Multiple sequence alignment - TraesCS3D01G237200

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 TraesCS3D01G237200 chr3D 100.000 8522 0 0 1 8522 328390824 328382303 0.000000e+00 15738
1 TraesCS3D01G237200 chr3A 96.434 7992 193 21 251 8199 442769111 442761169 0.000000e+00 13095
2 TraesCS3D01G237200 chr3A 94.257 296 15 2 8229 8522 442760950 442760655 1.300000e-122 451
3 TraesCS3D01G237200 chr3A 96.347 219 6 2 1 217 442769410 442769192 8.130000e-95 359
4 TraesCS3D01G237200 chr3A 86.592 179 23 1 3026 3204 745507307 745507484 6.750000e-46 196
5 TraesCS3D01G237200 chr3B 95.974 5291 116 42 251 5502 421662539 421667771 0.000000e+00 8501
6 TraesCS3D01G237200 chr3B 97.605 2672 60 4 5531 8200 421667770 421670439 0.000000e+00 4577
7 TraesCS3D01G237200 chr3B 93.515 293 13 2 8235 8522 421670583 421670874 1.700000e-116 431
8 TraesCS3D01G237200 chr3B 96.861 223 6 1 1 222 421662233 421662455 1.040000e-98 372
9 TraesCS3D01G237200 chr3B 87.222 180 22 1 3026 3204 828415517 828415696 4.030000e-48 204
10 TraesCS3D01G237200 chr3B 85.714 182 25 1 3026 3207 828769528 828769348 3.140000e-44 191


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 TraesCS3D01G237200 chr3D 328382303 328390824 8521 True 15738.00 15738 100.000000 1 8522 1 chr3D.!!$R1 8521
1 TraesCS3D01G237200 chr3A 442760655 442769410 8755 True 4635.00 13095 95.679333 1 8522 3 chr3A.!!$R1 8521
2 TraesCS3D01G237200 chr3B 421662233 421670874 8641 False 3470.25 8501 95.988750 1 8522 4 chr3B.!!$F2 8521

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
873 953 0.108233 CTGAGCCTTCAGCCTCAGAC 60.108 60.000 8.81 0.00 43.98 3.51 F
1288 1368 2.202566 GCCTATGCGAACTTCAGGTAC 58.797 52.381 0.00 0.00 0.00 3.34 F
1479 1559 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79 F
1485 1565 2.710096 ATATTGTGGGACGGTTGGAG 57.290 50.000 0.00 0.00 0.00 3.86 F
3561 3653 1.737838 ACAGTGGGTAATCATGCACG 58.262 50.000 0.00 0.00 0.00 5.34 F
3684 3776 2.881513 TGACCGAGACATCTGATAGCTC 59.118 50.000 0.00 8.21 0.00 4.09 F
4821 4927 0.543277 TAATGCTGGCAGGAGGAGTG 59.457 55.000 17.64 0.00 0.00 3.51 F
5513 5619 1.018910 ACTTTGGTCGTCCGGTTTTG 58.981 50.000 0.00 0.00 36.30 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2730 2810 1.230635 ATGCGTGCTGAGTGGTTGAC 61.231 55.000 0.00 0.00 0.00 3.18 R
2930 3010 8.897872 AGTTTTAGAGTATCAAAGAACGGAAA 57.102 30.769 0.00 0.00 37.82 3.13 R
3363 3443 5.690409 CACTACAACTTAGTATGGCATACCG 59.310 44.000 29.09 20.86 39.70 4.02 R
3655 3747 3.681897 CAGATGTCTCGGTCAAGGAAAAG 59.318 47.826 0.00 0.00 0.00 2.27 R
4821 4927 1.897560 AAGAACAGGTACCAAGCAGC 58.102 50.000 15.94 0.00 0.00 5.25 R
5095 5201 2.658285 GCAGACACATGAAGCAAACAG 58.342 47.619 0.00 0.00 0.00 3.16 R
6547 6661 0.462403 GCTCGTACCCTCTCGTCTCT 60.462 60.000 0.00 0.00 0.00 3.10 R
7676 7791 2.268298 CCGTTCGGTCATGAAACTAGG 58.732 52.381 0.00 0.00 0.00 3.02 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
166 168 3.323243 GCAATTGCAGTGCTTGAAGAAT 58.677 40.909 25.36 3.38 41.59 2.40
222 262 1.337167 GCAAAGAAACCCACATCAGCC 60.337 52.381 0.00 0.00 0.00 4.85
223 263 2.242043 CAAAGAAACCCACATCAGCCT 58.758 47.619 0.00 0.00 0.00 4.58
279 340 5.974370 AGATTTGTTCCTACTATTACCCCCA 59.026 40.000 0.00 0.00 0.00 4.96
280 341 5.440207 TTTGTTCCTACTATTACCCCCAC 57.560 43.478 0.00 0.00 0.00 4.61
281 342 3.387012 TGTTCCTACTATTACCCCCACC 58.613 50.000 0.00 0.00 0.00 4.61
282 343 2.707791 GTTCCTACTATTACCCCCACCC 59.292 54.545 0.00 0.00 0.00 4.61
283 344 1.223858 TCCTACTATTACCCCCACCCC 59.776 57.143 0.00 0.00 0.00 4.95
284 345 1.738474 CTACTATTACCCCCACCCCC 58.262 60.000 0.00 0.00 0.00 5.40
327 388 0.243636 GACAGCAAACCGAAATGGGG 59.756 55.000 0.00 0.00 44.64 4.96
342 412 3.161450 GGGCGGCAGGAGGATACA 61.161 66.667 12.47 0.00 41.41 2.29
370 440 4.777896 ACTAACCTGGATATGATACCGCAT 59.222 41.667 0.00 0.00 0.00 4.73
380 450 3.842732 TGATACCGCATATCGTCGAAT 57.157 42.857 0.00 0.00 42.51 3.34
717 790 0.181350 GCAACCCCGATGGATCTTCT 59.819 55.000 0.00 0.00 38.00 2.85
871 951 4.937193 CTGAGCCTTCAGCCTCAG 57.063 61.111 0.64 0.64 43.98 3.35
872 952 2.284824 CTGAGCCTTCAGCCTCAGA 58.715 57.895 8.81 0.00 43.98 3.27
873 953 0.108233 CTGAGCCTTCAGCCTCAGAC 60.108 60.000 8.81 0.00 43.98 3.51
958 1038 8.360390 CCCAGCTATTTTTCCTGAATAATAACC 58.640 37.037 0.00 1.19 0.00 2.85
1288 1368 2.202566 GCCTATGCGAACTTCAGGTAC 58.797 52.381 0.00 0.00 0.00 3.34
1356 1436 3.118038 GGGTGGAAACATGCTAGGTATGA 60.118 47.826 0.00 0.00 46.14 2.15
1392 1472 9.875691 GCCTTTGAAGTTTTTATAATTCTGGAT 57.124 29.630 0.00 0.00 0.00 3.41
1457 1537 6.070251 TCCTTGGCATCTGTACAAAGATAAGA 60.070 38.462 0.00 0.00 35.09 2.10
1458 1538 6.599244 CCTTGGCATCTGTACAAAGATAAGAA 59.401 38.462 0.00 0.00 35.09 2.52
1459 1539 6.985188 TGGCATCTGTACAAAGATAAGAAC 57.015 37.500 0.00 0.00 35.09 3.01
1460 1540 5.580691 TGGCATCTGTACAAAGATAAGAACG 59.419 40.000 0.00 0.00 35.09 3.95
1461 1541 5.493735 GCATCTGTACAAAGATAAGAACGC 58.506 41.667 0.00 0.00 35.09 4.84
1462 1542 5.292101 GCATCTGTACAAAGATAAGAACGCT 59.708 40.000 0.00 0.00 35.09 5.07
1463 1543 6.508721 GCATCTGTACAAAGATAAGAACGCTC 60.509 42.308 0.00 0.00 35.09 5.03
1464 1544 6.268825 TCTGTACAAAGATAAGAACGCTCT 57.731 37.500 0.00 0.00 0.00 4.09
1465 1545 6.688578 TCTGTACAAAGATAAGAACGCTCTT 58.311 36.000 6.30 6.30 44.37 2.85
1466 1546 7.823665 TCTGTACAAAGATAAGAACGCTCTTA 58.176 34.615 10.52 10.52 45.93 2.10
1476 1556 5.353394 AAGAACGCTCTTATATTGTGGGA 57.647 39.130 0.00 0.00 40.26 4.37
1477 1557 4.694339 AGAACGCTCTTATATTGTGGGAC 58.306 43.478 0.00 0.00 0.00 4.46
1478 1558 3.093717 ACGCTCTTATATTGTGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
1479 1559 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
1480 1560 2.223971 CGCTCTTATATTGTGGGACGGT 60.224 50.000 0.00 0.00 0.00 4.83
1481 1561 3.740141 CGCTCTTATATTGTGGGACGGTT 60.740 47.826 0.00 0.00 0.00 4.44
1482 1562 3.560068 GCTCTTATATTGTGGGACGGTTG 59.440 47.826 0.00 0.00 0.00 3.77
1483 1563 4.127171 CTCTTATATTGTGGGACGGTTGG 58.873 47.826 0.00 0.00 0.00 3.77
1484 1564 3.775866 TCTTATATTGTGGGACGGTTGGA 59.224 43.478 0.00 0.00 0.00 3.53
1485 1565 2.710096 ATATTGTGGGACGGTTGGAG 57.290 50.000 0.00 0.00 0.00 3.86
1646 1726 6.268387 AGTCATTTTGGAAGAATGTTGTCCAT 59.732 34.615 0.00 0.00 41.05 3.41
1661 1741 3.632333 TGTCCATACACCACACCAAAAA 58.368 40.909 0.00 0.00 0.00 1.94
1738 1818 6.507023 CACCTGATAGCAATGTTTAATTCCC 58.493 40.000 0.00 0.00 0.00 3.97
1806 1886 8.713737 TGTTGACTGAGAAGAATATTCTGATG 57.286 34.615 18.61 9.85 37.65 3.07
1807 1887 8.534496 TGTTGACTGAGAAGAATATTCTGATGA 58.466 33.333 18.61 4.22 37.65 2.92
1808 1888 9.033481 GTTGACTGAGAAGAATATTCTGATGAG 57.967 37.037 18.61 14.83 37.65 2.90
1829 1909 6.810911 TGAGAAGAGCCATCTTACTATGAAC 58.189 40.000 0.00 0.00 45.98 3.18
1847 1927 9.466497 ACTATGAACATCACATAATTTCCTTGT 57.534 29.630 0.00 0.00 31.26 3.16
1905 1985 9.979578 TGTACTTAAAAGTCATACCGAGTTAAA 57.020 29.630 0.00 0.00 40.37 1.52
2034 2114 7.816995 GGCAAATAATGAAATGTAGTTGTTCCA 59.183 33.333 0.00 0.00 30.13 3.53
2547 2627 5.488919 TCCTAGTTCATTGGTTCCTGAGATT 59.511 40.000 0.00 0.00 0.00 2.40
2635 2715 6.610075 ATTTTCAGTTGCTATTGTGGGATT 57.390 33.333 0.00 0.00 0.00 3.01
2730 2810 7.220599 TGCTTCGTTCTTTCAATTTTTCAAG 57.779 32.000 0.00 0.00 0.00 3.02
2930 3010 5.010516 TGTGTTGCCTGTGCTTAAATGTATT 59.989 36.000 0.00 0.00 38.71 1.89
2957 3037 7.095270 TCCGTTCTTTGATACTCTAAAACTCC 58.905 38.462 0.00 0.00 0.00 3.85
3209 3289 9.953565 TGGCATAATGTTATAGTAAGTTATCCC 57.046 33.333 0.00 0.00 0.00 3.85
3363 3443 8.861033 TGCAAACATCTATTTTCAATATCTGC 57.139 30.769 0.00 0.00 0.00 4.26
3561 3653 1.737838 ACAGTGGGTAATCATGCACG 58.262 50.000 0.00 0.00 0.00 5.34
3655 3747 8.747538 ATGTCTATAGTAAACCATTGGGAAAC 57.252 34.615 7.78 1.76 38.05 2.78
3684 3776 2.881513 TGACCGAGACATCTGATAGCTC 59.118 50.000 0.00 8.21 0.00 4.09
4697 4803 9.601971 GTAAGATTTTTGTTGCGAGTTATTACA 57.398 29.630 0.00 0.00 0.00 2.41
4748 4854 9.245962 CTTCATGCATAATCTTGAGGAATTTTC 57.754 33.333 0.00 0.00 0.00 2.29
4774 4880 7.120726 CCCCTTGTAGTAACAGTAATCCTTTTG 59.879 40.741 0.00 0.00 36.83 2.44
4821 4927 0.543277 TAATGCTGGCAGGAGGAGTG 59.457 55.000 17.64 0.00 0.00 3.51
4954 5060 4.873827 GCTACAAATGATAACTTCGGTCCA 59.126 41.667 0.00 0.00 0.00 4.02
5095 5201 9.750125 CCCTATATCTTGGAAAATTGTTTAAGC 57.250 33.333 0.00 0.00 0.00 3.09
5336 5442 7.797062 AGAAATCTAAGGAATTCAGGACCTAC 58.203 38.462 7.93 0.00 34.71 3.18
5513 5619 1.018910 ACTTTGGTCGTCCGGTTTTG 58.981 50.000 0.00 0.00 36.30 2.44
5635 5741 4.831710 GGTATACTTTCTAGATGGGGACGT 59.168 45.833 2.25 0.00 0.00 4.34
5817 5923 5.290386 CGTATCATGGGGTTCTCTCTAAAC 58.710 45.833 0.00 0.00 0.00 2.01
5909 6015 6.324819 CAAGATGCCTCGTTATGAAACAATT 58.675 36.000 0.00 0.00 35.16 2.32
6027 6134 3.947834 CGGCTTGTAGGAATTTTGGAGAT 59.052 43.478 0.00 0.00 0.00 2.75
6060 6167 5.081032 AGTGGGTATATTAGGAGCTCAGTC 58.919 45.833 17.19 0.00 0.00 3.51
6673 6787 0.475906 AGCTGGTGAGTGCCTTCTTT 59.524 50.000 0.00 0.00 0.00 2.52
6702 6816 3.423749 CGTTGGGGTAAGGTTTTATGGT 58.576 45.455 0.00 0.00 0.00 3.55
6768 6882 1.429463 GGTTTCGAACTGATGACGCT 58.571 50.000 0.00 0.00 0.00 5.07
6890 7004 8.517878 CCAAGATTAATCTCAATGAACAAGTGT 58.482 33.333 18.19 0.00 35.76 3.55
6906 7020 8.988934 TGAACAAGTGTTGTATCAAGATTAGAC 58.011 33.333 0.42 0.00 44.59 2.59
7044 7158 9.383519 CCAGTAGATGAAGTTTATTCTTAAGCA 57.616 33.333 0.00 0.00 0.00 3.91
7274 7388 7.050377 AGTTCCATGTGTTTACCTCATATCTG 58.950 38.462 0.00 0.00 0.00 2.90
7416 7530 2.625314 CGATCTAGGAAGATGACCAGCA 59.375 50.000 0.00 0.00 42.73 4.41
7756 7871 7.486407 AATGCCAAGATAAGGAACATTCTTT 57.514 32.000 0.00 0.00 0.00 2.52
7771 7886 4.462483 ACATTCTTTTCCCGTGCATATGTT 59.538 37.500 4.29 0.00 0.00 2.71
7831 7946 0.179020 CTCCAGGAACAAGCACACCA 60.179 55.000 0.00 0.00 0.00 4.17
7910 8026 4.005650 CACATGGCAGTAGTCAAGAATGT 58.994 43.478 0.00 0.00 30.06 2.71
7916 8032 5.412594 TGGCAGTAGTCAAGAATGTCAAATC 59.587 40.000 0.00 0.00 0.00 2.17
7932 8048 6.530120 TGTCAAATCTGCTAACCTTCAGTAA 58.470 36.000 0.00 0.00 0.00 2.24
7934 8050 7.665559 TGTCAAATCTGCTAACCTTCAGTAATT 59.334 33.333 0.00 0.00 0.00 1.40
7967 8083 0.253160 ATGGGCTTCAGGGGTCTACA 60.253 55.000 0.00 0.00 0.00 2.74
7985 8101 0.313043 CACAAAGCAAGCACCTCCAG 59.687 55.000 0.00 0.00 0.00 3.86
8015 8131 4.105697 AGTGGTAGGTTCATGGAGGAAAAA 59.894 41.667 0.00 0.00 0.00 1.94
8070 8186 2.165998 GACCTCTTTGGCTGCAGAATT 58.834 47.619 20.43 0.00 40.22 2.17
8184 8300 7.458397 ACAAGATAAATCAGTGAACCCTACAA 58.542 34.615 0.00 0.00 0.00 2.41
8221 8363 7.009357 GCAGTGTAGCTTAGTATGTTACTGTTC 59.991 40.741 0.00 1.92 39.81 3.18
8287 8675 2.398588 AGATAAGAATCCGACAGGCCA 58.601 47.619 5.01 0.00 37.47 5.36
8404 8796 5.188434 ACATGATACCCATCACAACAGAAG 58.812 41.667 0.00 0.00 43.89 2.85
8488 8880 0.729690 GCTCTTTCGGTCCATTCAGC 59.270 55.000 0.00 0.00 0.00 4.26
8489 8881 1.677217 GCTCTTTCGGTCCATTCAGCT 60.677 52.381 0.00 0.00 0.00 4.24
8505 8897 4.966965 TCAGCTAACTTAGGTTCTCGAG 57.033 45.455 5.93 5.93 36.92 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 285 3.494332 AGGAACAAATCTGAGCTGCTTT 58.506 40.909 2.53 0.00 0.00 3.51
248 288 3.604582 AGTAGGAACAAATCTGAGCTGC 58.395 45.455 0.00 0.00 0.00 5.25
249 289 7.439655 GGTAATAGTAGGAACAAATCTGAGCTG 59.560 40.741 0.00 0.00 0.00 4.24
279 340 4.039852 GTCATTTATTTTGTGTGTGGGGGT 59.960 41.667 0.00 0.00 0.00 4.95
280 341 4.562552 GGTCATTTATTTTGTGTGTGGGGG 60.563 45.833 0.00 0.00 0.00 5.40
281 342 4.283212 AGGTCATTTATTTTGTGTGTGGGG 59.717 41.667 0.00 0.00 0.00 4.96
282 343 5.467035 AGGTCATTTATTTTGTGTGTGGG 57.533 39.130 0.00 0.00 0.00 4.61
283 344 8.356657 TCTTAAGGTCATTTATTTTGTGTGTGG 58.643 33.333 1.85 0.00 0.00 4.17
284 345 9.180678 GTCTTAAGGTCATTTATTTTGTGTGTG 57.819 33.333 1.85 0.00 0.00 3.82
327 388 1.440145 GCTTTGTATCCTCCTGCCGC 61.440 60.000 0.00 0.00 0.00 6.53
342 412 6.534634 GGTATCATATCCAGGTTAGTGCTTT 58.465 40.000 0.00 0.00 0.00 3.51
370 440 1.473677 ACACGGTGGAATTCGACGATA 59.526 47.619 13.48 0.00 0.00 2.92
432 502 2.474561 CATGTGGCTCATGCGAGTT 58.525 52.632 15.70 0.00 45.69 3.01
709 782 2.182516 TCCCCCAGAAGAGAAGATCC 57.817 55.000 0.00 0.00 0.00 3.36
717 790 3.154473 CGGCGATCCCCCAGAAGA 61.154 66.667 0.00 0.00 0.00 2.87
870 950 0.885196 GCGGAACTCTCAGTCTGTCT 59.115 55.000 0.00 0.00 0.00 3.41
871 951 0.109039 GGCGGAACTCTCAGTCTGTC 60.109 60.000 0.00 0.00 0.00 3.51
872 952 0.827925 TGGCGGAACTCTCAGTCTGT 60.828 55.000 0.00 0.00 0.00 3.41
873 953 0.318441 TTGGCGGAACTCTCAGTCTG 59.682 55.000 0.00 0.00 0.00 3.51
936 1016 6.577427 CGCGGTTATTATTCAGGAAAAATAGC 59.423 38.462 0.00 0.00 0.00 2.97
1076 1156 3.753434 CGGAGCTCTCAGTGCGGT 61.753 66.667 14.64 0.00 35.28 5.68
1288 1368 7.140705 TGAAGACATAAATTTTGCAGTCACAG 58.859 34.615 0.00 0.00 0.00 3.66
1457 1537 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
1458 1538 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
1459 1539 2.223971 ACCGTCCCACAATATAAGAGCG 60.224 50.000 0.00 0.00 0.00 5.03
1460 1540 3.470645 ACCGTCCCACAATATAAGAGC 57.529 47.619 0.00 0.00 0.00 4.09
1461 1541 4.127171 CCAACCGTCCCACAATATAAGAG 58.873 47.826 0.00 0.00 0.00 2.85
1462 1542 3.775866 TCCAACCGTCCCACAATATAAGA 59.224 43.478 0.00 0.00 0.00 2.10
1463 1543 4.127171 CTCCAACCGTCCCACAATATAAG 58.873 47.826 0.00 0.00 0.00 1.73
1464 1544 3.520317 ACTCCAACCGTCCCACAATATAA 59.480 43.478 0.00 0.00 0.00 0.98
1465 1545 3.109151 ACTCCAACCGTCCCACAATATA 58.891 45.455 0.00 0.00 0.00 0.86
1466 1546 1.913419 ACTCCAACCGTCCCACAATAT 59.087 47.619 0.00 0.00 0.00 1.28
1467 1547 1.354101 ACTCCAACCGTCCCACAATA 58.646 50.000 0.00 0.00 0.00 1.90
1468 1548 1.002773 GTACTCCAACCGTCCCACAAT 59.997 52.381 0.00 0.00 0.00 2.71
1469 1549 0.393820 GTACTCCAACCGTCCCACAA 59.606 55.000 0.00 0.00 0.00 3.33
1470 1550 1.474332 GGTACTCCAACCGTCCCACA 61.474 60.000 0.00 0.00 0.00 4.17
1471 1551 1.294459 GGTACTCCAACCGTCCCAC 59.706 63.158 0.00 0.00 0.00 4.61
1472 1552 1.152290 TGGTACTCCAACCGTCCCA 60.152 57.895 0.00 0.00 42.91 4.37
1473 1553 3.795905 TGGTACTCCAACCGTCCC 58.204 61.111 0.00 0.00 42.91 4.46
1482 1562 7.608761 TGACTTGGTTAATGTAAATGGTACTCC 59.391 37.037 0.00 0.00 0.00 3.85
1483 1563 8.556213 TGACTTGGTTAATGTAAATGGTACTC 57.444 34.615 0.00 0.00 0.00 2.59
1484 1564 8.927675 TTGACTTGGTTAATGTAAATGGTACT 57.072 30.769 0.00 0.00 0.00 2.73
1485 1565 8.789762 ACTTGACTTGGTTAATGTAAATGGTAC 58.210 33.333 0.00 0.00 0.00 3.34
1612 1692 7.815840 TTCTTCCAAAATGACTTGATGTGTA 57.184 32.000 0.00 0.00 0.00 2.90
1661 1741 8.511604 CCAGATCGGCCAGAATATATTTTAAT 57.488 34.615 2.24 0.00 0.00 1.40
1679 1759 1.869767 GACCTTTAGCATGCCAGATCG 59.130 52.381 15.66 0.05 0.00 3.69
1786 1866 9.199645 TCTTCTCATCAGAATATTCTTCTCAGT 57.800 33.333 15.49 0.00 38.02 3.41
1806 1886 6.810911 TGTTCATAGTAAGATGGCTCTTCTC 58.189 40.000 3.06 0.43 40.92 2.87
1807 1887 6.798427 TGTTCATAGTAAGATGGCTCTTCT 57.202 37.500 3.06 4.28 40.92 2.85
1808 1888 7.170658 GTGATGTTCATAGTAAGATGGCTCTTC 59.829 40.741 3.06 0.00 40.92 2.87
1906 1986 5.928264 GCTCTGGTGTATCTGCAAAATTTTT 59.072 36.000 0.00 0.00 0.00 1.94
1908 1988 4.523943 TGCTCTGGTGTATCTGCAAAATTT 59.476 37.500 0.00 0.00 0.00 1.82
1909 1989 4.081406 TGCTCTGGTGTATCTGCAAAATT 58.919 39.130 0.00 0.00 0.00 1.82
1910 1990 3.689347 TGCTCTGGTGTATCTGCAAAAT 58.311 40.909 0.00 0.00 0.00 1.82
2284 2364 6.701340 TCAGCTCTATTCACACACTTATGTT 58.299 36.000 0.00 0.00 36.72 2.71
2635 2715 7.860373 GCGTCTAAAATATAATGCACCAATTGA 59.140 33.333 7.12 0.00 0.00 2.57
2730 2810 1.230635 ATGCGTGCTGAGTGGTTGAC 61.231 55.000 0.00 0.00 0.00 3.18
2930 3010 8.897872 AGTTTTAGAGTATCAAAGAACGGAAA 57.102 30.769 0.00 0.00 37.82 3.13
2957 3037 9.916397 GGAAGTAATATTATGAAACAACACTCG 57.084 33.333 0.00 0.00 0.00 4.18
3363 3443 5.690409 CACTACAACTTAGTATGGCATACCG 59.310 44.000 29.09 20.86 39.70 4.02
3655 3747 3.681897 CAGATGTCTCGGTCAAGGAAAAG 59.318 47.826 0.00 0.00 0.00 2.27
3829 3921 5.221441 TGCAGAAGTTTCTAGCTAGTGTCAA 60.221 40.000 20.10 4.62 35.34 3.18
4211 4317 5.191323 AGAAGATGATTGTGAGACTCCCATT 59.809 40.000 0.00 0.00 0.00 3.16
4697 4803 9.028284 AGACTCCAAATTCATTATGACATTGTT 57.972 29.630 14.18 3.35 0.00 2.83
4748 4854 5.952347 AGGATTACTGTTACTACAAGGGG 57.048 43.478 0.00 0.00 32.92 4.79
4821 4927 1.897560 AAGAACAGGTACCAAGCAGC 58.102 50.000 15.94 0.00 0.00 5.25
5095 5201 2.658285 GCAGACACATGAAGCAAACAG 58.342 47.619 0.00 0.00 0.00 3.16
5513 5619 5.673337 TCAAACTGAAGACATGCAACTAC 57.327 39.130 0.00 0.00 0.00 2.73
5635 5741 3.334691 CGTAAGGCAGTCTCCAAAATCA 58.665 45.455 0.00 0.00 0.00 2.57
5909 6015 6.486320 TCAACTTTTATCAATGTCAGAGTGCA 59.514 34.615 0.00 0.00 0.00 4.57
5973 6080 4.215827 TCCAAAATTTTGCACATGGAATGC 59.784 37.500 22.90 0.00 41.64 3.56
6027 6134 9.992442 CTCCTAATATACCCACTCTATTCCTTA 57.008 37.037 0.00 0.00 0.00 2.69
6060 6167 7.645058 AAAGATTGACAGTTATGGGTATTGG 57.355 36.000 0.00 0.00 0.00 3.16
6545 6659 1.137479 CTCGTACCCTCTCGTCTCTCT 59.863 57.143 0.00 0.00 0.00 3.10
6546 6660 1.574134 CTCGTACCCTCTCGTCTCTC 58.426 60.000 0.00 0.00 0.00 3.20
6547 6661 0.462403 GCTCGTACCCTCTCGTCTCT 60.462 60.000 0.00 0.00 0.00 3.10
6890 7004 8.902540 AACACACAAGTCTAATCTTGATACAA 57.097 30.769 12.38 0.00 45.11 2.41
6906 7020 5.440685 CGCTTTTCTTAGGTAACACACAAG 58.559 41.667 0.00 0.00 41.41 3.16
7044 7158 7.458409 ACAGTTGCTTTGATCTTCAATATGT 57.542 32.000 0.00 1.00 36.11 2.29
7292 7406 2.761786 ATGGCAATGCTACCTCCATT 57.238 45.000 4.82 0.00 34.09 3.16
7400 7514 3.701542 CACTACTGCTGGTCATCTTCCTA 59.298 47.826 0.00 0.00 0.00 2.94
7416 7530 5.277345 CGCAAAGCTGTAAGAAAACACTACT 60.277 40.000 0.00 0.00 34.07 2.57
7676 7791 2.268298 CCGTTCGGTCATGAAACTAGG 58.732 52.381 0.00 0.00 0.00 3.02
7771 7886 2.566010 GGCAAAATTCTCGCCGCA 59.434 55.556 0.00 0.00 35.79 5.69
7774 7889 0.887933 TTGAGGGCAAAATTCTCGCC 59.112 50.000 4.54 4.54 45.47 5.54
7831 7946 0.325296 TTCTACCTCAGGGTGCGGAT 60.325 55.000 0.00 0.00 46.75 4.18
7850 7965 7.718753 ACTTCTGTTGAGTCATCTGAAGAAAAT 59.281 33.333 34.40 21.09 39.36 1.82
7910 8026 8.635765 AAATTACTGAAGGTTAGCAGATTTGA 57.364 30.769 0.00 0.00 36.07 2.69
7916 8032 6.678900 GCATGGAAATTACTGAAGGTTAGCAG 60.679 42.308 0.00 0.00 38.10 4.24
7932 8048 2.433239 GCCCATCAGAAAGCATGGAAAT 59.567 45.455 0.17 0.00 42.11 2.17
7934 8050 1.006281 AGCCCATCAGAAAGCATGGAA 59.994 47.619 0.17 0.00 42.11 3.53
7967 8083 0.183492 TCTGGAGGTGCTTGCTTTGT 59.817 50.000 0.00 0.00 0.00 2.83
7985 8101 3.201290 CATGAACCTACCACTGATGCTC 58.799 50.000 0.00 0.00 0.00 4.26
8016 8132 3.381388 GGGCTCCCCATCAGTTTTT 57.619 52.632 0.00 0.00 44.65 1.94
8070 8186 4.398319 GGTTCCTTCCTGTGATCTTGAAA 58.602 43.478 0.00 0.00 0.00 2.69
8184 8300 5.941555 AAGCTACACTGCTACCTTAGAAT 57.058 39.130 0.00 0.00 43.24 2.40
8287 8675 4.787551 TCGCCATGGTTGGAAAATATACT 58.212 39.130 14.67 0.00 46.92 2.12
8404 8796 6.604735 TGTTCTTCTTTTTAGCTCACACTC 57.395 37.500 0.00 0.00 0.00 3.51
8488 8880 6.756299 AAGTACCTCGAGAACCTAAGTTAG 57.244 41.667 15.71 2.65 35.94 2.34
8489 8881 6.571150 GCAAAGTACCTCGAGAACCTAAGTTA 60.571 42.308 15.71 0.00 35.94 2.24


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

AutoCloner maintained by Alex Coulton.