Multiple sequence alignment - TraesCS3D01G138600

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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 TraesCS3D01G138600 chr3D 100.000 4807 0 0 1 4807 97110919 97115725 0.000000e+00 8877.0
1 TraesCS3D01G138600 chr3D 94.098 898 47 2 1 898 461559809 461558918 0.000000e+00 1360.0
2 TraesCS3D01G138600 chr3D 93.215 899 54 3 1 898 543499478 543498586 0.000000e+00 1315.0
3 TraesCS3D01G138600 chr3B 94.471 2876 140 11 1059 3917 147930087 147932960 0.000000e+00 4412.0
4 TraesCS3D01G138600 chr3B 93.108 740 44 1 4068 4807 147933247 147933979 0.000000e+00 1077.0
5 TraesCS3D01G138600 chr3A 91.877 2770 178 23 1366 4119 114707708 114710446 0.000000e+00 3825.0
6 TraesCS3D01G138600 chr3A 89.127 653 49 10 4171 4807 114712570 114713216 0.000000e+00 793.0
7 TraesCS3D01G138600 chr3A 85.981 428 35 8 959 1365 114707322 114707745 7.390000e-118 435.0
8 TraesCS3D01G138600 chr3A 88.587 184 11 6 3939 4119 114719845 114720021 1.050000e-51 215.0
9 TraesCS3D01G138600 chr2D 94.216 899 43 5 1 898 589513129 589512239 0.000000e+00 1363.0
10 TraesCS3D01G138600 chr2D 93.667 900 48 5 1 898 417191631 417190739 0.000000e+00 1338.0
11 TraesCS3D01G138600 chr2D 93.333 900 51 5 1 898 634062938 634063830 0.000000e+00 1321.0
12 TraesCS3D01G138600 chr4D 93.993 899 48 2 1 898 303073276 303072383 0.000000e+00 1356.0
13 TraesCS3D01G138600 chr4D 93.333 900 51 5 1 898 479372594 479373486 0.000000e+00 1321.0
14 TraesCS3D01G138600 chr4D 93.548 62 4 0 899 960 479373463 479373524 5.120000e-15 93.5
15 TraesCS3D01G138600 chr5D 93.743 895 46 6 6 898 238122292 238121406 0.000000e+00 1334.0
16 TraesCS3D01G138600 chr1A 93.581 888 48 2 6 893 587375236 587376114 0.000000e+00 1315.0


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 TraesCS3D01G138600 chr3D 97110919 97115725 4806 False 8877.000000 8877 100.0000 1 4807 1 chr3D.!!$F1 4806
1 TraesCS3D01G138600 chr3D 461558918 461559809 891 True 1360.000000 1360 94.0980 1 898 1 chr3D.!!$R1 897
2 TraesCS3D01G138600 chr3D 543498586 543499478 892 True 1315.000000 1315 93.2150 1 898 1 chr3D.!!$R2 897
3 TraesCS3D01G138600 chr3B 147930087 147933979 3892 False 2744.500000 4412 93.7895 1059 4807 2 chr3B.!!$F1 3748
4 TraesCS3D01G138600 chr3A 114707322 114713216 5894 False 1684.333333 3825 88.9950 959 4807 3 chr3A.!!$F2 3848
5 TraesCS3D01G138600 chr2D 589512239 589513129 890 True 1363.000000 1363 94.2160 1 898 1 chr2D.!!$R2 897
6 TraesCS3D01G138600 chr2D 417190739 417191631 892 True 1338.000000 1338 93.6670 1 898 1 chr2D.!!$R1 897
7 TraesCS3D01G138600 chr2D 634062938 634063830 892 False 1321.000000 1321 93.3330 1 898 1 chr2D.!!$F1 897
8 TraesCS3D01G138600 chr4D 303072383 303073276 893 True 1356.000000 1356 93.9930 1 898 1 chr4D.!!$R1 897
9 TraesCS3D01G138600 chr4D 479372594 479373524 930 False 707.250000 1321 93.4405 1 960 2 chr4D.!!$F1 959
10 TraesCS3D01G138600 chr5D 238121406 238122292 886 True 1334.000000 1334 93.7430 6 898 1 chr5D.!!$R1 892
11 TraesCS3D01G138600 chr1A 587375236 587376114 878 False 1315.000000 1315 93.5810 6 893 1 chr1A.!!$F1 887

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
806 812 0.039618 TTCTGATGTTTCCCCTGGGC 59.960 55.0 7.39 0.0 34.68 5.36 F
1933 1977 0.108585 TGAGGGAACGCTCTTTGCTT 59.891 50.0 17.16 0.0 40.11 3.91 F
3099 3144 0.530744 GTGCCTCCTGATGTACACGA 59.469 55.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2669 2714 0.097674 GCATCTCGCACATGGTTGTC 59.902 55.0 0.0 0.0 41.79 3.18 R
3672 3730 0.250513 CAGTGTCAGCCCTACTTCCC 59.749 60.0 0.0 0.0 0.00 3.97 R
3907 3969 0.383949 GGAACACCGCAAAGAAGCAA 59.616 50.0 0.0 0.0 0.00 3.91 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
71 72 7.047271 TGAAAGCAGAAGCATACATGTACATA 58.953 34.615 7.96 0.00 45.49 2.29
170 171 8.165239 ACATACATCTACAACAAACAACATGT 57.835 30.769 0.00 0.00 0.00 3.21
248 249 4.220602 AGCACAAGGTTCAACTTCAAACTT 59.779 37.500 0.00 0.00 0.00 2.66
447 450 2.194388 CTCACAGAGGCCATGGCTGT 62.194 60.000 34.70 27.47 43.16 4.40
473 476 2.758737 GACGATGGGGGACGGTCT 60.759 66.667 8.23 0.00 0.00 3.85
489 492 1.610624 GGTCTTGGAAGATCAACGCCA 60.611 52.381 0.00 0.00 36.18 5.69
559 563 1.585006 CTTACCTGCTCGTCGGTGT 59.415 57.895 0.00 0.00 34.76 4.16
674 678 1.153147 GTGAGCCGAAATCCTCCCC 60.153 63.158 0.00 0.00 0.00 4.81
732 737 4.069232 CTGCTCGCACGAGGGGAA 62.069 66.667 20.56 0.00 42.19 3.97
790 795 1.066587 GCGAGCTACTGCCGATTCT 59.933 57.895 0.00 0.00 40.80 2.40
792 797 0.382158 CGAGCTACTGCCGATTCTGA 59.618 55.000 0.00 0.00 40.80 3.27
802 808 1.408822 GCCGATTCTGATGTTTCCCCT 60.409 52.381 0.00 0.00 0.00 4.79
805 811 2.659428 GATTCTGATGTTTCCCCTGGG 58.341 52.381 5.50 5.50 0.00 4.45
806 812 0.039618 TTCTGATGTTTCCCCTGGGC 59.960 55.000 7.39 0.00 34.68 5.36
807 813 1.380380 CTGATGTTTCCCCTGGGCC 60.380 63.158 7.39 0.00 34.68 5.80
808 814 1.856873 TGATGTTTCCCCTGGGCCT 60.857 57.895 7.39 0.00 34.68 5.19
809 815 1.380380 GATGTTTCCCCTGGGCCTG 60.380 63.158 7.39 3.68 34.68 4.85
810 816 2.861271 GATGTTTCCCCTGGGCCTGG 62.861 65.000 21.83 21.83 34.68 4.45
811 817 3.590574 GTTTCCCCTGGGCCTGGT 61.591 66.667 25.76 0.00 34.68 4.00
832 838 2.103432 TCTGACCTGGACGTGCTTTAAA 59.897 45.455 8.99 0.00 0.00 1.52
835 841 3.886505 TGACCTGGACGTGCTTTAAATTT 59.113 39.130 8.99 0.00 0.00 1.82
848 854 5.153513 GCTTTAAATTTCGTGTGATGCAGA 58.846 37.500 0.00 0.00 0.00 4.26
852 858 0.249699 TTTCGTGTGATGCAGACCGT 60.250 50.000 0.00 0.00 0.00 4.83
858 864 3.002965 CGTGTGATGCAGACCGTATAGTA 59.997 47.826 0.00 0.00 0.00 1.82
911 917 4.699522 GCGGACGGGCCACTTTCT 62.700 66.667 4.39 0.00 35.94 2.52
912 918 2.032071 CGGACGGGCCACTTTCTT 59.968 61.111 4.39 0.00 35.94 2.52
913 919 2.033194 CGGACGGGCCACTTTCTTC 61.033 63.158 4.39 0.00 35.94 2.87
914 920 1.674651 GGACGGGCCACTTTCTTCC 60.675 63.158 4.39 0.00 36.34 3.46
915 921 1.674651 GACGGGCCACTTTCTTCCC 60.675 63.158 4.39 0.00 35.42 3.97
917 923 3.062466 GGGCCACTTTCTTCCCGC 61.062 66.667 4.39 0.00 0.00 6.13
918 924 3.431725 GGCCACTTTCTTCCCGCG 61.432 66.667 0.00 0.00 0.00 6.46
919 925 4.103103 GCCACTTTCTTCCCGCGC 62.103 66.667 0.00 0.00 0.00 6.86
920 926 3.788766 CCACTTTCTTCCCGCGCG 61.789 66.667 25.67 25.67 0.00 6.86
921 927 3.788766 CACTTTCTTCCCGCGCGG 61.789 66.667 41.00 41.00 0.00 6.46
939 945 1.461461 GGCTAGGGTGGGCCTGATA 60.461 63.158 4.53 0.00 44.48 2.15
960 966 1.899534 GGCAACCAAACACGCCCTA 60.900 57.895 0.00 0.00 38.67 3.53
961 967 1.579429 GCAACCAAACACGCCCTAG 59.421 57.895 0.00 0.00 0.00 3.02
962 968 1.579429 CAACCAAACACGCCCTAGC 59.421 57.895 0.00 0.00 0.00 3.42
974 980 3.955101 CCTAGCGACTCGGGCGAG 61.955 72.222 0.00 0.00 46.91 5.03
989 995 2.278661 GAGGACGATCGAACCGGC 60.279 66.667 24.34 16.46 0.00 6.13
990 996 4.189188 AGGACGATCGAACCGGCG 62.189 66.667 24.34 0.00 35.53 6.46
992 998 4.183686 GACGATCGAACCGGCGGA 62.184 66.667 35.78 10.94 31.91 5.54
1043 1056 2.507944 CATCCCTGAAGGCCCGAG 59.492 66.667 0.00 0.00 34.51 4.63
1254 1291 2.320587 CGTCTGCGCCTTGCTTCTT 61.321 57.895 4.18 0.00 46.63 2.52
1316 1353 1.557832 CTCCAACCCGAGGTATGGAAA 59.442 52.381 18.23 6.81 39.99 3.13
1753 1797 0.615850 TCATGTTGTATGTCCGGCCA 59.384 50.000 2.24 0.00 0.00 5.36
1770 1814 3.674682 CGGCCAAGACTACAGAGAAAGAG 60.675 52.174 2.24 0.00 0.00 2.85
1903 1947 1.982958 AGGGCTTCTTTCTTCGGGTTA 59.017 47.619 0.00 0.00 0.00 2.85
1933 1977 0.108585 TGAGGGAACGCTCTTTGCTT 59.891 50.000 17.16 0.00 40.11 3.91
1999 2043 5.745312 TCTTGATCACAGTAGGACACAAT 57.255 39.130 0.00 0.00 0.00 2.71
2018 2062 5.523916 CACAATCTTCGGAATAGGGTTGTAG 59.476 44.000 6.75 0.84 0.00 2.74
2019 2063 3.814005 TCTTCGGAATAGGGTTGTAGC 57.186 47.619 0.00 0.00 0.00 3.58
2068 2112 3.306166 CGGTTAGTCGCTATTTTGGACTG 59.694 47.826 3.35 0.00 40.94 3.51
2152 2196 1.213537 CAGAATTGCTGGCAACCCG 59.786 57.895 10.28 0.00 41.07 5.28
2186 2230 2.632377 ACTTCAAGGTATGACCATGCG 58.368 47.619 0.00 0.00 41.95 4.73
2268 2312 5.894298 TCATGTAGGATTGTATTGGAGCT 57.106 39.130 0.00 0.00 0.00 4.09
2287 2331 5.986135 GGAGCTATTGATTGTACACAGGTAG 59.014 44.000 0.00 0.15 0.00 3.18
2489 2533 7.416664 CCCATGTGTTCCTCAAGGTAATAAATG 60.417 40.741 0.00 0.24 36.34 2.32
2609 2654 1.507140 AGTGGAAGCCGGATATGGAA 58.493 50.000 5.05 0.00 0.00 3.53
2746 2791 5.163581 ACGAGTACCTATAGAACGTGCATTT 60.164 40.000 0.00 0.00 0.00 2.32
2748 2793 5.974108 AGTACCTATAGAACGTGCATTTGT 58.026 37.500 0.00 0.00 0.00 2.83
3010 3055 6.078456 TGGGAAGACCATCAAAACTATCAT 57.922 37.500 0.00 0.00 46.80 2.45
3083 3128 2.816087 ACAATCTTCAGTGATGGTGTGC 59.184 45.455 12.43 0.00 30.04 4.57
3095 3140 0.613260 TGGTGTGCCTCCTGATGTAC 59.387 55.000 0.00 0.00 35.27 2.90
3099 3144 0.530744 GTGCCTCCTGATGTACACGA 59.469 55.000 0.00 0.00 0.00 4.35
3181 3226 3.565905 AATGACACTTTTGCTGCTAGC 57.434 42.857 8.10 8.10 42.82 3.42
3209 3254 4.793201 AGAGTTTACACTGCCTTTTCCTT 58.207 39.130 0.00 0.00 31.22 3.36
3256 3301 5.129320 TGATTCCTCTAGCAGTAAAGCATCA 59.871 40.000 0.00 0.00 36.85 3.07
3283 3328 3.513515 GGGCCAAGGTAAACAATGATGAA 59.486 43.478 4.39 0.00 0.00 2.57
3322 3367 1.075374 ACCAGCCTTGATAACCTTGCA 59.925 47.619 0.00 0.00 0.00 4.08
3328 3373 3.588955 CCTTGATAACCTTGCAAAAGCC 58.411 45.455 0.00 0.00 0.00 4.35
3442 3487 6.597832 ACCCATTACTATGCTCATCTAGTC 57.402 41.667 0.00 0.00 30.98 2.59
3497 3542 5.138125 ACTTAGCATGTCCAACAAAATGG 57.862 39.130 0.00 0.00 42.12 3.16
3518 3563 5.528337 TGGCATGGGTAGCTAGATATATCA 58.472 41.667 15.08 0.77 0.00 2.15
3545 3600 8.697292 AGAACCACCTTTCTGAGTAGTATATTC 58.303 37.037 0.00 0.00 34.40 1.75
3558 3613 9.783081 TGAGTAGTATATTCGAACTATGTGGTA 57.217 33.333 0.00 0.00 31.25 3.25
3563 3618 8.358148 AGTATATTCGAACTATGTGGTAAGTGG 58.642 37.037 0.00 0.00 0.00 4.00
3564 3619 4.877378 TTCGAACTATGTGGTAAGTGGT 57.123 40.909 0.00 0.00 0.00 4.16
3567 3622 6.343716 TCGAACTATGTGGTAAGTGGTAAA 57.656 37.500 0.00 0.00 0.00 2.01
3581 3636 7.975058 GGTAAGTGGTAAAACTGCTTTTTGTTA 59.025 33.333 6.82 0.00 37.96 2.41
3588 3643 8.757789 GGTAAAACTGCTTTTTGTTACCAATAC 58.242 33.333 5.70 0.00 37.96 1.89
3589 3644 7.458038 AAAACTGCTTTTTGTTACCAATACG 57.542 32.000 0.00 0.00 35.98 3.06
3603 3659 4.901868 ACCAATACGGACAACAACTATGT 58.098 39.130 0.00 0.00 39.02 2.29
3606 3662 1.519408 ACGGACAACAACTATGTGGC 58.481 50.000 0.00 0.00 40.46 5.01
3628 3684 2.260869 GCCGTGCTGTGTCCATGTT 61.261 57.895 0.00 0.00 0.00 2.71
3654 3712 5.713792 TCTGTAACAGGCTATGCTATCTC 57.286 43.478 0.00 0.00 31.51 2.75
3672 3730 5.679734 ATCTCTGTTTGTTGTGCTACAAG 57.320 39.130 2.52 0.00 39.00 3.16
3677 3735 3.380004 TGTTTGTTGTGCTACAAGGGAAG 59.620 43.478 2.52 0.00 39.00 3.46
3724 3782 4.627611 ATTTCATGTGCATGCTAGTCAC 57.372 40.909 20.33 8.76 38.65 3.67
3733 3791 0.818296 ATGCTAGTCACACTCCGGAC 59.182 55.000 0.00 0.00 0.00 4.79
3768 3826 4.671377 TCGTTGCAAAATATCCTTGATGC 58.329 39.130 0.00 0.00 0.00 3.91
3800 3860 5.319140 TGGTTGATCTGAATTTCAGCATG 57.681 39.130 19.53 0.00 43.95 4.06
3807 3867 4.183865 TCTGAATTTCAGCATGTAGGACG 58.816 43.478 19.53 0.00 43.95 4.79
3820 3880 4.094830 TGTAGGACGGATAGTGATGCTA 57.905 45.455 0.00 0.00 0.00 3.49
3880 3940 5.903703 TCGTTAGTGTTTGTTTACGTATGC 58.096 37.500 0.00 0.00 0.00 3.14
3881 3941 5.074791 CGTTAGTGTTTGTTTACGTATGCC 58.925 41.667 0.00 0.00 0.00 4.40
3891 3953 4.767928 TGTTTACGTATGCCCCTGAATTTT 59.232 37.500 0.00 0.00 0.00 1.82
3892 3954 5.244178 TGTTTACGTATGCCCCTGAATTTTT 59.756 36.000 0.00 0.00 0.00 1.94
3910 3972 2.861462 TTTGTGCTGGTGTAAGTTGC 57.139 45.000 0.00 0.00 0.00 4.17
3930 3993 2.096013 GCTTCTTTGCGGTGTTCCTATC 59.904 50.000 0.00 0.00 0.00 2.08
3935 3998 0.892755 TGCGGTGTTCCTATCGAAGT 59.107 50.000 0.00 0.00 0.00 3.01
3942 4005 4.155462 GGTGTTCCTATCGAAGTTTTTCCC 59.845 45.833 0.00 0.00 0.00 3.97
3945 4008 5.828859 TGTTCCTATCGAAGTTTTTCCCAAA 59.171 36.000 0.00 0.00 0.00 3.28
3947 4010 4.763279 TCCTATCGAAGTTTTTCCCAAACC 59.237 41.667 0.00 0.00 0.00 3.27
3948 4011 4.765339 CCTATCGAAGTTTTTCCCAAACCT 59.235 41.667 0.00 0.00 0.00 3.50
3949 4012 4.584327 ATCGAAGTTTTTCCCAAACCTG 57.416 40.909 0.00 0.00 0.00 4.00
3980 4043 2.229792 TGCTGTAAAGCTCCTGGTTTG 58.770 47.619 6.43 0.00 42.86 2.93
3983 4046 3.222603 CTGTAAAGCTCCTGGTTTGGTT 58.777 45.455 0.00 0.00 42.86 3.67
4009 4217 6.204301 CAGGATACCAGAGCATGAAAACTATG 59.796 42.308 0.00 0.00 37.17 2.23
4033 4243 2.475200 GTGACAGCCACAAACTGAAC 57.525 50.000 0.00 0.00 45.03 3.18
4034 4244 2.017049 GTGACAGCCACAAACTGAACT 58.983 47.619 0.00 0.00 45.03 3.01
4036 4246 1.334869 GACAGCCACAAACTGAACTGG 59.665 52.381 0.00 0.00 38.55 4.00
4067 4277 9.875708 TTTAGTGGCCAAAGTATATTTCCATAT 57.124 29.630 7.24 0.00 0.00 1.78
4134 4344 3.611766 GCAAAACTCGATCCCAAAACCTC 60.612 47.826 0.00 0.00 0.00 3.85
4226 6508 8.278639 TCATACAAATATGGGAGCCTTTAAAGA 58.721 33.333 16.98 0.00 39.04 2.52
4240 6522 6.489022 AGCCTTTAAAGACGTAGGAACAAATT 59.511 34.615 16.98 0.00 0.00 1.82
4261 6543 3.510719 TGTTGCTGCAAAAAGACACTTC 58.489 40.909 17.80 0.99 0.00 3.01
4289 6578 1.902508 ACGATGAACATCACAGGACCT 59.097 47.619 13.92 0.00 37.69 3.85
4338 6632 0.447406 TGCTGTAATCACGCATGCAC 59.553 50.000 19.57 7.60 32.07 4.57
4339 6633 0.587242 GCTGTAATCACGCATGCACG 60.587 55.000 19.57 7.82 39.50 5.34
4340 6634 0.026674 CTGTAATCACGCATGCACGG 59.973 55.000 19.57 8.26 37.37 4.94
4341 6635 1.297598 GTAATCACGCATGCACGGC 60.298 57.895 19.57 1.88 37.37 5.68
4342 6636 1.743252 TAATCACGCATGCACGGCA 60.743 52.632 19.57 1.01 44.86 5.69
4384 6678 3.199727 GTGATGGCCATAAACCCCAAAAT 59.800 43.478 20.84 0.00 31.43 1.82
4399 6693 4.340617 CCCAAAATAGGCCTTGTCTTGTA 58.659 43.478 12.58 0.00 0.00 2.41
4590 6884 2.301902 GATCGCCTTCTTGCACTGCG 62.302 60.000 7.84 7.84 46.09 5.18
4653 6947 7.325338 GCATGATGTACTGCAATATGAACATTC 59.675 37.037 0.00 0.00 38.28 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 8.011844 TGTGCTTACTATGATAGTGATGAACT 57.988 34.615 15.08 0.00 43.40 3.01
170 171 4.929479 AGCTATTGGTGGTCCATTTGTAA 58.071 39.130 0.00 0.00 43.91 2.41
248 249 7.039923 GCATGTGGTAGGCTAGATTAGTAGTAA 60.040 40.741 0.00 0.00 32.24 2.24
310 311 5.872963 AGCTGATATGGTTGATTGCTATGA 58.127 37.500 0.00 0.00 0.00 2.15
473 476 0.960364 GGCTGGCGTTGATCTTCCAA 60.960 55.000 0.00 0.00 0.00 3.53
576 580 0.037232 CTCCCTCCGTTCGAGCTTTT 60.037 55.000 0.00 0.00 37.27 2.27
790 795 1.856873 AGGCCCAGGGGAAACATCA 60.857 57.895 7.91 0.00 37.50 3.07
792 797 2.772924 CAGGCCCAGGGGAAACAT 59.227 61.111 7.91 0.00 37.50 2.71
802 808 2.930019 CAGGTCAGACCAGGCCCA 60.930 66.667 22.31 0.00 41.95 5.36
805 811 2.665603 GTCCAGGTCAGACCAGGC 59.334 66.667 23.68 15.68 43.94 4.85
806 812 1.908793 ACGTCCAGGTCAGACCAGG 60.909 63.158 22.72 22.72 45.48 4.45
807 813 1.290324 CACGTCCAGGTCAGACCAG 59.710 63.158 22.31 13.81 41.95 4.00
808 814 2.867855 GCACGTCCAGGTCAGACCA 61.868 63.158 22.31 0.00 41.95 4.02
809 815 2.048127 GCACGTCCAGGTCAGACC 60.048 66.667 12.25 12.25 38.99 3.85
810 816 0.249911 AAAGCACGTCCAGGTCAGAC 60.250 55.000 0.00 0.00 0.00 3.51
811 817 1.334160 TAAAGCACGTCCAGGTCAGA 58.666 50.000 0.00 0.00 0.00 3.27
815 821 3.058501 CGAAATTTAAAGCACGTCCAGGT 60.059 43.478 0.00 0.00 0.00 4.00
832 838 1.078709 CGGTCTGCATCACACGAAAT 58.921 50.000 0.00 0.00 0.00 2.17
835 841 0.815095 ATACGGTCTGCATCACACGA 59.185 50.000 11.29 0.00 0.00 4.35
848 854 4.248058 GTTGCCTGTGTTTACTATACGGT 58.752 43.478 0.00 0.00 0.00 4.83
852 858 5.179742 CGTTTGGTTGCCTGTGTTTACTATA 59.820 40.000 0.00 0.00 0.00 1.31
858 864 0.174617 CCGTTTGGTTGCCTGTGTTT 59.825 50.000 0.00 0.00 0.00 2.83
898 904 2.434774 GGGAAGAAAGTGGCCCGT 59.565 61.111 0.00 0.00 0.00 5.28
900 906 3.062466 GCGGGAAGAAAGTGGCCC 61.062 66.667 0.00 0.00 37.21 5.80
901 907 3.431725 CGCGGGAAGAAAGTGGCC 61.432 66.667 0.00 0.00 0.00 5.36
902 908 4.103103 GCGCGGGAAGAAAGTGGC 62.103 66.667 8.83 0.00 0.00 5.01
903 909 3.788766 CGCGCGGGAAGAAAGTGG 61.789 66.667 24.84 0.00 0.00 4.00
904 910 3.788766 CCGCGCGGGAAGAAAGTG 61.789 66.667 40.50 11.24 38.47 3.16
936 942 0.167251 CGTGTTTGGTTGCCCGTATC 59.833 55.000 0.00 0.00 0.00 2.24
939 945 3.894947 GCGTGTTTGGTTGCCCGT 61.895 61.111 0.00 0.00 0.00 5.28
1027 1040 3.483869 GCTCGGGCCTTCAGGGAT 61.484 66.667 0.84 0.00 37.23 3.85
1254 1291 1.382695 GGGAGAGTGGATTCGGGGA 60.383 63.158 0.00 0.00 0.00 4.81
1316 1353 6.884295 TCAATGTAGGAATCGAAGAATTTGGT 59.116 34.615 0.00 0.00 43.58 3.67
1385 1422 6.259608 CCTCATAGTCACAAATCCAAGTCATC 59.740 42.308 0.00 0.00 0.00 2.92
1753 1797 6.779860 ACTCTCTCTCTTTCTCTGTAGTCTT 58.220 40.000 0.00 0.00 0.00 3.01
1770 1814 3.904339 TGGGCCATAGGAAATACTCTCTC 59.096 47.826 0.00 0.00 0.00 3.20
1863 1907 0.666274 CGTAAGCCTCAGCGTTGTCA 60.666 55.000 0.00 0.00 46.67 3.58
1903 1947 1.613437 CGTTCCCTCAAAACTTGGCAT 59.387 47.619 0.00 0.00 0.00 4.40
1999 2043 3.132289 CAGCTACAACCCTATTCCGAAGA 59.868 47.826 0.00 0.00 0.00 2.87
2018 2062 6.542370 TCACCTGACCTATTAAAAATAGCAGC 59.458 38.462 1.83 0.00 0.00 5.25
2019 2063 8.398665 GTTCACCTGACCTATTAAAAATAGCAG 58.601 37.037 1.83 4.88 0.00 4.24
2068 2112 3.556004 GCTGAACTATAGCATGGAGGACC 60.556 52.174 0.00 0.00 40.81 4.46
2152 2196 3.181450 CCTTGAAGTATGGGTCCCATCTC 60.181 52.174 27.49 20.48 40.74 2.75
2268 2312 5.661312 AGCCTCTACCTGTGTACAATCAATA 59.339 40.000 0.00 0.00 0.00 1.90
2609 2654 2.122768 TGGCAAAAATCCAGGTTTGGT 58.877 42.857 3.78 0.00 45.26 3.67
2669 2714 0.097674 GCATCTCGCACATGGTTGTC 59.902 55.000 0.00 0.00 41.79 3.18
2746 2791 7.602644 ACTTTAAATCTTCGCTTGAGTGATACA 59.397 33.333 0.00 0.00 34.19 2.29
2748 2793 8.547967 AACTTTAAATCTTCGCTTGAGTGATA 57.452 30.769 0.00 0.00 34.19 2.15
3083 3128 4.580995 ACTCTTATCGTGTACATCAGGAGG 59.419 45.833 0.00 0.00 42.83 4.30
3095 3140 3.119291 GCTCATCCACACTCTTATCGTG 58.881 50.000 0.00 0.00 38.32 4.35
3099 3144 5.426504 CAAGAAGCTCATCCACACTCTTAT 58.573 41.667 0.00 0.00 0.00 1.73
3126 3171 0.394216 TTCATTCCCGGCCACATCTG 60.394 55.000 2.24 0.00 0.00 2.90
3181 3226 3.131396 AGGCAGTGTAAACTCTTCAACG 58.869 45.455 0.00 0.00 0.00 4.10
3256 3301 4.410555 TCATTGTTTACCTTGGCCCTTTTT 59.589 37.500 0.00 0.00 0.00 1.94
3283 3328 4.338012 TGGTCATCAAATGCATCAACTCT 58.662 39.130 0.00 0.00 0.00 3.24
3322 3367 6.459298 CGCATTCAGATTTCTCTATGGCTTTT 60.459 38.462 0.00 0.00 0.00 2.27
3328 3373 9.071221 GTATCTACGCATTCAGATTTCTCTATG 57.929 37.037 0.00 0.00 33.58 2.23
3442 3487 3.461061 TCTAGCAATTGCAGGATTCTCG 58.539 45.455 30.89 6.03 45.16 4.04
3497 3542 7.353414 TCTTGATATATCTAGCTACCCATGC 57.647 40.000 16.57 0.00 31.18 4.06
3518 3563 6.936968 ATACTACTCAGAAAGGTGGTTCTT 57.063 37.500 0.00 0.00 35.63 2.52
3545 3600 6.647895 AGTTTTACCACTTACCACATAGTTCG 59.352 38.462 0.00 0.00 0.00 3.95
3558 3613 6.814644 GGTAACAAAAAGCAGTTTTACCACTT 59.185 34.615 9.51 0.00 37.32 3.16
3559 3614 6.334989 GGTAACAAAAAGCAGTTTTACCACT 58.665 36.000 9.51 0.00 37.32 4.00
3560 3615 6.578020 GGTAACAAAAAGCAGTTTTACCAC 57.422 37.500 9.51 4.12 37.32 4.16
3581 3636 4.693566 CACATAGTTGTTGTCCGTATTGGT 59.306 41.667 0.00 0.00 34.39 3.67
3588 3643 1.518325 TGCCACATAGTTGTTGTCCG 58.482 50.000 0.00 0.00 32.34 4.79
3589 3644 2.164219 CCATGCCACATAGTTGTTGTCC 59.836 50.000 0.00 0.00 32.34 4.02
3606 3662 3.434319 GGACACAGCACGGCCATG 61.434 66.667 2.24 0.00 0.00 3.66
3628 3684 4.286297 AGCATAGCCTGTTACAGAACAA 57.714 40.909 14.66 0.00 44.90 2.83
3654 3712 2.948979 TCCCTTGTAGCACAACAAACAG 59.051 45.455 1.71 0.00 38.81 3.16
3672 3730 0.250513 CAGTGTCAGCCCTACTTCCC 59.749 60.000 0.00 0.00 0.00 3.97
3677 3735 0.977395 AAGGTCAGTGTCAGCCCTAC 59.023 55.000 0.00 0.00 0.00 3.18
3724 3782 0.972983 ATCAGGTCCTGTCCGGAGTG 60.973 60.000 18.65 0.00 44.20 3.51
3733 3791 1.364626 GCAACGAGCATCAGGTCCTG 61.365 60.000 13.21 13.21 44.79 3.86
3756 3814 8.110743 ACCAATAGGATATGCATCAAGGATAT 57.889 34.615 0.19 0.00 43.08 1.63
3800 3860 4.700692 TCATAGCATCACTATCCGTCCTAC 59.299 45.833 0.00 0.00 39.71 3.18
3807 3867 7.976135 AATTCAGTTCATAGCATCACTATCC 57.024 36.000 0.00 0.00 39.71 2.59
3820 3880 7.383687 ACTCATGCATTGAAAATTCAGTTCAT 58.616 30.769 0.00 0.00 38.61 2.57
3856 3916 6.401367 GGCATACGTAAACAAACACTAACGAT 60.401 38.462 0.00 0.00 34.62 3.73
3891 3953 2.374184 AGCAACTTACACCAGCACAAA 58.626 42.857 0.00 0.00 0.00 2.83
3892 3954 2.051334 AGCAACTTACACCAGCACAA 57.949 45.000 0.00 0.00 0.00 3.33
3893 3955 1.946768 GAAGCAACTTACACCAGCACA 59.053 47.619 0.00 0.00 0.00 4.57
3900 3962 2.032924 ACCGCAAAGAAGCAACTTACAC 59.967 45.455 0.00 0.00 0.00 2.90
3907 3969 0.383949 GGAACACCGCAAAGAAGCAA 59.616 50.000 0.00 0.00 0.00 3.91
3910 3972 2.348666 CGATAGGAACACCGCAAAGAAG 59.651 50.000 0.00 0.00 0.00 2.85
3930 3993 2.801699 GCCAGGTTTGGGAAAAACTTCG 60.802 50.000 1.42 0.00 45.16 3.79
3935 3998 1.137282 GTTCGCCAGGTTTGGGAAAAA 59.863 47.619 0.00 0.00 45.16 1.94
3980 4043 2.435805 TCATGCTCTGGTATCCTGAACC 59.564 50.000 0.00 0.00 37.53 3.62
3983 4046 4.225942 AGTTTTCATGCTCTGGTATCCTGA 59.774 41.667 0.00 0.00 0.00 3.86
4009 4217 2.017049 AGTTTGTGGCTGTCACTGAAC 58.983 47.619 14.15 16.53 46.20 3.18
4031 4241 0.539669 GGCCACTAAACCTGCCAGTT 60.540 55.000 0.00 0.00 43.46 3.16
4032 4242 1.074951 GGCCACTAAACCTGCCAGT 59.925 57.895 0.00 0.00 43.46 4.00
4033 4243 4.002797 GGCCACTAAACCTGCCAG 57.997 61.111 0.00 0.00 43.46 4.85
4036 4246 1.328279 ACTTTGGCCACTAAACCTGC 58.672 50.000 3.88 0.00 0.00 4.85
4037 4247 7.404671 AAATATACTTTGGCCACTAAACCTG 57.595 36.000 3.88 0.00 0.00 4.00
4038 4248 6.605995 GGAAATATACTTTGGCCACTAAACCT 59.394 38.462 3.88 0.00 0.00 3.50
4119 4329 8.123639 CTCTATATTAGAGGTTTTGGGATCGA 57.876 38.462 4.01 0.00 46.70 3.59
4155 4367 9.285770 GGACTTAATAAAATTAGCGTTTTGAGG 57.714 33.333 7.48 0.00 33.62 3.86
4187 6469 1.939974 TGTATGATCTGTTGCTCGGC 58.060 50.000 0.00 0.00 0.00 5.54
4226 6508 3.550030 GCAGCAACAATTTGTTCCTACGT 60.550 43.478 11.78 0.00 38.77 3.57
4240 6522 3.510719 GAAGTGTCTTTTTGCAGCAACA 58.489 40.909 7.54 0.00 0.00 3.33
4250 6532 2.350498 CGTGGTTGTCGAAGTGTCTTTT 59.650 45.455 0.00 0.00 0.00 2.27
4261 6543 2.065512 TGATGTTCATCGTGGTTGTCG 58.934 47.619 8.04 0.00 0.00 4.35
4289 6578 3.299162 CTGTAACGTGTGTGTAAGCGTA 58.701 45.455 0.00 0.00 36.51 4.42
4338 6632 0.870393 CTGTATGCTTAGCCATGCCG 59.130 55.000 0.29 0.00 0.00 5.69
4339 6633 0.595095 GCTGTATGCTTAGCCATGCC 59.405 55.000 0.29 0.00 38.95 4.40
4384 6678 1.278127 GCCACTACAAGACAAGGCCTA 59.722 52.381 5.16 0.00 36.17 3.93
4590 6884 1.996191 GGACTGCGTGAAGATCTTGAC 59.004 52.381 14.00 14.22 0.00 3.18
4680 6974 6.092259 AGTTGCCACGAATACATAACTTCTTC 59.908 38.462 0.00 0.00 0.00 2.87
4738 7040 3.698040 ACATGATGAGCTCCATTCCAAAC 59.302 43.478 12.15 0.00 35.17 2.93
4739 7041 3.949754 GACATGATGAGCTCCATTCCAAA 59.050 43.478 12.15 0.00 35.17 3.28
4741 7043 2.484241 CGACATGATGAGCTCCATTCCA 60.484 50.000 12.15 2.27 35.17 3.53


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

AutoCloner maintained by Alex Coulton.