Multiple sequence alignment - TraesCS3B01G479500

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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 TraesCS3B01G479500 chr3B 100.000 3301 0 0 1 3301 727471706 727475006 0.000000e+00 6096
1 TraesCS3B01G479500 chr3B 86.924 673 74 12 1634 2297 732908091 732907424 0.000000e+00 743
2 TraesCS3B01G479500 chr3B 85.614 709 71 21 870 1559 732908955 732908259 0.000000e+00 715
3 TraesCS3B01G479500 chr3D 92.994 2341 108 29 1 2329 548681286 548683582 0.000000e+00 3363
4 TraesCS3B01G479500 chr3D 87.042 764 43 17 2365 3116 548683594 548684313 0.000000e+00 811
5 TraesCS3B01G479500 chr3D 96.795 156 5 0 3146 3301 548684307 548684462 9.090000e-66 261
6 TraesCS3B01G479500 chr3A 92.401 1987 105 17 331 2308 686169700 686171649 0.000000e+00 2791
7 TraesCS3B01G479500 chr3A 91.740 339 16 7 1 333 686169077 686169409 8.350000e-126 460
8 TraesCS3B01G479500 chr6D 73.747 499 95 22 966 1453 287955 288428 2.640000e-36 163


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 TraesCS3B01G479500 chr3B 727471706 727475006 3300 False 6096.000000 6096 100.0000 1 3301 1 chr3B.!!$F1 3300
1 TraesCS3B01G479500 chr3B 732907424 732908955 1531 True 729.000000 743 86.2690 870 2297 2 chr3B.!!$R1 1427
2 TraesCS3B01G479500 chr3D 548681286 548684462 3176 False 1478.333333 3363 92.2770 1 3301 3 chr3D.!!$F1 3300
3 TraesCS3B01G479500 chr3A 686169077 686171649 2572 False 1625.500000 2791 92.0705 1 2308 2 chr3A.!!$F1 2307

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
386 684 0.398664 AGGTACCCCCTTCGATCCAG 60.399 60.0 8.74 0.0 42.73 3.86 F
1897 2343 0.400213 TACAGGTGAAGCACAAGGGG 59.600 55.0 0.00 0.0 35.86 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 2681 0.317436 GTACGCCTCGATGAGCTCAG 60.317 60.0 22.96 9.67 0.00 3.35 R
3124 3598 0.107165 AAGATGGACGGGGCTTAAGC 60.107 55.0 19.53 19.53 41.14 3.09 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
84 85 7.759489 AGGTTTTATTTACTGAACTGATGCA 57.241 32.000 0.00 0.00 0.00 3.96
109 110 1.177895 TGCAGCGCCAGATTCCAAAA 61.178 50.000 2.29 0.00 0.00 2.44
112 113 1.473677 CAGCGCCAGATTCCAAAATCA 59.526 47.619 2.29 0.00 43.21 2.57
118 119 3.118884 GCCAGATTCCAAAATCAGCATGT 60.119 43.478 0.00 0.00 43.21 3.21
145 150 5.290493 TCCTCGTTATCAAAGGCACATAT 57.710 39.130 0.00 0.00 0.00 1.78
245 250 2.743928 GTTGCCACTCGCTCCCTG 60.744 66.667 0.00 0.00 38.78 4.45
246 251 2.922503 TTGCCACTCGCTCCCTGA 60.923 61.111 0.00 0.00 38.78 3.86
247 252 2.947532 TTGCCACTCGCTCCCTGAG 61.948 63.158 0.00 0.00 38.78 3.35
308 313 3.070159 AGGCTATCACATTCATGCTACGT 59.930 43.478 0.00 0.00 0.00 3.57
369 667 4.938080 CTGAACAGCTATACCACAGTAGG 58.062 47.826 0.00 0.00 0.00 3.18
373 671 4.213513 ACAGCTATACCACAGTAGGTACC 58.786 47.826 2.73 2.73 46.29 3.34
378 676 0.495008 ACCACAGTAGGTACCCCCTT 59.505 55.000 8.74 0.00 42.73 3.95
386 684 0.398664 AGGTACCCCCTTCGATCCAG 60.399 60.000 8.74 0.00 42.73 3.86
392 690 2.107141 CCTTCGATCCAGGTCGCC 59.893 66.667 0.00 0.00 41.22 5.54
418 716 7.376072 CGTTTTGAACTAAGATTGAGTGAAACC 59.624 37.037 0.00 0.00 37.80 3.27
424 722 7.881775 ACTAAGATTGAGTGAAACCTTTTGT 57.118 32.000 0.00 0.00 37.80 2.83
452 750 5.514169 TCAATCACTATTATTTGTGCCCCA 58.486 37.500 0.00 0.00 34.49 4.96
536 834 6.734137 TCAAAATAAAGTGTAGTTGCAGGTG 58.266 36.000 0.00 0.00 0.00 4.00
557 855 5.687730 GGTGTCTCGTATTCAGATACACATG 59.312 44.000 13.90 0.00 43.25 3.21
562 860 3.796717 CGTATTCAGATACACATGCACGT 59.203 43.478 0.00 0.00 38.42 4.49
578 876 6.203915 ACATGCACGTTTACTCTTTCACAATA 59.796 34.615 0.00 0.00 0.00 1.90
579 877 5.981174 TGCACGTTTACTCTTTCACAATAC 58.019 37.500 0.00 0.00 0.00 1.89
580 878 5.070862 GCACGTTTACTCTTTCACAATACG 58.929 41.667 0.00 0.00 0.00 3.06
581 879 5.070862 CACGTTTACTCTTTCACAATACGC 58.929 41.667 0.00 0.00 0.00 4.42
613 911 5.462068 GGTGGCAATTTCTTTAGAAACACAC 59.538 40.000 17.84 16.36 45.55 3.82
614 912 6.039616 GTGGCAATTTCTTTAGAAACACACA 58.960 36.000 7.05 3.14 45.55 3.72
655 953 2.986479 GGACTTGCTGTAAAAATTGCCG 59.014 45.455 0.00 0.00 0.00 5.69
712 1010 9.862371 ACAATATAATTGCCGTGAAAAATGTTA 57.138 25.926 0.00 0.00 0.00 2.41
723 1021 7.358830 CCGTGAAAAATGTTAATTTTGCCATT 58.641 30.769 0.00 0.00 43.63 3.16
726 1024 9.597999 GTGAAAAATGTTAATTTTGCCATTCTC 57.402 29.630 0.00 0.00 43.63 2.87
727 1025 9.558396 TGAAAAATGTTAATTTTGCCATTCTCT 57.442 25.926 0.00 0.00 43.63 3.10
729 1027 7.816945 AAATGTTAATTTTGCCATTCTCTCG 57.183 32.000 0.00 0.00 31.76 4.04
730 1028 4.732784 TGTTAATTTTGCCATTCTCTCGC 58.267 39.130 0.00 0.00 0.00 5.03
731 1029 4.217334 TGTTAATTTTGCCATTCTCTCGCA 59.783 37.500 0.00 0.00 0.00 5.10
732 1030 2.927553 ATTTTGCCATTCTCTCGCAC 57.072 45.000 0.00 0.00 30.84 5.34
733 1031 1.603456 TTTTGCCATTCTCTCGCACA 58.397 45.000 0.00 0.00 30.84 4.57
738 1036 0.803768 CCATTCTCTCGCACAGTCCG 60.804 60.000 0.00 0.00 0.00 4.79
767 1065 8.240682 TGAACTTTCATTGAATAACATTACCCG 58.759 33.333 0.00 0.00 31.01 5.28
801 1104 8.950208 ACTATTTATTTCTTCCTCTTTCTCCG 57.050 34.615 0.00 0.00 0.00 4.63
806 1109 2.594131 TCTTCCTCTTTCTCCGTGTCA 58.406 47.619 0.00 0.00 0.00 3.58
868 1171 3.575687 AGTGCCTTCTCAATCAAAAAGGG 59.424 43.478 2.48 0.00 38.96 3.95
873 1178 5.541845 CCTTCTCAATCAAAAAGGGGAAAC 58.458 41.667 0.00 0.00 35.63 2.78
924 1229 8.648557 TCAAACTAGTATAAGTGCATGTGATC 57.351 34.615 0.00 0.00 0.00 2.92
955 1263 6.954944 TGCAATACACACAGAAGAAAAGTAC 58.045 36.000 0.00 0.00 0.00 2.73
1087 1395 2.594592 GCCCTTGCAACCACGAGT 60.595 61.111 0.00 0.00 37.47 4.18
1177 1485 3.205338 CAGGTTATTGGCGACATCATGA 58.795 45.455 0.00 0.00 42.32 3.07
1179 1487 4.096231 CAGGTTATTGGCGACATCATGAAA 59.904 41.667 0.00 0.00 42.32 2.69
1559 1898 3.074412 ACAGCCAGAAACATTTCGGTAG 58.926 45.455 13.20 9.93 41.92 3.18
1586 1927 6.812160 AGTACATTCGTGTTGATTCCTCTTAC 59.188 38.462 0.00 0.00 0.00 2.34
1595 2038 4.703645 TGATTCCTCTTACTCTCACACG 57.296 45.455 0.00 0.00 0.00 4.49
1795 2241 2.123597 TACTACCCGCGATGCCCT 60.124 61.111 8.23 0.00 0.00 5.19
1798 2244 3.078196 TACCCGCGATGCCCTGAA 61.078 61.111 8.23 0.00 0.00 3.02
1801 2247 4.776322 CCGCGATGCCCTGAACCA 62.776 66.667 8.23 0.00 0.00 3.67
1867 2313 2.982130 GTCCTGTCACAGGGCGAT 59.018 61.111 24.36 0.00 46.58 4.58
1897 2343 0.400213 TACAGGTGAAGCACAAGGGG 59.600 55.000 0.00 0.00 35.86 4.79
1978 2424 4.673403 GTGAGGTCGCATCACACA 57.327 55.556 16.08 0.00 45.18 3.72
1994 2449 6.681368 GCATCACACATCGCATCTATCCTATA 60.681 42.308 0.00 0.00 0.00 1.31
2022 2485 8.998277 AGAAGAGAGTACATGGTAGCTAATTA 57.002 34.615 0.00 0.00 0.00 1.40
2178 2641 0.679640 GCCGGTGATGGTGAATGGAA 60.680 55.000 1.90 0.00 0.00 3.53
2218 2681 3.644335 AGTATAGGGACTTCACAGGGAC 58.356 50.000 0.00 0.00 41.75 4.46
2219 2682 2.950990 ATAGGGACTTCACAGGGACT 57.049 50.000 0.00 0.00 41.75 3.85
2237 2700 0.317436 CTGAGCTCATCGAGGCGTAC 60.317 60.000 18.63 0.00 0.00 3.67
2315 2778 1.227292 GTAGCTAGAGCCAACGCCC 60.227 63.158 0.00 0.00 43.38 6.13
2316 2779 2.432300 TAGCTAGAGCCAACGCCCC 61.432 63.158 0.00 0.00 43.38 5.80
2318 2781 2.668632 CTAGAGCCAACGCCCCAA 59.331 61.111 0.00 0.00 34.57 4.12
2329 2792 2.411290 GCCCCAAACACACACACG 59.589 61.111 0.00 0.00 0.00 4.49
2330 2793 2.411290 CCCCAAACACACACACGC 59.589 61.111 0.00 0.00 0.00 5.34
2331 2794 2.024022 CCCAAACACACACACGCG 59.976 61.111 3.53 3.53 0.00 6.01
2332 2795 2.650602 CCAAACACACACACGCGC 60.651 61.111 5.73 0.00 0.00 6.86
2333 2796 3.010692 CAAACACACACACGCGCG 61.011 61.111 30.96 30.96 0.00 6.86
2334 2797 4.879686 AAACACACACACGCGCGC 62.880 61.111 32.58 23.91 0.00 6.86
2388 2851 2.426522 CACATCCTGTCGACCATTGTT 58.573 47.619 14.12 0.00 0.00 2.83
2401 2864 7.012894 TGTCGACCATTGTTTTCTTAAGTTCAT 59.987 33.333 14.12 0.00 0.00 2.57
2404 2867 7.481798 CGACCATTGTTTTCTTAAGTTCATAGC 59.518 37.037 1.63 0.00 0.00 2.97
2407 2870 5.933187 TGTTTTCTTAAGTTCATAGCGCA 57.067 34.783 11.47 0.00 0.00 6.09
2408 2871 6.494893 TGTTTTCTTAAGTTCATAGCGCAT 57.505 33.333 11.47 0.00 0.00 4.73
2427 2890 8.886816 AGCGCATATAGTACGTAGTTTATTAC 57.113 34.615 11.47 4.82 37.78 1.89
2462 2925 5.689383 ATGATTGTTAATCCGTGTATGCC 57.311 39.130 0.00 0.00 37.09 4.40
2465 2928 3.462483 TGTTAATCCGTGTATGCCGAT 57.538 42.857 0.00 0.00 0.00 4.18
2479 2942 2.001357 CCGATCGACATGTGCAGTG 58.999 57.895 18.66 0.00 0.00 3.66
2483 2946 0.036732 ATCGACATGTGCAGTGGGTT 59.963 50.000 1.15 0.00 0.00 4.11
2491 2954 1.895798 TGTGCAGTGGGTTGTTTTGAA 59.104 42.857 0.00 0.00 0.00 2.69
2503 2967 7.061789 GTGGGTTGTTTTGAATTCGATATTGTC 59.938 37.037 0.04 0.00 0.00 3.18
2538 3002 5.390991 GCACTGCAATAAGGAACAGAGTAAC 60.391 44.000 0.00 0.00 34.25 2.50
2613 3077 8.768501 TGTATGATATACTCCAAGAACAGAGT 57.231 34.615 0.00 0.00 45.20 3.24
2614 3078 9.862149 TGTATGATATACTCCAAGAACAGAGTA 57.138 33.333 2.63 2.63 46.61 2.59
2619 3083 9.482627 GATATACTCCAAGAACAGAGTAATTGG 57.517 37.037 4.17 6.86 45.91 3.16
2620 3084 5.825593 ACTCCAAGAACAGAGTAATTGGA 57.174 39.130 12.57 12.57 45.38 3.53
2654 3118 5.643777 ACAAACTTCAGTGGTACATGATAGC 59.356 40.000 0.00 0.00 44.52 2.97
2678 3142 6.895040 GCTTCTCTTATGTGAAATAAACGTCG 59.105 38.462 0.00 0.00 0.00 5.12
2715 3179 1.599047 ACTGGATCCTTCAGTGGCG 59.401 57.895 14.23 0.00 43.07 5.69
2719 3183 1.144936 GATCCTTCAGTGGCGAGGG 59.855 63.158 7.85 0.00 33.50 4.30
2720 3184 2.317149 GATCCTTCAGTGGCGAGGGG 62.317 65.000 7.85 0.00 33.07 4.79
2721 3185 2.822643 ATCCTTCAGTGGCGAGGGGA 62.823 60.000 7.85 0.00 33.07 4.81
2722 3186 2.592993 CCTTCAGTGGCGAGGGGAA 61.593 63.158 0.00 0.00 0.00 3.97
2723 3187 1.078848 CTTCAGTGGCGAGGGGAAG 60.079 63.158 0.00 0.00 0.00 3.46
2724 3188 3.254024 TTCAGTGGCGAGGGGAAGC 62.254 63.158 0.00 0.00 0.00 3.86
2752 3216 1.140652 GAGGAGGCAATGGAGGAGAAG 59.859 57.143 0.00 0.00 0.00 2.85
2800 3265 3.987868 TGTTTGATTAGAGTCACTGCGTC 59.012 43.478 0.00 0.00 0.00 5.19
2802 3267 3.494045 TGATTAGAGTCACTGCGTCTG 57.506 47.619 0.00 0.00 0.00 3.51
2803 3268 3.081804 TGATTAGAGTCACTGCGTCTGA 58.918 45.455 0.00 0.00 0.00 3.27
2813 3287 1.338200 ACTGCGTCTGATTTGAGGGAC 60.338 52.381 0.00 0.00 0.00 4.46
2837 3311 0.906066 TATCCCAACTTGCGCCACTA 59.094 50.000 4.18 0.00 0.00 2.74
2843 3317 0.905357 AACTTGCGCCACTATCCTCT 59.095 50.000 4.18 0.00 0.00 3.69
2866 3340 2.047179 GCCTTCCACGTCTGGTCC 60.047 66.667 0.00 0.00 38.90 4.46
2867 3341 2.879233 GCCTTCCACGTCTGGTCCA 61.879 63.158 0.00 0.00 38.90 4.02
2894 3368 1.671742 CTATTAGGCCGCATCCCGT 59.328 57.895 0.00 0.00 34.38 5.28
2978 3452 0.616395 TGGGAGATTGTGCCGAGGTA 60.616 55.000 0.00 0.00 40.42 3.08
2989 3463 2.656646 CGAGGTACAGTGCCTGCA 59.343 61.111 16.07 0.00 36.29 4.41
3005 3479 2.756760 CCTGCATGTACTTGCCAGAAAT 59.243 45.455 25.78 0.00 42.06 2.17
3011 3485 5.335583 GCATGTACTTGCCAGAAATTGTGTA 60.336 40.000 20.17 0.00 36.60 2.90
3064 3538 4.442073 TCTCGTAAACACGTTTAAGCAGAC 59.558 41.667 9.78 0.00 36.86 3.51
3110 3584 0.037303 ACTGAAGCAGGGTCACATGG 59.963 55.000 0.00 0.00 35.51 3.66
3111 3585 0.325933 CTGAAGCAGGGTCACATGGA 59.674 55.000 0.00 0.00 0.00 3.41
3112 3586 0.994247 TGAAGCAGGGTCACATGGAT 59.006 50.000 0.00 0.00 0.00 3.41
3113 3587 1.355381 TGAAGCAGGGTCACATGGATT 59.645 47.619 0.00 0.00 0.00 3.01
3114 3588 2.225091 TGAAGCAGGGTCACATGGATTT 60.225 45.455 0.00 0.00 0.00 2.17
3115 3589 1.843368 AGCAGGGTCACATGGATTTG 58.157 50.000 0.00 0.00 0.00 2.32
3116 3590 0.819582 GCAGGGTCACATGGATTTGG 59.180 55.000 0.00 0.00 0.00 3.28
3117 3591 1.892329 GCAGGGTCACATGGATTTGGT 60.892 52.381 0.00 0.00 0.00 3.67
3118 3592 1.820519 CAGGGTCACATGGATTTGGTG 59.179 52.381 0.00 0.00 0.00 4.17
3119 3593 1.710244 AGGGTCACATGGATTTGGTGA 59.290 47.619 0.00 0.00 39.09 4.02
3120 3594 2.109834 AGGGTCACATGGATTTGGTGAA 59.890 45.455 0.00 0.00 42.59 3.18
3121 3595 2.231235 GGGTCACATGGATTTGGTGAAC 59.769 50.000 0.00 0.00 46.01 3.18
3122 3596 2.890311 GGTCACATGGATTTGGTGAACA 59.110 45.455 4.33 0.00 46.01 3.18
3123 3597 3.305335 GGTCACATGGATTTGGTGAACAC 60.305 47.826 4.33 0.00 46.01 3.32
3124 3598 2.551887 TCACATGGATTTGGTGAACACG 59.448 45.455 0.00 0.00 38.50 4.49
3125 3599 1.269448 ACATGGATTTGGTGAACACGC 59.731 47.619 0.00 0.00 0.00 5.34
3126 3600 1.541147 CATGGATTTGGTGAACACGCT 59.459 47.619 0.00 0.00 0.00 5.07
3127 3601 1.686355 TGGATTTGGTGAACACGCTT 58.314 45.000 0.00 0.00 0.00 4.68
3128 3602 2.852449 TGGATTTGGTGAACACGCTTA 58.148 42.857 0.00 0.00 0.00 3.09
3129 3603 3.215151 TGGATTTGGTGAACACGCTTAA 58.785 40.909 0.00 0.00 0.00 1.85
3130 3604 3.252215 TGGATTTGGTGAACACGCTTAAG 59.748 43.478 0.00 0.00 0.00 1.85
3131 3605 2.766970 TTTGGTGAACACGCTTAAGC 57.233 45.000 17.83 17.83 37.78 3.09
3132 3606 0.948678 TTGGTGAACACGCTTAAGCC 59.051 50.000 21.53 7.74 37.91 4.35
3133 3607 0.887387 TGGTGAACACGCTTAAGCCC 60.887 55.000 21.53 14.66 37.91 5.19
3134 3608 1.583495 GGTGAACACGCTTAAGCCCC 61.583 60.000 21.53 7.01 37.91 5.80
3135 3609 1.669760 TGAACACGCTTAAGCCCCG 60.670 57.895 21.53 12.19 37.91 5.73
3136 3610 1.670083 GAACACGCTTAAGCCCCGT 60.670 57.895 21.53 12.82 37.91 5.28
3137 3611 1.632948 GAACACGCTTAAGCCCCGTC 61.633 60.000 21.53 10.43 37.91 4.79
3138 3612 2.818274 CACGCTTAAGCCCCGTCC 60.818 66.667 21.53 0.00 37.91 4.79
3139 3613 3.315949 ACGCTTAAGCCCCGTCCA 61.316 61.111 21.53 0.00 37.91 4.02
3140 3614 2.189521 CGCTTAAGCCCCGTCCAT 59.810 61.111 21.53 0.00 37.91 3.41
3141 3615 1.887707 CGCTTAAGCCCCGTCCATC 60.888 63.158 21.53 0.00 37.91 3.51
3142 3616 1.527370 GCTTAAGCCCCGTCCATCT 59.473 57.895 17.00 0.00 34.31 2.90
3143 3617 0.107165 GCTTAAGCCCCGTCCATCTT 60.107 55.000 17.00 0.00 34.31 2.40
3144 3618 1.682087 GCTTAAGCCCCGTCCATCTTT 60.682 52.381 17.00 0.00 34.31 2.52
3155 3629 2.096496 CGTCCATCTTTGATCTTGCCAC 59.904 50.000 0.00 0.00 0.00 5.01
3180 3654 7.673082 ACCAAAAAGGAGATCAAAGATCAGATT 59.327 33.333 9.43 0.00 41.22 2.40
3193 3667 4.789807 AGATCAGATTAGCATTTGCCACT 58.210 39.130 0.00 0.00 43.38 4.00
3196 3670 4.529897 TCAGATTAGCATTTGCCACTGAT 58.470 39.130 0.00 0.00 43.38 2.90
3269 3743 6.094048 CAGTCAAGTTTTGAAGAAACTCCTCA 59.906 38.462 4.80 0.00 42.15 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 1.640428 CTTTGATAACGAGGAGCGCA 58.360 50.000 11.47 0.00 46.04 6.09
127 128 6.791887 AGATCATATGTGCCTTTGATAACG 57.208 37.500 1.90 0.00 0.00 3.18
145 150 2.632377 GGCTCATTTCGGTCAAGATCA 58.368 47.619 0.00 0.00 0.00 2.92
333 631 3.675698 GCTGTTCAGCTAACACTGTACTC 59.324 47.826 16.29 0.00 43.22 2.59
369 667 0.690077 ACCTGGATCGAAGGGGGTAC 60.690 60.000 15.47 0.00 39.30 3.34
373 671 2.815308 CGACCTGGATCGAAGGGG 59.185 66.667 15.47 1.64 45.13 4.79
378 676 2.162338 AAAACGGCGACCTGGATCGA 62.162 55.000 16.62 0.00 45.13 3.59
386 684 2.137523 TCTTAGTTCAAAACGGCGACC 58.862 47.619 16.62 0.00 36.23 4.79
392 690 7.376072 GGTTTCACTCAATCTTAGTTCAAAACG 59.624 37.037 0.00 0.00 36.23 3.60
424 722 8.682710 GGGCACAAATAATAGTGATTGAAACTA 58.317 33.333 0.00 0.00 37.97 2.24
441 739 5.128499 TGAATTTTATCGATGGGGCACAAAT 59.872 36.000 8.54 0.00 0.00 2.32
442 740 4.464244 TGAATTTTATCGATGGGGCACAAA 59.536 37.500 8.54 0.00 0.00 2.83
443 741 4.019858 TGAATTTTATCGATGGGGCACAA 58.980 39.130 8.54 0.00 0.00 3.33
489 787 9.539825 TTGATACAATTGCACTTATGTTTTTGT 57.460 25.926 5.05 0.00 32.01 2.83
536 834 5.174035 GTGCATGTGTATCTGAATACGAGAC 59.826 44.000 0.00 0.00 40.63 3.36
557 855 5.070862 CGTATTGTGAAAGAGTAAACGTGC 58.929 41.667 0.00 0.00 0.00 5.34
562 860 5.123186 CCCATGCGTATTGTGAAAGAGTAAA 59.877 40.000 0.00 0.00 0.00 2.01
580 878 1.887344 AAATTGCCACCGTCCCATGC 61.887 55.000 0.00 0.00 0.00 4.06
581 879 0.173255 GAAATTGCCACCGTCCCATG 59.827 55.000 0.00 0.00 0.00 3.66
613 911 8.574196 AGTCCTTATTTTTGTCGAAAATTGTG 57.426 30.769 14.63 6.88 43.65 3.33
614 912 9.030301 CAAGTCCTTATTTTTGTCGAAAATTGT 57.970 29.630 14.63 0.00 43.65 2.71
621 919 4.819630 ACAGCAAGTCCTTATTTTTGTCGA 59.180 37.500 0.00 0.00 0.00 4.20
655 953 3.059868 TGACAATTTCTCGAAGCGAACAC 60.060 43.478 0.00 0.00 34.74 3.32
712 1010 2.557924 TGTGCGAGAGAATGGCAAAATT 59.442 40.909 0.00 0.00 44.87 1.82
727 1025 1.007734 GTTCACTCGGACTGTGCGA 60.008 57.895 22.63 22.63 38.05 5.10
728 1026 0.597637 AAGTTCACTCGGACTGTGCG 60.598 55.000 15.86 15.86 35.58 5.34
729 1027 1.527311 GAAAGTTCACTCGGACTGTGC 59.473 52.381 0.00 0.00 35.58 4.57
730 1028 2.821546 TGAAAGTTCACTCGGACTGTG 58.178 47.619 0.00 0.00 36.82 3.66
731 1029 3.753294 ATGAAAGTTCACTCGGACTGT 57.247 42.857 0.00 0.00 40.49 3.55
732 1030 4.058124 TCAATGAAAGTTCACTCGGACTG 58.942 43.478 0.00 0.00 40.49 3.51
733 1031 4.336889 TCAATGAAAGTTCACTCGGACT 57.663 40.909 0.00 0.00 40.49 3.85
801 1104 3.683822 CCTCTGCATCTCTTCTTTGACAC 59.316 47.826 0.00 0.00 0.00 3.67
806 1109 4.630644 TGTTCCTCTGCATCTCTTCTTT 57.369 40.909 0.00 0.00 0.00 2.52
868 1171 4.576993 CCGCAGGCATTTGTTTCC 57.423 55.556 0.00 0.00 46.14 3.13
950 1258 9.311916 CGACTTCTGTACTGTATACTAGTACTT 57.688 37.037 27.31 16.22 46.66 2.24
951 1259 8.690884 TCGACTTCTGTACTGTATACTAGTACT 58.309 37.037 27.31 16.96 46.66 2.73
952 1260 8.864069 TCGACTTCTGTACTGTATACTAGTAC 57.136 38.462 24.10 24.10 46.69 2.73
953 1261 9.526713 CTTCGACTTCTGTACTGTATACTAGTA 57.473 37.037 4.77 4.77 0.00 1.82
954 1262 7.011295 GCTTCGACTTCTGTACTGTATACTAGT 59.989 40.741 0.00 0.00 0.00 2.57
955 1263 7.346695 GCTTCGACTTCTGTACTGTATACTAG 58.653 42.308 4.17 2.93 0.00 2.57
1066 1374 2.335011 GTGGTTGCAAGGGCGTTC 59.665 61.111 0.00 0.00 45.35 3.95
1087 1395 0.037303 ACTGAGAGGTCGTCCCGTAA 59.963 55.000 0.00 0.00 38.74 3.18
1170 1478 0.101759 CCTTGCCGGCTTTCATGATG 59.898 55.000 29.70 7.29 0.00 3.07
1177 1485 1.463553 CCAAACTCCTTGCCGGCTTT 61.464 55.000 29.70 15.72 33.27 3.51
1179 1487 2.282462 CCAAACTCCTTGCCGGCT 60.282 61.111 29.70 1.94 33.27 5.52
1252 1591 2.625639 AGAACTGGTCAGGATTCAGGT 58.374 47.619 0.00 0.00 33.19 4.00
1511 1850 1.135199 CAATGGTGCATCAGCTTGTCC 60.135 52.381 5.59 0.00 42.74 4.02
1559 1898 4.504858 AGGAATCAACACGAATGTACTCC 58.495 43.478 0.00 0.00 38.45 3.85
1586 1927 2.096169 CCGCTATAGCTACGTGTGAGAG 60.096 54.545 21.98 2.35 39.32 3.20
1595 2038 3.390135 TGAACAATGCCGCTATAGCTAC 58.610 45.455 21.98 13.95 39.32 3.58
1795 2241 0.817634 CCAACGTGAGGCTTGGTTCA 60.818 55.000 0.00 0.00 33.46 3.18
1798 2244 2.113139 CCCAACGTGAGGCTTGGT 59.887 61.111 1.85 0.00 35.99 3.67
1831 2277 2.107705 CGTGAGGATGTAGCGGTCT 58.892 57.895 0.00 0.00 0.00 3.85
1867 2313 3.804036 CTTCACCTGTAAACCACTGACA 58.196 45.455 0.00 0.00 0.00 3.58
1897 2343 4.451150 TGGACACCGATCCAGCGC 62.451 66.667 0.00 0.00 44.14 5.92
1977 2423 8.219546 TCTTCTTCTATAGGATAGATGCGATG 57.780 38.462 0.00 0.00 0.00 3.84
1978 2424 8.271458 TCTCTTCTTCTATAGGATAGATGCGAT 58.729 37.037 0.00 0.00 0.00 4.58
1994 2449 5.515106 AGCTACCATGTACTCTCTTCTTCT 58.485 41.667 0.00 0.00 0.00 2.85
2022 2485 8.150945 GGTCACCATCTACACAAGAACATATAT 58.849 37.037 0.00 0.00 37.89 0.86
2178 2641 3.633418 ACTTAGGACGATAGCTGGTCTT 58.367 45.455 12.28 8.61 42.67 3.01
2213 2676 0.754957 CCTCGATGAGCTCAGTCCCT 60.755 60.000 22.96 4.25 0.00 4.20
2218 2681 0.317436 GTACGCCTCGATGAGCTCAG 60.317 60.000 22.96 9.67 0.00 3.35
2219 2682 1.728069 GTACGCCTCGATGAGCTCA 59.272 57.895 20.79 20.79 0.00 4.26
2315 2778 2.650602 GCGCGTGTGTGTGTTTGG 60.651 61.111 8.43 0.00 0.00 3.28
2316 2779 3.010692 CGCGCGTGTGTGTGTTTG 61.011 61.111 24.19 0.00 0.00 2.93
2376 2839 6.721321 TGAACTTAAGAAAACAATGGTCGAC 58.279 36.000 10.09 7.13 0.00 4.20
2401 2864 9.973246 GTAATAAACTACGTACTATATGCGCTA 57.027 33.333 9.73 0.00 40.56 4.26
2404 2867 7.698130 GGGGTAATAAACTACGTACTATATGCG 59.302 40.741 0.00 0.00 42.90 4.73
2407 2870 9.600432 TTGGGGGTAATAAACTACGTACTATAT 57.400 33.333 0.00 0.00 0.00 0.86
2408 2871 8.856103 GTTGGGGGTAATAAACTACGTACTATA 58.144 37.037 0.00 0.00 0.00 1.31
2414 2877 4.906747 TGTTGGGGGTAATAAACTACGT 57.093 40.909 0.00 0.00 0.00 3.57
2451 2914 1.357690 GTCGATCGGCATACACGGA 59.642 57.895 16.20 0.00 0.00 4.69
2452 2915 0.318699 ATGTCGATCGGCATACACGG 60.319 55.000 32.31 0.00 38.84 4.94
2462 2925 1.423721 CCCACTGCACATGTCGATCG 61.424 60.000 9.36 9.36 0.00 3.69
2465 2928 0.884259 CAACCCACTGCACATGTCGA 60.884 55.000 0.00 0.00 0.00 4.20
2479 2942 7.506296 GACAATATCGAATTCAAAACAACCC 57.494 36.000 6.22 0.00 0.00 4.11
2547 3011 2.386661 AAGCTACATGTCGGTCCTTG 57.613 50.000 0.00 0.00 0.00 3.61
2595 3059 8.603898 TCCAATTACTCTGTTCTTGGAGTATA 57.396 34.615 0.00 0.00 42.32 1.47
2597 3061 6.928348 TCCAATTACTCTGTTCTTGGAGTA 57.072 37.500 0.00 0.00 40.21 2.59
2598 3062 5.825593 TCCAATTACTCTGTTCTTGGAGT 57.174 39.130 0.00 0.00 40.21 3.85
2600 3064 5.825593 ACTCCAATTACTCTGTTCTTGGA 57.174 39.130 0.00 0.00 42.22 3.53
2601 3065 9.265901 CATATACTCCAATTACTCTGTTCTTGG 57.734 37.037 0.00 0.00 38.14 3.61
2602 3066 9.265901 CCATATACTCCAATTACTCTGTTCTTG 57.734 37.037 0.00 0.00 0.00 3.02
2603 3067 8.993424 ACCATATACTCCAATTACTCTGTTCTT 58.007 33.333 0.00 0.00 0.00 2.52
2604 3068 8.554490 ACCATATACTCCAATTACTCTGTTCT 57.446 34.615 0.00 0.00 0.00 3.01
2605 3069 9.694137 GTACCATATACTCCAATTACTCTGTTC 57.306 37.037 0.00 0.00 0.00 3.18
2606 3070 9.209048 TGTACCATATACTCCAATTACTCTGTT 57.791 33.333 0.00 0.00 0.00 3.16
2607 3071 8.777578 TGTACCATATACTCCAATTACTCTGT 57.222 34.615 0.00 0.00 0.00 3.41
2614 3078 9.396022 CTGAAGTTTGTACCATATACTCCAATT 57.604 33.333 0.00 0.00 0.00 2.32
2615 3079 8.548877 ACTGAAGTTTGTACCATATACTCCAAT 58.451 33.333 0.00 0.00 0.00 3.16
2616 3080 7.822334 CACTGAAGTTTGTACCATATACTCCAA 59.178 37.037 0.00 0.00 0.00 3.53
2617 3081 7.327975 CACTGAAGTTTGTACCATATACTCCA 58.672 38.462 0.00 0.00 0.00 3.86
2618 3082 6.761714 CCACTGAAGTTTGTACCATATACTCC 59.238 42.308 0.00 0.00 0.00 3.85
2619 3083 7.328737 ACCACTGAAGTTTGTACCATATACTC 58.671 38.462 0.00 0.00 0.00 2.59
2620 3084 7.253905 ACCACTGAAGTTTGTACCATATACT 57.746 36.000 0.00 0.00 0.00 2.12
2621 3085 8.036575 TGTACCACTGAAGTTTGTACCATATAC 58.963 37.037 13.50 0.00 34.94 1.47
2654 3118 8.102716 GTCGACGTTTATTTCACATAAGAGAAG 58.897 37.037 0.00 0.00 0.00 2.85
2675 3139 4.323868 GTGTAGCATACTGAACTTGTCGAC 59.676 45.833 9.11 9.11 43.54 4.20
2678 3142 4.627467 CCAGTGTAGCATACTGAACTTGTC 59.373 45.833 14.27 0.00 46.52 3.18
2720 3184 3.839432 CTCCTCCCGGTCGGCTTC 61.839 72.222 0.00 0.00 0.00 3.86
2725 3189 3.470888 ATTGCCTCCTCCCGGTCG 61.471 66.667 0.00 0.00 0.00 4.79
2726 3190 2.190578 CATTGCCTCCTCCCGGTC 59.809 66.667 0.00 0.00 0.00 4.79
2727 3191 3.411517 CCATTGCCTCCTCCCGGT 61.412 66.667 0.00 0.00 0.00 5.28
2728 3192 3.089874 TCCATTGCCTCCTCCCGG 61.090 66.667 0.00 0.00 0.00 5.73
2729 3193 2.507944 CTCCATTGCCTCCTCCCG 59.492 66.667 0.00 0.00 0.00 5.14
2730 3194 1.694169 TCCTCCATTGCCTCCTCCC 60.694 63.158 0.00 0.00 0.00 4.30
2731 3195 0.692419 TCTCCTCCATTGCCTCCTCC 60.692 60.000 0.00 0.00 0.00 4.30
2732 3196 1.140652 CTTCTCCTCCATTGCCTCCTC 59.859 57.143 0.00 0.00 0.00 3.71
2733 3197 1.211456 CTTCTCCTCCATTGCCTCCT 58.789 55.000 0.00 0.00 0.00 3.69
2734 3198 0.182299 CCTTCTCCTCCATTGCCTCC 59.818 60.000 0.00 0.00 0.00 4.30
2735 3199 0.182299 CCCTTCTCCTCCATTGCCTC 59.818 60.000 0.00 0.00 0.00 4.70
2736 3200 1.284841 CCCCTTCTCCTCCATTGCCT 61.285 60.000 0.00 0.00 0.00 4.75
2737 3201 1.228510 CCCCTTCTCCTCCATTGCC 59.771 63.158 0.00 0.00 0.00 4.52
2741 3205 0.625683 ATGCACCCCTTCTCCTCCAT 60.626 55.000 0.00 0.00 0.00 3.41
2752 3216 2.758736 TGCAAAAATGTATGCACCCC 57.241 45.000 0.00 0.00 46.87 4.95
2800 3265 4.310769 GGATACGATGTCCCTCAAATCAG 58.689 47.826 0.00 0.00 0.00 2.90
2813 3287 0.304705 GCGCAAGTTGGGATACGATG 59.695 55.000 22.92 0.00 41.68 3.84
2837 3311 1.280421 GTGGAAGGCTGAACAGAGGAT 59.720 52.381 5.97 0.00 0.00 3.24
2843 3317 0.249868 CAGACGTGGAAGGCTGAACA 60.250 55.000 0.00 0.00 30.96 3.18
2930 3404 1.953138 CTCTCGCATGACCGCCATC 60.953 63.158 0.00 0.00 31.94 3.51
2931 3405 2.107750 CTCTCGCATGACCGCCAT 59.892 61.111 0.00 0.00 35.44 4.40
2941 3415 0.674581 CATGCCAAACTCCTCTCGCA 60.675 55.000 0.00 0.00 0.00 5.10
2989 3463 5.767665 TGTACACAATTTCTGGCAAGTACAT 59.232 36.000 0.00 0.00 36.60 2.29
3017 3491 5.316167 TCCATGTGACTCTTACTGCATTTT 58.684 37.500 0.00 0.00 0.00 1.82
3018 3492 4.910195 TCCATGTGACTCTTACTGCATTT 58.090 39.130 0.00 0.00 0.00 2.32
3064 3538 7.008719 GCACTACTCTGCATATGTTATATGTCG 59.991 40.741 4.29 3.25 37.11 4.35
3110 3584 3.234386 GCTTAAGCGTGTTCACCAAATC 58.766 45.455 12.53 0.00 0.00 2.17
3111 3585 2.030274 GGCTTAAGCGTGTTCACCAAAT 60.030 45.455 20.80 0.00 43.26 2.32
3112 3586 1.335496 GGCTTAAGCGTGTTCACCAAA 59.665 47.619 20.80 0.00 43.26 3.28
3113 3587 0.948678 GGCTTAAGCGTGTTCACCAA 59.051 50.000 20.80 0.00 43.26 3.67
3114 3588 0.887387 GGGCTTAAGCGTGTTCACCA 60.887 55.000 20.80 0.00 43.26 4.17
3115 3589 1.583495 GGGGCTTAAGCGTGTTCACC 61.583 60.000 20.80 13.76 43.26 4.02
3116 3590 1.873863 GGGGCTTAAGCGTGTTCAC 59.126 57.895 20.80 4.26 43.26 3.18
3117 3591 1.669760 CGGGGCTTAAGCGTGTTCA 60.670 57.895 20.80 0.00 43.26 3.18
3118 3592 1.632948 GACGGGGCTTAAGCGTGTTC 61.633 60.000 20.80 10.98 43.26 3.18
3119 3593 1.670083 GACGGGGCTTAAGCGTGTT 60.670 57.895 20.80 5.71 43.26 3.32
3120 3594 2.047560 GACGGGGCTTAAGCGTGT 60.048 61.111 20.80 17.64 43.26 4.49
3121 3595 2.818274 GGACGGGGCTTAAGCGTG 60.818 66.667 20.80 14.70 43.26 5.34
3122 3596 2.588856 GATGGACGGGGCTTAAGCGT 62.589 60.000 20.80 13.31 43.26 5.07
3123 3597 1.887707 GATGGACGGGGCTTAAGCG 60.888 63.158 20.80 10.10 43.26 4.68
3124 3598 0.107165 AAGATGGACGGGGCTTAAGC 60.107 55.000 19.53 19.53 41.14 3.09
3125 3599 2.017049 CAAAGATGGACGGGGCTTAAG 58.983 52.381 0.00 0.00 0.00 1.85
3126 3600 1.631388 TCAAAGATGGACGGGGCTTAA 59.369 47.619 0.00 0.00 0.00 1.85
3127 3601 1.281419 TCAAAGATGGACGGGGCTTA 58.719 50.000 0.00 0.00 0.00 3.09
3128 3602 0.625849 ATCAAAGATGGACGGGGCTT 59.374 50.000 0.00 0.00 0.00 4.35
3129 3603 0.181350 GATCAAAGATGGACGGGGCT 59.819 55.000 0.00 0.00 0.00 5.19
3130 3604 0.181350 AGATCAAAGATGGACGGGGC 59.819 55.000 0.00 0.00 0.00 5.80
3131 3605 2.292267 CAAGATCAAAGATGGACGGGG 58.708 52.381 0.00 0.00 0.00 5.73
3132 3606 1.672881 GCAAGATCAAAGATGGACGGG 59.327 52.381 0.00 0.00 0.00 5.28
3133 3607 1.672881 GGCAAGATCAAAGATGGACGG 59.327 52.381 0.00 0.00 0.00 4.79
3134 3608 2.096496 GTGGCAAGATCAAAGATGGACG 59.904 50.000 0.00 0.00 0.00 4.79
3135 3609 2.424956 GGTGGCAAGATCAAAGATGGAC 59.575 50.000 0.00 0.00 0.00 4.02
3136 3610 2.041485 TGGTGGCAAGATCAAAGATGGA 59.959 45.455 0.00 0.00 0.00 3.41
3137 3611 2.449464 TGGTGGCAAGATCAAAGATGG 58.551 47.619 0.00 0.00 0.00 3.51
3138 3612 4.524316 TTTGGTGGCAAGATCAAAGATG 57.476 40.909 0.00 0.00 0.00 2.90
3139 3613 5.511888 CCTTTTTGGTGGCAAGATCAAAGAT 60.512 40.000 0.00 0.00 31.89 2.40
3140 3614 4.202243 CCTTTTTGGTGGCAAGATCAAAGA 60.202 41.667 0.00 0.00 31.89 2.52
3141 3615 4.060205 CCTTTTTGGTGGCAAGATCAAAG 58.940 43.478 0.00 0.00 31.89 2.77
3142 3616 3.708631 TCCTTTTTGGTGGCAAGATCAAA 59.291 39.130 0.00 0.00 37.07 2.69
3143 3617 3.303938 TCCTTTTTGGTGGCAAGATCAA 58.696 40.909 0.00 0.00 37.07 2.57
3144 3618 2.892852 CTCCTTTTTGGTGGCAAGATCA 59.107 45.455 0.00 0.00 37.07 2.92
3155 3629 7.642082 ATCTGATCTTTGATCTCCTTTTTGG 57.358 36.000 8.71 0.00 37.10 3.28
3180 3654 5.185442 TCAATTTCATCAGTGGCAAATGCTA 59.815 36.000 5.25 0.00 41.70 3.49
3193 3667 2.487762 GCCGAAGTGGTCAATTTCATCA 59.512 45.455 0.00 0.00 41.21 3.07
3196 3670 1.243902 GGCCGAAGTGGTCAATTTCA 58.756 50.000 0.00 0.00 44.04 2.69


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

AutoCloner maintained by Alex Coulton.