Multiple sequence alignment - TraesCS7D01G452700

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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 TraesCS7D01G452700 chr7D 100.000 3583 0 0 1 3583 572537155 572540737 0.000000e+00 6617.0
1 TraesCS7D01G452700 chr7D 86.819 349 14 3 1968 2315 138312878 138312561 9.460000e-96 361.0
2 TraesCS7D01G452700 chr7B 90.945 2816 142 46 1 2768 629789587 629786837 0.000000e+00 3683.0
3 TraesCS7D01G452700 chr7B 90.607 511 23 14 2790 3285 629786853 629786353 0.000000e+00 654.0
4 TraesCS7D01G452700 chr7B 87.736 212 6 7 3374 3580 629786197 629786001 2.780000e-56 230.0
5 TraesCS7D01G452700 chr7B 85.222 203 25 4 81 281 629870104 629869905 1.690000e-48 204.0
6 TraesCS7D01G452700 chr7A 89.873 2992 122 42 681 3580 661575808 661578710 0.000000e+00 3679.0
7 TraesCS7D01G452700 chr1A 88.438 960 51 30 1775 2725 59587692 59586784 0.000000e+00 1103.0
8 TraesCS7D01G452700 chr1A 91.282 390 28 5 1279 1668 59588128 59587745 8.810000e-146 527.0
9 TraesCS7D01G452700 chr1A 91.473 129 9 2 2764 2890 59586783 59586655 3.680000e-40 176.0
10 TraesCS7D01G452700 chr1A 95.238 42 2 0 1668 1709 59587727 59587686 2.310000e-07 67.6
11 TraesCS7D01G452700 chr5A 87.409 961 60 22 1774 2725 328011010 328010102 0.000000e+00 1048.0
12 TraesCS7D01G452700 chr5A 87.409 961 60 22 1774 2725 328017251 328016343 0.000000e+00 1048.0
13 TraesCS7D01G452700 chr5A 92.381 210 10 2 1506 1709 328011212 328011003 9.730000e-76 294.0
14 TraesCS7D01G452700 chr5A 89.655 232 18 5 1279 1510 328023120 328022895 1.260000e-74 291.0
15 TraesCS7D01G452700 chr5A 90.698 129 10 2 2764 2890 328016342 328016214 1.710000e-38 171.0
16 TraesCS7D01G452700 chr5A 89.922 129 11 2 2764 2890 328010101 328009973 7.960000e-37 165.0
17 TraesCS7D01G452700 chr5A 96.491 57 2 0 1653 1709 328017300 328017244 1.060000e-15 95.3
18 TraesCS7D01G452700 chr6D 77.124 306 31 24 2005 2303 95248759 95248486 1.340000e-29 141.0
19 TraesCS7D01G452700 chr6B 76.774 310 37 22 1999 2303 177794292 177794571 1.340000e-29 141.0
20 TraesCS7D01G452700 chr6B 83.784 111 8 5 1302 1411 177793588 177793689 2.940000e-16 97.1


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 TraesCS7D01G452700 chr7D 572537155 572540737 3582 False 6617.000000 6617 100.000000 1 3583 1 chr7D.!!$F1 3582
1 TraesCS7D01G452700 chr7B 629786001 629789587 3586 True 1522.333333 3683 89.762667 1 3580 3 chr7B.!!$R2 3579
2 TraesCS7D01G452700 chr7A 661575808 661578710 2902 False 3679.000000 3679 89.873000 681 3580 1 chr7A.!!$F1 2899
3 TraesCS7D01G452700 chr1A 59586655 59588128 1473 True 468.400000 1103 91.607750 1279 2890 4 chr1A.!!$R1 1611
4 TraesCS7D01G452700 chr5A 328009973 328011212 1239 True 502.333333 1048 89.904000 1506 2890 3 chr5A.!!$R2 1384
5 TraesCS7D01G452700 chr5A 328016214 328017300 1086 True 438.100000 1048 91.532667 1653 2890 3 chr5A.!!$R3 1237

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
34 35 0.250989 TAGGGTTTGCAAGGGGTTCG 60.251 55.0 0.00 0.00 0.00 3.95 F
1062 1090 0.179150 CAGTCTGTCGTCTGGCTAGC 60.179 60.0 6.04 6.04 0.00 3.42 F
1264 1307 0.038251 CGGCTGTAGTGTCTTCTGCA 60.038 55.0 0.00 0.00 30.17 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1092 0.108898 GCAGATCGCACTCTCACACT 60.109 55.0 4.93 0.0 41.79 3.55 R
2512 2682 0.168128 AACCGAACAAAGCGCTATGC 59.832 50.0 12.05 0.0 46.98 3.14 R
2725 2937 0.673437 AAACAGCACCCGTTTGGATG 59.327 50.0 0.00 0.0 35.31 3.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.250989 TAGGGTTTGCAAGGGGTTCG 60.251 55.000 0.00 0.00 0.00 3.95
37 38 3.972276 TTTGCAAGGGGTTCGCGC 61.972 61.111 0.00 0.00 0.00 6.86
60 61 1.714899 GGCGGATCCCACAATGAACG 61.715 60.000 6.06 0.00 0.00 3.95
70 71 2.738846 CCACAATGAACGTTCCTCAGAG 59.261 50.000 24.78 11.33 0.00 3.35
75 76 6.035435 CACAATGAACGTTCCTCAGAGATTAG 59.965 42.308 24.78 12.22 0.00 1.73
86 87 8.581578 GTTCCTCAGAGATTAGGGTCTAATAAG 58.418 40.741 0.00 0.00 33.40 1.73
89 90 8.364142 CCTCAGAGATTAGGGTCTAATAAGTTG 58.636 40.741 0.00 0.00 0.00 3.16
100 101 4.076394 TCTAATAAGTTGGGTGGTGCAAC 58.924 43.478 0.00 0.00 0.00 4.17
149 150 6.368243 TGGAAAAAGTTAAACCCAAACGTTTC 59.632 34.615 11.37 0.00 37.48 2.78
151 152 5.402997 AAAGTTAAACCCAAACGTTTCCA 57.597 34.783 11.37 0.00 37.20 3.53
168 169 6.750039 ACGTTTCCAACTACATTTTGAAACAG 59.250 34.615 11.89 7.88 38.37 3.16
204 205 7.132213 ACTCAAACATTTGATGTGAACTAACG 58.868 34.615 7.48 0.00 45.26 3.18
230 231 9.537848 GTATTAACAACACATTCGTTCCTAAAG 57.462 33.333 0.00 0.00 0.00 1.85
263 264 0.387565 GCCTCCTCTTTCGAGCCTAG 59.612 60.000 0.00 0.00 35.90 3.02
265 266 1.679153 CCTCCTCTTTCGAGCCTAGAC 59.321 57.143 0.00 0.00 35.90 2.59
267 268 3.020984 CTCCTCTTTCGAGCCTAGACTT 58.979 50.000 0.00 0.00 35.90 3.01
274 275 0.749649 CGAGCCTAGACTTGCCAGAT 59.250 55.000 0.00 0.00 0.00 2.90
283 284 6.689177 GCCTAGACTTGCCAGATAATAAGGTT 60.689 42.308 0.00 0.00 0.00 3.50
295 296 6.322201 CAGATAATAAGGTTGGAGGTGCAAAT 59.678 38.462 0.00 0.00 0.00 2.32
296 297 6.897413 AGATAATAAGGTTGGAGGTGCAAATT 59.103 34.615 0.00 0.00 0.00 1.82
303 304 4.020662 GGTTGGAGGTGCAAATTTATCCAA 60.021 41.667 12.98 12.98 42.84 3.53
304 305 5.512232 GGTTGGAGGTGCAAATTTATCCAAA 60.512 40.000 16.27 4.60 45.58 3.28
326 327 7.500559 CCAAATTTTCCCAAAACTATTGGACAA 59.499 33.333 8.75 0.00 40.61 3.18
334 335 9.549078 TCCCAAAACTATTGGACAAATTAAAAC 57.451 29.630 8.75 0.00 42.06 2.43
336 337 9.250624 CCAAAACTATTGGACAAATTAAAACGA 57.749 29.630 0.87 0.00 42.06 3.85
371 372 8.375506 TCCAACTACATTTTGATACTCAGAAGT 58.624 33.333 0.00 0.00 39.66 3.01
372 373 8.660373 CCAACTACATTTTGATACTCAGAAGTC 58.340 37.037 0.00 0.00 36.92 3.01
373 374 8.376203 CAACTACATTTTGATACTCAGAAGTCG 58.624 37.037 0.00 0.00 36.92 4.18
375 376 5.794894 ACATTTTGATACTCAGAAGTCGGT 58.205 37.500 0.00 0.00 36.92 4.69
376 377 5.869888 ACATTTTGATACTCAGAAGTCGGTC 59.130 40.000 0.00 0.00 36.92 4.79
377 378 4.451629 TTTGATACTCAGAAGTCGGTCC 57.548 45.455 0.00 0.00 36.92 4.46
396 398 3.253432 GTCCTGAACCTTTGATGTGAACC 59.747 47.826 0.00 0.00 0.00 3.62
458 460 2.979240 AGTCCGATTCCTCTTTCAAGC 58.021 47.619 0.00 0.00 0.00 4.01
461 463 3.126000 GTCCGATTCCTCTTTCAAGCTTG 59.874 47.826 20.81 20.81 0.00 4.01
474 476 4.642445 TCAAGCTTGCATTGGTCATATG 57.358 40.909 21.99 0.00 0.00 1.78
487 489 3.008375 TGGTCATATGATAAGCTGGGAGC 59.992 47.826 9.02 0.00 42.84 4.70
501 503 0.947244 GGGAGCTGCAAACATATCCG 59.053 55.000 7.79 0.00 33.21 4.18
506 508 4.202050 GGAGCTGCAAACATATCCGAATTT 60.202 41.667 0.00 0.00 0.00 1.82
548 551 0.845337 AACCCCAACGTTTCCACCTA 59.155 50.000 0.00 0.00 0.00 3.08
557 560 5.450688 CCAACGTTTCCACCTACATTTTGAA 60.451 40.000 0.00 0.00 0.00 2.69
571 574 7.925483 CCTACATTTTGAAACAAAAGATGGTCA 59.075 33.333 13.54 0.00 0.00 4.02
588 591 3.119173 TGGTCAAACTTGAACCTTTGCTG 60.119 43.478 5.07 0.00 44.20 4.41
591 594 3.761218 TCAAACTTGAACCTTTGCTGTGA 59.239 39.130 0.00 0.00 33.55 3.58
610 613 3.375299 GTGAACTCACATATTGACAGCCC 59.625 47.826 4.96 0.00 45.75 5.19
616 619 4.858850 TCACATATTGACAGCCCATTCTT 58.141 39.130 0.00 0.00 0.00 2.52
632 635 6.678164 GCCCATTCTTTCCTTAAATCTCGTTC 60.678 42.308 0.00 0.00 0.00 3.95
638 644 8.848474 TCTTTCCTTAAATCTCGTTCATTCTT 57.152 30.769 0.00 0.00 0.00 2.52
647 653 4.893608 TCTCGTTCATTCTTCCACAATCA 58.106 39.130 0.00 0.00 0.00 2.57
650 656 5.491070 TCGTTCATTCTTCCACAATCAGAT 58.509 37.500 0.00 0.00 0.00 2.90
654 660 7.596248 CGTTCATTCTTCCACAATCAGATTTTT 59.404 33.333 0.00 0.00 0.00 1.94
678 687 2.362889 GGGGCCACATTGGTCAGG 60.363 66.667 4.39 0.00 45.98 3.86
679 688 2.763215 GGGCCACATTGGTCAGGA 59.237 61.111 4.39 0.00 45.98 3.86
696 707 3.069443 TCAGGAAAACCCAGCATCAAAAC 59.931 43.478 0.00 0.00 37.41 2.43
741 753 4.088762 CATGTTTGCCGCGCTCGT 62.089 61.111 5.56 0.00 0.00 4.18
835 857 0.953471 TGTATTTTGCCTCTGCGCGT 60.953 50.000 8.43 0.00 41.78 6.01
878 900 1.273606 TCTCCTCTGCTTTCCACGAAG 59.726 52.381 0.00 0.00 0.00 3.79
1062 1090 0.179150 CAGTCTGTCGTCTGGCTAGC 60.179 60.000 6.04 6.04 0.00 3.42
1063 1091 0.322997 AGTCTGTCGTCTGGCTAGCT 60.323 55.000 15.72 0.00 0.00 3.32
1064 1092 1.065345 AGTCTGTCGTCTGGCTAGCTA 60.065 52.381 15.72 7.83 0.00 3.32
1065 1093 1.332375 GTCTGTCGTCTGGCTAGCTAG 59.668 57.143 21.31 21.31 0.00 3.42
1231 1271 4.365505 TCGTTCGGCCGTGATGCA 62.366 61.111 27.15 0.06 0.00 3.96
1264 1307 0.038251 CGGCTGTAGTGTCTTCTGCA 60.038 55.000 0.00 0.00 30.17 4.41
1270 1313 0.894835 TAGTGTCTTCTGCATCGCCA 59.105 50.000 0.00 0.00 0.00 5.69
1272 1315 1.742880 TGTCTTCTGCATCGCCAGC 60.743 57.895 0.00 0.00 32.87 4.85
1624 1670 4.168291 CTCGGGCTCAAGAGGGCC 62.168 72.222 0.00 0.00 46.89 5.80
2303 2459 1.585006 GACAAGAAGGAGTCGGCGA 59.415 57.895 4.99 4.99 0.00 5.54
2320 2476 1.666011 GACCAGCAAGGACTCGTCA 59.334 57.895 1.83 0.00 41.22 4.35
2324 2480 1.751351 CCAGCAAGGACTCGTCATCTA 59.249 52.381 0.00 0.00 41.22 1.98
2426 2595 3.967335 GATCCGTCCGAGCCGAGG 61.967 72.222 0.00 0.00 0.00 4.63
2503 2673 0.548031 AGGGACGCAATGATGGATGT 59.452 50.000 0.00 0.00 0.00 3.06
2504 2674 0.664761 GGGACGCAATGATGGATGTG 59.335 55.000 0.00 0.00 0.00 3.21
2505 2675 1.667236 GGACGCAATGATGGATGTGA 58.333 50.000 0.00 0.00 0.00 3.58
2506 2676 2.016318 GGACGCAATGATGGATGTGAA 58.984 47.619 0.00 0.00 0.00 3.18
2507 2677 2.032550 GGACGCAATGATGGATGTGAAG 59.967 50.000 0.00 0.00 0.00 3.02
2508 2678 2.019249 ACGCAATGATGGATGTGAAGG 58.981 47.619 0.00 0.00 0.00 3.46
2509 2679 2.291365 CGCAATGATGGATGTGAAGGA 58.709 47.619 0.00 0.00 0.00 3.36
2510 2680 2.684374 CGCAATGATGGATGTGAAGGAA 59.316 45.455 0.00 0.00 0.00 3.36
2511 2681 3.317149 CGCAATGATGGATGTGAAGGAAT 59.683 43.478 0.00 0.00 0.00 3.01
2512 2682 4.617959 GCAATGATGGATGTGAAGGAATG 58.382 43.478 0.00 0.00 0.00 2.67
2533 2703 2.241722 CATAGCGCTTTGTTCGGTTTG 58.758 47.619 18.68 0.00 38.65 2.93
2605 2775 9.573133 TCAATTGACTGTTCTTCTTTTCTTTTC 57.427 29.630 3.38 0.00 0.00 2.29
2697 2867 5.072055 TCTGATTCTGATTTGGTTGCTTGA 58.928 37.500 0.00 0.00 0.00 3.02
2702 2872 5.186996 TCTGATTTGGTTGCTTGAAAGAC 57.813 39.130 0.00 0.00 0.00 3.01
2703 2873 3.963665 TGATTTGGTTGCTTGAAAGACG 58.036 40.909 0.00 0.00 0.00 4.18
2725 2937 6.438763 ACGAAAGATCACAAGATGTTTTTCC 58.561 36.000 0.00 0.00 44.81 3.13
2726 2938 6.039270 ACGAAAGATCACAAGATGTTTTTCCA 59.961 34.615 0.00 0.00 44.81 3.53
2727 2939 7.086376 CGAAAGATCACAAGATGTTTTTCCAT 58.914 34.615 0.00 0.00 44.81 3.41
2728 2940 7.272084 CGAAAGATCACAAGATGTTTTTCCATC 59.728 37.037 0.00 0.00 44.81 3.51
2729 2941 6.521151 AGATCACAAGATGTTTTTCCATCC 57.479 37.500 0.00 0.00 41.79 3.51
2730 2942 6.012113 AGATCACAAGATGTTTTTCCATCCA 58.988 36.000 0.00 0.00 41.79 3.41
2731 2943 6.494491 AGATCACAAGATGTTTTTCCATCCAA 59.506 34.615 0.00 0.00 41.79 3.53
2732 2944 6.477053 TCACAAGATGTTTTTCCATCCAAA 57.523 33.333 0.00 0.00 41.79 3.28
2733 2945 6.279882 TCACAAGATGTTTTTCCATCCAAAC 58.720 36.000 0.00 0.00 41.79 2.93
2734 2946 5.175491 CACAAGATGTTTTTCCATCCAAACG 59.825 40.000 0.00 0.00 41.79 3.60
2735 2947 4.519540 AGATGTTTTTCCATCCAAACGG 57.480 40.909 0.00 0.00 41.79 4.44
2736 2948 3.258123 AGATGTTTTTCCATCCAAACGGG 59.742 43.478 0.00 0.00 41.79 5.28
2737 2949 2.389715 TGTTTTTCCATCCAAACGGGT 58.610 42.857 0.00 0.00 35.93 5.28
2738 2950 2.101582 TGTTTTTCCATCCAAACGGGTG 59.898 45.455 0.00 0.00 35.93 4.61
2739 2951 0.676736 TTTTCCATCCAAACGGGTGC 59.323 50.000 0.00 0.00 38.11 5.01
2740 2952 0.178975 TTTCCATCCAAACGGGTGCT 60.179 50.000 0.00 0.00 38.11 4.40
2741 2953 0.893270 TTCCATCCAAACGGGTGCTG 60.893 55.000 0.00 0.00 38.11 4.41
2742 2954 1.603455 CCATCCAAACGGGTGCTGT 60.603 57.895 0.00 0.00 38.11 4.40
2743 2955 1.178534 CCATCCAAACGGGTGCTGTT 61.179 55.000 0.00 0.00 38.11 3.16
2744 2956 0.673437 CATCCAAACGGGTGCTGTTT 59.327 50.000 0.00 0.00 42.78 2.83
2745 2957 1.068434 CATCCAAACGGGTGCTGTTTT 59.932 47.619 0.00 0.00 40.45 2.43
2746 2958 1.187087 TCCAAACGGGTGCTGTTTTT 58.813 45.000 0.00 0.00 40.45 1.94
2747 2959 1.134965 TCCAAACGGGTGCTGTTTTTG 60.135 47.619 0.00 0.00 40.45 2.44
2748 2960 1.134965 CCAAACGGGTGCTGTTTTTGA 60.135 47.619 0.00 0.00 40.45 2.69
2749 2961 2.611518 CAAACGGGTGCTGTTTTTGAA 58.388 42.857 0.00 0.00 40.45 2.69
2750 2962 2.996621 CAAACGGGTGCTGTTTTTGAAA 59.003 40.909 0.00 0.00 40.45 2.69
2751 2963 3.320673 AACGGGTGCTGTTTTTGAAAA 57.679 38.095 0.00 0.00 27.13 2.29
2752 2964 2.887337 ACGGGTGCTGTTTTTGAAAAG 58.113 42.857 0.00 0.00 0.00 2.27
2753 2965 2.494073 ACGGGTGCTGTTTTTGAAAAGA 59.506 40.909 0.00 0.00 0.00 2.52
2754 2966 3.132111 ACGGGTGCTGTTTTTGAAAAGAT 59.868 39.130 0.00 0.00 0.00 2.40
2755 2967 3.490526 CGGGTGCTGTTTTTGAAAAGATG 59.509 43.478 0.00 0.00 0.00 2.90
2756 2968 3.248363 GGGTGCTGTTTTTGAAAAGATGC 59.752 43.478 0.00 0.00 0.00 3.91
2757 2969 3.870419 GGTGCTGTTTTTGAAAAGATGCA 59.130 39.130 8.59 8.59 0.00 3.96
2758 2970 4.260334 GGTGCTGTTTTTGAAAAGATGCAC 60.260 41.667 22.88 22.88 40.77 4.57
2759 2971 4.329528 GTGCTGTTTTTGAAAAGATGCACA 59.670 37.500 24.47 12.60 40.93 4.57
2760 2972 5.006941 GTGCTGTTTTTGAAAAGATGCACAT 59.993 36.000 24.47 0.00 40.93 3.21
2761 2973 5.234757 TGCTGTTTTTGAAAAGATGCACATC 59.765 36.000 2.28 2.28 38.09 3.06
2777 2989 4.153986 GCACATCTTGTCAACTTGATTCG 58.846 43.478 0.00 0.00 0.00 3.34
2844 3056 0.511653 CATTGCTCTGCCGATCGATG 59.488 55.000 18.66 5.71 0.00 3.84
3024 3244 1.311059 GGTCCAGGGCCCATTTCAT 59.689 57.895 27.56 0.00 0.00 2.57
3033 3262 2.378038 GGCCCATTTCATAGCTGAACA 58.622 47.619 0.00 0.00 41.05 3.18
3146 3375 1.449789 CGTCTGAATATTCGCGCAGAG 59.550 52.381 8.75 1.89 37.99 3.35
3162 3395 4.033472 GCGCAGAGAAGAAAATTACTCCTC 59.967 45.833 0.30 0.00 0.00 3.71
3468 3778 2.909965 AGGCTCTCGATCCGCTCC 60.910 66.667 0.00 0.00 0.00 4.70
3476 3786 2.892425 GATCCGCTCCCGTGCAAG 60.892 66.667 0.00 0.00 0.00 4.01
3522 3840 2.257409 GATGACACCATGAGCCCCGT 62.257 60.000 0.00 0.00 32.09 5.28
3549 3868 4.487412 GGCCGCTTGCACTGCATC 62.487 66.667 4.10 0.00 43.89 3.91
3550 3869 4.487412 GCCGCTTGCACTGCATCC 62.487 66.667 4.10 0.00 38.76 3.51
3551 3870 3.818787 CCGCTTGCACTGCATCCC 61.819 66.667 4.10 0.00 38.76 3.85
3552 3871 3.818787 CGCTTGCACTGCATCCCC 61.819 66.667 4.10 0.00 38.76 4.81
3553 3872 2.362120 GCTTGCACTGCATCCCCT 60.362 61.111 4.10 0.00 38.76 4.79
3563 3882 4.275508 CATCCCCTCGGCCATGGG 62.276 72.222 20.21 20.21 42.98 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.556592 TGCAAACCCTAGGTAATACGTT 57.443 40.909 8.29 0.22 33.12 3.99
7 8 4.204799 CCCTTGCAAACCCTAGGTAATAC 58.795 47.826 8.29 0.00 33.12 1.89
44 45 1.743394 GGAACGTTCATTGTGGGATCC 59.257 52.381 28.24 1.92 0.00 3.36
55 56 3.447586 CCCTAATCTCTGAGGAACGTTCA 59.552 47.826 28.24 9.41 34.46 3.18
60 61 6.987403 ATTAGACCCTAATCTCTGAGGAAC 57.013 41.667 4.59 0.00 34.46 3.62
70 71 6.126565 ACCACCCAACTTATTAGACCCTAATC 60.127 42.308 2.81 0.00 0.00 1.75
75 76 3.617284 CACCACCCAACTTATTAGACCC 58.383 50.000 0.00 0.00 0.00 4.46
86 87 0.891904 ATACGGTTGCACCACCCAAC 60.892 55.000 1.91 0.00 38.47 3.77
89 90 1.747745 GGATACGGTTGCACCACCC 60.748 63.158 1.91 0.00 38.47 4.61
100 101 6.709018 ATGGTTTTAGGAATTTGGATACGG 57.291 37.500 0.00 0.00 42.51 4.02
149 150 7.086376 CCATCTCTGTTTCAAAATGTAGTTGG 58.914 38.462 0.00 0.00 0.00 3.77
151 152 7.823745 ACCATCTCTGTTTCAAAATGTAGTT 57.176 32.000 0.00 0.00 0.00 2.24
168 169 6.738114 TCAAATGTTTGAGTTCAACCATCTC 58.262 36.000 5.53 0.00 41.88 2.75
204 205 9.537848 CTTTAGGAACGAATGTGTTGTTAATAC 57.462 33.333 0.00 0.00 30.75 1.89
230 231 6.679327 AAGAGGAGGCATAATTAACGAAAC 57.321 37.500 0.00 0.00 0.00 2.78
263 264 5.437060 TCCAACCTTATTATCTGGCAAGTC 58.563 41.667 0.00 0.00 0.00 3.01
265 266 4.823989 CCTCCAACCTTATTATCTGGCAAG 59.176 45.833 0.00 0.00 0.00 4.01
267 268 3.785887 ACCTCCAACCTTATTATCTGGCA 59.214 43.478 0.00 0.00 0.00 4.92
274 275 6.926630 AAATTTGCACCTCCAACCTTATTA 57.073 33.333 0.00 0.00 0.00 0.98
283 284 6.371595 AATTTGGATAAATTTGCACCTCCA 57.628 33.333 0.00 3.02 42.33 3.86
296 297 9.732130 CCAATAGTTTTGGGAAAATTTGGATAA 57.268 29.630 4.52 0.00 38.57 1.75
303 304 9.639563 AATTTGTCCAATAGTTTTGGGAAAATT 57.360 25.926 20.35 20.35 38.56 1.82
334 335 8.865001 TCAAAATGTAGTTGGAAAAGTTTTTCG 58.135 29.630 1.64 0.00 45.68 3.46
375 376 3.117701 TGGTTCACATCAAAGGTTCAGGA 60.118 43.478 0.00 0.00 0.00 3.86
376 377 3.221771 TGGTTCACATCAAAGGTTCAGG 58.778 45.455 0.00 0.00 0.00 3.86
377 378 3.885297 ACTGGTTCACATCAAAGGTTCAG 59.115 43.478 0.00 0.00 0.00 3.02
421 423 6.219302 TCGGACTTGACGAAATTTAAGAAC 57.781 37.500 5.62 0.85 37.42 3.01
458 460 6.379386 CAGCTTATCATATGACCAATGCAAG 58.621 40.000 7.78 4.62 0.00 4.01
461 463 4.157289 CCCAGCTTATCATATGACCAATGC 59.843 45.833 7.78 10.23 0.00 3.56
487 489 5.247507 TGGAAATTCGGATATGTTTGCAG 57.752 39.130 0.00 0.00 30.25 4.41
501 503 8.619546 TGATTTGTTCAATGGTTTTGGAAATTC 58.380 29.630 0.00 0.00 0.00 2.17
506 508 7.148171 GGTTTTGATTTGTTCAATGGTTTTGGA 60.148 33.333 0.00 0.00 43.73 3.53
548 551 8.450180 GTTTGACCATCTTTTGTTTCAAAATGT 58.550 29.630 7.87 4.53 37.26 2.71
557 560 6.070824 AGGTTCAAGTTTGACCATCTTTTGTT 60.071 34.615 12.67 0.00 36.83 2.83
571 574 4.220602 AGTTCACAGCAAAGGTTCAAGTTT 59.779 37.500 0.00 0.00 0.00 2.66
588 591 3.375299 GGGCTGTCAATATGTGAGTTCAC 59.625 47.826 5.33 5.33 46.59 3.18
591 594 3.719268 TGGGCTGTCAATATGTGAGTT 57.281 42.857 0.00 0.00 36.74 3.01
610 613 9.495754 GAATGAACGAGATTTAAGGAAAGAATG 57.504 33.333 0.00 0.00 0.00 2.67
616 619 7.119262 GTGGAAGAATGAACGAGATTTAAGGAA 59.881 37.037 0.00 0.00 0.00 3.36
654 660 1.476007 CCAATGTGGCCCCGGAAAAA 61.476 55.000 0.73 0.00 0.00 1.94
655 661 1.910772 CCAATGTGGCCCCGGAAAA 60.911 57.895 0.73 0.00 0.00 2.29
656 662 2.283532 CCAATGTGGCCCCGGAAA 60.284 61.111 0.73 0.00 0.00 3.13
657 663 3.577334 GACCAATGTGGCCCCGGAA 62.577 63.158 0.73 0.00 42.67 4.30
661 667 2.362889 CCTGACCAATGTGGCCCC 60.363 66.667 0.00 0.00 42.67 5.80
662 668 0.541764 TTTCCTGACCAATGTGGCCC 60.542 55.000 0.00 0.00 42.67 5.80
666 675 2.297033 CTGGGTTTTCCTGACCAATGTG 59.703 50.000 0.00 0.00 38.98 3.21
669 678 1.133199 TGCTGGGTTTTCCTGACCAAT 60.133 47.619 0.00 0.00 38.98 3.16
678 687 4.320608 TGAGTTTTGATGCTGGGTTTTC 57.679 40.909 0.00 0.00 0.00 2.29
679 688 4.961438 ATGAGTTTTGATGCTGGGTTTT 57.039 36.364 0.00 0.00 0.00 2.43
696 707 7.041440 GGTTTTGTTAATGGTTTTGGGAATGAG 60.041 37.037 0.00 0.00 0.00 2.90
741 753 2.041922 AGCTACGGCCAGATGGGA 60.042 61.111 2.24 0.00 40.01 4.37
745 757 1.735376 CGGTACAGCTACGGCCAGAT 61.735 60.000 2.24 0.00 39.73 2.90
835 857 1.250154 CGGTGTGGTCCTTACGGGTA 61.250 60.000 0.00 0.00 36.25 3.69
1062 1090 2.794282 GCAGATCGCACTCTCACACTAG 60.794 54.545 4.93 0.00 41.79 2.57
1063 1091 1.133216 GCAGATCGCACTCTCACACTA 59.867 52.381 4.93 0.00 41.79 2.74
1064 1092 0.108898 GCAGATCGCACTCTCACACT 60.109 55.000 4.93 0.00 41.79 3.55
1065 1093 0.108898 AGCAGATCGCACTCTCACAC 60.109 55.000 11.20 0.00 46.13 3.82
1546 1592 2.049802 AACACGTACTGGTCGGCG 60.050 61.111 0.00 0.00 0.00 6.46
2303 2459 0.247736 GATGACGAGTCCTTGCTGGT 59.752 55.000 0.34 0.00 37.07 4.00
2445 2614 4.994201 TGCACGACGACGCACTCC 62.994 66.667 7.30 0.00 43.96 3.85
2449 2618 3.850095 TTCCATGCACGACGACGCA 62.850 57.895 16.60 16.60 43.96 5.24
2512 2682 0.168128 AACCGAACAAAGCGCTATGC 59.832 50.000 12.05 0.00 46.98 3.14
2533 2703 6.478673 CCCAAAGAACAAACCAAATCAGTTAC 59.521 38.462 0.00 0.00 0.00 2.50
2601 2771 9.801873 CCAAATTTACAGTCAAGAGAAAGAAAA 57.198 29.630 0.00 0.00 0.00 2.29
2605 2775 8.159344 ACTCCAAATTTACAGTCAAGAGAAAG 57.841 34.615 0.00 0.00 0.00 2.62
2697 2867 6.867662 AACATCTTGTGATCTTTCGTCTTT 57.132 33.333 0.00 0.00 0.00 2.52
2702 2872 6.437928 TGGAAAAACATCTTGTGATCTTTCG 58.562 36.000 0.00 0.00 30.90 3.46
2703 2873 7.543520 GGATGGAAAAACATCTTGTGATCTTTC 59.456 37.037 6.20 0.00 45.11 2.62
2725 2937 0.673437 AAACAGCACCCGTTTGGATG 59.327 50.000 0.00 0.00 35.31 3.51
2726 2938 1.408969 AAAACAGCACCCGTTTGGAT 58.591 45.000 0.00 0.00 36.71 3.41
2727 2939 1.134965 CAAAAACAGCACCCGTTTGGA 60.135 47.619 0.00 0.00 36.71 3.53
2728 2940 1.134965 TCAAAAACAGCACCCGTTTGG 60.135 47.619 0.00 0.00 36.71 3.28
2729 2941 2.285827 TCAAAAACAGCACCCGTTTG 57.714 45.000 0.00 0.00 36.71 2.93
2730 2942 3.320673 TTTCAAAAACAGCACCCGTTT 57.679 38.095 0.00 0.00 38.19 3.60
2731 2943 3.056465 TCTTTTCAAAAACAGCACCCGTT 60.056 39.130 0.00 0.00 0.00 4.44
2732 2944 2.494073 TCTTTTCAAAAACAGCACCCGT 59.506 40.909 0.00 0.00 0.00 5.28
2733 2945 3.157932 TCTTTTCAAAAACAGCACCCG 57.842 42.857 0.00 0.00 0.00 5.28
2734 2946 3.248363 GCATCTTTTCAAAAACAGCACCC 59.752 43.478 0.00 0.00 0.00 4.61
2735 2947 3.870419 TGCATCTTTTCAAAAACAGCACC 59.130 39.130 0.13 0.00 0.00 5.01
2736 2948 4.329528 TGTGCATCTTTTCAAAAACAGCAC 59.670 37.500 18.93 18.93 40.90 4.40
2737 2949 4.502016 TGTGCATCTTTTCAAAAACAGCA 58.498 34.783 0.00 0.13 0.00 4.41
2738 2950 5.464389 AGATGTGCATCTTTTCAAAAACAGC 59.536 36.000 8.74 0.00 45.31 4.40
2752 2964 4.754372 TCAAGTTGACAAGATGTGCATC 57.246 40.909 0.08 4.12 38.09 3.91
2753 2965 5.618418 CGAATCAAGTTGACAAGATGTGCAT 60.618 40.000 7.96 0.00 0.00 3.96
2754 2966 4.319694 CGAATCAAGTTGACAAGATGTGCA 60.320 41.667 7.96 0.00 0.00 4.57
2755 2967 4.083855 TCGAATCAAGTTGACAAGATGTGC 60.084 41.667 7.96 0.00 0.00 4.57
2756 2968 5.596268 TCGAATCAAGTTGACAAGATGTG 57.404 39.130 7.96 0.00 0.00 3.21
2757 2969 6.427853 TCATTCGAATCAAGTTGACAAGATGT 59.572 34.615 7.92 0.00 0.00 3.06
2758 2970 6.834876 TCATTCGAATCAAGTTGACAAGATG 58.165 36.000 7.92 9.21 0.00 2.90
2759 2971 6.402983 GCTCATTCGAATCAAGTTGACAAGAT 60.403 38.462 7.92 0.00 0.00 2.40
2760 2972 5.106948 GCTCATTCGAATCAAGTTGACAAGA 60.107 40.000 7.92 4.88 0.00 3.02
2761 2973 5.084722 GCTCATTCGAATCAAGTTGACAAG 58.915 41.667 7.92 2.44 0.00 3.16
2762 2974 4.514816 TGCTCATTCGAATCAAGTTGACAA 59.485 37.500 7.92 0.00 0.00 3.18
2777 2989 6.192234 AGAGTGTGAATCATTTGCTCATTC 57.808 37.500 0.00 0.00 0.00 2.67
3013 3229 2.360165 CTGTTCAGCTATGAAATGGGCC 59.640 50.000 0.00 0.00 46.75 5.80
3024 3244 2.656069 GGACCGGCCTGTTCAGCTA 61.656 63.158 0.00 0.00 0.00 3.32
3127 3356 2.732366 TCTCTGCGCGAATATTCAGAC 58.268 47.619 12.10 4.27 32.73 3.51
3128 3357 3.066760 TCTTCTCTGCGCGAATATTCAGA 59.933 43.478 12.10 11.17 34.74 3.27
3129 3358 3.375642 TCTTCTCTGCGCGAATATTCAG 58.624 45.455 12.10 6.55 0.00 3.02
3146 3375 3.606687 TGGCGGAGGAGTAATTTTCTTC 58.393 45.455 0.00 0.00 0.00 2.87
3174 3407 5.862323 GTCAGCGTGTCTATTTTAGTTCTGA 59.138 40.000 0.00 0.00 0.00 3.27
3337 3606 1.153086 CGGGAGAGCAGGGAAATGG 60.153 63.158 0.00 0.00 0.00 3.16
3338 3607 1.907739 TCGGGAGAGCAGGGAAATG 59.092 57.895 0.00 0.00 0.00 2.32
3339 3608 4.480480 TCGGGAGAGCAGGGAAAT 57.520 55.556 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.