Multiple sequence alignment - TraesCS2D01G128300

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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 TraesCS2D01G128300 chr2D 100.000 3561 0 0 1 3561 74937320 74933760 0.000000e+00 6577.0
1 TraesCS2D01G128300 chr2D 79.935 618 99 16 2161 2774 79401645 79401049 7.060000e-117 431.0
2 TraesCS2D01G128300 chr2A 95.640 2913 92 14 1 2895 74107104 74104209 0.000000e+00 4643.0
3 TraesCS2D01G128300 chr2B 91.845 1631 100 18 1 1626 114047585 114045983 0.000000e+00 2244.0
4 TraesCS2D01G128300 chr2B 91.182 1168 70 18 1838 2980 114045905 114044746 0.000000e+00 1555.0
5 TraesCS2D01G128300 chr2B 89.899 198 14 4 3262 3458 114044162 114043970 2.120000e-62 250.0
6 TraesCS2D01G128300 chr2B 83.654 104 16 1 3233 3335 255571125 255571228 2.930000e-16 97.1
7 TraesCS2D01G128300 chr7B 81.042 691 77 20 1834 2509 15808162 15807511 5.310000e-138 501.0
8 TraesCS2D01G128300 chr7B 83.486 109 13 4 3232 3338 138654430 138654325 2.930000e-16 97.1
9 TraesCS2D01G128300 chr4A 83.133 332 29 10 1451 1780 428994811 428995117 9.740000e-71 278.0
10 TraesCS2D01G128300 chr4A 82.831 332 30 10 1451 1780 29364949 29364643 4.530000e-69 272.0
11 TraesCS2D01G128300 chr4A 81.924 343 35 10 1440 1780 708069681 708069998 7.580000e-67 265.0
12 TraesCS2D01G128300 chr4A 81.924 343 35 10 1440 1780 708092336 708092653 7.580000e-67 265.0
13 TraesCS2D01G128300 chrUn 81.924 343 35 10 1440 1780 50448493 50448810 7.580000e-67 265.0
14 TraesCS2D01G128300 chr4B 82.229 332 32 10 1451 1780 458278974 458279280 9.810000e-66 261.0
15 TraesCS2D01G128300 chr1B 82.229 332 31 11 1451 1780 280475689 280475994 9.810000e-66 261.0
16 TraesCS2D01G128300 chr7A 81.341 343 37 10 1440 1780 266940740 266941057 1.640000e-63 254.0
17 TraesCS2D01G128300 chr7A 84.404 109 12 4 3232 3338 175843862 175843757 6.290000e-18 102.0
18 TraesCS2D01G128300 chr1D 88.983 118 8 1 760 872 459048024 459047907 1.330000e-29 141.0
19 TraesCS2D01G128300 chr7D 82.569 109 14 4 3232 3338 173800033 173799928 1.360000e-14 91.6
20 TraesCS2D01G128300 chr6D 88.333 60 5 1 3235 3292 22703720 22703661 1.770000e-08 71.3
21 TraesCS2D01G128300 chr6D 88.333 60 5 1 3235 3292 86229707 86229766 1.770000e-08 71.3
22 TraesCS2D01G128300 chr6B 79.245 106 18 3 3235 3336 58619947 58619842 1.770000e-08 71.3
23 TraesCS2D01G128300 chr6B 88.333 60 5 1 3235 3292 128237426 128237485 1.770000e-08 71.3
24 TraesCS2D01G128300 chr5D 100.000 32 0 0 3474 3505 554514256 554514225 3.840000e-05 60.2
25 TraesCS2D01G128300 chr5D 97.059 34 1 0 3302 3335 142355926 142355959 1.380000e-04 58.4
26 TraesCS2D01G128300 chr5B 90.909 44 4 0 3301 3344 165085088 165085045 3.840000e-05 60.2
27 TraesCS2D01G128300 chr3A 100.000 30 0 0 3308 3337 686614899 686614928 4.970000e-04 56.5
28 TraesCS2D01G128300 chr3B 100.000 28 0 0 3308 3335 728751779 728751806 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G128300 chr2D 74933760 74937320 3560 True 6577.000000 6577 100.000000 1 3561 1 chr2D.!!$R1 3560
1 TraesCS2D01G128300 chr2D 79401049 79401645 596 True 431.000000 431 79.935000 2161 2774 1 chr2D.!!$R2 613
2 TraesCS2D01G128300 chr2A 74104209 74107104 2895 True 4643.000000 4643 95.640000 1 2895 1 chr2A.!!$R1 2894
3 TraesCS2D01G128300 chr2B 114043970 114047585 3615 True 1349.666667 2244 90.975333 1 3458 3 chr2B.!!$R1 3457
4 TraesCS2D01G128300 chr7B 15807511 15808162 651 True 501.000000 501 81.042000 1834 2509 1 chr7B.!!$R1 675

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
931 934 1.066358 CGGTCTCTAGGGTTTTGGGAC 60.066 57.143 0.0 0.0 0.00 4.46 F
1273 1276 0.179020 TTTATCTGGCTGGATGCGGG 60.179 55.000 0.0 0.0 44.05 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2395 1.683943 AGCTGCAAGAGTGAAAGCAA 58.316 45.0 1.02 0.00 38.05 3.91 R
2932 2973 1.192146 TGTCGAGGGCTTAAGGCTGT 61.192 55.0 26.23 15.29 41.46 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
74 75 5.552178 AGGACATTTCAGGTTCTCAAGTAC 58.448 41.667 0.00 0.00 0.00 2.73
294 295 1.073722 CTTGAGGACCAGCAGCCAA 59.926 57.895 0.00 0.00 0.00 4.52
414 415 3.056313 GCATCGGTTGGGCAGCTTC 62.056 63.158 0.00 0.00 0.00 3.86
613 614 4.980592 TGGTGCAGGCCCTGGAGA 62.981 66.667 13.78 0.00 31.31 3.71
664 665 4.838152 CGAGCGACACCATGGGGG 62.838 72.222 20.68 11.69 44.81 5.40
665 666 3.399181 GAGCGACACCATGGGGGA 61.399 66.667 20.68 0.00 41.15 4.81
666 667 3.391665 GAGCGACACCATGGGGGAG 62.392 68.421 20.68 12.89 41.15 4.30
667 668 4.489771 GCGACACCATGGGGGAGG 62.490 72.222 20.68 7.94 41.15 4.30
668 669 3.797353 CGACACCATGGGGGAGGG 61.797 72.222 20.68 0.00 41.15 4.30
931 934 1.066358 CGGTCTCTAGGGTTTTGGGAC 60.066 57.143 0.00 0.00 0.00 4.46
942 945 2.225041 GGTTTTGGGACTTTAGCCTCCT 60.225 50.000 0.00 0.00 0.00 3.69
1120 1123 1.671845 CTACCCTACTCACTCGCTGTC 59.328 57.143 0.00 0.00 0.00 3.51
1136 1139 1.000385 CTGTCCTCGATCAGATCTGCC 60.000 57.143 18.36 10.87 34.02 4.85
1198 1201 3.396560 TGATCTGCTCTGCGATATTTGG 58.603 45.455 0.00 0.00 0.00 3.28
1252 1255 5.691754 AGTTTCGAATTTTGCAAATCTGGTC 59.308 36.000 13.65 5.51 0.00 4.02
1273 1276 0.179020 TTTATCTGGCTGGATGCGGG 60.179 55.000 0.00 0.00 44.05 6.13
1288 1291 0.243636 GCGGGCTGTGTTTGCTTATT 59.756 50.000 0.00 0.00 0.00 1.40
1294 1297 4.201920 GGGCTGTGTTTGCTTATTAGTAGC 60.202 45.833 0.00 0.00 39.10 3.58
1644 1647 2.436417 GTTTGCTCCTGCTTGTCCATA 58.564 47.619 0.00 0.00 40.48 2.74
1688 1691 1.663135 GAGAGTTTGAGCAATCGAGCC 59.337 52.381 0.00 0.00 34.23 4.70
1972 1981 3.626670 CCTTCTTGCAGGATGAAGATGAC 59.373 47.826 16.50 0.00 39.69 3.06
2098 2107 8.083462 TCTACTAGTGTTGTGTGCTTAAATTG 57.917 34.615 5.39 0.00 0.00 2.32
2129 2145 5.061853 ACTTACTATCCTGCAGCATTCATG 58.938 41.667 8.66 0.00 0.00 3.07
2177 2193 3.023832 AGTTTGTGCTAACACCAAGCTT 58.976 40.909 0.00 0.00 46.86 3.74
2379 2395 6.310224 GCAACAGTTTGACAAAGTTAACACAT 59.690 34.615 8.61 0.00 34.24 3.21
2470 2495 2.672961 TCATCGATGACCTTGTGTCC 57.327 50.000 23.99 0.00 43.78 4.02
2497 2522 5.234466 ACACTCTTATTGAGGAAGTGCTT 57.766 39.130 0.00 0.00 46.72 3.91
2518 2543 2.435938 GAGGCGCCCATCAACGAA 60.436 61.111 26.15 0.00 0.00 3.85
2572 2597 9.784531 TTCAACAAGATCTAGAATCTTTGTTCT 57.215 29.630 17.24 4.13 41.18 3.01
2783 2817 8.451748 GTGGAGTAAAATCAGTCTTTGATAACC 58.548 37.037 0.00 0.00 45.82 2.85
2789 2823 6.910536 AATCAGTCTTTGATAACCGTGATC 57.089 37.500 0.00 0.00 45.82 2.92
2815 2849 6.825721 GGATGATCCAGATGTTCTTGTTTACT 59.174 38.462 6.60 0.00 36.28 2.24
2816 2850 7.337942 GGATGATCCAGATGTTCTTGTTTACTT 59.662 37.037 6.60 0.00 36.28 2.24
2817 2851 7.672983 TGATCCAGATGTTCTTGTTTACTTC 57.327 36.000 0.00 0.00 0.00 3.01
2818 2852 7.453393 TGATCCAGATGTTCTTGTTTACTTCT 58.547 34.615 0.00 0.00 31.28 2.85
2819 2853 7.388776 TGATCCAGATGTTCTTGTTTACTTCTG 59.611 37.037 0.00 0.00 42.04 3.02
2821 2855 7.054124 TCCAGATGTTCTTGTTTACTTCTGTT 58.946 34.615 13.55 0.00 41.39 3.16
2838 2872 6.597280 ACTTCTGTTTTTCCATATCTCAGCTC 59.403 38.462 0.00 0.00 0.00 4.09
2839 2873 5.111989 TCTGTTTTTCCATATCTCAGCTCG 58.888 41.667 0.00 0.00 0.00 5.03
2840 2874 4.832248 TGTTTTTCCATATCTCAGCTCGT 58.168 39.130 0.00 0.00 0.00 4.18
2844 2878 5.854010 TTTCCATATCTCAGCTCGTACTT 57.146 39.130 0.00 0.00 0.00 2.24
2857 2892 6.586463 TCAGCTCGTACTTGAAACTAATCTTG 59.414 38.462 0.00 0.00 0.00 3.02
2858 2893 6.366332 CAGCTCGTACTTGAAACTAATCTTGT 59.634 38.462 0.00 0.00 0.00 3.16
2898 2933 2.582498 GTGCCTAGCGCTGTACGG 60.582 66.667 22.90 15.72 43.93 4.02
2909 2944 1.996898 CGCTGTACGGTTGCTTAATCA 59.003 47.619 3.10 0.00 38.44 2.57
2915 2950 6.176975 TGTACGGTTGCTTAATCATTTCAG 57.823 37.500 0.00 0.00 0.00 3.02
2917 2952 5.046910 ACGGTTGCTTAATCATTTCAGTG 57.953 39.130 0.00 0.00 0.00 3.66
2918 2953 4.759693 ACGGTTGCTTAATCATTTCAGTGA 59.240 37.500 0.00 0.00 0.00 3.41
2919 2954 5.088739 CGGTTGCTTAATCATTTCAGTGAC 58.911 41.667 0.00 0.00 0.00 3.67
2921 2956 6.568462 CGGTTGCTTAATCATTTCAGTGACTT 60.568 38.462 0.00 0.00 0.00 3.01
2922 2957 7.360861 CGGTTGCTTAATCATTTCAGTGACTTA 60.361 37.037 0.00 0.00 0.00 2.24
2932 2973 4.890158 TTCAGTGACTTAGAGGATTGCA 57.110 40.909 0.00 0.00 0.00 4.08
2947 2988 0.609131 TTGCACAGCCTTAAGCCCTC 60.609 55.000 0.00 0.00 45.47 4.30
2948 2989 2.109126 GCACAGCCTTAAGCCCTCG 61.109 63.158 0.00 0.00 45.47 4.63
2964 3006 2.158943 CCCTCGACACTTTAGAATCCCC 60.159 54.545 0.00 0.00 0.00 4.81
3022 3376 1.269051 GCGCTGCACTTTTGGTTAGTT 60.269 47.619 0.00 0.00 0.00 2.24
3023 3377 2.798145 GCGCTGCACTTTTGGTTAGTTT 60.798 45.455 0.00 0.00 0.00 2.66
3024 3378 2.788786 CGCTGCACTTTTGGTTAGTTTG 59.211 45.455 0.00 0.00 0.00 2.93
3025 3379 2.539688 GCTGCACTTTTGGTTAGTTTGC 59.460 45.455 0.00 0.00 0.00 3.68
3026 3380 3.123050 CTGCACTTTTGGTTAGTTTGCC 58.877 45.455 0.00 0.00 0.00 4.52
3030 3384 4.501400 GCACTTTTGGTTAGTTTGCCAGAT 60.501 41.667 0.00 0.00 36.00 2.90
3032 3386 6.572314 GCACTTTTGGTTAGTTTGCCAGATAT 60.572 38.462 0.00 0.00 36.00 1.63
3045 3400 8.686334 AGTTTGCCAGATATAAATCACGATTTT 58.314 29.630 10.11 2.45 40.99 1.82
3046 3401 8.745837 GTTTGCCAGATATAAATCACGATTTTG 58.254 33.333 10.11 2.95 40.99 2.44
3048 3403 8.669946 TGCCAGATATAAATCACGATTTTGTA 57.330 30.769 10.11 5.38 40.99 2.41
3049 3404 9.114952 TGCCAGATATAAATCACGATTTTGTAA 57.885 29.630 10.11 0.00 40.99 2.41
3050 3405 9.944663 GCCAGATATAAATCACGATTTTGTAAA 57.055 29.630 10.11 0.00 40.99 2.01
3093 3491 6.780457 ACCAAACCATGAGAAATAGATTGG 57.220 37.500 0.00 0.00 40.39 3.16
3099 3497 9.838339 AAACCATGAGAAATAGATTGGTACTAG 57.162 33.333 0.00 0.00 36.49 2.57
3111 3509 3.906720 TGGTACTAGCAAATCCCACTC 57.093 47.619 0.00 0.00 0.00 3.51
3113 3511 2.504175 GGTACTAGCAAATCCCACTCCA 59.496 50.000 0.00 0.00 0.00 3.86
3115 3513 4.385310 GGTACTAGCAAATCCCACTCCAAT 60.385 45.833 0.00 0.00 0.00 3.16
3117 3515 5.450818 ACTAGCAAATCCCACTCCAATAA 57.549 39.130 0.00 0.00 0.00 1.40
3118 3516 5.826643 ACTAGCAAATCCCACTCCAATAAA 58.173 37.500 0.00 0.00 0.00 1.40
3119 3517 6.252995 ACTAGCAAATCCCACTCCAATAAAA 58.747 36.000 0.00 0.00 0.00 1.52
3122 3525 5.185828 AGCAAATCCCACTCCAATAAAAGAC 59.814 40.000 0.00 0.00 0.00 3.01
3127 3530 2.755103 CCACTCCAATAAAAGACCAGCC 59.245 50.000 0.00 0.00 0.00 4.85
3140 3543 2.564062 AGACCAGCCATGACAATTTTGG 59.436 45.455 0.00 0.00 0.00 3.28
3141 3544 1.624813 ACCAGCCATGACAATTTTGGG 59.375 47.619 0.00 0.00 0.00 4.12
3142 3545 1.901159 CCAGCCATGACAATTTTGGGA 59.099 47.619 0.00 0.00 0.00 4.37
3148 3551 4.568956 CCATGACAATTTTGGGAAAGACC 58.431 43.478 0.00 0.00 38.08 3.85
3160 3563 3.857549 GGAAAGACCCTCATTTTGCTC 57.142 47.619 0.00 0.00 0.00 4.26
3161 3564 2.493675 GGAAAGACCCTCATTTTGCTCC 59.506 50.000 0.00 0.00 0.00 4.70
3162 3565 2.978156 AAGACCCTCATTTTGCTCCA 57.022 45.000 0.00 0.00 0.00 3.86
3163 3566 2.206576 AGACCCTCATTTTGCTCCAC 57.793 50.000 0.00 0.00 0.00 4.02
3164 3567 1.425066 AGACCCTCATTTTGCTCCACA 59.575 47.619 0.00 0.00 0.00 4.17
3165 3568 2.042162 AGACCCTCATTTTGCTCCACAT 59.958 45.455 0.00 0.00 0.00 3.21
3166 3569 2.827921 GACCCTCATTTTGCTCCACATT 59.172 45.455 0.00 0.00 0.00 2.71
3167 3570 3.242011 ACCCTCATTTTGCTCCACATTT 58.758 40.909 0.00 0.00 0.00 2.32
3168 3571 3.007182 ACCCTCATTTTGCTCCACATTTG 59.993 43.478 0.00 0.00 0.00 2.32
3169 3572 3.258872 CCCTCATTTTGCTCCACATTTGA 59.741 43.478 0.00 0.00 0.00 2.69
3170 3573 4.081309 CCCTCATTTTGCTCCACATTTGAT 60.081 41.667 0.00 0.00 0.00 2.57
3171 3574 4.868171 CCTCATTTTGCTCCACATTTGATG 59.132 41.667 0.00 0.00 0.00 3.07
3172 3575 5.336929 CCTCATTTTGCTCCACATTTGATGA 60.337 40.000 0.00 0.00 0.00 2.92
3173 3576 6.099159 TCATTTTGCTCCACATTTGATGAA 57.901 33.333 0.00 0.00 0.00 2.57
3174 3577 6.522946 TCATTTTGCTCCACATTTGATGAAA 58.477 32.000 0.00 0.00 0.00 2.69
3175 3578 6.424509 TCATTTTGCTCCACATTTGATGAAAC 59.575 34.615 0.00 0.00 0.00 2.78
3178 3581 2.094026 GCTCCACATTTGATGAAACCCC 60.094 50.000 0.00 0.00 0.00 4.95
3182 3585 4.040217 TCCACATTTGATGAAACCCCTTTG 59.960 41.667 0.00 0.00 0.00 2.77
3183 3586 4.202346 CCACATTTGATGAAACCCCTTTGT 60.202 41.667 0.00 0.00 0.00 2.83
3184 3587 5.011533 CCACATTTGATGAAACCCCTTTGTA 59.988 40.000 0.00 0.00 0.00 2.41
3199 3602 4.200092 CCTTTGTATCTTTAGACCAGCCC 58.800 47.826 0.00 0.00 0.00 5.19
3200 3603 3.926058 TTGTATCTTTAGACCAGCCCC 57.074 47.619 0.00 0.00 0.00 5.80
3204 3607 0.620700 TCTTTAGACCAGCCCCTCCC 60.621 60.000 0.00 0.00 0.00 4.30
3206 3609 2.132946 TTTAGACCAGCCCCTCCCCT 62.133 60.000 0.00 0.00 0.00 4.79
3207 3610 2.840203 TTAGACCAGCCCCTCCCCTG 62.840 65.000 0.00 0.00 0.00 4.45
3249 3652 9.003145 TCATCCAAAAGAGGAATAGATTTAGGA 57.997 33.333 0.00 0.00 41.92 2.94
3252 3655 9.003145 TCCAAAAGAGGAATAGATTTAGGATGA 57.997 33.333 0.00 0.00 33.93 2.92
3253 3656 9.632638 CCAAAAGAGGAATAGATTTAGGATGAA 57.367 33.333 0.00 0.00 0.00 2.57
3381 3784 7.056635 ACATGATCTATGGTAACCAAAAGGAG 58.943 38.462 0.00 0.00 41.25 3.69
3382 3785 6.001449 TGATCTATGGTAACCAAAAGGAGG 57.999 41.667 0.00 0.00 36.95 4.30
3401 3804 6.213525 AGGAGGAGAGTCCAAAATTACCTAT 58.786 40.000 0.00 0.00 39.61 2.57
3403 3806 6.327887 GGAGGAGAGTCCAAAATTACCTATCT 59.672 42.308 0.00 0.00 39.61 1.98
3454 3857 9.346725 GAAATTTAGGAATGTAGCAAGTTCTTG 57.653 33.333 8.04 8.04 0.00 3.02
3458 3861 9.905713 TTTAGGAATGTAGCAAGTTCTTGATAT 57.094 29.630 15.52 0.28 0.00 1.63
3459 3862 9.905713 TTAGGAATGTAGCAAGTTCTTGATATT 57.094 29.630 15.52 7.44 0.00 1.28
3466 3869 9.982651 TGTAGCAAGTTCTTGATATTATACTCC 57.017 33.333 15.52 1.58 0.00 3.85
3467 3870 9.982651 GTAGCAAGTTCTTGATATTATACTCCA 57.017 33.333 15.52 0.00 0.00 3.86
3469 3872 9.717942 AGCAAGTTCTTGATATTATACTCCATC 57.282 33.333 15.52 0.00 0.00 3.51
3470 3873 9.717942 GCAAGTTCTTGATATTATACTCCATCT 57.282 33.333 15.52 0.00 0.00 2.90
3483 3886 6.668541 ATACTCCATCTGATCAAAACAACG 57.331 37.500 0.00 0.00 0.00 4.10
3484 3887 4.641396 ACTCCATCTGATCAAAACAACGA 58.359 39.130 0.00 0.00 0.00 3.85
3485 3888 4.452455 ACTCCATCTGATCAAAACAACGAC 59.548 41.667 0.00 0.00 0.00 4.34
3486 3889 4.384940 TCCATCTGATCAAAACAACGACA 58.615 39.130 0.00 0.00 0.00 4.35
3487 3890 4.213270 TCCATCTGATCAAAACAACGACAC 59.787 41.667 0.00 0.00 0.00 3.67
3488 3891 4.214119 CCATCTGATCAAAACAACGACACT 59.786 41.667 0.00 0.00 0.00 3.55
3489 3892 5.277974 CCATCTGATCAAAACAACGACACTT 60.278 40.000 0.00 0.00 0.00 3.16
3490 3893 6.073276 CCATCTGATCAAAACAACGACACTTA 60.073 38.462 0.00 0.00 0.00 2.24
3491 3894 7.361201 CCATCTGATCAAAACAACGACACTTAT 60.361 37.037 0.00 0.00 0.00 1.73
3492 3895 7.490962 TCTGATCAAAACAACGACACTTATT 57.509 32.000 0.00 0.00 0.00 1.40
3493 3896 7.925993 TCTGATCAAAACAACGACACTTATTT 58.074 30.769 0.00 0.00 0.00 1.40
3494 3897 8.402472 TCTGATCAAAACAACGACACTTATTTT 58.598 29.630 0.00 0.00 0.00 1.82
3495 3898 8.334016 TGATCAAAACAACGACACTTATTTTG 57.666 30.769 0.00 0.00 38.03 2.44
3496 3899 7.433719 TGATCAAAACAACGACACTTATTTTGG 59.566 33.333 0.00 0.00 37.53 3.28
3497 3900 6.853720 TCAAAACAACGACACTTATTTTGGA 58.146 32.000 7.24 0.00 37.53 3.53
3498 3901 7.484975 TCAAAACAACGACACTTATTTTGGAT 58.515 30.769 7.24 0.00 37.53 3.41
3499 3902 7.646130 TCAAAACAACGACACTTATTTTGGATC 59.354 33.333 7.24 0.00 37.53 3.36
3500 3903 6.627395 AACAACGACACTTATTTTGGATCA 57.373 33.333 0.00 0.00 0.00 2.92
3501 3904 6.241207 ACAACGACACTTATTTTGGATCAG 57.759 37.500 0.00 0.00 0.00 2.90
3502 3905 5.995282 ACAACGACACTTATTTTGGATCAGA 59.005 36.000 0.00 0.00 0.00 3.27
3503 3906 6.147821 ACAACGACACTTATTTTGGATCAGAG 59.852 38.462 0.00 0.00 0.00 3.35
3504 3907 5.178797 ACGACACTTATTTTGGATCAGAGG 58.821 41.667 0.00 0.00 0.00 3.69
3505 3908 5.046591 ACGACACTTATTTTGGATCAGAGGA 60.047 40.000 0.00 0.00 0.00 3.71
3506 3909 6.051717 CGACACTTATTTTGGATCAGAGGAT 58.948 40.000 0.00 0.00 36.13 3.24
3507 3910 6.018425 CGACACTTATTTTGGATCAGAGGATG 60.018 42.308 0.00 0.00 32.67 3.51
3508 3911 6.725364 ACACTTATTTTGGATCAGAGGATGT 58.275 36.000 0.00 0.00 32.67 3.06
3509 3912 7.861629 ACACTTATTTTGGATCAGAGGATGTA 58.138 34.615 0.00 0.00 32.67 2.29
3510 3913 7.770897 ACACTTATTTTGGATCAGAGGATGTAC 59.229 37.037 0.00 0.00 32.67 2.90
3511 3914 7.770433 CACTTATTTTGGATCAGAGGATGTACA 59.230 37.037 0.00 0.00 32.67 2.90
3512 3915 8.328758 ACTTATTTTGGATCAGAGGATGTACAA 58.671 33.333 0.00 0.00 32.67 2.41
3513 3916 9.347240 CTTATTTTGGATCAGAGGATGTACAAT 57.653 33.333 0.00 0.00 32.67 2.71
3516 3919 9.872684 ATTTTGGATCAGAGGATGTACAATATT 57.127 29.630 0.00 0.00 32.67 1.28
3517 3920 8.681486 TTTGGATCAGAGGATGTACAATATTG 57.319 34.615 14.01 14.01 32.67 1.90
3518 3921 7.379059 TGGATCAGAGGATGTACAATATTGT 57.621 36.000 23.80 23.80 38.34 2.71
3519 3922 7.805163 TGGATCAGAGGATGTACAATATTGTT 58.195 34.615 25.31 8.67 36.91 2.83
3520 3923 8.933653 TGGATCAGAGGATGTACAATATTGTTA 58.066 33.333 25.31 15.43 36.91 2.41
3521 3924 9.950496 GGATCAGAGGATGTACAATATTGTTAT 57.050 33.333 25.31 19.01 36.91 1.89
3560 3963 4.640771 AAAATCACCTCTCCTAACTGCA 57.359 40.909 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 9.322776 GATTATGAAGCAATTGAATTAGCTACG 57.677 33.333 10.34 0.00 36.07 3.51
453 454 3.069318 GAGCTCGGGTCCGACCTT 61.069 66.667 17.27 0.00 44.01 3.50
613 614 4.749310 CTCGCTGGCCTCGCAAGT 62.749 66.667 16.09 0.00 31.11 3.16
665 666 4.761058 TTCTCCGGCGAGCTCCCT 62.761 66.667 9.30 0.00 35.94 4.20
666 667 4.214327 CTTCTCCGGCGAGCTCCC 62.214 72.222 9.30 9.59 35.94 4.30
667 668 4.214327 CCTTCTCCGGCGAGCTCC 62.214 72.222 9.30 0.47 35.94 4.70
668 669 4.882396 GCCTTCTCCGGCGAGCTC 62.882 72.222 9.30 2.73 40.79 4.09
931 934 2.892425 CGGCGCAGGAGGCTAAAG 60.892 66.667 10.83 0.00 41.67 1.85
960 963 1.425428 CTTGTCGAATTCGCTGGGC 59.575 57.895 22.90 10.33 39.60 5.36
1120 1123 1.039068 ACTGGCAGATCTGATCGAGG 58.961 55.000 27.04 11.07 0.00 4.63
1136 1139 1.000163 ACTGCAGACCACTACGAACTG 60.000 52.381 23.35 0.00 0.00 3.16
1198 1201 6.851698 AGAAGAGATCTCATGTTGTAGGCAAC 60.852 42.308 24.39 3.77 44.03 4.17
1252 1255 1.538512 CCGCATCCAGCCAGATAAATG 59.461 52.381 0.00 0.00 41.38 2.32
1273 1276 4.092968 ACGCTACTAATAAGCAAACACAGC 59.907 41.667 0.00 0.00 40.08 4.40
1288 1291 3.926527 CAGAAGCATCACAAACGCTACTA 59.073 43.478 0.00 0.00 34.11 1.82
1644 1647 9.950680 CTCAAAGTAGTAATTGACACAACAAAT 57.049 29.630 0.00 0.00 32.46 2.32
1688 1691 4.054671 TCAAAGGGCAAATAAAAGCAACG 58.945 39.130 0.00 0.00 0.00 4.10
1812 1815 3.007940 AGAGCTTGGCATACACACAGTTA 59.992 43.478 0.00 0.00 0.00 2.24
1972 1981 4.024302 CCAAACAGATCCATGTCATCATCG 60.024 45.833 5.04 0.00 31.50 3.84
2098 2107 3.131223 TGCAGGATAGTAAGTCAGCAGAC 59.869 47.826 0.05 0.05 45.31 3.51
2129 2145 7.171678 GGACAATGACAATATAAGCCAGACTAC 59.828 40.741 0.00 0.00 0.00 2.73
2177 2193 4.204012 CGGAGGATTTGCCACCTAAATAA 58.796 43.478 0.00 0.00 44.54 1.40
2338 2354 3.528532 TGTTGCATCAGTGAGCTATGAG 58.471 45.455 13.40 0.00 0.00 2.90
2379 2395 1.683943 AGCTGCAAGAGTGAAAGCAA 58.316 45.000 1.02 0.00 38.05 3.91
2470 2495 3.759527 TCCTCAATAAGAGTGTCGACG 57.240 47.619 11.62 0.00 43.12 5.12
2789 2823 3.801698 ACAAGAACATCTGGATCATCCG 58.198 45.455 0.00 0.00 40.17 4.18
2815 2849 5.582269 CGAGCTGAGATATGGAAAAACAGAA 59.418 40.000 0.00 0.00 0.00 3.02
2816 2850 5.111989 CGAGCTGAGATATGGAAAAACAGA 58.888 41.667 0.00 0.00 0.00 3.41
2817 2851 4.872691 ACGAGCTGAGATATGGAAAAACAG 59.127 41.667 0.00 0.00 0.00 3.16
2818 2852 4.832248 ACGAGCTGAGATATGGAAAAACA 58.168 39.130 0.00 0.00 0.00 2.83
2819 2853 6.043411 AGTACGAGCTGAGATATGGAAAAAC 58.957 40.000 0.00 0.00 0.00 2.43
2821 2855 5.854010 AGTACGAGCTGAGATATGGAAAA 57.146 39.130 0.00 0.00 0.00 2.29
2833 2867 6.366332 ACAAGATTAGTTTCAAGTACGAGCTG 59.634 38.462 0.00 0.00 0.00 4.24
2838 2872 6.422701 TGGTGACAAGATTAGTTTCAAGTACG 59.577 38.462 0.00 0.00 37.44 3.67
2839 2873 7.724305 TGGTGACAAGATTAGTTTCAAGTAC 57.276 36.000 0.00 0.00 37.44 2.73
2857 2892 4.006319 AGAGCTTCTTATTGCTTGGTGAC 58.994 43.478 0.00 0.00 39.91 3.67
2858 2893 4.256920 GAGAGCTTCTTATTGCTTGGTGA 58.743 43.478 0.00 0.00 39.91 4.02
2898 2933 8.721478 TCTAAGTCACTGAAATGATTAAGCAAC 58.279 33.333 0.00 0.00 0.00 4.17
2909 2944 5.645497 GTGCAATCCTCTAAGTCACTGAAAT 59.355 40.000 0.00 0.00 0.00 2.17
2915 2950 2.675348 GCTGTGCAATCCTCTAAGTCAC 59.325 50.000 0.00 0.00 0.00 3.67
2917 2952 2.093235 AGGCTGTGCAATCCTCTAAGTC 60.093 50.000 0.00 0.00 0.00 3.01
2918 2953 1.912043 AGGCTGTGCAATCCTCTAAGT 59.088 47.619 0.00 0.00 0.00 2.24
2919 2954 2.706339 AGGCTGTGCAATCCTCTAAG 57.294 50.000 0.00 0.00 0.00 2.18
2921 2956 3.682718 GCTTAAGGCTGTGCAATCCTCTA 60.683 47.826 4.29 0.00 38.06 2.43
2922 2957 2.943199 GCTTAAGGCTGTGCAATCCTCT 60.943 50.000 4.29 0.00 38.06 3.69
2932 2973 1.192146 TGTCGAGGGCTTAAGGCTGT 61.192 55.000 26.23 15.29 41.46 4.40
2947 2988 3.689649 CCTTTGGGGATTCTAAAGTGTCG 59.310 47.826 0.00 0.00 37.23 4.35
2948 2989 4.918588 TCCTTTGGGGATTCTAAAGTGTC 58.081 43.478 0.00 0.00 39.58 3.67
2980 3049 2.559668 CTGCCCTCATGCTTCTCAAAAA 59.440 45.455 0.00 0.00 0.00 1.94
2981 3050 2.165167 CTGCCCTCATGCTTCTCAAAA 58.835 47.619 0.00 0.00 0.00 2.44
3008 3077 4.647424 TCTGGCAAACTAACCAAAAGTG 57.353 40.909 0.00 0.00 34.96 3.16
3015 3369 7.225931 TCGTGATTTATATCTGGCAAACTAACC 59.774 37.037 0.00 0.00 0.00 2.85
3022 3376 7.995289 ACAAAATCGTGATTTATATCTGGCAA 58.005 30.769 8.17 0.00 39.88 4.52
3023 3377 7.566760 ACAAAATCGTGATTTATATCTGGCA 57.433 32.000 8.17 0.00 39.88 4.92
3024 3378 9.944663 TTTACAAAATCGTGATTTATATCTGGC 57.055 29.630 8.17 0.00 39.88 4.85
3055 3410 9.397280 TCATGGTTTGGTTATAATTTATCGTCA 57.603 29.630 0.00 0.00 0.00 4.35
3089 3487 4.385310 GGAGTGGGATTTGCTAGTACCAAT 60.385 45.833 0.00 0.00 0.00 3.16
3090 3488 3.054655 GGAGTGGGATTTGCTAGTACCAA 60.055 47.826 0.00 0.00 0.00 3.67
3093 3491 3.906720 TGGAGTGGGATTTGCTAGTAC 57.093 47.619 0.00 0.00 0.00 2.73
3099 3497 5.410924 GTCTTTTATTGGAGTGGGATTTGC 58.589 41.667 0.00 0.00 0.00 3.68
3111 3509 3.763360 TGTCATGGCTGGTCTTTTATTGG 59.237 43.478 0.00 0.00 0.00 3.16
3113 3511 6.610075 AATTGTCATGGCTGGTCTTTTATT 57.390 33.333 0.00 0.00 0.00 1.40
3115 3513 6.222389 CAAAATTGTCATGGCTGGTCTTTTA 58.778 36.000 0.00 0.00 0.00 1.52
3117 3515 4.503643 CCAAAATTGTCATGGCTGGTCTTT 60.504 41.667 0.00 0.00 0.00 2.52
3118 3516 3.007182 CCAAAATTGTCATGGCTGGTCTT 59.993 43.478 0.00 0.00 0.00 3.01
3119 3517 2.564062 CCAAAATTGTCATGGCTGGTCT 59.436 45.455 0.00 0.00 0.00 3.85
3122 3525 1.901159 TCCCAAAATTGTCATGGCTGG 59.099 47.619 0.00 0.00 32.71 4.85
3140 3543 2.493675 GGAGCAAAATGAGGGTCTTTCC 59.506 50.000 0.00 0.00 0.00 3.13
3141 3544 3.057245 GTGGAGCAAAATGAGGGTCTTTC 60.057 47.826 0.00 0.00 0.00 2.62
3142 3545 2.893489 GTGGAGCAAAATGAGGGTCTTT 59.107 45.455 0.00 0.00 0.00 2.52
3148 3551 4.524316 TCAAATGTGGAGCAAAATGAGG 57.476 40.909 0.00 0.00 0.00 3.86
3149 3552 5.716094 TCATCAAATGTGGAGCAAAATGAG 58.284 37.500 0.00 0.00 0.00 2.90
3150 3553 5.725325 TCATCAAATGTGGAGCAAAATGA 57.275 34.783 0.00 0.00 0.00 2.57
3151 3554 6.347888 GGTTTCATCAAATGTGGAGCAAAATG 60.348 38.462 0.00 0.00 0.00 2.32
3152 3555 5.702209 GGTTTCATCAAATGTGGAGCAAAAT 59.298 36.000 0.00 0.00 0.00 1.82
3153 3556 5.055812 GGTTTCATCAAATGTGGAGCAAAA 58.944 37.500 0.00 0.00 0.00 2.44
3154 3557 4.502950 GGGTTTCATCAAATGTGGAGCAAA 60.503 41.667 0.00 0.00 0.00 3.68
3155 3558 3.006752 GGGTTTCATCAAATGTGGAGCAA 59.993 43.478 0.00 0.00 0.00 3.91
3156 3559 2.562298 GGGTTTCATCAAATGTGGAGCA 59.438 45.455 0.00 0.00 0.00 4.26
3157 3560 2.094026 GGGGTTTCATCAAATGTGGAGC 60.094 50.000 0.00 0.00 0.00 4.70
3158 3561 3.434309 AGGGGTTTCATCAAATGTGGAG 58.566 45.455 0.00 0.00 0.00 3.86
3159 3562 3.541242 AGGGGTTTCATCAAATGTGGA 57.459 42.857 0.00 0.00 0.00 4.02
3160 3563 4.202346 ACAAAGGGGTTTCATCAAATGTGG 60.202 41.667 0.00 0.00 0.00 4.17
3161 3564 4.959723 ACAAAGGGGTTTCATCAAATGTG 58.040 39.130 0.00 0.00 0.00 3.21
3162 3565 6.725834 AGATACAAAGGGGTTTCATCAAATGT 59.274 34.615 0.00 0.00 0.00 2.71
3163 3566 7.174107 AGATACAAAGGGGTTTCATCAAATG 57.826 36.000 0.00 0.00 0.00 2.32
3164 3567 7.797121 AAGATACAAAGGGGTTTCATCAAAT 57.203 32.000 0.00 0.00 0.00 2.32
3165 3568 7.610580 AAAGATACAAAGGGGTTTCATCAAA 57.389 32.000 0.00 0.00 0.00 2.69
3166 3569 8.167392 TCTAAAGATACAAAGGGGTTTCATCAA 58.833 33.333 0.00 0.00 0.00 2.57
3167 3570 7.610305 GTCTAAAGATACAAAGGGGTTTCATCA 59.390 37.037 0.00 0.00 0.00 3.07
3168 3571 7.067129 GGTCTAAAGATACAAAGGGGTTTCATC 59.933 40.741 0.00 0.00 0.00 2.92
3169 3572 6.890268 GGTCTAAAGATACAAAGGGGTTTCAT 59.110 38.462 0.00 0.00 0.00 2.57
3170 3573 6.183361 TGGTCTAAAGATACAAAGGGGTTTCA 60.183 38.462 0.00 0.00 0.00 2.69
3171 3574 6.243148 TGGTCTAAAGATACAAAGGGGTTTC 58.757 40.000 0.00 0.00 0.00 2.78
3172 3575 6.208840 TGGTCTAAAGATACAAAGGGGTTT 57.791 37.500 0.00 0.00 0.00 3.27
3173 3576 5.806734 GCTGGTCTAAAGATACAAAGGGGTT 60.807 44.000 0.00 0.00 0.00 4.11
3174 3577 4.324331 GCTGGTCTAAAGATACAAAGGGGT 60.324 45.833 0.00 0.00 0.00 4.95
3175 3578 4.200092 GCTGGTCTAAAGATACAAAGGGG 58.800 47.826 0.00 0.00 0.00 4.79
3178 3581 4.080299 AGGGGCTGGTCTAAAGATACAAAG 60.080 45.833 0.00 0.00 0.00 2.77
3182 3585 2.369203 GGAGGGGCTGGTCTAAAGATAC 59.631 54.545 0.00 0.00 0.00 2.24
3183 3586 2.690840 GGAGGGGCTGGTCTAAAGATA 58.309 52.381 0.00 0.00 0.00 1.98
3184 3587 1.512735 GGAGGGGCTGGTCTAAAGAT 58.487 55.000 0.00 0.00 0.00 2.40
3222 3625 9.632638 CCTAAATCTATTCCTCTTTTGGATGAA 57.367 33.333 0.00 0.00 35.83 2.57
3224 3627 9.804977 ATCCTAAATCTATTCCTCTTTTGGATG 57.195 33.333 8.39 0.00 39.81 3.51
3283 3686 9.541143 AACATGAAAACATTTACCCTAGTTTTG 57.459 29.630 0.00 0.00 42.33 2.44
3322 3725 7.555914 TGCCACTGCATATTCAAAATAGACTAA 59.444 33.333 0.00 0.00 44.23 2.24
3323 3726 7.053498 TGCCACTGCATATTCAAAATAGACTA 58.947 34.615 0.00 0.00 44.23 2.59
3381 3784 7.125792 TCAGATAGGTAATTTTGGACTCTCC 57.874 40.000 0.00 0.00 36.96 3.71
3458 3861 8.038351 TCGTTGTTTTGATCAGATGGAGTATAA 58.962 33.333 0.00 0.00 0.00 0.98
3459 3862 7.491372 GTCGTTGTTTTGATCAGATGGAGTATA 59.509 37.037 0.00 0.00 0.00 1.47
3460 3863 6.313905 GTCGTTGTTTTGATCAGATGGAGTAT 59.686 38.462 0.00 0.00 0.00 2.12
3461 3864 5.637810 GTCGTTGTTTTGATCAGATGGAGTA 59.362 40.000 0.00 0.00 0.00 2.59
3462 3865 4.452455 GTCGTTGTTTTGATCAGATGGAGT 59.548 41.667 0.00 0.00 0.00 3.85
3463 3866 4.452114 TGTCGTTGTTTTGATCAGATGGAG 59.548 41.667 0.00 0.00 0.00 3.86
3464 3867 4.213270 GTGTCGTTGTTTTGATCAGATGGA 59.787 41.667 0.00 0.00 0.00 3.41
3465 3868 4.214119 AGTGTCGTTGTTTTGATCAGATGG 59.786 41.667 0.00 0.00 0.00 3.51
3466 3869 5.348418 AGTGTCGTTGTTTTGATCAGATG 57.652 39.130 0.00 0.00 0.00 2.90
3467 3870 7.672983 ATAAGTGTCGTTGTTTTGATCAGAT 57.327 32.000 0.00 0.00 0.00 2.90
3468 3871 7.490962 AATAAGTGTCGTTGTTTTGATCAGA 57.509 32.000 0.00 0.00 0.00 3.27
3469 3872 8.471457 CAAAATAAGTGTCGTTGTTTTGATCAG 58.529 33.333 11.08 0.00 44.75 2.90
3470 3873 7.433719 CCAAAATAAGTGTCGTTGTTTTGATCA 59.566 33.333 15.79 0.00 44.75 2.92
3471 3874 7.646130 TCCAAAATAAGTGTCGTTGTTTTGATC 59.354 33.333 15.79 0.00 44.75 2.92
3472 3875 7.484975 TCCAAAATAAGTGTCGTTGTTTTGAT 58.515 30.769 15.79 0.00 44.75 2.57
3473 3876 6.853720 TCCAAAATAAGTGTCGTTGTTTTGA 58.146 32.000 15.79 4.48 44.75 2.69
3474 3877 7.433719 TGATCCAAAATAAGTGTCGTTGTTTTG 59.566 33.333 10.06 10.06 43.09 2.44
3475 3878 7.484975 TGATCCAAAATAAGTGTCGTTGTTTT 58.515 30.769 0.00 0.00 32.72 2.43
3476 3879 7.012894 TCTGATCCAAAATAAGTGTCGTTGTTT 59.987 33.333 0.00 0.00 0.00 2.83
3477 3880 6.485313 TCTGATCCAAAATAAGTGTCGTTGTT 59.515 34.615 0.00 0.00 0.00 2.83
3478 3881 5.995282 TCTGATCCAAAATAAGTGTCGTTGT 59.005 36.000 0.00 0.00 0.00 3.32
3479 3882 6.402550 CCTCTGATCCAAAATAAGTGTCGTTG 60.403 42.308 0.00 0.00 0.00 4.10
3480 3883 5.643777 CCTCTGATCCAAAATAAGTGTCGTT 59.356 40.000 0.00 0.00 0.00 3.85
3481 3884 5.046591 TCCTCTGATCCAAAATAAGTGTCGT 60.047 40.000 0.00 0.00 0.00 4.34
3482 3885 5.419542 TCCTCTGATCCAAAATAAGTGTCG 58.580 41.667 0.00 0.00 0.00 4.35
3483 3886 6.825721 ACATCCTCTGATCCAAAATAAGTGTC 59.174 38.462 0.00 0.00 0.00 3.67
3484 3887 6.725364 ACATCCTCTGATCCAAAATAAGTGT 58.275 36.000 0.00 0.00 0.00 3.55
3485 3888 7.770433 TGTACATCCTCTGATCCAAAATAAGTG 59.230 37.037 0.00 0.00 0.00 3.16
3486 3889 7.861629 TGTACATCCTCTGATCCAAAATAAGT 58.138 34.615 0.00 0.00 0.00 2.24
3487 3890 8.737168 TTGTACATCCTCTGATCCAAAATAAG 57.263 34.615 0.00 0.00 0.00 1.73
3490 3893 9.872684 AATATTGTACATCCTCTGATCCAAAAT 57.127 29.630 0.00 0.00 0.00 1.82
3491 3894 9.123902 CAATATTGTACATCCTCTGATCCAAAA 57.876 33.333 7.32 0.00 0.00 2.44
3492 3895 8.274322 ACAATATTGTACATCCTCTGATCCAAA 58.726 33.333 19.51 0.00 40.16 3.28
3493 3896 7.805163 ACAATATTGTACATCCTCTGATCCAA 58.195 34.615 19.51 0.00 40.16 3.53
3494 3897 7.379059 ACAATATTGTACATCCTCTGATCCA 57.621 36.000 19.51 0.00 40.16 3.41
3495 3898 9.950496 ATAACAATATTGTACATCCTCTGATCC 57.050 33.333 21.07 0.00 41.31 3.36
3538 3941 4.985538 TGCAGTTAGGAGAGGTGATTTTT 58.014 39.130 0.00 0.00 0.00 1.94
3539 3942 4.640771 TGCAGTTAGGAGAGGTGATTTT 57.359 40.909 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.