TraesCS4A01G436000 chr7A 90.764 1256 105 5 1080 2325 32583982 32582728 0.000000e+00 1666.0
7 TraesCS4A01G436000 chr7A 86.402 478 41 8 2873 3326 18960123 18960600 4.950000e-138 501.0
8 TraesCS4A01G436000 chr7A 87.123 365 31 12 536 887 645329013 645328652 1.860000e-107 399.0
9 TraesCS4A01G436000 chr7A 90.635 299 19 2 2489 2787 18959319 18959608 4.020000e-104 388.0
10 TraesCS4A01G436000 chr7A 91.200 125 11 0 2753 2877 18959613 18959737 1.590000e-38 171.0
11 TraesCS4A01G436000 chr7A 75.802 343 47 24 258 582 681252547 681252871 1.240000e-29 141.0
12 TraesCS4A01G436000 chr7A 79.775 178 23 9 2323 2490 32582701 32582527 2.100000e-22 117.0
13 TraesCS4A01G436000 chr3B 93.862 896 27 14 1 891 89091761 89092633 0.000000e+00 1325.0
14 TraesCS4A01G436000 chr7B 93.458 856 32 6 2493 3326 648758960 648758107 0.000000e+00 1249.0
15 TraesCS4A01G436000 chr7B 91.971 137 9 2 2489 2624 125371581 125371716 1.220000e-44 191.0
16 TraesCS4A01G436000 chr7B 85.333 75 8 3 827 899 624167536 624167463 1.280000e-09 75.0
17 TraesCS4A01G436000 chr1B 95.957 742 7 1 2493 3211 44735640 44736381 0.000000e+00 1182.0
18 TraesCS4A01G436000 chr1B 90.511 137 11 2 2492 2627 30947750 30947615 2.640000e-41 180.0
19 TraesCS4A01G436000 chrUn 95.687 742 9 1 2493 3211 388498574 388497833 0.000000e+00 1171.0
20 TraesCS4A01G436000 chrUn 95.553 742 10 7 2493 3211 169531537 169530796 0.000000e+00 1166.0
21 TraesCS4A01G436000 chrUn 99.031 516 5 0 2493 3008 169578861 169578346 0.000000e+00 926.0
22 TraesCS4A01G436000 chr6A 95.062 567 24 4 1 565 429385172 429384608 0.000000e+00 889.0
23 TraesCS4A01G436000 chr6A 91.040 346 17 3 557 890 429379153 429378810 3.910000e-124 455.0
24 TraesCS4A01G436000 chr6A 89.106 358 20 10 1 341 194790375 194790730 8.530000e-116 427.0
25 TraesCS4A01G436000 chr7D 88.840 681 70 4 1326 2001 32566455 32565776 0.000000e+00 832.0
26 TraesCS4A01G436000 chr7D 86.966 445 38 7 1999 2425 32559919 32559477 1.790000e-132 483.0
27 TraesCS4A01G436000 chr7D 90.000 60 5 1 832 891 413694259 413694201 3.560000e-10 76.8
28 TraesCS4A01G436000 chr2A 95.010 521 21 5 1 518 174443725 174444243 0.000000e+00 813.0
29 TraesCS4A01G436000 chr2A 93.176 381 22 4 513 890 174444549 174444928 1.040000e-154 556.0
30 TraesCS4A01G436000 chr2A 77.236 246 35 17 620 857 565168800 565169032 1.250000e-24 124.0
31 TraesCS4A01G436000 chr2D 95.258 485 16 5 1 482 22573082 22572602 0.000000e+00 761.0
32 TraesCS4A01G436000 chr2D 91.049 391 23 3 512 890 22572619 22572229 4.920000e-143 518.0
33 TraesCS4A01G436000 chr2D 87.654 405 24 11 1 381 5276601 5277003 6.550000e-122 448.0
34 TraesCS4A01G436000 chr2D 93.491 169 7 4 536 702 576451626 576451460 7.130000e-62 248.0
35 TraesCS4A01G436000 chr2D 85.350 157 16 4 737 890 22797356 22797204 4.440000e-34 156.0
36 TraesCS4A01G436000 chr2B 83.557 894 50 18 2492 3326 30327980 30327125 0.000000e+00 747.0
37 TraesCS4A01G436000 chr3D 88.303 436 25 16 1 415 591972464 591972034 1.780000e-137 499.0
38 TraesCS4A01G436000 chr6D 87.901 405 23 11 1 381 131641774 131641372 1.410000e-123 453.0
39 TraesCS4A01G436000 chr6D 88.473 347 23 9 1 332 38521309 38520965 1.440000e-108 403.0
40 TraesCS4A01G436000 chr6D 83.535 413 22 6 2486 2872 447660 447268 8.830000e-91 344.0
41 TraesCS4A01G436000 chr6B 90.152 132 11 2 2492 2622 40922418 40922288 1.590000e-38 171.0
42 TraesCS4A01G436000 chr4D 82.166 157 21 6 746 898 386548349 386548502 9.690000e-26 128.0
43 TraesCS4A01G436000 chr4D 100.000 31 0 0 1145 1175 79855054 79855084 1.290000e-04 58.4
44 TraesCS4A01G436000 chr4D 100.000 31 0 0 1145 1175 79947483 79947513 1.290000e-04 58.4
45 TraesCS4A01G436000 chr1D 82.759 145 20 5 750 890 481570634 481570491 1.250000e-24 124.0
46 TraesCS4A01G436000 chr5A 92.857 56 4 0 835 890 465318332 465318387 7.650000e-12 82.4


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 TraesCS4A01G436000 chr4A 705762229 705765554 3325 True 6143.000000 6143 100.000000 1 3326 1 chr4A.!!$R3 3325
1 TraesCS4A01G436000 chr4A 692393062 692394322 1260 True 1670.000000 1670 90.722000 1080 2329 1 chr4A.!!$R2 1249
2 TraesCS4A01G436000 chr4A 694755703 694756853 1150 False 738.000000 739 89.965500 1151 2323 2 chr4A.!!$F2 1172
3 TraesCS4A01G436000 chr7A 32582527 32583982 1455 True 891.500000 1666 85.269500 1080 2490 2 chr7A.!!$R2 1410
4 TraesCS4A01G436000 chr7A 18959319 18960600 1281 False 353.333333 501 89.412333 2489 3326 3 chr7A.!!$F2 837
5 TraesCS4A01G436000 chr3B 89091761 89092633 872 False 1325.000000 1325 93.862000 1 891 1 chr3B.!!$F1 890
6 TraesCS4A01G436000 chr7B 648758107 648758960 853 True 1249.000000 1249 93.458000 2493 3326 1 chr7B.!!$R2 833
7 TraesCS4A01G436000 chr1B 44735640 44736381 741 False 1182.000000 1182 95.957000 2493 3211 1 chr1B.!!$F1 718
8 TraesCS4A01G436000 chrUn 388497833 388498574 741 True 1171.000000 1171 95.687000 2493 3211 1 chrUn.!!$R3 718
9 TraesCS4A01G436000 chrUn 169530796 169531537 741 True 1166.000000 1166 95.553000 2493 3211 1 chrUn.!!$R1 718
10 TraesCS4A01G436000 chrUn 169578346 169578861 515 True 926.000000 926 99.031000 2493 3008 1 chrUn.!!$R2 515
11 TraesCS4A01G436000 chr6A 429384608 429385172 564 True 889.000000 889 95.062000 1 565 1 chr6A.!!$R2 564
12 TraesCS4A01G436000 chr7D 32565776 32566455 679 True 832.000000 832 88.840000 1326 2001 1 chr7D.!!$R2 675
13 TraesCS4A01G436000 chr2A 174443725 174444928 1203 False 684.500000 813 94.093000 1 890 2 chr2A.!!$F2 889
14 TraesCS4A01G436000 chr2D 22572229 22573082 853 True 639.500000 761 93.153500 1 890 2 chr2D.!!$R3 889
15 TraesCS4A01G436000 chr2B 30327125 30327980 855 True 747.000000 747 83.557000 2492 3326 1 chr2B.!!$R1 834

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
891 1232 1.130373 CTGATTTTTAGCAGCGCCGAA 59.870 47.619 2.29 0.0 0.0 4.30 F
1067 1408 0.106419 GGTATCCCCCATCGCCAAAA 60.106 55.000 0.00 0.0 0.0 2.44 F
1444 1792 0.174845 CCTCAATCCTACGTTCGCCA 59.825 55.000 0.00 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2350 0.107456 CCCCAGATTACGCAGCATCT 59.893 55.0 0.00 0.0 31.76 2.90 R
2208 2562 0.178767 CGAAGGGATGATCTGCCACA 59.821 55.0 6.73 0.0 37.96 4.17 R
2440 2837 0.387565 GAAGAGATGGAGAGCCGGTC 59.612 60.0 1.90 0.0 36.79 4.79 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
89 90 9.862371 TCTATTTTCAGACTAAGAAGCTAACAG 57.138 33.333 0.00 0.00 0.00 3.16
311 314 9.512748 AGCCTATAAATCCTGAGTCCATTATAT 57.487 33.333 0.00 0.00 0.00 0.86
406 409 6.397272 AGCATCAAACAAGAAACAAGACAAA 58.603 32.000 0.00 0.00 0.00 2.83
484 491 1.484653 CCTCTCTCTCTCGTCCTCTGA 59.515 57.143 0.00 0.00 0.00 3.27
573 891 2.311463 GGGAATGGAGAGAGACGATGA 58.689 52.381 0.00 0.00 0.00 2.92
707 1036 3.587933 GCCCGCACGGAAACACAA 61.588 61.111 11.42 0.00 37.50 3.33
727 1056 2.192861 CCAGCCCACAAAACGCTCA 61.193 57.895 0.00 0.00 0.00 4.26
765 1094 3.915569 CGACAGAAAAACAAACAAACGGT 59.084 39.130 0.00 0.00 0.00 4.83
891 1232 1.130373 CTGATTTTTAGCAGCGCCGAA 59.870 47.619 2.29 0.00 0.00 4.30
892 1233 1.537638 TGATTTTTAGCAGCGCCGAAA 59.462 42.857 2.29 0.00 0.00 3.46
893 1234 2.177173 GATTTTTAGCAGCGCCGAAAG 58.823 47.619 2.29 0.00 0.00 2.62
894 1235 1.231221 TTTTTAGCAGCGCCGAAAGA 58.769 45.000 2.29 0.00 0.00 2.52
895 1236 1.231221 TTTTAGCAGCGCCGAAAGAA 58.769 45.000 2.29 0.00 0.00 2.52
896 1237 1.231221 TTTAGCAGCGCCGAAAGAAA 58.769 45.000 2.29 0.00 0.00 2.52
897 1238 1.231221 TTAGCAGCGCCGAAAGAAAA 58.769 45.000 2.29 0.00 0.00 2.29
898 1239 1.231221 TAGCAGCGCCGAAAGAAAAA 58.769 45.000 2.29 0.00 0.00 1.94
915 1256 3.602205 AAAAACCTCCCTCTCTTTGCT 57.398 42.857 0.00 0.00 0.00 3.91
916 1257 3.602205 AAAACCTCCCTCTCTTTGCTT 57.398 42.857 0.00 0.00 0.00 3.91
917 1258 4.724279 AAAACCTCCCTCTCTTTGCTTA 57.276 40.909 0.00 0.00 0.00 3.09
918 1259 3.704800 AACCTCCCTCTCTTTGCTTAC 57.295 47.619 0.00 0.00 0.00 2.34
919 1260 1.550976 ACCTCCCTCTCTTTGCTTACG 59.449 52.381 0.00 0.00 0.00 3.18
920 1261 1.825474 CCTCCCTCTCTTTGCTTACGA 59.175 52.381 0.00 0.00 0.00 3.43
921 1262 2.159170 CCTCCCTCTCTTTGCTTACGAG 60.159 54.545 0.00 0.00 0.00 4.18
922 1263 2.494073 CTCCCTCTCTTTGCTTACGAGT 59.506 50.000 0.00 0.00 0.00 4.18
923 1264 2.897969 TCCCTCTCTTTGCTTACGAGTT 59.102 45.455 0.00 0.00 0.00 3.01
924 1265 4.084287 TCCCTCTCTTTGCTTACGAGTTA 58.916 43.478 0.00 0.00 0.00 2.24
925 1266 4.525487 TCCCTCTCTTTGCTTACGAGTTAA 59.475 41.667 0.00 0.00 0.00 2.01
926 1267 4.865365 CCCTCTCTTTGCTTACGAGTTAAG 59.135 45.833 0.00 0.00 40.40 1.85
927 1268 4.865365 CCTCTCTTTGCTTACGAGTTAAGG 59.135 45.833 0.00 0.00 38.15 2.69
928 1269 5.464030 TCTCTTTGCTTACGAGTTAAGGT 57.536 39.130 0.00 0.00 38.15 3.50
929 1270 5.850614 TCTCTTTGCTTACGAGTTAAGGTT 58.149 37.500 0.00 0.00 38.15 3.50
930 1271 6.285990 TCTCTTTGCTTACGAGTTAAGGTTT 58.714 36.000 0.00 0.00 38.15 3.27
931 1272 6.423001 TCTCTTTGCTTACGAGTTAAGGTTTC 59.577 38.462 0.00 0.00 38.15 2.78
932 1273 6.050432 TCTTTGCTTACGAGTTAAGGTTTCA 58.950 36.000 0.00 0.00 38.15 2.69
933 1274 6.708949 TCTTTGCTTACGAGTTAAGGTTTCAT 59.291 34.615 0.00 0.00 38.15 2.57
934 1275 6.870971 TTGCTTACGAGTTAAGGTTTCATT 57.129 33.333 0.00 0.00 38.15 2.57
935 1276 6.476243 TGCTTACGAGTTAAGGTTTCATTC 57.524 37.500 0.00 0.00 38.15 2.67
936 1277 5.410439 TGCTTACGAGTTAAGGTTTCATTCC 59.590 40.000 0.00 0.00 38.15 3.01
937 1278 5.642491 GCTTACGAGTTAAGGTTTCATTCCT 59.358 40.000 0.00 0.00 38.15 3.36
938 1279 6.148976 GCTTACGAGTTAAGGTTTCATTCCTT 59.851 38.462 0.00 2.81 45.72 3.36
939 1280 7.332678 GCTTACGAGTTAAGGTTTCATTCCTTA 59.667 37.037 0.00 0.00 43.84 2.69
940 1281 9.379791 CTTACGAGTTAAGGTTTCATTCCTTAT 57.620 33.333 5.45 0.00 43.98 1.73
941 1282 7.611213 ACGAGTTAAGGTTTCATTCCTTATG 57.389 36.000 5.45 0.00 43.98 1.90
942 1283 7.391620 ACGAGTTAAGGTTTCATTCCTTATGA 58.608 34.615 5.45 0.00 43.98 2.15
943 1284 7.549488 ACGAGTTAAGGTTTCATTCCTTATGAG 59.451 37.037 5.45 2.16 43.87 2.90
944 1285 7.549488 CGAGTTAAGGTTTCATTCCTTATGAGT 59.451 37.037 5.45 0.00 43.87 3.41
945 1286 9.232473 GAGTTAAGGTTTCATTCCTTATGAGTT 57.768 33.333 5.45 0.00 43.87 3.01
960 1301 7.396540 CTTATGAGTTAAGGTTGGATTGCTT 57.603 36.000 0.00 0.00 34.75 3.91
961 1302 8.506168 CTTATGAGTTAAGGTTGGATTGCTTA 57.494 34.615 0.00 0.00 34.75 3.09
962 1303 9.125026 CTTATGAGTTAAGGTTGGATTGCTTAT 57.875 33.333 0.00 0.00 34.75 1.73
963 1304 6.757897 TGAGTTAAGGTTGGATTGCTTATG 57.242 37.500 0.00 0.00 0.00 1.90
964 1305 6.480763 TGAGTTAAGGTTGGATTGCTTATGA 58.519 36.000 0.00 0.00 0.00 2.15
965 1306 6.599244 TGAGTTAAGGTTGGATTGCTTATGAG 59.401 38.462 0.00 0.00 0.00 2.90
966 1307 6.485171 AGTTAAGGTTGGATTGCTTATGAGT 58.515 36.000 0.00 0.00 0.00 3.41
967 1308 6.375455 AGTTAAGGTTGGATTGCTTATGAGTG 59.625 38.462 0.00 0.00 0.00 3.51
968 1309 4.574674 AGGTTGGATTGCTTATGAGTGA 57.425 40.909 0.00 0.00 0.00 3.41
969 1310 4.922206 AGGTTGGATTGCTTATGAGTGAA 58.078 39.130 0.00 0.00 0.00 3.18
970 1311 4.946157 AGGTTGGATTGCTTATGAGTGAAG 59.054 41.667 0.00 0.00 0.00 3.02
971 1312 4.943705 GGTTGGATTGCTTATGAGTGAAGA 59.056 41.667 0.00 0.00 0.00 2.87
972 1313 5.591877 GGTTGGATTGCTTATGAGTGAAGAT 59.408 40.000 0.00 0.00 0.00 2.40
973 1314 6.096001 GGTTGGATTGCTTATGAGTGAAGATT 59.904 38.462 0.00 0.00 0.00 2.40
974 1315 7.363268 GGTTGGATTGCTTATGAGTGAAGATTT 60.363 37.037 0.00 0.00 0.00 2.17
975 1316 7.325660 TGGATTGCTTATGAGTGAAGATTTC 57.674 36.000 0.00 0.00 0.00 2.17
976 1317 6.885918 TGGATTGCTTATGAGTGAAGATTTCA 59.114 34.615 0.00 0.00 37.33 2.69
996 1337 9.834628 GATTTCACTAAATCCATCGTGTTTAAA 57.165 29.630 0.00 0.00 43.49 1.52
998 1339 9.619316 TTTCACTAAATCCATCGTGTTTAAATG 57.381 29.630 0.00 0.00 0.00 2.32
999 1340 7.247728 TCACTAAATCCATCGTGTTTAAATGC 58.752 34.615 0.00 0.00 0.00 3.56
1000 1341 7.026562 CACTAAATCCATCGTGTTTAAATGCA 58.973 34.615 0.00 0.00 0.00 3.96
1001 1342 7.701924 CACTAAATCCATCGTGTTTAAATGCAT 59.298 33.333 0.00 0.00 0.00 3.96
1002 1343 6.890663 AAATCCATCGTGTTTAAATGCATG 57.109 33.333 0.00 0.00 0.00 4.06
1003 1344 3.768406 TCCATCGTGTTTAAATGCATGC 58.232 40.909 11.82 11.82 0.00 4.06
1004 1345 3.192212 TCCATCGTGTTTAAATGCATGCA 59.808 39.130 25.04 25.04 0.00 3.96
1005 1346 3.548668 CCATCGTGTTTAAATGCATGCAG 59.451 43.478 26.69 8.97 0.00 4.41
1006 1347 3.913548 TCGTGTTTAAATGCATGCAGT 57.086 38.095 26.69 21.79 0.00 4.40
1007 1348 3.820689 TCGTGTTTAAATGCATGCAGTC 58.179 40.909 26.69 11.90 0.00 3.51
1008 1349 2.916716 CGTGTTTAAATGCATGCAGTCC 59.083 45.455 26.69 12.46 0.00 3.85
1009 1350 3.611293 CGTGTTTAAATGCATGCAGTCCA 60.611 43.478 26.69 14.80 0.00 4.02
1010 1351 4.497300 GTGTTTAAATGCATGCAGTCCAT 58.503 39.130 26.69 11.30 33.39 3.41
1011 1352 4.931002 GTGTTTAAATGCATGCAGTCCATT 59.069 37.500 26.69 12.15 29.71 3.16
1012 1353 4.930405 TGTTTAAATGCATGCAGTCCATTG 59.070 37.500 26.69 0.00 29.71 2.82
1013 1354 4.804868 TTAAATGCATGCAGTCCATTGT 57.195 36.364 26.69 9.75 29.71 2.71
1014 1355 2.665649 AATGCATGCAGTCCATTGTG 57.334 45.000 26.69 0.00 29.71 3.33
1015 1356 0.821517 ATGCATGCAGTCCATTGTGG 59.178 50.000 26.69 0.00 39.43 4.17
1016 1357 1.153706 GCATGCAGTCCATTGTGGC 60.154 57.895 14.21 0.00 37.47 5.01
1017 1358 1.879737 GCATGCAGTCCATTGTGGCA 61.880 55.000 14.21 0.00 37.47 4.92
1018 1359 0.604073 CATGCAGTCCATTGTGGCAA 59.396 50.000 0.00 0.00 37.47 4.52
1019 1360 1.206132 CATGCAGTCCATTGTGGCAAT 59.794 47.619 0.00 0.00 37.47 3.56
1020 1361 0.889994 TGCAGTCCATTGTGGCAATC 59.110 50.000 0.00 0.00 37.47 2.67
1021 1362 0.174162 GCAGTCCATTGTGGCAATCC 59.826 55.000 0.00 0.00 37.47 3.01
1022 1363 1.548081 CAGTCCATTGTGGCAATCCA 58.452 50.000 0.00 0.00 37.47 3.41
1023 1364 1.475280 CAGTCCATTGTGGCAATCCAG 59.525 52.381 0.00 0.00 44.48 3.86
1024 1365 1.076024 AGTCCATTGTGGCAATCCAGT 59.924 47.619 0.00 0.00 44.48 4.00
1025 1366 1.474077 GTCCATTGTGGCAATCCAGTC 59.526 52.381 0.00 0.00 44.48 3.51
1026 1367 0.819582 CCATTGTGGCAATCCAGTCC 59.180 55.000 0.00 0.00 44.48 3.85
1027 1368 1.548081 CATTGTGGCAATCCAGTCCA 58.452 50.000 0.00 0.00 44.48 4.02
1028 1369 1.894466 CATTGTGGCAATCCAGTCCAA 59.106 47.619 0.00 0.00 44.48 3.53
1029 1370 2.079170 TTGTGGCAATCCAGTCCAAA 57.921 45.000 0.00 0.00 44.48 3.28
1030 1371 2.079170 TGTGGCAATCCAGTCCAAAA 57.921 45.000 0.00 0.00 44.48 2.44
1031 1372 1.962807 TGTGGCAATCCAGTCCAAAAG 59.037 47.619 0.00 0.00 44.48 2.27
1032 1373 2.238521 GTGGCAATCCAGTCCAAAAGA 58.761 47.619 0.00 0.00 44.48 2.52
1033 1374 2.827921 GTGGCAATCCAGTCCAAAAGAT 59.172 45.455 0.00 0.00 44.48 2.40
1034 1375 3.091545 TGGCAATCCAGTCCAAAAGATC 58.908 45.455 0.00 0.00 37.47 2.75
1035 1376 2.428530 GGCAATCCAGTCCAAAAGATCC 59.571 50.000 0.00 0.00 0.00 3.36
1036 1377 3.091545 GCAATCCAGTCCAAAAGATCCA 58.908 45.455 0.00 0.00 0.00 3.41
1037 1378 3.511146 GCAATCCAGTCCAAAAGATCCAA 59.489 43.478 0.00 0.00 0.00 3.53
1038 1379 4.619160 GCAATCCAGTCCAAAAGATCCAAC 60.619 45.833 0.00 0.00 0.00 3.77
1039 1380 4.664688 ATCCAGTCCAAAAGATCCAACT 57.335 40.909 0.00 0.00 0.00 3.16
1040 1381 5.779241 ATCCAGTCCAAAAGATCCAACTA 57.221 39.130 0.00 0.00 0.00 2.24
1041 1382 4.906618 TCCAGTCCAAAAGATCCAACTAC 58.093 43.478 0.00 0.00 0.00 2.73
1042 1383 4.597507 TCCAGTCCAAAAGATCCAACTACT 59.402 41.667 0.00 0.00 0.00 2.57
1043 1384 4.938226 CCAGTCCAAAAGATCCAACTACTC 59.062 45.833 0.00 0.00 0.00 2.59
1044 1385 4.627467 CAGTCCAAAAGATCCAACTACTCG 59.373 45.833 0.00 0.00 0.00 4.18
1045 1386 4.283722 AGTCCAAAAGATCCAACTACTCGT 59.716 41.667 0.00 0.00 0.00 4.18
1046 1387 4.995487 GTCCAAAAGATCCAACTACTCGTT 59.005 41.667 0.00 0.00 35.88 3.85
1047 1388 5.469084 GTCCAAAAGATCCAACTACTCGTTT 59.531 40.000 0.00 0.00 32.27 3.60
1048 1389 5.468746 TCCAAAAGATCCAACTACTCGTTTG 59.531 40.000 0.00 0.00 37.79 2.93
1049 1390 5.334879 CCAAAAGATCCAACTACTCGTTTGG 60.335 44.000 12.46 12.46 45.34 3.28
1050 1391 4.618920 AAGATCCAACTACTCGTTTGGT 57.381 40.909 0.50 0.00 32.27 3.67
1051 1392 5.733620 AAGATCCAACTACTCGTTTGGTA 57.266 39.130 0.50 0.00 32.27 3.25
1052 1393 5.934402 AGATCCAACTACTCGTTTGGTAT 57.066 39.130 0.50 0.00 32.27 2.73
1053 1394 5.903810 AGATCCAACTACTCGTTTGGTATC 58.096 41.667 0.50 3.47 32.27 2.24
1054 1395 4.460948 TCCAACTACTCGTTTGGTATCC 57.539 45.455 0.50 0.00 32.27 2.59
1055 1396 3.196254 TCCAACTACTCGTTTGGTATCCC 59.804 47.826 0.50 0.00 32.27 3.85
1056 1397 3.528532 CAACTACTCGTTTGGTATCCCC 58.471 50.000 0.00 0.00 32.27 4.81
1057 1398 2.113807 ACTACTCGTTTGGTATCCCCC 58.886 52.381 0.00 0.00 0.00 5.40
1058 1399 2.112998 CTACTCGTTTGGTATCCCCCA 58.887 52.381 0.00 0.00 0.00 4.96
1059 1400 1.591768 ACTCGTTTGGTATCCCCCAT 58.408 50.000 0.00 0.00 33.60 4.00
1060 1401 1.489230 ACTCGTTTGGTATCCCCCATC 59.511 52.381 0.00 0.00 33.60 3.51
1061 1402 0.466543 TCGTTTGGTATCCCCCATCG 59.533 55.000 0.00 0.00 33.60 3.84
1062 1403 1.164041 CGTTTGGTATCCCCCATCGC 61.164 60.000 0.00 0.00 33.60 4.58
1063 1404 0.822121 GTTTGGTATCCCCCATCGCC 60.822 60.000 0.00 0.00 33.60 5.54
1064 1405 1.282653 TTTGGTATCCCCCATCGCCA 61.283 55.000 0.00 0.00 33.60 5.69
1065 1406 1.282653 TTGGTATCCCCCATCGCCAA 61.283 55.000 0.00 0.00 33.60 4.52
1066 1407 1.282653 TGGTATCCCCCATCGCCAAA 61.283 55.000 0.00 0.00 0.00 3.28
1067 1408 0.106419 GGTATCCCCCATCGCCAAAA 60.106 55.000 0.00 0.00 0.00 2.44
1068 1409 1.686741 GGTATCCCCCATCGCCAAAAA 60.687 52.381 0.00 0.00 0.00 1.94
1098 1439 4.219392 ACTATCCATCTCCATTCCCTCA 57.781 45.455 0.00 0.00 0.00 3.86
1221 1568 1.371183 CACCAACCTCGCCTTCTCA 59.629 57.895 0.00 0.00 0.00 3.27
1419 1767 4.131088 GTCTGGGTCGACGCCTCC 62.131 72.222 27.39 15.04 0.00 4.30
1444 1792 0.174845 CCTCAATCCTACGTTCGCCA 59.825 55.000 0.00 0.00 0.00 5.69
1476 1824 3.484547 GTTTACCAGGCCGACGCG 61.485 66.667 3.53 3.53 35.02 6.01
1499 1847 0.249868 TCGGTGGACTTCAGCAACAG 60.250 55.000 0.00 0.00 43.59 3.16
1504 1852 1.973812 GACTTCAGCAACAGGCCCC 60.974 63.158 0.00 0.00 46.50 5.80
1524 1874 4.208686 GAGGCGACGGCGGAGATT 62.209 66.667 15.06 0.00 41.24 2.40
1558 1908 3.959975 GCAAAACACGCGGCCTCA 61.960 61.111 12.47 0.00 0.00 3.86
1559 1909 2.051345 CAAAACACGCGGCCTCAC 60.051 61.111 12.47 0.00 0.00 3.51
1570 1920 1.026718 CGGCCTCACCAAGAACATCC 61.027 60.000 0.00 0.00 39.03 3.51
1575 1925 2.568956 CCTCACCAAGAACATCCTCTCA 59.431 50.000 0.00 0.00 0.00 3.27
1580 1930 2.235650 CCAAGAACATCCTCTCAGAGCA 59.764 50.000 0.00 0.00 0.00 4.26
1609 1959 3.470567 GCTCCACGTCGCTTGTCG 61.471 66.667 0.00 0.00 40.15 4.35
1645 1995 4.680237 TCAGCGGCCACTGGAACG 62.680 66.667 20.47 3.71 38.26 3.95
1788 2141 4.039092 AAGGTCCTGCGCATGCCT 62.039 61.111 12.24 16.05 41.78 4.75
1791 2144 1.526917 GGTCCTGCGCATGCCTTAT 60.527 57.895 12.24 0.00 41.78 1.73
1797 2150 2.180204 GCGCATGCCTTATCGTGGT 61.180 57.895 13.15 0.00 33.98 4.16
1849 2202 1.285667 TGTACATCTACCTCCCCGACA 59.714 52.381 0.00 0.00 0.00 4.35
1853 2206 0.338814 ATCTACCTCCCCGACAACCT 59.661 55.000 0.00 0.00 0.00 3.50
1854 2207 0.613853 TCTACCTCCCCGACAACCTG 60.614 60.000 0.00 0.00 0.00 4.00
1975 2328 0.902531 GATCCCCAAGTTCGAGGTGA 59.097 55.000 0.00 0.00 0.00 4.02
1995 2348 3.775654 CTGAGGGTGGAGGCGTCC 61.776 72.222 18.69 18.69 44.24 4.79
2010 2363 0.530650 CGTCCCAGATGCTGCGTAAT 60.531 55.000 0.00 0.00 0.00 1.89
2118 2472 1.079681 GGTCCACCATTGCGTCGTA 60.080 57.895 0.00 0.00 35.64 3.43
2124 2478 2.570169 CACCATTGCGTCGTAAAAGTG 58.430 47.619 12.12 12.12 0.00 3.16
2127 2481 2.412325 CCATTGCGTCGTAAAAGTGGAC 60.412 50.000 8.07 0.00 0.00 4.02
2208 2562 0.321653 GTGATCGCCCTGTGGACTTT 60.322 55.000 0.00 0.00 0.00 2.66
2220 2574 2.224843 TGTGGACTTTGTGGCAGATCAT 60.225 45.455 0.00 0.00 0.00 2.45
2263 2621 3.583276 GATGTCGGTGGCGTGGTGA 62.583 63.158 0.00 0.00 0.00 4.02
2325 2685 1.759445 GGATTACCAGCTCTGCTCTGA 59.241 52.381 0.00 0.00 36.40 3.27
2362 2753 5.676532 TTTGTATCCTTGTTGGTGTAACG 57.323 39.130 0.00 0.00 42.34 3.18
2369 2760 0.250381 TGTTGGTGTAACGGCGGAAT 60.250 50.000 13.24 0.00 42.34 3.01
2372 2763 0.035036 TGGTGTAACGGCGGAATCAA 59.965 50.000 13.24 0.00 38.12 2.57
2373 2764 1.339247 TGGTGTAACGGCGGAATCAAT 60.339 47.619 13.24 0.00 38.12 2.57
2374 2765 1.741145 GGTGTAACGGCGGAATCAATT 59.259 47.619 13.24 0.00 38.12 2.32
2381 2772 3.016736 ACGGCGGAATCAATTTGATCTT 58.983 40.909 13.24 0.00 35.76 2.40
2422 2813 4.037927 TGGGAAGGGATTACTAGTTCAGG 58.962 47.826 0.00 0.00 0.00 3.86
2433 2830 2.280628 CTAGTTCAGGAATCCCGTTGC 58.719 52.381 0.00 0.00 37.58 4.17
2440 2837 1.503542 GAATCCCGTTGCTGCACAG 59.496 57.895 0.00 0.00 0.00 3.66
2441 2838 0.955428 GAATCCCGTTGCTGCACAGA 60.955 55.000 0.00 0.00 0.00 3.41
2459 2856 0.387565 GACCGGCTCTCCATCTCTTC 59.612 60.000 0.00 0.00 0.00 2.87
2462 2859 1.047002 CGGCTCTCCATCTCTTCCAT 58.953 55.000 0.00 0.00 0.00 3.41
2466 2863 3.072768 GGCTCTCCATCTCTTCCATTCAT 59.927 47.826 0.00 0.00 0.00 2.57
2469 2866 6.155910 GGCTCTCCATCTCTTCCATTCATATA 59.844 42.308 0.00 0.00 0.00 0.86
2477 2874 9.610705 CATCTCTTCCATTCATATATAACCAGG 57.389 37.037 0.00 0.00 0.00 4.45
2478 2875 8.972662 TCTCTTCCATTCATATATAACCAGGA 57.027 34.615 0.00 0.00 0.00 3.86
2504 2901 9.847224 AAATAATCTACATACACTACCCCAAAG 57.153 33.333 0.00 0.00 0.00 2.77
2779 3207 2.754254 TAGGAGCGAGCAAGGCGA 60.754 61.111 0.00 0.00 35.00 5.54
3173 4015 4.891727 CGCCTTCATCCCCGACGG 62.892 72.222 6.99 6.99 0.00 4.79
3286 4153 1.299468 CCCATCGACGTCTAGCAGC 60.299 63.158 14.70 0.00 0.00 5.25
3311 4178 2.741092 GTCGTCCAGCCACTCCAA 59.259 61.111 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 6.461092 GGGACCTCACTTTTTAGTCTTTTTGG 60.461 42.308 0.00 0.00 0.00 3.28
342 345 4.418359 GGGATTGGGGGTAGTTTTGTTTA 58.582 43.478 0.00 0.00 0.00 2.01
466 473 3.739830 CGAATCAGAGGACGAGAGAGAGA 60.740 52.174 0.00 0.00 0.00 3.10
484 491 3.476552 TGCAAGGTTCTCTTCAACGAAT 58.523 40.909 0.00 0.00 32.41 3.34
573 891 1.008206 AGGGAGTCAGAGCTCATTCCT 59.992 52.381 17.77 9.27 37.24 3.36
707 1036 3.223589 GCGTTTTGTGGGCTGGGT 61.224 61.111 0.00 0.00 0.00 4.51
765 1094 2.036098 TCTAAGGCGTGGACCGGA 59.964 61.111 9.46 0.00 36.94 5.14
895 1236 3.602205 AGCAAAGAGAGGGAGGTTTTT 57.398 42.857 0.00 0.00 0.00 1.94
896 1237 3.602205 AAGCAAAGAGAGGGAGGTTTT 57.398 42.857 0.00 0.00 0.00 2.43
897 1238 3.557264 CGTAAGCAAAGAGAGGGAGGTTT 60.557 47.826 0.00 0.00 0.00 3.27
898 1239 2.028020 CGTAAGCAAAGAGAGGGAGGTT 60.028 50.000 0.00 0.00 0.00 3.50
899 1240 1.550976 CGTAAGCAAAGAGAGGGAGGT 59.449 52.381 0.00 0.00 0.00 3.85
900 1241 1.825474 TCGTAAGCAAAGAGAGGGAGG 59.175 52.381 0.00 0.00 37.18 4.30
901 1242 2.494073 ACTCGTAAGCAAAGAGAGGGAG 59.506 50.000 8.59 0.00 37.18 4.30
902 1243 2.526432 ACTCGTAAGCAAAGAGAGGGA 58.474 47.619 8.59 0.00 37.18 4.20
903 1244 3.320673 AACTCGTAAGCAAAGAGAGGG 57.679 47.619 8.59 0.00 37.18 4.30
904 1245 4.865365 CCTTAACTCGTAAGCAAAGAGAGG 59.135 45.833 8.59 2.72 38.34 3.69
905 1246 5.471257 ACCTTAACTCGTAAGCAAAGAGAG 58.529 41.667 8.59 2.64 38.34 3.20
906 1247 5.464030 ACCTTAACTCGTAAGCAAAGAGA 57.536 39.130 8.59 0.00 38.34 3.10
907 1248 6.202188 TGAAACCTTAACTCGTAAGCAAAGAG 59.798 38.462 1.45 1.45 38.34 2.85
908 1249 6.050432 TGAAACCTTAACTCGTAAGCAAAGA 58.950 36.000 0.00 0.00 38.34 2.52
909 1250 6.295039 TGAAACCTTAACTCGTAAGCAAAG 57.705 37.500 0.00 0.00 38.34 2.77
910 1251 6.870971 ATGAAACCTTAACTCGTAAGCAAA 57.129 33.333 0.00 0.00 38.34 3.68
911 1252 6.072893 GGAATGAAACCTTAACTCGTAAGCAA 60.073 38.462 0.00 0.00 38.34 3.91
912 1253 5.410439 GGAATGAAACCTTAACTCGTAAGCA 59.590 40.000 0.00 0.00 38.34 3.91
913 1254 5.642491 AGGAATGAAACCTTAACTCGTAAGC 59.358 40.000 0.00 0.00 38.34 3.09
914 1255 7.668525 AAGGAATGAAACCTTAACTCGTAAG 57.331 36.000 0.00 0.00 44.62 2.34
936 1277 7.396540 AAGCAATCCAACCTTAACTCATAAG 57.603 36.000 0.00 0.00 40.67 1.73
937 1278 8.902806 CATAAGCAATCCAACCTTAACTCATAA 58.097 33.333 0.00 0.00 0.00 1.90
938 1279 8.271458 TCATAAGCAATCCAACCTTAACTCATA 58.729 33.333 0.00 0.00 0.00 2.15
939 1280 7.118723 TCATAAGCAATCCAACCTTAACTCAT 58.881 34.615 0.00 0.00 0.00 2.90
940 1281 6.480763 TCATAAGCAATCCAACCTTAACTCA 58.519 36.000 0.00 0.00 0.00 3.41
941 1282 6.599638 ACTCATAAGCAATCCAACCTTAACTC 59.400 38.462 0.00 0.00 0.00 3.01
942 1283 6.375455 CACTCATAAGCAATCCAACCTTAACT 59.625 38.462 0.00 0.00 0.00 2.24
943 1284 6.374333 TCACTCATAAGCAATCCAACCTTAAC 59.626 38.462 0.00 0.00 0.00 2.01
944 1285 6.480763 TCACTCATAAGCAATCCAACCTTAA 58.519 36.000 0.00 0.00 0.00 1.85
945 1286 6.061022 TCACTCATAAGCAATCCAACCTTA 57.939 37.500 0.00 0.00 0.00 2.69
946 1287 4.922206 TCACTCATAAGCAATCCAACCTT 58.078 39.130 0.00 0.00 0.00 3.50
947 1288 4.574674 TCACTCATAAGCAATCCAACCT 57.425 40.909 0.00 0.00 0.00 3.50
948 1289 4.943705 TCTTCACTCATAAGCAATCCAACC 59.056 41.667 0.00 0.00 0.00 3.77
949 1290 6.690194 ATCTTCACTCATAAGCAATCCAAC 57.310 37.500 0.00 0.00 0.00 3.77
950 1291 7.394077 TGAAATCTTCACTCATAAGCAATCCAA 59.606 33.333 0.00 0.00 34.08 3.53
951 1292 6.885918 TGAAATCTTCACTCATAAGCAATCCA 59.114 34.615 0.00 0.00 34.08 3.41
952 1293 7.325660 TGAAATCTTCACTCATAAGCAATCC 57.674 36.000 0.00 0.00 34.08 3.01
966 1307 6.878923 ACACGATGGATTTAGTGAAATCTTCA 59.121 34.615 9.58 2.36 46.93 3.02
967 1308 7.308782 ACACGATGGATTTAGTGAAATCTTC 57.691 36.000 9.58 6.94 46.93 2.87
968 1309 7.687941 AACACGATGGATTTAGTGAAATCTT 57.312 32.000 9.58 0.12 46.93 2.40
969 1310 7.687941 AAACACGATGGATTTAGTGAAATCT 57.312 32.000 9.58 0.00 46.93 2.40
972 1313 9.619316 CATTTAAACACGATGGATTTAGTGAAA 57.381 29.630 1.24 0.00 37.95 2.69
973 1314 7.753132 GCATTTAAACACGATGGATTTAGTGAA 59.247 33.333 1.24 0.00 37.95 3.18
974 1315 7.094592 TGCATTTAAACACGATGGATTTAGTGA 60.095 33.333 1.24 0.00 37.95 3.41
975 1316 7.026562 TGCATTTAAACACGATGGATTTAGTG 58.973 34.615 0.00 0.00 40.17 2.74
976 1317 7.151999 TGCATTTAAACACGATGGATTTAGT 57.848 32.000 0.00 0.00 0.00 2.24
977 1318 7.306167 GCATGCATTTAAACACGATGGATTTAG 60.306 37.037 14.21 0.00 30.76 1.85
978 1319 6.475076 GCATGCATTTAAACACGATGGATTTA 59.525 34.615 14.21 0.00 30.76 1.40
979 1320 5.291614 GCATGCATTTAAACACGATGGATTT 59.708 36.000 14.21 0.00 30.76 2.17
980 1321 4.805192 GCATGCATTTAAACACGATGGATT 59.195 37.500 14.21 0.00 30.76 3.01
981 1322 4.142204 TGCATGCATTTAAACACGATGGAT 60.142 37.500 18.46 0.00 32.96 3.41
982 1323 3.192212 TGCATGCATTTAAACACGATGGA 59.808 39.130 18.46 0.00 0.00 3.41
983 1324 3.509740 TGCATGCATTTAAACACGATGG 58.490 40.909 18.46 0.00 0.00 3.51
984 1325 4.168014 ACTGCATGCATTTAAACACGATG 58.832 39.130 22.97 7.02 0.00 3.84
985 1326 4.414852 GACTGCATGCATTTAAACACGAT 58.585 39.130 22.97 0.00 0.00 3.73
986 1327 3.365868 GGACTGCATGCATTTAAACACGA 60.366 43.478 22.97 0.00 0.00 4.35
987 1328 2.916716 GGACTGCATGCATTTAAACACG 59.083 45.455 22.97 8.59 0.00 4.49
988 1329 3.911868 TGGACTGCATGCATTTAAACAC 58.088 40.909 22.97 2.08 0.00 3.32
989 1330 4.804868 ATGGACTGCATGCATTTAAACA 57.195 36.364 22.97 14.44 35.46 2.83
990 1331 4.931002 ACAATGGACTGCATGCATTTAAAC 59.069 37.500 22.97 9.19 46.37 2.01
991 1332 4.930405 CACAATGGACTGCATGCATTTAAA 59.070 37.500 22.97 6.76 46.37 1.52
992 1333 4.496360 CACAATGGACTGCATGCATTTAA 58.504 39.130 22.97 8.41 46.37 1.52
993 1334 3.119065 CCACAATGGACTGCATGCATTTA 60.119 43.478 22.97 9.50 46.37 1.40
994 1335 2.354303 CCACAATGGACTGCATGCATTT 60.354 45.455 22.97 11.57 46.37 2.32
996 1337 0.821517 CCACAATGGACTGCATGCAT 59.178 50.000 22.97 11.62 40.96 3.96
997 1338 1.879737 GCCACAATGGACTGCATGCA 61.880 55.000 21.29 21.29 40.96 3.96
998 1339 1.153706 GCCACAATGGACTGCATGC 60.154 57.895 11.82 11.82 40.96 4.06
999 1340 0.604073 TTGCCACAATGGACTGCATG 59.396 50.000 0.00 0.00 40.96 4.06
1000 1341 1.479323 GATTGCCACAATGGACTGCAT 59.521 47.619 0.00 0.00 40.96 3.96
1001 1342 0.889994 GATTGCCACAATGGACTGCA 59.110 50.000 0.00 0.00 40.96 4.41
1002 1343 0.174162 GGATTGCCACAATGGACTGC 59.826 55.000 0.00 0.00 40.96 4.40
1003 1344 1.475280 CTGGATTGCCACAATGGACTG 59.525 52.381 0.00 0.00 40.96 3.51
1004 1345 1.076024 ACTGGATTGCCACAATGGACT 59.924 47.619 0.00 0.00 40.96 3.85
1005 1346 1.474077 GACTGGATTGCCACAATGGAC 59.526 52.381 0.00 0.00 40.96 4.02
1006 1347 1.616725 GGACTGGATTGCCACAATGGA 60.617 52.381 0.00 0.00 40.96 3.41
1007 1348 0.819582 GGACTGGATTGCCACAATGG 59.180 55.000 0.00 0.00 39.92 3.16
1008 1349 1.548081 TGGACTGGATTGCCACAATG 58.452 50.000 0.00 0.00 39.92 2.82
1009 1350 2.307496 TTGGACTGGATTGCCACAAT 57.693 45.000 0.00 0.00 39.92 2.71
1010 1351 2.079170 TTTGGACTGGATTGCCACAA 57.921 45.000 0.00 0.00 39.92 3.33
1011 1352 1.962807 CTTTTGGACTGGATTGCCACA 59.037 47.619 0.00 0.00 39.92 4.17
1012 1353 2.238521 TCTTTTGGACTGGATTGCCAC 58.761 47.619 0.00 0.00 39.92 5.01
1013 1354 2.673775 TCTTTTGGACTGGATTGCCA 57.326 45.000 0.00 0.00 43.47 4.92
1014 1355 2.428530 GGATCTTTTGGACTGGATTGCC 59.571 50.000 0.00 0.00 0.00 4.52
1015 1356 3.091545 TGGATCTTTTGGACTGGATTGC 58.908 45.455 0.00 0.00 0.00 3.56
1016 1357 4.768968 AGTTGGATCTTTTGGACTGGATTG 59.231 41.667 0.00 0.00 0.00 2.67
1017 1358 5.003096 AGTTGGATCTTTTGGACTGGATT 57.997 39.130 0.00 0.00 0.00 3.01
1018 1359 4.664688 AGTTGGATCTTTTGGACTGGAT 57.335 40.909 0.00 0.00 0.00 3.41
1019 1360 4.597507 AGTAGTTGGATCTTTTGGACTGGA 59.402 41.667 0.00 0.00 0.00 3.86
1020 1361 4.911390 AGTAGTTGGATCTTTTGGACTGG 58.089 43.478 0.00 0.00 0.00 4.00
1021 1362 4.627467 CGAGTAGTTGGATCTTTTGGACTG 59.373 45.833 0.00 0.00 0.00 3.51
1022 1363 4.283722 ACGAGTAGTTGGATCTTTTGGACT 59.716 41.667 0.00 0.00 0.00 3.85
1023 1364 4.566987 ACGAGTAGTTGGATCTTTTGGAC 58.433 43.478 0.00 0.00 0.00 4.02
1024 1365 4.884668 ACGAGTAGTTGGATCTTTTGGA 57.115 40.909 0.00 0.00 0.00 3.53
1025 1366 5.334879 CCAAACGAGTAGTTGGATCTTTTGG 60.335 44.000 7.68 7.68 43.37 3.28
1026 1367 5.238650 ACCAAACGAGTAGTTGGATCTTTTG 59.761 40.000 12.20 0.00 43.37 2.44
1027 1368 5.374071 ACCAAACGAGTAGTTGGATCTTTT 58.626 37.500 12.20 0.00 43.37 2.27
1028 1369 4.969484 ACCAAACGAGTAGTTGGATCTTT 58.031 39.130 12.20 0.00 43.37 2.52
1029 1370 4.618920 ACCAAACGAGTAGTTGGATCTT 57.381 40.909 12.20 0.00 43.37 2.40
1030 1371 5.163437 GGATACCAAACGAGTAGTTGGATCT 60.163 44.000 12.20 0.00 43.37 2.75
1031 1372 5.048507 GGATACCAAACGAGTAGTTGGATC 58.951 45.833 12.20 10.15 43.37 3.36
1032 1373 5.019785 GGATACCAAACGAGTAGTTGGAT 57.980 43.478 12.20 3.68 43.37 3.41
1033 1374 4.460948 GGATACCAAACGAGTAGTTGGA 57.539 45.455 12.20 0.00 43.37 3.53
1049 1390 1.770294 TTTTTGGCGATGGGGGATAC 58.230 50.000 0.00 0.00 0.00 2.24
1065 1406 8.375493 TGGAGATGGATAGTACAGTAGTTTTT 57.625 34.615 0.00 0.00 0.00 1.94
1066 1407 7.973048 TGGAGATGGATAGTACAGTAGTTTT 57.027 36.000 0.00 0.00 0.00 2.43
1067 1408 8.554490 AATGGAGATGGATAGTACAGTAGTTT 57.446 34.615 0.00 0.00 0.00 2.66
1068 1409 7.233757 GGAATGGAGATGGATAGTACAGTAGTT 59.766 40.741 0.00 0.00 0.00 2.24
1069 1410 6.722129 GGAATGGAGATGGATAGTACAGTAGT 59.278 42.308 0.00 0.00 0.00 2.73
1070 1411 6.153680 GGGAATGGAGATGGATAGTACAGTAG 59.846 46.154 0.00 0.00 0.00 2.57
1071 1412 6.017192 GGGAATGGAGATGGATAGTACAGTA 58.983 44.000 0.00 0.00 0.00 2.74
1072 1413 4.841246 GGGAATGGAGATGGATAGTACAGT 59.159 45.833 0.00 0.00 0.00 3.55
1073 1414 5.090139 AGGGAATGGAGATGGATAGTACAG 58.910 45.833 0.00 0.00 0.00 2.74
1074 1415 5.087323 GAGGGAATGGAGATGGATAGTACA 58.913 45.833 0.00 0.00 0.00 2.90
1075 1416 5.087323 TGAGGGAATGGAGATGGATAGTAC 58.913 45.833 0.00 0.00 0.00 2.73
1076 1417 5.336945 CTGAGGGAATGGAGATGGATAGTA 58.663 45.833 0.00 0.00 0.00 1.82
1077 1418 4.166539 CTGAGGGAATGGAGATGGATAGT 58.833 47.826 0.00 0.00 0.00 2.12
1078 1419 3.055240 GCTGAGGGAATGGAGATGGATAG 60.055 52.174 0.00 0.00 0.00 2.08
1098 1439 3.399046 TGGCCTACCATTGACGCT 58.601 55.556 3.32 0.00 42.67 5.07
1221 1568 1.949847 CTGCGTGGAAGGAGATCGGT 61.950 60.000 0.00 0.00 0.00 4.69
1338 1685 1.271871 ACGAAGGATGCAACCATGGAA 60.272 47.619 21.47 0.73 0.00 3.53
1374 1721 4.278513 CCGTGGGACTGGGCCAAA 62.279 66.667 8.04 0.00 0.00 3.28
1419 1767 1.030457 ACGTAGGATTGAGGCGTAGG 58.970 55.000 0.00 0.00 33.85 3.18
1476 1824 2.167861 GCTGAAGTCCACCGATCGC 61.168 63.158 10.32 0.00 0.00 4.58
1524 1874 3.953712 TTGCTCTCGAACCACTCATTA 57.046 42.857 0.00 0.00 0.00 1.90
1558 1908 2.235898 GCTCTGAGAGGATGTTCTTGGT 59.764 50.000 12.01 0.00 0.00 3.67
1559 1909 2.235650 TGCTCTGAGAGGATGTTCTTGG 59.764 50.000 12.01 0.00 0.00 3.61
1580 1930 4.063967 TGGAGCCGTCGCAATCGT 62.064 61.111 0.00 0.00 37.52 3.73
1605 1955 3.547249 GACCGAGTTGCCGACGACA 62.547 63.158 0.00 0.00 31.96 4.35
1609 1959 0.319641 AAGAAGACCGAGTTGCCGAC 60.320 55.000 0.00 0.00 0.00 4.79
1645 1995 3.798511 CTCCGGGAAGAAGGGGGC 61.799 72.222 0.00 0.00 0.00 5.80
1716 2069 1.303236 CCCCTTCATGAACGGCACA 60.303 57.895 15.78 0.00 0.00 4.57
1948 2301 1.283321 GAACTTGGGGATCCTGAGCTT 59.717 52.381 12.58 0.00 0.00 3.74
1955 2308 0.107654 CACCTCGAACTTGGGGATCC 60.108 60.000 1.92 1.92 0.00 3.36
1997 2350 0.107456 CCCCAGATTACGCAGCATCT 59.893 55.000 0.00 0.00 31.76 2.90
2091 2445 2.920912 TGGTGGACCACGGAGGAC 60.921 66.667 18.40 4.03 42.01 3.85
2109 2463 0.854062 CGTCCACTTTTACGACGCAA 59.146 50.000 0.00 0.00 42.37 4.85
2118 2472 0.473117 TCCCCCTCTCGTCCACTTTT 60.473 55.000 0.00 0.00 0.00 2.27
2124 2478 4.755507 ACGGTCCCCCTCTCGTCC 62.756 72.222 0.00 0.00 0.00 4.79
2208 2562 0.178767 CGAAGGGATGATCTGCCACA 59.821 55.000 6.73 0.00 37.96 4.17
2220 2574 0.544357 TGAGGAAGAAGGCGAAGGGA 60.544 55.000 0.00 0.00 0.00 4.20
2250 2604 1.487452 CGAATATCACCACGCCACCG 61.487 60.000 0.00 0.00 41.14 4.94
2251 2605 1.772063 GCGAATATCACCACGCCACC 61.772 60.000 0.00 0.00 44.27 4.61
2263 2621 2.224597 TGATGACATGGCCTGCGAATAT 60.225 45.455 3.32 0.00 0.00 1.28
2355 2743 3.120130 TCAAATTGATTCCGCCGTTACAC 60.120 43.478 0.00 0.00 0.00 2.90
2362 2753 4.637483 TCAAGATCAAATTGATTCCGCC 57.363 40.909 10.09 0.00 37.20 6.13
2374 2765 9.778741 ACTGTTAAGAGTACAAATCAAGATCAA 57.221 29.630 2.91 0.00 0.00 2.57
2381 2772 6.428083 TCCCACTGTTAAGAGTACAAATCA 57.572 37.500 4.74 0.00 0.00 2.57
2385 2776 4.041198 CCCTTCCCACTGTTAAGAGTACAA 59.959 45.833 4.74 0.00 0.00 2.41
2387 2778 3.836562 TCCCTTCCCACTGTTAAGAGTAC 59.163 47.826 4.74 0.00 0.00 2.73
2388 2779 4.136341 TCCCTTCCCACTGTTAAGAGTA 57.864 45.455 4.74 0.00 0.00 2.59
2389 2780 2.986050 TCCCTTCCCACTGTTAAGAGT 58.014 47.619 0.00 0.00 0.00 3.24
2390 2781 4.576330 AATCCCTTCCCACTGTTAAGAG 57.424 45.455 0.00 0.00 0.00 2.85
2392 2783 5.437191 AGTAATCCCTTCCCACTGTTAAG 57.563 43.478 0.00 0.00 0.00 1.85
2393 2784 6.027482 ACTAGTAATCCCTTCCCACTGTTAA 58.973 40.000 0.00 0.00 0.00 2.01
2397 2788 4.469945 TGAACTAGTAATCCCTTCCCACTG 59.530 45.833 0.00 0.00 0.00 3.66
2422 2813 0.955428 TCTGTGCAGCAACGGGATTC 60.955 55.000 0.00 0.00 0.00 2.52
2428 2825 3.716006 CCGGTCTGTGCAGCAACG 61.716 66.667 0.00 0.00 0.00 4.10
2433 2830 2.125753 GAGAGCCGGTCTGTGCAG 60.126 66.667 4.45 0.00 34.71 4.41
2440 2837 0.387565 GAAGAGATGGAGAGCCGGTC 59.612 60.000 1.90 0.00 36.79 4.79
2441 2838 1.045911 GGAAGAGATGGAGAGCCGGT 61.046 60.000 1.90 0.00 36.79 5.28
2477 2874 9.841295 TTTGGGGTAGTGTATGTAGATTATTTC 57.159 33.333 0.00 0.00 0.00 2.17
2478 2875 9.847224 CTTTGGGGTAGTGTATGTAGATTATTT 57.153 33.333 0.00 0.00 0.00 1.40
2481 2878 8.063153 TCTCTTTGGGGTAGTGTATGTAGATTA 58.937 37.037 0.00 0.00 0.00 1.75
2487 2884 4.426704 AGTCTCTTTGGGGTAGTGTATGT 58.573 43.478 0.00 0.00 0.00 2.29
2490 2887 5.899631 AAAAGTCTCTTTGGGGTAGTGTA 57.100 39.130 0.00 0.00 0.00 2.90
2504 2901 3.938778 AAACCGTCACGAAAAAGTCTC 57.061 42.857 0.00 0.00 0.00 3.36
2956 3775 1.932156 CGACCATGGGGGATTGGGAA 61.932 60.000 18.09 0.00 41.15 3.97
3264 4131 3.825833 CTAGACGTCGATGGGGCGC 62.826 68.421 10.46 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.