Multiple sequence alignment - TraesCS5D01G208400

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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 TraesCS5D01G208400 chr5D 100.000 6591 0 0 1 6591 314845646 314852236 0.000000e+00 12172.0
1 TraesCS5D01G208400 chr5D 91.549 71 2 3 1940 2006 251424153 251424223 1.960000e-15 95.3
2 TraesCS5D01G208400 chr5A 92.743 4065 176 46 2021 6028 408910708 408914710 0.000000e+00 5762.0
3 TraesCS5D01G208400 chr5A 92.558 1169 41 23 783 1921 408909436 408910588 0.000000e+00 1635.0
4 TraesCS5D01G208400 chr5A 85.370 540 68 9 7 540 408908645 408909179 3.470000e-152 549.0
5 TraesCS5D01G208400 chr5A 83.245 567 74 11 6044 6591 704956887 704956323 9.870000e-138 501.0
6 TraesCS5D01G208400 chr5A 87.209 172 8 5 609 767 408909280 408909450 4.060000e-42 183.0
7 TraesCS5D01G208400 chr5B 96.262 3264 87 17 1687 4932 362841273 362844519 0.000000e+00 5319.0
8 TraesCS5D01G208400 chr5B 96.113 1132 17 6 4915 6023 362844701 362845828 0.000000e+00 1821.0
9 TraesCS5D01G208400 chr5B 94.124 953 35 11 783 1723 362840322 362841265 0.000000e+00 1430.0
10 TraesCS5D01G208400 chr5B 88.504 548 49 11 1 540 362839537 362840078 0.000000e+00 651.0
11 TraesCS5D01G208400 chr5B 85.811 148 6 5 603 737 362840173 362840318 6.890000e-30 143.0
12 TraesCS5D01G208400 chr6B 82.979 564 76 9 6044 6588 497899978 497900540 5.940000e-135 492.0
13 TraesCS5D01G208400 chr6B 89.051 274 26 2 6318 6588 671754470 671754742 2.940000e-88 337.0
14 TraesCS5D01G208400 chr6B 87.319 276 21 3 6049 6311 671730423 671730697 2.990000e-78 303.0
15 TraesCS5D01G208400 chr1D 90.746 335 25 2 6260 6588 463062340 463062674 6.070000e-120 442.0
16 TraesCS5D01G208400 chr7D 88.953 344 20 6 6029 6360 132203410 132203073 6.150000e-110 409.0
17 TraesCS5D01G208400 chr7D 92.857 168 12 0 6424 6591 132202769 132202602 1.840000e-60 244.0
18 TraesCS5D01G208400 chr7D 90.541 74 3 1 1937 2006 199042473 199042546 1.960000e-15 95.3
19 TraesCS5D01G208400 chr3B 81.127 355 46 9 6082 6416 381972497 381972144 1.410000e-66 265.0
20 TraesCS5D01G208400 chr3B 82.659 173 19 6 117 288 687661885 687662047 6.890000e-30 143.0
21 TraesCS5D01G208400 chr3B 92.647 68 1 2 1937 2000 396880055 396880122 1.960000e-15 95.3
22 TraesCS5D01G208400 chr3B 90.541 74 3 2 1937 2006 556538508 556538581 1.960000e-15 95.3
23 TraesCS5D01G208400 chr3B 90.411 73 3 2 1937 2005 438545836 438545764 7.040000e-15 93.5
24 TraesCS5D01G208400 chr3B 100.000 28 0 0 345 372 565730125 565730152 1.200000e-02 52.8
25 TraesCS5D01G208400 chr1A 81.203 266 45 4 3625 3887 385658697 385658960 6.700000e-50 209.0
26 TraesCS5D01G208400 chr7A 80.822 146 18 9 202 341 188660178 188660319 9.040000e-19 106.0
27 TraesCS5D01G208400 chr3D 78.916 166 25 3 116 281 29164877 29164722 3.250000e-18 104.0
28 TraesCS5D01G208400 chr6D 91.429 70 5 1 1938 2006 212739803 212739872 1.960000e-15 95.3
29 TraesCS5D01G208400 chr3A 90.541 74 3 2 1937 2006 215955008 215955081 1.960000e-15 95.3
30 TraesCS5D01G208400 chr3A 90.541 74 3 2 1937 2006 400099498 400099425 1.960000e-15 95.3
31 TraesCS5D01G208400 chr3A 100.000 28 0 0 345 372 571412315 571412342 1.200000e-02 52.8


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 TraesCS5D01G208400 chr5D 314845646 314852236 6590 False 12172.00 12172 100.0000 1 6591 1 chr5D.!!$F2 6590
1 TraesCS5D01G208400 chr5A 408908645 408914710 6065 False 2032.25 5762 89.4700 7 6028 4 chr5A.!!$F1 6021
2 TraesCS5D01G208400 chr5A 704956323 704956887 564 True 501.00 501 83.2450 6044 6591 1 chr5A.!!$R1 547
3 TraesCS5D01G208400 chr5B 362839537 362845828 6291 False 1872.80 5319 92.1628 1 6023 5 chr5B.!!$F1 6022
4 TraesCS5D01G208400 chr6B 497899978 497900540 562 False 492.00 492 82.9790 6044 6588 1 chr6B.!!$F1 544
5 TraesCS5D01G208400 chr7D 132202602 132203410 808 True 326.50 409 90.9050 6029 6591 2 chr7D.!!$R1 562

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
635 704 0.034059 CACCTGATATGAGCCGTCCC 59.966 60.000 0.00 0.0 0.00 4.46 F
1583 1680 0.613777 AGAACGGGGAGTGATGAACC 59.386 55.000 0.00 0.0 0.00 3.62 F
1588 1685 0.830648 GGGGAGTGATGAACCGATGA 59.169 55.000 0.00 0.0 0.00 2.92 F
1818 1977 1.135286 GCTAAAATTTGCTCAGGCGCT 60.135 47.619 7.64 0.0 42.25 5.92 F
2195 2407 1.371558 GTCTCACCCCGACTTGCTT 59.628 57.895 0.00 0.0 0.00 3.91 F
4082 4307 1.065199 GCACTGGAGTCATCCCATGAA 60.065 52.381 0.00 0.0 46.04 2.57 F
4611 4847 1.206371 GGTTAGTGCCGGAGTGTGTAT 59.794 52.381 5.05 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1732 1.760613 TCAGAAAGGTTCACCACGAGT 59.239 47.619 0.00 0.0 38.89 4.18 R
2901 3124 2.034999 TCAAACCCACCCCATCGC 59.965 61.111 0.00 0.0 0.00 4.58 R
3297 3520 5.103000 ACACAAGAAGTACATCATCTACGC 58.897 41.667 0.31 0.0 0.00 4.42 R
3755 3980 2.745884 TCCCATGCGGCACTTTCG 60.746 61.111 4.03 0.0 0.00 3.46 R
4133 4366 3.462483 TCACTACATGAAACCACGTGT 57.538 42.857 15.65 0.0 41.85 4.49 R
5014 5455 3.019564 CCCATTCATCTTGTTCAGGGAC 58.980 50.000 0.00 0.0 37.22 4.46 R
6235 6720 1.028868 GGAAGAAGGCTGCGCTTGAT 61.029 55.000 9.73 0.0 0.00 2.57 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
78 79 4.453478 TGATCTCACTGAAAGCATGTGTTC 59.547 41.667 0.00 0.00 37.60 3.18
79 80 2.802247 TCTCACTGAAAGCATGTGTTCG 59.198 45.455 0.00 0.00 37.60 3.95
84 85 4.211164 CACTGAAAGCATGTGTTCGAGTTA 59.789 41.667 0.00 0.00 37.60 2.24
124 125 4.816385 CCCTAGTAAATGCTACACATGTGG 59.184 45.833 28.64 13.70 39.60 4.17
133 134 2.294979 CTACACATGTGGCATGAGCAT 58.705 47.619 28.64 7.84 44.61 3.79
138 139 3.058224 CACATGTGGCATGAGCATATGAG 60.058 47.826 18.51 0.00 44.61 2.90
148 149 5.241064 GCATGAGCATATGAGAACTCCAAAT 59.759 40.000 6.97 0.00 41.58 2.32
150 151 7.572724 GCATGAGCATATGAGAACTCCAAATAC 60.573 40.741 6.97 0.00 41.58 1.89
155 156 8.680903 AGCATATGAGAACTCCAAATACTTTTG 58.319 33.333 6.97 0.00 41.59 2.44
157 158 9.778993 CATATGAGAACTCCAAATACTTTTGTG 57.221 33.333 0.00 0.00 40.55 3.33
158 159 6.633500 TGAGAACTCCAAATACTTTTGTGG 57.367 37.500 0.00 0.00 40.55 4.17
159 160 5.009610 TGAGAACTCCAAATACTTTTGTGGC 59.990 40.000 0.00 0.00 40.55 5.01
161 162 5.362430 AGAACTCCAAATACTTTTGTGGCAA 59.638 36.000 0.00 0.00 40.55 4.52
162 163 5.200368 ACTCCAAATACTTTTGTGGCAAG 57.800 39.130 0.00 0.00 40.55 4.01
163 164 4.649218 ACTCCAAATACTTTTGTGGCAAGT 59.351 37.500 0.00 0.00 40.55 3.16
191 193 5.010719 AGTGACGTGAGGATGAGAACTTTAA 59.989 40.000 0.00 0.00 0.00 1.52
196 198 6.710744 ACGTGAGGATGAGAACTTTAATTGTT 59.289 34.615 0.00 0.00 0.00 2.83
227 229 5.495640 ACAACTTTCTTTTTGGATGGCAAA 58.504 33.333 0.00 0.00 0.00 3.68
299 303 4.558538 AAAATGTCAGACTGAAGTGCAC 57.441 40.909 9.40 9.40 0.00 4.57
304 308 1.482182 TCAGACTGAAGTGCACTGTGT 59.518 47.619 22.49 18.67 0.00 3.72
308 312 0.578683 CTGAAGTGCACTGTGTCACG 59.421 55.000 22.49 10.40 38.19 4.35
309 313 0.108377 TGAAGTGCACTGTGTCACGT 60.108 50.000 22.49 19.47 38.19 4.49
397 401 5.745227 ACTACCTGACCGATTGAATCAAAT 58.255 37.500 5.95 0.00 0.00 2.32
400 404 5.126067 ACCTGACCGATTGAATCAAATAGG 58.874 41.667 5.95 6.49 38.06 2.57
492 500 5.587844 AGTTCACATGTGCTATCTTCATTCC 59.412 40.000 21.38 0.00 0.00 3.01
593 662 8.934507 AATAAATTCGAAAAACAAACACCTGA 57.065 26.923 0.00 0.00 0.00 3.86
594 663 6.641176 AAATTCGAAAAACAAACACCTGAC 57.359 33.333 0.00 0.00 0.00 3.51
595 664 4.768130 TTCGAAAAACAAACACCTGACA 57.232 36.364 0.00 0.00 0.00 3.58
596 665 4.974368 TCGAAAAACAAACACCTGACAT 57.026 36.364 0.00 0.00 0.00 3.06
597 666 6.438259 TTCGAAAAACAAACACCTGACATA 57.562 33.333 0.00 0.00 0.00 2.29
598 667 6.627395 TCGAAAAACAAACACCTGACATAT 57.373 33.333 0.00 0.00 0.00 1.78
599 668 7.033530 TCGAAAAACAAACACCTGACATATT 57.966 32.000 0.00 0.00 0.00 1.28
600 669 7.484975 TCGAAAAACAAACACCTGACATATTT 58.515 30.769 0.00 0.00 0.00 1.40
601 670 7.976734 TCGAAAAACAAACACCTGACATATTTT 59.023 29.630 0.00 0.00 0.00 1.82
602 671 8.599774 CGAAAAACAAACACCTGACATATTTTT 58.400 29.630 0.00 0.00 31.37 1.94
627 696 7.815840 TTGAGAAAACAAACACCTGATATGA 57.184 32.000 0.00 0.00 0.00 2.15
635 704 0.034059 CACCTGATATGAGCCGTCCC 59.966 60.000 0.00 0.00 0.00 4.46
641 710 3.541632 TGATATGAGCCGTCCCTTTTTC 58.458 45.455 0.00 0.00 0.00 2.29
677 747 3.750639 TCCAACGGAAAACAATATCGC 57.249 42.857 0.00 0.00 0.00 4.58
764 845 2.768253 CCCCCTCAAAATCCAAAAGC 57.232 50.000 0.00 0.00 0.00 3.51
765 846 1.066929 CCCCCTCAAAATCCAAAAGCG 60.067 52.381 0.00 0.00 0.00 4.68
766 847 1.892474 CCCCTCAAAATCCAAAAGCGA 59.108 47.619 0.00 0.00 0.00 4.93
767 848 2.298729 CCCCTCAAAATCCAAAAGCGAA 59.701 45.455 0.00 0.00 0.00 4.70
768 849 3.317150 CCCTCAAAATCCAAAAGCGAAC 58.683 45.455 0.00 0.00 0.00 3.95
769 850 3.317150 CCTCAAAATCCAAAAGCGAACC 58.683 45.455 0.00 0.00 0.00 3.62
770 851 3.005791 CCTCAAAATCCAAAAGCGAACCT 59.994 43.478 0.00 0.00 0.00 3.50
771 852 4.229876 CTCAAAATCCAAAAGCGAACCTC 58.770 43.478 0.00 0.00 0.00 3.85
772 853 3.634448 TCAAAATCCAAAAGCGAACCTCA 59.366 39.130 0.00 0.00 0.00 3.86
773 854 4.098654 TCAAAATCCAAAAGCGAACCTCAA 59.901 37.500 0.00 0.00 0.00 3.02
774 855 4.664150 AAATCCAAAAGCGAACCTCAAA 57.336 36.364 0.00 0.00 0.00 2.69
775 856 4.664150 AATCCAAAAGCGAACCTCAAAA 57.336 36.364 0.00 0.00 0.00 2.44
776 857 4.664150 ATCCAAAAGCGAACCTCAAAAA 57.336 36.364 0.00 0.00 0.00 1.94
951 1048 3.707189 GGGGAGGGAGGGAGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
952 1049 2.040359 GGGAGGGAGGGAGGGAAG 60.040 72.222 0.00 0.00 0.00 3.46
953 1050 2.788589 GGAGGGAGGGAGGGAAGT 59.211 66.667 0.00 0.00 0.00 3.01
1583 1680 0.613777 AGAACGGGGAGTGATGAACC 59.386 55.000 0.00 0.00 0.00 3.62
1587 1684 3.386543 GGGGAGTGATGAACCGATG 57.613 57.895 0.00 0.00 0.00 3.84
1588 1685 0.830648 GGGGAGTGATGAACCGATGA 59.169 55.000 0.00 0.00 0.00 2.92
1590 1687 1.482593 GGGAGTGATGAACCGATGACT 59.517 52.381 0.00 0.00 0.00 3.41
1635 1732 6.599986 AATTGTGTAGGGGATAATGGGTTA 57.400 37.500 0.00 0.00 0.00 2.85
1658 1764 3.815401 CTCGTGGTGAACCTTTCTGAAAT 59.185 43.478 2.88 0.00 36.82 2.17
1736 1885 5.693814 AGCTTCGATGCTTTACTTTTCTTG 58.306 37.500 19.26 0.00 40.93 3.02
1818 1977 1.135286 GCTAAAATTTGCTCAGGCGCT 60.135 47.619 7.64 0.00 42.25 5.92
1851 2011 6.627395 TCAACCGACTTGAAATGTAACATT 57.373 33.333 0.00 0.00 35.84 2.71
1888 2048 6.183347 AGGAGGTCTGTTCCAAAATAGAATG 58.817 40.000 0.00 0.00 34.81 2.67
1944 2104 9.581099 TTTTATTTTTGACAGACTCTTGGTTTC 57.419 29.630 0.00 0.00 0.00 2.78
1988 2148 1.497286 AGCCTACCCCAACTTGTTTGA 59.503 47.619 0.00 0.00 37.39 2.69
2017 2181 4.626042 CTTTGCTGTTGACAGACTCTACT 58.374 43.478 14.98 0.00 46.59 2.57
2089 2301 8.665643 TTTGAACTGAAATGCATTTGAAGAAT 57.334 26.923 28.67 17.67 0.00 2.40
2092 2304 9.932207 TGAACTGAAATGCATTTGAAGAATATT 57.068 25.926 28.67 14.59 0.00 1.28
2116 2328 4.782019 TCCTGATGGTAATGTTGTTTGC 57.218 40.909 0.00 0.00 34.23 3.68
2195 2407 1.371558 GTCTCACCCCGACTTGCTT 59.628 57.895 0.00 0.00 0.00 3.91
2396 2619 5.989477 TGTCTGACTAATTATGGGTTCTGG 58.011 41.667 9.51 0.00 0.00 3.86
2590 2813 8.764524 ATGTGTGTTCTCTTTCTACAAGATAC 57.235 34.615 0.00 0.00 0.00 2.24
2620 2843 7.338800 ACAATTCAGTAGCCCATGAAATTAG 57.661 36.000 0.00 0.00 38.80 1.73
2652 2875 8.567948 AGTTCTAAACTGTTCAATAACCATGTG 58.432 33.333 0.00 0.00 41.01 3.21
2886 3109 2.575532 TCTGGTGACTTTTTGGCTCTG 58.424 47.619 0.00 0.00 0.00 3.35
2901 3124 2.275318 GCTCTGTCAAAGATTCGAGGG 58.725 52.381 0.00 0.00 33.29 4.30
2991 3214 3.438434 GCTTGAAAGATGAGAAGGGTGAC 59.562 47.826 0.00 0.00 0.00 3.67
3298 3521 8.975663 ATATACTCAAAAGGGTAAAGGTTAGC 57.024 34.615 0.00 0.00 0.00 3.09
3303 3526 5.011943 TCAAAAGGGTAAAGGTTAGCGTAGA 59.988 40.000 0.00 0.00 0.00 2.59
3322 3545 6.237595 GCGTAGATGATGTACTTCTTGTGTTC 60.238 42.308 9.87 0.00 35.23 3.18
3368 3593 4.010667 TGGTTTAAATACGTGCTGGACT 57.989 40.909 0.00 0.00 0.00 3.85
3435 3660 4.939052 GCTAGATTAGCCTTACACTGGA 57.061 45.455 0.00 0.00 45.95 3.86
3436 3661 4.623002 GCTAGATTAGCCTTACACTGGAC 58.377 47.826 0.00 0.00 45.95 4.02
3437 3662 4.099573 GCTAGATTAGCCTTACACTGGACA 59.900 45.833 0.00 0.00 45.95 4.02
3438 3663 5.221541 GCTAGATTAGCCTTACACTGGACAT 60.222 44.000 0.00 0.00 45.95 3.06
3439 3664 6.015350 GCTAGATTAGCCTTACACTGGACATA 60.015 42.308 0.00 0.00 45.95 2.29
3451 3676 4.870426 ACACTGGACATATTACTTTGCTCG 59.130 41.667 0.00 0.00 0.00 5.03
3537 3762 4.402474 ACACTAAAGCCAGCAGAACTTTTT 59.598 37.500 3.20 0.00 35.38 1.94
3755 3980 6.071840 ACCCTGATATACGCTCTAGATTCAAC 60.072 42.308 0.00 0.00 0.00 3.18
3987 4212 7.518161 TGTTCATACACATTCTCGTTGATTTC 58.482 34.615 0.00 0.00 0.00 2.17
4001 4226 4.176271 GTTGATTTCTTTGGTGCCTATGC 58.824 43.478 0.00 0.00 38.26 3.14
4082 4307 1.065199 GCACTGGAGTCATCCCATGAA 60.065 52.381 0.00 0.00 46.04 2.57
4095 4320 5.964477 TCATCCCATGAAACTTACCTACTCT 59.036 40.000 0.00 0.00 36.11 3.24
4229 4462 7.396540 AATCTTAGCAAACATACTGGGAAAG 57.603 36.000 0.00 0.00 0.00 2.62
4350 4586 4.985413 TGAGCACTTTGTCTTTCAAACTG 58.015 39.130 0.00 0.00 40.56 3.16
4533 4769 1.843368 ACATGTGGAATGAAGCCCTG 58.157 50.000 0.00 0.00 0.00 4.45
4593 4829 2.380064 TTGTGGCTTCCTTTGATGGT 57.620 45.000 0.00 0.00 0.00 3.55
4611 4847 1.206371 GGTTAGTGCCGGAGTGTGTAT 59.794 52.381 5.05 0.00 0.00 2.29
4646 4882 5.468540 TTGTAGTGATTACAGCTGACACT 57.531 39.130 27.55 27.55 42.92 3.55
4658 4894 3.681897 CAGCTGACACTAGGTTAAGCAAG 59.318 47.826 8.42 0.00 40.23 4.01
4829 5069 9.271828 CTTAGTTGGCCTTGAAATATTGTTTTT 57.728 29.630 3.32 0.00 0.00 1.94
5014 5455 1.391485 CTTTCGATCAGTTGCTCACCG 59.609 52.381 0.00 0.00 0.00 4.94
5212 5658 7.678947 AAGTGTTATTCTTCTCTGTTCATGG 57.321 36.000 0.00 0.00 0.00 3.66
5375 5821 5.104652 TGTTACTAAATTACCCTCTGCCTCC 60.105 44.000 0.00 0.00 0.00 4.30
5519 5965 4.703575 AGCTACCAGAGTACAACACGATAA 59.296 41.667 0.00 0.00 0.00 1.75
5602 6048 1.079612 CTGCTGACATGAGACGGCA 60.080 57.895 18.50 18.50 46.73 5.69
5673 6127 9.244799 CAAACTACGCTGTATATAGATGTTTGA 57.755 33.333 19.43 0.59 41.36 2.69
5805 6259 4.290969 TGCTCGCATAGATAGAACTTTCG 58.709 43.478 0.00 0.00 0.00 3.46
5815 6269 6.222038 AGATAGAACTTTCGAACCATAGCA 57.778 37.500 0.00 0.00 0.00 3.49
5822 6279 5.699839 ACTTTCGAACCATAGCATGAAAAC 58.300 37.500 0.00 0.00 0.00 2.43
5947 6419 1.958288 TTCAGAGGCTAGGGCTTTCT 58.042 50.000 0.00 0.00 38.98 2.52
6024 6496 7.757941 TTCCTATTGTGTTCATGATTTGTGA 57.242 32.000 0.00 0.00 0.00 3.58
6314 6799 0.607620 TCAGTGACATGGTGATCGCA 59.392 50.000 8.82 0.00 0.00 5.10
6326 6814 4.814294 ATCGCACCGGAAGACGCC 62.814 66.667 9.46 0.00 42.52 5.68
6376 6864 0.877649 CCGCCACCGATCATCAAGAG 60.878 60.000 0.00 0.00 36.29 2.85
6377 6865 0.179100 CGCCACCGATCATCAAGAGT 60.179 55.000 0.00 0.00 36.29 3.24
6383 6871 1.418334 CGATCATCAAGAGTCCCCCT 58.582 55.000 0.00 0.00 0.00 4.79
6409 6900 1.694150 CAAGTCTCCACCCAAGTCTCA 59.306 52.381 0.00 0.00 0.00 3.27
6410 6901 1.638529 AGTCTCCACCCAAGTCTCAG 58.361 55.000 0.00 0.00 0.00 3.35
6411 6902 0.610687 GTCTCCACCCAAGTCTCAGG 59.389 60.000 0.00 0.00 0.00 3.86
6416 6907 0.397941 CACCCAAGTCTCAGGCAAGA 59.602 55.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.815222 TGATACGTTCTCCAACCACATATTG 59.185 40.000 0.00 0.00 0.00 1.90
78 79 7.658982 AGGGTCCTACTTTTACTTTTTAACTCG 59.341 37.037 0.00 0.00 0.00 4.18
79 80 8.915057 AGGGTCCTACTTTTACTTTTTAACTC 57.085 34.615 0.00 0.00 0.00 3.01
124 125 3.736720 TGGAGTTCTCATATGCTCATGC 58.263 45.455 0.00 0.00 40.20 4.06
130 131 8.847444 CAAAAGTATTTGGAGTTCTCATATGC 57.153 34.615 0.00 0.00 41.81 3.14
148 149 6.557110 GTCACTAAAACTTGCCACAAAAGTA 58.443 36.000 0.00 0.00 36.87 2.24
150 151 4.499040 CGTCACTAAAACTTGCCACAAAAG 59.501 41.667 0.00 0.00 0.00 2.27
155 156 2.610374 TCACGTCACTAAAACTTGCCAC 59.390 45.455 0.00 0.00 0.00 5.01
157 158 2.223377 CCTCACGTCACTAAAACTTGCC 59.777 50.000 0.00 0.00 0.00 4.52
158 159 3.128349 TCCTCACGTCACTAAAACTTGC 58.872 45.455 0.00 0.00 0.00 4.01
159 160 4.988540 TCATCCTCACGTCACTAAAACTTG 59.011 41.667 0.00 0.00 0.00 3.16
161 162 4.523173 TCTCATCCTCACGTCACTAAAACT 59.477 41.667 0.00 0.00 0.00 2.66
162 163 4.806330 TCTCATCCTCACGTCACTAAAAC 58.194 43.478 0.00 0.00 0.00 2.43
163 164 5.010719 AGTTCTCATCCTCACGTCACTAAAA 59.989 40.000 0.00 0.00 0.00 1.52
191 193 5.779529 AGAAAGTTGTCATGCTCAACAAT 57.220 34.783 24.41 16.81 44.97 2.71
196 198 5.126869 TCCAAAAAGAAAGTTGTCATGCTCA 59.873 36.000 0.00 0.00 0.00 4.26
290 294 0.108377 ACGTGACACAGTGCACTTCA 60.108 50.000 18.94 16.22 32.98 3.02
292 296 0.391130 ACACGTGACACAGTGCACTT 60.391 50.000 25.01 2.02 41.72 3.16
308 312 9.853555 TTTATCCAAATGATAAATGTCACACAC 57.146 29.630 3.83 0.00 46.22 3.82
372 376 5.925506 TGATTCAATCGGTCAGGTAGTAA 57.074 39.130 0.00 0.00 0.00 2.24
375 379 6.425114 CCTATTTGATTCAATCGGTCAGGTAG 59.575 42.308 0.00 0.00 0.00 3.18
378 382 5.368145 TCCTATTTGATTCAATCGGTCAGG 58.632 41.667 0.00 0.00 0.00 3.86
446 454 8.843885 AACTAATAAAGTCTCGCCTAACTTTT 57.156 30.769 9.45 0.00 41.67 2.27
455 463 6.470160 CACATGTGAACTAATAAAGTCTCGC 58.530 40.000 21.64 0.00 37.50 5.03
600 669 9.311916 CATATCAGGTGTTTGTTTTCTCAAAAA 57.688 29.630 0.00 0.00 38.71 1.94
601 670 8.690884 TCATATCAGGTGTTTGTTTTCTCAAAA 58.309 29.630 0.00 0.00 38.71 2.44
602 671 8.231692 TCATATCAGGTGTTTGTTTTCTCAAA 57.768 30.769 0.00 0.00 35.36 2.69
603 672 7.522073 GCTCATATCAGGTGTTTGTTTTCTCAA 60.522 37.037 0.00 0.00 0.00 3.02
604 673 6.072508 GCTCATATCAGGTGTTTGTTTTCTCA 60.073 38.462 0.00 0.00 0.00 3.27
605 674 6.317857 GCTCATATCAGGTGTTTGTTTTCTC 58.682 40.000 0.00 0.00 0.00 2.87
606 675 5.183904 GGCTCATATCAGGTGTTTGTTTTCT 59.816 40.000 0.00 0.00 0.00 2.52
607 676 5.402398 GGCTCATATCAGGTGTTTGTTTTC 58.598 41.667 0.00 0.00 0.00 2.29
608 677 4.082787 CGGCTCATATCAGGTGTTTGTTTT 60.083 41.667 0.00 0.00 0.00 2.43
609 678 3.440173 CGGCTCATATCAGGTGTTTGTTT 59.560 43.478 0.00 0.00 0.00 2.83
624 693 1.534729 GTGAAAAAGGGACGGCTCAT 58.465 50.000 0.00 0.00 0.00 2.90
627 696 0.106419 TTGGTGAAAAAGGGACGGCT 60.106 50.000 0.00 0.00 0.00 5.52
641 710 3.490526 CGTTGGATTGCTTTTTCTTGGTG 59.509 43.478 0.00 0.00 0.00 4.17
752 833 4.664150 TTGAGGTTCGCTTTTGGATTTT 57.336 36.364 0.00 0.00 0.00 1.82
753 834 4.664150 TTTGAGGTTCGCTTTTGGATTT 57.336 36.364 0.00 0.00 0.00 2.17
754 835 4.664150 TTTTGAGGTTCGCTTTTGGATT 57.336 36.364 0.00 0.00 0.00 3.01
755 836 4.664150 TTTTTGAGGTTCGCTTTTGGAT 57.336 36.364 0.00 0.00 0.00 3.41
781 862 1.957877 TCCCGTCGCTTTTGGATTTTT 59.042 42.857 0.00 0.00 0.00 1.94
937 1034 1.690985 CCACTTCCCTCCCTCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
948 1045 2.265904 GCGGTTGGTTCCCACTTCC 61.266 63.158 0.00 0.00 30.78 3.46
949 1046 2.265904 GGCGGTTGGTTCCCACTTC 61.266 63.158 0.00 0.00 30.78 3.01
950 1047 2.203437 GGCGGTTGGTTCCCACTT 60.203 61.111 0.00 0.00 30.78 3.16
951 1048 4.636435 CGGCGGTTGGTTCCCACT 62.636 66.667 0.00 0.00 30.78 4.00
1583 1680 4.538917 CTCTCATCAGTCATCAGTCATCG 58.461 47.826 0.00 0.00 0.00 3.84
1584 1681 4.038282 AGCTCTCATCAGTCATCAGTCATC 59.962 45.833 0.00 0.00 0.00 2.92
1585 1682 3.962063 AGCTCTCATCAGTCATCAGTCAT 59.038 43.478 0.00 0.00 0.00 3.06
1586 1683 3.363627 AGCTCTCATCAGTCATCAGTCA 58.636 45.455 0.00 0.00 0.00 3.41
1587 1684 4.114073 CAAGCTCTCATCAGTCATCAGTC 58.886 47.826 0.00 0.00 0.00 3.51
1588 1685 3.679361 GCAAGCTCTCATCAGTCATCAGT 60.679 47.826 0.00 0.00 0.00 3.41
1590 1687 2.500504 AGCAAGCTCTCATCAGTCATCA 59.499 45.455 0.00 0.00 0.00 3.07
1635 1732 1.760613 TCAGAAAGGTTCACCACGAGT 59.239 47.619 0.00 0.00 38.89 4.18
1658 1764 6.809630 TCGGTCAACAAATCAATCAATACA 57.190 33.333 0.00 0.00 0.00 2.29
1818 1977 4.951254 TCAAGTCGGTTGATTTACAGTCA 58.049 39.130 0.00 0.00 40.45 3.41
1851 2011 5.965486 ACAGACCTCCTACCATATATGACA 58.035 41.667 14.54 0.54 0.00 3.58
1888 2048 9.630098 AAAATCAGAATTGTGTATGATGTTGTC 57.370 29.630 2.11 0.00 30.27 3.18
1926 2086 3.383505 TCTCGAAACCAAGAGTCTGTCAA 59.616 43.478 0.00 0.00 36.03 3.18
1930 2090 4.448537 AGATCTCGAAACCAAGAGTCTG 57.551 45.455 0.00 0.00 36.03 3.51
1940 2100 7.797819 AGTTGAAACACATAAGATCTCGAAAC 58.202 34.615 0.00 0.00 0.00 2.78
1944 2104 7.043722 GCTAGAGTTGAAACACATAAGATCTCG 60.044 40.741 0.00 0.00 0.00 4.04
1988 2148 2.360165 CTGTCAACAGCAAAGCCTTTCT 59.640 45.455 0.00 0.00 37.15 2.52
2089 2301 8.303156 CAAACAACATTACCATCAGGAACAATA 58.697 33.333 0.00 0.00 38.69 1.90
2092 2304 5.508825 GCAAACAACATTACCATCAGGAACA 60.509 40.000 0.00 0.00 38.69 3.18
2590 2813 5.652014 TCATGGGCTACTGAATTGTTTAAGG 59.348 40.000 0.00 0.00 0.00 2.69
2644 2867 6.266558 TGCTTAACCTGATTAAACACATGGTT 59.733 34.615 11.12 11.12 42.98 3.67
2652 2875 5.105756 ACCATGCTGCTTAACCTGATTAAAC 60.106 40.000 0.00 0.00 32.26 2.01
2886 3109 3.436001 TCGCCCTCGAATCTTTGAC 57.564 52.632 0.00 0.00 42.44 3.18
2901 3124 2.034999 TCAAACCCACCCCATCGC 59.965 61.111 0.00 0.00 0.00 4.58
3297 3520 5.103000 ACACAAGAAGTACATCATCTACGC 58.897 41.667 0.31 0.00 0.00 4.42
3298 3521 7.030165 AGAACACAAGAAGTACATCATCTACG 58.970 38.462 0.31 0.00 0.00 3.51
3303 3526 7.386299 GTGAGAAGAACACAAGAAGTACATCAT 59.614 37.037 0.31 0.00 38.05 2.45
3322 3545 8.507249 CAAAAGGATAAGTTTACTGGTGAGAAG 58.493 37.037 0.00 0.00 0.00 2.85
3432 3657 8.198778 TGTAATACGAGCAAAGTAATATGTCCA 58.801 33.333 0.00 0.00 0.00 4.02
3433 3658 8.583810 TGTAATACGAGCAAAGTAATATGTCC 57.416 34.615 0.00 0.00 0.00 4.02
3435 3660 9.042008 CCTTGTAATACGAGCAAAGTAATATGT 57.958 33.333 2.09 0.00 0.00 2.29
3436 3661 9.256477 TCCTTGTAATACGAGCAAAGTAATATG 57.744 33.333 2.09 0.00 0.00 1.78
3437 3662 9.998106 ATCCTTGTAATACGAGCAAAGTAATAT 57.002 29.630 2.09 0.00 0.00 1.28
3439 3664 9.826574 TTATCCTTGTAATACGAGCAAAGTAAT 57.173 29.630 2.09 0.00 0.00 1.89
3755 3980 2.745884 TCCCATGCGGCACTTTCG 60.746 61.111 4.03 0.00 0.00 3.46
4019 4244 7.961326 AGCATTACCACAAGATTTATTTCCT 57.039 32.000 0.00 0.00 0.00 3.36
4030 4255 5.705609 AGTTTGGTTAGCATTACCACAAG 57.294 39.130 4.32 0.00 45.00 3.16
4066 4291 4.324254 GGTAAGTTTCATGGGATGACTCCA 60.324 45.833 0.00 0.00 44.08 3.86
4082 4307 7.727634 GGTATGGGTGTATAGAGTAGGTAAGTT 59.272 40.741 0.00 0.00 0.00 2.66
4095 4320 6.670464 TCAAGAAAGAGTGGTATGGGTGTATA 59.330 38.462 0.00 0.00 0.00 1.47
4133 4366 3.462483 TCACTACATGAAACCACGTGT 57.538 42.857 15.65 0.00 41.85 4.49
4229 4462 5.064071 GTGCTTTCTTCTACCTTGATACAGC 59.936 44.000 0.00 0.00 0.00 4.40
4296 4529 5.466728 CAGGATATCAACATTACCACTTCGG 59.533 44.000 4.83 0.00 42.50 4.30
4301 4535 7.865706 AGTTTCAGGATATCAACATTACCAC 57.134 36.000 4.83 0.00 0.00 4.16
4315 4549 6.006449 ACAAAGTGCTCAATAGTTTCAGGAT 58.994 36.000 0.00 0.00 0.00 3.24
4350 4586 5.028375 GCAACCAATTTACAGCGTATCTTC 58.972 41.667 0.00 0.00 0.00 2.87
4533 4769 2.544267 CTCAGTCCCAAGTCGTTTGTTC 59.456 50.000 2.69 0.00 34.87 3.18
4593 4829 1.206132 CCATACACACTCCGGCACTAA 59.794 52.381 0.00 0.00 0.00 2.24
4611 4847 9.038072 TGTAATCACTACAAACTTATAGGACCA 57.962 33.333 0.00 0.00 37.58 4.02
4646 4882 2.059490 ACCACCACCTTGCTTAACCTA 58.941 47.619 0.00 0.00 0.00 3.08
4658 4894 5.908341 TGAAATTTAACAGAAACCACCACC 58.092 37.500 0.00 0.00 0.00 4.61
4862 5102 6.768381 GCAGGAGCACTATTTTACCTATCTTT 59.232 38.462 0.00 0.00 41.58 2.52
5014 5455 3.019564 CCCATTCATCTTGTTCAGGGAC 58.980 50.000 0.00 0.00 37.22 4.46
5212 5658 6.913132 TCGAAATCGTCTCAGATGTAGAAATC 59.087 38.462 2.41 0.00 40.80 2.17
5375 5821 3.116300 GCATATATGCGTCCCGTATCTG 58.884 50.000 21.33 0.00 44.67 2.90
5519 5965 3.057876 TCATTCATTTTTGCGTACGGCTT 60.058 39.130 18.39 0.00 44.05 4.35
5673 6127 3.764434 CCCGTGGATACTGCTATCTGTAT 59.236 47.826 0.00 0.00 39.20 2.29
5805 6259 6.446318 TCAACAAGTTTTCATGCTATGGTTC 58.554 36.000 0.00 0.00 0.00 3.62
5815 6269 8.033038 CCAAGATCATCATCAACAAGTTTTCAT 58.967 33.333 0.00 0.00 0.00 2.57
5822 6279 5.124936 TGAAGCCAAGATCATCATCAACAAG 59.875 40.000 0.00 0.00 0.00 3.16
5947 6419 3.068560 CCGGACACATAACCTCGAAAAA 58.931 45.455 0.00 0.00 0.00 1.94
6113 6585 1.805428 GCTTGGCCTTGGCGAAGAAA 61.805 55.000 31.00 10.16 0.00 2.52
6152 6625 2.370885 CTGCATGCAGTCGACTCTG 58.629 57.895 34.76 14.29 39.10 3.35
6235 6720 1.028868 GGAAGAAGGCTGCGCTTGAT 61.029 55.000 9.73 0.00 0.00 2.57
6362 6850 1.123928 GGGGACTCTTGATGATCGGT 58.876 55.000 0.00 0.00 0.00 4.69
6365 6853 1.696884 GGAGGGGGACTCTTGATGATC 59.303 57.143 0.00 0.00 45.83 2.92
6383 6871 4.373116 GGTGGAGACTTGCGCGGA 62.373 66.667 8.83 0.00 0.00 5.54
6411 6902 3.726144 AGCAGAGGGGGCTCTTGC 61.726 66.667 1.67 1.67 36.81 4.01
6416 6907 4.345286 ACAGGAGCAGAGGGGGCT 62.345 66.667 0.00 0.00 46.07 5.19
6454 7182 1.134699 GGACCGAGCAGTTCATCATCA 60.135 52.381 0.00 0.00 0.00 3.07
6530 7258 2.740981 CTGCACAGTCATCTTGTCCTTC 59.259 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.