Multiple sequence alignment - TraesCS7D01G180700

Loading Multiple Alignment...

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 TraesCS7D01G180700 chr7D 100.000 3909 0 0 1 3909 134100327 134104235 0.000000e+00 7219.0
1 TraesCS7D01G180700 chr7D 80.495 646 113 11 3209 3849 102547572 102546935 2.110000e-132 483.0
2 TraesCS7D01G180700 chr7D 77.692 130 28 1 2438 2567 8453050 8452922 1.160000e-10 78.7
3 TraesCS7D01G180700 chr7B 94.297 2788 100 23 206 2967 95916431 95919185 0.000000e+00 4213.0
4 TraesCS7D01G180700 chr7B 92.473 186 14 0 1 186 95894436 95894621 2.320000e-67 267.0
5 TraesCS7D01G180700 chr7B 81.102 127 18 5 2402 2525 444292484 444292607 3.210000e-16 97.1
6 TraesCS7D01G180700 chr7A 94.603 2038 94 12 1111 3139 133045902 133047932 0.000000e+00 3140.0
7 TraesCS7D01G180700 chr7A 89.912 1140 48 24 1 1083 133044778 133045907 0.000000e+00 1406.0
8 TraesCS7D01G180700 chr7A 80.301 731 127 15 3171 3896 510144884 510144166 1.600000e-148 536.0
9 TraesCS7D01G180700 chr7A 85.342 307 35 8 3610 3907 133048239 133048544 3.790000e-80 309.0
10 TraesCS7D01G180700 chr7A 84.000 125 18 2 1200 1323 441978663 441978786 6.860000e-23 119.0
11 TraesCS7D01G180700 chr7A 81.102 127 18 5 2402 2525 506155140 506155017 3.210000e-16 97.1
12 TraesCS7D01G180700 chr5D 97.585 414 9 1 2265 2678 126372581 126372169 0.000000e+00 708.0
13 TraesCS7D01G180700 chr5D 80.929 603 98 14 3198 3791 550375437 550376031 9.900000e-126 460.0
14 TraesCS7D01G180700 chr5D 73.756 442 94 19 2135 2562 416258232 416257799 1.880000e-33 154.0
15 TraesCS7D01G180700 chr5D 76.211 227 47 6 1200 1421 50678961 50678737 3.190000e-21 113.0
16 TraesCS7D01G180700 chr5D 100.000 39 0 0 2640 2678 446160545 446160507 5.420000e-09 73.1
17 TraesCS7D01G180700 chr2D 79.973 744 136 12 3157 3896 403179137 403178403 1.600000e-148 536.0
18 TraesCS7D01G180700 chr2D 88.060 134 15 1 1242 1375 315972868 315972736 1.450000e-34 158.0
19 TraesCS7D01G180700 chr2D 91.398 93 8 0 1577 1669 315972735 315972643 1.140000e-25 128.0
20 TraesCS7D01G180700 chr1D 79.866 745 135 11 3157 3896 270232992 270233726 7.440000e-147 531.0
21 TraesCS7D01G180700 chr1D 97.619 42 1 0 2637 2678 203955928 203955969 5.420000e-09 73.1
22 TraesCS7D01G180700 chr3A 79.542 743 132 16 3171 3907 629625023 629625751 2.690000e-141 512.0
23 TraesCS7D01G180700 chr5A 77.720 763 140 23 3157 3907 14489098 14489842 1.290000e-119 440.0
24 TraesCS7D01G180700 chr5A 73.394 436 100 14 2135 2562 529080083 529079656 8.750000e-32 148.0
25 TraesCS7D01G180700 chr5A 74.890 227 50 6 1200 1421 40080829 40080605 3.210000e-16 97.1
26 TraesCS7D01G180700 chr4A 77.837 749 139 20 3157 3896 516357242 516357972 4.640000e-119 438.0
27 TraesCS7D01G180700 chr5B 80.567 494 92 3 3170 3659 388734871 388735364 1.030000e-100 377.0
28 TraesCS7D01G180700 chr5B 74.536 377 81 13 2198 2562 503115650 503115277 2.430000e-32 150.0
29 TraesCS7D01G180700 chr5B 75.446 224 43 11 1205 1421 53553508 53553290 8.940000e-17 99.0


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 TraesCS7D01G180700 chr7D 134100327 134104235 3908 False 7219.000000 7219 100.000000 1 3909 1 chr7D.!!$F1 3908
1 TraesCS7D01G180700 chr7D 102546935 102547572 637 True 483.000000 483 80.495000 3209 3849 1 chr7D.!!$R2 640
2 TraesCS7D01G180700 chr7B 95916431 95919185 2754 False 4213.000000 4213 94.297000 206 2967 1 chr7B.!!$F2 2761
3 TraesCS7D01G180700 chr7A 133044778 133048544 3766 False 1618.333333 3140 89.952333 1 3907 3 chr7A.!!$F2 3906
4 TraesCS7D01G180700 chr7A 510144166 510144884 718 True 536.000000 536 80.301000 3171 3896 1 chr7A.!!$R2 725
5 TraesCS7D01G180700 chr5D 550375437 550376031 594 False 460.000000 460 80.929000 3198 3791 1 chr5D.!!$F1 593
6 TraesCS7D01G180700 chr2D 403178403 403179137 734 True 536.000000 536 79.973000 3157 3896 1 chr2D.!!$R1 739
7 TraesCS7D01G180700 chr1D 270232992 270233726 734 False 531.000000 531 79.866000 3157 3896 1 chr1D.!!$F2 739
8 TraesCS7D01G180700 chr3A 629625023 629625751 728 False 512.000000 512 79.542000 3171 3907 1 chr3A.!!$F1 736
9 TraesCS7D01G180700 chr5A 14489098 14489842 744 False 440.000000 440 77.720000 3157 3907 1 chr5A.!!$F1 750
10 TraesCS7D01G180700 chr4A 516357242 516357972 730 False 438.000000 438 77.837000 3157 3896 1 chr4A.!!$F1 739

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
109 110 0.601841 TGACTTTCGAAGGTTCCCGC 60.602 55.0 14.62 1.9 0.0 6.13 F
1036 1100 0.036294 CTAGCCCGCCTATTTAGCCC 60.036 60.0 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1102 1166 0.107831 GCACTTCCTACACACCCACA 59.892 55.0 0.0 0.00 0.0 4.17 R
3028 3110 0.865111 TTTGCATCCGTGTCTGAACG 59.135 50.0 0.0 5.72 43.2 3.95 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
29 30 3.445805 AGTGGAGCGGAAAAGAAAAACAA 59.554 39.130 0.00 0.00 0.00 2.83
34 35 5.155509 AGCGGAAAAGAAAAACAAATTGC 57.844 34.783 0.00 0.00 0.00 3.56
62 63 5.394224 TTTTCCAATTTCCGTATCCCAAC 57.606 39.130 0.00 0.00 0.00 3.77
63 64 4.310022 TTCCAATTTCCGTATCCCAACT 57.690 40.909 0.00 0.00 0.00 3.16
64 65 5.438698 TTCCAATTTCCGTATCCCAACTA 57.561 39.130 0.00 0.00 0.00 2.24
86 87 1.471684 ACGTAATAGGGCGATCCGATC 59.528 52.381 0.00 0.00 41.52 3.69
101 102 4.033990 TCCGATCTCATGACTTTCGAAG 57.966 45.455 15.23 0.00 31.74 3.79
109 110 0.601841 TGACTTTCGAAGGTTCCCGC 60.602 55.000 14.62 1.90 0.00 6.13
158 159 7.441157 TCAATCTTTCCACGGATATACAATGAC 59.559 37.037 0.00 0.00 0.00 3.06
173 174 9.836864 ATATACAATGACAATACAGTGATGTGT 57.163 29.630 0.00 0.00 38.85 3.72
190 191 8.857098 AGTGATGTGTTTTTACTAGACTGTAGA 58.143 33.333 0.00 0.00 0.00 2.59
241 249 2.097160 CGCGCACTCATCAGCAAC 59.903 61.111 8.75 0.00 0.00 4.17
252 260 0.744414 ATCAGCAACGGATGGGAACG 60.744 55.000 0.00 0.00 0.00 3.95
331 339 1.660560 CCTGGGGCTTCTCAATTGCG 61.661 60.000 0.00 0.00 0.00 4.85
333 341 1.678970 GGGGCTTCTCAATTGCGGT 60.679 57.895 0.00 0.00 0.00 5.68
430 438 4.566759 CGATGCTCGGAAGAATAGACAAAA 59.433 41.667 0.00 0.00 41.32 2.44
736 777 6.766084 TGGTTTTGCTTTTGTTTTTGTATCG 58.234 32.000 0.00 0.00 0.00 2.92
739 780 6.576551 TTTGCTTTTGTTTTTGTATCGGTC 57.423 33.333 0.00 0.00 0.00 4.79
748 789 4.617808 TTTTGTATCGGTCTCTCTCTCG 57.382 45.455 0.00 0.00 0.00 4.04
749 790 3.538634 TTGTATCGGTCTCTCTCTCGA 57.461 47.619 0.00 0.00 36.07 4.04
750 791 3.755112 TGTATCGGTCTCTCTCTCGAT 57.245 47.619 0.00 0.00 43.48 3.59
751 792 3.655486 TGTATCGGTCTCTCTCTCGATC 58.345 50.000 0.00 0.00 41.66 3.69
752 793 2.920724 ATCGGTCTCTCTCTCGATCA 57.079 50.000 0.00 0.00 37.77 2.92
753 794 2.232756 TCGGTCTCTCTCTCGATCAG 57.767 55.000 0.00 0.00 0.00 2.90
754 795 1.757699 TCGGTCTCTCTCTCGATCAGA 59.242 52.381 0.00 0.00 0.00 3.27
783 824 2.420642 ACTTGTGTAGCTAGTCGTCGA 58.579 47.619 0.00 0.00 0.00 4.20
785 826 1.799544 TGTGTAGCTAGTCGTCGACA 58.200 50.000 26.17 11.86 34.60 4.35
831 878 1.645710 GGTGAGACCAGGGAAGAAGA 58.354 55.000 0.00 0.00 38.42 2.87
1022 1086 2.102553 GACGACGACCAGCTAGCC 59.897 66.667 12.13 0.00 0.00 3.93
1035 1099 0.673956 GCTAGCCCGCCTATTTAGCC 60.674 60.000 2.29 0.00 32.58 3.93
1036 1100 0.036294 CTAGCCCGCCTATTTAGCCC 60.036 60.000 0.00 0.00 0.00 5.19
1083 1147 4.968259 AGGATGTGTTTGTACTTGTAGCA 58.032 39.130 0.00 0.00 0.00 3.49
1158 1222 0.749649 CTAGAGCTAGTGGTGCCAGG 59.250 60.000 0.00 0.00 0.00 4.45
1709 1780 5.497474 ACTTAGTGTTTCAATTATCGCCCT 58.503 37.500 0.00 0.00 0.00 5.19
1710 1781 5.585047 ACTTAGTGTTTCAATTATCGCCCTC 59.415 40.000 0.00 0.00 0.00 4.30
1711 1782 2.936498 AGTGTTTCAATTATCGCCCTCG 59.064 45.455 0.00 0.00 0.00 4.63
1774 1845 2.961721 CTGCACGTGTCGCACTGT 60.962 61.111 18.38 5.45 35.08 3.55
1821 1892 2.185004 ATCCGTGTCTGTTTCTTGGG 57.815 50.000 0.00 0.00 0.00 4.12
2304 2375 3.691342 TTCCTCTGGGTCGTGCGG 61.691 66.667 0.00 0.00 0.00 5.69
2370 2441 1.292223 CTTCCTCGCGGAGACCAAA 59.708 57.895 6.13 0.00 41.25 3.28
2373 2444 2.125512 CTCGCGGAGACCAAAGGG 60.126 66.667 6.13 0.00 41.29 3.95
2631 2702 3.474570 GAGGAGCTCATGGGCGGT 61.475 66.667 17.19 0.00 37.29 5.68
2988 3070 5.779529 ACTATGCAAATCATGGGCTTAAG 57.220 39.130 0.00 0.00 37.91 1.85
2990 3072 3.098774 TGCAAATCATGGGCTTAAGGA 57.901 42.857 4.29 0.00 0.00 3.36
3022 3104 0.177141 CGACCCGCAAAATCCCTCTA 59.823 55.000 0.00 0.00 0.00 2.43
3024 3106 1.209747 GACCCGCAAAATCCCTCTAGT 59.790 52.381 0.00 0.00 0.00 2.57
3027 3109 3.071167 ACCCGCAAAATCCCTCTAGTATC 59.929 47.826 0.00 0.00 0.00 2.24
3028 3110 3.557264 CCCGCAAAATCCCTCTAGTATCC 60.557 52.174 0.00 0.00 0.00 2.59
3029 3111 3.318017 CGCAAAATCCCTCTAGTATCCG 58.682 50.000 0.00 0.00 0.00 4.18
3030 3112 3.243771 CGCAAAATCCCTCTAGTATCCGT 60.244 47.826 0.00 0.00 0.00 4.69
3031 3113 4.704965 GCAAAATCCCTCTAGTATCCGTT 58.295 43.478 0.00 0.00 0.00 4.44
3032 3114 4.750598 GCAAAATCCCTCTAGTATCCGTTC 59.249 45.833 0.00 0.00 0.00 3.95
3033 3115 5.684030 GCAAAATCCCTCTAGTATCCGTTCA 60.684 44.000 0.00 0.00 0.00 3.18
3034 3116 5.793030 AAATCCCTCTAGTATCCGTTCAG 57.207 43.478 0.00 0.00 0.00 3.02
3035 3117 4.726035 ATCCCTCTAGTATCCGTTCAGA 57.274 45.455 0.00 0.00 0.00 3.27
3036 3118 3.818180 TCCCTCTAGTATCCGTTCAGAC 58.182 50.000 0.00 0.00 0.00 3.51
3037 3119 3.201487 TCCCTCTAGTATCCGTTCAGACA 59.799 47.826 0.00 0.00 0.00 3.41
3038 3120 3.315749 CCCTCTAGTATCCGTTCAGACAC 59.684 52.174 0.00 0.00 0.00 3.67
3039 3121 3.002451 CCTCTAGTATCCGTTCAGACACG 59.998 52.174 0.00 0.00 40.02 4.49
3045 3127 4.260194 CGTTCAGACACGGATGCA 57.740 55.556 0.00 0.00 36.47 3.96
3046 3128 2.527671 CGTTCAGACACGGATGCAA 58.472 52.632 0.00 0.00 36.47 4.08
3047 3129 0.865111 CGTTCAGACACGGATGCAAA 59.135 50.000 0.00 0.00 36.47 3.68
3048 3130 1.136252 CGTTCAGACACGGATGCAAAG 60.136 52.381 0.00 0.00 36.47 2.77
3049 3131 1.197721 GTTCAGACACGGATGCAAAGG 59.802 52.381 0.00 0.00 0.00 3.11
3050 3132 0.955428 TCAGACACGGATGCAAAGGC 60.955 55.000 0.00 0.00 41.68 4.35
3063 3145 2.716217 GCAAAGGCACTCATCTAAGGT 58.284 47.619 0.00 0.00 38.49 3.50
3064 3146 3.084786 GCAAAGGCACTCATCTAAGGTT 58.915 45.455 0.00 0.00 38.49 3.50
3065 3147 3.119708 GCAAAGGCACTCATCTAAGGTTG 60.120 47.826 0.00 0.00 38.49 3.77
3066 3148 4.074970 CAAAGGCACTCATCTAAGGTTGT 58.925 43.478 0.00 0.00 38.49 3.32
3067 3149 4.373156 AAGGCACTCATCTAAGGTTGTT 57.627 40.909 0.00 0.00 38.49 2.83
3068 3150 3.944087 AGGCACTCATCTAAGGTTGTTC 58.056 45.455 0.00 0.00 0.00 3.18
3069 3151 2.673368 GGCACTCATCTAAGGTTGTTCG 59.327 50.000 0.00 0.00 0.00 3.95
3070 3152 2.094417 GCACTCATCTAAGGTTGTTCGC 59.906 50.000 0.00 0.00 0.00 4.70
3071 3153 3.325870 CACTCATCTAAGGTTGTTCGCA 58.674 45.455 0.00 0.00 0.00 5.10
3072 3154 3.935203 CACTCATCTAAGGTTGTTCGCAT 59.065 43.478 0.00 0.00 0.00 4.73
3073 3155 5.109210 CACTCATCTAAGGTTGTTCGCATA 58.891 41.667 0.00 0.00 0.00 3.14
3074 3156 5.005779 CACTCATCTAAGGTTGTTCGCATAC 59.994 44.000 0.00 0.00 0.00 2.39
3075 3157 5.079689 TCATCTAAGGTTGTTCGCATACA 57.920 39.130 0.00 0.00 0.00 2.29
3076 3158 5.670485 TCATCTAAGGTTGTTCGCATACAT 58.330 37.500 0.00 0.00 0.00 2.29
3077 3159 6.112734 TCATCTAAGGTTGTTCGCATACATT 58.887 36.000 0.00 0.00 0.00 2.71
3078 3160 6.597672 TCATCTAAGGTTGTTCGCATACATTT 59.402 34.615 0.00 0.00 0.00 2.32
3079 3161 6.811253 TCTAAGGTTGTTCGCATACATTTT 57.189 33.333 0.00 0.00 0.00 1.82
3080 3162 7.908827 TCTAAGGTTGTTCGCATACATTTTA 57.091 32.000 0.00 0.00 0.00 1.52
3081 3163 7.970384 TCTAAGGTTGTTCGCATACATTTTAG 58.030 34.615 0.00 0.00 0.00 1.85
3082 3164 4.981794 AGGTTGTTCGCATACATTTTAGC 58.018 39.130 0.00 0.00 0.00 3.09
3083 3165 4.457603 AGGTTGTTCGCATACATTTTAGCA 59.542 37.500 0.00 0.00 0.00 3.49
3084 3166 5.048364 AGGTTGTTCGCATACATTTTAGCAA 60.048 36.000 0.00 0.00 0.00 3.91
3085 3167 5.804979 GGTTGTTCGCATACATTTTAGCAAT 59.195 36.000 0.00 0.00 0.00 3.56
3086 3168 6.310224 GGTTGTTCGCATACATTTTAGCAATT 59.690 34.615 0.00 0.00 0.00 2.32
3087 3169 7.148656 GGTTGTTCGCATACATTTTAGCAATTT 60.149 33.333 0.00 0.00 0.00 1.82
3088 3170 7.881643 TGTTCGCATACATTTTAGCAATTTT 57.118 28.000 0.00 0.00 0.00 1.82
3089 3171 8.304202 TGTTCGCATACATTTTAGCAATTTTT 57.696 26.923 0.00 0.00 0.00 1.94
3113 3195 9.571810 TTTTAGATCAATCGGACAAAATTCATG 57.428 29.630 0.00 0.00 0.00 3.07
3114 3196 5.585390 AGATCAATCGGACAAAATTCATGC 58.415 37.500 0.00 0.00 0.00 4.06
3115 3197 4.780275 TCAATCGGACAAAATTCATGCA 57.220 36.364 0.00 0.00 0.00 3.96
3116 3198 5.131594 TCAATCGGACAAAATTCATGCAA 57.868 34.783 0.00 0.00 0.00 4.08
3117 3199 4.922692 TCAATCGGACAAAATTCATGCAAC 59.077 37.500 0.00 0.00 0.00 4.17
3118 3200 3.998099 TCGGACAAAATTCATGCAACA 57.002 38.095 0.00 0.00 0.00 3.33
3119 3201 4.313277 TCGGACAAAATTCATGCAACAA 57.687 36.364 0.00 0.00 0.00 2.83
3120 3202 4.880759 TCGGACAAAATTCATGCAACAAT 58.119 34.783 0.00 0.00 0.00 2.71
3121 3203 4.685165 TCGGACAAAATTCATGCAACAATG 59.315 37.500 0.00 0.00 0.00 2.82
3122 3204 4.685165 CGGACAAAATTCATGCAACAATGA 59.315 37.500 0.00 0.00 34.75 2.57
3123 3205 5.388682 CGGACAAAATTCATGCAACAATGAC 60.389 40.000 0.00 0.00 36.31 3.06
3124 3206 5.388682 GGACAAAATTCATGCAACAATGACG 60.389 40.000 0.00 0.00 36.31 4.35
3125 3207 4.448395 ACAAAATTCATGCAACAATGACGG 59.552 37.500 0.00 0.00 36.31 4.79
3126 3208 4.517952 AAATTCATGCAACAATGACGGA 57.482 36.364 0.00 0.00 36.31 4.69
3127 3209 4.724074 AATTCATGCAACAATGACGGAT 57.276 36.364 0.00 0.00 36.31 4.18
3128 3210 4.724074 ATTCATGCAACAATGACGGATT 57.276 36.364 0.00 0.00 36.31 3.01
3129 3211 4.517952 TTCATGCAACAATGACGGATTT 57.482 36.364 0.00 0.00 36.31 2.17
3130 3212 4.095410 TCATGCAACAATGACGGATTTC 57.905 40.909 0.00 0.00 31.58 2.17
3131 3213 3.505293 TCATGCAACAATGACGGATTTCA 59.495 39.130 0.00 0.00 31.58 2.69
3132 3214 4.158209 TCATGCAACAATGACGGATTTCAT 59.842 37.500 0.00 0.00 37.87 2.57
3133 3215 5.356470 TCATGCAACAATGACGGATTTCATA 59.644 36.000 0.00 0.00 35.02 2.15
3134 3216 4.980590 TGCAACAATGACGGATTTCATAC 58.019 39.130 0.00 0.00 35.02 2.39
3135 3217 4.457257 TGCAACAATGACGGATTTCATACA 59.543 37.500 0.00 0.00 35.02 2.29
3136 3218 5.048434 TGCAACAATGACGGATTTCATACAA 60.048 36.000 0.00 0.00 35.02 2.41
3137 3219 5.861251 GCAACAATGACGGATTTCATACAAA 59.139 36.000 0.00 0.00 35.02 2.83
3164 3253 1.271325 ACACGGTTGCAGATCCAATGA 60.271 47.619 10.58 0.00 0.00 2.57
3331 3427 4.662961 CGGCGCCGGCAGATATCA 62.663 66.667 40.50 0.00 42.47 2.15
3339 3435 0.587768 CGGCAGATATCAATGCGCAA 59.412 50.000 17.11 0.00 43.49 4.85
3350 3446 1.396648 CAATGCGCAAGACACGGATAA 59.603 47.619 17.11 0.00 40.90 1.75
3366 3463 5.755375 CACGGATAACCTTACTAGTCTACGA 59.245 44.000 0.00 0.00 0.00 3.43
3390 3487 3.654020 GCGGCGGATCTCCATTGC 61.654 66.667 9.78 0.00 35.14 3.56
3406 3503 0.776810 TTGCCTTTCCCATGTCTGGA 59.223 50.000 0.00 0.00 46.37 3.86
3420 3517 3.589654 CTGGAAGCCCGCTCGTTGA 62.590 63.158 0.00 0.00 34.29 3.18
3459 3556 3.616219 AGGTATATGCCTCAACGCAAAA 58.384 40.909 6.53 0.00 43.24 2.44
3528 3630 1.656441 CCGCAATATGCTTCAGCCC 59.344 57.895 0.43 0.00 42.25 5.19
3529 3631 1.656441 CGCAATATGCTTCAGCCCC 59.344 57.895 0.43 0.00 42.25 5.80
3532 3634 1.751733 GCAATATGCTTCAGCCCCAGA 60.752 52.381 0.00 0.00 40.96 3.86
3665 3945 2.898729 TCTCCTCGATGATGGCTTTC 57.101 50.000 0.00 0.00 0.00 2.62
3689 3970 1.745115 CCGTCGGATGTGTTGGCAT 60.745 57.895 4.91 0.00 0.00 4.40
3708 3989 0.534873 TCATTTCGTCCATCTCCGCA 59.465 50.000 0.00 0.00 0.00 5.69
3712 3996 0.320374 TTCGTCCATCTCCGCAAAGT 59.680 50.000 0.00 0.00 0.00 2.66
3713 3997 0.320374 TCGTCCATCTCCGCAAAGTT 59.680 50.000 0.00 0.00 0.00 2.66
3803 4101 0.736325 GAGCAGCGGTACAACACGAT 60.736 55.000 0.00 0.00 0.00 3.73
3899 4198 3.557903 GAGCTGGGTTGGAGCAGCA 62.558 63.158 0.00 0.00 42.60 4.41
3901 4200 2.202395 GCTGGGTTGGAGCAGCAAA 61.202 57.895 0.00 0.00 40.14 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.457834 TTTGTTTTTCTTTTCCGCTCCA 57.542 36.364 0.00 0.00 0.00 3.86
11 12 5.197549 GCAATTTGTTTTTCTTTTCCGCTC 58.802 37.500 0.00 0.00 0.00 5.03
15 16 6.188400 TGTGGCAATTTGTTTTTCTTTTCC 57.812 33.333 0.00 0.00 0.00 3.13
29 30 5.048852 CGGAAATTGGAAAAATGTGGCAATT 60.049 36.000 0.00 0.00 0.00 2.32
34 35 5.810074 GGATACGGAAATTGGAAAAATGTGG 59.190 40.000 0.00 0.00 0.00 4.17
62 63 2.095532 CGGATCGCCCTATTACGTCTAG 59.904 54.545 0.00 0.00 0.00 2.43
63 64 2.079158 CGGATCGCCCTATTACGTCTA 58.921 52.381 0.00 0.00 0.00 2.59
64 65 0.879765 CGGATCGCCCTATTACGTCT 59.120 55.000 0.00 0.00 0.00 4.18
109 110 1.936547 GCTGTCTTTCTAAGATGGCGG 59.063 52.381 0.00 0.00 40.18 6.13
142 143 7.651704 TCACTGTATTGTCATTGTATATCCGTG 59.348 37.037 0.00 0.00 0.00 4.94
173 174 7.844493 TCCTTGGTCTACAGTCTAGTAAAAA 57.156 36.000 0.00 0.00 0.00 1.94
190 191 0.915364 GGATGCTCCTCTTCCTTGGT 59.085 55.000 0.00 0.00 36.40 3.67
241 249 2.147958 TCTTGTTTTCGTTCCCATCCG 58.852 47.619 0.00 0.00 0.00 4.18
252 260 0.383949 TGCAGGGCGTTCTTGTTTTC 59.616 50.000 0.00 0.00 0.00 2.29
331 339 2.263741 GCATGGGATGGCGATCACC 61.264 63.158 8.63 8.61 29.85 4.02
333 341 2.113774 GGCATGGGATGGCGATCA 59.886 61.111 11.07 0.00 46.11 2.92
430 438 8.195436 CCATTTTCATATGACTTGATTGAAGCT 58.805 33.333 4.48 0.00 34.68 3.74
509 518 3.458189 GTGAGATATGTTTACGGCAGCT 58.542 45.455 0.00 0.00 0.00 4.24
707 742 7.018235 ACAAAAACAAAAGCAAAACCAATACG 58.982 30.769 0.00 0.00 0.00 3.06
748 789 8.788806 AGCTACACAAGTATGTATACTCTGATC 58.211 37.037 4.17 0.00 42.47 2.92
749 790 8.698973 AGCTACACAAGTATGTATACTCTGAT 57.301 34.615 4.17 0.00 42.47 2.90
750 791 9.274206 CTAGCTACACAAGTATGTATACTCTGA 57.726 37.037 4.17 0.00 42.47 3.27
751 792 9.058174 ACTAGCTACACAAGTATGTATACTCTG 57.942 37.037 4.17 8.22 42.47 3.35
752 793 9.275398 GACTAGCTACACAAGTATGTATACTCT 57.725 37.037 4.17 0.00 42.47 3.24
753 794 8.222433 CGACTAGCTACACAAGTATGTATACTC 58.778 40.741 4.17 0.00 42.47 2.59
754 795 7.714377 ACGACTAGCTACACAAGTATGTATACT 59.286 37.037 4.17 0.00 45.04 2.12
755 796 7.859598 ACGACTAGCTACACAAGTATGTATAC 58.140 38.462 0.00 0.00 37.82 1.47
756 797 7.095899 CGACGACTAGCTACACAAGTATGTATA 60.096 40.741 0.00 0.00 37.82 1.47
757 798 6.292757 CGACGACTAGCTACACAAGTATGTAT 60.293 42.308 0.00 0.00 37.82 2.29
758 799 5.006068 CGACGACTAGCTACACAAGTATGTA 59.994 44.000 0.00 0.00 37.82 2.29
759 800 4.201792 CGACGACTAGCTACACAAGTATGT 60.202 45.833 0.00 0.00 41.61 2.29
760 801 4.033702 TCGACGACTAGCTACACAAGTATG 59.966 45.833 0.00 0.00 0.00 2.39
831 878 3.958860 AAAGCTGGTCGGGCTGCT 61.959 61.111 0.00 0.00 40.19 4.24
918 969 2.167861 GTCTGCCGGACAAGATCGC 61.168 63.158 5.05 0.00 43.94 4.58
1100 1164 0.763035 ACTTCCTACACACCCACACC 59.237 55.000 0.00 0.00 0.00 4.16
1101 1165 1.878953 CACTTCCTACACACCCACAC 58.121 55.000 0.00 0.00 0.00 3.82
1102 1166 0.107831 GCACTTCCTACACACCCACA 59.892 55.000 0.00 0.00 0.00 4.17
1103 1167 0.949105 CGCACTTCCTACACACCCAC 60.949 60.000 0.00 0.00 0.00 4.61
1104 1168 1.116536 TCGCACTTCCTACACACCCA 61.117 55.000 0.00 0.00 0.00 4.51
1688 1752 4.569162 CGAGGGCGATAATTGAAACACTAA 59.431 41.667 0.00 0.00 40.82 2.24
1689 1753 4.116961 CGAGGGCGATAATTGAAACACTA 58.883 43.478 0.00 0.00 40.82 2.74
1690 1754 2.936498 CGAGGGCGATAATTGAAACACT 59.064 45.455 0.00 0.00 40.82 3.55
1691 1755 2.031683 CCGAGGGCGATAATTGAAACAC 59.968 50.000 0.00 0.00 40.82 3.32
1692 1756 2.285083 CCGAGGGCGATAATTGAAACA 58.715 47.619 0.00 0.00 40.82 2.83
1693 1757 1.002792 GCCGAGGGCGATAATTGAAAC 60.003 52.381 0.00 0.00 39.62 2.78
1716 1787 0.302890 CGATCATCAAGCTTGGACGC 59.697 55.000 25.73 11.05 0.00 5.19
1774 1845 5.997129 ACATTTGCATCGATCCATATACACA 59.003 36.000 0.00 0.00 0.00 3.72
1821 1892 3.130164 TCAAGTAGCTCTCATCTGCAGAC 59.870 47.826 20.97 4.95 0.00 3.51
2638 2709 3.237741 CCTCATCTCCTCGCCCCC 61.238 72.222 0.00 0.00 0.00 5.40
2639 2710 3.934962 GCCTCATCTCCTCGCCCC 61.935 72.222 0.00 0.00 0.00 5.80
2706 2777 2.360350 TTCTCGTACGCCGACCCT 60.360 61.111 11.24 0.00 41.60 4.34
2813 2887 4.408821 TGGGACATGACGCTGCCC 62.409 66.667 12.86 7.45 39.29 5.36
2819 2893 1.868997 GCAACAGTGGGACATGACG 59.131 57.895 0.00 0.00 44.52 4.35
2988 3070 2.833582 TCGCCCTCGGAGATGTCC 60.834 66.667 6.58 0.00 39.88 4.02
2990 3072 3.148279 GGTCGCCCTCGGAGATGT 61.148 66.667 6.58 0.00 33.47 3.06
3007 3089 3.665190 GGATACTAGAGGGATTTTGCGG 58.335 50.000 0.00 0.00 0.00 5.69
3008 3090 3.243771 ACGGATACTAGAGGGATTTTGCG 60.244 47.826 0.00 0.00 0.00 4.85
3016 3098 3.315749 GTGTCTGAACGGATACTAGAGGG 59.684 52.174 0.00 0.00 0.00 4.30
3028 3110 0.865111 TTTGCATCCGTGTCTGAACG 59.135 50.000 0.00 5.72 43.20 3.95
3029 3111 1.197721 CCTTTGCATCCGTGTCTGAAC 59.802 52.381 0.00 0.00 0.00 3.18
3030 3112 1.522668 CCTTTGCATCCGTGTCTGAA 58.477 50.000 0.00 0.00 0.00 3.02
3031 3113 0.955428 GCCTTTGCATCCGTGTCTGA 60.955 55.000 0.00 0.00 37.47 3.27
3032 3114 1.236616 TGCCTTTGCATCCGTGTCTG 61.237 55.000 0.00 0.00 44.23 3.51
3033 3115 1.073025 TGCCTTTGCATCCGTGTCT 59.927 52.632 0.00 0.00 44.23 3.41
3034 3116 3.667087 TGCCTTTGCATCCGTGTC 58.333 55.556 0.00 0.00 44.23 3.67
3043 3125 2.716217 ACCTTAGATGAGTGCCTTTGC 58.284 47.619 0.00 0.00 38.26 3.68
3044 3126 4.074970 ACAACCTTAGATGAGTGCCTTTG 58.925 43.478 0.00 0.00 0.00 2.77
3045 3127 4.373156 ACAACCTTAGATGAGTGCCTTT 57.627 40.909 0.00 0.00 0.00 3.11
3046 3128 4.327680 GAACAACCTTAGATGAGTGCCTT 58.672 43.478 0.00 0.00 0.00 4.35
3047 3129 3.617531 CGAACAACCTTAGATGAGTGCCT 60.618 47.826 0.00 0.00 0.00 4.75
3048 3130 2.673368 CGAACAACCTTAGATGAGTGCC 59.327 50.000 0.00 0.00 0.00 5.01
3049 3131 2.094417 GCGAACAACCTTAGATGAGTGC 59.906 50.000 0.00 0.00 0.00 4.40
3050 3132 3.325870 TGCGAACAACCTTAGATGAGTG 58.674 45.455 0.00 0.00 0.00 3.51
3051 3133 3.678056 TGCGAACAACCTTAGATGAGT 57.322 42.857 0.00 0.00 0.00 3.41
3052 3134 5.109210 TGTATGCGAACAACCTTAGATGAG 58.891 41.667 0.00 0.00 0.00 2.90
3053 3135 5.079689 TGTATGCGAACAACCTTAGATGA 57.920 39.130 0.00 0.00 0.00 2.92
3054 3136 5.991328 ATGTATGCGAACAACCTTAGATG 57.009 39.130 0.00 0.00 32.02 2.90
3055 3137 7.391148 AAAATGTATGCGAACAACCTTAGAT 57.609 32.000 0.00 0.00 32.02 1.98
3056 3138 6.811253 AAAATGTATGCGAACAACCTTAGA 57.189 33.333 0.00 0.00 32.02 2.10
3057 3139 6.687105 GCTAAAATGTATGCGAACAACCTTAG 59.313 38.462 0.00 4.71 32.02 2.18
3058 3140 6.149640 TGCTAAAATGTATGCGAACAACCTTA 59.850 34.615 0.00 0.00 32.02 2.69
3059 3141 5.048364 TGCTAAAATGTATGCGAACAACCTT 60.048 36.000 0.00 0.00 32.02 3.50
3060 3142 4.457603 TGCTAAAATGTATGCGAACAACCT 59.542 37.500 0.00 0.00 32.02 3.50
3061 3143 4.728534 TGCTAAAATGTATGCGAACAACC 58.271 39.130 0.00 0.00 32.02 3.77
3062 3144 6.869421 ATTGCTAAAATGTATGCGAACAAC 57.131 33.333 0.00 0.00 32.02 3.32
3063 3145 7.881643 AAATTGCTAAAATGTATGCGAACAA 57.118 28.000 0.00 0.00 32.02 2.83
3064 3146 7.881643 AAAATTGCTAAAATGTATGCGAACA 57.118 28.000 0.00 0.00 0.00 3.18
3087 3169 9.571810 CATGAATTTTGTCCGATTGATCTAAAA 57.428 29.630 0.00 0.00 0.00 1.52
3088 3170 7.701924 GCATGAATTTTGTCCGATTGATCTAAA 59.298 33.333 0.00 0.00 0.00 1.85
3089 3171 7.148103 TGCATGAATTTTGTCCGATTGATCTAA 60.148 33.333 0.00 0.00 0.00 2.10
3090 3172 6.318396 TGCATGAATTTTGTCCGATTGATCTA 59.682 34.615 0.00 0.00 0.00 1.98
3091 3173 5.125900 TGCATGAATTTTGTCCGATTGATCT 59.874 36.000 0.00 0.00 0.00 2.75
3092 3174 5.342433 TGCATGAATTTTGTCCGATTGATC 58.658 37.500 0.00 0.00 0.00 2.92
3093 3175 5.327616 TGCATGAATTTTGTCCGATTGAT 57.672 34.783 0.00 0.00 0.00 2.57
3094 3176 4.780275 TGCATGAATTTTGTCCGATTGA 57.220 36.364 0.00 0.00 0.00 2.57
3095 3177 4.685165 TGTTGCATGAATTTTGTCCGATTG 59.315 37.500 0.00 0.00 0.00 2.67
3096 3178 4.880759 TGTTGCATGAATTTTGTCCGATT 58.119 34.783 0.00 0.00 0.00 3.34
3097 3179 4.517952 TGTTGCATGAATTTTGTCCGAT 57.482 36.364 0.00 0.00 0.00 4.18
3098 3180 3.998099 TGTTGCATGAATTTTGTCCGA 57.002 38.095 0.00 0.00 0.00 4.55
3099 3181 4.685165 TCATTGTTGCATGAATTTTGTCCG 59.315 37.500 0.00 0.00 0.00 4.79
3100 3182 5.388682 CGTCATTGTTGCATGAATTTTGTCC 60.389 40.000 0.00 0.00 0.00 4.02
3101 3183 5.388682 CCGTCATTGTTGCATGAATTTTGTC 60.389 40.000 0.00 0.00 0.00 3.18
3102 3184 4.448395 CCGTCATTGTTGCATGAATTTTGT 59.552 37.500 0.00 0.00 0.00 2.83
3103 3185 4.685165 TCCGTCATTGTTGCATGAATTTTG 59.315 37.500 0.00 0.00 0.00 2.44
3104 3186 4.880759 TCCGTCATTGTTGCATGAATTTT 58.119 34.783 0.00 0.00 0.00 1.82
3105 3187 4.517952 TCCGTCATTGTTGCATGAATTT 57.482 36.364 0.00 0.00 0.00 1.82
3106 3188 4.724074 ATCCGTCATTGTTGCATGAATT 57.276 36.364 0.00 0.00 0.00 2.17
3107 3189 4.724074 AATCCGTCATTGTTGCATGAAT 57.276 36.364 0.00 0.00 0.00 2.57
3108 3190 4.022503 TGAAATCCGTCATTGTTGCATGAA 60.023 37.500 0.00 0.00 0.00 2.57
3109 3191 3.505293 TGAAATCCGTCATTGTTGCATGA 59.495 39.130 0.00 0.00 0.00 3.07
3110 3192 3.835779 TGAAATCCGTCATTGTTGCATG 58.164 40.909 0.00 0.00 0.00 4.06
3111 3193 4.724074 ATGAAATCCGTCATTGTTGCAT 57.276 36.364 0.00 0.00 34.49 3.96
3112 3194 4.457257 TGTATGAAATCCGTCATTGTTGCA 59.543 37.500 0.00 0.00 39.07 4.08
3113 3195 4.980590 TGTATGAAATCCGTCATTGTTGC 58.019 39.130 0.00 0.00 39.07 4.17
3114 3196 6.307800 GGTTTGTATGAAATCCGTCATTGTTG 59.692 38.462 0.00 0.00 39.07 3.33
3115 3197 6.386654 GGTTTGTATGAAATCCGTCATTGTT 58.613 36.000 0.00 0.00 39.07 2.83
3116 3198 5.391523 CGGTTTGTATGAAATCCGTCATTGT 60.392 40.000 0.00 0.00 39.07 2.71
3117 3199 5.027737 CGGTTTGTATGAAATCCGTCATTG 58.972 41.667 0.00 0.00 39.07 2.82
3118 3200 5.229921 CGGTTTGTATGAAATCCGTCATT 57.770 39.130 0.00 0.00 39.07 2.57
3119 3201 4.875544 CGGTTTGTATGAAATCCGTCAT 57.124 40.909 0.00 0.00 41.21 3.06
3123 3205 3.004171 TCCACGGTTTGTATGAAATCCG 58.996 45.455 9.10 9.10 44.38 4.18
3124 3206 3.754323 TGTCCACGGTTTGTATGAAATCC 59.246 43.478 0.00 0.00 0.00 3.01
3125 3207 4.719040 GTGTCCACGGTTTGTATGAAATC 58.281 43.478 0.00 0.00 0.00 2.17
3126 3208 4.759516 GTGTCCACGGTTTGTATGAAAT 57.240 40.909 0.00 0.00 0.00 2.17
3154 3236 1.977056 ATGCGTGCATCATTGGATCT 58.023 45.000 0.51 0.00 29.42 2.75
3164 3253 3.846423 TGTTGAAATGTATGCGTGCAT 57.154 38.095 12.54 12.54 40.19 3.96
3331 3427 1.396996 GTTATCCGTGTCTTGCGCATT 59.603 47.619 12.75 0.00 0.00 3.56
3339 3435 5.753716 AGACTAGTAAGGTTATCCGTGTCT 58.246 41.667 0.00 0.00 39.05 3.41
3406 3503 1.961277 CAGTTCAACGAGCGGGCTT 60.961 57.895 0.00 0.00 0.00 4.35
3420 3517 4.003788 CCGGGGCTCACGACAGTT 62.004 66.667 0.00 0.00 0.00 3.16
3514 3616 1.144503 CCTCTGGGGCTGAAGCATATT 59.855 52.381 4.43 0.00 44.36 1.28
3517 3619 1.210204 TTCCTCTGGGGCTGAAGCAT 61.210 55.000 4.43 0.00 44.36 3.79
3528 3630 2.711922 CGTCGTCCCCTTCCTCTGG 61.712 68.421 0.00 0.00 0.00 3.86
3529 3631 1.038130 ATCGTCGTCCCCTTCCTCTG 61.038 60.000 0.00 0.00 0.00 3.35
3532 3634 2.058595 CCATCGTCGTCCCCTTCCT 61.059 63.158 0.00 0.00 0.00 3.36
3665 3945 1.726791 CAACACATCCGACGGAGAAAG 59.273 52.381 22.99 13.81 34.05 2.62
3689 3970 0.534873 TGCGGAGATGGACGAAATGA 59.465 50.000 0.00 0.00 0.00 2.57
3708 3989 4.065789 CGGTAGAGAAAGAAGCCAACTTT 58.934 43.478 0.00 0.00 39.76 2.66
3712 3996 1.338769 GCCGGTAGAGAAAGAAGCCAA 60.339 52.381 1.90 0.00 0.00 4.52
3713 3997 0.249398 GCCGGTAGAGAAAGAAGCCA 59.751 55.000 1.90 0.00 0.00 4.75
3862 4161 0.103208 CATCGAGGAGCGGCTAGTTT 59.897 55.000 0.60 0.00 41.33 2.66


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

AutoCloner maintained by Alex Coulton.