Multiple sequence alignment - TraesCS5B01G206800

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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 TraesCS5B01G206800 chr5B 100.000 3299 0 0 1 3299 375797616 375800914 0.000000e+00 6093.0
1 TraesCS5B01G206800 chr5D 95.210 3069 90 8 1 3066 324372397 324375411 0.000000e+00 4800.0
2 TraesCS5B01G206800 chr7A 96.078 204 8 0 3096 3299 287487112 287486909 1.900000e-87 333.0
3 TraesCS5B01G206800 chr4A 96.020 201 8 0 3099 3299 741028896 741029096 8.830000e-86 327.0
4 TraesCS5B01G206800 chr7D 95.098 204 10 0 3096 3299 631023539 631023336 4.110000e-84 322.0
5 TraesCS5B01G206800 chr3B 94.286 210 11 1 3091 3299 537872575 537872784 1.480000e-83 320.0
6 TraesCS5B01G206800 chr3B 93.827 81 5 0 2659 2739 556504507 556504587 4.470000e-24 122.0
7 TraesCS5B01G206800 chrUn 94.608 204 11 0 3096 3299 34095507 34095710 1.910000e-82 316.0
8 TraesCS5B01G206800 chrUn 94.608 204 11 0 3096 3299 234968278 234968075 1.910000e-82 316.0
9 TraesCS5B01G206800 chr6D 94.231 208 11 1 3093 3299 101206658 101206865 1.910000e-82 316.0
10 TraesCS5B01G206800 chr1A 95.025 201 9 1 3096 3296 579801368 579801169 6.870000e-82 315.0
11 TraesCS5B01G206800 chr6B 92.958 213 14 1 3088 3299 27825397 27825609 3.200000e-80 309.0
12 TraesCS5B01G206800 chr6B 92.683 82 6 0 2656 2737 58801815 58801734 5.780000e-23 119.0
13 TraesCS5B01G206800 chr3D 95.062 81 4 0 2657 2737 313178332 313178412 9.610000e-26 128.0
14 TraesCS5B01G206800 chr3D 91.860 86 7 0 2653 2738 489457440 489457525 1.610000e-23 121.0
15 TraesCS5B01G206800 chr4B 91.304 92 7 1 2659 2750 670403256 670403346 1.240000e-24 124.0
16 TraesCS5B01G206800 chr4D 94.872 78 4 0 2662 2739 509646365 509646442 4.470000e-24 122.0
17 TraesCS5B01G206800 chr3A 93.827 81 5 0 2657 2737 419336177 419336097 4.470000e-24 122.0
18 TraesCS5B01G206800 chr1D 92.045 88 6 1 2652 2739 348128523 348128609 4.470000e-24 122.0
19 TraesCS5B01G206800 chr2D 95.238 42 2 0 130 171 437642969 437643010 2.120000e-07 67.6


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 TraesCS5B01G206800 chr5B 375797616 375800914 3298 False 6093 6093 100.00 1 3299 1 chr5B.!!$F1 3298
1 TraesCS5B01G206800 chr5D 324372397 324375411 3014 False 4800 4800 95.21 1 3066 1 chr5D.!!$F1 3065

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
549 550 0.246635 CGATTCTTGTCGGGTCACCT 59.753 55.000 0.0 0.0 37.94 4.00 F
989 990 0.393077 AGTTTGACCCTCTGGACACG 59.607 55.000 0.0 0.0 36.01 4.49 F
993 994 0.834612 TGACCCTCTGGACACGTTTT 59.165 50.000 0.0 0.0 31.12 2.43 F
996 997 3.071892 TGACCCTCTGGACACGTTTTTAT 59.928 43.478 0.0 0.0 31.12 1.40 F
1868 1872 2.711542 TCTGCCTTTAGCTTAGTTGCC 58.288 47.619 0.0 0.0 44.23 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1867 0.108329 TGCTAGAGTTAGGCGGCAAC 60.108 55.0 13.08 13.47 0.0 4.17 R
1864 1868 0.175760 CTGCTAGAGTTAGGCGGCAA 59.824 55.0 13.08 0.11 0.0 4.52 R
1869 1873 0.249114 GGACGCTGCTAGAGTTAGGC 60.249 60.0 0.00 0.00 0.0 3.93 R
1870 1874 0.386113 GGGACGCTGCTAGAGTTAGG 59.614 60.0 0.00 0.00 0.0 2.69 R
3075 3079 0.179240 GCGAGCGTGTGAGTGATTTG 60.179 55.0 0.00 0.00 0.0 2.32 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
388 389 0.338120 CCTCCACTCCTCCCTCTTCT 59.662 60.000 0.00 0.00 0.00 2.85
411 412 3.357079 GCCCAACTCACGCACCTG 61.357 66.667 0.00 0.00 0.00 4.00
418 419 1.301244 CTCACGCACCTGAAGCTGT 60.301 57.895 0.00 0.00 0.00 4.40
419 420 1.563435 CTCACGCACCTGAAGCTGTG 61.563 60.000 0.00 0.00 37.63 3.66
423 424 4.410225 CACCTGAAGCTGTGCCAT 57.590 55.556 0.00 0.00 0.00 4.40
476 477 0.552848 GGATTCCCCATGCTCAAGGA 59.447 55.000 0.00 0.00 34.14 3.36
487 488 5.188434 CCATGCTCAAGGATCTAAAACTCA 58.812 41.667 0.00 0.00 0.00 3.41
490 491 4.019860 TGCTCAAGGATCTAAAACTCAGCT 60.020 41.667 0.00 0.00 0.00 4.24
498 499 5.408604 GGATCTAAAACTCAGCTTTGTCGAA 59.591 40.000 0.00 0.00 0.00 3.71
503 504 3.409026 ACTCAGCTTTGTCGAATTCCT 57.591 42.857 0.00 0.00 0.00 3.36
549 550 0.246635 CGATTCTTGTCGGGTCACCT 59.753 55.000 0.00 0.00 37.94 4.00
583 584 5.014123 ACCCTGAATCTTCACTTTGTGGATA 59.986 40.000 0.00 0.00 33.87 2.59
594 595 2.702592 TTGTGGATATCCGTGGGAAC 57.297 50.000 17.04 8.78 39.43 3.62
597 598 1.343465 GTGGATATCCGTGGGAACGAT 59.657 52.381 17.04 0.00 39.43 3.73
598 599 1.616865 TGGATATCCGTGGGAACGATC 59.383 52.381 17.04 0.00 39.43 3.69
653 654 1.684983 CCTCCGGAGCCTAACGATAAA 59.315 52.381 26.87 0.00 0.00 1.40
660 661 5.230942 CGGAGCCTAACGATAAATTCTGAT 58.769 41.667 0.00 0.00 0.00 2.90
666 667 8.616076 AGCCTAACGATAAATTCTGATTTTGAG 58.384 33.333 7.57 2.76 36.82 3.02
695 696 2.643551 GCAAGTTAAGGAGCTGCCATA 58.356 47.619 0.00 0.00 40.02 2.74
697 698 2.945668 CAAGTTAAGGAGCTGCCATACC 59.054 50.000 0.00 0.00 40.02 2.73
703 704 0.394565 GGAGCTGCCATACCTCGATT 59.605 55.000 0.00 0.00 36.34 3.34
707 708 1.801178 GCTGCCATACCTCGATTAAGC 59.199 52.381 0.00 0.00 0.00 3.09
710 711 1.000506 GCCATACCTCGATTAAGCCGA 59.999 52.381 3.28 3.28 34.61 5.54
720 721 2.153817 CGATTAAGCCGACATCGATGTG 59.846 50.000 34.48 23.88 41.96 3.21
735 736 2.609459 CGATGTGGGAAACTATGTGAGC 59.391 50.000 0.00 0.00 0.00 4.26
736 737 3.679917 CGATGTGGGAAACTATGTGAGCT 60.680 47.826 0.00 0.00 0.00 4.09
737 738 3.334583 TGTGGGAAACTATGTGAGCTC 57.665 47.619 6.82 6.82 0.00 4.09
744 745 6.100279 TGGGAAACTATGTGAGCTCTATCAAT 59.900 38.462 16.19 4.10 0.00 2.57
775 776 1.592131 CTTGCCAGCTTTGCGCAAA 60.592 52.632 31.75 31.75 41.63 3.68
785 786 2.672195 GCTTTGCGCAAATTAGGAAGCT 60.672 45.455 33.64 0.00 38.92 3.74
786 787 2.919666 TTGCGCAAATTAGGAAGCTC 57.080 45.000 22.78 0.00 0.00 4.09
787 788 2.113860 TGCGCAAATTAGGAAGCTCT 57.886 45.000 8.16 0.00 0.00 4.09
788 789 2.009774 TGCGCAAATTAGGAAGCTCTC 58.990 47.619 8.16 0.00 0.00 3.20
789 790 2.284190 GCGCAAATTAGGAAGCTCTCT 58.716 47.619 0.30 0.00 0.00 3.10
790 791 2.286563 GCGCAAATTAGGAAGCTCTCTC 59.713 50.000 0.30 0.00 0.00 3.20
798 799 3.287867 AGGAAGCTCTCTCTCTCTCTG 57.712 52.381 0.00 0.00 0.00 3.35
811 812 1.067743 CTCTCTGTGTGCGTGCTACG 61.068 60.000 4.61 4.61 45.88 3.51
872 873 9.293404 CCAATTATGAATAGTTCTGATCCACAT 57.707 33.333 0.00 0.00 0.00 3.21
934 935 0.394625 GTCTACTGGAGGCGGTCTCT 60.395 60.000 9.80 0.00 42.10 3.10
989 990 0.393077 AGTTTGACCCTCTGGACACG 59.607 55.000 0.00 0.00 36.01 4.49
993 994 0.834612 TGACCCTCTGGACACGTTTT 59.165 50.000 0.00 0.00 31.12 2.43
996 997 3.071892 TGACCCTCTGGACACGTTTTTAT 59.928 43.478 0.00 0.00 31.12 1.40
999 1000 3.684788 CCCTCTGGACACGTTTTTATGAG 59.315 47.826 0.00 0.00 0.00 2.90
1004 1005 3.124466 TGGACACGTTTTTATGAGATGCG 59.876 43.478 0.00 0.00 0.00 4.73
1006 1007 4.378046 GGACACGTTTTTATGAGATGCGTT 60.378 41.667 0.00 0.00 0.00 4.84
1011 1012 5.106317 ACGTTTTTATGAGATGCGTTCCATT 60.106 36.000 0.32 0.00 33.29 3.16
1027 1028 3.971150 TCCATTGTGTTAACCTTTTGCG 58.029 40.909 2.48 0.00 0.00 4.85
1039 1040 7.877097 TGTTAACCTTTTGCGTACTAAGGAATA 59.123 33.333 17.05 9.00 40.71 1.75
1143 1147 7.035004 GTCATCATTGCTATTTTTGGTGCTTA 58.965 34.615 0.00 0.00 0.00 3.09
1147 1151 7.385267 TCATTGCTATTTTTGGTGCTTAACAT 58.615 30.769 0.00 0.00 0.00 2.71
1208 1212 4.685924 CACCTGAAACAAATGCAGAGTTT 58.314 39.130 12.09 12.09 38.10 2.66
1449 1453 4.935702 TCGAGTCTTCTTTGACGGTAAAA 58.064 39.130 0.00 0.00 41.47 1.52
1450 1454 5.350633 TCGAGTCTTCTTTGACGGTAAAAA 58.649 37.500 0.00 0.00 41.47 1.94
1612 1616 7.368198 TGTGCTACCATTATTGTCTATACCA 57.632 36.000 0.00 0.00 0.00 3.25
1624 1628 3.792114 TGTCTATACCAGAGAGGAGGGAA 59.208 47.826 0.00 0.00 41.22 3.97
1628 1632 7.186268 GTCTATACCAGAGAGGAGGGAATATT 58.814 42.308 0.00 0.00 41.22 1.28
1651 1655 7.395190 TTGATGGAAATAGGATGAACACTTG 57.605 36.000 0.00 0.00 0.00 3.16
1658 1662 6.808008 AATAGGATGAACACTTGTGTCAAG 57.192 37.500 6.88 7.78 0.00 3.02
1858 1862 9.941664 CATGAATTTTGTACTATCTGCCTTTAG 57.058 33.333 0.00 0.00 0.00 1.85
1859 1863 7.985476 TGAATTTTGTACTATCTGCCTTTAGC 58.015 34.615 0.00 0.00 44.14 3.09
1860 1864 7.829211 TGAATTTTGTACTATCTGCCTTTAGCT 59.171 33.333 0.00 0.00 44.23 3.32
1861 1865 8.581253 AATTTTGTACTATCTGCCTTTAGCTT 57.419 30.769 0.00 0.00 44.23 3.74
1862 1866 9.681062 AATTTTGTACTATCTGCCTTTAGCTTA 57.319 29.630 0.00 0.00 44.23 3.09
1863 1867 8.718102 TTTTGTACTATCTGCCTTTAGCTTAG 57.282 34.615 0.00 0.00 44.23 2.18
1864 1868 7.419711 TTGTACTATCTGCCTTTAGCTTAGT 57.580 36.000 0.00 0.00 44.23 2.24
1865 1869 7.419711 TGTACTATCTGCCTTTAGCTTAGTT 57.580 36.000 0.00 0.00 44.23 2.24
1866 1870 7.265673 TGTACTATCTGCCTTTAGCTTAGTTG 58.734 38.462 0.00 0.00 44.23 3.16
1867 1871 5.119694 ACTATCTGCCTTTAGCTTAGTTGC 58.880 41.667 0.00 0.00 44.23 4.17
1868 1872 2.711542 TCTGCCTTTAGCTTAGTTGCC 58.288 47.619 0.00 0.00 44.23 4.52
1869 1873 1.398390 CTGCCTTTAGCTTAGTTGCCG 59.602 52.381 0.00 0.00 44.23 5.69
1870 1874 0.098905 GCCTTTAGCTTAGTTGCCGC 59.901 55.000 0.00 0.00 38.99 6.53
1871 1875 0.733150 CCTTTAGCTTAGTTGCCGCC 59.267 55.000 0.00 0.00 0.00 6.13
1872 1876 1.679032 CCTTTAGCTTAGTTGCCGCCT 60.679 52.381 0.00 0.00 0.00 5.52
1873 1877 2.419574 CCTTTAGCTTAGTTGCCGCCTA 60.420 50.000 0.00 0.00 0.00 3.93
1874 1878 3.267483 CTTTAGCTTAGTTGCCGCCTAA 58.733 45.455 0.00 0.00 0.00 2.69
1885 1889 1.299468 CCGCCTAACTCTAGCAGCG 60.299 63.158 0.00 0.00 36.28 5.18
1919 1923 1.001248 CGAAGGGAGGGTAGGGACA 59.999 63.158 0.00 0.00 0.00 4.02
1967 1971 2.303175 GGCCACAGAACAAACCACTTA 58.697 47.619 0.00 0.00 0.00 2.24
2072 2076 5.710099 GGGACAAAAAGTTGATAGTGATCCA 59.290 40.000 0.00 0.00 38.20 3.41
2134 2138 5.239359 TCATGCTTCACTGAATGCATTAC 57.761 39.130 12.97 6.91 43.24 1.89
2171 2175 3.360249 ACACGTACTGCTACTTCGTTT 57.640 42.857 0.00 0.00 32.47 3.60
2306 2310 6.493116 CAGGTAAAATGAAATGAGCTGCTAG 58.507 40.000 0.15 0.00 0.00 3.42
2649 2653 5.186198 AGTGGGATAGTAGCAATGACAAAC 58.814 41.667 0.00 0.00 0.00 2.93
2653 2657 6.070481 TGGGATAGTAGCAATGACAAACAGTA 60.070 38.462 0.00 0.00 0.00 2.74
2654 2658 6.992715 GGGATAGTAGCAATGACAAACAGTAT 59.007 38.462 0.00 0.00 0.00 2.12
2660 2664 6.500684 AGCAATGACAAACAGTATTACCTG 57.499 37.500 0.00 0.00 38.45 4.00
2784 2788 0.852842 TCCCTTTGCCCATCCCATAG 59.147 55.000 0.00 0.00 0.00 2.23
2821 2825 7.361894 CAACATGCCTTGGAAAAATTAAAAGG 58.638 34.615 0.00 0.00 40.35 3.11
2840 2844 1.538950 GGAGCAGGAGAAAAGCAACAG 59.461 52.381 0.00 0.00 0.00 3.16
3066 3070 8.937884 TGTAATTTCTGAAAATGCATTCCATTG 58.062 29.630 13.38 3.95 43.22 2.82
3067 3071 9.153721 GTAATTTCTGAAAATGCATTCCATTGA 57.846 29.630 13.38 6.10 43.22 2.57
3068 3072 7.843490 ATTTCTGAAAATGCATTCCATTGAG 57.157 32.000 13.38 7.40 43.22 3.02
3069 3073 5.333299 TCTGAAAATGCATTCCATTGAGG 57.667 39.130 13.38 2.64 43.22 3.86
3070 3074 3.864243 TGAAAATGCATTCCATTGAGGC 58.136 40.909 13.38 0.00 43.22 4.70
3071 3075 2.994186 AAATGCATTCCATTGAGGCC 57.006 45.000 13.38 0.00 43.22 5.19
3072 3076 1.868713 AATGCATTCCATTGAGGCCA 58.131 45.000 5.99 0.00 42.44 5.36
3073 3077 2.097110 ATGCATTCCATTGAGGCCAT 57.903 45.000 5.01 0.00 37.29 4.40
3074 3078 1.405872 TGCATTCCATTGAGGCCATC 58.594 50.000 5.01 0.00 37.29 3.51
3075 3079 0.677842 GCATTCCATTGAGGCCATCC 59.322 55.000 5.01 0.00 37.29 3.51
3076 3080 2.030571 GCATTCCATTGAGGCCATCCA 61.031 52.381 5.01 0.00 37.29 3.41
3077 3081 2.390696 CATTCCATTGAGGCCATCCAA 58.609 47.619 5.01 6.61 37.29 3.53
3078 3082 2.619697 TTCCATTGAGGCCATCCAAA 57.380 45.000 5.01 0.00 37.29 3.28
3079 3083 2.852714 TCCATTGAGGCCATCCAAAT 57.147 45.000 5.01 0.00 37.29 2.32
3080 3084 2.669781 TCCATTGAGGCCATCCAAATC 58.330 47.619 5.01 0.00 37.29 2.17
3081 3085 2.024177 TCCATTGAGGCCATCCAAATCA 60.024 45.455 5.01 0.00 37.29 2.57
3082 3086 2.101917 CCATTGAGGCCATCCAAATCAC 59.898 50.000 5.01 0.00 33.74 3.06
3083 3087 2.905415 TTGAGGCCATCCAAATCACT 57.095 45.000 5.01 0.00 33.74 3.41
3084 3088 2.425143 TGAGGCCATCCAAATCACTC 57.575 50.000 5.01 0.00 33.74 3.51
3085 3089 1.634973 TGAGGCCATCCAAATCACTCA 59.365 47.619 5.01 0.00 33.74 3.41
3086 3090 2.019984 GAGGCCATCCAAATCACTCAC 58.980 52.381 5.01 0.00 33.74 3.51
3087 3091 1.355381 AGGCCATCCAAATCACTCACA 59.645 47.619 5.01 0.00 33.74 3.58
3088 3092 1.474077 GGCCATCCAAATCACTCACAC 59.526 52.381 0.00 0.00 0.00 3.82
3089 3093 1.131126 GCCATCCAAATCACTCACACG 59.869 52.381 0.00 0.00 0.00 4.49
3090 3094 1.131126 CCATCCAAATCACTCACACGC 59.869 52.381 0.00 0.00 0.00 5.34
3091 3095 2.079158 CATCCAAATCACTCACACGCT 58.921 47.619 0.00 0.00 0.00 5.07
3092 3096 1.795768 TCCAAATCACTCACACGCTC 58.204 50.000 0.00 0.00 0.00 5.03
3093 3097 0.439985 CCAAATCACTCACACGCTCG 59.560 55.000 0.00 0.00 0.00 5.03
3094 3098 0.179240 CAAATCACTCACACGCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
3095 3099 1.617755 AAATCACTCACACGCTCGCG 61.618 55.000 10.06 10.06 46.03 5.87
3099 3103 4.767841 CTCACACGCTCGCGCTCT 62.768 66.667 11.65 0.00 44.19 4.09
3100 3104 4.760840 TCACACGCTCGCGCTCTC 62.761 66.667 11.65 0.00 44.19 3.20
3160 3164 4.862823 CCTCCCTCCTCCGGTCCC 62.863 77.778 0.00 0.00 0.00 4.46
3161 3165 4.862823 CTCCCTCCTCCGGTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
3165 3169 4.400251 CTCCTCCGGTCCCCACCT 62.400 72.222 0.00 0.00 41.17 4.00
3166 3170 4.393778 TCCTCCGGTCCCCACCTC 62.394 72.222 0.00 0.00 41.17 3.85
3167 3171 4.400251 CCTCCGGTCCCCACCTCT 62.400 72.222 0.00 0.00 41.17 3.69
3168 3172 2.760385 CTCCGGTCCCCACCTCTC 60.760 72.222 0.00 0.00 41.17 3.20
3169 3173 4.393778 TCCGGTCCCCACCTCTCC 62.394 72.222 0.00 0.00 41.17 3.71
3172 3176 4.026357 GGTCCCCACCTCTCCCCT 62.026 72.222 0.00 0.00 40.00 4.79
3173 3177 2.125225 GTCCCCACCTCTCCCCTT 59.875 66.667 0.00 0.00 0.00 3.95
3174 3178 1.996187 GTCCCCACCTCTCCCCTTC 60.996 68.421 0.00 0.00 0.00 3.46
3175 3179 2.692741 CCCCACCTCTCCCCTTCC 60.693 72.222 0.00 0.00 0.00 3.46
3176 3180 2.456840 CCCACCTCTCCCCTTCCT 59.543 66.667 0.00 0.00 0.00 3.36
3177 3181 1.690985 CCCACCTCTCCCCTTCCTC 60.691 68.421 0.00 0.00 0.00 3.71
3178 3182 1.690985 CCACCTCTCCCCTTCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
3179 3183 1.394151 CACCTCTCCCCTTCCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
3180 3184 0.980231 CACCTCTCCCCTTCCTCCTG 60.980 65.000 0.00 0.00 0.00 3.86
3181 3185 2.069430 CCTCTCCCCTTCCTCCTGC 61.069 68.421 0.00 0.00 0.00 4.85
3182 3186 2.041265 TCTCCCCTTCCTCCTGCC 59.959 66.667 0.00 0.00 0.00 4.85
3183 3187 3.474570 CTCCCCTTCCTCCTGCCG 61.475 72.222 0.00 0.00 0.00 5.69
3188 3192 4.821589 CTTCCTCCTGCCGCCGTC 62.822 72.222 0.00 0.00 0.00 4.79
3253 3257 2.692741 CCCCCTGACCTTCCCCTC 60.693 72.222 0.00 0.00 0.00 4.30
3254 3258 2.692741 CCCCTGACCTTCCCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
3255 3259 2.692741 CCCTGACCTTCCCCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
3256 3260 3.083997 CCTGACCTTCCCCTCCCG 61.084 72.222 0.00 0.00 0.00 5.14
3257 3261 3.083997 CTGACCTTCCCCTCCCGG 61.084 72.222 0.00 0.00 0.00 5.73
3258 3262 3.925914 CTGACCTTCCCCTCCCGGT 62.926 68.421 0.00 0.00 0.00 5.28
3259 3263 3.400054 GACCTTCCCCTCCCGGTG 61.400 72.222 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 4.227134 CGAGGCGGGTGAGGATGG 62.227 72.222 0.00 0.00 0.00 3.51
335 336 0.179000 GCATCGGAGGTTGATGGACT 59.821 55.000 5.25 0.00 42.73 3.85
388 389 3.883462 CGTGAGTTGGGCGCATAA 58.117 55.556 10.83 0.00 0.00 1.90
444 445 2.058593 GGAATCCAGTGAATCCCACC 57.941 55.000 0.00 0.00 46.87 4.61
476 477 7.361286 GGAATTCGACAAAGCTGAGTTTTAGAT 60.361 37.037 0.00 0.00 0.00 1.98
487 488 2.303022 TCTCCAGGAATTCGACAAAGCT 59.697 45.455 0.00 0.00 0.00 3.74
490 491 3.064207 CGTTCTCCAGGAATTCGACAAA 58.936 45.455 0.00 0.00 36.24 2.83
498 499 0.042731 TCTCCCCGTTCTCCAGGAAT 59.957 55.000 0.00 0.00 36.24 3.01
503 504 2.683933 GGCTCTCCCCGTTCTCCA 60.684 66.667 0.00 0.00 0.00 3.86
549 550 4.648762 TGAAGATTCAGGGTTTCAAGCAAA 59.351 37.500 0.00 0.00 32.50 3.68
594 595 3.561310 CCCACACATTTGAGTATGGATCG 59.439 47.826 0.00 0.00 0.00 3.69
597 598 3.329225 TCACCCACACATTTGAGTATGGA 59.671 43.478 0.00 0.00 0.00 3.41
598 599 3.684908 TCACCCACACATTTGAGTATGG 58.315 45.455 0.00 0.00 0.00 2.74
600 601 4.635765 CGAATCACCCACACATTTGAGTAT 59.364 41.667 0.00 0.00 0.00 2.12
609 610 2.358125 CCGCGAATCACCCACACA 60.358 61.111 8.23 0.00 0.00 3.72
611 612 4.402528 CCCCGCGAATCACCCACA 62.403 66.667 8.23 0.00 0.00 4.17
653 654 6.182627 TGCCAGTCATACTCAAAATCAGAAT 58.817 36.000 0.00 0.00 0.00 2.40
660 661 6.206634 CCTTAACTTGCCAGTCATACTCAAAA 59.793 38.462 0.00 0.00 30.45 2.44
666 667 3.623510 GCTCCTTAACTTGCCAGTCATAC 59.376 47.826 0.00 0.00 30.45 2.39
695 696 1.269102 CGATGTCGGCTTAATCGAGGT 60.269 52.381 2.34 0.00 44.57 3.85
697 698 2.401017 TCGATGTCGGCTTAATCGAG 57.599 50.000 6.81 0.00 45.18 4.04
703 704 0.104120 CCCACATCGATGTCGGCTTA 59.896 55.000 26.07 0.00 39.39 3.09
707 708 1.006832 GTTTCCCACATCGATGTCGG 58.993 55.000 29.91 29.91 39.96 4.79
710 711 4.081142 TCACATAGTTTCCCACATCGATGT 60.081 41.667 25.18 25.18 42.84 3.06
720 721 5.537300 TGATAGAGCTCACATAGTTTCCC 57.463 43.478 17.77 0.00 0.00 3.97
735 736 8.344098 GCAAGAAATCCTCTGAAATTGATAGAG 58.656 37.037 6.81 6.81 38.10 2.43
736 737 7.284034 GGCAAGAAATCCTCTGAAATTGATAGA 59.716 37.037 0.00 0.00 33.37 1.98
737 738 7.067859 TGGCAAGAAATCCTCTGAAATTGATAG 59.932 37.037 0.00 0.00 33.37 2.08
744 745 2.821969 GCTGGCAAGAAATCCTCTGAAA 59.178 45.455 0.00 0.00 33.37 2.69
775 776 5.103940 ACAGAGAGAGAGAGAGCTTCCTAAT 60.104 44.000 0.00 0.00 0.00 1.73
785 786 1.271108 ACGCACACAGAGAGAGAGAGA 60.271 52.381 0.00 0.00 0.00 3.10
786 787 1.135717 CACGCACACAGAGAGAGAGAG 60.136 57.143 0.00 0.00 0.00 3.20
787 788 0.877743 CACGCACACAGAGAGAGAGA 59.122 55.000 0.00 0.00 0.00 3.10
788 789 0.732196 GCACGCACACAGAGAGAGAG 60.732 60.000 0.00 0.00 0.00 3.20
789 790 1.175347 AGCACGCACACAGAGAGAGA 61.175 55.000 0.00 0.00 0.00 3.10
790 791 0.523519 TAGCACGCACACAGAGAGAG 59.476 55.000 0.00 0.00 0.00 3.20
811 812 6.128117 TGGTAAGAACAGAAAATTACCGATGC 60.128 38.462 8.09 0.00 46.67 3.91
858 859 5.244402 TCAATGCAAAATGTGGATCAGAACT 59.756 36.000 0.00 0.00 37.29 3.01
872 873 5.142061 AGCATGTGAATCTCAATGCAAAA 57.858 34.783 17.81 0.00 40.24 2.44
917 918 0.457851 CAAGAGACCGCCTCCAGTAG 59.542 60.000 0.00 0.00 42.97 2.57
989 990 6.033831 CACAATGGAACGCATCTCATAAAAAC 59.966 38.462 0.00 0.00 0.00 2.43
993 994 4.260985 ACACAATGGAACGCATCTCATAA 58.739 39.130 0.00 0.00 0.00 1.90
996 997 2.183478 ACACAATGGAACGCATCTCA 57.817 45.000 0.00 0.00 0.00 3.27
999 1000 3.190535 AGGTTAACACAATGGAACGCATC 59.809 43.478 8.10 0.00 0.00 3.91
1004 1005 4.208253 CGCAAAAGGTTAACACAATGGAAC 59.792 41.667 8.10 0.00 0.00 3.62
1006 1007 3.381908 ACGCAAAAGGTTAACACAATGGA 59.618 39.130 8.10 0.00 0.00 3.41
1011 1012 5.236911 CCTTAGTACGCAAAAGGTTAACACA 59.763 40.000 8.10 0.00 35.95 3.72
1048 1049 9.932207 TCATACCGTAATTTCAAGTTCTTCTAA 57.068 29.630 0.00 0.00 0.00 2.10
1114 1118 5.954150 ACCAAAAATAGCAATGATGACCTCT 59.046 36.000 0.00 0.00 0.00 3.69
1162 1166 1.846439 CCCCATCACCATAGGTCTTGT 59.154 52.381 0.00 0.00 31.02 3.16
1163 1167 2.126882 TCCCCATCACCATAGGTCTTG 58.873 52.381 0.00 0.00 31.02 3.02
1164 1168 2.587060 TCCCCATCACCATAGGTCTT 57.413 50.000 0.00 0.00 31.02 3.01
1165 1169 2.342659 CATCCCCATCACCATAGGTCT 58.657 52.381 0.00 0.00 31.02 3.85
1166 1170 1.271597 GCATCCCCATCACCATAGGTC 60.272 57.143 0.00 0.00 31.02 3.85
1167 1171 0.773644 GCATCCCCATCACCATAGGT 59.226 55.000 0.00 0.00 35.62 3.08
1168 1172 0.773014 TGCATCCCCATCACCATAGG 59.227 55.000 0.00 0.00 0.00 2.57
1169 1173 1.901591 GTGCATCCCCATCACCATAG 58.098 55.000 0.00 0.00 0.00 2.23
1208 1212 5.822519 GGCATCAGTCCATTGTGTATTTAGA 59.177 40.000 0.00 0.00 0.00 2.10
1252 1256 7.388500 ACCAGCCAATATTTTTCATTTTCACAG 59.612 33.333 0.00 0.00 0.00 3.66
1567 1571 5.418840 CACATAATATATCAACCCAAGGGCC 59.581 44.000 4.70 0.00 39.32 5.80
1612 1616 5.098575 TCCATCAATATTCCCTCCTCTCT 57.901 43.478 0.00 0.00 0.00 3.10
1624 1628 9.872684 AAGTGTTCATCCTATTTCCATCAATAT 57.127 29.630 0.00 0.00 0.00 1.28
1628 1632 6.375174 CACAAGTGTTCATCCTATTTCCATCA 59.625 38.462 0.00 0.00 0.00 3.07
1651 1655 5.929697 TCACATGTGATTTCTCTTGACAC 57.070 39.130 24.56 0.00 34.14 3.67
1858 1862 1.007580 GAGTTAGGCGGCAACTAAGC 58.992 55.000 20.72 9.80 36.38 3.09
1859 1863 2.674796 AGAGTTAGGCGGCAACTAAG 57.325 50.000 20.72 0.00 36.38 2.18
1860 1864 2.159142 GCTAGAGTTAGGCGGCAACTAA 60.159 50.000 20.72 13.72 36.38 2.24
1861 1865 1.407979 GCTAGAGTTAGGCGGCAACTA 59.592 52.381 20.72 11.51 36.38 2.24
1862 1866 0.175989 GCTAGAGTTAGGCGGCAACT 59.824 55.000 20.79 20.79 38.92 3.16
1863 1867 0.108329 TGCTAGAGTTAGGCGGCAAC 60.108 55.000 13.08 13.47 0.00 4.17
1864 1868 0.175760 CTGCTAGAGTTAGGCGGCAA 59.824 55.000 13.08 0.11 0.00 4.52
1865 1869 1.816537 CTGCTAGAGTTAGGCGGCA 59.183 57.895 13.08 0.00 0.00 5.69
1866 1870 4.740235 CTGCTAGAGTTAGGCGGC 57.260 61.111 0.00 0.00 0.00 6.53
1867 1871 1.299468 CGCTGCTAGAGTTAGGCGG 60.299 63.158 0.00 0.00 35.36 6.13
1868 1872 0.592754 GACGCTGCTAGAGTTAGGCG 60.593 60.000 0.00 0.00 40.85 5.52
1869 1873 0.249114 GGACGCTGCTAGAGTTAGGC 60.249 60.000 0.00 0.00 0.00 3.93
1870 1874 0.386113 GGGACGCTGCTAGAGTTAGG 59.614 60.000 0.00 0.00 0.00 2.69
1871 1875 1.394618 AGGGACGCTGCTAGAGTTAG 58.605 55.000 0.00 0.00 0.00 2.34
1872 1876 1.848652 AAGGGACGCTGCTAGAGTTA 58.151 50.000 0.00 0.00 0.00 2.24
1873 1877 0.977395 AAAGGGACGCTGCTAGAGTT 59.023 50.000 0.00 0.00 0.00 3.01
1874 1878 1.848652 TAAAGGGACGCTGCTAGAGT 58.151 50.000 0.00 0.00 0.00 3.24
1942 1946 1.607148 GGTTTGTTCTGTGGCCAGTAC 59.393 52.381 5.11 0.00 39.82 2.73
1967 1971 7.224949 GCCTTACTCGAAAGCTAAATTATCACT 59.775 37.037 0.00 0.00 0.00 3.41
1984 1988 2.332063 ATCCCAATGTGCCTTACTCG 57.668 50.000 0.00 0.00 0.00 4.18
2030 2034 7.392766 TTGTCCCATGAGATAAATCCATACT 57.607 36.000 0.00 0.00 0.00 2.12
2072 2076 3.399330 CCACTGTAATCGACAAGGTGTT 58.601 45.455 0.00 0.00 37.70 3.32
2157 2161 8.833493 ACAAAGTAATAAAAACGAAGTAGCAGT 58.167 29.630 0.00 0.00 45.00 4.40
2306 2310 3.181486 TGCATGGAAGACACGTCTCTATC 60.181 47.826 0.00 0.00 39.39 2.08
2766 2770 0.829182 GCTATGGGATGGGCAAAGGG 60.829 60.000 0.00 0.00 0.00 3.95
2784 2788 1.194495 GCATGTTGCTTCGCTAATGC 58.806 50.000 0.00 0.00 40.96 3.56
2792 2796 2.818130 TTTCCAAGGCATGTTGCTTC 57.182 45.000 0.00 0.00 44.28 3.86
2821 2825 1.068679 GCTGTTGCTTTTCTCCTGCTC 60.069 52.381 0.00 0.00 36.03 4.26
2840 2844 7.787725 AATAGTAACATACAAGGCTACAAGC 57.212 36.000 0.00 0.00 41.46 4.01
3046 3050 5.726397 CCTCAATGGAATGCATTTTCAGAA 58.274 37.500 14.33 4.82 38.35 3.02
3054 3058 1.968493 GATGGCCTCAATGGAATGCAT 59.032 47.619 3.32 0.00 38.35 3.96
3066 3070 2.019984 GTGAGTGATTTGGATGGCCTC 58.980 52.381 3.32 0.00 34.31 4.70
3067 3071 1.355381 TGTGAGTGATTTGGATGGCCT 59.645 47.619 3.32 0.00 34.31 5.19
3068 3072 1.474077 GTGTGAGTGATTTGGATGGCC 59.526 52.381 0.00 0.00 0.00 5.36
3069 3073 1.131126 CGTGTGAGTGATTTGGATGGC 59.869 52.381 0.00 0.00 0.00 4.40
3070 3074 1.131126 GCGTGTGAGTGATTTGGATGG 59.869 52.381 0.00 0.00 0.00 3.51
3071 3075 2.079158 AGCGTGTGAGTGATTTGGATG 58.921 47.619 0.00 0.00 0.00 3.51
3072 3076 2.350522 GAGCGTGTGAGTGATTTGGAT 58.649 47.619 0.00 0.00 0.00 3.41
3073 3077 1.795768 GAGCGTGTGAGTGATTTGGA 58.204 50.000 0.00 0.00 0.00 3.53
3074 3078 0.439985 CGAGCGTGTGAGTGATTTGG 59.560 55.000 0.00 0.00 0.00 3.28
3075 3079 0.179240 GCGAGCGTGTGAGTGATTTG 60.179 55.000 0.00 0.00 0.00 2.32
3076 3080 1.617755 CGCGAGCGTGTGAGTGATTT 61.618 55.000 0.00 0.00 34.35 2.17
3077 3081 2.088763 CGCGAGCGTGTGAGTGATT 61.089 57.895 0.00 0.00 34.35 2.57
3078 3082 2.504899 CGCGAGCGTGTGAGTGAT 60.505 61.111 0.00 0.00 34.35 3.06
3156 3160 1.996187 GAAGGGGAGAGGTGGGGAC 60.996 68.421 0.00 0.00 0.00 4.46
3157 3161 2.454941 GAAGGGGAGAGGTGGGGA 59.545 66.667 0.00 0.00 0.00 4.81
3158 3162 2.692741 GGAAGGGGAGAGGTGGGG 60.693 72.222 0.00 0.00 0.00 4.96
3159 3163 1.690985 GAGGAAGGGGAGAGGTGGG 60.691 68.421 0.00 0.00 0.00 4.61
3160 3164 1.690985 GGAGGAAGGGGAGAGGTGG 60.691 68.421 0.00 0.00 0.00 4.61
3161 3165 0.980231 CAGGAGGAAGGGGAGAGGTG 60.980 65.000 0.00 0.00 0.00 4.00
3162 3166 1.394151 CAGGAGGAAGGGGAGAGGT 59.606 63.158 0.00 0.00 0.00 3.85
3163 3167 2.069430 GCAGGAGGAAGGGGAGAGG 61.069 68.421 0.00 0.00 0.00 3.69
3164 3168 2.069430 GGCAGGAGGAAGGGGAGAG 61.069 68.421 0.00 0.00 0.00 3.20
3165 3169 2.041265 GGCAGGAGGAAGGGGAGA 59.959 66.667 0.00 0.00 0.00 3.71
3166 3170 3.474570 CGGCAGGAGGAAGGGGAG 61.475 72.222 0.00 0.00 0.00 4.30
3171 3175 4.821589 GACGGCGGCAGGAGGAAG 62.822 72.222 8.47 0.00 0.00 3.46
3236 3240 2.692741 GAGGGGAAGGTCAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
3237 3241 2.692741 GGAGGGGAAGGTCAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
3238 3242 2.692741 GGGAGGGGAAGGTCAGGG 60.693 72.222 0.00 0.00 0.00 4.45
3239 3243 3.083997 CGGGAGGGGAAGGTCAGG 61.084 72.222 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.