Multiple sequence alignment - TraesCS6D01G137500

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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 TraesCS6D01G137500 chr6D 100.000 2120 0 0 1 2120 106064675 106066794 0.000000e+00 3916
1 TraesCS6D01G137500 chr6D 84.106 906 116 15 1 894 62500215 62501104 0.000000e+00 850
2 TraesCS6D01G137500 chr6B 92.484 918 48 8 1 898 192868367 192869283 0.000000e+00 1293
3 TraesCS6D01G137500 chr6B 84.354 914 102 20 1 894 136115470 136116362 0.000000e+00 857
4 TraesCS6D01G137500 chr1B 88.998 918 81 6 1 898 42029773 42028856 0.000000e+00 1118
5 TraesCS6D01G137500 chr1B 93.065 447 28 3 1654 2100 42022368 42021925 0.000000e+00 651
6 TraesCS6D01G137500 chr2D 88.671 918 78 13 1 898 562900540 562899629 0.000000e+00 1096
7 TraesCS6D01G137500 chr2D 89.729 516 53 0 1584 2099 562899616 562899101 0.000000e+00 660
8 TraesCS6D01G137500 chr2D 98.026 304 6 0 899 1202 628288041 628287738 1.440000e-146 529
9 TraesCS6D01G137500 chr2D 98.013 302 6 0 899 1200 628284794 628284493 1.860000e-145 525
10 TraesCS6D01G137500 chr5D 88.017 918 90 8 1 898 340421634 340420717 0.000000e+00 1068
11 TraesCS6D01G137500 chr5D 88.760 516 54 1 1584 2099 340420704 340420193 1.380000e-176 628
12 TraesCS6D01G137500 chr5D 97.351 302 8 0 899 1200 6208563 6208864 4.030000e-142 514
13 TraesCS6D01G137500 chr5A 87.473 918 93 8 1 898 561986777 561985862 0.000000e+00 1038
14 TraesCS6D01G137500 chr5A 98.442 385 6 0 1199 1583 238862684 238863068 0.000000e+00 678
15 TraesCS6D01G137500 chr5A 90.116 516 51 0 1584 2099 561985849 561985334 0.000000e+00 671
16 TraesCS6D01G137500 chr3D 87.298 929 86 16 1 898 2068994 2069921 0.000000e+00 1033
17 TraesCS6D01G137500 chr3D 90.116 516 51 0 1584 2099 2069934 2070449 0.000000e+00 671
18 TraesCS6D01G137500 chr3D 97.682 302 7 0 899 1200 21896678 21896377 8.670000e-144 520
19 TraesCS6D01G137500 chr5B 87.255 918 97 8 1 898 78066354 78065437 0.000000e+00 1029
20 TraesCS6D01G137500 chr5B 89.922 516 52 0 1584 2099 586418624 586419139 0.000000e+00 665
21 TraesCS6D01G137500 chr5B 89.729 516 53 0 1584 2099 78065424 78064909 0.000000e+00 660
22 TraesCS6D01G137500 chr5B 84.861 502 57 11 416 898 586418110 586418611 2.440000e-134 488
23 TraesCS6D01G137500 chr6A 83.960 904 114 16 1 894 79948225 79949107 0.000000e+00 837
24 TraesCS6D01G137500 chr7B 98.182 385 7 0 1199 1583 742946549 742946165 0.000000e+00 673
25 TraesCS6D01G137500 chr7A 98.182 385 7 0 1199 1583 60166578 60166194 0.000000e+00 673
26 TraesCS6D01G137500 chr7A 98.182 385 7 0 1199 1583 708249694 708250078 0.000000e+00 673
27 TraesCS6D01G137500 chr7A 97.922 385 8 0 1199 1583 60087125 60087509 0.000000e+00 667
28 TraesCS6D01G137500 chr1A 98.182 385 7 0 1199 1583 334094091 334094475 0.000000e+00 673
29 TraesCS6D01G137500 chr1A 98.013 302 6 0 899 1200 554465912 554466213 1.860000e-145 525
30 TraesCS6D01G137500 chr1A 97.351 302 8 0 899 1200 256027043 256027344 4.030000e-142 514
31 TraesCS6D01G137500 chr1D 90.116 516 51 0 1584 2099 367004180 367003665 0.000000e+00 671
32 TraesCS6D01G137500 chr1D 97.922 385 8 0 1199 1583 212437918 212437534 0.000000e+00 667
33 TraesCS6D01G137500 chr1D 98.013 302 6 0 899 1200 394176973 394176672 1.860000e-145 525
34 TraesCS6D01G137500 chr1D 98.013 302 6 0 899 1200 394178026 394177725 1.860000e-145 525
35 TraesCS6D01G137500 chr7D 97.922 385 8 0 1199 1583 578999829 578999445 0.000000e+00 667
36 TraesCS6D01G137500 chrUn 97.662 385 9 0 1199 1583 209408067 209408451 0.000000e+00 662
37 TraesCS6D01G137500 chrUn 98.013 302 6 0 899 1200 405771441 405771742 1.860000e-145 525
38 TraesCS6D01G137500 chr4A 89.729 516 53 0 1584 2099 454760752 454761267 0.000000e+00 660
39 TraesCS6D01G137500 chr4A 92.771 83 5 1 816 898 454760658 454760739 3.700000e-23 119


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 TraesCS6D01G137500 chr6D 106064675 106066794 2119 False 3916.0 3916 100.0000 1 2120 1 chr6D.!!$F2 2119
1 TraesCS6D01G137500 chr6D 62500215 62501104 889 False 850.0 850 84.1060 1 894 1 chr6D.!!$F1 893
2 TraesCS6D01G137500 chr6B 192868367 192869283 916 False 1293.0 1293 92.4840 1 898 1 chr6B.!!$F2 897
3 TraesCS6D01G137500 chr6B 136115470 136116362 892 False 857.0 857 84.3540 1 894 1 chr6B.!!$F1 893
4 TraesCS6D01G137500 chr1B 42028856 42029773 917 True 1118.0 1118 88.9980 1 898 1 chr1B.!!$R2 897
5 TraesCS6D01G137500 chr2D 562899101 562900540 1439 True 878.0 1096 89.2000 1 2099 2 chr2D.!!$R1 2098
6 TraesCS6D01G137500 chr2D 628284493 628288041 3548 True 527.0 529 98.0195 899 1202 2 chr2D.!!$R2 303
7 TraesCS6D01G137500 chr5D 340420193 340421634 1441 True 848.0 1068 88.3885 1 2099 2 chr5D.!!$R1 2098
8 TraesCS6D01G137500 chr5A 561985334 561986777 1443 True 854.5 1038 88.7945 1 2099 2 chr5A.!!$R1 2098
9 TraesCS6D01G137500 chr3D 2068994 2070449 1455 False 852.0 1033 88.7070 1 2099 2 chr3D.!!$F1 2098
10 TraesCS6D01G137500 chr5B 78064909 78066354 1445 True 844.5 1029 88.4920 1 2099 2 chr5B.!!$R1 2098
11 TraesCS6D01G137500 chr5B 586418110 586419139 1029 False 576.5 665 87.3915 416 2099 2 chr5B.!!$F1 1683
12 TraesCS6D01G137500 chr6A 79948225 79949107 882 False 837.0 837 83.9600 1 894 1 chr6A.!!$F1 893
13 TraesCS6D01G137500 chr1D 367003665 367004180 515 True 671.0 671 90.1160 1584 2099 1 chr1D.!!$R2 515
14 TraesCS6D01G137500 chr1D 394176672 394178026 1354 True 525.0 525 98.0130 899 1200 2 chr1D.!!$R3 301
15 TraesCS6D01G137500 chr4A 454760658 454761267 609 False 389.5 660 91.2500 816 2099 2 chr4A.!!$F1 1283

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
894 927 0.468226 TCAAGCTTCTGTTCGGTGGT 59.532 50.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 4086 0.032403 TTGCTTTGCACACTGATGGC 59.968 50.0 0.0 0.0 38.71 4.4 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
146 150 2.706190 GGGCAATACTACATGGGAGAGT 59.294 50.000 0.00 0.00 0.00 3.24
181 185 3.201266 AGGGCTGATTAAACGTATTGGGA 59.799 43.478 0.00 0.00 0.00 4.37
201 205 4.932200 GGGAATGGAGCGAGTATTAAGATG 59.068 45.833 0.00 0.00 0.00 2.90
276 280 2.292559 GGGGGTTGCATGCACCAAT 61.293 57.895 28.69 0.00 0.00 3.16
434 448 7.014326 GGAGTTGGAGAGAAATGGTAACTTTTT 59.986 37.037 0.00 0.00 43.30 1.94
506 522 1.865865 GTCTTCGTCAGGAACAGCAA 58.134 50.000 0.00 0.00 0.00 3.91
610 626 3.178046 TGTGCCCTGTAAATCTGTCCTA 58.822 45.455 0.00 0.00 0.00 2.94
654 670 1.134401 CCCATTCTGCGACCTATGTGT 60.134 52.381 0.00 0.00 0.00 3.72
680 696 3.117663 GGAGGAAACTATAACCCATGCCA 60.118 47.826 0.00 0.00 44.43 4.92
740 756 5.795972 AGATGAAGACCATGATGCAGATAG 58.204 41.667 0.00 0.00 35.17 2.08
801 817 8.608598 AGATTTGATTGAAGGAAAAATGGGATT 58.391 29.630 0.00 0.00 0.00 3.01
894 927 0.468226 TCAAGCTTCTGTTCGGTGGT 59.532 50.000 0.00 0.00 0.00 4.16
916 949 3.007506 TCTCAGTATTTCACGGAAAGCCA 59.992 43.478 5.52 0.00 34.92 4.75
952 985 6.183360 CCGTTAATAACCGACCGTTTTGATTA 60.183 38.462 0.00 0.00 35.79 1.75
1053 1086 0.109153 TGCGATGGCTGGCTATTCAT 59.891 50.000 0.15 0.00 40.82 2.57
1115 1148 2.029739 CAGCAATGCAGTTCATCCAACA 60.030 45.455 8.35 0.00 37.48 3.33
1132 1165 8.213679 TCATCCAACAATAAACCAAATTCCAAA 58.786 29.630 0.00 0.00 0.00 3.28
1214 1254 9.627395 CCAGTCTATACTATATTTCTTGGTTCG 57.373 37.037 0.00 0.00 33.48 3.95
1215 1255 9.627395 CAGTCTATACTATATTTCTTGGTTCGG 57.373 37.037 0.00 0.00 33.48 4.30
1216 1256 9.584008 AGTCTATACTATATTTCTTGGTTCGGA 57.416 33.333 0.00 0.00 32.84 4.55
1221 1261 6.895782 ACTATATTTCTTGGTTCGGAATCCA 58.104 36.000 0.00 3.52 0.00 3.41
1222 1262 7.343357 ACTATATTTCTTGGTTCGGAATCCAA 58.657 34.615 17.72 17.72 40.77 3.53
1224 1264 5.582689 ATTTCTTGGTTCGGAATCCAATC 57.417 39.130 18.53 0.00 41.89 2.67
1225 1265 2.999331 TCTTGGTTCGGAATCCAATCC 58.001 47.619 18.53 5.79 41.89 3.01
1226 1266 2.307392 TCTTGGTTCGGAATCCAATCCA 59.693 45.455 18.53 7.92 41.89 3.41
1227 1267 2.418368 TGGTTCGGAATCCAATCCAG 57.582 50.000 0.00 0.00 39.61 3.86
1230 1270 2.423538 GGTTCGGAATCCAATCCAGTTG 59.576 50.000 0.00 0.00 39.61 3.16
1231 1271 3.343617 GTTCGGAATCCAATCCAGTTGA 58.656 45.455 0.00 0.00 40.37 3.18
1232 1272 3.712016 TCGGAATCCAATCCAGTTGAA 57.288 42.857 0.00 0.00 40.37 2.69
1233 1273 4.027674 TCGGAATCCAATCCAGTTGAAA 57.972 40.909 0.00 0.00 40.37 2.69
1235 1275 4.217550 TCGGAATCCAATCCAGTTGAAAAC 59.782 41.667 0.00 0.00 40.37 2.43
1236 1276 4.022416 CGGAATCCAATCCAGTTGAAAACA 60.022 41.667 0.00 0.00 42.49 2.83
1237 1277 5.508825 CGGAATCCAATCCAGTTGAAAACAA 60.509 40.000 0.00 0.00 42.49 2.83
1251 1291 5.987777 TGAAAACAAACAATTGCCTGATG 57.012 34.783 5.05 0.44 40.34 3.07
1265 1305 2.995283 CCTGATGGCAAAGTCAGATGA 58.005 47.619 16.23 0.00 43.50 2.92
1266 1306 3.349927 CCTGATGGCAAAGTCAGATGAA 58.650 45.455 16.23 0.00 43.50 2.57
1267 1307 3.760151 CCTGATGGCAAAGTCAGATGAAA 59.240 43.478 16.23 0.00 43.50 2.69
1268 1308 4.142447 CCTGATGGCAAAGTCAGATGAAAG 60.142 45.833 16.23 0.00 43.50 2.62
1269 1309 3.760151 TGATGGCAAAGTCAGATGAAAGG 59.240 43.478 0.00 0.00 0.00 3.11
1270 1310 1.888512 TGGCAAAGTCAGATGAAAGGC 59.111 47.619 0.00 0.00 0.00 4.35
1271 1311 1.888512 GGCAAAGTCAGATGAAAGGCA 59.111 47.619 0.00 0.00 0.00 4.75
1272 1312 2.297033 GGCAAAGTCAGATGAAAGGCAA 59.703 45.455 0.00 0.00 0.00 4.52
1273 1313 3.572584 GCAAAGTCAGATGAAAGGCAAG 58.427 45.455 0.00 0.00 0.00 4.01
1274 1314 3.613432 GCAAAGTCAGATGAAAGGCAAGG 60.613 47.826 0.00 0.00 0.00 3.61
1275 1315 3.795688 AAGTCAGATGAAAGGCAAGGA 57.204 42.857 0.00 0.00 0.00 3.36
1276 1316 3.347077 AGTCAGATGAAAGGCAAGGAG 57.653 47.619 0.00 0.00 0.00 3.69
1277 1317 2.641815 AGTCAGATGAAAGGCAAGGAGT 59.358 45.455 0.00 0.00 0.00 3.85
1278 1318 2.746362 GTCAGATGAAAGGCAAGGAGTG 59.254 50.000 0.00 0.00 0.00 3.51
1279 1319 2.373169 TCAGATGAAAGGCAAGGAGTGT 59.627 45.455 0.00 0.00 0.00 3.55
1280 1320 3.582647 TCAGATGAAAGGCAAGGAGTGTA 59.417 43.478 0.00 0.00 0.00 2.90
1281 1321 4.041567 TCAGATGAAAGGCAAGGAGTGTAA 59.958 41.667 0.00 0.00 0.00 2.41
1282 1322 4.761739 CAGATGAAAGGCAAGGAGTGTAAA 59.238 41.667 0.00 0.00 0.00 2.01
1283 1323 4.762251 AGATGAAAGGCAAGGAGTGTAAAC 59.238 41.667 0.00 0.00 0.00 2.01
1284 1324 3.219281 TGAAAGGCAAGGAGTGTAAACC 58.781 45.455 0.00 0.00 0.00 3.27
1285 1325 3.219281 GAAAGGCAAGGAGTGTAAACCA 58.781 45.455 0.00 0.00 0.00 3.67
1286 1326 2.271944 AGGCAAGGAGTGTAAACCAC 57.728 50.000 0.00 0.00 44.89 4.16
1295 1335 0.704551 GTGTAAACCACGTACGAGCG 59.295 55.000 24.41 10.68 33.61 5.03
1296 1336 0.310543 TGTAAACCACGTACGAGCGT 59.689 50.000 24.41 11.34 46.88 5.07
1311 1351 2.331098 CGTGGCGCAGAAAGCAAA 59.669 55.556 10.83 0.00 46.13 3.68
1312 1352 1.299014 CGTGGCGCAGAAAGCAAAA 60.299 52.632 10.83 0.00 46.13 2.44
1313 1353 0.664166 CGTGGCGCAGAAAGCAAAAT 60.664 50.000 10.83 0.00 46.13 1.82
1314 1354 0.785979 GTGGCGCAGAAAGCAAAATG 59.214 50.000 10.83 0.00 46.13 2.32
1315 1355 0.388659 TGGCGCAGAAAGCAAAATGT 59.611 45.000 10.83 0.00 46.13 2.71
1316 1356 1.202510 TGGCGCAGAAAGCAAAATGTT 60.203 42.857 10.83 0.00 46.13 2.71
1317 1357 1.866601 GGCGCAGAAAGCAAAATGTTT 59.133 42.857 10.83 0.00 46.13 2.83
1318 1358 2.287644 GGCGCAGAAAGCAAAATGTTTT 59.712 40.909 10.83 0.00 46.13 2.43
1331 1371 6.028040 CAAAATGTTTTGCAGTGAGTCAAG 57.972 37.500 5.39 0.00 40.76 3.02
1332 1372 2.849880 TGTTTTGCAGTGAGTCAAGC 57.150 45.000 10.96 10.96 0.00 4.01
1333 1373 1.063912 TGTTTTGCAGTGAGTCAAGCG 59.936 47.619 12.56 0.00 0.00 4.68
1334 1374 1.064060 GTTTTGCAGTGAGTCAAGCGT 59.936 47.619 12.56 0.00 0.00 5.07
1335 1375 2.232756 TTTGCAGTGAGTCAAGCGTA 57.767 45.000 12.56 2.93 0.00 4.42
1336 1376 2.232756 TTGCAGTGAGTCAAGCGTAA 57.767 45.000 12.56 2.15 0.00 3.18
1337 1377 2.455674 TGCAGTGAGTCAAGCGTAAT 57.544 45.000 12.56 0.00 0.00 1.89
1338 1378 3.586100 TGCAGTGAGTCAAGCGTAATA 57.414 42.857 12.56 0.00 0.00 0.98
1339 1379 3.250744 TGCAGTGAGTCAAGCGTAATAC 58.749 45.455 12.56 0.00 0.00 1.89
1340 1380 2.279136 GCAGTGAGTCAAGCGTAATACG 59.721 50.000 8.64 8.64 45.88 3.06
1341 1381 3.754955 CAGTGAGTCAAGCGTAATACGA 58.245 45.455 17.71 0.00 46.05 3.43
1342 1382 4.352039 CAGTGAGTCAAGCGTAATACGAT 58.648 43.478 17.71 7.51 44.59 3.73
1343 1383 4.438145 CAGTGAGTCAAGCGTAATACGATC 59.562 45.833 17.71 0.00 40.37 3.69
1344 1384 4.095932 AGTGAGTCAAGCGTAATACGATCA 59.904 41.667 17.71 0.94 40.37 2.92
1345 1385 4.796830 GTGAGTCAAGCGTAATACGATCAA 59.203 41.667 17.71 0.00 40.37 2.57
1346 1386 5.287752 GTGAGTCAAGCGTAATACGATCAAA 59.712 40.000 17.71 0.00 40.37 2.69
1347 1387 5.865013 TGAGTCAAGCGTAATACGATCAAAA 59.135 36.000 17.71 0.00 40.37 2.44
1348 1388 6.034577 TGAGTCAAGCGTAATACGATCAAAAG 59.965 38.462 17.71 0.00 40.37 2.27
1349 1389 5.291128 AGTCAAGCGTAATACGATCAAAAGG 59.709 40.000 17.71 0.00 40.37 3.11
1350 1390 5.290158 GTCAAGCGTAATACGATCAAAAGGA 59.710 40.000 17.71 0.00 40.37 3.36
1351 1391 5.870433 TCAAGCGTAATACGATCAAAAGGAA 59.130 36.000 17.71 0.00 40.37 3.36
1352 1392 6.369340 TCAAGCGTAATACGATCAAAAGGAAA 59.631 34.615 17.71 0.00 40.37 3.13
1353 1393 6.920569 AGCGTAATACGATCAAAAGGAAAT 57.079 33.333 17.71 0.00 46.05 2.17
1354 1394 6.715464 AGCGTAATACGATCAAAAGGAAATG 58.285 36.000 17.71 0.00 46.05 2.32
1355 1395 5.907391 GCGTAATACGATCAAAAGGAAATGG 59.093 40.000 17.71 0.00 46.05 3.16
1356 1396 6.427150 CGTAATACGATCAAAAGGAAATGGG 58.573 40.000 7.05 0.00 46.05 4.00
1357 1397 5.852282 AATACGATCAAAAGGAAATGGGG 57.148 39.130 0.00 0.00 0.00 4.96
1358 1398 3.169512 ACGATCAAAAGGAAATGGGGT 57.830 42.857 0.00 0.00 0.00 4.95
1359 1399 3.089284 ACGATCAAAAGGAAATGGGGTC 58.911 45.455 0.00 0.00 0.00 4.46
1360 1400 2.097466 CGATCAAAAGGAAATGGGGTCG 59.903 50.000 0.00 0.00 0.00 4.79
1361 1401 2.961531 TCAAAAGGAAATGGGGTCGA 57.038 45.000 0.00 0.00 0.00 4.20
1362 1402 3.449746 TCAAAAGGAAATGGGGTCGAT 57.550 42.857 0.00 0.00 0.00 3.59
1363 1403 3.088532 TCAAAAGGAAATGGGGTCGATG 58.911 45.455 0.00 0.00 0.00 3.84
1364 1404 1.474330 AAAGGAAATGGGGTCGATGC 58.526 50.000 0.00 0.00 0.00 3.91
1365 1405 0.625849 AAGGAAATGGGGTCGATGCT 59.374 50.000 0.00 0.00 0.00 3.79
1366 1406 1.507140 AGGAAATGGGGTCGATGCTA 58.493 50.000 0.00 0.00 0.00 3.49
1367 1407 1.843851 AGGAAATGGGGTCGATGCTAA 59.156 47.619 0.00 0.00 0.00 3.09
1368 1408 2.241176 AGGAAATGGGGTCGATGCTAAA 59.759 45.455 0.00 0.00 0.00 1.85
1369 1409 3.020984 GGAAATGGGGTCGATGCTAAAA 58.979 45.455 0.00 0.00 0.00 1.52
1370 1410 3.181490 GGAAATGGGGTCGATGCTAAAAC 60.181 47.826 0.00 0.00 0.00 2.43
1371 1411 3.366052 AATGGGGTCGATGCTAAAACT 57.634 42.857 0.00 0.00 0.00 2.66
1372 1412 2.396590 TGGGGTCGATGCTAAAACTC 57.603 50.000 0.00 0.00 0.00 3.01
1373 1413 1.626321 TGGGGTCGATGCTAAAACTCA 59.374 47.619 0.00 0.00 0.00 3.41
1374 1414 2.039216 TGGGGTCGATGCTAAAACTCAA 59.961 45.455 0.00 0.00 0.00 3.02
1375 1415 3.078837 GGGGTCGATGCTAAAACTCAAA 58.921 45.455 0.00 0.00 0.00 2.69
1376 1416 3.119955 GGGGTCGATGCTAAAACTCAAAC 60.120 47.826 0.00 0.00 0.00 2.93
1377 1417 3.500680 GGGTCGATGCTAAAACTCAAACA 59.499 43.478 0.00 0.00 0.00 2.83
1378 1418 4.378459 GGGTCGATGCTAAAACTCAAACAG 60.378 45.833 0.00 0.00 0.00 3.16
1379 1419 4.213482 GGTCGATGCTAAAACTCAAACAGT 59.787 41.667 0.00 0.00 36.64 3.55
1381 1421 5.846473 GTCGATGCTAAAACTCAAACAGTTC 59.154 40.000 0.00 0.00 45.32 3.01
1382 1422 5.049680 TCGATGCTAAAACTCAAACAGTTCC 60.050 40.000 0.00 0.00 45.32 3.62
1383 1423 4.911514 TGCTAAAACTCAAACAGTTCCC 57.088 40.909 0.00 0.00 45.32 3.97
1384 1424 3.634910 TGCTAAAACTCAAACAGTTCCCC 59.365 43.478 0.00 0.00 45.32 4.81
1385 1425 3.634910 GCTAAAACTCAAACAGTTCCCCA 59.365 43.478 0.00 0.00 45.32 4.96
1386 1426 4.261614 GCTAAAACTCAAACAGTTCCCCAG 60.262 45.833 0.00 0.00 45.32 4.45
1387 1427 3.662759 AAACTCAAACAGTTCCCCAGA 57.337 42.857 0.00 0.00 45.32 3.86
1388 1428 2.938956 ACTCAAACAGTTCCCCAGAG 57.061 50.000 0.00 0.00 26.56 3.35
1389 1429 1.421646 ACTCAAACAGTTCCCCAGAGG 59.578 52.381 0.00 0.00 26.56 3.69
1390 1430 5.345514 AACTCAAACAGTTCCCCAGAGGG 62.346 52.174 0.00 0.00 42.07 4.30
1407 1447 3.974293 GGGCCCCGGGTTGAAAGA 61.974 66.667 21.85 0.00 0.00 2.52
1408 1448 2.361230 GGCCCCGGGTTGAAAGAG 60.361 66.667 21.85 1.58 0.00 2.85
1409 1449 3.062466 GCCCCGGGTTGAAAGAGC 61.062 66.667 21.85 9.27 0.00 4.09
1410 1450 2.746277 CCCCGGGTTGAAAGAGCG 60.746 66.667 21.85 0.00 0.00 5.03
1411 1451 2.345991 CCCGGGTTGAAAGAGCGA 59.654 61.111 14.18 0.00 0.00 4.93
1412 1452 1.741770 CCCGGGTTGAAAGAGCGAG 60.742 63.158 14.18 0.00 0.00 5.03
1413 1453 2.391389 CCGGGTTGAAAGAGCGAGC 61.391 63.158 0.00 0.00 0.00 5.03
1414 1454 1.374758 CGGGTTGAAAGAGCGAGCT 60.375 57.895 0.00 0.00 0.00 4.09
1415 1455 0.108804 CGGGTTGAAAGAGCGAGCTA 60.109 55.000 0.00 0.00 0.00 3.32
1416 1456 1.360820 GGGTTGAAAGAGCGAGCTAC 58.639 55.000 0.00 0.00 0.00 3.58
1417 1457 1.337823 GGGTTGAAAGAGCGAGCTACA 60.338 52.381 0.00 0.00 0.00 2.74
1418 1458 2.622436 GGTTGAAAGAGCGAGCTACAT 58.378 47.619 0.00 0.00 0.00 2.29
1419 1459 3.003480 GGTTGAAAGAGCGAGCTACATT 58.997 45.455 0.00 0.00 0.00 2.71
1420 1460 3.062774 GGTTGAAAGAGCGAGCTACATTC 59.937 47.826 0.00 4.09 0.00 2.67
1421 1461 3.876274 TGAAAGAGCGAGCTACATTCT 57.124 42.857 0.00 0.00 0.00 2.40
1422 1462 4.193826 TGAAAGAGCGAGCTACATTCTT 57.806 40.909 0.00 0.00 0.00 2.52
1423 1463 4.569943 TGAAAGAGCGAGCTACATTCTTT 58.430 39.130 12.22 12.22 39.91 2.52
1424 1464 4.627467 TGAAAGAGCGAGCTACATTCTTTC 59.373 41.667 22.72 22.72 46.98 2.62
1425 1465 3.876274 AGAGCGAGCTACATTCTTTCA 57.124 42.857 0.00 0.00 0.00 2.69
1426 1466 4.399004 AGAGCGAGCTACATTCTTTCAT 57.601 40.909 0.00 0.00 0.00 2.57
1427 1467 5.521906 AGAGCGAGCTACATTCTTTCATA 57.478 39.130 0.00 0.00 0.00 2.15
1428 1468 5.527951 AGAGCGAGCTACATTCTTTCATAG 58.472 41.667 0.00 0.00 0.00 2.23
1433 1473 6.074569 GCGAGCTACATTCTTTCATAGAAGAC 60.075 42.308 0.00 0.00 45.69 3.01
1437 1477 8.535335 AGCTACATTCTTTCATAGAAGACAGAA 58.465 33.333 0.00 0.00 45.69 3.02
1448 1488 9.877178 TTCATAGAAGACAGAAAATAAGAGGAC 57.123 33.333 0.00 0.00 0.00 3.85
1450 1490 9.311916 CATAGAAGACAGAAAATAAGAGGACTG 57.688 37.037 0.00 0.00 0.00 3.51
1453 1493 5.486526 AGACAGAAAATAAGAGGACTGCTG 58.513 41.667 0.00 0.00 0.00 4.41
1454 1494 4.006319 ACAGAAAATAAGAGGACTGCTGC 58.994 43.478 0.00 0.00 0.00 5.25
1456 1496 4.699257 CAGAAAATAAGAGGACTGCTGCTT 59.301 41.667 0.00 0.00 0.00 3.91
1459 1499 4.566426 AATAAGAGGACTGCTGCTTTCT 57.434 40.909 0.00 0.00 0.00 2.52
1460 1500 2.947127 AAGAGGACTGCTGCTTTCTT 57.053 45.000 0.00 0.58 0.00 2.52
1462 1502 3.326836 AGAGGACTGCTGCTTTCTTAC 57.673 47.619 0.00 0.00 0.00 2.34
1465 1505 3.669536 AGGACTGCTGCTTTCTTACTTC 58.330 45.455 0.00 0.00 0.00 3.01
1466 1506 3.071602 AGGACTGCTGCTTTCTTACTTCA 59.928 43.478 0.00 0.00 0.00 3.02
1467 1507 4.006319 GGACTGCTGCTTTCTTACTTCAT 58.994 43.478 0.00 0.00 0.00 2.57
1468 1508 4.094146 GGACTGCTGCTTTCTTACTTCATC 59.906 45.833 0.00 0.00 0.00 2.92
1469 1509 4.904241 ACTGCTGCTTTCTTACTTCATCT 58.096 39.130 0.00 0.00 0.00 2.90
1470 1510 5.312079 ACTGCTGCTTTCTTACTTCATCTT 58.688 37.500 0.00 0.00 0.00 2.40
1472 1512 6.936900 ACTGCTGCTTTCTTACTTCATCTTAA 59.063 34.615 0.00 0.00 0.00 1.85
1473 1513 7.609532 ACTGCTGCTTTCTTACTTCATCTTAAT 59.390 33.333 0.00 0.00 0.00 1.40
1474 1514 9.102757 CTGCTGCTTTCTTACTTCATCTTAATA 57.897 33.333 0.00 0.00 0.00 0.98
1475 1515 9.618890 TGCTGCTTTCTTACTTCATCTTAATAT 57.381 29.630 0.00 0.00 0.00 1.28
1500 1540 9.872684 ATAGGGATTATAGCATTGGAATTATGG 57.127 33.333 0.00 0.00 0.00 2.74
1501 1541 7.943076 AGGGATTATAGCATTGGAATTATGGA 58.057 34.615 0.00 0.00 0.00 3.41
1502 1542 8.401105 AGGGATTATAGCATTGGAATTATGGAA 58.599 33.333 0.00 0.00 0.00 3.53
1516 1698 8.990203 TGGAATTATGGAATTTGAATGGATTGA 58.010 29.630 0.00 0.00 35.33 2.57
1524 1706 7.614974 TGGAATTTGAATGGATTGAGTACATCA 59.385 33.333 0.00 0.00 35.62 3.07
1542 1724 9.436957 AGTACATCAAGATGAAGAAATTAACGT 57.563 29.630 16.39 0.00 41.20 3.99
1570 1752 9.838339 ATAAGTGATATTCTCAAAAGATTCGGT 57.162 29.630 0.00 0.00 35.07 4.69
1572 1754 7.331026 AGTGATATTCTCAAAAGATTCGGTCA 58.669 34.615 0.00 0.00 35.07 4.02
1574 1756 8.066595 GTGATATTCTCAAAAGATTCGGTCATG 58.933 37.037 0.00 0.00 35.07 3.07
1575 1757 4.685169 TTCTCAAAAGATTCGGTCATGC 57.315 40.909 0.00 0.00 0.00 4.06
1577 1759 2.749076 CTCAAAAGATTCGGTCATGCCA 59.251 45.455 6.92 0.00 36.97 4.92
1579 1761 2.749076 CAAAAGATTCGGTCATGCCAGA 59.251 45.455 6.92 0.00 36.97 3.86
1580 1762 2.787473 AAGATTCGGTCATGCCAGAA 57.213 45.000 6.92 0.00 36.97 3.02
1581 1763 2.787473 AGATTCGGTCATGCCAGAAA 57.213 45.000 0.00 0.00 34.96 2.52
1592 1774 4.154918 GTCATGCCAGAAACTTGACCTTAG 59.845 45.833 0.00 0.00 36.63 2.18
1611 1799 5.221864 CCTTAGAACAACAGGGGAAACTACT 60.222 44.000 0.00 0.00 0.00 2.57
1623 1811 3.325716 GGGAAACTACTCAACCTGTGGTA 59.674 47.826 0.00 0.00 33.12 3.25
1637 1825 2.168728 CTGTGGTAACTAGGGAGGAAGC 59.831 54.545 0.00 0.00 37.61 3.86
1683 1931 4.156739 GGGACTCTGAAAATCAATGTGGAC 59.843 45.833 0.00 0.00 0.00 4.02
1689 1937 1.614996 AAATCAATGTGGACGTGGCA 58.385 45.000 0.00 0.00 0.00 4.92
1705 1971 0.604578 GGCATTTCTTGAGCAGGCAA 59.395 50.000 0.00 0.00 0.00 4.52
1710 1976 1.174712 TTCTTGAGCAGGCAAGGTGC 61.175 55.000 12.19 0.00 44.14 5.01
1731 1997 1.272807 GAAGTACAGGGCTGGTGGTA 58.727 55.000 0.00 0.00 34.19 3.25
1737 2003 1.001760 AGGGCTGGTGGTACGAGAT 59.998 57.895 0.00 0.00 0.00 2.75
1741 2007 1.641577 GCTGGTGGTACGAGATTCAC 58.358 55.000 0.00 0.00 0.00 3.18
1764 2030 2.222027 GGCAACCTAATTAGAGCGCAT 58.778 47.619 14.28 0.00 0.00 4.73
1965 3727 6.343716 TGCCATGAAATCAAAGAGCTTTTA 57.656 33.333 0.00 0.00 0.00 1.52
1998 3760 1.745087 AGCTGTGTTCTGGTGTTTGTG 59.255 47.619 0.00 0.00 0.00 3.33
2001 3763 1.889170 TGTGTTCTGGTGTTTGTGCAA 59.111 42.857 0.00 0.00 0.00 4.08
2019 4084 1.619827 CAAAGGGAAGCCAATGAAGCA 59.380 47.619 0.00 0.00 0.00 3.91
2021 4086 0.324091 AGGGAAGCCAATGAAGCAGG 60.324 55.000 0.00 0.00 0.00 4.85
2043 4108 1.000607 CATCAGTGTGCAAAGCAAGCT 60.001 47.619 0.00 0.00 41.47 3.74
2102 4627 7.857404 ATATGCCTCCTTTCTTAGCTAACTA 57.143 36.000 0.86 0.00 0.00 2.24
2103 4628 5.599999 TGCCTCCTTTCTTAGCTAACTAG 57.400 43.478 0.86 0.33 0.00 2.57
2106 4631 7.067421 TGCCTCCTTTCTTAGCTAACTAGATA 58.933 38.462 0.86 0.00 0.00 1.98
2107 4632 7.231722 TGCCTCCTTTCTTAGCTAACTAGATAG 59.768 40.741 0.86 0.00 0.00 2.08
2108 4633 7.309560 GCCTCCTTTCTTAGCTAACTAGATAGG 60.310 44.444 17.78 17.78 32.48 2.57
2109 4634 7.945664 CCTCCTTTCTTAGCTAACTAGATAGGA 59.054 40.741 21.95 21.95 34.86 2.94
2111 4636 9.710818 TCCTTTCTTAGCTAACTAGATAGGAAA 57.289 33.333 21.48 16.30 43.33 3.13
2112 4637 9.752961 CCTTTCTTAGCTAACTAGATAGGAAAC 57.247 37.037 18.55 0.00 41.85 2.78
2114 4639 6.968250 TCTTAGCTAACTAGATAGGAAACGC 58.032 40.000 0.86 0.00 29.17 4.84
2115 4640 4.226113 AGCTAACTAGATAGGAAACGCG 57.774 45.455 3.53 3.53 0.00 6.01
2117 4642 2.220479 AACTAGATAGGAAACGCGCC 57.780 50.000 5.73 0.00 0.00 6.53
2118 4643 1.400737 ACTAGATAGGAAACGCGCCT 58.599 50.000 5.73 7.64 39.56 5.52
2119 4644 1.755380 ACTAGATAGGAAACGCGCCTT 59.245 47.619 5.73 0.00 36.96 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 150 5.957771 AATCAGCCCTAGTTTCAGACATA 57.042 39.130 0.00 0.00 0.00 2.29
181 185 5.300752 CCACATCTTAATACTCGCTCCATT 58.699 41.667 0.00 0.00 0.00 3.16
258 262 2.292559 ATTGGTGCATGCAACCCCC 61.293 57.895 31.94 23.55 31.49 5.40
276 280 4.409901 TCATGATCAATAAGCTCCTCCACA 59.590 41.667 0.00 0.00 0.00 4.17
434 448 4.443063 CAGAATTATACGCCGATCGAACAA 59.557 41.667 18.66 0.00 41.67 2.83
506 522 7.667219 CCATAGTATGTTCCATAAGGCATTTCT 59.333 37.037 9.28 0.00 33.74 2.52
535 551 5.771666 CCTAACTCTTGGTGGTACCGATATA 59.228 44.000 7.57 0.00 42.58 0.86
610 626 6.388278 GGTCTTTTCTATGTGTCGAGTAAGT 58.612 40.000 0.00 0.00 0.00 2.24
654 670 5.631481 GCATGGGTTATAGTTTCCTCCTTGA 60.631 44.000 0.00 0.00 0.00 3.02
680 696 0.527565 GCCCAAGTGCATTCGAACAT 59.472 50.000 0.00 0.00 0.00 2.71
740 756 9.559958 CAATTGTGGATGTAACACTAAGATTTC 57.440 33.333 0.00 0.00 39.52 2.17
774 790 8.663209 TCCCATTTTTCCTTCAATCAAATCTA 57.337 30.769 0.00 0.00 0.00 1.98
801 817 2.765135 CCCATGCATACAAAATGGTCCA 59.235 45.455 0.00 0.00 39.43 4.02
894 927 3.007506 TGGCTTTCCGTGAAATACTGAGA 59.992 43.478 0.00 0.00 30.85 3.27
916 949 5.939296 TCGGTTATTAACGGAATTCCTTGTT 59.061 36.000 22.05 19.85 37.72 2.83
1053 1086 3.733883 ACAGTAGGTACAGCTAGTCCA 57.266 47.619 0.00 0.00 0.00 4.02
1132 1165 9.561069 GGGTTTGATTGTGTCATAGTTCTATAT 57.439 33.333 0.00 0.00 36.54 0.86
1202 1242 4.402474 GGATTGGATTCCGAACCAAGAAAT 59.598 41.667 13.20 0.00 46.95 2.17
1203 1243 3.761752 GGATTGGATTCCGAACCAAGAAA 59.238 43.478 13.20 0.00 46.95 2.52
1204 1244 3.245087 TGGATTGGATTCCGAACCAAGAA 60.245 43.478 17.44 0.00 46.95 2.52
1209 1249 2.420058 ACTGGATTGGATTCCGAACC 57.580 50.000 11.53 11.53 38.74 3.62
1210 1250 3.343617 TCAACTGGATTGGATTCCGAAC 58.656 45.455 0.00 0.00 38.74 3.95
1213 1253 4.022416 TGTTTTCAACTGGATTGGATTCCG 60.022 41.667 0.00 0.00 38.74 4.30
1214 1254 5.467035 TGTTTTCAACTGGATTGGATTCC 57.533 39.130 0.00 0.00 38.98 3.01
1215 1255 6.760770 TGTTTGTTTTCAACTGGATTGGATTC 59.239 34.615 0.00 0.00 39.73 2.52
1216 1256 6.648192 TGTTTGTTTTCAACTGGATTGGATT 58.352 32.000 0.00 0.00 39.73 3.01
1217 1257 6.232581 TGTTTGTTTTCAACTGGATTGGAT 57.767 33.333 0.00 0.00 39.73 3.41
1219 1259 6.923928 ATTGTTTGTTTTCAACTGGATTGG 57.076 33.333 0.00 0.00 39.73 3.16
1221 1261 6.183360 GGCAATTGTTTGTTTTCAACTGGATT 60.183 34.615 7.40 0.00 39.73 3.01
1222 1262 5.296531 GGCAATTGTTTGTTTTCAACTGGAT 59.703 36.000 7.40 0.00 39.73 3.41
1224 1264 4.635324 AGGCAATTGTTTGTTTTCAACTGG 59.365 37.500 7.40 0.00 39.73 4.00
1225 1265 5.350914 TCAGGCAATTGTTTGTTTTCAACTG 59.649 36.000 7.40 0.00 39.73 3.16
1226 1266 5.486526 TCAGGCAATTGTTTGTTTTCAACT 58.513 33.333 7.40 0.00 39.73 3.16
1227 1267 5.793026 TCAGGCAATTGTTTGTTTTCAAC 57.207 34.783 7.40 0.00 39.73 3.18
1230 1270 5.347012 CCATCAGGCAATTGTTTGTTTTC 57.653 39.130 7.40 0.00 35.17 2.29
1246 1286 4.142447 CCTTTCATCTGACTTTGCCATCAG 60.142 45.833 0.00 0.00 43.16 2.90
1247 1287 3.760151 CCTTTCATCTGACTTTGCCATCA 59.240 43.478 0.00 0.00 0.00 3.07
1248 1288 3.428589 GCCTTTCATCTGACTTTGCCATC 60.429 47.826 0.00 0.00 0.00 3.51
1249 1289 2.494870 GCCTTTCATCTGACTTTGCCAT 59.505 45.455 0.00 0.00 0.00 4.40
1250 1290 1.888512 GCCTTTCATCTGACTTTGCCA 59.111 47.619 0.00 0.00 0.00 4.92
1251 1291 1.888512 TGCCTTTCATCTGACTTTGCC 59.111 47.619 0.00 0.00 0.00 4.52
1253 1293 3.822735 TCCTTGCCTTTCATCTGACTTTG 59.177 43.478 0.00 0.00 0.00 2.77
1254 1294 4.077822 CTCCTTGCCTTTCATCTGACTTT 58.922 43.478 0.00 0.00 0.00 2.66
1256 1296 2.641815 ACTCCTTGCCTTTCATCTGACT 59.358 45.455 0.00 0.00 0.00 3.41
1257 1297 2.746362 CACTCCTTGCCTTTCATCTGAC 59.254 50.000 0.00 0.00 0.00 3.51
1258 1298 2.373169 ACACTCCTTGCCTTTCATCTGA 59.627 45.455 0.00 0.00 0.00 3.27
1259 1299 2.787994 ACACTCCTTGCCTTTCATCTG 58.212 47.619 0.00 0.00 0.00 2.90
1260 1300 4.640771 TTACACTCCTTGCCTTTCATCT 57.359 40.909 0.00 0.00 0.00 2.90
1261 1301 4.082733 GGTTTACACTCCTTGCCTTTCATC 60.083 45.833 0.00 0.00 0.00 2.92
1262 1302 3.826729 GGTTTACACTCCTTGCCTTTCAT 59.173 43.478 0.00 0.00 0.00 2.57
1263 1303 3.219281 GGTTTACACTCCTTGCCTTTCA 58.781 45.455 0.00 0.00 0.00 2.69
1264 1304 3.004419 GTGGTTTACACTCCTTGCCTTTC 59.996 47.826 0.00 0.00 46.72 2.62
1265 1305 2.956333 GTGGTTTACACTCCTTGCCTTT 59.044 45.455 0.00 0.00 46.72 3.11
1266 1306 2.583143 GTGGTTTACACTCCTTGCCTT 58.417 47.619 0.00 0.00 46.72 4.35
1267 1307 2.271944 GTGGTTTACACTCCTTGCCT 57.728 50.000 0.00 0.00 46.72 4.75
1276 1316 0.704551 CGCTCGTACGTGGTTTACAC 59.295 55.000 16.05 0.00 46.78 2.90
1277 1317 0.310543 ACGCTCGTACGTGGTTTACA 59.689 50.000 16.05 0.00 46.28 2.41
1278 1318 3.092081 ACGCTCGTACGTGGTTTAC 57.908 52.632 16.05 0.00 46.28 2.01
1294 1334 0.664166 ATTTTGCTTTCTGCGCCACG 60.664 50.000 4.18 0.00 46.63 4.94
1295 1335 0.785979 CATTTTGCTTTCTGCGCCAC 59.214 50.000 4.18 0.00 46.63 5.01
1296 1336 0.388659 ACATTTTGCTTTCTGCGCCA 59.611 45.000 4.18 0.00 46.63 5.69
1297 1337 1.501169 AACATTTTGCTTTCTGCGCC 58.499 45.000 4.18 0.00 46.63 6.53
1298 1338 3.282428 CAAAACATTTTGCTTTCTGCGC 58.718 40.909 0.00 0.00 46.63 6.09
1309 1349 4.567959 GCTTGACTCACTGCAAAACATTTT 59.432 37.500 0.00 0.00 0.00 1.82
1310 1350 4.114794 GCTTGACTCACTGCAAAACATTT 58.885 39.130 0.00 0.00 0.00 2.32
1311 1351 3.709987 GCTTGACTCACTGCAAAACATT 58.290 40.909 0.00 0.00 0.00 2.71
1312 1352 2.287188 CGCTTGACTCACTGCAAAACAT 60.287 45.455 0.00 0.00 0.00 2.71
1313 1353 1.063912 CGCTTGACTCACTGCAAAACA 59.936 47.619 0.00 0.00 0.00 2.83
1314 1354 1.064060 ACGCTTGACTCACTGCAAAAC 59.936 47.619 0.00 0.00 0.00 2.43
1315 1355 1.378531 ACGCTTGACTCACTGCAAAA 58.621 45.000 0.00 0.00 0.00 2.44
1316 1356 2.232756 TACGCTTGACTCACTGCAAA 57.767 45.000 0.00 0.00 0.00 3.68
1317 1357 2.232756 TTACGCTTGACTCACTGCAA 57.767 45.000 0.00 0.00 0.00 4.08
1318 1358 2.455674 ATTACGCTTGACTCACTGCA 57.544 45.000 0.00 0.00 0.00 4.41
1319 1359 2.279136 CGTATTACGCTTGACTCACTGC 59.721 50.000 2.88 0.00 33.65 4.40
1320 1360 3.754955 TCGTATTACGCTTGACTCACTG 58.245 45.455 11.33 0.00 42.21 3.66
1321 1361 4.095932 TGATCGTATTACGCTTGACTCACT 59.904 41.667 11.33 0.00 42.21 3.41
1322 1362 4.348656 TGATCGTATTACGCTTGACTCAC 58.651 43.478 11.33 0.00 42.21 3.51
1323 1363 4.625972 TGATCGTATTACGCTTGACTCA 57.374 40.909 11.33 4.84 42.21 3.41
1324 1364 5.944049 TTTGATCGTATTACGCTTGACTC 57.056 39.130 11.33 2.65 42.21 3.36
1325 1365 5.291128 CCTTTTGATCGTATTACGCTTGACT 59.709 40.000 11.33 0.00 42.21 3.41
1326 1366 5.290158 TCCTTTTGATCGTATTACGCTTGAC 59.710 40.000 11.33 2.21 42.21 3.18
1327 1367 5.412640 TCCTTTTGATCGTATTACGCTTGA 58.587 37.500 11.33 0.00 42.21 3.02
1328 1368 5.712217 TCCTTTTGATCGTATTACGCTTG 57.288 39.130 11.33 0.00 42.21 4.01
1329 1369 6.730960 TTTCCTTTTGATCGTATTACGCTT 57.269 33.333 11.33 1.58 42.21 4.68
1330 1370 6.238374 CCATTTCCTTTTGATCGTATTACGCT 60.238 38.462 11.33 1.46 42.21 5.07
1331 1371 5.907391 CCATTTCCTTTTGATCGTATTACGC 59.093 40.000 11.33 0.00 42.21 4.42
1332 1372 6.427150 CCCATTTCCTTTTGATCGTATTACG 58.573 40.000 9.95 9.95 44.19 3.18
1333 1373 6.320418 ACCCCATTTCCTTTTGATCGTATTAC 59.680 38.462 0.00 0.00 0.00 1.89
1334 1374 6.428295 ACCCCATTTCCTTTTGATCGTATTA 58.572 36.000 0.00 0.00 0.00 0.98
1335 1375 5.269189 ACCCCATTTCCTTTTGATCGTATT 58.731 37.500 0.00 0.00 0.00 1.89
1336 1376 4.867086 ACCCCATTTCCTTTTGATCGTAT 58.133 39.130 0.00 0.00 0.00 3.06
1337 1377 4.266714 GACCCCATTTCCTTTTGATCGTA 58.733 43.478 0.00 0.00 0.00 3.43
1338 1378 3.089284 GACCCCATTTCCTTTTGATCGT 58.911 45.455 0.00 0.00 0.00 3.73
1339 1379 2.097466 CGACCCCATTTCCTTTTGATCG 59.903 50.000 0.00 0.00 0.00 3.69
1340 1380 3.352648 TCGACCCCATTTCCTTTTGATC 58.647 45.455 0.00 0.00 0.00 2.92
1341 1381 3.449746 TCGACCCCATTTCCTTTTGAT 57.550 42.857 0.00 0.00 0.00 2.57
1342 1382 2.961531 TCGACCCCATTTCCTTTTGA 57.038 45.000 0.00 0.00 0.00 2.69
1343 1383 2.417243 GCATCGACCCCATTTCCTTTTG 60.417 50.000 0.00 0.00 0.00 2.44
1344 1384 1.824852 GCATCGACCCCATTTCCTTTT 59.175 47.619 0.00 0.00 0.00 2.27
1345 1385 1.005924 AGCATCGACCCCATTTCCTTT 59.994 47.619 0.00 0.00 0.00 3.11
1346 1386 0.625849 AGCATCGACCCCATTTCCTT 59.374 50.000 0.00 0.00 0.00 3.36
1347 1387 1.507140 TAGCATCGACCCCATTTCCT 58.493 50.000 0.00 0.00 0.00 3.36
1348 1388 2.341846 TTAGCATCGACCCCATTTCC 57.658 50.000 0.00 0.00 0.00 3.13
1349 1389 3.694566 AGTTTTAGCATCGACCCCATTTC 59.305 43.478 0.00 0.00 0.00 2.17
1350 1390 3.694566 GAGTTTTAGCATCGACCCCATTT 59.305 43.478 0.00 0.00 0.00 2.32
1351 1391 3.279434 GAGTTTTAGCATCGACCCCATT 58.721 45.455 0.00 0.00 0.00 3.16
1352 1392 2.238646 TGAGTTTTAGCATCGACCCCAT 59.761 45.455 0.00 0.00 0.00 4.00
1353 1393 1.626321 TGAGTTTTAGCATCGACCCCA 59.374 47.619 0.00 0.00 0.00 4.96
1354 1394 2.396590 TGAGTTTTAGCATCGACCCC 57.603 50.000 0.00 0.00 0.00 4.95
1355 1395 3.500680 TGTTTGAGTTTTAGCATCGACCC 59.499 43.478 0.00 0.00 0.00 4.46
1356 1396 4.213482 ACTGTTTGAGTTTTAGCATCGACC 59.787 41.667 0.00 0.00 0.00 4.79
1357 1397 5.344207 ACTGTTTGAGTTTTAGCATCGAC 57.656 39.130 0.00 0.00 0.00 4.20
1358 1398 5.049680 GGAACTGTTTGAGTTTTAGCATCGA 60.050 40.000 0.00 0.00 45.48 3.59
1359 1399 5.147162 GGAACTGTTTGAGTTTTAGCATCG 58.853 41.667 0.00 0.00 45.48 3.84
1360 1400 5.461526 GGGAACTGTTTGAGTTTTAGCATC 58.538 41.667 0.00 0.00 45.48 3.91
1361 1401 4.280929 GGGGAACTGTTTGAGTTTTAGCAT 59.719 41.667 0.00 0.00 45.48 3.79
1362 1402 3.634910 GGGGAACTGTTTGAGTTTTAGCA 59.365 43.478 0.00 0.00 45.48 3.49
1363 1403 3.634910 TGGGGAACTGTTTGAGTTTTAGC 59.365 43.478 0.00 0.00 45.48 3.09
1364 1404 5.130350 TCTGGGGAACTGTTTGAGTTTTAG 58.870 41.667 0.00 0.00 45.48 1.85
1365 1405 5.118729 TCTGGGGAACTGTTTGAGTTTTA 57.881 39.130 0.00 0.00 45.48 1.52
1366 1406 3.954258 CTCTGGGGAACTGTTTGAGTTTT 59.046 43.478 0.00 0.00 45.48 2.43
1367 1407 3.555966 CTCTGGGGAACTGTTTGAGTTT 58.444 45.455 0.00 0.00 45.48 2.66
1369 1409 1.421646 CCTCTGGGGAACTGTTTGAGT 59.578 52.381 0.00 0.00 37.23 3.41
1370 1410 2.191128 CCTCTGGGGAACTGTTTGAG 57.809 55.000 0.00 0.00 37.23 3.02
1390 1430 3.938637 CTCTTTCAACCCGGGGCCC 62.939 68.421 27.92 15.76 0.00 5.80
1391 1431 2.361230 CTCTTTCAACCCGGGGCC 60.361 66.667 27.92 0.00 0.00 5.80
1392 1432 3.062466 GCTCTTTCAACCCGGGGC 61.062 66.667 27.92 12.31 0.00 5.80
1393 1433 2.746277 CGCTCTTTCAACCCGGGG 60.746 66.667 27.92 12.73 0.00 5.73
1394 1434 1.741770 CTCGCTCTTTCAACCCGGG 60.742 63.158 22.25 22.25 0.00 5.73
1395 1435 2.391389 GCTCGCTCTTTCAACCCGG 61.391 63.158 0.00 0.00 0.00 5.73
1396 1436 0.108804 TAGCTCGCTCTTTCAACCCG 60.109 55.000 0.00 0.00 0.00 5.28
1397 1437 1.337823 TGTAGCTCGCTCTTTCAACCC 60.338 52.381 0.00 0.00 0.00 4.11
1398 1438 2.080286 TGTAGCTCGCTCTTTCAACC 57.920 50.000 0.00 0.00 0.00 3.77
1399 1439 3.929610 AGAATGTAGCTCGCTCTTTCAAC 59.070 43.478 0.00 0.00 0.00 3.18
1400 1440 4.193826 AGAATGTAGCTCGCTCTTTCAA 57.806 40.909 0.00 0.00 0.00 2.69
1401 1441 3.876274 AGAATGTAGCTCGCTCTTTCA 57.124 42.857 0.00 0.00 0.00 2.69
1402 1442 4.627467 TGAAAGAATGTAGCTCGCTCTTTC 59.373 41.667 21.84 21.84 46.32 2.62
1403 1443 4.569943 TGAAAGAATGTAGCTCGCTCTTT 58.430 39.130 10.93 10.93 38.67 2.52
1404 1444 4.193826 TGAAAGAATGTAGCTCGCTCTT 57.806 40.909 0.00 0.00 0.00 2.85
1405 1445 3.876274 TGAAAGAATGTAGCTCGCTCT 57.124 42.857 0.00 0.00 0.00 4.09
1406 1446 5.524284 TCTATGAAAGAATGTAGCTCGCTC 58.476 41.667 0.00 0.00 0.00 5.03
1407 1447 5.521906 TCTATGAAAGAATGTAGCTCGCT 57.478 39.130 0.00 0.00 0.00 4.93
1408 1448 5.980116 TCTTCTATGAAAGAATGTAGCTCGC 59.020 40.000 0.00 0.00 43.32 5.03
1409 1449 6.975197 TGTCTTCTATGAAAGAATGTAGCTCG 59.025 38.462 0.00 0.00 43.32 5.03
1410 1450 8.194104 TCTGTCTTCTATGAAAGAATGTAGCTC 58.806 37.037 0.00 0.00 43.32 4.09
1411 1451 8.072321 TCTGTCTTCTATGAAAGAATGTAGCT 57.928 34.615 0.00 0.00 43.32 3.32
1412 1452 8.709386 TTCTGTCTTCTATGAAAGAATGTAGC 57.291 34.615 0.00 0.00 43.32 3.58
1422 1462 9.877178 GTCCTCTTATTTTCTGTCTTCTATGAA 57.123 33.333 0.00 0.00 0.00 2.57
1423 1463 9.261035 AGTCCTCTTATTTTCTGTCTTCTATGA 57.739 33.333 0.00 0.00 0.00 2.15
1424 1464 9.311916 CAGTCCTCTTATTTTCTGTCTTCTATG 57.688 37.037 0.00 0.00 0.00 2.23
1425 1465 7.984617 GCAGTCCTCTTATTTTCTGTCTTCTAT 59.015 37.037 0.00 0.00 0.00 1.98
1426 1466 7.179338 AGCAGTCCTCTTATTTTCTGTCTTCTA 59.821 37.037 0.00 0.00 0.00 2.10
1427 1467 6.013812 AGCAGTCCTCTTATTTTCTGTCTTCT 60.014 38.462 0.00 0.00 0.00 2.85
1428 1468 6.091986 CAGCAGTCCTCTTATTTTCTGTCTTC 59.908 42.308 0.00 0.00 0.00 2.87
1433 1473 4.260170 AGCAGCAGTCCTCTTATTTTCTG 58.740 43.478 0.00 0.00 0.00 3.02
1437 1477 4.916183 AGAAAGCAGCAGTCCTCTTATTT 58.084 39.130 0.00 0.00 0.00 1.40
1439 1479 4.566426 AAGAAAGCAGCAGTCCTCTTAT 57.434 40.909 0.00 0.00 0.00 1.73
1443 1483 3.326836 AGTAAGAAAGCAGCAGTCCTC 57.673 47.619 0.00 0.00 0.00 3.71
1445 1485 3.403038 TGAAGTAAGAAAGCAGCAGTCC 58.597 45.455 0.00 0.00 0.00 3.85
1448 1488 5.876612 AAGATGAAGTAAGAAAGCAGCAG 57.123 39.130 0.00 0.00 0.00 4.24
1474 1514 9.872684 CCATAATTCCAATGCTATAATCCCTAT 57.127 33.333 0.00 0.00 0.00 2.57
1475 1515 9.067963 TCCATAATTCCAATGCTATAATCCCTA 57.932 33.333 0.00 0.00 0.00 3.53
1477 1517 8.593945 TTCCATAATTCCAATGCTATAATCCC 57.406 34.615 0.00 0.00 0.00 3.85
1484 1524 9.767228 CATTCAAATTCCATAATTCCAATGCTA 57.233 29.630 0.00 0.00 34.12 3.49
1486 1526 7.716123 TCCATTCAAATTCCATAATTCCAATGC 59.284 33.333 0.00 0.00 35.32 3.56
1487 1527 9.787435 ATCCATTCAAATTCCATAATTCCAATG 57.213 29.630 0.00 0.00 35.80 2.82
1489 1529 9.616156 CAATCCATTCAAATTCCATAATTCCAA 57.384 29.630 0.00 0.00 34.12 3.53
1490 1530 8.990203 TCAATCCATTCAAATTCCATAATTCCA 58.010 29.630 0.00 0.00 34.12 3.53
1491 1531 9.485206 CTCAATCCATTCAAATTCCATAATTCC 57.515 33.333 0.00 0.00 34.12 3.01
1495 1535 9.473007 TGTACTCAATCCATTCAAATTCCATAA 57.527 29.630 0.00 0.00 0.00 1.90
1496 1536 9.645128 ATGTACTCAATCCATTCAAATTCCATA 57.355 29.630 0.00 0.00 0.00 2.74
1497 1537 7.959658 TGTACTCAATCCATTCAAATTCCAT 57.040 32.000 0.00 0.00 0.00 3.41
1498 1538 7.614974 TGATGTACTCAATCCATTCAAATTCCA 59.385 33.333 0.00 0.00 0.00 3.53
1499 1539 7.999679 TGATGTACTCAATCCATTCAAATTCC 58.000 34.615 0.00 0.00 0.00 3.01
1500 1540 9.512435 CTTGATGTACTCAATCCATTCAAATTC 57.488 33.333 7.81 0.00 42.87 2.17
1501 1541 9.246670 TCTTGATGTACTCAATCCATTCAAATT 57.753 29.630 7.81 0.00 42.87 1.82
1502 1542 8.812513 TCTTGATGTACTCAATCCATTCAAAT 57.187 30.769 7.81 0.00 42.87 2.32
1504 1544 8.048514 TCATCTTGATGTACTCAATCCATTCAA 58.951 33.333 10.01 0.00 42.87 2.69
1506 1546 8.442632 TTCATCTTGATGTACTCAATCCATTC 57.557 34.615 10.01 0.00 42.87 2.67
1507 1547 8.270030 TCTTCATCTTGATGTACTCAATCCATT 58.730 33.333 10.01 0.00 42.87 3.16
1508 1548 7.799081 TCTTCATCTTGATGTACTCAATCCAT 58.201 34.615 10.01 0.00 42.87 3.41
1516 1698 9.436957 ACGTTAATTTCTTCATCTTGATGTACT 57.563 29.630 10.01 0.00 0.00 2.73
1544 1726 9.838339 ACCGAATCTTTTGAGAATATCACTTAT 57.162 29.630 0.00 0.00 37.77 1.73
1545 1727 9.314321 GACCGAATCTTTTGAGAATATCACTTA 57.686 33.333 0.00 0.00 37.77 2.24
1546 1728 7.824289 TGACCGAATCTTTTGAGAATATCACTT 59.176 33.333 0.00 0.00 37.77 3.16
1548 1730 7.539712 TGACCGAATCTTTTGAGAATATCAC 57.460 36.000 0.00 0.00 37.77 3.06
1551 1733 6.016777 GGCATGACCGAATCTTTTGAGAATAT 60.017 38.462 0.00 0.00 0.00 1.28
1552 1734 5.296780 GGCATGACCGAATCTTTTGAGAATA 59.703 40.000 0.00 0.00 0.00 1.75
1554 1736 3.440173 GGCATGACCGAATCTTTTGAGAA 59.560 43.478 0.00 0.00 0.00 2.87
1555 1737 3.009723 GGCATGACCGAATCTTTTGAGA 58.990 45.455 0.00 0.00 0.00 3.27
1556 1738 2.749076 TGGCATGACCGAATCTTTTGAG 59.251 45.455 0.00 0.00 43.94 3.02
1558 1740 2.749076 TCTGGCATGACCGAATCTTTTG 59.251 45.455 0.00 0.00 43.94 2.44
1563 1745 2.359900 AGTTTCTGGCATGACCGAATC 58.640 47.619 6.21 5.99 43.94 2.52
1564 1746 2.489329 CAAGTTTCTGGCATGACCGAAT 59.511 45.455 6.21 0.00 43.94 3.34
1566 1748 1.071542 TCAAGTTTCTGGCATGACCGA 59.928 47.619 0.00 0.00 43.94 4.69
1567 1749 1.197721 GTCAAGTTTCTGGCATGACCG 59.802 52.381 0.00 0.00 43.94 4.79
1569 1751 2.508526 AGGTCAAGTTTCTGGCATGAC 58.491 47.619 7.89 7.89 39.65 3.06
1570 1752 2.957402 AGGTCAAGTTTCTGGCATGA 57.043 45.000 0.00 0.00 0.00 3.07
1572 1754 4.640771 TCTAAGGTCAAGTTTCTGGCAT 57.359 40.909 0.00 0.00 0.00 4.40
1574 1756 4.134563 TGTTCTAAGGTCAAGTTTCTGGC 58.865 43.478 0.00 0.00 0.00 4.85
1575 1757 5.588648 TGTTGTTCTAAGGTCAAGTTTCTGG 59.411 40.000 0.00 0.00 0.00 3.86
1577 1759 5.823045 CCTGTTGTTCTAAGGTCAAGTTTCT 59.177 40.000 0.00 0.00 0.00 2.52
1579 1761 4.887655 CCCTGTTGTTCTAAGGTCAAGTTT 59.112 41.667 0.00 0.00 0.00 2.66
1580 1762 4.461198 CCCTGTTGTTCTAAGGTCAAGTT 58.539 43.478 0.00 0.00 0.00 2.66
1581 1763 3.181443 CCCCTGTTGTTCTAAGGTCAAGT 60.181 47.826 0.00 0.00 0.00 3.16
1592 1774 4.081322 TGAGTAGTTTCCCCTGTTGTTC 57.919 45.455 0.00 0.00 0.00 3.18
1611 1799 3.170717 CTCCCTAGTTACCACAGGTTGA 58.829 50.000 0.00 0.00 37.09 3.18
1623 1811 2.393646 CAGCTAGCTTCCTCCCTAGTT 58.606 52.381 16.46 0.00 34.81 2.24
1683 1931 0.169672 CCTGCTCAAGAAATGCCACG 59.830 55.000 0.00 0.00 0.00 4.94
1689 1937 1.891150 CACCTTGCCTGCTCAAGAAAT 59.109 47.619 13.07 0.16 44.61 2.17
1705 1971 2.955881 GCCCTGTACTTCCGCACCT 61.956 63.158 0.00 0.00 0.00 4.00
1710 1976 1.079127 CACCAGCCCTGTACTTCCG 60.079 63.158 0.00 0.00 0.00 4.30
1731 1997 0.321653 GGTTGCCCTGTGAATCTCGT 60.322 55.000 0.00 0.00 0.00 4.18
1737 2003 4.843728 CTCTAATTAGGTTGCCCTGTGAA 58.156 43.478 12.54 0.00 42.67 3.18
1741 2007 2.213499 CGCTCTAATTAGGTTGCCCTG 58.787 52.381 12.54 0.51 42.67 4.45
1794 2105 2.739292 GCGTATAGCTCCATCGTTTGA 58.261 47.619 0.00 0.00 44.04 2.69
1965 3727 4.472833 AGAACACAGCTCATAAATCCTCCT 59.527 41.667 0.00 0.00 0.00 3.69
1998 3760 1.673923 GCTTCATTGGCTTCCCTTTGC 60.674 52.381 0.00 0.00 0.00 3.68
2001 3763 1.553706 CTGCTTCATTGGCTTCCCTT 58.446 50.000 0.00 0.00 0.00 3.95
2019 4084 1.530013 GCTTTGCACACTGATGGCCT 61.530 55.000 3.32 0.00 0.00 5.19
2021 4086 0.032403 TTGCTTTGCACACTGATGGC 59.968 50.000 0.00 0.00 38.71 4.40
2043 4108 4.871871 ACATCTCCTCCTCTCTTCTGTA 57.128 45.455 0.00 0.00 0.00 2.74
2099 4624 1.400737 AGGCGCGTTTCCTATCTAGT 58.599 50.000 8.43 0.00 30.79 2.57


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

AutoCloner maintained by Alex Coulton.