Multiple sequence alignment - TraesCS1B01G240400

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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 TraesCS1B01G240400 chr1B 100.000 5871 0 0 1 5871 428074235 428068365 0.000000e+00 10842.0
1 TraesCS1B01G240400 chr1B 83.125 160 13 10 4693 4847 630935613 630935463 3.690000e-27 134.0
2 TraesCS1B01G240400 chr1B 95.833 48 2 0 4613 4660 630935659 630935612 1.750000e-10 78.7
3 TraesCS1B01G240400 chr1D 97.385 2715 48 14 2704 5411 315981281 315978583 0.000000e+00 4599.0
4 TraesCS1B01G240400 chr1D 94.788 2283 75 22 1 2260 315984121 315981860 0.000000e+00 3517.0
5 TraesCS1B01G240400 chr1D 97.406 424 8 3 2248 2669 315981698 315981276 0.000000e+00 719.0
6 TraesCS1B01G240400 chr1D 92.114 317 12 2 5499 5802 315978588 315978272 9.040000e-118 435.0
7 TraesCS1B01G240400 chr1D 100.000 67 0 0 5802 5868 315977977 315977911 2.220000e-24 124.0
8 TraesCS1B01G240400 chr1D 91.667 84 5 2 5408 5491 78965909 78965828 1.340000e-21 115.0
9 TraesCS1B01G240400 chr1A 94.910 2456 93 14 3362 5802 396429740 396427302 0.000000e+00 3814.0
10 TraesCS1B01G240400 chr1A 91.428 2718 127 37 1 2669 396433093 396430433 0.000000e+00 3631.0
11 TraesCS1B01G240400 chr1A 94.872 663 28 5 2704 3361 396430438 396429777 0.000000e+00 1031.0
12 TraesCS1B01G240400 chr5B 90.441 136 12 1 4522 4657 702235123 702234989 1.680000e-40 178.0
13 TraesCS1B01G240400 chr5B 90.722 97 8 1 5398 5494 133894180 133894085 1.720000e-25 128.0
14 TraesCS1B01G240400 chr4D 91.209 91 7 1 5408 5498 497058712 497058801 7.990000e-24 122.0
15 TraesCS1B01G240400 chr4D 89.773 88 7 2 5408 5495 504090794 504090709 1.730000e-20 111.0
16 TraesCS1B01G240400 chr3D 92.857 84 5 1 5408 5491 437189809 437189891 2.870000e-23 121.0
17 TraesCS1B01G240400 chr5D 91.667 84 5 2 5408 5491 122198431 122198512 1.340000e-21 115.0
18 TraesCS1B01G240400 chr4A 90.588 85 5 3 5408 5491 586778574 586778656 6.220000e-20 110.0
19 TraesCS1B01G240400 chr2B 90.476 84 7 1 5408 5491 14834325 14834407 6.220000e-20 110.0
20 TraesCS1B01G240400 chr3B 100.000 29 0 0 669 697 535561855 535561827 3.000000e-03 54.7


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 TraesCS1B01G240400 chr1B 428068365 428074235 5870 True 10842.000000 10842 100.000000 1 5871 1 chr1B.!!$R1 5870
1 TraesCS1B01G240400 chr1D 315977911 315984121 6210 True 1878.800000 4599 96.338600 1 5868 5 chr1D.!!$R2 5867
2 TraesCS1B01G240400 chr1A 396427302 396433093 5791 True 2825.333333 3814 93.736667 1 5802 3 chr1A.!!$R1 5801

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
238 240 0.744771 GATGGGCTTGAACGGGAGAC 60.745 60.000 0.00 0.0 0.00 3.36 F
837 868 0.898326 CCAAACCACAACCCTAGGCC 60.898 60.000 2.05 0.0 0.00 5.19 F
1491 1535 0.621280 TCTGCATGGAGGGGATGTCA 60.621 55.000 14.84 0.0 0.00 3.58 F
1652 1696 1.001633 TGGCCTTCTTACAGGTTCGTC 59.998 52.381 3.32 0.0 36.15 4.20 F
1952 2003 1.033574 CTTAGCTGTCCTACCCCGAG 58.966 60.000 0.00 0.0 0.00 4.63 F
3074 3307 1.137675 GGGCTTCCGTTAGACCGTTAT 59.862 52.381 0.00 0.0 32.51 1.89 F
3081 3314 2.190981 CGTTAGACCGTTATGTCCTGC 58.809 52.381 0.00 0.0 35.83 4.85 F
3999 4273 0.461961 GGAGTAAGAGCTGGTGCGAT 59.538 55.000 0.00 0.0 45.42 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1177 1208 0.108963 TACACCCCCAAACCGAACAG 59.891 55.000 0.00 0.0 0.00 3.16 R
1952 2003 1.740025 CGTGGGAGATTGGAAAAGAGC 59.260 52.381 0.00 0.0 0.00 4.09 R
2706 2939 1.765904 TCTGTGCACAACTAGGGTTCA 59.234 47.619 21.98 0.0 32.73 3.18 R
2708 2941 2.092646 TGTTCTGTGCACAACTAGGGTT 60.093 45.455 21.98 0.0 35.86 4.11 R
3554 3828 2.627699 CCCTAGAGAGAGTTGATGGCTC 59.372 54.545 0.00 0.0 0.00 4.70 R
3999 4273 0.322098 CGTGCCTTTGTATGGGACCA 60.322 55.000 0.00 0.0 41.94 4.02 R
4001 4275 0.322187 ACCGTGCCTTTGTATGGGAC 60.322 55.000 0.00 0.0 41.61 4.46 R
4879 5154 0.755686 GCAGGGATAGGACACAGGAG 59.244 60.000 0.00 0.0 0.00 3.69 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
33 35 1.376812 GGTCCCACGAACCCATCAC 60.377 63.158 0.00 0.00 0.00 3.06
148 150 3.188786 GGCAACGCTCAGCTACCG 61.189 66.667 0.00 0.00 0.00 4.02
237 239 1.602237 GATGGGCTTGAACGGGAGA 59.398 57.895 0.00 0.00 0.00 3.71
238 240 0.744771 GATGGGCTTGAACGGGAGAC 60.745 60.000 0.00 0.00 0.00 3.36
333 344 9.691362 AAATATTAACAAGCGAACAAGTTTCAT 57.309 25.926 0.00 0.00 0.00 2.57
335 346 9.691362 ATATTAACAAGCGAACAAGTTTCATTT 57.309 25.926 0.00 0.00 0.00 2.32
336 347 5.949233 AACAAGCGAACAAGTTTCATTTC 57.051 34.783 0.00 0.00 0.00 2.17
337 348 4.992688 ACAAGCGAACAAGTTTCATTTCA 58.007 34.783 0.00 0.00 0.00 2.69
338 349 4.798387 ACAAGCGAACAAGTTTCATTTCAC 59.202 37.500 0.00 0.00 0.00 3.18
339 350 4.900635 AGCGAACAAGTTTCATTTCACT 57.099 36.364 0.00 0.00 0.00 3.41
340 351 6.183360 ACAAGCGAACAAGTTTCATTTCACTA 60.183 34.615 0.00 0.00 0.00 2.74
507 525 2.278857 CGGCGTCGAGAATCCAGG 60.279 66.667 1.44 0.00 39.00 4.45
594 615 1.373435 CGAACAACCTAGGCCCACA 59.627 57.895 9.30 0.00 0.00 4.17
770 792 4.295051 GAAGGAATAGAGCAGCTTACGAG 58.705 47.826 0.00 0.00 0.00 4.18
837 868 0.898326 CCAAACCACAACCCTAGGCC 60.898 60.000 2.05 0.00 0.00 5.19
1167 1198 1.285578 GACAGCTCTCTCCATTTCGC 58.714 55.000 0.00 0.00 0.00 4.70
1172 1203 2.360801 AGCTCTCTCCATTTCGCTCTAC 59.639 50.000 0.00 0.00 0.00 2.59
1175 1206 2.690497 TCTCTCCATTTCGCTCTACTGG 59.310 50.000 0.00 0.00 0.00 4.00
1176 1207 2.428890 CTCTCCATTTCGCTCTACTGGT 59.571 50.000 0.00 0.00 0.00 4.00
1177 1208 2.427453 TCTCCATTTCGCTCTACTGGTC 59.573 50.000 0.00 0.00 0.00 4.02
1185 1216 0.889306 GCTCTACTGGTCTGTTCGGT 59.111 55.000 0.00 0.00 0.00 4.69
1198 1229 1.170442 GTTCGGTTTGGGGGTGTATG 58.830 55.000 0.00 0.00 0.00 2.39
1200 1231 2.049767 CGGTTTGGGGGTGTATGCC 61.050 63.158 0.00 0.00 0.00 4.40
1215 1250 6.240060 GGGTGTATGCCTATGGGAAGTAATTA 60.240 42.308 0.00 0.00 33.58 1.40
1219 1254 4.714632 TGCCTATGGGAAGTAATTACTGC 58.285 43.478 18.70 16.55 36.50 4.40
1361 1396 7.254727 GGTGAGCATTTCTTCAGATGAACTATC 60.255 40.741 0.00 0.00 35.97 2.08
1367 1402 4.926244 TCTTCAGATGAACTATCGCAGTC 58.074 43.478 0.00 0.00 40.86 3.51
1388 1424 0.948678 TTGCTTCAGTTTACGGCCAC 59.051 50.000 2.24 0.00 0.00 5.01
1398 1434 2.735134 GTTTACGGCCACAGTGTTAGAG 59.265 50.000 2.24 0.00 0.00 2.43
1452 1496 3.634504 TGATGCTGGGCTTGAATGTATT 58.365 40.909 0.00 0.00 0.00 1.89
1491 1535 0.621280 TCTGCATGGAGGGGATGTCA 60.621 55.000 14.84 0.00 0.00 3.58
1632 1676 6.065976 TGTTGGATCAGTTATGTCATCCTT 57.934 37.500 0.00 0.00 36.51 3.36
1652 1696 1.001633 TGGCCTTCTTACAGGTTCGTC 59.998 52.381 3.32 0.00 36.15 4.20
1672 1723 3.059570 GTCTCTTGCGTAATCGTCACTTG 59.940 47.826 0.00 0.00 39.49 3.16
1676 1727 4.983538 TCTTGCGTAATCGTCACTTGTTAA 59.016 37.500 0.00 0.00 39.49 2.01
1734 1785 2.101415 TCTGAGATTGCGTGACCTATGG 59.899 50.000 0.00 0.00 0.00 2.74
1735 1786 1.138859 TGAGATTGCGTGACCTATGGG 59.861 52.381 0.00 0.00 38.88 4.00
1752 1803 2.715046 TGGGATCTTGCATGTTGAGTC 58.285 47.619 0.00 0.00 0.00 3.36
1805 1856 2.728690 TGCATGTGAAAAGCATGGAC 57.271 45.000 7.29 0.00 42.72 4.02
1952 2003 1.033574 CTTAGCTGTCCTACCCCGAG 58.966 60.000 0.00 0.00 0.00 4.63
2304 2536 9.120538 TGTAAATAATAGCAATTGAAGAGACCC 57.879 33.333 10.34 0.00 0.00 4.46
2366 2598 1.912043 CTCCTCTGAGGGTTTGGATGT 59.088 52.381 23.00 0.00 35.59 3.06
2377 2609 2.029918 GGTTTGGATGTGCAGAAGGTTC 60.030 50.000 0.00 0.00 0.00 3.62
2525 2758 5.989168 TGATCTCATCTACGTGTTTTTGTGT 59.011 36.000 0.00 0.00 0.00 3.72
2617 2850 1.202114 TGGCTATTTTTCTTGGCAGCG 59.798 47.619 0.00 0.00 0.00 5.18
2633 2866 3.045688 GCAGCGCCTTCTAAAAATATGC 58.954 45.455 2.29 0.00 0.00 3.14
2657 2890 7.177216 TGCATTGGCTATTTTAGATGGGAATAG 59.823 37.037 0.00 0.00 41.91 1.73
2672 2905 9.265862 AGATGGGAATAGGTTATCTATGAGAAG 57.734 37.037 0.00 0.00 38.60 2.85
2673 2906 9.261035 GATGGGAATAGGTTATCTATGAGAAGA 57.739 37.037 0.00 0.00 38.60 2.87
2674 2907 8.423906 TGGGAATAGGTTATCTATGAGAAGAC 57.576 38.462 0.00 0.00 38.60 3.01
2675 2908 7.455008 TGGGAATAGGTTATCTATGAGAAGACC 59.545 40.741 0.00 4.35 38.60 3.85
2676 2909 7.455008 GGGAATAGGTTATCTATGAGAAGACCA 59.545 40.741 11.79 0.00 38.60 4.02
2677 2910 8.527810 GGAATAGGTTATCTATGAGAAGACCAG 58.472 40.741 11.79 0.00 38.60 4.00
2678 2911 9.303116 GAATAGGTTATCTATGAGAAGACCAGA 57.697 37.037 11.79 3.27 38.60 3.86
2679 2912 9.836179 AATAGGTTATCTATGAGAAGACCAGAT 57.164 33.333 11.79 0.00 38.60 2.90
2680 2913 7.775053 AGGTTATCTATGAGAAGACCAGATC 57.225 40.000 11.79 0.00 36.37 2.75
2681 2914 6.432783 AGGTTATCTATGAGAAGACCAGATCG 59.567 42.308 11.79 0.00 36.37 3.69
2682 2915 6.207810 GGTTATCTATGAGAAGACCAGATCGT 59.792 42.308 6.71 0.00 34.97 3.73
2683 2916 7.390996 GGTTATCTATGAGAAGACCAGATCGTA 59.609 40.741 6.71 0.00 34.97 3.43
2684 2917 8.784994 GTTATCTATGAGAAGACCAGATCGTAA 58.215 37.037 0.00 0.00 0.00 3.18
2685 2918 9.521841 TTATCTATGAGAAGACCAGATCGTAAT 57.478 33.333 0.00 0.00 0.00 1.89
2687 2920 8.919777 TCTATGAGAAGACCAGATCGTAATAA 57.080 34.615 0.00 0.00 0.00 1.40
2688 2921 9.521841 TCTATGAGAAGACCAGATCGTAATAAT 57.478 33.333 0.00 0.00 0.00 1.28
2712 2945 8.753497 ATATTTTTCTTGGAGACTATGAACCC 57.247 34.615 0.00 0.00 0.00 4.11
2735 2968 4.342862 AGTTGTGCACAGAACACTAGAT 57.657 40.909 20.59 0.00 37.08 1.98
2925 3158 1.963985 ACTCCAGGAGAAAGCCATCT 58.036 50.000 24.45 0.00 33.32 2.90
3062 3295 1.526575 AAATGTGTGCTGGGCTTCCG 61.527 55.000 0.00 0.00 0.00 4.30
3074 3307 1.137675 GGGCTTCCGTTAGACCGTTAT 59.862 52.381 0.00 0.00 32.51 1.89
3081 3314 2.190981 CGTTAGACCGTTATGTCCTGC 58.809 52.381 0.00 0.00 35.83 4.85
3822 4096 7.700234 CGTAATTAAATACATCCAGCTTGCAAA 59.300 33.333 0.00 0.00 0.00 3.68
3904 4178 7.849322 TTCAGTGGTCATACCTAGCATTATA 57.151 36.000 0.00 0.00 39.58 0.98
3905 4179 8.435931 TTCAGTGGTCATACCTAGCATTATAT 57.564 34.615 0.00 0.00 39.58 0.86
3999 4273 0.461961 GGAGTAAGAGCTGGTGCGAT 59.538 55.000 0.00 0.00 45.42 4.58
4001 4275 0.176680 AGTAAGAGCTGGTGCGATGG 59.823 55.000 0.00 0.00 45.42 3.51
4336 4611 5.010314 GGATGATCATGGCTGCTAAATTTGA 59.990 40.000 14.30 0.00 0.00 2.69
4527 4802 7.876582 TCAATCCTCTGCAATTATGATCTACTG 59.123 37.037 0.00 0.00 0.00 2.74
4879 5154 2.160417 GCTGAAGCATTGACTGTACCAC 59.840 50.000 0.00 0.00 41.59 4.16
4951 5226 2.879646 TCAAACGACGCCATTTACCTTT 59.120 40.909 0.00 0.00 0.00 3.11
4952 5227 2.977169 CAAACGACGCCATTTACCTTTG 59.023 45.455 0.00 0.00 0.00 2.77
4953 5228 2.172851 ACGACGCCATTTACCTTTGA 57.827 45.000 0.00 0.00 0.00 2.69
5047 5322 7.180408 AGGACAGGAATTAGTACTTGTGTATGT 59.820 37.037 0.00 0.23 0.00 2.29
5048 5323 8.472413 GGACAGGAATTAGTACTTGTGTATGTA 58.528 37.037 0.00 0.00 0.00 2.29
5050 5325 9.817809 ACAGGAATTAGTACTTGTGTATGTATG 57.182 33.333 0.00 0.00 0.00 2.39
5211 5486 1.678627 ACTTCGGGAGATCTGTGATCG 59.321 52.381 0.00 0.00 39.57 3.69
5265 5540 4.832248 TGGTGCTACTTATGGTTCTTGAG 58.168 43.478 0.00 0.00 0.00 3.02
5276 5551 4.008074 TGGTTCTTGAGATTTCGAGCTT 57.992 40.909 0.00 0.00 35.18 3.74
5287 5562 0.756294 TTCGAGCTTGACCAGGACAA 59.244 50.000 2.11 4.19 0.00 3.18
5412 5687 6.257193 GGTGGGTATGTTTTATGTCTTACTCG 59.743 42.308 0.00 0.00 0.00 4.18
5416 5691 6.979238 GGTATGTTTTATGTCTTACTCGCTCT 59.021 38.462 0.00 0.00 0.00 4.09
5420 5695 4.634184 TTATGTCTTACTCGCTCTGTCC 57.366 45.455 0.00 0.00 0.00 4.02
5455 5730 4.739195 TCGTTTTGCAAGCTAAAACAGTT 58.261 34.783 18.63 0.00 44.28 3.16
5491 5766 7.667575 TCTTATATTATGAGATGGAGGGAGC 57.332 40.000 0.00 0.00 0.00 4.70
5492 5767 7.191918 TCTTATATTATGAGATGGAGGGAGCA 58.808 38.462 0.00 0.00 0.00 4.26
5543 5818 2.420547 GGCACCATCTCAGCAAGTGATA 60.421 50.000 0.00 0.00 33.51 2.15
5547 5822 3.133721 ACCATCTCAGCAAGTGATAGTCC 59.866 47.826 0.00 0.00 33.51 3.85
5608 5895 3.072184 AGATTTAGATCATCTTGCCCGCT 59.928 43.478 0.00 0.00 34.60 5.52
5631 5918 8.003784 CGCTTCTGTTAATTGTTTTGAAAATCC 58.996 33.333 0.00 0.00 0.00 3.01
5647 5934 7.440523 TGAAAATCCTTAGAAACTCTGAAGC 57.559 36.000 0.00 0.00 0.00 3.86
5699 5986 3.491342 TGCTTACCATTTAAGTGCACCA 58.509 40.909 14.63 0.00 0.00 4.17
5714 6001 1.135689 GCACCATACCTGAGTTTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
5754 6041 5.055265 TCTGTTCTGGTGGTGGAATAAAA 57.945 39.130 0.00 0.00 0.00 1.52
5756 6043 5.534654 TCTGTTCTGGTGGTGGAATAAAAAG 59.465 40.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 239 1.288127 GAGACAAGGCCACGTACGT 59.712 57.895 16.72 16.72 0.00 3.57
238 240 1.800315 CGAGACAAGGCCACGTACG 60.800 63.158 15.01 15.01 0.00 3.67
239 241 2.092882 GCGAGACAAGGCCACGTAC 61.093 63.158 5.01 0.00 0.00 3.67
240 242 2.260434 GCGAGACAAGGCCACGTA 59.740 61.111 5.01 0.00 0.00 3.57
507 525 0.664166 CCTTGCATGAACACGTTGCC 60.664 55.000 6.70 0.00 35.51 4.52
580 601 1.375523 GACGTGTGGGCCTAGGTTG 60.376 63.158 11.31 0.00 0.00 3.77
594 615 2.335369 GTCCTCGCACACTGACGT 59.665 61.111 0.00 0.00 0.00 4.34
653 674 2.036256 AGGTGAACATGCCCCTGC 59.964 61.111 0.00 0.00 38.26 4.85
655 676 2.971598 CGGAGGTGAACATGCCCCT 61.972 63.158 0.00 0.00 0.00 4.79
770 792 3.400054 CAGGGAGGGACGGGGAAC 61.400 72.222 0.00 0.00 0.00 3.62
1167 1198 3.318017 CAAACCGAACAGACCAGTAGAG 58.682 50.000 0.00 0.00 0.00 2.43
1172 1203 0.889186 CCCCAAACCGAACAGACCAG 60.889 60.000 0.00 0.00 0.00 4.00
1175 1206 1.149854 ACCCCCAAACCGAACAGAC 59.850 57.895 0.00 0.00 0.00 3.51
1176 1207 1.149627 CACCCCCAAACCGAACAGA 59.850 57.895 0.00 0.00 0.00 3.41
1177 1208 0.108963 TACACCCCCAAACCGAACAG 59.891 55.000 0.00 0.00 0.00 3.16
1185 1216 1.216678 CCATAGGCATACACCCCCAAA 59.783 52.381 0.00 0.00 0.00 3.28
1198 1229 4.714632 TGCAGTAATTACTTCCCATAGGC 58.285 43.478 15.60 13.12 33.46 3.93
1200 1231 7.255590 CCCAAATGCAGTAATTACTTCCCATAG 60.256 40.741 15.60 12.79 33.46 2.23
1215 1250 1.152269 ACAAGCCCCCAAATGCAGT 60.152 52.632 0.00 0.00 0.00 4.40
1219 1254 2.262292 CGCACAAGCCCCCAAATG 59.738 61.111 0.00 0.00 37.52 2.32
1367 1402 1.606668 TGGCCGTAAACTGAAGCAAAG 59.393 47.619 0.00 0.00 0.00 2.77
1398 1434 3.617263 CCGAAAGTAGGTTCATGTAGTGC 59.383 47.826 0.00 0.00 0.00 4.40
1452 1496 0.964700 CACTCTGCTCTCACCAGTGA 59.035 55.000 0.00 0.00 37.28 3.41
1491 1535 9.569122 AAAAGACACCACAAACTAATACTACAT 57.431 29.630 0.00 0.00 0.00 2.29
1521 1565 4.714632 TCAACTCCCTAACTTTTGGACTG 58.285 43.478 0.00 0.00 0.00 3.51
1632 1676 1.001633 GACGAACCTGTAAGAAGGCCA 59.998 52.381 5.01 0.00 41.46 5.36
1652 1696 2.987149 ACAAGTGACGATTACGCAAGAG 59.013 45.455 0.00 0.00 43.96 2.85
1676 1727 7.068702 TGCCTCCCATATGATTCAAGTAATTT 58.931 34.615 3.65 0.00 0.00 1.82
1734 1785 2.621338 TCGACTCAACATGCAAGATCC 58.379 47.619 0.00 0.00 0.00 3.36
1735 1786 4.436584 CCTTTCGACTCAACATGCAAGATC 60.437 45.833 0.00 0.00 0.00 2.75
1805 1856 1.757574 CTGGTTGTTCATGCGTGTTG 58.242 50.000 5.68 0.00 0.00 3.33
1952 2003 1.740025 CGTGGGAGATTGGAAAAGAGC 59.260 52.381 0.00 0.00 0.00 4.09
2366 2598 1.888512 GCATCTTTGGAACCTTCTGCA 59.111 47.619 0.00 0.00 0.00 4.41
2377 2609 4.883585 TCCTGTAATTAGCTGCATCTTTGG 59.116 41.667 1.02 0.00 0.00 3.28
2525 2758 3.568007 GTGCAAAGGAACTCCACACATTA 59.432 43.478 0.00 0.00 38.49 1.90
2617 2850 5.604565 AGCCAATGCATATTTTTAGAAGGC 58.395 37.500 0.00 0.00 41.13 4.35
2633 2866 7.671398 ACCTATTCCCATCTAAAATAGCCAATG 59.329 37.037 0.00 0.00 33.55 2.82
2657 2890 6.207810 ACGATCTGGTCTTCTCATAGATAACC 59.792 42.308 0.00 0.00 32.69 2.85
2686 2919 9.190317 GGGTTCATAGTCTCCAAGAAAAATATT 57.810 33.333 0.00 0.00 0.00 1.28
2687 2920 8.560903 AGGGTTCATAGTCTCCAAGAAAAATAT 58.439 33.333 0.00 0.00 0.00 1.28
2688 2921 7.928873 AGGGTTCATAGTCTCCAAGAAAAATA 58.071 34.615 0.00 0.00 0.00 1.40
2689 2922 6.794534 AGGGTTCATAGTCTCCAAGAAAAAT 58.205 36.000 0.00 0.00 0.00 1.82
2690 2923 6.200878 AGGGTTCATAGTCTCCAAGAAAAA 57.799 37.500 0.00 0.00 0.00 1.94
2691 2924 5.843019 AGGGTTCATAGTCTCCAAGAAAA 57.157 39.130 0.00 0.00 0.00 2.29
2692 2925 6.023603 ACTAGGGTTCATAGTCTCCAAGAAA 58.976 40.000 0.00 0.00 0.00 2.52
2693 2926 5.590818 ACTAGGGTTCATAGTCTCCAAGAA 58.409 41.667 0.00 0.00 0.00 2.52
2694 2927 5.208294 ACTAGGGTTCATAGTCTCCAAGA 57.792 43.478 0.00 0.00 0.00 3.02
2695 2928 5.187967 ACAACTAGGGTTCATAGTCTCCAAG 59.812 44.000 0.00 0.00 32.29 3.61
2696 2929 5.046591 CACAACTAGGGTTCATAGTCTCCAA 60.047 44.000 0.00 0.00 32.29 3.53
2697 2930 4.466370 CACAACTAGGGTTCATAGTCTCCA 59.534 45.833 0.00 0.00 32.29 3.86
2698 2931 4.680975 GCACAACTAGGGTTCATAGTCTCC 60.681 50.000 0.00 0.00 32.29 3.71
2699 2932 4.081642 TGCACAACTAGGGTTCATAGTCTC 60.082 45.833 0.00 0.00 32.29 3.36
2700 2933 3.838317 TGCACAACTAGGGTTCATAGTCT 59.162 43.478 0.00 0.00 32.29 3.24
2701 2934 3.933332 GTGCACAACTAGGGTTCATAGTC 59.067 47.826 13.17 0.00 32.29 2.59
2702 2935 3.326588 TGTGCACAACTAGGGTTCATAGT 59.673 43.478 19.28 0.00 34.96 2.12
2703 2936 3.935203 CTGTGCACAACTAGGGTTCATAG 59.065 47.826 21.98 0.00 32.73 2.23
2704 2937 3.580895 TCTGTGCACAACTAGGGTTCATA 59.419 43.478 21.98 0.00 32.73 2.15
2705 2938 2.371841 TCTGTGCACAACTAGGGTTCAT 59.628 45.455 21.98 0.00 32.73 2.57
2706 2939 1.765904 TCTGTGCACAACTAGGGTTCA 59.234 47.619 21.98 0.00 32.73 3.18
2707 2940 2.543777 TCTGTGCACAACTAGGGTTC 57.456 50.000 21.98 0.00 32.73 3.62
2708 2941 2.092646 TGTTCTGTGCACAACTAGGGTT 60.093 45.455 21.98 0.00 35.86 4.11
2712 2945 4.871513 TCTAGTGTTCTGTGCACAACTAG 58.128 43.478 32.31 32.31 39.17 2.57
3062 3295 3.187700 CAGCAGGACATAACGGTCTAAC 58.812 50.000 0.00 0.00 37.91 2.34
3554 3828 2.627699 CCCTAGAGAGAGTTGATGGCTC 59.372 54.545 0.00 0.00 0.00 4.70
3794 4068 6.632834 GCAAGCTGGATGTATTTAATTACGTG 59.367 38.462 0.00 0.00 0.00 4.49
3822 4096 4.712476 CATGCTAGCTAAAGATGGTTCCT 58.288 43.478 17.23 0.00 0.00 3.36
3867 4141 3.248024 ACCACTGAATACAAGAGACCCA 58.752 45.455 0.00 0.00 0.00 4.51
3904 4178 8.280258 TCTACTGGGATCATATTTCTTGGAAT 57.720 34.615 0.00 0.00 0.00 3.01
3905 4179 7.690454 TCTACTGGGATCATATTTCTTGGAA 57.310 36.000 0.00 0.00 0.00 3.53
3958 4232 5.126384 TCCTTGGGTCTACAAAACAAAACAG 59.874 40.000 0.00 0.00 0.00 3.16
3999 4273 0.322098 CGTGCCTTTGTATGGGACCA 60.322 55.000 0.00 0.00 41.94 4.02
4001 4275 0.322187 ACCGTGCCTTTGTATGGGAC 60.322 55.000 0.00 0.00 41.61 4.46
4657 4932 0.468214 CCCCTCTGTATCTCGCCTCA 60.468 60.000 0.00 0.00 0.00 3.86
4879 5154 0.755686 GCAGGGATAGGACACAGGAG 59.244 60.000 0.00 0.00 0.00 3.69
4965 5240 4.233789 TGTTGCGATACCAAAATCTTTGC 58.766 39.130 0.00 0.00 0.00 3.68
4968 5243 5.705609 ACTTGTTGCGATACCAAAATCTT 57.294 34.783 0.00 0.00 0.00 2.40
5047 5322 6.512297 TGCGTGCTATCAAGACTAATTCATA 58.488 36.000 0.00 0.00 0.00 2.15
5048 5323 5.359756 TGCGTGCTATCAAGACTAATTCAT 58.640 37.500 0.00 0.00 0.00 2.57
5049 5324 4.754322 TGCGTGCTATCAAGACTAATTCA 58.246 39.130 0.00 0.00 0.00 2.57
5050 5325 4.806247 ACTGCGTGCTATCAAGACTAATTC 59.194 41.667 0.00 0.00 0.00 2.17
5150 5425 6.910433 GGCAATTATTCGTGTACCAACAATAG 59.090 38.462 0.00 0.00 37.36 1.73
5188 5463 4.202020 CGATCACAGATCTCCCGAAGTAAA 60.202 45.833 0.00 0.00 0.00 2.01
5189 5464 3.315470 CGATCACAGATCTCCCGAAGTAA 59.685 47.826 0.00 0.00 0.00 2.24
5190 5465 2.879026 CGATCACAGATCTCCCGAAGTA 59.121 50.000 0.00 0.00 0.00 2.24
5211 5486 6.743575 AAAGTGCTCCAAGATAATGTACAC 57.256 37.500 0.00 0.00 0.00 2.90
5265 5540 2.003301 GTCCTGGTCAAGCTCGAAATC 58.997 52.381 0.00 0.00 0.00 2.17
5276 5551 5.126384 CAGTTTAAACCTTTTGTCCTGGTCA 59.874 40.000 14.72 0.00 32.98 4.02
5287 5562 8.576442 CAGATATGTCAACCAGTTTAAACCTTT 58.424 33.333 14.72 3.10 0.00 3.11
5420 5695 8.292448 AGCTTGCAAAACGATCTTATATTATGG 58.708 33.333 0.00 0.00 0.00 2.74
5463 5738 9.431690 TCCCTCCATCTCATAATATAAGATCAG 57.568 37.037 0.00 0.00 0.00 2.90
5471 5746 5.096521 TGTGCTCCCTCCATCTCATAATAT 58.903 41.667 0.00 0.00 0.00 1.28
5479 5754 2.769209 AGTATTGTGCTCCCTCCATCT 58.231 47.619 0.00 0.00 0.00 2.90
5547 5822 4.545610 TGTATTTTCAGAGCGCAAAAAGG 58.454 39.130 11.47 0.00 0.00 3.11
5631 5918 6.692486 TCCACTTAGCTTCAGAGTTTCTAAG 58.308 40.000 0.00 0.00 40.97 2.18
5647 5934 9.784531 ATATGAAGATGTACCATTTCCACTTAG 57.215 33.333 0.00 0.00 0.00 2.18
5699 5986 3.074412 CAGAACCGCAAAACTCAGGTAT 58.926 45.455 0.00 0.00 35.68 2.73
5714 6001 1.407618 AGAAAACGCCCAAACAGAACC 59.592 47.619 0.00 0.00 0.00 3.62
5754 6041 5.047802 CAGATAAAGATGCACCAAACACCTT 60.048 40.000 0.00 0.00 0.00 3.50
5756 6043 4.458989 TCAGATAAAGATGCACCAAACACC 59.541 41.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.