Multiple sequence alignment - TraesCS6A01G222000

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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 TraesCS6A01G222000 chr6A 100.000 5144 0 0 1 5144 414864158 414869301 0.000000e+00 9500
1 TraesCS6A01G222000 chr6A 94.667 75 3 1 5070 5144 418022660 418022733 1.170000e-21 115
2 TraesCS6A01G222000 chr6B 97.757 4413 95 3 543 4954 467461351 467456942 0.000000e+00 7598
3 TraesCS6A01G222000 chr6B 91.992 487 13 5 30 513 467465387 467464924 0.000000e+00 660
4 TraesCS6A01G222000 chr6B 91.818 110 7 2 4951 5058 411556650 411556541 8.920000e-33 152
5 TraesCS6A01G222000 chr6D 97.282 4195 82 10 276 4453 302061363 302057184 0.000000e+00 7086
6 TraesCS6A01G222000 chr6D 97.222 504 14 0 4452 4955 302057023 302056520 0.000000e+00 854
7 TraesCS6A01G222000 chr6D 94.224 277 5 6 1 277 302061790 302061525 3.710000e-111 412
8 TraesCS6A01G222000 chr7D 97.826 92 2 0 4953 5044 540399160 540399251 5.330000e-35 159
9 TraesCS6A01G222000 chr1D 96.809 94 2 1 4950 5043 268929833 268929925 6.900000e-34 156
10 TraesCS6A01G222000 chrUn 94.949 99 4 1 4949 5046 37006358 37006456 2.480000e-33 154
11 TraesCS6A01G222000 chrUn 94.949 99 4 1 4949 5046 38258579 38258677 2.480000e-33 154
12 TraesCS6A01G222000 chrUn 94.949 99 4 1 4949 5046 196709651 196709553 2.480000e-33 154
13 TraesCS6A01G222000 chr7A 94.059 101 6 0 4953 5053 250807288 250807188 2.480000e-33 154
14 TraesCS6A01G222000 chr4B 95.833 96 3 1 4953 5048 117191101 117191195 2.480000e-33 154
15 TraesCS6A01G222000 chr2B 91.589 107 7 2 4941 5046 415996645 415996540 4.150000e-31 147
16 TraesCS6A01G222000 chr4A 97.183 71 2 0 5074 5144 218166905 218166835 2.520000e-23 121
17 TraesCS6A01G222000 chr4A 94.667 75 3 1 5070 5144 555000111 555000038 1.170000e-21 115
18 TraesCS6A01G222000 chr1A 97.183 71 2 0 5074 5144 547029891 547029821 2.520000e-23 121
19 TraesCS6A01G222000 chr1A 97.143 70 2 0 5075 5144 90099313 90099382 9.050000e-23 119
20 TraesCS6A01G222000 chr1A 97.143 70 2 0 5075 5144 118495538 118495607 9.050000e-23 119
21 TraesCS6A01G222000 chr1A 97.143 70 2 0 5075 5144 189314898 189314829 9.050000e-23 119
22 TraesCS6A01G222000 chr1A 97.143 70 2 0 5075 5144 315181687 315181618 9.050000e-23 119
23 TraesCS6A01G222000 chr1A 97.143 70 2 0 5075 5144 550461937 550461868 9.050000e-23 119


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 TraesCS6A01G222000 chr6A 414864158 414869301 5143 False 9500 9500 100.000000 1 5144 1 chr6A.!!$F1 5143
1 TraesCS6A01G222000 chr6B 467456942 467465387 8445 True 4129 7598 94.874500 30 4954 2 chr6B.!!$R2 4924
2 TraesCS6A01G222000 chr6D 302056520 302061790 5270 True 2784 7086 96.242667 1 4955 3 chr6D.!!$R1 4954

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
994 4729 0.031917 TCCTGCATCAATGGGGCATT 60.032 50.000 0.00 0.00 36.87 3.56 F
1077 4812 0.318441 TTCTCTTGCTGTCTCCGGTG 59.682 55.000 0.00 0.00 0.00 4.94 F
1519 5254 0.692476 TCCCACACTCCATGGTTCAG 59.308 55.000 12.58 4.33 35.23 3.02 F
3012 6747 1.202818 GGCTTATCCCCATGTCAGTCC 60.203 57.143 0.00 0.00 0.00 3.85 F
3524 7259 4.830046 GCTCCTGATCTACTCTTACATGGA 59.170 45.833 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 5664 1.881973 TGAGACAATGAAGCAGGCAAC 59.118 47.619 0.00 0.00 0.00 4.17 R
3012 6747 3.753797 CAGAGATGATGGGAGCATGATTG 59.246 47.826 0.00 0.00 0.00 2.67 R
3201 6936 1.968017 CAGTGACGCTGGTGCCAAT 60.968 57.895 8.20 0.00 41.42 3.16 R
4114 7849 1.603802 TGCTTCACTGCTAGCACAAAC 59.396 47.619 14.93 3.23 42.12 2.93 R
5098 8996 0.674534 GGCTACTCGGTGACCCTATG 59.325 60.000 0.00 0.00 0.00 2.23 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
20 21 3.829886 GAGCACGAATGATTTCACCAA 57.170 42.857 0.00 0.00 0.00 3.67
21 22 4.159377 GAGCACGAATGATTTCACCAAA 57.841 40.909 0.00 0.00 0.00 3.28
22 23 4.545610 GAGCACGAATGATTTCACCAAAA 58.454 39.130 0.00 0.00 0.00 2.44
23 24 4.549458 AGCACGAATGATTTCACCAAAAG 58.451 39.130 0.00 0.00 0.00 2.27
24 25 3.674753 GCACGAATGATTTCACCAAAAGG 59.325 43.478 0.00 0.00 0.00 3.11
25 26 4.558496 GCACGAATGATTTCACCAAAAGGA 60.558 41.667 0.00 0.00 0.00 3.36
54 55 3.664107 TGCAGAGCACGAGTAGAATTTT 58.336 40.909 0.00 0.00 31.71 1.82
55 56 3.679980 TGCAGAGCACGAGTAGAATTTTC 59.320 43.478 0.00 0.00 31.71 2.29
368 532 1.305219 TGCCAGCGTCCACTAAATGC 61.305 55.000 0.00 0.00 0.00 3.56
377 544 5.180117 AGCGTCCACTAAATGCAATCATATC 59.820 40.000 0.00 0.00 31.46 1.63
435 602 2.229792 TGCTTTGCCTGTTTAGACTGG 58.770 47.619 5.07 5.07 45.04 4.00
514 4248 5.221382 GGCACAAATGGAGAAGCATAATCAT 60.221 40.000 0.00 0.00 0.00 2.45
516 4250 7.428020 GCACAAATGGAGAAGCATAATCATTA 58.572 34.615 0.00 0.00 0.00 1.90
517 4251 7.922278 GCACAAATGGAGAAGCATAATCATTAA 59.078 33.333 0.00 0.00 0.00 1.40
518 4252 9.241317 CACAAATGGAGAAGCATAATCATTAAC 57.759 33.333 0.00 0.00 0.00 2.01
519 4253 8.416329 ACAAATGGAGAAGCATAATCATTAACC 58.584 33.333 0.00 0.00 0.00 2.85
520 4254 8.415553 CAAATGGAGAAGCATAATCATTAACCA 58.584 33.333 0.00 0.00 0.00 3.67
521 4255 8.537728 AATGGAGAAGCATAATCATTAACCAA 57.462 30.769 0.00 0.00 0.00 3.67
522 4256 7.953005 TGGAGAAGCATAATCATTAACCAAA 57.047 32.000 0.00 0.00 0.00 3.28
523 4257 7.999679 TGGAGAAGCATAATCATTAACCAAAG 58.000 34.615 0.00 0.00 0.00 2.77
541 4275 4.690748 CCAAAGTCTTCGAACATCTAGCAA 59.309 41.667 0.00 0.00 0.00 3.91
876 4611 2.045926 ATCCTTCACTGCCGCCAC 60.046 61.111 0.00 0.00 0.00 5.01
923 4658 5.733091 GCTTAGATATCGCATAGCTCCTGAG 60.733 48.000 0.00 0.00 32.96 3.35
972 4707 1.671979 TCAACAGCATCAGCATAGCC 58.328 50.000 0.00 0.00 45.49 3.93
994 4729 0.031917 TCCTGCATCAATGGGGCATT 60.032 50.000 0.00 0.00 36.87 3.56
1012 4747 2.073117 TTTCTTGATGCGACGCACTA 57.927 45.000 27.06 14.37 43.04 2.74
1077 4812 0.318441 TTCTCTTGCTGTCTCCGGTG 59.682 55.000 0.00 0.00 0.00 4.94
1188 4923 1.009389 CGCTCTCAAACACGACCTCC 61.009 60.000 0.00 0.00 0.00 4.30
1201 4936 2.359975 CCTCCGAAGTGGCCAACC 60.360 66.667 7.24 0.00 37.80 3.77
1362 5097 3.716195 CTCCGTGGTGCCATCCCA 61.716 66.667 0.00 0.00 0.00 4.37
1386 5121 1.413662 CCCCTCCTTCAGCTCCATAGA 60.414 57.143 0.00 0.00 0.00 1.98
1443 5178 2.359478 ACATTCCCGGCCAACGTC 60.359 61.111 2.24 0.00 42.24 4.34
1519 5254 0.692476 TCCCACACTCCATGGTTCAG 59.308 55.000 12.58 4.33 35.23 3.02
1539 5274 1.738099 GCAGCTCACGGTGTTCGAT 60.738 57.895 8.17 0.00 42.43 3.59
1545 5280 2.047274 ACGGTGTTCGATGCAGGG 60.047 61.111 0.00 0.00 42.43 4.45
1566 5301 3.133362 GGTACAATATGTTCACCGGGAGA 59.867 47.826 6.32 0.00 0.00 3.71
1620 5355 5.127845 AGTGATCCGTGTGATAAGATTCACT 59.872 40.000 6.20 0.00 45.07 3.41
1667 5402 1.620323 GGAAGGCTTTGGAAACTGCAT 59.380 47.619 0.00 0.00 0.00 3.96
1726 5461 2.435059 GGAGCTTGCCAGACGACC 60.435 66.667 0.00 0.00 0.00 4.79
1756 5491 7.980662 TCAAGTTGCAATTTCTGAAGAATTTGA 59.019 29.630 22.58 11.02 42.98 2.69
2099 5834 1.376543 AGCTTGTCAGATTGCCATCG 58.623 50.000 0.00 0.00 34.17 3.84
3012 6747 1.202818 GGCTTATCCCCATGTCAGTCC 60.203 57.143 0.00 0.00 0.00 3.85
3524 7259 4.830046 GCTCCTGATCTACTCTTACATGGA 59.170 45.833 0.00 0.00 0.00 3.41
3780 7515 5.245075 TGATACACATGTGACAACTGACCTA 59.755 40.000 31.94 10.13 0.00 3.08
4077 7812 5.723672 TTAGTGAGTCACCTAAACTGAGG 57.276 43.478 19.71 0.00 42.89 3.86
4114 7849 1.442769 AGTGCTATGGCTTGACAACG 58.557 50.000 1.68 0.00 39.59 4.10
4171 7907 2.702592 AACAGTGACCTTCGTGGAAA 57.297 45.000 0.00 0.00 39.71 3.13
4199 7935 2.234908 ACTCACAGCCCATGAACTAGTC 59.765 50.000 0.00 0.00 0.00 2.59
4306 8042 7.777440 ACTCAATTTCTCCCCTCTTGAATAATC 59.223 37.037 0.00 0.00 0.00 1.75
4649 8547 4.281182 AGTCAAAGTCGTGTACTGGAGATT 59.719 41.667 0.00 0.00 38.88 2.40
4662 8560 7.819900 GTGTACTGGAGATTGTAGAAGTCAAAT 59.180 37.037 0.00 0.00 0.00 2.32
4665 8563 7.227156 ACTGGAGATTGTAGAAGTCAAATGTT 58.773 34.615 0.00 0.00 0.00 2.71
4743 8641 9.624373 AGTAAATGAGATTTTGTGATAGCTCAT 57.376 29.630 0.00 0.00 42.89 2.90
4744 8642 9.661187 GTAAATGAGATTTTGTGATAGCTCATG 57.339 33.333 0.00 0.00 40.92 3.07
4870 8768 6.959639 TTGATATTTCCCTGCATTTACCTC 57.040 37.500 0.00 0.00 0.00 3.85
4957 8855 2.409975 TGCGTGTTAGCAAAGTACTCC 58.590 47.619 0.00 0.00 45.06 3.85
4958 8856 1.730612 GCGTGTTAGCAAAGTACTCCC 59.269 52.381 0.00 0.00 37.05 4.30
4959 8857 2.344025 CGTGTTAGCAAAGTACTCCCC 58.656 52.381 0.00 0.00 0.00 4.81
4960 8858 2.708051 GTGTTAGCAAAGTACTCCCCC 58.292 52.381 0.00 0.00 0.00 5.40
4961 8859 2.305052 GTGTTAGCAAAGTACTCCCCCT 59.695 50.000 0.00 0.00 0.00 4.79
4962 8860 2.304761 TGTTAGCAAAGTACTCCCCCTG 59.695 50.000 0.00 0.00 0.00 4.45
4963 8861 2.305052 GTTAGCAAAGTACTCCCCCTGT 59.695 50.000 0.00 0.00 0.00 4.00
4964 8862 0.984995 AGCAAAGTACTCCCCCTGTC 59.015 55.000 0.00 0.00 0.00 3.51
4965 8863 0.035343 GCAAAGTACTCCCCCTGTCC 60.035 60.000 0.00 0.00 0.00 4.02
4966 8864 0.618981 CAAAGTACTCCCCCTGTCCC 59.381 60.000 0.00 0.00 0.00 4.46
4967 8865 0.195096 AAAGTACTCCCCCTGTCCCA 59.805 55.000 0.00 0.00 0.00 4.37
4968 8866 0.195096 AAGTACTCCCCCTGTCCCAA 59.805 55.000 0.00 0.00 0.00 4.12
4969 8867 0.195096 AGTACTCCCCCTGTCCCAAA 59.805 55.000 0.00 0.00 0.00 3.28
4970 8868 1.069775 GTACTCCCCCTGTCCCAAAA 58.930 55.000 0.00 0.00 0.00 2.44
4971 8869 1.639108 GTACTCCCCCTGTCCCAAAAT 59.361 52.381 0.00 0.00 0.00 1.82
4972 8870 2.068831 ACTCCCCCTGTCCCAAAATA 57.931 50.000 0.00 0.00 0.00 1.40
4973 8871 2.584773 ACTCCCCCTGTCCCAAAATAT 58.415 47.619 0.00 0.00 0.00 1.28
4974 8872 3.754976 ACTCCCCCTGTCCCAAAATATA 58.245 45.455 0.00 0.00 0.00 0.86
4975 8873 4.123745 ACTCCCCCTGTCCCAAAATATAA 58.876 43.478 0.00 0.00 0.00 0.98
4976 8874 4.168088 ACTCCCCCTGTCCCAAAATATAAG 59.832 45.833 0.00 0.00 0.00 1.73
4977 8875 4.385386 TCCCCCTGTCCCAAAATATAAGA 58.615 43.478 0.00 0.00 0.00 2.10
4978 8876 4.796816 TCCCCCTGTCCCAAAATATAAGAA 59.203 41.667 0.00 0.00 0.00 2.52
4979 8877 4.893524 CCCCCTGTCCCAAAATATAAGAAC 59.106 45.833 0.00 0.00 0.00 3.01
4980 8878 4.578928 CCCCTGTCCCAAAATATAAGAACG 59.421 45.833 0.00 0.00 0.00 3.95
4981 8879 5.190677 CCCTGTCCCAAAATATAAGAACGT 58.809 41.667 0.00 0.00 0.00 3.99
4982 8880 5.650703 CCCTGTCCCAAAATATAAGAACGTT 59.349 40.000 0.00 0.00 0.00 3.99
4983 8881 6.152154 CCCTGTCCCAAAATATAAGAACGTTT 59.848 38.462 0.46 0.00 0.00 3.60
4984 8882 7.309560 CCCTGTCCCAAAATATAAGAACGTTTT 60.310 37.037 0.46 0.00 0.00 2.43
4985 8883 8.085909 CCTGTCCCAAAATATAAGAACGTTTTT 58.914 33.333 9.22 9.22 0.00 1.94
4999 8897 8.707938 AAGAACGTTTTTAACACTACACTAGT 57.292 30.769 0.46 0.00 40.28 2.57
5012 8910 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
5013 8911 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
5014 8912 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
5015 8913 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
5016 8914 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
5017 8915 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
5018 8916 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
5024 8922 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
5025 8923 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
5028 8926 9.677567 CAAAAACGTTCTTATATTATGGGATGG 57.322 33.333 0.00 0.00 0.00 3.51
5029 8927 9.635404 AAAAACGTTCTTATATTATGGGATGGA 57.365 29.630 0.00 0.00 0.00 3.41
5030 8928 8.848474 AAACGTTCTTATATTATGGGATGGAG 57.152 34.615 0.00 0.00 0.00 3.86
5031 8929 6.947464 ACGTTCTTATATTATGGGATGGAGG 58.053 40.000 0.00 0.00 0.00 4.30
5032 8930 6.070194 ACGTTCTTATATTATGGGATGGAGGG 60.070 42.308 0.00 0.00 0.00 4.30
5033 8931 6.156256 CGTTCTTATATTATGGGATGGAGGGA 59.844 42.308 0.00 0.00 0.00 4.20
5034 8932 7.569240 GTTCTTATATTATGGGATGGAGGGAG 58.431 42.308 0.00 0.00 0.00 4.30
5035 8933 6.826727 TCTTATATTATGGGATGGAGGGAGT 58.173 40.000 0.00 0.00 0.00 3.85
5036 8934 7.961940 TCTTATATTATGGGATGGAGGGAGTA 58.038 38.462 0.00 0.00 0.00 2.59
5037 8935 7.844779 TCTTATATTATGGGATGGAGGGAGTAC 59.155 40.741 0.00 0.00 0.00 2.73
5038 8936 3.717507 TTATGGGATGGAGGGAGTACA 57.282 47.619 0.00 0.00 0.00 2.90
5039 8937 2.587060 ATGGGATGGAGGGAGTACAA 57.413 50.000 0.00 0.00 0.00 2.41
5040 8938 2.587060 TGGGATGGAGGGAGTACAAT 57.413 50.000 0.00 0.00 0.00 2.71
5041 8939 3.717507 TGGGATGGAGGGAGTACAATA 57.282 47.619 0.00 0.00 0.00 1.90
5042 8940 4.228237 TGGGATGGAGGGAGTACAATAT 57.772 45.455 0.00 0.00 0.00 1.28
5043 8941 5.363124 TGGGATGGAGGGAGTACAATATA 57.637 43.478 0.00 0.00 0.00 0.86
5044 8942 5.342017 TGGGATGGAGGGAGTACAATATAG 58.658 45.833 0.00 0.00 0.00 1.31
5045 8943 5.162760 TGGGATGGAGGGAGTACAATATAGT 60.163 44.000 0.00 0.00 0.00 2.12
5046 8944 5.422650 GGGATGGAGGGAGTACAATATAGTC 59.577 48.000 0.00 0.00 0.00 2.59
5047 8945 6.257586 GGATGGAGGGAGTACAATATAGTCT 58.742 44.000 0.00 0.00 0.00 3.24
5048 8946 6.726764 GGATGGAGGGAGTACAATATAGTCTT 59.273 42.308 0.00 0.00 0.00 3.01
5049 8947 6.978674 TGGAGGGAGTACAATATAGTCTTG 57.021 41.667 0.00 0.00 0.00 3.02
5050 8948 5.304614 TGGAGGGAGTACAATATAGTCTTGC 59.695 44.000 0.00 0.00 0.00 4.01
5051 8949 5.540719 GGAGGGAGTACAATATAGTCTTGCT 59.459 44.000 0.00 0.00 0.00 3.91
5052 8950 6.294843 GGAGGGAGTACAATATAGTCTTGCTC 60.295 46.154 0.00 0.00 0.00 4.26
5053 8951 6.136857 AGGGAGTACAATATAGTCTTGCTCA 58.863 40.000 0.00 0.00 0.00 4.26
5054 8952 6.611642 AGGGAGTACAATATAGTCTTGCTCAA 59.388 38.462 0.00 0.00 0.00 3.02
5055 8953 7.125811 AGGGAGTACAATATAGTCTTGCTCAAA 59.874 37.037 0.00 0.00 0.00 2.69
5056 8954 7.769044 GGGAGTACAATATAGTCTTGCTCAAAA 59.231 37.037 0.00 0.00 0.00 2.44
5057 8955 9.162764 GGAGTACAATATAGTCTTGCTCAAAAA 57.837 33.333 0.00 0.00 0.00 1.94
5079 8977 6.731292 AAAAAGCCCTGTTCAAGATTAACT 57.269 33.333 0.00 0.00 0.00 2.24
5080 8978 6.731292 AAAAGCCCTGTTCAAGATTAACTT 57.269 33.333 0.00 0.00 39.70 2.66
5094 8992 7.881775 AAGATTAACTTGCCGATTAATCCTT 57.118 32.000 9.87 0.48 43.95 3.36
5095 8993 8.974060 AAGATTAACTTGCCGATTAATCCTTA 57.026 30.769 9.87 0.00 43.95 2.69
5096 8994 8.379457 AGATTAACTTGCCGATTAATCCTTAC 57.621 34.615 9.87 0.00 43.95 2.34
5097 8995 8.211629 AGATTAACTTGCCGATTAATCCTTACT 58.788 33.333 9.87 0.00 43.95 2.24
5098 8996 7.781548 TTAACTTGCCGATTAATCCTTACTC 57.218 36.000 9.87 0.00 0.00 2.59
5099 8997 5.353394 ACTTGCCGATTAATCCTTACTCA 57.647 39.130 9.87 0.00 0.00 3.41
5100 8998 5.930135 ACTTGCCGATTAATCCTTACTCAT 58.070 37.500 9.87 0.00 0.00 2.90
5101 8999 7.062749 ACTTGCCGATTAATCCTTACTCATA 57.937 36.000 9.87 0.00 0.00 2.15
5102 9000 7.155328 ACTTGCCGATTAATCCTTACTCATAG 58.845 38.462 9.87 0.00 0.00 2.23
5103 9001 6.037786 TGCCGATTAATCCTTACTCATAGG 57.962 41.667 9.87 2.61 0.00 2.57
5104 9002 5.046591 TGCCGATTAATCCTTACTCATAGGG 60.047 44.000 9.87 2.13 33.41 3.53
5105 9003 5.046520 GCCGATTAATCCTTACTCATAGGGT 60.047 44.000 9.87 0.00 33.41 4.34
5106 9004 6.631962 CCGATTAATCCTTACTCATAGGGTC 58.368 44.000 9.87 0.00 33.41 4.46
5107 9005 6.210784 CCGATTAATCCTTACTCATAGGGTCA 59.789 42.308 9.87 0.00 33.41 4.02
5108 9006 7.091443 CGATTAATCCTTACTCATAGGGTCAC 58.909 42.308 9.87 0.00 33.41 3.67
5109 9007 6.742559 TTAATCCTTACTCATAGGGTCACC 57.257 41.667 0.00 0.00 33.41 4.02
5110 9008 2.662866 TCCTTACTCATAGGGTCACCG 58.337 52.381 0.00 0.00 43.47 4.94
5111 9009 2.242965 TCCTTACTCATAGGGTCACCGA 59.757 50.000 0.00 0.00 43.47 4.69
5112 9010 2.623889 CCTTACTCATAGGGTCACCGAG 59.376 54.545 0.00 0.00 43.47 4.63
5113 9011 3.288964 CTTACTCATAGGGTCACCGAGT 58.711 50.000 7.23 7.23 43.47 4.18
5114 9012 4.458397 CTTACTCATAGGGTCACCGAGTA 58.542 47.826 5.46 5.46 43.47 2.59
5115 9013 2.933573 ACTCATAGGGTCACCGAGTAG 58.066 52.381 0.48 0.00 43.47 2.57
5116 9014 1.609555 CTCATAGGGTCACCGAGTAGC 59.390 57.143 0.00 0.00 43.47 3.58
5117 9015 0.674534 CATAGGGTCACCGAGTAGCC 59.325 60.000 0.00 0.00 43.47 3.93
5118 9016 0.822532 ATAGGGTCACCGAGTAGCCG 60.823 60.000 0.00 0.00 43.47 5.52
5119 9017 1.913951 TAGGGTCACCGAGTAGCCGA 61.914 60.000 0.00 0.00 43.47 5.54
5120 9018 2.125961 GGGTCACCGAGTAGCCGAT 61.126 63.158 0.00 0.00 0.00 4.18
5121 9019 0.820891 GGGTCACCGAGTAGCCGATA 60.821 60.000 0.00 0.00 0.00 2.92
5122 9020 1.027357 GGTCACCGAGTAGCCGATAA 58.973 55.000 0.00 0.00 0.00 1.75
5123 9021 1.406539 GGTCACCGAGTAGCCGATAAA 59.593 52.381 0.00 0.00 0.00 1.40
5124 9022 2.457970 GTCACCGAGTAGCCGATAAAC 58.542 52.381 0.00 0.00 0.00 2.01
5125 9023 1.406539 TCACCGAGTAGCCGATAAACC 59.593 52.381 0.00 0.00 0.00 3.27
5126 9024 1.135527 CACCGAGTAGCCGATAAACCA 59.864 52.381 0.00 0.00 0.00 3.67
5127 9025 1.826720 ACCGAGTAGCCGATAAACCAA 59.173 47.619 0.00 0.00 0.00 3.67
5128 9026 2.234414 ACCGAGTAGCCGATAAACCAAA 59.766 45.455 0.00 0.00 0.00 3.28
5129 9027 3.264104 CCGAGTAGCCGATAAACCAAAA 58.736 45.455 0.00 0.00 0.00 2.44
5130 9028 3.685756 CCGAGTAGCCGATAAACCAAAAA 59.314 43.478 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.347490 GACAAAGGGCTGGCGAGA 59.653 61.111 0.00 0.00 0.00 4.04
55 56 2.747855 GGACAAAGGGCTGGCGAG 60.748 66.667 0.00 0.00 0.00 5.03
116 117 0.036765 GCCCGTGAACATACACAGGA 60.037 55.000 0.00 0.00 39.79 3.86
299 463 9.947433 TCAATTTGGAATGCTTTTCATAAGATT 57.053 25.926 0.00 0.00 34.33 2.40
435 602 3.575399 CAACAAGTGCTCAAAGGGC 57.425 52.632 0.00 0.00 0.00 5.19
514 4248 6.367969 GCTAGATGTTCGAAGACTTTGGTTAA 59.632 38.462 0.00 0.00 34.32 2.01
516 4250 4.691216 GCTAGATGTTCGAAGACTTTGGTT 59.309 41.667 0.00 0.00 34.32 3.67
517 4251 4.246458 GCTAGATGTTCGAAGACTTTGGT 58.754 43.478 0.00 0.00 34.32 3.67
518 4252 4.245660 TGCTAGATGTTCGAAGACTTTGG 58.754 43.478 0.00 0.00 34.32 3.28
519 4253 5.845985 TTGCTAGATGTTCGAAGACTTTG 57.154 39.130 0.00 0.00 34.32 2.77
520 4254 6.256757 GCTATTGCTAGATGTTCGAAGACTTT 59.743 38.462 0.00 0.00 33.42 2.66
521 4255 5.751028 GCTATTGCTAGATGTTCGAAGACTT 59.249 40.000 0.00 0.00 33.42 3.01
522 4256 5.163509 TGCTATTGCTAGATGTTCGAAGACT 60.164 40.000 0.00 0.87 40.48 3.24
523 4257 5.043903 TGCTATTGCTAGATGTTCGAAGAC 58.956 41.667 0.00 0.00 40.48 3.01
541 4275 7.578189 GCCTGCATACAAAATGGATATTGCTAT 60.578 37.037 0.00 0.00 0.00 2.97
876 4611 1.766625 TTGGCCCCAAGCAACAATGG 61.767 55.000 0.00 0.00 46.50 3.16
923 4658 3.378427 AGAGAGGTTCTTGTTTGTTGTGC 59.622 43.478 0.00 0.00 29.61 4.57
972 4707 1.397390 GCCCCATTGATGCAGGAAGG 61.397 60.000 0.00 0.00 0.00 3.46
994 4729 1.346365 GTAGTGCGTCGCATCAAGAA 58.654 50.000 24.65 2.72 41.91 2.52
1004 4739 2.106683 GGCCATGTGGTAGTGCGTC 61.107 63.158 0.00 0.00 37.57 5.19
1012 4747 0.760189 AAACAGCTTGGCCATGTGGT 60.760 50.000 19.05 14.23 37.57 4.16
1077 4812 2.615747 GGAGCTTTGGTTGAGGGAGTAC 60.616 54.545 0.00 0.00 0.00 2.73
1188 4923 3.726517 CAGCGGTTGGCCACTTCG 61.727 66.667 3.88 11.31 45.17 3.79
1362 5097 2.204059 AGCTGAAGGAGGGGTGCT 60.204 61.111 0.00 0.00 0.00 4.40
1419 5154 2.361104 GCCGGGAATGTGCCAGAA 60.361 61.111 2.18 0.00 0.00 3.02
1443 5178 1.227089 CTCAATCACCGGGAGCGAG 60.227 63.158 6.32 6.69 0.00 5.03
1519 5254 4.077188 GAACACCGTGAGCTGCGC 62.077 66.667 5.28 0.00 0.00 6.09
1539 5274 3.616219 GGTGAACATATTGTACCCTGCA 58.384 45.455 0.00 0.00 0.00 4.41
1545 5280 4.395959 TCTCCCGGTGAACATATTGTAC 57.604 45.455 0.00 0.00 0.00 2.90
1566 5301 5.708697 TGACTCACAGATGCTTGAATCAATT 59.291 36.000 0.00 0.00 0.00 2.32
1620 5355 0.392461 CCCCGGCAAAGAGATTCGAA 60.392 55.000 0.00 0.00 0.00 3.71
1726 5461 9.635520 ATTCTTCAGAAATTGCAACTTGAATAG 57.364 29.630 0.00 0.00 37.61 1.73
1756 5491 1.481772 GAGCTGATTCTCCTGCAGAGT 59.518 52.381 17.39 0.00 43.71 3.24
1929 5664 1.881973 TGAGACAATGAAGCAGGCAAC 59.118 47.619 0.00 0.00 0.00 4.17
3012 6747 3.753797 CAGAGATGATGGGAGCATGATTG 59.246 47.826 0.00 0.00 0.00 2.67
3201 6936 1.968017 CAGTGACGCTGGTGCCAAT 60.968 57.895 8.20 0.00 41.42 3.16
3524 7259 0.543749 GTGGTCTAGGCTGCCATTCT 59.456 55.000 22.65 1.88 34.52 2.40
3780 7515 0.548989 TGTAACCCAGTGTGCCAACT 59.451 50.000 0.00 0.00 0.00 3.16
4077 7812 4.342092 AGCACTAATTCATGGGTTAATGGC 59.658 41.667 0.00 0.00 0.00 4.40
4114 7849 1.603802 TGCTTCACTGCTAGCACAAAC 59.396 47.619 14.93 3.23 42.12 2.93
4171 7907 2.158623 TCATGGGCTGTGAGTTCAAGTT 60.159 45.455 0.00 0.00 0.00 2.66
4306 8042 6.042777 TCTTACAGTGTTCACTCTGACAAAG 58.957 40.000 14.42 13.13 39.17 2.77
4441 8177 8.995027 ATTTATGTGCCTTCTATTATGGAACA 57.005 30.769 0.00 0.00 43.43 3.18
4624 8522 4.823442 TCTCCAGTACACGACTTTGACTAA 59.177 41.667 0.00 0.00 35.64 2.24
4665 8563 6.069673 TGCTCCTCTGTTCCAAAATATAAGGA 60.070 38.462 0.00 0.00 0.00 3.36
4743 8641 8.791675 TCATAAAAGACACAGATAACATTTGCA 58.208 29.630 0.00 0.00 0.00 4.08
4744 8642 9.793252 ATCATAAAAGACACAGATAACATTTGC 57.207 29.630 0.00 0.00 0.00 3.68
4786 8684 6.851222 AAACATCTTCCATAGCTTCATACG 57.149 37.500 0.00 0.00 0.00 3.06
4834 8732 7.010738 CAGGGAAATATCAAACATGTGAATTGC 59.989 37.037 0.00 0.00 0.00 3.56
4870 8768 3.826157 TGGCTAACTGGAAAGATTGGTTG 59.174 43.478 0.00 0.00 0.00 3.77
4955 8853 4.385386 TCTTATATTTTGGGACAGGGGGA 58.615 43.478 0.00 0.00 42.39 4.81
4956 8854 4.806952 TCTTATATTTTGGGACAGGGGG 57.193 45.455 0.00 0.00 42.39 5.40
4957 8855 4.578928 CGTTCTTATATTTTGGGACAGGGG 59.421 45.833 0.00 0.00 42.39 4.79
4958 8856 5.190677 ACGTTCTTATATTTTGGGACAGGG 58.809 41.667 0.00 0.00 42.39 4.45
4959 8857 6.753107 AACGTTCTTATATTTTGGGACAGG 57.247 37.500 0.00 0.00 42.39 4.00
4973 8871 9.801873 ACTAGTGTAGTGTTAAAAACGTTCTTA 57.198 29.630 0.00 0.00 37.69 2.10
4974 8872 8.707938 ACTAGTGTAGTGTTAAAAACGTTCTT 57.292 30.769 0.00 0.00 37.69 2.52
4989 8887 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
4990 8888 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
4991 8889 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
4998 8896 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
4999 8897 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
5002 8900 9.677567 CCATCCCATAATATAAGAACGTTTTTG 57.322 33.333 13.87 0.00 0.00 2.44
5003 8901 9.635404 TCCATCCCATAATATAAGAACGTTTTT 57.365 29.630 9.22 9.22 0.00 1.94
5004 8902 9.284968 CTCCATCCCATAATATAAGAACGTTTT 57.715 33.333 0.46 0.00 0.00 2.43
5005 8903 7.883311 CCTCCATCCCATAATATAAGAACGTTT 59.117 37.037 0.46 0.00 0.00 3.60
5006 8904 7.394816 CCTCCATCCCATAATATAAGAACGTT 58.605 38.462 0.00 0.00 0.00 3.99
5007 8905 6.070194 CCCTCCATCCCATAATATAAGAACGT 60.070 42.308 0.00 0.00 0.00 3.99
5008 8906 6.156256 TCCCTCCATCCCATAATATAAGAACG 59.844 42.308 0.00 0.00 0.00 3.95
5009 8907 7.182930 ACTCCCTCCATCCCATAATATAAGAAC 59.817 40.741 0.00 0.00 0.00 3.01
5010 8908 7.263901 ACTCCCTCCATCCCATAATATAAGAA 58.736 38.462 0.00 0.00 0.00 2.52
5011 8909 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
5012 8910 7.623677 TGTACTCCCTCCATCCCATAATATAAG 59.376 40.741 0.00 0.00 0.00 1.73
5013 8911 7.492552 TGTACTCCCTCCATCCCATAATATAA 58.507 38.462 0.00 0.00 0.00 0.98
5014 8912 7.063801 TGTACTCCCTCCATCCCATAATATA 57.936 40.000 0.00 0.00 0.00 0.86
5015 8913 5.927465 TGTACTCCCTCCATCCCATAATAT 58.073 41.667 0.00 0.00 0.00 1.28
5016 8914 5.363124 TGTACTCCCTCCATCCCATAATA 57.637 43.478 0.00 0.00 0.00 0.98
5017 8915 4.228237 TGTACTCCCTCCATCCCATAAT 57.772 45.455 0.00 0.00 0.00 1.28
5018 8916 3.717507 TGTACTCCCTCCATCCCATAA 57.282 47.619 0.00 0.00 0.00 1.90
5019 8917 3.717507 TTGTACTCCCTCCATCCCATA 57.282 47.619 0.00 0.00 0.00 2.74
5020 8918 2.587060 TTGTACTCCCTCCATCCCAT 57.413 50.000 0.00 0.00 0.00 4.00
5021 8919 2.587060 ATTGTACTCCCTCCATCCCA 57.413 50.000 0.00 0.00 0.00 4.37
5022 8920 5.342866 ACTATATTGTACTCCCTCCATCCC 58.657 45.833 0.00 0.00 0.00 3.85
5023 8921 6.257586 AGACTATATTGTACTCCCTCCATCC 58.742 44.000 0.00 0.00 0.00 3.51
5024 8922 7.607250 CAAGACTATATTGTACTCCCTCCATC 58.393 42.308 0.00 0.00 0.00 3.51
5025 8923 6.014156 GCAAGACTATATTGTACTCCCTCCAT 60.014 42.308 0.00 0.00 0.00 3.41
5026 8924 5.304614 GCAAGACTATATTGTACTCCCTCCA 59.695 44.000 0.00 0.00 0.00 3.86
5027 8925 5.540719 AGCAAGACTATATTGTACTCCCTCC 59.459 44.000 0.00 0.00 0.00 4.30
5028 8926 6.265649 TGAGCAAGACTATATTGTACTCCCTC 59.734 42.308 0.00 1.71 0.00 4.30
5029 8927 6.136857 TGAGCAAGACTATATTGTACTCCCT 58.863 40.000 0.00 0.00 0.00 4.20
5030 8928 6.406692 TGAGCAAGACTATATTGTACTCCC 57.593 41.667 0.00 0.00 0.00 4.30
5031 8929 8.718102 TTTTGAGCAAGACTATATTGTACTCC 57.282 34.615 0.00 0.00 0.00 3.85
5056 8954 6.731292 AGTTAATCTTGAACAGGGCTTTTT 57.269 33.333 0.00 0.00 0.00 1.94
5057 8955 6.731292 AAGTTAATCTTGAACAGGGCTTTT 57.269 33.333 0.00 0.00 34.77 2.27
5070 8968 7.881775 AAGGATTAATCGGCAAGTTAATCTT 57.118 32.000 18.30 12.57 42.63 2.40
5071 8969 8.211629 AGTAAGGATTAATCGGCAAGTTAATCT 58.788 33.333 18.30 8.86 42.63 2.40
5072 8970 8.379457 AGTAAGGATTAATCGGCAAGTTAATC 57.621 34.615 9.32 13.94 42.45 1.75
5073 8971 8.379457 GAGTAAGGATTAATCGGCAAGTTAAT 57.621 34.615 9.32 0.67 35.86 1.40
5074 8972 7.781548 GAGTAAGGATTAATCGGCAAGTTAA 57.218 36.000 9.32 0.00 35.86 2.01
5084 8982 7.387643 GGTGACCCTATGAGTAAGGATTAATC 58.612 42.308 6.93 6.93 45.16 1.75
5085 8983 6.014499 CGGTGACCCTATGAGTAAGGATTAAT 60.014 42.308 0.00 0.00 36.08 1.40
5086 8984 5.303589 CGGTGACCCTATGAGTAAGGATTAA 59.696 44.000 0.00 0.00 36.08 1.40
5087 8985 4.831155 CGGTGACCCTATGAGTAAGGATTA 59.169 45.833 0.00 0.00 36.08 1.75
5088 8986 3.641906 CGGTGACCCTATGAGTAAGGATT 59.358 47.826 0.00 0.00 36.08 3.01
5089 8987 3.117246 TCGGTGACCCTATGAGTAAGGAT 60.117 47.826 0.00 0.00 36.08 3.24
5090 8988 2.242965 TCGGTGACCCTATGAGTAAGGA 59.757 50.000 0.00 0.00 36.08 3.36
5091 8989 2.623889 CTCGGTGACCCTATGAGTAAGG 59.376 54.545 0.00 0.00 0.00 2.69
5092 8990 3.288964 ACTCGGTGACCCTATGAGTAAG 58.711 50.000 7.93 0.00 38.09 2.34
5093 8991 3.377253 ACTCGGTGACCCTATGAGTAA 57.623 47.619 7.93 0.00 38.09 2.24
5094 8992 3.746751 GCTACTCGGTGACCCTATGAGTA 60.747 52.174 13.87 13.87 40.22 2.59
5095 8993 2.933573 CTACTCGGTGACCCTATGAGT 58.066 52.381 13.18 13.18 42.22 3.41
5096 8994 1.609555 GCTACTCGGTGACCCTATGAG 59.390 57.143 0.00 0.00 0.00 2.90
5097 8995 1.688772 GCTACTCGGTGACCCTATGA 58.311 55.000 0.00 0.00 0.00 2.15
5098 8996 0.674534 GGCTACTCGGTGACCCTATG 59.325 60.000 0.00 0.00 0.00 2.23
5099 8997 0.822532 CGGCTACTCGGTGACCCTAT 60.823 60.000 0.00 0.00 0.00 2.57
5100 8998 1.452651 CGGCTACTCGGTGACCCTA 60.453 63.158 0.00 0.00 0.00 3.53
5101 8999 2.569218 ATCGGCTACTCGGTGACCCT 62.569 60.000 0.00 0.00 0.00 4.34
5102 9000 0.820891 TATCGGCTACTCGGTGACCC 60.821 60.000 0.00 0.00 0.00 4.46
5103 9001 1.027357 TTATCGGCTACTCGGTGACC 58.973 55.000 0.00 0.00 0.00 4.02
5104 9002 2.457970 GTTTATCGGCTACTCGGTGAC 58.542 52.381 0.00 0.00 0.00 3.67
5105 9003 1.406539 GGTTTATCGGCTACTCGGTGA 59.593 52.381 0.00 0.00 0.00 4.02
5106 9004 1.135527 TGGTTTATCGGCTACTCGGTG 59.864 52.381 0.00 0.00 0.00 4.94
5107 9005 1.477553 TGGTTTATCGGCTACTCGGT 58.522 50.000 0.00 0.00 0.00 4.69
5108 9006 2.589798 TTGGTTTATCGGCTACTCGG 57.410 50.000 0.00 0.00 0.00 4.63
5109 9007 4.932268 TTTTTGGTTTATCGGCTACTCG 57.068 40.909 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.