Multiple sequence alignment - TraesCS2B01G529500

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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 TraesCS2B01G529500 chr2B 100.000 3628 0 0 1 3628 724547738 724551365 0.000000e+00 6700.0
1 TraesCS2B01G529500 chr2A 84.743 2045 140 68 18 1945 729771528 729773517 0.000000e+00 1890.0
2 TraesCS2B01G529500 chr2A 92.315 1028 46 15 2358 3371 729773993 729775001 0.000000e+00 1430.0
3 TraesCS2B01G529500 chr2A 90.432 324 17 7 2000 2317 729773678 729773993 7.250000e-112 414.0
4 TraesCS2B01G529500 chr2A 90.840 262 22 2 3368 3628 729775047 729775307 2.070000e-92 350.0
5 TraesCS2B01G529500 chr2A 97.297 37 1 0 3326 3362 729774916 729774952 3.020000e-06 63.9
6 TraesCS2B01G529500 chr2D 88.896 1549 111 26 18 1516 596118453 596119990 0.000000e+00 1851.0
7 TraesCS2B01G529500 chr2D 89.871 1313 64 35 2360 3628 596121083 596122370 0.000000e+00 1624.0
8 TraesCS2B01G529500 chr2D 89.223 399 17 9 1550 1945 596120177 596120552 3.280000e-130 475.0
9 TraesCS2B01G529500 chr2D 89.908 327 18 8 1996 2317 596120765 596121081 1.210000e-109 407.0
10 TraesCS2B01G529500 chr2D 89.404 151 13 2 85 232 596117704 596117854 1.720000e-43 187.0
11 TraesCS2B01G529500 chr2D 95.652 46 1 1 3326 3371 596122032 596122076 5.030000e-09 73.1
12 TraesCS2B01G529500 chr3B 93.548 93 5 1 3179 3271 776359634 776359543 1.760000e-28 137.0
13 TraesCS2B01G529500 chr3B 90.909 99 9 0 3184 3282 135685091 135684993 2.270000e-27 134.0
14 TraesCS2B01G529500 chr7A 95.238 84 4 0 3186 3269 252187600 252187683 2.270000e-27 134.0
15 TraesCS2B01G529500 chr3A 92.473 93 6 1 3179 3271 716368720 716368629 8.170000e-27 132.0
16 TraesCS2B01G529500 chr1A 93.258 89 6 0 3187 3275 320523098 320523010 8.170000e-27 132.0
17 TraesCS2B01G529500 chr3D 89.899 99 10 0 3184 3282 85447130 85447032 1.060000e-25 128.0
18 TraesCS2B01G529500 chr3D 92.308 91 6 1 3186 3276 450878785 450878874 1.060000e-25 128.0
19 TraesCS2B01G529500 chr4D 89.216 102 10 1 3172 3272 418387173 418387274 3.800000e-25 126.0


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 TraesCS2B01G529500 chr2B 724547738 724551365 3627 False 6700.000000 6700 100.000000 1 3628 1 chr2B.!!$F1 3627
1 TraesCS2B01G529500 chr2A 729771528 729775307 3779 False 829.580000 1890 91.125400 18 3628 5 chr2A.!!$F1 3610
2 TraesCS2B01G529500 chr2D 596117704 596122370 4666 False 769.516667 1851 90.492333 18 3628 6 chr2D.!!$F1 3610

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
269 1004 0.108615 CTTTGTCGATCGAGGCACCT 60.109 55.0 20.09 0.0 0.00 4.00 F
464 1203 0.108804 CGCCGTTTCTTAGCCTCTGA 60.109 55.0 0.00 0.0 0.00 3.27 F
756 1498 0.307760 GGGACATGCTTTAATCGGCG 59.692 55.0 0.00 0.0 0.00 6.46 F
1824 2815 0.317799 TCACAAATTTGCATGCGCCT 59.682 45.0 18.12 0.0 37.32 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 2050 0.032678 ACGCAGGGAATCGCAGATAG 59.967 55.0 0.00 0.0 45.12 2.08 R
2124 3288 0.036483 TGGTGACGCACTGCATACAT 60.036 50.0 1.11 0.0 34.40 2.29 R
2343 3515 1.091771 CATGCGGTAGCTCCTTGGTG 61.092 60.0 0.00 0.0 45.42 4.17 R
2829 4010 0.179073 ATTTGGGAGCGACGATGGAG 60.179 55.0 0.00 0.0 0.00 3.86 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
59 792 1.534235 AGTCGTGGCAAGAGGAGGT 60.534 57.895 2.57 0.00 0.00 3.85
98 831 4.827835 CACTACCCTTCTAGGAATCATCGA 59.172 45.833 0.00 0.00 37.67 3.59
110 843 2.996249 ATCATCGATGCCACACTTCT 57.004 45.000 20.81 0.00 0.00 2.85
163 898 5.720041 AGGACAGATAGTTGTAGGCTTGTAA 59.280 40.000 0.00 0.00 0.00 2.41
243 978 1.715585 CCGCTACAAGGCAATGTCG 59.284 57.895 0.00 0.00 34.75 4.35
269 1004 0.108615 CTTTGTCGATCGAGGCACCT 60.109 55.000 20.09 0.00 0.00 4.00
291 1026 2.355108 GCCATCAAGTCTAAGAGCCACA 60.355 50.000 0.00 0.00 0.00 4.17
300 1036 4.018960 AGTCTAAGAGCCACATTCAACCAT 60.019 41.667 0.00 0.00 0.00 3.55
301 1037 5.189736 AGTCTAAGAGCCACATTCAACCATA 59.810 40.000 0.00 0.00 0.00 2.74
303 1039 3.287867 AGAGCCACATTCAACCATAGG 57.712 47.619 0.00 0.00 0.00 2.57
322 1058 1.725665 CAAGGATCGCTACCGTCGA 59.274 57.895 0.00 0.00 40.45 4.20
325 1061 2.052414 GATCGCTACCGTCGACCG 60.052 66.667 10.58 6.12 38.88 4.79
360 1096 1.408822 GGCGGTGAATGGGAAGAAGAT 60.409 52.381 0.00 0.00 0.00 2.40
387 1125 2.751837 GTGGTGGCAGCTTAGGGC 60.752 66.667 18.53 0.00 42.19 5.19
411 1149 1.325476 GGTACCACCCTAGTCACCCG 61.325 65.000 7.15 0.00 30.04 5.28
430 1168 3.329889 TTGGGAGCGATGCAGGGT 61.330 61.111 0.00 0.00 0.00 4.34
432 1170 3.474570 GGGAGCGATGCAGGGTCT 61.475 66.667 16.33 0.77 32.69 3.85
464 1203 0.108804 CGCCGTTTCTTAGCCTCTGA 60.109 55.000 0.00 0.00 0.00 3.27
468 1207 2.860735 CCGTTTCTTAGCCTCTGAATCG 59.139 50.000 0.00 0.00 34.61 3.34
470 1209 3.548268 CGTTTCTTAGCCTCTGAATCGTC 59.452 47.826 0.00 0.00 32.01 4.20
505 1244 8.358148 GTGAAGCATAATCAATGAGGAAATGAT 58.642 33.333 0.00 0.00 37.86 2.45
510 1249 9.706691 GCATAATCAATGAGGAAATGATGAAAT 57.293 29.630 0.00 0.00 37.86 2.17
599 1339 4.649674 TCGACTAAAAGTGGGATCTGCTAT 59.350 41.667 0.00 0.00 0.00 2.97
740 1482 4.042435 ACGAAAGTCTAAAATTGGGAGGGA 59.958 41.667 0.00 0.00 44.19 4.20
756 1498 0.307760 GGGACATGCTTTAATCGGCG 59.692 55.000 0.00 0.00 0.00 6.46
788 1553 0.458669 GAATGCAAGTCATGGGCCTG 59.541 55.000 4.53 0.24 35.13 4.85
934 1699 0.758685 CTTCCTCGCCATCTCCCTCT 60.759 60.000 0.00 0.00 0.00 3.69
937 1702 0.831288 CCTCGCCATCTCCCTCTCAT 60.831 60.000 0.00 0.00 0.00 2.90
1038 1827 4.329545 TGGCAGAAGGCGGTGGTC 62.330 66.667 0.00 0.00 46.16 4.02
1111 1900 0.603707 ACAGCATGGTGAGTCAACCG 60.604 55.000 30.46 1.59 43.73 4.44
1118 1925 0.391597 GGTGAGTCAACCGACCTTGA 59.608 55.000 0.00 0.00 43.73 3.02
1123 1930 0.517316 GTCAACCGACCTTGACATGC 59.483 55.000 12.85 0.00 46.38 4.06
1128 1935 1.378882 CCGACCTTGACATGCCCATG 61.379 60.000 6.71 6.71 44.15 3.66
1129 1936 0.392863 CGACCTTGACATGCCCATGA 60.393 55.000 14.69 0.00 41.20 3.07
1130 1937 1.386533 GACCTTGACATGCCCATGAG 58.613 55.000 14.69 2.46 41.20 2.90
1136 1943 2.927028 TGACATGCCCATGAGATCTTG 58.073 47.619 14.69 0.00 41.20 3.02
1156 1963 2.159184 TGTGCTGATCTCCATCGAGTTC 60.159 50.000 0.00 0.00 37.40 3.01
1170 1977 3.061322 TCGAGTTCCACGGTTAAACATG 58.939 45.455 0.00 0.00 0.00 3.21
1175 1982 4.155280 AGTTCCACGGTTAAACATGCATAC 59.845 41.667 0.00 0.00 0.00 2.39
1176 1983 2.673862 TCCACGGTTAAACATGCATACG 59.326 45.455 0.00 0.00 0.00 3.06
1188 1995 1.314534 TGCATACGCATGGCAGCTTT 61.315 50.000 0.00 0.00 45.36 3.51
1190 1997 0.452987 CATACGCATGGCAGCTTTGT 59.547 50.000 0.00 0.00 0.00 2.83
1193 2000 0.958091 ACGCATGGCAGCTTTGTTTA 59.042 45.000 0.00 0.00 0.00 2.01
1194 2001 1.335872 ACGCATGGCAGCTTTGTTTAC 60.336 47.619 0.00 0.00 0.00 2.01
1208 2015 5.277538 GCTTTGTTTACTCTCTTGGTCACTG 60.278 44.000 0.00 0.00 0.00 3.66
1210 2017 5.808366 TGTTTACTCTCTTGGTCACTGAT 57.192 39.130 0.00 0.00 0.00 2.90
1211 2018 5.541845 TGTTTACTCTCTTGGTCACTGATG 58.458 41.667 0.00 0.00 0.00 3.07
1236 2050 1.749634 AGCAGCAAAGCTTGATCCATC 59.250 47.619 0.00 0.00 43.70 3.51
1512 2347 3.807538 CAGGACACGCCATGCAGC 61.808 66.667 0.00 0.00 40.02 5.25
1571 2559 2.036958 TACACTACACATGCATGCCC 57.963 50.000 26.53 0.00 0.00 5.36
1677 2665 1.902508 CACACCACTGGACTCCATAGT 59.097 52.381 0.71 0.00 39.21 2.12
1695 2685 3.118454 CGACGACCATGCCACACC 61.118 66.667 0.00 0.00 0.00 4.16
1696 2686 2.347490 GACGACCATGCCACACCT 59.653 61.111 0.00 0.00 0.00 4.00
1697 2687 2.032528 ACGACCATGCCACACCTG 59.967 61.111 0.00 0.00 0.00 4.00
1698 2688 3.434319 CGACCATGCCACACCTGC 61.434 66.667 0.00 0.00 0.00 4.85
1699 2689 2.282391 GACCATGCCACACCTGCA 60.282 61.111 0.00 0.00 43.97 4.41
1700 2690 2.598394 ACCATGCCACACCTGCAC 60.598 61.111 0.00 0.00 42.38 4.57
1701 2691 3.740397 CCATGCCACACCTGCACG 61.740 66.667 0.00 0.00 42.38 5.34
1702 2692 4.409218 CATGCCACACCTGCACGC 62.409 66.667 0.00 0.00 42.38 5.34
1703 2693 4.953010 ATGCCACACCTGCACGCA 62.953 61.111 0.00 0.00 42.38 5.24
1810 2801 7.445121 CCTGTATATCTAATCAGGCTTCACAA 58.555 38.462 0.00 0.00 40.43 3.33
1811 2802 7.933577 CCTGTATATCTAATCAGGCTTCACAAA 59.066 37.037 0.00 0.00 40.43 2.83
1812 2803 9.499479 CTGTATATCTAATCAGGCTTCACAAAT 57.501 33.333 0.00 0.00 0.00 2.32
1813 2804 9.851686 TGTATATCTAATCAGGCTTCACAAATT 57.148 29.630 0.00 0.00 0.00 1.82
1816 2807 5.713025 TCTAATCAGGCTTCACAAATTTGC 58.287 37.500 18.12 3.49 0.00 3.68
1817 2808 4.339872 AATCAGGCTTCACAAATTTGCA 57.660 36.364 18.12 2.13 0.00 4.08
1818 2809 4.546829 ATCAGGCTTCACAAATTTGCAT 57.453 36.364 18.12 0.00 0.00 3.96
1819 2810 3.655486 TCAGGCTTCACAAATTTGCATG 58.345 40.909 18.12 11.36 36.87 4.06
1820 2811 2.158841 CAGGCTTCACAAATTTGCATGC 59.841 45.455 18.12 11.82 0.00 4.06
1821 2812 1.127213 GGCTTCACAAATTTGCATGCG 59.873 47.619 18.12 0.00 0.00 4.73
1822 2813 1.462869 GCTTCACAAATTTGCATGCGC 60.463 47.619 18.12 0.00 39.24 6.09
1823 2814 1.127213 CTTCACAAATTTGCATGCGCC 59.873 47.619 18.12 0.00 37.32 6.53
1824 2815 0.317799 TCACAAATTTGCATGCGCCT 59.682 45.000 18.12 0.00 37.32 5.52
1825 2816 0.717224 CACAAATTTGCATGCGCCTC 59.283 50.000 18.12 0.00 37.32 4.70
1851 2842 3.368427 GGATGACGATGAGTTTGTCCAGA 60.368 47.826 0.00 0.00 37.88 3.86
1868 2861 3.895041 TCCAGAGGGAATGTTTGTTTTCC 59.105 43.478 0.00 0.00 41.32 3.13
1873 2869 3.678056 GGAATGTTTGTTTTCCCTCCC 57.322 47.619 0.00 0.00 36.24 4.30
1874 2870 3.239449 GGAATGTTTGTTTTCCCTCCCT 58.761 45.455 0.00 0.00 36.24 4.20
1888 2884 4.307259 TCCCTCCCTAGTAAATGCTCATT 58.693 43.478 0.00 0.00 0.00 2.57
1895 2891 7.727181 TCCCTAGTAAATGCTCATTTAGAGTC 58.273 38.462 13.55 4.61 46.47 3.36
1896 2892 6.642950 CCCTAGTAAATGCTCATTTAGAGTCG 59.357 42.308 13.55 5.39 46.47 4.18
1900 2896 8.136057 AGTAAATGCTCATTTAGAGTCGAATG 57.864 34.615 13.55 13.12 46.47 2.67
1901 2897 5.998454 AATGCTCATTTAGAGTCGAATGG 57.002 39.130 16.97 11.38 46.47 3.16
1908 2906 7.170393 TCATTTAGAGTCGAATGGAAGAGAA 57.830 36.000 16.97 0.55 34.74 2.87
1912 2910 8.480643 TTTAGAGTCGAATGGAAGAGAAATTC 57.519 34.615 0.00 0.00 0.00 2.17
1917 2915 4.091424 CGAATGGAAGAGAAATTCGTTGC 58.909 43.478 8.45 0.00 44.66 4.17
1942 2940 9.599322 GCGAATTAATCATATCGATCTTGTTTT 57.401 29.630 0.00 3.41 37.48 2.43
1950 2948 8.131455 TCATATCGATCTTGTTTTTGTAGAGC 57.869 34.615 0.00 0.00 0.00 4.09
1952 2950 9.249457 CATATCGATCTTGTTTTTGTAGAGCTA 57.751 33.333 0.00 0.00 0.00 3.32
1953 2951 9.817809 ATATCGATCTTGTTTTTGTAGAGCTAA 57.182 29.630 0.00 0.00 0.00 3.09
1954 2952 7.956420 TCGATCTTGTTTTTGTAGAGCTAAA 57.044 32.000 0.00 0.00 0.00 1.85
1955 2953 8.373048 TCGATCTTGTTTTTGTAGAGCTAAAA 57.627 30.769 0.00 0.00 31.38 1.52
1956 2954 8.832521 TCGATCTTGTTTTTGTAGAGCTAAAAA 58.167 29.630 1.57 1.57 34.60 1.94
1982 3059 6.403866 AAATTGTAGCACATTTCAGGTGAA 57.596 33.333 0.00 0.00 38.54 3.18
1983 3060 6.403866 AATTGTAGCACATTTCAGGTGAAA 57.596 33.333 7.58 7.58 46.60 2.69
1984 3061 5.843673 TTGTAGCACATTTCAGGTGAAAA 57.156 34.783 9.13 0.00 45.81 2.29
1985 3062 5.843673 TGTAGCACATTTCAGGTGAAAAA 57.156 34.783 9.13 0.00 45.81 1.94
1986 3063 5.830912 TGTAGCACATTTCAGGTGAAAAAG 58.169 37.500 9.13 7.72 45.81 2.27
1988 3065 2.802247 GCACATTTCAGGTGAAAAAGGC 59.198 45.455 9.13 8.90 45.81 4.35
1989 3066 3.740764 GCACATTTCAGGTGAAAAAGGCA 60.741 43.478 9.13 0.00 45.81 4.75
1990 3067 3.803778 CACATTTCAGGTGAAAAAGGCAC 59.196 43.478 9.13 0.00 45.81 5.01
1991 3068 2.861462 TTTCAGGTGAAAAAGGCACG 57.139 45.000 2.59 0.00 40.68 5.34
1992 3069 1.757682 TTCAGGTGAAAAAGGCACGT 58.242 45.000 0.00 0.00 37.13 4.49
1994 3071 2.489971 TCAGGTGAAAAAGGCACGTAG 58.510 47.619 0.00 0.00 37.13 3.51
1997 3161 2.104281 AGGTGAAAAAGGCACGTAGAGT 59.896 45.455 0.00 0.00 37.13 3.24
2002 3166 3.314541 AAAAGGCACGTAGAGTAGGTG 57.685 47.619 0.00 3.03 44.83 4.00
2007 3171 1.132643 GCACGTAGAGTAGGTGGACAG 59.867 57.143 8.42 0.00 42.91 3.51
2013 3177 1.305046 AGTAGGTGGACAGGGACGG 60.305 63.158 0.00 0.00 0.00 4.79
2061 3225 1.893808 CAACTGCCACTTCCTGCGT 60.894 57.895 0.00 0.00 0.00 5.24
2089 3253 1.250328 TCGCCGTTCTTCAGTCCTTA 58.750 50.000 0.00 0.00 0.00 2.69
2098 3262 6.159988 CGTTCTTCAGTCCTTATTGTCTCTT 58.840 40.000 0.00 0.00 0.00 2.85
2099 3263 6.090088 CGTTCTTCAGTCCTTATTGTCTCTTG 59.910 42.308 0.00 0.00 0.00 3.02
2121 3285 1.581934 GCCACTGGCCAAAAGAAAAC 58.418 50.000 7.01 0.00 44.06 2.43
2122 3286 1.134551 GCCACTGGCCAAAAGAAAACA 60.135 47.619 7.01 0.00 44.06 2.83
2124 3288 2.093764 CCACTGGCCAAAAGAAAACACA 60.094 45.455 7.01 0.00 0.00 3.72
2125 3289 3.432046 CCACTGGCCAAAAGAAAACACAT 60.432 43.478 7.01 0.00 0.00 3.21
2131 3298 4.152223 GGCCAAAAGAAAACACATGTATGC 59.848 41.667 0.00 0.00 0.00 3.14
2320 3492 3.726517 CGGAAGCCACCTGCAACG 61.727 66.667 0.00 0.00 44.83 4.10
2321 3493 2.281484 GGAAGCCACCTGCAACGA 60.281 61.111 0.00 0.00 44.83 3.85
2322 3494 1.896660 GGAAGCCACCTGCAACGAA 60.897 57.895 0.00 0.00 44.83 3.85
2323 3495 1.282875 GAAGCCACCTGCAACGAAC 59.717 57.895 0.00 0.00 44.83 3.95
2324 3496 2.130073 GAAGCCACCTGCAACGAACC 62.130 60.000 0.00 0.00 44.83 3.62
2325 3497 4.025401 GCCACCTGCAACGAACCG 62.025 66.667 0.00 0.00 40.77 4.44
2326 3498 4.025401 CCACCTGCAACGAACCGC 62.025 66.667 0.00 0.00 0.00 5.68
2327 3499 4.025401 CACCTGCAACGAACCGCC 62.025 66.667 0.00 0.00 0.00 6.13
2333 3505 3.656045 CAACGAACCGCCCCACAC 61.656 66.667 0.00 0.00 0.00 3.82
2334 3506 4.941309 AACGAACCGCCCCACACC 62.941 66.667 0.00 0.00 0.00 4.16
2337 3509 4.572571 GAACCGCCCCACACCACA 62.573 66.667 0.00 0.00 0.00 4.17
2338 3510 4.887190 AACCGCCCCACACCACAC 62.887 66.667 0.00 0.00 0.00 3.82
2352 3524 4.988598 ACACCGCGCACCAAGGAG 62.989 66.667 8.75 0.57 0.00 3.69
2355 3527 4.451150 CCGCGCACCAAGGAGCTA 62.451 66.667 8.75 0.00 0.00 3.32
2356 3528 3.188786 CGCGCACCAAGGAGCTAC 61.189 66.667 8.75 0.00 0.00 3.58
2357 3529 2.820037 GCGCACCAAGGAGCTACC 60.820 66.667 0.30 0.00 39.35 3.18
2398 3573 4.032900 CCAGATGTAATGTACGTGTTGCTC 59.967 45.833 0.00 0.00 0.00 4.26
2419 3594 8.801715 TGCTCATGACTGAAACTTTTTATTTC 57.198 30.769 0.00 0.00 36.73 2.17
2718 3899 3.758755 TGCATATAGCTCCTTGGTCTG 57.241 47.619 0.00 0.00 45.94 3.51
2783 3964 8.268878 AGATACCAGTCTCTTTATATGCCTTT 57.731 34.615 0.00 0.00 0.00 3.11
2794 3975 1.448985 TATGCCTTTTGCGTCAGTCC 58.551 50.000 0.00 0.00 45.60 3.85
2815 3996 3.594134 CCTCACCTAGCTTCAGAAGTTG 58.406 50.000 11.94 2.73 0.00 3.16
2816 3997 3.259374 CCTCACCTAGCTTCAGAAGTTGA 59.741 47.826 11.94 6.30 0.00 3.18
2817 3998 4.262635 CCTCACCTAGCTTCAGAAGTTGAA 60.263 45.833 11.94 0.00 43.40 2.69
2829 4010 4.876107 TCAGAAGTTGAAGTTCAGAACCAC 59.124 41.667 14.56 5.17 31.34 4.16
2831 4012 5.007136 CAGAAGTTGAAGTTCAGAACCACTC 59.993 44.000 14.56 5.35 30.04 3.51
2840 4021 1.078759 CAGAACCACTCCATCGTCGC 61.079 60.000 0.00 0.00 0.00 5.19
2939 4121 0.179134 ATCCAGTTCAGTCGCTACGC 60.179 55.000 0.00 0.00 0.00 4.42
3072 4254 4.569719 TCATAAACCTCCAGGGAAAGTC 57.430 45.455 0.00 0.00 40.27 3.01
3073 4255 4.175962 TCATAAACCTCCAGGGAAAGTCT 58.824 43.478 0.00 0.00 40.27 3.24
3074 4256 2.959465 AAACCTCCAGGGAAAGTCTG 57.041 50.000 0.00 0.00 40.27 3.51
3075 4257 2.118403 AACCTCCAGGGAAAGTCTGA 57.882 50.000 0.00 0.00 40.27 3.27
3076 4258 2.118403 ACCTCCAGGGAAAGTCTGAA 57.882 50.000 0.00 0.00 40.27 3.02
3077 4259 2.418669 ACCTCCAGGGAAAGTCTGAAA 58.581 47.619 0.00 0.00 40.27 2.69
3087 4269 4.881850 GGGAAAGTCTGAAACTGAAACAGA 59.118 41.667 5.76 0.00 38.58 3.41
3405 4665 5.049818 GTGCTCTGCAACAGGTATTGATATC 60.050 44.000 0.00 0.00 41.47 1.63
3412 4672 5.536161 GCAACAGGTATTGATATCCCAACAT 59.464 40.000 0.00 0.00 0.00 2.71
3424 4684 6.273026 TGATATCCCAACATATCCATGTCAGT 59.727 38.462 0.00 0.00 44.83 3.41
3425 4685 4.155063 TCCCAACATATCCATGTCAGTG 57.845 45.455 0.00 0.00 44.83 3.66
3475 4735 8.850156 CATAAAAGGTTATCCATAGTTCCCTTG 58.150 37.037 0.00 0.00 35.89 3.61
3497 4757 7.094205 CCTTGCCATATTTAGAAACAACAGACT 60.094 37.037 0.00 0.00 0.00 3.24
3602 4862 6.763610 TGACAGTGTGTATGTACAATGAAACA 59.236 34.615 15.42 0.00 46.33 2.83
3604 4864 6.079763 CAGTGTGTATGTACAATGAAACAGC 58.920 40.000 0.00 0.00 46.33 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 767 1.170290 TCTTGCCACGACTCTCGACA 61.170 55.000 0.00 0.00 43.74 4.35
59 792 0.837691 AGTGTCAGGGCAGTGGATGA 60.838 55.000 0.00 0.00 0.00 2.92
68 801 1.757699 CTAGAAGGGTAGTGTCAGGGC 59.242 57.143 0.00 0.00 0.00 5.19
71 804 4.956700 TGATTCCTAGAAGGGTAGTGTCAG 59.043 45.833 0.00 0.00 35.59 3.51
98 831 4.125207 GCCCTTCTTTAGAAGTGTGGCAT 61.125 47.826 22.58 0.00 46.73 4.40
145 880 5.720261 GCAGTTACAAGCCTACAACTATC 57.280 43.478 0.00 0.00 30.31 2.08
215 950 3.305177 TTGTAGCGGCGGTTCTCCC 62.305 63.158 19.60 1.13 0.00 4.30
243 978 0.731514 TCGATCGACAAAGGCACGTC 60.732 55.000 15.15 0.00 0.00 4.34
269 1004 1.908619 TGGCTCTTAGACTTGATGGCA 59.091 47.619 0.00 0.00 0.00 4.92
272 1007 5.181009 TGAATGTGGCTCTTAGACTTGATG 58.819 41.667 0.00 0.00 0.00 3.07
291 1026 3.480470 CGATCCTTGCCTATGGTTGAAT 58.520 45.455 0.00 0.00 0.00 2.57
300 1036 0.754217 ACGGTAGCGATCCTTGCCTA 60.754 55.000 22.88 0.00 0.00 3.93
301 1037 2.017559 GACGGTAGCGATCCTTGCCT 62.018 60.000 22.88 0.00 0.00 4.75
303 1039 1.944676 CGACGGTAGCGATCCTTGC 60.945 63.158 22.88 0.39 0.00 4.01
341 1077 1.672881 CATCTTCTTCCCATTCACCGC 59.327 52.381 0.00 0.00 0.00 5.68
342 1078 2.292267 CCATCTTCTTCCCATTCACCG 58.708 52.381 0.00 0.00 0.00 4.94
347 1083 2.158755 CCTACGCCATCTTCTTCCCATT 60.159 50.000 0.00 0.00 0.00 3.16
411 1149 3.207669 CCTGCATCGCTCCCAAGC 61.208 66.667 0.00 0.00 45.56 4.01
419 1157 0.598065 ACAAAAAGACCCTGCATCGC 59.402 50.000 0.00 0.00 0.00 4.58
427 1165 1.197036 GCGCTAGTGACAAAAAGACCC 59.803 52.381 7.68 0.00 0.00 4.46
430 1168 1.144969 CGGCGCTAGTGACAAAAAGA 58.855 50.000 10.36 0.00 0.00 2.52
432 1170 1.301423 AACGGCGCTAGTGACAAAAA 58.699 45.000 10.36 0.00 0.00 1.94
510 1249 9.764363 ATGATCTATGCGTAAAATAAGAGACAA 57.236 29.630 0.00 0.00 0.00 3.18
511 1250 9.764363 AATGATCTATGCGTAAAATAAGAGACA 57.236 29.630 0.00 0.00 0.00 3.41
556 1295 7.029925 GTCGAATCGACGCACATATAATTAA 57.970 36.000 20.24 0.00 46.56 1.40
571 1310 4.401519 AGATCCCACTTTTAGTCGAATCGA 59.598 41.667 0.00 0.00 0.00 3.59
713 1455 7.937394 CCCTCCCAATTTTAGACTTTCGTATAT 59.063 37.037 0.00 0.00 0.00 0.86
714 1456 7.126115 TCCCTCCCAATTTTAGACTTTCGTATA 59.874 37.037 0.00 0.00 0.00 1.47
740 1482 1.732941 TCACGCCGATTAAAGCATGT 58.267 45.000 0.00 0.00 0.00 3.21
756 1498 6.486248 TGACTTGCATTCGCTAATTAATCAC 58.514 36.000 0.00 0.00 39.64 3.06
766 1508 1.660560 GCCCATGACTTGCATTCGCT 61.661 55.000 0.00 0.00 39.64 4.93
788 1553 2.302157 CCATTCCTAATACGACCCCTCC 59.698 54.545 0.00 0.00 0.00 4.30
934 1699 2.176798 GAGAGAGGGAGAGGGAGAATGA 59.823 54.545 0.00 0.00 0.00 2.57
937 1702 0.548989 CGAGAGAGGGAGAGGGAGAA 59.451 60.000 0.00 0.00 0.00 2.87
1111 1900 1.065199 TCTCATGGGCATGTCAAGGTC 60.065 52.381 0.00 0.00 39.72 3.85
1118 1925 2.651455 CACAAGATCTCATGGGCATGT 58.349 47.619 0.00 0.00 39.72 3.21
1123 1930 2.704464 TCAGCACAAGATCTCATGGG 57.296 50.000 0.00 0.00 0.00 4.00
1130 1937 3.058450 CGATGGAGATCAGCACAAGATC 58.942 50.000 0.00 0.00 41.68 2.75
1136 1943 2.468831 GAACTCGATGGAGATCAGCAC 58.531 52.381 12.14 0.00 43.27 4.40
1156 1963 2.789779 GCGTATGCATGTTTAACCGTGG 60.790 50.000 10.16 0.00 42.15 4.94
1170 1977 0.868602 CAAAGCTGCCATGCGTATGC 60.869 55.000 8.12 0.00 43.20 3.14
1175 1982 1.068333 AGTAAACAAAGCTGCCATGCG 60.068 47.619 0.00 0.00 38.13 4.73
1176 1983 2.229784 AGAGTAAACAAAGCTGCCATGC 59.770 45.455 0.00 0.00 0.00 4.06
1181 1988 3.565902 ACCAAGAGAGTAAACAAAGCTGC 59.434 43.478 0.00 0.00 0.00 5.25
1182 1989 4.816385 TGACCAAGAGAGTAAACAAAGCTG 59.184 41.667 0.00 0.00 0.00 4.24
1183 1990 4.816925 GTGACCAAGAGAGTAAACAAAGCT 59.183 41.667 0.00 0.00 0.00 3.74
1188 1995 5.511373 CCATCAGTGACCAAGAGAGTAAACA 60.511 44.000 0.00 0.00 0.00 2.83
1190 1997 4.838423 TCCATCAGTGACCAAGAGAGTAAA 59.162 41.667 0.00 0.00 0.00 2.01
1193 2000 2.564947 GTCCATCAGTGACCAAGAGAGT 59.435 50.000 0.00 0.00 0.00 3.24
1194 2001 2.564504 TGTCCATCAGTGACCAAGAGAG 59.435 50.000 0.00 0.00 31.60 3.20
1208 2015 0.886563 AGCTTTGCTGCTTGTCCATC 59.113 50.000 0.00 0.00 40.93 3.51
1210 2017 4.585070 AGCTTTGCTGCTTGTCCA 57.415 50.000 0.00 0.00 40.93 4.02
1236 2050 0.032678 ACGCAGGGAATCGCAGATAG 59.967 55.000 0.00 0.00 45.12 2.08
1353 2170 3.881092 CTCGCTCGCTCACGTGTGT 62.881 63.158 16.51 0.00 42.30 3.72
1571 2559 1.809567 GCCACAAACTTCCAGGCAGG 61.810 60.000 0.00 0.00 44.59 4.85
1677 2665 2.048597 GTGTGGCATGGTCGTCGA 60.049 61.111 0.00 0.00 0.00 4.20
1810 2801 1.338973 CCATAGAGGCGCATGCAAATT 59.661 47.619 19.57 0.00 45.35 1.82
1811 2802 0.956633 CCATAGAGGCGCATGCAAAT 59.043 50.000 19.57 1.27 45.35 2.32
1812 2803 0.107263 TCCATAGAGGCGCATGCAAA 60.107 50.000 19.57 0.00 45.35 3.68
1813 2804 0.109153 ATCCATAGAGGCGCATGCAA 59.891 50.000 19.57 0.00 45.35 4.08
1814 2805 0.604511 CATCCATAGAGGCGCATGCA 60.605 55.000 19.57 0.00 45.35 3.96
1815 2806 0.321034 TCATCCATAGAGGCGCATGC 60.321 55.000 10.83 7.91 41.71 4.06
1816 2807 1.436600 GTCATCCATAGAGGCGCATG 58.563 55.000 10.83 3.77 37.29 4.06
1817 2808 0.037882 CGTCATCCATAGAGGCGCAT 60.038 55.000 10.83 0.00 37.29 4.73
1818 2809 1.106944 TCGTCATCCATAGAGGCGCA 61.107 55.000 10.83 0.00 37.29 6.09
1819 2810 0.244994 ATCGTCATCCATAGAGGCGC 59.755 55.000 0.00 0.00 37.29 6.53
1820 2811 1.541588 TCATCGTCATCCATAGAGGCG 59.458 52.381 0.00 0.00 37.29 5.52
1821 2812 2.560542 ACTCATCGTCATCCATAGAGGC 59.439 50.000 0.00 0.00 37.29 4.70
1822 2813 4.862902 AACTCATCGTCATCCATAGAGG 57.137 45.455 0.00 0.00 39.47 3.69
1823 2814 5.595885 ACAAACTCATCGTCATCCATAGAG 58.404 41.667 0.00 0.00 0.00 2.43
1824 2815 5.451937 GGACAAACTCATCGTCATCCATAGA 60.452 44.000 0.00 0.00 0.00 1.98
1825 2816 4.747108 GGACAAACTCATCGTCATCCATAG 59.253 45.833 0.00 0.00 0.00 2.23
1868 2861 7.067496 TCTAAATGAGCATTTACTAGGGAGG 57.933 40.000 10.69 1.52 40.99 4.30
1873 2869 8.858003 TTCGACTCTAAATGAGCATTTACTAG 57.142 34.615 10.69 12.45 46.41 2.57
1874 2870 9.249457 CATTCGACTCTAAATGAGCATTTACTA 57.751 33.333 10.69 3.44 46.41 1.82
1896 2892 4.091424 CGCAACGAATTTCTCTTCCATTC 58.909 43.478 0.00 0.00 0.00 2.67
1900 2896 3.806316 TTCGCAACGAATTTCTCTTCC 57.194 42.857 0.00 0.00 41.05 3.46
1912 2910 6.982809 AGATCGATATGATTAATTCGCAACG 58.017 36.000 0.00 0.00 37.47 4.10
1913 2911 8.223769 ACAAGATCGATATGATTAATTCGCAAC 58.776 33.333 15.46 0.00 37.47 4.17
1914 2912 8.310406 ACAAGATCGATATGATTAATTCGCAA 57.690 30.769 15.46 0.00 37.47 4.85
1957 2955 6.815089 TCACCTGAAATGTGCTACAATTTTT 58.185 32.000 0.00 0.00 32.09 1.94
1958 2956 6.403866 TCACCTGAAATGTGCTACAATTTT 57.596 33.333 0.00 0.00 32.09 1.82
1959 2957 6.403866 TTCACCTGAAATGTGCTACAATTT 57.596 33.333 0.00 0.00 32.09 1.82
1960 2958 6.403866 TTTCACCTGAAATGTGCTACAATT 57.596 33.333 0.00 0.00 38.94 2.32
1961 2959 6.403866 TTTTCACCTGAAATGTGCTACAAT 57.596 33.333 1.35 0.00 42.83 2.71
1964 3041 5.222631 CCTTTTTCACCTGAAATGTGCTAC 58.777 41.667 1.35 0.00 42.83 3.58
1974 3051 2.103432 TCTACGTGCCTTTTTCACCTGA 59.897 45.455 0.00 0.00 0.00 3.86
1976 3053 2.104281 ACTCTACGTGCCTTTTTCACCT 59.896 45.455 0.00 0.00 0.00 4.00
1977 3054 2.490991 ACTCTACGTGCCTTTTTCACC 58.509 47.619 0.00 0.00 0.00 4.02
1978 3055 3.678548 CCTACTCTACGTGCCTTTTTCAC 59.321 47.826 0.00 0.00 0.00 3.18
1979 3056 3.322828 ACCTACTCTACGTGCCTTTTTCA 59.677 43.478 0.00 0.00 0.00 2.69
1980 3057 3.678548 CACCTACTCTACGTGCCTTTTTC 59.321 47.826 0.00 0.00 0.00 2.29
1982 3059 2.028385 CCACCTACTCTACGTGCCTTTT 60.028 50.000 0.00 0.00 0.00 2.27
1983 3060 1.549170 CCACCTACTCTACGTGCCTTT 59.451 52.381 0.00 0.00 0.00 3.11
1984 3061 1.183549 CCACCTACTCTACGTGCCTT 58.816 55.000 0.00 0.00 0.00 4.35
1985 3062 0.330604 TCCACCTACTCTACGTGCCT 59.669 55.000 0.00 0.00 0.00 4.75
1986 3063 0.455005 GTCCACCTACTCTACGTGCC 59.545 60.000 0.00 0.00 0.00 5.01
1988 3065 1.743958 CCTGTCCACCTACTCTACGTG 59.256 57.143 0.00 0.00 0.00 4.49
1989 3066 1.340795 CCCTGTCCACCTACTCTACGT 60.341 57.143 0.00 0.00 0.00 3.57
1990 3067 1.064906 TCCCTGTCCACCTACTCTACG 60.065 57.143 0.00 0.00 0.00 3.51
1991 3068 2.377073 GTCCCTGTCCACCTACTCTAC 58.623 57.143 0.00 0.00 0.00 2.59
1992 3069 1.064906 CGTCCCTGTCCACCTACTCTA 60.065 57.143 0.00 0.00 0.00 2.43
1994 3071 1.321074 CCGTCCCTGTCCACCTACTC 61.321 65.000 0.00 0.00 0.00 2.59
1997 3161 0.686441 CATCCGTCCCTGTCCACCTA 60.686 60.000 0.00 0.00 0.00 3.08
2002 3166 2.687566 ACCCATCCGTCCCTGTCC 60.688 66.667 0.00 0.00 0.00 4.02
2089 3253 1.546323 CCAGTGGCCACAAGAGACAAT 60.546 52.381 36.39 10.81 0.00 2.71
2119 3283 1.464608 GACGCACTGCATACATGTGTT 59.535 47.619 9.11 0.00 37.21 3.32
2120 3284 1.078709 GACGCACTGCATACATGTGT 58.921 50.000 9.11 0.00 39.68 3.72
2121 3285 1.077915 TGACGCACTGCATACATGTG 58.922 50.000 9.11 0.00 35.08 3.21
2122 3286 1.078709 GTGACGCACTGCATACATGT 58.921 50.000 2.69 2.69 0.00 3.21
2124 3288 0.036483 TGGTGACGCACTGCATACAT 60.036 50.000 1.11 0.00 34.40 2.29
2125 3289 0.036483 ATGGTGACGCACTGCATACA 60.036 50.000 1.11 0.00 34.40 2.29
2131 3298 4.571250 ACGTATGGTGACGCACTG 57.429 55.556 9.31 0.09 46.87 3.66
2317 3489 4.941309 GGTGTGGGGCGGTTCGTT 62.941 66.667 0.00 0.00 0.00 3.85
2320 3492 4.572571 TGTGGTGTGGGGCGGTTC 62.573 66.667 0.00 0.00 0.00 3.62
2321 3493 4.887190 GTGTGGTGTGGGGCGGTT 62.887 66.667 0.00 0.00 0.00 4.44
2335 3507 4.988598 CTCCTTGGTGCGCGGTGT 62.989 66.667 8.83 0.00 0.00 4.16
2338 3510 4.451150 TAGCTCCTTGGTGCGCGG 62.451 66.667 8.83 0.00 0.00 6.46
2339 3511 3.188786 GTAGCTCCTTGGTGCGCG 61.189 66.667 0.00 0.00 0.00 6.86
2340 3512 2.820037 GGTAGCTCCTTGGTGCGC 60.820 66.667 0.00 0.00 0.00 6.09
2341 3513 2.509336 CGGTAGCTCCTTGGTGCG 60.509 66.667 7.88 0.00 0.00 5.34
2342 3514 2.820037 GCGGTAGCTCCTTGGTGC 60.820 66.667 5.65 5.65 41.01 5.01
2343 3515 1.091771 CATGCGGTAGCTCCTTGGTG 61.092 60.000 0.00 0.00 45.42 4.17
2344 3516 1.221840 CATGCGGTAGCTCCTTGGT 59.778 57.895 0.00 0.00 45.42 3.67
2345 3517 1.524621 CCATGCGGTAGCTCCTTGG 60.525 63.158 0.00 0.00 45.42 3.61
2346 3518 2.182842 GCCATGCGGTAGCTCCTTG 61.183 63.158 0.00 0.00 45.42 3.61
2347 3519 2.190578 GCCATGCGGTAGCTCCTT 59.809 61.111 0.00 0.00 45.42 3.36
2495 3674 1.445716 GCTGCAGCATCTCCCACATC 61.446 60.000 33.36 0.00 41.59 3.06
2713 3894 6.382869 AATATTTACATCAAGCAGCAGACC 57.617 37.500 0.00 0.00 0.00 3.85
2718 3899 6.532657 ACTGCAAAATATTTACATCAAGCAGC 59.467 34.615 19.81 0.00 46.92 5.25
2783 3964 0.541063 TAGGTGAGGGACTGACGCAA 60.541 55.000 0.00 0.00 45.62 4.85
2794 3975 3.259374 TCAACTTCTGAAGCTAGGTGAGG 59.741 47.826 17.00 0.00 31.02 3.86
2815 3996 2.996621 CGATGGAGTGGTTCTGAACTTC 59.003 50.000 19.05 13.76 0.00 3.01
2816 3997 2.368875 ACGATGGAGTGGTTCTGAACTT 59.631 45.455 19.05 6.49 0.00 2.66
2817 3998 1.971357 ACGATGGAGTGGTTCTGAACT 59.029 47.619 19.05 0.12 0.00 3.01
2818 3999 2.338500 GACGATGGAGTGGTTCTGAAC 58.662 52.381 12.05 12.05 0.00 3.18
2819 4000 1.067846 CGACGATGGAGTGGTTCTGAA 60.068 52.381 0.00 0.00 0.00 3.02
2820 4001 0.526211 CGACGATGGAGTGGTTCTGA 59.474 55.000 0.00 0.00 0.00 3.27
2829 4010 0.179073 ATTTGGGAGCGACGATGGAG 60.179 55.000 0.00 0.00 0.00 3.86
2831 4012 1.439353 CCATTTGGGAGCGACGATGG 61.439 60.000 0.00 0.00 40.01 3.51
2853 4034 2.288186 GGCGAATTTCTCCCGATTCTTC 59.712 50.000 0.00 0.00 31.63 2.87
2856 4037 0.582005 CGGCGAATTTCTCCCGATTC 59.418 55.000 15.94 0.00 39.12 2.52
2857 4038 0.814010 CCGGCGAATTTCTCCCGATT 60.814 55.000 20.25 0.00 39.12 3.34
2939 4121 1.003008 GCAATTTGTTTTTGCCACGGG 60.003 47.619 0.00 0.00 42.84 5.28
2982 4164 7.624549 TCTACTGAAGATGGCTAAGTCAAAAT 58.375 34.615 0.00 0.00 0.00 1.82
3072 4254 5.163723 TGCTCTGTTTCTGTTTCAGTTTCAG 60.164 40.000 0.00 0.00 32.61 3.02
3073 4255 4.699735 TGCTCTGTTTCTGTTTCAGTTTCA 59.300 37.500 0.00 0.00 32.61 2.69
3074 4256 5.065218 TCTGCTCTGTTTCTGTTTCAGTTTC 59.935 40.000 0.00 0.00 32.61 2.78
3075 4257 4.943705 TCTGCTCTGTTTCTGTTTCAGTTT 59.056 37.500 0.00 0.00 32.61 2.66
3076 4258 4.517285 TCTGCTCTGTTTCTGTTTCAGTT 58.483 39.130 0.00 0.00 32.61 3.16
3077 4259 4.125703 CTCTGCTCTGTTTCTGTTTCAGT 58.874 43.478 0.00 0.00 32.61 3.41
3262 4469 6.071984 CACACTGGATAGATACTACTCCCTT 58.928 44.000 0.00 0.00 0.00 3.95
3294 4501 4.282496 TCTCTGGACAGGATTAACTCTCC 58.718 47.826 0.00 0.00 0.00 3.71
3307 4514 6.368791 CGTGTTCTATTTTTCATCTCTGGACA 59.631 38.462 0.00 0.00 0.00 4.02
3337 4544 7.340232 CCATTTTTCATCTCTGGACTGGATTAA 59.660 37.037 0.00 0.00 0.00 1.40
3412 4672 1.210234 CCTGGTGCACTGACATGGATA 59.790 52.381 17.98 0.00 0.00 2.59
3424 4684 1.075374 ACTTGCTATTTCCCTGGTGCA 59.925 47.619 0.00 0.00 0.00 4.57
3425 4685 1.839424 ACTTGCTATTTCCCTGGTGC 58.161 50.000 0.00 0.00 0.00 5.01
3475 4735 6.030228 GCAGTCTGTTGTTTCTAAATATGGC 58.970 40.000 0.93 0.00 0.00 4.40
3497 4757 0.239082 CTTGATGAGTTGCTTGCGCA 59.761 50.000 5.66 5.66 46.24 6.09
3514 4774 4.744237 TCTACCTACCCTGTGTGTTACTT 58.256 43.478 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.