Multiple sequence alignment - TraesCS6D01G187700

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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 TraesCS6D01G187700 chr6D 100.000 2961 0 0 1 2961 254235368 254238328 0.000000e+00 5469.0
1 TraesCS6D01G187700 chr6D 92.708 96 7 0 301 396 108483180 108483275 3.980000e-29 139.0
2 TraesCS6D01G187700 chr6D 91.954 87 7 0 785 871 254236238 254236152 4.010000e-24 122.0
3 TraesCS6D01G187700 chr6A 92.516 1109 24 19 877 1969 364626321 364625256 0.000000e+00 1533.0
4 TraesCS6D01G187700 chr6A 91.336 958 38 9 2042 2961 364624845 364623895 0.000000e+00 1267.0
5 TraesCS6D01G187700 chr6A 88.067 771 75 8 1 758 364627108 364626342 0.000000e+00 898.0
6 TraesCS6D01G187700 chr6B 91.595 583 39 2 2388 2961 372316723 372317304 0.000000e+00 797.0
7 TraesCS6D01G187700 chr6B 92.628 529 28 6 1562 2090 372307505 372308022 0.000000e+00 750.0
8 TraesCS6D01G187700 chr6B 87.071 495 19 6 1084 1566 372305272 372305733 4.370000e-143 518.0
9 TraesCS6D01G187700 chr6B 94.208 259 15 0 2089 2347 372309793 372310051 2.140000e-106 396.0
10 TraesCS6D01G187700 chr6B 88.850 287 19 7 477 756 372303119 372303399 1.020000e-89 340.0
11 TraesCS6D01G187700 chr6B 95.098 204 9 1 877 1079 372303690 372303893 1.320000e-83 320.0
12 TraesCS6D01G187700 chr6B 83.495 103 8 4 780 873 27775350 27775452 1.460000e-13 87.9
13 TraesCS6D01G187700 chr5D 90.179 112 11 0 2848 2959 555440887 555440776 2.380000e-31 147.0
14 TraesCS6D01G187700 chrUn 92.708 96 7 0 301 396 217905640 217905735 3.980000e-29 139.0
15 TraesCS6D01G187700 chrUn 92.708 96 7 0 301 396 430768477 430768572 3.980000e-29 139.0
16 TraesCS6D01G187700 chr7D 92.708 96 7 0 301 396 382114042 382114137 3.980000e-29 139.0
17 TraesCS6D01G187700 chr7D 85.321 109 13 3 2848 2955 18760454 18760560 3.120000e-20 110.0
18 TraesCS6D01G187700 chr3D 92.708 96 7 0 301 396 501840400 501840305 3.980000e-29 139.0
19 TraesCS6D01G187700 chr3D 84.685 111 17 0 2849 2959 518141945 518141835 8.680000e-21 111.0
20 TraesCS6D01G187700 chr3B 92.708 96 7 0 301 396 6012794 6012699 3.980000e-29 139.0
21 TraesCS6D01G187700 chr3B 88.764 89 10 0 785 873 738284166 738284254 3.120000e-20 110.0
22 TraesCS6D01G187700 chr3B 85.567 97 14 0 779 875 738284258 738284162 5.220000e-18 102.0
23 TraesCS6D01G187700 chr1B 92.708 96 7 0 301 396 461438092 461438187 3.980000e-29 139.0
24 TraesCS6D01G187700 chr1B 92.708 96 7 0 301 396 619197340 619197245 3.980000e-29 139.0
25 TraesCS6D01G187700 chr1B 89.189 111 11 1 2849 2959 512784760 512784869 1.430000e-28 137.0
26 TraesCS6D01G187700 chr2D 85.345 116 17 0 2844 2959 9601286 9601401 1.440000e-23 121.0
27 TraesCS6D01G187700 chr2D 85.437 103 14 1 2856 2958 640602253 640602152 4.040000e-19 106.0
28 TraesCS6D01G187700 chr5A 85.321 109 16 0 2848 2956 659315887 659315995 2.410000e-21 113.0
29 TraesCS6D01G187700 chr5A 83.036 112 19 0 2848 2959 709225044 709224933 5.220000e-18 102.0
30 TraesCS6D01G187700 chr5A 81.818 99 11 6 780 873 63371641 63371545 3.160000e-10 76.8
31 TraesCS6D01G187700 chr1A 83.186 113 19 0 2847 2959 27315780 27315668 1.450000e-18 104.0
32 TraesCS6D01G187700 chr7B 85.263 95 14 0 779 873 553654381 553654475 6.750000e-17 99.0
33 TraesCS6D01G187700 chr1D 85.263 95 14 0 779 873 189199032 189199126 6.750000e-17 99.0
34 TraesCS6D01G187700 chr4A 82.979 94 15 1 780 873 568711618 568711710 1.890000e-12 84.2
35 TraesCS6D01G187700 chr4B 82.105 95 13 1 780 870 577011693 577011787 8.800000e-11 78.7


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 TraesCS6D01G187700 chr6D 254235368 254238328 2960 False 5469.000000 5469 100.000000 1 2961 1 chr6D.!!$F2 2960
1 TraesCS6D01G187700 chr6A 364623895 364627108 3213 True 1232.666667 1533 90.639667 1 2961 3 chr6A.!!$R1 2960
2 TraesCS6D01G187700 chr6B 372316723 372317304 581 False 797.000000 797 91.595000 2388 2961 1 chr6B.!!$F2 573
3 TraesCS6D01G187700 chr6B 372303119 372310051 6932 False 464.800000 750 91.571000 477 2347 5 chr6B.!!$F3 1870

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
367 369 0.034896 AACGTCTAACCCACCTGCTG 59.965 55.000 0.00 0.00 0.0 4.41 F
568 572 1.266989 CAAAGTCTTCCGGCCAAAGTC 59.733 52.381 2.24 3.75 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 5040 0.034089 TCCTCAGCTCCACGATCTCA 60.034 55.000 0.0 0.0 0.0 3.27 R
1983 5465 1.475751 GCGGAGATGGATGGATGTTGT 60.476 52.381 0.0 0.0 0.0 3.32 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
27 28 2.443016 ACTAGGGCCAGCCTCGAG 60.443 66.667 6.18 5.13 36.10 4.04
121 123 4.899239 CATCGGACCTCAGCGCCC 62.899 72.222 2.29 0.00 0.00 6.13
159 161 1.002250 CAACACGGACGAGGAAGACG 61.002 60.000 0.00 0.00 0.00 4.18
172 174 3.883744 AAGACGAGGCCACAAGCGG 62.884 63.158 5.01 0.00 45.17 5.52
182 184 2.529389 ACAAGCGGAGGGGAAGGT 60.529 61.111 0.00 0.00 0.00 3.50
189 191 2.359967 GGAGGGGAAGGTGACGAGG 61.360 68.421 0.00 0.00 0.00 4.63
191 193 3.003763 GGGGAAGGTGACGAGGCT 61.004 66.667 0.00 0.00 0.00 4.58
193 195 2.283529 GGGAAGGTGACGAGGCTGA 61.284 63.158 0.00 0.00 0.00 4.26
195 197 1.444553 GAAGGTGACGAGGCTGACG 60.445 63.158 0.00 0.00 0.00 4.35
203 205 1.444553 CGAGGCTGACGACAAGGAC 60.445 63.158 0.00 0.00 0.00 3.85
220 222 1.152030 ACAGCTGACCAGGGAGGAA 60.152 57.895 23.35 0.00 41.22 3.36
226 228 1.690985 GACCAGGGAGGAAGGAGGG 60.691 68.421 0.00 0.00 41.22 4.30
227 229 2.182858 GACCAGGGAGGAAGGAGGGA 62.183 65.000 0.00 0.00 41.22 4.20
228 230 1.383803 CCAGGGAGGAAGGAGGGAG 60.384 68.421 0.00 0.00 41.22 4.30
229 231 1.383803 CAGGGAGGAAGGAGGGAGG 60.384 68.421 0.00 0.00 0.00 4.30
236 238 1.503347 AGGAAGGAGGGAGGAGAGATC 59.497 57.143 0.00 0.00 0.00 2.75
246 248 2.026879 GAGAGATCCAGCGACCGC 59.973 66.667 6.25 6.25 42.33 5.68
247 249 2.755876 AGAGATCCAGCGACCGCA 60.756 61.111 16.97 0.00 44.88 5.69
308 310 2.989824 ACGACCACGACCCAGAGG 60.990 66.667 0.00 0.00 42.66 3.69
330 332 0.254178 ATCATCACCACCTGCACCTC 59.746 55.000 0.00 0.00 0.00 3.85
337 339 0.037303 CCACCTGCACCTCACATCTT 59.963 55.000 0.00 0.00 0.00 2.40
342 344 0.890542 TGCACCTCACATCTTGGCAC 60.891 55.000 0.00 0.00 0.00 5.01
350 352 0.889186 ACATCTTGGCACCGTGGAAC 60.889 55.000 0.00 0.00 0.00 3.62
365 367 0.672711 GGAACGTCTAACCCACCTGC 60.673 60.000 0.00 0.00 0.00 4.85
367 369 0.034896 AACGTCTAACCCACCTGCTG 59.965 55.000 0.00 0.00 0.00 4.41
396 398 5.998363 AGTCAACCACTGAATTTCCTCTAAC 59.002 40.000 0.00 0.00 35.22 2.34
425 427 4.790790 AGATCTTTGGTCTTCCCCTGTAAT 59.209 41.667 0.00 0.00 0.00 1.89
426 428 5.254032 AGATCTTTGGTCTTCCCCTGTAATT 59.746 40.000 0.00 0.00 0.00 1.40
466 470 5.885230 TCACTCCTTATGCATTTGTTCAG 57.115 39.130 3.54 0.00 0.00 3.02
470 474 7.828717 TCACTCCTTATGCATTTGTTCAGAATA 59.171 33.333 3.54 0.00 0.00 1.75
543 547 8.726988 TCTAATGGAATTCTTACCGACAAAAAG 58.273 33.333 5.23 0.00 37.87 2.27
547 551 5.472478 GGAATTCTTACCGACAAAAAGGAGT 59.528 40.000 5.23 0.00 0.00 3.85
568 572 1.266989 CAAAGTCTTCCGGCCAAAGTC 59.733 52.381 2.24 3.75 0.00 3.01
605 609 3.987220 CGAACTTGGGGCTTTTGTTTATG 59.013 43.478 0.00 0.00 0.00 1.90
614 618 3.181476 GGCTTTTGTTTATGGGCGATGAT 60.181 43.478 0.00 0.00 0.00 2.45
616 620 4.268405 GCTTTTGTTTATGGGCGATGATTG 59.732 41.667 0.00 0.00 0.00 2.67
758 772 6.313905 GTGTTGGAAATATGAGTAGTGTCAGG 59.686 42.308 0.00 0.00 0.00 3.86
759 773 5.023533 TGGAAATATGAGTAGTGTCAGGC 57.976 43.478 0.00 0.00 0.00 4.85
770 1049 2.359230 GTCAGGCTGTCAGCACCC 60.359 66.667 25.68 9.19 44.75 4.61
772 1051 2.359602 CAGGCTGTCAGCACCCTG 60.360 66.667 25.68 18.77 44.75 4.45
781 1065 2.988010 TCAGCACCCTGATGTCATAC 57.012 50.000 0.00 0.00 42.98 2.39
782 1066 2.470990 TCAGCACCCTGATGTCATACT 58.529 47.619 0.00 0.00 42.98 2.12
783 1067 2.840038 TCAGCACCCTGATGTCATACTT 59.160 45.455 0.00 0.00 42.98 2.24
784 1068 3.118629 TCAGCACCCTGATGTCATACTTC 60.119 47.826 0.00 0.00 42.98 3.01
785 1069 2.171448 AGCACCCTGATGTCATACTTCC 59.829 50.000 0.00 0.00 0.00 3.46
786 1070 2.171448 GCACCCTGATGTCATACTTCCT 59.829 50.000 0.00 0.00 0.00 3.36
787 1071 3.742640 GCACCCTGATGTCATACTTCCTC 60.743 52.174 0.00 0.00 0.00 3.71
788 1072 3.041946 ACCCTGATGTCATACTTCCTCC 58.958 50.000 0.00 0.00 0.00 4.30
789 1073 2.036475 CCCTGATGTCATACTTCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
790 1074 2.695666 CCTGATGTCATACTTCCTCCGT 59.304 50.000 0.00 0.00 0.00 4.69
791 1075 3.133003 CCTGATGTCATACTTCCTCCGTT 59.867 47.826 0.00 0.00 0.00 4.44
792 1076 4.383118 CCTGATGTCATACTTCCTCCGTTT 60.383 45.833 0.00 0.00 0.00 3.60
793 1077 5.160607 TGATGTCATACTTCCTCCGTTTT 57.839 39.130 0.00 0.00 0.00 2.43
794 1078 6.288941 TGATGTCATACTTCCTCCGTTTTA 57.711 37.500 0.00 0.00 0.00 1.52
795 1079 6.703319 TGATGTCATACTTCCTCCGTTTTAA 58.297 36.000 0.00 0.00 0.00 1.52
796 1080 7.162761 TGATGTCATACTTCCTCCGTTTTAAA 58.837 34.615 0.00 0.00 0.00 1.52
797 1081 7.662258 TGATGTCATACTTCCTCCGTTTTAAAA 59.338 33.333 0.00 0.00 0.00 1.52
798 1082 7.989416 TGTCATACTTCCTCCGTTTTAAAAT 57.011 32.000 3.52 0.00 0.00 1.82
799 1083 9.675464 ATGTCATACTTCCTCCGTTTTAAAATA 57.325 29.630 3.52 0.00 0.00 1.40
800 1084 9.504708 TGTCATACTTCCTCCGTTTTAAAATAA 57.495 29.630 3.52 0.00 0.00 1.40
806 1090 8.301720 ACTTCCTCCGTTTTAAAATAAATGACC 58.698 33.333 3.52 0.00 0.00 4.02
807 1091 7.160547 TCCTCCGTTTTAAAATAAATGACCC 57.839 36.000 3.52 0.00 0.00 4.46
808 1092 6.720288 TCCTCCGTTTTAAAATAAATGACCCA 59.280 34.615 3.52 0.00 0.00 4.51
809 1093 7.232941 TCCTCCGTTTTAAAATAAATGACCCAA 59.767 33.333 3.52 0.00 0.00 4.12
810 1094 8.038351 CCTCCGTTTTAAAATAAATGACCCAAT 58.962 33.333 3.52 0.00 0.00 3.16
811 1095 9.430623 CTCCGTTTTAAAATAAATGACCCAATT 57.569 29.630 3.52 0.00 0.00 2.32
812 1096 9.780186 TCCGTTTTAAAATAAATGACCCAATTT 57.220 25.926 3.52 0.00 34.24 1.82
866 1150 7.665561 AAATTGGGTCATTTATTTTGGAACG 57.334 32.000 0.00 0.00 0.00 3.95
867 1151 4.792521 TGGGTCATTTATTTTGGAACGG 57.207 40.909 0.00 0.00 0.00 4.44
868 1152 4.408276 TGGGTCATTTATTTTGGAACGGA 58.592 39.130 0.00 0.00 0.00 4.69
869 1153 4.461081 TGGGTCATTTATTTTGGAACGGAG 59.539 41.667 0.00 0.00 0.00 4.63
870 1154 4.142249 GGGTCATTTATTTTGGAACGGAGG 60.142 45.833 0.00 0.00 0.00 4.30
871 1155 4.142249 GGTCATTTATTTTGGAACGGAGGG 60.142 45.833 0.00 0.00 0.00 4.30
872 1156 4.703093 GTCATTTATTTTGGAACGGAGGGA 59.297 41.667 0.00 0.00 0.00 4.20
873 1157 5.184287 GTCATTTATTTTGGAACGGAGGGAA 59.816 40.000 0.00 0.00 0.00 3.97
874 1158 5.955355 TCATTTATTTTGGAACGGAGGGAAT 59.045 36.000 0.00 0.00 0.00 3.01
875 1159 5.652994 TTTATTTTGGAACGGAGGGAATG 57.347 39.130 0.00 0.00 0.00 2.67
1060 1345 4.574599 ATCACTCACCTTTCTTGTTTGC 57.425 40.909 0.00 0.00 0.00 3.68
1065 1350 4.160252 ACTCACCTTTCTTGTTTGCATGTT 59.840 37.500 0.00 0.00 0.00 2.71
1106 2765 7.445402 TCTTCTTCTTTGGGACTATTTTGTCTG 59.555 37.037 0.00 0.00 37.16 3.51
1171 2865 7.594824 GCATATTTGCGTAACTTATGAACTG 57.405 36.000 15.25 0.00 39.49 3.16
1172 2866 7.186804 GCATATTTGCGTAACTTATGAACTGT 58.813 34.615 15.25 0.00 39.49 3.55
1173 2867 7.696453 GCATATTTGCGTAACTTATGAACTGTT 59.304 33.333 15.25 0.00 39.49 3.16
1174 2868 9.210426 CATATTTGCGTAACTTATGAACTGTTC 57.790 33.333 13.49 13.49 0.00 3.18
1175 2869 5.600908 TTGCGTAACTTATGAACTGTTCC 57.399 39.130 17.26 1.11 0.00 3.62
1176 2870 4.890088 TGCGTAACTTATGAACTGTTCCT 58.110 39.130 17.26 10.47 0.00 3.36
1177 2871 5.302360 TGCGTAACTTATGAACTGTTCCTT 58.698 37.500 17.26 7.99 0.00 3.36
1178 2872 5.761234 TGCGTAACTTATGAACTGTTCCTTT 59.239 36.000 17.26 5.68 0.00 3.11
1179 2873 6.261381 TGCGTAACTTATGAACTGTTCCTTTT 59.739 34.615 17.26 6.63 0.00 2.27
1180 2874 7.441760 TGCGTAACTTATGAACTGTTCCTTTTA 59.558 33.333 17.26 5.80 0.00 1.52
1181 2875 7.743400 GCGTAACTTATGAACTGTTCCTTTTAC 59.257 37.037 17.26 14.38 0.00 2.01
1182 2876 8.767085 CGTAACTTATGAACTGTTCCTTTTACA 58.233 33.333 17.26 0.00 0.00 2.41
1185 2879 8.747538 ACTTATGAACTGTTCCTTTTACAACT 57.252 30.769 17.26 0.00 0.00 3.16
1291 2985 7.238559 GCTACGGCTAGCGGTACGTATATAG 62.239 52.000 26.09 18.20 45.21 1.31
1317 3011 6.401047 CCATATGCTGGTTCATCATTCTTT 57.599 37.500 0.00 0.00 40.49 2.52
1783 5265 4.498520 GGCAGCAGCTACTCGCGA 62.499 66.667 9.26 9.26 45.59 5.87
1867 5349 3.202467 GAGCACTCCTCCTCGTCC 58.798 66.667 0.00 0.00 34.35 4.79
1868 5350 2.752238 AGCACTCCTCCTCGTCCG 60.752 66.667 0.00 0.00 0.00 4.79
1869 5351 3.827898 GCACTCCTCCTCGTCCGG 61.828 72.222 0.00 0.00 0.00 5.14
1870 5352 3.827898 CACTCCTCCTCGTCCGGC 61.828 72.222 0.00 0.00 0.00 6.13
1871 5353 4.361971 ACTCCTCCTCGTCCGGCA 62.362 66.667 0.00 0.00 0.00 5.69
1872 5354 3.522731 CTCCTCCTCGTCCGGCAG 61.523 72.222 0.00 0.00 0.00 4.85
1969 5451 1.143838 CATACAGTAGCAGGCGCCA 59.856 57.895 31.54 4.11 39.83 5.69
1994 5476 0.966875 TGGCCTGCACAACATCCATC 60.967 55.000 3.32 0.00 0.00 3.51
2077 5897 1.053424 TTGGAAGGTTGTAGCCGACT 58.947 50.000 0.00 0.00 0.00 4.18
2367 7966 1.402852 GCTTTGGCCGGACTTCAAATC 60.403 52.381 9.82 3.67 31.21 2.17
2368 7967 0.878416 TTTGGCCGGACTTCAAATCG 59.122 50.000 9.82 0.00 0.00 3.34
2467 8066 6.655003 TGAGATTTAGAATGACAAGTGGAACC 59.345 38.462 0.00 0.00 37.80 3.62
2487 8086 7.017551 TGGAACCATCCTAGATATTTAGCACAT 59.982 37.037 0.00 0.00 46.70 3.21
2578 8191 6.605849 CAATCCAACTACATCTTTGTCACTG 58.394 40.000 0.00 0.00 37.28 3.66
2638 8258 2.026356 CGGGGCCAATCCATGTGATATA 60.026 50.000 4.39 0.00 36.21 0.86
2730 8351 3.610114 GCATCAGTGTGCACGAAATTTCT 60.610 43.478 15.92 0.92 44.43 2.52
2786 8407 0.941542 CACACGTTTCGTCCACCAAT 59.058 50.000 0.00 0.00 38.32 3.16
2803 8424 3.062763 CCAATTCTCTGGCGCACTATAG 58.937 50.000 10.83 0.00 0.00 1.31
2808 8429 2.496070 TCTCTGGCGCACTATAGTTTGT 59.504 45.455 10.83 0.00 0.00 2.83
2809 8430 2.860735 CTCTGGCGCACTATAGTTTGTC 59.139 50.000 10.83 0.54 0.00 3.18
2891 8521 3.087031 CCATCTCAAACAGCCTTCATGT 58.913 45.455 0.00 0.00 0.00 3.21
2953 8583 1.153309 CATGCATGAGAGGCACCGA 60.153 57.895 22.59 0.00 45.23 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.442272 GTCTCGAGGCTGGCCCTA 60.442 66.667 10.47 0.00 46.60 3.53
27 28 1.033574 CCCTAGGGTCAGATGACGTC 58.966 60.000 20.88 9.11 45.65 4.34
139 141 1.006571 TCTTCCTCGTCCGTGTTGC 60.007 57.895 0.00 0.00 0.00 4.17
142 144 1.575576 CTCGTCTTCCTCGTCCGTGT 61.576 60.000 0.00 0.00 0.00 4.49
147 149 2.341101 TGGCCTCGTCTTCCTCGTC 61.341 63.158 3.32 0.00 0.00 4.20
149 151 2.154798 TTGTGGCCTCGTCTTCCTCG 62.155 60.000 3.32 0.00 0.00 4.63
159 161 4.785453 CCCTCCGCTTGTGGCCTC 62.785 72.222 3.32 0.00 37.74 4.70
172 174 3.020237 GCCTCGTCACCTTCCCCTC 62.020 68.421 0.00 0.00 0.00 4.30
182 184 1.285950 CTTGTCGTCAGCCTCGTCA 59.714 57.895 0.00 0.00 0.00 4.35
189 191 3.555428 GCTGTCCTTGTCGTCAGC 58.445 61.111 0.00 0.00 44.50 4.26
191 193 0.032130 GTCAGCTGTCCTTGTCGTCA 59.968 55.000 14.67 0.00 0.00 4.35
193 195 1.367840 GGTCAGCTGTCCTTGTCGT 59.632 57.895 21.09 0.00 0.00 4.34
195 197 0.321122 CCTGGTCAGCTGTCCTTGTC 60.321 60.000 26.86 4.64 0.00 3.18
203 205 1.601171 CTTCCTCCCTGGTCAGCTG 59.399 63.158 7.63 7.63 37.07 4.24
220 222 0.859760 CTGGATCTCTCCTCCCTCCT 59.140 60.000 0.00 0.00 42.59 3.69
226 228 1.791103 CGGTCGCTGGATCTCTCCTC 61.791 65.000 0.00 0.00 42.59 3.71
227 229 1.826054 CGGTCGCTGGATCTCTCCT 60.826 63.158 0.00 0.00 42.59 3.69
228 230 2.725008 CGGTCGCTGGATCTCTCC 59.275 66.667 0.00 0.00 42.45 3.71
229 231 2.026879 GCGGTCGCTGGATCTCTC 59.973 66.667 8.20 0.00 38.26 3.20
308 310 1.089920 GTGCAGGTGGTGATGATCAC 58.910 55.000 16.95 16.95 46.23 3.06
330 332 0.888736 TTCCACGGTGCCAAGATGTG 60.889 55.000 1.68 0.00 0.00 3.21
350 352 0.389948 GACAGCAGGTGGGTTAGACG 60.390 60.000 4.26 0.00 0.00 4.18
351 353 0.036294 GGACAGCAGGTGGGTTAGAC 60.036 60.000 4.26 0.00 0.00 2.59
353 355 0.400213 TTGGACAGCAGGTGGGTTAG 59.600 55.000 4.26 0.00 0.00 2.34
358 360 0.179020 TTGACTTGGACAGCAGGTGG 60.179 55.000 4.26 0.00 0.00 4.61
365 367 2.620251 TCAGTGGTTGACTTGGACAG 57.380 50.000 0.00 0.00 29.75 3.51
367 369 4.261614 GGAAATTCAGTGGTTGACTTGGAC 60.262 45.833 0.00 0.00 34.94 4.02
396 398 2.675348 GGAAGACCAAAGATCTTGCTCG 59.325 50.000 9.17 0.00 40.34 5.03
446 450 8.579850 TTATTCTGAACAAATGCATAAGGAGT 57.420 30.769 0.00 0.00 0.00 3.85
494 498 7.351166 AGAGCACCTTCTACTTCTAATAGACT 58.649 38.462 0.00 0.00 0.00 3.24
543 547 0.673956 GGCCGGAAGACTTTGACTCC 60.674 60.000 5.05 0.00 0.00 3.85
547 551 1.133915 ACTTTGGCCGGAAGACTTTGA 60.134 47.619 21.59 0.00 0.00 2.69
568 572 5.263185 CCAAGTTCGAATATTTAAGTGGCG 58.737 41.667 0.00 0.00 0.00 5.69
605 609 2.044123 AGAAAGACCAATCATCGCCC 57.956 50.000 0.00 0.00 0.00 6.13
635 639 8.877864 ATTAGTAACCAAATCAAAGATCACCA 57.122 30.769 0.00 0.00 0.00 4.17
733 747 6.313905 CCTGACACTACTCATATTTCCAACAC 59.686 42.308 0.00 0.00 0.00 3.32
736 750 5.189736 AGCCTGACACTACTCATATTTCCAA 59.810 40.000 0.00 0.00 0.00 3.53
739 753 5.665459 ACAGCCTGACACTACTCATATTTC 58.335 41.667 0.00 0.00 0.00 2.17
758 772 1.002868 ACATCAGGGTGCTGACAGC 60.003 57.895 20.86 20.86 43.74 4.40
759 773 0.322648 TGACATCAGGGTGCTGACAG 59.677 55.000 0.00 0.00 36.05 3.51
770 1049 4.392921 AACGGAGGAAGTATGACATCAG 57.607 45.455 0.00 0.00 0.00 2.90
772 1051 7.605410 TTTAAAACGGAGGAAGTATGACATC 57.395 36.000 0.00 0.00 0.00 3.06
781 1065 7.758076 GGGTCATTTATTTTAAAACGGAGGAAG 59.242 37.037 1.97 0.00 0.00 3.46
782 1066 7.232941 TGGGTCATTTATTTTAAAACGGAGGAA 59.767 33.333 1.97 0.00 0.00 3.36
783 1067 6.720288 TGGGTCATTTATTTTAAAACGGAGGA 59.280 34.615 1.97 0.00 0.00 3.71
784 1068 6.926313 TGGGTCATTTATTTTAAAACGGAGG 58.074 36.000 1.97 0.00 0.00 4.30
785 1069 8.996024 ATTGGGTCATTTATTTTAAAACGGAG 57.004 30.769 1.97 0.00 0.00 4.63
786 1070 9.780186 AAATTGGGTCATTTATTTTAAAACGGA 57.220 25.926 1.97 0.00 0.00 4.69
840 1124 9.209175 CGTTCCAAAATAAATGACCCAATTTTA 57.791 29.630 0.00 0.00 31.97 1.52
841 1125 7.174080 CCGTTCCAAAATAAATGACCCAATTTT 59.826 33.333 0.00 0.00 33.07 1.82
842 1126 6.652900 CCGTTCCAAAATAAATGACCCAATTT 59.347 34.615 0.00 0.00 34.24 1.82
843 1127 6.014156 TCCGTTCCAAAATAAATGACCCAATT 60.014 34.615 0.00 0.00 0.00 2.32
844 1128 5.482175 TCCGTTCCAAAATAAATGACCCAAT 59.518 36.000 0.00 0.00 0.00 3.16
845 1129 4.833380 TCCGTTCCAAAATAAATGACCCAA 59.167 37.500 0.00 0.00 0.00 4.12
846 1130 4.408276 TCCGTTCCAAAATAAATGACCCA 58.592 39.130 0.00 0.00 0.00 4.51
847 1131 4.142249 CCTCCGTTCCAAAATAAATGACCC 60.142 45.833 0.00 0.00 0.00 4.46
848 1132 4.142249 CCCTCCGTTCCAAAATAAATGACC 60.142 45.833 0.00 0.00 0.00 4.02
849 1133 4.703093 TCCCTCCGTTCCAAAATAAATGAC 59.297 41.667 0.00 0.00 0.00 3.06
850 1134 4.924625 TCCCTCCGTTCCAAAATAAATGA 58.075 39.130 0.00 0.00 0.00 2.57
851 1135 5.652994 TTCCCTCCGTTCCAAAATAAATG 57.347 39.130 0.00 0.00 0.00 2.32
852 1136 5.395214 GCATTCCCTCCGTTCCAAAATAAAT 60.395 40.000 0.00 0.00 0.00 1.40
853 1137 4.081917 GCATTCCCTCCGTTCCAAAATAAA 60.082 41.667 0.00 0.00 0.00 1.40
854 1138 3.445805 GCATTCCCTCCGTTCCAAAATAA 59.554 43.478 0.00 0.00 0.00 1.40
855 1139 3.020984 GCATTCCCTCCGTTCCAAAATA 58.979 45.455 0.00 0.00 0.00 1.40
856 1140 1.824852 GCATTCCCTCCGTTCCAAAAT 59.175 47.619 0.00 0.00 0.00 1.82
857 1141 1.253100 GCATTCCCTCCGTTCCAAAA 58.747 50.000 0.00 0.00 0.00 2.44
858 1142 0.111446 TGCATTCCCTCCGTTCCAAA 59.889 50.000 0.00 0.00 0.00 3.28
859 1143 0.331278 ATGCATTCCCTCCGTTCCAA 59.669 50.000 0.00 0.00 0.00 3.53
860 1144 0.394216 CATGCATTCCCTCCGTTCCA 60.394 55.000 0.00 0.00 0.00 3.53
861 1145 0.394352 ACATGCATTCCCTCCGTTCC 60.394 55.000 0.00 0.00 0.00 3.62
862 1146 1.017387 GACATGCATTCCCTCCGTTC 58.983 55.000 0.00 0.00 0.00 3.95
863 1147 0.620556 AGACATGCATTCCCTCCGTT 59.379 50.000 0.00 0.00 0.00 4.44
864 1148 1.414181 CTAGACATGCATTCCCTCCGT 59.586 52.381 0.00 0.00 0.00 4.69
865 1149 1.688735 TCTAGACATGCATTCCCTCCG 59.311 52.381 0.00 0.00 0.00 4.63
866 1150 3.135530 ACTTCTAGACATGCATTCCCTCC 59.864 47.826 0.00 0.00 0.00 4.30
867 1151 4.125703 CACTTCTAGACATGCATTCCCTC 58.874 47.826 0.00 0.00 0.00 4.30
868 1152 3.521126 ACACTTCTAGACATGCATTCCCT 59.479 43.478 0.00 0.00 0.00 4.20
869 1153 3.624861 CACACTTCTAGACATGCATTCCC 59.375 47.826 0.00 0.00 0.00 3.97
870 1154 4.256920 ACACACTTCTAGACATGCATTCC 58.743 43.478 0.00 0.00 0.00 3.01
871 1155 5.004821 CGTACACACTTCTAGACATGCATTC 59.995 44.000 0.00 0.00 0.00 2.67
872 1156 4.864806 CGTACACACTTCTAGACATGCATT 59.135 41.667 0.00 0.00 0.00 3.56
873 1157 4.424626 CGTACACACTTCTAGACATGCAT 58.575 43.478 0.00 0.00 0.00 3.96
874 1158 3.366985 CCGTACACACTTCTAGACATGCA 60.367 47.826 0.00 0.00 0.00 3.96
875 1159 3.179830 CCGTACACACTTCTAGACATGC 58.820 50.000 0.00 0.00 0.00 4.06
1030 1315 6.382869 AGAAAGGTGAGTGATTTGTTTCAG 57.617 37.500 0.00 0.00 0.00 3.02
1040 1325 3.351740 TGCAAACAAGAAAGGTGAGTGA 58.648 40.909 0.00 0.00 0.00 3.41
1060 1345 8.606040 AGAAGAAGAAGAAGAAGAAGAACATG 57.394 34.615 0.00 0.00 0.00 3.21
1065 1350 9.323985 CAAAGAAGAAGAAGAAGAAGAAGAAGA 57.676 33.333 0.00 0.00 0.00 2.87
1106 2765 6.971602 TGGATGTATTGAGAGATAAGACGAC 58.028 40.000 0.00 0.00 0.00 4.34
1570 5040 0.034089 TCCTCAGCTCCACGATCTCA 60.034 55.000 0.00 0.00 0.00 3.27
1983 5465 1.475751 GCGGAGATGGATGGATGTTGT 60.476 52.381 0.00 0.00 0.00 3.32
1994 5476 3.448686 CTGTAACTGTAAGCGGAGATGG 58.551 50.000 0.00 0.00 37.60 3.51
2077 5897 9.685828 GACAACCAGCTAATTAACATTTACAAA 57.314 29.630 0.00 0.00 0.00 2.83
2367 7966 1.577328 CTACTGCTGGGTTGCCAACG 61.577 60.000 0.74 0.00 0.00 4.10
2368 7967 1.866853 GCTACTGCTGGGTTGCCAAC 61.867 60.000 0.00 0.00 33.26 3.77
2451 8050 3.690460 AGGATGGTTCCACTTGTCATTC 58.310 45.455 0.00 0.00 45.30 2.67
2467 8066 9.800433 CTACTGATGTGCTAAATATCTAGGATG 57.200 37.037 0.00 0.00 0.00 3.51
2578 8191 4.437390 CGCTGTGTCAATTGGGACTATTTC 60.437 45.833 5.42 0.00 38.61 2.17
2638 8258 1.352622 TGGGGAGGCACAGACAAACT 61.353 55.000 0.00 0.00 0.00 2.66
2730 8351 3.361786 TCTATGGTCCATCTCACGTTCA 58.638 45.455 7.92 0.00 0.00 3.18
2786 8407 3.056107 ACAAACTATAGTGCGCCAGAGAA 60.056 43.478 6.06 0.00 0.00 2.87
2803 8424 0.310854 CTCAACTTGCGGGGACAAAC 59.689 55.000 0.00 0.00 0.00 2.93
2808 8429 0.181587 TGTTTCTCAACTTGCGGGGA 59.818 50.000 0.00 0.00 33.58 4.81
2809 8430 0.310854 GTGTTTCTCAACTTGCGGGG 59.689 55.000 0.00 0.00 33.58 5.73
2932 8562 0.682209 GGTGCCTCTCATGCATGGTT 60.682 55.000 25.97 0.00 41.46 3.67


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

AutoCloner maintained by Alex Coulton.