Multiple sequence alignment - TraesCS7D01G373800

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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 TraesCS7D01G373800 chr7D 100.000 4080 0 0 1 4080 484360674 484364753 0.000000e+00 7535
1 TraesCS7D01G373800 chr7B 93.676 3384 128 32 669 4030 511062023 511065342 0.000000e+00 4985
2 TraesCS7D01G373800 chr7B 83.453 278 32 9 231 504 511061669 511061936 3.150000e-61 246
3 TraesCS7D01G373800 chr7A 94.361 3139 106 28 912 4030 552678993 552682080 0.000000e+00 4750
4 TraesCS7D01G373800 chr7A 84.795 901 58 25 1 847 552677712 552678587 0.000000e+00 832
5 TraesCS7D01G373800 chr6D 76.736 1771 371 31 1319 3070 155542104 155543852 0.000000e+00 950
6 TraesCS7D01G373800 chr6B 76.736 1771 371 31 1319 3070 278539918 278541666 0.000000e+00 950
7 TraesCS7D01G373800 chr6A 76.567 1771 374 31 1319 3070 209267068 209268816 0.000000e+00 933


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 TraesCS7D01G373800 chr7D 484360674 484364753 4079 False 7535.0 7535 100.0000 1 4080 1 chr7D.!!$F1 4079
1 TraesCS7D01G373800 chr7B 511061669 511065342 3673 False 2615.5 4985 88.5645 231 4030 2 chr7B.!!$F1 3799
2 TraesCS7D01G373800 chr7A 552677712 552682080 4368 False 2791.0 4750 89.5780 1 4030 2 chr7A.!!$F1 4029
3 TraesCS7D01G373800 chr6D 155542104 155543852 1748 False 950.0 950 76.7360 1319 3070 1 chr6D.!!$F1 1751
4 TraesCS7D01G373800 chr6B 278539918 278541666 1748 False 950.0 950 76.7360 1319 3070 1 chr6B.!!$F1 1751
5 TraesCS7D01G373800 chr6A 209267068 209268816 1748 False 933.0 933 76.5670 1319 3070 1 chr6A.!!$F1 1751

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
33 34 0.307146 GATCTGCGCTTCTTCATGGC 59.693 55.0 9.73 0.0 0.0 4.40 F
90 91 0.378257 CCTTCGGCATTTCATCACGG 59.622 55.0 0.00 0.0 0.0 4.94 F
1053 1457 0.537371 GGCCCCGAATCGAATTGGAT 60.537 55.0 8.46 0.0 0.0 3.41 F
2026 2447 0.460987 CTGGTCTCATCTGTTCCGCC 60.461 60.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1053 1457 0.028770 CGGCGAAACACAGCAAGAAA 59.971 50.0 0.00 0.0 34.54 2.52 R
1139 1554 0.322816 AGACCGCCATCTGCACAAAT 60.323 50.0 0.00 0.0 41.33 2.32 R
2101 2522 0.168128 GGTTTGTGATCGCCTTTCCG 59.832 55.0 3.31 0.0 0.00 4.30 R
3898 4322 0.031994 ATCACAAAGGTTGCGGTTGC 59.968 50.0 0.00 0.0 43.20 4.17 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
26 27 1.409064 TCGGTATTGATCTGCGCTTCT 59.591 47.619 9.73 0.00 0.00 2.85
33 34 0.307146 GATCTGCGCTTCTTCATGGC 59.693 55.000 9.73 0.00 0.00 4.40
39 40 2.355756 TGCGCTTCTTCATGGCTTATTC 59.644 45.455 9.73 0.00 0.00 1.75
40 41 2.600792 GCGCTTCTTCATGGCTTATTCG 60.601 50.000 0.00 0.00 0.00 3.34
43 44 3.623060 GCTTCTTCATGGCTTATTCGACA 59.377 43.478 0.00 0.00 0.00 4.35
44 45 4.274459 GCTTCTTCATGGCTTATTCGACAT 59.726 41.667 0.00 0.00 31.24 3.06
50 51 3.179443 TGGCTTATTCGACATGACCTC 57.821 47.619 0.00 0.00 0.00 3.85
51 52 2.128035 GGCTTATTCGACATGACCTCG 58.872 52.381 0.00 0.00 0.00 4.63
52 53 2.481449 GGCTTATTCGACATGACCTCGT 60.481 50.000 0.00 0.00 32.77 4.18
53 54 2.789893 GCTTATTCGACATGACCTCGTC 59.210 50.000 0.00 0.00 32.77 4.20
62 63 4.421948 GACATGACCTCGTCGTAAAAGAT 58.578 43.478 0.00 0.00 34.95 2.40
66 67 3.256383 TGACCTCGTCGTAAAAGATTCCA 59.744 43.478 0.00 0.00 34.95 3.53
67 68 3.846360 ACCTCGTCGTAAAAGATTCCAG 58.154 45.455 0.00 0.00 0.00 3.86
77 78 2.409948 AAGATTCCAGAAGCCTTCGG 57.590 50.000 8.46 8.46 34.02 4.30
90 91 0.378257 CCTTCGGCATTTCATCACGG 59.622 55.000 0.00 0.00 0.00 4.94
108 110 1.605712 CGGCCTATTCAATCCGACCTC 60.606 57.143 0.00 0.00 44.23 3.85
114 116 4.021894 CCTATTCAATCCGACCTCGATCTT 60.022 45.833 0.00 0.00 43.02 2.40
122 135 5.686159 TCCGACCTCGATCTTAGAATTAC 57.314 43.478 0.00 0.00 43.02 1.89
125 138 6.095860 TCCGACCTCGATCTTAGAATTACAAA 59.904 38.462 0.00 0.00 43.02 2.83
132 145 8.948631 TCGATCTTAGAATTACAAAAGCTCAT 57.051 30.769 0.00 0.00 0.00 2.90
205 231 2.046700 GTCCGGGCCGATTGAACA 60.047 61.111 30.79 0.00 0.00 3.18
208 234 1.748879 CCGGGCCGATTGAACATGT 60.749 57.895 30.79 0.00 0.00 3.21
223 249 5.996219 TGAACATGTCATACGAAACCAAAG 58.004 37.500 0.00 0.00 0.00 2.77
225 251 6.261158 TGAACATGTCATACGAAACCAAAGAA 59.739 34.615 0.00 0.00 0.00 2.52
229 255 4.273969 TGTCATACGAAACCAAAGAACCAC 59.726 41.667 0.00 0.00 0.00 4.16
261 287 9.502091 TGCTCATTATGGAAGGTATACAATTAC 57.498 33.333 5.01 0.41 0.00 1.89
265 291 8.946085 CATTATGGAAGGTATACAATTACGCAT 58.054 33.333 5.01 0.00 0.00 4.73
270 299 8.614346 TGGAAGGTATACAATTACGCATAAAAC 58.386 33.333 5.01 0.00 0.00 2.43
277 306 6.051646 ACAATTACGCATAAAACGTATCCC 57.948 37.500 0.00 0.00 44.66 3.85
343 372 6.114767 TCATCGATCAATTGAGAATCCACAA 58.885 36.000 14.54 0.00 0.00 3.33
345 374 4.877823 TCGATCAATTGAGAATCCACAAGG 59.122 41.667 14.54 0.00 0.00 3.61
379 410 8.487313 AACCTTCTATTTTTGTTTGTTGTTCC 57.513 30.769 0.00 0.00 0.00 3.62
411 442 2.478746 CGCGGGGATTGTTGTTCG 59.521 61.111 0.00 0.00 0.00 3.95
441 472 4.020839 GCATGCTTGCTTCCCCATATATTT 60.021 41.667 16.80 0.00 45.77 1.40
485 516 1.203376 TCCATCTAGACCACCAACCCA 60.203 52.381 0.00 0.00 0.00 4.51
522 553 9.026074 CAAAAGCAAGCATTTGAAATTTGAAAT 57.974 25.926 15.36 9.48 36.94 2.17
533 564 6.572167 TGAAATTTGAAATGAAAATGCCCC 57.428 33.333 0.00 0.00 0.00 5.80
577 610 6.066690 TGAAATTTGAAATGAAAATGCCCCA 58.933 32.000 0.00 0.00 0.00 4.96
583 616 4.582240 TGAAATGAAAATGCCCCAAAAACC 59.418 37.500 0.00 0.00 0.00 3.27
619 664 1.309347 TCAGCCAGAGAGAGAGGGG 59.691 63.158 0.00 0.00 0.00 4.79
779 838 2.031120 TCATTGAATCCCGGCAAATCC 58.969 47.619 0.00 0.00 0.00 3.01
780 839 7.999153 GATTCATTGAATCCCGGCAAATCCG 62.999 48.000 23.26 0.00 46.01 4.18
849 908 0.672401 ACATAAGAACCACCACCGCG 60.672 55.000 0.00 0.00 0.00 6.46
868 927 4.904590 CCCAAACCCACCACCGCA 62.905 66.667 0.00 0.00 0.00 5.69
871 930 4.906537 AAACCCACCACCGCACCC 62.907 66.667 0.00 0.00 0.00 4.61
896 955 2.287194 CCCCACCCCATTCCTCCT 60.287 66.667 0.00 0.00 0.00 3.69
899 958 1.308216 CCACCCCATTCCTCCTCCT 60.308 63.158 0.00 0.00 0.00 3.69
962 1362 1.334419 CGCCGCCTGATTGATTGATTC 60.334 52.381 0.00 0.00 0.00 2.52
963 1363 1.334419 GCCGCCTGATTGATTGATTCG 60.334 52.381 0.00 0.00 0.00 3.34
1019 1423 0.625849 ATGCCTCCCTTCCACGATTT 59.374 50.000 0.00 0.00 0.00 2.17
1044 1448 1.101635 GTAAGCAAGGGCCCCGAATC 61.102 60.000 21.43 3.28 42.56 2.52
1053 1457 0.537371 GGCCCCGAATCGAATTGGAT 60.537 55.000 8.46 0.00 0.00 3.41
1056 1460 2.287608 GCCCCGAATCGAATTGGATTTC 60.288 50.000 15.72 9.02 36.79 2.17
1057 1461 3.214328 CCCCGAATCGAATTGGATTTCT 58.786 45.455 15.72 0.00 36.79 2.52
1061 1476 4.201950 CCGAATCGAATTGGATTTCTTGCT 60.202 41.667 15.72 0.00 36.79 3.91
1089 1504 1.270571 GCCGGAGATCTGGAGGATTTC 60.271 57.143 5.05 0.00 45.36 2.17
1090 1505 2.324541 CCGGAGATCTGGAGGATTTCT 58.675 52.381 0.00 0.00 45.36 2.52
1091 1506 2.703007 CCGGAGATCTGGAGGATTTCTT 59.297 50.000 0.00 0.00 45.36 2.52
1092 1507 3.494048 CCGGAGATCTGGAGGATTTCTTG 60.494 52.174 0.00 0.00 45.36 3.02
1093 1508 3.475575 GGAGATCTGGAGGATTTCTTGC 58.524 50.000 0.00 0.00 36.27 4.01
1094 1509 3.136260 GGAGATCTGGAGGATTTCTTGCT 59.864 47.826 0.00 0.00 36.27 3.91
1095 1510 4.128643 GAGATCTGGAGGATTTCTTGCTG 58.871 47.826 0.00 0.00 34.07 4.41
1096 1511 2.119801 TCTGGAGGATTTCTTGCTGC 57.880 50.000 0.00 0.00 34.56 5.25
1097 1512 0.731417 CTGGAGGATTTCTTGCTGCG 59.269 55.000 0.00 0.00 36.90 5.18
1098 1513 0.677731 TGGAGGATTTCTTGCTGCGG 60.678 55.000 0.00 0.00 36.90 5.69
1099 1514 1.431036 GAGGATTTCTTGCTGCGGC 59.569 57.895 11.65 11.65 39.26 6.53
1100 1515 1.001641 AGGATTTCTTGCTGCGGCT 60.002 52.632 20.27 0.00 39.59 5.52
1101 1516 1.138247 GGATTTCTTGCTGCGGCTG 59.862 57.895 20.27 11.76 39.59 4.85
1102 1517 1.138247 GATTTCTTGCTGCGGCTGG 59.862 57.895 20.27 11.33 39.59 4.85
1103 1518 2.275547 GATTTCTTGCTGCGGCTGGG 62.276 60.000 20.27 8.74 39.59 4.45
1104 1519 3.790416 TTTCTTGCTGCGGCTGGGT 62.790 57.895 20.27 0.00 39.59 4.51
1105 1520 3.790416 TTCTTGCTGCGGCTGGGTT 62.790 57.895 20.27 0.00 39.59 4.11
1139 1554 5.098893 GTGTGCTGATTTTGTGTGTGTTTA 58.901 37.500 0.00 0.00 0.00 2.01
1146 1561 6.998338 TGATTTTGTGTGTGTTTATTTGTGC 58.002 32.000 0.00 0.00 0.00 4.57
1177 1592 4.760047 CTTGTCCTGGACCCGGCG 62.760 72.222 23.42 0.00 0.00 6.46
1466 1881 4.918201 CCGAGATCAAGCGGGCCC 62.918 72.222 13.57 13.57 43.67 5.80
1467 1882 4.161295 CGAGATCAAGCGGGCCCA 62.161 66.667 24.92 0.53 0.00 5.36
1524 1945 4.517703 CGACGACGAGGACGAGGC 62.518 72.222 0.00 0.00 42.66 4.70
1855 2276 4.373116 GACAAGGGCCTCGTCGCA 62.373 66.667 9.22 0.00 0.00 5.10
2026 2447 0.460987 CTGGTCTCATCTGTTCCGCC 60.461 60.000 0.00 0.00 0.00 6.13
2101 2522 4.081642 TCTCTTGCTGTGATTGGGTACTAC 60.082 45.833 0.00 0.00 0.00 2.73
2314 2735 1.818642 AGTGCAGCCAAATCTCAGAC 58.181 50.000 0.00 0.00 0.00 3.51
2713 3134 1.996191 GGTTGCGAGAATCTCACAGAC 59.004 52.381 11.18 7.77 24.00 3.51
2716 3137 1.467556 GCGAGAATCTCACAGACGCG 61.468 60.000 11.18 3.53 35.78 6.01
2762 3183 0.877071 CGGCACTTCTCTTGCACATT 59.123 50.000 0.00 0.00 42.12 2.71
2789 3210 0.841961 TGAGGGCTGCAGCAAGATAT 59.158 50.000 37.63 17.34 44.36 1.63
2962 3383 1.006102 CACACCGAAGAGCGTTCCT 60.006 57.895 0.00 0.00 38.67 3.36
3414 3838 4.333926 GTGGGAGCTCAAATATTGTCAGTC 59.666 45.833 17.19 0.00 0.00 3.51
3415 3839 4.019411 TGGGAGCTCAAATATTGTCAGTCA 60.019 41.667 17.19 0.00 0.00 3.41
3416 3840 4.574013 GGGAGCTCAAATATTGTCAGTCAG 59.426 45.833 17.19 0.00 0.00 3.51
3417 3841 5.181748 GGAGCTCAAATATTGTCAGTCAGT 58.818 41.667 17.19 0.00 0.00 3.41
3515 3939 5.779806 AGTTCTATTTGTCGGATTTGTCG 57.220 39.130 0.00 0.00 0.00 4.35
3516 3940 4.630069 AGTTCTATTTGTCGGATTTGTCGG 59.370 41.667 0.00 0.00 0.00 4.79
3521 3945 2.046700 TCGGATTTGTCGGGGTGC 60.047 61.111 0.00 0.00 0.00 5.01
3543 3967 0.037232 GCCTGTCGTAGAAGCTTGGT 60.037 55.000 2.10 0.00 39.69 3.67
3616 4040 3.278574 TGGTTGTTCCAGTTTCAGTCTG 58.721 45.455 0.00 0.00 41.93 3.51
3630 4054 2.552743 TCAGTCTGTTCACGGTCTGTAG 59.447 50.000 11.31 0.00 38.77 2.74
3631 4055 1.269998 AGTCTGTTCACGGTCTGTAGC 59.730 52.381 0.00 0.00 0.00 3.58
3754 4178 0.746659 GCAAGGTGCAACATATCCCC 59.253 55.000 3.64 0.00 44.26 4.81
3757 4181 0.986019 AGGTGCAACATATCCCCGGA 60.986 55.000 3.64 0.00 39.98 5.14
3826 4250 0.869880 GTTTTTGCAGGCGTGTGGTC 60.870 55.000 8.40 0.00 0.00 4.02
3889 4313 7.989416 AATTTGTTTTCGTCCAAGTCCTATA 57.011 32.000 0.00 0.00 0.00 1.31
3890 4314 8.575649 AATTTGTTTTCGTCCAAGTCCTATAT 57.424 30.769 0.00 0.00 0.00 0.86
3891 4315 6.978343 TTGTTTTCGTCCAAGTCCTATATG 57.022 37.500 0.00 0.00 0.00 1.78
3892 4316 4.873827 TGTTTTCGTCCAAGTCCTATATGC 59.126 41.667 0.00 0.00 0.00 3.14
3895 4319 4.585955 TCGTCCAAGTCCTATATGCTTC 57.414 45.455 0.00 0.00 0.00 3.86
3898 4322 4.051922 GTCCAAGTCCTATATGCTTCACG 58.948 47.826 0.00 0.00 0.00 4.35
3899 4323 2.802816 CCAAGTCCTATATGCTTCACGC 59.197 50.000 0.00 0.00 39.77 5.34
3912 4336 1.658686 TTCACGCAACCGCAACCTTT 61.659 50.000 0.00 0.00 38.40 3.11
3913 4337 1.943693 CACGCAACCGCAACCTTTG 60.944 57.895 0.00 0.00 38.40 2.77
3914 4338 2.411290 CGCAACCGCAACCTTTGT 59.589 55.556 0.00 0.00 38.40 2.83
3915 4339 1.943693 CGCAACCGCAACCTTTGTG 60.944 57.895 0.00 0.00 40.74 3.33
3916 4340 1.435515 GCAACCGCAACCTTTGTGA 59.564 52.632 1.01 0.00 43.66 3.58
3919 4343 2.393764 CAACCGCAACCTTTGTGATTC 58.606 47.619 1.01 0.00 43.66 2.52
3927 4351 6.092092 CGCAACCTTTGTGATTCATGAATTA 58.908 36.000 21.57 15.20 43.66 1.40
3937 4361 7.925993 TGTGATTCATGAATTATTACGTTCCC 58.074 34.615 21.57 5.54 0.00 3.97
3942 4366 9.793259 ATTCATGAATTATTACGTTCCCTGTAT 57.207 29.630 15.36 0.00 0.00 2.29
3948 4372 8.570068 AATTATTACGTTCCCTGTATTGTGTT 57.430 30.769 0.00 0.00 0.00 3.32
3958 4382 8.357402 GTTCCCTGTATTGTGTTTAAATGTCTT 58.643 33.333 0.00 0.00 0.00 3.01
3959 4383 7.881142 TCCCTGTATTGTGTTTAAATGTCTTG 58.119 34.615 0.00 0.00 0.00 3.02
3967 4395 2.279935 TTAAATGTCTTGTGGCCGGT 57.720 45.000 1.90 0.00 0.00 5.28
3997 4427 1.208776 TGATGCCACCACTGAGATGAG 59.791 52.381 0.00 0.00 0.00 2.90
3998 4428 1.483827 GATGCCACCACTGAGATGAGA 59.516 52.381 0.00 0.00 0.00 3.27
3999 4429 1.576577 TGCCACCACTGAGATGAGAT 58.423 50.000 0.00 0.00 0.00 2.75
4000 4430 1.208776 TGCCACCACTGAGATGAGATG 59.791 52.381 0.00 0.00 0.00 2.90
4001 4431 1.483827 GCCACCACTGAGATGAGATGA 59.516 52.381 0.00 0.00 0.00 2.92
4016 4446 1.140452 AGATGAACATCTCGCAGCCAT 59.860 47.619 10.99 0.00 44.37 4.40
4030 4460 0.610232 AGCCATCCTTGACAACTGCC 60.610 55.000 0.00 0.00 0.00 4.85
4031 4461 0.610232 GCCATCCTTGACAACTGCCT 60.610 55.000 0.00 0.00 0.00 4.75
4032 4462 1.171308 CCATCCTTGACAACTGCCTG 58.829 55.000 0.00 0.00 0.00 4.85
4033 4463 1.546323 CCATCCTTGACAACTGCCTGT 60.546 52.381 0.00 0.00 0.00 4.00
4034 4464 1.808945 CATCCTTGACAACTGCCTGTC 59.191 52.381 4.24 4.24 45.01 3.51
4038 4468 2.031163 GACAACTGCCTGTCGCCT 59.969 61.111 0.00 0.00 36.64 5.52
4039 4469 2.029844 GACAACTGCCTGTCGCCTC 61.030 63.158 0.00 0.00 36.64 4.70
4040 4470 2.345244 CAACTGCCTGTCGCCTCT 59.655 61.111 0.00 0.00 36.24 3.69
4041 4471 2.031516 CAACTGCCTGTCGCCTCTG 61.032 63.158 0.00 0.00 36.24 3.35
4042 4472 2.210013 AACTGCCTGTCGCCTCTGA 61.210 57.895 0.00 0.00 36.24 3.27
4043 4473 1.758440 AACTGCCTGTCGCCTCTGAA 61.758 55.000 0.00 0.00 36.24 3.02
4044 4474 1.220206 CTGCCTGTCGCCTCTGAAT 59.780 57.895 0.00 0.00 36.24 2.57
4045 4475 0.392193 CTGCCTGTCGCCTCTGAATT 60.392 55.000 0.00 0.00 36.24 2.17
4046 4476 0.391661 TGCCTGTCGCCTCTGAATTC 60.392 55.000 0.00 0.00 36.24 2.17
4047 4477 0.107945 GCCTGTCGCCTCTGAATTCT 60.108 55.000 7.05 0.00 0.00 2.40
4048 4478 1.649664 CCTGTCGCCTCTGAATTCTG 58.350 55.000 7.05 6.50 0.00 3.02
4049 4479 1.066573 CCTGTCGCCTCTGAATTCTGT 60.067 52.381 7.05 0.00 0.00 3.41
4050 4480 2.613977 CCTGTCGCCTCTGAATTCTGTT 60.614 50.000 7.05 0.00 0.00 3.16
4051 4481 2.414481 CTGTCGCCTCTGAATTCTGTTG 59.586 50.000 7.05 3.68 0.00 3.33
4052 4482 2.037121 TGTCGCCTCTGAATTCTGTTGA 59.963 45.455 7.05 1.63 0.00 3.18
4053 4483 3.067106 GTCGCCTCTGAATTCTGTTGAA 58.933 45.455 7.05 0.00 36.54 2.69
4054 4484 3.124297 GTCGCCTCTGAATTCTGTTGAAG 59.876 47.826 7.05 0.00 35.44 3.02
4055 4485 3.070018 CGCCTCTGAATTCTGTTGAAGT 58.930 45.455 7.05 0.00 35.44 3.01
4056 4486 3.499918 CGCCTCTGAATTCTGTTGAAGTT 59.500 43.478 7.05 0.00 35.44 2.66
4057 4487 4.023707 CGCCTCTGAATTCTGTTGAAGTTT 60.024 41.667 7.05 0.00 35.44 2.66
4058 4488 5.506317 CGCCTCTGAATTCTGTTGAAGTTTT 60.506 40.000 7.05 0.00 35.44 2.43
4059 4489 6.293407 CGCCTCTGAATTCTGTTGAAGTTTTA 60.293 38.462 7.05 0.00 35.44 1.52
4060 4490 7.080724 GCCTCTGAATTCTGTTGAAGTTTTAG 58.919 38.462 7.05 0.00 35.44 1.85
4061 4491 7.588512 CCTCTGAATTCTGTTGAAGTTTTAGG 58.411 38.462 7.05 1.62 35.44 2.69
4062 4492 6.970484 TCTGAATTCTGTTGAAGTTTTAGGC 58.030 36.000 7.05 0.00 35.44 3.93
4063 4493 6.772716 TCTGAATTCTGTTGAAGTTTTAGGCT 59.227 34.615 7.05 0.00 35.44 4.58
4064 4494 6.738114 TGAATTCTGTTGAAGTTTTAGGCTG 58.262 36.000 7.05 0.00 35.44 4.85
4065 4495 6.545666 TGAATTCTGTTGAAGTTTTAGGCTGA 59.454 34.615 7.05 0.00 35.44 4.26
4066 4496 7.231317 TGAATTCTGTTGAAGTTTTAGGCTGAT 59.769 33.333 7.05 0.00 35.44 2.90
4067 4497 6.959639 TTCTGTTGAAGTTTTAGGCTGATT 57.040 33.333 0.00 0.00 0.00 2.57
4068 4498 6.317789 TCTGTTGAAGTTTTAGGCTGATTG 57.682 37.500 0.00 0.00 0.00 2.67
4069 4499 6.061441 TCTGTTGAAGTTTTAGGCTGATTGA 58.939 36.000 0.00 0.00 0.00 2.57
4070 4500 6.545666 TCTGTTGAAGTTTTAGGCTGATTGAA 59.454 34.615 0.00 0.00 0.00 2.69
4071 4501 7.068103 TCTGTTGAAGTTTTAGGCTGATTGAAA 59.932 33.333 0.00 0.00 0.00 2.69
4072 4502 6.978080 TGTTGAAGTTTTAGGCTGATTGAAAC 59.022 34.615 0.00 1.09 0.00 2.78
4073 4503 6.707440 TGAAGTTTTAGGCTGATTGAAACA 57.293 33.333 0.00 0.00 33.77 2.83
4074 4504 7.106439 TGAAGTTTTAGGCTGATTGAAACAA 57.894 32.000 0.00 0.00 33.77 2.83
4075 4505 6.978080 TGAAGTTTTAGGCTGATTGAAACAAC 59.022 34.615 0.00 0.00 33.77 3.32
4076 4506 6.463995 AGTTTTAGGCTGATTGAAACAACA 57.536 33.333 0.00 0.00 33.77 3.33
4077 4507 6.273071 AGTTTTAGGCTGATTGAAACAACAC 58.727 36.000 0.00 0.00 33.77 3.32
4078 4508 4.846779 TTAGGCTGATTGAAACAACACC 57.153 40.909 0.00 0.00 0.00 4.16
4079 4509 1.963515 AGGCTGATTGAAACAACACCC 59.036 47.619 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.198068 TGAAGAAGCGCAGATCAATACC 58.802 45.455 11.47 0.00 0.00 2.73
16 17 0.321919 AAGCCATGAAGAAGCGCAGA 60.322 50.000 11.47 0.00 0.00 4.26
20 21 2.866156 TCGAATAAGCCATGAAGAAGCG 59.134 45.455 0.00 0.00 0.00 4.68
26 27 3.876914 GGTCATGTCGAATAAGCCATGAA 59.123 43.478 13.72 0.00 43.66 2.57
40 41 3.829948 TCTTTTACGACGAGGTCATGTC 58.170 45.455 0.00 0.00 32.09 3.06
43 44 4.081862 TGGAATCTTTTACGACGAGGTCAT 60.082 41.667 0.00 0.00 32.09 3.06
44 45 3.256383 TGGAATCTTTTACGACGAGGTCA 59.744 43.478 0.00 0.00 32.09 4.02
50 51 3.062234 GGCTTCTGGAATCTTTTACGACG 59.938 47.826 0.00 0.00 0.00 5.12
51 52 4.254492 AGGCTTCTGGAATCTTTTACGAC 58.746 43.478 0.00 0.00 0.00 4.34
52 53 4.553330 AGGCTTCTGGAATCTTTTACGA 57.447 40.909 0.00 0.00 0.00 3.43
53 54 4.201724 CGAAGGCTTCTGGAATCTTTTACG 60.202 45.833 23.74 3.43 0.00 3.18
77 78 2.618241 TGAATAGGCCGTGATGAAATGC 59.382 45.455 0.00 0.00 0.00 3.56
81 82 3.476552 GGATTGAATAGGCCGTGATGAA 58.523 45.455 0.00 0.00 0.00 2.57
82 83 2.547855 CGGATTGAATAGGCCGTGATGA 60.548 50.000 0.00 0.00 38.99 2.92
84 85 1.691976 TCGGATTGAATAGGCCGTGAT 59.308 47.619 0.00 0.00 43.92 3.06
87 88 0.106149 GGTCGGATTGAATAGGCCGT 59.894 55.000 0.00 0.00 43.92 5.68
88 89 0.393077 AGGTCGGATTGAATAGGCCG 59.607 55.000 0.00 0.00 44.83 6.13
90 91 1.340248 TCGAGGTCGGATTGAATAGGC 59.660 52.381 0.00 0.00 40.29 3.93
108 110 8.607459 ACATGAGCTTTTGTAATTCTAAGATCG 58.393 33.333 0.00 0.00 36.19 3.69
185 210 1.451207 TTCAATCGGCCCGGACATG 60.451 57.895 0.73 0.00 0.00 3.21
186 211 1.451387 GTTCAATCGGCCCGGACAT 60.451 57.895 0.73 0.00 0.00 3.06
187 212 2.046700 GTTCAATCGGCCCGGACA 60.047 61.111 0.73 0.00 0.00 4.02
188 213 1.451387 ATGTTCAATCGGCCCGGAC 60.451 57.895 0.73 0.00 0.00 4.79
205 231 5.048991 GTGGTTCTTTGGTTTCGTATGACAT 60.049 40.000 0.00 0.00 0.00 3.06
208 234 3.816523 GGTGGTTCTTTGGTTTCGTATGA 59.183 43.478 0.00 0.00 0.00 2.15
229 255 1.942657 CTTCCATAATGAGCACGTGGG 59.057 52.381 18.88 7.29 0.00 4.61
261 287 5.418310 AGAAATGGGATACGTTTTATGCG 57.582 39.130 0.00 0.00 38.38 4.73
265 291 8.801882 AAGATCAAGAAATGGGATACGTTTTA 57.198 30.769 0.00 0.00 38.38 1.52
270 299 7.559590 AAGAAAGATCAAGAAATGGGATACG 57.440 36.000 0.00 0.00 37.60 3.06
277 306 7.530010 TCGCCTTTAAGAAAGATCAAGAAATG 58.470 34.615 0.00 0.00 41.02 2.32
343 372 8.870116 ACAAAAATAGAAGGTTTTTATCTGCCT 58.130 29.630 0.00 0.00 36.82 4.75
390 421 1.739338 AACAACAATCCCCGCGCAAA 61.739 50.000 8.75 0.00 0.00 3.68
391 422 2.136196 GAACAACAATCCCCGCGCAA 62.136 55.000 8.75 0.00 0.00 4.85
394 425 1.015085 TACGAACAACAATCCCCGCG 61.015 55.000 0.00 0.00 0.00 6.46
441 472 1.926827 GCGGTTTCGGCGATTTGAAAA 60.927 47.619 11.76 0.00 35.99 2.29
485 516 6.930667 ATGCTTGCTTTTGAAAATTGAACT 57.069 29.167 0.00 0.00 0.00 3.01
522 553 4.142293 GCTTTTGTTTTTGGGGCATTTTCA 60.142 37.500 0.00 0.00 0.00 2.69
533 564 7.564044 TTTCAAATGCTTGCTTTTGTTTTTG 57.436 28.000 23.59 7.52 35.01 2.44
577 610 4.263025 GGAAGATGCTGATTTGGGGTTTTT 60.263 41.667 0.00 0.00 0.00 1.94
583 616 2.950309 CTGAGGAAGATGCTGATTTGGG 59.050 50.000 0.00 0.00 0.00 4.12
685 730 3.945434 GATGTGCTGGGATGCGCG 61.945 66.667 0.00 0.00 45.42 6.86
800 859 2.590092 GGGGAATCCGGTCCAGTG 59.410 66.667 12.84 0.00 39.70 3.66
949 1349 4.265320 CGACGAGAACGAATCAATCAATCA 59.735 41.667 0.00 0.00 42.66 2.57
962 1362 3.832171 GCTGCTGCGACGAGAACG 61.832 66.667 0.00 0.00 45.75 3.95
963 1363 2.431601 AGCTGCTGCGACGAGAAC 60.432 61.111 10.14 0.00 45.42 3.01
1019 1423 4.770874 GCCCTTGCTTACCGCGGA 62.771 66.667 35.90 13.31 43.27 5.54
1044 1448 4.164822 ACACAGCAAGAAATCCAATTCG 57.835 40.909 0.00 0.00 34.46 3.34
1053 1457 0.028770 CGGCGAAACACAGCAAGAAA 59.971 50.000 0.00 0.00 34.54 2.52
1056 1460 2.175184 CTCCGGCGAAACACAGCAAG 62.175 60.000 9.30 0.00 34.54 4.01
1057 1461 2.203084 TCCGGCGAAACACAGCAA 60.203 55.556 9.30 0.00 34.54 3.91
1061 1476 0.389817 CAGATCTCCGGCGAAACACA 60.390 55.000 9.30 0.00 0.00 3.72
1089 1504 3.297620 AAACCCAGCCGCAGCAAG 61.298 61.111 0.00 0.00 43.56 4.01
1090 1505 3.604667 CAAACCCAGCCGCAGCAA 61.605 61.111 0.00 0.00 43.56 3.91
1093 1508 4.047059 CAGCAAACCCAGCCGCAG 62.047 66.667 0.00 0.00 0.00 5.18
1096 1511 3.673484 CACCAGCAAACCCAGCCG 61.673 66.667 0.00 0.00 0.00 5.52
1097 1512 3.994853 GCACCAGCAAACCCAGCC 61.995 66.667 0.00 0.00 41.58 4.85
1098 1513 4.347453 CGCACCAGCAAACCCAGC 62.347 66.667 0.00 0.00 42.27 4.85
1099 1514 3.673484 CCGCACCAGCAAACCCAG 61.673 66.667 0.00 0.00 42.27 4.45
1100 1515 4.514585 ACCGCACCAGCAAACCCA 62.515 61.111 0.00 0.00 42.27 4.51
1101 1516 3.977244 CACCGCACCAGCAAACCC 61.977 66.667 0.00 0.00 42.27 4.11
1102 1517 3.216292 ACACCGCACCAGCAAACC 61.216 61.111 0.00 0.00 42.27 3.27
1103 1518 2.026014 CACACCGCACCAGCAAAC 59.974 61.111 0.00 0.00 42.27 2.93
1104 1519 3.898509 GCACACCGCACCAGCAAA 61.899 61.111 0.00 0.00 42.27 3.68
1105 1520 4.873810 AGCACACCGCACCAGCAA 62.874 61.111 0.00 0.00 46.13 3.91
1139 1554 0.322816 AGACCGCCATCTGCACAAAT 60.323 50.000 0.00 0.00 41.33 2.32
2026 2447 2.974489 CTTGGCAAGCGAGGCTGTG 61.974 63.158 15.25 0.00 39.62 3.66
2101 2522 0.168128 GGTTTGTGATCGCCTTTCCG 59.832 55.000 3.31 0.00 0.00 4.30
2314 2735 1.661112 GCGAAATCCTTGAGAAGACCG 59.339 52.381 0.00 0.00 0.00 4.79
2608 3029 2.281070 ACTGCACCAAGACCGCTG 60.281 61.111 0.00 0.00 0.00 5.18
2789 3210 1.432514 GCAAACAGACTCGCATCAGA 58.567 50.000 0.00 0.00 0.00 3.27
2962 3383 0.612732 CAGGCATGCTTCCCAGGAAA 60.613 55.000 18.92 0.00 33.34 3.13
3414 3838 5.584649 TGTACTGGAAAAGAAGACACAACTG 59.415 40.000 0.00 0.00 0.00 3.16
3415 3839 5.741011 TGTACTGGAAAAGAAGACACAACT 58.259 37.500 0.00 0.00 0.00 3.16
3416 3840 6.431198 TTGTACTGGAAAAGAAGACACAAC 57.569 37.500 0.00 0.00 0.00 3.32
3417 3841 7.012327 CAGATTGTACTGGAAAAGAAGACACAA 59.988 37.037 0.00 0.00 34.64 3.33
3516 3940 4.367023 TACGACAGGCACGCACCC 62.367 66.667 0.00 0.00 0.00 4.61
3521 3945 0.388649 AAGCTTCTACGACAGGCACG 60.389 55.000 0.00 0.00 0.00 5.34
3609 4033 1.399714 ACAGACCGTGAACAGACTGA 58.600 50.000 10.08 0.00 0.00 3.41
3616 4040 4.959446 ACGCTACAGACCGTGAAC 57.041 55.556 0.00 0.00 36.18 3.18
3630 4054 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
3631 4055 1.225991 GCACACACACACACACACG 60.226 57.895 0.00 0.00 0.00 4.49
3632 4056 0.179192 CAGCACACACACACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
3633 4057 0.605050 ACAGCACACACACACACACA 60.605 50.000 0.00 0.00 0.00 3.72
3634 4058 0.179192 CACAGCACACACACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
3635 4059 1.921045 GCACAGCACACACACACACA 61.921 55.000 0.00 0.00 0.00 3.72
3636 4060 1.226379 GCACAGCACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
3637 4061 2.748843 CGCACAGCACACACACACA 61.749 57.895 0.00 0.00 0.00 3.72
3752 4176 3.727258 TCATGGCAAGGGTCCGGG 61.727 66.667 0.00 0.00 0.00 5.73
3753 4177 2.438434 GTCATGGCAAGGGTCCGG 60.438 66.667 0.00 0.00 0.00 5.14
3754 4178 1.303236 TTGTCATGGCAAGGGTCCG 60.303 57.895 9.09 0.00 0.00 4.79
3757 4181 0.188342 AAGGTTGTCATGGCAAGGGT 59.812 50.000 14.22 0.00 0.00 4.34
3826 4250 1.225855 TGCAAAGGTTACAGCACTCG 58.774 50.000 0.00 0.00 31.05 4.18
3874 4298 3.958147 TGAAGCATATAGGACTTGGACGA 59.042 43.478 0.00 0.00 0.00 4.20
3898 4322 0.031994 ATCACAAAGGTTGCGGTTGC 59.968 50.000 0.00 0.00 43.20 4.17
3899 4323 2.223688 TGAATCACAAAGGTTGCGGTTG 60.224 45.455 0.00 0.00 0.00 3.77
3901 4325 1.686355 TGAATCACAAAGGTTGCGGT 58.314 45.000 0.00 0.00 0.00 5.68
3903 4327 3.557577 TCATGAATCACAAAGGTTGCG 57.442 42.857 0.00 0.00 0.00 4.85
3912 4336 7.773224 AGGGAACGTAATAATTCATGAATCACA 59.227 33.333 20.95 10.08 0.00 3.58
3913 4337 8.070171 CAGGGAACGTAATAATTCATGAATCAC 58.930 37.037 20.95 14.49 0.00 3.06
3914 4338 7.773224 ACAGGGAACGTAATAATTCATGAATCA 59.227 33.333 20.95 7.66 0.00 2.57
3915 4339 8.154649 ACAGGGAACGTAATAATTCATGAATC 57.845 34.615 20.95 7.60 0.00 2.52
3916 4340 9.793259 ATACAGGGAACGTAATAATTCATGAAT 57.207 29.630 15.36 15.36 0.00 2.57
3919 4343 8.836413 ACAATACAGGGAACGTAATAATTCATG 58.164 33.333 0.00 0.00 0.00 3.07
3927 4351 7.982761 TTAAACACAATACAGGGAACGTAAT 57.017 32.000 0.00 0.00 0.00 1.89
3937 4361 7.114811 GCCACAAGACATTTAAACACAATACAG 59.885 37.037 0.00 0.00 0.00 2.74
3942 4366 4.688021 GGCCACAAGACATTTAAACACAA 58.312 39.130 0.00 0.00 0.00 3.33
3948 4372 1.883275 CACCGGCCACAAGACATTTAA 59.117 47.619 0.00 0.00 0.00 1.52
3997 4427 1.530293 GATGGCTGCGAGATGTTCATC 59.470 52.381 4.80 4.80 0.00 2.92
3998 4428 1.590932 GATGGCTGCGAGATGTTCAT 58.409 50.000 0.00 0.00 0.00 2.57
3999 4429 0.462581 GGATGGCTGCGAGATGTTCA 60.463 55.000 0.00 0.00 0.00 3.18
4000 4430 0.179062 AGGATGGCTGCGAGATGTTC 60.179 55.000 0.00 0.00 0.00 3.18
4001 4431 0.254178 AAGGATGGCTGCGAGATGTT 59.746 50.000 0.00 0.00 0.00 2.71
4016 4446 0.249868 CGACAGGCAGTTGTCAAGGA 60.250 55.000 13.42 0.00 46.11 3.36
4030 4460 2.376808 ACAGAATTCAGAGGCGACAG 57.623 50.000 8.44 0.00 0.00 3.51
4031 4461 2.037121 TCAACAGAATTCAGAGGCGACA 59.963 45.455 8.44 0.00 0.00 4.35
4032 4462 2.688507 TCAACAGAATTCAGAGGCGAC 58.311 47.619 8.44 0.00 0.00 5.19
4033 4463 3.244215 ACTTCAACAGAATTCAGAGGCGA 60.244 43.478 8.44 0.00 0.00 5.54
4034 4464 3.070018 ACTTCAACAGAATTCAGAGGCG 58.930 45.455 8.44 0.00 0.00 5.52
4035 4465 5.444663 AAACTTCAACAGAATTCAGAGGC 57.555 39.130 8.44 0.00 0.00 4.70
4036 4466 7.588512 CCTAAAACTTCAACAGAATTCAGAGG 58.411 38.462 8.44 3.42 0.00 3.69
4037 4467 7.040823 AGCCTAAAACTTCAACAGAATTCAGAG 60.041 37.037 8.44 0.00 0.00 3.35
4038 4468 6.772716 AGCCTAAAACTTCAACAGAATTCAGA 59.227 34.615 8.44 0.00 0.00 3.27
4039 4469 6.860023 CAGCCTAAAACTTCAACAGAATTCAG 59.140 38.462 8.44 1.65 0.00 3.02
4040 4470 6.545666 TCAGCCTAAAACTTCAACAGAATTCA 59.454 34.615 8.44 0.00 0.00 2.57
4041 4471 6.970484 TCAGCCTAAAACTTCAACAGAATTC 58.030 36.000 0.00 0.00 0.00 2.17
4042 4472 6.959639 TCAGCCTAAAACTTCAACAGAATT 57.040 33.333 0.00 0.00 0.00 2.17
4043 4473 7.231317 TCAATCAGCCTAAAACTTCAACAGAAT 59.769 33.333 0.00 0.00 0.00 2.40
4044 4474 6.545666 TCAATCAGCCTAAAACTTCAACAGAA 59.454 34.615 0.00 0.00 0.00 3.02
4045 4475 6.061441 TCAATCAGCCTAAAACTTCAACAGA 58.939 36.000 0.00 0.00 0.00 3.41
4046 4476 6.317789 TCAATCAGCCTAAAACTTCAACAG 57.682 37.500 0.00 0.00 0.00 3.16
4047 4477 6.707440 TTCAATCAGCCTAAAACTTCAACA 57.293 33.333 0.00 0.00 0.00 3.33
4048 4478 6.978080 TGTTTCAATCAGCCTAAAACTTCAAC 59.022 34.615 0.00 0.00 32.44 3.18
4049 4479 7.106439 TGTTTCAATCAGCCTAAAACTTCAA 57.894 32.000 0.00 0.00 32.44 2.69
4050 4480 6.707440 TGTTTCAATCAGCCTAAAACTTCA 57.293 33.333 0.00 0.00 32.44 3.02
4051 4481 6.978080 TGTTGTTTCAATCAGCCTAAAACTTC 59.022 34.615 0.00 0.00 32.44 3.01
4052 4482 6.756542 GTGTTGTTTCAATCAGCCTAAAACTT 59.243 34.615 0.00 0.00 32.44 2.66
4053 4483 6.273071 GTGTTGTTTCAATCAGCCTAAAACT 58.727 36.000 0.00 0.00 32.44 2.66
4054 4484 5.462068 GGTGTTGTTTCAATCAGCCTAAAAC 59.538 40.000 0.00 0.00 0.00 2.43
4055 4485 5.452636 GGGTGTTGTTTCAATCAGCCTAAAA 60.453 40.000 17.20 0.00 42.74 1.52
4056 4486 4.038642 GGGTGTTGTTTCAATCAGCCTAAA 59.961 41.667 17.20 0.00 42.74 1.85
4057 4487 3.572255 GGGTGTTGTTTCAATCAGCCTAA 59.428 43.478 17.20 0.00 42.74 2.69
4058 4488 3.153919 GGGTGTTGTTTCAATCAGCCTA 58.846 45.455 17.20 0.00 42.74 3.93
4059 4489 1.963515 GGGTGTTGTTTCAATCAGCCT 59.036 47.619 17.20 0.00 42.74 4.58
4060 4490 2.438868 GGGTGTTGTTTCAATCAGCC 57.561 50.000 13.01 13.01 40.36 4.85


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

AutoCloner maintained by Alex Coulton.