Multiple sequence alignment - TraesCS3D01G039000

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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 TraesCS3D01G039000 chr3D 100.000 3041 0 0 1 3041 14556907 14553867 0.000000e+00 5616.0
1 TraesCS3D01G039000 chr3D 100.000 33 0 0 2736 2768 14545616 14545584 9.100000e-06 62.1
2 TraesCS3D01G039000 chr3A 90.007 3072 199 51 1 2994 21786305 21789346 0.000000e+00 3873.0
3 TraesCS3D01G039000 chr3B 90.000 2130 139 29 1 2071 21772154 21770040 0.000000e+00 2686.0
4 TraesCS3D01G039000 chr3B 90.634 726 37 14 2073 2769 21769747 21769024 0.000000e+00 935.0
5 TraesCS3D01G039000 chr7A 93.157 453 21 6 1988 2438 532123299 532122855 0.000000e+00 656.0
6 TraesCS3D01G039000 chr1A 94.161 411 21 2 1985 2392 44861242 44861652 9.260000e-175 623.0
7 TraesCS3D01G039000 chr2D 98.182 55 0 1 434 487 6095182 6095128 8.980000e-16 95.3


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 TraesCS3D01G039000 chr3D 14553867 14556907 3040 True 5616.0 5616 100.000 1 3041 1 chr3D.!!$R2 3040
1 TraesCS3D01G039000 chr3A 21786305 21789346 3041 False 3873.0 3873 90.007 1 2994 1 chr3A.!!$F1 2993
2 TraesCS3D01G039000 chr3B 21769024 21772154 3130 True 1810.5 2686 90.317 1 2769 2 chr3B.!!$R1 2768

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
201 206 0.248743 TCTGTCAAAACGTCGCGACT 60.249 50.0 33.94 19.7 0.0 4.18 F
1072 1148 0.322816 GCCCAAGACCAAGATGCTCA 60.323 55.0 0.00 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1801 0.250727 ACAACATGACGGGAACTGGG 60.251 55.000 0.0 0.0 40.47 4.45 R
2884 3307 1.002990 TGCACAGCATCACTCCTGG 60.003 57.895 0.0 0.0 31.71 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
20 21 3.365297 GCTCGCGTTTCTTACCTAAAC 57.635 47.619 5.77 0.00 34.25 2.01
23 24 4.622740 GCTCGCGTTTCTTACCTAAACTTA 59.377 41.667 5.77 0.00 35.20 2.24
25 26 6.012658 TCGCGTTTCTTACCTAAACTTAGA 57.987 37.500 5.77 0.00 35.20 2.10
26 27 6.624423 TCGCGTTTCTTACCTAAACTTAGAT 58.376 36.000 5.77 0.00 35.20 1.98
27 28 7.092716 TCGCGTTTCTTACCTAAACTTAGATT 58.907 34.615 5.77 0.00 35.20 2.40
86 90 4.404654 CGGACAAAAGGCCAGCGC 62.405 66.667 5.01 0.00 0.00 5.92
103 107 1.749258 GCGGTTCCAGACCCATTCC 60.749 63.158 0.00 0.00 46.35 3.01
166 170 2.124983 CGGTGGGCCTCTGATGTG 60.125 66.667 8.79 0.00 0.00 3.21
177 181 3.295304 CTGATGTGCGTCGGTCCCA 62.295 63.158 0.00 0.00 0.00 4.37
184 188 2.970639 CGTCGGTCCCACATGTCT 59.029 61.111 0.00 0.00 0.00 3.41
188 192 0.830023 TCGGTCCCACATGTCTGTCA 60.830 55.000 0.00 0.00 31.62 3.58
195 200 2.032030 CCCACATGTCTGTCAAAACGTC 60.032 50.000 0.00 0.00 31.62 4.34
197 202 1.260561 ACATGTCTGTCAAAACGTCGC 59.739 47.619 0.00 0.00 0.00 5.19
201 206 0.248743 TCTGTCAAAACGTCGCGACT 60.249 50.000 33.94 19.70 0.00 4.18
251 256 3.697045 TCAACCGTGTCACTTTCCATTTT 59.303 39.130 0.65 0.00 0.00 1.82
253 258 4.301637 ACCGTGTCACTTTCCATTTTTC 57.698 40.909 0.65 0.00 0.00 2.29
254 259 3.697045 ACCGTGTCACTTTCCATTTTTCA 59.303 39.130 0.65 0.00 0.00 2.69
257 262 4.051237 GTGTCACTTTCCATTTTTCAGCC 58.949 43.478 0.00 0.00 0.00 4.85
259 264 2.061028 CACTTTCCATTTTTCAGCCGC 58.939 47.619 0.00 0.00 0.00 6.53
263 268 1.444212 CCATTTTTCAGCCGCACGG 60.444 57.895 4.30 4.30 38.57 4.94
335 340 4.906537 GCGGGTGGTTGGGTGGTT 62.907 66.667 0.00 0.00 0.00 3.67
336 341 2.123640 CGGGTGGTTGGGTGGTTT 60.124 61.111 0.00 0.00 0.00 3.27
363 368 1.747367 CGGCGATTTAGGTGGGCAA 60.747 57.895 0.00 0.00 0.00 4.52
365 370 0.679960 GGCGATTTAGGTGGGCAAGT 60.680 55.000 0.00 0.00 0.00 3.16
368 373 0.451783 GATTTAGGTGGGCAAGTGCG 59.548 55.000 0.00 0.00 43.26 5.34
519 533 0.673956 GAAGAAGAAGACGCCCCACC 60.674 60.000 0.00 0.00 0.00 4.61
689 706 1.226717 GTCGATGCTCAGGTCCGTC 60.227 63.158 0.00 0.00 0.00 4.79
691 708 2.105128 GATGCTCAGGTCCGTCCG 59.895 66.667 0.00 0.00 41.99 4.79
692 711 2.680352 ATGCTCAGGTCCGTCCGT 60.680 61.111 0.00 0.00 41.99 4.69
731 762 3.764885 ATTTCTCATCTTTTTCGCCGG 57.235 42.857 0.00 0.00 0.00 6.13
786 842 3.118992 GGTTTTGATGGATTCTTGCTCCC 60.119 47.826 0.00 0.00 31.32 4.30
794 857 2.555227 GGATTCTTGCTCCCCTTGTTGA 60.555 50.000 0.00 0.00 0.00 3.18
982 1048 4.572389 AGTTTTGCTAGTCAGTCAGTGTTG 59.428 41.667 0.00 0.00 0.00 3.33
985 1051 2.698274 TGCTAGTCAGTCAGTGTTGGAA 59.302 45.455 0.00 0.00 0.00 3.53
994 1060 4.509600 CAGTCAGTGTTGGAAGAAGAAGAC 59.490 45.833 0.00 0.00 0.00 3.01
1005 1081 1.139853 AGAAGAAGACGATCCATGGCC 59.860 52.381 6.96 0.00 0.00 5.36
1034 1110 3.503363 GCACCAGATGCGCCTCAC 61.503 66.667 15.26 0.00 46.55 3.51
1072 1148 0.322816 GCCCAAGACCAAGATGCTCA 60.323 55.000 0.00 0.00 0.00 4.26
1093 1169 2.592287 GGTTCGGCGTCAAACCCA 60.592 61.111 15.81 0.00 39.23 4.51
1471 1553 2.432628 CCTTCGACACTGCCGACC 60.433 66.667 0.00 0.00 35.61 4.79
1608 1690 2.738846 GACGTCGTCTTCTACTACACCA 59.261 50.000 18.09 0.00 0.00 4.17
1650 1732 4.081185 TCGGCTGCTCCATTCGCA 62.081 61.111 0.00 0.00 35.80 5.10
1677 1759 2.716017 GCCGTCCTCTGTCCTGGAG 61.716 68.421 0.00 0.00 32.36 3.86
1719 1801 4.803426 CTGTCGCCTGAGCCGACC 62.803 72.222 13.56 0.00 39.91 4.79
1728 1810 4.097361 GAGCCGACCCCAGTTCCC 62.097 72.222 0.00 0.00 0.00 3.97
1735 1832 1.838073 GACCCCAGTTCCCGTCATGT 61.838 60.000 0.00 0.00 0.00 3.21
1806 1903 2.574399 GACCTCCTGCGTGGTCTC 59.426 66.667 5.05 0.00 45.40 3.36
1899 1996 1.079127 CTTGGACGGCGAACAGGAT 60.079 57.895 16.62 0.00 0.00 3.24
2128 2521 0.920763 TGTGCATTGGGAGGGAGGAT 60.921 55.000 0.00 0.00 0.00 3.24
2160 2553 2.439553 TTTTCCCCGGGCAGCTCAAT 62.440 55.000 17.73 0.00 0.00 2.57
2202 2595 2.904434 GTCTGTTTTCCCTAGTCTCCCA 59.096 50.000 0.00 0.00 0.00 4.37
2301 2701 5.431765 CTGCTGGTTATGTTATGTTCCTCT 58.568 41.667 0.00 0.00 0.00 3.69
2341 2742 2.744202 GTTGGTCCAGACATTGTAGCTG 59.256 50.000 0.00 0.00 0.00 4.24
2438 2844 1.530876 TTTGCCGCTTGCTTGCCATA 61.531 50.000 0.00 0.00 42.00 2.74
2482 2888 8.700973 TGTCTTACCTGCTCATTTGTATGTATA 58.299 33.333 0.00 0.00 33.34 1.47
2510 2919 2.490903 GTTGCTGAAGTGCTGATGGATT 59.509 45.455 0.00 0.00 0.00 3.01
2511 2920 2.089201 TGCTGAAGTGCTGATGGATTG 58.911 47.619 0.00 0.00 0.00 2.67
2538 2948 6.100404 CAAGTTCTGGAATGAAATTTGGGA 57.900 37.500 0.00 0.00 36.07 4.37
2552 2962 1.225373 TTGGGAGATTCCATCCAGGG 58.775 55.000 0.00 0.00 38.64 4.45
2578 2995 4.098055 TGTTGTTTAGCTCGTTTTGCAA 57.902 36.364 0.00 0.00 0.00 4.08
2605 3025 7.439108 ACCCTAGTACTATGCTGAAAAAGAT 57.561 36.000 2.33 0.00 0.00 2.40
2646 3066 2.847327 TCTCCACTTCCTGCTCTTTG 57.153 50.000 0.00 0.00 0.00 2.77
2647 3067 2.329267 TCTCCACTTCCTGCTCTTTGA 58.671 47.619 0.00 0.00 0.00 2.69
2650 3070 2.909006 TCCACTTCCTGCTCTTTGAGAT 59.091 45.455 0.00 0.00 0.00 2.75
2651 3071 3.328931 TCCACTTCCTGCTCTTTGAGATT 59.671 43.478 0.00 0.00 0.00 2.40
2652 3072 4.532126 TCCACTTCCTGCTCTTTGAGATTA 59.468 41.667 0.00 0.00 0.00 1.75
2653 3073 4.874966 CCACTTCCTGCTCTTTGAGATTAG 59.125 45.833 0.00 0.00 0.00 1.73
2654 3074 5.486526 CACTTCCTGCTCTTTGAGATTAGT 58.513 41.667 0.00 0.00 0.00 2.24
2655 3075 5.580297 CACTTCCTGCTCTTTGAGATTAGTC 59.420 44.000 0.00 0.00 0.00 2.59
2657 3077 5.336150 TCCTGCTCTTTGAGATTAGTCTG 57.664 43.478 0.00 0.00 33.97 3.51
2658 3078 5.019470 TCCTGCTCTTTGAGATTAGTCTGA 58.981 41.667 0.00 0.00 33.97 3.27
2666 3086 8.046294 TCTTTGAGATTAGTCTGACTGTACTC 57.954 38.462 20.19 20.95 33.97 2.59
2698 3118 5.491070 TGTATGCATCTTACTTGCTGAACT 58.509 37.500 0.19 0.00 40.77 3.01
2727 3150 4.498682 GGATGCTCATTTGTATCTTGTGCC 60.499 45.833 0.00 0.00 31.28 5.01
2769 3192 7.455058 TGTTATAGTTTGACCAGTGGTGTTAT 58.545 34.615 22.50 11.75 35.25 1.89
2770 3193 8.595421 TGTTATAGTTTGACCAGTGGTGTTATA 58.405 33.333 22.50 10.82 35.25 0.98
2786 3209 5.527582 GGTGTTATACCTTCCAGCATTAGTG 59.472 44.000 0.00 0.00 46.51 2.74
2787 3210 6.346096 GTGTTATACCTTCCAGCATTAGTGA 58.654 40.000 0.00 0.00 0.00 3.41
2790 3213 5.894298 ATACCTTCCAGCATTAGTGATGA 57.106 39.130 4.90 0.00 44.34 2.92
2791 3214 4.148128 ACCTTCCAGCATTAGTGATGAG 57.852 45.455 4.90 0.00 44.34 2.90
2792 3215 2.877168 CCTTCCAGCATTAGTGATGAGC 59.123 50.000 4.90 0.00 44.34 4.26
2793 3216 3.433314 CCTTCCAGCATTAGTGATGAGCT 60.433 47.826 4.90 0.00 44.34 4.09
2796 3219 2.562635 CAGCATTAGTGATGAGCTGCT 58.437 47.619 0.00 0.00 44.34 4.24
2797 3220 2.544686 CAGCATTAGTGATGAGCTGCTC 59.455 50.000 22.38 22.38 44.34 4.26
2798 3221 2.169978 AGCATTAGTGATGAGCTGCTCA 59.830 45.455 32.07 32.07 44.99 4.26
2810 3233 3.955650 AGCTGCTCATTTTGCTCATTT 57.044 38.095 0.00 0.00 0.00 2.32
2811 3234 3.846360 AGCTGCTCATTTTGCTCATTTC 58.154 40.909 0.00 0.00 0.00 2.17
2812 3235 2.928116 GCTGCTCATTTTGCTCATTTCC 59.072 45.455 0.00 0.00 0.00 3.13
2813 3236 3.368116 GCTGCTCATTTTGCTCATTTCCT 60.368 43.478 0.00 0.00 0.00 3.36
2814 3237 4.174009 CTGCTCATTTTGCTCATTTCCTG 58.826 43.478 0.00 0.00 0.00 3.86
2815 3238 2.928116 GCTCATTTTGCTCATTTCCTGC 59.072 45.455 0.00 0.00 0.00 4.85
2816 3239 3.368116 GCTCATTTTGCTCATTTCCTGCT 60.368 43.478 0.00 0.00 0.00 4.24
2817 3240 4.421948 CTCATTTTGCTCATTTCCTGCTC 58.578 43.478 0.00 0.00 0.00 4.26
2818 3241 3.827876 TCATTTTGCTCATTTCCTGCTCA 59.172 39.130 0.00 0.00 0.00 4.26
2824 3247 4.334552 TGCTCATTTCCTGCTCATTTGTA 58.665 39.130 0.00 0.00 0.00 2.41
2826 3249 5.163591 TGCTCATTTCCTGCTCATTTGTATG 60.164 40.000 0.00 0.00 0.00 2.39
2831 3254 6.942532 TTTCCTGCTCATTTGTATGTATCC 57.057 37.500 0.00 0.00 33.34 2.59
2833 3256 5.614308 TCCTGCTCATTTGTATGTATCCTG 58.386 41.667 0.00 0.00 33.34 3.86
2839 3262 6.569226 GCTCATTTGTATGTATCCTGCATTCC 60.569 42.308 0.00 0.00 33.34 3.01
2841 3264 6.832900 TCATTTGTATGTATCCTGCATTCCAA 59.167 34.615 0.00 0.00 33.34 3.53
2857 3280 5.702209 GCATTCCAATGGATGTTTTCAACTT 59.298 36.000 1.39 0.00 36.90 2.66
2860 3283 5.599732 TCCAATGGATGTTTTCAACTTGTG 58.400 37.500 0.00 0.00 0.00 3.33
2864 3287 5.667539 TGGATGTTTTCAACTTGTGGAAA 57.332 34.783 0.00 0.00 31.83 3.13
2868 3291 4.887748 TGTTTTCAACTTGTGGAAAGCAA 58.112 34.783 14.74 3.06 39.95 3.91
2870 3293 5.580297 TGTTTTCAACTTGTGGAAAGCAATC 59.420 36.000 14.74 3.07 39.95 2.67
2884 3307 5.163673 GGAAAGCAATCTGTGAGAATCCTTC 60.164 44.000 0.00 0.00 0.00 3.46
2885 3308 3.883669 AGCAATCTGTGAGAATCCTTCC 58.116 45.455 0.00 0.00 0.00 3.46
2901 3324 0.321919 TTCCAGGAGTGATGCTGTGC 60.322 55.000 0.00 0.00 0.00 4.57
2919 3342 5.295431 TGTGCAGCTCATTTTGTATGTAC 57.705 39.130 0.00 0.00 0.00 2.90
2924 3347 5.728255 CAGCTCATTTTGTATGTACGCTAC 58.272 41.667 0.00 0.00 0.00 3.58
2925 3348 5.520288 CAGCTCATTTTGTATGTACGCTACT 59.480 40.000 6.88 0.00 0.00 2.57
2926 3349 6.695713 CAGCTCATTTTGTATGTACGCTACTA 59.304 38.462 6.88 0.00 0.00 1.82
2927 3350 7.222031 CAGCTCATTTTGTATGTACGCTACTAA 59.778 37.037 6.88 3.61 0.00 2.24
2935 3358 9.616634 TTTGTATGTACGCTACTAATACTATGC 57.383 33.333 6.88 0.00 0.00 3.14
2940 3363 7.358066 TGTACGCTACTAATACTATGCTGAAC 58.642 38.462 0.00 0.00 0.00 3.18
2953 3376 6.820335 ACTATGCTGAACTGCTATTCATACA 58.180 36.000 4.04 6.35 37.93 2.29
2958 3381 7.829725 TGCTGAACTGCTATTCATACAAAAAT 58.170 30.769 4.04 0.00 37.93 1.82
2986 3409 3.825328 ACTCCTGAACTGAATGCAACTT 58.175 40.909 0.00 0.00 0.00 2.66
2994 3417 5.300034 TGAACTGAATGCAACTTGTGAGATT 59.700 36.000 0.00 0.00 0.00 2.40
2995 3418 5.117355 ACTGAATGCAACTTGTGAGATTG 57.883 39.130 0.00 0.00 0.00 2.67
2996 3419 4.022589 ACTGAATGCAACTTGTGAGATTGG 60.023 41.667 0.00 0.00 0.00 3.16
2997 3420 3.890756 TGAATGCAACTTGTGAGATTGGT 59.109 39.130 0.00 0.00 0.00 3.67
2998 3421 4.341806 TGAATGCAACTTGTGAGATTGGTT 59.658 37.500 0.00 0.00 0.00 3.67
2999 3422 3.713858 TGCAACTTGTGAGATTGGTTG 57.286 42.857 0.00 0.00 39.83 3.77
3000 3423 2.361757 TGCAACTTGTGAGATTGGTTGG 59.638 45.455 0.00 0.00 38.05 3.77
3001 3424 2.362077 GCAACTTGTGAGATTGGTTGGT 59.638 45.455 0.00 0.00 38.05 3.67
3002 3425 3.568007 GCAACTTGTGAGATTGGTTGGTA 59.432 43.478 0.00 0.00 38.05 3.25
3003 3426 4.037446 GCAACTTGTGAGATTGGTTGGTAA 59.963 41.667 0.00 0.00 38.05 2.85
3004 3427 5.519722 CAACTTGTGAGATTGGTTGGTAAC 58.480 41.667 0.00 0.00 35.18 2.50
3023 3446 7.870826 TGGTAACAGTTCATAAACATTGACTG 58.129 34.615 0.00 0.00 46.17 3.51
3024 3447 7.717436 TGGTAACAGTTCATAAACATTGACTGA 59.283 33.333 8.15 0.00 46.17 3.41
3025 3448 8.730680 GGTAACAGTTCATAAACATTGACTGAT 58.269 33.333 8.15 0.00 37.88 2.90
3026 3449 9.546909 GTAACAGTTCATAAACATTGACTGATG 57.453 33.333 8.15 0.00 37.88 3.07
3027 3450 6.615088 ACAGTTCATAAACATTGACTGATGC 58.385 36.000 8.15 0.00 37.88 3.91
3028 3451 6.432162 ACAGTTCATAAACATTGACTGATGCT 59.568 34.615 8.15 0.00 37.88 3.79
3029 3452 6.745907 CAGTTCATAAACATTGACTGATGCTG 59.254 38.462 0.00 0.00 37.88 4.41
3030 3453 6.656270 AGTTCATAAACATTGACTGATGCTGA 59.344 34.615 0.00 0.00 37.88 4.26
3031 3454 7.338703 AGTTCATAAACATTGACTGATGCTGAT 59.661 33.333 0.00 0.00 37.88 2.90
3032 3455 7.023197 TCATAAACATTGACTGATGCTGATG 57.977 36.000 0.00 0.00 0.00 3.07
3033 3456 4.713824 AAACATTGACTGATGCTGATGG 57.286 40.909 0.00 0.00 0.00 3.51
3034 3457 3.639672 ACATTGACTGATGCTGATGGA 57.360 42.857 0.00 0.00 0.00 3.41
3035 3458 3.542648 ACATTGACTGATGCTGATGGAG 58.457 45.455 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.124457 CCCACCAGTCATTGACAAATCTAAG 59.876 44.000 18.57 1.32 34.60 2.18
23 24 3.424703 CCCACCAGTCATTGACAAATCT 58.575 45.455 18.57 0.00 34.60 2.40
25 26 2.528564 CCCCACCAGTCATTGACAAAT 58.471 47.619 18.57 0.62 34.60 2.32
26 27 1.993956 CCCCACCAGTCATTGACAAA 58.006 50.000 18.57 0.00 34.60 2.83
27 28 0.539438 GCCCCACCAGTCATTGACAA 60.539 55.000 18.57 0.00 34.60 3.18
32 33 4.047125 CCGGCCCCACCAGTCATT 62.047 66.667 0.00 0.00 39.03 2.57
103 107 0.313043 AGGTAACCCATCGTATCGCG 59.687 55.000 0.00 0.00 39.00 5.87
156 160 1.517257 GACCGACGCACATCAGAGG 60.517 63.158 0.00 0.00 0.00 3.69
159 163 2.509336 GGGACCGACGCACATCAG 60.509 66.667 0.00 0.00 0.00 2.90
160 164 3.307108 TGGGACCGACGCACATCA 61.307 61.111 0.00 0.00 36.54 3.07
166 170 2.813908 GACATGTGGGACCGACGC 60.814 66.667 1.15 0.00 0.00 5.19
177 181 1.260561 GCGACGTTTTGACAGACATGT 59.739 47.619 0.00 0.00 44.31 3.21
184 188 1.717113 CATAGTCGCGACGTTTTGACA 59.283 47.619 31.56 11.95 36.20 3.58
188 192 0.389426 AGCCATAGTCGCGACGTTTT 60.389 50.000 31.56 18.01 36.20 2.43
195 200 0.585357 ACGTACTAGCCATAGTCGCG 59.415 55.000 0.00 0.00 41.46 5.87
197 202 3.363772 GCTGTACGTACTAGCCATAGTCG 60.364 52.174 26.31 0.00 41.46 4.18
201 206 1.265095 GCGCTGTACGTACTAGCCATA 59.735 52.381 28.44 10.60 46.11 2.74
251 256 1.227883 TTTTACCCGTGCGGCTGAA 60.228 52.632 4.91 0.00 33.26 3.02
253 258 2.559330 GTTTTACCCGTGCGGCTG 59.441 61.111 4.91 0.00 33.26 4.85
254 259 3.045492 CGTTTTACCCGTGCGGCT 61.045 61.111 4.91 0.00 33.26 5.52
257 262 1.062873 CATTGCGTTTTACCCGTGCG 61.063 55.000 0.00 0.00 0.00 5.34
259 264 1.264557 TGTCATTGCGTTTTACCCGTG 59.735 47.619 0.00 0.00 0.00 4.94
519 533 4.051922 GGGCAAGAAGACATATACGAGTG 58.948 47.826 0.00 0.00 0.00 3.51
701 720 2.196595 AGATGAGAAATTGACGGGGGA 58.803 47.619 0.00 0.00 0.00 4.81
704 723 5.088739 CGAAAAAGATGAGAAATTGACGGG 58.911 41.667 0.00 0.00 0.00 5.28
731 762 1.379642 CCAGATCTGGGCGAAAAGGC 61.380 60.000 31.14 0.00 46.81 4.35
786 842 1.308069 CCGTCCCTGCATCAACAAGG 61.308 60.000 0.00 0.00 0.00 3.61
794 857 4.096003 CCGAACCCGTCCCTGCAT 62.096 66.667 0.00 0.00 0.00 3.96
895 958 5.532406 TCTCTCTCTTGGGTGTCAAAAATTG 59.468 40.000 0.00 0.00 34.56 2.32
982 1048 3.462021 CCATGGATCGTCTTCTTCTTCC 58.538 50.000 5.56 0.00 0.00 3.46
985 1051 1.139853 GGCCATGGATCGTCTTCTTCT 59.860 52.381 18.40 0.00 0.00 2.85
1009 1085 4.105727 CATCTGGTGCTCGCTCAG 57.894 61.111 6.53 6.53 0.00 3.35
1089 1165 2.032681 GAGAAAGCAGCGGTGGGT 59.967 61.111 17.54 0.00 0.00 4.51
1093 1169 4.386413 CTTGGAGAAAGCAGCGGT 57.614 55.556 0.00 0.00 0.00 5.68
1212 1288 3.053849 GACAGCCTCCTCGTCGTCC 62.054 68.421 0.00 0.00 0.00 4.79
1608 1690 1.445582 GGACGACGAAGATGCCGTT 60.446 57.895 0.00 0.00 40.67 4.44
1695 1777 3.057547 CTCAGGCGACAGGGACTCG 62.058 68.421 0.00 0.00 34.60 4.18
1719 1801 0.250727 ACAACATGACGGGAACTGGG 60.251 55.000 0.00 0.00 40.47 4.45
1728 1810 1.565156 CCGTGGTGGACAACATGACG 61.565 60.000 10.98 1.81 42.00 4.35
1735 1832 2.137528 TCTCAGCCGTGGTGGACAA 61.138 57.895 3.77 0.00 42.00 3.18
1806 1903 4.147449 TCGATGTCCGGCAGCTGG 62.147 66.667 15.05 15.05 39.14 4.85
1899 1996 2.601666 AGGTCACCGAGCAGCAGA 60.602 61.111 0.00 0.00 31.89 4.26
2160 2553 1.078918 CATCTTGGGCACGAGCTGA 60.079 57.895 0.32 0.00 41.70 4.26
2202 2595 2.682856 CCACCATAACGCTAATGTGCTT 59.317 45.455 0.00 0.00 0.00 3.91
2301 2701 7.255660 GGACCAACATTGACAGGTAACATAAAA 60.256 37.037 0.00 0.00 41.41 1.52
2438 2844 8.738645 GTAAGACATACCCATCTCAAAGAAAT 57.261 34.615 0.00 0.00 0.00 2.17
2482 2888 3.574396 TCAGCACTTCAGCAACTAGTACT 59.426 43.478 0.00 0.00 36.85 2.73
2538 2948 2.854967 ACATCAACCCTGGATGGAATCT 59.145 45.455 0.00 0.00 45.01 2.40
2552 2962 5.331532 GCAAAACGAGCTAAACAACATCAAC 60.332 40.000 0.00 0.00 0.00 3.18
2646 3066 5.588648 AGCAGAGTACAGTCAGACTAATCTC 59.411 44.000 1.67 10.59 30.42 2.75
2647 3067 5.505780 AGCAGAGTACAGTCAGACTAATCT 58.494 41.667 1.67 0.00 34.57 2.40
2650 3070 4.652822 TGAGCAGAGTACAGTCAGACTAA 58.347 43.478 1.67 0.00 0.00 2.24
2651 3071 4.287766 TGAGCAGAGTACAGTCAGACTA 57.712 45.455 1.67 0.00 0.00 2.59
2652 3072 3.147553 TGAGCAGAGTACAGTCAGACT 57.852 47.619 0.00 0.00 0.00 3.24
2653 3073 3.694072 AGATGAGCAGAGTACAGTCAGAC 59.306 47.826 0.00 0.00 0.00 3.51
2654 3074 3.693578 CAGATGAGCAGAGTACAGTCAGA 59.306 47.826 0.00 0.00 0.00 3.27
2655 3075 3.443329 ACAGATGAGCAGAGTACAGTCAG 59.557 47.826 0.00 0.00 0.00 3.51
2657 3077 5.518812 CATACAGATGAGCAGAGTACAGTC 58.481 45.833 0.00 0.00 34.73 3.51
2658 3078 4.202101 GCATACAGATGAGCAGAGTACAGT 60.202 45.833 0.00 0.00 34.73 3.55
2666 3086 5.539979 AGTAAGATGCATACAGATGAGCAG 58.460 41.667 0.00 0.00 40.71 4.24
2698 3118 5.748402 AGATACAAATGAGCATCCAAGACA 58.252 37.500 0.00 0.00 0.00 3.41
2727 3150 3.559238 AACAAAATTAGCTCCAGCACG 57.441 42.857 0.48 0.00 45.16 5.34
2769 3192 4.443457 GCTCATCACTAATGCTGGAAGGTA 60.443 45.833 0.00 0.00 35.17 3.08
2770 3193 3.683847 GCTCATCACTAATGCTGGAAGGT 60.684 47.826 0.00 0.00 35.17 3.50
2772 3195 3.560481 CAGCTCATCACTAATGCTGGAAG 59.440 47.826 0.00 0.00 44.95 3.46
2773 3196 3.538591 CAGCTCATCACTAATGCTGGAA 58.461 45.455 0.00 0.00 44.95 3.53
2776 3199 5.276812 ATGAGCAGCTCATCACTAATGCTG 61.277 45.833 29.28 8.67 46.83 4.41
2777 3200 2.169978 TGAGCAGCTCATCACTAATGCT 59.830 45.455 21.85 0.00 46.06 3.79
2790 3213 3.368116 GGAAATGAGCAAAATGAGCAGCT 60.368 43.478 0.00 0.00 40.60 4.24
2791 3214 2.928116 GGAAATGAGCAAAATGAGCAGC 59.072 45.455 0.00 0.00 0.00 5.25
2792 3215 4.174009 CAGGAAATGAGCAAAATGAGCAG 58.826 43.478 0.00 0.00 0.00 4.24
2793 3216 3.615592 GCAGGAAATGAGCAAAATGAGCA 60.616 43.478 0.00 0.00 0.00 4.26
2794 3217 2.928116 GCAGGAAATGAGCAAAATGAGC 59.072 45.455 0.00 0.00 0.00 4.26
2795 3218 4.082408 TGAGCAGGAAATGAGCAAAATGAG 60.082 41.667 0.00 0.00 0.00 2.90
2796 3219 3.827876 TGAGCAGGAAATGAGCAAAATGA 59.172 39.130 0.00 0.00 0.00 2.57
2797 3220 4.182693 TGAGCAGGAAATGAGCAAAATG 57.817 40.909 0.00 0.00 0.00 2.32
2798 3221 5.416271 AATGAGCAGGAAATGAGCAAAAT 57.584 34.783 0.00 0.00 0.00 1.82
2800 3223 4.039488 ACAAATGAGCAGGAAATGAGCAAA 59.961 37.500 0.00 0.00 0.00 3.68
2801 3224 3.575256 ACAAATGAGCAGGAAATGAGCAA 59.425 39.130 0.00 0.00 0.00 3.91
2803 3226 3.863142 ACAAATGAGCAGGAAATGAGC 57.137 42.857 0.00 0.00 0.00 4.26
2804 3227 6.446781 ACATACAAATGAGCAGGAAATGAG 57.553 37.500 0.00 0.00 36.54 2.90
2805 3228 7.229306 GGATACATACAAATGAGCAGGAAATGA 59.771 37.037 0.00 0.00 36.54 2.57
2806 3229 7.230108 AGGATACATACAAATGAGCAGGAAATG 59.770 37.037 0.00 0.00 36.54 2.32
2808 3231 6.543465 CAGGATACATACAAATGAGCAGGAAA 59.457 38.462 0.00 0.00 36.54 3.13
2809 3232 6.057533 CAGGATACATACAAATGAGCAGGAA 58.942 40.000 0.00 0.00 36.54 3.36
2810 3233 5.614308 CAGGATACATACAAATGAGCAGGA 58.386 41.667 0.00 0.00 36.54 3.86
2811 3234 4.214971 GCAGGATACATACAAATGAGCAGG 59.785 45.833 0.00 0.00 36.54 4.85
2812 3235 4.818005 TGCAGGATACATACAAATGAGCAG 59.182 41.667 0.00 0.00 36.54 4.24
2813 3236 4.779696 TGCAGGATACATACAAATGAGCA 58.220 39.130 0.00 0.00 36.54 4.26
2814 3237 5.954296 ATGCAGGATACATACAAATGAGC 57.046 39.130 0.00 0.00 36.54 4.26
2815 3238 6.487668 TGGAATGCAGGATACATACAAATGAG 59.512 38.462 0.00 0.00 36.54 2.90
2816 3239 6.363882 TGGAATGCAGGATACATACAAATGA 58.636 36.000 0.00 0.00 36.54 2.57
2817 3240 6.638096 TGGAATGCAGGATACATACAAATG 57.362 37.500 0.00 0.00 39.17 2.32
2818 3241 7.256048 CCATTGGAATGCAGGATACATACAAAT 60.256 37.037 0.00 0.00 35.13 2.32
2824 3247 4.458256 TCCATTGGAATGCAGGATACAT 57.542 40.909 1.94 0.00 35.13 2.29
2826 3249 4.147321 ACATCCATTGGAATGCAGGATAC 58.853 43.478 9.98 0.00 36.99 2.24
2831 3254 4.823157 TGAAAACATCCATTGGAATGCAG 58.177 39.130 9.98 0.65 34.34 4.41
2857 3280 3.490439 TCTCACAGATTGCTTTCCACA 57.510 42.857 0.00 0.00 0.00 4.17
2860 3283 4.268359 AGGATTCTCACAGATTGCTTTCC 58.732 43.478 0.00 0.00 0.00 3.13
2864 3287 3.265221 TGGAAGGATTCTCACAGATTGCT 59.735 43.478 0.00 0.00 46.56 3.91
2884 3307 1.002990 TGCACAGCATCACTCCTGG 60.003 57.895 0.00 0.00 31.71 4.45
2885 3308 2.467962 CTGCACAGCATCACTCCTG 58.532 57.895 0.00 0.00 38.13 3.86
2901 3324 4.864916 AGCGTACATACAAAATGAGCTG 57.135 40.909 0.00 0.00 31.36 4.24
2919 3342 5.343593 GCAGTTCAGCATAGTATTAGTAGCG 59.656 44.000 0.00 0.00 0.00 4.26
2924 3347 9.650539 ATGAATAGCAGTTCAGCATAGTATTAG 57.349 33.333 9.25 0.00 41.05 1.73
2926 3349 9.429359 GTATGAATAGCAGTTCAGCATAGTATT 57.571 33.333 9.25 0.00 41.05 1.89
2927 3350 8.588472 TGTATGAATAGCAGTTCAGCATAGTAT 58.412 33.333 9.25 0.00 41.05 2.12
2958 3381 6.530120 TGCATTCAGTTCAGGAGTAGTTTTA 58.470 36.000 0.00 0.00 0.00 1.52
2961 3384 4.623932 TGCATTCAGTTCAGGAGTAGTT 57.376 40.909 0.00 0.00 0.00 2.24
2963 3386 4.573900 AGTTGCATTCAGTTCAGGAGTAG 58.426 43.478 0.00 0.00 0.00 2.57
2964 3387 4.623932 AGTTGCATTCAGTTCAGGAGTA 57.376 40.909 0.00 0.00 0.00 2.59
2965 3388 3.498774 AGTTGCATTCAGTTCAGGAGT 57.501 42.857 0.00 0.00 0.00 3.85
2967 3390 3.316029 CACAAGTTGCATTCAGTTCAGGA 59.684 43.478 1.81 0.00 0.00 3.86
2968 3391 3.316029 TCACAAGTTGCATTCAGTTCAGG 59.684 43.478 1.81 0.00 0.00 3.86
2969 3392 4.274214 TCTCACAAGTTGCATTCAGTTCAG 59.726 41.667 1.81 0.00 0.00 3.02
2970 3393 4.198530 TCTCACAAGTTGCATTCAGTTCA 58.801 39.130 1.81 0.00 0.00 3.18
2972 3395 5.508489 CCAATCTCACAAGTTGCATTCAGTT 60.508 40.000 1.81 0.00 0.00 3.16
2973 3396 4.022589 CCAATCTCACAAGTTGCATTCAGT 60.023 41.667 1.81 0.00 0.00 3.41
2974 3397 4.022589 ACCAATCTCACAAGTTGCATTCAG 60.023 41.667 1.81 0.00 0.00 3.02
2975 3398 3.890756 ACCAATCTCACAAGTTGCATTCA 59.109 39.130 1.81 0.00 0.00 2.57
2986 3409 4.431416 ACTGTTACCAACCAATCTCACA 57.569 40.909 0.00 0.00 0.00 3.58
2994 3417 7.285629 TCAATGTTTATGAACTGTTACCAACCA 59.714 33.333 1.75 0.00 36.70 3.67
2995 3418 7.593644 GTCAATGTTTATGAACTGTTACCAACC 59.406 37.037 1.75 0.00 36.70 3.77
2996 3419 8.349983 AGTCAATGTTTATGAACTGTTACCAAC 58.650 33.333 1.75 0.00 36.70 3.77
2997 3420 8.349245 CAGTCAATGTTTATGAACTGTTACCAA 58.651 33.333 1.75 0.00 36.70 3.67
2998 3421 7.717436 TCAGTCAATGTTTATGAACTGTTACCA 59.283 33.333 1.75 0.00 36.70 3.25
2999 3422 8.094798 TCAGTCAATGTTTATGAACTGTTACC 57.905 34.615 1.75 0.00 36.70 2.85
3000 3423 9.546909 CATCAGTCAATGTTTATGAACTGTTAC 57.453 33.333 1.75 0.00 36.70 2.50
3001 3424 8.236586 GCATCAGTCAATGTTTATGAACTGTTA 58.763 33.333 1.75 0.00 36.70 2.41
3002 3425 7.040201 AGCATCAGTCAATGTTTATGAACTGTT 60.040 33.333 1.75 0.00 36.70 3.16
3003 3426 6.432162 AGCATCAGTCAATGTTTATGAACTGT 59.568 34.615 1.75 0.00 36.70 3.55
3004 3427 6.745907 CAGCATCAGTCAATGTTTATGAACTG 59.254 38.462 1.75 0.00 36.70 3.16
3005 3428 6.656270 TCAGCATCAGTCAATGTTTATGAACT 59.344 34.615 1.75 0.00 36.70 3.01
3006 3429 6.845302 TCAGCATCAGTCAATGTTTATGAAC 58.155 36.000 0.00 0.00 36.29 3.18
3007 3430 7.415877 CCATCAGCATCAGTCAATGTTTATGAA 60.416 37.037 0.00 0.00 0.00 2.57
3008 3431 6.038936 CCATCAGCATCAGTCAATGTTTATGA 59.961 38.462 0.00 0.00 0.00 2.15
3009 3432 6.038936 TCCATCAGCATCAGTCAATGTTTATG 59.961 38.462 0.00 0.00 0.00 1.90
3010 3433 6.124340 TCCATCAGCATCAGTCAATGTTTAT 58.876 36.000 0.00 0.00 0.00 1.40
3011 3434 5.499313 TCCATCAGCATCAGTCAATGTTTA 58.501 37.500 0.00 0.00 0.00 2.01
3012 3435 4.338012 TCCATCAGCATCAGTCAATGTTT 58.662 39.130 0.00 0.00 0.00 2.83
3013 3436 3.945921 CTCCATCAGCATCAGTCAATGTT 59.054 43.478 0.00 0.00 0.00 2.71
3014 3437 3.542648 CTCCATCAGCATCAGTCAATGT 58.457 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.