Multiple sequence alignment - TraesCS2A01G325000

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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 TraesCS2A01G325000 chr2A 100.000 4540 0 0 1 4540 554823265 554827804 0.000000e+00 8384.0
1 TraesCS2A01G325000 chr2A 91.814 794 63 2 3746 4539 11663648 11664439 0.000000e+00 1105.0
2 TraesCS2A01G325000 chr2A 96.970 33 0 1 3198 3230 554826433 554826464 2.000000e-03 54.7
3 TraesCS2A01G325000 chr2A 96.970 33 0 1 3169 3200 554826462 554826494 2.000000e-03 54.7
4 TraesCS2A01G325000 chr2B 95.214 3218 122 12 1 3200 510400816 510397613 0.000000e+00 5060.0
5 TraesCS2A01G325000 chr2B 90.714 560 29 8 3198 3740 510397645 510397092 0.000000e+00 725.0
6 TraesCS2A01G325000 chr2D 95.597 3134 106 13 1 3123 431515945 431512833 0.000000e+00 4994.0
7 TraesCS2A01G325000 chr2D 90.050 794 75 4 3749 4540 419606001 419605210 0.000000e+00 1026.0
8 TraesCS2A01G325000 chr2D 90.184 326 22 4 3321 3643 431512434 431512116 2.530000e-112 416.0
9 TraesCS2A01G325000 chr2D 94.118 102 6 0 3639 3740 431503847 431503746 6.080000e-34 156.0
10 TraesCS2A01G325000 chr2D 95.455 88 3 1 3114 3200 431512543 431512456 6.120000e-29 139.0
11 TraesCS2A01G325000 chr2D 94.643 56 3 0 3198 3253 431512488 431512433 2.250000e-13 87.9
12 TraesCS2A01G325000 chr1D 91.844 797 58 5 3747 4539 426553194 426553987 0.000000e+00 1105.0
13 TraesCS2A01G325000 chr1D 91.343 797 61 6 3747 4539 426552063 426552855 0.000000e+00 1083.0
14 TraesCS2A01G325000 chr1D 91.643 694 52 4 3850 4539 426551033 426551724 0.000000e+00 955.0
15 TraesCS2A01G325000 chr6B 90.542 793 70 5 3747 4536 714464142 714464932 0.000000e+00 1044.0
16 TraesCS2A01G325000 chr6D 89.001 791 72 7 3747 4536 468687987 468688763 0.000000e+00 965.0
17 TraesCS2A01G325000 chr3D 88.035 794 71 12 3747 4538 151069121 151068350 0.000000e+00 918.0
18 TraesCS2A01G325000 chr6A 87.863 791 83 6 3747 4536 11531995 11532773 0.000000e+00 917.0
19 TraesCS2A01G325000 chr5A 88.571 105 11 1 4432 4536 306897107 306897210 4.770000e-25 126.0


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 TraesCS2A01G325000 chr2A 554823265 554827804 4539 False 2831.133333 8384 97.98000 1 4540 3 chr2A.!!$F2 4539
1 TraesCS2A01G325000 chr2A 11663648 11664439 791 False 1105.000000 1105 91.81400 3746 4539 1 chr2A.!!$F1 793
2 TraesCS2A01G325000 chr2B 510397092 510400816 3724 True 2892.500000 5060 92.96400 1 3740 2 chr2B.!!$R1 3739
3 TraesCS2A01G325000 chr2D 431512116 431515945 3829 True 1409.225000 4994 93.96975 1 3643 4 chr2D.!!$R3 3642
4 TraesCS2A01G325000 chr2D 419605210 419606001 791 True 1026.000000 1026 90.05000 3749 4540 1 chr2D.!!$R1 791
5 TraesCS2A01G325000 chr1D 426551033 426553987 2954 False 1047.666667 1105 91.61000 3747 4539 3 chr1D.!!$F1 792
6 TraesCS2A01G325000 chr6B 714464142 714464932 790 False 1044.000000 1044 90.54200 3747 4536 1 chr6B.!!$F1 789
7 TraesCS2A01G325000 chr6D 468687987 468688763 776 False 965.000000 965 89.00100 3747 4536 1 chr6D.!!$F1 789
8 TraesCS2A01G325000 chr3D 151068350 151069121 771 True 918.000000 918 88.03500 3747 4538 1 chr3D.!!$R1 791
9 TraesCS2A01G325000 chr6A 11531995 11532773 778 False 917.000000 917 87.86300 3747 4536 1 chr6A.!!$F1 789

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
916 934 0.906066 GAGTCCTTCCACTCCTTCCC 59.094 60.0 0.00 0.0 37.43 3.97 F
1566 1584 0.534877 AACTGCGCTGGTTGACATGA 60.535 50.0 18.98 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2901 2921 0.041535 AGGTGACCCCGGTGTACATA 59.958 55.0 0.00 0.0 38.74 2.29 R
3556 3885 0.027455 CGCGTCAGCTTTGTTGACAA 59.973 50.0 13.27 0.0 42.45 3.18 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
91 98 6.756074 GGAATCCGAATAAACAAATGCAATCA 59.244 34.615 0.00 0.00 0.00 2.57
132 143 3.242316 CCTCGGTTATTTAAAGCGCTGAC 60.242 47.826 12.58 1.26 40.50 3.51
621 632 3.214328 CGGATCTGGAGTTTAAATGGGG 58.786 50.000 0.00 0.00 0.00 4.96
684 695 1.503542 CACGGATTGGTTGCTGCTC 59.496 57.895 0.00 0.00 0.00 4.26
707 718 2.704725 TAAGCAAAGAAAGGCAAGCG 57.295 45.000 0.00 0.00 0.00 4.68
711 722 2.919494 AAAGAAAGGCAAGCGGCGG 61.919 57.895 9.78 0.00 46.16 6.13
916 934 0.906066 GAGTCCTTCCACTCCTTCCC 59.094 60.000 0.00 0.00 37.43 3.97
927 945 2.365105 CCTTCCCCGAGGCTACCA 60.365 66.667 0.00 0.00 0.00 3.25
1142 1160 2.870372 GACCAGCACACGATTGCC 59.130 61.111 9.00 0.00 44.14 4.52
1284 1302 1.048160 TGCGAGCTGTGGGGATATCA 61.048 55.000 4.83 0.00 0.00 2.15
1313 1331 2.150397 AGGTACTGTTCAACGCAGTC 57.850 50.000 0.95 0.00 44.96 3.51
1328 1346 1.797025 CAGTCGAGGAAAAGGGTGTC 58.203 55.000 0.00 0.00 0.00 3.67
1391 1409 1.826096 GACTGGAAGGAGGTAGTGGAC 59.174 57.143 0.00 0.00 39.30 4.02
1424 1442 3.972227 CTTGAGGTTCAGGCACCG 58.028 61.111 0.00 0.00 42.33 4.94
1566 1584 0.534877 AACTGCGCTGGTTGACATGA 60.535 50.000 18.98 0.00 0.00 3.07
1700 1718 3.437049 GTCGAGAGGCACTTGCTATTTTT 59.563 43.478 0.38 0.00 41.55 1.94
1737 1755 1.411246 CCGAGGTGAACCCGAATGATA 59.589 52.381 10.68 0.00 38.74 2.15
1830 1848 5.191722 TCATACATAAGGAGAAAGGCCTTGT 59.808 40.000 21.33 12.55 45.05 3.16
1847 1865 4.461198 CCTTGTCCCTTACAGTTGTTCTT 58.539 43.478 0.00 0.00 39.87 2.52
1982 2000 1.600916 GGCAAGCAACGGAAGAGGT 60.601 57.895 0.00 0.00 0.00 3.85
2006 2024 1.981312 AGCGCTGGAGCTCTTCTCA 60.981 57.895 10.39 1.66 45.67 3.27
2016 2034 4.173622 GAGCTCTTCTCATCCATGCGGA 62.174 54.545 6.43 0.00 41.51 5.54
2078 2096 1.002868 CCTAGCTTGCAGCCACAGT 60.003 57.895 0.00 0.00 43.77 3.55
2203 2221 2.450476 GGCAGGTTTGATTGATGAGGT 58.550 47.619 0.00 0.00 0.00 3.85
2233 2251 7.201938 CCAGTTTATCAGGAATATGCCAATTGT 60.202 37.037 1.47 0.00 0.00 2.71
2642 2660 2.210116 GAGAAGCAAGTGTCCGTTTCA 58.790 47.619 0.00 0.00 0.00 2.69
2732 2750 4.693283 TGTCGAAGAATTTGAGAGTGTGT 58.307 39.130 0.00 0.00 39.66 3.72
2768 2786 2.066262 GCCACGAAGTTGATCTCGAAA 58.934 47.619 8.86 0.00 41.61 3.46
2870 2888 8.894768 ATTACTGGTGAGTATAAATTCTCTGC 57.105 34.615 0.00 0.00 34.53 4.26
2898 2918 8.557029 CGTCAAGGTTTTTCTCTTACATAAGTT 58.443 33.333 0.00 0.00 34.93 2.66
2914 2934 6.527423 ACATAAGTTTATATGTACACCGGGG 58.473 40.000 0.00 0.00 43.04 5.73
2915 2935 6.100134 ACATAAGTTTATATGTACACCGGGGT 59.900 38.462 16.91 16.91 43.04 4.95
2957 2977 7.891183 CTGTACAGCACTTTGTAAGTAATCT 57.109 36.000 10.54 0.00 40.46 2.40
2958 2978 7.652300 TGTACAGCACTTTGTAAGTAATCTG 57.348 36.000 0.00 11.02 40.46 2.90
2959 2979 7.214381 TGTACAGCACTTTGTAAGTAATCTGT 58.786 34.615 17.31 17.31 42.69 3.41
2960 2980 8.361889 TGTACAGCACTTTGTAAGTAATCTGTA 58.638 33.333 16.09 16.09 41.55 2.74
2961 2981 9.199982 GTACAGCACTTTGTAAGTAATCTGTAA 57.800 33.333 18.87 9.36 42.58 2.41
2962 2982 8.311650 ACAGCACTTTGTAAGTAATCTGTAAG 57.688 34.615 14.21 0.00 40.59 2.34
2963 2983 7.931948 ACAGCACTTTGTAAGTAATCTGTAAGT 59.068 33.333 14.21 0.00 40.59 2.24
2964 2984 9.419297 CAGCACTTTGTAAGTAATCTGTAAGTA 57.581 33.333 0.00 0.00 40.46 2.24
2965 2985 9.420551 AGCACTTTGTAAGTAATCTGTAAGTAC 57.579 33.333 0.00 0.00 40.46 2.73
2966 2986 9.199982 GCACTTTGTAAGTAATCTGTAAGTACA 57.800 33.333 0.00 0.00 40.46 2.90
3177 3496 6.726490 TCTCCTTACCTCATGTAACATACC 57.274 41.667 0.00 0.00 34.50 2.73
3178 3497 6.199376 TCTCCTTACCTCATGTAACATACCA 58.801 40.000 0.00 0.00 34.50 3.25
3179 3498 6.097839 TCTCCTTACCTCATGTAACATACCAC 59.902 42.308 0.00 0.00 34.50 4.16
3180 3499 5.962031 TCCTTACCTCATGTAACATACCACT 59.038 40.000 0.00 0.00 34.50 4.00
3181 3500 7.127405 TCCTTACCTCATGTAACATACCACTA 58.873 38.462 0.00 0.00 34.50 2.74
3182 3501 7.787904 TCCTTACCTCATGTAACATACCACTAT 59.212 37.037 0.00 0.00 34.50 2.12
3183 3502 8.429641 CCTTACCTCATGTAACATACCACTATT 58.570 37.037 0.00 0.00 34.50 1.73
3187 3506 9.778741 ACCTCATGTAACATACCACTATTAATG 57.221 33.333 0.00 0.00 0.00 1.90
3188 3507 9.996554 CCTCATGTAACATACCACTATTAATGA 57.003 33.333 0.00 0.00 0.00 2.57
3293 3612 2.416638 AGATTCCTAGCCTGCCAGAAT 58.583 47.619 0.00 0.00 0.00 2.40
3319 3638 2.346766 TGGTTCTGCAGCTTCAAGAA 57.653 45.000 9.47 0.00 0.00 2.52
3340 3661 2.293677 ACGAGAACTGAGTGTGTACAGG 59.706 50.000 0.00 0.00 38.30 4.00
3431 3758 4.632538 AAAGAAACTGTGGTGTGCTTAC 57.367 40.909 0.00 0.00 0.00 2.34
3448 3776 7.683676 GTGTGCTTACATAAAATTTCAAATGCG 59.316 33.333 0.00 0.00 0.00 4.73
3474 3802 4.685924 CAGCACAGTTTCCTTTCATTGTT 58.314 39.130 0.00 0.00 0.00 2.83
3516 3845 0.036010 CTGGGTCGACTTTGATGGCT 60.036 55.000 16.46 0.00 0.00 4.75
3524 3853 2.673368 CGACTTTGATGGCTCAACCTAC 59.327 50.000 0.00 0.00 41.05 3.18
3527 3856 0.392461 TTGATGGCTCAACCTACGGC 60.392 55.000 0.00 0.00 36.46 5.68
3552 3881 2.364632 TCTGGTGAGTTGGTGTTGTTG 58.635 47.619 0.00 0.00 0.00 3.33
3553 3882 2.091541 CTGGTGAGTTGGTGTTGTTGT 58.908 47.619 0.00 0.00 0.00 3.32
3554 3883 2.491693 CTGGTGAGTTGGTGTTGTTGTT 59.508 45.455 0.00 0.00 0.00 2.83
3555 3884 2.230025 TGGTGAGTTGGTGTTGTTGTTG 59.770 45.455 0.00 0.00 0.00 3.33
3556 3885 2.230266 GGTGAGTTGGTGTTGTTGTTGT 59.770 45.455 0.00 0.00 0.00 3.32
3557 3886 3.305744 GGTGAGTTGGTGTTGTTGTTGTT 60.306 43.478 0.00 0.00 0.00 2.83
3636 3971 8.677148 ATAATCTTTGTTGTAATATCGGCTGT 57.323 30.769 0.00 0.00 0.00 4.40
3644 3979 9.549078 TTGTTGTAATATCGGCTGTTGATATAA 57.451 29.630 0.00 0.00 37.91 0.98
3666 4003 3.132289 ACCACTTATCTGTACATCGGGTG 59.868 47.826 0.00 2.92 0.00 4.61
3719 4056 1.271379 ACCTTTCAAGTGTCATCCGGG 60.271 52.381 0.00 0.00 0.00 5.73
3740 4077 2.485903 CGGCAAGTACACCAAGTTGTA 58.514 47.619 1.45 0.00 33.21 2.41
3741 4078 2.873472 CGGCAAGTACACCAAGTTGTAA 59.127 45.455 1.45 0.00 33.73 2.41
3742 4079 3.059188 CGGCAAGTACACCAAGTTGTAAG 60.059 47.826 1.45 0.00 33.73 2.34
3743 4080 3.304458 GGCAAGTACACCAAGTTGTAAGC 60.304 47.826 1.45 0.00 33.73 3.09
3744 4081 3.314080 GCAAGTACACCAAGTTGTAAGCA 59.686 43.478 1.45 0.00 33.73 3.91
3789 4126 1.799181 CGACGACGCTCATTGGAATCT 60.799 52.381 0.00 0.00 0.00 2.40
3835 5313 2.299013 CTCACGCACTATAATAGCCCCA 59.701 50.000 0.00 0.00 0.00 4.96
3844 5322 7.094377 CGCACTATAATAGCCCCAATTGTATTT 60.094 37.037 4.43 0.00 0.00 1.40
3882 5361 8.832735 ACTAGTATTTATCTTTCCCCTGTTCAA 58.167 33.333 0.00 0.00 0.00 2.69
3883 5362 7.939784 AGTATTTATCTTTCCCCTGTTCAAC 57.060 36.000 0.00 0.00 0.00 3.18
3928 5407 4.582656 TGTTTCTGTTCCCCACACATTAAG 59.417 41.667 0.00 0.00 0.00 1.85
3965 5444 0.478072 TGTTCCAACTCCACTGGCAT 59.522 50.000 0.00 0.00 33.63 4.40
3971 5450 2.749621 CCAACTCCACTGGCATAAGTTC 59.250 50.000 0.00 0.00 0.00 3.01
4049 5528 6.260271 GTGCTCTCTTTTTACCACTTACACTT 59.740 38.462 0.00 0.00 0.00 3.16
4122 5601 0.889994 TGACGGTTAAGAAGGCGCTA 59.110 50.000 7.64 0.00 0.00 4.26
4131 5610 3.636153 AAGAAGGCGCTAGGATTCTTT 57.364 42.857 7.64 0.00 38.51 2.52
4167 5647 7.918076 AGACTTTCTTGTCCAACCTATCAATA 58.082 34.615 0.00 0.00 37.66 1.90
4170 5650 8.109634 ACTTTCTTGTCCAACCTATCAATACAT 58.890 33.333 0.00 0.00 0.00 2.29
4173 5653 7.402054 TCTTGTCCAACCTATCAATACATTGT 58.598 34.615 2.08 0.00 38.84 2.71
4214 5697 3.341823 AGCATGCATGGCTAGTAATAGC 58.658 45.455 27.34 13.72 40.47 2.97
4226 5709 6.884295 TGGCTAGTAATAGCTTGAACACAAAT 59.116 34.615 20.53 0.00 42.45 2.32
4239 5722 7.465379 GCTTGAACACAAATGTAAAGGAAAACC 60.465 37.037 0.00 0.00 38.45 3.27
4387 5872 5.531287 AGAAACTTAAGCCACGTTCATCTTT 59.469 36.000 1.29 0.00 0.00 2.52
4473 5961 7.462109 TGACTATTTTGTTTTTGTGCACATC 57.538 32.000 22.39 10.69 0.00 3.06
4501 5989 8.458052 TCTATTTTGTGCACATTATGTAACCTG 58.542 33.333 22.39 3.48 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 98 1.777272 GGTTATCCCCTGAGAAGCCAT 59.223 52.381 0.00 0.00 34.87 4.40
132 143 2.046314 CCGGGTAGGTGGTTGCTG 60.046 66.667 0.00 0.00 34.51 4.41
621 632 2.362760 TGGCCCCACATGTCATGC 60.363 61.111 12.91 0.00 0.00 4.06
684 695 3.762779 CTTGCCTTTCTTTGCTTATCCG 58.237 45.455 0.00 0.00 0.00 4.18
711 722 2.200170 CTTAAGCGCACCAGGCCAAC 62.200 60.000 11.47 0.00 40.31 3.77
916 934 4.208686 GGAGCGTGGTAGCCTCGG 62.209 72.222 10.86 0.00 40.31 4.63
1019 1037 3.131396 GGCACGGATAAGGATGTTGTAG 58.869 50.000 0.00 0.00 0.00 2.74
1136 1154 2.095415 GGACTTTACGGTGTTGGCAATC 60.095 50.000 1.92 0.00 0.00 2.67
1142 1160 0.511221 CGCAGGACTTTACGGTGTTG 59.489 55.000 0.00 0.00 0.00 3.33
1265 1283 1.048160 TGATATCCCCACAGCTCGCA 61.048 55.000 0.00 0.00 0.00 5.10
1284 1302 0.251165 AACAGTACCTTTGCCGCCAT 60.251 50.000 0.00 0.00 0.00 4.40
1313 1331 2.064014 GTAACGACACCCTTTTCCTCG 58.936 52.381 0.00 0.00 0.00 4.63
1328 1346 4.434725 GCTATCATCGCATTCCATGTAACG 60.435 45.833 0.00 0.00 0.00 3.18
1391 1409 4.949856 ACCTCAAGCATACCCTTAAACATG 59.050 41.667 0.00 0.00 0.00 3.21
1424 1442 3.820467 TCACCAATGTGACCTCATCAAAC 59.180 43.478 0.00 0.00 46.40 2.93
1566 1584 2.624838 CAAGTTCTCCACACTTGGCATT 59.375 45.455 5.10 0.00 45.06 3.56
1700 1718 2.297315 CTCGGTAGCCTGCATCTCATTA 59.703 50.000 0.00 0.00 0.00 1.90
1737 1755 2.573462 AGAGCACACTGACCATGGTTAT 59.427 45.455 20.85 4.62 0.00 1.89
1830 1848 2.173782 TGCCAAGAACAACTGTAAGGGA 59.826 45.455 0.00 0.00 39.30 4.20
2006 2024 1.754234 GTTGGCCTTCCGCATGGAT 60.754 57.895 3.32 0.00 45.91 3.41
2016 2034 1.075374 TGTAGGCTCAATGTTGGCCTT 59.925 47.619 23.39 13.26 46.00 4.35
2078 2096 1.275291 CGACCCTCCTCAACTAAGCAA 59.725 52.381 0.00 0.00 0.00 3.91
2203 2221 4.580167 GCATATTCCTGATAAACTGGTGCA 59.420 41.667 0.00 0.00 36.57 4.57
2399 2417 1.143305 CCTTCCGAATCATAGCTGCG 58.857 55.000 0.00 0.00 0.00 5.18
2480 2498 6.319658 TGTCTTCAGCAAAGAACTCAAAGATT 59.680 34.615 3.40 0.00 45.50 2.40
2705 2723 2.029380 TCTCAAATTCTTCGACAGCCGA 60.029 45.455 0.00 0.00 46.94 5.54
2721 2739 1.473257 GCAGTCCACACACACTCTCAA 60.473 52.381 0.00 0.00 0.00 3.02
2768 2786 4.389374 CAACAATCTCCCTGTTGTACACT 58.611 43.478 0.00 0.00 45.58 3.55
2793 2811 3.648067 TGATGAAACCTGTTCCTGTCTCT 59.352 43.478 0.00 0.00 0.00 3.10
2870 2888 3.246699 TGTAAGAGAAAAACCTTGACGCG 59.753 43.478 3.53 3.53 0.00 6.01
2898 2918 2.699846 GGTGACCCCGGTGTACATATAA 59.300 50.000 0.00 0.00 0.00 0.98
2899 2919 2.091166 AGGTGACCCCGGTGTACATATA 60.091 50.000 0.00 0.00 38.74 0.86
2900 2920 1.125633 GGTGACCCCGGTGTACATAT 58.874 55.000 0.00 0.00 0.00 1.78
2901 2921 0.041535 AGGTGACCCCGGTGTACATA 59.958 55.000 0.00 0.00 38.74 2.29
2914 2934 1.896694 CCTCTCTGGCTCAGGTGAC 59.103 63.158 2.86 0.00 31.51 3.67
2915 2935 4.449638 CCTCTCTGGCTCAGGTGA 57.550 61.111 2.86 2.10 31.51 4.02
2954 2974 6.479001 GTGAACGGCATTATGTACTTACAGAT 59.521 38.462 0.00 0.00 39.92 2.90
2955 2975 5.808540 GTGAACGGCATTATGTACTTACAGA 59.191 40.000 0.00 0.00 39.92 3.41
2956 2976 5.810587 AGTGAACGGCATTATGTACTTACAG 59.189 40.000 0.00 0.00 39.92 2.74
2957 2977 5.726397 AGTGAACGGCATTATGTACTTACA 58.274 37.500 0.00 0.00 40.98 2.41
2958 2978 6.040878 AGAGTGAACGGCATTATGTACTTAC 58.959 40.000 0.00 0.00 0.00 2.34
2959 2979 6.127563 TGAGAGTGAACGGCATTATGTACTTA 60.128 38.462 0.00 0.00 0.00 2.24
2960 2980 5.086104 AGAGTGAACGGCATTATGTACTT 57.914 39.130 0.00 0.00 0.00 2.24
2961 2981 4.159693 TGAGAGTGAACGGCATTATGTACT 59.840 41.667 0.00 0.00 0.00 2.73
2962 2982 4.430007 TGAGAGTGAACGGCATTATGTAC 58.570 43.478 0.00 0.00 0.00 2.90
2963 2983 4.729227 TGAGAGTGAACGGCATTATGTA 57.271 40.909 0.00 0.00 0.00 2.29
2964 2984 3.610040 TGAGAGTGAACGGCATTATGT 57.390 42.857 0.00 0.00 0.00 2.29
2965 2985 4.154015 TGTTTGAGAGTGAACGGCATTATG 59.846 41.667 0.00 0.00 0.00 1.90
2966 2986 4.323417 TGTTTGAGAGTGAACGGCATTAT 58.677 39.130 0.00 0.00 0.00 1.28
2967 2987 3.734463 TGTTTGAGAGTGAACGGCATTA 58.266 40.909 0.00 0.00 0.00 1.90
3028 3048 2.434428 CAAGCCTGAAACTCTGCAGAT 58.566 47.619 18.63 1.53 34.06 2.90
3264 3583 4.100189 GCAGGCTAGGAATCTTCTCTAACA 59.900 45.833 0.00 0.00 0.00 2.41
3269 3588 1.765314 TGGCAGGCTAGGAATCTTCTC 59.235 52.381 0.00 0.00 0.00 2.87
3271 3590 1.765314 TCTGGCAGGCTAGGAATCTTC 59.235 52.381 15.73 0.00 0.00 2.87
3293 3612 3.181455 TGAAGCTGCAGAACCAACTTCTA 60.181 43.478 20.43 7.54 37.08 2.10
3319 3638 2.293677 CCTGTACACACTCAGTTCTCGT 59.706 50.000 0.00 0.00 0.00 4.18
3422 3749 7.683676 CGCATTTGAAATTTTATGTAAGCACAC 59.316 33.333 0.00 0.00 37.54 3.82
3425 3752 7.093354 TCCGCATTTGAAATTTTATGTAAGCA 58.907 30.769 0.00 0.00 0.00 3.91
3431 3758 5.501252 GCTGCTCCGCATTTGAAATTTTATG 60.501 40.000 0.00 0.00 38.13 1.90
3448 3776 1.268079 GAAAGGAAACTGTGCTGCTCC 59.732 52.381 0.00 0.00 42.68 4.70
3474 3802 3.587933 GCCGTCGTTGTGGCCAAA 61.588 61.111 7.24 0.00 45.73 3.28
3524 3853 1.302033 AACTCACCAGAAGCAGCCG 60.302 57.895 0.00 0.00 0.00 5.52
3527 3856 1.233019 CACCAACTCACCAGAAGCAG 58.767 55.000 0.00 0.00 0.00 4.24
3554 3883 1.202132 GCGTCAGCTTTGTTGACAACA 60.202 47.619 17.02 17.02 42.45 3.33
3555 3884 1.466855 GCGTCAGCTTTGTTGACAAC 58.533 50.000 11.54 11.54 42.45 3.32
3556 3885 0.027455 CGCGTCAGCTTTGTTGACAA 59.973 50.000 13.27 0.00 42.45 3.18
3557 3886 1.087202 ACGCGTCAGCTTTGTTGACA 61.087 50.000 5.58 0.00 42.45 3.58
3615 3949 5.935206 TCAACAGCCGATATTACAACAAAGA 59.065 36.000 0.00 0.00 0.00 2.52
3616 3950 6.176975 TCAACAGCCGATATTACAACAAAG 57.823 37.500 0.00 0.00 0.00 2.77
3621 3956 8.151596 TGGTTATATCAACAGCCGATATTACAA 58.848 33.333 9.96 0.00 37.22 2.41
3628 3963 4.689612 AGTGGTTATATCAACAGCCGAT 57.310 40.909 0.00 0.00 0.00 4.18
3629 3964 4.481368 AAGTGGTTATATCAACAGCCGA 57.519 40.909 0.00 0.00 0.00 5.54
3636 3971 9.908152 CGATGTACAGATAAGTGGTTATATCAA 57.092 33.333 0.33 0.00 32.17 2.57
3644 3979 3.132289 CACCCGATGTACAGATAAGTGGT 59.868 47.826 0.33 0.00 0.00 4.16
3666 4003 5.010112 TGTCGGATATGGAGATTTCTCACTC 59.990 44.000 9.65 0.00 44.60 3.51
3719 4056 0.040425 CAACTTGGTGTACTTGCCGC 60.040 55.000 0.00 0.00 0.00 6.53
3740 4077 0.447801 CCTACGCAATTTCGCTGCTT 59.552 50.000 0.00 0.00 37.67 3.91
3741 4078 0.391130 TCCTACGCAATTTCGCTGCT 60.391 50.000 0.00 0.00 37.67 4.24
3742 4079 0.026803 CTCCTACGCAATTTCGCTGC 59.973 55.000 0.00 0.00 36.41 5.25
3743 4080 0.026803 GCTCCTACGCAATTTCGCTG 59.973 55.000 0.00 0.00 0.00 5.18
3744 4081 0.391130 TGCTCCTACGCAATTTCGCT 60.391 50.000 0.00 0.00 36.89 4.93
3789 4126 1.067000 CCAAAGCGATTTGATGGGCAA 60.067 47.619 26.63 0.00 33.95 4.52
3882 5361 4.409570 CGTGTACTTTACGTCTGCTATGT 58.590 43.478 0.00 0.00 36.83 2.29
3883 5362 4.993560 CGTGTACTTTACGTCTGCTATG 57.006 45.455 0.00 0.00 36.83 2.23
3905 5384 2.746279 ATGTGTGGGGAACAGAAACA 57.254 45.000 0.00 0.00 40.26 2.83
3910 5389 3.154827 ACCTTAATGTGTGGGGAACAG 57.845 47.619 0.00 0.00 40.26 3.16
3928 5407 3.113260 ACAGTGTAGCAGACAGAAACC 57.887 47.619 0.00 0.00 39.29 3.27
3971 5450 6.256975 CCAGCAATGTTAAATGACATGAATGG 59.743 38.462 0.00 0.00 40.03 3.16
4058 5537 4.281435 TGACCGGACTTGTAGTAACAATCA 59.719 41.667 9.46 0.00 44.43 2.57
4069 5548 5.607939 TTATATCACATGACCGGACTTGT 57.392 39.130 17.39 17.39 0.00 3.16
4107 5586 2.912690 ATCCTAGCGCCTTCTTAACC 57.087 50.000 2.29 0.00 0.00 2.85
4113 5592 2.633488 ACAAAGAATCCTAGCGCCTTC 58.367 47.619 2.29 0.00 0.00 3.46
4122 5601 2.871096 TTGCCCGTACAAAGAATCCT 57.129 45.000 0.00 0.00 0.00 3.24
4131 5610 2.875933 CAAGAAAGTCTTTGCCCGTACA 59.124 45.455 1.60 0.00 33.78 2.90
4167 5647 2.501723 CCTAGTGGCCTAGACACAATGT 59.498 50.000 16.49 0.00 45.35 2.71
4214 5697 7.905126 GGTTTTCCTTTACATTTGTGTTCAAG 58.095 34.615 0.00 0.00 34.44 3.02
4232 5715 6.877981 GGTCTTTACCCCAGGAGGTTTTCC 62.878 54.167 5.03 0.00 42.31 3.13
4239 5722 3.654273 TCTATGGTCTTTACCCCAGGAG 58.346 50.000 0.00 0.00 46.16 3.69
4307 5791 2.022195 TGTCGCTCGAATTAGCTACCT 58.978 47.619 0.00 0.00 40.49 3.08
4370 5855 4.537135 AGAGAAAGATGAACGTGGCTTA 57.463 40.909 0.00 0.00 0.00 3.09
4387 5872 2.741930 CATCGCGTGCAAGAAGAGA 58.258 52.632 5.77 0.00 0.00 3.10
4473 5961 9.236691 GGTTACATAATGTGCACAAAATAGATG 57.763 33.333 25.72 20.21 0.00 2.90


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

AutoCloner maintained by Alex Coulton.