Multiple sequence alignment - TraesCS1A01G389100

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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 TraesCS1A01G389100 chr1A 100.000 3398 0 0 1 3398 557153396 557156793 0.000000e+00 6276.0
1 TraesCS1A01G389100 chr1A 93.293 164 10 1 3210 3372 425068286 425068123 1.220000e-59 241.0
2 TraesCS1A01G389100 chr1A 91.566 166 13 1 3210 3374 406654907 406655072 9.490000e-56 228.0
3 TraesCS1A01G389100 chr1A 91.667 48 2 2 3170 3216 31162175 31162221 7.870000e-07 65.8
4 TraesCS1A01G389100 chr1A 100.000 30 0 0 3169 3198 203818633 203818662 4.740000e-04 56.5
5 TraesCS1A01G389100 chr1D 92.291 2335 97 40 867 3156 464863544 464865840 0.000000e+00 3238.0
6 TraesCS1A01G389100 chr1D 88.919 740 54 14 1 728 464862677 464863400 0.000000e+00 887.0
7 TraesCS1A01G389100 chr1D 94.595 148 7 1 3237 3383 464865837 464865984 9.490000e-56 228.0
8 TraesCS1A01G389100 chr1D 95.238 42 1 1 3172 3212 19408067 19408026 7.870000e-07 65.8
9 TraesCS1A01G389100 chr1B 86.658 2376 155 71 389 2679 641630830 641633128 0.000000e+00 2483.0
10 TraesCS1A01G389100 chr1B 94.297 491 22 5 2911 3398 641633123 641633610 0.000000e+00 747.0
11 TraesCS1A01G389100 chr1B 92.547 322 18 2 1 316 641630355 641630676 1.110000e-124 457.0
12 TraesCS1A01G389100 chr1B 100.000 30 0 0 3169 3198 237010340 237010369 4.740000e-04 56.5
13 TraesCS1A01G389100 chr3B 87.673 1955 123 61 922 2790 657945728 657947650 0.000000e+00 2167.0
14 TraesCS1A01G389100 chr5D 90.153 782 77 0 1012 1793 271481226 271480445 0.000000e+00 1018.0
15 TraesCS1A01G389100 chr5D 88.363 782 91 0 1012 1793 271465590 271464809 0.000000e+00 941.0
16 TraesCS1A01G389100 chr5D 88.962 761 84 0 1033 1793 271470785 271470025 0.000000e+00 941.0
17 TraesCS1A01G389100 chr5D 88.962 761 83 1 1033 1793 271475985 271475226 0.000000e+00 939.0
18 TraesCS1A01G389100 chr5D 86.594 276 31 6 1 275 271708182 271708452 1.980000e-77 300.0
19 TraesCS1A01G389100 chr5A 86.473 414 55 1 1380 1793 361365010 361364598 1.440000e-123 453.0
20 TraesCS1A01G389100 chr5A 77.706 776 123 33 1 759 361447488 361446746 2.420000e-116 429.0
21 TraesCS1A01G389100 chr5B 88.722 266 25 5 1 266 307881239 307880979 1.520000e-83 320.0
22 TraesCS1A01G389100 chr5B 93.939 165 9 1 3210 3373 101902543 101902379 7.280000e-62 248.0
23 TraesCS1A01G389100 chr3D 93.939 165 9 1 3210 3373 209469090 209468926 7.280000e-62 248.0
24 TraesCS1A01G389100 chrUn 82.456 285 38 3 1015 1299 31027386 31027114 4.380000e-59 239.0
25 TraesCS1A01G389100 chr6B 91.329 173 13 2 3210 3381 92348663 92348492 5.670000e-58 235.0
26 TraesCS1A01G389100 chr4B 90.419 167 14 2 3210 3374 604114403 604114569 5.710000e-53 219.0
27 TraesCS1A01G389100 chr3A 97.500 40 0 1 3173 3211 442290691 442290652 2.190000e-07 67.6
28 TraesCS1A01G389100 chr4A 95.122 41 1 1 3172 3211 279471366 279471326 2.830000e-06 63.9
29 TraesCS1A01G389100 chr6D 96.875 32 0 1 3168 3199 366703428 366703398 6.000000e-03 52.8
30 TraesCS1A01G389100 chr6A 96.875 32 0 1 3168 3199 507148714 507148684 6.000000e-03 52.8


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 TraesCS1A01G389100 chr1A 557153396 557156793 3397 False 6276 6276 100.000000 1 3398 1 chr1A.!!$F4 3397
1 TraesCS1A01G389100 chr1D 464862677 464865984 3307 False 1451 3238 91.935000 1 3383 3 chr1D.!!$F1 3382
2 TraesCS1A01G389100 chr1B 641630355 641633610 3255 False 1229 2483 91.167333 1 3398 3 chr1B.!!$F2 3397
3 TraesCS1A01G389100 chr3B 657945728 657947650 1922 False 2167 2167 87.673000 922 2790 1 chr3B.!!$F1 1868
4 TraesCS1A01G389100 chr5D 271480445 271481226 781 True 1018 1018 90.153000 1012 1793 1 chr5D.!!$R4 781
5 TraesCS1A01G389100 chr5D 271464809 271465590 781 True 941 941 88.363000 1012 1793 1 chr5D.!!$R1 781
6 TraesCS1A01G389100 chr5D 271470025 271470785 760 True 941 941 88.962000 1033 1793 1 chr5D.!!$R2 760
7 TraesCS1A01G389100 chr5D 271475226 271475985 759 True 939 939 88.962000 1033 1793 1 chr5D.!!$R3 760
8 TraesCS1A01G389100 chr5A 361446746 361447488 742 True 429 429 77.706000 1 759 1 chr5A.!!$R2 758

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
562 665 0.031178 GGCACAAGTCAAGCAAGGTG 59.969 55.0 0.00 0.0 0.0 4.00 F
2105 2292 0.038166 GCATTGGACAAGGAGGTGGA 59.962 55.0 0.35 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2294 0.179702 TCTGCAGGACTGGCATCATC 59.820 55.000 15.13 0.0 41.06 2.92 R
2993 3284 1.483827 AGGCATTTCATCGAGCAGAGA 59.516 47.619 0.00 0.0 0.00 3.10 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
30 31 2.921634 TCTTCGAGAACATCCGACAG 57.078 50.000 0.00 0.00 34.26 3.51
251 257 3.955101 TTTCCACCAAACGCGCCG 61.955 61.111 5.73 0.00 0.00 6.46
287 294 1.153249 GGTTATGCAGCGGCTGGTA 60.153 57.895 29.44 11.73 41.91 3.25
290 297 1.798813 GTTATGCAGCGGCTGGTATAC 59.201 52.381 29.44 14.00 41.91 1.47
341 350 0.389426 ATGACGGGTAACACGCTGAC 60.389 55.000 0.00 0.00 39.74 3.51
357 366 0.032130 TGACGGAGCACAGAGTTGTC 59.968 55.000 0.00 0.00 34.62 3.18
387 396 7.715265 ACGCCAGATATCTAAATGTAACAAG 57.285 36.000 4.54 0.00 0.00 3.16
450 545 3.444703 AGGAGATGAATCGGAAAGACG 57.555 47.619 0.00 0.00 0.00 4.18
461 556 1.737008 GAAAGACGCGTCCTCACCC 60.737 63.158 34.08 14.59 0.00 4.61
515 610 4.418401 GATGCCGGCGCTTGCAAA 62.418 61.111 23.90 0.49 41.50 3.68
541 644 4.885426 ACTGCAGGTGACACAAGG 57.115 55.556 19.93 0.00 0.00 3.61
542 645 1.526917 ACTGCAGGTGACACAAGGC 60.527 57.895 19.93 8.05 0.00 4.35
555 658 1.283793 CAAGGCGGCACAAGTCAAG 59.716 57.895 13.08 0.00 0.00 3.02
562 665 0.031178 GGCACAAGTCAAGCAAGGTG 59.969 55.000 0.00 0.00 0.00 4.00
601 707 2.197605 TCGAACAGGTCAGGTGCGA 61.198 57.895 0.00 0.00 43.70 5.10
610 716 3.818787 CAGGTGCGAGCCCAATGC 61.819 66.667 0.00 0.00 41.71 3.56
624 734 1.535226 CCAATGCCATGCACAGATTCG 60.535 52.381 0.00 0.00 43.04 3.34
627 737 3.113745 CCATGCACAGATTCGCCC 58.886 61.111 0.00 0.00 0.00 6.13
629 739 1.430632 CATGCACAGATTCGCCCAC 59.569 57.895 0.00 0.00 0.00 4.61
630 740 1.750399 ATGCACAGATTCGCCCACC 60.750 57.895 0.00 0.00 0.00 4.61
631 741 2.359850 GCACAGATTCGCCCACCA 60.360 61.111 0.00 0.00 0.00 4.17
632 742 1.971167 GCACAGATTCGCCCACCAA 60.971 57.895 0.00 0.00 0.00 3.67
633 743 1.523154 GCACAGATTCGCCCACCAAA 61.523 55.000 0.00 0.00 0.00 3.28
634 744 0.523072 CACAGATTCGCCCACCAAAG 59.477 55.000 0.00 0.00 0.00 2.77
635 745 1.244019 ACAGATTCGCCCACCAAAGC 61.244 55.000 0.00 0.00 0.00 3.51
636 746 0.962356 CAGATTCGCCCACCAAAGCT 60.962 55.000 0.00 0.00 0.00 3.74
637 747 0.678048 AGATTCGCCCACCAAAGCTC 60.678 55.000 0.00 0.00 0.00 4.09
638 748 0.960364 GATTCGCCCACCAAAGCTCA 60.960 55.000 0.00 0.00 0.00 4.26
639 749 0.323725 ATTCGCCCACCAAAGCTCAT 60.324 50.000 0.00 0.00 0.00 2.90
672 793 2.046292 TGAGACACTCACAATGGTGGA 58.954 47.619 0.00 0.00 45.32 4.02
676 797 2.037772 GACACTCACAATGGTGGAGTCT 59.962 50.000 0.00 0.00 45.32 3.24
690 812 3.423154 GTCTGCGCGGTTCCCTTG 61.423 66.667 17.37 0.00 0.00 3.61
695 817 2.677979 GCGCGGTTCCCTTGAGAAC 61.678 63.158 8.83 0.00 44.45 3.01
699 821 1.270893 GCGGTTCCCTTGAGAACTCTT 60.271 52.381 4.58 0.00 44.56 2.85
756 888 4.408821 ATGAAGCCGGCCAGCGAA 62.409 61.111 26.15 3.19 38.01 4.70
765 897 2.498726 GCCAGCGAAGGAGGAGAG 59.501 66.667 0.00 0.00 0.00 3.20
766 898 2.498726 CCAGCGAAGGAGGAGAGC 59.501 66.667 0.00 0.00 0.00 4.09
773 919 1.734388 GAAGGAGGAGAGCGAGAGGC 61.734 65.000 0.00 0.00 44.05 4.70
786 932 1.025812 GAGAGGCTTCTCGATCGGAA 58.974 55.000 16.41 15.69 40.43 4.30
787 933 1.405821 GAGAGGCTTCTCGATCGGAAA 59.594 52.381 16.41 8.95 40.43 3.13
790 936 0.530870 GGCTTCTCGATCGGAAAGGG 60.531 60.000 22.96 12.74 0.00 3.95
791 937 0.530870 GCTTCTCGATCGGAAAGGGG 60.531 60.000 22.96 12.49 0.00 4.79
793 939 1.968050 TTCTCGATCGGAAAGGGGGC 61.968 60.000 16.41 0.00 0.00 5.80
794 940 2.365105 TCGATCGGAAAGGGGGCT 60.365 61.111 16.41 0.00 0.00 5.19
795 941 1.075822 TCGATCGGAAAGGGGGCTA 60.076 57.895 16.41 0.00 0.00 3.93
797 943 0.532196 CGATCGGAAAGGGGGCTAAC 60.532 60.000 7.38 0.00 0.00 2.34
798 944 0.544697 GATCGGAAAGGGGGCTAACA 59.455 55.000 0.00 0.00 0.00 2.41
799 945 0.996583 ATCGGAAAGGGGGCTAACAA 59.003 50.000 0.00 0.00 0.00 2.83
800 946 0.772384 TCGGAAAGGGGGCTAACAAA 59.228 50.000 0.00 0.00 0.00 2.83
801 947 1.145325 TCGGAAAGGGGGCTAACAAAA 59.855 47.619 0.00 0.00 0.00 2.44
805 951 1.951209 AAGGGGGCTAACAAAATGGG 58.049 50.000 0.00 0.00 0.00 4.00
808 954 0.536724 GGGGCTAACAAAATGGGCTG 59.463 55.000 0.00 0.00 0.00 4.85
809 955 0.536724 GGGCTAACAAAATGGGCTGG 59.463 55.000 0.00 0.00 0.00 4.85
810 956 0.536724 GGCTAACAAAATGGGCTGGG 59.463 55.000 0.00 0.00 0.00 4.45
811 957 0.108186 GCTAACAAAATGGGCTGGGC 60.108 55.000 0.00 0.00 0.00 5.36
812 958 1.560505 CTAACAAAATGGGCTGGGCT 58.439 50.000 0.00 0.00 0.00 5.19
825 971 2.440539 CTGGGCTAGCTAATGGTACG 57.559 55.000 15.72 0.00 0.00 3.67
827 973 1.684983 TGGGCTAGCTAATGGTACGTC 59.315 52.381 15.72 0.00 0.00 4.34
828 974 1.000618 GGGCTAGCTAATGGTACGTCC 59.999 57.143 15.72 0.00 0.00 4.79
829 975 1.335689 GGCTAGCTAATGGTACGTCCG 60.336 57.143 15.72 0.00 39.52 4.79
830 976 1.605710 GCTAGCTAATGGTACGTCCGA 59.394 52.381 7.70 0.00 39.52 4.55
831 977 2.033801 GCTAGCTAATGGTACGTCCGAA 59.966 50.000 7.70 0.00 39.52 4.30
832 978 2.573941 AGCTAATGGTACGTCCGAAC 57.426 50.000 0.00 0.00 39.52 3.95
842 988 3.961729 GTCCGAACGACCTTTGGG 58.038 61.111 0.00 0.00 34.33 4.12
844 990 2.281208 CCGAACGACCTTTGGGCA 60.281 61.111 0.00 0.00 35.63 5.36
845 991 1.894756 CCGAACGACCTTTGGGCAA 60.895 57.895 0.00 0.00 35.63 4.52
852 1006 1.152052 ACCTTTGGGCAATTGGGCT 60.152 52.632 7.72 0.00 42.84 5.19
895 1055 1.071567 GCGTAAGGTGCAGTCTCGTC 61.072 60.000 0.00 0.00 38.28 4.20
897 1057 1.466024 CGTAAGGTGCAGTCTCGTCTC 60.466 57.143 0.00 0.00 0.00 3.36
899 1059 0.315568 AAGGTGCAGTCTCGTCTCAC 59.684 55.000 0.00 0.00 0.00 3.51
901 1061 0.244994 GGTGCAGTCTCGTCTCACAT 59.755 55.000 0.00 0.00 0.00 3.21
902 1062 1.472878 GGTGCAGTCTCGTCTCACATA 59.527 52.381 0.00 0.00 0.00 2.29
903 1063 2.099921 GGTGCAGTCTCGTCTCACATAT 59.900 50.000 0.00 0.00 0.00 1.78
904 1064 3.315470 GGTGCAGTCTCGTCTCACATATA 59.685 47.826 0.00 0.00 0.00 0.86
905 1065 4.202020 GGTGCAGTCTCGTCTCACATATAA 60.202 45.833 0.00 0.00 0.00 0.98
906 1066 5.508153 GGTGCAGTCTCGTCTCACATATAAT 60.508 44.000 0.00 0.00 0.00 1.28
907 1067 6.294010 GGTGCAGTCTCGTCTCACATATAATA 60.294 42.308 0.00 0.00 0.00 0.98
908 1068 7.139392 GTGCAGTCTCGTCTCACATATAATAA 58.861 38.462 0.00 0.00 0.00 1.40
909 1069 7.324856 GTGCAGTCTCGTCTCACATATAATAAG 59.675 40.741 0.00 0.00 0.00 1.73
910 1070 6.804295 GCAGTCTCGTCTCACATATAATAAGG 59.196 42.308 0.00 0.00 0.00 2.69
911 1071 7.522399 GCAGTCTCGTCTCACATATAATAAGGT 60.522 40.741 0.00 0.00 0.00 3.50
912 1072 8.018520 CAGTCTCGTCTCACATATAATAAGGTC 58.981 40.741 0.00 0.00 0.00 3.85
913 1073 7.940137 AGTCTCGTCTCACATATAATAAGGTCT 59.060 37.037 0.00 0.00 0.00 3.85
914 1074 8.231837 GTCTCGTCTCACATATAATAAGGTCTC 58.768 40.741 0.00 0.00 0.00 3.36
915 1075 7.117956 TCTCGTCTCACATATAATAAGGTCTCG 59.882 40.741 0.00 0.00 0.00 4.04
916 1076 5.795939 CGTCTCACATATAATAAGGTCTCGC 59.204 44.000 0.00 0.00 0.00 5.03
917 1077 6.567891 CGTCTCACATATAATAAGGTCTCGCA 60.568 42.308 0.00 0.00 0.00 5.10
948 1108 2.517402 CCTCCCGTCCTCCTCTCG 60.517 72.222 0.00 0.00 0.00 4.04
956 1116 1.399089 CGTCCTCCTCTCGTCTTTCTC 59.601 57.143 0.00 0.00 0.00 2.87
967 1127 4.394712 CTTTCTCCCGCCGCCACT 62.395 66.667 0.00 0.00 0.00 4.00
985 1145 1.302671 TCCAAACCCTAAACCGCCG 60.303 57.895 0.00 0.00 0.00 6.46
986 1146 2.564458 CAAACCCTAAACCGCCGC 59.436 61.111 0.00 0.00 0.00 6.53
987 1147 2.674033 AAACCCTAAACCGCCGCC 60.674 61.111 0.00 0.00 0.00 6.13
988 1148 3.494736 AAACCCTAAACCGCCGCCA 62.495 57.895 0.00 0.00 0.00 5.69
989 1149 4.710167 ACCCTAAACCGCCGCCAC 62.710 66.667 0.00 0.00 0.00 5.01
990 1150 4.708386 CCCTAAACCGCCGCCACA 62.708 66.667 0.00 0.00 0.00 4.17
1101 1270 1.746615 CCTCACCAAGTGGATGCGG 60.747 63.158 3.83 0.00 38.94 5.69
1215 1384 4.954970 ACCACCAAGCCGCACCTG 62.955 66.667 0.00 0.00 0.00 4.00
1793 1965 1.135721 GTTGGGCATGAAGATTGAGGC 59.864 52.381 0.00 0.00 0.00 4.70
1892 2064 3.416156 GCAAGGACAAGAAGATGAAGGT 58.584 45.455 0.00 0.00 0.00 3.50
2025 2212 1.203199 AGGAGGAAGAAGGAGTCGGTT 60.203 52.381 0.00 0.00 0.00 4.44
2064 2251 2.512056 TGAAGACCTGAAGACCCCAAAA 59.488 45.455 0.00 0.00 0.00 2.44
2105 2292 0.038166 GCATTGGACAAGGAGGTGGA 59.962 55.000 0.35 0.00 0.00 4.02
2106 2293 1.952367 GCATTGGACAAGGAGGTGGAG 60.952 57.143 0.35 0.00 0.00 3.86
2107 2294 0.995024 ATTGGACAAGGAGGTGGAGG 59.005 55.000 0.00 0.00 0.00 4.30
2150 2337 3.511477 AGAAGGGTAAGAAGAGTGAGCA 58.489 45.455 0.00 0.00 0.00 4.26
2153 2340 2.093235 AGGGTAAGAAGAGTGAGCATGC 60.093 50.000 10.51 10.51 0.00 4.06
2157 2344 1.937278 AGAAGAGTGAGCATGCATCG 58.063 50.000 21.98 0.00 0.00 3.84
2186 2373 3.317993 GCCAGCAACAAGAAAAGTAAGGA 59.682 43.478 0.00 0.00 0.00 3.36
2200 2402 0.476338 TAAGGACAAGCAAGCACCCA 59.524 50.000 0.00 0.00 0.00 4.51
2235 2437 5.336690 GGATGTTGGCAGCAAGAAGAATAAA 60.337 40.000 8.44 0.00 31.62 1.40
2254 2480 3.712016 AAGGGAAGAAGAAGAAGAGCC 57.288 47.619 0.00 0.00 0.00 4.70
2366 2592 2.171003 GGGGAAGAAATCAAGTGGTGG 58.829 52.381 0.00 0.00 0.00 4.61
2400 2627 1.077429 CAGGGCAAGGGTCTAAGGC 60.077 63.158 0.00 0.00 0.00 4.35
2405 2632 1.134371 GGCAAGGGTCTAAGGCTGTAG 60.134 57.143 0.00 0.00 0.00 2.74
2476 2703 0.807496 GAGACCAAGCTGCATGTTCC 59.193 55.000 1.02 0.00 0.00 3.62
2499 2726 7.513856 TCCATGCATAGTTAAGCTGGTTAATA 58.486 34.615 14.33 8.84 33.11 0.98
2562 2814 4.445453 TGCACTTGAGATTATACTGCTGG 58.555 43.478 0.00 0.00 0.00 4.85
2579 2831 2.433994 GGGTGTAATACGGGGGCGA 61.434 63.158 0.00 0.00 0.00 5.54
2595 2847 0.464554 GCGAGGGGGAATTTCTGGAG 60.465 60.000 0.00 0.00 0.00 3.86
2621 2873 8.874816 GGTAGTTTCTTCAGATTTTAGTAGCTG 58.125 37.037 0.00 0.00 0.00 4.24
2631 2896 7.719633 TCAGATTTTAGTAGCTGAAACCTTTGT 59.280 33.333 0.00 0.00 34.71 2.83
2716 2982 3.777465 TTGTGCGAGTCTGATACTACC 57.223 47.619 0.00 0.00 39.07 3.18
2719 2985 3.699538 TGTGCGAGTCTGATACTACCATT 59.300 43.478 0.00 0.00 39.07 3.16
2723 2989 4.202020 GCGAGTCTGATACTACCATTCACA 60.202 45.833 0.00 0.00 39.07 3.58
2751 3017 4.265073 GTCTGTCTTCAATAATGCACCCT 58.735 43.478 0.00 0.00 0.00 4.34
2810 3101 5.809562 GGTACTCATCTTTGACAGTCATCTG 59.190 44.000 3.45 0.40 46.18 2.90
2811 3102 4.829968 ACTCATCTTTGACAGTCATCTGG 58.170 43.478 3.45 0.00 45.14 3.86
2812 3103 4.529769 ACTCATCTTTGACAGTCATCTGGA 59.470 41.667 3.45 1.33 45.14 3.86
2837 3128 7.795047 ACTATTACATGATCCAACATCTGTGA 58.205 34.615 0.00 0.00 0.00 3.58
2838 3129 6.932356 ATTACATGATCCAACATCTGTGAC 57.068 37.500 0.00 0.00 0.00 3.67
2839 3130 4.290711 ACATGATCCAACATCTGTGACA 57.709 40.909 0.00 0.00 0.00 3.58
2840 3131 4.259356 ACATGATCCAACATCTGTGACAG 58.741 43.478 6.18 6.18 0.00 3.51
2841 3132 4.259356 CATGATCCAACATCTGTGACAGT 58.741 43.478 12.93 0.00 32.61 3.55
2842 3133 3.930336 TGATCCAACATCTGTGACAGTC 58.070 45.455 12.93 0.62 32.61 3.51
2843 3134 3.324556 TGATCCAACATCTGTGACAGTCA 59.675 43.478 12.93 0.00 32.61 3.41
2844 3135 3.391506 TCCAACATCTGTGACAGTCAG 57.608 47.619 12.93 6.34 32.61 3.51
2845 3136 1.802960 CCAACATCTGTGACAGTCAGC 59.197 52.381 12.93 0.00 32.61 4.26
2846 3137 2.486918 CAACATCTGTGACAGTCAGCA 58.513 47.619 12.93 4.69 32.61 4.41
2847 3138 2.452295 ACATCTGTGACAGTCAGCAG 57.548 50.000 12.93 19.38 32.61 4.24
2848 3139 1.001746 ACATCTGTGACAGTCAGCAGG 59.998 52.381 22.53 14.84 31.26 4.85
2849 3140 1.001746 CATCTGTGACAGTCAGCAGGT 59.998 52.381 22.53 17.33 31.26 4.00
2850 3141 1.995376 TCTGTGACAGTCAGCAGGTA 58.005 50.000 22.53 9.97 31.26 3.08
2851 3142 2.529632 TCTGTGACAGTCAGCAGGTAT 58.470 47.619 22.53 0.00 31.26 2.73
2852 3143 3.697166 TCTGTGACAGTCAGCAGGTATA 58.303 45.455 22.53 9.23 31.26 1.47
2853 3144 3.696548 TCTGTGACAGTCAGCAGGTATAG 59.303 47.826 22.53 3.75 31.26 1.31
2854 3145 3.696548 CTGTGACAGTCAGCAGGTATAGA 59.303 47.826 18.38 0.00 0.00 1.98
2877 3168 8.193953 AGAACCAAAGAATGATTTACCAACAT 57.806 30.769 0.00 0.00 0.00 2.71
2918 3209 8.243426 GTGCTTATCCAATTTGAATAACACAGA 58.757 33.333 12.03 0.00 0.00 3.41
2945 3236 7.364522 TCATGCTTTCATATCTAATTACGGC 57.635 36.000 0.00 0.00 0.00 5.68
2968 3259 5.291858 GCGATCAATCACTTGTGACTTGATA 59.708 40.000 24.07 11.51 36.85 2.15
2969 3260 6.018425 GCGATCAATCACTTGTGACTTGATAT 60.018 38.462 24.07 14.59 36.85 1.63
2971 3262 9.201127 CGATCAATCACTTGTGACTTGATATAT 57.799 33.333 24.07 13.97 36.85 0.86
2986 3277 6.540189 ACTTGATATATTGTGTGCTGGACTTC 59.460 38.462 0.00 0.00 0.00 3.01
2993 3284 2.840038 TGTGTGCTGGACTTCCATATCT 59.160 45.455 0.00 0.00 46.46 1.98
3181 3472 9.277783 CTTTTTCATTGGTATATACTCCCTCTG 57.722 37.037 12.54 3.35 0.00 3.35
3222 3513 7.224949 AGCGTTTAGATCCTAACTTTTAGATGC 59.775 37.037 6.13 0.00 0.00 3.91
3322 3613 8.470040 TGCATTTTCATCTTAATTGCTTCTTC 57.530 30.769 0.00 0.00 34.59 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.634940 TCTTGCTTGCCTGAAGTCTACT 59.365 45.455 0.00 0.00 33.73 2.57
287 294 9.067986 TCACTAACTTGACATCATAGATCGTAT 57.932 33.333 0.00 0.00 0.00 3.06
290 297 7.328005 CCATCACTAACTTGACATCATAGATCG 59.672 40.741 0.00 0.00 0.00 3.69
341 350 1.734477 CCGACAACTCTGTGCTCCG 60.734 63.158 0.00 0.00 35.30 4.63
387 396 4.720649 TGTAGTAGGTTCATGCTCACTC 57.279 45.455 0.00 0.00 0.00 3.51
461 556 0.109597 GTGCTTGGGAAATGAGTGCG 60.110 55.000 0.00 0.00 0.00 5.34
515 610 1.825191 CACCTGCAGTGTTGGTGCT 60.825 57.895 13.81 0.00 43.61 4.40
540 643 2.737932 CTTGCTTGACTTGTGCCGCC 62.738 60.000 0.00 0.00 0.00 6.13
541 644 1.370900 CTTGCTTGACTTGTGCCGC 60.371 57.895 0.00 0.00 0.00 6.53
542 645 1.283793 CCTTGCTTGACTTGTGCCG 59.716 57.895 0.00 0.00 0.00 5.69
555 658 0.179145 GCATGATGTCTGCACCTTGC 60.179 55.000 0.00 0.00 45.29 4.01
562 665 1.202211 TGAAATGCGCATGATGTCTGC 60.202 47.619 26.09 6.04 36.26 4.26
565 668 2.032636 TCGATGAAATGCGCATGATGTC 60.033 45.455 26.09 18.42 0.00 3.06
566 669 1.941975 TCGATGAAATGCGCATGATGT 59.058 42.857 26.09 11.03 0.00 3.06
567 670 2.673976 TCGATGAAATGCGCATGATG 57.326 45.000 26.09 11.00 0.00 3.07
568 671 2.355444 TGTTCGATGAAATGCGCATGAT 59.645 40.909 26.09 16.50 0.00 2.45
569 672 1.736681 TGTTCGATGAAATGCGCATGA 59.263 42.857 26.09 12.90 0.00 3.07
571 674 1.064505 CCTGTTCGATGAAATGCGCAT 59.935 47.619 19.28 19.28 0.00 4.73
572 675 0.447406 CCTGTTCGATGAAATGCGCA 59.553 50.000 14.96 14.96 0.00 6.09
573 676 0.447801 ACCTGTTCGATGAAATGCGC 59.552 50.000 0.00 0.00 0.00 6.09
601 707 2.284039 TGTGCATGGCATTGGGCT 60.284 55.556 0.00 0.00 41.91 5.19
610 716 1.750018 TGGGCGAATCTGTGCATGG 60.750 57.895 0.00 0.00 0.00 3.66
624 734 1.885871 GTCATGAGCTTTGGTGGGC 59.114 57.895 0.00 0.00 0.00 5.36
627 737 1.236616 TGGCGTCATGAGCTTTGGTG 61.237 55.000 14.20 0.00 34.52 4.17
629 739 1.651240 CCTGGCGTCATGAGCTTTGG 61.651 60.000 14.20 10.78 34.52 3.28
630 740 0.674581 TCCTGGCGTCATGAGCTTTG 60.675 55.000 14.20 0.00 34.52 2.77
631 741 0.392193 CTCCTGGCGTCATGAGCTTT 60.392 55.000 9.40 0.00 30.95 3.51
632 742 1.220206 CTCCTGGCGTCATGAGCTT 59.780 57.895 9.40 0.00 30.95 3.74
633 743 1.047596 ATCTCCTGGCGTCATGAGCT 61.048 55.000 16.42 5.17 36.16 4.09
634 744 0.879400 CATCTCCTGGCGTCATGAGC 60.879 60.000 16.42 1.82 36.16 4.26
635 745 0.749049 TCATCTCCTGGCGTCATGAG 59.251 55.000 15.27 15.27 37.11 2.90
636 746 0.749049 CTCATCTCCTGGCGTCATGA 59.251 55.000 0.00 0.00 0.00 3.07
637 747 0.749049 TCTCATCTCCTGGCGTCATG 59.251 55.000 0.00 0.00 0.00 3.07
638 748 0.749649 GTCTCATCTCCTGGCGTCAT 59.250 55.000 0.00 0.00 0.00 3.06
639 749 0.611896 TGTCTCATCTCCTGGCGTCA 60.612 55.000 0.00 0.00 0.00 4.35
652 766 2.037641 CTCCACCATTGTGAGTGTCTCA 59.962 50.000 0.00 0.00 45.76 3.27
690 812 0.456995 CTCCGGCGTGAAGAGTTCTC 60.457 60.000 6.01 0.00 0.00 2.87
728 860 2.974698 GCTTCATCCATCCGCCCG 60.975 66.667 0.00 0.00 0.00 6.13
729 861 2.595754 GGCTTCATCCATCCGCCC 60.596 66.667 0.00 0.00 34.75 6.13
730 862 2.974698 CGGCTTCATCCATCCGCC 60.975 66.667 0.00 0.00 35.20 6.13
731 863 2.974698 CCGGCTTCATCCATCCGC 60.975 66.667 0.00 0.00 40.49 5.54
732 864 2.974698 GCCGGCTTCATCCATCCG 60.975 66.667 22.15 0.00 41.41 4.18
733 865 2.595754 GGCCGGCTTCATCCATCC 60.596 66.667 28.56 0.41 0.00 3.51
734 866 1.895707 CTGGCCGGCTTCATCCATC 60.896 63.158 28.56 6.48 0.00 3.51
735 867 2.194056 CTGGCCGGCTTCATCCAT 59.806 61.111 28.56 0.00 0.00 3.41
736 868 4.802051 GCTGGCCGGCTTCATCCA 62.802 66.667 30.01 13.75 0.00 3.41
756 888 2.123897 GCCTCTCGCTCTCCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
773 919 0.105039 CCCCCTTTCCGATCGAGAAG 59.895 60.000 18.66 18.21 0.00 2.85
774 920 1.968050 GCCCCCTTTCCGATCGAGAA 61.968 60.000 18.66 15.19 0.00 2.87
775 921 2.432300 GCCCCCTTTCCGATCGAGA 61.432 63.158 18.66 9.51 0.00 4.04
777 923 0.688418 TTAGCCCCCTTTCCGATCGA 60.688 55.000 18.66 0.00 0.00 3.59
778 924 0.532196 GTTAGCCCCCTTTCCGATCG 60.532 60.000 8.51 8.51 0.00 3.69
779 925 0.544697 TGTTAGCCCCCTTTCCGATC 59.455 55.000 0.00 0.00 0.00 3.69
780 926 0.996583 TTGTTAGCCCCCTTTCCGAT 59.003 50.000 0.00 0.00 0.00 4.18
782 928 1.623163 TTTTGTTAGCCCCCTTTCCG 58.377 50.000 0.00 0.00 0.00 4.30
786 932 1.951209 CCCATTTTGTTAGCCCCCTT 58.049 50.000 0.00 0.00 0.00 3.95
787 933 0.617535 GCCCATTTTGTTAGCCCCCT 60.618 55.000 0.00 0.00 0.00 4.79
790 936 0.536724 CCAGCCCATTTTGTTAGCCC 59.463 55.000 0.00 0.00 0.00 5.19
791 937 0.536724 CCCAGCCCATTTTGTTAGCC 59.463 55.000 0.00 0.00 0.00 3.93
793 939 1.560505 AGCCCAGCCCATTTTGTTAG 58.439 50.000 0.00 0.00 0.00 2.34
794 940 2.733956 CTAGCCCAGCCCATTTTGTTA 58.266 47.619 0.00 0.00 0.00 2.41
795 941 1.560505 CTAGCCCAGCCCATTTTGTT 58.439 50.000 0.00 0.00 0.00 2.83
797 943 1.818555 GCTAGCCCAGCCCATTTTG 59.181 57.895 2.29 0.00 45.23 2.44
798 944 4.362479 GCTAGCCCAGCCCATTTT 57.638 55.556 2.29 0.00 45.23 1.82
808 954 1.000618 GGACGTACCATTAGCTAGCCC 59.999 57.143 12.13 0.00 38.79 5.19
809 955 1.335689 CGGACGTACCATTAGCTAGCC 60.336 57.143 12.13 0.00 38.90 3.93
810 956 1.605710 TCGGACGTACCATTAGCTAGC 59.394 52.381 6.62 6.62 38.90 3.42
811 957 3.625938 GTTCGGACGTACCATTAGCTAG 58.374 50.000 0.00 0.00 38.90 3.42
812 958 2.032054 CGTTCGGACGTACCATTAGCTA 59.968 50.000 8.45 0.00 44.08 3.32
825 971 2.322830 GCCCAAAGGTCGTTCGGAC 61.323 63.158 0.00 0.00 45.31 4.79
827 973 1.241315 ATTGCCCAAAGGTCGTTCGG 61.241 55.000 0.00 0.00 34.57 4.30
828 974 0.596082 AATTGCCCAAAGGTCGTTCG 59.404 50.000 0.00 0.00 34.57 3.95
829 975 1.336795 CCAATTGCCCAAAGGTCGTTC 60.337 52.381 0.00 0.00 34.57 3.95
830 976 0.678950 CCAATTGCCCAAAGGTCGTT 59.321 50.000 0.00 0.00 34.57 3.85
831 977 1.184970 CCCAATTGCCCAAAGGTCGT 61.185 55.000 0.00 0.00 34.57 4.34
832 978 1.591183 CCCAATTGCCCAAAGGTCG 59.409 57.895 0.00 0.00 34.57 4.79
834 980 1.152052 AGCCCAATTGCCCAAAGGT 60.152 52.632 0.00 0.00 34.57 3.50
835 981 1.297364 CAGCCCAATTGCCCAAAGG 59.703 57.895 0.00 0.00 0.00 3.11
836 982 1.297364 CCAGCCCAATTGCCCAAAG 59.703 57.895 0.00 0.00 0.00 2.77
837 983 2.222727 CCCAGCCCAATTGCCCAAA 61.223 57.895 0.00 0.00 0.00 3.28
866 1020 3.861797 CCTTACGCGGCCCATCCT 61.862 66.667 12.47 0.00 0.00 3.24
887 1047 7.940137 AGACCTTATTATATGTGAGACGAGACT 59.060 37.037 0.00 0.00 0.00 3.24
895 1055 6.470556 CGATGCGAGACCTTATTATATGTGAG 59.529 42.308 0.00 0.00 0.00 3.51
897 1057 5.004821 GCGATGCGAGACCTTATTATATGTG 59.995 44.000 0.00 0.00 0.00 3.21
899 1059 5.102313 TGCGATGCGAGACCTTATTATATG 58.898 41.667 0.00 0.00 0.00 1.78
901 1061 4.733850 CTGCGATGCGAGACCTTATTATA 58.266 43.478 0.00 0.00 0.00 0.98
902 1062 3.579709 CTGCGATGCGAGACCTTATTAT 58.420 45.455 0.00 0.00 0.00 1.28
903 1063 2.862530 GCTGCGATGCGAGACCTTATTA 60.863 50.000 0.00 0.00 0.00 0.98
904 1064 1.858091 CTGCGATGCGAGACCTTATT 58.142 50.000 0.00 0.00 0.00 1.40
905 1065 0.598680 GCTGCGATGCGAGACCTTAT 60.599 55.000 0.00 0.00 0.00 1.73
906 1066 1.226974 GCTGCGATGCGAGACCTTA 60.227 57.895 0.00 0.00 0.00 2.69
907 1067 2.510238 GCTGCGATGCGAGACCTT 60.510 61.111 0.00 0.00 0.00 3.50
908 1068 4.521062 GGCTGCGATGCGAGACCT 62.521 66.667 0.00 0.00 0.00 3.85
937 1097 1.746787 GGAGAAAGACGAGAGGAGGAC 59.253 57.143 0.00 0.00 0.00 3.85
939 1099 1.107945 GGGAGAAAGACGAGAGGAGG 58.892 60.000 0.00 0.00 0.00 4.30
948 1108 4.388499 TGGCGGCGGGAGAAAGAC 62.388 66.667 9.78 0.00 0.00 3.01
967 1127 1.302671 CGGCGGTTTAGGGTTTGGA 60.303 57.895 0.00 0.00 0.00 3.53
987 1147 3.807538 GACATGGCAGCGGCTGTG 61.808 66.667 28.88 21.61 40.87 3.66
1710 1882 1.683011 GCCTTCAAATGCAGAGCCCTA 60.683 52.381 0.00 0.00 0.00 3.53
1793 1965 4.383602 CCAAACGCGCAACCGGAG 62.384 66.667 9.46 0.15 34.32 4.63
1806 1978 1.691196 CACCAACTCCTGCTTCCAAA 58.309 50.000 0.00 0.00 0.00 3.28
1892 2064 1.546923 CACCATTGGCATCTTTCAGCA 59.453 47.619 1.54 0.00 0.00 4.41
2064 2251 2.290960 ACGCTTCTTATCCTTGCCCTTT 60.291 45.455 0.00 0.00 0.00 3.11
2105 2292 1.276859 TGCAGGACTGGCATCATCCT 61.277 55.000 8.81 8.81 43.95 3.24
2106 2293 0.818445 CTGCAGGACTGGCATCATCC 60.818 60.000 5.57 4.79 41.06 3.51
2107 2294 0.179702 TCTGCAGGACTGGCATCATC 59.820 55.000 15.13 0.00 41.06 2.92
2150 2337 1.099879 GCTGGCTTCCTTCGATGCAT 61.100 55.000 0.00 0.00 40.16 3.96
2153 2340 0.449388 GTTGCTGGCTTCCTTCGATG 59.551 55.000 0.00 0.00 0.00 3.84
2157 2344 1.609208 TCTTGTTGCTGGCTTCCTTC 58.391 50.000 0.00 0.00 0.00 3.46
2186 2373 0.825010 CTCCTTGGGTGCTTGCTTGT 60.825 55.000 0.00 0.00 0.00 3.16
2200 2402 0.995024 CCAACATCCTCCACCTCCTT 59.005 55.000 0.00 0.00 0.00 3.36
2235 2437 2.571202 CAGGCTCTTCTTCTTCTTCCCT 59.429 50.000 0.00 0.00 0.00 4.20
2254 2480 4.135306 CCATCATCAGAATCACCCTTCAG 58.865 47.826 0.00 0.00 0.00 3.02
2366 2592 3.389329 TGCCCTGGATCTCTTCATCTTAC 59.611 47.826 0.00 0.00 0.00 2.34
2400 2627 7.083875 TCAACTTCAGGAAAAACAACTACAG 57.916 36.000 0.00 0.00 0.00 2.74
2405 2632 5.351458 AGCATCAACTTCAGGAAAAACAAC 58.649 37.500 0.00 0.00 0.00 3.32
2476 2703 9.002600 TCATATTAACCAGCTTAACTATGCATG 57.997 33.333 10.16 1.82 0.00 4.06
2485 2712 9.256477 CGACAGTAATCATATTAACCAGCTTAA 57.744 33.333 0.00 0.00 0.00 1.85
2499 2726 5.752472 CAGAAGCAGATTCGACAGTAATCAT 59.248 40.000 0.00 0.00 43.16 2.45
2562 2814 1.068585 CTCGCCCCCGTATTACACC 59.931 63.158 0.00 0.00 35.54 4.16
2579 2831 2.226170 ACTACCTCCAGAAATTCCCCCT 60.226 50.000 0.00 0.00 0.00 4.79
2595 2847 8.874816 CAGCTACTAAAATCTGAAGAAACTACC 58.125 37.037 0.00 0.00 0.00 3.18
2631 2896 7.648039 AAACAGTTCCACATAACTTTTACCA 57.352 32.000 0.00 0.00 37.61 3.25
2716 2982 4.516321 TGAAGACAGACCAACATGTGAATG 59.484 41.667 0.00 0.00 0.00 2.67
2719 2985 3.836365 TGAAGACAGACCAACATGTGA 57.164 42.857 0.00 0.00 0.00 3.58
2723 2989 5.711506 TGCATTATTGAAGACAGACCAACAT 59.288 36.000 0.00 0.00 0.00 2.71
2766 3032 5.579753 ACCTGCTATCCAGAATCATCAAT 57.420 39.130 0.00 0.00 44.64 2.57
2810 3101 7.172190 CACAGATGTTGGATCATGTAATAGTCC 59.828 40.741 0.00 0.00 31.66 3.85
2811 3102 7.928167 TCACAGATGTTGGATCATGTAATAGTC 59.072 37.037 0.00 0.00 0.00 2.59
2812 3103 7.712639 GTCACAGATGTTGGATCATGTAATAGT 59.287 37.037 0.00 0.00 0.00 2.12
2813 3104 7.712205 TGTCACAGATGTTGGATCATGTAATAG 59.288 37.037 0.00 0.00 0.00 1.73
2819 3110 4.259356 ACTGTCACAGATGTTGGATCATG 58.741 43.478 13.14 0.00 35.18 3.07
2850 3141 9.308000 TGTTGGTAAATCATTCTTTGGTTCTAT 57.692 29.630 0.00 0.00 0.00 1.98
2851 3142 8.698973 TGTTGGTAAATCATTCTTTGGTTCTA 57.301 30.769 0.00 0.00 0.00 2.10
2852 3143 7.595819 TGTTGGTAAATCATTCTTTGGTTCT 57.404 32.000 0.00 0.00 0.00 3.01
2853 3144 8.831715 AATGTTGGTAAATCATTCTTTGGTTC 57.168 30.769 0.00 0.00 0.00 3.62
2854 3145 9.625747 AAAATGTTGGTAAATCATTCTTTGGTT 57.374 25.926 0.00 0.00 32.39 3.67
2945 3236 5.791367 ATCAAGTCACAAGTGATTGATCG 57.209 39.130 21.57 6.67 40.04 3.69
2968 3259 3.719268 TGGAAGTCCAGCACACAATAT 57.281 42.857 0.00 0.00 42.01 1.28
2986 3277 4.780275 TTCATCGAGCAGAGAGATATGG 57.220 45.455 0.00 0.00 0.00 2.74
2993 3284 1.483827 AGGCATTTCATCGAGCAGAGA 59.516 47.619 0.00 0.00 0.00 3.10
3148 3439 9.284968 AGTATATACCAATGAAAAAGGAATCCG 57.715 33.333 9.32 0.00 0.00 4.18
3222 3513 8.926710 AGAGAACGCGGAAAATGAATATATAAG 58.073 33.333 12.47 0.00 0.00 1.73
3322 3613 4.590850 AAGGCTGCTTTAAAACTGAAGG 57.409 40.909 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.