Multiple sequence alignment - TraesCS5D01G059300

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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 TraesCS5D01G059300 chr5D 100.000 3782 0 0 584 4365 56121909 56125690 0.000000e+00 6985.0
1 TraesCS5D01G059300 chr5D 100.000 241 0 0 1 241 56121326 56121566 3.100000e-121 446.0
2 TraesCS5D01G059300 chr5D 95.652 46 0 2 4315 4360 381914487 381914444 6.060000e-09 73.1
3 TraesCS5D01G059300 chr5A 92.481 3817 212 45 584 4353 44944981 44948769 0.000000e+00 5389.0
4 TraesCS5D01G059300 chr5A 80.843 261 23 13 1 240 44944698 44944952 3.470000e-41 180.0
5 TraesCS5D01G059300 chr5A 93.478 46 1 2 4315 4360 10905 10862 2.820000e-07 67.6
6 TraesCS5D01G059300 chr5B 94.231 1664 69 15 2574 4223 58893507 58895157 0.000000e+00 2516.0
7 TraesCS5D01G059300 chr5B 90.590 1849 110 30 707 2527 58891701 58893513 0.000000e+00 2392.0
8 TraesCS5D01G059300 chr5B 99.099 111 1 0 4205 4315 58895337 58895447 2.660000e-47 200.0
9 TraesCS5D01G059300 chr5B 93.478 46 1 2 4315 4360 1739567 1739524 2.820000e-07 67.6
10 TraesCS5D01G059300 chr4B 95.745 47 0 2 4315 4359 70256633 70256679 1.680000e-09 75.0
11 TraesCS5D01G059300 chr2A 100.000 40 0 0 4315 4354 733925428 733925467 1.680000e-09 75.0
12 TraesCS5D01G059300 chr2A 90.385 52 3 2 4316 4365 675304129 675304180 2.820000e-07 67.6
13 TraesCS5D01G059300 chr2B 92.157 51 4 0 4315 4365 587169385 587169335 6.060000e-09 73.1
14 TraesCS5D01G059300 chr4A 93.617 47 1 1 4315 4359 549879054 549879008 7.830000e-08 69.4


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 TraesCS5D01G059300 chr5D 56121326 56125690 4364 False 3715.500000 6985 100.000 1 4365 2 chr5D.!!$F1 4364
1 TraesCS5D01G059300 chr5A 44944698 44948769 4071 False 2784.500000 5389 86.662 1 4353 2 chr5A.!!$F1 4352
2 TraesCS5D01G059300 chr5B 58891701 58895447 3746 False 1702.666667 2516 94.640 707 4315 3 chr5B.!!$F1 3608

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
737 761 0.177604 CTGCGCCTCAGAGGAAGAAT 59.822 55.0 21.89 0.0 45.72 2.40 F
1067 1121 0.320771 CCTGTGTTCCGGTGGAAGAG 60.321 60.0 0.00 0.0 42.88 2.85 F
2751 2815 0.967380 GGCCCACTGGTTCTGGATTG 60.967 60.0 0.00 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 1972 1.040646 GATATGTGAGACCCTCGGCA 58.959 55.0 0.00 0.00 32.35 5.69 R
3003 3074 0.391793 GTAGAGTGTCCAAGCCTGGC 60.392 60.0 11.65 11.65 43.17 4.85 R
3803 3877 2.094100 TTGGCATTTCAGGGTGGAAA 57.906 45.0 0.00 0.00 40.72 3.13 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
26 27 4.482990 TCCTTTTCTCCCTTTTGCTGAAT 58.517 39.130 0.00 0.00 0.00 2.57
33 34 2.647299 TCCCTTTTGCTGAATCTACCCA 59.353 45.455 0.00 0.00 0.00 4.51
36 37 4.098501 CCCTTTTGCTGAATCTACCCAATC 59.901 45.833 0.00 0.00 0.00 2.67
37 38 4.201950 CCTTTTGCTGAATCTACCCAATCG 60.202 45.833 0.00 0.00 0.00 3.34
44 45 2.056906 ATCTACCCAATCGCCCTGGC 62.057 60.000 0.00 0.00 37.85 4.85
50 51 0.976641 CCAATCGCCCTGGCTAGATA 59.023 55.000 6.60 0.00 39.32 1.98
62 63 6.302269 CCCTGGCTAGATATGTTTTGAGAAT 58.698 40.000 0.00 0.00 0.00 2.40
63 64 6.774656 CCCTGGCTAGATATGTTTTGAGAATT 59.225 38.462 0.00 0.00 0.00 2.17
65 66 8.689972 CCTGGCTAGATATGTTTTGAGAATTTT 58.310 33.333 0.00 0.00 0.00 1.82
84 85 9.435688 AGAATTTTAATTGTCCTATGTTTTGCC 57.564 29.630 0.00 0.00 0.00 4.52
85 86 7.826260 ATTTTAATTGTCCTATGTTTTGCCG 57.174 32.000 0.00 0.00 0.00 5.69
87 88 4.434713 AATTGTCCTATGTTTTGCCGTC 57.565 40.909 0.00 0.00 0.00 4.79
89 90 2.422597 TGTCCTATGTTTTGCCGTCTG 58.577 47.619 0.00 0.00 0.00 3.51
90 91 2.224426 TGTCCTATGTTTTGCCGTCTGT 60.224 45.455 0.00 0.00 0.00 3.41
93 94 2.584791 CTATGTTTTGCCGTCTGTTGC 58.415 47.619 0.00 0.00 0.00 4.17
104 109 2.019249 CGTCTGTTGCAATCCATCCAT 58.981 47.619 0.59 0.00 0.00 3.41
135 152 6.655003 TCATTTGATTCGCTTCTAGTTCCTTT 59.345 34.615 0.00 0.00 0.00 3.11
136 153 6.481954 TTTGATTCGCTTCTAGTTCCTTTC 57.518 37.500 0.00 0.00 0.00 2.62
137 154 5.147330 TGATTCGCTTCTAGTTCCTTTCA 57.853 39.130 0.00 0.00 0.00 2.69
140 157 6.313905 TGATTCGCTTCTAGTTCCTTTCATTC 59.686 38.462 0.00 0.00 0.00 2.67
148 165 8.519799 TTCTAGTTCCTTTCATTCTTGTGTTT 57.480 30.769 0.00 0.00 0.00 2.83
149 166 8.519799 TCTAGTTCCTTTCATTCTTGTGTTTT 57.480 30.769 0.00 0.00 0.00 2.43
150 167 9.621629 TCTAGTTCCTTTCATTCTTGTGTTTTA 57.378 29.630 0.00 0.00 0.00 1.52
174 191 7.636150 ATCTTAAACCATCAAGTTCATCTGG 57.364 36.000 0.00 0.00 0.00 3.86
182 199 5.106396 CCATCAAGTTCATCTGGTTCTGTTC 60.106 44.000 0.00 0.00 0.00 3.18
183 200 4.389374 TCAAGTTCATCTGGTTCTGTTCC 58.611 43.478 0.00 0.00 0.00 3.62
240 260 1.478105 GGGGTCATGCTGAAAATGGTC 59.522 52.381 0.00 0.00 0.00 4.02
658 678 4.759693 TGTCCATTAACTGTAACCAGCTTG 59.240 41.667 0.00 0.00 42.81 4.01
667 687 6.013842 ACTGTAACCAGCTTGCTTAATTTC 57.986 37.500 0.00 0.00 42.81 2.17
668 688 5.770162 ACTGTAACCAGCTTGCTTAATTTCT 59.230 36.000 0.00 0.00 42.81 2.52
669 689 6.940298 ACTGTAACCAGCTTGCTTAATTTCTA 59.060 34.615 0.00 0.00 42.81 2.10
676 696 8.971073 ACCAGCTTGCTTAATTTCTACATTATT 58.029 29.630 0.00 0.00 0.00 1.40
699 719 6.601741 TTCATTGGAATTTCACACAAAAGC 57.398 33.333 0.00 0.00 0.00 3.51
700 720 5.668471 TCATTGGAATTTCACACAAAAGCA 58.332 33.333 0.00 0.00 0.00 3.91
703 723 7.599621 TCATTGGAATTTCACACAAAAGCATAG 59.400 33.333 0.00 0.00 0.00 2.23
705 725 6.215121 TGGAATTTCACACAAAAGCATAGTG 58.785 36.000 0.00 0.00 39.12 2.74
709 733 8.491331 AATTTCACACAAAAGCATAGTGTTTT 57.509 26.923 0.00 0.00 43.40 2.43
737 761 0.177604 CTGCGCCTCAGAGGAAGAAT 59.822 55.000 21.89 0.00 45.72 2.40
744 768 4.509600 CGCCTCAGAGGAAGAATAAACATC 59.490 45.833 21.89 0.00 37.67 3.06
745 769 5.431765 GCCTCAGAGGAAGAATAAACATCA 58.568 41.667 21.89 0.00 37.67 3.07
746 770 5.526846 GCCTCAGAGGAAGAATAAACATCAG 59.473 44.000 21.89 0.00 37.67 2.90
776 810 2.224426 TGAATTACGAGTGCCACCTGTT 60.224 45.455 0.00 0.00 0.00 3.16
790 824 4.159506 GCCACCTGTTATGCCATTTTCTTA 59.840 41.667 0.00 0.00 0.00 2.10
795 829 7.703621 CACCTGTTATGCCATTTTCTTATCTTG 59.296 37.037 0.00 0.00 0.00 3.02
796 830 7.147846 ACCTGTTATGCCATTTTCTTATCTTGG 60.148 37.037 0.00 0.00 0.00 3.61
797 831 7.068593 CCTGTTATGCCATTTTCTTATCTTGGA 59.931 37.037 0.00 0.00 0.00 3.53
798 832 7.999679 TGTTATGCCATTTTCTTATCTTGGAG 58.000 34.615 0.00 0.00 0.00 3.86
800 834 5.191727 TGCCATTTTCTTATCTTGGAGGA 57.808 39.130 0.00 0.00 0.00 3.71
801 835 4.949856 TGCCATTTTCTTATCTTGGAGGAC 59.050 41.667 0.00 0.00 0.00 3.85
802 836 4.949856 GCCATTTTCTTATCTTGGAGGACA 59.050 41.667 0.00 0.00 0.00 4.02
803 837 5.595952 GCCATTTTCTTATCTTGGAGGACAT 59.404 40.000 0.00 0.00 0.00 3.06
804 838 6.238869 GCCATTTTCTTATCTTGGAGGACATC 60.239 42.308 0.00 0.00 0.00 3.06
805 839 7.059156 CCATTTTCTTATCTTGGAGGACATCT 58.941 38.462 0.00 0.00 0.00 2.90
806 840 7.559170 CCATTTTCTTATCTTGGAGGACATCTT 59.441 37.037 0.00 0.00 0.00 2.40
807 841 9.618890 CATTTTCTTATCTTGGAGGACATCTTA 57.381 33.333 0.00 0.00 0.00 2.10
808 842 9.620259 ATTTTCTTATCTTGGAGGACATCTTAC 57.380 33.333 0.00 0.00 0.00 2.34
809 843 6.732896 TCTTATCTTGGAGGACATCTTACC 57.267 41.667 0.00 0.00 0.00 2.85
810 844 6.202331 TCTTATCTTGGAGGACATCTTACCA 58.798 40.000 0.00 0.00 0.00 3.25
819 853 4.684724 AGGACATCTTACCACTTACCAGA 58.315 43.478 0.00 0.00 0.00 3.86
830 864 5.491982 ACCACTTACCAGATTAGCTTCTTG 58.508 41.667 0.00 0.00 0.00 3.02
831 865 5.248477 ACCACTTACCAGATTAGCTTCTTGA 59.752 40.000 0.00 0.00 0.00 3.02
839 874 8.870075 ACCAGATTAGCTTCTTGAAGTTAAAT 57.130 30.769 18.52 12.31 31.05 1.40
840 875 9.301897 ACCAGATTAGCTTCTTGAAGTTAAATT 57.698 29.630 18.52 10.32 31.05 1.82
874 909 5.590530 AGTAGCTTCATTCTGTGTAGGAG 57.409 43.478 0.00 0.00 0.00 3.69
877 927 6.663953 AGTAGCTTCATTCTGTGTAGGAGTTA 59.336 38.462 0.00 0.00 0.00 2.24
882 932 9.162764 GCTTCATTCTGTGTAGGAGTTATTTTA 57.837 33.333 0.00 0.00 0.00 1.52
895 945 5.248870 AGTTATTTTATGCGGCTGAAAGG 57.751 39.130 0.00 0.00 0.00 3.11
899 949 4.799564 TTTTATGCGGCTGAAAGGAAAT 57.200 36.364 0.00 0.00 0.00 2.17
900 950 4.799564 TTTATGCGGCTGAAAGGAAATT 57.200 36.364 0.00 0.00 0.00 1.82
901 951 5.906113 TTTATGCGGCTGAAAGGAAATTA 57.094 34.783 0.00 0.00 0.00 1.40
931 984 9.614792 AACTCCAACAAGATACTTACATAATCC 57.385 33.333 0.00 0.00 0.00 3.01
963 1017 5.125417 TGTTGTTCTTTTCCTCAGGTTCTTG 59.875 40.000 0.00 0.00 0.00 3.02
988 1042 4.320057 CGAACTCTTCTTTGCATGAGCTTT 60.320 41.667 0.00 0.00 42.74 3.51
993 1047 6.092955 TCTTCTTTGCATGAGCTTTTGAAT 57.907 33.333 0.00 0.00 42.74 2.57
996 1050 5.713025 TCTTTGCATGAGCTTTTGAATACC 58.287 37.500 0.00 0.00 42.74 2.73
1000 1054 8.518430 TTTGCATGAGCTTTTGAATACCTATA 57.482 30.769 0.00 0.00 42.74 1.31
1026 1080 5.635417 AGCTTCTAAGAAGCAAATTCCAC 57.365 39.130 21.30 0.00 45.30 4.02
1027 1081 5.320277 AGCTTCTAAGAAGCAAATTCCACT 58.680 37.500 21.30 0.00 45.30 4.00
1029 1083 5.392487 GCTTCTAAGAAGCAAATTCCACTCC 60.392 44.000 10.31 0.00 42.56 3.85
1054 1108 2.224606 CAATGACTTGCTGTCCTGTGT 58.775 47.619 7.71 0.00 44.75 3.72
1067 1121 0.320771 CCTGTGTTCCGGTGGAAGAG 60.321 60.000 0.00 0.00 42.88 2.85
1079 1133 4.072131 CGGTGGAAGAGAAAATCCAGAAA 58.928 43.478 0.00 0.00 46.01 2.52
1188 1243 5.515797 TCCTATTCTGTTCAGACATACCG 57.484 43.478 1.72 0.00 34.72 4.02
1245 1300 1.341209 CTCAAAAGGGCCACAAGGAAC 59.659 52.381 6.18 0.00 36.89 3.62
1343 1398 5.697633 CAGTTTGCACCATAAAAGCTTTGAT 59.302 36.000 13.54 8.01 0.00 2.57
1368 1423 6.531503 TTTCCAAGTTCAAACACCACAATA 57.468 33.333 0.00 0.00 0.00 1.90
1370 1425 7.825331 TTCCAAGTTCAAACACCACAATATA 57.175 32.000 0.00 0.00 0.00 0.86
1407 1462 4.847198 TGTCTTATGCACCAATCAGTCAT 58.153 39.130 0.00 0.00 0.00 3.06
1449 1504 5.857471 TTAGAAAGCGGCAGGTTATACTA 57.143 39.130 1.45 4.33 37.04 1.82
1468 1523 5.455056 ACTATTCCTGCCGTAGTGATTAG 57.545 43.478 0.00 0.00 0.00 1.73
1572 1627 2.751806 GGGAAAGCTGAAGAATGGTCAG 59.248 50.000 0.00 0.00 44.48 3.51
1850 1905 2.231964 CCCCTGGTTTGTCATGATGTTG 59.768 50.000 0.00 0.00 0.00 3.33
1917 1972 1.470098 GCGAAGATCTGCATTGGTGTT 59.530 47.619 0.51 0.00 0.00 3.32
1923 1978 1.210931 CTGCATTGGTGTTGCCGAG 59.789 57.895 0.00 0.00 41.21 4.63
2025 2080 2.091885 GGACCTGAGCCCCAAAATATCA 60.092 50.000 0.00 0.00 0.00 2.15
2235 2290 2.899339 GCAATCCGAGGGCAGCTC 60.899 66.667 0.00 0.00 0.00 4.09
2265 2320 2.907910 CTGATGTGTACAGCTTTGGC 57.092 50.000 0.00 0.00 39.06 4.52
2271 2326 1.194772 GTGTACAGCTTTGGCGTTCTC 59.805 52.381 0.00 0.00 44.37 2.87
2292 2347 1.277273 CTGCTGGAGATTGTCAGTGGA 59.723 52.381 0.00 0.00 33.81 4.02
2547 2611 8.530311 TGCACATGGTTGAACAATTTAGATAAT 58.470 29.630 0.00 0.00 0.00 1.28
2716 2780 6.179756 TGCCAGCTTTCATTGTCTTATCTTA 58.820 36.000 0.00 0.00 0.00 2.10
2751 2815 0.967380 GGCCCACTGGTTCTGGATTG 60.967 60.000 0.00 0.00 0.00 2.67
2945 3015 7.642071 TTTCAAAAATAGCTGAAGCATTGTC 57.358 32.000 4.90 0.00 45.16 3.18
3097 3168 2.599082 CACCGACGAAGCTCATAAGTTC 59.401 50.000 0.00 0.00 0.00 3.01
3112 3183 8.608317 GCTCATAAGTTCTTGAAAATAGGACTC 58.392 37.037 0.00 0.00 30.03 3.36
3185 3256 1.065126 AGATGCTAAAGGGTGAGTGCC 60.065 52.381 0.00 0.00 0.00 5.01
3284 3355 5.788450 CTCTTCAGTTAAGTGTGTCTCCAT 58.212 41.667 10.08 0.00 36.51 3.41
3295 3366 2.094026 TGTGTCTCCATCAATGTCTCCG 60.094 50.000 0.00 0.00 0.00 4.63
3372 3443 0.179936 GACAGCCCCTGATGAGAAGG 59.820 60.000 0.00 0.00 35.18 3.46
3492 3566 6.985188 TGTGTTTCTGGATTGCTTAGATAC 57.015 37.500 0.00 0.00 0.00 2.24
3677 3751 4.518970 CACCTTTCCTAAGTTAAGCAAGCA 59.481 41.667 0.00 0.00 0.00 3.91
3678 3752 5.009610 CACCTTTCCTAAGTTAAGCAAGCAA 59.990 40.000 0.00 0.00 0.00 3.91
3679 3753 5.241728 ACCTTTCCTAAGTTAAGCAAGCAAG 59.758 40.000 0.00 0.00 0.00 4.01
3680 3754 4.766404 TTCCTAAGTTAAGCAAGCAAGC 57.234 40.909 0.00 0.00 0.00 4.01
3803 3877 4.401022 TCTGCATGAAAGACCTGTGAAAT 58.599 39.130 0.00 0.00 0.00 2.17
3810 3884 4.340950 TGAAAGACCTGTGAAATTTCCACC 59.659 41.667 15.48 4.46 33.80 4.61
3826 3900 3.096092 TCCACCCTGAAATGCCAATAAC 58.904 45.455 0.00 0.00 0.00 1.89
3836 3910 7.230849 TGAAATGCCAATAACTCAAACTGAT 57.769 32.000 0.00 0.00 0.00 2.90
3877 3951 9.764870 CGATAAAATACATCAGCAGATTATTGG 57.235 33.333 0.00 0.00 30.20 3.16
3889 3963 6.491062 CAGCAGATTATTGGGGATGATTGTAA 59.509 38.462 0.00 0.00 0.00 2.41
4016 4090 9.646522 AACTGCAGTTCCAAAAATATATATCCT 57.353 29.630 26.36 0.00 31.64 3.24
4057 4131 3.319122 ACTGAAAGCAGGGATTGACAAAC 59.681 43.478 0.00 0.00 46.60 2.93
4075 4149 4.216687 ACAAACGAACCTTCAAAACACTGA 59.783 37.500 0.00 0.00 0.00 3.41
4198 4274 0.036306 CAAACAGTCCGGGTAAGCCT 59.964 55.000 0.00 0.00 34.45 4.58
4315 4589 7.653311 ACAGCAAAAACTTTCATCCATCTAAAC 59.347 33.333 0.00 0.00 0.00 2.01
4316 4590 7.869429 CAGCAAAAACTTTCATCCATCTAAACT 59.131 33.333 0.00 0.00 0.00 2.66
4317 4591 8.084684 AGCAAAAACTTTCATCCATCTAAACTC 58.915 33.333 0.00 0.00 0.00 3.01
4318 4592 7.329471 GCAAAAACTTTCATCCATCTAAACTCC 59.671 37.037 0.00 0.00 0.00 3.85
4353 4627 7.281549 ACAAATGTAAGACGTTTTAGGTCACTT 59.718 33.333 0.00 0.00 35.31 3.16
4354 4628 8.767085 CAAATGTAAGACGTTTTAGGTCACTTA 58.233 33.333 0.00 0.00 35.31 2.24
4355 4629 7.880059 ATGTAAGACGTTTTAGGTCACTTAC 57.120 36.000 0.00 0.00 35.60 2.34
4356 4630 6.804677 TGTAAGACGTTTTAGGTCACTTACA 58.195 36.000 13.51 13.51 34.37 2.41
4357 4631 7.436118 TGTAAGACGTTTTAGGTCACTTACAT 58.564 34.615 13.51 0.00 33.12 2.29
4358 4632 7.927629 TGTAAGACGTTTTAGGTCACTTACATT 59.072 33.333 13.51 0.00 33.12 2.71
4359 4633 7.797038 AAGACGTTTTAGGTCACTTACATTT 57.203 32.000 0.00 0.00 35.60 2.32
4360 4634 7.186021 AGACGTTTTAGGTCACTTACATTTG 57.814 36.000 0.00 0.00 35.60 2.32
4361 4635 6.764560 AGACGTTTTAGGTCACTTACATTTGT 59.235 34.615 0.00 0.00 35.60 2.83
4362 4636 7.281549 AGACGTTTTAGGTCACTTACATTTGTT 59.718 33.333 0.00 0.00 35.60 2.83
4363 4637 7.764331 ACGTTTTAGGTCACTTACATTTGTTT 58.236 30.769 0.00 0.00 0.00 2.83
4364 4638 8.891720 ACGTTTTAGGTCACTTACATTTGTTTA 58.108 29.630 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.742116 GCCAGGGCGATTGGGTAGA 61.742 63.158 0.00 0.00 36.19 2.59
37 38 3.817647 CTCAAAACATATCTAGCCAGGGC 59.182 47.826 0.97 0.97 42.33 5.19
62 63 6.750148 ACGGCAAAACATAGGACAATTAAAA 58.250 32.000 0.00 0.00 0.00 1.52
63 64 6.207810 AGACGGCAAAACATAGGACAATTAAA 59.792 34.615 0.00 0.00 0.00 1.52
65 66 5.123186 CAGACGGCAAAACATAGGACAATTA 59.877 40.000 0.00 0.00 0.00 1.40
67 68 3.440173 CAGACGGCAAAACATAGGACAAT 59.560 43.478 0.00 0.00 0.00 2.71
72 73 2.668279 GCAACAGACGGCAAAACATAGG 60.668 50.000 0.00 0.00 0.00 2.57
76 77 0.528017 TTGCAACAGACGGCAAAACA 59.472 45.000 0.00 0.00 46.11 2.83
77 78 3.337398 TTGCAACAGACGGCAAAAC 57.663 47.368 0.00 0.00 46.11 2.43
82 83 0.099436 GATGGATTGCAACAGACGGC 59.901 55.000 0.00 0.00 0.00 5.68
83 84 0.734889 GGATGGATTGCAACAGACGG 59.265 55.000 0.00 0.00 0.00 4.79
84 85 1.452110 TGGATGGATTGCAACAGACG 58.548 50.000 0.00 0.00 0.00 4.18
85 86 3.431922 CATGGATGGATTGCAACAGAC 57.568 47.619 0.00 0.00 0.00 3.51
93 94 7.474222 AATCAAATGATTCCCATGGATGGATTG 60.474 37.037 15.22 9.46 44.51 2.67
107 112 7.011857 AGGAACTAGAAGCGAATCAAATGATTC 59.988 37.037 20.98 20.98 46.51 2.52
110 127 5.734720 AGGAACTAGAAGCGAATCAAATGA 58.265 37.500 0.00 0.00 36.02 2.57
140 157 9.965824 ACTTGATGGTTTAAGATAAAACACAAG 57.034 29.630 23.30 23.30 42.93 3.16
148 165 9.177608 CCAGATGAACTTGATGGTTTAAGATAA 57.822 33.333 0.00 0.00 0.00 1.75
149 166 8.328758 ACCAGATGAACTTGATGGTTTAAGATA 58.671 33.333 0.00 0.00 41.44 1.98
150 167 7.177878 ACCAGATGAACTTGATGGTTTAAGAT 58.822 34.615 0.00 0.00 41.44 2.40
596 616 7.770366 TGTGTGGAGTACTCTACTTTTGATA 57.230 36.000 31.66 13.42 41.04 2.15
597 617 6.665992 TGTGTGGAGTACTCTACTTTTGAT 57.334 37.500 31.66 0.00 41.04 2.57
605 625 9.871238 GAAGAATATTTTGTGTGGAGTACTCTA 57.129 33.333 21.88 14.08 0.00 2.43
611 631 9.466497 ACATATGAAGAATATTTTGTGTGGAGT 57.534 29.630 10.38 0.00 28.26 3.85
614 634 8.685427 TGGACATATGAAGAATATTTTGTGTGG 58.315 33.333 10.38 0.00 28.26 4.17
641 661 7.519032 AATTAAGCAAGCTGGTTACAGTTAA 57.481 32.000 0.00 0.00 46.62 2.01
647 667 7.141100 TGTAGAAATTAAGCAAGCTGGTTAC 57.859 36.000 0.00 0.00 39.68 2.50
669 689 9.775854 TTGTGTGAAATTCCAATGAAATAATGT 57.224 25.926 0.00 0.00 33.32 2.71
676 696 6.111382 TGCTTTTGTGTGAAATTCCAATGAA 58.889 32.000 0.00 0.00 34.33 2.57
678 698 5.987777 TGCTTTTGTGTGAAATTCCAATG 57.012 34.783 0.00 0.00 0.00 2.82
679 699 7.385752 CACTATGCTTTTGTGTGAAATTCCAAT 59.614 33.333 0.00 0.00 0.00 3.16
681 701 6.183360 ACACTATGCTTTTGTGTGAAATTCCA 60.183 34.615 9.23 0.00 42.43 3.53
682 702 6.215845 ACACTATGCTTTTGTGTGAAATTCC 58.784 36.000 9.23 0.00 42.43 3.01
683 703 7.698836 AACACTATGCTTTTGTGTGAAATTC 57.301 32.000 10.31 0.00 43.11 2.17
684 704 8.491331 AAAACACTATGCTTTTGTGTGAAATT 57.509 26.923 10.31 1.87 43.11 1.82
685 705 8.491331 AAAAACACTATGCTTTTGTGTGAAAT 57.509 26.923 10.31 0.00 43.11 2.17
744 768 7.438160 TGGCACTCGTAATTCAAATAGATACTG 59.562 37.037 0.00 0.00 0.00 2.74
745 769 7.438459 GTGGCACTCGTAATTCAAATAGATACT 59.562 37.037 11.13 0.00 0.00 2.12
746 770 7.307219 GGTGGCACTCGTAATTCAAATAGATAC 60.307 40.741 18.45 0.00 0.00 2.24
752 781 3.440173 CAGGTGGCACTCGTAATTCAAAT 59.560 43.478 18.45 0.00 0.00 2.32
758 787 3.531538 CATAACAGGTGGCACTCGTAAT 58.468 45.455 18.45 3.70 0.00 1.89
762 791 1.369091 GGCATAACAGGTGGCACTCG 61.369 60.000 18.45 11.23 41.35 4.18
776 810 6.772716 GTCCTCCAAGATAAGAAAATGGCATA 59.227 38.462 0.00 0.00 0.00 3.14
790 824 4.366267 AGTGGTAAGATGTCCTCCAAGAT 58.634 43.478 0.00 0.00 0.00 2.40
795 829 3.773119 TGGTAAGTGGTAAGATGTCCTCC 59.227 47.826 0.00 0.00 0.00 4.30
796 830 4.710375 TCTGGTAAGTGGTAAGATGTCCTC 59.290 45.833 0.00 0.00 0.00 3.71
797 831 4.684724 TCTGGTAAGTGGTAAGATGTCCT 58.315 43.478 0.00 0.00 0.00 3.85
798 832 5.615925 ATCTGGTAAGTGGTAAGATGTCC 57.384 43.478 0.00 0.00 0.00 4.02
800 834 6.384305 AGCTAATCTGGTAAGTGGTAAGATGT 59.616 38.462 0.00 0.00 0.00 3.06
801 835 6.821388 AGCTAATCTGGTAAGTGGTAAGATG 58.179 40.000 0.00 0.00 0.00 2.90
802 836 7.345914 AGAAGCTAATCTGGTAAGTGGTAAGAT 59.654 37.037 0.00 0.00 0.00 2.40
803 837 6.668283 AGAAGCTAATCTGGTAAGTGGTAAGA 59.332 38.462 0.00 0.00 0.00 2.10
804 838 6.879400 AGAAGCTAATCTGGTAAGTGGTAAG 58.121 40.000 0.00 0.00 0.00 2.34
805 839 6.869206 AGAAGCTAATCTGGTAAGTGGTAA 57.131 37.500 0.00 0.00 0.00 2.85
806 840 6.439375 TCAAGAAGCTAATCTGGTAAGTGGTA 59.561 38.462 0.00 0.00 0.00 3.25
807 841 5.248477 TCAAGAAGCTAATCTGGTAAGTGGT 59.752 40.000 0.00 0.00 0.00 4.16
808 842 5.734720 TCAAGAAGCTAATCTGGTAAGTGG 58.265 41.667 0.00 0.00 0.00 4.00
809 843 6.876257 ACTTCAAGAAGCTAATCTGGTAAGTG 59.124 38.462 9.62 0.00 41.99 3.16
810 844 7.010339 ACTTCAAGAAGCTAATCTGGTAAGT 57.990 36.000 9.62 0.00 41.99 2.24
848 883 7.492524 TCCTACACAGAATGAAGCTACTTATG 58.507 38.462 0.00 0.00 39.69 1.90
853 888 5.331876 ACTCCTACACAGAATGAAGCTAC 57.668 43.478 0.00 0.00 39.69 3.58
864 899 5.277345 GCCGCATAAAATAACTCCTACACAG 60.277 44.000 0.00 0.00 0.00 3.66
866 901 4.814771 AGCCGCATAAAATAACTCCTACAC 59.185 41.667 0.00 0.00 0.00 2.90
874 909 5.243426 TCCTTTCAGCCGCATAAAATAAC 57.757 39.130 0.00 0.00 0.00 1.89
877 927 4.799564 TTTCCTTTCAGCCGCATAAAAT 57.200 36.364 0.00 0.00 0.00 1.82
882 932 4.799564 TTTAATTTCCTTTCAGCCGCAT 57.200 36.364 0.00 0.00 0.00 4.73
930 983 6.985645 TGAGGAAAAGAACAACAATCAAATGG 59.014 34.615 0.00 0.00 0.00 3.16
931 984 7.170320 CCTGAGGAAAAGAACAACAATCAAATG 59.830 37.037 0.00 0.00 0.00 2.32
937 990 5.893824 AGAACCTGAGGAAAAGAACAACAAT 59.106 36.000 4.99 0.00 0.00 2.71
938 991 5.261216 AGAACCTGAGGAAAAGAACAACAA 58.739 37.500 4.99 0.00 0.00 2.83
943 996 4.024809 CGACAAGAACCTGAGGAAAAGAAC 60.025 45.833 4.99 0.00 0.00 3.01
963 1017 3.424170 GCTCATGCAAAGAAGAGTTCGAC 60.424 47.826 3.77 0.00 39.41 4.20
972 1026 6.015180 AGGTATTCAAAAGCTCATGCAAAGAA 60.015 34.615 3.77 0.00 42.74 2.52
993 1047 8.478775 TGCTTCTTAGAAGCTTCATATAGGTA 57.521 34.615 36.46 16.87 43.38 3.08
1000 1054 6.435277 TGGAATTTGCTTCTTAGAAGCTTCAT 59.565 34.615 36.46 25.38 43.38 2.57
1046 1100 0.602905 CTTCCACCGGAACACAGGAC 60.603 60.000 9.46 0.00 36.71 3.85
1049 1103 0.679505 TCTCTTCCACCGGAACACAG 59.320 55.000 9.46 0.00 36.71 3.66
1051 1105 2.249844 TTTCTCTTCCACCGGAACAC 57.750 50.000 9.46 0.00 36.71 3.32
1054 1108 2.373836 TGGATTTTCTCTTCCACCGGAA 59.626 45.455 9.46 0.00 39.66 4.30
1067 1121 7.095649 GCTGTACAATTTGGTTTCTGGATTTTC 60.096 37.037 0.00 0.00 0.00 2.29
1079 1133 3.222173 TGTCCTGCTGTACAATTTGGT 57.778 42.857 0.00 0.00 0.00 3.67
1188 1243 0.955428 TCTTCACGTTGCCATGGAGC 60.955 55.000 18.40 0.45 0.00 4.70
1245 1300 4.498682 CCAAGTTTGTTTCCTGAGCAGAAG 60.499 45.833 0.00 0.00 0.00 2.85
1343 1398 6.531503 TTGTGGTGTTTGAACTTGGAAATA 57.468 33.333 0.00 0.00 0.00 1.40
1379 1434 6.658816 ACTGATTGGTGCATAAGACATGTTAA 59.341 34.615 0.00 0.00 0.00 2.01
1386 1441 5.220931 GGAATGACTGATTGGTGCATAAGAC 60.221 44.000 0.00 0.00 0.00 3.01
1388 1443 4.641541 TGGAATGACTGATTGGTGCATAAG 59.358 41.667 0.00 0.00 0.00 1.73
1389 1444 4.598022 TGGAATGACTGATTGGTGCATAA 58.402 39.130 0.00 0.00 0.00 1.90
1449 1504 2.434336 TGCTAATCACTACGGCAGGAAT 59.566 45.455 0.00 0.00 0.00 3.01
1468 1523 1.734465 GTCCAAGTGCTACAGTGATGC 59.266 52.381 0.00 0.75 0.00 3.91
1520 1575 1.229145 ACCAGAGCCTGAGCACTCT 60.229 57.895 4.00 0.00 44.06 3.24
1572 1627 1.615392 AGCACCTTGATGGCAACTTTC 59.385 47.619 0.00 0.00 40.22 2.62
1917 1972 1.040646 GATATGTGAGACCCTCGGCA 58.959 55.000 0.00 0.00 32.35 5.69
1923 1978 3.758755 TCATGCAGATATGTGAGACCC 57.241 47.619 3.61 0.00 0.00 4.46
2025 2080 1.383523 GCTTTGCTAGCCCGAAATCT 58.616 50.000 13.29 0.00 44.48 2.40
2235 2290 3.814842 TGTACACATCAGCCTTCTTTGTG 59.185 43.478 0.00 0.00 38.69 3.33
2271 2326 1.678123 CCACTGACAATCTCCAGCAGG 60.678 57.143 0.00 0.00 33.90 4.85
2304 2359 1.144936 GAGAGGCAATCTGGGGTCG 59.855 63.158 0.00 0.00 38.84 4.79
2455 2519 8.927411 TGTGGAACATCTTGAATCTATCATAGA 58.073 33.333 0.00 0.00 45.67 1.98
2547 2611 7.602753 AGTATATTATGCGCATCTACTTGTGA 58.397 34.615 29.11 2.22 0.00 3.58
2602 2666 6.373005 TCCAACTGTATTTCCTCTTCATCA 57.627 37.500 0.00 0.00 0.00 3.07
2603 2667 6.881602 ACTTCCAACTGTATTTCCTCTTCATC 59.118 38.462 0.00 0.00 0.00 2.92
2604 2668 6.784031 ACTTCCAACTGTATTTCCTCTTCAT 58.216 36.000 0.00 0.00 0.00 2.57
2751 2815 6.928492 TGGCATAGAAAACATTTTCAGAAACC 59.072 34.615 17.12 12.11 46.81 3.27
3003 3074 0.391793 GTAGAGTGTCCAAGCCTGGC 60.392 60.000 11.65 11.65 43.17 4.85
3097 3168 4.154918 GTGCACAGGAGTCCTATTTTCAAG 59.845 45.833 12.53 0.00 29.64 3.02
3185 3256 2.582498 GATCTTGTCGCCGACGGG 60.582 66.667 17.22 7.79 40.63 5.28
3191 3262 1.162800 GGCCTCATGATCTTGTCGCC 61.163 60.000 18.67 18.67 0.00 5.54
3284 3355 2.158957 GGTTATCCAGCGGAGACATTGA 60.159 50.000 3.76 0.00 34.05 2.57
3295 3366 2.029838 CCAGTGAGTGGTTATCCAGC 57.970 55.000 0.00 0.00 45.24 4.85
3330 3401 0.459899 TATCACAGTGCTACCAGCGG 59.540 55.000 0.00 0.00 46.26 5.52
3363 3434 5.415701 TCATGTGCCTTTTTACCTTCTCATC 59.584 40.000 0.00 0.00 0.00 2.92
3372 3443 5.705609 TTCTCCTTCATGTGCCTTTTTAC 57.294 39.130 0.00 0.00 0.00 2.01
3492 3566 8.073167 TGCAACATATACAAACAACTAACAGTG 58.927 33.333 0.00 0.00 0.00 3.66
3803 3877 2.094100 TTGGCATTTCAGGGTGGAAA 57.906 45.000 0.00 0.00 40.72 3.13
3810 3884 5.865552 CAGTTTGAGTTATTGGCATTTCAGG 59.134 40.000 0.00 0.00 0.00 3.86
3845 3919 8.131455 TCTGCTGATGTATTTTATCGAAAGAC 57.869 34.615 0.00 0.00 46.97 3.01
3855 3929 7.068702 TCCCCAATAATCTGCTGATGTATTTT 58.931 34.615 6.88 0.00 32.44 1.82
3889 3963 9.567848 CACTTGTTTCAGTTTACAGTTTATTGT 57.432 29.630 0.00 0.00 35.09 2.71
3962 4036 5.548056 TGGTTCCTCTTAGATTCAAGACCTT 59.452 40.000 0.00 0.00 31.34 3.50
4011 4085 7.565398 AGTGTTGAGCTTCCTCTTATAAGGATA 59.435 37.037 12.54 0.00 44.87 2.59
4012 4086 6.385467 AGTGTTGAGCTTCCTCTTATAAGGAT 59.615 38.462 12.54 0.00 44.87 3.24
4013 4087 5.721960 AGTGTTGAGCTTCCTCTTATAAGGA 59.278 40.000 12.54 0.65 43.84 3.36
4014 4088 5.814705 CAGTGTTGAGCTTCCTCTTATAAGG 59.185 44.000 12.54 0.00 38.93 2.69
4016 4090 6.605471 TCAGTGTTGAGCTTCCTCTTATAA 57.395 37.500 0.00 0.00 38.93 0.98
4018 4092 5.489792 TTCAGTGTTGAGCTTCCTCTTAT 57.510 39.130 0.00 0.00 38.93 1.73
4057 4131 4.265320 GCTTTTCAGTGTTTTGAAGGTTCG 59.735 41.667 0.00 0.00 38.25 3.95
4198 4274 7.119992 TGACAGCAAGTACTTTTGTTTAACTCA 59.880 33.333 18.62 11.03 0.00 3.41
4315 4589 6.090898 CGTCTTACATTTGTTTACAGAGGGAG 59.909 42.308 0.00 0.00 0.00 4.30
4316 4590 5.929992 CGTCTTACATTTGTTTACAGAGGGA 59.070 40.000 0.00 0.00 0.00 4.20
4317 4591 5.699458 ACGTCTTACATTTGTTTACAGAGGG 59.301 40.000 0.00 0.00 0.00 4.30
4318 4592 6.780706 ACGTCTTACATTTGTTTACAGAGG 57.219 37.500 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.