Multiple sequence alignment - TraesCS1A01G317200

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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 TraesCS1A01G317200 chr1A 100.000 3715 0 0 1 3715 508643831 508640117 0.000000e+00 6861.0
1 TraesCS1A01G317200 chr1B 92.918 3304 152 41 2 3237 555640924 555637635 0.000000e+00 4730.0
2 TraesCS1A01G317200 chr1B 87.361 269 13 8 3453 3715 555637257 555637004 4.690000e-74 289.0
3 TraesCS1A01G317200 chr1D 94.866 1344 34 11 582 1922 412091059 412089748 0.000000e+00 2067.0
4 TraesCS1A01G317200 chr1D 94.658 1273 44 14 1951 3207 412089750 412088486 0.000000e+00 1953.0
5 TraesCS1A01G317200 chr1D 87.230 556 44 7 2 542 412091600 412091057 3.170000e-170 608.0
6 TraesCS1A01G317200 chr1D 88.835 206 9 4 3513 3715 412088248 412088054 1.330000e-59 241.0
7 TraesCS1A01G317200 chr1D 93.846 65 4 0 3376 3440 216726043 216726107 8.490000e-17 99.0
8 TraesCS1A01G317200 chr1D 93.939 66 2 2 3376 3440 361156260 361156196 8.490000e-17 99.0
9 TraesCS1A01G317200 chr1D 94.595 37 1 1 3455 3491 412088285 412088250 5.180000e-04 56.5
10 TraesCS1A01G317200 chr7A 95.385 65 3 0 3376 3440 727851198 727851262 1.830000e-18 104.0
11 TraesCS1A01G317200 chr2B 95.385 65 3 0 3376 3440 38399634 38399698 1.830000e-18 104.0
12 TraesCS1A01G317200 chr7D 96.721 61 2 0 3376 3436 562201737 562201677 6.560000e-18 102.0
13 TraesCS1A01G317200 chr7D 86.154 65 9 0 3376 3440 94439167 94439103 1.850000e-08 71.3
14 TraesCS1A01G317200 chr4D 93.846 65 4 0 3376 3440 61780304 61780368 8.490000e-17 99.0
15 TraesCS1A01G317200 chr4D 93.846 65 4 0 3376 3440 180441261 180441325 8.490000e-17 99.0
16 TraesCS1A01G317200 chr6B 82.203 118 16 4 3328 3440 15398362 15398245 3.050000e-16 97.1
17 TraesCS1A01G317200 chr6D 80.734 109 17 3 3336 3440 351111795 351111687 8.550000e-12 82.4
18 TraesCS1A01G317200 chr6D 81.609 87 10 5 3324 3404 351111885 351111799 2.390000e-07 67.6
19 TraesCS1A01G317200 chr5B 91.525 59 5 0 3382 3440 318396486 318396428 8.550000e-12 82.4
20 TraesCS1A01G317200 chr4B 89.231 65 7 0 3376 3440 407061261 407061197 8.550000e-12 82.4
21 TraesCS1A01G317200 chr7B 83.333 78 6 3 3288 3364 311345631 311345702 8.610000e-07 65.8
22 TraesCS1A01G317200 chr3B 87.719 57 2 4 3308 3364 689511322 689511271 1.110000e-05 62.1
23 TraesCS1A01G317200 chr2A 82.895 76 6 6 3290 3364 668451495 668451564 1.110000e-05 62.1


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 TraesCS1A01G317200 chr1A 508640117 508643831 3714 True 6861.0 6861 100.0000 1 3715 1 chr1A.!!$R1 3714
1 TraesCS1A01G317200 chr1B 555637004 555640924 3920 True 2509.5 4730 90.1395 2 3715 2 chr1B.!!$R1 3713
2 TraesCS1A01G317200 chr1D 412088054 412091600 3546 True 985.1 2067 92.0368 2 3715 5 chr1D.!!$R2 3713

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
262 278 0.396139 ATGGGGAGTAGCGTTCCGTA 60.396 55.000 0.0 0.0 35.48 4.02 F
524 550 2.032620 GGGATCAGAAAGCGAGGAGTA 58.967 52.381 0.0 0.0 0.00 2.59 F
1798 1839 0.555769 ATGGGGTGTTTGAGGTGTGT 59.444 50.000 0.0 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 1181 0.544357 TCAGGGACGGTGTTCATCCT 60.544 55.000 0.00 0.0 32.70 3.24 R
2229 2270 1.068402 CCAAGACGCATGTGCATTTGA 60.068 47.619 6.08 0.0 42.21 2.69 R
3609 3911 0.107848 GTCCTGGGATGTGTTACCGG 60.108 60.000 0.00 0.0 0.00 5.28 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
135 137 2.413765 GCCACGGTCTCGATCCTC 59.586 66.667 5.48 0.00 40.11 3.71
137 139 2.716244 CACGGTCTCGATCCTCCG 59.284 66.667 13.35 13.35 46.98 4.63
138 140 3.210528 ACGGTCTCGATCCTCCGC 61.211 66.667 14.37 0.00 45.76 5.54
140 142 3.967335 GGTCTCGATCCTCCGCCG 61.967 72.222 0.00 0.00 0.00 6.46
243 259 3.731728 GGGTGGCAGATCTGGGCA 61.732 66.667 23.89 18.57 38.62 5.36
261 277 1.684734 ATGGGGAGTAGCGTTCCGT 60.685 57.895 0.00 0.00 35.48 4.69
262 278 0.396139 ATGGGGAGTAGCGTTCCGTA 60.396 55.000 0.00 0.00 35.48 4.02
278 294 5.513376 GTTCCGTAAAATTCGGTTCAAAGT 58.487 37.500 4.21 0.00 46.86 2.66
281 297 4.913345 CCGTAAAATTCGGTTCAAAGTTCC 59.087 41.667 0.00 0.00 42.62 3.62
335 351 2.076863 CTTCTGGGTGACGAATTGGTC 58.923 52.381 13.18 13.18 37.45 4.02
363 382 6.953843 AGAATTTTTAATTTTGTGCGGTTGG 58.046 32.000 0.00 0.00 0.00 3.77
376 395 4.873827 TGTGCGGTTGGAAGATAGATTTAC 59.126 41.667 0.00 0.00 0.00 2.01
384 403 9.939802 GGTTGGAAGATAGATTTACGGTATTAT 57.060 33.333 0.00 0.00 0.00 1.28
434 460 6.324042 TCATGAACATGAATTGAAATGGTCG 58.676 36.000 14.00 0.00 44.14 4.79
441 467 5.365403 TGAATTGAAATGGTCGGTGTTAC 57.635 39.130 0.00 0.00 0.00 2.50
453 479 4.037089 GGTCGGTGTTACTTCCATTTGTTT 59.963 41.667 0.00 0.00 0.00 2.83
454 480 5.450826 GGTCGGTGTTACTTCCATTTGTTTT 60.451 40.000 0.00 0.00 0.00 2.43
524 550 2.032620 GGGATCAGAAAGCGAGGAGTA 58.967 52.381 0.00 0.00 0.00 2.59
558 584 5.277250 TCATGGGAGAAGTACAACAGGATA 58.723 41.667 0.00 0.00 0.00 2.59
632 668 2.112297 TCGAAACTTGCCCGCCTT 59.888 55.556 0.00 0.00 0.00 4.35
918 956 6.130298 TGTCCTATGGTGCATTTATTTTCG 57.870 37.500 0.00 0.00 0.00 3.46
919 957 5.650266 TGTCCTATGGTGCATTTATTTTCGT 59.350 36.000 0.00 0.00 0.00 3.85
920 958 6.824196 TGTCCTATGGTGCATTTATTTTCGTA 59.176 34.615 0.00 0.00 0.00 3.43
922 960 7.855904 GTCCTATGGTGCATTTATTTTCGTAAG 59.144 37.037 0.00 0.00 0.00 2.34
923 961 6.636850 CCTATGGTGCATTTATTTTCGTAAGC 59.363 38.462 0.00 0.00 37.18 3.09
924 962 5.378292 TGGTGCATTTATTTTCGTAAGCA 57.622 34.783 0.00 0.00 37.18 3.91
925 963 5.398169 TGGTGCATTTATTTTCGTAAGCAG 58.602 37.500 0.00 0.00 37.18 4.24
926 964 4.798387 GGTGCATTTATTTTCGTAAGCAGG 59.202 41.667 0.00 0.00 37.18 4.85
927 965 5.392595 GGTGCATTTATTTTCGTAAGCAGGA 60.393 40.000 0.00 0.00 37.18 3.86
928 966 6.265577 GTGCATTTATTTTCGTAAGCAGGAT 58.734 36.000 0.00 0.00 37.18 3.24
929 967 7.414436 GTGCATTTATTTTCGTAAGCAGGATA 58.586 34.615 0.00 0.00 37.18 2.59
1141 1181 6.182627 AGGATGAATGACTTTGAGTATGCAA 58.817 36.000 0.00 0.00 0.00 4.08
1181 1221 3.084536 TGTGAAGCAATGGGATAAGCA 57.915 42.857 0.00 0.00 0.00 3.91
1254 1294 7.050377 TCATGAACCTGGATCTTAAGATGAAC 58.950 38.462 22.61 12.46 34.37 3.18
1317 1357 4.610945 GCAACATGGCCTATAACATGAAC 58.389 43.478 3.32 0.00 45.55 3.18
1320 1360 3.157087 CATGGCCTATAACATGAACCCC 58.843 50.000 3.32 0.00 45.55 4.95
1494 1534 4.560136 TGACAAGCGCTTCAAAACATTA 57.440 36.364 22.21 0.00 0.00 1.90
1600 1640 4.216257 TCAAGAGACAGCTTTTTGGTATGC 59.784 41.667 0.00 0.00 0.00 3.14
1798 1839 0.555769 ATGGGGTGTTTGAGGTGTGT 59.444 50.000 0.00 0.00 0.00 3.72
1812 1853 5.590145 TGAGGTGTGTGATTGTTTCATTTG 58.410 37.500 0.00 0.00 36.54 2.32
1821 1862 7.596248 GTGTGATTGTTTCATTTGCTGATAACT 59.404 33.333 0.00 0.00 36.54 2.24
1824 1865 7.962373 TGATTGTTTCATTTGCTGATAACTACG 59.038 33.333 0.00 0.00 32.72 3.51
1837 1878 6.726490 TGATAACTACGAGCCTCCTTATTT 57.274 37.500 0.00 0.00 0.00 1.40
1846 1887 4.035675 CGAGCCTCCTTATTTGAATGGAAC 59.964 45.833 0.00 0.00 0.00 3.62
1868 1909 3.943381 CTGCAAGCCTCTTCATGAATACA 59.057 43.478 8.96 0.00 0.00 2.29
1880 1921 9.764870 CTCTTCATGAATACATTGTAACAGTTG 57.235 33.333 8.96 2.27 34.15 3.16
1922 1963 8.818622 ATGCTTATATCATTTGCATGGATAGT 57.181 30.769 0.00 0.00 41.93 2.12
1925 1966 9.565213 GCTTATATCATTTGCATGGATAGTTTC 57.435 33.333 0.00 0.00 0.00 2.78
1926 1967 9.764870 CTTATATCATTTGCATGGATAGTTTCG 57.235 33.333 0.00 0.00 0.00 3.46
1937 1978 3.496884 TGGATAGTTTCGTGTGCTGTTTC 59.503 43.478 0.00 0.00 0.00 2.78
2035 2076 5.415077 GCGGTGTAGATACTCTACCATATGT 59.585 44.000 10.86 0.00 46.64 2.29
2143 2184 4.265073 AGCCAACATTCTCCTGATGTTAC 58.735 43.478 2.54 0.00 36.83 2.50
2144 2185 3.063997 GCCAACATTCTCCTGATGTTACG 59.936 47.826 2.54 0.00 36.83 3.18
2146 2187 4.695455 CCAACATTCTCCTGATGTTACGTT 59.305 41.667 0.00 0.00 36.83 3.99
2180 2221 2.747855 GCTTCTGTGGCCCTTCCG 60.748 66.667 0.00 0.00 37.80 4.30
2183 2224 2.411765 CTTCTGTGGCCCTTCCGGTT 62.412 60.000 0.00 0.00 37.80 4.44
2210 2251 3.267483 TGGCTGAAATTAGAAGCGTACC 58.733 45.455 0.00 0.00 37.83 3.34
2229 2270 5.238650 CGTACCTGTTCTCAAAGTTCCATTT 59.761 40.000 0.00 0.00 0.00 2.32
2243 2284 2.608268 TCCATTTCAAATGCACATGCG 58.392 42.857 4.40 0.00 45.83 4.73
2247 2288 3.367992 TTTCAAATGCACATGCGTCTT 57.632 38.095 0.00 0.00 45.83 3.01
2255 2296 1.925946 GCACATGCGTCTTGGTTGAAC 60.926 52.381 0.00 0.00 0.00 3.18
2263 2304 2.731976 CGTCTTGGTTGAACTCTAGCAC 59.268 50.000 0.00 0.00 0.00 4.40
2264 2305 3.728845 GTCTTGGTTGAACTCTAGCACA 58.271 45.455 0.00 0.00 0.00 4.57
2265 2306 4.127171 GTCTTGGTTGAACTCTAGCACAA 58.873 43.478 0.00 0.00 0.00 3.33
2293 2334 4.645535 AGTGCTTGTTCTTCAGCATTCTA 58.354 39.130 0.00 0.00 39.57 2.10
2412 2453 4.953579 TCCCAGCACAGGTAATTAATTTCC 59.046 41.667 14.32 14.32 0.00 3.13
2528 2594 2.174360 GCCTTGGAAGAGGATGCTTTT 58.826 47.619 0.00 0.00 39.25 2.27
2615 2684 0.902531 TACCTTACTCCAGCTGCCAC 59.097 55.000 8.66 0.00 0.00 5.01
2633 2702 3.124297 GCCACGATAATAGATGCTTGAGC 59.876 47.826 0.00 0.00 42.50 4.26
2702 2772 2.320587 GCTGGACCTGTGCAAGACG 61.321 63.158 0.00 0.00 0.00 4.18
2722 2792 1.677217 GGAAGACGCCTGATCTGCTTT 60.677 52.381 6.30 0.00 0.00 3.51
2877 2948 0.111253 CCAGAAAGGACCTGGTGCTT 59.889 55.000 25.65 25.65 45.62 3.91
2955 3026 5.518847 CGTAATCTCGGTGATGTGTATGTTT 59.481 40.000 0.00 0.00 35.21 2.83
3069 3143 1.244019 AAAGTGAGGGCGGTTGATGC 61.244 55.000 0.00 0.00 0.00 3.91
3237 3338 1.812922 GCCTCCTGATGACGCTGTG 60.813 63.158 0.00 0.00 0.00 3.66
3238 3339 1.812922 CCTCCTGATGACGCTGTGC 60.813 63.158 0.00 0.00 0.00 4.57
3240 3341 2.821366 CCTGATGACGCTGTGCCC 60.821 66.667 0.00 0.00 0.00 5.36
3241 3342 2.046988 CTGATGACGCTGTGCCCA 60.047 61.111 0.00 0.00 0.00 5.36
3242 3343 1.672030 CTGATGACGCTGTGCCCAA 60.672 57.895 0.00 0.00 0.00 4.12
3244 3345 0.821301 TGATGACGCTGTGCCCAAAA 60.821 50.000 0.00 0.00 0.00 2.44
3245 3346 0.527565 GATGACGCTGTGCCCAAAAT 59.472 50.000 0.00 0.00 0.00 1.82
3246 3347 1.742831 GATGACGCTGTGCCCAAAATA 59.257 47.619 0.00 0.00 0.00 1.40
3247 3348 0.878416 TGACGCTGTGCCCAAAATAC 59.122 50.000 0.00 0.00 0.00 1.89
3248 3349 0.878416 GACGCTGTGCCCAAAATACA 59.122 50.000 0.00 0.00 0.00 2.29
3249 3350 0.596082 ACGCTGTGCCCAAAATACAC 59.404 50.000 0.00 0.00 34.86 2.90
3251 3352 0.732538 GCTGTGCCCAAAATACACGC 60.733 55.000 0.00 0.00 37.11 5.34
3252 3353 0.881118 CTGTGCCCAAAATACACGCT 59.119 50.000 0.00 0.00 37.11 5.07
3254 3355 0.170339 GTGCCCAAAATACACGCTCC 59.830 55.000 0.00 0.00 0.00 4.70
3255 3356 1.302383 TGCCCAAAATACACGCTCCG 61.302 55.000 0.00 0.00 0.00 4.63
3256 3357 1.303091 GCCCAAAATACACGCTCCGT 61.303 55.000 0.00 0.00 42.36 4.69
3259 3360 1.801771 CCAAAATACACGCTCCGTTCA 59.198 47.619 0.00 0.00 38.32 3.18
3261 3362 3.485216 CCAAAATACACGCTCCGTTCATC 60.485 47.826 0.00 0.00 38.32 2.92
3274 3375 4.124238 TCCGTTCATCTTTCTTTCACGTT 58.876 39.130 0.00 0.00 0.00 3.99
3278 3379 5.276868 CGTTCATCTTTCTTTCACGTTCAGT 60.277 40.000 0.00 0.00 0.00 3.41
3289 3390 3.034721 CACGTTCAGTGGCTTAGGTAA 57.965 47.619 0.00 0.00 46.77 2.85
3290 3391 3.596214 CACGTTCAGTGGCTTAGGTAAT 58.404 45.455 0.00 0.00 46.77 1.89
3291 3392 3.617263 CACGTTCAGTGGCTTAGGTAATC 59.383 47.826 0.00 0.00 46.77 1.75
3292 3393 3.514309 ACGTTCAGTGGCTTAGGTAATCT 59.486 43.478 0.00 0.00 0.00 2.40
3293 3394 4.020485 ACGTTCAGTGGCTTAGGTAATCTT 60.020 41.667 0.00 0.00 0.00 2.40
3294 3395 4.567159 CGTTCAGTGGCTTAGGTAATCTTC 59.433 45.833 0.00 0.00 0.00 2.87
3295 3396 5.488341 GTTCAGTGGCTTAGGTAATCTTCA 58.512 41.667 0.00 0.00 0.00 3.02
3296 3397 5.957771 TCAGTGGCTTAGGTAATCTTCAT 57.042 39.130 0.00 0.00 0.00 2.57
3299 3400 6.599244 TCAGTGGCTTAGGTAATCTTCATTTG 59.401 38.462 0.00 0.00 0.00 2.32
3300 3401 5.888161 AGTGGCTTAGGTAATCTTCATTTGG 59.112 40.000 0.00 0.00 0.00 3.28
3301 3402 5.885912 GTGGCTTAGGTAATCTTCATTTGGA 59.114 40.000 0.00 0.00 0.00 3.53
3303 3404 6.547141 TGGCTTAGGTAATCTTCATTTGGATG 59.453 38.462 0.00 0.00 34.46 3.51
3304 3405 6.772716 GGCTTAGGTAATCTTCATTTGGATGA 59.227 38.462 0.00 0.00 40.46 2.92
3305 3406 7.449704 GGCTTAGGTAATCTTCATTTGGATGAT 59.550 37.037 0.00 0.00 41.71 2.45
3306 3407 8.295288 GCTTAGGTAATCTTCATTTGGATGATG 58.705 37.037 0.00 0.00 41.71 3.07
3307 3408 9.347240 CTTAGGTAATCTTCATTTGGATGATGT 57.653 33.333 0.00 0.00 41.71 3.06
3310 3411 9.293404 AGGTAATCTTCATTTGGATGATGTATG 57.707 33.333 0.00 0.00 41.71 2.39
3311 3412 9.288576 GGTAATCTTCATTTGGATGATGTATGA 57.711 33.333 0.00 0.00 41.71 2.15
3315 3416 8.756486 TCTTCATTTGGATGATGTATGAATGT 57.244 30.769 0.00 0.00 41.71 2.71
3316 3417 9.850198 TCTTCATTTGGATGATGTATGAATGTA 57.150 29.630 0.00 0.00 41.71 2.29
3317 3418 9.888878 CTTCATTTGGATGATGTATGAATGTAC 57.111 33.333 0.00 0.00 41.71 2.90
3318 3419 9.631257 TTCATTTGGATGATGTATGAATGTACT 57.369 29.630 0.00 0.00 41.71 2.73
3319 3420 9.276590 TCATTTGGATGATGTATGAATGTACTC 57.723 33.333 0.00 0.00 37.37 2.59
3320 3421 8.509690 CATTTGGATGATGTATGAATGTACTCC 58.490 37.037 0.00 0.00 35.16 3.85
3321 3422 6.114187 TGGATGATGTATGAATGTACTCCC 57.886 41.667 0.00 0.00 0.00 4.30
3322 3423 5.846164 TGGATGATGTATGAATGTACTCCCT 59.154 40.000 0.00 0.00 0.00 4.20
3323 3424 6.014242 TGGATGATGTATGAATGTACTCCCTC 60.014 42.308 0.00 0.00 0.00 4.30
3324 3425 6.212388 GGATGATGTATGAATGTACTCCCTCT 59.788 42.308 0.00 0.00 0.00 3.69
3325 3426 6.656632 TGATGTATGAATGTACTCCCTCTC 57.343 41.667 0.00 0.00 0.00 3.20
3326 3427 5.540337 TGATGTATGAATGTACTCCCTCTCC 59.460 44.000 0.00 0.00 0.00 3.71
3327 3428 4.223953 TGTATGAATGTACTCCCTCTCCC 58.776 47.826 0.00 0.00 0.00 4.30
3328 3429 2.176247 TGAATGTACTCCCTCTCCCC 57.824 55.000 0.00 0.00 0.00 4.81
3332 3433 1.002069 TGTACTCCCTCTCCCCGTTA 58.998 55.000 0.00 0.00 0.00 3.18
3334 3435 0.259938 TACTCCCTCTCCCCGTTACC 59.740 60.000 0.00 0.00 0.00 2.85
3343 3444 5.512576 CCCTCTCCCCGTTACCAAATATAAG 60.513 48.000 0.00 0.00 0.00 1.73
3344 3445 5.071384 CCTCTCCCCGTTACCAAATATAAGT 59.929 44.000 0.00 0.00 0.00 2.24
3345 3446 6.165700 TCTCCCCGTTACCAAATATAAGTC 57.834 41.667 0.00 0.00 0.00 3.01
3346 3447 5.901276 TCTCCCCGTTACCAAATATAAGTCT 59.099 40.000 0.00 0.00 0.00 3.24
3349 3450 6.824704 TCCCCGTTACCAAATATAAGTCTTTG 59.175 38.462 0.00 0.00 33.20 2.77
3371 3472 5.952347 GGAGAGATTCCACTAAACCCTAA 57.048 43.478 0.00 0.00 46.01 2.69
3373 3474 6.114089 GGAGAGATTCCACTAAACCCTAAAC 58.886 44.000 0.00 0.00 46.01 2.01
3374 3475 6.063496 AGAGATTCCACTAAACCCTAAACC 57.937 41.667 0.00 0.00 0.00 3.27
3380 3499 9.081204 GATTCCACTAAACCCTAAACCTTTTAA 57.919 33.333 0.00 0.00 0.00 1.52
3405 3524 6.233434 AGTGTAGATTCACTCATTTTGCTCA 58.767 36.000 0.00 0.00 44.07 4.26
3406 3525 6.148480 AGTGTAGATTCACTCATTTTGCTCAC 59.852 38.462 0.00 0.00 44.07 3.51
3410 3529 7.317842 AGATTCACTCATTTTGCTCACTATG 57.682 36.000 0.00 0.00 0.00 2.23
3412 3531 8.043113 AGATTCACTCATTTTGCTCACTATGTA 58.957 33.333 0.00 0.00 0.00 2.29
3415 3534 7.161404 TCACTCATTTTGCTCACTATGTAGTT 58.839 34.615 0.00 0.00 33.46 2.24
3416 3535 7.331934 TCACTCATTTTGCTCACTATGTAGTTC 59.668 37.037 0.00 0.00 33.46 3.01
3458 3760 3.668447 ACTCAAGGTTGTGTAGATGCAG 58.332 45.455 0.00 0.00 33.60 4.41
3491 3793 3.181445 TGGTGAGCTGAAGTGGTTACATT 60.181 43.478 0.00 0.00 0.00 2.71
3493 3795 3.815401 GTGAGCTGAAGTGGTTACATTGT 59.185 43.478 0.00 0.00 0.00 2.71
3495 3797 4.275689 TGAGCTGAAGTGGTTACATTGTTG 59.724 41.667 0.00 0.00 0.00 3.33
3529 3831 2.660572 TGTGTTGTAGGTGCACCAAAT 58.339 42.857 36.39 19.55 38.89 2.32
3534 3836 5.183140 GTGTTGTAGGTGCACCAAATCTTAT 59.817 40.000 36.39 16.49 38.89 1.73
3535 3837 6.373216 GTGTTGTAGGTGCACCAAATCTTATA 59.627 38.462 36.39 15.41 38.89 0.98
3536 3838 6.597672 TGTTGTAGGTGCACCAAATCTTATAG 59.402 38.462 36.39 0.00 38.89 1.31
3537 3839 6.308015 TGTAGGTGCACCAAATCTTATAGT 57.692 37.500 36.39 14.45 38.89 2.12
3538 3840 7.426606 TGTAGGTGCACCAAATCTTATAGTA 57.573 36.000 36.39 13.39 38.89 1.82
3544 3846 5.808540 TGCACCAAATCTTATAGTACGTGTC 59.191 40.000 0.00 0.00 0.00 3.67
3606 3908 2.354259 CATCAGTTCAACTGCTCCTCC 58.646 52.381 13.15 0.00 45.54 4.30
3607 3909 1.722034 TCAGTTCAACTGCTCCTCCT 58.278 50.000 13.15 0.00 45.54 3.69
3608 3910 1.620819 TCAGTTCAACTGCTCCTCCTC 59.379 52.381 13.15 0.00 45.54 3.71
3609 3911 0.980423 AGTTCAACTGCTCCTCCTCC 59.020 55.000 0.00 0.00 0.00 4.30
3610 3912 0.035915 GTTCAACTGCTCCTCCTCCC 60.036 60.000 0.00 0.00 0.00 4.30
3651 3956 4.724279 AGTAGTCCCATCACCTGTTTTT 57.276 40.909 0.00 0.00 0.00 1.94
3652 3957 5.836024 AGTAGTCCCATCACCTGTTTTTA 57.164 39.130 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.517694 GCCGTCGGATGCTACGAAA 60.518 57.895 17.49 0.00 42.55 3.46
21 22 0.676782 AGAAACGGGGAAAGCGGATG 60.677 55.000 0.00 0.00 0.00 3.51
22 23 0.392595 GAGAAACGGGGAAAGCGGAT 60.393 55.000 0.00 0.00 0.00 4.18
121 123 3.210528 GCGGAGGATCGAGACCGT 61.211 66.667 18.26 1.80 45.91 4.83
152 154 3.941657 GAGTGCCACTCGCCAGGAC 62.942 68.421 9.45 0.00 35.28 3.85
216 228 3.346734 TGCCACCCCTTCCCATCC 61.347 66.667 0.00 0.00 0.00 3.51
220 236 2.003548 AGATCTGCCACCCCTTCCC 61.004 63.158 0.00 0.00 0.00 3.97
261 277 6.658188 ATGGGAACTTTGAACCGAATTTTA 57.342 33.333 0.00 0.00 0.00 1.52
262 278 5.545063 ATGGGAACTTTGAACCGAATTTT 57.455 34.783 0.00 0.00 0.00 1.82
278 294 9.029368 CACAACTATCATCTAGATCTATGGGAA 57.971 37.037 1.03 0.00 38.19 3.97
376 395 7.316544 ACTTAAACCAAGCTTCATAATACCG 57.683 36.000 0.00 0.00 37.83 4.02
384 403 6.524101 ACTTTCAACTTAAACCAAGCTTCA 57.476 33.333 0.00 0.00 37.83 3.02
434 460 7.708998 TCTACAAAACAAATGGAAGTAACACC 58.291 34.615 0.00 0.00 0.00 4.16
441 467 8.190784 ACAAACTCTCTACAAAACAAATGGAAG 58.809 33.333 0.00 0.00 0.00 3.46
497 523 2.125147 TTTCTGATCCCGCGCTGG 60.125 61.111 12.26 12.26 37.55 4.85
524 550 2.278245 TCTCCCATGAACACAATCCCT 58.722 47.619 0.00 0.00 0.00 4.20
558 584 1.173444 CGTCCACGCTCTAGCCCTAT 61.173 60.000 0.00 0.00 37.91 2.57
632 668 2.945440 GCCCACCAAGAATAGTGCATCA 60.945 50.000 0.00 0.00 32.48 3.07
819 857 9.793252 AACTTCATGCATGTTGTAATTCTATTC 57.207 29.630 25.43 0.00 0.00 1.75
829 867 9.709495 AATTACAAATAACTTCATGCATGTTGT 57.291 25.926 25.43 24.68 0.00 3.32
917 955 7.303634 ACACTTGTAAAATATCCTGCTTACG 57.696 36.000 0.00 0.00 0.00 3.18
918 956 8.512138 ACAACACTTGTAAAATATCCTGCTTAC 58.488 33.333 0.00 0.00 43.27 2.34
919 957 8.630054 ACAACACTTGTAAAATATCCTGCTTA 57.370 30.769 0.00 0.00 43.27 3.09
920 958 7.524717 ACAACACTTGTAAAATATCCTGCTT 57.475 32.000 0.00 0.00 43.27 3.91
922 960 7.651704 ACAAACAACACTTGTAAAATATCCTGC 59.348 33.333 0.00 0.00 44.59 4.85
923 961 9.180678 GACAAACAACACTTGTAAAATATCCTG 57.819 33.333 0.00 0.00 44.59 3.86
924 962 8.908903 TGACAAACAACACTTGTAAAATATCCT 58.091 29.630 0.00 0.00 44.59 3.24
925 963 8.964150 GTGACAAACAACACTTGTAAAATATCC 58.036 33.333 0.00 0.00 44.59 2.59
926 964 8.964150 GGTGACAAACAACACTTGTAAAATATC 58.036 33.333 0.00 0.00 44.59 1.63
927 965 8.691797 AGGTGACAAACAACACTTGTAAAATAT 58.308 29.630 0.00 0.00 44.59 1.28
928 966 7.971168 CAGGTGACAAACAACACTTGTAAAATA 59.029 33.333 0.00 0.00 44.59 1.40
929 967 6.811170 CAGGTGACAAACAACACTTGTAAAAT 59.189 34.615 0.00 0.00 44.59 1.82
936 976 7.665559 ACATATATCAGGTGACAAACAACACTT 59.334 33.333 0.00 0.00 38.92 3.16
1141 1181 0.544357 TCAGGGACGGTGTTCATCCT 60.544 55.000 0.00 0.00 32.70 3.24
1181 1221 4.104102 TGTTGTCTTCTTGGTGGTAGGATT 59.896 41.667 0.00 0.00 0.00 3.01
1254 1294 2.123342 GCCTCGTTCATCTTGAGATCG 58.877 52.381 0.00 0.00 31.21 3.69
1320 1360 2.560981 GTTGTTTCCCTTGGGGTACATG 59.439 50.000 5.78 0.00 44.74 3.21
1515 1555 4.453480 TCCACCAAGAACTTCATTCCTT 57.547 40.909 0.00 0.00 38.16 3.36
1656 1697 7.441458 AGAACAAACCATGAGTAACAGAGTAAC 59.559 37.037 0.00 0.00 0.00 2.50
1798 1839 7.962373 CGTAGTTATCAGCAAATGAAACAATCA 59.038 33.333 0.00 0.00 42.53 2.57
1812 1853 1.957877 AGGAGGCTCGTAGTTATCAGC 59.042 52.381 8.15 0.00 0.00 4.26
1821 1862 4.407621 TCCATTCAAATAAGGAGGCTCGTA 59.592 41.667 10.52 4.58 0.00 3.43
1824 1865 5.067023 CAGTTCCATTCAAATAAGGAGGCTC 59.933 44.000 5.78 5.78 0.00 4.70
1837 1878 1.074405 AGAGGCTTGCAGTTCCATTCA 59.926 47.619 0.00 0.00 0.00 2.57
1846 1887 3.943381 TGTATTCATGAAGAGGCTTGCAG 59.057 43.478 14.54 0.00 0.00 4.41
1922 1963 4.630894 AATTCAGAAACAGCACACGAAA 57.369 36.364 0.00 0.00 0.00 3.46
1925 1966 3.003689 AGGAAATTCAGAAACAGCACACG 59.996 43.478 0.00 0.00 0.00 4.49
1926 1967 4.574599 AGGAAATTCAGAAACAGCACAC 57.425 40.909 0.00 0.00 0.00 3.82
2128 2169 6.732896 ATAGGAACGTAACATCAGGAGAAT 57.267 37.500 0.00 0.00 0.00 2.40
2143 2184 2.222953 GCACGTTTGGCTAATAGGAACG 60.223 50.000 2.88 2.88 45.96 3.95
2144 2185 3.007635 AGCACGTTTGGCTAATAGGAAC 58.992 45.455 0.00 0.00 40.47 3.62
2146 2187 3.055385 AGAAGCACGTTTGGCTAATAGGA 60.055 43.478 0.00 0.00 41.66 2.94
2180 2221 2.549064 AATTTCAGCCAGGCAAAACC 57.451 45.000 15.80 0.00 39.61 3.27
2183 2224 3.056607 GCTTCTAATTTCAGCCAGGCAAA 60.057 43.478 15.80 6.82 0.00 3.68
2210 2251 7.306983 GCATTTGAAATGGAACTTTGAGAACAG 60.307 37.037 18.52 0.00 0.00 3.16
2229 2270 1.068402 CCAAGACGCATGTGCATTTGA 60.068 47.619 6.08 0.00 42.21 2.69
2243 2284 3.728845 TGTGCTAGAGTTCAACCAAGAC 58.271 45.455 0.00 0.00 0.00 3.01
2247 2288 8.100791 ACTATAATTTGTGCTAGAGTTCAACCA 58.899 33.333 0.00 0.00 0.00 3.67
2263 2304 7.307694 TGCTGAAGAACAAGCACTATAATTTG 58.692 34.615 0.00 0.00 31.54 2.32
2264 2305 7.452880 TGCTGAAGAACAAGCACTATAATTT 57.547 32.000 0.00 0.00 31.54 1.82
2265 2306 7.636150 ATGCTGAAGAACAAGCACTATAATT 57.364 32.000 0.00 0.00 36.25 1.40
2293 2334 5.182760 GCCTGAGACACAAGAAAATCTGATT 59.817 40.000 0.00 0.00 0.00 2.57
2351 2392 2.352960 GCACTTCTTATCTTCCCAAGCG 59.647 50.000 0.00 0.00 0.00 4.68
2528 2594 3.248418 TGGTGCAGCACTGGCCTA 61.248 61.111 24.75 2.71 42.56 3.93
2633 2702 2.620251 TGTTCAGTCCACCTGTCTTG 57.380 50.000 0.00 0.00 42.19 3.02
2639 2708 3.843027 AGATGAGAATGTTCAGTCCACCT 59.157 43.478 0.00 0.00 0.00 4.00
2640 2709 4.187694 GAGATGAGAATGTTCAGTCCACC 58.812 47.826 0.00 0.00 0.00 4.61
2687 2757 0.951040 CTTCCGTCTTGCACAGGTCC 60.951 60.000 0.00 0.00 0.00 4.46
2702 2772 0.107945 AAGCAGATCAGGCGTCTTCC 60.108 55.000 0.00 0.00 36.08 3.46
2722 2792 0.749649 GCAACCACAACCATGTTCCA 59.250 50.000 0.00 0.00 37.82 3.53
2874 2945 1.557371 AGAGGCCTACTTCTTCCAAGC 59.443 52.381 4.42 0.00 0.00 4.01
2877 2948 4.684724 TCTTTAGAGGCCTACTTCTTCCA 58.315 43.478 4.42 0.00 0.00 3.53
3069 3143 3.766591 AGAGACAACAGATACACTCCCAG 59.233 47.826 0.00 0.00 0.00 4.45
3224 3324 1.236616 TTTGGGCACAGCGTCATCAG 61.237 55.000 0.00 0.00 0.00 2.90
3237 3338 1.303091 ACGGAGCGTGTATTTTGGGC 61.303 55.000 0.00 0.00 39.18 5.36
3238 3339 1.129811 GAACGGAGCGTGTATTTTGGG 59.870 52.381 0.00 0.00 39.99 4.12
3240 3341 3.370978 AGATGAACGGAGCGTGTATTTTG 59.629 43.478 0.00 0.00 39.99 2.44
3241 3342 3.596214 AGATGAACGGAGCGTGTATTTT 58.404 40.909 0.00 0.00 39.99 1.82
3242 3343 3.247006 AGATGAACGGAGCGTGTATTT 57.753 42.857 0.00 0.00 39.99 1.40
3244 3345 2.961526 AAGATGAACGGAGCGTGTAT 57.038 45.000 0.00 0.00 39.99 2.29
3245 3346 2.230508 AGAAAGATGAACGGAGCGTGTA 59.769 45.455 0.00 0.00 39.99 2.90
3246 3347 1.000955 AGAAAGATGAACGGAGCGTGT 59.999 47.619 0.00 0.00 39.99 4.49
3247 3348 1.714794 AGAAAGATGAACGGAGCGTG 58.285 50.000 0.00 0.00 39.99 5.34
3248 3349 2.457366 AAGAAAGATGAACGGAGCGT 57.543 45.000 0.00 0.00 43.97 5.07
3249 3350 2.736721 TGAAAGAAAGATGAACGGAGCG 59.263 45.455 0.00 0.00 0.00 5.03
3251 3352 3.741344 ACGTGAAAGAAAGATGAACGGAG 59.259 43.478 0.00 0.00 34.06 4.63
3252 3353 3.724374 ACGTGAAAGAAAGATGAACGGA 58.276 40.909 0.00 0.00 34.06 4.69
3254 3355 5.078153 TGAACGTGAAAGAAAGATGAACG 57.922 39.130 0.00 0.00 35.78 3.95
3255 3356 5.904080 CACTGAACGTGAAAGAAAGATGAAC 59.096 40.000 0.00 0.00 46.81 3.18
3256 3357 5.007626 CCACTGAACGTGAAAGAAAGATGAA 59.992 40.000 0.00 0.00 46.81 2.57
3259 3360 3.251004 GCCACTGAACGTGAAAGAAAGAT 59.749 43.478 0.00 0.00 46.81 2.40
3261 3362 2.614057 AGCCACTGAACGTGAAAGAAAG 59.386 45.455 0.00 0.00 46.81 2.62
3274 3375 5.957771 ATGAAGATTACCTAAGCCACTGA 57.042 39.130 0.00 0.00 0.00 3.41
3278 3379 6.073447 TCCAAATGAAGATTACCTAAGCCA 57.927 37.500 0.00 0.00 0.00 4.75
3279 3380 6.772716 TCATCCAAATGAAGATTACCTAAGCC 59.227 38.462 0.00 0.00 38.97 4.35
3280 3381 7.807977 TCATCCAAATGAAGATTACCTAAGC 57.192 36.000 0.00 0.00 38.97 3.09
3289 3390 9.363401 ACATTCATACATCATCCAAATGAAGAT 57.637 29.630 0.00 0.00 44.85 2.40
3290 3391 8.756486 ACATTCATACATCATCCAAATGAAGA 57.244 30.769 0.00 0.00 44.85 2.87
3291 3392 9.888878 GTACATTCATACATCATCCAAATGAAG 57.111 33.333 0.00 0.00 44.85 3.02
3292 3393 9.631257 AGTACATTCATACATCATCCAAATGAA 57.369 29.630 0.00 0.00 44.85 2.57
3293 3394 9.276590 GAGTACATTCATACATCATCCAAATGA 57.723 33.333 0.00 0.00 45.73 2.57
3294 3395 8.509690 GGAGTACATTCATACATCATCCAAATG 58.490 37.037 0.00 0.00 0.00 2.32
3295 3396 7.667219 GGGAGTACATTCATACATCATCCAAAT 59.333 37.037 0.00 0.00 0.00 2.32
3296 3397 6.998074 GGGAGTACATTCATACATCATCCAAA 59.002 38.462 0.00 0.00 0.00 3.28
3299 3400 6.212388 AGAGGGAGTACATTCATACATCATCC 59.788 42.308 0.00 0.00 0.00 3.51
3300 3401 7.238486 AGAGGGAGTACATTCATACATCATC 57.762 40.000 0.00 0.00 0.00 2.92
3301 3402 6.212388 GGAGAGGGAGTACATTCATACATCAT 59.788 42.308 0.00 0.00 0.00 2.45
3303 3404 5.046950 GGGAGAGGGAGTACATTCATACATC 60.047 48.000 0.00 0.00 0.00 3.06
3304 3405 4.841246 GGGAGAGGGAGTACATTCATACAT 59.159 45.833 0.00 0.00 0.00 2.29
3305 3406 4.223953 GGGAGAGGGAGTACATTCATACA 58.776 47.826 0.00 0.00 0.00 2.29
3306 3407 3.579151 GGGGAGAGGGAGTACATTCATAC 59.421 52.174 0.00 0.00 0.00 2.39
3307 3408 3.754172 CGGGGAGAGGGAGTACATTCATA 60.754 52.174 0.00 0.00 0.00 2.15
3308 3409 2.695585 GGGGAGAGGGAGTACATTCAT 58.304 52.381 0.00 0.00 0.00 2.57
3310 3411 1.041437 CGGGGAGAGGGAGTACATTC 58.959 60.000 0.00 0.00 0.00 2.67
3311 3412 0.338814 ACGGGGAGAGGGAGTACATT 59.661 55.000 0.00 0.00 0.00 2.71
3312 3413 0.338814 AACGGGGAGAGGGAGTACAT 59.661 55.000 0.00 0.00 0.00 2.29
3314 3415 1.397672 GTAACGGGGAGAGGGAGTAC 58.602 60.000 0.00 0.00 0.00 2.73
3315 3416 0.259938 GGTAACGGGGAGAGGGAGTA 59.740 60.000 0.00 0.00 0.00 2.59
3316 3417 1.001376 GGTAACGGGGAGAGGGAGT 59.999 63.158 0.00 0.00 0.00 3.85
3317 3418 0.616679 TTGGTAACGGGGAGAGGGAG 60.617 60.000 0.00 0.00 42.51 4.30
3318 3419 0.178897 TTTGGTAACGGGGAGAGGGA 60.179 55.000 0.00 0.00 42.51 4.20
3319 3420 0.916809 ATTTGGTAACGGGGAGAGGG 59.083 55.000 0.00 0.00 42.51 4.30
3320 3421 5.071384 ACTTATATTTGGTAACGGGGAGAGG 59.929 44.000 0.00 0.00 42.51 3.69
3321 3422 6.041751 AGACTTATATTTGGTAACGGGGAGAG 59.958 42.308 0.00 0.00 42.51 3.20
3322 3423 5.901276 AGACTTATATTTGGTAACGGGGAGA 59.099 40.000 0.00 0.00 42.51 3.71
3323 3424 6.170846 AGACTTATATTTGGTAACGGGGAG 57.829 41.667 0.00 0.00 42.51 4.30
3324 3425 6.564557 AAGACTTATATTTGGTAACGGGGA 57.435 37.500 0.00 0.00 42.51 4.81
3325 3426 7.023197 CAAAGACTTATATTTGGTAACGGGG 57.977 40.000 0.00 0.00 34.09 5.73
3349 3450 5.952347 TTAGGGTTTAGTGGAATCTCTCC 57.048 43.478 0.00 0.00 45.64 3.71
3350 3451 6.070136 AGGTTTAGGGTTTAGTGGAATCTCTC 60.070 42.308 0.00 0.00 0.00 3.20
3358 3459 8.139350 CACTTTAAAAGGTTTAGGGTTTAGTGG 58.861 37.037 0.00 0.00 0.00 4.00
3364 3465 9.650714 AATCTACACTTTAAAAGGTTTAGGGTT 57.349 29.630 3.78 0.00 0.00 4.11
3365 3466 9.293404 GAATCTACACTTTAAAAGGTTTAGGGT 57.707 33.333 3.78 0.00 0.00 4.34
3366 3467 9.292195 TGAATCTACACTTTAAAAGGTTTAGGG 57.708 33.333 3.78 0.00 0.00 3.53
3420 3608 9.660180 AACCTTGAGTCTTTATAGAGATTTCAC 57.340 33.333 8.87 0.00 0.00 3.18
3432 3620 5.932303 GCATCTACACAACCTTGAGTCTTTA 59.068 40.000 0.00 0.00 33.99 1.85
3442 3630 1.905215 AGCTCTGCATCTACACAACCT 59.095 47.619 0.00 0.00 0.00 3.50
3443 3631 2.005451 CAGCTCTGCATCTACACAACC 58.995 52.381 0.00 0.00 0.00 3.77
3444 3632 2.928757 CTCAGCTCTGCATCTACACAAC 59.071 50.000 0.00 0.00 0.00 3.32
3458 3760 2.008329 CAGCTCACCAATTCTCAGCTC 58.992 52.381 0.00 0.00 38.40 4.09
3491 3793 3.181445 ACACAACCTTGATCTAGCCAACA 60.181 43.478 0.00 0.00 0.00 3.33
3493 3795 3.788227 ACACAACCTTGATCTAGCCAA 57.212 42.857 0.00 0.00 0.00 4.52
3495 3797 3.412386 ACAACACAACCTTGATCTAGCC 58.588 45.455 0.00 0.00 0.00 3.93
3529 3831 8.098220 TGTAACACTTGACACGTACTATAAGA 57.902 34.615 0.00 0.00 0.00 2.10
3534 3836 6.151691 GGATTGTAACACTTGACACGTACTA 58.848 40.000 0.00 0.00 0.00 1.82
3535 3837 4.986659 GGATTGTAACACTTGACACGTACT 59.013 41.667 0.00 0.00 0.00 2.73
3536 3838 4.746115 TGGATTGTAACACTTGACACGTAC 59.254 41.667 0.00 0.00 0.00 3.67
3537 3839 4.946445 TGGATTGTAACACTTGACACGTA 58.054 39.130 0.00 0.00 0.00 3.57
3538 3840 3.799366 TGGATTGTAACACTTGACACGT 58.201 40.909 0.00 0.00 0.00 4.49
3544 3846 5.056480 TGTCACTCTGGATTGTAACACTTG 58.944 41.667 0.00 0.00 0.00 3.16
3606 3908 0.178068 CTGGGATGTGTTACCGGGAG 59.822 60.000 6.32 0.00 0.00 4.30
3607 3909 2.292866 CTGGGATGTGTTACCGGGA 58.707 57.895 6.32 0.00 0.00 5.14
3608 3910 1.223487 CCTGGGATGTGTTACCGGG 59.777 63.158 6.32 0.00 43.92 5.73
3609 3911 0.107848 GTCCTGGGATGTGTTACCGG 60.108 60.000 0.00 0.00 0.00 5.28
3610 3912 0.611200 TGTCCTGGGATGTGTTACCG 59.389 55.000 0.00 0.00 0.00 4.02
3651 3956 0.988145 CCTGAGACAGGCCCCCAATA 60.988 60.000 0.00 0.00 45.13 1.90
3652 3957 2.311854 CCTGAGACAGGCCCCCAAT 61.312 63.158 0.00 0.00 45.13 3.16
3671 3976 2.244946 GGTTTCAACCTGCCGAGAC 58.755 57.895 1.08 0.00 45.75 3.36


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

AutoCloner maintained by Alex Coulton.