Multiple sequence alignment - TraesCS1D01G113300

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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 TraesCS1D01G113300 chr1D 100.000 2288 0 0 1 2288 109801958 109804245 0.000000e+00 4226
1 TraesCS1D01G113300 chr1A 89.468 864 90 1 457 1320 540374294 540373432 0.000000e+00 1090
2 TraesCS1D01G113300 chr1A 89.356 404 43 0 53 456 540374736 540374333 2.030000e-140 508
3 TraesCS1D01G113300 chr1A 93.496 246 10 3 2008 2247 113484508 113484753 6.010000e-96 361
4 TraesCS1D01G113300 chr1A 93.361 241 14 1 1701 1941 113484254 113484492 2.800000e-94 355
5 TraesCS1D01G113300 chr2A 89.394 858 83 3 457 1313 474745688 474744838 0.000000e+00 1074
6 TraesCS1D01G113300 chr2A 93.069 404 28 0 53 456 688251626 688251223 1.960000e-165 592
7 TraesCS1D01G113300 chr1B 88.747 862 91 6 457 1316 615620865 615621722 0.000000e+00 1050
8 TraesCS1D01G113300 chr1B 86.816 804 82 13 1365 2158 165767615 165768404 0.000000e+00 876
9 TraesCS1D01G113300 chr1B 89.346 413 44 0 44 456 615620414 615620826 9.370000e-144 520
10 TraesCS1D01G113300 chr1B 95.312 64 3 0 2189 2252 165768773 165768836 4.020000e-18 102
11 TraesCS1D01G113300 chr3A 86.295 861 116 1 457 1315 649950497 649951357 0.000000e+00 935
12 TraesCS1D01G113300 chr3A 79.460 852 163 12 470 1315 12942066 12941221 5.440000e-166 593
13 TraesCS1D01G113300 chr3A 87.561 410 49 2 47 455 649950049 649950457 7.400000e-130 473
14 TraesCS1D01G113300 chr6A 87.011 793 101 2 457 1249 375006330 375005540 0.000000e+00 893
15 TraesCS1D01G113300 chr6A 86.759 793 103 2 457 1249 375057666 375056876 0.000000e+00 881
16 TraesCS1D01G113300 chr6A 87.383 745 94 0 470 1214 603427320 603428064 0.000000e+00 856
17 TraesCS1D01G113300 chr6A 89.926 407 41 0 50 456 375058111 375057705 2.010000e-145 525
18 TraesCS1D01G113300 chr6A 89.294 411 40 1 50 456 375006779 375006369 1.570000e-141 512
19 TraesCS1D01G113300 chr6A 85.610 410 57 2 47 455 603426859 603427267 1.620000e-116 429
20 TraesCS1D01G113300 chr2B 79.210 861 169 10 461 1316 639029029 639028174 7.040000e-165 590
21 TraesCS1D01G113300 chr7B 91.133 406 36 0 51 456 191476999 191476594 3.320000e-153 551
22 TraesCS1D01G113300 chr3B 79.525 337 67 2 115 450 450138875 450139210 2.940000e-59 239


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 TraesCS1D01G113300 chr1D 109801958 109804245 2287 False 4226.0 4226 100.0000 1 2288 1 chr1D.!!$F1 2287
1 TraesCS1D01G113300 chr1A 540373432 540374736 1304 True 799.0 1090 89.4120 53 1320 2 chr1A.!!$R1 1267
2 TraesCS1D01G113300 chr2A 474744838 474745688 850 True 1074.0 1074 89.3940 457 1313 1 chr2A.!!$R1 856
3 TraesCS1D01G113300 chr1B 615620414 615621722 1308 False 785.0 1050 89.0465 44 1316 2 chr1B.!!$F2 1272
4 TraesCS1D01G113300 chr1B 165767615 165768836 1221 False 489.0 876 91.0640 1365 2252 2 chr1B.!!$F1 887
5 TraesCS1D01G113300 chr3A 649950049 649951357 1308 False 704.0 935 86.9280 47 1315 2 chr3A.!!$F1 1268
6 TraesCS1D01G113300 chr3A 12941221 12942066 845 True 593.0 593 79.4600 470 1315 1 chr3A.!!$R1 845
7 TraesCS1D01G113300 chr6A 375056876 375058111 1235 True 703.0 881 88.3425 50 1249 2 chr6A.!!$R2 1199
8 TraesCS1D01G113300 chr6A 375005540 375006779 1239 True 702.5 893 88.1525 50 1249 2 chr6A.!!$R1 1199
9 TraesCS1D01G113300 chr6A 603426859 603428064 1205 False 642.5 856 86.4965 47 1214 2 chr6A.!!$F1 1167
10 TraesCS1D01G113300 chr2B 639028174 639029029 855 True 590.0 590 79.2100 461 1316 1 chr2B.!!$R1 855

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
20 21 0.319641 GTTCTCCCGCGTCCATATCC 60.32 60.0 4.92 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1763 0.026674 CGACTAACCGTACGCGATCA 59.973 55.0 15.93 0.0 41.33 2.92 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
17 18 4.021559 TGTTCTCCCGCGTCCATA 57.978 55.556 4.92 0.00 0.00 2.74
18 19 2.511818 TGTTCTCCCGCGTCCATAT 58.488 52.632 4.92 0.00 0.00 1.78
19 20 0.387929 TGTTCTCCCGCGTCCATATC 59.612 55.000 4.92 0.00 0.00 1.63
20 21 0.319641 GTTCTCCCGCGTCCATATCC 60.320 60.000 4.92 0.00 0.00 2.59
21 22 0.757561 TTCTCCCGCGTCCATATCCA 60.758 55.000 4.92 0.00 0.00 3.41
22 23 0.541998 TCTCCCGCGTCCATATCCAT 60.542 55.000 4.92 0.00 0.00 3.41
23 24 0.390340 CTCCCGCGTCCATATCCATG 60.390 60.000 4.92 0.00 0.00 3.66
42 43 2.900528 GACTGGTCCACTGTTCGTG 58.099 57.895 0.00 0.00 43.41 4.35
45 46 1.217882 CTGGTCCACTGTTCGTGAAC 58.782 55.000 5.80 5.80 46.81 3.18
71 72 1.600663 CCGTCGACTGTATCCATGAGC 60.601 57.143 14.70 0.00 0.00 4.26
82 83 2.673775 TCCATGAGCCCACTTTTCAA 57.326 45.000 0.00 0.00 0.00 2.69
96 97 0.526662 TTTCAAACCGCCAAACACGT 59.473 45.000 0.00 0.00 0.00 4.49
106 107 0.790207 CCAAACACGTCGATCACCAG 59.210 55.000 0.00 0.00 0.00 4.00
173 174 2.030007 CCTTGTCCGTGCAACATTCATT 60.030 45.455 0.00 0.00 35.74 2.57
180 181 3.687212 CCGTGCAACATTCATTACACCTA 59.313 43.478 0.00 0.00 35.74 3.08
236 241 0.903236 GTGGTGGGGAGGACTTCTAC 59.097 60.000 0.00 0.00 0.00 2.59
248 253 0.602905 ACTTCTACGCTTGGGCACAC 60.603 55.000 0.00 0.00 38.60 3.82
313 318 5.724328 TCTAATGAATCAGAAAGAGCGTGT 58.276 37.500 0.00 0.00 0.00 4.49
330 335 3.018149 CGTGTAGCTCTAGAAGAAGGGT 58.982 50.000 0.00 0.00 0.00 4.34
359 364 0.379669 GGCCATCAGCGAATGAACAG 59.620 55.000 0.00 0.00 45.17 3.16
371 376 1.747709 ATGAACAGCAGATGTGGAGC 58.252 50.000 0.00 0.00 43.00 4.70
385 390 1.968540 GGAGCGCCATATGGAAGCC 60.969 63.158 28.11 21.53 39.90 4.35
401 406 3.580895 GGAAGCCCAAATTAGTTCCCAAA 59.419 43.478 0.00 0.00 32.05 3.28
408 413 5.076873 CCAAATTAGTTCCCAAAGTCAGGA 58.923 41.667 0.00 0.00 0.00 3.86
1027 1071 0.249911 GCAACTGGAGACCGACTGTT 60.250 55.000 0.00 0.00 0.00 3.16
1034 1078 1.070289 GGAGACCGACTGTTTTGAGGT 59.930 52.381 0.00 0.00 38.00 3.85
1070 1114 6.152323 TGGAACTCTAGCTACACTAATCGTTT 59.848 38.462 0.00 0.00 0.00 3.60
1130 1174 4.207165 TCTGCTAGCTTTTTGTCCTTTGT 58.793 39.130 17.23 0.00 0.00 2.83
1141 1185 8.730680 GCTTTTTGTCCTTTGTTATCTCTCATA 58.269 33.333 0.00 0.00 0.00 2.15
1229 1273 1.034838 AGCTGGCTAGACTCCACTCG 61.035 60.000 0.00 0.00 0.00 4.18
1298 1344 9.113838 TGCCTTTATTCAATAAAGCTCTCTAAG 57.886 33.333 20.50 8.59 46.49 2.18
1341 1387 9.415544 AGATGTGAAAGAAAATTTACAGATTGC 57.584 29.630 0.00 0.00 33.10 3.56
1342 1388 7.945033 TGTGAAAGAAAATTTACAGATTGCC 57.055 32.000 0.00 0.00 0.00 4.52
1343 1389 6.640499 TGTGAAAGAAAATTTACAGATTGCCG 59.360 34.615 0.00 0.00 0.00 5.69
1344 1390 6.640907 GTGAAAGAAAATTTACAGATTGCCGT 59.359 34.615 0.00 0.00 0.00 5.68
1345 1391 7.169140 GTGAAAGAAAATTTACAGATTGCCGTT 59.831 33.333 0.00 0.00 0.00 4.44
1346 1392 8.353684 TGAAAGAAAATTTACAGATTGCCGTTA 58.646 29.630 0.00 0.00 0.00 3.18
1347 1393 9.187455 GAAAGAAAATTTACAGATTGCCGTTAA 57.813 29.630 0.00 0.00 0.00 2.01
1348 1394 9.535878 AAAGAAAATTTACAGATTGCCGTTAAA 57.464 25.926 0.00 0.00 0.00 1.52
1349 1395 9.535878 AAGAAAATTTACAGATTGCCGTTAAAA 57.464 25.926 0.00 0.00 0.00 1.52
1350 1396 9.535878 AGAAAATTTACAGATTGCCGTTAAAAA 57.464 25.926 0.00 0.00 0.00 1.94
1353 1399 6.698359 TTTACAGATTGCCGTTAAAAATGC 57.302 33.333 0.00 0.00 0.00 3.56
1354 1400 3.584834 ACAGATTGCCGTTAAAAATGCC 58.415 40.909 0.00 0.00 0.00 4.40
1355 1401 2.929398 CAGATTGCCGTTAAAAATGCCC 59.071 45.455 0.00 0.00 0.00 5.36
1356 1402 2.831526 AGATTGCCGTTAAAAATGCCCT 59.168 40.909 0.00 0.00 0.00 5.19
1357 1403 3.260632 AGATTGCCGTTAAAAATGCCCTT 59.739 39.130 0.00 0.00 0.00 3.95
1358 1404 4.464597 AGATTGCCGTTAAAAATGCCCTTA 59.535 37.500 0.00 0.00 0.00 2.69
1359 1405 3.579335 TGCCGTTAAAAATGCCCTTAC 57.421 42.857 0.00 0.00 0.00 2.34
1360 1406 2.891580 TGCCGTTAAAAATGCCCTTACA 59.108 40.909 0.00 0.00 0.00 2.41
1361 1407 3.321111 TGCCGTTAAAAATGCCCTTACAA 59.679 39.130 0.00 0.00 0.00 2.41
1362 1408 4.202223 TGCCGTTAAAAATGCCCTTACAAA 60.202 37.500 0.00 0.00 0.00 2.83
1363 1409 4.387559 GCCGTTAAAAATGCCCTTACAAAG 59.612 41.667 0.00 0.00 0.00 2.77
1367 1413 6.516028 CGTTAAAAATGCCCTTACAAAGAGGT 60.516 38.462 0.00 0.00 32.15 3.85
1374 1420 2.582052 CCTTACAAAGAGGTTGCCACA 58.418 47.619 0.00 0.00 41.31 4.17
1389 1435 1.609635 CCACACCCACATGCATGCAT 61.610 55.000 27.46 27.46 37.08 3.96
1407 1453 2.089201 CATGCAGCAATCAGTCTTCCA 58.911 47.619 0.00 0.00 0.00 3.53
1413 1459 3.567164 CAGCAATCAGTCTTCCACAACTT 59.433 43.478 0.00 0.00 0.00 2.66
1422 1468 4.335594 AGTCTTCCACAACTTTGCTAACAC 59.664 41.667 0.00 0.00 0.00 3.32
1443 1489 3.381272 ACCCCGAAACATGATGCTAAATG 59.619 43.478 0.00 0.00 0.00 2.32
1460 1506 1.890876 ATGCAAGTCCAGCACGTTTA 58.109 45.000 0.00 0.00 45.95 2.01
1520 1566 1.079819 GCTGTCGTGCTAGCTGGAA 60.080 57.895 17.23 0.00 36.99 3.53
1521 1567 1.080995 GCTGTCGTGCTAGCTGGAAG 61.081 60.000 17.23 12.70 36.99 3.46
1591 1637 1.207329 CAAGACACCTACCTACCCTGC 59.793 57.143 0.00 0.00 0.00 4.85
1592 1638 0.683504 AGACACCTACCTACCCTGCG 60.684 60.000 0.00 0.00 0.00 5.18
1593 1639 2.294132 GACACCTACCTACCCTGCGC 62.294 65.000 0.00 0.00 0.00 6.09
1594 1640 2.058595 CACCTACCTACCCTGCGCT 61.059 63.158 9.73 0.00 0.00 5.92
1595 1641 2.058595 ACCTACCTACCCTGCGCTG 61.059 63.158 9.73 8.47 0.00 5.18
1636 1682 4.416738 GGAGGAGGTGTGGCAGCC 62.417 72.222 3.66 3.66 31.60 4.85
1656 1702 1.983605 CAGTGTCGACCGAATACACAC 59.016 52.381 14.12 1.33 44.68 3.82
1657 1703 0.979811 GTGTCGACCGAATACACACG 59.020 55.000 14.12 0.00 42.40 4.49
1658 1704 0.592637 TGTCGACCGAATACACACGT 59.407 50.000 14.12 0.00 0.00 4.49
1661 1707 2.076100 TCGACCGAATACACACGTACT 58.924 47.619 0.00 0.00 0.00 2.73
1662 1708 2.159667 TCGACCGAATACACACGTACTG 60.160 50.000 0.00 0.00 0.00 2.74
1663 1709 2.523015 GACCGAATACACACGTACTGG 58.477 52.381 0.00 0.00 0.00 4.00
1664 1710 1.888512 ACCGAATACACACGTACTGGT 59.111 47.619 0.00 0.00 0.00 4.00
1665 1711 2.095059 ACCGAATACACACGTACTGGTC 60.095 50.000 0.00 0.00 28.56 4.02
1666 1712 2.171567 CGAATACACACGTACTGGTCG 58.828 52.381 0.00 0.00 0.00 4.79
1667 1713 1.916000 GAATACACACGTACTGGTCGC 59.084 52.381 0.00 0.00 0.00 5.19
1702 1754 1.343377 TGAGCCTGAGCAGAGGGATAA 60.343 52.381 0.00 0.00 43.56 1.75
1711 1763 2.578021 AGCAGAGGGATAACACAATGGT 59.422 45.455 0.00 0.00 0.00 3.55
1739 1791 1.574134 ACGGTTAGTCGTTGGTGTTG 58.426 50.000 0.00 0.00 40.85 3.33
1752 1804 0.512952 GGTGTTGTGAGCATGTCGAC 59.487 55.000 9.11 9.11 0.00 4.20
1802 1854 3.809013 GGGATGGGCGGGACACAT 61.809 66.667 0.00 0.00 0.00 3.21
1808 1860 2.813908 GGCGGGACACATGTCGAC 60.814 66.667 9.11 9.11 45.65 4.20
1832 1884 1.711060 CCGACCACGCGGCATTTAAT 61.711 55.000 12.47 0.00 45.38 1.40
1882 1934 1.463553 CCGGCCTGGGATTAATTGGC 61.464 60.000 0.00 11.70 42.56 4.52
1883 1935 0.754957 CGGCCTGGGATTAATTGGCA 60.755 55.000 17.94 0.00 44.85 4.92
1949 2001 2.202878 GCGCGCTCCAGGTTGATA 60.203 61.111 26.67 0.00 0.00 2.15
1950 2002 1.813753 GCGCGCTCCAGGTTGATAA 60.814 57.895 26.67 0.00 0.00 1.75
1951 2003 1.160329 GCGCGCTCCAGGTTGATAAT 61.160 55.000 26.67 0.00 0.00 1.28
1952 2004 1.299541 CGCGCTCCAGGTTGATAATT 58.700 50.000 5.56 0.00 0.00 1.40
1953 2005 1.670811 CGCGCTCCAGGTTGATAATTT 59.329 47.619 5.56 0.00 0.00 1.82
1954 2006 2.097466 CGCGCTCCAGGTTGATAATTTT 59.903 45.455 5.56 0.00 0.00 1.82
1955 2007 3.427503 CGCGCTCCAGGTTGATAATTTTT 60.428 43.478 5.56 0.00 0.00 1.94
1991 2043 3.775316 AGGACTCCAGGTTGATATTCGTT 59.225 43.478 0.00 0.00 0.00 3.85
1995 2063 3.680490 TCCAGGTTGATATTCGTTTGCA 58.320 40.909 0.00 0.00 0.00 4.08
1998 2066 4.799949 CCAGGTTGATATTCGTTTGCAATG 59.200 41.667 0.00 0.00 0.00 2.82
2022 2090 5.639757 CATGCACATACGATTTCTTTGGAA 58.360 37.500 0.00 0.00 0.00 3.53
2112 2181 1.337071 GGATCGATCGAGTAGTTGGCA 59.663 52.381 23.84 0.00 0.00 4.92
2118 2187 0.037326 TCGAGTAGTTGGCAGGCAAG 60.037 55.000 10.23 0.00 0.00 4.01
2124 2193 1.999648 AGTTGGCAGGCAAGATGAAA 58.000 45.000 10.23 0.00 0.00 2.69
2125 2194 2.318908 AGTTGGCAGGCAAGATGAAAA 58.681 42.857 10.23 0.00 0.00 2.29
2126 2195 2.699846 AGTTGGCAGGCAAGATGAAAAA 59.300 40.909 10.23 0.00 0.00 1.94
2127 2196 3.325716 AGTTGGCAGGCAAGATGAAAAAT 59.674 39.130 10.23 0.00 0.00 1.82
2158 2227 4.507756 GCTATTCATGCTGACACGTATTCA 59.492 41.667 0.00 0.00 0.00 2.57
2167 2562 2.677337 TGACACGTATTCATGCACATGG 59.323 45.455 10.58 0.00 39.24 3.66
2184 2579 1.865865 TGGCAAGTCTCAAGAACGAC 58.134 50.000 0.00 0.00 0.00 4.34
2217 2624 0.384725 GCATGCGTCATTATGTCCGC 60.385 55.000 19.07 19.07 45.92 5.54
2252 2659 4.446371 TCGCCCATTTTTCATGTTTTTGT 58.554 34.783 0.00 0.00 0.00 2.83
2253 2660 4.878397 TCGCCCATTTTTCATGTTTTTGTT 59.122 33.333 0.00 0.00 0.00 2.83
2254 2661 5.355350 TCGCCCATTTTTCATGTTTTTGTTT 59.645 32.000 0.00 0.00 0.00 2.83
2255 2662 5.454877 CGCCCATTTTTCATGTTTTTGTTTG 59.545 36.000 0.00 0.00 0.00 2.93
2256 2663 5.231779 GCCCATTTTTCATGTTTTTGTTTGC 59.768 36.000 0.00 0.00 0.00 3.68
2257 2664 6.562518 CCCATTTTTCATGTTTTTGTTTGCT 58.437 32.000 0.00 0.00 0.00 3.91
2258 2665 6.472808 CCCATTTTTCATGTTTTTGTTTGCTG 59.527 34.615 0.00 0.00 0.00 4.41
2259 2666 7.028361 CCATTTTTCATGTTTTTGTTTGCTGT 58.972 30.769 0.00 0.00 0.00 4.40
2260 2667 7.008447 CCATTTTTCATGTTTTTGTTTGCTGTG 59.992 33.333 0.00 0.00 0.00 3.66
2261 2668 5.542616 TTTCATGTTTTTGTTTGCTGTGG 57.457 34.783 0.00 0.00 0.00 4.17
2262 2669 3.529533 TCATGTTTTTGTTTGCTGTGGG 58.470 40.909 0.00 0.00 0.00 4.61
2263 2670 1.731720 TGTTTTTGTTTGCTGTGGGC 58.268 45.000 0.00 0.00 42.22 5.36
2264 2671 1.013596 GTTTTTGTTTGCTGTGGGCC 58.986 50.000 0.00 0.00 40.92 5.80
2265 2672 0.908198 TTTTTGTTTGCTGTGGGCCT 59.092 45.000 4.53 0.00 40.92 5.19
2266 2673 1.781786 TTTTGTTTGCTGTGGGCCTA 58.218 45.000 4.53 0.00 40.92 3.93
2267 2674 1.036707 TTTGTTTGCTGTGGGCCTAC 58.963 50.000 13.24 13.24 40.92 3.18
2268 2675 1.169661 TTGTTTGCTGTGGGCCTACG 61.170 55.000 15.22 10.45 40.92 3.51
2269 2676 2.033448 TTTGCTGTGGGCCTACGG 59.967 61.111 23.17 23.17 40.92 4.02
2270 2677 2.824880 TTTGCTGTGGGCCTACGGT 61.825 57.895 27.01 0.00 40.92 4.83
2271 2678 3.545124 TTGCTGTGGGCCTACGGTG 62.545 63.158 27.01 14.75 40.92 4.94
2272 2679 4.016706 GCTGTGGGCCTACGGTGT 62.017 66.667 27.01 0.00 34.27 4.16
2273 2680 2.264794 CTGTGGGCCTACGGTGTC 59.735 66.667 19.59 0.00 0.00 3.67
2274 2681 2.524640 TGTGGGCCTACGGTGTCA 60.525 61.111 15.22 0.00 0.00 3.58
2275 2682 2.264794 GTGGGCCTACGGTGTCAG 59.735 66.667 2.40 0.00 0.00 3.51
2276 2683 2.118732 TGGGCCTACGGTGTCAGA 59.881 61.111 4.53 0.00 0.00 3.27
2277 2684 1.305802 TGGGCCTACGGTGTCAGAT 60.306 57.895 4.53 0.00 0.00 2.90
2278 2685 1.144057 GGGCCTACGGTGTCAGATG 59.856 63.158 0.84 0.00 0.00 2.90
2279 2686 1.327690 GGGCCTACGGTGTCAGATGA 61.328 60.000 0.84 0.00 0.00 2.92
2280 2687 0.753262 GGCCTACGGTGTCAGATGAT 59.247 55.000 0.00 0.00 0.00 2.45
2281 2688 1.961394 GGCCTACGGTGTCAGATGATA 59.039 52.381 0.00 0.00 0.00 2.15
2282 2689 2.288273 GGCCTACGGTGTCAGATGATAC 60.288 54.545 0.00 1.43 35.73 2.24
2283 2690 2.623889 GCCTACGGTGTCAGATGATACT 59.376 50.000 9.22 0.00 36.56 2.12
2284 2691 3.819337 GCCTACGGTGTCAGATGATACTA 59.181 47.826 9.22 0.00 36.56 1.82
2285 2692 4.459685 GCCTACGGTGTCAGATGATACTAT 59.540 45.833 9.22 1.87 36.56 2.12
2286 2693 5.047943 GCCTACGGTGTCAGATGATACTATT 60.048 44.000 9.22 0.00 36.56 1.73
2287 2694 6.150641 GCCTACGGTGTCAGATGATACTATTA 59.849 42.308 9.22 0.00 36.56 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.387929 GATATGGACGCGGGAGAACA 59.612 55.000 12.47 0.00 0.00 3.18
1 2 0.319641 GGATATGGACGCGGGAGAAC 60.320 60.000 12.47 0.00 0.00 3.01
2 3 0.757561 TGGATATGGACGCGGGAGAA 60.758 55.000 12.47 0.00 0.00 2.87
3 4 0.541998 ATGGATATGGACGCGGGAGA 60.542 55.000 12.47 0.00 0.00 3.71
4 5 0.390340 CATGGATATGGACGCGGGAG 60.390 60.000 12.47 0.00 0.00 4.30
5 6 1.671166 CATGGATATGGACGCGGGA 59.329 57.895 12.47 0.00 0.00 5.14
6 7 4.284123 CATGGATATGGACGCGGG 57.716 61.111 12.47 0.00 0.00 6.13
24 25 2.900528 CACGAACAGTGGACCAGTC 58.099 57.895 0.00 0.00 46.77 3.51
33 34 0.949105 GGCATCCGTTCACGAACAGT 60.949 55.000 10.35 0.00 43.02 3.55
34 35 1.787847 GGCATCCGTTCACGAACAG 59.212 57.895 10.35 0.00 43.02 3.16
35 36 2.024868 CGGCATCCGTTCACGAACA 61.025 57.895 10.35 0.00 42.73 3.18
36 37 2.776072 CGGCATCCGTTCACGAAC 59.224 61.111 0.00 0.00 42.73 3.95
48 49 2.500352 TGGATACAGTCGACGGCAT 58.500 52.632 15.92 8.47 46.17 4.40
71 72 0.461961 TTGGCGGTTTGAAAAGTGGG 59.538 50.000 0.00 0.00 0.00 4.61
82 83 1.562575 GATCGACGTGTTTGGCGGTT 61.563 55.000 0.00 0.00 0.00 4.44
173 174 1.226745 CGCGTCCGCATTAGGTGTA 60.227 57.895 12.58 0.00 42.06 2.90
236 241 2.842394 ATCTCTCGTGTGCCCAAGCG 62.842 60.000 0.00 0.00 44.31 4.68
248 253 2.294791 AGAATAAGTGCCGGATCTCTCG 59.705 50.000 5.05 0.00 0.00 4.04
313 318 6.478129 GCTATCTACCCTTCTTCTAGAGCTA 58.522 44.000 0.00 0.00 0.00 3.32
330 335 1.544825 GCTGATGGCCCCGCTATCTA 61.545 60.000 0.00 0.00 44.86 1.98
359 364 0.604780 ATATGGCGCTCCACATCTGC 60.605 55.000 7.64 0.00 46.92 4.26
371 376 1.331214 ATTTGGGCTTCCATATGGCG 58.669 50.000 17.58 11.27 40.80 5.69
385 390 5.076873 TCCTGACTTTGGGAACTAATTTGG 58.923 41.667 0.00 0.00 0.00 3.28
390 395 4.993705 ACATCCTGACTTTGGGAACTAA 57.006 40.909 0.00 0.00 35.08 2.24
401 406 1.905215 CTCCACCAGAACATCCTGACT 59.095 52.381 0.00 0.00 36.29 3.41
408 413 4.466370 TCGAATAACTCTCCACCAGAACAT 59.534 41.667 0.00 0.00 0.00 2.71
466 509 1.208052 CATCAGGTCCTCGTCCATTGT 59.792 52.381 0.00 0.00 0.00 2.71
468 511 0.179000 GCATCAGGTCCTCGTCCATT 59.821 55.000 0.00 0.00 0.00 3.16
584 627 5.217393 GTTGTTCACAGAGTATGTCGTGTA 58.783 41.667 0.00 0.00 41.41 2.90
587 630 3.305964 CGTTGTTCACAGAGTATGTCGT 58.694 45.455 0.00 0.00 41.41 4.34
849 892 4.789075 GCACCTGCATTGCCAGCG 62.789 66.667 6.12 1.73 41.59 5.18
987 1031 1.749063 ACGTGCATGTATCCTCGAAGA 59.251 47.619 10.57 0.00 0.00 2.87
1017 1061 3.382048 ACTACCTCAAAACAGTCGGTC 57.618 47.619 0.00 0.00 0.00 4.79
1034 1078 5.828871 AGCTAGAGTTCCAGAGGTTTACTA 58.171 41.667 0.00 0.00 0.00 1.82
1070 1114 3.767673 AGAAAGAATCGGTGCTACTACCA 59.232 43.478 0.00 0.00 40.89 3.25
1141 1185 6.471146 CAGGACCATTAGCAGCTCTTATTAT 58.529 40.000 0.00 0.00 0.00 1.28
1177 1221 3.380479 AAGTGTACAAGCACGCTTAGA 57.620 42.857 3.53 0.00 45.09 2.10
1229 1273 1.137282 GGCTACTGACCAGGAAGCTAC 59.863 57.143 19.14 6.77 39.78 3.58
1320 1366 6.744112 ACGGCAATCTGTAAATTTTCTTTCA 58.256 32.000 0.00 0.00 0.00 2.69
1321 1367 7.637709 AACGGCAATCTGTAAATTTTCTTTC 57.362 32.000 0.00 0.00 0.00 2.62
1322 1368 9.535878 TTTAACGGCAATCTGTAAATTTTCTTT 57.464 25.926 0.00 0.00 0.00 2.52
1323 1369 9.535878 TTTTAACGGCAATCTGTAAATTTTCTT 57.464 25.926 0.00 0.00 0.00 2.52
1324 1370 9.535878 TTTTTAACGGCAATCTGTAAATTTTCT 57.464 25.926 0.00 0.00 0.00 2.52
1327 1373 8.227119 GCATTTTTAACGGCAATCTGTAAATTT 58.773 29.630 0.00 0.00 0.00 1.82
1328 1374 7.148490 GGCATTTTTAACGGCAATCTGTAAATT 60.148 33.333 0.00 0.00 0.00 1.82
1329 1375 6.312672 GGCATTTTTAACGGCAATCTGTAAAT 59.687 34.615 0.00 0.00 0.00 1.40
1330 1376 5.635700 GGCATTTTTAACGGCAATCTGTAAA 59.364 36.000 0.00 0.00 0.00 2.01
1331 1377 5.164954 GGCATTTTTAACGGCAATCTGTAA 58.835 37.500 0.00 0.00 0.00 2.41
1332 1378 4.381079 GGGCATTTTTAACGGCAATCTGTA 60.381 41.667 0.00 0.00 0.00 2.74
1333 1379 3.584834 GGCATTTTTAACGGCAATCTGT 58.415 40.909 0.00 0.00 0.00 3.41
1334 1380 2.929398 GGGCATTTTTAACGGCAATCTG 59.071 45.455 0.00 0.00 0.00 2.90
1335 1381 2.831526 AGGGCATTTTTAACGGCAATCT 59.168 40.909 0.00 0.00 0.00 2.40
1336 1382 3.245518 AGGGCATTTTTAACGGCAATC 57.754 42.857 0.00 0.00 0.00 2.67
1337 1383 3.694043 AAGGGCATTTTTAACGGCAAT 57.306 38.095 0.00 0.00 0.00 3.56
1338 1384 3.321111 TGTAAGGGCATTTTTAACGGCAA 59.679 39.130 0.00 0.00 0.00 4.52
1339 1385 2.891580 TGTAAGGGCATTTTTAACGGCA 59.108 40.909 0.00 0.00 0.00 5.69
1340 1386 3.579335 TGTAAGGGCATTTTTAACGGC 57.421 42.857 0.00 0.00 0.00 5.68
1341 1387 5.774630 TCTTTGTAAGGGCATTTTTAACGG 58.225 37.500 0.00 0.00 0.00 4.44
1342 1388 5.861787 CCTCTTTGTAAGGGCATTTTTAACG 59.138 40.000 0.00 0.00 0.00 3.18
1343 1389 6.755206 ACCTCTTTGTAAGGGCATTTTTAAC 58.245 36.000 0.00 0.00 38.29 2.01
1344 1390 6.987403 ACCTCTTTGTAAGGGCATTTTTAA 57.013 33.333 0.00 0.00 38.29 1.52
1345 1391 6.740122 GCAACCTCTTTGTAAGGGCATTTTTA 60.740 38.462 0.00 0.00 38.29 1.52
1346 1392 5.610398 CAACCTCTTTGTAAGGGCATTTTT 58.390 37.500 0.00 0.00 38.29 1.94
1347 1393 4.503123 GCAACCTCTTTGTAAGGGCATTTT 60.503 41.667 0.00 0.00 38.29 1.82
1348 1394 3.006859 GCAACCTCTTTGTAAGGGCATTT 59.993 43.478 0.00 0.00 38.29 2.32
1349 1395 2.562738 GCAACCTCTTTGTAAGGGCATT 59.437 45.455 0.00 0.00 38.29 3.56
1350 1396 2.171003 GCAACCTCTTTGTAAGGGCAT 58.829 47.619 0.00 0.00 38.29 4.40
1351 1397 1.616159 GCAACCTCTTTGTAAGGGCA 58.384 50.000 0.00 0.00 38.29 5.36
1352 1398 0.888619 GGCAACCTCTTTGTAAGGGC 59.111 55.000 0.00 0.00 38.29 5.19
1353 1399 1.886542 GTGGCAACCTCTTTGTAAGGG 59.113 52.381 0.00 0.00 38.29 3.95
1354 1400 2.293399 GTGTGGCAACCTCTTTGTAAGG 59.707 50.000 0.00 0.00 37.54 2.69
1355 1401 2.293399 GGTGTGGCAACCTCTTTGTAAG 59.707 50.000 10.41 0.00 37.54 2.34
1356 1402 2.303175 GGTGTGGCAACCTCTTTGTAA 58.697 47.619 10.41 0.00 37.54 2.41
1357 1403 1.477923 GGGTGTGGCAACCTCTTTGTA 60.478 52.381 15.29 0.00 38.38 2.41
1358 1404 0.755327 GGGTGTGGCAACCTCTTTGT 60.755 55.000 15.29 0.00 38.38 2.83
1359 1405 0.754957 TGGGTGTGGCAACCTCTTTG 60.755 55.000 15.29 0.00 42.67 2.77
1360 1406 0.755327 GTGGGTGTGGCAACCTCTTT 60.755 55.000 15.29 0.00 42.67 2.52
1361 1407 1.152756 GTGGGTGTGGCAACCTCTT 60.153 57.895 15.29 0.00 42.67 2.85
1362 1408 1.719063 ATGTGGGTGTGGCAACCTCT 61.719 55.000 15.29 0.63 42.67 3.69
1363 1409 1.228552 ATGTGGGTGTGGCAACCTC 60.229 57.895 15.29 1.70 42.67 3.85
1367 1413 1.533513 ATGCATGTGGGTGTGGCAA 60.534 52.632 0.00 0.00 38.08 4.52
1389 1435 1.202794 TGTGGAAGACTGATTGCTGCA 60.203 47.619 0.00 0.00 0.00 4.41
1390 1436 1.527034 TGTGGAAGACTGATTGCTGC 58.473 50.000 0.00 0.00 0.00 5.25
1391 1437 3.144506 AGTTGTGGAAGACTGATTGCTG 58.855 45.455 0.00 0.00 0.00 4.41
1392 1438 3.498774 AGTTGTGGAAGACTGATTGCT 57.501 42.857 0.00 0.00 0.00 3.91
1396 1442 3.825328 AGCAAAGTTGTGGAAGACTGAT 58.175 40.909 0.00 0.00 0.00 2.90
1401 1447 3.630312 GGTGTTAGCAAAGTTGTGGAAGA 59.370 43.478 0.00 0.00 0.00 2.87
1407 1453 1.134037 TCGGGGTGTTAGCAAAGTTGT 60.134 47.619 0.00 0.00 0.00 3.32
1413 1459 1.883275 CATGTTTCGGGGTGTTAGCAA 59.117 47.619 0.00 0.00 0.00 3.91
1422 1468 3.796504 GCATTTAGCATCATGTTTCGGGG 60.797 47.826 0.00 0.00 44.79 5.73
1443 1489 0.110192 GCTAAACGTGCTGGACTTGC 60.110 55.000 0.00 0.00 0.00 4.01
1474 1520 4.383602 CCAACAGGCCGAAACGCG 62.384 66.667 3.53 3.53 40.47 6.01
1533 1579 0.240145 CGCCTGTACGAACTGTCAGA 59.760 55.000 6.91 0.00 34.06 3.27
1535 1581 1.287815 CCGCCTGTACGAACTGTCA 59.712 57.895 0.00 0.00 34.06 3.58
1592 1638 3.777925 CACTACGCACGGCACAGC 61.778 66.667 0.00 0.00 0.00 4.40
1593 1639 3.777925 GCACTACGCACGGCACAG 61.778 66.667 0.00 0.00 41.79 3.66
1607 1653 4.408821 TCCTCCATGGGCGTGCAC 62.409 66.667 13.02 6.82 36.20 4.57
1614 1660 3.001514 CCACACCTCCTCCATGGG 58.998 66.667 13.02 2.26 36.20 4.00
1616 1662 1.077930 CTGCCACACCTCCTCCATG 60.078 63.158 0.00 0.00 0.00 3.66
1636 1682 1.983605 GTGTGTATTCGGTCGACACTG 59.016 52.381 18.91 6.62 43.15 3.66
1656 1702 2.202440 CACCGAGCGACCAGTACG 60.202 66.667 0.00 0.00 0.00 3.67
1657 1703 2.181021 CCACCGAGCGACCAGTAC 59.819 66.667 0.00 0.00 0.00 2.73
1658 1704 3.066190 CCCACCGAGCGACCAGTA 61.066 66.667 0.00 0.00 0.00 2.74
1686 1738 1.833630 TGTGTTATCCCTCTGCTCAGG 59.166 52.381 0.00 0.00 0.00 3.86
1702 1754 1.355971 GTACGCGATCACCATTGTGT 58.644 50.000 15.93 0.00 43.26 3.72
1711 1763 0.026674 CGACTAACCGTACGCGATCA 59.973 55.000 15.93 0.00 41.33 2.92
1716 1768 0.387239 ACCAACGACTAACCGTACGC 60.387 55.000 10.49 0.00 42.54 4.42
1739 1791 0.450583 TACTCCGTCGACATGCTCAC 59.549 55.000 17.16 0.00 0.00 3.51
1752 1804 0.659427 TCATTCGGCTACGTACTCCG 59.341 55.000 19.88 19.88 44.16 4.63
1766 1818 6.093219 CCATCCCATACTCATTTCGATCATTC 59.907 42.308 0.00 0.00 0.00 2.67
1774 1826 2.154462 CGCCCATCCCATACTCATTTC 58.846 52.381 0.00 0.00 0.00 2.17
1822 1874 3.623060 ACTAGCAGTGTGATTAAATGCCG 59.377 43.478 0.00 0.00 37.61 5.69
1865 1917 0.752658 GTGCCAATTAATCCCAGGCC 59.247 55.000 14.69 0.00 44.60 5.19
1867 1919 1.032014 CCGTGCCAATTAATCCCAGG 58.968 55.000 0.00 0.00 0.00 4.45
1871 1923 2.758423 ACTTTCCCGTGCCAATTAATCC 59.242 45.455 0.00 0.00 0.00 3.01
1882 1934 0.877213 AACCGACGAACTTTCCCGTG 60.877 55.000 0.00 0.00 39.30 4.94
1883 1935 0.179076 AAACCGACGAACTTTCCCGT 60.179 50.000 0.00 0.00 42.17 5.28
1957 2009 2.159327 GGAGTCCTCCGTTTCGAAAA 57.841 50.000 13.10 0.00 40.36 2.29
1958 2010 3.900446 GGAGTCCTCCGTTTCGAAA 57.100 52.632 6.47 6.47 40.36 3.46
1968 2020 3.385111 ACGAATATCAACCTGGAGTCCTC 59.615 47.826 11.33 0.00 0.00 3.71
1969 2021 3.375699 ACGAATATCAACCTGGAGTCCT 58.624 45.455 11.33 0.00 0.00 3.85
1970 2022 3.821421 ACGAATATCAACCTGGAGTCC 57.179 47.619 0.73 0.73 0.00 3.85
1971 2023 4.201822 GCAAACGAATATCAACCTGGAGTC 60.202 45.833 0.00 0.00 0.00 3.36
1972 2024 3.689649 GCAAACGAATATCAACCTGGAGT 59.310 43.478 0.00 0.00 0.00 3.85
1979 2031 5.720239 CATGCATTGCAAACGAATATCAAC 58.280 37.500 16.46 0.00 43.62 3.18
1995 2063 4.906065 AGAAATCGTATGTGCATGCATT 57.094 36.364 25.64 16.89 0.00 3.56
1998 2066 3.792956 CCAAAGAAATCGTATGTGCATGC 59.207 43.478 11.82 11.82 0.00 4.06
2003 2071 6.898041 TCTTGTTCCAAAGAAATCGTATGTG 58.102 36.000 0.00 0.00 33.25 3.21
2022 2090 0.739813 GCCCACGCGTCTTATCTTGT 60.740 55.000 9.86 0.00 0.00 3.16
2078 2146 2.523412 ATCCCATGCATGCCTGGC 60.523 61.111 30.45 12.87 31.59 4.85
2112 2181 5.821995 GCTCTCTCTATTTTTCATCTTGCCT 59.178 40.000 0.00 0.00 0.00 4.75
2124 2193 7.300556 TCAGCATGAATAGCTCTCTCTATTT 57.699 36.000 0.00 0.00 45.97 1.40
2125 2194 6.914654 TCAGCATGAATAGCTCTCTCTATT 57.085 37.500 0.00 0.00 45.97 1.73
2167 2562 0.784778 CGGTCGTTCTTGAGACTTGC 59.215 55.000 0.00 0.00 37.52 4.01
2205 2612 1.737236 GTTGTGCAGCGGACATAATGA 59.263 47.619 4.05 0.00 0.00 2.57
2206 2613 1.739466 AGTTGTGCAGCGGACATAATG 59.261 47.619 4.05 0.00 0.00 1.90
2217 2624 1.008538 GGGCGAACAAGTTGTGCAG 60.009 57.895 14.48 7.93 0.00 4.41
2252 2659 2.033448 CCGTAGGCCCACAGCAAA 59.967 61.111 0.00 0.00 46.14 3.68


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

AutoCloner maintained by Alex Coulton.