Multiple sequence alignment - TraesCS4B01G081400

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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 TraesCS4B01G081400 chr4B 100.000 2784 0 0 1 2784 79606804 79604021 0.000000e+00 5142.0
1 TraesCS4B01G081400 chr4D 94.690 791 24 5 1207 1997 54053236 54052464 0.000000e+00 1212.0
2 TraesCS4B01G081400 chr4D 90.167 600 31 9 1984 2564 54051109 54050519 0.000000e+00 756.0
3 TraesCS4B01G081400 chr4D 91.729 532 19 5 145 671 54056429 54055918 0.000000e+00 715.0
4 TraesCS4B01G081400 chr4D 98.316 297 3 2 911 1207 54055620 54055326 1.140000e-143 520.0
5 TraesCS4B01G081400 chr4D 91.441 222 17 2 2563 2784 54050257 54050038 1.250000e-78 303.0
6 TraesCS4B01G081400 chr4D 92.105 152 12 0 2 153 54056755 54056604 6.040000e-52 215.0
7 TraesCS4B01G081400 chr4A 85.484 806 68 17 1988 2784 543176478 543177243 0.000000e+00 795.0
8 TraesCS4B01G081400 chr4A 91.367 278 19 1 522 799 543175606 543175878 2.620000e-100 375.0
9 TraesCS4B01G081400 chr4A 85.185 270 19 7 256 524 543084641 543084890 9.890000e-65 257.0
10 TraesCS4B01G081400 chr4A 88.816 152 17 0 2 153 542995504 542995655 1.320000e-43 187.0
11 TraesCS4B01G081400 chr4A 86.719 128 11 3 145 267 542995831 542995957 1.340000e-28 137.0
12 TraesCS4B01G081400 chr1D 78.481 316 54 9 2432 2742 24060548 24060854 7.870000e-46 195.0
13 TraesCS4B01G081400 chr7A 75.141 177 40 3 2470 2645 70817886 70817713 2.300000e-11 80.5
14 TraesCS4B01G081400 chr7D 84.146 82 10 2 2594 2675 69009951 69010029 2.970000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G081400 chr4B 79604021 79606804 2783 True 5142.000000 5142 100.000000 1 2784 1 chr4B.!!$R1 2783
1 TraesCS4B01G081400 chr4D 54050038 54056755 6717 True 620.166667 1212 93.074667 2 2784 6 chr4D.!!$R1 2782
2 TraesCS4B01G081400 chr4A 543175606 543177243 1637 False 585.000000 795 88.425500 522 2784 2 chr4A.!!$F3 2262

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
589 778 0.032540 GTTTTGGCTGGGAGCAACTG 59.967 55.0 0.00 0.0 44.75 3.16 F
836 1048 0.036732 TTACCAAGCAGGGCAGAGTG 59.963 55.0 0.04 0.0 43.89 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 4119 0.036952 ACTGCCTCATGGTCTTGTCG 60.037 55.0 0.0 0.0 35.27 4.35 R
2497 6504 0.172803 CGGACAGGTCTCGGTTAAGG 59.827 60.0 0.0 0.0 0.00 2.69 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
66 67 0.109964 GCCTAACAATGAAACGCGCA 60.110 50.000 5.73 0.00 0.00 6.09
87 88 1.281899 GCGAGTGCTGGAGTACAATC 58.718 55.000 0.00 0.00 38.39 2.67
98 99 0.606604 AGTACAATCCGACGCCTTGT 59.393 50.000 14.84 14.84 37.00 3.16
99 100 0.719465 GTACAATCCGACGCCTTGTG 59.281 55.000 18.08 3.14 35.00 3.33
104 105 0.178068 ATCCGACGCCTTGTGCTAAT 59.822 50.000 0.00 0.00 38.05 1.73
128 129 5.012458 TGAGGAGCTCTCTGAATTTGAAAGA 59.988 40.000 14.64 0.00 42.86 2.52
141 142 7.250569 TGAATTTGAAAGATGCGATTACCTTC 58.749 34.615 0.00 0.00 0.00 3.46
143 144 5.801350 TTGAAAGATGCGATTACCTTCAG 57.199 39.130 0.00 0.00 0.00 3.02
166 350 0.108774 TGGCCGTCATGTGTGGTTTA 59.891 50.000 0.00 0.00 0.00 2.01
178 362 1.079681 TGGTTTACTAGCACGCCGG 60.080 57.895 0.00 0.00 0.00 6.13
230 414 7.979115 TGGTTCAATAAAGTTGTTTTTCTCG 57.021 32.000 0.00 0.00 0.00 4.04
231 415 7.540299 TGGTTCAATAAAGTTGTTTTTCTCGT 58.460 30.769 0.00 0.00 0.00 4.18
322 511 5.515797 AACTAACCCTGTTTTCTCAAAGC 57.484 39.130 0.00 0.00 0.00 3.51
332 521 4.862018 TGTTTTCTCAAAGCGAAAAAGGTG 59.138 37.500 0.00 0.00 40.72 4.00
350 539 4.638304 AGGTGATTGCAAAAGTAGTACGT 58.362 39.130 1.71 0.00 0.00 3.57
351 540 4.451096 AGGTGATTGCAAAAGTAGTACGTG 59.549 41.667 1.71 0.00 0.00 4.49
352 541 4.378046 GGTGATTGCAAAAGTAGTACGTGG 60.378 45.833 1.71 0.00 0.00 4.94
353 542 4.449743 GTGATTGCAAAAGTAGTACGTGGA 59.550 41.667 1.71 0.00 0.00 4.02
354 543 5.121768 GTGATTGCAAAAGTAGTACGTGGAT 59.878 40.000 1.71 0.00 0.00 3.41
355 544 6.311935 GTGATTGCAAAAGTAGTACGTGGATA 59.688 38.462 1.71 0.00 0.00 2.59
356 545 6.874664 TGATTGCAAAAGTAGTACGTGGATAA 59.125 34.615 1.71 0.00 0.00 1.75
357 546 6.715344 TTGCAAAAGTAGTACGTGGATAAG 57.285 37.500 0.00 0.00 0.00 1.73
358 547 5.786311 TGCAAAAGTAGTACGTGGATAAGT 58.214 37.500 0.00 0.00 0.00 2.24
359 548 5.865552 TGCAAAAGTAGTACGTGGATAAGTC 59.134 40.000 0.00 0.00 0.00 3.01
360 549 5.004156 GCAAAAGTAGTACGTGGATAAGTCG 59.996 44.000 0.00 0.00 0.00 4.18
361 550 3.959573 AGTAGTACGTGGATAAGTCGC 57.040 47.619 0.00 0.00 0.00 5.19
362 551 3.273434 AGTAGTACGTGGATAAGTCGCA 58.727 45.455 0.00 0.00 0.00 5.10
363 552 3.881688 AGTAGTACGTGGATAAGTCGCAT 59.118 43.478 0.00 0.00 0.00 4.73
364 553 3.079960 AGTACGTGGATAAGTCGCATG 57.920 47.619 0.00 0.00 0.00 4.06
365 554 2.124903 GTACGTGGATAAGTCGCATGG 58.875 52.381 0.00 0.00 0.00 3.66
366 555 0.535335 ACGTGGATAAGTCGCATGGT 59.465 50.000 0.00 0.00 0.00 3.55
367 556 1.066430 ACGTGGATAAGTCGCATGGTT 60.066 47.619 0.00 0.00 0.00 3.67
368 557 2.006888 CGTGGATAAGTCGCATGGTTT 58.993 47.619 0.00 0.00 0.00 3.27
381 570 4.699735 TCGCATGGTTTCATTTCAGTACAT 59.300 37.500 0.00 0.00 0.00 2.29
396 585 1.480954 GTACATGGATCACACGACCCT 59.519 52.381 0.00 0.00 0.00 4.34
412 601 3.429135 CGACCCTAGTAGCTTTCTGGAAC 60.429 52.174 0.00 0.00 0.00 3.62
419 608 1.082756 GCTTTCTGGAACACACGCG 60.083 57.895 3.53 3.53 0.00 6.01
423 612 2.042520 TTCTGGAACACACGCGTTGC 62.043 55.000 10.22 0.00 37.69 4.17
584 773 1.005748 GCTTGTTTTGGCTGGGAGC 60.006 57.895 0.00 0.00 41.46 4.70
589 778 0.032540 GTTTTGGCTGGGAGCAACTG 59.967 55.000 0.00 0.00 44.75 3.16
704 916 1.961277 CTGGGCACAGGAACACGTC 60.961 63.158 8.54 0.00 41.13 4.34
714 926 2.733552 CAGGAACACGTCTCACAAGATG 59.266 50.000 0.00 0.00 43.13 2.90
715 927 2.628178 AGGAACACGTCTCACAAGATGA 59.372 45.455 1.82 0.00 40.43 2.92
716 928 3.259374 AGGAACACGTCTCACAAGATGAT 59.741 43.478 1.82 0.00 40.43 2.45
717 929 4.462834 AGGAACACGTCTCACAAGATGATA 59.537 41.667 1.82 0.00 40.43 2.15
718 930 4.800993 GGAACACGTCTCACAAGATGATAG 59.199 45.833 1.82 0.00 40.43 2.08
739 951 5.880054 AGGATAGGACACAAAATTTGACG 57.120 39.130 13.19 5.62 0.00 4.35
757 969 3.377798 TGACGGTTACCCAAGTGAAAAAC 59.622 43.478 0.00 0.00 0.00 2.43
785 997 3.118992 ACTCGCTCTTGAATAGATGTGCA 60.119 43.478 0.00 0.00 30.92 4.57
788 1000 3.606384 CGCTCTTGAATAGATGTGCATGC 60.606 47.826 11.82 11.82 30.92 4.06
807 1019 4.875544 TGCGTGCTCATTATAACTTTCC 57.124 40.909 0.00 0.00 0.00 3.13
812 1024 5.062934 CGTGCTCATTATAACTTTCCGTGAA 59.937 40.000 0.00 0.00 0.00 3.18
813 1025 6.248631 GTGCTCATTATAACTTTCCGTGAAC 58.751 40.000 0.00 0.00 0.00 3.18
814 1026 5.353123 TGCTCATTATAACTTTCCGTGAACC 59.647 40.000 0.00 0.00 0.00 3.62
815 1027 5.585047 GCTCATTATAACTTTCCGTGAACCT 59.415 40.000 0.00 0.00 0.00 3.50
819 1031 9.504708 TCATTATAACTTTCCGTGAACCTTTTA 57.495 29.630 0.00 0.00 0.00 1.52
820 1032 9.550811 CATTATAACTTTCCGTGAACCTTTTAC 57.449 33.333 0.00 0.00 0.00 2.01
821 1033 4.906065 AACTTTCCGTGAACCTTTTACC 57.094 40.909 0.00 0.00 0.00 2.85
822 1034 3.888583 ACTTTCCGTGAACCTTTTACCA 58.111 40.909 0.00 0.00 0.00 3.25
823 1035 4.271661 ACTTTCCGTGAACCTTTTACCAA 58.728 39.130 0.00 0.00 0.00 3.67
824 1036 4.337274 ACTTTCCGTGAACCTTTTACCAAG 59.663 41.667 0.00 0.00 0.00 3.61
828 1040 2.031157 CGTGAACCTTTTACCAAGCAGG 60.031 50.000 0.00 0.00 45.67 4.85
829 1041 2.296190 GTGAACCTTTTACCAAGCAGGG 59.704 50.000 0.04 0.00 43.89 4.45
831 1043 0.187361 ACCTTTTACCAAGCAGGGCA 59.813 50.000 0.04 0.00 43.89 5.36
832 1044 0.890683 CCTTTTACCAAGCAGGGCAG 59.109 55.000 0.04 0.00 43.89 4.85
833 1045 1.547675 CCTTTTACCAAGCAGGGCAGA 60.548 52.381 0.04 0.00 43.89 4.26
836 1048 0.036732 TTACCAAGCAGGGCAGAGTG 59.963 55.000 0.04 0.00 43.89 3.51
837 1049 1.127567 TACCAAGCAGGGCAGAGTGT 61.128 55.000 0.04 0.00 43.89 3.55
838 1050 1.970114 CCAAGCAGGGCAGAGTGTG 60.970 63.158 0.00 0.00 0.00 3.82
839 1051 1.970114 CAAGCAGGGCAGAGTGTGG 60.970 63.158 0.00 0.00 0.00 4.17
841 1053 4.729918 GCAGGGCAGAGTGTGGGG 62.730 72.222 0.00 0.00 0.00 4.96
842 1054 3.252284 CAGGGCAGAGTGTGGGGT 61.252 66.667 0.00 0.00 0.00 4.95
843 1055 2.450502 AGGGCAGAGTGTGGGGTT 60.451 61.111 0.00 0.00 0.00 4.11
844 1056 2.084930 AGGGCAGAGTGTGGGGTTT 61.085 57.895 0.00 0.00 0.00 3.27
846 1058 0.331616 GGGCAGAGTGTGGGGTTTAT 59.668 55.000 0.00 0.00 0.00 1.40
847 1059 1.682087 GGGCAGAGTGTGGGGTTTATC 60.682 57.143 0.00 0.00 0.00 1.75
848 1060 1.369625 GCAGAGTGTGGGGTTTATCG 58.630 55.000 0.00 0.00 0.00 2.92
849 1061 1.338769 GCAGAGTGTGGGGTTTATCGT 60.339 52.381 0.00 0.00 0.00 3.73
850 1062 2.618053 CAGAGTGTGGGGTTTATCGTC 58.382 52.381 0.00 0.00 0.00 4.20
852 1064 0.390735 AGTGTGGGGTTTATCGTCGC 60.391 55.000 0.00 0.00 0.00 5.19
855 1067 2.586914 GGGGTTTATCGTCGCCGG 60.587 66.667 0.00 0.00 33.95 6.13
856 1068 3.267118 GGGTTTATCGTCGCCGGC 61.267 66.667 19.07 19.07 33.95 6.13
857 1069 2.509786 GGTTTATCGTCGCCGGCA 60.510 61.111 28.98 11.20 33.95 5.69
859 1071 0.598158 GGTTTATCGTCGCCGGCATA 60.598 55.000 28.98 13.87 33.95 3.14
860 1072 1.425412 GTTTATCGTCGCCGGCATAT 58.575 50.000 28.98 15.52 33.95 1.78
862 1074 1.705256 TTATCGTCGCCGGCATATTC 58.295 50.000 28.98 10.09 33.95 1.75
863 1075 0.108992 TATCGTCGCCGGCATATTCC 60.109 55.000 28.98 5.58 33.95 3.01
864 1076 1.816863 ATCGTCGCCGGCATATTCCT 61.817 55.000 28.98 0.62 33.95 3.36
865 1077 2.022129 CGTCGCCGGCATATTCCTC 61.022 63.158 28.98 5.73 0.00 3.71
866 1078 1.668151 GTCGCCGGCATATTCCTCC 60.668 63.158 28.98 0.00 0.00 4.30
868 1080 1.961277 CGCCGGCATATTCCTCCAC 60.961 63.158 28.98 0.00 0.00 4.02
869 1081 1.451936 GCCGGCATATTCCTCCACT 59.548 57.895 24.80 0.00 0.00 4.00
870 1082 0.886490 GCCGGCATATTCCTCCACTG 60.886 60.000 24.80 0.00 0.00 3.66
873 1085 1.134401 CGGCATATTCCTCCACTGTGT 60.134 52.381 7.08 0.00 0.00 3.72
875 1087 2.684881 GGCATATTCCTCCACTGTGTTG 59.315 50.000 7.08 0.00 0.00 3.33
877 1089 2.489938 TATTCCTCCACTGTGTTGCC 57.510 50.000 7.08 0.00 0.00 4.52
878 1090 0.251341 ATTCCTCCACTGTGTTGCCC 60.251 55.000 7.08 0.00 0.00 5.36
880 1092 1.898574 CCTCCACTGTGTTGCCCAC 60.899 63.158 7.08 0.00 44.78 4.61
887 1099 2.932905 GTGTTGCCCACGTACGTG 59.067 61.111 35.57 35.57 45.02 4.49
891 1103 2.572149 TTGCCCACGTACGTGCCTA 61.572 57.895 36.76 24.19 44.16 3.93
896 1108 1.673626 CCCACGTACGTGCCTACAAAT 60.674 52.381 36.76 2.18 44.16 2.32
897 1109 2.417107 CCCACGTACGTGCCTACAAATA 60.417 50.000 36.76 0.00 44.16 1.40
988 1241 4.337836 TCTCTCTCTCTCATACACATGCAC 59.662 45.833 0.00 0.00 31.73 4.57
1132 1556 4.748892 CTTCTCCGTCTTCATGTATGTGT 58.251 43.478 0.00 0.00 0.00 3.72
1155 1579 6.798476 TGTGCGCGTTGATATATACTTACTAC 59.202 38.462 8.43 0.00 0.00 2.73
1203 1627 9.239551 TCTACGTAATACATGCTCCATATTAGT 57.760 33.333 0.00 0.00 0.00 2.24
1227 3740 9.136323 AGTATATACTAGTAGCATGCATGCATA 57.864 33.333 43.55 31.50 44.75 3.14
1236 3749 1.070376 CATGCATGCATACTCGAACGG 60.070 52.381 31.73 13.15 34.91 4.44
1392 3905 4.752879 GGCGCTTGTGGCCGTAGA 62.753 66.667 7.64 0.00 41.39 2.59
1526 4039 0.595053 ATCGATCGATGTTCGCGCTT 60.595 50.000 28.90 1.98 40.21 4.68
1527 4040 1.084666 CGATCGATGTTCGCGCTTG 60.085 57.895 10.26 0.00 40.21 4.01
1528 4041 1.742900 CGATCGATGTTCGCGCTTGT 61.743 55.000 10.26 0.00 40.21 3.16
1529 4042 0.043822 GATCGATGTTCGCGCTTGTC 60.044 55.000 0.54 0.00 40.21 3.18
1530 4043 1.742900 ATCGATGTTCGCGCTTGTCG 61.743 55.000 5.56 9.34 40.21 4.35
1531 4044 2.395690 GATGTTCGCGCTTGTCGG 59.604 61.111 5.56 0.00 38.94 4.79
1532 4045 3.702334 GATGTTCGCGCTTGTCGGC 62.702 63.158 5.56 0.00 38.94 5.54
1533 4046 4.961511 TGTTCGCGCTTGTCGGCT 62.962 61.111 5.56 0.00 38.94 5.52
1534 4047 3.712881 GTTCGCGCTTGTCGGCTT 61.713 61.111 5.56 0.00 38.94 4.35
1562 4075 4.025858 AGGTCATGCTGCACGCCT 62.026 61.111 3.57 10.05 38.05 5.52
1578 4091 3.130160 CTTCTTCGCTGCTGGGGC 61.130 66.667 7.80 0.00 39.26 5.80
1719 4232 1.748403 CCGTCCCGGTCATCATCAT 59.252 57.895 0.00 0.00 42.73 2.45
1737 4250 2.011947 CATCATGTTCCGTCTGCATGT 58.988 47.619 0.00 0.00 40.40 3.21
1743 4256 1.662629 GTTCCGTCTGCATGTGATCTG 59.337 52.381 0.00 0.00 0.00 2.90
1747 4260 1.405933 CGTCTGCATGTGATCTGGGAA 60.406 52.381 0.00 0.00 0.00 3.97
1791 4304 1.142965 CCCATGCATGACGTACGGA 59.857 57.895 28.31 5.92 0.00 4.69
1803 4316 1.717791 CGTACGGATACTCCACGGCA 61.718 60.000 7.57 0.00 35.91 5.69
1805 4318 0.742505 TACGGATACTCCACGGCAAG 59.257 55.000 0.00 0.00 35.91 4.01
1858 4371 1.005630 CCGGCGATCTCTGGGATTC 60.006 63.158 9.30 0.00 34.33 2.52
1873 4386 9.101325 TCTCTGGGATTCGGAAACTAATTATAT 57.899 33.333 0.00 0.00 0.00 0.86
1896 4409 5.719173 TGTTTTCTTTGGCTATGGTTATGC 58.281 37.500 0.00 0.00 0.00 3.14
1913 4426 9.899661 ATGGTTATGCAGAAGTAGTACATTTAA 57.100 29.630 2.52 0.00 0.00 1.52
1956 4469 3.010200 AGCTTTGCTTTGCCTAGCTAT 57.990 42.857 11.80 0.00 40.60 2.97
1969 4482 3.737047 GCCTAGCTATCTTTGTGTGCGTA 60.737 47.826 0.00 0.00 0.00 4.42
1970 4483 4.045104 CCTAGCTATCTTTGTGTGCGTAG 58.955 47.826 0.00 0.00 0.00 3.51
2004 4624 6.695713 TGTGCACTTATCTTCGTATACATGAC 59.304 38.462 19.41 0.00 0.00 3.06
2054 6049 7.278875 ACTATTTCAGATGAATTCCCAGTCTC 58.721 38.462 2.27 0.00 33.54 3.36
2196 6191 0.249238 ACTGTGCTCGCTATAGCTGC 60.249 55.000 21.98 23.06 43.19 5.25
2333 6332 5.748152 GCTTGTGTGCTGTCAATTTTAAAGA 59.252 36.000 0.00 0.00 0.00 2.52
2339 6338 7.277760 GTGTGCTGTCAATTTTAAAGACCTTTT 59.722 33.333 0.00 0.00 34.23 2.27
2398 6397 0.032815 TTGCTGTCGATCAACGGACA 59.967 50.000 0.00 0.00 42.82 4.02
2399 6398 0.246360 TGCTGTCGATCAACGGACAT 59.754 50.000 0.00 0.00 42.82 3.06
2400 6399 0.924090 GCTGTCGATCAACGGACATC 59.076 55.000 0.00 0.00 42.82 3.06
2402 6401 0.800683 TGTCGATCAACGGACATCGC 60.801 55.000 7.14 4.37 41.41 4.58
2403 6402 1.226859 TCGATCAACGGACATCGCC 60.227 57.895 7.14 0.00 41.41 5.54
2404 6403 2.237751 CGATCAACGGACATCGCCC 61.238 63.158 0.00 0.00 43.89 6.13
2405 6404 1.887707 GATCAACGGACATCGCCCC 60.888 63.158 0.00 0.00 43.89 5.80
2449 6456 1.839894 CCAACTCTAGCCCATCCCC 59.160 63.158 0.00 0.00 0.00 4.81
2450 6457 0.695803 CCAACTCTAGCCCATCCCCT 60.696 60.000 0.00 0.00 0.00 4.79
2451 6458 1.414538 CCAACTCTAGCCCATCCCCTA 60.415 57.143 0.00 0.00 0.00 3.53
2452 6459 2.408565 CAACTCTAGCCCATCCCCTAA 58.591 52.381 0.00 0.00 0.00 2.69
2453 6460 2.777692 CAACTCTAGCCCATCCCCTAAA 59.222 50.000 0.00 0.00 0.00 1.85
2454 6461 3.145559 ACTCTAGCCCATCCCCTAAAA 57.854 47.619 0.00 0.00 0.00 1.52
2455 6462 3.049344 ACTCTAGCCCATCCCCTAAAAG 58.951 50.000 0.00 0.00 0.00 2.27
2456 6463 2.373502 CTCTAGCCCATCCCCTAAAAGG 59.626 54.545 0.00 0.00 34.30 3.11
2465 6472 4.572007 CCATCCCCTAAAAGGCTAAAACCT 60.572 45.833 0.00 0.00 43.91 3.50
2489 6496 8.121167 CTCAATTAGAGGAGTACAAATTCGTC 57.879 38.462 0.00 0.00 40.84 4.20
2497 6504 6.644191 GGAGTACAAATTCGTCTTTACTCC 57.356 41.667 9.28 9.28 43.43 3.85
2499 6506 6.356186 AGTACAAATTCGTCTTTACTCCCT 57.644 37.500 0.00 0.00 0.00 4.20
2512 6519 1.558233 ACTCCCTTAACCGAGACCTG 58.442 55.000 1.86 0.00 0.00 4.00
2534 6541 5.828747 TGTCCGATCTCTTAAAACCGATAG 58.171 41.667 0.00 0.00 0.00 2.08
2558 6565 8.008513 AGAGGAGTATAAAATTTACTCGAGCA 57.991 34.615 13.61 0.00 44.22 4.26
2627 6897 2.759973 CCACGCCTCCTCTGCCTA 60.760 66.667 0.00 0.00 0.00 3.93
2644 6914 1.974236 CCTAGATCCGCCTCCTCAATT 59.026 52.381 0.00 0.00 0.00 2.32
2711 6981 3.860605 CATGGCCGGATCCCGTGA 61.861 66.667 5.05 0.00 46.80 4.35
2758 7028 3.838271 GTGGGCGCATCCTCGAGA 61.838 66.667 15.71 0.00 34.39 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.978934 ACACGTATCTTTTCTTCACGTTT 57.021 34.783 0.00 0.00 42.69 3.60
20 21 4.904154 GTGCAACACGTATCTTTTCTTCAC 59.096 41.667 0.00 0.00 36.32 3.18
34 35 1.076332 GTTAGGCCTAGTGCAACACG 58.924 55.000 13.36 0.00 43.89 4.49
36 37 2.940994 TTGTTAGGCCTAGTGCAACA 57.059 45.000 13.36 13.15 43.89 3.33
66 67 1.185618 TTGTACTCCAGCACTCGCCT 61.186 55.000 0.00 0.00 39.83 5.52
98 99 3.023939 TCAGAGAGCTCCTCATTAGCA 57.976 47.619 10.93 0.00 44.40 3.49
99 100 4.605640 ATTCAGAGAGCTCCTCATTAGC 57.394 45.455 10.93 0.00 44.40 3.09
104 105 4.897509 TTCAAATTCAGAGAGCTCCTCA 57.102 40.909 10.93 0.00 44.40 3.86
128 129 3.316308 GCCAAATCTGAAGGTAATCGCAT 59.684 43.478 0.00 0.00 0.00 4.73
141 142 1.135603 CACACATGACGGCCAAATCTG 60.136 52.381 2.24 0.00 0.00 2.90
143 144 0.171007 CCACACATGACGGCCAAATC 59.829 55.000 2.24 0.00 0.00 2.17
166 350 2.040009 ATAATGCCCGGCGTGCTAGT 62.040 55.000 16.55 4.06 0.00 2.57
178 362 5.295787 TGTTCATCGGAGTACAAATAATGCC 59.704 40.000 0.00 0.00 0.00 4.40
322 511 5.977129 ACTACTTTTGCAATCACCTTTTTCG 59.023 36.000 0.00 0.00 0.00 3.46
332 521 5.796350 ATCCACGTACTACTTTTGCAATC 57.204 39.130 0.00 0.00 0.00 2.67
350 539 3.342377 TGAAACCATGCGACTTATCCA 57.658 42.857 0.00 0.00 0.00 3.41
351 540 4.900635 AATGAAACCATGCGACTTATCC 57.099 40.909 0.00 0.00 0.00 2.59
352 541 5.879237 TGAAATGAAACCATGCGACTTATC 58.121 37.500 0.00 0.00 0.00 1.75
353 542 5.415701 ACTGAAATGAAACCATGCGACTTAT 59.584 36.000 0.00 0.00 0.00 1.73
354 543 4.759693 ACTGAAATGAAACCATGCGACTTA 59.240 37.500 0.00 0.00 0.00 2.24
355 544 3.569701 ACTGAAATGAAACCATGCGACTT 59.430 39.130 0.00 0.00 0.00 3.01
356 545 3.149196 ACTGAAATGAAACCATGCGACT 58.851 40.909 0.00 0.00 0.00 4.18
357 546 3.559238 ACTGAAATGAAACCATGCGAC 57.441 42.857 0.00 0.00 0.00 5.19
358 547 4.068599 TGTACTGAAATGAAACCATGCGA 58.931 39.130 0.00 0.00 0.00 5.10
359 548 4.418013 TGTACTGAAATGAAACCATGCG 57.582 40.909 0.00 0.00 0.00 4.73
360 549 5.104374 CCATGTACTGAAATGAAACCATGC 58.896 41.667 0.00 0.00 0.00 4.06
361 550 6.513806 TCCATGTACTGAAATGAAACCATG 57.486 37.500 0.00 0.00 0.00 3.66
362 551 6.891361 TGATCCATGTACTGAAATGAAACCAT 59.109 34.615 0.00 0.00 0.00 3.55
363 552 6.150976 GTGATCCATGTACTGAAATGAAACCA 59.849 38.462 0.00 0.00 0.00 3.67
364 553 6.150976 TGTGATCCATGTACTGAAATGAAACC 59.849 38.462 0.00 0.00 0.00 3.27
365 554 7.023575 GTGTGATCCATGTACTGAAATGAAAC 58.976 38.462 0.00 0.00 0.00 2.78
366 555 6.128309 CGTGTGATCCATGTACTGAAATGAAA 60.128 38.462 0.00 0.00 0.00 2.69
367 556 5.351189 CGTGTGATCCATGTACTGAAATGAA 59.649 40.000 0.00 0.00 0.00 2.57
368 557 4.869861 CGTGTGATCCATGTACTGAAATGA 59.130 41.667 0.00 0.00 0.00 2.57
396 585 3.859627 GCGTGTGTTCCAGAAAGCTACTA 60.860 47.826 0.00 0.00 0.00 1.82
419 608 1.156736 TCTGCCTTAAGCTTCGCAAC 58.843 50.000 0.00 0.00 44.23 4.17
437 626 2.032680 AATGCCAAATGCCATGCTTC 57.967 45.000 0.00 0.00 40.16 3.86
443 632 2.273538 AAAGCAAATGCCAAATGCCA 57.726 40.000 0.94 0.00 43.38 4.92
564 753 1.075674 TCCCAGCCAAAACAAGCCA 60.076 52.632 0.00 0.00 0.00 4.75
584 773 1.004745 AGGCATTACACCCTCCAGTTG 59.995 52.381 0.00 0.00 0.00 3.16
589 778 1.037579 GGCAAGGCATTACACCCTCC 61.038 60.000 0.00 0.00 0.00 4.30
676 888 0.543277 CTGTGCCCAGAATGCCTCTA 59.457 55.000 0.00 0.00 41.50 2.43
704 916 6.266330 TGTGTCCTATCCTATCATCTTGTGAG 59.734 42.308 0.00 0.00 40.92 3.51
714 926 7.254795 CCGTCAAATTTTGTGTCCTATCCTATC 60.255 40.741 8.89 0.00 0.00 2.08
715 927 6.542370 CCGTCAAATTTTGTGTCCTATCCTAT 59.458 38.462 8.89 0.00 0.00 2.57
716 928 5.878116 CCGTCAAATTTTGTGTCCTATCCTA 59.122 40.000 8.89 0.00 0.00 2.94
717 929 4.700213 CCGTCAAATTTTGTGTCCTATCCT 59.300 41.667 8.89 0.00 0.00 3.24
718 930 4.457949 ACCGTCAAATTTTGTGTCCTATCC 59.542 41.667 8.89 0.00 0.00 2.59
757 969 0.459237 ATTCAAGAGCGAGTCGGCTG 60.459 55.000 15.52 2.05 44.93 4.85
785 997 4.024893 CGGAAAGTTATAATGAGCACGCAT 60.025 41.667 0.00 0.00 0.00 4.73
788 1000 4.565166 TCACGGAAAGTTATAATGAGCACG 59.435 41.667 0.00 0.00 0.00 5.34
799 1011 5.435291 TGGTAAAAGGTTCACGGAAAGTTA 58.565 37.500 0.00 0.00 0.00 2.24
801 1013 3.888583 TGGTAAAAGGTTCACGGAAAGT 58.111 40.909 0.00 0.00 0.00 2.66
802 1014 4.791734 GCTTGGTAAAAGGTTCACGGAAAG 60.792 45.833 0.00 0.00 0.00 2.62
805 1017 2.223745 GCTTGGTAAAAGGTTCACGGA 58.776 47.619 0.00 0.00 0.00 4.69
806 1018 1.950909 TGCTTGGTAAAAGGTTCACGG 59.049 47.619 0.00 0.00 0.00 4.94
807 1019 2.031157 CCTGCTTGGTAAAAGGTTCACG 60.031 50.000 0.00 0.00 0.00 4.35
812 1024 0.187361 TGCCCTGCTTGGTAAAAGGT 59.813 50.000 0.00 0.00 0.00 3.50
813 1025 0.890683 CTGCCCTGCTTGGTAAAAGG 59.109 55.000 0.00 0.00 0.00 3.11
814 1026 1.815003 CTCTGCCCTGCTTGGTAAAAG 59.185 52.381 0.00 0.00 0.00 2.27
815 1027 1.144913 ACTCTGCCCTGCTTGGTAAAA 59.855 47.619 0.00 0.00 0.00 1.52
819 1031 2.433446 CACTCTGCCCTGCTTGGT 59.567 61.111 0.00 0.00 0.00 3.67
820 1032 1.970114 CACACTCTGCCCTGCTTGG 60.970 63.158 0.00 0.00 0.00 3.61
821 1033 1.970114 CCACACTCTGCCCTGCTTG 60.970 63.158 0.00 0.00 0.00 4.01
822 1034 2.433446 CCACACTCTGCCCTGCTT 59.567 61.111 0.00 0.00 0.00 3.91
823 1035 3.644606 CCCACACTCTGCCCTGCT 61.645 66.667 0.00 0.00 0.00 4.24
824 1036 4.729918 CCCCACACTCTGCCCTGC 62.730 72.222 0.00 0.00 0.00 4.85
828 1040 1.751437 GATAAACCCCACACTCTGCC 58.249 55.000 0.00 0.00 0.00 4.85
829 1041 1.338769 ACGATAAACCCCACACTCTGC 60.339 52.381 0.00 0.00 0.00 4.26
831 1043 1.203994 CGACGATAAACCCCACACTCT 59.796 52.381 0.00 0.00 0.00 3.24
832 1044 1.636988 CGACGATAAACCCCACACTC 58.363 55.000 0.00 0.00 0.00 3.51
833 1045 0.390735 GCGACGATAAACCCCACACT 60.391 55.000 0.00 0.00 0.00 3.55
836 1048 3.803886 GGCGACGATAAACCCCAC 58.196 61.111 0.00 0.00 0.00 4.61
848 1060 1.668151 GGAGGAATATGCCGGCGAC 60.668 63.158 23.90 10.60 0.00 5.19
849 1061 2.137528 TGGAGGAATATGCCGGCGA 61.138 57.895 23.90 13.33 0.00 5.54
850 1062 1.961277 GTGGAGGAATATGCCGGCG 60.961 63.158 23.90 0.00 0.00 6.46
852 1064 0.469917 ACAGTGGAGGAATATGCCGG 59.530 55.000 0.00 0.00 0.00 6.13
855 1067 2.098117 GCAACACAGTGGAGGAATATGC 59.902 50.000 5.31 0.00 0.00 3.14
856 1068 2.684881 GGCAACACAGTGGAGGAATATG 59.315 50.000 5.31 0.00 0.00 1.78
857 1069 2.357154 GGGCAACACAGTGGAGGAATAT 60.357 50.000 5.31 0.00 39.74 1.28
859 1071 0.251341 GGGCAACACAGTGGAGGAAT 60.251 55.000 5.31 0.00 39.74 3.01
860 1072 1.150536 GGGCAACACAGTGGAGGAA 59.849 57.895 5.31 0.00 39.74 3.36
862 1074 2.515398 TGGGCAACACAGTGGAGG 59.485 61.111 5.31 0.00 39.74 4.30
870 1082 2.932905 CACGTACGTGGGCAACAC 59.067 61.111 35.09 1.02 46.78 3.32
873 1085 2.572149 TAGGCACGTACGTGGGCAA 61.572 57.895 40.17 21.18 45.49 4.52
875 1087 2.507769 GTAGGCACGTACGTGGGC 60.508 66.667 40.17 32.24 45.49 5.36
877 1089 1.717194 ATTTGTAGGCACGTACGTGG 58.283 50.000 40.17 25.91 45.49 4.94
880 1092 3.789756 CAGACTATTTGTAGGCACGTACG 59.210 47.826 15.01 15.01 0.00 3.67
882 1094 4.097437 CCTCAGACTATTTGTAGGCACGTA 59.903 45.833 0.00 0.00 0.00 3.57
885 1097 4.081642 TCACCTCAGACTATTTGTAGGCAC 60.082 45.833 0.00 0.00 0.00 5.01
887 1099 4.737855 TCACCTCAGACTATTTGTAGGC 57.262 45.455 0.00 0.00 0.00 3.93
891 1103 5.777732 AGAGAGTTCACCTCAGACTATTTGT 59.222 40.000 0.00 0.00 43.12 2.83
896 1108 4.534500 AGAGAGAGAGTTCACCTCAGACTA 59.466 45.833 0.00 0.00 43.12 2.59
897 1109 3.330701 AGAGAGAGAGTTCACCTCAGACT 59.669 47.826 0.00 0.00 43.12 3.24
1132 1556 6.072563 TGGTAGTAAGTATATATCAACGCGCA 60.073 38.462 5.73 0.00 0.00 6.09
1155 1579 9.482627 GTAGAAGTGAGAAAGATGGTAATATGG 57.517 37.037 0.00 0.00 0.00 2.74
1227 3740 6.638468 GGATAAATTAATACGTCCGTTCGAGT 59.362 38.462 0.00 0.00 34.70 4.18
1392 3905 6.521151 AAGTAGTAGTAGCACGTACCAAAT 57.479 37.500 0.00 0.00 31.06 2.32
1526 4039 1.965930 GGATGCACACAAGCCGACA 60.966 57.895 0.00 0.00 0.00 4.35
1527 4040 1.915614 CTGGATGCACACAAGCCGAC 61.916 60.000 0.00 0.00 0.00 4.79
1528 4041 1.672030 CTGGATGCACACAAGCCGA 60.672 57.895 0.00 0.00 0.00 5.54
1529 4042 2.693762 CCTGGATGCACACAAGCCG 61.694 63.158 0.00 0.00 0.00 5.52
1530 4043 1.589716 GACCTGGATGCACACAAGCC 61.590 60.000 0.00 0.00 0.00 4.35
1531 4044 0.890542 TGACCTGGATGCACACAAGC 60.891 55.000 0.00 0.00 0.00 4.01
1532 4045 1.471287 CATGACCTGGATGCACACAAG 59.529 52.381 0.00 0.00 0.00 3.16
1533 4046 1.536940 CATGACCTGGATGCACACAA 58.463 50.000 0.00 0.00 0.00 3.33
1534 4047 0.961857 GCATGACCTGGATGCACACA 60.962 55.000 13.75 0.00 44.74 3.72
1597 4110 1.542492 TGGTCTTGTCGAGGTAGTCC 58.458 55.000 0.00 0.00 0.00 3.85
1604 4117 0.247460 TGCCTCATGGTCTTGTCGAG 59.753 55.000 0.00 0.00 35.27 4.04
1606 4119 0.036952 ACTGCCTCATGGTCTTGTCG 60.037 55.000 0.00 0.00 35.27 4.35
1705 4218 2.556144 ACATGATGATGATGACCGGG 57.444 50.000 6.32 0.00 33.36 5.73
1719 4232 1.001860 TCACATGCAGACGGAACATGA 59.998 47.619 14.32 0.00 0.00 3.07
1737 4250 1.417517 CGTGATCCCATTCCCAGATCA 59.582 52.381 0.00 0.00 43.06 2.92
1743 4256 2.591715 CGGCGTGATCCCATTCCC 60.592 66.667 0.00 0.00 0.00 3.97
1772 4285 2.534019 CCGTACGTCATGCATGGGC 61.534 63.158 25.97 17.44 41.68 5.36
1773 4286 0.249868 ATCCGTACGTCATGCATGGG 60.250 55.000 25.97 19.61 0.00 4.00
1774 4287 2.058798 GTATCCGTACGTCATGCATGG 58.941 52.381 25.97 13.66 0.00 3.66
1791 4304 2.590092 GGCCTTGCCGTGGAGTAT 59.410 61.111 0.00 0.00 39.62 2.12
1803 4316 1.004044 CTCCAGTGTCATCTTGGCCTT 59.996 52.381 3.32 0.00 0.00 4.35
1805 4318 0.326264 ACTCCAGTGTCATCTTGGCC 59.674 55.000 0.00 0.00 0.00 5.36
1816 4329 1.448540 GCGTGATCCCACTCCAGTG 60.449 63.158 0.00 0.00 45.23 3.66
1873 4386 5.244851 TGCATAACCATAGCCAAAGAAAACA 59.755 36.000 0.00 0.00 0.00 2.83
1896 4409 7.861372 ACGGATCGATTAAATGTACTACTTCTG 59.139 37.037 0.00 0.00 0.00 3.02
1913 4426 5.871396 AAATATATGGCCTACGGATCGAT 57.129 39.130 3.32 0.00 0.00 3.59
1956 4469 1.877637 ACATGCTACGCACACAAAGA 58.122 45.000 0.00 0.00 43.04 2.52
1969 4482 2.448926 TAAGTGCACACGTACATGCT 57.551 45.000 21.04 0.00 42.55 3.79
1970 4483 2.930040 AGATAAGTGCACACGTACATGC 59.070 45.455 21.04 10.76 42.40 4.06
1971 4484 4.259411 CGAAGATAAGTGCACACGTACATG 60.259 45.833 21.04 0.00 36.20 3.21
1972 4485 3.857665 CGAAGATAAGTGCACACGTACAT 59.142 43.478 21.04 2.14 36.20 2.29
2004 4624 7.946655 TTGCTTCACTTTAGATCCGTATATG 57.053 36.000 0.00 0.00 0.00 1.78
2081 6076 3.802685 ACACACTCACGAAAACTAAGCTC 59.197 43.478 0.00 0.00 0.00 4.09
2333 6332 1.111277 AAAGTTGCGAGCCAAAAGGT 58.889 45.000 0.00 0.00 34.68 3.50
2339 6338 1.536766 CATCTTCAAAGTTGCGAGCCA 59.463 47.619 0.00 0.00 0.00 4.75
2407 6406 1.400846 TCTTGCTACGTCTTCGCCTAG 59.599 52.381 0.00 0.00 41.18 3.02
2408 6407 1.400846 CTCTTGCTACGTCTTCGCCTA 59.599 52.381 0.00 0.00 41.18 3.93
2465 6472 7.837863 AGACGAATTTGTACTCCTCTAATTGA 58.162 34.615 0.00 0.00 0.00 2.57
2480 6487 6.401796 CGGTTAAGGGAGTAAAGACGAATTTG 60.402 42.308 0.00 0.00 0.00 2.32
2489 6496 3.768215 AGGTCTCGGTTAAGGGAGTAAAG 59.232 47.826 3.39 0.00 0.00 1.85
2497 6504 0.172803 CGGACAGGTCTCGGTTAAGG 59.827 60.000 0.00 0.00 0.00 2.69
2499 6506 1.747355 GATCGGACAGGTCTCGGTTAA 59.253 52.381 0.00 0.00 0.00 2.01
2512 6519 6.069684 TCTATCGGTTTTAAGAGATCGGAC 57.930 41.667 0.00 0.00 0.00 4.79
2534 6541 7.921745 AGTGCTCGAGTAAATTTTATACTCCTC 59.078 37.037 15.13 4.66 44.08 3.71
2558 6565 6.824704 GGAGTAGATATACTCGGCAGATAAGT 59.175 42.308 18.71 0.00 45.51 2.24
2627 6897 0.761802 GGAATTGAGGAGGCGGATCT 59.238 55.000 0.00 0.00 0.00 2.75
2644 6914 2.125832 GATTCGTCGGCGGTTGGA 60.126 61.111 10.62 0.00 38.89 3.53
2741 7011 3.838271 TCTCGAGGATGCGCCCAC 61.838 66.667 13.56 0.00 37.37 4.61
2742 7012 3.838271 GTCTCGAGGATGCGCCCA 61.838 66.667 13.56 0.00 37.37 5.36
2749 7019 3.518998 CGGTGGCGTCTCGAGGAT 61.519 66.667 13.56 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.