Multiple sequence alignment - TraesCS6A01G372300

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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 TraesCS6A01G372300 chr6A 100.000 4460 0 0 1 4460 596162200 596166659 0.000000e+00 8237.0
1 TraesCS6A01G372300 chr6D 93.209 1664 86 9 1395 3035 450642248 450643907 0.000000e+00 2422.0
2 TraesCS6A01G372300 chr6D 93.407 1259 61 8 3040 4277 450643956 450645213 0.000000e+00 1845.0
3 TraesCS6A01G372300 chr6D 86.903 1298 97 40 23 1280 450640901 450642165 0.000000e+00 1387.0
4 TraesCS6A01G372300 chr6D 94.391 624 32 2 1036 1659 76080446 76079826 0.000000e+00 955.0
5 TraesCS6A01G372300 chr6D 93.258 178 10 1 4283 4460 450646102 450646277 1.230000e-65 261.0
6 TraesCS6A01G372300 chr6D 100.000 31 0 0 4152 4182 263042724 263042694 1.730000e-04 58.4
7 TraesCS6A01G372300 chr6B 94.524 1187 57 4 2025 3210 684387355 684388534 0.000000e+00 1825.0
8 TraesCS6A01G372300 chr6B 89.825 855 60 16 1179 2013 684386439 684387286 0.000000e+00 1072.0
9 TraesCS6A01G372300 chr6B 84.072 1105 101 30 3214 4277 684388575 684389645 0.000000e+00 996.0
10 TraesCS6A01G372300 chr6B 86.400 750 45 22 1 732 684384940 684385650 0.000000e+00 767.0
11 TraesCS6A01G372300 chr6B 83.377 385 31 13 725 1080 684385692 684386072 4.300000e-85 326.0
12 TraesCS6A01G372300 chr6B 100.000 33 0 0 1155 1187 684386403 684386435 1.340000e-05 62.1
13 TraesCS6A01G372300 chr3D 94.822 618 29 2 1036 1653 382820008 382820622 0.000000e+00 961.0
14 TraesCS6A01G372300 chr3D 94.822 618 29 2 1036 1653 554658693 554659307 0.000000e+00 961.0
15 TraesCS6A01G372300 chr1D 94.391 624 32 2 1036 1659 207148746 207148126 0.000000e+00 955.0
16 TraesCS6A01G372300 chr7B 85.897 312 29 8 1546 1842 745863126 745862815 7.200000e-83 318.0
17 TraesCS6A01G372300 chr7B 85.577 312 30 9 1546 1842 745807125 745806814 3.350000e-81 313.0
18 TraesCS6A01G372300 chr7B 85.032 314 32 8 1544 1842 745923937 745923624 5.600000e-79 305.0
19 TraesCS6A01G372300 chr7B 95.213 188 9 0 386 573 33805613 33805426 9.380000e-77 298.0
20 TraesCS6A01G372300 chr7B 84.076 314 31 9 1544 1842 745841136 745840827 7.300000e-73 285.0
21 TraesCS6A01G372300 chr7D 95.745 188 8 0 386 573 84178441 84178254 2.020000e-78 303.0
22 TraesCS6A01G372300 chr7A 93.617 188 12 0 386 573 85588906 85588719 9.450000e-72 281.0
23 TraesCS6A01G372300 chrUn 100.000 37 0 0 4149 4185 373283842 373283878 8.010000e-08 69.4


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 TraesCS6A01G372300 chr6A 596162200 596166659 4459 False 8237.00 8237 100.000000 1 4460 1 chr6A.!!$F1 4459
1 TraesCS6A01G372300 chr6D 450640901 450646277 5376 False 1478.75 2422 91.694250 23 4460 4 chr6D.!!$F1 4437
2 TraesCS6A01G372300 chr6D 76079826 76080446 620 True 955.00 955 94.391000 1036 1659 1 chr6D.!!$R1 623
3 TraesCS6A01G372300 chr6B 684384940 684389645 4705 False 841.35 1825 89.699667 1 4277 6 chr6B.!!$F1 4276
4 TraesCS6A01G372300 chr3D 382820008 382820622 614 False 961.00 961 94.822000 1036 1653 1 chr3D.!!$F1 617
5 TraesCS6A01G372300 chr3D 554658693 554659307 614 False 961.00 961 94.822000 1036 1653 1 chr3D.!!$F2 617
6 TraesCS6A01G372300 chr1D 207148126 207148746 620 True 955.00 955 94.391000 1036 1659 1 chr1D.!!$R1 623

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
345 354 0.103208 GGATCACAGCTACTGACGGG 59.897 60.0 0.78 0.0 35.18 5.28 F
619 632 0.106918 ACCAAGAAGAACCACGGCAA 60.107 50.0 0.00 0.0 0.00 4.52 F
623 636 0.180406 AGAAGAACCACGGCAACAGT 59.820 50.0 0.00 0.0 0.00 3.55 F
931 1033 0.456995 CGAGAGAACAGAACCCTCGC 60.457 60.0 0.00 0.0 39.88 5.03 F
932 1034 0.603569 GAGAGAACAGAACCCTCGCA 59.396 55.0 0.00 0.0 32.52 5.10 F
1715 2135 0.668535 GTTTGGGTCACAGCTTGTCC 59.331 55.0 0.00 0.0 32.91 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2526 0.103390 TGTGAAAAGGTCGACGCAGA 59.897 50.000 9.92 0.00 0.00 4.26 R
2614 3100 1.134401 AGGCATCCACATAAGTCCACG 60.134 52.381 0.00 0.00 0.00 4.94 R
2757 3243 3.451526 TCGTTGCTCTCATCATCATCAC 58.548 45.455 0.00 0.00 0.00 3.06 R
2763 3249 2.169144 TGGTCATCGTTGCTCTCATCAT 59.831 45.455 0.00 0.00 0.00 2.45 R
2914 3400 2.421775 TGCAACTGGTTTGTGTACACAG 59.578 45.455 26.52 17.75 42.94 3.66 R
3847 4425 0.608035 TCCATGGAAAACAGCCCGTC 60.608 55.000 13.46 0.00 0.00 4.79 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
35 36 7.511959 AGGAAGTACAGAAGTTTTCAAATCC 57.488 36.000 0.00 0.00 0.00 3.01
60 61 1.251251 AAGCATCAGCAACAAGACCC 58.749 50.000 0.00 0.00 45.49 4.46
90 91 1.668419 GCTGGTACACTATTGCTGGG 58.332 55.000 0.00 0.00 0.00 4.45
93 94 2.236146 CTGGTACACTATTGCTGGGTCA 59.764 50.000 0.00 0.00 0.00 4.02
113 114 4.271291 GTCATTCAGCTAAGGATTCGTTCC 59.729 45.833 0.00 0.00 45.85 3.62
126 127 4.332819 GGATTCGTTCCAACCACTAATCAG 59.667 45.833 2.81 0.00 44.74 2.90
127 128 4.345859 TTCGTTCCAACCACTAATCAGT 57.654 40.909 0.00 0.00 34.42 3.41
128 129 5.471556 TTCGTTCCAACCACTAATCAGTA 57.528 39.130 0.00 0.00 32.21 2.74
129 130 4.813027 TCGTTCCAACCACTAATCAGTAC 58.187 43.478 0.00 0.00 32.21 2.73
131 132 4.863131 CGTTCCAACCACTAATCAGTACTC 59.137 45.833 0.00 0.00 32.21 2.59
132 133 5.336531 CGTTCCAACCACTAATCAGTACTCT 60.337 44.000 0.00 0.00 32.21 3.24
133 134 5.661056 TCCAACCACTAATCAGTACTCTG 57.339 43.478 0.00 0.00 42.54 3.35
181 182 8.562892 CAGACCATATAAAATAACAGAAGCAGG 58.437 37.037 0.00 0.00 0.00 4.85
208 209 6.409704 GCCACAAGCAGGATAATATGAGATA 58.590 40.000 0.00 0.00 42.97 1.98
272 275 6.484288 AGATTTCCATTACCAACATCACAGA 58.516 36.000 0.00 0.00 0.00 3.41
304 310 9.482175 ACAGATACTTGATTAGGTCTTCTTACT 57.518 33.333 0.00 0.00 0.00 2.24
320 326 6.986817 TCTTCTTACTTCTTAGCATGCATACC 59.013 38.462 21.98 0.00 0.00 2.73
341 350 1.476891 GGAACGGATCACAGCTACTGA 59.523 52.381 0.78 0.00 35.18 3.41
342 351 2.531206 GAACGGATCACAGCTACTGAC 58.469 52.381 0.78 0.00 35.18 3.51
343 352 0.452184 ACGGATCACAGCTACTGACG 59.548 55.000 0.78 0.00 35.18 4.35
344 353 0.248661 CGGATCACAGCTACTGACGG 60.249 60.000 0.78 0.00 35.18 4.79
345 354 0.103208 GGATCACAGCTACTGACGGG 59.897 60.000 0.78 0.00 35.18 5.28
346 355 1.103803 GATCACAGCTACTGACGGGA 58.896 55.000 0.78 0.00 35.18 5.14
348 357 1.334160 TCACAGCTACTGACGGGAAA 58.666 50.000 0.78 0.00 35.18 3.13
349 358 1.000506 TCACAGCTACTGACGGGAAAC 59.999 52.381 0.78 0.00 35.18 2.78
397 410 3.816523 CCACCTAGATCTACTTCTCGGAC 59.183 52.174 9.75 0.00 33.79 4.79
608 621 1.672356 CCGGGTCAGCACCAAGAAG 60.672 63.158 0.00 0.00 45.94 2.85
609 622 1.371183 CGGGTCAGCACCAAGAAGA 59.629 57.895 0.00 0.00 45.94 2.87
612 625 1.239347 GGTCAGCACCAAGAAGAACC 58.761 55.000 0.00 0.00 43.17 3.62
615 628 0.588252 CAGCACCAAGAAGAACCACG 59.412 55.000 0.00 0.00 0.00 4.94
616 629 0.535102 AGCACCAAGAAGAACCACGG 60.535 55.000 0.00 0.00 0.00 4.94
619 632 0.106918 ACCAAGAAGAACCACGGCAA 60.107 50.000 0.00 0.00 0.00 4.52
620 633 0.310854 CCAAGAAGAACCACGGCAAC 59.689 55.000 0.00 0.00 0.00 4.17
623 636 0.180406 AGAAGAACCACGGCAACAGT 59.820 50.000 0.00 0.00 0.00 3.55
624 637 1.414919 AGAAGAACCACGGCAACAGTA 59.585 47.619 0.00 0.00 0.00 2.74
625 638 1.798813 GAAGAACCACGGCAACAGTAG 59.201 52.381 0.00 0.00 0.00 2.57
644 658 0.688087 GGATAGGGATCTAGCGGGGG 60.688 65.000 0.00 0.00 32.98 5.40
661 677 2.069430 GGGAAGAGGGGGAGCAGAG 61.069 68.421 0.00 0.00 0.00 3.35
785 861 3.008049 CGGGTGGGAGATTTTATAGAGGG 59.992 52.174 0.00 0.00 0.00 4.30
887 979 1.068121 AAAAGAGGTGGGGAGTGGAG 58.932 55.000 0.00 0.00 0.00 3.86
907 999 2.328589 CCTCCTCCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
931 1033 0.456995 CGAGAGAACAGAACCCTCGC 60.457 60.000 0.00 0.00 39.88 5.03
932 1034 0.603569 GAGAGAACAGAACCCTCGCA 59.396 55.000 0.00 0.00 32.52 5.10
934 1036 0.603569 GAGAACAGAACCCTCGCAGA 59.396 55.000 0.00 0.00 0.00 4.26
935 1037 1.000955 GAGAACAGAACCCTCGCAGAA 59.999 52.381 0.00 0.00 34.09 3.02
1187 1555 3.181464 CCCGGGTTATCTCCTTCTTCTTC 60.181 52.174 14.18 0.00 0.00 2.87
1188 1556 3.491104 CCGGGTTATCTCCTTCTTCTTCG 60.491 52.174 0.00 0.00 0.00 3.79
1276 1656 1.485838 GATGCTGCTCGACATCGGTG 61.486 60.000 0.00 0.00 40.29 4.94
1287 1667 2.025155 GACATCGGTGAGCTTCCTCTA 58.975 52.381 0.65 0.00 38.93 2.43
1326 1706 6.711645 AGTACCATAGAACTACTCGATTCTCC 59.288 42.308 2.36 0.00 36.56 3.71
1334 1714 1.997669 ACTCGATTCTCCGTTGCTTC 58.002 50.000 0.00 0.00 0.00 3.86
1380 1787 2.542766 ATTGCTGGCGTTTACAATCG 57.457 45.000 0.00 0.00 0.00 3.34
1501 1911 2.276827 CCATGCTTGGTGAGGAACTCG 61.277 57.143 10.48 0.00 46.85 4.18
1576 1987 3.632145 TGAGAGCTTCAGTTTTGTTTCCC 59.368 43.478 0.00 0.00 0.00 3.97
1677 2088 2.508526 GGCATTGGATTAGCCGAGAAT 58.491 47.619 0.00 0.00 38.86 2.40
1705 2117 2.575735 TCCAGATGCTATGTTTGGGTCA 59.424 45.455 0.00 0.00 0.00 4.02
1706 2118 2.684881 CCAGATGCTATGTTTGGGTCAC 59.315 50.000 0.00 0.00 0.00 3.67
1715 2135 0.668535 GTTTGGGTCACAGCTTGTCC 59.331 55.000 0.00 0.00 32.91 4.02
1735 2155 8.579850 TTGTCCTATGCAATTCTTCTTGTTAT 57.420 30.769 0.00 0.00 0.00 1.89
1822 2243 4.687948 ACTTGTGTTCAACATGATCTCGAG 59.312 41.667 5.93 5.93 38.99 4.04
1827 2248 3.790152 TCAACATGATCTCGAGGTCAG 57.210 47.619 30.49 23.50 0.00 3.51
1882 2303 2.418746 CGAACCTATGTCTGGTGGGAAG 60.419 54.545 0.00 0.00 37.93 3.46
1930 2358 6.463995 TGAACATTTCAGTACTGCCTTTTT 57.536 33.333 18.45 8.11 34.08 1.94
1936 2364 7.389053 ACATTTCAGTACTGCCTTTTTCTCTAG 59.611 37.037 18.45 0.00 0.00 2.43
1957 2385 7.276658 TCTAGAATAATTGTATGGTTGCCGAA 58.723 34.615 0.00 0.00 0.00 4.30
1974 2402 4.065088 GCCGAATGGTATCTTCTATTGCA 58.935 43.478 0.00 0.00 37.67 4.08
1986 2414 2.009051 TCTATTGCACATGCTGAACCG 58.991 47.619 5.31 0.00 42.66 4.44
1987 2415 2.009051 CTATTGCACATGCTGAACCGA 58.991 47.619 5.31 0.00 42.66 4.69
2041 2526 6.543465 TGATTTCCAATCTTCGCTTCATACAT 59.457 34.615 0.00 0.00 0.00 2.29
2046 2531 2.463876 TCTTCGCTTCATACATCTGCG 58.536 47.619 0.00 0.00 46.71 5.18
2061 2546 1.148310 CTGCGTCGACCTTTTCACAT 58.852 50.000 10.58 0.00 0.00 3.21
2067 2552 2.096218 GTCGACCTTTTCACATCTGTGC 60.096 50.000 3.51 0.00 45.25 4.57
2094 2579 3.881795 CAGTTTGCTGTTACTTGAGCTG 58.118 45.455 0.00 0.00 37.92 4.24
2591 3077 1.670811 GGAGCCATGGTTGTATGAACG 59.329 52.381 14.67 0.00 0.00 3.95
2592 3078 1.064060 GAGCCATGGTTGTATGAACGC 59.936 52.381 14.67 0.00 0.00 4.84
2614 3100 4.036144 GCTCTTATGGATTTCTTGTCTGCC 59.964 45.833 0.00 0.00 0.00 4.85
2757 3243 0.741927 TGCAGCAGTGATGATGACGG 60.742 55.000 13.68 0.00 0.00 4.79
2763 3249 2.739609 GCAGTGATGATGACGGTGATGA 60.740 50.000 0.00 0.00 0.00 2.92
2839 3325 8.915654 GTTTCCTGTTTATACATTTTGAGCTTG 58.084 33.333 0.00 0.00 32.86 4.01
2841 3327 8.579850 TCCTGTTTATACATTTTGAGCTTGAT 57.420 30.769 0.00 0.00 32.86 2.57
2845 3331 7.545265 TGTTTATACATTTTGAGCTTGATTGCC 59.455 33.333 0.00 0.00 0.00 4.52
2860 3346 6.571150 GCTTGATTGCCTTTAATCTCTGTGTT 60.571 38.462 0.00 0.00 37.81 3.32
2914 3400 3.877508 GGAACTATATGTGACCCAGTTGC 59.122 47.826 0.00 0.00 31.84 4.17
3011 3504 8.251383 TGGGATGGAAATGTTTGTTACTTTTA 57.749 30.769 0.00 0.00 35.09 1.52
3012 3505 8.705594 TGGGATGGAAATGTTTGTTACTTTTAA 58.294 29.630 0.00 0.00 35.09 1.52
3037 3530 5.185249 GGTGATCTTTCTACCTGTCTGTGTA 59.815 44.000 0.00 0.00 0.00 2.90
3053 3590 6.170506 GTCTGTGTAATATTCCCTGTGTCAA 58.829 40.000 0.00 0.00 0.00 3.18
3128 3665 4.749245 AAACTGTTGCTATCTTGAACGG 57.251 40.909 0.00 0.00 33.06 4.44
3130 3667 4.002906 ACTGTTGCTATCTTGAACGGAA 57.997 40.909 0.00 0.00 31.58 4.30
3250 3823 2.507058 TGATGAAGCCTTGGTGCTCTAT 59.493 45.455 0.00 0.00 41.80 1.98
3266 3839 3.750130 GCTCTATTGGCAGTGATACATGG 59.250 47.826 0.00 0.00 0.00 3.66
3402 3977 2.287769 GAGCAGATGAGGAAAAGAGGC 58.712 52.381 0.00 0.00 0.00 4.70
3469 4044 1.730612 CCCGCTTCTAAGTCGGTTTTC 59.269 52.381 17.93 0.00 41.14 2.29
3470 4045 2.409975 CCGCTTCTAAGTCGGTTTTCA 58.590 47.619 13.80 0.00 39.32 2.69
3483 4058 3.188460 TCGGTTTTCAGCAGTCATTTAGC 59.812 43.478 0.00 0.00 0.00 3.09
3537 4112 2.826128 TCTGAAGAGTTGGCTGTATCGT 59.174 45.455 0.00 0.00 0.00 3.73
3544 4119 0.323302 TTGGCTGTATCGTGCTTCCA 59.677 50.000 0.00 0.00 0.00 3.53
3650 4225 7.984050 TGTAATGATGACATTGTTGGTTGTTTT 59.016 29.630 0.00 0.00 44.97 2.43
3651 4226 6.847956 ATGATGACATTGTTGGTTGTTTTG 57.152 33.333 0.00 0.00 32.21 2.44
3661 4236 4.516698 TGTTGGTTGTTTTGTGTTTGCATT 59.483 33.333 0.00 0.00 0.00 3.56
3693 4268 9.410556 GTGAAAGTATGCACAATTTTGTATCTT 57.589 29.630 0.00 1.37 39.91 2.40
3719 4294 5.516696 CAGTAATCGCGATGATATACCCTTG 59.483 44.000 24.47 11.33 35.84 3.61
3747 4324 4.551702 TGTAAGCATGTGGTGTAGATGT 57.448 40.909 0.00 0.00 32.84 3.06
3805 4383 1.408422 GCACTAGGCGCAAAAACAAG 58.592 50.000 10.83 0.00 0.00 3.16
3828 4406 6.876804 AGCGCAACATAAAAATTTCTGTTTC 58.123 32.000 11.47 2.99 35.95 2.78
3847 4425 9.161629 TCTGTTTCTGTGTATTACATTGTATGG 57.838 33.333 0.00 0.00 38.92 2.74
3851 4429 6.277605 TCTGTGTATTACATTGTATGGACGG 58.722 40.000 0.00 0.00 38.92 4.79
3860 4459 1.816074 TGTATGGACGGGCTGTTTTC 58.184 50.000 0.00 0.00 0.00 2.29
3871 4470 3.096092 GGGCTGTTTTCCATGGAATACA 58.904 45.455 34.42 34.42 41.34 2.29
3899 4498 4.130286 TGCATGGTATACGTCACAATCA 57.870 40.909 0.00 0.00 0.00 2.57
3934 4551 0.109597 GTTGCGCTTGACCTTCATGG 60.110 55.000 9.73 0.00 42.93 3.66
3953 4570 2.434336 TGGTACTTTGCGCATCCTCTAT 59.566 45.455 12.75 0.00 0.00 1.98
3961 4579 2.289631 TGCGCATCCTCTATAACATGGG 60.290 50.000 5.66 0.00 33.49 4.00
3963 4581 3.589988 CGCATCCTCTATAACATGGGTC 58.410 50.000 0.00 0.00 0.00 4.46
3966 4584 2.605257 TCCTCTATAACATGGGTCGGG 58.395 52.381 0.00 0.00 0.00 5.14
4013 4631 2.170187 GAGTCCTTGCTCATGGAGATGT 59.830 50.000 4.91 0.00 35.61 3.06
4015 4633 1.911357 TCCTTGCTCATGGAGATGTGT 59.089 47.619 0.00 0.00 31.81 3.72
4074 4692 1.170919 ACGTCAGTGTGCTACCTCGT 61.171 55.000 0.00 0.00 0.00 4.18
4087 4707 1.153745 CCTCGTTGAGGCCTCTTCG 60.154 63.158 32.28 30.93 43.29 3.79
4102 4722 2.412870 TCTTCGCTGTGGTATTGTGTG 58.587 47.619 0.00 0.00 0.00 3.82
4121 4741 2.032030 GTGTGGAGTATGTTGTGTGTGC 60.032 50.000 0.00 0.00 0.00 4.57
4147 4767 2.027625 CGGTTTGTGGCGGTCTCTC 61.028 63.158 0.00 0.00 0.00 3.20
4166 4786 7.411264 GGTCTCTCTCGGTTTTTCGTTAATTAC 60.411 40.741 0.00 0.00 0.00 1.89
4208 4828 3.383185 TGCACCCGTTTCAAGAAAGAAAT 59.617 39.130 0.00 0.00 39.46 2.17
4214 4834 5.140177 CCGTTTCAAGAAAGAAATGACTCG 58.860 41.667 9.52 1.26 43.76 4.18
4220 4840 6.464222 TCAAGAAAGAAATGACTCGGTGTAT 58.536 36.000 0.00 0.00 0.00 2.29
4223 4843 6.644347 AGAAAGAAATGACTCGGTGTATCAT 58.356 36.000 0.00 0.00 34.52 2.45
4225 4845 5.344743 AGAAATGACTCGGTGTATCATGT 57.655 39.130 0.00 0.00 33.37 3.21
4234 4854 5.466728 ACTCGGTGTATCATGTATGCAAATC 59.533 40.000 0.00 0.00 31.46 2.17
4237 4857 5.181811 CGGTGTATCATGTATGCAAATCCAT 59.818 40.000 0.00 0.00 31.46 3.41
4253 4874 6.238130 GCAAATCCATCTAACTAACCTCGTTC 60.238 42.308 0.00 0.00 0.00 3.95
4277 4898 5.034152 GTGAGAGATTCAGATCGAGACAAC 58.966 45.833 0.00 0.00 36.21 3.32
4278 4899 4.097135 TGAGAGATTCAGATCGAGACAACC 59.903 45.833 0.00 0.00 37.37 3.77
4285 5789 3.956848 TCAGATCGAGACAACCTCATCAT 59.043 43.478 0.00 0.00 42.06 2.45
4303 5807 2.480037 TCATCAGCACAACATCGAACAC 59.520 45.455 0.00 0.00 0.00 3.32
4304 5808 1.946745 TCAGCACAACATCGAACACA 58.053 45.000 0.00 0.00 0.00 3.72
4415 5919 5.333299 ACATTGCTCATAATGCACATTGT 57.667 34.783 6.13 0.00 40.80 2.71
4419 5923 2.223317 GCTCATAATGCACATTGTCGCA 60.223 45.455 13.64 13.64 43.45 5.10
4432 5936 6.292061 GCACATTGTCGCATAAAAAGAAAACA 60.292 34.615 6.41 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.060421 TGGATTTGAAAACTTCTGTACTTCCT 58.940 34.615 0.00 0.00 0.00 3.36
12 13 7.228706 TCTGGATTTGAAAACTTCTGTACTTCC 59.771 37.037 0.00 0.00 0.00 3.46
13 14 8.070769 GTCTGGATTTGAAAACTTCTGTACTTC 58.929 37.037 0.00 0.00 0.00 3.01
15 16 7.054124 TGTCTGGATTTGAAAACTTCTGTACT 58.946 34.615 0.00 0.00 0.00 2.73
16 17 7.259290 TGTCTGGATTTGAAAACTTCTGTAC 57.741 36.000 0.00 0.00 0.00 2.90
18 19 6.773976 TTGTCTGGATTTGAAAACTTCTGT 57.226 33.333 0.00 0.00 0.00 3.41
19 20 6.199719 GCTTTGTCTGGATTTGAAAACTTCTG 59.800 38.462 0.00 0.00 0.00 3.02
21 22 6.042143 TGCTTTGTCTGGATTTGAAAACTTC 58.958 36.000 0.00 0.00 0.00 3.01
35 36 3.004002 TCTTGTTGCTGATGCTTTGTCTG 59.996 43.478 0.00 0.00 40.48 3.51
69 70 1.065491 CCAGCAATAGTGTACCAGCCA 60.065 52.381 0.00 0.00 0.00 4.75
71 72 1.065418 ACCCAGCAATAGTGTACCAGC 60.065 52.381 0.00 0.00 0.00 4.85
76 77 4.769688 CTGAATGACCCAGCAATAGTGTA 58.230 43.478 0.00 0.00 0.00 2.90
90 91 4.271291 GGAACGAATCCTTAGCTGAATGAC 59.729 45.833 0.00 0.00 45.56 3.06
113 114 5.407407 ACCAGAGTACTGATTAGTGGTTG 57.593 43.478 0.00 0.00 46.03 3.77
160 161 7.649306 GGCAACCTGCTTCTGTTATTTTATATG 59.351 37.037 0.00 0.00 44.28 1.78
161 162 7.341769 TGGCAACCTGCTTCTGTTATTTTATAT 59.658 33.333 0.00 0.00 44.28 0.86
162 163 6.661377 TGGCAACCTGCTTCTGTTATTTTATA 59.339 34.615 0.00 0.00 44.28 0.98
303 309 3.111853 TCCGGTATGCATGCTAAGAAG 57.888 47.619 20.33 5.99 0.00 2.85
304 310 3.202906 GTTCCGGTATGCATGCTAAGAA 58.797 45.455 20.33 11.55 0.00 2.52
305 311 2.801699 CGTTCCGGTATGCATGCTAAGA 60.802 50.000 20.33 6.33 0.00 2.10
306 312 1.526887 CGTTCCGGTATGCATGCTAAG 59.473 52.381 20.33 5.80 0.00 2.18
307 313 1.577468 CGTTCCGGTATGCATGCTAA 58.423 50.000 20.33 3.61 0.00 3.09
308 314 0.249699 CCGTTCCGGTATGCATGCTA 60.250 55.000 20.33 5.73 42.73 3.49
309 315 1.523711 CCGTTCCGGTATGCATGCT 60.524 57.895 20.33 7.07 42.73 3.79
320 326 0.456221 AGTAGCTGTGATCCGTTCCG 59.544 55.000 0.00 0.00 0.00 4.30
593 606 1.239347 GGTTCTTCTTGGTGCTGACC 58.761 55.000 0.00 0.00 43.48 4.02
603 616 1.308998 CTGTTGCCGTGGTTCTTCTT 58.691 50.000 0.00 0.00 0.00 2.52
605 618 1.798813 CTACTGTTGCCGTGGTTCTTC 59.201 52.381 0.00 0.00 0.00 2.87
608 621 0.034337 TCCTACTGTTGCCGTGGTTC 59.966 55.000 0.00 0.00 0.00 3.62
609 622 0.690762 ATCCTACTGTTGCCGTGGTT 59.309 50.000 0.00 0.00 0.00 3.67
612 625 1.202533 CCCTATCCTACTGTTGCCGTG 60.203 57.143 0.00 0.00 0.00 4.94
615 628 3.243724 AGATCCCTATCCTACTGTTGCC 58.756 50.000 0.00 0.00 31.98 4.52
616 629 4.081917 GCTAGATCCCTATCCTACTGTTGC 60.082 50.000 0.00 0.00 31.98 4.17
619 632 3.308545 CCGCTAGATCCCTATCCTACTGT 60.309 52.174 0.00 0.00 31.98 3.55
620 633 3.283751 CCGCTAGATCCCTATCCTACTG 58.716 54.545 0.00 0.00 31.98 2.74
623 636 1.569548 CCCCGCTAGATCCCTATCCTA 59.430 57.143 0.00 0.00 31.98 2.94
624 637 0.336737 CCCCGCTAGATCCCTATCCT 59.663 60.000 0.00 0.00 31.98 3.24
625 638 0.688087 CCCCCGCTAGATCCCTATCC 60.688 65.000 0.00 0.00 31.98 2.59
644 658 2.741055 GCTCTGCTCCCCCTCTTCC 61.741 68.421 0.00 0.00 0.00 3.46
645 659 2.907236 GCTCTGCTCCCCCTCTTC 59.093 66.667 0.00 0.00 0.00 2.87
647 661 2.516048 TAACGCTCTGCTCCCCCTCT 62.516 60.000 0.00 0.00 0.00 3.69
648 662 2.058595 TAACGCTCTGCTCCCCCTC 61.059 63.158 0.00 0.00 0.00 4.30
649 663 2.038975 TAACGCTCTGCTCCCCCT 59.961 61.111 0.00 0.00 0.00 4.79
785 861 1.095807 GCATAACAACGGAGCCCTCC 61.096 60.000 4.19 4.19 46.18 4.30
887 979 1.231928 GAGGAGGAGGGAGGAGGTC 59.768 68.421 0.00 0.00 0.00 3.85
907 999 1.192803 GGTTCTGTTCTCTCGGGGGT 61.193 60.000 0.00 0.00 0.00 4.95
1023 1135 1.254026 TGTAGAATATCTCCGGCGGG 58.746 55.000 27.98 17.02 0.00 6.13
1287 1667 0.822164 GGTACTGTGGGTGAGCGTAT 59.178 55.000 0.00 0.00 0.00 3.06
1326 1706 1.192534 GGTTTCTCTGTCGAAGCAACG 59.807 52.381 0.00 0.00 0.00 4.10
1334 1714 3.032017 AGACACATGGTTTCTCTGTCG 57.968 47.619 0.00 0.00 37.03 4.35
1380 1787 0.463654 TTCACAGCACACAGGACCAC 60.464 55.000 0.00 0.00 0.00 4.16
1501 1911 3.989817 CCATAAGAGCAACAAACAAAGGC 59.010 43.478 0.00 0.00 0.00 4.35
1593 2004 3.068691 CTCCGTCTCCCGCTCCAA 61.069 66.667 0.00 0.00 34.38 3.53
1625 2036 1.549243 TTACCTCGCCCATGTCTGCA 61.549 55.000 0.00 0.00 0.00 4.41
1677 2088 6.222389 CCAAACATAGCATCTGGAACAAAAA 58.778 36.000 0.00 0.00 38.70 1.94
1705 2117 3.960571 AGAATTGCATAGGACAAGCTGT 58.039 40.909 0.00 0.00 0.00 4.40
1706 2118 4.639310 AGAAGAATTGCATAGGACAAGCTG 59.361 41.667 0.00 0.00 0.00 4.24
1822 2243 2.037772 ACAGTGTCAATCAGGTCTGACC 59.962 50.000 19.20 19.20 43.11 4.02
1827 2248 7.724305 TTACTTTTACAGTGTCAATCAGGTC 57.276 36.000 0.00 0.00 35.97 3.85
1882 2303 8.997323 CAGGTTCTTTGGATTCATACTCATATC 58.003 37.037 0.00 0.00 0.00 1.63
1930 2358 6.929049 CGGCAACCATACAATTATTCTAGAGA 59.071 38.462 0.00 0.00 0.00 3.10
1936 2364 5.920273 CCATTCGGCAACCATACAATTATTC 59.080 40.000 0.00 0.00 0.00 1.75
1957 2385 5.472478 CAGCATGTGCAATAGAAGATACCAT 59.528 40.000 7.83 0.00 45.16 3.55
2015 2443 6.543465 TGTATGAAGCGAAGATTGGAAATCAT 59.457 34.615 3.03 0.00 34.67 2.45
2041 2526 0.103390 TGTGAAAAGGTCGACGCAGA 59.897 50.000 9.92 0.00 0.00 4.26
2046 2531 7.966484 GTTGCACAGATGTGAAAAGGTCGAC 62.966 48.000 16.92 7.13 44.57 4.20
2447 2933 9.448438 ACATTATCAGCATAAAACTGTAGAACA 57.552 29.630 0.00 0.00 36.50 3.18
2591 3077 4.036144 GGCAGACAAGAAATCCATAAGAGC 59.964 45.833 0.00 0.00 0.00 4.09
2592 3078 4.272018 CGGCAGACAAGAAATCCATAAGAG 59.728 45.833 0.00 0.00 0.00 2.85
2614 3100 1.134401 AGGCATCCACATAAGTCCACG 60.134 52.381 0.00 0.00 0.00 4.94
2757 3243 3.451526 TCGTTGCTCTCATCATCATCAC 58.548 45.455 0.00 0.00 0.00 3.06
2763 3249 2.169144 TGGTCATCGTTGCTCTCATCAT 59.831 45.455 0.00 0.00 0.00 2.45
2839 3325 7.147976 ACAAAACACAGAGATTAAAGGCAATC 58.852 34.615 0.00 0.00 35.53 2.67
2841 3327 6.321181 AGACAAAACACAGAGATTAAAGGCAA 59.679 34.615 0.00 0.00 0.00 4.52
2845 3331 8.012241 GCAGTAGACAAAACACAGAGATTAAAG 58.988 37.037 0.00 0.00 0.00 1.85
2860 3346 4.072131 GGTGGAATGAAGCAGTAGACAAA 58.928 43.478 0.00 0.00 0.00 2.83
2914 3400 2.421775 TGCAACTGGTTTGTGTACACAG 59.578 45.455 26.52 17.75 42.94 3.66
3006 3499 8.097662 AGACAGGTAGAAAGATCACCTTAAAAG 58.902 37.037 0.00 0.00 40.77 2.27
3011 3504 4.841246 ACAGACAGGTAGAAAGATCACCTT 59.159 41.667 0.00 0.00 40.77 3.50
3012 3505 4.221703 CACAGACAGGTAGAAAGATCACCT 59.778 45.833 0.00 0.00 43.56 4.00
3037 3530 4.307032 AGCAGTTGACACAGGGAATATT 57.693 40.909 0.00 0.00 0.00 1.28
3053 3590 4.142049 GGTAGAACTGAAGATGCTAGCAGT 60.142 45.833 23.89 11.33 42.91 4.40
3128 3665 3.594134 AGCACAGACAGTTAGCTCATTC 58.406 45.455 0.00 0.00 0.00 2.67
3130 3667 3.007290 TCAAGCACAGACAGTTAGCTCAT 59.993 43.478 0.00 0.00 33.83 2.90
3250 3823 7.013178 CACATTATTACCATGTATCACTGCCAA 59.987 37.037 0.00 0.00 32.88 4.52
3266 3839 8.819974 CCTGCATTGGAAAAATCACATTATTAC 58.180 33.333 0.00 0.00 0.00 1.89
3469 4044 4.394300 ACAAGCTAAGCTAAATGACTGCTG 59.606 41.667 0.00 0.00 38.25 4.41
3470 4045 4.583871 ACAAGCTAAGCTAAATGACTGCT 58.416 39.130 0.00 0.00 38.25 4.24
3483 4058 2.420642 TGCTGCTTCTGACAAGCTAAG 58.579 47.619 7.78 0.00 43.38 2.18
3537 4112 2.502130 TCGGTGGTATACAATGGAAGCA 59.498 45.455 5.01 0.00 0.00 3.91
3544 4119 5.775701 AGAATAGCTCTCGGTGGTATACAAT 59.224 40.000 5.01 0.00 0.00 2.71
3650 4225 5.873712 ACTTTCACAAATCAATGCAAACACA 59.126 32.000 0.00 0.00 0.00 3.72
3651 4226 6.348621 ACTTTCACAAATCAATGCAAACAC 57.651 33.333 0.00 0.00 0.00 3.32
3693 4268 4.421058 GGTATATCATCGCGATTACTGCA 58.579 43.478 21.14 1.87 35.39 4.41
3719 4294 5.385509 ACACCACATGCTTACAAATAACC 57.614 39.130 0.00 0.00 0.00 2.85
3747 4324 9.844257 AATAATCTCCAAACCATTTTGTTTCAA 57.156 25.926 0.00 0.00 40.61 2.69
3828 4406 5.465390 CCCGTCCATACAATGTAATACACAG 59.535 44.000 0.00 0.00 41.51 3.66
3837 4415 0.618458 ACAGCCCGTCCATACAATGT 59.382 50.000 0.00 0.00 0.00 2.71
3838 4416 1.750193 AACAGCCCGTCCATACAATG 58.250 50.000 0.00 0.00 0.00 2.82
3847 4425 0.608035 TCCATGGAAAACAGCCCGTC 60.608 55.000 13.46 0.00 0.00 4.79
3851 4429 4.799564 TTGTATTCCATGGAAAACAGCC 57.200 40.909 30.28 14.46 37.69 4.85
3860 4459 5.699001 CCATGCATGATTTTGTATTCCATGG 59.301 40.000 28.31 4.97 40.58 3.66
3871 4470 5.588246 TGTGACGTATACCATGCATGATTTT 59.412 36.000 28.31 11.59 0.00 1.82
3899 4498 0.877649 CAACGCGGCATCATAGCTCT 60.878 55.000 12.47 0.00 34.17 4.09
3934 4551 5.047847 TGTTATAGAGGATGCGCAAAGTAC 58.952 41.667 17.11 0.00 0.00 2.73
3935 4552 5.270893 TGTTATAGAGGATGCGCAAAGTA 57.729 39.130 17.11 2.16 0.00 2.24
3953 4570 3.021473 GCCGACCCGACCCATGTTA 62.021 63.158 0.00 0.00 0.00 2.41
4013 4631 2.095617 CGAGCAAGCATCATCACAAACA 60.096 45.455 0.00 0.00 0.00 2.83
4015 4633 2.417586 CTCGAGCAAGCATCATCACAAA 59.582 45.455 0.00 0.00 0.00 2.83
4074 4692 1.004560 CACAGCGAAGAGGCCTCAA 60.005 57.895 33.90 0.00 0.00 3.02
4087 4707 1.806542 CTCCACACACAATACCACAGC 59.193 52.381 0.00 0.00 0.00 4.40
4102 4722 1.535462 GGCACACACAACATACTCCAC 59.465 52.381 0.00 0.00 0.00 4.02
4121 4741 1.080569 GCCACAAACCGCAGAATGG 60.081 57.895 0.00 0.00 35.86 3.16
4147 4767 5.391203 CCCAGGTAATTAACGAAAAACCGAG 60.391 44.000 0.00 0.00 34.10 4.63
4166 4786 3.615834 GCAAAAGAAGAGAATTGCCCAGG 60.616 47.826 0.00 0.00 41.67 4.45
4208 4828 3.383185 TGCATACATGATACACCGAGTCA 59.617 43.478 0.00 0.00 0.00 3.41
4214 4834 6.432162 AGATGGATTTGCATACATGATACACC 59.568 38.462 0.00 0.00 33.58 4.16
4220 4840 9.056005 GTTAGTTAGATGGATTTGCATACATGA 57.944 33.333 0.00 0.00 33.58 3.07
4223 4843 7.573710 AGGTTAGTTAGATGGATTTGCATACA 58.426 34.615 0.00 0.00 0.00 2.29
4225 4845 6.929049 CGAGGTTAGTTAGATGGATTTGCATA 59.071 38.462 0.00 0.00 0.00 3.14
4234 4854 4.103357 CACGAACGAGGTTAGTTAGATGG 58.897 47.826 0.14 0.00 29.58 3.51
4237 4857 4.318332 TCTCACGAACGAGGTTAGTTAGA 58.682 43.478 0.14 2.80 32.23 2.10
4253 4874 3.311048 TGTCTCGATCTGAATCTCTCACG 59.689 47.826 0.00 0.00 0.00 4.35
4277 4898 2.287103 CGATGTTGTGCTGATGATGAGG 59.713 50.000 0.00 0.00 0.00 3.86
4278 4899 3.192466 TCGATGTTGTGCTGATGATGAG 58.808 45.455 0.00 0.00 0.00 2.90
4285 5789 1.946745 TGTGTTCGATGTTGTGCTGA 58.053 45.000 0.00 0.00 0.00 4.26
4303 5807 4.815846 TGTGGTAAATGATGATCCGTGATG 59.184 41.667 0.00 0.00 0.00 3.07
4304 5808 5.034852 TGTGGTAAATGATGATCCGTGAT 57.965 39.130 0.00 0.00 0.00 3.06
4415 5919 8.973378 CATAAAAGGTGTTTTCTTTTTATGCGA 58.027 29.630 15.44 0.00 42.36 5.10
4432 5936 7.151976 GGCAACTAATTGAACACATAAAAGGT 58.848 34.615 0.00 0.00 38.15 3.50


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

AutoCloner maintained by Alex Coulton.