Multiple sequence alignment - TraesCS4D01G307600

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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 TraesCS4D01G307600 chr4D 100.000 2726 0 0 1 2726 475203014 475200289 0.000000e+00 5035.0
1 TraesCS4D01G307600 chr4B 94.302 2264 76 20 1 2234 599958705 599956465 0.000000e+00 3417.0
2 TraesCS4D01G307600 chr4A 89.995 2019 113 48 737 2726 681935001 681933043 0.000000e+00 2527.0
3 TraesCS4D01G307600 chr4A 85.035 715 71 18 1 713 681935884 681935204 0.000000e+00 695.0
4 TraesCS4D01G307600 chr7A 84.524 924 62 32 1016 1880 496085939 496085038 0.000000e+00 839.0
5 TraesCS4D01G307600 chr7A 94.444 54 3 0 1878 1931 496084886 496084833 1.740000e-12 84.2
6 TraesCS4D01G307600 chr7D 84.372 915 68 34 1016 1877 445459926 445460818 0.000000e+00 828.0
7 TraesCS4D01G307600 chr7D 86.916 107 11 3 620 724 436961948 436961843 1.720000e-22 117.0
8 TraesCS4D01G307600 chr7D 91.228 57 5 0 1875 1931 445460963 445461019 8.090000e-11 78.7
9 TraesCS4D01G307600 chr7D 96.970 33 0 1 2424 2456 20593513 20593544 1.000000e-03 54.7
10 TraesCS4D01G307600 chr7B 83.388 921 75 35 1016 1877 462060805 462061706 0.000000e+00 782.0
11 TraesCS4D01G307600 chr7B 86.916 107 11 3 620 724 453623443 453623338 1.720000e-22 117.0
12 TraesCS4D01G307600 chr7B 88.542 96 9 2 620 714 567999015 567998921 6.170000e-22 115.0
13 TraesCS4D01G307600 chr7B 92.982 57 4 0 1875 1931 462061841 462061897 1.740000e-12 84.2
14 TraesCS4D01G307600 chr7B 94.737 38 1 1 2357 2394 577143924 577143960 1.050000e-04 58.4
15 TraesCS4D01G307600 chr5A 86.916 107 12 2 619 724 366635327 366635432 4.770000e-23 119.0
16 TraesCS4D01G307600 chr2A 85.714 112 14 2 617 727 587277762 587277872 1.720000e-22 117.0
17 TraesCS4D01G307600 chr2A 89.247 93 8 2 619 711 329688021 329688111 6.170000e-22 115.0
18 TraesCS4D01G307600 chr5D 85.981 107 13 2 619 724 277561453 277561558 2.220000e-21 113.0
19 TraesCS4D01G307600 chr6A 85.714 105 9 6 611 711 532026766 532026868 3.710000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G307600 chr4D 475200289 475203014 2725 True 5035.00 5035 100.000 1 2726 1 chr4D.!!$R1 2725
1 TraesCS4D01G307600 chr4B 599956465 599958705 2240 True 3417.00 3417 94.302 1 2234 1 chr4B.!!$R1 2233
2 TraesCS4D01G307600 chr4A 681933043 681935884 2841 True 1611.00 2527 87.515 1 2726 2 chr4A.!!$R1 2725
3 TraesCS4D01G307600 chr7A 496084833 496085939 1106 True 461.60 839 89.484 1016 1931 2 chr7A.!!$R1 915
4 TraesCS4D01G307600 chr7D 445459926 445461019 1093 False 453.35 828 87.800 1016 1931 2 chr7D.!!$F2 915
5 TraesCS4D01G307600 chr7B 462060805 462061897 1092 False 433.10 782 88.185 1016 1931 2 chr7B.!!$F2 915

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
77 78 0.707616 TCCCACCAATTAACCTGGGG 59.292 55.0 9.64 5.7 43.38 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2370 0.985549 GCGCAAAACAACGACAACAA 59.014 45.0 0.3 0.0 0.0 2.83 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
30 31 8.853345 CGATTGTCAAAATGGTCTTTATTCTTG 58.147 33.333 0.00 0.00 0.00 3.02
43 44 7.222999 GGTCTTTATTCTTGTCTCGGTGATAAG 59.777 40.741 9.44 9.44 42.81 1.73
77 78 0.707616 TCCCACCAATTAACCTGGGG 59.292 55.000 9.64 5.70 43.38 4.96
198 200 5.314923 CAAAGGTGGAATTCGATGTGATT 57.685 39.130 0.00 0.00 0.00 2.57
199 201 6.435430 CAAAGGTGGAATTCGATGTGATTA 57.565 37.500 0.00 0.00 0.00 1.75
221 223 1.370414 CCCTTTGAAACAGCGCACG 60.370 57.895 11.47 1.85 0.00 5.34
258 261 6.855763 TGAATGGATGCCAAGTAAAATTCT 57.144 33.333 0.00 0.00 36.95 2.40
288 291 1.364626 CCAGATGCAGGCAAGACGTC 61.365 60.000 7.70 7.70 0.00 4.34
345 348 5.913137 AAGACATGTTTCTGAAAACCACA 57.087 34.783 4.09 0.00 43.44 4.17
478 481 7.550551 TGTCTCTCATGATGAACCATCTTTAAC 59.449 37.037 0.00 0.38 41.06 2.01
598 602 8.649841 CACAGATTGCACCTTAATACATTTTTG 58.350 33.333 0.00 0.00 0.00 2.44
623 627 6.656314 TTTAACGATGGTTGTATGCTACTG 57.344 37.500 3.01 0.00 36.90 2.74
714 762 7.906611 TGTGTTTGTTCACTTATTTCAATCG 57.093 32.000 0.00 0.00 38.90 3.34
739 789 7.359431 CGGCGTGTAGTATTAAAAGAAAAGTCA 60.359 37.037 0.00 0.00 0.00 3.41
753 936 3.928727 AAAGTCATGTTCTGGCATGTG 57.071 42.857 6.04 0.00 44.68 3.21
774 957 2.952310 GTGCACTTCCTTTTCAGTCCTT 59.048 45.455 10.32 0.00 0.00 3.36
780 963 4.335594 ACTTCCTTTTCAGTCCTTGTTTCG 59.664 41.667 0.00 0.00 0.00 3.46
781 964 2.616842 TCCTTTTCAGTCCTTGTTTCGC 59.383 45.455 0.00 0.00 0.00 4.70
782 965 2.618709 CCTTTTCAGTCCTTGTTTCGCT 59.381 45.455 0.00 0.00 0.00 4.93
783 966 3.304057 CCTTTTCAGTCCTTGTTTCGCTC 60.304 47.826 0.00 0.00 0.00 5.03
784 967 2.910688 TTCAGTCCTTGTTTCGCTCT 57.089 45.000 0.00 0.00 0.00 4.09
849 1035 5.887598 AGTTCCATTATACTGATGCTTGCAA 59.112 36.000 0.00 0.00 0.00 4.08
1221 1416 3.419580 TCGGATGCCTGCCCCAAT 61.420 61.111 0.00 0.00 0.00 3.16
1428 1647 2.103934 GACGCGCTGATGAGCTCT 59.896 61.111 16.19 0.00 43.77 4.09
1638 1872 4.832608 GGCGACCGGATGGACACC 62.833 72.222 9.46 0.00 39.21 4.16
1993 2401 3.516615 TGTTTTGCGCTTAGTGCTTTTT 58.483 36.364 18.81 0.00 40.03 1.94
2027 2435 6.044046 TGTGTTTACCTAGGCACATATTACG 58.956 40.000 9.30 0.00 37.00 3.18
2040 2448 6.251589 GGCACATATTACGAGATCACTAATCG 59.748 42.308 0.00 0.00 39.55 3.34
2045 2453 1.609555 ACGAGATCACTAATCGAGGGC 59.390 52.381 8.15 0.00 39.55 5.19
2086 2494 1.271871 CCACCTTGGGTTGAGCATGTA 60.272 52.381 0.00 0.00 31.02 2.29
2088 2496 1.423541 ACCTTGGGTTGAGCATGTACA 59.576 47.619 0.00 0.00 27.29 2.90
2097 2505 5.336690 GGGTTGAGCATGTACATCATTTGTT 60.337 40.000 5.07 0.00 39.87 2.83
2100 2508 4.217983 TGAGCATGTACATCATTTGTTGCA 59.782 37.500 5.07 0.00 40.50 4.08
2102 2510 5.539979 AGCATGTACATCATTTGTTGCAAA 58.460 33.333 5.07 0.00 40.50 3.68
2103 2511 5.406175 AGCATGTACATCATTTGTTGCAAAC 59.594 36.000 5.07 0.00 40.50 2.93
2115 2523 3.245518 GTTGCAAACTGTGGGTTTTCT 57.754 42.857 0.00 0.00 44.77 2.52
2120 2528 4.453819 TGCAAACTGTGGGTTTTCTTTTTG 59.546 37.500 0.00 0.00 44.77 2.44
2122 2530 5.616645 GCAAACTGTGGGTTTTCTTTTTGTG 60.617 40.000 0.00 0.00 44.77 3.33
2129 2537 6.154363 TGTGGGTTTTCTTTTTGTGAGATTCT 59.846 34.615 0.00 0.00 0.00 2.40
2177 2585 3.132289 AGCCATGCATCAAAATCCTGAAG 59.868 43.478 0.00 0.00 0.00 3.02
2195 2604 6.206634 TCCTGAAGCGTTTTCACTATTGAATT 59.793 34.615 0.00 0.00 41.50 2.17
2250 2659 8.634335 TCATGTCAATAAGTTTCAAGGAATCA 57.366 30.769 0.00 0.00 0.00 2.57
2296 2705 4.660789 AAAAACAAGCTGAGAGCACAAT 57.339 36.364 0.00 0.00 45.56 2.71
2323 2732 8.541899 TTTTCACTTTTTCCCCTTATAGTTGT 57.458 30.769 0.00 0.00 0.00 3.32
2324 2733 7.519032 TTCACTTTTTCCCCTTATAGTTGTG 57.481 36.000 0.00 0.00 0.00 3.33
2325 2734 5.475564 TCACTTTTTCCCCTTATAGTTGTGC 59.524 40.000 0.00 0.00 0.00 4.57
2326 2735 4.770531 ACTTTTTCCCCTTATAGTTGTGCC 59.229 41.667 0.00 0.00 0.00 5.01
2327 2736 4.668138 TTTTCCCCTTATAGTTGTGCCT 57.332 40.909 0.00 0.00 0.00 4.75
2328 2737 4.668138 TTTCCCCTTATAGTTGTGCCTT 57.332 40.909 0.00 0.00 0.00 4.35
2329 2738 4.668138 TTCCCCTTATAGTTGTGCCTTT 57.332 40.909 0.00 0.00 0.00 3.11
2330 2739 4.230745 TCCCCTTATAGTTGTGCCTTTC 57.769 45.455 0.00 0.00 0.00 2.62
2331 2740 3.589735 TCCCCTTATAGTTGTGCCTTTCA 59.410 43.478 0.00 0.00 0.00 2.69
2332 2741 3.694566 CCCCTTATAGTTGTGCCTTTCAC 59.305 47.826 0.00 0.00 45.82 3.18
2342 2751 2.825205 GTGCCTTTCACACAAGCAAAT 58.175 42.857 0.00 0.00 44.98 2.32
2345 2754 4.386652 GTGCCTTTCACACAAGCAAATATG 59.613 41.667 0.00 0.00 44.98 1.78
2346 2755 4.039004 TGCCTTTCACACAAGCAAATATGT 59.961 37.500 0.00 0.00 0.00 2.29
2354 2763 4.171005 CACAAGCAAATATGTGCCTCTTG 58.829 43.478 14.50 14.16 46.14 3.02
2361 2781 4.851639 AATATGTGCCTCTTGGAGAAGT 57.148 40.909 0.00 0.00 34.57 3.01
2366 2786 4.579869 TGTGCCTCTTGGAGAAGTAAATC 58.420 43.478 0.00 0.00 34.57 2.17
2368 2788 4.633565 GTGCCTCTTGGAGAAGTAAATCTG 59.366 45.833 0.00 0.00 34.57 2.90
2377 2797 5.702670 TGGAGAAGTAAATCTGTGCTTCTTG 59.297 40.000 6.93 0.00 45.09 3.02
2499 2920 5.949735 TCCTGTGTGAAAGAGAAACAAAAC 58.050 37.500 0.00 0.00 0.00 2.43
2500 2921 4.793216 CCTGTGTGAAAGAGAAACAAAACG 59.207 41.667 0.00 0.00 0.00 3.60
2501 2922 4.162812 TGTGTGAAAGAGAAACAAAACGC 58.837 39.130 0.00 0.00 0.00 4.84
2502 2923 4.162812 GTGTGAAAGAGAAACAAAACGCA 58.837 39.130 0.00 0.00 0.00 5.24
2503 2924 4.798387 GTGTGAAAGAGAAACAAAACGCAT 59.202 37.500 0.00 0.00 0.00 4.73
2506 2927 6.034470 TGTGAAAGAGAAACAAAACGCATTTC 59.966 34.615 0.00 0.00 33.40 2.17
2508 2929 3.977427 AGAGAAACAAAACGCATTTCCC 58.023 40.909 0.00 0.00 33.64 3.97
2509 2930 3.057019 GAGAAACAAAACGCATTTCCCC 58.943 45.455 0.00 0.00 33.64 4.81
2548 2984 5.532406 GCATAGAAGAAAATATGTGCCTCCA 59.468 40.000 0.00 0.00 32.94 3.86
2549 2985 6.208204 GCATAGAAGAAAATATGTGCCTCCAT 59.792 38.462 0.00 0.00 32.94 3.41
2550 2986 7.591165 CATAGAAGAAAATATGTGCCTCCATG 58.409 38.462 0.00 0.00 0.00 3.66
2552 2988 6.189859 AGAAGAAAATATGTGCCTCCATGAA 58.810 36.000 0.00 0.00 0.00 2.57
2555 2991 6.633856 AGAAAATATGTGCCTCCATGAAAAC 58.366 36.000 0.00 0.00 0.00 2.43
2559 2995 2.607499 TGTGCCTCCATGAAAACCAAT 58.393 42.857 0.00 0.00 0.00 3.16
2560 2996 2.971330 TGTGCCTCCATGAAAACCAATT 59.029 40.909 0.00 0.00 0.00 2.32
2562 2998 4.776837 TGTGCCTCCATGAAAACCAATTAT 59.223 37.500 0.00 0.00 0.00 1.28
2563 2999 5.111293 GTGCCTCCATGAAAACCAATTATG 58.889 41.667 0.00 0.00 0.00 1.90
2564 3000 4.776837 TGCCTCCATGAAAACCAATTATGT 59.223 37.500 0.00 0.00 0.00 2.29
2565 3001 5.111293 GCCTCCATGAAAACCAATTATGTG 58.889 41.667 0.00 0.00 0.00 3.21
2566 3002 5.111293 CCTCCATGAAAACCAATTATGTGC 58.889 41.667 0.00 0.00 0.00 4.57
2567 3003 5.083533 TCCATGAAAACCAATTATGTGCC 57.916 39.130 0.00 0.00 0.00 5.01
2568 3004 4.776837 TCCATGAAAACCAATTATGTGCCT 59.223 37.500 0.00 0.00 0.00 4.75
2569 3005 5.105392 TCCATGAAAACCAATTATGTGCCTC 60.105 40.000 0.00 0.00 0.00 4.70
2570 3006 5.105228 CCATGAAAACCAATTATGTGCCTCT 60.105 40.000 0.00 0.00 0.00 3.69
2571 3007 5.643379 TGAAAACCAATTATGTGCCTCTC 57.357 39.130 0.00 0.00 0.00 3.20
2572 3008 4.155826 TGAAAACCAATTATGTGCCTCTCG 59.844 41.667 0.00 0.00 0.00 4.04
2573 3009 3.350219 AACCAATTATGTGCCTCTCGT 57.650 42.857 0.00 0.00 0.00 4.18
2574 3010 4.481368 AACCAATTATGTGCCTCTCGTA 57.519 40.909 0.00 0.00 0.00 3.43
2575 3011 4.060038 ACCAATTATGTGCCTCTCGTAG 57.940 45.455 0.00 0.00 0.00 3.51
2576 3012 3.704566 ACCAATTATGTGCCTCTCGTAGA 59.295 43.478 0.00 0.00 0.00 2.59
2577 3013 4.161565 ACCAATTATGTGCCTCTCGTAGAA 59.838 41.667 0.00 0.00 34.09 2.10
2578 3014 4.747108 CCAATTATGTGCCTCTCGTAGAAG 59.253 45.833 0.00 0.00 34.09 2.85
2579 3015 5.451937 CCAATTATGTGCCTCTCGTAGAAGA 60.452 44.000 0.00 0.00 34.09 2.87
2580 3016 5.854010 ATTATGTGCCTCTCGTAGAAGAA 57.146 39.130 0.00 0.00 34.09 2.52
2581 3017 3.512033 ATGTGCCTCTCGTAGAAGAAC 57.488 47.619 0.00 0.00 34.09 3.01
2582 3018 1.199327 TGTGCCTCTCGTAGAAGAACG 59.801 52.381 0.00 0.00 44.19 3.95
2583 3019 0.170561 TGCCTCTCGTAGAAGAACGC 59.829 55.000 0.00 0.00 42.56 4.84
2584 3020 0.170561 GCCTCTCGTAGAAGAACGCA 59.829 55.000 0.00 0.00 42.56 5.24
2620 3056 3.118261 TCAAGAGGCACAACTTTGTCTCT 60.118 43.478 1.36 1.36 41.41 3.10
2661 3097 5.048573 TGCCTCCCGTGTAAGAAAATAAAAC 60.049 40.000 0.00 0.00 0.00 2.43
2664 3100 6.016943 CCTCCCGTGTAAGAAAATAAAACACA 60.017 38.462 4.95 0.00 40.29 3.72
2703 3140 3.866651 TGTAGAAGCAAATCTCTGCCTC 58.133 45.455 0.00 0.00 43.73 4.70
2718 3155 3.569701 TCTGCCTCCACAAGAAACAAATC 59.430 43.478 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.760077 TTTTAATATCTTCCTTATCACCGAGAC 57.240 33.333 0.00 0.00 0.00 3.36
77 78 9.269415 GTCAATATTTGTCGTGTTAACCATAAC 57.731 33.333 2.48 0.00 41.50 1.89
87 88 4.454504 GGAACTGGTCAATATTTGTCGTGT 59.545 41.667 0.00 0.00 0.00 4.49
221 223 5.737063 GCATCCATTCAACATTGATGTACCC 60.737 44.000 0.00 0.00 40.80 3.69
258 261 2.782222 GCATCTGGACGGCCGAGTA 61.782 63.158 35.90 15.87 36.79 2.59
288 291 0.608130 TGGTCTCGACAATGTCTGGG 59.392 55.000 11.92 5.39 0.00 4.45
345 348 5.127682 GTGGCCATTTCAAAATCCACTAGAT 59.872 40.000 9.72 0.00 38.90 1.98
358 361 5.538053 TGATTTAGACTTTGTGGCCATTTCA 59.462 36.000 9.72 0.00 0.00 2.69
478 481 2.930682 GGTCGAGCTAGGCTTTACAAAG 59.069 50.000 7.51 0.00 39.88 2.77
598 602 6.959311 CAGTAGCATACAACCATCGTTAAAAC 59.041 38.462 0.00 0.00 46.26 2.43
608 612 1.209504 GGAGGCAGTAGCATACAACCA 59.790 52.381 0.00 0.00 46.26 3.67
613 617 1.136305 TGAACGGAGGCAGTAGCATAC 59.864 52.381 0.00 0.00 44.61 2.39
623 627 6.456501 ACATCTTATAATAGTGAACGGAGGC 58.543 40.000 0.00 0.00 0.00 4.70
679 683 5.808030 AGTGAACAAACACATTAAAAACGGG 59.192 36.000 0.00 0.00 42.45 5.28
714 762 7.799784 TGACTTTTCTTTTAATACTACACGCC 58.200 34.615 0.00 0.00 0.00 5.68
753 936 2.576615 AGGACTGAAAAGGAAGTGCAC 58.423 47.619 9.40 9.40 37.23 4.57
766 949 1.873903 GCAGAGCGAAACAAGGACTGA 60.874 52.381 0.00 0.00 0.00 3.41
774 957 0.668706 GAGCAGAGCAGAGCGAAACA 60.669 55.000 0.00 0.00 35.48 2.83
780 963 0.737019 GTGTGAGAGCAGAGCAGAGC 60.737 60.000 0.00 0.00 0.00 4.09
781 964 0.889994 AGTGTGAGAGCAGAGCAGAG 59.110 55.000 0.00 0.00 0.00 3.35
782 965 1.000618 CAAGTGTGAGAGCAGAGCAGA 59.999 52.381 0.00 0.00 0.00 4.26
783 966 1.000618 TCAAGTGTGAGAGCAGAGCAG 59.999 52.381 0.00 0.00 0.00 4.24
784 967 1.043022 TCAAGTGTGAGAGCAGAGCA 58.957 50.000 0.00 0.00 0.00 4.26
1083 1278 1.549203 ACCGGTCGTTGGTGTAGTAT 58.451 50.000 0.00 0.00 38.60 2.12
1960 2368 1.979469 CGCAAAACAACGACAACAACA 59.021 42.857 0.00 0.00 0.00 3.33
1961 2369 1.266163 GCGCAAAACAACGACAACAAC 60.266 47.619 0.30 0.00 0.00 3.32
1962 2370 0.985549 GCGCAAAACAACGACAACAA 59.014 45.000 0.30 0.00 0.00 2.83
1993 2401 7.388500 GTGCCTAGGTAAACACAAACACTATTA 59.612 37.037 11.31 0.00 33.23 0.98
2027 2435 2.288518 GGTGCCCTCGATTAGTGATCTC 60.289 54.545 0.00 0.00 32.30 2.75
2045 2453 4.161942 TGGGAATAATCATTGCAAAGGGTG 59.838 41.667 1.71 0.00 34.35 4.61
2086 2494 4.121317 CCACAGTTTGCAACAAATGATGT 58.879 39.130 0.00 0.52 46.82 3.06
2088 2496 3.134442 ACCCACAGTTTGCAACAAATGAT 59.866 39.130 0.00 0.00 0.00 2.45
2102 2510 4.770010 TCTCACAAAAAGAAAACCCACAGT 59.230 37.500 0.00 0.00 0.00 3.55
2103 2511 5.323371 TCTCACAAAAAGAAAACCCACAG 57.677 39.130 0.00 0.00 0.00 3.66
2149 2557 6.372103 CAGGATTTTGATGCATGGCTTAAAAA 59.628 34.615 2.46 2.01 32.92 1.94
2151 2559 5.187381 TCAGGATTTTGATGCATGGCTTAAA 59.813 36.000 2.46 0.00 0.00 1.52
2156 2564 3.454375 CTTCAGGATTTTGATGCATGGC 58.546 45.455 2.46 0.00 0.00 4.40
2177 2585 5.002561 GCGAGAAATTCAATAGTGAAAACGC 59.997 40.000 9.98 16.42 46.66 4.84
2302 2711 5.336451 GGCACAACTATAAGGGGAAAAAGTG 60.336 44.000 0.00 0.00 0.00 3.16
2303 2712 4.770531 GGCACAACTATAAGGGGAAAAAGT 59.229 41.667 0.00 0.00 0.00 2.66
2304 2713 5.016831 AGGCACAACTATAAGGGGAAAAAG 58.983 41.667 0.00 0.00 0.00 2.27
2305 2714 5.005628 AGGCACAACTATAAGGGGAAAAA 57.994 39.130 0.00 0.00 0.00 1.94
2306 2715 4.668138 AGGCACAACTATAAGGGGAAAA 57.332 40.909 0.00 0.00 0.00 2.29
2311 2720 4.965119 GTGAAAGGCACAACTATAAGGG 57.035 45.455 0.00 0.00 46.91 3.95
2323 2732 4.039004 ACATATTTGCTTGTGTGAAAGGCA 59.961 37.500 0.00 0.00 0.00 4.75
2324 2733 4.386652 CACATATTTGCTTGTGTGAAAGGC 59.613 41.667 6.08 0.00 43.41 4.35
2325 2734 4.386652 GCACATATTTGCTTGTGTGAAAGG 59.613 41.667 6.60 0.00 44.01 3.11
2326 2735 4.386652 GGCACATATTTGCTTGTGTGAAAG 59.613 41.667 13.29 0.00 44.01 2.62
2327 2736 4.039004 AGGCACATATTTGCTTGTGTGAAA 59.961 37.500 13.29 0.00 44.01 2.69
2328 2737 3.573538 AGGCACATATTTGCTTGTGTGAA 59.426 39.130 13.29 0.00 44.01 3.18
2329 2738 3.156293 AGGCACATATTTGCTTGTGTGA 58.844 40.909 13.29 0.00 44.01 3.58
2330 2739 3.192001 AGAGGCACATATTTGCTTGTGTG 59.808 43.478 13.29 0.00 44.01 3.82
2331 2740 3.424703 AGAGGCACATATTTGCTTGTGT 58.575 40.909 13.29 0.00 44.01 3.72
2332 2741 4.171005 CAAGAGGCACATATTTGCTTGTG 58.829 43.478 13.29 0.79 44.75 3.33
2333 2742 3.194116 CCAAGAGGCACATATTTGCTTGT 59.806 43.478 13.29 1.79 42.56 3.16
2334 2743 3.444742 TCCAAGAGGCACATATTTGCTTG 59.555 43.478 13.29 9.82 42.56 4.01
2335 2744 3.698040 CTCCAAGAGGCACATATTTGCTT 59.302 43.478 13.29 5.98 42.56 3.91
2336 2745 3.054139 TCTCCAAGAGGCACATATTTGCT 60.054 43.478 13.29 0.24 42.56 3.91
2337 2746 3.282021 TCTCCAAGAGGCACATATTTGC 58.718 45.455 5.23 5.23 42.18 3.68
2339 2748 5.184892 ACTTCTCCAAGAGGCACATATTT 57.815 39.130 0.00 0.00 33.34 1.40
2340 2749 4.851639 ACTTCTCCAAGAGGCACATATT 57.148 40.909 0.00 0.00 33.34 1.28
2342 2751 5.755409 TTTACTTCTCCAAGAGGCACATA 57.245 39.130 0.00 0.00 33.34 2.29
2345 2754 4.633565 CAGATTTACTTCTCCAAGAGGCAC 59.366 45.833 0.00 0.00 33.34 5.01
2346 2755 4.287067 ACAGATTTACTTCTCCAAGAGGCA 59.713 41.667 0.00 0.00 33.34 4.75
2347 2756 4.633565 CACAGATTTACTTCTCCAAGAGGC 59.366 45.833 0.00 0.00 33.34 4.70
2348 2757 4.633565 GCACAGATTTACTTCTCCAAGAGG 59.366 45.833 0.00 0.00 33.34 3.69
2349 2758 5.486526 AGCACAGATTTACTTCTCCAAGAG 58.513 41.667 0.00 0.00 33.34 2.85
2351 2760 5.936956 AGAAGCACAGATTTACTTCTCCAAG 59.063 40.000 0.00 0.00 44.14 3.61
2352 2761 5.869579 AGAAGCACAGATTTACTTCTCCAA 58.130 37.500 0.00 0.00 44.14 3.53
2354 2763 5.391416 GCAAGAAGCACAGATTTACTTCTCC 60.391 44.000 4.72 0.00 46.13 3.71
2361 2781 3.052455 TCCGCAAGAAGCACAGATTTA 57.948 42.857 0.00 0.00 46.13 1.40
2377 2797 1.487482 GTGGTTTTTCTTGCTTCCGC 58.513 50.000 0.00 0.00 0.00 5.54
2406 2827 5.300752 AGCATAATTGTACCTCTCGGAATG 58.699 41.667 0.00 0.00 0.00 2.67
2407 2828 5.552870 AGCATAATTGTACCTCTCGGAAT 57.447 39.130 0.00 0.00 0.00 3.01
2410 2831 4.950050 AGAAGCATAATTGTACCTCTCGG 58.050 43.478 0.00 0.00 0.00 4.63
2417 2838 4.318121 CTTCCGCGAGAAGCATAATTGTAC 60.318 45.833 19.55 0.00 45.38 2.90
2418 2839 3.802139 CTTCCGCGAGAAGCATAATTGTA 59.198 43.478 19.55 0.00 45.38 2.41
2429 2850 2.351418 CACATATTTGCTTCCGCGAGAA 59.649 45.455 8.23 8.88 39.65 2.87
2455 2876 5.250774 AGGAGGCACAAATTTACTTCTCCTA 59.749 40.000 21.04 0.00 45.43 2.94
2508 2929 0.627986 ATGCCTCTCAGAAAAGGGGG 59.372 55.000 1.54 0.00 37.39 5.40
2509 2930 2.774234 TCTATGCCTCTCAGAAAAGGGG 59.226 50.000 1.54 0.00 40.19 4.79
2514 2935 9.334947 CATATTTTCTTCTATGCCTCTCAGAAA 57.665 33.333 0.00 0.00 0.00 2.52
2548 2984 5.163622 CGAGAGGCACATAATTGGTTTTCAT 60.164 40.000 0.00 0.00 0.00 2.57
2549 2985 4.155826 CGAGAGGCACATAATTGGTTTTCA 59.844 41.667 0.00 0.00 0.00 2.69
2550 2986 4.156008 ACGAGAGGCACATAATTGGTTTTC 59.844 41.667 0.00 0.00 0.00 2.29
2552 2988 3.686016 ACGAGAGGCACATAATTGGTTT 58.314 40.909 0.00 0.00 0.00 3.27
2555 2991 4.322080 TCTACGAGAGGCACATAATTGG 57.678 45.455 0.00 0.00 0.00 3.16
2559 2995 4.438336 CGTTCTTCTACGAGAGGCACATAA 60.438 45.833 0.00 0.00 43.99 1.90
2560 2996 3.064958 CGTTCTTCTACGAGAGGCACATA 59.935 47.826 0.00 0.00 43.99 2.29
2562 2998 1.199327 CGTTCTTCTACGAGAGGCACA 59.801 52.381 0.00 0.00 43.99 4.57
2563 2999 1.897641 CGTTCTTCTACGAGAGGCAC 58.102 55.000 0.00 0.00 43.99 5.01
2564 3000 0.170561 GCGTTCTTCTACGAGAGGCA 59.829 55.000 0.00 0.00 43.99 4.75
2565 3001 0.170561 TGCGTTCTTCTACGAGAGGC 59.829 55.000 0.00 0.00 43.99 4.70
2566 3002 2.853731 ATGCGTTCTTCTACGAGAGG 57.146 50.000 0.00 0.00 43.99 3.69
2567 3003 5.517037 AAAAATGCGTTCTTCTACGAGAG 57.483 39.130 0.00 0.00 43.99 3.20
2592 3028 2.639065 AGTTGTGCCTCTTGAAAACGA 58.361 42.857 0.00 0.00 0.00 3.85
2594 3030 4.494484 ACAAAGTTGTGCCTCTTGAAAAC 58.506 39.130 0.00 0.00 40.49 2.43
2620 3056 1.202627 GGCACACATTTGCTTTTGGGA 60.203 47.619 0.00 0.00 42.56 4.37
2675 3112 6.746364 GCAGAGATTTGCTTCTACATGAAAAG 59.254 38.462 0.00 0.85 40.89 2.27
2684 3121 2.840038 TGGAGGCAGAGATTTGCTTCTA 59.160 45.455 9.46 1.66 46.07 2.10
2685 3122 1.632409 TGGAGGCAGAGATTTGCTTCT 59.368 47.619 9.46 0.00 46.07 2.85
2703 3140 4.311816 AGCACAGATTTGTTTCTTGTGG 57.688 40.909 5.24 0.00 34.62 4.17


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

AutoCloner maintained by Alex Coulton.