Multiple sequence alignment - TraesCS2B01G495400

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 TraesCS2B01G495400 chr2B 100.000 3095 0 0 1 3095 692161270 692164364 0.000000e+00 5716.0
1 TraesCS2B01G495400 chr2B 98.361 61 1 0 3035 3095 485894153 485894213 1.170000e-19 108.0
2 TraesCS2B01G495400 chr2B 90.244 41 4 0 1114 1154 690666757 690666717 2.000000e-03 54.7
3 TraesCS2B01G495400 chr2D 92.680 2978 134 41 96 3040 576190465 576193391 0.000000e+00 4215.0
4 TraesCS2B01G495400 chr2A 91.936 3063 162 50 14 3040 714206321 714209334 0.000000e+00 4209.0
5 TraesCS2B01G495400 chr6B 80.447 537 71 21 2219 2747 173816986 173817496 2.250000e-101 379.0
6 TraesCS2B01G495400 chr6B 98.361 61 1 0 3035 3095 680728657 680728597 1.170000e-19 108.0
7 TraesCS2B01G495400 chr7B 78.090 534 64 34 2219 2750 171091131 171090649 3.910000e-74 289.0
8 TraesCS2B01G495400 chr1B 79.661 295 38 14 2219 2513 87189656 87189384 3.150000e-45 193.0
9 TraesCS2B01G495400 chr1B 100.000 60 0 0 3036 3095 370161818 370161759 9.070000e-21 111.0
10 TraesCS2B01G495400 chr5D 81.102 254 32 9 2219 2472 181607413 181607176 4.070000e-44 189.0
11 TraesCS2B01G495400 chr5D 95.385 65 2 1 3030 3094 381812026 381812089 5.460000e-18 102.0
12 TraesCS2B01G495400 chr4A 92.683 82 5 1 2230 2310 20573249 20573330 1.950000e-22 117.0
13 TraesCS2B01G495400 chr4D 95.652 69 2 1 3027 3095 505322499 505322432 3.260000e-20 110.0
14 TraesCS2B01G495400 chr7A 95.385 65 2 1 3031 3095 655447229 655447292 5.460000e-18 102.0
15 TraesCS2B01G495400 chr7D 88.372 86 6 4 3010 3095 535938349 535938430 1.960000e-17 100.0
16 TraesCS2B01G495400 chr3B 94.030 67 3 1 3029 3095 243784214 243784149 1.960000e-17 100.0
17 TraesCS2B01G495400 chr3B 91.781 73 5 1 3024 3095 724932114 724932186 1.960000e-17 100.0


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 TraesCS2B01G495400 chr2B 692161270 692164364 3094 False 5716 5716 100.000 1 3095 1 chr2B.!!$F2 3094
1 TraesCS2B01G495400 chr2D 576190465 576193391 2926 False 4215 4215 92.680 96 3040 1 chr2D.!!$F1 2944
2 TraesCS2B01G495400 chr2A 714206321 714209334 3013 False 4209 4209 91.936 14 3040 1 chr2A.!!$F1 3026
3 TraesCS2B01G495400 chr6B 173816986 173817496 510 False 379 379 80.447 2219 2747 1 chr6B.!!$F1 528

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
482 517 0.76551 AGAAGAAACAAGTCCCCGCT 59.234 50.0 0.0 0.0 0.0 5.52 F
484 519 0.76551 AAGAAACAAGTCCCCGCTCT 59.234 50.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1484 0.456995 GGCAGTCGTTCTCGAGGAAG 60.457 60.0 13.56 6.43 46.96 3.46 R
2413 2472 0.766674 TGTTAGACCAGCCAGGGTGT 60.767 55.0 17.61 5.71 42.53 4.16 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
42 43 5.840693 CCCTTCAAAAAGATATGGCCCTTAT 59.159 40.000 0.00 0.00 34.14 1.73
53 54 9.605951 AAGATATGGCCCTTATTAACATCAAAT 57.394 29.630 0.00 0.00 0.00 2.32
54 55 9.247861 AGATATGGCCCTTATTAACATCAAATC 57.752 33.333 0.00 0.00 0.00 2.17
55 56 6.670695 ATGGCCCTTATTAACATCAAATCC 57.329 37.500 0.00 0.00 0.00 3.01
56 57 5.523588 TGGCCCTTATTAACATCAAATCCA 58.476 37.500 0.00 0.00 0.00 3.41
57 58 5.960811 TGGCCCTTATTAACATCAAATCCAA 59.039 36.000 0.00 0.00 0.00 3.53
58 59 6.441924 TGGCCCTTATTAACATCAAATCCAAA 59.558 34.615 0.00 0.00 0.00 3.28
59 60 6.761242 GGCCCTTATTAACATCAAATCCAAAC 59.239 38.462 0.00 0.00 0.00 2.93
60 61 7.364673 GGCCCTTATTAACATCAAATCCAAACT 60.365 37.037 0.00 0.00 0.00 2.66
61 62 8.040727 GCCCTTATTAACATCAAATCCAAACTT 58.959 33.333 0.00 0.00 0.00 2.66
62 63 9.586435 CCCTTATTAACATCAAATCCAAACTTC 57.414 33.333 0.00 0.00 0.00 3.01
63 64 9.586435 CCTTATTAACATCAAATCCAAACTTCC 57.414 33.333 0.00 0.00 0.00 3.46
64 65 9.586435 CTTATTAACATCAAATCCAAACTTCCC 57.414 33.333 0.00 0.00 0.00 3.97
65 66 4.890158 AACATCAAATCCAAACTTCCCC 57.110 40.909 0.00 0.00 0.00 4.81
66 67 3.855668 ACATCAAATCCAAACTTCCCCA 58.144 40.909 0.00 0.00 0.00 4.96
67 68 4.230455 ACATCAAATCCAAACTTCCCCAA 58.770 39.130 0.00 0.00 0.00 4.12
68 69 4.657969 ACATCAAATCCAAACTTCCCCAAA 59.342 37.500 0.00 0.00 0.00 3.28
69 70 5.131809 ACATCAAATCCAAACTTCCCCAAAA 59.868 36.000 0.00 0.00 0.00 2.44
70 71 5.700402 TCAAATCCAAACTTCCCCAAAAA 57.300 34.783 0.00 0.00 0.00 1.94
71 72 6.259346 TCAAATCCAAACTTCCCCAAAAAT 57.741 33.333 0.00 0.00 0.00 1.82
72 73 6.667661 TCAAATCCAAACTTCCCCAAAAATT 58.332 32.000 0.00 0.00 0.00 1.82
73 74 7.806180 TCAAATCCAAACTTCCCCAAAAATTA 58.194 30.769 0.00 0.00 0.00 1.40
74 75 8.443979 TCAAATCCAAACTTCCCCAAAAATTAT 58.556 29.630 0.00 0.00 0.00 1.28
75 76 9.076781 CAAATCCAAACTTCCCCAAAAATTATT 57.923 29.630 0.00 0.00 0.00 1.40
77 78 9.958180 AATCCAAACTTCCCCAAAAATTATTAG 57.042 29.630 0.00 0.00 0.00 1.73
78 79 8.499288 TCCAAACTTCCCCAAAAATTATTAGT 57.501 30.769 0.00 0.00 0.00 2.24
79 80 8.371699 TCCAAACTTCCCCAAAAATTATTAGTG 58.628 33.333 0.00 0.00 0.00 2.74
80 81 8.154203 CCAAACTTCCCCAAAAATTATTAGTGT 58.846 33.333 0.00 0.00 0.00 3.55
81 82 9.203421 CAAACTTCCCCAAAAATTATTAGTGTC 57.797 33.333 0.00 0.00 0.00 3.67
82 83 8.485578 AACTTCCCCAAAAATTATTAGTGTCA 57.514 30.769 0.00 0.00 0.00 3.58
83 84 8.485578 ACTTCCCCAAAAATTATTAGTGTCAA 57.514 30.769 0.00 0.00 0.00 3.18
84 85 8.929487 ACTTCCCCAAAAATTATTAGTGTCAAA 58.071 29.630 0.00 0.00 0.00 2.69
97 98 4.437682 AGTGTCAAATCCAGAACTTCCA 57.562 40.909 0.00 0.00 0.00 3.53
98 99 4.792068 AGTGTCAAATCCAGAACTTCCAA 58.208 39.130 0.00 0.00 0.00 3.53
178 193 9.478768 TTCTCAGACTAATACTATAGACGTCAG 57.521 37.037 19.50 9.14 0.00 3.51
183 198 9.263538 AGACTAATACTATAGACGTCAGTGAAG 57.736 37.037 19.50 12.83 0.00 3.02
185 200 9.781633 ACTAATACTATAGACGTCAGTGAAGAT 57.218 33.333 19.50 3.73 0.00 2.40
199 214 7.336679 CGTCAGTGAAGATATCCTATCTCATCT 59.663 40.741 0.00 0.00 0.00 2.90
213 228 7.290948 TCCTATCTCATCTTATCTTTTCCTGCA 59.709 37.037 0.00 0.00 0.00 4.41
214 229 7.935755 CCTATCTCATCTTATCTTTTCCTGCAA 59.064 37.037 0.00 0.00 0.00 4.08
232 247 6.798315 CTGCAAGGAAAGACATATCCTATG 57.202 41.667 0.00 0.00 45.33 2.23
298 315 1.326548 CCTAAAGACGCACGCCATTAC 59.673 52.381 0.00 0.00 0.00 1.89
299 316 2.268298 CTAAAGACGCACGCCATTACT 58.732 47.619 0.00 0.00 0.00 2.24
300 317 2.373540 AAAGACGCACGCCATTACTA 57.626 45.000 0.00 0.00 0.00 1.82
316 333 7.545615 CGCCATTACTAGAATTGTATAGCATGA 59.454 37.037 0.00 0.00 0.00 3.07
444 468 2.158943 AGCCTCCTCCACGCTATAAAAC 60.159 50.000 0.00 0.00 0.00 2.43
470 505 1.909302 AGCAATCCCCTCGAGAAGAAA 59.091 47.619 15.71 0.00 0.00 2.52
471 506 2.010497 GCAATCCCCTCGAGAAGAAAC 58.990 52.381 15.71 0.69 0.00 2.78
473 508 3.674997 CAATCCCCTCGAGAAGAAACAA 58.325 45.455 15.71 0.00 0.00 2.83
474 509 3.618690 ATCCCCTCGAGAAGAAACAAG 57.381 47.619 15.71 0.00 0.00 3.16
475 510 2.326428 TCCCCTCGAGAAGAAACAAGT 58.674 47.619 15.71 0.00 0.00 3.16
477 512 2.613223 CCCCTCGAGAAGAAACAAGTCC 60.613 54.545 15.71 0.00 0.00 3.85
478 513 2.613223 CCCTCGAGAAGAAACAAGTCCC 60.613 54.545 15.71 0.00 0.00 4.46
480 515 1.000506 TCGAGAAGAAACAAGTCCCCG 59.999 52.381 0.00 0.00 0.00 5.73
481 516 1.157585 GAGAAGAAACAAGTCCCCGC 58.842 55.000 0.00 0.00 0.00 6.13
482 517 0.765510 AGAAGAAACAAGTCCCCGCT 59.234 50.000 0.00 0.00 0.00 5.52
483 518 1.157585 GAAGAAACAAGTCCCCGCTC 58.842 55.000 0.00 0.00 0.00 5.03
484 519 0.765510 AAGAAACAAGTCCCCGCTCT 59.234 50.000 0.00 0.00 0.00 4.09
485 520 0.765510 AGAAACAAGTCCCCGCTCTT 59.234 50.000 0.00 0.00 0.00 2.85
486 521 1.157585 GAAACAAGTCCCCGCTCTTC 58.842 55.000 0.00 0.00 0.00 2.87
489 524 1.374947 CAAGTCCCCGCTCTTCCAA 59.625 57.895 0.00 0.00 0.00 3.53
491 526 2.046217 GTCCCCGCTCTTCCAACC 60.046 66.667 0.00 0.00 0.00 3.77
492 527 3.702048 TCCCCGCTCTTCCAACCG 61.702 66.667 0.00 0.00 0.00 4.44
496 544 2.556287 CGCTCTTCCAACCGCAAC 59.444 61.111 0.00 0.00 0.00 4.17
511 559 2.915659 AACCACGAGCCTCCACGA 60.916 61.111 0.00 0.00 0.00 4.35
517 565 4.803426 GAGCCTCCACGACGCCTG 62.803 72.222 0.00 0.00 0.00 4.85
657 715 2.284552 TGGGGCAGGCAATTTCCC 60.285 61.111 0.00 0.00 38.03 3.97
822 881 2.283809 CTCCACGGATCCTCCCCT 59.716 66.667 10.75 0.00 31.13 4.79
823 882 1.383248 CTCCACGGATCCTCCCCTT 60.383 63.158 10.75 0.00 31.13 3.95
824 883 1.689233 TCCACGGATCCTCCCCTTG 60.689 63.158 10.75 0.00 31.13 3.61
830 889 1.575447 GGATCCTCCCCTTGCTGGTT 61.575 60.000 3.84 0.00 0.00 3.67
973 1032 2.460330 CTGATAATCATCGGCCCGC 58.540 57.895 0.00 0.00 33.51 6.13
975 1034 1.745489 GATAATCATCGGCCCGCCC 60.745 63.158 0.00 0.00 0.00 6.13
1371 1430 1.880340 CACATTCTCTCCGGCGAGC 60.880 63.158 16.85 0.00 35.94 5.03
1476 1535 1.669115 CCTGCTCACCGTCACCAAG 60.669 63.158 0.00 0.00 0.00 3.61
1498 1557 4.308458 CCCGCACCCAAGACGTCA 62.308 66.667 19.50 0.00 0.00 4.35
1559 1618 0.248215 GATTTCGGGAACATGCTGCG 60.248 55.000 0.00 0.00 0.00 5.18
1572 1631 4.003788 CTGCGTGACGGGGAAGGT 62.004 66.667 7.25 0.00 0.00 3.50
1578 1637 4.754667 GACGGGGAAGGTGCGGAC 62.755 72.222 0.00 0.00 0.00 4.79
1693 1752 3.867600 GCTGAGAGAAAATGCCACAGAGA 60.868 47.826 0.00 0.00 0.00 3.10
1779 1838 1.285962 ACCCTGCCTGATAACTGCAAT 59.714 47.619 0.00 0.00 34.06 3.56
1849 1908 2.572284 GCGTCGACAGGCTAAGGT 59.428 61.111 17.16 0.00 0.00 3.50
1863 1922 2.878406 GCTAAGGTTGCTGTGTGAAAGA 59.122 45.455 0.00 0.00 0.00 2.52
1875 1934 2.287915 GTGTGAAAGAAAGCTGAGCGAA 59.712 45.455 0.00 0.00 0.00 4.70
2097 2156 2.729882 GCGCGACAAGTCTTCTTAGAAA 59.270 45.455 12.10 0.00 32.07 2.52
2135 2194 3.511540 CCTTATCATGGACTGATAGGCGA 59.488 47.826 0.00 0.00 45.36 5.54
2158 2217 7.036220 CGATACTGTTTTACTCTGGTTCAGAT 58.964 38.462 0.00 0.00 39.92 2.90
2216 2275 5.107645 CCGTGTAAGCCTTTAAAATTTGCAC 60.108 40.000 12.81 12.81 33.09 4.57
2320 2379 6.306987 TGGGCATCCTTCTCCTTATTATTTC 58.693 40.000 0.00 0.00 0.00 2.17
2373 2432 9.695526 TTTGTATGTTTTCCTGATTCTTGATTG 57.304 29.630 0.00 0.00 0.00 2.67
2425 2484 1.341080 AAATCAAACACCCTGGCTGG 58.659 50.000 2.96 2.96 0.00 4.85
2476 2535 8.714906 ACCACATTCTTTAGCTTATACTACCAT 58.285 33.333 0.00 0.00 0.00 3.55
2477 2536 9.209175 CCACATTCTTTAGCTTATACTACCATC 57.791 37.037 0.00 0.00 0.00 3.51
2506 2565 1.891150 CAGCCCTGAAACATCTTTGCT 59.109 47.619 0.00 0.00 0.00 3.91
2508 2567 2.165998 GCCCTGAAACATCTTTGCTCT 58.834 47.619 0.00 0.00 0.00 4.09
2553 2619 4.627467 GCAGTCAGACCAAATGTAGTACTG 59.373 45.833 5.39 0.00 35.94 2.74
2554 2620 5.784177 CAGTCAGACCAAATGTAGTACTGT 58.216 41.667 5.39 0.00 0.00 3.55
2568 2634 3.996480 AGTACTGTCTGAAAGTTCTGGC 58.004 45.455 5.69 0.00 33.76 4.85
2751 2819 7.623770 ACTGTTACACAACTTTTACACATACG 58.376 34.615 0.00 0.00 35.56 3.06
2866 2938 1.172812 GCCCTGTCCCGCCATATTTC 61.173 60.000 0.00 0.00 0.00 2.17
2877 2949 4.059511 CCGCCATATTTCGTTGTATGGTA 58.940 43.478 17.53 0.00 45.87 3.25
2886 2958 7.639113 ATTTCGTTGTATGGTAATCATTGGT 57.361 32.000 0.00 0.00 37.30 3.67
2966 3038 5.107375 CCGAAAGAACCAGCAAAAATGAATG 60.107 40.000 0.00 0.00 0.00 2.67
2979 3051 9.932207 AGCAAAAATGAATGAGAAACATATTCA 57.068 25.926 0.00 0.00 42.83 2.57
3040 3112 6.017687 TGCAAACTATGATCATGCAGATGTAC 60.018 38.462 18.72 0.71 41.67 2.90
3041 3113 6.204301 GCAAACTATGATCATGCAGATGTACT 59.796 38.462 18.72 0.00 37.00 2.73
3042 3114 7.570875 GCAAACTATGATCATGCAGATGTACTC 60.571 40.741 18.72 0.00 37.00 2.59
3043 3115 6.035368 ACTATGATCATGCAGATGTACTCC 57.965 41.667 18.72 0.00 37.00 3.85
3044 3116 3.758755 TGATCATGCAGATGTACTCCC 57.241 47.619 0.00 0.00 37.00 4.30
3045 3117 3.311990 TGATCATGCAGATGTACTCCCT 58.688 45.455 0.00 0.00 37.00 4.20
3046 3118 3.323115 TGATCATGCAGATGTACTCCCTC 59.677 47.826 0.00 0.00 37.00 4.30
3047 3119 2.042464 TCATGCAGATGTACTCCCTCC 58.958 52.381 0.00 0.00 0.00 4.30
3048 3120 1.043816 ATGCAGATGTACTCCCTCCG 58.956 55.000 0.00 0.00 0.00 4.63
3049 3121 0.324368 TGCAGATGTACTCCCTCCGT 60.324 55.000 0.00 0.00 0.00 4.69
3050 3122 0.824759 GCAGATGTACTCCCTCCGTT 59.175 55.000 0.00 0.00 0.00 4.44
3051 3123 1.202428 GCAGATGTACTCCCTCCGTTC 60.202 57.143 0.00 0.00 0.00 3.95
3052 3124 1.409427 CAGATGTACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
3053 3125 1.288335 AGATGTACTCCCTCCGTTCCT 59.712 52.381 0.00 0.00 0.00 3.36
3054 3126 2.512896 AGATGTACTCCCTCCGTTCCTA 59.487 50.000 0.00 0.00 0.00 2.94
3055 3127 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3056 3128 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3057 3129 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3058 3130 3.449737 TGTACTCCCTCCGTTCCTAAATG 59.550 47.826 0.00 0.00 0.00 2.32
3059 3131 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
3060 3132 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
3061 3133 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
3062 3134 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
3063 3135 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
3064 3136 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
3065 3137 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
3066 3138 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3067 3139 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3068 3140 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
3069 3141 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
3070 3142 7.669427 TCCGTTCCTAAATGTAAGTCTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
3071 3143 7.816031 TCCGTTCCTAAATGTAAGTCTTTGTAG 59.184 37.037 0.00 0.00 0.00 2.74
3072 3144 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
3073 3145 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
3074 3146 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
3080 3152 8.779354 AATGTAAGTCTTTGTAGAGATTCCAC 57.221 34.615 0.00 0.00 0.00 4.02
3081 3153 7.540474 TGTAAGTCTTTGTAGAGATTCCACT 57.460 36.000 0.00 0.00 0.00 4.00
3082 3154 8.645814 TGTAAGTCTTTGTAGAGATTCCACTA 57.354 34.615 0.00 0.00 0.00 2.74
3083 3155 9.256228 TGTAAGTCTTTGTAGAGATTCCACTAT 57.744 33.333 0.00 0.00 0.00 2.12
3084 3156 9.522804 GTAAGTCTTTGTAGAGATTCCACTATG 57.477 37.037 0.00 0.00 0.00 2.23
3085 3157 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
3086 3158 8.367660 AGTCTTTGTAGAGATTCCACTATGAA 57.632 34.615 0.00 0.00 0.00 2.57
3087 3159 8.254508 AGTCTTTGTAGAGATTCCACTATGAAC 58.745 37.037 0.00 0.00 0.00 3.18
3088 3160 7.492994 GTCTTTGTAGAGATTCCACTATGAACC 59.507 40.741 0.00 0.00 0.00 3.62
3089 3161 6.867519 TTGTAGAGATTCCACTATGAACCA 57.132 37.500 0.00 0.00 0.00 3.67
3090 3162 6.222038 TGTAGAGATTCCACTATGAACCAC 57.778 41.667 0.00 0.00 0.00 4.16
3091 3163 5.719563 TGTAGAGATTCCACTATGAACCACA 59.280 40.000 0.00 0.00 0.00 4.17
3092 3164 5.965033 AGAGATTCCACTATGAACCACAT 57.035 39.130 0.00 0.00 42.39 3.21
3093 3165 7.563556 TGTAGAGATTCCACTATGAACCACATA 59.436 37.037 0.00 0.00 40.07 2.29
3094 3166 6.821388 AGAGATTCCACTATGAACCACATAC 58.179 40.000 0.00 0.00 40.07 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.886132 TTTGAAGGGTAATATTGTAACTCTCTC 57.114 33.333 0.00 0.00 0.00 3.20
10 11 9.696917 GCCATATCTTTTTGAAGGGTAATATTG 57.303 33.333 0.00 0.00 0.00 1.90
11 12 8.870116 GGCCATATCTTTTTGAAGGGTAATATT 58.130 33.333 0.00 0.00 0.00 1.28
12 13 7.454694 GGGCCATATCTTTTTGAAGGGTAATAT 59.545 37.037 4.39 0.00 0.00 1.28
35 36 7.555965 AGTTTGGATTTGATGTTAATAAGGGC 58.444 34.615 0.00 0.00 0.00 5.19
42 43 5.841237 TGGGGAAGTTTGGATTTGATGTTAA 59.159 36.000 0.00 0.00 0.00 2.01
53 54 8.371699 CACTAATAATTTTTGGGGAAGTTTGGA 58.628 33.333 0.00 0.00 0.00 3.53
54 55 8.154203 ACACTAATAATTTTTGGGGAAGTTTGG 58.846 33.333 1.39 0.00 0.00 3.28
55 56 9.203421 GACACTAATAATTTTTGGGGAAGTTTG 57.797 33.333 1.39 0.00 0.00 2.93
56 57 8.929487 TGACACTAATAATTTTTGGGGAAGTTT 58.071 29.630 1.39 0.00 0.00 2.66
57 58 8.485578 TGACACTAATAATTTTTGGGGAAGTT 57.514 30.769 1.39 0.00 0.00 2.66
58 59 8.485578 TTGACACTAATAATTTTTGGGGAAGT 57.514 30.769 1.39 0.00 0.00 3.01
59 60 9.942850 ATTTGACACTAATAATTTTTGGGGAAG 57.057 29.630 1.39 0.00 0.00 3.46
60 61 9.936759 GATTTGACACTAATAATTTTTGGGGAA 57.063 29.630 1.39 0.00 0.00 3.97
61 62 8.536175 GGATTTGACACTAATAATTTTTGGGGA 58.464 33.333 1.39 0.00 0.00 4.81
62 63 8.317679 TGGATTTGACACTAATAATTTTTGGGG 58.682 33.333 0.00 0.00 0.00 4.96
63 64 9.369904 CTGGATTTGACACTAATAATTTTTGGG 57.630 33.333 0.00 0.00 0.00 4.12
70 71 9.178758 GGAAGTTCTGGATTTGACACTAATAAT 57.821 33.333 2.25 0.00 0.00 1.28
71 72 8.160765 TGGAAGTTCTGGATTTGACACTAATAA 58.839 33.333 2.25 0.00 0.00 1.40
72 73 7.685481 TGGAAGTTCTGGATTTGACACTAATA 58.315 34.615 2.25 0.00 0.00 0.98
73 74 6.542821 TGGAAGTTCTGGATTTGACACTAAT 58.457 36.000 2.25 0.00 0.00 1.73
74 75 5.935945 TGGAAGTTCTGGATTTGACACTAA 58.064 37.500 2.25 0.00 0.00 2.24
75 76 5.560722 TGGAAGTTCTGGATTTGACACTA 57.439 39.130 2.25 0.00 0.00 2.74
76 77 4.437682 TGGAAGTTCTGGATTTGACACT 57.562 40.909 2.25 0.00 0.00 3.55
77 78 5.712152 ATTGGAAGTTCTGGATTTGACAC 57.288 39.130 2.25 0.00 0.00 3.67
78 79 6.729690 AAATTGGAAGTTCTGGATTTGACA 57.270 33.333 2.25 0.00 0.00 3.58
127 142 6.431234 ACTCACATTAATTGTCTTCCAGAACC 59.569 38.462 0.00 0.00 36.00 3.62
208 223 4.162040 AGGATATGTCTTTCCTTGCAGG 57.838 45.455 0.00 0.00 39.36 4.85
254 271 7.181665 AGGGAGATAGCTCTTGATTAATGCATA 59.818 37.037 8.10 0.00 41.06 3.14
266 283 3.319689 GCGTCTTTAGGGAGATAGCTCTT 59.680 47.826 8.10 0.00 41.06 2.85
450 485 1.573108 TTCTTCTCGAGGGGATTGCT 58.427 50.000 13.56 0.00 0.00 3.91
451 486 2.010497 GTTTCTTCTCGAGGGGATTGC 58.990 52.381 13.56 1.75 0.00 3.56
452 487 3.334583 TGTTTCTTCTCGAGGGGATTG 57.665 47.619 13.56 0.00 0.00 2.67
453 488 3.328050 ACTTGTTTCTTCTCGAGGGGATT 59.672 43.478 13.56 0.00 0.00 3.01
454 489 2.907042 ACTTGTTTCTTCTCGAGGGGAT 59.093 45.455 13.56 0.00 0.00 3.85
455 490 2.299297 GACTTGTTTCTTCTCGAGGGGA 59.701 50.000 13.56 8.32 0.00 4.81
456 491 2.613223 GGACTTGTTTCTTCTCGAGGGG 60.613 54.545 13.56 5.91 0.00 4.79
457 492 2.613223 GGGACTTGTTTCTTCTCGAGGG 60.613 54.545 13.56 6.29 0.00 4.30
458 493 2.613223 GGGGACTTGTTTCTTCTCGAGG 60.613 54.545 13.56 0.00 0.00 4.63
470 505 1.415672 TTGGAAGAGCGGGGACTTGT 61.416 55.000 0.00 0.00 0.00 3.16
471 506 0.955919 GTTGGAAGAGCGGGGACTTG 60.956 60.000 0.00 0.00 0.00 3.16
473 508 2.593956 GGTTGGAAGAGCGGGGACT 61.594 63.158 0.00 0.00 0.00 3.85
474 509 2.046217 GGTTGGAAGAGCGGGGAC 60.046 66.667 0.00 0.00 0.00 4.46
475 510 3.702048 CGGTTGGAAGAGCGGGGA 61.702 66.667 0.00 0.00 36.92 4.81
477 512 4.697756 TGCGGTTGGAAGAGCGGG 62.698 66.667 0.00 0.00 40.59 6.13
478 513 2.668212 TTGCGGTTGGAAGAGCGG 60.668 61.111 0.00 0.00 40.59 5.52
480 515 1.896660 TGGTTGCGGTTGGAAGAGC 60.897 57.895 0.00 0.00 0.00 4.09
481 516 1.841663 CGTGGTTGCGGTTGGAAGAG 61.842 60.000 0.00 0.00 0.00 2.85
482 517 1.890041 CGTGGTTGCGGTTGGAAGA 60.890 57.895 0.00 0.00 0.00 2.87
483 518 1.841663 CTCGTGGTTGCGGTTGGAAG 61.842 60.000 0.00 0.00 0.00 3.46
484 519 1.890041 CTCGTGGTTGCGGTTGGAA 60.890 57.895 0.00 0.00 0.00 3.53
485 520 2.280524 CTCGTGGTTGCGGTTGGA 60.281 61.111 0.00 0.00 0.00 3.53
486 521 4.025401 GCTCGTGGTTGCGGTTGG 62.025 66.667 0.00 0.00 0.00 3.77
489 524 4.681978 GAGGCTCGTGGTTGCGGT 62.682 66.667 0.00 0.00 0.00 5.68
491 526 4.680237 TGGAGGCTCGTGGTTGCG 62.680 66.667 8.69 0.00 0.00 4.85
492 527 3.050275 GTGGAGGCTCGTGGTTGC 61.050 66.667 8.69 0.00 0.00 4.17
493 528 2.738521 CGTGGAGGCTCGTGGTTG 60.739 66.667 8.69 0.00 0.00 3.77
496 544 4.778415 CGTCGTGGAGGCTCGTGG 62.778 72.222 8.69 0.00 0.00 4.94
537 587 1.651240 CCTTAGCGACGAGGGAACGA 61.651 60.000 0.00 0.00 37.03 3.85
592 650 0.249955 TCCGCCCGTACCCTTTTAAG 59.750 55.000 0.00 0.00 0.00 1.85
657 715 1.611977 GGAAAACCCCGGAAACTGAAG 59.388 52.381 0.73 0.00 0.00 3.02
763 822 4.785453 CAGGCCTGACGGGAAGCC 62.785 72.222 29.88 0.00 46.13 4.35
786 845 1.376812 GTCGGGGCGGAAGTGAATT 60.377 57.895 0.00 0.00 0.00 2.17
830 889 2.441532 GGAGACGACCATCGGGGA 60.442 66.667 2.97 0.00 45.59 4.81
973 1032 4.101077 AGGAGGAGGAGCAGGGGG 62.101 72.222 0.00 0.00 0.00 5.40
975 1034 2.445654 GGAGGAGGAGGAGCAGGG 60.446 72.222 0.00 0.00 0.00 4.45
978 1037 1.522917 AAGGAGGAGGAGGAGGAGCA 61.523 60.000 0.00 0.00 0.00 4.26
979 1038 0.759060 GAAGGAGGAGGAGGAGGAGC 60.759 65.000 0.00 0.00 0.00 4.70
982 1041 0.267356 ATGGAAGGAGGAGGAGGAGG 59.733 60.000 0.00 0.00 0.00 4.30
983 1042 1.422531 CATGGAAGGAGGAGGAGGAG 58.577 60.000 0.00 0.00 0.00 3.69
984 1043 0.030705 CCATGGAAGGAGGAGGAGGA 60.031 60.000 5.56 0.00 0.00 3.71
985 1044 1.059006 CCCATGGAAGGAGGAGGAGG 61.059 65.000 15.22 0.00 0.00 4.30
986 1045 0.327000 ACCCATGGAAGGAGGAGGAG 60.327 60.000 15.22 0.00 0.00 3.69
987 1046 0.621571 CACCCATGGAAGGAGGAGGA 60.622 60.000 15.22 0.00 0.00 3.71
988 1047 0.621571 TCACCCATGGAAGGAGGAGG 60.622 60.000 15.22 0.00 0.00 4.30
1144 1203 2.659610 GCTGGAGCTGACGAACCT 59.340 61.111 0.00 0.00 38.21 3.50
1146 1205 2.049063 ACGCTGGAGCTGACGAAC 60.049 61.111 0.00 0.00 39.32 3.95
1323 1382 1.657804 AGGAGTTGGTTACCTGGGAG 58.342 55.000 2.07 0.00 32.39 4.30
1371 1430 1.462616 TGATGAAGCCCCAATTGTCG 58.537 50.000 4.43 0.00 0.00 4.35
1425 1484 0.456995 GGCAGTCGTTCTCGAGGAAG 60.457 60.000 13.56 6.43 46.96 3.46
1476 1535 3.319198 TCTTGGGTGCGGGACTCC 61.319 66.667 0.00 0.00 0.00 3.85
1498 1557 2.762535 ACCACGATCGAATTGGTCTT 57.237 45.000 24.34 0.41 39.57 3.01
1572 1631 2.656007 GTGAACGTCACGTCCGCA 60.656 61.111 1.67 0.00 39.99 5.69
1693 1752 5.795972 CTCCATGTCATCTATCTTGATGCT 58.204 41.667 0.00 0.00 42.44 3.79
1779 1838 1.909459 TAGCCGCAGCCTTTCCATCA 61.909 55.000 0.00 0.00 41.25 3.07
1849 1908 3.016031 TCAGCTTTCTTTCACACAGCAA 58.984 40.909 0.00 0.00 32.58 3.91
1863 1922 1.881973 TCAATTGCTTCGCTCAGCTTT 59.118 42.857 0.00 0.00 40.79 3.51
1875 1934 3.638160 ACACTGTTTCCACATCAATTGCT 59.362 39.130 0.00 0.00 30.39 3.91
2107 2166 4.471904 TCAGTCCATGATAAGGTGTCAC 57.528 45.455 0.00 0.00 31.12 3.67
2193 2252 5.689961 AGTGCAAATTTTAAAGGCTTACACG 59.310 36.000 0.00 0.00 0.00 4.49
2325 2384 9.504708 ACAAATAAATTGCAATTCCAAGATTCA 57.495 25.926 24.28 3.20 43.13 2.57
2413 2472 0.766674 TGTTAGACCAGCCAGGGTGT 60.767 55.000 17.61 5.71 42.53 4.16
2425 2484 9.069078 GTTTACAGTTTCCTTGTTTTGTTAGAC 57.931 33.333 0.00 0.00 0.00 2.59
2553 2619 1.876156 CCTGTGCCAGAACTTTCAGAC 59.124 52.381 4.00 0.00 32.44 3.51
2554 2620 1.768275 TCCTGTGCCAGAACTTTCAGA 59.232 47.619 4.00 0.00 32.44 3.27
2568 2634 1.688197 ACAATGGGCAAAACTCCTGTG 59.312 47.619 0.00 0.00 0.00 3.66
2611 2677 0.389426 GCCTTGCACAATTCCTGCAG 60.389 55.000 6.78 6.78 45.21 4.41
2738 2806 6.693545 TGTTTTTGCCTTCGTATGTGTAAAAG 59.306 34.615 0.00 0.00 0.00 2.27
2802 2873 6.801862 GCAGTTGGTATGTATTTGTTCAGTTC 59.198 38.462 0.00 0.00 0.00 3.01
2866 2938 6.017523 TGCATACCAATGATTACCATACAACG 60.018 38.462 0.00 0.00 34.84 4.10
2886 2958 7.438160 CGTTTCTGTTCAAGAGGTATATGCATA 59.562 37.037 9.27 9.27 35.91 3.14
2987 3059 8.698973 TTTCACTTGACAGGGAAACATTTATA 57.301 30.769 0.00 0.00 45.86 0.98
3040 3112 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3041 3113 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3042 3114 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3043 3115 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3044 3116 6.649557 ACAAAGACTTACATTTAGGAACGGAG 59.350 38.462 0.00 0.00 0.00 4.63
3045 3117 6.527423 ACAAAGACTTACATTTAGGAACGGA 58.473 36.000 0.00 0.00 0.00 4.69
3046 3118 6.796705 ACAAAGACTTACATTTAGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44
3047 3119 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95
3048 3120 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
3054 3126 9.220767 GTGGAATCTCTACAAAGACTTACATTT 57.779 33.333 0.00 0.00 0.00 2.32
3055 3127 8.598041 AGTGGAATCTCTACAAAGACTTACATT 58.402 33.333 0.00 0.00 29.47 2.71
3056 3128 8.140112 AGTGGAATCTCTACAAAGACTTACAT 57.860 34.615 0.00 0.00 29.47 2.29
3057 3129 7.540474 AGTGGAATCTCTACAAAGACTTACA 57.460 36.000 0.00 0.00 29.47 2.41
3058 3130 9.522804 CATAGTGGAATCTCTACAAAGACTTAC 57.477 37.037 0.00 0.00 29.47 2.34
3059 3131 9.475620 TCATAGTGGAATCTCTACAAAGACTTA 57.524 33.333 0.00 0.00 29.47 2.24
3060 3132 8.367660 TCATAGTGGAATCTCTACAAAGACTT 57.632 34.615 0.00 0.00 29.47 3.01
3061 3133 7.962995 TCATAGTGGAATCTCTACAAAGACT 57.037 36.000 0.00 0.00 29.47 3.24
3062 3134 7.492994 GGTTCATAGTGGAATCTCTACAAAGAC 59.507 40.741 0.00 0.00 29.47 3.01
3063 3135 7.180229 TGGTTCATAGTGGAATCTCTACAAAGA 59.820 37.037 0.00 0.00 29.47 2.52
3064 3136 7.278868 GTGGTTCATAGTGGAATCTCTACAAAG 59.721 40.741 0.00 0.00 29.47 2.77
3065 3137 7.103641 GTGGTTCATAGTGGAATCTCTACAAA 58.896 38.462 0.00 0.00 29.47 2.83
3066 3138 6.212589 TGTGGTTCATAGTGGAATCTCTACAA 59.787 38.462 0.00 0.00 29.47 2.41
3067 3139 5.719563 TGTGGTTCATAGTGGAATCTCTACA 59.280 40.000 0.00 0.00 29.47 2.74
3068 3140 6.222038 TGTGGTTCATAGTGGAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
3069 3141 7.952671 GTATGTGGTTCATAGTGGAATCTCTA 58.047 38.462 0.00 0.00 39.36 2.43
3070 3142 5.965033 ATGTGGTTCATAGTGGAATCTCT 57.035 39.130 0.00 0.00 34.67 3.10


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

AutoCloner maintained by Alex Coulton.