Multiple sequence alignment - TraesCS3B01G042200

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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 TraesCS3B01G042200 chr3B 100.000 3939 0 0 1 3939 21388054 21384116 0.000000e+00 7275.0
1 TraesCS3B01G042200 chr3B 88.073 1048 101 12 673 1709 21346698 21345664 0.000000e+00 1221.0
2 TraesCS3B01G042200 chr3B 77.759 1214 221 26 744 1938 11187219 11186036 0.000000e+00 701.0
3 TraesCS3B01G042200 chr3B 81.203 798 100 27 2023 2779 21334666 21333878 7.290000e-167 597.0
4 TraesCS3B01G042200 chr3B 85.918 561 49 12 54 595 21347228 21346679 4.420000e-159 571.0
5 TraesCS3B01G042200 chr3B 88.393 336 35 3 1695 2026 21337085 21336750 6.130000e-108 401.0
6 TraesCS3B01G042200 chr3B 81.768 362 53 6 221 572 11231516 11231874 1.380000e-74 291.0
7 TraesCS3B01G042200 chr3B 85.185 243 31 4 2450 2690 11182387 11182148 1.090000e-60 244.0
8 TraesCS3B01G042200 chr3B 95.000 40 2 0 1906 1945 11233169 11233208 3.290000e-06 63.9
9 TraesCS3B01G042200 chr3D 91.267 3332 222 34 632 3920 14416156 14412851 0.000000e+00 4477.0
10 TraesCS3B01G042200 chr3D 86.891 1602 135 31 146 1709 14407225 14405661 0.000000e+00 1725.0
11 TraesCS3B01G042200 chr3D 79.640 1277 199 34 704 1946 9105585 9106834 0.000000e+00 861.0
12 TraesCS3B01G042200 chr3D 89.875 642 48 5 43 669 14416710 14416071 0.000000e+00 809.0
13 TraesCS3B01G042200 chr3D 79.000 600 77 26 2825 3414 14391105 14390545 8.040000e-97 364.0
14 TraesCS3B01G042200 chr3D 83.792 327 39 7 1711 2026 14396463 14396140 8.270000e-77 298.0
15 TraesCS3B01G042200 chr3D 82.581 155 21 1 2631 2779 14393693 14393539 8.880000e-27 132.0
16 TraesCS3B01G042200 chr3A 94.934 1599 55 12 571 2153 22247956 22249544 0.000000e+00 2481.0
17 TraesCS3B01G042200 chr3A 84.397 1410 154 41 2156 3531 22249609 22250986 0.000000e+00 1325.0
18 TraesCS3B01G042200 chr3A 87.994 683 53 12 24 680 22247431 22248110 0.000000e+00 780.0
19 TraesCS3B01G042200 chr3A 77.439 492 78 21 221 692 11882914 11882436 3.020000e-66 263.0
20 TraesCS3B01G042200 chr7A 77.982 1635 263 56 279 1875 635552574 635554149 0.000000e+00 935.0
21 TraesCS3B01G042200 chr7A 75.000 312 44 27 1954 2232 635554850 635555160 3.220000e-21 113.0
22 TraesCS3B01G042200 chr7B 76.276 1724 255 85 193 1875 594763553 594765163 0.000000e+00 776.0
23 TraesCS3B01G042200 chr6A 78.272 382 59 20 199 558 106986286 106985907 1.420000e-54 224.0
24 TraesCS3B01G042200 chr5B 76.724 348 56 19 224 552 525447611 525447952 1.880000e-38 171.0
25 TraesCS3B01G042200 chr5D 76.504 349 55 23 224 552 432781794 432782135 8.760000e-37 165.0


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 TraesCS3B01G042200 chr3B 21384116 21388054 3938 True 7275.000000 7275 100.000000 1 3939 1 chr3B.!!$R1 3938
1 TraesCS3B01G042200 chr3B 21345664 21347228 1564 True 896.000000 1221 86.995500 54 1709 2 chr3B.!!$R4 1655
2 TraesCS3B01G042200 chr3B 21333878 21337085 3207 True 499.000000 597 84.798000 1695 2779 2 chr3B.!!$R3 1084
3 TraesCS3B01G042200 chr3B 11182148 11187219 5071 True 472.500000 701 81.472000 744 2690 2 chr3B.!!$R2 1946
4 TraesCS3B01G042200 chr3D 14412851 14416710 3859 True 2643.000000 4477 90.571000 43 3920 2 chr3D.!!$R3 3877
5 TraesCS3B01G042200 chr3D 14405661 14407225 1564 True 1725.000000 1725 86.891000 146 1709 1 chr3D.!!$R1 1563
6 TraesCS3B01G042200 chr3D 9105585 9106834 1249 False 861.000000 861 79.640000 704 1946 1 chr3D.!!$F1 1242
7 TraesCS3B01G042200 chr3D 14390545 14396463 5918 True 264.666667 364 81.791000 1711 3414 3 chr3D.!!$R2 1703
8 TraesCS3B01G042200 chr3A 22247431 22250986 3555 False 1528.666667 2481 89.108333 24 3531 3 chr3A.!!$F1 3507
9 TraesCS3B01G042200 chr7A 635552574 635555160 2586 False 524.000000 935 76.491000 279 2232 2 chr7A.!!$F1 1953
10 TraesCS3B01G042200 chr7B 594763553 594765163 1610 False 776.000000 776 76.276000 193 1875 1 chr7B.!!$F1 1682

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
722 787 0.041135 GAAGACGACGGCGAGGATAG 60.041 60.0 22.49 0.0 41.64 2.08 F
1374 1535 0.459585 TAGCTGGAATCGTTCGGTGC 60.460 55.0 0.00 0.0 0.00 5.01 F
2381 4812 0.105964 TGTCACAAACAGACCCGGAG 59.894 55.0 0.73 0.0 35.15 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1740 2.685897 GCTGTGTACCAACCAAAGAACA 59.314 45.455 0.00 0.00 0.00 3.18 R
2749 8574 1.133976 CCCTGCCTGATAAACCTGGAG 60.134 57.143 0.00 0.00 0.00 3.86 R
3582 11815 0.455410 TTCACCTTGTTGTGCAGCAC 59.545 50.000 19.37 19.37 36.17 4.40 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
124 131 4.720902 TGCATGTCGGCCTGGTGG 62.721 66.667 0.00 0.00 0.00 4.61
179 189 1.003580 CCCACACAATAGTCACTGCCT 59.996 52.381 0.00 0.00 0.00 4.75
185 197 4.286032 ACACAATAGTCACTGCCTCCTTTA 59.714 41.667 0.00 0.00 0.00 1.85
275 288 0.771755 GAAGAAACCCCCACCACTCT 59.228 55.000 0.00 0.00 0.00 3.24
277 290 1.003718 GAAACCCCCACCACTCTCG 60.004 63.158 0.00 0.00 0.00 4.04
283 296 3.680786 CCACCACTCTCGCCGACA 61.681 66.667 0.00 0.00 0.00 4.35
313 326 0.752376 CCCTCGACCTAGACACCCTC 60.752 65.000 0.00 0.00 0.00 4.30
319 332 2.050350 CCTAGACACCCTCCGCGAA 61.050 63.158 8.23 0.00 0.00 4.70
435 461 4.181010 CTCCATCCACCCCCGCTG 62.181 72.222 0.00 0.00 0.00 5.18
444 470 3.164269 CCCCCGCTGCTAGGTCAT 61.164 66.667 0.00 0.00 0.00 3.06
596 631 4.754667 GTCCGTTCCTGTCCCCGC 62.755 72.222 0.00 0.00 0.00 6.13
614 649 3.702048 CCCCGCCCTCGAAGACAA 61.702 66.667 0.00 0.00 38.10 3.18
615 650 2.434359 CCCGCCCTCGAAGACAAC 60.434 66.667 0.00 0.00 38.10 3.32
616 651 2.809601 CCGCCCTCGAAGACAACG 60.810 66.667 0.00 0.00 38.10 4.10
617 652 2.809601 CGCCCTCGAAGACAACGG 60.810 66.667 0.00 0.00 38.10 4.44
618 653 3.119096 GCCCTCGAAGACAACGGC 61.119 66.667 0.00 0.00 0.00 5.68
619 654 2.809601 CCCTCGAAGACAACGGCG 60.810 66.667 4.80 4.80 0.00 6.46
620 655 2.257371 CCTCGAAGACAACGGCGA 59.743 61.111 16.62 0.00 0.00 5.54
621 656 1.153823 CCTCGAAGACAACGGCGAT 60.154 57.895 16.62 0.00 31.87 4.58
622 657 1.413767 CCTCGAAGACAACGGCGATG 61.414 60.000 16.62 16.22 31.87 3.84
623 658 1.413767 CTCGAAGACAACGGCGATGG 61.414 60.000 21.20 8.72 31.87 3.51
624 659 2.785258 GAAGACAACGGCGATGGC 59.215 61.111 21.20 18.77 38.90 4.40
633 668 2.742372 GGCGATGGCGTGTCTGTT 60.742 61.111 0.00 0.00 41.24 3.16
634 669 2.740714 GGCGATGGCGTGTCTGTTC 61.741 63.158 0.00 0.00 41.24 3.18
635 670 2.740714 GCGATGGCGTGTCTGTTCC 61.741 63.158 0.00 0.00 40.36 3.62
636 671 1.079819 CGATGGCGTGTCTGTTCCT 60.080 57.895 0.00 0.00 0.00 3.36
637 672 1.354337 CGATGGCGTGTCTGTTCCTG 61.354 60.000 0.00 0.00 0.00 3.86
638 673 0.320771 GATGGCGTGTCTGTTCCTGT 60.321 55.000 0.00 0.00 0.00 4.00
639 674 0.320771 ATGGCGTGTCTGTTCCTGTC 60.321 55.000 0.00 0.00 0.00 3.51
640 675 1.668151 GGCGTGTCTGTTCCTGTCC 60.668 63.158 0.00 0.00 0.00 4.02
641 676 1.668151 GCGTGTCTGTTCCTGTCCC 60.668 63.158 0.00 0.00 0.00 4.46
642 677 1.004918 CGTGTCTGTTCCTGTCCCC 60.005 63.158 0.00 0.00 0.00 4.81
643 678 1.004918 GTGTCTGTTCCTGTCCCCG 60.005 63.158 0.00 0.00 0.00 5.73
644 679 2.047179 GTCTGTTCCTGTCCCCGC 60.047 66.667 0.00 0.00 0.00 6.13
721 786 1.769098 CGAAGACGACGGCGAGGATA 61.769 60.000 22.49 0.00 42.66 2.59
722 787 0.041135 GAAGACGACGGCGAGGATAG 60.041 60.000 22.49 0.00 41.64 2.08
742 857 1.587043 CGTCTCTGGCTCCGAAGACA 61.587 60.000 15.97 0.00 38.59 3.41
1076 1224 3.272031 GCTCTGGCCTCAAACTGC 58.728 61.111 3.32 0.00 0.00 4.40
1374 1535 0.459585 TAGCTGGAATCGTTCGGTGC 60.460 55.000 0.00 0.00 0.00 5.01
1579 1740 0.464373 CTACATCATGCCGTGGCCTT 60.464 55.000 8.69 0.00 41.09 4.35
1702 1878 2.929641 TGAACTGTTGTCTTGCCATGA 58.070 42.857 0.00 0.00 0.00 3.07
1829 2021 6.554982 TCCTACTCTATGCATACTGGAAATGT 59.445 38.462 1.16 0.00 0.00 2.71
2034 4383 9.515226 TCATTTTACTTCTGTTAGCAAGGTTAT 57.485 29.630 0.00 0.00 0.00 1.89
2106 4460 2.437281 AGCTGGCTGTGCTATGTAGAAT 59.563 45.455 0.00 0.00 39.21 2.40
2139 4494 4.342092 AGTGTAATTCTTTTTGCAGGTGCT 59.658 37.500 3.18 0.00 42.66 4.40
2153 4508 3.676646 GCAGGTGCTCATCATTTGTTTTC 59.323 43.478 0.00 0.00 38.21 2.29
2157 4574 7.262772 CAGGTGCTCATCATTTGTTTTCATAT 58.737 34.615 0.00 0.00 0.00 1.78
2217 4636 6.807230 GGTCCTAGCAATATATCACTAACACG 59.193 42.308 0.00 0.00 0.00 4.49
2381 4812 0.105964 TGTCACAAACAGACCCGGAG 59.894 55.000 0.73 0.00 35.15 4.63
2408 4839 5.296283 CAGGAAAGATGGTCAGCTATTTCTG 59.704 44.000 0.00 0.00 35.46 3.02
2442 8239 6.957631 ACAAGTTATACAATGTCATCTCCCA 58.042 36.000 0.00 0.00 0.00 4.37
2749 8574 5.586243 TGAAATGATAGCAACCTAGAGCAAC 59.414 40.000 0.00 0.00 0.00 4.17
2755 8580 1.677217 GCAACCTAGAGCAACTCCAGG 60.677 57.143 7.43 7.43 43.34 4.45
2808 11016 3.988976 TTCTCTGATTTAGCAGCCAGT 57.011 42.857 0.00 0.00 35.86 4.00
2886 11110 4.869297 GGGCTGATCGAATTGATATCTCTG 59.131 45.833 3.98 0.00 37.47 3.35
2938 11162 5.282055 AGACACACAATTCTCTTCTGTGA 57.718 39.130 8.32 0.00 42.48 3.58
2951 11175 7.664082 TCTCTTCTGTGATCTTGAATTGAAC 57.336 36.000 0.00 0.00 0.00 3.18
3015 11240 4.843220 AAGGTGCAGAAGAAGAAACATG 57.157 40.909 0.00 0.00 0.00 3.21
3115 11343 1.470979 GCAAGCAGGGCTTCATCAATG 60.471 52.381 0.00 0.00 46.77 2.82
3121 11349 1.005097 AGGGCTTCATCAATGTGCTGA 59.995 47.619 9.30 0.00 0.00 4.26
3148 11376 5.255687 TGTTGGTTCACATGCAGAATCTAT 58.744 37.500 11.62 0.00 0.00 1.98
3208 11436 1.178276 CCGTAGAGCTCTCAAGGTGT 58.822 55.000 22.17 0.00 32.07 4.16
3285 11514 6.533819 TGTATTGAAACAGTTTCGGTACAG 57.466 37.500 25.00 0.00 42.55 2.74
3302 11531 5.637810 CGGTACAGCAATTAGAGAAGAAACA 59.362 40.000 0.00 0.00 0.00 2.83
3306 11535 7.750229 ACAGCAATTAGAGAAGAAACAATCA 57.250 32.000 0.00 0.00 0.00 2.57
3326 11555 3.758023 TCAGAATTTGCCATTGTCGTCAT 59.242 39.130 0.00 0.00 0.00 3.06
3409 11639 6.741992 AACAGAGCGAATGTGAATTTGATA 57.258 33.333 0.00 0.00 0.00 2.15
3420 11650 6.415798 TGTGAATTTGATATACACACACCG 57.584 37.500 0.00 0.00 36.72 4.94
3444 11674 6.128902 CGGAAGACAAATACGTAGCAATATCC 60.129 42.308 0.08 3.05 0.00 2.59
3482 11713 7.062956 GCAAACAAAAATAACCTATAGTGGTGC 59.937 37.037 0.00 0.00 40.73 5.01
3483 11714 6.769134 ACAAAAATAACCTATAGTGGTGCC 57.231 37.500 0.00 0.00 40.73 5.01
3485 11716 5.362105 AAAATAACCTATAGTGGTGCCGA 57.638 39.130 0.00 0.00 40.73 5.54
3490 11721 2.158445 ACCTATAGTGGTGCCGAGAGAT 60.158 50.000 0.00 0.00 39.17 2.75
3491 11722 2.894126 CCTATAGTGGTGCCGAGAGATT 59.106 50.000 0.00 0.00 0.00 2.40
3492 11723 3.057174 CCTATAGTGGTGCCGAGAGATTC 60.057 52.174 0.00 0.00 0.00 2.52
3493 11724 1.112113 TAGTGGTGCCGAGAGATTCC 58.888 55.000 0.00 0.00 0.00 3.01
3494 11725 0.904865 AGTGGTGCCGAGAGATTCCA 60.905 55.000 0.00 0.00 0.00 3.53
3495 11726 0.179000 GTGGTGCCGAGAGATTCCAT 59.821 55.000 0.00 0.00 0.00 3.41
3540 11772 1.001641 AGATTGCTGGTGTGGCCTC 60.002 57.895 3.32 0.00 38.35 4.70
3541 11773 2.360350 ATTGCTGGTGTGGCCTCG 60.360 61.111 3.32 0.00 38.35 4.63
3582 11815 0.549950 AGATGGGTGGCCTCATTCTG 59.450 55.000 3.32 0.00 0.00 3.02
3614 11847 2.127651 AGGTGAACCCTTGTCCCTAA 57.872 50.000 0.00 0.00 42.73 2.69
3616 11849 2.375509 AGGTGAACCCTTGTCCCTAAAG 59.624 50.000 0.00 0.00 42.73 1.85
3621 11854 5.361571 GTGAACCCTTGTCCCTAAAGAAAAA 59.638 40.000 0.00 0.00 0.00 1.94
3682 11915 7.363431 GGGCTATGTAAATAACTTCTCATTGC 58.637 38.462 0.00 0.00 33.76 3.56
3720 11953 5.898061 GCTTTTGCATTTTCTCGAAAAACAG 59.102 36.000 8.69 4.27 46.58 3.16
3727 11960 7.012515 TGCATTTTCTCGAAAAACAGTAAGGTA 59.987 33.333 8.69 0.00 42.71 3.08
3758 11991 9.817809 GAAAACTAGAACTGGGAATTTCTTTTT 57.182 29.630 0.00 0.00 33.96 1.94
3759 11992 9.599866 AAAACTAGAACTGGGAATTTCTTTTTG 57.400 29.630 0.00 0.00 33.96 2.44
3891 12124 6.638096 TCAAGATGTTGATGTGTTGTTGAT 57.362 33.333 0.23 0.00 37.79 2.57
3907 12140 3.216800 GTTGATGATTGCTGGCCATCTA 58.783 45.455 5.51 0.00 37.97 1.98
3920 12153 3.130869 TGGCCATCTATGCACATTTGAAC 59.869 43.478 0.00 0.00 0.00 3.18
3921 12154 3.130869 GGCCATCTATGCACATTTGAACA 59.869 43.478 0.00 0.00 0.00 3.18
3924 12157 5.916883 GCCATCTATGCACATTTGAACATAC 59.083 40.000 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.185680 GGGTAGACTGAAACCAATGTTTATTAT 57.814 33.333 0.00 0.00 44.57 1.28
11 12 7.334921 CGGGTAGACTGAAACCAATGTTTATTA 59.665 37.037 0.00 0.00 44.57 0.98
12 13 6.150474 CGGGTAGACTGAAACCAATGTTTATT 59.850 38.462 0.00 0.00 44.57 1.40
13 14 5.646360 CGGGTAGACTGAAACCAATGTTTAT 59.354 40.000 0.00 0.00 44.57 1.40
14 15 4.998672 CGGGTAGACTGAAACCAATGTTTA 59.001 41.667 0.00 0.00 44.57 2.01
16 17 3.408634 CGGGTAGACTGAAACCAATGTT 58.591 45.455 0.00 0.00 37.51 2.71
17 18 2.874457 GCGGGTAGACTGAAACCAATGT 60.874 50.000 0.00 0.00 37.51 2.71
18 19 1.737793 GCGGGTAGACTGAAACCAATG 59.262 52.381 0.00 0.00 37.51 2.82
19 20 1.349688 TGCGGGTAGACTGAAACCAAT 59.650 47.619 0.00 0.00 37.51 3.16
20 21 0.759959 TGCGGGTAGACTGAAACCAA 59.240 50.000 0.00 0.00 37.51 3.67
21 22 0.759959 TTGCGGGTAGACTGAAACCA 59.240 50.000 0.00 0.00 37.51 3.67
22 23 1.886886 TTTGCGGGTAGACTGAAACC 58.113 50.000 0.00 0.00 34.85 3.27
89 95 2.267426 GCAAGAAAACGTGCCACTTTT 58.733 42.857 0.00 0.00 34.58 2.27
90 96 1.203523 TGCAAGAAAACGTGCCACTTT 59.796 42.857 0.00 0.00 40.14 2.66
91 97 0.814457 TGCAAGAAAACGTGCCACTT 59.186 45.000 0.00 0.00 40.14 3.16
179 189 3.143728 GGGTTTCGTTTCAGCTAAAGGA 58.856 45.455 0.00 0.00 39.54 3.36
185 197 2.568623 ATGAGGGTTTCGTTTCAGCT 57.431 45.000 0.00 0.00 0.00 4.24
275 288 1.807981 CGCTTATGGTTGTCGGCGA 60.808 57.895 4.99 4.99 44.36 5.54
277 290 2.403586 GCGCTTATGGTTGTCGGC 59.596 61.111 0.00 0.00 0.00 5.54
283 296 1.153429 GTCGAGGGCGCTTATGGTT 60.153 57.895 7.64 0.00 37.46 3.67
313 326 1.432270 GGCAGAGGAAGATTTCGCGG 61.432 60.000 6.13 0.00 0.00 6.46
319 332 0.045469 AGGGGAGGCAGAGGAAGATT 59.955 55.000 0.00 0.00 0.00 2.40
435 461 2.633488 GTGGTGAGGAAATGACCTAGC 58.367 52.381 0.00 0.00 40.73 3.42
444 470 1.133915 GTGTCTTGGGTGGTGAGGAAA 60.134 52.381 0.00 0.00 0.00 3.13
597 632 3.702048 TTGTCTTCGAGGGCGGGG 61.702 66.667 0.00 0.00 38.28 5.73
598 633 2.434359 GTTGTCTTCGAGGGCGGG 60.434 66.667 0.00 0.00 38.28 6.13
599 634 2.809601 CGTTGTCTTCGAGGGCGG 60.810 66.667 0.00 0.00 38.28 6.13
600 635 2.809601 CCGTTGTCTTCGAGGGCG 60.810 66.667 0.00 0.00 39.35 6.13
601 636 3.119096 GCCGTTGTCTTCGAGGGC 61.119 66.667 0.00 0.00 46.98 5.19
602 637 2.558554 ATCGCCGTTGTCTTCGAGGG 62.559 60.000 0.00 0.00 36.41 4.30
603 638 1.153823 ATCGCCGTTGTCTTCGAGG 60.154 57.895 0.00 0.00 34.30 4.63
604 639 1.413767 CCATCGCCGTTGTCTTCGAG 61.414 60.000 0.00 0.00 34.30 4.04
605 640 1.445410 CCATCGCCGTTGTCTTCGA 60.445 57.895 0.00 0.00 35.34 3.71
606 641 3.081133 CCATCGCCGTTGTCTTCG 58.919 61.111 0.00 0.00 0.00 3.79
607 642 2.785258 GCCATCGCCGTTGTCTTC 59.215 61.111 0.00 0.00 0.00 2.87
608 643 3.118454 CGCCATCGCCGTTGTCTT 61.118 61.111 0.00 0.00 0.00 3.01
609 644 4.373116 ACGCCATCGCCGTTGTCT 62.373 61.111 0.00 0.00 39.84 3.41
610 645 4.147322 CACGCCATCGCCGTTGTC 62.147 66.667 0.00 0.00 39.84 3.18
611 646 4.980805 ACACGCCATCGCCGTTGT 62.981 61.111 0.00 0.00 39.84 3.32
612 647 4.147322 GACACGCCATCGCCGTTG 62.147 66.667 0.00 0.00 39.84 4.10
613 648 4.373116 AGACACGCCATCGCCGTT 62.373 61.111 0.00 0.00 39.84 4.44
616 651 2.740714 GAACAGACACGCCATCGCC 61.741 63.158 0.00 0.00 39.84 5.54
617 652 2.740714 GGAACAGACACGCCATCGC 61.741 63.158 0.00 0.00 39.84 4.58
618 653 1.079819 AGGAACAGACACGCCATCG 60.080 57.895 0.00 0.00 42.43 3.84
619 654 0.320771 ACAGGAACAGACACGCCATC 60.321 55.000 0.00 0.00 0.00 3.51
620 655 0.320771 GACAGGAACAGACACGCCAT 60.321 55.000 0.00 0.00 0.00 4.40
621 656 1.069090 GACAGGAACAGACACGCCA 59.931 57.895 0.00 0.00 0.00 5.69
622 657 1.668151 GGACAGGAACAGACACGCC 60.668 63.158 0.00 0.00 0.00 5.68
623 658 1.668151 GGGACAGGAACAGACACGC 60.668 63.158 0.00 0.00 0.00 5.34
624 659 1.004918 GGGGACAGGAACAGACACG 60.005 63.158 0.00 0.00 0.00 4.49
625 660 1.004918 CGGGGACAGGAACAGACAC 60.005 63.158 0.00 0.00 0.00 3.67
626 661 2.879233 GCGGGGACAGGAACAGACA 61.879 63.158 0.00 0.00 0.00 3.41
627 662 2.047179 GCGGGGACAGGAACAGAC 60.047 66.667 0.00 0.00 0.00 3.51
628 663 3.319198 GGCGGGGACAGGAACAGA 61.319 66.667 0.00 0.00 0.00 3.41
629 664 4.410400 GGGCGGGGACAGGAACAG 62.410 72.222 0.00 0.00 0.00 3.16
666 701 2.264794 GGAACGGACACGCCATCT 59.735 61.111 0.00 0.00 46.04 2.90
721 786 2.676822 TTCGGAGCCAGAGACGCT 60.677 61.111 0.00 0.00 39.95 5.07
722 787 2.202676 CTTCGGAGCCAGAGACGC 60.203 66.667 0.00 0.00 0.00 5.19
742 857 3.194719 GACGGGATCCTCGTCGTT 58.805 61.111 28.25 10.32 45.53 3.85
1076 1224 0.737219 GCAGCCATTCACCAGCTTAG 59.263 55.000 0.00 0.00 33.70 2.18
1374 1535 8.970691 ATTTAACATTGTCTTCCTTGAATTCG 57.029 30.769 0.04 0.00 0.00 3.34
1579 1740 2.685897 GCTGTGTACCAACCAAAGAACA 59.314 45.455 0.00 0.00 0.00 3.18
1862 2054 9.614792 GGAATCTCTAGCAAATTACTCCTTTTA 57.385 33.333 0.00 0.00 0.00 1.52
2034 4383 9.665719 TGTGCATGATAAACAAGAGAACTTATA 57.334 29.630 0.00 0.00 34.70 0.98
2071 4423 3.560481 CAGCCAGCTATTTGATGTCTCTG 59.440 47.826 0.00 0.00 0.00 3.35
2106 4460 7.489757 GCAAAAAGAATTACACTACAAACCACA 59.510 33.333 0.00 0.00 0.00 4.17
2171 4588 7.564660 AGGACCAATATGCCTCATAAAAATCAA 59.435 33.333 0.00 0.00 29.74 2.57
2252 4682 7.335422 ACAAACTTGAGATAGTAATGCCAAGAG 59.665 37.037 0.00 0.00 36.03 2.85
2350 4781 3.252944 TGTTTGTGACACGATGCAATCAT 59.747 39.130 0.22 0.00 36.82 2.45
2381 4812 3.557228 AGCTGACCATCTTTCCTGATC 57.443 47.619 0.00 0.00 0.00 2.92
2749 8574 1.133976 CCCTGCCTGATAAACCTGGAG 60.134 57.143 0.00 0.00 0.00 3.86
2755 8580 1.559682 TCCTCACCCTGCCTGATAAAC 59.440 52.381 0.00 0.00 0.00 2.01
2886 11110 5.161358 GGATAAGCTGGTTTGCTGTAAAAC 58.839 41.667 0.00 0.00 43.24 2.43
2938 11162 5.944599 AGCAGACATCAGTTCAATTCAAGAT 59.055 36.000 0.00 0.00 0.00 2.40
3015 11240 3.101019 GCCATTACAAACGGCACAC 57.899 52.632 0.00 0.00 45.52 3.82
3115 11343 3.779759 TGTGAACCAACAATTTCAGCAC 58.220 40.909 0.00 0.00 32.40 4.40
3121 11349 4.669206 TCTGCATGTGAACCAACAATTT 57.331 36.364 0.00 0.00 32.81 1.82
3148 11376 6.280855 TGCAAGTTCTAACTGCAGATAGTA 57.719 37.500 25.12 16.36 39.66 1.82
3208 11436 3.435275 AGACTGACAGACATTAGCTCCA 58.565 45.455 10.08 0.00 0.00 3.86
3285 11514 9.852091 AATTCTGATTGTTTCTTCTCTAATTGC 57.148 29.630 0.00 0.00 0.00 3.56
3302 11531 4.218200 TGACGACAATGGCAAATTCTGATT 59.782 37.500 0.00 0.00 0.00 2.57
3306 11535 4.460382 AGAATGACGACAATGGCAAATTCT 59.540 37.500 0.00 3.02 0.00 2.40
3326 11555 4.473643 CCGTGTGGCAGGAAAGAA 57.526 55.556 0.00 0.00 0.00 2.52
3390 11620 7.584123 GTGTGTATATCAAATTCACATTCGCTC 59.416 37.037 0.00 0.00 40.31 5.03
3400 11630 6.537301 TCTTCCGGTGTGTGTATATCAAATTC 59.463 38.462 0.00 0.00 0.00 2.17
3409 11639 3.478857 TTTGTCTTCCGGTGTGTGTAT 57.521 42.857 0.00 0.00 0.00 2.29
3420 11650 6.929606 AGGATATTGCTACGTATTTGTCTTCC 59.070 38.462 0.00 0.00 0.00 3.46
3444 11674 9.801714 GTTATTTTTGTTTGCATCAATCTGAAG 57.198 29.630 5.83 0.00 0.00 3.02
3482 11713 1.139654 TCCAGCAATGGAATCTCTCGG 59.860 52.381 0.00 0.00 34.56 4.63
3483 11714 2.208431 GTCCAGCAATGGAATCTCTCG 58.792 52.381 0.00 0.00 40.06 4.04
3485 11716 3.265221 TCTTGTCCAGCAATGGAATCTCT 59.735 43.478 0.00 0.00 40.06 3.10
3490 11721 2.655090 TGTCTTGTCCAGCAATGGAA 57.345 45.000 0.00 0.00 40.06 3.53
3491 11722 2.885135 ATGTCTTGTCCAGCAATGGA 57.115 45.000 0.00 0.00 36.36 3.41
3492 11723 2.165030 GGAATGTCTTGTCCAGCAATGG 59.835 50.000 0.00 0.00 36.36 3.16
3493 11724 2.821378 TGGAATGTCTTGTCCAGCAATG 59.179 45.455 0.00 0.00 39.04 2.82
3494 11725 3.159213 TGGAATGTCTTGTCCAGCAAT 57.841 42.857 0.00 0.00 39.04 3.56
3495 11726 2.655090 TGGAATGTCTTGTCCAGCAA 57.345 45.000 0.00 0.00 39.04 3.91
3582 11815 0.455410 TTCACCTTGTTGTGCAGCAC 59.545 50.000 19.37 19.37 36.17 4.40
3621 11854 6.098266 AGCAAAGAAGTTATTCACCTTGGTTT 59.902 34.615 0.00 0.00 37.94 3.27
3622 11855 5.598417 AGCAAAGAAGTTATTCACCTTGGTT 59.402 36.000 0.00 0.00 37.94 3.67
3623 11856 5.140454 AGCAAAGAAGTTATTCACCTTGGT 58.860 37.500 0.00 0.00 37.94 3.67
3624 11857 5.712152 AGCAAAGAAGTTATTCACCTTGG 57.288 39.130 0.00 0.00 37.94 3.61
3682 11915 8.937634 AAATGCAAAAGCTTTGAATAGATAGG 57.062 30.769 13.54 0.00 0.00 2.57
3711 11944 7.486802 TTTCTTCCTACCTTACTGTTTTTCG 57.513 36.000 0.00 0.00 0.00 3.46
3720 11953 7.818446 CCAGTTCTAGTTTTCTTCCTACCTTAC 59.182 40.741 0.00 0.00 0.00 2.34
3727 11960 5.906772 TTCCCAGTTCTAGTTTTCTTCCT 57.093 39.130 0.00 0.00 0.00 3.36
3802 12035 9.337396 CATTTGTACTAAAACCATAGATAGGCA 57.663 33.333 0.00 0.00 0.00 4.75
3825 12058 9.872684 ATGAATAAATCTAACCAGGATCACATT 57.127 29.630 0.00 0.00 0.00 2.71
3862 12095 8.356533 ACAACACATCAACATCTTGATTTTTC 57.643 30.769 0.00 0.00 43.48 2.29
3868 12101 6.262720 TCATCAACAACACATCAACATCTTGA 59.737 34.615 0.00 0.00 40.77 3.02
3886 12119 2.029623 AGATGGCCAGCAATCATCAAC 58.970 47.619 25.38 0.00 39.59 3.18
3890 12123 2.168496 GCATAGATGGCCAGCAATCAT 58.832 47.619 25.38 7.68 0.00 2.45
3891 12124 1.133730 TGCATAGATGGCCAGCAATCA 60.134 47.619 25.38 12.22 31.42 2.57


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

AutoCloner maintained by Alex Coulton.