Multiple sequence alignment - TraesCS6D01G129600

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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 TraesCS6D01G129600 chr6D 100.000 3307 0 0 1 3307 94763508 94766814 0.000000e+00 6107.0
1 TraesCS6D01G129600 chr3B 90.109 1658 86 28 1709 3307 432261900 432260262 0.000000e+00 2082.0
2 TraesCS6D01G129600 chr3B 79.054 1289 208 33 1045 2279 71430530 71429250 0.000000e+00 828.0
3 TraesCS6D01G129600 chr3B 87.413 572 61 10 1 566 299121455 299120889 0.000000e+00 647.0
4 TraesCS6D01G129600 chr3B 86.934 574 64 11 1 568 326239281 326238713 4.660000e-178 634.0
5 TraesCS6D01G129600 chr3B 87.774 548 56 10 1 543 752510690 752511231 6.020000e-177 630.0
6 TraesCS6D01G129600 chr3B 90.950 221 17 1 1053 1273 432262116 432261899 8.970000e-76 294.0
7 TraesCS6D01G129600 chr3D 90.335 1614 98 27 1053 2613 333012680 333011072 0.000000e+00 2063.0
8 TraesCS6D01G129600 chr3D 94.356 567 26 4 2747 3307 333010874 333010308 0.000000e+00 865.0
9 TraesCS6D01G129600 chr3D 79.065 1070 167 28 1242 2272 45766386 45765335 0.000000e+00 682.0
10 TraesCS6D01G129600 chr3D 82.759 203 22 7 813 1014 333012878 333012688 5.680000e-38 169.0
11 TraesCS6D01G129600 chr3A 91.953 1454 96 15 1053 2490 450712958 450711510 0.000000e+00 2017.0
12 TraesCS6D01G129600 chr3A 90.000 510 43 5 1 506 291798849 291798344 0.000000e+00 652.0
13 TraesCS6D01G129600 chr3A 91.740 339 25 3 2672 3007 450711478 450711140 5.000000e-128 468.0
14 TraesCS6D01G129600 chr3A 93.137 306 18 1 3005 3307 450702298 450701993 2.340000e-121 446.0
15 TraesCS6D01G129600 chr6B 98.523 745 10 1 1419 2163 178019329 178018586 0.000000e+00 1314.0
16 TraesCS6D01G129600 chr6B 95.736 469 6 4 2120 2576 178018590 178018124 0.000000e+00 743.0
17 TraesCS6D01G129600 chr6B 98.155 271 2 1 2972 3242 178017790 178017523 1.390000e-128 470.0
18 TraesCS6D01G129600 chr6B 97.683 259 6 0 2714 2972 178018123 178017865 2.340000e-121 446.0
19 TraesCS6D01G129600 chr6B 75.240 832 162 24 1073 1886 678822553 678823358 4.060000e-94 355.0
20 TraesCS6D01G129600 chr6B 88.889 81 0 3 569 647 178020736 178020663 1.260000e-14 91.6
21 TraesCS6D01G129600 chr6B 100.000 28 0 0 3212 3239 178017512 178017485 6.000000e-03 52.8
22 TraesCS6D01G129600 chrUn 94.903 569 25 3 1 566 60924383 60924950 0.000000e+00 887.0
23 TraesCS6D01G129600 chr4D 94.903 569 25 3 1 566 3521484 3520917 0.000000e+00 887.0
24 TraesCS6D01G129600 chr2D 95.104 531 23 2 1 528 617910664 617910134 0.000000e+00 833.0
25 TraesCS6D01G129600 chr4B 87.215 571 62 10 1 566 507970227 507969663 1.000000e-179 640.0
26 TraesCS6D01G129600 chr5B 86.667 570 64 10 1 566 419095502 419096063 3.620000e-174 621.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G129600 chr6D 94763508 94766814 3306 False 6107.000000 6107 100.000000 1 3307 1 chr6D.!!$F1 3306
1 TraesCS6D01G129600 chr3B 432260262 432262116 1854 True 1188.000000 2082 90.529500 1053 3307 2 chr3B.!!$R4 2254
2 TraesCS6D01G129600 chr3B 71429250 71430530 1280 True 828.000000 828 79.054000 1045 2279 1 chr3B.!!$R1 1234
3 TraesCS6D01G129600 chr3B 299120889 299121455 566 True 647.000000 647 87.413000 1 566 1 chr3B.!!$R2 565
4 TraesCS6D01G129600 chr3B 326238713 326239281 568 True 634.000000 634 86.934000 1 568 1 chr3B.!!$R3 567
5 TraesCS6D01G129600 chr3B 752510690 752511231 541 False 630.000000 630 87.774000 1 543 1 chr3B.!!$F1 542
6 TraesCS6D01G129600 chr3D 333010308 333012878 2570 True 1032.333333 2063 89.150000 813 3307 3 chr3D.!!$R2 2494
7 TraesCS6D01G129600 chr3D 45765335 45766386 1051 True 682.000000 682 79.065000 1242 2272 1 chr3D.!!$R1 1030
8 TraesCS6D01G129600 chr3A 450711140 450712958 1818 True 1242.500000 2017 91.846500 1053 3007 2 chr3A.!!$R3 1954
9 TraesCS6D01G129600 chr3A 291798344 291798849 505 True 652.000000 652 90.000000 1 506 1 chr3A.!!$R1 505
10 TraesCS6D01G129600 chr6B 178017485 178020736 3251 True 519.566667 1314 96.497667 569 3242 6 chr6B.!!$R1 2673
11 TraesCS6D01G129600 chr6B 678822553 678823358 805 False 355.000000 355 75.240000 1073 1886 1 chr6B.!!$F1 813
12 TraesCS6D01G129600 chrUn 60924383 60924950 567 False 887.000000 887 94.903000 1 566 1 chrUn.!!$F1 565
13 TraesCS6D01G129600 chr4D 3520917 3521484 567 True 887.000000 887 94.903000 1 566 1 chr4D.!!$R1 565
14 TraesCS6D01G129600 chr2D 617910134 617910664 530 True 833.000000 833 95.104000 1 528 1 chr2D.!!$R1 527
15 TraesCS6D01G129600 chr4B 507969663 507970227 564 True 640.000000 640 87.215000 1 566 1 chr4B.!!$R1 565
16 TraesCS6D01G129600 chr5B 419095502 419096063 561 False 621.000000 621 86.667000 1 566 1 chr5B.!!$F1 565

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
915 2177 0.036765 CCAACTCCGATTCCGAACCA 60.037 55.0 0.0 0.0 38.22 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 4045 1.305297 CCTGAGGGGGCTTTTTCCC 60.305 63.158 0.0 0.0 45.8 3.97 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
88 89 0.855349 CGTGCGAGATTGTATGGAGC 59.145 55.000 0.00 0.00 0.00 4.70
174 175 1.885388 CGGGCGCGTCCATTTCATA 60.885 57.895 31.65 0.00 36.21 2.15
370 371 1.484240 CCTGGTCTTGGTCTCTGATCC 59.516 57.143 0.00 0.00 0.00 3.36
405 406 1.446099 GAGCGACACTTGCGGATCA 60.446 57.895 0.00 0.00 37.44 2.92
458 462 4.342378 AGTCCTGTACGATGCATAAGATGT 59.658 41.667 0.00 0.00 0.00 3.06
502 508 1.945662 GCGTTGTGGCAGCACAAAG 60.946 57.895 14.27 14.27 45.26 2.77
528 535 3.006859 TCGCAAGTTCATCTTCTTCCTCA 59.993 43.478 0.00 0.00 33.63 3.86
530 539 4.377841 CGCAAGTTCATCTTCTTCCTCAAC 60.378 45.833 0.00 0.00 33.63 3.18
536 545 5.878406 TCATCTTCTTCCTCAACCTATCC 57.122 43.478 0.00 0.00 0.00 2.59
548 557 2.962421 CAACCTATCCCTCTCTGACTCC 59.038 54.545 0.00 0.00 0.00 3.85
568 577 2.096406 CGATCGGCAACAACAGCG 59.904 61.111 7.38 0.00 0.00 5.18
569 578 2.379634 CGATCGGCAACAACAGCGA 61.380 57.895 7.38 0.00 0.00 4.93
570 579 1.132640 GATCGGCAACAACAGCGAC 59.867 57.895 0.00 0.00 0.00 5.19
571 580 1.565156 GATCGGCAACAACAGCGACA 61.565 55.000 0.00 0.00 0.00 4.35
572 581 1.568612 ATCGGCAACAACAGCGACAG 61.569 55.000 0.00 0.00 0.00 3.51
655 664 3.866883 GCCTCAGGCTCACTATCTATC 57.133 52.381 9.09 0.00 46.69 2.08
656 665 3.430453 GCCTCAGGCTCACTATCTATCT 58.570 50.000 9.09 0.00 46.69 1.98
667 1919 8.673711 GGCTCACTATCTATCTTCTACAGTATG 58.326 40.741 0.00 0.00 46.00 2.39
690 1952 1.299976 GATTTGTGCCCGACCTCCT 59.700 57.895 0.00 0.00 0.00 3.69
691 1953 0.322546 GATTTGTGCCCGACCTCCTT 60.323 55.000 0.00 0.00 0.00 3.36
694 1956 1.122632 TTGTGCCCGACCTCCTTACA 61.123 55.000 0.00 0.00 0.00 2.41
706 1968 5.401674 CGACCTCCTTACAATCGCTAAATAC 59.598 44.000 0.00 0.00 0.00 1.89
722 1984 2.876368 ATACAAGAGCCACAGCGCCC 62.876 60.000 2.29 0.00 46.67 6.13
742 2004 4.845580 CCGCAGCCCTAGCCACAG 62.846 72.222 0.00 0.00 41.25 3.66
774 2036 3.878519 CGCCTCTCCCGTCTCGAC 61.879 72.222 0.00 0.00 0.00 4.20
775 2037 3.519930 GCCTCTCCCGTCTCGACC 61.520 72.222 0.00 0.00 0.00 4.79
776 2038 2.829458 CCTCTCCCGTCTCGACCC 60.829 72.222 0.00 0.00 0.00 4.46
777 2039 3.203412 CTCTCCCGTCTCGACCCG 61.203 72.222 0.00 0.00 0.00 5.28
780 2042 4.100084 TCCCGTCTCGACCCGCTA 62.100 66.667 0.00 0.00 0.00 4.26
781 2043 3.584052 CCCGTCTCGACCCGCTAG 61.584 72.222 0.00 0.00 0.00 3.42
782 2044 2.823147 CCGTCTCGACCCGCTAGT 60.823 66.667 0.00 0.00 0.00 2.57
783 2045 2.404995 CCGTCTCGACCCGCTAGTT 61.405 63.158 0.00 0.00 0.00 2.24
784 2046 1.062206 CGTCTCGACCCGCTAGTTC 59.938 63.158 0.00 0.00 0.00 3.01
785 2047 1.432657 GTCTCGACCCGCTAGTTCC 59.567 63.158 0.00 0.00 0.00 3.62
786 2048 1.031029 GTCTCGACCCGCTAGTTCCT 61.031 60.000 0.00 0.00 0.00 3.36
787 2049 0.747283 TCTCGACCCGCTAGTTCCTC 60.747 60.000 0.00 0.00 0.00 3.71
788 2050 2.049475 CTCGACCCGCTAGTTCCTCG 62.049 65.000 0.00 0.00 0.00 4.63
789 2051 2.104530 GACCCGCTAGTTCCTCGC 59.895 66.667 0.00 0.00 0.00 5.03
790 2052 3.427598 GACCCGCTAGTTCCTCGCC 62.428 68.421 0.00 0.00 0.00 5.54
791 2053 4.222847 CCCGCTAGTTCCTCGCCC 62.223 72.222 0.00 0.00 0.00 6.13
792 2054 4.222847 CCGCTAGTTCCTCGCCCC 62.223 72.222 0.00 0.00 0.00 5.80
793 2055 4.222847 CGCTAGTTCCTCGCCCCC 62.223 72.222 0.00 0.00 0.00 5.40
794 2056 3.081409 GCTAGTTCCTCGCCCCCA 61.081 66.667 0.00 0.00 0.00 4.96
795 2057 2.901042 CTAGTTCCTCGCCCCCAC 59.099 66.667 0.00 0.00 0.00 4.61
796 2058 2.686106 TAGTTCCTCGCCCCCACC 60.686 66.667 0.00 0.00 0.00 4.61
811 2073 4.677151 ACCCCACCCCCTCTGGTC 62.677 72.222 0.00 0.00 36.12 4.02
821 2083 2.182030 CTCTGGTCCGTTCTCCGC 59.818 66.667 0.00 0.00 34.38 5.54
853 2115 1.758592 CTTCCCGGAACCAACTCCA 59.241 57.895 0.73 0.00 34.91 3.86
854 2116 0.109723 CTTCCCGGAACCAACTCCAA 59.890 55.000 0.73 0.00 34.91 3.53
855 2117 0.179012 TTCCCGGAACCAACTCCAAC 60.179 55.000 0.73 0.00 34.91 3.77
856 2118 1.057851 TCCCGGAACCAACTCCAACT 61.058 55.000 0.73 0.00 34.91 3.16
857 2119 0.605589 CCCGGAACCAACTCCAACTC 60.606 60.000 0.73 0.00 34.91 3.01
858 2120 0.605589 CCGGAACCAACTCCAACTCC 60.606 60.000 0.00 0.00 34.91 3.85
859 2121 0.107831 CGGAACCAACTCCAACTCCA 59.892 55.000 0.00 0.00 34.91 3.86
864 2126 1.202651 ACCAACTCCAACTCCAACTCG 60.203 52.381 0.00 0.00 0.00 4.18
888 2150 1.604023 AGACTCGTGCTCCCGTCTT 60.604 57.895 0.00 0.00 33.21 3.01
890 2152 2.182030 CTCGTGCTCCCGTCTTCC 59.818 66.667 0.00 0.00 0.00 3.46
892 2154 4.796231 CGTGCTCCCGTCTTCCCG 62.796 72.222 0.00 0.00 0.00 5.14
900 2162 3.961729 CGTCTTCCCGGAACCAAC 58.038 61.111 0.73 0.00 0.00 3.77
901 2163 1.370064 CGTCTTCCCGGAACCAACT 59.630 57.895 0.73 0.00 0.00 3.16
902 2164 0.669625 CGTCTTCCCGGAACCAACTC 60.670 60.000 0.73 0.00 0.00 3.01
910 2172 2.763651 GGAACCAACTCCGATTCCG 58.236 57.895 0.00 0.00 31.82 4.30
911 2173 0.248289 GGAACCAACTCCGATTCCGA 59.752 55.000 0.00 0.00 38.22 4.55
912 2174 1.338389 GGAACCAACTCCGATTCCGAA 60.338 52.381 0.00 0.00 38.22 4.30
915 2177 0.036765 CCAACTCCGATTCCGAACCA 60.037 55.000 0.00 0.00 38.22 3.67
916 2178 1.609580 CCAACTCCGATTCCGAACCAA 60.610 52.381 0.00 0.00 38.22 3.67
918 2180 0.974383 ACTCCGATTCCGAACCAACT 59.026 50.000 0.00 0.00 38.22 3.16
919 2181 1.067071 ACTCCGATTCCGAACCAACTC 60.067 52.381 0.00 0.00 38.22 3.01
920 2182 0.248289 TCCGATTCCGAACCAACTCC 59.752 55.000 0.00 0.00 38.22 3.85
921 2183 1.082117 CCGATTCCGAACCAACTCCG 61.082 60.000 0.00 0.00 38.22 4.63
947 2209 4.493747 CTCCTTCCCGTCCGCGAC 62.494 72.222 8.23 2.72 41.33 5.19
966 2228 2.930682 GACTTGGTTTCGAGGTATGAGC 59.069 50.000 0.00 0.00 0.00 4.26
967 2229 2.567615 ACTTGGTTTCGAGGTATGAGCT 59.432 45.455 0.00 0.00 0.00 4.09
970 2232 3.628008 TGGTTTCGAGGTATGAGCTCTA 58.372 45.455 16.19 1.49 40.38 2.43
988 2250 8.044309 TGAGCTCTATATATATCTAGATCCGCC 58.956 40.741 16.19 4.84 0.00 6.13
992 2254 3.878237 ATATATCTAGATCCGCCCCGA 57.122 47.619 8.95 0.00 0.00 5.14
994 2256 0.675837 TATCTAGATCCGCCCCGACG 60.676 60.000 8.95 0.00 0.00 5.12
1004 2266 2.508928 CCCCGACGCCCACAATAT 59.491 61.111 0.00 0.00 0.00 1.28
1007 2269 0.880278 CCCGACGCCCACAATATCAG 60.880 60.000 0.00 0.00 0.00 2.90
1008 2270 0.104120 CCGACGCCCACAATATCAGA 59.896 55.000 0.00 0.00 0.00 3.27
1009 2271 1.270305 CCGACGCCCACAATATCAGAT 60.270 52.381 0.00 0.00 0.00 2.90
1010 2272 2.061773 CGACGCCCACAATATCAGATC 58.938 52.381 0.00 0.00 0.00 2.75
1025 2287 0.312102 AGATCGATCGATTGCGCTGA 59.688 50.000 29.89 0.49 37.46 4.26
1026 2288 1.067985 AGATCGATCGATTGCGCTGAT 60.068 47.619 29.89 6.93 37.46 2.90
1027 2289 1.723542 GATCGATCGATTGCGCTGATT 59.276 47.619 29.89 6.14 37.46 2.57
1028 2290 2.415697 TCGATCGATTGCGCTGATTA 57.584 45.000 15.15 0.00 37.46 1.75
1029 2291 2.946564 TCGATCGATTGCGCTGATTAT 58.053 42.857 15.15 0.00 37.46 1.28
1030 2292 3.317150 TCGATCGATTGCGCTGATTATT 58.683 40.909 15.15 0.00 37.46 1.40
1031 2293 4.481463 TCGATCGATTGCGCTGATTATTA 58.519 39.130 15.15 0.00 37.46 0.98
1032 2294 5.102313 TCGATCGATTGCGCTGATTATTAT 58.898 37.500 15.15 0.00 37.46 1.28
1033 2295 6.262601 TCGATCGATTGCGCTGATTATTATA 58.737 36.000 15.15 0.00 37.46 0.98
1034 2296 6.750039 TCGATCGATTGCGCTGATTATTATAA 59.250 34.615 15.15 0.00 37.46 0.98
1035 2297 6.836337 CGATCGATTGCGCTGATTATTATAAC 59.164 38.462 10.26 0.00 37.46 1.89
1036 2298 7.462724 CGATCGATTGCGCTGATTATTATAACA 60.463 37.037 10.26 0.00 37.46 2.41
1037 2299 7.414814 TCGATTGCGCTGATTATTATAACAA 57.585 32.000 9.73 0.00 37.46 2.83
1038 2300 7.287950 TCGATTGCGCTGATTATTATAACAAC 58.712 34.615 9.73 0.00 37.46 3.32
1039 2301 7.042389 TCGATTGCGCTGATTATTATAACAACA 60.042 33.333 9.73 0.00 37.46 3.33
1040 2302 7.266966 CGATTGCGCTGATTATTATAACAACAG 59.733 37.037 9.73 9.54 0.00 3.16
1041 2303 5.747565 TGCGCTGATTATTATAACAACAGC 58.252 37.500 20.00 20.00 43.48 4.40
1042 2304 5.295540 TGCGCTGATTATTATAACAACAGCA 59.704 36.000 24.67 15.72 45.99 4.41
1043 2305 6.183360 TGCGCTGATTATTATAACAACAGCAA 60.183 34.615 24.67 16.49 45.99 3.91
1065 2327 5.885449 AAAAATCCCATCTTTTGTGTCCA 57.115 34.783 0.00 0.00 0.00 4.02
1308 2579 1.526917 GGGCGGCAACATCATAGCT 60.527 57.895 12.47 0.00 0.00 3.32
1311 2582 1.541233 GGCGGCAACATCATAGCTACT 60.541 52.381 3.07 0.00 0.00 2.57
1355 2626 1.269413 GGTCTTCGACACGGAAACTGA 60.269 52.381 0.00 0.00 33.68 3.41
1414 2685 1.904287 TGATGCGGCCAACTACTTTT 58.096 45.000 2.24 0.00 0.00 2.27
1614 2903 2.434185 CCGGACGGACACACCATG 60.434 66.667 4.40 0.00 38.90 3.66
1675 2967 2.123589 TCTCCTTTGACACCAAGACCA 58.876 47.619 0.00 0.00 33.23 4.02
1727 3019 0.954452 CCTTTCGTGCTTGAAGGCTT 59.046 50.000 0.00 0.00 0.00 4.35
2068 3387 2.099141 TCTGCGAATCAAAGACAGGG 57.901 50.000 0.00 0.00 0.00 4.45
2202 3573 4.077300 TGTCAGCTATGTTCATCATCCC 57.923 45.455 0.00 0.00 37.91 3.85
2314 3686 7.941795 ATATGTTATACTCCACGCAAAGTAC 57.058 36.000 0.00 0.00 31.15 2.73
2449 3825 4.403113 ACCGTTTATTGTGTGGAACCTTTT 59.597 37.500 0.00 0.00 34.36 2.27
2555 3956 9.717942 AGATGTGAGTTGGAATCTAAATATAGC 57.282 33.333 0.00 0.00 0.00 2.97
2619 4035 2.739885 TCTCTGCAGTTCTCTCTTGC 57.260 50.000 14.67 0.00 0.00 4.01
2691 4227 6.885247 ACTTCAAGTAAAGTTAACTAAGCGC 58.115 36.000 8.92 0.00 36.02 5.92
2699 4235 3.724374 AGTTAACTAAGCGCAGTGTGAA 58.276 40.909 11.47 0.90 0.00 3.18
2703 4239 1.197721 ACTAAGCGCAGTGTGAATTGC 59.802 47.619 11.47 0.00 36.97 3.56
2712 4248 5.097529 CGCAGTGTGAATTGCTCATAATTT 58.902 37.500 0.00 0.00 38.16 1.82
2888 4426 3.403038 AGAACACAATCAGGTTTCGGAG 58.597 45.455 0.00 0.00 0.00 4.63
2918 4457 2.773661 TGGAGAAGCTAGCCATTGATCA 59.226 45.455 12.13 0.00 0.00 2.92
3084 4704 6.594937 CCCATGTTTAGTTGCTTTTATGCATT 59.405 34.615 3.54 0.00 42.96 3.56
3085 4705 7.763528 CCCATGTTTAGTTGCTTTTATGCATTA 59.236 33.333 3.54 0.00 42.96 1.90
3086 4706 9.316730 CCATGTTTAGTTGCTTTTATGCATTAT 57.683 29.630 3.54 0.00 42.96 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 6.711194 ACATGATCTATCTCCATTTGCTTCTG 59.289 38.462 0.00 0.00 0.00 3.02
174 175 2.763292 AGCCTCTGCCGCATCTCT 60.763 61.111 0.00 0.00 38.69 3.10
458 462 4.819630 AGCGTTTTCTGTTCTGTTATTCCA 59.180 37.500 0.00 0.00 0.00 3.53
510 517 5.574970 AGGTTGAGGAAGAAGATGAACTT 57.425 39.130 0.00 0.00 42.03 2.66
528 535 2.090999 GGGAGTCAGAGAGGGATAGGTT 60.091 54.545 0.00 0.00 0.00 3.50
530 539 1.786441 AGGGAGTCAGAGAGGGATAGG 59.214 57.143 0.00 0.00 0.00 2.57
536 545 1.604604 GATCGAGGGAGTCAGAGAGG 58.395 60.000 0.00 0.00 0.00 3.69
548 557 1.970917 GCTGTTGTTGCCGATCGAGG 61.971 60.000 18.66 1.12 0.00 4.63
614 623 1.065701 GAGGCAATCTGCTGAATGCTG 59.934 52.381 26.49 10.87 45.62 4.41
615 624 1.390565 GAGGCAATCTGCTGAATGCT 58.609 50.000 26.49 15.97 45.62 3.79
616 625 0.029035 CGAGGCAATCTGCTGAATGC 59.971 55.000 21.63 21.63 45.61 3.56
617 626 0.029035 GCGAGGCAATCTGCTGAATG 59.971 55.000 4.39 4.39 44.28 2.67
618 627 1.099879 GGCGAGGCAATCTGCTGAAT 61.100 55.000 0.00 0.00 44.28 2.57
619 628 1.746615 GGCGAGGCAATCTGCTGAA 60.747 57.895 0.00 0.00 44.28 3.02
654 663 8.668353 GCACAAATCAAATCATACTGTAGAAGA 58.332 33.333 0.00 0.00 0.00 2.87
655 664 7.912250 GGCACAAATCAAATCATACTGTAGAAG 59.088 37.037 0.00 0.00 0.00 2.85
656 665 7.148086 GGGCACAAATCAAATCATACTGTAGAA 60.148 37.037 0.00 0.00 0.00 2.10
667 1919 1.818674 AGGTCGGGCACAAATCAAATC 59.181 47.619 0.00 0.00 0.00 2.17
678 1930 0.539986 GATTGTAAGGAGGTCGGGCA 59.460 55.000 0.00 0.00 0.00 5.36
690 1952 6.036735 GTGGCTCTTGTATTTAGCGATTGTAA 59.963 38.462 0.00 0.00 37.11 2.41
691 1953 5.522460 GTGGCTCTTGTATTTAGCGATTGTA 59.478 40.000 0.00 0.00 37.11 2.41
694 1956 4.513442 TGTGGCTCTTGTATTTAGCGATT 58.487 39.130 0.00 0.00 37.11 3.34
725 1987 4.845580 CTGTGGCTAGGGCTGCGG 62.846 72.222 0.00 0.00 38.73 5.69
757 2019 3.878519 GTCGAGACGGGAGAGGCG 61.879 72.222 0.00 0.00 0.00 5.52
758 2020 3.519930 GGTCGAGACGGGAGAGGC 61.520 72.222 0.00 0.00 0.00 4.70
759 2021 2.829458 GGGTCGAGACGGGAGAGG 60.829 72.222 0.00 0.00 0.00 3.69
760 2022 3.203412 CGGGTCGAGACGGGAGAG 61.203 72.222 1.00 0.00 0.00 3.20
763 2025 4.100084 TAGCGGGTCGAGACGGGA 62.100 66.667 10.24 0.00 0.00 5.14
764 2026 3.584052 CTAGCGGGTCGAGACGGG 61.584 72.222 10.24 0.00 0.00 5.28
765 2027 2.320339 GAACTAGCGGGTCGAGACGG 62.320 65.000 10.24 1.19 0.00 4.79
766 2028 1.062206 GAACTAGCGGGTCGAGACG 59.938 63.158 4.45 4.45 0.00 4.18
767 2029 1.031029 AGGAACTAGCGGGTCGAGAC 61.031 60.000 0.00 0.00 36.02 3.36
768 2030 0.747283 GAGGAACTAGCGGGTCGAGA 60.747 60.000 0.00 0.00 41.55 4.04
769 2031 1.728672 GAGGAACTAGCGGGTCGAG 59.271 63.158 0.00 0.00 41.55 4.04
770 2032 2.110967 CGAGGAACTAGCGGGTCGA 61.111 63.158 0.00 0.00 41.55 4.20
771 2033 2.408022 CGAGGAACTAGCGGGTCG 59.592 66.667 0.00 0.00 41.55 4.79
778 2040 2.732619 GGTGGGGGCGAGGAACTAG 61.733 68.421 0.00 0.00 41.55 2.57
779 2041 2.686106 GGTGGGGGCGAGGAACTA 60.686 66.667 0.00 0.00 41.55 2.24
794 2056 4.677151 GACCAGAGGGGGTGGGGT 62.677 72.222 0.00 0.00 42.53 4.95
798 2060 2.928396 AACGGACCAGAGGGGGTG 60.928 66.667 0.00 0.00 42.53 4.61
799 2061 2.606826 GAACGGACCAGAGGGGGT 60.607 66.667 0.00 0.00 46.02 4.95
800 2062 2.284699 AGAACGGACCAGAGGGGG 60.285 66.667 0.00 0.00 42.91 5.40
801 2063 2.359967 GGAGAACGGACCAGAGGGG 61.360 68.421 0.00 0.00 44.81 4.79
802 2064 2.711922 CGGAGAACGGACCAGAGGG 61.712 68.421 0.00 0.00 39.42 4.30
803 2065 2.885861 CGGAGAACGGACCAGAGG 59.114 66.667 0.00 0.00 39.42 3.69
804 2066 2.182030 GCGGAGAACGGACCAGAG 59.818 66.667 0.00 0.00 44.51 3.35
805 2067 3.379445 GGCGGAGAACGGACCAGA 61.379 66.667 0.00 0.00 44.51 3.86
806 2068 4.796231 CGGCGGAGAACGGACCAG 62.796 72.222 0.00 0.00 44.51 4.00
821 2083 4.821589 GAAGGAGACAGGCGGCGG 62.822 72.222 9.78 7.74 0.00 6.13
837 2099 1.057851 AGTTGGAGTTGGTTCCGGGA 61.058 55.000 0.00 0.00 40.27 5.14
857 2119 1.269621 ACGAGTCTGTTTCCGAGTTGG 60.270 52.381 0.00 0.00 40.09 3.77
858 2120 1.787155 CACGAGTCTGTTTCCGAGTTG 59.213 52.381 0.00 0.00 0.00 3.16
859 2121 1.868519 GCACGAGTCTGTTTCCGAGTT 60.869 52.381 0.00 0.00 0.00 3.01
864 2126 0.670854 GGGAGCACGAGTCTGTTTCC 60.671 60.000 0.00 0.00 0.00 3.13
892 2154 0.248289 TCGGAATCGGAGTTGGTTCC 59.752 55.000 0.00 0.00 37.38 3.62
893 2155 1.730612 GTTCGGAATCGGAGTTGGTTC 59.269 52.381 0.00 0.00 36.95 3.62
895 2157 0.036671 GGTTCGGAATCGGAGTTGGT 60.037 55.000 0.00 0.00 36.95 3.67
896 2158 0.036765 TGGTTCGGAATCGGAGTTGG 60.037 55.000 0.00 0.00 36.95 3.77
898 2160 1.346722 AGTTGGTTCGGAATCGGAGTT 59.653 47.619 0.00 0.00 36.95 3.01
899 2161 0.974383 AGTTGGTTCGGAATCGGAGT 59.026 50.000 0.00 0.00 36.95 3.85
900 2162 1.641577 GAGTTGGTTCGGAATCGGAG 58.358 55.000 0.00 0.00 36.95 4.63
901 2163 0.248289 GGAGTTGGTTCGGAATCGGA 59.752 55.000 0.00 0.00 36.95 4.55
902 2164 1.082117 CGGAGTTGGTTCGGAATCGG 61.082 60.000 0.00 0.00 36.95 4.18
905 2167 1.376812 GGCGGAGTTGGTTCGGAAT 60.377 57.895 0.00 0.00 0.00 3.01
906 2168 2.031465 GGCGGAGTTGGTTCGGAA 59.969 61.111 0.00 0.00 0.00 4.30
907 2169 4.367023 CGGCGGAGTTGGTTCGGA 62.367 66.667 0.00 0.00 0.00 4.55
910 2172 4.699522 AGGCGGCGGAGTTGGTTC 62.700 66.667 9.78 0.00 0.00 3.62
915 2177 4.070552 GAGACAGGCGGCGGAGTT 62.071 66.667 17.37 0.08 0.00 3.01
919 2181 4.821589 GAAGGAGACAGGCGGCGG 62.822 72.222 9.78 7.74 0.00 6.13
920 2182 4.821589 GGAAGGAGACAGGCGGCG 62.822 72.222 0.51 0.51 0.00 6.46
921 2183 4.475135 GGGAAGGAGACAGGCGGC 62.475 72.222 0.00 0.00 0.00 6.53
947 2209 3.118956 AGAGCTCATACCTCGAAACCAAG 60.119 47.826 17.77 0.00 34.56 3.61
966 2228 6.764085 CGGGGCGGATCTAGATATATATAGAG 59.236 46.154 19.10 9.49 34.48 2.43
967 2229 6.442885 TCGGGGCGGATCTAGATATATATAGA 59.557 42.308 17.21 17.21 35.36 1.98
970 2232 5.254901 GTCGGGGCGGATCTAGATATATAT 58.745 45.833 4.89 0.00 0.00 0.86
988 2250 0.880278 CTGATATTGTGGGCGTCGGG 60.880 60.000 0.00 0.00 0.00 5.14
992 2254 1.686587 TCGATCTGATATTGTGGGCGT 59.313 47.619 0.00 0.00 0.00 5.68
994 2256 2.926200 CGATCGATCTGATATTGTGGGC 59.074 50.000 22.43 0.00 37.47 5.36
1002 2264 2.162408 AGCGCAATCGATCGATCTGATA 59.838 45.455 29.48 1.51 37.47 2.15
1004 2266 0.312102 AGCGCAATCGATCGATCTGA 59.688 50.000 29.48 19.85 38.10 3.27
1007 2269 1.344458 ATCAGCGCAATCGATCGATC 58.656 50.000 29.48 17.46 38.10 3.69
1008 2270 1.788258 AATCAGCGCAATCGATCGAT 58.212 45.000 24.60 24.60 38.10 3.59
1009 2271 2.415697 TAATCAGCGCAATCGATCGA 57.584 45.000 21.86 21.86 38.10 3.59
1010 2272 3.712162 AATAATCAGCGCAATCGATCG 57.288 42.857 11.47 9.36 38.10 3.69
1043 2305 5.366477 ACTGGACACAAAAGATGGGATTTTT 59.634 36.000 0.00 0.00 35.35 1.94
1051 2313 5.530915 TCCTACAAACTGGACACAAAAGATG 59.469 40.000 0.00 0.00 0.00 2.90
1061 2323 4.870991 GCTTAGACATCCTACAAACTGGAC 59.129 45.833 0.00 0.00 34.90 4.02
1144 2415 4.215109 AGAACCAGATAGAGGCTCTTCTC 58.785 47.826 24.13 18.79 27.26 2.87
1145 2416 4.264373 AGAACCAGATAGAGGCTCTTCT 57.736 45.455 24.13 20.19 27.26 2.85
1146 2417 5.381757 TCTAGAACCAGATAGAGGCTCTTC 58.618 45.833 24.13 18.38 33.78 2.87
1308 2579 6.053005 GGTTGCAGTATATTGGTTGCTAGTA 58.947 40.000 0.00 0.00 37.45 1.82
1311 2582 3.874543 CGGTTGCAGTATATTGGTTGCTA 59.125 43.478 0.00 0.00 37.45 3.49
1614 2903 4.207635 TCGTTGATGTACGAAGACACAAAC 59.792 41.667 0.00 0.00 46.50 2.93
1638 2927 0.110486 AGAAGGTGCCACGGTTGATT 59.890 50.000 0.00 0.00 0.00 2.57
2202 3573 8.525290 AAAATGGAGGGAGTAATTTACAGATG 57.475 34.615 9.15 0.00 0.00 2.90
2289 3660 7.804600 CGTACTTTGCGTGGAGTATAACATATA 59.195 37.037 0.00 0.00 31.62 0.86
2290 3661 6.639686 CGTACTTTGCGTGGAGTATAACATAT 59.360 38.462 0.00 0.00 31.62 1.78
2291 3662 5.972973 CGTACTTTGCGTGGAGTATAACATA 59.027 40.000 0.00 0.00 31.62 2.29
2292 3663 4.802039 CGTACTTTGCGTGGAGTATAACAT 59.198 41.667 0.00 0.00 31.62 2.71
2293 3664 4.168014 CGTACTTTGCGTGGAGTATAACA 58.832 43.478 0.00 0.00 31.62 2.41
2294 3665 3.549070 CCGTACTTTGCGTGGAGTATAAC 59.451 47.826 0.00 0.00 31.62 1.89
2295 3666 3.429272 CCCGTACTTTGCGTGGAGTATAA 60.429 47.826 0.00 0.00 31.62 0.98
2314 3686 8.859156 GCAACAAAATTATATGTTATATGCCCG 58.141 33.333 4.47 0.00 37.66 6.13
2449 3825 6.658816 TGCAGAATTAACAATTAAGAGCTCCA 59.341 34.615 10.93 0.00 0.00 3.86
2552 3953 9.306777 ACAGATAAGATGAGAATATGTCAGCTA 57.693 33.333 6.55 0.00 39.74 3.32
2553 3954 8.192743 ACAGATAAGATGAGAATATGTCAGCT 57.807 34.615 1.19 1.19 42.42 4.24
2554 3955 8.087136 TGACAGATAAGATGAGAATATGTCAGC 58.913 37.037 7.66 0.00 43.26 4.26
2555 3956 9.409312 GTGACAGATAAGATGAGAATATGTCAG 57.591 37.037 11.10 0.00 46.56 3.51
2629 4045 1.305297 CCTGAGGGGGCTTTTTCCC 60.305 63.158 0.00 0.00 45.80 3.97
2685 4221 1.464608 GAGCAATTCACACTGCGCTTA 59.535 47.619 9.73 0.00 43.51 3.09
2691 4227 5.865013 TGCAAATTATGAGCAATTCACACTG 59.135 36.000 0.00 0.00 38.99 3.66
2888 4426 4.123506 GGCTAGCTTCTCCATAAAGTGAC 58.876 47.826 15.72 0.00 0.00 3.67
2918 4457 9.632638 ACAAGCATCCTAATGAGTTTACATATT 57.367 29.630 0.00 0.00 34.61 1.28


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

AutoCloner maintained by Alex Coulton.