Multiple sequence alignment - TraesCS1D01G077400

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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 TraesCS1D01G077400 chr1D 100.000 3479 0 0 1 3479 59514220 59517698 0.000000e+00 6425.0
1 TraesCS1D01G077400 chr1D 96.429 56 2 0 3373 3428 254384870 254384925 3.700000e-15 93.5
2 TraesCS1D01G077400 chr1A 87.574 3541 183 97 1 3428 58122938 58126334 0.000000e+00 3864.0
3 TraesCS1D01G077400 chr1A 82.707 133 9 8 3133 3252 58166095 58166226 4.750000e-19 106.0
4 TraesCS1D01G077400 chr1B 91.396 2092 102 38 2 2035 94955324 94957395 0.000000e+00 2795.0
5 TraesCS1D01G077400 chr1B 83.709 1418 91 56 2032 3387 94957680 94959019 0.000000e+00 1210.0
6 TraesCS1D01G077400 chr5B 96.429 56 2 0 3373 3428 432719375 432719320 3.700000e-15 93.5
7 TraesCS1D01G077400 chr3B 96.429 56 2 0 3373 3428 201536672 201536617 3.700000e-15 93.5
8 TraesCS1D01G077400 chrUn 94.643 56 3 0 3373 3428 216508966 216509021 1.720000e-13 87.9
9 TraesCS1D01G077400 chrUn 94.643 56 3 0 3373 3428 398828945 398828890 1.720000e-13 87.9
10 TraesCS1D01G077400 chrUn 94.643 56 3 0 3373 3428 440226712 440226767 1.720000e-13 87.9
11 TraesCS1D01G077400 chrUn 94.643 56 3 0 3373 3428 453113839 453113784 1.720000e-13 87.9
12 TraesCS1D01G077400 chr6D 94.643 56 3 0 3373 3428 389249526 389249471 1.720000e-13 87.9
13 TraesCS1D01G077400 chr3D 90.769 65 6 0 3373 3437 164942879 164942815 1.720000e-13 87.9


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 TraesCS1D01G077400 chr1D 59514220 59517698 3478 False 6425.0 6425 100.0000 1 3479 1 chr1D.!!$F1 3478
1 TraesCS1D01G077400 chr1A 58122938 58126334 3396 False 3864.0 3864 87.5740 1 3428 1 chr1A.!!$F1 3427
2 TraesCS1D01G077400 chr1B 94955324 94959019 3695 False 2002.5 2795 87.5525 2 3387 2 chr1B.!!$F1 3385

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
322 331 0.179189 CATTTGTTTCTCGGCTCGCC 60.179 55.0 0.00 0.0 0.00 5.54 F
635 683 0.250770 GGACTTTGGTGGTGTCTCCC 60.251 60.0 0.00 0.0 34.77 4.30 F
2338 2748 0.253327 GGAGCCTCTCCCATTTCGTT 59.747 55.0 1.44 0.0 44.36 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1199 0.448990 CATCCTTGGTGTGCATGACG 59.551 55.000 0.0 0.0 0.0 4.35 R
2375 2785 1.133823 TGCAGAGGTTGAAGGAAAGCA 60.134 47.619 0.0 0.0 0.0 3.91 R
3434 3940 1.001974 TCATAGCACCGACAAAGCACT 59.998 47.619 0.0 0.0 0.0 4.40 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
131 136 1.063031 GGAAATTTGCGTGCTTCTGC 58.937 50.000 0.00 0.00 40.20 4.26
225 234 1.142748 CCGCTCGCCAGATTCTTCT 59.857 57.895 0.00 0.00 0.00 2.85
295 304 4.726334 GGTTCCATGCCGTAACCA 57.274 55.556 10.76 0.00 41.89 3.67
296 305 0.322098 TGGTTCCATGCCGTAACCAG 60.322 55.000 13.15 0.00 45.85 4.00
297 306 1.654023 GGTTCCATGCCGTAACCAGC 61.654 60.000 10.76 0.00 41.89 4.85
299 308 2.828549 CCATGCCGTAACCAGCCC 60.829 66.667 0.00 0.00 0.00 5.19
300 309 2.828549 CATGCCGTAACCAGCCCC 60.829 66.667 0.00 0.00 0.00 5.80
301 310 3.015145 ATGCCGTAACCAGCCCCT 61.015 61.111 0.00 0.00 0.00 4.79
316 325 1.463674 CCCCTCCATTTGTTTCTCGG 58.536 55.000 0.00 0.00 0.00 4.63
322 331 0.179189 CATTTGTTTCTCGGCTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
323 332 1.305930 ATTTGTTTCTCGGCTCGCCC 61.306 55.000 1.72 0.00 0.00 6.13
439 469 2.617274 GGTGCGTGTGAAAGGAGGC 61.617 63.158 0.00 0.00 0.00 4.70
635 683 0.250770 GGACTTTGGTGGTGTCTCCC 60.251 60.000 0.00 0.00 34.77 4.30
655 703 3.831911 CCCACCATTGTTATCCTTGTGTT 59.168 43.478 0.00 0.00 0.00 3.32
656 704 4.321899 CCCACCATTGTTATCCTTGTGTTG 60.322 45.833 0.00 0.00 0.00 3.33
657 705 4.280677 CCACCATTGTTATCCTTGTGTTGT 59.719 41.667 0.00 0.00 0.00 3.32
658 706 5.221880 CACCATTGTTATCCTTGTGTTGTG 58.778 41.667 0.00 0.00 0.00 3.33
659 707 4.892934 ACCATTGTTATCCTTGTGTTGTGT 59.107 37.500 0.00 0.00 0.00 3.72
660 708 5.221224 ACCATTGTTATCCTTGTGTTGTGTG 60.221 40.000 0.00 0.00 0.00 3.82
661 709 5.221224 CCATTGTTATCCTTGTGTTGTGTGT 60.221 40.000 0.00 0.00 0.00 3.72
662 710 5.906113 TTGTTATCCTTGTGTTGTGTGTT 57.094 34.783 0.00 0.00 0.00 3.32
663 711 7.421599 CATTGTTATCCTTGTGTTGTGTGTTA 58.578 34.615 0.00 0.00 0.00 2.41
712 764 4.027755 CGATTAGGCGCGGTTCAT 57.972 55.556 8.83 0.00 0.00 2.57
727 779 3.609853 GGTTCATGGTGCTGATCTGTTA 58.390 45.455 1.27 0.00 0.00 2.41
756 808 2.304761 TGGTAATTCTGGCGGAGAAAGT 59.695 45.455 0.00 0.00 44.11 2.66
773 825 6.417930 GGAGAAAGTCTTGAATTTTGTTTCCG 59.582 38.462 0.00 0.00 0.00 4.30
809 862 3.146066 TGGTTACAACTCTGTGGAATGC 58.854 45.455 0.00 0.00 36.96 3.56
851 904 2.143876 ACTTGTGGCCAAACTTGTCT 57.856 45.000 7.24 0.00 0.00 3.41
910 963 1.628340 TCTTGCGATTTTGGGAGGAGA 59.372 47.619 0.00 0.00 0.00 3.71
935 988 0.834261 TGATCCGAGTGTTGGTCCCA 60.834 55.000 0.00 0.00 0.00 4.37
1058 1111 0.610687 GACCTGGAGAGTGGGAACAG 59.389 60.000 0.00 0.00 44.46 3.16
1200 1253 3.202706 GATTGTTCCTCGCCCGCC 61.203 66.667 0.00 0.00 0.00 6.13
1263 1316 2.304831 GGAGGAGAAGCTGGGCCTT 61.305 63.158 4.53 0.00 0.00 4.35
1320 1373 1.377856 GTCCAGCTCCAAGAAGCCC 60.378 63.158 0.00 0.00 43.56 5.19
1550 1603 6.727394 TCTGGCAAGGTATACCAAATTAGTT 58.273 36.000 23.87 4.64 38.89 2.24
1608 1688 5.255687 TGTCATGCTTGTATGGAAGAACAT 58.744 37.500 0.00 0.00 34.90 2.71
1611 1691 7.557358 TGTCATGCTTGTATGGAAGAACATAAT 59.443 33.333 0.00 0.00 35.29 1.28
1613 1693 8.970020 TCATGCTTGTATGGAAGAACATAATTT 58.030 29.630 0.00 0.00 35.29 1.82
1793 1903 9.923143 AATTTACCTTATTTTAACAGCCAGTTC 57.077 29.630 0.00 0.00 41.64 3.01
1864 1981 8.673711 TGTTCACATTATAGTTTCTTACCATGC 58.326 33.333 0.00 0.00 0.00 4.06
1892 2009 4.628333 GCTTGTCAAATTGTTCATCCATGG 59.372 41.667 4.97 4.97 0.00 3.66
1974 2091 1.551883 GGGCAATGCAAAGATCCACTT 59.448 47.619 7.79 0.00 40.98 3.16
1975 2092 2.613691 GGCAATGCAAAGATCCACTTG 58.386 47.619 7.79 0.00 38.98 3.16
2043 2448 5.590530 AACTGTTTGTTAAGCCATGTTGA 57.409 34.783 0.00 0.00 37.07 3.18
2044 2449 4.932146 ACTGTTTGTTAAGCCATGTTGAC 58.068 39.130 0.00 0.00 0.00 3.18
2067 2472 0.537371 AAAGCCGTTGGTCTTCAGGG 60.537 55.000 0.00 0.00 0.00 4.45
2072 2477 2.514803 CCGTTGGTCTTCAGGGAAAAT 58.485 47.619 0.00 0.00 0.00 1.82
2098 2503 5.465390 GGCACACTAAAATCCCTTGTTTTTC 59.535 40.000 0.00 0.00 31.71 2.29
2119 2526 2.271944 ACACTACAGGGTTTTGCTCC 57.728 50.000 0.00 0.00 0.00 4.70
2164 2571 2.093500 CCACGGATCACCTGAATCTTCA 60.093 50.000 0.00 0.00 35.57 3.02
2274 2683 3.820467 CCCAAGTATGCAAACTCAGTCAA 59.180 43.478 0.00 0.00 0.00 3.18
2282 2692 5.336150 TGCAAACTCAGTCAATTTCCAAA 57.664 34.783 0.00 0.00 0.00 3.28
2295 2705 6.592607 GTCAATTTCCAAACAATGCATCTCAT 59.407 34.615 0.00 0.00 36.87 2.90
2329 2739 5.483892 AATCTCAAGATCTGGAGCCTCTCC 61.484 50.000 20.85 5.94 41.39 3.71
2338 2748 0.253327 GGAGCCTCTCCCATTTCGTT 59.747 55.000 1.44 0.00 44.36 3.85
2340 2750 1.740025 GAGCCTCTCCCATTTCGTTTG 59.260 52.381 0.00 0.00 0.00 2.93
2341 2751 1.073923 AGCCTCTCCCATTTCGTTTGT 59.926 47.619 0.00 0.00 0.00 2.83
2342 2752 2.304761 AGCCTCTCCCATTTCGTTTGTA 59.695 45.455 0.00 0.00 0.00 2.41
2343 2753 2.418976 GCCTCTCCCATTTCGTTTGTAC 59.581 50.000 0.00 0.00 0.00 2.90
2344 2754 3.007635 CCTCTCCCATTTCGTTTGTACC 58.992 50.000 0.00 0.00 0.00 3.34
2345 2755 3.558321 CCTCTCCCATTTCGTTTGTACCA 60.558 47.826 0.00 0.00 0.00 3.25
2360 2770 4.502105 TGTACCAACCATGCTATGATGT 57.498 40.909 0.00 0.00 0.00 3.06
2375 2785 0.815734 GATGTGCTGCTGATGCCTTT 59.184 50.000 0.00 0.00 38.71 3.11
2376 2786 0.530744 ATGTGCTGCTGATGCCTTTG 59.469 50.000 0.00 0.00 38.71 2.77
2391 2802 2.288457 GCCTTTGCTTTCCTTCAACCTC 60.288 50.000 0.00 0.00 33.53 3.85
2535 2965 2.566010 GCTCGCCGCCATTTTGAA 59.434 55.556 0.00 0.00 0.00 2.69
2751 3189 2.849294 TGATGACGGTGATGGTTTCA 57.151 45.000 0.00 0.00 0.00 2.69
2786 3227 9.726438 ATAATACTAATAAGGCTTGCTAGTTGG 57.274 33.333 21.07 9.37 0.00 3.77
2861 3303 2.279741 GCTCACACTGTTGACTGTTGA 58.720 47.619 0.00 0.41 0.00 3.18
2862 3304 2.286294 GCTCACACTGTTGACTGTTGAG 59.714 50.000 17.95 17.95 36.82 3.02
2863 3305 2.868583 CTCACACTGTTGACTGTTGAGG 59.131 50.000 16.27 2.39 34.09 3.86
2864 3306 1.942657 CACACTGTTGACTGTTGAGGG 59.057 52.381 0.00 0.00 0.00 4.30
2865 3307 1.559682 ACACTGTTGACTGTTGAGGGT 59.440 47.619 0.00 0.00 0.00 4.34
2866 3308 2.026262 ACACTGTTGACTGTTGAGGGTT 60.026 45.455 0.00 0.00 0.00 4.11
2867 3309 2.355756 CACTGTTGACTGTTGAGGGTTG 59.644 50.000 0.00 0.00 0.00 3.77
2868 3310 2.238646 ACTGTTGACTGTTGAGGGTTGA 59.761 45.455 0.00 0.00 0.00 3.18
2882 3324 1.001406 GGGTTGAGAGAGTGTCACTGG 59.999 57.143 11.04 0.00 0.00 4.00
2883 3325 1.606737 GGTTGAGAGAGTGTCACTGGC 60.607 57.143 11.04 1.77 0.00 4.85
2884 3326 1.342819 GTTGAGAGAGTGTCACTGGCT 59.657 52.381 11.04 7.06 0.00 4.75
2885 3327 1.252175 TGAGAGAGTGTCACTGGCTC 58.748 55.000 11.04 15.83 0.00 4.70
2886 3328 1.202989 TGAGAGAGTGTCACTGGCTCT 60.203 52.381 19.23 19.23 41.72 4.09
2887 3329 1.202114 GAGAGAGTGTCACTGGCTCTG 59.798 57.143 22.54 0.00 39.43 3.35
2888 3330 0.246086 GAGAGTGTCACTGGCTCTGG 59.754 60.000 11.04 0.00 39.43 3.86
2889 3331 1.190833 AGAGTGTCACTGGCTCTGGG 61.191 60.000 11.04 0.00 38.09 4.45
2890 3332 2.177594 GAGTGTCACTGGCTCTGGGG 62.178 65.000 11.04 0.00 0.00 4.96
2891 3333 2.122413 TGTCACTGGCTCTGGGGT 60.122 61.111 0.00 0.00 0.00 4.95
2892 3334 2.217038 TGTCACTGGCTCTGGGGTC 61.217 63.158 0.00 0.00 0.00 4.46
2893 3335 1.915769 GTCACTGGCTCTGGGGTCT 60.916 63.158 0.00 0.00 0.00 3.85
2894 3336 1.915266 TCACTGGCTCTGGGGTCTG 60.915 63.158 0.00 0.00 0.00 3.51
2895 3337 2.608988 ACTGGCTCTGGGGTCTGG 60.609 66.667 0.00 0.00 0.00 3.86
2896 3338 3.406200 CTGGCTCTGGGGTCTGGG 61.406 72.222 0.00 0.00 0.00 4.45
3064 3532 3.245518 TGTCTCTCTCTCACTCTCTCG 57.754 52.381 0.00 0.00 0.00 4.04
3065 3533 2.565391 TGTCTCTCTCTCACTCTCTCGT 59.435 50.000 0.00 0.00 0.00 4.18
3066 3534 3.187700 GTCTCTCTCTCACTCTCTCGTC 58.812 54.545 0.00 0.00 0.00 4.20
3085 3553 0.163788 CGCGTGTGTTTCTCATGGTC 59.836 55.000 0.00 0.00 0.00 4.02
3088 3556 2.413239 GCGTGTGTTTCTCATGGTCATG 60.413 50.000 4.67 4.67 40.09 3.07
3089 3557 2.160219 CGTGTGTTTCTCATGGTCATGG 59.840 50.000 10.61 2.91 39.24 3.66
3091 3559 4.323417 GTGTGTTTCTCATGGTCATGGTA 58.677 43.478 10.61 0.00 39.24 3.25
3093 3561 4.285775 TGTGTTTCTCATGGTCATGGTAGA 59.714 41.667 10.61 5.01 39.24 2.59
3164 3632 2.093394 TGGCATTAAGTACGCCTGCTTA 60.093 45.455 9.69 0.00 46.39 3.09
3168 3636 4.035208 GCATTAAGTACGCCTGCTTAACAT 59.965 41.667 7.84 0.00 39.18 2.71
3186 3661 1.941294 CATGAGATGGCTTGAGTGCTC 59.059 52.381 0.00 0.00 0.00 4.26
3225 3702 1.377366 CGGTTCTGGAGCGCTCTCTA 61.377 60.000 34.46 20.53 42.83 2.43
3228 3705 1.107114 TTCTGGAGCGCTCTCTAAGG 58.893 55.000 34.46 18.15 39.31 2.69
3231 3708 0.257905 TGGAGCGCTCTCTAAGGGTA 59.742 55.000 34.46 9.10 40.03 3.69
3236 3713 1.202313 GCGCTCTCTAAGGGTACACAG 60.202 57.143 0.00 0.00 40.03 3.66
3252 3729 4.085357 ACACAGGTTTGACTGCTGATTA 57.915 40.909 0.00 0.00 42.21 1.75
3291 3779 3.192844 ACGACTATGGTACTGTGAAGGTG 59.807 47.826 0.00 0.00 0.00 4.00
3299 3787 2.584492 ACTGTGAAGGTGCTTTTTGC 57.416 45.000 0.00 0.00 43.25 3.68
3301 3789 1.065401 CTGTGAAGGTGCTTTTTGCGA 59.935 47.619 0.00 0.00 46.63 5.10
3304 3792 2.535574 GTGAAGGTGCTTTTTGCGAAAG 59.464 45.455 0.00 3.78 46.63 2.62
3309 3815 2.284150 GGTGCTTTTTGCGAAAGTTTCC 59.716 45.455 10.01 3.92 46.63 3.13
3317 3823 2.302260 TGCGAAAGTTTCCAATGTCCA 58.698 42.857 10.01 0.00 0.00 4.02
3369 3875 3.821421 AATCTACCGTGGGAACTCATC 57.179 47.619 0.00 0.00 0.00 2.92
3370 3876 2.225382 TCTACCGTGGGAACTCATCA 57.775 50.000 0.00 0.00 0.00 3.07
3371 3877 2.747177 TCTACCGTGGGAACTCATCAT 58.253 47.619 0.00 0.00 0.00 2.45
3399 3905 3.667497 TGACTATGGATTCGAGCCATC 57.333 47.619 20.95 11.59 44.70 3.51
3419 3925 5.916883 CCATCGCTCATGGTTTCATAAAATC 59.083 40.000 3.80 0.00 46.72 2.17
3420 3926 6.459985 CCATCGCTCATGGTTTCATAAAATCA 60.460 38.462 3.80 0.00 46.72 2.57
3429 3935 9.687210 CATGGTTTCATAAAATCAGTATGATGG 57.313 33.333 0.00 0.00 43.10 3.51
3439 3945 4.760530 TCAGTATGATGGCTTAAGTGCT 57.239 40.909 4.02 0.00 42.56 4.40
3440 3946 5.102953 TCAGTATGATGGCTTAAGTGCTT 57.897 39.130 4.02 0.00 42.56 3.91
3441 3947 5.500234 TCAGTATGATGGCTTAAGTGCTTT 58.500 37.500 4.02 0.00 42.56 3.51
3442 3948 5.355071 TCAGTATGATGGCTTAAGTGCTTTG 59.645 40.000 4.02 0.00 42.56 2.77
3443 3949 5.124457 CAGTATGATGGCTTAAGTGCTTTGT 59.876 40.000 4.02 0.00 39.69 2.83
3444 3950 4.708726 ATGATGGCTTAAGTGCTTTGTC 57.291 40.909 4.02 0.00 0.00 3.18
3445 3951 2.483877 TGATGGCTTAAGTGCTTTGTCG 59.516 45.455 4.02 0.00 0.00 4.35
3446 3952 1.234821 TGGCTTAAGTGCTTTGTCGG 58.765 50.000 4.02 0.00 0.00 4.79
3447 3953 1.235724 GGCTTAAGTGCTTTGTCGGT 58.764 50.000 4.02 0.00 0.00 4.69
3448 3954 1.069227 GGCTTAAGTGCTTTGTCGGTG 60.069 52.381 4.02 0.00 0.00 4.94
3449 3955 1.663161 GCTTAAGTGCTTTGTCGGTGC 60.663 52.381 4.02 0.00 0.00 5.01
3450 3956 1.873591 CTTAAGTGCTTTGTCGGTGCT 59.126 47.619 0.00 0.00 0.00 4.40
3451 3957 2.823924 TAAGTGCTTTGTCGGTGCTA 57.176 45.000 0.00 0.00 0.00 3.49
3452 3958 2.185004 AAGTGCTTTGTCGGTGCTAT 57.815 45.000 0.00 0.00 0.00 2.97
3453 3959 1.442769 AGTGCTTTGTCGGTGCTATG 58.557 50.000 0.00 0.00 0.00 2.23
3454 3960 1.001974 AGTGCTTTGTCGGTGCTATGA 59.998 47.619 0.00 0.00 0.00 2.15
3455 3961 1.128692 GTGCTTTGTCGGTGCTATGAC 59.871 52.381 0.00 0.00 35.67 3.06
3456 3962 1.001974 TGCTTTGTCGGTGCTATGACT 59.998 47.619 4.81 0.00 36.10 3.41
3457 3963 1.394917 GCTTTGTCGGTGCTATGACTG 59.605 52.381 4.81 0.00 36.10 3.51
3458 3964 2.688507 CTTTGTCGGTGCTATGACTGT 58.311 47.619 4.81 0.00 36.10 3.55
3459 3965 2.363788 TTGTCGGTGCTATGACTGTC 57.636 50.000 0.00 0.00 36.10 3.51
3460 3966 1.545841 TGTCGGTGCTATGACTGTCT 58.454 50.000 9.51 0.00 36.10 3.41
3461 3967 1.472878 TGTCGGTGCTATGACTGTCTC 59.527 52.381 9.51 0.00 36.10 3.36
3462 3968 1.746220 GTCGGTGCTATGACTGTCTCT 59.254 52.381 9.51 0.00 32.37 3.10
3463 3969 2.164624 GTCGGTGCTATGACTGTCTCTT 59.835 50.000 9.51 0.00 32.37 2.85
3464 3970 3.377485 GTCGGTGCTATGACTGTCTCTTA 59.623 47.826 9.51 0.00 32.37 2.10
3465 3971 3.628032 TCGGTGCTATGACTGTCTCTTAG 59.372 47.826 9.51 8.55 32.17 2.18
3466 3972 3.628032 CGGTGCTATGACTGTCTCTTAGA 59.372 47.826 9.51 0.00 31.07 2.10
3467 3973 4.277174 CGGTGCTATGACTGTCTCTTAGAT 59.723 45.833 9.51 0.00 31.07 1.98
3468 3974 5.561919 CGGTGCTATGACTGTCTCTTAGATC 60.562 48.000 9.51 0.00 31.07 2.75
3469 3975 5.278758 GGTGCTATGACTGTCTCTTAGATCC 60.279 48.000 9.51 9.13 31.07 3.36
3470 3976 5.534654 GTGCTATGACTGTCTCTTAGATCCT 59.465 44.000 9.51 0.00 31.07 3.24
3471 3977 5.534278 TGCTATGACTGTCTCTTAGATCCTG 59.466 44.000 9.51 0.00 31.07 3.86
3472 3978 5.048083 GCTATGACTGTCTCTTAGATCCTGG 60.048 48.000 9.51 0.00 31.07 4.45
3473 3979 4.592997 TGACTGTCTCTTAGATCCTGGA 57.407 45.455 9.51 0.00 0.00 3.86
3474 3980 5.136068 TGACTGTCTCTTAGATCCTGGAT 57.864 43.478 9.42 9.42 0.00 3.41
3475 3981 5.523588 TGACTGTCTCTTAGATCCTGGATT 58.476 41.667 11.17 3.85 0.00 3.01
3476 3982 5.596361 TGACTGTCTCTTAGATCCTGGATTC 59.404 44.000 11.17 4.48 0.00 2.52
3477 3983 4.582656 ACTGTCTCTTAGATCCTGGATTCG 59.417 45.833 11.17 0.36 0.00 3.34
3478 3984 4.793201 TGTCTCTTAGATCCTGGATTCGA 58.207 43.478 11.17 4.62 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 234 5.638530 ATTTTTAGCTTTCCCCAAAACCA 57.361 34.783 0.00 0.00 0.00 3.67
295 304 1.614317 CGAGAAACAAATGGAGGGGCT 60.614 52.381 0.00 0.00 0.00 5.19
296 305 0.811281 CGAGAAACAAATGGAGGGGC 59.189 55.000 0.00 0.00 0.00 5.80
297 306 1.463674 CCGAGAAACAAATGGAGGGG 58.536 55.000 0.00 0.00 0.00 4.79
299 308 1.740025 GAGCCGAGAAACAAATGGAGG 59.260 52.381 0.00 0.00 0.00 4.30
300 309 1.394917 CGAGCCGAGAAACAAATGGAG 59.605 52.381 0.00 0.00 0.00 3.86
301 310 1.438651 CGAGCCGAGAAACAAATGGA 58.561 50.000 0.00 0.00 0.00 3.41
439 469 4.514577 CCGCCGCTACCCACTCTG 62.515 72.222 0.00 0.00 0.00 3.35
635 683 5.221224 ACACAACACAAGGATAACAATGGTG 60.221 40.000 0.00 0.00 0.00 4.17
637 685 5.221224 ACACACAACACAAGGATAACAATGG 60.221 40.000 0.00 0.00 0.00 3.16
655 703 3.181449 ACCAGCCATGTAACTAACACACA 60.181 43.478 0.00 0.00 42.09 3.72
656 704 3.408634 ACCAGCCATGTAACTAACACAC 58.591 45.455 0.00 0.00 42.09 3.82
657 705 3.780804 ACCAGCCATGTAACTAACACA 57.219 42.857 0.00 0.00 42.09 3.72
658 706 5.447624 AAAACCAGCCATGTAACTAACAC 57.552 39.130 0.00 0.00 42.09 3.32
659 707 4.521256 GGAAAACCAGCCATGTAACTAACA 59.479 41.667 0.00 0.00 43.86 2.41
660 708 4.521256 TGGAAAACCAGCCATGTAACTAAC 59.479 41.667 0.00 0.00 0.00 2.34
661 709 4.730966 TGGAAAACCAGCCATGTAACTAA 58.269 39.130 0.00 0.00 0.00 2.24
662 710 4.374689 TGGAAAACCAGCCATGTAACTA 57.625 40.909 0.00 0.00 0.00 2.24
663 711 3.237268 TGGAAAACCAGCCATGTAACT 57.763 42.857 0.00 0.00 0.00 2.24
712 764 2.840038 ACCATCTAACAGATCAGCACCA 59.160 45.455 0.00 0.00 31.32 4.17
727 779 3.016736 CGCCAGAATTACCAAACCATCT 58.983 45.455 0.00 0.00 0.00 2.90
756 808 6.868864 TCAAACAACGGAAACAAAATTCAAGA 59.131 30.769 0.00 0.00 0.00 3.02
773 825 5.012328 TGTAACCATGGGTTTCAAACAAC 57.988 39.130 18.09 2.00 44.33 3.32
809 862 3.473625 AGGTCAGTTGGTTAAAAGTCCG 58.526 45.455 0.00 0.00 0.00 4.79
851 904 3.248418 TGCCTGCCTACCTGCACA 61.248 61.111 0.00 0.00 36.04 4.57
910 963 3.486383 ACCAACACTCGGATCAAATGTT 58.514 40.909 0.00 0.00 33.86 2.71
935 988 0.768221 TCTGGCTCCCACTTTGACCT 60.768 55.000 0.00 0.00 0.00 3.85
1038 1091 0.105194 TGTTCCCACTCTCCAGGTCA 60.105 55.000 0.00 0.00 0.00 4.02
1058 1111 0.652592 ATGCTCGCTGATAACAACGC 59.347 50.000 0.00 0.00 35.87 4.84
1146 1199 0.448990 CATCCTTGGTGTGCATGACG 59.551 55.000 0.00 0.00 0.00 4.35
1263 1316 1.133167 TCACCTCCAGAACTGTCCAGA 60.133 52.381 0.40 0.00 0.00 3.86
1580 1660 6.594744 TCTTCCATACAAGCATGACATATGT 58.405 36.000 8.43 8.43 0.00 2.29
1581 1661 7.012610 TGTTCTTCCATACAAGCATGACATATG 59.987 37.037 0.00 0.00 0.00 1.78
1582 1662 7.056006 TGTTCTTCCATACAAGCATGACATAT 58.944 34.615 0.00 0.00 0.00 1.78
1584 1664 5.255687 TGTTCTTCCATACAAGCATGACAT 58.744 37.500 0.00 0.00 0.00 3.06
1611 1691 9.660180 AAGGTTTTGCTTCATTTGTAAACTAAA 57.340 25.926 0.00 0.00 0.00 1.85
1613 1693 9.308318 GAAAGGTTTTGCTTCATTTGTAAACTA 57.692 29.630 0.00 0.00 0.00 2.24
1614 1694 8.040727 AGAAAGGTTTTGCTTCATTTGTAAACT 58.959 29.630 0.00 0.00 0.00 2.66
1781 1891 6.649155 TGCTCAATAATAGAACTGGCTGTTA 58.351 36.000 9.88 0.00 39.30 2.41
1864 1981 4.057406 TGAACAATTTGACAAGCAAGGG 57.943 40.909 2.79 0.00 37.87 3.95
2009 2126 9.807386 GCTTAACAAACAGTTAACAGTATGTAG 57.193 33.333 8.61 4.69 45.65 2.74
2067 2472 5.793817 AGGGATTTTAGTGTGCCAATTTTC 58.206 37.500 0.00 0.00 0.00 2.29
2072 2477 3.571590 ACAAGGGATTTTAGTGTGCCAA 58.428 40.909 0.00 0.00 0.00 4.52
2098 2503 3.244422 TGGAGCAAAACCCTGTAGTGTAG 60.244 47.826 0.00 0.00 0.00 2.74
2119 2526 2.286872 CTTACTCCAGATGCTTGCCTG 58.713 52.381 0.00 0.00 0.00 4.85
2164 2571 2.364970 CAGGCTGCTATGCTCTCTAACT 59.635 50.000 0.00 0.00 0.00 2.24
2295 2705 5.412594 CAGATCTTGAGATTTCGGGTTTCAA 59.587 40.000 0.00 0.00 34.37 2.69
2340 2750 3.003689 GCACATCATAGCATGGTTGGTAC 59.996 47.826 1.12 0.00 38.56 3.34
2341 2751 3.117926 AGCACATCATAGCATGGTTGGTA 60.118 43.478 1.12 0.00 39.94 3.25
2342 2752 2.026641 GCACATCATAGCATGGTTGGT 58.973 47.619 1.12 0.00 37.36 3.67
2343 2753 2.034179 CAGCACATCATAGCATGGTTGG 59.966 50.000 1.12 0.00 0.00 3.77
2344 2754 2.543031 GCAGCACATCATAGCATGGTTG 60.543 50.000 1.12 0.00 0.00 3.77
2345 2755 1.679680 GCAGCACATCATAGCATGGTT 59.320 47.619 1.12 0.00 0.00 3.67
2360 2770 1.183030 AAGCAAAGGCATCAGCAGCA 61.183 50.000 0.00 0.00 44.61 4.41
2375 2785 1.133823 TGCAGAGGTTGAAGGAAAGCA 60.134 47.619 0.00 0.00 0.00 3.91
2376 2786 1.538950 CTGCAGAGGTTGAAGGAAAGC 59.461 52.381 8.42 0.00 0.00 3.51
2391 2802 1.678269 GCGTCTCGTAGTTGCTGCAG 61.678 60.000 10.11 10.11 0.00 4.41
2535 2965 3.322466 CCTGTCGTGGGGGAGCTT 61.322 66.667 0.00 0.00 0.00 3.74
2703 3138 1.592400 CGCTCGGGACTGACTTACCA 61.592 60.000 0.00 0.00 0.00 3.25
2861 3303 1.967066 CAGTGACACTCTCTCAACCCT 59.033 52.381 4.74 0.00 0.00 4.34
2862 3304 1.001406 CCAGTGACACTCTCTCAACCC 59.999 57.143 4.74 0.00 0.00 4.11
2863 3305 1.606737 GCCAGTGACACTCTCTCAACC 60.607 57.143 4.74 0.00 0.00 3.77
2864 3306 1.342819 AGCCAGTGACACTCTCTCAAC 59.657 52.381 4.74 0.00 0.00 3.18
2865 3307 1.615883 GAGCCAGTGACACTCTCTCAA 59.384 52.381 20.56 0.00 0.00 3.02
2866 3308 1.202989 AGAGCCAGTGACACTCTCTCA 60.203 52.381 24.43 0.00 35.96 3.27
2867 3309 1.202114 CAGAGCCAGTGACACTCTCTC 59.798 57.143 19.10 19.02 38.72 3.20
2868 3310 1.255882 CAGAGCCAGTGACACTCTCT 58.744 55.000 17.12 17.12 38.72 3.10
2904 3346 2.109181 GGATCTACACCGCCCAGC 59.891 66.667 0.00 0.00 0.00 4.85
2905 3347 0.469331 TAGGGATCTACACCGCCCAG 60.469 60.000 0.00 0.00 43.20 4.45
2985 3436 6.682113 GCTTGCTTAACCATCATCATTGACAT 60.682 38.462 0.00 0.00 33.85 3.06
3064 3532 0.163788 CCATGAGAAACACACGCGAC 59.836 55.000 15.93 0.00 0.00 5.19
3065 3533 0.249699 ACCATGAGAAACACACGCGA 60.250 50.000 15.93 0.00 0.00 5.87
3066 3534 0.163788 GACCATGAGAAACACACGCG 59.836 55.000 3.53 3.53 0.00 6.01
3085 3553 2.103771 CCATGTGAGGAGGTCTACCATG 59.896 54.545 1.26 0.00 38.89 3.66
3088 3556 0.466124 GCCATGTGAGGAGGTCTACC 59.534 60.000 0.00 0.00 0.00 3.18
3089 3557 0.103208 CGCCATGTGAGGAGGTCTAC 59.897 60.000 0.00 0.00 0.00 2.59
3091 3559 1.194781 AACGCCATGTGAGGAGGTCT 61.195 55.000 0.00 0.00 32.16 3.85
3093 3561 1.003355 CAACGCCATGTGAGGAGGT 60.003 57.895 0.00 0.00 32.16 3.85
3164 3632 2.089980 GCACTCAAGCCATCTCATGTT 58.910 47.619 0.00 0.00 0.00 2.71
3168 3636 1.066358 CAGAGCACTCAAGCCATCTCA 60.066 52.381 0.00 0.00 34.23 3.27
3186 3661 1.066303 GGAGAGTCATAGCACCGACAG 59.934 57.143 0.00 0.00 34.48 3.51
3225 3702 2.748465 GCAGTCAAACCTGTGTACCCTT 60.748 50.000 0.00 0.00 34.84 3.95
3228 3705 1.873591 CAGCAGTCAAACCTGTGTACC 59.126 52.381 0.00 0.00 34.84 3.34
3231 3708 2.645838 ATCAGCAGTCAAACCTGTGT 57.354 45.000 0.00 0.00 34.84 3.72
3267 3755 4.639310 ACCTTCACAGTACCATAGTCGTAG 59.361 45.833 0.00 0.00 0.00 3.51
3268 3756 4.397103 CACCTTCACAGTACCATAGTCGTA 59.603 45.833 0.00 0.00 0.00 3.43
3269 3757 3.192844 CACCTTCACAGTACCATAGTCGT 59.807 47.826 0.00 0.00 0.00 4.34
3270 3758 3.770666 CACCTTCACAGTACCATAGTCG 58.229 50.000 0.00 0.00 0.00 4.18
3271 3759 3.195825 AGCACCTTCACAGTACCATAGTC 59.804 47.826 0.00 0.00 0.00 2.59
3272 3760 3.173965 AGCACCTTCACAGTACCATAGT 58.826 45.455 0.00 0.00 0.00 2.12
3273 3761 3.895232 AGCACCTTCACAGTACCATAG 57.105 47.619 0.00 0.00 0.00 2.23
3274 3762 4.634012 AAAGCACCTTCACAGTACCATA 57.366 40.909 0.00 0.00 0.00 2.74
3275 3763 3.508845 AAAGCACCTTCACAGTACCAT 57.491 42.857 0.00 0.00 0.00 3.55
3276 3764 3.290948 AAAAGCACCTTCACAGTACCA 57.709 42.857 0.00 0.00 0.00 3.25
3277 3765 3.795488 GCAAAAAGCACCTTCACAGTACC 60.795 47.826 0.00 0.00 44.79 3.34
3291 3779 4.033932 ACATTGGAAACTTTCGCAAAAAGC 59.966 37.500 8.16 0.00 40.87 3.51
3299 3787 4.932146 ACTTTGGACATTGGAAACTTTCG 58.068 39.130 0.00 0.00 0.00 3.46
3301 3789 6.127196 TGCTTACTTTGGACATTGGAAACTTT 60.127 34.615 0.00 0.00 0.00 2.66
3304 3792 5.195001 TGCTTACTTTGGACATTGGAAAC 57.805 39.130 0.00 0.00 0.00 2.78
3309 3815 4.911610 CGAGTTTGCTTACTTTGGACATTG 59.088 41.667 0.00 0.00 0.00 2.82
3317 3823 5.682943 TGTATTGCGAGTTTGCTTACTTT 57.317 34.783 0.00 0.00 35.36 2.66
3369 3875 6.691508 TCGAATCCATAGTCAATCCTACATG 58.308 40.000 0.00 0.00 0.00 3.21
3370 3876 6.573289 GCTCGAATCCATAGTCAATCCTACAT 60.573 42.308 0.00 0.00 0.00 2.29
3371 3877 5.279006 GCTCGAATCCATAGTCAATCCTACA 60.279 44.000 0.00 0.00 0.00 2.74
3399 3905 5.883661 ACTGATTTTATGAAACCATGAGCG 58.116 37.500 0.00 0.00 0.00 5.03
3419 3925 5.124457 ACAAAGCACTTAAGCCATCATACTG 59.876 40.000 1.29 0.00 34.23 2.74
3420 3926 5.256474 ACAAAGCACTTAAGCCATCATACT 58.744 37.500 1.29 0.00 34.23 2.12
3428 3934 1.069227 CACCGACAAAGCACTTAAGCC 60.069 52.381 1.29 0.00 34.23 4.35
3429 3935 1.663161 GCACCGACAAAGCACTTAAGC 60.663 52.381 1.29 0.00 0.00 3.09
3430 3936 1.873591 AGCACCGACAAAGCACTTAAG 59.126 47.619 0.00 0.00 0.00 1.85
3431 3937 1.961793 AGCACCGACAAAGCACTTAA 58.038 45.000 0.00 0.00 0.00 1.85
3432 3938 2.823924 TAGCACCGACAAAGCACTTA 57.176 45.000 0.00 0.00 0.00 2.24
3433 3939 1.806542 CATAGCACCGACAAAGCACTT 59.193 47.619 0.00 0.00 0.00 3.16
3434 3940 1.001974 TCATAGCACCGACAAAGCACT 59.998 47.619 0.00 0.00 0.00 4.40
3435 3941 1.128692 GTCATAGCACCGACAAAGCAC 59.871 52.381 0.00 0.00 32.24 4.40
3436 3942 1.001974 AGTCATAGCACCGACAAAGCA 59.998 47.619 0.00 0.00 34.48 3.91
3437 3943 1.394917 CAGTCATAGCACCGACAAAGC 59.605 52.381 0.00 0.00 34.48 3.51
3438 3944 2.668457 GACAGTCATAGCACCGACAAAG 59.332 50.000 0.00 0.00 34.48 2.77
3439 3945 2.299013 AGACAGTCATAGCACCGACAAA 59.701 45.455 2.66 0.00 34.48 2.83
3440 3946 1.893137 AGACAGTCATAGCACCGACAA 59.107 47.619 2.66 0.00 34.48 3.18
3441 3947 1.472878 GAGACAGTCATAGCACCGACA 59.527 52.381 2.66 0.00 34.48 4.35
3442 3948 1.746220 AGAGACAGTCATAGCACCGAC 59.254 52.381 2.66 0.00 0.00 4.79
3443 3949 2.130272 AGAGACAGTCATAGCACCGA 57.870 50.000 2.66 0.00 0.00 4.69
3444 3950 2.949451 AAGAGACAGTCATAGCACCG 57.051 50.000 2.66 0.00 0.00 4.94
3445 3951 5.278758 GGATCTAAGAGACAGTCATAGCACC 60.279 48.000 2.66 5.75 0.00 5.01
3446 3952 5.534654 AGGATCTAAGAGACAGTCATAGCAC 59.465 44.000 2.66 1.14 0.00 4.40
3447 3953 5.534278 CAGGATCTAAGAGACAGTCATAGCA 59.466 44.000 2.66 0.00 0.00 3.49
3448 3954 5.048083 CCAGGATCTAAGAGACAGTCATAGC 60.048 48.000 2.66 0.00 0.00 2.97
3449 3955 6.303054 TCCAGGATCTAAGAGACAGTCATAG 58.697 44.000 2.66 2.85 0.00 2.23
3450 3956 6.267492 TCCAGGATCTAAGAGACAGTCATA 57.733 41.667 2.66 0.00 0.00 2.15
3451 3957 5.136068 TCCAGGATCTAAGAGACAGTCAT 57.864 43.478 2.66 0.00 0.00 3.06
3452 3958 4.592997 TCCAGGATCTAAGAGACAGTCA 57.407 45.455 2.66 0.00 0.00 3.41
3453 3959 5.278266 CGAATCCAGGATCTAAGAGACAGTC 60.278 48.000 1.11 0.00 0.00 3.51
3454 3960 4.582656 CGAATCCAGGATCTAAGAGACAGT 59.417 45.833 1.11 0.00 0.00 3.55
3455 3961 4.824537 TCGAATCCAGGATCTAAGAGACAG 59.175 45.833 1.11 0.00 0.00 3.51
3456 3962 4.793201 TCGAATCCAGGATCTAAGAGACA 58.207 43.478 1.11 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.