Multiple sequence alignment - TraesCS6A01G031100

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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 TraesCS6A01G031100 chr6A 100.000 3524 0 0 1 3524 15764983 15768506 0.000000e+00 6508
1 TraesCS6A01G031100 chr6A 90.097 1545 148 4 986 2527 15727828 15729370 0.000000e+00 2001
2 TraesCS6A01G031100 chr6A 90.111 1527 151 0 1001 2527 15734520 15736046 0.000000e+00 1984
3 TraesCS6A01G031100 chr6A 86.711 1821 192 31 709 2514 15756382 15758167 0.000000e+00 1977
4 TraesCS6A01G031100 chr6D 94.043 2585 114 11 1 2564 14626985 14624420 0.000000e+00 3884
5 TraesCS6A01G031100 chr6D 86.947 1831 189 25 710 2526 14633254 14631460 0.000000e+00 2012
6 TraesCS6A01G031100 chr6D 88.958 1612 164 12 1001 2608 14680775 14679174 0.000000e+00 1978
7 TraesCS6A01G031100 chr6D 90.033 1525 152 0 1001 2525 14656589 14655065 0.000000e+00 1975
8 TraesCS6A01G031100 chr6D 90.315 413 21 6 2606 3018 14624422 14624029 1.120000e-144 523
9 TraesCS6A01G031100 chr6D 91.727 278 21 2 3249 3524 14623976 14623699 5.520000e-103 385
10 TraesCS6A01G031100 chr6D 92.233 103 7 1 3017 3118 374820303 374820201 1.020000e-30 145
11 TraesCS6A01G031100 chr6D 88.596 114 10 3 3015 3127 9063737 9063848 6.140000e-28 135
12 TraesCS6A01G031100 chr6B 92.264 2301 131 19 502 2762 26598280 26595987 0.000000e+00 3219
13 TraesCS6A01G031100 chr6B 90.439 1527 146 0 1001 2527 26634792 26633266 0.000000e+00 2012
14 TraesCS6A01G031100 chr6B 92.444 450 16 5 1 441 26598725 26598285 8.300000e-176 627
15 TraesCS6A01G031100 chr6B 86.182 275 34 4 2742 3014 26595964 26595692 9.570000e-76 294
16 TraesCS6A01G031100 chr6B 92.157 102 7 1 3016 3116 309754924 309755025 3.670000e-30 143
17 TraesCS6A01G031100 chr4A 96.842 95 3 0 3164 3258 95187560 95187466 3.640000e-35 159
18 TraesCS6A01G031100 chr4D 98.864 88 1 0 3168 3255 437508896 437508983 1.310000e-34 158
19 TraesCS6A01G031100 chr4D 92.308 104 7 1 3150 3252 428390079 428390182 2.830000e-31 147
20 TraesCS6A01G031100 chr4D 92.157 102 6 2 3162 3262 182071709 182071809 3.670000e-30 143
21 TraesCS6A01G031100 chr4B 95.789 95 4 0 3162 3256 180553961 180553867 1.690000e-33 154
22 TraesCS6A01G031100 chr4B 92.929 99 7 0 3015 3113 664775616 664775714 1.020000e-30 145
23 TraesCS6A01G031100 chr4B 90.000 110 11 0 3014 3123 409939564 409939673 3.670000e-30 143
24 TraesCS6A01G031100 chr2B 94.898 98 3 2 3161 3256 478114367 478114464 6.090000e-33 152
25 TraesCS6A01G031100 chr2B 86.777 121 13 3 3162 3281 575874897 575875015 7.940000e-27 132
26 TraesCS6A01G031100 chr2D 93.939 99 6 0 3015 3113 427953773 427953675 2.190000e-32 150
27 TraesCS6A01G031100 chr7B 93.000 100 7 0 3015 3114 134634119 134634218 2.830000e-31 147
28 TraesCS6A01G031100 chr7B 93.000 100 6 1 3162 3261 661996482 661996384 1.020000e-30 145
29 TraesCS6A01G031100 chr7D 92.157 102 8 0 3157 3258 49828871 49828770 1.020000e-30 145
30 TraesCS6A01G031100 chr1D 92.079 101 8 0 3017 3117 225943942 225944042 3.670000e-30 143
31 TraesCS6A01G031100 chr1D 89.815 108 11 0 3006 3113 490538105 490538212 4.740000e-29 139


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 TraesCS6A01G031100 chr6A 15764983 15768506 3523 False 6508.000000 6508 100.000000 1 3524 1 chr6A.!!$F4 3523
1 TraesCS6A01G031100 chr6A 15727828 15729370 1542 False 2001.000000 2001 90.097000 986 2527 1 chr6A.!!$F1 1541
2 TraesCS6A01G031100 chr6A 15734520 15736046 1526 False 1984.000000 1984 90.111000 1001 2527 1 chr6A.!!$F2 1526
3 TraesCS6A01G031100 chr6A 15756382 15758167 1785 False 1977.000000 1977 86.711000 709 2514 1 chr6A.!!$F3 1805
4 TraesCS6A01G031100 chr6D 14631460 14633254 1794 True 2012.000000 2012 86.947000 710 2526 1 chr6D.!!$R1 1816
5 TraesCS6A01G031100 chr6D 14679174 14680775 1601 True 1978.000000 1978 88.958000 1001 2608 1 chr6D.!!$R3 1607
6 TraesCS6A01G031100 chr6D 14655065 14656589 1524 True 1975.000000 1975 90.033000 1001 2525 1 chr6D.!!$R2 1524
7 TraesCS6A01G031100 chr6D 14623699 14626985 3286 True 1597.333333 3884 92.028333 1 3524 3 chr6D.!!$R5 3523
8 TraesCS6A01G031100 chr6B 26633266 26634792 1526 True 2012.000000 2012 90.439000 1001 2527 1 chr6B.!!$R1 1526
9 TraesCS6A01G031100 chr6B 26595692 26598725 3033 True 1380.000000 3219 90.296667 1 3014 3 chr6B.!!$R2 3013

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
303 312 0.040646 TCCTACTTGGCTCCCTCGAA 59.959 55.0 0.0 0.0 35.26 3.71 F
1875 1917 0.408700 ACTTCCACCTAGACCTCCGT 59.591 55.0 0.0 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2019 1.021390 AGATGTTCCAAAGGCGAGCG 61.021 55.0 0.0 0.0 0.00 5.03 R
2811 2929 0.692476 TAACTGAGTGCCACTGCCAT 59.308 50.0 0.0 0.0 36.33 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
35 36 0.395311 CTCCCCTTGCATGCTGTCAT 60.395 55.000 20.33 0.00 0.00 3.06
244 247 6.719370 TGCTCCCATTTCAGTAACAAACTAAT 59.281 34.615 0.00 0.00 35.76 1.73
261 264 2.579410 AATAACAACCTGTCGGCCTT 57.421 45.000 0.00 0.00 0.00 4.35
299 308 1.646977 ACTAGTCCTACTTGGCTCCCT 59.353 52.381 0.00 0.00 35.26 4.20
301 310 0.684805 AGTCCTACTTGGCTCCCTCG 60.685 60.000 0.00 0.00 35.26 4.63
303 312 0.040646 TCCTACTTGGCTCCCTCGAA 59.959 55.000 0.00 0.00 35.26 3.71
319 329 3.499918 CCTCGAAGCAAACTGTCATCTTT 59.500 43.478 0.00 0.00 0.00 2.52
328 338 7.491682 AGCAAACTGTCATCTTTTTACACATT 58.508 30.769 0.00 0.00 0.00 2.71
329 339 7.981225 AGCAAACTGTCATCTTTTTACACATTT 59.019 29.630 0.00 0.00 0.00 2.32
330 340 8.603181 GCAAACTGTCATCTTTTTACACATTTT 58.397 29.630 0.00 0.00 0.00 1.82
404 423 6.000246 TCATATGCATGAAGGTTCCTTGTA 58.000 37.500 10.16 0.00 38.25 2.41
463 482 9.807386 GTTATACTTGTTAGACACATGTTTGTC 57.193 33.333 8.10 8.10 45.45 3.18
475 497 5.025826 CACATGTTTGTCACATCATGATCG 58.974 41.667 22.28 4.49 43.17 3.69
479 501 6.348621 TGTTTGTCACATCATGATCGTATG 57.651 37.500 4.86 0.00 40.28 2.39
481 503 7.466320 ATGTTTGTCACATCATGATCGTATGTG 60.466 37.037 20.53 20.53 43.17 3.21
487 509 6.818142 TCACATCATGATCGTATGTGTTTTCT 59.182 34.615 23.31 0.00 46.73 2.52
490 512 7.334171 ACATCATGATCGTATGTGTTTTCTTCA 59.666 33.333 4.86 0.00 32.74 3.02
578 604 3.490759 CGCATCCTGTGACGTGCC 61.491 66.667 0.00 0.00 34.20 5.01
665 691 4.826274 TTACTTAGCTGTCCTGCTCATT 57.174 40.909 0.00 0.00 42.97 2.57
801 829 6.127869 CGGTTAAGAGATGAGAGTTGAGAGAA 60.128 42.308 0.00 0.00 0.00 2.87
881 909 5.620205 CGCATCTGTCTATAAATACCTCGCT 60.620 44.000 0.00 0.00 0.00 4.93
978 1020 2.301296 AGCTGCTCATAGTTGTGAGTGT 59.699 45.455 0.00 0.00 45.80 3.55
1366 1408 1.003355 CCCACCGTCTTCTGCATGT 60.003 57.895 0.00 0.00 0.00 3.21
1422 1464 1.676916 CGCTTCCTCATTGGCTTCTCA 60.677 52.381 0.00 0.00 35.26 3.27
1443 1485 1.667830 CGCCACCTTCGTGTCATGT 60.668 57.895 0.00 0.00 38.41 3.21
1875 1917 0.408700 ACTTCCACCTAGACCTCCGT 59.591 55.000 0.00 0.00 0.00 4.69
1977 2019 3.925238 CGGTACTTCGGCATGCGC 61.925 66.667 12.44 0.00 37.44 6.09
2079 2121 0.675837 CCTCAGTGACTGCCATGGTG 60.676 60.000 14.67 9.43 0.00 4.17
2542 2584 9.787532 ACGTATAAGATTGGATTGTTTTTCATG 57.212 29.630 0.00 0.00 0.00 3.07
2574 2623 7.597369 TGTACAAGTACTAAACTACAGTGCATG 59.403 37.037 11.27 0.00 37.50 4.06
2575 2624 5.408604 ACAAGTACTAAACTACAGTGCATGC 59.591 40.000 11.82 11.82 37.50 4.06
2577 2626 5.547465 AGTACTAAACTACAGTGCATGCAA 58.453 37.500 24.58 5.68 36.36 4.08
2624 2700 2.287009 GCAACATCGGCTGTAATAAGGC 60.287 50.000 0.00 0.00 36.98 4.35
2646 2722 6.696148 AGGCGTACGAATTTAGATTTCTAGTG 59.304 38.462 21.65 0.00 0.00 2.74
2652 2728 6.985059 ACGAATTTAGATTTCTAGTGTAGGCC 59.015 38.462 0.00 0.00 0.00 5.19
2793 2911 3.703001 TTCCTCTCCTGGCAAGTTTAG 57.297 47.619 0.00 0.00 0.00 1.85
2822 2940 1.828081 TGCAAAAATGGCAGTGGCA 59.172 47.368 22.88 22.88 43.71 4.92
2961 3079 8.961294 TCAAATTTGAGGTTTCACATTTCAAT 57.039 26.923 16.91 0.00 40.13 2.57
2962 3080 9.393512 TCAAATTTGAGGTTTCACATTTCAATT 57.606 25.926 16.91 0.00 40.13 2.32
2977 3097 9.706846 CACATTTCAATTTTTCTTTTGAGGTTC 57.293 29.630 0.00 0.00 33.68 3.62
3016 3136 2.507058 TCCACATCTCCTGCAAGCTAAT 59.493 45.455 0.00 0.00 0.00 1.73
3017 3137 3.711190 TCCACATCTCCTGCAAGCTAATA 59.289 43.478 0.00 0.00 0.00 0.98
3018 3138 3.812053 CCACATCTCCTGCAAGCTAATAC 59.188 47.826 0.00 0.00 0.00 1.89
3019 3139 4.444022 CCACATCTCCTGCAAGCTAATACT 60.444 45.833 0.00 0.00 0.00 2.12
3020 3140 4.749099 CACATCTCCTGCAAGCTAATACTC 59.251 45.833 0.00 0.00 0.00 2.59
3021 3141 4.202305 ACATCTCCTGCAAGCTAATACTCC 60.202 45.833 0.00 0.00 0.00 3.85
3022 3142 2.700897 TCTCCTGCAAGCTAATACTCCC 59.299 50.000 0.00 0.00 0.00 4.30
3023 3143 2.703007 CTCCTGCAAGCTAATACTCCCT 59.297 50.000 0.00 0.00 0.00 4.20
3024 3144 2.700897 TCCTGCAAGCTAATACTCCCTC 59.299 50.000 0.00 0.00 0.00 4.30
3025 3145 2.224402 CCTGCAAGCTAATACTCCCTCC 60.224 54.545 0.00 0.00 0.00 4.30
3026 3146 1.412710 TGCAAGCTAATACTCCCTCCG 59.587 52.381 0.00 0.00 0.00 4.63
3027 3147 1.413077 GCAAGCTAATACTCCCTCCGT 59.587 52.381 0.00 0.00 0.00 4.69
3028 3148 2.546162 GCAAGCTAATACTCCCTCCGTC 60.546 54.545 0.00 0.00 0.00 4.79
3029 3149 1.998222 AGCTAATACTCCCTCCGTCC 58.002 55.000 0.00 0.00 0.00 4.79
3030 3150 0.967662 GCTAATACTCCCTCCGTCCC 59.032 60.000 0.00 0.00 0.00 4.46
3031 3151 1.756690 GCTAATACTCCCTCCGTCCCA 60.757 57.143 0.00 0.00 0.00 4.37
3032 3152 2.674420 CTAATACTCCCTCCGTCCCAA 58.326 52.381 0.00 0.00 0.00 4.12
3033 3153 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3034 3154 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3035 3155 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3036 3156 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3037 3157 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3038 3158 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3039 3159 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3040 3160 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3041 3161 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3042 3162 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3043 3163 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3044 3164 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3045 3165 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3046 3166 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3047 3167 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3048 3168 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3049 3169 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3050 3170 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3051 3171 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3052 3172 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3053 3173 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3054 3174 8.576442 CCCAAAATAAGTGTCTCAACTTTGTAT 58.424 33.333 0.00 0.00 40.77 2.29
3055 3175 9.965824 CCAAAATAAGTGTCTCAACTTTGTATT 57.034 29.630 0.00 0.00 40.77 1.89
3088 3208 9.694137 AGTACATAGTTGAACTAAAGTCAAGAC 57.306 33.333 9.35 6.51 33.89 3.01
3089 3209 9.472361 GTACATAGTTGAACTAAAGTCAAGACA 57.528 33.333 9.35 0.00 33.89 3.41
3090 3210 8.366671 ACATAGTTGAACTAAAGTCAAGACAC 57.633 34.615 9.35 0.00 33.89 3.67
3091 3211 8.204836 ACATAGTTGAACTAAAGTCAAGACACT 58.795 33.333 9.35 0.00 33.89 3.55
3092 3212 9.046296 CATAGTTGAACTAAAGTCAAGACACTT 57.954 33.333 9.35 0.00 38.30 3.16
3095 3215 9.614792 AGTTGAACTAAAGTCAAGACACTTATT 57.385 29.630 0.00 0.00 35.45 1.40
3099 3219 9.665264 GAACTAAAGTCAAGACACTTATTTTGG 57.335 33.333 2.72 0.00 35.45 3.28
3100 3220 8.166422 ACTAAAGTCAAGACACTTATTTTGGG 57.834 34.615 2.72 0.00 35.45 4.12
3101 3221 7.996644 ACTAAAGTCAAGACACTTATTTTGGGA 59.003 33.333 2.72 0.00 35.45 4.37
3102 3222 6.635030 AAGTCAAGACACTTATTTTGGGAC 57.365 37.500 2.72 0.00 34.70 4.46
3103 3223 5.690865 AGTCAAGACACTTATTTTGGGACA 58.309 37.500 2.72 0.00 0.00 4.02
3104 3224 6.605594 AAGTCAAGACACTTATTTTGGGACAA 59.394 34.615 2.72 0.00 38.08 3.18
3105 3225 7.123547 AAGTCAAGACACTTATTTTGGGACAAA 59.876 33.333 2.72 0.00 38.08 2.83
3125 3245 5.301805 ACAAAGGGAGTAGTTGTTTCATTGG 59.698 40.000 0.00 0.00 31.52 3.16
3130 3250 4.217767 GGAGTAGTTGTTTCATTGGGGAAC 59.782 45.833 0.00 0.00 0.00 3.62
3133 3253 4.670896 AGTTGTTTCATTGGGGAACAAG 57.329 40.909 1.32 0.00 43.48 3.16
3151 3271 1.343069 AGACTTCCACTCTCACCCAC 58.657 55.000 0.00 0.00 0.00 4.61
3152 3272 1.048601 GACTTCCACTCTCACCCACA 58.951 55.000 0.00 0.00 0.00 4.17
3169 3289 8.514330 TCACCCACATTCCAAATAAATAGTAC 57.486 34.615 0.00 0.00 0.00 2.73
3171 3291 8.621286 CACCCACATTCCAAATAAATAGTACTC 58.379 37.037 0.00 0.00 0.00 2.59
3172 3292 7.778382 ACCCACATTCCAAATAAATAGTACTCC 59.222 37.037 0.00 0.00 0.00 3.85
3173 3293 7.230712 CCCACATTCCAAATAAATAGTACTCCC 59.769 40.741 0.00 0.00 0.00 4.30
3174 3294 7.998964 CCACATTCCAAATAAATAGTACTCCCT 59.001 37.037 0.00 0.00 0.00 4.20
3175 3295 9.408648 CACATTCCAAATAAATAGTACTCCCTT 57.591 33.333 0.00 0.00 0.00 3.95
3176 3296 9.628500 ACATTCCAAATAAATAGTACTCCCTTC 57.372 33.333 0.00 0.00 0.00 3.46
3177 3297 8.774586 CATTCCAAATAAATAGTACTCCCTTCG 58.225 37.037 0.00 0.00 0.00 3.79
3178 3298 7.427989 TCCAAATAAATAGTACTCCCTTCGT 57.572 36.000 0.00 0.00 0.00 3.85
3179 3299 7.495055 TCCAAATAAATAGTACTCCCTTCGTC 58.505 38.462 0.00 0.00 0.00 4.20
3180 3300 7.343833 TCCAAATAAATAGTACTCCCTTCGTCT 59.656 37.037 0.00 0.00 0.00 4.18
3181 3301 7.652507 CCAAATAAATAGTACTCCCTTCGTCTC 59.347 40.741 0.00 0.00 0.00 3.36
3182 3302 7.893124 AATAAATAGTACTCCCTTCGTCTCA 57.107 36.000 0.00 0.00 0.00 3.27
3183 3303 8.480133 AATAAATAGTACTCCCTTCGTCTCAT 57.520 34.615 0.00 0.00 0.00 2.90
3184 3304 9.584008 AATAAATAGTACTCCCTTCGTCTCATA 57.416 33.333 0.00 0.00 0.00 2.15
3185 3305 7.893124 AAATAGTACTCCCTTCGTCTCATAA 57.107 36.000 0.00 0.00 0.00 1.90
3186 3306 8.480133 AAATAGTACTCCCTTCGTCTCATAAT 57.520 34.615 0.00 0.00 0.00 1.28
3187 3307 5.776173 AGTACTCCCTTCGTCTCATAATG 57.224 43.478 0.00 0.00 0.00 1.90
3188 3308 5.202004 AGTACTCCCTTCGTCTCATAATGT 58.798 41.667 0.00 0.00 0.00 2.71
3189 3309 6.363065 AGTACTCCCTTCGTCTCATAATGTA 58.637 40.000 0.00 0.00 0.00 2.29
3190 3310 6.832384 AGTACTCCCTTCGTCTCATAATGTAA 59.168 38.462 0.00 0.00 0.00 2.41
3191 3311 6.150396 ACTCCCTTCGTCTCATAATGTAAG 57.850 41.667 0.00 0.00 0.00 2.34
3192 3312 5.892119 ACTCCCTTCGTCTCATAATGTAAGA 59.108 40.000 0.00 0.00 0.00 2.10
3193 3313 6.145338 TCCCTTCGTCTCATAATGTAAGAC 57.855 41.667 0.00 0.00 36.82 3.01
3247 3367 3.990369 TCCTATATTATGGGACGGAGGG 58.010 50.000 4.74 0.00 34.71 4.30
3248 3368 3.599240 TCCTATATTATGGGACGGAGGGA 59.401 47.826 4.74 0.00 34.71 4.20
3249 3369 3.961408 CCTATATTATGGGACGGAGGGAG 59.039 52.174 0.00 0.00 31.57 4.30
3250 3370 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3251 3371 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3252 3372 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
3253 3373 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
3331 3451 8.049721 AGAGTTTAGGTATTTTGATTGAGAGGG 58.950 37.037 0.00 0.00 0.00 4.30
3357 3477 2.679450 CGGAAGTACGGAACATGTTGA 58.321 47.619 17.58 0.00 0.00 3.18
3358 3478 2.410730 CGGAAGTACGGAACATGTTGAC 59.589 50.000 17.58 7.80 0.00 3.18
3363 3483 0.949105 ACGGAACATGTTGACGAGGC 60.949 55.000 28.55 10.11 0.00 4.70
3369 3489 2.571212 ACATGTTGACGAGGCTTGAAA 58.429 42.857 9.20 0.00 0.00 2.69
3425 3546 1.841556 TCCAGCCTTCCGTGGACTT 60.842 57.895 0.00 0.00 37.96 3.01
3426 3547 1.376037 CCAGCCTTCCGTGGACTTC 60.376 63.158 0.00 0.00 35.67 3.01
3441 3562 6.801862 CCGTGGACTTCTAATTGAATTTCAAC 59.198 38.462 13.80 0.00 39.45 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 3.709880 TACCGGCGAGGCGACAATG 62.710 63.158 20.49 5.72 46.52 2.82
134 135 3.426117 CTACCGGCGAGGCGACAAT 62.426 63.158 20.49 5.61 46.52 2.71
244 247 0.250553 CCAAGGCCGACAGGTTGTTA 60.251 55.000 0.00 0.00 40.50 2.41
261 264 6.360370 ACTAGTGTAGAATCTTCAAAGCCA 57.640 37.500 0.00 0.00 0.00 4.75
299 308 5.499139 AAAAAGATGACAGTTTGCTTCGA 57.501 34.783 0.00 0.00 0.00 3.71
301 310 6.972328 TGTGTAAAAAGATGACAGTTTGCTTC 59.028 34.615 0.00 0.00 0.00 3.86
303 312 6.449635 TGTGTAAAAAGATGACAGTTTGCT 57.550 33.333 0.00 0.00 0.00 3.91
404 423 5.786311 TGTGTACAAAGATTACTTAGCGGT 58.214 37.500 0.00 0.00 35.05 5.68
441 460 6.819146 TGTGACAAACATGTGTCTAACAAGTA 59.181 34.615 15.23 0.00 46.70 2.24
442 461 5.645929 TGTGACAAACATGTGTCTAACAAGT 59.354 36.000 15.23 0.00 46.70 3.16
457 476 6.349973 ACATACGATCATGATGTGACAAAC 57.650 37.500 14.30 0.00 40.28 2.93
481 503 2.857748 CGGCCTTTGTGTTGAAGAAAAC 59.142 45.455 0.00 0.00 0.00 2.43
487 509 0.106918 ACTCCGGCCTTTGTGTTGAA 60.107 50.000 0.00 0.00 0.00 2.69
490 512 0.106918 TTCACTCCGGCCTTTGTGTT 60.107 50.000 15.21 0.00 0.00 3.32
496 518 2.040544 CGCATTTCACTCCGGCCTT 61.041 57.895 0.00 0.00 0.00 4.35
499 521 4.520846 CGCGCATTTCACTCCGGC 62.521 66.667 8.75 0.00 0.00 6.13
500 522 3.864686 CCGCGCATTTCACTCCGG 61.865 66.667 8.75 0.00 0.00 5.14
578 604 3.470709 ACCAAGGATCAGAATATGCACG 58.529 45.455 0.00 0.00 0.00 5.34
665 691 1.639628 AGGGTCGAGAGAGGTAGGAAA 59.360 52.381 0.00 0.00 43.49 3.13
801 829 5.327732 AGTTGACATTGGGATGATTGAACT 58.672 37.500 0.00 0.00 36.73 3.01
865 893 5.722021 TGCATCAGCGAGGTATTTATAGA 57.278 39.130 0.00 0.00 46.23 1.98
881 909 4.587584 TTGTGCTTTTGATCTTGCATCA 57.412 36.364 0.00 0.00 37.76 3.07
990 1032 3.415212 CTGCACCTCCATCTTTCTTGAA 58.585 45.455 0.00 0.00 0.00 2.69
1143 1185 2.354203 GGAGACGAAGCAGGTGAAGAAT 60.354 50.000 0.00 0.00 0.00 2.40
1366 1408 1.405105 TGACGCATCATCGATGACAGA 59.595 47.619 29.49 8.68 42.09 3.41
1443 1485 3.200605 ACATGGTGCTCATCCAATACTGA 59.799 43.478 0.00 0.00 38.52 3.41
1977 2019 1.021390 AGATGTTCCAAAGGCGAGCG 61.021 55.000 0.00 0.00 0.00 5.03
2079 2121 1.886777 GGCGCAGATGGAGAAGAGC 60.887 63.158 10.83 0.00 0.00 4.09
2560 2604 7.094420 TGTGTATATTTGCATGCACTGTAGTTT 60.094 33.333 22.58 0.25 40.80 2.66
2563 2607 6.362210 TGTGTATATTTGCATGCACTGTAG 57.638 37.500 22.58 0.00 40.80 2.74
2564 2608 6.292811 CGATGTGTATATTTGCATGCACTGTA 60.293 38.462 22.58 13.70 40.80 2.74
2565 2609 5.504501 CGATGTGTATATTTGCATGCACTGT 60.505 40.000 22.58 11.71 40.80 3.55
2566 2610 4.907582 CGATGTGTATATTTGCATGCACTG 59.092 41.667 22.58 0.00 40.80 3.66
2568 2617 4.847633 ACGATGTGTATATTTGCATGCAC 58.152 39.130 22.58 8.45 40.65 4.57
2569 2618 6.799926 ATACGATGTGTATATTTGCATGCA 57.200 33.333 18.46 18.46 42.03 3.96
2624 2700 9.167239 CCTACACTAGAAATCTAAATTCGTACG 57.833 37.037 9.53 9.53 32.04 3.67
2646 2722 1.734163 AACGCATTACACAGGCCTAC 58.266 50.000 3.98 0.00 0.00 3.18
2811 2929 0.692476 TAACTGAGTGCCACTGCCAT 59.308 50.000 0.00 0.00 36.33 4.40
2822 2940 9.388506 CTCATGTATGGAGAAAATTAACTGAGT 57.611 33.333 0.00 0.00 34.24 3.41
2866 2984 7.452501 ACGATTTAGGTATACTATTGGCACCTA 59.547 37.037 2.25 0.00 40.14 3.08
2961 3079 4.383661 GGGCTTGGAACCTCAAAAGAAAAA 60.384 41.667 0.00 0.00 0.00 1.94
2962 3080 3.133901 GGGCTTGGAACCTCAAAAGAAAA 59.866 43.478 0.00 0.00 0.00 2.29
2963 3081 2.698274 GGGCTTGGAACCTCAAAAGAAA 59.302 45.455 0.00 0.00 0.00 2.52
2964 3082 2.316108 GGGCTTGGAACCTCAAAAGAA 58.684 47.619 0.00 0.00 0.00 2.52
2965 3083 1.216678 TGGGCTTGGAACCTCAAAAGA 59.783 47.619 0.00 0.00 0.00 2.52
2966 3084 1.341209 GTGGGCTTGGAACCTCAAAAG 59.659 52.381 0.00 0.00 0.00 2.27
2977 3097 2.836981 TGGAATTATTTGGTGGGCTTGG 59.163 45.455 0.00 0.00 0.00 3.61
3016 3136 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3017 3137 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3018 3138 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3019 3139 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3020 3140 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3021 3141 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3022 3142 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3023 3143 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
3024 3144 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3025 3145 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
3026 3146 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3027 3147 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
3028 3148 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
3029 3149 9.965824 AATACAAAGTTGAGACACTTATTTTGG 57.034 29.630 0.00 0.00 35.87 3.28
3062 3182 9.694137 GTCTTGACTTTAGTTCAACTATGTACT 57.306 33.333 0.00 0.00 39.98 2.73
3063 3183 9.472361 TGTCTTGACTTTAGTTCAACTATGTAC 57.528 33.333 0.00 0.00 29.64 2.90
3064 3184 9.472361 GTGTCTTGACTTTAGTTCAACTATGTA 57.528 33.333 0.00 0.00 29.64 2.29
3065 3185 8.204836 AGTGTCTTGACTTTAGTTCAACTATGT 58.795 33.333 0.00 0.90 29.64 2.29
3066 3186 8.594881 AGTGTCTTGACTTTAGTTCAACTATG 57.405 34.615 0.00 0.00 29.64 2.23
3069 3189 9.614792 AATAAGTGTCTTGACTTTAGTTCAACT 57.385 29.630 0.00 0.00 37.38 3.16
3073 3193 9.665264 CCAAAATAAGTGTCTTGACTTTAGTTC 57.335 33.333 2.35 0.00 37.38 3.01
3074 3194 8.630037 CCCAAAATAAGTGTCTTGACTTTAGTT 58.370 33.333 2.35 4.56 37.38 2.24
3075 3195 7.996644 TCCCAAAATAAGTGTCTTGACTTTAGT 59.003 33.333 2.35 0.00 37.38 2.24
3076 3196 8.290325 GTCCCAAAATAAGTGTCTTGACTTTAG 58.710 37.037 2.35 0.00 37.38 1.85
3077 3197 7.776030 TGTCCCAAAATAAGTGTCTTGACTTTA 59.224 33.333 2.35 2.51 37.38 1.85
3078 3198 6.605594 TGTCCCAAAATAAGTGTCTTGACTTT 59.394 34.615 2.35 0.51 37.38 2.66
3079 3199 6.126409 TGTCCCAAAATAAGTGTCTTGACTT 58.874 36.000 2.35 0.00 39.54 3.01
3080 3200 5.690865 TGTCCCAAAATAAGTGTCTTGACT 58.309 37.500 2.35 0.00 0.00 3.41
3081 3201 6.385649 TTGTCCCAAAATAAGTGTCTTGAC 57.614 37.500 0.00 0.00 0.00 3.18
3082 3202 6.040391 CCTTTGTCCCAAAATAAGTGTCTTGA 59.960 38.462 0.00 0.00 0.00 3.02
3083 3203 6.215845 CCTTTGTCCCAAAATAAGTGTCTTG 58.784 40.000 0.00 0.00 0.00 3.02
3084 3204 5.304357 CCCTTTGTCCCAAAATAAGTGTCTT 59.696 40.000 0.00 0.00 0.00 3.01
3085 3205 4.832823 CCCTTTGTCCCAAAATAAGTGTCT 59.167 41.667 0.00 0.00 0.00 3.41
3086 3206 4.830600 TCCCTTTGTCCCAAAATAAGTGTC 59.169 41.667 0.00 0.00 0.00 3.67
3087 3207 4.810345 TCCCTTTGTCCCAAAATAAGTGT 58.190 39.130 0.00 0.00 0.00 3.55
3088 3208 4.832823 ACTCCCTTTGTCCCAAAATAAGTG 59.167 41.667 0.00 0.00 0.00 3.16
3089 3209 5.074746 ACTCCCTTTGTCCCAAAATAAGT 57.925 39.130 0.00 0.00 0.00 2.24
3090 3210 6.246163 ACTACTCCCTTTGTCCCAAAATAAG 58.754 40.000 0.00 0.00 0.00 1.73
3091 3211 6.208840 ACTACTCCCTTTGTCCCAAAATAA 57.791 37.500 0.00 0.00 0.00 1.40
3092 3212 5.853572 ACTACTCCCTTTGTCCCAAAATA 57.146 39.130 0.00 0.00 0.00 1.40
3093 3213 4.741928 ACTACTCCCTTTGTCCCAAAAT 57.258 40.909 0.00 0.00 0.00 1.82
3094 3214 4.211920 CAACTACTCCCTTTGTCCCAAAA 58.788 43.478 0.00 0.00 0.00 2.44
3095 3215 3.203487 ACAACTACTCCCTTTGTCCCAAA 59.797 43.478 0.00 0.00 0.00 3.28
3096 3216 2.781174 ACAACTACTCCCTTTGTCCCAA 59.219 45.455 0.00 0.00 0.00 4.12
3097 3217 2.414612 ACAACTACTCCCTTTGTCCCA 58.585 47.619 0.00 0.00 0.00 4.37
3098 3218 3.503800 AACAACTACTCCCTTTGTCCC 57.496 47.619 0.00 0.00 32.24 4.46
3099 3219 4.457466 TGAAACAACTACTCCCTTTGTCC 58.543 43.478 0.00 0.00 32.24 4.02
3100 3220 6.438763 CAATGAAACAACTACTCCCTTTGTC 58.561 40.000 0.00 0.00 32.24 3.18
3101 3221 5.301805 CCAATGAAACAACTACTCCCTTTGT 59.698 40.000 0.00 0.00 34.92 2.83
3102 3222 5.278957 CCCAATGAAACAACTACTCCCTTTG 60.279 44.000 0.00 0.00 0.00 2.77
3103 3223 4.832823 CCCAATGAAACAACTACTCCCTTT 59.167 41.667 0.00 0.00 0.00 3.11
3104 3224 4.407365 CCCAATGAAACAACTACTCCCTT 58.593 43.478 0.00 0.00 0.00 3.95
3105 3225 3.245264 CCCCAATGAAACAACTACTCCCT 60.245 47.826 0.00 0.00 0.00 4.20
3106 3226 3.089284 CCCCAATGAAACAACTACTCCC 58.911 50.000 0.00 0.00 0.00 4.30
3107 3227 4.028993 TCCCCAATGAAACAACTACTCC 57.971 45.455 0.00 0.00 0.00 3.85
3108 3228 4.825085 TGTTCCCCAATGAAACAACTACTC 59.175 41.667 0.00 0.00 0.00 2.59
3109 3229 4.798882 TGTTCCCCAATGAAACAACTACT 58.201 39.130 0.00 0.00 0.00 2.57
3110 3230 5.300792 TCTTGTTCCCCAATGAAACAACTAC 59.699 40.000 5.05 0.00 31.20 2.73
3133 3253 1.048601 TGTGGGTGAGAGTGGAAGTC 58.951 55.000 0.00 0.00 36.21 3.01
3151 3271 8.774586 CGAAGGGAGTACTATTTATTTGGAATG 58.225 37.037 0.00 0.00 0.00 2.67
3152 3272 8.491958 ACGAAGGGAGTACTATTTATTTGGAAT 58.508 33.333 0.00 0.00 0.00 3.01
3169 3289 6.210078 GTCTTACATTATGAGACGAAGGGAG 58.790 44.000 0.00 0.00 34.53 4.30
3225 3345 3.705072 CCCTCCGTCCCATAATATAGGAC 59.295 52.174 7.65 7.65 45.49 3.85
3226 3346 3.599240 TCCCTCCGTCCCATAATATAGGA 59.401 47.826 0.00 0.00 0.00 2.94
3227 3347 3.961408 CTCCCTCCGTCCCATAATATAGG 59.039 52.174 0.00 0.00 0.00 2.57
3228 3348 4.611367 ACTCCCTCCGTCCCATAATATAG 58.389 47.826 0.00 0.00 0.00 1.31
3229 3349 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3230 3350 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3231 3351 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3232 3352 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3233 3353 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3234 3354 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3235 3355 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
3236 3356 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
3237 3357 2.374839 AGTATACTACTCCCTCCGTCCC 59.625 54.545 2.75 0.00 32.47 4.46
3238 3358 3.786368 AGTATACTACTCCCTCCGTCC 57.214 52.381 2.75 0.00 32.47 4.79
3239 3359 6.371271 GTCATTAGTATACTACTCCCTCCGTC 59.629 46.154 12.25 0.00 40.14 4.79
3240 3360 6.044171 AGTCATTAGTATACTACTCCCTCCGT 59.956 42.308 12.25 0.00 40.14 4.69
3241 3361 6.474630 AGTCATTAGTATACTACTCCCTCCG 58.525 44.000 12.25 0.00 40.14 4.63
3242 3362 8.824783 TCTAGTCATTAGTATACTACTCCCTCC 58.175 40.741 12.25 0.00 40.14 4.30
3319 3439 0.749091 CGCCATGCCCTCTCAATCAA 60.749 55.000 0.00 0.00 0.00 2.57
3331 3451 1.448893 TTCCGTACTTCCGCCATGC 60.449 57.895 0.00 0.00 0.00 4.06
3357 3477 8.570068 TTTATAAAGGTTATTTCAAGCCTCGT 57.430 30.769 0.00 0.00 0.00 4.18
3358 3478 9.450807 CATTTATAAAGGTTATTTCAAGCCTCG 57.549 33.333 3.94 0.00 0.00 4.63
3448 3569 9.921637 GGTCAAATTGAAACTTCCATTGTAATA 57.078 29.630 0.00 0.00 0.00 0.98
3449 3570 8.650490 AGGTCAAATTGAAACTTCCATTGTAAT 58.350 29.630 0.00 0.00 0.00 1.89
3482 3603 4.696455 AGCTTGTCCAAACCATTGAAAAG 58.304 39.130 0.00 0.00 38.94 2.27


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

AutoCloner maintained by Alex Coulton.