Multiple sequence alignment - TraesCS3D01G239700

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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 TraesCS3D01G239700 chr3D 100.000 4122 0 0 1 4122 332165922 332161801 0.000000e+00 7613.0
1 TraesCS3D01G239700 chr3D 89.958 239 12 4 441 667 332233494 332233256 8.660000e-77 298.0
2 TraesCS3D01G239700 chr3D 88.024 167 19 1 47 212 360383196 360383362 3.250000e-46 196.0
3 TraesCS3D01G239700 chr3B 94.419 3494 139 27 650 4118 431212424 431208962 0.000000e+00 5321.0
4 TraesCS3D01G239700 chr3B 88.333 360 35 4 1 359 431213457 431213104 3.810000e-115 425.0
5 TraesCS3D01G239700 chr3B 90.625 224 7 4 440 649 431212799 431212576 6.740000e-73 285.0
6 TraesCS3D01G239700 chr3A 96.022 2564 67 14 922 3473 449124241 449121701 0.000000e+00 4137.0
7 TraesCS3D01G239700 chr3A 96.798 531 16 1 3522 4051 449121267 449120737 0.000000e+00 885.0
8 TraesCS3D01G239700 chr3A 87.008 254 18 7 426 667 449506412 449506162 5.250000e-69 272.0
9 TraesCS3D01G239700 chr3A 96.250 80 2 1 4044 4122 449120701 449120622 3.340000e-26 130.0
10 TraesCS3D01G239700 chr5A 93.182 352 23 1 3403 3753 37109847 37110198 2.200000e-142 516.0
11 TraesCS3D01G239700 chr5A 92.614 352 23 2 3403 3753 298336833 298337182 1.710000e-138 503.0
12 TraesCS3D01G239700 chr5A 91.477 352 28 2 3403 3753 546857717 546857367 2.230000e-132 483.0
13 TraesCS3D01G239700 chr5A 93.077 130 9 0 1 130 139521514 139521643 1.510000e-44 191.0
14 TraesCS3D01G239700 chr4A 93.182 352 22 2 3403 3753 559212269 559211919 2.200000e-142 516.0
15 TraesCS3D01G239700 chr2A 92.330 352 26 1 3403 3753 607534896 607534545 2.210000e-137 499.0
16 TraesCS3D01G239700 chr6A 91.761 352 27 2 3403 3753 419205290 419204940 4.790000e-134 488.0
17 TraesCS3D01G239700 chr6A 88.618 246 26 2 1 245 178409541 178409297 8.660000e-77 298.0
18 TraesCS3D01G239700 chr1A 86.313 453 47 7 1 438 584319429 584319881 2.880000e-131 479.0
19 TraesCS3D01G239700 chr6B 91.753 291 22 2 3403 3692 92069084 92069373 1.780000e-108 403.0
20 TraesCS3D01G239700 chr6B 90.076 262 25 1 1 261 719335497 719335236 5.100000e-89 339.0
21 TraesCS3D01G239700 chr2D 83.636 440 47 11 1 438 555872838 555872422 1.390000e-104 390.0
22 TraesCS3D01G239700 chr2D 89.726 146 14 1 658 802 461085685 461085830 7.040000e-43 185.0
23 TraesCS3D01G239700 chr2D 88.435 147 14 3 658 802 547766539 547766394 1.520000e-39 174.0
24 TraesCS3D01G239700 chr2B 81.771 384 49 11 73 437 39989514 39989133 6.700000e-78 302.0
25 TraesCS3D01G239700 chr2B 93.182 44 3 0 6 49 743910242 743910199 9.560000e-07 65.8
26 TraesCS3D01G239700 chr7A 82.709 347 43 8 78 408 287523504 287523159 4.030000e-75 292.0
27 TraesCS3D01G239700 chr7B 96.491 57 2 0 3697 3753 202304306 202304362 1.220000e-15 95.3


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 TraesCS3D01G239700 chr3D 332161801 332165922 4121 True 7613.000000 7613 100.000000 1 4122 1 chr3D.!!$R1 4121
1 TraesCS3D01G239700 chr3B 431208962 431213457 4495 True 2010.333333 5321 91.125667 1 4118 3 chr3B.!!$R1 4117
2 TraesCS3D01G239700 chr3A 449120622 449124241 3619 True 1717.333333 4137 96.356667 922 4122 3 chr3A.!!$R2 3200

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
359 361 0.110486 GTGGAGGTTGCCCAAAGAGA 59.890 55.0 0.00 0.0 35.12 3.1 F
760 1151 0.606401 CATCCAACGGTCAGCAAGGT 60.606 55.0 0.00 0.0 0.00 3.5 F
1534 1947 0.030705 AGCTCCCATGGCTCCTTCTA 60.031 55.0 6.09 0.0 34.70 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1935 1.049289 GGGACGGTAGAAGGAGCCAT 61.049 60.000 0.00 0.0 0.00 4.40 R
2728 3142 0.178961 AGGGTTCCACAAAAGGGAGC 60.179 55.000 0.00 0.0 35.46 4.70 R
3152 3567 4.707030 TGATGATTCGAGCTGCAAAAAT 57.293 36.364 1.02 0.0 0.00 1.82 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
65 66 4.430765 ACACGGATCGACGCCACC 62.431 66.667 6.92 0.00 37.37 4.61
232 234 4.704833 CTCCCCACCGCACACCTG 62.705 72.222 0.00 0.00 0.00 4.00
242 244 2.747460 CACACCTGGGCATCCACG 60.747 66.667 0.00 0.00 38.32 4.94
304 306 2.894387 GCCTCGCAGATCTGGTGC 60.894 66.667 23.89 15.49 37.58 5.01
354 356 1.152830 GAAGGTGGAGGTTGCCCAA 59.847 57.895 0.00 0.00 35.12 4.12
359 361 0.110486 GTGGAGGTTGCCCAAAGAGA 59.890 55.000 0.00 0.00 35.12 3.10
361 363 0.955919 GGAGGTTGCCCAAAGAGACG 60.956 60.000 0.00 0.00 0.00 4.18
362 364 1.578206 GAGGTTGCCCAAAGAGACGC 61.578 60.000 0.00 0.00 0.00 5.19
363 365 2.626780 GGTTGCCCAAAGAGACGCC 61.627 63.158 0.00 0.00 0.00 5.68
364 366 2.282180 TTGCCCAAAGAGACGCCC 60.282 61.111 0.00 0.00 0.00 6.13
365 367 2.829384 TTGCCCAAAGAGACGCCCT 61.829 57.895 0.00 0.00 0.00 5.19
366 368 2.747855 GCCCAAAGAGACGCCCTG 60.748 66.667 0.00 0.00 0.00 4.45
367 369 2.747855 CCCAAAGAGACGCCCTGC 60.748 66.667 0.00 0.00 0.00 4.85
368 370 2.747855 CCAAAGAGACGCCCTGCC 60.748 66.667 0.00 0.00 0.00 4.85
369 371 3.121030 CAAAGAGACGCCCTGCCG 61.121 66.667 0.00 0.00 0.00 5.69
387 389 3.443045 CCGCCCTCATTGGTGCAC 61.443 66.667 8.80 8.80 34.46 4.57
388 390 3.803082 CGCCCTCATTGGTGCACG 61.803 66.667 11.45 0.00 33.44 5.34
389 391 4.120331 GCCCTCATTGGTGCACGC 62.120 66.667 11.45 4.50 33.85 5.34
390 392 3.443045 CCCTCATTGGTGCACGCC 61.443 66.667 11.45 0.00 0.00 5.68
391 393 3.443045 CCTCATTGGTGCACGCCC 61.443 66.667 11.45 0.00 0.00 6.13
392 394 3.803082 CTCATTGGTGCACGCCCG 61.803 66.667 11.45 0.00 0.00 6.13
421 423 4.821589 GGCGGCGAGACAGGAAGG 62.822 72.222 12.98 0.00 0.00 3.46
422 424 4.821589 GCGGCGAGACAGGAAGGG 62.822 72.222 12.98 0.00 0.00 3.95
423 425 4.148825 CGGCGAGACAGGAAGGGG 62.149 72.222 0.00 0.00 0.00 4.79
424 426 3.787001 GGCGAGACAGGAAGGGGG 61.787 72.222 0.00 0.00 0.00 5.40
425 427 2.683933 GCGAGACAGGAAGGGGGA 60.684 66.667 0.00 0.00 0.00 4.81
426 428 2.726351 GCGAGACAGGAAGGGGGAG 61.726 68.421 0.00 0.00 0.00 4.30
427 429 2.060980 CGAGACAGGAAGGGGGAGG 61.061 68.421 0.00 0.00 0.00 4.30
428 430 1.690985 GAGACAGGAAGGGGGAGGG 60.691 68.421 0.00 0.00 0.00 4.30
429 431 2.182858 GAGACAGGAAGGGGGAGGGA 62.183 65.000 0.00 0.00 0.00 4.20
430 432 1.690985 GACAGGAAGGGGGAGGGAG 60.691 68.421 0.00 0.00 0.00 4.30
431 433 2.182858 GACAGGAAGGGGGAGGGAGA 62.183 65.000 0.00 0.00 0.00 3.71
432 434 1.383803 CAGGAAGGGGGAGGGAGAG 60.384 68.421 0.00 0.00 0.00 3.20
433 435 2.040359 GGAAGGGGGAGGGAGAGG 60.040 72.222 0.00 0.00 0.00 3.69
434 436 2.647949 GGAAGGGGGAGGGAGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
435 437 1.383386 GAAGGGGGAGGGAGAGGAC 60.383 68.421 0.00 0.00 0.00 3.85
436 438 2.900269 GAAGGGGGAGGGAGAGGACC 62.900 70.000 0.00 0.00 0.00 4.46
549 778 7.331193 AGTGGAGTAATACGTGTCTTTCATTTC 59.669 37.037 0.00 0.00 0.00 2.17
610 841 5.997843 AGGATTACCGCTAACCAAAACTAT 58.002 37.500 0.00 0.00 41.83 2.12
624 864 5.189736 ACCAAAACTATCAGAGGCATCTACA 59.810 40.000 0.00 0.00 33.22 2.74
668 1059 9.747898 TGACCATTATAATACCAGAACTTGTTT 57.252 29.630 0.00 0.00 0.00 2.83
695 1086 2.294791 CACCGCCTTTGTTGTAAATGGA 59.705 45.455 0.00 0.00 0.00 3.41
698 1089 3.574614 CGCCTTTGTTGTAAATGGAAGG 58.425 45.455 0.00 0.00 36.03 3.46
701 1092 4.799255 GCCTTTGTTGTAAATGGAAGGTGG 60.799 45.833 0.00 0.00 35.64 4.61
702 1093 4.306600 CTTTGTTGTAAATGGAAGGTGGC 58.693 43.478 0.00 0.00 0.00 5.01
704 1095 1.883926 GTTGTAAATGGAAGGTGGCGT 59.116 47.619 0.00 0.00 0.00 5.68
722 1113 2.550606 GCGTTTGTGAGTGGGTTAATCA 59.449 45.455 0.00 0.00 0.00 2.57
726 1117 5.872617 CGTTTGTGAGTGGGTTAATCAGATA 59.127 40.000 0.00 0.00 33.47 1.98
736 1127 5.243954 TGGGTTAATCAGATAGACATCCTCG 59.756 44.000 0.00 0.00 0.00 4.63
751 1142 3.642778 CTCGCGTCCATCCAACGGT 62.643 63.158 5.77 0.00 40.41 4.83
760 1151 0.606401 CATCCAACGGTCAGCAAGGT 60.606 55.000 0.00 0.00 0.00 3.50
763 1154 1.525995 CAACGGTCAGCAAGGTGGT 60.526 57.895 0.00 0.00 0.00 4.16
782 1173 4.816925 GTGGTGGATGTTTTCTAGCTATCC 59.183 45.833 0.00 0.00 38.20 2.59
786 1177 3.982058 GGATGTTTTCTAGCTATCCGTCG 59.018 47.826 0.00 0.00 0.00 5.12
834 1233 4.727507 TTTGTGTAGCCAAAATGTGTGT 57.272 36.364 0.00 0.00 31.66 3.72
835 1234 3.706802 TGTGTAGCCAAAATGTGTGTG 57.293 42.857 0.00 0.00 0.00 3.82
842 1241 3.894427 AGCCAAAATGTGTGTGTGGATAA 59.106 39.130 0.00 0.00 0.00 1.75
843 1242 4.527816 AGCCAAAATGTGTGTGTGGATAAT 59.472 37.500 0.00 0.00 0.00 1.28
867 1266 2.564975 GCAGCATCACACCTGTGC 59.435 61.111 0.17 0.00 45.25 4.57
902 1301 0.613012 GAGAATTGCCTGGGCCTGTT 60.613 55.000 4.53 1.43 41.09 3.16
956 1357 3.308832 CCCACTAGTCAGTTCTCTCTCCT 60.309 52.174 0.00 0.00 30.46 3.69
1063 1467 0.831288 CTCATCCGGCCTCCAGAGAT 60.831 60.000 0.00 0.00 0.00 2.75
1292 1696 1.059942 CAGATTTGTTTTTCCGGCGC 58.940 50.000 0.00 0.00 0.00 6.53
1311 1715 2.111460 TTGCAGCGTTAACCCCGT 59.889 55.556 0.00 0.00 0.00 5.28
1338 1751 4.397010 GGCTGCCCCCAAATCCCA 62.397 66.667 7.66 0.00 0.00 4.37
1534 1947 0.030705 AGCTCCCATGGCTCCTTCTA 60.031 55.000 6.09 0.00 34.70 2.10
1909 2322 1.745489 GAACGGGCACTGGATCACC 60.745 63.158 0.00 0.00 40.47 4.02
2098 2511 3.630148 CGCGCTGATTACAGGCCG 61.630 66.667 5.56 0.00 43.62 6.13
2728 3142 5.916883 CCTGAACATTGTTAGAGCTTGTTTG 59.083 40.000 1.15 0.00 31.09 2.93
2755 3170 5.281037 CCCTTTTGTGGAACCCTAATCTAGT 60.281 44.000 0.00 0.00 34.36 2.57
2986 3401 1.281199 TAGGGCATGCCATGTGAGGT 61.281 55.000 36.56 13.08 37.98 3.85
3152 3567 8.153221 TGGAGGAACCAATGATTTAGTAGTTA 57.847 34.615 0.00 0.00 46.75 2.24
3182 3600 4.150274 CAGCTCGAATCATCAATCTACAGC 59.850 45.833 0.00 0.00 0.00 4.40
3193 3611 5.722021 TCAATCTACAGCAGTTACAGTCA 57.278 39.130 0.00 0.00 0.00 3.41
3194 3612 6.096673 TCAATCTACAGCAGTTACAGTCAA 57.903 37.500 0.00 0.00 0.00 3.18
3195 3613 6.701340 TCAATCTACAGCAGTTACAGTCAAT 58.299 36.000 0.00 0.00 0.00 2.57
3196 3614 6.813649 TCAATCTACAGCAGTTACAGTCAATC 59.186 38.462 0.00 0.00 0.00 2.67
3197 3615 5.984695 TCTACAGCAGTTACAGTCAATCT 57.015 39.130 0.00 0.00 0.00 2.40
3198 3616 7.646548 ATCTACAGCAGTTACAGTCAATCTA 57.353 36.000 0.00 0.00 0.00 1.98
3199 3617 6.853720 TCTACAGCAGTTACAGTCAATCTAC 58.146 40.000 0.00 0.00 0.00 2.59
3200 3618 5.468540 ACAGCAGTTACAGTCAATCTACA 57.531 39.130 0.00 0.00 0.00 2.74
3201 3619 5.473931 ACAGCAGTTACAGTCAATCTACAG 58.526 41.667 0.00 0.00 0.00 2.74
3202 3620 4.328440 CAGCAGTTACAGTCAATCTACAGC 59.672 45.833 0.00 0.00 0.00 4.40
3203 3621 4.021104 AGCAGTTACAGTCAATCTACAGCA 60.021 41.667 0.00 0.00 0.00 4.41
3204 3622 4.328440 GCAGTTACAGTCAATCTACAGCAG 59.672 45.833 0.00 0.00 0.00 4.24
3205 3623 5.473931 CAGTTACAGTCAATCTACAGCAGT 58.526 41.667 0.00 0.00 0.00 4.40
3206 3624 5.928839 CAGTTACAGTCAATCTACAGCAGTT 59.071 40.000 0.00 0.00 0.00 3.16
3207 3625 7.090808 CAGTTACAGTCAATCTACAGCAGTTA 58.909 38.462 0.00 0.00 0.00 2.24
3208 3626 7.062371 CAGTTACAGTCAATCTACAGCAGTTAC 59.938 40.741 0.00 0.00 0.00 2.50
3209 3627 5.468540 ACAGTCAATCTACAGCAGTTACA 57.531 39.130 0.00 0.00 0.00 2.41
3210 3628 5.473931 ACAGTCAATCTACAGCAGTTACAG 58.526 41.667 0.00 0.00 0.00 2.74
3211 3629 5.011125 ACAGTCAATCTACAGCAGTTACAGT 59.989 40.000 0.00 0.00 0.00 3.55
3212 3630 5.574830 CAGTCAATCTACAGCAGTTACAGTC 59.425 44.000 0.00 0.00 0.00 3.51
3232 3650 7.783042 ACAGTCCTTATTCTGGATTACACTAC 58.217 38.462 0.00 0.00 35.87 2.73
3299 3717 7.741554 AATTTAGTCCCACTGATAGACTTCT 57.258 36.000 0.00 0.00 41.09 2.85
3486 3905 5.367937 AGGAATGATGGCTTCTAGCTTTAGA 59.632 40.000 0.00 0.00 41.99 2.10
3494 3913 3.307129 GCTTCTAGCTTTAGATAGCCCCC 60.307 52.174 0.00 0.00 42.20 5.40
3703 4508 0.249489 GGCTACCATGCGTCTAGTGG 60.249 60.000 0.00 0.00 38.96 4.00
3993 4798 2.349590 TGACATGTTTCAGATGCCTCG 58.650 47.619 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.111878 CGATGGTGGATGGAGCCC 59.888 66.667 0.00 0.00 0.00 5.19
83 84 2.592861 GCGATGGTGGATGGAGCC 60.593 66.667 0.00 0.00 0.00 4.70
86 87 2.297129 TGTGGCGATGGTGGATGGA 61.297 57.895 0.00 0.00 0.00 3.41
139 140 1.444553 CTGTCGTGGTCTTCCTCGC 60.445 63.158 4.23 1.63 46.27 5.03
146 147 4.008933 GGGCTGCTGTCGTGGTCT 62.009 66.667 0.00 0.00 0.00 3.85
212 214 3.717294 GTGTGCGGTGGGGAGGAT 61.717 66.667 0.00 0.00 0.00 3.24
284 286 4.598894 CCAGATCTGCGAGGCCCG 62.599 72.222 17.76 3.77 42.21 6.13
287 289 2.894387 GCACCAGATCTGCGAGGC 60.894 66.667 17.76 12.81 0.00 4.70
307 309 3.310860 CTCTTTAGGGCGTGGCGGT 62.311 63.158 0.00 0.00 0.00 5.68
331 333 0.402121 GCAACCTCCACCTTCTCCTT 59.598 55.000 0.00 0.00 0.00 3.36
370 372 3.443045 GTGCACCAATGAGGGCGG 61.443 66.667 5.22 0.00 43.89 6.13
371 373 3.803082 CGTGCACCAATGAGGGCG 61.803 66.667 12.15 0.00 43.89 6.13
372 374 4.120331 GCGTGCACCAATGAGGGC 62.120 66.667 12.15 1.93 43.89 5.19
373 375 3.443045 GGCGTGCACCAATGAGGG 61.443 66.667 12.15 0.00 43.89 4.30
374 376 3.443045 GGGCGTGCACCAATGAGG 61.443 66.667 12.15 0.00 45.67 3.86
375 377 3.803082 CGGGCGTGCACCAATGAG 61.803 66.667 12.15 0.00 0.00 2.90
404 406 4.821589 CCTTCCTGTCTCGCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
405 407 4.821589 CCCTTCCTGTCTCGCCGC 62.822 72.222 0.00 0.00 0.00 6.53
406 408 4.148825 CCCCTTCCTGTCTCGCCG 62.149 72.222 0.00 0.00 0.00 6.46
407 409 3.787001 CCCCCTTCCTGTCTCGCC 61.787 72.222 0.00 0.00 0.00 5.54
408 410 2.683933 TCCCCCTTCCTGTCTCGC 60.684 66.667 0.00 0.00 0.00 5.03
409 411 2.060980 CCTCCCCCTTCCTGTCTCG 61.061 68.421 0.00 0.00 0.00 4.04
410 412 1.690985 CCCTCCCCCTTCCTGTCTC 60.691 68.421 0.00 0.00 0.00 3.36
411 413 2.184631 TCCCTCCCCCTTCCTGTCT 61.185 63.158 0.00 0.00 0.00 3.41
412 414 1.690985 CTCCCTCCCCCTTCCTGTC 60.691 68.421 0.00 0.00 0.00 3.51
413 415 2.184631 TCTCCCTCCCCCTTCCTGT 61.185 63.158 0.00 0.00 0.00 4.00
414 416 1.383803 CTCTCCCTCCCCCTTCCTG 60.384 68.421 0.00 0.00 0.00 3.86
415 417 2.652113 CCTCTCCCTCCCCCTTCCT 61.652 68.421 0.00 0.00 0.00 3.36
416 418 2.040359 CCTCTCCCTCCCCCTTCC 60.040 72.222 0.00 0.00 0.00 3.46
417 419 1.383386 GTCCTCTCCCTCCCCCTTC 60.383 68.421 0.00 0.00 0.00 3.46
418 420 2.788589 GTCCTCTCCCTCCCCCTT 59.211 66.667 0.00 0.00 0.00 3.95
419 421 3.369388 GGTCCTCTCCCTCCCCCT 61.369 72.222 0.00 0.00 0.00 4.79
420 422 4.500826 GGGTCCTCTCCCTCCCCC 62.501 77.778 0.00 0.00 43.85 5.40
427 429 2.640332 AGAAAAACTCTGGGTCCTCTCC 59.360 50.000 0.00 0.00 31.12 3.71
428 430 5.685520 ATAGAAAAACTCTGGGTCCTCTC 57.314 43.478 0.00 0.00 35.41 3.20
429 431 6.241645 CAAATAGAAAAACTCTGGGTCCTCT 58.758 40.000 0.00 0.00 35.41 3.69
430 432 5.416013 CCAAATAGAAAAACTCTGGGTCCTC 59.584 44.000 0.00 0.00 35.41 3.71
431 433 5.074515 TCCAAATAGAAAAACTCTGGGTCCT 59.925 40.000 0.00 0.00 35.41 3.85
432 434 5.321927 TCCAAATAGAAAAACTCTGGGTCC 58.678 41.667 0.00 0.00 35.41 4.46
433 435 6.071896 CCTTCCAAATAGAAAAACTCTGGGTC 60.072 42.308 0.00 0.00 35.41 4.46
434 436 5.775195 CCTTCCAAATAGAAAAACTCTGGGT 59.225 40.000 0.00 0.00 35.41 4.51
435 437 5.336770 GCCTTCCAAATAGAAAAACTCTGGG 60.337 44.000 0.00 0.00 35.41 4.45
436 438 5.336770 GGCCTTCCAAATAGAAAAACTCTGG 60.337 44.000 0.00 0.00 35.41 3.86
437 439 5.243730 TGGCCTTCCAAATAGAAAAACTCTG 59.756 40.000 3.32 0.00 39.99 3.35
438 440 5.393866 TGGCCTTCCAAATAGAAAAACTCT 58.606 37.500 3.32 0.00 39.99 3.24
516 742 8.064336 AGACACGTATTACTCCACTCTAAAAT 57.936 34.615 0.00 0.00 0.00 1.82
517 743 7.458409 AGACACGTATTACTCCACTCTAAAA 57.542 36.000 0.00 0.00 0.00 1.52
520 746 6.656270 TGAAAGACACGTATTACTCCACTCTA 59.344 38.462 0.00 0.00 0.00 2.43
549 778 8.327941 TGAAGAATGGACAGAGTTTTATTGAG 57.672 34.615 0.00 0.00 0.00 3.02
587 816 4.296621 AGTTTTGGTTAGCGGTAATCCT 57.703 40.909 14.67 2.11 0.00 3.24
610 841 2.121948 AGCCATTGTAGATGCCTCTGA 58.878 47.619 1.22 0.00 32.66 3.27
645 885 7.855904 GCGAAACAAGTTCTGGTATTATAATGG 59.144 37.037 8.28 0.00 33.70 3.16
668 1059 2.115911 AACAAAGGCGGTGTTGCGA 61.116 52.632 7.86 0.00 37.80 5.10
688 1079 2.294791 CACAAACGCCACCTTCCATTTA 59.705 45.455 0.00 0.00 0.00 1.40
695 1086 1.101049 CCACTCACAAACGCCACCTT 61.101 55.000 0.00 0.00 0.00 3.50
698 1089 1.381165 AACCCACTCACAAACGCCAC 61.381 55.000 0.00 0.00 0.00 5.01
701 1092 2.550606 TGATTAACCCACTCACAAACGC 59.449 45.455 0.00 0.00 0.00 4.84
702 1093 4.062293 TCTGATTAACCCACTCACAAACG 58.938 43.478 0.00 0.00 0.00 3.60
704 1095 7.103641 GTCTATCTGATTAACCCACTCACAAA 58.896 38.462 0.00 0.00 0.00 2.83
722 1113 1.240256 GGACGCGAGGATGTCTATCT 58.760 55.000 15.93 0.00 35.45 1.98
726 1117 1.736586 GATGGACGCGAGGATGTCT 59.263 57.895 15.93 0.00 35.45 3.41
736 1127 2.047655 TGACCGTTGGATGGACGC 60.048 61.111 0.00 0.00 39.09 5.19
751 1142 0.478072 AACATCCACCACCTTGCTGA 59.522 50.000 0.00 0.00 0.00 4.26
760 1151 4.442893 CGGATAGCTAGAAAACATCCACCA 60.443 45.833 9.52 0.00 35.85 4.17
763 1154 4.499188 CGACGGATAGCTAGAAAACATCCA 60.499 45.833 9.52 0.00 35.85 3.41
792 1183 1.440353 CACTTTTGGCACGCTACGC 60.440 57.895 0.00 0.00 0.00 4.42
793 1184 0.584396 TTCACTTTTGGCACGCTACG 59.416 50.000 0.00 0.00 0.00 3.51
794 1185 2.989422 ATTCACTTTTGGCACGCTAC 57.011 45.000 0.00 0.00 0.00 3.58
795 1186 3.067461 ACAAATTCACTTTTGGCACGCTA 59.933 39.130 0.00 0.00 40.20 4.26
796 1187 2.159114 ACAAATTCACTTTTGGCACGCT 60.159 40.909 0.00 0.00 40.20 5.07
797 1188 2.033832 CACAAATTCACTTTTGGCACGC 60.034 45.455 0.00 0.00 40.20 5.34
798 1189 3.186119 ACACAAATTCACTTTTGGCACG 58.814 40.909 0.00 0.00 40.20 5.34
800 1191 4.367450 GCTACACAAATTCACTTTTGGCA 58.633 39.130 2.42 0.00 40.20 4.92
801 1192 3.740832 GGCTACACAAATTCACTTTTGGC 59.259 43.478 2.42 0.00 40.20 4.52
802 1193 4.942852 TGGCTACACAAATTCACTTTTGG 58.057 39.130 2.42 0.00 40.20 3.28
803 1194 6.900568 TTTGGCTACACAAATTCACTTTTG 57.099 33.333 0.00 0.00 41.37 2.44
804 1195 7.552330 ACATTTTGGCTACACAAATTCACTTTT 59.448 29.630 0.00 0.00 39.80 2.27
805 1196 7.011295 CACATTTTGGCTACACAAATTCACTTT 59.989 33.333 0.00 0.00 39.80 2.66
806 1197 6.479660 CACATTTTGGCTACACAAATTCACTT 59.520 34.615 0.00 0.00 39.80 3.16
808 1199 5.752955 ACACATTTTGGCTACACAAATTCAC 59.247 36.000 0.00 0.00 39.80 3.18
809 1200 5.752472 CACACATTTTGGCTACACAAATTCA 59.248 36.000 0.00 0.00 39.80 2.57
842 1241 1.270518 GGTGTGATGCTGCGAGGATAT 60.271 52.381 0.00 0.00 0.00 1.63
843 1242 0.104855 GGTGTGATGCTGCGAGGATA 59.895 55.000 0.00 0.00 0.00 2.59
902 1301 3.759618 AGGTTTTTCAGGACACGAAACAA 59.240 39.130 0.00 0.00 32.27 2.83
956 1357 4.341487 TCGAAGAAGTTAGGTGAGATGGA 58.659 43.478 0.00 0.00 0.00 3.41
1021 1425 2.967615 GAAGGATACGGCGGCAGC 60.968 66.667 13.24 0.00 46.39 5.25
1022 1426 1.300233 GAGAAGGATACGGCGGCAG 60.300 63.158 13.24 0.00 46.39 4.85
1023 1427 2.812499 GAGAAGGATACGGCGGCA 59.188 61.111 13.24 0.00 46.39 5.69
1030 1434 2.226912 CGGATGAGGACGAGAAGGATAC 59.773 54.545 0.00 0.00 0.00 2.24
1292 1696 2.559330 GGGGTTAACGCTGCAACG 59.441 61.111 20.55 8.18 39.50 4.10
1311 1715 2.281484 GGGCAGCCGTCTTTGACA 60.281 61.111 5.00 0.00 32.09 3.58
1522 1935 1.049289 GGGACGGTAGAAGGAGCCAT 61.049 60.000 0.00 0.00 0.00 4.40
1846 2259 2.581354 GAGGCGCTGGAGACATGT 59.419 61.111 7.64 0.00 41.51 3.21
1873 2286 2.117156 CATTCCAGGCCGCCAGAAG 61.117 63.158 13.15 5.04 0.00 2.85
1885 2298 1.303236 CCAGTGCCCGTTCATTCCA 60.303 57.895 0.00 0.00 0.00 3.53
2098 2511 2.139118 GACTTGCGCCTGAGATTATCC 58.861 52.381 4.18 0.00 0.00 2.59
2728 3142 0.178961 AGGGTTCCACAAAAGGGAGC 60.179 55.000 0.00 0.00 35.46 4.70
2755 3170 6.676950 AGCACAATTATCACAAAATTCGACA 58.323 32.000 0.00 0.00 0.00 4.35
2986 3401 7.825270 TGAAACCTGACTACAAGTTGACTAAAA 59.175 33.333 10.54 0.00 31.99 1.52
3070 3485 9.590451 AACTGCATAACAATCATATTTGGAAAG 57.410 29.630 0.00 0.00 0.00 2.62
3112 3527 4.919774 TCCTCCAGCCATAGTGTAAAAA 57.080 40.909 0.00 0.00 0.00 1.94
3152 3567 4.707030 TGATGATTCGAGCTGCAAAAAT 57.293 36.364 1.02 0.00 0.00 1.82
3182 3600 5.473931 ACTGCTGTAGATTGACTGTAACTG 58.526 41.667 0.00 0.00 0.00 3.16
3193 3611 5.746990 AAGGACTGTAACTGCTGTAGATT 57.253 39.130 0.00 0.00 0.00 2.40
3194 3612 7.343316 AGAATAAGGACTGTAACTGCTGTAGAT 59.657 37.037 0.00 0.00 0.00 1.98
3195 3613 6.663953 AGAATAAGGACTGTAACTGCTGTAGA 59.336 38.462 0.00 0.00 0.00 2.59
3196 3614 6.754209 CAGAATAAGGACTGTAACTGCTGTAG 59.246 42.308 0.00 0.00 0.00 2.74
3197 3615 6.351033 CCAGAATAAGGACTGTAACTGCTGTA 60.351 42.308 0.00 0.00 32.93 2.74
3198 3616 5.482908 CAGAATAAGGACTGTAACTGCTGT 58.517 41.667 0.00 0.00 0.00 4.40
3199 3617 4.872691 CCAGAATAAGGACTGTAACTGCTG 59.127 45.833 0.00 0.00 32.93 4.41
3200 3618 4.777896 TCCAGAATAAGGACTGTAACTGCT 59.222 41.667 0.00 0.00 32.93 4.24
3201 3619 5.086104 TCCAGAATAAGGACTGTAACTGC 57.914 43.478 0.00 0.00 32.93 4.40
3202 3620 8.258007 TGTAATCCAGAATAAGGACTGTAACTG 58.742 37.037 0.00 0.00 38.13 3.16
3203 3621 8.258708 GTGTAATCCAGAATAAGGACTGTAACT 58.741 37.037 0.00 0.00 38.13 2.24
3204 3622 8.258708 AGTGTAATCCAGAATAAGGACTGTAAC 58.741 37.037 0.00 0.00 38.13 2.50
3205 3623 8.375493 AGTGTAATCCAGAATAAGGACTGTAA 57.625 34.615 0.00 0.00 38.13 2.41
3206 3624 7.973048 AGTGTAATCCAGAATAAGGACTGTA 57.027 36.000 0.00 0.00 38.13 2.74
3207 3625 6.875972 AGTGTAATCCAGAATAAGGACTGT 57.124 37.500 0.00 0.00 38.13 3.55
3208 3626 7.782049 TGTAGTGTAATCCAGAATAAGGACTG 58.218 38.462 0.00 0.00 38.13 3.51
3209 3627 7.973048 TGTAGTGTAATCCAGAATAAGGACT 57.027 36.000 0.00 0.00 38.13 3.85
3210 3628 8.421784 TCATGTAGTGTAATCCAGAATAAGGAC 58.578 37.037 0.00 0.00 38.13 3.85
3211 3629 8.547481 TCATGTAGTGTAATCCAGAATAAGGA 57.453 34.615 0.00 0.00 39.97 3.36
3212 3630 9.265901 CTTCATGTAGTGTAATCCAGAATAAGG 57.734 37.037 0.00 0.00 0.00 2.69
3299 3717 8.862325 TTTCATCACCTATCTTAGCTTCAAAA 57.138 30.769 0.00 0.00 0.00 2.44
3420 3838 9.423061 GCAAATTGTAACAAATGGAATACTCTT 57.577 29.630 0.00 0.00 0.00 2.85
3582 4385 1.897802 GGGTCTGGGTCGTAGAAGAAA 59.102 52.381 0.00 0.00 39.69 2.52
3584 4387 0.406750 TGGGTCTGGGTCGTAGAAGA 59.593 55.000 0.00 0.00 39.69 2.87
3629 4433 6.270231 AGGTCAAATTCTGAACCAGTACTACT 59.730 38.462 0.00 0.00 43.49 2.57
3703 4508 3.471495 ACGAGTTTGCCAAATCGATTC 57.529 42.857 24.40 0.00 38.50 2.52
3993 4798 3.883669 ACATCTCCCTGAAATCTGAAGC 58.116 45.455 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.