Multiple sequence alignment - TraesCS1A01G219800

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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 TraesCS1A01G219800 chr1A 100.000 5215 0 0 1 5215 388838136 388832922 0.000000e+00 9631.0
1 TraesCS1A01G219800 chr1A 89.516 124 10 3 3125 3247 52458340 52458219 2.510000e-33 154.0
2 TraesCS1A01G219800 chr1A 90.090 111 8 3 3122 3231 235661274 235661166 1.960000e-29 141.0
3 TraesCS1A01G219800 chr1A 77.733 247 32 9 4682 4906 510700452 510700697 4.240000e-26 130.0
4 TraesCS1A01G219800 chr1B 95.467 2978 104 18 178 3139 418809375 418806413 0.000000e+00 4723.0
5 TraesCS1A01G219800 chr1B 96.347 1177 30 4 3224 4399 418806411 418805247 0.000000e+00 1923.0
6 TraesCS1A01G219800 chr1B 92.773 512 33 3 4704 5215 418804703 418804196 0.000000e+00 737.0
7 TraesCS1A01G219800 chr1B 91.456 316 8 4 4398 4702 418805071 418804764 2.900000e-112 416.0
8 TraesCS1A01G219800 chr1B 92.818 181 13 0 17 197 418809670 418809490 4.000000e-66 263.0
9 TraesCS1A01G219800 chr1B 90.000 70 4 2 4691 4760 341336792 341336726 2.590000e-13 87.9
10 TraesCS1A01G219800 chr1B 90.741 54 5 0 2198 2251 665275920 665275973 7.240000e-09 73.1
11 TraesCS1A01G219800 chr1D 93.821 3156 152 20 1 3140 309077862 309074734 0.000000e+00 4708.0
12 TraesCS1A01G219800 chr1D 86.185 2034 160 50 3222 5215 309074735 309072783 0.000000e+00 2087.0
13 TraesCS1A01G219800 chr2A 83.465 254 38 3 4963 5215 757962637 757962887 3.140000e-57 233.0
14 TraesCS1A01G219800 chr2A 94.737 95 5 0 3132 3226 714302910 714303004 1.170000e-31 148.0
15 TraesCS1A01G219800 chr2A 76.190 273 48 15 4630 4899 746727636 746727378 1.520000e-25 128.0
16 TraesCS1A01G219800 chr2A 96.774 31 1 0 4877 4907 753250788 753250758 9.000000e-03 52.8
17 TraesCS1A01G219800 chr7D 82.869 251 35 7 4971 5215 461395690 461395442 8.790000e-53 219.0
18 TraesCS1A01G219800 chr3B 76.399 411 74 15 1856 2251 501420263 501420665 3.180000e-47 200.0
19 TraesCS1A01G219800 chr5A 85.052 194 27 2 5023 5215 11777974 11777782 4.120000e-46 196.0
20 TraesCS1A01G219800 chr5A 93.000 100 5 2 3126 3224 112221130 112221032 1.510000e-30 145.0
21 TraesCS1A01G219800 chr5A 82.550 149 20 4 4763 4906 672508141 672508288 5.480000e-25 126.0
22 TraesCS1A01G219800 chr5A 75.926 216 39 9 5013 5215 535646214 535646429 1.200000e-16 99.0
23 TraesCS1A01G219800 chr2D 79.181 293 38 16 4622 4906 172394461 172394184 1.150000e-41 182.0
24 TraesCS1A01G219800 chr2D 95.876 97 3 1 3129 3224 108886677 108886581 6.990000e-34 156.0
25 TraesCS1A01G219800 chr2D 93.939 99 4 1 3133 3229 564440787 564440689 1.170000e-31 148.0
26 TraesCS1A01G219800 chr2D 91.346 104 7 2 3131 3234 436111431 436111330 1.960000e-29 141.0
27 TraesCS1A01G219800 chr2D 91.803 61 5 0 4702 4762 307577146 307577086 9.300000e-13 86.1
28 TraesCS1A01G219800 chr5B 94.792 96 5 0 3135 3230 504177847 504177752 3.250000e-32 150.0
29 TraesCS1A01G219800 chr4B 94.792 96 5 0 3136 3231 303647930 303648025 3.250000e-32 150.0
30 TraesCS1A01G219800 chr4B 83.108 148 21 2 4763 4906 631072533 631072386 1.180000e-26 132.0
31 TraesCS1A01G219800 chr4D 83.108 148 21 2 4763 4906 492813348 492813495 1.180000e-26 132.0
32 TraesCS1A01G219800 chrUn 81.295 139 24 2 4769 4906 32095371 32095234 1.540000e-20 111.0
33 TraesCS1A01G219800 chr3A 79.856 139 26 2 4769 4906 57085229 57085366 3.320000e-17 100.0
34 TraesCS1A01G219800 chr7A 86.585 82 9 1 4682 4761 368949290 368949371 7.190000e-14 89.8
35 TraesCS1A01G219800 chr4A 86.585 82 9 2 4682 4761 16502041 16502122 7.190000e-14 89.8


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 TraesCS1A01G219800 chr1A 388832922 388838136 5214 True 9631.0 9631 100.0000 1 5215 1 chr1A.!!$R3 5214
1 TraesCS1A01G219800 chr1B 418804196 418809670 5474 True 1612.4 4723 93.7722 17 5215 5 chr1B.!!$R2 5198
2 TraesCS1A01G219800 chr1D 309072783 309077862 5079 True 3397.5 4708 90.0030 1 5215 2 chr1D.!!$R1 5214

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
622 763 0.820074 CGAGAGGGAGTCGCACCTAT 60.820 60.0 10.15 0.0 37.18 2.57 F
1796 1941 0.106149 AAAAAGAGGTCCAGCGTCGT 59.894 50.0 0.00 0.0 37.10 4.34 F
3154 3311 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2157 1.349026 AGGCGAATCCCATCGATGATT 59.651 47.619 26.86 18.2 45.48 2.57 R
3462 3635 0.877071 AGCACGGATGTTTGAAGCAG 59.123 50.000 0.00 0.0 0.00 4.24 R
4960 5424 0.111253 ACAGACCAAAGGAAGCCTGG 59.889 55.000 0.00 0.0 32.13 4.45 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
87 88 6.245408 TCCAAAGACAAATTACTGCATACCT 58.755 36.000 0.00 0.00 0.00 3.08
89 90 7.885922 TCCAAAGACAAATTACTGCATACCTAA 59.114 33.333 0.00 0.00 0.00 2.69
97 98 9.507280 CAAATTACTGCATACCTAATGACAAAG 57.493 33.333 0.00 0.00 37.86 2.77
108 109 4.278170 CCTAATGACAAAGTGGCAACTGAA 59.722 41.667 0.00 0.00 39.86 3.02
111 112 4.734398 TGACAAAGTGGCAACTGAAAAT 57.266 36.364 0.00 0.00 36.51 1.82
166 167 3.486584 GCTCGAAGAAAAGCAATCACAG 58.513 45.455 0.00 0.00 38.42 3.66
301 436 5.721960 ACCAGGTCTACAGAAAGTATCACAT 59.278 40.000 0.00 0.00 30.93 3.21
622 763 0.820074 CGAGAGGGAGTCGCACCTAT 60.820 60.000 10.15 0.00 37.18 2.57
625 766 1.214673 AGAGGGAGTCGCACCTATACA 59.785 52.381 10.15 0.00 37.18 2.29
763 904 2.735762 GCTTGACCGAGACATGACTACC 60.736 54.545 0.00 0.00 0.00 3.18
834 978 1.603455 CAATCGGTTGTGGGCCTGT 60.603 57.895 4.53 0.00 0.00 4.00
856 1000 6.354130 TGTGGCCCAATATAGTCTTTAACTC 58.646 40.000 0.00 0.00 39.55 3.01
882 1026 1.779061 ATCCTGGTTGGGCTGACGTT 61.779 55.000 0.00 0.00 36.20 3.99
883 1027 2.260869 CCTGGTTGGGCTGACGTTG 61.261 63.158 0.00 0.00 0.00 4.10
884 1028 1.525995 CTGGTTGGGCTGACGTTGT 60.526 57.895 0.00 0.00 0.00 3.32
892 1036 1.275657 GCTGACGTTGTTGGTCACG 59.724 57.895 0.00 0.00 39.36 4.35
925 1069 1.448540 CCGCTCTGTCATGTGACCC 60.449 63.158 10.40 0.00 44.15 4.46
1220 1364 2.564771 GCAGCAGGCAGTGTCAATATA 58.435 47.619 0.00 0.00 43.97 0.86
1221 1365 2.289002 GCAGCAGGCAGTGTCAATATAC 59.711 50.000 0.00 0.00 43.97 1.47
1225 1369 3.733337 CAGGCAGTGTCAATATACCTCC 58.267 50.000 0.00 0.00 0.00 4.30
1235 1379 2.016905 ATATACCTCCCTTGCTCGCT 57.983 50.000 0.00 0.00 0.00 4.93
1241 1385 1.603172 CCTCCCTTGCTCGCTATAACG 60.603 57.143 0.00 0.00 0.00 3.18
1255 1399 3.995048 GCTATAACGCCCTAGACAATTCC 59.005 47.826 0.00 0.00 0.00 3.01
1261 1405 2.210961 GCCCTAGACAATTCCGCTTAC 58.789 52.381 0.00 0.00 0.00 2.34
1263 1407 3.069158 GCCCTAGACAATTCCGCTTACTA 59.931 47.826 0.00 0.00 0.00 1.82
1264 1408 4.262506 GCCCTAGACAATTCCGCTTACTAT 60.263 45.833 0.00 0.00 0.00 2.12
1268 1412 7.282450 CCCTAGACAATTCCGCTTACTATTTTT 59.718 37.037 0.00 0.00 0.00 1.94
1269 1413 8.122952 CCTAGACAATTCCGCTTACTATTTTTG 58.877 37.037 0.00 0.00 0.00 2.44
1271 1415 5.961272 ACAATTCCGCTTACTATTTTTGGG 58.039 37.500 0.00 0.00 0.00 4.12
1272 1416 5.479027 ACAATTCCGCTTACTATTTTTGGGT 59.521 36.000 0.00 0.00 0.00 4.51
1273 1417 5.576447 ATTCCGCTTACTATTTTTGGGTG 57.424 39.130 0.00 0.00 0.00 4.61
1274 1418 4.023726 TCCGCTTACTATTTTTGGGTGT 57.976 40.909 0.00 0.00 0.00 4.16
1276 1420 5.558818 TCCGCTTACTATTTTTGGGTGTTA 58.441 37.500 0.00 0.00 0.00 2.41
1277 1421 6.181908 TCCGCTTACTATTTTTGGGTGTTAT 58.818 36.000 0.00 0.00 0.00 1.89
1278 1422 6.660094 TCCGCTTACTATTTTTGGGTGTTATT 59.340 34.615 0.00 0.00 0.00 1.40
1279 1423 7.828223 TCCGCTTACTATTTTTGGGTGTTATTA 59.172 33.333 0.00 0.00 0.00 0.98
1280 1424 8.460428 CCGCTTACTATTTTTGGGTGTTATTAA 58.540 33.333 0.00 0.00 0.00 1.40
1424 1569 9.787532 TTATATTGCACTTTCAAGATTTACTGC 57.212 29.630 0.00 0.00 31.29 4.40
1796 1941 0.106149 AAAAAGAGGTCCAGCGTCGT 59.894 50.000 0.00 0.00 37.10 4.34
1857 2005 6.560253 TGCATCCTCACTTTAGAGTTTTTC 57.440 37.500 0.00 0.00 32.54 2.29
1958 2106 2.200337 GGCGGTTGGCAGAAAACCT 61.200 57.895 4.68 0.00 44.16 3.50
2009 2157 2.092049 AGATGCCCTGAATCATGCTTCA 60.092 45.455 11.28 11.28 34.14 3.02
2641 2790 2.884012 TGACATAAGTGTTGGCACCTTG 59.116 45.455 0.00 0.00 46.35 3.61
2698 2847 4.396166 GCATGCAGGTAAACAGACACTTAT 59.604 41.667 14.21 0.00 0.00 1.73
2741 2890 2.050691 CACACTTTTGTACATTGCGGC 58.949 47.619 0.00 0.00 33.30 6.53
2755 2904 4.457603 ACATTGCGGCACTGATTTTAGTAA 59.542 37.500 24.59 0.00 0.00 2.24
2803 2952 7.405292 AGTGATTTTCAAGGTTCTGGATCATA 58.595 34.615 0.00 0.00 0.00 2.15
2864 3013 6.270463 TGCCCCATGCTTATAATTCAATGAAT 59.730 34.615 2.07 2.07 42.00 2.57
2914 3071 8.989131 ACTGTATATTTATGGTACTGGACACTT 58.011 33.333 0.00 0.00 0.00 3.16
3140 3297 9.609346 AGGTAATATTCACAACATACCAACTAC 57.391 33.333 0.00 0.00 36.18 2.73
3141 3298 9.609346 GGTAATATTCACAACATACCAACTACT 57.391 33.333 0.00 0.00 34.35 2.57
3143 3300 8.732746 AATATTCACAACATACCAACTACTCC 57.267 34.615 0.00 0.00 0.00 3.85
3144 3301 4.546829 TCACAACATACCAACTACTCCC 57.453 45.455 0.00 0.00 0.00 4.30
3145 3302 4.164981 TCACAACATACCAACTACTCCCT 58.835 43.478 0.00 0.00 0.00 4.20
3146 3303 4.222145 TCACAACATACCAACTACTCCCTC 59.778 45.833 0.00 0.00 0.00 4.30
3147 3304 3.518303 ACAACATACCAACTACTCCCTCC 59.482 47.826 0.00 0.00 0.00 4.30
3148 3305 2.385803 ACATACCAACTACTCCCTCCG 58.614 52.381 0.00 0.00 0.00 4.63
3149 3306 2.292061 ACATACCAACTACTCCCTCCGT 60.292 50.000 0.00 0.00 0.00 4.69
3150 3307 2.134789 TACCAACTACTCCCTCCGTC 57.865 55.000 0.00 0.00 0.00 4.79
3151 3308 0.614134 ACCAACTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
3152 3309 1.328430 CCAACTACTCCCTCCGTCCC 61.328 65.000 0.00 0.00 0.00 4.46
3153 3310 0.613853 CAACTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
3154 3311 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3155 3312 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3156 3313 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3157 3314 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3158 3315 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3159 3316 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3160 3317 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3161 3318 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3162 3319 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3163 3320 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3164 3321 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
3165 3322 6.269194 TCCCTCCGTCCCATAATATAAGAAT 58.731 40.000 0.00 0.00 0.00 2.40
3166 3323 6.156256 TCCCTCCGTCCCATAATATAAGAATG 59.844 42.308 0.00 0.00 0.00 2.67
3167 3324 6.070194 CCCTCCGTCCCATAATATAAGAATGT 60.070 42.308 0.00 0.00 0.00 2.71
3168 3325 7.394816 CCTCCGTCCCATAATATAAGAATGTT 58.605 38.462 0.00 0.00 0.00 2.71
3169 3326 7.883311 CCTCCGTCCCATAATATAAGAATGTTT 59.117 37.037 0.00 0.00 0.00 2.83
3170 3327 9.284968 CTCCGTCCCATAATATAAGAATGTTTT 57.715 33.333 0.00 0.00 0.00 2.43
3171 3328 9.635404 TCCGTCCCATAATATAAGAATGTTTTT 57.365 29.630 0.00 0.00 0.00 1.94
3172 3329 9.677567 CCGTCCCATAATATAAGAATGTTTTTG 57.322 33.333 0.00 0.00 0.00 2.44
3185 3342 8.732746 AAGAATGTTTTTGACACTAGTGTAGT 57.267 30.769 27.98 10.32 45.05 2.73
3198 3355 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
3199 3356 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
3200 3357 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
3201 3358 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
3202 3359 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
3203 3360 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
3204 3361 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
3210 3367 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3211 3368 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3212 3369 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3213 3370 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3214 3371 8.605746 CAAAAACGTTCTTATATTATGGGACGA 58.394 33.333 0.00 0.00 0.00 4.20
3215 3372 8.721019 AAAACGTTCTTATATTATGGGACGAA 57.279 30.769 0.00 0.00 0.00 3.85
3216 3373 7.941795 AACGTTCTTATATTATGGGACGAAG 57.058 36.000 14.76 0.00 0.00 3.79
3217 3374 6.453092 ACGTTCTTATATTATGGGACGAAGG 58.547 40.000 14.76 0.00 0.00 3.46
3218 3375 5.867716 CGTTCTTATATTATGGGACGAAGGG 59.132 44.000 0.00 0.00 0.00 3.95
3219 3376 6.294899 CGTTCTTATATTATGGGACGAAGGGA 60.295 42.308 0.00 0.00 0.00 4.20
3220 3377 6.852420 TCTTATATTATGGGACGAAGGGAG 57.148 41.667 0.00 0.00 0.00 4.30
3221 3378 6.320518 TCTTATATTATGGGACGAAGGGAGT 58.679 40.000 0.00 0.00 0.00 3.85
3222 3379 7.472741 TCTTATATTATGGGACGAAGGGAGTA 58.527 38.462 0.00 0.00 0.00 2.59
3406 3579 2.742589 GGGTACAAACACTTCAGCTAGC 59.257 50.000 6.62 6.62 0.00 3.42
3472 3645 6.203723 AGAGAAACTATCACACTGCTTCAAAC 59.796 38.462 0.00 0.00 0.00 2.93
3489 3662 3.003275 TCAAACATCCGTGCTGTTTTCTC 59.997 43.478 0.00 0.00 42.58 2.87
3493 3666 3.569701 ACATCCGTGCTGTTTTCTCATTT 59.430 39.130 0.00 0.00 0.00 2.32
3536 3709 0.541863 AAGGAACGATGGCGGAGATT 59.458 50.000 0.00 0.00 43.17 2.40
3634 3807 2.875094 AGGAAGTGAAGAAGCAGCAT 57.125 45.000 0.00 0.00 0.00 3.79
3811 3987 2.371259 GCAGGTCCCTCCTCCCTTC 61.371 68.421 0.00 0.00 46.24 3.46
3813 3989 0.980231 CAGGTCCCTCCTCCCTTCTG 60.980 65.000 0.00 0.00 46.24 3.02
3858 4034 6.204688 GTGTCTTGTCATGAACTTCACCAATA 59.795 38.462 0.00 0.00 0.00 1.90
3900 4076 4.748701 TCCAAGTAACTGGACTAGGACTT 58.251 43.478 0.00 3.47 40.71 3.01
3902 4078 5.605488 TCCAAGTAACTGGACTAGGACTTTT 59.395 40.000 5.87 0.00 40.71 2.27
3988 4166 3.949842 TCTATGGATTCCTGCTCGATG 57.050 47.619 3.95 0.00 0.00 3.84
4000 4178 4.036852 TCCTGCTCGATGTTAGTACAGATG 59.963 45.833 0.00 0.00 37.77 2.90
4045 4223 3.926616 ACTGTCGACCAAGATTAACTGG 58.073 45.455 14.12 0.00 0.00 4.00
4121 4299 0.247736 ACATCAAGAGGCTGGTCGAC 59.752 55.000 7.13 7.13 0.00 4.20
4455 4810 1.155042 GAGCTTGAGCCTGTTCTGTG 58.845 55.000 0.00 0.00 43.38 3.66
4460 4815 0.250038 TGAGCCTGTTCTGTGACTGC 60.250 55.000 0.00 0.00 0.00 4.40
4514 4869 3.501062 GCTACCAAACTGTCTGGTAAACC 59.499 47.826 13.63 2.81 46.34 3.27
4515 4870 2.567985 ACCAAACTGTCTGGTAAACCG 58.432 47.619 3.45 0.00 45.58 4.44
4516 4871 2.092807 ACCAAACTGTCTGGTAAACCGT 60.093 45.455 3.45 0.00 45.58 4.83
4518 4873 4.128643 CCAAACTGTCTGGTAAACCGTAA 58.871 43.478 0.00 0.00 39.43 3.18
4519 4874 4.575645 CCAAACTGTCTGGTAAACCGTAAA 59.424 41.667 0.00 0.00 39.43 2.01
4521 4876 4.405116 ACTGTCTGGTAAACCGTAAACA 57.595 40.909 0.00 0.00 39.43 2.83
4522 4877 4.768583 ACTGTCTGGTAAACCGTAAACAA 58.231 39.130 0.00 0.00 39.43 2.83
4523 4878 4.571984 ACTGTCTGGTAAACCGTAAACAAC 59.428 41.667 0.00 0.00 39.43 3.32
4533 4888 1.749153 CGTAAACAACGGCCTGTTTG 58.251 50.000 25.63 16.97 46.42 2.93
4597 4964 0.257328 TGGCCTGTTTGGAACACAGA 59.743 50.000 3.32 0.00 43.90 3.41
4626 5001 2.235891 GGGAAATTCCACTCGTTTGGT 58.764 47.619 14.68 0.00 38.64 3.67
4628 5003 3.305131 GGGAAATTCCACTCGTTTGGTTC 60.305 47.826 14.68 2.86 38.64 3.62
4633 5011 5.818136 ATTCCACTCGTTTGGTTCATATG 57.182 39.130 0.00 0.00 37.93 1.78
4696 5160 9.218525 TCTCAATTTCTATAGGGAAAGAGATGT 57.781 33.333 0.00 0.00 38.38 3.06
4697 5161 9.844257 CTCAATTTCTATAGGGAAAGAGATGTT 57.156 33.333 0.00 0.00 38.38 2.71
4703 5167 9.716556 TTCTATAGGGAAAGAGATGTTACTTCT 57.283 33.333 0.16 0.16 0.00 2.85
4704 5168 9.357161 TCTATAGGGAAAGAGATGTTACTTCTC 57.643 37.037 17.23 17.23 39.96 2.87
4705 5169 7.979786 ATAGGGAAAGAGATGTTACTTCTCA 57.020 36.000 23.87 7.54 41.72 3.27
4706 5170 6.688073 AGGGAAAGAGATGTTACTTCTCAA 57.312 37.500 23.87 0.00 41.72 3.02
4707 5171 7.264294 AGGGAAAGAGATGTTACTTCTCAAT 57.736 36.000 23.87 14.88 41.72 2.57
4708 5172 7.694093 AGGGAAAGAGATGTTACTTCTCAATT 58.306 34.615 23.87 18.84 41.72 2.32
4709 5173 7.826744 AGGGAAAGAGATGTTACTTCTCAATTC 59.173 37.037 23.87 23.38 41.72 2.17
4710 5174 7.066404 GGGAAAGAGATGTTACTTCTCAATTCC 59.934 40.741 30.72 30.72 45.76 3.01
4711 5175 7.826744 GGAAAGAGATGTTACTTCTCAATTCCT 59.173 37.037 30.94 14.16 44.66 3.36
4712 5176 9.877178 GAAAGAGATGTTACTTCTCAATTCCTA 57.123 33.333 23.87 0.00 41.72 2.94
4741 5205 8.715191 AGAAAGAGATGTCACTTGATTCATAC 57.285 34.615 0.00 0.00 0.00 2.39
4899 5363 9.635404 TCTTACAAAATTCCTCTAAACCAAAGA 57.365 29.630 0.00 0.00 0.00 2.52
4950 5414 6.563222 TTGTAAAAACACCGGAATAGGAAG 57.437 37.500 9.46 0.00 34.73 3.46
4960 5424 5.696724 CACCGGAATAGGAAGAATACATGAC 59.303 44.000 9.46 0.00 34.73 3.06
4961 5425 5.221661 ACCGGAATAGGAAGAATACATGACC 60.222 44.000 9.46 0.00 34.73 4.02
4966 5430 3.118531 AGGAAGAATACATGACCAGGCT 58.881 45.455 0.00 0.00 0.00 4.58
5052 5516 3.167485 TCGGAGCCCTTTACTTTGTAGA 58.833 45.455 0.00 0.00 0.00 2.59
5061 5525 8.113462 AGCCCTTTACTTTGTAGAAATGGATTA 58.887 33.333 0.00 0.00 0.00 1.75
5177 5642 5.354767 TCGAATGACATCTCTTTCTCCATG 58.645 41.667 0.00 0.00 31.31 3.66
5178 5643 5.127682 TCGAATGACATCTCTTTCTCCATGA 59.872 40.000 0.00 0.00 31.31 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 5.843673 TTTCAGTTGCCACTTTGTCATTA 57.156 34.783 0.00 0.00 0.00 1.90
89 90 4.734398 TTTTCAGTTGCCACTTTGTCAT 57.266 36.364 0.00 0.00 0.00 3.06
97 98 5.880054 TCTTAGCTATTTTCAGTTGCCAC 57.120 39.130 0.00 0.00 0.00 5.01
111 112 7.805163 TGGGATTTGAGAATGATTCTTAGCTA 58.195 34.615 9.35 0.00 40.87 3.32
166 167 7.337942 ACATTGATGGATTCCTGTCTTTTCTAC 59.662 37.037 3.95 0.00 0.00 2.59
474 613 0.104120 TGCCGGATCCGTCTGTTATG 59.896 55.000 31.22 15.10 37.81 1.90
479 618 1.800586 CAATTATGCCGGATCCGTCTG 59.199 52.381 31.22 18.01 37.81 3.51
497 636 1.324383 TCTGCTACGTCCTGTCACAA 58.676 50.000 0.00 0.00 0.00 3.33
834 978 5.454187 CCGAGTTAAAGACTATATTGGGCCA 60.454 44.000 0.00 0.00 39.19 5.36
856 1000 4.856801 CCAACCAGGATCGGCCCG 62.857 72.222 0.00 0.00 41.22 6.13
1211 1355 3.069586 CGAGCAAGGGAGGTATATTGACA 59.930 47.826 0.00 0.00 0.00 3.58
1220 1364 1.413077 GTTATAGCGAGCAAGGGAGGT 59.587 52.381 0.00 0.00 0.00 3.85
1221 1365 1.603172 CGTTATAGCGAGCAAGGGAGG 60.603 57.143 2.40 0.00 0.00 4.30
1225 1369 1.222115 GGGCGTTATAGCGAGCAAGG 61.222 60.000 13.56 0.00 38.18 3.61
1235 1379 3.553508 GCGGAATTGTCTAGGGCGTTATA 60.554 47.826 0.00 0.00 0.00 0.98
1241 1385 2.158943 AGTAAGCGGAATTGTCTAGGGC 60.159 50.000 0.00 0.00 0.00 5.19
1276 1420 9.745018 ACAGCAAGGCATCAAGTATATATTAAT 57.255 29.630 0.00 0.00 0.00 1.40
1277 1421 9.002600 CACAGCAAGGCATCAAGTATATATTAA 57.997 33.333 0.00 0.00 0.00 1.40
1278 1422 8.156820 ACACAGCAAGGCATCAAGTATATATTA 58.843 33.333 0.00 0.00 0.00 0.98
1279 1423 7.000472 ACACAGCAAGGCATCAAGTATATATT 59.000 34.615 0.00 0.00 0.00 1.28
1280 1424 6.429078 CACACAGCAAGGCATCAAGTATATAT 59.571 38.462 0.00 0.00 0.00 0.86
1281 1425 5.759763 CACACAGCAAGGCATCAAGTATATA 59.240 40.000 0.00 0.00 0.00 0.86
1282 1426 4.577693 CACACAGCAAGGCATCAAGTATAT 59.422 41.667 0.00 0.00 0.00 0.86
1283 1427 3.940852 CACACAGCAAGGCATCAAGTATA 59.059 43.478 0.00 0.00 0.00 1.47
1284 1428 2.751259 CACACAGCAAGGCATCAAGTAT 59.249 45.455 0.00 0.00 0.00 2.12
1285 1429 2.153645 CACACAGCAAGGCATCAAGTA 58.846 47.619 0.00 0.00 0.00 2.24
1286 1430 0.956633 CACACAGCAAGGCATCAAGT 59.043 50.000 0.00 0.00 0.00 3.16
1291 1435 0.179009 ACAGTCACACAGCAAGGCAT 60.179 50.000 0.00 0.00 0.00 4.40
1424 1569 3.193263 CAAGCCATGTAGTGAGCACTAG 58.807 50.000 10.42 1.20 43.84 2.57
1611 1756 6.097981 TCGATTCAGAGTACTCTACAGTCCTA 59.902 42.308 24.75 8.14 37.98 2.94
1857 2005 2.559440 GCAGAGAAGGCAATCCTGTAG 58.441 52.381 0.00 0.00 43.40 2.74
1958 2106 1.806542 GCAATTCTCTCGTCCTTTGCA 59.193 47.619 0.00 0.00 39.30 4.08
2009 2157 1.349026 AGGCGAATCCCATCGATGATT 59.651 47.619 26.86 18.20 45.48 2.57
2335 2484 3.819368 TCTGAATTTGGTGCTCTGACAA 58.181 40.909 0.00 0.00 0.00 3.18
2698 2847 4.808895 GTGCATTCATACGACAACCTGATA 59.191 41.667 0.00 0.00 0.00 2.15
2773 2922 7.885297 TCCAGAACCTTGAAAATCACTTTATG 58.115 34.615 0.00 0.00 0.00 1.90
2914 3071 3.386078 GGAGTGCTGATATTCCAGAGTCA 59.614 47.826 0.00 0.00 36.29 3.41
3008 3165 1.341852 TGCTGCTCAACACATTGCAAT 59.658 42.857 5.99 5.99 35.63 3.56
3140 3297 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3141 3298 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
3142 3299 6.070194 ACATTCTTATATTATGGGACGGAGGG 60.070 42.308 0.00 0.00 0.00 4.30
3143 3300 6.947464 ACATTCTTATATTATGGGACGGAGG 58.053 40.000 0.00 0.00 0.00 4.30
3144 3301 8.848474 AAACATTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
3145 3302 9.635404 AAAAACATTCTTATATTATGGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
3146 3303 9.677567 CAAAAACATTCTTATATTATGGGACGG 57.322 33.333 0.00 0.00 0.00 4.79
3159 3316 9.826574 ACTACACTAGTGTCAAAAACATTCTTA 57.173 29.630 31.11 8.36 43.74 2.10
3160 3317 8.732746 ACTACACTAGTGTCAAAAACATTCTT 57.267 30.769 31.11 4.99 43.74 2.52
3175 3332 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
3176 3333 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
3177 3334 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
3178 3335 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
3184 3341 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3185 3342 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3186 3343 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3187 3344 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3188 3345 8.605746 TCGTCCCATAATATAAGAACGTTTTTG 58.394 33.333 13.87 0.00 0.00 2.44
3189 3346 8.721019 TCGTCCCATAATATAAGAACGTTTTT 57.279 30.769 9.22 9.22 0.00 1.94
3190 3347 8.721019 TTCGTCCCATAATATAAGAACGTTTT 57.279 30.769 0.46 0.00 0.00 2.43
3191 3348 7.440255 CCTTCGTCCCATAATATAAGAACGTTT 59.560 37.037 0.46 0.00 0.00 3.60
3192 3349 6.927381 CCTTCGTCCCATAATATAAGAACGTT 59.073 38.462 0.00 0.00 0.00 3.99
3193 3350 6.453092 CCTTCGTCCCATAATATAAGAACGT 58.547 40.000 0.00 0.00 0.00 3.99
3194 3351 5.867716 CCCTTCGTCCCATAATATAAGAACG 59.132 44.000 0.00 0.00 0.00 3.95
3195 3352 7.001099 TCCCTTCGTCCCATAATATAAGAAC 57.999 40.000 0.00 0.00 0.00 3.01
3196 3353 6.785963 ACTCCCTTCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
3197 3354 6.320518 ACTCCCTTCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
3198 3355 6.607004 ACTCCCTTCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
3199 3356 7.676893 ACATACTCCCTTCGTCCCATAATATAA 59.323 37.037 0.00 0.00 0.00 0.98
3200 3357 7.186972 ACATACTCCCTTCGTCCCATAATATA 58.813 38.462 0.00 0.00 0.00 0.86
3201 3358 6.023603 ACATACTCCCTTCGTCCCATAATAT 58.976 40.000 0.00 0.00 0.00 1.28
3202 3359 5.399991 ACATACTCCCTTCGTCCCATAATA 58.600 41.667 0.00 0.00 0.00 0.98
3203 3360 4.232091 ACATACTCCCTTCGTCCCATAAT 58.768 43.478 0.00 0.00 0.00 1.28
3204 3361 3.640029 GACATACTCCCTTCGTCCCATAA 59.360 47.826 0.00 0.00 0.00 1.90
3205 3362 3.228453 GACATACTCCCTTCGTCCCATA 58.772 50.000 0.00 0.00 0.00 2.74
3206 3363 2.040178 GACATACTCCCTTCGTCCCAT 58.960 52.381 0.00 0.00 0.00 4.00
3207 3364 1.272816 TGACATACTCCCTTCGTCCCA 60.273 52.381 0.00 0.00 0.00 4.37
3208 3365 1.481871 TGACATACTCCCTTCGTCCC 58.518 55.000 0.00 0.00 0.00 4.46
3209 3366 4.142790 TCTATGACATACTCCCTTCGTCC 58.857 47.826 0.00 0.00 0.00 4.79
3210 3367 5.507650 GGTTCTATGACATACTCCCTTCGTC 60.508 48.000 0.00 0.00 0.00 4.20
3211 3368 4.341520 GGTTCTATGACATACTCCCTTCGT 59.658 45.833 0.00 0.00 0.00 3.85
3212 3369 4.262079 GGGTTCTATGACATACTCCCTTCG 60.262 50.000 13.44 0.00 0.00 3.79
3213 3370 4.902448 AGGGTTCTATGACATACTCCCTTC 59.098 45.833 15.91 0.39 40.79 3.46
3214 3371 4.897051 AGGGTTCTATGACATACTCCCTT 58.103 43.478 15.91 1.86 40.79 3.95
3215 3372 4.171044 AGAGGGTTCTATGACATACTCCCT 59.829 45.833 19.24 19.24 45.47 4.20
3216 3373 4.484912 AGAGGGTTCTATGACATACTCCC 58.515 47.826 13.08 13.08 0.00 4.30
3217 3374 7.598759 TTTAGAGGGTTCTATGACATACTCC 57.401 40.000 6.46 3.19 35.88 3.85
3218 3375 9.482627 CATTTTAGAGGGTTCTATGACATACTC 57.517 37.037 0.00 0.00 35.88 2.59
3219 3376 9.213777 TCATTTTAGAGGGTTCTATGACATACT 57.786 33.333 0.00 0.00 35.88 2.12
3220 3377 9.832445 TTCATTTTAGAGGGTTCTATGACATAC 57.168 33.333 0.00 0.00 35.88 2.39
3462 3635 0.877071 AGCACGGATGTTTGAAGCAG 59.123 50.000 0.00 0.00 0.00 4.24
3472 3645 3.837213 AATGAGAAAACAGCACGGATG 57.163 42.857 0.00 0.00 0.00 3.51
3498 3671 2.491621 CTCGAGACATGGAGCGCA 59.508 61.111 11.47 0.00 0.00 6.09
3536 3709 1.408683 GCACATGCCTCCAGACCAATA 60.409 52.381 0.00 0.00 34.31 1.90
3634 3807 1.590591 TATAACCTGCCAGCCCTCAA 58.409 50.000 0.00 0.00 0.00 3.02
3819 3995 2.254546 AGACACTGGATTGCAAACGA 57.745 45.000 1.71 0.00 0.00 3.85
3820 3996 2.033299 ACAAGACACTGGATTGCAAACG 59.967 45.455 1.71 0.00 0.00 3.60
3821 3997 3.066621 TGACAAGACACTGGATTGCAAAC 59.933 43.478 1.71 0.00 0.00 2.93
3858 4034 1.705186 ACACAGGGTTGCAGGTTCTAT 59.295 47.619 0.00 0.00 0.00 1.98
3900 4076 5.616270 TGTGCTATATGCCCTTAATCGAAA 58.384 37.500 0.00 0.00 42.00 3.46
3902 4078 4.882842 TGTGCTATATGCCCTTAATCGA 57.117 40.909 0.00 0.00 42.00 3.59
3988 4166 7.436673 GTCTCATTGGTGATCATCTGTACTAAC 59.563 40.741 7.64 0.00 32.98 2.34
4000 4178 5.240891 TGAAACAGAGTCTCATTGGTGATC 58.759 41.667 1.94 0.00 32.98 2.92
4381 4559 9.915629 CTACATCAATAGTATCTTTCAGGGTAC 57.084 37.037 0.00 0.00 0.00 3.34
4455 4810 1.336240 GCACCAAGGATGTTTGCAGTC 60.336 52.381 0.00 0.00 35.03 3.51
4460 4815 1.080569 GCGGCACCAAGGATGTTTG 60.081 57.895 0.00 0.00 0.00 2.93
4514 4869 1.598430 CCAAACAGGCCGTTGTTTACG 60.598 52.381 19.48 10.58 46.49 3.18
4515 4870 1.677052 TCCAAACAGGCCGTTGTTTAC 59.323 47.619 19.48 0.00 46.49 2.01
4516 4871 2.054232 TCCAAACAGGCCGTTGTTTA 57.946 45.000 19.48 6.01 46.49 2.01
4518 4873 1.068434 CATTCCAAACAGGCCGTTGTT 59.932 47.619 12.63 8.92 42.82 2.83
4519 4874 0.673437 CATTCCAAACAGGCCGTTGT 59.327 50.000 12.63 2.78 38.07 3.32
4521 4876 1.112315 TGCATTCCAAACAGGCCGTT 61.112 50.000 7.08 7.08 40.50 4.44
4522 4877 1.526575 CTGCATTCCAAACAGGCCGT 61.527 55.000 0.00 0.00 37.29 5.68
4523 4878 1.213537 CTGCATTCCAAACAGGCCG 59.786 57.895 0.00 0.00 37.29 6.13
4524 4879 1.593265 CCTGCATTCCAAACAGGCC 59.407 57.895 0.00 0.00 44.16 5.19
4527 4882 3.318839 TGAAGTTCCTGCATTCCAAACAG 59.681 43.478 0.00 0.00 0.00 3.16
4528 4883 3.068024 GTGAAGTTCCTGCATTCCAAACA 59.932 43.478 0.00 0.00 0.00 2.83
4529 4884 3.068024 TGTGAAGTTCCTGCATTCCAAAC 59.932 43.478 0.00 0.00 0.00 2.93
4530 4885 3.295093 TGTGAAGTTCCTGCATTCCAAA 58.705 40.909 0.00 0.00 0.00 3.28
4533 4888 3.084039 TCATGTGAAGTTCCTGCATTCC 58.916 45.455 0.00 0.00 0.00 3.01
4545 4912 5.075448 CGAATCGAACAGTTTCATGTGAAG 58.925 41.667 0.00 0.00 35.21 3.02
4619 4994 8.094548 TCCTATTCCTATCATATGAACCAAACG 58.905 37.037 9.99 0.00 0.00 3.60
4620 4995 9.793259 TTCCTATTCCTATCATATGAACCAAAC 57.207 33.333 9.99 0.00 0.00 2.93
4623 4998 8.383175 GGTTTCCTATTCCTATCATATGAACCA 58.617 37.037 9.99 0.00 0.00 3.67
4633 5011 8.437274 TCTTCCTATGGTTTCCTATTCCTATC 57.563 38.462 0.00 0.00 0.00 2.08
4701 5165 9.653516 ACATCTCTTTCTCTATAGGAATTGAGA 57.346 33.333 21.74 21.74 40.68 3.27
4702 5166 9.912634 GACATCTCTTTCTCTATAGGAATTGAG 57.087 37.037 16.99 16.99 36.61 3.02
4703 5167 9.426534 TGACATCTCTTTCTCTATAGGAATTGA 57.573 33.333 0.00 4.25 0.00 2.57
4704 5168 9.474920 GTGACATCTCTTTCTCTATAGGAATTG 57.525 37.037 0.00 0.60 0.00 2.32
4705 5169 9.432982 AGTGACATCTCTTTCTCTATAGGAATT 57.567 33.333 0.00 0.00 0.00 2.17
4706 5170 9.432982 AAGTGACATCTCTTTCTCTATAGGAAT 57.567 33.333 0.00 0.00 0.00 3.01
4707 5171 8.690884 CAAGTGACATCTCTTTCTCTATAGGAA 58.309 37.037 0.00 0.00 0.00 3.36
4708 5172 8.055790 TCAAGTGACATCTCTTTCTCTATAGGA 58.944 37.037 0.00 0.00 0.00 2.94
4709 5173 8.231692 TCAAGTGACATCTCTTTCTCTATAGG 57.768 38.462 0.00 0.00 0.00 2.57
4712 5176 8.756927 TGAATCAAGTGACATCTCTTTCTCTAT 58.243 33.333 0.00 0.00 0.00 1.98
4713 5177 8.127150 TGAATCAAGTGACATCTCTTTCTCTA 57.873 34.615 0.00 0.00 0.00 2.43
4714 5178 7.002250 TGAATCAAGTGACATCTCTTTCTCT 57.998 36.000 0.00 0.00 0.00 3.10
4715 5179 7.846644 ATGAATCAAGTGACATCTCTTTCTC 57.153 36.000 0.00 0.00 0.00 2.87
4716 5180 7.490725 CGTATGAATCAAGTGACATCTCTTTCT 59.509 37.037 0.00 0.00 0.00 2.52
4828 5292 1.347378 GGCAAAATTCCTTTGGAGCCA 59.653 47.619 8.38 0.00 44.03 4.75
4899 5363 3.947834 CGAATGAAATAAGTCCAGGCCTT 59.052 43.478 0.00 0.00 0.00 4.35
4950 5414 3.567478 AGGAAGCCTGGTCATGTATTC 57.433 47.619 0.00 0.00 29.57 1.75
4960 5424 0.111253 ACAGACCAAAGGAAGCCTGG 59.889 55.000 0.00 0.00 32.13 4.45
4961 5425 2.616510 CCTACAGACCAAAGGAAGCCTG 60.617 54.545 0.00 0.00 32.13 4.85
5061 5525 9.670442 TTGGTTCCTATCCTACATAAGAATAGT 57.330 33.333 0.00 0.00 0.00 2.12
5068 5532 8.582437 CGAAGTATTGGTTCCTATCCTACATAA 58.418 37.037 0.00 0.00 0.00 1.90
5114 5579 7.921786 TTTTGTCATTGAGTCTAGGGTAATG 57.078 36.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.