Multiple sequence alignment - TraesCS2A01G316400

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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 TraesCS2A01G316400 chr2A 100.000 7719 0 0 1 7719 542453914 542461632 0.000000e+00 14255.0
1 TraesCS2A01G316400 chr2A 82.096 1212 172 36 2903 4082 542385555 542386753 0.000000e+00 994.0
2 TraesCS2A01G316400 chr2A 82.749 1084 149 25 5015 6070 542387975 542389048 0.000000e+00 931.0
3 TraesCS2A01G316400 chr2A 86.792 212 26 2 1 212 646626835 646627044 1.300000e-57 235.0
4 TraesCS2A01G316400 chr2A 75.000 340 62 12 4242 4580 542387031 542387348 1.350000e-27 135.0
5 TraesCS2A01G316400 chr2A 85.981 107 12 3 1926 2030 1883355 1883460 2.280000e-20 111.0
6 TraesCS2A01G316400 chr2D 97.148 6136 116 19 1 6126 404085626 404091712 0.000000e+00 10307.0
7 TraesCS2A01G316400 chr2D 92.401 1566 38 39 6167 7686 404091710 404093240 0.000000e+00 2158.0
8 TraesCS2A01G316400 chr2D 81.439 1293 177 47 2903 4148 404040538 404041814 0.000000e+00 1000.0
9 TraesCS2A01G316400 chr2D 82.778 1080 148 24 5015 6066 404042957 404044026 0.000000e+00 929.0
10 TraesCS2A01G316400 chr2D 94.565 92 5 0 1945 2036 534925464 534925555 8.070000e-30 143.0
11 TraesCS2A01G316400 chr2D 75.294 340 61 15 4242 4580 404042014 404042331 2.900000e-29 141.0
12 TraesCS2A01G316400 chr2D 88.889 108 11 1 1946 2052 302248097 302247990 1.750000e-26 132.0
13 TraesCS2A01G316400 chr2D 90.323 62 3 1 1198 1256 404086861 404086922 2.310000e-10 78.7
14 TraesCS2A01G316400 chr2B 94.080 5321 221 49 2421 7684 478115112 478120395 0.000000e+00 7995.0
15 TraesCS2A01G316400 chr2B 94.932 1697 74 9 2 1694 478112689 478114377 0.000000e+00 2647.0
16 TraesCS2A01G316400 chr2B 81.599 1288 184 38 2903 4148 478104189 478105465 0.000000e+00 1016.0
17 TraesCS2A01G316400 chr2B 95.478 575 23 3 1693 2266 478114459 478115031 0.000000e+00 915.0
18 TraesCS2A01G316400 chr2B 82.392 1045 151 22 5046 6066 478106676 478107711 0.000000e+00 880.0
19 TraesCS2A01G316400 chr2B 82.622 328 44 10 6558 6874 709836103 709835778 2.120000e-70 278.0
20 TraesCS2A01G316400 chr2B 94.505 91 5 0 1943 2033 354879122 354879212 2.900000e-29 141.0
21 TraesCS2A01G316400 chr2B 88.073 109 9 3 1922 2030 396927490 396927386 8.130000e-25 126.0
22 TraesCS2A01G316400 chr2B 74.412 340 65 11 4242 4580 478105665 478105983 8.130000e-25 126.0
23 TraesCS2A01G316400 chr2B 90.769 65 3 1 1198 1259 478113944 478114008 4.960000e-12 84.2
24 TraesCS2A01G316400 chr7A 82.569 327 46 9 6558 6874 685399766 685400091 2.120000e-70 278.0
25 TraesCS2A01G316400 chr7A 82.317 328 45 10 6558 6874 650540520 650540845 9.870000e-69 272.0
26 TraesCS2A01G316400 chr7A 90.909 110 8 2 2320 2427 203965937 203965828 6.240000e-31 147.0
27 TraesCS2A01G316400 chr3A 88.835 206 21 2 1 205 220639263 220639467 1.290000e-62 252.0
28 TraesCS2A01G316400 chr3A 86.893 206 25 2 1 205 749182602 749182806 6.030000e-56 230.0
29 TraesCS2A01G316400 chr3A 86.667 105 12 2 1927 2030 293585531 293585634 1.760000e-21 115.0
30 TraesCS2A01G316400 chr1A 89.637 193 19 1 1 193 554783203 554783394 2.150000e-60 244.0
31 TraesCS2A01G316400 chr1A 88.793 116 11 2 2326 2441 357777915 357777802 2.900000e-29 141.0
32 TraesCS2A01G316400 chr1A 87.619 105 9 4 1927 2030 320522997 320523098 1.360000e-22 119.0
33 TraesCS2A01G316400 chr1A 85.965 114 13 3 1924 2035 518662867 518662755 1.360000e-22 119.0
34 TraesCS2A01G316400 chr4D 85.185 243 27 7 6641 6874 468439360 468439118 2.780000e-59 241.0
35 TraesCS2A01G316400 chr4D 94.059 101 6 0 2323 2423 375382015 375381915 3.730000e-33 154.0
36 TraesCS2A01G316400 chr3D 85.185 243 27 6 6641 6874 562008993 562008751 2.780000e-59 241.0
37 TraesCS2A01G316400 chr1D 84.774 243 28 7 6641 6874 419285194 419284952 1.300000e-57 235.0
38 TraesCS2A01G316400 chrUn 83.270 263 35 7 6621 6874 478215791 478216053 4.660000e-57 233.0
39 TraesCS2A01G316400 chr7D 86.321 212 26 3 1 210 469225098 469224888 2.170000e-55 228.0
40 TraesCS2A01G316400 chr5A 85.849 212 28 2 1 211 699519362 699519572 2.800000e-54 224.0
41 TraesCS2A01G316400 chr5A 88.288 111 10 3 1925 2033 533835085 533835194 6.290000e-26 130.0
42 TraesCS2A01G316400 chr5A 88.889 108 9 3 1945 2052 679658441 679658545 6.290000e-26 130.0
43 TraesCS2A01G316400 chr4A 86.473 207 24 4 1 205 685783782 685783578 2.800000e-54 224.0
44 TraesCS2A01G316400 chr5D 94.059 101 6 0 2323 2423 266749353 266749453 3.730000e-33 154.0
45 TraesCS2A01G316400 chr5D 91.589 107 7 2 2317 2422 180472167 180472062 6.240000e-31 147.0
46 TraesCS2A01G316400 chr5D 85.816 141 15 5 2325 2463 266749453 266749316 2.250000e-30 145.0
47 TraesCS2A01G316400 chr6D 94.000 100 6 0 2323 2422 467773577 467773478 1.340000e-32 152.0
48 TraesCS2A01G316400 chr3B 93.204 103 7 0 2325 2427 479298476 479298374 1.340000e-32 152.0
49 TraesCS2A01G316400 chr7B 91.919 99 8 0 1932 2030 740996254 740996156 1.040000e-28 139.0
50 TraesCS2A01G316400 chr6B 93.617 94 5 1 1939 2031 485061194 485061287 1.040000e-28 139.0
51 TraesCS2A01G316400 chr6B 85.849 106 10 3 1927 2030 642350338 642350236 2.950000e-19 108.0


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 TraesCS2A01G316400 chr2A 542453914 542461632 7718 False 14255.000000 14255 100.000000 1 7719 1 chr2A.!!$F2 7718
1 TraesCS2A01G316400 chr2A 542385555 542389048 3493 False 686.666667 994 79.948333 2903 6070 3 chr2A.!!$F4 3167
2 TraesCS2A01G316400 chr2D 404085626 404091712 6086 False 10307.000000 10307 97.148000 1 6126 1 chr2D.!!$F1 6125
3 TraesCS2A01G316400 chr2D 404091710 404093240 1530 False 2158.000000 2158 92.401000 6167 7686 1 chr2D.!!$F3 1519
4 TraesCS2A01G316400 chr2D 404040538 404044026 3488 False 690.000000 1000 79.837000 2903 6066 3 chr2D.!!$F5 3163
5 TraesCS2A01G316400 chr2B 478112689 478120395 7706 False 2910.300000 7995 93.814750 2 7684 4 chr2B.!!$F3 7682
6 TraesCS2A01G316400 chr2B 478104189 478107711 3522 False 674.000000 1016 79.467667 2903 6066 3 chr2B.!!$F2 3163

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
813 840 0.036306 AGAGTTAGGGTTTGGTGCGG 59.964 55.000 0.00 0.0 0.00 5.69 F
935 962 0.673644 GGAGGACATTGGTGGTCGTG 60.674 60.000 0.00 0.0 36.12 4.35 F
2286 2418 1.244019 AAGCAAATGCAGTCCGGTCC 61.244 55.000 8.28 0.0 45.16 4.46 F
2711 2843 3.650942 ACAGGGACACAAAGGATACAAGA 59.349 43.478 0.00 0.0 41.41 3.02 F
4907 5494 2.297033 ACATGTCTGCATTTTGTGGGAC 59.703 45.455 0.00 0.0 31.99 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2762 2896 0.250234 AAGAGTATGCAGCGCAGGAA 59.750 50.000 11.47 0.0 43.65 3.36 R
4007 4158 7.756395 TCTTTCTTCAATCTTTTGAGCATCT 57.244 32.000 0.00 0.0 42.60 2.90 R
4044 4204 0.526524 GATGAAGGCGTCAGAGGTCG 60.527 60.000 9.38 0.0 40.43 4.79 R
5128 5748 1.768870 ACAGGACCATTAGAATCCCCG 59.231 52.381 0.00 0.0 32.47 5.73 R
7504 8198 1.211190 CCGAAAGCAGCCAAAGAGC 59.789 57.895 0.00 0.0 0.00 4.09 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
30 31 5.864418 TTCCGGCTATCTACTACAACAAT 57.136 39.130 0.00 0.00 0.00 2.71
34 35 5.462398 CCGGCTATCTACTACAACAATGTTC 59.538 44.000 0.00 0.00 41.05 3.18
35 36 6.040247 CGGCTATCTACTACAACAATGTTCA 58.960 40.000 0.00 0.00 41.05 3.18
65 66 2.587060 ATGAGGGAGGGGTAATGACA 57.413 50.000 0.00 0.00 0.00 3.58
115 116 0.807496 GTAGTCGTCGCTAGGTGGTT 59.193 55.000 0.00 0.00 0.00 3.67
522 528 1.745320 CGAATCCCGACGAATCCCCT 61.745 60.000 0.00 0.00 41.76 4.79
543 549 3.153919 TCGAAATTTTCCAACCCTCCAG 58.846 45.455 3.61 0.00 0.00 3.86
627 633 2.807045 GTCGCTGACTCGCTGGTG 60.807 66.667 2.10 0.00 0.00 4.17
714 722 1.881591 ACCGATAGCTACGAGAGGAC 58.118 55.000 14.62 0.00 0.00 3.85
790 798 5.746245 GTGTGTCTGAGATAGATTGTACTGC 59.254 44.000 0.00 0.00 37.83 4.40
810 837 2.931320 GCGAGAGAGTTAGGGTTTGGTG 60.931 54.545 0.00 0.00 0.00 4.17
811 838 2.701107 GAGAGAGTTAGGGTTTGGTGC 58.299 52.381 0.00 0.00 0.00 5.01
812 839 1.002087 AGAGAGTTAGGGTTTGGTGCG 59.998 52.381 0.00 0.00 0.00 5.34
813 840 0.036306 AGAGTTAGGGTTTGGTGCGG 59.964 55.000 0.00 0.00 0.00 5.69
814 841 0.958876 GAGTTAGGGTTTGGTGCGGG 60.959 60.000 0.00 0.00 0.00 6.13
815 842 1.974875 GTTAGGGTTTGGTGCGGGG 60.975 63.158 0.00 0.00 0.00 5.73
816 843 3.212796 TTAGGGTTTGGTGCGGGGG 62.213 63.158 0.00 0.00 0.00 5.40
819 846 4.354162 GGTTTGGTGCGGGGGCTA 62.354 66.667 0.00 0.00 0.00 3.93
820 847 2.750237 GTTTGGTGCGGGGGCTAG 60.750 66.667 0.00 0.00 0.00 3.42
821 848 4.041762 TTTGGTGCGGGGGCTAGG 62.042 66.667 0.00 0.00 0.00 3.02
825 852 4.043100 GTGCGGGGGCTAGGGTTT 62.043 66.667 0.00 0.00 0.00 3.27
826 853 4.041762 TGCGGGGGCTAGGGTTTG 62.042 66.667 0.00 0.00 0.00 2.93
827 854 4.815108 GCGGGGGCTAGGGTTTGG 62.815 72.222 0.00 0.00 0.00 3.28
828 855 3.335729 CGGGGGCTAGGGTTTGGT 61.336 66.667 0.00 0.00 0.00 3.67
912 939 1.372087 GCCTTCAGTGATTGGCGAGG 61.372 60.000 18.05 10.94 35.79 4.63
921 948 1.306141 ATTGGCGAGGAGTGGAGGA 60.306 57.895 0.00 0.00 0.00 3.71
932 959 0.693049 AGTGGAGGACATTGGTGGTC 59.307 55.000 0.00 0.00 34.52 4.02
935 962 0.673644 GGAGGACATTGGTGGTCGTG 60.674 60.000 0.00 0.00 36.12 4.35
989 1016 2.567615 GGAAGTGTAGATGGTGAGTGGT 59.432 50.000 0.00 0.00 0.00 4.16
1062 1089 2.433664 GGGGTTGCTACACCGACG 60.434 66.667 3.14 0.00 38.28 5.12
1152 1179 6.528537 TTGCTATTTTGGTGCATATTCTGT 57.471 33.333 0.00 0.00 36.55 3.41
1273 1300 6.202954 CACCAGCTGTAGTTGTTATTATAGGC 59.797 42.308 13.81 0.00 0.00 3.93
1285 1312 1.457823 TTATAGGCGTCGCACCGGAT 61.458 55.000 20.50 6.67 0.00 4.18
2173 2284 4.245660 TCTTTTCTTGATACAGCGGACAG 58.754 43.478 0.00 0.00 0.00 3.51
2211 2322 5.643777 TCTTCCTAAGCTAGTTGTTCAATGC 59.356 40.000 0.00 0.00 0.00 3.56
2227 2338 2.386661 ATGCAGTGTACTGGTAGCAC 57.613 50.000 13.41 0.00 43.94 4.40
2286 2418 1.244019 AAGCAAATGCAGTCCGGTCC 61.244 55.000 8.28 0.00 45.16 4.46
2397 2529 9.322773 GTACTAAAGTTAGTCCAAAGTTGAGTT 57.677 33.333 6.99 0.00 42.66 3.01
2711 2843 3.650942 ACAGGGACACAAAGGATACAAGA 59.349 43.478 0.00 0.00 41.41 3.02
2854 2988 5.470368 TGTTGATGTGCTAGTAAGACTGTC 58.530 41.667 0.00 0.00 0.00 3.51
3952 4096 8.786826 TTTGGTCTGTAATCATATTTCGTTCT 57.213 30.769 0.00 0.00 0.00 3.01
4044 4204 7.984617 AGATTGAAGAAAGAACTATGAGGCTAC 59.015 37.037 0.00 0.00 0.00 3.58
4129 4301 4.388469 TCTTGTTTTGTTGTTTGCTGCTTC 59.612 37.500 0.00 0.00 0.00 3.86
4810 5397 4.569761 TGTCTGAGTACACTTCACTGTC 57.430 45.455 0.00 0.00 0.00 3.51
4907 5494 2.297033 ACATGTCTGCATTTTGTGGGAC 59.703 45.455 0.00 0.00 31.99 4.46
4976 5563 2.998772 TGCAGACATTTTCGAACTTGC 58.001 42.857 0.00 2.77 0.00 4.01
5026 5613 6.545666 TGTTTCACTTGTTTATGGAGTGATGT 59.454 34.615 6.29 0.00 46.36 3.06
5041 5661 8.997621 TGGAGTGATGTGTTATACTAAAGAAC 57.002 34.615 0.00 0.00 0.00 3.01
5128 5748 4.790765 AAAAATTAGAGGTGCAAGAGCC 57.209 40.909 0.00 0.00 41.13 4.70
5434 6054 2.304180 ACAAGGTTCATCTGGTGAGAGG 59.696 50.000 0.00 0.00 38.29 3.69
5436 6056 2.183679 AGGTTCATCTGGTGAGAGGAC 58.816 52.381 0.00 0.00 38.73 3.85
5507 6127 4.419522 TCTTTAAATGGTTCAAGCGCTC 57.580 40.909 12.06 0.00 0.00 5.03
5572 6192 4.022849 CCCTCTGTTGATTTGTCCTTGTTC 60.023 45.833 0.00 0.00 0.00 3.18
5914 6558 4.158020 GGAATCGTATCCTACCGAAGAC 57.842 50.000 2.56 0.00 36.57 3.01
6133 6777 6.821031 ACTCTCAATGAAGTACTCGTAACT 57.179 37.500 0.00 0.00 0.00 2.24
6157 6801 7.926018 ACTTTTTGGGTCATCAACACTATTTTC 59.074 33.333 0.00 0.00 30.14 2.29
6242 6886 2.156098 TCATAGTTTTGTTGTCCCCGC 58.844 47.619 0.00 0.00 0.00 6.13
6285 6929 6.899393 ACAGCTCCAAATACTTTCATTTCA 57.101 33.333 0.00 0.00 0.00 2.69
6612 7261 3.115554 GGAATGCACACACACTTGTTTC 58.884 45.455 0.00 0.00 31.66 2.78
6648 7297 8.026607 TGCCTATCATTTACTGCTTTTTAACAC 58.973 33.333 0.00 0.00 0.00 3.32
6655 7304 7.817418 TTTACTGCTTTTTAACACATCTCCT 57.183 32.000 0.00 0.00 0.00 3.69
6731 7380 2.092753 AGGGGCTAATGACATGACACAG 60.093 50.000 0.00 1.89 0.00 3.66
6843 7492 3.281727 TGGGGTGATTAGCTTAGCAAG 57.718 47.619 7.07 0.00 0.00 4.01
6884 7551 4.283363 ACTTCAGCTCTGTGATTGATGT 57.717 40.909 0.00 0.00 0.00 3.06
7100 7768 3.119955 GGTCTTTACATGAAAAGGACGCC 60.120 47.826 15.84 5.67 37.13 5.68
7207 7876 2.512745 TTCAGTTGCGCACCGTGT 60.513 55.556 11.12 0.00 0.00 4.49
7264 7937 9.713684 TTTTATTGGGTCCAGATATCTCATTTT 57.286 29.630 1.03 0.00 0.00 1.82
7288 7961 4.000988 GTCATACAGACGGTGGTCAATTT 58.999 43.478 0.00 0.00 45.92 1.82
7296 7969 4.007659 GACGGTGGTCAATTTGGTAATCT 58.992 43.478 0.00 0.00 42.91 2.40
7330 8003 4.077108 GAGGTATTTAATTTAGGCCCCCG 58.923 47.826 0.00 0.00 0.00 5.73
7346 8019 2.423577 CCCCGTCCTACACTTTCAAAG 58.576 52.381 0.00 0.00 0.00 2.77
7349 8022 4.323257 CCCCGTCCTACACTTTCAAAGTAT 60.323 45.833 1.43 0.00 40.46 2.12
7352 8025 6.127535 CCCGTCCTACACTTTCAAAGTATAGA 60.128 42.308 15.94 2.86 40.18 1.98
7403 8076 8.768019 TGATAAATTATCAGATTGCTCAACTCG 58.232 33.333 11.32 0.00 40.09 4.18
7420 8093 2.548057 ACTCGTGGCATGTTACTGTTTG 59.452 45.455 6.60 0.00 0.00 2.93
7421 8094 2.548057 CTCGTGGCATGTTACTGTTTGT 59.452 45.455 6.60 0.00 0.00 2.83
7423 8096 3.042189 CGTGGCATGTTACTGTTTGTTG 58.958 45.455 0.00 0.00 0.00 3.33
7425 8098 2.223923 TGGCATGTTACTGTTTGTTGGC 60.224 45.455 0.00 0.00 0.00 4.52
7471 8145 2.599677 GGAAACAATGGTGGGGTACAA 58.400 47.619 0.00 0.00 0.00 2.41
7477 8151 6.749036 AACAATGGTGGGGTACAATTTTTA 57.251 33.333 0.00 0.00 30.24 1.52
7478 8152 6.353404 ACAATGGTGGGGTACAATTTTTAG 57.647 37.500 0.00 0.00 30.24 1.85
7482 8156 7.619512 ATGGTGGGGTACAATTTTTAGAAAA 57.380 32.000 0.00 0.00 0.00 2.29
7483 8157 7.433537 TGGTGGGGTACAATTTTTAGAAAAA 57.566 32.000 2.82 2.82 41.59 1.94
7484 8158 7.501844 TGGTGGGGTACAATTTTTAGAAAAAG 58.498 34.615 6.36 0.00 40.78 2.27
7485 8159 6.932400 GGTGGGGTACAATTTTTAGAAAAAGG 59.068 38.462 6.36 4.08 40.78 3.11
7503 8197 9.740710 AGAAAAAGGCATGTAATAAGTTAGAGT 57.259 29.630 0.00 0.00 0.00 3.24
7504 8198 9.774742 GAAAAAGGCATGTAATAAGTTAGAGTG 57.225 33.333 0.00 0.00 0.00 3.51
7541 8265 1.606531 GGCTGAAGCACTCCCAGAT 59.393 57.895 4.43 0.00 44.36 2.90
7547 8271 2.286872 GAAGCACTCCCAGATGATGTG 58.713 52.381 0.00 0.00 0.00 3.21
7569 8301 0.911769 TAAGTGCCATGAGGACCAGG 59.088 55.000 0.00 0.00 36.89 4.45
7687 8422 9.717942 ACTAATCTAGATAAGCAGCTTTTATGG 57.282 33.333 14.29 5.07 0.00 2.74
7688 8423 9.935241 CTAATCTAGATAAGCAGCTTTTATGGA 57.065 33.333 14.29 10.75 0.00 3.41
7690 8425 9.632638 AATCTAGATAAGCAGCTTTTATGGAAA 57.367 29.630 14.29 0.00 0.00 3.13
7691 8426 9.632638 ATCTAGATAAGCAGCTTTTATGGAAAA 57.367 29.630 14.29 0.00 33.48 2.29
7692 8427 9.461312 TCTAGATAAGCAGCTTTTATGGAAAAA 57.539 29.630 14.29 0.00 34.16 1.94
7693 8428 9.727627 CTAGATAAGCAGCTTTTATGGAAAAAG 57.272 33.333 14.29 5.98 39.55 2.27
7708 8443 9.874205 TTATGGAAAAAGCTTCTAATCAATTGG 57.126 29.630 5.42 0.00 0.00 3.16
7709 8444 6.165577 TGGAAAAAGCTTCTAATCAATTGGC 58.834 36.000 5.42 0.00 0.00 4.52
7710 8445 5.582269 GGAAAAAGCTTCTAATCAATTGGCC 59.418 40.000 5.42 0.00 0.00 5.36
7711 8446 4.376340 AAAGCTTCTAATCAATTGGCCG 57.624 40.909 5.42 0.00 0.00 6.13
7712 8447 3.281727 AGCTTCTAATCAATTGGCCGA 57.718 42.857 5.42 0.00 0.00 5.54
7713 8448 3.825328 AGCTTCTAATCAATTGGCCGAT 58.175 40.909 5.42 0.00 0.00 4.18
7714 8449 3.817647 AGCTTCTAATCAATTGGCCGATC 59.182 43.478 5.76 0.00 0.00 3.69
7715 8450 3.817647 GCTTCTAATCAATTGGCCGATCT 59.182 43.478 5.76 0.00 0.00 2.75
7716 8451 4.276926 GCTTCTAATCAATTGGCCGATCTT 59.723 41.667 5.76 3.46 0.00 2.40
7717 8452 5.221126 GCTTCTAATCAATTGGCCGATCTTT 60.221 40.000 5.76 3.28 0.00 2.52
7718 8453 6.681368 GCTTCTAATCAATTGGCCGATCTTTT 60.681 38.462 5.76 2.92 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.647853 ACATTGTTGTAGTAGATAGCCGGA 59.352 41.667 5.05 0.00 33.16 5.14
14 15 6.475727 CGGGTGAACATTGTTGTAGTAGATAG 59.524 42.308 6.80 0.00 34.06 2.08
16 17 5.175859 CGGGTGAACATTGTTGTAGTAGAT 58.824 41.667 6.80 0.00 34.06 1.98
30 31 0.616395 TCATAGGAGCCGGGTGAACA 60.616 55.000 12.94 0.00 0.00 3.18
34 35 2.511452 CCCTCATAGGAGCCGGGTG 61.511 68.421 12.94 0.00 37.67 4.61
35 36 2.122813 CCCTCATAGGAGCCGGGT 60.123 66.667 5.45 5.45 37.67 5.28
115 116 7.396418 AGTAAAAATTACATCCAGGTCCGTAA 58.604 34.615 3.37 0.00 0.00 3.18
219 220 3.730215 TGGCCTGGTTACATAACATGT 57.270 42.857 3.32 0.00 46.92 3.21
457 460 1.533965 GGATTTGGAGCGCCGATTTTC 60.534 52.381 2.29 0.00 36.79 2.29
522 528 3.153919 CTGGAGGGTTGGAAAATTTCGA 58.846 45.455 0.00 0.00 0.00 3.71
714 722 2.489751 GGGCAAAAATCGCTCCCG 59.510 61.111 0.00 0.00 0.00 5.14
790 798 2.931320 GCACCAAACCCTAACTCTCTCG 60.931 54.545 0.00 0.00 0.00 4.04
810 837 4.815108 CCAAACCCTAGCCCCCGC 62.815 72.222 0.00 0.00 0.00 6.13
811 838 3.335729 ACCAAACCCTAGCCCCCG 61.336 66.667 0.00 0.00 0.00 5.73
812 839 2.359011 CACCAAACCCTAGCCCCC 59.641 66.667 0.00 0.00 0.00 5.40
813 840 2.359011 CCACCAAACCCTAGCCCC 59.641 66.667 0.00 0.00 0.00 5.80
814 841 1.001269 GACCACCAAACCCTAGCCC 60.001 63.158 0.00 0.00 0.00 5.19
815 842 0.035343 GAGACCACCAAACCCTAGCC 60.035 60.000 0.00 0.00 0.00 3.93
816 843 0.984995 AGAGACCACCAAACCCTAGC 59.015 55.000 0.00 0.00 0.00 3.42
817 844 1.339151 GCAGAGACCACCAAACCCTAG 60.339 57.143 0.00 0.00 0.00 3.02
818 845 0.690762 GCAGAGACCACCAAACCCTA 59.309 55.000 0.00 0.00 0.00 3.53
819 846 1.062488 AGCAGAGACCACCAAACCCT 61.062 55.000 0.00 0.00 0.00 4.34
820 847 0.606673 GAGCAGAGACCACCAAACCC 60.607 60.000 0.00 0.00 0.00 4.11
821 848 0.606673 GGAGCAGAGACCACCAAACC 60.607 60.000 0.00 0.00 0.00 3.27
822 849 0.951040 CGGAGCAGAGACCACCAAAC 60.951 60.000 0.00 0.00 0.00 2.93
823 850 1.371183 CGGAGCAGAGACCACCAAA 59.629 57.895 0.00 0.00 0.00 3.28
824 851 3.059982 CGGAGCAGAGACCACCAA 58.940 61.111 0.00 0.00 0.00 3.67
869 896 0.531974 ACAGCACACGATTCAACGGT 60.532 50.000 0.00 0.00 37.61 4.83
912 939 0.693049 ACCACCAATGTCCTCCACTC 59.307 55.000 0.00 0.00 0.00 3.51
921 948 1.879380 CAATGACACGACCACCAATGT 59.121 47.619 0.00 0.00 0.00 2.71
932 959 1.082169 CCGGCACAACAATGACACG 60.082 57.895 0.00 0.00 0.00 4.49
935 962 0.238289 CAGTCCGGCACAACAATGAC 59.762 55.000 0.00 0.00 0.00 3.06
1152 1179 7.949690 TCTATAAACAGCAGTAACCACTAGA 57.050 36.000 0.00 0.00 32.21 2.43
1273 1300 1.736249 GAAACGTATCCGGTGCGACG 61.736 60.000 17.97 16.52 39.38 5.12
1285 1312 3.965379 TCCAATGCCACTAGAAACGTA 57.035 42.857 0.00 0.00 0.00 3.57
1865 1975 6.070995 ACGTGTCATACCTCTCCAAGAATTTA 60.071 38.462 0.00 0.00 0.00 1.40
2211 2322 3.181495 GCTCTAGTGCTACCAGTACACTG 60.181 52.174 9.52 2.23 44.12 3.66
2286 2418 7.396540 AATCAAAGCAGGTTATGGTAAGAAG 57.603 36.000 0.00 0.00 39.18 2.85
2397 2529 4.533311 ACTTCCTCCGTCCCAAAATAAGTA 59.467 41.667 0.00 0.00 0.00 2.24
2711 2843 1.486310 TGCACGGATGAAGCTTAGGAT 59.514 47.619 0.00 0.00 0.00 3.24
2762 2896 0.250234 AAGAGTATGCAGCGCAGGAA 59.750 50.000 11.47 0.00 43.65 3.36
4007 4158 7.756395 TCTTTCTTCAATCTTTTGAGCATCT 57.244 32.000 0.00 0.00 42.60 2.90
4044 4204 0.526524 GATGAAGGCGTCAGAGGTCG 60.527 60.000 9.38 0.00 40.43 4.79
4129 4301 9.997482 GTAATAACACAACCATGGTAATAACAG 57.003 33.333 20.12 6.81 0.00 3.16
4663 4943 8.537016 TGTCCATTGTATAGTTAGTAAAGCACT 58.463 33.333 0.00 0.00 41.62 4.40
4738 5019 4.142687 ACCAGTGAAAGTTTTGTCAGAACG 60.143 41.667 0.91 0.00 32.38 3.95
4810 5397 6.650807 ACCCAATGCTGATCAAGTAATATACG 59.349 38.462 0.00 0.00 0.00 3.06
5026 5613 8.519526 CCAAAATGCTGGTTCTTTAGTATAACA 58.480 33.333 0.00 0.00 0.00 2.41
5041 5661 1.868498 CAGTGCAAACCAAAATGCTGG 59.132 47.619 0.00 0.00 42.97 4.85
5128 5748 1.768870 ACAGGACCATTAGAATCCCCG 59.231 52.381 0.00 0.00 32.47 5.73
5434 6054 6.230849 TGCTTTGATTTTGCAATTGATGTC 57.769 33.333 10.34 0.06 33.48 3.06
5436 6056 9.781834 ATTTATGCTTTGATTTTGCAATTGATG 57.218 25.926 10.34 0.00 40.24 3.07
5507 6127 3.331150 AGCTAGATGAGGACTCGATACG 58.669 50.000 0.00 0.00 0.00 3.06
5572 6192 6.558771 TCAATACACTTGATTCCACTGTTG 57.441 37.500 0.00 0.00 0.00 3.33
5914 6558 3.189287 CCATTTCTTCTGGACTTGGTTCG 59.811 47.826 0.00 0.00 35.70 3.95
6133 6777 7.070571 AGGAAAATAGTGTTGATGACCCAAAAA 59.929 33.333 0.00 0.00 0.00 1.94
6377 7021 6.053650 TGCCTCATCAGAAGTTCATTGATAG 58.946 40.000 5.50 5.51 30.77 2.08
6447 7091 7.454260 ACTAGGATTTCATTTCCACTTCAAC 57.546 36.000 0.00 0.00 35.59 3.18
6485 7129 9.699410 ACCAAATCCTGAATCTCACAATTTATA 57.301 29.630 0.00 0.00 0.00 0.98
6486 7130 8.599624 ACCAAATCCTGAATCTCACAATTTAT 57.400 30.769 0.00 0.00 0.00 1.40
6612 7261 6.648310 CAGTAAATGATAGGCACAGATGGTAG 59.352 42.308 0.00 0.00 0.00 3.18
6648 7297 9.315525 GCCTTAACTAAAAAGTAGTAGGAGATG 57.684 37.037 6.54 0.00 29.07 2.90
6655 7304 7.710475 ACGTTGTGCCTTAACTAAAAAGTAGTA 59.290 33.333 0.00 0.00 0.00 1.82
6664 7313 3.395639 CCTCACGTTGTGCCTTAACTAA 58.604 45.455 0.00 0.00 32.98 2.24
6731 7380 3.398406 CAACCCCAGTAATTTTGGTTGC 58.602 45.455 6.77 0.00 46.49 4.17
6884 7551 3.020984 ACCTCTTTTCAGCACGGAAAAA 58.979 40.909 9.42 2.22 43.82 1.94
6989 7656 4.202461 ACAACCTATTCTTTCTGAGCACCA 60.202 41.667 0.00 0.00 0.00 4.17
7070 7737 7.610305 TCCTTTTCATGTAAAGACCCAAGTATC 59.390 37.037 22.24 0.00 37.31 2.24
7100 7768 1.224592 GACCATGGTAGCCACAGGG 59.775 63.158 19.80 2.51 44.83 4.45
7204 7873 6.434340 AGACCTTTTTGATCCCATTAAGACAC 59.566 38.462 0.00 0.00 0.00 3.67
7207 7876 5.418840 GCAGACCTTTTTGATCCCATTAAGA 59.581 40.000 0.00 0.00 0.00 2.10
7264 7937 3.076079 TGACCACCGTCTGTATGACTA 57.924 47.619 0.00 0.00 43.25 2.59
7288 7961 6.484288 ACCTCATGATCAAACAAGATTACCA 58.516 36.000 0.00 0.00 0.00 3.25
7349 8022 9.362151 ACCTTGAAATAACCAATCTGTTTTCTA 57.638 29.630 0.00 0.00 0.00 2.10
7352 8025 9.108284 CAAACCTTGAAATAACCAATCTGTTTT 57.892 29.630 0.00 0.00 0.00 2.43
7372 8045 9.412460 TGAGCAATCTGATAATTTATCAAACCT 57.588 29.630 17.49 10.64 43.98 3.50
7395 8068 2.413112 CAGTAACATGCCACGAGTTGAG 59.587 50.000 0.00 0.00 0.00 3.02
7403 8076 3.380142 CCAACAAACAGTAACATGCCAC 58.620 45.455 0.00 0.00 0.00 5.01
7420 8093 8.731275 AAAATAATAATTAAAGCCAGGCCAAC 57.269 30.769 8.22 0.00 0.00 3.77
7477 8151 9.740710 ACTCTAACTTATTACATGCCTTTTTCT 57.259 29.630 0.00 0.00 0.00 2.52
7478 8152 9.774742 CACTCTAACTTATTACATGCCTTTTTC 57.225 33.333 0.00 0.00 0.00 2.29
7482 8156 6.653989 AGCACTCTAACTTATTACATGCCTT 58.346 36.000 0.00 0.00 0.00 4.35
7483 8157 6.098982 AGAGCACTCTAACTTATTACATGCCT 59.901 38.462 0.00 0.00 38.35 4.75
7484 8158 6.284459 AGAGCACTCTAACTTATTACATGCC 58.716 40.000 0.00 0.00 38.35 4.40
7485 8159 7.778470 AAGAGCACTCTAACTTATTACATGC 57.222 36.000 0.00 0.00 39.39 4.06
7503 8197 1.518056 CCGAAAGCAGCCAAAGAGCA 61.518 55.000 0.00 0.00 34.23 4.26
7504 8198 1.211190 CCGAAAGCAGCCAAAGAGC 59.789 57.895 0.00 0.00 0.00 4.09
7541 8265 3.011818 CTCATGGCACTTAAGCACATCA 58.988 45.455 1.29 0.00 35.83 3.07
7547 8271 1.340017 TGGTCCTCATGGCACTTAAGC 60.340 52.381 1.29 0.00 0.00 3.09
7569 8301 4.021925 ACCGGCTCAGCAAGACCC 62.022 66.667 0.00 0.00 0.00 4.46
7597 8329 6.603201 TGGAAATCAAACACTAGGATTCCATC 59.397 38.462 5.29 0.00 31.26 3.51
7686 8421 5.582269 GGCCAATTGATTAGAAGCTTTTTCC 59.418 40.000 7.12 0.00 0.00 3.13
7687 8422 5.289434 CGGCCAATTGATTAGAAGCTTTTTC 59.711 40.000 7.12 0.00 0.00 2.29
7688 8423 5.047377 TCGGCCAATTGATTAGAAGCTTTTT 60.047 36.000 7.12 0.00 0.00 1.94
7689 8424 4.462483 TCGGCCAATTGATTAGAAGCTTTT 59.538 37.500 7.12 0.00 0.00 2.27
7690 8425 4.016444 TCGGCCAATTGATTAGAAGCTTT 58.984 39.130 7.12 0.00 0.00 3.51
7691 8426 3.620488 TCGGCCAATTGATTAGAAGCTT 58.380 40.909 7.12 0.00 0.00 3.74
7692 8427 3.281727 TCGGCCAATTGATTAGAAGCT 57.718 42.857 7.12 0.00 0.00 3.74
7693 8428 3.817647 AGATCGGCCAATTGATTAGAAGC 59.182 43.478 7.12 0.00 0.00 3.86
7694 8429 6.382869 AAAGATCGGCCAATTGATTAGAAG 57.617 37.500 7.12 0.00 0.00 2.85
7695 8430 6.773976 AAAAGATCGGCCAATTGATTAGAA 57.226 33.333 7.12 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.