Multiple sequence alignment - TraesCS1B01G097000

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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 TraesCS1B01G097000 chr1B 100.000 2158 0 0 1 2158 101234759 101232602 0.000000e+00 3986
1 TraesCS1B01G097000 chr1B 100.000 206 0 0 2491 2696 101232269 101232064 5.450000e-102 381
2 TraesCS1B01G097000 chr1B 98.837 86 1 0 258 343 101523788 101523873 1.290000e-33 154
3 TraesCS1B01G097000 chr1D 89.537 1491 102 26 616 2083 63381807 63380348 0.000000e+00 1840
4 TraesCS1B01G097000 chr1D 79.310 232 34 10 122 344 63428052 63427826 1.670000e-32 150
5 TraesCS1B01G097000 chr1A 88.475 1102 61 20 758 1839 62013960 62015015 0.000000e+00 1271
6 TraesCS1B01G097000 chr1A 92.992 371 24 2 346 715 62012869 62013238 8.490000e-150 540
7 TraesCS1B01G097000 chr1A 87.464 351 34 8 1 343 62012053 62012401 1.950000e-106 396


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 TraesCS1B01G097000 chr1B 101232064 101234759 2695 True 2183.500000 3986 100.000000 1 2696 2 chr1B.!!$R1 2695
1 TraesCS1B01G097000 chr1D 63380348 63381807 1459 True 1840.000000 1840 89.537000 616 2083 1 chr1D.!!$R1 1467
2 TraesCS1B01G097000 chr1A 62012053 62015015 2962 False 735.666667 1271 89.643667 1 1839 3 chr1A.!!$F1 1838

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
23 24 0.758734 TCAGAGGTGTTGTGGGTGAG 59.241 55.0 0.0 0.0 0.00 3.51 F
517 991 0.759060 ACCCCAAGCCTTTGACAACC 60.759 55.0 0.0 0.0 36.36 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 2364 0.669625 GGACAAGAGAACGAACCCGG 60.670 60.0 0.0 0.0 40.78 5.73 R
2115 3300 0.036010 ACAATGAGAGGCGAACAGGG 60.036 55.0 0.0 0.0 0.00 4.45 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
23 24 0.758734 TCAGAGGTGTTGTGGGTGAG 59.241 55.000 0.00 0.00 0.00 3.51
41 42 1.067821 GAGTATCTCGTGCTCCCAAGG 59.932 57.143 0.00 0.00 33.88 3.61
58 59 1.396653 AGGCTTTGGTGCTATCATGC 58.603 50.000 0.00 0.00 0.00 4.06
60 61 1.336125 GGCTTTGGTGCTATCATGCTC 59.664 52.381 0.00 0.00 0.00 4.26
65 66 2.042686 GGTGCTATCATGCTCCAACA 57.957 50.000 0.00 0.00 43.67 3.33
66 67 2.579873 GGTGCTATCATGCTCCAACAT 58.420 47.619 0.00 0.00 43.67 2.71
67 68 3.743521 GGTGCTATCATGCTCCAACATA 58.256 45.455 0.00 0.00 43.67 2.29
71 72 6.405731 GGTGCTATCATGCTCCAACATAAAAA 60.406 38.462 0.00 0.00 43.67 1.94
233 242 8.987890 TCACAAAAAGATAAAAGCTAAATTGGC 58.012 29.630 0.00 0.00 0.00 4.52
244 253 6.780457 AAGCTAAATTGGCACTATTCACAT 57.220 33.333 3.77 0.00 0.00 3.21
279 288 5.585500 TTTTTGTATCTCCGTGTCTTTCG 57.415 39.130 0.00 0.00 0.00 3.46
281 290 3.759527 TGTATCTCCGTGTCTTTCGAG 57.240 47.619 0.00 0.00 0.00 4.04
291 300 4.201783 CCGTGTCTTTCGAGTTTGAAGTTT 60.202 41.667 0.00 0.00 0.00 2.66
328 337 7.760340 GGTTTGTAAACACCTATTTTGTGAACA 59.240 33.333 9.44 0.00 40.63 3.18
329 338 9.308318 GTTTGTAAACACCTATTTTGTGAACAT 57.692 29.630 2.77 0.00 38.74 2.71
442 916 8.896320 TCTAGTTTGCTTGATGTTAGTTTGTA 57.104 30.769 0.00 0.00 0.00 2.41
479 953 4.406456 ACAATATGTCACCACCAATGTGT 58.594 39.130 0.00 0.00 41.09 3.72
483 957 3.500448 TGTCACCACCAATGTGTATGT 57.500 42.857 0.00 0.00 41.09 2.29
517 991 0.759060 ACCCCAAGCCTTTGACAACC 60.759 55.000 0.00 0.00 36.36 3.77
527 1001 3.411446 CCTTTGACAACCAGCTGTATCA 58.589 45.455 13.81 7.60 0.00 2.15
544 1018 6.695713 GCTGTATCATGAATACGTGACACTAA 59.304 38.462 0.00 0.00 43.52 2.24
631 1105 0.967662 CCAATGTGAATGTGCACCCA 59.032 50.000 15.69 6.99 37.99 4.51
673 1147 3.643763 CACGCTCACTTCACTAAAGTCT 58.356 45.455 0.00 0.00 45.28 3.24
698 1172 2.171448 GACACCCAGCTGTATCCTGATT 59.829 50.000 13.81 0.00 32.03 2.57
709 1184 6.554982 AGCTGTATCCTGATTATACCTGACAA 59.445 38.462 0.00 0.00 0.00 3.18
815 1969 3.868200 CTCCTTTTGCCCCTGCCGT 62.868 63.158 0.00 0.00 36.33 5.68
894 2048 3.346734 ACCATGCCCGTCCCCAAT 61.347 61.111 0.00 0.00 0.00 3.16
896 2050 2.834505 CATGCCCGTCCCCAATGG 60.835 66.667 0.00 0.00 0.00 3.16
897 2051 4.839706 ATGCCCGTCCCCAATGGC 62.840 66.667 0.00 0.00 44.27 4.40
921 2075 3.052082 CTCCGCTGCCCAACACAG 61.052 66.667 0.00 0.00 38.22 3.66
1045 2209 1.463214 TTGGCTCTGGGTCTGGGAA 60.463 57.895 0.00 0.00 0.00 3.97
1082 2246 4.863984 GACGTTGGTCGAGGACTC 57.136 61.111 0.00 0.00 42.86 3.36
1233 2397 2.029518 GTCCGTCCGTTCCCGTTT 59.970 61.111 0.00 0.00 0.00 3.60
1251 2415 5.061684 CCCGTTTTTGGCGATTATTCTTTTC 59.938 40.000 0.00 0.00 0.00 2.29
1252 2416 5.631512 CCGTTTTTGGCGATTATTCTTTTCA 59.368 36.000 0.00 0.00 0.00 2.69
1256 2420 9.877137 GTTTTTGGCGATTATTCTTTTCATTTT 57.123 25.926 0.00 0.00 0.00 1.82
1258 2422 9.487790 TTTTGGCGATTATTCTTTTCATTTTCT 57.512 25.926 0.00 0.00 0.00 2.52
1317 2481 2.259204 CGTGAACGGCCGAACCTA 59.741 61.111 35.90 10.30 35.61 3.08
1324 2488 1.949465 ACGGCCGAACCTATGATTTC 58.051 50.000 35.90 0.00 35.61 2.17
1692 2856 5.026462 GCAGATATTATTAGCAGCAATGCG 58.974 41.667 0.00 0.00 40.27 4.73
1741 2905 3.717400 TCAGCTATGTCGTCTTGGATC 57.283 47.619 0.00 0.00 0.00 3.36
1748 2912 2.014857 TGTCGTCTTGGATCCTCGTAG 58.985 52.381 14.23 5.45 0.00 3.51
1765 2929 4.048504 TCGTAGTATTATCGTTCGGTCGA 58.951 43.478 5.49 5.49 43.86 4.20
1771 2935 3.362581 ATCGTTCGGTCGATGCATT 57.637 47.368 0.00 0.00 46.58 3.56
1789 2957 4.761739 TGCATTTCTCCTCGAATTTTGACT 59.238 37.500 0.00 0.00 0.00 3.41
1791 2959 5.123027 GCATTTCTCCTCGAATTTTGACTCT 59.877 40.000 0.00 0.00 0.00 3.24
1823 2996 0.682292 TCAGACAACCGTATGCCACA 59.318 50.000 0.00 0.00 34.24 4.17
1832 3005 2.221169 CCGTATGCCACAATGCTGTAT 58.779 47.619 0.00 0.00 33.22 2.29
1852 3025 6.573434 TGTATATATCTCCTATTTGCCAGCG 58.427 40.000 0.00 0.00 0.00 5.18
1857 3030 3.507924 CTATTTGCCAGCGCGCCA 61.508 61.111 30.33 16.76 38.08 5.69
1878 3055 4.036734 CCATAAACATGGCAGTACACCATC 59.963 45.833 15.50 0.00 44.85 3.51
1879 3056 3.439857 AAACATGGCAGTACACCATCT 57.560 42.857 15.50 4.10 44.85 2.90
1883 3060 4.261801 ACATGGCAGTACACCATCTAAAC 58.738 43.478 15.50 0.00 44.85 2.01
1890 3067 5.568825 GCAGTACACCATCTAAACTCTTCCA 60.569 44.000 0.00 0.00 0.00 3.53
1895 3072 5.248477 ACACCATCTAAACTCTTCCAAGCTA 59.752 40.000 0.00 0.00 0.00 3.32
1896 3073 6.173339 CACCATCTAAACTCTTCCAAGCTAA 58.827 40.000 0.00 0.00 0.00 3.09
1952 3134 9.228949 CAGATTAGATTTAGCTATGCCTCATTT 57.771 33.333 0.00 0.00 0.00 2.32
1958 3140 9.061435 AGATTTAGCTATGCCTCATTTAAGTTC 57.939 33.333 0.00 0.00 0.00 3.01
1962 3144 9.712305 TTAGCTATGCCTCATTTAAGTTCTATC 57.288 33.333 0.00 0.00 0.00 2.08
1963 3145 6.870965 AGCTATGCCTCATTTAAGTTCTATCG 59.129 38.462 0.00 0.00 0.00 2.92
1964 3146 6.868864 GCTATGCCTCATTTAAGTTCTATCGA 59.131 38.462 0.00 0.00 0.00 3.59
1965 3147 7.385205 GCTATGCCTCATTTAAGTTCTATCGAA 59.615 37.037 0.00 0.00 0.00 3.71
1966 3148 9.429359 CTATGCCTCATTTAAGTTCTATCGAAT 57.571 33.333 0.00 0.00 0.00 3.34
1967 3149 7.482654 TGCCTCATTTAAGTTCTATCGAATG 57.517 36.000 0.00 0.00 0.00 2.67
1968 3150 7.272244 TGCCTCATTTAAGTTCTATCGAATGA 58.728 34.615 0.00 0.00 33.80 2.57
1969 3151 7.933577 TGCCTCATTTAAGTTCTATCGAATGAT 59.066 33.333 0.00 0.00 34.26 2.45
1970 3152 8.439286 GCCTCATTTAAGTTCTATCGAATGATC 58.561 37.037 0.00 0.00 34.26 2.92
1971 3153 9.481340 CCTCATTTAAGTTCTATCGAATGATCA 57.519 33.333 0.00 0.00 34.26 2.92
1995 3179 9.128107 TCAGATTTTCTAAATTTCGTGCAAATC 57.872 29.630 0.00 5.16 33.16 2.17
2001 3185 6.602179 TCTAAATTTCGTGCAAATCTGTGAG 58.398 36.000 0.00 0.00 33.16 3.51
2030 3214 4.437587 GCATGGGGCCTGCTGTCT 62.438 66.667 10.32 0.00 36.68 3.41
2040 3224 1.586541 CTGCTGTCTCCGTGTGCTA 59.413 57.895 0.00 0.00 0.00 3.49
2043 3227 1.424493 GCTGTCTCCGTGTGCTATGC 61.424 60.000 0.00 0.00 0.00 3.14
2056 3240 2.161609 GTGCTATGCAGGCTACGTTTTT 59.838 45.455 14.14 0.00 40.08 1.94
2083 3268 8.742777 TCTTGAAATCCGAATTGAAAGAATCAT 58.257 29.630 0.00 0.00 38.03 2.45
2084 3269 9.362539 CTTGAAATCCGAATTGAAAGAATCATT 57.637 29.630 0.00 0.00 38.03 2.57
2088 3273 9.793252 AAATCCGAATTGAAAGAATCATTAGTG 57.207 29.630 0.00 0.00 38.03 2.74
2089 3274 7.921786 TCCGAATTGAAAGAATCATTAGTGT 57.078 32.000 0.00 0.00 38.03 3.55
2090 3275 7.974675 TCCGAATTGAAAGAATCATTAGTGTC 58.025 34.615 0.00 0.00 38.03 3.67
2091 3276 7.824289 TCCGAATTGAAAGAATCATTAGTGTCT 59.176 33.333 0.00 0.00 38.03 3.41
2092 3277 9.098355 CCGAATTGAAAGAATCATTAGTGTCTA 57.902 33.333 0.00 0.00 38.03 2.59
2093 3278 9.907576 CGAATTGAAAGAATCATTAGTGTCTAC 57.092 33.333 0.00 0.00 38.03 2.59
2097 3282 8.722480 TGAAAGAATCATTAGTGTCTACATGG 57.278 34.615 0.00 0.00 31.50 3.66
2098 3283 8.539544 TGAAAGAATCATTAGTGTCTACATGGA 58.460 33.333 0.00 0.00 31.50 3.41
2099 3284 9.553064 GAAAGAATCATTAGTGTCTACATGGAT 57.447 33.333 0.00 0.00 0.00 3.41
2100 3285 9.911788 AAAGAATCATTAGTGTCTACATGGATT 57.088 29.630 0.00 0.00 0.00 3.01
2101 3286 9.911788 AAGAATCATTAGTGTCTACATGGATTT 57.088 29.630 0.00 0.00 0.00 2.17
2102 3287 9.334947 AGAATCATTAGTGTCTACATGGATTTG 57.665 33.333 0.00 0.00 0.00 2.32
2103 3288 9.113838 GAATCATTAGTGTCTACATGGATTTGT 57.886 33.333 0.00 0.00 0.00 2.83
2105 3290 8.942338 TCATTAGTGTCTACATGGATTTGTAC 57.058 34.615 0.00 0.00 0.00 2.90
2106 3291 7.985184 TCATTAGTGTCTACATGGATTTGTACC 59.015 37.037 0.00 0.00 0.00 3.34
2107 3292 5.099042 AGTGTCTACATGGATTTGTACCC 57.901 43.478 0.00 0.00 0.00 3.69
2108 3293 3.869246 GTGTCTACATGGATTTGTACCCG 59.131 47.826 0.00 0.00 0.00 5.28
2109 3294 3.118555 TGTCTACATGGATTTGTACCCGG 60.119 47.826 0.00 0.00 0.00 5.73
2110 3295 2.436542 TCTACATGGATTTGTACCCGGG 59.563 50.000 22.25 22.25 0.00 5.73
2111 3296 1.291109 ACATGGATTTGTACCCGGGA 58.709 50.000 32.02 8.25 0.00 5.14
2112 3297 1.636519 ACATGGATTTGTACCCGGGAA 59.363 47.619 32.02 11.95 0.00 3.97
2113 3298 2.243736 ACATGGATTTGTACCCGGGAAT 59.756 45.455 32.02 17.07 0.00 3.01
2114 3299 3.295973 CATGGATTTGTACCCGGGAATT 58.704 45.455 32.02 7.60 0.00 2.17
2115 3300 3.007473 TGGATTTGTACCCGGGAATTC 57.993 47.619 32.02 15.96 0.00 2.17
2116 3301 2.304092 GGATTTGTACCCGGGAATTCC 58.696 52.381 32.02 21.22 0.00 3.01
2127 3312 2.781911 GGAATTCCCTGTTCGCCTC 58.218 57.895 14.03 0.00 0.00 4.70
2128 3313 0.253327 GGAATTCCCTGTTCGCCTCT 59.747 55.000 14.03 0.00 0.00 3.69
2129 3314 1.657822 GAATTCCCTGTTCGCCTCTC 58.342 55.000 0.00 0.00 0.00 3.20
2130 3315 0.984230 AATTCCCTGTTCGCCTCTCA 59.016 50.000 0.00 0.00 0.00 3.27
2131 3316 1.207791 ATTCCCTGTTCGCCTCTCAT 58.792 50.000 0.00 0.00 0.00 2.90
2132 3317 0.984230 TTCCCTGTTCGCCTCTCATT 59.016 50.000 0.00 0.00 0.00 2.57
2133 3318 0.250234 TCCCTGTTCGCCTCTCATTG 59.750 55.000 0.00 0.00 0.00 2.82
2134 3319 0.036010 CCCTGTTCGCCTCTCATTGT 60.036 55.000 0.00 0.00 0.00 2.71
2135 3320 1.363744 CCTGTTCGCCTCTCATTGTC 58.636 55.000 0.00 0.00 0.00 3.18
2136 3321 1.066573 CCTGTTCGCCTCTCATTGTCT 60.067 52.381 0.00 0.00 0.00 3.41
2137 3322 2.266554 CTGTTCGCCTCTCATTGTCTC 58.733 52.381 0.00 0.00 0.00 3.36
2138 3323 1.272781 GTTCGCCTCTCATTGTCTCG 58.727 55.000 0.00 0.00 0.00 4.04
2139 3324 0.458543 TTCGCCTCTCATTGTCTCGC 60.459 55.000 0.00 0.00 0.00 5.03
2140 3325 2.226896 CGCCTCTCATTGTCTCGCG 61.227 63.158 0.00 0.00 0.00 5.87
2141 3326 2.520904 GCCTCTCATTGTCTCGCGC 61.521 63.158 0.00 0.00 0.00 6.86
2142 3327 1.140589 CCTCTCATTGTCTCGCGCT 59.859 57.895 5.56 0.00 0.00 5.92
2143 3328 1.144565 CCTCTCATTGTCTCGCGCTG 61.145 60.000 5.56 0.00 0.00 5.18
2144 3329 0.457509 CTCTCATTGTCTCGCGCTGT 60.458 55.000 5.56 0.00 0.00 4.40
2145 3330 0.038251 TCTCATTGTCTCGCGCTGTT 60.038 50.000 5.56 0.00 0.00 3.16
2146 3331 0.792640 CTCATTGTCTCGCGCTGTTT 59.207 50.000 5.56 0.00 0.00 2.83
2147 3332 1.195448 CTCATTGTCTCGCGCTGTTTT 59.805 47.619 5.56 0.00 0.00 2.43
2148 3333 1.601903 TCATTGTCTCGCGCTGTTTTT 59.398 42.857 5.56 0.00 0.00 1.94
2521 3706 7.865706 AGTACATGAACACTTTTTCTGAAGT 57.134 32.000 0.00 0.00 40.37 3.01
2530 3715 4.843728 ACTTTTTCTGAAGTGTGAGGACA 58.156 39.130 0.00 0.00 38.39 4.02
2547 3732 8.999431 TGTGAGGACACTTTTTAGAATTCATAC 58.001 33.333 8.44 0.00 46.07 2.39
2548 3733 8.451748 GTGAGGACACTTTTTAGAATTCATACC 58.548 37.037 8.44 0.00 42.99 2.73
2549 3734 8.383175 TGAGGACACTTTTTAGAATTCATACCT 58.617 33.333 8.44 0.00 0.00 3.08
2550 3735 9.232473 GAGGACACTTTTTAGAATTCATACCTT 57.768 33.333 8.44 0.00 0.00 3.50
2551 3736 9.588096 AGGACACTTTTTAGAATTCATACCTTT 57.412 29.630 8.44 0.00 0.00 3.11
2676 3861 9.651913 ATTTTGTTTTACAAATCTTGTGTGACT 57.348 25.926 5.88 0.00 46.17 3.41
2678 3863 9.781834 TTTGTTTTACAAATCTTGTGTGACTAG 57.218 29.630 2.30 0.00 42.55 2.57
2679 3864 8.500753 TGTTTTACAAATCTTGTGTGACTAGT 57.499 30.769 0.00 0.00 45.03 2.57
2680 3865 8.952278 TGTTTTACAAATCTTGTGTGACTAGTT 58.048 29.630 0.00 0.00 45.03 2.24
2681 3866 9.221775 GTTTTACAAATCTTGTGTGACTAGTTG 57.778 33.333 0.00 0.00 45.03 3.16
2682 3867 5.424121 ACAAATCTTGTGTGACTAGTTGC 57.576 39.130 0.00 0.00 43.48 4.17
2683 3868 4.881273 ACAAATCTTGTGTGACTAGTTGCA 59.119 37.500 0.00 0.00 43.48 4.08
2684 3869 5.532406 ACAAATCTTGTGTGACTAGTTGCAT 59.468 36.000 0.00 0.00 43.48 3.96
2685 3870 5.618056 AATCTTGTGTGACTAGTTGCATG 57.382 39.130 0.00 0.00 0.00 4.06
2686 3871 4.071961 TCTTGTGTGACTAGTTGCATGT 57.928 40.909 0.00 0.00 0.00 3.21
2687 3872 4.058124 TCTTGTGTGACTAGTTGCATGTC 58.942 43.478 0.00 0.00 0.00 3.06
2688 3873 2.766313 TGTGTGACTAGTTGCATGTCC 58.234 47.619 0.00 0.00 0.00 4.02
2689 3874 2.103941 TGTGTGACTAGTTGCATGTCCA 59.896 45.455 0.00 0.00 0.00 4.02
2690 3875 2.480419 GTGTGACTAGTTGCATGTCCAC 59.520 50.000 0.00 0.00 0.00 4.02
2691 3876 2.103941 TGTGACTAGTTGCATGTCCACA 59.896 45.455 0.00 1.00 0.00 4.17
2692 3877 3.138304 GTGACTAGTTGCATGTCCACAA 58.862 45.455 0.00 0.00 0.00 3.33
2693 3878 3.753272 GTGACTAGTTGCATGTCCACAAT 59.247 43.478 0.00 0.00 0.00 2.71
2694 3879 4.216257 GTGACTAGTTGCATGTCCACAATT 59.784 41.667 0.00 0.00 0.00 2.32
2695 3880 4.826733 TGACTAGTTGCATGTCCACAATTT 59.173 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.530870 GCCTTGGGAGCACGAGATAC 60.531 60.000 0.00 0.00 0.00 2.24
41 42 1.336125 GGAGCATGATAGCACCAAAGC 59.664 52.381 0.00 0.00 43.62 3.51
47 48 5.756195 TTTATGTTGGAGCATGATAGCAC 57.244 39.130 0.00 0.00 36.85 4.40
113 114 5.235305 ACATTTATCTTGTGAACATCCGC 57.765 39.130 0.00 0.00 0.00 5.54
209 218 8.773645 GTGCCAATTTAGCTTTTATCTTTTTGT 58.226 29.630 0.00 0.00 0.00 2.83
210 219 8.992073 AGTGCCAATTTAGCTTTTATCTTTTTG 58.008 29.630 0.00 0.00 0.00 2.44
218 227 8.116651 TGTGAATAGTGCCAATTTAGCTTTTA 57.883 30.769 0.00 0.00 0.00 1.52
227 236 8.723311 CAAATTTCAATGTGAATAGTGCCAATT 58.277 29.630 0.00 0.00 36.11 2.32
228 237 7.879160 ACAAATTTCAATGTGAATAGTGCCAAT 59.121 29.630 0.00 0.00 36.11 3.16
231 240 7.092716 AGACAAATTTCAATGTGAATAGTGCC 58.907 34.615 0.00 0.00 36.11 5.01
232 241 8.524870 AAGACAAATTTCAATGTGAATAGTGC 57.475 30.769 0.00 0.00 36.11 4.40
269 278 4.516092 AACTTCAAACTCGAAAGACACG 57.484 40.909 0.93 0.00 35.39 4.49
291 300 8.080363 AGGTGTTTACAAACCCTAAAAATTGA 57.920 30.769 11.07 0.00 37.62 2.57
406 880 9.539825 CATCAAGCAAACTAGAGTGATTACTAT 57.460 33.333 0.00 0.00 37.25 2.12
413 887 6.759272 ACTAACATCAAGCAAACTAGAGTGA 58.241 36.000 0.00 0.00 0.00 3.41
418 892 9.944663 TTTACAAACTAACATCAAGCAAACTAG 57.055 29.630 0.00 0.00 0.00 2.57
454 928 4.462483 ACATTGGTGGTGACATATTGTTCC 59.538 41.667 0.00 0.00 46.14 3.62
479 953 3.492337 GGTGAAAACTTGGGTGGACATA 58.508 45.455 0.00 0.00 0.00 2.29
483 957 0.105913 GGGGTGAAAACTTGGGTGGA 60.106 55.000 0.00 0.00 0.00 4.02
517 991 5.043248 TGTCACGTATTCATGATACAGCTG 58.957 41.667 13.48 13.48 40.58 4.24
527 1001 5.523916 GGCATCTTTAGTGTCACGTATTCAT 59.476 40.000 0.00 0.00 0.00 2.57
544 1018 4.089361 CAAGAAAAAGTAGGGGGCATCTT 58.911 43.478 0.00 0.00 0.00 2.40
596 1070 4.935702 ACATTGGTTGTGAACTTGTGATG 58.064 39.130 0.00 0.00 37.11 3.07
631 1105 4.077108 TGCAGCATCTTTGATCTGAACTT 58.923 39.130 0.00 0.00 0.00 2.66
673 1147 2.375174 AGGATACAGCTGGGTGTCAAAA 59.625 45.455 19.93 0.00 41.41 2.44
698 1172 7.311675 GGGGGCATCTTTATATTGTCAGGTATA 60.312 40.741 0.00 0.00 0.00 1.47
709 1184 3.198827 GGGGTAGGGGGCATCTTTATAT 58.801 50.000 0.00 0.00 0.00 0.86
756 1910 2.810852 CCTCCTCAAGAGAAAACTGCAC 59.189 50.000 0.00 0.00 46.50 4.57
766 1920 0.323908 ACCCTCGTCCTCCTCAAGAG 60.324 60.000 0.00 0.00 42.83 2.85
904 2058 3.052082 CTGTGTTGGGCAGCGGAG 61.052 66.667 0.00 0.00 0.00 4.63
905 2059 3.535629 CTCTGTGTTGGGCAGCGGA 62.536 63.158 0.00 0.00 34.21 5.54
921 2075 4.509737 GCGAGCCGGGGTACACTC 62.510 72.222 2.18 0.00 0.00 3.51
942 2097 3.690460 AGTGCCTCTCTGTTTTTATGGG 58.310 45.455 0.00 0.00 0.00 4.00
946 2101 2.413837 GCGAGTGCCTCTCTGTTTTTA 58.586 47.619 0.00 0.00 40.75 1.52
980 2139 3.661131 CGGGGCGATCGATCTCGT 61.661 66.667 21.57 0.00 40.73 4.18
1027 2191 1.463214 TTCCCAGACCCAGAGCCAA 60.463 57.895 0.00 0.00 0.00 4.52
1077 2241 2.126424 GCACGAGTCACCGAGTCC 60.126 66.667 0.00 0.00 0.00 3.85
1078 2242 2.502080 CGCACGAGTCACCGAGTC 60.502 66.667 0.00 0.00 0.00 3.36
1079 2243 4.039357 CCGCACGAGTCACCGAGT 62.039 66.667 0.00 0.00 0.00 4.18
1080 2244 4.778415 CCCGCACGAGTCACCGAG 62.778 72.222 0.00 0.00 0.00 4.63
1147 2311 2.456119 CGAAGAGCACGGACATGGC 61.456 63.158 0.00 0.00 0.00 4.40
1200 2364 0.669625 GGACAAGAGAACGAACCCGG 60.670 60.000 0.00 0.00 40.78 5.73
1233 2397 9.139174 GAGAAAATGAAAAGAATAATCGCCAAA 57.861 29.630 0.00 0.00 0.00 3.28
1251 2415 2.858344 AGATACGAACGCCGAGAAAATG 59.142 45.455 4.79 0.00 41.76 2.32
1252 2416 2.858344 CAGATACGAACGCCGAGAAAAT 59.142 45.455 4.79 0.00 41.76 1.82
1256 2420 1.063649 GCAGATACGAACGCCGAGA 59.936 57.895 4.79 0.00 41.76 4.04
1257 2421 1.944676 GGCAGATACGAACGCCGAG 60.945 63.158 4.79 0.00 41.76 4.63
1258 2422 2.103538 GGCAGATACGAACGCCGA 59.896 61.111 4.79 0.00 41.76 5.54
1312 2476 2.292267 CTGCGCCAGAAATCATAGGTT 58.708 47.619 4.18 0.00 32.44 3.50
1316 2480 1.159713 CGCCTGCGCCAGAAATCATA 61.160 55.000 4.18 0.00 32.44 2.15
1317 2481 2.475466 CGCCTGCGCCAGAAATCAT 61.475 57.895 4.18 0.00 32.44 2.45
1340 2504 4.175489 CGTCGACGATGTCCGCCT 62.175 66.667 33.35 0.00 43.32 5.52
1348 2512 3.912907 GATGGCCCCGTCGACGAT 61.913 66.667 37.65 22.92 43.02 3.73
1482 2646 3.644399 GAAGCACGACGTCTCCCCC 62.644 68.421 14.70 0.00 0.00 5.40
1585 2749 2.355481 GTTTCGCGAGACGGTGGT 60.355 61.111 14.40 0.00 43.89 4.16
1614 2778 4.295119 GTGGTGACCGTGACCGCT 62.295 66.667 12.92 0.00 40.30 5.52
1692 2856 5.126222 TCATTCAGTAGGACTCATCACTCAC 59.874 44.000 0.00 0.00 0.00 3.51
1741 2905 4.665142 CGACCGAACGATAATACTACGAGG 60.665 50.000 0.00 0.00 35.09 4.63
1765 2929 5.416952 AGTCAAAATTCGAGGAGAAATGCAT 59.583 36.000 0.00 0.00 42.91 3.96
1768 2932 6.734104 AGAGTCAAAATTCGAGGAGAAATG 57.266 37.500 0.00 0.00 42.91 2.32
1771 2935 4.452455 GCAAGAGTCAAAATTCGAGGAGAA 59.548 41.667 0.00 0.00 43.93 2.87
1823 2996 8.551440 TGGCAAATAGGAGATATATACAGCATT 58.449 33.333 0.00 0.00 0.00 3.56
1832 3005 3.676049 CGCGCTGGCAAATAGGAGATATA 60.676 47.826 5.56 0.00 39.92 0.86
1857 3030 5.116084 AGATGGTGTACTGCCATGTTTAT 57.884 39.130 21.55 3.59 45.87 1.40
1883 3060 9.003658 TCTGTAAAGAAAATTAGCTTGGAAGAG 57.996 33.333 0.00 0.00 0.00 2.85
1890 3067 8.572855 AGCAGATCTGTAAAGAAAATTAGCTT 57.427 30.769 23.38 0.00 0.00 3.74
1923 3105 8.600668 TGAGGCATAGCTAAATCTAATCTGAAT 58.399 33.333 0.00 0.00 0.00 2.57
1926 3108 8.789825 AATGAGGCATAGCTAAATCTAATCTG 57.210 34.615 0.00 0.00 0.00 2.90
1962 3144 9.708222 ACGAAATTTAGAAAATCTGATCATTCG 57.292 29.630 14.32 14.32 39.24 3.34
1964 3146 9.294030 GCACGAAATTTAGAAAATCTGATCATT 57.706 29.630 5.22 0.00 0.00 2.57
1965 3147 8.461222 TGCACGAAATTTAGAAAATCTGATCAT 58.539 29.630 5.22 0.00 0.00 2.45
1966 3148 7.815641 TGCACGAAATTTAGAAAATCTGATCA 58.184 30.769 5.22 0.00 0.00 2.92
1967 3149 8.673626 TTGCACGAAATTTAGAAAATCTGATC 57.326 30.769 5.22 0.00 0.00 2.92
1968 3150 9.643693 ATTTGCACGAAATTTAGAAAATCTGAT 57.356 25.926 5.22 0.00 29.22 2.90
1969 3151 9.128107 GATTTGCACGAAATTTAGAAAATCTGA 57.872 29.630 16.56 0.00 34.18 3.27
1970 3152 9.132521 AGATTTGCACGAAATTTAGAAAATCTG 57.867 29.630 21.46 6.50 40.05 2.90
1971 3153 9.132521 CAGATTTGCACGAAATTTAGAAAATCT 57.867 29.630 18.84 18.84 41.43 2.40
1972 3154 8.915654 ACAGATTTGCACGAAATTTAGAAAATC 58.084 29.630 16.30 16.30 34.18 2.17
1974 3156 7.918033 TCACAGATTTGCACGAAATTTAGAAAA 59.082 29.630 5.22 0.00 34.18 2.29
1975 3157 7.421599 TCACAGATTTGCACGAAATTTAGAAA 58.578 30.769 5.22 0.00 34.18 2.52
1984 3168 0.874390 GGCTCACAGATTTGCACGAA 59.126 50.000 0.00 0.00 0.00 3.85
1995 3179 3.052082 CCAACGCAGGGCTCACAG 61.052 66.667 0.00 0.00 0.00 3.66
2019 3203 4.008933 ACACGGAGACAGCAGGCC 62.009 66.667 0.00 0.00 0.00 5.19
2025 3209 0.108662 TGCATAGCACACGGAGACAG 60.109 55.000 0.00 0.00 31.71 3.51
2027 3211 0.807667 CCTGCATAGCACACGGAGAC 60.808 60.000 0.00 0.00 33.79 3.36
2030 3214 1.326951 TAGCCTGCATAGCACACGGA 61.327 55.000 11.08 0.00 33.79 4.69
2056 3240 8.575589 TGATTCTTTCAATTCGGATTTCAAGAA 58.424 29.630 16.87 16.87 36.31 2.52
2064 3249 8.511604 ACACTAATGATTCTTTCAATTCGGAT 57.488 30.769 0.00 0.00 38.03 4.18
2067 3252 9.907576 GTAGACACTAATGATTCTTTCAATTCG 57.092 33.333 0.00 0.00 38.03 3.34
2074 3259 9.911788 AATCCATGTAGACACTAATGATTCTTT 57.088 29.630 0.00 0.00 0.00 2.52
2083 3268 6.628621 CGGGTACAAATCCATGTAGACACTAA 60.629 42.308 0.00 0.00 36.51 2.24
2084 3269 5.163488 CGGGTACAAATCCATGTAGACACTA 60.163 44.000 0.00 0.00 36.51 2.74
2085 3270 4.382685 CGGGTACAAATCCATGTAGACACT 60.383 45.833 0.00 0.00 36.51 3.55
2086 3271 3.869246 CGGGTACAAATCCATGTAGACAC 59.131 47.826 0.00 0.00 36.51 3.67
2087 3272 3.118555 CCGGGTACAAATCCATGTAGACA 60.119 47.826 0.00 0.00 36.51 3.41
2088 3273 3.463944 CCGGGTACAAATCCATGTAGAC 58.536 50.000 0.00 0.00 36.51 2.59
2089 3274 2.436542 CCCGGGTACAAATCCATGTAGA 59.563 50.000 14.18 0.00 36.51 2.59
2090 3275 2.436542 TCCCGGGTACAAATCCATGTAG 59.563 50.000 22.86 0.00 36.51 2.74
2091 3276 2.479340 TCCCGGGTACAAATCCATGTA 58.521 47.619 22.86 0.00 34.75 2.29
2092 3277 1.291109 TCCCGGGTACAAATCCATGT 58.709 50.000 22.86 0.00 37.32 3.21
2093 3278 2.428544 TTCCCGGGTACAAATCCATG 57.571 50.000 22.86 0.00 0.00 3.66
2094 3279 3.562182 GAATTCCCGGGTACAAATCCAT 58.438 45.455 22.86 0.00 0.00 3.41
2095 3280 2.357361 GGAATTCCCGGGTACAAATCCA 60.357 50.000 22.86 0.00 0.00 3.41
2096 3281 2.304092 GGAATTCCCGGGTACAAATCC 58.696 52.381 22.86 15.78 0.00 3.01
2109 3294 0.253327 AGAGGCGAACAGGGAATTCC 59.747 55.000 16.74 16.74 0.00 3.01
2110 3295 1.066143 TGAGAGGCGAACAGGGAATTC 60.066 52.381 0.00 0.00 0.00 2.17
2111 3296 0.984230 TGAGAGGCGAACAGGGAATT 59.016 50.000 0.00 0.00 0.00 2.17
2112 3297 1.207791 ATGAGAGGCGAACAGGGAAT 58.792 50.000 0.00 0.00 0.00 3.01
2113 3298 0.984230 AATGAGAGGCGAACAGGGAA 59.016 50.000 0.00 0.00 0.00 3.97
2114 3299 0.250234 CAATGAGAGGCGAACAGGGA 59.750 55.000 0.00 0.00 0.00 4.20
2115 3300 0.036010 ACAATGAGAGGCGAACAGGG 60.036 55.000 0.00 0.00 0.00 4.45
2116 3301 1.066573 AGACAATGAGAGGCGAACAGG 60.067 52.381 0.00 0.00 0.00 4.00
2117 3302 2.266554 GAGACAATGAGAGGCGAACAG 58.733 52.381 0.00 0.00 0.00 3.16
2118 3303 1.402852 CGAGACAATGAGAGGCGAACA 60.403 52.381 0.00 0.00 0.00 3.18
2119 3304 1.272781 CGAGACAATGAGAGGCGAAC 58.727 55.000 0.00 0.00 0.00 3.95
2120 3305 0.458543 GCGAGACAATGAGAGGCGAA 60.459 55.000 0.00 0.00 0.00 4.70
2121 3306 1.139734 GCGAGACAATGAGAGGCGA 59.860 57.895 0.00 0.00 0.00 5.54
2122 3307 2.226896 CGCGAGACAATGAGAGGCG 61.227 63.158 0.00 0.00 36.05 5.52
2123 3308 2.520904 GCGCGAGACAATGAGAGGC 61.521 63.158 12.10 0.00 0.00 4.70
2124 3309 1.140589 AGCGCGAGACAATGAGAGG 59.859 57.895 12.10 0.00 0.00 3.69
2125 3310 0.457509 ACAGCGCGAGACAATGAGAG 60.458 55.000 12.10 0.00 0.00 3.20
2126 3311 0.038251 AACAGCGCGAGACAATGAGA 60.038 50.000 12.10 0.00 0.00 3.27
2127 3312 0.792640 AAACAGCGCGAGACAATGAG 59.207 50.000 12.10 0.00 0.00 2.90
2128 3313 1.225855 AAAACAGCGCGAGACAATGA 58.774 45.000 12.10 0.00 0.00 2.57
2129 3314 2.036556 AAAAACAGCGCGAGACAATG 57.963 45.000 12.10 0.00 0.00 2.82
2495 3680 9.391006 ACTTCAGAAAAAGTGTTCATGTACTAA 57.609 29.630 4.01 0.00 38.06 2.24
2496 3681 8.958119 ACTTCAGAAAAAGTGTTCATGTACTA 57.042 30.769 4.01 0.00 38.06 1.82
2497 3682 7.865706 ACTTCAGAAAAAGTGTTCATGTACT 57.134 32.000 4.01 0.00 38.06 2.73
2508 3693 4.843728 TGTCCTCACACTTCAGAAAAAGT 58.156 39.130 0.00 0.00 40.08 2.66
2521 3706 8.999431 GTATGAATTCTAAAAAGTGTCCTCACA 58.001 33.333 7.05 0.00 46.01 3.58
2522 3707 8.451748 GGTATGAATTCTAAAAAGTGTCCTCAC 58.548 37.037 7.05 0.00 44.15 3.51
2523 3708 8.383175 AGGTATGAATTCTAAAAAGTGTCCTCA 58.617 33.333 7.05 0.00 0.00 3.86
2524 3709 8.794335 AGGTATGAATTCTAAAAAGTGTCCTC 57.206 34.615 7.05 0.00 0.00 3.71
2525 3710 9.588096 AAAGGTATGAATTCTAAAAAGTGTCCT 57.412 29.630 7.05 0.00 0.00 3.85
2653 3838 8.952278 ACTAGTCACACAAGATTTGTAAAACAA 58.048 29.630 0.00 0.00 43.23 2.83
2654 3839 8.500753 ACTAGTCACACAAGATTTGTAAAACA 57.499 30.769 0.00 0.00 43.23 2.83
2655 3840 9.221775 CAACTAGTCACACAAGATTTGTAAAAC 57.778 33.333 0.00 0.00 43.23 2.43
2656 3841 7.913297 GCAACTAGTCACACAAGATTTGTAAAA 59.087 33.333 0.00 0.00 43.23 1.52
2657 3842 7.066404 TGCAACTAGTCACACAAGATTTGTAAA 59.934 33.333 0.00 0.00 43.23 2.01
2658 3843 6.540551 TGCAACTAGTCACACAAGATTTGTAA 59.459 34.615 0.00 0.00 43.23 2.41
2659 3844 6.052360 TGCAACTAGTCACACAAGATTTGTA 58.948 36.000 0.00 0.00 43.23 2.41
2660 3845 4.881273 TGCAACTAGTCACACAAGATTTGT 59.119 37.500 0.00 0.00 46.75 2.83
2661 3846 5.422666 TGCAACTAGTCACACAAGATTTG 57.577 39.130 0.00 0.00 0.00 2.32
2662 3847 5.532406 ACATGCAACTAGTCACACAAGATTT 59.468 36.000 0.00 0.00 0.00 2.17
2663 3848 5.065914 ACATGCAACTAGTCACACAAGATT 58.934 37.500 0.00 0.00 0.00 2.40
2664 3849 4.645535 ACATGCAACTAGTCACACAAGAT 58.354 39.130 0.00 0.00 0.00 2.40
2665 3850 4.058124 GACATGCAACTAGTCACACAAGA 58.942 43.478 0.00 0.00 32.68 3.02
2666 3851 3.187227 GGACATGCAACTAGTCACACAAG 59.813 47.826 0.00 0.00 34.04 3.16
2667 3852 3.138304 GGACATGCAACTAGTCACACAA 58.862 45.455 0.00 0.00 34.04 3.33
2668 3853 2.103941 TGGACATGCAACTAGTCACACA 59.896 45.455 0.00 0.00 34.04 3.72
2669 3854 2.480419 GTGGACATGCAACTAGTCACAC 59.520 50.000 0.00 12.43 34.04 3.82
2670 3855 2.103941 TGTGGACATGCAACTAGTCACA 59.896 45.455 0.00 0.41 34.04 3.58
2671 3856 2.766313 TGTGGACATGCAACTAGTCAC 58.234 47.619 0.00 0.00 34.04 3.67
2672 3857 3.483808 TTGTGGACATGCAACTAGTCA 57.516 42.857 0.00 0.00 34.04 3.41
2673 3858 5.376854 AAATTGTGGACATGCAACTAGTC 57.623 39.130 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.