Multiple sequence alignment - TraesCS3D01G541000

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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 TraesCS3D01G541000 chr3D 100.000 3518 0 0 1 3518 612292809 612289292 0.000000e+00 6497.0
1 TraesCS3D01G541000 chr3D 91.837 49 4 0 1108 1156 123517119 123517071 6.300000e-08 69.4
2 TraesCS3D01G541000 chr3A 88.847 1318 71 40 888 2164 746945527 746944245 0.000000e+00 1550.0
3 TraesCS3D01G541000 chr3A 89.501 762 49 17 2183 2923 746944186 746943435 0.000000e+00 935.0
4 TraesCS3D01G541000 chr3A 86.808 849 42 20 1 844 746946310 746945527 0.000000e+00 883.0
5 TraesCS3D01G541000 chr3A 77.119 354 59 15 18 367 1930771 1930436 6.000000e-43 185.0
6 TraesCS3D01G541000 chr3B 90.685 891 60 11 1 882 826710299 826711175 0.000000e+00 1164.0
7 TraesCS3D01G541000 chr3B 81.738 1369 148 50 2198 3518 826712648 826713962 0.000000e+00 1050.0
8 TraesCS3D01G541000 chr3B 91.392 697 33 14 879 1562 826711290 826711972 0.000000e+00 929.0
9 TraesCS3D01G541000 chr3B 95.417 480 20 2 1686 2164 826712091 826712569 0.000000e+00 763.0
10 TraesCS3D01G541000 chr3B 85.974 549 51 12 2985 3518 826933890 826933353 6.590000e-157 564.0
11 TraesCS3D01G541000 chr1D 93.166 439 30 0 1689 2127 139979689 139980127 0.000000e+00 645.0
12 TraesCS3D01G541000 chr1D 88.225 552 39 15 1033 1562 139979037 139979584 1.380000e-178 636.0
13 TraesCS3D01G541000 chr1D 90.675 311 19 6 2216 2519 139980809 139981116 4.230000e-109 405.0
14 TraesCS3D01G541000 chr1D 75.789 190 37 7 2302 2485 461506367 461506181 1.740000e-13 87.9
15 TraesCS3D01G541000 chr1D 75.263 190 38 7 2302 2485 461485695 461485509 8.090000e-12 82.4
16 TraesCS3D01G541000 chr1B 93.166 439 30 0 1689 2127 198644546 198644108 0.000000e+00 645.0
17 TraesCS3D01G541000 chr1B 85.664 565 40 19 1032 1562 198645174 198644617 1.100000e-154 556.0
18 TraesCS3D01G541000 chr1B 91.694 301 14 8 2220 2519 198643303 198643013 1.180000e-109 407.0
19 TraesCS3D01G541000 chr1B 90.566 53 5 0 1584 1636 491038052 491038000 1.750000e-08 71.3
20 TraesCS3D01G541000 chr1A 92.938 439 31 0 1689 2127 150901386 150900948 1.060000e-179 640.0
21 TraesCS3D01G541000 chr1A 88.212 509 35 15 1078 1562 150901986 150901479 5.060000e-163 584.0
22 TraesCS3D01G541000 chr1A 95.385 260 12 0 2260 2519 150900019 150899760 7.030000e-112 414.0
23 TraesCS3D01G541000 chrUn 75.661 189 33 9 2302 2482 218156143 218156326 8.090000e-12 82.4
24 TraesCS3D01G541000 chrUn 75.521 192 34 8 2302 2485 246422226 246422040 8.090000e-12 82.4
25 TraesCS3D01G541000 chr4B 89.583 48 5 0 1587 1634 624187876 624187923 1.050000e-05 62.1
26 TraesCS3D01G541000 chr2B 89.583 48 5 0 1586 1633 232248465 232248418 1.050000e-05 62.1
27 TraesCS3D01G541000 chr5A 88.000 50 6 0 1585 1634 645417858 645417907 3.790000e-05 60.2
28 TraesCS3D01G541000 chr2D 86.538 52 7 0 1586 1637 19222918 19222867 1.360000e-04 58.4
29 TraesCS3D01G541000 chr4D 100.000 30 0 0 1607 1636 468807568 468807597 4.910000e-04 56.5


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 TraesCS3D01G541000 chr3D 612289292 612292809 3517 True 6497.000000 6497 100.000000 1 3518 1 chr3D.!!$R2 3517
1 TraesCS3D01G541000 chr3A 746943435 746946310 2875 True 1122.666667 1550 88.385333 1 2923 3 chr3A.!!$R2 2922
2 TraesCS3D01G541000 chr3B 826710299 826713962 3663 False 976.500000 1164 89.808000 1 3518 4 chr3B.!!$F1 3517
3 TraesCS3D01G541000 chr3B 826933353 826933890 537 True 564.000000 564 85.974000 2985 3518 1 chr3B.!!$R1 533
4 TraesCS3D01G541000 chr1D 139979037 139981116 2079 False 562.000000 645 90.688667 1033 2519 3 chr1D.!!$F1 1486
5 TraesCS3D01G541000 chr1B 198643013 198645174 2161 True 536.000000 645 90.174667 1032 2519 3 chr1B.!!$R2 1487
6 TraesCS3D01G541000 chr1A 150899760 150901986 2226 True 546.000000 640 92.178333 1078 2519 3 chr1A.!!$R1 1441

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
196 198 0.108992 GTTGTATGTCGTCGGCCTCA 60.109 55.0 0.00 0.00 0.00 3.86 F
256 258 0.110295 TTGCTAGGTGAAGCTTGCCA 59.890 50.0 2.10 0.00 43.19 4.92 F
852 1025 0.179065 GCGGCCCCGATTAGTAAACT 60.179 55.0 11.48 0.00 42.83 2.66 F
1296 1525 0.516877 CCAACATGTACACGTGCCTG 59.483 55.0 17.22 10.36 36.36 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1463 0.526211 TGTTGGATCGACGACAGAGG 59.474 55.000 0.00 0.00 31.33 3.69 R
2141 2453 1.202545 GGAAGAAGACGTAGGGGATGC 60.203 57.143 0.00 0.00 0.00 3.91 R
2319 3756 0.035176 TGTTGTAGTTGTACGGGCCC 59.965 55.000 13.57 13.57 30.95 5.80 R
3058 4516 1.210931 CTTCAACACATGCGGCTGG 59.789 57.895 0.00 0.00 0.00 4.85 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
62 63 4.493618 TCCTTTCGGAGATATCATCCCTT 58.506 43.478 5.32 0.00 35.04 3.95
65 66 5.012561 CCTTTCGGAGATATCATCCCTTTCT 59.987 44.000 5.32 0.00 35.04 2.52
66 67 5.474578 TTCGGAGATATCATCCCTTTCTG 57.525 43.478 5.32 0.00 35.04 3.02
108 110 1.017387 GCTTGTGGTGGATCGGATTC 58.983 55.000 0.00 0.00 0.00 2.52
120 122 1.809619 CGGATTCATGCGACGGTGT 60.810 57.895 0.00 0.00 44.78 4.16
146 148 2.823154 TGCACTTAATTTGGTAGTGGCC 59.177 45.455 0.00 0.00 39.66 5.36
154 156 1.847798 TTGGTAGTGGCCAAGGCGAT 61.848 55.000 7.24 0.00 42.98 4.58
182 184 1.227704 CCTGGCCGTGTGTGTTGTA 60.228 57.895 0.00 0.00 0.00 2.41
186 188 0.515564 GGCCGTGTGTGTTGTATGTC 59.484 55.000 0.00 0.00 0.00 3.06
196 198 0.108992 GTTGTATGTCGTCGGCCTCA 60.109 55.000 0.00 0.00 0.00 3.86
250 252 3.068165 ACTTGGTTTTTGCTAGGTGAAGC 59.932 43.478 0.00 0.00 43.08 3.86
256 258 0.110295 TTGCTAGGTGAAGCTTGCCA 59.890 50.000 2.10 0.00 43.19 4.92
280 283 2.032071 AGGTTTTCGCCCGGTCTG 59.968 61.111 0.00 0.00 0.00 3.51
304 307 4.214119 TCTTCAATAAACTGAGCAGTGTGC 59.786 41.667 3.57 0.00 45.46 4.57
434 437 1.131937 AGGATGGGGGAGATAGCCAAT 60.132 52.381 0.00 0.00 0.00 3.16
575 578 3.044156 AGCCCTGCTCAGATGAATTCTA 58.956 45.455 7.05 0.00 30.62 2.10
610 613 8.722480 TTTCTTCATCATTGAGTAGTACATGG 57.278 34.615 2.52 0.00 32.27 3.66
613 616 7.343057 TCTTCATCATTGAGTAGTACATGGAGT 59.657 37.037 2.52 0.00 32.27 3.85
663 669 1.081892 AGTGTCAGCGATGATGTTGC 58.918 50.000 6.66 0.00 37.51 4.17
845 1018 4.263572 CCATGGCGGCCCCGATTA 62.264 66.667 17.97 0.00 42.83 1.75
846 1019 2.669569 CATGGCGGCCCCGATTAG 60.670 66.667 17.97 0.00 42.83 1.73
847 1020 3.168528 ATGGCGGCCCCGATTAGT 61.169 61.111 17.97 0.00 42.83 2.24
848 1021 1.839747 ATGGCGGCCCCGATTAGTA 60.840 57.895 17.97 0.00 42.83 1.82
849 1022 1.412453 ATGGCGGCCCCGATTAGTAA 61.412 55.000 17.97 0.00 42.83 2.24
850 1023 1.146707 GGCGGCCCCGATTAGTAAA 59.853 57.895 8.12 0.00 42.83 2.01
851 1024 1.162181 GGCGGCCCCGATTAGTAAAC 61.162 60.000 8.12 0.00 42.83 2.01
852 1025 0.179065 GCGGCCCCGATTAGTAAACT 60.179 55.000 11.48 0.00 42.83 2.66
853 1026 1.578583 CGGCCCCGATTAGTAAACTG 58.421 55.000 0.00 0.00 42.83 3.16
854 1027 1.808891 CGGCCCCGATTAGTAAACTGG 60.809 57.143 0.00 0.00 42.83 4.00
855 1028 1.211212 GGCCCCGATTAGTAAACTGGT 59.789 52.381 0.00 0.00 0.00 4.00
856 1029 2.435437 GGCCCCGATTAGTAAACTGGTA 59.565 50.000 0.00 0.00 0.00 3.25
857 1030 3.118298 GGCCCCGATTAGTAAACTGGTAA 60.118 47.826 0.00 0.00 0.00 2.85
858 1031 4.445305 GGCCCCGATTAGTAAACTGGTAAT 60.445 45.833 0.00 0.00 0.00 1.89
859 1032 5.128205 GCCCCGATTAGTAAACTGGTAATT 58.872 41.667 1.00 0.00 0.00 1.40
860 1033 5.591472 GCCCCGATTAGTAAACTGGTAATTT 59.409 40.000 1.00 0.00 0.00 1.82
861 1034 6.095860 GCCCCGATTAGTAAACTGGTAATTTT 59.904 38.462 1.00 0.00 0.00 1.82
862 1035 7.282901 GCCCCGATTAGTAAACTGGTAATTTTA 59.717 37.037 1.00 0.00 0.00 1.52
863 1036 8.615211 CCCCGATTAGTAAACTGGTAATTTTAC 58.385 37.037 1.00 0.00 38.12 2.01
864 1037 8.330302 CCCGATTAGTAAACTGGTAATTTTACG 58.670 37.037 0.00 0.00 41.24 3.18
865 1038 8.330302 CCGATTAGTAAACTGGTAATTTTACGG 58.670 37.037 0.00 0.00 41.24 4.02
866 1039 8.330302 CGATTAGTAAACTGGTAATTTTACGGG 58.670 37.037 0.00 0.00 41.24 5.28
867 1040 7.920160 TTAGTAAACTGGTAATTTTACGGGG 57.080 36.000 0.00 0.00 41.24 5.73
868 1041 4.701651 AGTAAACTGGTAATTTTACGGGGC 59.298 41.667 0.00 0.00 41.24 5.80
869 1042 1.741528 ACTGGTAATTTTACGGGGCG 58.258 50.000 0.00 0.00 34.50 6.13
870 1043 1.003464 ACTGGTAATTTTACGGGGCGT 59.997 47.619 0.00 0.00 44.35 5.68
871 1044 1.667212 CTGGTAATTTTACGGGGCGTC 59.333 52.381 0.00 0.00 41.54 5.19
872 1045 0.652071 GGTAATTTTACGGGGCGTCG 59.348 55.000 0.00 0.00 41.54 5.12
873 1046 1.358877 GTAATTTTACGGGGCGTCGT 58.641 50.000 9.29 9.29 45.88 4.34
874 1047 1.324435 GTAATTTTACGGGGCGTCGTC 59.676 52.381 7.73 0.00 42.82 4.20
875 1048 1.353609 AATTTTACGGGGCGTCGTCG 61.354 55.000 7.73 0.00 42.82 5.12
876 1049 2.211619 ATTTTACGGGGCGTCGTCGA 62.212 55.000 6.17 0.00 42.82 4.20
877 1050 2.801113 TTTTACGGGGCGTCGTCGAG 62.801 60.000 6.17 0.95 42.82 4.04
895 1068 0.626916 AGGCCCGCCCTTATAACAAA 59.373 50.000 0.00 0.00 43.06 2.83
944 1117 1.005924 TCCCATTTCCTCTTCCCTTGC 59.994 52.381 0.00 0.00 0.00 4.01
981 1155 1.228124 TGTTTCGTGAGGGGCCAAG 60.228 57.895 4.39 0.00 0.00 3.61
1041 1221 4.922026 GGGTTGCCGTCGTGGTGT 62.922 66.667 0.00 0.00 41.21 4.16
1042 1222 2.029369 GGTTGCCGTCGTGGTGTA 59.971 61.111 0.00 0.00 41.21 2.90
1043 1223 1.375013 GGTTGCCGTCGTGGTGTAT 60.375 57.895 0.00 0.00 41.21 2.29
1242 1428 1.736645 CAACGGCCGTCTCGTCATT 60.737 57.895 34.29 10.72 40.18 2.57
1263 1463 1.747924 GACTTCCTGGGTACGTACCTC 59.252 57.143 36.70 27.90 45.72 3.85
1296 1525 0.516877 CCAACATGTACACGTGCCTG 59.483 55.000 17.22 10.36 36.36 4.85
1319 1548 5.533528 TGCTGAATCGAAATGGATGATTGAT 59.466 36.000 0.00 0.00 32.74 2.57
1348 1587 1.739466 GATTGATGTTTGCAGCCGAGA 59.261 47.619 0.00 0.00 0.00 4.04
1349 1588 1.159285 TTGATGTTTGCAGCCGAGAG 58.841 50.000 0.00 0.00 0.00 3.20
1554 1793 1.690633 GACCATCTGCTCCTCCCCA 60.691 63.158 0.00 0.00 0.00 4.96
1566 1805 1.913419 TCCTCCCCACAAGGTAATCAC 59.087 52.381 0.00 0.00 35.29 3.06
1567 1806 1.064685 CCTCCCCACAAGGTAATCACC 60.065 57.143 0.00 0.00 46.19 4.02
1635 1900 4.778534 ACTCAAAATGGAGCATCAAGTG 57.221 40.909 0.00 0.00 38.50 3.16
1665 1934 6.852664 TCAGTTTTCTTGTTGGTTTCTCTTC 58.147 36.000 0.00 0.00 0.00 2.87
1782 2094 3.394836 GGAAGGCGGAGTGGAGCT 61.395 66.667 0.00 0.00 0.00 4.09
1787 2099 2.347490 GCGGAGTGGAGCTTGGAA 59.653 61.111 0.00 0.00 0.00 3.53
2128 2440 0.811915 CCTCACCTCTACGGTCAGTG 59.188 60.000 0.00 0.00 44.93 3.66
2141 2453 2.669569 CAGTGCCACTCCCAACCG 60.670 66.667 0.00 0.00 0.00 4.44
2144 2456 3.965258 TGCCACTCCCAACCGCAT 61.965 61.111 0.00 0.00 0.00 4.73
2151 2463 2.192175 CCCAACCGCATCCCCTAC 59.808 66.667 0.00 0.00 0.00 3.18
2157 2469 1.067582 CCGCATCCCCTACGTCTTC 59.932 63.158 0.00 0.00 0.00 2.87
2180 2546 5.243283 TCTTCCTTTCCTACTAGTGTGTGTC 59.757 44.000 5.39 0.00 0.00 3.67
2206 3360 5.591643 TGTTTCAATGAGAAAGAGTACGC 57.408 39.130 0.00 0.00 46.34 4.42
2246 3636 9.450807 GTATTTGTCCAAGATAATGTGTAATGC 57.549 33.333 0.00 0.00 0.00 3.56
2525 3962 6.453092 ACGATATGGTCTATTAACGGGAAAG 58.547 40.000 0.00 0.00 0.00 2.62
2668 4110 6.586463 GTGGAAAGCTTTAGCAATTTAACCTC 59.414 38.462 12.68 2.41 45.16 3.85
2772 4214 3.548014 GCTATACCATTTCGCGTGCAAAT 60.548 43.478 5.77 1.68 0.00 2.32
2849 4291 4.448640 CCCTTTTTCCCCCTTACTTTCAGA 60.449 45.833 0.00 0.00 0.00 3.27
2851 4293 6.490492 CCTTTTTCCCCCTTACTTTCAGATA 58.510 40.000 0.00 0.00 0.00 1.98
2867 4310 8.049117 ACTTTCAGATATGACAGATTTTAGCCA 58.951 33.333 10.36 0.00 0.00 4.75
2894 4338 7.171508 GGCTGTCTATTTTTCTTTTCTTTTGGG 59.828 37.037 0.00 0.00 0.00 4.12
2933 4377 6.636454 TTTCCCCACTATCTTGTATCTGTT 57.364 37.500 0.00 0.00 0.00 3.16
2935 4379 5.529289 TCCCCACTATCTTGTATCTGTTCT 58.471 41.667 0.00 0.00 0.00 3.01
2936 4380 5.964477 TCCCCACTATCTTGTATCTGTTCTT 59.036 40.000 0.00 0.00 0.00 2.52
2937 4381 7.130099 TCCCCACTATCTTGTATCTGTTCTTA 58.870 38.462 0.00 0.00 0.00 2.10
2938 4382 7.789831 TCCCCACTATCTTGTATCTGTTCTTAT 59.210 37.037 0.00 0.00 0.00 1.73
2939 4383 9.090103 CCCCACTATCTTGTATCTGTTCTTATA 57.910 37.037 0.00 0.00 0.00 0.98
2950 4394 8.154856 TGTATCTGTTCTTATATAAAGTGGGGC 58.845 37.037 0.00 0.00 0.00 5.80
2951 4395 5.607477 TCTGTTCTTATATAAAGTGGGGCG 58.393 41.667 0.00 0.00 0.00 6.13
2957 4415 6.655930 TCTTATATAAAGTGGGGCGAAAACT 58.344 36.000 0.00 0.00 0.00 2.66
3058 4516 3.521947 ACTTTGCGTACTCCTACCATC 57.478 47.619 0.00 0.00 0.00 3.51
3081 4539 0.729116 CCGCATGTGTTGAAGCTAGG 59.271 55.000 5.38 0.00 0.00 3.02
3094 4552 0.322906 AGCTAGGCTGAAAGGTTGCC 60.323 55.000 0.00 0.00 46.42 4.52
3159 4621 9.474313 GTATAGGAGAGTCCAATCAGATAAGAT 57.526 37.037 0.00 0.00 39.61 2.40
3166 4628 8.547173 AGAGTCCAATCAGATAAGATGAAAGTT 58.453 33.333 0.00 0.00 0.00 2.66
3178 4640 8.934023 ATAAGATGAAAGTTGGTTAGGAAACA 57.066 30.769 0.00 0.00 37.34 2.83
3179 4641 7.839680 AAGATGAAAGTTGGTTAGGAAACAT 57.160 32.000 0.00 0.00 37.34 2.71
3272 4736 5.165961 TCTCCCAAAAGAATAGTCACCTG 57.834 43.478 0.00 0.00 0.00 4.00
3300 4764 6.502136 AAATTTGATCCTCTCCTTCGTTTC 57.498 37.500 0.00 0.00 0.00 2.78
3429 4901 9.603921 TCCCGTATAATTAGAAAGTAAAACAGG 57.396 33.333 0.00 0.00 0.00 4.00
3447 4929 1.123928 GGATCGAAGGGTGTGGAGAT 58.876 55.000 0.00 0.00 0.00 2.75
3450 4932 0.902531 TCGAAGGGTGTGGAGATTCC 59.097 55.000 0.00 0.00 36.96 3.01
3470 4952 2.807045 CACGCAGCTCACCGAGTC 60.807 66.667 5.11 0.00 31.39 3.36
3471 4953 4.406173 ACGCAGCTCACCGAGTCG 62.406 66.667 5.29 5.29 31.39 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.179111 GCCGTTCCGATCTGATGACA 60.179 55.000 0.00 0.00 0.00 3.58
13 14 2.300152 ACATATGCCGTTCCGATCTGAT 59.700 45.455 1.58 0.00 0.00 2.90
15 16 2.061773 GACATATGCCGTTCCGATCTG 58.938 52.381 1.58 0.00 0.00 2.90
16 17 1.964223 AGACATATGCCGTTCCGATCT 59.036 47.619 1.58 0.00 0.00 2.75
50 51 3.416156 GCCACCAGAAAGGGATGATATC 58.584 50.000 0.00 0.00 43.89 1.63
56 57 0.107017 CATCGCCACCAGAAAGGGAT 60.107 55.000 0.00 0.00 43.89 3.85
62 63 1.191489 TCACCTCATCGCCACCAGAA 61.191 55.000 0.00 0.00 0.00 3.02
65 66 2.662596 GTCACCTCATCGCCACCA 59.337 61.111 0.00 0.00 0.00 4.17
66 67 2.125106 GGTCACCTCATCGCCACC 60.125 66.667 0.00 0.00 0.00 4.61
97 99 0.597377 CGTCGCATGAATCCGATCCA 60.597 55.000 0.00 0.00 35.76 3.41
108 110 2.664851 ACACCACACCGTCGCATG 60.665 61.111 0.00 0.00 0.00 4.06
120 122 4.277174 CACTACCAAATTAAGTGCACACCA 59.723 41.667 21.04 1.49 34.73 4.17
196 198 0.600782 AACACATACGAAACGCCGGT 60.601 50.000 1.90 0.00 0.00 5.28
250 252 3.052036 CGAAAACCTGAACAATGGCAAG 58.948 45.455 0.00 0.00 0.00 4.01
256 258 0.596082 CGGGCGAAAACCTGAACAAT 59.404 50.000 0.00 0.00 38.48 2.71
280 283 5.683859 CACACTGCTCAGTTTATTGAAGAC 58.316 41.667 0.00 0.00 40.20 3.01
434 437 7.040686 GGCGCTAGAAAATTAATTATTGGAGGA 60.041 37.037 7.64 0.00 0.00 3.71
452 455 1.133450 ACTCCCAAGATAGGCGCTAGA 60.133 52.381 7.64 0.00 0.00 2.43
610 613 5.304614 TGGGGAAGTATACTCTATGCAACTC 59.695 44.000 5.70 0.00 0.00 3.01
613 616 5.464069 TCTGGGGAAGTATACTCTATGCAA 58.536 41.667 5.70 0.00 0.00 4.08
663 669 5.702865 TCGCTGATTCCATGAAAGAAAAAG 58.297 37.500 0.00 0.00 0.00 2.27
764 775 1.091771 CATTGACAATCGCTCCCGCT 61.092 55.000 0.00 0.00 0.00 5.52
844 1017 5.879777 GCCCCGTAAAATTACCAGTTTACTA 59.120 40.000 4.40 0.00 40.01 1.82
845 1018 4.701651 GCCCCGTAAAATTACCAGTTTACT 59.298 41.667 4.40 0.00 40.01 2.24
846 1019 4.437255 CGCCCCGTAAAATTACCAGTTTAC 60.437 45.833 0.00 0.00 39.19 2.01
847 1020 3.688673 CGCCCCGTAAAATTACCAGTTTA 59.311 43.478 0.00 0.00 0.00 2.01
848 1021 2.488937 CGCCCCGTAAAATTACCAGTTT 59.511 45.455 0.00 0.00 0.00 2.66
849 1022 2.086094 CGCCCCGTAAAATTACCAGTT 58.914 47.619 0.00 0.00 0.00 3.16
850 1023 1.003464 ACGCCCCGTAAAATTACCAGT 59.997 47.619 0.00 0.00 38.73 4.00
851 1024 1.667212 GACGCCCCGTAAAATTACCAG 59.333 52.381 0.00 0.00 41.37 4.00
852 1025 1.736612 GACGCCCCGTAAAATTACCA 58.263 50.000 0.00 0.00 41.37 3.25
853 1026 0.652071 CGACGCCCCGTAAAATTACC 59.348 55.000 0.00 0.00 41.37 2.85
854 1027 1.324435 GACGACGCCCCGTAAAATTAC 59.676 52.381 0.00 0.00 43.49 1.89
855 1028 1.639280 GACGACGCCCCGTAAAATTA 58.361 50.000 0.00 0.00 43.49 1.40
856 1029 1.353609 CGACGACGCCCCGTAAAATT 61.354 55.000 0.00 0.00 43.49 1.82
857 1030 1.806758 CGACGACGCCCCGTAAAAT 60.807 57.895 0.00 0.00 43.49 1.82
858 1031 2.430582 CGACGACGCCCCGTAAAA 60.431 61.111 0.00 0.00 43.49 1.52
859 1032 3.326889 CTCGACGACGCCCCGTAAA 62.327 63.158 1.48 0.00 43.49 2.01
860 1033 3.803082 CTCGACGACGCCCCGTAA 61.803 66.667 1.48 0.00 43.49 3.18
873 1046 1.458020 TTATAAGGGCGGGCCTCGA 60.458 57.895 24.62 15.21 42.43 4.04
874 1047 1.301479 GTTATAAGGGCGGGCCTCG 60.301 63.158 24.62 5.90 42.76 4.63
875 1048 0.181824 TTGTTATAAGGGCGGGCCTC 59.818 55.000 24.62 11.34 36.10 4.70
876 1049 0.626916 TTTGTTATAAGGGCGGGCCT 59.373 50.000 18.71 18.71 36.10 5.19
877 1050 0.742505 GTTTGTTATAAGGGCGGGCC 59.257 55.000 13.58 13.58 0.00 5.80
878 1051 0.742505 GGTTTGTTATAAGGGCGGGC 59.257 55.000 0.00 0.00 0.00 6.13
879 1052 1.395635 GGGTTTGTTATAAGGGCGGG 58.604 55.000 0.00 0.00 0.00 6.13
880 1053 1.064240 AGGGGTTTGTTATAAGGGCGG 60.064 52.381 0.00 0.00 0.00 6.13
881 1054 2.430248 AGGGGTTTGTTATAAGGGCG 57.570 50.000 0.00 0.00 0.00 6.13
882 1055 3.635373 GCTTAGGGGTTTGTTATAAGGGC 59.365 47.826 0.00 0.00 0.00 5.19
883 1056 4.643334 GTGCTTAGGGGTTTGTTATAAGGG 59.357 45.833 0.00 0.00 0.00 3.95
884 1057 5.506708 AGTGCTTAGGGGTTTGTTATAAGG 58.493 41.667 0.00 0.00 0.00 2.69
885 1058 5.589050 GGAGTGCTTAGGGGTTTGTTATAAG 59.411 44.000 0.00 0.00 0.00 1.73
886 1059 5.252164 AGGAGTGCTTAGGGGTTTGTTATAA 59.748 40.000 0.00 0.00 0.00 0.98
887 1060 4.786454 AGGAGTGCTTAGGGGTTTGTTATA 59.214 41.667 0.00 0.00 0.00 0.98
895 1068 2.349445 AGAAAAGGAGTGCTTAGGGGT 58.651 47.619 0.00 0.00 0.00 4.95
944 1117 1.002468 CAGTGTGCGGAAGAAACAAGG 60.002 52.381 0.00 0.00 32.21 3.61
981 1155 1.066752 GGTCACCGCCAAACCAAAC 59.933 57.895 0.00 0.00 33.11 2.93
987 1161 1.303236 CTCCATGGTCACCGCCAAA 60.303 57.895 12.58 0.00 42.48 3.28
1041 1221 0.824109 CCAGGCACAAGAGGACGATA 59.176 55.000 0.00 0.00 0.00 2.92
1042 1222 1.599047 CCAGGCACAAGAGGACGAT 59.401 57.895 0.00 0.00 0.00 3.73
1043 1223 3.059982 CCAGGCACAAGAGGACGA 58.940 61.111 0.00 0.00 0.00 4.20
1242 1428 1.549203 GGTACGTACCCAGGAAGTCA 58.451 55.000 30.84 0.00 40.53 3.41
1263 1463 0.526211 TGTTGGATCGACGACAGAGG 59.474 55.000 0.00 0.00 31.33 3.69
1296 1525 5.428496 TCAATCATCCATTTCGATTCAGC 57.572 39.130 0.00 0.00 0.00 4.26
1319 1548 5.335113 GCTGCAAACATCAATCAGTCAACTA 60.335 40.000 0.00 0.00 0.00 2.24
1348 1587 4.335647 CAGCGGCACTCCCAACCT 62.336 66.667 1.45 0.00 0.00 3.50
1607 1872 9.859427 CTTGATGCTCCATTTTGAGTTAATAAA 57.141 29.630 0.00 0.00 34.74 1.40
1617 1882 2.564062 ACCCACTTGATGCTCCATTTTG 59.436 45.455 0.00 0.00 0.00 2.44
1627 1892 4.823989 AGAAAACTGAGAACCCACTTGATG 59.176 41.667 0.00 0.00 0.00 3.07
1635 1900 3.699538 ACCAACAAGAAAACTGAGAACCC 59.300 43.478 0.00 0.00 0.00 4.11
1782 2094 2.512056 TCTGGGTCTTCACCTTTTCCAA 59.488 45.455 0.00 0.00 43.22 3.53
1787 2099 2.887151 CCATCTGGGTCTTCACCTTT 57.113 50.000 0.00 0.00 43.22 3.11
2128 2440 3.134127 GATGCGGTTGGGAGTGGC 61.134 66.667 0.00 0.00 0.00 5.01
2141 2453 1.202545 GGAAGAAGACGTAGGGGATGC 60.203 57.143 0.00 0.00 0.00 3.91
2144 2456 2.617840 AAGGAAGAAGACGTAGGGGA 57.382 50.000 0.00 0.00 0.00 4.81
2151 2463 5.183522 ACACTAGTAGGAAAGGAAGAAGACG 59.816 44.000 1.45 0.00 0.00 4.18
2157 2469 5.244178 AGACACACACTAGTAGGAAAGGAAG 59.756 44.000 1.45 0.00 0.00 3.46
2180 2546 7.505646 CGTACTCTTTCTCATTGAAACAGAAG 58.494 38.462 0.00 0.00 39.50 2.85
2201 3355 1.823610 ACTCTGTCCCTAAAGGCGTAC 59.176 52.381 0.00 0.00 34.51 3.67
2205 3359 4.844884 ACAAATACTCTGTCCCTAAAGGC 58.155 43.478 0.00 0.00 34.51 4.35
2246 3636 6.038356 GGCCACAAATCTCATCTTGTTATTG 58.962 40.000 0.00 0.00 33.51 1.90
2319 3756 0.035176 TGTTGTAGTTGTACGGGCCC 59.965 55.000 13.57 13.57 30.95 5.80
2668 4110 3.378112 TGTTCACCTTGTCTTTTCTGCAG 59.622 43.478 7.63 7.63 0.00 4.41
2725 4167 7.707893 GCATTGCCTTGTCAGTGAAATAATAAT 59.292 33.333 0.00 0.00 0.00 1.28
2818 4260 4.777877 AGGGGGAAAAAGGGATTTACTT 57.222 40.909 0.00 0.00 0.00 2.24
2849 4291 5.068636 CAGCCTGGCTAAAATCTGTCATAT 58.931 41.667 22.90 0.00 36.40 1.78
2851 4293 3.285484 CAGCCTGGCTAAAATCTGTCAT 58.715 45.455 22.90 0.00 36.40 3.06
2864 4307 4.790765 AAAGAAAAATAGACAGCCTGGC 57.209 40.909 11.65 11.65 0.00 4.85
2867 4310 7.928167 CCAAAAGAAAAGAAAAATAGACAGCCT 59.072 33.333 0.00 0.00 0.00 4.58
2933 4377 6.655930 AGTTTTCGCCCCACTTTATATAAGA 58.344 36.000 0.00 0.00 0.00 2.10
2935 4379 6.660094 ACAAGTTTTCGCCCCACTTTATATAA 59.340 34.615 0.00 0.00 0.00 0.98
2936 4380 6.181908 ACAAGTTTTCGCCCCACTTTATATA 58.818 36.000 0.00 0.00 0.00 0.86
2937 4381 5.014202 ACAAGTTTTCGCCCCACTTTATAT 58.986 37.500 0.00 0.00 0.00 0.86
2938 4382 4.400120 ACAAGTTTTCGCCCCACTTTATA 58.600 39.130 0.00 0.00 0.00 0.98
2939 4383 3.227614 ACAAGTTTTCGCCCCACTTTAT 58.772 40.909 0.00 0.00 0.00 1.40
2941 4385 1.480789 ACAAGTTTTCGCCCCACTTT 58.519 45.000 0.00 0.00 0.00 2.66
2942 4386 1.480789 AACAAGTTTTCGCCCCACTT 58.519 45.000 0.00 0.00 0.00 3.16
2943 4387 1.480789 AAACAAGTTTTCGCCCCACT 58.519 45.000 0.00 0.00 0.00 4.00
2944 4388 1.930503 CAAAACAAGTTTTCGCCCCAC 59.069 47.619 7.89 0.00 40.45 4.61
2945 4389 1.825474 TCAAAACAAGTTTTCGCCCCA 59.175 42.857 7.89 0.00 40.45 4.96
2946 4390 2.100087 TCTCAAAACAAGTTTTCGCCCC 59.900 45.455 7.89 0.00 40.45 5.80
2947 4391 3.430333 TCTCAAAACAAGTTTTCGCCC 57.570 42.857 7.89 0.00 40.45 6.13
2948 4392 4.359706 ACATCTCAAAACAAGTTTTCGCC 58.640 39.130 7.89 0.00 40.45 5.54
2949 4393 5.717251 CAACATCTCAAAACAAGTTTTCGC 58.283 37.500 7.89 0.00 40.45 4.70
2950 4394 5.516339 AGCAACATCTCAAAACAAGTTTTCG 59.484 36.000 7.89 5.14 40.45 3.46
2951 4395 6.753744 AGAGCAACATCTCAAAACAAGTTTTC 59.246 34.615 7.89 0.00 40.45 2.29
2957 4415 5.357878 AGACAAGAGCAACATCTCAAAACAA 59.642 36.000 0.00 0.00 35.59 2.83
3058 4516 1.210931 CTTCAACACATGCGGCTGG 59.789 57.895 0.00 0.00 0.00 4.85
3113 4572 8.417884 CCTATACACCTTGGTTTTTCAAAGAAA 58.582 33.333 0.00 0.00 0.00 2.52
3119 4578 6.043938 ACTCTCCTATACACCTTGGTTTTTCA 59.956 38.462 0.00 0.00 0.00 2.69
3121 4580 6.449830 ACTCTCCTATACACCTTGGTTTTT 57.550 37.500 0.00 0.00 0.00 1.94
3127 4586 5.363868 TGATTGGACTCTCCTATACACCTTG 59.636 44.000 0.00 0.00 37.46 3.61
3129 4588 5.103473 TCTGATTGGACTCTCCTATACACCT 60.103 44.000 0.00 0.00 37.46 4.00
3131 4590 6.909550 ATCTGATTGGACTCTCCTATACAC 57.090 41.667 0.00 0.00 37.46 2.90
3272 4736 6.371825 ACGAAGGAGAGGATCAAATTTACAAC 59.628 38.462 0.00 0.00 37.82 3.32
3300 4764 2.725203 TTTTGGAGCTGGGTCGTCCG 62.725 60.000 0.00 0.00 38.76 4.79
3362 4827 7.691993 ATACTAGGTGATCATGGGTTAGTTT 57.308 36.000 0.00 0.00 0.00 2.66
3420 4892 3.435671 CACACCCTTCGATCCTGTTTTAC 59.564 47.826 0.00 0.00 0.00 2.01
3429 4901 2.483889 GGAATCTCCACACCCTTCGATC 60.484 54.545 0.00 0.00 36.28 3.69
3433 4905 1.680249 GCAGGAATCTCCACACCCTTC 60.680 57.143 0.00 0.00 39.61 3.46
3435 4917 0.842030 TGCAGGAATCTCCACACCCT 60.842 55.000 0.00 0.00 39.61 4.34
3447 4929 2.666190 GTGAGCTGCGTGCAGGAA 60.666 61.111 22.22 0.00 45.94 3.36
3466 4948 0.388649 ATTCATATCGGCGGCGACTC 60.389 55.000 37.06 0.00 0.00 3.36
3467 4949 0.667487 CATTCATATCGGCGGCGACT 60.667 55.000 37.06 25.41 0.00 4.18
3468 4950 1.781555 CATTCATATCGGCGGCGAC 59.218 57.895 37.06 7.01 0.00 5.19
3469 4951 2.027073 GCATTCATATCGGCGGCGA 61.027 57.895 36.40 36.40 0.00 5.54
3470 4952 2.029288 AGCATTCATATCGGCGGCG 61.029 57.895 27.15 27.15 0.00 6.46
3471 4953 1.499056 CAGCATTCATATCGGCGGC 59.501 57.895 7.21 0.00 0.00 6.53
3472 4954 0.603707 ACCAGCATTCATATCGGCGG 60.604 55.000 7.21 0.00 0.00 6.13
3473 4955 2.078849 TACCAGCATTCATATCGGCG 57.921 50.000 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.