Multiple sequence alignment - TraesCS4B01G396200

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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 TraesCS4B01G396200 chr4B 100.000 3182 0 0 1 3182 670714208 670711027 0.000000e+00 5877.0
1 TraesCS4B01G396200 chrUn 92.954 2654 123 19 553 3182 28412536 28409923 0.000000e+00 3807.0
2 TraesCS4B01G396200 chr7D 83.442 1377 214 11 1208 2577 629434966 629433597 0.000000e+00 1267.0
3 TraesCS4B01G396200 chr7D 79.931 1455 278 9 1078 2527 28578504 28577059 0.000000e+00 1057.0
4 TraesCS4B01G396200 chr7D 78.125 128 13 10 6 119 511363936 511364062 2.050000e-07 67.6
5 TraesCS4B01G396200 chr1A 81.806 1451 258 6 1078 2527 32111214 32112659 0.000000e+00 1212.0
6 TraesCS4B01G396200 chr4A 80.672 1459 266 15 1078 2530 702327739 702326291 0.000000e+00 1118.0
7 TraesCS4B01G396200 chr4A 88.158 76 4 5 63 134 418052834 418052908 5.660000e-13 86.1
8 TraesCS4B01G396200 chr7A 80.495 1456 274 8 1078 2530 29009186 29007738 0.000000e+00 1107.0
9 TraesCS4B01G396200 chr7A 80.302 1457 275 11 1078 2530 28968967 28967519 0.000000e+00 1090.0
10 TraesCS4B01G396200 chr7A 80.165 1457 278 10 1078 2530 28808870 28807421 0.000000e+00 1079.0
11 TraesCS4B01G396200 chr7A 97.368 38 1 0 518 555 200195029 200194992 7.370000e-07 65.8
12 TraesCS4B01G396200 chr2B 80.371 1457 274 12 1078 2530 742172678 742171230 0.000000e+00 1096.0
13 TraesCS4B01G396200 chr2B 92.780 554 38 1 1 554 765300512 765299961 0.000000e+00 800.0
14 TraesCS4B01G396200 chr2B 92.394 447 23 3 1 447 72963681 72963246 7.490000e-176 627.0
15 TraesCS4B01G396200 chr2B 86.207 87 12 0 292 378 762960759 762960845 9.400000e-16 95.3
16 TraesCS4B01G396200 chr5B 94.937 553 23 2 1 553 300846625 300846078 0.000000e+00 861.0
17 TraesCS4B01G396200 chr2A 93.153 555 34 3 1 555 610172588 610172038 0.000000e+00 811.0
18 TraesCS4B01G396200 chr3B 92.780 554 37 3 1 553 612713147 612713698 0.000000e+00 798.0
19 TraesCS4B01G396200 chr3B 91.950 559 39 5 1 554 85455540 85454983 0.000000e+00 778.0
20 TraesCS4B01G396200 chr3B 87.523 553 48 3 1 553 68356973 68356442 1.250000e-173 619.0
21 TraesCS4B01G396200 chr7B 78.740 508 105 3 1208 1713 732578232 732577726 1.410000e-88 337.0
22 TraesCS4B01G396200 chr3D 92.063 63 5 0 1 63 554131109 554131047 4.370000e-14 89.8
23 TraesCS4B01G396200 chr3D 83.099 71 4 6 524 592 522120600 522120664 1.230000e-04 58.4
24 TraesCS4B01G396200 chr6A 91.935 62 4 1 304 364 145997993 145998054 5.660000e-13 86.1
25 TraesCS4B01G396200 chr6A 87.671 73 5 4 63 134 63582028 63582097 7.320000e-12 82.4
26 TraesCS4B01G396200 chr6B 77.059 170 20 11 19 178 522800682 522800522 2.630000e-11 80.5
27 TraesCS4B01G396200 chr6B 97.222 36 0 1 2740 2774 566632680 566632645 3.430000e-05 60.2
28 TraesCS4B01G396200 chr4D 95.122 41 2 0 513 553 374076729 374076689 7.370000e-07 65.8


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 TraesCS4B01G396200 chr4B 670711027 670714208 3181 True 5877 5877 100.000 1 3182 1 chr4B.!!$R1 3181
1 TraesCS4B01G396200 chrUn 28409923 28412536 2613 True 3807 3807 92.954 553 3182 1 chrUn.!!$R1 2629
2 TraesCS4B01G396200 chr7D 629433597 629434966 1369 True 1267 1267 83.442 1208 2577 1 chr7D.!!$R2 1369
3 TraesCS4B01G396200 chr7D 28577059 28578504 1445 True 1057 1057 79.931 1078 2527 1 chr7D.!!$R1 1449
4 TraesCS4B01G396200 chr1A 32111214 32112659 1445 False 1212 1212 81.806 1078 2527 1 chr1A.!!$F1 1449
5 TraesCS4B01G396200 chr4A 702326291 702327739 1448 True 1118 1118 80.672 1078 2530 1 chr4A.!!$R1 1452
6 TraesCS4B01G396200 chr7A 29007738 29009186 1448 True 1107 1107 80.495 1078 2530 1 chr7A.!!$R3 1452
7 TraesCS4B01G396200 chr7A 28967519 28968967 1448 True 1090 1090 80.302 1078 2530 1 chr7A.!!$R2 1452
8 TraesCS4B01G396200 chr7A 28807421 28808870 1449 True 1079 1079 80.165 1078 2530 1 chr7A.!!$R1 1452
9 TraesCS4B01G396200 chr2B 742171230 742172678 1448 True 1096 1096 80.371 1078 2530 1 chr2B.!!$R2 1452
10 TraesCS4B01G396200 chr2B 765299961 765300512 551 True 800 800 92.780 1 554 1 chr2B.!!$R3 553
11 TraesCS4B01G396200 chr5B 300846078 300846625 547 True 861 861 94.937 1 553 1 chr5B.!!$R1 552
12 TraesCS4B01G396200 chr2A 610172038 610172588 550 True 811 811 93.153 1 555 1 chr2A.!!$R1 554
13 TraesCS4B01G396200 chr3B 612713147 612713698 551 False 798 798 92.780 1 553 1 chr3B.!!$F1 552
14 TraesCS4B01G396200 chr3B 85454983 85455540 557 True 778 778 91.950 1 554 1 chr3B.!!$R2 553
15 TraesCS4B01G396200 chr3B 68356442 68356973 531 True 619 619 87.523 1 553 1 chr3B.!!$R1 552
16 TraesCS4B01G396200 chr7B 732577726 732578232 506 True 337 337 78.740 1208 1713 1 chr7B.!!$R1 505

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
844 855 0.996583 TAACAAGTGTCCCCATCCCC 59.003 55.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2259 0.313672 TTCGAACAACTTGGCCATGC 59.686 50.0 18.17 0.0 0.0 4.06 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
296 300 2.221055 ACGAGATGTGCGTGTCTTTTTC 59.779 45.455 0.00 0.00 40.94 2.29
474 482 4.809496 CATGCGCTTCCCTGCCCT 62.809 66.667 9.73 0.00 0.00 5.19
543 552 1.863491 GTTGCAACGCACGGACATA 59.137 52.632 14.90 0.00 38.71 2.29
545 554 1.661617 GTTGCAACGCACGGACATATA 59.338 47.619 14.90 0.00 38.71 0.86
575 584 5.827568 AAATAACAAAAGCAGAACGCATG 57.172 34.783 0.00 0.00 46.13 4.06
576 585 2.138596 AACAAAAGCAGAACGCATGG 57.861 45.000 0.00 0.00 46.13 3.66
608 617 2.025510 CAGAAGGAAAGAGGGATTGGCT 60.026 50.000 0.00 0.00 0.00 4.75
710 721 1.197430 AGCTCCCAGAACAGTCCAGG 61.197 60.000 0.00 0.00 0.00 4.45
711 722 1.194781 GCTCCCAGAACAGTCCAGGA 61.195 60.000 0.00 0.00 0.00 3.86
739 750 2.104859 CACAGCACGCATCTCAGGG 61.105 63.158 0.00 0.00 0.00 4.45
785 796 8.017418 ACTGACTGAACCAAAATTAAAATCCA 57.983 30.769 0.00 0.00 0.00 3.41
786 797 8.143835 ACTGACTGAACCAAAATTAAAATCCAG 58.856 33.333 0.00 0.00 0.00 3.86
787 798 7.441017 TGACTGAACCAAAATTAAAATCCAGG 58.559 34.615 0.00 0.00 0.00 4.45
788 799 6.768483 ACTGAACCAAAATTAAAATCCAGGG 58.232 36.000 0.00 0.00 0.00 4.45
789 800 6.120507 TGAACCAAAATTAAAATCCAGGGG 57.879 37.500 0.00 0.00 0.00 4.79
790 801 5.846714 TGAACCAAAATTAAAATCCAGGGGA 59.153 36.000 0.00 0.00 35.55 4.81
791 802 5.755409 ACCAAAATTAAAATCCAGGGGAC 57.245 39.130 0.00 0.00 32.98 4.46
792 803 5.411493 ACCAAAATTAAAATCCAGGGGACT 58.589 37.500 0.00 0.00 46.44 3.85
793 804 5.849475 ACCAAAATTAAAATCCAGGGGACTT 59.151 36.000 0.00 0.00 40.21 3.01
834 845 8.771920 TTCATCGAAGTTCATATAACAAGTGT 57.228 30.769 3.32 0.00 0.00 3.55
835 846 8.407457 TCATCGAAGTTCATATAACAAGTGTC 57.593 34.615 3.32 0.00 0.00 3.67
836 847 7.491372 TCATCGAAGTTCATATAACAAGTGTCC 59.509 37.037 3.32 0.00 0.00 4.02
837 848 6.103997 TCGAAGTTCATATAACAAGTGTCCC 58.896 40.000 3.32 0.00 0.00 4.46
838 849 5.293569 CGAAGTTCATATAACAAGTGTCCCC 59.706 44.000 3.32 0.00 0.00 4.81
839 850 5.772393 AGTTCATATAACAAGTGTCCCCA 57.228 39.130 0.00 0.00 0.00 4.96
840 851 6.327386 AGTTCATATAACAAGTGTCCCCAT 57.673 37.500 0.00 0.00 0.00 4.00
841 852 6.357367 AGTTCATATAACAAGTGTCCCCATC 58.643 40.000 0.00 0.00 0.00 3.51
842 853 5.304686 TCATATAACAAGTGTCCCCATCC 57.695 43.478 0.00 0.00 0.00 3.51
843 854 4.104102 TCATATAACAAGTGTCCCCATCCC 59.896 45.833 0.00 0.00 0.00 3.85
844 855 0.996583 TAACAAGTGTCCCCATCCCC 59.003 55.000 0.00 0.00 0.00 4.81
845 856 1.071314 AACAAGTGTCCCCATCCCCA 61.071 55.000 0.00 0.00 0.00 4.96
846 857 1.000896 CAAGTGTCCCCATCCCCAC 60.001 63.158 0.00 0.00 0.00 4.61
847 858 1.151587 AAGTGTCCCCATCCCCACT 60.152 57.895 0.00 0.00 39.73 4.00
1071 1086 1.008194 CGACGACGTGAAGGAACCA 60.008 57.895 4.58 0.00 34.56 3.67
1234 1249 2.588877 CGCCAACCTATCCCGCAG 60.589 66.667 0.00 0.00 0.00 5.18
1323 1338 1.797025 ACTTCTTCGCTTTCTTCCCG 58.203 50.000 0.00 0.00 0.00 5.14
1452 1468 2.464459 GCTTAACTGGCTCGCGCAT 61.464 57.895 8.75 0.00 38.10 4.73
1890 1909 3.446570 GCTGCATCCTTTGGCGCT 61.447 61.111 7.64 0.00 0.00 5.92
2181 2200 2.031012 CGTGGGCTCAAGCTGTGA 59.969 61.111 1.46 0.00 41.70 3.58
2195 2214 0.736636 CTGTGAATGGTCATGCGCAT 59.263 50.000 19.28 19.28 36.36 4.73
2238 2257 0.460109 AGCACATTCGCAGCGATGTA 60.460 50.000 20.32 3.80 35.23 2.29
2240 2259 1.593070 GCACATTCGCAGCGATGTAAG 60.593 52.381 20.32 13.88 35.23 2.34
2266 2286 2.833794 CCAAGTTGTTCGAAGGTCTCA 58.166 47.619 0.00 0.00 0.00 3.27
2458 2478 0.036010 CAACAGGATCTTGCTCCGGT 60.036 55.000 4.46 0.00 44.29 5.28
2491 2511 0.805614 CGTCGCTTCAAGAGGAGAGA 59.194 55.000 0.00 0.00 0.00 3.10
2533 2553 2.419297 GCTCATCAAGAGGACGACCAAT 60.419 50.000 6.71 0.00 44.86 3.16
2541 2561 2.232452 AGAGGACGACCAATGACTTGAG 59.768 50.000 6.71 0.00 38.94 3.02
2577 2598 7.175467 AGTGTGTGCATTCATAGAGAATTTGAA 59.825 33.333 0.00 0.00 44.48 2.69
2633 2654 5.991328 ATGCTCGACAATTGTAATACAGG 57.009 39.130 11.95 0.00 0.00 4.00
2637 2658 5.681437 GCTCGACAATTGTAATACAGGGAGA 60.681 44.000 11.95 0.00 0.00 3.71
2639 2660 6.513180 TCGACAATTGTAATACAGGGAGATC 58.487 40.000 11.95 0.00 0.00 2.75
2644 2665 8.894592 ACAATTGTAATACAGGGAGATCCATAT 58.105 33.333 9.97 0.00 38.24 1.78
2653 2674 5.308237 ACAGGGAGATCCATATTACAACCTC 59.692 44.000 0.47 0.00 38.24 3.85
2654 2675 5.307976 CAGGGAGATCCATATTACAACCTCA 59.692 44.000 0.47 0.00 38.24 3.86
2655 2676 5.308237 AGGGAGATCCATATTACAACCTCAC 59.692 44.000 0.47 0.00 38.24 3.51
2656 2677 5.071788 GGGAGATCCATATTACAACCTCACA 59.928 44.000 0.47 0.00 37.91 3.58
2658 2679 7.038302 GGGAGATCCATATTACAACCTCACATA 60.038 40.741 0.47 0.00 37.91 2.29
2699 2752 5.186021 ACAACCTCACATACAAAACCAAACA 59.814 36.000 0.00 0.00 0.00 2.83
2727 2780 4.095782 TCAACCTTTCTCAAGTCAAAACCG 59.904 41.667 0.00 0.00 0.00 4.44
2728 2781 2.949644 ACCTTTCTCAAGTCAAAACCGG 59.050 45.455 0.00 0.00 0.00 5.28
2729 2782 2.949644 CCTTTCTCAAGTCAAAACCGGT 59.050 45.455 0.00 0.00 0.00 5.28
2730 2783 3.380320 CCTTTCTCAAGTCAAAACCGGTT 59.620 43.478 15.86 15.86 0.00 4.44
2731 2784 4.142249 CCTTTCTCAAGTCAAAACCGGTTT 60.142 41.667 26.87 26.87 0.00 3.27
2732 2785 5.066764 CCTTTCTCAAGTCAAAACCGGTTTA 59.933 40.000 31.80 15.67 31.63 2.01
2733 2786 6.238925 CCTTTCTCAAGTCAAAACCGGTTTAT 60.239 38.462 31.80 18.85 31.63 1.40
2734 2787 5.934935 TCTCAAGTCAAAACCGGTTTATC 57.065 39.130 31.80 22.64 31.63 1.75
2735 2788 4.758165 TCTCAAGTCAAAACCGGTTTATCC 59.242 41.667 31.80 20.78 31.63 2.59
2736 2789 3.822167 TCAAGTCAAAACCGGTTTATCCC 59.178 43.478 31.80 19.14 31.63 3.85
2737 2790 3.801307 AGTCAAAACCGGTTTATCCCT 57.199 42.857 31.80 20.87 31.63 4.20
2738 2791 3.418047 AGTCAAAACCGGTTTATCCCTG 58.582 45.455 31.80 24.39 31.63 4.45
2739 2792 3.151554 GTCAAAACCGGTTTATCCCTGT 58.848 45.455 31.80 12.58 31.63 4.00
2740 2793 3.570975 GTCAAAACCGGTTTATCCCTGTT 59.429 43.478 31.80 11.81 31.63 3.16
2741 2794 4.038282 GTCAAAACCGGTTTATCCCTGTTT 59.962 41.667 31.80 11.05 38.48 2.83
2742 2795 4.650131 TCAAAACCGGTTTATCCCTGTTTT 59.350 37.500 31.80 10.28 42.81 2.43
2743 2796 5.832060 TCAAAACCGGTTTATCCCTGTTTTA 59.168 36.000 31.80 8.16 41.49 1.52
2744 2797 5.710513 AAACCGGTTTATCCCTGTTTTAC 57.289 39.130 30.76 0.00 35.51 2.01
2745 2798 4.645863 ACCGGTTTATCCCTGTTTTACT 57.354 40.909 0.00 0.00 0.00 2.24
2746 2799 4.329392 ACCGGTTTATCCCTGTTTTACTG 58.671 43.478 0.00 0.00 0.00 2.74
2747 2800 3.692593 CCGGTTTATCCCTGTTTTACTGG 59.307 47.826 0.00 0.00 37.01 4.00
2748 2801 4.329392 CGGTTTATCCCTGTTTTACTGGT 58.671 43.478 0.00 0.00 35.67 4.00
2749 2802 4.763279 CGGTTTATCCCTGTTTTACTGGTT 59.237 41.667 0.00 0.00 35.67 3.67
2750 2803 5.242171 CGGTTTATCCCTGTTTTACTGGTTT 59.758 40.000 0.00 0.00 35.67 3.27
2751 2804 6.239092 CGGTTTATCCCTGTTTTACTGGTTTT 60.239 38.462 0.00 0.00 35.67 2.43
2752 2805 6.926826 GGTTTATCCCTGTTTTACTGGTTTTG 59.073 38.462 0.00 0.00 35.67 2.44
2753 2806 7.201929 GGTTTATCCCTGTTTTACTGGTTTTGA 60.202 37.037 0.00 0.00 35.67 2.69
2754 2807 5.784578 ATCCCTGTTTTACTGGTTTTGAC 57.215 39.130 0.00 0.00 35.67 3.18
2755 2808 3.955551 TCCCTGTTTTACTGGTTTTGACC 59.044 43.478 0.00 0.00 35.67 4.02
2822 2875 2.949644 CCCGAAATATGAAAGTCACCCC 59.050 50.000 0.00 0.00 0.00 4.95
2833 2886 2.285069 TCACCCCGCCACATAGGT 60.285 61.111 0.00 0.00 40.61 3.08
2839 2892 0.608640 CCCGCCACATAGGTATCCTC 59.391 60.000 0.00 0.00 40.61 3.71
2867 2920 1.621814 AGATGGTTTCGAAGTTCGGGA 59.378 47.619 24.18 11.29 40.88 5.14
2883 2936 7.342769 AGTTCGGGATTGTTCTTAAACTTTT 57.657 32.000 0.00 0.00 36.30 2.27
2915 2968 5.428253 TCAGGGTTGTAATATGTGCTTCTC 58.572 41.667 0.00 0.00 0.00 2.87
2934 2987 6.018994 GCTTCTCTCTTTGTAACACGAAAAGA 60.019 38.462 0.00 0.00 37.54 2.52
2999 3062 6.199937 CCTTATATTCAAGGCATATGCACC 57.800 41.667 28.07 12.58 44.36 5.01
3016 3079 2.954868 CGCTCGCGACGCCTTATT 60.955 61.111 15.34 0.00 42.83 1.40
3031 3094 3.139211 GCCTTATTCCCTCCCAATCTTCT 59.861 47.826 0.00 0.00 0.00 2.85
3037 3100 1.493871 CCCTCCCAATCTTCTGCATCT 59.506 52.381 0.00 0.00 0.00 2.90
3042 3105 2.172082 CCCAATCTTCTGCATCTCCTCA 59.828 50.000 0.00 0.00 0.00 3.86
3051 3114 3.773667 TCTGCATCTCCTCATTTCTGTCT 59.226 43.478 0.00 0.00 0.00 3.41
3054 3117 4.224594 TGCATCTCCTCATTTCTGTCTCTT 59.775 41.667 0.00 0.00 0.00 2.85
3069 3132 0.994995 CTCTTCCAACATCGACGCAG 59.005 55.000 0.00 0.00 0.00 5.18
3073 3136 0.602638 TCCAACATCGACGCAGCTTT 60.603 50.000 0.00 0.00 0.00 3.51
3086 3149 1.003233 AGCTTTCCTTCTCGTGCCC 60.003 57.895 0.00 0.00 0.00 5.36
3097 3160 4.148825 CGTGCCCCTCTCCTTCCG 62.149 72.222 0.00 0.00 0.00 4.30
3179 3242 0.394899 CCAGCACCCTTTCATCCTCC 60.395 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
296 300 6.019479 GCATTTCACGTAGAAGGTATTCTCTG 60.019 42.308 0.00 0.00 42.25 3.35
378 384 5.796935 GCATGCGTGGATATTGAATTGATAC 59.203 40.000 8.27 0.00 0.00 2.24
440 447 3.243877 CGCATGTCGAGGTATCAAAGAAG 59.756 47.826 3.85 0.00 41.67 2.85
545 554 7.962918 CGTTCTGCTTTTGTTATTTACTAGCAT 59.037 33.333 0.00 0.00 36.51 3.79
575 584 6.980978 CCTCTTTCCTTCTGTTTTTCTTTTCC 59.019 38.462 0.00 0.00 0.00 3.13
576 585 6.980978 CCCTCTTTCCTTCTGTTTTTCTTTTC 59.019 38.462 0.00 0.00 0.00 2.29
608 617 1.071071 GCCCATTACATGTACCGCCTA 59.929 52.381 4.68 0.00 0.00 3.93
678 689 2.116125 GAGCTGGGTTTGGGCTGT 59.884 61.111 0.00 0.00 36.37 4.40
739 750 4.631813 AGTTTCTCGGCTGTTGATTCATAC 59.368 41.667 0.00 0.00 0.00 2.39
785 796 4.295905 TGATTCATACCCTAAGTCCCCT 57.704 45.455 0.00 0.00 0.00 4.79
786 797 5.382664 TTTGATTCATACCCTAAGTCCCC 57.617 43.478 0.00 0.00 0.00 4.81
787 798 7.060421 TGAATTTGATTCATACCCTAAGTCCC 58.940 38.462 0.00 0.00 43.84 4.46
833 844 1.616628 AGTCAGTGGGGATGGGGAC 60.617 63.158 0.00 0.00 0.00 4.46
834 845 1.616327 CAGTCAGTGGGGATGGGGA 60.616 63.158 0.00 0.00 0.00 4.81
835 846 2.683465 CCAGTCAGTGGGGATGGGG 61.683 68.421 0.00 0.00 43.63 4.96
836 847 3.001514 CCAGTCAGTGGGGATGGG 58.998 66.667 0.00 0.00 43.63 4.00
923 934 2.633509 GGGAGTGCTTGCTTGCTGG 61.634 63.158 3.47 0.00 0.00 4.85
924 935 2.960170 GGGAGTGCTTGCTTGCTG 59.040 61.111 3.47 0.00 0.00 4.41
926 937 4.410743 GCGGGAGTGCTTGCTTGC 62.411 66.667 0.00 0.00 0.00 4.01
1071 1086 2.516225 GGCTTAAGCGGCCGGAAT 60.516 61.111 29.38 2.70 43.26 3.01
1122 1137 3.377485 TGTAGTAGTCGCAGATGAAGTCC 59.623 47.826 0.00 0.00 40.67 3.85
1452 1468 3.706373 GCGGGCAGGTGAAGGAGA 61.706 66.667 0.00 0.00 0.00 3.71
1594 1613 1.728971 GCCAAACACTCTCACAGATCG 59.271 52.381 0.00 0.00 0.00 3.69
1616 1635 0.109412 GTAGACAACCAGACCCGACG 60.109 60.000 0.00 0.00 0.00 5.12
1618 1637 1.870055 GCGTAGACAACCAGACCCGA 61.870 60.000 0.00 0.00 0.00 5.14
1890 1909 4.651008 GCGTCGACGTGGACCCAA 62.651 66.667 35.48 0.00 42.22 4.12
1962 1981 2.643272 GAGTCCACGCACTCGACA 59.357 61.111 0.00 0.00 39.41 4.35
1969 1988 2.265739 GCTGATGGAGTCCACGCA 59.734 61.111 15.86 14.77 35.80 5.24
2181 2200 2.156917 CCATAGATGCGCATGACCATT 58.843 47.619 30.76 1.03 0.00 3.16
2238 2257 0.314935 CGAACAACTTGGCCATGCTT 59.685 50.000 18.17 9.13 0.00 3.91
2240 2259 0.313672 TTCGAACAACTTGGCCATGC 59.686 50.000 18.17 0.00 0.00 4.06
2440 2460 0.693049 AACCGGAGCAAGATCCTGTT 59.307 50.000 9.46 8.12 40.66 3.16
2458 2478 2.592287 GACGACCCCACCGCAAAA 60.592 61.111 0.00 0.00 0.00 2.44
2491 2511 1.004560 CCATGCACTCCTCACGTGT 60.005 57.895 16.51 0.00 34.91 4.49
2533 2553 5.013079 ACACACTTAATCCATCCTCAAGTCA 59.987 40.000 0.00 0.00 0.00 3.41
2541 2561 4.398988 TGAATGCACACACTTAATCCATCC 59.601 41.667 0.00 0.00 0.00 3.51
2592 2613 8.130469 TCGAGCATATAAATAGTCGTGTGTTTA 58.870 33.333 0.00 0.00 0.00 2.01
2611 2632 4.816385 CCCTGTATTACAATTGTCGAGCAT 59.184 41.667 15.85 3.66 0.00 3.79
2615 2636 5.925506 TCTCCCTGTATTACAATTGTCGA 57.074 39.130 15.85 5.67 0.00 4.20
2630 2651 5.307976 TGAGGTTGTAATATGGATCTCCCTG 59.692 44.000 0.00 0.00 35.38 4.45
2633 2654 6.174720 TGTGAGGTTGTAATATGGATCTCC 57.825 41.667 0.00 0.00 0.00 3.71
2637 2658 9.693739 TTTTGTATGTGAGGTTGTAATATGGAT 57.306 29.630 0.00 0.00 0.00 3.41
2639 2660 8.188139 GGTTTTGTATGTGAGGTTGTAATATGG 58.812 37.037 0.00 0.00 0.00 2.74
2644 2665 5.124645 ACGGTTTTGTATGTGAGGTTGTAA 58.875 37.500 0.00 0.00 0.00 2.41
2653 2674 7.410800 TGTAAAGTAGACGGTTTTGTATGTG 57.589 36.000 0.00 0.00 0.00 3.21
2654 2675 7.041848 GGTTGTAAAGTAGACGGTTTTGTATGT 60.042 37.037 0.00 0.00 0.00 2.29
2655 2676 7.172019 AGGTTGTAAAGTAGACGGTTTTGTATG 59.828 37.037 0.00 0.00 0.00 2.39
2656 2677 7.219322 AGGTTGTAAAGTAGACGGTTTTGTAT 58.781 34.615 0.00 0.00 0.00 2.29
2658 2679 5.430886 AGGTTGTAAAGTAGACGGTTTTGT 58.569 37.500 0.00 0.00 0.00 2.83
2699 2752 8.935844 GTTTTGACTTGAGAAAGGTTGATTTTT 58.064 29.630 0.00 0.00 0.00 1.94
2727 2780 6.659745 AAACCAGTAAAACAGGGATAAACC 57.340 37.500 0.00 0.00 38.08 3.27
2728 2781 7.650504 GTCAAAACCAGTAAAACAGGGATAAAC 59.349 37.037 0.00 0.00 0.00 2.01
2729 2782 7.201929 GGTCAAAACCAGTAAAACAGGGATAAA 60.202 37.037 0.00 0.00 45.68 1.40
2730 2783 6.265876 GGTCAAAACCAGTAAAACAGGGATAA 59.734 38.462 0.00 0.00 45.68 1.75
2731 2784 5.771165 GGTCAAAACCAGTAAAACAGGGATA 59.229 40.000 0.00 0.00 45.68 2.59
2732 2785 4.587262 GGTCAAAACCAGTAAAACAGGGAT 59.413 41.667 0.00 0.00 45.68 3.85
2733 2786 3.955551 GGTCAAAACCAGTAAAACAGGGA 59.044 43.478 0.00 0.00 45.68 4.20
2734 2787 4.316205 GGTCAAAACCAGTAAAACAGGG 57.684 45.455 0.00 0.00 45.68 4.45
2750 2803 3.788227 ACTAGGCATTTGACTGGTCAA 57.212 42.857 11.53 11.53 41.34 3.18
2754 2807 2.012673 GCTGACTAGGCATTTGACTGG 58.987 52.381 0.00 0.00 37.70 4.00
2755 2808 2.703416 TGCTGACTAGGCATTTGACTG 58.297 47.619 0.00 0.00 33.72 3.51
2822 2875 0.959553 ACGAGGATACCTATGTGGCG 59.040 55.000 0.00 0.00 40.22 5.69
2833 2886 6.543465 TCGAAACCATCTAGTTTACGAGGATA 59.457 38.462 0.00 0.00 40.01 2.59
2839 2892 6.452090 CGAACTTCGAAACCATCTAGTTTACG 60.452 42.308 5.15 0.00 43.74 3.18
2883 2936 8.303156 CACATATTACAACCCTGAATTGTCAAA 58.697 33.333 0.00 0.00 40.68 2.69
2915 2968 7.461107 TCAGTTTCTTTTCGTGTTACAAAGAG 58.539 34.615 0.00 0.00 37.72 2.85
2934 2987 2.750237 GGCCGCCCGATTCAGTTT 60.750 61.111 0.00 0.00 0.00 2.66
2999 3062 2.917656 GAATAAGGCGTCGCGAGCG 61.918 63.158 10.24 17.64 41.35 5.03
3010 3073 4.723309 CAGAAGATTGGGAGGGAATAAGG 58.277 47.826 0.00 0.00 0.00 2.69
3016 3079 1.492176 GATGCAGAAGATTGGGAGGGA 59.508 52.381 0.00 0.00 0.00 4.20
3031 3094 3.773667 AGAGACAGAAATGAGGAGATGCA 59.226 43.478 0.00 0.00 0.00 3.96
3037 3100 4.347876 TGTTGGAAGAGACAGAAATGAGGA 59.652 41.667 0.00 0.00 0.00 3.71
3042 3105 4.932200 GTCGATGTTGGAAGAGACAGAAAT 59.068 41.667 0.00 0.00 0.00 2.17
3051 3114 1.014044 GCTGCGTCGATGTTGGAAGA 61.014 55.000 6.48 0.00 0.00 2.87
3054 3117 0.602638 AAAGCTGCGTCGATGTTGGA 60.603 50.000 6.48 0.00 0.00 3.53
3069 3132 2.041115 GGGGCACGAGAAGGAAAGC 61.041 63.158 0.00 0.00 0.00 3.51
3073 3136 1.682684 GAGAGGGGCACGAGAAGGA 60.683 63.158 0.00 0.00 0.00 3.36
3097 3160 1.349067 ACCTTGTGGTAGAGGTGACC 58.651 55.000 0.00 0.00 46.43 4.02
3123 3186 2.568090 GCATTGTTGTGAGCCGGG 59.432 61.111 2.18 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.