Multiple sequence alignment - TraesCS3D01G094500

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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 TraesCS3D01G094500 chr3D 100.000 3068 0 0 1 3068 48069609 48072676 0.000000e+00 5666.0
1 TraesCS3D01G094500 chr3D 94.690 113 4 2 1289 1400 19269703 19269814 1.130000e-39 174.0
2 TraesCS3D01G094500 chr3A 88.902 1685 100 42 1398 3068 60297765 60299376 0.000000e+00 1995.0
3 TraesCS3D01G094500 chr3A 92.652 1320 59 18 2 1303 60296469 60297768 0.000000e+00 1866.0
4 TraesCS3D01G094500 chr3A 98.077 104 2 0 1301 1404 692869669 692869566 6.760000e-42 182.0
5 TraesCS3D01G094500 chr3A 87.879 66 8 0 1157 1222 476385475 476385540 9.120000e-11 78.7
6 TraesCS3D01G094500 chr3B 89.213 1474 102 26 1425 2887 75735863 75737290 0.000000e+00 1788.0
7 TraesCS3D01G094500 chr3B 88.006 1334 83 36 10 1292 75734538 75735845 0.000000e+00 1506.0
8 TraesCS3D01G094500 chr3B 87.879 66 8 0 1157 1222 458343136 458343201 9.120000e-11 78.7
9 TraesCS3D01G094500 chr2B 98.990 99 1 0 1302 1400 629108531 629108629 8.740000e-41 178.0
10 TraesCS3D01G094500 chr2B 86.747 83 11 0 1495 1577 550213837 550213755 3.260000e-15 93.5
11 TraesCS3D01G094500 chr7B 98.020 101 2 0 1302 1402 700426539 700426639 3.140000e-40 176.0
12 TraesCS3D01G094500 chr6B 94.737 114 4 2 1288 1400 52799532 52799644 3.140000e-40 176.0
13 TraesCS3D01G094500 chr6B 85.542 83 12 0 1495 1577 477691822 477691904 1.520000e-13 87.9
14 TraesCS3D01G094500 chr6B 100.000 29 0 0 1062 1090 476841206 476841234 2.000000e-03 54.7
15 TraesCS3D01G094500 chr7D 94.690 113 5 1 1304 1415 617181760 617181648 1.130000e-39 174.0
16 TraesCS3D01G094500 chr7D 92.647 68 3 2 1495 1561 13097810 13097744 2.520000e-16 97.1
17 TraesCS3D01G094500 chr4B 95.370 108 5 0 1301 1408 658978257 658978364 4.070000e-39 172.0
18 TraesCS3D01G094500 chr4B 81.707 164 20 8 1132 1290 637621888 637622046 8.930000e-26 128.0
19 TraesCS3D01G094500 chr1D 93.805 113 6 1 1297 1408 268409329 268409441 5.260000e-38 169.0
20 TraesCS3D01G094500 chr2D 91.057 123 8 3 1303 1424 227086965 227086845 2.450000e-36 163.0
21 TraesCS3D01G094500 chr2D 85.057 87 13 0 1494 1580 165468020 165467934 4.210000e-14 89.8
22 TraesCS3D01G094500 chr4D 81.707 164 20 8 1132 1290 497126146 497126304 8.930000e-26 128.0
23 TraesCS3D01G094500 chr5A 81.098 164 21 8 1132 1290 676887007 676887165 4.150000e-24 122.0
24 TraesCS3D01G094500 chr2A 85.057 87 13 0 1494 1580 185285275 185285361 4.210000e-14 89.8
25 TraesCS3D01G094500 chr2A 96.875 32 1 0 1062 1093 613175733 613175702 2.000000e-03 54.7
26 TraesCS3D01G094500 chr6D 85.542 83 12 0 1495 1577 309719548 309719630 1.520000e-13 87.9
27 TraesCS3D01G094500 chr6D 100.000 29 0 0 1062 1090 309341541 309341569 2.000000e-03 54.7
28 TraesCS3D01G094500 chr6A 85.542 83 12 0 1495 1577 446521693 446521775 1.520000e-13 87.9
29 TraesCS3D01G094500 chr6A 100.000 28 0 0 1062 1089 446091951 446091978 6.000000e-03 52.8
30 TraesCS3D01G094500 chr5D 77.381 168 24 11 1062 1222 130188037 130188197 1.520000e-13 87.9


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 TraesCS3D01G094500 chr3D 48069609 48072676 3067 False 5666.0 5666 100.0000 1 3068 1 chr3D.!!$F2 3067
1 TraesCS3D01G094500 chr3A 60296469 60299376 2907 False 1930.5 1995 90.7770 2 3068 2 chr3A.!!$F2 3066
2 TraesCS3D01G094500 chr3B 75734538 75737290 2752 False 1647.0 1788 88.6095 10 2887 2 chr3B.!!$F2 2877

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
984 1037 1.338655 GTAGCTAGCTAGGCCACTCAC 59.661 57.143 24.78 8.68 0.0 3.51 F
1317 1370 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1976 1.068741 GCGCAGTAGTAGTAATGCCCT 59.931 52.381 20.96 0.0 45.52 5.19 R
3037 3116 1.000827 AGAGAGCTGTCTTGTGTGTCG 60.001 52.381 7.74 0.0 30.97 4.35 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
38 39 2.877786 TGTCTTTGCTTCGCTCAAATCA 59.122 40.909 0.00 0.00 33.54 2.57
361 369 8.375506 CAAGGGAATACTAAGATGGCATAGTTA 58.624 37.037 6.70 4.52 34.37 2.24
392 400 5.188948 ACTGTCTAACATAGGCAATGGTGTA 59.811 40.000 0.00 0.00 40.35 2.90
455 463 4.890158 TCATCAAAAGGAGTAGCTGACA 57.110 40.909 0.00 0.00 0.00 3.58
587 616 4.469657 AGTCATTGTCAAGGGTGCTTTAA 58.530 39.130 0.00 0.00 0.00 1.52
591 620 6.146021 GTCATTGTCAAGGGTGCTTTAATTTG 59.854 38.462 0.00 0.00 0.00 2.32
594 623 4.837860 TGTCAAGGGTGCTTTAATTTGGAT 59.162 37.500 0.00 0.00 0.00 3.41
597 627 2.501316 AGGGTGCTTTAATTTGGATGGC 59.499 45.455 0.00 0.00 0.00 4.40
607 637 9.546428 GCTTTAATTTGGATGGCTAATTACAAT 57.454 29.630 0.00 0.00 0.00 2.71
640 670 6.667386 GCGACACAAATTAACATGCTTTTAGC 60.667 38.462 0.00 0.00 42.82 3.09
682 719 4.386711 CACATGCATGATGGAGATACACT 58.613 43.478 32.75 2.54 36.23 3.55
683 720 4.213482 CACATGCATGATGGAGATACACTG 59.787 45.833 32.75 11.78 36.23 3.66
748 788 3.100111 GGATGCCCTCCACCCTTT 58.900 61.111 0.00 0.00 44.26 3.11
853 906 7.138631 CCATATTTGGTAGGGAAAGTACCCAC 61.139 46.154 0.00 0.00 44.00 4.61
876 929 5.013183 ACCCTATAAATGTAGTGCAGATCCC 59.987 44.000 0.00 0.00 0.00 3.85
921 974 4.023878 AGCTGCGATAAGTACACTAGCTAC 60.024 45.833 0.00 0.00 38.38 3.58
933 986 3.056749 ACACTAGCTACCTGAACTTTCCG 60.057 47.826 0.00 0.00 0.00 4.30
957 1010 3.272574 ACGCAGTAGTAGTAGTAGCCA 57.727 47.619 0.00 0.00 41.94 4.75
958 1011 3.204526 ACGCAGTAGTAGTAGTAGCCAG 58.795 50.000 0.00 0.00 41.94 4.85
959 1012 2.031857 CGCAGTAGTAGTAGTAGCCAGC 60.032 54.545 0.00 0.00 0.00 4.85
960 1013 3.215975 GCAGTAGTAGTAGTAGCCAGCT 58.784 50.000 0.00 0.00 0.00 4.24
961 1014 4.387598 GCAGTAGTAGTAGTAGCCAGCTA 58.612 47.826 0.00 0.00 0.00 3.32
962 1015 5.005094 GCAGTAGTAGTAGTAGCCAGCTAT 58.995 45.833 2.12 0.00 0.00 2.97
963 1016 5.474189 GCAGTAGTAGTAGTAGCCAGCTATT 59.526 44.000 2.12 1.07 0.00 1.73
964 1017 6.568844 GCAGTAGTAGTAGTAGCCAGCTATTG 60.569 46.154 2.12 0.00 0.00 1.90
965 1018 6.487331 CAGTAGTAGTAGTAGCCAGCTATTGT 59.513 42.308 2.12 0.00 0.00 2.71
966 1019 7.660617 CAGTAGTAGTAGTAGCCAGCTATTGTA 59.339 40.741 2.12 0.00 0.00 2.41
984 1037 1.338655 GTAGCTAGCTAGGCCACTCAC 59.661 57.143 24.78 8.68 0.00 3.51
987 1040 1.472376 GCTAGCTAGGCCACTCACAAG 60.472 57.143 22.10 0.00 0.00 3.16
1212 1265 1.335132 GGATGAACTACCTCCGGCCA 61.335 60.000 2.24 0.00 0.00 5.36
1218 1271 2.363795 TACCTCCGGCCAGACCTG 60.364 66.667 2.24 0.00 35.61 4.00
1248 1301 1.153568 CATCTCCAAGCGCGAGGAA 60.154 57.895 21.43 14.04 32.57 3.36
1272 1325 1.411977 ACCATCATCTCGCTCCAGAAG 59.588 52.381 0.00 0.00 0.00 2.85
1303 1356 6.101997 GGCAACAGGTACTTAATTACGTACT 58.898 40.000 23.70 12.39 34.60 2.73
1304 1357 7.257722 GGCAACAGGTACTTAATTACGTACTA 58.742 38.462 23.70 0.00 34.60 1.82
1305 1358 7.220875 GGCAACAGGTACTTAATTACGTACTAC 59.779 40.741 23.70 13.20 34.60 2.73
1306 1359 7.970614 GCAACAGGTACTTAATTACGTACTACT 59.029 37.037 23.70 14.71 34.60 2.57
1307 1360 9.495754 CAACAGGTACTTAATTACGTACTACTC 57.504 37.037 23.70 12.41 34.60 2.59
1308 1361 8.214721 ACAGGTACTTAATTACGTACTACTCC 57.785 38.462 23.70 12.38 34.60 3.85
1309 1362 7.283354 ACAGGTACTTAATTACGTACTACTCCC 59.717 40.741 23.70 11.84 34.60 4.30
1310 1363 7.500559 CAGGTACTTAATTACGTACTACTCCCT 59.499 40.741 23.70 13.41 34.60 4.20
1311 1364 7.717436 AGGTACTTAATTACGTACTACTCCCTC 59.283 40.741 23.70 10.57 36.94 4.30
1312 1365 6.951062 ACTTAATTACGTACTACTCCCTCC 57.049 41.667 0.00 0.00 0.00 4.30
1313 1366 5.529060 ACTTAATTACGTACTACTCCCTCCG 59.471 44.000 0.00 0.00 0.00 4.63
1314 1367 3.567478 ATTACGTACTACTCCCTCCGT 57.433 47.619 0.00 0.00 0.00 4.69
1315 1368 3.350219 TTACGTACTACTCCCTCCGTT 57.650 47.619 0.00 0.00 0.00 4.44
1316 1369 1.743996 ACGTACTACTCCCTCCGTTC 58.256 55.000 0.00 0.00 0.00 3.95
1317 1370 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
1318 1371 1.679944 CGTACTACTCCCTCCGTTCCA 60.680 57.143 0.00 0.00 0.00 3.53
1319 1372 2.450476 GTACTACTCCCTCCGTTCCAA 58.550 52.381 0.00 0.00 0.00 3.53
1320 1373 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1321 1374 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1322 1375 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1323 1376 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1324 1377 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1325 1378 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1326 1379 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1327 1380 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1328 1381 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1329 1382 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1330 1383 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1331 1384 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1332 1385 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1333 1386 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1334 1387 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1335 1388 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1336 1389 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1337 1390 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1338 1391 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1339 1392 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1340 1393 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1341 1394 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1342 1395 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1386 1439 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1387 1440 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1388 1441 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1389 1442 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1390 1443 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1391 1444 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1392 1445 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1393 1446 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1394 1447 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1395 1448 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1396 1449 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1397 1450 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1398 1451 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1399 1452 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1400 1453 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1407 1460 3.318557 GGAACGGAGGGAGTACATTCTAG 59.681 52.174 0.00 0.00 0.00 2.43
1408 1461 3.947612 ACGGAGGGAGTACATTCTAGA 57.052 47.619 0.00 0.00 0.00 2.43
1417 1470 9.357161 GAGGGAGTACATTCTAGAAGATTTCTA 57.643 37.037 11.53 0.00 41.14 2.10
1460 1513 6.645306 TGTACAAGAACATTTGGGATCGATA 58.355 36.000 0.00 0.00 32.32 2.92
1478 1531 4.039245 TCGATAGTCCAGGAGGCTAAATTG 59.961 45.833 0.00 0.00 33.74 2.32
1503 1556 6.574073 GCCATGAAATTTTTATCAGGTGGTCA 60.574 38.462 0.00 0.00 31.35 4.02
1585 1638 2.293318 ATCAGGAAGCGCCAGACCA 61.293 57.895 2.29 0.00 40.02 4.02
1632 1688 4.112341 GGCCTCGCAAAGCAGCAG 62.112 66.667 0.00 0.00 0.00 4.24
1675 1731 3.316573 AAGGCCTCCGTGCTAGCAC 62.317 63.158 33.47 33.47 43.01 4.40
1676 1732 4.840005 GGCCTCCGTGCTAGCACC 62.840 72.222 35.76 23.43 43.49 5.01
1711 1767 1.378911 CTGGTTAGCAGCATGGCCA 60.379 57.895 8.56 8.56 35.86 5.36
1767 1823 2.432456 CTGTTCGCGTGCCAGCTA 60.432 61.111 5.77 0.00 34.40 3.32
1770 1826 2.126071 TTCGCGTGCCAGCTACTC 60.126 61.111 5.77 0.00 34.40 2.59
1914 1979 3.771160 CAGGACGGTCGGGAAGGG 61.771 72.222 1.43 0.00 0.00 3.95
2230 2295 7.724305 TGATCGAGTGGTAATTAATTAAGGC 57.276 36.000 9.48 3.42 0.00 4.35
2231 2296 6.708949 TGATCGAGTGGTAATTAATTAAGGCC 59.291 38.462 9.48 7.74 0.00 5.19
2232 2297 6.243216 TCGAGTGGTAATTAATTAAGGCCT 57.757 37.500 9.48 0.00 0.00 5.19
2233 2298 6.053005 TCGAGTGGTAATTAATTAAGGCCTG 58.947 40.000 5.69 0.57 0.00 4.85
2234 2299 5.820947 CGAGTGGTAATTAATTAAGGCCTGT 59.179 40.000 5.69 0.00 0.00 4.00
2248 2313 4.251543 AGGCCTGTTTATTTTTGTTCCG 57.748 40.909 3.11 0.00 0.00 4.30
2249 2314 3.639561 AGGCCTGTTTATTTTTGTTCCGT 59.360 39.130 3.11 0.00 0.00 4.69
2296 2361 6.100668 TCAAAACCGGTTGAAACTTTTTAGG 58.899 36.000 23.08 0.00 34.59 2.69
2354 2420 9.623350 AATAGTTCGTGACTAAAGTAACTCTTC 57.377 33.333 5.72 0.00 43.76 2.87
2509 2575 2.106683 GGTCTCGCCATTGGGTTCG 61.107 63.158 4.53 0.00 37.17 3.95
2510 2576 1.079405 GTCTCGCCATTGGGTTCGA 60.079 57.895 4.53 4.36 36.17 3.71
2511 2577 0.462047 GTCTCGCCATTGGGTTCGAT 60.462 55.000 4.53 0.00 36.17 3.59
2512 2578 0.251916 TCTCGCCATTGGGTTCGATT 59.748 50.000 4.53 0.00 36.17 3.34
2513 2579 0.378257 CTCGCCATTGGGTTCGATTG 59.622 55.000 4.53 0.00 36.17 2.67
2514 2580 1.226660 CGCCATTGGGTTCGATTGC 60.227 57.895 4.53 0.00 36.17 3.56
2525 2596 3.802685 GGGTTCGATTGCATCACTAGTAC 59.197 47.826 0.00 0.00 0.00 2.73
2527 2598 5.050490 GGTTCGATTGCATCACTAGTACAT 58.950 41.667 0.00 0.00 0.00 2.29
2574 2645 3.570125 TGTTGTGTTGTGTGGAACTTTCA 59.430 39.130 0.00 0.00 38.04 2.69
2601 2672 4.065088 GCCATGGATATATTGTGACGTGT 58.935 43.478 18.40 0.00 0.00 4.49
2699 2770 1.369625 CGGAGCAACCACCAGATAAC 58.630 55.000 1.20 0.00 38.90 1.89
2701 2772 1.004277 GGAGCAACCACCAGATAACCA 59.996 52.381 0.00 0.00 38.79 3.67
2721 2792 7.784633 AACCAAGTTTCCATTGTACATTTTG 57.215 32.000 0.00 0.00 0.00 2.44
2817 2890 4.503910 GAGTTTGAGTTTTGGCTTTTGGT 58.496 39.130 0.00 0.00 0.00 3.67
2820 2893 5.872617 AGTTTGAGTTTTGGCTTTTGGTAAC 59.127 36.000 0.00 0.00 0.00 2.50
2919 2998 4.634004 TGAGTAATACAATGCTTTCACCCG 59.366 41.667 0.00 0.00 0.00 5.28
2920 2999 4.585879 AGTAATACAATGCTTTCACCCGT 58.414 39.130 0.00 0.00 0.00 5.28
2945 3024 6.452244 AAAAAGAAAAATATGACAGCGCAC 57.548 33.333 11.47 0.51 0.00 5.34
2946 3025 5.376854 AAAGAAAAATATGACAGCGCACT 57.623 34.783 11.47 0.00 0.00 4.40
2947 3026 6.494893 AAAGAAAAATATGACAGCGCACTA 57.505 33.333 11.47 0.00 0.00 2.74
2948 3027 6.494893 AAGAAAAATATGACAGCGCACTAA 57.505 33.333 11.47 0.00 0.00 2.24
2949 3028 6.494893 AGAAAAATATGACAGCGCACTAAA 57.505 33.333 11.47 0.00 0.00 1.85
2953 3032 5.818136 AATATGACAGCGCACTAAACAAT 57.182 34.783 11.47 0.00 0.00 2.71
2963 3042 3.432252 CGCACTAAACAATTCTCTTCCGT 59.568 43.478 0.00 0.00 0.00 4.69
2964 3043 4.666655 CGCACTAAACAATTCTCTTCCGTG 60.667 45.833 0.00 0.00 0.00 4.94
2976 3055 2.738846 CTCTTCCGTGTTCAACATCCTG 59.261 50.000 0.00 0.00 0.00 3.86
2978 3057 2.631160 TCCGTGTTCAACATCCTGTT 57.369 45.000 0.00 0.00 42.08 3.16
2990 3069 8.564574 GTTCAACATCCTGTTTTAATAGTGTCA 58.435 33.333 0.00 0.00 38.77 3.58
2997 3076 6.043938 TCCTGTTTTAATAGTGTCACTTCCCT 59.956 38.462 11.54 0.00 0.00 4.20
3011 3090 6.710744 TGTCACTTCCCTAAGACTTGAAATTC 59.289 38.462 0.00 0.00 36.50 2.17
3015 3094 6.486993 ACTTCCCTAAGACTTGAAATTCACAC 59.513 38.462 0.00 0.00 36.50 3.82
3017 3096 7.311092 TCCCTAAGACTTGAAATTCACACTA 57.689 36.000 0.00 0.00 0.00 2.74
3037 3116 9.994432 CACACTATCACTAAAAATTGGAGAATC 57.006 33.333 0.00 0.00 0.00 2.52
3042 3121 7.129109 TCACTAAAAATTGGAGAATCGACAC 57.871 36.000 0.00 0.00 34.37 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.232913 TGGTTAATTTGTGAGTTCTAGCTTTT 57.767 30.769 0.00 0.00 0.00 2.27
145 151 7.502895 CCCTAGCTACTTTCAACTAGAGTATGA 59.497 40.741 0.00 0.00 35.21 2.15
318 326 6.240549 TCCCTTGAGGAAGAGACAAATATC 57.759 41.667 0.00 0.00 43.78 1.63
361 369 5.446860 TGCCTATGTTAGACAGTAGTAGCT 58.553 41.667 0.00 0.00 0.00 3.32
392 400 2.411628 TTGTGGTTACTGTGCACTGT 57.588 45.000 28.89 28.89 0.00 3.55
587 616 8.424133 GGAAAGATTGTAATTAGCCATCCAAAT 58.576 33.333 0.00 0.00 0.00 2.32
591 620 6.515696 GCTGGAAAGATTGTAATTAGCCATCC 60.516 42.308 0.00 0.00 0.00 3.51
594 623 4.335315 CGCTGGAAAGATTGTAATTAGCCA 59.665 41.667 0.00 0.00 0.00 4.75
597 627 6.092122 TGTGTCGCTGGAAAGATTGTAATTAG 59.908 38.462 0.00 0.00 0.00 1.73
607 637 4.576873 TGTTAATTTGTGTCGCTGGAAAGA 59.423 37.500 0.00 0.00 0.00 2.52
640 670 2.549329 TGCAAGCCAGTAATATCATGCG 59.451 45.455 0.00 0.00 35.40 4.73
682 719 6.614160 GCATGCATGTGCTTATAATGTATCA 58.386 36.000 26.79 0.00 41.82 2.15
796 836 8.676401 CATCTGTACACATTAATCAATTGTCCA 58.324 33.333 5.13 0.00 0.00 4.02
853 906 5.013079 TGGGATCTGCACTACATTTATAGGG 59.987 44.000 0.00 0.00 0.00 3.53
876 929 5.734220 GCTGGTGCTTAATTATGTGGTGATG 60.734 44.000 0.84 0.00 36.03 3.07
907 960 6.295180 GGAAAGTTCAGGTAGCTAGTGTACTT 60.295 42.308 16.42 16.42 34.44 2.24
921 974 1.615107 GCGTCGACGGAAAGTTCAGG 61.615 60.000 36.13 7.18 40.23 3.86
933 986 3.060607 GCTACTACTACTACTGCGTCGAC 60.061 52.174 5.18 5.18 0.00 4.20
959 1012 3.829601 AGTGGCCTAGCTAGCTACAATAG 59.170 47.826 20.67 12.15 43.52 1.73
960 1013 3.827302 GAGTGGCCTAGCTAGCTACAATA 59.173 47.826 20.67 1.82 43.52 1.90
961 1014 2.630580 GAGTGGCCTAGCTAGCTACAAT 59.369 50.000 20.67 15.81 43.52 2.71
962 1015 2.032620 GAGTGGCCTAGCTAGCTACAA 58.967 52.381 20.67 2.75 43.52 2.41
963 1016 1.063942 TGAGTGGCCTAGCTAGCTACA 60.064 52.381 20.67 14.20 43.52 2.74
964 1017 1.338655 GTGAGTGGCCTAGCTAGCTAC 59.661 57.143 20.67 16.96 41.60 3.58
965 1018 1.063942 TGTGAGTGGCCTAGCTAGCTA 60.064 52.381 22.85 22.85 0.00 3.32
966 1019 0.324738 TGTGAGTGGCCTAGCTAGCT 60.325 55.000 23.12 23.12 0.00 3.32
969 1022 2.103373 CTCTTGTGAGTGGCCTAGCTA 58.897 52.381 3.32 0.00 35.67 3.32
973 1026 2.231716 TAGCTCTTGTGAGTGGCCTA 57.768 50.000 3.32 0.00 42.13 3.93
976 1029 1.082690 GCTTAGCTCTTGTGAGTGGC 58.917 55.000 0.00 0.00 42.13 5.01
978 1031 3.657634 TCTTGCTTAGCTCTTGTGAGTG 58.342 45.455 5.60 0.00 42.13 3.51
984 1037 3.128242 CCACCATTCTTGCTTAGCTCTTG 59.872 47.826 5.60 0.00 0.00 3.02
987 1040 2.941720 CTCCACCATTCTTGCTTAGCTC 59.058 50.000 5.60 0.00 0.00 4.09
1128 1181 3.075005 GCCACGGAGCTCCAGGTA 61.075 66.667 31.25 0.00 34.39 3.08
1212 1265 0.178891 TGGGCTCCTTCTTCAGGTCT 60.179 55.000 0.00 0.00 44.37 3.85
1248 1301 1.327303 GGAGCGAGATGATGGTCTCT 58.673 55.000 2.83 0.00 41.95 3.10
1272 1325 0.317479 AGTACCTGTTGCCGAGTGAC 59.683 55.000 0.00 0.00 0.00 3.67
1303 1356 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1304 1357 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1305 1358 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1306 1359 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1307 1360 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1308 1361 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1309 1362 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1310 1363 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1311 1364 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1312 1365 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1313 1366 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1314 1367 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1315 1368 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1316 1369 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1360 1413 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1361 1414 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1362 1415 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1363 1416 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1364 1417 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1365 1418 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1366 1419 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1367 1420 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1368 1421 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1369 1422 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1370 1423 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1371 1424 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1372 1425 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1373 1426 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1374 1427 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1375 1428 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1376 1429 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1377 1430 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1378 1431 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1379 1432 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
1380 1433 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
1381 1434 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
1382 1435 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
1383 1436 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
1384 1437 1.829222 GAATGTACTCCCTCCGTTCCA 59.171 52.381 0.00 0.00 0.00 3.53
1385 1438 2.108970 AGAATGTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
1386 1439 4.205587 TCTAGAATGTACTCCCTCCGTTC 58.794 47.826 0.00 0.00 0.00 3.95
1387 1440 4.246712 TCTAGAATGTACTCCCTCCGTT 57.753 45.455 0.00 0.00 0.00 4.44
1388 1441 3.947612 TCTAGAATGTACTCCCTCCGT 57.052 47.619 0.00 0.00 0.00 4.69
1389 1442 4.462133 TCTTCTAGAATGTACTCCCTCCG 58.538 47.826 5.44 0.00 0.00 4.63
1390 1443 6.987403 AATCTTCTAGAATGTACTCCCTCC 57.013 41.667 5.44 0.00 0.00 4.30
1391 1444 8.245195 AGAAATCTTCTAGAATGTACTCCCTC 57.755 38.462 5.44 0.00 38.49 4.30
1421 1474 9.562408 TGTTCTTGTACAATCAATTACCAAGTA 57.438 29.630 9.13 0.00 0.00 2.24
1422 1475 8.458573 TGTTCTTGTACAATCAATTACCAAGT 57.541 30.769 9.13 0.00 0.00 3.16
1440 1493 5.237344 GGACTATCGATCCCAAATGTTCTTG 59.763 44.000 0.00 0.00 0.00 3.02
1441 1494 5.104527 TGGACTATCGATCCCAAATGTTCTT 60.105 40.000 0.00 0.00 35.12 2.52
1442 1495 4.408921 TGGACTATCGATCCCAAATGTTCT 59.591 41.667 0.00 0.00 35.12 3.01
1460 1513 2.426842 GCAATTTAGCCTCCTGGACT 57.573 50.000 0.00 0.00 34.57 3.85
1478 1531 5.733676 ACCACCTGATAAAAATTTCATGGC 58.266 37.500 0.00 0.00 29.03 4.40
1490 1543 2.159099 GCGATCACTGACCACCTGATAA 60.159 50.000 0.00 0.00 0.00 1.75
1503 1556 1.589993 CATCTTCGCCGCGATCACT 60.590 57.895 17.62 0.00 35.23 3.41
1675 1731 3.075005 TTCCTTCTCTCCGGGCGG 61.075 66.667 0.00 0.00 0.00 6.13
1676 1732 2.184579 GTTCCTTCTCTCCGGGCG 59.815 66.667 0.00 0.00 0.00 6.13
1681 1737 2.567615 TGCTAACCAGTTCCTTCTCTCC 59.432 50.000 0.00 0.00 0.00 3.71
1685 1741 1.699634 TGCTGCTAACCAGTTCCTTCT 59.300 47.619 0.00 0.00 43.71 2.85
1694 1750 1.678635 GTGGCCATGCTGCTAACCA 60.679 57.895 9.72 0.54 0.00 3.67
1790 1846 2.908940 CAATGGCCGCATCCCCTC 60.909 66.667 0.00 0.00 0.00 4.30
1793 1849 3.908081 CTGCAATGGCCGCATCCC 61.908 66.667 4.14 0.00 39.02 3.85
1897 1956 3.771160 CCCTTCCCGACCGTCCTG 61.771 72.222 0.00 0.00 0.00 3.86
1911 1976 1.068741 GCGCAGTAGTAGTAATGCCCT 59.931 52.381 20.96 0.00 45.52 5.19
1914 1979 1.129326 CGGCGCAGTAGTAGTAATGC 58.871 55.000 17.92 17.92 44.97 3.56
1980 2045 4.832608 CCGGCCGGGTACTCAAGC 62.833 72.222 37.42 0.00 0.00 4.01
2225 2290 5.302313 ACGGAACAAAAATAAACAGGCCTTA 59.698 36.000 0.00 0.00 0.00 2.69
2226 2291 4.100344 ACGGAACAAAAATAAACAGGCCTT 59.900 37.500 0.00 0.00 0.00 4.35
2227 2292 3.639561 ACGGAACAAAAATAAACAGGCCT 59.360 39.130 0.00 0.00 0.00 5.19
2228 2293 3.985008 ACGGAACAAAAATAAACAGGCC 58.015 40.909 0.00 0.00 0.00 5.19
2230 2295 6.153067 TGCATACGGAACAAAAATAAACAGG 58.847 36.000 0.00 0.00 0.00 4.00
2231 2296 7.630470 TTGCATACGGAACAAAAATAAACAG 57.370 32.000 0.00 0.00 0.00 3.16
2232 2297 8.594881 ATTTGCATACGGAACAAAAATAAACA 57.405 26.923 3.58 0.00 36.90 2.83
2322 2387 6.656003 ACTTTAGTCACGAACTATTGCAAAC 58.344 36.000 1.71 0.00 40.18 2.93
2354 2420 7.133891 AGATACCACTCTCAAATTTGTTTCG 57.866 36.000 17.47 7.76 0.00 3.46
2449 2515 8.659925 TTTACATTGTGTAAGAAAAGGTCGTA 57.340 30.769 0.00 0.00 42.93 3.43
2468 2534 9.174166 GACCACCACTAGTTCATAAATTTACAT 57.826 33.333 0.00 0.00 0.00 2.29
2509 2575 7.169982 GGAGTGTTATGTACTAGTGATGCAATC 59.830 40.741 5.39 9.38 45.83 2.67
2510 2576 6.986817 GGAGTGTTATGTACTAGTGATGCAAT 59.013 38.462 5.39 1.60 0.00 3.56
2511 2577 6.338146 GGAGTGTTATGTACTAGTGATGCAA 58.662 40.000 5.39 0.00 0.00 4.08
2512 2578 5.163447 GGGAGTGTTATGTACTAGTGATGCA 60.163 44.000 5.39 0.00 0.00 3.96
2513 2579 5.069251 AGGGAGTGTTATGTACTAGTGATGC 59.931 44.000 5.39 0.00 0.00 3.91
2514 2580 6.716934 AGGGAGTGTTATGTACTAGTGATG 57.283 41.667 5.39 0.00 0.00 3.07
2547 2618 5.129634 AGTTCCACACAACACAACATATCA 58.870 37.500 0.00 0.00 0.00 2.15
2548 2619 5.689383 AGTTCCACACAACACAACATATC 57.311 39.130 0.00 0.00 0.00 1.63
2549 2620 6.096141 TGAAAGTTCCACACAACACAACATAT 59.904 34.615 0.00 0.00 0.00 1.78
2550 2621 5.416013 TGAAAGTTCCACACAACACAACATA 59.584 36.000 0.00 0.00 0.00 2.29
2551 2622 4.219507 TGAAAGTTCCACACAACACAACAT 59.780 37.500 0.00 0.00 0.00 2.71
2574 2645 5.645067 CGTCACAATATATCCATGGCTCATT 59.355 40.000 6.96 0.90 0.00 2.57
2601 2672 7.172361 TGTCTTTCACAACGACATATCATTTCA 59.828 33.333 0.00 0.00 33.15 2.69
2693 2764 8.650143 AATGTACAATGGAAACTTGGTTATCT 57.350 30.769 0.00 0.00 0.00 1.98
2699 2770 6.520272 TCCAAAATGTACAATGGAAACTTGG 58.480 36.000 20.09 12.57 38.95 3.61
2721 2792 1.294857 GCTGAGAGCCTCGAATTTCC 58.705 55.000 0.00 0.00 34.48 3.13
2927 3006 6.083630 TGTTTAGTGCGCTGTCATATTTTTC 58.916 36.000 10.80 0.00 0.00 2.29
2929 3008 5.621197 TGTTTAGTGCGCTGTCATATTTT 57.379 34.783 10.80 0.00 0.00 1.82
2931 3010 5.818136 ATTGTTTAGTGCGCTGTCATATT 57.182 34.783 10.80 0.00 0.00 1.28
2932 3011 5.586243 AGAATTGTTTAGTGCGCTGTCATAT 59.414 36.000 10.80 0.00 0.00 1.78
2933 3012 4.935205 AGAATTGTTTAGTGCGCTGTCATA 59.065 37.500 10.80 0.00 0.00 2.15
2934 3013 3.753272 AGAATTGTTTAGTGCGCTGTCAT 59.247 39.130 10.80 0.00 0.00 3.06
2935 3014 3.138304 AGAATTGTTTAGTGCGCTGTCA 58.862 40.909 10.80 3.44 0.00 3.58
2936 3015 3.433615 AGAGAATTGTTTAGTGCGCTGTC 59.566 43.478 10.80 0.00 0.00 3.51
2937 3016 3.403038 AGAGAATTGTTTAGTGCGCTGT 58.597 40.909 10.80 0.00 0.00 4.40
2939 3018 3.437049 GGAAGAGAATTGTTTAGTGCGCT 59.563 43.478 9.73 4.58 0.00 5.92
2940 3019 3.725010 CGGAAGAGAATTGTTTAGTGCGC 60.725 47.826 0.00 0.00 0.00 6.09
2941 3020 3.432252 ACGGAAGAGAATTGTTTAGTGCG 59.568 43.478 0.00 0.00 0.00 5.34
2942 3021 4.213482 ACACGGAAGAGAATTGTTTAGTGC 59.787 41.667 0.00 0.00 0.00 4.40
2943 3022 5.924475 ACACGGAAGAGAATTGTTTAGTG 57.076 39.130 0.00 0.00 0.00 2.74
2944 3023 6.053005 TGAACACGGAAGAGAATTGTTTAGT 58.947 36.000 0.00 0.00 30.60 2.24
2945 3024 6.539649 TGAACACGGAAGAGAATTGTTTAG 57.460 37.500 0.00 0.00 30.60 1.85
2946 3025 6.316640 TGTTGAACACGGAAGAGAATTGTTTA 59.683 34.615 0.00 0.00 30.60 2.01
2947 3026 5.124776 TGTTGAACACGGAAGAGAATTGTTT 59.875 36.000 0.00 0.00 30.60 2.83
2948 3027 4.638421 TGTTGAACACGGAAGAGAATTGTT 59.362 37.500 0.00 0.00 33.12 2.83
2949 3028 4.196193 TGTTGAACACGGAAGAGAATTGT 58.804 39.130 0.00 0.00 0.00 2.71
2953 3032 3.071023 AGGATGTTGAACACGGAAGAGAA 59.929 43.478 0.00 0.00 0.00 2.87
2976 3055 8.933807 GTCTTAGGGAAGTGACACTATTAAAAC 58.066 37.037 8.91 0.00 34.03 2.43
2978 3057 8.431910 AGTCTTAGGGAAGTGACACTATTAAA 57.568 34.615 8.91 0.00 34.03 1.52
2990 3069 6.486993 GTGTGAATTTCAAGTCTTAGGGAAGT 59.513 38.462 0.00 0.00 34.03 3.01
3011 3090 9.994432 GATTCTCCAATTTTTAGTGATAGTGTG 57.006 33.333 0.00 0.00 0.00 3.82
3015 3094 9.098355 TGTCGATTCTCCAATTTTTAGTGATAG 57.902 33.333 0.00 0.00 0.00 2.08
3017 3096 7.390440 TGTGTCGATTCTCCAATTTTTAGTGAT 59.610 33.333 0.00 0.00 0.00 3.06
3030 3109 2.989840 CTGTCTTGTGTGTCGATTCTCC 59.010 50.000 0.00 0.00 0.00 3.71
3037 3116 1.000827 AGAGAGCTGTCTTGTGTGTCG 60.001 52.381 7.74 0.00 30.97 4.35
3042 3121 4.213059 GGAAAAGAAGAGAGCTGTCTTGTG 59.787 45.833 29.07 0.00 36.89 3.33


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

AutoCloner maintained by Alex Coulton.