Multiple sequence alignment - TraesCS5A01G166500

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 TraesCS5A01G166500 chr5A 100.000 3254 0 0 1 3254 355463026 355466279 0.000000e+00 6010.0
1 TraesCS5A01G166500 chr5B 92.200 2782 141 30 227 2990 303581816 303584539 0.000000e+00 3866.0
2 TraesCS5A01G166500 chr5B 87.866 239 17 4 1 230 303575604 303575839 1.490000e-68 270.0
3 TraesCS5A01G166500 chr5B 97.059 102 2 1 3154 3254 303584540 303584641 1.550000e-38 171.0
4 TraesCS5A01G166500 chr5B 76.866 268 43 9 2323 2581 415671012 415670755 2.040000e-27 134.0
5 TraesCS5A01G166500 chr5B 89.130 46 5 0 499 544 591480895 591480850 1.260000e-04 58.4
6 TraesCS5A01G166500 chr5D 94.865 2220 89 10 1 2206 268278293 268280501 0.000000e+00 3445.0
7 TraesCS5A01G166500 chr5D 94.364 763 34 4 2236 2994 268280781 268281538 0.000000e+00 1162.0
8 TraesCS5A01G166500 chr5D 97.143 175 4 1 2993 3166 42949724 42949550 8.830000e-76 294.0
9 TraesCS5A01G166500 chr5D 98.990 99 1 0 3156 3254 268281537 268281635 9.280000e-41 178.0
10 TraesCS5A01G166500 chr5D 76.265 257 44 9 2334 2581 352699169 352698921 1.590000e-23 121.0
11 TraesCS5A01G166500 chr4D 98.810 168 2 0 2993 3160 93336684 93336851 1.900000e-77 300.0
12 TraesCS5A01G166500 chr4D 95.882 170 7 0 2988 3157 243613441 243613272 3.200000e-70 276.0
13 TraesCS5A01G166500 chr6B 97.605 167 4 0 2991 3157 520090688 520090522 1.480000e-73 287.0
14 TraesCS5A01G166500 chr6B 83.537 164 25 2 526 688 578776522 578776360 5.620000e-33 152.0
15 TraesCS5A01G166500 chr3D 97.605 167 4 0 2991 3157 22383603 22383437 1.480000e-73 287.0
16 TraesCS5A01G166500 chr3D 85.227 88 10 3 2364 2450 461952575 461952660 1.610000e-13 87.9
17 TraesCS5A01G166500 chr3D 78.151 119 22 3 2331 2447 588408418 588408302 4.500000e-09 73.1
18 TraesCS5A01G166500 chr3B 95.055 182 8 1 2977 3158 822199989 822199809 5.310000e-73 285.0
19 TraesCS5A01G166500 chr3B 88.889 63 6 1 2398 2460 10634237 10634298 3.480000e-10 76.8
20 TraesCS5A01G166500 chr3B 88.889 63 6 1 2388 2450 719827286 719827225 3.480000e-10 76.8
21 TraesCS5A01G166500 chr1D 97.041 169 5 0 2993 3161 458805377 458805545 5.310000e-73 285.0
22 TraesCS5A01G166500 chr4A 95.455 176 6 1 2993 3168 141122831 141122658 2.470000e-71 279.0
23 TraesCS5A01G166500 chr7D 93.956 182 11 0 2983 3164 530406726 530406907 3.200000e-70 276.0
24 TraesCS5A01G166500 chr7D 78.750 240 44 6 469 706 617232394 617232628 1.560000e-33 154.0
25 TraesCS5A01G166500 chr7D 77.489 231 41 8 231 452 591221489 591221261 9.480000e-26 128.0
26 TraesCS5A01G166500 chr2D 82.707 133 22 1 243 375 546219901 546220032 2.050000e-22 117.0
27 TraesCS5A01G166500 chr7B 75.591 254 44 16 231 469 666626807 666626557 3.430000e-20 110.0
28 TraesCS5A01G166500 chr3A 77.841 176 24 10 2388 2560 680969969 680969806 9.610000e-16 95.3
29 TraesCS5A01G166500 chr6A 77.869 122 25 1 2342 2463 514401840 514401721 1.250000e-09 75.0


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 TraesCS5A01G166500 chr5A 355463026 355466279 3253 False 6010.0 6010 100.0000 1 3254 1 chr5A.!!$F1 3253
1 TraesCS5A01G166500 chr5B 303581816 303584641 2825 False 2018.5 3866 94.6295 227 3254 2 chr5B.!!$F2 3027
2 TraesCS5A01G166500 chr5D 268278293 268281635 3342 False 1595.0 3445 96.0730 1 3254 3 chr5D.!!$F1 3253

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
520 533 0.040425 AAGCATGTCAAACCGAACGC 60.04 50.0 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2734 0.108186 CTAGTCGGTGAGCATGGCAA 60.108 55.0 0.0 0.0 0.0 4.52 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
33 34 3.569701 TGAGTGATGGGAAAGACAAAAGC 59.430 43.478 0.00 0.00 0.00 3.51
34 35 3.565307 AGTGATGGGAAAGACAAAAGCA 58.435 40.909 0.00 0.00 0.00 3.91
75 76 1.834822 CGTCTCTCCCTCCCCATCC 60.835 68.421 0.00 0.00 0.00 3.51
78 79 1.152139 CTCTCCCTCCCCATCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
85 86 1.721691 CCTCCCCATCCCTCTCTCTAT 59.278 57.143 0.00 0.00 0.00 1.98
89 90 2.381618 CCCCATCCCTCTCTCTATCTCA 59.618 54.545 0.00 0.00 0.00 3.27
95 96 3.650942 TCCCTCTCTCTATCTCAGGAGTC 59.349 52.174 0.00 0.00 0.00 3.36
147 149 5.717078 TTATCTTATCCGCACGGTCTAAT 57.283 39.130 9.23 0.00 36.47 1.73
176 178 1.833630 CCTGAGATGTGGGCACTCTAA 59.166 52.381 0.00 0.00 0.00 2.10
226 236 7.206687 TGCGACCATTTCATTACTTTTCTTTT 58.793 30.769 0.00 0.00 0.00 2.27
286 299 5.499139 AATGTTTCACTTTTCTTCTCGCA 57.501 34.783 0.00 0.00 0.00 5.10
305 318 2.514803 CAATCCCTTCGTCCAACCTTT 58.485 47.619 0.00 0.00 0.00 3.11
319 332 6.479001 CGTCCAACCTTTCTCGTATGATAATT 59.521 38.462 0.00 0.00 0.00 1.40
354 367 5.476091 TTATTTGCCTTCCGAACCAATTT 57.524 34.783 0.00 0.00 0.00 1.82
396 409 3.195002 CGCACGGGCATGATTCGT 61.195 61.111 11.77 0.00 41.24 3.85
398 411 1.506262 GCACGGGCATGATTCGTTT 59.494 52.632 3.77 0.00 40.72 3.60
508 521 6.875195 CCTGAATGTTTGGATTTTAAGCATGT 59.125 34.615 0.00 0.00 30.85 3.21
520 533 0.040425 AAGCATGTCAAACCGAACGC 60.040 50.000 0.00 0.00 0.00 4.84
547 560 2.634600 TGGCAACTTTAGTTCACACGT 58.365 42.857 0.00 0.00 35.83 4.49
615 630 7.283625 ACAAAGTTGCCATGTCTTAATAACA 57.716 32.000 0.00 0.00 0.00 2.41
629 644 8.962679 TGTCTTAATAACAAAAGTTGTCACCTT 58.037 29.630 0.00 0.00 44.59 3.50
683 698 7.601856 TGTTCGGAATGAAATGCTTAAAATCT 58.398 30.769 0.00 0.00 38.60 2.40
694 709 4.059511 TGCTTAAAATCTGAACCGTTCGA 58.940 39.130 6.78 7.37 0.00 3.71
818 835 7.083858 ACGTGAATCAACATTTTGGTTAGATG 58.916 34.615 0.00 0.00 36.10 2.90
850 867 8.673711 CGGGATTAACTTTTCATAACAATCTCA 58.326 33.333 0.00 0.00 0.00 3.27
1233 1251 1.202188 GGCTTCTTTATCTGCAACGGC 60.202 52.381 0.00 0.00 41.68 5.68
1495 1513 4.394712 CCTTGTCCCGCCGCTCTT 62.395 66.667 0.00 0.00 0.00 2.85
1770 1788 1.261938 ATGGCTGCGTGTACTGGGTA 61.262 55.000 0.00 0.00 0.00 3.69
1835 1853 2.222027 CACAAAGGAGTTCTCCACCAC 58.778 52.381 19.28 0.00 0.00 4.16
1965 1983 2.168106 GCTCCATATCTGGCATCTCGAT 59.832 50.000 0.00 0.00 42.80 3.59
1969 1987 3.703556 CCATATCTGGCATCTCGATAGGT 59.296 47.826 5.72 0.00 35.23 3.08
2001 2019 3.407967 GGCCGATGGGTGAGGGAA 61.408 66.667 0.00 0.00 34.97 3.97
2091 2110 0.954449 GGATCATGGATGCCTGCGAG 60.954 60.000 0.00 0.00 0.00 5.03
2296 2566 7.715249 TGTTTTGCTTCTACTCAACTATGAACT 59.285 33.333 0.00 0.00 34.49 3.01
2297 2567 9.204570 GTTTTGCTTCTACTCAACTATGAACTA 57.795 33.333 0.00 0.00 34.49 2.24
2298 2568 8.758633 TTTGCTTCTACTCAACTATGAACTAC 57.241 34.615 0.00 0.00 34.49 2.73
2299 2569 6.552629 TGCTTCTACTCAACTATGAACTACG 58.447 40.000 0.00 0.00 34.49 3.51
2343 2613 2.362169 TGATGATCAGCGAACGTTCA 57.638 45.000 26.71 8.77 0.00 3.18
2377 2647 7.436080 GGATGACAATTGCAAACATTTCGATAT 59.564 33.333 1.71 0.00 0.00 1.63
2424 2694 1.846541 TTTTAGTTTGCAAGCACGGC 58.153 45.000 16.04 0.00 0.00 5.68
2478 2748 3.803082 CCGTTGCCATGCTCACCG 61.803 66.667 0.00 0.00 0.00 4.94
2489 2759 3.430790 CCATGCTCACCGACTAGAATTGA 60.431 47.826 0.00 0.00 0.00 2.57
2534 2804 6.136071 GCGATCAAAATGATACGTAAATGCT 58.864 36.000 0.00 0.00 37.20 3.79
2601 2871 8.944212 AAAAACTACGCACTACATTCATAAAC 57.056 30.769 0.00 0.00 0.00 2.01
2676 2949 4.584874 TCAAACAGTTGTTCCTTCACAGA 58.415 39.130 0.00 0.00 37.25 3.41
2748 3021 5.808366 AATGTCAAGGACTCAGAGTTGTA 57.192 39.130 4.05 0.00 33.15 2.41
2760 3033 8.035394 GGACTCAGAGTTGTACATTGAGAATTA 58.965 37.037 22.98 0.00 35.65 1.40
2762 3035 9.950496 ACTCAGAGTTGTACATTGAGAATTATT 57.050 29.630 22.98 6.89 35.65 1.40
2992 3270 6.972885 AGGAGACTTATGGCTCTGCCTTCT 62.973 50.000 11.06 4.09 45.01 2.85
2993 3271 7.647806 AGGAGACTTATGGCTCTGCCTTCTA 62.648 48.000 11.06 0.00 45.01 2.10
2998 3276 1.826709 GGCTCTGCCTTCTACTCCC 59.173 63.158 0.73 0.00 46.69 4.30
2999 3277 0.689412 GGCTCTGCCTTCTACTCCCT 60.689 60.000 0.73 0.00 46.69 4.20
3000 3278 0.750249 GCTCTGCCTTCTACTCCCTC 59.250 60.000 0.00 0.00 0.00 4.30
3001 3279 1.408969 CTCTGCCTTCTACTCCCTCC 58.591 60.000 0.00 0.00 0.00 4.30
3002 3280 0.395862 TCTGCCTTCTACTCCCTCCG 60.396 60.000 0.00 0.00 0.00 4.63
3003 3281 0.684805 CTGCCTTCTACTCCCTCCGT 60.685 60.000 0.00 0.00 0.00 4.69
3004 3282 0.252103 TGCCTTCTACTCCCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
3005 3283 0.460722 GCCTTCTACTCCCTCCGTTC 59.539 60.000 0.00 0.00 0.00 3.95
3006 3284 1.112950 CCTTCTACTCCCTCCGTTCC 58.887 60.000 0.00 0.00 0.00 3.62
3007 3285 1.112950 CTTCTACTCCCTCCGTTCCC 58.887 60.000 0.00 0.00 0.00 3.97
3008 3286 0.410663 TTCTACTCCCTCCGTTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
3009 3287 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
3010 3288 1.203212 TCTACTCCCTCCGTTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
3011 3289 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
3012 3290 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3013 3291 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3014 3292 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3015 3293 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3016 3294 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3017 3295 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
3018 3296 4.102054 TCCCTCCGTTCCCAAATATAAGTC 59.898 45.833 0.00 0.00 0.00 3.01
3019 3297 4.102681 CCCTCCGTTCCCAAATATAAGTCT 59.897 45.833 0.00 0.00 0.00 3.24
3020 3298 5.397559 CCCTCCGTTCCCAAATATAAGTCTT 60.398 44.000 0.00 0.00 0.00 3.01
3021 3299 6.120220 CCTCCGTTCCCAAATATAAGTCTTT 58.880 40.000 0.00 0.00 0.00 2.52
3022 3300 6.260271 CCTCCGTTCCCAAATATAAGTCTTTC 59.740 42.308 0.00 0.00 0.00 2.62
3023 3301 6.954232 TCCGTTCCCAAATATAAGTCTTTCT 58.046 36.000 0.00 0.00 0.00 2.52
3024 3302 8.081517 TCCGTTCCCAAATATAAGTCTTTCTA 57.918 34.615 0.00 0.00 0.00 2.10
3025 3303 8.202137 TCCGTTCCCAAATATAAGTCTTTCTAG 58.798 37.037 0.00 0.00 0.00 2.43
3026 3304 8.202137 CCGTTCCCAAATATAAGTCTTTCTAGA 58.798 37.037 0.00 0.00 0.00 2.43
3027 3305 9.250624 CGTTCCCAAATATAAGTCTTTCTAGAG 57.749 37.037 0.00 0.00 0.00 2.43
3038 3316 9.883142 ATAAGTCTTTCTAGAGATTCCAACAAG 57.117 33.333 0.00 0.00 0.00 3.16
3039 3317 7.309770 AGTCTTTCTAGAGATTCCAACAAGT 57.690 36.000 0.00 0.00 0.00 3.16
3040 3318 7.158021 AGTCTTTCTAGAGATTCCAACAAGTG 58.842 38.462 0.00 0.00 0.00 3.16
3041 3319 7.015682 AGTCTTTCTAGAGATTCCAACAAGTGA 59.984 37.037 0.00 0.00 0.00 3.41
3042 3320 7.117092 GTCTTTCTAGAGATTCCAACAAGTGAC 59.883 40.741 0.00 0.00 0.00 3.67
3043 3321 6.672266 TTCTAGAGATTCCAACAAGTGACT 57.328 37.500 0.00 0.00 0.00 3.41
3044 3322 7.776618 TTCTAGAGATTCCAACAAGTGACTA 57.223 36.000 0.00 0.00 0.00 2.59
3045 3323 7.159322 TCTAGAGATTCCAACAAGTGACTAC 57.841 40.000 0.00 0.00 0.00 2.73
3046 3324 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
3047 3325 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
3048 3326 7.482169 AGAGATTCCAACAAGTGACTACATA 57.518 36.000 0.00 0.00 0.00 2.29
3049 3327 7.324178 AGAGATTCCAACAAGTGACTACATAC 58.676 38.462 0.00 0.00 0.00 2.39
3050 3328 6.100004 AGATTCCAACAAGTGACTACATACG 58.900 40.000 0.00 0.00 0.00 3.06
3051 3329 4.182693 TCCAACAAGTGACTACATACGG 57.817 45.455 0.00 0.00 0.00 4.02
3052 3330 3.827876 TCCAACAAGTGACTACATACGGA 59.172 43.478 0.00 0.00 0.00 4.69
3053 3331 4.082408 TCCAACAAGTGACTACATACGGAG 60.082 45.833 0.00 0.00 0.00 4.63
3054 3332 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3055 3333 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3056 3334 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3057 3335 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3058 3336 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3059 3337 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3060 3338 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3061 3339 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3062 3340 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3063 3341 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3064 3342 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3065 3343 3.674997 ACATACGGAGCAAAATGAGTGT 58.325 40.909 0.00 0.00 0.00 3.55
3066 3344 4.827692 ACATACGGAGCAAAATGAGTGTA 58.172 39.130 0.00 0.00 0.00 2.90
3067 3345 5.428253 ACATACGGAGCAAAATGAGTGTAT 58.572 37.500 0.00 0.00 0.00 2.29
3068 3346 5.523916 ACATACGGAGCAAAATGAGTGTATC 59.476 40.000 0.00 0.00 0.00 2.24
3069 3347 4.207891 ACGGAGCAAAATGAGTGTATCT 57.792 40.909 0.00 0.00 0.00 1.98
3070 3348 5.339008 ACGGAGCAAAATGAGTGTATCTA 57.661 39.130 0.00 0.00 0.00 1.98
3071 3349 5.109903 ACGGAGCAAAATGAGTGTATCTAC 58.890 41.667 0.00 0.00 0.00 2.59
3072 3350 5.109210 CGGAGCAAAATGAGTGTATCTACA 58.891 41.667 0.00 0.00 0.00 2.74
3106 3384 6.954487 TGTCTAGATACATCCGTATGTTGT 57.046 37.500 0.00 0.00 44.07 3.32
3107 3385 8.631480 ATGTCTAGATACATCCGTATGTTGTA 57.369 34.615 0.00 0.00 44.07 2.41
3108 3386 8.095937 TGTCTAGATACATCCGTATGTTGTAG 57.904 38.462 0.00 1.01 44.07 2.74
3109 3387 7.718314 TGTCTAGATACATCCGTATGTTGTAGT 59.282 37.037 0.00 0.00 44.07 2.73
3110 3388 8.229137 GTCTAGATACATCCGTATGTTGTAGTC 58.771 40.741 0.00 0.00 44.07 2.59
3111 3389 6.328641 AGATACATCCGTATGTTGTAGTCC 57.671 41.667 0.00 0.00 44.07 3.85
3112 3390 5.831525 AGATACATCCGTATGTTGTAGTCCA 59.168 40.000 0.00 0.00 44.07 4.02
3113 3391 6.493802 AGATACATCCGTATGTTGTAGTCCAT 59.506 38.462 0.00 0.00 44.07 3.41
3114 3392 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
3115 3393 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
3116 3394 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
3117 3395 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
3118 3396 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
3119 3397 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
3120 3398 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
3121 3399 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
3122 3400 7.361713 CCGTATGTTGTAGTCCATTTGAAATGT 60.362 37.037 15.93 1.43 0.00 2.71
3123 3401 7.692291 CGTATGTTGTAGTCCATTTGAAATGTC 59.308 37.037 15.93 9.10 0.00 3.06
3124 3402 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
3125 3403 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
3126 3404 8.684386 TGTTGTAGTCCATTTGAAATGTCTAA 57.316 30.769 15.93 4.89 0.00 2.10
3127 3405 9.126151 TGTTGTAGTCCATTTGAAATGTCTAAA 57.874 29.630 15.93 10.39 0.00 1.85
3128 3406 9.959749 GTTGTAGTCCATTTGAAATGTCTAAAA 57.040 29.630 15.93 14.59 0.00 1.52
3133 3411 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
3134 3412 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
3151 3429 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3152 3430 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.956848 GGGAGAATCTCAATCCCCTTTTG 59.043 47.826 12.79 0.00 46.03 2.44
34 35 4.256983 GGGAGAATCTCAATCCCCTTTT 57.743 45.455 12.79 0.00 46.03 2.27
75 76 3.244911 GGGACTCCTGAGATAGAGAGAGG 60.245 56.522 0.22 0.00 34.13 3.69
78 79 3.874383 TGGGACTCCTGAGATAGAGAG 57.126 52.381 0.22 0.00 34.13 3.20
85 86 3.943671 TTTTTGTTGGGACTCCTGAGA 57.056 42.857 0.22 0.00 0.00 3.27
89 90 3.117131 AGGTGATTTTTGTTGGGACTCCT 60.117 43.478 0.00 0.00 0.00 3.69
95 96 7.090173 CACTATTGTAGGTGATTTTTGTTGGG 58.910 38.462 0.00 0.00 35.69 4.12
124 125 5.717078 TTAGACCGTGCGGATAAGATAAT 57.283 39.130 18.16 0.00 38.96 1.28
125 126 5.717078 ATTAGACCGTGCGGATAAGATAA 57.283 39.130 18.16 6.93 38.96 1.75
127 128 4.281182 AGAATTAGACCGTGCGGATAAGAT 59.719 41.667 18.16 8.73 38.96 2.40
128 129 3.635373 AGAATTAGACCGTGCGGATAAGA 59.365 43.478 18.16 0.00 38.96 2.10
129 130 3.978687 AGAATTAGACCGTGCGGATAAG 58.021 45.455 18.16 0.00 38.96 1.73
130 131 5.518848 TTAGAATTAGACCGTGCGGATAA 57.481 39.130 18.16 14.72 38.96 1.75
147 149 1.134699 CCACATCTCAGGCGCTTAGAA 60.135 52.381 7.64 0.00 0.00 2.10
176 178 2.835764 TCTAATTCTACACCGGGCACTT 59.164 45.455 6.32 0.00 0.00 3.16
278 288 1.281899 GACGAAGGGATTGCGAGAAG 58.718 55.000 0.00 0.00 0.00 2.85
286 299 2.375509 AGAAAGGTTGGACGAAGGGATT 59.624 45.455 0.00 0.00 0.00 3.01
323 336 8.626526 GGTTCGGAAGGCAAATAAATTAAGATA 58.373 33.333 0.00 0.00 0.00 1.98
325 338 6.434652 TGGTTCGGAAGGCAAATAAATTAAGA 59.565 34.615 0.00 0.00 0.00 2.10
354 367 9.165035 CGAGGGTTGGTATGTAAATTAAAGTAA 57.835 33.333 0.00 0.00 0.00 2.24
368 381 2.582436 CCGTGCGAGGGTTGGTAT 59.418 61.111 0.00 0.00 0.00 2.73
482 495 5.792741 TGCTTAAAATCCAAACATTCAGGG 58.207 37.500 0.00 0.00 0.00 4.45
493 506 4.520874 TCGGTTTGACATGCTTAAAATCCA 59.479 37.500 0.00 0.00 0.00 3.41
508 521 2.287308 CCATGAAAAGCGTTCGGTTTGA 60.287 45.455 19.91 11.93 36.21 2.69
520 533 6.198966 GTGTGAACTAAAGTTGCCATGAAAAG 59.801 38.462 0.00 0.00 38.56 2.27
547 560 6.910536 AAAAATTGTCGTGTTTGCCAATAA 57.089 29.167 0.00 0.00 0.00 1.40
582 595 0.168128 GGCAACTTTGTCCCGATTCG 59.832 55.000 0.00 0.00 0.00 3.34
587 600 0.240945 GACATGGCAACTTTGTCCCG 59.759 55.000 7.56 0.00 41.58 5.14
588 601 1.620822 AGACATGGCAACTTTGTCCC 58.379 50.000 13.75 0.00 45.63 4.46
615 630 8.570068 TTAGTTGACTTAAGGTGACAACTTTT 57.430 30.769 27.12 15.95 45.37 2.27
657 672 8.253113 AGATTTTAAGCATTTCATTCCGAACAT 58.747 29.630 0.00 0.00 31.73 2.71
658 673 7.541783 CAGATTTTAAGCATTTCATTCCGAACA 59.458 33.333 0.00 0.00 31.73 3.18
659 674 7.754924 TCAGATTTTAAGCATTTCATTCCGAAC 59.245 33.333 0.00 0.00 31.73 3.95
663 678 7.009540 CGGTTCAGATTTTAAGCATTTCATTCC 59.990 37.037 0.00 0.00 0.00 3.01
683 698 3.371591 CCCGATAAATTTCGAACGGTTCA 59.628 43.478 19.91 5.46 41.62 3.18
818 835 7.548075 TGTTATGAAAAGTTAATCCCGAGTCTC 59.452 37.037 0.00 0.00 0.00 3.36
850 867 4.679373 AAGGTTCAGTGAGATATGCGAT 57.321 40.909 0.00 0.00 0.00 4.58
994 1012 0.808125 TTTTTGCCGCGCATCTATGT 59.192 45.000 8.75 0.00 38.76 2.29
1233 1251 0.392998 CCCTCTCCACATGGAAACCG 60.393 60.000 1.50 0.00 44.91 4.44
1582 1600 2.462723 GAAGGAGAGGGTACTTGAGCT 58.537 52.381 0.00 0.00 0.00 4.09
1770 1788 1.429825 CTCGCTCTCGTCGTCCATT 59.570 57.895 0.00 0.00 36.96 3.16
1965 1983 0.615331 CTTTCCTGCTCCTGCACCTA 59.385 55.000 0.00 0.00 45.31 3.08
2091 2110 0.679505 GCTTGAGGAAAACAACCCCC 59.320 55.000 0.00 0.00 0.00 5.40
2343 2613 2.292389 TGCAATTGTCATCCCTCCCAAT 60.292 45.455 7.40 0.00 0.00 3.16
2392 2662 7.230849 TGCAAACTAAAATTGTCATCCTCAT 57.769 32.000 0.00 0.00 0.00 2.90
2464 2734 0.108186 CTAGTCGGTGAGCATGGCAA 60.108 55.000 0.00 0.00 0.00 4.52
2478 2748 3.628942 TGGCATGCATGTCAATTCTAGTC 59.371 43.478 30.82 7.69 39.82 2.59
2489 2759 2.809119 CAATTTGTGTTGGCATGCATGT 59.191 40.909 26.79 0.78 0.00 3.21
2600 2870 8.736244 ACGCAAAATAGTACTCCATAAAAATGT 58.264 29.630 0.00 0.00 0.00 2.71
2810 3087 6.102897 AGATTGTAGAGCCGCTAAATACAT 57.897 37.500 11.39 4.90 0.00 2.29
2992 3270 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2993 3271 1.961133 TATTTGGGAACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2994 3272 4.102681 ACTTATATTTGGGAACGGAGGGAG 59.897 45.833 0.00 0.00 0.00 4.30
2995 3273 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
2996 3274 4.102681 AGACTTATATTTGGGAACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
2997 3275 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
2998 3276 7.048512 AGAAAGACTTATATTTGGGAACGGAG 58.951 38.462 0.00 0.00 0.00 4.63
2999 3277 6.954232 AGAAAGACTTATATTTGGGAACGGA 58.046 36.000 0.00 0.00 0.00 4.69
3000 3278 8.202137 TCTAGAAAGACTTATATTTGGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
3001 3279 9.250624 CTCTAGAAAGACTTATATTTGGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
3012 3290 9.883142 CTTGTTGGAATCTCTAGAAAGACTTAT 57.117 33.333 0.00 0.00 0.00 1.73
3013 3291 8.871125 ACTTGTTGGAATCTCTAGAAAGACTTA 58.129 33.333 0.00 0.00 0.00 2.24
3014 3292 7.659390 CACTTGTTGGAATCTCTAGAAAGACTT 59.341 37.037 0.00 0.00 0.00 3.01
3015 3293 7.015682 TCACTTGTTGGAATCTCTAGAAAGACT 59.984 37.037 0.00 0.00 0.00 3.24
3016 3294 7.117092 GTCACTTGTTGGAATCTCTAGAAAGAC 59.883 40.741 0.00 0.00 0.00 3.01
3017 3295 7.015682 AGTCACTTGTTGGAATCTCTAGAAAGA 59.984 37.037 0.00 0.00 0.00 2.52
3018 3296 7.158021 AGTCACTTGTTGGAATCTCTAGAAAG 58.842 38.462 0.00 0.00 0.00 2.62
3019 3297 7.067496 AGTCACTTGTTGGAATCTCTAGAAA 57.933 36.000 0.00 0.00 0.00 2.52
3020 3298 6.672266 AGTCACTTGTTGGAATCTCTAGAA 57.328 37.500 0.00 0.00 0.00 2.10
3021 3299 6.719829 TGTAGTCACTTGTTGGAATCTCTAGA 59.280 38.462 0.00 0.00 0.00 2.43
3022 3300 6.925211 TGTAGTCACTTGTTGGAATCTCTAG 58.075 40.000 0.00 0.00 0.00 2.43
3023 3301 6.911250 TGTAGTCACTTGTTGGAATCTCTA 57.089 37.500 0.00 0.00 0.00 2.43
3024 3302 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
3025 3303 6.253727 CGTATGTAGTCACTTGTTGGAATCTC 59.746 42.308 0.00 0.00 0.00 2.75
3026 3304 6.100004 CGTATGTAGTCACTTGTTGGAATCT 58.900 40.000 0.00 0.00 0.00 2.40
3027 3305 5.291128 CCGTATGTAGTCACTTGTTGGAATC 59.709 44.000 0.00 0.00 0.00 2.52
3028 3306 5.046878 TCCGTATGTAGTCACTTGTTGGAAT 60.047 40.000 0.00 0.00 0.00 3.01
3029 3307 4.281435 TCCGTATGTAGTCACTTGTTGGAA 59.719 41.667 0.00 0.00 0.00 3.53
3030 3308 3.827876 TCCGTATGTAGTCACTTGTTGGA 59.172 43.478 0.00 0.00 0.00 3.53
3031 3309 4.174009 CTCCGTATGTAGTCACTTGTTGG 58.826 47.826 0.00 0.00 0.00 3.77
3032 3310 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3033 3311 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3034 3312 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3035 3313 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3036 3314 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3037 3315 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3038 3316 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3039 3317 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3040 3318 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3041 3319 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3042 3320 4.870426 ACACTCATTTTGCTCCGTATGTAG 59.130 41.667 0.00 0.00 0.00 2.74
3043 3321 4.827692 ACACTCATTTTGCTCCGTATGTA 58.172 39.130 0.00 0.00 0.00 2.29
3044 3322 3.674997 ACACTCATTTTGCTCCGTATGT 58.325 40.909 0.00 0.00 0.00 2.29
3045 3323 5.755375 AGATACACTCATTTTGCTCCGTATG 59.245 40.000 0.00 0.00 0.00 2.39
3046 3324 5.918608 AGATACACTCATTTTGCTCCGTAT 58.081 37.500 0.00 0.00 0.00 3.06
3047 3325 5.339008 AGATACACTCATTTTGCTCCGTA 57.661 39.130 0.00 0.00 0.00 4.02
3048 3326 4.207891 AGATACACTCATTTTGCTCCGT 57.792 40.909 0.00 0.00 0.00 4.69
3049 3327 5.109210 TGTAGATACACTCATTTTGCTCCG 58.891 41.667 0.00 0.00 0.00 4.63
3080 3358 9.244292 ACAACATACGGATGTATCTAGACATAT 57.756 33.333 15.10 0.00 45.93 1.78
3081 3359 8.631480 ACAACATACGGATGTATCTAGACATA 57.369 34.615 15.10 0.00 45.93 2.29
3082 3360 7.526142 ACAACATACGGATGTATCTAGACAT 57.474 36.000 15.10 0.00 45.93 3.06
3083 3361 6.954487 ACAACATACGGATGTATCTAGACA 57.046 37.500 15.10 0.00 45.93 3.41
3084 3362 8.097078 ACTACAACATACGGATGTATCTAGAC 57.903 38.462 15.10 0.00 45.93 2.59
3085 3363 7.389884 GGACTACAACATACGGATGTATCTAGA 59.610 40.741 15.10 0.00 45.93 2.43
3086 3364 7.174426 TGGACTACAACATACGGATGTATCTAG 59.826 40.741 15.10 14.29 45.93 2.43
3087 3365 6.999871 TGGACTACAACATACGGATGTATCTA 59.000 38.462 15.10 2.92 45.93 1.98
3088 3366 5.831525 TGGACTACAACATACGGATGTATCT 59.168 40.000 15.10 1.76 45.93 1.98
3089 3367 6.080648 TGGACTACAACATACGGATGTATC 57.919 41.667 15.10 6.98 45.93 2.24
3090 3368 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
3091 3369 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
3093 3371 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
3094 3372 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
3095 3373 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
3096 3374 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
3097 3375 7.526608 ACATTTCAAATGGACTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
3098 3376 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
3099 3377 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
3100 3378 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
3101 3379 8.684386 TTAGACATTTCAAATGGACTACAACA 57.316 30.769 14.70 1.25 0.00 3.33
3102 3380 9.959749 TTTTAGACATTTCAAATGGACTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
3107 3385 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
3108 3386 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
3125 3403 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3126 3404 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3127 3405 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3128 3406 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3129 3407 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3130 3408 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3131 3409 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3132 3410 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3134 3412 9.638176 GATATACTCCCTCCGTTCCTAAATATA 57.362 37.037 0.00 0.00 0.00 0.86
3135 3413 8.345306 AGATATACTCCCTCCGTTCCTAAATAT 58.655 37.037 0.00 0.00 0.00 1.28
3136 3414 7.614583 CAGATATACTCCCTCCGTTCCTAAATA 59.385 40.741 0.00 0.00 0.00 1.40
3137 3415 6.437793 CAGATATACTCCCTCCGTTCCTAAAT 59.562 42.308 0.00 0.00 0.00 1.40
3138 3416 5.773680 CAGATATACTCCCTCCGTTCCTAAA 59.226 44.000 0.00 0.00 0.00 1.85
3139 3417 5.074102 TCAGATATACTCCCTCCGTTCCTAA 59.926 44.000 0.00 0.00 0.00 2.69
3140 3418 4.600547 TCAGATATACTCCCTCCGTTCCTA 59.399 45.833 0.00 0.00 0.00 2.94
3141 3419 3.398292 TCAGATATACTCCCTCCGTTCCT 59.602 47.826 0.00 0.00 0.00 3.36
3142 3420 3.506844 GTCAGATATACTCCCTCCGTTCC 59.493 52.174 0.00 0.00 0.00 3.62
3143 3421 3.188873 CGTCAGATATACTCCCTCCGTTC 59.811 52.174 0.00 0.00 0.00 3.95
3144 3422 3.147629 CGTCAGATATACTCCCTCCGTT 58.852 50.000 0.00 0.00 0.00 4.44
3145 3423 2.371179 TCGTCAGATATACTCCCTCCGT 59.629 50.000 0.00 0.00 0.00 4.69
3146 3424 3.055209 TCGTCAGATATACTCCCTCCG 57.945 52.381 0.00 0.00 0.00 4.63
3147 3425 5.986501 AATTCGTCAGATATACTCCCTCC 57.013 43.478 0.00 0.00 0.00 4.30
3148 3426 6.864165 GTCAAATTCGTCAGATATACTCCCTC 59.136 42.308 0.00 0.00 0.00 4.30
3149 3427 6.239345 GGTCAAATTCGTCAGATATACTCCCT 60.239 42.308 0.00 0.00 0.00 4.20
3150 3428 5.927115 GGTCAAATTCGTCAGATATACTCCC 59.073 44.000 0.00 0.00 0.00 4.30
3151 3429 6.513180 TGGTCAAATTCGTCAGATATACTCC 58.487 40.000 0.00 0.00 0.00 3.85
3152 3430 7.168302 CACTGGTCAAATTCGTCAGATATACTC 59.832 40.741 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.