Multiple sequence alignment - TraesCS7D01G393300

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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 TraesCS7D01G393300 chr7D 100.000 4255 0 0 1 4255 508617415 508613161 0.000000e+00 7858.0
1 TraesCS7D01G393300 chr7D 94.265 680 26 2 5 671 396105533 396104854 0.000000e+00 1027.0
2 TraesCS7D01G393300 chr7D 93.548 682 30 3 1 668 10824838 10825519 0.000000e+00 1003.0
3 TraesCS7D01G393300 chr7D 91.892 259 8 2 424 669 616137446 616137188 2.430000e-92 350.0
4 TraesCS7D01G393300 chr7D 91.085 258 10 2 424 668 99972282 99972539 1.900000e-88 337.0
5 TraesCS7D01G393300 chr7B 89.097 1972 115 37 680 2586 536682753 536680817 0.000000e+00 2359.0
6 TraesCS7D01G393300 chr7B 95.667 600 25 1 2839 3437 536680500 536679901 0.000000e+00 963.0
7 TraesCS7D01G393300 chr7B 90.685 569 29 7 3692 4253 536667470 536666919 0.000000e+00 736.0
8 TraesCS7D01G393300 chr7B 90.962 343 23 5 2497 2839 536680861 536680527 5.020000e-124 455.0
9 TraesCS7D01G393300 chr7A 90.386 1581 76 37 2723 4255 578997870 578996318 0.000000e+00 2008.0
10 TraesCS7D01G393300 chr7A 94.152 1026 45 9 1671 2685 578999236 578998215 0.000000e+00 1548.0
11 TraesCS7D01G393300 chr7A 86.029 952 76 17 680 1592 579000212 578999279 0.000000e+00 968.0
12 TraesCS7D01G393300 chr6D 96.499 657 11 1 24 668 452927034 452927690 0.000000e+00 1075.0
13 TraesCS7D01G393300 chr6D 98.157 597 11 0 24 620 443755700 443755104 0.000000e+00 1042.0
14 TraesCS7D01G393300 chr6D 91.120 259 10 2 424 669 345768257 345767999 5.270000e-89 339.0
15 TraesCS7D01G393300 chr2D 94.860 681 22 2 1 668 81835413 81836093 0.000000e+00 1051.0
16 TraesCS7D01G393300 chr2D 90.698 258 10 3 424 668 598318876 598319132 8.820000e-87 331.0
17 TraesCS7D01G393300 chr2D 89.952 209 9 1 472 668 182739512 182739720 4.220000e-65 259.0
18 TraesCS7D01G393300 chr3D 94.567 681 24 5 1 668 129354182 129354862 0.000000e+00 1040.0
19 TraesCS7D01G393300 chr3D 89.565 230 12 1 451 668 55363343 55363572 9.010000e-72 281.0
20 TraesCS7D01G393300 chr3D 90.278 216 9 1 465 668 50069711 50069926 5.420000e-69 272.0
21 TraesCS7D01G393300 chr1D 94.682 677 23 2 5 668 76925920 76926596 0.000000e+00 1038.0
22 TraesCS7D01G393300 chr1D 94.039 671 35 5 1 668 400134563 400135231 0.000000e+00 1013.0
23 TraesCS7D01G393300 chr5D 96.135 621 23 1 1 620 431155111 431154491 0.000000e+00 1013.0
24 TraesCS7D01G393300 chr5B 87.500 56 7 0 3717 3772 699933832 699933777 9.880000e-07 65.8


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 TraesCS7D01G393300 chr7D 508613161 508617415 4254 True 7858 7858 100.000000 1 4255 1 chr7D.!!$R2 4254
1 TraesCS7D01G393300 chr7D 396104854 396105533 679 True 1027 1027 94.265000 5 671 1 chr7D.!!$R1 666
2 TraesCS7D01G393300 chr7D 10824838 10825519 681 False 1003 1003 93.548000 1 668 1 chr7D.!!$F1 667
3 TraesCS7D01G393300 chr7B 536679901 536682753 2852 True 1259 2359 91.908667 680 3437 3 chr7B.!!$R2 2757
4 TraesCS7D01G393300 chr7B 536666919 536667470 551 True 736 736 90.685000 3692 4253 1 chr7B.!!$R1 561
5 TraesCS7D01G393300 chr7A 578996318 579000212 3894 True 1508 2008 90.189000 680 4255 3 chr7A.!!$R1 3575
6 TraesCS7D01G393300 chr6D 452927034 452927690 656 False 1075 1075 96.499000 24 668 1 chr6D.!!$F1 644
7 TraesCS7D01G393300 chr6D 443755104 443755700 596 True 1042 1042 98.157000 24 620 1 chr6D.!!$R2 596
8 TraesCS7D01G393300 chr2D 81835413 81836093 680 False 1051 1051 94.860000 1 668 1 chr2D.!!$F1 667
9 TraesCS7D01G393300 chr3D 129354182 129354862 680 False 1040 1040 94.567000 1 668 1 chr3D.!!$F3 667
10 TraesCS7D01G393300 chr1D 76925920 76926596 676 False 1038 1038 94.682000 5 668 1 chr1D.!!$F1 663
11 TraesCS7D01G393300 chr1D 400134563 400135231 668 False 1013 1013 94.039000 1 668 1 chr1D.!!$F2 667
12 TraesCS7D01G393300 chr5D 431154491 431155111 620 True 1013 1013 96.135000 1 620 1 chr5D.!!$R1 619

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
675 690 0.544120 ATCAAATTTGCCGGGGGTGT 60.544 50.0 13.54 0.00 0.00 4.16 F
1388 1448 0.310232 GTACTGGGAGGTCGCGATAC 59.690 60.0 14.06 9.11 0.00 2.24 F
2051 2121 0.033090 TGTGCTCAGTGTCAGCTCTG 59.967 55.0 5.51 0.00 37.79 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1999 0.699577 TGTGAAGGTGGGGAAGGGAA 60.700 55.000 0.00 0.00 0.0 3.97 R
2897 3378 0.460811 TGGTCAGATGCTGCGTGATC 60.461 55.000 0.00 0.71 0.0 2.92 R
3372 3857 1.196808 ACTGCGCCGTAAAGTTCAATG 59.803 47.619 4.18 0.00 0.0 2.82 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
461 464 0.933097 CTAGGCGCTGCACATTACAG 59.067 55.000 7.64 0.00 38.22 2.74
600 603 1.669760 CGGGCGCTACACAAAAGGA 60.670 57.895 7.64 0.00 0.00 3.36
650 665 6.853872 TGTGAATTTATTTCGTTTTCTGGTCG 59.146 34.615 0.00 0.00 37.13 4.79
668 683 5.098893 TGGTCGAAATTATCAAATTTGCCG 58.901 37.500 13.54 7.72 43.69 5.69
671 686 3.801594 CGAAATTATCAAATTTGCCGGGG 59.198 43.478 13.54 0.00 43.69 5.73
672 687 3.836365 AATTATCAAATTTGCCGGGGG 57.164 42.857 13.54 0.00 30.98 5.40
673 688 2.239681 TTATCAAATTTGCCGGGGGT 57.760 45.000 13.54 0.00 0.00 4.95
674 689 1.479709 TATCAAATTTGCCGGGGGTG 58.520 50.000 13.54 0.00 0.00 4.61
675 690 0.544120 ATCAAATTTGCCGGGGGTGT 60.544 50.000 13.54 0.00 0.00 4.16
676 691 1.005156 CAAATTTGCCGGGGGTGTG 60.005 57.895 5.01 0.00 0.00 3.82
677 692 2.878089 AAATTTGCCGGGGGTGTGC 61.878 57.895 2.18 0.00 0.00 4.57
678 693 3.826265 AATTTGCCGGGGGTGTGCT 62.826 57.895 2.18 0.00 0.00 4.40
709 724 1.613437 CAAATCCCAACAAAGCGAGGT 59.387 47.619 0.00 0.00 0.00 3.85
750 765 3.412408 GCCCCCTGTTCTCCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
859 874 1.376037 CGACCAGGAGCCCAAGAAC 60.376 63.158 0.00 0.00 0.00 3.01
860 875 1.761174 GACCAGGAGCCCAAGAACA 59.239 57.895 0.00 0.00 0.00 3.18
861 876 0.606673 GACCAGGAGCCCAAGAACAC 60.607 60.000 0.00 0.00 0.00 3.32
865 898 2.617274 GGAGCCCAAGAACACGCAC 61.617 63.158 0.00 0.00 0.00 5.34
956 990 2.967397 CACTTCCGTCCGGTAGCA 59.033 61.111 11.65 0.00 36.32 3.49
989 1023 2.279517 CCCGTGATCGCTACCAGC 60.280 66.667 4.48 0.00 38.02 4.85
1025 1059 1.142314 GCTCTCTGCTCCTGCTCTG 59.858 63.158 0.00 0.00 40.48 3.35
1169 1206 1.767289 GACGGTATGTATGTGCTCCG 58.233 55.000 0.00 0.00 42.94 4.63
1189 1226 6.708949 GCTCCGGTGTTCATATTTATCCTTTA 59.291 38.462 0.00 0.00 0.00 1.85
1261 1298 1.160870 TCTGGCCTTTCCCTCTCCA 59.839 57.895 3.32 0.00 0.00 3.86
1288 1327 0.598065 CCCCTTTCTTTCCTTGTGCG 59.402 55.000 0.00 0.00 0.00 5.34
1298 1337 2.325583 TCCTTGTGCGTTTTCTCTGT 57.674 45.000 0.00 0.00 0.00 3.41
1302 1341 3.745975 CCTTGTGCGTTTTCTCTGTATGA 59.254 43.478 0.00 0.00 0.00 2.15
1303 1342 4.213270 CCTTGTGCGTTTTCTCTGTATGAA 59.787 41.667 0.00 0.00 0.00 2.57
1304 1343 5.106555 CCTTGTGCGTTTTCTCTGTATGAAT 60.107 40.000 0.00 0.00 0.00 2.57
1305 1344 5.281693 TGTGCGTTTTCTCTGTATGAATG 57.718 39.130 0.00 0.00 0.00 2.67
1356 1398 4.553330 AAGATGAGACGGTGTGGTATTT 57.447 40.909 0.00 0.00 0.00 1.40
1388 1448 0.310232 GTACTGGGAGGTCGCGATAC 59.690 60.000 14.06 9.11 0.00 2.24
1392 1452 0.828022 TGGGAGGTCGCGATACAAAT 59.172 50.000 14.06 0.00 0.00 2.32
1401 1461 3.060272 GTCGCGATACAAATCAGATGTGG 60.060 47.826 14.06 0.00 32.27 4.17
1424 1484 5.882557 GGAGATTTGATCTTGGAAGTTGCTA 59.117 40.000 0.00 0.00 40.38 3.49
1500 1563 1.337071 CCATGGATGTTCTGCAGATGC 59.663 52.381 19.04 14.09 42.50 3.91
1547 1610 7.921786 TTTATTGTGATTTGTGAGAGGGTAG 57.078 36.000 0.00 0.00 0.00 3.18
1549 1612 4.808414 TGTGATTTGTGAGAGGGTAGAG 57.192 45.455 0.00 0.00 0.00 2.43
1553 1616 5.186021 GTGATTTGTGAGAGGGTAGAGAAGA 59.814 44.000 0.00 0.00 0.00 2.87
1567 1630 9.052365 AGGGTAGAGAAGAGTTTCTTTGATAAT 57.948 33.333 0.00 0.00 43.63 1.28
1615 1682 5.183904 GCTGTCCTTACCATCAACATTTTCT 59.816 40.000 0.00 0.00 0.00 2.52
1616 1683 6.374333 GCTGTCCTTACCATCAACATTTTCTA 59.626 38.462 0.00 0.00 0.00 2.10
1617 1684 7.067494 GCTGTCCTTACCATCAACATTTTCTAT 59.933 37.037 0.00 0.00 0.00 1.98
1618 1685 9.613428 CTGTCCTTACCATCAACATTTTCTATA 57.387 33.333 0.00 0.00 0.00 1.31
1669 1736 9.151471 CATTTTAGTGTGTTAGTGCACTACTAT 57.849 33.333 26.02 9.85 44.73 2.12
1674 1741 8.294954 AGTGTGTTAGTGCACTACTATTATCT 57.705 34.615 26.02 14.59 43.30 1.98
1980 2047 4.379813 CCTTCACGAAGATCCACCAAAATG 60.380 45.833 8.38 0.00 40.79 2.32
2001 2070 4.678256 TGTACTCTGAATCCTGAAGACCT 58.322 43.478 0.00 0.00 0.00 3.85
2046 2116 1.723220 CATCCTGTGCTCAGTGTCAG 58.277 55.000 14.31 0.00 39.82 3.51
2047 2117 0.036577 ATCCTGTGCTCAGTGTCAGC 60.037 55.000 14.31 0.00 39.82 4.26
2048 2118 1.117749 TCCTGTGCTCAGTGTCAGCT 61.118 55.000 14.31 0.00 39.82 4.24
2049 2119 0.669932 CCTGTGCTCAGTGTCAGCTC 60.670 60.000 14.31 2.79 39.82 4.09
2051 2121 0.033090 TGTGCTCAGTGTCAGCTCTG 59.967 55.000 5.51 0.00 37.79 3.35
2052 2122 0.669932 GTGCTCAGTGTCAGCTCTGG 60.670 60.000 5.51 0.00 37.79 3.86
2053 2123 1.079266 GCTCAGTGTCAGCTCTGGG 60.079 63.158 0.72 0.00 39.13 4.45
2054 2124 1.539560 GCTCAGTGTCAGCTCTGGGA 61.540 60.000 4.25 0.00 38.59 4.37
2055 2125 1.193323 CTCAGTGTCAGCTCTGGGAT 58.807 55.000 0.00 0.00 38.59 3.85
2056 2126 2.382882 CTCAGTGTCAGCTCTGGGATA 58.617 52.381 0.00 0.00 38.59 2.59
2057 2127 2.762887 CTCAGTGTCAGCTCTGGGATAA 59.237 50.000 0.00 0.00 38.59 1.75
2058 2128 3.378512 TCAGTGTCAGCTCTGGGATAAT 58.621 45.455 0.72 0.00 36.98 1.28
2059 2129 3.133542 TCAGTGTCAGCTCTGGGATAATG 59.866 47.826 0.72 0.00 36.98 1.90
2060 2130 3.110705 AGTGTCAGCTCTGGGATAATGT 58.889 45.455 0.00 0.00 0.00 2.71
2062 2132 3.624861 GTGTCAGCTCTGGGATAATGTTG 59.375 47.826 0.00 0.00 0.00 3.33
2063 2133 2.615912 GTCAGCTCTGGGATAATGTTGC 59.384 50.000 0.00 0.00 0.00 4.17
2064 2134 2.239402 TCAGCTCTGGGATAATGTTGCA 59.761 45.455 0.00 0.00 0.00 4.08
2066 2136 4.102996 TCAGCTCTGGGATAATGTTGCATA 59.897 41.667 0.00 0.00 0.00 3.14
2067 2137 4.823442 CAGCTCTGGGATAATGTTGCATAA 59.177 41.667 0.00 0.00 0.00 1.90
2068 2138 5.300034 CAGCTCTGGGATAATGTTGCATAAA 59.700 40.000 0.00 0.00 0.00 1.40
2069 2139 5.893255 AGCTCTGGGATAATGTTGCATAAAA 59.107 36.000 0.00 0.00 0.00 1.52
2072 2142 7.631377 GCTCTGGGATAATGTTGCATAAAAACT 60.631 37.037 0.00 0.00 0.00 2.66
2073 2143 7.546358 TCTGGGATAATGTTGCATAAAAACTG 58.454 34.615 0.00 0.00 0.00 3.16
2322 2403 4.678743 GCCCCCAACTTCGGCCTT 62.679 66.667 0.00 0.00 36.63 4.35
2471 2554 5.514204 CGGTTCTTGATGCAAATTTCATCTC 59.486 40.000 21.04 7.62 40.59 2.75
2472 2555 6.624423 CGGTTCTTGATGCAAATTTCATCTCT 60.624 38.462 21.04 0.00 40.59 3.10
2475 2558 7.317842 TCTTGATGCAAATTTCATCTCTCTC 57.682 36.000 21.04 6.19 40.59 3.20
2522 2609 2.672961 TGGCAGTATCGTTCTTGAGG 57.327 50.000 0.00 0.00 0.00 3.86
2546 2633 5.625311 GTGTGCATCTGTTGTAGTTAAAAGC 59.375 40.000 0.00 0.00 0.00 3.51
2558 2645 6.176896 TGTAGTTAAAAGCATGGCACTATCA 58.823 36.000 0.00 0.00 0.00 2.15
2567 2654 3.304525 GCATGGCACTATCATTCTTGAGC 60.305 47.826 0.00 0.00 34.73 4.26
2576 2663 2.362736 TCATTCTTGAGCTGTGCATCC 58.637 47.619 0.00 0.00 0.00 3.51
2619 2749 4.863491 GCTTTTGCAGAAGTTCAGAATGA 58.137 39.130 17.43 0.00 45.39 2.57
2688 2818 1.610038 TGTCTGAAGCCACTTTGCATG 59.390 47.619 0.00 0.00 0.00 4.06
2742 3195 1.270907 GAGAGGGTGCTGAGGAAAGA 58.729 55.000 0.00 0.00 0.00 2.52
2753 3206 4.676849 CTGAGGAAAGAGCAGCTTTAAC 57.323 45.455 0.00 2.54 46.52 2.01
2754 3207 3.067106 TGAGGAAAGAGCAGCTTTAACG 58.933 45.455 0.00 0.00 46.52 3.18
2755 3208 2.416893 GAGGAAAGAGCAGCTTTAACGG 59.583 50.000 0.00 0.00 46.52 4.44
2757 3210 0.517316 AAAGAGCAGCTTTAACGGCG 59.483 50.000 4.80 4.80 44.78 6.46
2848 3328 6.204301 CAGTCCAATGCTATGAGTATCCTTTG 59.796 42.308 0.00 0.00 0.00 2.77
2864 3344 5.086104 TCCTTTGTAGTGCAGGATAAGAC 57.914 43.478 0.00 0.00 0.00 3.01
2868 3348 7.038587 TCCTTTGTAGTGCAGGATAAGACTAAA 60.039 37.037 0.00 0.00 0.00 1.85
2894 3375 1.814394 GTCCAGTTTGATCAGCATGCA 59.186 47.619 21.98 0.00 34.76 3.96
2897 3378 2.481276 CCAGTTTGATCAGCATGCATGG 60.481 50.000 27.34 12.41 34.76 3.66
2914 3395 0.460811 TGGATCACGCAGCATCTGAC 60.461 55.000 0.00 0.00 32.44 3.51
2916 3397 0.460811 GATCACGCAGCATCTGACCA 60.461 55.000 0.00 0.00 32.44 4.02
2923 3404 2.481854 GCAGCATCTGACCATGACTAG 58.518 52.381 0.00 0.00 32.44 2.57
3070 3551 0.037232 GTGAAGGTGAAGGGGTCGAG 60.037 60.000 0.00 0.00 0.00 4.04
3260 3741 2.582687 CAGTTCGTCGAGTAGGTGAAC 58.417 52.381 0.00 0.00 39.28 3.18
3305 3786 7.172019 CGACTGTAATTACAACTACAAGGGTTT 59.828 37.037 18.55 0.00 35.50 3.27
3340 3825 2.621526 ACCCAAGAACGTGAATGGTTTC 59.378 45.455 11.45 0.00 0.00 2.78
3372 3857 1.064505 CCATGCACGTCCAACATGATC 59.935 52.381 15.33 0.00 43.04 2.92
3384 3869 6.742718 CGTCCAACATGATCATTGAACTTTAC 59.257 38.462 5.16 0.00 0.00 2.01
3434 3919 2.649331 ACCACGTCAGTCTATTTCCG 57.351 50.000 0.00 0.00 0.00 4.30
3514 4008 2.289565 CCCCGAAGCATCCTTCTAAAC 58.710 52.381 0.00 0.00 44.24 2.01
3515 4009 2.289565 CCCGAAGCATCCTTCTAAACC 58.710 52.381 0.00 0.00 44.24 3.27
3516 4010 2.289565 CCGAAGCATCCTTCTAAACCC 58.710 52.381 0.00 0.00 44.24 4.11
3523 4017 2.068831 TCCTTCTAAACCCCCACCAT 57.931 50.000 0.00 0.00 0.00 3.55
3524 4018 2.364190 TCCTTCTAAACCCCCACCATT 58.636 47.619 0.00 0.00 0.00 3.16
3525 4019 2.310647 TCCTTCTAAACCCCCACCATTC 59.689 50.000 0.00 0.00 0.00 2.67
3529 4023 3.265489 TCTAAACCCCCACCATTCTTCT 58.735 45.455 0.00 0.00 0.00 2.85
3531 4025 0.704664 AACCCCCACCATTCTTCTCC 59.295 55.000 0.00 0.00 0.00 3.71
3553 4047 2.354729 CCGTCAGCCCATCCCAAA 59.645 61.111 0.00 0.00 0.00 3.28
3591 4092 1.377987 AACAACACCACTGCCGTGT 60.378 52.632 7.53 0.00 46.25 4.49
3618 4119 3.963383 GTGAAACGGCTCTCTCAAAAA 57.037 42.857 0.00 0.00 0.00 1.94
3619 4120 4.489679 GTGAAACGGCTCTCTCAAAAAT 57.510 40.909 0.00 0.00 0.00 1.82
3620 4121 5.607119 GTGAAACGGCTCTCTCAAAAATA 57.393 39.130 0.00 0.00 0.00 1.40
3621 4122 5.997385 GTGAAACGGCTCTCTCAAAAATAA 58.003 37.500 0.00 0.00 0.00 1.40
3622 4123 6.435428 GTGAAACGGCTCTCTCAAAAATAAA 58.565 36.000 0.00 0.00 0.00 1.40
3623 4124 6.915843 GTGAAACGGCTCTCTCAAAAATAAAA 59.084 34.615 0.00 0.00 0.00 1.52
3624 4125 7.595130 GTGAAACGGCTCTCTCAAAAATAAAAT 59.405 33.333 0.00 0.00 0.00 1.82
3837 4338 6.014669 AGAGACATCACTCTCTGTAGCTTTTT 60.015 38.462 0.00 0.00 44.54 1.94
3845 4346 3.321111 TCTCTGTAGCTTTTTGGACGACT 59.679 43.478 0.00 0.00 0.00 4.18
3880 4381 2.086869 CTTGGCCCACTGTGTGAATAG 58.913 52.381 0.00 0.00 35.23 1.73
4126 4627 3.368571 GCTGCAGCACCCAGGAAC 61.369 66.667 33.36 0.00 41.59 3.62
4127 4628 3.052082 CTGCAGCACCCAGGAACG 61.052 66.667 0.00 0.00 0.00 3.95
4128 4629 3.832237 CTGCAGCACCCAGGAACGT 62.832 63.158 0.00 0.00 0.00 3.99
4129 4630 2.594592 GCAGCACCCAGGAACGTT 60.595 61.111 0.00 0.00 0.00 3.99
4130 4631 2.617274 GCAGCACCCAGGAACGTTC 61.617 63.158 20.14 20.14 0.00 3.95
4147 4653 3.059166 CGTTCCAAGGAAATTTTGCTGG 58.941 45.455 3.76 8.03 35.75 4.85
4234 4743 7.020827 TGACCAAAATCTAGAGAAAGGACAT 57.979 36.000 10.11 0.00 0.00 3.06
4246 4755 9.658799 CTAGAGAAAGGACATGAGTAAAATGAA 57.341 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
600 603 7.557719 CAGAATGAACTATTTCACACCCCTAAT 59.442 37.037 0.00 0.00 44.66 1.73
645 660 5.098893 CGGCAAATTTGATAATTTCGACCA 58.901 37.500 22.31 0.00 40.97 4.02
650 665 4.126437 CCCCCGGCAAATTTGATAATTTC 58.874 43.478 22.31 1.89 40.97 2.17
656 671 0.544120 ACACCCCCGGCAAATTTGAT 60.544 50.000 22.31 0.00 0.00 2.57
677 692 2.105528 GATTTGCGGCCATGGCAG 59.894 61.111 36.56 33.25 42.12 4.85
678 693 3.459965 GGATTTGCGGCCATGGCA 61.460 61.111 36.56 17.73 44.11 4.92
709 724 2.668185 TTTCGCCACGCCCTTTCTGA 62.668 55.000 0.00 0.00 0.00 3.27
750 765 2.613696 TGGGACATGGGACTGGGG 60.614 66.667 0.00 0.00 0.00 4.96
851 866 4.025401 GCGGTGCGTGTTCTTGGG 62.025 66.667 0.00 0.00 0.00 4.12
893 927 2.564721 GGAAGGGGCTTGTGTGTGC 61.565 63.158 0.00 0.00 0.00 4.57
1011 1045 2.284478 AGGCAGAGCAGGAGCAGA 60.284 61.111 0.00 0.00 45.49 4.26
1025 1059 1.318158 CCCAGAAATCACCAGCAGGC 61.318 60.000 0.00 0.00 39.06 4.85
1086 1123 1.388065 CCAGCCTCCAGTCCTCGTAG 61.388 65.000 0.00 0.00 0.00 3.51
1113 1150 2.840651 CTGGGACTCCTTGATGTAGGTT 59.159 50.000 0.00 0.00 36.63 3.50
1149 1186 1.767289 GGAGCACATACATACCGTCG 58.233 55.000 0.00 0.00 0.00 5.12
1194 1231 8.880878 TGTTCTTGACGCTGCTAATAATAATA 57.119 30.769 0.00 0.00 0.00 0.98
1195 1232 7.786178 TGTTCTTGACGCTGCTAATAATAAT 57.214 32.000 0.00 0.00 0.00 1.28
1196 1233 7.494298 TGATGTTCTTGACGCTGCTAATAATAA 59.506 33.333 0.00 0.00 0.00 1.40
1197 1234 6.983890 TGATGTTCTTGACGCTGCTAATAATA 59.016 34.615 0.00 0.00 0.00 0.98
1198 1235 5.817296 TGATGTTCTTGACGCTGCTAATAAT 59.183 36.000 0.00 0.00 0.00 1.28
1199 1236 5.175127 TGATGTTCTTGACGCTGCTAATAA 58.825 37.500 0.00 0.00 0.00 1.40
1200 1237 4.754322 TGATGTTCTTGACGCTGCTAATA 58.246 39.130 0.00 0.00 0.00 0.98
1210 1247 2.479566 TCCTGCCTGATGTTCTTGAC 57.520 50.000 0.00 0.00 0.00 3.18
1288 1327 7.554118 TCCAATCTCCATTCATACAGAGAAAAC 59.446 37.037 0.00 0.00 38.76 2.43
1298 1337 5.608015 TCACCATCTCCAATCTCCATTCATA 59.392 40.000 0.00 0.00 0.00 2.15
1302 1341 4.868172 TTCACCATCTCCAATCTCCATT 57.132 40.909 0.00 0.00 0.00 3.16
1303 1342 4.726583 CATTCACCATCTCCAATCTCCAT 58.273 43.478 0.00 0.00 0.00 3.41
1304 1343 3.686405 GCATTCACCATCTCCAATCTCCA 60.686 47.826 0.00 0.00 0.00 3.86
1305 1344 2.883386 GCATTCACCATCTCCAATCTCC 59.117 50.000 0.00 0.00 0.00 3.71
1336 1375 3.369471 CCAAATACCACACCGTCTCATCT 60.369 47.826 0.00 0.00 0.00 2.90
1344 1383 3.463944 GGATCTACCAAATACCACACCG 58.536 50.000 0.00 0.00 38.79 4.94
1356 1398 1.105167 CCAGTACGCCGGATCTACCA 61.105 60.000 5.05 0.00 38.90 3.25
1392 1452 5.190330 TCCAAGATCAAATCTCCACATCTGA 59.810 40.000 0.00 0.00 39.08 3.27
1401 1461 5.893897 AGCAACTTCCAAGATCAAATCTC 57.106 39.130 0.00 0.00 39.08 2.75
1409 1469 6.543735 AGTAAAAGGTAGCAACTTCCAAGAT 58.456 36.000 0.00 0.00 0.00 2.40
1411 1471 5.998363 AGAGTAAAAGGTAGCAACTTCCAAG 59.002 40.000 0.00 0.00 0.00 3.61
1424 1484 6.211584 TCTCAATGAGTAGCAGAGTAAAAGGT 59.788 38.462 10.36 0.00 0.00 3.50
1525 1588 6.667848 TCTCTACCCTCTCACAAATCACAATA 59.332 38.462 0.00 0.00 0.00 1.90
1540 1603 6.347859 TCAAAGAAACTCTTCTCTACCCTC 57.652 41.667 0.00 0.00 41.23 4.30
1567 1630 3.868757 AGCGTCAAGACTGCACTATAA 57.131 42.857 15.46 0.00 34.80 0.98
1637 1704 7.376072 GTGCACTAACACACTAAAATGAAGTTC 59.624 37.037 10.32 0.00 40.40 3.01
1650 1717 8.928270 AAGATAATAGTAGTGCACTAACACAC 57.072 34.615 27.61 17.58 43.00 3.82
1669 1736 7.392113 TGGTTTTCTTTCGGCTGATTAAGATAA 59.608 33.333 9.89 8.92 0.00 1.75
1674 1741 5.776173 TTGGTTTTCTTTCGGCTGATTAA 57.224 34.783 0.00 0.00 0.00 1.40
1856 1923 3.863400 GCAGGCAATGACAGCAAGAAAAT 60.863 43.478 0.00 0.00 0.00 1.82
1858 1925 1.000060 GCAGGCAATGACAGCAAGAAA 60.000 47.619 0.00 0.00 0.00 2.52
1932 1999 0.699577 TGTGAAGGTGGGGAAGGGAA 60.700 55.000 0.00 0.00 0.00 3.97
1980 2047 5.669164 AAGGTCTTCAGGATTCAGAGTAC 57.331 43.478 0.00 0.00 0.00 2.73
2046 2116 5.772825 TTTATGCAACATTATCCCAGAGC 57.227 39.130 0.00 0.00 0.00 4.09
2047 2117 7.703621 CAGTTTTTATGCAACATTATCCCAGAG 59.296 37.037 0.00 0.00 0.00 3.35
2048 2118 7.395772 TCAGTTTTTATGCAACATTATCCCAGA 59.604 33.333 0.00 0.00 0.00 3.86
2049 2119 7.546358 TCAGTTTTTATGCAACATTATCCCAG 58.454 34.615 0.00 0.00 0.00 4.45
2051 2121 8.770438 TTTCAGTTTTTATGCAACATTATCCC 57.230 30.769 0.00 0.00 0.00 3.85
2056 2126 9.719279 CAACATTTTCAGTTTTTATGCAACATT 57.281 25.926 0.00 0.00 0.00 2.71
2057 2127 8.891720 ACAACATTTTCAGTTTTTATGCAACAT 58.108 25.926 0.00 0.00 0.00 2.71
2058 2128 8.261492 ACAACATTTTCAGTTTTTATGCAACA 57.739 26.923 0.00 0.00 0.00 3.33
2059 2129 8.997960 CAACAACATTTTCAGTTTTTATGCAAC 58.002 29.630 0.00 0.00 0.00 4.17
2060 2130 8.725148 ACAACAACATTTTCAGTTTTTATGCAA 58.275 25.926 0.00 0.00 0.00 4.08
2062 2132 8.603181 AGACAACAACATTTTCAGTTTTTATGC 58.397 29.630 0.00 0.00 0.00 3.14
2063 2133 9.904647 CAGACAACAACATTTTCAGTTTTTATG 57.095 29.630 0.00 0.00 0.00 1.90
2064 2134 9.868277 TCAGACAACAACATTTTCAGTTTTTAT 57.132 25.926 0.00 0.00 0.00 1.40
2066 2136 8.658609 CATCAGACAACAACATTTTCAGTTTTT 58.341 29.630 0.00 0.00 0.00 1.94
2067 2137 7.201548 GCATCAGACAACAACATTTTCAGTTTT 60.202 33.333 0.00 0.00 0.00 2.43
2068 2138 6.256321 GCATCAGACAACAACATTTTCAGTTT 59.744 34.615 0.00 0.00 0.00 2.66
2069 2139 5.750067 GCATCAGACAACAACATTTTCAGTT 59.250 36.000 0.00 0.00 0.00 3.16
2072 2142 5.259832 TGCATCAGACAACAACATTTTCA 57.740 34.783 0.00 0.00 0.00 2.69
2073 2143 6.347079 CCATTGCATCAGACAACAACATTTTC 60.347 38.462 0.00 0.00 0.00 2.29
2248 2329 4.445699 CCGCAGGCAATAGAGGAC 57.554 61.111 0.00 0.00 46.14 3.85
2471 2554 8.429493 TGCACACATATATTCAGAAAAGAGAG 57.571 34.615 0.00 0.00 0.00 3.20
2472 2555 8.791327 TTGCACACATATATTCAGAAAAGAGA 57.209 30.769 0.00 0.00 0.00 3.10
2475 2558 8.589629 GCTTTTGCACACATATATTCAGAAAAG 58.410 33.333 0.00 0.00 46.58 2.27
2522 2609 5.625311 GCTTTTAACTACAACAGATGCACAC 59.375 40.000 0.00 0.00 0.00 3.82
2546 2633 4.023963 CAGCTCAAGAATGATAGTGCCATG 60.024 45.833 0.00 0.00 34.37 3.66
2558 2645 1.376543 CGGATGCACAGCTCAAGAAT 58.623 50.000 0.00 0.00 0.00 2.40
2567 2654 2.386661 AAACTACTCCGGATGCACAG 57.613 50.000 3.57 0.20 0.00 3.66
2591 2721 0.957362 ACTTCTGCAAAAGCAGGCTC 59.043 50.000 16.47 0.00 38.27 4.70
2688 2818 2.137177 TTTCTACCCAGCAGCCCACC 62.137 60.000 0.00 0.00 0.00 4.61
2742 3195 2.033194 GTCCGCCGTTAAAGCTGCT 61.033 57.895 0.00 0.00 0.00 4.24
2753 3206 1.566018 AAAGAAGAAAGCGTCCGCCG 61.566 55.000 8.23 0.00 43.17 6.46
2754 3207 0.591659 AAAAGAAGAAAGCGTCCGCC 59.408 50.000 8.23 0.00 43.17 6.13
2755 3208 2.401017 AAAAAGAAGAAAGCGTCCGC 57.599 45.000 2.94 2.94 42.33 5.54
2788 3241 5.842907 AGTACTCATGATTAGCATACGCAA 58.157 37.500 0.00 0.00 42.27 4.85
2789 3242 5.453567 AGTACTCATGATTAGCATACGCA 57.546 39.130 0.00 0.00 42.27 5.24
2790 3243 5.346281 GGAAGTACTCATGATTAGCATACGC 59.654 44.000 0.00 0.00 34.82 4.42
2848 3328 9.250624 CACTATTTTAGTCTTATCCTGCACTAC 57.749 37.037 0.00 0.00 36.76 2.73
2864 3344 7.119699 TGCTGATCAAACTGGACACTATTTTAG 59.880 37.037 0.00 0.00 0.00 1.85
2868 3348 4.910195 TGCTGATCAAACTGGACACTATT 58.090 39.130 0.00 0.00 0.00 1.73
2894 3375 0.466963 TCAGATGCTGCGTGATCCAT 59.533 50.000 0.00 0.00 0.00 3.41
2897 3378 0.460811 TGGTCAGATGCTGCGTGATC 60.461 55.000 0.00 0.71 0.00 2.92
2914 3395 2.602257 TCGTCAATGGCTAGTCATGG 57.398 50.000 11.34 8.18 0.00 3.66
3070 3551 1.835712 ATCGGTATCCACCCGGTCC 60.836 63.158 0.00 0.00 45.51 4.46
3260 3741 1.600636 TTGGAGCTTGCAACCCTCG 60.601 57.895 13.38 0.00 0.00 4.63
3305 3786 2.039216 TCTTGGGTCACGGCATTTTAGA 59.961 45.455 0.00 0.00 0.00 2.10
3355 3840 2.112380 ATGATCATGTTGGACGTGCA 57.888 45.000 5.33 5.33 35.17 4.57
3372 3857 1.196808 ACTGCGCCGTAAAGTTCAATG 59.803 47.619 4.18 0.00 0.00 2.82
3384 3869 1.922570 ACTTACAGATAACTGCGCCG 58.077 50.000 4.18 0.00 46.95 6.46
3514 4008 1.224592 CGGAGAAGAATGGTGGGGG 59.775 63.158 0.00 0.00 0.00 5.40
3515 4009 1.224592 CCGGAGAAGAATGGTGGGG 59.775 63.158 0.00 0.00 0.00 4.96
3516 4010 1.452108 GCCGGAGAAGAATGGTGGG 60.452 63.158 5.05 0.00 0.00 4.61
3547 4041 2.305927 GAGAGGAGTTGATGGTTTGGGA 59.694 50.000 0.00 0.00 0.00 4.37
3553 4047 1.280457 GGTGGAGAGGAGTTGATGGT 58.720 55.000 0.00 0.00 0.00 3.55
3631 4132 2.044650 GAGCTGGGGATGCAGCAA 60.045 61.111 3.51 0.00 46.10 3.91
3837 4338 1.764134 AGTGGTTTGGTAAGTCGTCCA 59.236 47.619 0.00 0.00 0.00 4.02
3845 4346 2.303175 GCCAAGTCAGTGGTTTGGTAA 58.697 47.619 20.53 0.00 42.60 2.85
3911 4412 2.822764 CTATAACTCCCGTTGCACTCC 58.177 52.381 0.00 0.00 34.59 3.85
3912 4413 2.202566 GCTATAACTCCCGTTGCACTC 58.797 52.381 0.00 0.00 34.59 3.51
3913 4414 1.553248 TGCTATAACTCCCGTTGCACT 59.447 47.619 0.00 0.00 34.59 4.40
3914 4415 2.018542 TGCTATAACTCCCGTTGCAC 57.981 50.000 0.00 0.00 34.59 4.57
4124 4625 4.119136 CAGCAAAATTTCCTTGGAACGTT 58.881 39.130 0.00 0.00 0.00 3.99
4126 4627 3.059166 CCAGCAAAATTTCCTTGGAACG 58.941 45.455 0.98 0.00 0.00 3.95
4127 4628 2.807967 GCCAGCAAAATTTCCTTGGAAC 59.192 45.455 15.22 0.00 0.00 3.62
4128 4629 2.705127 AGCCAGCAAAATTTCCTTGGAA 59.295 40.909 15.22 0.00 0.00 3.53
4129 4630 2.037511 CAGCCAGCAAAATTTCCTTGGA 59.962 45.455 15.22 0.00 0.00 3.53
4130 4631 2.224354 ACAGCCAGCAAAATTTCCTTGG 60.224 45.455 9.34 9.34 0.00 3.61
4131 4632 3.116079 ACAGCCAGCAAAATTTCCTTG 57.884 42.857 0.00 0.00 0.00 3.61
4176 4683 5.934625 TCTTCTGTCTTTTTATCTGCCTCAC 59.065 40.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.