Multiple sequence alignment - TraesCS7D01G344500

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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 TraesCS7D01G344500 chr7D 100.000 5492 0 0 1 5492 442197936 442203427 0.000000e+00 10142.0
1 TraesCS7D01G344500 chr7D 86.515 749 101 0 3 751 528098032 528097284 0.000000e+00 824.0
2 TraesCS7D01G344500 chr7D 86.851 578 73 3 176 751 89954426 89955002 1.290000e-180 643.0
3 TraesCS7D01G344500 chr7B 94.292 2190 64 14 746 2905 458781581 458783739 0.000000e+00 3295.0
4 TraesCS7D01G344500 chr7B 97.756 1025 18 3 3498 4518 458786297 458787320 0.000000e+00 1760.0
5 TraesCS7D01G344500 chr7B 93.624 643 24 4 4546 5188 458787309 458787934 0.000000e+00 944.0
6 TraesCS7D01G344500 chr7B 96.464 509 8 5 2918 3420 458783725 458784229 0.000000e+00 832.0
7 TraesCS7D01G344500 chr7B 89.189 296 23 6 5180 5470 458787964 458788255 1.450000e-95 361.0
8 TraesCS7D01G344500 chr7B 98.837 86 1 0 3414 3499 458786118 458786203 2.650000e-33 154.0
9 TraesCS7D01G344500 chr7B 100.000 29 0 0 5464 5492 458788606 458788634 3.000000e-03 54.7
10 TraesCS7D01G344500 chr7A 91.857 2149 112 30 3066 5179 493087903 493090023 0.000000e+00 2940.0
11 TraesCS7D01G344500 chr7A 90.583 2283 113 43 826 3054 493085694 493087928 0.000000e+00 2931.0
12 TraesCS7D01G344500 chr7A 80.982 326 41 11 5180 5492 493090075 493090392 7.110000e-59 239.0
13 TraesCS7D01G344500 chr2B 94.267 750 43 0 3 752 584735761 584735012 0.000000e+00 1147.0
14 TraesCS7D01G344500 chr2B 89.655 58 6 0 4407 4464 386497035 386497092 2.120000e-09 75.0
15 TraesCS7D01G344500 chr2B 87.500 64 3 1 2915 2978 227853300 227853358 9.870000e-08 69.4
16 TraesCS7D01G344500 chr5A 86.382 749 102 0 3 751 30030262 30029514 0.000000e+00 819.0
17 TraesCS7D01G344500 chr5A 85.581 749 108 0 3 751 491576812 491576064 0.000000e+00 785.0
18 TraesCS7D01G344500 chr5A 84.685 111 17 0 5382 5492 320212314 320212204 1.620000e-20 111.0
19 TraesCS7D01G344500 chr5A 77.941 136 24 6 5353 5485 595496948 595496816 4.560000e-11 80.5
20 TraesCS7D01G344500 chr5A 89.831 59 1 2 2920 2978 395056152 395056099 2.740000e-08 71.3
21 TraesCS7D01G344500 chr5D 83.099 142 21 3 5352 5492 234147093 234147232 5.780000e-25 126.0
22 TraesCS7D01G344500 chr5D 91.228 57 1 1 2922 2978 473790976 473790924 2.120000e-09 75.0
23 TraesCS7D01G344500 chr2D 92.045 88 2 1 2891 2978 226598411 226598329 9.660000e-23 119.0
24 TraesCS7D01G344500 chr2D 92.045 88 2 1 2891 2978 643593209 643593291 9.660000e-23 119.0
25 TraesCS7D01G344500 chr2D 91.667 48 4 0 4417 4464 318404986 318405033 3.550000e-07 67.6
26 TraesCS7D01G344500 chr4A 88.172 93 11 0 5399 5491 191414890 191414982 1.620000e-20 111.0
27 TraesCS7D01G344500 chr1D 91.892 74 1 1 2905 2978 352662585 352662517 1.260000e-16 99.0
28 TraesCS7D01G344500 chr2A 93.750 64 1 1 4487 4547 413187474 413187537 5.860000e-15 93.5
29 TraesCS7D01G344500 chrUn 89.610 77 1 3 2904 2978 87273717 87273788 2.110000e-14 91.6
30 TraesCS7D01G344500 chr1B 91.429 70 1 1 2909 2978 119963105 119963169 2.110000e-14 91.6
31 TraesCS7D01G344500 chr4B 89.286 56 6 0 5436 5491 367280498 367280443 2.740000e-08 71.3
32 TraesCS7D01G344500 chr3D 84.507 71 11 0 6 76 584469753 584469683 2.740000e-08 71.3
33 TraesCS7D01G344500 chr3A 94.286 35 2 0 5451 5485 80278890 80278924 3.000000e-03 54.7


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 TraesCS7D01G344500 chr7D 442197936 442203427 5491 False 10142.000000 10142 100.000000 1 5492 1 chr7D.!!$F2 5491
1 TraesCS7D01G344500 chr7D 528097284 528098032 748 True 824.000000 824 86.515000 3 751 1 chr7D.!!$R1 748
2 TraesCS7D01G344500 chr7D 89954426 89955002 576 False 643.000000 643 86.851000 176 751 1 chr7D.!!$F1 575
3 TraesCS7D01G344500 chr7B 458781581 458788634 7053 False 1057.242857 3295 95.737429 746 5492 7 chr7B.!!$F1 4746
4 TraesCS7D01G344500 chr7A 493085694 493090392 4698 False 2036.666667 2940 87.807333 826 5492 3 chr7A.!!$F1 4666
5 TraesCS7D01G344500 chr2B 584735012 584735761 749 True 1147.000000 1147 94.267000 3 752 1 chr2B.!!$R1 749
6 TraesCS7D01G344500 chr5A 30029514 30030262 748 True 819.000000 819 86.382000 3 751 1 chr5A.!!$R1 748
7 TraesCS7D01G344500 chr5A 491576064 491576812 748 True 785.000000 785 85.581000 3 751 1 chr5A.!!$R4 748

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
51 52 0.178990 GGACCTGGAGCTTTGGTTGT 60.179 55.000 0.00 0.00 33.74 3.32 F
1444 1447 0.332972 AGAAGGAGATTTGGCCACCC 59.667 55.000 3.88 1.61 0.00 4.61 F
1763 1796 0.108472 TGACTGAGCTGCTTCATCCG 60.108 55.000 2.53 0.00 0.00 4.18 F
1864 1897 2.787129 GCGGCAACAGTGTTTTAAGTTC 59.213 45.455 5.57 0.00 0.00 3.01 F
2770 2827 3.250744 GGGTTTCCAGCTTAAAAATCGC 58.749 45.455 0.00 0.00 0.00 4.58 F
3959 6052 1.408702 GACTGCCAAACAAAAGAGCCA 59.591 47.619 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1778 0.108424 ACGGATGAAGCAGCTCAGTC 60.108 55.000 0.00 0.00 0.00 3.51 R
2779 2837 3.214328 AGTCCCATGAATAATTCGTGCC 58.786 45.455 0.00 0.00 43.66 5.01 R
3345 3423 3.389925 TTGCTTTCCCTTCAATGCAAG 57.610 42.857 0.00 0.00 39.94 4.01 R
3461 5439 8.432110 TGTATCATGTAACTCGCAACATTAAT 57.568 30.769 0.00 0.00 34.12 1.40 R
4131 6224 2.361119 AGAACTCACGCTGTACTTGTGA 59.639 45.455 12.57 12.57 40.12 3.58 R
5047 7150 1.075542 TGTATTTCTCTTGCACGCCG 58.924 50.000 0.00 0.00 0.00 6.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.455383 AAAACTGTGCAGGGAAGCCG 61.455 55.000 4.11 0.00 0.00 5.52
51 52 0.178990 GGACCTGGAGCTTTGGTTGT 60.179 55.000 0.00 0.00 33.74 3.32
101 102 2.871133 CAGCATTTGTGTATGGTGCAG 58.129 47.619 0.00 0.00 44.18 4.41
107 108 5.745294 GCATTTGTGTATGGTGCAGATAAAG 59.255 40.000 0.00 0.00 35.93 1.85
121 122 4.742659 GCAGATAAAGTCTCGTTCATCTCC 59.257 45.833 0.00 0.00 34.00 3.71
124 125 1.835494 AAGTCTCGTTCATCTCCGGA 58.165 50.000 2.93 2.93 0.00 5.14
137 138 1.356738 TCTCCGGAGTAACCTTCCTCA 59.643 52.381 30.17 4.05 36.31 3.86
287 288 4.580580 GTGCCCGGATCATATTCTTCTTTT 59.419 41.667 0.73 0.00 0.00 2.27
369 370 2.835431 CCGGGATCTCTGACGCCT 60.835 66.667 0.00 0.00 0.00 5.52
454 455 1.298413 CCTCGTACGCACTGGATCG 60.298 63.158 11.24 0.00 0.00 3.69
494 495 6.122964 AGTTGGGTCTTTATCTGCTTTATCC 58.877 40.000 0.00 0.00 0.00 2.59
530 531 2.038033 CCGAAAGTTTCCCTACTCCACA 59.962 50.000 10.01 0.00 0.00 4.17
586 587 1.129058 GGAAGTCACCGACCCCATAT 58.871 55.000 0.00 0.00 32.18 1.78
588 589 0.750850 AAGTCACCGACCCCATATCG 59.249 55.000 0.00 0.00 39.33 2.92
700 701 3.361917 GCTTTGTATTGTTTTGTGCAGCG 60.362 43.478 0.00 0.00 0.00 5.18
976 977 2.703007 CAATCGATCCCCTTCTTCTCCT 59.297 50.000 0.00 0.00 0.00 3.69
1162 1163 1.133668 AGGCCTGCAAGTTCAAGAAGT 60.134 47.619 3.11 0.00 0.00 3.01
1163 1164 1.683385 GGCCTGCAAGTTCAAGAAGTT 59.317 47.619 0.00 0.00 34.50 2.66
1202 1203 2.268920 GAGAAGCCGATGCACCCA 59.731 61.111 0.00 0.00 41.13 4.51
1444 1447 0.332972 AGAAGGAGATTTGGCCACCC 59.667 55.000 3.88 1.61 0.00 4.61
1463 1466 5.645497 CCACCCTGTTTAGATCTTTCTTCAG 59.355 44.000 0.00 3.63 33.17 3.02
1470 1484 7.386851 TGTTTAGATCTTTCTTCAGTACCCAG 58.613 38.462 0.00 0.00 33.17 4.45
1520 1534 1.064758 TGATTTCTGGGGATTCCGTGG 60.065 52.381 0.00 0.00 38.76 4.94
1595 1613 7.296628 AGTACAATCTTGCTCTATTCCCTAG 57.703 40.000 0.00 0.00 0.00 3.02
1763 1796 0.108472 TGACTGAGCTGCTTCATCCG 60.108 55.000 2.53 0.00 0.00 4.18
1864 1897 2.787129 GCGGCAACAGTGTTTTAAGTTC 59.213 45.455 5.57 0.00 0.00 3.01
2051 2084 5.625150 GACATTCCCCATAATAGCAAGACT 58.375 41.667 0.00 0.00 0.00 3.24
2052 2085 5.625150 ACATTCCCCATAATAGCAAGACTC 58.375 41.667 0.00 0.00 0.00 3.36
2053 2086 5.132648 ACATTCCCCATAATAGCAAGACTCA 59.867 40.000 0.00 0.00 0.00 3.41
2054 2087 5.708736 TTCCCCATAATAGCAAGACTCAA 57.291 39.130 0.00 0.00 0.00 3.02
2055 2088 5.708736 TCCCCATAATAGCAAGACTCAAA 57.291 39.130 0.00 0.00 0.00 2.69
2056 2089 6.073447 TCCCCATAATAGCAAGACTCAAAA 57.927 37.500 0.00 0.00 0.00 2.44
2430 2463 4.851639 AATCCTTCTTCCATAGTGCAGT 57.148 40.909 0.00 0.00 0.00 4.40
2670 2704 7.972832 TTAGTGGTTTGATCTTATCGTTGTT 57.027 32.000 0.00 0.00 0.00 2.83
2768 2825 4.882842 TGGGGTTTCCAGCTTAAAAATC 57.117 40.909 0.00 0.00 41.46 2.17
2770 2827 3.250744 GGGTTTCCAGCTTAAAAATCGC 58.749 45.455 0.00 0.00 0.00 4.58
2771 2828 3.250744 GGTTTCCAGCTTAAAAATCGCC 58.749 45.455 0.00 0.00 0.00 5.54
2772 2829 3.305744 GGTTTCCAGCTTAAAAATCGCCA 60.306 43.478 0.00 0.00 0.00 5.69
2773 2830 4.494484 GTTTCCAGCTTAAAAATCGCCAT 58.506 39.130 0.00 0.00 0.00 4.40
2774 2831 5.393678 GGTTTCCAGCTTAAAAATCGCCATA 60.394 40.000 0.00 0.00 0.00 2.74
2881 2943 6.790350 CAGTCAACATAAATCACGTACAACAC 59.210 38.462 0.00 0.00 0.00 3.32
2883 2945 7.868922 AGTCAACATAAATCACGTACAACACTA 59.131 33.333 0.00 0.00 0.00 2.74
2890 2952 6.476243 AATCACGTACAACACTAAATGTCC 57.524 37.500 0.00 0.00 42.31 4.02
2891 2953 4.946445 TCACGTACAACACTAAATGTCCA 58.054 39.130 0.00 0.00 42.31 4.02
2892 2954 5.358090 TCACGTACAACACTAAATGTCCAA 58.642 37.500 0.00 0.00 42.31 3.53
2893 2955 5.992829 TCACGTACAACACTAAATGTCCAAT 59.007 36.000 0.00 0.00 42.31 3.16
2894 2956 7.153315 TCACGTACAACACTAAATGTCCAATA 58.847 34.615 0.00 0.00 42.31 1.90
2895 2957 7.656542 TCACGTACAACACTAAATGTCCAATAA 59.343 33.333 0.00 0.00 42.31 1.40
2896 2958 7.742963 CACGTACAACACTAAATGTCCAATAAC 59.257 37.037 0.00 0.00 42.31 1.89
2897 2959 7.441760 ACGTACAACACTAAATGTCCAATAACA 59.558 33.333 0.00 0.00 42.31 2.41
2898 2960 8.283992 CGTACAACACTAAATGTCCAATAACAA 58.716 33.333 0.00 0.00 42.31 2.83
2899 2961 9.389570 GTACAACACTAAATGTCCAATAACAAC 57.610 33.333 0.00 0.00 42.31 3.32
2900 2962 8.001881 ACAACACTAAATGTCCAATAACAACA 57.998 30.769 0.00 0.00 42.31 3.33
2901 2963 8.470805 ACAACACTAAATGTCCAATAACAACAA 58.529 29.630 0.00 0.00 42.31 2.83
2902 2964 8.751335 CAACACTAAATGTCCAATAACAACAAC 58.249 33.333 0.00 0.00 42.31 3.32
2903 2965 8.001881 ACACTAAATGTCCAATAACAACAACA 57.998 30.769 0.00 0.00 36.54 3.33
2904 2966 8.470805 ACACTAAATGTCCAATAACAACAACAA 58.529 29.630 0.00 0.00 36.54 2.83
2905 2967 8.751335 CACTAAATGTCCAATAACAACAACAAC 58.249 33.333 0.00 0.00 31.81 3.32
2906 2968 8.470805 ACTAAATGTCCAATAACAACAACAACA 58.529 29.630 0.00 0.00 31.81 3.33
2907 2969 9.307121 CTAAATGTCCAATAACAACAACAACAA 57.693 29.630 0.00 0.00 31.81 2.83
2908 2970 7.532682 AATGTCCAATAACAACAACAACAAC 57.467 32.000 0.00 0.00 31.81 3.32
2909 2971 6.025749 TGTCCAATAACAACAACAACAACA 57.974 33.333 0.00 0.00 0.00 3.33
2910 2972 6.455647 TGTCCAATAACAACAACAACAACAA 58.544 32.000 0.00 0.00 0.00 2.83
2911 2973 6.366332 TGTCCAATAACAACAACAACAACAAC 59.634 34.615 0.00 0.00 0.00 3.32
2912 2974 6.366332 GTCCAATAACAACAACAACAACAACA 59.634 34.615 0.00 0.00 0.00 3.33
2913 2975 6.929049 TCCAATAACAACAACAACAACAACAA 59.071 30.769 0.00 0.00 0.00 2.83
2914 2976 7.012358 CCAATAACAACAACAACAACAACAAC 58.988 34.615 0.00 0.00 0.00 3.32
2915 2977 7.307396 CCAATAACAACAACAACAACAACAACA 60.307 33.333 0.00 0.00 0.00 3.33
2916 2978 7.715265 ATAACAACAACAACAACAACAACAA 57.285 28.000 0.00 0.00 0.00 2.83
2984 3051 5.105064 GGGTAGCCTAGAGTTGAACATGTTA 60.105 44.000 11.95 0.00 0.00 2.41
3046 3120 6.525629 ACGATGAATAAGCCAAATAGTAGCT 58.474 36.000 0.00 0.00 38.88 3.32
3061 3135 8.821894 CAAATAGTAGCTGTAGGATCTTGTTTC 58.178 37.037 0.00 0.00 0.00 2.78
3062 3136 7.661536 ATAGTAGCTGTAGGATCTTGTTTCA 57.338 36.000 0.00 0.00 0.00 2.69
3063 3137 6.360370 AGTAGCTGTAGGATCTTGTTTCAA 57.640 37.500 0.00 0.00 0.00 2.69
3064 3138 6.769512 AGTAGCTGTAGGATCTTGTTTCAAA 58.230 36.000 0.00 0.00 0.00 2.69
3065 3139 7.224297 AGTAGCTGTAGGATCTTGTTTCAAAA 58.776 34.615 0.00 0.00 0.00 2.44
3066 3140 6.959639 AGCTGTAGGATCTTGTTTCAAAAA 57.040 33.333 0.00 0.00 0.00 1.94
3159 3237 7.951591 TCTTTTCTGCTTTTGTTTATAGGCTT 58.048 30.769 0.00 0.00 0.00 4.35
3371 3449 4.152938 GCATTGAAGGGAAAGCAAATCAAC 59.847 41.667 0.00 0.00 30.46 3.18
3461 5439 3.786368 TGGATGTGAAGTGGTCATCAA 57.214 42.857 0.00 0.00 38.90 2.57
3959 6052 1.408702 GACTGCCAAACAAAAGAGCCA 59.591 47.619 0.00 0.00 0.00 4.75
3990 6083 3.891977 AGAAGACAGTGAGACACTTGCTA 59.108 43.478 0.00 0.00 42.59 3.49
4131 6224 9.244292 GACAATTATCTAAAGTCCTTTTCCCTT 57.756 33.333 0.00 0.00 34.23 3.95
4145 6238 1.045407 TCCCTTCACAAGTACAGCGT 58.955 50.000 0.00 0.00 0.00 5.07
4254 6347 6.874134 AGAATACTGTTTTGCACGAGAAGTAT 59.126 34.615 0.00 0.00 32.25 2.12
4449 6542 1.276989 CAAGCCAATTCCCTTGCACAT 59.723 47.619 0.00 0.00 32.94 3.21
4692 6785 5.894298 TCTAGCATATCAAGGTCATGGTT 57.106 39.130 0.00 0.00 32.92 3.67
4693 6786 6.994421 TCTAGCATATCAAGGTCATGGTTA 57.006 37.500 0.00 0.00 32.92 2.85
4694 6787 7.559335 TCTAGCATATCAAGGTCATGGTTAT 57.441 36.000 0.00 0.00 32.92 1.89
4695 6788 7.615403 TCTAGCATATCAAGGTCATGGTTATC 58.385 38.462 0.00 0.00 32.92 1.75
4696 6789 6.191657 AGCATATCAAGGTCATGGTTATCA 57.808 37.500 0.00 0.00 0.00 2.15
4697 6790 6.000219 AGCATATCAAGGTCATGGTTATCAC 59.000 40.000 0.00 0.00 0.00 3.06
4698 6791 6.000219 GCATATCAAGGTCATGGTTATCACT 59.000 40.000 0.00 0.00 0.00 3.41
4699 6792 6.488006 GCATATCAAGGTCATGGTTATCACTT 59.512 38.462 0.00 0.00 0.00 3.16
4700 6793 7.661437 GCATATCAAGGTCATGGTTATCACTTA 59.339 37.037 0.00 0.00 0.00 2.24
4701 6794 9.212641 CATATCAAGGTCATGGTTATCACTTAG 57.787 37.037 0.00 0.00 0.00 2.18
4738 6841 8.168681 ACAACTTTTGTGTGAATAAAAGAACG 57.831 30.769 14.25 6.34 43.25 3.95
4806 6909 9.562583 TTTACATTCAGTTAAACTGTTTGTGAC 57.437 29.630 15.69 10.98 46.03 3.67
4834 6937 9.403110 CATGCTTTATAATAAGACCAGAAATGC 57.597 33.333 0.00 0.00 0.00 3.56
4920 7023 5.906073 TGATGATCGTACAGACAATGTGAT 58.094 37.500 0.00 0.00 43.80 3.06
4921 7024 7.038154 TGATGATCGTACAGACAATGTGATA 57.962 36.000 0.00 0.00 43.80 2.15
4922 7025 7.661040 TGATGATCGTACAGACAATGTGATAT 58.339 34.615 0.00 0.00 43.80 1.63
4923 7026 7.596248 TGATGATCGTACAGACAATGTGATATG 59.404 37.037 0.00 0.00 43.80 1.78
5047 7150 2.111756 CTTTTTCACACAACAGCTCGC 58.888 47.619 0.00 0.00 0.00 5.03
5078 7181 9.187996 TGCAAGAGAAATACATCCATTTCATTA 57.812 29.630 10.29 0.00 44.09 1.90
5167 7278 5.860941 TTTACCAAAAGATCAACCAAGCA 57.139 34.783 0.00 0.00 0.00 3.91
5219 7383 9.672086 CCAACTAATTACAACAAAATTCGAAGA 57.328 29.630 3.35 0.00 0.00 2.87
5375 7554 6.840705 AGTACTACATCCTTCCGGGTTTATTA 59.159 38.462 0.00 0.00 36.25 0.98
5384 7563 5.816258 CCTTCCGGGTTTATTAGTTCTCTTC 59.184 44.000 0.00 0.00 0.00 2.87
5390 7569 7.168804 CCGGGTTTATTAGTTCTCTTCGTATTC 59.831 40.741 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.238289 CTGCACAGTTTTACCAGCGG 59.762 55.000 0.00 0.00 0.00 5.52
28 29 0.322008 CCAAAGCTCCAGGTCCTGAC 60.322 60.000 21.23 9.25 32.44 3.51
51 52 5.534207 AAATGCCTTGTTTCAGATGTTCA 57.466 34.783 0.00 0.00 0.00 3.18
97 98 5.330455 AGATGAACGAGACTTTATCTGCA 57.670 39.130 0.00 0.00 38.00 4.41
101 102 4.036498 TCCGGAGATGAACGAGACTTTATC 59.964 45.833 0.00 0.00 0.00 1.75
107 108 1.096416 ACTCCGGAGATGAACGAGAC 58.904 55.000 37.69 0.00 0.00 3.36
121 122 3.087031 TGTACTGAGGAAGGTTACTCCG 58.913 50.000 0.00 0.00 37.34 4.63
124 125 3.197983 GGCATGTACTGAGGAAGGTTACT 59.802 47.826 0.00 0.00 0.00 2.24
137 138 2.038557 ACGAGGTTTTGAGGCATGTACT 59.961 45.455 0.00 0.00 0.00 2.73
369 370 9.815306 AGCTATACCATAGAGAAGAGTTAATGA 57.185 33.333 0.00 0.00 0.00 2.57
494 495 0.941542 TTCGGCAGTGTTCGAAAAGG 59.058 50.000 16.84 0.00 41.54 3.11
553 554 4.995487 GGTGACTTCCGAGATAAGTTGTTT 59.005 41.667 0.00 0.00 37.31 2.83
568 569 1.269621 CGATATGGGGTCGGTGACTTC 60.270 57.143 0.00 0.00 35.55 3.01
700 701 4.825634 GGGCCCATATTAGTAAAGTTGGAC 59.174 45.833 19.95 1.40 0.00 4.02
802 803 3.235200 GAGATAGCTAGGCTTTCTGGGA 58.765 50.000 14.99 0.00 44.43 4.37
879 880 2.682582 GAATGGGGGCGGTCATCCTC 62.683 65.000 0.00 0.00 0.00 3.71
884 885 4.041762 GTGGAATGGGGGCGGTCA 62.042 66.667 0.00 0.00 0.00 4.02
976 977 1.774254 TGTTGGCTGGAGAAAGGAGAA 59.226 47.619 0.00 0.00 0.00 2.87
1088 1089 4.779733 TCCACGGAGAGGGGGAGC 62.780 72.222 0.00 0.00 45.91 4.70
1390 1392 2.263945 GCGCTGAAGAGGAGAAACTAC 58.736 52.381 0.00 0.00 0.00 2.73
1444 1447 7.386851 TGGGTACTGAAGAAAGATCTAAACAG 58.613 38.462 0.00 4.89 37.42 3.16
1463 1466 5.801531 ATTTTGGGAAGAAAACTGGGTAC 57.198 39.130 0.00 0.00 0.00 3.34
1470 1484 5.877564 TGGTGACAAATTTTGGGAAGAAAAC 59.122 36.000 13.42 0.82 37.44 2.43
1520 1534 4.519540 ACCATTGATAGTTGGTTGTTGC 57.480 40.909 0.00 0.00 43.73 4.17
1745 1778 0.108424 ACGGATGAAGCAGCTCAGTC 60.108 55.000 0.00 0.00 0.00 3.51
1750 1783 1.160137 GTGAAACGGATGAAGCAGCT 58.840 50.000 0.00 0.00 0.00 4.24
1763 1796 0.736053 TCAAGTGCCAACCGTGAAAC 59.264 50.000 0.00 0.00 0.00 2.78
1864 1897 2.832129 TCCTGCAACAGAAGGTAGGTAG 59.168 50.000 0.00 0.00 38.01 3.18
2051 2084 9.814899 TCTTTCTTAACAGCATTTTGATTTTGA 57.185 25.926 0.00 0.00 0.00 2.69
2052 2085 9.853921 GTCTTTCTTAACAGCATTTTGATTTTG 57.146 29.630 0.00 0.00 0.00 2.44
2053 2086 9.598517 TGTCTTTCTTAACAGCATTTTGATTTT 57.401 25.926 0.00 0.00 0.00 1.82
2054 2087 9.598517 TTGTCTTTCTTAACAGCATTTTGATTT 57.401 25.926 0.00 0.00 0.00 2.17
2055 2088 9.598517 TTTGTCTTTCTTAACAGCATTTTGATT 57.401 25.926 0.00 0.00 0.00 2.57
2056 2089 9.598517 TTTTGTCTTTCTTAACAGCATTTTGAT 57.401 25.926 0.00 0.00 0.00 2.57
2430 2463 9.112725 CATCAGTGTATCATCACCAATTTTAGA 57.887 33.333 0.00 0.00 38.91 2.10
2670 2704 5.005740 AGATATCAAACAGCTCTTGCAACA 58.994 37.500 5.32 0.00 42.74 3.33
2759 2816 5.905480 GCCCATTTATGGCGATTTTTAAG 57.095 39.130 3.11 0.00 46.70 1.85
2770 2827 6.587226 CATGAATAATTCGTGCCCATTTATGG 59.413 38.462 1.59 1.59 41.15 2.74
2771 2828 6.587226 CCATGAATAATTCGTGCCCATTTATG 59.413 38.462 0.00 0.00 43.66 1.90
2772 2829 6.295236 CCCATGAATAATTCGTGCCCATTTAT 60.295 38.462 0.00 0.00 43.66 1.40
2773 2830 5.010516 CCCATGAATAATTCGTGCCCATTTA 59.989 40.000 0.00 0.00 43.66 1.40
2774 2831 4.202243 CCCATGAATAATTCGTGCCCATTT 60.202 41.667 0.00 0.00 43.66 2.32
2779 2837 3.214328 AGTCCCATGAATAATTCGTGCC 58.786 45.455 0.00 0.00 43.66 5.01
2881 2943 8.864069 TGTTGTTGTTGTTATTGGACATTTAG 57.136 30.769 0.00 0.00 0.00 1.85
2883 2945 7.604164 TGTTGTTGTTGTTGTTATTGGACATTT 59.396 29.630 0.00 0.00 0.00 2.32
2890 2952 7.567571 TGTTGTTGTTGTTGTTGTTGTTATTG 58.432 30.769 0.00 0.00 0.00 1.90
2891 2953 7.715265 TGTTGTTGTTGTTGTTGTTGTTATT 57.285 28.000 0.00 0.00 0.00 1.40
2892 2954 7.224753 TGTTGTTGTTGTTGTTGTTGTTGTTAT 59.775 29.630 0.00 0.00 0.00 1.89
2893 2955 6.533723 TGTTGTTGTTGTTGTTGTTGTTGTTA 59.466 30.769 0.00 0.00 0.00 2.41
2894 2956 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2895 2957 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2896 2958 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2897 2959 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2898 2960 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2899 2961 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2900 2962 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2901 2963 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2902 2964 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2903 2965 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2904 2966 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2905 2967 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2906 2968 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
2907 2969 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2908 2970 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2909 2971 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
2910 2972 5.503194 GCTTTGTTGTTGTTGTTGTTGTTGT 60.503 36.000 0.00 0.00 0.00 3.32
2911 2973 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
2912 2974 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
2913 2975 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
2914 2976 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
2915 2977 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
2916 2978 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
2984 3051 7.942341 TGGTATGTTGACTCTGGAAGTATTTTT 59.058 33.333 0.00 0.00 38.74 1.94
3075 3149 9.941325 GACTATACAACTATCCTACTGCTACTA 57.059 37.037 0.00 0.00 0.00 1.82
3159 3237 6.653526 ACATCCAAATGACATCAAACTTGA 57.346 33.333 0.00 0.00 37.83 3.02
3345 3423 3.389925 TTGCTTTCCCTTCAATGCAAG 57.610 42.857 0.00 0.00 39.94 4.01
3371 3449 8.964420 ACAAATAATAAACAGACAACATTCCG 57.036 30.769 0.00 0.00 0.00 4.30
3461 5439 8.432110 TGTATCATGTAACTCGCAACATTAAT 57.568 30.769 0.00 0.00 34.12 1.40
3959 6052 5.221521 TGTCTCACTGTCTTCTGTGCTAATT 60.222 40.000 0.00 0.00 41.26 1.40
3990 6083 3.766051 GGTCAATGAGGGAATGCTTCTTT 59.234 43.478 0.00 0.00 0.00 2.52
4131 6224 2.361119 AGAACTCACGCTGTACTTGTGA 59.639 45.455 12.57 12.57 40.12 3.58
4145 6238 3.568430 TCTCTTACGTGCTGAAGAACTCA 59.432 43.478 0.00 0.00 31.46 3.41
4254 6347 6.785337 TCTCTTCGGGTCAACTGATTAATA 57.215 37.500 0.00 0.00 33.61 0.98
4449 6542 3.621268 CGTCTTCACTGTTTTCCAGAACA 59.379 43.478 0.00 0.00 44.49 3.18
4701 6794 8.984764 TCACACAAAAGTTGTAGTATGTGATAC 58.015 33.333 10.34 0.00 43.23 2.24
4738 6841 4.992381 AATGAAGCGAACAGAGTTGTAC 57.008 40.909 0.00 0.00 36.23 2.90
4771 6874 2.738743 ACTGAATGTAAATGGGCCTGG 58.261 47.619 4.53 0.00 0.00 4.45
4806 6909 6.785488 TCTGGTCTTATTATAAAGCATGCG 57.215 37.500 13.01 0.00 0.00 4.73
4834 6937 3.314635 GCTCTGAGAATTACCTTGCATGG 59.685 47.826 16.76 16.76 0.00 3.66
5047 7150 1.075542 TGTATTTCTCTTGCACGCCG 58.924 50.000 0.00 0.00 0.00 6.46
5106 7217 3.830744 TTCGAACAAAGGGAGACTTCA 57.169 42.857 0.00 0.00 38.85 3.02
5107 7218 4.127907 AGTTTCGAACAAAGGGAGACTTC 58.872 43.478 0.00 0.00 38.85 3.01
5109 7220 3.840124 AGTTTCGAACAAAGGGAGACT 57.160 42.857 0.00 0.00 0.00 3.24
5110 7221 4.451435 CCTAAGTTTCGAACAAAGGGAGAC 59.549 45.833 0.00 0.00 34.00 3.36
5111 7222 4.345837 TCCTAAGTTTCGAACAAAGGGAGA 59.654 41.667 0.00 0.00 36.65 3.71
5112 7223 4.638304 TCCTAAGTTTCGAACAAAGGGAG 58.362 43.478 0.00 0.00 36.65 4.30
5167 7278 4.410099 CACATGGCCTATGGGATGTAATT 58.590 43.478 16.39 0.00 43.15 1.40
5338 7516 3.820195 TGTAGTACTTCTGTCTCCCCA 57.180 47.619 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.