Multiple sequence alignment - TraesCS7D01G252400

Loading Multiple Alignment...

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 TraesCS7D01G252400 chr7D 100.000 3466 0 0 1 3466 227564985 227568450 0.000000e+00 6401.0
1 TraesCS7D01G252400 chr7B 93.226 1801 66 22 135 1897 199281495 199283277 0.000000e+00 2599.0
2 TraesCS7D01G252400 chr7B 93.152 1066 55 10 1936 2997 199283270 199284321 0.000000e+00 1548.0
3 TraesCS7D01G252400 chr7B 94.915 413 18 1 3054 3466 199284537 199284946 0.000000e+00 643.0
4 TraesCS7D01G252400 chr7A 94.389 1497 61 9 406 1881 239755346 239756840 0.000000e+00 2278.0
5 TraesCS7D01G252400 chr7A 88.724 1614 113 37 1876 3454 239756862 239758441 0.000000e+00 1908.0
6 TraesCS7D01G252400 chr7A 87.582 306 23 10 119 421 239754893 239755186 1.190000e-89 340.0
7 TraesCS7D01G252400 chr5D 76.671 853 126 55 1036 1861 384471251 384472057 4.170000e-109 405.0
8 TraesCS7D01G252400 chr5D 80.000 120 24 0 4 123 291480426 291480545 4.760000e-14 89.8
9 TraesCS7D01G252400 chr5B 77.150 779 121 40 1094 1861 461292421 461293153 1.940000e-107 399.0
10 TraesCS7D01G252400 chr5A 78.719 437 58 25 1094 1523 485375614 485376022 3.430000e-65 259.0
11 TraesCS7D01G252400 chr4B 88.333 120 14 0 1 120 18000244 18000125 1.000000e-30 145.0
12 TraesCS7D01G252400 chr6A 87.963 108 11 2 15 122 242199472 242199367 3.630000e-25 126.0
13 TraesCS7D01G252400 chr3B 83.333 120 20 0 4 123 21174950 21175069 1.020000e-20 111.0


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 TraesCS7D01G252400 chr7D 227564985 227568450 3465 False 6401.000000 6401 100.000000 1 3466 1 chr7D.!!$F1 3465
1 TraesCS7D01G252400 chr7B 199281495 199284946 3451 False 1596.666667 2599 93.764333 135 3466 3 chr7B.!!$F1 3331
2 TraesCS7D01G252400 chr7A 239754893 239758441 3548 False 1508.666667 2278 90.231667 119 3454 3 chr7A.!!$F1 3335
3 TraesCS7D01G252400 chr5D 384471251 384472057 806 False 405.000000 405 76.671000 1036 1861 1 chr5D.!!$F2 825
4 TraesCS7D01G252400 chr5B 461292421 461293153 732 False 399.000000 399 77.150000 1094 1861 1 chr5B.!!$F1 767

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
72 73 0.247537 GCCGACTCGCATTTTAACGG 60.248 55.0 0.0 0.0 41.44 4.44 F
914 1112 0.249868 TCACCAAGCAACTCACTCCG 60.250 55.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2321 0.110486 ACCTGTGTGAACCATGGGTC 59.890 55.0 23.74 23.74 33.12 4.46 R
2469 2753 0.106318 GGCTGGCCTTTCATGGAGAT 60.106 55.0 3.32 0.00 0.00 2.75 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
36 37 4.038080 CGTTTGCGGGGCCTGTTC 62.038 66.667 15.16 0.00 0.00 3.18
37 38 4.038080 GTTTGCGGGGCCTGTTCG 62.038 66.667 15.16 4.72 0.00 3.95
46 47 4.796495 GCCTGTTCGGGCGGGATT 62.796 66.667 6.91 0.00 42.82 3.01
47 48 2.045340 CCTGTTCGGGCGGGATTT 60.045 61.111 0.00 0.00 37.06 2.17
48 49 1.677633 CCTGTTCGGGCGGGATTTT 60.678 57.895 0.00 0.00 37.06 1.82
49 50 1.654023 CCTGTTCGGGCGGGATTTTC 61.654 60.000 0.00 0.00 37.06 2.29
50 51 0.958382 CTGTTCGGGCGGGATTTTCA 60.958 55.000 0.00 0.00 0.00 2.69
51 52 0.958382 TGTTCGGGCGGGATTTTCAG 60.958 55.000 0.00 0.00 0.00 3.02
52 53 2.043980 TTCGGGCGGGATTTTCAGC 61.044 57.895 0.00 0.00 0.00 4.26
53 54 3.876198 CGGGCGGGATTTTCAGCG 61.876 66.667 0.00 0.00 0.00 5.18
54 55 4.193334 GGGCGGGATTTTCAGCGC 62.193 66.667 0.00 0.00 35.54 5.92
55 56 4.193334 GGCGGGATTTTCAGCGCC 62.193 66.667 2.29 0.00 35.36 6.53
56 57 4.536687 GCGGGATTTTCAGCGCCG 62.537 66.667 2.29 0.00 0.00 6.46
57 58 2.817834 CGGGATTTTCAGCGCCGA 60.818 61.111 2.29 0.00 0.00 5.54
58 59 2.791927 GGGATTTTCAGCGCCGAC 59.208 61.111 2.29 0.00 0.00 4.79
59 60 1.745489 GGGATTTTCAGCGCCGACT 60.745 57.895 2.29 0.00 0.00 4.18
60 61 1.706287 GGGATTTTCAGCGCCGACTC 61.706 60.000 2.29 0.00 0.00 3.36
61 62 1.345176 GATTTTCAGCGCCGACTCG 59.655 57.895 2.29 0.00 0.00 4.18
70 71 3.198680 CGCCGACTCGCATTTTAAC 57.801 52.632 0.00 0.00 0.00 2.01
71 72 0.583083 CGCCGACTCGCATTTTAACG 60.583 55.000 0.00 0.00 0.00 3.18
72 73 0.247537 GCCGACTCGCATTTTAACGG 60.248 55.000 0.00 0.00 41.44 4.44
73 74 1.073177 CCGACTCGCATTTTAACGGT 58.927 50.000 0.00 0.00 35.21 4.83
74 75 1.461897 CCGACTCGCATTTTAACGGTT 59.538 47.619 0.00 0.00 35.21 4.44
75 76 2.667481 CCGACTCGCATTTTAACGGTTA 59.333 45.455 0.00 0.00 35.21 2.85
76 77 3.307782 CCGACTCGCATTTTAACGGTTAT 59.692 43.478 0.73 0.00 35.21 1.89
77 78 4.201744 CCGACTCGCATTTTAACGGTTATT 60.202 41.667 0.73 0.00 35.21 1.40
78 79 5.318349 CGACTCGCATTTTAACGGTTATTT 58.682 37.500 0.73 0.00 0.00 1.40
79 80 5.791480 CGACTCGCATTTTAACGGTTATTTT 59.209 36.000 0.73 0.00 0.00 1.82
80 81 6.236838 CGACTCGCATTTTAACGGTTATTTTG 60.237 38.462 0.73 1.57 0.00 2.44
81 82 5.343860 ACTCGCATTTTAACGGTTATTTTGC 59.656 36.000 14.44 14.44 0.00 3.68
82 83 5.220381 TCGCATTTTAACGGTTATTTTGCA 58.780 33.333 19.96 10.70 0.00 4.08
83 84 5.343593 TCGCATTTTAACGGTTATTTTGCAG 59.656 36.000 19.96 15.16 0.00 4.41
84 85 5.343593 CGCATTTTAACGGTTATTTTGCAGA 59.656 36.000 19.96 0.00 0.00 4.26
85 86 6.034470 CGCATTTTAACGGTTATTTTGCAGAT 59.966 34.615 19.96 0.00 0.00 2.90
86 87 7.391016 GCATTTTAACGGTTATTTTGCAGATC 58.609 34.615 17.36 0.00 0.00 2.75
87 88 7.600039 CATTTTAACGGTTATTTTGCAGATCG 58.400 34.615 0.73 0.00 0.00 3.69
88 89 3.757745 AACGGTTATTTTGCAGATCGG 57.242 42.857 0.00 0.00 0.00 4.18
89 90 2.980568 ACGGTTATTTTGCAGATCGGA 58.019 42.857 0.00 0.00 0.00 4.55
90 91 2.936498 ACGGTTATTTTGCAGATCGGAG 59.064 45.455 0.00 0.00 0.00 4.63
91 92 2.286418 CGGTTATTTTGCAGATCGGAGC 60.286 50.000 0.00 0.00 0.00 4.70
92 93 2.945668 GGTTATTTTGCAGATCGGAGCT 59.054 45.455 0.00 0.00 0.00 4.09
93 94 3.378427 GGTTATTTTGCAGATCGGAGCTT 59.622 43.478 0.00 0.00 0.00 3.74
94 95 4.142381 GGTTATTTTGCAGATCGGAGCTTT 60.142 41.667 0.00 0.00 0.00 3.51
95 96 5.402398 GTTATTTTGCAGATCGGAGCTTTT 58.598 37.500 0.00 0.00 0.00 2.27
96 97 4.525912 ATTTTGCAGATCGGAGCTTTTT 57.474 36.364 0.00 0.00 0.00 1.94
97 98 2.995466 TTGCAGATCGGAGCTTTTTG 57.005 45.000 0.00 0.00 0.00 2.44
98 99 0.523072 TGCAGATCGGAGCTTTTTGC 59.477 50.000 0.00 0.00 43.29 3.68
99 100 0.523072 GCAGATCGGAGCTTTTTGCA 59.477 50.000 0.00 0.00 45.94 4.08
100 101 1.467035 GCAGATCGGAGCTTTTTGCAG 60.467 52.381 0.00 0.00 45.94 4.41
101 102 1.131883 CAGATCGGAGCTTTTTGCAGG 59.868 52.381 0.00 0.00 45.94 4.85
102 103 0.453390 GATCGGAGCTTTTTGCAGGG 59.547 55.000 0.00 0.00 45.94 4.45
103 104 0.251341 ATCGGAGCTTTTTGCAGGGT 60.251 50.000 0.00 0.00 45.94 4.34
104 105 0.889186 TCGGAGCTTTTTGCAGGGTC 60.889 55.000 0.00 0.00 45.94 4.46
105 106 0.890996 CGGAGCTTTTTGCAGGGTCT 60.891 55.000 0.00 0.00 45.94 3.85
106 107 0.600057 GGAGCTTTTTGCAGGGTCTG 59.400 55.000 0.00 0.00 45.94 3.51
122 123 3.602390 GTCTGCTAGAGACGCTCTTAG 57.398 52.381 13.34 10.22 41.91 2.18
149 150 8.976986 AAGTTATACTACGAACTGGTACTTTG 57.023 34.615 0.00 0.00 36.05 2.77
162 163 8.611051 AACTGGTACTTTGAAGGATCTACTAT 57.389 34.615 0.00 0.00 0.00 2.12
170 171 9.751542 ACTTTGAAGGATCTACTATTTGTATCG 57.248 33.333 0.00 0.00 0.00 2.92
310 311 2.614057 CTGATGGGTAAGACGGCATTTC 59.386 50.000 0.00 0.00 0.00 2.17
320 321 1.129437 GACGGCATTTCTGTTCTCTGC 59.871 52.381 0.00 0.00 33.57 4.26
463 656 1.234615 TACTGCCGCAAAGCCAAGTC 61.235 55.000 0.00 0.00 0.00 3.01
517 715 2.949177 ACACCATAGAGTTGTGCCAA 57.051 45.000 0.00 0.00 33.30 4.52
530 728 4.220602 AGTTGTGCCAAAAATGGGATAGTC 59.779 41.667 0.00 0.00 0.00 2.59
576 774 9.952030 TGGTCCCCTTCAAAAATTTATTTTATC 57.048 29.630 1.19 0.00 38.92 1.75
657 855 2.029828 GGTAGATAGAGCACGGGACATG 60.030 54.545 0.00 0.00 0.00 3.21
674 872 2.616256 ACATGCATGTACAGGACACTGG 60.616 50.000 30.50 0.00 42.17 4.00
705 903 6.127647 TGCTCTTTTGGTTATGGTGATCATTC 60.128 38.462 0.00 0.00 37.30 2.67
735 933 7.340487 GGAAAATGAGGATTGGTTTAGACTGAT 59.660 37.037 0.00 0.00 0.00 2.90
768 966 5.138125 ACCTTGTGTGAAATTAAGGCATG 57.862 39.130 0.00 0.00 42.66 4.06
875 1073 3.338250 TGAGGCCACCCCATCCAC 61.338 66.667 5.01 0.00 35.39 4.02
889 1087 2.099098 CCATCCACGGGAAATGCTAAAC 59.901 50.000 0.00 0.00 34.34 2.01
914 1112 0.249868 TCACCAAGCAACTCACTCCG 60.250 55.000 0.00 0.00 0.00 4.63
919 1117 2.099098 CCAAGCAACTCACTCCGTTTTT 59.901 45.455 0.00 0.00 0.00 1.94
988 1190 6.136541 ACAAGTGACAAGGAAATCAAGAAC 57.863 37.500 0.00 0.00 0.00 3.01
1116 1321 3.699538 TCACGATATCCAACTACTGCACT 59.300 43.478 0.00 0.00 0.00 4.40
1185 1390 2.283388 ACGACGGGGTTCAGGCTA 60.283 61.111 0.00 0.00 0.00 3.93
1191 1396 3.321445 GGGTTCAGGCTAGACCCC 58.679 66.667 21.24 13.14 40.58 4.95
1556 1776 6.304356 GCATGTAGCATAACTATGAAGCAA 57.696 37.500 0.77 0.00 44.79 3.91
1583 1822 4.522789 TGCAGAAGTGTATACTCTGACACA 59.477 41.667 19.54 8.99 46.83 3.72
1586 1825 6.915300 GCAGAAGTGTATACTCTGACACATAG 59.085 42.308 19.54 3.70 46.83 2.23
1732 1975 4.409218 TACGCGACGCCAGACACC 62.409 66.667 15.93 0.00 0.00 4.16
1849 2092 1.933041 CGTCGACTACACCATCGCG 60.933 63.158 14.70 0.00 38.24 5.87
1874 2117 2.686106 TCCCTCCAGCCGGGTAAC 60.686 66.667 5.47 0.00 42.56 2.50
1890 2158 2.347452 GGTAACCAATCACGTCGACATG 59.653 50.000 17.16 11.43 0.00 3.21
1926 2194 7.596995 GCAATTTGCAACCAGTAGTAATTAACA 59.403 33.333 16.35 0.00 44.26 2.41
1927 2195 9.638239 CAATTTGCAACCAGTAGTAATTAACAT 57.362 29.630 0.00 0.00 0.00 2.71
1930 2198 7.151999 TGCAACCAGTAGTAATTAACATTGG 57.848 36.000 7.28 7.28 0.00 3.16
1932 2200 7.094549 TGCAACCAGTAGTAATTAACATTGGTC 60.095 37.037 12.44 5.31 0.00 4.02
2039 2321 7.350744 TGAAATACTGGGAATTTGATGGATG 57.649 36.000 0.00 0.00 0.00 3.51
2082 2366 0.306840 CATGCCTGCTGATGCTAACG 59.693 55.000 0.00 0.00 40.48 3.18
2172 2456 2.184579 GGAGCGTCTACCAGCCAC 59.815 66.667 0.00 0.00 0.00 5.01
2195 2479 0.527565 CTGCAGGTAACAATGGTGCC 59.472 55.000 5.57 0.00 41.41 5.01
2213 2497 2.125106 GGAAGTGCCTACCAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
2469 2753 5.617609 CGCTCGTGTTCTTTAAATGATCAA 58.382 37.500 0.00 0.00 0.00 2.57
2520 2804 4.459089 AGCCGGCCTTCGAGCTTC 62.459 66.667 26.15 0.00 40.60 3.86
2528 2812 1.470979 GCCTTCGAGCTTCCGAATACA 60.471 52.381 10.30 0.00 45.85 2.29
2630 2916 6.451393 AGTTTCTGACAGATTCACAGTAGTC 58.549 40.000 5.87 0.00 33.93 2.59
2638 2934 5.161358 CAGATTCACAGTAGTCGCAACTTA 58.839 41.667 0.00 0.00 36.92 2.24
2681 2977 3.954904 ACTAGATAGTACTGGTGGTGCAG 59.045 47.826 5.39 0.00 34.13 4.41
2716 3012 9.193806 AGATGTAAATATTGGCTTCTTTCATGT 57.806 29.630 0.00 0.00 0.00 3.21
2719 3015 9.679661 TGTAAATATTGGCTTCTTTCATGTAGA 57.320 29.630 0.00 0.00 0.00 2.59
2738 3034 8.607459 CATGTAGACCAACAATGAAATCTACTC 58.393 37.037 9.81 0.00 37.29 2.59
2739 3035 7.103641 TGTAGACCAACAATGAAATCTACTCC 58.896 38.462 9.81 0.00 37.29 3.85
2740 3036 6.126863 AGACCAACAATGAAATCTACTCCA 57.873 37.500 0.00 0.00 0.00 3.86
2741 3037 6.176183 AGACCAACAATGAAATCTACTCCAG 58.824 40.000 0.00 0.00 0.00 3.86
2742 3038 5.880901 ACCAACAATGAAATCTACTCCAGT 58.119 37.500 0.00 0.00 0.00 4.00
2853 3151 2.094762 AGCACTGTCGGGTGATAAAC 57.905 50.000 7.94 0.00 39.34 2.01
2877 3175 6.990939 ACCTTCTCCTTTTTCTGTAGTGTTAC 59.009 38.462 0.00 0.00 0.00 2.50
2900 3200 6.002062 CGATAGTTTGAATTGAATAGCCCC 57.998 41.667 0.00 0.00 0.00 5.80
2946 3246 4.697514 TCATCCCAAGAAATCTGACGATC 58.302 43.478 0.00 0.00 0.00 3.69
2948 3248 4.551702 TCCCAAGAAATCTGACGATCAA 57.448 40.909 0.00 0.00 0.00 2.57
2950 3250 4.695455 TCCCAAGAAATCTGACGATCAAAC 59.305 41.667 0.00 0.00 0.00 2.93
2953 3253 6.437928 CCAAGAAATCTGACGATCAAACAAA 58.562 36.000 0.00 0.00 0.00 2.83
2954 3254 6.360681 CCAAGAAATCTGACGATCAAACAAAC 59.639 38.462 0.00 0.00 0.00 2.93
2956 3256 7.026631 AGAAATCTGACGATCAAACAAACAA 57.973 32.000 0.00 0.00 0.00 2.83
2957 3257 7.134815 AGAAATCTGACGATCAAACAAACAAG 58.865 34.615 0.00 0.00 0.00 3.16
2962 3263 6.966632 TCTGACGATCAAACAAACAAGAAAAG 59.033 34.615 0.00 0.00 0.00 2.27
2977 3278 3.157881 AGAAAAGGAAGCAACTAAGGGC 58.842 45.455 0.00 0.00 0.00 5.19
2992 3293 1.527457 AGGGCCTCTTTGGATAGCAT 58.473 50.000 0.00 0.00 38.35 3.79
2997 3298 4.835056 GGGCCTCTTTGGATAGCATAAAAT 59.165 41.667 0.84 0.00 38.35 1.82
2998 3299 5.047731 GGGCCTCTTTGGATAGCATAAAATC 60.048 44.000 0.84 0.00 38.35 2.17
2999 3300 5.772169 GGCCTCTTTGGATAGCATAAAATCT 59.228 40.000 0.00 0.00 38.35 2.40
3000 3301 6.072230 GGCCTCTTTGGATAGCATAAAATCTC 60.072 42.308 0.00 0.00 38.35 2.75
3003 3304 9.075678 CCTCTTTGGATAGCATAAAATCTCAAT 57.924 33.333 0.00 0.00 38.35 2.57
3013 3314 8.193250 AGCATAAAATCTCAATTGAAATGTGC 57.807 30.769 9.88 12.60 0.00 4.57
3014 3315 8.038944 AGCATAAAATCTCAATTGAAATGTGCT 58.961 29.630 9.88 14.32 0.00 4.40
3015 3316 9.304731 GCATAAAATCTCAATTGAAATGTGCTA 57.695 29.630 9.88 0.00 0.00 3.49
3019 3320 9.985730 AAAATCTCAATTGAAATGTGCTAAGAA 57.014 25.926 9.88 0.00 0.00 2.52
3020 3321 9.985730 AAATCTCAATTGAAATGTGCTAAGAAA 57.014 25.926 9.88 0.00 0.00 2.52
3058 3529 3.815401 CCGGAACATGACTTATGGATTCC 59.185 47.826 0.00 0.00 41.25 3.01
3063 3534 6.708054 GGAACATGACTTATGGATTCCTACAG 59.292 42.308 0.00 0.00 41.25 2.74
3068 3539 5.598830 TGACTTATGGATTCCTACAGGACTC 59.401 44.000 3.95 7.01 45.39 3.36
3071 3542 2.656002 TGGATTCCTACAGGACTCGAG 58.344 52.381 11.84 11.84 45.39 4.04
3081 3552 0.605589 AGGACTCGAGGCACAAGAAG 59.394 55.000 22.31 0.00 0.00 2.85
3082 3553 0.318762 GGACTCGAGGCACAAGAAGT 59.681 55.000 22.31 0.00 0.00 3.01
3120 3591 5.608437 TGCCTAAGGATGGATCACTAGAAAT 59.392 40.000 0.00 0.00 0.00 2.17
3121 3592 6.787458 TGCCTAAGGATGGATCACTAGAAATA 59.213 38.462 0.00 0.00 0.00 1.40
3126 3597 8.970859 AAGGATGGATCACTAGAAATAAACAG 57.029 34.615 0.00 0.00 0.00 3.16
3266 3737 0.253044 GTCACAGGATTGCTGGCCTA 59.747 55.000 10.12 0.00 32.03 3.93
3284 3755 1.133025 CTAGCCAAAATCCAGCAACCG 59.867 52.381 0.00 0.00 0.00 4.44
3326 3797 5.765677 GGGCTCTTATAGGGAAAGAAATCAC 59.234 44.000 0.00 0.00 32.77 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.038080 GAACAGGCCCCGCAAACG 62.038 66.667 0.00 0.00 39.67 3.60
20 21 4.038080 CGAACAGGCCCCGCAAAC 62.038 66.667 0.00 0.00 0.00 2.93
30 31 1.654023 GAAAATCCCGCCCGAACAGG 61.654 60.000 0.00 0.00 40.63 4.00
31 32 0.958382 TGAAAATCCCGCCCGAACAG 60.958 55.000 0.00 0.00 0.00 3.16
32 33 0.958382 CTGAAAATCCCGCCCGAACA 60.958 55.000 0.00 0.00 0.00 3.18
33 34 1.800681 CTGAAAATCCCGCCCGAAC 59.199 57.895 0.00 0.00 0.00 3.95
34 35 2.043980 GCTGAAAATCCCGCCCGAA 61.044 57.895 0.00 0.00 0.00 4.30
35 36 2.437716 GCTGAAAATCCCGCCCGA 60.438 61.111 0.00 0.00 0.00 5.14
36 37 3.876198 CGCTGAAAATCCCGCCCG 61.876 66.667 0.00 0.00 0.00 6.13
37 38 4.193334 GCGCTGAAAATCCCGCCC 62.193 66.667 0.00 0.00 40.51 6.13
39 40 4.536687 CGGCGCTGAAAATCCCGC 62.537 66.667 11.90 0.00 45.15 6.13
40 41 2.817834 TCGGCGCTGAAAATCCCG 60.818 61.111 18.55 3.13 40.25 5.14
41 42 1.706287 GAGTCGGCGCTGAAAATCCC 61.706 60.000 22.89 7.39 0.00 3.85
42 43 1.716172 GAGTCGGCGCTGAAAATCC 59.284 57.895 22.89 8.21 0.00 3.01
43 44 1.345176 CGAGTCGGCGCTGAAAATC 59.655 57.895 22.89 17.63 0.00 2.17
44 45 3.474806 CGAGTCGGCGCTGAAAAT 58.525 55.556 22.89 10.23 0.00 1.82
52 53 0.583083 CGTTAAAATGCGAGTCGGCG 60.583 55.000 15.52 0.00 35.06 6.46
53 54 0.247537 CCGTTAAAATGCGAGTCGGC 60.248 55.000 15.52 7.33 0.00 5.54
54 55 1.073177 ACCGTTAAAATGCGAGTCGG 58.927 50.000 15.52 0.00 41.77 4.79
55 56 2.867456 AACCGTTAAAATGCGAGTCG 57.133 45.000 8.54 8.54 0.00 4.18
56 57 6.451960 GCAAAATAACCGTTAAAATGCGAGTC 60.452 38.462 8.75 0.00 0.00 3.36
57 58 5.343860 GCAAAATAACCGTTAAAATGCGAGT 59.656 36.000 8.75 0.00 0.00 4.18
58 59 5.343593 TGCAAAATAACCGTTAAAATGCGAG 59.656 36.000 15.16 0.00 34.16 5.03
59 60 5.220381 TGCAAAATAACCGTTAAAATGCGA 58.780 33.333 15.16 7.03 34.16 5.10
60 61 5.343593 TCTGCAAAATAACCGTTAAAATGCG 59.656 36.000 15.16 11.84 34.16 4.73
61 62 6.698359 TCTGCAAAATAACCGTTAAAATGC 57.302 33.333 14.09 14.09 0.00 3.56
62 63 7.253618 CCGATCTGCAAAATAACCGTTAAAATG 60.254 37.037 0.00 0.00 0.00 2.32
63 64 6.750039 CCGATCTGCAAAATAACCGTTAAAAT 59.250 34.615 0.00 0.00 0.00 1.82
64 65 6.072618 TCCGATCTGCAAAATAACCGTTAAAA 60.073 34.615 0.00 0.00 0.00 1.52
65 66 5.411977 TCCGATCTGCAAAATAACCGTTAAA 59.588 36.000 0.00 0.00 0.00 1.52
66 67 4.936411 TCCGATCTGCAAAATAACCGTTAA 59.064 37.500 0.00 0.00 0.00 2.01
67 68 4.505808 TCCGATCTGCAAAATAACCGTTA 58.494 39.130 0.00 0.00 0.00 3.18
68 69 3.340034 TCCGATCTGCAAAATAACCGTT 58.660 40.909 0.00 0.00 0.00 4.44
69 70 2.936498 CTCCGATCTGCAAAATAACCGT 59.064 45.455 0.00 0.00 0.00 4.83
70 71 2.286418 GCTCCGATCTGCAAAATAACCG 60.286 50.000 0.00 0.00 0.00 4.44
71 72 2.945668 AGCTCCGATCTGCAAAATAACC 59.054 45.455 0.00 0.00 0.00 2.85
72 73 4.622701 AAGCTCCGATCTGCAAAATAAC 57.377 40.909 0.00 0.00 0.00 1.89
73 74 5.643379 AAAAGCTCCGATCTGCAAAATAA 57.357 34.783 0.00 0.00 0.00 1.40
74 75 5.401550 CAAAAAGCTCCGATCTGCAAAATA 58.598 37.500 0.00 0.00 0.00 1.40
75 76 4.240096 CAAAAAGCTCCGATCTGCAAAAT 58.760 39.130 0.00 0.00 0.00 1.82
76 77 3.641648 CAAAAAGCTCCGATCTGCAAAA 58.358 40.909 0.00 0.00 0.00 2.44
77 78 2.607771 GCAAAAAGCTCCGATCTGCAAA 60.608 45.455 0.00 0.00 41.15 3.68
78 79 1.068333 GCAAAAAGCTCCGATCTGCAA 60.068 47.619 0.00 0.00 41.15 4.08
79 80 0.523072 GCAAAAAGCTCCGATCTGCA 59.477 50.000 0.00 0.00 41.15 4.41
80 81 0.523072 TGCAAAAAGCTCCGATCTGC 59.477 50.000 0.00 0.00 45.94 4.26
81 82 1.131883 CCTGCAAAAAGCTCCGATCTG 59.868 52.381 0.00 0.00 45.94 2.90
82 83 1.457346 CCTGCAAAAAGCTCCGATCT 58.543 50.000 0.00 0.00 45.94 2.75
83 84 0.453390 CCCTGCAAAAAGCTCCGATC 59.547 55.000 0.00 0.00 45.94 3.69
84 85 0.251341 ACCCTGCAAAAAGCTCCGAT 60.251 50.000 0.00 0.00 45.94 4.18
85 86 0.889186 GACCCTGCAAAAAGCTCCGA 60.889 55.000 0.00 0.00 45.94 4.55
86 87 0.890996 AGACCCTGCAAAAAGCTCCG 60.891 55.000 0.00 0.00 45.94 4.63
87 88 0.600057 CAGACCCTGCAAAAAGCTCC 59.400 55.000 0.00 0.00 45.94 4.70
103 104 3.545366 TCTAAGAGCGTCTCTAGCAGA 57.455 47.619 9.33 9.46 40.28 4.26
104 105 4.095782 ACTTTCTAAGAGCGTCTCTAGCAG 59.904 45.833 9.33 7.77 40.28 4.24
105 106 4.011023 ACTTTCTAAGAGCGTCTCTAGCA 58.989 43.478 9.33 0.00 40.28 3.49
106 107 4.625972 ACTTTCTAAGAGCGTCTCTAGC 57.374 45.455 9.33 0.00 40.28 3.42
107 108 9.048446 AGTATAACTTTCTAAGAGCGTCTCTAG 57.952 37.037 9.33 6.09 40.28 2.43
108 109 8.961294 AGTATAACTTTCTAAGAGCGTCTCTA 57.039 34.615 9.33 0.00 40.28 2.43
109 110 7.868906 AGTATAACTTTCTAAGAGCGTCTCT 57.131 36.000 3.88 3.88 43.37 3.10
110 111 7.793427 CGTAGTATAACTTTCTAAGAGCGTCTC 59.207 40.741 0.00 0.00 0.00 3.36
111 112 7.493971 TCGTAGTATAACTTTCTAAGAGCGTCT 59.506 37.037 0.00 0.00 0.00 4.18
112 113 7.625553 TCGTAGTATAACTTTCTAAGAGCGTC 58.374 38.462 0.00 0.00 0.00 5.19
113 114 7.545362 TCGTAGTATAACTTTCTAAGAGCGT 57.455 36.000 0.00 0.00 0.00 5.07
114 115 8.121708 AGTTCGTAGTATAACTTTCTAAGAGCG 58.878 37.037 0.00 0.00 32.00 5.03
115 116 9.224058 CAGTTCGTAGTATAACTTTCTAAGAGC 57.776 37.037 0.00 0.00 33.72 4.09
116 117 9.719279 CCAGTTCGTAGTATAACTTTCTAAGAG 57.281 37.037 0.00 0.00 33.72 2.85
117 118 9.236006 ACCAGTTCGTAGTATAACTTTCTAAGA 57.764 33.333 0.00 0.00 33.72 2.10
120 121 9.672673 AGTACCAGTTCGTAGTATAACTTTCTA 57.327 33.333 0.00 0.00 33.72 2.10
121 122 8.572855 AGTACCAGTTCGTAGTATAACTTTCT 57.427 34.615 0.00 0.00 33.72 2.52
122 123 9.631452 AAAGTACCAGTTCGTAGTATAACTTTC 57.369 33.333 0.00 0.00 33.72 2.62
149 150 8.569641 ACTCACGATACAAATAGTAGATCCTTC 58.430 37.037 0.00 0.00 35.85 3.46
162 163 4.870991 TGTGTCACAAACTCACGATACAAA 59.129 37.500 2.31 0.00 35.20 2.83
168 169 2.951457 TCTGTGTCACAAACTCACGA 57.049 45.000 7.18 0.00 35.20 4.35
169 170 2.348872 GCATCTGTGTCACAAACTCACG 60.349 50.000 7.18 0.00 35.20 4.35
170 171 2.874701 AGCATCTGTGTCACAAACTCAC 59.125 45.455 7.18 0.00 0.00 3.51
463 656 2.787473 TCAGGGGATGTAAACTGCAG 57.213 50.000 13.48 13.48 0.00 4.41
517 715 5.041191 AGAGCATTCGACTATCCCATTTT 57.959 39.130 0.00 0.00 0.00 1.82
530 728 6.369059 ACCATTCTCAAATTAGAGCATTCG 57.631 37.500 0.00 0.00 35.59 3.34
576 774 3.688185 CAGTCCACATTGACCAATCTCAG 59.312 47.826 0.00 0.00 35.83 3.35
657 855 0.036010 AGCCAGTGTCCTGTACATGC 60.036 55.000 0.00 0.00 41.10 4.06
674 872 4.082026 ACCATAACCAAAAGAGCATTGAGC 60.082 41.667 0.00 0.00 46.19 4.26
705 903 8.624776 GTCTAAACCAATCCTCATTTTCCATAG 58.375 37.037 0.00 0.00 0.00 2.23
875 1073 3.694072 TGAGATTGGTTTAGCATTTCCCG 59.306 43.478 0.00 0.00 0.00 5.14
889 1087 2.227388 GTGAGTTGCTTGGTGAGATTGG 59.773 50.000 0.00 0.00 0.00 3.16
919 1117 0.250945 TAATGCCGTGCAGGGTTCAA 60.251 50.000 25.40 10.43 43.65 2.69
988 1190 0.747283 GCCTCCATGGTCTTGAGCTG 60.747 60.000 12.58 0.00 38.35 4.24
1062 1267 1.080501 CGTCGAGACACTGCACCAT 60.081 57.895 4.02 0.00 0.00 3.55
1098 1303 4.806247 GTGTGAGTGCAGTAGTTGGATATC 59.194 45.833 0.00 0.00 0.00 1.63
1116 1321 3.716195 CCCGGCCAGATGGTGTGA 61.716 66.667 2.24 0.00 37.57 3.58
1556 1776 5.124776 GTCAGAGTATACACTTCTGCAGAGT 59.875 44.000 17.43 14.00 34.21 3.24
1573 1812 4.459337 TGATTGTCGTCTATGTGTCAGAGT 59.541 41.667 0.00 0.00 0.00 3.24
1583 1822 5.660460 TGCAGTAACATGATTGTCGTCTAT 58.340 37.500 0.00 0.00 34.06 1.98
1586 1825 3.484229 GCTGCAGTAACATGATTGTCGTC 60.484 47.826 16.64 0.00 34.06 4.20
1726 1969 4.008933 GTCGGGCTGCAGGTGTCT 62.009 66.667 17.12 0.00 0.00 3.41
1849 2092 2.270527 GCTGGAGGGAGGCAGAAC 59.729 66.667 0.00 0.00 0.00 3.01
1874 2117 3.125146 ACATTTCATGTCGACGTGATTGG 59.875 43.478 34.40 27.12 39.92 3.16
1910 2178 5.583457 GCGACCAATGTTAATTACTACTGGT 59.417 40.000 7.78 7.78 36.79 4.00
1917 2185 7.008266 CACATTTCAGCGACCAATGTTAATTAC 59.992 37.037 4.46 0.00 38.75 1.89
1918 2186 7.026562 CACATTTCAGCGACCAATGTTAATTA 58.973 34.615 4.46 0.00 38.75 1.40
1919 2187 5.863397 CACATTTCAGCGACCAATGTTAATT 59.137 36.000 4.46 0.00 38.75 1.40
1926 2194 1.538047 AGCACATTTCAGCGACCAAT 58.462 45.000 0.00 0.00 35.48 3.16
1927 2195 1.266718 GAAGCACATTTCAGCGACCAA 59.733 47.619 0.00 0.00 35.48 3.67
1930 2198 1.800586 TCAGAAGCACATTTCAGCGAC 59.199 47.619 0.00 0.00 35.48 5.19
1932 2200 2.975410 TTCAGAAGCACATTTCAGCG 57.025 45.000 0.00 0.00 35.48 5.18
1967 2249 2.270275 TGTTGAAGTTTGGCACGTTG 57.730 45.000 0.00 0.00 0.00 4.10
2039 2321 0.110486 ACCTGTGTGAACCATGGGTC 59.890 55.000 23.74 23.74 33.12 4.46
2082 2366 2.116983 TTGTCAGCAGGAGGAGCACC 62.117 60.000 0.00 0.00 0.00 5.01
2156 2440 2.184579 GGTGGCTGGTAGACGCTC 59.815 66.667 0.00 0.00 33.29 5.03
2160 2444 2.285442 AGGGGGTGGCTGGTAGAC 60.285 66.667 0.00 0.00 0.00 2.59
2172 2456 0.684153 CCATTGTTACCTGCAGGGGG 60.684 60.000 35.42 19.68 40.27 5.40
2279 2563 0.601558 GTGTCTCGTAGGTGCTTCCA 59.398 55.000 1.79 0.00 39.02 3.53
2469 2753 0.106318 GGCTGGCCTTTCATGGAGAT 60.106 55.000 3.32 0.00 0.00 2.75
2520 2804 3.769739 TCCAATCCCTCATGTATTCGG 57.230 47.619 0.00 0.00 0.00 4.30
2528 2812 4.018597 GCCTAAGATCATCCAATCCCTCAT 60.019 45.833 0.00 0.00 0.00 2.90
2630 2916 2.227194 ACAGGAGGGTTTTAAGTTGCG 58.773 47.619 0.00 0.00 0.00 4.85
2681 2977 5.185828 GCCAATATTTACATCTCCCCCAATC 59.814 44.000 0.00 0.00 0.00 2.67
2716 3012 7.038302 ACTGGAGTAGATTTCATTGTTGGTCTA 60.038 37.037 0.00 0.00 0.00 2.59
2719 3015 5.880901 ACTGGAGTAGATTTCATTGTTGGT 58.119 37.500 0.00 0.00 0.00 3.67
2810 3106 8.300286 GCTAAAGTTCCTAAAAGCAGAGAAATT 58.700 33.333 0.00 0.00 0.00 1.82
2812 3108 6.770785 TGCTAAAGTTCCTAAAAGCAGAGAAA 59.229 34.615 0.00 0.00 35.20 2.52
2813 3109 6.204882 GTGCTAAAGTTCCTAAAAGCAGAGAA 59.795 38.462 0.00 0.00 40.36 2.87
2814 3110 5.701290 GTGCTAAAGTTCCTAAAAGCAGAGA 59.299 40.000 0.00 0.00 40.36 3.10
2815 3111 5.703130 AGTGCTAAAGTTCCTAAAAGCAGAG 59.297 40.000 0.00 0.00 40.36 3.35
2816 3112 5.470098 CAGTGCTAAAGTTCCTAAAAGCAGA 59.530 40.000 0.00 0.00 40.36 4.26
2817 3113 5.239525 ACAGTGCTAAAGTTCCTAAAAGCAG 59.760 40.000 0.00 0.00 40.36 4.24
2818 3114 5.130350 ACAGTGCTAAAGTTCCTAAAAGCA 58.870 37.500 0.00 0.00 37.62 3.91
2853 3151 6.145696 CGTAACACTACAGAAAAAGGAGAAGG 59.854 42.308 0.00 0.00 0.00 3.46
2865 3163 9.135843 CAATTCAAACTATCGTAACACTACAGA 57.864 33.333 0.00 0.00 0.00 3.41
2877 3175 5.530915 TGGGGCTATTCAATTCAAACTATCG 59.469 40.000 0.00 0.00 0.00 2.92
2942 3242 6.291796 GCTTCCTTTTCTTGTTTGTTTGATCG 60.292 38.462 0.00 0.00 0.00 3.69
2946 3246 6.147656 AGTTGCTTCCTTTTCTTGTTTGTTTG 59.852 34.615 0.00 0.00 0.00 2.93
2948 3248 5.793817 AGTTGCTTCCTTTTCTTGTTTGTT 58.206 33.333 0.00 0.00 0.00 2.83
2950 3250 6.476706 CCTTAGTTGCTTCCTTTTCTTGTTTG 59.523 38.462 0.00 0.00 0.00 2.93
2953 3253 4.584743 CCCTTAGTTGCTTCCTTTTCTTGT 59.415 41.667 0.00 0.00 0.00 3.16
2954 3254 4.559502 GCCCTTAGTTGCTTCCTTTTCTTG 60.560 45.833 0.00 0.00 0.00 3.02
2956 3256 3.157881 GCCCTTAGTTGCTTCCTTTTCT 58.842 45.455 0.00 0.00 0.00 2.52
2957 3257 2.231478 GGCCCTTAGTTGCTTCCTTTTC 59.769 50.000 0.00 0.00 0.00 2.29
2962 3263 0.621082 AGAGGCCCTTAGTTGCTTCC 59.379 55.000 0.00 0.00 34.42 3.46
2977 3278 8.455903 TTGAGATTTTATGCTATCCAAAGAGG 57.544 34.615 0.00 0.00 39.47 3.69
3021 3322 9.754382 GTCATGTTCCGGTATTATTTTCTACTA 57.246 33.333 0.00 0.00 0.00 1.82
3022 3323 8.483758 AGTCATGTTCCGGTATTATTTTCTACT 58.516 33.333 0.00 0.00 0.00 2.57
3023 3324 8.658499 AGTCATGTTCCGGTATTATTTTCTAC 57.342 34.615 0.00 0.00 0.00 2.59
3035 3336 4.451900 GAATCCATAAGTCATGTTCCGGT 58.548 43.478 0.00 0.00 32.21 5.28
3037 3338 4.708177 AGGAATCCATAAGTCATGTTCCG 58.292 43.478 0.61 0.00 41.48 4.30
3038 3339 6.591935 TGTAGGAATCCATAAGTCATGTTCC 58.408 40.000 0.61 0.00 38.91 3.62
3039 3340 6.708054 CCTGTAGGAATCCATAAGTCATGTTC 59.292 42.308 0.61 0.00 37.39 3.18
3041 3342 5.905331 TCCTGTAGGAATCCATAAGTCATGT 59.095 40.000 0.61 0.00 42.18 3.21
3058 3529 0.888619 TTGTGCCTCGAGTCCTGTAG 59.111 55.000 12.31 0.00 0.00 2.74
3063 3534 0.318762 ACTTCTTGTGCCTCGAGTCC 59.681 55.000 12.31 2.40 0.00 3.85
3102 3573 8.324191 TCTGTTTATTTCTAGTGATCCATCCT 57.676 34.615 0.00 0.00 0.00 3.24
3104 3575 8.424918 TCCTCTGTTTATTTCTAGTGATCCATC 58.575 37.037 0.00 0.00 0.00 3.51
3120 3591 7.394359 CCCATTTCTCTGAAATTCCTCTGTTTA 59.606 37.037 3.13 0.00 0.00 2.01
3121 3592 6.210185 CCCATTTCTCTGAAATTCCTCTGTTT 59.790 38.462 3.13 0.00 0.00 2.83
3126 3597 4.860022 TCCCCATTTCTCTGAAATTCCTC 58.140 43.478 3.13 0.00 0.00 3.71
3244 3715 1.003355 CCAGCAATCCTGTGACCGT 60.003 57.895 0.00 0.00 40.06 4.83
3266 3737 1.966762 CGGTTGCTGGATTTTGGCT 59.033 52.632 0.00 0.00 0.00 4.75
3284 3755 2.485814 GCCCTTCGGATCATAGAATTGC 59.514 50.000 0.00 0.02 0.00 3.56


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

AutoCloner maintained by Alex Coulton.