Multiple sequence alignment - TraesCS6D01G108900

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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 TraesCS6D01G108900 chr6D 100.000 7134 0 0 1 7134 73518641 73525774 0.000000e+00 13175.0
1 TraesCS6D01G108900 chr6D 95.122 41 2 0 4900 4940 68863785 68863825 1.660000e-06 65.8
2 TraesCS6D01G108900 chr6B 95.123 4142 138 18 2390 6506 147883609 147887711 0.000000e+00 6471.0
3 TraesCS6D01G108900 chr6B 95.235 1469 57 8 913 2376 147882166 147883626 0.000000e+00 2313.0
4 TraesCS6D01G108900 chr6B 89.683 630 39 19 1 614 147881171 147881790 0.000000e+00 780.0
5 TraesCS6D01G108900 chr6B 98.238 227 3 1 6696 6921 147953825 147954051 5.190000e-106 396.0
6 TraesCS6D01G108900 chr6B 98.113 212 3 1 6498 6708 147953597 147953808 1.130000e-97 368.0
7 TraesCS6D01G108900 chr6B 92.130 216 17 0 6918 7133 147957887 147958102 8.990000e-79 305.0
8 TraesCS6D01G108900 chr6B 95.122 41 2 0 4900 4940 143769272 143769312 1.660000e-06 65.8
9 TraesCS6D01G108900 chr6A 94.317 2921 108 18 634 3517 89968173 89971072 0.000000e+00 4421.0
10 TraesCS6D01G108900 chr6A 93.798 1693 80 12 4960 6632 89972678 89974365 0.000000e+00 2521.0
11 TraesCS6D01G108900 chr6A 97.241 1450 38 1 3514 4963 89971152 89972599 0.000000e+00 2455.0
12 TraesCS6D01G108900 chr6A 92.445 503 30 4 6632 7134 90028431 90028925 0.000000e+00 712.0
13 TraesCS6D01G108900 chr6A 85.619 299 28 6 294 586 89967888 89968177 4.180000e-77 300.0
14 TraesCS6D01G108900 chr6A 85.217 230 19 7 1 227 89967669 89967886 9.310000e-54 222.0
15 TraesCS6D01G108900 chr6A 95.122 41 2 0 4900 4940 86461904 86461944 1.660000e-06 65.8
16 TraesCS6D01G108900 chr7A 77.322 829 167 16 3751 4573 615339912 615340725 3.010000e-128 470.0
17 TraesCS6D01G108900 chr7A 83.871 124 18 2 7000 7122 730828178 730828056 4.520000e-22 117.0
18 TraesCS6D01G108900 chr7A 85.714 105 15 0 2951 3055 615339168 615339272 2.100000e-20 111.0
19 TraesCS6D01G108900 chr7D 77.229 830 166 18 3751 4573 535328082 535328895 1.400000e-126 464.0
20 TraesCS6D01G108900 chr7D 85.714 105 15 0 2951 3055 535327337 535327441 2.100000e-20 111.0
21 TraesCS6D01G108900 chr7B 77.229 830 166 18 3751 4573 575380757 575381570 1.400000e-126 464.0
22 TraesCS6D01G108900 chr7B 85.714 105 15 0 2951 3055 575380013 575380117 2.100000e-20 111.0
23 TraesCS6D01G108900 chr7B 100.000 30 0 0 4845 4874 692828850 692828821 1.000000e-03 56.5
24 TraesCS6D01G108900 chr3A 83.088 136 17 6 7000 7132 126119577 126119445 1.260000e-22 119.0
25 TraesCS6D01G108900 chr3A 83.333 114 19 0 7000 7113 69662536 69662649 9.790000e-19 106.0
26 TraesCS6D01G108900 chr3A 84.112 107 15 2 7011 7116 9518852 9518747 1.270000e-17 102.0
27 TraesCS6D01G108900 chr3A 90.566 53 4 1 4899 4951 17624706 17624757 1.280000e-07 69.4
28 TraesCS6D01G108900 chr3A 85.714 63 8 1 4899 4961 221275027 221274966 1.660000e-06 65.8
29 TraesCS6D01G108900 chr3B 85.088 114 17 0 7000 7113 97755886 97755999 4.520000e-22 117.0
30 TraesCS6D01G108900 chrUn 82.456 114 20 0 7000 7113 87229948 87229835 4.550000e-17 100.0
31 TraesCS6D01G108900 chr5A 82.456 114 20 0 7000 7113 221611653 221611540 4.550000e-17 100.0
32 TraesCS6D01G108900 chr1A 91.837 49 2 2 4899 4946 557424107 557424060 4.620000e-07 67.6
33 TraesCS6D01G108900 chr3D 85.714 63 8 1 4899 4961 178651863 178651802 1.660000e-06 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 TraesCS6D01G108900 chr6D 73518641 73525774 7133 False 13175.000000 13175 100.000000 1 7134 1 chr6D.!!$F2 7133
1 TraesCS6D01G108900 chr6B 147881171 147887711 6540 False 3188.000000 6471 93.347000 1 6506 3 chr6B.!!$F2 6505
2 TraesCS6D01G108900 chr6B 147953597 147958102 4505 False 356.333333 396 96.160333 6498 7133 3 chr6B.!!$F3 635
3 TraesCS6D01G108900 chr6A 89967669 89974365 6696 False 1983.800000 4421 91.238400 1 6632 5 chr6A.!!$F3 6631
4 TraesCS6D01G108900 chr7A 615339168 615340725 1557 False 290.500000 470 81.518000 2951 4573 2 chr7A.!!$F1 1622
5 TraesCS6D01G108900 chr7D 535327337 535328895 1558 False 287.500000 464 81.471500 2951 4573 2 chr7D.!!$F1 1622
6 TraesCS6D01G108900 chr7B 575380013 575381570 1557 False 287.500000 464 81.471500 2951 4573 2 chr7B.!!$F1 1622

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
300 308 0.032316 AGCATGCAGAGGAGAGGAGA 60.032 55.000 21.98 0.00 0.00 3.71 F
599 613 0.037139 TTGGTGGCTTGCATTGCATC 60.037 50.000 12.95 7.47 38.76 3.91 F
2007 2112 0.809241 GCTTGGCCTGATCGAGACTG 60.809 60.000 3.32 0.00 0.00 3.51 F
2190 2295 1.001406 CTCACCTATGGCCTTCGATCC 59.999 57.143 3.32 0.00 0.00 3.36 F
2301 2406 1.908619 TGTTAGCTCTGCCCTCAATCA 59.091 47.619 0.00 0.00 0.00 2.57 F
3918 4252 0.108615 AAGCTCATCCGGTCAGTTCG 60.109 55.000 0.00 0.00 0.00 3.95 F
4807 5141 2.890945 ACAACAAATTAGGACAGGTGCC 59.109 45.455 0.00 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2112 0.319728 TCAGCAAGGTCTGACAGCTC 59.680 55.000 15.58 1.21 38.11 4.09 R
2284 2389 0.461548 CGTGATTGAGGGCAGAGCTA 59.538 55.000 0.00 0.00 0.00 3.32 R
2927 3052 2.307934 TCACATGCAGCGCAAGTATA 57.692 45.000 11.47 1.68 43.62 1.47 R
3918 4252 3.544285 CAGCTTGAACTCGTCGATACTTC 59.456 47.826 0.00 0.00 0.00 3.01 R
3931 4265 6.593382 AGAGTTTGATCTATGTCAGCTTGAAC 59.407 38.462 0.00 0.00 0.00 3.18 R
5357 5774 0.101219 CCCTGCTTATCAAAAGCGCC 59.899 55.000 2.29 0.00 45.80 6.53 R
6324 6771 0.453793 CCAACAAGCACGGTGACAAA 59.546 50.000 13.29 0.00 0.00 2.83 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
47 48 0.883370 GTTCCAAACCCTTCGTCGCT 60.883 55.000 0.00 0.00 0.00 4.93
51 52 0.921347 CAAACCCTTCGTCGCTATCG 59.079 55.000 0.00 0.00 0.00 2.92
70 71 1.206371 CGAACCCATCGTAGTTTCCCT 59.794 52.381 0.00 0.00 46.52 4.20
74 75 0.468648 CCATCGTAGTTTCCCTCCCC 59.531 60.000 0.00 0.00 0.00 4.81
75 76 1.200519 CATCGTAGTTTCCCTCCCCA 58.799 55.000 0.00 0.00 0.00 4.96
76 77 1.557832 CATCGTAGTTTCCCTCCCCAA 59.442 52.381 0.00 0.00 0.00 4.12
83 85 1.514864 TTTCCCTCCCCAATCCCCAC 61.515 60.000 0.00 0.00 0.00 4.61
84 86 3.429580 CCCTCCCCAATCCCCACC 61.430 72.222 0.00 0.00 0.00 4.61
85 87 2.287194 CCTCCCCAATCCCCACCT 60.287 66.667 0.00 0.00 0.00 4.00
88 90 2.616893 CCCCAATCCCCACCTCCA 60.617 66.667 0.00 0.00 0.00 3.86
96 98 1.979809 TCCCCACCTCCAATGTACAT 58.020 50.000 1.41 1.41 0.00 2.29
102 104 3.440173 CCACCTCCAATGTACATTCACAC 59.560 47.826 18.25 0.00 0.00 3.82
110 112 2.073056 TGTACATTCACACGCACCATC 58.927 47.619 0.00 0.00 0.00 3.51
113 115 1.270785 ACATTCACACGCACCATCTCA 60.271 47.619 0.00 0.00 0.00 3.27
114 116 1.805943 CATTCACACGCACCATCTCAA 59.194 47.619 0.00 0.00 0.00 3.02
115 117 1.225855 TTCACACGCACCATCTCAAC 58.774 50.000 0.00 0.00 0.00 3.18
117 119 0.884259 CACACGCACCATCTCAACCA 60.884 55.000 0.00 0.00 0.00 3.67
118 120 0.036732 ACACGCACCATCTCAACCAT 59.963 50.000 0.00 0.00 0.00 3.55
119 121 0.729116 CACGCACCATCTCAACCATC 59.271 55.000 0.00 0.00 0.00 3.51
120 122 0.324614 ACGCACCATCTCAACCATCA 59.675 50.000 0.00 0.00 0.00 3.07
132 134 4.761739 TCTCAACCATCACAGTGATTTTCC 59.238 41.667 13.79 0.00 34.28 3.13
143 145 3.753272 CAGTGATTTTCCCGTGTTGAGAT 59.247 43.478 0.00 0.00 0.00 2.75
179 186 3.864789 ATGGTCATACAATCAGGGGTC 57.135 47.619 0.00 0.00 0.00 4.46
257 264 1.222113 TGGCACGTTCAGTTCCACA 59.778 52.632 0.00 0.00 41.20 4.17
274 281 7.012327 CAGTTCCACACTTTGATGTTCTTCTTA 59.988 37.037 0.00 0.00 30.92 2.10
297 305 0.530211 CGAAGCATGCAGAGGAGAGG 60.530 60.000 21.98 0.00 0.00 3.69
298 306 0.829333 GAAGCATGCAGAGGAGAGGA 59.171 55.000 21.98 0.00 0.00 3.71
299 307 0.831966 AAGCATGCAGAGGAGAGGAG 59.168 55.000 21.98 0.00 0.00 3.69
300 308 0.032316 AGCATGCAGAGGAGAGGAGA 60.032 55.000 21.98 0.00 0.00 3.71
301 309 0.390124 GCATGCAGAGGAGAGGAGAG 59.610 60.000 14.21 0.00 0.00 3.20
395 406 6.665680 ACATGTTATGAGAACTGGTAGAGACT 59.334 38.462 0.00 0.00 0.00 3.24
449 460 6.350103 TGGAAGTGACAAATACAGTACACAA 58.650 36.000 0.00 0.00 0.00 3.33
593 607 2.202395 AGCGTTTGGTGGCTTGCAT 61.202 52.632 0.00 0.00 35.61 3.96
599 613 0.037139 TTGGTGGCTTGCATTGCATC 60.037 50.000 12.95 7.47 38.76 3.91
641 677 1.475280 CATTGCATTCCCTGGTGTCTG 59.525 52.381 0.00 0.00 0.00 3.51
711 747 1.438814 CAGGCCCATTGCGATTTCC 59.561 57.895 0.00 0.00 42.61 3.13
880 916 2.277072 CTCCCCCGCTCTCTCTCA 59.723 66.667 0.00 0.00 0.00 3.27
882 918 3.151022 CCCCCGCTCTCTCTCACC 61.151 72.222 0.00 0.00 0.00 4.02
884 920 2.363018 CCCGCTCTCTCTCACCCA 60.363 66.667 0.00 0.00 0.00 4.51
886 922 1.680651 CCGCTCTCTCTCACCCACT 60.681 63.158 0.00 0.00 0.00 4.00
887 923 1.254284 CCGCTCTCTCTCACCCACTT 61.254 60.000 0.00 0.00 0.00 3.16
908 944 1.838073 TTCTTCTTCCCCACGCCTCC 61.838 60.000 0.00 0.00 0.00 4.30
1738 1838 3.243301 CCGTGCCGTTCTAAGCTAATCTA 60.243 47.826 0.00 0.00 0.00 1.98
1744 1844 5.175856 GCCGTTCTAAGCTAATCTATGTGTG 59.824 44.000 0.00 0.00 0.00 3.82
1746 1846 6.757010 CCGTTCTAAGCTAATCTATGTGTGTT 59.243 38.462 0.00 0.00 0.00 3.32
1748 1848 8.321716 CGTTCTAAGCTAATCTATGTGTGTTTC 58.678 37.037 0.00 0.00 0.00 2.78
1749 1849 9.372369 GTTCTAAGCTAATCTATGTGTGTTTCT 57.628 33.333 0.00 0.00 0.00 2.52
1751 1851 6.992063 AAGCTAATCTATGTGTGTTTCTGG 57.008 37.500 0.00 0.00 0.00 3.86
1752 1852 6.054860 AGCTAATCTATGTGTGTTTCTGGT 57.945 37.500 0.00 0.00 0.00 4.00
1839 1939 3.382111 CTCCAGGTGAGCCGACTT 58.618 61.111 0.00 0.00 40.50 3.01
1856 1956 3.059597 CGACTTTGATGAGCTTTCACGTT 60.060 43.478 0.15 0.00 0.00 3.99
1859 1959 6.371809 ACTTTGATGAGCTTTCACGTTTTA 57.628 33.333 0.15 0.00 0.00 1.52
1863 1963 5.053811 TGATGAGCTTTCACGTTTTAGTCA 58.946 37.500 0.00 0.00 0.00 3.41
1874 1974 4.318071 CACGTTTTAGTCACATGCATTTCG 59.682 41.667 0.00 0.00 0.00 3.46
1954 2054 3.319198 GGGTTCTCGGCCTGTGGA 61.319 66.667 0.00 0.00 0.00 4.02
1963 2068 2.281761 GCCTGTGGAGTGTGTGGG 60.282 66.667 0.00 0.00 0.00 4.61
1964 2069 2.431683 CCTGTGGAGTGTGTGGGG 59.568 66.667 0.00 0.00 0.00 4.96
2007 2112 0.809241 GCTTGGCCTGATCGAGACTG 60.809 60.000 3.32 0.00 0.00 3.51
2071 2176 3.577848 TGGGTTTGATTTGAGGTCAATGG 59.422 43.478 0.00 0.00 35.68 3.16
2078 2183 5.852827 TGATTTGAGGTCAATGGAAAAACC 58.147 37.500 0.00 0.00 35.55 3.27
2104 2209 2.089980 GCCATCTGTCATTCTTGTGCT 58.910 47.619 0.00 0.00 0.00 4.40
2190 2295 1.001406 CTCACCTATGGCCTTCGATCC 59.999 57.143 3.32 0.00 0.00 3.36
2248 2353 6.801539 AGCTTTTCTCGTGTTTGATAATCA 57.198 33.333 0.00 0.00 0.00 2.57
2255 2360 9.863845 TTTCTCGTGTTTGATAATCAGTATGTA 57.136 29.630 0.00 0.00 37.40 2.29
2259 2364 6.073765 CGTGTTTGATAATCAGTATGTAGGCC 60.074 42.308 0.00 0.00 37.40 5.19
2284 2389 4.702612 TGTGATGGTGTTGTACAGTTTGTT 59.297 37.500 0.00 0.00 0.00 2.83
2301 2406 1.908619 TGTTAGCTCTGCCCTCAATCA 59.091 47.619 0.00 0.00 0.00 2.57
2526 2651 9.660180 AATTTTGTTAGTGCACTTTAGGAAAAA 57.340 25.926 27.06 20.53 0.00 1.94
2586 2711 5.605488 TCTGTTACTTCTGGGTTTACCTCTT 59.395 40.000 0.00 0.00 41.11 2.85
2600 2725 3.584406 ACCTCTTGTCTCGAACATCTG 57.416 47.619 2.09 0.00 37.82 2.90
2601 2726 2.232452 ACCTCTTGTCTCGAACATCTGG 59.768 50.000 2.09 6.58 37.82 3.86
2639 2764 7.555195 TCAAGCATGTGAATTGATCTGTTCTAT 59.445 33.333 10.56 4.69 0.00 1.98
2706 2831 4.422506 GCTTCATGCGTGTTCACG 57.577 55.556 19.03 19.03 0.00 4.35
2869 2994 4.837972 AGTTCCTAAGTTCTCAAGCCATC 58.162 43.478 0.00 0.00 0.00 3.51
2927 3052 6.983906 ACTTCTGTTTCCATTTTGAATCCT 57.016 33.333 0.00 0.00 0.00 3.24
2936 3070 6.618287 TCCATTTTGAATCCTATACTTGCG 57.382 37.500 0.00 0.00 0.00 4.85
3097 3231 5.900865 ACTTTGAGCTACTGGTACTAGAC 57.099 43.478 13.86 2.15 0.00 2.59
3110 3244 4.818642 GGTACTAGACCCACTTTCAGTTC 58.181 47.826 0.00 0.00 43.25 3.01
3199 3333 7.413988 GCATACATTACTACACAGAAACATGCA 60.414 37.037 0.00 0.00 34.26 3.96
3219 3353 7.177921 ACATGCATATTTTGATCTCCATAAGGG 59.822 37.037 0.00 0.00 34.83 3.95
3336 3484 3.064931 GTTGAAAGAGAAGTACCACCCG 58.935 50.000 0.00 0.00 0.00 5.28
3918 4252 0.108615 AAGCTCATCCGGTCAGTTCG 60.109 55.000 0.00 0.00 0.00 3.95
4244 4578 2.988493 CTGACAACAAAATTGCCGATGG 59.012 45.455 0.00 0.00 0.00 3.51
4317 4651 3.244561 ACGAAAGACTGGTGAATGGTGAT 60.245 43.478 0.00 0.00 0.00 3.06
4338 4672 7.417911 GGTGATGATCCTCTAGTTGTATTGACA 60.418 40.741 0.00 0.00 0.00 3.58
4473 4807 3.416156 AGTTTTCCATGCTCCTGAGTTC 58.584 45.455 0.00 0.00 0.00 3.01
4807 5141 2.890945 ACAACAAATTAGGACAGGTGCC 59.109 45.455 0.00 0.00 0.00 5.01
5010 5426 7.513190 TTGTTGTCAAAATAACAAAAGGTCG 57.487 32.000 0.00 0.00 41.66 4.79
5041 5457 3.586618 GAGAAGATTGCCTCCCATATCCT 59.413 47.826 0.00 0.00 0.00 3.24
5143 5559 9.906660 TTACATATTACTTCCTGCAAACTTTTG 57.093 29.630 0.00 0.00 41.03 2.44
5356 5773 6.765036 GCAGAATGAGAAGAATACCAGATGAA 59.235 38.462 0.00 0.00 39.69 2.57
5357 5774 7.041916 GCAGAATGAGAAGAATACCAGATGAAG 60.042 40.741 0.00 0.00 39.69 3.02
5358 5775 7.441760 CAGAATGAGAAGAATACCAGATGAAGG 59.558 40.741 0.00 0.00 39.69 3.46
5359 5776 5.028549 TGAGAAGAATACCAGATGAAGGC 57.971 43.478 0.00 0.00 0.00 4.35
5360 5777 4.054671 GAGAAGAATACCAGATGAAGGCG 58.945 47.826 0.00 0.00 0.00 5.52
5361 5778 2.246719 AGAATACCAGATGAAGGCGC 57.753 50.000 0.00 0.00 0.00 6.53
5362 5779 1.765314 AGAATACCAGATGAAGGCGCT 59.235 47.619 7.64 0.00 0.00 5.92
5363 5780 2.171448 AGAATACCAGATGAAGGCGCTT 59.829 45.455 7.64 0.00 0.00 4.68
5364 5781 2.717639 ATACCAGATGAAGGCGCTTT 57.282 45.000 3.65 3.65 0.00 3.51
5365 5782 2.489938 TACCAGATGAAGGCGCTTTT 57.510 45.000 6.11 1.22 0.00 2.27
5366 5783 0.883833 ACCAGATGAAGGCGCTTTTG 59.116 50.000 6.11 0.00 0.00 2.44
5367 5784 1.167851 CCAGATGAAGGCGCTTTTGA 58.832 50.000 6.11 0.00 0.00 2.69
5368 5785 1.747355 CCAGATGAAGGCGCTTTTGAT 59.253 47.619 6.11 1.57 0.00 2.57
5369 5786 2.945008 CCAGATGAAGGCGCTTTTGATA 59.055 45.455 6.11 0.00 0.00 2.15
5370 5787 3.378112 CCAGATGAAGGCGCTTTTGATAA 59.622 43.478 6.11 0.00 0.00 1.75
5518 5959 2.159240 CGTATGAAGTGCAGGCAGAGTA 60.159 50.000 0.00 0.00 0.00 2.59
5569 6010 5.896678 CCATTGGGACCATTTGTTCCTATAA 59.103 40.000 0.00 0.00 43.96 0.98
5792 6233 7.378181 TCCAAAATCTTTATTGAGGTGCTTTC 58.622 34.615 0.00 0.00 0.00 2.62
5807 6248 4.212636 GGTGCTTTCTGTTACATGTAACGT 59.787 41.667 32.75 1.27 46.19 3.99
5850 6291 9.342308 CTGAATTTTATCTTCAGCCCTTGTATA 57.658 33.333 0.58 0.00 42.11 1.47
5885 6326 6.642707 AACAACCGACCATTCTTCATTTAA 57.357 33.333 0.00 0.00 0.00 1.52
5929 6370 5.422145 AGTTTGGCCTCATGCATTTTTATC 58.578 37.500 3.32 0.00 43.89 1.75
5947 6388 1.043816 TCGAGGCTGAGGAATCATCC 58.956 55.000 0.00 0.00 46.98 3.51
5971 6412 3.679980 CACCCTGTTGTATTTCTCACTCG 59.320 47.826 0.00 0.00 0.00 4.18
5974 6415 3.679980 CCTGTTGTATTTCTCACTCGTGG 59.320 47.826 0.00 0.00 0.00 4.94
5975 6416 4.556233 CTGTTGTATTTCTCACTCGTGGA 58.444 43.478 0.00 0.00 0.00 4.02
6026 6469 3.603158 TCTATTTCCACGCTGCACTTA 57.397 42.857 0.00 0.00 0.00 2.24
6060 6503 3.869246 AGTATCGCATAACCTGTTTTCGG 59.131 43.478 0.00 0.00 0.00 4.30
6237 6680 1.668151 GGCAACGACAGACAGGGAC 60.668 63.158 0.00 0.00 0.00 4.46
6297 6740 0.038343 CATTTTCTGCAACACCCCCG 60.038 55.000 0.00 0.00 0.00 5.73
6312 6759 1.681780 CCCCCGCTCAAAATAGCAAGA 60.682 52.381 0.00 0.00 42.91 3.02
6319 6766 6.980397 CCCGCTCAAAATAGCAAGAATTTTAT 59.020 34.615 0.00 0.00 42.91 1.40
6320 6767 7.043192 CCCGCTCAAAATAGCAAGAATTTTATG 60.043 37.037 0.00 0.00 42.91 1.90
6321 6768 7.701924 CCGCTCAAAATAGCAAGAATTTTATGA 59.298 33.333 0.00 0.00 42.91 2.15
6322 6769 8.740369 CGCTCAAAATAGCAAGAATTTTATGAG 58.260 33.333 0.00 0.00 42.91 2.90
6323 6770 9.793252 GCTCAAAATAGCAAGAATTTTATGAGA 57.207 29.630 11.59 0.00 42.30 3.27
6349 6798 1.106351 ACCGTGCTTGTTGGAATGCA 61.106 50.000 0.00 0.00 0.00 3.96
6412 6861 3.858238 GCTCGTATTCACAGTTGGAGTAC 59.142 47.826 0.00 0.00 0.00 2.73
6431 6880 6.342338 AGTACGGAGAACTTCTATGTTTGT 57.658 37.500 0.00 0.00 0.00 2.83
6432 6881 6.756221 AGTACGGAGAACTTCTATGTTTGTT 58.244 36.000 0.00 0.00 0.00 2.83
6433 6882 7.215085 AGTACGGAGAACTTCTATGTTTGTTT 58.785 34.615 0.00 0.00 0.00 2.83
6434 6883 6.300354 ACGGAGAACTTCTATGTTTGTTTG 57.700 37.500 0.00 0.00 0.00 2.93
6435 6884 5.820947 ACGGAGAACTTCTATGTTTGTTTGT 59.179 36.000 0.00 0.00 0.00 2.83
6436 6885 6.987992 ACGGAGAACTTCTATGTTTGTTTGTA 59.012 34.615 0.00 0.00 0.00 2.41
6437 6886 7.042254 ACGGAGAACTTCTATGTTTGTTTGTAC 60.042 37.037 0.00 0.00 0.00 2.90
6495 6951 0.865111 TTGATGTGGTCGTTTGCTCG 59.135 50.000 0.00 0.00 0.00 5.03
6627 7087 3.189287 CCGTAAGAAAAGCATCTTGCAGT 59.811 43.478 12.76 0.00 44.17 4.40
6688 7148 6.490040 TCAATCATTTTCTTCCTCTTTTCCGT 59.510 34.615 0.00 0.00 0.00 4.69
6743 7232 0.884704 GCTGGACTCCACGCTTTTCA 60.885 55.000 10.60 0.00 0.00 2.69
6754 7243 4.038522 TCCACGCTTTTCATTTTTGGATCA 59.961 37.500 0.00 0.00 0.00 2.92
6815 7304 4.764823 ACCGCATTTTCACTAGGATTTTGA 59.235 37.500 0.00 0.00 0.00 2.69
6921 7411 9.357161 ACACACCTAACCAATTATTTGACTTTA 57.643 29.630 0.00 0.00 34.60 1.85
6924 7414 9.716507 CACCTAACCAATTATTTGACTTTATCG 57.283 33.333 0.00 0.00 34.60 2.92
7028 11357 7.776500 TCCATCCATTCCATAATATAGTGCATG 59.224 37.037 0.00 0.00 0.00 4.06
7069 11398 7.621102 GTCAAATTTAGCAAACTTTGACCAAG 58.379 34.615 16.82 0.00 45.88 3.61
7083 11412 8.250143 ACTTTGACCAAGTTTATGGAGAAAAT 57.750 30.769 0.00 0.00 43.89 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.813184 TCGATAGCGACGAAGGGTTT 59.187 50.000 0.00 0.00 42.51 3.27
51 52 2.419713 GGAGGGAAACTACGATGGGTTC 60.420 54.545 0.00 0.00 0.00 3.62
55 56 0.468648 GGGGAGGGAAACTACGATGG 59.531 60.000 0.00 0.00 0.00 3.51
58 59 1.835531 GATTGGGGAGGGAAACTACGA 59.164 52.381 0.00 0.00 0.00 3.43
70 71 2.286885 GGAGGTGGGGATTGGGGA 60.287 66.667 0.00 0.00 0.00 4.81
74 75 2.025416 TGTACATTGGAGGTGGGGATTG 60.025 50.000 0.00 0.00 0.00 2.67
75 76 2.283834 TGTACATTGGAGGTGGGGATT 58.716 47.619 0.00 0.00 0.00 3.01
76 77 1.979809 TGTACATTGGAGGTGGGGAT 58.020 50.000 0.00 0.00 0.00 3.85
83 85 2.095853 GCGTGTGAATGTACATTGGAGG 59.904 50.000 25.42 14.04 32.43 4.30
84 86 2.741517 TGCGTGTGAATGTACATTGGAG 59.258 45.455 25.42 12.40 32.43 3.86
85 87 2.482336 GTGCGTGTGAATGTACATTGGA 59.518 45.455 25.42 9.21 32.43 3.53
88 90 2.499197 TGGTGCGTGTGAATGTACATT 58.501 42.857 20.93 20.93 32.43 2.71
96 98 1.225855 GTTGAGATGGTGCGTGTGAA 58.774 50.000 0.00 0.00 0.00 3.18
102 104 0.729116 GTGATGGTTGAGATGGTGCG 59.271 55.000 0.00 0.00 0.00 5.34
110 112 4.082571 GGGAAAATCACTGTGATGGTTGAG 60.083 45.833 22.91 0.00 37.15 3.02
113 115 2.819608 CGGGAAAATCACTGTGATGGTT 59.180 45.455 22.91 18.88 37.15 3.67
114 116 2.224769 ACGGGAAAATCACTGTGATGGT 60.225 45.455 22.91 14.02 37.15 3.55
115 117 2.162208 CACGGGAAAATCACTGTGATGG 59.838 50.000 22.91 11.04 44.70 3.51
117 119 3.140325 ACACGGGAAAATCACTGTGAT 57.860 42.857 17.24 17.24 44.70 3.06
118 120 2.616376 CAACACGGGAAAATCACTGTGA 59.384 45.455 13.60 13.60 44.70 3.58
119 121 2.616376 TCAACACGGGAAAATCACTGTG 59.384 45.455 0.17 0.17 46.69 3.66
120 122 2.878406 CTCAACACGGGAAAATCACTGT 59.122 45.455 0.00 0.00 0.00 3.55
132 134 3.393800 ACTGTTTCTCATCTCAACACGG 58.606 45.455 0.00 0.00 0.00 4.94
179 186 4.929808 GGTAATCAGTGGTCTTACTGTGTG 59.070 45.833 5.89 0.00 46.32 3.82
192 199 6.566564 GCATACATTTCATCCGGTAATCAGTG 60.567 42.308 0.00 0.00 0.00 3.66
257 264 6.049955 TCGGGATAAGAAGAACATCAAAGT 57.950 37.500 0.00 0.00 0.00 2.66
274 281 1.147824 CCTCTGCATGCTTCGGGAT 59.852 57.895 20.33 0.00 0.00 3.85
374 383 5.163499 CCCAGTCTCTACCAGTTCTCATAAC 60.163 48.000 0.00 0.00 0.00 1.89
395 406 1.694150 CTCTGAACAGAACACTCCCCA 59.306 52.381 6.01 0.00 36.94 4.96
449 460 3.276857 CTCCAGCATGCATACTCACTTT 58.723 45.455 21.98 0.00 31.97 2.66
620 656 0.819582 GACACCAGGGAATGCAATGG 59.180 55.000 0.00 0.00 38.83 3.16
631 667 3.978272 GCTGAAGCAGACACCAGG 58.022 61.111 0.00 0.00 41.59 4.45
641 677 1.470098 ACGAACCAATCATGCTGAAGC 59.530 47.619 0.00 0.00 42.50 3.86
652 688 1.068434 CACAGGGCAAAACGAACCAAT 59.932 47.619 0.00 0.00 0.00 3.16
653 689 0.457851 CACAGGGCAAAACGAACCAA 59.542 50.000 0.00 0.00 0.00 3.67
690 726 1.669999 AAATCGCAATGGGCCTGCTC 61.670 55.000 14.92 0.00 40.31 4.26
880 916 1.705745 GGGGAAGAAGAAGAAGTGGGT 59.294 52.381 0.00 0.00 0.00 4.51
882 918 2.784347 GTGGGGAAGAAGAAGAAGTGG 58.216 52.381 0.00 0.00 0.00 4.00
884 920 1.270893 GCGTGGGGAAGAAGAAGAAGT 60.271 52.381 0.00 0.00 0.00 3.01
886 922 0.036306 GGCGTGGGGAAGAAGAAGAA 59.964 55.000 0.00 0.00 0.00 2.52
887 923 0.836400 AGGCGTGGGGAAGAAGAAGA 60.836 55.000 0.00 0.00 0.00 2.87
908 944 2.124695 GGTTTAGCAGGCGGAGGG 60.125 66.667 0.00 0.00 0.00 4.30
1297 1397 4.501714 GTCGGCGTCCATGCGGTA 62.502 66.667 6.85 0.00 36.64 4.02
1738 1838 0.944386 GCACGACCAGAAACACACAT 59.056 50.000 0.00 0.00 0.00 3.21
1744 1844 2.617274 GCCAGGCACGACCAGAAAC 61.617 63.158 6.55 0.00 43.14 2.78
1746 1846 4.329545 GGCCAGGCACGACCAGAA 62.330 66.667 15.19 0.00 43.14 3.02
1839 1939 5.525745 TGACTAAAACGTGAAAGCTCATCAA 59.474 36.000 3.91 0.00 33.05 2.57
1856 1956 4.759693 AGGTTCGAAATGCATGTGACTAAA 59.240 37.500 0.00 0.00 0.00 1.85
1859 1959 2.485426 CAGGTTCGAAATGCATGTGACT 59.515 45.455 0.00 0.00 0.00 3.41
1863 1963 4.361451 GAATCAGGTTCGAAATGCATGT 57.639 40.909 0.00 0.00 0.00 3.21
1874 1974 2.165437 AGAGACAGAGCGAATCAGGTTC 59.835 50.000 0.00 0.00 0.00 3.62
1954 2054 1.283613 TCTCAAAACACCCCACACACT 59.716 47.619 0.00 0.00 0.00 3.55
1963 2068 3.994392 TCGCTTCACTATCTCAAAACACC 59.006 43.478 0.00 0.00 0.00 4.16
1964 2069 5.786401 ATCGCTTCACTATCTCAAAACAC 57.214 39.130 0.00 0.00 0.00 3.32
2007 2112 0.319728 TCAGCAAGGTCTGACAGCTC 59.680 55.000 15.58 1.21 38.11 4.09
2071 2176 4.051237 GACAGATGGCAAACAGGTTTTTC 58.949 43.478 0.00 0.00 0.00 2.29
2078 2183 4.022589 ACAAGAATGACAGATGGCAAACAG 60.023 41.667 0.00 0.00 36.16 3.16
2104 2209 8.301720 ACATGATAGTTACGTACAAGTCTTTGA 58.698 33.333 0.00 0.00 37.73 2.69
2178 2283 2.272146 GCTTGGGATCGAAGGCCA 59.728 61.111 5.01 0.00 0.00 5.36
2190 2295 0.588252 CTTTCAGGTCACGTGCTTGG 59.412 55.000 11.67 0.47 0.00 3.61
2248 2353 3.777106 CCATCACATGGCCTACATACT 57.223 47.619 3.32 0.00 44.70 2.12
2259 2364 5.214417 CAAACTGTACAACACCATCACATG 58.786 41.667 0.00 0.00 0.00 3.21
2278 2383 2.185004 TGAGGGCAGAGCTAACAAAC 57.815 50.000 0.00 0.00 0.00 2.93
2284 2389 0.461548 CGTGATTGAGGGCAGAGCTA 59.538 55.000 0.00 0.00 0.00 3.32
2395 2517 1.068264 GCCCACAAGTCAAGCTTTAGC 60.068 52.381 0.00 0.00 42.49 3.09
2526 2651 2.065799 ACCACAGGTCTCCCATTTTCT 58.934 47.619 0.00 0.00 0.00 2.52
2586 2711 4.808414 AGAATTCCAGATGTTCGAGACA 57.192 40.909 0.65 3.49 43.71 3.41
2600 2725 7.792374 TCACATGCTTGATACTAAGAATTCC 57.208 36.000 6.60 0.00 0.00 3.01
2628 2753 4.061596 GCAGGCTGGTAATAGAACAGATC 58.938 47.826 17.64 0.00 34.21 2.75
2700 2825 5.120208 ACAGCAAGTAATACATGACGTGAAC 59.880 40.000 0.00 0.00 0.00 3.18
2706 2831 9.708222 CTGAAATAACAGCAAGTAATACATGAC 57.292 33.333 0.00 0.00 0.00 3.06
2791 2916 6.827586 TCGGTTATAAGGCAACAATTTCTT 57.172 33.333 0.00 0.00 41.41 2.52
2927 3052 2.307934 TCACATGCAGCGCAAGTATA 57.692 45.000 11.47 1.68 43.62 1.47
2936 3070 7.021790 CAGAATCATATACAATCACATGCAGC 58.978 38.462 0.00 0.00 0.00 5.25
3110 3244 9.573133 GTTTAATCAATCAATTAGGTGGTTCTG 57.427 33.333 0.00 0.00 0.00 3.02
3148 3282 6.170506 TGTCTTGTATTCATGGTACCTTGTC 58.829 40.000 23.17 14.23 0.00 3.18
3160 3294 9.529325 GTAGTAATGTATGCTGTCTTGTATTCA 57.471 33.333 0.00 0.00 0.00 2.57
3199 3333 9.965902 GTATCACCCTTATGGAGATCAAAATAT 57.034 33.333 0.00 0.00 42.69 1.28
3297 3432 5.181690 TCAACCTGCAATTACAGTCAAAC 57.818 39.130 4.98 0.00 35.83 2.93
3918 4252 3.544285 CAGCTTGAACTCGTCGATACTTC 59.456 47.826 0.00 0.00 0.00 3.01
3931 4265 6.593382 AGAGTTTGATCTATGTCAGCTTGAAC 59.407 38.462 0.00 0.00 0.00 3.18
3981 4315 6.739331 ATGTTTCCAACAATACCCTTTTCA 57.261 33.333 0.00 0.00 45.86 2.69
4317 4651 5.163405 GGCTGTCAATACAACTAGAGGATCA 60.163 44.000 0.00 0.00 33.70 2.92
4338 4672 2.633967 TGCATCAATTTTGTCCTTGGCT 59.366 40.909 0.00 0.00 0.00 4.75
4473 4807 3.433274 TGAGCTTTAGATGCTTGTGAACG 59.567 43.478 0.00 0.00 41.30 3.95
4607 4941 7.262048 ACATCACCTTTTAACACGTTTGAAAT 58.738 30.769 0.00 0.00 0.00 2.17
4737 5071 3.347216 AGCTAAATGTACCAAGCCACTG 58.653 45.455 0.00 0.00 35.54 3.66
4807 5141 2.569059 TGGAGGGAGTATCTACGAACG 58.431 52.381 0.00 0.00 33.73 3.95
4891 5225 7.013942 GGTTTGTCCTAAGTCAAACTGGTAATT 59.986 37.037 16.44 0.00 45.51 1.40
4892 5226 6.489022 GGTTTGTCCTAAGTCAAACTGGTAAT 59.511 38.462 16.44 0.00 45.51 1.89
5010 5426 5.298026 GGGAGGCAATCTTCTCTTTTACATC 59.702 44.000 0.00 0.00 0.00 3.06
5041 5457 7.337167 TGGTTACAAGTAAACTTCAGGTAACA 58.663 34.615 22.71 13.61 40.65 2.41
5356 5773 1.098050 CCTGCTTATCAAAAGCGCCT 58.902 50.000 2.29 0.00 45.80 5.52
5357 5774 0.101219 CCCTGCTTATCAAAAGCGCC 59.899 55.000 2.29 0.00 45.80 6.53
5358 5775 0.811281 ACCCTGCTTATCAAAAGCGC 59.189 50.000 0.00 0.00 45.80 5.92
5359 5776 2.487762 TGAACCCTGCTTATCAAAAGCG 59.512 45.455 5.37 1.13 45.80 4.68
5360 5777 3.758554 TCTGAACCCTGCTTATCAAAAGC 59.241 43.478 2.81 2.81 43.29 3.51
5361 5778 5.678107 GCATCTGAACCCTGCTTATCAAAAG 60.678 44.000 0.00 0.00 33.15 2.27
5362 5779 4.158394 GCATCTGAACCCTGCTTATCAAAA 59.842 41.667 0.00 0.00 33.15 2.44
5363 5780 3.696051 GCATCTGAACCCTGCTTATCAAA 59.304 43.478 0.00 0.00 33.15 2.69
5364 5781 3.282021 GCATCTGAACCCTGCTTATCAA 58.718 45.455 0.00 0.00 33.15 2.57
5365 5782 2.421952 GGCATCTGAACCCTGCTTATCA 60.422 50.000 1.51 0.00 36.18 2.15
5366 5783 2.225467 GGCATCTGAACCCTGCTTATC 58.775 52.381 1.51 0.00 36.18 1.75
5367 5784 1.133668 GGGCATCTGAACCCTGCTTAT 60.134 52.381 10.96 0.00 43.36 1.73
5368 5785 0.255890 GGGCATCTGAACCCTGCTTA 59.744 55.000 10.96 0.00 43.36 3.09
5369 5786 1.000396 GGGCATCTGAACCCTGCTT 60.000 57.895 10.96 0.00 43.36 3.91
5370 5787 2.679716 GGGCATCTGAACCCTGCT 59.320 61.111 10.96 0.00 43.36 4.24
5518 5959 1.203050 ACAAGGGCAGCCAATGTTAGT 60.203 47.619 15.19 0.00 0.00 2.24
5569 6010 0.908910 TGAACGGCCATATCTGGTGT 59.091 50.000 2.24 0.00 45.10 4.16
5792 6233 7.173863 ACAAAAGAGACGTTACATGTAACAG 57.826 36.000 35.70 30.15 44.12 3.16
5807 6248 6.579666 AATTCAGCATAGCAACAAAAGAGA 57.420 33.333 0.00 0.00 0.00 3.10
5850 6291 7.696992 ATGGTCGGTTGTTAAGTATGAAAAT 57.303 32.000 0.00 0.00 0.00 1.82
5947 6388 4.899502 AGTGAGAAATACAACAGGGTGAG 58.100 43.478 0.00 0.00 0.00 3.51
5952 6393 3.679980 CCACGAGTGAGAAATACAACAGG 59.320 47.826 4.59 0.00 0.00 4.00
5971 6412 5.705609 TTTACAGAAGAAATTGCCTCCAC 57.294 39.130 0.00 0.00 0.00 4.02
6026 6469 1.686587 TGCGATACTCATGGAACGGAT 59.313 47.619 0.00 0.00 0.00 4.18
6237 6680 2.821969 CCAGGACTTCACAAAATCCCAG 59.178 50.000 0.00 0.00 30.99 4.45
6297 6740 9.793252 TCTCATAAAATTCTTGCTATTTTGAGC 57.207 29.630 0.00 0.00 43.16 4.26
6312 6759 6.071952 AGCACGGTGACAAATCTCATAAAATT 60.072 34.615 13.29 0.00 0.00 1.82
6319 6766 1.872952 CAAGCACGGTGACAAATCTCA 59.127 47.619 13.29 0.00 0.00 3.27
6320 6767 1.873591 ACAAGCACGGTGACAAATCTC 59.126 47.619 13.29 0.00 0.00 2.75
6321 6768 1.967319 ACAAGCACGGTGACAAATCT 58.033 45.000 13.29 0.00 0.00 2.40
6322 6769 2.384382 CAACAAGCACGGTGACAAATC 58.616 47.619 13.29 0.00 0.00 2.17
6323 6770 1.066908 CCAACAAGCACGGTGACAAAT 59.933 47.619 13.29 0.00 0.00 2.32
6324 6771 0.453793 CCAACAAGCACGGTGACAAA 59.546 50.000 13.29 0.00 0.00 2.83
6327 6774 0.951558 ATTCCAACAAGCACGGTGAC 59.048 50.000 13.29 3.33 0.00 3.67
6328 6775 0.950836 CATTCCAACAAGCACGGTGA 59.049 50.000 13.29 0.00 0.00 4.02
6329 6776 0.664166 GCATTCCAACAAGCACGGTG 60.664 55.000 3.15 3.15 0.00 4.94
6330 6777 1.106351 TGCATTCCAACAAGCACGGT 61.106 50.000 0.00 0.00 31.05 4.83
6349 6798 2.859165 TTTCCAGCTTCTGATTCGGT 57.141 45.000 0.00 0.00 32.44 4.69
6412 6861 6.300354 ACAAACAAACATAGAAGTTCTCCG 57.700 37.500 9.12 4.29 0.00 4.63
6431 6880 6.127591 ACAAACACATGCCTACAAAGTACAAA 60.128 34.615 0.00 0.00 0.00 2.83
6432 6881 5.358442 ACAAACACATGCCTACAAAGTACAA 59.642 36.000 0.00 0.00 0.00 2.41
6433 6882 4.884744 ACAAACACATGCCTACAAAGTACA 59.115 37.500 0.00 0.00 0.00 2.90
6434 6883 5.212194 CACAAACACATGCCTACAAAGTAC 58.788 41.667 0.00 0.00 0.00 2.73
6435 6884 4.277174 CCACAAACACATGCCTACAAAGTA 59.723 41.667 0.00 0.00 0.00 2.24
6436 6885 3.068024 CCACAAACACATGCCTACAAAGT 59.932 43.478 0.00 0.00 0.00 2.66
6437 6886 3.068024 ACCACAAACACATGCCTACAAAG 59.932 43.478 0.00 0.00 0.00 2.77
6495 6951 4.522971 GGCATCACCTTCTCGTCC 57.477 61.111 0.00 0.00 34.51 4.79
6688 7148 5.451908 CAATTCAAAGAAAAGCTGCTACGA 58.548 37.500 0.90 0.00 0.00 3.43
6743 7232 9.927081 ATAGAGTCCAGTTTATGATCCAAAAAT 57.073 29.630 0.00 0.00 0.00 1.82
6754 7243 6.284459 GCTACAAGCATAGAGTCCAGTTTAT 58.716 40.000 0.00 0.00 41.89 1.40
6815 7304 2.703007 AGGAGCGGCTGAGAAAGATTAT 59.297 45.455 7.50 0.00 0.00 1.28
6922 7412 9.483916 TCAAATGTTAATAGAGAAACTTCACGA 57.516 29.630 0.00 0.00 0.00 4.35
6955 11284 9.438228 AAAATTGTCATTGCATCACATTCATTA 57.562 25.926 0.00 0.00 0.00 1.90
6967 11296 4.004196 TGGCATCAAAATTGTCATTGCA 57.996 36.364 11.81 0.00 0.00 4.08
6969 11298 6.548441 AGTTTGGCATCAAAATTGTCATTG 57.452 33.333 0.00 0.00 43.56 2.82


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

AutoCloner maintained by Alex Coulton.