Multiple sequence alignment - TraesCS7D01G266500

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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 TraesCS7D01G266500 chr7D 100.000 3883 0 0 1 3883 249418519 249414637 0.000000e+00 7171
1 TraesCS7D01G266500 chr7D 95.145 865 36 6 1 861 617988984 617988122 0.000000e+00 1360
2 TraesCS7D01G266500 chr7B 97.548 2732 63 3 863 3592 226429281 226426552 0.000000e+00 4671
3 TraesCS7D01G266500 chr7B 93.981 216 10 1 3668 3883 226426563 226426351 1.350000e-84 324
4 TraesCS7D01G266500 chr7B 94.937 79 3 1 3589 3667 536117585 536117662 5.270000e-24 122
5 TraesCS7D01G266500 chr7A 96.852 2732 81 3 863 3592 271736807 271739535 0.000000e+00 4564
6 TraesCS7D01G266500 chr7A 93.548 217 10 2 3668 3883 271739524 271739737 1.740000e-83 320
7 TraesCS7D01G266500 chr7A 97.297 74 2 0 3594 3667 700603722 700603649 4.070000e-25 126
8 TraesCS7D01G266500 chr7A 91.954 87 5 1 3583 3667 481695187 481695273 1.890000e-23 121
9 TraesCS7D01G266500 chr1D 95.266 866 35 6 1 862 223187635 223186772 0.000000e+00 1367
10 TraesCS7D01G266500 chr1D 77.778 864 177 11 874 1728 8613793 8614650 5.750000e-143 518
11 TraesCS7D01G266500 chr4D 94.919 866 41 3 1 864 156844841 156843977 0.000000e+00 1352
12 TraesCS7D01G266500 chr4D 94.913 865 42 2 1 863 195287788 195286924 0.000000e+00 1352
13 TraesCS7D01G266500 chr4D 94.798 865 41 4 1 862 42070814 42069951 0.000000e+00 1345
14 TraesCS7D01G266500 chr5D 94.907 864 41 3 1 862 57511869 57512731 0.000000e+00 1349
15 TraesCS7D01G266500 chr3D 94.804 866 41 4 1 864 482032402 482033265 0.000000e+00 1347
16 TraesCS7D01G266500 chr3D 94.566 865 44 3 1 862 254670665 254669801 0.000000e+00 1334
17 TraesCS7D01G266500 chr3D 78.474 878 166 18 861 1727 605332774 605331909 1.580000e-153 553
18 TraesCS7D01G266500 chr3D 96.053 76 3 0 3592 3667 21580636 21580711 1.460000e-24 124
19 TraesCS7D01G266500 chr6D 94.573 866 42 5 1 863 392690326 392689463 0.000000e+00 1334
20 TraesCS7D01G266500 chrUn 100.000 394 0 0 1515 1908 479476300 479476693 0.000000e+00 728
21 TraesCS7D01G266500 chr4A 78.929 859 171 10 870 1723 674937916 674938769 3.360000e-160 575
22 TraesCS7D01G266500 chr3B 78.629 875 170 14 861 1727 814613532 814612667 7.280000e-157 564
23 TraesCS7D01G266500 chr3B 77.675 869 181 10 861 1723 814651722 814650861 5.750000e-143 518
24 TraesCS7D01G266500 chr3B 77.549 873 179 12 864 1727 815034642 815033778 9.620000e-141 510
25 TraesCS7D01G266500 chr3B 77.133 879 176 18 860 1727 814843161 814842297 1.620000e-133 486
26 TraesCS7D01G266500 chr3B 76.403 873 195 8 860 1727 814797454 814796588 9.830000e-126 460
27 TraesCS7D01G266500 chr5B 77.333 900 191 13 867 1759 25330034 25329141 1.600000e-143 520
28 TraesCS7D01G266500 chr5B 93.023 86 4 2 3588 3672 604872355 604872439 1.460000e-24 124
29 TraesCS7D01G266500 chr5B 96.053 76 3 0 3592 3667 618264532 618264607 1.460000e-24 124
30 TraesCS7D01G266500 chr5A 76.863 899 197 11 867 1759 22595849 22596742 7.490000e-137 497
31 TraesCS7D01G266500 chr6A 96.104 77 3 0 3591 3667 11164629 11164705 4.070000e-25 126
32 TraesCS7D01G266500 chr1A 96.053 76 3 0 3592 3667 515551481 515551406 1.460000e-24 124
33 TraesCS7D01G266500 chr4B 94.937 79 3 1 3589 3667 444048920 444048997 5.270000e-24 122


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 TraesCS7D01G266500 chr7D 249414637 249418519 3882 True 7171.0 7171 100.0000 1 3883 1 chr7D.!!$R1 3882
1 TraesCS7D01G266500 chr7D 617988122 617988984 862 True 1360.0 1360 95.1450 1 861 1 chr7D.!!$R2 860
2 TraesCS7D01G266500 chr7B 226426351 226429281 2930 True 2497.5 4671 95.7645 863 3883 2 chr7B.!!$R1 3020
3 TraesCS7D01G266500 chr7A 271736807 271739737 2930 False 2442.0 4564 95.2000 863 3883 2 chr7A.!!$F2 3020
4 TraesCS7D01G266500 chr1D 223186772 223187635 863 True 1367.0 1367 95.2660 1 862 1 chr1D.!!$R1 861
5 TraesCS7D01G266500 chr1D 8613793 8614650 857 False 518.0 518 77.7780 874 1728 1 chr1D.!!$F1 854
6 TraesCS7D01G266500 chr4D 156843977 156844841 864 True 1352.0 1352 94.9190 1 864 1 chr4D.!!$R2 863
7 TraesCS7D01G266500 chr4D 195286924 195287788 864 True 1352.0 1352 94.9130 1 863 1 chr4D.!!$R3 862
8 TraesCS7D01G266500 chr4D 42069951 42070814 863 True 1345.0 1345 94.7980 1 862 1 chr4D.!!$R1 861
9 TraesCS7D01G266500 chr5D 57511869 57512731 862 False 1349.0 1349 94.9070 1 862 1 chr5D.!!$F1 861
10 TraesCS7D01G266500 chr3D 482032402 482033265 863 False 1347.0 1347 94.8040 1 864 1 chr3D.!!$F2 863
11 TraesCS7D01G266500 chr3D 254669801 254670665 864 True 1334.0 1334 94.5660 1 862 1 chr3D.!!$R1 861
12 TraesCS7D01G266500 chr3D 605331909 605332774 865 True 553.0 553 78.4740 861 1727 1 chr3D.!!$R2 866
13 TraesCS7D01G266500 chr6D 392689463 392690326 863 True 1334.0 1334 94.5730 1 863 1 chr6D.!!$R1 862
14 TraesCS7D01G266500 chr4A 674937916 674938769 853 False 575.0 575 78.9290 870 1723 1 chr4A.!!$F1 853
15 TraesCS7D01G266500 chr3B 814612667 814613532 865 True 564.0 564 78.6290 861 1727 1 chr3B.!!$R1 866
16 TraesCS7D01G266500 chr3B 814650861 814651722 861 True 518.0 518 77.6750 861 1723 1 chr3B.!!$R2 862
17 TraesCS7D01G266500 chr3B 815033778 815034642 864 True 510.0 510 77.5490 864 1727 1 chr3B.!!$R5 863
18 TraesCS7D01G266500 chr3B 814842297 814843161 864 True 486.0 486 77.1330 860 1727 1 chr3B.!!$R4 867
19 TraesCS7D01G266500 chr3B 814796588 814797454 866 True 460.0 460 76.4030 860 1727 1 chr3B.!!$R3 867
20 TraesCS7D01G266500 chr5B 25329141 25330034 893 True 520.0 520 77.3330 867 1759 1 chr5B.!!$R1 892
21 TraesCS7D01G266500 chr5A 22595849 22596742 893 False 497.0 497 76.8630 867 1759 1 chr5A.!!$F1 892

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
558 563 0.033090 GTTCGACGAGGACCTTGGTT 59.967 55.000 13.62 0.0 0.00 3.67 F
855 864 0.530744 GATATAGCCGCATCGTGGGA 59.469 55.000 0.00 0.0 33.18 4.37 F
864 873 1.801771 CGCATCGTGGGAGTTACAAAA 59.198 47.619 0.00 0.0 31.21 2.44 F
2410 2423 1.143183 CTGGCCATCCTGCATTTGC 59.857 57.895 5.51 0.0 42.50 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 2362 0.106369 CCACATCACCATCATGCCCT 60.106 55.000 0.00 0.00 0.00 5.19 R
2410 2423 1.344763 ACCCTGAAACGACTTCTCCAG 59.655 52.381 0.00 0.00 34.86 3.86 R
2585 2598 2.549754 ACTTCATTCGCAGAACAACCAG 59.450 45.455 0.00 0.00 45.90 4.00 R
3641 3655 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46 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
171 172 3.576982 TCCGGTTGTAGAGAACTTGACAT 59.423 43.478 0.00 0.00 0.00 3.06
202 203 0.595588 AAAATGCATCAACCGCGTGA 59.404 45.000 4.92 3.05 0.00 4.35
398 400 1.654954 GCTGCAGCTCCACCTCATTG 61.655 60.000 31.33 0.00 38.21 2.82
484 488 3.927142 GTGACTCACGGATACTTCCAAAG 59.073 47.826 0.00 0.00 42.74 2.77
558 563 0.033090 GTTCGACGAGGACCTTGGTT 59.967 55.000 13.62 0.00 0.00 3.67
652 659 6.481976 GGGGTTGTCTTCTTTTATTTTGGTTG 59.518 38.462 0.00 0.00 0.00 3.77
716 725 3.749226 TCATGTATTGTGTGAAGTGGCA 58.251 40.909 0.00 0.00 0.00 4.92
855 864 0.530744 GATATAGCCGCATCGTGGGA 59.469 55.000 0.00 0.00 33.18 4.37
864 873 1.801771 CGCATCGTGGGAGTTACAAAA 59.198 47.619 0.00 0.00 31.21 2.44
865 874 2.159707 CGCATCGTGGGAGTTACAAAAG 60.160 50.000 0.00 0.00 31.21 2.27
930 939 2.231235 CCATAGGTGGTTTCTTGGCAAC 59.769 50.000 0.00 0.00 40.83 4.17
939 948 2.675844 GTTTCTTGGCAACCCAACAAAC 59.324 45.455 9.47 9.47 45.88 2.93
1265 1277 8.059798 ACAATCAATTCATGGTAGAAAAGGAG 57.940 34.615 0.00 0.00 0.00 3.69
1328 1340 5.469421 AGCATCAAGAAGTCAACTGAAGAAG 59.531 40.000 0.00 0.00 0.00 2.85
1370 1382 3.532542 GAAGGTTACGGCTTAAGCAGAT 58.467 45.455 30.43 17.94 44.36 2.90
1908 1920 6.510478 CGTCGTTTTGGTTATTCTGAAGACAA 60.510 38.462 0.00 0.00 0.00 3.18
1912 1924 8.076178 CGTTTTGGTTATTCTGAAGACAAGAAT 58.924 33.333 4.28 4.28 36.42 2.40
1913 1925 9.750125 GTTTTGGTTATTCTGAAGACAAGAATT 57.250 29.630 4.16 0.00 34.55 2.17
2186 2199 4.929211 CCGTCTTGAGTCATTGTCAATACA 59.071 41.667 0.00 0.00 33.02 2.29
2199 2212 4.614475 TGTCAATACAGTCAGAGGGAGAT 58.386 43.478 0.00 0.00 0.00 2.75
2276 2289 2.726760 GCCTCAAGCTGTACGATAATCG 59.273 50.000 0.00 0.00 41.78 3.34
2311 2324 3.791586 GGGTCCAGAGGCTCCAGC 61.792 72.222 11.71 5.14 41.14 4.85
2334 2347 5.390885 GCATCTTGTGAAGCTGAATTTACGA 60.391 40.000 0.00 0.00 34.45 3.43
2410 2423 1.143183 CTGGCCATCCTGCATTTGC 59.857 57.895 5.51 0.00 42.50 3.68
2441 2454 2.806745 CGTTTCAGGGTGAAGAGCTTCA 60.807 50.000 8.76 8.76 46.27 3.02
2585 2598 2.224548 ACTGGAGGGTAAGTGCTGAAAC 60.225 50.000 0.00 0.00 0.00 2.78
2617 2630 4.366586 TGCGAATGAAGTTGCATTTTCAA 58.633 34.783 14.88 0.00 38.53 2.69
2619 2632 4.445385 GCGAATGAAGTTGCATTTTCAAGT 59.555 37.500 14.88 8.13 38.53 3.16
2652 2665 0.677731 CAAGCATCAAGGAAGCCCGA 60.678 55.000 0.00 0.00 37.58 5.14
2787 2800 4.344237 CCCATTCTGAAGGTGGGC 57.656 61.111 14.44 0.00 45.50 5.36
2800 2813 4.116328 TGGGCGAGCTCGAGAACG 62.116 66.667 38.74 20.32 43.02 3.95
2855 2868 1.055040 TGTTGCCAATCCAAAAGGGG 58.945 50.000 0.00 0.00 37.22 4.79
2916 2929 5.290493 TGTTGTATCCCTATACAGCTTGG 57.710 43.478 11.83 0.00 46.58 3.61
2964 2977 8.691661 TTTTACTCTAAAGCATTCCTCTTGTT 57.308 30.769 0.00 0.00 0.00 2.83
3149 3162 8.993121 GTGCATATAAGTGAAATGTGCTAGTAT 58.007 33.333 0.00 0.00 40.79 2.12
3212 3225 6.368243 CCTCATATATCACATGTGCTCTGTTC 59.632 42.308 21.38 0.00 0.00 3.18
3298 3312 4.753233 TGGATTGCGTGAAAATTAATGGG 58.247 39.130 0.00 0.00 0.00 4.00
3376 3390 0.901580 TTAAAGGGCGTCTCCGAGGT 60.902 55.000 0.00 0.00 35.63 3.85
3557 3571 8.773645 CAATAGACACACATCAAAGTTACTGAA 58.226 33.333 0.00 0.00 0.00 3.02
3581 3595 5.654603 ACTGATACCATGAACACTCGTAA 57.345 39.130 0.00 0.00 0.00 3.18
3582 3596 6.032956 ACTGATACCATGAACACTCGTAAA 57.967 37.500 0.00 0.00 0.00 2.01
3583 3597 5.867716 ACTGATACCATGAACACTCGTAAAC 59.132 40.000 0.00 0.00 0.00 2.01
3584 3598 5.785243 TGATACCATGAACACTCGTAAACA 58.215 37.500 0.00 0.00 0.00 2.83
3585 3599 5.867174 TGATACCATGAACACTCGTAAACAG 59.133 40.000 0.00 0.00 0.00 3.16
3586 3600 2.806244 ACCATGAACACTCGTAAACAGC 59.194 45.455 0.00 0.00 0.00 4.40
3587 3601 2.159627 CCATGAACACTCGTAAACAGCC 59.840 50.000 0.00 0.00 0.00 4.85
3588 3602 1.493772 TGAACACTCGTAAACAGCCG 58.506 50.000 0.00 0.00 0.00 5.52
3589 3603 1.067364 TGAACACTCGTAAACAGCCGA 59.933 47.619 0.00 0.00 0.00 5.54
3590 3604 2.129607 GAACACTCGTAAACAGCCGAA 58.870 47.619 0.00 0.00 0.00 4.30
3591 3605 2.228138 ACACTCGTAAACAGCCGAAA 57.772 45.000 0.00 0.00 0.00 3.46
3592 3606 2.762745 ACACTCGTAAACAGCCGAAAT 58.237 42.857 0.00 0.00 0.00 2.17
3593 3607 3.916761 ACACTCGTAAACAGCCGAAATA 58.083 40.909 0.00 0.00 0.00 1.40
3594 3608 4.309099 ACACTCGTAAACAGCCGAAATAA 58.691 39.130 0.00 0.00 0.00 1.40
3595 3609 4.751098 ACACTCGTAAACAGCCGAAATAAA 59.249 37.500 0.00 0.00 0.00 1.40
3596 3610 5.236911 ACACTCGTAAACAGCCGAAATAAAA 59.763 36.000 0.00 0.00 0.00 1.52
3597 3611 6.137415 CACTCGTAAACAGCCGAAATAAAAA 58.863 36.000 0.00 0.00 0.00 1.94
3617 3631 2.360600 GGCAACCCGGTGCATGTA 60.361 61.111 17.82 0.00 46.81 2.29
3618 3632 2.406616 GGCAACCCGGTGCATGTAG 61.407 63.158 17.82 0.00 46.81 2.74
3619 3633 3.051392 GCAACCCGGTGCATGTAGC 62.051 63.158 11.92 2.56 44.29 3.58
3620 3634 1.377202 CAACCCGGTGCATGTAGCT 60.377 57.895 11.25 0.00 45.94 3.32
3621 3635 1.078426 AACCCGGTGCATGTAGCTC 60.078 57.895 11.25 0.00 45.94 4.09
3640 3654 4.077184 TGCTTACGCAGGGTCCGG 62.077 66.667 0.00 0.00 42.25 5.14
3641 3655 4.832608 GCTTACGCAGGGTCCGGG 62.833 72.222 0.00 0.00 35.78 5.73
3642 3656 4.157120 CTTACGCAGGGTCCGGGG 62.157 72.222 0.00 2.98 0.00 5.73
3643 3657 4.700448 TTACGCAGGGTCCGGGGA 62.700 66.667 0.00 0.00 0.00 4.81
3644 3658 4.700448 TACGCAGGGTCCGGGGAA 62.700 66.667 0.00 0.00 0.00 3.97
3649 3663 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
3656 3670 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
3657 3671 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3658 3672 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3659 3673 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3660 3674 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3661 3675 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3662 3676 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3663 3677 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3709 3723 9.930693 TTTACTAATAATCCGGCAAAACAAAAT 57.069 25.926 0.00 0.00 0.00 1.82
3787 3801 4.517075 CCACCCTCTTTTCTGAAAGTTCTC 59.483 45.833 2.75 0.00 42.32 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.364626 CCATCACAAGCTCTCACGGC 61.365 60.000 0.00 0.00 0.00 5.68
94 95 1.796459 GCACGGCTCTCGAAAGTTTAA 59.204 47.619 0.00 0.00 42.43 1.52
202 203 1.853963 AAGAGACCATCACGGCTACT 58.146 50.000 0.00 0.00 39.03 2.57
398 400 1.353091 CTTATGGGTAGGAGAGGGGC 58.647 60.000 0.00 0.00 0.00 5.80
484 488 3.414700 CGTCGGCACCTGCAACTC 61.415 66.667 0.00 0.00 44.36 3.01
558 563 7.156000 TCATCAGGAAACGAAACATAGTAACA 58.844 34.615 0.00 0.00 0.00 2.41
652 659 3.314541 ACAATCAAGGTCCGACTACAC 57.685 47.619 0.00 0.00 0.00 2.90
716 725 6.252995 TGGGATAAAGAGTTGGCTTACAATT 58.747 36.000 0.00 0.00 41.95 2.32
855 864 7.939588 ACTTCTTTAGGATCAGCTTTTGTAACT 59.060 33.333 0.00 0.00 0.00 2.24
864 873 3.262915 ACTGCACTTCTTTAGGATCAGCT 59.737 43.478 0.00 0.00 0.00 4.24
865 874 3.373439 CACTGCACTTCTTTAGGATCAGC 59.627 47.826 0.00 0.00 0.00 4.26
930 939 1.134551 CCAAAGGTGTGGTTTGTTGGG 60.135 52.381 0.00 0.00 33.75 4.12
939 948 1.075374 TCCTCCATTCCAAAGGTGTGG 59.925 52.381 0.00 0.00 40.33 4.17
1230 1242 6.127535 ACCATGAATTGATTGTTGAGATGGTC 60.128 38.462 0.00 0.00 37.12 4.02
1265 1277 0.966875 TGGACCTGGCATGCATCAAC 60.967 55.000 21.36 7.41 0.00 3.18
1328 1340 5.514274 TCCTCCAGTGTGAAAACAAAATC 57.486 39.130 0.00 0.00 0.00 2.17
1908 1920 5.240183 GCAGTACATATGTCATGGCAATTCT 59.760 40.000 12.68 0.00 0.00 2.40
1912 1924 3.878699 CAGCAGTACATATGTCATGGCAA 59.121 43.478 12.68 0.00 0.00 4.52
1913 1925 3.469739 CAGCAGTACATATGTCATGGCA 58.530 45.455 12.68 0.60 0.00 4.92
2186 2199 1.313889 TCCAGGATCTCCCTCTGACT 58.686 55.000 0.00 0.00 45.60 3.41
2199 2212 3.005684 GCAAACATTCACACAATCCAGGA 59.994 43.478 0.00 0.00 0.00 3.86
2270 2283 4.780815 TCTTGGCAGTTTGATCCGATTAT 58.219 39.130 0.00 0.00 0.00 1.28
2276 2289 1.753073 CCCATCTTGGCAGTTTGATCC 59.247 52.381 0.00 0.00 35.79 3.36
2311 2324 6.169419 TCGTAAATTCAGCTTCACAAGATG 57.831 37.500 0.00 0.00 45.90 2.90
2349 2362 0.106369 CCACATCACCATCATGCCCT 60.106 55.000 0.00 0.00 0.00 5.19
2410 2423 1.344763 ACCCTGAAACGACTTCTCCAG 59.655 52.381 0.00 0.00 34.86 3.86
2441 2454 6.351626 GCTTCTGAAAATCCCAATCTGGAAAT 60.352 38.462 0.00 0.00 40.96 2.17
2482 2495 6.648879 TTTGATGTCCCCAAAGTTTCTAAG 57.351 37.500 0.00 0.00 0.00 2.18
2485 2498 5.221702 CCAATTTGATGTCCCCAAAGTTTCT 60.222 40.000 0.00 0.00 37.00 2.52
2585 2598 2.549754 ACTTCATTCGCAGAACAACCAG 59.450 45.455 0.00 0.00 45.90 4.00
2617 2630 3.511477 TGCTTGGGAGAAAGTCTAGACT 58.489 45.455 20.00 20.00 44.94 3.24
2619 2632 4.096681 TGATGCTTGGGAGAAAGTCTAGA 58.903 43.478 0.00 0.00 0.00 2.43
2652 2665 6.134535 TCCGGGATAATGTTTAGCCATAAT 57.865 37.500 0.00 0.00 0.00 1.28
2659 2672 6.542370 AGTTGTTCATCCGGGATAATGTTTAG 59.458 38.462 9.68 0.00 0.00 1.85
2916 2929 7.559590 AAAACATATTCTCCAGTAGCATGTC 57.440 36.000 0.00 0.00 0.00 3.06
2964 2977 9.382307 AGGGTTTAACCTGTATTTATGGAAAAA 57.618 29.630 14.27 0.00 40.04 1.94
2970 2983 8.966868 ACATTGAGGGTTTAACCTGTATTTATG 58.033 33.333 14.27 10.53 42.10 1.90
3178 3191 6.560304 ACATGTGATATATGAGGAAAGGGTCT 59.440 38.462 0.00 0.00 0.00 3.85
3212 3225 4.083643 ACTGCTCAATCACGACAAAATGAG 60.084 41.667 0.00 0.00 37.83 2.90
3275 3289 5.104982 ACCCATTAATTTTCACGCAATCCAT 60.105 36.000 0.00 0.00 0.00 3.41
3376 3390 7.001674 TGGGTTCAGAACAAGAAGCTTAAATA 58.998 34.615 15.36 0.00 41.76 1.40
3540 3554 9.599322 GTATCAGTTTTCAGTAACTTTGATGTG 57.401 33.333 0.00 0.00 36.24 3.21
3557 3571 4.894784 ACGAGTGTTCATGGTATCAGTTT 58.105 39.130 0.00 0.00 0.00 2.66
3594 3608 2.802724 GCACCGGGTTGCCCTTTTT 61.803 57.895 6.32 0.00 42.67 1.94
3595 3609 3.230990 GCACCGGGTTGCCCTTTT 61.231 61.111 6.32 0.00 42.67 2.27
3596 3610 3.826265 ATGCACCGGGTTGCCCTTT 62.826 57.895 13.95 0.00 42.67 3.11
3597 3611 4.299796 ATGCACCGGGTTGCCCTT 62.300 61.111 13.95 0.00 42.67 3.95
3599 3613 3.929334 TACATGCACCGGGTTGCCC 62.929 63.158 13.95 0.00 42.25 5.36
3600 3614 2.360600 TACATGCACCGGGTTGCC 60.361 61.111 13.95 1.69 42.25 4.52
3601 3615 3.051392 GCTACATGCACCGGGTTGC 62.051 63.158 6.32 8.50 43.31 4.17
3602 3616 1.369091 GAGCTACATGCACCGGGTTG 61.369 60.000 6.32 0.00 45.94 3.77
3603 3617 1.078426 GAGCTACATGCACCGGGTT 60.078 57.895 6.32 0.00 45.94 4.11
3604 3618 2.584608 GAGCTACATGCACCGGGT 59.415 61.111 6.32 0.00 45.94 5.28
3605 3619 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
3625 3639 4.157120 CCCCGGACCCTGCGTAAG 62.157 72.222 0.73 0.00 43.44 2.34
3626 3640 4.700448 TCCCCGGACCCTGCGTAA 62.700 66.667 0.73 0.00 0.00 3.18
3627 3641 4.700448 TTCCCCGGACCCTGCGTA 62.700 66.667 0.73 0.00 0.00 4.42
3632 3646 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
3639 3653 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
3640 3654 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3641 3655 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3642 3656 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3643 3657 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3644 3658 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3645 3659 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3646 3660 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3647 3661 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3652 3666 2.956333 GCTGTTTTAGACCCAAAGTGGT 59.044 45.455 0.00 0.00 42.79 4.16
3653 3667 2.296190 GGCTGTTTTAGACCCAAAGTGG 59.704 50.000 0.00 0.00 37.25 4.00
3654 3668 2.031157 CGGCTGTTTTAGACCCAAAGTG 60.031 50.000 0.00 0.00 0.00 3.16
3655 3669 2.158726 TCGGCTGTTTTAGACCCAAAGT 60.159 45.455 0.00 0.00 0.00 2.66
3656 3670 2.500229 TCGGCTGTTTTAGACCCAAAG 58.500 47.619 0.00 0.00 0.00 2.77
3657 3671 2.642154 TCGGCTGTTTTAGACCCAAA 57.358 45.000 0.00 0.00 0.00 3.28
3658 3672 2.619646 GTTTCGGCTGTTTTAGACCCAA 59.380 45.455 0.00 0.00 0.00 4.12
3659 3673 2.223745 GTTTCGGCTGTTTTAGACCCA 58.776 47.619 0.00 0.00 0.00 4.51
3660 3674 1.196127 CGTTTCGGCTGTTTTAGACCC 59.804 52.381 0.00 0.00 0.00 4.46
3661 3675 2.137523 TCGTTTCGGCTGTTTTAGACC 58.862 47.619 0.00 0.00 0.00 3.85
3662 3676 3.865224 TTCGTTTCGGCTGTTTTAGAC 57.135 42.857 0.00 0.00 0.00 2.59
3663 3677 5.427036 AAATTCGTTTCGGCTGTTTTAGA 57.573 34.783 0.00 0.00 0.00 2.10
3664 3678 6.368213 AGTAAATTCGTTTCGGCTGTTTTAG 58.632 36.000 0.00 0.00 0.00 1.85
3665 3679 6.303021 AGTAAATTCGTTTCGGCTGTTTTA 57.697 33.333 0.00 0.00 0.00 1.52
3666 3680 5.177725 AGTAAATTCGTTTCGGCTGTTTT 57.822 34.783 0.00 0.00 0.00 2.43
3667 3681 4.823790 AGTAAATTCGTTTCGGCTGTTT 57.176 36.364 0.00 0.00 0.00 2.83
3732 3746 6.904463 TCACCACACTATCTAGTTTGTACA 57.096 37.500 0.00 0.00 33.35 2.90
3733 3747 6.310711 GCTTCACCACACTATCTAGTTTGTAC 59.689 42.308 3.56 0.00 33.35 2.90
3769 3783 5.176590 CAGGTCGAGAACTTTCAGAAAAGAG 59.823 44.000 4.99 0.00 43.90 2.85
3852 3866 8.703604 TCTGCTTTCACTGTATTAGAACATAC 57.296 34.615 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.