Multiple sequence alignment - TraesCS3B01G061300

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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 TraesCS3B01G061300 chr3B 100.000 2275 0 0 1 2275 33098932 33096658 0.000000e+00 4202.0
1 TraesCS3B01G061300 chr3B 93.272 327 22 0 1949 2275 32991995 32991669 1.220000e-132 483.0
2 TraesCS3B01G061300 chr3B 83.432 338 44 8 1941 2275 33299096 33298768 1.020000e-78 303.0
3 TraesCS3B01G061300 chr7B 96.777 1303 36 2 1 1303 503279660 503280956 0.000000e+00 2169.0
4 TraesCS3B01G061300 chr7B 77.273 286 37 27 1339 1608 254679680 254679407 2.360000e-30 143.0
5 TraesCS3B01G061300 chr7B 76.408 284 39 26 1339 1608 254678466 254678197 6.600000e-26 128.0
6 TraesCS3B01G061300 chr2B 93.654 1308 78 3 1 1307 1653178 1651875 0.000000e+00 1951.0
7 TraesCS3B01G061300 chr2B 89.820 167 7 6 1358 1519 763054362 763054201 2.960000e-49 206.0
8 TraesCS3B01G061300 chr4B 93.027 1305 89 1 1 1305 661249021 661247719 0.000000e+00 1905.0
9 TraesCS3B01G061300 chr4B 86.634 202 17 9 1320 1519 624475251 624475058 4.920000e-52 215.0
10 TraesCS3B01G061300 chr5D 90.483 1303 121 3 1 1303 332802660 332803959 0.000000e+00 1716.0
11 TraesCS3B01G061300 chr5D 89.759 166 11 5 1356 1519 97369198 97369037 8.240000e-50 207.0
12 TraesCS3B01G061300 chr5D 89.157 166 12 5 1356 1519 97357482 97357321 3.830000e-48 202.0
13 TraesCS3B01G061300 chr2D 90.038 1305 123 6 1 1304 132690767 132689469 0.000000e+00 1683.0
14 TraesCS3B01G061300 chr6A 89.695 1310 133 1 1 1310 612193841 612192534 0.000000e+00 1670.0
15 TraesCS3B01G061300 chr1A 89.647 1304 132 3 1 1304 492268559 492269859 0.000000e+00 1657.0
16 TraesCS3B01G061300 chr6B 89.661 1209 120 4 1 1208 647476310 647475106 0.000000e+00 1535.0
17 TraesCS3B01G061300 chr3D 87.107 1303 164 3 2 1304 553376258 553374960 0.000000e+00 1472.0
18 TraesCS3B01G061300 chr3D 86.386 617 40 14 1688 2275 20708653 20708052 3.190000e-178 634.0
19 TraesCS3B01G061300 chr3A 84.017 707 67 28 1613 2275 28231777 28231073 2.460000e-179 638.0
20 TraesCS3B01G061300 chr3A 87.356 348 31 5 1939 2275 28322786 28322441 9.860000e-104 387.0
21 TraesCS3B01G061300 chr3A 78.779 344 55 10 1941 2275 28391317 28390983 4.920000e-52 215.0
22 TraesCS3B01G061300 chr3A 83.333 192 16 10 1741 1925 28391563 28391381 1.810000e-36 163.0
23 TraesCS3B01G061300 chr3A 90.769 65 4 2 1544 1608 750642452 750642514 4.030000e-13 86.1


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 TraesCS3B01G061300 chr3B 33096658 33098932 2274 True 4202 4202 100.000 1 2275 1 chr3B.!!$R2 2274
1 TraesCS3B01G061300 chr7B 503279660 503280956 1296 False 2169 2169 96.777 1 1303 1 chr7B.!!$F1 1302
2 TraesCS3B01G061300 chr2B 1651875 1653178 1303 True 1951 1951 93.654 1 1307 1 chr2B.!!$R1 1306
3 TraesCS3B01G061300 chr4B 661247719 661249021 1302 True 1905 1905 93.027 1 1305 1 chr4B.!!$R2 1304
4 TraesCS3B01G061300 chr5D 332802660 332803959 1299 False 1716 1716 90.483 1 1303 1 chr5D.!!$F1 1302
5 TraesCS3B01G061300 chr2D 132689469 132690767 1298 True 1683 1683 90.038 1 1304 1 chr2D.!!$R1 1303
6 TraesCS3B01G061300 chr6A 612192534 612193841 1307 True 1670 1670 89.695 1 1310 1 chr6A.!!$R1 1309
7 TraesCS3B01G061300 chr1A 492268559 492269859 1300 False 1657 1657 89.647 1 1304 1 chr1A.!!$F1 1303
8 TraesCS3B01G061300 chr6B 647475106 647476310 1204 True 1535 1535 89.661 1 1208 1 chr6B.!!$R1 1207
9 TraesCS3B01G061300 chr3D 553374960 553376258 1298 True 1472 1472 87.107 2 1304 1 chr3D.!!$R2 1302
10 TraesCS3B01G061300 chr3D 20708052 20708653 601 True 634 634 86.386 1688 2275 1 chr3D.!!$R1 587
11 TraesCS3B01G061300 chr3A 28231073 28231777 704 True 638 638 84.017 1613 2275 1 chr3A.!!$R1 662

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
622 623 0.693049 AGAGAGTGACCGGGCAAAAT 59.307 50.0 14.43 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1874 0.034896 GAGTAGTGGTGGTGGTGGTG 59.965 60.0 0.0 0.0 0.0 4.17 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
402 403 1.821136 GGCATCCTTCCAGTGGAAAAG 59.179 52.381 24.59 18.42 41.54 2.27
409 410 4.410883 TCCTTCCAGTGGAAAAGACACTAA 59.589 41.667 24.59 0.00 46.76 2.24
622 623 0.693049 AGAGAGTGACCGGGCAAAAT 59.307 50.000 14.43 0.00 0.00 1.82
878 879 1.371558 GAGTGGCACGGACTTCCTT 59.628 57.895 12.71 0.00 0.00 3.36
951 952 3.518998 GCCGAGGCGTCTGCTCTA 61.519 66.667 14.55 0.00 42.25 2.43
964 965 2.045524 CTGCTCTATGAGATGGGGTGT 58.954 52.381 0.00 0.00 0.00 4.16
1045 1046 1.300465 CAGCTATGGCACTCGCGAT 60.300 57.895 10.36 0.00 41.70 4.58
1131 1132 7.990541 TCTTTCTTTTGATGTTCAACATGTG 57.009 32.000 8.05 0.00 39.27 3.21
1132 1133 7.546358 TCTTTCTTTTGATGTTCAACATGTGT 58.454 30.769 8.05 0.00 39.27 3.72
1144 1145 6.597672 TGTTCAACATGTGTACTGAGAAACTT 59.402 34.615 0.00 0.00 0.00 2.66
1239 1244 1.300963 GGCTTCCTCATGACCAGCA 59.699 57.895 14.86 0.00 31.71 4.41
1261 1266 2.203070 GGCTGATCGTGCGGGAAT 60.203 61.111 4.75 0.00 0.00 3.01
1321 1326 1.675552 AAAAAGGGTCGTGTGAGTGG 58.324 50.000 0.00 0.00 0.00 4.00
1322 1327 0.179029 AAAAGGGTCGTGTGAGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
1323 1328 2.676163 AAAGGGTCGTGTGAGTGGGC 62.676 60.000 0.00 0.00 0.00 5.36
1324 1329 3.626924 GGGTCGTGTGAGTGGGCT 61.627 66.667 0.00 0.00 0.00 5.19
1325 1330 2.280552 GGGTCGTGTGAGTGGGCTA 61.281 63.158 0.00 0.00 0.00 3.93
1326 1331 1.669440 GGTCGTGTGAGTGGGCTAA 59.331 57.895 0.00 0.00 0.00 3.09
1327 1332 0.249398 GGTCGTGTGAGTGGGCTAAT 59.751 55.000 0.00 0.00 0.00 1.73
1328 1333 1.641577 GTCGTGTGAGTGGGCTAATC 58.358 55.000 0.00 0.00 0.00 1.75
1329 1334 1.204941 GTCGTGTGAGTGGGCTAATCT 59.795 52.381 0.00 0.00 0.00 2.40
1330 1335 1.476891 TCGTGTGAGTGGGCTAATCTC 59.523 52.381 0.00 0.00 0.00 2.75
1331 1336 1.478510 CGTGTGAGTGGGCTAATCTCT 59.521 52.381 0.00 0.00 0.00 3.10
1332 1337 2.480416 CGTGTGAGTGGGCTAATCTCTC 60.480 54.545 0.00 0.00 0.00 3.20
1333 1338 2.111384 TGTGAGTGGGCTAATCTCTCC 58.889 52.381 0.00 0.00 0.00 3.71
1334 1339 2.292521 TGTGAGTGGGCTAATCTCTCCT 60.293 50.000 0.00 0.00 0.00 3.69
1335 1340 2.102252 GTGAGTGGGCTAATCTCTCCTG 59.898 54.545 0.00 0.00 0.00 3.86
1336 1341 2.292521 TGAGTGGGCTAATCTCTCCTGT 60.293 50.000 0.00 0.00 0.00 4.00
1337 1342 2.102252 GAGTGGGCTAATCTCTCCTGTG 59.898 54.545 0.00 0.00 0.00 3.66
1338 1343 1.834263 GTGGGCTAATCTCTCCTGTGT 59.166 52.381 0.00 0.00 0.00 3.72
1339 1344 3.031736 GTGGGCTAATCTCTCCTGTGTA 58.968 50.000 0.00 0.00 0.00 2.90
1340 1345 3.643792 GTGGGCTAATCTCTCCTGTGTAT 59.356 47.826 0.00 0.00 0.00 2.29
1341 1346 4.833380 GTGGGCTAATCTCTCCTGTGTATA 59.167 45.833 0.00 0.00 0.00 1.47
1342 1347 5.304614 GTGGGCTAATCTCTCCTGTGTATAA 59.695 44.000 0.00 0.00 0.00 0.98
1343 1348 5.540337 TGGGCTAATCTCTCCTGTGTATAAG 59.460 44.000 0.00 0.00 0.00 1.73
1344 1349 5.540719 GGGCTAATCTCTCCTGTGTATAAGT 59.459 44.000 0.00 0.00 0.00 2.24
1345 1350 6.720288 GGGCTAATCTCTCCTGTGTATAAGTA 59.280 42.308 0.00 0.00 0.00 2.24
1346 1351 7.397761 GGGCTAATCTCTCCTGTGTATAAGTAT 59.602 40.741 0.00 0.00 0.00 2.12
1347 1352 8.463607 GGCTAATCTCTCCTGTGTATAAGTATC 58.536 40.741 0.00 0.00 0.00 2.24
1348 1353 8.463607 GCTAATCTCTCCTGTGTATAAGTATCC 58.536 40.741 0.00 0.00 0.00 2.59
1349 1354 7.784470 AATCTCTCCTGTGTATAAGTATCCC 57.216 40.000 0.00 0.00 0.00 3.85
1350 1355 6.532119 TCTCTCCTGTGTATAAGTATCCCT 57.468 41.667 0.00 0.00 0.00 4.20
1351 1356 6.923670 TCTCTCCTGTGTATAAGTATCCCTT 58.076 40.000 0.00 0.00 37.17 3.95
1352 1357 6.778069 TCTCTCCTGTGTATAAGTATCCCTTG 59.222 42.308 0.00 0.00 34.46 3.61
1353 1358 6.679542 TCTCCTGTGTATAAGTATCCCTTGA 58.320 40.000 0.00 0.00 34.46 3.02
1354 1359 6.778069 TCTCCTGTGTATAAGTATCCCTTGAG 59.222 42.308 0.00 0.00 34.46 3.02
1355 1360 6.441222 TCCTGTGTATAAGTATCCCTTGAGT 58.559 40.000 0.00 0.00 34.46 3.41
1356 1361 6.901300 TCCTGTGTATAAGTATCCCTTGAGTT 59.099 38.462 0.00 0.00 34.46 3.01
1357 1362 8.063153 TCCTGTGTATAAGTATCCCTTGAGTTA 58.937 37.037 0.00 0.00 34.46 2.24
1358 1363 8.701895 CCTGTGTATAAGTATCCCTTGAGTTAA 58.298 37.037 0.00 0.00 34.46 2.01
1366 1371 8.794335 AAGTATCCCTTGAGTTAATGAGAAAC 57.206 34.615 0.00 0.00 30.18 2.78
1367 1372 7.918076 AGTATCCCTTGAGTTAATGAGAAACA 58.082 34.615 0.00 0.00 0.00 2.83
1368 1373 8.043710 AGTATCCCTTGAGTTAATGAGAAACAG 58.956 37.037 0.00 0.00 0.00 3.16
1369 1374 6.433847 TCCCTTGAGTTAATGAGAAACAGA 57.566 37.500 0.00 0.00 0.00 3.41
1370 1375 6.467677 TCCCTTGAGTTAATGAGAAACAGAG 58.532 40.000 0.00 0.00 0.00 3.35
1371 1376 6.270000 TCCCTTGAGTTAATGAGAAACAGAGA 59.730 38.462 0.00 0.00 0.00 3.10
1372 1377 6.593382 CCCTTGAGTTAATGAGAAACAGAGAG 59.407 42.308 0.00 0.00 0.00 3.20
1373 1378 6.593382 CCTTGAGTTAATGAGAAACAGAGAGG 59.407 42.308 0.00 0.00 0.00 3.69
1374 1379 5.482908 TGAGTTAATGAGAAACAGAGAGGC 58.517 41.667 0.00 0.00 0.00 4.70
1375 1380 4.837972 AGTTAATGAGAAACAGAGAGGCC 58.162 43.478 0.00 0.00 0.00 5.19
1376 1381 2.393271 AATGAGAAACAGAGAGGCCG 57.607 50.000 0.00 0.00 0.00 6.13
1377 1382 1.270907 ATGAGAAACAGAGAGGCCGT 58.729 50.000 0.00 0.00 0.00 5.68
1378 1383 0.318441 TGAGAAACAGAGAGGCCGTG 59.682 55.000 0.00 0.00 0.00 4.94
1379 1384 0.603569 GAGAAACAGAGAGGCCGTGA 59.396 55.000 0.00 0.00 0.00 4.35
1380 1385 0.605589 AGAAACAGAGAGGCCGTGAG 59.394 55.000 0.00 0.00 0.00 3.51
1392 1397 3.385384 CGTGAGGGCTGAGGCAGA 61.385 66.667 8.68 0.00 40.87 4.26
1393 1398 2.947532 CGTGAGGGCTGAGGCAGAA 61.948 63.158 8.68 0.00 40.87 3.02
1394 1399 1.376466 GTGAGGGCTGAGGCAGAAA 59.624 57.895 8.68 0.00 40.87 2.52
1395 1400 0.250901 GTGAGGGCTGAGGCAGAAAA 60.251 55.000 8.68 0.00 40.87 2.29
1396 1401 0.250901 TGAGGGCTGAGGCAGAAAAC 60.251 55.000 8.68 0.00 40.87 2.43
1397 1402 0.250901 GAGGGCTGAGGCAGAAAACA 60.251 55.000 8.68 0.00 40.87 2.83
1398 1403 0.185901 AGGGCTGAGGCAGAAAACAA 59.814 50.000 8.68 0.00 40.87 2.83
1399 1404 1.203100 AGGGCTGAGGCAGAAAACAAT 60.203 47.619 8.68 0.00 40.87 2.71
1400 1405 1.067354 GGGCTGAGGCAGAAAACAATG 60.067 52.381 8.68 0.00 40.87 2.82
1401 1406 1.615392 GGCTGAGGCAGAAAACAATGT 59.385 47.619 0.00 0.00 40.87 2.71
1402 1407 2.819608 GGCTGAGGCAGAAAACAATGTA 59.180 45.455 0.00 0.00 40.87 2.29
1403 1408 3.119708 GGCTGAGGCAGAAAACAATGTAG 60.120 47.826 0.00 0.00 40.87 2.74
1404 1409 3.671702 GCTGAGGCAGAAAACAATGTAGC 60.672 47.826 0.00 0.00 38.54 3.58
1405 1410 2.483877 TGAGGCAGAAAACAATGTAGCG 59.516 45.455 0.00 0.00 0.00 4.26
1406 1411 1.200020 AGGCAGAAAACAATGTAGCGC 59.800 47.619 0.00 0.00 0.00 5.92
1407 1412 1.200020 GGCAGAAAACAATGTAGCGCT 59.800 47.619 17.26 17.26 0.00 5.92
1408 1413 2.351738 GGCAGAAAACAATGTAGCGCTT 60.352 45.455 18.68 0.00 0.00 4.68
1409 1414 2.658325 GCAGAAAACAATGTAGCGCTTG 59.342 45.455 18.68 10.84 0.00 4.01
1410 1415 3.853307 GCAGAAAACAATGTAGCGCTTGT 60.853 43.478 18.68 11.65 37.19 3.16
1411 1416 3.665409 CAGAAAACAATGTAGCGCTTGTG 59.335 43.478 18.68 11.49 35.82 3.33
1412 1417 3.315191 AGAAAACAATGTAGCGCTTGTGT 59.685 39.130 18.68 12.20 35.82 3.72
1413 1418 2.686558 AACAATGTAGCGCTTGTGTG 57.313 45.000 18.68 12.27 35.82 3.82
1414 1419 1.877637 ACAATGTAGCGCTTGTGTGA 58.122 45.000 18.68 0.00 34.43 3.58
1415 1420 1.531149 ACAATGTAGCGCTTGTGTGAC 59.469 47.619 18.68 7.09 34.43 3.67
1416 1421 1.530720 CAATGTAGCGCTTGTGTGACA 59.469 47.619 18.68 13.83 0.00 3.58
1417 1422 1.432514 ATGTAGCGCTTGTGTGACAG 58.567 50.000 18.68 0.00 0.00 3.51
1418 1423 0.599991 TGTAGCGCTTGTGTGACAGG 60.600 55.000 18.68 0.00 0.00 4.00
1419 1424 0.319555 GTAGCGCTTGTGTGACAGGA 60.320 55.000 18.68 0.00 0.00 3.86
1420 1425 0.038251 TAGCGCTTGTGTGACAGGAG 60.038 55.000 18.68 0.00 0.00 3.69
1421 1426 2.320587 GCGCTTGTGTGACAGGAGG 61.321 63.158 0.00 0.00 0.00 4.30
1422 1427 1.367471 CGCTTGTGTGACAGGAGGA 59.633 57.895 0.00 0.00 0.00 3.71
1423 1428 0.668706 CGCTTGTGTGACAGGAGGAG 60.669 60.000 0.00 0.00 0.00 3.69
1424 1429 0.681733 GCTTGTGTGACAGGAGGAGA 59.318 55.000 0.00 0.00 0.00 3.71
1425 1430 1.337635 GCTTGTGTGACAGGAGGAGAG 60.338 57.143 0.00 0.00 0.00 3.20
1426 1431 0.681733 TTGTGTGACAGGAGGAGAGC 59.318 55.000 0.00 0.00 0.00 4.09
1427 1432 1.188219 TGTGTGACAGGAGGAGAGCC 61.188 60.000 0.00 0.00 0.00 4.70
1446 1451 3.515330 CCTCTTGGCAAAGCTAATTGG 57.485 47.619 0.00 0.00 33.06 3.16
1456 1461 2.443958 AGCTAATTGGCTTCCTTCCC 57.556 50.000 10.99 0.00 39.86 3.97
1457 1462 1.925959 AGCTAATTGGCTTCCTTCCCT 59.074 47.619 10.99 0.00 39.86 4.20
1458 1463 2.027385 GCTAATTGGCTTCCTTCCCTG 58.973 52.381 6.53 0.00 0.00 4.45
1459 1464 2.659428 CTAATTGGCTTCCTTCCCTGG 58.341 52.381 0.00 0.00 0.00 4.45
1460 1465 0.786435 AATTGGCTTCCTTCCCTGGT 59.214 50.000 0.00 0.00 0.00 4.00
1461 1466 1.681229 ATTGGCTTCCTTCCCTGGTA 58.319 50.000 0.00 0.00 0.00 3.25
1462 1467 0.696501 TTGGCTTCCTTCCCTGGTAC 59.303 55.000 0.00 0.00 0.00 3.34
1463 1468 0.474854 TGGCTTCCTTCCCTGGTACA 60.475 55.000 0.00 0.00 0.00 2.90
1464 1469 0.919710 GGCTTCCTTCCCTGGTACAT 59.080 55.000 0.00 0.00 38.20 2.29
1465 1470 1.408822 GGCTTCCTTCCCTGGTACATG 60.409 57.143 0.00 0.00 38.20 3.21
1466 1471 2.019156 GCTTCCTTCCCTGGTACATGC 61.019 57.143 0.00 0.00 38.20 4.06
1467 1472 0.251916 TTCCTTCCCTGGTACATGCG 59.748 55.000 0.00 0.00 38.20 4.73
1468 1473 0.907704 TCCTTCCCTGGTACATGCGT 60.908 55.000 0.00 0.00 38.20 5.24
1469 1474 0.744414 CCTTCCCTGGTACATGCGTG 60.744 60.000 3.82 3.82 38.20 5.34
1470 1475 1.369091 CTTCCCTGGTACATGCGTGC 61.369 60.000 5.64 0.00 38.20 5.34
1471 1476 3.195002 CCCTGGTACATGCGTGCG 61.195 66.667 5.64 0.00 38.20 5.34
1472 1477 2.434185 CCTGGTACATGCGTGCGT 60.434 61.111 5.64 0.00 38.20 5.24
1473 1478 2.739704 CCTGGTACATGCGTGCGTG 61.740 63.158 12.31 12.31 38.20 5.34
1474 1479 2.027073 CTGGTACATGCGTGCGTGT 61.027 57.895 21.91 21.91 46.53 4.49
1475 1480 2.226712 CTGGTACATGCGTGCGTGTG 62.227 60.000 25.62 8.57 44.79 3.82
1476 1481 2.314647 GGTACATGCGTGCGTGTGT 61.315 57.895 25.62 14.25 44.79 3.72
1477 1482 1.154672 GTACATGCGTGCGTGTGTG 60.155 57.895 25.62 5.02 44.79 3.82
1478 1483 1.592939 TACATGCGTGCGTGTGTGT 60.593 52.632 25.62 9.97 44.79 3.72
1479 1484 1.826299 TACATGCGTGCGTGTGTGTG 61.826 55.000 25.62 0.00 44.79 3.82
1480 1485 2.894879 ATGCGTGCGTGTGTGTGT 60.895 55.556 0.00 0.00 0.00 3.72
1481 1486 3.166953 ATGCGTGCGTGTGTGTGTG 62.167 57.895 0.00 0.00 0.00 3.82
1482 1487 3.860125 GCGTGCGTGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
1483 1488 2.781957 CGTGCGTGTGTGTGTGTT 59.218 55.556 0.00 0.00 0.00 3.32
1484 1489 1.133664 CGTGCGTGTGTGTGTGTTT 59.866 52.632 0.00 0.00 0.00 2.83
1485 1490 0.855670 CGTGCGTGTGTGTGTGTTTC 60.856 55.000 0.00 0.00 0.00 2.78
1486 1491 0.446222 GTGCGTGTGTGTGTGTTTCT 59.554 50.000 0.00 0.00 0.00 2.52
1487 1492 0.724549 TGCGTGTGTGTGTGTTTCTC 59.275 50.000 0.00 0.00 0.00 2.87
1488 1493 0.724549 GCGTGTGTGTGTGTTTCTCA 59.275 50.000 0.00 0.00 0.00 3.27
1489 1494 1.267532 GCGTGTGTGTGTGTTTCTCAG 60.268 52.381 0.00 0.00 0.00 3.35
1490 1495 1.999735 CGTGTGTGTGTGTTTCTCAGT 59.000 47.619 0.00 0.00 0.00 3.41
1491 1496 2.415168 CGTGTGTGTGTGTTTCTCAGTT 59.585 45.455 0.00 0.00 0.00 3.16
1492 1497 3.120338 CGTGTGTGTGTGTTTCTCAGTTT 60.120 43.478 0.00 0.00 0.00 2.66
1493 1498 4.612712 CGTGTGTGTGTGTTTCTCAGTTTT 60.613 41.667 0.00 0.00 0.00 2.43
1494 1499 5.219633 GTGTGTGTGTGTTTCTCAGTTTTT 58.780 37.500 0.00 0.00 0.00 1.94
1513 1518 4.981806 TTTTCCTTGGAGTGTGTTCTTG 57.018 40.909 0.00 0.00 0.00 3.02
1514 1519 3.924114 TTCCTTGGAGTGTGTTCTTGA 57.076 42.857 0.00 0.00 0.00 3.02
1515 1520 3.475566 TCCTTGGAGTGTGTTCTTGAG 57.524 47.619 0.00 0.00 0.00 3.02
1516 1521 3.038280 TCCTTGGAGTGTGTTCTTGAGA 58.962 45.455 0.00 0.00 0.00 3.27
1517 1522 3.070159 TCCTTGGAGTGTGTTCTTGAGAG 59.930 47.826 0.00 0.00 0.00 3.20
1518 1523 3.070159 CCTTGGAGTGTGTTCTTGAGAGA 59.930 47.826 0.00 0.00 0.00 3.10
1519 1524 4.262808 CCTTGGAGTGTGTTCTTGAGAGAT 60.263 45.833 0.00 0.00 0.00 2.75
1520 1525 5.047021 CCTTGGAGTGTGTTCTTGAGAGATA 60.047 44.000 0.00 0.00 0.00 1.98
1521 1526 6.351711 CCTTGGAGTGTGTTCTTGAGAGATAT 60.352 42.308 0.00 0.00 0.00 1.63
1522 1527 7.147828 CCTTGGAGTGTGTTCTTGAGAGATATA 60.148 40.741 0.00 0.00 0.00 0.86
1523 1528 7.904558 TGGAGTGTGTTCTTGAGAGATATAT 57.095 36.000 0.00 0.00 0.00 0.86
1524 1529 8.996651 TGGAGTGTGTTCTTGAGAGATATATA 57.003 34.615 0.00 0.00 0.00 0.86
1525 1530 9.593565 TGGAGTGTGTTCTTGAGAGATATATAT 57.406 33.333 0.00 0.00 0.00 0.86
1548 1553 9.812347 ATATAGAGAGAGAAACATCATGAGAGT 57.188 33.333 0.09 0.00 0.00 3.24
1549 1554 6.855763 AGAGAGAGAAACATCATGAGAGTT 57.144 37.500 9.77 9.77 0.00 3.01
1550 1555 6.632909 AGAGAGAGAAACATCATGAGAGTTG 58.367 40.000 14.80 5.00 0.00 3.16
1551 1556 6.211184 AGAGAGAGAAACATCATGAGAGTTGT 59.789 38.462 14.80 5.60 0.00 3.32
1552 1557 6.164876 AGAGAGAAACATCATGAGAGTTGTG 58.835 40.000 14.80 3.99 0.00 3.33
1553 1558 4.694509 AGAGAAACATCATGAGAGTTGTGC 59.305 41.667 14.80 9.13 0.00 4.57
1554 1559 4.649692 AGAAACATCATGAGAGTTGTGCT 58.350 39.130 14.80 10.72 0.00 4.40
1555 1560 5.798132 AGAAACATCATGAGAGTTGTGCTA 58.202 37.500 14.80 0.00 0.00 3.49
1556 1561 5.873712 AGAAACATCATGAGAGTTGTGCTAG 59.126 40.000 14.80 0.00 0.00 3.42
1557 1562 4.134379 ACATCATGAGAGTTGTGCTAGG 57.866 45.455 0.09 0.00 0.00 3.02
1558 1563 2.680312 TCATGAGAGTTGTGCTAGGC 57.320 50.000 0.00 0.00 0.00 3.93
1559 1564 1.901833 TCATGAGAGTTGTGCTAGGCA 59.098 47.619 0.00 0.00 35.60 4.75
1560 1565 2.093816 TCATGAGAGTTGTGCTAGGCAG 60.094 50.000 0.00 0.00 40.08 4.85
1569 1574 3.211288 GCTAGGCAGCTCGAGGAA 58.789 61.111 15.58 0.00 44.93 3.36
1570 1575 1.067250 GCTAGGCAGCTCGAGGAAG 59.933 63.158 15.58 0.00 44.93 3.46
1571 1576 1.388065 GCTAGGCAGCTCGAGGAAGA 61.388 60.000 15.58 0.00 44.93 2.87
1572 1577 1.107114 CTAGGCAGCTCGAGGAAGAA 58.893 55.000 15.58 0.00 0.00 2.52
1573 1578 1.066908 CTAGGCAGCTCGAGGAAGAAG 59.933 57.143 15.58 0.00 0.00 2.85
1574 1579 0.613292 AGGCAGCTCGAGGAAGAAGA 60.613 55.000 15.58 0.00 0.00 2.87
1575 1580 0.247736 GGCAGCTCGAGGAAGAAGAA 59.752 55.000 15.58 0.00 0.00 2.52
1576 1581 1.639280 GCAGCTCGAGGAAGAAGAAG 58.361 55.000 15.58 0.00 0.00 2.85
1577 1582 1.203523 GCAGCTCGAGGAAGAAGAAGA 59.796 52.381 15.58 0.00 0.00 2.87
1578 1583 2.735126 GCAGCTCGAGGAAGAAGAAGAG 60.735 54.545 15.58 0.00 0.00 2.85
1579 1584 1.921243 GCTCGAGGAAGAAGAAGAGC 58.079 55.000 15.58 0.00 43.11 4.09
1580 1585 1.797348 GCTCGAGGAAGAAGAAGAGCG 60.797 57.143 15.58 0.00 41.03 5.03
1581 1586 0.811915 TCGAGGAAGAAGAAGAGCGG 59.188 55.000 0.00 0.00 0.00 5.52
1582 1587 0.804156 CGAGGAAGAAGAAGAGCGGC 60.804 60.000 0.00 0.00 0.00 6.53
1583 1588 0.804156 GAGGAAGAAGAAGAGCGGCG 60.804 60.000 0.51 0.51 0.00 6.46
1584 1589 2.456948 GGAAGAAGAAGAGCGGCGC 61.457 63.158 26.86 26.86 0.00 6.53
1585 1590 1.446966 GAAGAAGAAGAGCGGCGCT 60.447 57.895 37.11 37.11 43.88 5.92
1586 1591 1.691215 GAAGAAGAAGAGCGGCGCTG 61.691 60.000 41.51 13.18 39.88 5.18
1587 1592 3.858989 GAAGAAGAGCGGCGCTGC 61.859 66.667 41.51 33.71 39.88 5.25
1657 1662 2.504244 CTGACGACCCGAAGACGC 60.504 66.667 0.00 0.00 38.29 5.19
1703 1709 1.066071 TCACAAGGTGTTGGACGAACA 60.066 47.619 0.00 0.00 42.55 3.18
1771 1777 0.875059 GAACCCGGACTCTGCTTTTG 59.125 55.000 0.73 0.00 0.00 2.44
1779 1785 4.587436 GGACTCTGCTTTTGCTAGGCCT 62.587 54.545 11.78 11.78 46.80 5.19
1785 1805 0.915364 CTTTTGCTAGGCCTCCTCCT 59.085 55.000 9.68 0.00 40.21 3.69
1798 1818 2.050351 CTCCTCACACGTCGCGTT 60.050 61.111 5.77 0.00 38.32 4.84
1826 1846 3.432051 CTCATCGTCTCGGCACCCC 62.432 68.421 0.00 0.00 0.00 4.95
1845 1865 2.963782 CCCGAGCATATATACCCCTACC 59.036 54.545 0.00 0.00 0.00 3.18
1846 1866 3.629025 CCCGAGCATATATACCCCTACCA 60.629 52.174 0.00 0.00 0.00 3.25
1847 1867 3.383825 CCGAGCATATATACCCCTACCAC 59.616 52.174 0.00 0.00 0.00 4.16
1848 1868 3.383825 CGAGCATATATACCCCTACCACC 59.616 52.174 0.00 0.00 0.00 4.61
1849 1869 4.359105 GAGCATATATACCCCTACCACCA 58.641 47.826 0.00 0.00 0.00 4.17
1850 1870 4.101856 AGCATATATACCCCTACCACCAC 58.898 47.826 0.00 0.00 0.00 4.16
1851 1871 3.841845 GCATATATACCCCTACCACCACA 59.158 47.826 0.00 0.00 0.00 4.17
1852 1872 4.287585 GCATATATACCCCTACCACCACAA 59.712 45.833 0.00 0.00 0.00 3.33
1853 1873 5.801380 CATATATACCCCTACCACCACAAC 58.199 45.833 0.00 0.00 0.00 3.32
1854 1874 1.292085 ATACCCCTACCACCACAACC 58.708 55.000 0.00 0.00 0.00 3.77
1855 1875 0.104567 TACCCCTACCACCACAACCA 60.105 55.000 0.00 0.00 0.00 3.67
1856 1876 1.074248 CCCCTACCACCACAACCAC 59.926 63.158 0.00 0.00 0.00 4.16
1857 1877 1.074248 CCCTACCACCACAACCACC 59.926 63.158 0.00 0.00 0.00 4.61
1858 1878 1.710996 CCCTACCACCACAACCACCA 61.711 60.000 0.00 0.00 0.00 4.17
1859 1879 0.536460 CCTACCACCACAACCACCAC 60.536 60.000 0.00 0.00 0.00 4.16
1900 1920 0.835941 ACAGCCAGATAAGCCTCCTG 59.164 55.000 0.00 0.00 0.00 3.86
1919 1939 1.039233 GGGTGCACATCCAATCCAGG 61.039 60.000 20.43 0.00 0.00 4.45
1946 2020 2.743928 CAGGAAGTCCGCCAGCAC 60.744 66.667 0.00 0.00 42.08 4.40
2105 2182 3.691342 CCTCCGACCACAAGCCGA 61.691 66.667 0.00 0.00 0.00 5.54
2141 2218 0.972471 TCAGCGGGCTCTTGATGAGA 60.972 55.000 0.00 0.00 45.39 3.27
2149 2226 0.179062 CTCTTGATGAGAAGGGGCGG 60.179 60.000 0.00 0.00 45.39 6.13
2237 2314 0.595567 CTATTACGCCGCCTACGCAA 60.596 55.000 0.00 0.00 38.22 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.148310 CCACGACCAGTTCACATCAC 58.852 55.000 0.00 0.00 0.00 3.06
402 403 6.898041 TGCAATATGTCTGTGTTTTAGTGTC 58.102 36.000 0.00 0.00 0.00 3.67
409 410 5.509501 CCAAGGTTGCAATATGTCTGTGTTT 60.510 40.000 0.59 0.00 0.00 2.83
453 454 3.332034 CATCATATCTTCATCTGCGCCA 58.668 45.455 4.18 0.00 0.00 5.69
622 623 1.202830 AGCCCACATGACCGTAACAAA 60.203 47.619 0.00 0.00 0.00 2.83
878 879 1.073722 CAGGCAGCCAAGAAGGTCA 59.926 57.895 15.80 0.00 40.61 4.02
951 952 2.172505 TGCGAATAACACCCCATCTCAT 59.827 45.455 0.00 0.00 0.00 2.90
964 965 1.075542 CCACGAAGCTGTGCGAATAA 58.924 50.000 10.35 0.00 38.55 1.40
1018 1019 2.162681 GTGCCATAGCTGAACCAGTTT 58.837 47.619 0.00 0.00 40.80 2.66
1045 1046 1.169661 ACAATGGAGCGCGAAAACCA 61.170 50.000 12.10 13.39 36.83 3.67
1131 1132 6.237861 GCCGACATATTGAAGTTTCTCAGTAC 60.238 42.308 0.00 0.00 0.00 2.73
1132 1133 5.810587 GCCGACATATTGAAGTTTCTCAGTA 59.189 40.000 0.00 0.00 0.00 2.74
1144 1145 1.280710 ACAAGTGGGCCGACATATTGA 59.719 47.619 20.91 0.00 0.00 2.57
1239 1244 1.656818 CCCGCACGATCAGCCAAAAT 61.657 55.000 0.00 0.00 0.00 1.82
1307 1312 1.823169 TTAGCCCACTCACACGACCC 61.823 60.000 0.00 0.00 0.00 4.46
1310 1315 1.476891 GAGATTAGCCCACTCACACGA 59.523 52.381 0.00 0.00 0.00 4.35
1311 1316 1.478510 AGAGATTAGCCCACTCACACG 59.521 52.381 0.00 0.00 33.69 4.49
1312 1317 2.159028 GGAGAGATTAGCCCACTCACAC 60.159 54.545 0.00 0.00 33.69 3.82
1313 1318 2.111384 GGAGAGATTAGCCCACTCACA 58.889 52.381 0.00 0.00 33.69 3.58
1314 1319 2.102252 CAGGAGAGATTAGCCCACTCAC 59.898 54.545 0.00 0.00 33.69 3.51
1315 1320 2.292521 ACAGGAGAGATTAGCCCACTCA 60.293 50.000 0.00 0.00 33.69 3.41
1316 1321 2.102252 CACAGGAGAGATTAGCCCACTC 59.898 54.545 0.00 0.00 0.00 3.51
1317 1322 2.114616 CACAGGAGAGATTAGCCCACT 58.885 52.381 0.00 0.00 0.00 4.00
1318 1323 1.834263 ACACAGGAGAGATTAGCCCAC 59.166 52.381 0.00 0.00 0.00 4.61
1319 1324 2.254152 ACACAGGAGAGATTAGCCCA 57.746 50.000 0.00 0.00 0.00 5.36
1320 1325 5.540719 ACTTATACACAGGAGAGATTAGCCC 59.459 44.000 0.00 0.00 0.00 5.19
1321 1326 6.658188 ACTTATACACAGGAGAGATTAGCC 57.342 41.667 0.00 0.00 0.00 3.93
1322 1327 8.463607 GGATACTTATACACAGGAGAGATTAGC 58.536 40.741 0.00 0.00 0.00 3.09
1323 1328 8.962679 GGGATACTTATACACAGGAGAGATTAG 58.037 40.741 0.00 0.00 0.00 1.73
1324 1329 8.679725 AGGGATACTTATACACAGGAGAGATTA 58.320 37.037 0.00 0.00 0.00 1.75
1325 1330 7.540183 AGGGATACTTATACACAGGAGAGATT 58.460 38.462 0.00 0.00 0.00 2.40
1326 1331 7.109901 AGGGATACTTATACACAGGAGAGAT 57.890 40.000 0.00 0.00 0.00 2.75
1327 1332 6.532119 AGGGATACTTATACACAGGAGAGA 57.468 41.667 0.00 0.00 0.00 3.10
1328 1333 6.778069 TCAAGGGATACTTATACACAGGAGAG 59.222 42.308 0.00 0.00 37.29 3.20
1329 1334 6.679542 TCAAGGGATACTTATACACAGGAGA 58.320 40.000 0.00 0.00 37.29 3.71
1330 1335 6.551601 ACTCAAGGGATACTTATACACAGGAG 59.448 42.308 0.00 0.00 37.29 3.69
1331 1336 6.441222 ACTCAAGGGATACTTATACACAGGA 58.559 40.000 0.00 0.00 37.29 3.86
1332 1337 6.732896 ACTCAAGGGATACTTATACACAGG 57.267 41.667 0.00 0.00 37.29 4.00
1340 1345 9.886132 GTTTCTCATTAACTCAAGGGATACTTA 57.114 33.333 0.00 0.00 37.29 2.24
1341 1346 8.383175 TGTTTCTCATTAACTCAAGGGATACTT 58.617 33.333 0.00 0.00 41.00 2.24
1342 1347 7.918076 TGTTTCTCATTAACTCAAGGGATACT 58.082 34.615 0.00 0.00 0.00 2.12
1343 1348 8.041323 TCTGTTTCTCATTAACTCAAGGGATAC 58.959 37.037 0.00 0.00 0.00 2.24
1344 1349 8.146053 TCTGTTTCTCATTAACTCAAGGGATA 57.854 34.615 0.00 0.00 0.00 2.59
1345 1350 7.020827 TCTGTTTCTCATTAACTCAAGGGAT 57.979 36.000 0.00 0.00 0.00 3.85
1346 1351 6.270000 TCTCTGTTTCTCATTAACTCAAGGGA 59.730 38.462 0.00 0.00 0.00 4.20
1347 1352 6.467677 TCTCTGTTTCTCATTAACTCAAGGG 58.532 40.000 0.00 0.00 0.00 3.95
1348 1353 6.593382 CCTCTCTGTTTCTCATTAACTCAAGG 59.407 42.308 0.00 0.00 0.00 3.61
1349 1354 6.091986 GCCTCTCTGTTTCTCATTAACTCAAG 59.908 42.308 0.00 0.00 0.00 3.02
1350 1355 5.934625 GCCTCTCTGTTTCTCATTAACTCAA 59.065 40.000 0.00 0.00 0.00 3.02
1351 1356 5.482908 GCCTCTCTGTTTCTCATTAACTCA 58.517 41.667 0.00 0.00 0.00 3.41
1352 1357 4.873259 GGCCTCTCTGTTTCTCATTAACTC 59.127 45.833 0.00 0.00 0.00 3.01
1353 1358 4.621747 CGGCCTCTCTGTTTCTCATTAACT 60.622 45.833 0.00 0.00 0.00 2.24
1354 1359 3.619038 CGGCCTCTCTGTTTCTCATTAAC 59.381 47.826 0.00 0.00 0.00 2.01
1355 1360 3.260884 ACGGCCTCTCTGTTTCTCATTAA 59.739 43.478 0.00 0.00 0.00 1.40
1356 1361 2.832129 ACGGCCTCTCTGTTTCTCATTA 59.168 45.455 0.00 0.00 0.00 1.90
1357 1362 1.625818 ACGGCCTCTCTGTTTCTCATT 59.374 47.619 0.00 0.00 0.00 2.57
1358 1363 1.066573 CACGGCCTCTCTGTTTCTCAT 60.067 52.381 0.00 0.00 30.14 2.90
1359 1364 0.318441 CACGGCCTCTCTGTTTCTCA 59.682 55.000 0.00 0.00 30.14 3.27
1360 1365 0.603569 TCACGGCCTCTCTGTTTCTC 59.396 55.000 0.00 0.00 30.14 2.87
1361 1366 0.605589 CTCACGGCCTCTCTGTTTCT 59.394 55.000 0.00 0.00 30.14 2.52
1362 1367 0.390472 CCTCACGGCCTCTCTGTTTC 60.390 60.000 0.00 0.00 30.14 2.78
1363 1368 1.674057 CCTCACGGCCTCTCTGTTT 59.326 57.895 0.00 0.00 30.14 2.83
1364 1369 2.286523 CCCTCACGGCCTCTCTGTT 61.287 63.158 0.00 0.00 30.14 3.16
1365 1370 2.681778 CCCTCACGGCCTCTCTGT 60.682 66.667 0.00 0.00 33.70 3.41
1374 1379 4.463879 CTGCCTCAGCCCTCACGG 62.464 72.222 0.00 0.00 38.69 4.94
1375 1380 2.454832 TTTCTGCCTCAGCCCTCACG 62.455 60.000 0.00 0.00 38.69 4.35
1376 1381 0.250901 TTTTCTGCCTCAGCCCTCAC 60.251 55.000 0.00 0.00 38.69 3.51
1377 1382 0.250901 GTTTTCTGCCTCAGCCCTCA 60.251 55.000 0.00 0.00 38.69 3.86
1378 1383 0.250901 TGTTTTCTGCCTCAGCCCTC 60.251 55.000 0.00 0.00 38.69 4.30
1379 1384 0.185901 TTGTTTTCTGCCTCAGCCCT 59.814 50.000 0.00 0.00 38.69 5.19
1380 1385 1.067354 CATTGTTTTCTGCCTCAGCCC 60.067 52.381 0.00 0.00 38.69 5.19
1381 1386 1.615392 ACATTGTTTTCTGCCTCAGCC 59.385 47.619 0.00 0.00 38.69 4.85
1382 1387 3.671702 GCTACATTGTTTTCTGCCTCAGC 60.672 47.826 0.00 0.00 40.48 4.26
1383 1388 3.425359 CGCTACATTGTTTTCTGCCTCAG 60.425 47.826 0.00 0.00 0.00 3.35
1384 1389 2.483877 CGCTACATTGTTTTCTGCCTCA 59.516 45.455 0.00 0.00 0.00 3.86
1385 1390 2.729156 GCGCTACATTGTTTTCTGCCTC 60.729 50.000 0.00 0.00 0.00 4.70
1386 1391 1.200020 GCGCTACATTGTTTTCTGCCT 59.800 47.619 0.00 0.00 0.00 4.75
1387 1392 1.200020 AGCGCTACATTGTTTTCTGCC 59.800 47.619 8.99 0.00 0.00 4.85
1388 1393 2.619013 AGCGCTACATTGTTTTCTGC 57.381 45.000 8.99 0.00 0.00 4.26
1389 1394 3.665409 CACAAGCGCTACATTGTTTTCTG 59.335 43.478 12.05 2.50 37.54 3.02
1390 1395 3.315191 ACACAAGCGCTACATTGTTTTCT 59.685 39.130 12.05 0.00 37.54 2.52
1391 1396 3.421888 CACACAAGCGCTACATTGTTTTC 59.578 43.478 12.05 0.00 37.54 2.29
1392 1397 3.066064 TCACACAAGCGCTACATTGTTTT 59.934 39.130 12.05 0.00 37.54 2.43
1393 1398 2.616376 TCACACAAGCGCTACATTGTTT 59.384 40.909 12.05 0.63 37.54 2.83
1394 1399 2.032030 GTCACACAAGCGCTACATTGTT 60.032 45.455 12.05 0.00 37.54 2.83
1395 1400 1.531149 GTCACACAAGCGCTACATTGT 59.469 47.619 12.05 8.84 40.18 2.71
1396 1401 1.530720 TGTCACACAAGCGCTACATTG 59.469 47.619 12.05 8.02 0.00 2.82
1397 1402 1.800586 CTGTCACACAAGCGCTACATT 59.199 47.619 12.05 0.00 0.00 2.71
1398 1403 1.432514 CTGTCACACAAGCGCTACAT 58.567 50.000 12.05 0.00 0.00 2.29
1399 1404 0.599991 CCTGTCACACAAGCGCTACA 60.600 55.000 12.05 9.59 0.00 2.74
1400 1405 0.319555 TCCTGTCACACAAGCGCTAC 60.320 55.000 12.05 4.18 0.00 3.58
1401 1406 0.038251 CTCCTGTCACACAAGCGCTA 60.038 55.000 12.05 0.00 0.00 4.26
1402 1407 1.301244 CTCCTGTCACACAAGCGCT 60.301 57.895 2.64 2.64 0.00 5.92
1403 1408 2.320587 CCTCCTGTCACACAAGCGC 61.321 63.158 0.00 0.00 0.00 5.92
1404 1409 0.668706 CTCCTCCTGTCACACAAGCG 60.669 60.000 0.00 0.00 0.00 4.68
1405 1410 0.681733 TCTCCTCCTGTCACACAAGC 59.318 55.000 0.00 0.00 0.00 4.01
1406 1411 1.337635 GCTCTCCTCCTGTCACACAAG 60.338 57.143 0.00 0.00 0.00 3.16
1407 1412 0.681733 GCTCTCCTCCTGTCACACAA 59.318 55.000 0.00 0.00 0.00 3.33
1408 1413 1.188219 GGCTCTCCTCCTGTCACACA 61.188 60.000 0.00 0.00 0.00 3.72
1409 1414 0.902516 AGGCTCTCCTCCTGTCACAC 60.903 60.000 0.00 0.00 38.72 3.82
1410 1415 1.466979 AGGCTCTCCTCCTGTCACA 59.533 57.895 0.00 0.00 38.72 3.58
1411 1416 4.451544 AGGCTCTCCTCCTGTCAC 57.548 61.111 0.00 0.00 38.72 3.67
1426 1431 2.417787 GCCAATTAGCTTTGCCAAGAGG 60.418 50.000 0.86 0.00 38.23 3.69
1427 1432 2.494870 AGCCAATTAGCTTTGCCAAGAG 59.505 45.455 0.86 0.00 41.41 2.85
1428 1433 2.528564 AGCCAATTAGCTTTGCCAAGA 58.471 42.857 0.86 0.00 41.41 3.02
1438 1443 2.027385 CAGGGAAGGAAGCCAATTAGC 58.973 52.381 0.00 0.00 0.00 3.09
1439 1444 2.024941 ACCAGGGAAGGAAGCCAATTAG 60.025 50.000 0.00 0.00 0.00 1.73
1440 1445 2.000048 ACCAGGGAAGGAAGCCAATTA 59.000 47.619 0.00 0.00 0.00 1.40
1441 1446 0.786435 ACCAGGGAAGGAAGCCAATT 59.214 50.000 0.00 0.00 0.00 2.32
1442 1447 1.285078 GTACCAGGGAAGGAAGCCAAT 59.715 52.381 0.00 0.00 0.00 3.16
1443 1448 0.696501 GTACCAGGGAAGGAAGCCAA 59.303 55.000 0.00 0.00 0.00 4.52
1444 1449 0.474854 TGTACCAGGGAAGGAAGCCA 60.475 55.000 0.00 0.00 0.00 4.75
1445 1450 0.919710 ATGTACCAGGGAAGGAAGCC 59.080 55.000 0.00 0.00 0.00 4.35
1446 1451 2.019156 GCATGTACCAGGGAAGGAAGC 61.019 57.143 0.00 0.00 0.00 3.86
1447 1452 1.743772 CGCATGTACCAGGGAAGGAAG 60.744 57.143 0.00 0.00 0.00 3.46
1448 1453 0.251916 CGCATGTACCAGGGAAGGAA 59.748 55.000 0.00 0.00 0.00 3.36
1449 1454 0.907704 ACGCATGTACCAGGGAAGGA 60.908 55.000 5.85 0.00 0.00 3.36
1450 1455 0.744414 CACGCATGTACCAGGGAAGG 60.744 60.000 5.85 0.00 0.00 3.46
1451 1456 1.369091 GCACGCATGTACCAGGGAAG 61.369 60.000 5.85 0.64 0.00 3.46
1452 1457 1.376683 GCACGCATGTACCAGGGAA 60.377 57.895 5.85 0.00 0.00 3.97
1453 1458 2.267642 GCACGCATGTACCAGGGA 59.732 61.111 5.85 0.00 0.00 4.20
1454 1459 3.195002 CGCACGCATGTACCAGGG 61.195 66.667 0.00 0.00 0.00 4.45
1455 1460 2.434185 ACGCACGCATGTACCAGG 60.434 61.111 0.00 0.00 0.00 4.45
1456 1461 2.027073 ACACGCACGCATGTACCAG 61.027 57.895 0.00 0.00 0.00 4.00
1457 1462 2.029815 ACACGCACGCATGTACCA 59.970 55.556 0.00 0.00 0.00 3.25
1458 1463 2.314647 ACACACGCACGCATGTACC 61.315 57.895 0.00 0.00 0.00 3.34
1459 1464 1.154672 CACACACGCACGCATGTAC 60.155 57.895 0.00 0.00 0.00 2.90
1460 1465 1.592939 ACACACACGCACGCATGTA 60.593 52.632 0.00 0.00 0.00 2.29
1461 1466 2.894879 ACACACACGCACGCATGT 60.895 55.556 0.00 0.00 0.00 3.21
1462 1467 2.425610 CACACACACGCACGCATG 60.426 61.111 0.00 0.00 0.00 4.06
1463 1468 2.894879 ACACACACACGCACGCAT 60.895 55.556 0.00 0.00 0.00 4.73
1464 1469 3.858989 CACACACACACGCACGCA 61.859 61.111 0.00 0.00 0.00 5.24
1465 1470 2.842588 AAACACACACACACGCACGC 62.843 55.000 0.00 0.00 0.00 5.34
1466 1471 0.855670 GAAACACACACACACGCACG 60.856 55.000 0.00 0.00 0.00 5.34
1467 1472 0.446222 AGAAACACACACACACGCAC 59.554 50.000 0.00 0.00 0.00 5.34
1468 1473 0.724549 GAGAAACACACACACACGCA 59.275 50.000 0.00 0.00 0.00 5.24
1469 1474 0.724549 TGAGAAACACACACACACGC 59.275 50.000 0.00 0.00 0.00 5.34
1470 1475 1.999735 ACTGAGAAACACACACACACG 59.000 47.619 0.00 0.00 0.00 4.49
1471 1476 4.419522 AAACTGAGAAACACACACACAC 57.580 40.909 0.00 0.00 0.00 3.82
1472 1477 5.446143 AAAAACTGAGAAACACACACACA 57.554 34.783 0.00 0.00 0.00 3.72
1491 1496 5.013547 TCAAGAACACACTCCAAGGAAAAA 58.986 37.500 0.00 0.00 0.00 1.94
1492 1497 4.594970 TCAAGAACACACTCCAAGGAAAA 58.405 39.130 0.00 0.00 0.00 2.29
1493 1498 4.080582 TCTCAAGAACACACTCCAAGGAAA 60.081 41.667 0.00 0.00 0.00 3.13
1494 1499 3.454447 TCTCAAGAACACACTCCAAGGAA 59.546 43.478 0.00 0.00 0.00 3.36
1495 1500 3.038280 TCTCAAGAACACACTCCAAGGA 58.962 45.455 0.00 0.00 0.00 3.36
1496 1501 3.070159 TCTCTCAAGAACACACTCCAAGG 59.930 47.826 0.00 0.00 0.00 3.61
1497 1502 4.327982 TCTCTCAAGAACACACTCCAAG 57.672 45.455 0.00 0.00 0.00 3.61
1498 1503 4.963318 ATCTCTCAAGAACACACTCCAA 57.037 40.909 0.00 0.00 34.49 3.53
1499 1504 7.904558 ATATATCTCTCAAGAACACACTCCA 57.095 36.000 0.00 0.00 34.49 3.86
1522 1527 9.812347 ACTCTCATGATGTTTCTCTCTCTATAT 57.188 33.333 0.00 0.00 0.00 0.86
1523 1528 9.639563 AACTCTCATGATGTTTCTCTCTCTATA 57.360 33.333 0.00 0.00 0.00 1.31
1524 1529 8.415553 CAACTCTCATGATGTTTCTCTCTCTAT 58.584 37.037 10.38 0.00 0.00 1.98
1525 1530 7.395772 ACAACTCTCATGATGTTTCTCTCTCTA 59.604 37.037 10.38 0.00 0.00 2.43
1526 1531 6.211184 ACAACTCTCATGATGTTTCTCTCTCT 59.789 38.462 10.38 0.00 0.00 3.10
1527 1532 6.310956 CACAACTCTCATGATGTTTCTCTCTC 59.689 42.308 10.38 0.00 0.00 3.20
1528 1533 6.164876 CACAACTCTCATGATGTTTCTCTCT 58.835 40.000 10.38 0.00 0.00 3.10
1529 1534 5.163874 GCACAACTCTCATGATGTTTCTCTC 60.164 44.000 10.38 0.00 0.00 3.20
1530 1535 4.694509 GCACAACTCTCATGATGTTTCTCT 59.305 41.667 10.38 0.00 0.00 3.10
1531 1536 4.694509 AGCACAACTCTCATGATGTTTCTC 59.305 41.667 10.38 4.61 0.00 2.87
1532 1537 4.649692 AGCACAACTCTCATGATGTTTCT 58.350 39.130 10.38 3.31 0.00 2.52
1533 1538 5.064452 CCTAGCACAACTCTCATGATGTTTC 59.936 44.000 10.38 1.44 0.00 2.78
1534 1539 4.940046 CCTAGCACAACTCTCATGATGTTT 59.060 41.667 10.38 0.68 0.00 2.83
1535 1540 4.511527 CCTAGCACAACTCTCATGATGTT 58.488 43.478 0.00 2.00 0.00 2.71
1536 1541 3.681034 GCCTAGCACAACTCTCATGATGT 60.681 47.826 0.00 0.00 0.00 3.06
1537 1542 2.871022 GCCTAGCACAACTCTCATGATG 59.129 50.000 0.00 0.00 0.00 3.07
1538 1543 2.502947 TGCCTAGCACAACTCTCATGAT 59.497 45.455 0.00 0.00 31.71 2.45
1539 1544 1.901833 TGCCTAGCACAACTCTCATGA 59.098 47.619 0.00 0.00 31.71 3.07
1540 1545 2.277969 CTGCCTAGCACAACTCTCATG 58.722 52.381 0.00 0.00 33.79 3.07
1541 1546 2.687700 CTGCCTAGCACAACTCTCAT 57.312 50.000 0.00 0.00 33.79 2.90
1553 1558 1.066908 CTTCTTCCTCGAGCTGCCTAG 59.933 57.143 6.99 0.00 0.00 3.02
1554 1559 1.107114 CTTCTTCCTCGAGCTGCCTA 58.893 55.000 6.99 0.00 0.00 3.93
1555 1560 0.613292 TCTTCTTCCTCGAGCTGCCT 60.613 55.000 6.99 0.00 0.00 4.75
1556 1561 0.247736 TTCTTCTTCCTCGAGCTGCC 59.752 55.000 6.99 0.00 0.00 4.85
1557 1562 1.203523 TCTTCTTCTTCCTCGAGCTGC 59.796 52.381 6.99 0.00 0.00 5.25
1558 1563 2.735126 GCTCTTCTTCTTCCTCGAGCTG 60.735 54.545 6.99 0.00 40.37 4.24
1559 1564 1.476488 GCTCTTCTTCTTCCTCGAGCT 59.524 52.381 6.99 0.00 40.37 4.09
1560 1565 1.797348 CGCTCTTCTTCTTCCTCGAGC 60.797 57.143 6.99 0.00 40.19 5.03
1561 1566 1.202245 CCGCTCTTCTTCTTCCTCGAG 60.202 57.143 5.13 5.13 0.00 4.04
1562 1567 0.811915 CCGCTCTTCTTCTTCCTCGA 59.188 55.000 0.00 0.00 0.00 4.04
1563 1568 0.804156 GCCGCTCTTCTTCTTCCTCG 60.804 60.000 0.00 0.00 0.00 4.63
1564 1569 0.804156 CGCCGCTCTTCTTCTTCCTC 60.804 60.000 0.00 0.00 0.00 3.71
1565 1570 1.216710 CGCCGCTCTTCTTCTTCCT 59.783 57.895 0.00 0.00 0.00 3.36
1566 1571 2.456948 GCGCCGCTCTTCTTCTTCC 61.457 63.158 0.00 0.00 0.00 3.46
1567 1572 1.446966 AGCGCCGCTCTTCTTCTTC 60.447 57.895 5.39 0.00 30.62 2.87
1568 1573 1.739562 CAGCGCCGCTCTTCTTCTT 60.740 57.895 9.54 0.00 36.40 2.52
1569 1574 2.125753 CAGCGCCGCTCTTCTTCT 60.126 61.111 9.54 0.00 36.40 2.85
1570 1575 3.858989 GCAGCGCCGCTCTTCTTC 61.859 66.667 9.54 0.00 36.40 2.87
1597 1602 4.465512 GTGATGCTGTTGGCGCCG 62.466 66.667 23.90 8.53 45.43 6.46
1598 1603 4.120331 GGTGATGCTGTTGGCGCC 62.120 66.667 22.73 22.73 45.43 6.53
1599 1604 3.364441 TGGTGATGCTGTTGGCGC 61.364 61.111 0.00 0.00 45.43 6.53
1600 1605 2.562912 GTGGTGATGCTGTTGGCG 59.437 61.111 0.00 0.00 45.43 5.69
1601 1606 1.902918 TGGTGGTGATGCTGTTGGC 60.903 57.895 0.00 0.00 42.22 4.52
1602 1607 1.526575 GGTGGTGGTGATGCTGTTGG 61.527 60.000 0.00 0.00 0.00 3.77
1603 1608 0.822944 TGGTGGTGGTGATGCTGTTG 60.823 55.000 0.00 0.00 0.00 3.33
1604 1609 0.823356 GTGGTGGTGGTGATGCTGTT 60.823 55.000 0.00 0.00 0.00 3.16
1605 1610 1.228245 GTGGTGGTGGTGATGCTGT 60.228 57.895 0.00 0.00 0.00 4.40
1606 1611 1.073722 AGTGGTGGTGGTGATGCTG 59.926 57.895 0.00 0.00 0.00 4.41
1607 1612 1.073722 CAGTGGTGGTGGTGATGCT 59.926 57.895 0.00 0.00 0.00 3.79
1608 1613 1.228245 ACAGTGGTGGTGGTGATGC 60.228 57.895 0.00 0.00 0.00 3.91
1609 1614 1.518056 GCACAGTGGTGGTGGTGATG 61.518 60.000 1.84 0.00 45.38 3.07
1610 1615 1.228245 GCACAGTGGTGGTGGTGAT 60.228 57.895 1.84 0.00 45.38 3.06
1611 1616 2.191908 GCACAGTGGTGGTGGTGA 59.808 61.111 1.84 0.00 45.38 4.02
1640 1645 2.504244 GCGTCTTCGGGTCGTCAG 60.504 66.667 0.00 0.00 37.56 3.51
1657 1662 1.153745 CTTCTCTTCACCCGGAGCG 60.154 63.158 0.73 0.00 0.00 5.03
1660 1665 1.874345 GCGTCTTCTCTTCACCCGGA 61.874 60.000 0.73 0.00 0.00 5.14
1661 1666 1.446272 GCGTCTTCTCTTCACCCGG 60.446 63.158 0.00 0.00 0.00 5.73
1663 1668 2.095252 GCGCGTCTTCTCTTCACCC 61.095 63.158 8.43 0.00 0.00 4.61
1703 1709 2.588620 GTCCCGATCTACAGAGGTCAT 58.411 52.381 0.00 0.00 31.57 3.06
1771 1777 1.381872 TGTGAGGAGGAGGCCTAGC 60.382 63.158 4.42 0.00 38.73 3.42
1779 1785 3.733960 CGCGACGTGTGAGGAGGA 61.734 66.667 0.00 0.00 0.00 3.71
1780 1786 3.553437 AACGCGACGTGTGAGGAGG 62.553 63.158 15.93 0.00 39.99 4.30
1785 1805 3.028019 GCTGAACGCGACGTGTGA 61.028 61.111 15.93 4.11 39.99 3.58
1826 1846 3.383825 GGTGGTAGGGGTATATATGCTCG 59.616 52.174 0.62 0.00 0.00 5.03
1845 1865 2.124693 GGTGGTGGTGGTTGTGGTG 61.125 63.158 0.00 0.00 0.00 4.17
1846 1866 2.277404 GGTGGTGGTGGTTGTGGT 59.723 61.111 0.00 0.00 0.00 4.16
1847 1867 2.124693 GTGGTGGTGGTGGTTGTGG 61.125 63.158 0.00 0.00 0.00 4.17
1848 1868 2.124693 GGTGGTGGTGGTGGTTGTG 61.125 63.158 0.00 0.00 0.00 3.33
1849 1869 2.277404 GGTGGTGGTGGTGGTTGT 59.723 61.111 0.00 0.00 0.00 3.32
1850 1870 2.124693 GTGGTGGTGGTGGTGGTTG 61.125 63.158 0.00 0.00 0.00 3.77
1851 1871 0.989212 TAGTGGTGGTGGTGGTGGTT 60.989 55.000 0.00 0.00 0.00 3.67
1852 1872 1.384783 TAGTGGTGGTGGTGGTGGT 60.385 57.895 0.00 0.00 0.00 4.16
1853 1873 1.072505 GTAGTGGTGGTGGTGGTGG 59.927 63.158 0.00 0.00 0.00 4.61
1854 1874 0.034896 GAGTAGTGGTGGTGGTGGTG 59.965 60.000 0.00 0.00 0.00 4.17
1855 1875 1.469335 CGAGTAGTGGTGGTGGTGGT 61.469 60.000 0.00 0.00 0.00 4.16
1856 1876 1.183030 TCGAGTAGTGGTGGTGGTGG 61.183 60.000 0.00 0.00 0.00 4.61
1857 1877 0.243907 CTCGAGTAGTGGTGGTGGTG 59.756 60.000 3.62 0.00 0.00 4.17
1858 1878 0.178970 ACTCGAGTAGTGGTGGTGGT 60.179 55.000 18.46 0.00 36.93 4.16
1859 1879 1.830279 TACTCGAGTAGTGGTGGTGG 58.170 55.000 21.25 0.00 39.39 4.61
1900 1920 1.039233 CCTGGATTGGATGTGCACCC 61.039 60.000 15.69 9.94 0.00 4.61
1919 1939 1.677052 CGGACTTCCTGGCTAGACTAC 59.323 57.143 0.00 0.00 0.00 2.73
2090 2167 4.351938 CGTCGGCTTGTGGTCGGA 62.352 66.667 0.00 0.00 44.01 4.55
2122 2199 0.972471 TCTCATCAAGAGCCCGCTGA 60.972 55.000 0.00 0.00 44.35 4.26
2237 2314 1.362717 CGTCGTGGACCTTGTCAGT 59.637 57.895 0.00 0.00 33.68 3.41


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

AutoCloner maintained by Alex Coulton.