Multiple sequence alignment - TraesCS6D01G202000

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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 TraesCS6D01G202000 chr6D 100.000 3054 0 0 1 3054 284848813 284851866 0.000000e+00 5640.0
1 TraesCS6D01G202000 chr6D 98.592 568 4 3 2301 2867 450099102 450099666 0.000000e+00 1002.0
2 TraesCS6D01G202000 chr6A 92.285 1698 62 33 643 2300 405166485 405168153 0.000000e+00 2346.0
3 TraesCS6D01G202000 chr6A 92.379 643 31 8 1 626 405165857 405166498 0.000000e+00 900.0
4 TraesCS6D01G202000 chr6A 97.143 35 1 0 2866 2900 405168164 405168198 3.290000e-05 60.2
5 TraesCS6D01G202000 chr6B 92.449 1629 67 16 643 2262 445851998 445853579 0.000000e+00 2276.0
6 TraesCS6D01G202000 chr6B 92.051 629 38 5 1 626 445851392 445852011 0.000000e+00 874.0
7 TraesCS6D01G202000 chr3D 99.091 550 5 0 2317 2866 466755976 466755427 0.000000e+00 989.0
8 TraesCS6D01G202000 chr3D 96.552 551 18 1 2317 2866 91803503 91802953 0.000000e+00 911.0
9 TraesCS6D01G202000 chr5D 98.370 552 8 1 2316 2866 58020845 58020294 0.000000e+00 968.0
10 TraesCS6D01G202000 chr5D 95.699 558 21 3 2310 2866 373567331 373566776 0.000000e+00 894.0
11 TraesCS6D01G202000 chr7D 96.739 552 17 1 2317 2867 608121971 608122522 0.000000e+00 918.0
12 TraesCS6D01G202000 chr2D 96.209 554 18 3 2317 2869 544881953 544881402 0.000000e+00 904.0
13 TraesCS6D01G202000 chr2D 96.196 552 20 1 2317 2867 612544014 612544565 0.000000e+00 902.0
14 TraesCS6D01G202000 chr1D 95.871 557 21 2 2312 2866 410455845 410455289 0.000000e+00 900.0
15 TraesCS6D01G202000 chr4A 98.171 164 3 0 2890 3053 501966163 501966326 1.390000e-73 287.0
16 TraesCS6D01G202000 chr7B 99.355 155 0 1 2897 3051 712632046 712631893 2.320000e-71 279.0
17 TraesCS6D01G202000 chr7B 90.132 152 15 0 2900 3051 704278882 704279033 6.680000e-47 198.0
18 TraesCS6D01G202000 chr5B 99.355 155 0 1 2901 3054 9618026 9618180 2.320000e-71 279.0
19 TraesCS6D01G202000 chr2B 100.000 151 0 0 2901 3051 400625424 400625574 2.320000e-71 279.0
20 TraesCS6D01G202000 chr2B 87.245 196 16 6 1763 1956 530307271 530307459 6.630000e-52 215.0
21 TraesCS6D01G202000 chr2B 90.066 151 15 0 2901 3051 685740977 685741127 2.400000e-46 196.0
22 TraesCS6D01G202000 chr7A 99.338 151 1 0 2901 3051 519850756 519850906 1.080000e-69 274.0
23 TraesCS6D01G202000 chr3B 98.693 153 2 0 2899 3051 378720119 378720271 3.880000e-69 272.0
24 TraesCS6D01G202000 chr2A 89.595 173 17 1 1782 1954 594581043 594581214 5.130000e-53 219.0
25 TraesCS6D01G202000 chr2A 90.066 151 15 0 2901 3051 175462418 175462268 2.400000e-46 196.0


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 TraesCS6D01G202000 chr6D 284848813 284851866 3053 False 5640.000000 5640 100.000000 1 3054 1 chr6D.!!$F1 3053
1 TraesCS6D01G202000 chr6D 450099102 450099666 564 False 1002.000000 1002 98.592000 2301 2867 1 chr6D.!!$F2 566
2 TraesCS6D01G202000 chr6A 405165857 405168198 2341 False 1102.066667 2346 93.935667 1 2900 3 chr6A.!!$F1 2899
3 TraesCS6D01G202000 chr6B 445851392 445853579 2187 False 1575.000000 2276 92.250000 1 2262 2 chr6B.!!$F1 2261
4 TraesCS6D01G202000 chr3D 466755427 466755976 549 True 989.000000 989 99.091000 2317 2866 1 chr3D.!!$R2 549
5 TraesCS6D01G202000 chr3D 91802953 91803503 550 True 911.000000 911 96.552000 2317 2866 1 chr3D.!!$R1 549
6 TraesCS6D01G202000 chr5D 58020294 58020845 551 True 968.000000 968 98.370000 2316 2866 1 chr5D.!!$R1 550
7 TraesCS6D01G202000 chr5D 373566776 373567331 555 True 894.000000 894 95.699000 2310 2866 1 chr5D.!!$R2 556
8 TraesCS6D01G202000 chr7D 608121971 608122522 551 False 918.000000 918 96.739000 2317 2867 1 chr7D.!!$F1 550
9 TraesCS6D01G202000 chr2D 544881402 544881953 551 True 904.000000 904 96.209000 2317 2869 1 chr2D.!!$R1 552
10 TraesCS6D01G202000 chr2D 612544014 612544565 551 False 902.000000 902 96.196000 2317 2867 1 chr2D.!!$F1 550
11 TraesCS6D01G202000 chr1D 410455289 410455845 556 True 900.000000 900 95.871000 2312 2866 1 chr1D.!!$R1 554

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
226 234 0.040794 AACTGGACCCGCCTACTACT 59.959 55.0 0.0 0.0 37.63 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2140 0.166814 GCGCCAAAACTACAGCAGAG 59.833 55.0 0.0 0.0 0.0 3.35 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
127 128 2.658707 GCACGACAGTCGGACTTGC 61.659 63.158 26.31 21.48 45.59 4.01
226 234 0.040794 AACTGGACCCGCCTACTACT 59.959 55.000 0.00 0.00 37.63 2.57
491 515 1.153469 TGTGCAGCTGACGTGAACA 60.153 52.632 20.43 8.19 30.44 3.18
526 550 0.512952 CGCCGACCTGAAACTGAAAG 59.487 55.000 0.00 0.00 42.29 2.62
553 577 2.888414 TGCCCAGAATCATATACGTCGA 59.112 45.455 0.00 0.00 0.00 4.20
606 630 2.159043 CGACTGAGGAATGGTATGCAGT 60.159 50.000 0.00 0.00 39.10 4.40
622 646 1.466558 GCAGTAAAGCAGGAGTGAAGC 59.533 52.381 0.00 0.00 0.00 3.86
623 647 2.771089 CAGTAAAGCAGGAGTGAAGCA 58.229 47.619 0.00 0.00 0.00 3.91
624 648 2.740981 CAGTAAAGCAGGAGTGAAGCAG 59.259 50.000 0.00 0.00 0.00 4.24
625 649 2.079925 GTAAAGCAGGAGTGAAGCAGG 58.920 52.381 0.00 0.00 0.00 4.85
626 650 0.475906 AAAGCAGGAGTGAAGCAGGT 59.524 50.000 0.00 0.00 0.00 4.00
627 651 1.352083 AAGCAGGAGTGAAGCAGGTA 58.648 50.000 0.00 0.00 0.00 3.08
628 652 0.610687 AGCAGGAGTGAAGCAGGTAC 59.389 55.000 0.00 0.00 0.00 3.34
629 653 0.391793 GCAGGAGTGAAGCAGGTACC 60.392 60.000 2.73 2.73 0.00 3.34
630 654 0.250513 CAGGAGTGAAGCAGGTACCC 59.749 60.000 8.74 0.00 0.00 3.69
631 655 1.218316 GGAGTGAAGCAGGTACCCG 59.782 63.158 8.74 0.00 0.00 5.28
632 656 1.448013 GAGTGAAGCAGGTACCCGC 60.448 63.158 12.49 12.49 0.00 6.13
633 657 2.167398 GAGTGAAGCAGGTACCCGCA 62.167 60.000 22.01 4.42 0.00 5.69
634 658 1.302192 GTGAAGCAGGTACCCGCAA 60.302 57.895 22.01 4.57 0.00 4.85
635 659 0.887387 GTGAAGCAGGTACCCGCAAA 60.887 55.000 22.01 4.20 0.00 3.68
636 660 0.179015 TGAAGCAGGTACCCGCAAAA 60.179 50.000 22.01 3.84 0.00 2.44
637 661 0.955905 GAAGCAGGTACCCGCAAAAA 59.044 50.000 22.01 0.00 0.00 1.94
675 699 1.135431 GCGACAGCAATGGCAAACATA 60.135 47.619 0.00 0.00 44.61 2.29
676 700 2.480073 GCGACAGCAATGGCAAACATAT 60.480 45.455 0.00 0.00 44.61 1.78
707 731 4.441695 TCAGCCGAGGCAAGCTCG 62.442 66.667 17.18 4.12 44.88 5.03
708 732 4.749310 CAGCCGAGGCAAGCTCGT 62.749 66.667 17.18 0.00 44.88 4.18
709 733 3.068691 AGCCGAGGCAAGCTCGTA 61.069 61.111 17.18 0.00 44.88 3.43
817 841 4.421479 CCCGAAGTGTCTCGCGCT 62.421 66.667 5.56 0.00 40.11 5.92
818 842 2.876645 CCGAAGTGTCTCGCGCTC 60.877 66.667 5.56 0.00 36.85 5.03
819 843 3.234041 CGAAGTGTCTCGCGCTCG 61.234 66.667 5.56 0.61 36.85 5.03
820 844 3.537297 GAAGTGTCTCGCGCTCGC 61.537 66.667 5.56 3.90 36.85 5.03
945 988 5.043248 CAGAAAGAAACGCACCAAATCTTT 58.957 37.500 0.00 0.00 41.60 2.52
946 989 6.205784 CAGAAAGAAACGCACCAAATCTTTA 58.794 36.000 0.00 0.00 39.66 1.85
947 990 6.863126 CAGAAAGAAACGCACCAAATCTTTAT 59.137 34.615 0.00 0.00 39.66 1.40
948 991 7.061094 CAGAAAGAAACGCACCAAATCTTTATC 59.939 37.037 0.00 0.00 39.66 1.75
952 995 2.025321 ACGCACCAAATCTTTATCCCCT 60.025 45.455 0.00 0.00 0.00 4.79
953 996 2.358898 CGCACCAAATCTTTATCCCCTG 59.641 50.000 0.00 0.00 0.00 4.45
958 1001 3.225940 CAAATCTTTATCCCCTGCCCTC 58.774 50.000 0.00 0.00 0.00 4.30
959 1002 2.212752 ATCTTTATCCCCTGCCCTCA 57.787 50.000 0.00 0.00 0.00 3.86
960 1003 1.511613 TCTTTATCCCCTGCCCTCAG 58.488 55.000 0.00 0.00 40.02 3.35
987 1030 3.222855 CCTGAGCGCCGGAGATCT 61.223 66.667 23.85 4.92 0.00 2.75
1489 1535 0.741221 CAGCACCGCTACCTTCTTCC 60.741 60.000 0.00 0.00 36.40 3.46
1491 1537 1.900545 GCACCGCTACCTTCTTCCCT 61.901 60.000 0.00 0.00 0.00 4.20
1582 1628 4.194720 CCCCTTCCGAGCTCGACG 62.195 72.222 36.59 21.07 43.02 5.12
1626 1672 1.156736 CCGAACACTCCATGAACCAC 58.843 55.000 0.00 0.00 0.00 4.16
1649 1705 1.940613 CGTAAGCCTTTCTGCCATACC 59.059 52.381 0.00 0.00 0.00 2.73
1650 1706 2.420129 CGTAAGCCTTTCTGCCATACCT 60.420 50.000 0.00 0.00 0.00 3.08
1651 1707 2.426842 AAGCCTTTCTGCCATACCTC 57.573 50.000 0.00 0.00 0.00 3.85
1652 1708 0.179000 AGCCTTTCTGCCATACCTCG 59.821 55.000 0.00 0.00 0.00 4.63
1653 1709 0.107654 GCCTTTCTGCCATACCTCGT 60.108 55.000 0.00 0.00 0.00 4.18
1654 1710 1.941325 CCTTTCTGCCATACCTCGTC 58.059 55.000 0.00 0.00 0.00 4.20
1655 1711 1.482593 CCTTTCTGCCATACCTCGTCT 59.517 52.381 0.00 0.00 0.00 4.18
1656 1712 2.482142 CCTTTCTGCCATACCTCGTCTC 60.482 54.545 0.00 0.00 0.00 3.36
1657 1713 1.847328 TTCTGCCATACCTCGTCTCA 58.153 50.000 0.00 0.00 0.00 3.27
1658 1714 1.103803 TCTGCCATACCTCGTCTCAC 58.896 55.000 0.00 0.00 0.00 3.51
1659 1715 0.103208 CTGCCATACCTCGTCTCACC 59.897 60.000 0.00 0.00 0.00 4.02
1660 1716 0.613572 TGCCATACCTCGTCTCACCA 60.614 55.000 0.00 0.00 0.00 4.17
1706 1768 6.474427 ACGTACGTGGTGATAAATAATGTCTG 59.526 38.462 22.14 0.00 0.00 3.51
1708 1770 4.574828 ACGTGGTGATAAATAATGTCTGCC 59.425 41.667 0.00 0.00 0.00 4.85
1868 1930 1.374252 GAGAAGCGCAAGAACCGGA 60.374 57.895 9.46 0.00 43.02 5.14
2099 2161 2.501865 GCTGTAGTTTTGGCGCGC 60.502 61.111 25.94 25.94 0.00 6.86
2233 2299 6.483307 CCTGATGTACTCACTGTTTTTCTTCA 59.517 38.462 0.00 0.00 0.00 3.02
2238 2304 2.290641 CTCACTGTTTTTCTTCACCCCG 59.709 50.000 0.00 0.00 0.00 5.73
2246 2312 2.241281 TTCTTCACCCCGATCCAGTA 57.759 50.000 0.00 0.00 0.00 2.74
2300 2373 2.245159 TCAGCAACTGTGACCTTCAG 57.755 50.000 0.00 0.00 38.68 3.02
2308 2381 0.916086 TGTGACCTTCAGTTGGGTGT 59.084 50.000 0.00 0.00 35.77 4.16
2309 2382 1.283613 TGTGACCTTCAGTTGGGTGTT 59.716 47.619 0.00 0.00 35.77 3.32
2310 2383 1.676006 GTGACCTTCAGTTGGGTGTTG 59.324 52.381 0.00 0.00 35.77 3.33
2311 2384 0.668535 GACCTTCAGTTGGGTGTTGC 59.331 55.000 0.00 0.00 35.77 4.17
2312 2385 0.033601 ACCTTCAGTTGGGTGTTGCA 60.034 50.000 0.00 0.00 34.16 4.08
2313 2386 0.670162 CCTTCAGTTGGGTGTTGCAG 59.330 55.000 0.00 0.00 0.00 4.41
2314 2387 0.031178 CTTCAGTTGGGTGTTGCAGC 59.969 55.000 0.00 0.00 0.00 5.25
2682 2757 9.487790 TGGATTTCAATCTGTTCAAATAAAACC 57.512 29.630 0.00 0.00 35.73 3.27
2737 2812 5.826737 AGCTTATTGATGTTTGCTGCTATCT 59.173 36.000 0.00 0.00 0.00 1.98
2812 2887 5.554747 AGGATGTGGATTGGATGGAGATTAT 59.445 40.000 0.00 0.00 0.00 1.28
2870 2945 3.056628 CTGGATCTCAGTCCGTTGC 57.943 57.895 0.00 0.00 41.35 4.17
2913 2988 3.488048 CGTAGGAGAGCTGCTATGC 57.512 57.895 7.77 7.77 35.96 3.14
2914 2989 0.670706 CGTAGGAGAGCTGCTATGCA 59.329 55.000 17.86 1.57 35.96 3.96
2915 2990 1.601663 CGTAGGAGAGCTGCTATGCAC 60.602 57.143 17.86 12.06 35.96 4.57
2916 2991 1.410517 GTAGGAGAGCTGCTATGCACA 59.589 52.381 17.86 2.46 35.96 4.57
2917 2992 0.177604 AGGAGAGCTGCTATGCACAC 59.822 55.000 17.86 0.00 33.79 3.82
2918 2993 1.150567 GGAGAGCTGCTATGCACACG 61.151 60.000 11.01 0.00 33.79 4.49
2919 2994 0.179127 GAGAGCTGCTATGCACACGA 60.179 55.000 0.00 0.00 33.79 4.35
2920 2995 0.459237 AGAGCTGCTATGCACACGAC 60.459 55.000 0.15 0.00 33.79 4.34
2921 2996 1.746727 GAGCTGCTATGCACACGACG 61.747 60.000 0.15 0.00 33.79 5.12
2922 2997 2.697425 CTGCTATGCACACGACGC 59.303 61.111 0.00 0.00 33.79 5.19
2923 2998 2.048690 TGCTATGCACACGACGCA 60.049 55.556 0.00 0.00 44.94 5.24
2928 3003 2.048690 TGCACACGACGCATAGCA 60.049 55.556 0.00 0.00 33.55 3.49
2929 3004 2.094066 TGCACACGACGCATAGCAG 61.094 57.895 0.00 0.00 33.55 4.24
2930 3005 1.805539 GCACACGACGCATAGCAGA 60.806 57.895 0.00 0.00 0.00 4.26
2931 3006 1.991430 CACACGACGCATAGCAGAC 59.009 57.895 0.00 0.00 0.00 3.51
2932 3007 1.514228 ACACGACGCATAGCAGACG 60.514 57.895 0.00 0.00 0.00 4.18
2933 3008 1.226295 CACGACGCATAGCAGACGA 60.226 57.895 0.00 0.00 0.00 4.20
2934 3009 0.592500 CACGACGCATAGCAGACGAT 60.593 55.000 0.00 0.00 0.00 3.73
2935 3010 0.100682 ACGACGCATAGCAGACGATT 59.899 50.000 0.00 0.00 0.00 3.34
2936 3011 1.200483 CGACGCATAGCAGACGATTT 58.800 50.000 0.00 0.00 0.00 2.17
2937 3012 1.071894 CGACGCATAGCAGACGATTTG 60.072 52.381 0.00 0.00 0.00 2.32
2938 3013 1.927174 GACGCATAGCAGACGATTTGT 59.073 47.619 0.00 0.00 0.00 2.83
2939 3014 1.660607 ACGCATAGCAGACGATTTGTG 59.339 47.619 0.00 0.00 0.00 3.33
2940 3015 1.593070 CGCATAGCAGACGATTTGTGC 60.593 52.381 0.00 0.00 37.48 4.57
2941 3016 1.398041 GCATAGCAGACGATTTGTGCA 59.602 47.619 0.00 0.00 39.80 4.57
2942 3017 2.789092 GCATAGCAGACGATTTGTGCAC 60.789 50.000 10.75 10.75 39.80 4.57
2943 3018 1.067693 TAGCAGACGATTTGTGCACG 58.932 50.000 13.13 1.70 39.80 5.34
2944 3019 0.599991 AGCAGACGATTTGTGCACGA 60.600 50.000 13.13 7.71 39.80 4.35
2945 3020 0.443869 GCAGACGATTTGTGCACGAT 59.556 50.000 13.13 8.85 37.16 3.73
2946 3021 1.658596 GCAGACGATTTGTGCACGATA 59.341 47.619 13.13 0.00 37.16 2.92
2947 3022 2.534939 GCAGACGATTTGTGCACGATAC 60.535 50.000 13.13 6.65 37.16 2.24
2948 3023 2.666022 CAGACGATTTGTGCACGATACA 59.334 45.455 13.13 0.00 0.00 2.29
2949 3024 2.923655 AGACGATTTGTGCACGATACAG 59.076 45.455 13.13 4.49 0.00 2.74
2950 3025 1.393539 ACGATTTGTGCACGATACAGC 59.606 47.619 13.13 0.00 0.00 4.40
2951 3026 1.393196 CGATTTGTGCACGATACAGCA 59.607 47.619 13.13 0.00 38.65 4.41
2956 3031 3.830679 TGCACGATACAGCACATCA 57.169 47.368 0.00 0.00 35.51 3.07
2957 3032 1.643880 TGCACGATACAGCACATCAG 58.356 50.000 0.00 0.00 35.51 2.90
2958 3033 1.066929 TGCACGATACAGCACATCAGT 60.067 47.619 0.00 0.00 35.51 3.41
2967 3042 3.159070 CACATCAGTGCGTCCGTG 58.841 61.111 0.00 0.00 39.21 4.94
2968 3043 2.738521 ACATCAGTGCGTCCGTGC 60.739 61.111 0.00 0.00 0.00 5.34
2969 3044 2.738139 CATCAGTGCGTCCGTGCA 60.738 61.111 0.00 0.00 43.95 4.57
2977 3052 2.812358 TGCGTCCGTGCATATTATCT 57.188 45.000 0.00 0.00 40.62 1.98
2978 3053 3.926821 TGCGTCCGTGCATATTATCTA 57.073 42.857 0.00 0.00 40.62 1.98
2979 3054 4.245845 TGCGTCCGTGCATATTATCTAA 57.754 40.909 0.00 0.00 40.62 2.10
2980 3055 4.234574 TGCGTCCGTGCATATTATCTAAG 58.765 43.478 0.00 0.00 40.62 2.18
2981 3056 4.235360 GCGTCCGTGCATATTATCTAAGT 58.765 43.478 0.00 0.00 34.15 2.24
2982 3057 4.090066 GCGTCCGTGCATATTATCTAAGTG 59.910 45.833 0.00 0.00 34.15 3.16
2983 3058 4.090066 CGTCCGTGCATATTATCTAAGTGC 59.910 45.833 0.00 0.00 33.80 4.40
2984 3059 4.988540 GTCCGTGCATATTATCTAAGTGCA 59.011 41.667 0.00 8.06 37.96 4.57
2985 3060 5.465390 GTCCGTGCATATTATCTAAGTGCAA 59.535 40.000 11.85 0.00 40.20 4.08
2986 3061 5.465390 TCCGTGCATATTATCTAAGTGCAAC 59.535 40.000 11.85 7.72 40.20 4.17
2987 3062 5.236263 CCGTGCATATTATCTAAGTGCAACA 59.764 40.000 11.85 0.00 40.20 3.33
2988 3063 6.357980 CGTGCATATTATCTAAGTGCAACAG 58.642 40.000 11.85 0.00 40.20 3.16
2989 3064 6.200854 CGTGCATATTATCTAAGTGCAACAGA 59.799 38.462 11.85 0.00 40.20 3.41
2990 3065 7.095481 CGTGCATATTATCTAAGTGCAACAGAT 60.095 37.037 11.85 9.98 40.20 2.90
2991 3066 8.013947 GTGCATATTATCTAAGTGCAACAGATG 58.986 37.037 13.52 2.85 40.20 2.90
2992 3067 7.173735 TGCATATTATCTAAGTGCAACAGATGG 59.826 37.037 13.52 3.21 41.43 3.51
2993 3068 7.524912 CATATTATCTAAGTGCAACAGATGGC 58.475 38.462 13.52 0.00 41.43 4.40
2994 3069 3.641434 ATCTAAGTGCAACAGATGGCT 57.359 42.857 5.42 0.00 41.43 4.75
2995 3070 4.760530 ATCTAAGTGCAACAGATGGCTA 57.239 40.909 5.42 0.00 41.43 3.93
2996 3071 4.128925 TCTAAGTGCAACAGATGGCTAG 57.871 45.455 0.00 0.00 41.43 3.42
2997 3072 3.769300 TCTAAGTGCAACAGATGGCTAGA 59.231 43.478 0.00 0.00 41.43 2.43
2998 3073 3.641434 AAGTGCAACAGATGGCTAGAT 57.359 42.857 0.00 0.00 41.43 1.98
2999 3074 3.641434 AGTGCAACAGATGGCTAGATT 57.359 42.857 0.00 0.00 41.43 2.40
3000 3075 3.276857 AGTGCAACAGATGGCTAGATTG 58.723 45.455 0.00 0.00 41.43 2.67
3001 3076 3.054875 AGTGCAACAGATGGCTAGATTGA 60.055 43.478 0.00 0.00 41.43 2.57
3002 3077 3.064545 GTGCAACAGATGGCTAGATTGAC 59.935 47.826 0.00 0.00 36.32 3.18
3003 3078 3.273434 GCAACAGATGGCTAGATTGACA 58.727 45.455 0.00 0.00 0.00 3.58
3004 3079 3.881688 GCAACAGATGGCTAGATTGACAT 59.118 43.478 0.00 0.00 38.59 3.06
3009 3084 1.939974 TGGCTAGATTGACATCGTGC 58.060 50.000 0.00 0.00 34.17 5.34
3010 3085 1.206849 TGGCTAGATTGACATCGTGCA 59.793 47.619 0.00 0.00 35.52 4.57
3011 3086 1.863454 GGCTAGATTGACATCGTGCAG 59.137 52.381 0.00 0.00 35.52 4.41
3012 3087 1.260033 GCTAGATTGACATCGTGCAGC 59.740 52.381 0.00 0.00 34.61 5.25
3013 3088 2.819115 CTAGATTGACATCGTGCAGCT 58.181 47.619 0.00 0.00 34.17 4.24
3014 3089 1.366679 AGATTGACATCGTGCAGCTG 58.633 50.000 10.11 10.11 34.17 4.24
3015 3090 1.081892 GATTGACATCGTGCAGCTGT 58.918 50.000 16.64 0.00 30.94 4.40
3016 3091 1.061711 GATTGACATCGTGCAGCTGTC 59.938 52.381 16.64 13.62 44.02 3.51
3017 3092 1.284297 TTGACATCGTGCAGCTGTCG 61.284 55.000 16.64 19.39 46.01 4.35
3018 3093 1.734477 GACATCGTGCAGCTGTCGT 60.734 57.895 24.17 14.00 36.44 4.34
3019 3094 1.949015 GACATCGTGCAGCTGTCGTG 61.949 60.000 24.17 22.26 36.44 4.35
3020 3095 3.114616 ATCGTGCAGCTGTCGTGC 61.115 61.111 24.17 10.01 41.59 5.34
3024 3099 2.281002 TGCAGCTGTCGTGCATGT 60.281 55.556 16.64 0.00 45.96 3.21
3025 3100 1.005156 TGCAGCTGTCGTGCATGTA 60.005 52.632 16.64 0.00 45.96 2.29
3026 3101 1.015607 TGCAGCTGTCGTGCATGTAG 61.016 55.000 16.64 7.15 45.96 2.74
3027 3102 1.016130 GCAGCTGTCGTGCATGTAGT 61.016 55.000 16.64 0.00 40.86 2.73
3028 3103 0.717784 CAGCTGTCGTGCATGTAGTG 59.282 55.000 5.25 4.17 34.99 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 1.078497 CCGTGGATGCTGGCTGTAA 60.078 57.895 0.00 0.00 0.00 2.41
93 94 2.821366 GCTCACCCGTGGATGCTG 60.821 66.667 0.00 0.00 0.00 4.41
136 137 3.252284 AGGTGAGGGTGGCAGGTG 61.252 66.667 0.00 0.00 0.00 4.00
137 138 2.930562 GAGGTGAGGGTGGCAGGT 60.931 66.667 0.00 0.00 0.00 4.00
138 139 3.721706 GGAGGTGAGGGTGGCAGG 61.722 72.222 0.00 0.00 0.00 4.85
139 140 4.087892 CGGAGGTGAGGGTGGCAG 62.088 72.222 0.00 0.00 0.00 4.85
140 141 4.954118 ACGGAGGTGAGGGTGGCA 62.954 66.667 0.00 0.00 0.00 4.92
141 142 4.083862 GACGGAGGTGAGGGTGGC 62.084 72.222 0.00 0.00 0.00 5.01
181 189 0.681887 TGTCCTGATGCCATTGCCAG 60.682 55.000 0.00 0.00 36.33 4.85
226 234 1.583986 CGATGCCCTTGCCGAAAAA 59.416 52.632 0.00 0.00 36.33 1.94
338 361 3.192922 CGGAATGGGGACGCGTTC 61.193 66.667 15.53 12.55 0.00 3.95
342 366 4.851179 GGGACGGAATGGGGACGC 62.851 72.222 0.00 0.00 0.00 5.19
396 420 1.130561 GCCATTAGTGAGACGTTTGGC 59.869 52.381 0.00 0.00 41.09 4.52
431 455 2.092882 GCGTGAGGCCGTTAGTCAC 61.093 63.158 11.17 11.17 37.77 3.67
451 475 1.794222 GGTGATAACGCAGCACACC 59.206 57.895 8.09 0.00 45.65 4.16
500 524 2.515996 TTTCAGGTCGGCGGCCTAAG 62.516 60.000 34.96 22.37 34.45 2.18
553 577 2.410638 TTTGCACGCTACTCCGACGT 62.411 55.000 0.00 0.00 41.45 4.34
606 630 1.699634 ACCTGCTTCACTCCTGCTTTA 59.300 47.619 0.00 0.00 0.00 1.85
638 662 2.814336 GTCGCCTGATTCACTCCTTTTT 59.186 45.455 0.00 0.00 0.00 1.94
639 663 2.224523 TGTCGCCTGATTCACTCCTTTT 60.225 45.455 0.00 0.00 0.00 2.27
640 664 1.347707 TGTCGCCTGATTCACTCCTTT 59.652 47.619 0.00 0.00 0.00 3.11
641 665 0.976641 TGTCGCCTGATTCACTCCTT 59.023 50.000 0.00 0.00 0.00 3.36
642 666 0.534412 CTGTCGCCTGATTCACTCCT 59.466 55.000 0.00 0.00 0.00 3.69
643 667 1.086634 GCTGTCGCCTGATTCACTCC 61.087 60.000 0.00 0.00 0.00 3.85
644 668 0.390340 TGCTGTCGCCTGATTCACTC 60.390 55.000 0.00 0.00 34.43 3.51
645 669 0.035317 TTGCTGTCGCCTGATTCACT 59.965 50.000 0.00 0.00 34.43 3.41
646 670 1.089920 ATTGCTGTCGCCTGATTCAC 58.910 50.000 0.00 0.00 34.43 3.18
647 671 1.089112 CATTGCTGTCGCCTGATTCA 58.911 50.000 0.00 0.00 34.43 2.57
648 672 0.379669 CCATTGCTGTCGCCTGATTC 59.620 55.000 0.00 0.00 34.43 2.52
649 673 1.660560 GCCATTGCTGTCGCCTGATT 61.661 55.000 0.00 0.00 34.43 2.57
650 674 2.117156 GCCATTGCTGTCGCCTGAT 61.117 57.895 0.00 0.00 34.43 2.90
651 675 2.747460 GCCATTGCTGTCGCCTGA 60.747 61.111 0.00 0.00 34.43 3.86
958 1001 2.433838 CTCAGGTCGGCACTGCTG 60.434 66.667 3.14 3.14 35.94 4.41
959 1002 4.385405 GCTCAGGTCGGCACTGCT 62.385 66.667 0.00 0.00 35.94 4.24
987 1030 3.641159 TTTCATCTCGCTCGCCGCA 62.641 57.895 0.00 0.00 39.08 5.69
1308 1354 3.952628 GAAAGGCGTGACGGGGAGG 62.953 68.421 7.25 0.00 0.00 4.30
1479 1525 1.356738 TCCGAGTCAGGGAAGAAGGTA 59.643 52.381 0.00 0.00 0.00 3.08
1489 1535 2.099831 GTACGCGTCCGAGTCAGG 59.900 66.667 18.63 0.00 38.29 3.86
1491 1537 2.359107 AGGTACGCGTCCGAGTCA 60.359 61.111 18.63 0.00 38.29 3.41
1530 1576 0.692756 TGGCCTTGATCCCGTCCATA 60.693 55.000 3.32 0.00 0.00 2.74
1626 1672 0.955428 TGGCAGAAAGGCTTACGCTG 60.955 55.000 16.00 16.00 44.55 5.18
1643 1689 3.328382 TTTTGGTGAGACGAGGTATGG 57.672 47.619 0.00 0.00 0.00 2.74
1658 1714 5.466393 GTCCATGTCAAGAAAACCATTTTGG 59.534 40.000 0.00 0.00 45.02 3.28
1659 1715 5.175491 CGTCCATGTCAAGAAAACCATTTTG 59.825 40.000 0.00 0.00 31.94 2.44
1660 1716 5.163457 ACGTCCATGTCAAGAAAACCATTTT 60.163 36.000 0.00 0.00 35.12 1.82
1677 1733 3.872511 TTTATCACCACGTACGTCCAT 57.127 42.857 19.94 10.18 0.00 3.41
1706 1768 2.180017 CATCTGCAAAGGCGTGGC 59.820 61.111 0.00 0.00 45.35 5.01
1708 1770 0.592637 TTGACATCTGCAAAGGCGTG 59.407 50.000 0.00 0.00 45.35 5.34
1807 1869 2.367202 CCGCTCCTTCCCCTTGCTA 61.367 63.158 0.00 0.00 0.00 3.49
1868 1930 0.905357 CGGATGGTCTTCTGGAACCT 59.095 55.000 0.00 0.00 0.00 3.50
2047 2109 2.046864 TCGCCGGTCTCCTCAGAAG 61.047 63.158 1.90 0.00 0.00 2.85
2073 2135 1.461127 CAAAACTACAGCAGAGTCGCC 59.539 52.381 3.79 0.00 0.00 5.54
2074 2136 1.461127 CCAAAACTACAGCAGAGTCGC 59.539 52.381 0.00 0.00 0.00 5.19
2075 2137 1.461127 GCCAAAACTACAGCAGAGTCG 59.539 52.381 0.00 0.00 0.00 4.18
2076 2138 1.461127 CGCCAAAACTACAGCAGAGTC 59.539 52.381 0.00 0.00 0.00 3.36
2077 2139 1.512926 CGCCAAAACTACAGCAGAGT 58.487 50.000 0.00 0.00 0.00 3.24
2078 2140 0.166814 GCGCCAAAACTACAGCAGAG 59.833 55.000 0.00 0.00 0.00 3.35
2081 2143 2.942879 CGCGCCAAAACTACAGCA 59.057 55.556 0.00 0.00 0.00 4.41
2143 2208 7.539712 ACAGATTATTCAATGTTACACGGAG 57.460 36.000 0.00 0.00 0.00 4.63
2233 2299 2.436911 GGTACAAATACTGGATCGGGGT 59.563 50.000 0.00 0.00 0.00 4.95
2238 2304 3.136626 AGGCAGGGTACAAATACTGGATC 59.863 47.826 0.00 0.00 0.00 3.36
2246 2312 3.181423 TGGAAGAAAGGCAGGGTACAAAT 60.181 43.478 0.00 0.00 0.00 2.32
2300 2373 1.827789 TCCTGCTGCAACACCCAAC 60.828 57.895 3.02 0.00 0.00 3.77
2302 2375 2.203337 GTCCTGCTGCAACACCCA 60.203 61.111 3.02 0.00 0.00 4.51
2303 2376 2.113986 AGTCCTGCTGCAACACCC 59.886 61.111 3.02 0.00 0.00 4.61
2304 2377 1.227943 TCAGTCCTGCTGCAACACC 60.228 57.895 3.02 0.00 44.66 4.16
2305 2378 0.250038 TCTCAGTCCTGCTGCAACAC 60.250 55.000 3.02 3.05 44.66 3.32
2308 2381 0.251354 GGATCTCAGTCCTGCTGCAA 59.749 55.000 3.02 0.00 44.66 4.08
2309 2382 0.906282 TGGATCTCAGTCCTGCTGCA 60.906 55.000 0.88 0.88 44.66 4.41
2310 2383 0.179078 CTGGATCTCAGTCCTGCTGC 60.179 60.000 0.00 0.00 44.66 5.25
2682 2757 1.571460 GCAGTGGCACTTGAACTCG 59.429 57.895 19.43 5.93 40.72 4.18
2737 2812 5.220854 GCTCTCAACACTTAGCAGTTTTCAA 60.221 40.000 0.00 0.00 35.05 2.69
2812 2887 2.161855 CATGCTGCAACTTTACCCTGA 58.838 47.619 6.36 0.00 0.00 3.86
2870 2945 0.376152 GCACTGATGAACCGATGCTG 59.624 55.000 0.00 0.00 0.00 4.41
2900 2975 0.179127 TCGTGTGCATAGCAGCTCTC 60.179 55.000 0.00 0.00 40.08 3.20
2901 2976 0.459237 GTCGTGTGCATAGCAGCTCT 60.459 55.000 0.00 0.00 40.08 4.09
2902 2977 1.746727 CGTCGTGTGCATAGCAGCTC 61.747 60.000 0.00 0.00 40.08 4.09
2903 2978 1.807165 CGTCGTGTGCATAGCAGCT 60.807 57.895 0.00 0.00 40.08 4.24
2904 2979 2.697425 CGTCGTGTGCATAGCAGC 59.303 61.111 0.00 0.00 40.08 5.25
2905 2980 2.094066 TGCGTCGTGTGCATAGCAG 61.094 57.895 0.00 0.00 40.08 4.24
2906 2981 2.048690 TGCGTCGTGTGCATAGCA 60.049 55.556 0.00 0.00 37.44 3.49
2912 2987 1.805539 TCTGCTATGCGTCGTGTGC 60.806 57.895 0.00 0.00 0.00 4.57
2913 2988 1.733416 CGTCTGCTATGCGTCGTGTG 61.733 60.000 0.00 0.00 0.00 3.82
2914 2989 1.514228 CGTCTGCTATGCGTCGTGT 60.514 57.895 0.00 0.00 0.00 4.49
2915 2990 0.592500 ATCGTCTGCTATGCGTCGTG 60.593 55.000 0.00 0.00 0.00 4.35
2916 2991 0.100682 AATCGTCTGCTATGCGTCGT 59.899 50.000 0.00 0.00 0.00 4.34
2917 2992 1.071894 CAAATCGTCTGCTATGCGTCG 60.072 52.381 0.00 0.00 0.00 5.12
2918 2993 1.927174 ACAAATCGTCTGCTATGCGTC 59.073 47.619 0.00 0.00 0.00 5.19
2919 2994 1.660607 CACAAATCGTCTGCTATGCGT 59.339 47.619 0.00 0.00 0.00 5.24
2920 2995 1.593070 GCACAAATCGTCTGCTATGCG 60.593 52.381 0.00 0.00 0.00 4.73
2921 2996 1.398041 TGCACAAATCGTCTGCTATGC 59.602 47.619 0.00 0.00 0.00 3.14
2922 2997 2.535534 CGTGCACAAATCGTCTGCTATG 60.536 50.000 18.64 0.00 0.00 2.23
2923 2998 1.660607 CGTGCACAAATCGTCTGCTAT 59.339 47.619 18.64 0.00 0.00 2.97
2924 2999 1.067693 CGTGCACAAATCGTCTGCTA 58.932 50.000 18.64 0.00 0.00 3.49
2925 3000 0.599991 TCGTGCACAAATCGTCTGCT 60.600 50.000 18.64 0.00 0.00 4.24
2926 3001 0.443869 ATCGTGCACAAATCGTCTGC 59.556 50.000 18.64 0.00 0.00 4.26
2927 3002 2.666022 TGTATCGTGCACAAATCGTCTG 59.334 45.455 18.64 0.00 0.00 3.51
2928 3003 2.923655 CTGTATCGTGCACAAATCGTCT 59.076 45.455 18.64 0.00 0.00 4.18
2929 3004 2.534939 GCTGTATCGTGCACAAATCGTC 60.535 50.000 18.64 5.17 0.00 4.20
2930 3005 1.393539 GCTGTATCGTGCACAAATCGT 59.606 47.619 18.64 0.00 0.00 3.73
2931 3006 1.393196 TGCTGTATCGTGCACAAATCG 59.607 47.619 18.64 1.94 33.94 3.34
2938 3013 1.066929 ACTGATGTGCTGTATCGTGCA 60.067 47.619 0.00 0.00 36.79 4.57
2939 3014 1.325640 CACTGATGTGCTGTATCGTGC 59.674 52.381 0.00 0.00 37.38 5.34
2950 3025 3.015293 GCACGGACGCACTGATGTG 62.015 63.158 0.00 0.00 46.37 3.21
2951 3026 2.738521 GCACGGACGCACTGATGT 60.739 61.111 0.00 0.00 0.00 3.06
2952 3027 0.805711 TATGCACGGACGCACTGATG 60.806 55.000 0.00 0.00 46.56 3.07
2953 3028 0.104855 ATATGCACGGACGCACTGAT 59.895 50.000 0.00 0.00 46.56 2.90
2954 3029 0.108377 AATATGCACGGACGCACTGA 60.108 50.000 0.00 0.00 46.56 3.41
2955 3030 1.566404 TAATATGCACGGACGCACTG 58.434 50.000 0.00 0.00 46.56 3.66
2956 3031 2.035961 AGATAATATGCACGGACGCACT 59.964 45.455 0.00 0.00 46.56 4.40
2957 3032 2.404215 AGATAATATGCACGGACGCAC 58.596 47.619 0.00 0.00 46.56 5.34
2959 3034 4.090066 CACTTAGATAATATGCACGGACGC 59.910 45.833 0.00 0.00 0.00 5.19
2960 3035 4.090066 GCACTTAGATAATATGCACGGACG 59.910 45.833 0.00 0.00 36.30 4.79
2961 3036 4.988540 TGCACTTAGATAATATGCACGGAC 59.011 41.667 0.00 0.00 41.18 4.79
2962 3037 5.208463 TGCACTTAGATAATATGCACGGA 57.792 39.130 0.00 0.00 41.18 4.69
2963 3038 5.236263 TGTTGCACTTAGATAATATGCACGG 59.764 40.000 9.84 0.00 45.45 4.94
2964 3039 6.200854 TCTGTTGCACTTAGATAATATGCACG 59.799 38.462 9.84 0.00 45.45 5.34
2965 3040 7.482654 TCTGTTGCACTTAGATAATATGCAC 57.517 36.000 9.84 7.39 45.45 4.57
2966 3041 7.173735 CCATCTGTTGCACTTAGATAATATGCA 59.826 37.037 6.30 0.00 44.19 3.96
2967 3042 7.524912 CCATCTGTTGCACTTAGATAATATGC 58.475 38.462 6.30 0.00 36.81 3.14
2968 3043 7.389884 AGCCATCTGTTGCACTTAGATAATATG 59.610 37.037 6.30 0.00 30.43 1.78
2969 3044 7.456725 AGCCATCTGTTGCACTTAGATAATAT 58.543 34.615 6.30 0.00 30.43 1.28
2970 3045 6.830912 AGCCATCTGTTGCACTTAGATAATA 58.169 36.000 6.30 0.00 30.43 0.98
2971 3046 5.688807 AGCCATCTGTTGCACTTAGATAAT 58.311 37.500 6.30 0.00 30.43 1.28
2972 3047 5.102953 AGCCATCTGTTGCACTTAGATAA 57.897 39.130 6.30 0.00 30.43 1.75
2973 3048 4.760530 AGCCATCTGTTGCACTTAGATA 57.239 40.909 6.30 0.00 30.43 1.98
2974 3049 3.641434 AGCCATCTGTTGCACTTAGAT 57.359 42.857 0.00 0.00 0.00 1.98
2975 3050 3.769300 TCTAGCCATCTGTTGCACTTAGA 59.231 43.478 0.00 0.00 0.00 2.10
2976 3051 4.128925 TCTAGCCATCTGTTGCACTTAG 57.871 45.455 0.00 0.00 0.00 2.18
2977 3052 4.760530 ATCTAGCCATCTGTTGCACTTA 57.239 40.909 0.00 0.00 0.00 2.24
2978 3053 3.641434 ATCTAGCCATCTGTTGCACTT 57.359 42.857 0.00 0.00 0.00 3.16
2979 3054 3.054875 TCAATCTAGCCATCTGTTGCACT 60.055 43.478 0.00 0.00 0.00 4.40
2980 3055 3.064545 GTCAATCTAGCCATCTGTTGCAC 59.935 47.826 0.00 0.00 0.00 4.57
2981 3056 3.273434 GTCAATCTAGCCATCTGTTGCA 58.727 45.455 0.00 0.00 0.00 4.08
2982 3057 3.273434 TGTCAATCTAGCCATCTGTTGC 58.727 45.455 0.00 0.00 0.00 4.17
2983 3058 4.210746 CGATGTCAATCTAGCCATCTGTTG 59.789 45.833 0.00 0.00 33.24 3.33
2984 3059 4.141846 ACGATGTCAATCTAGCCATCTGTT 60.142 41.667 0.00 0.00 33.24 3.16
2985 3060 3.386078 ACGATGTCAATCTAGCCATCTGT 59.614 43.478 0.00 0.00 33.24 3.41
2986 3061 3.739810 CACGATGTCAATCTAGCCATCTG 59.260 47.826 0.00 0.00 33.24 2.90
2987 3062 3.801638 GCACGATGTCAATCTAGCCATCT 60.802 47.826 0.00 0.00 33.24 2.90
2988 3063 2.478134 GCACGATGTCAATCTAGCCATC 59.522 50.000 0.00 0.00 0.00 3.51
2989 3064 2.158914 TGCACGATGTCAATCTAGCCAT 60.159 45.455 0.00 0.00 32.39 4.40
2990 3065 1.206849 TGCACGATGTCAATCTAGCCA 59.793 47.619 0.00 0.00 32.39 4.75
2991 3066 1.863454 CTGCACGATGTCAATCTAGCC 59.137 52.381 0.00 0.00 32.39 3.93
2992 3067 1.260033 GCTGCACGATGTCAATCTAGC 59.740 52.381 0.00 0.00 33.38 3.42
2993 3068 2.538861 CAGCTGCACGATGTCAATCTAG 59.461 50.000 0.00 0.00 0.00 2.43
2994 3069 2.094026 ACAGCTGCACGATGTCAATCTA 60.094 45.455 15.27 0.00 37.86 1.98
2995 3070 1.338484 ACAGCTGCACGATGTCAATCT 60.338 47.619 15.27 0.00 37.86 2.40
2996 3071 1.081892 ACAGCTGCACGATGTCAATC 58.918 50.000 15.27 0.00 37.86 2.67
2997 3072 3.238232 ACAGCTGCACGATGTCAAT 57.762 47.368 15.27 0.00 37.86 2.57
2998 3073 4.777384 ACAGCTGCACGATGTCAA 57.223 50.000 15.27 0.00 37.86 3.18
3001 3076 2.023771 CACGACAGCTGCACGATGT 61.024 57.895 30.57 13.14 46.62 3.06
3002 3077 2.774126 CACGACAGCTGCACGATG 59.226 61.111 30.57 22.23 34.52 3.84
3003 3078 3.114616 GCACGACAGCTGCACGAT 61.115 61.111 30.57 17.14 34.56 3.73
3004 3079 4.583866 TGCACGACAGCTGCACGA 62.584 61.111 30.57 13.14 39.76 4.35
3008 3083 1.016130 ACTACATGCACGACAGCTGC 61.016 55.000 15.27 5.81 34.99 5.25
3009 3084 0.717784 CACTACATGCACGACAGCTG 59.282 55.000 13.48 13.48 34.99 4.24
3010 3085 3.128259 CACTACATGCACGACAGCT 57.872 52.632 0.00 0.00 34.99 4.24


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

AutoCloner maintained by Alex Coulton.