Multiple sequence alignment - TraesCS2A01G414700

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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 TraesCS2A01G414700 chr2A 100.000 3014 0 0 1 3014 671713638 671710625 0.000000e+00 5566
1 TraesCS2A01G414700 chr2B 94.494 2143 74 11 891 3014 622922937 622920820 0.000000e+00 3264
2 TraesCS2A01G414700 chr2D 97.374 1333 31 2 891 2220 526527140 526525809 0.000000e+00 2265
3 TraesCS2A01G414700 chr2D 93.447 702 26 7 2246 2936 526525811 526525119 0.000000e+00 1024
4 TraesCS2A01G414700 chr2D 92.405 79 6 0 2936 3014 526524957 526524879 2.460000e-21 113
5 TraesCS2A01G414700 chr6D 86.941 850 109 2 1164 2012 325821249 325820401 0.000000e+00 953
6 TraesCS2A01G414700 chr6A 86.926 849 111 0 1164 2012 464690795 464689947 0.000000e+00 953
7 TraesCS2A01G414700 chr6A 80.627 351 65 1 1236 1586 12367546 12367199 4.950000e-68 268
8 TraesCS2A01G414700 chr6B 86.690 849 113 0 1164 2012 496986735 496987583 0.000000e+00 942
9 TraesCS2A01G414700 chr4D 93.289 447 28 2 1 446 32760340 32760785 0.000000e+00 658
10 TraesCS2A01G414700 chr4D 86.932 352 22 10 485 815 32760781 32761129 1.020000e-99 374
11 TraesCS2A01G414700 chr3A 80.282 568 85 13 1177 1734 648104233 648104783 1.300000e-108 403
12 TraesCS2A01G414700 chr5D 80.911 461 68 11 1151 1595 547059981 547060437 2.220000e-91 346
13 TraesCS2A01G414700 chr5B 82.169 415 63 8 1175 1578 690230581 690230995 2.220000e-91 346


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 TraesCS2A01G414700 chr2A 671710625 671713638 3013 True 5566 5566 100.000000 1 3014 1 chr2A.!!$R1 3013
1 TraesCS2A01G414700 chr2B 622920820 622922937 2117 True 3264 3264 94.494000 891 3014 1 chr2B.!!$R1 2123
2 TraesCS2A01G414700 chr2D 526524879 526527140 2261 True 1134 2265 94.408667 891 3014 3 chr2D.!!$R1 2123
3 TraesCS2A01G414700 chr6D 325820401 325821249 848 True 953 953 86.941000 1164 2012 1 chr6D.!!$R1 848
4 TraesCS2A01G414700 chr6A 464689947 464690795 848 True 953 953 86.926000 1164 2012 1 chr6A.!!$R2 848
5 TraesCS2A01G414700 chr6B 496986735 496987583 848 False 942 942 86.690000 1164 2012 1 chr6B.!!$F1 848
6 TraesCS2A01G414700 chr4D 32760340 32761129 789 False 516 658 90.110500 1 815 2 chr4D.!!$F1 814
7 TraesCS2A01G414700 chr3A 648104233 648104783 550 False 403 403 80.282000 1177 1734 1 chr3A.!!$F1 557

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
816 839 0.105039 CCGAGAGATGCCCAGGTTAC 59.895 60.0 0.0 0.0 0.0 2.50 F
839 862 0.114364 ACCCCAATTCACCACTTCCC 59.886 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1918 0.703488 TTGGGATCATTCCACCAGCA 59.297 50.0 0.0 0.0 44.60 4.41 R
2683 2751 0.741221 CCGGTAAGACTGCAAGAGGC 60.741 60.0 0.0 0.0 45.13 4.70 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
103 104 7.448420 AGAGATGAAGTCAAAAGAGTCATCAA 58.552 34.615 12.91 0.00 36.08 2.57
114 115 8.184192 TCAAAAGAGTCATCAACTTGTTTCTTC 58.816 33.333 0.00 0.00 38.74 2.87
116 117 5.360591 AGAGTCATCAACTTGTTTCTTCGT 58.639 37.500 0.00 0.00 38.74 3.85
149 150 7.984422 ATGATGTTCTGTAATGAACTTGTCA 57.016 32.000 8.52 9.63 44.63 3.58
156 157 8.651588 GTTCTGTAATGAACTTGTCAGACTATG 58.348 37.037 1.31 0.00 42.03 2.23
170 171 7.066781 TGTCAGACTATGTTATGGAGTATGGA 58.933 38.462 1.31 0.00 34.07 3.41
182 183 9.155975 GTTATGGAGTATGGACTTGCTATTATG 57.844 37.037 0.00 0.00 35.45 1.90
217 218 8.709386 ACAGACTAGCTATTTGTTATCTTGTG 57.291 34.615 0.00 0.00 0.00 3.33
218 219 8.531982 ACAGACTAGCTATTTGTTATCTTGTGA 58.468 33.333 0.00 0.00 0.00 3.58
294 295 8.729805 TGATGCTGTTATGTAATGATGTAACA 57.270 30.769 0.00 0.00 36.13 2.41
337 339 8.845227 TCTTGTGAAGAATTTATGTTGCTGTTA 58.155 29.630 0.00 0.00 33.83 2.41
352 354 8.334263 TGTTGCTGTTATGTGAAGATTTCATA 57.666 30.769 0.00 0.00 42.47 2.15
419 421 7.604545 TGATGTTTTGTTCGGATAACATGTCTA 59.395 33.333 0.00 0.00 40.29 2.59
427 429 7.704899 TGTTCGGATAACATGTCTATAGTGTTG 59.295 37.037 14.39 7.08 36.78 3.33
432 434 9.162764 GGATAACATGTCTATAGTGTTGTTTGT 57.837 33.333 14.39 8.49 36.78 2.83
435 437 7.202016 ACATGTCTATAGTGTTGTTTGTTGG 57.798 36.000 0.00 0.00 0.00 3.77
469 471 8.988064 ATATAGTGTTGTGAAGAGTAGTTGTG 57.012 34.615 0.00 0.00 0.00 3.33
470 472 5.086104 AGTGTTGTGAAGAGTAGTTGTGT 57.914 39.130 0.00 0.00 0.00 3.72
471 473 6.216801 AGTGTTGTGAAGAGTAGTTGTGTA 57.783 37.500 0.00 0.00 0.00 2.90
472 474 6.817184 AGTGTTGTGAAGAGTAGTTGTGTAT 58.183 36.000 0.00 0.00 0.00 2.29
473 475 7.948357 AGTGTTGTGAAGAGTAGTTGTGTATA 58.052 34.615 0.00 0.00 0.00 1.47
474 476 8.585881 AGTGTTGTGAAGAGTAGTTGTGTATAT 58.414 33.333 0.00 0.00 0.00 0.86
475 477 9.850628 GTGTTGTGAAGAGTAGTTGTGTATATA 57.149 33.333 0.00 0.00 0.00 0.86
477 479 9.517609 GTTGTGAAGAGTAGTTGTGTATATAGG 57.482 37.037 0.00 0.00 0.00 2.57
478 480 7.713750 TGTGAAGAGTAGTTGTGTATATAGGC 58.286 38.462 0.00 0.00 0.00 3.93
479 481 7.560262 TGTGAAGAGTAGTTGTGTATATAGGCT 59.440 37.037 0.00 0.00 0.00 4.58
480 482 7.863375 GTGAAGAGTAGTTGTGTATATAGGCTG 59.137 40.741 0.00 0.00 0.00 4.85
481 483 6.334102 AGAGTAGTTGTGTATATAGGCTGC 57.666 41.667 0.00 0.00 0.00 5.25
482 484 6.071984 AGAGTAGTTGTGTATATAGGCTGCT 58.928 40.000 0.00 0.00 0.00 4.24
483 485 6.015856 AGAGTAGTTGTGTATATAGGCTGCTG 60.016 42.308 0.00 0.00 0.00 4.41
484 486 5.598830 AGTAGTTGTGTATATAGGCTGCTGT 59.401 40.000 0.00 0.00 0.00 4.40
485 487 6.776116 AGTAGTTGTGTATATAGGCTGCTGTA 59.224 38.462 0.00 0.00 0.00 2.74
490 492 7.718334 TGTGTATATAGGCTGCTGTATATGT 57.282 36.000 17.79 7.03 0.00 2.29
523 525 4.676196 GCTGTTTGCTGGAATAGTGGAATG 60.676 45.833 0.00 0.00 38.95 2.67
537 539 5.125100 AGTGGAATGTATGTGCTGTTTTG 57.875 39.130 0.00 0.00 0.00 2.44
546 548 7.503521 TGTATGTGCTGTTTTGTAAAGATCA 57.496 32.000 0.00 0.00 0.00 2.92
578 580 8.752766 ATTGTTTGCTGAAATATATATGCTGC 57.247 30.769 15.14 15.14 0.00 5.25
593 595 4.694760 ATGCTGCTGTGAAGATACCATA 57.305 40.909 0.00 0.00 0.00 2.74
614 616 8.950210 ACCATATATATGCTGCTATTTTGTGAC 58.050 33.333 16.08 0.00 32.40 3.67
661 663 8.732093 GTTTTGTAAAACGTTGATGTTCAATG 57.268 30.769 0.00 7.69 46.08 2.82
671 675 5.959527 CGTTGATGTTCAATGTGCTGTATAC 59.040 40.000 0.00 0.00 38.79 1.47
677 681 4.406648 TCAATGTGCTGTATACCAGGAG 57.593 45.455 0.00 0.00 42.77 3.69
681 685 3.297391 GCTGTATACCAGGAGCAGC 57.703 57.895 7.79 11.39 44.24 5.25
700 723 1.543944 CCGGGCTTTGGGCTTTTCAT 61.544 55.000 0.00 0.00 41.46 2.57
708 731 3.518068 GGCTTTTCATCCGGGCCG 61.518 66.667 21.46 21.46 33.30 6.13
756 779 4.696805 GGGGGCTTTTTCCGGGCT 62.697 66.667 0.00 0.00 0.00 5.19
758 781 2.282887 GGGCTTTTTCCGGGCTCA 60.283 61.111 0.00 0.00 0.00 4.26
815 838 1.048724 CCCGAGAGATGCCCAGGTTA 61.049 60.000 0.00 0.00 0.00 2.85
816 839 0.105039 CCGAGAGATGCCCAGGTTAC 59.895 60.000 0.00 0.00 0.00 2.50
817 840 1.115467 CGAGAGATGCCCAGGTTACT 58.885 55.000 0.00 0.00 0.00 2.24
818 841 1.067821 CGAGAGATGCCCAGGTTACTC 59.932 57.143 0.00 0.00 0.00 2.59
819 842 2.111384 GAGAGATGCCCAGGTTACTCA 58.889 52.381 0.00 0.00 0.00 3.41
820 843 2.501723 GAGAGATGCCCAGGTTACTCAA 59.498 50.000 0.00 0.00 0.00 3.02
821 844 2.237392 AGAGATGCCCAGGTTACTCAAC 59.763 50.000 0.00 0.00 0.00 3.18
833 856 3.492337 GTTACTCAACCCCAATTCACCA 58.508 45.455 0.00 0.00 0.00 4.17
834 857 1.995376 ACTCAACCCCAATTCACCAC 58.005 50.000 0.00 0.00 0.00 4.16
835 858 1.499007 ACTCAACCCCAATTCACCACT 59.501 47.619 0.00 0.00 0.00 4.00
836 859 2.091333 ACTCAACCCCAATTCACCACTT 60.091 45.455 0.00 0.00 0.00 3.16
837 860 2.558359 CTCAACCCCAATTCACCACTTC 59.442 50.000 0.00 0.00 0.00 3.01
838 861 1.618343 CAACCCCAATTCACCACTTCC 59.382 52.381 0.00 0.00 0.00 3.46
839 862 0.114364 ACCCCAATTCACCACTTCCC 59.886 55.000 0.00 0.00 0.00 3.97
840 863 0.614697 CCCCAATTCACCACTTCCCC 60.615 60.000 0.00 0.00 0.00 4.81
841 864 0.409484 CCCAATTCACCACTTCCCCT 59.591 55.000 0.00 0.00 0.00 4.79
842 865 1.549203 CCAATTCACCACTTCCCCTG 58.451 55.000 0.00 0.00 0.00 4.45
843 866 0.890683 CAATTCACCACTTCCCCTGC 59.109 55.000 0.00 0.00 0.00 4.85
844 867 0.251787 AATTCACCACTTCCCCTGCC 60.252 55.000 0.00 0.00 0.00 4.85
845 868 2.155197 ATTCACCACTTCCCCTGCCC 62.155 60.000 0.00 0.00 0.00 5.36
846 869 4.722700 CACCACTTCCCCTGCCCG 62.723 72.222 0.00 0.00 0.00 6.13
866 889 3.279116 GCACGCACCTGCAGTCAA 61.279 61.111 13.81 0.00 42.21 3.18
867 890 2.633657 CACGCACCTGCAGTCAAC 59.366 61.111 13.81 0.00 42.21 3.18
868 891 2.179547 CACGCACCTGCAGTCAACA 61.180 57.895 13.81 0.00 42.21 3.33
869 892 2.180204 ACGCACCTGCAGTCAACAC 61.180 57.895 13.81 0.00 42.21 3.32
870 893 2.896801 CGCACCTGCAGTCAACACC 61.897 63.158 13.81 0.00 42.21 4.16
871 894 1.526917 GCACCTGCAGTCAACACCT 60.527 57.895 13.81 0.00 41.59 4.00
872 895 1.103398 GCACCTGCAGTCAACACCTT 61.103 55.000 13.81 0.00 41.59 3.50
873 896 1.392589 CACCTGCAGTCAACACCTTT 58.607 50.000 13.81 0.00 0.00 3.11
874 897 1.066002 CACCTGCAGTCAACACCTTTG 59.934 52.381 13.81 0.00 0.00 2.77
875 898 1.340991 ACCTGCAGTCAACACCTTTGT 60.341 47.619 13.81 0.00 37.67 2.83
876 899 1.334869 CCTGCAGTCAACACCTTTGTC 59.665 52.381 13.81 0.00 33.55 3.18
877 900 2.292267 CTGCAGTCAACACCTTTGTCT 58.708 47.619 5.25 0.00 33.55 3.41
878 901 2.288666 TGCAGTCAACACCTTTGTCTC 58.711 47.619 0.00 0.00 33.55 3.36
879 902 2.288666 GCAGTCAACACCTTTGTCTCA 58.711 47.619 0.00 0.00 33.55 3.27
880 903 2.682856 GCAGTCAACACCTTTGTCTCAA 59.317 45.455 0.00 0.00 33.55 3.02
881 904 3.128589 GCAGTCAACACCTTTGTCTCAAA 59.871 43.478 0.00 0.00 33.55 2.69
882 905 4.380444 GCAGTCAACACCTTTGTCTCAAAA 60.380 41.667 0.00 0.00 33.55 2.44
883 906 5.708948 CAGTCAACACCTTTGTCTCAAAAA 58.291 37.500 0.00 0.00 33.55 1.94
1063 1089 3.192922 CGCCGCTCTTTAACCCCG 61.193 66.667 0.00 0.00 0.00 5.73
1141 1188 4.916293 GCATCTCCGCCGCATCCA 62.916 66.667 0.00 0.00 0.00 3.41
1142 1189 2.969238 CATCTCCGCCGCATCCAC 60.969 66.667 0.00 0.00 0.00 4.02
1143 1190 4.592192 ATCTCCGCCGCATCCACG 62.592 66.667 0.00 0.00 0.00 4.94
1503 1558 2.721167 CCTCATCAACCTCGCCGGA 61.721 63.158 5.05 0.00 36.31 5.14
1641 1696 2.446848 CCCCATCATCGCCTCTGGT 61.447 63.158 0.00 0.00 0.00 4.00
1803 1858 1.153229 GGACCGTAATGACCCTGGC 60.153 63.158 0.00 0.00 0.00 4.85
1863 1918 2.676265 GGTATCCGGTGGGCAGGTT 61.676 63.158 0.00 0.00 0.00 3.50
1900 1955 2.324014 AAAGGTGGAGTGCTGCGTGA 62.324 55.000 0.00 0.00 0.00 4.35
1905 1960 2.813042 GAGTGCTGCGTGAGAGCC 60.813 66.667 0.00 0.00 34.69 4.70
2138 2193 4.348168 AGAGTACCTTCCTGACATTTGTGT 59.652 41.667 0.00 0.00 0.00 3.72
2155 2210 8.035394 ACATTTGTGTACTGTAGGAGAGTAATG 58.965 37.037 0.00 0.00 0.00 1.90
2168 2223 4.180057 GAGAGTAATGCTGACTGAGGTTG 58.820 47.826 0.00 0.00 0.00 3.77
2174 2229 1.610038 TGCTGACTGAGGTTGCATTTG 59.390 47.619 0.00 0.00 33.11 2.32
2450 2515 4.323562 GGGTAGCTGGTGATTTCAGTAAGT 60.324 45.833 0.00 0.00 34.89 2.24
2518 2585 9.553064 AATGTTGTTTCACAAAAATATTGCCTA 57.447 25.926 0.00 0.00 40.15 3.93
2683 2751 1.143813 AAGGCCATCCATCACTAGGG 58.856 55.000 5.01 0.00 33.74 3.53
2702 2770 0.741221 GCCTCTTGCAGTCTTACCGG 60.741 60.000 0.00 0.00 40.77 5.28
2719 2787 7.712205 GTCTTACCGGAGCTAACCAAATTATAA 59.288 37.037 9.46 0.00 0.00 0.98
2882 2955 5.592054 ACAAGAGCTAAACTTTGCCTTTTC 58.408 37.500 0.00 0.00 0.00 2.29
2906 2979 2.325484 TGCTCTTGACTTCACTACCCA 58.675 47.619 0.00 0.00 0.00 4.51
2914 2987 5.762179 TGACTTCACTACCCAATCATTCT 57.238 39.130 0.00 0.00 0.00 2.40
3010 3245 6.362248 TGGGTTTATCCTTTATAGGTTGCTC 58.638 40.000 0.00 0.00 42.60 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 8.152309 ACTCTTTTGACTTCATCTCTTTCTTG 57.848 34.615 0.00 0.00 0.00 3.02
85 86 7.396540 AACAAGTTGATGACTCTTTTGACTT 57.603 32.000 10.54 0.00 37.72 3.01
133 134 8.539770 AACATAGTCTGACAAGTTCATTACAG 57.460 34.615 10.88 0.00 32.17 2.74
149 150 7.472100 GCAAGTCCATACTCCATAACATAGTCT 60.472 40.741 0.00 0.00 33.75 3.24
156 157 9.155975 CATAATAGCAAGTCCATACTCCATAAC 57.844 37.037 0.00 0.00 33.75 1.89
193 194 8.932945 TCACAAGATAACAAATAGCTAGTCTG 57.067 34.615 0.00 1.02 27.90 3.51
194 195 8.972127 TCTCACAAGATAACAAATAGCTAGTCT 58.028 33.333 0.00 0.00 27.90 3.24
238 239 8.486210 TCTTGTTCATAATAGCAAGTCCATACT 58.514 33.333 0.00 0.00 39.28 2.12
329 330 8.959548 ACATATGAAATCTTCACATAACAGCAA 58.040 29.630 10.38 0.00 43.48 3.91
352 354 5.009310 CCAGCAAACATCAGCATATACACAT 59.991 40.000 0.00 0.00 0.00 3.21
395 397 6.817765 AGACATGTTATCCGAACAAAACAT 57.182 33.333 0.00 0.00 41.87 2.71
444 446 8.585881 ACACAACTACTCTTCACAACACTATAT 58.414 33.333 0.00 0.00 0.00 0.86
445 447 7.948357 ACACAACTACTCTTCACAACACTATA 58.052 34.615 0.00 0.00 0.00 1.31
446 448 6.817184 ACACAACTACTCTTCACAACACTAT 58.183 36.000 0.00 0.00 0.00 2.12
447 449 6.216801 ACACAACTACTCTTCACAACACTA 57.783 37.500 0.00 0.00 0.00 2.74
448 450 5.086104 ACACAACTACTCTTCACAACACT 57.914 39.130 0.00 0.00 0.00 3.55
449 451 8.758633 ATATACACAACTACTCTTCACAACAC 57.241 34.615 0.00 0.00 0.00 3.32
451 453 9.517609 CCTATATACACAACTACTCTTCACAAC 57.482 37.037 0.00 0.00 0.00 3.32
452 454 8.195436 GCCTATATACACAACTACTCTTCACAA 58.805 37.037 0.00 0.00 0.00 3.33
453 455 7.560262 AGCCTATATACACAACTACTCTTCACA 59.440 37.037 0.00 0.00 0.00 3.58
454 456 7.863375 CAGCCTATATACACAACTACTCTTCAC 59.137 40.741 0.00 0.00 0.00 3.18
455 457 7.470147 GCAGCCTATATACACAACTACTCTTCA 60.470 40.741 0.00 0.00 0.00 3.02
456 458 6.864165 GCAGCCTATATACACAACTACTCTTC 59.136 42.308 0.00 0.00 0.00 2.87
457 459 6.551601 AGCAGCCTATATACACAACTACTCTT 59.448 38.462 0.00 0.00 0.00 2.85
458 460 6.015856 CAGCAGCCTATATACACAACTACTCT 60.016 42.308 0.00 0.00 0.00 3.24
459 461 6.153067 CAGCAGCCTATATACACAACTACTC 58.847 44.000 0.00 0.00 0.00 2.59
460 462 5.598830 ACAGCAGCCTATATACACAACTACT 59.401 40.000 0.00 0.00 0.00 2.57
461 463 5.844004 ACAGCAGCCTATATACACAACTAC 58.156 41.667 0.00 0.00 0.00 2.73
462 464 7.776618 ATACAGCAGCCTATATACACAACTA 57.223 36.000 0.00 0.00 0.00 2.24
463 465 6.672266 ATACAGCAGCCTATATACACAACT 57.328 37.500 0.00 0.00 0.00 3.16
464 466 8.035394 ACATATACAGCAGCCTATATACACAAC 58.965 37.037 0.00 0.00 0.00 3.32
465 467 8.134202 ACATATACAGCAGCCTATATACACAA 57.866 34.615 0.00 0.00 0.00 3.33
466 468 7.718334 ACATATACAGCAGCCTATATACACA 57.282 36.000 0.00 0.00 0.00 3.72
467 469 7.010552 GCAACATATACAGCAGCCTATATACAC 59.989 40.741 0.00 0.00 0.00 2.90
468 470 7.041721 GCAACATATACAGCAGCCTATATACA 58.958 38.462 0.00 0.00 0.00 2.29
469 471 7.223582 CAGCAACATATACAGCAGCCTATATAC 59.776 40.741 0.00 0.00 0.00 1.47
470 472 7.124147 TCAGCAACATATACAGCAGCCTATATA 59.876 37.037 0.00 0.00 0.00 0.86
471 473 6.070596 TCAGCAACATATACAGCAGCCTATAT 60.071 38.462 0.00 0.00 0.00 0.86
472 474 5.245977 TCAGCAACATATACAGCAGCCTATA 59.754 40.000 0.00 0.00 0.00 1.31
473 475 4.040829 TCAGCAACATATACAGCAGCCTAT 59.959 41.667 0.00 0.00 0.00 2.57
474 476 3.387699 TCAGCAACATATACAGCAGCCTA 59.612 43.478 0.00 0.00 0.00 3.93
475 477 2.171237 TCAGCAACATATACAGCAGCCT 59.829 45.455 0.00 0.00 0.00 4.58
476 478 2.289002 GTCAGCAACATATACAGCAGCC 59.711 50.000 0.00 0.00 0.00 4.85
477 479 2.289002 GGTCAGCAACATATACAGCAGC 59.711 50.000 0.00 0.00 0.00 5.25
478 480 3.558829 CAGGTCAGCAACATATACAGCAG 59.441 47.826 0.00 0.00 0.00 4.24
479 481 3.534554 CAGGTCAGCAACATATACAGCA 58.465 45.455 0.00 0.00 0.00 4.41
480 482 2.289002 GCAGGTCAGCAACATATACAGC 59.711 50.000 0.00 0.00 0.00 4.40
481 483 3.558829 CAGCAGGTCAGCAACATATACAG 59.441 47.826 0.00 0.00 36.85 2.74
482 484 3.055167 ACAGCAGGTCAGCAACATATACA 60.055 43.478 0.00 0.00 36.85 2.29
483 485 3.535561 ACAGCAGGTCAGCAACATATAC 58.464 45.455 0.00 0.00 36.85 1.47
484 486 3.912496 ACAGCAGGTCAGCAACATATA 57.088 42.857 0.00 0.00 36.85 0.86
485 487 2.795231 ACAGCAGGTCAGCAACATAT 57.205 45.000 0.00 0.00 36.85 1.78
490 492 1.735360 GCAAACAGCAGGTCAGCAA 59.265 52.632 0.00 0.00 44.79 3.91
516 518 4.870363 ACAAAACAGCACATACATTCCAC 58.130 39.130 0.00 0.00 0.00 4.02
553 555 8.582437 AGCAGCATATATATTTCAGCAAACAAT 58.418 29.630 0.00 0.00 0.00 2.71
578 580 8.202811 AGCAGCATATATATGGTATCTTCACAG 58.797 37.037 23.37 11.41 41.99 3.66
589 591 8.949177 TGTCACAAAATAGCAGCATATATATGG 58.051 33.333 21.50 9.17 34.32 2.74
647 649 3.272439 ACAGCACATTGAACATCAACG 57.728 42.857 0.00 0.00 39.45 4.10
649 651 5.942826 TGGTATACAGCACATTGAACATCAA 59.057 36.000 5.01 0.00 41.09 2.57
653 655 4.019771 TCCTGGTATACAGCACATTGAACA 60.020 41.667 5.01 0.00 46.14 3.18
658 660 2.505407 TGCTCCTGGTATACAGCACATT 59.495 45.455 10.64 0.00 46.14 2.71
660 662 1.482182 CTGCTCCTGGTATACAGCACA 59.518 52.381 10.64 0.00 46.14 4.57
661 663 2.231215 CTGCTCCTGGTATACAGCAC 57.769 55.000 10.64 0.00 46.14 4.40
663 665 3.297391 GCTGCTCCTGGTATACAGC 57.703 57.895 5.01 13.88 46.14 4.40
681 685 1.543944 ATGAAAAGCCCAAAGCCCGG 61.544 55.000 0.00 0.00 45.47 5.73
708 731 2.861147 AGATTTATAAGCCCGAGCCC 57.139 50.000 0.00 0.00 41.25 5.19
739 762 4.696805 AGCCCGGAAAAAGCCCCC 62.697 66.667 0.73 0.00 0.00 5.40
740 763 3.068691 GAGCCCGGAAAAAGCCCC 61.069 66.667 0.73 0.00 0.00 5.80
749 772 3.706373 GTGAAGCCTGAGCCCGGA 61.706 66.667 0.73 0.00 41.25 5.14
756 779 1.001974 ACGCTACAATGTGAAGCCTGA 59.998 47.619 0.00 0.00 32.50 3.86
758 781 1.726853 GACGCTACAATGTGAAGCCT 58.273 50.000 0.00 0.00 32.50 4.58
795 818 2.444706 CCTGGGCATCTCTCGGGA 60.445 66.667 0.00 0.00 0.00 5.14
796 819 1.048724 TAACCTGGGCATCTCTCGGG 61.049 60.000 0.00 0.00 0.00 5.14
815 838 1.499007 AGTGGTGAATTGGGGTTGAGT 59.501 47.619 0.00 0.00 0.00 3.41
816 839 2.292828 AGTGGTGAATTGGGGTTGAG 57.707 50.000 0.00 0.00 0.00 3.02
817 840 2.593026 GAAGTGGTGAATTGGGGTTGA 58.407 47.619 0.00 0.00 0.00 3.18
818 841 1.618343 GGAAGTGGTGAATTGGGGTTG 59.382 52.381 0.00 0.00 0.00 3.77
819 842 1.482365 GGGAAGTGGTGAATTGGGGTT 60.482 52.381 0.00 0.00 0.00 4.11
820 843 0.114364 GGGAAGTGGTGAATTGGGGT 59.886 55.000 0.00 0.00 0.00 4.95
821 844 0.614697 GGGGAAGTGGTGAATTGGGG 60.615 60.000 0.00 0.00 0.00 4.96
822 845 0.409484 AGGGGAAGTGGTGAATTGGG 59.591 55.000 0.00 0.00 0.00 4.12
823 846 1.549203 CAGGGGAAGTGGTGAATTGG 58.451 55.000 0.00 0.00 0.00 3.16
824 847 0.890683 GCAGGGGAAGTGGTGAATTG 59.109 55.000 0.00 0.00 0.00 2.32
825 848 0.251787 GGCAGGGGAAGTGGTGAATT 60.252 55.000 0.00 0.00 0.00 2.17
826 849 1.384191 GGCAGGGGAAGTGGTGAAT 59.616 57.895 0.00 0.00 0.00 2.57
827 850 2.840753 GGGCAGGGGAAGTGGTGAA 61.841 63.158 0.00 0.00 0.00 3.18
828 851 3.256960 GGGCAGGGGAAGTGGTGA 61.257 66.667 0.00 0.00 0.00 4.02
829 852 4.722700 CGGGCAGGGGAAGTGGTG 62.723 72.222 0.00 0.00 0.00 4.17
849 872 3.279116 TTGACTGCAGGTGCGTGC 61.279 61.111 19.93 9.59 45.83 5.34
850 873 2.179547 TGTTGACTGCAGGTGCGTG 61.180 57.895 19.93 0.00 45.83 5.34
851 874 2.180204 GTGTTGACTGCAGGTGCGT 61.180 57.895 19.93 0.00 45.83 5.24
852 875 2.633657 GTGTTGACTGCAGGTGCG 59.366 61.111 19.93 0.00 45.83 5.34
853 876 1.103398 AAGGTGTTGACTGCAGGTGC 61.103 55.000 19.93 7.61 42.50 5.01
854 877 1.066002 CAAAGGTGTTGACTGCAGGTG 59.934 52.381 19.93 0.00 0.00 4.00
855 878 1.340991 ACAAAGGTGTTGACTGCAGGT 60.341 47.619 19.93 3.31 32.58 4.00
856 879 1.334869 GACAAAGGTGTTGACTGCAGG 59.665 52.381 19.93 0.00 38.41 4.85
857 880 2.289002 GAGACAAAGGTGTTGACTGCAG 59.711 50.000 13.48 13.48 38.41 4.41
858 881 2.288666 GAGACAAAGGTGTTGACTGCA 58.711 47.619 0.00 0.00 38.41 4.41
859 882 2.288666 TGAGACAAAGGTGTTGACTGC 58.711 47.619 0.00 0.00 38.41 4.40
860 883 4.963276 TTTGAGACAAAGGTGTTGACTG 57.037 40.909 0.00 0.00 38.41 3.51
861 884 5.975693 TTTTTGAGACAAAGGTGTTGACT 57.024 34.783 0.00 0.00 38.41 3.41
886 909 2.456577 AGGTGTTGACTGCAGGTTTTT 58.543 42.857 19.93 0.00 0.00 1.94
887 910 2.143876 AGGTGTTGACTGCAGGTTTT 57.856 45.000 19.93 0.00 0.00 2.43
888 911 2.172717 AGTAGGTGTTGACTGCAGGTTT 59.827 45.455 19.93 0.00 0.00 3.27
889 912 1.768870 AGTAGGTGTTGACTGCAGGTT 59.231 47.619 19.93 0.00 0.00 3.50
890 913 1.424638 AGTAGGTGTTGACTGCAGGT 58.575 50.000 19.93 3.31 0.00 4.00
891 914 2.671351 CGTAGTAGGTGTTGACTGCAGG 60.671 54.545 19.93 0.00 0.00 4.85
892 915 2.596452 CGTAGTAGGTGTTGACTGCAG 58.404 52.381 13.48 13.48 0.00 4.41
893 916 1.336517 GCGTAGTAGGTGTTGACTGCA 60.337 52.381 0.00 0.00 0.00 4.41
1023 1049 1.340889 GATGCGAGCAGAGAGGAAGAT 59.659 52.381 3.58 0.00 0.00 2.40
1063 1089 1.809207 CGTGGTTGGGATTGGATGC 59.191 57.895 0.00 0.00 0.00 3.91
1135 1182 4.160635 CGAAACCGCCGTGGATGC 62.161 66.667 4.58 0.00 42.00 3.91
1136 1183 4.160635 GCGAAACCGCCGTGGATG 62.161 66.667 4.58 0.00 46.48 3.51
1353 1400 0.540923 GCAGCCAGGAGTTGATCTCT 59.459 55.000 0.00 0.00 42.40 3.10
1641 1696 1.077787 GGCAATGACCGGGATGTGA 60.078 57.895 6.32 0.00 0.00 3.58
1803 1858 1.280133 TCAATCTCCTTCACCAGGCTG 59.720 52.381 7.75 7.75 43.55 4.85
1863 1918 0.703488 TTGGGATCATTCCACCAGCA 59.297 50.000 0.00 0.00 44.60 4.41
2020 2075 2.649816 AGGAAGTACCAAGGAGGCATTT 59.350 45.455 0.00 0.00 43.14 2.32
2138 2193 5.590663 CAGTCAGCATTACTCTCCTACAGTA 59.409 44.000 0.00 0.00 0.00 2.74
2155 2210 1.881973 TCAAATGCAACCTCAGTCAGC 59.118 47.619 0.00 0.00 0.00 4.26
2174 2229 8.498358 CCCAACAAAAGAAGCTTTATCAAAATC 58.502 33.333 0.00 0.00 0.00 2.17
2683 2751 0.741221 CCGGTAAGACTGCAAGAGGC 60.741 60.000 0.00 0.00 45.13 4.70
2882 2955 4.214332 GGGTAGTGAAGTCAAGAGCAAAAG 59.786 45.833 0.00 0.00 0.00 2.27
2960 3195 6.152323 AGCCAGAATACTACGTAAACTTGAGA 59.848 38.462 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.