Multiple sequence alignment - TraesCS5A01G277000

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 TraesCS5A01G277000 chr5A 100.000 3599 0 0 1 3599 486756339 486759937 0.000000e+00 6647.0
1 TraesCS5A01G277000 chr5A 85.224 1428 167 21 653 2069 486748729 486750123 0.000000e+00 1428.0
2 TraesCS5A01G277000 chr5A 84.674 522 68 5 2160 2671 486750143 486750662 8.910000e-141 510.0
3 TraesCS5A01G277000 chr5A 83.237 519 60 19 662 1162 485534193 485534702 5.480000e-123 451.0
4 TraesCS5A01G277000 chr5A 78.967 542 83 18 651 1171 485603900 485603369 1.240000e-89 340.0
5 TraesCS5A01G277000 chr5A 84.536 291 41 4 3295 3584 676758902 676759189 5.880000e-73 285.0
6 TraesCS5A01G277000 chr5A 87.500 232 25 3 384 614 486748342 486748570 7.660000e-67 265.0
7 TraesCS5A01G277000 chr5A 84.052 232 32 4 384 611 485533562 485533792 6.050000e-53 219.0
8 TraesCS5A01G277000 chr5A 88.372 129 12 2 21 149 485533256 485533381 6.220000e-33 152.0
9 TraesCS5A01G277000 chr5A 83.234 167 17 4 20 176 486747967 486748132 3.750000e-30 143.0
10 TraesCS5A01G277000 chr5B 95.679 2291 79 10 680 2952 462325301 462327589 0.000000e+00 3664.0
11 TraesCS5A01G277000 chr5B 85.633 1399 157 21 683 2069 462309716 462311082 0.000000e+00 1430.0
12 TraesCS5A01G277000 chr5B 88.244 689 41 14 9 690 462322759 462323414 0.000000e+00 787.0
13 TraesCS5A01G277000 chr5B 77.372 1370 243 46 1272 2600 461581157 461582500 0.000000e+00 750.0
14 TraesCS5A01G277000 chr5B 82.759 725 86 24 2160 2865 462311102 462311806 8.540000e-171 610.0
15 TraesCS5A01G277000 chr5B 95.082 305 12 2 3295 3597 462328863 462329166 9.040000e-131 477.0
16 TraesCS5A01G277000 chr5B 85.327 443 52 9 724 1162 461699538 461699971 2.550000e-121 446.0
17 TraesCS5A01G277000 chr5B 87.931 290 32 2 3295 3584 459046294 459046580 4.450000e-89 339.0
18 TraesCS5A01G277000 chr5B 95.588 204 7 1 2949 3150 462327808 462328011 3.470000e-85 326.0
19 TraesCS5A01G277000 chr5B 79.412 442 60 19 182 614 462309120 462309539 2.120000e-72 283.0
20 TraesCS5A01G277000 chr5B 84.052 232 31 4 384 612 461580159 461580387 6.050000e-53 219.0
21 TraesCS5A01G277000 chr5B 84.431 167 15 4 20 176 462308920 462309085 1.730000e-33 154.0
22 TraesCS5A01G277000 chr5D 94.228 1542 59 16 9 1540 384981039 384982560 0.000000e+00 2327.0
23 TraesCS5A01G277000 chr5D 85.999 2007 228 27 675 2669 384739174 384737209 0.000000e+00 2100.0
24 TraesCS5A01G277000 chr5D 85.094 1429 158 28 653 2069 384975846 384977231 0.000000e+00 1408.0
25 TraesCS5A01G277000 chr5D 97.778 405 9 0 1542 1946 384982691 384983095 0.000000e+00 699.0
26 TraesCS5A01G277000 chr5D 95.584 385 17 0 2201 2585 384983094 384983478 5.110000e-173 617.0
27 TraesCS5A01G277000 chr5D 82.507 726 88 24 2160 2866 384977253 384977958 5.140000e-168 601.0
28 TraesCS5A01G277000 chr5D 92.468 385 16 4 2581 2952 384983620 384984004 4.090000e-149 538.0
29 TraesCS5A01G277000 chr5D 77.512 836 143 31 1798 2598 384670314 384669489 9.100000e-126 460.0
30 TraesCS5A01G277000 chr5D 85.398 452 50 11 720 1165 384683518 384683077 4.240000e-124 455.0
31 TraesCS5A01G277000 chr5D 93.115 305 16 3 3295 3597 384984976 384985277 3.300000e-120 442.0
32 TraesCS5A01G277000 chr5D 96.970 198 5 1 2949 3146 384984057 384984253 7.450000e-87 331.0
33 TraesCS5A01G277000 chr5D 80.682 440 53 21 182 614 384975273 384975687 2.700000e-81 313.0
34 TraesCS5A01G277000 chr5D 85.345 232 26 4 384 614 384683961 384683737 2.160000e-57 233.0
35 TraesCS5A01G277000 chr2A 86.219 283 35 3 3295 3576 17864234 17863955 1.620000e-78 303.0
36 TraesCS5A01G277000 chr2A 96.875 32 1 0 3030 3061 735331526 735331495 2.000000e-03 54.7
37 TraesCS5A01G277000 chr1B 85.714 287 38 2 3300 3584 16425933 16425648 2.100000e-77 300.0
38 TraesCS5A01G277000 chr1B 84.669 287 42 1 3300 3584 39819153 39818867 5.880000e-73 285.0
39 TraesCS5A01G277000 chr3A 83.803 284 43 3 3301 3584 542228057 542227777 2.130000e-67 267.0
40 TraesCS5A01G277000 chr3B 83.219 292 46 2 3295 3584 208755166 208755456 7.660000e-67 265.0


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 TraesCS5A01G277000 chr5A 486756339 486759937 3598 False 6647.000000 6647 100.000000 1 3599 1 chr5A.!!$F1 3598
1 TraesCS5A01G277000 chr5A 486747967 486750662 2695 False 586.500000 1428 85.158000 20 2671 4 chr5A.!!$F4 2651
2 TraesCS5A01G277000 chr5A 485603369 485603900 531 True 340.000000 340 78.967000 651 1171 1 chr5A.!!$R1 520
3 TraesCS5A01G277000 chr5A 485533256 485534702 1446 False 274.000000 451 85.220333 21 1162 3 chr5A.!!$F3 1141
4 TraesCS5A01G277000 chr5B 462322759 462329166 6407 False 1313.500000 3664 93.648250 9 3597 4 chr5B.!!$F5 3588
5 TraesCS5A01G277000 chr5B 462308920 462311806 2886 False 619.250000 1430 83.058750 20 2865 4 chr5B.!!$F4 2845
6 TraesCS5A01G277000 chr5B 461580159 461582500 2341 False 484.500000 750 80.712000 384 2600 2 chr5B.!!$F3 2216
7 TraesCS5A01G277000 chr5D 384737209 384739174 1965 True 2100.000000 2100 85.999000 675 2669 1 chr5D.!!$R2 1994
8 TraesCS5A01G277000 chr5D 384975273 384985277 10004 False 808.444444 2327 90.936222 9 3597 9 chr5D.!!$F1 3588
9 TraesCS5A01G277000 chr5D 384669489 384670314 825 True 460.000000 460 77.512000 1798 2598 1 chr5D.!!$R1 800
10 TraesCS5A01G277000 chr5D 384683077 384683961 884 True 344.000000 455 85.371500 384 1165 2 chr5D.!!$R3 781

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
136 145 0.894184 TCCCTAGCTCGGCCTATTCG 60.894 60.000 0.00 0.0 0.00 3.34 F
322 365 0.958822 ATTGTGTCGGCTGTTTTCCC 59.041 50.000 0.00 0.0 0.00 3.97 F
1333 9577 1.068895 CGATCCAGCAGCTTCATCTCT 59.931 52.381 0.00 0.0 0.00 3.10 F
1691 10064 0.521735 GGTCGCCAAGATGTTGTTCC 59.478 55.000 1.49 0.0 30.95 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 9318 1.913778 TGACAGCAATGTGAAGCCAT 58.086 45.0 0.00 0.0 0.00 4.40 R
1691 10064 2.370189 AGAAGATCGGCCCAAGGATAAG 59.630 50.0 0.00 0.0 0.00 1.73 R
2334 10763 0.322975 ACTCAACCATGCTCTTCGCT 59.677 50.0 0.00 0.0 40.11 4.93 R
3370 12969 0.937304 GTGGTAGTATGCATGTGCCG 59.063 55.0 10.16 0.0 41.18 5.69 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
88 89 2.975799 GTCGCCGGCCAACTCAAA 60.976 61.111 23.46 0.00 0.00 2.69
89 90 2.203224 TCGCCGGCCAACTCAAAA 60.203 55.556 23.46 0.00 0.00 2.44
90 91 2.255252 CGCCGGCCAACTCAAAAG 59.745 61.111 23.46 0.00 0.00 2.27
91 92 2.650778 GCCGGCCAACTCAAAAGG 59.349 61.111 18.11 0.00 0.00 3.11
102 103 3.679824 ACTCAAAAGGCGTAGTAAGCT 57.320 42.857 8.01 0.00 34.52 3.74
110 111 2.582436 GTAGTAAGCTGCCCGCCA 59.418 61.111 0.00 0.00 40.39 5.69
136 145 0.894184 TCCCTAGCTCGGCCTATTCG 60.894 60.000 0.00 0.00 0.00 3.34
137 146 0.894184 CCCTAGCTCGGCCTATTCGA 60.894 60.000 0.00 0.00 35.24 3.71
149 158 2.748605 CCTATTCGACTCTGCCATGTC 58.251 52.381 0.00 0.00 0.00 3.06
169 180 1.471287 CTTGTGTGCATGTCCTGATGG 59.529 52.381 0.00 0.00 0.00 3.51
176 187 2.374170 TGCATGTCCTGATGGCATCTAT 59.626 45.455 26.49 11.27 31.15 1.98
177 188 3.583966 TGCATGTCCTGATGGCATCTATA 59.416 43.478 26.49 11.88 31.15 1.31
179 190 4.575236 GCATGTCCTGATGGCATCTATATG 59.425 45.833 26.49 22.47 36.09 1.78
268 311 2.665649 TGTTTGCGGTCGATCTGTAT 57.334 45.000 0.00 0.00 0.00 2.29
270 313 4.316205 TGTTTGCGGTCGATCTGTATAT 57.684 40.909 0.00 0.00 0.00 0.86
271 314 4.048504 TGTTTGCGGTCGATCTGTATATG 58.951 43.478 0.00 0.00 0.00 1.78
310 353 1.927895 CGGGAGCACTCTATTGTGTC 58.072 55.000 0.00 0.00 39.89 3.67
311 354 1.799181 CGGGAGCACTCTATTGTGTCG 60.799 57.143 0.00 0.00 39.89 4.35
322 365 0.958822 ATTGTGTCGGCTGTTTTCCC 59.041 50.000 0.00 0.00 0.00 3.97
337 380 5.768317 TGTTTTCCCAAGATAAAAAGAGCG 58.232 37.500 0.00 0.00 0.00 5.03
358 442 5.104900 AGCGGTATACTTGTTCTCTTCCATT 60.105 40.000 2.25 0.00 0.00 3.16
367 451 2.948315 GTTCTCTTCCATTGGCATCTCC 59.052 50.000 0.00 0.00 0.00 3.71
368 452 1.492176 TCTCTTCCATTGGCATCTCCC 59.508 52.381 0.00 0.00 0.00 4.30
380 465 7.069826 CCATTGGCATCTCCCTTATTCTAAAAA 59.930 37.037 0.00 0.00 0.00 1.94
381 466 8.645110 CATTGGCATCTCCCTTATTCTAAAAAT 58.355 33.333 0.00 0.00 0.00 1.82
382 467 7.587037 TGGCATCTCCCTTATTCTAAAAATG 57.413 36.000 0.00 0.00 0.00 2.32
437 522 2.943036 TCCGTAGCCAAAAGAAAGGT 57.057 45.000 0.00 0.00 0.00 3.50
542 636 9.602568 TCATTAAATGCTGATAATTTGCAACAT 57.397 25.926 0.00 0.00 40.24 2.71
986 3360 1.942657 GGTGGATGGATTGTCATGTCG 59.057 52.381 0.00 0.00 0.00 4.35
1019 3393 3.181483 GCGATGGATCTTGCAAGGAAAAT 60.181 43.478 25.73 12.14 0.00 1.82
1162 9361 3.138283 ACCAGGGATTGAAGAACTTGACA 59.862 43.478 0.00 0.00 0.00 3.58
1333 9577 1.068895 CGATCCAGCAGCTTCATCTCT 59.931 52.381 0.00 0.00 0.00 3.10
1341 9585 3.626670 AGCAGCTTCATCTCTACAATTGC 59.373 43.478 5.05 0.00 0.00 3.56
1389 9633 3.195825 GCCACTTAAGAAGCCTGACTAGA 59.804 47.826 10.09 0.00 0.00 2.43
1691 10064 0.521735 GGTCGCCAAGATGTTGTTCC 59.478 55.000 1.49 0.00 30.95 3.62
1741 10114 2.941720 GTGCCACATCTTGAAGATCTCC 59.058 50.000 4.39 0.00 31.32 3.71
1836 10212 4.806056 GCAACTTGCATTTCGTTATGAC 57.194 40.909 8.97 0.00 44.26 3.06
1996 10372 4.104738 TGTCCTTCCTTGGAGACTTTCATT 59.895 41.667 9.47 0.00 36.69 2.57
2113 10530 8.547967 TTCTACACTCAACCTTAAAATAGCAG 57.452 34.615 0.00 0.00 0.00 4.24
2143 10561 9.158097 ACATTTATTTTTATATGCCTGGTGGAT 57.842 29.630 0.00 0.00 34.57 3.41
2167 10585 7.439157 TCCATGCATTAGTTTGAGTATATGC 57.561 36.000 0.00 0.00 38.97 3.14
2252 10681 2.747446 TGAGGCAAGAATCGGTTTTAGC 59.253 45.455 0.00 0.00 0.00 3.09
2334 10763 6.577103 TGTGTTTATCATTGGCTTTTGTTCA 58.423 32.000 0.00 0.00 0.00 3.18
2337 10766 2.420628 TCATTGGCTTTTGTTCAGCG 57.579 45.000 0.00 0.00 38.24 5.18
2483 10912 3.396560 CGATGAGCAAGCATATGAGGAA 58.603 45.455 6.97 0.00 0.00 3.36
2600 11176 6.093495 CGGTGCAATACTCTTGAAATTTAGGA 59.907 38.462 0.00 0.00 0.00 2.94
2706 11305 6.987404 TCGCAAGTATAAGTGGTATTTGCATA 59.013 34.615 11.89 0.00 41.83 3.14
2798 11401 8.893727 GTCTTTATTTGGCTGTATCTGTATTGT 58.106 33.333 0.00 0.00 0.00 2.71
2897 11502 3.607641 CACAACATTTAAATGATGCGCGT 59.392 39.130 30.18 12.80 41.30 6.01
2904 11509 4.718858 TTAAATGATGCGCGTACCATAC 57.281 40.909 3.86 0.00 0.00 2.39
3148 11978 7.937649 ACTAGCGAAACATGTATACTATGTCA 58.062 34.615 16.29 0.00 37.77 3.58
3149 11979 8.577296 ACTAGCGAAACATGTATACTATGTCAT 58.423 33.333 16.29 11.11 37.77 3.06
3150 11980 7.643528 AGCGAAACATGTATACTATGTCATG 57.356 36.000 16.29 8.57 42.00 3.07
3151 11981 7.433680 AGCGAAACATGTATACTATGTCATGA 58.566 34.615 16.29 0.00 39.68 3.07
3152 11982 7.926018 AGCGAAACATGTATACTATGTCATGAA 59.074 33.333 16.29 0.00 39.68 2.57
3153 11983 8.217115 GCGAAACATGTATACTATGTCATGAAG 58.783 37.037 16.29 0.00 39.68 3.02
3154 11984 9.463443 CGAAACATGTATACTATGTCATGAAGA 57.537 33.333 16.29 0.00 39.68 2.87
3179 12009 9.495572 GAATCTAACTATACTTCCTTTGGATGG 57.504 37.037 4.84 0.00 32.06 3.51
3180 12010 8.798975 ATCTAACTATACTTCCTTTGGATGGA 57.201 34.615 4.84 0.00 32.06 3.41
3181 12011 8.618240 TCTAACTATACTTCCTTTGGATGGAA 57.382 34.615 4.84 0.00 40.85 3.53
3182 12012 9.053472 TCTAACTATACTTCCTTTGGATGGAAA 57.947 33.333 0.00 0.00 42.29 3.13
3183 12013 9.853177 CTAACTATACTTCCTTTGGATGGAAAT 57.147 33.333 0.00 0.00 42.29 2.17
3190 12020 8.697507 ACTTCCTTTGGATGGAAATATATGTC 57.302 34.615 0.00 0.00 42.29 3.06
3191 12021 8.281531 ACTTCCTTTGGATGGAAATATATGTCA 58.718 33.333 5.26 0.00 42.29 3.58
3192 12022 9.305555 CTTCCTTTGGATGGAAATATATGTCAT 57.694 33.333 5.26 1.12 42.29 3.06
3193 12023 8.640063 TCCTTTGGATGGAAATATATGTCATG 57.360 34.615 5.26 0.00 0.00 3.07
3194 12024 8.447200 TCCTTTGGATGGAAATATATGTCATGA 58.553 33.333 5.26 0.00 0.00 3.07
3195 12025 9.251440 CCTTTGGATGGAAATATATGTCATGAT 57.749 33.333 0.00 0.00 0.00 2.45
3197 12027 9.810870 TTTGGATGGAAATATATGTCATGATGA 57.189 29.630 0.00 0.00 0.00 2.92
3235 12065 4.946160 ACTCCCTTTGGATGGAAATACA 57.054 40.909 0.00 0.00 40.80 2.29
3236 12066 5.269554 ACTCCCTTTGGATGGAAATACAA 57.730 39.130 0.00 0.00 40.80 2.41
3237 12067 5.650283 ACTCCCTTTGGATGGAAATACAAA 58.350 37.500 0.00 0.00 40.80 2.83
3239 12069 6.730507 ACTCCCTTTGGATGGAAATACAAATT 59.269 34.615 0.00 0.00 40.80 1.82
3243 12073 7.365831 CCCTTTGGATGGAAATACAAATTGGAT 60.366 37.037 0.00 0.00 32.99 3.41
3244 12074 7.712205 CCTTTGGATGGAAATACAAATTGGATC 59.288 37.037 0.00 0.00 32.99 3.36
3245 12075 6.389830 TGGATGGAAATACAAATTGGATCG 57.610 37.500 0.00 0.00 0.00 3.69
3246 12076 5.890985 TGGATGGAAATACAAATTGGATCGT 59.109 36.000 0.00 0.00 0.00 3.73
3247 12077 6.039270 TGGATGGAAATACAAATTGGATCGTC 59.961 38.462 0.00 0.00 0.00 4.20
3248 12078 6.039270 GGATGGAAATACAAATTGGATCGTCA 59.961 38.462 0.00 0.00 0.00 4.35
3249 12079 6.825944 TGGAAATACAAATTGGATCGTCAA 57.174 33.333 0.00 0.00 0.00 3.18
3250 12080 7.403312 TGGAAATACAAATTGGATCGTCAAT 57.597 32.000 0.00 0.00 38.84 2.57
3259 12089 4.837093 TTGGATCGTCAATTTACTCCCT 57.163 40.909 0.00 0.00 0.00 4.20
3260 12090 4.837093 TGGATCGTCAATTTACTCCCTT 57.163 40.909 0.00 0.00 0.00 3.95
3261 12091 5.174037 TGGATCGTCAATTTACTCCCTTT 57.826 39.130 0.00 0.00 0.00 3.11
3262 12092 4.941263 TGGATCGTCAATTTACTCCCTTTG 59.059 41.667 0.00 0.00 0.00 2.77
3263 12093 4.335594 GGATCGTCAATTTACTCCCTTTGG 59.664 45.833 0.00 0.00 0.00 3.28
3266 12096 6.302535 TCGTCAATTTACTCCCTTTGGATA 57.697 37.500 0.00 0.00 40.80 2.59
3267 12097 6.110707 TCGTCAATTTACTCCCTTTGGATAC 58.889 40.000 0.00 0.00 40.80 2.24
3347 12946 7.010460 GTGCCCACAATTTCTTTCAATTATAGC 59.990 37.037 0.00 0.00 0.00 2.97
3363 12962 9.420118 TCAATTATAGCCAACCAACATATTCTT 57.580 29.630 0.00 0.00 0.00 2.52
3440 13041 2.533535 GCTCATGATTCTCGAGACAACG 59.466 50.000 16.36 7.01 0.00 4.10
3463 13064 5.552178 GTCCTTACTTTCAGTCAATCACCT 58.448 41.667 0.00 0.00 0.00 4.00
3485 13086 6.624021 ACCTTATTTCCATACAACCTAGGGAT 59.376 38.462 14.81 0.00 0.00 3.85
3532 13133 2.808906 AAGCTCCAAGGTGGGATTAC 57.191 50.000 0.00 0.00 38.32 1.89
3540 13141 3.006967 CCAAGGTGGGATTACTCCTATCG 59.993 52.174 0.00 0.00 38.17 2.92
3547 13148 5.638234 GTGGGATTACTCCTATCGTAATTGC 59.362 44.000 0.00 0.00 41.74 3.56
3584 13185 3.130340 GGTTTTGTCCATCGGCACAATAT 59.870 43.478 0.00 0.00 32.60 1.28
3597 13198 2.869801 GCACAATATGATCCGACGGAAA 59.130 45.455 22.55 12.98 34.34 3.13
3598 13199 3.311322 GCACAATATGATCCGACGGAAAA 59.689 43.478 22.55 12.58 34.34 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.706729 GTGTGACGACGAACCGATTC 59.293 55.000 0.00 0.00 0.00 2.52
2 3 0.665369 GGTGTGACGACGAACCGATT 60.665 55.000 0.00 0.00 0.00 3.34
3 4 1.080974 GGTGTGACGACGAACCGAT 60.081 57.895 0.00 0.00 0.00 4.18
4 5 1.798234 ATGGTGTGACGACGAACCGA 61.798 55.000 0.00 0.00 35.33 4.69
5 6 1.372499 ATGGTGTGACGACGAACCG 60.372 57.895 0.00 0.00 35.33 4.44
6 7 1.289109 CCATGGTGTGACGACGAACC 61.289 60.000 2.57 4.39 0.00 3.62
7 8 1.289109 CCCATGGTGTGACGACGAAC 61.289 60.000 11.73 0.00 0.00 3.95
88 89 1.221021 GGGCAGCTTACTACGCCTT 59.779 57.895 10.06 0.00 44.27 4.35
89 90 2.901042 GGGCAGCTTACTACGCCT 59.099 61.111 10.06 0.00 44.27 5.52
90 91 2.585247 CGGGCAGCTTACTACGCC 60.585 66.667 1.90 1.90 44.10 5.68
91 92 3.262686 GCGGGCAGCTTACTACGC 61.263 66.667 1.25 9.22 44.04 4.42
136 145 1.802960 CACACAAGACATGGCAGAGTC 59.197 52.381 13.25 13.25 35.02 3.36
137 146 1.888215 CACACAAGACATGGCAGAGT 58.112 50.000 0.00 0.00 0.00 3.24
149 158 1.471287 CCATCAGGACATGCACACAAG 59.529 52.381 0.00 0.00 36.89 3.16
268 311 5.954349 CGCGCAAAAACAAAAGAAAAACATA 59.046 32.000 8.75 0.00 0.00 2.29
270 313 4.144555 CGCGCAAAAACAAAAGAAAAACA 58.855 34.783 8.75 0.00 0.00 2.83
271 314 3.536449 CCGCGCAAAAACAAAAGAAAAAC 59.464 39.130 8.75 0.00 0.00 2.43
297 340 2.370281 ACAGCCGACACAATAGAGTG 57.630 50.000 0.00 0.00 44.93 3.51
310 353 4.513198 TTTTATCTTGGGAAAACAGCCG 57.487 40.909 0.00 0.00 0.00 5.52
311 354 6.096673 TCTTTTTATCTTGGGAAAACAGCC 57.903 37.500 0.00 0.00 0.00 4.85
322 365 8.197988 ACAAGTATACCGCTCTTTTTATCTTG 57.802 34.615 0.00 0.00 35.20 3.02
337 380 5.297029 GCCAATGGAAGAGAACAAGTATACC 59.703 44.000 2.05 0.00 0.00 2.73
358 442 7.353525 TCATTTTTAGAATAAGGGAGATGCCA 58.646 34.615 0.00 0.00 38.95 4.92
367 451 8.131100 ACACGATGCATCATTTTTAGAATAAGG 58.869 33.333 25.70 6.53 0.00 2.69
437 522 1.764723 CATCATGTAGGCAGGGTGAGA 59.235 52.381 0.00 0.00 39.65 3.27
569 663 1.457303 CGCAGCTAGAACAGACACAAC 59.543 52.381 0.00 0.00 0.00 3.32
570 664 1.783284 CGCAGCTAGAACAGACACAA 58.217 50.000 0.00 0.00 0.00 3.33
958 3332 0.183492 AATCCATCCACCCCGTCATG 59.817 55.000 0.00 0.00 0.00 3.07
986 3360 5.616424 GCAAGATCCATCGCTATTTCACATC 60.616 44.000 0.00 0.00 0.00 3.06
1019 3393 3.314080 GTGGTTTTTGAGAATGTGGTCGA 59.686 43.478 0.00 0.00 0.00 4.20
1119 9318 1.913778 TGACAGCAATGTGAAGCCAT 58.086 45.000 0.00 0.00 0.00 4.40
1162 9361 9.401058 AGCTACATAAGTTGATAAAAGCTTCAT 57.599 29.630 0.00 0.00 34.26 2.57
1333 9577 2.822255 GCGGAGGGCGCAATTGTA 60.822 61.111 10.83 0.00 0.00 2.41
1408 9652 7.982354 GCACCTTAACTCATCTTCTGTAATACT 59.018 37.037 0.00 0.00 0.00 2.12
1691 10064 2.370189 AGAAGATCGGCCCAAGGATAAG 59.630 50.000 0.00 0.00 0.00 1.73
1741 10114 5.403897 ACCGCACAATACGAAGATATTTG 57.596 39.130 0.00 0.00 0.00 2.32
2143 10561 7.226441 AGCATATACTCAAACTAATGCATGGA 58.774 34.615 0.00 0.00 41.61 3.41
2167 10585 7.686938 GTCAATCATAACGGTTAAAAGACGAAG 59.313 37.037 4.47 0.00 0.00 3.79
2252 10681 4.152045 GCCTTAGATCATGCGAAGATTCTG 59.848 45.833 0.00 0.00 0.00 3.02
2314 10743 4.922692 CGCTGAACAAAAGCCAATGATAAA 59.077 37.500 0.00 0.00 37.37 1.40
2334 10763 0.322975 ACTCAACCATGCTCTTCGCT 59.677 50.000 0.00 0.00 40.11 4.93
2337 10766 5.634896 CATGTTAACTCAACCATGCTCTTC 58.365 41.667 7.22 0.00 36.20 2.87
2600 11176 7.175104 TGGCTTAAAAGATCACTTATTCCTGT 58.825 34.615 0.00 0.00 35.05 4.00
2710 11311 8.837389 AGTTAGTAACTCAATGGAACAGAAAAC 58.163 33.333 9.85 0.00 38.96 2.43
2798 11401 9.961265 CCGACTATAATCATTACTCAACTACAA 57.039 33.333 0.00 0.00 0.00 2.41
2822 11427 2.032894 CGCATCACAGCTTTTATACCCG 60.033 50.000 0.00 0.00 0.00 5.28
2879 11484 3.375610 TGGTACGCGCATCATTTAAATGT 59.624 39.130 23.95 11.50 37.65 2.71
3065 11893 7.061688 AGGGAGTAAATACAGTACTAGGTGAG 58.938 42.308 0.00 0.00 31.88 3.51
3066 11894 6.978261 AGGGAGTAAATACAGTACTAGGTGA 58.022 40.000 0.00 0.00 31.88 4.02
3153 11983 9.495572 CCATCCAAAGGAAGTATAGTTAGATTC 57.504 37.037 0.00 0.00 34.34 2.52
3154 11984 9.225682 TCCATCCAAAGGAAGTATAGTTAGATT 57.774 33.333 0.00 0.00 34.34 2.40
3155 11985 8.798975 TCCATCCAAAGGAAGTATAGTTAGAT 57.201 34.615 0.00 0.00 34.34 1.98
3156 11986 8.618240 TTCCATCCAAAGGAAGTATAGTTAGA 57.382 34.615 0.00 0.00 40.11 2.10
3157 11987 9.853177 ATTTCCATCCAAAGGAAGTATAGTTAG 57.147 33.333 0.00 0.00 45.25 2.34
3164 11994 9.793259 GACATATATTTCCATCCAAAGGAAGTA 57.207 33.333 0.00 0.00 45.25 2.24
3165 11995 8.281531 TGACATATATTTCCATCCAAAGGAAGT 58.718 33.333 0.00 0.00 45.25 3.01
3166 11996 8.696043 TGACATATATTTCCATCCAAAGGAAG 57.304 34.615 0.00 0.00 45.25 3.46
3167 11997 9.081204 CATGACATATATTTCCATCCAAAGGAA 57.919 33.333 0.00 0.00 43.13 3.36
3168 11998 8.447200 TCATGACATATATTTCCATCCAAAGGA 58.553 33.333 0.00 0.00 35.55 3.36
3169 11999 8.640063 TCATGACATATATTTCCATCCAAAGG 57.360 34.615 0.00 0.00 0.00 3.11
3171 12001 9.810870 TCATCATGACATATATTTCCATCCAAA 57.189 29.630 0.00 0.00 0.00 3.28
3172 12002 9.234827 GTCATCATGACATATATTTCCATCCAA 57.765 33.333 13.26 0.00 46.22 3.53
3173 12003 8.797350 GTCATCATGACATATATTTCCATCCA 57.203 34.615 13.26 0.00 46.22 3.41
3221 12051 6.379703 ACGATCCAATTTGTATTTCCATCCAA 59.620 34.615 0.00 0.00 0.00 3.53
3222 12052 5.890985 ACGATCCAATTTGTATTTCCATCCA 59.109 36.000 0.00 0.00 0.00 3.41
3224 12054 7.026631 TGACGATCCAATTTGTATTTCCATC 57.973 36.000 0.00 0.00 0.00 3.51
3225 12055 7.403312 TTGACGATCCAATTTGTATTTCCAT 57.597 32.000 0.00 0.00 0.00 3.41
3226 12056 6.825944 TTGACGATCCAATTTGTATTTCCA 57.174 33.333 0.00 0.00 0.00 3.53
3236 12066 5.755849 AGGGAGTAAATTGACGATCCAATT 58.244 37.500 4.11 4.61 45.58 2.32
3237 12067 5.373812 AGGGAGTAAATTGACGATCCAAT 57.626 39.130 4.11 0.00 38.30 3.16
3239 12069 4.837093 AAGGGAGTAAATTGACGATCCA 57.163 40.909 4.11 0.00 0.00 3.41
3243 12073 4.627284 TCCAAAGGGAGTAAATTGACGA 57.373 40.909 0.00 0.00 38.64 4.20
3257 12087 4.881273 TGACGATCCAATTGTATCCAAAGG 59.119 41.667 4.43 0.00 33.44 3.11
3258 12088 6.435430 TTGACGATCCAATTGTATCCAAAG 57.565 37.500 4.43 0.00 33.44 2.77
3259 12089 7.026631 GATTGACGATCCAATTGTATCCAAA 57.973 36.000 4.43 0.00 36.93 3.28
3260 12090 6.618287 GATTGACGATCCAATTGTATCCAA 57.382 37.500 4.43 5.13 36.93 3.53
3273 12103 4.081586 GGTATAAGGGAGGGATTGACGATC 60.082 50.000 0.00 0.00 0.00 3.69
3274 12104 3.838903 GGTATAAGGGAGGGATTGACGAT 59.161 47.826 0.00 0.00 0.00 3.73
3275 12105 3.236896 GGTATAAGGGAGGGATTGACGA 58.763 50.000 0.00 0.00 0.00 4.20
3276 12106 2.969950 TGGTATAAGGGAGGGATTGACG 59.030 50.000 0.00 0.00 0.00 4.35
3277 12107 4.597507 TGATGGTATAAGGGAGGGATTGAC 59.402 45.833 0.00 0.00 0.00 3.18
3279 12109 5.786121 ATGATGGTATAAGGGAGGGATTG 57.214 43.478 0.00 0.00 0.00 2.67
3280 12110 7.688534 TGAATATGATGGTATAAGGGAGGGATT 59.311 37.037 0.00 0.00 0.00 3.01
3285 12115 9.799106 AAAAGTGAATATGATGGTATAAGGGAG 57.201 33.333 0.00 0.00 0.00 4.30
3293 12123 9.194972 TGCCAATAAAAAGTGAATATGATGGTA 57.805 29.630 0.00 0.00 0.00 3.25
3363 12962 5.008217 GGTAGTATGCATGTGCCGATAAAAA 59.992 40.000 10.16 0.00 41.18 1.94
3370 12969 0.937304 GTGGTAGTATGCATGTGCCG 59.063 55.000 10.16 0.00 41.18 5.69
3496 13097 6.953101 TGGAGCTTTATACTAAATCACACCA 58.047 36.000 0.00 0.00 0.00 4.17
3532 13133 5.533482 ACTAGCTTGCAATTACGATAGGAG 58.467 41.667 11.82 0.00 43.77 3.69
3540 13141 5.048713 ACCAACTCAACTAGCTTGCAATTAC 60.049 40.000 0.00 0.00 0.00 1.89
3547 13148 5.248870 ACAAAACCAACTCAACTAGCTTG 57.751 39.130 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.