Multiple sequence alignment - TraesCS6D01G017300

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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 TraesCS6D01G017300 chr6D 100.000 2709 0 0 1 2709 7162993 7165701 0.000000e+00 5003.0
1 TraesCS6D01G017300 chr6D 86.641 262 34 1 2429 2689 299905032 299904771 3.410000e-74 289.0
2 TraesCS6D01G017300 chr6A 90.080 1129 50 21 904 1995 6826261 6827364 0.000000e+00 1408.0
3 TraesCS6D01G017300 chr6A 93.230 901 26 14 1 892 6825343 6826217 0.000000e+00 1293.0
4 TraesCS6D01G017300 chr6A 93.359 512 33 1 2036 2546 6827597 6828108 0.000000e+00 756.0
5 TraesCS6D01G017300 chr6B 90.838 764 45 14 989 1750 12731068 12731808 0.000000e+00 1000.0
6 TraesCS6D01G017300 chr6B 87.898 471 35 8 440 892 12730428 12730894 3.970000e-148 534.0
7 TraesCS6D01G017300 chr6B 83.871 124 15 3 1942 2062 28018703 28018824 2.200000e-21 113.0
8 TraesCS6D01G017300 chr6B 80.851 141 20 4 1934 2070 203956 204093 1.330000e-18 104.0
9 TraesCS6D01G017300 chr4D 78.324 752 99 35 1966 2689 47746122 47745407 6.930000e-116 427.0
10 TraesCS6D01G017300 chr4D 78.788 132 22 5 1941 2071 201706849 201706723 1.730000e-12 84.2
11 TraesCS6D01G017300 chr3D 87.879 264 27 4 2425 2685 3965136 3964875 3.390000e-79 305.0
12 TraesCS6D01G017300 chr5D 88.400 250 27 2 2427 2675 411612398 411612150 1.580000e-77 300.0
13 TraesCS6D01G017300 chr5D 87.747 253 30 1 2429 2680 238902501 238902753 7.340000e-76 294.0
14 TraesCS6D01G017300 chr2D 88.142 253 28 2 2429 2680 572213545 572213796 1.580000e-77 300.0
15 TraesCS6D01G017300 chr3B 87.597 258 30 2 2429 2685 7141808 7142064 5.670000e-77 298.0
16 TraesCS6D01G017300 chr3B 82.857 140 19 4 1934 2070 769053162 769053025 1.320000e-23 121.0
17 TraesCS6D01G017300 chr7B 86.466 266 34 2 2425 2689 600651182 600650918 9.490000e-75 291.0
18 TraesCS6D01G017300 chr7B 79.808 104 16 4 1947 2049 590254333 590254234 1.350000e-08 71.3
19 TraesCS6D01G017300 chr1D 86.142 267 36 1 2425 2690 413402571 413402305 1.230000e-73 287.0
20 TraesCS6D01G017300 chr4B 89.189 111 12 0 2144 2254 70055100 70054990 3.640000e-29 139.0
21 TraesCS6D01G017300 chrUn 78.505 214 40 5 1940 2151 178700577 178700368 4.700000e-28 135.0
22 TraesCS6D01G017300 chr1B 82.143 140 20 4 1934 2070 32987807 32987670 6.130000e-22 115.0
23 TraesCS6D01G017300 chr1A 81.022 137 23 3 1936 2071 482222448 482222314 3.690000e-19 106.0


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 TraesCS6D01G017300 chr6D 7162993 7165701 2708 False 5003.000000 5003 100.000 1 2709 1 chr6D.!!$F1 2708
1 TraesCS6D01G017300 chr6A 6825343 6828108 2765 False 1152.333333 1408 92.223 1 2546 3 chr6A.!!$F1 2545
2 TraesCS6D01G017300 chr6B 12730428 12731808 1380 False 767.000000 1000 89.368 440 1750 2 chr6B.!!$F3 1310
3 TraesCS6D01G017300 chr4D 47745407 47746122 715 True 427.000000 427 78.324 1966 2689 1 chr4D.!!$R1 723

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
935 989 0.17907 TATGCATGGCGCCGTTTAGA 60.179 50.0 21.21 5.15 41.33 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2554 2913 0.458889 CAAAATGCCGCCATCACCTG 60.459 55.0 0.0 0.0 0.0 4.0 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
80 81 3.052082 CGCAAGCCACACCTCCTG 61.052 66.667 0.00 0.00 0.00 3.86
143 144 2.046314 CCATGCCGTCGGGAACTT 60.046 61.111 10.37 0.00 34.06 2.66
153 154 2.186125 GGGAACTTAGCCGTCGGG 59.814 66.667 14.38 0.00 0.00 5.14
175 176 2.158986 CCTCTGTGCACAAGATCTAGGG 60.159 54.545 21.98 12.55 0.00 3.53
220 221 2.963101 CCCCACGTCACCATATAGAAGA 59.037 50.000 0.00 0.00 0.00 2.87
246 247 0.832559 AGGAGGATAAGCCCCGCTAC 60.833 60.000 0.00 0.00 38.25 3.58
342 343 0.815615 GTGGGAATGGAAGCGCTAGG 60.816 60.000 12.05 0.00 0.00 3.02
382 383 3.377656 GGAGTGTCTCCGGCTGAA 58.622 61.111 0.00 0.00 41.08 3.02
383 384 1.079750 GGAGTGTCTCCGGCTGAAC 60.080 63.158 0.00 0.00 41.08 3.18
384 385 1.536943 GGAGTGTCTCCGGCTGAACT 61.537 60.000 0.00 0.00 41.08 3.01
385 386 1.174783 GAGTGTCTCCGGCTGAACTA 58.825 55.000 0.00 0.00 0.00 2.24
386 387 1.751924 GAGTGTCTCCGGCTGAACTAT 59.248 52.381 0.00 0.00 0.00 2.12
410 411 4.682778 TTTTCTTTCTTCCGAGACCTGA 57.317 40.909 0.00 0.00 0.00 3.86
412 413 4.891992 TTCTTTCTTCCGAGACCTGATT 57.108 40.909 0.00 0.00 0.00 2.57
444 445 5.085390 CAGCGATGACACTATTCGATCTAG 58.915 45.833 0.00 0.00 34.92 2.43
500 501 5.017294 TGTGTCATGTCTTACACTTCACA 57.983 39.130 14.38 0.00 44.99 3.58
705 712 8.701908 ACTCCATATATTTCAGTCATGCAATT 57.298 30.769 0.00 0.00 0.00 2.32
820 838 7.173907 CCAAACTAATGTGATGATCTGGATACC 59.826 40.741 0.00 0.00 0.00 2.73
894 916 7.966753 TGAAGATATATGAAATACGAGGTACGC 59.033 37.037 0.00 0.00 46.94 4.42
896 918 2.521105 ATGAAATACGAGGTACGCCC 57.479 50.000 0.00 0.00 46.94 6.13
897 919 0.461135 TGAAATACGAGGTACGCCCC 59.539 55.000 0.00 0.00 46.94 5.80
898 920 0.595825 GAAATACGAGGTACGCCCCG 60.596 60.000 0.00 0.00 46.94 5.73
899 921 1.037030 AAATACGAGGTACGCCCCGA 61.037 55.000 0.00 0.00 46.94 5.14
900 922 1.728490 AATACGAGGTACGCCCCGAC 61.728 60.000 0.00 0.00 46.94 4.79
911 965 1.291272 GCCCCGACGACTTGTAACT 59.709 57.895 0.00 0.00 0.00 2.24
935 989 0.179070 TATGCATGGCGCCGTTTAGA 60.179 50.000 21.21 5.15 41.33 2.10
936 990 0.819259 ATGCATGGCGCCGTTTAGAT 60.819 50.000 21.21 3.02 41.33 1.98
937 991 1.009675 GCATGGCGCCGTTTAGATG 60.010 57.895 21.21 17.95 32.94 2.90
938 992 1.648720 CATGGCGCCGTTTAGATGG 59.351 57.895 21.21 1.18 34.87 3.51
942 996 1.517694 GCGCCGTTTAGATGGACGA 60.518 57.895 0.00 0.00 41.53 4.20
943 997 0.874607 GCGCCGTTTAGATGGACGAT 60.875 55.000 0.00 0.00 41.53 3.73
945 999 1.499049 GCCGTTTAGATGGACGATCC 58.501 55.000 0.00 0.00 41.53 3.36
954 1008 3.083686 TGGACGATCCATGCATGTG 57.916 52.632 24.58 15.94 42.67 3.21
956 1010 0.659427 GGACGATCCATGCATGTGTG 59.341 55.000 24.58 13.66 36.28 3.82
957 1011 1.372582 GACGATCCATGCATGTGTGT 58.627 50.000 24.58 16.55 0.00 3.72
958 1012 1.063027 GACGATCCATGCATGTGTGTG 59.937 52.381 24.58 12.67 0.00 3.82
962 1016 2.857186 TCCATGCATGTGTGTGTACT 57.143 45.000 24.58 0.00 0.00 2.73
963 1017 2.698803 TCCATGCATGTGTGTGTACTC 58.301 47.619 24.58 0.00 0.00 2.59
964 1018 2.038295 TCCATGCATGTGTGTGTACTCA 59.962 45.455 24.58 0.00 35.08 3.41
965 1019 2.813172 CCATGCATGTGTGTGTACTCAA 59.187 45.455 24.58 0.00 34.37 3.02
969 1072 4.306600 TGCATGTGTGTGTACTCAAGTAG 58.693 43.478 0.00 0.00 34.37 2.57
975 1078 5.301045 TGTGTGTGTACTCAAGTAGTTAGCT 59.699 40.000 0.00 0.00 39.80 3.32
976 1079 5.629849 GTGTGTGTACTCAAGTAGTTAGCTG 59.370 44.000 0.00 0.00 39.80 4.24
1027 1130 0.905357 AGCAAGGTTGGCTCTACGAT 59.095 50.000 0.00 0.00 36.81 3.73
1058 1164 6.482973 CACCAGCATACATACATACATTGTCA 59.517 38.462 0.00 0.00 39.87 3.58
1076 1182 8.762645 ACATTGTCATCCTCTTCTCTTGTAATA 58.237 33.333 0.00 0.00 0.00 0.98
1077 1183 9.605275 CATTGTCATCCTCTTCTCTTGTAATAA 57.395 33.333 0.00 0.00 0.00 1.40
1101 1232 5.772825 TTGTAATAATGGCTTCATGGAGC 57.227 39.130 18.45 18.45 41.96 4.70
1575 1706 2.423892 GACAACTCGAGGACTGCATCTA 59.576 50.000 18.41 0.00 0.00 1.98
1576 1707 3.027412 ACAACTCGAGGACTGCATCTAT 58.973 45.455 18.41 0.00 0.00 1.98
1577 1708 3.067461 ACAACTCGAGGACTGCATCTATC 59.933 47.826 18.41 0.00 0.00 2.08
1668 1803 1.393539 CGCATTACGCTGCTTGTAACT 59.606 47.619 0.00 0.00 40.06 2.24
1669 1804 2.774007 GCATTACGCTGCTTGTAACTG 58.226 47.619 0.00 2.82 39.12 3.16
1670 1805 2.476185 GCATTACGCTGCTTGTAACTGG 60.476 50.000 0.00 0.00 39.12 4.00
1671 1806 2.823924 TTACGCTGCTTGTAACTGGA 57.176 45.000 0.00 0.00 0.00 3.86
1672 1807 2.363788 TACGCTGCTTGTAACTGGAG 57.636 50.000 0.00 0.00 0.00 3.86
1779 1914 7.793927 AAGGTAGTTCTCTTGTTTTCAGAAG 57.206 36.000 0.00 0.00 0.00 2.85
1780 1915 6.890293 AGGTAGTTCTCTTGTTTTCAGAAGT 58.110 36.000 0.00 0.00 0.00 3.01
1781 1916 7.339482 AGGTAGTTCTCTTGTTTTCAGAAGTT 58.661 34.615 0.00 0.00 0.00 2.66
1782 1917 8.483758 AGGTAGTTCTCTTGTTTTCAGAAGTTA 58.516 33.333 0.00 0.00 0.00 2.24
1783 1918 8.549548 GGTAGTTCTCTTGTTTTCAGAAGTTAC 58.450 37.037 0.00 0.00 0.00 2.50
1786 1921 8.041323 AGTTCTCTTGTTTTCAGAAGTTACAGA 58.959 33.333 0.00 0.00 0.00 3.41
1825 1967 8.896320 AAATAAAGGAAGTTGCGGTTTAAAAT 57.104 26.923 0.00 0.00 0.00 1.82
1891 2034 6.303839 ACAGAAAGGCTAATTTACCACAAGA 58.696 36.000 0.00 0.00 0.00 3.02
1897 2040 5.710567 AGGCTAATTTACCACAAGAAAGACC 59.289 40.000 0.00 0.00 0.00 3.85
1919 2062 5.070847 ACCAAATTAATGGCAGATTGATCCC 59.929 40.000 0.00 0.00 44.75 3.85
1931 2074 2.203451 GATCCCCGCGACCCTCTA 60.203 66.667 8.23 0.00 0.00 2.43
1985 2128 4.215742 CCCGATCTACGCCGCCAA 62.216 66.667 0.00 0.00 41.07 4.52
2287 2627 1.093159 CGTGCGGAGGTTACTACTCT 58.907 55.000 0.00 0.00 35.34 3.24
2311 2652 3.958860 GGTGGCAGTGGCTGAGGT 61.959 66.667 18.53 0.00 40.87 3.85
2359 2717 2.016961 CGGTTGGCAGATTGGATCG 58.983 57.895 0.00 0.00 0.00 3.69
2422 2781 2.236395 ACCTCAAGTTCGGATTCGGATT 59.764 45.455 0.00 0.00 36.95 3.01
2445 2804 2.114616 AGTGGTGGTGATCATCTCCTC 58.885 52.381 23.88 20.61 31.62 3.71
2498 2857 3.738482 GATCTCGAGATCCGTCGTG 57.262 57.895 35.46 0.00 43.85 4.35
2511 2870 3.755628 TCGTGTAGTCCCGGCTGC 61.756 66.667 0.00 0.00 0.00 5.25
2543 2902 2.858745 ACATAGTTGCCGGTGAAAACT 58.141 42.857 1.90 10.88 37.82 2.66
2553 2912 0.599204 GGTGAAAACTGAGCCGACGA 60.599 55.000 0.00 0.00 0.00 4.20
2554 2913 0.507358 GTGAAAACTGAGCCGACGAC 59.493 55.000 0.00 0.00 0.00 4.34
2555 2914 0.103390 TGAAAACTGAGCCGACGACA 59.897 50.000 0.00 0.00 0.00 4.35
2558 2917 1.745320 AAACTGAGCCGACGACAGGT 61.745 55.000 16.30 10.11 36.17 4.00
2571 2930 1.304381 ACAGGTGATGGCGGCATTT 60.304 52.632 26.52 5.09 0.00 2.32
2574 2933 1.810853 GGTGATGGCGGCATTTTGC 60.811 57.895 26.52 13.45 44.08 3.68
2576 2935 2.181525 GATGGCGGCATTTTGCGT 59.818 55.556 26.52 1.49 46.21 5.24
2577 2936 1.445926 GATGGCGGCATTTTGCGTT 60.446 52.632 26.52 0.59 46.21 4.84
2578 2937 0.179150 GATGGCGGCATTTTGCGTTA 60.179 50.000 26.52 0.00 46.21 3.18
2610 2969 3.129813 TGAAGGCATCGTCGTGTAACTAT 59.870 43.478 0.00 0.00 31.75 2.12
2614 2973 3.242248 GGCATCGTCGTGTAACTATTGTC 59.758 47.826 0.00 0.00 31.75 3.18
2617 2976 3.736213 TCGTCGTGTAACTATTGTCGAC 58.264 45.455 9.11 9.11 42.33 4.20
2622 2981 3.366679 CGTGTAACTATTGTCGACCCACT 60.367 47.826 14.12 0.00 31.75 4.00
2624 2983 2.649331 AACTATTGTCGACCCACTCG 57.351 50.000 14.12 0.00 44.44 4.18
2629 2988 2.430921 GTCGACCCACTCGTGCTG 60.431 66.667 3.51 0.00 43.45 4.41
2665 3025 4.842948 CCCTAGGATCCATCTTTCAGATCA 59.157 45.833 15.82 0.00 38.52 2.92
2666 3026 5.046448 CCCTAGGATCCATCTTTCAGATCAG 60.046 48.000 15.82 0.00 38.52 2.90
2669 3029 4.967442 AGGATCCATCTTTCAGATCAGACA 59.033 41.667 15.82 0.00 38.52 3.41
2676 3036 2.768253 TTCAGATCAGACAATGGCGT 57.232 45.000 0.00 0.00 0.00 5.68
2680 3040 1.276138 AGATCAGACAATGGCGTCACA 59.724 47.619 0.00 0.00 38.43 3.58
2681 3041 2.076100 GATCAGACAATGGCGTCACAA 58.924 47.619 0.00 0.00 38.43 3.33
2691 3051 2.657296 CGTCACAACGGCGTCACT 60.657 61.111 15.17 0.00 45.21 3.41
2692 3052 2.927618 CGTCACAACGGCGTCACTG 61.928 63.158 15.17 11.28 45.21 3.66
2693 3053 2.964925 TCACAACGGCGTCACTGC 60.965 61.111 15.17 0.00 0.00 4.40
2694 3054 4.354212 CACAACGGCGTCACTGCG 62.354 66.667 15.17 0.00 35.06 5.18
2703 3063 3.335534 GTCACTGCGGCGTCGTTT 61.336 61.111 12.58 0.00 38.89 3.60
2704 3064 3.033764 TCACTGCGGCGTCGTTTC 61.034 61.111 12.58 0.00 38.89 2.78
2705 3065 3.036084 CACTGCGGCGTCGTTTCT 61.036 61.111 12.58 0.00 38.89 2.52
2706 3066 2.733593 ACTGCGGCGTCGTTTCTC 60.734 61.111 12.58 0.00 38.89 2.87
2707 3067 2.430921 CTGCGGCGTCGTTTCTCT 60.431 61.111 12.58 0.00 38.89 3.10
2708 3068 2.430244 TGCGGCGTCGTTTCTCTC 60.430 61.111 12.58 0.00 38.89 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.213013 CGACTCCCGGTCTTGACTG 59.787 63.158 0.00 2.77 42.44 3.51
153 154 2.548875 CTAGATCTTGTGCACAGAGGC 58.451 52.381 20.59 14.33 0.00 4.70
158 159 0.253044 GGCCCTAGATCTTGTGCACA 59.747 55.000 17.42 17.42 0.00 4.57
220 221 2.624293 GGGGCTTATCCTCCTTTTTGCT 60.624 50.000 0.00 0.00 34.39 3.91
365 366 1.079750 GTTCAGCCGGAGACACTCC 60.080 63.158 5.05 7.65 46.44 3.85
366 367 1.174783 TAGTTCAGCCGGAGACACTC 58.825 55.000 5.05 0.00 0.00 3.51
367 368 1.853963 ATAGTTCAGCCGGAGACACT 58.146 50.000 5.05 10.77 0.00 3.55
368 369 2.674796 AATAGTTCAGCCGGAGACAC 57.325 50.000 5.05 3.81 0.00 3.67
369 370 3.695830 AAAATAGTTCAGCCGGAGACA 57.304 42.857 5.05 0.00 0.00 3.41
399 400 0.965866 AGCGTGAATCAGGTCTCGGA 60.966 55.000 4.81 0.00 35.59 4.55
444 445 2.092598 ATGGGCCAAATGGGAGAATC 57.907 50.000 11.89 0.00 40.01 2.52
474 475 7.072030 GTGAAGTGTAAGACATGACACAATTC 58.928 38.462 16.12 16.12 46.83 2.17
555 556 7.825331 ACGGATCTATCTTGATCTCTTTGTA 57.175 36.000 0.00 0.00 41.72 2.41
820 838 2.106511 TCCAAAGTTGACAAGGAGAGGG 59.893 50.000 0.00 0.00 0.00 4.30
870 892 7.256286 GGCGTACCTCGTATTTCATATATCTT 58.744 38.462 0.00 0.00 42.13 2.40
872 894 5.975939 GGGCGTACCTCGTATTTCATATATC 59.024 44.000 0.00 0.00 42.13 1.63
886 908 4.185059 GTCGTCGGGGCGTACCTC 62.185 72.222 0.00 0.00 40.03 3.85
892 914 2.090524 GTTACAAGTCGTCGGGGCG 61.091 63.158 0.00 0.00 0.00 6.13
893 915 0.320160 AAGTTACAAGTCGTCGGGGC 60.320 55.000 0.00 0.00 0.00 5.80
894 916 1.425412 CAAGTTACAAGTCGTCGGGG 58.575 55.000 0.00 0.00 0.00 5.73
896 918 1.493772 TGCAAGTTACAAGTCGTCGG 58.506 50.000 0.00 0.00 0.00 4.79
897 919 4.779082 GCATATGCAAGTTACAAGTCGTCG 60.779 45.833 22.84 0.00 41.59 5.12
898 920 4.578601 GCATATGCAAGTTACAAGTCGTC 58.421 43.478 22.84 0.00 41.59 4.20
899 921 4.600012 GCATATGCAAGTTACAAGTCGT 57.400 40.909 22.84 0.00 41.59 4.34
937 991 0.659427 CACACATGCATGGATCGTCC 59.341 55.000 29.41 0.00 36.96 4.79
938 992 1.063027 CACACACATGCATGGATCGTC 59.937 52.381 29.41 0.00 0.00 4.20
942 996 3.273434 GAGTACACACACATGCATGGAT 58.727 45.455 29.41 14.85 0.00 3.41
943 997 2.038295 TGAGTACACACACATGCATGGA 59.962 45.455 29.41 0.00 0.00 3.41
945 999 3.499537 ACTTGAGTACACACACATGCATG 59.500 43.478 25.09 25.09 0.00 4.06
946 1000 3.743521 ACTTGAGTACACACACATGCAT 58.256 40.909 0.00 0.00 0.00 3.96
947 1001 3.192541 ACTTGAGTACACACACATGCA 57.807 42.857 0.00 0.00 0.00 3.96
948 1002 4.307432 ACTACTTGAGTACACACACATGC 58.693 43.478 0.00 0.00 36.27 4.06
950 1004 6.015350 AGCTAACTACTTGAGTACACACACAT 60.015 38.462 0.00 0.00 37.44 3.21
951 1005 5.301045 AGCTAACTACTTGAGTACACACACA 59.699 40.000 0.00 0.00 37.44 3.72
952 1006 5.629849 CAGCTAACTACTTGAGTACACACAC 59.370 44.000 0.00 0.00 37.44 3.82
953 1007 5.278808 CCAGCTAACTACTTGAGTACACACA 60.279 44.000 0.00 0.00 37.44 3.72
954 1008 5.048224 TCCAGCTAACTACTTGAGTACACAC 60.048 44.000 0.00 0.00 37.44 3.82
956 1010 5.393243 CCTCCAGCTAACTACTTGAGTACAC 60.393 48.000 0.00 0.00 37.44 2.90
957 1011 4.705507 CCTCCAGCTAACTACTTGAGTACA 59.294 45.833 0.00 0.00 37.44 2.90
958 1012 4.098196 CCCTCCAGCTAACTACTTGAGTAC 59.902 50.000 0.00 0.00 37.44 2.73
962 1016 2.467880 CCCCTCCAGCTAACTACTTGA 58.532 52.381 0.00 0.00 0.00 3.02
963 1017 1.486726 CCCCCTCCAGCTAACTACTTG 59.513 57.143 0.00 0.00 0.00 3.16
964 1018 1.080666 ACCCCCTCCAGCTAACTACTT 59.919 52.381 0.00 0.00 0.00 2.24
965 1019 0.717196 ACCCCCTCCAGCTAACTACT 59.283 55.000 0.00 0.00 0.00 2.57
969 1072 2.272471 GCACCCCCTCCAGCTAAC 59.728 66.667 0.00 0.00 0.00 2.34
1027 1130 2.708325 TGTATGTATGCTGGTGCCCATA 59.292 45.455 0.00 0.00 38.71 2.74
1076 1182 7.212274 GCTCCATGAAGCCATTATTACAAATT 58.788 34.615 0.00 0.00 36.22 1.82
1077 1183 6.515531 CGCTCCATGAAGCCATTATTACAAAT 60.516 38.462 0.00 0.00 39.17 2.32
1079 1185 4.275689 CGCTCCATGAAGCCATTATTACAA 59.724 41.667 0.00 0.00 39.17 2.41
1081 1187 3.365364 GCGCTCCATGAAGCCATTATTAC 60.365 47.826 0.00 0.00 39.17 1.89
1097 1228 2.510238 CCACTACAGCTGCGCTCC 60.510 66.667 15.27 0.00 36.40 4.70
1098 1229 2.510238 CCCACTACAGCTGCGCTC 60.510 66.667 15.27 0.00 36.40 5.03
1419 1550 2.730672 GCACCTACTCTTGCACGCG 61.731 63.158 3.53 3.53 38.68 6.01
1575 1706 7.010460 GCATGCGTACATACATACATACATGAT 59.990 37.037 0.00 0.00 35.03 2.45
1576 1707 6.310224 GCATGCGTACATACATACATACATGA 59.690 38.462 0.00 0.00 35.03 3.07
1577 1708 6.090628 TGCATGCGTACATACATACATACATG 59.909 38.462 14.09 0.00 35.58 3.21
1595 1726 0.164432 CATAGCCACGTATGCATGCG 59.836 55.000 31.52 31.52 41.71 4.73
1668 1803 2.496070 CGAGGTCCAAACATCTACTCCA 59.504 50.000 0.00 0.00 34.05 3.86
1669 1804 2.496470 ACGAGGTCCAAACATCTACTCC 59.504 50.000 0.00 0.00 34.05 3.85
1670 1805 3.870633 ACGAGGTCCAAACATCTACTC 57.129 47.619 0.00 0.00 34.05 2.59
1671 1806 3.323979 ACAACGAGGTCCAAACATCTACT 59.676 43.478 0.00 0.00 34.05 2.57
1672 1807 3.660865 ACAACGAGGTCCAAACATCTAC 58.339 45.455 0.00 0.00 34.05 2.59
1803 1945 9.813446 TTTTATTTTAAACCGCAACTTCCTTTA 57.187 25.926 0.00 0.00 0.00 1.85
1825 1967 7.760794 TGACTTCGTACTGACTTTCTGTTTTTA 59.239 33.333 0.00 0.00 31.00 1.52
1891 2034 7.243604 TCAATCTGCCATTAATTTGGTCTTT 57.756 32.000 0.00 0.00 39.11 2.52
1897 2040 5.544650 GGGGATCAATCTGCCATTAATTTG 58.455 41.667 0.00 0.00 0.00 2.32
2064 2399 2.288152 GCGAGAAGAAGATCTAGCCCTG 60.288 54.545 0.00 0.00 40.78 4.45
2065 2400 1.960689 GCGAGAAGAAGATCTAGCCCT 59.039 52.381 0.00 0.00 40.78 5.19
2106 2446 2.045242 CCCTGACCCGACGAGAGA 60.045 66.667 0.00 0.00 0.00 3.10
2269 2609 1.404748 GGAGAGTAGTAACCTCCGCAC 59.595 57.143 0.00 0.00 35.04 5.34
2311 2652 1.827344 CACATGAGAGCTCCACCACTA 59.173 52.381 10.93 0.00 0.00 2.74
2399 2758 2.827322 TCCGAATCCGAACTTGAGGTTA 59.173 45.455 0.00 0.00 38.41 2.85
2422 2781 0.986527 AGATGATCACCACCACTGCA 59.013 50.000 0.00 0.00 0.00 4.41
2445 2804 2.567049 GTCGACCACCTCAGACGG 59.433 66.667 3.51 0.00 0.00 4.79
2498 2857 3.003113 AACTCGCAGCCGGGACTAC 62.003 63.158 2.18 0.00 36.99 2.73
2511 2870 2.161609 GCAACTATGTTTCCCCAACTCG 59.838 50.000 0.00 0.00 36.21 4.18
2543 2902 1.977009 ATCACCTGTCGTCGGCTCA 60.977 57.895 0.00 0.00 0.00 4.26
2553 2912 0.899717 AAAATGCCGCCATCACCTGT 60.900 50.000 0.00 0.00 0.00 4.00
2554 2913 0.458889 CAAAATGCCGCCATCACCTG 60.459 55.000 0.00 0.00 0.00 4.00
2555 2914 1.892338 CAAAATGCCGCCATCACCT 59.108 52.632 0.00 0.00 0.00 4.00
2558 2917 2.152297 AACGCAAAATGCCGCCATCA 62.152 50.000 0.00 0.00 41.12 3.07
2571 2930 5.811399 CCTTCATCAAGGTAATAACGCAA 57.189 39.130 0.00 0.00 44.11 4.85
2617 2976 2.433838 CAGAGCAGCACGAGTGGG 60.434 66.667 5.32 0.00 0.00 4.61
2624 2983 1.973812 GTTTCCCCCAGAGCAGCAC 60.974 63.158 0.00 0.00 0.00 4.40
2652 3011 8.361297 GACGCCATTGTCTGATCTGAAAGATG 62.361 46.154 3.59 8.47 44.07 2.90
2653 3012 6.423855 GACGCCATTGTCTGATCTGAAAGAT 61.424 44.000 3.59 0.00 45.50 2.40
2654 3013 5.152879 GACGCCATTGTCTGATCTGAAAGA 61.153 45.833 3.59 0.00 40.97 2.52
2655 3014 3.005554 ACGCCATTGTCTGATCTGAAAG 58.994 45.455 3.59 0.00 0.00 2.62
2665 3025 2.234613 CGTTGTGACGCCATTGTCT 58.765 52.632 0.00 0.00 43.03 3.41
2666 3026 4.818417 CGTTGTGACGCCATTGTC 57.182 55.556 0.00 0.00 43.03 3.18
2676 3036 2.964925 GCAGTGACGCCGTTGTGA 60.965 61.111 0.00 0.00 0.00 3.58
2686 3046 3.277742 GAAACGACGCCGCAGTGAC 62.278 63.158 0.00 0.00 39.95 3.67
2689 3049 2.733593 GAGAAACGACGCCGCAGT 60.734 61.111 0.00 0.00 39.95 4.40
2690 3050 2.430921 AGAGAAACGACGCCGCAG 60.431 61.111 0.00 0.00 39.95 5.18
2691 3051 2.430244 GAGAGAAACGACGCCGCA 60.430 61.111 0.00 0.00 39.95 5.69


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

AutoCloner maintained by Alex Coulton.