Multiple sequence alignment - TraesCS5A01G379200

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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 TraesCS5A01G379200 chr5A 100.000 3434 0 0 1 3434 576336730 576340163 0.000000e+00 6342.0
1 TraesCS5A01G379200 chr5A 75.260 578 117 19 1307 1868 69140929 69141496 5.690000e-63 252.0
2 TraesCS5A01G379200 chr5D 95.655 2854 90 16 559 3402 458453584 458456413 0.000000e+00 4553.0
3 TraesCS5A01G379200 chr5B 96.863 2136 50 9 773 2905 561687151 561689272 0.000000e+00 3557.0
4 TraesCS5A01G379200 chr5B 83.456 816 95 18 1 785 561686381 561687187 0.000000e+00 723.0
5 TraesCS5A01G379200 chr5B 72.843 939 189 47 1307 2197 78221002 78220082 9.450000e-66 261.0
6 TraesCS5A01G379200 chr7A 90.230 174 16 1 1246 1419 202520830 202520658 3.450000e-55 226.0
7 TraesCS5A01G379200 chr7A 95.385 65 3 0 1874 1938 202520655 202520591 1.690000e-18 104.0
8 TraesCS5A01G379200 chr7B 89.308 159 16 1 1261 1419 156428587 156428430 7.520000e-47 198.0
9 TraesCS5A01G379200 chr7D 86.034 179 16 5 1246 1419 192928841 192928667 2.100000e-42 183.0
10 TraesCS5A01G379200 chr7D 94.805 77 4 0 1862 1938 192928669 192928593 1.670000e-23 121.0
11 TraesCS5A01G379200 chr6B 94.737 38 1 1 608 644 154307697 154307734 1.330000e-04 58.4
12 TraesCS5A01G379200 chr2D 94.286 35 1 1 456 489 18240957 18240923 6.000000e-03 52.8
13 TraesCS5A01G379200 chr2A 94.286 35 1 1 456 489 19372149 19372115 6.000000e-03 52.8


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 TraesCS5A01G379200 chr5A 576336730 576340163 3433 False 6342 6342 100.0000 1 3434 1 chr5A.!!$F2 3433
1 TraesCS5A01G379200 chr5A 69140929 69141496 567 False 252 252 75.2600 1307 1868 1 chr5A.!!$F1 561
2 TraesCS5A01G379200 chr5D 458453584 458456413 2829 False 4553 4553 95.6550 559 3402 1 chr5D.!!$F1 2843
3 TraesCS5A01G379200 chr5B 561686381 561689272 2891 False 2140 3557 90.1595 1 2905 2 chr5B.!!$F1 2904
4 TraesCS5A01G379200 chr5B 78220082 78221002 920 True 261 261 72.8430 1307 2197 1 chr5B.!!$R1 890

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
145 146 1.067142 GGTGTGCTGATGTCCTAACGA 60.067 52.381 0.00 0.0 0.00 3.85 F
594 625 1.344763 CGAAGGACTGGTTTGAGGAGT 59.655 52.381 0.00 0.0 0.00 3.85 F
2157 2224 2.125753 GTGCACTCCTGCCTCTCG 60.126 66.667 10.32 0.0 43.51 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1149 1183 0.108329 AGTCATTGTAGAACCCGCCG 60.108 55.000 0.00 0.00 0.00 6.46 R
2265 2332 1.807886 GCTGTAGACGATCCACCGT 59.192 57.895 0.00 0.00 46.43 4.83 R
3402 3479 0.580578 CGTGATCGTAGATCGTCGGT 59.419 55.000 14.56 5.58 45.12 4.69 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
25 26 8.062065 TCCTATGGGTTTTGTAAAGCTTAATG 57.938 34.615 0.00 0.00 0.00 1.90
26 27 7.891183 TCCTATGGGTTTTGTAAAGCTTAATGA 59.109 33.333 0.00 0.00 0.00 2.57
33 34 7.253750 GGTTTTGTAAAGCTTAATGATGATGCG 60.254 37.037 0.00 0.00 0.00 4.73
35 36 3.360249 AAAGCTTAATGATGATGCGCC 57.640 42.857 4.18 0.00 0.00 6.53
46 47 4.136051 TGATGATGCGCCTTTTGATCATA 58.864 39.130 15.99 5.40 36.02 2.15
59 60 5.708736 TTTGATCATAACCTGCTTAGGGA 57.291 39.130 0.00 0.00 0.00 4.20
63 64 5.843969 TGATCATAACCTGCTTAGGGATACA 59.156 40.000 0.00 0.00 39.74 2.29
64 65 5.808366 TCATAACCTGCTTAGGGATACAG 57.192 43.478 0.00 0.00 39.74 2.74
65 66 5.216622 TCATAACCTGCTTAGGGATACAGT 58.783 41.667 0.00 0.00 39.74 3.55
66 67 6.378745 TCATAACCTGCTTAGGGATACAGTA 58.621 40.000 0.00 0.00 39.74 2.74
69 70 3.052033 ACCTGCTTAGGGATACAGTAGGT 60.052 47.826 2.65 2.65 45.72 3.08
78 79 4.954826 AGGGATACAGTAGGTGTTGTACTC 59.045 45.833 0.00 0.00 40.94 2.59
85 86 6.482524 ACAGTAGGTGTTGTACTCAGAGATA 58.517 40.000 3.79 0.00 34.94 1.98
142 143 3.008923 TGATTGGTGTGCTGATGTCCTAA 59.991 43.478 0.00 0.00 0.00 2.69
145 146 1.067142 GGTGTGCTGATGTCCTAACGA 60.067 52.381 0.00 0.00 0.00 3.85
192 193 3.760684 AGGCTTATCTCTTGCACAAAAGG 59.239 43.478 0.00 0.00 0.00 3.11
193 194 3.507622 GGCTTATCTCTTGCACAAAAGGT 59.492 43.478 0.00 0.00 0.00 3.50
215 216 4.634443 GTGAGATACAACCGCCTTGTTATT 59.366 41.667 2.44 0.00 40.45 1.40
220 221 8.967664 AGATACAACCGCCTTGTTATTAATTA 57.032 30.769 0.00 0.00 40.45 1.40
255 256 8.493607 TGAAGGTCATCAATACCATGAAGAATA 58.506 33.333 0.00 0.00 39.64 1.75
260 261 8.370940 GTCATCAATACCATGAAGAATAGAGGA 58.629 37.037 0.00 0.00 31.98 3.71
265 266 8.997323 CAATACCATGAAGAATAGAGGATGTTC 58.003 37.037 0.00 0.00 0.00 3.18
270 271 3.742433 AGAATAGAGGATGTTCTGCGG 57.258 47.619 0.00 0.00 37.90 5.69
271 272 2.366916 AGAATAGAGGATGTTCTGCGGG 59.633 50.000 0.00 0.00 37.90 6.13
339 341 2.317040 CTCCTCTTGGAACCGGCTATA 58.683 52.381 0.00 0.00 42.66 1.31
340 342 2.900546 CTCCTCTTGGAACCGGCTATAT 59.099 50.000 0.00 0.00 42.66 0.86
347 349 5.129815 TCTTGGAACCGGCTATATGTAAGTT 59.870 40.000 0.00 0.00 0.00 2.66
348 350 4.699637 TGGAACCGGCTATATGTAAGTTG 58.300 43.478 0.00 0.00 0.00 3.16
395 398 9.319143 AGTCGATTTTCTGAACCATTAGATTAG 57.681 33.333 0.00 0.00 0.00 1.73
418 421 9.798994 TTAGAAATCTAACGGTTGATCTACTTC 57.201 33.333 3.07 0.00 33.83 3.01
420 423 6.540438 AATCTAACGGTTGATCTACTTCCA 57.460 37.500 3.07 0.00 0.00 3.53
421 424 5.578005 TCTAACGGTTGATCTACTTCCAG 57.422 43.478 3.07 1.41 0.00 3.86
422 425 5.014858 TCTAACGGTTGATCTACTTCCAGT 58.985 41.667 3.07 0.00 0.00 4.00
425 428 4.969484 ACGGTTGATCTACTTCCAGTTTT 58.031 39.130 7.24 0.00 0.00 2.43
426 429 5.374071 ACGGTTGATCTACTTCCAGTTTTT 58.626 37.500 7.24 0.00 0.00 1.94
451 461 2.368875 TCTCCTTCAACTGTTCACCCTC 59.631 50.000 0.00 0.00 0.00 4.30
455 465 4.065789 CCTTCAACTGTTCACCCTCTTAC 58.934 47.826 0.00 0.00 0.00 2.34
459 469 5.123227 TCAACTGTTCACCCTCTTACAAAG 58.877 41.667 0.00 0.00 0.00 2.77
469 479 5.469084 CACCCTCTTACAAAGTTGACTTACC 59.531 44.000 0.00 0.00 34.61 2.85
556 566 4.638304 TGTAATAGGGAAGCGAATAAGGC 58.362 43.478 0.00 0.00 0.00 4.35
567 598 3.623510 AGCGAATAAGGCAGCTAGTTTTC 59.376 43.478 0.00 0.00 38.29 2.29
575 606 2.095718 GGCAGCTAGTTTTCCTTCAACG 60.096 50.000 0.00 0.00 0.00 4.10
594 625 1.344763 CGAAGGACTGGTTTGAGGAGT 59.655 52.381 0.00 0.00 0.00 3.85
608 639 7.841729 TGGTTTGAGGAGTCTCTTCTTATAGAT 59.158 37.037 12.72 0.00 40.58 1.98
718 752 8.147642 AGTAATTTATCAGCTGAAGAAATCGG 57.852 34.615 27.32 0.00 37.49 4.18
1065 1099 2.616458 GCACCCCTCCAACATCCCT 61.616 63.158 0.00 0.00 0.00 4.20
1173 1207 3.175109 GGGTTCTACAATGACTACCCG 57.825 52.381 0.00 0.00 36.21 5.28
2157 2224 2.125753 GTGCACTCCTGCCTCTCG 60.126 66.667 10.32 0.00 43.51 4.04
2265 2332 4.980805 GACAACAGCGGCGTGGGA 62.981 66.667 9.37 0.00 0.00 4.37
2452 2519 3.219603 GTCGTCGACACGTACGCG 61.220 66.667 20.28 8.78 46.76 6.01
2644 2711 0.670162 GTTTGCTGCCTTTCAGAGCA 59.330 50.000 0.00 0.00 45.72 4.26
2793 2863 9.745018 TGTGGATCTTTTCTTTTTAGATGATCT 57.255 29.630 0.00 0.00 32.31 2.75
2829 2899 9.522804 TGTAACTGTGACCAAAAATTACATTTC 57.477 29.630 0.00 0.00 0.00 2.17
2831 2901 7.360113 ACTGTGACCAAAAATTACATTTCCT 57.640 32.000 0.00 0.00 0.00 3.36
2933 3005 1.152383 GATTGGGCTTAGACGCGTCC 61.152 60.000 34.08 20.00 0.00 4.79
2956 3028 7.223777 GTCCTATTTCTACTCACTCTTTCATGC 59.776 40.741 0.00 0.00 0.00 4.06
2960 3032 7.807977 TTTCTACTCACTCTTTCATGCTTTT 57.192 32.000 0.00 0.00 0.00 2.27
3038 3110 5.768333 GCTATTTGCAAGTTGCCTAAAAG 57.232 39.130 24.59 17.08 44.23 2.27
3063 3135 4.393062 ACAACTTGCATCAGTCGATTTAGG 59.607 41.667 0.00 0.00 0.00 2.69
3072 3144 4.856509 TCAGTCGATTTAGGAAGAGGAGA 58.143 43.478 0.00 0.00 0.00 3.71
3073 3145 5.262009 TCAGTCGATTTAGGAAGAGGAGAA 58.738 41.667 0.00 0.00 0.00 2.87
3112 3184 2.128507 GGAGGAGACAGGGGTAGCG 61.129 68.421 0.00 0.00 0.00 4.26
3134 3206 2.509336 CGACCATGACGTCCCAGC 60.509 66.667 14.12 0.00 0.00 4.85
3137 3209 1.298859 GACCATGACGTCCCAGCAAC 61.299 60.000 14.12 0.00 0.00 4.17
3162 3234 2.808315 CGGGAGTGATCCGGAGTG 59.192 66.667 11.34 0.00 43.45 3.51
3163 3235 2.786495 CGGGAGTGATCCGGAGTGG 61.786 68.421 11.34 0.00 43.45 4.00
3183 3255 2.032681 GGACCGAAGCAGCTGGTT 59.967 61.111 30.06 30.06 35.75 3.67
3185 3257 1.598130 GACCGAAGCAGCTGGTTGT 60.598 57.895 34.11 25.57 35.75 3.32
3187 3259 1.597854 CCGAAGCAGCTGGTTGTCA 60.598 57.895 34.11 0.00 35.69 3.58
3189 3261 1.845809 CGAAGCAGCTGGTTGTCACC 61.846 60.000 34.11 18.39 44.56 4.02
3201 3278 2.111999 TTGTCACCTGCGAAGGGGAG 62.112 60.000 17.23 3.14 42.93 4.30
3204 3281 3.382832 ACCTGCGAAGGGGAGTCG 61.383 66.667 15.83 0.00 41.46 4.18
3269 3346 4.760530 TGTGATTAGAGAGATGGTTGGG 57.239 45.455 0.00 0.00 0.00 4.12
3276 3353 2.204291 AGATGGTTGGGGGAGGCA 60.204 61.111 0.00 0.00 0.00 4.75
3282 3359 2.780924 TTGGGGGAGGCAGTGGTT 60.781 61.111 0.00 0.00 0.00 3.67
3283 3360 3.145473 TTGGGGGAGGCAGTGGTTG 62.145 63.158 0.00 0.00 0.00 3.77
3342 3419 6.126623 GGAGGAGGTAGGAGAAGATGAAAATT 60.127 42.308 0.00 0.00 0.00 1.82
3343 3420 6.894682 AGGAGGTAGGAGAAGATGAAAATTC 58.105 40.000 0.00 0.00 0.00 2.17
3344 3421 5.755861 GGAGGTAGGAGAAGATGAAAATTCG 59.244 44.000 0.00 0.00 0.00 3.34
3345 3422 5.119694 AGGTAGGAGAAGATGAAAATTCGC 58.880 41.667 0.00 0.00 0.00 4.70
3349 3426 3.691609 GGAGAAGATGAAAATTCGCAGGT 59.308 43.478 0.00 0.00 0.00 4.00
3350 3427 4.437930 GGAGAAGATGAAAATTCGCAGGTG 60.438 45.833 0.00 0.00 0.00 4.00
3402 3479 6.014584 TCAACTGTCAAATAGAGCTCCTTACA 60.015 38.462 10.93 6.15 0.00 2.41
3403 3480 5.725362 ACTGTCAAATAGAGCTCCTTACAC 58.275 41.667 10.93 5.68 0.00 2.90
3404 3481 5.086104 TGTCAAATAGAGCTCCTTACACC 57.914 43.478 10.93 0.00 0.00 4.16
3405 3482 4.113354 GTCAAATAGAGCTCCTTACACCG 58.887 47.826 10.93 0.00 0.00 4.94
3406 3483 4.021229 TCAAATAGAGCTCCTTACACCGA 58.979 43.478 10.93 0.00 0.00 4.69
3407 3484 4.113354 CAAATAGAGCTCCTTACACCGAC 58.887 47.826 10.93 0.00 0.00 4.79
3408 3485 1.376543 TAGAGCTCCTTACACCGACG 58.623 55.000 10.93 0.00 0.00 5.12
3409 3486 0.322277 AGAGCTCCTTACACCGACGA 60.322 55.000 10.93 0.00 0.00 4.20
3410 3487 0.739561 GAGCTCCTTACACCGACGAT 59.260 55.000 0.87 0.00 0.00 3.73
3411 3488 0.739561 AGCTCCTTACACCGACGATC 59.260 55.000 0.00 0.00 0.00 3.69
3412 3489 0.739561 GCTCCTTACACCGACGATCT 59.260 55.000 0.00 0.00 0.00 2.75
3413 3490 1.945394 GCTCCTTACACCGACGATCTA 59.055 52.381 0.00 0.00 0.00 1.98
3414 3491 2.286891 GCTCCTTACACCGACGATCTAC 60.287 54.545 0.00 0.00 0.00 2.59
3416 3493 1.935873 CCTTACACCGACGATCTACGA 59.064 52.381 0.00 0.00 45.77 3.43
3417 3494 2.547211 CCTTACACCGACGATCTACGAT 59.453 50.000 0.00 0.00 45.77 3.73
3418 3495 3.363772 CCTTACACCGACGATCTACGATC 60.364 52.174 0.00 0.00 45.77 3.69
3419 3496 1.660167 ACACCGACGATCTACGATCA 58.340 50.000 0.00 0.00 45.77 2.92
3420 3497 1.329906 ACACCGACGATCTACGATCAC 59.670 52.381 0.00 0.00 45.77 3.06
3421 3498 0.580578 ACCGACGATCTACGATCACG 59.419 55.000 0.00 8.41 45.77 4.35
3422 3499 0.857287 CCGACGATCTACGATCACGA 59.143 55.000 16.15 0.00 45.77 4.35
3423 3500 1.459975 CCGACGATCTACGATCACGAT 59.540 52.381 16.15 0.00 45.77 3.73
3424 3501 2.472560 CCGACGATCTACGATCACGATC 60.473 54.545 16.15 0.00 45.77 3.69
3425 3502 2.409041 CGACGATCTACGATCACGATCT 59.591 50.000 5.55 0.00 45.77 2.75
3426 3503 3.607209 CGACGATCTACGATCACGATCTA 59.393 47.826 5.55 0.00 45.77 1.98
3427 3504 4.489048 CGACGATCTACGATCACGATCTAC 60.489 50.000 5.55 6.67 45.77 2.59
3428 3505 3.364322 ACGATCTACGATCACGATCTACG 59.636 47.826 5.55 0.00 45.77 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.382227 TGATCAAAAGGCGCATCATCATT 59.618 39.130 10.83 0.00 0.00 2.57
23 24 2.953648 TGATCAAAAGGCGCATCATCAT 59.046 40.909 10.83 0.00 0.00 2.45
25 26 3.637998 ATGATCAAAAGGCGCATCATC 57.362 42.857 10.83 3.00 31.59 2.92
26 27 4.261741 GGTTATGATCAAAAGGCGCATCAT 60.262 41.667 18.85 18.85 39.01 2.45
33 34 4.725790 AAGCAGGTTATGATCAAAAGGC 57.274 40.909 0.00 0.00 0.00 4.35
35 36 6.122277 TCCCTAAGCAGGTTATGATCAAAAG 58.878 40.000 0.00 0.00 40.79 2.27
46 47 3.967987 CCTACTGTATCCCTAAGCAGGTT 59.032 47.826 0.00 0.00 40.79 3.50
59 60 6.482524 TCTCTGAGTACAACACCTACTGTAT 58.517 40.000 4.32 0.00 31.05 2.29
63 64 9.696572 TTATTATCTCTGAGTACAACACCTACT 57.303 33.333 4.32 0.00 0.00 2.57
66 67 9.036980 ACTTTATTATCTCTGAGTACAACACCT 57.963 33.333 4.32 0.00 0.00 4.00
111 112 5.748402 TCAGCACACCAATCAATCTTCTAT 58.252 37.500 0.00 0.00 0.00 1.98
115 116 4.084287 ACATCAGCACACCAATCAATCTT 58.916 39.130 0.00 0.00 0.00 2.40
118 119 2.756760 GGACATCAGCACACCAATCAAT 59.243 45.455 0.00 0.00 0.00 2.57
148 149 7.233553 AGCCTAATCTAAGAGCCAAAACTTTTT 59.766 33.333 0.00 0.00 0.00 1.94
149 150 6.721668 AGCCTAATCTAAGAGCCAAAACTTTT 59.278 34.615 0.00 0.00 0.00 2.27
150 151 6.249192 AGCCTAATCTAAGAGCCAAAACTTT 58.751 36.000 0.00 0.00 0.00 2.66
162 163 7.212976 TGTGCAAGAGATAAGCCTAATCTAAG 58.787 38.462 0.00 0.00 33.82 2.18
167 168 6.096001 CCTTTTGTGCAAGAGATAAGCCTAAT 59.904 38.462 4.32 0.00 0.00 1.73
170 171 3.760684 CCTTTTGTGCAAGAGATAAGCCT 59.239 43.478 4.32 0.00 0.00 4.58
225 226 9.948964 CTTCATGGTATTGATGACCTTCATATA 57.051 33.333 0.00 0.00 37.20 0.86
236 237 9.163899 CATCCTCTATTCTTCATGGTATTGATG 57.836 37.037 0.00 0.00 0.00 3.07
243 244 6.590068 CAGAACATCCTCTATTCTTCATGGT 58.410 40.000 0.00 0.00 30.17 3.55
255 256 1.965754 GCTCCCGCAGAACATCCTCT 61.966 60.000 0.00 0.00 35.78 3.69
281 282 6.973229 AAATAACAATCATCAAAAGCTGCC 57.027 33.333 0.00 0.00 0.00 4.85
311 313 3.756117 GGTTCCAAGAGGAGTTTCACAT 58.244 45.455 0.00 0.00 46.74 3.21
319 321 1.123928 ATAGCCGGTTCCAAGAGGAG 58.876 55.000 1.90 0.00 46.74 3.69
347 349 9.340695 CGACTAACTCAAAATAAATTTCATGCA 57.659 29.630 0.00 0.00 0.00 3.96
348 350 9.554724 TCGACTAACTCAAAATAAATTTCATGC 57.445 29.630 0.00 0.00 0.00 4.06
364 367 6.969828 ATGGTTCAGAAAATCGACTAACTC 57.030 37.500 0.00 0.00 0.00 3.01
365 368 8.311836 TCTAATGGTTCAGAAAATCGACTAACT 58.688 33.333 0.00 0.00 0.00 2.24
395 398 7.039882 TGGAAGTAGATCAACCGTTAGATTTC 58.960 38.462 0.00 0.00 0.00 2.17
425 428 4.881850 GGTGAACAGTTGAAGGAGAGAAAA 59.118 41.667 0.00 0.00 0.00 2.29
426 429 4.451900 GGTGAACAGTTGAAGGAGAGAAA 58.548 43.478 0.00 0.00 0.00 2.52
427 430 3.181454 GGGTGAACAGTTGAAGGAGAGAA 60.181 47.826 0.00 0.00 0.00 2.87
428 431 2.368875 GGGTGAACAGTTGAAGGAGAGA 59.631 50.000 0.00 0.00 0.00 3.10
429 432 2.370189 AGGGTGAACAGTTGAAGGAGAG 59.630 50.000 0.00 0.00 0.00 3.20
430 433 2.368875 GAGGGTGAACAGTTGAAGGAGA 59.631 50.000 0.00 0.00 0.00 3.71
431 434 2.370189 AGAGGGTGAACAGTTGAAGGAG 59.630 50.000 0.00 0.00 0.00 3.69
434 437 4.703897 TGTAAGAGGGTGAACAGTTGAAG 58.296 43.478 0.00 0.00 0.00 3.02
437 440 4.881850 ACTTTGTAAGAGGGTGAACAGTTG 59.118 41.667 0.00 0.00 0.00 3.16
438 441 5.112129 ACTTTGTAAGAGGGTGAACAGTT 57.888 39.130 0.00 0.00 0.00 3.16
439 442 4.772886 ACTTTGTAAGAGGGTGAACAGT 57.227 40.909 0.00 0.00 0.00 3.55
440 443 5.007724 GTCAACTTTGTAAGAGGGTGAACAG 59.992 44.000 0.00 0.00 0.00 3.16
506 516 8.208903 TGCTTAAAACTAGTAAGAGGAAACACT 58.791 33.333 7.87 0.00 31.37 3.55
521 531 8.899771 GCTTCCCTATTACAATGCTTAAAACTA 58.100 33.333 0.00 0.00 0.00 2.24
528 538 4.150897 TCGCTTCCCTATTACAATGCTT 57.849 40.909 0.00 0.00 0.00 3.91
530 540 6.348540 CCTTATTCGCTTCCCTATTACAATGC 60.349 42.308 0.00 0.00 0.00 3.56
541 551 0.464554 AGCTGCCTTATTCGCTTCCC 60.465 55.000 0.00 0.00 0.00 3.97
556 566 5.023551 CTTCGTTGAAGGAAAACTAGCTG 57.976 43.478 0.00 0.00 36.16 4.24
575 606 2.635427 AGACTCCTCAAACCAGTCCTTC 59.365 50.000 0.00 0.00 37.82 3.46
581 612 4.615588 AAGAAGAGACTCCTCAAACCAG 57.384 45.455 3.93 0.00 41.87 4.00
665 696 2.159028 AGCCTCCTAAAGAATGAGTCGC 60.159 50.000 0.00 0.00 0.00 5.19
705 739 0.392998 TCCTGCCCGATTTCTTCAGC 60.393 55.000 0.00 0.00 0.00 4.26
708 742 5.278512 GGATAATTTCCTGCCCGATTTCTTC 60.279 44.000 0.00 0.00 41.78 2.87
711 745 3.058224 CGGATAATTTCCTGCCCGATTTC 60.058 47.826 0.00 0.00 42.99 2.17
718 752 4.022849 CAGGAATTCGGATAATTTCCTGCC 60.023 45.833 15.35 0.00 42.99 4.85
732 766 1.202348 GTTTTGGAGCCCAGGAATTCG 59.798 52.381 0.00 0.00 33.81 3.34
733 767 2.529632 AGTTTTGGAGCCCAGGAATTC 58.470 47.619 0.00 0.00 33.81 2.17
741 775 3.392882 CATTTCACAAGTTTTGGAGCCC 58.607 45.455 0.00 0.00 34.12 5.19
1065 1099 2.181777 GAGTGCGACATCGGCAGA 59.818 61.111 3.08 0.00 40.23 4.26
1147 1181 2.124860 ATTGTAGAACCCGCCGCC 60.125 61.111 0.00 0.00 0.00 6.13
1148 1182 1.448893 TCATTGTAGAACCCGCCGC 60.449 57.895 0.00 0.00 0.00 6.53
1149 1183 0.108329 AGTCATTGTAGAACCCGCCG 60.108 55.000 0.00 0.00 0.00 6.46
1173 1207 4.742201 TCGCCGCTGAAGCTGGAC 62.742 66.667 14.60 7.18 39.32 4.02
2181 2248 4.457496 ACGGCGAGGCACCTGATG 62.457 66.667 16.62 0.00 0.00 3.07
2265 2332 1.807886 GCTGTAGACGATCCACCGT 59.192 57.895 0.00 0.00 46.43 4.83
2452 2519 2.051345 CTTGTGCGTTCCGTTGGC 60.051 61.111 0.00 0.00 0.00 4.52
2644 2711 0.712380 AAATGTCCCTTGGCCCTGAT 59.288 50.000 0.00 0.00 0.00 2.90
2792 2862 8.918961 TTGGTCACAGTTACAAACAAAATAAG 57.081 30.769 0.00 0.00 0.00 1.73
2793 2863 9.706691 TTTTGGTCACAGTTACAAACAAAATAA 57.293 25.926 0.00 0.00 33.31 1.40
2829 2899 4.573900 ACAAGACAGAAGATAAGCACAGG 58.426 43.478 0.00 0.00 0.00 4.00
2831 2901 6.054941 TGAAACAAGACAGAAGATAAGCACA 58.945 36.000 0.00 0.00 0.00 4.57
2912 2982 0.460284 ACGCGTCTAAGCCCAATCTG 60.460 55.000 5.58 0.00 0.00 2.90
2914 2984 1.152383 GGACGCGTCTAAGCCCAATC 61.152 60.000 35.50 13.58 0.00 2.67
2916 2986 0.966875 TAGGACGCGTCTAAGCCCAA 60.967 55.000 35.50 10.45 0.00 4.12
2917 2987 0.754217 ATAGGACGCGTCTAAGCCCA 60.754 55.000 35.50 11.85 0.00 5.36
2918 2988 0.388294 AATAGGACGCGTCTAAGCCC 59.612 55.000 35.50 20.73 0.00 5.19
2920 2990 3.081329 AGAAATAGGACGCGTCTAAGC 57.919 47.619 35.50 20.66 0.00 3.09
2921 2991 5.007430 TGAGTAGAAATAGGACGCGTCTAAG 59.993 44.000 35.50 0.00 0.00 2.18
2922 2992 4.877823 TGAGTAGAAATAGGACGCGTCTAA 59.122 41.667 35.50 24.64 0.00 2.10
2923 2993 4.272018 GTGAGTAGAAATAGGACGCGTCTA 59.728 45.833 35.50 25.19 0.00 2.59
2924 2994 3.065095 GTGAGTAGAAATAGGACGCGTCT 59.935 47.826 35.50 23.99 0.00 4.18
2933 3005 8.715191 AAGCATGAAAGAGTGAGTAGAAATAG 57.285 34.615 0.00 0.00 0.00 1.73
3038 3110 4.928661 AATCGACTGATGCAAGTTGTAC 57.071 40.909 4.48 0.00 34.24 2.90
3063 3135 3.465871 GCATCACCATCTTCTCCTCTTC 58.534 50.000 0.00 0.00 0.00 2.87
3072 3144 2.117156 GGCTGCGCATCACCATCTT 61.117 57.895 12.24 0.00 0.00 2.40
3073 3145 2.515523 GGCTGCGCATCACCATCT 60.516 61.111 12.24 0.00 0.00 2.90
3118 3190 1.003839 TTGCTGGGACGTCATGGTC 60.004 57.895 18.91 0.00 36.18 4.02
3123 3195 4.980805 GGCGTTGCTGGGACGTCA 62.981 66.667 18.91 0.00 43.98 4.35
3154 3226 4.753662 CGGTCCTCCCACTCCGGA 62.754 72.222 2.93 2.93 39.41 5.14
3162 3234 3.394836 AGCTGCTTCGGTCCTCCC 61.395 66.667 0.00 0.00 0.00 4.30
3163 3235 2.125350 CAGCTGCTTCGGTCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
3183 3255 2.525629 TCCCCTTCGCAGGTGACA 60.526 61.111 0.00 0.00 38.79 3.58
3185 3257 2.203788 ACTCCCCTTCGCAGGTGA 60.204 61.111 0.00 0.00 38.79 4.02
3187 3259 3.382832 CGACTCCCCTTCGCAGGT 61.383 66.667 0.00 0.00 38.79 4.00
3189 3261 3.068691 TCCGACTCCCCTTCGCAG 61.069 66.667 0.00 0.00 35.06 5.18
3193 3270 0.903454 TCAACCTCCGACTCCCCTTC 60.903 60.000 0.00 0.00 0.00 3.46
3201 3278 2.126031 GCTCCGTCAACCTCCGAC 60.126 66.667 0.00 0.00 0.00 4.79
3204 3281 2.240162 ATTCCGCTCCGTCAACCTCC 62.240 60.000 0.00 0.00 0.00 4.30
3228 3305 2.494530 CCTCCTCTCTAGCGTGGGC 61.495 68.421 1.19 0.00 40.37 5.36
3269 3346 4.284550 TGCCAACCACTGCCTCCC 62.285 66.667 0.00 0.00 0.00 4.30
3276 3353 1.764571 TAGCCGAACTGCCAACCACT 61.765 55.000 0.00 0.00 0.00 4.00
3282 3359 0.739462 CGACATTAGCCGAACTGCCA 60.739 55.000 0.00 0.00 0.00 4.92
3283 3360 0.739813 ACGACATTAGCCGAACTGCC 60.740 55.000 0.00 0.00 0.00 4.85
3344 3421 4.295051 TGAAAAACTAAAATCGCACCTGC 58.705 39.130 0.00 0.00 37.78 4.85
3345 3422 5.283717 CGATGAAAAACTAAAATCGCACCTG 59.716 40.000 0.00 0.00 34.42 4.00
3349 3426 4.162812 GCCGATGAAAAACTAAAATCGCA 58.837 39.130 0.00 0.00 38.97 5.10
3350 3427 4.162812 TGCCGATGAAAAACTAAAATCGC 58.837 39.130 0.00 0.00 38.97 4.58
3352 3429 8.017587 ACAATTGCCGATGAAAAACTAAAATC 57.982 30.769 5.05 0.00 0.00 2.17
3402 3479 0.580578 CGTGATCGTAGATCGTCGGT 59.419 55.000 14.56 5.58 45.12 4.69
3403 3480 0.857287 TCGTGATCGTAGATCGTCGG 59.143 55.000 18.82 5.78 45.12 4.79
3404 3481 2.409041 AGATCGTGATCGTAGATCGTCG 59.591 50.000 14.86 15.53 45.12 5.12
3405 3482 4.489048 CGTAGATCGTGATCGTAGATCGTC 60.489 50.000 14.86 11.98 43.87 4.20
3406 3483 3.364322 CGTAGATCGTGATCGTAGATCGT 59.636 47.826 14.86 9.07 43.87 3.73
3407 3484 3.902085 CGTAGATCGTGATCGTAGATCG 58.098 50.000 14.86 5.28 43.87 3.69


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

AutoCloner maintained by Alex Coulton.