Multiple sequence alignment - TraesCS7A01G460900

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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 TraesCS7A01G460900 chr7A 100.000 3355 0 0 1 3355 657092687 657089333 0.000000e+00 6196.0
1 TraesCS7A01G460900 chr7B 87.089 2649 179 72 707 3288 623977345 623974793 0.000000e+00 2846.0
2 TraesCS7A01G460900 chr7B 93.744 1087 53 10 1658 2741 624148623 624147549 0.000000e+00 1616.0
3 TraesCS7A01G460900 chr7B 91.527 956 50 15 707 1643 624149548 624148605 0.000000e+00 1288.0
4 TraesCS7A01G460900 chr7B 84.840 686 54 26 9 662 624150223 624149556 0.000000e+00 645.0
5 TraesCS7A01G460900 chr7B 81.264 443 47 25 2932 3354 624147267 624146841 3.230000e-85 326.0
6 TraesCS7A01G460900 chr7B 90.987 233 12 5 438 662 623977584 623977353 4.210000e-79 305.0
7 TraesCS7A01G460900 chr7B 84.530 181 20 6 2765 2941 624147474 624147298 4.450000e-39 172.0
8 TraesCS7A01G460900 chr7B 94.872 78 3 1 1 77 623977777 623977700 1.630000e-23 121.0
9 TraesCS7A01G460900 chr7D 91.013 1491 98 19 514 1978 568393862 568392382 0.000000e+00 1978.0
10 TraesCS7A01G460900 chr7D 93.294 507 24 4 2040 2545 568392363 568391866 0.000000e+00 739.0
11 TraesCS7A01G460900 chr7D 77.970 867 89 50 2539 3353 568389003 568388187 1.840000e-122 449.0
12 TraesCS7A01G460900 chr7D 77.807 757 124 22 1674 2401 181009016 181009757 8.600000e-116 427.0
13 TraesCS7A01G460900 chr7D 78.358 536 87 18 1004 1537 181008435 181008943 1.500000e-83 320.0
14 TraesCS7A01G460900 chr7D 84.242 165 21 4 151 312 568394054 568393892 4.480000e-34 156.0
15 TraesCS7A01G460900 chr7D 85.965 114 6 5 44 147 568395420 568395307 2.740000e-21 113.0
16 TraesCS7A01G460900 chr7D 100.000 29 0 0 1975 2003 509699900 509699928 2.000000e-03 54.7
17 TraesCS7A01G460900 chr7D 100.000 29 0 0 1975 2003 509836002 509835974 2.000000e-03 54.7
18 TraesCS7A01G460900 chr1B 73.861 746 156 26 1674 2398 610970532 610969805 9.230000e-66 261.0
19 TraesCS7A01G460900 chr1B 80.870 230 39 4 1324 1549 608403169 608403397 3.440000e-40 176.0
20 TraesCS7A01G460900 chr1B 80.870 230 39 4 1324 1549 608421317 608421545 3.440000e-40 176.0
21 TraesCS7A01G460900 chr1B 78.696 230 39 5 1324 1549 608439815 608440038 9.700000e-31 145.0
22 TraesCS7A01G460900 chr2B 84.496 258 35 5 2145 2400 736409007 736408753 2.000000e-62 250.0
23 TraesCS7A01G460900 chr2B 100.000 32 0 0 2801 2832 769253476 769253507 3.610000e-05 60.2
24 TraesCS7A01G460900 chr1D 73.635 751 150 38 1700 2435 445263517 445264234 2.590000e-61 246.0
25 TraesCS7A01G460900 chr1A 73.535 563 104 31 1007 1536 541146507 541147057 4.450000e-39 172.0
26 TraesCS7A01G460900 chr1A 74.286 490 74 34 1092 1536 541399768 541399286 3.460000e-35 159.0
27 TraesCS7A01G460900 chr2D 80.000 170 17 8 503 662 161647282 161647120 3.540000e-20 110.0
28 TraesCS7A01G460900 chr4A 89.130 46 4 1 1975 2019 650312220 650312175 4.680000e-04 56.5
29 TraesCS7A01G460900 chr3B 100.000 29 0 0 1975 2003 70312895 70312923 2.000000e-03 54.7
30 TraesCS7A01G460900 chr3A 100.000 29 0 0 1975 2003 56770947 56770975 2.000000e-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 TraesCS7A01G460900 chr7A 657089333 657092687 3354 True 6196.000000 6196 100.000000 1 3355 1 chr7A.!!$R1 3354
1 TraesCS7A01G460900 chr7B 623974793 623977777 2984 True 1090.666667 2846 90.982667 1 3288 3 chr7B.!!$R1 3287
2 TraesCS7A01G460900 chr7B 624146841 624150223 3382 True 809.400000 1616 87.181000 9 3354 5 chr7B.!!$R2 3345
3 TraesCS7A01G460900 chr7D 568388187 568395420 7233 True 687.000000 1978 86.496800 44 3353 5 chr7D.!!$R2 3309
4 TraesCS7A01G460900 chr7D 181008435 181009757 1322 False 373.500000 427 78.082500 1004 2401 2 chr7D.!!$F2 1397
5 TraesCS7A01G460900 chr1B 610969805 610970532 727 True 261.000000 261 73.861000 1674 2398 1 chr1B.!!$R1 724
6 TraesCS7A01G460900 chr1D 445263517 445264234 717 False 246.000000 246 73.635000 1700 2435 1 chr1D.!!$F1 735

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
164 1427 0.387929 TCTTACTTAGGCATCGGGCG 59.612 55.000 0.00 0.00 46.16 6.13 F
579 1885 1.296715 GCCAGACCTACACCAGTGG 59.703 63.158 7.91 7.91 34.19 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 2712 0.239347 CGCAAGGGCAAGAAACTCTG 59.761 55.000 0.00 0.0 41.24 3.35 R
2405 3837 1.205655 CATCTGGATGACACGACACCT 59.794 52.381 4.72 0.0 41.20 4.00 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
28 29 5.191722 TGGTCTTGATTAGCTCCAGGTTATT 59.808 40.000 0.00 0.00 0.00 1.40
86 92 2.014093 CTACGCTGCTGCTTACACGC 62.014 60.000 14.03 0.00 36.97 5.34
87 93 4.489795 CGCTGCTGCTTACACGCG 62.490 66.667 14.03 3.53 36.97 6.01
88 94 4.152625 GCTGCTGCTTACACGCGG 62.153 66.667 12.47 1.27 39.29 6.46
164 1427 0.387929 TCTTACTTAGGCATCGGGCG 59.612 55.000 0.00 0.00 46.16 6.13
181 1444 1.494824 GCGGATCCGTGTATGTTACC 58.505 55.000 33.33 10.49 42.09 2.85
215 1483 8.282124 ACATATATGATTCAAGACACGTAACG 57.718 34.615 19.63 0.00 0.00 3.18
219 1487 3.732219 TGATTCAAGACACGTAACGACAC 59.268 43.478 0.00 0.00 0.00 3.67
221 1489 1.330213 TCAAGACACGTAACGACACGA 59.670 47.619 17.77 0.00 44.69 4.35
222 1490 2.031769 TCAAGACACGTAACGACACGAT 60.032 45.455 17.77 7.43 44.69 3.73
223 1491 2.238245 AGACACGTAACGACACGATC 57.762 50.000 17.77 14.07 44.69 3.69
252 1520 8.050121 CGTAAGGTTTATTGCTGATTATTTGC 57.950 34.615 0.00 0.00 0.00 3.68
302 1577 4.558178 CTTAGAGCATGCAGAGGTAGATG 58.442 47.826 21.98 0.00 0.00 2.90
309 1584 1.556451 TGCAGAGGTAGATGCATGTGT 59.444 47.619 2.46 0.00 46.97 3.72
328 1603 6.650427 TGTGTCATCTCTTGTAGTTGTAGT 57.350 37.500 0.00 0.00 0.00 2.73
359 1634 8.506168 TTGATCTATATTGTCTCACCCAAAAC 57.494 34.615 0.00 0.00 0.00 2.43
360 1635 7.861629 TGATCTATATTGTCTCACCCAAAACT 58.138 34.615 0.00 0.00 0.00 2.66
361 1636 8.988060 TGATCTATATTGTCTCACCCAAAACTA 58.012 33.333 0.00 0.00 0.00 2.24
373 1653 8.822805 TCTCACCCAAAACTATTAACTCATACT 58.177 33.333 0.00 0.00 0.00 2.12
416 1696 7.654116 GGTAGAGCTAGTTGTTAATTCCTCATC 59.346 40.741 0.00 0.00 0.00 2.92
518 1824 4.022329 TCAATTGTTCAGAGTCTCGCACTA 60.022 41.667 5.13 0.00 34.41 2.74
579 1885 1.296715 GCCAGACCTACACCAGTGG 59.703 63.158 7.91 7.91 34.19 4.00
580 1886 1.296715 CCAGACCTACACCAGTGGC 59.703 63.158 9.78 0.00 34.19 5.01
618 1924 6.648879 TGATAACATATTTTAGCCAAGCCC 57.351 37.500 0.00 0.00 0.00 5.19
665 1971 9.793259 AGGAAACATGTATTCAAAGTTTCTAGA 57.207 29.630 21.60 0.00 43.65 2.43
681 1987 8.697507 AGTTTCTAGACAACAAAATTGGAGAT 57.302 30.769 15.53 0.00 0.00 2.75
792 2098 4.097892 ACACCCTGTGAATTCAACTCAAAC 59.902 41.667 10.35 0.00 36.96 2.93
819 2125 1.722677 GCCCGTGAGACGAGTCTAG 59.277 63.158 5.65 1.44 46.05 2.43
839 2145 6.369615 GTCTAGCAAAACTCCGGTAAACATAA 59.630 38.462 0.00 0.00 0.00 1.90
942 2258 7.887996 TCTATTGAAAATGCAACACAAATCC 57.112 32.000 0.00 0.00 0.00 3.01
1081 2398 1.829096 AATGCACACACCAGCAGCA 60.829 52.632 0.00 0.00 44.94 4.41
1185 2502 2.047830 GGTCGGGAGGATGGTCTTTAT 58.952 52.381 0.00 0.00 0.00 1.40
1227 2549 6.090358 GCATCAATCAGGTGACAATTCTTTTG 59.910 38.462 0.00 0.00 0.00 2.44
1228 2550 6.713762 TCAATCAGGTGACAATTCTTTTGT 57.286 33.333 0.00 0.00 34.97 2.83
1260 2583 8.933438 TTATTAGTTTCATACGTATCGTACCG 57.067 34.615 4.74 0.00 45.07 4.02
1263 2586 3.607422 TTCATACGTATCGTACCGTGG 57.393 47.619 4.74 0.00 45.07 4.94
1273 2596 2.084681 GTACCGTGGCGAGTTGACG 61.085 63.158 0.00 0.00 0.00 4.35
1342 2665 6.636705 ACATCTGTAGGTCGTTGCTATAAAA 58.363 36.000 0.00 0.00 0.00 1.52
1507 2830 2.351726 GGTTCACGAGTACATGCCATTC 59.648 50.000 0.00 0.00 0.00 2.67
1538 2861 0.824759 AGATCACCTCCACGGTAAGC 59.175 55.000 0.00 0.00 46.94 3.09
1639 3000 5.048991 GGTTGTGTTAGTTAACCACCTGATG 60.049 44.000 0.88 0.00 42.60 3.07
1640 3001 5.554437 TGTGTTAGTTAACCACCTGATGA 57.446 39.130 0.88 0.00 35.37 2.92
1641 3002 6.121776 TGTGTTAGTTAACCACCTGATGAT 57.878 37.500 0.88 0.00 35.37 2.45
1642 3003 6.170506 TGTGTTAGTTAACCACCTGATGATC 58.829 40.000 0.88 0.00 35.37 2.92
1643 3004 6.170506 GTGTTAGTTAACCACCTGATGATCA 58.829 40.000 0.00 0.00 35.37 2.92
1644 3005 6.653320 GTGTTAGTTAACCACCTGATGATCAA 59.347 38.462 0.00 0.00 35.37 2.57
1645 3006 7.336931 GTGTTAGTTAACCACCTGATGATCAAT 59.663 37.037 0.00 0.00 35.37 2.57
1646 3007 7.888021 TGTTAGTTAACCACCTGATGATCAATT 59.112 33.333 0.00 0.00 35.37 2.32
1647 3008 9.391006 GTTAGTTAACCACCTGATGATCAATTA 57.609 33.333 0.00 0.00 0.00 1.40
1648 3009 9.967451 TTAGTTAACCACCTGATGATCAATTAA 57.033 29.630 0.00 0.00 0.00 1.40
1649 3010 8.511604 AGTTAACCACCTGATGATCAATTAAG 57.488 34.615 0.00 0.00 0.00 1.85
1650 3011 8.328758 AGTTAACCACCTGATGATCAATTAAGA 58.671 33.333 0.00 0.00 0.00 2.10
1651 3012 8.956426 GTTAACCACCTGATGATCAATTAAGAA 58.044 33.333 0.00 0.00 0.00 2.52
1886 3275 1.645704 GCATGACCAGCTGTCTGCAG 61.646 60.000 13.81 7.63 44.75 4.41
1887 3276 0.321387 CATGACCAGCTGTCTGCAGT 60.321 55.000 14.67 1.33 44.75 4.40
1901 3290 4.547859 CAGTGGCTGCTATCACCC 57.452 61.111 0.00 0.00 34.67 4.61
1972 3382 1.269012 TTCCGGGGTCGAGTGTTTAT 58.731 50.000 0.00 0.00 39.00 1.40
2432 3867 0.746659 TGTCATCCAGATGCGTCGAT 59.253 50.000 0.00 0.00 38.65 3.59
2433 3868 1.269257 TGTCATCCAGATGCGTCGATC 60.269 52.381 0.00 0.00 38.65 3.69
2434 3869 1.032014 TCATCCAGATGCGTCGATCA 58.968 50.000 0.00 0.00 38.65 2.92
2435 3870 1.615392 TCATCCAGATGCGTCGATCAT 59.385 47.619 0.00 3.23 38.65 2.45
2436 3871 1.725164 CATCCAGATGCGTCGATCATG 59.275 52.381 7.70 0.00 31.39 3.07
2437 3872 1.032014 TCCAGATGCGTCGATCATGA 58.968 50.000 0.00 0.00 0.00 3.07
2438 3873 1.408702 TCCAGATGCGTCGATCATGAA 59.591 47.619 0.00 0.00 0.00 2.57
2439 3874 2.036346 TCCAGATGCGTCGATCATGAAT 59.964 45.455 0.00 0.00 0.00 2.57
2588 6900 4.760204 GTGTAACTGGCAGAGGTTAATTGT 59.240 41.667 23.66 0.00 31.07 2.71
2620 6932 3.498018 GTGGATTTGGAAATTGTGTTGGC 59.502 43.478 0.00 0.00 0.00 4.52
2621 6933 3.073678 GGATTTGGAAATTGTGTTGGCC 58.926 45.455 0.00 0.00 0.00 5.36
2705 7018 6.125029 GCATCATCAAGGCCCATATTACTAT 58.875 40.000 0.00 0.00 0.00 2.12
2816 7182 7.663043 ATATCCTCTTCTTTTCTTCTACCGT 57.337 36.000 0.00 0.00 0.00 4.83
2832 7198 8.717821 TCTTCTACCGTTTGTATTCAAGAAATG 58.282 33.333 0.00 0.00 34.88 2.32
2849 7215 6.139679 AGAAATGGATTCTTCCCTTGTACA 57.860 37.500 0.00 0.00 46.39 2.90
2912 7282 6.676950 TCAAATCACGCTGAATGTTAAATGT 58.323 32.000 0.00 0.00 0.00 2.71
2918 7288 5.738693 CACGCTGAATGTTAAATGTACCATG 59.261 40.000 0.00 0.00 0.00 3.66
2921 7291 7.119992 ACGCTGAATGTTAAATGTACCATGTAA 59.880 33.333 0.00 0.00 0.00 2.41
2922 7292 7.965655 CGCTGAATGTTAAATGTACCATGTAAA 59.034 33.333 0.00 0.00 0.00 2.01
2923 7293 9.072294 GCTGAATGTTAAATGTACCATGTAAAC 57.928 33.333 0.00 0.00 0.00 2.01
2954 7360 8.042515 ACTGATGAATTAATTTTGGTGGGATTG 58.957 33.333 1.43 0.00 0.00 2.67
2956 7362 8.770322 TGATGAATTAATTTTGGTGGGATTGAT 58.230 29.630 1.43 0.00 0.00 2.57
2957 7363 8.967664 ATGAATTAATTTTGGTGGGATTGATG 57.032 30.769 1.43 0.00 0.00 3.07
2968 7374 5.373555 TGGTGGGATTGATGGAGAGATAAAT 59.626 40.000 0.00 0.00 0.00 1.40
3003 7409 4.156455 AGAAGCACCAAACAGAGAAAGA 57.844 40.909 0.00 0.00 0.00 2.52
3006 7412 2.945668 AGCACCAAACAGAGAAAGACAC 59.054 45.455 0.00 0.00 0.00 3.67
3011 7417 1.772182 AACAGAGAAAGACACGAGCG 58.228 50.000 0.00 0.00 0.00 5.03
3020 7426 1.372997 GACACGAGCGGCAAGAAGA 60.373 57.895 1.45 0.00 0.00 2.87
3030 7436 2.744494 GCGGCAAGAAGAAGAGGATCAT 60.744 50.000 0.00 0.00 37.82 2.45
3031 7437 3.129871 CGGCAAGAAGAAGAGGATCATC 58.870 50.000 0.00 0.00 37.82 2.92
3032 7438 3.181467 CGGCAAGAAGAAGAGGATCATCT 60.181 47.826 3.52 3.52 46.47 2.90
3083 7503 8.753133 GGTTCCTCTATTTCCATTTCAAAGAAT 58.247 33.333 0.00 0.00 0.00 2.40
3100 7520 8.534954 TCAAAGAATATACCTAGTGTGCTACT 57.465 34.615 0.12 0.12 43.56 2.57
3103 7523 8.991783 AAGAATATACCTAGTGTGCTACTACA 57.008 34.615 0.00 0.00 40.89 2.74
3104 7524 8.991783 AGAATATACCTAGTGTGCTACTACAA 57.008 34.615 0.00 0.00 40.89 2.41
3105 7525 8.848182 AGAATATACCTAGTGTGCTACTACAAC 58.152 37.037 0.00 0.00 40.89 3.32
3106 7526 5.848833 ATACCTAGTGTGCTACTACAACC 57.151 43.478 0.00 0.00 40.89 3.77
3107 7527 3.503365 ACCTAGTGTGCTACTACAACCA 58.497 45.455 0.00 0.00 40.89 3.67
3108 7528 4.094476 ACCTAGTGTGCTACTACAACCAT 58.906 43.478 0.00 0.00 40.89 3.55
3109 7529 4.530946 ACCTAGTGTGCTACTACAACCATT 59.469 41.667 0.00 0.00 40.89 3.16
3110 7530 5.012768 ACCTAGTGTGCTACTACAACCATTT 59.987 40.000 0.00 0.00 40.89 2.32
3111 7531 5.581085 CCTAGTGTGCTACTACAACCATTTC 59.419 44.000 0.00 0.00 40.89 2.17
3112 7532 4.968259 AGTGTGCTACTACAACCATTTCA 58.032 39.130 0.00 0.00 38.04 2.69
3113 7533 4.755123 AGTGTGCTACTACAACCATTTCAC 59.245 41.667 0.00 0.00 38.04 3.18
3114 7534 3.743911 TGTGCTACTACAACCATTTCACG 59.256 43.478 0.00 0.00 0.00 4.35
3215 7643 5.069501 AGACAAGGAATACAAGACCGTAC 57.930 43.478 0.00 0.00 0.00 3.67
3221 7649 3.429960 GGAATACAAGACCGTACCAGTCC 60.430 52.174 7.00 0.00 34.67 3.85
3244 7698 3.437049 ACAGCTTAGCCGAGAATTTTGAC 59.563 43.478 0.00 0.00 0.00 3.18
3248 7702 2.286365 AGCCGAGAATTTTGACCCAA 57.714 45.000 0.00 0.00 0.00 4.12
3259 7713 6.761242 AGAATTTTGACCCAAGCTTACAAAAC 59.239 34.615 22.53 15.95 41.10 2.43
3260 7714 5.407407 TTTTGACCCAAGCTTACAAAACA 57.593 34.783 19.28 7.23 36.16 2.83
3288 7742 0.328258 TCCAGAAGCTAAGCCCCAAC 59.672 55.000 0.00 0.00 0.00 3.77
3303 7757 1.534729 CCAACCCTGGCTTCAAGTAC 58.465 55.000 0.00 0.00 35.39 2.73
3322 7776 6.334102 AGTACGAAATTTTAACCATTGCCA 57.666 33.333 0.00 0.00 0.00 4.92
3324 7778 7.210873 AGTACGAAATTTTAACCATTGCCAAA 58.789 30.769 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 4.152625 CCGCGTGTAAGCAGCAGC 62.153 66.667 4.92 0.00 42.56 5.25
86 92 2.226330 TGTTTCACAAATCTCACCCCG 58.774 47.619 0.00 0.00 0.00 5.73
87 93 3.486383 TCTGTTTCACAAATCTCACCCC 58.514 45.455 0.00 0.00 0.00 4.95
88 94 4.761739 TGATCTGTTTCACAAATCTCACCC 59.238 41.667 0.00 0.00 0.00 4.61
204 1472 1.463034 CGATCGTGTCGTTACGTGTCT 60.463 52.381 7.03 0.00 45.19 3.41
215 1483 0.449388 ACCTTACGGACGATCGTGTC 59.551 55.000 28.12 16.19 43.70 3.67
219 1487 3.060740 GCAATAAACCTTACGGACGATCG 60.061 47.826 14.88 14.88 0.00 3.69
220 1488 4.025979 CAGCAATAAACCTTACGGACGATC 60.026 45.833 0.00 0.00 0.00 3.69
221 1489 3.869246 CAGCAATAAACCTTACGGACGAT 59.131 43.478 0.00 0.00 0.00 3.73
222 1490 3.056678 TCAGCAATAAACCTTACGGACGA 60.057 43.478 0.00 0.00 0.00 4.20
223 1491 3.255725 TCAGCAATAAACCTTACGGACG 58.744 45.455 0.00 0.00 0.00 4.79
224 1492 5.813080 AATCAGCAATAAACCTTACGGAC 57.187 39.130 0.00 0.00 0.00 4.79
225 1493 8.402472 CAAATAATCAGCAATAAACCTTACGGA 58.598 33.333 0.00 0.00 0.00 4.69
227 1495 7.097047 CGCAAATAATCAGCAATAAACCTTACG 60.097 37.037 0.00 0.00 0.00 3.18
228 1496 7.167468 CCGCAAATAATCAGCAATAAACCTTAC 59.833 37.037 0.00 0.00 0.00 2.34
229 1497 7.147983 ACCGCAAATAATCAGCAATAAACCTTA 60.148 33.333 0.00 0.00 0.00 2.69
230 1498 6.042143 CCGCAAATAATCAGCAATAAACCTT 58.958 36.000 0.00 0.00 0.00 3.50
231 1499 5.127031 ACCGCAAATAATCAGCAATAAACCT 59.873 36.000 0.00 0.00 0.00 3.50
241 1509 3.814842 TGGATAGCACCGCAAATAATCAG 59.185 43.478 0.00 0.00 0.00 2.90
252 1520 3.069586 TGAAGATAAGGTGGATAGCACCG 59.930 47.826 0.00 0.00 46.77 4.94
302 1577 4.692625 ACAACTACAAGAGATGACACATGC 59.307 41.667 0.00 0.00 32.40 4.06
309 1584 8.728337 ATACGTACTACAACTACAAGAGATGA 57.272 34.615 0.00 0.00 32.40 2.92
328 1603 8.737175 GGGTGAGACAATATAGATCAATACGTA 58.263 37.037 0.00 0.00 0.00 3.57
378 1658 9.417561 ACAACTAGCTCTACCATTATACAGTTA 57.582 33.333 0.00 0.00 0.00 2.24
379 1659 8.307582 ACAACTAGCTCTACCATTATACAGTT 57.692 34.615 0.00 0.00 0.00 3.16
380 1660 7.899648 ACAACTAGCTCTACCATTATACAGT 57.100 36.000 0.00 0.00 0.00 3.55
397 1677 7.989741 ACTGATGGATGAGGAATTAACAACTAG 59.010 37.037 0.00 0.00 0.00 2.57
416 1696 3.559655 TCGTTTTTCTGTGACACTGATGG 59.440 43.478 14.99 4.78 0.00 3.51
518 1824 6.041296 ACATTTTCATTTCTGAACTTGGCTCT 59.959 34.615 0.00 0.00 41.05 4.09
575 1881 0.036732 TCCTCAAGAAATGCGCCACT 59.963 50.000 4.18 0.00 0.00 4.00
576 1882 1.098050 ATCCTCAAGAAATGCGCCAC 58.902 50.000 4.18 0.00 0.00 5.01
579 1885 4.035558 TGTTATCATCCTCAAGAAATGCGC 59.964 41.667 0.00 0.00 0.00 6.09
580 1886 5.739752 TGTTATCATCCTCAAGAAATGCG 57.260 39.130 0.00 0.00 0.00 4.73
618 1924 0.883833 GTGTGCCTTGAATGACCAGG 59.116 55.000 0.00 0.00 0.00 4.45
665 1971 5.705609 AGCGTTATCTCCAATTTTGTTGT 57.294 34.783 0.00 0.00 0.00 3.32
751 2057 7.031372 CAGGGTGTGAAGAAATAACATGAATG 58.969 38.462 0.00 0.00 0.00 2.67
819 2125 5.110940 TGTTATGTTTACCGGAGTTTTGC 57.889 39.130 9.46 0.00 0.00 3.68
839 2145 6.801862 GTCGCTAAAAGTTCAAATAGCAATGT 59.198 34.615 4.73 0.00 40.55 2.71
861 2167 6.474427 ACATTGTACTACGGAAACATATGTCG 59.526 38.462 9.23 11.13 0.00 4.35
933 2248 3.632145 GTCAACCAGAACAGGATTTGTGT 59.368 43.478 0.00 0.00 40.74 3.72
937 2252 3.632145 GTGTGTCAACCAGAACAGGATTT 59.368 43.478 0.00 0.00 0.00 2.17
942 2258 2.905075 TCTGTGTGTCAACCAGAACAG 58.095 47.619 1.22 0.00 39.04 3.16
1185 2502 3.264193 TGATGCTCTTGAGGAAGCCTTTA 59.736 43.478 0.00 0.00 31.76 1.85
1260 2583 0.666274 TCATGTCGTCAACTCGCCAC 60.666 55.000 0.00 0.00 0.00 5.01
1263 2586 0.567968 CGATCATGTCGTCAACTCGC 59.432 55.000 8.84 0.00 45.19 5.03
1273 2596 3.459232 TTCCCTCACATCGATCATGTC 57.541 47.619 0.00 0.00 44.60 3.06
1318 2641 5.847111 TTATAGCAACGACCTACAGATGT 57.153 39.130 0.00 0.00 0.00 3.06
1364 2687 1.817099 CTTGCTCCGCTGATCCACC 60.817 63.158 0.00 0.00 0.00 4.61
1389 2712 0.239347 CGCAAGGGCAAGAAACTCTG 59.761 55.000 0.00 0.00 41.24 3.35
1473 2796 1.439679 GTGAACCAAGATCCGGTGAC 58.560 55.000 0.00 2.71 36.67 3.67
1507 2830 1.827969 AGGTGATCTTCCAGAGAACCG 59.172 52.381 9.47 0.00 38.19 4.44
1538 2861 1.545614 AAGTCGCACGTACGCACTTG 61.546 55.000 16.72 7.24 34.47 3.16
1552 2881 4.550577 TTGTTGGCATGCATATAAGTCG 57.449 40.909 21.36 0.00 0.00 4.18
1598 2929 5.241506 ACACAACCTCAAACGAATCATGAAT 59.758 36.000 0.00 0.00 0.00 2.57
1752 3113 3.388024 GTGCATATACTCCAACCCTCTGA 59.612 47.826 0.00 0.00 0.00 3.27
1836 3200 1.410153 CATATTGGGACAGCTTTGGGC 59.590 52.381 0.00 0.00 42.39 5.36
1901 3290 1.469335 ATAGTACCCCATGTCCCGCG 61.469 60.000 0.00 0.00 0.00 6.46
2032 3442 1.437573 GTGCCGATCCTCGACATCA 59.562 57.895 0.00 0.00 43.74 3.07
2097 3514 4.002906 TCATGGCGAAACAAGAAGTAGT 57.997 40.909 0.00 0.00 0.00 2.73
2350 3782 3.278574 GTGATGATTCGGGTGGATCAAA 58.721 45.455 0.00 0.00 0.00 2.69
2401 3833 2.217750 TGGATGACACGACACCTTTTG 58.782 47.619 0.00 0.00 0.00 2.44
2405 3837 1.205655 CATCTGGATGACACGACACCT 59.794 52.381 4.72 0.00 41.20 4.00
2433 3868 7.033185 TCAAGCAACTTGATCATGAATTCATG 58.967 34.615 33.47 33.47 46.90 3.07
2434 3869 7.165460 TCAAGCAACTTGATCATGAATTCAT 57.835 32.000 15.36 15.36 44.27 2.57
2435 3870 6.578163 TCAAGCAACTTGATCATGAATTCA 57.422 33.333 11.26 11.26 44.27 2.57
2493 3928 4.237724 TCTAGAACAAGCAACGATCACAG 58.762 43.478 0.00 0.00 0.00 3.66
2588 6900 2.626785 TCCAAATCCACCACTACTGGA 58.373 47.619 0.00 0.00 40.55 3.86
2620 6932 3.003173 TTCGCTCCACCTCTGGGG 61.003 66.667 0.00 0.00 41.80 4.96
2621 6933 2.232298 GACTTCGCTCCACCTCTGGG 62.232 65.000 0.00 0.00 38.25 4.45
2634 6946 5.006165 GGTTCTTGCTCATATCTTGACTTCG 59.994 44.000 0.00 0.00 0.00 3.79
2705 7018 8.861086 TGCCTAACTAATTGTTTATGTTTTCCA 58.139 29.630 0.00 0.00 39.89 3.53
2832 7198 7.939784 ATAAAGTTGTACAAGGGAAGAATCC 57.060 36.000 8.98 0.00 45.77 3.01
2838 7204 7.174253 CACTGCTTATAAAGTTGTACAAGGGAA 59.826 37.037 8.98 0.00 0.00 3.97
2849 7215 6.934645 TGACACTTAGCACTGCTTATAAAGTT 59.065 34.615 9.30 4.34 40.44 2.66
2924 7294 9.717942 CCCACCAAAATTAATTCATCAGTTTAA 57.282 29.630 0.10 0.00 0.00 1.52
2925 7295 9.094578 TCCCACCAAAATTAATTCATCAGTTTA 57.905 29.630 0.10 0.00 0.00 2.01
2927 7297 7.552050 TCCCACCAAAATTAATTCATCAGTT 57.448 32.000 0.10 0.00 0.00 3.16
2930 7336 8.143673 TCAATCCCACCAAAATTAATTCATCA 57.856 30.769 0.10 0.00 0.00 3.07
2939 7345 4.686891 TCTCCATCAATCCCACCAAAATT 58.313 39.130 0.00 0.00 0.00 1.82
2968 7374 6.707440 TGGTGCTTCTATTTTCAGTTCAAA 57.293 33.333 0.00 0.00 0.00 2.69
2981 7387 5.057149 GTCTTTCTCTGTTTGGTGCTTCTA 58.943 41.667 0.00 0.00 0.00 2.10
3003 7409 0.946221 CTTCTTCTTGCCGCTCGTGT 60.946 55.000 0.00 0.00 0.00 4.49
3006 7412 1.080995 CCTCTTCTTCTTGCCGCTCG 61.081 60.000 0.00 0.00 0.00 5.03
3011 7417 4.420522 AGATGATCCTCTTCTTCTTGCC 57.579 45.455 0.00 0.00 27.79 4.52
3020 7426 8.169393 AGGAAAAAGAAAGAAGATGATCCTCTT 58.831 33.333 12.47 12.47 38.18 2.85
3036 7442 9.483489 GGAACCCCTTTATATTAGGAAAAAGAA 57.517 33.333 5.39 0.00 34.56 2.52
3037 7443 8.852894 AGGAACCCCTTTATATTAGGAAAAAGA 58.147 33.333 5.39 0.00 40.78 2.52
3038 7444 9.132923 GAGGAACCCCTTTATATTAGGAAAAAG 57.867 37.037 5.39 0.00 44.53 2.27
3083 7503 6.425735 TGGTTGTAGTAGCACACTAGGTATA 58.574 40.000 0.00 0.00 40.48 1.47
3189 7617 4.159879 CGGTCTTGTATTCCTTGTCTAGGT 59.840 45.833 0.00 0.00 45.03 3.08
3215 7643 1.448540 CGGCTAAGCTGTGGACTGG 60.449 63.158 0.00 0.00 0.00 4.00
3221 7649 3.436704 TCAAAATTCTCGGCTAAGCTGTG 59.563 43.478 0.00 0.00 36.18 3.66
3244 7698 3.383185 TCAGGTTGTTTTGTAAGCTTGGG 59.617 43.478 9.86 0.00 33.95 4.12
3248 7702 4.278419 GGATGTCAGGTTGTTTTGTAAGCT 59.722 41.667 0.00 0.00 36.39 3.74
3259 7713 2.486472 AGCTTCTGGATGTCAGGTTG 57.514 50.000 0.00 0.00 43.53 3.77
3260 7714 3.620966 GCTTAGCTTCTGGATGTCAGGTT 60.621 47.826 0.00 0.00 43.53 3.50
3288 7742 2.178912 TTTCGTACTTGAAGCCAGGG 57.821 50.000 0.00 0.00 0.00 4.45
3303 7757 5.334491 GGGTTTGGCAATGGTTAAAATTTCG 60.334 40.000 0.00 0.00 0.00 3.46
3336 7790 4.704833 GCAGAGGCACTTCGGGCA 62.705 66.667 0.00 0.00 41.55 5.36


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

AutoCloner maintained by Alex Coulton.