Multiple sequence alignment - TraesCS1B01G401700

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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 TraesCS1B01G401700 chr1B 100.000 3023 0 0 1 3023 631968718 631965696 0.000000e+00 5583.0
1 TraesCS1B01G401700 chr1B 91.595 583 39 5 2446 3023 631961082 631960505 0.000000e+00 797.0
2 TraesCS1B01G401700 chr1B 90.252 595 41 10 2439 3023 631957932 631957345 0.000000e+00 761.0
3 TraesCS1B01G401700 chr1B 91.892 333 21 5 2694 3023 631904304 631903975 7.640000e-126 460.0
4 TraesCS1B01G401700 chr1B 89.394 264 23 3 2446 2709 631947376 631947118 8.080000e-86 327.0
5 TraesCS1B01G401700 chr1B 88.811 143 14 1 2304 2446 631958103 631957963 1.110000e-39 174.0
6 TraesCS1B01G401700 chr1B 81.034 116 12 3 2128 2243 631901110 631901005 1.930000e-12 84.2
7 TraesCS1B01G401700 chr1A 88.330 2245 107 59 121 2246 551594096 551591888 0.000000e+00 2551.0
8 TraesCS1B01G401700 chr1A 86.656 607 46 14 2303 2885 551591752 551591157 9.140000e-180 640.0
9 TraesCS1B01G401700 chr1A 86.147 462 38 11 2439 2887 551587546 551587098 2.730000e-130 475.0
10 TraesCS1B01G401700 chr1D 88.678 1528 89 39 739 2201 459880936 459879428 0.000000e+00 1786.0
11 TraesCS1B01G401700 chr1D 87.043 602 59 12 2438 3023 459879003 459878405 0.000000e+00 662.0
12 TraesCS1B01G401700 chr1D 87.170 569 25 19 213 736 459881540 459880975 1.200000e-168 603.0
13 TraesCS1B01G401700 chr1D 89.583 144 12 2 2303 2446 459879174 459879034 2.390000e-41 180.0
14 TraesCS1B01G401700 chr1D 84.211 171 20 4 2304 2471 459862840 459862674 3.120000e-35 159.0
15 TraesCS1B01G401700 chr1D 83.562 146 18 3 2304 2446 459876202 459876060 6.800000e-27 132.0
16 TraesCS1B01G401700 chr1D 84.615 117 8 5 2128 2243 459863055 459862948 1.150000e-19 108.0
17 TraesCS1B01G401700 chr7B 77.149 442 88 10 1001 1432 561280847 561280409 8.370000e-61 244.0
18 TraesCS1B01G401700 chr7A 86.977 215 28 0 1218 1432 604853731 604853517 3.010000e-60 243.0
19 TraesCS1B01G401700 chr7D 86.512 215 29 0 1218 1432 524915884 524915670 1.400000e-58 237.0
20 TraesCS1B01G401700 chr5A 85.446 213 29 2 1216 1427 436089393 436089604 1.410000e-53 220.0
21 TraesCS1B01G401700 chr5A 82.576 132 21 2 1218 1348 691677520 691677390 6.850000e-22 115.0
22 TraesCS1B01G401700 chr5B 76.286 447 83 15 997 1427 391144727 391145166 1.830000e-52 217.0
23 TraesCS1B01G401700 chr5D 83.019 212 36 0 1216 1427 334255462 334255673 3.080000e-45 193.0
24 TraesCS1B01G401700 chr3D 88.514 148 14 3 1001 1146 367236964 367236818 3.100000e-40 176.0
25 TraesCS1B01G401700 chr3D 92.553 94 7 0 1352 1445 367236373 367236280 5.260000e-28 135.0
26 TraesCS1B01G401700 chr3B 87.417 151 16 3 995 1143 478323400 478323251 1.440000e-38 171.0
27 TraesCS1B01G401700 chr3A 87.333 150 16 3 995 1142 489311970 489311822 5.180000e-38 169.0


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 TraesCS1B01G401700 chr1B 631965696 631968718 3022 True 5583.000000 5583 100.000000 1 3023 1 chr1B.!!$R2 3022
1 TraesCS1B01G401700 chr1B 631957345 631961082 3737 True 577.333333 797 90.219333 2304 3023 3 chr1B.!!$R4 719
2 TraesCS1B01G401700 chr1B 631901005 631904304 3299 True 272.100000 460 86.463000 2128 3023 2 chr1B.!!$R3 895
3 TraesCS1B01G401700 chr1A 551587098 551594096 6998 True 1222.000000 2551 87.044333 121 2887 3 chr1A.!!$R1 2766
4 TraesCS1B01G401700 chr1D 459876060 459881540 5480 True 672.600000 1786 87.207200 213 3023 5 chr1D.!!$R2 2810

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
360 387 0.036388 CTCCGTCCTGGCAAAGCTTA 60.036 55.0 0.0 0.0 37.8 3.09 F
993 1117 0.170561 GTGCTCCGACGTGTGTAGAT 59.829 55.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1325 0.179100 ACTCGATGAGCATGGGAACG 60.179 55.0 0.00 0.0 32.04 3.95 R
2243 2425 0.464036 ATCGATCGGCCTAAGCACAA 59.536 50.0 16.41 0.0 42.56 3.33 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
19 20 2.416680 GTCAGAGTACCTACCGGACT 57.583 55.000 9.46 0.00 0.00 3.85
20 21 2.287769 GTCAGAGTACCTACCGGACTC 58.712 57.143 9.46 10.68 37.55 3.36
21 22 2.093021 GTCAGAGTACCTACCGGACTCT 60.093 54.545 15.18 15.18 42.95 3.24
22 23 2.170187 TCAGAGTACCTACCGGACTCTC 59.830 54.545 17.45 11.20 41.61 3.20
23 24 1.490069 AGAGTACCTACCGGACTCTCC 59.510 57.143 15.18 0.00 40.59 3.71
24 25 0.550432 AGTACCTACCGGACTCTCCC 59.450 60.000 9.46 0.00 31.13 4.30
25 26 0.257039 GTACCTACCGGACTCTCCCA 59.743 60.000 9.46 0.00 31.13 4.37
26 27 0.257039 TACCTACCGGACTCTCCCAC 59.743 60.000 9.46 0.00 31.13 4.61
27 28 2.119655 CCTACCGGACTCTCCCACG 61.120 68.421 9.46 0.00 31.13 4.94
30 31 2.995574 CCGGACTCTCCCACGGTT 60.996 66.667 0.00 0.00 41.34 4.44
31 32 2.572284 CGGACTCTCCCACGGTTC 59.428 66.667 0.00 0.00 31.13 3.62
32 33 2.979649 GGACTCTCCCACGGTTCC 59.020 66.667 0.00 0.00 0.00 3.62
33 34 2.657066 GGACTCTCCCACGGTTCCC 61.657 68.421 0.00 0.00 0.00 3.97
34 35 1.911766 GACTCTCCCACGGTTCCCA 60.912 63.158 0.00 0.00 0.00 4.37
35 36 2.168666 GACTCTCCCACGGTTCCCAC 62.169 65.000 0.00 0.00 0.00 4.61
36 37 2.926242 TCTCCCACGGTTCCCACC 60.926 66.667 0.00 0.00 40.16 4.61
37 38 3.246112 CTCCCACGGTTCCCACCA 61.246 66.667 0.00 0.00 44.53 4.17
38 39 2.530661 TCCCACGGTTCCCACCAT 60.531 61.111 0.00 0.00 44.53 3.55
39 40 2.361104 CCCACGGTTCCCACCATG 60.361 66.667 0.00 0.00 44.53 3.66
40 41 3.061848 CCACGGTTCCCACCATGC 61.062 66.667 0.00 0.00 44.53 4.06
41 42 2.282110 CACGGTTCCCACCATGCA 60.282 61.111 0.00 0.00 44.53 3.96
42 43 1.678635 CACGGTTCCCACCATGCAT 60.679 57.895 0.00 0.00 44.53 3.96
43 44 1.378514 ACGGTTCCCACCATGCATC 60.379 57.895 0.00 0.00 44.53 3.91
44 45 2.120909 CGGTTCCCACCATGCATCC 61.121 63.158 0.00 0.00 44.53 3.51
45 46 1.000233 GGTTCCCACCATGCATCCA 60.000 57.895 0.00 0.00 43.61 3.41
46 47 0.397535 GGTTCCCACCATGCATCCAT 60.398 55.000 0.00 0.00 43.61 3.41
47 48 0.748450 GTTCCCACCATGCATCCATG 59.252 55.000 0.00 0.00 46.70 3.66
69 70 1.746470 TGCATGACTCTTGCATGAGG 58.254 50.000 27.63 14.42 44.73 3.86
70 71 1.022735 GCATGACTCTTGCATGAGGG 58.977 55.000 27.63 17.05 44.49 4.30
71 72 1.407851 GCATGACTCTTGCATGAGGGA 60.408 52.381 27.63 16.66 44.49 4.20
72 73 2.562635 CATGACTCTTGCATGAGGGAG 58.437 52.381 27.63 14.09 44.49 4.30
73 74 0.907486 TGACTCTTGCATGAGGGAGG 59.093 55.000 27.63 8.92 38.32 4.30
74 75 1.198713 GACTCTTGCATGAGGGAGGA 58.801 55.000 27.63 0.00 38.32 3.71
75 76 1.138661 GACTCTTGCATGAGGGAGGAG 59.861 57.143 27.63 7.66 45.01 3.69
76 77 1.273495 ACTCTTGCATGAGGGAGGAGA 60.273 52.381 27.63 6.66 42.63 3.71
77 78 1.836166 CTCTTGCATGAGGGAGGAGAA 59.164 52.381 19.36 0.00 42.63 2.87
78 79 1.836166 TCTTGCATGAGGGAGGAGAAG 59.164 52.381 0.00 0.00 0.00 2.85
79 80 1.836166 CTTGCATGAGGGAGGAGAAGA 59.164 52.381 0.00 0.00 0.00 2.87
80 81 1.956869 TGCATGAGGGAGGAGAAGAA 58.043 50.000 0.00 0.00 0.00 2.52
81 82 1.836166 TGCATGAGGGAGGAGAAGAAG 59.164 52.381 0.00 0.00 0.00 2.85
82 83 2.114616 GCATGAGGGAGGAGAAGAAGA 58.885 52.381 0.00 0.00 0.00 2.87
83 84 2.102925 GCATGAGGGAGGAGAAGAAGAG 59.897 54.545 0.00 0.00 0.00 2.85
84 85 1.859302 TGAGGGAGGAGAAGAAGAGC 58.141 55.000 0.00 0.00 0.00 4.09
85 86 1.360852 TGAGGGAGGAGAAGAAGAGCT 59.639 52.381 0.00 0.00 0.00 4.09
86 87 1.756538 GAGGGAGGAGAAGAAGAGCTG 59.243 57.143 0.00 0.00 0.00 4.24
87 88 0.177836 GGGAGGAGAAGAAGAGCTGC 59.822 60.000 0.00 0.00 0.00 5.25
88 89 0.177836 GGAGGAGAAGAAGAGCTGCC 59.822 60.000 0.00 0.00 0.00 4.85
89 90 0.177836 GAGGAGAAGAAGAGCTGCCC 59.822 60.000 0.00 0.00 0.00 5.36
90 91 1.223211 GGAGAAGAAGAGCTGCCCC 59.777 63.158 0.00 0.00 0.00 5.80
91 92 1.271127 GGAGAAGAAGAGCTGCCCCT 61.271 60.000 0.00 0.00 0.00 4.79
92 93 0.107752 GAGAAGAAGAGCTGCCCCTG 60.108 60.000 0.00 0.00 0.00 4.45
93 94 1.077858 GAAGAAGAGCTGCCCCTGG 60.078 63.158 0.00 0.00 0.00 4.45
94 95 2.549169 GAAGAAGAGCTGCCCCTGGG 62.549 65.000 5.50 5.50 38.57 4.45
107 108 2.285368 CTGGGCAGGACCACCCTA 60.285 66.667 20.30 5.43 45.60 3.53
108 109 2.609610 TGGGCAGGACCACCCTAC 60.610 66.667 20.30 0.00 45.60 3.18
109 110 3.408853 GGGCAGGACCACCCTACC 61.409 72.222 14.11 0.00 45.60 3.18
110 111 2.609610 GGCAGGACCACCCTACCA 60.610 66.667 0.00 0.00 46.20 3.25
111 112 2.669240 GCAGGACCACCCTACCAC 59.331 66.667 0.00 0.00 45.60 4.16
112 113 2.967946 GCAGGACCACCCTACCACC 61.968 68.421 0.00 0.00 45.60 4.61
113 114 2.124312 AGGACCACCCTACCACCC 59.876 66.667 0.00 0.00 45.48 4.61
114 115 2.204029 GGACCACCCTACCACCCA 60.204 66.667 0.00 0.00 0.00 4.51
115 116 2.599757 GGACCACCCTACCACCCAC 61.600 68.421 0.00 0.00 0.00 4.61
116 117 2.530916 ACCACCCTACCACCCACC 60.531 66.667 0.00 0.00 0.00 4.61
117 118 3.335729 CCACCCTACCACCCACCC 61.336 72.222 0.00 0.00 0.00 4.61
118 119 3.712907 CACCCTACCACCCACCCG 61.713 72.222 0.00 0.00 0.00 5.28
152 153 2.553602 ACGAAACAGAAAGCATGCATCA 59.446 40.909 21.98 0.00 0.00 3.07
360 387 0.036388 CTCCGTCCTGGCAAAGCTTA 60.036 55.000 0.00 0.00 37.80 3.09
365 392 2.095718 CGTCCTGGCAAAGCTTACTTTC 60.096 50.000 0.00 0.00 44.41 2.62
378 405 3.435671 GCTTACTTTCAGAGCCGCTTTAA 59.564 43.478 0.00 0.00 0.00 1.52
387 414 2.188469 CCGCTTTAAGCCCGGCTA 59.812 61.111 13.73 0.00 38.25 3.93
415 453 4.322385 GTTTGGACGCACACCCGC 62.322 66.667 0.00 0.00 0.00 6.13
416 454 4.555709 TTTGGACGCACACCCGCT 62.556 61.111 0.00 0.00 0.00 5.52
638 694 1.135972 CACGGCGAGGTTGATCTTTTG 60.136 52.381 16.62 0.00 0.00 2.44
722 778 4.182693 TGGAGACGTTGAACAATACGAT 57.817 40.909 0.00 0.00 40.03 3.73
838 936 1.075536 TGGCAGAGGTAGACAGACAGA 59.924 52.381 0.00 0.00 0.00 3.41
877 975 4.662145 CCAGTTAATGCGAAGAACATTCC 58.338 43.478 0.00 0.00 38.62 3.01
878 976 4.155826 CCAGTTAATGCGAAGAACATTCCA 59.844 41.667 0.00 0.00 38.62 3.53
879 977 5.163622 CCAGTTAATGCGAAGAACATTCCAT 60.164 40.000 0.00 0.00 38.62 3.41
903 1002 0.319383 CCATCGCTAGCTAGCTGTGG 60.319 60.000 33.31 33.31 46.85 4.17
904 1003 0.387202 CATCGCTAGCTAGCTGTGGT 59.613 55.000 36.02 19.40 46.85 4.16
910 1025 1.821753 CTAGCTAGCTGTGGTGTGAGT 59.178 52.381 27.68 0.00 0.00 3.41
912 1027 0.318441 GCTAGCTGTGGTGTGAGTGA 59.682 55.000 7.70 0.00 0.00 3.41
915 1030 0.322975 AGCTGTGGTGTGAGTGATCC 59.677 55.000 0.00 0.00 0.00 3.36
945 1069 0.175989 GTCGGAACTAGCTTGGAGGG 59.824 60.000 0.00 0.00 0.00 4.30
992 1116 1.577922 GTGCTCCGACGTGTGTAGA 59.422 57.895 0.00 0.00 0.00 2.59
993 1117 0.170561 GTGCTCCGACGTGTGTAGAT 59.829 55.000 0.00 0.00 0.00 1.98
994 1118 1.399440 GTGCTCCGACGTGTGTAGATA 59.601 52.381 0.00 0.00 0.00 1.98
996 1120 1.597445 GCTCCGACGTGTGTAGATAGC 60.597 57.143 0.00 0.00 0.00 2.97
997 1121 0.654160 TCCGACGTGTGTAGATAGCG 59.346 55.000 0.00 0.00 0.00 4.26
1099 1226 1.745320 CTACGTCCGGGCTAATGGCT 61.745 60.000 3.66 0.00 41.46 4.75
1198 1343 0.877649 CCGTTCCCATGCTCATCGAG 60.878 60.000 0.00 0.00 0.00 4.04
1199 1344 0.179100 CGTTCCCATGCTCATCGAGT 60.179 55.000 0.00 0.00 31.39 4.18
1200 1345 1.293924 GTTCCCATGCTCATCGAGTG 58.706 55.000 0.00 0.00 31.39 3.51
1201 1346 1.134699 GTTCCCATGCTCATCGAGTGA 60.135 52.381 0.00 0.00 35.05 3.41
1202 1347 1.417288 TCCCATGCTCATCGAGTGAT 58.583 50.000 0.00 0.00 35.97 3.06
1489 1652 4.856607 GCCTCGGACTCGAAGCCG 62.857 72.222 16.96 16.96 44.48 5.52
1493 1656 4.856607 CGGACTCGAAGCCGGAGC 62.857 72.222 5.05 0.00 43.67 4.70
1494 1657 4.516195 GGACTCGAAGCCGGAGCC 62.516 72.222 5.05 0.00 41.25 4.70
1495 1658 4.856607 GACTCGAAGCCGGAGCCG 62.857 72.222 5.05 4.27 41.25 5.52
1531 1694 2.363795 CCACGCCCTCAGGTCCTA 60.364 66.667 0.00 0.00 34.57 2.94
1532 1695 2.722201 CCACGCCCTCAGGTCCTAC 61.722 68.421 0.00 0.00 34.57 3.18
1533 1696 1.682684 CACGCCCTCAGGTCCTACT 60.683 63.158 0.00 0.00 34.57 2.57
1534 1697 1.380112 ACGCCCTCAGGTCCTACTC 60.380 63.158 0.00 0.00 34.57 2.59
1535 1698 2.128507 CGCCCTCAGGTCCTACTCC 61.129 68.421 0.00 0.00 34.57 3.85
1950 2113 1.376609 GCTACTTCCCCAACATGGCG 61.377 60.000 0.00 0.00 35.79 5.69
2058 2221 1.737838 TGCTCCATTGGATTCGTCAC 58.262 50.000 5.70 0.00 0.00 3.67
2059 2222 1.278985 TGCTCCATTGGATTCGTCACT 59.721 47.619 5.70 0.00 0.00 3.41
2076 2239 5.093457 CGTCACTACACACGTAATTGAGAT 58.907 41.667 0.00 0.00 0.00 2.75
2080 2243 7.008447 GTCACTACACACGTAATTGAGATCTTC 59.992 40.741 0.00 0.00 0.00 2.87
2086 2249 4.100189 CACGTAATTGAGATCTTCCTCCCT 59.900 45.833 0.00 0.00 32.32 4.20
2172 2351 8.908786 ATTTAGGTCTGGATTACATACATGTG 57.091 34.615 9.11 0.00 41.89 3.21
2203 2385 4.642429 ACTCAACTGAGGTGTGGATTTAC 58.358 43.478 11.31 0.00 46.13 2.01
2204 2386 3.659786 TCAACTGAGGTGTGGATTTACG 58.340 45.455 0.00 0.00 0.00 3.18
2205 2387 2.742053 CAACTGAGGTGTGGATTTACGG 59.258 50.000 0.00 0.00 0.00 4.02
2206 2388 2.253610 ACTGAGGTGTGGATTTACGGA 58.746 47.619 0.00 0.00 0.00 4.69
2207 2389 2.838202 ACTGAGGTGTGGATTTACGGAT 59.162 45.455 0.00 0.00 0.00 4.18
2208 2390 3.263425 ACTGAGGTGTGGATTTACGGATT 59.737 43.478 0.00 0.00 0.00 3.01
2209 2391 4.261801 CTGAGGTGTGGATTTACGGATTT 58.738 43.478 0.00 0.00 0.00 2.17
2261 2503 0.464036 ATTGTGCTTAGGCCGATCGA 59.536 50.000 18.66 0.00 37.74 3.59
2262 2504 0.464036 TTGTGCTTAGGCCGATCGAT 59.536 50.000 18.66 0.00 37.74 3.59
2263 2505 0.464036 TGTGCTTAGGCCGATCGATT 59.536 50.000 18.66 3.89 37.74 3.34
2275 2517 3.555956 GCCGATCGATTGACACAATAACT 59.444 43.478 18.66 0.00 0.00 2.24
2282 2610 9.425893 GATCGATTGACACAATAACTTTATGTG 57.574 33.333 0.00 3.76 36.65 3.21
2307 2635 3.453559 CGGTTTACGCCTTCCTCAT 57.546 52.632 0.00 0.00 34.82 2.90
2308 2636 2.589798 CGGTTTACGCCTTCCTCATA 57.410 50.000 0.00 0.00 34.82 2.15
2309 2637 3.107642 CGGTTTACGCCTTCCTCATAT 57.892 47.619 0.00 0.00 34.82 1.78
2310 2638 2.800544 CGGTTTACGCCTTCCTCATATG 59.199 50.000 0.00 0.00 34.82 1.78
2312 2640 3.433173 GGTTTACGCCTTCCTCATATGGT 60.433 47.826 2.13 0.00 0.00 3.55
2330 2676 2.422479 TGGTCTCCTCGACAAGAATACG 59.578 50.000 0.00 0.00 44.68 3.06
2332 2678 1.063616 TCTCCTCGACAAGAATACGCG 59.936 52.381 3.53 3.53 0.00 6.01
2348 2694 3.056952 ACGCGTATACTACACCGAAAG 57.943 47.619 11.67 0.00 0.00 2.62
2349 2695 1.777461 CGCGTATACTACACCGAAAGC 59.223 52.381 0.00 0.00 0.00 3.51
2358 2704 1.081376 CACCGAAAGCGACGAGACT 60.081 57.895 0.00 0.00 40.82 3.24
2359 2705 0.167470 CACCGAAAGCGACGAGACTA 59.833 55.000 0.00 0.00 40.82 2.59
2395 2741 4.408821 GTCTGGTGATGCCGGCCA 62.409 66.667 26.77 13.42 43.46 5.36
2396 2742 3.645660 TCTGGTGATGCCGGCCAA 61.646 61.111 26.77 6.41 43.46 4.52
2398 2744 1.152984 CTGGTGATGCCGGCCAATA 60.153 57.895 26.77 4.98 41.21 1.90
2399 2745 1.447317 CTGGTGATGCCGGCCAATAC 61.447 60.000 26.77 17.15 41.21 1.89
2400 2746 2.542907 GGTGATGCCGGCCAATACG 61.543 63.158 26.77 0.00 0.00 3.06
2433 2779 2.971307 TGCGCAAGAGTGACATGAATA 58.029 42.857 8.16 0.00 43.02 1.75
2434 2780 3.534554 TGCGCAAGAGTGACATGAATAT 58.465 40.909 8.16 0.00 43.02 1.28
2509 2892 3.054361 GGAACCTTTGCAAGATCCTCCTA 60.054 47.826 0.00 0.00 33.86 2.94
2525 2908 6.039415 TCCTCCTATCTGTAGGGTTTGTAT 57.961 41.667 1.92 0.00 46.37 2.29
2532 2915 5.927281 TCTGTAGGGTTTGTATACACTCC 57.073 43.478 4.68 10.59 32.95 3.85
2533 2916 4.400251 TCTGTAGGGTTTGTATACACTCCG 59.600 45.833 4.68 0.00 32.95 4.63
2556 2939 6.749578 CCGATCTCTCCTATGATTTGATTACG 59.250 42.308 0.00 0.00 0.00 3.18
2557 2940 6.749578 CGATCTCTCCTATGATTTGATTACGG 59.250 42.308 0.00 0.00 0.00 4.02
2635 3026 2.479049 GCATGCATGTCTCCATTGTCAC 60.479 50.000 26.79 2.60 0.00 3.67
2660 3051 7.122948 ACCTCTAGTAGTAAAGTGATTGGAGTG 59.877 40.741 0.00 0.00 0.00 3.51
2686 3077 3.728845 ACTTTGAGCTCAGCGACTAAAA 58.271 40.909 17.43 4.79 0.00 1.52
2701 3092 4.387862 CGACTAAAAAGCCGTACATTGACT 59.612 41.667 0.00 0.00 0.00 3.41
2801 3193 0.242017 GGTGGCATTTCAGCAGTGTC 59.758 55.000 0.00 0.00 35.45 3.67
2957 3412 8.969267 CACGTCATGGAATACTTTTATAGACTC 58.031 37.037 0.00 0.00 0.00 3.36
2985 3440 8.693504 GTGTGACTTGTCAATACAAAATGATTG 58.306 33.333 4.93 0.00 44.79 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.093021 AGAGTCCGGTAGGTACTCTGAC 60.093 54.545 19.04 0.00 45.07 3.51
1 2 2.170187 GAGAGTCCGGTAGGTACTCTGA 59.830 54.545 23.33 0.00 45.89 3.27
2 3 2.563702 GAGAGTCCGGTAGGTACTCTG 58.436 57.143 23.33 0.00 45.89 3.35
4 5 1.476652 GGGAGAGTCCGGTAGGTACTC 60.477 61.905 11.35 11.35 41.16 2.59
5 6 0.550432 GGGAGAGTCCGGTAGGTACT 59.450 60.000 0.00 0.00 39.36 2.73
6 7 0.257039 TGGGAGAGTCCGGTAGGTAC 59.743 60.000 0.00 0.00 37.43 3.34
7 8 0.257039 GTGGGAGAGTCCGGTAGGTA 59.743 60.000 0.00 0.00 37.43 3.08
8 9 1.000107 GTGGGAGAGTCCGGTAGGT 60.000 63.158 0.00 0.00 37.43 3.08
9 10 2.119655 CGTGGGAGAGTCCGGTAGG 61.120 68.421 0.00 0.00 37.43 3.18
10 11 2.119655 CCGTGGGAGAGTCCGGTAG 61.120 68.421 0.00 0.00 37.43 3.18
11 12 2.044650 CCGTGGGAGAGTCCGGTA 60.045 66.667 0.00 0.00 37.43 4.02
13 14 2.995574 AACCGTGGGAGAGTCCGG 60.996 66.667 0.00 0.00 45.72 5.14
14 15 2.572284 GAACCGTGGGAGAGTCCG 59.428 66.667 0.00 0.00 37.43 4.79
15 16 2.657066 GGGAACCGTGGGAGAGTCC 61.657 68.421 0.00 0.00 40.86 3.85
16 17 2.979649 GGGAACCGTGGGAGAGTC 59.020 66.667 0.00 0.00 40.86 3.36
28 29 0.748450 CATGGATGCATGGTGGGAAC 59.252 55.000 18.76 0.00 0.00 3.62
29 30 3.210733 CATGGATGCATGGTGGGAA 57.789 52.632 18.76 0.00 0.00 3.97
51 52 1.022735 CCCTCATGCAAGAGTCATGC 58.977 55.000 17.11 13.34 44.08 4.06
52 53 2.562635 CTCCCTCATGCAAGAGTCATG 58.437 52.381 17.11 2.47 41.87 3.07
53 54 1.489649 CCTCCCTCATGCAAGAGTCAT 59.510 52.381 17.11 0.00 33.75 3.06
54 55 0.907486 CCTCCCTCATGCAAGAGTCA 59.093 55.000 17.11 2.96 33.75 3.41
55 56 1.138661 CTCCTCCCTCATGCAAGAGTC 59.861 57.143 17.11 0.00 33.75 3.36
56 57 1.202330 CTCCTCCCTCATGCAAGAGT 58.798 55.000 17.11 0.00 33.75 3.24
57 58 1.493861 TCTCCTCCCTCATGCAAGAG 58.506 55.000 12.01 12.01 35.39 2.85
58 59 1.836166 CTTCTCCTCCCTCATGCAAGA 59.164 52.381 0.00 0.00 0.00 3.02
59 60 1.836166 TCTTCTCCTCCCTCATGCAAG 59.164 52.381 0.00 0.00 0.00 4.01
60 61 1.956869 TCTTCTCCTCCCTCATGCAA 58.043 50.000 0.00 0.00 0.00 4.08
61 62 1.836166 CTTCTTCTCCTCCCTCATGCA 59.164 52.381 0.00 0.00 0.00 3.96
62 63 2.102925 CTCTTCTTCTCCTCCCTCATGC 59.897 54.545 0.00 0.00 0.00 4.06
63 64 2.102925 GCTCTTCTTCTCCTCCCTCATG 59.897 54.545 0.00 0.00 0.00 3.07
64 65 2.023113 AGCTCTTCTTCTCCTCCCTCAT 60.023 50.000 0.00 0.00 0.00 2.90
65 66 1.360852 AGCTCTTCTTCTCCTCCCTCA 59.639 52.381 0.00 0.00 0.00 3.86
66 67 1.756538 CAGCTCTTCTTCTCCTCCCTC 59.243 57.143 0.00 0.00 0.00 4.30
67 68 1.864669 CAGCTCTTCTTCTCCTCCCT 58.135 55.000 0.00 0.00 0.00 4.20
68 69 0.177836 GCAGCTCTTCTTCTCCTCCC 59.822 60.000 0.00 0.00 0.00 4.30
69 70 0.177836 GGCAGCTCTTCTTCTCCTCC 59.822 60.000 0.00 0.00 0.00 4.30
70 71 0.177836 GGGCAGCTCTTCTTCTCCTC 59.822 60.000 0.00 0.00 0.00 3.71
71 72 1.271127 GGGGCAGCTCTTCTTCTCCT 61.271 60.000 0.00 0.00 0.00 3.69
72 73 1.223211 GGGGCAGCTCTTCTTCTCC 59.777 63.158 0.00 0.00 0.00 3.71
73 74 0.107752 CAGGGGCAGCTCTTCTTCTC 60.108 60.000 0.00 0.00 0.00 2.87
74 75 1.560866 CCAGGGGCAGCTCTTCTTCT 61.561 60.000 0.00 0.00 0.00 2.85
75 76 1.077858 CCAGGGGCAGCTCTTCTTC 60.078 63.158 0.00 0.00 0.00 2.87
76 77 2.610519 CCCAGGGGCAGCTCTTCTT 61.611 63.158 0.00 0.00 0.00 2.52
77 78 3.013932 CCCAGGGGCAGCTCTTCT 61.014 66.667 0.00 0.00 0.00 2.85
97 98 2.204029 TGGGTGGTAGGGTGGTCC 60.204 66.667 0.00 0.00 0.00 4.46
98 99 2.599757 GGTGGGTGGTAGGGTGGTC 61.600 68.421 0.00 0.00 0.00 4.02
99 100 2.530916 GGTGGGTGGTAGGGTGGT 60.531 66.667 0.00 0.00 0.00 4.16
100 101 3.335729 GGGTGGGTGGTAGGGTGG 61.336 72.222 0.00 0.00 0.00 4.61
101 102 3.712907 CGGGTGGGTGGTAGGGTG 61.713 72.222 0.00 0.00 0.00 4.61
118 119 3.919973 TTTCGTCCTACGCACGGCC 62.920 63.158 0.00 0.00 42.21 6.13
119 120 2.431260 TTTCGTCCTACGCACGGC 60.431 61.111 0.00 0.00 42.21 5.68
129 130 1.266718 TGCATGCTTTCTGTTTCGTCC 59.733 47.619 20.33 0.00 0.00 4.79
138 139 1.476891 CTTGGCTGATGCATGCTTTCT 59.523 47.619 20.33 0.46 41.91 2.52
152 153 1.302511 CACCACGGTTAGCTTGGCT 60.303 57.895 6.85 0.00 43.41 4.75
312 321 2.983592 GGGTCAGGCAACCAACCG 60.984 66.667 10.72 0.00 41.40 4.44
313 322 2.983592 CGGGTCAGGCAACCAACC 60.984 66.667 10.72 0.76 41.40 3.77
315 324 2.112297 GACGGGTCAGGCAACCAA 59.888 61.111 10.72 0.00 41.40 3.67
317 326 4.309950 ACGACGGGTCAGGCAACC 62.310 66.667 0.00 0.69 38.69 3.77
319 328 4.351938 CGACGACGGGTCAGGCAA 62.352 66.667 0.00 0.00 46.42 4.52
321 330 4.773117 GACGACGACGGGTCAGGC 62.773 72.222 12.58 1.52 46.42 4.85
322 331 4.456253 CGACGACGACGGGTCAGG 62.456 72.222 12.58 3.12 46.42 3.86
360 387 1.807142 GCTTAAAGCGGCTCTGAAAGT 59.193 47.619 1.45 0.00 33.76 2.66
365 392 2.464459 CGGGCTTAAAGCGGCTCTG 61.464 63.158 1.45 0.00 43.62 3.35
378 405 1.367840 CTAGCGATTTAGCCGGGCT 59.632 57.895 26.95 26.95 43.41 5.19
387 414 0.719465 CGTCCAAACGCTAGCGATTT 59.281 50.000 41.33 30.60 42.82 2.17
412 450 0.811281 GGGGTTGATTCTTTCAGCGG 59.189 55.000 0.00 0.00 36.49 5.52
415 453 4.321230 CCTTTTCGGGGTTGATTCTTTCAG 60.321 45.833 0.00 0.00 35.27 3.02
416 454 3.572255 CCTTTTCGGGGTTGATTCTTTCA 59.428 43.478 0.00 0.00 0.00 2.69
553 595 6.204108 CGGTCAATAGTCAACACCTTTTTACT 59.796 38.462 0.00 0.00 0.00 2.24
554 596 6.368213 CGGTCAATAGTCAACACCTTTTTAC 58.632 40.000 0.00 0.00 0.00 2.01
555 597 5.049267 GCGGTCAATAGTCAACACCTTTTTA 60.049 40.000 0.00 0.00 0.00 1.52
556 598 4.261447 GCGGTCAATAGTCAACACCTTTTT 60.261 41.667 0.00 0.00 0.00 1.94
689 745 0.179205 CGTCTCCAAGGTCGTCGTAC 60.179 60.000 0.00 0.00 0.00 3.67
838 936 2.574955 GGCGGAGGACACTGTCTGT 61.575 63.158 9.08 0.00 34.96 3.41
877 975 2.478134 GCTAGCTAGCGATGGAACAATG 59.522 50.000 28.89 0.00 40.44 2.82
878 976 2.760374 GCTAGCTAGCGATGGAACAAT 58.240 47.619 28.89 0.00 40.44 2.71
879 977 2.225068 GCTAGCTAGCGATGGAACAA 57.775 50.000 28.89 0.00 40.44 2.83
903 1002 2.560542 AGTCAGTCTGGATCACTCACAC 59.439 50.000 0.00 0.00 0.00 3.82
904 1003 2.560105 CAGTCAGTCTGGATCACTCACA 59.440 50.000 0.00 0.00 40.23 3.58
915 1030 0.962489 AGTTCCGACCAGTCAGTCTG 59.038 55.000 0.00 0.00 43.27 3.51
945 1069 3.530398 GAGAGTCCTCGATCGCCGC 62.530 68.421 11.09 0.41 38.37 6.53
979 1103 0.316772 CCGCTATCTACACACGTCGG 60.317 60.000 0.00 0.00 0.00 4.79
1079 1206 1.366366 CCATTAGCCCGGACGTAGG 59.634 63.158 0.73 2.74 0.00 3.18
1099 1226 2.435938 GATCCAGTTGCCGCCGAA 60.436 61.111 0.00 0.00 0.00 4.30
1180 1325 0.179100 ACTCGATGAGCATGGGAACG 60.179 55.000 0.00 0.00 32.04 3.95
1198 1343 0.730494 GCAGCGCCACAAGAAATCAC 60.730 55.000 2.29 0.00 0.00 3.06
1199 1344 1.171549 TGCAGCGCCACAAGAAATCA 61.172 50.000 2.29 0.00 0.00 2.57
1200 1345 0.455633 CTGCAGCGCCACAAGAAATC 60.456 55.000 2.29 0.00 0.00 2.17
1201 1346 1.582968 CTGCAGCGCCACAAGAAAT 59.417 52.632 2.29 0.00 0.00 2.17
1202 1347 2.554636 CCTGCAGCGCCACAAGAAA 61.555 57.895 8.66 0.00 0.00 2.52
1488 1651 4.214327 GAGAAGGCTCCGGCTCCG 62.214 72.222 0.00 0.48 37.50 4.63
1530 1693 2.363795 CAGGACCGGGCAGGAGTA 60.364 66.667 11.00 0.00 45.00 2.59
1761 1924 4.451150 GACGACGCCCAGATGCCA 62.451 66.667 0.00 0.00 0.00 4.92
2058 2221 6.565234 AGGAAGATCTCAATTACGTGTGTAG 58.435 40.000 0.00 0.00 0.00 2.74
2059 2222 6.405508 GGAGGAAGATCTCAATTACGTGTGTA 60.406 42.308 0.00 0.00 35.58 2.90
2076 2239 2.398754 TCACAACTCAGGGAGGAAGA 57.601 50.000 0.00 0.00 33.35 2.87
2138 2316 8.768397 TGTAATCCAGACCTAAATTGAGTACAT 58.232 33.333 0.00 0.00 31.03 2.29
2155 2334 5.125356 TCCAAGCACATGTATGTAATCCAG 58.875 41.667 0.00 0.00 39.39 3.86
2172 2351 3.686726 CACCTCAGTTGAGTATTCCAAGC 59.313 47.826 8.23 0.00 40.48 4.01
2243 2425 0.464036 ATCGATCGGCCTAAGCACAA 59.536 50.000 16.41 0.00 42.56 3.33
2261 2503 8.306038 ACATGCACATAAAGTTATTGTGTCAAT 58.694 29.630 15.59 0.80 33.49 2.57
2262 2504 7.594386 CACATGCACATAAAGTTATTGTGTCAA 59.406 33.333 15.59 6.44 33.49 3.18
2263 2505 7.083230 CACATGCACATAAAGTTATTGTGTCA 58.917 34.615 15.59 14.08 33.49 3.58
2275 2517 3.668226 CGTAAACCGCACATGCACATAAA 60.668 43.478 4.49 0.00 42.21 1.40
2312 2640 1.063616 CGCGTATTCTTGTCGAGGAGA 59.936 52.381 0.00 0.00 0.00 3.71
2332 2678 3.031812 CGTCGCTTTCGGTGTAGTATAC 58.968 50.000 0.00 0.00 38.03 1.47
2348 2694 8.350238 TGTAGACATATATATAGTCTCGTCGC 57.650 38.462 21.20 11.65 41.39 5.19
2359 2705 9.121658 CACCAGACCGTATGTAGACATATATAT 57.878 37.037 5.69 0.00 40.53 0.86
2394 2740 4.431986 GCGCATACATTACGTACCGTATTG 60.432 45.833 0.30 13.84 44.13 1.90
2395 2741 3.670055 GCGCATACATTACGTACCGTATT 59.330 43.478 0.30 0.00 41.97 1.89
2396 2742 3.236816 GCGCATACATTACGTACCGTAT 58.763 45.455 0.30 9.31 41.97 3.06
2398 2744 1.202279 TGCGCATACATTACGTACCGT 60.202 47.619 5.66 0.00 44.35 4.83
2399 2745 1.479170 TGCGCATACATTACGTACCG 58.521 50.000 5.66 0.00 33.56 4.02
2400 2746 3.117794 TCTTGCGCATACATTACGTACC 58.882 45.455 12.75 0.00 31.27 3.34
2401 2747 3.795101 ACTCTTGCGCATACATTACGTAC 59.205 43.478 12.75 0.00 31.27 3.67
2406 2752 3.855858 TGTCACTCTTGCGCATACATTA 58.144 40.909 12.75 0.00 0.00 1.90
2509 2892 5.068723 CGGAGTGTATACAAACCCTACAGAT 59.931 44.000 7.25 0.00 0.00 2.90
2525 2908 4.976540 TCATAGGAGAGATCGGAGTGTA 57.023 45.455 0.00 0.00 0.00 2.90
2532 2915 6.749578 CCGTAATCAAATCATAGGAGAGATCG 59.250 42.308 0.00 0.00 0.00 3.69
2533 2916 7.831753 TCCGTAATCAAATCATAGGAGAGATC 58.168 38.462 0.00 0.00 0.00 2.75
2556 2939 4.757149 GTGCTCCAAGATGGTATACAATCC 59.243 45.833 15.47 1.63 39.03 3.01
2557 2940 5.368145 TGTGCTCCAAGATGGTATACAATC 58.632 41.667 11.79 11.79 39.03 2.67
2601 2986 9.185192 GGAGACATGCATGCTTAATAATTAAAC 57.815 33.333 26.53 7.75 0.00 2.01
2635 3026 7.416890 CCACTCCAATCACTTTACTACTAGAGG 60.417 44.444 0.00 0.00 0.00 3.69
2660 3051 1.074752 CGCTGAGCTCAAAGTCTTCC 58.925 55.000 18.85 0.00 0.00 3.46
2686 3077 2.143122 CACACAGTCAATGTACGGCTT 58.857 47.619 0.00 0.00 41.41 4.35
2701 3092 3.323691 TGCTAGCTCTTAGTTTCCACACA 59.676 43.478 17.23 0.00 0.00 3.72
2957 3412 7.416817 TCATTTTGTATTGACAAGTCACACTG 58.583 34.615 1.73 0.07 46.11 3.66
2985 3440 8.744568 ATGGAAAATCTCTATCTTTTCTGGTC 57.255 34.615 7.46 0.00 39.92 4.02


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

AutoCloner maintained by Alex Coulton.