Multiple sequence alignment - TraesCS2D01G198700

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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 TraesCS2D01G198700 chr2D 100.000 3666 0 0 1 3666 147425038 147428703 0.000000e+00 6770.0
1 TraesCS2D01G198700 chr2D 92.478 1715 107 9 961 2674 147937899 147939592 0.000000e+00 2433.0
2 TraesCS2D01G198700 chr2D 82.344 1365 235 6 1213 2574 147953717 147955078 0.000000e+00 1181.0
3 TraesCS2D01G198700 chr2B 97.864 1732 37 0 954 2685 207100411 207102142 0.000000e+00 2994.0
4 TraesCS2D01G198700 chr2B 92.509 1722 112 8 954 2674 207471164 207472869 0.000000e+00 2449.0
5 TraesCS2D01G198700 chr2B 82.331 1364 235 6 1213 2573 207482275 207483635 0.000000e+00 1179.0
6 TraesCS2D01G198700 chr2B 89.060 521 48 5 3002 3519 207118395 207118909 3.990000e-179 638.0
7 TraesCS2D01G198700 chr2B 91.837 98 7 1 3569 3666 207119193 207119289 6.390000e-28 135.0
8 TraesCS2D01G198700 chr2B 97.143 35 1 0 2862 2896 207102235 207102269 3.950000e-05 60.2
9 TraesCS2D01G198700 chr2A 96.673 1683 56 0 954 2636 155074933 155073251 0.000000e+00 2798.0
10 TraesCS2D01G198700 chr2A 91.895 1678 117 9 1000 2676 154849656 154847997 0.000000e+00 2327.0
11 TraesCS2D01G198700 chr2A 82.151 1367 234 9 1213 2574 154422566 154421205 0.000000e+00 1164.0
12 TraesCS2D01G198700 chr2A 91.667 108 9 0 2860 2967 155072852 155072745 2.280000e-32 150.0
13 TraesCS2D01G198700 chr7D 98.951 953 9 1 5 956 262346887 262347839 0.000000e+00 1703.0
14 TraesCS2D01G198700 chr7D 98.846 953 9 2 5 956 391211172 391210221 0.000000e+00 1698.0
15 TraesCS2D01G198700 chr5D 98.951 953 9 1 5 956 450112836 450111884 0.000000e+00 1703.0
16 TraesCS2D01G198700 chr5D 98.738 951 11 1 6 955 549580760 549579810 0.000000e+00 1688.0
17 TraesCS2D01G198700 chr5D 85.938 192 24 3 2949 3138 517752340 517752150 6.210000e-48 202.0
18 TraesCS2D01G198700 chr5D 86.503 163 22 0 3135 3297 517743555 517743393 2.910000e-41 180.0
19 TraesCS2D01G198700 chr6D 98.433 957 13 2 5 959 449270148 449271104 0.000000e+00 1683.0
20 TraesCS2D01G198700 chr3D 97.687 951 18 4 6 954 573040513 573041461 0.000000e+00 1631.0
21 TraesCS2D01G198700 chr1D 97.492 957 19 5 5 958 451282970 451283924 0.000000e+00 1629.0
22 TraesCS2D01G198700 chr1D 82.180 1358 232 10 1213 2565 483972824 483974176 0.000000e+00 1158.0
23 TraesCS2D01G198700 chr1D 85.833 120 15 1 2742 2861 85844631 85844748 3.840000e-25 126.0
24 TraesCS2D01G198700 chr1D 83.594 128 19 1 2734 2861 46360099 46359974 6.430000e-23 119.0
25 TraesCS2D01G198700 chr1D 81.818 121 20 1 2743 2863 326014985 326014867 2.330000e-17 100.0
26 TraesCS2D01G198700 chrUn 97.382 955 22 3 6 958 19190874 19189921 0.000000e+00 1622.0
27 TraesCS2D01G198700 chr6A 97.167 953 25 2 5 955 2696048 2695096 0.000000e+00 1609.0
28 TraesCS2D01G198700 chr3B 86.066 122 14 2 2744 2865 309414739 309414857 1.070000e-25 128.0
29 TraesCS2D01G198700 chr3B 82.787 122 19 2 2743 2864 49149469 49149350 1.390000e-19 108.0
30 TraesCS2D01G198700 chr3B 82.645 121 16 4 2743 2861 720269033 720268916 6.480000e-18 102.0
31 TraesCS2D01G198700 chr4A 83.200 125 19 1 2738 2862 730293179 730293301 2.990000e-21 113.0
32 TraesCS2D01G198700 chr4A 86.869 99 12 1 2949 3047 314667897 314667800 3.870000e-20 110.0
33 TraesCS2D01G198700 chr7B 86.275 102 12 2 2743 2844 496220163 496220262 3.870000e-20 110.0
34 TraesCS2D01G198700 chr6B 81.890 127 19 3 2740 2865 527586364 527586487 1.800000e-18 104.0


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 TraesCS2D01G198700 chr2D 147425038 147428703 3665 False 6770.0 6770 100.0000 1 3666 1 chr2D.!!$F1 3665
1 TraesCS2D01G198700 chr2D 147937899 147939592 1693 False 2433.0 2433 92.4780 961 2674 1 chr2D.!!$F2 1713
2 TraesCS2D01G198700 chr2D 147953717 147955078 1361 False 1181.0 1181 82.3440 1213 2574 1 chr2D.!!$F3 1361
3 TraesCS2D01G198700 chr2B 207471164 207472869 1705 False 2449.0 2449 92.5090 954 2674 1 chr2B.!!$F1 1720
4 TraesCS2D01G198700 chr2B 207100411 207102269 1858 False 1527.1 2994 97.5035 954 2896 2 chr2B.!!$F3 1942
5 TraesCS2D01G198700 chr2B 207482275 207483635 1360 False 1179.0 1179 82.3310 1213 2573 1 chr2B.!!$F2 1360
6 TraesCS2D01G198700 chr2B 207118395 207119289 894 False 386.5 638 90.4485 3002 3666 2 chr2B.!!$F4 664
7 TraesCS2D01G198700 chr2A 154847997 154849656 1659 True 2327.0 2327 91.8950 1000 2676 1 chr2A.!!$R2 1676
8 TraesCS2D01G198700 chr2A 155072745 155074933 2188 True 1474.0 2798 94.1700 954 2967 2 chr2A.!!$R3 2013
9 TraesCS2D01G198700 chr2A 154421205 154422566 1361 True 1164.0 1164 82.1510 1213 2574 1 chr2A.!!$R1 1361
10 TraesCS2D01G198700 chr7D 262346887 262347839 952 False 1703.0 1703 98.9510 5 956 1 chr7D.!!$F1 951
11 TraesCS2D01G198700 chr7D 391210221 391211172 951 True 1698.0 1698 98.8460 5 956 1 chr7D.!!$R1 951
12 TraesCS2D01G198700 chr5D 450111884 450112836 952 True 1703.0 1703 98.9510 5 956 1 chr5D.!!$R1 951
13 TraesCS2D01G198700 chr5D 549579810 549580760 950 True 1688.0 1688 98.7380 6 955 1 chr5D.!!$R4 949
14 TraesCS2D01G198700 chr6D 449270148 449271104 956 False 1683.0 1683 98.4330 5 959 1 chr6D.!!$F1 954
15 TraesCS2D01G198700 chr3D 573040513 573041461 948 False 1631.0 1631 97.6870 6 954 1 chr3D.!!$F1 948
16 TraesCS2D01G198700 chr1D 451282970 451283924 954 False 1629.0 1629 97.4920 5 958 1 chr1D.!!$F2 953
17 TraesCS2D01G198700 chr1D 483972824 483974176 1352 False 1158.0 1158 82.1800 1213 2565 1 chr1D.!!$F3 1352
18 TraesCS2D01G198700 chrUn 19189921 19190874 953 True 1622.0 1622 97.3820 6 958 1 chrUn.!!$R1 952
19 TraesCS2D01G198700 chr6A 2695096 2696048 952 True 1609.0 1609 97.1670 5 955 1 chr6A.!!$R1 950

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
884 887 0.748005 CCCGCCGGATGAAAAGATGT 60.748 55.000 5.05 0.0 0.0 3.06 F
1036 1039 2.266055 CAGAGGCAGTCGAACCCC 59.734 66.667 0.00 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2103 0.468226 GGAACATGGCGACCAGGATA 59.532 55.0 15.63 0.0 37.52 2.59 R
2921 3249 0.878416 GCGGTGGACTATTGCAAACA 59.122 50.0 1.71 0.0 0.00 2.83 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
731 733 6.313519 ACACATCAAGGCCTCTAAGATTTA 57.686 37.500 5.23 0.00 0.00 1.40
884 887 0.748005 CCCGCCGGATGAAAAGATGT 60.748 55.000 5.05 0.00 0.00 3.06
1036 1039 2.266055 CAGAGGCAGTCGAACCCC 59.734 66.667 0.00 0.00 0.00 4.95
1882 1887 2.685380 CCCAGGAAGAGAGGCGGT 60.685 66.667 0.00 0.00 0.00 5.68
2098 2103 2.733593 GTCGCCAAGACGCTCGTT 60.734 61.111 0.00 0.00 40.43 3.85
2425 2430 2.325661 TGTCCATGACCTTCCTCTCA 57.674 50.000 0.00 0.00 0.00 3.27
2426 2431 2.619931 TGTCCATGACCTTCCTCTCAA 58.380 47.619 0.00 0.00 0.00 3.02
2620 2625 3.559657 GACACAGGACGCGAGCTGT 62.560 63.158 15.93 6.23 35.27 4.40
2685 2690 4.961438 AATCACATGAATATTTGGGGCC 57.039 40.909 0.00 0.00 0.00 5.80
2731 3059 1.000506 GGCTAGTTGTGTTGGTCTCGA 59.999 52.381 0.00 0.00 0.00 4.04
2740 3068 5.828299 TGTGTTGGTCTCGATTTTCTTTT 57.172 34.783 0.00 0.00 0.00 2.27
2757 3085 2.460757 TTTTTACTCCCTTCGTCCGG 57.539 50.000 0.00 0.00 0.00 5.14
2758 3086 1.631405 TTTTACTCCCTTCGTCCGGA 58.369 50.000 0.00 0.00 0.00 5.14
2759 3087 1.631405 TTTACTCCCTTCGTCCGGAA 58.369 50.000 5.23 0.00 0.00 4.30
2760 3088 1.631405 TTACTCCCTTCGTCCGGAAA 58.369 50.000 5.23 0.00 33.34 3.13
2761 3089 1.856629 TACTCCCTTCGTCCGGAAAT 58.143 50.000 5.23 0.00 33.34 2.17
2762 3090 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
2763 3091 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
2764 3092 1.755380 CTCCCTTCGTCCGGAAATACT 59.245 52.381 5.23 0.00 33.34 2.12
2765 3093 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
2766 3094 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
2767 3095 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
2768 3096 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
2769 3097 3.581755 CTTCGTCCGGAAATACTTGTCA 58.418 45.455 5.23 0.00 33.34 3.58
2770 3098 3.226346 TCGTCCGGAAATACTTGTCAG 57.774 47.619 5.23 0.00 0.00 3.51
2771 3099 2.821378 TCGTCCGGAAATACTTGTCAGA 59.179 45.455 5.23 0.00 0.00 3.27
2772 3100 3.446161 TCGTCCGGAAATACTTGTCAGAT 59.554 43.478 5.23 0.00 0.00 2.90
2773 3101 4.641541 TCGTCCGGAAATACTTGTCAGATA 59.358 41.667 5.23 0.00 0.00 1.98
2774 3102 5.125900 TCGTCCGGAAATACTTGTCAGATAA 59.874 40.000 5.23 0.00 0.00 1.75
2775 3103 5.808540 CGTCCGGAAATACTTGTCAGATAAA 59.191 40.000 5.23 0.00 0.00 1.40
2776 3104 6.479001 CGTCCGGAAATACTTGTCAGATAAAT 59.521 38.462 5.23 0.00 0.00 1.40
2777 3105 7.516785 CGTCCGGAAATACTTGTCAGATAAATG 60.517 40.741 5.23 0.00 0.00 2.32
2778 3106 7.494625 GTCCGGAAATACTTGTCAGATAAATGA 59.505 37.037 5.23 0.00 0.00 2.57
2779 3107 8.044309 TCCGGAAATACTTGTCAGATAAATGAA 58.956 33.333 0.00 0.00 0.00 2.57
2780 3108 8.840321 CCGGAAATACTTGTCAGATAAATGAAT 58.160 33.333 0.00 0.00 0.00 2.57
2781 3109 9.655769 CGGAAATACTTGTCAGATAAATGAATG 57.344 33.333 0.00 0.00 0.00 2.67
2847 3175 7.372451 TCCATTTCTACAACAAGTATTTCCG 57.628 36.000 0.00 0.00 30.93 4.30
2848 3176 7.162761 TCCATTTCTACAACAAGTATTTCCGA 58.837 34.615 0.00 0.00 30.93 4.55
2849 3177 7.662258 TCCATTTCTACAACAAGTATTTCCGAA 59.338 33.333 0.00 0.00 30.93 4.30
2850 3178 7.749126 CCATTTCTACAACAAGTATTTCCGAAC 59.251 37.037 0.00 0.00 30.93 3.95
2851 3179 7.789273 TTTCTACAACAAGTATTTCCGAACA 57.211 32.000 0.00 0.00 30.93 3.18
2852 3180 7.416154 TTCTACAACAAGTATTTCCGAACAG 57.584 36.000 0.00 0.00 30.93 3.16
2853 3181 6.751157 TCTACAACAAGTATTTCCGAACAGA 58.249 36.000 0.00 0.00 30.93 3.41
2854 3182 5.924475 ACAACAAGTATTTCCGAACAGAG 57.076 39.130 0.00 0.00 0.00 3.35
2855 3183 4.755123 ACAACAAGTATTTCCGAACAGAGG 59.245 41.667 0.00 0.00 0.00 3.69
2856 3184 4.618920 ACAAGTATTTCCGAACAGAGGT 57.381 40.909 0.00 0.00 0.00 3.85
2857 3185 5.733620 ACAAGTATTTCCGAACAGAGGTA 57.266 39.130 0.00 0.00 0.00 3.08
2858 3186 5.721232 ACAAGTATTTCCGAACAGAGGTAG 58.279 41.667 0.00 0.00 0.00 3.18
2899 3227 5.009610 GCTTCTTACATTTTGGAACACCTCA 59.990 40.000 0.00 0.00 39.29 3.86
2909 3237 1.537202 GGAACACCTCAACACATCTGC 59.463 52.381 0.00 0.00 0.00 4.26
2913 3241 2.224185 ACACCTCAACACATCTGCGTTA 60.224 45.455 0.00 0.00 0.00 3.18
2921 3249 1.733912 CACATCTGCGTTACACTGCAT 59.266 47.619 0.00 0.00 40.89 3.96
2924 3252 1.877637 TCTGCGTTACACTGCATGTT 58.122 45.000 7.02 0.00 43.19 2.71
2955 3283 1.206132 CACCGCATGGACCACTAGTAA 59.794 52.381 0.00 0.00 39.21 2.24
2963 3291 2.285977 GGACCACTAGTAAAATGCCCG 58.714 52.381 0.00 0.00 0.00 6.13
2967 3295 2.418628 CCACTAGTAAAATGCCCGTGTG 59.581 50.000 0.00 0.00 0.00 3.82
2968 3296 3.071479 CACTAGTAAAATGCCCGTGTGT 58.929 45.455 0.00 0.00 0.00 3.72
2969 3297 3.500680 CACTAGTAAAATGCCCGTGTGTT 59.499 43.478 0.00 0.00 0.00 3.32
2970 3298 3.500680 ACTAGTAAAATGCCCGTGTGTTG 59.499 43.478 0.00 0.00 0.00 3.33
2971 3299 2.303175 AGTAAAATGCCCGTGTGTTGT 58.697 42.857 0.00 0.00 0.00 3.32
2972 3300 2.691011 AGTAAAATGCCCGTGTGTTGTT 59.309 40.909 0.00 0.00 0.00 2.83
2973 3301 3.884091 AGTAAAATGCCCGTGTGTTGTTA 59.116 39.130 0.00 0.00 0.00 2.41
2974 3302 4.521256 AGTAAAATGCCCGTGTGTTGTTAT 59.479 37.500 0.00 0.00 0.00 1.89
2975 3303 3.296322 AAATGCCCGTGTGTTGTTATG 57.704 42.857 0.00 0.00 0.00 1.90
2976 3304 1.173043 ATGCCCGTGTGTTGTTATGG 58.827 50.000 0.00 0.00 0.00 2.74
2977 3305 0.108774 TGCCCGTGTGTTGTTATGGA 59.891 50.000 0.00 0.00 0.00 3.41
2978 3306 0.519961 GCCCGTGTGTTGTTATGGAC 59.480 55.000 0.00 0.00 0.00 4.02
2979 3307 1.880646 GCCCGTGTGTTGTTATGGACT 60.881 52.381 0.00 0.00 0.00 3.85
2980 3308 2.613474 GCCCGTGTGTTGTTATGGACTA 60.613 50.000 0.00 0.00 0.00 2.59
2981 3309 3.869065 CCCGTGTGTTGTTATGGACTAT 58.131 45.455 0.00 0.00 0.00 2.12
2982 3310 4.681244 GCCCGTGTGTTGTTATGGACTATA 60.681 45.833 0.00 0.00 0.00 1.31
2983 3311 5.421277 CCCGTGTGTTGTTATGGACTATAA 58.579 41.667 0.00 0.00 0.00 0.98
2984 3312 6.053005 CCCGTGTGTTGTTATGGACTATAAT 58.947 40.000 0.00 0.00 33.99 1.28
2985 3313 7.211573 CCCGTGTGTTGTTATGGACTATAATA 58.788 38.462 0.00 0.00 33.99 0.98
2986 3314 7.876068 CCCGTGTGTTGTTATGGACTATAATAT 59.124 37.037 0.00 0.00 33.99 1.28
2987 3315 9.917129 CCGTGTGTTGTTATGGACTATAATATA 57.083 33.333 0.00 0.00 33.99 0.86
3043 3371 5.695851 TTCAAGGTTGAAGCTCATTTCTC 57.304 39.130 0.00 0.00 41.88 2.87
3051 3379 5.543507 TGAAGCTCATTTCTCCCTATCTC 57.456 43.478 0.00 0.00 0.00 2.75
3063 3391 4.140924 TCTCCCTATCTCTAGGCATGTTCA 60.141 45.833 0.00 0.00 42.95 3.18
3067 3395 5.163258 CCCTATCTCTAGGCATGTTCAAACT 60.163 44.000 0.00 0.00 42.95 2.66
3072 3400 1.238439 AGGCATGTTCAAACTGTCCG 58.762 50.000 0.00 0.00 0.00 4.79
3079 3407 1.871676 GTTCAAACTGTCCGGACTTCC 59.128 52.381 33.39 9.62 0.00 3.46
3096 3424 5.300286 GGACTTCCCAAATCCAACTCATATG 59.700 44.000 0.00 0.00 32.35 1.78
3178 3507 0.893727 AGAAACCCATCCCACAACGC 60.894 55.000 0.00 0.00 0.00 4.84
3194 3523 2.723124 ACGCGCATTTCATTTTCCTT 57.277 40.000 5.73 0.00 0.00 3.36
3195 3524 2.595386 ACGCGCATTTCATTTTCCTTC 58.405 42.857 5.73 0.00 0.00 3.46
3200 3529 3.608073 CGCATTTCATTTTCCTTCCGAAC 59.392 43.478 0.00 0.00 0.00 3.95
3205 3534 2.642807 TCATTTTCCTTCCGAACCCTCT 59.357 45.455 0.00 0.00 0.00 3.69
3214 3543 1.219393 CGAACCCTCTCCTTCCTGC 59.781 63.158 0.00 0.00 0.00 4.85
3215 3544 1.261238 CGAACCCTCTCCTTCCTGCT 61.261 60.000 0.00 0.00 0.00 4.24
3223 3552 0.391793 CTCCTTCCTGCTCGGTTTCC 60.392 60.000 0.00 0.00 0.00 3.13
3234 3563 2.159181 CGGTTTCCTGCCGTAACAG 58.841 57.895 0.00 0.00 43.84 3.16
3244 3573 3.074412 CTGCCGTAACAGGACAATTCTT 58.926 45.455 0.00 0.00 33.85 2.52
3246 3575 2.414161 GCCGTAACAGGACAATTCTTGC 60.414 50.000 0.00 0.00 31.94 4.01
3248 3577 3.125316 CCGTAACAGGACAATTCTTGCTC 59.875 47.826 0.00 0.00 31.94 4.26
3256 3585 1.271597 ACAATTCTTGCTCGAGCCCTT 60.272 47.619 33.23 16.32 41.18 3.95
3259 3588 0.687354 TTCTTGCTCGAGCCCTTTCT 59.313 50.000 33.23 0.00 41.18 2.52
3278 3607 7.200455 CCTTTCTTTTAAAACCGAATGACACT 58.800 34.615 13.20 0.00 0.00 3.55
3290 3619 0.037882 ATGACACTCGGCTCACACTG 60.038 55.000 0.00 0.00 0.00 3.66
3292 3621 0.596577 GACACTCGGCTCACACTGTA 59.403 55.000 0.00 0.00 0.00 2.74
3329 3658 2.447714 GCTCCACCCTGATCCCCTC 61.448 68.421 0.00 0.00 0.00 4.30
3349 3678 4.195334 CCCTTGCCCCATCCCTCG 62.195 72.222 0.00 0.00 0.00 4.63
3373 3702 2.398588 TCCTACTGATCCACCACCATC 58.601 52.381 0.00 0.00 0.00 3.51
3378 3707 2.092753 ACTGATCCACCACCATCATCAC 60.093 50.000 0.00 0.00 0.00 3.06
3391 3720 3.470888 ATCACGGGGAAGGAGGCG 61.471 66.667 0.00 0.00 0.00 5.52
3397 3726 4.021925 GGGAAGGAGGCGTGCACT 62.022 66.667 16.19 0.00 0.00 4.40
3400 3729 1.598130 GAAGGAGGCGTGCACTGTT 60.598 57.895 16.19 0.00 0.00 3.16
3440 3769 0.616111 AAGGCAGATCCGGTGTCTCT 60.616 55.000 0.00 0.00 40.77 3.10
3451 3780 2.271800 CGGTGTCTCTTGAGCCATTAC 58.728 52.381 0.00 0.00 0.00 1.89
3453 3782 3.674997 GGTGTCTCTTGAGCCATTACAA 58.325 45.455 0.00 0.00 0.00 2.41
3476 3805 6.389830 ACTGAATGTTGTGCATTTTCACTA 57.610 33.333 0.00 0.00 46.90 2.74
3519 3848 7.255695 CCATTATTGGACATGCAACTGATACAT 60.256 37.037 0.00 0.00 46.92 2.29
3520 3849 4.968812 TTGGACATGCAACTGATACATG 57.031 40.909 0.00 0.00 45.28 3.21
3521 3850 2.684374 TGGACATGCAACTGATACATGC 59.316 45.455 0.00 0.00 43.96 4.06
3522 3851 2.033801 GGACATGCAACTGATACATGCC 59.966 50.000 0.00 0.00 43.96 4.40
3523 3852 1.672363 ACATGCAACTGATACATGCCG 59.328 47.619 0.00 0.00 43.96 5.69
3533 3883 7.345192 CAACTGATACATGCCGTTATTAACTC 58.655 38.462 5.11 0.00 0.00 3.01
3534 3884 6.817184 ACTGATACATGCCGTTATTAACTCT 58.183 36.000 5.11 0.00 0.00 3.24
3543 3893 5.239744 TGCCGTTATTAACTCTTGAAGCAAA 59.760 36.000 5.11 0.00 0.00 3.68
3544 3894 6.146898 GCCGTTATTAACTCTTGAAGCAAAA 58.853 36.000 5.11 0.00 0.00 2.44
3568 4117 9.816787 AAAAACCAGTGAATTTACCCTTCTATA 57.183 29.630 0.00 0.00 0.00 1.31
3582 4131 3.823873 CCTTCTATACCGCTCACTCTCAT 59.176 47.826 0.00 0.00 0.00 2.90
3588 4150 1.344438 ACCGCTCACTCTCATCACAAA 59.656 47.619 0.00 0.00 0.00 2.83
3618 4180 8.070171 CACTAACTCATGTTTTAAGTGAACCAG 58.930 37.037 10.40 0.00 40.22 4.00
3626 4188 9.912634 CATGTTTTAAGTGAACCAGTGATTAAT 57.087 29.630 0.00 0.00 0.00 1.40
3627 4189 9.912634 ATGTTTTAAGTGAACCAGTGATTAATG 57.087 29.630 0.00 0.00 0.00 1.90
3660 4222 1.474077 GCTAGCAACAAGGGACAATGG 59.526 52.381 10.63 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.107017 CCCCGTTGCCATCTTGAGAT 60.107 55.000 0.00 0.00 34.56 2.75
3 4 1.198094 TCCCCGTTGCCATCTTGAGA 61.198 55.000 0.00 0.00 0.00 3.27
353 354 4.776435 TGGAGATGTGAAAGATGCCATA 57.224 40.909 0.00 0.00 0.00 2.74
731 733 1.290130 ACCGTAGTCATCTTACCCCCT 59.710 52.381 0.00 0.00 0.00 4.79
884 887 0.868894 TATTAGGGGACGGGGATGGA 59.131 55.000 0.00 0.00 0.00 3.41
1036 1039 3.349927 TGATGTTGCCCTTCTTCATCTG 58.650 45.455 0.00 0.00 36.74 2.90
1631 1636 2.898840 CATGAAGCGCCAGCCGAT 60.899 61.111 2.29 0.00 46.67 4.18
1882 1887 0.471780 TCCACACCTGCTTCTCCTCA 60.472 55.000 0.00 0.00 0.00 3.86
1928 1933 2.896801 GCAGTATTCGCCGCATGGG 61.897 63.158 2.06 2.06 39.58 4.00
2098 2103 0.468226 GGAACATGGCGACCAGGATA 59.532 55.000 15.63 0.00 37.52 2.59
2425 2430 2.824041 GTGATGGCGCCGGACATT 60.824 61.111 23.90 1.28 43.76 2.71
2482 2487 1.006571 GAAGAACACCCACGCGAGA 60.007 57.895 15.93 0.00 0.00 4.04
2620 2625 2.058595 GCCCAAGAGTCTCGCCCTA 61.059 63.158 0.00 0.00 0.00 3.53
2685 2690 8.177663 CCTTGGCAGCATATTTTTATATACTCG 58.822 37.037 0.00 0.00 0.00 4.18
2713 3041 5.696724 AGAAAATCGAGACCAACACAACTAG 59.303 40.000 0.00 0.00 0.00 2.57
2714 3042 5.607477 AGAAAATCGAGACCAACACAACTA 58.393 37.500 0.00 0.00 0.00 2.24
2716 3044 4.813296 AGAAAATCGAGACCAACACAAC 57.187 40.909 0.00 0.00 0.00 3.32
2718 3046 5.828299 AAAAGAAAATCGAGACCAACACA 57.172 34.783 0.00 0.00 0.00 3.72
2740 3068 1.631405 TTCCGGACGAAGGGAGTAAA 58.369 50.000 1.83 0.00 33.01 2.01
2742 3070 1.856629 ATTTCCGGACGAAGGGAGTA 58.143 50.000 1.83 0.00 33.01 2.59
2743 3071 1.479730 GTATTTCCGGACGAAGGGAGT 59.520 52.381 1.83 0.00 33.01 3.85
2744 3072 1.755380 AGTATTTCCGGACGAAGGGAG 59.245 52.381 1.83 0.00 33.01 4.30
2745 3073 1.856629 AGTATTTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 0.00 4.20
2746 3074 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
2747 3075 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
2748 3076 3.581755 TGACAAGTATTTCCGGACGAAG 58.418 45.455 1.83 0.00 0.00 3.79
2749 3077 3.256383 TCTGACAAGTATTTCCGGACGAA 59.744 43.478 1.83 0.00 0.00 3.85
2750 3078 2.821378 TCTGACAAGTATTTCCGGACGA 59.179 45.455 1.83 0.00 0.00 4.20
2751 3079 3.226346 TCTGACAAGTATTTCCGGACG 57.774 47.619 1.83 0.00 0.00 4.79
2752 3080 7.494625 TCATTTATCTGACAAGTATTTCCGGAC 59.505 37.037 1.83 0.00 0.00 4.79
2753 3081 7.561251 TCATTTATCTGACAAGTATTTCCGGA 58.439 34.615 0.00 0.00 0.00 5.14
2754 3082 7.786178 TCATTTATCTGACAAGTATTTCCGG 57.214 36.000 0.00 0.00 0.00 5.14
2755 3083 9.655769 CATTCATTTATCTGACAAGTATTTCCG 57.344 33.333 0.00 0.00 0.00 4.30
2821 3149 9.104965 CGGAAATACTTGTTGTAGAAATGGATA 57.895 33.333 0.00 0.00 34.24 2.59
2822 3150 7.827236 TCGGAAATACTTGTTGTAGAAATGGAT 59.173 33.333 0.00 0.00 34.24 3.41
2823 3151 7.162761 TCGGAAATACTTGTTGTAGAAATGGA 58.837 34.615 0.00 0.00 34.24 3.41
2824 3152 7.372451 TCGGAAATACTTGTTGTAGAAATGG 57.628 36.000 0.00 0.00 34.24 3.16
2825 3153 8.286800 TGTTCGGAAATACTTGTTGTAGAAATG 58.713 33.333 0.00 0.00 34.24 2.32
2826 3154 8.385898 TGTTCGGAAATACTTGTTGTAGAAAT 57.614 30.769 0.00 0.00 34.24 2.17
2827 3155 7.711772 TCTGTTCGGAAATACTTGTTGTAGAAA 59.288 33.333 0.00 0.00 34.24 2.52
2828 3156 7.211573 TCTGTTCGGAAATACTTGTTGTAGAA 58.788 34.615 0.00 0.00 34.24 2.10
2829 3157 6.751157 TCTGTTCGGAAATACTTGTTGTAGA 58.249 36.000 0.00 0.00 34.24 2.59
2830 3158 6.090898 CCTCTGTTCGGAAATACTTGTTGTAG 59.909 42.308 0.00 0.00 34.24 2.74
2831 3159 5.929992 CCTCTGTTCGGAAATACTTGTTGTA 59.070 40.000 0.00 0.00 35.37 2.41
2832 3160 4.755123 CCTCTGTTCGGAAATACTTGTTGT 59.245 41.667 0.00 0.00 0.00 3.32
2833 3161 4.755123 ACCTCTGTTCGGAAATACTTGTTG 59.245 41.667 0.00 0.00 0.00 3.33
2834 3162 4.969484 ACCTCTGTTCGGAAATACTTGTT 58.031 39.130 0.00 0.00 0.00 2.83
2835 3163 4.618920 ACCTCTGTTCGGAAATACTTGT 57.381 40.909 0.00 0.00 0.00 3.16
2836 3164 5.721232 ACTACCTCTGTTCGGAAATACTTG 58.279 41.667 0.00 0.00 0.00 3.16
2837 3165 5.997384 ACTACCTCTGTTCGGAAATACTT 57.003 39.130 0.00 0.00 0.00 2.24
2838 3166 6.186234 AGTACTACCTCTGTTCGGAAATACT 58.814 40.000 0.00 0.00 0.00 2.12
2839 3167 6.448207 AGTACTACCTCTGTTCGGAAATAC 57.552 41.667 0.00 0.00 0.00 1.89
2840 3168 7.318141 CAAAGTACTACCTCTGTTCGGAAATA 58.682 38.462 0.00 0.00 0.00 1.40
2841 3169 5.997384 AAGTACTACCTCTGTTCGGAAAT 57.003 39.130 0.00 0.00 0.00 2.17
2842 3170 5.535333 CAAAGTACTACCTCTGTTCGGAAA 58.465 41.667 0.00 0.00 0.00 3.13
2843 3171 4.560108 GCAAAGTACTACCTCTGTTCGGAA 60.560 45.833 0.00 0.00 0.00 4.30
2844 3172 3.057033 GCAAAGTACTACCTCTGTTCGGA 60.057 47.826 0.00 0.00 0.00 4.55
2845 3173 3.251571 GCAAAGTACTACCTCTGTTCGG 58.748 50.000 0.00 0.00 0.00 4.30
2846 3174 3.909430 TGCAAAGTACTACCTCTGTTCG 58.091 45.455 0.00 0.00 0.00 3.95
2847 3175 4.924462 GTCTGCAAAGTACTACCTCTGTTC 59.076 45.833 0.00 0.00 0.00 3.18
2848 3176 4.589374 AGTCTGCAAAGTACTACCTCTGTT 59.411 41.667 0.00 0.00 0.00 3.16
2849 3177 4.153411 AGTCTGCAAAGTACTACCTCTGT 58.847 43.478 0.00 0.00 0.00 3.41
2850 3178 4.792521 AGTCTGCAAAGTACTACCTCTG 57.207 45.455 0.00 0.00 0.00 3.35
2851 3179 5.810080 AAAGTCTGCAAAGTACTACCTCT 57.190 39.130 0.00 0.00 0.00 3.69
2852 3180 5.334182 GCAAAAGTCTGCAAAGTACTACCTC 60.334 44.000 0.00 0.00 42.17 3.85
2853 3181 4.515567 GCAAAAGTCTGCAAAGTACTACCT 59.484 41.667 0.00 0.00 42.17 3.08
2854 3182 4.515567 AGCAAAAGTCTGCAAAGTACTACC 59.484 41.667 0.00 0.00 45.18 3.18
2855 3183 5.674933 AGCAAAAGTCTGCAAAGTACTAC 57.325 39.130 0.00 0.00 45.18 2.73
2856 3184 6.055588 AGAAGCAAAAGTCTGCAAAGTACTA 58.944 36.000 0.00 0.00 45.18 1.82
2857 3185 4.884164 AGAAGCAAAAGTCTGCAAAGTACT 59.116 37.500 0.00 0.00 45.18 2.73
2858 3186 5.175090 AGAAGCAAAAGTCTGCAAAGTAC 57.825 39.130 0.00 0.00 45.18 2.73
2899 3227 4.359774 ATGCAGTGTAACGCAGATGTGTT 61.360 43.478 15.37 15.37 45.96 3.32
2909 3237 2.397777 TGCAAACATGCAGTGTAACG 57.602 45.000 0.00 0.00 45.86 3.18
2913 3241 3.057315 GGACTATTGCAAACATGCAGTGT 60.057 43.478 1.71 6.99 46.21 3.55
2921 3249 0.878416 GCGGTGGACTATTGCAAACA 59.122 50.000 1.71 0.00 0.00 2.83
2924 3252 1.093972 CATGCGGTGGACTATTGCAA 58.906 50.000 0.00 0.00 39.26 4.08
2946 3274 2.418628 CACACGGGCATTTTACTAGTGG 59.581 50.000 5.39 0.00 32.98 4.00
2955 3283 2.029470 CCATAACAACACACGGGCATTT 60.029 45.455 0.00 0.00 0.00 2.32
3023 3351 3.192212 GGGAGAAATGAGCTTCAACCTTG 59.808 47.826 0.00 0.00 0.00 3.61
3025 3353 2.646798 AGGGAGAAATGAGCTTCAACCT 59.353 45.455 0.00 0.00 32.20 3.50
3026 3354 3.078891 AGGGAGAAATGAGCTTCAACC 57.921 47.619 0.00 0.00 0.00 3.77
3043 3371 4.963318 TTGAACATGCCTAGAGATAGGG 57.037 45.455 3.61 0.00 37.69 3.53
3051 3379 2.416547 CGGACAGTTTGAACATGCCTAG 59.583 50.000 0.00 0.00 0.00 3.02
3063 3391 0.841289 TTGGGAAGTCCGGACAGTTT 59.159 50.000 35.00 21.41 38.76 2.66
3067 3395 0.326927 GGATTTGGGAAGTCCGGACA 59.673 55.000 35.00 14.19 38.76 4.02
3072 3400 3.154827 TGAGTTGGATTTGGGAAGTCC 57.845 47.619 0.00 0.00 0.00 3.85
3096 3424 4.764823 TCCAACAACCACATATTCTCCAAC 59.235 41.667 0.00 0.00 0.00 3.77
3103 3431 6.721318 ACAGATAGTCCAACAACCACATATT 58.279 36.000 0.00 0.00 0.00 1.28
3138 3467 0.878416 GTATTGGGCTTGCGTGTTGA 59.122 50.000 0.00 0.00 0.00 3.18
3139 3468 0.595588 TGTATTGGGCTTGCGTGTTG 59.404 50.000 0.00 0.00 0.00 3.33
3140 3469 1.269448 CTTGTATTGGGCTTGCGTGTT 59.731 47.619 0.00 0.00 0.00 3.32
3141 3470 0.881118 CTTGTATTGGGCTTGCGTGT 59.119 50.000 0.00 0.00 0.00 4.49
3178 3507 3.485947 TCGGAAGGAAAATGAAATGCG 57.514 42.857 0.00 0.00 0.00 4.73
3194 3523 0.614979 CAGGAAGGAGAGGGTTCGGA 60.615 60.000 0.00 0.00 0.00 4.55
3195 3524 1.901085 CAGGAAGGAGAGGGTTCGG 59.099 63.158 0.00 0.00 0.00 4.30
3200 3529 2.430610 CCGAGCAGGAAGGAGAGGG 61.431 68.421 0.00 0.00 45.00 4.30
3205 3534 0.836400 AGGAAACCGAGCAGGAAGGA 60.836 55.000 5.19 0.00 45.00 3.36
3223 3552 2.699954 AGAATTGTCCTGTTACGGCAG 58.300 47.619 0.00 0.00 36.31 4.85
3244 3573 2.851263 TAAAAGAAAGGGCTCGAGCA 57.149 45.000 36.27 11.18 44.36 4.26
3246 3575 4.612939 CGGTTTTAAAAGAAAGGGCTCGAG 60.613 45.833 8.45 8.45 0.00 4.04
3248 3577 3.251487 TCGGTTTTAAAAGAAAGGGCTCG 59.749 43.478 0.00 0.00 0.00 5.03
3256 3585 6.423862 CGAGTGTCATTCGGTTTTAAAAGAA 58.576 36.000 9.72 3.13 34.56 2.52
3278 3607 1.583495 CGGAGTACAGTGTGAGCCGA 61.583 60.000 20.88 0.00 39.62 5.54
3281 3610 1.446272 GGCGGAGTACAGTGTGAGC 60.446 63.158 5.88 4.04 0.00 4.26
3309 3638 4.554036 GGGATCAGGGTGGAGCGC 62.554 72.222 0.00 0.00 0.00 5.92
3311 3640 2.367512 AGGGGATCAGGGTGGAGC 60.368 66.667 0.00 0.00 0.00 4.70
3336 3665 2.933287 AACACGAGGGATGGGGCA 60.933 61.111 0.00 0.00 0.00 5.36
3349 3678 2.354805 GGTGGTGGATCAGTAGGAACAC 60.355 54.545 0.00 0.00 36.98 3.32
3373 3702 2.190578 GCCTCCTTCCCCGTGATG 59.809 66.667 0.00 0.00 0.00 3.07
3395 3724 2.351276 GGGGGCATCACGAACAGT 59.649 61.111 0.00 0.00 0.00 3.55
3397 3726 3.309436 CTCGGGGGCATCACGAACA 62.309 63.158 5.22 0.00 36.08 3.18
3427 3756 0.179097 GGCTCAAGAGACACCGGATC 60.179 60.000 9.46 5.22 36.17 3.36
3501 3830 2.033801 GGCATGTATCAGTTGCATGTCC 59.966 50.000 10.27 8.50 44.46 4.02
3502 3831 2.286595 CGGCATGTATCAGTTGCATGTC 60.287 50.000 10.27 7.52 46.64 3.06
3519 3848 4.320023 TGCTTCAAGAGTTAATAACGGCA 58.680 39.130 0.00 0.00 36.23 5.69
3520 3849 4.939509 TGCTTCAAGAGTTAATAACGGC 57.060 40.909 0.00 0.00 36.23 5.68
3543 3893 9.239551 GTATAGAAGGGTAAATTCACTGGTTTT 57.760 33.333 0.00 0.00 0.00 2.43
3544 3894 7.832685 GGTATAGAAGGGTAAATTCACTGGTTT 59.167 37.037 0.00 0.00 0.00 3.27
3547 3897 5.989777 CGGTATAGAAGGGTAAATTCACTGG 59.010 44.000 0.00 0.00 0.00 4.00
3550 3900 5.608449 AGCGGTATAGAAGGGTAAATTCAC 58.392 41.667 0.00 0.00 0.00 3.18
3553 3903 5.365895 AGTGAGCGGTATAGAAGGGTAAATT 59.634 40.000 0.00 0.00 0.00 1.82
3568 4117 0.969149 TTGTGATGAGAGTGAGCGGT 59.031 50.000 0.00 0.00 0.00 5.68
3582 4131 7.581213 AAACATGAGTTAGTGGATTTTGTGA 57.419 32.000 0.00 0.00 36.84 3.58
3588 4150 8.918202 TCACTTAAAACATGAGTTAGTGGATT 57.082 30.769 0.00 0.00 40.10 3.01
3642 4204 1.544724 GCCATTGTCCCTTGTTGCTA 58.455 50.000 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.