Multiple sequence alignment - TraesCS4B01G286200

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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 TraesCS4B01G286200 chr4B 100.000 3554 0 0 1 3554 569760993 569764546 0.000000e+00 6564.0
1 TraesCS4B01G286200 chr4D 91.229 2018 117 21 857 2841 455756950 455758940 0.000000e+00 2691.0
2 TraesCS4B01G286200 chr4D 84.735 642 45 32 2833 3453 455758984 455759593 8.500000e-166 593.0
3 TraesCS4B01G286200 chr4D 96.552 58 1 1 808 864 455756855 455756912 1.050000e-15 95.3
4 TraesCS4B01G286200 chr4A 90.684 2061 126 16 810 2841 11776337 11774314 0.000000e+00 2682.0
5 TraesCS4B01G286200 chr4A 94.514 638 29 5 1 636 733390516 733391149 0.000000e+00 979.0
6 TraesCS4B01G286200 chr4A 87.064 688 72 7 2833 3519 11774273 11773602 0.000000e+00 761.0
7 TraesCS4B01G286200 chr7A 98.399 812 8 2 1 809 81147590 81146781 0.000000e+00 1423.0
8 TraesCS4B01G286200 chr2D 95.320 812 28 8 1 809 425476497 425475693 0.000000e+00 1280.0
9 TraesCS4B01G286200 chr2D 94.843 795 33 5 1 794 298847845 298847058 0.000000e+00 1234.0
10 TraesCS4B01G286200 chr3D 94.002 817 38 8 1 815 559263267 559264074 0.000000e+00 1227.0
11 TraesCS4B01G286200 chr1D 93.635 817 43 7 1 814 296613913 296613103 0.000000e+00 1212.0
12 TraesCS4B01G286200 chr6D 92.584 836 34 8 1 814 203757818 203756989 0.000000e+00 1175.0
13 TraesCS4B01G286200 chr2B 93.358 813 24 6 1 786 451120096 451119287 0.000000e+00 1175.0
14 TraesCS4B01G286200 chr7D 92.034 816 33 13 1 815 636607510 636606726 0.000000e+00 1118.0
15 TraesCS4B01G286200 chr7B 90.482 809 59 14 7 812 68187070 68187863 0.000000e+00 1051.0
16 TraesCS4B01G286200 chr7B 90.637 267 16 8 559 820 44267665 44267403 2.630000e-91 346.0
17 TraesCS4B01G286200 chr6A 90.447 806 57 15 7 808 310195388 310194599 0.000000e+00 1044.0


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 TraesCS4B01G286200 chr4B 569760993 569764546 3553 False 6564.000000 6564 100.000000 1 3554 1 chr4B.!!$F1 3553
1 TraesCS4B01G286200 chr4D 455756855 455759593 2738 False 1126.433333 2691 90.838667 808 3453 3 chr4D.!!$F1 2645
2 TraesCS4B01G286200 chr4A 11773602 11776337 2735 True 1721.500000 2682 88.874000 810 3519 2 chr4A.!!$R1 2709
3 TraesCS4B01G286200 chr4A 733390516 733391149 633 False 979.000000 979 94.514000 1 636 1 chr4A.!!$F1 635
4 TraesCS4B01G286200 chr7A 81146781 81147590 809 True 1423.000000 1423 98.399000 1 809 1 chr7A.!!$R1 808
5 TraesCS4B01G286200 chr2D 425475693 425476497 804 True 1280.000000 1280 95.320000 1 809 1 chr2D.!!$R2 808
6 TraesCS4B01G286200 chr2D 298847058 298847845 787 True 1234.000000 1234 94.843000 1 794 1 chr2D.!!$R1 793
7 TraesCS4B01G286200 chr3D 559263267 559264074 807 False 1227.000000 1227 94.002000 1 815 1 chr3D.!!$F1 814
8 TraesCS4B01G286200 chr1D 296613103 296613913 810 True 1212.000000 1212 93.635000 1 814 1 chr1D.!!$R1 813
9 TraesCS4B01G286200 chr6D 203756989 203757818 829 True 1175.000000 1175 92.584000 1 814 1 chr6D.!!$R1 813
10 TraesCS4B01G286200 chr2B 451119287 451120096 809 True 1175.000000 1175 93.358000 1 786 1 chr2B.!!$R1 785
11 TraesCS4B01G286200 chr7D 636606726 636607510 784 True 1118.000000 1118 92.034000 1 815 1 chr7D.!!$R1 814
12 TraesCS4B01G286200 chr7B 68187070 68187863 793 False 1051.000000 1051 90.482000 7 812 1 chr7B.!!$F1 805
13 TraesCS4B01G286200 chr6A 310194599 310195388 789 True 1044.000000 1044 90.447000 7 808 1 chr6A.!!$R1 801

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
704 773 0.321996 GAAGAAGCTGGGGACGAGTT 59.678 55.0 0.0 0.0 0.00 3.01 F
1617 1779 0.382515 GGGACGTGATCTCCTTCTCG 59.617 60.0 0.0 0.0 38.28 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1785 0.096628 CTTTGAGATGCGCAGTGAGC 59.903 55.0 18.32 12.4 40.87 4.26 R
2984 3207 0.543277 TTCTAGCCCATGCCAGACAG 59.457 55.0 0.00 0.0 34.87 3.51 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
593 605 4.388499 GGCGAGGGTTGGAAGCGA 62.388 66.667 0.00 0.00 0.00 4.93
703 772 0.543174 AGAAGAAGCTGGGGACGAGT 60.543 55.000 0.00 0.00 0.00 4.18
704 773 0.321996 GAAGAAGCTGGGGACGAGTT 59.678 55.000 0.00 0.00 0.00 3.01
893 1021 5.502606 GTTAACAGCACACTTCACTTCTTC 58.497 41.667 0.00 0.00 0.00 2.87
908 1036 5.755375 TCACTTCTTCACTCAACTTTGCTAG 59.245 40.000 0.00 0.00 0.00 3.42
916 1044 0.807496 CAACTTTGCTAGCAGAGGGC 59.193 55.000 31.86 0.50 45.30 5.19
929 1057 1.753078 GAGGGCGGGGGAATTTCAC 60.753 63.158 0.00 0.00 0.00 3.18
930 1058 2.036572 GGGCGGGGGAATTTCACA 59.963 61.111 0.29 0.00 0.00 3.58
941 1069 5.497474 GGGGAATTTCACATGTAGTACAGT 58.503 41.667 9.25 4.58 0.00 3.55
970 1098 3.510388 TCTACATGGAGCGAACAGAAG 57.490 47.619 0.00 0.00 0.00 2.85
982 1110 3.063452 GCGAACAGAAGAGTTGAACACAA 59.937 43.478 0.00 0.00 0.00 3.33
1054 1207 4.657824 CAACGTCCACCTCGCCGT 62.658 66.667 0.00 0.00 34.56 5.68
1055 1208 4.353437 AACGTCCACCTCGCCGTC 62.353 66.667 0.00 0.00 32.30 4.79
1239 1392 3.869272 CGCCAAGCAGCCGTGATC 61.869 66.667 0.00 0.00 0.00 2.92
1257 1410 3.077556 CTCTCCACCCACCTCCCG 61.078 72.222 0.00 0.00 0.00 5.14
1263 1416 1.378762 CACCCACCTCCCGTTCATT 59.621 57.895 0.00 0.00 0.00 2.57
1296 1449 1.345715 CCCACCCCGCCTTCTTCTAT 61.346 60.000 0.00 0.00 0.00 1.98
1617 1779 0.382515 GGGACGTGATCTCCTTCTCG 59.617 60.000 0.00 0.00 38.28 4.04
1623 1785 1.045350 TGATCTCCTTCTCGGGGCTG 61.045 60.000 0.00 0.00 31.12 4.85
1646 1808 0.890542 ACTGCGCATCTCAAAGCCAA 60.891 50.000 12.24 0.00 0.00 4.52
1651 1813 2.857489 GCGCATCTCAAAGCCAATGATC 60.857 50.000 0.30 0.00 0.00 2.92
1659 1821 0.254178 AAGCCAATGATCTGGACGCT 59.746 50.000 5.19 0.00 38.96 5.07
1779 1941 1.676314 GCATTGTTTGATGCCATGCCA 60.676 47.619 0.00 0.00 45.16 4.92
1818 1980 2.930040 GACCATGGTGAGTATTGTGTCG 59.070 50.000 25.52 0.00 0.00 4.35
1897 2059 2.381618 TCCCTTGGTTTTGGATGGATGA 59.618 45.455 0.00 0.00 0.00 2.92
2004 2166 1.287146 AGGAGCTTGGCATCTTGGAAT 59.713 47.619 0.00 0.00 0.00 3.01
2043 2205 1.881072 GCATCACATGGCGATCTGGAT 60.881 52.381 0.00 0.00 0.00 3.41
2082 2244 1.210538 ATCAGATGCTGGCAGAAGGA 58.789 50.000 20.86 7.75 31.51 3.36
2093 2255 2.297701 GGCAGAAGGAAACACTGTGAA 58.702 47.619 15.86 0.00 38.59 3.18
2142 2304 2.478894 GCTTATGGCGTACGCATACAAT 59.521 45.455 37.99 24.12 44.11 2.71
2186 2348 2.597520 CATGTTCAATGCGATGCAACA 58.402 42.857 0.00 0.00 43.62 3.33
2192 2354 2.546645 AATGCGATGCAACAAGGCGG 62.547 55.000 0.00 0.00 43.62 6.13
2211 2373 2.679639 CGGCTATGGCAAAGTGGAACTA 60.680 50.000 2.58 0.00 44.27 2.24
2226 2388 3.057736 TGGAACTAACAGTCGAGCACTAC 60.058 47.826 0.00 0.00 32.21 2.73
2250 2412 1.902918 TGTGGTGGACATGCTTGGC 60.903 57.895 4.44 0.00 0.00 4.52
2325 2487 0.682209 GCAATGCTGTGATCTGGGGT 60.682 55.000 0.00 0.00 0.00 4.95
2388 2550 4.704833 GAGCGGGCTGTGCAGGAA 62.705 66.667 0.00 0.00 33.85 3.36
2403 2565 5.067954 GTGCAGGAACTAAGGAACCTAAAA 58.932 41.667 0.00 0.00 36.02 1.52
2501 2663 2.306341 AGACGTGCCATGAATGAGAG 57.694 50.000 0.00 0.00 0.00 3.20
2550 2712 0.608582 CTGCCTTTCTGCCTCAGCTT 60.609 55.000 0.00 0.00 40.80 3.74
2589 2754 9.927081 ATCTGGTTATCCTTAAGATCACAATTT 57.073 29.630 3.36 0.00 36.33 1.82
2598 2763 9.513906 TCCTTAAGATCACAATTTACAATCACA 57.486 29.630 3.36 0.00 0.00 3.58
2601 2766 9.624697 TTAAGATCACAATTTACAATCACAAGC 57.375 29.630 0.00 0.00 0.00 4.01
2602 2767 7.218228 AGATCACAATTTACAATCACAAGCA 57.782 32.000 0.00 0.00 0.00 3.91
2603 2768 7.833786 AGATCACAATTTACAATCACAAGCAT 58.166 30.769 0.00 0.00 0.00 3.79
2604 2769 8.308931 AGATCACAATTTACAATCACAAGCATT 58.691 29.630 0.00 0.00 0.00 3.56
2605 2770 8.836268 ATCACAATTTACAATCACAAGCATTT 57.164 26.923 0.00 0.00 0.00 2.32
2606 2771 8.659925 TCACAATTTACAATCACAAGCATTTT 57.340 26.923 0.00 0.00 0.00 1.82
2623 2788 5.117355 CATTTTATGCTAGCCAGATGGTG 57.883 43.478 13.29 0.00 37.57 4.17
2663 2828 3.327757 TCTTCACACCAGACAAGCCTATT 59.672 43.478 0.00 0.00 0.00 1.73
2692 2857 6.183360 TGGTCACATTTGTCTCAGTCTTCTTA 60.183 38.462 0.00 0.00 0.00 2.10
2706 2871 4.003648 GTCTTCTTACCAAGGTGTGATGG 58.996 47.826 1.07 0.00 42.60 3.51
2715 2880 3.561310 CCAAGGTGTGATGGTTGATATCG 59.439 47.826 0.00 0.00 31.84 2.92
2722 2887 3.187227 GTGATGGTTGATATCGATGGTGC 59.813 47.826 8.54 0.00 0.00 5.01
2740 2905 0.462789 GCAAGGCTGCTGGCAATTAT 59.537 50.000 19.23 0.00 45.74 1.28
2741 2906 1.537562 GCAAGGCTGCTGGCAATTATC 60.538 52.381 19.23 0.00 45.74 1.75
2758 2924 6.086765 GCAATTATCGCTCGGTAATCAAAATG 59.913 38.462 8.07 4.48 0.00 2.32
2872 3094 6.149308 TCCATACTTGATGCTTACACACAAAG 59.851 38.462 0.00 0.00 33.79 2.77
2878 3100 5.122519 TGATGCTTACACACAAAGAAGTGA 58.877 37.500 0.57 0.00 42.05 3.41
2887 3109 3.128589 ACACAAAGAAGTGACATTTGCGT 59.871 39.130 0.57 3.02 42.05 5.24
2894 3116 3.120321 AGTGACATTTGCGTTACTGGA 57.880 42.857 0.00 0.00 34.70 3.86
2900 3122 2.623878 TTTGCGTTACTGGACCTTGA 57.376 45.000 0.00 0.00 0.00 3.02
2972 3195 2.079158 CAGGTGCACACAGTCATTAGG 58.921 52.381 20.43 0.00 0.00 2.69
2973 3196 1.977854 AGGTGCACACAGTCATTAGGA 59.022 47.619 20.43 0.00 0.00 2.94
2974 3197 2.573462 AGGTGCACACAGTCATTAGGAT 59.427 45.455 20.43 0.00 0.00 3.24
2975 3198 3.009473 AGGTGCACACAGTCATTAGGATT 59.991 43.478 20.43 0.00 0.00 3.01
2976 3199 3.127548 GGTGCACACAGTCATTAGGATTG 59.872 47.826 20.43 0.00 39.04 2.67
2977 3200 2.749076 TGCACACAGTCATTAGGATTGC 59.251 45.455 0.00 0.00 36.76 3.56
2978 3201 2.098117 GCACACAGTCATTAGGATTGCC 59.902 50.000 0.00 0.00 36.76 4.52
2981 3204 3.521126 ACACAGTCATTAGGATTGCCTCT 59.479 43.478 0.00 0.00 45.54 3.69
2982 3205 3.875727 CACAGTCATTAGGATTGCCTCTG 59.124 47.826 0.00 0.00 45.54 3.35
2983 3206 3.118112 ACAGTCATTAGGATTGCCTCTGG 60.118 47.826 0.00 0.00 45.54 3.86
2999 3222 4.437587 GGCTGTCTGGCATGGGCT 62.438 66.667 0.00 0.00 41.37 5.19
3011 3234 2.162681 GCATGGGCTAGAAACAAGTGT 58.837 47.619 0.00 0.00 36.96 3.55
3081 3311 1.751927 GGCTGCCAGAAGGTGATGG 60.752 63.158 15.17 0.00 39.73 3.51
3123 3353 4.040755 AGTGATTATACCTTGTGGGCTCT 58.959 43.478 0.00 0.00 39.10 4.09
3127 3357 0.753262 ATACCTTGTGGGCTCTAGCG 59.247 55.000 0.00 0.00 43.26 4.26
3138 3368 3.568853 TGGGCTCTAGCGATAGTTACTTC 59.431 47.826 7.70 0.00 43.26 3.01
3300 3542 4.927425 TCCGTTGAACTATTAGCAAGTGAC 59.073 41.667 0.00 0.00 0.00 3.67
3305 3547 6.599356 TGAACTATTAGCAAGTGACAGGTA 57.401 37.500 0.00 0.00 0.00 3.08
3375 3617 7.780745 TCCTTTTAGAACCCAATAAACTGACAA 59.219 33.333 0.00 0.00 0.00 3.18
3493 3735 5.479724 TGTATGATTGGCAATTCCTTGTTCA 59.520 36.000 14.93 6.27 34.69 3.18
3501 3743 5.538053 TGGCAATTCCTTGTTCACATCTTTA 59.462 36.000 0.00 0.00 34.69 1.85
3504 3746 8.250332 GGCAATTCCTTGTTCACATCTTTATTA 58.750 33.333 0.00 0.00 34.69 0.98
3514 3756 9.665719 TGTTCACATCTTTATTATACAAGCTCA 57.334 29.630 0.00 0.00 0.00 4.26
3530 3772 7.951347 ACAAGCTCATCATAAGGAAATTTCT 57.049 32.000 17.42 1.79 0.00 2.52
3531 3773 8.358582 ACAAGCTCATCATAAGGAAATTTCTT 57.641 30.769 17.42 7.61 0.00 2.52
3532 3774 8.810041 ACAAGCTCATCATAAGGAAATTTCTTT 58.190 29.630 18.24 18.24 0.00 2.52
3533 3775 9.649167 CAAGCTCATCATAAGGAAATTTCTTTT 57.351 29.630 19.22 14.77 0.00 2.27
3534 3776 9.866798 AAGCTCATCATAAGGAAATTTCTTTTC 57.133 29.630 19.22 2.76 42.57 2.29
3535 3777 9.028284 AGCTCATCATAAGGAAATTTCTTTTCA 57.972 29.630 19.22 4.63 44.67 2.69
3536 3778 9.080915 GCTCATCATAAGGAAATTTCTTTTCAC 57.919 33.333 19.22 1.71 44.67 3.18
3541 3783 8.796475 TCATAAGGAAATTTCTTTTCACTCTGG 58.204 33.333 19.22 3.34 44.67 3.86
3542 3784 6.410942 AAGGAAATTTCTTTTCACTCTGGG 57.589 37.500 17.42 0.00 44.67 4.45
3543 3785 5.458595 AGGAAATTTCTTTTCACTCTGGGT 58.541 37.500 17.42 0.00 44.67 4.51
3544 3786 5.302823 AGGAAATTTCTTTTCACTCTGGGTG 59.697 40.000 17.42 0.00 44.67 4.61
3545 3787 4.590850 AATTTCTTTTCACTCTGGGTGC 57.409 40.909 1.88 0.00 44.98 5.01
3546 3788 3.297134 TTTCTTTTCACTCTGGGTGCT 57.703 42.857 1.88 0.00 44.98 4.40
3547 3789 3.297134 TTCTTTTCACTCTGGGTGCTT 57.703 42.857 1.88 0.00 44.98 3.91
3548 3790 4.431416 TTCTTTTCACTCTGGGTGCTTA 57.569 40.909 1.88 0.00 44.98 3.09
3549 3791 4.008074 TCTTTTCACTCTGGGTGCTTAG 57.992 45.455 1.88 0.00 44.98 2.18
3550 3792 2.185004 TTTCACTCTGGGTGCTTAGC 57.815 50.000 1.88 0.00 44.98 3.09
3551 3793 1.352083 TTCACTCTGGGTGCTTAGCT 58.648 50.000 5.60 0.00 44.98 3.32
3552 3794 1.352083 TCACTCTGGGTGCTTAGCTT 58.648 50.000 5.60 0.00 44.98 3.74
3553 3795 2.536066 TCACTCTGGGTGCTTAGCTTA 58.464 47.619 5.60 0.00 44.98 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
822 898 6.649141 TCTGTTAACCAAACATAGCAGTACAG 59.351 38.462 2.48 0.00 46.81 2.74
865 949 4.461081 AGTGAAGTGTGCTGTTAACCAAAA 59.539 37.500 2.48 0.00 0.00 2.44
866 950 4.013728 AGTGAAGTGTGCTGTTAACCAAA 58.986 39.130 2.48 0.00 0.00 3.28
867 951 3.616219 AGTGAAGTGTGCTGTTAACCAA 58.384 40.909 2.48 0.00 0.00 3.67
868 952 3.275617 AGTGAAGTGTGCTGTTAACCA 57.724 42.857 2.48 0.00 0.00 3.67
870 954 5.064707 TGAAGAAGTGAAGTGTGCTGTTAAC 59.935 40.000 0.00 0.00 0.00 2.01
871 955 5.064707 GTGAAGAAGTGAAGTGTGCTGTTAA 59.935 40.000 0.00 0.00 0.00 2.01
872 956 4.570772 GTGAAGAAGTGAAGTGTGCTGTTA 59.429 41.667 0.00 0.00 0.00 2.41
878 971 4.872691 AGTTGAGTGAAGAAGTGAAGTGTG 59.127 41.667 0.00 0.00 0.00 3.82
893 1021 2.740981 CCTCTGCTAGCAAAGTTGAGTG 59.259 50.000 19.86 10.90 0.00 3.51
908 1036 3.662117 AAATTCCCCCGCCCTCTGC 62.662 63.158 0.00 0.00 0.00 4.26
916 1044 2.999331 ACTACATGTGAAATTCCCCCG 58.001 47.619 9.11 0.00 0.00 5.73
929 1057 9.110502 TGTAGAAGAGTATGACTGTACTACATG 57.889 37.037 0.00 0.00 35.14 3.21
930 1058 9.854668 ATGTAGAAGAGTATGACTGTACTACAT 57.145 33.333 0.00 0.00 38.18 2.29
941 1069 4.461198 TCGCTCCATGTAGAAGAGTATGA 58.539 43.478 0.00 0.00 0.00 2.15
1235 1388 0.325671 GAGGTGGGTGGAGAGGATCA 60.326 60.000 0.00 0.00 37.82 2.92
1239 1392 2.689034 GGGAGGTGGGTGGAGAGG 60.689 72.222 0.00 0.00 0.00 3.69
1257 1410 0.539986 TGGAGGCCGAGGTAATGAAC 59.460 55.000 0.00 0.00 0.00 3.18
1263 1416 4.000620 TGGGTGGAGGCCGAGGTA 62.001 66.667 0.00 0.00 0.00 3.08
1296 1449 2.125310 CCGCGCATGAGGGTGTTA 60.125 61.111 8.75 0.00 36.55 2.41
1446 1599 0.172803 CGTGGAGGTCGGAAGGTAAG 59.827 60.000 0.00 0.00 0.00 2.34
1566 1728 1.723608 CTTCAAACACCCTGCACGCA 61.724 55.000 0.00 0.00 0.00 5.24
1623 1785 0.096628 CTTTGAGATGCGCAGTGAGC 59.903 55.000 18.32 12.40 40.87 4.26
1646 1808 2.507944 GGGCAGCGTCCAGATCAT 59.492 61.111 0.00 0.00 0.00 2.45
1668 1830 0.716108 GAGGCATCTTGTCGAACACG 59.284 55.000 0.00 0.00 0.00 4.49
1779 1941 1.376424 CACCTCGTCTGGCTGCATT 60.376 57.895 0.50 0.00 0.00 3.56
1897 2059 1.466167 GAGTGCATTGCGAAGTGACAT 59.534 47.619 3.84 0.00 0.00 3.06
2004 2166 1.402852 GCATATGCCGAGATCAGCGTA 60.403 52.381 17.26 1.10 35.10 4.42
2082 2244 1.238439 CATCCGGCTTCACAGTGTTT 58.762 50.000 0.00 0.00 0.00 2.83
2106 2268 1.136690 TAAGCACTGCGAGAAACGTG 58.863 50.000 0.00 0.00 44.60 4.49
2110 2272 1.086696 GCCATAAGCACTGCGAGAAA 58.913 50.000 0.00 0.00 42.97 2.52
2142 2304 2.528818 CCCCTCCTCAACACAGCCA 61.529 63.158 0.00 0.00 0.00 4.75
2186 2348 1.000896 ACTTTGCCATAGCCGCCTT 60.001 52.632 0.00 0.00 38.69 4.35
2192 2354 3.756434 TGTTAGTTCCACTTTGCCATAGC 59.244 43.478 0.00 0.00 40.48 2.97
2211 2373 1.177256 ACCCGTAGTGCTCGACTGTT 61.177 55.000 0.00 0.00 35.96 3.16
2226 2388 1.965930 CATGTCCACCACACACCCG 60.966 63.158 0.00 0.00 38.04 5.28
2250 2412 3.665675 CTCGAGTTTCCCTGCCCGG 62.666 68.421 3.62 0.00 0.00 5.73
2325 2487 1.227823 ACAAGCACCAAGTAGCGCA 60.228 52.632 11.47 0.00 35.48 6.09
2388 2550 5.160386 TCCTCTGGTTTTAGGTTCCTTAGT 58.840 41.667 0.00 0.00 34.30 2.24
2389 2551 5.338463 CCTCCTCTGGTTTTAGGTTCCTTAG 60.338 48.000 0.00 0.00 34.30 2.18
2403 2565 1.080538 GTACCCACCCTCCTCTGGT 59.919 63.158 0.00 0.00 36.21 4.00
2448 2610 2.590704 TGCTATCCGACCAGCAGAA 58.409 52.632 2.98 0.00 42.68 3.02
2601 2766 4.558095 GCACCATCTGGCTAGCATAAAATG 60.558 45.833 18.24 11.59 39.32 2.32
2602 2767 3.571401 GCACCATCTGGCTAGCATAAAAT 59.429 43.478 18.24 0.00 39.32 1.82
2603 2768 2.951642 GCACCATCTGGCTAGCATAAAA 59.048 45.455 18.24 0.00 39.32 1.52
2604 2769 2.092484 TGCACCATCTGGCTAGCATAAA 60.092 45.455 18.24 0.00 36.37 1.40
2605 2770 1.490069 TGCACCATCTGGCTAGCATAA 59.510 47.619 18.24 0.33 36.37 1.90
2606 2771 1.130777 TGCACCATCTGGCTAGCATA 58.869 50.000 18.24 3.74 36.37 3.14
2623 2788 7.170658 GTGTGAAGAGAAGATAGATTGGTATGC 59.829 40.741 0.00 0.00 0.00 3.14
2663 2828 4.717877 ACTGAGACAAATGTGACCAATCA 58.282 39.130 0.00 0.00 0.00 2.57
2706 2871 2.031682 GCCTTGCACCATCGATATCAAC 60.032 50.000 0.00 0.00 0.00 3.18
2722 2887 1.268896 CGATAATTGCCAGCAGCCTTG 60.269 52.381 0.00 0.00 42.71 3.61
2737 2902 4.024387 GGCATTTTGATTACCGAGCGATAA 60.024 41.667 0.00 0.00 0.00 1.75
2740 2905 1.668751 GGCATTTTGATTACCGAGCGA 59.331 47.619 0.00 0.00 0.00 4.93
2741 2906 1.670811 AGGCATTTTGATTACCGAGCG 59.329 47.619 0.00 0.00 0.00 5.03
2758 2924 3.131223 TCAACTAGTCTATCAGCACAGGC 59.869 47.826 0.00 0.00 41.61 4.85
2813 2979 2.456577 ACTGAAACTGGCTTTGGTGTT 58.543 42.857 0.00 0.00 0.00 3.32
2872 3094 3.496884 TCCAGTAACGCAAATGTCACTTC 59.503 43.478 0.00 0.00 0.00 3.01
2878 3100 2.552315 CAAGGTCCAGTAACGCAAATGT 59.448 45.455 0.00 0.00 0.00 2.71
2887 3109 1.351017 CAGGCCTTCAAGGTCCAGTAA 59.649 52.381 16.56 0.00 42.20 2.24
2894 3116 1.777272 AGAAGTTCAGGCCTTCAAGGT 59.223 47.619 0.00 0.00 40.62 3.50
2900 3122 4.959839 TGGTTTTAAAGAAGTTCAGGCCTT 59.040 37.500 0.00 0.00 0.00 4.35
2977 3200 1.451567 CATGCCAGACAGCCAGAGG 60.452 63.158 0.00 0.00 0.00 3.69
2978 3201 1.451567 CCATGCCAGACAGCCAGAG 60.452 63.158 0.00 0.00 0.00 3.35
2979 3202 2.672908 CCATGCCAGACAGCCAGA 59.327 61.111 0.00 0.00 0.00 3.86
2981 3204 4.746309 GCCCATGCCAGACAGCCA 62.746 66.667 0.00 0.00 0.00 4.75
2982 3205 2.955022 CTAGCCCATGCCAGACAGCC 62.955 65.000 0.00 0.00 38.69 4.85
2983 3206 1.525535 CTAGCCCATGCCAGACAGC 60.526 63.158 0.00 0.00 38.69 4.40
2984 3207 0.543277 TTCTAGCCCATGCCAGACAG 59.457 55.000 0.00 0.00 34.87 3.51
2985 3208 0.991146 TTTCTAGCCCATGCCAGACA 59.009 50.000 0.00 0.00 34.87 3.41
2986 3209 1.340017 TGTTTCTAGCCCATGCCAGAC 60.340 52.381 0.00 0.00 34.87 3.51
2999 3222 7.170320 GGTCTTCGAAATACACACTTGTTTCTA 59.830 37.037 0.00 0.00 37.15 2.10
3011 3234 7.068226 TGAGATGATACTGGTCTTCGAAATACA 59.932 37.037 0.00 0.00 0.00 2.29
3123 3353 6.187125 AGTTCGTTGAAGTAACTATCGCTA 57.813 37.500 0.00 0.00 37.13 4.26
3127 3357 8.295569 ACTTGAAGTTCGTTGAAGTAACTATC 57.704 34.615 4.89 0.00 40.43 2.08
3138 3368 7.459394 TTCACTACTTACTTGAAGTTCGTTG 57.541 36.000 1.97 5.05 46.79 4.10
3300 3542 7.981225 CCACCAAATTAATTCCAAGAATACCTG 59.019 37.037 0.10 0.00 0.00 4.00
3347 3589 8.803235 GTCAGTTTATTGGGTTCTAAAAGGAAT 58.197 33.333 0.00 0.00 0.00 3.01
3348 3590 7.780745 TGTCAGTTTATTGGGTTCTAAAAGGAA 59.219 33.333 0.00 0.00 0.00 3.36
3350 3592 7.519032 TGTCAGTTTATTGGGTTCTAAAAGG 57.481 36.000 0.00 0.00 0.00 3.11
3351 3593 9.981114 AATTGTCAGTTTATTGGGTTCTAAAAG 57.019 29.630 0.00 0.00 0.00 2.27
3360 3602 7.812669 GTGGACTTTAATTGTCAGTTTATTGGG 59.187 37.037 10.11 0.00 36.26 4.12
3369 3611 7.542130 GGCATTTTAGTGGACTTTAATTGTCAG 59.458 37.037 10.11 0.00 36.26 3.51
3375 3617 9.528489 TCTTAAGGCATTTTAGTGGACTTTAAT 57.472 29.630 1.85 0.00 0.00 1.40
3458 3700 7.974482 TTGCCAATCATACATAGAGAATGAG 57.026 36.000 0.00 0.00 39.07 2.90
3459 3701 8.929260 AATTGCCAATCATACATAGAGAATGA 57.071 30.769 0.00 0.00 39.07 2.57
3476 3718 3.896888 AGATGTGAACAAGGAATTGCCAA 59.103 39.130 0.00 0.00 40.02 4.52
3504 3746 9.638176 AGAAATTTCCTTATGATGAGCTTGTAT 57.362 29.630 14.61 0.00 0.00 2.29
3519 3761 5.899547 ACCCAGAGTGAAAAGAAATTTCCTT 59.100 36.000 14.61 5.36 45.67 3.36
3520 3762 5.458595 ACCCAGAGTGAAAAGAAATTTCCT 58.541 37.500 14.61 3.46 45.67 3.36
3521 3763 5.791336 ACCCAGAGTGAAAAGAAATTTCC 57.209 39.130 14.61 0.07 45.67 3.13


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

AutoCloner maintained by Alex Coulton.