Multiple sequence alignment - TraesCS6A01G317600

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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 TraesCS6A01G317600 chr6A 100.000 3582 0 0 1 3582 553914297 553910716 0.000000e+00 6615.0
1 TraesCS6A01G317600 chr6A 94.308 1757 77 11 889 2625 553767091 553765338 0.000000e+00 2669.0
2 TraesCS6A01G317600 chr6A 91.368 1089 83 6 1600 2683 563485402 563486484 0.000000e+00 1480.0
3 TraesCS6A01G317600 chr6A 92.642 530 34 4 999 1527 563484764 563485289 0.000000e+00 758.0
4 TraesCS6A01G317600 chr6A 86.905 252 22 4 875 1125 573014291 573014050 4.560000e-69 272.0
5 TraesCS6A01G317600 chr6A 81.771 192 19 8 540 728 553767279 553767101 2.880000e-31 147.0
6 TraesCS6A01G317600 chr6A 94.444 72 4 0 2621 2692 553764592 553764521 1.050000e-20 111.0
7 TraesCS6A01G317600 chr6D 89.951 2846 207 40 440 3241 59089645 59086835 0.000000e+00 3598.0
8 TraesCS6A01G317600 chr6D 88.441 2483 167 57 262 2670 408157832 408155396 0.000000e+00 2885.0
9 TraesCS6A01G317600 chr6D 91.280 1078 81 6 1609 2683 420568513 420567446 0.000000e+00 1458.0
10 TraesCS6A01G317600 chr6D 90.976 1086 87 5 1600 2683 420559890 420560966 0.000000e+00 1452.0
11 TraesCS6A01G317600 chr6D 90.104 576 48 6 1001 1571 420559264 420559835 0.000000e+00 739.0
12 TraesCS6A01G317600 chr6D 91.165 532 43 2 999 1530 420569155 420568628 0.000000e+00 719.0
13 TraesCS6A01G317600 chr6D 90.169 295 29 0 3288 3582 59086832 59086538 5.610000e-103 385.0
14 TraesCS6A01G317600 chr6D 88.686 274 17 7 185 448 59091266 59090997 4.460000e-84 322.0
15 TraesCS6A01G317600 chr6D 91.489 141 9 1 81 221 408157973 408157836 1.310000e-44 191.0
16 TraesCS6A01G317600 chr6D 89.091 110 5 2 81 186 59099131 59099025 2.900000e-26 130.0
17 TraesCS6A01G317600 chr6B 89.182 2274 158 45 518 2751 612745634 612743409 0.000000e+00 2756.0
18 TraesCS6A01G317600 chr6B 92.111 1876 125 9 864 2739 612271579 612269727 0.000000e+00 2623.0
19 TraesCS6A01G317600 chr6B 88.547 1720 150 25 999 2684 633730677 633732383 0.000000e+00 2041.0
20 TraesCS6A01G317600 chr6B 96.078 51 2 0 731 781 612271677 612271627 2.290000e-12 84.2
21 TraesCS6A01G317600 chr6B 88.571 70 5 1 2592 2661 612269334 612269268 8.240000e-12 82.4
22 TraesCS6A01G317600 chr4B 84.469 631 70 9 874 1503 514492855 514492252 6.620000e-167 597.0
23 TraesCS6A01G317600 chr7B 85.315 143 16 5 2794 2932 684755155 684755296 3.730000e-30 143.0
24 TraesCS6A01G317600 chr3A 85.385 130 14 5 2773 2898 9271699 9271827 2.900000e-26 130.0
25 TraesCS6A01G317600 chr3B 85.156 128 14 5 2773 2897 6173490 6173615 3.750000e-25 126.0
26 TraesCS6A01G317600 chr3B 95.238 42 1 1 2825 2865 578229091 578229050 8.300000e-07 65.8
27 TraesCS6A01G317600 chr1D 83.333 132 17 5 2786 2917 458130947 458130821 2.260000e-22 117.0
28 TraesCS6A01G317600 chr7A 78.363 171 24 8 3146 3316 367011436 367011593 8.180000e-17 99.0
29 TraesCS6A01G317600 chr3D 100.000 35 0 0 913 947 557798731 557798765 8.300000e-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 TraesCS6A01G317600 chr6A 553910716 553914297 3581 True 6615.000000 6615 100.000000 1 3582 1 chr6A.!!$R1 3581
1 TraesCS6A01G317600 chr6A 563484764 563486484 1720 False 1119.000000 1480 92.005000 999 2683 2 chr6A.!!$F1 1684
2 TraesCS6A01G317600 chr6A 553764521 553767279 2758 True 975.666667 2669 90.174333 540 2692 3 chr6A.!!$R3 2152
3 TraesCS6A01G317600 chr6D 408155396 408157973 2577 True 1538.000000 2885 89.965000 81 2670 2 chr6D.!!$R3 2589
4 TraesCS6A01G317600 chr6D 59086538 59091266 4728 True 1435.000000 3598 89.602000 185 3582 3 chr6D.!!$R2 3397
5 TraesCS6A01G317600 chr6D 420559264 420560966 1702 False 1095.500000 1452 90.540000 1001 2683 2 chr6D.!!$F1 1682
6 TraesCS6A01G317600 chr6D 420567446 420569155 1709 True 1088.500000 1458 91.222500 999 2683 2 chr6D.!!$R4 1684
7 TraesCS6A01G317600 chr6B 612743409 612745634 2225 True 2756.000000 2756 89.182000 518 2751 1 chr6B.!!$R1 2233
8 TraesCS6A01G317600 chr6B 633730677 633732383 1706 False 2041.000000 2041 88.547000 999 2684 1 chr6B.!!$F1 1685
9 TraesCS6A01G317600 chr6B 612269268 612271677 2409 True 929.866667 2623 92.253333 731 2739 3 chr6B.!!$R2 2008
10 TraesCS6A01G317600 chr4B 514492252 514492855 603 True 597.000000 597 84.469000 874 1503 1 chr4B.!!$R1 629

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
78 79 0.036388 ACGTGCCGAGGATGTCAAAT 60.036 50.0 1.5 0.0 0.00 2.32 F
963 2389 0.179045 CCATCGACCCATCTTGGACC 60.179 60.0 0.0 0.0 40.96 4.46 F
1405 2852 0.459899 CGTCATCGGGTTCTCCATGA 59.540 55.0 0.0 0.0 33.64 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 2822 0.658368 CCGATGACGACGTCAGAGAT 59.342 55.000 31.72 17.93 46.04 2.75 R
2557 4059 0.541063 TCTTGGGTAGGAGCACGTCA 60.541 55.000 0.00 0.00 0.00 4.35 R
3202 5640 1.333619 GTTGTGACAATGTTCGTGGCT 59.666 47.619 0.00 0.00 0.00 4.75 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
43 44 4.724074 TTTTCTTGCACATCCATCCATC 57.276 40.909 0.00 0.00 0.00 3.51
44 45 2.353357 TCTTGCACATCCATCCATCC 57.647 50.000 0.00 0.00 0.00 3.51
45 46 1.565288 TCTTGCACATCCATCCATCCA 59.435 47.619 0.00 0.00 0.00 3.41
46 47 1.954382 CTTGCACATCCATCCATCCAG 59.046 52.381 0.00 0.00 0.00 3.86
47 48 0.184211 TGCACATCCATCCATCCAGG 59.816 55.000 0.00 0.00 39.47 4.45
48 49 0.184451 GCACATCCATCCATCCAGGT 59.816 55.000 0.00 0.00 39.02 4.00
49 50 1.816961 GCACATCCATCCATCCAGGTC 60.817 57.143 0.00 0.00 39.02 3.85
50 51 1.143813 ACATCCATCCATCCAGGTCC 58.856 55.000 0.00 0.00 39.02 4.46
51 52 1.142936 CATCCATCCATCCAGGTCCA 58.857 55.000 0.00 0.00 39.02 4.02
52 53 1.073444 CATCCATCCATCCAGGTCCAG 59.927 57.143 0.00 0.00 39.02 3.86
53 54 1.150081 CCATCCATCCAGGTCCAGC 59.850 63.158 0.00 0.00 39.02 4.85
54 55 1.351080 CCATCCATCCAGGTCCAGCT 61.351 60.000 0.00 0.00 39.02 4.24
55 56 0.179026 CATCCATCCAGGTCCAGCTG 60.179 60.000 6.78 6.78 39.02 4.24
56 57 1.351080 ATCCATCCAGGTCCAGCTGG 61.351 60.000 27.87 27.87 41.85 4.85
57 58 2.304056 CCATCCAGGTCCAGCTGGT 61.304 63.158 31.58 10.90 41.28 4.00
58 59 1.687612 CATCCAGGTCCAGCTGGTT 59.312 57.895 31.58 16.07 41.28 3.67
59 60 0.911769 CATCCAGGTCCAGCTGGTTA 59.088 55.000 31.58 11.73 41.28 2.85
60 61 0.912486 ATCCAGGTCCAGCTGGTTAC 59.088 55.000 31.58 22.76 41.28 2.50
61 62 1.079127 CCAGGTCCAGCTGGTTACG 60.079 63.158 31.58 18.26 36.08 3.18
62 63 1.671742 CAGGTCCAGCTGGTTACGT 59.328 57.895 31.58 21.38 36.34 3.57
63 64 0.670546 CAGGTCCAGCTGGTTACGTG 60.671 60.000 31.58 27.39 36.34 4.49
64 65 2.033194 GGTCCAGCTGGTTACGTGC 61.033 63.158 31.58 13.58 36.34 5.34
65 66 2.033194 GTCCAGCTGGTTACGTGCC 61.033 63.158 31.58 7.52 36.34 5.01
66 67 3.118454 CCAGCTGGTTACGTGCCG 61.118 66.667 25.53 0.00 0.00 5.69
67 68 2.048597 CAGCTGGTTACGTGCCGA 60.049 61.111 5.57 0.00 0.00 5.54
68 69 2.094659 CAGCTGGTTACGTGCCGAG 61.095 63.158 5.57 2.66 0.00 4.63
69 70 2.813908 GCTGGTTACGTGCCGAGG 60.814 66.667 0.00 0.00 0.00 4.63
70 71 2.967397 CTGGTTACGTGCCGAGGA 59.033 61.111 0.00 0.00 0.00 3.71
71 72 1.515954 CTGGTTACGTGCCGAGGAT 59.484 57.895 0.00 0.00 0.00 3.24
72 73 0.806102 CTGGTTACGTGCCGAGGATG 60.806 60.000 0.00 0.00 0.00 3.51
73 74 1.217244 GGTTACGTGCCGAGGATGT 59.783 57.895 0.00 0.00 0.00 3.06
74 75 0.804933 GGTTACGTGCCGAGGATGTC 60.805 60.000 0.00 0.00 0.00 3.06
75 76 0.108992 GTTACGTGCCGAGGATGTCA 60.109 55.000 0.00 0.00 0.00 3.58
76 77 0.604073 TTACGTGCCGAGGATGTCAA 59.396 50.000 0.00 0.00 0.00 3.18
77 78 0.604073 TACGTGCCGAGGATGTCAAA 59.396 50.000 0.00 0.00 0.00 2.69
78 79 0.036388 ACGTGCCGAGGATGTCAAAT 60.036 50.000 1.50 0.00 0.00 2.32
79 80 0.374758 CGTGCCGAGGATGTCAAATG 59.625 55.000 0.00 0.00 0.00 2.32
216 217 9.319223 GAAAACGAATTATGTTCAGAGAGTTTC 57.681 33.333 0.00 0.00 0.00 2.78
259 260 4.106925 CCCAGGACAGGCCAGAGC 62.107 72.222 5.01 0.00 40.02 4.09
260 261 3.007920 CCAGGACAGGCCAGAGCT 61.008 66.667 5.01 0.00 40.02 4.09
261 262 2.268280 CAGGACAGGCCAGAGCTG 59.732 66.667 5.01 0.00 40.02 4.24
272 276 4.385405 AGAGCTGGCCACGCTGAC 62.385 66.667 27.52 17.01 37.96 3.51
298 308 2.644992 CACGCCAAAGAGCCCAAC 59.355 61.111 0.00 0.00 0.00 3.77
337 347 7.303634 AGTAGATGTACAAATTTGCTAACCG 57.696 36.000 18.12 0.00 0.00 4.44
343 353 2.873472 ACAAATTTGCTAACCGTCGACA 59.127 40.909 18.12 0.00 0.00 4.35
347 357 3.581024 TTTGCTAACCGTCGACATAGT 57.419 42.857 17.16 6.71 0.00 2.12
395 405 2.747460 CACCGCCACTGTGGATGG 60.747 66.667 30.23 28.48 45.51 3.51
522 1912 1.227645 TGCTGTAGATCATGCCGGC 60.228 57.895 22.73 22.73 0.00 6.13
576 1967 3.479269 GCTGCACACGTAGCGACC 61.479 66.667 7.54 0.00 41.19 4.79
577 1968 2.258591 CTGCACACGTAGCGACCT 59.741 61.111 7.54 0.00 33.85 3.85
617 2014 4.688419 CACACGCCGGCTGCTTTG 62.688 66.667 26.68 15.24 38.05 2.77
638 2035 1.287146 TGTGGAGGTAGGAGTAGGACC 59.713 57.143 0.00 0.00 0.00 4.46
639 2036 1.287146 GTGGAGGTAGGAGTAGGACCA 59.713 57.143 0.00 0.00 35.56 4.02
640 2037 2.005350 TGGAGGTAGGAGTAGGACCAA 58.995 52.381 0.00 0.00 35.56 3.67
747 2152 4.328983 CCTAATACGTCATCACTTGCGTTT 59.671 41.667 0.00 0.00 38.45 3.60
778 2183 2.996249 ATGGCGATTCTCACTGTCAT 57.004 45.000 0.00 0.00 0.00 3.06
785 2195 0.615331 TTCTCACTGTCATGCCCCTC 59.385 55.000 0.00 0.00 0.00 4.30
809 2231 0.465705 TATGGAGTAGTGCTGCCTGC 59.534 55.000 0.00 0.00 43.25 4.85
839 2261 1.939838 GCCTATAAATACAGCCGCGCT 60.940 52.381 5.56 0.00 40.77 5.92
842 2264 1.784525 ATAAATACAGCCGCGCTCTC 58.215 50.000 5.56 0.00 36.40 3.20
953 2379 1.809207 CCATTGTTGCCATCGACCC 59.191 57.895 0.00 0.00 0.00 4.46
961 2387 1.271127 TGCCATCGACCCATCTTGGA 61.271 55.000 3.16 0.00 40.96 3.53
962 2388 0.815615 GCCATCGACCCATCTTGGAC 60.816 60.000 3.16 0.00 40.96 4.02
963 2389 0.179045 CCATCGACCCATCTTGGACC 60.179 60.000 0.00 0.00 40.96 4.46
964 2390 0.530650 CATCGACCCATCTTGGACCG 60.531 60.000 0.00 0.00 40.96 4.79
965 2391 1.686325 ATCGACCCATCTTGGACCGG 61.686 60.000 0.00 0.00 40.96 5.28
989 2428 4.913126 GGAACGCTCGGAGTCATT 57.087 55.556 6.90 0.00 0.00 2.57
1016 2458 2.105806 GAGATGGGCTCGATGGGACC 62.106 65.000 0.00 0.00 33.17 4.46
1017 2459 2.040464 ATGGGCTCGATGGGACCT 60.040 61.111 0.00 0.00 0.00 3.85
1018 2460 2.388890 GATGGGCTCGATGGGACCTG 62.389 65.000 0.00 0.00 0.00 4.00
1213 2660 2.607750 TCCCAGGCTTCCGCTTCT 60.608 61.111 0.00 0.00 36.09 2.85
1293 2740 1.072159 GCTCTGCAAGTCCACCACT 59.928 57.895 0.00 0.00 36.64 4.00
1375 2822 2.738139 CAGCGGTCACATGCGTCA 60.738 61.111 0.00 0.00 35.87 4.35
1392 2839 2.710760 GTCATCTCTGACGTCGTCATC 58.289 52.381 27.10 1.83 41.94 2.92
1405 2852 0.459899 CGTCATCGGGTTCTCCATGA 59.540 55.000 0.00 0.00 33.64 3.07
1467 2914 2.281345 GCCAGCGCCATCAGCTAT 60.281 61.111 2.29 0.00 44.06 2.97
1530 2989 1.208776 GCCCCACTCAAAGGTACGTAT 59.791 52.381 0.00 0.00 0.00 3.06
1598 3094 2.514592 CTCGGTGCGGCCATTGAT 60.515 61.111 2.24 0.00 36.97 2.57
1629 3125 8.187480 GCTGATCGAAGCTCTTATCTGAATATA 58.813 37.037 1.75 0.00 40.20 0.86
1840 3342 0.671796 TCCTCAACAGCTTCGACGAA 59.328 50.000 10.34 10.34 0.00 3.85
2044 3546 0.956633 TCTACGTCAACTTCGGCAGT 59.043 50.000 0.00 0.00 37.30 4.40
2122 3624 2.450476 GGGAAGCAGTTCATGTGGATT 58.550 47.619 0.00 0.00 33.93 3.01
2128 3630 2.426522 CAGTTCATGTGGATTGTCCGT 58.573 47.619 0.00 0.00 40.17 4.69
2539 4041 4.913126 GGCTCGTCTCACCGAAAT 57.087 55.556 0.00 0.00 36.24 2.17
2557 4059 1.874345 ATTTCGACGAGCTGGTCCGT 61.874 55.000 21.44 10.56 42.17 4.69
2569 4071 2.338015 GGTCCGTGACGTGCTCCTA 61.338 63.158 3.64 0.00 32.65 2.94
2619 4880 9.074576 TCTTCACTGTAATTAGAGAACACTACA 57.925 33.333 16.03 0.00 0.00 2.74
2626 4887 9.903682 TGTAATTAGAGAACACTACAACTGTAC 57.096 33.333 0.00 0.00 0.00 2.90
2698 4960 4.321230 CCTGAGTGGAGTAACAAAAATGCC 60.321 45.833 0.00 0.00 38.35 4.40
2710 4973 3.070302 ACAAAAATGCCAAACATACGGGT 59.930 39.130 0.00 0.00 38.34 5.28
2723 4986 5.106876 ACATACGGGTAGCTTTTTATGGT 57.893 39.130 0.00 0.00 0.00 3.55
2760 5023 9.308000 AGACCATGGTAAATTTTACTTCATGAA 57.692 29.630 24.82 8.12 34.26 2.57
2761 5024 9.921637 GACCATGGTAAATTTTACTTCATGAAA 57.078 29.630 24.82 0.00 34.26 2.69
2762 5025 9.705290 ACCATGGTAAATTTTACTTCATGAAAC 57.295 29.630 24.82 1.23 34.26 2.78
2781 5047 7.144722 TGAAACAAGATGGCAATTACTACTG 57.855 36.000 0.00 0.00 0.00 2.74
2911 5177 6.380846 ACATATTTTTGCCACCATGTACAGAT 59.619 34.615 0.33 0.00 0.00 2.90
2919 5185 4.426416 CCACCATGTACAGATGCAAATTG 58.574 43.478 0.33 0.00 0.00 2.32
3024 5456 6.993786 TTGCCATGTTACGATTTTCAGATA 57.006 33.333 0.00 0.00 0.00 1.98
3131 5569 2.565391 TGTAACATGGATGGACGTCTGT 59.435 45.455 16.46 7.80 0.00 3.41
3164 5602 3.259902 GAGATCTTAAACCCGACCACAC 58.740 50.000 0.00 0.00 0.00 3.82
3170 5608 1.052124 AAACCCGACCACACCTCTCA 61.052 55.000 0.00 0.00 0.00 3.27
3189 5627 4.148825 CTCGCCACCCTTCTCCGG 62.149 72.222 0.00 0.00 0.00 5.14
3202 5640 4.490606 TCCGGGCAGGGGCTGATA 62.491 66.667 0.00 0.00 41.52 2.15
3234 5672 0.027586 GTCACAACACAGTTGACGCC 59.972 55.000 15.99 0.00 0.00 5.68
3236 5674 0.662619 CACAACACAGTTGACGCCAT 59.337 50.000 15.99 0.00 0.00 4.40
3241 5679 0.179181 CACAGTTGACGCCATCATGC 60.179 55.000 0.00 0.00 37.11 4.06
3242 5680 1.308069 ACAGTTGACGCCATCATGCC 61.308 55.000 0.00 0.00 37.11 4.40
3243 5681 1.750399 AGTTGACGCCATCATGCCC 60.750 57.895 0.00 0.00 37.11 5.36
3244 5682 2.823593 TTGACGCCATCATGCCCG 60.824 61.111 0.00 0.00 37.11 6.13
3245 5683 3.322318 TTGACGCCATCATGCCCGA 62.322 57.895 3.31 0.00 37.11 5.14
3246 5684 2.281070 GACGCCATCATGCCCGAT 60.281 61.111 3.31 0.00 0.00 4.18
3247 5685 2.592574 ACGCCATCATGCCCGATG 60.593 61.111 5.65 5.65 42.09 3.84
3248 5686 2.281002 CGCCATCATGCCCGATGA 60.281 61.111 12.71 1.14 44.67 2.92
3249 5687 2.610694 CGCCATCATGCCCGATGAC 61.611 63.158 12.71 2.06 44.12 3.06
3250 5688 1.526686 GCCATCATGCCCGATGACA 60.527 57.895 12.71 0.00 44.12 3.58
3251 5689 1.102809 GCCATCATGCCCGATGACAA 61.103 55.000 12.71 0.00 44.12 3.18
3252 5690 1.612676 CCATCATGCCCGATGACAAT 58.387 50.000 12.71 0.00 44.12 2.71
3253 5691 1.538512 CCATCATGCCCGATGACAATC 59.461 52.381 12.71 0.00 44.12 2.67
3263 5701 2.635141 GATGACAATCGATCACACGC 57.365 50.000 0.00 0.00 0.00 5.34
3264 5702 2.196749 GATGACAATCGATCACACGCT 58.803 47.619 0.00 0.00 0.00 5.07
3265 5703 2.931512 TGACAATCGATCACACGCTA 57.068 45.000 0.00 0.00 0.00 4.26
3266 5704 3.436700 TGACAATCGATCACACGCTAT 57.563 42.857 0.00 0.00 0.00 2.97
3267 5705 3.372060 TGACAATCGATCACACGCTATC 58.628 45.455 0.00 0.00 0.00 2.08
3268 5706 3.181491 TGACAATCGATCACACGCTATCA 60.181 43.478 0.00 0.00 0.00 2.15
3269 5707 3.982475 ACAATCGATCACACGCTATCAT 58.018 40.909 0.00 0.00 0.00 2.45
3270 5708 4.371786 ACAATCGATCACACGCTATCATT 58.628 39.130 0.00 0.00 0.00 2.57
3271 5709 4.445718 ACAATCGATCACACGCTATCATTC 59.554 41.667 0.00 0.00 0.00 2.67
3272 5710 3.990318 TCGATCACACGCTATCATTCT 57.010 42.857 0.00 0.00 0.00 2.40
3273 5711 4.307443 TCGATCACACGCTATCATTCTT 57.693 40.909 0.00 0.00 0.00 2.52
3274 5712 4.682787 TCGATCACACGCTATCATTCTTT 58.317 39.130 0.00 0.00 0.00 2.52
3275 5713 5.827666 TCGATCACACGCTATCATTCTTTA 58.172 37.500 0.00 0.00 0.00 1.85
3276 5714 5.915196 TCGATCACACGCTATCATTCTTTAG 59.085 40.000 0.00 0.00 0.00 1.85
3277 5715 5.915196 CGATCACACGCTATCATTCTTTAGA 59.085 40.000 0.00 0.00 0.00 2.10
3278 5716 6.584184 CGATCACACGCTATCATTCTTTAGAT 59.416 38.462 0.00 0.00 0.00 1.98
3279 5717 7.750903 CGATCACACGCTATCATTCTTTAGATA 59.249 37.037 0.00 0.00 0.00 1.98
3280 5718 8.978564 ATCACACGCTATCATTCTTTAGATAG 57.021 34.615 0.00 0.00 44.09 2.08
3281 5719 7.941919 TCACACGCTATCATTCTTTAGATAGT 58.058 34.615 10.18 0.00 43.49 2.12
3300 5738 7.105588 AGATAGTGTTTCATCACATAGCAACA 58.894 34.615 0.00 0.00 40.37 3.33
3304 5742 4.151070 GTTTCATCACATAGCAACACACG 58.849 43.478 0.00 0.00 0.00 4.49
3328 5766 9.439500 ACGTGTATTTAGCTGGTTAATAAGAAA 57.561 29.630 0.00 0.00 0.00 2.52
3336 5774 5.875359 AGCTGGTTAATAAGAAAGGAGAACG 59.125 40.000 0.00 0.00 0.00 3.95
3337 5775 5.642491 GCTGGTTAATAAGAAAGGAGAACGT 59.358 40.000 0.00 0.00 0.00 3.99
3341 5779 8.149647 TGGTTAATAAGAAAGGAGAACGTTGTA 58.850 33.333 5.00 0.00 0.00 2.41
3419 5857 3.257375 TCTCCTAAAGTTGCTCTTACGCA 59.743 43.478 0.00 0.00 38.31 5.24
3425 5863 4.408182 AAGTTGCTCTTACGCAGGATAT 57.592 40.909 0.00 0.00 41.55 1.63
3451 5889 3.064324 AAATGCCGACTGCTGCCC 61.064 61.111 0.00 0.00 42.00 5.36
3453 5891 2.196997 AAATGCCGACTGCTGCCCTA 62.197 55.000 0.00 0.00 42.00 3.53
3460 5898 1.473965 CGACTGCTGCCCTATCACAAT 60.474 52.381 0.00 0.00 0.00 2.71
3461 5899 2.224042 CGACTGCTGCCCTATCACAATA 60.224 50.000 0.00 0.00 0.00 1.90
3474 5912 5.011125 CCTATCACAATAGGTCTCAATCGGT 59.989 44.000 3.71 0.00 46.63 4.69
3525 5963 7.186021 TCTTTGTAAGTGATTTCCGAAAGTC 57.814 36.000 0.00 0.00 0.00 3.01
3534 5972 6.715264 AGTGATTTCCGAAAGTCCAAAATAGT 59.285 34.615 0.00 0.00 0.00 2.12
3537 5975 4.759516 TCCGAAAGTCCAAAATAGTTGC 57.240 40.909 0.00 0.00 0.00 4.17
3542 5980 5.179368 CGAAAGTCCAAAATAGTTGCTCAGA 59.821 40.000 0.00 0.00 0.00 3.27
3543 5981 6.293407 CGAAAGTCCAAAATAGTTGCTCAGAA 60.293 38.462 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.081531 GGATGGATGGATGTGCAAGAAAAA 60.082 41.667 0.00 0.00 0.00 1.94
22 23 3.448301 GGATGGATGGATGTGCAAGAAAA 59.552 43.478 0.00 0.00 0.00 2.29
23 24 3.025978 GGATGGATGGATGTGCAAGAAA 58.974 45.455 0.00 0.00 0.00 2.52
24 25 2.025131 TGGATGGATGGATGTGCAAGAA 60.025 45.455 0.00 0.00 0.00 2.52
25 26 1.565288 TGGATGGATGGATGTGCAAGA 59.435 47.619 0.00 0.00 0.00 3.02
26 27 1.954382 CTGGATGGATGGATGTGCAAG 59.046 52.381 0.00 0.00 0.00 4.01
27 28 1.410507 CCTGGATGGATGGATGTGCAA 60.411 52.381 0.00 0.00 38.35 4.08
28 29 0.184211 CCTGGATGGATGGATGTGCA 59.816 55.000 0.00 0.00 38.35 4.57
29 30 0.184451 ACCTGGATGGATGGATGTGC 59.816 55.000 0.00 0.00 39.71 4.57
30 31 1.202855 GGACCTGGATGGATGGATGTG 60.203 57.143 0.00 0.00 39.71 3.21
31 32 1.143813 GGACCTGGATGGATGGATGT 58.856 55.000 0.00 0.00 39.71 3.06
32 33 1.073444 CTGGACCTGGATGGATGGATG 59.927 57.143 0.00 0.00 39.71 3.51
33 34 1.442773 CTGGACCTGGATGGATGGAT 58.557 55.000 0.00 0.00 39.71 3.41
34 35 1.348008 GCTGGACCTGGATGGATGGA 61.348 60.000 0.00 0.00 39.71 3.41
35 36 1.150081 GCTGGACCTGGATGGATGG 59.850 63.158 0.00 0.00 39.71 3.51
36 37 0.179026 CAGCTGGACCTGGATGGATG 60.179 60.000 5.57 0.00 39.71 3.51
37 38 2.228711 CAGCTGGACCTGGATGGAT 58.771 57.895 5.57 0.00 39.71 3.41
38 39 3.731547 CAGCTGGACCTGGATGGA 58.268 61.111 5.57 0.00 39.71 3.41
44 45 0.670546 CACGTAACCAGCTGGACCTG 60.671 60.000 39.19 25.24 38.94 4.00
45 46 1.671742 CACGTAACCAGCTGGACCT 59.328 57.895 39.19 23.27 38.94 3.85
46 47 2.033194 GCACGTAACCAGCTGGACC 61.033 63.158 39.19 22.67 38.94 4.46
47 48 2.033194 GGCACGTAACCAGCTGGAC 61.033 63.158 39.19 25.45 38.94 4.02
48 49 2.345991 GGCACGTAACCAGCTGGA 59.654 61.111 39.19 15.70 38.94 3.86
61 62 0.099436 GCATTTGACATCCTCGGCAC 59.901 55.000 0.00 0.00 0.00 5.01
62 63 0.322366 TGCATTTGACATCCTCGGCA 60.322 50.000 0.00 0.00 0.00 5.69
63 64 0.810648 TTGCATTTGACATCCTCGGC 59.189 50.000 0.00 0.00 0.00 5.54
64 65 4.898829 TTATTGCATTTGACATCCTCGG 57.101 40.909 0.00 0.00 0.00 4.63
65 66 7.157050 CAAATTATTGCATTTGACATCCTCG 57.843 36.000 4.80 0.00 43.99 4.63
101 102 2.222729 GCACGGTGTGATCGTTCATTAC 60.223 50.000 10.24 2.91 38.94 1.89
102 103 1.996898 GCACGGTGTGATCGTTCATTA 59.003 47.619 10.24 0.00 38.94 1.90
103 104 0.796312 GCACGGTGTGATCGTTCATT 59.204 50.000 10.24 0.00 38.94 2.57
104 105 0.320334 TGCACGGTGTGATCGTTCAT 60.320 50.000 10.24 0.00 38.94 2.57
132 133 1.296056 GATTGGGTCCACAACGACGG 61.296 60.000 0.00 0.00 33.30 4.79
155 156 1.153978 CATGTGGCATGCAACGGAC 60.154 57.895 20.19 8.18 0.00 4.79
216 217 3.650070 GGAACCAAAGAAAGAAGGCAG 57.350 47.619 0.00 0.00 0.00 4.85
298 308 2.086869 TCTACTCCTTGACCCGTAACG 58.913 52.381 0.00 0.00 0.00 3.18
337 347 8.127954 CCTACTCCTAAAACTAACTATGTCGAC 58.872 40.741 9.11 9.11 0.00 4.20
343 353 6.832900 ACGCTCCTACTCCTAAAACTAACTAT 59.167 38.462 0.00 0.00 0.00 2.12
347 357 5.065218 CGTACGCTCCTACTCCTAAAACTAA 59.935 44.000 0.52 0.00 0.00 2.24
399 409 1.569479 GCTTCGGTTCTGCTGGTGAC 61.569 60.000 0.00 0.00 0.00 3.67
413 433 6.073548 CCTTATTAGCACTCTTTATGGCTTCG 60.074 42.308 0.00 0.00 37.79 3.79
560 1951 1.801913 GAGGTCGCTACGTGTGCAG 60.802 63.158 14.10 8.00 0.00 4.41
564 1955 1.874562 GTGAGAGGTCGCTACGTGT 59.125 57.895 0.00 0.00 0.00 4.49
566 1957 3.175724 CGTGAGAGGTCGCTACGT 58.824 61.111 0.00 0.00 0.00 3.57
576 1967 4.056125 TGCGGGTCAGCGTGAGAG 62.056 66.667 0.00 0.00 40.67 3.20
577 1968 4.357947 GTGCGGGTCAGCGTGAGA 62.358 66.667 0.00 0.00 40.67 3.27
617 2014 2.377073 GTCCTACTCCTACCTCCACAC 58.623 57.143 0.00 0.00 0.00 3.82
618 2015 1.287146 GGTCCTACTCCTACCTCCACA 59.713 57.143 0.00 0.00 0.00 4.17
638 2035 3.065371 GGAGACTTGTTGGTCACTTGTTG 59.935 47.826 0.00 0.00 38.57 3.33
639 2036 3.279434 GGAGACTTGTTGGTCACTTGTT 58.721 45.455 0.00 0.00 38.57 2.83
640 2037 2.238646 TGGAGACTTGTTGGTCACTTGT 59.761 45.455 0.00 0.00 38.57 3.16
747 2152 5.049336 TGAGAATCGCCATTTTGTTACGAAA 60.049 36.000 0.00 0.00 38.61 3.46
785 2195 3.580458 AGGCAGCACTACTCCATATTAGG 59.420 47.826 0.00 0.00 0.00 2.69
839 2261 0.899720 AATTGGTTACCTCGGCGAGA 59.100 50.000 36.47 16.53 0.00 4.04
842 2264 1.663695 ATGAATTGGTTACCTCGGCG 58.336 50.000 0.00 0.00 0.00 6.46
852 2274 3.560025 GCTGGGGATCGATATGAATTGGT 60.560 47.826 0.00 0.00 0.00 3.67
953 2379 1.817099 GAGCTGCCGGTCCAAGATG 60.817 63.158 1.90 0.00 0.00 2.90
989 2428 3.687321 GAGCCCATCTCCGCTGCAA 62.687 63.158 0.00 0.00 34.84 4.08
1360 2807 1.756375 GAGATGACGCATGTGACCGC 61.756 60.000 14.43 1.66 0.00 5.68
1375 2822 0.658368 CCGATGACGACGTCAGAGAT 59.342 55.000 31.72 17.93 46.04 2.75
1392 2839 1.452108 GGCCTTCATGGAGAACCCG 60.452 63.158 1.24 0.00 38.35 5.28
1530 2989 4.083590 GGAAACAAAACAAAAAGCAGTGCA 60.084 37.500 19.20 0.00 0.00 4.57
1629 3125 1.660607 CGTCTGCATGCGTAAAGACAT 59.339 47.619 26.35 0.00 39.19 3.06
2044 3546 1.471501 GCGCTGGTCATGACAGTGATA 60.472 52.381 27.97 10.60 46.53 2.15
2122 3624 2.114625 ACCAGGTCTCGACGGACA 59.885 61.111 15.29 0.00 37.91 4.02
2128 3630 2.283529 GCCCTTCACCAGGTCTCGA 61.284 63.158 0.00 0.00 42.02 4.04
2416 3918 1.138036 CGTGATAAGTCGGGCGACA 59.862 57.895 0.00 0.00 46.76 4.35
2539 4041 2.257371 CGGACCAGCTCGTCGAAA 59.743 61.111 5.34 0.00 33.30 3.46
2557 4059 0.541063 TCTTGGGTAGGAGCACGTCA 60.541 55.000 0.00 0.00 0.00 4.35
2569 4071 3.381908 CGATGTAGAGCTAGTTCTTGGGT 59.618 47.826 14.78 0.00 0.00 4.51
2619 4880 8.685838 TCTTAACAAGCAAATAAGGTACAGTT 57.314 30.769 0.00 0.00 0.00 3.16
2626 4887 7.860872 ACGAACTTTCTTAACAAGCAAATAAGG 59.139 33.333 0.00 0.00 0.00 2.69
2698 4960 6.127842 ACCATAAAAAGCTACCCGTATGTTTG 60.128 38.462 0.00 0.00 0.00 2.93
2710 4973 5.009631 ACATCAGCACACCATAAAAAGCTA 58.990 37.500 0.00 0.00 0.00 3.32
2723 4986 1.908619 ACCATGGTCTACATCAGCACA 59.091 47.619 13.00 0.00 37.84 4.57
2760 5023 6.714810 TGTTCAGTAGTAATTGCCATCTTGTT 59.285 34.615 0.00 0.00 0.00 2.83
2761 5024 6.237901 TGTTCAGTAGTAATTGCCATCTTGT 58.762 36.000 0.00 0.00 0.00 3.16
2762 5025 6.741992 TGTTCAGTAGTAATTGCCATCTTG 57.258 37.500 0.00 0.00 0.00 3.02
2964 5230 4.215399 TGTTCTCTCACATTAAAAAGGCCG 59.785 41.667 0.00 0.00 0.00 6.13
3065 5503 9.723601 AATTGCAAAATGTGGTTATCACTAAAT 57.276 25.926 1.71 0.00 46.20 1.40
3099 5537 8.562892 GTCCATCCATGTTACATAGATCAAAAG 58.437 37.037 3.40 0.00 0.00 2.27
3104 5542 5.784177 ACGTCCATCCATGTTACATAGATC 58.216 41.667 3.40 0.00 0.00 2.75
3113 5551 1.404181 CGACAGACGTCCATCCATGTT 60.404 52.381 13.01 0.00 39.11 2.71
3141 5579 2.094338 GTGGTCGGGTTTAAGATCTCGT 60.094 50.000 0.00 0.00 0.00 4.18
3142 5580 2.094390 TGTGGTCGGGTTTAAGATCTCG 60.094 50.000 0.00 0.00 0.00 4.04
3164 5602 1.333636 AAGGGTGGCGAGATGAGAGG 61.334 60.000 0.00 0.00 0.00 3.69
3170 5608 2.427245 CGGAGAAGGGTGGCGAGAT 61.427 63.158 0.00 0.00 0.00 2.75
3202 5640 1.333619 GTTGTGACAATGTTCGTGGCT 59.666 47.619 0.00 0.00 0.00 4.75
3208 5646 4.793216 GTCAACTGTGTTGTGACAATGTTC 59.207 41.667 0.00 0.00 37.57 3.18
3234 5672 2.983402 GATTGTCATCGGGCATGATG 57.017 50.000 11.48 11.48 43.72 3.07
3244 5682 2.196749 AGCGTGTGATCGATTGTCATC 58.803 47.619 0.00 0.00 0.00 2.92
3245 5683 2.299993 AGCGTGTGATCGATTGTCAT 57.700 45.000 0.00 0.00 0.00 3.06
3246 5684 2.931512 TAGCGTGTGATCGATTGTCA 57.068 45.000 0.00 0.00 0.00 3.58
3247 5685 3.372060 TGATAGCGTGTGATCGATTGTC 58.628 45.455 0.00 0.00 0.00 3.18
3248 5686 3.436700 TGATAGCGTGTGATCGATTGT 57.563 42.857 0.00 0.00 0.00 2.71
3249 5687 4.683320 AGAATGATAGCGTGTGATCGATTG 59.317 41.667 0.00 0.00 0.00 2.67
3250 5688 4.876125 AGAATGATAGCGTGTGATCGATT 58.124 39.130 0.00 0.00 0.00 3.34
3251 5689 4.511617 AGAATGATAGCGTGTGATCGAT 57.488 40.909 0.00 0.00 0.00 3.59
3252 5690 3.990318 AGAATGATAGCGTGTGATCGA 57.010 42.857 0.00 0.00 0.00 3.59
3253 5691 5.915196 TCTAAAGAATGATAGCGTGTGATCG 59.085 40.000 0.00 0.00 0.00 3.69
3254 5692 7.881643 ATCTAAAGAATGATAGCGTGTGATC 57.118 36.000 0.00 0.00 0.00 2.92
3255 5693 8.580720 ACTATCTAAAGAATGATAGCGTGTGAT 58.419 33.333 9.18 0.00 43.38 3.06
3256 5694 7.862873 CACTATCTAAAGAATGATAGCGTGTGA 59.137 37.037 9.18 0.00 43.38 3.58
3257 5695 7.649705 ACACTATCTAAAGAATGATAGCGTGTG 59.350 37.037 9.18 0.00 43.38 3.82
3258 5696 7.717568 ACACTATCTAAAGAATGATAGCGTGT 58.282 34.615 9.18 6.22 43.38 4.49
3259 5697 8.581057 AACACTATCTAAAGAATGATAGCGTG 57.419 34.615 9.18 5.73 43.38 5.34
3260 5698 9.250624 GAAACACTATCTAAAGAATGATAGCGT 57.749 33.333 9.18 4.49 43.38 5.07
3261 5699 9.249457 TGAAACACTATCTAAAGAATGATAGCG 57.751 33.333 9.18 3.96 43.38 4.26
3266 5704 9.942850 TGTGATGAAACACTATCTAAAGAATGA 57.057 29.630 0.00 0.00 40.87 2.57
3270 5708 9.534565 GCTATGTGATGAAACACTATCTAAAGA 57.465 33.333 0.00 0.00 40.87 2.52
3271 5709 9.317936 TGCTATGTGATGAAACACTATCTAAAG 57.682 33.333 0.00 0.00 40.87 1.85
3272 5710 9.665719 TTGCTATGTGATGAAACACTATCTAAA 57.334 29.630 0.00 0.00 40.87 1.85
3273 5711 9.098355 GTTGCTATGTGATGAAACACTATCTAA 57.902 33.333 0.00 0.00 40.87 2.10
3274 5712 8.257306 TGTTGCTATGTGATGAAACACTATCTA 58.743 33.333 0.00 0.00 40.87 1.98
3275 5713 7.065085 GTGTTGCTATGTGATGAAACACTATCT 59.935 37.037 9.08 0.00 42.44 1.98
3276 5714 7.148423 TGTGTTGCTATGTGATGAAACACTATC 60.148 37.037 15.26 0.00 44.73 2.08
3277 5715 6.654582 TGTGTTGCTATGTGATGAAACACTAT 59.345 34.615 15.26 0.00 44.73 2.12
3278 5716 5.994668 TGTGTTGCTATGTGATGAAACACTA 59.005 36.000 15.26 3.10 44.73 2.74
3279 5717 4.821260 TGTGTTGCTATGTGATGAAACACT 59.179 37.500 15.26 0.00 44.73 3.55
3280 5718 4.911610 GTGTGTTGCTATGTGATGAAACAC 59.088 41.667 9.34 9.34 44.70 3.32
3281 5719 4.319405 CGTGTGTTGCTATGTGATGAAACA 60.319 41.667 0.00 0.00 0.00 2.83
3282 5720 4.151070 CGTGTGTTGCTATGTGATGAAAC 58.849 43.478 0.00 0.00 0.00 2.78
3283 5721 3.812609 ACGTGTGTTGCTATGTGATGAAA 59.187 39.130 0.00 0.00 0.00 2.69
3284 5722 3.186205 CACGTGTGTTGCTATGTGATGAA 59.814 43.478 7.58 0.00 0.00 2.57
3285 5723 2.736192 CACGTGTGTTGCTATGTGATGA 59.264 45.455 7.58 0.00 0.00 2.92
3286 5724 2.480037 ACACGTGTGTTGCTATGTGATG 59.520 45.455 22.71 0.00 41.83 3.07
3300 5738 8.036575 TCTTATTAACCAGCTAAATACACGTGT 58.963 33.333 26.52 26.52 0.00 4.49
3328 5766 6.154706 ACTTCTATGGAATACAACGTTCTCCT 59.845 38.462 0.00 0.00 0.00 3.69
3341 5779 8.224620 AGCTTATTATGGGACTTCTATGGAAT 57.775 34.615 0.00 0.00 0.00 3.01
3390 5828 6.552445 AGAGCAACTTTAGGAGATACACAT 57.448 37.500 0.00 0.00 0.00 3.21
3451 5889 6.090483 ACCGATTGAGACCTATTGTGATAG 57.910 41.667 0.00 0.00 35.92 2.08
3453 5891 4.499865 CGACCGATTGAGACCTATTGTGAT 60.500 45.833 0.00 0.00 0.00 3.06
3460 5898 1.725665 CGCGACCGATTGAGACCTA 59.274 57.895 0.00 0.00 36.29 3.08
3461 5899 2.490217 CGCGACCGATTGAGACCT 59.510 61.111 0.00 0.00 36.29 3.85
3469 5907 4.814294 GTCCCTTGCGCGACCGAT 62.814 66.667 12.10 0.00 36.29 4.18
3474 5912 1.527380 AAAAAGGTCCCTTGCGCGA 60.527 52.632 12.10 0.00 36.26 5.87


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

AutoCloner maintained by Alex Coulton.