Multiple sequence alignment - TraesCS7D01G260700

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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 TraesCS7D01G260700 chr7D 100.000 7068 0 0 1 7068 236638377 236645444 0.000000e+00 13053.0
1 TraesCS7D01G260700 chr7D 87.137 241 24 5 1978 2214 368913880 368914117 4.200000e-67 267.0
2 TraesCS7D01G260700 chr7D 88.182 220 22 3 2011 2227 13688480 13688698 7.030000e-65 259.0
3 TraesCS7D01G260700 chr7A 95.212 5806 211 20 1275 7068 251742569 251748319 0.000000e+00 9119.0
4 TraesCS7D01G260700 chr7A 92.633 733 36 12 431 1151 251741725 251742451 0.000000e+00 1038.0
5 TraesCS7D01G260700 chr7A 88.030 401 41 5 3 398 251741324 251741722 1.070000e-127 468.0
6 TraesCS7D01G260700 chr7A 91.089 303 26 1 1654 1955 571440801 571441103 6.600000e-110 409.0
7 TraesCS7D01G260700 chr7A 89.457 313 31 2 1649 1960 352359172 352358861 1.850000e-105 394.0
8 TraesCS7D01G260700 chr7A 100.000 32 0 0 1622 1653 571440721 571440752 7.660000e-05 60.2
9 TraesCS7D01G260700 chr7B 95.165 3247 121 13 113 3341 213245982 213249210 0.000000e+00 5094.0
10 TraesCS7D01G260700 chr7B 96.367 2780 78 7 3404 6174 213249203 213251968 0.000000e+00 4553.0
11 TraesCS7D01G260700 chr7B 88.983 472 22 10 6172 6624 213252049 213252509 2.230000e-154 556.0
12 TraesCS7D01G260700 chr7B 85.714 252 32 3 1977 2225 313691549 313691299 5.440000e-66 263.0
13 TraesCS7D01G260700 chr7B 86.806 144 14 3 6446 6587 63972565 63972705 9.490000e-34 156.0
14 TraesCS7D01G260700 chr4A 90.096 313 27 3 1649 1960 544290462 544290771 3.070000e-108 403.0
15 TraesCS7D01G260700 chr4A 91.411 163 13 1 1649 1810 309477680 309477518 9.230000e-54 222.0
16 TraesCS7D01G260700 chr4A 91.111 90 8 0 3586 3675 27643525 27643614 9.630000e-24 122.0
17 TraesCS7D01G260700 chr4A 100.000 32 0 0 1622 1653 544290386 544290417 7.660000e-05 60.2
18 TraesCS7D01G260700 chr4D 91.844 282 21 2 1680 1960 19881125 19881405 6.650000e-105 392.0
19 TraesCS7D01G260700 chr4D 77.556 401 51 19 5234 5603 499290840 499291232 9.290000e-49 206.0
20 TraesCS7D01G260700 chr4D 100.000 31 0 0 1622 1652 19881052 19881082 2.750000e-04 58.4
21 TraesCS7D01G260700 chr3D 84.962 266 38 1 1960 2223 170240244 170240509 1.170000e-67 268.0
22 TraesCS7D01G260700 chr3D 83.588 262 37 6 1963 2222 100179516 100179259 2.550000e-59 241.0
23 TraesCS7D01G260700 chr3D 85.976 164 21 2 6464 6627 104391416 104391255 2.620000e-39 174.0
24 TraesCS7D01G260700 chr3D 91.111 90 7 1 3587 3676 477907443 477907355 3.460000e-23 121.0
25 TraesCS7D01G260700 chr3B 84.270 267 38 3 1960 2223 245514213 245514478 2.530000e-64 257.0
26 TraesCS7D01G260700 chr3B 91.111 90 7 1 3587 3676 637089781 637089693 3.460000e-23 121.0
27 TraesCS7D01G260700 chr5A 78.638 426 57 17 5204 5603 680075672 680076089 1.180000e-62 252.0
28 TraesCS7D01G260700 chr5A 100.000 32 0 0 1622 1653 674570855 674570824 7.660000e-05 60.2
29 TraesCS7D01G260700 chr4B 78.422 431 54 19 5204 5603 642086625 642087047 1.970000e-60 244.0
30 TraesCS7D01G260700 chr4B 92.941 85 6 0 3587 3671 41531417 41531501 2.680000e-24 124.0
31 TraesCS7D01G260700 chr2A 83.459 266 38 3 1962 2223 46113311 46113048 7.080000e-60 243.0
32 TraesCS7D01G260700 chr2A 100.000 28 0 0 6855 6882 18897259 18897232 1.300000e-02 52.8
33 TraesCS7D01G260700 chr5B 91.176 170 14 1 1649 1818 688995881 688995713 5.510000e-56 230.0
34 TraesCS7D01G260700 chr6B 92.617 149 10 1 1680 1828 318650710 318650857 5.550000e-51 213.0
35 TraesCS7D01G260700 chr1D 86.982 169 11 8 6464 6624 246940513 246940678 5.630000e-41 180.0
36 TraesCS7D01G260700 chr1D 91.111 90 8 0 3587 3676 101285148 101285237 9.630000e-24 122.0
37 TraesCS7D01G260700 chr1D 100.000 31 0 0 1622 1652 246464720 246464750 2.750000e-04 58.4
38 TraesCS7D01G260700 chr6D 93.182 88 6 0 3587 3674 389976960 389976873 5.750000e-26 130.0
39 TraesCS7D01G260700 chr6D 100.000 31 0 0 1622 1652 429815877 429815847 2.750000e-04 58.4
40 TraesCS7D01G260700 chr1A 91.111 90 8 0 3587 3676 104216547 104216458 9.630000e-24 122.0
41 TraesCS7D01G260700 chr1A 92.857 56 2 2 1557 1612 154075337 154075390 5.880000e-11 80.5
42 TraesCS7D01G260700 chrUn 100.000 31 0 0 1622 1652 414538479 414538449 2.750000e-04 58.4


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 TraesCS7D01G260700 chr7D 236638377 236645444 7067 False 13053.000000 13053 100.000000 1 7068 1 chr7D.!!$F2 7067
1 TraesCS7D01G260700 chr7A 251741324 251748319 6995 False 3541.666667 9119 91.958333 3 7068 3 chr7A.!!$F1 7065
2 TraesCS7D01G260700 chr7B 213245982 213252509 6527 False 3401.000000 5094 93.505000 113 6624 3 chr7B.!!$F2 6511

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
564 571 1.139654 TCCTGCAGATTTCCTCCATCG 59.860 52.381 17.39 0.00 0.00 3.84 F
1988 2008 0.808453 ACGTCCGGAAATACATGCCG 60.808 55.000 5.23 4.48 44.42 5.69 F
2813 2834 0.321564 TGTTTCCATCAGTGGCCTCG 60.322 55.000 3.32 0.00 45.63 4.63 F
3183 3204 0.875059 GGTAAGAGGCGCATTATGGC 59.125 55.000 10.83 0.00 0.00 4.40 F
4570 4607 0.447801 CCTGTGTTGCTATGTTCCGC 59.552 55.000 0.00 0.00 0.00 5.54 F
5167 5204 2.571212 CCGGAGGCTGTTTGCATATTA 58.429 47.619 0.00 0.00 46.14 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 2348 1.003851 AAACACACGGACAAGTCACG 58.996 50.000 2.29 6.12 0.00 4.35 R
3627 3658 3.626028 AGACGTTTTTGCAGGCTAAAG 57.374 42.857 0.00 0.00 0.00 1.85 R
4002 4033 1.091771 AATGCGCAATCACCTCTCCG 61.092 55.000 17.11 0.00 0.00 4.63 R
5167 5204 2.092968 TGGCAGATAATCGCAAGGAAGT 60.093 45.455 0.00 0.00 38.47 3.01 R
5607 5649 0.665369 GAGCATGCAAACCAGTGTGC 60.665 55.000 21.98 5.98 41.29 4.57 R
6755 6899 0.107459 GACAGAGGATGAGGTTGGCC 60.107 60.000 0.00 0.00 0.00 5.36 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
24 25 4.966005 TCGGCAAGAGAACGACAG 57.034 55.556 0.00 0.00 0.00 3.51
49 51 4.639135 ACTGAAGAAACTCAAACAAGCC 57.361 40.909 0.00 0.00 0.00 4.35
91 93 1.534729 AAAAAGAGGTGGCCGACATC 58.465 50.000 10.71 10.71 35.49 3.06
121 127 3.402628 ACTCGTGAGGCTTATTTGTGT 57.597 42.857 1.43 0.00 0.00 3.72
133 139 5.221880 GCTTATTTGTGTCATTGCTCAACA 58.778 37.500 0.00 0.00 0.00 3.33
150 156 1.248785 ACAGCTAAGGCCTCGTTCGA 61.249 55.000 5.23 0.00 39.73 3.71
164 170 4.868171 CCTCGTTCGAAATGGATGTTTAGA 59.132 41.667 0.00 0.00 0.00 2.10
220 226 6.869206 AATTGAGGTGCTAGTAGAAACCTA 57.131 37.500 19.63 9.86 43.12 3.08
243 249 6.764308 ATGAATGTAGAAACATGTGAAGGG 57.236 37.500 0.00 0.00 45.79 3.95
285 291 1.491332 TCGTGGGAAAGGAAACAAGGA 59.509 47.619 0.00 0.00 0.00 3.36
291 297 2.562738 GGAAAGGAAACAAGGACCATGG 59.437 50.000 11.19 11.19 0.00 3.66
301 307 4.739793 ACAAGGACCATGGAGAAAAATGA 58.260 39.130 21.47 0.00 0.00 2.57
405 411 2.045045 CCCATGCTTGGCCTCGAA 60.045 61.111 13.15 0.00 42.15 3.71
424 430 2.640316 AACTCCGCCAGAAAAAGAGT 57.360 45.000 0.00 0.00 39.42 3.24
429 435 1.266989 CCGCCAGAAAAAGAGTTCACC 59.733 52.381 0.00 0.00 0.00 4.02
437 443 4.219288 AGAAAAAGAGTTCACCATGGATGC 59.781 41.667 21.47 5.50 0.00 3.91
450 456 3.213506 CATGGATGCTTGATTTCCCGTA 58.786 45.455 0.00 0.00 0.00 4.02
459 465 5.708230 TGCTTGATTTCCCGTAAAAGTACAT 59.292 36.000 0.00 0.00 0.00 2.29
519 525 2.416701 CCTGCAAACCAAACGACACTTT 60.417 45.455 0.00 0.00 0.00 2.66
534 540 6.861144 ACGACACTTTAGTATAACTTCCTCC 58.139 40.000 0.00 0.00 0.00 4.30
559 566 7.547019 CCTTTTTATTTTCCTGCAGATTTCCTC 59.453 37.037 17.39 0.00 0.00 3.71
564 571 1.139654 TCCTGCAGATTTCCTCCATCG 59.860 52.381 17.39 0.00 0.00 3.84
580 587 2.356135 CATCGTTCCTCCAAACCGAAT 58.644 47.619 0.00 0.00 0.00 3.34
584 591 1.611491 GTTCCTCCAAACCGAATGCAA 59.389 47.619 0.00 0.00 0.00 4.08
593 601 4.216687 CCAAACCGAATGCAACCTAAGTTA 59.783 41.667 0.00 0.00 33.27 2.24
597 605 6.584185 ACCGAATGCAACCTAAGTTATTTT 57.416 33.333 0.00 0.00 33.27 1.82
638 646 6.325286 GGAGACCATAGGTAGACTTGAGAATT 59.675 42.308 0.00 0.00 35.25 2.17
676 684 5.873179 TCACAATAAATCCTCACGGTTTC 57.127 39.130 0.00 0.00 0.00 2.78
1250 1268 3.492545 TTTATGCCGTGGCGCGTC 61.493 61.111 20.01 2.29 45.51 5.19
1496 1514 7.732025 TGAATTTCTCACAAGTTGTAGGAGTA 58.268 34.615 18.04 9.75 0.00 2.59
1497 1515 7.872993 TGAATTTCTCACAAGTTGTAGGAGTAG 59.127 37.037 18.04 2.90 0.00 2.57
1501 1519 6.776744 TCTCACAAGTTGTAGGAGTAGAGTA 58.223 40.000 18.04 5.04 0.00 2.59
1503 1521 7.889073 TCTCACAAGTTGTAGGAGTAGAGTAAT 59.111 37.037 18.04 0.00 0.00 1.89
1572 1590 2.004017 ACACGCAAACTCGAACTTTCA 58.996 42.857 0.00 0.00 0.00 2.69
1724 1742 1.993301 CCCTTTTCTTCTACCCCAGGT 59.007 52.381 0.00 0.00 40.16 4.00
1731 1749 2.162681 CTTCTACCCCAGGTTTTGCAG 58.837 52.381 0.00 0.00 37.09 4.41
1800 1818 7.099120 GGAACAATTAGCAGATTTGGATTTGT 58.901 34.615 0.00 0.00 0.00 2.83
1837 1855 1.180029 TCCTTAGTCGAACGGAAGGG 58.820 55.000 16.68 5.47 36.98 3.95
1988 2008 0.808453 ACGTCCGGAAATACATGCCG 60.808 55.000 5.23 4.48 44.42 5.69
2002 2022 3.793559 ACATGCCGTATAAACTGAGTCC 58.206 45.455 0.00 0.00 0.00 3.85
2019 2039 4.037923 TGAGTCCAAAAGTCAATGCTTTCC 59.962 41.667 3.84 0.00 37.68 3.13
2040 2060 6.489127 TCCAAGTTTGACCAAATGTATACG 57.511 37.500 0.00 0.00 32.36 3.06
2216 2236 2.357154 GCCATGTATTTGGGGACAGAGT 60.357 50.000 0.00 0.00 44.54 3.24
2362 2382 6.015010 TCCGTGTGTTTTGGATTAATTTGGAT 60.015 34.615 0.00 0.00 0.00 3.41
2365 2385 7.158021 GTGTGTTTTGGATTAATTTGGATGGA 58.842 34.615 0.00 0.00 0.00 3.41
2691 2711 8.906867 TGATGATATCTCAAGGTTTCCATTTTC 58.093 33.333 3.98 0.00 34.37 2.29
2813 2834 0.321564 TGTTTCCATCAGTGGCCTCG 60.322 55.000 3.32 0.00 45.63 4.63
3049 3070 9.360093 GGCTAATGTATGAGTATTGCTAGTAAG 57.640 37.037 0.00 0.00 0.00 2.34
3183 3204 0.875059 GGTAAGAGGCGCATTATGGC 59.125 55.000 10.83 0.00 0.00 4.40
3377 3408 4.228824 AGTACAAGTGGAGGGAGTTTACA 58.771 43.478 0.00 0.00 0.00 2.41
3452 3483 7.978975 GTCTCAGTGCTTTCATAGACTATTCTT 59.021 37.037 0.00 0.00 32.75 2.52
3454 3485 9.809096 CTCAGTGCTTTCATAGACTATTCTTTA 57.191 33.333 0.00 0.00 32.75 1.85
3504 3535 7.338800 AGAACAATACCCTGCTTGATTATTG 57.661 36.000 0.00 0.00 36.58 1.90
3592 3623 6.300354 ACAATTTTGTTCTCTTGTACTCCG 57.700 37.500 0.00 0.00 38.47 4.63
3661 3692 7.113684 TGCAAAAACGTCTTATATTTTGGAACG 59.886 33.333 17.78 0.00 39.20 3.95
3681 3712 5.588958 ACGGAGGTAGTAGTTTGGTTATC 57.411 43.478 0.00 0.00 0.00 1.75
3879 3910 1.003464 TCAGCAGCAATCCTTGTAGCA 59.997 47.619 0.00 0.00 35.83 3.49
4002 4033 6.771076 TGTGTTACTCGCATATGAAATGAAC 58.229 36.000 6.97 5.24 0.00 3.18
4391 4426 9.243637 CTGAAGCTTCTCTTACTGAACATATAC 57.756 37.037 26.09 0.00 34.56 1.47
4570 4607 0.447801 CCTGTGTTGCTATGTTCCGC 59.552 55.000 0.00 0.00 0.00 5.54
4931 4968 7.772332 TTCTTCTCTTGTCTGTTGAAGTAAC 57.228 36.000 0.00 0.00 39.80 2.50
5008 5045 7.832503 AAACATCTTTTTCTTTGTCAACTGG 57.167 32.000 0.00 0.00 0.00 4.00
5009 5046 6.773976 ACATCTTTTTCTTTGTCAACTGGA 57.226 33.333 0.00 0.00 0.00 3.86
5010 5047 6.799512 ACATCTTTTTCTTTGTCAACTGGAG 58.200 36.000 0.00 0.00 0.00 3.86
5020 5057 4.271696 TGTCAACTGGAGTACAATGGAG 57.728 45.455 0.00 0.00 0.00 3.86
5066 5103 9.151471 GACATTACAATATACCGCAGTTATGAT 57.849 33.333 0.00 0.00 0.00 2.45
5099 5136 2.687935 TGCCCTGTGAACAGAAAAGTTC 59.312 45.455 12.05 0.00 46.59 3.01
5167 5204 2.571212 CCGGAGGCTGTTTGCATATTA 58.429 47.619 0.00 0.00 46.14 0.98
5248 5285 9.225682 TCTAGATGGGTTCTAAGTTTATGGAAT 57.774 33.333 0.00 0.00 36.50 3.01
5526 5568 7.324388 TGTTATCAAGGAAGGAAAGGTTAGA 57.676 36.000 0.00 0.00 0.00 2.10
5756 5798 5.864418 ATCAGAAAAGCAATGTGCCATAT 57.136 34.783 0.00 0.00 46.52 1.78
5865 5907 2.760581 AGGCGGTAAGTAGAATTCCCT 58.239 47.619 0.65 0.00 0.00 4.20
5928 5970 1.270785 TGAGTCTGAAAATGCGCCTCA 60.271 47.619 4.18 3.79 0.00 3.86
6040 6082 6.428159 GGCATCGGATCAAAATACAGAATACT 59.572 38.462 0.00 0.00 0.00 2.12
6058 6100 6.427242 AGAATACTTCGTGCGTATCTAGATCA 59.573 38.462 8.95 0.00 34.02 2.92
6144 6186 9.466497 TCCATGATATCTCCAAATAATAAAGCC 57.534 33.333 3.98 0.00 0.00 4.35
6147 6189 8.635765 TGATATCTCCAAATAATAAAGCCACC 57.364 34.615 3.98 0.00 0.00 4.61
6148 6190 8.224025 TGATATCTCCAAATAATAAAGCCACCA 58.776 33.333 3.98 0.00 0.00 4.17
6150 6192 4.638421 TCTCCAAATAATAAAGCCACCACG 59.362 41.667 0.00 0.00 0.00 4.94
6193 6318 7.634671 TCGTATAGACTTTGTCATGGAACTA 57.365 36.000 0.00 0.00 34.60 2.24
6247 6372 4.576053 TGCTTGTGTTGGCTGATATGATAC 59.424 41.667 0.00 0.00 0.00 2.24
6256 6381 6.114187 TGGCTGATATGATACGAGGAAATT 57.886 37.500 0.00 0.00 0.00 1.82
6257 6382 7.239763 TGGCTGATATGATACGAGGAAATTA 57.760 36.000 0.00 0.00 0.00 1.40
6356 6481 1.256812 GGCATAACAGCAGGTGGTTT 58.743 50.000 4.26 0.00 35.83 3.27
6371 6496 5.887598 CAGGTGGTTTGATGGAGAATTATCA 59.112 40.000 1.97 0.00 0.00 2.15
6374 6499 6.547141 GGTGGTTTGATGGAGAATTATCATGA 59.453 38.462 0.00 0.00 33.68 3.07
6441 6569 5.858381 TGCTCACTATCCTTAGCCTTATTG 58.142 41.667 0.00 0.00 33.99 1.90
6442 6570 5.602561 TGCTCACTATCCTTAGCCTTATTGA 59.397 40.000 0.00 0.00 33.99 2.57
6478 6621 5.750352 ATGACTGAGGGCAATTGAAAATT 57.250 34.783 10.34 0.00 0.00 1.82
6498 6641 1.841302 TTCATCTCCAACGGCTGCCT 61.841 55.000 17.92 0.55 0.00 4.75
6528 6671 4.040217 AGGGCACTTCAAACATGCAAATAA 59.960 37.500 0.00 0.00 41.27 1.40
6603 6747 6.778834 TGAACATCCAAACATTGCATAGAT 57.221 33.333 0.00 0.00 0.00 1.98
6654 6798 7.582352 TCATTCTAACATTACGATAGACTCCG 58.418 38.462 0.00 0.00 41.38 4.63
6682 6826 1.508632 CCTACAGGTTGTTGTGGTCG 58.491 55.000 0.00 0.00 32.56 4.79
6702 6846 2.755650 GATGTTGTCGGACTTGTCACT 58.244 47.619 9.88 0.00 0.00 3.41
6711 6855 1.203523 GGACTTGTCACTCTCATCGCT 59.796 52.381 3.08 0.00 0.00 4.93
6723 6867 0.174389 TCATCGCTGAGCTCAACCTC 59.826 55.000 18.85 6.39 0.00 3.85
6726 6870 1.803519 CGCTGAGCTCAACCTCGTC 60.804 63.158 18.85 1.66 34.56 4.20
6728 6872 1.581954 CTGAGCTCAACCTCGTCGT 59.418 57.895 18.85 0.00 34.56 4.34
6736 6880 0.040692 CAACCTCGTCGTCGAACTCA 60.041 55.000 6.19 0.00 45.61 3.41
6737 6881 0.237761 AACCTCGTCGTCGAACTCAG 59.762 55.000 6.19 0.00 45.61 3.35
6738 6882 1.512310 CCTCGTCGTCGAACTCAGC 60.512 63.158 6.19 0.00 45.61 4.26
6739 6883 1.498166 CTCGTCGTCGAACTCAGCT 59.502 57.895 6.19 0.00 45.61 4.24
6742 6886 1.532437 TCGTCGTCGAACTCAGCTTTA 59.468 47.619 1.37 0.00 43.34 1.85
6743 6887 1.642843 CGTCGTCGAACTCAGCTTTAC 59.357 52.381 0.00 0.00 39.71 2.01
6744 6888 1.984297 GTCGTCGAACTCAGCTTTACC 59.016 52.381 0.00 0.00 0.00 2.85
6745 6889 1.610038 TCGTCGAACTCAGCTTTACCA 59.390 47.619 0.00 0.00 0.00 3.25
6746 6890 1.719780 CGTCGAACTCAGCTTTACCAC 59.280 52.381 0.00 0.00 0.00 4.16
6747 6891 2.750948 GTCGAACTCAGCTTTACCACA 58.249 47.619 0.00 0.00 0.00 4.17
6748 6892 2.475487 GTCGAACTCAGCTTTACCACAC 59.525 50.000 0.00 0.00 0.00 3.82
6749 6893 1.798813 CGAACTCAGCTTTACCACACC 59.201 52.381 0.00 0.00 0.00 4.16
6750 6894 1.798813 GAACTCAGCTTTACCACACCG 59.201 52.381 0.00 0.00 0.00 4.94
6751 6895 0.034896 ACTCAGCTTTACCACACCGG 59.965 55.000 0.00 0.00 42.50 5.28
6752 6896 0.320374 CTCAGCTTTACCACACCGGA 59.680 55.000 9.46 0.00 38.63 5.14
6753 6897 0.320374 TCAGCTTTACCACACCGGAG 59.680 55.000 9.46 1.26 38.63 4.63
6778 6922 2.304180 CCAACCTCATCCTCTGTCTTGT 59.696 50.000 0.00 0.00 0.00 3.16
6784 6928 1.277273 CATCCTCTGTCTTGTGCTCCA 59.723 52.381 0.00 0.00 0.00 3.86
6793 6937 0.595095 CTTGTGCTCCACCTTCTTGC 59.405 55.000 0.00 0.00 32.73 4.01
6794 6938 0.106769 TTGTGCTCCACCTTCTTGCA 60.107 50.000 0.00 0.00 32.73 4.08
6795 6939 1.952263 GTGCTCCACCTTCTTGCAC 59.048 57.895 0.00 0.00 45.23 4.57
6801 6945 1.689813 TCCACCTTCTTGCACTCGTTA 59.310 47.619 0.00 0.00 0.00 3.18
6813 6957 3.007506 TGCACTCGTTATCCCTCTTTCAA 59.992 43.478 0.00 0.00 0.00 2.69
6828 6972 3.564225 TCTTTCAAAAGAACTCCTTCGCC 59.436 43.478 2.74 0.00 41.75 5.54
6837 6981 1.220206 CTCCTTCGCCTGCATGAGT 59.780 57.895 0.00 0.00 0.00 3.41
6878 7022 1.442526 CTTGCCATCACCGCCTCATC 61.443 60.000 0.00 0.00 0.00 2.92
6880 7024 2.969238 CCATCACCGCCTCATCGC 60.969 66.667 0.00 0.00 0.00 4.58
6890 7034 1.604378 CCTCATCGCTTTCCCTGGT 59.396 57.895 0.00 0.00 0.00 4.00
6934 7078 0.685660 GGTCTTCCTCTTTGTCGGGT 59.314 55.000 0.00 0.00 0.00 5.28
6945 7089 0.178955 TTGTCGGGTGGGACTCACTA 60.179 55.000 5.23 0.00 45.38 2.74
6975 7119 1.556911 AGCCCGATGAACTTCACATCT 59.443 47.619 0.00 0.00 41.06 2.90
6977 7121 2.283298 CCCGATGAACTTCACATCTGG 58.717 52.381 0.00 0.00 40.60 3.86
6982 7126 0.955428 GAACTTCACATCTGGCCGCA 60.955 55.000 0.00 0.00 0.00 5.69
6987 7131 1.153309 CACATCTGGCCGCATCTCA 60.153 57.895 0.00 0.00 0.00 3.27
7004 7148 4.277515 TCTCAATCACCAGGAAGTTGAG 57.722 45.455 18.46 18.46 44.31 3.02
7015 7159 1.891060 GAAGTTGAGCTCGTGCCACG 61.891 60.000 11.80 11.80 44.19 4.94
7044 7188 1.584495 CCTCCACACGACGATGTCA 59.416 57.895 0.00 0.00 32.09 3.58
7049 7193 1.134367 CCACACGACGATGTCATAGGT 59.866 52.381 0.00 0.00 32.09 3.08
7058 7202 2.890474 GTCATAGGTGCGTGCGGG 60.890 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.135933 CGTTCTCTTGCCGAGTTTTCT 58.864 47.619 0.73 0.00 40.75 2.52
1 2 2.096860 GTCGTTCTCTTGCCGAGTTTTC 60.097 50.000 0.73 0.00 40.75 2.29
10 11 4.049186 TCAGTAAACTGTCGTTCTCTTGC 58.951 43.478 9.81 0.00 44.12 4.01
22 23 7.218963 GCTTGTTTGAGTTTCTTCAGTAAACTG 59.781 37.037 5.98 3.64 44.94 3.16
24 25 6.472486 GGCTTGTTTGAGTTTCTTCAGTAAAC 59.528 38.462 0.00 0.00 37.14 2.01
49 51 2.223971 GGCATTGGCAAGATCATCCTTG 60.224 50.000 5.96 0.00 44.67 3.61
81 83 2.270352 AAACTTCTTGATGTCGGCCA 57.730 45.000 2.24 0.00 0.00 5.36
91 93 3.654414 AGCCTCACGAGTAAACTTCTTG 58.346 45.455 0.00 0.00 0.00 3.02
133 139 0.606604 TTTCGAACGAGGCCTTAGCT 59.393 50.000 6.77 0.00 39.73 3.32
182 188 6.881065 GCACCTCAATTATATTCCTATGCAGA 59.119 38.462 0.00 0.00 0.00 4.26
212 218 8.950210 CACATGTTTCTACATTCATAGGTTTCT 58.050 33.333 0.00 0.00 42.29 2.52
220 226 6.484288 TCCCTTCACATGTTTCTACATTCAT 58.516 36.000 0.00 0.00 42.29 2.57
258 264 3.502123 TTCCTTTCCCACGAACAGAAT 57.498 42.857 0.00 0.00 0.00 2.40
285 291 3.075882 TGGGTCTCATTTTTCTCCATGGT 59.924 43.478 12.58 0.00 0.00 3.55
291 297 6.331369 TGATTGTTGGGTCTCATTTTTCTC 57.669 37.500 0.00 0.00 0.00 2.87
301 307 4.927267 TTGTATCCTGATTGTTGGGTCT 57.073 40.909 0.00 0.00 0.00 3.85
345 351 7.551974 CCACAACATGAGAGAGAAAGTTCATAT 59.448 37.037 0.00 0.00 0.00 1.78
346 352 6.875726 CCACAACATGAGAGAGAAAGTTCATA 59.124 38.462 0.00 0.00 0.00 2.15
363 369 0.185901 ACAGTTGAGGCCCACAACAT 59.814 50.000 31.16 21.56 46.58 2.71
405 411 2.640316 ACTCTTTTTCTGGCGGAGTT 57.360 45.000 0.00 0.00 34.13 3.01
424 430 3.448301 GGAAATCAAGCATCCATGGTGAA 59.552 43.478 12.58 0.00 38.70 3.18
429 435 2.026641 ACGGGAAATCAAGCATCCATG 58.973 47.619 0.00 0.00 34.82 3.66
437 443 6.027749 GCATGTACTTTTACGGGAAATCAAG 58.972 40.000 0.00 0.00 0.00 3.02
450 456 5.520376 AAGTTTCTGCAGCATGTACTTTT 57.480 34.783 9.47 0.00 39.31 2.27
459 465 4.019792 TCATAGGAAAGTTTCTGCAGCA 57.980 40.909 9.47 0.00 0.00 4.41
534 540 7.547019 GGAGGAAATCTGCAGGAAAATAAAAAG 59.453 37.037 15.13 0.00 33.66 2.27
544 551 1.139654 CGATGGAGGAAATCTGCAGGA 59.860 52.381 15.13 0.57 46.85 3.86
559 566 0.036765 TCGGTTTGGAGGAACGATGG 60.037 55.000 0.00 0.00 0.00 3.51
564 571 1.243902 TGCATTCGGTTTGGAGGAAC 58.756 50.000 0.00 0.00 0.00 3.62
593 601 5.938125 TCTCCGCTGCTAGTAAAAGAAAAAT 59.062 36.000 0.00 0.00 0.00 1.82
597 605 3.368116 GGTCTCCGCTGCTAGTAAAAGAA 60.368 47.826 0.00 0.00 0.00 2.52
665 673 7.583860 TTTTTAACAAAAAGAAACCGTGAGG 57.416 32.000 0.00 0.00 45.58 3.86
866 882 2.665185 GGTGTGTGGTGAGTCGGC 60.665 66.667 0.00 0.00 0.00 5.54
1082 1100 4.408396 TAGGAAGGAGGGCGGGCA 62.408 66.667 3.27 0.00 0.00 5.36
1121 1139 4.459331 CGCGACATGCCAAACCCG 62.459 66.667 0.00 0.00 42.08 5.28
1250 1268 1.670406 GGCTCATATCAGCAGCCGG 60.670 63.158 0.00 0.00 43.35 6.13
1465 1483 6.742109 ACAACTTGTGAGAAATTCAGGAATG 58.258 36.000 0.00 0.00 36.21 2.67
1496 1514 6.065374 TCGCCTAGAGAAATCAGATTACTCT 58.935 40.000 0.00 0.00 40.37 3.24
1497 1515 6.320494 TCGCCTAGAGAAATCAGATTACTC 57.680 41.667 0.00 0.00 0.00 2.59
1501 1519 9.213799 GAATAAATCGCCTAGAGAAATCAGATT 57.786 33.333 0.00 0.00 0.00 2.40
1503 1521 6.863645 CGAATAAATCGCCTAGAGAAATCAGA 59.136 38.462 0.00 0.00 45.89 3.27
1724 1742 4.869215 TCTGATTTCGAAATGCTGCAAAA 58.131 34.783 27.27 2.31 0.00 2.44
1731 1749 6.155691 TGCAATTTTCTGATTTCGAAATGC 57.844 33.333 27.27 21.03 37.11 3.56
1837 1855 3.952967 ACTACACCCCTCGTCTTCTAATC 59.047 47.826 0.00 0.00 0.00 1.75
1921 1941 6.994992 TGTTTGAATAAAAAGTTTCGCCAAC 58.005 32.000 0.00 0.00 35.32 3.77
1988 2008 7.750903 GCATTGACTTTTGGACTCAGTTTATAC 59.249 37.037 0.00 0.00 0.00 1.47
2019 2039 8.789881 TTTTCGTATACATTTGGTCAAACTTG 57.210 30.769 3.32 0.00 32.51 3.16
2216 2236 5.467035 TTCACAGACATGTCACATACTCA 57.533 39.130 27.02 1.15 37.65 3.41
2328 2348 1.003851 AAACACACGGACAAGTCACG 58.996 50.000 2.29 6.12 0.00 4.35
2339 2359 6.090628 CCATCCAAATTAATCCAAAACACACG 59.909 38.462 0.00 0.00 0.00 4.49
2362 2382 5.958380 ACTGAGAATACATCAACCTAGTCCA 59.042 40.000 0.00 0.00 0.00 4.02
2365 2385 7.680730 ACAAACTGAGAATACATCAACCTAGT 58.319 34.615 0.00 0.00 0.00 2.57
2409 2429 5.408356 ATAAGCAATGACTTACGACGAAGT 58.592 37.500 0.00 7.12 42.42 3.01
2813 2834 4.453819 GGACAGCTGGATATGCTTATTCAC 59.546 45.833 19.93 0.00 38.92 3.18
3315 3346 6.897259 TTCTTGTGGTACGCTAAATATGTC 57.103 37.500 0.00 0.00 40.97 3.06
3377 3408 5.163754 GCAAGTAAAAAGGCTCACGATACAT 60.164 40.000 0.00 0.00 0.00 2.29
3454 3485 9.661563 TTCATTACGTAGATGAAACAAAGGTAT 57.338 29.630 20.83 0.00 39.75 2.73
3592 3623 9.977762 AAAAACGTCTTATATTTTGATACGGAC 57.022 29.630 0.00 0.00 33.44 4.79
3627 3658 3.626028 AGACGTTTTTGCAGGCTAAAG 57.374 42.857 0.00 0.00 0.00 1.85
3661 3692 6.608808 TGTAGGATAACCAAACTACTACCTCC 59.391 42.308 0.00 0.00 37.34 4.30
3681 3712 6.512297 AGTGCAAAGGTAAAAACATTGTAGG 58.488 36.000 0.00 0.00 0.00 3.18
3879 3910 8.478877 ACGAAAGTCTCAAGATTATTGAGGTAT 58.521 33.333 18.31 5.54 44.19 2.73
4002 4033 1.091771 AATGCGCAATCACCTCTCCG 61.092 55.000 17.11 0.00 0.00 4.63
4391 4426 3.242739 GCACAATAAGCTTACGGTGGATG 60.243 47.826 27.47 15.27 0.00 3.51
4526 4563 7.609532 GGAGCCATAACAGCAGAATATTTAGAT 59.390 37.037 0.00 0.00 0.00 1.98
4527 4564 6.936900 GGAGCCATAACAGCAGAATATTTAGA 59.063 38.462 0.00 0.00 0.00 2.10
5020 5057 8.460831 AATGTCTTTTATTTGCGTGGATTTAC 57.539 30.769 0.00 0.00 0.00 2.01
5117 5154 9.238368 AGTATCTGCCATTCTTCTCTATAGTAC 57.762 37.037 0.00 0.00 0.00 2.73
5167 5204 2.092968 TGGCAGATAATCGCAAGGAAGT 60.093 45.455 0.00 0.00 38.47 3.01
5238 5275 6.543831 AGGACACAGCATTCTATTCCATAAAC 59.456 38.462 0.00 0.00 0.00 2.01
5248 5285 1.279496 AGGCAGGACACAGCATTCTA 58.721 50.000 0.00 0.00 0.00 2.10
5526 5568 8.506083 ACATCCCTTTCTATCATGGAAGTAATT 58.494 33.333 0.00 0.00 0.00 1.40
5571 5613 6.325028 AGAATGTACTGATGCTACCTACACAT 59.675 38.462 0.00 0.00 0.00 3.21
5607 5649 0.665369 GAGCATGCAAACCAGTGTGC 60.665 55.000 21.98 5.98 41.29 4.57
5684 5726 5.726793 ACCCCCATCAACAGATATATCTACC 59.273 44.000 14.92 0.00 34.85 3.18
5756 5798 2.354503 GCTTTGAGCTCCATCAGAGACA 60.355 50.000 12.15 0.00 46.50 3.41
5928 5970 1.340017 CCGAATCCACCTGTTGTCCAT 60.340 52.381 0.00 0.00 0.00 3.41
6040 6082 6.533723 ACATTTTTGATCTAGATACGCACGAA 59.466 34.615 4.89 0.00 0.00 3.85
6058 6100 8.641541 ACATCAACATACTTCCTTCACATTTTT 58.358 29.630 0.00 0.00 0.00 1.94
6144 6186 2.811431 TCACAGAAATTAAGCCGTGGTG 59.189 45.455 0.00 0.00 0.00 4.17
6147 6189 5.283717 CGAAAATCACAGAAATTAAGCCGTG 59.716 40.000 0.00 0.00 0.00 4.94
6148 6190 5.048991 ACGAAAATCACAGAAATTAAGCCGT 60.049 36.000 0.00 0.00 0.00 5.68
6150 6192 9.651718 CTATACGAAAATCACAGAAATTAAGCC 57.348 33.333 0.00 0.00 0.00 4.35
6247 6372 5.812642 AGCACAAGTCATAGTAATTTCCTCG 59.187 40.000 0.00 0.00 0.00 4.63
6256 6381 6.035650 GCATTCGTAAAGCACAAGTCATAGTA 59.964 38.462 0.00 0.00 0.00 1.82
6257 6382 5.163854 GCATTCGTAAAGCACAAGTCATAGT 60.164 40.000 0.00 0.00 0.00 2.12
6478 6621 0.960364 GGCAGCCGTTGGAGATGAAA 60.960 55.000 0.00 0.00 0.00 2.69
6498 6641 6.162777 GCATGTTTGAAGTGCCCTATTTTAA 58.837 36.000 0.00 0.00 32.88 1.52
6627 6771 9.562583 GGAGTCTATCGTAATGTTAGAATGATC 57.437 37.037 0.00 0.00 32.16 2.92
6644 6788 2.959707 AGGGTGTTCATCGGAGTCTATC 59.040 50.000 0.00 0.00 0.00 2.08
6682 6826 2.731976 GAGTGACAAGTCCGACAACATC 59.268 50.000 0.40 0.00 0.00 3.06
6696 6840 0.172127 GCTCAGCGATGAGAGTGACA 59.828 55.000 33.37 0.00 38.13 3.58
6702 6846 0.174389 GGTTGAGCTCAGCGATGAGA 59.826 55.000 33.37 10.80 38.13 3.27
6711 6855 1.579932 GACGACGAGGTTGAGCTCA 59.420 57.895 13.74 13.74 0.00 4.26
6723 6867 1.642843 GTAAAGCTGAGTTCGACGACG 59.357 52.381 0.00 0.00 41.26 5.12
6726 6870 1.719780 GTGGTAAAGCTGAGTTCGACG 59.280 52.381 0.00 0.00 0.00 5.12
6728 6872 2.547218 GGTGTGGTAAAGCTGAGTTCGA 60.547 50.000 0.00 0.00 0.00 3.71
6736 6880 1.677552 CCTCCGGTGTGGTAAAGCT 59.322 57.895 0.00 0.00 39.52 3.74
6737 6881 1.376812 CCCTCCGGTGTGGTAAAGC 60.377 63.158 0.00 0.00 39.52 3.51
6738 6882 1.298667 CCCCTCCGGTGTGGTAAAG 59.701 63.158 0.00 0.00 39.52 1.85
6739 6883 2.897762 GCCCCTCCGGTGTGGTAAA 61.898 63.158 6.89 0.00 39.52 2.01
6752 6896 2.003548 GAGGATGAGGTTGGCCCCT 61.004 63.158 0.00 0.00 37.62 4.79
6753 6897 2.003548 AGAGGATGAGGTTGGCCCC 61.004 63.158 0.00 0.00 34.57 5.80
6754 6898 1.225704 CAGAGGATGAGGTTGGCCC 59.774 63.158 0.00 0.00 34.57 5.80
6755 6899 0.107459 GACAGAGGATGAGGTTGGCC 60.107 60.000 0.00 0.00 0.00 5.36
6756 6900 0.908198 AGACAGAGGATGAGGTTGGC 59.092 55.000 0.00 0.00 0.00 4.52
6757 6901 2.304180 ACAAGACAGAGGATGAGGTTGG 59.696 50.000 0.00 0.00 0.00 3.77
6758 6902 3.332919 CACAAGACAGAGGATGAGGTTG 58.667 50.000 0.00 0.00 0.00 3.77
6759 6903 2.289945 GCACAAGACAGAGGATGAGGTT 60.290 50.000 0.00 0.00 0.00 3.50
6760 6904 1.277557 GCACAAGACAGAGGATGAGGT 59.722 52.381 0.00 0.00 0.00 3.85
6761 6905 1.554160 AGCACAAGACAGAGGATGAGG 59.446 52.381 0.00 0.00 0.00 3.86
6762 6906 2.418471 GGAGCACAAGACAGAGGATGAG 60.418 54.545 0.00 0.00 0.00 2.90
6763 6907 1.552337 GGAGCACAAGACAGAGGATGA 59.448 52.381 0.00 0.00 0.00 2.92
6764 6908 1.277273 TGGAGCACAAGACAGAGGATG 59.723 52.381 0.00 0.00 0.00 3.51
6765 6909 1.277557 GTGGAGCACAAGACAGAGGAT 59.722 52.381 0.00 0.00 34.08 3.24
6766 6910 0.681733 GTGGAGCACAAGACAGAGGA 59.318 55.000 0.00 0.00 34.08 3.71
6778 6922 0.250467 GAGTGCAAGAAGGTGGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
6784 6928 2.354805 GGGATAACGAGTGCAAGAAGGT 60.355 50.000 0.00 0.00 0.00 3.50
6793 6937 5.932303 TCTTTTGAAAGAGGGATAACGAGTG 59.068 40.000 2.16 0.00 39.95 3.51
6794 6938 6.110411 TCTTTTGAAAGAGGGATAACGAGT 57.890 37.500 2.16 0.00 39.95 4.18
6795 6939 6.651225 AGTTCTTTTGAAAGAGGGATAACGAG 59.349 38.462 6.32 0.00 45.01 4.18
6801 6945 5.590976 AGGAGTTCTTTTGAAAGAGGGAT 57.409 39.130 6.32 0.00 45.01 3.85
6813 6957 0.108585 TGCAGGCGAAGGAGTTCTTT 59.891 50.000 0.00 0.00 35.50 2.52
6837 6981 0.395862 TCACAAGGGAAAACCCGCAA 60.396 50.000 0.00 0.00 41.63 4.85
6847 6991 0.482446 ATGGCAAGGTTCACAAGGGA 59.518 50.000 0.00 0.00 0.00 4.20
6852 6996 0.888736 CGGTGATGGCAAGGTTCACA 60.889 55.000 17.84 0.00 41.17 3.58
6878 7022 2.359975 GGGACACCAGGGAAAGCG 60.360 66.667 0.00 0.00 36.50 4.68
6880 7024 1.555533 GTAGAGGGACACCAGGGAAAG 59.444 57.143 0.00 0.00 40.13 2.62
6945 7089 3.005539 ATCGGGCTGCCAGTGACT 61.006 61.111 22.05 0.82 0.00 3.41
6975 7119 1.451927 GGTGATTGAGATGCGGCCA 60.452 57.895 2.24 0.00 0.00 5.36
6977 7121 1.442526 CCTGGTGATTGAGATGCGGC 61.443 60.000 0.00 0.00 0.00 6.53
6982 7126 4.841422 CTCAACTTCCTGGTGATTGAGAT 58.159 43.478 21.43 0.00 45.96 2.75
6987 7131 2.613977 CGAGCTCAACTTCCTGGTGATT 60.614 50.000 15.40 0.00 42.19 2.57
7020 7164 2.433318 GTCGTGTGGAGGCTCAGC 60.433 66.667 17.69 8.67 0.00 4.26
7035 7179 1.200483 CACGCACCTATGACATCGTC 58.800 55.000 0.00 0.00 0.00 4.20
7044 7188 4.175337 ATGCCCGCACGCACCTAT 62.175 61.111 0.00 0.00 42.70 2.57


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

AutoCloner maintained by Alex Coulton.