Multiple sequence alignment - TraesCS3D01G171800

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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 TraesCS3D01G171800 chr3D 100.000 4225 0 0 1 4225 152559133 152554909 0.000000e+00 7803
1 TraesCS3D01G171800 chr3D 95.677 694 29 1 1 693 117516107 117515414 0.000000e+00 1114
2 TraesCS3D01G171800 chr3A 93.268 1946 106 9 1456 3398 178131236 178133159 0.000000e+00 2844
3 TraesCS3D01G171800 chr3A 87.979 574 31 17 811 1364 178130607 178131162 0.000000e+00 643
4 TraesCS3D01G171800 chr3A 88.759 427 21 8 3801 4225 178133649 178134050 8.160000e-137 497
5 TraesCS3D01G171800 chr3A 89.242 409 26 3 3394 3802 178133235 178133625 2.930000e-136 496
6 TraesCS3D01G171800 chr3A 88.298 94 4 1 691 777 178129958 178130051 5.780000e-19 106
7 TraesCS3D01G171800 chr3B 93.487 1735 91 10 1666 3398 223038039 223036325 0.000000e+00 2558
8 TraesCS3D01G171800 chr3B 82.274 1038 63 37 719 1671 223039090 223038089 0.000000e+00 785
9 TraesCS3D01G171800 chr3B 90.602 415 27 7 3394 3805 223036217 223035812 1.340000e-149 540
10 TraesCS3D01G171800 chr3B 96.970 231 7 0 3995 4225 223035622 223035392 5.120000e-104 388
11 TraesCS3D01G171800 chr3B 95.312 192 8 1 3801 3991 223035791 223035600 1.910000e-78 303
12 TraesCS3D01G171800 chr3B 82.278 158 23 5 3534 3689 640671997 640671843 9.530000e-27 132
13 TraesCS3D01G171800 chr3B 82.166 157 22 6 3534 3688 647175912 647176064 3.430000e-26 130
14 TraesCS3D01G171800 chr6D 96.676 692 20 2 1 691 10675182 10674493 0.000000e+00 1147
15 TraesCS3D01G171800 chr4D 95.435 701 22 4 1 693 81327666 81326968 0.000000e+00 1109
16 TraesCS3D01G171800 chr7D 94.864 701 26 4 1 691 630613183 630612483 0.000000e+00 1086
17 TraesCS3D01G171800 chr7D 94.437 701 29 4 1 693 474004137 474004835 0.000000e+00 1070
18 TraesCS3D01G171800 chr7D 89.216 102 11 0 4124 4225 535728030 535727929 1.230000e-25 128
19 TraesCS3D01G171800 chr1D 94.971 696 30 4 1 691 425565422 425564727 0.000000e+00 1086
20 TraesCS3D01G171800 chr1D 94.564 699 28 5 1 691 334053878 334053182 0.000000e+00 1072
21 TraesCS3D01G171800 chr1D 84.034 119 14 4 3533 3651 100313846 100313959 4.470000e-20 110
22 TraesCS3D01G171800 chr2D 94.587 702 28 5 1 693 525939163 525939863 0.000000e+00 1077
23 TraesCS3D01G171800 chr2D 94.294 701 30 3 1 691 563966499 563965799 0.000000e+00 1064
24 TraesCS3D01G171800 chr4B 86.585 164 19 3 3526 3688 22464772 22464611 1.210000e-40 178
25 TraesCS3D01G171800 chr7A 87.179 156 17 3 3534 3688 579808374 579808527 1.560000e-39 174
26 TraesCS3D01G171800 chr5A 85.417 144 18 3 3534 3676 556687382 556687523 3.400000e-31 147
27 TraesCS3D01G171800 chr7B 90.196 102 10 0 4124 4225 577563655 577563554 2.650000e-27 134
28 TraesCS3D01G171800 chr5B 81.250 160 25 5 3534 3691 405561798 405561954 1.600000e-24 124


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 TraesCS3D01G171800 chr3D 152554909 152559133 4224 True 7803.0 7803 100.0000 1 4225 1 chr3D.!!$R2 4224
1 TraesCS3D01G171800 chr3D 117515414 117516107 693 True 1114.0 1114 95.6770 1 693 1 chr3D.!!$R1 692
2 TraesCS3D01G171800 chr3A 178129958 178134050 4092 False 917.2 2844 89.5092 691 4225 5 chr3A.!!$F1 3534
3 TraesCS3D01G171800 chr3B 223035392 223039090 3698 True 914.8 2558 91.7290 719 4225 5 chr3B.!!$R2 3506
4 TraesCS3D01G171800 chr6D 10674493 10675182 689 True 1147.0 1147 96.6760 1 691 1 chr6D.!!$R1 690
5 TraesCS3D01G171800 chr4D 81326968 81327666 698 True 1109.0 1109 95.4350 1 693 1 chr4D.!!$R1 692
6 TraesCS3D01G171800 chr7D 630612483 630613183 700 True 1086.0 1086 94.8640 1 691 1 chr7D.!!$R2 690
7 TraesCS3D01G171800 chr7D 474004137 474004835 698 False 1070.0 1070 94.4370 1 693 1 chr7D.!!$F1 692
8 TraesCS3D01G171800 chr1D 425564727 425565422 695 True 1086.0 1086 94.9710 1 691 1 chr1D.!!$R2 690
9 TraesCS3D01G171800 chr1D 334053182 334053878 696 True 1072.0 1072 94.5640 1 691 1 chr1D.!!$R1 690
10 TraesCS3D01G171800 chr2D 525939163 525939863 700 False 1077.0 1077 94.5870 1 693 1 chr2D.!!$F1 692
11 TraesCS3D01G171800 chr2D 563965799 563966499 700 True 1064.0 1064 94.2940 1 691 1 chr2D.!!$R1 690

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
167 168 0.103026 TCATCGAGAATGAGCGTGGG 59.897 55.0 0.00 0.0 39.52 4.61 F
563 571 0.940519 GCATTTTTGCGCACTGCTGA 60.941 50.0 11.12 0.0 46.63 4.26 F
1371 1961 0.099968 CGCTGAAATGCCCACTCATG 59.900 55.0 0.00 0.0 0.00 3.07 F
1515 2142 0.110295 TGGTTGGCATCGATATGGGG 59.890 55.0 0.00 0.0 33.38 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1942 0.099968 CATGAGTGGGCATTTCAGCG 59.900 55.000 0.00 0.00 34.64 5.18 R
1374 1964 0.318762 GCGAGGCGAGAAATAGGGAT 59.681 55.000 0.00 0.00 0.00 3.85 R
3065 3752 1.178276 TCACAAAAACCTTGGCACGT 58.822 45.000 0.00 0.00 0.00 4.49 R
3446 4247 2.005451 AGAACTTGCATCGCATGTCTC 58.995 47.619 7.81 7.95 44.18 3.36 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
43 44 4.630644 AAGATGTGGAGAGAGCTTTTGA 57.369 40.909 0.00 0.00 0.00 2.69
73 74 3.874392 AGCCCAATTTGCTATTGTGAC 57.126 42.857 10.03 1.89 37.28 3.67
167 168 0.103026 TCATCGAGAATGAGCGTGGG 59.897 55.000 0.00 0.00 39.52 4.61
528 534 3.618150 GGAATGCATATGTTGTTTGTGCC 59.382 43.478 0.00 0.00 35.03 5.01
563 571 0.940519 GCATTTTTGCGCACTGCTGA 60.941 50.000 11.12 0.00 46.63 4.26
698 713 3.119245 TGTTGGAGATGCTCTAACCGTAC 60.119 47.826 17.28 0.00 46.56 3.67
866 1413 6.367969 TCGTAATAAGCAGACAAAAGAGGTTC 59.632 38.462 0.00 0.00 0.00 3.62
1011 1577 3.876198 CCGCTAATGCACCGCCAC 61.876 66.667 0.00 0.00 39.64 5.01
1012 1578 2.819595 CGCTAATGCACCGCCACT 60.820 61.111 0.00 0.00 39.64 4.00
1013 1579 2.813179 CGCTAATGCACCGCCACTC 61.813 63.158 0.00 0.00 39.64 3.51
1157 1729 2.540910 TCCCACTCCCTCCTCCCT 60.541 66.667 0.00 0.00 0.00 4.20
1158 1730 2.184631 TCCCACTCCCTCCTCCCTT 61.185 63.158 0.00 0.00 0.00 3.95
1244 1819 1.004320 TAACAATCTGCGTGCGGGT 60.004 52.632 0.03 0.00 0.00 5.28
1251 1826 1.743623 CTGCGTGCGGGTTATTCCA 60.744 57.895 0.00 0.00 38.11 3.53
1262 1837 4.879545 GCGGGTTATTCCAAATCTGAACTA 59.120 41.667 0.00 0.00 38.11 2.24
1277 1852 6.951256 TCTGAACTATGTCGTCTTGATTTG 57.049 37.500 0.00 0.00 0.00 2.32
1340 1930 3.423154 CGTCAAAGCCACCCTCGC 61.423 66.667 0.00 0.00 0.00 5.03
1341 1931 2.032681 GTCAAAGCCACCCTCGCT 59.967 61.111 0.00 0.00 38.53 4.93
1351 1941 4.803426 CCCTCGCTGTCTGCCGTC 62.803 72.222 0.00 0.00 38.78 4.79
1352 1942 4.803426 CCTCGCTGTCTGCCGTCC 62.803 72.222 0.00 0.00 38.78 4.79
1364 1954 3.508840 CCGTCCGCTGAAATGCCC 61.509 66.667 0.00 0.00 0.00 5.36
1365 1955 2.745884 CGTCCGCTGAAATGCCCA 60.746 61.111 0.00 0.00 0.00 5.36
1368 1958 1.377202 TCCGCTGAAATGCCCACTC 60.377 57.895 0.00 0.00 0.00 3.51
1369 1959 1.675310 CCGCTGAAATGCCCACTCA 60.675 57.895 0.00 0.00 0.00 3.41
1370 1960 1.033746 CCGCTGAAATGCCCACTCAT 61.034 55.000 0.00 0.00 0.00 2.90
1371 1961 0.099968 CGCTGAAATGCCCACTCATG 59.900 55.000 0.00 0.00 0.00 3.07
1373 1963 1.547372 GCTGAAATGCCCACTCATGTT 59.453 47.619 0.00 0.00 0.00 2.71
1374 1964 2.754552 GCTGAAATGCCCACTCATGTTA 59.245 45.455 0.00 0.00 0.00 2.41
1375 1965 3.382546 GCTGAAATGCCCACTCATGTTAT 59.617 43.478 0.00 0.00 0.00 1.89
1376 1966 4.498682 GCTGAAATGCCCACTCATGTTATC 60.499 45.833 0.00 0.00 0.00 1.75
1380 2000 2.770447 TGCCCACTCATGTTATCCCTA 58.230 47.619 0.00 0.00 0.00 3.53
1417 2037 4.489810 CTCTGTCGAAGCTGAAATACTGT 58.510 43.478 0.00 0.00 0.00 3.55
1422 2042 4.092091 GTCGAAGCTGAAATACTGTCTTGG 59.908 45.833 0.00 0.00 0.00 3.61
1423 2043 3.181516 CGAAGCTGAAATACTGTCTTGGC 60.182 47.826 0.00 0.00 0.00 4.52
1424 2044 2.716217 AGCTGAAATACTGTCTTGGCC 58.284 47.619 0.00 0.00 0.00 5.36
1425 2045 1.398390 GCTGAAATACTGTCTTGGCCG 59.602 52.381 0.00 0.00 0.00 6.13
1426 2046 2.699954 CTGAAATACTGTCTTGGCCGT 58.300 47.619 0.00 0.00 0.00 5.68
1428 2048 1.737793 GAAATACTGTCTTGGCCGTGG 59.262 52.381 0.00 0.00 0.00 4.94
1453 2080 4.887071 TGTCTATCTTGCCTGTTGTTTTGT 59.113 37.500 0.00 0.00 0.00 2.83
1468 2095 2.687935 GTTTTGTTTGAGTCAGCTGGGA 59.312 45.455 15.13 0.00 0.00 4.37
1507 2134 4.377370 TGACACTGGTTGGCATCG 57.623 55.556 0.00 0.00 38.87 3.84
1515 2142 0.110295 TGGTTGGCATCGATATGGGG 59.890 55.000 0.00 0.00 33.38 4.96
1606 2236 2.180946 TCAGGCCCTATGAGTGTGAT 57.819 50.000 0.00 0.00 0.00 3.06
1609 2239 3.834813 TCAGGCCCTATGAGTGTGATATC 59.165 47.826 0.00 0.00 0.00 1.63
1625 2255 4.752101 GTGATATCGGATCCTGTTCAAAGG 59.248 45.833 10.75 0.00 38.84 3.11
1690 2375 7.978982 ACAGTGTACTTGATCAAAATAGATGC 58.021 34.615 9.88 0.00 0.00 3.91
1704 2389 9.974980 TCAAAATAGATGCGACATGTTATACTA 57.025 29.630 0.00 1.83 0.00 1.82
1767 2453 4.889995 AGCCCTATAGGATTTCTTTTGTGC 59.110 41.667 21.07 9.94 38.24 4.57
1808 2494 9.530129 CAGTGTCGATGTTTTACTCTAAATTTC 57.470 33.333 0.00 0.00 0.00 2.17
1811 2497 9.226606 TGTCGATGTTTTACTCTAAATTTCCAT 57.773 29.630 0.00 0.00 0.00 3.41
1850 2537 6.542005 TGAGTGTAGAAAGCATGTTTTTCTCA 59.458 34.615 22.35 18.64 42.30 3.27
1859 2546 4.037208 AGCATGTTTTTCTCACTGGTCAAG 59.963 41.667 0.00 0.00 0.00 3.02
1861 2548 2.687935 TGTTTTTCTCACTGGTCAAGGC 59.312 45.455 0.00 0.00 0.00 4.35
1865 2552 1.673665 CTCACTGGTCAAGGCTGCC 60.674 63.158 11.65 11.65 0.00 4.85
1946 2633 6.146510 TGCCACGTTAGACTTTATTAGTTGTG 59.853 38.462 0.00 0.00 37.17 3.33
1970 2657 1.399440 CAGGGAATTGTGTCATGAGCG 59.601 52.381 0.00 0.00 0.00 5.03
1971 2658 1.003580 AGGGAATTGTGTCATGAGCGT 59.996 47.619 0.00 0.00 0.00 5.07
1972 2659 1.131126 GGGAATTGTGTCATGAGCGTG 59.869 52.381 0.00 0.00 0.00 5.34
1973 2660 1.806542 GGAATTGTGTCATGAGCGTGT 59.193 47.619 0.00 0.00 0.00 4.49
1974 2661 2.159653 GGAATTGTGTCATGAGCGTGTC 60.160 50.000 0.00 0.00 0.00 3.67
1975 2662 2.168326 ATTGTGTCATGAGCGTGTCA 57.832 45.000 0.00 0.00 40.38 3.58
1998 2685 6.992715 TCATGAGCTTTTAAGGCCTTAGTATC 59.007 38.462 23.96 17.94 0.00 2.24
2000 2687 6.113411 TGAGCTTTTAAGGCCTTAGTATCAC 58.887 40.000 23.96 15.72 0.00 3.06
2055 2742 0.322816 TGGCATGGTTCTTGCTCTCC 60.323 55.000 0.00 0.00 40.03 3.71
2067 2754 7.615365 TGGTTCTTGCTCTCCATATAATTTGTT 59.385 33.333 0.00 0.00 0.00 2.83
2150 2837 8.707796 AGGAGTGTTATTCTTCCGATATCTTA 57.292 34.615 0.34 0.00 0.00 2.10
2211 2898 3.066380 GCCATGCCTTTTTACAACAAGG 58.934 45.455 3.04 3.04 42.39 3.61
2226 2913 4.202315 ACAACAAGGCTAGTGATGTGTGTA 60.202 41.667 1.80 0.00 31.56 2.90
2237 2924 6.201226 AGTGATGTGTGTAGTACTGATGAG 57.799 41.667 5.39 0.00 0.00 2.90
2288 2975 5.774690 TCCCAACTACAGAAGAATTGCAATT 59.225 36.000 24.33 24.33 0.00 2.32
2306 2993 4.558178 CAATTTCATGTTTAGTGCAGGCA 58.442 39.130 0.00 0.00 0.00 4.75
2497 3184 1.414181 CTGGATAATGCGGAGACCTGT 59.586 52.381 0.00 0.00 0.00 4.00
2687 3374 3.255017 CAACAATGTGTGCGTTGCT 57.745 47.368 0.00 0.00 43.49 3.91
2714 3401 2.579201 CTAGGGGCCGGATATGCG 59.421 66.667 5.05 9.98 0.00 4.73
2765 3452 2.541556 GGAGTCTTCGTAGAATGCCAC 58.458 52.381 0.00 0.00 45.90 5.01
2834 3521 4.188247 TCAGGATAAAGTCGACAAGGTG 57.812 45.455 19.50 5.69 0.00 4.00
2872 3559 3.181967 CAGCTCTTCGAACGCCGG 61.182 66.667 0.00 0.00 39.14 6.13
2878 3565 0.320073 TCTTCGAACGCCGGTGAAAT 60.320 50.000 24.59 7.26 39.14 2.17
2892 3579 2.084546 GTGAAATTTCTCACCCGGGAG 58.915 52.381 32.02 21.98 39.93 4.30
2909 3596 1.279558 GGAGAGAAGGGGGAAACTGTC 59.720 57.143 0.00 0.00 0.00 3.51
2927 3614 5.792741 ACTGTCTCTGAAATTGGAGAAGAG 58.207 41.667 7.36 8.64 39.81 2.85
2960 3647 1.077429 GGTGAAGAGATGGGTGCCC 60.077 63.158 0.00 0.00 0.00 5.36
3002 3689 3.242123 GCGACTACATTTGCTGCTTCTAC 60.242 47.826 0.00 0.00 0.00 2.59
3023 3710 1.876497 TTGACCGTAGTGGCGTACCC 61.876 60.000 0.00 0.00 43.94 3.69
3035 3722 0.320073 GCGTACCCACTGTTACTGCA 60.320 55.000 0.00 0.00 0.00 4.41
3044 3731 1.341531 ACTGTTACTGCAGAGAAGCGT 59.658 47.619 23.35 10.35 39.62 5.07
3059 3746 4.082523 CGTGGCGATGGTCACCCT 62.083 66.667 6.89 0.00 46.04 4.34
3065 3752 2.659063 CGATGGTCACCCTGAGGCA 61.659 63.158 0.00 0.00 36.11 4.75
3089 3776 2.170187 TGCCAAGGTTTTTGTGATTGCT 59.830 40.909 0.00 0.00 0.00 3.91
3095 3782 5.869649 AGGTTTTTGTGATTGCTAAAGGT 57.130 34.783 0.00 0.00 0.00 3.50
3098 3785 5.221441 GGTTTTTGTGATTGCTAAAGGTCCT 60.221 40.000 0.00 0.00 0.00 3.85
3104 3791 5.003804 GTGATTGCTAAAGGTCCTCAGAAA 58.996 41.667 0.00 0.00 0.00 2.52
3235 3922 5.466058 TGAAAGAAACGTAGCGAAACCAATA 59.534 36.000 0.00 0.00 0.00 1.90
3276 3963 3.321497 CTGTTGTCTCCTGTTCTGTAGC 58.679 50.000 0.00 0.00 0.00 3.58
3283 3970 4.021368 GTCTCCTGTTCTGTAGCCAAGTAA 60.021 45.833 0.00 0.00 0.00 2.24
3284 3971 4.591498 TCTCCTGTTCTGTAGCCAAGTAAA 59.409 41.667 0.00 0.00 0.00 2.01
3296 3984 7.645402 TGTAGCCAAGTAAACTTTTAAAGCTC 58.355 34.615 4.42 0.00 33.11 4.09
3337 4025 5.686753 TCCTGCAAACCTTTTAGTCAGTTA 58.313 37.500 0.00 0.00 0.00 2.24
3342 4030 6.134061 GCAAACCTTTTAGTCAGTTAACTCG 58.866 40.000 4.77 2.02 0.00 4.18
3343 4031 6.238293 GCAAACCTTTTAGTCAGTTAACTCGT 60.238 38.462 4.77 0.00 0.00 4.18
3344 4032 7.042523 GCAAACCTTTTAGTCAGTTAACTCGTA 60.043 37.037 4.77 0.00 0.00 3.43
3345 4033 8.985805 CAAACCTTTTAGTCAGTTAACTCGTAT 58.014 33.333 4.77 0.00 0.00 3.06
3346 4034 8.754230 AACCTTTTAGTCAGTTAACTCGTATC 57.246 34.615 4.77 0.00 0.00 2.24
3433 4234 2.159014 AGGCGTTCTACTGTTGTGTTGA 60.159 45.455 0.00 0.00 0.00 3.18
3454 4255 2.894387 GCCTCTGGCGAGACATGC 60.894 66.667 0.00 0.00 39.62 4.06
3455 4256 2.584418 CCTCTGGCGAGACATGCG 60.584 66.667 0.00 0.00 39.74 4.73
3474 4275 3.306973 TGCGATGCAAGTTCTCTTTATCG 59.693 43.478 14.36 14.36 43.34 2.92
3524 4327 8.877864 ATTCAGAACCATAATACAAGGAAACA 57.122 30.769 0.00 0.00 0.00 2.83
3553 4356 2.474410 ACTCCCTCCGTTCACAAATC 57.526 50.000 0.00 0.00 0.00 2.17
3557 4360 4.122776 CTCCCTCCGTTCACAAATCATAG 58.877 47.826 0.00 0.00 0.00 2.23
3569 4372 8.398665 GTTCACAAATCATAGGATGTTCTAACC 58.601 37.037 0.00 0.00 32.92 2.85
3599 4403 6.263754 TCTGAATCAGATGTATATAGGCCCA 58.736 40.000 9.18 0.00 35.39 5.36
3626 4430 4.202441 AGTGTGCTTGTTCACTCATTTCT 58.798 39.130 0.00 0.00 40.28 2.52
3629 4433 4.035558 TGTGCTTGTTCACTCATTTCTGTC 59.964 41.667 0.00 0.00 37.81 3.51
3663 4467 9.479549 AGTTCATATTGAAATACCCTGAACATT 57.520 29.630 19.93 7.06 39.03 2.71
3704 4508 4.702131 GGGAGTAGAACCGTAAGAACTGTA 59.298 45.833 0.00 0.00 43.02 2.74
3717 4533 4.685169 AGAACTGTAATTTGTGGCATCG 57.315 40.909 0.00 0.00 0.00 3.84
3718 4534 4.323417 AGAACTGTAATTTGTGGCATCGA 58.677 39.130 0.00 0.00 0.00 3.59
3719 4535 4.943705 AGAACTGTAATTTGTGGCATCGAT 59.056 37.500 0.00 0.00 0.00 3.59
3720 4536 4.882671 ACTGTAATTTGTGGCATCGATC 57.117 40.909 0.00 0.00 0.00 3.69
3721 4537 3.627577 ACTGTAATTTGTGGCATCGATCC 59.372 43.478 0.00 0.59 0.00 3.36
3722 4538 2.948979 TGTAATTTGTGGCATCGATCCC 59.051 45.455 0.00 0.00 0.00 3.85
3723 4539 1.402787 AATTTGTGGCATCGATCCCC 58.597 50.000 2.06 3.76 0.00 4.81
3724 4540 0.468029 ATTTGTGGCATCGATCCCCC 60.468 55.000 2.06 1.10 0.00 5.40
3725 4541 1.857638 TTTGTGGCATCGATCCCCCA 61.858 55.000 2.06 3.91 0.00 4.96
3726 4542 1.857638 TTGTGGCATCGATCCCCCAA 61.858 55.000 2.06 0.10 0.00 4.12
3727 4543 1.151450 GTGGCATCGATCCCCCAAT 59.849 57.895 2.06 0.00 0.00 3.16
3728 4544 0.890996 GTGGCATCGATCCCCCAATC 60.891 60.000 2.06 0.00 0.00 2.67
3775 4591 1.147473 TGCAGATGTACAAGTGCGTG 58.853 50.000 21.41 6.69 38.84 5.34
3821 4663 1.047002 CAATGGTGGTTCCTTTGGCA 58.953 50.000 0.00 0.00 43.40 4.92
3916 4760 5.828747 TGCTAGTACAGTATAAGAAAGCCG 58.171 41.667 0.00 0.00 0.00 5.52
3979 4824 6.680810 TCAAGGTTATTTGAGCATTCACAAG 58.319 36.000 0.00 0.00 32.39 3.16
3980 4825 5.649782 AGGTTATTTGAGCATTCACAAGG 57.350 39.130 0.00 0.00 31.71 3.61
3981 4826 4.082026 AGGTTATTTGAGCATTCACAAGGC 60.082 41.667 0.00 0.00 38.73 4.35
3982 4827 4.321899 GGTTATTTGAGCATTCACAAGGCA 60.322 41.667 0.00 0.00 41.41 4.75
3983 4828 5.229423 GTTATTTGAGCATTCACAAGGCAA 58.771 37.500 0.00 0.00 41.41 4.52
3984 4829 3.374220 TTTGAGCATTCACAAGGCAAG 57.626 42.857 0.00 0.00 41.41 4.01
3985 4830 1.250328 TGAGCATTCACAAGGCAAGG 58.750 50.000 0.00 0.00 41.41 3.61
3986 4831 1.251251 GAGCATTCACAAGGCAAGGT 58.749 50.000 0.00 0.00 41.41 3.50
3987 4832 2.224744 TGAGCATTCACAAGGCAAGGTA 60.225 45.455 0.00 0.00 41.41 3.08
3988 4833 2.421424 GAGCATTCACAAGGCAAGGTAG 59.579 50.000 0.00 0.00 41.41 3.18
3989 4834 2.162681 GCATTCACAAGGCAAGGTAGT 58.837 47.619 0.00 0.00 38.24 2.73
3990 4835 2.162408 GCATTCACAAGGCAAGGTAGTC 59.838 50.000 0.00 0.00 38.24 2.59
3991 4836 2.561478 TTCACAAGGCAAGGTAGTCC 57.439 50.000 0.00 0.00 0.00 3.85
3992 4837 0.690762 TCACAAGGCAAGGTAGTCCC 59.309 55.000 0.00 0.00 0.00 4.46
3993 4838 0.400213 CACAAGGCAAGGTAGTCCCA 59.600 55.000 0.00 0.00 34.66 4.37
3994 4839 1.145571 ACAAGGCAAGGTAGTCCCAA 58.854 50.000 0.00 0.00 34.66 4.12
3995 4840 1.073923 ACAAGGCAAGGTAGTCCCAAG 59.926 52.381 0.00 0.00 34.66 3.61
3996 4841 0.038310 AAGGCAAGGTAGTCCCAAGC 59.962 55.000 0.00 0.00 35.27 4.01
3997 4842 1.133809 AGGCAAGGTAGTCCCAAGCA 61.134 55.000 0.00 0.00 37.09 3.91
3998 4843 0.034089 GGCAAGGTAGTCCCAAGCAT 60.034 55.000 0.00 0.00 37.09 3.79
3999 4844 1.098050 GCAAGGTAGTCCCAAGCATG 58.902 55.000 0.00 0.00 35.86 4.06
4000 4845 1.098050 CAAGGTAGTCCCAAGCATGC 58.902 55.000 10.51 10.51 34.66 4.06
4001 4846 0.698238 AAGGTAGTCCCAAGCATGCA 59.302 50.000 21.98 0.00 34.66 3.96
4002 4847 0.035056 AGGTAGTCCCAAGCATGCAC 60.035 55.000 21.98 8.85 34.66 4.57
4003 4848 0.322456 GGTAGTCCCAAGCATGCACA 60.322 55.000 21.98 0.00 0.00 4.57
4004 4849 1.533625 GTAGTCCCAAGCATGCACAA 58.466 50.000 21.98 0.00 0.00 3.33
4052 4897 5.766150 TTTGTGACCATAACAAGGACTTG 57.234 39.130 10.34 10.34 45.58 3.16
4067 4912 3.077359 GGACTTGGTTCTCCTTGTCATG 58.923 50.000 0.00 0.00 37.89 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.815503 GCAAATTGGGCTTGCAAAATCT 59.184 40.909 0.00 0.00 46.78 2.40
73 74 1.668419 CCAAAATCTAGCCGGTCCTG 58.332 55.000 1.90 0.00 0.00 3.86
167 168 5.828299 ACTGAGAGTAGTCTACATCTTGC 57.172 43.478 12.54 3.16 30.97 4.01
226 227 3.984732 GGGCCACCCTTTCAGCCT 61.985 66.667 4.39 0.00 45.07 4.58
470 476 9.776451 GCAAAAAGATCAAACAAAAACAAAAAC 57.224 25.926 0.00 0.00 0.00 2.43
480 486 7.903995 AAACAGAAGCAAAAAGATCAAACAA 57.096 28.000 0.00 0.00 0.00 2.83
577 591 2.358737 AGCAGCCGCGCTAAAAGT 60.359 55.556 5.56 0.00 45.49 2.66
618 633 0.457166 CGCGTCCATCGTCTGGTTTA 60.457 55.000 0.00 0.00 46.08 2.01
633 648 2.317685 AAAACTGCTTTGTCGCGCGT 62.318 50.000 30.98 3.31 0.00 6.01
866 1413 2.416547 CCACTGGTCATTTCTTACTGCG 59.583 50.000 0.00 0.00 0.00 5.18
1170 1745 1.868109 GCTATCGTGCCATGCGTTCTA 60.868 52.381 0.00 0.00 0.00 2.10
1213 1788 2.991190 AGATTGTTACCAACAGTACGCG 59.009 45.455 3.53 3.53 43.27 6.01
1214 1789 3.424433 GCAGATTGTTACCAACAGTACGC 60.424 47.826 0.00 0.00 43.27 4.42
1215 1790 3.181534 CGCAGATTGTTACCAACAGTACG 60.182 47.826 0.00 0.00 43.27 3.67
1216 1791 3.744426 ACGCAGATTGTTACCAACAGTAC 59.256 43.478 0.00 0.00 43.27 2.73
1217 1792 3.743911 CACGCAGATTGTTACCAACAGTA 59.256 43.478 0.00 0.00 43.27 2.74
1218 1793 2.548057 CACGCAGATTGTTACCAACAGT 59.452 45.455 0.00 0.00 43.27 3.55
1236 1811 2.014128 AGATTTGGAATAACCCGCACG 58.986 47.619 0.00 0.00 38.00 5.34
1244 1819 8.258007 AGACGACATAGTTCAGATTTGGAATAA 58.742 33.333 0.00 0.00 0.00 1.40
1251 1826 8.446273 CAAATCAAGACGACATAGTTCAGATTT 58.554 33.333 0.00 0.00 33.01 2.17
1277 1852 2.808906 ATCCCCAAACCTAGACTTGC 57.191 50.000 0.00 0.00 0.00 4.01
1351 1941 1.033746 ATGAGTGGGCATTTCAGCGG 61.034 55.000 0.00 0.00 34.64 5.52
1352 1942 0.099968 CATGAGTGGGCATTTCAGCG 59.900 55.000 0.00 0.00 34.64 5.18
1364 1954 5.406780 GCGAGAAATAGGGATAACATGAGTG 59.593 44.000 0.00 0.00 0.00 3.51
1365 1955 5.511545 GGCGAGAAATAGGGATAACATGAGT 60.512 44.000 0.00 0.00 0.00 3.41
1368 1958 4.899502 AGGCGAGAAATAGGGATAACATG 58.100 43.478 0.00 0.00 0.00 3.21
1369 1959 4.322049 CGAGGCGAGAAATAGGGATAACAT 60.322 45.833 0.00 0.00 0.00 2.71
1370 1960 3.005472 CGAGGCGAGAAATAGGGATAACA 59.995 47.826 0.00 0.00 0.00 2.41
1371 1961 3.576648 CGAGGCGAGAAATAGGGATAAC 58.423 50.000 0.00 0.00 0.00 1.89
1373 1963 1.544691 GCGAGGCGAGAAATAGGGATA 59.455 52.381 0.00 0.00 0.00 2.59
1374 1964 0.318762 GCGAGGCGAGAAATAGGGAT 59.681 55.000 0.00 0.00 0.00 3.85
1375 1965 1.740285 GCGAGGCGAGAAATAGGGA 59.260 57.895 0.00 0.00 0.00 4.20
1376 1966 1.301009 GGCGAGGCGAGAAATAGGG 60.301 63.158 0.00 0.00 0.00 3.53
1380 2000 2.060980 AGAGGGCGAGGCGAGAAAT 61.061 57.895 0.00 0.00 0.00 2.17
1417 2037 1.264749 ATAGACAGCCACGGCCAAGA 61.265 55.000 2.24 0.00 43.17 3.02
1422 2042 1.432270 GCAAGATAGACAGCCACGGC 61.432 60.000 0.00 0.00 42.33 5.68
1423 2043 0.811616 GGCAAGATAGACAGCCACGG 60.812 60.000 0.00 0.00 46.26 4.94
1424 2044 2.682893 GGCAAGATAGACAGCCACG 58.317 57.895 0.00 0.00 46.26 4.94
1428 2048 2.704572 ACAACAGGCAAGATAGACAGC 58.295 47.619 0.00 0.00 0.00 4.40
1453 2080 0.401356 TGCATCCCAGCTGACTCAAA 59.599 50.000 17.39 0.00 34.99 2.69
1468 2095 2.593346 TGAAACAACGCCTTTTGCAT 57.407 40.000 0.00 0.00 41.33 3.96
1479 2106 5.460646 CCAACCAGTGTCATATGAAACAAC 58.539 41.667 24.75 13.06 34.73 3.32
1488 2115 1.552792 TCGATGCCAACCAGTGTCATA 59.447 47.619 0.00 0.00 0.00 2.15
1507 2134 0.988832 TACGCCCCATTCCCCATATC 59.011 55.000 0.00 0.00 0.00 1.63
1515 2142 3.504520 TGAAAACTCTTTACGCCCCATTC 59.495 43.478 0.00 0.00 0.00 2.67
1580 2210 4.101741 ACACTCATAGGGCCTGAATTCTAC 59.898 45.833 18.53 0.00 0.00 2.59
1625 2255 4.833390 AGGTACTGCTTCCACTTGTAATC 58.167 43.478 0.00 0.00 37.18 1.75
1632 2262 4.565652 CCAACAATAGGTACTGCTTCCACT 60.566 45.833 0.00 0.00 41.52 4.00
1690 2375 8.237949 CCCTATTCTGAGTAGTATAACATGTCG 58.762 40.741 0.00 0.00 0.00 4.35
1704 2389 0.919710 GGTTGGGCCCTATTCTGAGT 59.080 55.000 25.70 0.00 0.00 3.41
1767 2453 3.067106 GACACTGACAACATACACTGGG 58.933 50.000 0.00 0.00 0.00 4.45
1808 2494 5.668471 ACACTCATGACACTTAGATGATGG 58.332 41.667 0.00 0.00 0.00 3.51
1811 2497 7.703058 TTCTACACTCATGACACTTAGATGA 57.297 36.000 0.00 0.00 0.00 2.92
1850 2537 1.529244 GTTGGCAGCCTTGACCAGT 60.529 57.895 14.15 0.00 33.86 4.00
1859 2546 2.186826 AGTCAACGTGTTGGCAGCC 61.187 57.895 18.46 3.66 46.84 4.85
1861 2548 1.003545 CTTCAGTCAACGTGTTGGCAG 60.004 52.381 18.46 11.24 46.84 4.85
1865 2552 2.821546 TCTCCTTCAGTCAACGTGTTG 58.178 47.619 6.39 6.39 41.71 3.33
1909 2596 6.748658 AGTCTAACGTGGCAAAAAGTTAAAAC 59.251 34.615 0.00 0.70 0.00 2.43
1916 2603 8.287503 ACTAATAAAGTCTAACGTGGCAAAAAG 58.712 33.333 0.00 0.00 30.33 2.27
1930 2617 6.042781 TCCCTGTCACACAACTAATAAAGTCT 59.957 38.462 0.00 0.00 37.50 3.24
1970 2657 3.084786 AGGCCTTAAAAGCTCATGACAC 58.915 45.455 0.00 0.00 0.00 3.67
1971 2658 3.439857 AGGCCTTAAAAGCTCATGACA 57.560 42.857 0.00 0.00 0.00 3.58
1972 2659 4.944317 ACTAAGGCCTTAAAAGCTCATGAC 59.056 41.667 25.14 0.00 0.00 3.06
1973 2660 5.179452 ACTAAGGCCTTAAAAGCTCATGA 57.821 39.130 25.14 1.28 0.00 3.07
1974 2661 6.767902 TGATACTAAGGCCTTAAAAGCTCATG 59.232 38.462 25.14 12.90 0.00 3.07
1975 2662 6.768381 GTGATACTAAGGCCTTAAAAGCTCAT 59.232 38.462 25.14 10.41 0.00 2.90
1976 2663 6.070194 AGTGATACTAAGGCCTTAAAAGCTCA 60.070 38.462 25.14 17.66 0.00 4.26
1977 2664 6.350103 AGTGATACTAAGGCCTTAAAAGCTC 58.650 40.000 25.14 17.82 0.00 4.09
1978 2665 6.314899 AGTGATACTAAGGCCTTAAAAGCT 57.685 37.500 25.14 15.07 0.00 3.74
1979 2666 6.374613 ACAAGTGATACTAAGGCCTTAAAAGC 59.625 38.462 25.14 18.27 0.00 3.51
1980 2667 7.923414 ACAAGTGATACTAAGGCCTTAAAAG 57.077 36.000 25.14 18.17 0.00 2.27
2150 2837 5.133221 AGTGACCAAAAATACAAGCAGAGT 58.867 37.500 0.00 0.00 0.00 3.24
2204 2891 3.141398 ACACACATCACTAGCCTTGTTG 58.859 45.455 0.00 0.00 0.00 3.33
2211 2898 5.562506 TCAGTACTACACACATCACTAGC 57.437 43.478 0.00 0.00 0.00 3.42
2226 2913 9.703892 GAGTCATTATATTTGCTCATCAGTACT 57.296 33.333 0.00 0.00 0.00 2.73
2237 2924 4.065088 TCCTGCGGAGTCATTATATTTGC 58.935 43.478 2.36 0.00 0.00 3.68
2288 2975 1.541147 GCTGCCTGCACTAAACATGAA 59.459 47.619 0.00 0.00 42.31 2.57
2306 2993 3.248266 GTCAAACTCCAATACGTACGCT 58.752 45.455 16.72 5.36 0.00 5.07
2312 2999 2.422597 TGCCTGTCAAACTCCAATACG 58.577 47.619 0.00 0.00 0.00 3.06
2316 3003 2.172505 TCTCTTGCCTGTCAAACTCCAA 59.827 45.455 0.00 0.00 33.65 3.53
2714 3401 3.191371 CCAAAGTCTTACCAACCTGCATC 59.809 47.826 0.00 0.00 0.00 3.91
2765 3452 4.503741 CACTGATGGTGGGTTAAACAAG 57.496 45.455 0.00 0.00 41.90 3.16
2834 3521 1.258982 CCGCTGATGTATCGCTTCAAC 59.741 52.381 6.96 0.00 31.98 3.18
2867 3554 3.676091 GTGAGAAATTTCACCGGCG 57.324 52.632 19.99 0.00 41.24 6.46
2872 3559 2.084546 CTCCCGGGTGAGAAATTTCAC 58.915 52.381 22.86 14.20 45.28 3.18
2878 3565 1.267121 CTTCTCTCCCGGGTGAGAAA 58.733 55.000 44.01 33.63 46.86 2.52
2892 3579 2.027653 CAGAGACAGTTTCCCCCTTCTC 60.028 54.545 0.00 0.00 0.00 2.87
2909 3596 7.329499 TCAGATTCTCTTCTCCAATTTCAGAG 58.671 38.462 0.00 0.00 33.56 3.35
2927 3614 5.128499 TCTCTTCACCTCCTTGATCAGATTC 59.872 44.000 0.00 0.00 0.00 2.52
2960 3647 3.606846 CGCTGTTGTTGATGTACAGGTTG 60.607 47.826 0.33 0.00 39.66 3.77
3023 3710 1.723542 CGCTTCTCTGCAGTAACAGTG 59.276 52.381 14.67 8.61 38.84 3.66
3035 3722 2.185350 CCATCGCCACGCTTCTCT 59.815 61.111 0.00 0.00 0.00 3.10
3065 3752 1.178276 TCACAAAAACCTTGGCACGT 58.822 45.000 0.00 0.00 0.00 4.49
3089 3776 8.793592 GCTTTTAGAAATTTCTGAGGACCTTTA 58.206 33.333 27.37 3.64 38.19 1.85
3095 3782 7.121759 CCATGAGCTTTTAGAAATTTCTGAGGA 59.878 37.037 27.37 12.69 38.19 3.71
3098 3785 6.350445 GCCCATGAGCTTTTAGAAATTTCTGA 60.350 38.462 27.37 18.51 38.19 3.27
3104 3791 3.131755 GCAGCCCATGAGCTTTTAGAAAT 59.868 43.478 0.00 0.00 42.61 2.17
3235 3922 4.715792 ACAGGAGACAGAGATCACAATGAT 59.284 41.667 0.00 0.00 40.34 2.45
3276 3963 8.567948 TCATGAGAGCTTTAAAAGTTTACTTGG 58.432 33.333 0.00 0.00 36.12 3.61
3283 3970 6.890979 AGCTTCATGAGAGCTTTAAAAGTT 57.109 33.333 20.08 0.00 35.02 2.66
3284 3971 7.281999 GGATAGCTTCATGAGAGCTTTAAAAGT 59.718 37.037 26.50 11.06 39.79 2.66
3296 3984 4.686191 AGGAACTGGATAGCTTCATGAG 57.314 45.455 0.00 0.00 37.18 2.90
3337 4025 7.159372 ACTGACAGTTAATTTGGATACGAGTT 58.841 34.615 1.07 0.00 42.51 3.01
3345 4033 9.295825 ACATTTCATACTGACAGTTAATTTGGA 57.704 29.630 14.50 0.00 0.00 3.53
3346 4034 9.345517 CACATTTCATACTGACAGTTAATTTGG 57.654 33.333 14.50 2.47 0.00 3.28
3446 4247 2.005451 AGAACTTGCATCGCATGTCTC 58.995 47.619 7.81 7.95 44.18 3.36
3451 4252 4.025396 CGATAAAGAGAACTTGCATCGCAT 60.025 41.667 0.00 0.00 40.91 4.73
3452 4253 3.306973 CGATAAAGAGAACTTGCATCGCA 59.693 43.478 0.00 0.00 40.91 5.10
3453 4254 3.854881 CGATAAAGAGAACTTGCATCGC 58.145 45.455 0.00 0.00 40.91 4.58
3454 4255 3.553511 AGCGATAAAGAGAACTTGCATCG 59.446 43.478 15.94 15.94 44.89 3.84
3455 4256 4.568359 TCAGCGATAAAGAGAACTTGCATC 59.432 41.667 0.00 0.00 36.39 3.91
3524 4327 4.960469 TGAACGGAGGGAGTAACATTCTAT 59.040 41.667 0.00 0.00 0.00 1.98
3599 4403 6.639632 ATGAGTGAACAAGCACACTAAAAT 57.360 33.333 0.00 0.00 45.54 1.82
3626 4430 5.017294 TCAATATGAACTACATGCGGACA 57.983 39.130 0.00 0.00 39.77 4.02
3629 4433 7.298122 GGTATTTCAATATGAACTACATGCGG 58.702 38.462 17.06 0.00 41.45 5.69
3653 4457 8.786898 CCACTCACATATATAAAATGTTCAGGG 58.213 37.037 2.21 3.35 35.39 4.45
3663 4467 8.453681 TCTACTCCCTCCACTCACATATATAAA 58.546 37.037 0.00 0.00 0.00 1.40
3676 4480 2.134789 TACGGTTCTACTCCCTCCAC 57.865 55.000 0.00 0.00 0.00 4.02
3704 4508 1.402787 GGGGATCGATGCCACAAATT 58.597 50.000 33.38 0.00 40.49 1.82
3717 4533 3.768757 TGTTGAAATGTGATTGGGGGATC 59.231 43.478 0.00 0.00 0.00 3.36
3718 4534 3.515104 GTGTTGAAATGTGATTGGGGGAT 59.485 43.478 0.00 0.00 0.00 3.85
3719 4535 2.896685 GTGTTGAAATGTGATTGGGGGA 59.103 45.455 0.00 0.00 0.00 4.81
3720 4536 2.899256 AGTGTTGAAATGTGATTGGGGG 59.101 45.455 0.00 0.00 0.00 5.40
3721 4537 4.039004 TCAAGTGTTGAAATGTGATTGGGG 59.961 41.667 0.00 0.00 36.59 4.96
3722 4538 5.199024 TCAAGTGTTGAAATGTGATTGGG 57.801 39.130 0.00 0.00 36.59 4.12
3753 4569 3.370672 CACGCACTTGTACATCTGCATTA 59.629 43.478 19.78 0.00 0.00 1.90
3775 4591 0.391661 TCTCTGCTCAACGCCATTCC 60.392 55.000 0.00 0.00 38.05 3.01
3979 4824 0.034089 ATGCTTGGGACTACCTTGCC 60.034 55.000 0.00 0.00 41.11 4.52
3980 4825 1.098050 CATGCTTGGGACTACCTTGC 58.902 55.000 0.00 0.00 41.11 4.01
3981 4826 1.098050 GCATGCTTGGGACTACCTTG 58.902 55.000 11.37 0.00 41.11 3.61
3982 4827 0.698238 TGCATGCTTGGGACTACCTT 59.302 50.000 20.33 0.00 41.11 3.50
3983 4828 0.035056 GTGCATGCTTGGGACTACCT 60.035 55.000 20.33 0.00 41.11 3.08
3984 4829 0.322456 TGTGCATGCTTGGGACTACC 60.322 55.000 20.33 0.00 40.81 3.18
3985 4830 1.470098 CTTGTGCATGCTTGGGACTAC 59.530 52.381 20.33 6.41 0.00 2.73
3986 4831 1.614051 CCTTGTGCATGCTTGGGACTA 60.614 52.381 20.33 4.20 0.00 2.59
3987 4832 0.896940 CCTTGTGCATGCTTGGGACT 60.897 55.000 20.33 0.00 0.00 3.85
3988 4833 1.588082 CCTTGTGCATGCTTGGGAC 59.412 57.895 20.33 8.76 0.00 4.46
3989 4834 2.277591 GCCTTGTGCATGCTTGGGA 61.278 57.895 20.33 0.00 40.77 4.37
3990 4835 2.263540 GCCTTGTGCATGCTTGGG 59.736 61.111 20.33 15.71 40.77 4.12
3999 4844 1.270839 TGAGACTACCTTGCCTTGTGC 60.271 52.381 0.00 0.00 41.77 4.57
4000 4845 2.839486 TGAGACTACCTTGCCTTGTG 57.161 50.000 0.00 0.00 0.00 3.33
4001 4846 3.584848 AGATTGAGACTACCTTGCCTTGT 59.415 43.478 0.00 0.00 0.00 3.16
4002 4847 3.937706 CAGATTGAGACTACCTTGCCTTG 59.062 47.826 0.00 0.00 0.00 3.61
4003 4848 3.840666 TCAGATTGAGACTACCTTGCCTT 59.159 43.478 0.00 0.00 0.00 4.35
4004 4849 3.445008 TCAGATTGAGACTACCTTGCCT 58.555 45.455 0.00 0.00 0.00 4.75
4052 4897 3.084039 TCAATGCATGACAAGGAGAACC 58.916 45.455 0.00 0.00 31.50 3.62


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

AutoCloner maintained by Alex Coulton.