Multiple sequence alignment - TraesCS5A01G183800

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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 TraesCS5A01G183800 chr5A 100.000 5088 0 0 1 5088 383467793 383462706 0.000000e+00 9396.0
1 TraesCS5A01G183800 chr5B 93.490 4301 217 31 831 5088 331655966 331651686 0.000000e+00 6333.0
2 TraesCS5A01G183800 chr5B 87.893 413 49 1 392 803 331656484 331656072 7.660000e-133 484.0
3 TraesCS5A01G183800 chr5B 87.805 410 26 7 6 397 331657053 331656650 4.640000e-125 459.0
4 TraesCS5A01G183800 chr5D 95.942 2760 105 2 831 3584 291253193 291250435 0.000000e+00 4470.0
5 TraesCS5A01G183800 chr5D 90.216 1298 78 21 3689 4977 291250254 291248997 0.000000e+00 1648.0
6 TraesCS5A01G183800 chr5D 91.945 807 51 7 1 803 291254067 291253271 0.000000e+00 1118.0
7 TraesCS5A01G183800 chr6D 94.875 761 33 1 2071 2825 415402286 415403046 0.000000e+00 1184.0
8 TraesCS5A01G183800 chr6D 87.037 54 7 0 3765 3818 78302571 78302518 1.530000e-05 62.1
9 TraesCS5A01G183800 chr4B 84.043 94 15 0 3733 3826 94208702 94208609 1.950000e-14 91.6
10 TraesCS5A01G183800 chr6B 87.273 55 7 0 3764 3818 151149194 151149140 4.250000e-06 63.9
11 TraesCS5A01G183800 chr6A 87.273 55 7 0 3764 3818 93890453 93890399 4.250000e-06 63.9


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 TraesCS5A01G183800 chr5A 383462706 383467793 5087 True 9396.000000 9396 100.000000 1 5088 1 chr5A.!!$R1 5087
1 TraesCS5A01G183800 chr5B 331651686 331657053 5367 True 2425.333333 6333 89.729333 6 5088 3 chr5B.!!$R1 5082
2 TraesCS5A01G183800 chr5D 291248997 291254067 5070 True 2412.000000 4470 92.701000 1 4977 3 chr5D.!!$R1 4976
3 TraesCS5A01G183800 chr6D 415402286 415403046 760 False 1184.000000 1184 94.875000 2071 2825 1 chr6D.!!$F1 754

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
828 1070 0.178975 ATAGGAGTCAGAGGCTCGGG 60.179 60.0 14.68 8.73 34.0 5.14 F
1076 1355 0.105039 CTACTCCCACTCCCGATTGC 59.895 60.0 0.00 0.00 0.0 3.56 F
2833 3124 0.039764 AGTCCACCTGATCGTCTCCA 59.960 55.0 0.00 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2508 0.174389 GCTCGAGCATCTGGACAAGA 59.826 55.0 31.91 0.0 41.59 3.02 R
2850 3141 0.107508 AACCCATGAGCAGGACGATG 60.108 55.0 0.00 0.0 0.00 3.84 R
4767 5155 0.253327 GTAGTCAAGGGGAGGCCAAG 59.747 60.0 5.01 0.0 0.00 3.61 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
44 45 4.322650 GGCTGGAAAATAAGTTGAATGCCA 60.323 41.667 0.00 0.00 35.94 4.92
81 82 3.879998 TGTAGAACTCAACTTTGTGGCA 58.120 40.909 0.00 0.00 0.00 4.92
96 97 4.233632 TGTGGCATCAATTGGTCTATCA 57.766 40.909 5.42 0.00 0.00 2.15
169 185 9.376075 CATATAATCTCAGTAATGGCTAGTTGG 57.624 37.037 0.00 0.00 0.00 3.77
259 275 6.849588 CATCCGATGATGTTACTCAATTCA 57.150 37.500 1.78 0.00 42.87 2.57
273 289 8.543774 GTTACTCAATTCAAGATGAATACGAGG 58.456 37.037 22.88 13.06 45.57 4.63
453 644 5.469479 CAACTCAACTTTTGTCAACCAGTT 58.531 37.500 4.20 4.20 0.00 3.16
525 717 6.294899 GCATATGGCCAACACATATCATCTTT 60.295 38.462 10.96 0.00 38.98 2.52
541 733 4.095782 TCATCTTTATAACGGCAAGCCAAC 59.904 41.667 12.19 0.00 35.37 3.77
559 751 2.262292 GGTGTGCGCATTTGGCAT 59.738 55.556 15.91 0.00 45.17 4.40
583 775 8.693504 CATCATCTGAACACAATAAAACACAAC 58.306 33.333 0.00 0.00 0.00 3.32
584 776 7.995289 TCATCTGAACACAATAAAACACAACT 58.005 30.769 0.00 0.00 0.00 3.16
648 841 2.889756 GCTCCCCATTTCCTTGGAACAT 60.890 50.000 0.98 0.00 39.25 2.71
661 854 5.885912 TCCTTGGAACATAGGCATTTAAGAC 59.114 40.000 0.00 0.00 39.30 3.01
673 866 4.319177 GCATTTAAGACTGCCTCCGATAT 58.681 43.478 0.00 0.00 32.15 1.63
692 885 8.304596 TCCGATATATGTTACTCAATTCCACTC 58.695 37.037 0.00 0.00 0.00 3.51
709 902 4.025563 TCCACTCGAACACAACAAAATACG 60.026 41.667 0.00 0.00 0.00 3.06
751 944 1.269012 CAACCAATGGCATGAACCCT 58.731 50.000 0.00 0.00 0.00 4.34
768 961 1.500844 CTCTCCGACACGCGTTACT 59.499 57.895 10.22 0.00 38.67 2.24
811 1053 3.592898 AGTGTGCATGACTCGTCAATA 57.407 42.857 3.60 0.00 43.58 1.90
815 1057 3.119291 GTGCATGACTCGTCAATAGGAG 58.881 50.000 3.60 0.00 43.58 3.69
828 1070 0.178975 ATAGGAGTCAGAGGCTCGGG 60.179 60.000 14.68 8.73 34.00 5.14
1038 1317 1.290732 CTCCTTCTCCTCCTCCTTCCT 59.709 57.143 0.00 0.00 0.00 3.36
1047 1326 2.776913 CCTCCTTCCTCTCGTCGGC 61.777 68.421 0.00 0.00 0.00 5.54
1061 1340 1.746516 CGTCGGCCTCCTAGTTCTACT 60.747 57.143 0.00 0.00 0.00 2.57
1071 1350 2.299521 CTAGTTCTACTCCCACTCCCG 58.700 57.143 0.00 0.00 0.00 5.14
1076 1355 0.105039 CTACTCCCACTCCCGATTGC 59.895 60.000 0.00 0.00 0.00 3.56
1082 1361 3.717294 ACTCCCGATTGCCGCCTT 61.717 61.111 0.00 0.00 36.84 4.35
1155 1434 2.444895 GCCCTCTCCGTCTGGGAT 60.445 66.667 0.91 0.00 46.04 3.85
1221 1500 2.874751 GGAAAATCCACCGCCGTG 59.125 61.111 0.00 0.00 36.28 4.94
1500 1779 2.525592 CCCTGGTTCCTGGCCAAA 59.474 61.111 7.01 0.00 35.32 3.28
1545 1824 2.468532 GCCTACAACGCGTTCACG 59.531 61.111 23.92 14.08 43.27 4.35
1633 1912 1.475213 CCCTGAGCGGTAAAATCCCTC 60.475 57.143 0.00 0.00 0.00 4.30
1677 1956 1.407258 CTCGTCAATCTGGACCTCTCC 59.593 57.143 0.00 0.00 37.04 3.71
1707 1986 2.520982 TCCGGCGAGATACCCAGG 60.521 66.667 9.30 0.00 0.00 4.45
1805 2084 1.219393 GGGGTCTCAAGAAGCTCCG 59.781 63.158 0.00 0.00 0.00 4.63
1893 2172 2.283298 CTGGAGAGCGTGCACATTTAT 58.717 47.619 18.64 0.00 0.00 1.40
1908 2187 5.619981 GCACATTTATCAGAACAACCTGACC 60.620 44.000 0.00 0.00 44.93 4.02
2196 2475 2.035442 GCAGAACAACCGCCTCTCC 61.035 63.158 0.00 0.00 0.00 3.71
2226 2505 2.438434 CCGGAATTCTGGGCGCTT 60.438 61.111 23.77 0.00 38.76 4.68
2229 2508 1.077429 GGAATTCTGGGCGCTTCCT 60.077 57.895 14.67 0.00 35.36 3.36
2577 2856 1.460273 GGACGATCCCTCCAGAGCTC 61.460 65.000 5.27 5.27 0.00 4.09
2805 3096 4.028490 GACCACGGTGCCATCCCA 62.028 66.667 1.68 0.00 0.00 4.37
2833 3124 0.039764 AGTCCACCTGATCGTCTCCA 59.960 55.000 0.00 0.00 0.00 3.86
2841 3132 1.081774 GATCGTCTCCATCCTCGCG 60.082 63.158 0.00 0.00 0.00 5.87
2847 3138 2.839632 TCCATCCTCGCGGCATCT 60.840 61.111 6.13 0.00 0.00 2.90
2883 3174 2.969821 TGGGTTTAGCATGGTTCACT 57.030 45.000 1.12 0.00 0.00 3.41
3054 3345 1.144298 GGGAAGGTGTACAAGGTGGTT 59.856 52.381 0.00 0.00 0.00 3.67
3098 3389 0.322975 GCTGTCAAGAAGCTCTGGGA 59.677 55.000 0.00 0.00 37.69 4.37
3099 3390 1.943507 GCTGTCAAGAAGCTCTGGGAC 60.944 57.143 0.00 0.00 37.69 4.46
3267 3558 4.432741 GGCAGCCTGGGGGACTTC 62.433 72.222 3.29 0.00 33.58 3.01
3327 3618 2.492484 GAGGTATAAGATCGCGGTCCAT 59.508 50.000 17.38 12.41 0.00 3.41
3599 3935 3.795877 ACATGCAGTTTTTCCCTTGTTG 58.204 40.909 0.00 0.00 0.00 3.33
3600 3936 3.450457 ACATGCAGTTTTTCCCTTGTTGA 59.550 39.130 0.00 0.00 0.00 3.18
3601 3937 4.081198 ACATGCAGTTTTTCCCTTGTTGAA 60.081 37.500 0.00 0.00 0.00 2.69
3602 3938 4.543590 TGCAGTTTTTCCCTTGTTGAAA 57.456 36.364 0.00 0.00 0.00 2.69
3603 3939 4.502962 TGCAGTTTTTCCCTTGTTGAAAG 58.497 39.130 0.00 0.00 33.58 2.62
3683 4066 2.882137 TGGCACTGCTAAAACCTTGTAC 59.118 45.455 0.00 0.00 0.00 2.90
3684 4067 3.146847 GGCACTGCTAAAACCTTGTACT 58.853 45.455 0.00 0.00 0.00 2.73
3685 4068 3.188667 GGCACTGCTAAAACCTTGTACTC 59.811 47.826 0.00 0.00 0.00 2.59
3686 4069 3.188667 GCACTGCTAAAACCTTGTACTCC 59.811 47.826 0.00 0.00 0.00 3.85
3687 4070 4.385825 CACTGCTAAAACCTTGTACTCCA 58.614 43.478 0.00 0.00 0.00 3.86
3688 4071 5.003804 CACTGCTAAAACCTTGTACTCCAT 58.996 41.667 0.00 0.00 0.00 3.41
3689 4072 6.170506 CACTGCTAAAACCTTGTACTCCATA 58.829 40.000 0.00 0.00 0.00 2.74
3690 4073 6.823689 CACTGCTAAAACCTTGTACTCCATAT 59.176 38.462 0.00 0.00 0.00 1.78
3694 4077 9.742144 TGCTAAAACCTTGTACTCCATATTTTA 57.258 29.630 0.00 0.00 0.00 1.52
3787 4170 0.314302 AGAGCGACGTGTACAGCTTT 59.686 50.000 8.56 0.98 40.39 3.51
3862 4245 1.374758 CGAGAAGCACCTGGTGGTC 60.375 63.158 29.63 21.71 46.60 4.02
3985 4368 2.928361 CTGTGCGTCAACACCGTC 59.072 61.111 0.00 0.00 39.93 4.79
3990 4373 2.732094 CGTCAACACCGTCCCGAC 60.732 66.667 0.00 0.00 0.00 4.79
3997 4380 3.539791 ACCGTCCCGACCAAACGT 61.540 61.111 0.00 0.00 34.71 3.99
4030 4413 1.241165 CTGTGGTGAAGATGCTGCAA 58.759 50.000 6.36 0.00 0.00 4.08
4043 4426 1.303643 CTGCAAGAGGTTGGGGGAC 60.304 63.158 0.00 0.00 34.07 4.46
4054 4437 2.035783 GGGGGACAGAACAAGCCC 59.964 66.667 0.00 0.00 39.93 5.19
4079 4462 3.523681 AAGGAGGAGGTGGCCCCTT 62.524 63.158 13.39 7.70 46.51 3.95
4167 4551 8.701908 ATTACCGTTAACTAGGAGTCATATCA 57.298 34.615 3.71 0.00 0.00 2.15
4170 4554 6.262720 ACCGTTAACTAGGAGTCATATCAGAC 59.737 42.308 3.71 0.00 38.81 3.51
4174 4558 9.352191 GTTAACTAGGAGTCATATCAGACCTTA 57.648 37.037 0.00 0.00 39.34 2.69
4211 4595 7.033530 CTGATAGCAGCTAGTAGTAGTTTGT 57.966 40.000 8.43 0.00 34.95 2.83
4251 4635 4.159506 TGCACTTTGGTAAACTCAAAAGCT 59.840 37.500 0.00 0.00 36.76 3.74
4318 4702 2.221169 GCTGTCAACCAATCTGTGACA 58.779 47.619 5.67 5.67 37.81 3.58
4366 4750 3.635331 CTTGATGCTTTTGTGGTGACTG 58.365 45.455 0.00 0.00 0.00 3.51
4436 4821 5.994668 TGTTTCTTTTTCACACAGCCTTTTT 59.005 32.000 0.00 0.00 0.00 1.94
4437 4822 6.147000 TGTTTCTTTTTCACACAGCCTTTTTC 59.853 34.615 0.00 0.00 0.00 2.29
4439 4824 5.976458 TCTTTTTCACACAGCCTTTTTCAT 58.024 33.333 0.00 0.00 0.00 2.57
4460 4845 2.807967 TCGTGAAGATGCTTTGGAACAG 59.192 45.455 0.00 0.00 42.39 3.16
4575 4960 3.526931 TGATAGCTCTGTTACCAGCAC 57.473 47.619 0.00 0.00 38.66 4.40
4592 4977 2.693797 CACTAGTGCTTGGTGCTTTG 57.306 50.000 10.54 0.00 43.37 2.77
4594 4979 0.242017 CTAGTGCTTGGTGCTTTGGC 59.758 55.000 0.00 0.00 43.37 4.52
4752 5140 2.236766 GCATAAGCTGGAGATGGCATT 58.763 47.619 0.00 0.00 37.91 3.56
4767 5155 3.990318 GGCATTGCCTTTATGTACTCC 57.010 47.619 20.66 0.00 46.69 3.85
4858 5246 6.457799 CCAGGACAAGTAAACTGTACACAAAC 60.458 42.308 0.00 0.00 0.00 2.93
4875 5263 9.059260 GTACACAAACTTATAGGGACAAAGAAA 57.941 33.333 0.00 0.00 0.00 2.52
4898 5286 5.902613 TTTATTGGGATGCAGTTCTGAAG 57.097 39.130 3.84 0.00 0.00 3.02
4931 5320 7.313646 TCAGTAGAACACATAACTGTCTTAGC 58.686 38.462 0.00 0.00 40.18 3.09
4935 5324 6.166982 AGAACACATAACTGTCTTAGCTTCC 58.833 40.000 0.00 0.00 31.62 3.46
4956 5348 3.762293 TGGCACACATGTCCTTGC 58.238 55.556 13.07 13.07 0.00 4.01
4972 5368 0.251922 TTGCTAGGACCGGTGTACCT 60.252 55.000 14.63 16.06 37.76 3.08
4981 5377 4.106019 AGGACCGGTGTACCTAGATCTAAT 59.894 45.833 14.63 0.00 31.78 1.73
4990 5386 7.201705 GGTGTACCTAGATCTAATTTTGCAACC 60.202 40.741 0.00 1.67 0.00 3.77
4992 5388 7.552687 TGTACCTAGATCTAATTTTGCAACCTG 59.447 37.037 0.00 0.00 0.00 4.00
5002 5398 3.663995 TTTGCAACCTGTCATTGGATG 57.336 42.857 0.00 0.00 0.00 3.51
5004 5400 2.439409 TGCAACCTGTCATTGGATGAG 58.561 47.619 0.00 0.00 40.53 2.90
5017 5413 1.098050 GGATGAGTTGACATGGTGCC 58.902 55.000 0.00 0.00 0.00 5.01
5018 5414 1.614051 GGATGAGTTGACATGGTGCCA 60.614 52.381 0.00 0.00 0.00 4.92
5019 5415 1.470098 GATGAGTTGACATGGTGCCAC 59.530 52.381 0.00 0.00 0.00 5.01
5020 5416 0.473755 TGAGTTGACATGGTGCCACT 59.526 50.000 0.00 0.00 0.00 4.00
5021 5417 0.877071 GAGTTGACATGGTGCCACTG 59.123 55.000 0.00 0.00 0.00 3.66
5022 5418 1.174712 AGTTGACATGGTGCCACTGC 61.175 55.000 0.00 0.00 38.26 4.40
5037 5433 0.536233 ACTGCCATGGCGTGTGTTTA 60.536 50.000 30.87 10.57 45.51 2.01
5063 5459 5.067283 TCAGTGTTTAGCCCTTTCTGTTTTC 59.933 40.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.885912 TCAACTTATTTTCCAGCCAGATACC 59.114 40.000 0.00 0.00 0.00 2.73
44 45 8.849168 TGAGTTCTACAAACATGTCAAAATGAT 58.151 29.630 0.00 0.00 0.00 2.45
169 185 2.450160 GCGCCAAATGCTATTGTACAC 58.550 47.619 0.00 0.00 38.05 2.90
195 211 4.278419 GGGTCAGCTTATCTTGTTGTGTTT 59.722 41.667 0.00 0.00 0.00 2.83
259 275 8.567285 AAGTCATTTTTCCTCGTATTCATCTT 57.433 30.769 0.00 0.00 0.00 2.40
347 364 1.196104 TACGCTACAAGGGCAAGGGT 61.196 55.000 0.00 0.00 39.43 4.34
348 365 0.462047 CTACGCTACAAGGGCAAGGG 60.462 60.000 0.00 0.00 0.00 3.95
349 366 0.535335 TCTACGCTACAAGGGCAAGG 59.465 55.000 0.00 0.00 0.00 3.61
350 367 2.380084 TTCTACGCTACAAGGGCAAG 57.620 50.000 0.00 0.00 0.00 4.01
351 368 4.344102 AGATATTCTACGCTACAAGGGCAA 59.656 41.667 0.00 0.00 0.00 4.52
352 369 3.895656 AGATATTCTACGCTACAAGGGCA 59.104 43.478 0.00 0.00 0.00 5.36
453 644 5.223449 AGAACCAAGGAAGTTATCGACAA 57.777 39.130 0.00 0.00 0.00 3.18
495 687 1.339535 TGTGTTGGCCATATGCTTCGA 60.340 47.619 6.09 0.00 40.92 3.71
525 717 0.036199 ACCGTTGGCTTGCCGTTATA 60.036 50.000 7.18 0.00 0.00 0.98
541 733 3.629883 ATGCCAAATGCGCACACCG 62.630 57.895 14.90 1.38 45.60 4.94
559 751 7.995289 AGTTGTGTTTTATTGTGTTCAGATGA 58.005 30.769 0.00 0.00 0.00 2.92
661 854 5.644977 TGAGTAACATATATCGGAGGCAG 57.355 43.478 0.00 0.00 0.00 4.85
673 866 6.588756 GTGTTCGAGTGGAATTGAGTAACATA 59.411 38.462 0.00 0.00 36.92 2.29
692 885 3.178814 GCCAACGTATTTTGTTGTGTTCG 59.821 43.478 5.28 0.00 44.00 3.95
709 902 1.967319 TGAACTCCTTGTGAGCCAAC 58.033 50.000 0.00 0.00 45.61 3.77
751 944 1.229975 TGAGTAACGCGTGTCGGAGA 61.230 55.000 14.98 0.00 43.86 3.71
768 961 5.553290 TTGACACGTGTTTCTCAAATTGA 57.447 34.783 24.26 0.00 0.00 2.57
811 1053 2.043450 CCCGAGCCTCTGACTCCT 60.043 66.667 0.00 0.00 0.00 3.69
815 1057 1.142748 CATGACCCGAGCCTCTGAC 59.857 63.158 0.00 0.00 0.00 3.51
828 1070 0.180406 AATGAGGTACCCGGCATGAC 59.820 55.000 8.74 0.00 0.00 3.06
1038 1317 0.747283 GAACTAGGAGGCCGACGAGA 60.747 60.000 14.72 0.00 0.00 4.04
1047 1326 3.558033 GAGTGGGAGTAGAACTAGGAGG 58.442 54.545 0.00 0.00 0.00 4.30
1061 1340 3.781307 CGGCAATCGGGAGTGGGA 61.781 66.667 0.00 0.00 34.75 4.37
1082 1361 2.562912 GGTAACTGGCGTCGTCGA 59.437 61.111 6.17 0.00 39.71 4.20
1195 1474 1.899054 TGGATTTTCCGGCGCACAA 60.899 52.632 10.83 0.00 40.17 3.33
1238 1517 3.452786 CGGCGAGGGAGAGCTTGA 61.453 66.667 0.00 0.00 0.00 3.02
1273 1552 0.250338 AGGGACCTCAACGAGCAAAC 60.250 55.000 0.00 0.00 0.00 2.93
1359 1638 0.108585 GGGTGAGGTTCAAGAGTGCA 59.891 55.000 0.00 0.00 0.00 4.57
1500 1779 2.305095 CTCCTGGAGGGTGCTGATT 58.695 57.895 16.19 0.00 36.25 2.57
1590 1869 0.603975 AGTTGGCGAGAAACAGCTCC 60.604 55.000 0.00 0.00 0.00 4.70
1624 1903 2.205342 TCCGATGGAAGGAGGGATTTT 58.795 47.619 0.00 0.00 33.19 1.82
1633 1912 0.462047 CCGAGGTTTCCGATGGAAGG 60.462 60.000 0.00 0.00 43.06 3.46
1677 1956 2.202932 CCGGAGAGGGCGTTCATG 60.203 66.667 0.00 0.00 35.97 3.07
1707 1986 4.704057 AGAGAACTCAAATTCCCAATGCTC 59.296 41.667 4.64 0.00 0.00 4.26
1893 2172 1.752198 CCCGGTCAGGTTGTTCTGA 59.248 57.895 0.00 0.00 41.03 3.27
2016 2295 1.221840 CATGTCCAGGAACCCGAGG 59.778 63.158 0.00 0.00 0.00 4.63
2160 2439 4.680537 AGCCGGACCCTCGTCAGT 62.681 66.667 5.05 0.00 41.13 3.41
2223 2502 1.065564 AGCATCTGGACAAGAGGAAGC 60.066 52.381 0.00 0.00 39.10 3.86
2226 2505 0.820226 CGAGCATCTGGACAAGAGGA 59.180 55.000 0.00 0.00 39.10 3.71
2229 2508 0.174389 GCTCGAGCATCTGGACAAGA 59.826 55.000 31.91 0.00 41.59 3.02
2451 2730 3.947173 CTCAGGTCGAGCTGGGAT 58.053 61.111 35.50 2.67 34.18 3.85
2500 2779 2.434428 CTGCTTCAGCTGTCCAATCTT 58.566 47.619 14.67 0.00 42.66 2.40
2561 2840 2.560119 CCGAGCTCTGGAGGGATCG 61.560 68.421 16.62 7.21 0.00 3.69
2577 2856 1.525995 CATCCGGTGGATTTCCCCG 60.526 63.158 15.51 15.51 39.79 5.73
2770 3061 2.399611 GTCGTTGCCTGCGCATAC 59.600 61.111 12.24 6.72 46.67 2.39
2847 3138 1.153309 CATGAGCAGGACGATGGCA 60.153 57.895 0.00 0.00 0.00 4.92
2850 3141 0.107508 AACCCATGAGCAGGACGATG 60.108 55.000 0.00 0.00 0.00 3.84
2883 3174 6.645415 GCTTCTTGTAGCTTCTGTACTTGTAA 59.355 38.462 0.00 0.00 38.15 2.41
2930 3221 0.966920 GAGGTCCCAACTTGACTCGA 59.033 55.000 0.00 0.00 33.22 4.04
3042 3333 0.671796 GCCCAACAACCACCTTGTAC 59.328 55.000 0.00 0.00 42.70 2.90
3054 3345 1.679311 CTCACTGCTAGGCCCAACA 59.321 57.895 0.00 0.00 0.00 3.33
3098 3389 1.548973 CTTGCTTTCGACGTCGCTGT 61.549 55.000 32.19 0.00 39.60 4.40
3099 3390 1.128611 CTTGCTTTCGACGTCGCTG 59.871 57.895 32.19 22.97 39.60 5.18
3223 3514 2.854777 GCATGTACTCGTAGACAAGCAG 59.145 50.000 0.00 0.00 39.46 4.24
3228 3519 1.741528 TCGGCATGTACTCGTAGACA 58.258 50.000 0.00 0.00 0.00 3.41
3265 3556 0.823356 GCTTTGGCACTGTGGAGGAA 60.823 55.000 10.21 0.00 38.54 3.36
3267 3558 2.270986 GGCTTTGGCACTGTGGAGG 61.271 63.158 10.21 0.00 40.87 4.30
3486 3777 1.986757 ACAGGAGCCAGCGATGACT 60.987 57.895 0.06 0.00 0.00 3.41
3578 3869 3.450457 TCAACAAGGGAAAAACTGCATGT 59.550 39.130 0.00 0.00 0.00 3.21
3599 3935 9.846248 AGAAAATGTCATGTAAATGTAGCTTTC 57.154 29.630 0.00 0.35 0.00 2.62
3600 3936 9.630098 CAGAAAATGTCATGTAAATGTAGCTTT 57.370 29.630 0.00 0.00 0.00 3.51
3601 3937 7.756722 GCAGAAAATGTCATGTAAATGTAGCTT 59.243 33.333 0.00 0.00 0.00 3.74
3602 3938 7.094248 TGCAGAAAATGTCATGTAAATGTAGCT 60.094 33.333 0.00 0.00 0.00 3.32
3603 3939 7.028962 TGCAGAAAATGTCATGTAAATGTAGC 58.971 34.615 0.00 0.00 0.00 3.58
3636 3972 5.861251 CAGTGCACAAGAACAAAGTTACAAA 59.139 36.000 21.04 0.00 0.00 2.83
3638 3974 4.142491 CCAGTGCACAAGAACAAAGTTACA 60.142 41.667 21.04 0.00 0.00 2.41
3683 4066 6.598064 ACACGGTCCTTTCTTAAAATATGGAG 59.402 38.462 0.00 0.00 0.00 3.86
3684 4067 6.373216 CACACGGTCCTTTCTTAAAATATGGA 59.627 38.462 0.00 0.00 0.00 3.41
3685 4068 6.150474 ACACACGGTCCTTTCTTAAAATATGG 59.850 38.462 0.00 0.00 0.00 2.74
3686 4069 7.021196 CACACACGGTCCTTTCTTAAAATATG 58.979 38.462 0.00 0.00 0.00 1.78
3687 4070 6.713450 ACACACACGGTCCTTTCTTAAAATAT 59.287 34.615 0.00 0.00 0.00 1.28
3688 4071 6.017770 CACACACACGGTCCTTTCTTAAAATA 60.018 38.462 0.00 0.00 0.00 1.40
3689 4072 4.885325 ACACACACGGTCCTTTCTTAAAAT 59.115 37.500 0.00 0.00 0.00 1.82
3690 4073 4.095185 CACACACACGGTCCTTTCTTAAAA 59.905 41.667 0.00 0.00 0.00 1.52
3694 4077 1.208535 TCACACACACGGTCCTTTCTT 59.791 47.619 0.00 0.00 0.00 2.52
3703 4086 2.357637 AGGAACAAAATCACACACACGG 59.642 45.455 0.00 0.00 0.00 4.94
3787 4170 1.296392 CTCCAGAATGACCACGCCA 59.704 57.895 0.00 0.00 39.69 5.69
3862 4245 3.773117 GACATTGTCGCAAACCCAG 57.227 52.632 0.13 0.00 0.00 4.45
3930 4313 1.954382 CCTTGCACATCTCATCATGGG 59.046 52.381 0.00 0.00 0.00 4.00
3990 4373 1.019278 CCTCATCGGTGGACGTTTGG 61.019 60.000 0.00 0.00 44.69 3.28
3997 4380 2.284625 ACAGCCCTCATCGGTGGA 60.285 61.111 0.00 0.00 33.01 4.02
4030 4413 0.401395 TGTTCTGTCCCCCAACCTCT 60.401 55.000 0.00 0.00 0.00 3.69
4054 4437 1.078848 CACCTCCTCCTTCGCCTTG 60.079 63.158 0.00 0.00 0.00 3.61
4079 4462 4.898265 CCTATCCATGGTTCTTCAGAGAGA 59.102 45.833 12.58 0.00 32.44 3.10
4167 4551 2.370189 AGCAGTGCACTTCTTAAGGTCT 59.630 45.455 18.94 3.21 0.00 3.85
4170 4554 2.771089 TCAGCAGTGCACTTCTTAAGG 58.229 47.619 18.94 5.91 0.00 2.69
4174 4558 2.354259 GCTATCAGCAGTGCACTTCTT 58.646 47.619 18.94 6.26 41.89 2.52
4211 4595 6.942532 AAGTGCAGTTCTAAATGTTCAGAA 57.057 33.333 0.00 0.00 0.00 3.02
4227 4611 4.504097 GCTTTTGAGTTTACCAAAGTGCAG 59.496 41.667 0.00 0.00 36.17 4.41
4251 4635 3.569701 CAGAGCAAAAGGTTAGCTTCCAA 59.430 43.478 9.72 0.00 39.02 3.53
4318 4702 2.768253 TGCAACAACATCGGATCTCT 57.232 45.000 0.00 0.00 0.00 3.10
4366 4750 2.288213 GGAGGCAACAAAAGTTACAGCC 60.288 50.000 0.00 0.00 40.85 4.85
4439 4824 2.807967 CTGTTCCAAAGCATCTTCACGA 59.192 45.455 0.00 0.00 0.00 4.35
4460 4845 1.540267 CATGGCAGCATCTCCATAAGC 59.460 52.381 0.00 0.00 40.88 3.09
4524 4909 6.045955 GCTTTAGATGGGACTTCTAGACTTG 58.954 44.000 0.00 0.00 0.00 3.16
4584 4969 0.676782 ATCACTACCGCCAAAGCACC 60.677 55.000 0.00 0.00 39.83 5.01
4592 4977 1.268032 CGAAATGCAATCACTACCGCC 60.268 52.381 0.00 0.00 0.00 6.13
4594 4979 2.006888 ACCGAAATGCAATCACTACCG 58.993 47.619 0.00 0.00 0.00 4.02
4693 5080 1.573108 CCATGGGTACTGGAGACTGT 58.427 55.000 2.85 0.00 45.27 3.55
4752 5140 2.356741 GGCCAAGGAGTACATAAAGGCA 60.357 50.000 16.84 0.00 42.49 4.75
4767 5155 0.253327 GTAGTCAAGGGGAGGCCAAG 59.747 60.000 5.01 0.00 0.00 3.61
4818 5206 2.614057 GTCCTGGCGACCAATGATTTAG 59.386 50.000 0.00 0.00 35.23 1.85
4875 5263 5.163478 GCTTCAGAACTGCATCCCAATAAAT 60.163 40.000 0.00 0.00 0.00 1.40
4883 5271 2.698855 TAGGCTTCAGAACTGCATCC 57.301 50.000 0.00 0.00 0.00 3.51
4919 5307 3.260884 CCACTGGGAAGCTAAGACAGTTA 59.739 47.826 9.66 0.00 40.14 2.24
4931 5320 0.538057 ACATGTGTGCCACTGGGAAG 60.538 55.000 0.00 0.00 35.11 3.46
4935 5324 0.538057 AAGGACATGTGTGCCACTGG 60.538 55.000 1.15 0.00 37.04 4.00
4972 5368 8.461222 CAATGACAGGTTGCAAAATTAGATCTA 58.539 33.333 0.00 0.00 0.00 1.98
4981 5377 3.640498 TCATCCAATGACAGGTTGCAAAA 59.360 39.130 0.00 0.00 33.59 2.44
4992 5388 4.012374 ACCATGTCAACTCATCCAATGAC 58.988 43.478 0.00 0.00 41.90 3.06
5002 5398 0.877071 CAGTGGCACCATGTCAACTC 59.123 55.000 15.27 0.00 31.67 3.01
5004 5400 1.286880 GCAGTGGCACCATGTCAAC 59.713 57.895 15.27 0.00 40.72 3.18
5017 5413 2.074230 AAACACACGCCATGGCAGTG 62.074 55.000 37.96 37.96 45.78 3.66
5018 5414 0.536233 TAAACACACGCCATGGCAGT 60.536 50.000 34.93 28.28 42.06 4.40
5019 5415 0.595588 TTAAACACACGCCATGGCAG 59.404 50.000 34.93 27.62 42.06 4.85
5020 5416 1.201181 GATTAAACACACGCCATGGCA 59.799 47.619 34.93 13.77 42.06 4.92
5021 5417 1.201181 TGATTAAACACACGCCATGGC 59.799 47.619 27.67 27.67 37.85 4.40
5022 5418 2.487762 ACTGATTAAACACACGCCATGG 59.512 45.455 7.63 7.63 0.00 3.66
5037 5433 4.729868 ACAGAAAGGGCTAAACACTGATT 58.270 39.130 0.00 0.00 0.00 2.57
5063 5459 3.553105 GCAAAAACCAGAGAAAGCAACAG 59.447 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.