Multiple sequence alignment - TraesCS5A01G288200

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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 TraesCS5A01G288200 chr5A 100.000 3945 0 0 1 3945 495867399 495863455 0.000000e+00 7286.0
1 TraesCS5A01G288200 chr5A 88.178 516 56 5 3429 3941 32741488 32742001 9.370000e-171 610.0
2 TraesCS5A01G288200 chr5A 91.406 128 7 2 1 124 422030516 422030643 5.240000e-39 172.0
3 TraesCS5A01G288200 chr5A 77.114 201 33 9 1945 2134 593352632 593352830 1.940000e-18 104.0
4 TraesCS5A01G288200 chr5A 87.273 55 7 0 1260 1314 593352463 593352517 3.290000e-06 63.9
5 TraesCS5A01G288200 chr5D 89.042 3112 195 73 1 3025 393803874 393800822 0.000000e+00 3723.0
6 TraesCS5A01G288200 chr5D 94.259 540 31 0 3406 3945 393763854 393763315 0.000000e+00 826.0
7 TraesCS5A01G288200 chr5D 93.862 391 22 2 3019 3408 393766072 393765683 4.390000e-164 588.0
8 TraesCS5A01G288200 chr5D 76.142 197 34 8 1949 2134 473853282 473853476 1.510000e-14 91.6
9 TraesCS5A01G288200 chr5D 87.037 54 7 0 1260 1313 473853135 473853188 1.180000e-05 62.1
10 TraesCS5A01G288200 chr5B 89.325 2014 114 39 184 2146 473640526 473638563 0.000000e+00 2435.0
11 TraesCS5A01G288200 chr5B 90.046 874 59 15 2169 3024 473638509 473637646 0.000000e+00 1107.0
12 TraesCS5A01G288200 chr5B 89.333 825 84 4 3019 3840 473637177 473636354 0.000000e+00 1033.0
13 TraesCS5A01G288200 chr5B 86.839 813 90 11 3141 3945 672836378 672835575 0.000000e+00 893.0
14 TraesCS5A01G288200 chr5B 87.938 514 59 3 3429 3941 80604249 80604760 1.570000e-168 603.0
15 TraesCS5A01G288200 chr5B 93.048 187 8 2 1 184 473640783 473640599 6.500000e-68 268.0
16 TraesCS5A01G288200 chr5B 81.308 107 13 5 1949 2050 580849641 580849745 3.270000e-11 80.5
17 TraesCS5A01G288200 chr5B 77.143 105 24 0 1209 1313 580849444 580849548 1.180000e-05 62.1
18 TraesCS5A01G288200 chr7A 87.715 814 82 11 3140 3945 11279396 11280199 0.000000e+00 933.0
19 TraesCS5A01G288200 chr7A 87.500 96 9 3 2031 2125 617385889 617385796 1.500000e-19 108.0
20 TraesCS5A01G288200 chr7A 100.000 37 0 0 1279 1315 516151995 516152031 7.070000e-08 69.4
21 TraesCS5A01G288200 chr7A 100.000 37 0 0 1279 1315 516514847 516514811 7.070000e-08 69.4
22 TraesCS5A01G288200 chr6D 88.189 508 58 2 3435 3941 6391171 6390665 4.360000e-169 604.0
23 TraesCS5A01G288200 chr6D 81.944 144 20 5 1997 2140 89308680 89308543 2.490000e-22 117.0
24 TraesCS5A01G288200 chr2B 87.814 517 59 3 3430 3945 742653033 742653546 1.570000e-168 603.0
25 TraesCS5A01G288200 chr4B 87.743 514 60 3 3429 3941 459068573 459068062 7.300000e-167 597.0
26 TraesCS5A01G288200 chr4B 91.057 123 8 1 1 120 178081142 178081264 3.150000e-36 163.0
27 TraesCS5A01G288200 chr4B 89.844 128 10 3 1 125 159566814 159566687 1.130000e-35 161.0
28 TraesCS5A01G288200 chr1B 81.975 405 54 14 3026 3421 35472800 35472406 3.800000e-85 326.0
29 TraesCS5A01G288200 chr1B 81.728 405 55 10 3026 3421 35495323 35494929 1.770000e-83 320.0
30 TraesCS5A01G288200 chr1B 92.105 38 2 1 3026 3063 35031523 35031487 7.000000e-03 52.8
31 TraesCS5A01G288200 chr7D 91.870 123 5 3 1 119 82296584 82296705 2.440000e-37 167.0
32 TraesCS5A01G288200 chr7D 81.538 130 19 5 1997 2125 535967380 535967505 6.970000e-18 102.0
33 TraesCS5A01G288200 chr1A 90.400 125 11 1 1 124 249049918 249050042 3.150000e-36 163.0
34 TraesCS5A01G288200 chr2A 90.400 125 9 1 1 122 578387595 578387719 1.130000e-35 161.0
35 TraesCS5A01G288200 chr2A 90.323 124 11 1 1 123 656371996 656371873 1.130000e-35 161.0
36 TraesCS5A01G288200 chr6B 81.944 144 20 5 1997 2140 171709468 171709331 2.490000e-22 117.0
37 TraesCS5A01G288200 chr6A 89.655 87 9 0 2054 2140 107686128 107686042 1.160000e-20 111.0
38 TraesCS5A01G288200 chr7B 82.308 130 18 5 1997 2125 578438877 578439002 1.500000e-19 108.0
39 TraesCS5A01G288200 chr7B 100.000 37 0 0 1279 1315 504495459 504495495 7.070000e-08 69.4
40 TraesCS5A01G288200 chrUn 79.221 154 22 6 1993 2144 124826904 124827049 9.020000e-17 99.0
41 TraesCS5A01G288200 chr4D 86.275 51 4 2 1285 1332 97508803 97508853 7.000000e-03 52.8


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 TraesCS5A01G288200 chr5A 495863455 495867399 3944 True 7286.00 7286 100.0000 1 3945 1 chr5A.!!$R1 3944
1 TraesCS5A01G288200 chr5A 32741488 32742001 513 False 610.00 610 88.1780 3429 3941 1 chr5A.!!$F1 512
2 TraesCS5A01G288200 chr5D 393800822 393803874 3052 True 3723.00 3723 89.0420 1 3025 1 chr5D.!!$R1 3024
3 TraesCS5A01G288200 chr5D 393763315 393766072 2757 True 707.00 826 94.0605 3019 3945 2 chr5D.!!$R2 926
4 TraesCS5A01G288200 chr5B 473636354 473640783 4429 True 1210.75 2435 90.4380 1 3840 4 chr5B.!!$R2 3839
5 TraesCS5A01G288200 chr5B 672835575 672836378 803 True 893.00 893 86.8390 3141 3945 1 chr5B.!!$R1 804
6 TraesCS5A01G288200 chr5B 80604249 80604760 511 False 603.00 603 87.9380 3429 3941 1 chr5B.!!$F1 512
7 TraesCS5A01G288200 chr7A 11279396 11280199 803 False 933.00 933 87.7150 3140 3945 1 chr7A.!!$F1 805
8 TraesCS5A01G288200 chr6D 6390665 6391171 506 True 604.00 604 88.1890 3435 3941 1 chr6D.!!$R1 506
9 TraesCS5A01G288200 chr2B 742653033 742653546 513 False 603.00 603 87.8140 3430 3945 1 chr2B.!!$F1 515
10 TraesCS5A01G288200 chr4B 459068062 459068573 511 True 597.00 597 87.7430 3429 3941 1 chr4B.!!$R2 512

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
548 631 0.604780 CAGCCTCAGTCAACCCACAG 60.605 60.0 0.0 0.0 0.0 3.66 F
1565 1719 0.106519 ATGTGACCCCATTAGCCAGC 60.107 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2365 0.179000 GACGGGAGGTGCAATGAGAT 59.821 55.0 0.0 0.0 0.00 2.75 R
3120 3823 0.320683 CGATGCAGTGTTCTCACCCA 60.321 55.0 0.0 0.0 44.83 4.51 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
388 468 3.956199 ACAGGCCATGTTTCCAATGATAG 59.044 43.478 5.01 0.00 39.96 2.08
466 549 5.748402 TGATCTGATTGCCTGTTACAAGAT 58.252 37.500 0.00 0.00 0.00 2.40
502 585 2.092212 ACGATGCCAAATCCAAGGAGAT 60.092 45.455 0.00 0.00 0.00 2.75
510 593 4.381292 CCAAATCCAAGGAGATGAAACAGC 60.381 45.833 5.71 0.00 0.00 4.40
511 594 2.496899 TCCAAGGAGATGAAACAGCC 57.503 50.000 0.00 0.00 0.00 4.85
512 595 1.004745 TCCAAGGAGATGAAACAGCCC 59.995 52.381 0.00 0.00 0.00 5.19
513 596 1.467920 CAAGGAGATGAAACAGCCCC 58.532 55.000 0.00 0.00 0.00 5.80
537 620 3.640257 ATGTGCAGCCCAGCCTCAG 62.640 63.158 0.00 0.00 0.00 3.35
539 622 4.025858 TGCAGCCCAGCCTCAGTC 62.026 66.667 0.00 0.00 0.00 3.51
548 631 0.604780 CAGCCTCAGTCAACCCACAG 60.605 60.000 0.00 0.00 0.00 3.66
583 666 6.213397 TCTCTAGATTTGATTGGTTCCACAGA 59.787 38.462 0.00 0.00 0.00 3.41
590 673 2.910688 TTGGTTCCACAGAGTCTCAC 57.089 50.000 1.94 0.00 0.00 3.51
594 677 2.103263 GGTTCCACAGAGTCTCACACTT 59.897 50.000 1.94 0.00 34.41 3.16
596 679 4.299978 GTTCCACAGAGTCTCACACTTAC 58.700 47.826 1.94 0.00 34.41 2.34
658 745 1.018148 CCGTCTCTCACTAGCATCGT 58.982 55.000 0.00 0.00 0.00 3.73
687 774 6.012745 GGAATATATCCCTTTTCAGTGCCAT 58.987 40.000 0.00 0.00 43.00 4.40
700 787 7.974482 TTTCAGTGCCATGATCATAATCTAG 57.026 36.000 8.15 0.00 32.75 2.43
717 804 4.104696 TCTAGGCGCTTTTAAAAATGGC 57.895 40.909 7.64 14.28 0.00 4.40
738 825 5.178623 TGGCTCACATAACTAACGAACAAAG 59.821 40.000 0.00 0.00 0.00 2.77
743 830 4.387862 ACATAACTAACGAACAAAGCCTCG 59.612 41.667 0.00 0.00 40.87 4.63
764 852 6.346919 CCTCGTTGGAATAATATCTTTCAGCG 60.347 42.308 8.38 8.38 38.35 5.18
798 886 7.338800 ACAGATAATACAGCTTCCAATTTGG 57.661 36.000 9.28 9.28 39.43 3.28
801 889 4.888326 AATACAGCTTCCAATTTGGCAA 57.112 36.364 10.76 0.00 37.47 4.52
802 890 5.425196 AATACAGCTTCCAATTTGGCAAT 57.575 34.783 10.76 0.00 37.47 3.56
805 893 3.816523 ACAGCTTCCAATTTGGCAATTTG 59.183 39.130 21.88 21.88 37.47 2.32
829 917 6.653740 TGCATTATCCTCATCTCAATCATCAC 59.346 38.462 0.00 0.00 0.00 3.06
832 920 5.908562 ATCCTCATCTCAATCATCACCTT 57.091 39.130 0.00 0.00 0.00 3.50
833 921 5.287674 TCCTCATCTCAATCATCACCTTC 57.712 43.478 0.00 0.00 0.00 3.46
837 925 5.618236 TCATCTCAATCATCACCTTCATCC 58.382 41.667 0.00 0.00 0.00 3.51
910 1004 1.000396 GGCCCATCTTTGCTGTCCT 60.000 57.895 0.00 0.00 0.00 3.85
915 1009 1.004044 CCATCTTTGCTGTCCTCTGGT 59.996 52.381 0.00 0.00 0.00 4.00
944 1038 2.035961 TCACTGTCACTCACTTGTAGCC 59.964 50.000 0.00 0.00 0.00 3.93
949 1045 1.344438 TCACTCACTTGTAGCCAGTGG 59.656 52.381 4.20 4.20 36.04 4.00
1082 1185 2.284921 CTGACCTCCAGGGCCAGA 60.285 66.667 6.18 0.21 44.80 3.86
1229 1338 2.483745 GAGTCGATCGTGCGGTCA 59.516 61.111 15.94 0.00 0.00 4.02
1271 1380 3.621892 GACCTTCGTCACCGTCCCG 62.622 68.421 0.00 0.00 38.99 5.14
1341 1450 2.642129 CGCCGCTGAGATCGATCT 59.358 61.111 27.63 27.63 40.50 2.75
1342 1451 1.728778 CGCCGCTGAGATCGATCTG 60.729 63.158 31.88 19.14 37.25 2.90
1343 1452 2.021039 GCCGCTGAGATCGATCTGC 61.021 63.158 31.88 26.11 37.25 4.26
1347 1456 0.321021 GCTGAGATCGATCTGCCCAT 59.679 55.000 31.88 7.53 37.98 4.00
1359 1468 3.301746 TGCCCATGCATCATTGGAA 57.698 47.368 5.61 0.00 44.23 3.53
1414 1524 6.180472 TCTTCCCTGTAAACTTCCATGATTC 58.820 40.000 0.00 0.00 0.00 2.52
1419 1529 3.930229 TGTAAACTTCCATGATTCCGTCG 59.070 43.478 0.00 0.00 0.00 5.12
1477 1608 4.983538 TGCATTTACAGATTGCAAACAGTG 59.016 37.500 13.83 4.94 40.55 3.66
1535 1670 3.782244 GGCACGAGCAGCTTGTCG 61.782 66.667 12.89 11.99 44.61 4.35
1565 1719 0.106519 ATGTGACCCCATTAGCCAGC 60.107 55.000 0.00 0.00 0.00 4.85
1625 1779 3.702548 TGCAATTGGCTGATTAATCTGCT 59.297 39.130 32.99 19.23 46.78 4.24
1890 2061 2.166459 TCCACGTCACTTGAGGATGATC 59.834 50.000 5.95 0.00 34.35 2.92
1897 2068 5.218885 GTCACTTGAGGATGATCATCTACG 58.781 45.833 29.85 18.03 37.92 3.51
1899 2070 6.017026 GTCACTTGAGGATGATCATCTACGTA 60.017 42.308 29.85 16.34 37.92 3.57
1900 2071 6.717084 TCACTTGAGGATGATCATCTACGTAT 59.283 38.462 29.85 13.10 37.92 3.06
1901 2072 7.026562 CACTTGAGGATGATCATCTACGTATC 58.973 42.308 29.85 19.08 37.92 2.24
1902 2073 6.151985 ACTTGAGGATGATCATCTACGTATCC 59.848 42.308 29.85 15.97 37.92 2.59
1921 2092 3.674997 TCCTTTTACTGCTCATGGTCAC 58.325 45.455 0.00 0.00 0.00 3.67
1981 2152 3.024609 CGGTGATGATCGCGTCCG 61.025 66.667 5.77 6.69 0.00 4.79
2146 2317 0.448990 CGACGTCGTCTCCATGGTAA 59.551 55.000 29.08 0.00 34.11 2.85
2147 2318 1.135603 CGACGTCGTCTCCATGGTAAA 60.136 52.381 29.08 0.00 34.11 2.01
2148 2319 2.257034 GACGTCGTCTCCATGGTAAAC 58.743 52.381 18.09 7.67 0.00 2.01
2149 2320 1.614903 ACGTCGTCTCCATGGTAAACA 59.385 47.619 12.58 0.00 0.00 2.83
2150 2321 2.232941 ACGTCGTCTCCATGGTAAACAT 59.767 45.455 12.58 0.00 41.57 2.71
2163 2365 3.323115 TGGTAAACATGCCATCTTTTGCA 59.677 39.130 0.00 0.00 42.52 4.08
2166 2368 4.546829 AAACATGCCATCTTTTGCATCT 57.453 36.364 0.00 0.00 45.98 2.90
2179 2381 2.412605 GCATCTCATTGCACCTCCC 58.587 57.895 0.00 0.00 42.31 4.30
2192 2400 1.077930 CCTCCCGTCGTGTCCTCTA 60.078 63.158 0.00 0.00 0.00 2.43
2198 2406 1.202734 CCGTCGTGTCCTCTATCCCTA 60.203 57.143 0.00 0.00 0.00 3.53
2204 2412 4.583489 TCGTGTCCTCTATCCCTAACAATC 59.417 45.833 0.00 0.00 0.00 2.67
2206 2414 5.768662 CGTGTCCTCTATCCCTAACAATCTA 59.231 44.000 0.00 0.00 0.00 1.98
2207 2415 6.072397 CGTGTCCTCTATCCCTAACAATCTAG 60.072 46.154 0.00 0.00 0.00 2.43
2208 2416 6.778559 GTGTCCTCTATCCCTAACAATCTAGT 59.221 42.308 0.00 0.00 0.00 2.57
2209 2417 7.005296 TGTCCTCTATCCCTAACAATCTAGTC 58.995 42.308 0.00 0.00 0.00 2.59
2211 2419 5.416326 CCTCTATCCCTAACAATCTAGTCCG 59.584 48.000 0.00 0.00 0.00 4.79
2600 2808 0.303493 CCACCGTGTTCGACAACAAG 59.697 55.000 0.00 0.00 44.32 3.16
2747 2955 1.751927 GGAGGCCATGGTGAAGCTG 60.752 63.158 14.67 0.00 0.00 4.24
2804 3012 4.057428 AGACGAGACTGCACCGCC 62.057 66.667 0.00 0.00 0.00 6.13
2824 3035 3.634910 GCCTTCAACTAGTAGGAGAGGAG 59.365 52.174 13.46 1.79 36.96 3.69
2825 3036 4.211920 CCTTCAACTAGTAGGAGAGGAGG 58.788 52.174 4.37 2.35 36.96 4.30
2826 3037 4.079672 CCTTCAACTAGTAGGAGAGGAGGA 60.080 50.000 4.37 0.00 36.96 3.71
2827 3038 4.781775 TCAACTAGTAGGAGAGGAGGAG 57.218 50.000 0.00 0.00 0.00 3.69
2828 3039 3.460340 TCAACTAGTAGGAGAGGAGGAGG 59.540 52.174 0.00 0.00 0.00 4.30
2863 3074 2.163010 GCGGTGACACTAGCTTGTACTA 59.837 50.000 15.79 0.00 0.00 1.82
2865 3076 3.439476 CGGTGACACTAGCTTGTACTACT 59.561 47.826 5.39 0.00 0.00 2.57
2867 3078 5.122869 CGGTGACACTAGCTTGTACTACTAA 59.877 44.000 5.39 0.00 0.00 2.24
2869 3080 7.545489 GGTGACACTAGCTTGTACTACTAATT 58.455 38.462 5.39 0.00 0.00 1.40
2870 3081 7.488471 GGTGACACTAGCTTGTACTACTAATTG 59.512 40.741 5.39 0.00 0.00 2.32
2889 3102 9.886132 ACTAATTGAGAAATGTTATACGGTCTT 57.114 29.630 0.00 0.00 0.00 3.01
2891 3104 8.786826 AATTGAGAAATGTTATACGGTCTTGA 57.213 30.769 0.00 0.00 0.00 3.02
2892 3105 8.964476 ATTGAGAAATGTTATACGGTCTTGAT 57.036 30.769 0.00 0.00 0.00 2.57
2893 3106 7.770801 TGAGAAATGTTATACGGTCTTGATG 57.229 36.000 0.00 0.00 0.00 3.07
2959 3181 0.389556 AGCACGCACAGTCTGATCTG 60.390 55.000 6.91 0.00 40.80 2.90
2960 3182 1.964290 GCACGCACAGTCTGATCTGC 61.964 60.000 6.91 5.34 38.84 4.26
2963 3185 1.338484 ACGCACAGTCTGATCTGCAAT 60.338 47.619 6.91 0.00 38.84 3.56
2971 3193 4.267214 CAGTCTGATCTGCAATTGTCTACG 59.733 45.833 7.40 0.00 0.00 3.51
2974 3196 5.045872 TCTGATCTGCAATTGTCTACGATG 58.954 41.667 7.40 0.00 0.00 3.84
2977 3205 4.926860 TCTGCAATTGTCTACGATGTTG 57.073 40.909 7.40 0.00 0.00 3.33
3090 3792 2.735857 ACGCGAAGGTACCGTTGC 60.736 61.111 25.47 25.47 0.00 4.17
3120 3823 1.203441 TGGGGATCTGCACTTGCTCT 61.203 55.000 2.33 0.00 42.66 4.09
3131 3834 1.131638 ACTTGCTCTGGGTGAGAACA 58.868 50.000 0.00 0.00 45.39 3.18
3160 3863 1.573829 TTTTGTCGATGCTGACGGCC 61.574 55.000 3.22 0.00 41.87 6.13
3173 3881 3.687102 CGGCCACAGGTGTCCGTA 61.687 66.667 13.26 0.00 37.33 4.02
3209 3917 3.730761 CTGCCGTGGAGCTTGTGC 61.731 66.667 0.00 0.00 40.05 4.57
3212 3920 4.335647 CCGTGGAGCTTGTGCCCT 62.336 66.667 0.00 0.00 40.80 5.19
3238 3946 0.981183 TGCCTGGTTTCGTGGTATCT 59.019 50.000 0.00 0.00 0.00 1.98
3347 4056 2.028476 TCGTGAAGACCCAAATGACGAT 60.028 45.455 0.00 0.00 30.00 3.73
3350 4059 4.669197 CGTGAAGACCCAAATGACGATTTC 60.669 45.833 0.00 0.00 28.65 2.17
3374 4084 0.951558 ATTGCGTGTGGTTGAAGGTC 59.048 50.000 0.00 0.00 0.00 3.85
3532 6074 1.070134 CTCTTTGGACCACCTCGTTCA 59.930 52.381 0.00 0.00 37.04 3.18
3538 6080 3.367321 TGGACCACCTCGTTCATGTATA 58.633 45.455 0.00 0.00 37.04 1.47
3616 6159 2.906389 ACTCACCTTGCTTGGTCAGATA 59.094 45.455 6.60 0.00 38.45 1.98
3623 6166 5.188434 CCTTGCTTGGTCAGATAAAGATGA 58.812 41.667 0.31 0.00 0.00 2.92
3636 6179 8.378565 TCAGATAAAGATGAAAGTTGAGACCTT 58.621 33.333 0.00 0.00 0.00 3.50
3664 6208 3.732849 CCAAGCCCAGGTCCTCCC 61.733 72.222 0.00 0.00 0.00 4.30
3720 6264 3.782523 ACCCTTCTTGAAGGCATCATCTA 59.217 43.478 20.71 0.00 38.03 1.98
3785 6330 2.980233 GTGGTGGTGCAGCTGGAC 60.980 66.667 28.46 28.46 35.50 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
89 90 7.883311 CCCTCTGTTTCTAAATAGTCCTTTTCA 59.117 37.037 0.06 0.00 0.00 2.69
95 96 6.547930 ACTCCCTCTGTTTCTAAATAGTCC 57.452 41.667 0.06 0.00 0.00 3.85
110 114 4.216708 GGTTAGCACATACTACTCCCTCT 58.783 47.826 0.00 0.00 0.00 3.69
430 510 5.706369 GCAATCAGATCAAGGAATCATAGCT 59.294 40.000 0.00 0.00 0.00 3.32
484 567 3.675348 TCATCTCCTTGGATTTGGCAT 57.325 42.857 0.00 0.00 0.00 4.40
502 585 0.831288 CATGGGTTGGGGCTGTTTCA 60.831 55.000 0.00 0.00 0.00 2.69
510 593 3.384532 GCTGCACATGGGTTGGGG 61.385 66.667 0.00 0.00 0.00 4.96
511 594 3.384532 GGCTGCACATGGGTTGGG 61.385 66.667 0.50 0.00 0.00 4.12
512 595 3.384532 GGGCTGCACATGGGTTGG 61.385 66.667 0.50 0.00 0.00 3.77
513 596 2.601067 TGGGCTGCACATGGGTTG 60.601 61.111 0.00 0.00 0.00 3.77
537 620 2.104963 AGAAGAGGAACTGTGGGTTGAC 59.895 50.000 0.00 0.00 41.55 3.18
539 622 2.370189 AGAGAAGAGGAACTGTGGGTTG 59.630 50.000 0.00 0.00 41.55 3.77
548 631 7.710475 CCAATCAAATCTAGAGAGAAGAGGAAC 59.290 40.741 0.00 0.00 34.61 3.62
583 666 3.944055 AATGCTCGTAAGTGTGAGACT 57.056 42.857 0.00 0.00 35.94 3.24
590 673 5.147162 GGACTTTTCAAATGCTCGTAAGTG 58.853 41.667 0.00 0.00 39.48 3.16
594 677 3.745799 TGGGACTTTTCAAATGCTCGTA 58.254 40.909 0.00 0.00 0.00 3.43
596 679 3.243367 TGTTGGGACTTTTCAAATGCTCG 60.243 43.478 0.00 0.00 0.00 5.03
658 745 5.134339 ACTGAAAAGGGATATATTCCTGGCA 59.866 40.000 13.74 10.63 44.75 4.92
687 774 8.445275 TTTTAAAAGCGCCTAGATTATGATCA 57.555 30.769 2.29 0.00 34.60 2.92
700 787 2.411748 GTGAGCCATTTTTAAAAGCGCC 59.588 45.455 2.29 5.89 0.00 6.53
717 804 5.408604 AGGCTTTGTTCGTTAGTTATGTGAG 59.591 40.000 0.00 0.00 0.00 3.51
738 825 6.566753 GCTGAAAGATATTATTCCAACGAGGC 60.567 42.308 0.00 0.00 33.77 4.70
743 830 7.742089 CGATTCGCTGAAAGATATTATTCCAAC 59.258 37.037 0.00 0.00 34.07 3.77
744 831 7.441157 ACGATTCGCTGAAAGATATTATTCCAA 59.559 33.333 5.86 0.00 34.07 3.53
788 876 6.095160 GGATAATGCAAATTGCCAAATTGGAA 59.905 34.615 17.47 1.03 44.23 3.53
789 877 5.589452 GGATAATGCAAATTGCCAAATTGGA 59.411 36.000 17.47 4.68 44.23 3.53
790 878 5.591067 AGGATAATGCAAATTGCCAAATTGG 59.409 36.000 15.98 7.84 44.23 3.16
791 879 6.316640 TGAGGATAATGCAAATTGCCAAATTG 59.683 34.615 15.98 0.77 44.23 2.32
792 880 6.416415 TGAGGATAATGCAAATTGCCAAATT 58.584 32.000 15.98 10.88 44.23 1.82
793 881 5.991861 TGAGGATAATGCAAATTGCCAAAT 58.008 33.333 15.98 5.67 44.23 2.32
794 882 5.417754 TGAGGATAATGCAAATTGCCAAA 57.582 34.783 15.98 0.51 44.23 3.28
795 883 5.364446 AGATGAGGATAATGCAAATTGCCAA 59.636 36.000 15.98 0.00 44.23 4.52
798 886 6.080648 TGAGATGAGGATAATGCAAATTGC 57.919 37.500 11.58 11.58 45.29 3.56
801 889 8.651589 ATGATTGAGATGAGGATAATGCAAAT 57.348 30.769 0.00 0.00 0.00 2.32
802 890 7.722285 TGATGATTGAGATGAGGATAATGCAAA 59.278 33.333 0.00 0.00 0.00 3.68
805 893 6.093771 GGTGATGATTGAGATGAGGATAATGC 59.906 42.308 0.00 0.00 0.00 3.56
817 905 4.042884 AGGGATGAAGGTGATGATTGAGA 58.957 43.478 0.00 0.00 0.00 3.27
856 944 5.530543 ACAGCTTTCCTCTCTTCTTTTTCTG 59.469 40.000 0.00 0.00 0.00 3.02
910 1004 1.979155 CAGTGAGAGGCGGACCAGA 60.979 63.158 0.00 0.00 39.06 3.86
915 1009 1.228583 AGTGACAGTGAGAGGCGGA 60.229 57.895 0.00 0.00 0.00 5.54
944 1038 2.623915 GCTGCCTCACTTGCCACTG 61.624 63.158 0.00 0.00 0.00 3.66
949 1045 2.979197 CTGCTGCTGCCTCACTTGC 61.979 63.158 13.47 0.00 38.71 4.01
951 1047 2.672307 GCTGCTGCTGCCTCACTT 60.672 61.111 19.30 0.00 38.71 3.16
1082 1185 4.172512 CTCCGCTGCTCCATGGCT 62.173 66.667 6.96 0.00 0.00 4.75
1160 1269 4.742201 GACAGCTTCGCCTCGCCA 62.742 66.667 0.00 0.00 0.00 5.69
1342 1451 0.105408 GGTTCCAATGATGCATGGGC 59.895 55.000 2.46 0.00 35.02 5.36
1343 1452 1.684983 GAGGTTCCAATGATGCATGGG 59.315 52.381 2.46 0.00 36.32 4.00
1347 1456 2.942752 GCTGAGAGGTTCCAATGATGCA 60.943 50.000 0.00 0.00 0.00 3.96
1358 1467 2.317371 TCCAAGAGAGCTGAGAGGTT 57.683 50.000 0.00 0.00 0.00 3.50
1359 1468 2.317371 TTCCAAGAGAGCTGAGAGGT 57.683 50.000 0.00 0.00 0.00 3.85
1414 1524 1.169661 ATCCTCTCTAGCAGCGACGG 61.170 60.000 0.00 0.00 0.00 4.79
1419 1529 3.727726 GGAAGAAATCCTCTCTAGCAGC 58.272 50.000 0.00 0.00 45.56 5.25
1461 1587 1.401761 TGCCACTGTTTGCAATCTGT 58.598 45.000 12.68 12.68 33.87 3.41
1477 1608 3.300765 AGCTGGCTGCAAGTTGCC 61.301 61.111 24.59 10.51 44.23 4.52
1501 1636 1.138247 CCGCTGAGCTGGAAATTGC 59.862 57.895 9.22 0.00 0.00 3.56
1504 1639 2.042831 GTGCCGCTGAGCTGGAAAT 61.043 57.895 17.21 0.00 0.00 2.17
1535 1670 1.676014 GGGGTCACATCACTAGTGCAC 60.676 57.143 18.45 9.40 36.93 4.57
1576 1730 3.314307 TCTACTGTACTCAGGATGGGG 57.686 52.381 0.00 0.00 44.94 4.96
1625 1779 0.473755 TCTCTGCTTTGCTGGGACAA 59.526 50.000 0.00 0.00 38.70 3.18
1651 1805 5.864474 AGAAAAGTACTACTCATCAAGTGCG 59.136 40.000 0.00 0.00 39.11 5.34
1790 1961 0.877071 GTCACAACTCACATGGCAGG 59.123 55.000 0.00 0.00 0.00 4.85
1792 1963 0.884259 CGGTCACAACTCACATGGCA 60.884 55.000 0.00 0.00 0.00 4.92
1797 1968 1.880796 CGTGCGGTCACAACTCACA 60.881 57.895 4.05 0.00 43.28 3.58
1798 1969 1.590525 TCGTGCGGTCACAACTCAC 60.591 57.895 4.05 0.00 43.28 3.51
1799 1970 1.590525 GTCGTGCGGTCACAACTCA 60.591 57.895 4.05 0.00 43.28 3.41
1800 1971 2.308039 GGTCGTGCGGTCACAACTC 61.308 63.158 4.05 0.00 43.28 3.01
1801 1972 2.279918 GGTCGTGCGGTCACAACT 60.280 61.111 4.05 0.00 43.28 3.16
1802 1973 1.828331 GAAGGTCGTGCGGTCACAAC 61.828 60.000 4.05 0.00 43.28 3.32
1803 1974 1.593209 GAAGGTCGTGCGGTCACAA 60.593 57.895 4.05 0.00 43.28 3.33
1820 1991 4.329545 GCAGCCGGGTTGACAGGA 62.330 66.667 15.64 0.00 0.00 3.86
1878 2049 6.376864 AGGATACGTAGATGATCATCCTCAAG 59.623 42.308 28.23 18.71 38.26 3.02
1890 2061 6.504398 TGAGCAGTAAAAGGATACGTAGATG 58.496 40.000 0.08 0.00 46.39 2.90
1897 2068 5.294552 GTGACCATGAGCAGTAAAAGGATAC 59.705 44.000 0.00 0.00 0.00 2.24
1899 2070 4.265073 GTGACCATGAGCAGTAAAAGGAT 58.735 43.478 0.00 0.00 0.00 3.24
1900 2071 3.674997 GTGACCATGAGCAGTAAAAGGA 58.325 45.455 0.00 0.00 0.00 3.36
1901 2072 2.416547 CGTGACCATGAGCAGTAAAAGG 59.583 50.000 0.00 0.00 0.00 3.11
1902 2073 2.159653 GCGTGACCATGAGCAGTAAAAG 60.160 50.000 0.00 0.00 0.00 2.27
2150 2321 3.677700 GCAATGAGATGCAAAAGATGGCA 60.678 43.478 0.00 0.00 45.70 4.92
2163 2365 0.179000 GACGGGAGGTGCAATGAGAT 59.821 55.000 0.00 0.00 0.00 2.75
2166 2368 2.264480 CGACGGGAGGTGCAATGA 59.736 61.111 0.00 0.00 0.00 2.57
2179 2381 2.251409 TAGGGATAGAGGACACGACG 57.749 55.000 0.00 0.00 0.00 5.12
2192 2400 4.585162 CAGACGGACTAGATTGTTAGGGAT 59.415 45.833 0.00 0.00 0.00 3.85
2198 2406 4.950475 TCAGATCAGACGGACTAGATTGTT 59.050 41.667 0.00 0.00 0.00 2.83
2204 2412 2.817258 GGGATCAGATCAGACGGACTAG 59.183 54.545 12.66 0.00 0.00 2.57
2206 2414 1.216678 AGGGATCAGATCAGACGGACT 59.783 52.381 12.66 0.00 0.00 3.85
2207 2415 1.339610 CAGGGATCAGATCAGACGGAC 59.660 57.143 12.66 0.00 0.00 4.79
2208 2416 1.063642 ACAGGGATCAGATCAGACGGA 60.064 52.381 12.66 0.00 0.00 4.69
2209 2417 1.068281 CACAGGGATCAGATCAGACGG 59.932 57.143 12.66 5.39 0.00 4.79
2211 2419 1.202627 GGCACAGGGATCAGATCAGAC 60.203 57.143 12.66 2.21 0.00 3.51
2240 2448 2.819595 CCCGACGACTGCCATTGG 60.820 66.667 0.00 0.00 0.00 3.16
2291 2499 3.706373 GCCTTGGAGACGAGCCCA 61.706 66.667 0.00 0.00 40.85 5.36
2482 2690 1.590792 GGGCTTAACGACGGATCCG 60.591 63.158 32.20 32.20 46.03 4.18
2486 2694 2.568090 GACGGGCTTAACGACGGA 59.432 61.111 0.00 0.00 34.93 4.69
2588 2796 2.406357 GGCGTAGTACTTGTTGTCGAAC 59.594 50.000 0.00 0.00 0.00 3.95
2804 3012 5.118729 TCCTCCTCTCCTACTAGTTGAAG 57.881 47.826 0.00 0.00 0.00 3.02
2842 3053 1.067776 AGTACAAGCTAGTGTCACCGC 60.068 52.381 0.00 3.01 32.75 5.68
2863 3074 9.886132 AAGACCGTATAACATTTCTCAATTAGT 57.114 29.630 0.00 0.00 0.00 2.24
2865 3076 9.878667 TCAAGACCGTATAACATTTCTCAATTA 57.121 29.630 0.00 0.00 0.00 1.40
2867 3078 8.830580 CATCAAGACCGTATAACATTTCTCAAT 58.169 33.333 0.00 0.00 0.00 2.57
2869 3080 6.761242 CCATCAAGACCGTATAACATTTCTCA 59.239 38.462 0.00 0.00 0.00 3.27
2870 3081 6.984474 TCCATCAAGACCGTATAACATTTCTC 59.016 38.462 0.00 0.00 0.00 2.87
2876 3089 4.141824 TGCATCCATCAAGACCGTATAACA 60.142 41.667 0.00 0.00 0.00 2.41
2889 3102 9.722184 TTTTTCTTTTTATCAATGCATCCATCA 57.278 25.926 0.00 0.00 0.00 3.07
2918 3131 6.145534 TGCTACTACTTGCGTGCATTTATATC 59.854 38.462 0.00 0.00 0.00 1.63
2922 3135 3.369756 GTGCTACTACTTGCGTGCATTTA 59.630 43.478 0.00 0.00 32.98 1.40
2923 3136 2.159627 GTGCTACTACTTGCGTGCATTT 59.840 45.455 0.00 0.00 32.98 2.32
2939 3158 1.135286 CAGATCAGACTGTGCGTGCTA 60.135 52.381 1.59 0.00 33.73 3.49
2940 3159 0.389556 CAGATCAGACTGTGCGTGCT 60.390 55.000 1.59 0.00 33.73 4.40
2941 3160 1.964290 GCAGATCAGACTGTGCGTGC 61.964 60.000 1.59 4.48 39.73 5.34
2945 3164 2.486982 ACAATTGCAGATCAGACTGTGC 59.513 45.455 5.05 9.08 39.73 4.57
2959 3181 5.029650 TGAACAACATCGTAGACAATTGC 57.970 39.130 5.05 0.00 42.51 3.56
2960 3182 7.077605 ACAATGAACAACATCGTAGACAATTG 58.922 34.615 3.24 3.24 42.51 2.32
2963 3185 5.755861 TGACAATGAACAACATCGTAGACAA 59.244 36.000 0.00 0.00 42.51 3.18
2971 3193 4.383649 GTGCACATGACAATGAACAACATC 59.616 41.667 13.17 0.00 38.38 3.06
2974 3196 3.968649 AGTGCACATGACAATGAACAAC 58.031 40.909 21.04 0.00 37.24 3.32
2977 3205 5.097529 CCAATAGTGCACATGACAATGAAC 58.902 41.667 21.04 0.00 37.24 3.18
3057 3759 2.125512 GTGTAGCCCAGCTCCGTG 60.126 66.667 0.00 0.00 40.44 4.94
3120 3823 0.320683 CGATGCAGTGTTCTCACCCA 60.321 55.000 0.00 0.00 44.83 4.51
3131 3834 1.808411 ATCGACAAAACCGATGCAGT 58.192 45.000 0.00 0.00 44.06 4.40
3160 3863 2.140717 GGAAAACTACGGACACCTGTG 58.859 52.381 0.00 0.00 33.18 3.66
3212 3920 2.347490 GAAACCAGGCAGCGAGGA 59.653 61.111 8.64 0.00 0.00 3.71
3238 3946 2.682563 GCCGATCATAGGTTTTCACCCA 60.683 50.000 0.00 0.00 45.63 4.51
3347 4056 1.595466 ACCACACGCAATAACGGAAA 58.405 45.000 0.00 0.00 37.37 3.13
3350 4059 0.869068 TCAACCACACGCAATAACGG 59.131 50.000 0.00 0.00 37.37 4.44
3374 4084 2.029964 ACCGCCACCTAACACACG 59.970 61.111 0.00 0.00 0.00 4.49
3532 6074 4.561254 AGAGGGGAGAGGTGTTATACAT 57.439 45.455 0.00 0.00 0.00 2.29
3538 6080 0.324460 CCGTAGAGGGGAGAGGTGTT 60.324 60.000 0.00 0.00 35.97 3.32
3595 6138 1.131638 TCTGACCAAGCAAGGTGAGT 58.868 50.000 12.39 0.00 42.63 3.41
3616 6159 4.829492 CCCAAGGTCTCAACTTTCATCTTT 59.171 41.667 0.00 0.00 0.00 2.52
3623 6166 1.529744 TCCCCCAAGGTCTCAACTTT 58.470 50.000 0.00 0.00 36.75 2.66
3720 6264 1.456287 GTCAACCAAGCAGACCCCT 59.544 57.895 0.00 0.00 0.00 4.79
3785 6330 2.822255 CATACCACCGCCAACCCG 60.822 66.667 0.00 0.00 0.00 5.28
3904 6449 4.828939 TGAGCAAAGATGAACCAAGACAAT 59.171 37.500 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.