Multiple sequence alignment - TraesCS6A01G342600

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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 TraesCS6A01G342600 chr6A 100.000 2249 0 0 1 2249 575201247 575198999 0.000000e+00 4154.0
1 TraesCS6A01G342600 chr6A 86.279 860 54 29 520 1368 575143777 575142971 0.000000e+00 876.0
2 TraesCS6A01G342600 chr6A 88.527 584 34 8 1556 2115 575142975 575142401 0.000000e+00 676.0
3 TraesCS6A01G342600 chr6A 89.355 310 28 2 1021 1330 574911655 574911959 3.500000e-103 385.0
4 TraesCS6A01G342600 chr6B 86.795 621 63 6 1 610 647955069 647954457 0.000000e+00 675.0
5 TraesCS6A01G342600 chr6B 83.671 692 78 17 79 757 647846702 647846033 8.820000e-174 619.0
6 TraesCS6A01G342600 chr6B 87.016 439 35 5 934 1368 647952526 647952106 2.020000e-130 475.0
7 TraesCS6A01G342600 chr6B 90.116 344 27 5 893 1232 647837456 647837116 7.370000e-120 440.0
8 TraesCS6A01G342600 chr6B 92.941 255 10 3 1004 1258 647588897 647589143 4.560000e-97 364.0
9 TraesCS6A01G342600 chr6B 84.840 376 42 7 961 1330 647690997 647691363 4.560000e-97 364.0
10 TraesCS6A01G342600 chr6B 87.983 233 18 7 1742 1968 647951854 647951626 1.320000e-67 267.0
11 TraesCS6A01G342600 chr6B 90.278 144 8 2 743 886 647837636 647837499 1.370000e-42 183.0
12 TraesCS6A01G342600 chr6B 88.652 141 8 2 1594 1734 647952092 647951960 4.970000e-37 165.0
13 TraesCS6A01G342600 chr6D 87.768 327 26 5 1004 1330 429666524 429666836 9.810000e-99 370.0
14 TraesCS6A01G342600 chr4A 88.346 266 25 3 969 1233 109843116 109843376 4.660000e-82 315.0
15 TraesCS6A01G342600 chr4D 87.970 266 26 3 969 1233 354890731 354890471 2.170000e-80 309.0
16 TraesCS6A01G342600 chr7D 89.855 207 15 3 1354 1556 625764010 625763806 6.160000e-66 261.0
17 TraesCS6A01G342600 chr7D 90.761 184 13 3 1367 1550 364301919 364301740 2.230000e-60 243.0
18 TraesCS6A01G342600 chr5B 90.761 184 15 1 1367 1550 229749826 229750007 6.200000e-61 244.0
19 TraesCS6A01G342600 chr5B 90.761 184 15 1 1367 1550 300265433 300265614 6.200000e-61 244.0
20 TraesCS6A01G342600 chr5B 90.761 184 14 2 1367 1550 298640340 298640520 2.230000e-60 243.0
21 TraesCS6A01G342600 chr5B 90.270 185 14 3 1367 1550 543565828 543566009 2.890000e-59 239.0
22 TraesCS6A01G342600 chr2B 90.761 184 15 1 1367 1550 798105921 798106102 6.200000e-61 244.0
23 TraesCS6A01G342600 chr2B 100.000 31 0 0 2207 2237 291587739 291587709 8.680000e-05 58.4
24 TraesCS6A01G342600 chr3B 90.761 184 14 2 1367 1550 349759892 349759712 2.230000e-60 243.0
25 TraesCS6A01G342600 chr7A 87.624 202 22 3 1363 1562 669697870 669698070 4.830000e-57 231.0
26 TraesCS6A01G342600 chr4B 86.486 74 9 1 559 631 31643382 31643309 1.850000e-11 80.5
27 TraesCS6A01G342600 chr2A 95.000 40 2 0 2208 2247 622856146 622856185 1.860000e-06 63.9
28 TraesCS6A01G342600 chr2A 100.000 31 0 0 2207 2237 240460529 240460499 8.680000e-05 58.4
29 TraesCS6A01G342600 chr2D 100.000 31 0 0 2207 2237 220959663 220959633 8.680000e-05 58.4
30 TraesCS6A01G342600 chr1B 100.000 28 0 0 2213 2240 558933341 558933368 4.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G342600 chr6A 575198999 575201247 2248 True 4154.0 4154 100.0000 1 2249 1 chr6A.!!$R1 2248
1 TraesCS6A01G342600 chr6A 575142401 575143777 1376 True 776.0 876 87.4030 520 2115 2 chr6A.!!$R2 1595
2 TraesCS6A01G342600 chr6B 647846033 647846702 669 True 619.0 619 83.6710 79 757 1 chr6B.!!$R1 678
3 TraesCS6A01G342600 chr6B 647951626 647955069 3443 True 395.5 675 87.6115 1 1968 4 chr6B.!!$R3 1967
4 TraesCS6A01G342600 chr6B 647837116 647837636 520 True 311.5 440 90.1970 743 1232 2 chr6B.!!$R2 489

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
769 785 0.321671 ACCTCCAATGGTGTGACGAG 59.678 55.0 0.0 0.0 39.17 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 3935 0.099968 GTCGCACTCGCACATACCTA 59.9 55.0 0.0 0.0 38.4 3.08 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
45 46 4.369809 TCTCCCTTTCCTTCCCTCTATT 57.630 45.455 0.00 0.00 0.00 1.73
48 49 4.444611 TCCCTTTCCTTCCCTCTATTTCA 58.555 43.478 0.00 0.00 0.00 2.69
66 67 0.686224 CATCTCCATGCCTCCCTCTC 59.314 60.000 0.00 0.00 0.00 3.20
246 249 3.200593 GGGCTGAGCTGTGCATCG 61.201 66.667 3.72 0.00 0.00 3.84
284 287 1.004918 CTCGTGCCCGACCTTTCTT 60.005 57.895 0.00 0.00 38.40 2.52
294 297 1.615107 GACCTTTCTTCGCCACGTCG 61.615 60.000 0.00 0.00 0.00 5.12
308 311 1.371267 CGTCGTTGTTCCTCTCGCA 60.371 57.895 0.00 0.00 0.00 5.10
357 360 2.970324 GTTTGTCGCCTCACGCCA 60.970 61.111 0.00 0.00 43.23 5.69
378 381 1.069204 GTTGATCCTCTGCATCGCCTA 59.931 52.381 0.00 0.00 0.00 3.93
381 384 3.165071 TGATCCTCTGCATCGCCTATAA 58.835 45.455 0.00 0.00 0.00 0.98
390 393 2.030185 GCATCGCCTATAACCGAGAGAA 60.030 50.000 0.00 0.00 36.86 2.87
418 421 0.324552 CCCATGGGTTGCATCCTTGA 60.325 55.000 23.93 0.00 32.96 3.02
419 422 1.559368 CCATGGGTTGCATCCTTGAA 58.441 50.000 13.47 0.00 32.96 2.69
538 547 1.331756 CTATTGCAATGGTGGAGACGC 59.668 52.381 22.27 0.00 41.20 5.19
547 560 2.678934 TGGAGACGCCGGCTACTT 60.679 61.111 26.68 7.13 40.66 2.24
553 566 2.434185 CGCCGGCTACTTGAAGCA 60.434 61.111 26.68 0.00 44.64 3.91
562 575 4.276183 CGGCTACTTGAAGCACTAGATCTA 59.724 45.833 1.69 1.69 44.64 1.98
565 578 6.183360 GGCTACTTGAAGCACTAGATCTAACT 60.183 42.308 3.57 0.00 44.64 2.24
572 585 2.223595 GCACTAGATCTAACTGCTCGCA 60.224 50.000 18.69 0.00 0.00 5.10
576 589 1.827969 AGATCTAACTGCTCGCAACCT 59.172 47.619 0.00 0.00 0.00 3.50
703 717 8.692110 TCAGTGATCAAATGCATTTTGTTATC 57.308 30.769 21.95 19.51 44.25 1.75
769 785 0.321671 ACCTCCAATGGTGTGACGAG 59.678 55.000 0.00 0.00 39.17 4.18
821 861 3.623060 CCCTTCATTTCACGGAGTACATG 59.377 47.826 0.00 0.00 41.61 3.21
822 862 4.253685 CCTTCATTTCACGGAGTACATGT 58.746 43.478 2.69 2.69 41.61 3.21
823 863 5.416083 CCTTCATTTCACGGAGTACATGTA 58.584 41.667 0.08 0.08 41.61 2.29
824 864 5.291128 CCTTCATTTCACGGAGTACATGTAC 59.709 44.000 25.51 25.51 41.61 2.90
825 865 5.394224 TCATTTCACGGAGTACATGTACA 57.606 39.130 32.02 13.55 41.61 2.90
826 866 5.972935 TCATTTCACGGAGTACATGTACAT 58.027 37.500 32.02 19.61 41.61 2.29
827 867 6.403049 TCATTTCACGGAGTACATGTACATT 58.597 36.000 32.02 16.67 41.61 2.71
945 2607 4.626604 CACTACGCGTTTAAATAGAACCCA 59.373 41.667 20.78 0.00 0.00 4.51
984 2646 3.589288 ACACTATTCCTTTTCCTCTGCCT 59.411 43.478 0.00 0.00 0.00 4.75
991 2654 4.030216 TCCTTTTCCTCTGCCTTTTTGTT 58.970 39.130 0.00 0.00 0.00 2.83
994 2657 1.774110 TCCTCTGCCTTTTTGTTGCA 58.226 45.000 0.00 0.00 0.00 4.08
1007 2670 0.681887 TGTTGCATGGAGATGGCAGG 60.682 55.000 0.00 0.00 38.97 4.85
1009 2672 0.332293 TTGCATGGAGATGGCAGGAA 59.668 50.000 0.00 0.00 38.97 3.36
1010 2673 0.394762 TGCATGGAGATGGCAGGAAC 60.395 55.000 0.00 0.00 32.95 3.62
1011 2674 1.442526 GCATGGAGATGGCAGGAACG 61.443 60.000 0.00 0.00 0.00 3.95
1013 2676 0.911769 ATGGAGATGGCAGGAACGAA 59.088 50.000 0.00 0.00 0.00 3.85
1015 2678 0.462759 GGAGATGGCAGGAACGAAGG 60.463 60.000 0.00 0.00 0.00 3.46
1016 2679 0.462759 GAGATGGCAGGAACGAAGGG 60.463 60.000 0.00 0.00 0.00 3.95
1017 2680 2.044946 ATGGCAGGAACGAAGGGC 60.045 61.111 0.00 0.00 0.00 5.19
1019 2682 4.388499 GGCAGGAACGAAGGGCGA 62.388 66.667 0.00 0.00 44.57 5.54
1270 2933 3.139077 CTGCCACCTACGAATATTTCCC 58.861 50.000 0.00 0.00 0.00 3.97
1303 2969 7.041098 AGTGGTAGCTGTTCTGTTCTTTAATTG 60.041 37.037 0.00 0.00 0.00 2.32
1348 3014 4.897856 ACGGCGTTTTGTGCGTGC 62.898 61.111 6.77 0.00 0.00 5.34
1367 3033 7.955324 GTGCGTGCGTTACATATATTGAATTAT 59.045 33.333 0.00 0.00 0.00 1.28
1368 3034 8.166066 TGCGTGCGTTACATATATTGAATTATC 58.834 33.333 0.00 0.00 0.00 1.75
1369 3035 8.166066 GCGTGCGTTACATATATTGAATTATCA 58.834 33.333 0.00 0.00 0.00 2.15
1423 3089 8.561738 TTTTAAGGATGTCACATCTAAACTCC 57.438 34.615 17.46 0.18 0.00 3.85
1424 3090 4.762289 AGGATGTCACATCTAAACTCCC 57.238 45.455 17.46 0.00 0.00 4.30
1425 3091 4.104086 AGGATGTCACATCTAAACTCCCA 58.896 43.478 17.46 0.00 0.00 4.37
1426 3092 4.080863 AGGATGTCACATCTAAACTCCCAC 60.081 45.833 17.46 0.00 0.00 4.61
1427 3093 4.323485 GGATGTCACATCTAAACTCCCACA 60.323 45.833 17.46 0.00 0.00 4.17
1428 3094 4.698201 TGTCACATCTAAACTCCCACAA 57.302 40.909 0.00 0.00 0.00 3.33
1429 3095 5.042463 TGTCACATCTAAACTCCCACAAA 57.958 39.130 0.00 0.00 0.00 2.83
1430 3096 5.630121 TGTCACATCTAAACTCCCACAAAT 58.370 37.500 0.00 0.00 0.00 2.32
1431 3097 6.774673 TGTCACATCTAAACTCCCACAAATA 58.225 36.000 0.00 0.00 0.00 1.40
1432 3098 7.402054 TGTCACATCTAAACTCCCACAAATAT 58.598 34.615 0.00 0.00 0.00 1.28
1433 3099 8.544622 TGTCACATCTAAACTCCCACAAATATA 58.455 33.333 0.00 0.00 0.00 0.86
1434 3100 9.561069 GTCACATCTAAACTCCCACAAATATAT 57.439 33.333 0.00 0.00 0.00 0.86
1502 3168 8.723942 AGATTACAAATAGAGTGGACATCAAC 57.276 34.615 0.00 0.00 0.00 3.18
1503 3169 8.543774 AGATTACAAATAGAGTGGACATCAACT 58.456 33.333 0.00 0.00 0.00 3.16
1504 3170 9.167311 GATTACAAATAGAGTGGACATCAACTT 57.833 33.333 0.00 0.00 0.00 2.66
1506 3172 9.653287 TTACAAATAGAGTGGACATCAACTTAG 57.347 33.333 0.00 0.00 0.00 2.18
1507 3173 7.907389 ACAAATAGAGTGGACATCAACTTAGA 58.093 34.615 0.00 0.00 0.00 2.10
1508 3174 8.543774 ACAAATAGAGTGGACATCAACTTAGAT 58.456 33.333 0.00 0.00 0.00 1.98
1537 3203 9.973450 AACATAACTATGTCACATCTAGATGTC 57.027 33.333 31.17 22.30 45.54 3.06
1538 3204 9.360901 ACATAACTATGTCACATCTAGATGTCT 57.639 33.333 31.17 19.23 44.27 3.41
1563 3229 9.906660 CTCCTAGACAGACTCATTATTATTGAC 57.093 37.037 0.00 0.00 0.00 3.18
1662 3328 2.414559 CCTCAGTTGCCAAATGCTTACG 60.415 50.000 0.00 0.00 42.00 3.18
1663 3329 1.068610 TCAGTTGCCAAATGCTTACGC 60.069 47.619 0.00 0.00 42.00 4.42
1664 3330 1.068333 CAGTTGCCAAATGCTTACGCT 60.068 47.619 0.00 0.00 42.00 5.07
1665 3331 1.068333 AGTTGCCAAATGCTTACGCTG 60.068 47.619 0.00 0.00 42.00 5.18
1667 3333 0.958091 TGCCAAATGCTTACGCTGTT 59.042 45.000 0.00 0.00 42.00 3.16
1668 3334 2.155279 TGCCAAATGCTTACGCTGTTA 58.845 42.857 0.00 0.00 42.00 2.41
1669 3335 2.095466 TGCCAAATGCTTACGCTGTTAC 60.095 45.455 0.00 0.00 42.00 2.50
1670 3336 2.769376 CCAAATGCTTACGCTGTTACG 58.231 47.619 0.00 0.00 36.97 3.18
1707 3373 4.371624 TTCCAGCATCTTTTCTTCCAGA 57.628 40.909 0.00 0.00 0.00 3.86
1737 3403 7.087409 TCATATTGTTCTGTGCCATTTACTG 57.913 36.000 0.00 0.00 0.00 2.74
1835 3599 6.038997 AGAACCTCTTTAAGTAGCACGATT 57.961 37.500 0.00 0.00 0.00 3.34
1902 3706 3.923827 ACTTGCGCAAAATGTTGTTTC 57.076 38.095 25.01 0.00 37.06 2.78
1969 3773 5.523552 CAGTGGAAAACTTTTGGTGAAATCC 59.476 40.000 0.00 0.00 36.83 3.01
1995 3799 8.798153 CGCAAACTAATATTTAGGAAAAGCAAG 58.202 33.333 0.00 0.00 0.00 4.01
2023 3827 6.694411 GCATGATACATTTCTCAAATCACACC 59.306 38.462 0.00 0.00 29.93 4.16
2046 3850 7.968405 CACCAGCACATAAAAAGTTATAGGAAC 59.032 37.037 0.00 0.00 0.00 3.62
2053 3857 8.528643 ACATAAAAAGTTATAGGAACCCAAAGC 58.471 33.333 0.00 0.00 0.00 3.51
2065 3869 4.158579 GGAACCCAAAGCTCCTATGAAAAG 59.841 45.833 0.00 0.00 0.00 2.27
2086 3890 1.811965 TCTTGCAATCAATGTGGTCCG 59.188 47.619 0.00 0.00 0.00 4.79
2087 3891 0.887247 TTGCAATCAATGTGGTCCGG 59.113 50.000 0.00 0.00 0.00 5.14
2096 3900 0.613777 ATGTGGTCCGGAGAGGTTTC 59.386 55.000 3.06 0.00 41.99 2.78
2110 3914 6.014156 CGGAGAGGTTTCTTATGGAGGATATT 60.014 42.308 0.00 0.00 32.53 1.28
2115 3919 5.162980 GGTTTCTTATGGAGGATATTGGGGT 60.163 44.000 0.00 0.00 0.00 4.95
2116 3920 6.373759 GTTTCTTATGGAGGATATTGGGGTT 58.626 40.000 0.00 0.00 0.00 4.11
2117 3921 5.582950 TCTTATGGAGGATATTGGGGTTG 57.417 43.478 0.00 0.00 0.00 3.77
2118 3922 5.231552 TCTTATGGAGGATATTGGGGTTGA 58.768 41.667 0.00 0.00 0.00 3.18
2119 3923 5.857283 TCTTATGGAGGATATTGGGGTTGAT 59.143 40.000 0.00 0.00 0.00 2.57
2120 3924 3.882102 TGGAGGATATTGGGGTTGATG 57.118 47.619 0.00 0.00 0.00 3.07
2121 3925 3.130450 TGGAGGATATTGGGGTTGATGT 58.870 45.455 0.00 0.00 0.00 3.06
2122 3926 3.117550 TGGAGGATATTGGGGTTGATGTG 60.118 47.826 0.00 0.00 0.00 3.21
2123 3927 3.117512 GGAGGATATTGGGGTTGATGTGT 60.118 47.826 0.00 0.00 0.00 3.72
2124 3928 4.536765 GAGGATATTGGGGTTGATGTGTT 58.463 43.478 0.00 0.00 0.00 3.32
2125 3929 4.280819 AGGATATTGGGGTTGATGTGTTG 58.719 43.478 0.00 0.00 0.00 3.33
2126 3930 4.017591 AGGATATTGGGGTTGATGTGTTGA 60.018 41.667 0.00 0.00 0.00 3.18
2127 3931 4.895297 GGATATTGGGGTTGATGTGTTGAT 59.105 41.667 0.00 0.00 0.00 2.57
2128 3932 6.068010 GGATATTGGGGTTGATGTGTTGATA 58.932 40.000 0.00 0.00 0.00 2.15
2129 3933 6.207417 GGATATTGGGGTTGATGTGTTGATAG 59.793 42.308 0.00 0.00 0.00 2.08
2130 3934 4.380843 TTGGGGTTGATGTGTTGATAGT 57.619 40.909 0.00 0.00 0.00 2.12
2131 3935 4.380843 TGGGGTTGATGTGTTGATAGTT 57.619 40.909 0.00 0.00 0.00 2.24
2132 3936 5.506730 TGGGGTTGATGTGTTGATAGTTA 57.493 39.130 0.00 0.00 0.00 2.24
2133 3937 5.496556 TGGGGTTGATGTGTTGATAGTTAG 58.503 41.667 0.00 0.00 0.00 2.34
2134 3938 4.881850 GGGGTTGATGTGTTGATAGTTAGG 59.118 45.833 0.00 0.00 0.00 2.69
2135 3939 5.497474 GGGTTGATGTGTTGATAGTTAGGT 58.503 41.667 0.00 0.00 0.00 3.08
2136 3940 6.352394 GGGGTTGATGTGTTGATAGTTAGGTA 60.352 42.308 0.00 0.00 0.00 3.08
2137 3941 7.280356 GGGTTGATGTGTTGATAGTTAGGTAT 58.720 38.462 0.00 0.00 0.00 2.73
2138 3942 7.226720 GGGTTGATGTGTTGATAGTTAGGTATG 59.773 40.741 0.00 0.00 0.00 2.39
2139 3943 7.769044 GGTTGATGTGTTGATAGTTAGGTATGT 59.231 37.037 0.00 0.00 0.00 2.29
2140 3944 8.604035 GTTGATGTGTTGATAGTTAGGTATGTG 58.396 37.037 0.00 0.00 0.00 3.21
2141 3945 6.761242 TGATGTGTTGATAGTTAGGTATGTGC 59.239 38.462 0.00 0.00 0.00 4.57
2142 3946 5.106442 TGTGTTGATAGTTAGGTATGTGCG 58.894 41.667 0.00 0.00 0.00 5.34
2143 3947 5.105675 TGTGTTGATAGTTAGGTATGTGCGA 60.106 40.000 0.00 0.00 0.00 5.10
2144 3948 5.459107 GTGTTGATAGTTAGGTATGTGCGAG 59.541 44.000 0.00 0.00 0.00 5.03
2145 3949 5.126545 TGTTGATAGTTAGGTATGTGCGAGT 59.873 40.000 0.00 0.00 0.00 4.18
2146 3950 5.183014 TGATAGTTAGGTATGTGCGAGTG 57.817 43.478 0.00 0.00 0.00 3.51
2147 3951 2.295253 AGTTAGGTATGTGCGAGTGC 57.705 50.000 0.00 0.00 43.20 4.40
2157 3961 2.202222 GCGAGTGCGACATGTTGC 60.202 61.111 28.13 28.13 40.82 4.17
2158 3962 2.953605 GCGAGTGCGACATGTTGCA 61.954 57.895 32.48 32.48 46.95 4.08
2165 3969 2.363683 TGCGACATGTTGCAATATCCA 58.636 42.857 33.67 12.56 46.20 3.41
2166 3970 2.950975 TGCGACATGTTGCAATATCCAT 59.049 40.909 33.67 0.00 46.20 3.41
2167 3971 4.133078 TGCGACATGTTGCAATATCCATA 58.867 39.130 33.67 11.14 46.20 2.74
2168 3972 4.213906 TGCGACATGTTGCAATATCCATAG 59.786 41.667 33.67 0.00 46.20 2.23
2169 3973 4.214119 GCGACATGTTGCAATATCCATAGT 59.786 41.667 29.49 0.84 39.74 2.12
2170 3974 5.277974 GCGACATGTTGCAATATCCATAGTT 60.278 40.000 29.49 0.00 39.74 2.24
2171 3975 6.073276 GCGACATGTTGCAATATCCATAGTTA 60.073 38.462 29.49 0.00 39.74 2.24
2172 3976 7.519809 GCGACATGTTGCAATATCCATAGTTAA 60.520 37.037 29.49 0.00 39.74 2.01
2173 3977 8.506437 CGACATGTTGCAATATCCATAGTTAAT 58.494 33.333 5.61 0.00 0.00 1.40
2201 4005 8.680039 TCTGGAAAGTATTTTCGGAACTTTAA 57.320 30.769 5.72 0.00 45.71 1.52
2202 4006 9.122779 TCTGGAAAGTATTTTCGGAACTTTAAA 57.877 29.630 5.72 0.00 45.71 1.52
2203 4007 9.177304 CTGGAAAGTATTTTCGGAACTTTAAAC 57.823 33.333 5.72 2.12 42.82 2.01
2204 4008 8.684520 TGGAAAGTATTTTCGGAACTTTAAACA 58.315 29.630 5.72 4.09 42.06 2.83
2205 4009 9.518906 GGAAAGTATTTTCGGAACTTTAAACAA 57.481 29.630 5.72 0.00 42.06 2.83
2215 4019 9.887406 TTCGGAACTTTAAACAAATACTTCATC 57.113 29.630 0.00 0.00 0.00 2.92
2216 4020 8.508875 TCGGAACTTTAAACAAATACTTCATCC 58.491 33.333 0.00 0.00 0.00 3.51
2217 4021 7.480542 CGGAACTTTAAACAAATACTTCATCCG 59.519 37.037 0.00 0.00 36.95 4.18
2218 4022 8.294577 GGAACTTTAAACAAATACTTCATCCGT 58.705 33.333 0.00 0.00 0.00 4.69
2219 4023 9.673454 GAACTTTAAACAAATACTTCATCCGTT 57.327 29.630 0.00 0.00 0.00 4.44
2220 4024 9.673454 AACTTTAAACAAATACTTCATCCGTTC 57.327 29.630 0.00 0.00 0.00 3.95
2221 4025 8.842280 ACTTTAAACAAATACTTCATCCGTTCA 58.158 29.630 0.00 0.00 0.00 3.18
2222 4026 9.840427 CTTTAAACAAATACTTCATCCGTTCAT 57.160 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.082690 GGAGAAAGAAAGAGCGGCAG 58.917 55.000 1.45 0.00 0.00 4.85
10 11 0.321653 GGGAGAAAGAAAGAGCGGCA 60.322 55.000 1.45 0.00 0.00 5.69
45 46 1.135094 GAGGGAGGCATGGAGATGAA 58.865 55.000 0.00 0.00 0.00 2.57
48 49 0.831288 CGAGAGGGAGGCATGGAGAT 60.831 60.000 0.00 0.00 0.00 2.75
66 67 2.428890 AGCTTCAGAGATGGTTCCTACG 59.571 50.000 0.00 0.00 0.00 3.51
77 78 1.077930 GCCATGGCAGCTTCAGAGA 60.078 57.895 32.08 0.00 41.49 3.10
112 115 4.072088 GTTGTCGGCAGGTTCGCG 62.072 66.667 0.00 0.00 0.00 5.87
134 137 3.532155 GCAGAGCGGACCGGAGAT 61.532 66.667 17.22 0.00 0.00 2.75
163 166 2.670148 GGGAGCAGTGGTGGGGTAG 61.670 68.421 0.00 0.00 0.00 3.18
220 223 2.190578 GCTCAGCCCCGCATAGTT 59.809 61.111 0.00 0.00 0.00 2.24
231 234 3.873883 GGCGATGCACAGCTCAGC 61.874 66.667 13.87 0.00 0.00 4.26
284 287 2.659244 GGAACAACGACGTGGCGA 60.659 61.111 0.25 0.00 34.83 5.54
294 297 1.696832 GGCGATGCGAGAGGAACAAC 61.697 60.000 0.00 0.00 32.68 3.32
330 333 0.669318 GGCGACAAACTGATCCACGA 60.669 55.000 0.00 0.00 0.00 4.35
337 340 1.954146 GCGTGAGGCGACAAACTGA 60.954 57.895 0.00 0.00 44.77 3.41
338 341 2.551270 GCGTGAGGCGACAAACTG 59.449 61.111 0.00 0.00 44.77 3.16
357 360 0.179062 GGCGATGCAGAGGATCAACT 60.179 55.000 0.00 0.00 37.82 3.16
378 381 1.207329 GTGGTGGCTTCTCTCGGTTAT 59.793 52.381 0.00 0.00 0.00 1.89
381 384 2.584391 GGTGGTGGCTTCTCTCGGT 61.584 63.158 0.00 0.00 0.00 4.69
454 461 9.382275 ACAGAAGTCTTGTTGCATTTTTATTTT 57.618 25.926 0.00 0.00 0.00 1.82
455 462 8.947055 ACAGAAGTCTTGTTGCATTTTTATTT 57.053 26.923 0.00 0.00 0.00 1.40
456 463 8.947055 AACAGAAGTCTTGTTGCATTTTTATT 57.053 26.923 0.00 0.00 0.00 1.40
458 465 9.862371 TTTAACAGAAGTCTTGTTGCATTTTTA 57.138 25.926 0.00 0.00 0.00 1.52
459 466 8.770438 TTTAACAGAAGTCTTGTTGCATTTTT 57.230 26.923 0.00 0.00 0.00 1.94
507 516 6.543465 CCACCATTGCAATAGAGATCTTGTTA 59.457 38.462 12.53 0.00 0.00 2.41
538 547 1.476891 TCTAGTGCTTCAAGTAGCCGG 59.523 52.381 0.00 0.00 40.49 6.13
547 560 4.201960 CGAGCAGTTAGATCTAGTGCTTCA 60.202 45.833 28.86 4.05 44.42 3.02
553 566 3.181485 GGTTGCGAGCAGTTAGATCTAGT 60.181 47.826 2.02 0.00 0.00 2.57
562 575 2.980233 GCCAGGTTGCGAGCAGTT 60.980 61.111 5.82 0.00 0.00 3.16
572 585 4.830600 TCTTTTTAAAAGATCGGCCAGGTT 59.169 37.500 15.24 0.00 0.00 3.50
576 589 5.393027 GCTCATCTTTTTAAAAGATCGGCCA 60.393 40.000 24.82 9.82 34.96 5.36
665 678 4.318332 TGATCACTGATTGCTCTTTTCGT 58.682 39.130 0.00 0.00 0.00 3.85
723 739 8.304596 GCAAGATTGATGGTCATCATATTTCAT 58.695 33.333 13.58 4.31 46.12 2.57
724 740 7.285858 TGCAAGATTGATGGTCATCATATTTCA 59.714 33.333 13.58 7.62 46.12 2.69
725 741 7.594015 GTGCAAGATTGATGGTCATCATATTTC 59.406 37.037 13.58 9.07 46.12 2.17
726 742 7.431249 GTGCAAGATTGATGGTCATCATATTT 58.569 34.615 13.58 6.52 46.12 1.40
727 743 6.015688 GGTGCAAGATTGATGGTCATCATATT 60.016 38.462 13.58 7.08 46.12 1.28
728 744 5.475909 GGTGCAAGATTGATGGTCATCATAT 59.524 40.000 13.58 10.16 46.12 1.78
738 754 3.181479 CCATTGGAGGTGCAAGATTGATG 60.181 47.826 0.00 0.00 0.00 3.07
751 767 0.608130 TCTCGTCACACCATTGGAGG 59.392 55.000 10.37 3.62 0.00 4.30
766 782 3.777465 TTGAATCCGGTAGAGTTCTCG 57.223 47.619 0.00 0.00 0.00 4.04
767 783 4.271291 GCATTTGAATCCGGTAGAGTTCTC 59.729 45.833 0.00 0.00 0.00 2.87
769 785 3.938963 TGCATTTGAATCCGGTAGAGTTC 59.061 43.478 0.00 0.54 0.00 3.01
821 861 6.526674 GCAGTAATTACACAAGCCAAATGTAC 59.473 38.462 17.65 0.00 0.00 2.90
822 862 6.432783 AGCAGTAATTACACAAGCCAAATGTA 59.567 34.615 17.65 0.00 0.00 2.29
823 863 5.243730 AGCAGTAATTACACAAGCCAAATGT 59.756 36.000 17.65 0.00 0.00 2.71
824 864 5.574055 CAGCAGTAATTACACAAGCCAAATG 59.426 40.000 17.65 4.41 0.00 2.32
825 865 5.476599 TCAGCAGTAATTACACAAGCCAAAT 59.523 36.000 17.65 0.00 0.00 2.32
826 866 4.824537 TCAGCAGTAATTACACAAGCCAAA 59.175 37.500 17.65 2.79 0.00 3.28
827 867 4.393834 TCAGCAGTAATTACACAAGCCAA 58.606 39.130 17.65 4.82 0.00 4.52
945 2607 0.537143 TGTGACGCTTGGGAATTGCT 60.537 50.000 0.00 0.00 0.00 3.91
984 2646 2.367894 TGCCATCTCCATGCAACAAAAA 59.632 40.909 0.00 0.00 0.00 1.94
991 2654 0.394762 GTTCCTGCCATCTCCATGCA 60.395 55.000 0.00 0.00 0.00 3.96
994 2657 0.911769 TTCGTTCCTGCCATCTCCAT 59.088 50.000 0.00 0.00 0.00 3.41
1007 2670 3.170585 CGTCGTCGCCCTTCGTTC 61.171 66.667 0.00 0.00 39.67 3.95
1011 2674 4.790861 GGTCCGTCGTCGCCCTTC 62.791 72.222 0.00 0.00 35.54 3.46
1054 2717 3.075005 GGCCACGCAGGAGTAGGA 61.075 66.667 0.00 0.00 41.22 2.94
1185 2848 2.440796 ATGGCGGCCTGGTTCATG 60.441 61.111 21.46 0.00 0.00 3.07
1186 2849 2.440796 CATGGCGGCCTGGTTCAT 60.441 61.111 21.46 0.39 0.00 2.57
1281 2944 8.089115 ACTCAATTAAAGAACAGAACAGCTAC 57.911 34.615 0.00 0.00 0.00 3.58
1284 2947 8.131731 AGAAACTCAATTAAAGAACAGAACAGC 58.868 33.333 0.00 0.00 0.00 4.40
1303 2969 4.353383 AACCCACTAACCTGAGAAACTC 57.647 45.455 0.00 0.00 0.00 3.01
1397 3063 9.010029 GGAGTTTAGATGTGACATCCTTAAAAA 57.990 33.333 21.05 11.39 0.00 1.94
1398 3064 7.610305 GGGAGTTTAGATGTGACATCCTTAAAA 59.390 37.037 21.05 13.52 0.00 1.52
1399 3065 7.110155 GGGAGTTTAGATGTGACATCCTTAAA 58.890 38.462 21.05 16.39 0.00 1.52
1400 3066 6.214615 TGGGAGTTTAGATGTGACATCCTTAA 59.785 38.462 21.05 11.73 0.00 1.85
1401 3067 5.724370 TGGGAGTTTAGATGTGACATCCTTA 59.276 40.000 21.05 6.22 0.00 2.69
1402 3068 4.536090 TGGGAGTTTAGATGTGACATCCTT 59.464 41.667 21.05 7.22 0.00 3.36
1403 3069 4.080863 GTGGGAGTTTAGATGTGACATCCT 60.081 45.833 21.05 11.37 0.00 3.24
1404 3070 4.192317 GTGGGAGTTTAGATGTGACATCC 58.808 47.826 21.05 6.28 0.00 3.51
1405 3071 4.832248 TGTGGGAGTTTAGATGTGACATC 58.168 43.478 17.46 17.46 0.00 3.06
1406 3072 4.908601 TGTGGGAGTTTAGATGTGACAT 57.091 40.909 0.00 0.00 0.00 3.06
1407 3073 4.698201 TTGTGGGAGTTTAGATGTGACA 57.302 40.909 0.00 0.00 0.00 3.58
1408 3074 7.865706 ATATTTGTGGGAGTTTAGATGTGAC 57.134 36.000 0.00 0.00 0.00 3.67
1476 3142 9.817809 GTTGATGTCCACTCTATTTGTAATCTA 57.182 33.333 0.00 0.00 0.00 1.98
1477 3143 8.543774 AGTTGATGTCCACTCTATTTGTAATCT 58.456 33.333 0.00 0.00 0.00 2.40
1478 3144 8.723942 AGTTGATGTCCACTCTATTTGTAATC 57.276 34.615 0.00 0.00 0.00 1.75
1480 3146 9.653287 CTAAGTTGATGTCCACTCTATTTGTAA 57.347 33.333 0.00 0.00 0.00 2.41
1481 3147 9.031537 TCTAAGTTGATGTCCACTCTATTTGTA 57.968 33.333 0.00 0.00 0.00 2.41
1482 3148 7.907389 TCTAAGTTGATGTCCACTCTATTTGT 58.093 34.615 0.00 0.00 0.00 2.83
1483 3149 8.824781 CATCTAAGTTGATGTCCACTCTATTTG 58.175 37.037 6.97 0.00 39.05 2.32
1484 3150 8.954950 CATCTAAGTTGATGTCCACTCTATTT 57.045 34.615 6.97 0.00 39.05 1.40
1535 3201 9.906660 CAATAATAATGAGTCTGTCTAGGAGAC 57.093 37.037 12.53 12.53 45.26 3.36
1536 3202 9.868160 TCAATAATAATGAGTCTGTCTAGGAGA 57.132 33.333 0.00 0.00 0.00 3.71
1537 3203 9.906660 GTCAATAATAATGAGTCTGTCTAGGAG 57.093 37.037 0.00 0.00 0.00 3.69
1538 3204 9.647918 AGTCAATAATAATGAGTCTGTCTAGGA 57.352 33.333 0.00 0.00 0.00 2.94
1555 3221 8.888419 ACTGGGATCATCTCAATAGTCAATAAT 58.112 33.333 0.00 0.00 0.00 1.28
1563 3229 7.554476 TCGATACTACTGGGATCATCTCAATAG 59.446 40.741 1.22 1.22 0.00 1.73
1670 3336 2.992543 CTGGAATCGAATAGCTAGCTGC 59.007 50.000 27.68 14.75 43.29 5.25
1862 3634 7.043565 GCAAGTTTAATCACATGGGAATTGAT 58.956 34.615 0.00 0.00 0.00 2.57
1902 3706 8.586570 TTTTTGTGTTTTCCTATGCTGTAATG 57.413 30.769 0.00 0.00 0.00 1.90
1929 3733 4.776349 TCCACTGACTTAAAACTTGCTGA 58.224 39.130 0.00 0.00 0.00 4.26
1930 3734 5.499139 TTCCACTGACTTAAAACTTGCTG 57.501 39.130 0.00 0.00 0.00 4.41
1969 3773 8.682128 TTGCTTTTCCTAAATATTAGTTTGCG 57.318 30.769 0.00 0.00 0.00 4.85
1991 3795 4.201980 TGAGAAATGTATCATGCAGCTTGC 60.202 41.667 3.32 1.70 45.29 4.01
1995 3799 6.417044 GTGATTTGAGAAATGTATCATGCAGC 59.583 38.462 0.00 0.00 0.00 5.25
2023 3827 7.122055 TGGGTTCCTATAACTTTTTATGTGCTG 59.878 37.037 0.00 0.00 0.00 4.41
2046 3850 4.593956 AGACTTTTCATAGGAGCTTTGGG 58.406 43.478 0.00 0.00 0.00 4.12
2053 3857 6.748333 TGATTGCAAGACTTTTCATAGGAG 57.252 37.500 4.94 0.00 0.00 3.69
2059 3863 5.163426 ACCACATTGATTGCAAGACTTTTCA 60.163 36.000 4.94 0.00 37.45 2.69
2065 3869 2.414559 CGGACCACATTGATTGCAAGAC 60.415 50.000 4.94 2.22 37.45 3.01
2086 3890 6.943899 ATATCCTCCATAAGAAACCTCTCC 57.056 41.667 0.00 0.00 0.00 3.71
2087 3891 7.164803 CCAATATCCTCCATAAGAAACCTCTC 58.835 42.308 0.00 0.00 0.00 3.20
2096 3900 5.582950 TCAACCCCAATATCCTCCATAAG 57.417 43.478 0.00 0.00 0.00 1.73
2110 3914 4.380843 AACTATCAACACATCAACCCCA 57.619 40.909 0.00 0.00 0.00 4.96
2115 3919 7.279981 GCACATACCTAACTATCAACACATCAA 59.720 37.037 0.00 0.00 0.00 2.57
2116 3920 6.761242 GCACATACCTAACTATCAACACATCA 59.239 38.462 0.00 0.00 0.00 3.07
2117 3921 6.074302 CGCACATACCTAACTATCAACACATC 60.074 42.308 0.00 0.00 0.00 3.06
2118 3922 5.753438 CGCACATACCTAACTATCAACACAT 59.247 40.000 0.00 0.00 0.00 3.21
2119 3923 5.105675 TCGCACATACCTAACTATCAACACA 60.106 40.000 0.00 0.00 0.00 3.72
2120 3924 5.345702 TCGCACATACCTAACTATCAACAC 58.654 41.667 0.00 0.00 0.00 3.32
2121 3925 5.126545 ACTCGCACATACCTAACTATCAACA 59.873 40.000 0.00 0.00 0.00 3.33
2122 3926 5.459107 CACTCGCACATACCTAACTATCAAC 59.541 44.000 0.00 0.00 0.00 3.18
2123 3927 5.588240 CACTCGCACATACCTAACTATCAA 58.412 41.667 0.00 0.00 0.00 2.57
2124 3928 4.499188 GCACTCGCACATACCTAACTATCA 60.499 45.833 0.00 0.00 38.36 2.15
2125 3929 3.982058 GCACTCGCACATACCTAACTATC 59.018 47.826 0.00 0.00 38.36 2.08
2126 3930 3.550233 CGCACTCGCACATACCTAACTAT 60.550 47.826 0.00 0.00 38.40 2.12
2127 3931 2.223409 CGCACTCGCACATACCTAACTA 60.223 50.000 0.00 0.00 38.40 2.24
2128 3932 1.469251 CGCACTCGCACATACCTAACT 60.469 52.381 0.00 0.00 38.40 2.24
2129 3933 0.921347 CGCACTCGCACATACCTAAC 59.079 55.000 0.00 0.00 38.40 2.34
2130 3934 0.812549 TCGCACTCGCACATACCTAA 59.187 50.000 0.00 0.00 38.40 2.69
2131 3935 0.099968 GTCGCACTCGCACATACCTA 59.900 55.000 0.00 0.00 38.40 3.08
2132 3936 1.153823 GTCGCACTCGCACATACCT 60.154 57.895 0.00 0.00 38.40 3.08
2133 3937 0.806102 ATGTCGCACTCGCACATACC 60.806 55.000 0.00 0.00 35.93 2.73
2134 3938 0.298707 CATGTCGCACTCGCACATAC 59.701 55.000 0.00 0.00 35.93 2.39
2135 3939 0.108851 ACATGTCGCACTCGCACATA 60.109 50.000 0.00 0.00 35.93 2.29
2136 3940 0.950555 AACATGTCGCACTCGCACAT 60.951 50.000 0.00 0.00 37.13 3.21
2137 3941 1.594021 AACATGTCGCACTCGCACA 60.594 52.632 0.00 0.00 38.40 4.57
2138 3942 1.154599 CAACATGTCGCACTCGCAC 60.155 57.895 0.00 0.00 38.40 5.34
2139 3943 2.953605 GCAACATGTCGCACTCGCA 61.954 57.895 3.28 0.00 38.40 5.10
2140 3944 2.202222 GCAACATGTCGCACTCGC 60.202 61.111 3.28 0.00 35.26 5.03
2141 3945 0.166597 ATTGCAACATGTCGCACTCG 59.833 50.000 11.86 0.00 38.00 4.18
2142 3946 3.546815 GGATATTGCAACATGTCGCACTC 60.547 47.826 11.86 8.62 38.00 3.51
2143 3947 2.355756 GGATATTGCAACATGTCGCACT 59.644 45.455 11.86 9.07 38.00 4.40
2144 3948 2.097304 TGGATATTGCAACATGTCGCAC 59.903 45.455 11.86 0.00 38.00 5.34
2145 3949 2.363683 TGGATATTGCAACATGTCGCA 58.636 42.857 7.54 7.54 36.05 5.10
2146 3950 3.631145 ATGGATATTGCAACATGTCGC 57.369 42.857 0.00 0.57 0.00 5.19
2147 3951 5.929697 ACTATGGATATTGCAACATGTCG 57.070 39.130 0.00 0.00 0.00 4.35
2171 3975 9.462606 AGTTCCGAAAATACTTTCCAGATAATT 57.537 29.630 0.00 0.00 38.17 1.40
2172 3976 9.462606 AAGTTCCGAAAATACTTTCCAGATAAT 57.537 29.630 0.00 0.00 38.17 1.28
2173 3977 8.857694 AAGTTCCGAAAATACTTTCCAGATAA 57.142 30.769 0.00 0.00 38.17 1.75
2174 3978 8.857694 AAAGTTCCGAAAATACTTTCCAGATA 57.142 30.769 0.00 0.00 37.51 1.98
2175 3979 7.761038 AAAGTTCCGAAAATACTTTCCAGAT 57.239 32.000 0.00 0.00 37.51 2.90
2176 3980 8.680039 TTAAAGTTCCGAAAATACTTTCCAGA 57.320 30.769 0.00 0.00 41.12 3.86
2177 3981 9.177304 GTTTAAAGTTCCGAAAATACTTTCCAG 57.823 33.333 0.00 0.00 41.12 3.86
2178 3982 8.684520 TGTTTAAAGTTCCGAAAATACTTTCCA 58.315 29.630 0.00 0.00 41.12 3.53
2179 3983 9.518906 TTGTTTAAAGTTCCGAAAATACTTTCC 57.481 29.630 0.00 0.00 41.12 3.13
2189 3993 9.887406 GATGAAGTATTTGTTTAAAGTTCCGAA 57.113 29.630 0.00 0.00 0.00 4.30
2190 3994 8.508875 GGATGAAGTATTTGTTTAAAGTTCCGA 58.491 33.333 0.00 0.00 0.00 4.55
2191 3995 7.480542 CGGATGAAGTATTTGTTTAAAGTTCCG 59.519 37.037 0.00 0.00 0.00 4.30
2192 3996 8.294577 ACGGATGAAGTATTTGTTTAAAGTTCC 58.705 33.333 0.00 0.00 0.00 3.62
2193 3997 9.673454 AACGGATGAAGTATTTGTTTAAAGTTC 57.327 29.630 0.00 0.00 0.00 3.01
2194 3998 9.673454 GAACGGATGAAGTATTTGTTTAAAGTT 57.327 29.630 0.00 0.00 0.00 2.66
2195 3999 8.842280 TGAACGGATGAAGTATTTGTTTAAAGT 58.158 29.630 0.00 0.00 0.00 2.66
2196 4000 9.840427 ATGAACGGATGAAGTATTTGTTTAAAG 57.160 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.