Multiple sequence alignment - TraesCS1A01G007300

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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 TraesCS1A01G007300 chr1A 100.000 1646 0 0 1723 3368 3846428 3844783 0.000000e+00 3040.0
1 TraesCS1A01G007300 chr1A 100.000 1319 0 0 1 1319 3848150 3846832 0.000000e+00 2436.0
2 TraesCS1A01G007300 chr1A 88.812 1296 94 17 48 1319 3909454 3910722 0.000000e+00 1543.0
3 TraesCS1A01G007300 chr1A 88.382 1162 121 12 2150 3308 4041963 4043113 0.000000e+00 1386.0
4 TraesCS1A01G007300 chr1A 88.210 1162 122 13 2150 3308 4033978 4035127 0.000000e+00 1373.0
5 TraesCS1A01G007300 chr1A 89.659 967 83 4 2153 3114 3911053 3912007 0.000000e+00 1216.0
6 TraesCS1A01G007300 chr1A 84.773 1169 107 25 186 1319 4032537 4033669 0.000000e+00 1107.0
7 TraesCS1A01G007300 chr1A 84.773 1169 107 24 186 1319 4040522 4041654 0.000000e+00 1107.0
8 TraesCS1A01G007300 chr1A 95.844 409 17 0 1723 2131 4033587 4033995 0.000000e+00 662.0
9 TraesCS1A01G007300 chr1A 95.355 409 19 0 1723 2131 4041572 4041980 0.000000e+00 651.0
10 TraesCS1A01G007300 chr1A 89.720 428 22 7 1723 2128 3910640 3911067 8.280000e-146 527.0
11 TraesCS1A01G007300 chr1A 89.453 256 24 3 3114 3368 3913740 3913993 1.510000e-83 320.0
12 TraesCS1A01G007300 chr1D 85.190 1580 191 21 1742 3293 260292 258728 0.000000e+00 1581.0
13 TraesCS1A01G007300 chr1D 84.635 1601 196 29 1723 3286 322576 320989 0.000000e+00 1548.0
14 TraesCS1A01G007300 chr1D 86.442 1158 124 16 186 1319 252192 251044 0.000000e+00 1238.0
15 TraesCS1A01G007300 chr1D 86.969 1082 89 21 273 1319 261293 260229 0.000000e+00 1170.0
16 TraesCS1A01G007300 chr1D 86.106 1130 100 24 186 1297 382975 381885 0.000000e+00 1164.0
17 TraesCS1A01G007300 chr1D 90.552 815 75 2 2153 2966 381151 380338 0.000000e+00 1077.0
18 TraesCS1A01G007300 chr1D 83.956 910 113 16 1742 2624 251107 250204 0.000000e+00 841.0
19 TraesCS1A01G007300 chr1D 84.891 642 88 6 2658 3293 236679 236041 1.020000e-179 640.0
20 TraesCS1A01G007300 chr1D 89.286 392 21 3 1761 2131 381528 381137 3.930000e-129 472.0
21 TraesCS1A01G007300 chr1D 88.028 142 12 4 48 185 261916 261776 2.690000e-36 163.0
22 TraesCS1A01G007300 chr1D 85.906 149 15 5 48 191 252726 252579 1.620000e-33 154.0
23 TraesCS1A01G007300 chr1B 83.550 1386 173 25 1723 3057 5057307 5058688 0.000000e+00 1245.0
24 TraesCS1A01G007300 chr1B 86.849 1133 88 20 186 1298 4993441 4992350 0.000000e+00 1210.0
25 TraesCS1A01G007300 chr1B 85.616 1161 126 21 186 1319 5141216 5142362 0.000000e+00 1181.0
26 TraesCS1A01G007300 chr1B 84.372 1203 153 14 2114 3286 5137833 5139030 0.000000e+00 1147.0
27 TraesCS1A01G007300 chr1B 86.089 1028 101 27 320 1310 5098629 5099651 0.000000e+00 1068.0
28 TraesCS1A01G007300 chr1B 85.827 1016 88 25 298 1308 4965001 4965965 0.000000e+00 1027.0
29 TraesCS1A01G007300 chr1B 85.106 1034 114 22 312 1319 5056241 5057260 0.000000e+00 1020.0
30 TraesCS1A01G007300 chr1B 84.765 978 131 11 2317 3286 5100315 5101282 0.000000e+00 965.0
31 TraesCS1A01G007300 chr1B 87.775 818 68 5 2150 2966 4966354 4967140 0.000000e+00 928.0
32 TraesCS1A01G007300 chr1B 83.257 657 71 14 1723 2343 5099656 5100309 4.880000e-158 568.0
33 TraesCS1A01G007300 chr1B 89.640 444 46 0 1724 2167 5137395 5137838 1.750000e-157 566.0
34 TraesCS1A01G007300 chr1B 89.302 430 25 3 1723 2131 4992378 4991949 1.390000e-143 520.0
35 TraesCS1A01G007300 chr1B 88.078 411 28 6 1742 2131 4965961 4966371 5.090000e-128 468.0
36 TraesCS1A01G007300 chr1B 85.906 149 14 6 48 191 5140862 5141008 5.820000e-33 152.0
37 TraesCS1A01G007300 chr1B 86.364 88 6 1 186 267 4962190 4962277 1.290000e-14 91.6


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 TraesCS1A01G007300 chr1A 3844783 3848150 3367 True 2738.000000 3040 100.000000 1 3368 2 chr1A.!!$R1 3367
1 TraesCS1A01G007300 chr1A 4040522 4043113 2591 False 1048.000000 1386 89.503333 186 3308 3 chr1A.!!$F3 3122
2 TraesCS1A01G007300 chr1A 4032537 4035127 2590 False 1047.333333 1373 89.609000 186 3308 3 chr1A.!!$F2 3122
3 TraesCS1A01G007300 chr1A 3909454 3913993 4539 False 901.500000 1543 89.411000 48 3368 4 chr1A.!!$F1 3320
4 TraesCS1A01G007300 chr1D 320989 322576 1587 True 1548.000000 1548 84.635000 1723 3286 1 chr1D.!!$R2 1563
5 TraesCS1A01G007300 chr1D 258728 261916 3188 True 971.333333 1581 86.729000 48 3293 3 chr1D.!!$R4 3245
6 TraesCS1A01G007300 chr1D 380338 382975 2637 True 904.333333 1164 88.648000 186 2966 3 chr1D.!!$R5 2780
7 TraesCS1A01G007300 chr1D 250204 252726 2522 True 744.333333 1238 85.434667 48 2624 3 chr1D.!!$R3 2576
8 TraesCS1A01G007300 chr1D 236041 236679 638 True 640.000000 640 84.891000 2658 3293 1 chr1D.!!$R1 635
9 TraesCS1A01G007300 chr1B 5056241 5058688 2447 False 1132.500000 1245 84.328000 312 3057 2 chr1B.!!$F2 2745
10 TraesCS1A01G007300 chr1B 5098629 5101282 2653 False 867.000000 1068 84.703667 320 3286 3 chr1B.!!$F3 2966
11 TraesCS1A01G007300 chr1B 4991949 4993441 1492 True 865.000000 1210 88.075500 186 2131 2 chr1B.!!$R1 1945
12 TraesCS1A01G007300 chr1B 5137395 5142362 4967 False 761.500000 1181 86.383500 48 3286 4 chr1B.!!$F4 3238
13 TraesCS1A01G007300 chr1B 4962190 4967140 4950 False 628.650000 1027 87.011000 186 2966 4 chr1B.!!$F1 2780

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
36 37 0.107897 AAACGACTGAGCACACACCA 60.108 50.0 0.0 0.0 0.0 4.17 F
37 38 0.107897 AACGACTGAGCACACACCAA 60.108 50.0 0.0 0.0 0.0 3.67 F
1314 4760 0.104725 AACAATTTCCCCAGCCCCAA 60.105 50.0 0.0 0.0 0.0 4.12 F
1316 4762 0.835543 CAATTTCCCCAGCCCCAACA 60.836 55.0 0.0 0.0 0.0 3.33 F
1317 4763 0.104725 AATTTCCCCAGCCCCAACAA 60.105 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 4744 0.104725 TTGTTGGGGCTGGGGAAATT 60.105 50.0 0.00 0.00 0.00 1.82 R
2017 5506 0.244450 CATTGTTGCCGCATCACCTT 59.756 50.0 3.55 0.00 0.00 3.50 R
2179 5794 0.107017 AGCTGAAATAGTGGCCGCAT 60.107 50.0 20.59 7.25 0.00 4.73 R
2297 5936 0.108585 GGAGCACTCAGGTGGAACAA 59.891 55.0 0.00 0.00 44.16 2.83 R
2568 6268 0.322322 TGCGGTTAGGGACGAACATT 59.678 50.0 0.00 0.00 45.69 2.71 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
17 18 3.546009 CGGGGGATAGGCGAGAAA 58.454 61.111 0.00 0.00 0.00 2.52
18 19 1.827394 CGGGGGATAGGCGAGAAAA 59.173 57.895 0.00 0.00 0.00 2.29
19 20 0.179468 CGGGGGATAGGCGAGAAAAA 59.821 55.000 0.00 0.00 0.00 1.94
20 21 1.676746 GGGGGATAGGCGAGAAAAAC 58.323 55.000 0.00 0.00 0.00 2.43
21 22 1.296727 GGGGATAGGCGAGAAAAACG 58.703 55.000 0.00 0.00 0.00 3.60
22 23 1.134610 GGGGATAGGCGAGAAAAACGA 60.135 52.381 0.00 0.00 0.00 3.85
23 24 1.931841 GGGATAGGCGAGAAAAACGAC 59.068 52.381 0.00 0.00 39.24 4.34
28 29 0.164002 GGCGAGAAAAACGACTGAGC 59.836 55.000 0.00 0.00 35.75 4.26
29 30 0.859232 GCGAGAAAAACGACTGAGCA 59.141 50.000 0.00 0.00 0.00 4.26
30 31 1.397315 GCGAGAAAAACGACTGAGCAC 60.397 52.381 0.00 0.00 0.00 4.40
31 32 1.858458 CGAGAAAAACGACTGAGCACA 59.142 47.619 0.00 0.00 0.00 4.57
32 33 2.347661 CGAGAAAAACGACTGAGCACAC 60.348 50.000 0.00 0.00 0.00 3.82
33 34 2.607635 GAGAAAAACGACTGAGCACACA 59.392 45.455 0.00 0.00 0.00 3.72
34 35 2.351726 AGAAAAACGACTGAGCACACAC 59.648 45.455 0.00 0.00 0.00 3.82
35 36 1.014352 AAAACGACTGAGCACACACC 58.986 50.000 0.00 0.00 0.00 4.16
36 37 0.107897 AAACGACTGAGCACACACCA 60.108 50.000 0.00 0.00 0.00 4.17
37 38 0.107897 AACGACTGAGCACACACCAA 60.108 50.000 0.00 0.00 0.00 3.67
38 39 0.530650 ACGACTGAGCACACACCAAG 60.531 55.000 0.00 0.00 0.00 3.61
39 40 0.249447 CGACTGAGCACACACCAAGA 60.249 55.000 0.00 0.00 0.00 3.02
40 41 1.221414 GACTGAGCACACACCAAGAC 58.779 55.000 0.00 0.00 0.00 3.01
41 42 0.179045 ACTGAGCACACACCAAGACC 60.179 55.000 0.00 0.00 0.00 3.85
42 43 0.886490 CTGAGCACACACCAAGACCC 60.886 60.000 0.00 0.00 0.00 4.46
43 44 1.961277 GAGCACACACCAAGACCCG 60.961 63.158 0.00 0.00 0.00 5.28
44 45 2.978010 GCACACACCAAGACCCGG 60.978 66.667 0.00 0.00 0.00 5.73
45 46 2.281484 CACACACCAAGACCCGGG 60.281 66.667 22.25 22.25 0.00 5.73
46 47 2.770904 ACACACCAAGACCCGGGT 60.771 61.111 30.81 30.81 38.10 5.28
114 118 2.141517 CAAGCTCAGGAGTCAACTGTG 58.858 52.381 0.00 0.00 37.25 3.66
116 120 0.394565 GCTCAGGAGTCAACTGTGGT 59.605 55.000 0.00 0.00 37.25 4.16
120 124 2.367567 TCAGGAGTCAACTGTGGTTACC 59.632 50.000 0.00 0.00 37.25 2.85
199 807 4.089065 GCTTGCTTTTTCGACTAAATGCAG 59.911 41.667 17.39 14.04 44.05 4.41
260 877 3.703556 TCAATTGAAGCCAGAACAAACCA 59.296 39.130 5.45 0.00 0.00 3.67
267 884 5.538053 TGAAGCCAGAACAAACCATCAAATA 59.462 36.000 0.00 0.00 0.00 1.40
268 885 5.391312 AGCCAGAACAAACCATCAAATAC 57.609 39.130 0.00 0.00 0.00 1.89
347 3658 6.891908 ACTTGCATAGAATTACAACCCTTGAT 59.108 34.615 0.00 0.00 0.00 2.57
441 3752 9.880064 GAGAATTTGATGAGTCATGTATTGATG 57.120 33.333 11.20 0.00 36.54 3.07
518 3857 9.099454 ACACTACAAGTTAGTTGAAGAAAGAAG 57.901 33.333 6.80 0.00 38.60 2.85
551 3890 6.018669 CAGAACGAACATAAGAATTCTAGCCC 60.019 42.308 8.75 0.00 0.00 5.19
559 3898 8.824756 ACATAAGAATTCTAGCCCGATCTATA 57.175 34.615 8.75 0.00 0.00 1.31
602 3946 2.884639 CAAATTTAGTCCCCCGCTATGG 59.115 50.000 0.00 0.00 37.55 2.74
639 3983 7.851387 TGTCTAACAACTTGTACAACATGAA 57.149 32.000 18.17 8.31 0.00 2.57
742 4106 7.155328 TCAAGTTTTCCTCACTCTTAGATGAC 58.845 38.462 0.00 0.00 0.00 3.06
813 4178 2.447443 TGTAGTGCCACCAAACACAAA 58.553 42.857 0.00 0.00 39.30 2.83
907 4277 5.228945 TCATGGTAGCTATAAAAGAGCCC 57.771 43.478 0.00 0.00 41.06 5.19
951 4321 3.942829 TCATCCATCCTTCACACAACTC 58.057 45.455 0.00 0.00 0.00 3.01
1027 4398 5.026121 AGACCTTACTCATCCTGACAATCA 58.974 41.667 0.00 0.00 0.00 2.57
1103 4474 2.660572 AGTACAATGGCCACAACAACA 58.339 42.857 8.16 0.00 0.00 3.33
1104 4475 3.027412 AGTACAATGGCCACAACAACAA 58.973 40.909 8.16 0.00 0.00 2.83
1105 4476 2.307934 ACAATGGCCACAACAACAAC 57.692 45.000 8.16 0.00 0.00 3.32
1140 4511 1.482177 CCCCAACAACCATTCTCCCAA 60.482 52.381 0.00 0.00 0.00 4.12
1289 4729 0.321346 CAACCATTTCCCCAGCAACC 59.679 55.000 0.00 0.00 0.00 3.77
1298 4744 1.326213 CCCCAGCAACCACAACAACA 61.326 55.000 0.00 0.00 0.00 3.33
1310 4756 1.416030 ACAACAACAATTTCCCCAGCC 59.584 47.619 0.00 0.00 0.00 4.85
1311 4757 1.055849 AACAACAATTTCCCCAGCCC 58.944 50.000 0.00 0.00 0.00 5.19
1313 4759 0.835543 CAACAATTTCCCCAGCCCCA 60.836 55.000 0.00 0.00 0.00 4.96
1314 4760 0.104725 AACAATTTCCCCAGCCCCAA 60.105 50.000 0.00 0.00 0.00 4.12
1315 4761 0.835971 ACAATTTCCCCAGCCCCAAC 60.836 55.000 0.00 0.00 0.00 3.77
1316 4762 0.835543 CAATTTCCCCAGCCCCAACA 60.836 55.000 0.00 0.00 0.00 3.33
1317 4763 0.104725 AATTTCCCCAGCCCCAACAA 60.105 50.000 0.00 0.00 0.00 2.83
1318 4764 0.835971 ATTTCCCCAGCCCCAACAAC 60.836 55.000 0.00 0.00 0.00 3.32
1767 5213 1.816224 CAACCCCAACTACCATTTCCG 59.184 52.381 0.00 0.00 0.00 4.30
1848 5316 3.093057 ACAGCAACCACAACAACCTTTA 58.907 40.909 0.00 0.00 0.00 1.85
1873 5362 1.227118 CCCCAACAACCGCAACAAC 60.227 57.895 0.00 0.00 0.00 3.32
1911 5400 4.989279 ACAACCATTGATTCAGCCATAC 57.011 40.909 0.00 0.00 0.00 2.39
2131 5716 2.605030 TGCAGCAAGAACAACAACAAC 58.395 42.857 0.00 0.00 0.00 3.32
2132 5717 2.029560 TGCAGCAAGAACAACAACAACA 60.030 40.909 0.00 0.00 0.00 3.33
2133 5718 2.992543 GCAGCAAGAACAACAACAACAA 59.007 40.909 0.00 0.00 0.00 2.83
2134 5719 3.181531 GCAGCAAGAACAACAACAACAAC 60.182 43.478 0.00 0.00 0.00 3.32
2135 5720 3.986572 CAGCAAGAACAACAACAACAACA 59.013 39.130 0.00 0.00 0.00 3.33
2136 5721 4.447054 CAGCAAGAACAACAACAACAACAA 59.553 37.500 0.00 0.00 0.00 2.83
2137 5722 4.447389 AGCAAGAACAACAACAACAACAAC 59.553 37.500 0.00 0.00 0.00 3.32
2138 5723 4.210120 GCAAGAACAACAACAACAACAACA 59.790 37.500 0.00 0.00 0.00 3.33
2139 5724 5.277058 GCAAGAACAACAACAACAACAACAA 60.277 36.000 0.00 0.00 0.00 2.83
2140 5725 5.898630 AGAACAACAACAACAACAACAAC 57.101 34.783 0.00 0.00 0.00 3.32
2141 5726 5.352284 AGAACAACAACAACAACAACAACA 58.648 33.333 0.00 0.00 0.00 3.33
2142 5727 5.812642 AGAACAACAACAACAACAACAACAA 59.187 32.000 0.00 0.00 0.00 2.83
2143 5728 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2144 5729 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2145 5730 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2146 5731 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2147 5732 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2148 5733 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2149 5734 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2150 5735 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2151 5736 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2152 5737 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2153 5738 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2154 5739 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2155 5740 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2179 5794 4.397420 ACAACAACAAGGCATACAGATCA 58.603 39.130 0.00 0.00 0.00 2.92
2269 5908 3.885297 GGTGATCAGGTCATTGGTATTGG 59.115 47.826 0.00 0.00 39.48 3.16
2321 5960 1.302033 CACCTGAGTGCTCCACCAC 60.302 63.158 0.00 0.00 37.14 4.16
2351 6022 2.514510 TTTGCCAGCATAGTCGCCGA 62.515 55.000 0.00 0.00 0.00 5.54
2374 6045 2.181954 TGGTGGCCAATGAAAAATGC 57.818 45.000 7.24 0.00 0.00 3.56
2375 6046 1.419012 TGGTGGCCAATGAAAAATGCA 59.581 42.857 7.24 0.00 0.00 3.96
2376 6047 2.158711 TGGTGGCCAATGAAAAATGCAA 60.159 40.909 7.24 0.00 0.00 4.08
2377 6048 2.485038 GGTGGCCAATGAAAAATGCAAG 59.515 45.455 7.24 0.00 0.00 4.01
2378 6049 2.095617 GTGGCCAATGAAAAATGCAAGC 60.096 45.455 7.24 0.00 0.00 4.01
2379 6050 2.152830 GGCCAATGAAAAATGCAAGCA 58.847 42.857 0.00 0.00 0.00 3.91
2380 6051 2.750712 GGCCAATGAAAAATGCAAGCAT 59.249 40.909 0.00 0.86 38.46 3.79
2568 6268 8.690884 TCACTGTTCCATTCACTTTTTATTTCA 58.309 29.630 0.00 0.00 0.00 2.69
2590 6290 1.549620 TGTTCGTCCCTAACCGCAATA 59.450 47.619 0.00 0.00 0.00 1.90
2600 6300 4.557205 CCTAACCGCAATACTAGCCTTAG 58.443 47.826 0.00 0.00 0.00 2.18
2616 6316 4.590647 AGCCTTAGACATCAATAGCTAGCA 59.409 41.667 18.83 3.19 0.00 3.49
2634 6334 0.242825 CAGCTTGTGATGGCAGGTTG 59.757 55.000 0.00 0.00 0.00 3.77
2683 6383 8.844244 GTCGACCTATTAATCTAGTTAACAGGA 58.156 37.037 20.01 5.73 45.79 3.86
2735 6435 3.562973 CCGACCGAGTAGCTATCAGTTAA 59.437 47.826 0.00 0.00 0.00 2.01
2756 6456 8.120465 AGTTAACGATTTCCTAAATATTGCACG 58.880 33.333 0.00 0.00 0.00 5.34
2820 6521 4.379652 CCATTTTAGCACCAAAACAAGCT 58.620 39.130 0.00 0.00 40.92 3.74
2845 6546 5.530171 CCTGATTAGAAACCATCCATCACTG 59.470 44.000 0.00 0.00 29.44 3.66
2853 6554 6.375455 AGAAACCATCCATCACTGTAAATGTC 59.625 38.462 2.79 0.00 0.00 3.06
2925 6626 8.528295 CAAAGCATTTTTCAAAAGCAATTCTTG 58.472 29.630 0.00 0.00 35.03 3.02
2932 6633 4.419282 TCAAAAGCAATTCTTGAGGGGAT 58.581 39.130 0.00 0.00 34.67 3.85
2950 6651 4.081476 GGGGATTCCAAAGAGGTGAAAATG 60.081 45.833 4.80 0.00 39.02 2.32
2954 6655 7.389232 GGATTCCAAAGAGGTGAAAATGAAAT 58.611 34.615 0.00 0.00 39.02 2.17
3028 6729 1.060937 GTCACAATAGCAAGCGCCG 59.939 57.895 2.29 0.00 39.83 6.46
3040 6741 0.733566 AAGCGCCGAACATGCAATTG 60.734 50.000 2.29 0.00 0.00 2.32
3196 8635 6.039159 TGCATTGTGTATTGACTTGTCTCAAA 59.961 34.615 2.35 0.00 33.85 2.69
3221 8660 8.319143 ACTACGAACACAAAGCAAATATTACT 57.681 30.769 0.00 0.00 0.00 2.24
3231 8671 9.626045 ACAAAGCAAATATTACTTTTACAGCTC 57.374 29.630 11.71 0.00 31.43 4.09
3278 8719 6.069331 TCAGTCTGTGTAGAAGTTCCTTAGT 58.931 40.000 0.00 0.00 34.01 2.24
3346 11280 8.871629 TCTAATATAGTAGAAGGAAGAGCTGG 57.128 38.462 7.44 0.00 0.00 4.85
3350 11284 9.830186 AATATAGTAGAAGGAAGAGCTGGAATA 57.170 33.333 0.00 0.00 0.00 1.75
3355 11289 0.767998 GGAAGAGCTGGAATAGGGGG 59.232 60.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.676746 GTTTTTCTCGCCTATCCCCC 58.323 55.000 0.00 0.00 0.00 5.40
2 3 1.134610 TCGTTTTTCTCGCCTATCCCC 60.135 52.381 0.00 0.00 0.00 4.81
3 4 1.931841 GTCGTTTTTCTCGCCTATCCC 59.068 52.381 0.00 0.00 0.00 3.85
4 5 2.603560 CAGTCGTTTTTCTCGCCTATCC 59.396 50.000 0.00 0.00 0.00 2.59
5 6 3.508762 TCAGTCGTTTTTCTCGCCTATC 58.491 45.455 0.00 0.00 0.00 2.08
6 7 3.512680 CTCAGTCGTTTTTCTCGCCTAT 58.487 45.455 0.00 0.00 0.00 2.57
7 8 2.925306 GCTCAGTCGTTTTTCTCGCCTA 60.925 50.000 0.00 0.00 0.00 3.93
8 9 1.784525 CTCAGTCGTTTTTCTCGCCT 58.215 50.000 0.00 0.00 0.00 5.52
9 10 0.164002 GCTCAGTCGTTTTTCTCGCC 59.836 55.000 0.00 0.00 0.00 5.54
10 11 0.859232 TGCTCAGTCGTTTTTCTCGC 59.141 50.000 0.00 0.00 0.00 5.03
11 12 1.858458 TGTGCTCAGTCGTTTTTCTCG 59.142 47.619 0.00 0.00 0.00 4.04
12 13 2.607635 TGTGTGCTCAGTCGTTTTTCTC 59.392 45.455 0.00 0.00 0.00 2.87
13 14 2.351726 GTGTGTGCTCAGTCGTTTTTCT 59.648 45.455 0.00 0.00 0.00 2.52
14 15 2.538939 GGTGTGTGCTCAGTCGTTTTTC 60.539 50.000 0.00 0.00 0.00 2.29
15 16 1.400494 GGTGTGTGCTCAGTCGTTTTT 59.600 47.619 0.00 0.00 0.00 1.94
16 17 1.014352 GGTGTGTGCTCAGTCGTTTT 58.986 50.000 0.00 0.00 0.00 2.43
17 18 0.107897 TGGTGTGTGCTCAGTCGTTT 60.108 50.000 0.00 0.00 0.00 3.60
18 19 0.107897 TTGGTGTGTGCTCAGTCGTT 60.108 50.000 0.00 0.00 0.00 3.85
19 20 0.530650 CTTGGTGTGTGCTCAGTCGT 60.531 55.000 0.00 0.00 0.00 4.34
20 21 0.249447 TCTTGGTGTGTGCTCAGTCG 60.249 55.000 0.00 0.00 0.00 4.18
21 22 1.221414 GTCTTGGTGTGTGCTCAGTC 58.779 55.000 0.00 0.00 0.00 3.51
22 23 0.179045 GGTCTTGGTGTGTGCTCAGT 60.179 55.000 0.00 0.00 0.00 3.41
23 24 0.886490 GGGTCTTGGTGTGTGCTCAG 60.886 60.000 0.00 0.00 0.00 3.35
24 25 1.148273 GGGTCTTGGTGTGTGCTCA 59.852 57.895 0.00 0.00 0.00 4.26
25 26 1.961277 CGGGTCTTGGTGTGTGCTC 60.961 63.158 0.00 0.00 0.00 4.26
26 27 2.111043 CGGGTCTTGGTGTGTGCT 59.889 61.111 0.00 0.00 0.00 4.40
27 28 2.978010 CCGGGTCTTGGTGTGTGC 60.978 66.667 0.00 0.00 0.00 4.57
28 29 1.760479 TACCCGGGTCTTGGTGTGTG 61.760 60.000 34.27 0.00 36.04 3.82
29 30 1.459921 TACCCGGGTCTTGGTGTGT 60.460 57.895 34.27 3.16 36.04 3.72
30 31 1.004200 GTACCCGGGTCTTGGTGTG 60.004 63.158 34.27 0.00 36.04 3.82
31 32 0.838987 ATGTACCCGGGTCTTGGTGT 60.839 55.000 34.27 5.01 36.04 4.16
32 33 0.392461 CATGTACCCGGGTCTTGGTG 60.392 60.000 34.27 18.81 36.04 4.17
33 34 0.838987 ACATGTACCCGGGTCTTGGT 60.839 55.000 34.27 21.71 38.69 3.67
34 35 0.326927 AACATGTACCCGGGTCTTGG 59.673 55.000 34.27 20.99 0.00 3.61
35 36 3.337694 TTAACATGTACCCGGGTCTTG 57.662 47.619 34.27 27.71 0.00 3.02
36 37 4.074259 GTTTTAACATGTACCCGGGTCTT 58.926 43.478 34.27 16.82 0.00 3.01
37 38 3.328637 AGTTTTAACATGTACCCGGGTCT 59.671 43.478 34.27 13.84 0.00 3.85
38 39 3.678289 AGTTTTAACATGTACCCGGGTC 58.322 45.455 34.27 22.12 0.00 4.46
39 40 3.793819 AGTTTTAACATGTACCCGGGT 57.206 42.857 32.66 32.66 0.00 5.28
40 41 4.073549 TCAAGTTTTAACATGTACCCGGG 58.926 43.478 22.25 22.25 0.00 5.73
41 42 4.758165 ACTCAAGTTTTAACATGTACCCGG 59.242 41.667 0.00 0.00 0.00 5.73
42 43 5.685841 CACTCAAGTTTTAACATGTACCCG 58.314 41.667 0.00 0.00 0.00 5.28
43 44 5.009210 TGCACTCAAGTTTTAACATGTACCC 59.991 40.000 0.00 0.00 0.00 3.69
44 45 6.067263 TGCACTCAAGTTTTAACATGTACC 57.933 37.500 0.00 0.00 0.00 3.34
45 46 6.725246 ACTGCACTCAAGTTTTAACATGTAC 58.275 36.000 0.00 0.00 0.00 2.90
46 47 6.935741 ACTGCACTCAAGTTTTAACATGTA 57.064 33.333 0.00 0.00 0.00 2.29
114 118 8.631797 TCTTGTTTGTTTAATTACCTGGTAACC 58.368 33.333 20.90 7.95 30.49 2.85
151 155 7.661040 CAAGAAGAGGTGGTAAAATTGTCATT 58.339 34.615 0.00 0.00 0.00 2.57
267 884 6.861065 ACACGTCTTAATTGATTCAAGTGT 57.139 33.333 9.49 10.20 34.75 3.55
268 885 9.318041 CTTTACACGTCTTAATTGATTCAAGTG 57.682 33.333 9.49 9.64 0.00 3.16
347 3658 9.511272 CATGACTCATCATATTCCCTTTCAATA 57.489 33.333 0.00 0.00 44.13 1.90
441 3752 6.034591 AGCTGATAGTAATGTTGTACACGTC 58.965 40.000 0.00 0.00 0.00 4.34
508 3846 5.404066 CGTTCTGGACTCTTCTTCTTTCTTC 59.596 44.000 0.00 0.00 0.00 2.87
511 3850 4.872664 TCGTTCTGGACTCTTCTTCTTTC 58.127 43.478 0.00 0.00 0.00 2.62
518 3857 5.710984 TCTTATGTTCGTTCTGGACTCTTC 58.289 41.667 0.00 0.00 0.00 2.87
551 3890 8.011673 CCTTGTGCATGTTGTTAATATAGATCG 58.988 37.037 0.00 0.00 0.00 3.69
559 3898 6.832520 TGTATCCTTGTGCATGTTGTTAAT 57.167 33.333 0.00 0.00 0.00 1.40
602 3946 9.612620 CAAGTTGTTAGACATAAACCAAATCTC 57.387 33.333 0.00 0.00 0.00 2.75
742 4106 8.586570 TCAAAGTTGCCTTTTTATTGTACATG 57.413 30.769 0.00 0.00 38.87 3.21
813 4178 9.868277 TGCTTATCGAATTGATTATTTGGTTTT 57.132 25.926 0.00 0.00 38.57 2.43
857 4225 7.734942 AGGTTTCTTTTCATTATTGCTTTCCA 58.265 30.769 0.00 0.00 0.00 3.53
885 4255 4.262463 CGGGCTCTTTTATAGCTACCATGA 60.262 45.833 0.00 0.00 39.97 3.07
907 4277 5.134202 TGGTATGGAGTCTACATATTGCG 57.866 43.478 8.07 0.00 33.77 4.85
951 4321 4.142534 ACTTGGATTTGATGATTGTGCTCG 60.143 41.667 0.00 0.00 0.00 5.03
990 4361 6.214615 TGAGTAAGGTCTTCATGGTGGATTTA 59.785 38.462 0.00 0.00 0.00 1.40
1046 4417 1.593196 CTGTATATTGGCGGTGGTGG 58.407 55.000 0.00 0.00 0.00 4.61
1103 4474 1.229177 GGCTGGGGGAATGGTTGTT 60.229 57.895 0.00 0.00 0.00 2.83
1104 4475 2.445155 GGCTGGGGGAATGGTTGT 59.555 61.111 0.00 0.00 0.00 3.32
1105 4476 2.364186 GGGCTGGGGGAATGGTTG 60.364 66.667 0.00 0.00 0.00 3.77
1140 4511 4.263506 TGGGGAAAAATTTGTTGTGGTTGT 60.264 37.500 0.00 0.00 0.00 3.32
1289 4729 2.482864 GCTGGGGAAATTGTTGTTGTG 58.517 47.619 0.00 0.00 0.00 3.33
1298 4744 0.104725 TTGTTGGGGCTGGGGAAATT 60.105 50.000 0.00 0.00 0.00 1.82
1767 5213 2.307934 ATGGTTGTTGTGGTTGTTGC 57.692 45.000 0.00 0.00 0.00 4.17
1848 5316 4.233558 GGTTGTTGGGGCTGGGGT 62.234 66.667 0.00 0.00 0.00 4.95
1873 5362 0.831288 TGTTGTTGCTGGGGGAATGG 60.831 55.000 0.00 0.00 0.00 3.16
1911 5400 3.081804 GGGGTTCATCTGTTGTTGTAGG 58.918 50.000 0.00 0.00 0.00 3.18
2017 5506 0.244450 CATTGTTGCCGCATCACCTT 59.756 50.000 3.55 0.00 0.00 3.50
2089 5578 0.956633 ATGATGGAATGCACGATGCC 59.043 50.000 7.38 0.00 44.23 4.40
2131 5716 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2132 5717 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2133 5718 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2134 5719 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2135 5720 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2136 5721 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2137 5722 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2138 5723 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2139 5724 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2140 5725 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2141 5726 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2142 5727 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2143 5728 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2144 5729 5.007136 CCTTGTTGTTGTTGTTGTTGTTGTT 59.993 36.000 0.00 0.00 0.00 2.83
2145 5730 4.509600 CCTTGTTGTTGTTGTTGTTGTTGT 59.490 37.500 0.00 0.00 0.00 3.32
2146 5731 4.610231 GCCTTGTTGTTGTTGTTGTTGTTG 60.610 41.667 0.00 0.00 0.00 3.33
2147 5732 3.496507 GCCTTGTTGTTGTTGTTGTTGTT 59.503 39.130 0.00 0.00 0.00 2.83
2148 5733 3.063485 GCCTTGTTGTTGTTGTTGTTGT 58.937 40.909 0.00 0.00 0.00 3.32
2149 5734 3.062763 TGCCTTGTTGTTGTTGTTGTTG 58.937 40.909 0.00 0.00 0.00 3.33
2150 5735 3.393089 TGCCTTGTTGTTGTTGTTGTT 57.607 38.095 0.00 0.00 0.00 2.83
2151 5736 3.608316 ATGCCTTGTTGTTGTTGTTGT 57.392 38.095 0.00 0.00 0.00 3.32
2152 5737 4.428209 TGTATGCCTTGTTGTTGTTGTTG 58.572 39.130 0.00 0.00 0.00 3.33
2153 5738 4.400884 TCTGTATGCCTTGTTGTTGTTGTT 59.599 37.500 0.00 0.00 0.00 2.83
2154 5739 3.951037 TCTGTATGCCTTGTTGTTGTTGT 59.049 39.130 0.00 0.00 0.00 3.32
2155 5740 4.566545 TCTGTATGCCTTGTTGTTGTTG 57.433 40.909 0.00 0.00 0.00 3.33
2179 5794 0.107017 AGCTGAAATAGTGGCCGCAT 60.107 50.000 20.59 7.25 0.00 4.73
2297 5936 0.108585 GGAGCACTCAGGTGGAACAA 59.891 55.000 0.00 0.00 44.16 2.83
2301 5940 2.217038 GGTGGAGCACTCAGGTGGA 61.217 63.158 0.00 0.00 43.18 4.02
2377 6048 8.206867 TGATCCATCTACCTATTAGCATAATGC 58.793 37.037 0.00 0.00 45.46 3.56
2380 6051 8.633561 CGATGATCCATCTACCTATTAGCATAA 58.366 37.037 5.54 0.00 38.59 1.90
2381 6052 7.780271 ACGATGATCCATCTACCTATTAGCATA 59.220 37.037 5.54 0.00 38.59 3.14
2568 6268 0.322322 TGCGGTTAGGGACGAACATT 59.678 50.000 0.00 0.00 45.69 2.71
2590 6290 6.071616 GCTAGCTATTGATGTCTAAGGCTAGT 60.072 42.308 7.70 0.00 45.35 2.57
2616 6316 1.530013 GCAACCTGCCATCACAAGCT 61.530 55.000 0.00 0.00 37.42 3.74
2624 6324 7.233632 TGATAGATTAAATAGCAACCTGCCAT 58.766 34.615 0.00 0.00 46.52 4.40
2735 6435 4.334203 TGCGTGCAATATTTAGGAAATCGT 59.666 37.500 0.00 0.00 32.38 3.73
2820 6521 5.429762 AGTGATGGATGGTTTCTAATCAGGA 59.570 40.000 0.00 0.00 32.01 3.86
2925 6626 1.916181 TCACCTCTTTGGAATCCCCTC 59.084 52.381 0.00 0.00 39.71 4.30
2950 6651 7.954788 TTTACCATGTGGCAACTTTAATTTC 57.045 32.000 0.00 0.00 39.32 2.17
2954 6655 6.716934 TCTTTTACCATGTGGCAACTTTAA 57.283 33.333 0.00 0.00 39.32 1.52
2988 6689 5.374921 ACTCAATATTCCCTCTTGCTCATG 58.625 41.667 0.00 0.00 0.00 3.07
3001 6702 6.132056 CGCTTGCTATTGTGACTCAATATTC 58.868 40.000 9.71 6.58 44.69 1.75
3028 6729 4.771590 TCAAGAGTCCAATTGCATGTTC 57.228 40.909 0.00 0.00 0.00 3.18
3040 6741 6.227298 TCTCTGAAACCATATCAAGAGTCC 57.773 41.667 0.00 0.00 0.00 3.85
3146 8584 9.219603 CATGTTTAAAGAGATAACAACTGAGGA 57.780 33.333 0.00 0.00 35.62 3.71
3147 8585 7.965107 GCATGTTTAAAGAGATAACAACTGAGG 59.035 37.037 0.00 0.00 35.62 3.86
3196 8635 8.319143 AGTAATATTTGCTTTGTGTTCGTAGT 57.681 30.769 0.00 0.00 0.00 2.73
3221 8660 4.134563 GTTTGGAGTCCAGAGCTGTAAAA 58.865 43.478 12.67 0.00 33.81 1.52
3231 8671 3.969287 TCTCATCTGTTTGGAGTCCAG 57.031 47.619 12.67 0.38 33.81 3.86
3323 8887 9.830186 ATTCCAGCTCTTCCTTCTACTATATTA 57.170 33.333 0.00 0.00 0.00 0.98
3326 8890 7.891183 CCTATTCCAGCTCTTCCTTCTACTATA 59.109 40.741 0.00 0.00 0.00 1.31
3327 8891 6.723977 CCTATTCCAGCTCTTCCTTCTACTAT 59.276 42.308 0.00 0.00 0.00 2.12
3328 8892 6.071984 CCTATTCCAGCTCTTCCTTCTACTA 58.928 44.000 0.00 0.00 0.00 1.82
3330 8894 4.039852 CCCTATTCCAGCTCTTCCTTCTAC 59.960 50.000 0.00 0.00 0.00 2.59
3331 8895 4.227197 CCCTATTCCAGCTCTTCCTTCTA 58.773 47.826 0.00 0.00 0.00 2.10
3340 11274 1.847088 AGTTTCCCCCTATTCCAGCTC 59.153 52.381 0.00 0.00 0.00 4.09
3342 11276 1.410224 CCAGTTTCCCCCTATTCCAGC 60.410 57.143 0.00 0.00 0.00 4.85
3346 11280 1.475213 CGCTCCAGTTTCCCCCTATTC 60.475 57.143 0.00 0.00 0.00 1.75
3350 11284 4.035102 GCGCTCCAGTTTCCCCCT 62.035 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.