Multiple sequence alignment - TraesCS7D01G320000

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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 TraesCS7D01G320000 chr7D 100.000 4199 0 0 768 4966 409516253 409512055 0.000000e+00 7755
1 TraesCS7D01G320000 chr7D 100.000 437 0 0 1 437 409517020 409516584 0.000000e+00 808
2 TraesCS7D01G320000 chr7A 94.809 1830 69 19 768 2581 470600787 470598968 0.000000e+00 2830
3 TraesCS7D01G320000 chr7A 91.531 1169 62 14 3126 4269 470598195 470597039 0.000000e+00 1576
4 TraesCS7D01G320000 chr7A 93.763 481 23 6 2616 3092 470598672 470598195 0.000000e+00 715
5 TraesCS7D01G320000 chr7A 93.067 375 10 5 4606 4966 470596778 470596406 7.320000e-148 534
6 TraesCS7D01G320000 chr7A 92.975 242 15 1 4337 4578 470597000 470596761 7.910000e-93 351
7 TraesCS7D01G320000 chr7A 86.207 319 34 5 1 309 470601240 470600922 2.210000e-88 337
8 TraesCS7D01G320000 chr7B 89.773 1672 89 45 771 2418 424064726 424063113 0.000000e+00 2065
9 TraesCS7D01G320000 chr7B 89.666 1616 98 34 3386 4966 424061945 424060364 0.000000e+00 1995
10 TraesCS7D01G320000 chr7B 92.135 445 19 8 1 437 424065229 424064793 9.140000e-172 614


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 TraesCS7D01G320000 chr7D 409512055 409517020 4965 True 4281.500000 7755 100.000000 1 4966 2 chr7D.!!$R1 4965
1 TraesCS7D01G320000 chr7A 470596406 470601240 4834 True 1057.166667 2830 92.058667 1 4966 6 chr7A.!!$R1 4965
2 TraesCS7D01G320000 chr7B 424060364 424065229 4865 True 1558.000000 2065 90.524667 1 4966 3 chr7B.!!$R1 4965

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
925 944 0.108945 GAGGTCCAGTAAACGTCCCG 60.109 60.000 0.0 0.0 0.0 5.14 F
1554 1580 0.031817 CCCCATTCTTTCCCAGGCAT 60.032 55.000 0.0 0.0 0.0 4.40 F
1556 1582 1.063417 CCCATTCTTTCCCAGGCATCT 60.063 52.381 0.0 0.0 0.0 2.90 F
2237 2281 1.270412 CCGCACAACCTGTACCTGTAA 60.270 52.381 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1908 0.381801 CATGAAGGCGTGGCAATACC 59.618 55.000 0.00 0.0 39.84 2.73 R
2587 2637 0.701310 GGGGGTGGGGGAATCTACAT 60.701 60.000 0.00 0.0 0.00 2.29 R
2588 2638 1.308392 GGGGGTGGGGGAATCTACA 60.308 63.158 0.00 0.0 0.00 2.74 R
3969 4532 1.044611 CAACCGGGAAAACCCAACAT 58.955 50.000 6.32 0.0 36.34 2.71 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
37 38 3.119884 CGGCTAGCTAGAGATGAGTGATG 60.120 52.174 25.15 0.00 0.00 3.07
70 75 0.784495 TAGGTGTCCACTCTCCCACT 59.216 55.000 0.00 0.00 0.00 4.00
291 303 1.199789 GATTGCAATCACCGTGCTTCA 59.800 47.619 30.15 0.00 42.69 3.02
293 305 1.028130 TGCAATCACCGTGCTTCAAA 58.972 45.000 0.00 0.00 42.69 2.69
353 365 0.745486 CGATGCAGCTTGATCCCACA 60.745 55.000 0.00 0.00 0.00 4.17
368 380 1.967066 CCCACAATTGGTACTTTGGCA 59.033 47.619 10.83 0.00 42.10 4.92
379 391 3.119137 GGTACTTTGGCATGTGAAATCCC 60.119 47.826 0.00 0.00 0.00 3.85
431 445 1.179152 TCGGTGATAGGCTCAAACGA 58.821 50.000 0.00 0.00 40.84 3.85
432 446 1.134367 TCGGTGATAGGCTCAAACGAG 59.866 52.381 0.00 0.00 39.29 4.18
433 447 1.135083 CGGTGATAGGCTCAAACGAGT 60.135 52.381 0.00 0.00 38.23 4.18
434 448 2.541556 GGTGATAGGCTCAAACGAGTC 58.458 52.381 0.00 0.00 35.07 3.36
435 449 2.094182 GGTGATAGGCTCAAACGAGTCA 60.094 50.000 0.00 0.00 37.61 3.41
436 450 2.924290 GTGATAGGCTCAAACGAGTCAC 59.076 50.000 0.00 0.00 37.61 3.67
804 818 9.463443 ACGAAAAGTTTGAAGGATATGAAAAAG 57.537 29.630 0.00 0.00 0.00 2.27
818 832 4.817318 TGAAAAAGGAGGTGCAGTTTTT 57.183 36.364 0.00 0.00 35.36 1.94
819 833 4.754322 TGAAAAAGGAGGTGCAGTTTTTC 58.246 39.130 16.45 16.45 44.04 2.29
885 904 3.901797 AAGACGGCGGCCCAAAGAG 62.902 63.158 10.28 0.00 0.00 2.85
925 944 0.108945 GAGGTCCAGTAAACGTCCCG 60.109 60.000 0.00 0.00 0.00 5.14
1535 1561 3.113260 CCTCGTCCAGGTAATTCCATC 57.887 52.381 0.00 0.00 37.53 3.51
1537 1563 1.766496 TCGTCCAGGTAATTCCATCCC 59.234 52.381 0.00 0.00 39.02 3.85
1550 1576 1.570501 TCCATCCCCATTCTTTCCCAG 59.429 52.381 0.00 0.00 0.00 4.45
1551 1577 1.412074 CCATCCCCATTCTTTCCCAGG 60.412 57.143 0.00 0.00 0.00 4.45
1554 1580 0.031817 CCCCATTCTTTCCCAGGCAT 60.032 55.000 0.00 0.00 0.00 4.40
1556 1582 1.063417 CCCATTCTTTCCCAGGCATCT 60.063 52.381 0.00 0.00 0.00 2.90
1564 1590 6.073447 TCTTTCCCAGGCATCTTTAACATA 57.927 37.500 0.00 0.00 0.00 2.29
1571 1597 6.339730 CCAGGCATCTTTAACATAATTTGCA 58.660 36.000 0.00 0.00 0.00 4.08
1572 1598 6.987992 CCAGGCATCTTTAACATAATTTGCAT 59.012 34.615 0.00 0.00 0.00 3.96
1592 1618 4.679639 GCATCATGTCAGCAATGTGGATTT 60.680 41.667 0.00 0.00 0.00 2.17
1613 1639 4.901197 TTATGCTTAGGTCAGGTGTGAA 57.099 40.909 0.00 0.00 33.27 3.18
1614 1640 5.435686 TTATGCTTAGGTCAGGTGTGAAT 57.564 39.130 0.00 0.00 33.27 2.57
1618 1644 4.278170 TGCTTAGGTCAGGTGTGAATTTTG 59.722 41.667 0.00 0.00 33.27 2.44
1682 1708 3.570125 TGGTCGCATATCTAGAGTCCTTG 59.430 47.826 0.00 0.00 0.00 3.61
1869 1897 6.925211 TCAAAGTAATCTACTGACTGTGAGG 58.075 40.000 0.00 0.00 39.39 3.86
1880 1908 1.732259 GACTGTGAGGTGGTTATTGCG 59.268 52.381 0.00 0.00 0.00 4.85
1901 1929 1.949525 GTATTGCCACGCCTTCATGAT 59.050 47.619 0.00 0.00 0.00 2.45
1955 1983 7.432350 AACAAGATGTCAGATTGTCTTCTTC 57.568 36.000 6.05 0.00 36.18 2.87
1956 1984 6.767456 ACAAGATGTCAGATTGTCTTCTTCT 58.233 36.000 0.70 0.00 31.46 2.85
1967 1999 7.706179 CAGATTGTCTTCTTCTTCATCCTCTAC 59.294 40.741 0.00 0.00 0.00 2.59
2120 2154 8.161699 CCTTTTGGTATGTAGTGTTTACAAGT 57.838 34.615 0.00 0.00 34.07 3.16
2218 2262 5.470047 TTCTGAACCTTTCACTCTACTCC 57.530 43.478 0.00 0.00 35.46 3.85
2237 2281 1.270412 CCGCACAACCTGTACCTGTAA 60.270 52.381 0.00 0.00 0.00 2.41
2389 2433 3.071602 AGTCTGTGACAGTGCCAGTTAAT 59.928 43.478 12.93 0.00 34.60 1.40
2426 2473 7.497595 TGGATGACCATATACTTTGTCTACAC 58.502 38.462 0.00 0.00 41.77 2.90
2434 2481 7.649705 CCATATACTTTGTCTACACTAGCACTG 59.350 40.741 0.00 0.00 0.00 3.66
2444 2491 3.668447 ACACTAGCACTGAGGAAATGTG 58.332 45.455 0.00 0.00 35.08 3.21
2471 2518 5.467738 TCTTCCTGTGGATGGTCATATACT 58.532 41.667 0.00 0.00 0.00 2.12
2483 2530 9.262358 GGATGGTCATATACTTCTTTTGTCTAC 57.738 37.037 0.00 0.00 0.00 2.59
2494 2544 3.385433 TCTTTTGTCTACGTCACCCAAGA 59.615 43.478 0.00 0.00 0.00 3.02
2510 2560 7.391833 GTCACCCAAGATATATCAATTCTTCCC 59.608 40.741 15.08 0.00 0.00 3.97
2529 2579 1.815003 CCATCCTCTTTCAGTTGTGCC 59.185 52.381 0.00 0.00 0.00 5.01
2582 2632 6.827586 TGGGAACAGTTAAACATATGAACC 57.172 37.500 10.38 0.00 35.01 3.62
2583 2633 6.307776 TGGGAACAGTTAAACATATGAACCA 58.692 36.000 10.38 0.00 35.01 3.67
2584 2634 6.207810 TGGGAACAGTTAAACATATGAACCAC 59.792 38.462 10.38 0.99 35.01 4.16
2585 2635 6.207810 GGGAACAGTTAAACATATGAACCACA 59.792 38.462 10.38 0.00 0.00 4.17
2586 2636 7.305474 GGAACAGTTAAACATATGAACCACAG 58.695 38.462 10.38 0.87 0.00 3.66
2587 2637 7.174253 GGAACAGTTAAACATATGAACCACAGA 59.826 37.037 10.38 0.00 0.00 3.41
2588 2638 8.635765 AACAGTTAAACATATGAACCACAGAT 57.364 30.769 10.38 0.00 0.00 2.90
2597 2647 7.664082 CATATGAACCACAGATGTAGATTCC 57.336 40.000 0.00 0.00 41.55 3.01
2598 2648 4.487714 TGAACCACAGATGTAGATTCCC 57.512 45.455 0.00 0.00 0.00 3.97
2599 2649 3.199946 TGAACCACAGATGTAGATTCCCC 59.800 47.826 0.00 0.00 0.00 4.81
2600 2650 2.127708 ACCACAGATGTAGATTCCCCC 58.872 52.381 0.00 0.00 0.00 5.40
2601 2651 2.126882 CCACAGATGTAGATTCCCCCA 58.873 52.381 0.00 0.00 0.00 4.96
2602 2652 2.158755 CCACAGATGTAGATTCCCCCAC 60.159 54.545 0.00 0.00 0.00 4.61
2603 2653 2.127708 ACAGATGTAGATTCCCCCACC 58.872 52.381 0.00 0.00 0.00 4.61
2604 2654 1.421646 CAGATGTAGATTCCCCCACCC 59.578 57.143 0.00 0.00 0.00 4.61
2605 2655 0.771755 GATGTAGATTCCCCCACCCC 59.228 60.000 0.00 0.00 0.00 4.95
2606 2656 0.701310 ATGTAGATTCCCCCACCCCC 60.701 60.000 0.00 0.00 0.00 5.40
2741 3053 6.491745 TCTGGAACAATGTGGTTTGCTTATAA 59.508 34.615 0.00 0.00 38.70 0.98
2766 3078 5.877491 ACTTAAAGGGCTAGCTGTTTTACT 58.123 37.500 15.72 0.00 0.00 2.24
2767 3079 5.705905 ACTTAAAGGGCTAGCTGTTTTACTG 59.294 40.000 15.72 12.94 0.00 2.74
2777 3089 7.415653 GGCTAGCTGTTTTACTGAGCATATTTT 60.416 37.037 15.72 0.00 35.03 1.82
2792 3104 7.831690 TGAGCATATTTTGTGGTATGGTTTCTA 59.168 33.333 0.00 0.00 38.66 2.10
2793 3105 8.766994 AGCATATTTTGTGGTATGGTTTCTAT 57.233 30.769 0.00 0.00 36.04 1.98
2828 3146 5.990120 ATCTGCATCTTTGTTAGCCTTTT 57.010 34.783 0.00 0.00 0.00 2.27
2857 3175 6.822667 TGCTCTGTTAATCAACATCAACAT 57.177 33.333 0.00 0.00 43.58 2.71
2858 3176 6.614160 TGCTCTGTTAATCAACATCAACATG 58.386 36.000 0.00 0.00 43.58 3.21
2940 3258 5.660460 GTGAAACAAAGATGGAGGTTTTGT 58.340 37.500 0.00 0.00 44.39 2.83
2962 3281 7.997107 TGTTTGTTACTAATATCAGTAGCCG 57.003 36.000 0.00 0.00 32.86 5.52
2985 3304 6.632834 CCGTTTTGAACACAATCAGTTTAGAG 59.367 38.462 0.00 0.00 0.00 2.43
2999 3318 6.075984 TCAGTTTAGAGTTCCTAACCAGACT 58.924 40.000 0.00 0.00 37.10 3.24
3095 3416 5.192327 CTTGGAGATTTTGCAAGTTCTGT 57.808 39.130 15.53 0.00 46.63 3.41
3108 3429 4.374399 CAAGTTCTGTACGGTTTACACCT 58.626 43.478 0.64 0.00 41.64 4.00
3238 3561 5.950544 TTAGTATCTGTTGCCCAGTATGT 57.049 39.130 0.96 0.00 42.19 2.29
3253 3577 9.150028 TGCCCAGTATGTATTGTAATAACTAGA 57.850 33.333 0.00 0.00 0.00 2.43
3292 3616 8.321650 TCTTTTTGTTTTCTGTGCTTCATTTT 57.678 26.923 0.00 0.00 0.00 1.82
3462 3995 7.362401 GGTGATTAATTGCATCTCAAGTTGACT 60.362 37.037 0.08 0.00 38.22 3.41
3499 4032 6.735130 ACGGAAAAACTGAAAACCTTCTATG 58.265 36.000 0.00 0.00 32.33 2.23
3534 4067 8.564574 TGTGTTAGTGGAAAAAGATAACATGTC 58.435 33.333 0.00 0.00 38.28 3.06
3660 4214 4.561530 GCTTAGTGGACAACTGTCATGAGA 60.562 45.833 11.76 0.00 46.47 3.27
3675 4229 6.475504 TGTCATGAGAGACCATGTGTTAATT 58.524 36.000 0.00 0.00 43.22 1.40
3751 4308 1.033574 TAAAGTGGGGCACAAAACCG 58.966 50.000 0.00 0.00 36.74 4.44
3753 4310 3.532155 GTGGGGCACAAAACCGCA 61.532 61.111 0.00 0.00 46.77 5.69
3873 4436 4.832248 TGCCTGTAACTGAACTATTCCTG 58.168 43.478 0.00 0.00 0.00 3.86
3959 4522 7.050377 TCCACTTTAAGATCAAGCCTATTCAG 58.950 38.462 0.00 0.00 0.00 3.02
4124 4687 4.142315 CCTGAGGTTATTGGATTGTGCAAG 60.142 45.833 0.00 0.00 29.36 4.01
4210 4778 2.812613 GCAGTAGCACCTTTTACCACCA 60.813 50.000 0.00 0.00 41.58 4.17
4274 4846 4.870426 CGTCCATAACTAGTTTGCATGTCT 59.130 41.667 14.49 0.00 0.00 3.41
4275 4847 5.220472 CGTCCATAACTAGTTTGCATGTCTG 60.220 44.000 14.49 0.13 0.00 3.51
4277 4849 6.149474 GTCCATAACTAGTTTGCATGTCTGTT 59.851 38.462 14.49 0.00 0.00 3.16
4313 4885 0.887933 TGGCCGCTCTTTCCATTTTC 59.112 50.000 0.00 0.00 0.00 2.29
4314 4886 0.887933 GGCCGCTCTTTCCATTTTCA 59.112 50.000 0.00 0.00 0.00 2.69
4335 4907 1.312815 GGATGCAGCATGAGGGTAAC 58.687 55.000 14.22 0.00 39.69 2.50
4380 4952 8.058667 TCTTTTATGAATCATGACTTGTGCAT 57.941 30.769 5.91 0.00 0.00 3.96
4414 4986 8.632679 AGCAAAACTGACAAATAAAAGAGATCA 58.367 29.630 0.00 0.00 0.00 2.92
4437 5009 4.644103 CAAGTGGCATTGGAGATAAAGG 57.356 45.455 0.00 0.00 0.00 3.11
4478 5050 1.596603 TCATGAGTTGTGCACCTGTG 58.403 50.000 15.69 6.58 0.00 3.66
4479 5051 1.134128 TCATGAGTTGTGCACCTGTGT 60.134 47.619 15.69 0.00 0.00 3.72
4557 5129 6.091305 GGATCCTTTATTTTGCAAAGCAGAAC 59.909 38.462 12.41 4.23 40.61 3.01
4571 5143 5.695851 AAGCAGAACAGTGTGATTAAAGG 57.304 39.130 0.00 0.00 0.00 3.11
4746 5318 7.921041 AGGAGGTCAGATCTTATTACATGAA 57.079 36.000 0.00 0.00 0.00 2.57
4747 5319 7.731054 AGGAGGTCAGATCTTATTACATGAAC 58.269 38.462 0.00 0.00 0.00 3.18
4748 5320 6.642950 GGAGGTCAGATCTTATTACATGAACG 59.357 42.308 0.00 0.00 29.78 3.95
4749 5321 7.113658 AGGTCAGATCTTATTACATGAACGT 57.886 36.000 0.00 0.00 29.78 3.99
4750 5322 6.980978 AGGTCAGATCTTATTACATGAACGTG 59.019 38.462 0.00 0.00 29.78 4.49
4751 5323 6.978659 GGTCAGATCTTATTACATGAACGTGA 59.021 38.462 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.141937 TGGACACCTAAGAGACATACATGC 60.142 45.833 0.00 0.00 0.00 4.06
70 75 9.371136 TGTGTTTTTGCACAAAATTCTACATAA 57.629 25.926 9.21 2.43 45.17 1.90
97 102 1.153353 GACCGGTCGCTCATCAAAAA 58.847 50.000 20.85 0.00 0.00 1.94
334 346 0.745486 TGTGGGATCAAGCTGCATCG 60.745 55.000 1.02 0.00 0.00 3.84
353 365 5.543507 TTTCACATGCCAAAGTACCAATT 57.456 34.783 0.00 0.00 0.00 2.32
368 380 3.524095 TCCACACAAGGGATTTCACAT 57.476 42.857 0.00 0.00 0.00 3.21
379 391 2.744202 GCACCTCACTTATCCACACAAG 59.256 50.000 0.00 0.00 0.00 3.16
794 808 6.670695 AAAACTGCACCTCCTTTTTCATAT 57.329 33.333 0.00 0.00 0.00 1.78
797 811 4.466015 AGAAAAACTGCACCTCCTTTTTCA 59.534 37.500 13.89 0.00 41.76 2.69
798 812 5.011090 AGAAAAACTGCACCTCCTTTTTC 57.989 39.130 6.41 6.41 40.54 2.29
799 813 5.420725 AAGAAAAACTGCACCTCCTTTTT 57.579 34.783 0.00 0.00 0.00 1.94
804 818 4.134563 TGTCTAAGAAAAACTGCACCTCC 58.865 43.478 0.00 0.00 0.00 4.30
818 832 0.601558 AGGCGCGAGTTTGTCTAAGA 59.398 50.000 12.10 0.00 0.00 2.10
819 833 2.273370 TAGGCGCGAGTTTGTCTAAG 57.727 50.000 12.10 0.00 0.00 2.18
885 904 4.930696 TCCCCTTTCTGTTTATTCTTCCC 58.069 43.478 0.00 0.00 0.00 3.97
925 944 1.009389 CGGCACTTCGTCTGAACCTC 61.009 60.000 0.00 0.00 0.00 3.85
1047 1068 1.987855 CAGGTAGAACTCGGCCCCA 60.988 63.158 0.00 0.00 0.00 4.96
1344 1370 4.023980 TGTCGTCCTCCTTCATTATCTGT 58.976 43.478 0.00 0.00 0.00 3.41
1530 1556 1.570501 CTGGGAAAGAATGGGGATGGA 59.429 52.381 0.00 0.00 0.00 3.41
1535 1561 0.031817 ATGCCTGGGAAAGAATGGGG 60.032 55.000 0.00 0.00 0.00 4.96
1537 1563 2.449137 AGATGCCTGGGAAAGAATGG 57.551 50.000 0.00 0.00 0.00 3.16
1550 1576 8.492748 CATGATGCAAATTATGTTAAAGATGCC 58.507 33.333 0.00 0.00 0.00 4.40
1551 1577 9.037737 ACATGATGCAAATTATGTTAAAGATGC 57.962 29.630 0.00 0.00 30.05 3.91
1554 1580 9.791820 CTGACATGATGCAAATTATGTTAAAGA 57.208 29.630 0.00 0.00 34.18 2.52
1556 1582 8.033626 TGCTGACATGATGCAAATTATGTTAAA 58.966 29.630 0.00 0.00 34.18 1.52
1571 1597 5.670792 AAAATCCACATTGCTGACATGAT 57.329 34.783 0.00 0.00 0.00 2.45
1572 1598 6.566141 CATAAAATCCACATTGCTGACATGA 58.434 36.000 0.00 0.00 0.00 3.07
1592 1618 4.901197 TTCACACCTGACCTAAGCATAA 57.099 40.909 0.00 0.00 0.00 1.90
1642 1668 5.502544 GCGACCAAGTGAATAAGACTAATGC 60.503 44.000 0.00 0.00 0.00 3.56
1682 1708 3.821033 ACATTTGAGTTTCTGCTACCACC 59.179 43.478 0.00 0.00 0.00 4.61
1869 1897 1.746220 TGGCAATACCGCAATAACCAC 59.254 47.619 0.00 0.00 43.94 4.16
1880 1908 0.381801 CATGAAGGCGTGGCAATACC 59.618 55.000 0.00 0.00 39.84 2.73
1915 1943 3.985279 TCTTGTTAACCATTGACTCGTCG 59.015 43.478 2.48 0.00 0.00 5.12
1955 1983 5.344743 TGCTTGGTTAGTAGAGGATGAAG 57.655 43.478 0.00 0.00 0.00 3.02
1956 1984 5.483937 TCTTGCTTGGTTAGTAGAGGATGAA 59.516 40.000 0.00 0.00 0.00 2.57
1967 1999 6.089249 AGAAATTGGTTCTTGCTTGGTTAG 57.911 37.500 0.00 0.00 44.64 2.34
2024 2056 3.908103 TGCTAGGTTCCTATGGGGTATTC 59.092 47.826 0.00 0.00 36.25 1.75
2025 2057 3.949430 TGCTAGGTTCCTATGGGGTATT 58.051 45.455 0.00 0.00 36.25 1.89
2120 2154 4.636648 TGTTTCGAGTTTTTAGCTTGGTCA 59.363 37.500 0.00 0.00 0.00 4.02
2218 2262 2.066262 CTTACAGGTACAGGTTGTGCG 58.934 52.381 0.00 0.00 33.61 5.34
2237 2281 5.843019 TTTTCTTCCTTAGACCACATCCT 57.157 39.130 0.00 0.00 30.90 3.24
2426 2473 2.935201 GCTCACATTTCCTCAGTGCTAG 59.065 50.000 0.00 0.00 33.44 3.42
2434 2481 3.269178 CAGGAAGAGCTCACATTTCCTC 58.731 50.000 24.84 6.75 45.73 3.71
2444 2491 0.908198 ACCATCCACAGGAAGAGCTC 59.092 55.000 5.27 5.27 34.34 4.09
2471 2518 3.823281 TGGGTGACGTAGACAAAAGAA 57.177 42.857 0.00 0.00 32.13 2.52
2483 2530 7.118390 GGAAGAATTGATATATCTTGGGTGACG 59.882 40.741 13.79 0.00 33.73 4.35
2494 2544 9.972106 GAAAGAGGATGGGAAGAATTGATATAT 57.028 33.333 0.00 0.00 0.00 0.86
2510 2560 2.746362 GAGGCACAACTGAAAGAGGATG 59.254 50.000 0.00 0.00 37.43 3.51
2554 2604 8.698973 TCATATGTTTAACTGTTCCCAGAAAA 57.301 30.769 1.90 0.00 41.50 2.29
2558 2608 6.432783 TGGTTCATATGTTTAACTGTTCCCAG 59.567 38.462 1.90 0.00 44.68 4.45
2562 2612 8.094798 TCTGTGGTTCATATGTTTAACTGTTC 57.905 34.615 1.90 0.00 0.00 3.18
2581 2631 2.126882 TGGGGGAATCTACATCTGTGG 58.873 52.381 0.00 0.00 0.00 4.17
2582 2632 2.158755 GGTGGGGGAATCTACATCTGTG 60.159 54.545 0.00 0.00 0.00 3.66
2583 2633 2.127708 GGTGGGGGAATCTACATCTGT 58.872 52.381 0.00 0.00 0.00 3.41
2584 2634 1.421646 GGGTGGGGGAATCTACATCTG 59.578 57.143 0.00 0.00 0.00 2.90
2585 2635 1.699257 GGGGTGGGGGAATCTACATCT 60.699 57.143 0.00 0.00 0.00 2.90
2586 2636 0.771755 GGGGTGGGGGAATCTACATC 59.228 60.000 0.00 0.00 0.00 3.06
2587 2637 0.701310 GGGGGTGGGGGAATCTACAT 60.701 60.000 0.00 0.00 0.00 2.29
2588 2638 1.308392 GGGGGTGGGGGAATCTACA 60.308 63.158 0.00 0.00 0.00 2.74
2589 2639 3.670191 GGGGGTGGGGGAATCTAC 58.330 66.667 0.00 0.00 0.00 2.59
2627 2939 8.585881 TGTACTGAGTGCTCTTACTTTAAGATT 58.414 33.333 1.74 0.00 43.32 2.40
2741 3053 6.776116 AGTAAAACAGCTAGCCCTTTAAGTTT 59.224 34.615 12.13 8.44 0.00 2.66
2766 3078 6.663093 AGAAACCATACCACAAAATATGCTCA 59.337 34.615 0.00 0.00 0.00 4.26
2767 3079 7.100458 AGAAACCATACCACAAAATATGCTC 57.900 36.000 0.00 0.00 0.00 4.26
2777 3089 7.681679 TGACAGTTAATAGAAACCATACCACA 58.318 34.615 0.00 0.00 0.00 4.17
2793 3105 9.013229 ACAAAGATGCAGATTATTGACAGTTAA 57.987 29.630 0.00 0.00 0.00 2.01
2828 3146 5.843673 TGTTGATTAACAGAGCAACCAAA 57.156 34.783 0.00 0.00 41.66 3.28
2857 3175 9.109393 GTGAAAGCAGGAGATATATTACAAACA 57.891 33.333 0.00 0.00 0.00 2.83
2858 3176 9.331282 AGTGAAAGCAGGAGATATATTACAAAC 57.669 33.333 0.00 0.00 0.00 2.93
2940 3258 9.439500 AAAACGGCTACTGATATTAGTAACAAA 57.561 29.630 8.55 0.00 33.09 2.83
2959 3278 3.078594 ACTGATTGTGTTCAAAACGGC 57.921 42.857 0.00 0.00 37.11 5.68
2962 3281 8.911247 AACTCTAAACTGATTGTGTTCAAAAC 57.089 30.769 0.00 0.00 37.11 2.43
2985 3304 7.055378 TCTAGATAGTCAGTCTGGTTAGGAAC 58.945 42.308 0.00 0.00 0.00 3.62
3116 3437 8.140112 ACCTTATTATGAACTCAGTCAAGTCT 57.860 34.615 0.00 0.00 0.00 3.24
3273 3597 8.655092 CAGTTTAAAAATGAAGCACAGAAAACA 58.345 29.630 0.00 0.00 0.00 2.83
3274 3598 8.116136 CCAGTTTAAAAATGAAGCACAGAAAAC 58.884 33.333 3.77 0.00 0.00 2.43
3292 3616 8.050778 CAAATATGCTGAGGTTACCAGTTTAA 57.949 34.615 3.51 0.00 34.29 1.52
3366 3759 7.768120 TGCAACAAACAATAATTTTTCTCCTGT 59.232 29.630 0.00 0.00 0.00 4.00
3414 3946 8.598916 TCACCTAATTCACTAAACAATAGGTCA 58.401 33.333 0.00 0.00 33.59 4.02
3476 4009 6.636850 CACATAGAAGGTTTTCAGTTTTTCCG 59.363 38.462 0.00 0.00 35.70 4.30
3499 4032 1.349688 TCCACTAACACACCCCATCAC 59.650 52.381 0.00 0.00 0.00 3.06
3534 4067 6.632909 TGTCATCAGAAATAAGGCAAAATGG 58.367 36.000 0.00 0.00 0.00 3.16
3585 4118 8.153221 TGGTACAGAAGAGGTTGGATATTTTA 57.847 34.615 0.00 0.00 0.00 1.52
3660 4214 7.502561 GCCTAGGAAATAATTAACACATGGTCT 59.497 37.037 14.75 0.00 0.00 3.85
3675 4229 7.054124 CAGTTCCTTAATGTGCCTAGGAAATA 58.946 38.462 14.75 0.00 45.55 1.40
3840 4397 6.294361 TCAGTTACAGGCATACAGTATTGT 57.706 37.500 0.00 0.00 41.39 2.71
3873 4436 5.964751 GCAAACAAAAACATCCACAAATGTC 59.035 36.000 0.00 0.00 38.92 3.06
3959 4522 3.942130 AAACCCAACATAGCTCAAAGC 57.058 42.857 0.00 0.00 42.84 3.51
3969 4532 1.044611 CAACCGGGAAAACCCAACAT 58.955 50.000 6.32 0.00 36.34 2.71
4124 4687 5.415415 AAATATCAATGAGCACTCGAAGC 57.585 39.130 1.47 1.47 0.00 3.86
4193 4761 3.393278 AGAAGTGGTGGTAAAAGGTGCTA 59.607 43.478 0.00 0.00 0.00 3.49
4210 4778 6.012745 AGGCCTTTGATCATAAACAAGAAGT 58.987 36.000 0.00 0.00 0.00 3.01
4274 4846 3.211288 CCAACGGTTTGGCCAACA 58.789 55.556 20.35 6.99 46.09 3.33
4313 4885 0.467474 ACCCTCATGCTGCATCCATG 60.467 55.000 13.10 17.05 41.03 3.66
4314 4886 1.142936 TACCCTCATGCTGCATCCAT 58.857 50.000 13.10 0.00 0.00 3.41
4380 4952 4.710423 TTGTCAGTTTTGCTAGCACAAA 57.290 36.364 19.17 17.26 37.74 2.83
4414 4986 3.737559 TTATCTCCAATGCCACTTGGT 57.262 42.857 8.99 0.00 44.99 3.67
4437 5009 6.913170 TGAAAGAATCTGTAGATGCCAAAAC 58.087 36.000 0.00 0.00 34.49 2.43
4478 5050 2.222027 ACTAGTCAGTTTTGCCAGCAC 58.778 47.619 0.00 0.00 0.00 4.40
4479 5051 2.638480 ACTAGTCAGTTTTGCCAGCA 57.362 45.000 0.00 0.00 0.00 4.41
4557 5129 4.142315 CCAATGGAGCCTTTAATCACACTG 60.142 45.833 0.00 0.00 0.00 3.66
4571 5143 1.846261 TCCATAGGCCCAATGGAGC 59.154 57.895 26.41 2.08 46.29 4.70
4746 5318 4.405680 TCTGATGGGAGAACATAATCACGT 59.594 41.667 0.00 0.00 0.00 4.49
4747 5319 4.948847 TCTGATGGGAGAACATAATCACG 58.051 43.478 0.00 0.00 0.00 4.35
4748 5320 5.180868 GCATCTGATGGGAGAACATAATCAC 59.819 44.000 18.60 0.00 0.00 3.06
4749 5321 5.163174 TGCATCTGATGGGAGAACATAATCA 60.163 40.000 18.60 1.37 0.00 2.57
4750 5322 5.311265 TGCATCTGATGGGAGAACATAATC 58.689 41.667 18.60 0.00 0.00 1.75
4751 5323 5.314529 CTGCATCTGATGGGAGAACATAAT 58.685 41.667 18.60 0.00 0.00 1.28
4782 5368 7.036220 CACGAGAGGGTAAATGCTATAATAGG 58.964 42.308 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.