Multiple sequence alignment - TraesCS6A01G254200

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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 TraesCS6A01G254200 chr6A 100.000 3083 0 0 1 3083 470410631 470413713 0.000000e+00 5694.0
1 TraesCS6A01G254200 chr6D 95.425 1989 72 12 854 2829 331531359 331533341 0.000000e+00 3151.0
2 TraesCS6A01G254200 chr6D 78.009 673 108 16 1 664 331529510 331530151 1.340000e-103 387.0
3 TraesCS6A01G254200 chr6D 78.731 268 53 3 100 366 315977389 315977125 3.160000e-40 176.0
4 TraesCS6A01G254200 chr6D 91.753 97 8 0 765 861 331530213 331530309 5.360000e-28 135.0
5 TraesCS6A01G254200 chr6B 91.850 2233 132 22 792 2988 489540902 489538684 0.000000e+00 3070.0
6 TraesCS6A01G254200 chr6B 74.916 594 117 25 88 667 659671757 659672332 3.070000e-60 243.0
7 TraesCS6A01G254200 chr7A 77.029 579 113 15 104 667 670685999 670686572 6.420000e-82 315.0
8 TraesCS6A01G254200 chrUn 76.173 554 112 15 120 658 434813789 434814337 1.090000e-69 274.0
9 TraesCS6A01G254200 chr7D 75.648 579 115 17 104 667 116601861 116602428 6.560000e-67 265.0
10 TraesCS6A01G254200 chr7D 92.500 40 3 0 592 631 621613050 621613011 1.190000e-04 58.4
11 TraesCS6A01G254200 chr3D 76.008 521 108 16 151 659 517266196 517266711 1.420000e-63 254.0
12 TraesCS6A01G254200 chr3D 73.369 567 107 27 118 667 20940287 20940826 1.470000e-38 171.0
13 TraesCS6A01G254200 chr3D 73.194 526 104 26 118 631 2681201 2681701 4.120000e-34 156.0
14 TraesCS6A01G254200 chr2D 74.561 570 124 14 104 659 491424900 491425462 2.390000e-56 230.0
15 TraesCS6A01G254200 chr2D 74.946 463 91 20 219 665 629380570 629380117 4.060000e-44 189.0
16 TraesCS6A01G254200 chr1B 76.519 362 70 13 179 532 350634389 350634035 1.890000e-42 183.0
17 TraesCS6A01G254200 chr2B 93.182 88 6 0 2982 3069 584118585 584118672 2.490000e-26 130.0
18 TraesCS6A01G254200 chr2B 89.474 95 10 0 2987 3081 718968489 718968583 1.500000e-23 121.0
19 TraesCS6A01G254200 chr2B 87.500 104 11 2 2978 3080 52717978 52717876 5.400000e-23 119.0
20 TraesCS6A01G254200 chr5B 90.625 96 8 1 2986 3081 711940363 711940457 3.230000e-25 126.0
21 TraesCS6A01G254200 chr4B 88.571 105 11 1 2978 3081 94353184 94353288 3.230000e-25 126.0
22 TraesCS6A01G254200 chr7B 88.542 96 11 0 2986 3081 717178143 717178048 1.940000e-22 117.0
23 TraesCS6A01G254200 chr7B 88.542 96 11 0 2986 3081 717252796 717252701 1.940000e-22 117.0
24 TraesCS6A01G254200 chr3B 87.129 101 13 0 2981 3081 245962953 245963053 6.990000e-22 115.0
25 TraesCS6A01G254200 chr3B 87.879 99 11 1 2984 3081 561099072 561098974 6.990000e-22 115.0
26 TraesCS6A01G254200 chr5D 71.295 533 109 27 142 659 448439024 448438521 2.530000e-16 97.1


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 TraesCS6A01G254200 chr6A 470410631 470413713 3082 False 5694.000000 5694 100.000000 1 3083 1 chr6A.!!$F1 3082
1 TraesCS6A01G254200 chr6D 331529510 331533341 3831 False 1224.333333 3151 88.395667 1 2829 3 chr6D.!!$F1 2828
2 TraesCS6A01G254200 chr6B 489538684 489540902 2218 True 3070.000000 3070 91.850000 792 2988 1 chr6B.!!$R1 2196
3 TraesCS6A01G254200 chr6B 659671757 659672332 575 False 243.000000 243 74.916000 88 667 1 chr6B.!!$F1 579
4 TraesCS6A01G254200 chr7A 670685999 670686572 573 False 315.000000 315 77.029000 104 667 1 chr7A.!!$F1 563
5 TraesCS6A01G254200 chrUn 434813789 434814337 548 False 274.000000 274 76.173000 120 658 1 chrUn.!!$F1 538
6 TraesCS6A01G254200 chr7D 116601861 116602428 567 False 265.000000 265 75.648000 104 667 1 chr7D.!!$F1 563
7 TraesCS6A01G254200 chr3D 517266196 517266711 515 False 254.000000 254 76.008000 151 659 1 chr3D.!!$F3 508
8 TraesCS6A01G254200 chr2D 491424900 491425462 562 False 230.000000 230 74.561000 104 659 1 chr2D.!!$F1 555

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
412 417 0.105039 GGTGGATCCGCTCGAATCTT 59.895 55.000 24.15 0.0 0.00 2.40 F
588 598 0.249657 GCCAGGATGATGAGGACGAC 60.250 60.000 0.00 0.0 39.69 4.34 F
904 1978 1.002868 GCCATAGAGCATCGCCCAT 60.003 57.895 0.00 0.0 42.67 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2815 0.109689 GGAGAAGTCCACGTCGTCAG 60.110 60.0 0.0 0.0 43.31 3.51 R
2076 3152 0.895559 CCCCTGACTTTGTTCAGCCC 60.896 60.0 0.0 0.0 41.61 5.19 R
2855 3949 0.025001 CGCGTGCTTTCCATTCTACG 59.975 55.0 0.0 0.0 34.93 3.51 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
76 80 3.124686 GCTCCTCCTAGCGACCAG 58.875 66.667 0.00 0.00 31.76 4.00
94 98 1.021390 AGCAGCGAACATGTGGCTAC 61.021 55.000 20.48 16.30 34.75 3.58
96 100 0.735978 CAGCGAACATGTGGCTACGA 60.736 55.000 20.48 0.00 34.75 3.43
98 102 1.407618 AGCGAACATGTGGCTACGATA 59.592 47.619 19.78 0.00 34.75 2.92
140 144 3.675086 GCGATCTGCCTCATCTTCA 57.325 52.632 0.00 0.00 37.76 3.02
175 179 4.176752 GGGGCACGGTGGATCTCC 62.177 72.222 10.60 1.68 0.00 3.71
185 189 1.541118 TGGATCTCCACCCTTGCCA 60.541 57.895 0.00 0.00 42.01 4.92
187 191 1.566298 GGATCTCCACCCTTGCCAGT 61.566 60.000 0.00 0.00 35.64 4.00
192 196 2.520458 CACCCTTGCCAGTGGGAA 59.480 61.111 16.05 16.05 46.15 3.97
200 204 4.567318 CCAGTGGGAAGGCTATGC 57.433 61.111 0.00 0.00 35.59 3.14
209 213 5.104109 AGTGGGAAGGCTATGCTTTTATACA 60.104 40.000 0.00 0.00 0.00 2.29
262 266 1.210931 CAGGTAAACGAGACGGCGA 59.789 57.895 16.62 0.00 34.83 5.54
265 269 0.179156 GGTAAACGAGACGGCGATGA 60.179 55.000 16.62 0.00 34.83 2.92
275 280 1.066303 GACGGCGATGACTCTCTGAAT 59.934 52.381 16.62 0.00 0.00 2.57
303 308 1.939980 AGTTTCTTCCCGTCTAGCCT 58.060 50.000 0.00 0.00 0.00 4.58
366 371 1.277557 GGTGTGTCTCCAGCAGATCTT 59.722 52.381 0.00 0.00 32.08 2.40
407 412 2.721167 CCTTGGTGGATCCGCTCGA 61.721 63.158 24.15 13.13 39.52 4.04
412 417 0.105039 GGTGGATCCGCTCGAATCTT 59.895 55.000 24.15 0.00 0.00 2.40
420 425 0.296056 CGCTCGAATCTTGTCTTCGC 59.704 55.000 0.83 0.00 43.86 4.70
429 434 1.605232 TCTTGTCTTCGCACGTCTACA 59.395 47.619 0.00 0.00 0.00 2.74
438 443 3.495193 TCGCACGTCTACATTAGTGTTC 58.505 45.455 0.00 0.00 39.77 3.18
439 444 3.189910 TCGCACGTCTACATTAGTGTTCT 59.810 43.478 0.00 0.00 39.77 3.01
458 463 3.260205 TCTTTCAGGTTGGATCCTTCCT 58.740 45.455 14.23 16.69 43.07 3.36
465 470 3.134804 AGGTTGGATCCTTCCTATCAACG 59.865 47.826 21.16 0.00 43.07 4.10
483 489 0.597637 CGCTTATCTTCATCGGCGGT 60.598 55.000 7.21 0.00 39.12 5.68
484 490 1.335597 CGCTTATCTTCATCGGCGGTA 60.336 52.381 7.21 0.00 39.12 4.02
490 496 0.739462 CTTCATCGGCGGTAGTTGCA 60.739 55.000 7.21 0.00 0.00 4.08
492 498 1.153647 CATCGGCGGTAGTTGCAGA 60.154 57.895 7.21 0.00 40.68 4.26
494 501 2.573609 ATCGGCGGTAGTTGCAGACC 62.574 60.000 7.21 4.78 39.29 3.85
521 528 2.188817 CTGGTCCTGTTAGGCCTTAGT 58.811 52.381 12.58 0.00 34.61 2.24
525 532 2.100418 GTCCTGTTAGGCCTTAGTACGG 59.900 54.545 12.58 9.61 34.61 4.02
535 542 2.098117 GCCTTAGTACGGCGACTTTCTA 59.902 50.000 16.62 5.60 37.87 2.10
541 548 2.521105 ACGGCGACTTTCTAACTGTT 57.479 45.000 16.62 0.00 0.00 3.16
544 551 4.563061 ACGGCGACTTTCTAACTGTTTAT 58.437 39.130 16.62 0.00 0.00 1.40
581 591 3.170672 CCCCGGCCAGGATGATGA 61.171 66.667 6.57 0.00 45.00 2.92
583 593 2.429058 CCGGCCAGGATGATGAGG 59.571 66.667 2.24 0.00 45.00 3.86
584 594 2.142761 CCGGCCAGGATGATGAGGA 61.143 63.158 2.24 0.00 45.00 3.71
585 595 1.070445 CGGCCAGGATGATGAGGAC 59.930 63.158 2.24 0.00 39.69 3.85
586 596 1.070445 GGCCAGGATGATGAGGACG 59.930 63.158 0.00 0.00 39.69 4.79
587 597 1.402896 GGCCAGGATGATGAGGACGA 61.403 60.000 0.00 0.00 39.69 4.20
588 598 0.249657 GCCAGGATGATGAGGACGAC 60.250 60.000 0.00 0.00 39.69 4.34
606 623 1.065701 GACATCTTCGGCTCGCTTCTA 59.934 52.381 0.00 0.00 0.00 2.10
631 648 1.066215 TGTAGTCGTCGCTAGGTGGTA 60.066 52.381 0.00 0.00 0.00 3.25
632 649 1.596727 GTAGTCGTCGCTAGGTGGTAG 59.403 57.143 0.00 0.00 0.00 3.18
634 651 1.452651 TCGTCGCTAGGTGGTAGGG 60.453 63.158 0.00 0.00 41.98 3.53
635 652 1.452651 CGTCGCTAGGTGGTAGGGA 60.453 63.158 0.00 0.00 45.88 4.20
636 653 4.672251 TCGCTAGGTGGTAGGGAC 57.328 61.111 0.00 0.00 43.84 4.46
637 654 1.076485 TCGCTAGGTGGTAGGGACC 60.076 63.158 0.00 0.00 43.84 4.46
649 666 4.838904 GGTAGGGACCTTGATGTAGTTT 57.161 45.455 0.00 0.00 43.16 2.66
650 667 5.175388 GGTAGGGACCTTGATGTAGTTTT 57.825 43.478 0.00 0.00 43.16 2.43
651 668 5.567430 GGTAGGGACCTTGATGTAGTTTTT 58.433 41.667 0.00 0.00 43.16 1.94
652 669 6.714278 GGTAGGGACCTTGATGTAGTTTTTA 58.286 40.000 0.00 0.00 43.16 1.52
653 670 7.344134 GGTAGGGACCTTGATGTAGTTTTTAT 58.656 38.462 0.00 0.00 43.16 1.40
654 671 7.832685 GGTAGGGACCTTGATGTAGTTTTTATT 59.167 37.037 0.00 0.00 43.16 1.40
655 672 9.895138 GTAGGGACCTTGATGTAGTTTTTATTA 57.105 33.333 0.00 0.00 0.00 0.98
657 674 9.990868 AGGGACCTTGATGTAGTTTTTATTATT 57.009 29.630 0.00 0.00 0.00 1.40
715 732 9.833917 TGTTCGTTGTATTATCATAATGGGTAA 57.166 29.630 0.00 0.00 0.00 2.85
869 1943 5.472478 GGAAGGAGACCGATAAACAAAAACT 59.528 40.000 0.00 0.00 0.00 2.66
904 1978 1.002868 GCCATAGAGCATCGCCCAT 60.003 57.895 0.00 0.00 42.67 4.00
961 2035 3.030652 CAACCGAGCCCACACAAC 58.969 61.111 0.00 0.00 0.00 3.32
973 2049 1.542547 CCACACAACCTAGAAACGCCT 60.543 52.381 0.00 0.00 0.00 5.52
1347 2423 3.854669 CTCGCCGCATCCCTCCTT 61.855 66.667 0.00 0.00 0.00 3.36
1368 2444 4.452733 CCCTTCACCGGCTCCGTC 62.453 72.222 0.00 0.00 37.81 4.79
1401 2477 4.840005 CTCCCCGCCTTCTTCGCC 62.840 72.222 0.00 0.00 0.00 5.54
1640 2716 4.077184 GGTCACGGCCGTCATCCA 62.077 66.667 31.80 7.10 0.00 3.41
1641 2717 2.509336 GTCACGGCCGTCATCCAG 60.509 66.667 31.80 16.95 0.00 3.86
1695 2771 2.110213 GTCGTGGTGGCTGGTGAA 59.890 61.111 0.00 0.00 0.00 3.18
1739 2815 4.813027 TCCAAGTGGATGTACGTCTTTAC 58.187 43.478 14.61 11.10 39.78 2.01
2067 3143 2.146342 GCATCGTGGATCATACCAAGG 58.854 52.381 0.00 0.00 41.87 3.61
2076 3152 4.141413 TGGATCATACCAAGGGTGAATGAG 60.141 45.833 6.90 0.00 36.19 2.90
2116 3192 2.544844 ATCGGAGGTCCTGGTTCTTA 57.455 50.000 0.00 0.00 0.00 2.10
2130 3206 5.163269 CCTGGTTCTTATCTGATGATGGTGA 60.163 44.000 0.00 0.00 34.32 4.02
2177 3253 3.574614 CCAAATTCTTGGTACCTTTGCG 58.425 45.455 14.36 5.74 46.25 4.85
2202 3278 6.486253 TTGCATATGTTCTGAAGTGAAGTC 57.514 37.500 4.29 0.00 0.00 3.01
2212 3288 4.398044 TCTGAAGTGAAGTCAAAACCAACC 59.602 41.667 0.00 0.00 0.00 3.77
2330 3411 4.582869 TCTGTGAGATGTATTTGCTGCTT 58.417 39.130 0.00 0.00 0.00 3.91
2331 3412 5.733676 TCTGTGAGATGTATTTGCTGCTTA 58.266 37.500 0.00 0.00 0.00 3.09
2332 3413 6.172630 TCTGTGAGATGTATTTGCTGCTTAA 58.827 36.000 0.00 0.00 0.00 1.85
2357 3438 6.591935 ACTCTCAAGTTTCATTGTCCACTTA 58.408 36.000 0.00 0.00 28.74 2.24
2453 3535 2.930682 GTTTCAGTAATGGACTCGGAGC 59.069 50.000 4.58 0.00 35.64 4.70
2501 3585 2.611722 GGAGTCTCAGAAGCTGGACAAC 60.612 54.545 1.47 9.58 35.60 3.32
2606 3696 7.220030 AGCATAATGGATAACTGAGTACCAAG 58.780 38.462 9.39 0.00 34.28 3.61
2630 3720 2.093553 CCGGCAAATGGGATCAATTTGT 60.094 45.455 23.43 0.00 37.54 2.83
2724 3815 1.608590 ACCTGAACAGCAACGAAATGG 59.391 47.619 0.00 0.00 0.00 3.16
2730 3821 0.527113 CAGCAACGAAATGGCATCCA 59.473 50.000 0.00 0.00 38.19 3.41
2732 3823 1.406539 AGCAACGAAATGGCATCCATC 59.593 47.619 0.00 0.00 44.40 3.51
2733 3824 1.536709 GCAACGAAATGGCATCCATCC 60.537 52.381 0.00 0.00 44.40 3.51
2736 3827 0.534877 CGAAATGGCATCCATCCGGA 60.535 55.000 6.61 6.61 44.40 5.14
2754 3847 2.165030 CGGATTGCTTGAAAAGGATGCT 59.835 45.455 0.00 0.00 46.19 3.79
2759 3852 4.970662 TGCTTGAAAAGGATGCTACATC 57.029 40.909 0.00 0.00 46.35 3.06
2816 3910 1.931841 CCAAGCGACTGATGTCATGAG 59.068 52.381 0.00 0.00 43.06 2.90
2837 3931 4.503741 GCATGTTTTTGCTAGTGGAGAA 57.496 40.909 0.00 0.00 39.57 2.87
2838 3932 4.479619 GCATGTTTTTGCTAGTGGAGAAG 58.520 43.478 0.00 0.00 39.57 2.85
2839 3933 4.022849 GCATGTTTTTGCTAGTGGAGAAGT 60.023 41.667 0.00 0.00 39.57 3.01
2841 3935 6.293955 GCATGTTTTTGCTAGTGGAGAAGTAA 60.294 38.462 0.00 0.00 39.57 2.24
2842 3936 6.861065 TGTTTTTGCTAGTGGAGAAGTAAG 57.139 37.500 0.00 0.00 0.00 2.34
2843 3937 5.763204 TGTTTTTGCTAGTGGAGAAGTAAGG 59.237 40.000 0.00 0.00 0.00 2.69
2845 3939 5.818678 TTTGCTAGTGGAGAAGTAAGGAA 57.181 39.130 0.00 0.00 0.00 3.36
2846 3940 5.818678 TTGCTAGTGGAGAAGTAAGGAAA 57.181 39.130 0.00 0.00 0.00 3.13
2847 3941 5.818678 TGCTAGTGGAGAAGTAAGGAAAA 57.181 39.130 0.00 0.00 0.00 2.29
2848 3942 5.794894 TGCTAGTGGAGAAGTAAGGAAAAG 58.205 41.667 0.00 0.00 0.00 2.27
2850 3944 6.213600 TGCTAGTGGAGAAGTAAGGAAAAGAT 59.786 38.462 0.00 0.00 0.00 2.40
2851 3945 6.759356 GCTAGTGGAGAAGTAAGGAAAAGATC 59.241 42.308 0.00 0.00 0.00 2.75
2872 3971 2.159707 CCAACGTAGAATGGAAAGCACG 60.160 50.000 0.00 0.00 39.61 5.34
2873 3972 1.076332 ACGTAGAATGGAAAGCACGC 58.924 50.000 0.00 0.00 32.90 5.34
2876 3975 0.248012 TAGAATGGAAAGCACGCGGA 59.752 50.000 12.47 0.00 0.00 5.54
2877 3976 0.605319 AGAATGGAAAGCACGCGGAA 60.605 50.000 12.47 0.00 0.00 4.30
2878 3977 0.454452 GAATGGAAAGCACGCGGAAC 60.454 55.000 12.47 0.00 0.00 3.62
2912 4025 2.015736 AGCAGTGGTTATCGAGCAAG 57.984 50.000 0.00 0.00 37.53 4.01
2919 4032 2.213499 GGTTATCGAGCAAGATGGGTG 58.787 52.381 4.46 0.00 32.39 4.61
2924 4037 3.179443 TCGAGCAAGATGGGTGTAATC 57.821 47.619 0.00 0.00 0.00 1.75
2925 4038 2.766263 TCGAGCAAGATGGGTGTAATCT 59.234 45.455 0.00 0.00 35.89 2.40
2932 4045 8.366359 AGCAAGATGGGTGTAATCTTATTTTT 57.634 30.769 0.00 0.00 41.39 1.94
2943 4056 9.129209 GTGTAATCTTATTTTTGCAGTTCCTTC 57.871 33.333 0.00 0.00 0.00 3.46
2961 4074 6.452494 TCCTTCTAAAACATACTCTCTCCG 57.548 41.667 0.00 0.00 0.00 4.63
2969 4082 3.757270 ACATACTCTCTCCGTCCTATGG 58.243 50.000 0.00 0.00 0.00 2.74
2979 4092 4.291513 TCTCCGTCCTATGGTATATGGAGT 59.708 45.833 8.80 0.00 41.88 3.85
2999 4112 6.940831 GAGTATATTATACTCCCTCCGTCC 57.059 45.833 24.42 5.51 38.33 4.79
3000 4113 6.655376 AGTATATTATACTCCCTCCGTCCT 57.345 41.667 10.04 0.00 0.00 3.85
3001 4114 7.761981 AGTATATTATACTCCCTCCGTCCTA 57.238 40.000 10.04 0.00 0.00 2.94
3002 4115 8.167691 AGTATATTATACTCCCTCCGTCCTAA 57.832 38.462 10.04 0.00 0.00 2.69
3003 4116 8.618385 AGTATATTATACTCCCTCCGTCCTAAA 58.382 37.037 10.04 0.00 0.00 1.85
3004 4117 9.247861 GTATATTATACTCCCTCCGTCCTAAAA 57.752 37.037 6.59 0.00 0.00 1.52
3005 4118 8.912614 ATATTATACTCCCTCCGTCCTAAAAT 57.087 34.615 0.00 0.00 0.00 1.82
3007 4120 8.731591 ATTATACTCCCTCCGTCCTAAAATAA 57.268 34.615 0.00 0.00 0.00 1.40
3008 4121 8.731591 TTATACTCCCTCCGTCCTAAAATAAT 57.268 34.615 0.00 0.00 0.00 1.28
3009 4122 5.970501 ACTCCCTCCGTCCTAAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
3010 4123 5.681639 ACTCCCTCCGTCCTAAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
3011 4124 5.191124 ACTCCCTCCGTCCTAAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
3012 4125 5.677567 TCCCTCCGTCCTAAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
3013 4126 5.427481 TCCCTCCGTCCTAAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
3014 4127 5.758784 CCCTCCGTCCTAAAATAATTGTCTC 59.241 44.000 0.00 0.00 0.00 3.36
3015 4128 6.346096 CCTCCGTCCTAAAATAATTGTCTCA 58.654 40.000 0.00 0.00 0.00 3.27
3016 4129 6.821665 CCTCCGTCCTAAAATAATTGTCTCAA 59.178 38.462 0.00 0.00 0.00 3.02
3017 4130 7.201617 CCTCCGTCCTAAAATAATTGTCTCAAC 60.202 40.741 0.00 0.00 0.00 3.18
3018 4131 7.391620 TCCGTCCTAAAATAATTGTCTCAACT 58.608 34.615 0.00 0.00 0.00 3.16
3019 4132 7.881232 TCCGTCCTAAAATAATTGTCTCAACTT 59.119 33.333 0.00 0.00 0.00 2.66
3020 4133 8.512138 CCGTCCTAAAATAATTGTCTCAACTTT 58.488 33.333 0.00 0.00 0.00 2.66
3073 4186 7.406799 AATTTGAGGCACTTATTTTGAAACG 57.593 32.000 0.00 0.00 41.55 3.60
3074 4187 4.497473 TGAGGCACTTATTTTGAAACGG 57.503 40.909 0.00 0.00 41.55 4.44
3075 4188 4.138290 TGAGGCACTTATTTTGAAACGGA 58.862 39.130 0.00 0.00 41.55 4.69
3076 4189 4.764823 TGAGGCACTTATTTTGAAACGGAT 59.235 37.500 0.00 0.00 41.55 4.18
3077 4190 5.059404 AGGCACTTATTTTGAAACGGATG 57.941 39.130 0.00 0.00 27.25 3.51
3078 4191 4.082245 AGGCACTTATTTTGAAACGGATGG 60.082 41.667 0.00 0.00 27.25 3.51
3079 4192 4.082463 GGCACTTATTTTGAAACGGATGGA 60.082 41.667 0.00 0.00 0.00 3.41
3080 4193 5.095490 GCACTTATTTTGAAACGGATGGAG 58.905 41.667 0.00 0.00 0.00 3.86
3081 4194 5.640732 CACTTATTTTGAAACGGATGGAGG 58.359 41.667 0.00 0.00 0.00 4.30
3082 4195 5.414454 CACTTATTTTGAAACGGATGGAGGA 59.586 40.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.868277 GTCCTGTATATAAAGGATTCATGAGAG 57.132 37.037 22.27 0.00 44.30 3.20
23 24 9.607333 AGTCCTGTATATAAAGGATTCATGAGA 57.393 33.333 22.27 0.00 44.30 3.27
53 54 4.261701 GCTAGGAGGAGCGAAGGA 57.738 61.111 0.00 0.00 31.57 3.36
72 76 1.968017 CCACATGTTCGCTGCTGGT 60.968 57.895 0.00 0.00 0.00 4.00
76 80 1.425428 GTAGCCACATGTTCGCTGC 59.575 57.895 22.02 18.24 34.03 5.25
79 83 1.847818 TATCGTAGCCACATGTTCGC 58.152 50.000 0.00 0.20 0.00 4.70
94 98 0.032952 TCGGCGGGAGGAAAATATCG 59.967 55.000 7.21 0.00 0.00 2.92
96 100 0.249741 CGTCGGCGGGAGGAAAATAT 60.250 55.000 7.21 0.00 32.22 1.28
98 102 2.125269 CGTCGGCGGGAGGAAAAT 60.125 61.111 7.21 0.00 32.22 1.82
175 179 1.604593 CTTCCCACTGGCAAGGGTG 60.605 63.158 20.54 10.78 45.64 4.61
185 189 2.907458 AAAAGCATAGCCTTCCCACT 57.093 45.000 0.00 0.00 0.00 4.00
187 191 5.381184 TGTATAAAAGCATAGCCTTCCCA 57.619 39.130 0.00 0.00 0.00 4.37
360 365 2.166459 TCGACCGAATTCTGCAAGATCT 59.834 45.455 3.52 0.00 46.36 2.75
366 371 0.249120 ACCATCGACCGAATTCTGCA 59.751 50.000 3.52 0.00 0.00 4.41
371 376 1.278127 AGGACAACCATCGACCGAATT 59.722 47.619 0.00 0.00 38.94 2.17
407 412 2.440539 AGACGTGCGAAGACAAGATT 57.559 45.000 0.00 0.00 0.00 2.40
412 417 2.717580 AATGTAGACGTGCGAAGACA 57.282 45.000 0.00 0.00 0.00 3.41
420 425 6.089551 CCTGAAAGAACACTAATGTAGACGTG 59.910 42.308 0.00 0.00 38.45 4.49
429 434 5.946377 GGATCCAACCTGAAAGAACACTAAT 59.054 40.000 6.95 0.00 34.07 1.73
458 463 3.987868 GCCGATGAAGATAAGCGTTGATA 59.012 43.478 0.00 0.00 0.00 2.15
465 470 2.288273 ACTACCGCCGATGAAGATAAGC 60.288 50.000 0.00 0.00 0.00 3.09
483 489 2.048597 CGCACCGGTCTGCAACTA 60.049 61.111 16.41 0.00 36.94 2.24
494 501 3.583276 TAACAGGACCAGCGCACCG 62.583 63.158 11.47 0.00 0.00 4.94
521 528 3.648339 AACAGTTAGAAAGTCGCCGTA 57.352 42.857 0.00 0.00 0.00 4.02
571 581 2.627221 AGATGTCGTCCTCATCATCCTG 59.373 50.000 8.30 0.00 42.63 3.86
575 585 3.361794 CGAAGATGTCGTCCTCATCAT 57.638 47.619 8.30 0.00 45.09 2.45
576 586 2.851805 CGAAGATGTCGTCCTCATCA 57.148 50.000 8.30 0.00 45.09 3.07
586 596 0.179124 AGAAGCGAGCCGAAGATGTC 60.179 55.000 0.00 0.00 0.00 3.06
587 597 1.103803 TAGAAGCGAGCCGAAGATGT 58.896 50.000 0.00 0.00 0.00 3.06
588 598 2.057316 CATAGAAGCGAGCCGAAGATG 58.943 52.381 0.00 0.00 0.00 2.90
606 623 1.065701 CCTAGCGACGACTACAAGCAT 59.934 52.381 0.00 0.00 0.00 3.79
631 648 9.990868 AATAATAAAAACTACATCAAGGTCCCT 57.009 29.630 0.00 0.00 0.00 4.20
707 724 9.479549 AAGTTTATGATCTGTTCATTACCCATT 57.520 29.630 6.54 0.00 42.62 3.16
747 764 9.196552 GCACGCATCAGAGCAATTATATATATA 57.803 33.333 0.00 0.00 0.00 0.86
748 765 7.095899 CGCACGCATCAGAGCAATTATATATAT 60.096 37.037 0.00 0.00 0.00 0.86
749 766 6.198966 CGCACGCATCAGAGCAATTATATATA 59.801 38.462 0.00 0.00 0.00 0.86
750 767 5.006068 CGCACGCATCAGAGCAATTATATAT 59.994 40.000 0.00 0.00 0.00 0.86
752 769 3.124128 CGCACGCATCAGAGCAATTATAT 59.876 43.478 0.00 0.00 0.00 0.86
753 770 2.476241 CGCACGCATCAGAGCAATTATA 59.524 45.455 0.00 0.00 0.00 0.98
754 771 1.262417 CGCACGCATCAGAGCAATTAT 59.738 47.619 0.00 0.00 0.00 1.28
755 772 0.652071 CGCACGCATCAGAGCAATTA 59.348 50.000 0.00 0.00 0.00 1.40
756 773 1.426621 CGCACGCATCAGAGCAATT 59.573 52.632 0.00 0.00 0.00 2.32
759 776 4.377708 ACCGCACGCATCAGAGCA 62.378 61.111 0.00 0.00 0.00 4.26
760 777 3.857854 CACCGCACGCATCAGAGC 61.858 66.667 0.00 0.00 0.00 4.09
761 778 3.857854 GCACCGCACGCATCAGAG 61.858 66.667 0.00 0.00 0.00 3.35
762 779 4.678499 TGCACCGCACGCATCAGA 62.678 61.111 0.00 0.00 33.55 3.27
771 788 1.528076 ATCAAACTGGTGCACCGCA 60.528 52.632 30.07 13.62 39.43 5.69
772 789 1.081242 CATCAAACTGGTGCACCGC 60.081 57.895 30.07 8.85 39.43 5.68
812 829 2.125106 GTAGGGTGCCGCTCTTGG 60.125 66.667 0.00 0.00 0.00 3.61
813 830 2.125106 GGTAGGGTGCCGCTCTTG 60.125 66.667 0.00 0.00 0.00 3.02
904 1978 2.136298 TTGCTCGGATTTAATGGGCA 57.864 45.000 0.00 0.00 0.00 5.36
910 1984 6.399639 AAAAACCTCTTTGCTCGGATTTAA 57.600 33.333 0.00 0.00 0.00 1.52
959 2033 2.304761 TGGAATCAGGCGTTTCTAGGTT 59.695 45.455 0.00 0.00 0.00 3.50
961 2035 2.691409 TGGAATCAGGCGTTTCTAGG 57.309 50.000 0.00 0.00 0.00 3.02
973 2049 2.212652 CGCGATCTGGAATTGGAATCA 58.787 47.619 0.00 0.00 0.00 2.57
1338 2414 0.121197 TGAAGGGGTGAAGGAGGGAT 59.879 55.000 0.00 0.00 0.00 3.85
1347 2423 3.319198 GAGCCGGTGAAGGGGTGA 61.319 66.667 1.90 0.00 34.92 4.02
1401 2477 2.105128 GCCAGGTCATCCGTCTCG 59.895 66.667 0.00 0.00 39.05 4.04
1695 2771 2.208132 TGACGAGAAGGAAGAGCTCT 57.792 50.000 11.45 11.45 0.00 4.09
1739 2815 0.109689 GGAGAAGTCCACGTCGTCAG 60.110 60.000 0.00 0.00 43.31 3.51
1839 2915 1.437986 GAACCCGTGGAGAGGATCG 59.562 63.158 0.00 0.00 42.67 3.69
1866 2942 2.737376 GTGAACCCTGCCGTCGTC 60.737 66.667 0.00 0.00 0.00 4.20
1867 2943 4.657824 CGTGAACCCTGCCGTCGT 62.658 66.667 0.00 0.00 0.00 4.34
1868 2944 3.851845 TTCGTGAACCCTGCCGTCG 62.852 63.158 0.00 0.00 0.00 5.12
2067 3143 1.909700 TTGTTCAGCCCTCATTCACC 58.090 50.000 0.00 0.00 0.00 4.02
2076 3152 0.895559 CCCCTGACTTTGTTCAGCCC 60.896 60.000 0.00 0.00 41.61 5.19
2116 3192 4.677673 TCATTCGTCACCATCATCAGAT 57.322 40.909 0.00 0.00 33.87 2.90
2130 3206 3.055591 CGAGCAAGCAGATATCATTCGT 58.944 45.455 5.32 0.00 0.00 3.85
2177 3253 4.952262 TCACTTCAGAACATATGCAAGC 57.048 40.909 1.58 0.00 0.00 4.01
2183 3259 7.502226 TGGTTTTGACTTCACTTCAGAACATAT 59.498 33.333 7.73 0.00 38.97 1.78
2202 3278 3.541996 AAAAGAGGCTGGTTGGTTTTG 57.458 42.857 0.00 0.00 0.00 2.44
2212 3288 4.572389 AGAACATGCGTATAAAAGAGGCTG 59.428 41.667 0.00 0.00 0.00 4.85
2269 3348 7.714377 GCTGATCAGAAATTCAGAATCTAGGAA 59.286 37.037 27.04 0.00 41.53 3.36
2463 3545 6.543465 TGAGACTCCGATTCAATTAATGCATT 59.457 34.615 17.56 17.56 0.00 3.56
2468 3551 6.481644 GCTTCTGAGACTCCGATTCAATTAAT 59.518 38.462 0.00 0.00 0.00 1.40
2469 3552 5.812642 GCTTCTGAGACTCCGATTCAATTAA 59.187 40.000 0.00 0.00 0.00 1.40
2480 3564 1.261480 TGTCCAGCTTCTGAGACTCC 58.739 55.000 0.00 0.00 34.85 3.85
2606 3696 3.226537 GATCCCATTTGCCGGGCC 61.227 66.667 17.97 0.00 44.11 5.80
2630 3720 7.445096 TGCATTTTCTGTTCAATCAACTAGAGA 59.555 33.333 0.00 0.00 35.79 3.10
2684 3774 1.879380 TGTTCCCATCACAAAGCTTCG 59.121 47.619 0.00 0.00 0.00 3.79
2713 3804 1.536709 GGATGGATGCCATTTCGTTGC 60.537 52.381 0.00 0.00 45.26 4.17
2730 3821 3.085952 TCCTTTTCAAGCAATCCGGAT 57.914 42.857 12.38 12.38 0.00 4.18
2732 3823 2.736400 GCATCCTTTTCAAGCAATCCGG 60.736 50.000 0.00 0.00 0.00 5.14
2733 3824 2.165030 AGCATCCTTTTCAAGCAATCCG 59.835 45.455 0.00 0.00 0.00 4.18
2736 3827 5.655532 AGATGTAGCATCCTTTTCAAGCAAT 59.344 36.000 5.59 0.00 0.00 3.56
2737 3828 5.012239 AGATGTAGCATCCTTTTCAAGCAA 58.988 37.500 5.59 0.00 0.00 3.91
2740 3833 4.397103 TGCAGATGTAGCATCCTTTTCAAG 59.603 41.667 5.59 0.00 37.02 3.02
2754 3847 3.205338 CAATCGGGTCATTGCAGATGTA 58.795 45.455 8.19 0.00 0.00 2.29
2816 3910 4.022849 ACTTCTCCACTAGCAAAAACATGC 60.023 41.667 0.00 0.00 46.78 4.06
2830 3924 5.805728 TGGATCTTTTCCTTACTTCTCCAC 58.194 41.667 0.00 0.00 45.68 4.02
2831 3925 6.238648 GTTGGATCTTTTCCTTACTTCTCCA 58.761 40.000 0.00 0.00 45.68 3.86
2832 3926 5.351740 CGTTGGATCTTTTCCTTACTTCTCC 59.648 44.000 0.00 0.00 45.68 3.71
2833 3927 5.932883 ACGTTGGATCTTTTCCTTACTTCTC 59.067 40.000 0.00 0.00 45.68 2.87
2834 3928 5.866207 ACGTTGGATCTTTTCCTTACTTCT 58.134 37.500 0.00 0.00 45.68 2.85
2835 3929 7.095270 TCTACGTTGGATCTTTTCCTTACTTC 58.905 38.462 0.00 0.00 45.68 3.01
2836 3930 7.001099 TCTACGTTGGATCTTTTCCTTACTT 57.999 36.000 0.00 0.00 45.68 2.24
2837 3931 6.600882 TCTACGTTGGATCTTTTCCTTACT 57.399 37.500 0.00 0.00 45.68 2.24
2838 3932 7.201617 CCATTCTACGTTGGATCTTTTCCTTAC 60.202 40.741 0.00 0.00 45.68 2.34
2839 3933 6.821665 CCATTCTACGTTGGATCTTTTCCTTA 59.178 38.462 0.00 0.00 45.68 2.69
2841 3935 5.045869 TCCATTCTACGTTGGATCTTTTCCT 60.046 40.000 2.50 0.00 45.68 3.36
2842 3936 5.183228 TCCATTCTACGTTGGATCTTTTCC 58.817 41.667 2.50 0.00 45.69 3.13
2843 3937 6.737254 TTCCATTCTACGTTGGATCTTTTC 57.263 37.500 7.50 0.00 41.52 2.29
2845 3939 5.123979 GCTTTCCATTCTACGTTGGATCTTT 59.876 40.000 7.50 0.00 41.52 2.52
2846 3940 4.636206 GCTTTCCATTCTACGTTGGATCTT 59.364 41.667 7.50 0.00 41.52 2.40
2847 3941 4.192317 GCTTTCCATTCTACGTTGGATCT 58.808 43.478 7.50 0.00 41.52 2.75
2848 3942 3.938963 TGCTTTCCATTCTACGTTGGATC 59.061 43.478 7.50 2.07 41.52 3.36
2850 3944 3.071479 GTGCTTTCCATTCTACGTTGGA 58.929 45.455 2.50 2.50 40.24 3.53
2851 3945 2.159707 CGTGCTTTCCATTCTACGTTGG 60.160 50.000 0.00 0.00 0.00 3.77
2852 3946 2.724839 GCGTGCTTTCCATTCTACGTTG 60.725 50.000 0.00 0.00 34.37 4.10
2853 3947 1.463444 GCGTGCTTTCCATTCTACGTT 59.537 47.619 0.00 0.00 34.37 3.99
2854 3948 1.076332 GCGTGCTTTCCATTCTACGT 58.924 50.000 0.00 0.00 34.37 3.57
2855 3949 0.025001 CGCGTGCTTTCCATTCTACG 59.975 55.000 0.00 0.00 34.93 3.51
2878 3977 3.112580 CACTGCTTAAACAAACCGGTTG 58.887 45.455 23.08 17.07 43.43 3.77
2890 3989 3.603158 TGCTCGATAACCACTGCTTAA 57.397 42.857 0.00 0.00 0.00 1.85
2912 4025 7.547227 ACTGCAAAAATAAGATTACACCCATC 58.453 34.615 0.00 0.00 0.00 3.51
2924 4037 9.528018 TGTTTTAGAAGGAACTGCAAAAATAAG 57.472 29.630 0.00 0.00 40.86 1.73
2932 4045 6.769512 AGAGTATGTTTTAGAAGGAACTGCA 58.230 36.000 0.00 0.00 40.86 4.41
2943 4056 5.838531 AGGACGGAGAGAGTATGTTTTAG 57.161 43.478 0.00 0.00 0.00 1.85
2988 4101 5.681639 ACAATTATTTTAGGACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2989 4102 5.427481 AGACAATTATTTTAGGACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2990 4103 5.681639 AGACAATTATTTTAGGACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2991 4104 6.346096 TGAGACAATTATTTTAGGACGGAGG 58.654 40.000 0.00 0.00 0.00 4.30
2992 4105 7.549488 AGTTGAGACAATTATTTTAGGACGGAG 59.451 37.037 0.00 0.00 0.00 4.63
2993 4106 7.391620 AGTTGAGACAATTATTTTAGGACGGA 58.608 34.615 0.00 0.00 0.00 4.69
2994 4107 7.611213 AGTTGAGACAATTATTTTAGGACGG 57.389 36.000 0.00 0.00 0.00 4.79
3008 4121 9.463902 ACTAGAGCTAGTATAAAGTTGAGACAA 57.536 33.333 8.35 0.00 43.98 3.18
3035 4148 9.297037 AGTGCCTCAAATTTAGTATAACTTTGT 57.703 29.630 10.33 0.00 0.00 2.83
3047 4160 8.973378 CGTTTCAAAATAAGTGCCTCAAATTTA 58.027 29.630 0.00 0.00 0.00 1.40
3048 4161 7.042119 CCGTTTCAAAATAAGTGCCTCAAATTT 60.042 33.333 0.00 0.00 0.00 1.82
3049 4162 6.423604 CCGTTTCAAAATAAGTGCCTCAAATT 59.576 34.615 0.00 0.00 0.00 1.82
3050 4163 5.925969 CCGTTTCAAAATAAGTGCCTCAAAT 59.074 36.000 0.00 0.00 0.00 2.32
3051 4164 5.067936 TCCGTTTCAAAATAAGTGCCTCAAA 59.932 36.000 0.00 0.00 0.00 2.69
3052 4165 4.580995 TCCGTTTCAAAATAAGTGCCTCAA 59.419 37.500 0.00 0.00 0.00 3.02
3053 4166 4.138290 TCCGTTTCAAAATAAGTGCCTCA 58.862 39.130 0.00 0.00 0.00 3.86
3054 4167 4.759516 TCCGTTTCAAAATAAGTGCCTC 57.240 40.909 0.00 0.00 0.00 4.70
3055 4168 4.082245 CCATCCGTTTCAAAATAAGTGCCT 60.082 41.667 0.00 0.00 0.00 4.75
3056 4169 4.082463 TCCATCCGTTTCAAAATAAGTGCC 60.082 41.667 0.00 0.00 0.00 5.01
3057 4170 5.054390 TCCATCCGTTTCAAAATAAGTGC 57.946 39.130 0.00 0.00 0.00 4.40
3058 4171 5.414454 TCCTCCATCCGTTTCAAAATAAGTG 59.586 40.000 0.00 0.00 0.00 3.16
3059 4172 5.566469 TCCTCCATCCGTTTCAAAATAAGT 58.434 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.