Multiple sequence alignment - TraesCS1A01G109900

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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 TraesCS1A01G109900 chr1A 100.000 2276 0 0 1 2276 108920279 108918004 0.000000e+00 4204
1 TraesCS1A01G109900 chr3A 96.777 1303 41 1 1 1302 508528753 508530055 0.000000e+00 2172
2 TraesCS1A01G109900 chr3A 95.362 345 10 2 962 1305 25004872 25005211 5.530000e-151 544
3 TraesCS1A01G109900 chr7B 91.648 1305 108 1 1 1304 11598177 11599481 0.000000e+00 1805
4 TraesCS1A01G109900 chr7B 74.625 1265 281 36 59 1302 640268260 640269505 2.590000e-144 521
5 TraesCS1A01G109900 chr1B 91.545 1301 107 3 1 1300 545433178 545434476 0.000000e+00 1790
6 TraesCS1A01G109900 chr1B 90.345 1305 122 4 1 1303 659718245 659716943 0.000000e+00 1709
7 TraesCS1A01G109900 chr1B 92.208 847 65 1 1 846 584318557 584319403 0.000000e+00 1197
8 TraesCS1A01G109900 chr1B 91.831 710 56 2 595 1303 624872815 624873523 0.000000e+00 989
9 TraesCS1A01G109900 chr1B 88.854 323 30 3 1898 2216 121402917 121402597 2.120000e-105 392
10 TraesCS1A01G109900 chr1B 86.174 311 30 8 1373 1670 121403555 121403245 7.840000e-85 324
11 TraesCS1A01G109900 chr4B 91.362 1285 108 3 2 1283 278429766 278428482 0.000000e+00 1755
12 TraesCS1A01G109900 chr3B 89.671 1307 130 5 1 1304 773031742 773030438 0.000000e+00 1661
13 TraesCS1A01G109900 chr1D 88.274 452 35 7 1718 2169 77837478 77837045 2.000000e-145 525
14 TraesCS1A01G109900 chr1D 85.674 356 28 14 1373 1711 77837860 77837511 1.000000e-93 353
15 TraesCS1A01G109900 chr6B 73.232 1244 295 33 59 1283 471152720 471153944 3.500000e-113 418
16 TraesCS1A01G109900 chr6B 72.990 1244 299 32 59 1283 683422486 683421261 3.520000e-108 401
17 TraesCS1A01G109900 chr4A 72.638 1016 249 26 183 1182 73168009 73169011 2.200000e-80 309


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 TraesCS1A01G109900 chr1A 108918004 108920279 2275 True 4204 4204 100.000 1 2276 1 chr1A.!!$R1 2275
1 TraesCS1A01G109900 chr3A 508528753 508530055 1302 False 2172 2172 96.777 1 1302 1 chr3A.!!$F2 1301
2 TraesCS1A01G109900 chr7B 11598177 11599481 1304 False 1805 1805 91.648 1 1304 1 chr7B.!!$F1 1303
3 TraesCS1A01G109900 chr7B 640268260 640269505 1245 False 521 521 74.625 59 1302 1 chr7B.!!$F2 1243
4 TraesCS1A01G109900 chr1B 545433178 545434476 1298 False 1790 1790 91.545 1 1300 1 chr1B.!!$F1 1299
5 TraesCS1A01G109900 chr1B 659716943 659718245 1302 True 1709 1709 90.345 1 1303 1 chr1B.!!$R1 1302
6 TraesCS1A01G109900 chr1B 584318557 584319403 846 False 1197 1197 92.208 1 846 1 chr1B.!!$F2 845
7 TraesCS1A01G109900 chr1B 624872815 624873523 708 False 989 989 91.831 595 1303 1 chr1B.!!$F3 708
8 TraesCS1A01G109900 chr1B 121402597 121403555 958 True 358 392 87.514 1373 2216 2 chr1B.!!$R2 843
9 TraesCS1A01G109900 chr4B 278428482 278429766 1284 True 1755 1755 91.362 2 1283 1 chr4B.!!$R1 1281
10 TraesCS1A01G109900 chr3B 773030438 773031742 1304 True 1661 1661 89.671 1 1304 1 chr3B.!!$R1 1303
11 TraesCS1A01G109900 chr1D 77837045 77837860 815 True 439 525 86.974 1373 2169 2 chr1D.!!$R1 796
12 TraesCS1A01G109900 chr6B 471152720 471153944 1224 False 418 418 73.232 59 1283 1 chr6B.!!$F1 1224
13 TraesCS1A01G109900 chr6B 683421261 683422486 1225 True 401 401 72.990 59 1283 1 chr6B.!!$R1 1224
14 TraesCS1A01G109900 chr4A 73168009 73169011 1002 False 309 309 72.638 183 1182 1 chr4A.!!$F1 999

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
498 499 0.528684 GCTCTACTTAGGTGCAGCCG 60.529 60.0 13.29 4.04 43.7 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2368 0.034767 AGCACCCTCATCACATGTGG 60.035 55.0 25.16 10.9 42.17 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
33 34 5.440610 CATAGCCAACTTTATTCCCACTCT 58.559 41.667 0.00 0.00 0.00 3.24
291 292 0.759436 GAGGAAGGGCAGGATACCGA 60.759 60.000 0.00 0.00 37.17 4.69
302 303 3.681594 GCAGGATACCGAAACTCCAATCA 60.682 47.826 0.00 0.00 37.17 2.57
478 479 4.333926 GCTTATGATGAGGACTTGGAACAC 59.666 45.833 0.00 0.00 39.29 3.32
498 499 0.528684 GCTCTACTTAGGTGCAGCCG 60.529 60.000 13.29 4.04 43.70 5.52
588 589 2.173356 CCTGGGCAAAGGATGTCATCTA 59.827 50.000 12.54 0.00 40.02 1.98
606 607 0.747852 TACAGCGACACACTCACCAA 59.252 50.000 0.00 0.00 0.00 3.67
632 633 4.422840 GGATCGATCGATACTAGTCTCGA 58.577 47.826 29.26 28.55 46.71 4.04
704 705 3.064987 CTTGATCCGGCGACCTCGT 62.065 63.158 9.30 0.00 42.22 4.18
705 706 2.938539 CTTGATCCGGCGACCTCGTC 62.939 65.000 9.30 0.00 42.22 4.20
816 818 2.993220 CGGATTCGTCAAGATCAACACA 59.007 45.455 0.00 0.00 0.00 3.72
956 959 3.868200 AAGCTTTGGCGGTGAGGGG 62.868 63.158 0.00 0.00 44.37 4.79
1044 1047 2.097825 GTAAACCTCTGGGCTACTCGA 58.902 52.381 0.00 0.00 35.63 4.04
1317 1322 2.499214 AAAAAGCAACGCTGGGTGA 58.501 47.368 0.00 0.00 39.62 4.02
1318 1323 1.039856 AAAAAGCAACGCTGGGTGAT 58.960 45.000 0.00 0.00 39.62 3.06
1319 1324 1.904287 AAAAGCAACGCTGGGTGATA 58.096 45.000 0.00 0.00 39.62 2.15
1320 1325 1.453155 AAAGCAACGCTGGGTGATAG 58.547 50.000 0.00 0.00 39.62 2.08
1321 1326 0.324943 AAGCAACGCTGGGTGATAGT 59.675 50.000 0.00 0.00 39.62 2.12
1322 1327 0.324943 AGCAACGCTGGGTGATAGTT 59.675 50.000 0.00 0.00 37.57 2.24
1323 1328 1.165270 GCAACGCTGGGTGATAGTTT 58.835 50.000 0.00 0.00 0.00 2.66
1324 1329 1.539827 GCAACGCTGGGTGATAGTTTT 59.460 47.619 0.00 0.00 0.00 2.43
1325 1330 2.030274 GCAACGCTGGGTGATAGTTTTT 60.030 45.455 0.00 0.00 0.00 1.94
1340 1345 4.905836 TTTTTCGAAACGGAGCGC 57.094 50.000 10.79 0.00 0.00 5.92
1341 1346 2.313267 TTTTTCGAAACGGAGCGCT 58.687 47.368 11.27 11.27 0.00 5.92
1342 1347 0.041663 TTTTTCGAAACGGAGCGCTG 60.042 50.000 18.48 3.12 0.00 5.18
1343 1348 1.837538 TTTTCGAAACGGAGCGCTGG 61.838 55.000 18.48 9.49 0.00 4.85
1344 1349 4.735132 TCGAAACGGAGCGCTGGG 62.735 66.667 18.48 9.04 0.00 4.45
1346 1351 3.423154 GAAACGGAGCGCTGGGTG 61.423 66.667 18.48 3.57 0.00 4.61
1347 1352 3.876589 GAAACGGAGCGCTGGGTGA 62.877 63.158 18.48 0.00 0.00 4.02
1348 1353 3.254024 AAACGGAGCGCTGGGTGAT 62.254 57.895 18.48 2.26 0.00 3.06
1349 1354 1.895020 AAACGGAGCGCTGGGTGATA 61.895 55.000 18.48 0.00 0.00 2.15
1350 1355 2.028190 CGGAGCGCTGGGTGATAG 59.972 66.667 18.48 0.00 0.00 2.08
1351 1356 2.786495 CGGAGCGCTGGGTGATAGT 61.786 63.158 18.48 0.00 0.00 2.12
1352 1357 1.227380 GGAGCGCTGGGTGATAGTG 60.227 63.158 18.48 0.00 0.00 2.74
1353 1358 1.227380 GAGCGCTGGGTGATAGTGG 60.227 63.158 18.48 0.00 0.00 4.00
1354 1359 1.676678 GAGCGCTGGGTGATAGTGGA 61.677 60.000 18.48 0.00 0.00 4.02
1355 1360 1.220749 GCGCTGGGTGATAGTGGAA 59.779 57.895 0.00 0.00 0.00 3.53
1356 1361 0.811616 GCGCTGGGTGATAGTGGAAG 60.812 60.000 0.00 0.00 0.00 3.46
1357 1362 0.811616 CGCTGGGTGATAGTGGAAGC 60.812 60.000 0.00 0.00 0.00 3.86
1358 1363 0.543749 GCTGGGTGATAGTGGAAGCT 59.456 55.000 0.00 0.00 0.00 3.74
1359 1364 1.762957 GCTGGGTGATAGTGGAAGCTA 59.237 52.381 0.00 0.00 0.00 3.32
1360 1365 2.483889 GCTGGGTGATAGTGGAAGCTAC 60.484 54.545 0.00 0.00 0.00 3.58
1361 1366 3.034635 CTGGGTGATAGTGGAAGCTACT 58.965 50.000 0.00 0.00 0.00 2.57
1362 1367 3.031736 TGGGTGATAGTGGAAGCTACTC 58.968 50.000 0.00 0.00 0.00 2.59
1363 1368 2.365941 GGGTGATAGTGGAAGCTACTCC 59.634 54.545 0.00 0.00 35.88 3.85
1364 1369 2.365941 GGTGATAGTGGAAGCTACTCCC 59.634 54.545 1.91 0.00 34.22 4.30
1365 1370 3.031736 GTGATAGTGGAAGCTACTCCCA 58.968 50.000 1.91 0.00 34.22 4.37
1369 1374 2.100605 GTGGAAGCTACTCCCACTTG 57.899 55.000 15.88 0.00 45.08 3.16
1370 1375 0.324943 TGGAAGCTACTCCCACTTGC 59.675 55.000 1.91 0.00 34.22 4.01
1371 1376 0.324943 GGAAGCTACTCCCACTTGCA 59.675 55.000 0.00 0.00 32.62 4.08
1429 1434 1.863454 AGCATCAAACGCGATCTGATC 59.137 47.619 15.93 7.60 0.00 2.92
1504 1516 1.631072 CTTATGCGCTGGTCGTTCG 59.369 57.895 9.73 0.00 41.07 3.95
1569 1594 0.463295 ATGTTGAGCGGCCAGATGAG 60.463 55.000 2.24 0.00 0.00 2.90
1639 1665 4.433805 CGTACGTGCACAATACTCTTTTCC 60.434 45.833 18.64 0.00 0.00 3.13
1641 1667 3.498397 ACGTGCACAATACTCTTTTCCAG 59.502 43.478 18.64 0.00 0.00 3.86
1644 1670 4.702131 GTGCACAATACTCTTTTCCAGGAT 59.298 41.667 13.17 0.00 0.00 3.24
1645 1671 4.943705 TGCACAATACTCTTTTCCAGGATC 59.056 41.667 0.00 0.00 0.00 3.36
1646 1672 5.189180 GCACAATACTCTTTTCCAGGATCT 58.811 41.667 0.00 0.00 0.00 2.75
1647 1673 5.649831 GCACAATACTCTTTTCCAGGATCTT 59.350 40.000 0.00 0.00 0.00 2.40
1663 1692 6.043706 CCAGGATCTTATTACAGGTCAAGGAT 59.956 42.308 0.00 0.00 0.00 3.24
1664 1693 7.158021 CAGGATCTTATTACAGGTCAAGGATC 58.842 42.308 0.00 0.00 0.00 3.36
1665 1694 6.015010 AGGATCTTATTACAGGTCAAGGATCG 60.015 42.308 0.00 0.00 0.00 3.69
1666 1695 4.945246 TCTTATTACAGGTCAAGGATCGC 58.055 43.478 0.00 0.00 0.00 4.58
1667 1696 4.404394 TCTTATTACAGGTCAAGGATCGCA 59.596 41.667 0.00 0.00 0.00 5.10
1668 1697 2.672961 TTACAGGTCAAGGATCGCAG 57.327 50.000 0.00 0.00 0.00 5.18
1669 1698 0.175760 TACAGGTCAAGGATCGCAGC 59.824 55.000 0.00 0.00 0.00 5.25
1673 1702 4.081185 TCAAGGATCGCAGCGGCA 62.081 61.111 16.42 0.00 41.24 5.69
1685 1714 1.823470 AGCGGCAAGCAACTTGTCA 60.823 52.632 12.00 0.00 45.19 3.58
1688 1721 1.005294 CGGCAAGCAACTTGTCATGC 61.005 55.000 12.00 5.26 45.19 4.06
1689 1722 0.668401 GGCAAGCAACTTGTCATGCC 60.668 55.000 14.67 14.67 44.43 4.40
1692 1725 0.963962 AAGCAACTTGTCATGCCCTG 59.036 50.000 0.00 0.00 43.57 4.45
1696 1729 0.178981 AACTTGTCATGCCCTGCAGT 60.179 50.000 13.81 0.00 43.65 4.40
1711 1744 2.199291 GCAGTGGCACTTGCATTATC 57.801 50.000 26.33 5.93 44.36 1.75
1712 1745 1.473677 GCAGTGGCACTTGCATTATCA 59.526 47.619 26.33 0.00 44.36 2.15
1713 1746 2.100252 GCAGTGGCACTTGCATTATCAT 59.900 45.455 26.33 0.33 44.36 2.45
1714 1747 3.702330 CAGTGGCACTTGCATTATCATG 58.298 45.455 19.43 0.00 44.36 3.07
1716 1749 4.336153 CAGTGGCACTTGCATTATCATGTA 59.664 41.667 19.43 0.00 44.36 2.29
1717 1750 4.336433 AGTGGCACTTGCATTATCATGTAC 59.664 41.667 15.88 0.00 44.36 2.90
1718 1751 3.631686 TGGCACTTGCATTATCATGTACC 59.368 43.478 3.15 0.00 44.36 3.34
1719 1752 3.004734 GGCACTTGCATTATCATGTACCC 59.995 47.826 3.15 0.00 44.36 3.69
1720 1753 3.885297 GCACTTGCATTATCATGTACCCT 59.115 43.478 0.00 0.00 41.59 4.34
1721 1754 4.261322 GCACTTGCATTATCATGTACCCTG 60.261 45.833 0.00 0.00 41.59 4.45
1722 1755 3.885297 ACTTGCATTATCATGTACCCTGC 59.115 43.478 0.00 0.00 32.28 4.85
1723 1756 2.493035 TGCATTATCATGTACCCTGCG 58.507 47.619 0.00 0.00 32.28 5.18
1727 1786 1.119684 TATCATGTACCCTGCGTGCT 58.880 50.000 0.00 0.00 0.00 4.40
1759 1818 7.497249 AGAAACTTAGCAAGCTGGTTATCATAG 59.503 37.037 4.53 0.00 0.00 2.23
1765 1824 4.558095 GCAAGCTGGTTATCATAGCATTGG 60.558 45.833 0.00 0.00 39.84 3.16
1788 1847 2.924290 GTTTAGCTGTTCTGTCCGCTAG 59.076 50.000 0.00 0.00 36.46 3.42
1804 1863 2.483714 CGCTAGCCAGAATCCAGCTTAA 60.484 50.000 9.66 0.00 38.06 1.85
1838 1897 0.753848 AGTTGACGTTTTGGGTGGGG 60.754 55.000 0.00 0.00 0.00 4.96
1994 2134 5.066893 TCTGGCATATCTTTTTGACAGCATC 59.933 40.000 0.85 0.00 46.54 3.91
1996 2136 5.419788 TGGCATATCTTTTTGACAGCATCTT 59.580 36.000 0.00 0.00 0.00 2.40
2064 2204 4.853924 AGAGAAAATGCCATGAAAACGT 57.146 36.364 0.00 0.00 0.00 3.99
2069 2209 4.320608 AAATGCCATGAAAACGTTGACT 57.679 36.364 0.00 0.00 0.00 3.41
2084 2224 3.871594 CGTTGACTAATGGAATGGGTCTC 59.128 47.826 0.00 0.00 32.35 3.36
2087 2227 3.118775 TGACTAATGGAATGGGTCTCGTG 60.119 47.826 0.00 0.00 32.35 4.35
2104 2244 3.105187 TGCTTATGCATGGGCTGAG 57.895 52.632 20.68 7.22 45.31 3.35
2111 2251 2.512692 TGCATGGGCTGAGTTACATT 57.487 45.000 0.00 0.00 41.91 2.71
2117 2257 4.150897 TGGGCTGAGTTACATTGGTATC 57.849 45.455 0.00 0.00 0.00 2.24
2120 2260 5.606749 TGGGCTGAGTTACATTGGTATCTAT 59.393 40.000 0.00 0.00 31.33 1.98
2122 2262 6.239600 GGGCTGAGTTACATTGGTATCTATGA 60.240 42.308 4.34 0.00 31.33 2.15
2134 2274 7.786178 TTGGTATCTATGAGTACAAATGTGC 57.214 36.000 0.00 0.00 0.00 4.57
2171 2311 6.422776 ACCAAAAGCAAATCGAGTACATAG 57.577 37.500 0.00 0.00 0.00 2.23
2186 2326 7.603784 TCGAGTACATAGATATACAAAGGCGTA 59.396 37.037 0.00 0.00 0.00 4.42
2192 2332 7.966753 ACATAGATATACAAAGGCGTATACGTG 59.033 37.037 25.04 17.54 37.20 4.49
2210 2350 0.682292 TGTGTGATGTCCGTTGGCTA 59.318 50.000 0.00 0.00 0.00 3.93
2216 2356 2.434336 TGATGTCCGTTGGCTAGCTTAT 59.566 45.455 15.72 0.00 0.00 1.73
2217 2357 2.309528 TGTCCGTTGGCTAGCTTATG 57.690 50.000 15.72 8.14 0.00 1.90
2218 2358 1.134521 TGTCCGTTGGCTAGCTTATGG 60.135 52.381 15.72 16.47 0.00 2.74
2219 2359 0.179056 TCCGTTGGCTAGCTTATGGC 60.179 55.000 15.72 0.00 42.19 4.40
2229 2369 4.929707 CTTATGGCGGCGACCCCC 62.930 72.222 11.74 1.40 0.00 5.40
2237 2377 4.028490 GGCGACCCCCACATGTGA 62.028 66.667 27.46 0.00 0.00 3.58
2238 2378 2.272146 GCGACCCCCACATGTGAT 59.728 61.111 27.46 9.36 0.00 3.06
2239 2379 2.114670 GCGACCCCCACATGTGATG 61.115 63.158 27.46 16.64 0.00 3.07
2240 2380 1.601703 CGACCCCCACATGTGATGA 59.398 57.895 27.46 0.00 0.00 2.92
2241 2381 0.462581 CGACCCCCACATGTGATGAG 60.463 60.000 27.46 14.31 0.00 2.90
2242 2382 0.107017 GACCCCCACATGTGATGAGG 60.107 60.000 27.46 21.12 40.24 3.86
2246 2386 2.485677 CCACATGTGATGAGGGTGC 58.514 57.895 27.46 0.00 37.37 5.01
2247 2387 0.034767 CCACATGTGATGAGGGTGCT 60.035 55.000 27.46 0.00 37.37 4.40
2248 2388 1.376543 CACATGTGATGAGGGTGCTC 58.623 55.000 21.64 0.00 0.00 4.26
2249 2389 0.254178 ACATGTGATGAGGGTGCTCC 59.746 55.000 0.00 0.00 0.00 4.70
2250 2390 0.253894 CATGTGATGAGGGTGCTCCA 59.746 55.000 7.20 0.00 38.24 3.86
2251 2391 1.133884 CATGTGATGAGGGTGCTCCAT 60.134 52.381 7.20 0.00 38.24 3.41
2252 2392 0.253894 TGTGATGAGGGTGCTCCATG 59.746 55.000 7.20 0.00 38.24 3.66
2253 2393 1.099879 GTGATGAGGGTGCTCCATGC 61.100 60.000 7.20 0.00 43.25 4.06
2254 2394 1.890979 GATGAGGGTGCTCCATGCG 60.891 63.158 7.20 0.00 46.63 4.73
2255 2395 2.315781 GATGAGGGTGCTCCATGCGA 62.316 60.000 7.20 0.00 46.63 5.10
2256 2396 2.202987 GAGGGTGCTCCATGCGAG 60.203 66.667 7.20 6.79 46.63 5.03
2257 2397 3.746949 GAGGGTGCTCCATGCGAGG 62.747 68.421 7.20 0.00 46.63 4.63
2258 2398 4.864334 GGGTGCTCCATGCGAGGG 62.864 72.222 7.20 0.00 46.63 4.30
2259 2399 4.101448 GGTGCTCCATGCGAGGGT 62.101 66.667 11.63 0.00 46.63 4.34
2260 2400 2.731571 GGTGCTCCATGCGAGGGTA 61.732 63.158 11.63 0.00 46.63 3.69
2261 2401 1.521681 GTGCTCCATGCGAGGGTAC 60.522 63.158 11.63 0.00 46.63 3.34
2262 2402 1.685765 TGCTCCATGCGAGGGTACT 60.686 57.895 11.63 0.00 46.63 2.73
2263 2403 1.068250 GCTCCATGCGAGGGTACTC 59.932 63.158 11.63 0.00 39.22 2.59
2264 2404 1.395826 GCTCCATGCGAGGGTACTCT 61.396 60.000 0.00 0.00 41.71 3.24
2265 2405 1.982660 CTCCATGCGAGGGTACTCTA 58.017 55.000 0.00 0.00 41.71 2.43
2266 2406 2.520069 CTCCATGCGAGGGTACTCTAT 58.480 52.381 0.00 0.00 41.71 1.98
2267 2407 2.230025 CTCCATGCGAGGGTACTCTATG 59.770 54.545 0.00 0.00 41.71 2.23
2268 2408 1.273606 CCATGCGAGGGTACTCTATGG 59.726 57.143 8.36 8.36 43.40 2.74
2269 2409 1.964223 CATGCGAGGGTACTCTATGGT 59.036 52.381 0.00 0.00 41.71 3.55
2270 2410 1.399714 TGCGAGGGTACTCTATGGTG 58.600 55.000 0.00 0.00 41.71 4.17
2271 2411 1.341679 TGCGAGGGTACTCTATGGTGT 60.342 52.381 0.00 0.00 41.71 4.16
2272 2412 1.067212 GCGAGGGTACTCTATGGTGTG 59.933 57.143 0.00 0.00 41.71 3.82
2273 2413 2.376109 CGAGGGTACTCTATGGTGTGT 58.624 52.381 0.00 0.00 41.71 3.72
2274 2414 2.358267 CGAGGGTACTCTATGGTGTGTC 59.642 54.545 0.00 0.00 41.71 3.67
2275 2415 3.633418 GAGGGTACTCTATGGTGTGTCT 58.367 50.000 0.00 0.00 40.68 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.519107 TGACACCAAATCTGCTATCCTGA 59.481 43.478 0.00 0.00 0.00 3.86
176 177 2.562738 GTGCCCATGCTAAAAAGTCCTT 59.437 45.455 0.00 0.00 38.71 3.36
291 292 4.021719 CCTGTTGCTCATTGATTGGAGTTT 60.022 41.667 0.00 0.00 33.66 2.66
302 303 2.308570 TGTCCCATACCTGTTGCTCATT 59.691 45.455 0.00 0.00 0.00 2.57
451 452 4.166725 TCCAAGTCCTCATCATAAGCCAAT 59.833 41.667 0.00 0.00 0.00 3.16
478 479 0.528684 GGCTGCACCTAAGTAGAGCG 60.529 60.000 0.50 0.00 32.53 5.03
498 499 2.159114 TCTTCCCAAAACTGCTTTGCAC 60.159 45.455 0.00 0.00 42.74 4.57
549 550 1.061546 GGTGAGGGGTTGGAGTGTTA 58.938 55.000 0.00 0.00 0.00 2.41
588 589 0.810031 GTTGGTGAGTGTGTCGCTGT 60.810 55.000 0.00 0.00 35.82 4.40
606 607 4.020039 AGACTAGTATCGATCGATCCCTGT 60.020 45.833 32.50 24.68 36.17 4.00
632 633 4.594491 TGAGTGCCATATAGACCACATCAT 59.406 41.667 0.00 0.00 0.00 2.45
705 706 4.803426 GTCTCCCTCGTGCGGCAG 62.803 72.222 1.18 0.00 0.00 4.85
816 818 1.482182 TCAAGATGTATGGCTGCGTCT 59.518 47.619 0.00 0.00 35.15 4.18
1304 1309 1.165270 AAACTATCACCCAGCGTTGC 58.835 50.000 0.00 0.00 0.00 4.17
1305 1310 3.915437 AAAAACTATCACCCAGCGTTG 57.085 42.857 0.00 0.00 0.00 4.10
1323 1328 0.041663 CAGCGCTCCGTTTCGAAAAA 60.042 50.000 13.10 0.44 0.00 1.94
1324 1329 1.567537 CAGCGCTCCGTTTCGAAAA 59.432 52.632 13.10 0.00 0.00 2.29
1325 1330 2.314647 CCAGCGCTCCGTTTCGAAA 61.315 57.895 7.13 6.47 0.00 3.46
1326 1331 2.736995 CCAGCGCTCCGTTTCGAA 60.737 61.111 7.13 0.00 0.00 3.71
1327 1332 4.735132 CCCAGCGCTCCGTTTCGA 62.735 66.667 7.13 0.00 0.00 3.71
1329 1334 3.423154 CACCCAGCGCTCCGTTTC 61.423 66.667 7.13 0.00 0.00 2.78
1330 1335 1.895020 TATCACCCAGCGCTCCGTTT 61.895 55.000 7.13 0.00 0.00 3.60
1331 1336 2.298158 CTATCACCCAGCGCTCCGTT 62.298 60.000 7.13 0.00 0.00 4.44
1332 1337 2.758327 TATCACCCAGCGCTCCGT 60.758 61.111 7.13 2.81 0.00 4.69
1333 1338 2.028190 CTATCACCCAGCGCTCCG 59.972 66.667 7.13 1.99 0.00 4.63
1334 1339 1.227380 CACTATCACCCAGCGCTCC 60.227 63.158 7.13 0.00 0.00 4.70
1335 1340 1.227380 CCACTATCACCCAGCGCTC 60.227 63.158 7.13 0.00 0.00 5.03
1336 1341 1.264749 TTCCACTATCACCCAGCGCT 61.265 55.000 2.64 2.64 0.00 5.92
1337 1342 0.811616 CTTCCACTATCACCCAGCGC 60.812 60.000 0.00 0.00 0.00 5.92
1338 1343 0.811616 GCTTCCACTATCACCCAGCG 60.812 60.000 0.00 0.00 0.00 5.18
1339 1344 0.543749 AGCTTCCACTATCACCCAGC 59.456 55.000 0.00 0.00 0.00 4.85
1340 1345 3.034635 AGTAGCTTCCACTATCACCCAG 58.965 50.000 0.00 0.00 0.00 4.45
1341 1346 3.031736 GAGTAGCTTCCACTATCACCCA 58.968 50.000 0.00 0.00 0.00 4.51
1342 1347 2.365941 GGAGTAGCTTCCACTATCACCC 59.634 54.545 0.00 0.00 37.20 4.61
1343 1348 2.365941 GGGAGTAGCTTCCACTATCACC 59.634 54.545 6.77 0.00 39.09 4.02
1344 1349 3.031736 TGGGAGTAGCTTCCACTATCAC 58.968 50.000 6.77 0.00 33.52 3.06
1345 1350 3.398318 TGGGAGTAGCTTCCACTATCA 57.602 47.619 6.77 0.00 33.52 2.15
1351 1356 0.324943 GCAAGTGGGAGTAGCTTCCA 59.675 55.000 6.77 0.72 36.67 3.53
1352 1357 0.324943 TGCAAGTGGGAGTAGCTTCC 59.675 55.000 0.00 0.00 36.46 3.46
1353 1358 2.185004 TTGCAAGTGGGAGTAGCTTC 57.815 50.000 0.00 0.00 0.00 3.86
1354 1359 2.508526 CTTTGCAAGTGGGAGTAGCTT 58.491 47.619 0.00 0.00 0.00 3.74
1355 1360 1.884067 GCTTTGCAAGTGGGAGTAGCT 60.884 52.381 7.98 0.00 0.00 3.32
1356 1361 0.523519 GCTTTGCAAGTGGGAGTAGC 59.476 55.000 0.00 0.00 0.00 3.58
1357 1362 1.168714 GGCTTTGCAAGTGGGAGTAG 58.831 55.000 0.00 0.00 0.00 2.57
1358 1363 0.476338 TGGCTTTGCAAGTGGGAGTA 59.524 50.000 0.00 0.00 0.00 2.59
1359 1364 1.109323 GTGGCTTTGCAAGTGGGAGT 61.109 55.000 0.00 0.00 0.00 3.85
1360 1365 1.662044 GTGGCTTTGCAAGTGGGAG 59.338 57.895 0.00 0.00 0.00 4.30
1361 1366 2.192861 CGTGGCTTTGCAAGTGGGA 61.193 57.895 0.00 0.00 0.00 4.37
1362 1367 2.133742 CTCGTGGCTTTGCAAGTGGG 62.134 60.000 0.00 0.00 0.00 4.61
1363 1368 1.283793 CTCGTGGCTTTGCAAGTGG 59.716 57.895 0.00 0.00 0.00 4.00
1364 1369 1.283793 CCTCGTGGCTTTGCAAGTG 59.716 57.895 0.00 0.00 0.00 3.16
1365 1370 1.152963 ACCTCGTGGCTTTGCAAGT 60.153 52.632 2.76 0.00 36.63 3.16
1366 1371 1.283793 CACCTCGTGGCTTTGCAAG 59.716 57.895 2.76 0.00 36.63 4.01
1367 1372 2.844451 GCACCTCGTGGCTTTGCAA 61.844 57.895 11.45 0.00 34.26 4.08
1368 1373 2.390306 TAGCACCTCGTGGCTTTGCA 62.390 55.000 16.82 3.95 41.41 4.08
1369 1374 1.671054 TAGCACCTCGTGGCTTTGC 60.671 57.895 2.76 6.46 41.41 3.68
1370 1375 1.298859 GGTAGCACCTCGTGGCTTTG 61.299 60.000 2.76 0.00 41.41 2.77
1371 1376 1.003718 GGTAGCACCTCGTGGCTTT 60.004 57.895 2.76 0.00 41.41 3.51
1429 1434 1.821332 GGAGGCGAGATTTGCTGGG 60.821 63.158 0.00 0.00 0.00 4.45
1475 1484 2.006772 CGCATAAGCACGAGAACCC 58.993 57.895 0.00 0.00 42.27 4.11
1486 1495 1.631072 CGAACGACCAGCGCATAAG 59.369 57.895 11.47 0.00 46.04 1.73
1504 1516 8.352942 GTGTCATTATTCATGGAAGGATTAACC 58.647 37.037 0.00 0.00 34.48 2.85
1569 1594 1.364626 CTCTGCATCCAACCTGTCGC 61.365 60.000 0.00 0.00 0.00 5.19
1639 1665 6.485830 TCCTTGACCTGTAATAAGATCCTG 57.514 41.667 0.00 0.00 0.00 3.86
1641 1667 6.159988 CGATCCTTGACCTGTAATAAGATCC 58.840 44.000 0.00 0.00 0.00 3.36
1644 1670 4.404394 TGCGATCCTTGACCTGTAATAAGA 59.596 41.667 0.00 0.00 0.00 2.10
1645 1671 4.693283 TGCGATCCTTGACCTGTAATAAG 58.307 43.478 0.00 0.00 0.00 1.73
1646 1672 4.693283 CTGCGATCCTTGACCTGTAATAA 58.307 43.478 0.00 0.00 0.00 1.40
1647 1673 3.492656 GCTGCGATCCTTGACCTGTAATA 60.493 47.826 0.00 0.00 0.00 0.98
1664 1693 4.332637 AAGTTGCTTGCCGCTGCG 62.333 61.111 16.34 16.34 41.78 5.18
1665 1694 2.732094 CAAGTTGCTTGCCGCTGC 60.732 61.111 0.00 0.00 40.11 5.25
1666 1695 1.370900 GACAAGTTGCTTGCCGCTG 60.371 57.895 1.81 0.00 44.43 5.18
1667 1696 1.174712 ATGACAAGTTGCTTGCCGCT 61.175 50.000 1.81 0.00 44.43 5.52
1668 1697 1.005294 CATGACAAGTTGCTTGCCGC 61.005 55.000 1.81 0.71 44.43 6.53
1669 1698 1.005294 GCATGACAAGTTGCTTGCCG 61.005 55.000 18.70 1.79 44.43 5.69
1673 1702 0.963962 CAGGGCATGACAAGTTGCTT 59.036 50.000 0.00 0.00 38.88 3.91
1692 1725 1.473677 TGATAATGCAAGTGCCACTGC 59.526 47.619 0.00 5.22 41.18 4.40
1696 1729 3.631686 GGTACATGATAATGCAAGTGCCA 59.368 43.478 0.00 0.00 40.45 4.92
1711 1744 0.447801 GAAAGCACGCAGGGTACATG 59.552 55.000 0.00 0.00 0.00 3.21
1712 1745 1.019278 CGAAAGCACGCAGGGTACAT 61.019 55.000 0.00 0.00 0.00 2.29
1713 1746 1.666553 CGAAAGCACGCAGGGTACA 60.667 57.895 0.00 0.00 0.00 2.90
1714 1747 0.947180 TTCGAAAGCACGCAGGGTAC 60.947 55.000 0.00 0.00 0.00 3.34
1716 1749 1.961277 CTTCGAAAGCACGCAGGGT 60.961 57.895 0.00 0.00 0.00 4.34
1717 1750 1.227999 TTCTTCGAAAGCACGCAGGG 61.228 55.000 0.00 0.00 0.00 4.45
1718 1751 0.586319 TTTCTTCGAAAGCACGCAGG 59.414 50.000 0.00 0.00 0.00 4.85
1719 1752 1.261619 AGTTTCTTCGAAAGCACGCAG 59.738 47.619 0.00 0.00 0.00 5.18
1720 1753 1.295792 AGTTTCTTCGAAAGCACGCA 58.704 45.000 0.00 0.00 0.00 5.24
1721 1754 2.384899 AAGTTTCTTCGAAAGCACGC 57.615 45.000 0.00 0.00 0.00 5.34
1722 1755 3.059868 TGCTAAGTTTCTTCGAAAGCACG 60.060 43.478 13.01 0.00 33.84 5.34
1723 1756 4.468095 TGCTAAGTTTCTTCGAAAGCAC 57.532 40.909 13.01 3.74 33.84 4.40
1727 1786 4.024048 CCAGCTTGCTAAGTTTCTTCGAAA 60.024 41.667 0.00 0.00 0.00 3.46
1759 1818 3.503748 ACAGAACAGCTAAACTCCAATGC 59.496 43.478 0.00 0.00 0.00 3.56
1765 1824 1.727335 GCGGACAGAACAGCTAAACTC 59.273 52.381 0.00 0.00 0.00 3.01
1804 1863 3.734231 CGTCAACTGATAAACACGACAGT 59.266 43.478 0.00 0.00 43.92 3.55
1870 1931 9.680315 ACGCAGAGAATTACTATAATACAGTTC 57.320 33.333 0.00 0.00 0.00 3.01
1990 2130 1.012841 CTTCCGGAGCAAGAAGATGC 58.987 55.000 3.34 0.00 46.78 3.91
1994 2134 4.116238 GACTAATCTTCCGGAGCAAGAAG 58.884 47.826 8.37 5.33 0.00 2.85
1996 2136 3.366396 AGACTAATCTTCCGGAGCAAGA 58.634 45.455 3.34 5.36 0.00 3.02
2013 2153 2.826725 AGCTAACGAAAGCAGGTAGACT 59.173 45.455 14.46 0.00 45.30 3.24
2052 2192 4.083003 TCCATTAGTCAACGTTTTCATGGC 60.083 41.667 0.00 0.00 31.62 4.40
2064 2204 3.517901 ACGAGACCCATTCCATTAGTCAA 59.482 43.478 0.00 0.00 0.00 3.18
2069 2209 1.837439 AGCACGAGACCCATTCCATTA 59.163 47.619 0.00 0.00 0.00 1.90
2087 2227 1.396653 AACTCAGCCCATGCATAAGC 58.603 50.000 11.26 11.26 41.13 3.09
2111 2251 6.761242 GTGCACATTTGTACTCATAGATACCA 59.239 38.462 13.17 0.00 35.57 3.25
2117 2257 5.861222 TGTGTGCACATTTGTACTCATAG 57.139 39.130 24.69 0.00 37.05 2.23
2161 2301 6.609533 ACGCCTTTGTATATCTATGTACTCG 58.390 40.000 0.00 0.00 0.00 4.18
2166 2306 7.966753 CACGTATACGCCTTTGTATATCTATGT 59.033 37.037 24.64 0.00 44.43 2.29
2171 2311 5.916883 ACACACGTATACGCCTTTGTATATC 59.083 40.000 24.64 0.00 44.43 1.63
2181 2321 1.850441 GACATCACACACGTATACGCC 59.150 52.381 24.64 0.00 44.43 5.68
2186 2326 2.333926 CAACGGACATCACACACGTAT 58.666 47.619 0.00 0.00 36.69 3.06
2192 2332 1.359848 CTAGCCAACGGACATCACAC 58.640 55.000 0.00 0.00 0.00 3.82
2210 2350 4.547367 GGGTCGCCGCCATAAGCT 62.547 66.667 0.33 0.00 40.39 3.74
2220 2360 3.344137 ATCACATGTGGGGGTCGCC 62.344 63.158 25.16 0.00 0.00 5.54
2221 2361 2.114670 CATCACATGTGGGGGTCGC 61.115 63.158 25.16 0.00 0.00 5.19
2222 2362 0.462581 CTCATCACATGTGGGGGTCG 60.463 60.000 25.16 8.11 0.00 4.79
2223 2363 0.107017 CCTCATCACATGTGGGGGTC 60.107 60.000 25.16 0.00 39.60 4.46
2224 2364 2.001803 CCTCATCACATGTGGGGGT 58.998 57.895 25.16 7.03 39.60 4.95
2225 2365 4.993307 CCTCATCACATGTGGGGG 57.007 61.111 25.16 15.64 39.60 5.40
2228 2368 0.034767 AGCACCCTCATCACATGTGG 60.035 55.000 25.16 10.90 42.17 4.17
2229 2369 1.376543 GAGCACCCTCATCACATGTG 58.623 55.000 20.18 20.18 38.03 3.21
2230 2370 0.254178 GGAGCACCCTCATCACATGT 59.746 55.000 0.00 0.00 39.96 3.21
2231 2371 0.253894 TGGAGCACCCTCATCACATG 59.746 55.000 0.00 0.00 39.96 3.21
2232 2372 1.133884 CATGGAGCACCCTCATCACAT 60.134 52.381 0.00 0.00 39.96 3.21
2233 2373 0.253894 CATGGAGCACCCTCATCACA 59.746 55.000 0.00 0.00 39.96 3.58
2234 2374 1.099879 GCATGGAGCACCCTCATCAC 61.100 60.000 0.00 0.00 44.79 3.06
2235 2375 1.225426 GCATGGAGCACCCTCATCA 59.775 57.895 0.00 0.00 44.79 3.07
2236 2376 1.890979 CGCATGGAGCACCCTCATC 60.891 63.158 0.00 0.00 46.13 2.92
2237 2377 2.191375 CGCATGGAGCACCCTCAT 59.809 61.111 0.00 0.00 46.13 2.90
2238 2378 3.002583 TCGCATGGAGCACCCTCA 61.003 61.111 0.00 0.00 46.13 3.86
2239 2379 2.202987 CTCGCATGGAGCACCCTC 60.203 66.667 0.00 0.00 46.13 4.30
2240 2380 3.790437 CCTCGCATGGAGCACCCT 61.790 66.667 0.00 0.00 46.13 4.34
2241 2381 4.864334 CCCTCGCATGGAGCACCC 62.864 72.222 0.00 0.00 46.13 4.61
2242 2382 2.731571 TACCCTCGCATGGAGCACC 61.732 63.158 0.00 0.00 46.13 5.01
2243 2383 1.521681 GTACCCTCGCATGGAGCAC 60.522 63.158 0.00 0.00 46.13 4.40
2244 2384 1.676678 GAGTACCCTCGCATGGAGCA 61.677 60.000 0.00 0.00 46.13 4.26
2245 2385 1.068250 GAGTACCCTCGCATGGAGC 59.932 63.158 0.00 0.00 41.71 4.70
2246 2386 1.982660 TAGAGTACCCTCGCATGGAG 58.017 55.000 0.00 0.00 42.86 3.86
2247 2387 2.239400 CATAGAGTACCCTCGCATGGA 58.761 52.381 0.00 0.00 42.86 3.41
2248 2388 1.273606 CCATAGAGTACCCTCGCATGG 59.726 57.143 10.15 10.15 43.06 3.66
2249 2389 1.964223 ACCATAGAGTACCCTCGCATG 59.036 52.381 0.00 0.00 42.86 4.06
2250 2390 1.964223 CACCATAGAGTACCCTCGCAT 59.036 52.381 0.00 0.00 42.86 4.73
2251 2391 1.341679 ACACCATAGAGTACCCTCGCA 60.342 52.381 0.00 0.00 42.86 5.10
2252 2392 1.067212 CACACCATAGAGTACCCTCGC 59.933 57.143 0.00 0.00 42.86 5.03
2253 2393 2.358267 GACACACCATAGAGTACCCTCG 59.642 54.545 0.00 0.00 42.86 4.63
2254 2394 3.633418 AGACACACCATAGAGTACCCTC 58.367 50.000 0.00 0.00 38.04 4.30
2255 2395 3.759815 AGACACACCATAGAGTACCCT 57.240 47.619 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.