Multiple sequence alignment - TraesCS5A01G229200

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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 TraesCS5A01G229200 chr5A 100.000 5183 0 0 1 5183 444939448 444944630 0.000000e+00 9572
1 TraesCS5A01G229200 chr5A 87.557 884 88 17 1 870 597423689 597424564 0.000000e+00 1003
2 TraesCS5A01G229200 chr5A 87.472 886 84 19 5 871 636296621 636295744 0.000000e+00 996
3 TraesCS5A01G229200 chr5B 92.009 3817 183 52 890 4608 404186203 404189995 0.000000e+00 5247
4 TraesCS5A01G229200 chr5B 95.950 642 17 3 4543 5183 404190002 404190635 0.000000e+00 1033
5 TraesCS5A01G229200 chr5D 91.067 3806 175 79 890 4608 346641760 346638033 0.000000e+00 4992
6 TraesCS5A01G229200 chr5D 95.643 459 14 3 4543 4996 346638026 346637569 0.000000e+00 732
7 TraesCS5A01G229200 chr5D 94.886 176 6 3 5009 5183 346637502 346637329 6.610000e-69 272
8 TraesCS5A01G229200 chr6A 87.906 893 81 20 1 874 495671992 495671108 0.000000e+00 1026
9 TraesCS5A01G229200 chr6A 87.177 889 93 15 1 874 49470866 49469984 0.000000e+00 990
10 TraesCS5A01G229200 chr6A 91.018 167 14 1 2691 2856 411770253 411770419 1.880000e-54 224
11 TraesCS5A01G229200 chr7A 87.682 893 83 20 1 874 474820947 474821831 0.000000e+00 1014
12 TraesCS5A01G229200 chr7A 87.108 892 93 15 1 874 283158098 283157211 0.000000e+00 990
13 TraesCS5A01G229200 chr7A 87.385 872 88 15 1 859 510903780 510904642 0.000000e+00 981
14 TraesCS5A01G229200 chr2A 87.148 887 91 18 1 873 38784925 38785802 0.000000e+00 985
15 TraesCS5A01G229200 chr6D 86.981 891 90 18 1 874 126630000 126629119 0.000000e+00 979
16 TraesCS5A01G229200 chr4B 92.500 160 12 0 2684 2843 106227402 106227561 4.040000e-56 230
17 TraesCS5A01G229200 chrUn 90.566 159 15 0 2689 2847 126680632 126680474 1.460000e-50 211
18 TraesCS5A01G229200 chr7D 90.625 160 14 1 2684 2843 447053662 447053504 1.460000e-50 211
19 TraesCS5A01G229200 chr7D 90.062 161 16 0 2683 2843 34757026 34756866 5.260000e-50 209
20 TraesCS5A01G229200 chr7D 89.157 166 17 1 2679 2843 454079065 454079230 6.800000e-49 206
21 TraesCS5A01G229200 chr4A 90.062 161 15 1 2683 2843 690411282 690411441 1.890000e-49 207


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 TraesCS5A01G229200 chr5A 444939448 444944630 5182 False 9572.000000 9572 100.000000 1 5183 1 chr5A.!!$F1 5182
1 TraesCS5A01G229200 chr5A 597423689 597424564 875 False 1003.000000 1003 87.557000 1 870 1 chr5A.!!$F2 869
2 TraesCS5A01G229200 chr5A 636295744 636296621 877 True 996.000000 996 87.472000 5 871 1 chr5A.!!$R1 866
3 TraesCS5A01G229200 chr5B 404186203 404190635 4432 False 3140.000000 5247 93.979500 890 5183 2 chr5B.!!$F1 4293
4 TraesCS5A01G229200 chr5D 346637329 346641760 4431 True 1998.666667 4992 93.865333 890 5183 3 chr5D.!!$R1 4293
5 TraesCS5A01G229200 chr6A 495671108 495671992 884 True 1026.000000 1026 87.906000 1 874 1 chr6A.!!$R2 873
6 TraesCS5A01G229200 chr6A 49469984 49470866 882 True 990.000000 990 87.177000 1 874 1 chr6A.!!$R1 873
7 TraesCS5A01G229200 chr7A 474820947 474821831 884 False 1014.000000 1014 87.682000 1 874 1 chr7A.!!$F1 873
8 TraesCS5A01G229200 chr7A 283157211 283158098 887 True 990.000000 990 87.108000 1 874 1 chr7A.!!$R1 873
9 TraesCS5A01G229200 chr7A 510903780 510904642 862 False 981.000000 981 87.385000 1 859 1 chr7A.!!$F2 858
10 TraesCS5A01G229200 chr2A 38784925 38785802 877 False 985.000000 985 87.148000 1 873 1 chr2A.!!$F1 872
11 TraesCS5A01G229200 chr6D 126629119 126630000 881 True 979.000000 979 86.981000 1 874 1 chr6D.!!$R1 873

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
147 159 0.108615 CCGTGCCTCTCGTGAAATCT 60.109 55.000 0.00 0.00 0.00 2.40 F
253 273 0.737715 GCCATGACTCTCGCGAAAGT 60.738 55.000 16.32 16.32 0.00 2.66 F
1198 1279 1.226773 GCCGGTGTAGCGTCGTATT 60.227 57.895 1.90 0.00 0.00 1.89 F
1278 1359 0.103208 CTTTCCCGAGTCCGATCCTG 59.897 60.000 0.00 0.00 38.22 3.86 F
1318 1411 0.107361 GGATTGGTACGGTTGGGGAG 60.107 60.000 0.00 0.00 0.00 4.30 F
1319 1412 0.616891 GATTGGTACGGTTGGGGAGT 59.383 55.000 0.00 0.00 0.00 3.85 F
1320 1413 0.616891 ATTGGTACGGTTGGGGAGTC 59.383 55.000 0.00 0.00 0.00 3.36 F
1342 1436 1.140161 CATGTGCAGGGCGAAATGG 59.860 57.895 0.00 0.00 0.00 3.16 F
3437 3582 0.953960 GTGACTTTGGCGGTGGTAGG 60.954 60.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1278 0.039617 CAGAAAATCGCCAACGCCAA 60.040 50.000 0.0 0.0 39.84 4.52 R
1200 1281 0.387239 AAGCAGAAAATCGCCAACGC 60.387 50.000 0.0 0.0 39.84 4.84 R
2473 2616 0.601311 AACTCTCTTGTGCTCCACGC 60.601 55.000 0.0 0.0 37.14 5.34 R
3086 3230 1.497278 CAGGCGTTGAATGTCCACG 59.503 57.895 0.0 0.0 0.00 4.94 R
3227 3371 7.012138 CCATCCTGATCTGTGTTTTCTTCTATG 59.988 40.741 0.0 0.0 0.00 2.23 R
3228 3372 7.052873 CCATCCTGATCTGTGTTTTCTTCTAT 58.947 38.462 0.0 0.0 0.00 1.98 R
3437 3582 3.156511 GCCAGAGCTAATTTTTCAGCC 57.843 47.619 0.0 0.0 38.61 4.85 R
3638 3785 4.215908 TCCACTATGGAGAATAAGCGAGT 58.784 43.478 0.0 0.0 42.67 4.18 R
4481 4636 2.231478 CCGGACACAGATGTAGAACAGT 59.769 50.000 0.0 0.0 39.95 3.55 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
27 28 9.725019 TTGAAAACTAGATCACATGTTGATAGT 57.275 29.630 0.00 0.00 45.67 2.12
147 159 0.108615 CCGTGCCTCTCGTGAAATCT 60.109 55.000 0.00 0.00 0.00 2.40
167 179 2.283529 AACCGTGCCTCTCGTGGAT 61.284 57.895 0.00 0.00 0.00 3.41
253 273 0.737715 GCCATGACTCTCGCGAAAGT 60.738 55.000 16.32 16.32 0.00 2.66
260 280 1.338973 ACTCTCGCGAAAGTACAACCA 59.661 47.619 14.61 0.00 0.00 3.67
515 547 3.463944 GGAAGAAAAACCGTGACTCTCA 58.536 45.455 0.00 0.00 0.00 3.27
757 808 4.684877 ACCATTTAAAAAGCCGAAAACGT 58.315 34.783 0.00 0.00 0.00 3.99
840 898 3.127533 GAGAGCGCGCCAAATGGT 61.128 61.111 30.33 7.05 37.57 3.55
847 905 4.798288 CGCCAAATGGTGCTGATG 57.202 55.556 0.00 0.00 39.04 3.07
883 941 2.279784 GAGCGCTCCATTCTCCCG 60.280 66.667 27.22 0.00 0.00 5.14
884 942 3.077556 AGCGCTCCATTCTCCCGT 61.078 61.111 2.64 0.00 0.00 5.28
885 943 2.586357 GCGCTCCATTCTCCCGTC 60.586 66.667 0.00 0.00 0.00 4.79
886 944 2.107141 CGCTCCATTCTCCCGTCC 59.893 66.667 0.00 0.00 0.00 4.79
887 945 2.107141 GCTCCATTCTCCCGTCCG 59.893 66.667 0.00 0.00 0.00 4.79
888 946 2.423898 GCTCCATTCTCCCGTCCGA 61.424 63.158 0.00 0.00 0.00 4.55
1147 1225 1.392710 ATTCTCGGTGCGTCCCCTAG 61.393 60.000 0.00 0.00 0.00 3.02
1148 1226 2.754658 CTCGGTGCGTCCCCTAGT 60.755 66.667 0.00 0.00 0.00 2.57
1149 1227 2.753043 TCGGTGCGTCCCCTAGTC 60.753 66.667 0.00 0.00 0.00 2.59
1150 1228 3.834799 CGGTGCGTCCCCTAGTCC 61.835 72.222 0.00 0.00 0.00 3.85
1152 1230 2.682494 GTGCGTCCCCTAGTCCCA 60.682 66.667 0.00 0.00 0.00 4.37
1156 1237 1.837499 CGTCCCCTAGTCCCATCCC 60.837 68.421 0.00 0.00 0.00 3.85
1197 1278 2.056481 GAGCCGGTGTAGCGTCGTAT 62.056 60.000 1.90 0.00 34.64 3.06
1198 1279 1.226773 GCCGGTGTAGCGTCGTATT 60.227 57.895 1.90 0.00 0.00 1.89
1199 1280 1.477030 GCCGGTGTAGCGTCGTATTG 61.477 60.000 1.90 0.00 0.00 1.90
1200 1281 0.868602 CCGGTGTAGCGTCGTATTGG 60.869 60.000 0.00 0.00 0.00 3.16
1201 1282 1.477030 CGGTGTAGCGTCGTATTGGC 61.477 60.000 0.00 0.00 0.00 4.52
1202 1283 1.477030 GGTGTAGCGTCGTATTGGCG 61.477 60.000 0.00 0.00 0.00 5.69
1211 1292 0.741574 TCGTATTGGCGTTGGCGATT 60.742 50.000 0.00 0.00 41.24 3.34
1263 1344 2.884639 TCCTTGCTAGTTTGCCACTTTC 59.115 45.455 0.00 0.00 36.88 2.62
1275 1356 0.179108 CCACTTTCCCGAGTCCGATC 60.179 60.000 0.00 0.00 38.22 3.69
1276 1357 0.179108 CACTTTCCCGAGTCCGATCC 60.179 60.000 0.00 0.00 38.22 3.36
1278 1359 0.103208 CTTTCCCGAGTCCGATCCTG 59.897 60.000 0.00 0.00 38.22 3.86
1285 1366 1.677637 GAGTCCGATCCTGTGGGGTC 61.678 65.000 0.00 0.00 39.31 4.46
1286 1367 1.686110 GTCCGATCCTGTGGGGTCT 60.686 63.158 0.00 0.00 40.50 3.85
1287 1368 1.080354 TCCGATCCTGTGGGGTCTT 59.920 57.895 0.00 0.00 40.50 3.01
1288 1369 1.221840 CCGATCCTGTGGGGTCTTG 59.778 63.158 0.00 0.00 40.50 3.02
1291 1372 1.216990 GATCCTGTGGGGTCTTGGAT 58.783 55.000 0.00 0.00 39.58 3.41
1293 1374 1.879575 TCCTGTGGGGTCTTGGATAG 58.120 55.000 0.00 0.00 36.25 2.08
1309 1402 3.817084 TGGATAGTAGACGGATTGGTACG 59.183 47.826 0.00 0.00 37.80 3.67
1317 1410 1.901654 CGGATTGGTACGGTTGGGGA 61.902 60.000 0.00 0.00 0.00 4.81
1318 1411 0.107361 GGATTGGTACGGTTGGGGAG 60.107 60.000 0.00 0.00 0.00 4.30
1319 1412 0.616891 GATTGGTACGGTTGGGGAGT 59.383 55.000 0.00 0.00 0.00 3.85
1320 1413 0.616891 ATTGGTACGGTTGGGGAGTC 59.383 55.000 0.00 0.00 0.00 3.36
1321 1414 1.482748 TTGGTACGGTTGGGGAGTCC 61.483 60.000 0.00 0.00 0.00 3.85
1332 1426 2.821366 GGAGTCCGGCATGTGCAG 60.821 66.667 7.36 2.57 44.36 4.41
1342 1436 1.140161 CATGTGCAGGGCGAAATGG 59.860 57.895 0.00 0.00 0.00 3.16
1359 1453 5.564455 CGAAATGGTGTGGTGAATTCATGAA 60.564 40.000 12.12 11.26 0.00 2.57
1361 1455 6.363167 AATGGTGTGGTGAATTCATGAATT 57.637 33.333 29.31 29.31 43.14 2.17
1363 1457 6.172136 TGGTGTGGTGAATTCATGAATTTT 57.828 33.333 29.44 13.78 40.77 1.82
1364 1458 6.222389 TGGTGTGGTGAATTCATGAATTTTC 58.778 36.000 29.44 23.63 40.77 2.29
1366 1460 6.587608 GGTGTGGTGAATTCATGAATTTTCTC 59.412 38.462 29.44 20.10 40.77 2.87
1367 1461 7.373493 GTGTGGTGAATTCATGAATTTTCTCT 58.627 34.615 29.44 10.97 40.77 3.10
1370 1464 7.967303 GTGGTGAATTCATGAATTTTCTCTCTC 59.033 37.037 29.44 17.23 40.77 3.20
1372 1466 8.397148 GGTGAATTCATGAATTTTCTCTCTCTC 58.603 37.037 29.44 16.01 40.77 3.20
1374 1468 7.821359 TGAATTCATGAATTTTCTCTCTCTCGT 59.179 33.333 29.44 7.10 40.77 4.18
1375 1469 8.558973 AATTCATGAATTTTCTCTCTCTCGTT 57.441 30.769 24.83 1.36 37.74 3.85
1376 1470 6.957984 TCATGAATTTTCTCTCTCTCGTTG 57.042 37.500 0.00 0.00 0.00 4.10
1378 1472 6.931281 TCATGAATTTTCTCTCTCTCGTTGTT 59.069 34.615 0.00 0.00 0.00 2.83
1379 1473 8.088365 TCATGAATTTTCTCTCTCTCGTTGTTA 58.912 33.333 0.00 0.00 0.00 2.41
1417 1516 8.319143 AGTTTAGTTGGTGTATGTATGTTGAC 57.681 34.615 0.00 0.00 0.00 3.18
1519 1632 4.753233 TGCATCGAATATTTTGGTTTGGG 58.247 39.130 0.00 0.00 0.00 4.12
1544 1657 6.622896 GCAGTGGTCTACAATGTTTGATTACC 60.623 42.308 0.00 0.00 46.36 2.85
1546 1659 6.430000 AGTGGTCTACAATGTTTGATTACCAC 59.570 38.462 21.34 21.34 46.98 4.16
1547 1660 6.430000 GTGGTCTACAATGTTTGATTACCACT 59.570 38.462 21.46 0.00 45.38 4.00
1548 1661 6.653320 TGGTCTACAATGTTTGATTACCACTC 59.347 38.462 0.00 0.00 35.61 3.51
1549 1662 6.093633 GGTCTACAATGTTTGATTACCACTCC 59.906 42.308 0.00 0.00 32.90 3.85
1562 1677 3.806625 ACCACTCCATATGCATTTTGC 57.193 42.857 3.54 0.00 45.29 3.68
1591 1717 4.775253 TGTGGGACTGTATGAGTACATGAA 59.225 41.667 0.00 0.00 37.23 2.57
1593 1719 6.170506 GTGGGACTGTATGAGTACATGAAAA 58.829 40.000 0.00 0.00 37.23 2.29
1596 1722 7.985184 TGGGACTGTATGAGTACATGAAAATAC 59.015 37.037 0.00 1.25 37.23 1.89
1597 1723 7.441458 GGGACTGTATGAGTACATGAAAATACC 59.559 40.741 0.00 0.00 37.23 2.73
1655 1784 6.946340 TGAAGATAGATTGGCAACTCAAGTA 58.054 36.000 0.00 0.00 37.61 2.24
1667 1796 6.100668 GGCAACTCAAGTAGACCTTAGTAAG 58.899 44.000 2.65 2.65 0.00 2.34
1718 1847 9.294030 CTTTTTAAGATTAATCATGTGGACAGC 57.706 33.333 17.56 0.00 0.00 4.40
1723 1860 2.760634 AATCATGTGGACAGCGTGTA 57.239 45.000 0.00 0.00 0.00 2.90
1738 1875 2.483876 CGTGTATATTGCAGGAGTGGG 58.516 52.381 0.00 0.00 0.00 4.61
1759 1896 1.682005 GCCCCTAAGCCAATGCACA 60.682 57.895 0.00 0.00 41.13 4.57
1773 1910 4.741676 CCAATGCACAAGTCTCTTTTGAAC 59.258 41.667 0.00 0.00 0.00 3.18
1775 1912 2.223249 TGCACAAGTCTCTTTTGAACGC 60.223 45.455 0.69 0.00 0.00 4.84
1806 1943 5.753438 GCGATGGACAATAGTGAGTATTCAA 59.247 40.000 0.00 0.00 34.49 2.69
1864 2007 8.451908 AAGTCTATTTGTAACTTGCTTTCTGT 57.548 30.769 0.00 0.00 32.22 3.41
1890 2033 4.392445 CAGCCAGATGAACAAAAGAGAGAG 59.608 45.833 0.00 0.00 0.00 3.20
1891 2034 4.285517 AGCCAGATGAACAAAAGAGAGAGA 59.714 41.667 0.00 0.00 0.00 3.10
1911 2054 1.302832 CTGGACACCCTTGCCTGAC 60.303 63.158 0.00 0.00 0.00 3.51
2184 2327 7.066766 GCTTGGTTGAGATTTTAGATCATCTGT 59.933 37.037 0.00 0.00 29.41 3.41
2313 2456 3.443099 AGGTGCTTTTGAAGTTTCAGC 57.557 42.857 0.00 0.00 38.61 4.26
2379 2522 6.827586 TGGAAGTGAAAGTTTTAGTTGTGT 57.172 33.333 5.27 0.00 0.00 3.72
2471 2614 5.449553 AGTGAGAACTCCACCAAAAGAATT 58.550 37.500 0.00 0.00 35.23 2.17
2473 2616 5.979517 GTGAGAACTCCACCAAAAGAATTTG 59.020 40.000 0.00 0.00 44.50 2.32
2624 2767 8.367660 TCTTTGGTCATATAGTCACTTCTCTT 57.632 34.615 0.00 0.00 0.00 2.85
2644 2788 4.019321 TCTTGACCCCTTGATAAGTGAAGG 60.019 45.833 0.00 0.00 38.33 3.46
2695 2839 7.486802 TGTTGCAAAACTAAACTACTACTCC 57.513 36.000 0.00 0.00 0.00 3.85
2762 2906 7.539710 TCAGATGTATGTACACACGTTTTAGTC 59.460 37.037 0.00 0.00 39.30 2.59
2803 2947 6.072119 TGCAGTCCGTATGTAGTCCATATTAG 60.072 42.308 0.00 0.00 38.29 1.73
3086 3230 2.940410 CCTTGCATTTGATGATTTGCCC 59.060 45.455 0.00 0.00 34.20 5.36
3128 3272 5.748592 CGCTGTAAAGTTAACTTTGAAGCT 58.251 37.500 36.02 21.55 44.55 3.74
3132 3276 7.254795 GCTGTAAAGTTAACTTTGAAGCTCTGA 60.255 37.037 34.65 19.13 45.01 3.27
3227 3371 3.383761 CACTGAATTTGCCCAACAAGTC 58.616 45.455 0.00 0.00 40.06 3.01
3228 3372 3.030291 ACTGAATTTGCCCAACAAGTCA 58.970 40.909 0.00 0.00 40.06 3.41
3328 3472 6.037062 TCTGCAATATTTGGAAGTCGTATGTG 59.963 38.462 0.00 0.00 0.00 3.21
3437 3582 0.953960 GTGACTTTGGCGGTGGTAGG 60.954 60.000 0.00 0.00 0.00 3.18
3638 3785 2.170397 TCACAAGGTTTGACTCTCTGCA 59.830 45.455 0.00 0.00 0.00 4.41
3920 4067 2.421424 CTGTTGGCTTCTGCTGTATTCC 59.579 50.000 0.00 0.00 39.59 3.01
3922 4069 1.289160 TGGCTTCTGCTGTATTCCCT 58.711 50.000 0.00 0.00 39.59 4.20
3925 4072 2.436173 GGCTTCTGCTGTATTCCCTAGT 59.564 50.000 0.00 0.00 39.59 2.57
3929 4076 5.416013 GCTTCTGCTGTATTCCCTAGTTTTT 59.584 40.000 0.00 0.00 36.03 1.94
3999 4146 0.255033 ACCGGGCCTACAGGAATTTC 59.745 55.000 6.32 0.00 37.90 2.17
4043 4190 2.383368 TTGCTTGGCCACATATTTGC 57.617 45.000 3.88 1.96 0.00 3.68
4161 4308 5.299782 GTCTATCTATACTTATCCTGCCCCG 59.700 48.000 0.00 0.00 0.00 5.73
4185 4332 3.838244 TGTATGTGCCAAGGGTAGATC 57.162 47.619 0.00 0.00 0.00 2.75
4208 4355 0.040958 GAGTTTTCTGCAGTGCACCG 60.041 55.000 15.37 5.78 33.79 4.94
4224 4371 2.393764 CACCGACAAAAGAAATGTGCC 58.606 47.619 0.00 0.00 0.00 5.01
4239 4386 1.671054 TGCCGAGTTACTTGCAGCC 60.671 57.895 6.45 0.00 0.00 4.85
4387 4537 3.258971 AGGACTCTAATCTTGTGCTGC 57.741 47.619 0.00 0.00 31.41 5.25
4405 4555 1.277326 GCTGCACATTCGATACGACA 58.723 50.000 0.00 0.00 34.89 4.35
4436 4586 8.984764 TGTAGTTTTGTGACTGATGTTGTATAC 58.015 33.333 0.00 0.00 0.00 1.47
4481 4636 7.896383 TCCTTTTTCTTCTTCTTTGATTCCA 57.104 32.000 0.00 0.00 0.00 3.53
4496 4651 5.745312 TGATTCCACTGTTCTACATCTGT 57.255 39.130 0.00 0.00 0.00 3.41
4498 4653 4.955811 TTCCACTGTTCTACATCTGTGT 57.044 40.909 0.00 0.00 42.39 3.72
4499 4654 4.521130 TCCACTGTTCTACATCTGTGTC 57.479 45.455 0.00 0.00 39.77 3.67
4501 4656 3.245797 CACTGTTCTACATCTGTGTCCG 58.754 50.000 0.00 0.00 39.77 4.79
4502 4657 2.231478 ACTGTTCTACATCTGTGTCCGG 59.769 50.000 0.00 0.00 39.77 5.14
4503 4658 2.231478 CTGTTCTACATCTGTGTCCGGT 59.769 50.000 0.00 0.00 39.77 5.28
4519 4675 3.810941 GTCCGGTGTTTGTATGAAGTTCA 59.189 43.478 8.27 8.27 0.00 3.18
4537 4693 8.023128 TGAAGTTCAGCTTTGATTTACTATTGC 58.977 33.333 0.08 0.00 37.59 3.56
4549 4774 8.315391 TGATTTACTATTGCTATCATCACAGC 57.685 34.615 0.00 0.00 38.31 4.40
4561 4786 1.253800 CATCACAGCGAATTCGAGACG 59.746 52.381 31.01 16.56 43.02 4.18
4627 4852 4.024893 CACGCATGGGTGATATTACAAGTC 60.025 45.833 32.85 0.00 40.38 3.01
4688 4913 1.029681 GTTTCACCACCGGAGCTTTT 58.970 50.000 9.46 0.00 0.00 2.27
4954 5179 1.740718 GCCAGTCTCCCTGAACGAATC 60.741 57.143 0.00 0.00 44.49 2.52
5023 5253 0.514691 GGTGAAGCAAGCAGAGAACG 59.485 55.000 0.00 0.00 0.00 3.95
5024 5254 1.502231 GTGAAGCAAGCAGAGAACGA 58.498 50.000 0.00 0.00 0.00 3.85
5025 5255 2.072298 GTGAAGCAAGCAGAGAACGAT 58.928 47.619 0.00 0.00 0.00 3.73
5026 5256 2.071540 TGAAGCAAGCAGAGAACGATG 58.928 47.619 0.00 0.00 0.00 3.84
5027 5257 1.396301 GAAGCAAGCAGAGAACGATGG 59.604 52.381 0.00 0.00 0.00 3.51
5029 5259 0.723981 GCAAGCAGAGAACGATGGAC 59.276 55.000 0.00 0.00 0.00 4.02
5030 5260 1.674221 GCAAGCAGAGAACGATGGACT 60.674 52.381 0.00 0.00 0.00 3.85
5031 5261 2.266554 CAAGCAGAGAACGATGGACTC 58.733 52.381 0.00 0.00 0.00 3.36
5111 5394 3.621805 TTGAAGACGCTGCCGGGA 61.622 61.111 2.18 0.00 39.22 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.259290 AGTTCGTCAAAAACTATCAACATGT 57.741 32.000 0.00 0.00 35.25 3.21
147 159 2.338620 CACGAGAGGCACGGTTGA 59.661 61.111 0.00 0.00 34.93 3.18
167 179 0.179094 ACGAGAGTCACGGTTTTGCA 60.179 50.000 14.49 0.00 44.19 4.08
206 220 3.517974 GGAAACGGAAAAACGCGC 58.482 55.556 5.73 0.00 37.37 6.86
253 273 1.153647 CGCGAGAGGCATGGTTGTA 60.154 57.895 0.00 0.00 43.84 2.41
260 280 0.955428 TTTGCTTTCGCGAGAGGCAT 60.955 50.000 25.84 0.00 45.05 4.40
322 343 2.677037 CGTGCCTCTCGGAAAGGTAAAT 60.677 50.000 0.00 0.00 36.21 1.40
326 349 2.657237 CGTGCCTCTCGGAAAGGT 59.343 61.111 0.00 0.00 36.21 3.50
347 374 1.790755 TGTGCTTACGCGAAAGTCAT 58.209 45.000 15.93 0.00 39.65 3.06
459 491 1.372997 TGCTTTCGCGAGAGTCACC 60.373 57.895 25.34 11.07 43.69 4.02
481 513 0.816018 TTCTTCCGCGAAAGGCACAA 60.816 50.000 8.23 0.00 43.84 3.33
482 514 0.816018 TTTCTTCCGCGAAAGGCACA 60.816 50.000 8.23 0.00 43.84 4.57
569 603 3.934457 TGTGCTTTATCGAGAGTCACA 57.066 42.857 13.79 13.79 31.98 3.58
784 842 0.667487 CGCTTTGGACGCTCTCTTCA 60.667 55.000 0.00 0.00 0.00 3.02
840 898 0.890542 AAGCTTCGCAACCATCAGCA 60.891 50.000 0.00 0.00 32.58 4.41
874 932 0.108992 TTTCGTCGGACGGGAGAATG 60.109 55.000 28.07 0.00 42.81 2.67
875 933 0.822164 ATTTCGTCGGACGGGAGAAT 59.178 50.000 28.07 19.08 42.81 2.40
876 934 0.108992 CATTTCGTCGGACGGGAGAA 60.109 55.000 28.07 17.89 42.81 2.87
877 935 1.509463 CATTTCGTCGGACGGGAGA 59.491 57.895 28.07 13.21 42.81 3.71
878 936 1.518572 CCATTTCGTCGGACGGGAG 60.519 63.158 28.07 15.98 42.81 4.30
879 937 1.324740 ATCCATTTCGTCGGACGGGA 61.325 55.000 28.07 24.91 42.81 5.14
880 938 1.143183 ATCCATTTCGTCGGACGGG 59.857 57.895 28.07 20.96 42.81 5.28
881 939 1.151777 CCATCCATTTCGTCGGACGG 61.152 60.000 28.07 13.24 42.81 4.79
882 940 1.151777 CCCATCCATTTCGTCGGACG 61.152 60.000 23.73 23.73 44.19 4.79
883 941 1.436983 GCCCATCCATTTCGTCGGAC 61.437 60.000 0.00 0.00 33.05 4.79
884 942 1.153249 GCCCATCCATTTCGTCGGA 60.153 57.895 0.00 0.00 35.27 4.55
885 943 2.186826 GGCCCATCCATTTCGTCGG 61.187 63.158 0.00 0.00 34.01 4.79
886 944 1.029408 TTGGCCCATCCATTTCGTCG 61.029 55.000 0.00 0.00 46.04 5.12
887 945 1.402787 ATTGGCCCATCCATTTCGTC 58.597 50.000 0.00 0.00 46.04 4.20
888 946 1.864669 AATTGGCCCATCCATTTCGT 58.135 45.000 0.00 0.00 46.04 3.85
1147 1225 1.768077 CTGGAGAGGGGGATGGGAC 60.768 68.421 0.00 0.00 0.00 4.46
1148 1226 2.705410 CTGGAGAGGGGGATGGGA 59.295 66.667 0.00 0.00 0.00 4.37
1149 1227 2.449322 CCTGGAGAGGGGGATGGG 60.449 72.222 0.00 0.00 35.40 4.00
1150 1228 3.174265 GCCTGGAGAGGGGGATGG 61.174 72.222 0.00 0.00 40.19 3.51
1156 1237 4.148825 CGAACCGCCTGGAGAGGG 62.149 72.222 0.00 0.00 40.19 4.30
1197 1278 0.039617 CAGAAAATCGCCAACGCCAA 60.040 50.000 0.00 0.00 39.84 4.52
1198 1279 1.578926 CAGAAAATCGCCAACGCCA 59.421 52.632 0.00 0.00 39.84 5.69
1199 1280 1.801512 GCAGAAAATCGCCAACGCC 60.802 57.895 0.00 0.00 39.84 5.68
1200 1281 0.387239 AAGCAGAAAATCGCCAACGC 60.387 50.000 0.00 0.00 39.84 4.84
1201 1282 2.050477 AAAGCAGAAAATCGCCAACG 57.950 45.000 0.00 0.00 42.01 4.10
1202 1283 3.642705 AGAAAAGCAGAAAATCGCCAAC 58.357 40.909 0.00 0.00 0.00 3.77
1263 1344 2.786495 CCACAGGATCGGACTCGGG 61.786 68.421 0.00 0.00 36.95 5.14
1275 1356 1.584724 ACTATCCAAGACCCCACAGG 58.415 55.000 0.00 0.00 43.78 4.00
1276 1357 3.385111 GTCTACTATCCAAGACCCCACAG 59.615 52.174 0.00 0.00 36.86 3.66
1278 1359 2.361438 CGTCTACTATCCAAGACCCCAC 59.639 54.545 0.00 0.00 39.16 4.61
1285 1366 4.939052 ACCAATCCGTCTACTATCCAAG 57.061 45.455 0.00 0.00 0.00 3.61
1286 1367 4.276678 CGTACCAATCCGTCTACTATCCAA 59.723 45.833 0.00 0.00 0.00 3.53
1287 1368 3.817084 CGTACCAATCCGTCTACTATCCA 59.183 47.826 0.00 0.00 0.00 3.41
1288 1369 3.190118 CCGTACCAATCCGTCTACTATCC 59.810 52.174 0.00 0.00 0.00 2.59
1291 1372 3.281727 ACCGTACCAATCCGTCTACTA 57.718 47.619 0.00 0.00 0.00 1.82
1293 1374 2.533266 CAACCGTACCAATCCGTCTAC 58.467 52.381 0.00 0.00 0.00 2.59
1309 1402 3.728373 ATGCCGGACTCCCCAACC 61.728 66.667 5.05 0.00 34.14 3.77
1317 1410 4.415150 CCCTGCACATGCCGGACT 62.415 66.667 15.19 0.00 46.66 3.85
1322 1415 2.713967 ATTTCGCCCTGCACATGCC 61.714 57.895 0.49 0.00 41.18 4.40
1323 1416 1.517694 CATTTCGCCCTGCACATGC 60.518 57.895 0.00 0.00 42.50 4.06
1324 1417 1.140161 CCATTTCGCCCTGCACATG 59.860 57.895 0.00 0.00 0.00 3.21
1330 1424 1.603455 ACCACACCATTTCGCCCTG 60.603 57.895 0.00 0.00 0.00 4.45
1332 1426 1.175983 TTCACCACACCATTTCGCCC 61.176 55.000 0.00 0.00 0.00 6.13
1335 1429 3.913548 TGAATTCACCACACCATTTCG 57.086 42.857 3.38 0.00 0.00 3.46
1342 1436 7.373493 AGAGAAAATTCATGAATTCACCACAC 58.627 34.615 29.08 17.60 39.88 3.82
1359 1453 8.888579 TTTCTTAACAACGAGAGAGAGAAAAT 57.111 30.769 0.00 0.00 31.27 1.82
1361 1455 8.888579 AATTTCTTAACAACGAGAGAGAGAAA 57.111 30.769 0.00 0.00 36.62 2.52
1363 1457 8.573885 TGTAATTTCTTAACAACGAGAGAGAGA 58.426 33.333 0.00 0.00 0.00 3.10
1364 1458 8.744008 TGTAATTTCTTAACAACGAGAGAGAG 57.256 34.615 0.00 0.00 0.00 3.20
1392 1491 7.117236 CGTCAACATACATACACCAACTAAACT 59.883 37.037 0.00 0.00 0.00 2.66
1398 1497 3.433957 TGCGTCAACATACATACACCAAC 59.566 43.478 0.00 0.00 0.00 3.77
1403 1502 4.450082 ACTCTGCGTCAACATACATACA 57.550 40.909 0.00 0.00 0.00 2.29
1451 1550 7.281774 TCAAAAGAATCCAGATCTTCACATAGC 59.718 37.037 0.00 0.00 36.14 2.97
1454 1553 7.068348 CCATCAAAAGAATCCAGATCTTCACAT 59.932 37.037 0.00 0.00 36.14 3.21
1456 1555 6.600822 TCCATCAAAAGAATCCAGATCTTCAC 59.399 38.462 0.00 0.00 36.14 3.18
1457 1556 6.724351 TCCATCAAAAGAATCCAGATCTTCA 58.276 36.000 0.00 0.00 36.14 3.02
1458 1557 7.820578 ATCCATCAAAAGAATCCAGATCTTC 57.179 36.000 0.00 0.00 36.14 2.87
1502 1615 3.925913 CACTGCCCAAACCAAAATATTCG 59.074 43.478 0.00 0.00 0.00 3.34
1519 1632 5.376854 AATCAAACATTGTAGACCACTGC 57.623 39.130 0.00 0.00 0.00 4.40
1534 1647 6.639632 ATGCATATGGAGTGGTAATCAAAC 57.360 37.500 0.00 0.00 0.00 2.93
1544 1657 2.734670 CCGCAAAATGCATATGGAGTG 58.265 47.619 0.00 3.15 45.36 3.51
1546 1659 1.067364 TGCCGCAAAATGCATATGGAG 59.933 47.619 0.00 0.00 45.36 3.86
1547 1660 1.067364 CTGCCGCAAAATGCATATGGA 59.933 47.619 0.00 1.06 45.36 3.41
1548 1661 1.202440 ACTGCCGCAAAATGCATATGG 60.202 47.619 0.00 0.00 45.36 2.74
1549 1662 1.855978 CACTGCCGCAAAATGCATATG 59.144 47.619 0.00 3.61 45.36 1.78
1585 1711 8.792633 CATATGTTATTCCCGGTATTTTCATGT 58.207 33.333 0.00 0.00 0.00 3.21
1591 1717 7.881232 CCAGTACATATGTTATTCCCGGTATTT 59.119 37.037 14.77 0.00 0.00 1.40
1593 1719 6.727231 TCCAGTACATATGTTATTCCCGGTAT 59.273 38.462 14.77 0.00 0.00 2.73
1596 1722 5.477607 TCCAGTACATATGTTATTCCCGG 57.522 43.478 14.77 0.00 0.00 5.73
1597 1723 8.311836 AGTAATCCAGTACATATGTTATTCCCG 58.688 37.037 14.77 0.00 0.00 5.14
1628 1757 8.049117 ACTTGAGTTGCCAATCTATCTTCATAA 58.951 33.333 0.00 0.00 0.00 1.90
1655 1784 8.376270 AGTTTGCAGAAATACTTACTAAGGTCT 58.624 33.333 0.88 0.00 0.00 3.85
1692 1821 9.294030 GCTGTCCACATGATTAATCTTAAAAAG 57.706 33.333 16.24 6.23 0.00 2.27
1717 1846 1.867233 CCACTCCTGCAATATACACGC 59.133 52.381 0.00 0.00 0.00 5.34
1718 1847 2.102420 TCCCACTCCTGCAATATACACG 59.898 50.000 0.00 0.00 0.00 4.49
1723 1860 1.202976 GGCATCCCACTCCTGCAATAT 60.203 52.381 0.00 0.00 37.64 1.28
1759 1896 2.822764 AGACGCGTTCAAAAGAGACTT 58.177 42.857 15.53 0.00 0.00 3.01
1775 1912 2.930040 ACTATTGTCCATCGCAAAGACG 59.070 45.455 0.00 0.00 33.09 4.18
1806 1943 8.697507 ACTACTTCCATTTTTCATCTGAGTTT 57.302 30.769 0.00 0.00 0.00 2.66
1849 1992 4.274950 TGGCTGTAACAGAAAGCAAGTTAC 59.725 41.667 0.00 0.00 44.72 2.50
1850 1993 4.456535 TGGCTGTAACAGAAAGCAAGTTA 58.543 39.130 0.00 0.00 38.73 2.24
1851 1994 3.287222 TGGCTGTAACAGAAAGCAAGTT 58.713 40.909 0.00 0.00 38.73 2.66
1864 2007 5.620206 TCTCTTTTGTTCATCTGGCTGTAA 58.380 37.500 0.00 0.00 0.00 2.41
1890 2033 0.393537 CAGGCAAGGGTGTCCAGATC 60.394 60.000 0.00 0.00 34.83 2.75
1891 2034 0.842030 TCAGGCAAGGGTGTCCAGAT 60.842 55.000 0.00 0.00 34.83 2.90
1911 2054 1.984026 GCATGGTTTCCACCCCTGG 60.984 63.158 0.00 0.00 43.49 4.45
2339 2482 9.581289 TTCACTTCCAATTTAACAGGAGAATAA 57.419 29.630 0.00 0.00 32.11 1.40
2379 2522 3.758755 ATATCTCCGAATGAGCTGCAA 57.241 42.857 1.02 0.00 41.18 4.08
2421 2564 1.980036 ACCTCGCCTTTTAGGGTGTTA 59.020 47.619 0.00 0.00 37.18 2.41
2473 2616 0.601311 AACTCTCTTGTGCTCCACGC 60.601 55.000 0.00 0.00 37.14 5.34
2624 2767 3.256704 ACCTTCACTTATCAAGGGGTCA 58.743 45.455 2.88 0.00 43.25 4.02
2695 2839 9.347240 AGAACATCTTATATTTGTGAATGGAGG 57.653 33.333 0.00 0.00 0.00 4.30
2762 2906 5.215160 GGACTGCAATGAGTAAACAAACAG 58.785 41.667 0.00 0.00 0.00 3.16
2821 2965 7.888021 TCAAATACTCCCACTGTTCACAAATAT 59.112 33.333 0.00 0.00 0.00 1.28
3086 3230 1.497278 CAGGCGTTGAATGTCCACG 59.503 57.895 0.00 0.00 0.00 4.94
3128 3272 8.579850 AGATAATGTAAGGCACAAAAATCAGA 57.420 30.769 0.00 0.00 41.55 3.27
3132 3276 9.590451 CAATGAGATAATGTAAGGCACAAAAAT 57.410 29.630 0.00 0.00 41.55 1.82
3227 3371 7.012138 CCATCCTGATCTGTGTTTTCTTCTATG 59.988 40.741 0.00 0.00 0.00 2.23
3228 3372 7.052873 CCATCCTGATCTGTGTTTTCTTCTAT 58.947 38.462 0.00 0.00 0.00 1.98
3437 3582 3.156511 GCCAGAGCTAATTTTTCAGCC 57.843 47.619 0.00 0.00 38.61 4.85
3638 3785 4.215908 TCCACTATGGAGAATAAGCGAGT 58.784 43.478 0.00 0.00 42.67 4.18
3897 4044 0.764890 TACAGCAGAAGCCAACAGGT 59.235 50.000 0.00 0.00 43.56 4.00
3929 4076 3.756434 CAGGACCAATAAAGAAAGCGGAA 59.244 43.478 0.00 0.00 0.00 4.30
3933 4080 6.407202 TCTAGTCAGGACCAATAAAGAAAGC 58.593 40.000 0.00 0.00 0.00 3.51
3999 4146 3.689161 TCATGTTTGGCCTTATCGTCTTG 59.311 43.478 3.32 0.00 0.00 3.02
4043 4190 1.081892 CCACTCCATGCTCTTGTTCG 58.918 55.000 0.00 0.00 0.00 3.95
4161 4308 2.143876 ACCCTTGGCACATACAATCC 57.856 50.000 0.00 0.00 39.30 3.01
4185 4332 1.205064 CACTGCAGAAAACTCGGCG 59.795 57.895 23.35 0.00 33.59 6.46
4208 4355 3.626028 ACTCGGCACATTTCTTTTGTC 57.374 42.857 0.00 0.00 0.00 3.18
4224 4371 0.457853 TAGCGGCTGCAAGTAACTCG 60.458 55.000 21.93 0.00 46.23 4.18
4239 4386 5.349817 CCACATGAGCTTATCCTAATTAGCG 59.650 44.000 6.99 1.18 41.36 4.26
4271 4420 8.970691 ATTCAACCGAAAATTGAGAACTAATG 57.029 30.769 0.00 0.00 37.38 1.90
4281 4430 4.150451 GCCAACTGATTCAACCGAAAATTG 59.850 41.667 0.00 0.00 34.01 2.32
4387 4537 3.367932 ACTTTGTCGTATCGAATGTGCAG 59.632 43.478 0.00 0.00 37.72 4.41
4397 4547 7.581600 GTCACAAAACTACAACTTTGTCGTATC 59.418 37.037 0.00 0.00 42.41 2.24
4405 4555 7.391148 ACATCAGTCACAAAACTACAACTTT 57.609 32.000 0.00 0.00 0.00 2.66
4436 4586 5.541868 AGGATCCAGTATATCAAGTCACAGG 59.458 44.000 15.82 0.00 0.00 4.00
4481 4636 2.231478 CCGGACACAGATGTAGAACAGT 59.769 50.000 0.00 0.00 39.95 3.55
4496 4651 3.478857 ACTTCATACAAACACCGGACA 57.521 42.857 9.46 0.00 0.00 4.02
4498 4653 4.062293 CTGAACTTCATACAAACACCGGA 58.938 43.478 9.46 0.00 0.00 5.14
4499 4654 3.364964 GCTGAACTTCATACAAACACCGG 60.365 47.826 0.00 0.00 0.00 5.28
4501 4656 5.438761 AAGCTGAACTTCATACAAACACC 57.561 39.130 0.00 0.00 30.77 4.16
4502 4657 6.494842 TCAAAGCTGAACTTCATACAAACAC 58.505 36.000 0.00 0.00 37.75 3.32
4503 4658 6.691754 TCAAAGCTGAACTTCATACAAACA 57.308 33.333 0.00 0.00 37.75 2.83
4519 4675 9.565090 TGATGATAGCAATAGTAAATCAAAGCT 57.435 29.630 0.00 0.00 30.90 3.74
4537 4693 4.381270 GTCTCGAATTCGCTGTGATGATAG 59.619 45.833 22.90 10.76 39.60 2.08
4688 4913 8.194104 ACAGTGCAAAAATGTGTTGTAATCTTA 58.806 29.630 0.00 0.00 0.00 2.10
4954 5179 8.795786 TCTTGTTAATCTTTGGATGTTTTTCG 57.204 30.769 0.00 0.00 31.75 3.46
5023 5253 2.427742 GGTACCTCCCGAGTCCATC 58.572 63.158 4.06 0.00 0.00 3.51
5024 5254 4.701286 GGTACCTCCCGAGTCCAT 57.299 61.111 4.06 0.00 0.00 3.41
5032 5262 3.366739 CTCGCCAACGGTACCTCCC 62.367 68.421 10.90 0.00 40.63 4.30
5111 5394 3.849951 CCCCACGAGTGCGGCTAT 61.850 66.667 0.00 0.00 43.17 2.97


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

AutoCloner maintained by Alex Coulton.