Multiple sequence alignment - TraesCS2D01G128400

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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 TraesCS2D01G128400 chr2D 100.000 3860 0 0 1 3860 74935661 74939520 0.000000e+00 7129.0
1 TraesCS2D01G128400 chr2D 84.118 510 26 18 3024 3521 365349041 365349507 3.540000e-120 442.0
2 TraesCS2D01G128400 chr2D 88.393 112 5 1 2810 2921 365348913 365349016 1.130000e-25 128.0
3 TraesCS2D01G128400 chr2A 95.562 3200 123 11 1 3196 74105450 74108634 0.000000e+00 5105.0
4 TraesCS2D01G128400 chr2B 92.250 3045 175 25 35 3050 114045983 114048995 0.000000e+00 4259.0
5 TraesCS2D01G128400 chr2B 90.180 611 27 12 3034 3633 114049007 114049595 0.000000e+00 765.0
6 TraesCS2D01G128400 chr1A 86.600 597 46 19 3049 3633 551483752 551484326 2.530000e-176 628.0
7 TraesCS2D01G128400 chr1A 88.372 215 15 4 2669 2873 551483197 551483411 2.300000e-62 250.0
8 TraesCS2D01G128400 chr1A 91.200 125 5 3 2868 2987 551483613 551483736 8.580000e-37 165.0
9 TraesCS2D01G128400 chr1A 95.652 46 2 0 3726 3771 551487871 551487916 1.490000e-09 75.0
10 TraesCS2D01G128400 chr1A 93.750 48 1 2 3633 3679 551484355 551484401 1.920000e-08 71.3
11 TraesCS2D01G128400 chr1D 89.222 501 29 10 3138 3633 459049210 459049690 1.530000e-168 603.0
12 TraesCS2D01G128400 chr1D 84.895 523 23 17 3024 3536 215043364 215042888 9.700000e-131 477.0
13 TraesCS2D01G128400 chr1D 89.516 372 21 5 2624 2987 459048580 459048941 4.550000e-124 455.0
14 TraesCS2D01G128400 chr1D 87.202 336 23 10 3244 3568 339905557 339905231 7.880000e-97 364.0
15 TraesCS2D01G128400 chr1D 88.983 118 8 1 789 901 459047907 459048024 1.450000e-29 141.0
16 TraesCS2D01G128400 chr1D 95.588 68 3 0 3024 3091 66760381 66760314 4.080000e-20 110.0
17 TraesCS2D01G128400 chr1D 97.222 36 0 1 3645 3679 459049730 459049765 4.160000e-05 60.2
18 TraesCS2D01G128400 chr1B 82.609 529 46 15 2467 2987 631227858 631228348 3.560000e-115 425.0
19 TraesCS2D01G128400 chr1B 89.637 193 17 3 19 210 280475879 280475689 3.850000e-60 243.0
20 TraesCS2D01G128400 chr1B 82.373 295 25 9 1699 1986 631227316 631227590 8.340000e-57 231.0
21 TraesCS2D01G128400 chr1B 95.588 68 3 0 3024 3091 513973843 513973776 4.080000e-20 110.0
22 TraesCS2D01G128400 chr1B 95.588 68 3 0 3024 3091 542807930 542807863 4.080000e-20 110.0
23 TraesCS2D01G128400 chr1B 94.444 36 0 2 2036 2071 631227630 631227663 2.000000e-03 54.7
24 TraesCS2D01G128400 chr1B 94.444 36 1 1 3645 3679 631228913 631228948 2.000000e-03 54.7
25 TraesCS2D01G128400 chr4A 90.155 193 16 3 19 210 29364759 29364949 8.280000e-62 248.0
26 TraesCS2D01G128400 chr4A 90.155 193 16 3 19 210 428995001 428994811 8.280000e-62 248.0
27 TraesCS2D01G128400 chr4A 88.725 204 20 3 19 221 708069882 708069681 2.980000e-61 246.0
28 TraesCS2D01G128400 chr4A 88.725 204 20 3 19 221 708092537 708092336 2.980000e-61 246.0
29 TraesCS2D01G128400 chrUn 88.725 204 20 3 19 221 50448694 50448493 2.980000e-61 246.0
30 TraesCS2D01G128400 chrUn 95.588 68 3 0 3024 3091 93959203 93959136 4.080000e-20 110.0
31 TraesCS2D01G128400 chr4B 89.637 193 17 3 19 210 458279164 458278974 3.850000e-60 243.0
32 TraesCS2D01G128400 chr7A 88.235 204 21 3 19 221 266940941 266940740 1.390000e-59 241.0
33 TraesCS2D01G128400 chr7A 95.588 68 3 0 3024 3091 727859951 727859884 4.080000e-20 110.0
34 TraesCS2D01G128400 chr7D 95.588 68 3 0 3024 3091 568459043 568458976 4.080000e-20 110.0
35 TraesCS2D01G128400 chr5B 95.588 68 3 0 3024 3091 43858160 43858227 4.080000e-20 110.0


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 TraesCS2D01G128400 chr2D 74935661 74939520 3859 False 7129.00 7129 100.00000 1 3860 1 chr2D.!!$F1 3859
1 TraesCS2D01G128400 chr2D 365348913 365349507 594 False 285.00 442 86.25550 2810 3521 2 chr2D.!!$F2 711
2 TraesCS2D01G128400 chr2A 74105450 74108634 3184 False 5105.00 5105 95.56200 1 3196 1 chr2A.!!$F1 3195
3 TraesCS2D01G128400 chr2B 114045983 114049595 3612 False 2512.00 4259 91.21500 35 3633 2 chr2B.!!$F1 3598
4 TraesCS2D01G128400 chr1A 551483197 551487916 4719 False 237.86 628 91.11480 2669 3771 5 chr1A.!!$F1 1102
5 TraesCS2D01G128400 chr1D 459047907 459049765 1858 False 314.80 603 91.23575 789 3679 4 chr1D.!!$F1 2890

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
523 524 1.000163 ACTGCAGACCACTACGAACTG 60.000 52.381 23.35 0.00 0.0 3.16 F
539 540 1.039068 ACTGGCAGATCTGATCGAGG 58.961 55.000 27.04 11.07 0.0 4.63 F
2319 2372 0.596082 AAAGGGTTTTCGATGCGGTG 59.404 50.000 0.00 0.00 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1373 1.073722 CTTGAGGACCAGCAGCCAA 59.926 57.895 0.0 0.0 0.00 4.52 R
2453 2506 1.893137 TGAGTATCAAGGCGACACACT 59.107 47.619 0.0 0.0 45.97 3.55 R
3528 4064 0.320247 GAGGCCGATGAGCGATGATT 60.320 55.000 0.0 0.0 44.57 2.57 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
371 372 3.926527 CAGAAGCATCACAAACGCTACTA 59.073 43.478 0.00 0.00 34.11 1.82
386 387 4.092968 ACGCTACTAATAAGCAAACACAGC 59.907 41.667 0.00 0.00 40.08 4.40
407 408 1.538512 CCGCATCCAGCCAGATAAATG 59.461 52.381 0.00 0.00 41.38 2.32
523 524 1.000163 ACTGCAGACCACTACGAACTG 60.000 52.381 23.35 0.00 0.00 3.16
539 540 1.039068 ACTGGCAGATCTGATCGAGG 58.961 55.000 27.04 11.07 0.00 4.63
699 700 1.425428 CTTGTCGAATTCGCTGGGC 59.575 57.895 22.90 10.33 39.60 5.36
728 729 2.892425 CGGCGCAGGAGGCTAAAG 60.892 66.667 10.83 0.00 41.67 1.85
991 999 4.882396 GCCTTCTCCGGCGAGCTC 62.882 72.222 9.30 2.73 40.79 4.09
992 1000 4.214327 CCTTCTCCGGCGAGCTCC 62.214 72.222 9.30 0.47 35.94 4.70
993 1001 4.214327 CTTCTCCGGCGAGCTCCC 62.214 72.222 9.30 9.59 35.94 4.30
994 1002 4.761058 TTCTCCGGCGAGCTCCCT 62.761 66.667 9.30 0.00 35.94 4.20
1046 1054 4.749310 CTCGCTGGCCTCGCAAGT 62.749 66.667 16.09 0.00 31.11 3.16
1206 1214 3.069318 GAGCTCGGGTCCGACCTT 61.069 66.667 17.27 0.00 44.01 3.50
1585 1620 9.322776 GATTATGAAGCAATTGAATTAGCTACG 57.677 33.333 10.34 0.00 36.07 3.51
1695 1745 8.464404 TGAGATTTTATTTGCTTGGAGAATGAG 58.536 33.333 0.00 0.00 0.00 2.90
1714 1764 4.424626 TGAGCATGCTCTTAGTTTACTCG 58.575 43.478 39.46 0.00 43.12 4.18
1829 1882 4.877378 ATTGCATCAATGGTGACTGTTT 57.123 36.364 0.00 0.00 36.31 2.83
2302 2355 1.378514 GATTCAGAGGGGGCGCAAA 60.379 57.895 10.83 0.00 0.00 3.68
2319 2372 0.596082 AAAGGGTTTTCGATGCGGTG 59.404 50.000 0.00 0.00 0.00 4.94
2453 2506 1.593209 GACTGGAACCGTGCGACAA 60.593 57.895 0.00 0.00 0.00 3.18
2473 2526 1.893137 AGTGTGTCGCCTTGATACTCA 59.107 47.619 0.00 0.00 39.29 3.41
2651 2704 5.184287 AGGAAGTGAGTAAGAGTAGCAAGAC 59.816 44.000 0.00 0.00 0.00 3.01
2692 2746 1.618837 TGAAGGAAGGGACGAAGAGTG 59.381 52.381 0.00 0.00 0.00 3.51
2789 2876 1.637553 ACCCAGCATTTCAGTCCAGAT 59.362 47.619 0.00 0.00 0.00 2.90
2816 2903 0.595095 GCAACCAACAGGAAGAGCAG 59.405 55.000 0.00 0.00 0.00 4.24
2873 2961 4.846779 TTTTGTAACTCCAGTGCCATTC 57.153 40.909 0.00 0.00 0.00 2.67
2986 3287 6.621613 TGTGAGTAAGTGTATGTAGCTGAAG 58.378 40.000 0.00 0.00 0.00 3.02
3015 3316 5.814705 AGTGCAGAAGAGAAATAAGATTCCG 59.185 40.000 0.00 0.00 0.00 4.30
3030 3331 2.343163 TTCCGCAAAACCAGGCAACG 62.343 55.000 0.00 0.00 46.39 4.10
3093 3424 0.601311 AAGCAGACTCGAGTGCAACC 60.601 55.000 25.58 8.06 42.47 3.77
3172 3672 5.359009 CCTCAAAATGTATCCAAGTGCAGAT 59.641 40.000 0.00 0.00 0.00 2.90
3288 3803 4.836125 AATGCAAGACCAAACTACTGTG 57.164 40.909 0.00 0.00 0.00 3.66
3310 3831 4.775780 TGGTGCAACAGGACTACTTACTAT 59.224 41.667 0.00 0.00 39.98 2.12
3311 3832 5.953548 TGGTGCAACAGGACTACTTACTATA 59.046 40.000 0.00 0.00 39.98 1.31
3312 3833 6.610020 TGGTGCAACAGGACTACTTACTATAT 59.390 38.462 0.00 0.00 39.98 0.86
3313 3834 6.924060 GGTGCAACAGGACTACTTACTATATG 59.076 42.308 0.00 0.00 39.98 1.78
3319 3840 8.380743 ACAGGACTACTTACTATATGACGAAG 57.619 38.462 0.00 0.00 0.00 3.79
3392 3917 6.938596 TCAATCCATGCTCTTCCACATTATAG 59.061 38.462 0.00 0.00 0.00 1.31
3394 3919 5.858381 TCCATGCTCTTCCACATTATAGAC 58.142 41.667 0.00 0.00 0.00 2.59
3395 3920 4.999950 CCATGCTCTTCCACATTATAGACC 59.000 45.833 0.00 0.00 0.00 3.85
3396 3921 5.221803 CCATGCTCTTCCACATTATAGACCT 60.222 44.000 0.00 0.00 0.00 3.85
3397 3922 5.537300 TGCTCTTCCACATTATAGACCTC 57.463 43.478 0.00 0.00 0.00 3.85
3398 3923 4.962362 TGCTCTTCCACATTATAGACCTCA 59.038 41.667 0.00 0.00 0.00 3.86
3448 3979 6.531503 TGAAAGATTCAATAGTCGAGACCT 57.468 37.500 0.00 0.00 36.59 3.85
3534 4070 9.308318 GAACAAAGAGGTTCTAGTCTAATCATC 57.692 37.037 0.00 0.00 42.98 2.92
3535 4071 7.484975 ACAAAGAGGTTCTAGTCTAATCATCG 58.515 38.462 0.00 0.00 0.00 3.84
3536 4072 5.699097 AGAGGTTCTAGTCTAATCATCGC 57.301 43.478 0.00 0.00 0.00 4.58
3633 4169 3.882888 AGCATCACGGTTCTTCTTTTTCA 59.117 39.130 0.00 0.00 0.00 2.69
3635 4171 4.853743 GCATCACGGTTCTTCTTTTTCATC 59.146 41.667 0.00 0.00 0.00 2.92
3636 4172 4.725556 TCACGGTTCTTCTTTTTCATCG 57.274 40.909 0.00 0.00 0.00 3.84
3637 4173 3.059188 TCACGGTTCTTCTTTTTCATCGC 60.059 43.478 0.00 0.00 0.00 4.58
3639 4175 2.225491 CGGTTCTTCTTTTTCATCGCCA 59.775 45.455 0.00 0.00 0.00 5.69
3641 4177 4.615912 CGGTTCTTCTTTTTCATCGCCATT 60.616 41.667 0.00 0.00 0.00 3.16
3643 4179 5.460646 GTTCTTCTTTTTCATCGCCATTGA 58.539 37.500 0.00 0.00 0.00 2.57
3676 4240 0.189822 GATCCTGGGGCTCCTCTAGT 59.810 60.000 3.07 0.00 0.00 2.57
3678 4242 0.325671 TCCTGGGGCTCCTCTAGTTG 60.326 60.000 3.07 0.00 0.00 3.16
3680 4244 1.977293 CTGGGGCTCCTCTAGTTGGC 61.977 65.000 3.07 0.00 0.00 4.52
3681 4245 1.995626 GGGGCTCCTCTAGTTGGCA 60.996 63.158 0.00 0.00 0.00 4.92
3682 4246 1.348775 GGGGCTCCTCTAGTTGGCAT 61.349 60.000 0.00 0.00 0.00 4.40
3683 4247 0.107643 GGGCTCCTCTAGTTGGCATC 59.892 60.000 0.00 0.00 0.00 3.91
3684 4248 0.833287 GGCTCCTCTAGTTGGCATCA 59.167 55.000 0.00 0.00 0.00 3.07
3692 7583 4.460382 CCTCTAGTTGGCATCACACAATTT 59.540 41.667 0.00 0.00 0.00 1.82
3696 7587 6.939730 TCTAGTTGGCATCACACAATTTTCTA 59.060 34.615 0.00 0.00 0.00 2.10
3707 7598 5.304357 CACACAATTTTCTACCCCTCCTTTT 59.696 40.000 0.00 0.00 0.00 2.27
3713 7604 4.772886 TTCTACCCCTCCTTTTGCTATC 57.227 45.455 0.00 0.00 0.00 2.08
3718 7609 4.055094 ACCCCTCCTTTTGCTATCCTAAT 58.945 43.478 0.00 0.00 0.00 1.73
3719 7610 4.141158 ACCCCTCCTTTTGCTATCCTAATG 60.141 45.833 0.00 0.00 0.00 1.90
3721 7612 5.073144 CCCCTCCTTTTGCTATCCTAATGTA 59.927 44.000 0.00 0.00 0.00 2.29
3722 7613 6.410388 CCCCTCCTTTTGCTATCCTAATGTAA 60.410 42.308 0.00 0.00 0.00 2.41
3724 7615 7.559897 CCCTCCTTTTGCTATCCTAATGTAAAA 59.440 37.037 0.00 0.00 0.00 1.52
3725 7616 8.966868 CCTCCTTTTGCTATCCTAATGTAAAAA 58.033 33.333 0.00 0.00 0.00 1.94
3761 7749 2.993220 TGTACTGTGAAACTGCTATGCG 59.007 45.455 0.00 0.00 39.67 4.73
3771 7759 1.269778 ACTGCTATGCGCACGATACAT 60.270 47.619 14.90 0.00 45.47 2.29
3772 7760 1.125566 CTGCTATGCGCACGATACATG 59.874 52.381 14.90 0.00 45.47 3.21
3773 7761 0.439985 GCTATGCGCACGATACATGG 59.560 55.000 14.90 0.00 38.92 3.66
3774 7762 1.070821 CTATGCGCACGATACATGGG 58.929 55.000 14.90 0.00 0.00 4.00
3775 7763 0.391228 TATGCGCACGATACATGGGT 59.609 50.000 14.90 0.00 32.82 4.51
3776 7764 0.880278 ATGCGCACGATACATGGGTC 60.880 55.000 14.90 0.00 32.82 4.46
3777 7765 1.227263 GCGCACGATACATGGGTCT 60.227 57.895 0.30 0.00 32.82 3.85
3778 7766 0.031585 GCGCACGATACATGGGTCTA 59.968 55.000 0.30 0.00 32.82 2.59
3779 7767 1.336887 GCGCACGATACATGGGTCTAT 60.337 52.381 0.30 0.00 32.82 1.98
3780 7768 2.866460 GCGCACGATACATGGGTCTATT 60.866 50.000 0.30 0.00 32.82 1.73
3781 7769 2.987149 CGCACGATACATGGGTCTATTC 59.013 50.000 0.00 0.00 0.00 1.75
3782 7770 3.305403 CGCACGATACATGGGTCTATTCT 60.305 47.826 0.00 0.00 0.00 2.40
3783 7771 4.632153 GCACGATACATGGGTCTATTCTT 58.368 43.478 0.00 0.00 0.00 2.52
3784 7772 4.686554 GCACGATACATGGGTCTATTCTTC 59.313 45.833 0.00 0.00 0.00 2.87
3785 7773 4.917998 CACGATACATGGGTCTATTCTTCG 59.082 45.833 0.00 0.00 0.00 3.79
3786 7774 4.583489 ACGATACATGGGTCTATTCTTCGT 59.417 41.667 0.00 0.00 0.00 3.85
3787 7775 5.068723 ACGATACATGGGTCTATTCTTCGTT 59.931 40.000 0.00 0.00 32.81 3.85
3788 7776 6.263842 ACGATACATGGGTCTATTCTTCGTTA 59.736 38.462 0.00 0.00 32.81 3.18
3789 7777 6.581542 CGATACATGGGTCTATTCTTCGTTAC 59.418 42.308 0.00 0.00 0.00 2.50
3790 7778 5.934402 ACATGGGTCTATTCTTCGTTACT 57.066 39.130 0.00 0.00 0.00 2.24
3791 7779 5.661458 ACATGGGTCTATTCTTCGTTACTG 58.339 41.667 0.00 0.00 0.00 2.74
3792 7780 5.421056 ACATGGGTCTATTCTTCGTTACTGA 59.579 40.000 0.00 0.00 0.00 3.41
3793 7781 5.988310 TGGGTCTATTCTTCGTTACTGAA 57.012 39.130 0.00 0.00 0.00 3.02
3794 7782 6.540438 TGGGTCTATTCTTCGTTACTGAAT 57.460 37.500 0.00 0.00 35.08 2.57
3795 7783 6.942976 TGGGTCTATTCTTCGTTACTGAATT 58.057 36.000 0.00 0.00 33.24 2.17
3796 7784 7.039882 TGGGTCTATTCTTCGTTACTGAATTC 58.960 38.462 0.00 0.00 33.24 2.17
3797 7785 7.093465 TGGGTCTATTCTTCGTTACTGAATTCT 60.093 37.037 7.05 0.00 33.24 2.40
3798 7786 7.764901 GGGTCTATTCTTCGTTACTGAATTCTT 59.235 37.037 7.05 0.00 33.24 2.52
3799 7787 8.809478 GGTCTATTCTTCGTTACTGAATTCTTC 58.191 37.037 7.05 0.00 33.24 2.87
3800 7788 9.575783 GTCTATTCTTCGTTACTGAATTCTTCT 57.424 33.333 7.05 0.00 33.24 2.85
3803 7791 8.833231 ATTCTTCGTTACTGAATTCTTCTTCA 57.167 30.769 7.05 0.00 34.14 3.02
3804 7792 7.639162 TCTTCGTTACTGAATTCTTCTTCAC 57.361 36.000 7.05 0.00 31.98 3.18
3805 7793 7.207383 TCTTCGTTACTGAATTCTTCTTCACA 58.793 34.615 7.05 0.00 31.98 3.58
3806 7794 7.709182 TCTTCGTTACTGAATTCTTCTTCACAA 59.291 33.333 7.05 0.00 31.98 3.33
3807 7795 7.962964 TCGTTACTGAATTCTTCTTCACAAT 57.037 32.000 7.05 0.00 31.98 2.71
3808 7796 8.378172 TCGTTACTGAATTCTTCTTCACAATT 57.622 30.769 7.05 0.00 31.98 2.32
3809 7797 8.282592 TCGTTACTGAATTCTTCTTCACAATTG 58.717 33.333 7.05 3.24 31.98 2.32
3810 7798 7.059945 CGTTACTGAATTCTTCTTCACAATTGC 59.940 37.037 5.05 0.00 31.98 3.56
3811 7799 6.645790 ACTGAATTCTTCTTCACAATTGCT 57.354 33.333 5.05 0.00 31.98 3.91
3812 7800 7.750229 ACTGAATTCTTCTTCACAATTGCTA 57.250 32.000 5.05 0.00 31.98 3.49
3813 7801 7.588512 ACTGAATTCTTCTTCACAATTGCTAC 58.411 34.615 5.05 0.00 31.98 3.58
3814 7802 7.446625 ACTGAATTCTTCTTCACAATTGCTACT 59.553 33.333 5.05 0.00 31.98 2.57
3815 7803 7.587629 TGAATTCTTCTTCACAATTGCTACTG 58.412 34.615 5.05 0.00 30.34 2.74
3816 7804 5.362556 TTCTTCTTCACAATTGCTACTGC 57.637 39.130 5.05 0.00 40.20 4.40
3817 7805 4.645535 TCTTCTTCACAATTGCTACTGCT 58.354 39.130 5.05 0.00 40.48 4.24
3818 7806 5.793817 TCTTCTTCACAATTGCTACTGCTA 58.206 37.500 5.05 0.00 40.48 3.49
3819 7807 5.639506 TCTTCTTCACAATTGCTACTGCTAC 59.360 40.000 5.05 0.00 40.48 3.58
3820 7808 4.253685 TCTTCACAATTGCTACTGCTACC 58.746 43.478 5.05 0.00 40.48 3.18
3821 7809 2.616960 TCACAATTGCTACTGCTACCG 58.383 47.619 5.05 0.00 40.48 4.02
3822 7810 2.028476 TCACAATTGCTACTGCTACCGT 60.028 45.455 5.05 0.00 40.48 4.83
3823 7811 2.742053 CACAATTGCTACTGCTACCGTT 59.258 45.455 5.05 0.00 40.48 4.44
3824 7812 3.188460 CACAATTGCTACTGCTACCGTTT 59.812 43.478 5.05 0.00 40.48 3.60
3825 7813 3.818773 ACAATTGCTACTGCTACCGTTTT 59.181 39.130 5.05 0.00 40.48 2.43
3826 7814 4.158384 CAATTGCTACTGCTACCGTTTTG 58.842 43.478 0.00 0.00 40.48 2.44
3827 7815 1.153353 TGCTACTGCTACCGTTTTGC 58.847 50.000 0.00 0.00 40.48 3.68
3828 7816 0.446616 GCTACTGCTACCGTTTTGCC 59.553 55.000 0.00 0.00 36.03 4.52
3829 7817 1.944430 GCTACTGCTACCGTTTTGCCT 60.944 52.381 0.00 0.00 36.03 4.75
3830 7818 2.423577 CTACTGCTACCGTTTTGCCTT 58.576 47.619 0.00 0.00 0.00 4.35
3831 7819 0.951558 ACTGCTACCGTTTTGCCTTG 59.048 50.000 0.00 0.00 0.00 3.61
3832 7820 0.387239 CTGCTACCGTTTTGCCTTGC 60.387 55.000 0.00 0.00 0.00 4.01
3833 7821 0.821711 TGCTACCGTTTTGCCTTGCT 60.822 50.000 0.00 0.00 0.00 3.91
3834 7822 1.161843 GCTACCGTTTTGCCTTGCTA 58.838 50.000 0.00 0.00 0.00 3.49
3835 7823 1.743394 GCTACCGTTTTGCCTTGCTAT 59.257 47.619 0.00 0.00 0.00 2.97
3836 7824 2.223272 GCTACCGTTTTGCCTTGCTATC 60.223 50.000 0.00 0.00 0.00 2.08
3837 7825 1.904287 ACCGTTTTGCCTTGCTATCA 58.096 45.000 0.00 0.00 0.00 2.15
3838 7826 2.235016 ACCGTTTTGCCTTGCTATCAA 58.765 42.857 0.00 0.00 0.00 2.57
3839 7827 2.825532 ACCGTTTTGCCTTGCTATCAAT 59.174 40.909 0.00 0.00 0.00 2.57
3840 7828 3.258123 ACCGTTTTGCCTTGCTATCAATT 59.742 39.130 0.00 0.00 0.00 2.32
3841 7829 4.461081 ACCGTTTTGCCTTGCTATCAATTA 59.539 37.500 0.00 0.00 0.00 1.40
3842 7830 5.127031 ACCGTTTTGCCTTGCTATCAATTAT 59.873 36.000 0.00 0.00 0.00 1.28
3843 7831 5.687285 CCGTTTTGCCTTGCTATCAATTATC 59.313 40.000 0.00 0.00 0.00 1.75
3844 7832 6.460123 CCGTTTTGCCTTGCTATCAATTATCT 60.460 38.462 0.00 0.00 0.00 1.98
3845 7833 6.634436 CGTTTTGCCTTGCTATCAATTATCTC 59.366 38.462 0.00 0.00 0.00 2.75
3846 7834 7.467811 CGTTTTGCCTTGCTATCAATTATCTCT 60.468 37.037 0.00 0.00 0.00 3.10
3847 7835 8.840321 GTTTTGCCTTGCTATCAATTATCTCTA 58.160 33.333 0.00 0.00 0.00 2.43
3848 7836 9.578576 TTTTGCCTTGCTATCAATTATCTCTAT 57.421 29.630 0.00 0.00 0.00 1.98
3849 7837 8.783833 TTGCCTTGCTATCAATTATCTCTATC 57.216 34.615 0.00 0.00 0.00 2.08
3850 7838 7.910584 TGCCTTGCTATCAATTATCTCTATCA 58.089 34.615 0.00 0.00 0.00 2.15
3851 7839 7.821359 TGCCTTGCTATCAATTATCTCTATCAC 59.179 37.037 0.00 0.00 0.00 3.06
3852 7840 8.040132 GCCTTGCTATCAATTATCTCTATCACT 58.960 37.037 0.00 0.00 0.00 3.41
3853 7841 9.941325 CCTTGCTATCAATTATCTCTATCACTT 57.059 33.333 0.00 0.00 0.00 3.16
3855 7843 9.716531 TTGCTATCAATTATCTCTATCACTTGG 57.283 33.333 0.00 0.00 0.00 3.61
3856 7844 8.316946 TGCTATCAATTATCTCTATCACTTGGG 58.683 37.037 0.00 0.00 0.00 4.12
3857 7845 8.317679 GCTATCAATTATCTCTATCACTTGGGT 58.682 37.037 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.436417 GTTTGCTCCTGCTTGTCCATA 58.564 47.619 0.00 0.00 40.48 2.74
365 366 4.201920 GGGCTGTGTTTGCTTATTAGTAGC 60.202 45.833 0.00 0.00 39.10 3.58
371 372 0.243636 GCGGGCTGTGTTTGCTTATT 59.756 50.000 0.00 0.00 0.00 1.40
386 387 0.179020 TTTATCTGGCTGGATGCGGG 60.179 55.000 0.00 0.00 44.05 6.13
407 408 5.691754 AGTTTCGAATTTTGCAAATCTGGTC 59.308 36.000 13.65 5.51 0.00 4.02
523 524 1.000385 CTGTCCTCGATCAGATCTGCC 60.000 57.143 18.36 10.87 34.02 4.85
539 540 1.671845 CTACCCTACTCACTCGCTGTC 59.328 57.143 0.00 0.00 0.00 3.51
717 718 2.225041 GGTTTTGGGACTTTAGCCTCCT 60.225 50.000 0.00 0.00 0.00 3.69
728 729 1.066358 CGGTCTCTAGGGTTTTGGGAC 60.066 57.143 0.00 0.00 0.00 4.46
991 999 3.797353 CGACACCATGGGGGAGGG 61.797 72.222 20.68 0.00 41.15 4.30
992 1000 4.489771 GCGACACCATGGGGGAGG 62.490 72.222 20.68 7.94 41.15 4.30
993 1001 3.391665 GAGCGACACCATGGGGGAG 62.392 68.421 20.68 12.89 41.15 4.30
994 1002 3.399181 GAGCGACACCATGGGGGA 61.399 66.667 20.68 0.00 41.15 4.81
995 1003 4.838152 CGAGCGACACCATGGGGG 62.838 72.222 20.68 11.69 44.81 5.40
1046 1054 4.980592 TGGTGCAGGCCCTGGAGA 62.981 66.667 13.78 0.00 31.31 3.71
1245 1253 3.056313 GCATCGGTTGGGCAGCTTC 62.056 63.158 0.00 0.00 0.00 3.86
1365 1373 1.073722 CTTGAGGACCAGCAGCCAA 59.926 57.895 0.00 0.00 0.00 4.52
1585 1620 5.552178 AGGACATTTCAGGTTCTCAAGTAC 58.448 41.667 0.00 0.00 0.00 2.73
1695 1745 2.930040 TGCGAGTAAACTAAGAGCATGC 59.070 45.455 10.51 10.51 0.00 4.06
1714 1764 7.163001 ACTCAAAATTCCCTAAAGAAGATGC 57.837 36.000 0.00 0.00 0.00 3.91
1829 1882 6.475076 GTCACATTGCCGATAAAATTAATGCA 59.525 34.615 0.00 0.00 0.00 3.96
2302 2355 2.332654 GCACCGCATCGAAAACCCT 61.333 57.895 0.00 0.00 0.00 4.34
2346 2399 4.996434 AGGAGCGCGCACAGCTTT 62.996 61.111 35.10 10.81 46.13 3.51
2453 2506 1.893137 TGAGTATCAAGGCGACACACT 59.107 47.619 0.00 0.00 45.97 3.55
2473 2526 4.493747 GGCCTTCTCGTACGCGCT 62.494 66.667 11.24 0.00 38.14 5.92
2541 2594 1.493950 GCTCTTGGCCGATCACGATG 61.494 60.000 0.00 0.00 42.66 3.84
2542 2595 1.227380 GCTCTTGGCCGATCACGAT 60.227 57.895 0.00 0.00 42.66 3.73
2651 2704 1.876156 GGACTGAAACACTCTGCTTGG 59.124 52.381 0.00 0.00 0.00 3.61
2692 2746 0.250338 ACACCGTCTTTGCTCTTCCC 60.250 55.000 0.00 0.00 0.00 3.97
2789 2876 0.758685 CCTGTTGGTTGCCCCTTTCA 60.759 55.000 0.00 0.00 0.00 2.69
2816 2903 5.355596 CAGAGGTAATGGACTGAGTGATTC 58.644 45.833 0.00 0.00 32.90 2.52
2986 3287 6.568869 TCTTATTTCTCTTCTGCACTAGAGC 58.431 40.000 13.21 5.07 38.20 4.09
3015 3316 0.386113 TTACCGTTGCCTGGTTTTGC 59.614 50.000 0.00 0.00 40.96 3.68
3084 3415 1.448013 GAGTAGCCCGGTTGCACTC 60.448 63.158 14.46 14.46 34.61 3.51
3159 3659 9.553064 CTAAGTTATTTCTATCTGCACTTGGAT 57.447 33.333 0.00 0.00 0.00 3.41
3184 3684 7.099120 GCCTGGTTTTGTCAAATCATATTTCT 58.901 34.615 0.00 0.00 32.35 2.52
3191 3691 4.686191 ATTGCCTGGTTTTGTCAAATCA 57.314 36.364 0.00 0.87 31.84 2.57
3288 3803 3.679824 AGTAAGTAGTCCTGTTGCACC 57.320 47.619 0.00 0.00 0.00 5.01
3310 3831 2.820330 TGCGATTCATGCTTCGTCATA 58.180 42.857 15.46 2.14 37.66 2.15
3311 3832 1.655484 TGCGATTCATGCTTCGTCAT 58.345 45.000 15.46 0.00 37.66 3.06
3312 3833 1.437625 TTGCGATTCATGCTTCGTCA 58.562 45.000 15.46 11.86 37.66 4.35
3313 3834 2.525750 TTTGCGATTCATGCTTCGTC 57.474 45.000 15.46 10.06 37.66 4.20
3392 3917 4.479619 GTGCTGATCACATTTTTGAGGTC 58.520 43.478 0.00 0.00 44.98 3.85
3527 4063 0.969149 AGGCCGATGAGCGATGATTA 59.031 50.000 0.00 0.00 44.57 1.75
3528 4064 0.320247 GAGGCCGATGAGCGATGATT 60.320 55.000 0.00 0.00 44.57 2.57
3529 4065 1.291588 GAGGCCGATGAGCGATGAT 59.708 57.895 0.00 0.00 44.57 2.45
3531 4067 2.732468 CGAGGCCGATGAGCGATG 60.732 66.667 0.00 0.00 44.57 3.84
3534 4070 4.514577 AACCGAGGCCGATGAGCG 62.515 66.667 0.00 0.00 38.22 5.03
3535 4071 1.745489 AAAACCGAGGCCGATGAGC 60.745 57.895 0.00 0.00 38.22 4.26
3536 4072 1.369091 CCAAAACCGAGGCCGATGAG 61.369 60.000 0.00 0.00 38.22 2.90
3567 4103 2.026449 CAGCCACAGAAGGGAAGAAGAT 60.026 50.000 0.00 0.00 0.00 2.40
3603 4139 0.608130 AACCGTGATGCTGCAGAGTA 59.392 50.000 20.43 2.64 0.00 2.59
3636 4172 0.465824 AGAGATGGCAGCTCAATGGC 60.466 55.000 31.81 7.15 45.50 4.40
3637 4173 1.676529 CAAGAGATGGCAGCTCAATGG 59.323 52.381 31.81 15.37 34.85 3.16
3639 4175 3.478509 GATCAAGAGATGGCAGCTCAAT 58.521 45.455 31.81 21.69 33.72 2.57
3641 4177 1.140452 GGATCAAGAGATGGCAGCTCA 59.860 52.381 31.81 14.22 33.72 4.26
3643 4179 1.141254 CAGGATCAAGAGATGGCAGCT 59.859 52.381 4.21 4.21 33.72 4.24
3676 4240 4.021544 GGGTAGAAAATTGTGTGATGCCAA 60.022 41.667 0.00 0.00 0.00 4.52
3678 4242 3.119137 GGGGTAGAAAATTGTGTGATGCC 60.119 47.826 0.00 0.00 0.00 4.40
3680 4244 4.399303 GGAGGGGTAGAAAATTGTGTGATG 59.601 45.833 0.00 0.00 0.00 3.07
3681 4245 4.292306 AGGAGGGGTAGAAAATTGTGTGAT 59.708 41.667 0.00 0.00 0.00 3.06
3682 4246 3.655777 AGGAGGGGTAGAAAATTGTGTGA 59.344 43.478 0.00 0.00 0.00 3.58
3683 4247 4.034285 AGGAGGGGTAGAAAATTGTGTG 57.966 45.455 0.00 0.00 0.00 3.82
3684 4248 4.741928 AAGGAGGGGTAGAAAATTGTGT 57.258 40.909 0.00 0.00 0.00 3.72
3692 7583 3.458487 GGATAGCAAAAGGAGGGGTAGAA 59.542 47.826 0.00 0.00 0.00 2.10
3696 7587 1.987080 AGGATAGCAAAAGGAGGGGT 58.013 50.000 0.00 0.00 0.00 4.95
3728 7619 6.716628 AGTTTCACAGTACAAATGGTGATCAT 59.283 34.615 0.00 0.00 39.73 2.45
3730 7621 6.373779 CAGTTTCACAGTACAAATGGTGATC 58.626 40.000 0.00 0.00 39.73 2.92
3761 7749 4.258702 AGAATAGACCCATGTATCGTGC 57.741 45.455 0.00 0.00 0.00 5.34
3771 7759 5.988310 TTCAGTAACGAAGAATAGACCCA 57.012 39.130 0.00 0.00 0.00 4.51
3772 7760 7.266400 AGAATTCAGTAACGAAGAATAGACCC 58.734 38.462 8.44 0.00 32.11 4.46
3773 7761 8.705048 AAGAATTCAGTAACGAAGAATAGACC 57.295 34.615 8.44 0.00 32.11 3.85
3790 7778 7.786060 GCAGTAGCAATTGTGAAGAAGAATTCA 60.786 37.037 8.44 0.00 44.39 2.57
3791 7779 6.525976 GCAGTAGCAATTGTGAAGAAGAATTC 59.474 38.462 7.40 0.00 43.05 2.17
3792 7780 6.208204 AGCAGTAGCAATTGTGAAGAAGAATT 59.792 34.615 7.40 0.00 45.49 2.17
3793 7781 5.709164 AGCAGTAGCAATTGTGAAGAAGAAT 59.291 36.000 7.40 0.00 45.49 2.40
3794 7782 5.065914 AGCAGTAGCAATTGTGAAGAAGAA 58.934 37.500 7.40 0.00 45.49 2.52
3795 7783 4.645535 AGCAGTAGCAATTGTGAAGAAGA 58.354 39.130 7.40 0.00 45.49 2.87
3796 7784 5.163814 GGTAGCAGTAGCAATTGTGAAGAAG 60.164 44.000 7.40 0.00 45.49 2.85
3797 7785 4.695455 GGTAGCAGTAGCAATTGTGAAGAA 59.305 41.667 7.40 0.00 45.49 2.52
3798 7786 4.253685 GGTAGCAGTAGCAATTGTGAAGA 58.746 43.478 7.40 0.00 45.49 2.87
3799 7787 3.062639 CGGTAGCAGTAGCAATTGTGAAG 59.937 47.826 7.40 0.00 45.49 3.02
3800 7788 3.000041 CGGTAGCAGTAGCAATTGTGAA 59.000 45.455 7.40 0.00 45.49 3.18
3801 7789 2.028476 ACGGTAGCAGTAGCAATTGTGA 60.028 45.455 7.40 0.00 45.49 3.58
3802 7790 2.346803 ACGGTAGCAGTAGCAATTGTG 58.653 47.619 7.40 0.00 45.49 3.33
3803 7791 2.762535 ACGGTAGCAGTAGCAATTGT 57.237 45.000 7.40 0.00 45.49 2.71
3804 7792 4.158384 CAAAACGGTAGCAGTAGCAATTG 58.842 43.478 0.00 0.00 45.49 2.32
3805 7793 3.365969 GCAAAACGGTAGCAGTAGCAATT 60.366 43.478 0.00 0.00 45.49 2.32
3806 7794 2.161609 GCAAAACGGTAGCAGTAGCAAT 59.838 45.455 0.00 0.00 45.49 3.56
3807 7795 1.533731 GCAAAACGGTAGCAGTAGCAA 59.466 47.619 0.00 0.00 45.49 3.91
3808 7796 1.153353 GCAAAACGGTAGCAGTAGCA 58.847 50.000 0.00 0.00 45.49 3.49
3809 7797 0.446616 GGCAAAACGGTAGCAGTAGC 59.553 55.000 0.04 0.00 42.56 3.58
3810 7798 2.094762 AGGCAAAACGGTAGCAGTAG 57.905 50.000 0.04 0.00 0.00 2.57
3811 7799 2.147958 CAAGGCAAAACGGTAGCAGTA 58.852 47.619 0.04 0.00 0.00 2.74
3812 7800 0.951558 CAAGGCAAAACGGTAGCAGT 59.048 50.000 0.04 0.00 0.00 4.40
3813 7801 0.387239 GCAAGGCAAAACGGTAGCAG 60.387 55.000 0.04 0.00 0.00 4.24
3814 7802 0.821711 AGCAAGGCAAAACGGTAGCA 60.822 50.000 0.04 0.00 0.00 3.49
3815 7803 1.161843 TAGCAAGGCAAAACGGTAGC 58.838 50.000 0.00 0.00 0.00 3.58
3816 7804 3.006940 TGATAGCAAGGCAAAACGGTAG 58.993 45.455 0.00 0.00 0.00 3.18
3817 7805 3.060736 TGATAGCAAGGCAAAACGGTA 57.939 42.857 0.00 0.00 0.00 4.02
3818 7806 1.904287 TGATAGCAAGGCAAAACGGT 58.096 45.000 0.00 0.00 0.00 4.83
3819 7807 3.508744 ATTGATAGCAAGGCAAAACGG 57.491 42.857 0.00 0.00 37.45 4.44
3820 7808 6.498304 AGATAATTGATAGCAAGGCAAAACG 58.502 36.000 0.00 0.00 37.45 3.60
3821 7809 7.710896 AGAGATAATTGATAGCAAGGCAAAAC 58.289 34.615 0.00 0.00 37.45 2.43
3822 7810 7.886629 AGAGATAATTGATAGCAAGGCAAAA 57.113 32.000 0.00 0.00 37.45 2.44
3823 7811 9.224267 GATAGAGATAATTGATAGCAAGGCAAA 57.776 33.333 0.00 0.00 37.45 3.68
3824 7812 8.377799 TGATAGAGATAATTGATAGCAAGGCAA 58.622 33.333 0.00 0.00 37.45 4.52
3825 7813 7.821359 GTGATAGAGATAATTGATAGCAAGGCA 59.179 37.037 0.00 0.00 37.45 4.75
3826 7814 8.040132 AGTGATAGAGATAATTGATAGCAAGGC 58.960 37.037 0.00 0.00 37.45 4.35
3827 7815 9.941325 AAGTGATAGAGATAATTGATAGCAAGG 57.059 33.333 0.00 0.00 37.45 3.61
3829 7817 9.716531 CCAAGTGATAGAGATAATTGATAGCAA 57.283 33.333 0.00 0.00 38.60 3.91
3830 7818 8.316946 CCCAAGTGATAGAGATAATTGATAGCA 58.683 37.037 0.00 0.00 0.00 3.49
3831 7819 8.317679 ACCCAAGTGATAGAGATAATTGATAGC 58.682 37.037 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.