Multiple sequence alignment - TraesCS6A01G343600

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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 TraesCS6A01G343600 chr6A 100.000 3859 0 0 1 3859 577783282 577779424 0.000000e+00 7127.0
1 TraesCS6A01G343600 chr6A 90.141 142 13 1 1 142 577835118 577834978 2.370000e-42 183.0
2 TraesCS6A01G343600 chr6A 88.596 114 11 2 2814 2926 577780355 577780243 1.870000e-28 137.0
3 TraesCS6A01G343600 chr6A 88.596 114 11 2 2928 3040 577780469 577780357 1.870000e-28 137.0
4 TraesCS6A01G343600 chr6D 93.021 2608 101 17 1270 3856 430948029 430945482 0.000000e+00 3733.0
5 TraesCS6A01G343600 chr6D 91.634 777 49 9 1 765 430949339 430948567 0.000000e+00 1061.0
6 TraesCS6A01G343600 chr6D 84.936 312 35 6 747 1049 430948544 430948236 4.840000e-79 305.0
7 TraesCS6A01G343600 chr6D 87.692 130 11 3 2912 3040 430946497 430946372 3.110000e-31 147.0
8 TraesCS6A01G343600 chr6D 92.000 75 6 0 2814 2888 430946370 430946296 5.270000e-19 106.0
9 TraesCS6A01G343600 chr6D 86.957 92 11 1 1068 1158 46454400 46454309 6.820000e-18 102.0
10 TraesCS6A01G343600 chr6D 93.548 62 2 1 2586 2645 430946652 430946591 1.480000e-14 91.6
11 TraesCS6A01G343600 chr6B 93.863 1499 76 6 1156 2645 650051015 650049524 0.000000e+00 2244.0
12 TraesCS6A01G343600 chr6B 89.831 1003 61 13 2646 3632 650049585 650048608 0.000000e+00 1249.0
13 TraesCS6A01G343600 chr6B 91.243 708 48 9 2933 3632 650046025 650045324 0.000000e+00 952.0
14 TraesCS6A01G343600 chr6B 92.727 495 29 6 1 490 650053897 650053405 0.000000e+00 708.0
15 TraesCS6A01G343600 chr6B 91.304 299 24 2 751 1049 650051426 650051130 1.290000e-109 407.0
16 TraesCS6A01G343600 chr6B 90.429 303 29 0 747 1049 650053018 650052716 2.160000e-107 399.0
17 TraesCS6A01G343600 chr6B 91.007 278 21 4 463 740 650051973 650051700 4.710000e-99 372.0
18 TraesCS6A01G343600 chr6B 89.273 289 28 2 489 777 650053311 650053026 3.670000e-95 359.0
19 TraesCS6A01G343600 chr6B 92.771 166 9 2 119 281 650052531 650052366 1.790000e-58 237.0
20 TraesCS6A01G343600 chr6B 89.560 182 16 3 1 179 9011345 9011164 1.080000e-55 228.0
21 TraesCS6A01G343600 chr6B 93.162 117 7 1 2912 3028 650049425 650049310 1.840000e-38 171.0
22 TraesCS6A01G343600 chr6B 91.000 100 9 0 2814 2913 650049295 650049196 6.730000e-28 135.0
23 TraesCS6A01G343600 chr7A 89.011 91 7 3 1067 1155 280845848 280845937 4.080000e-20 110.0
24 TraesCS6A01G343600 chr5B 88.636 88 9 1 1071 1157 466429594 466429681 5.270000e-19 106.0
25 TraesCS6A01G343600 chr5B 86.813 91 11 1 1066 1155 372649060 372648970 2.450000e-17 100.0
26 TraesCS6A01G343600 chr5A 88.506 87 9 1 1070 1155 499657511 499657425 1.900000e-18 104.0
27 TraesCS6A01G343600 chr3D 88.372 86 8 2 1077 1160 32010701 32010616 6.820000e-18 102.0
28 TraesCS6A01G343600 chr1B 89.157 83 7 2 1077 1157 358393930 358393848 6.820000e-18 102.0
29 TraesCS6A01G343600 chr3A 86.957 92 9 3 1066 1154 482094286 482094377 2.450000e-17 100.0
30 TraesCS6A01G343600 chr3A 89.744 78 6 2 1088 1163 168540398 168540321 8.820000e-17 99.0


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 TraesCS6A01G343600 chr6A 577779424 577783282 3858 True 2467.000000 7127 92.397333 1 3859 3 chr6A.!!$R2 3858
1 TraesCS6A01G343600 chr6D 430945482 430949339 3857 True 907.266667 3733 90.471833 1 3856 6 chr6D.!!$R2 3855
2 TraesCS6A01G343600 chr6B 650045324 650053897 8573 True 657.545455 2244 91.510000 1 3632 11 chr6B.!!$R2 3631

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
798 945 0.252193 CAAAGAGGGGAATGGGCCAA 60.252 55.0 11.89 0.0 0.00 4.52 F
1209 3019 0.181824 ACTGTTAACCACTTGGGCGT 59.818 50.0 2.48 0.0 42.05 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3635 0.108662 GCGGCTTGAAAGGGGAAATG 60.109 55.0 0.0 0.0 0.0 2.32 R
3112 4986 0.186630 GTACACAACCCCCAAACCCT 59.813 55.0 0.0 0.0 0.0 4.34 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 34 8.328758 AGAAATCCCAAACTGATTATCACAGTA 58.671 33.333 0.00 0.00 46.01 2.74
122 127 3.247006 AGACGGAGCGACATTTTGTAT 57.753 42.857 0.00 0.00 0.00 2.29
132 137 9.037737 GGAGCGACATTTTGTATAACTATAACA 57.962 33.333 0.00 0.00 0.00 2.41
357 365 3.790437 CGTCCAGCCATCCTGCCT 61.790 66.667 0.00 0.00 40.36 4.75
359 367 3.473647 TCCAGCCATCCTGCCTCG 61.474 66.667 0.00 0.00 40.36 4.63
399 407 9.205719 CCATCAACAAAATCACATAATCAACAA 57.794 29.630 0.00 0.00 0.00 2.83
430 438 1.410517 CATCTAGCTTCCTGCCTTCGA 59.589 52.381 0.00 0.00 44.23 3.71
448 456 7.145985 GCCTTCGAATATACTAGAATGTGACA 58.854 38.462 0.00 0.00 0.00 3.58
452 460 6.017357 TCGAATATACTAGAATGTGACACGCT 60.017 38.462 0.00 1.16 0.00 5.07
458 467 1.001378 AGAATGTGACACGCTTTTGCC 60.001 47.619 0.22 0.00 43.93 4.52
595 702 1.006825 CAACCGCTCGATGAACGTCA 61.007 55.000 0.00 0.00 43.13 4.35
614 721 1.063027 CATGAATGATGACGCACGCTT 59.937 47.619 0.00 0.00 33.31 4.68
680 787 0.397816 ACCCGGATCCAAGAGAGGAG 60.398 60.000 13.41 0.91 41.90 3.69
716 823 0.612174 AGACAAGGCGAGCAGTAGGA 60.612 55.000 0.00 0.00 0.00 2.94
718 825 1.517257 CAAGGCGAGCAGTAGGACG 60.517 63.158 0.00 0.00 0.00 4.79
742 849 2.108168 CCTTCGTCCCTGTAATCTGGA 58.892 52.381 0.00 0.00 35.11 3.86
745 852 2.317040 TCGTCCCTGTAATCTGGATCC 58.683 52.381 4.20 4.20 35.11 3.36
749 896 3.392616 GTCCCTGTAATCTGGATCCATGT 59.607 47.826 16.63 3.82 35.11 3.21
791 938 2.922283 ACACAGGATCAAAGAGGGGAAT 59.078 45.455 0.00 0.00 0.00 3.01
798 945 0.252193 CAAAGAGGGGAATGGGCCAA 60.252 55.000 11.89 0.00 0.00 4.52
813 960 1.365699 GCCAAAATAGCTCGAACGGA 58.634 50.000 0.00 0.00 0.00 4.69
839 986 0.606604 TGGACCTACAACCGAGCTTC 59.393 55.000 0.00 0.00 0.00 3.86
852 999 1.534235 AGCTTCTCAGGGTGTCGGT 60.534 57.895 0.00 0.00 0.00 4.69
856 1003 0.469331 TTCTCAGGGTGTCGGTCAGT 60.469 55.000 0.00 0.00 0.00 3.41
863 1010 0.602905 GGTGTCGGTCAGTCTTTGGG 60.603 60.000 0.00 0.00 0.00 4.12
942 1096 1.714899 AAACGTGCTTGTCTGCGCTT 61.715 50.000 9.73 0.00 40.87 4.68
962 1116 4.440663 GCTTCCACTTGAACTGCTTTTCTT 60.441 41.667 0.00 0.00 0.00 2.52
1011 2751 5.238650 CCGAAAAGTCAGTATTTTGGTGAGT 59.761 40.000 0.00 0.00 35.97 3.41
1019 2759 6.262273 GTCAGTATTTTGGTGAGTTCAAAGGA 59.738 38.462 0.00 0.00 35.81 3.36
1028 2768 4.626172 GGTGAGTTCAAAGGATTCTCGTAC 59.374 45.833 0.00 0.00 31.41 3.67
1043 2783 3.572682 TCTCGTACTGTGTGAAAGGTCAT 59.427 43.478 0.00 0.00 35.80 3.06
1129 2939 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
1130 2940 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
1131 2941 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
1132 2942 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
1133 2943 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
1134 2944 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
1135 2945 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
1141 2951 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
1142 2952 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
1150 2960 9.947189 ACGTTCTTATATTATGGGATATAGGGA 57.053 33.333 0.00 0.00 0.00 4.20
1178 2988 0.613012 TGAGGCTAGAGTGAGCTGCA 60.613 55.000 1.02 0.00 42.43 4.41
1208 3018 0.872388 GACTGTTAACCACTTGGGCG 59.128 55.000 2.48 0.00 42.05 6.13
1209 3019 0.181824 ACTGTTAACCACTTGGGCGT 59.818 50.000 2.48 0.00 42.05 5.68
1210 3020 1.314730 CTGTTAACCACTTGGGCGTT 58.685 50.000 2.48 0.00 42.05 4.84
1211 3021 1.001815 CTGTTAACCACTTGGGCGTTG 60.002 52.381 2.48 0.00 42.05 4.10
1212 3022 0.312729 GTTAACCACTTGGGCGTTGG 59.687 55.000 0.00 0.00 42.05 3.77
1213 3023 0.824182 TTAACCACTTGGGCGTTGGG 60.824 55.000 0.00 0.00 42.05 4.12
1255 3065 4.323477 GGCGTGTGTGGGCTGGTA 62.323 66.667 0.00 0.00 0.00 3.25
1256 3066 2.742372 GCGTGTGTGGGCTGGTAG 60.742 66.667 0.00 0.00 0.00 3.18
1257 3067 2.742372 CGTGTGTGGGCTGGTAGC 60.742 66.667 0.00 0.00 41.46 3.58
1449 3302 2.394563 GCAAGAGGAAGAGCACCGC 61.395 63.158 0.00 0.00 0.00 5.68
1773 3626 2.947652 TCTACCAGGTAATCGAACGAGG 59.052 50.000 0.00 0.28 0.00 4.63
1782 3635 4.084888 CGAACGAGGCGCCCAAAC 62.085 66.667 26.15 11.66 0.00 2.93
1783 3636 2.975799 GAACGAGGCGCCCAAACA 60.976 61.111 26.15 0.00 0.00 2.83
1784 3637 2.282180 AACGAGGCGCCCAAACAT 60.282 55.556 26.15 1.92 0.00 2.71
1785 3638 1.862602 GAACGAGGCGCCCAAACATT 61.863 55.000 26.15 9.37 0.00 2.71
1797 3650 3.806858 GCCCAAACATTTCCCCTTTCAAG 60.807 47.826 0.00 0.00 0.00 3.02
1802 3655 1.257750 ATTTCCCCTTTCAAGCCGCC 61.258 55.000 0.00 0.00 0.00 6.13
1846 3699 8.582437 AGATTTGATTGATTGATGAGTTTGTGT 58.418 29.630 0.00 0.00 0.00 3.72
1851 3704 0.234625 TTGATGAGTTTGTGTCGCGC 59.765 50.000 0.00 0.00 0.00 6.86
1854 3707 3.033764 GAGTTTGTGTCGCGCCGA 61.034 61.111 0.00 0.00 0.00 5.54
2243 4096 4.687215 GCAGCAGTGCGAGGACCA 62.687 66.667 10.00 0.00 40.71 4.02
2572 4425 3.922171 AGATCATCTGTTCCTGAACCC 57.078 47.619 7.51 0.00 40.46 4.11
2595 4448 3.204526 AGAGAAGCATCAGCAATGTAGC 58.795 45.455 0.00 0.00 45.49 3.58
2635 4488 7.694784 GTCTTCTCTAGTCTCGTTGAAGTATTG 59.305 40.741 0.00 0.00 34.37 1.90
2660 4513 3.543680 GCCTTAGCAATGTAGTCCTGA 57.456 47.619 0.00 0.00 39.53 3.86
2754 4612 3.845781 AGTTGCTTCCAGTCTCTCAAA 57.154 42.857 0.00 0.00 0.00 2.69
2852 4713 3.568007 GGTGTTTGATTGGAGTTGCAGTA 59.432 43.478 0.00 0.00 0.00 2.74
3031 4905 7.675962 ATGATGCTTGTTTGCAATGTTTATT 57.324 28.000 0.00 0.00 46.61 1.40
3048 4922 7.523293 TGTTTATTCTTTCAATCTGCTTGGA 57.477 32.000 0.00 0.00 35.43 3.53
3050 4924 8.587608 TGTTTATTCTTTCAATCTGCTTGGATT 58.412 29.630 0.00 0.00 36.49 3.01
3051 4925 9.428097 GTTTATTCTTTCAATCTGCTTGGATTT 57.572 29.630 0.00 0.00 34.15 2.17
3052 4926 8.991243 TTATTCTTTCAATCTGCTTGGATTTG 57.009 30.769 0.00 0.00 34.15 2.32
3053 4927 6.409524 TTCTTTCAATCTGCTTGGATTTGT 57.590 33.333 0.00 0.00 34.15 2.83
3054 4928 6.409524 TCTTTCAATCTGCTTGGATTTGTT 57.590 33.333 0.00 0.00 34.15 2.83
3110 4984 6.143118 GCTGCTTCTGTCTACTGTAATAATCG 59.857 42.308 0.00 0.00 0.00 3.34
3112 4986 5.977725 GCTTCTGTCTACTGTAATAATCGCA 59.022 40.000 0.00 0.00 0.00 5.10
3117 4991 5.128171 TGTCTACTGTAATAATCGCAGGGTT 59.872 40.000 0.00 0.00 34.79 4.11
3256 5134 9.817809 GTAGAAGTTCCACAATATACAAGATGA 57.182 33.333 0.00 0.00 0.00 2.92
3288 5166 6.425504 CAAGCCAAAGAATCTAGCGAATAAG 58.574 40.000 0.00 0.00 0.00 1.73
3293 5175 7.641802 GCCAAAGAATCTAGCGAATAAGAAAAG 59.358 37.037 0.00 0.00 0.00 2.27
3295 5177 8.883731 CAAAGAATCTAGCGAATAAGAAAAGGA 58.116 33.333 0.00 0.00 0.00 3.36
3332 5215 7.827729 ACACAAAAGGAGAGTTAAACTAGTTGT 59.172 33.333 9.34 2.40 0.00 3.32
3354 5237 7.759489 TGTTGAGCAATAACTTAATCCAACT 57.241 32.000 0.00 0.00 34.30 3.16
3486 5369 7.710044 TGCAATTCAAATCTTCAAAAGCTGTTA 59.290 29.630 0.00 0.00 0.00 2.41
3514 5398 8.533569 AGGGGTATTTTATGTAAACTTGATGG 57.466 34.615 0.00 0.00 0.00 3.51
3697 5581 3.876320 CTGGCAGAAGGAGAGAAAATAGC 59.124 47.826 9.42 0.00 0.00 2.97
3708 5592 5.812642 GGAGAGAAAATAGCATTGTTCGAGA 59.187 40.000 0.00 0.00 0.00 4.04
3716 5600 4.670227 AGCATTGTTCGAGAAAGCTAAC 57.330 40.909 7.08 0.00 0.00 2.34
3775 6042 5.468540 AGCACGTCTAGATATGCCATAAA 57.531 39.130 21.35 0.00 38.92 1.40
3823 8564 3.239587 TGTCATTGATCTTACGCGGAA 57.760 42.857 12.47 7.57 0.00 4.30
3832 8573 3.529634 TCTTACGCGGAAATTTGTGTG 57.470 42.857 12.47 0.00 0.00 3.82
3833 8574 2.224549 TCTTACGCGGAAATTTGTGTGG 59.775 45.455 12.47 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 137 3.181434 TGTGCCTTGACTGGGAACTATTT 60.181 43.478 0.00 0.00 33.62 1.40
301 308 2.889045 GGGCTGACAATGACATGCATAT 59.111 45.455 0.00 0.00 35.78 1.78
357 365 2.168313 TGATGGAAGTATTGCTGCTCGA 59.832 45.455 0.00 0.00 37.31 4.04
359 367 3.691118 TGTTGATGGAAGTATTGCTGCTC 59.309 43.478 0.00 0.00 37.31 4.26
392 400 7.040201 AGCTAGATGTGTGATTTTGTTGTTGAT 60.040 33.333 0.00 0.00 0.00 2.57
399 407 5.413833 CAGGAAGCTAGATGTGTGATTTTGT 59.586 40.000 0.00 0.00 0.00 2.83
430 438 8.604035 CAAAAGCGTGTCACATTCTAGTATATT 58.396 33.333 3.42 0.00 0.00 1.28
452 460 2.589442 AAGGACGACGCGGCAAAA 60.589 55.556 14.85 0.00 36.10 2.44
458 467 0.732880 AATGAGTGAAGGACGACGCG 60.733 55.000 3.53 3.53 0.00 6.01
462 471 0.976641 AGCCAATGAGTGAAGGACGA 59.023 50.000 0.00 0.00 0.00 4.20
464 473 3.935828 GACTTAGCCAATGAGTGAAGGAC 59.064 47.826 0.00 0.00 0.00 3.85
496 600 6.145048 ACCGTAAAAAGACTTCGTACAGAATG 59.855 38.462 0.00 0.00 46.00 2.67
595 702 1.063027 CAAGCGTGCGTCATCATTCAT 59.937 47.619 0.00 0.00 0.00 2.57
628 735 0.524862 TCGACGACCTAAGCAACTCC 59.475 55.000 0.00 0.00 0.00 3.85
680 787 1.066502 GTCTCCTTGCTCCAACTCTCC 60.067 57.143 0.00 0.00 0.00 3.71
716 823 4.052229 CAGGGACGAAGGCGACGT 62.052 66.667 11.14 11.14 46.58 4.34
718 825 0.175073 ATTACAGGGACGAAGGCGAC 59.825 55.000 0.00 0.00 41.64 5.19
742 849 1.215423 GCCAACCCCTTCTACATGGAT 59.785 52.381 0.00 0.00 0.00 3.41
745 852 0.748005 CCGCCAACCCCTTCTACATG 60.748 60.000 0.00 0.00 0.00 3.21
749 896 2.931105 TGCCGCCAACCCCTTCTA 60.931 61.111 0.00 0.00 0.00 2.10
791 938 1.459450 GTTCGAGCTATTTTGGCCCA 58.541 50.000 0.00 0.00 0.00 5.36
798 945 3.056749 ACTTGAGTCCGTTCGAGCTATTT 60.057 43.478 0.00 0.00 32.72 1.40
813 960 1.343465 CGGTTGTAGGTCCACTTGAGT 59.657 52.381 0.00 0.00 0.00 3.41
839 986 0.896019 AGACTGACCGACACCCTGAG 60.896 60.000 0.00 0.00 0.00 3.35
852 999 1.068588 CGACTGTCACCCAAAGACTGA 59.931 52.381 8.73 0.00 38.05 3.41
856 1003 1.300620 CGCGACTGTCACCCAAAGA 60.301 57.895 0.00 0.00 0.00 2.52
863 1010 2.179517 CTCCTCCGCGACTGTCAC 59.820 66.667 8.23 0.00 0.00 3.67
926 1080 2.171940 GAAGCGCAGACAAGCACG 59.828 61.111 11.47 0.00 35.48 5.34
942 1096 5.659440 AAAAGAAAAGCAGTTCAAGTGGA 57.341 34.783 0.00 0.00 0.00 4.02
978 1132 2.963782 ACTGACTTTTCGGTCACTAGGT 59.036 45.455 0.00 0.00 36.54 3.08
984 1138 5.008217 CACCAAAATACTGACTTTTCGGTCA 59.992 40.000 0.00 0.00 40.79 4.02
988 2728 6.300354 ACTCACCAAAATACTGACTTTTCG 57.700 37.500 0.00 0.00 0.00 3.46
1011 2751 4.988540 CACACAGTACGAGAATCCTTTGAA 59.011 41.667 0.00 0.00 0.00 2.69
1019 2759 4.038763 TGACCTTTCACACAGTACGAGAAT 59.961 41.667 0.00 0.00 0.00 2.40
1028 2768 5.579904 CACTCTCATATGACCTTTCACACAG 59.420 44.000 0.00 0.00 33.38 3.66
1106 2916 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
1107 2917 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
1115 2925 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
1116 2926 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
1124 2934 9.947189 TCCCTATATCCCATAATATAAGAACGT 57.053 33.333 0.00 0.00 0.00 3.99
1137 2947 9.230477 CCTCAAAATATACTCCCTATATCCCAT 57.770 37.037 0.00 0.00 29.00 4.00
1138 2948 7.127339 GCCTCAAAATATACTCCCTATATCCCA 59.873 40.741 0.00 0.00 29.00 4.37
1139 2949 7.348537 AGCCTCAAAATATACTCCCTATATCCC 59.651 40.741 0.00 0.00 29.00 3.85
1140 2950 8.325477 AGCCTCAAAATATACTCCCTATATCC 57.675 38.462 0.00 0.00 29.00 2.59
1143 2953 9.702253 CTCTAGCCTCAAAATATACTCCCTATA 57.298 37.037 0.00 0.00 0.00 1.31
1144 2954 8.180844 ACTCTAGCCTCAAAATATACTCCCTAT 58.819 37.037 0.00 0.00 0.00 2.57
1145 2955 7.451877 CACTCTAGCCTCAAAATATACTCCCTA 59.548 40.741 0.00 0.00 0.00 3.53
1146 2956 6.268847 CACTCTAGCCTCAAAATATACTCCCT 59.731 42.308 0.00 0.00 0.00 4.20
1147 2957 6.267928 TCACTCTAGCCTCAAAATATACTCCC 59.732 42.308 0.00 0.00 0.00 4.30
1148 2958 7.291411 TCACTCTAGCCTCAAAATATACTCC 57.709 40.000 0.00 0.00 0.00 3.85
1149 2959 6.866248 GCTCACTCTAGCCTCAAAATATACTC 59.134 42.308 0.00 0.00 36.45 2.59
1150 2960 6.553100 AGCTCACTCTAGCCTCAAAATATACT 59.447 38.462 0.00 0.00 43.86 2.12
1151 2961 6.644592 CAGCTCACTCTAGCCTCAAAATATAC 59.355 42.308 0.00 0.00 43.86 1.47
1152 2962 6.739843 GCAGCTCACTCTAGCCTCAAAATATA 60.740 42.308 0.00 0.00 43.86 0.86
1153 2963 5.609423 CAGCTCACTCTAGCCTCAAAATAT 58.391 41.667 0.00 0.00 43.86 1.28
1154 2964 4.681781 GCAGCTCACTCTAGCCTCAAAATA 60.682 45.833 0.00 0.00 43.86 1.40
1155 2965 3.871485 CAGCTCACTCTAGCCTCAAAAT 58.129 45.455 0.00 0.00 43.86 1.82
1156 2966 2.613977 GCAGCTCACTCTAGCCTCAAAA 60.614 50.000 0.00 0.00 43.86 2.44
1157 2967 1.066573 GCAGCTCACTCTAGCCTCAAA 60.067 52.381 0.00 0.00 43.86 2.69
1158 2968 0.534412 GCAGCTCACTCTAGCCTCAA 59.466 55.000 0.00 0.00 43.86 3.02
1159 2969 0.613012 TGCAGCTCACTCTAGCCTCA 60.613 55.000 0.00 0.00 43.86 3.86
1160 2970 0.102844 CTGCAGCTCACTCTAGCCTC 59.897 60.000 0.00 0.00 43.86 4.70
1178 2988 2.480845 GTTAACAGTCAGGTCGTTGCT 58.519 47.619 0.00 0.00 0.00 3.91
1208 3018 1.349357 ACTCTCTTTCTCAGGCCCAAC 59.651 52.381 0.00 0.00 0.00 3.77
1209 3019 1.349026 CACTCTCTTTCTCAGGCCCAA 59.651 52.381 0.00 0.00 0.00 4.12
1210 3020 0.979665 CACTCTCTTTCTCAGGCCCA 59.020 55.000 0.00 0.00 0.00 5.36
1211 3021 0.251634 CCACTCTCTTTCTCAGGCCC 59.748 60.000 0.00 0.00 0.00 5.80
1212 3022 0.251634 CCCACTCTCTTTCTCAGGCC 59.748 60.000 0.00 0.00 0.00 5.19
1213 3023 0.392327 GCCCACTCTCTTTCTCAGGC 60.392 60.000 0.00 0.00 0.00 4.85
1214 3024 0.251634 GGCCCACTCTCTTTCTCAGG 59.748 60.000 0.00 0.00 0.00 3.86
1217 3027 0.321996 AACGGCCCACTCTCTTTCTC 59.678 55.000 0.00 0.00 0.00 2.87
1255 3065 5.580022 AGAGAGAAGTAAAGGAGAAGAGCT 58.420 41.667 0.00 0.00 0.00 4.09
1256 3066 5.163550 GGAGAGAGAAGTAAAGGAGAAGAGC 60.164 48.000 0.00 0.00 0.00 4.09
1257 3067 5.065988 CGGAGAGAGAAGTAAAGGAGAAGAG 59.934 48.000 0.00 0.00 0.00 2.85
1604 3457 4.271816 CTCGGATCTGGGCGACGG 62.272 72.222 0.62 0.00 0.00 4.79
1773 3626 1.826340 AAGGGGAAATGTTTGGGCGC 61.826 55.000 0.00 0.00 0.00 6.53
1782 3635 0.108662 GCGGCTTGAAAGGGGAAATG 60.109 55.000 0.00 0.00 0.00 2.32
1783 3636 1.257750 GGCGGCTTGAAAGGGGAAAT 61.258 55.000 0.00 0.00 0.00 2.17
1784 3637 1.906333 GGCGGCTTGAAAGGGGAAA 60.906 57.895 0.00 0.00 0.00 3.13
1785 3638 2.282887 GGCGGCTTGAAAGGGGAA 60.283 61.111 0.00 0.00 0.00 3.97
1814 3667 5.422650 TCATCAATCAATCAAATCTTGGCCA 59.577 36.000 0.00 0.00 0.00 5.36
2319 4172 1.120184 TACCCCTAACGCACACCACA 61.120 55.000 0.00 0.00 0.00 4.17
2412 4265 2.347490 GCCGCCACCTTCTTCTCA 59.653 61.111 0.00 0.00 0.00 3.27
2572 4425 4.496010 GCTACATTGCTGATGCTTCTCTTG 60.496 45.833 0.88 0.00 39.47 3.02
2675 4528 5.357314 TCCAATACTTCAACGAGACTAGAGG 59.643 44.000 0.00 0.00 0.00 3.69
2754 4612 6.380079 AGTTCTCAACTGAACCCTGAATAT 57.620 37.500 4.08 0.00 45.25 1.28
2803 4661 4.665833 TCACGGATAGATTCAACCGAAT 57.334 40.909 17.99 0.00 46.94 3.34
2880 4741 8.243426 GCAAACAAGTATCATTCCAAATACTCA 58.757 33.333 0.00 0.00 37.64 3.41
2992 4853 5.841957 AGCATCATTCCAAAATACTCCAC 57.158 39.130 0.00 0.00 0.00 4.02
3031 4905 6.266103 AGAACAAATCCAAGCAGATTGAAAGA 59.734 34.615 0.00 0.00 41.83 2.52
3048 4922 5.360714 TCCAAGCACAAAGAAGAGAACAAAT 59.639 36.000 0.00 0.00 0.00 2.32
3050 4924 4.269183 TCCAAGCACAAAGAAGAGAACAA 58.731 39.130 0.00 0.00 0.00 2.83
3051 4925 3.879295 CTCCAAGCACAAAGAAGAGAACA 59.121 43.478 0.00 0.00 0.00 3.18
3052 4926 3.251972 CCTCCAAGCACAAAGAAGAGAAC 59.748 47.826 0.00 0.00 0.00 3.01
3053 4927 3.117888 ACCTCCAAGCACAAAGAAGAGAA 60.118 43.478 0.00 0.00 0.00 2.87
3054 4928 2.439507 ACCTCCAAGCACAAAGAAGAGA 59.560 45.455 0.00 0.00 0.00 3.10
3110 4984 2.123033 ACAACCCCCAAACCCTGC 60.123 61.111 0.00 0.00 0.00 4.85
3112 4986 0.186630 GTACACAACCCCCAAACCCT 59.813 55.000 0.00 0.00 0.00 4.34
3117 4991 3.458857 TCAACTTAGTACACAACCCCCAA 59.541 43.478 0.00 0.00 0.00 4.12
3232 5107 8.543774 AGTCATCTTGTATATTGTGGAACTTCT 58.456 33.333 0.00 0.00 38.04 2.85
3237 5112 9.613428 CCTTAAGTCATCTTGTATATTGTGGAA 57.387 33.333 0.97 0.00 35.36 3.53
3256 5134 4.411013 AGATTCTTTGGCTTGCCTTAAGT 58.589 39.130 13.18 2.47 38.70 2.24
3354 5237 9.755804 CACATATATCTTCTTGAGCTCACTTTA 57.244 33.333 18.03 0.00 0.00 1.85
3490 5374 8.528044 TCCATCAAGTTTACATAAAATACCCC 57.472 34.615 0.00 0.00 0.00 4.95
3514 5398 7.727331 AAATGCTCAGAGTGCTTATCTATTC 57.273 36.000 0.00 0.00 0.00 1.75
3649 5533 9.692749 GCGGCTTTAGCATGATAATATATAGTA 57.307 33.333 3.91 0.00 44.36 1.82
3650 5534 8.424918 AGCGGCTTTAGCATGATAATATATAGT 58.575 33.333 3.91 0.00 44.36 2.12
3651 5535 8.706936 CAGCGGCTTTAGCATGATAATATATAG 58.293 37.037 3.91 0.00 44.36 1.31
3652 5536 7.657354 CCAGCGGCTTTAGCATGATAATATATA 59.343 37.037 3.91 0.00 44.36 0.86
3653 5537 6.484643 CCAGCGGCTTTAGCATGATAATATAT 59.515 38.462 3.91 0.00 44.36 0.86
3654 5538 5.817296 CCAGCGGCTTTAGCATGATAATATA 59.183 40.000 3.91 0.00 44.36 0.86
3697 5581 3.678072 TCCGTTAGCTTTCTCGAACAATG 59.322 43.478 0.00 0.00 0.00 2.82
3708 5592 7.690952 TTTGGTAATGTAATCCGTTAGCTTT 57.309 32.000 0.00 0.00 41.51 3.51
3796 6063 5.631096 CGCGTAAGATCAATGACATATGACT 59.369 40.000 10.38 0.00 43.02 3.41
3797 6064 5.164051 CCGCGTAAGATCAATGACATATGAC 60.164 44.000 10.38 3.62 43.02 3.06
3799 6066 4.923281 TCCGCGTAAGATCAATGACATATG 59.077 41.667 4.92 0.00 43.02 1.78
3800 6067 5.134202 TCCGCGTAAGATCAATGACATAT 57.866 39.130 4.92 0.00 43.02 1.78
3801 6068 4.577834 TCCGCGTAAGATCAATGACATA 57.422 40.909 4.92 0.00 43.02 2.29
3802 6069 3.452755 TCCGCGTAAGATCAATGACAT 57.547 42.857 4.92 0.00 43.02 3.06


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

AutoCloner maintained by Alex Coulton.