Multiple sequence alignment - TraesCS4B01G246900

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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 TraesCS4B01G246900 chr4B 100.000 3895 0 0 845 4739 511158059 511161953 0.000000e+00 7193.0
1 TraesCS4B01G246900 chr4B 100.000 324 0 0 1 324 511157215 511157538 2.440000e-167 599.0
2 TraesCS4B01G246900 chr4A 91.788 3373 199 27 845 4199 48533168 48529856 0.000000e+00 4623.0
3 TraesCS4B01G246900 chr4A 95.152 330 9 4 1 324 48533607 48533279 9.090000e-142 514.0
4 TraesCS4B01G246900 chr4A 82.918 562 36 29 4231 4739 48529745 48529191 7.230000e-123 451.0
5 TraesCS4B01G246900 chr4A 95.833 48 1 1 4200 4247 48529823 48529777 5.090000e-10 76.8
6 TraesCS4B01G246900 chr4D 91.426 3359 194 36 861 4199 414993986 414997270 0.000000e+00 4521.0
7 TraesCS4B01G246900 chr4D 86.481 540 31 18 4231 4739 414997354 414997882 5.360000e-154 555.0
8 TraesCS4B01G246900 chr4D 95.062 324 14 2 1 324 414993560 414993881 4.230000e-140 508.0
9 TraesCS4B01G246900 chr6B 86.508 126 11 3 2806 2925 54417521 54417646 2.980000e-27 134.0
10 TraesCS4B01G246900 chr7A 91.765 85 7 0 2635 2719 450089287 450089203 8.330000e-23 119.0


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 TraesCS4B01G246900 chr4B 511157215 511161953 4738 False 3896.000000 7193 100.000000 1 4739 2 chr4B.!!$F1 4738
1 TraesCS4B01G246900 chr4A 48529191 48533607 4416 True 1416.200000 4623 91.422750 1 4739 4 chr4A.!!$R1 4738
2 TraesCS4B01G246900 chr4D 414993560 414997882 4322 False 1861.333333 4521 90.989667 1 4739 3 chr4D.!!$F1 4738

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
961 969 0.034477 CTCCATTTTGCCCCGTACCT 60.034 55.0 0.0 0.0 0.00 3.08 F
1887 1906 0.819582 CCACCATGTTCAATGAGCCC 59.180 55.0 0.0 0.0 0.00 5.19 F
3517 3540 0.447011 GCTTGCTCTGTGATCTGTGC 59.553 55.0 0.0 0.0 34.33 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2305 1.518102 GCAACAACAATGTCACGCTTG 59.482 47.619 0.00 0.00 39.4 4.01 R
3696 3722 0.107116 TCTCCTCGAGCTGGTACCTC 60.107 60.000 14.36 5.02 0.0 3.85 R
4515 4669 0.037326 TTAGTGGCTGGCTTCTCACG 60.037 55.000 2.00 0.00 35.5 4.35 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
170 172 0.047802 ATCCCATCCCCTCTCCCAAA 59.952 55.000 0.00 0.00 0.00 3.28
182 184 1.063717 TCTCCCAAATCCAAGCCATCC 60.064 52.381 0.00 0.00 0.00 3.51
246 253 4.771356 TTCCGGAAGACGCGCGAG 62.771 66.667 39.36 18.41 42.52 5.03
870 877 0.387878 GTAGCATCTCGCCGGATCTG 60.388 60.000 5.05 0.00 44.04 2.90
873 880 1.006805 CATCTCGCCGGATCTGTCC 60.007 63.158 5.05 0.00 41.40 4.02
897 904 0.249073 CTTCTGCGCGTAGGCATAGT 60.249 55.000 24.11 0.00 42.99 2.12
934 942 4.143221 GCTCGTTTGTCTTCAGAATCTGTC 60.143 45.833 10.36 1.17 32.61 3.51
961 969 0.034477 CTCCATTTTGCCCCGTACCT 60.034 55.000 0.00 0.00 0.00 3.08
983 991 4.454678 TGCACAGATCTGTTCTTCTTTGT 58.545 39.130 25.84 0.00 42.83 2.83
990 998 4.265904 TCTGTTCTTCTTTGTGCCGATA 57.734 40.909 0.00 0.00 0.00 2.92
1004 1012 1.906574 GCCGATATCCCCCTGTATGAA 59.093 52.381 0.00 0.00 0.00 2.57
1010 1018 5.513094 CGATATCCCCCTGTATGAAATGTGT 60.513 44.000 0.00 0.00 0.00 3.72
1011 1019 4.608170 ATCCCCCTGTATGAAATGTGTT 57.392 40.909 0.00 0.00 0.00 3.32
1029 1037 2.223971 TGTTCCTGACGGACTGTTCTTC 60.224 50.000 0.00 0.00 39.60 2.87
1036 1044 1.270358 ACGGACTGTTCTTCTTGCCTC 60.270 52.381 0.00 0.00 0.00 4.70
1131 1139 2.037136 CGGCAAGCTCCAGAACCTG 61.037 63.158 0.00 0.00 0.00 4.00
1254 1262 1.691976 TCATCCTTCACTGAACACCGT 59.308 47.619 0.00 0.00 0.00 4.83
1285 1293 0.908910 TACACGGCAGGATGGTGATT 59.091 50.000 0.00 0.00 33.34 2.57
1321 1329 2.045926 GTGTCCCAGGCGCTTGAT 60.046 61.111 22.50 0.00 0.00 2.57
1348 1356 2.662006 TCAAGAGCGAGGTCAAGATG 57.338 50.000 5.06 0.00 0.00 2.90
1462 1470 3.103911 CACGACGTGAAGTCCGCC 61.104 66.667 23.39 0.00 46.92 6.13
1508 1516 3.124297 CGGAAAGTAAGCTCTTCTTGCAG 59.876 47.826 0.00 0.00 39.49 4.41
1549 1557 5.766222 ACTGTTCTGCTGATGAAATTTGTC 58.234 37.500 0.00 0.00 0.00 3.18
1742 1750 1.611673 CGTGGAGAAGGCCATGTCTTT 60.612 52.381 5.01 0.00 40.68 2.52
1784 1800 5.501156 GAGGATGTAAGTTCCCTGTCAAAT 58.499 41.667 0.00 0.00 33.45 2.32
1790 1806 4.326504 AAGTTCCCTGTCAAATGCTTTG 57.673 40.909 3.17 3.17 41.96 2.77
1806 1822 5.911378 TGCTTTGATACATGTATTTGCCA 57.089 34.783 19.19 9.93 0.00 4.92
1817 1833 4.744795 TGTATTTGCCAAACCAAGTTGT 57.255 36.364 1.45 0.00 0.00 3.32
1833 1849 5.177696 CCAAGTTGTAACTGTAAGCTGACTC 59.822 44.000 2.06 0.00 39.66 3.36
1887 1906 0.819582 CCACCATGTTCAATGAGCCC 59.180 55.000 0.00 0.00 0.00 5.19
1959 1978 1.377202 GGGGTCGCTCAGAATTGCA 60.377 57.895 0.00 0.00 0.00 4.08
2006 2025 5.539574 AGAATGACTATGAGATGACCCTGAG 59.460 44.000 0.00 0.00 0.00 3.35
2037 2056 2.172505 TGTTGTTGAAGAAGCTGAGGGA 59.827 45.455 0.00 0.00 0.00 4.20
2052 2071 4.125703 CTGAGGGAGAATCTTTCATTCCG 58.874 47.826 0.00 0.00 33.73 4.30
2169 2188 8.258007 AGTGAGCTATATTAGTAACTTGTTGCA 58.742 33.333 4.58 0.00 0.00 4.08
2175 2194 9.869844 CTATATTAGTAACTTGTTGCATTCAGC 57.130 33.333 4.58 0.00 45.96 4.26
2180 2199 2.522185 ACTTGTTGCATTCAGCCTGAT 58.478 42.857 0.00 0.00 44.83 2.90
2189 2209 6.147864 TGCATTCAGCCTGATTAATTTACC 57.852 37.500 0.00 0.00 44.83 2.85
2196 2216 5.888161 CAGCCTGATTAATTTACCCTGTTCT 59.112 40.000 0.00 0.00 0.00 3.01
2415 2436 9.065871 GTTCTGATGTACAACTAATTTGATTGC 57.934 33.333 0.00 0.00 38.73 3.56
2556 2577 3.244596 ACTTTCAAGGTAGGCTCTTGGTC 60.245 47.826 13.99 0.00 41.23 4.02
2582 2604 7.784550 CCCCTTCCATAAATTCTTTTCTGGATA 59.215 37.037 6.45 0.12 43.59 2.59
2583 2605 9.200817 CCCTTCCATAAATTCTTTTCTGGATAA 57.799 33.333 6.45 0.00 43.59 1.75
2605 2627 4.006319 ACAATTTTGTTGTTGTTGTGGGG 58.994 39.130 0.00 0.00 38.47 4.96
2731 2753 2.159114 GCCTGAGACTGAGAAGCTTAGG 60.159 54.545 0.00 0.00 38.17 2.69
2780 2802 6.183360 ACGATGCTTCTTTTGATTAGCTCTTC 60.183 38.462 0.00 0.00 34.35 2.87
2953 2975 4.532126 TCTCACATCACAAGTGACCCTAAT 59.468 41.667 4.84 0.00 43.11 1.73
3029 3051 8.565416 GCATCTGAATCTGAATAATTCATGACA 58.435 33.333 0.00 0.00 41.10 3.58
3061 3084 1.747709 CTGCCTGCAGTAAGCTGATT 58.252 50.000 13.81 0.00 45.28 2.57
3063 3086 1.003464 TGCCTGCAGTAAGCTGATTCA 59.997 47.619 13.81 0.00 45.28 2.57
3065 3088 2.489329 GCCTGCAGTAAGCTGATTCAAA 59.511 45.455 13.81 0.00 45.28 2.69
3067 3090 4.732938 GCCTGCAGTAAGCTGATTCAAATC 60.733 45.833 13.81 0.00 45.28 2.17
3176 3199 2.092968 TGCAACAAGAAGGTGACTGAGT 60.093 45.455 0.00 0.00 42.68 3.41
3192 3215 3.117851 ACTGAGTCACTCGGATCAGGATA 60.118 47.826 21.16 0.00 42.76 2.59
3223 3246 2.912956 AGGGTGCCAGAAGAACTATGAA 59.087 45.455 0.00 0.00 0.00 2.57
3310 3333 4.839121 TCCGTGAAATACCAATGCTAAGT 58.161 39.130 0.00 0.00 0.00 2.24
3412 3435 2.775911 TCAATGACCAAGCAGAGAGG 57.224 50.000 0.00 0.00 0.00 3.69
3427 3450 1.078848 GAGGATCGTTGGCTGCAGT 60.079 57.895 16.64 0.00 0.00 4.40
3469 3492 6.149640 GGATCAGGAAAGAGGTAAAAACTCAC 59.850 42.308 0.00 0.00 37.43 3.51
3474 3497 3.041508 AGAGGTAAAAACTCACGCCTC 57.958 47.619 0.00 0.00 41.90 4.70
3475 3498 2.367567 AGAGGTAAAAACTCACGCCTCA 59.632 45.455 10.49 0.00 43.47 3.86
3488 3511 1.003580 ACGCCTCACCATTCAGAATGT 59.996 47.619 19.79 7.26 37.18 2.71
3517 3540 0.447011 GCTTGCTCTGTGATCTGTGC 59.553 55.000 0.00 0.00 34.33 4.57
3606 3632 1.749258 GATTCCCCACCTGTTCCGC 60.749 63.158 0.00 0.00 0.00 5.54
3612 3638 2.029073 CACCTGTTCCGCGTCAGT 59.971 61.111 4.92 0.00 0.00 3.41
3636 3662 1.067142 GTGCAGAACGAGTACATGGGA 60.067 52.381 0.00 0.00 0.00 4.37
3638 3664 1.204941 GCAGAACGAGTACATGGGAGT 59.795 52.381 0.00 0.00 0.00 3.85
3718 3744 1.477923 GGTACCAGCTCGAGGAGATCT 60.478 57.143 15.58 0.00 0.00 2.75
3772 3798 1.348775 GGAGTATGCCTGCTCCCCTT 61.349 60.000 13.99 0.00 45.73 3.95
3823 3849 4.080695 TGCTGGAAGAAGATGCAAGAGTAT 60.081 41.667 0.00 0.00 34.07 2.12
3824 3850 4.880696 GCTGGAAGAAGATGCAAGAGTATT 59.119 41.667 0.00 0.00 34.07 1.89
3825 3851 5.220815 GCTGGAAGAAGATGCAAGAGTATTG 60.221 44.000 0.00 0.00 34.07 1.90
3826 3852 4.637534 TGGAAGAAGATGCAAGAGTATTGC 59.362 41.667 15.52 15.52 45.11 3.56
3827 3853 4.036144 GGAAGAAGATGCAAGAGTATTGCC 59.964 45.833 19.22 5.40 44.32 4.52
3856 3882 3.850752 TCCCCTTGAGGAGATATGAGAC 58.149 50.000 0.00 0.00 38.24 3.36
3875 3901 1.377725 ATCCAGGCTCACCGCTTTG 60.378 57.895 0.00 0.00 42.76 2.77
3876 3902 3.741476 CCAGGCTCACCGCTTTGC 61.741 66.667 0.00 0.00 42.76 3.68
3877 3903 2.670934 CAGGCTCACCGCTTTGCT 60.671 61.111 0.00 0.00 42.76 3.91
3967 3994 2.560981 TGTCGCTCCTCAAATGTAGTGA 59.439 45.455 0.00 0.00 0.00 3.41
3969 3996 3.799420 GTCGCTCCTCAAATGTAGTGATC 59.201 47.826 0.00 0.00 31.72 2.92
3988 4015 5.458779 GTGATCACTTAAAAACGCTTTTGCT 59.541 36.000 18.83 0.00 44.80 3.91
3989 4016 5.458452 TGATCACTTAAAAACGCTTTTGCTG 59.542 36.000 6.79 0.21 44.80 4.41
4010 4037 7.658261 TGCTGTCCTGTGTTATATATGTAGAC 58.342 38.462 0.00 0.00 0.00 2.59
4014 4041 8.347771 TGTCCTGTGTTATATATGTAGACGTTC 58.652 37.037 0.00 0.00 0.00 3.95
4016 4043 6.800408 CCTGTGTTATATATGTAGACGTTCGG 59.200 42.308 0.00 0.00 0.00 4.30
4032 4059 0.901114 TCGGTTTGGAGGACATCGGA 60.901 55.000 0.00 0.00 0.00 4.55
4078 4108 4.885907 TGATCTGCAAATTCCTTCTCCATC 59.114 41.667 0.00 0.00 0.00 3.51
4079 4109 4.305539 TCTGCAAATTCCTTCTCCATCA 57.694 40.909 0.00 0.00 0.00 3.07
4086 4116 3.340814 TTCCTTCTCCATCAGACAAGC 57.659 47.619 0.00 0.00 0.00 4.01
4090 4120 3.370209 CCTTCTCCATCAGACAAGCATGA 60.370 47.826 0.00 0.00 0.00 3.07
4123 4153 5.817296 CCACTGCTAGCTGATGTTAAACATA 59.183 40.000 26.29 0.00 39.27 2.29
4124 4154 6.484643 CCACTGCTAGCTGATGTTAAACATAT 59.515 38.462 26.29 0.00 39.27 1.78
4132 4162 8.565896 AGCTGATGTTAAACATATGTTCTGAA 57.434 30.769 21.02 12.69 39.27 3.02
4181 4212 7.337689 TGCAAGAATCACTGCACTATTCTTTAT 59.662 33.333 17.41 2.45 43.85 1.40
4190 4221 6.070538 ACTGCACTATTCTTTATCTGTGTCCT 60.071 38.462 0.00 0.00 0.00 3.85
4209 4272 6.495872 GTGTCCTGGGAATGTATAGGTGTATA 59.504 42.308 0.00 0.00 0.00 1.47
4266 4377 0.247736 AAGGTAGTCTCAGCCTTGCG 59.752 55.000 0.00 0.00 40.71 4.85
4291 4415 1.194121 GGGCTTGCTGGGTTGGATTT 61.194 55.000 0.00 0.00 0.00 2.17
4292 4416 0.037046 GGCTTGCTGGGTTGGATTTG 60.037 55.000 0.00 0.00 0.00 2.32
4295 4419 1.693606 CTTGCTGGGTTGGATTTGGTT 59.306 47.619 0.00 0.00 0.00 3.67
4296 4420 1.799933 TGCTGGGTTGGATTTGGTTT 58.200 45.000 0.00 0.00 0.00 3.27
4310 4434 0.324738 TGGTTTGTTGGTTGCTGGGA 60.325 50.000 0.00 0.00 0.00 4.37
4327 4451 0.259065 GGAAGGTTTGGGGGAGGATC 59.741 60.000 0.00 0.00 0.00 3.36
4350 4474 6.665695 TCTTTTGACTTTGTAGGGGTTAACT 58.334 36.000 5.42 0.00 0.00 2.24
4351 4475 7.804147 TCTTTTGACTTTGTAGGGGTTAACTA 58.196 34.615 5.42 0.00 0.00 2.24
4380 4504 4.642429 TCTTCTCTAAACTGAACAAGCCC 58.358 43.478 0.00 0.00 0.00 5.19
4388 4512 2.787994 ACTGAACAAGCCCTGAAGATG 58.212 47.619 0.00 0.00 0.00 2.90
4390 4514 3.327757 ACTGAACAAGCCCTGAAGATGTA 59.672 43.478 0.00 0.00 0.00 2.29
4436 4563 3.646162 TGGAAAGCTACCAACTCAGAAGA 59.354 43.478 9.68 0.00 34.25 2.87
4441 4568 2.544685 CTACCAACTCAGAAGATGCGG 58.455 52.381 0.00 0.00 0.00 5.69
4442 4569 0.687354 ACCAACTCAGAAGATGCGGT 59.313 50.000 0.00 0.00 0.00 5.68
4461 4589 4.391830 GCGGTTAAGATGTTCATCACTTCA 59.608 41.667 14.05 0.00 32.90 3.02
4515 4669 2.360475 GACTGGTTGCTGGGAGCC 60.360 66.667 0.00 0.00 41.51 4.70
4542 4696 1.484240 AGCCAGCCACTAAGATCAGTC 59.516 52.381 0.00 0.00 0.00 3.51
4622 4797 2.391926 TCAGTTGTAGGGTGTCAGGA 57.608 50.000 0.00 0.00 0.00 3.86
4631 4806 2.344592 AGGGTGTCAGGAACATGGTTA 58.655 47.619 0.00 0.00 40.80 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 172 4.209866 GGCGGGGATGGCTTGGAT 62.210 66.667 0.00 0.00 0.00 3.41
844 851 1.365633 GCGAGATGCTACAGGGGAG 59.634 63.158 0.00 0.00 41.73 4.30
845 852 2.134287 GGCGAGATGCTACAGGGGA 61.134 63.158 0.00 0.00 45.43 4.81
846 853 2.423446 GGCGAGATGCTACAGGGG 59.577 66.667 0.00 0.00 45.43 4.79
847 854 2.028190 CGGCGAGATGCTACAGGG 59.972 66.667 0.00 0.00 45.43 4.45
848 855 1.810606 ATCCGGCGAGATGCTACAGG 61.811 60.000 9.30 0.00 45.43 4.00
849 856 0.387878 GATCCGGCGAGATGCTACAG 60.388 60.000 9.30 0.00 45.43 2.74
850 857 0.823769 AGATCCGGCGAGATGCTACA 60.824 55.000 9.30 0.00 45.43 2.74
856 863 3.449349 GGACAGATCCGGCGAGAT 58.551 61.111 9.30 9.76 34.48 2.75
897 904 2.434185 GAGCGATTCCGTGGTGCA 60.434 61.111 0.00 0.00 38.24 4.57
934 942 3.749226 GGGGCAAAATGGAGAGATCTAG 58.251 50.000 0.00 0.00 0.00 2.43
961 969 4.274214 CACAAAGAAGAACAGATCTGTGCA 59.726 41.667 31.34 0.00 44.13 4.57
983 991 1.203250 TCATACAGGGGGATATCGGCA 60.203 52.381 0.00 0.00 0.00 5.69
990 998 4.536765 GAACACATTTCATACAGGGGGAT 58.463 43.478 0.00 0.00 0.00 3.85
1011 1019 1.996798 AGAAGAACAGTCCGTCAGGA 58.003 50.000 0.00 0.00 46.11 3.86
1029 1037 0.169672 CCATGAAACTGCGAGGCAAG 59.830 55.000 0.00 0.00 38.41 4.01
1036 1044 2.180017 GCTGGCCATGAAACTGCG 59.820 61.111 5.51 0.00 0.00 5.18
1254 1262 0.945265 GCCGTGTACCGTACAAAGCA 60.945 55.000 21.16 0.00 40.93 3.91
1285 1293 0.172578 CGACCTCGCACTTGGTGATA 59.827 55.000 1.57 0.00 36.59 2.15
1321 1329 1.435105 CTCGCTCTTGATCTCGGCA 59.565 57.895 0.00 0.00 0.00 5.69
1462 1470 1.134699 TGCTCGCTAACAATCTGGGAG 60.135 52.381 0.00 0.00 41.64 4.30
1508 1516 3.759618 ACAGTAGAGTAAGGACACAGCTC 59.240 47.826 0.00 0.00 0.00 4.09
1512 1520 4.022242 GCAGAACAGTAGAGTAAGGACACA 60.022 45.833 0.00 0.00 0.00 3.72
1514 1522 4.218635 CAGCAGAACAGTAGAGTAAGGACA 59.781 45.833 0.00 0.00 0.00 4.02
1558 1566 1.683917 AGAAGTGACAGAAGTGAGCGT 59.316 47.619 0.00 0.00 0.00 5.07
1559 1567 2.057316 CAGAAGTGACAGAAGTGAGCG 58.943 52.381 0.00 0.00 0.00 5.03
1690 1698 1.352622 TGACCTGAGGTTGCCCTTGT 61.353 55.000 5.21 0.00 42.86 3.16
1742 1750 2.671888 CTCGTCAGTGAGCTCTACGTTA 59.328 50.000 16.19 4.44 34.55 3.18
1784 1800 5.911378 TGGCAAATACATGTATCAAAGCA 57.089 34.783 18.52 8.54 0.00 3.91
1790 1806 6.630071 ACTTGGTTTGGCAAATACATGTATC 58.370 36.000 24.19 7.03 0.00 2.24
1806 1822 5.883673 TCAGCTTACAGTTACAACTTGGTTT 59.116 36.000 0.00 0.00 37.08 3.27
1833 1849 2.625737 CCCTGTACACAGATCAAGCAG 58.374 52.381 10.96 0.00 46.59 4.24
1887 1906 2.348666 CACGGGATAGAACTTCTTTGCG 59.651 50.000 0.00 0.00 0.00 4.85
1959 1978 3.378427 GGACTGTCTTGAACTGCTTGTTT 59.622 43.478 7.85 0.00 39.30 2.83
2006 2025 4.818534 TCTTCAACAACAGCATTCTCAC 57.181 40.909 0.00 0.00 0.00 3.51
2037 2056 3.012518 CACTGGCGGAATGAAAGATTCT 58.987 45.455 0.00 0.00 0.00 2.40
2052 2071 3.243367 TGACAAAGTTGTATTGCACTGGC 60.243 43.478 0.00 0.00 42.43 4.85
2169 2188 6.435164 ACAGGGTAAATTAATCAGGCTGAAT 58.565 36.000 22.84 16.38 0.00 2.57
2175 2194 9.853177 AAGATAGAACAGGGTAAATTAATCAGG 57.147 33.333 0.00 0.00 0.00 3.86
2285 2305 1.518102 GCAACAACAATGTCACGCTTG 59.482 47.619 0.00 0.00 39.40 4.01
2367 2387 2.875296 TGCACCACCTTTCAAGCTATT 58.125 42.857 0.00 0.00 0.00 1.73
2583 2605 4.006319 CCCCACAACAACAACAAAATTGT 58.994 39.130 0.00 0.00 44.72 2.71
2584 2606 4.256920 TCCCCACAACAACAACAAAATTG 58.743 39.130 0.00 0.00 0.00 2.32
2585 2607 4.559862 TCCCCACAACAACAACAAAATT 57.440 36.364 0.00 0.00 0.00 1.82
2586 2608 4.257731 GTTCCCCACAACAACAACAAAAT 58.742 39.130 0.00 0.00 0.00 1.82
2587 2609 3.071023 TGTTCCCCACAACAACAACAAAA 59.929 39.130 0.00 0.00 33.21 2.44
2588 2610 2.632996 TGTTCCCCACAACAACAACAAA 59.367 40.909 0.00 0.00 33.21 2.83
2589 2611 2.248248 TGTTCCCCACAACAACAACAA 58.752 42.857 0.00 0.00 33.21 2.83
2590 2612 1.924731 TGTTCCCCACAACAACAACA 58.075 45.000 0.00 0.00 33.21 3.33
2599 2621 9.853177 ACAAATAAAATAAAATTGTTCCCCACA 57.147 25.926 0.00 0.00 30.50 4.17
2601 2623 8.787852 GCACAAATAAAATAAAATTGTTCCCCA 58.212 29.630 0.00 0.00 32.25 4.96
2602 2624 9.008965 AGCACAAATAAAATAAAATTGTTCCCC 57.991 29.630 0.00 0.00 32.25 4.81
2799 2821 4.141981 TGTTCAGCAAACAATGTGGTCATT 60.142 37.500 2.51 0.00 44.83 2.57
2811 2833 5.412594 TCAGATTCATACCTGTTCAGCAAAC 59.587 40.000 0.00 0.00 38.43 2.93
2855 2877 2.165167 CATTCCAGCACCAACTGATGT 58.835 47.619 0.00 0.00 40.25 3.06
2953 2975 3.194620 TCTTACCTTATCCTGGCCCAAA 58.805 45.455 0.00 0.00 0.00 3.28
3029 3051 1.338020 GCAGGCAGTTGCAAGTTTACT 59.662 47.619 3.38 0.15 43.53 2.24
3063 3086 2.888834 AACAGGCTGCAAAACGATTT 57.111 40.000 15.89 0.00 0.00 2.17
3065 3088 2.362077 AGAAAACAGGCTGCAAAACGAT 59.638 40.909 15.89 0.00 0.00 3.73
3067 3090 2.208326 AGAAAACAGGCTGCAAAACG 57.792 45.000 15.89 0.00 0.00 3.60
3176 3199 2.091830 ACCAGTATCCTGATCCGAGTGA 60.092 50.000 0.00 0.00 41.50 3.41
3192 3215 2.343475 CTGGCACCCTTCACACCAGT 62.343 60.000 0.00 0.00 42.42 4.00
3223 3246 3.071602 ACTGTTACCTCAATGAGCACTGT 59.928 43.478 4.40 8.14 0.00 3.55
3310 3333 1.821759 CCACGGTGAACAAGGCACA 60.822 57.895 10.28 0.00 37.99 4.57
3412 3435 2.327343 TGCACTGCAGCCAACGATC 61.327 57.895 15.27 0.00 33.32 3.69
3427 3450 0.826062 TCCGATCAAGCTCATCTGCA 59.174 50.000 0.00 0.00 34.99 4.41
3469 3492 1.742761 ACATTCTGAATGGTGAGGCG 58.257 50.000 28.41 6.88 43.21 5.52
3474 3497 6.549061 CAACATGTCTACATTCTGAATGGTG 58.451 40.000 28.41 20.97 43.21 4.17
3475 3498 5.124457 GCAACATGTCTACATTCTGAATGGT 59.876 40.000 28.41 18.28 43.21 3.55
3488 3511 3.069289 CACAGAGCAAGCAACATGTCTA 58.931 45.455 0.00 0.00 0.00 2.59
3517 3540 6.145535 GCAAACAGAATTTGACAGTCTTAGG 58.854 40.000 1.31 0.00 0.00 2.69
3606 3632 1.846648 GTTCTGCACGACACTGACG 59.153 57.895 0.00 0.00 0.00 4.35
3636 3662 1.830477 GTGATCCTCTGCCTCTTCACT 59.170 52.381 0.00 0.00 32.69 3.41
3638 3664 1.198713 GGTGATCCTCTGCCTCTTCA 58.801 55.000 0.00 0.00 0.00 3.02
3696 3722 0.107116 TCTCCTCGAGCTGGTACCTC 60.107 60.000 14.36 5.02 0.00 3.85
3718 3744 0.252239 TAGCTGGAGGTGAGCTTGGA 60.252 55.000 0.00 0.00 44.65 3.53
3772 3798 0.115152 TGAGCTTGGGAGTCTCCTCA 59.885 55.000 18.58 10.85 39.64 3.86
3806 3832 4.639310 CAGGCAATACTCTTGCATCTTCTT 59.361 41.667 11.59 0.00 46.58 2.52
3826 3852 3.333219 TCAAGGGGAGCAGGCAGG 61.333 66.667 0.00 0.00 0.00 4.85
3827 3853 2.271497 CTCAAGGGGAGCAGGCAG 59.729 66.667 0.00 0.00 36.69 4.85
3851 3877 1.607801 CGGTGAGCCTGGATGTCTCA 61.608 60.000 0.00 0.00 34.78 3.27
3852 3878 1.142748 CGGTGAGCCTGGATGTCTC 59.857 63.158 0.00 0.00 0.00 3.36
3853 3879 3.023949 GCGGTGAGCCTGGATGTCT 62.024 63.158 0.00 0.00 40.81 3.41
3875 3901 4.037858 CCAAAACATGGCTTCATCTAGC 57.962 45.455 0.00 0.00 43.80 3.42
3931 3958 0.874175 CGACACGGCAGAAAGACACA 60.874 55.000 0.00 0.00 0.00 3.72
3967 3994 5.348164 ACAGCAAAAGCGTTTTTAAGTGAT 58.652 33.333 9.75 0.00 34.81 3.06
3969 3996 4.026886 GGACAGCAAAAGCGTTTTTAAGTG 60.027 41.667 9.75 9.74 34.81 3.16
3988 4015 7.812690 ACGTCTACATATATAACACAGGACA 57.187 36.000 0.00 0.00 0.00 4.02
3989 4016 7.533222 CGAACGTCTACATATATAACACAGGAC 59.467 40.741 0.00 0.00 0.00 3.85
4010 4037 1.076332 GATGTCCTCCAAACCGAACG 58.924 55.000 0.00 0.00 0.00 3.95
4014 4041 0.460284 CTCCGATGTCCTCCAAACCG 60.460 60.000 0.00 0.00 0.00 4.44
4016 4043 3.821421 ATACTCCGATGTCCTCCAAAC 57.179 47.619 0.00 0.00 0.00 2.93
4123 4153 3.181465 ACGAGGACACTTGTTCAGAACAT 60.181 43.478 16.89 1.63 41.79 2.71
4124 4154 2.167693 ACGAGGACACTTGTTCAGAACA 59.832 45.455 12.24 12.24 38.17 3.18
4132 4162 1.000955 CTAAGCCACGAGGACACTTGT 59.999 52.381 1.86 0.00 42.17 3.16
4181 4212 3.967326 CCTATACATTCCCAGGACACAGA 59.033 47.826 0.00 0.00 0.00 3.41
4190 4221 7.364149 ACGTTTATACACCTATACATTCCCA 57.636 36.000 0.00 0.00 0.00 4.37
4209 4272 4.906618 AGATAGGTGGATTCACAACGTTT 58.093 39.130 6.44 0.00 45.32 3.60
4273 4384 0.037046 CAAATCCAACCCAGCAAGCC 60.037 55.000 0.00 0.00 0.00 4.35
4274 4385 0.037046 CCAAATCCAACCCAGCAAGC 60.037 55.000 0.00 0.00 0.00 4.01
4275 4386 1.341080 ACCAAATCCAACCCAGCAAG 58.659 50.000 0.00 0.00 0.00 4.01
4276 4387 1.799933 AACCAAATCCAACCCAGCAA 58.200 45.000 0.00 0.00 0.00 3.91
4277 4388 1.415659 CAAACCAAATCCAACCCAGCA 59.584 47.619 0.00 0.00 0.00 4.41
4278 4389 1.416030 ACAAACCAAATCCAACCCAGC 59.584 47.619 0.00 0.00 0.00 4.85
4279 4390 3.465871 CAACAAACCAAATCCAACCCAG 58.534 45.455 0.00 0.00 0.00 4.45
4280 4391 2.171448 CCAACAAACCAAATCCAACCCA 59.829 45.455 0.00 0.00 0.00 4.51
4282 4393 3.552132 ACCAACAAACCAAATCCAACC 57.448 42.857 0.00 0.00 0.00 3.77
4283 4394 3.064682 GCAACCAACAAACCAAATCCAAC 59.935 43.478 0.00 0.00 0.00 3.77
4291 4415 0.324738 TCCCAGCAACCAACAAACCA 60.325 50.000 0.00 0.00 0.00 3.67
4292 4416 0.827368 TTCCCAGCAACCAACAAACC 59.173 50.000 0.00 0.00 0.00 3.27
4295 4419 0.032615 ACCTTCCCAGCAACCAACAA 60.033 50.000 0.00 0.00 0.00 2.83
4296 4420 0.032615 AACCTTCCCAGCAACCAACA 60.033 50.000 0.00 0.00 0.00 3.33
4310 4434 1.773541 AAGATCCTCCCCCAAACCTT 58.226 50.000 0.00 0.00 0.00 3.50
4327 4451 6.954487 AGTTAACCCCTACAAAGTCAAAAG 57.046 37.500 0.88 0.00 0.00 2.27
4350 4474 6.657966 TGTTCAGTTTAGAGAAGATCGAGGTA 59.342 38.462 0.00 0.00 0.00 3.08
4351 4475 5.477291 TGTTCAGTTTAGAGAAGATCGAGGT 59.523 40.000 0.00 0.00 0.00 3.85
4356 4480 5.352846 GGGCTTGTTCAGTTTAGAGAAGATC 59.647 44.000 0.00 0.00 0.00 2.75
4360 4484 4.102524 TCAGGGCTTGTTCAGTTTAGAGAA 59.897 41.667 0.00 0.00 0.00 2.87
4380 4504 9.254133 CATTGTTAGTCTGGTATACATCTTCAG 57.746 37.037 5.01 2.67 0.00 3.02
4388 4512 9.998106 ATGGAATACATTGTTAGTCTGGTATAC 57.002 33.333 0.00 0.00 35.97 1.47
4390 4514 7.939039 CCATGGAATACATTGTTAGTCTGGTAT 59.061 37.037 5.56 0.00 37.84 2.73
4409 4533 3.073798 TGAGTTGGTAGCTTTCCATGGAA 59.926 43.478 23.63 23.63 34.75 3.53
4411 4535 3.012518 CTGAGTTGGTAGCTTTCCATGG 58.987 50.000 4.97 4.97 34.75 3.66
4436 4563 4.517285 AGTGATGAACATCTTAACCGCAT 58.483 39.130 14.50 0.00 38.60 4.73
4441 4568 7.148507 CCAGTCTGAAGTGATGAACATCTTAAC 60.149 40.741 14.50 6.13 38.60 2.01
4442 4569 6.875726 CCAGTCTGAAGTGATGAACATCTTAA 59.124 38.462 14.50 0.00 38.60 1.85
4494 4648 1.340017 GCTCCCAGCAACCAGTCATTA 60.340 52.381 0.00 0.00 41.89 1.90
4496 4650 1.001641 GCTCCCAGCAACCAGTCAT 60.002 57.895 0.00 0.00 41.89 3.06
4515 4669 0.037326 TTAGTGGCTGGCTTCTCACG 60.037 55.000 2.00 0.00 35.50 4.35
4622 4797 3.838317 TGGAGTCAGTAGCTAACCATGTT 59.162 43.478 0.00 0.00 0.00 2.71
4631 4806 3.055530 CCAGTTTCATGGAGTCAGTAGCT 60.056 47.826 0.00 0.00 43.57 3.32
4700 4875 1.299541 CAGCGACTGGTCAGTTGTTT 58.700 50.000 16.92 6.12 43.25 2.83


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

AutoCloner maintained by Alex Coulton.