Multiple sequence alignment - TraesCS6B01G265600

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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 TraesCS6B01G265600 chr6B 100.000 3649 0 0 1 3649 477788103 477791751 0.000000e+00 6739
1 TraesCS6B01G265600 chr6A 94.655 2881 122 10 1 2872 446726408 446729265 0.000000e+00 4438
2 TraesCS6B01G265600 chr6A 91.553 438 22 5 3220 3649 446729618 446730048 1.130000e-164 590
3 TraesCS6B01G265600 chr6A 84.709 327 20 14 2906 3224 446729262 446729566 2.130000e-77 300
4 TraesCS6B01G265600 chr6D 94.758 2213 101 9 668 2872 309951860 309954065 0.000000e+00 3430
5 TraesCS6B01G265600 chr6D 91.811 635 29 8 1 633 309951246 309951859 0.000000e+00 863
6 TraesCS6B01G265600 chr6D 91.076 437 23 5 3220 3649 309954439 309954866 8.790000e-161 577
7 TraesCS6B01G265600 chr6D 88.485 330 21 9 2906 3223 309954062 309954386 2.060000e-102 383
8 TraesCS6B01G265600 chr5A 84.395 314 49 0 2082 2395 32703181 32703494 3.540000e-80 309
9 TraesCS6B01G265600 chr5A 76.776 366 82 3 1166 1530 32702683 32703046 6.180000e-48 202
10 TraesCS6B01G265600 chr5D 83.758 314 51 0 2082 2395 42922906 42923219 7.660000e-77 298
11 TraesCS6B01G265600 chr5D 76.602 359 82 2 1166 1523 42922393 42922750 2.870000e-46 196
12 TraesCS6B01G265600 chr5B 77.596 366 79 3 1166 1530 38168277 38167914 6.130000e-53 219
13 TraesCS6B01G265600 chr4A 78.662 314 65 2 2085 2397 598590780 598591092 1.330000e-49 207


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 TraesCS6B01G265600 chr6B 477788103 477791751 3648 False 6739.00 6739 100.000000 1 3649 1 chr6B.!!$F1 3648
1 TraesCS6B01G265600 chr6A 446726408 446730048 3640 False 1776.00 4438 90.305667 1 3649 3 chr6A.!!$F1 3648
2 TraesCS6B01G265600 chr6D 309951246 309954866 3620 False 1313.25 3430 91.532500 1 3649 4 chr6D.!!$F1 3648
3 TraesCS6B01G265600 chr5A 32702683 32703494 811 False 255.50 309 80.585500 1166 2395 2 chr5A.!!$F1 1229
4 TraesCS6B01G265600 chr5D 42922393 42923219 826 False 247.00 298 80.180000 1166 2395 2 chr5D.!!$F1 1229


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
155 156 0.249868 TTGGTGCCTCTTCTGTGACG 60.250 55.000 0.00 0.0 0.0 4.35 F
157 158 0.601558 GGTGCCTCTTCTGTGACGTA 59.398 55.000 0.00 0.0 0.0 3.57 F
806 828 1.003355 ATGGCCACCTCACAACTCG 60.003 57.895 8.16 0.0 0.0 4.18 F
2461 2584 0.244450 ATGCTCCAAATGTGTTGCCG 59.756 50.000 0.00 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1406 1.148273 GTGGTGACTGGTCCAGCAA 59.852 57.895 19.40 4.30 42.63 3.91 R
1483 1505 1.601903 GCGGTCAAATGTGTCAGTTGA 59.398 47.619 8.22 8.22 44.27 3.18 R
2573 2696 0.371301 CTAGCACGTAGTACGACGCA 59.629 55.000 29.56 19.73 46.05 5.24 R
3438 3631 1.065126 GGGCATAAGAAGCACCTCAGT 60.065 52.381 0.00 0.00 0.00 3.41 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
123 124 4.632688 AGGTCGTTTGGAATAATGGTAACG 59.367 41.667 0.00 0.00 39.55 3.18
151 152 3.228188 TGAATTTGGTGCCTCTTCTGT 57.772 42.857 0.00 0.00 0.00 3.41
152 153 2.886523 TGAATTTGGTGCCTCTTCTGTG 59.113 45.455 0.00 0.00 0.00 3.66
153 154 2.957402 ATTTGGTGCCTCTTCTGTGA 57.043 45.000 0.00 0.00 0.00 3.58
154 155 1.967319 TTTGGTGCCTCTTCTGTGAC 58.033 50.000 0.00 0.00 0.00 3.67
155 156 0.249868 TTGGTGCCTCTTCTGTGACG 60.250 55.000 0.00 0.00 0.00 4.35
156 157 1.367840 GGTGCCTCTTCTGTGACGT 59.632 57.895 0.00 0.00 0.00 4.34
157 158 0.601558 GGTGCCTCTTCTGTGACGTA 59.398 55.000 0.00 0.00 0.00 3.57
158 159 1.204941 GGTGCCTCTTCTGTGACGTAT 59.795 52.381 0.00 0.00 0.00 3.06
159 160 2.353803 GGTGCCTCTTCTGTGACGTATT 60.354 50.000 0.00 0.00 0.00 1.89
160 161 3.326747 GTGCCTCTTCTGTGACGTATTT 58.673 45.455 0.00 0.00 0.00 1.40
161 162 4.491676 GTGCCTCTTCTGTGACGTATTTA 58.508 43.478 0.00 0.00 0.00 1.40
162 163 5.109903 GTGCCTCTTCTGTGACGTATTTAT 58.890 41.667 0.00 0.00 0.00 1.40
163 164 5.005779 GTGCCTCTTCTGTGACGTATTTATG 59.994 44.000 0.00 0.00 0.00 1.90
229 244 2.555199 CTCCATTCCGATCCACTGTTC 58.445 52.381 0.00 0.00 0.00 3.18
340 355 4.020839 TGCAGTTAAGAGGTACCCACTTAC 60.021 45.833 21.29 17.19 36.66 2.34
398 413 8.439971 AGGACCAGTAATTATCTGATGCAAATA 58.560 33.333 13.42 0.00 35.20 1.40
500 515 9.643693 AACAAAAGATTAATTGCTTATGTGGAG 57.356 29.630 0.00 0.00 0.00 3.86
546 561 9.076596 GTAATATTTGAATGGCAAGTTCAAGAC 57.923 33.333 14.02 7.28 43.90 3.01
583 598 4.022762 TCCACAACCATAAATTCACAACCG 60.023 41.667 0.00 0.00 0.00 4.44
767 789 3.612860 CCGGACTTAGAAATGAGTTGACG 59.387 47.826 0.00 0.00 0.00 4.35
806 828 1.003355 ATGGCCACCTCACAACTCG 60.003 57.895 8.16 0.00 0.00 4.18
861 883 9.981460 ATTTTCCTTACAAGTCTATGGAAGAAT 57.019 29.630 0.87 0.00 42.81 2.40
888 910 6.577427 CGCAAAGATTTGTTTAGGAGTTACAC 59.423 38.462 7.12 0.00 40.24 2.90
889 911 7.519970 CGCAAAGATTTGTTTAGGAGTTACACT 60.520 37.037 7.12 0.00 40.24 3.55
890 912 8.780249 GCAAAGATTTGTTTAGGAGTTACACTA 58.220 33.333 7.12 0.00 40.24 2.74
986 1008 8.523523 TTCACAATTTGATCTAACTTTGCATG 57.476 30.769 2.79 0.00 32.84 4.06
1096 1118 3.644966 TGAGAAACAAAGGTGGTGTCT 57.355 42.857 0.00 0.00 0.00 3.41
1102 1124 1.308998 CAAAGGTGGTGTCTGGTCAC 58.691 55.000 0.00 0.00 37.57 3.67
1120 1142 4.181578 GTCACGAGCAAAGTATGTGGTAT 58.818 43.478 0.00 0.00 31.55 2.73
1137 1159 2.609491 GGTATCAACGTGTGCAGTCTCA 60.609 50.000 0.00 0.00 0.00 3.27
1290 1312 1.164041 CGTTGGAACCCGCTGAACTT 61.164 55.000 0.00 0.00 0.00 2.66
1356 1378 3.443681 GGTTCACTACATTGGGGATTGTG 59.556 47.826 0.00 0.00 0.00 3.33
1384 1406 1.140052 TGGACAACGACAATGTGACCT 59.860 47.619 0.00 0.00 0.00 3.85
1483 1505 0.772124 TGCTGAGGACCTCCCCTTTT 60.772 55.000 19.11 0.00 36.49 2.27
1598 1620 4.954875 ACTGATCTTATACCAGCTTGAGC 58.045 43.478 0.00 0.00 42.49 4.26
1648 1670 5.869888 CCTTTCCTGTTGCTACTTACTACTG 59.130 44.000 0.00 0.00 0.00 2.74
1735 1757 7.496346 TTACTTGACTAAATCCATCTGACCT 57.504 36.000 0.00 0.00 0.00 3.85
1844 1866 4.468713 TGTTTCCAGTTGTCCATGATTCA 58.531 39.130 0.00 0.00 0.00 2.57
1890 1912 5.946942 ACTCTGCTGGAAGAAATGATCTA 57.053 39.130 0.00 0.00 37.42 1.98
1891 1913 6.305272 ACTCTGCTGGAAGAAATGATCTAA 57.695 37.500 0.00 0.00 37.42 2.10
1892 1914 6.897986 ACTCTGCTGGAAGAAATGATCTAAT 58.102 36.000 0.00 0.00 37.42 1.73
1893 1915 7.344913 ACTCTGCTGGAAGAAATGATCTAATT 58.655 34.615 0.00 0.00 37.42 1.40
1946 1968 5.424252 ACAGATACCTTTGGTCGATCCTTTA 59.576 40.000 0.00 0.00 37.09 1.85
1947 1969 6.099845 ACAGATACCTTTGGTCGATCCTTTAT 59.900 38.462 0.00 0.00 37.09 1.40
1951 1973 9.503399 GATACCTTTGGTCGATCCTTTATTATT 57.497 33.333 0.00 0.00 37.09 1.40
1965 1991 8.348285 TCCTTTATTATTTGTTAAGCTGCTGT 57.652 30.769 1.35 0.00 0.00 4.40
2024 2051 9.679661 TGGCTTAGATTTTATTATTGTGAGTCA 57.320 29.630 0.00 0.00 0.00 3.41
2034 2061 6.683974 ATTATTGTGAGTCAAGTGCCATAC 57.316 37.500 0.00 0.00 39.55 2.39
2228 2351 1.742761 CCGACATGTGGATGCTCTTT 58.257 50.000 9.73 0.00 32.14 2.52
2232 2355 1.637553 ACATGTGGATGCTCTTTCCCT 59.362 47.619 0.00 0.00 32.14 4.20
2397 2520 0.541863 CGACTCCCCTTTGCAGGTAT 59.458 55.000 0.00 0.00 38.79 2.73
2427 2550 0.246635 TCCGTAGCTGCCAGACTTTC 59.753 55.000 0.00 0.00 0.00 2.62
2445 2568 6.150809 AGACTTTCTTTTCTCCATCTCAATGC 59.849 38.462 0.00 0.00 0.00 3.56
2451 2574 4.305539 TTCTCCATCTCAATGCTCCAAA 57.694 40.909 0.00 0.00 0.00 3.28
2459 2582 2.991190 CTCAATGCTCCAAATGTGTTGC 59.009 45.455 0.00 0.00 0.00 4.17
2461 2584 0.244450 ATGCTCCAAATGTGTTGCCG 59.756 50.000 0.00 0.00 0.00 5.69
2469 2592 3.364964 CCAAATGTGTTGCCGTCTCTTAC 60.365 47.826 0.00 0.00 0.00 2.34
2470 2593 2.094762 ATGTGTTGCCGTCTCTTACC 57.905 50.000 0.00 0.00 0.00 2.85
2524 2647 1.680249 GGCTGAGGATGTTGAGGAACC 60.680 57.143 0.00 0.00 0.00 3.62
2534 2657 2.901192 TGTTGAGGAACCGGTGAATCTA 59.099 45.455 8.52 0.00 0.00 1.98
2651 2774 1.376609 AAGGCCAGCCGATTTAAGCG 61.377 55.000 5.01 0.00 41.95 4.68
2654 2777 1.508632 GCCAGCCGATTTAAGCGATA 58.491 50.000 3.56 0.00 0.00 2.92
2660 2783 4.617645 CAGCCGATTTAAGCGATAGTAGTC 59.382 45.833 3.56 0.00 39.35 2.59
2673 2796 7.952671 AGCGATAGTAGTCAAGATCCAATTTA 58.047 34.615 0.00 0.00 39.35 1.40
2705 2830 2.680913 GCCACCTGTAGTGCTTGCG 61.681 63.158 0.00 0.00 45.83 4.85
2729 2854 6.628621 CGGTTCCCTACTCATGTATGTTTGTA 60.629 42.308 0.00 0.00 0.00 2.41
2744 2869 5.133707 TGTTTGTACTTTTCTTGTCGTCG 57.866 39.130 0.00 0.00 0.00 5.12
2745 2870 4.033129 TGTTTGTACTTTTCTTGTCGTCGG 59.967 41.667 0.00 0.00 0.00 4.79
2842 2967 3.518590 GATGAAATGCAAAGGAGCTTGG 58.481 45.455 0.00 0.00 34.99 3.61
2872 2997 6.802608 CATCAAAATGCATCCTCTAACATGT 58.197 36.000 0.00 0.00 0.00 3.21
2873 2998 6.198650 TCAAAATGCATCCTCTAACATGTG 57.801 37.500 0.00 0.00 0.00 3.21
2874 2999 4.644103 AAATGCATCCTCTAACATGTGC 57.356 40.909 0.00 0.00 0.00 4.57
2875 3000 2.042686 TGCATCCTCTAACATGTGCC 57.957 50.000 0.00 0.00 0.00 5.01
2876 3001 1.561076 TGCATCCTCTAACATGTGCCT 59.439 47.619 0.00 0.00 0.00 4.75
2877 3002 1.945394 GCATCCTCTAACATGTGCCTG 59.055 52.381 0.00 0.00 0.00 4.85
2878 3003 2.681976 GCATCCTCTAACATGTGCCTGT 60.682 50.000 0.00 0.00 0.00 4.00
2879 3004 2.768253 TCCTCTAACATGTGCCTGTG 57.232 50.000 0.00 0.00 0.00 3.66
2880 3005 1.278985 TCCTCTAACATGTGCCTGTGG 59.721 52.381 0.00 1.10 0.00 4.17
2881 3006 1.278985 CCTCTAACATGTGCCTGTGGA 59.721 52.381 0.00 0.00 0.00 4.02
2882 3007 2.290260 CCTCTAACATGTGCCTGTGGAA 60.290 50.000 0.00 0.00 0.00 3.53
2883 3008 3.614092 CTCTAACATGTGCCTGTGGAAT 58.386 45.455 0.00 0.00 0.00 3.01
2884 3009 3.346315 TCTAACATGTGCCTGTGGAATG 58.654 45.455 0.00 0.00 0.00 2.67
2885 3010 2.291209 AACATGTGCCTGTGGAATGA 57.709 45.000 0.00 0.00 0.00 2.57
2886 3011 1.538047 ACATGTGCCTGTGGAATGAC 58.462 50.000 0.00 0.00 0.00 3.06
2887 3012 1.202915 ACATGTGCCTGTGGAATGACA 60.203 47.619 0.00 0.00 0.00 3.58
2888 3013 2.097036 CATGTGCCTGTGGAATGACAT 58.903 47.619 0.00 0.00 0.00 3.06
2889 3014 2.291209 TGTGCCTGTGGAATGACATT 57.709 45.000 0.00 0.00 0.00 2.71
2890 3015 2.161855 TGTGCCTGTGGAATGACATTC 58.838 47.619 18.24 18.24 38.55 2.67
2891 3016 2.161855 GTGCCTGTGGAATGACATTCA 58.838 47.619 25.59 11.94 41.03 2.57
2892 3017 2.756760 GTGCCTGTGGAATGACATTCAT 59.243 45.455 25.59 0.00 41.03 2.57
2893 3018 3.947196 GTGCCTGTGGAATGACATTCATA 59.053 43.478 25.59 13.63 41.03 2.15
2894 3019 3.947196 TGCCTGTGGAATGACATTCATAC 59.053 43.478 25.59 22.34 41.03 2.39
2895 3020 3.316308 GCCTGTGGAATGACATTCATACC 59.684 47.826 25.59 12.39 41.03 2.73
2896 3021 3.885297 CCTGTGGAATGACATTCATACCC 59.115 47.826 25.59 12.06 41.03 3.69
2897 3022 3.540617 TGTGGAATGACATTCATACCCG 58.459 45.455 25.59 0.00 41.03 5.28
2898 3023 3.054728 TGTGGAATGACATTCATACCCGT 60.055 43.478 25.59 0.00 41.03 5.28
2899 3024 4.162509 TGTGGAATGACATTCATACCCGTA 59.837 41.667 25.59 8.72 41.03 4.02
2900 3025 5.163248 TGTGGAATGACATTCATACCCGTAT 60.163 40.000 25.59 0.00 41.03 3.06
2901 3026 5.408604 GTGGAATGACATTCATACCCGTATC 59.591 44.000 25.59 8.22 41.03 2.24
2902 3027 5.071115 TGGAATGACATTCATACCCGTATCA 59.929 40.000 25.59 10.39 41.03 2.15
2903 3028 5.995282 GGAATGACATTCATACCCGTATCAA 59.005 40.000 25.59 0.00 41.03 2.57
2904 3029 6.073222 GGAATGACATTCATACCCGTATCAAC 60.073 42.308 25.59 3.65 41.03 3.18
2989 3114 2.215196 GTGGCGAACTTGTTAGGTTCA 58.785 47.619 7.24 0.00 41.99 3.18
2990 3115 2.614983 GTGGCGAACTTGTTAGGTTCAA 59.385 45.455 7.24 0.00 41.99 2.69
2991 3116 3.252458 GTGGCGAACTTGTTAGGTTCAAT 59.748 43.478 7.24 0.00 41.99 2.57
2992 3117 3.886505 TGGCGAACTTGTTAGGTTCAATT 59.113 39.130 7.24 0.00 41.99 2.32
2993 3118 4.023536 TGGCGAACTTGTTAGGTTCAATTC 60.024 41.667 7.24 0.00 41.99 2.17
3014 3139 2.124277 AATTCGGTAAGTCCCCTTGC 57.876 50.000 0.00 0.00 33.03 4.01
3023 3148 0.111253 AGTCCCCTTGCTGTCTTTGG 59.889 55.000 0.00 0.00 0.00 3.28
3032 3157 5.440610 CCTTGCTGTCTTTGGTATATCCTT 58.559 41.667 0.00 0.00 37.07 3.36
3042 3167 9.628500 GTCTTTGGTATATCCTTTATTCCTGTT 57.372 33.333 0.00 0.00 37.07 3.16
3043 3168 9.627123 TCTTTGGTATATCCTTTATTCCTGTTG 57.373 33.333 0.00 0.00 37.07 3.33
3056 3187 1.202639 TCCTGTTGCCTACATATGCCG 60.203 52.381 1.58 0.00 35.85 5.69
3057 3188 1.475034 CCTGTTGCCTACATATGCCGT 60.475 52.381 1.58 0.00 35.85 5.68
3078 3209 4.134563 GTCATTACCAAGACCACACACTT 58.865 43.478 0.00 0.00 0.00 3.16
3079 3210 4.213482 GTCATTACCAAGACCACACACTTC 59.787 45.833 0.00 0.00 0.00 3.01
3122 3253 8.363390 TGTCATGGAAAGAGTAGCATCTTATAG 58.637 37.037 0.00 0.00 38.59 1.31
3137 3272 9.902684 AGCATCTTATAGATAAAATCCATGAGG 57.097 33.333 0.00 0.00 32.12 3.86
3149 3284 3.555527 TCCATGAGGCAAGAAGAGATG 57.444 47.619 0.00 0.00 33.74 2.90
3251 3444 3.242518 TGATCTTAGACAACGCGAACAG 58.757 45.455 15.93 1.12 0.00 3.16
3254 3447 1.455786 CTTAGACAACGCGAACAGTGG 59.544 52.381 15.93 0.00 33.90 4.00
3291 3484 4.081198 ACCACCAAAAATCTGTCTTTGCAA 60.081 37.500 0.00 0.00 32.31 4.08
3299 3492 6.956299 AAATCTGTCTTTGCAATTACATGC 57.044 33.333 13.05 0.00 46.58 4.06
3315 3508 6.756299 TTACATGCTATGCAACATGAAGAA 57.244 33.333 25.60 16.36 45.23 2.52
3369 3562 6.366332 ACATGAAGAGTAGCAAACTTAACTCG 59.634 38.462 0.00 0.00 42.51 4.18
3379 3572 4.796312 GCAAACTTAACTCGCAGAAAACAA 59.204 37.500 0.00 0.00 34.09 2.83
3398 3591 7.760131 AAACAAGACACATTTTCAGAACATG 57.240 32.000 7.62 7.62 0.00 3.21
3412 3605 4.758674 TCAGAACATGAAGAAGGAAAGCAG 59.241 41.667 0.00 0.00 34.02 4.24
3422 3615 2.758736 AGGAAAGCAGCTACACAGAG 57.241 50.000 0.00 0.00 0.00 3.35
3425 3618 2.146342 GAAAGCAGCTACACAGAGCAA 58.854 47.619 0.00 0.00 45.43 3.91
3437 3630 3.087031 CACAGAGCAAATCACCTCCAAT 58.913 45.455 0.00 0.00 0.00 3.16
3438 3631 4.263462 ACACAGAGCAAATCACCTCCAATA 60.263 41.667 0.00 0.00 0.00 1.90
3520 3721 1.009829 GGTACTTTGCTGCCATCTCG 58.990 55.000 0.00 0.00 0.00 4.04
3583 3784 3.164268 TGCTCTCTTCTCTTCAGCTTCT 58.836 45.455 0.00 0.00 0.00 2.85
3622 3823 6.238842 CCTTTTTGTTCTTCATCTTCTCAGCA 60.239 38.462 0.00 0.00 0.00 4.41
3627 3828 7.783090 TGTTCTTCATCTTCTCAGCATATTC 57.217 36.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 6.272822 AGAGGCACCAAATTCATTTAGTTC 57.727 37.500 0.00 0.00 0.00 3.01
229 244 1.349026 TCTGCCAAGAGACCCAAGAAG 59.651 52.381 0.00 0.00 0.00 2.85
497 512 6.534634 ACACCTTATTTGCTGGATATACTCC 58.465 40.000 0.00 0.00 45.19 3.85
583 598 2.988010 TCTACTGATGTGGACATGGC 57.012 50.000 0.00 0.00 36.57 4.40
767 789 2.155279 GGAGACAAGTTCTTGGCCTTC 58.845 52.381 13.91 6.89 33.22 3.46
806 828 0.250234 TCACATACCAGTGCTCCTGC 59.750 55.000 0.00 0.00 40.06 4.85
861 883 6.385649 AACTCCTAAACAAATCTTTGCGAA 57.614 33.333 2.63 0.00 41.79 4.70
986 1008 3.442977 ACAAGCCATTTCTTGATCTCTGC 59.557 43.478 10.10 0.00 44.61 4.26
1096 1118 2.412870 CACATACTTTGCTCGTGACCA 58.587 47.619 0.00 0.00 0.00 4.02
1102 1124 4.259810 CGTTGATACCACATACTTTGCTCG 60.260 45.833 0.00 0.00 0.00 5.03
1120 1142 1.341209 AGATGAGACTGCACACGTTGA 59.659 47.619 0.00 0.00 0.00 3.18
1236 1258 1.565390 CCTCAGTCCAATGCCCTGGA 61.565 60.000 0.00 0.00 43.45 3.86
1290 1312 6.767524 ACAACCTTGAACTCATTGTTGTAA 57.232 33.333 18.46 0.00 43.14 2.41
1356 1378 1.225855 TGTCGTTGTCCACATGCTTC 58.774 50.000 0.00 0.00 0.00 3.86
1384 1406 1.148273 GTGGTGACTGGTCCAGCAA 59.852 57.895 19.40 4.30 42.63 3.91
1483 1505 1.601903 GCGGTCAAATGTGTCAGTTGA 59.398 47.619 8.22 8.22 44.27 3.18
1605 1627 9.997172 AGGAAAGGATGAAGGTTAAGAAAATAT 57.003 29.630 0.00 0.00 0.00 1.28
1648 1670 7.200455 GGCAATAACAAGGTATTGACATTACC 58.800 38.462 19.19 15.77 45.32 2.85
1720 1742 8.988060 TGTTTATACTGAGGTCAGATGGATTTA 58.012 33.333 13.99 0.00 46.59 1.40
1844 1866 9.965902 AGTATCAGGACTTCAATAACATTTCTT 57.034 29.630 0.00 0.00 0.00 2.52
1946 1968 7.925483 TGTTCAAACAGCAGCTTAACAAATAAT 59.075 29.630 0.00 0.00 34.30 1.28
1947 1969 7.261325 TGTTCAAACAGCAGCTTAACAAATAA 58.739 30.769 0.00 0.00 34.30 1.40
1951 1973 4.710423 TGTTCAAACAGCAGCTTAACAA 57.290 36.364 0.00 0.00 34.30 2.83
2034 2061 2.691409 TGAAACGGAGGCATAAGAGG 57.309 50.000 0.00 0.00 0.00 3.69
2228 2351 6.069323 ACTCTATGTACTCTTCTTCTGAGGGA 60.069 42.308 0.00 0.00 35.98 4.20
2232 2355 6.486056 ACCACTCTATGTACTCTTCTTCTGA 58.514 40.000 0.00 0.00 0.00 3.27
2397 2520 3.044235 CAGCTACGGATGCATGGAATA 57.956 47.619 2.46 0.00 0.00 1.75
2427 2550 4.267536 TGGAGCATTGAGATGGAGAAAAG 58.732 43.478 0.00 0.00 33.72 2.27
2445 2568 1.197721 GAGACGGCAACACATTTGGAG 59.802 52.381 0.00 0.00 0.00 3.86
2451 2574 1.338769 GGGTAAGAGACGGCAACACAT 60.339 52.381 0.00 0.00 0.00 3.21
2469 2592 2.674747 GCAGCAACAACATACCAATGGG 60.675 50.000 3.55 0.00 37.43 4.00
2470 2593 2.029200 TGCAGCAACAACATACCAATGG 60.029 45.455 0.00 0.00 37.43 3.16
2524 2647 1.536284 GGAAGGCGAGTAGATTCACCG 60.536 57.143 0.00 0.00 0.00 4.94
2534 2657 3.007973 GCGGAAGAGGAAGGCGAGT 62.008 63.158 0.00 0.00 0.00 4.18
2573 2696 0.371301 CTAGCACGTAGTACGACGCA 59.629 55.000 29.56 19.73 46.05 5.24
2651 2774 8.371699 AGCCTAAATTGGATCTTGACTACTATC 58.628 37.037 0.00 0.00 0.00 2.08
2654 2777 6.567602 AGCCTAAATTGGATCTTGACTACT 57.432 37.500 0.00 0.00 0.00 2.57
2660 2783 7.814264 ACATAGAAGCCTAAATTGGATCTTG 57.186 36.000 0.00 0.00 0.00 3.02
2729 2854 3.991367 AGATTCCGACGACAAGAAAAGT 58.009 40.909 0.00 0.00 0.00 2.66
2738 2863 3.369756 TGCATAAACAAGATTCCGACGAC 59.630 43.478 0.00 0.00 0.00 4.34
2744 2869 5.185828 AGTCCCTTTGCATAAACAAGATTCC 59.814 40.000 0.00 0.00 0.00 3.01
2745 2870 6.272822 AGTCCCTTTGCATAAACAAGATTC 57.727 37.500 0.00 0.00 0.00 2.52
2773 2898 2.699954 CCTCTACAATTCCGCAAGTGT 58.300 47.619 0.00 0.00 43.19 3.55
2842 2967 4.110482 GAGGATGCATTTTGATGCTTCAC 58.890 43.478 21.21 14.00 46.93 3.18
2868 2993 1.536940 TGTCATTCCACAGGCACATG 58.463 50.000 0.00 0.00 0.00 3.21
2869 2994 2.519771 ATGTCATTCCACAGGCACAT 57.480 45.000 0.00 0.00 0.00 3.21
2870 2995 2.161855 GAATGTCATTCCACAGGCACA 58.838 47.619 13.74 0.00 33.17 4.57
2871 2996 2.161855 TGAATGTCATTCCACAGGCAC 58.838 47.619 20.41 0.00 38.50 5.01
2872 2997 2.583024 TGAATGTCATTCCACAGGCA 57.417 45.000 20.41 0.55 38.50 4.75
2873 2998 3.316308 GGTATGAATGTCATTCCACAGGC 59.684 47.826 20.41 6.98 42.00 4.85
2874 2999 3.885297 GGGTATGAATGTCATTCCACAGG 59.115 47.826 20.41 0.00 43.55 4.00
2875 3000 3.561310 CGGGTATGAATGTCATTCCACAG 59.439 47.826 20.41 12.60 43.55 3.66
2876 3001 3.054728 ACGGGTATGAATGTCATTCCACA 60.055 43.478 20.41 5.62 43.55 4.17
2877 3002 3.541632 ACGGGTATGAATGTCATTCCAC 58.458 45.455 20.41 17.19 43.55 4.02
2878 3003 3.924114 ACGGGTATGAATGTCATTCCA 57.076 42.857 20.41 10.59 43.55 3.53
2879 3004 5.547465 TGATACGGGTATGAATGTCATTCC 58.453 41.667 20.41 7.01 41.78 3.01
2880 3005 6.073222 GGTTGATACGGGTATGAATGTCATTC 60.073 42.308 17.21 17.21 38.26 2.67
2881 3006 5.763204 GGTTGATACGGGTATGAATGTCATT 59.237 40.000 0.00 0.00 38.26 2.57
2882 3007 5.163248 TGGTTGATACGGGTATGAATGTCAT 60.163 40.000 0.00 0.00 40.72 3.06
2883 3008 4.162509 TGGTTGATACGGGTATGAATGTCA 59.837 41.667 0.00 0.00 0.00 3.58
2884 3009 4.699637 TGGTTGATACGGGTATGAATGTC 58.300 43.478 0.00 0.00 0.00 3.06
2885 3010 4.764050 TGGTTGATACGGGTATGAATGT 57.236 40.909 0.00 0.00 0.00 2.71
2886 3011 4.455533 CCATGGTTGATACGGGTATGAATG 59.544 45.833 2.57 0.00 0.00 2.67
2887 3012 4.104102 ACCATGGTTGATACGGGTATGAAT 59.896 41.667 13.00 0.00 0.00 2.57
2888 3013 3.456644 ACCATGGTTGATACGGGTATGAA 59.543 43.478 13.00 0.00 0.00 2.57
2889 3014 3.042682 ACCATGGTTGATACGGGTATGA 58.957 45.455 13.00 0.00 0.00 2.15
2890 3015 3.138304 CACCATGGTTGATACGGGTATG 58.862 50.000 16.84 0.00 0.00 2.39
2891 3016 3.042682 TCACCATGGTTGATACGGGTAT 58.957 45.455 16.84 0.00 0.00 2.73
2892 3017 2.468915 TCACCATGGTTGATACGGGTA 58.531 47.619 16.84 0.00 0.00 3.69
2893 3018 1.281419 TCACCATGGTTGATACGGGT 58.719 50.000 16.84 0.00 0.00 5.28
2894 3019 2.411628 TTCACCATGGTTGATACGGG 57.588 50.000 16.84 0.77 0.00 5.28
2895 3020 3.756434 AGTTTTCACCATGGTTGATACGG 59.244 43.478 16.84 1.62 0.00 4.02
2896 3021 4.722194 CAGTTTTCACCATGGTTGATACG 58.278 43.478 16.84 2.47 0.00 3.06
2897 3022 4.485163 GCAGTTTTCACCATGGTTGATAC 58.515 43.478 16.84 15.50 0.00 2.24
2898 3023 3.509575 GGCAGTTTTCACCATGGTTGATA 59.490 43.478 16.84 8.82 0.00 2.15
2899 3024 2.299867 GGCAGTTTTCACCATGGTTGAT 59.700 45.455 16.84 0.00 0.00 2.57
2900 3025 1.686052 GGCAGTTTTCACCATGGTTGA 59.314 47.619 16.84 13.57 0.00 3.18
2901 3026 1.411977 TGGCAGTTTTCACCATGGTTG 59.588 47.619 16.84 11.33 0.00 3.77
2902 3027 1.786937 TGGCAGTTTTCACCATGGTT 58.213 45.000 16.84 0.00 0.00 3.67
2903 3028 2.014010 ATGGCAGTTTTCACCATGGT 57.986 45.000 13.00 13.00 42.59 3.55
2904 3029 3.355378 TCTATGGCAGTTTTCACCATGG 58.645 45.455 11.19 11.19 43.93 3.66
2956 3081 1.153353 TCGCCACCGAATTTTCAGTC 58.847 50.000 0.00 0.00 41.17 3.51
2989 3114 4.930696 AGGGGACTTACCGAATTTGAATT 58.069 39.130 0.00 0.00 37.44 2.17
2990 3115 4.586306 AGGGGACTTACCGAATTTGAAT 57.414 40.909 0.00 0.00 37.44 2.57
3014 3139 9.277783 CAGGAATAAAGGATATACCAAAGACAG 57.722 37.037 0.00 0.00 42.04 3.51
3023 3148 8.154856 TGTAGGCAACAGGAATAAAGGATATAC 58.845 37.037 0.00 0.00 41.41 1.47
3032 3157 5.070001 GGCATATGTAGGCAACAGGAATAA 58.930 41.667 4.29 0.00 42.70 1.40
3042 3167 2.928801 AATGACGGCATATGTAGGCA 57.071 45.000 2.90 9.88 34.14 4.75
3043 3168 3.000727 GGTAATGACGGCATATGTAGGC 58.999 50.000 2.90 1.52 33.44 3.93
3056 3187 3.740115 AGTGTGTGGTCTTGGTAATGAC 58.260 45.455 0.00 0.00 0.00 3.06
3057 3188 4.141597 TGAAGTGTGTGGTCTTGGTAATGA 60.142 41.667 0.00 0.00 0.00 2.57
3078 3209 4.206375 TGACAATGCTTGTTTCCTCTTGA 58.794 39.130 3.56 0.00 45.52 3.02
3079 3210 4.572985 TGACAATGCTTGTTTCCTCTTG 57.427 40.909 3.56 0.00 45.52 3.02
3122 3253 6.769822 TCTCTTCTTGCCTCATGGATTTTATC 59.230 38.462 0.00 0.00 34.57 1.75
3137 3272 6.336566 TGTTCAGAGTATCATCTCTTCTTGC 58.663 40.000 0.00 0.00 42.10 4.01
3149 3284 5.840715 TCTGCATGAGATGTTCAGAGTATC 58.159 41.667 0.00 0.00 39.68 2.24
3236 3429 0.669619 TCCACTGTTCGCGTTGTCTA 59.330 50.000 5.77 0.00 0.00 2.59
3251 3444 6.294361 TGGTGGTACATATATAGCATCCAC 57.706 41.667 15.51 15.51 44.52 4.02
3291 3484 6.947644 TCTTCATGTTGCATAGCATGTAAT 57.052 33.333 19.15 0.00 43.52 1.89
3299 3492 5.180868 GGGAGCTATTCTTCATGTTGCATAG 59.819 44.000 0.00 0.00 0.00 2.23
3335 3528 8.940952 GTTTGCTACTCTTCATGTTATCTTTCT 58.059 33.333 0.00 0.00 0.00 2.52
3336 3529 8.940952 AGTTTGCTACTCTTCATGTTATCTTTC 58.059 33.333 0.00 0.00 28.23 2.62
3355 3548 4.095782 TGTTTTCTGCGAGTTAAGTTTGCT 59.904 37.500 9.14 0.00 0.00 3.91
3369 3562 6.035843 TCTGAAAATGTGTCTTGTTTTCTGC 58.964 36.000 10.11 0.00 40.62 4.26
3379 3572 7.255381 CCTTCTTCATGTTCTGAAAATGTGTCT 60.255 37.037 17.74 0.00 43.20 3.41
3398 3591 3.403038 TGTGTAGCTGCTTTCCTTCTTC 58.597 45.455 7.79 0.00 0.00 2.87
3405 3598 1.800805 TGCTCTGTGTAGCTGCTTTC 58.199 50.000 7.79 2.35 43.19 2.62
3409 3602 2.079158 TGATTTGCTCTGTGTAGCTGC 58.921 47.619 0.00 0.00 43.19 5.25
3412 3605 2.675348 GAGGTGATTTGCTCTGTGTAGC 59.325 50.000 0.00 0.00 43.08 3.58
3422 3615 3.629398 CCTCAGTATTGGAGGTGATTTGC 59.371 47.826 0.00 0.00 45.59 3.68
3437 3630 2.170607 GGGCATAAGAAGCACCTCAGTA 59.829 50.000 0.00 0.00 0.00 2.74
3438 3631 1.065126 GGGCATAAGAAGCACCTCAGT 60.065 52.381 0.00 0.00 0.00 3.41
3520 3721 2.070028 GAAGAAGTTCTCAAGGCCGAC 58.930 52.381 5.70 0.00 0.00 4.79
3622 3823 4.855340 TGGAAAAGAAGAAGGCCGAATAT 58.145 39.130 0.00 0.00 0.00 1.28
3627 3828 2.226674 GAGTTGGAAAAGAAGAAGGCCG 59.773 50.000 0.00 0.00 0.00 6.13



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

AutoCloner maintained by Alex Coulton.