Multiple sequence alignment - TraesCS5B01G185300

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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 TraesCS5B01G185300 chr5B 100.000 4702 0 0 1 4702 336777280 336772579 0.000000e+00 8684.0
1 TraesCS5B01G185300 chr5B 92.923 862 40 11 1 842 456330416 456331276 0.000000e+00 1234.0
2 TraesCS5B01G185300 chr5B 91.926 867 46 11 1 843 575851268 575852134 0.000000e+00 1192.0
3 TraesCS5B01G185300 chr5B 91.561 865 50 10 1 842 614992132 614991268 0.000000e+00 1171.0
4 TraesCS5B01G185300 chr5B 91.455 866 49 17 1 842 89644758 89645622 0.000000e+00 1166.0
5 TraesCS5B01G185300 chr5B 90.281 854 56 11 1 842 41398613 41397775 0.000000e+00 1092.0
6 TraesCS5B01G185300 chr5D 93.336 3031 135 26 882 3887 294954778 294951790 0.000000e+00 4416.0
7 TraesCS5B01G185300 chr5D 87.600 750 62 16 3966 4702 294951793 294951062 0.000000e+00 841.0
8 TraesCS5B01G185300 chr5A 92.566 3067 160 32 842 3887 388636698 388633679 0.000000e+00 4338.0
9 TraesCS5B01G185300 chr5A 83.247 776 55 29 3966 4702 388633678 388632939 1.100000e-180 643.0
10 TraesCS5B01G185300 chr3B 93.240 858 40 7 1 843 741700651 741701505 0.000000e+00 1247.0
11 TraesCS5B01G185300 chr3B 92.317 859 46 9 1 842 527028904 527028049 0.000000e+00 1203.0
12 TraesCS5B01G185300 chr3B 92.182 857 52 5 1 842 249987934 249988790 0.000000e+00 1197.0
13 TraesCS5B01G185300 chr3B 92.453 53 3 1 3731 3783 42628395 42628344 1.810000e-09 75.0
14 TraesCS5B01G185300 chr7B 92.907 860 42 9 1 842 378616696 378617554 0.000000e+00 1232.0
15 TraesCS5B01G185300 chr7B 91.132 857 51 11 1 842 409918995 409918149 0.000000e+00 1138.0
16 TraesCS5B01G185300 chr7B 82.301 113 15 4 4284 4392 39929632 39929743 5.010000e-15 93.5
17 TraesCS5B01G185300 chr7B 93.478 46 3 0 3881 3926 437368292 437368337 8.440000e-08 69.4
18 TraesCS5B01G185300 chr4B 92.708 864 42 12 1 844 1074943 1075805 0.000000e+00 1227.0
19 TraesCS5B01G185300 chr4B 91.908 865 51 9 1 851 548122282 548121423 0.000000e+00 1192.0
20 TraesCS5B01G185300 chr4B 95.056 708 26 3 1 699 472491514 472492221 0.000000e+00 1105.0
21 TraesCS5B01G185300 chr2B 91.735 859 55 6 1 844 782133303 782134160 0.000000e+00 1179.0
22 TraesCS5B01G185300 chr1B 91.399 872 47 16 1 844 449992194 449991323 0.000000e+00 1170.0
23 TraesCS5B01G185300 chr1B 100.000 32 0 0 3884 3915 22056484 22056453 5.080000e-05 60.2
24 TraesCS5B01G185300 chrUn 90.262 534 37 9 328 846 465884852 465884319 0.000000e+00 684.0
25 TraesCS5B01G185300 chr1A 88.235 85 7 3 3886 3967 312612134 312612050 1.080000e-16 99.0
26 TraesCS5B01G185300 chr1A 100.000 30 0 0 3885 3914 47204518 47204547 6.570000e-04 56.5
27 TraesCS5B01G185300 chr4A 96.000 50 0 1 3736 3783 622919206 622919255 3.900000e-11 80.5
28 TraesCS5B01G185300 chr4A 95.918 49 0 1 3737 3783 622895386 622895434 1.400000e-10 78.7
29 TraesCS5B01G185300 chr4A 95.918 49 0 1 3737 3783 622900271 622900319 1.400000e-10 78.7
30 TraesCS5B01G185300 chr4A 95.918 49 0 1 3737 3783 622944968 622945016 1.400000e-10 78.7
31 TraesCS5B01G185300 chr4A 95.918 49 0 1 3737 3783 622969009 622969057 1.400000e-10 78.7
32 TraesCS5B01G185300 chr4A 90.000 60 2 3 3727 3783 622959167 622959225 1.810000e-09 75.0


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 TraesCS5B01G185300 chr5B 336772579 336777280 4701 True 8684.0 8684 100.0000 1 4702 1 chr5B.!!$R2 4701
1 TraesCS5B01G185300 chr5B 456330416 456331276 860 False 1234.0 1234 92.9230 1 842 1 chr5B.!!$F2 841
2 TraesCS5B01G185300 chr5B 575851268 575852134 866 False 1192.0 1192 91.9260 1 843 1 chr5B.!!$F3 842
3 TraesCS5B01G185300 chr5B 614991268 614992132 864 True 1171.0 1171 91.5610 1 842 1 chr5B.!!$R3 841
4 TraesCS5B01G185300 chr5B 89644758 89645622 864 False 1166.0 1166 91.4550 1 842 1 chr5B.!!$F1 841
5 TraesCS5B01G185300 chr5B 41397775 41398613 838 True 1092.0 1092 90.2810 1 842 1 chr5B.!!$R1 841
6 TraesCS5B01G185300 chr5D 294951062 294954778 3716 True 2628.5 4416 90.4680 882 4702 2 chr5D.!!$R1 3820
7 TraesCS5B01G185300 chr5A 388632939 388636698 3759 True 2490.5 4338 87.9065 842 4702 2 chr5A.!!$R1 3860
8 TraesCS5B01G185300 chr3B 741700651 741701505 854 False 1247.0 1247 93.2400 1 843 1 chr3B.!!$F2 842
9 TraesCS5B01G185300 chr3B 527028049 527028904 855 True 1203.0 1203 92.3170 1 842 1 chr3B.!!$R2 841
10 TraesCS5B01G185300 chr3B 249987934 249988790 856 False 1197.0 1197 92.1820 1 842 1 chr3B.!!$F1 841
11 TraesCS5B01G185300 chr7B 378616696 378617554 858 False 1232.0 1232 92.9070 1 842 1 chr7B.!!$F2 841
12 TraesCS5B01G185300 chr7B 409918149 409918995 846 True 1138.0 1138 91.1320 1 842 1 chr7B.!!$R1 841
13 TraesCS5B01G185300 chr4B 1074943 1075805 862 False 1227.0 1227 92.7080 1 844 1 chr4B.!!$F1 843
14 TraesCS5B01G185300 chr4B 548121423 548122282 859 True 1192.0 1192 91.9080 1 851 1 chr4B.!!$R1 850
15 TraesCS5B01G185300 chr4B 472491514 472492221 707 False 1105.0 1105 95.0560 1 699 1 chr4B.!!$F2 698
16 TraesCS5B01G185300 chr2B 782133303 782134160 857 False 1179.0 1179 91.7350 1 844 1 chr2B.!!$F1 843
17 TraesCS5B01G185300 chr1B 449991323 449992194 871 True 1170.0 1170 91.3990 1 844 1 chr1B.!!$R2 843
18 TraesCS5B01G185300 chrUn 465884319 465884852 533 True 684.0 684 90.2620 328 846 1 chrUn.!!$R1 518

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
743 800 1.162951 AGGAAGAGGGAGGGGGAGAA 61.163 60.0 0.00 0.0 0.0 2.87 F
1285 1349 0.036483 TCCGTCCATGGTGTGTGATG 60.036 55.0 12.58 0.0 0.0 3.07 F
2375 2457 0.739561 ATAGAGAACTGGACGTCGCC 59.260 55.0 9.92 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 2510 0.322277 ACTAGACGAGCTCCAACGGA 60.322 55.0 8.47 0.0 0.0 4.69 R
2429 2511 0.526662 AACTAGACGAGCTCCAACGG 59.473 55.0 8.47 0.0 0.0 4.44 R
4077 4169 0.030773 TGAGCGAGCCGATGTGTATC 59.969 55.0 0.00 0.0 0.0 2.24 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
51 52 2.203938 GGGGACTGGACCACTGGA 60.204 66.667 0.71 0.00 0.00 3.86
264 276 1.551452 TGGGGCCAAAAGGAAATACG 58.449 50.000 4.39 0.00 0.00 3.06
422 436 9.361315 GGTGAACATTTTAGTTTTACTGTTTGT 57.639 29.630 0.00 0.00 0.00 2.83
638 661 2.092968 TCAGTCAAGCTCACCACAAGTT 60.093 45.455 0.00 0.00 0.00 2.66
665 688 9.897744 CACACATTATTGTCAATTGAGTAAGTT 57.102 29.630 8.80 0.00 32.34 2.66
696 719 3.136626 GGGGAGAATAGGCTATGTGTGTT 59.863 47.826 7.99 0.00 0.00 3.32
697 720 4.130118 GGGAGAATAGGCTATGTGTGTTG 58.870 47.826 7.99 0.00 0.00 3.33
698 721 4.384208 GGGAGAATAGGCTATGTGTGTTGT 60.384 45.833 7.99 0.00 0.00 3.32
743 800 1.162951 AGGAAGAGGGAGGGGGAGAA 61.163 60.000 0.00 0.00 0.00 2.87
875 937 1.270839 ACACGGTTTGGATGTCTGGAG 60.271 52.381 0.00 0.00 0.00 3.86
1108 1170 1.684049 CTCCTCTTCCTCCGTGGCT 60.684 63.158 0.00 0.00 35.26 4.75
1150 1212 1.591863 GAAGATGTAGGTCGCGGCC 60.592 63.158 25.39 25.39 0.00 6.13
1184 1246 0.616891 GTGGTCACCGGGGTAATCTT 59.383 55.000 2.12 0.00 0.00 2.40
1196 1258 3.053917 GGGGTAATCTTGAACTGCCCTAA 60.054 47.826 0.00 0.00 35.19 2.69
1200 1262 2.859165 TCTTGAACTGCCCTAACAGG 57.141 50.000 0.00 0.00 42.21 4.00
1201 1263 2.334977 TCTTGAACTGCCCTAACAGGA 58.665 47.619 0.00 0.00 42.21 3.86
1225 1287 8.086522 GGAGTGTCTGCCTATTTTATCGTATTA 58.913 37.037 0.00 0.00 0.00 0.98
1250 1314 1.080569 CTGTTTTCCATGGTGCGCC 60.081 57.895 12.58 10.11 0.00 6.53
1283 1347 1.671166 CTCCGTCCATGGTGTGTGA 59.329 57.895 12.58 2.12 0.00 3.58
1285 1349 0.036483 TCCGTCCATGGTGTGTGATG 60.036 55.000 12.58 0.00 0.00 3.07
1348 1412 1.457643 CTGGCGAGGGAGGGATACA 60.458 63.158 0.00 0.00 39.74 2.29
1349 1413 1.457643 TGGCGAGGGAGGGATACAG 60.458 63.158 0.00 0.00 39.74 2.74
1350 1414 2.737830 GCGAGGGAGGGATACAGC 59.262 66.667 0.00 0.00 39.74 4.40
1464 1528 6.425721 GTGCCCTTTGTTGAACGCTATATATA 59.574 38.462 0.00 0.00 0.00 0.86
1569 1633 4.034858 TGCTGCATCTTGAATTCTCGATTC 59.965 41.667 7.05 4.05 43.67 2.52
1618 1690 4.582656 CCTTGTTGTGGGACTTGTATTCAA 59.417 41.667 0.00 0.00 0.00 2.69
1913 1987 3.446516 AGCCTTCCATTCAGCTTTTGATC 59.553 43.478 0.00 0.00 35.27 2.92
1943 2017 2.568062 TGGGATGCTTGCAAAATCACAT 59.432 40.909 18.31 9.53 28.85 3.21
1973 2047 3.517100 CCGAGGATGGGATTGATGAGTAT 59.483 47.826 0.00 0.00 35.02 2.12
1996 2070 5.713025 TGTGCTTTCCTTGCAATTATTCTC 58.287 37.500 0.00 0.00 42.41 2.87
2091 2172 3.472652 AGTGAACCTTAATGCGTGTGAA 58.527 40.909 0.00 0.00 0.00 3.18
2147 2228 5.009410 CCATTTATCCTGACCAGCATTCTTC 59.991 44.000 0.00 0.00 0.00 2.87
2319 2401 3.032459 TGGACATTGCCACATTATGCAT 58.968 40.909 3.79 3.79 37.33 3.96
2354 2436 9.882996 ATTGCATACATTAGTTTTCACATATCG 57.117 29.630 0.00 0.00 0.00 2.92
2357 2439 8.721478 GCATACATTAGTTTTCACATATCGGAT 58.279 33.333 0.00 0.00 0.00 4.18
2375 2457 0.739561 ATAGAGAACTGGACGTCGCC 59.260 55.000 9.92 0.00 0.00 5.54
2419 2501 4.431131 CCGAGCCCACCTGCCAAT 62.431 66.667 0.00 0.00 0.00 3.16
2420 2502 2.825836 CGAGCCCACCTGCCAATC 60.826 66.667 0.00 0.00 0.00 2.67
2421 2503 2.440980 GAGCCCACCTGCCAATCC 60.441 66.667 0.00 0.00 0.00 3.01
2422 2504 4.066139 AGCCCACCTGCCAATCCC 62.066 66.667 0.00 0.00 0.00 3.85
2423 2505 4.066139 GCCCACCTGCCAATCCCT 62.066 66.667 0.00 0.00 0.00 4.20
2424 2506 2.043652 CCCACCTGCCAATCCCTG 60.044 66.667 0.00 0.00 0.00 4.45
2434 2516 3.159298 CAATCCCTGGACTCCGTTG 57.841 57.895 0.00 0.00 0.00 4.10
2435 2517 0.392998 CAATCCCTGGACTCCGTTGG 60.393 60.000 0.00 0.00 0.00 3.77
2436 2518 0.546747 AATCCCTGGACTCCGTTGGA 60.547 55.000 0.00 3.26 0.00 3.53
2444 2526 3.279183 CTCCGTTGGAGCTCGTCT 58.721 61.111 7.83 0.00 43.29 4.18
2445 2527 2.478989 CTCCGTTGGAGCTCGTCTA 58.521 57.895 7.83 0.00 43.29 2.59
2454 2536 6.032094 CGTTGGAGCTCGTCTAGTTTATTTA 58.968 40.000 7.83 0.00 0.00 1.40
2529 2611 4.640201 TGTAGTAGCTCCATTGCCAAAATC 59.360 41.667 0.00 0.00 0.00 2.17
2532 2614 5.128919 AGTAGCTCCATTGCCAAAATCTAG 58.871 41.667 0.00 0.00 0.00 2.43
2576 2658 6.128391 TGTTGCGTCTATTTTGAATCTGGTAC 60.128 38.462 0.00 0.00 0.00 3.34
2613 2695 1.610522 GTTCTTGCAGCTGGTCACATT 59.389 47.619 17.12 0.00 0.00 2.71
2628 2710 4.876107 GGTCACATTGTACCACCATTCTAG 59.124 45.833 9.30 0.00 35.73 2.43
2790 2874 8.093927 CCCTTAGCTAGTACTTACGAGTATACT 58.906 40.741 4.68 4.68 40.33 2.12
2829 2913 5.355071 TGCTTTAGTATTCACTTCATGCAGG 59.645 40.000 0.00 0.00 36.14 4.85
2850 2934 9.330063 TGCAGGTCTTATCTACAAAATCTATTG 57.670 33.333 0.00 0.00 36.37 1.90
2996 3080 5.957168 TCCCTTCCATTTATTCTTCATGCAA 59.043 36.000 0.00 0.00 0.00 4.08
3088 3175 2.426522 ACATGTCTGACCCAAATGTCG 58.573 47.619 5.17 0.00 38.11 4.35
3096 3183 2.289444 TGACCCAAATGTCGAAGTCCTC 60.289 50.000 0.00 0.00 38.11 3.71
3139 3226 9.326413 CTGTAGTTCTGTTCTCTTTTCCTTTTA 57.674 33.333 0.00 0.00 0.00 1.52
3140 3227 9.106070 TGTAGTTCTGTTCTCTTTTCCTTTTAC 57.894 33.333 0.00 0.00 0.00 2.01
3146 3234 7.501225 TCTGTTCTCTTTTCCTTTTACCGAAAT 59.499 33.333 0.00 0.00 0.00 2.17
3149 3237 7.811117 TCTCTTTTCCTTTTACCGAAATTCA 57.189 32.000 0.00 0.00 0.00 2.57
3199 3287 1.747924 CGAAGGCTCATCTCTCTGTCA 59.252 52.381 0.00 0.00 0.00 3.58
3209 3297 3.729862 TCTCTCTGTCATGCTATGCTG 57.270 47.619 0.00 0.00 0.00 4.41
3225 3313 3.100207 TGCTGCCTTAAGCCCTTTTAT 57.900 42.857 0.00 0.00 42.83 1.40
3289 3378 7.231519 AGTCTTAAATTTCATGCTTATAGGGCC 59.768 37.037 0.00 0.00 0.00 5.80
3305 3394 3.770040 CCGCGGATCCAGGTGTGA 61.770 66.667 24.07 0.00 0.00 3.58
3348 3437 0.914644 CTCCCTCCATGCCTTTCTCA 59.085 55.000 0.00 0.00 0.00 3.27
3433 3522 2.979676 CTTGACGCAGCCTTGGCA 60.980 61.111 14.54 0.00 0.00 4.92
3495 3584 8.836268 TTCTGCTATTTTGATGCAAGAAAAAT 57.164 26.923 16.65 16.65 37.32 1.82
3653 3742 1.676635 GTGGGCAGCATCTTCAGCA 60.677 57.895 0.00 0.00 0.00 4.41
3654 3743 1.676635 TGGGCAGCATCTTCAGCAC 60.677 57.895 0.00 0.00 0.00 4.40
3661 3750 0.675837 GCATCTTCAGCACTGCTCCA 60.676 55.000 0.00 0.00 36.40 3.86
3687 3776 1.336887 TGCGGCTTAGAGACTGTGAAC 60.337 52.381 0.00 0.00 0.00 3.18
3688 3777 1.067495 GCGGCTTAGAGACTGTGAACT 60.067 52.381 0.00 0.00 0.00 3.01
3750 3839 0.312416 CATCTCTAGCCGTCCCTTCG 59.688 60.000 0.00 0.00 0.00 3.79
3773 3862 4.832823 GGGGACATCCGATAAAATTGGAAT 59.167 41.667 0.00 0.00 45.74 3.01
3783 3872 7.173218 TCCGATAAAATTGGAATGATACAGAGC 59.827 37.037 0.00 0.00 39.91 4.09
3798 3887 3.177883 GAGCGCATCTCTAGCAGAC 57.822 57.895 11.47 0.00 38.78 3.51
3827 3918 6.575162 AAGTCGCACTTGAGGAATTTATTT 57.425 33.333 1.44 0.00 37.00 1.40
3828 3919 6.575162 AGTCGCACTTGAGGAATTTATTTT 57.425 33.333 0.00 0.00 0.00 1.82
3829 3920 7.681939 AGTCGCACTTGAGGAATTTATTTTA 57.318 32.000 0.00 0.00 0.00 1.52
3830 3921 8.281212 AGTCGCACTTGAGGAATTTATTTTAT 57.719 30.769 0.00 0.00 0.00 1.40
3875 3966 8.776061 AGCCCTATCTAACAGATCCTATATTC 57.224 38.462 0.00 0.00 36.20 1.75
3877 3968 7.787424 GCCCTATCTAACAGATCCTATATTCCT 59.213 40.741 0.00 0.00 36.20 3.36
3896 3987 6.469782 TTCCTATAAAAATACTCCGTCCGT 57.530 37.500 0.00 0.00 0.00 4.69
3897 3988 7.581213 TTCCTATAAAAATACTCCGTCCGTA 57.419 36.000 0.00 0.00 0.00 4.02
3898 3989 7.581213 TCCTATAAAAATACTCCGTCCGTAA 57.419 36.000 0.00 0.00 0.00 3.18
3899 3990 8.006298 TCCTATAAAAATACTCCGTCCGTAAA 57.994 34.615 0.00 0.00 0.00 2.01
3900 3991 8.137437 TCCTATAAAAATACTCCGTCCGTAAAG 58.863 37.037 0.00 0.00 0.00 1.85
3901 3992 8.137437 CCTATAAAAATACTCCGTCCGTAAAGA 58.863 37.037 0.00 0.00 0.00 2.52
3902 3993 9.520204 CTATAAAAATACTCCGTCCGTAAAGAA 57.480 33.333 0.00 0.00 0.00 2.52
3903 3994 8.776376 ATAAAAATACTCCGTCCGTAAAGAAA 57.224 30.769 0.00 0.00 0.00 2.52
3904 3995 7.677454 AAAAATACTCCGTCCGTAAAGAAAT 57.323 32.000 0.00 0.00 0.00 2.17
3905 3996 8.776376 AAAAATACTCCGTCCGTAAAGAAATA 57.224 30.769 0.00 0.00 0.00 1.40
3906 3997 8.953368 AAAATACTCCGTCCGTAAAGAAATAT 57.047 30.769 0.00 0.00 0.00 1.28
3909 4000 9.688592 AATACTCCGTCCGTAAAGAAATATAAG 57.311 33.333 0.00 0.00 0.00 1.73
3910 4001 7.338800 ACTCCGTCCGTAAAGAAATATAAGA 57.661 36.000 0.00 0.00 0.00 2.10
3911 4002 7.424001 ACTCCGTCCGTAAAGAAATATAAGAG 58.576 38.462 0.00 0.00 0.00 2.85
3912 4003 6.211515 TCCGTCCGTAAAGAAATATAAGAGC 58.788 40.000 0.00 0.00 0.00 4.09
3913 4004 5.116680 CCGTCCGTAAAGAAATATAAGAGCG 59.883 44.000 0.00 0.00 0.00 5.03
3914 4005 5.684626 CGTCCGTAAAGAAATATAAGAGCGT 59.315 40.000 0.00 0.00 0.00 5.07
3915 4006 6.197842 CGTCCGTAAAGAAATATAAGAGCGTT 59.802 38.462 0.00 0.00 0.00 4.84
3916 4007 7.253883 CGTCCGTAAAGAAATATAAGAGCGTTT 60.254 37.037 0.00 0.00 0.00 3.60
3917 4008 8.385858 GTCCGTAAAGAAATATAAGAGCGTTTT 58.614 33.333 0.00 0.00 0.00 2.43
3918 4009 8.385111 TCCGTAAAGAAATATAAGAGCGTTTTG 58.615 33.333 0.00 0.00 0.00 2.44
3919 4010 7.163682 CCGTAAAGAAATATAAGAGCGTTTTGC 59.836 37.037 0.00 0.00 46.98 3.68
3991 4082 5.167303 AGGAATTAAGACACTTCCTGGAC 57.833 43.478 6.52 0.00 45.45 4.02
3996 4087 0.759436 AGACACTTCCTGGACACGGT 60.759 55.000 0.00 0.00 0.00 4.83
4005 4096 2.635915 TCCTGGACACGGTTTCAATACT 59.364 45.455 0.00 0.00 0.00 2.12
4045 4136 0.327000 ATACCAAGCTCCAGGCCTCT 60.327 55.000 0.00 0.00 43.05 3.69
4054 4146 0.693049 TCCAGGCCTCTGTTTTCCTC 59.307 55.000 0.00 0.00 39.31 3.71
4083 4175 1.883084 CGCCCCGCAGAAGATACAC 60.883 63.158 0.00 0.00 0.00 2.90
4105 4218 1.862806 GGCTCGCTCACAGTGAAAC 59.137 57.895 4.41 0.00 33.88 2.78
4110 4223 2.473816 TCGCTCACAGTGAAACAGAAG 58.526 47.619 4.41 0.00 41.43 2.85
4145 4259 1.395826 GGCACTAGGAGCTCGACCAT 61.396 60.000 7.83 0.00 0.00 3.55
4169 4283 1.078528 TTCTTCCTCTCCCCGCTCA 59.921 57.895 0.00 0.00 0.00 4.26
4228 4342 3.473647 CGCTGCCCATCCTCTCCA 61.474 66.667 0.00 0.00 0.00 3.86
4275 4389 1.333636 CCTCAAGATCTGTCGCCCCT 61.334 60.000 0.00 0.00 0.00 4.79
4330 4444 5.697633 ACAGAACATCCAAACATGAAATTGC 59.302 36.000 0.00 0.00 0.00 3.56
4354 4468 2.247358 TGCCTCCTTTGTTGAATTCCC 58.753 47.619 2.27 0.00 0.00 3.97
4358 4472 2.228822 CTCCTTTGTTGAATTCCCACCG 59.771 50.000 2.27 0.00 0.00 4.94
4472 4588 7.402054 AGGTTCTCAATACATACATCCAAACA 58.598 34.615 0.00 0.00 0.00 2.83
4483 4599 3.149196 ACATCCAAACAGAGCGTGAATT 58.851 40.909 0.00 0.00 0.00 2.17
4484 4600 3.058016 ACATCCAAACAGAGCGTGAATTG 60.058 43.478 0.00 1.93 0.00 2.32
4485 4601 2.571212 TCCAAACAGAGCGTGAATTGT 58.429 42.857 0.00 0.00 0.00 2.71
4486 4602 2.548057 TCCAAACAGAGCGTGAATTGTC 59.452 45.455 0.00 0.00 0.00 3.18
4488 4604 3.548587 CAAACAGAGCGTGAATTGTCTG 58.451 45.455 0.00 0.00 41.88 3.51
4489 4605 2.820059 ACAGAGCGTGAATTGTCTGA 57.180 45.000 5.24 0.00 39.04 3.27
4490 4606 2.681706 ACAGAGCGTGAATTGTCTGAG 58.318 47.619 5.24 0.00 39.04 3.35
4491 4607 2.036475 ACAGAGCGTGAATTGTCTGAGT 59.964 45.455 5.24 0.00 39.04 3.41
4492 4608 2.411069 CAGAGCGTGAATTGTCTGAGTG 59.589 50.000 0.00 0.00 39.04 3.51
4499 4625 3.316308 GTGAATTGTCTGAGTGTTTGGCT 59.684 43.478 0.00 0.00 0.00 4.75
4520 4646 2.103432 TCTTAGCTGTTCACGGAACCAA 59.897 45.455 12.35 3.66 41.35 3.67
4552 4682 4.613394 CGACACATTGTAGCTTTTGATGCA 60.613 41.667 0.00 0.00 0.00 3.96
4560 4690 5.304778 TGTAGCTTTTGATGCACTAGTGAA 58.695 37.500 27.08 17.61 0.00 3.18
4594 4724 1.074775 CCAAGCACCTGCCCTTGTA 59.925 57.895 0.00 0.00 43.38 2.41
4629 4759 9.850628 CATATTGGGTGCTTCTTCATATTAATG 57.149 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 100 5.845391 AACCAAAAGGACGATGAAAAAGA 57.155 34.783 0.00 0.00 0.00 2.52
242 254 3.055458 CGTATTTCCTTTTGGCCCCAAAT 60.055 43.478 12.84 0.67 44.14 2.32
460 476 5.011943 TGCCACTTGATAAAAATCAAAGCCT 59.988 36.000 2.74 0.00 39.73 4.58
638 661 9.283768 ACTTACTCAATTGACAATAATGTGTGA 57.716 29.630 3.38 7.47 40.74 3.58
665 688 3.714798 AGCCTATTCTCCCCGTCAATAAA 59.285 43.478 0.00 0.00 0.00 1.40
672 695 1.971357 CACATAGCCTATTCTCCCCGT 59.029 52.381 0.00 0.00 0.00 5.28
719 765 0.252927 CCCCTCCCTCTTCCTCACTT 60.253 60.000 0.00 0.00 0.00 3.16
1155 1217 2.436646 GTGACCACGCAGATGGGG 60.437 66.667 3.87 0.00 44.81 4.96
1184 1246 1.347707 CACTCCTGTTAGGGCAGTTCA 59.652 52.381 0.00 0.00 35.59 3.18
1196 1258 5.675538 GATAAAATAGGCAGACACTCCTGT 58.324 41.667 0.00 0.00 36.57 4.00
1200 1262 7.948278 AATACGATAAAATAGGCAGACACTC 57.052 36.000 0.00 0.00 0.00 3.51
1201 1263 9.998106 AATAATACGATAAAATAGGCAGACACT 57.002 29.630 0.00 0.00 0.00 3.55
1225 1287 4.394920 CGCACCATGGAAAACAGTAGTAAT 59.605 41.667 21.47 0.00 0.00 1.89
1250 1314 2.811317 GAGCACCGTCAGAAGGCG 60.811 66.667 1.64 0.00 0.00 5.52
1336 1400 1.828660 CGACGCTGTATCCCTCCCT 60.829 63.158 0.00 0.00 0.00 4.20
1349 1413 4.702081 ACTCACCGAGCACGACGC 62.702 66.667 4.70 0.00 42.66 5.19
1350 1414 2.502080 GACTCACCGAGCACGACG 60.502 66.667 4.70 0.00 42.66 5.12
1417 1481 2.565391 TCTATTTTGCACGAGACCAGGA 59.435 45.455 0.00 0.00 0.00 3.86
1464 1528 5.575957 GTTTGCAGATTCATCGAATGTCAT 58.424 37.500 0.00 0.00 31.89 3.06
1618 1690 9.832445 AATAGAACATGTATCATTTTAGTCCGT 57.168 29.630 0.00 0.00 0.00 4.69
1913 1987 2.101750 TGCAAGCATCCCAGCATTATTG 59.898 45.455 0.00 0.00 36.85 1.90
1943 2017 3.895656 CAATCCCATCCTCGGTAACTCTA 59.104 47.826 0.00 0.00 0.00 2.43
1973 2047 5.619757 CGAGAATAATTGCAAGGAAAGCACA 60.620 40.000 4.94 0.00 42.54 4.57
1996 2070 6.480524 TGAAGACCACATAATTCTTTCACG 57.519 37.500 0.00 0.00 29.54 4.35
2091 2172 5.068636 AGTTTGTCTGCATCACTCTGAAAT 58.931 37.500 0.00 0.00 0.00 2.17
2345 2427 5.473846 GTCCAGTTCTCTATCCGATATGTGA 59.526 44.000 0.00 0.00 0.00 3.58
2348 2430 4.456222 ACGTCCAGTTCTCTATCCGATATG 59.544 45.833 0.00 0.00 0.00 1.78
2349 2431 4.653868 ACGTCCAGTTCTCTATCCGATAT 58.346 43.478 0.00 0.00 0.00 1.63
2354 2436 1.268640 GCGACGTCCAGTTCTCTATCC 60.269 57.143 10.58 0.00 0.00 2.59
2357 2439 1.310933 GGGCGACGTCCAGTTCTCTA 61.311 60.000 15.00 0.00 0.00 2.43
2359 2441 2.126031 GGGCGACGTCCAGTTCTC 60.126 66.667 15.00 0.00 0.00 2.87
2375 2457 1.079819 CACGCACCTAGACACCTGG 60.080 63.158 0.00 0.00 0.00 4.45
2404 2486 2.440980 GGATTGGCAGGTGGGCTC 60.441 66.667 0.00 0.00 43.83 4.70
2414 2496 2.198304 AACGGAGTCCAGGGATTGGC 62.198 60.000 10.49 0.00 45.00 4.52
2415 2497 0.392998 CAACGGAGTCCAGGGATTGG 60.393 60.000 10.49 0.00 45.00 3.16
2417 2499 0.546747 TCCAACGGAGTCCAGGGATT 60.547 55.000 10.49 0.00 45.00 3.01
2418 2500 0.978146 CTCCAACGGAGTCCAGGGAT 60.978 60.000 10.49 0.00 45.00 3.85
2419 2501 1.609501 CTCCAACGGAGTCCAGGGA 60.610 63.158 10.49 11.23 45.00 4.20
2420 2502 2.982130 CTCCAACGGAGTCCAGGG 59.018 66.667 10.49 7.19 45.00 4.45
2428 2510 0.322277 ACTAGACGAGCTCCAACGGA 60.322 55.000 8.47 0.00 0.00 4.69
2429 2511 0.526662 AACTAGACGAGCTCCAACGG 59.473 55.000 8.47 0.00 0.00 4.44
2430 2512 2.349297 AAACTAGACGAGCTCCAACG 57.651 50.000 8.47 0.00 0.00 4.10
2431 2513 7.034397 ACTAAATAAACTAGACGAGCTCCAAC 58.966 38.462 8.47 0.00 0.00 3.77
2432 2514 7.166691 ACTAAATAAACTAGACGAGCTCCAA 57.833 36.000 8.47 0.00 0.00 3.53
2433 2515 6.770746 ACTAAATAAACTAGACGAGCTCCA 57.229 37.500 8.47 0.00 0.00 3.86
2434 2516 7.464311 GCAAACTAAATAAACTAGACGAGCTCC 60.464 40.741 8.47 0.00 0.00 4.70
2435 2517 7.063074 TGCAAACTAAATAAACTAGACGAGCTC 59.937 37.037 2.73 2.73 0.00 4.09
2436 2518 6.872020 TGCAAACTAAATAAACTAGACGAGCT 59.128 34.615 0.00 0.00 0.00 4.09
2437 2519 7.057149 TGCAAACTAAATAAACTAGACGAGC 57.943 36.000 0.00 0.00 0.00 5.03
2438 2520 9.088512 AGATGCAAACTAAATAAACTAGACGAG 57.911 33.333 0.00 0.00 0.00 4.18
2439 2521 8.997621 AGATGCAAACTAAATAAACTAGACGA 57.002 30.769 0.00 0.00 0.00 4.20
2500 2582 3.756434 GCAATGGAGCTACTACAACCAAA 59.244 43.478 0.00 0.00 34.28 3.28
2529 2611 3.716872 AGGGAAATATGTGGTCCACCTAG 59.283 47.826 19.57 0.00 36.82 3.02
2532 2614 2.025321 ACAGGGAAATATGTGGTCCACC 60.025 50.000 19.57 1.56 32.73 4.61
2576 2658 8.045810 CTGCAAGAACAAATGGTACACATAGTG 61.046 40.741 0.00 0.00 37.35 2.74
2594 2676 1.610038 CAATGTGACCAGCTGCAAGAA 59.390 47.619 8.66 0.00 34.07 2.52
2613 2695 4.564821 GGAAACTGCTAGAATGGTGGTACA 60.565 45.833 0.00 0.00 0.00 2.90
2628 2710 1.262640 TACGGGGAGAGGGAAACTGC 61.263 60.000 0.00 0.00 0.00 4.40
2849 2933 3.091545 GCAATGGGAGAAAATGAGACCA 58.908 45.455 0.00 0.00 0.00 4.02
2850 2934 3.091545 TGCAATGGGAGAAAATGAGACC 58.908 45.455 0.00 0.00 0.00 3.85
3088 3175 6.183309 AGAACATAATTTTGCGAGGACTTC 57.817 37.500 0.00 0.00 0.00 3.01
3096 3183 8.230486 AGAACTACAGAAGAACATAATTTTGCG 58.770 33.333 0.00 0.00 0.00 4.85
3139 3226 8.575649 ACCAAAGATAACTAATGAATTTCGGT 57.424 30.769 0.00 0.00 0.00 4.69
3140 3227 9.931210 GTACCAAAGATAACTAATGAATTTCGG 57.069 33.333 0.00 0.00 0.00 4.30
3146 3234 9.444600 GTCCTTGTACCAAAGATAACTAATGAA 57.555 33.333 0.00 0.00 0.00 2.57
3149 3237 7.046033 CCGTCCTTGTACCAAAGATAACTAAT 58.954 38.462 0.00 0.00 0.00 1.73
3172 3260 2.131183 GAGATGAGCCTTCGAAATCCG 58.869 52.381 0.00 0.00 40.25 4.18
3199 3287 1.613836 GGCTTAAGGCAGCATAGCAT 58.386 50.000 23.15 0.00 42.10 3.79
3289 3378 0.319040 CTATCACACCTGGATCCGCG 60.319 60.000 7.39 0.00 0.00 6.46
3433 3522 2.284699 AGGAAGGCTACAGGCGGT 60.285 61.111 0.00 0.00 46.23 5.68
3443 3532 1.202940 AGAGGGTTTTGACAGGAAGGC 60.203 52.381 0.00 0.00 0.00 4.35
3485 3574 7.697710 TGAATGTCGATACATCATTTTTCTTGC 59.302 33.333 0.00 0.00 45.79 4.01
3495 3584 5.736207 GCTGGTACTGAATGTCGATACATCA 60.736 44.000 0.00 0.00 45.79 3.07
3653 3742 2.345244 CGCAGTTCCTGGAGCAGT 59.655 61.111 13.26 0.00 31.21 4.40
3654 3743 2.435586 CCGCAGTTCCTGGAGCAG 60.436 66.667 13.26 5.94 31.21 4.24
3661 3750 0.533032 GTCTCTAAGCCGCAGTTCCT 59.467 55.000 0.00 0.00 0.00 3.36
3750 3839 3.827722 TCCAATTTTATCGGATGTCCCC 58.172 45.455 0.00 0.00 0.00 4.81
3783 3872 1.365633 GGGGTCTGCTAGAGATGCG 59.634 63.158 0.00 0.00 31.63 4.73
3827 3918 9.278978 GGCTTAATTCCTCAAAACCAAAAATAA 57.721 29.630 0.00 0.00 0.00 1.40
3828 3919 7.880713 GGGCTTAATTCCTCAAAACCAAAAATA 59.119 33.333 0.00 0.00 0.00 1.40
3829 3920 6.714810 GGGCTTAATTCCTCAAAACCAAAAAT 59.285 34.615 0.00 0.00 0.00 1.82
3830 3921 6.058833 GGGCTTAATTCCTCAAAACCAAAAA 58.941 36.000 0.00 0.00 0.00 1.94
3842 3933 7.037945 GGATCTGTTAGATAGGGCTTAATTCCT 60.038 40.741 0.00 2.83 34.53 3.36
3887 3978 6.362820 GCTCTTATATTTCTTTACGGACGGAG 59.637 42.308 0.00 0.00 0.00 4.63
3888 3979 6.211515 GCTCTTATATTTCTTTACGGACGGA 58.788 40.000 0.00 0.00 0.00 4.69
3889 3980 5.116680 CGCTCTTATATTTCTTTACGGACGG 59.883 44.000 0.00 0.00 0.00 4.79
3890 3981 5.684626 ACGCTCTTATATTTCTTTACGGACG 59.315 40.000 0.00 0.00 0.00 4.79
3891 3982 7.460751 AACGCTCTTATATTTCTTTACGGAC 57.539 36.000 0.00 0.00 0.00 4.79
3892 3983 8.385111 CAAAACGCTCTTATATTTCTTTACGGA 58.615 33.333 0.00 0.00 0.00 4.69
3893 3984 7.163682 GCAAAACGCTCTTATATTTCTTTACGG 59.836 37.037 0.00 0.00 37.77 4.02
3894 3985 8.025217 GCAAAACGCTCTTATATTTCTTTACG 57.975 34.615 0.00 0.00 37.77 3.18
3953 4044 9.947189 TCTTAATTCCTTATACTCCCTCTGTAA 57.053 33.333 0.00 0.00 0.00 2.41
3954 4045 9.364653 GTCTTAATTCCTTATACTCCCTCTGTA 57.635 37.037 0.00 0.00 0.00 2.74
3955 4046 7.844779 TGTCTTAATTCCTTATACTCCCTCTGT 59.155 37.037 0.00 0.00 0.00 3.41
3956 4047 8.145122 GTGTCTTAATTCCTTATACTCCCTCTG 58.855 40.741 0.00 0.00 0.00 3.35
3957 4048 8.068733 AGTGTCTTAATTCCTTATACTCCCTCT 58.931 37.037 0.00 0.00 0.00 3.69
3958 4049 8.252624 AGTGTCTTAATTCCTTATACTCCCTC 57.747 38.462 0.00 0.00 0.00 4.30
3959 4050 8.625467 AAGTGTCTTAATTCCTTATACTCCCT 57.375 34.615 0.00 0.00 0.00 4.20
3960 4051 8.890124 GAAGTGTCTTAATTCCTTATACTCCC 57.110 38.462 0.00 0.00 0.00 4.30
3991 4082 4.556233 TCACTCTCAGTATTGAAACCGTG 58.444 43.478 0.00 0.00 31.69 4.94
4045 4136 2.736721 CGAGCGATTTCAGAGGAAAACA 59.263 45.455 0.00 0.00 45.52 2.83
4054 4146 3.264897 CGGGGCGAGCGATTTCAG 61.265 66.667 0.00 0.00 0.00 3.02
4074 4166 1.132588 GCGAGCCGATGTGTATCTTC 58.867 55.000 0.00 0.00 0.00 2.87
4077 4169 0.030773 TGAGCGAGCCGATGTGTATC 59.969 55.000 0.00 0.00 0.00 2.24
4083 4175 2.163390 CACTGTGAGCGAGCCGATG 61.163 63.158 0.32 0.00 0.00 3.84
4105 4218 0.734253 CTCCCTTGTCGTCGCTTCTG 60.734 60.000 0.00 0.00 0.00 3.02
4110 4223 2.432628 CCACTCCCTTGTCGTCGC 60.433 66.667 0.00 0.00 0.00 5.19
4145 4259 0.903454 GGGGAGAGGAAGAACCGTCA 60.903 60.000 0.00 0.00 44.74 4.35
4169 4283 1.039068 CGAGGAGCAGAGATGATGGT 58.961 55.000 0.00 0.00 0.00 3.55
4219 4333 1.519719 GTTGCGAGCTGGAGAGGAT 59.480 57.895 0.00 0.00 0.00 3.24
4248 4362 0.035725 CAGATCTTGAGGTGCAGGCA 60.036 55.000 0.00 0.00 0.00 4.75
4330 4444 5.394553 GGGAATTCAACAAAGGAGGCAATAG 60.395 44.000 7.93 0.00 0.00 1.73
4354 4468 0.038435 TGCACATGAAATTGCCGGTG 60.038 50.000 1.90 1.16 38.00 4.94
4358 4472 2.166821 TGGTTGCACATGAAATTGCC 57.833 45.000 0.00 0.00 38.00 4.52
4440 4555 9.553064 GATGTATGTATTGAGAACCTCTGAATT 57.447 33.333 0.00 0.00 32.66 2.17
4472 4588 2.036475 ACACTCAGACAATTCACGCTCT 59.964 45.455 0.00 0.00 0.00 4.09
4483 4599 3.803715 GCTAAGAGCCAAACACTCAGACA 60.804 47.826 0.00 0.00 36.58 3.41
4484 4600 2.739379 GCTAAGAGCCAAACACTCAGAC 59.261 50.000 0.00 0.00 36.58 3.51
4485 4601 2.634940 AGCTAAGAGCCAAACACTCAGA 59.365 45.455 0.00 0.00 43.77 3.27
4486 4602 2.740981 CAGCTAAGAGCCAAACACTCAG 59.259 50.000 0.00 0.00 43.77 3.35
4488 4604 2.772287 ACAGCTAAGAGCCAAACACTC 58.228 47.619 0.00 0.00 43.77 3.51
4489 4605 2.938956 ACAGCTAAGAGCCAAACACT 57.061 45.000 0.00 0.00 43.77 3.55
4490 4606 2.878406 TGAACAGCTAAGAGCCAAACAC 59.122 45.455 0.00 0.00 43.77 3.32
4491 4607 2.878406 GTGAACAGCTAAGAGCCAAACA 59.122 45.455 0.00 0.00 43.77 2.83
4492 4608 2.096218 CGTGAACAGCTAAGAGCCAAAC 60.096 50.000 0.00 0.00 43.77 2.93
4499 4625 1.689813 TGGTTCCGTGAACAGCTAAGA 59.310 47.619 15.57 0.00 43.54 2.10
4520 4646 5.423015 AGCTACAATGTGTCGATTGATTCT 58.577 37.500 3.59 0.00 36.89 2.40
4552 4682 7.472804 TGGTACAAATCAGTGTCATTCACTAGT 60.473 37.037 0.00 0.00 46.35 2.57
4594 4724 2.240667 AGCACCCAATATGAGCAAGAGT 59.759 45.455 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.