Multiple sequence alignment - TraesCS4D01G229700

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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 TraesCS4D01G229700 chr4D 100.000 3942 0 0 1 3942 389479357 389483298 0.000000e+00 7280
1 TraesCS4D01G229700 chr4D 89.831 767 45 18 1 747 283855618 283854865 0.000000e+00 953
2 TraesCS4D01G229700 chr4A 92.216 2518 123 28 804 3290 71122758 71125233 0.000000e+00 3496
3 TraesCS4D01G229700 chr4A 90.977 665 40 8 3287 3942 71125313 71125966 0.000000e+00 878
4 TraesCS4D01G229700 chr4B 92.406 2423 120 30 1562 3942 479227629 479230029 0.000000e+00 3397
5 TraesCS4D01G229700 chr4B 94.274 716 30 5 804 1515 479226619 479227327 0.000000e+00 1085
6 TraesCS4D01G229700 chr5D 91.241 822 43 18 9 807 410840815 410841630 0.000000e+00 1092
7 TraesCS4D01G229700 chr5D 90.865 832 42 15 1 803 478460129 478459303 0.000000e+00 1085
8 TraesCS4D01G229700 chr6D 88.954 851 41 22 1 803 147646733 147647578 0.000000e+00 1002
9 TraesCS4D01G229700 chr2D 90.296 742 40 15 1 716 552532691 552531956 0.000000e+00 942
10 TraesCS4D01G229700 chr2D 90.741 432 32 5 376 803 36547511 36547938 1.590000e-158 569
11 TraesCS4D01G229700 chr3D 87.342 790 53 15 45 803 369418423 369417650 0.000000e+00 861
12 TraesCS4D01G229700 chr3D 90.443 429 34 5 382 803 601085565 601085993 3.440000e-155 558
13 TraesCS4D01G229700 chr7B 86.403 809 82 19 10 803 725524054 725523259 0.000000e+00 859
14 TraesCS4D01G229700 chr6A 85.943 811 97 14 6 804 101542377 101543182 0.000000e+00 850
15 TraesCS4D01G229700 chr6A 83.427 356 39 12 451 798 33030459 33030802 2.960000e-81 313
16 TraesCS4D01G229700 chr7D 87.429 700 42 24 140 804 126659402 126658714 0.000000e+00 763
17 TraesCS4D01G229700 chr1B 83.951 810 98 30 9 798 10837292 10838089 0.000000e+00 747
18 TraesCS4D01G229700 chr1B 82.469 405 55 10 406 798 416635279 416635679 1.360000e-89 340
19 TraesCS4D01G229700 chr3A 83.231 817 98 31 1 803 690214699 690215490 0.000000e+00 713


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 TraesCS4D01G229700 chr4D 389479357 389483298 3941 False 7280 7280 100.0000 1 3942 1 chr4D.!!$F1 3941
1 TraesCS4D01G229700 chr4D 283854865 283855618 753 True 953 953 89.8310 1 747 1 chr4D.!!$R1 746
2 TraesCS4D01G229700 chr4A 71122758 71125966 3208 False 2187 3496 91.5965 804 3942 2 chr4A.!!$F1 3138
3 TraesCS4D01G229700 chr4B 479226619 479230029 3410 False 2241 3397 93.3400 804 3942 2 chr4B.!!$F1 3138
4 TraesCS4D01G229700 chr5D 410840815 410841630 815 False 1092 1092 91.2410 9 807 1 chr5D.!!$F1 798
5 TraesCS4D01G229700 chr5D 478459303 478460129 826 True 1085 1085 90.8650 1 803 1 chr5D.!!$R1 802
6 TraesCS4D01G229700 chr6D 147646733 147647578 845 False 1002 1002 88.9540 1 803 1 chr6D.!!$F1 802
7 TraesCS4D01G229700 chr2D 552531956 552532691 735 True 942 942 90.2960 1 716 1 chr2D.!!$R1 715
8 TraesCS4D01G229700 chr3D 369417650 369418423 773 True 861 861 87.3420 45 803 1 chr3D.!!$R1 758
9 TraesCS4D01G229700 chr7B 725523259 725524054 795 True 859 859 86.4030 10 803 1 chr7B.!!$R1 793
10 TraesCS4D01G229700 chr6A 101542377 101543182 805 False 850 850 85.9430 6 804 1 chr6A.!!$F2 798
11 TraesCS4D01G229700 chr7D 126658714 126659402 688 True 763 763 87.4290 140 804 1 chr7D.!!$R1 664
12 TraesCS4D01G229700 chr1B 10837292 10838089 797 False 747 747 83.9510 9 798 1 chr1B.!!$F1 789
13 TraesCS4D01G229700 chr3A 690214699 690215490 791 False 713 713 83.2310 1 803 1 chr3A.!!$F1 802

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
120 127 1.068895 TCTCGTGGAAGCAAAACCGTA 59.931 47.619 0.00 0.0 0.00 4.02 F
774 897 1.221840 GATCCTTGCGAGGCTTCCA 59.778 57.895 16.01 0.0 43.21 3.53 F
1604 2003 0.106419 AAGGGGACGAAAAAGCACCA 60.106 50.000 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1036 1168 0.525668 TCGATCGAAGCGGAAGAAGC 60.526 55.0 16.99 0.0 0.00 3.86 R
1942 2343 0.618458 TATCTTCACCCACACCCAGC 59.382 55.0 0.00 0.0 0.00 4.85 R
3326 3853 0.234106 CGATCATGAATGGCGTGCTC 59.766 55.0 0.00 0.0 33.39 4.26 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
120 127 1.068895 TCTCGTGGAAGCAAAACCGTA 59.931 47.619 0.00 0.00 0.00 4.02
238 249 4.497340 GCAAAATCAAAACCGTGACTCTCA 60.497 41.667 0.00 0.00 0.00 3.27
598 709 5.343593 TCGCGCAAATTGTTTTTATCGAAAT 59.656 32.000 8.75 0.00 0.00 2.17
614 725 2.418197 CGAAATGCTAAGGAAGACCGGA 60.418 50.000 9.46 0.00 41.83 5.14
737 860 2.031919 ACGTGGCGAATGGCTGAA 59.968 55.556 0.00 0.00 42.94 3.02
774 897 1.221840 GATCCTTGCGAGGCTTCCA 59.778 57.895 16.01 0.00 43.21 3.53
810 933 1.276989 ACTAGTTGATCCCGCCGAAAA 59.723 47.619 0.00 0.00 0.00 2.29
835 958 6.479205 GCTCTCGGCCTAAGTAATGGAACA 62.479 50.000 0.00 0.00 37.71 3.18
924 1051 2.197643 GAAGGAGACCGACGCGACTT 62.198 60.000 15.93 3.50 0.00 3.01
946 1073 4.489771 CCACCTGTCCATCCGCCC 62.490 72.222 0.00 0.00 0.00 6.13
952 1079 2.836360 GTCCATCCGCCCCGTAGA 60.836 66.667 0.00 0.00 0.00 2.59
954 1081 2.520982 CCATCCGCCCCGTAGAGA 60.521 66.667 0.00 0.00 0.00 3.10
955 1082 2.728817 CATCCGCCCCGTAGAGAC 59.271 66.667 0.00 0.00 0.00 3.36
956 1083 2.521224 ATCCGCCCCGTAGAGACC 60.521 66.667 0.00 0.00 0.00 3.85
957 1084 3.369410 ATCCGCCCCGTAGAGACCA 62.369 63.158 0.00 0.00 0.00 4.02
958 1085 3.528370 CCGCCCCGTAGAGACCAG 61.528 72.222 0.00 0.00 0.00 4.00
959 1086 3.528370 CGCCCCGTAGAGACCAGG 61.528 72.222 0.00 0.00 0.00 4.45
960 1087 3.851128 GCCCCGTAGAGACCAGGC 61.851 72.222 0.00 0.00 34.18 4.85
983 1110 1.728971 CAGAGACACGCACTCATTTCC 59.271 52.381 0.00 0.00 36.91 3.13
1045 1177 3.549150 CGCGAGCAGCTTCTTCCG 61.549 66.667 0.00 0.00 45.59 4.30
1193 1325 3.140225 GATCGTCGGGCTCACCTCC 62.140 68.421 0.00 0.00 36.97 4.30
1247 1379 2.269241 GCCGCCTTCCAGCTACTT 59.731 61.111 0.00 0.00 0.00 2.24
1316 1448 1.273886 GAAGCTTCTCCTCGGTTCAGT 59.726 52.381 19.44 0.00 37.53 3.41
1327 1459 2.160205 TCGGTTCAGTCTCTGACGATT 58.840 47.619 7.88 0.00 40.46 3.34
1342 1474 3.978217 TGACGATTGATTTGCGTTTTTCC 59.022 39.130 0.00 0.00 38.51 3.13
1343 1475 3.313690 ACGATTGATTTGCGTTTTTCCC 58.686 40.909 0.00 0.00 34.12 3.97
1462 1594 3.927142 CCGTGAGTGAATTGAGACCTTAC 59.073 47.826 0.00 0.00 0.00 2.34
1493 1625 6.367969 CGAATTTGTCGGTATATTTCTAGGGG 59.632 42.308 0.00 0.00 46.45 4.79
1499 1631 7.068702 TGTCGGTATATTTCTAGGGGTTTCTA 58.931 38.462 0.00 0.00 0.00 2.10
1525 1657 5.050567 CGTTTGGTTCAGTAAGTACAGTTCC 60.051 44.000 0.00 0.00 0.00 3.62
1560 1959 2.987149 CGGTAACTGTTGCTGTAGAGTG 59.013 50.000 9.02 0.00 0.00 3.51
1581 1980 2.095053 GGTAGAGTACACGTCTTCGGTC 59.905 54.545 0.00 0.00 41.85 4.79
1593 1992 2.227089 CTTCGGTCTGGAAGGGGACG 62.227 65.000 0.00 0.00 39.76 4.79
1599 1998 2.152016 GTCTGGAAGGGGACGAAAAAG 58.848 52.381 0.00 0.00 0.00 2.27
1600 1999 0.881796 CTGGAAGGGGACGAAAAAGC 59.118 55.000 0.00 0.00 0.00 3.51
1601 2000 0.183971 TGGAAGGGGACGAAAAAGCA 59.816 50.000 0.00 0.00 0.00 3.91
1603 2002 0.596577 GAAGGGGACGAAAAAGCACC 59.403 55.000 0.00 0.00 0.00 5.01
1604 2003 0.106419 AAGGGGACGAAAAAGCACCA 60.106 50.000 0.00 0.00 0.00 4.17
1605 2004 0.537371 AGGGGACGAAAAAGCACCAG 60.537 55.000 0.00 0.00 0.00 4.00
1606 2005 0.822121 GGGGACGAAAAAGCACCAGT 60.822 55.000 0.00 0.00 0.00 4.00
1607 2006 1.029681 GGGACGAAAAAGCACCAGTT 58.970 50.000 0.00 0.00 0.00 3.16
1608 2007 1.269051 GGGACGAAAAAGCACCAGTTG 60.269 52.381 0.00 0.00 0.00 3.16
1704 2104 2.271800 CCAGATCGTAGCTGTTTCCAC 58.728 52.381 0.00 0.00 0.00 4.02
1831 2232 8.918202 TGGAGATTCTGTTGTTACTAAAATGT 57.082 30.769 0.00 0.00 0.00 2.71
1942 2343 9.167311 ACCTATTTGCATTCTAGTTTGAAGTAG 57.833 33.333 0.00 0.13 34.04 2.57
1945 2346 6.486253 TTGCATTCTAGTTTGAAGTAGCTG 57.514 37.500 0.00 3.43 33.02 4.24
2104 2511 2.610976 GCTGGATTGTGCAAAATCAGCA 60.611 45.455 29.58 20.47 38.79 4.41
2129 2536 5.473039 AGCATGCTCTTGTTATTTTTGTCC 58.527 37.500 16.30 0.00 0.00 4.02
2138 2545 3.185594 TGTTATTTTTGTCCGCTCACTCG 59.814 43.478 0.00 0.00 0.00 4.18
2155 2562 2.162681 CTCGGAAACTGGCAATCCTTT 58.837 47.619 10.72 0.00 0.00 3.11
2156 2563 3.244770 ACTCGGAAACTGGCAATCCTTTA 60.245 43.478 10.72 0.00 0.00 1.85
2263 2670 6.865411 TGGTTAGATACTAATTGCACGTACA 58.135 36.000 0.00 0.00 0.00 2.90
2269 2676 4.640805 ACTAATTGCACGTACAAACTCG 57.359 40.909 5.10 0.00 32.27 4.18
2401 2809 3.689347 TCACTTGTGGCATAGATTTGCT 58.311 40.909 6.59 0.00 42.38 3.91
2470 2878 9.892130 GGTATCTTTTTCTTCCTTGATAGAAGA 57.108 33.333 0.00 0.00 46.11 2.87
2506 2914 1.003580 CCCATCAGCCAACTGTACAGT 59.996 52.381 22.95 22.95 44.77 3.55
2527 2935 4.396790 AGTTTTCAGCCGTTTACACAAAGA 59.603 37.500 0.00 0.00 0.00 2.52
2556 2964 6.620678 TGTGCTCTATTGTTGCTTTATTTCC 58.379 36.000 0.00 0.00 0.00 3.13
2572 2980 6.578163 TTATTTCCCCCGTTTCACTTTTAG 57.422 37.500 0.00 0.00 0.00 1.85
2860 3268 4.487019 TGAACACGACTCAACGCATTATA 58.513 39.130 0.00 0.00 36.70 0.98
3010 3433 7.291411 AGGAGTAGACATCGCTAAATAATGT 57.709 36.000 0.00 0.00 36.37 2.71
3014 3437 7.497595 AGTAGACATCGCTAAATAATGTTGGA 58.502 34.615 0.00 0.00 33.91 3.53
3015 3438 6.851222 AGACATCGCTAAATAATGTTGGAG 57.149 37.500 0.00 0.00 33.91 3.86
3041 3464 7.423199 CGTGCTACACTGGAACTTAGATAATA 58.577 38.462 0.00 0.00 31.34 0.98
3062 3485 0.108709 TCGGCAAATTCCTGCATTGC 60.109 50.000 12.50 12.50 46.60 3.56
3190 3632 6.122277 AGGTATTACAAACATCTGGACATGG 58.878 40.000 0.00 0.00 0.00 3.66
3193 3635 2.440409 ACAAACATCTGGACATGGCTC 58.560 47.619 0.00 0.00 0.00 4.70
3219 3661 6.546484 ACTAATGATGCCTGCCTAAATATGT 58.454 36.000 0.00 0.00 0.00 2.29
3302 3829 7.655328 GCTTCATTGATACTAGTTAGTGCTCAT 59.345 37.037 0.00 0.00 37.10 2.90
3326 3853 8.867935 CATGGATCGATTATAGTAAAGCTTGAG 58.132 37.037 0.00 0.00 0.00 3.02
3327 3854 8.178313 TGGATCGATTATAGTAAAGCTTGAGA 57.822 34.615 0.00 0.00 0.00 3.27
3328 3855 8.300286 TGGATCGATTATAGTAAAGCTTGAGAG 58.700 37.037 0.00 0.00 0.00 3.20
3365 3893 6.868339 TGATCGGACATGTGAACATATGATAC 59.132 38.462 10.38 5.83 34.26 2.24
3368 3896 7.216494 TCGGACATGTGAACATATGATACATT 58.784 34.615 10.38 7.58 34.26 2.71
3369 3897 7.384932 TCGGACATGTGAACATATGATACATTC 59.615 37.037 10.38 13.82 34.26 2.67
3370 3898 7.171337 CGGACATGTGAACATATGATACATTCA 59.829 37.037 10.38 5.68 34.77 2.57
3371 3899 9.006839 GGACATGTGAACATATGATACATTCAT 57.993 33.333 10.38 4.75 46.86 2.57
3387 3915 8.938801 ATACATTCATACATATGCCTTTTCCA 57.061 30.769 1.58 0.00 33.76 3.53
3420 3948 6.042143 TGGAATTTCTGAACTGTGCTTTTTC 58.958 36.000 0.00 0.00 0.00 2.29
3421 3949 6.127366 TGGAATTTCTGAACTGTGCTTTTTCT 60.127 34.615 0.00 0.00 0.00 2.52
3422 3950 6.419116 GGAATTTCTGAACTGTGCTTTTTCTC 59.581 38.462 0.00 0.00 0.00 2.87
3424 3952 3.214328 TCTGAACTGTGCTTTTTCTCCC 58.786 45.455 0.00 0.00 0.00 4.30
3445 3973 3.113322 CGCAAGCTGATGAATTCCAATG 58.887 45.455 2.27 0.00 0.00 2.82
3467 3996 0.982704 CCCATGGCAAAAATGGTCCA 59.017 50.000 6.09 0.00 42.68 4.02
3487 4016 8.764558 TGGTCCATTAGTTTGTTAGCTAGATAA 58.235 33.333 0.00 0.00 0.00 1.75
3502 4031 9.542462 TTAGCTAGATAAATTGATTACAACGCT 57.458 29.630 0.00 0.00 38.90 5.07
3543 4072 2.421424 GCTAGTTTCATGGTGGCAGAAG 59.579 50.000 0.00 0.00 0.00 2.85
3599 4128 5.913137 TTCAGGAACAGACAAACAACAAT 57.087 34.783 0.00 0.00 0.00 2.71
3608 4137 5.066505 ACAGACAAACAACAATCTGACTTCC 59.933 40.000 7.08 0.00 40.92 3.46
3697 4227 9.162764 ACAGATTCGTAATAGTGTGCTTATTTT 57.837 29.630 0.00 0.00 0.00 1.82
3716 4246 9.398170 CTTATTTTACACTTCAAGATTGGTGTG 57.602 33.333 14.18 13.74 41.97 3.82
3756 4293 0.170116 TTTCATCGCATTTCCGTGCC 59.830 50.000 0.00 0.00 42.06 5.01
3762 4300 0.096976 CGCATTTCCGTGCCTGTAAG 59.903 55.000 0.00 0.00 42.06 2.34
3781 4319 9.883142 CCTGTAAGTTTCTAATCAGAGAGAAAT 57.117 33.333 11.63 2.83 42.15 2.17
3850 4388 0.393808 GTATTCCCGGCCTTCAGCAA 60.394 55.000 0.00 0.00 46.50 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 173 1.512156 GGCGTGCCTCTTTCGGAAAA 61.512 55.000 2.98 0.00 0.00 2.29
585 691 7.696872 GGTCTTCCTTAGCATTTCGATAAAAAC 59.303 37.037 0.00 0.00 0.00 2.43
598 709 1.933021 TTCTCCGGTCTTCCTTAGCA 58.067 50.000 0.00 0.00 0.00 3.49
760 883 1.198637 CTTCTTTGGAAGCCTCGCAAG 59.801 52.381 0.00 0.00 41.80 4.01
774 897 5.932303 TCAACTAGTTAATGAGCGCTTCTTT 59.068 36.000 13.26 11.67 0.00 2.52
786 909 2.696707 TCGGCGGGATCAACTAGTTAAT 59.303 45.455 8.04 0.00 0.00 1.40
822 945 5.417580 GGCCTTGTGATTGTTCCATTACTTA 59.582 40.000 0.00 0.00 0.00 2.24
825 948 3.119137 GGGCCTTGTGATTGTTCCATTAC 60.119 47.826 0.84 0.00 0.00 1.89
835 958 1.260544 GCTTTCTGGGCCTTGTGATT 58.739 50.000 4.53 0.00 0.00 2.57
839 962 1.600916 GTCGCTTTCTGGGCCTTGT 60.601 57.895 4.53 0.00 0.00 3.16
901 1024 1.446272 GCGTCGGTCTCCTTCCTTG 60.446 63.158 0.00 0.00 0.00 3.61
924 1051 1.134220 GCGGATGGACAGGTGGATAAA 60.134 52.381 0.00 0.00 0.00 1.40
946 1073 1.949847 CTGGTGCCTGGTCTCTACGG 61.950 65.000 0.00 0.00 0.00 4.02
952 1079 1.152247 TGTCTCTGGTGCCTGGTCT 60.152 57.895 0.00 0.00 0.00 3.85
954 1081 2.872388 CGTGTCTCTGGTGCCTGGT 61.872 63.158 0.00 0.00 0.00 4.00
955 1082 2.047844 CGTGTCTCTGGTGCCTGG 60.048 66.667 0.00 0.00 0.00 4.45
956 1083 2.740055 GCGTGTCTCTGGTGCCTG 60.740 66.667 0.00 0.00 0.00 4.85
957 1084 3.233980 TGCGTGTCTCTGGTGCCT 61.234 61.111 0.00 0.00 0.00 4.75
958 1085 3.044305 GTGCGTGTCTCTGGTGCC 61.044 66.667 0.00 0.00 0.00 5.01
959 1086 2.024319 GAGTGCGTGTCTCTGGTGC 61.024 63.158 0.00 0.00 0.00 5.01
960 1087 0.037882 ATGAGTGCGTGTCTCTGGTG 60.038 55.000 0.00 0.00 33.59 4.17
983 1110 1.678627 CTCCGATCTGTGTAGTCCTGG 59.321 57.143 0.00 0.00 0.00 4.45
1036 1168 0.525668 TCGATCGAAGCGGAAGAAGC 60.526 55.000 16.99 0.00 0.00 3.86
1045 1177 0.857935 CTTGCTGGATCGATCGAAGC 59.142 55.000 30.38 30.38 37.56 3.86
1316 1448 2.959516 ACGCAAATCAATCGTCAGAGA 58.040 42.857 0.00 0.00 0.00 3.10
1342 1474 4.682563 AGATATCTACACATCAGAGGGGG 58.317 47.826 2.53 0.00 0.00 5.40
1343 1475 6.767524 GTAGATATCTACACATCAGAGGGG 57.232 45.833 29.91 0.00 46.08 4.79
1481 1613 6.819947 AACGGTAGAAACCCCTAGAAATAT 57.180 37.500 0.00 0.00 43.54 1.28
1493 1625 5.525012 ACTTACTGAACCAAACGGTAGAAAC 59.475 40.000 0.00 0.00 34.92 2.78
1499 1631 4.141869 ACTGTACTTACTGAACCAAACGGT 60.142 41.667 0.00 0.00 38.95 4.83
1511 1643 4.296056 CCCCCATAGGAACTGTACTTACT 58.704 47.826 0.00 0.00 41.52 2.24
1512 1644 4.684484 CCCCCATAGGAACTGTACTTAC 57.316 50.000 0.00 0.00 41.52 2.34
1535 1667 4.491676 TCTACAGCAACAGTTACCGATTC 58.508 43.478 0.00 0.00 0.00 2.52
1560 1959 2.079925 ACCGAAGACGTGTACTCTACC 58.920 52.381 0.00 0.00 37.88 3.18
1581 1980 0.881796 GCTTTTTCGTCCCCTTCCAG 59.118 55.000 0.00 0.00 0.00 3.86
1704 2104 2.418746 CCAGATCACCACTAAACCTCCG 60.419 54.545 0.00 0.00 0.00 4.63
1802 2203 8.547967 TTTAGTAACAACAGAATCTCCATGTC 57.452 34.615 0.00 0.00 0.00 3.06
1831 2232 9.575868 CTATAGTAATGACCTCTAAGTTCAGGA 57.424 37.037 7.63 0.00 33.52 3.86
1860 2261 8.503458 TCCATTTTCTCTTTTCAATTGCAAAA 57.497 26.923 1.71 9.29 0.00 2.44
1942 2343 0.618458 TATCTTCACCCACACCCAGC 59.382 55.000 0.00 0.00 0.00 4.85
1945 2346 2.092914 CCTCTTATCTTCACCCACACCC 60.093 54.545 0.00 0.00 0.00 4.61
2005 2406 2.317371 ACCCACATTGGCAAATGGTA 57.683 45.000 24.35 0.00 46.34 3.25
2014 2415 8.924511 ATATATAGAACTGAAACCCACATTGG 57.075 34.615 0.00 0.00 37.25 3.16
2129 2536 2.383527 GCCAGTTTCCGAGTGAGCG 61.384 63.158 0.00 0.00 0.00 5.03
2138 2545 3.092301 AGCTAAAGGATTGCCAGTTTCC 58.908 45.455 0.00 0.00 36.29 3.13
2155 2562 9.074576 TCGAACCTCAATATAACAGAATAGCTA 57.925 33.333 0.00 0.00 0.00 3.32
2156 2563 7.952671 TCGAACCTCAATATAACAGAATAGCT 58.047 34.615 0.00 0.00 0.00 3.32
2179 2586 7.776933 TGACATAAGAGATTGAAATTCCTCG 57.223 36.000 0.00 0.00 0.00 4.63
2263 2670 3.944055 AGTCAGCTATGTGTCGAGTTT 57.056 42.857 0.00 0.00 0.00 2.66
2269 2676 5.062809 GCAAGTTCTAAGTCAGCTATGTGTC 59.937 44.000 0.00 0.00 0.00 3.67
2322 2729 4.492494 TGCTGCAGAGATGAAGGATTTA 57.508 40.909 20.43 0.00 0.00 1.40
2401 2809 9.108284 TGACGCTTTTCATTCTTGAATATGATA 57.892 29.630 0.00 0.00 41.38 2.15
2443 2851 9.114952 CTTCTATCAAGGAAGAAAAAGATACCC 57.885 37.037 0.00 0.00 41.71 3.69
2456 2864 9.601217 GCTTAATTACACTCTTCTATCAAGGAA 57.399 33.333 0.00 0.00 0.00 3.36
2470 2878 5.431765 CTGATGGGTCAGCTTAATTACACT 58.568 41.667 0.00 0.00 44.86 3.55
2506 2914 4.966965 TCTTTGTGTAAACGGCTGAAAA 57.033 36.364 0.00 0.00 0.00 2.29
2527 2935 9.492973 AATAAAGCAACAATAGAGCACAATTTT 57.507 25.926 0.00 0.00 0.00 1.82
2556 2964 4.642445 AACAACTAAAAGTGAAACGGGG 57.358 40.909 0.00 0.00 45.86 5.73
2572 2980 6.311200 ACTTGAAAATCTGCACAAGAAACAAC 59.689 34.615 16.69 0.00 41.16 3.32
2860 3268 5.751243 AAACGCATTGTCTAAGTCAACTT 57.249 34.783 0.46 0.46 39.85 2.66
2965 3388 1.587547 TAAGCACATCAACGCACACA 58.412 45.000 0.00 0.00 0.00 3.72
3010 3433 1.005037 CCAGTGTAGCACGCTCCAA 60.005 57.895 0.00 0.00 36.71 3.53
3014 3437 0.393077 AAGTTCCAGTGTAGCACGCT 59.607 50.000 0.00 0.00 39.99 5.07
3015 3438 1.993370 CTAAGTTCCAGTGTAGCACGC 59.007 52.381 0.00 0.00 39.64 5.34
3041 3464 2.896168 CAATGCAGGAATTTGCCGAAT 58.104 42.857 0.00 0.00 43.43 3.34
3062 3485 7.169982 CCTTAACTTCACAGAGTTAGTGAGTTG 59.830 40.741 15.04 6.51 45.72 3.16
3190 3632 0.864455 GCAGGCATCATTAGTCGAGC 59.136 55.000 0.00 0.00 0.00 5.03
3193 3635 2.820059 TAGGCAGGCATCATTAGTCG 57.180 50.000 0.00 0.00 0.00 4.18
3280 3724 7.436933 TCCATGAGCACTAACTAGTATCAATG 58.563 38.462 0.00 0.00 35.88 2.82
3302 3829 8.178313 TCTCAAGCTTTACTATAATCGATCCA 57.822 34.615 0.00 0.00 0.00 3.41
3326 3853 0.234106 CGATCATGAATGGCGTGCTC 59.766 55.000 0.00 0.00 33.39 4.26
3327 3854 1.162181 CCGATCATGAATGGCGTGCT 61.162 55.000 0.00 0.00 33.39 4.40
3328 3855 1.159713 TCCGATCATGAATGGCGTGC 61.160 55.000 0.00 0.00 33.39 5.34
3365 3893 8.984764 CAATTGGAAAAGGCATATGTATGAATG 58.015 33.333 4.29 0.00 35.75 2.67
3368 3896 6.610830 ACCAATTGGAAAAGGCATATGTATGA 59.389 34.615 31.22 0.00 38.94 2.15
3369 3897 6.702723 CACCAATTGGAAAAGGCATATGTATG 59.297 38.462 31.22 8.71 38.94 2.39
3370 3898 6.610830 TCACCAATTGGAAAAGGCATATGTAT 59.389 34.615 31.22 0.00 38.94 2.29
3371 3899 5.954752 TCACCAATTGGAAAAGGCATATGTA 59.045 36.000 31.22 2.66 38.94 2.29
3372 3900 4.776837 TCACCAATTGGAAAAGGCATATGT 59.223 37.500 31.22 0.05 38.94 2.29
3373 3901 5.341872 TCACCAATTGGAAAAGGCATATG 57.658 39.130 31.22 14.04 38.94 1.78
3374 3902 5.163280 CCATCACCAATTGGAAAAGGCATAT 60.163 40.000 31.22 0.85 38.94 1.78
3375 3903 4.161942 CCATCACCAATTGGAAAAGGCATA 59.838 41.667 31.22 5.37 38.94 3.14
3387 3915 6.268387 ACAGTTCAGAAATTCCATCACCAATT 59.732 34.615 0.00 0.00 0.00 2.32
3420 3948 1.332997 GAATTCATCAGCTTGCGGGAG 59.667 52.381 0.00 0.00 0.00 4.30
3421 3949 1.382522 GAATTCATCAGCTTGCGGGA 58.617 50.000 0.00 0.00 0.00 5.14
3422 3950 0.383231 GGAATTCATCAGCTTGCGGG 59.617 55.000 7.93 0.00 0.00 6.13
3424 3952 2.925578 TTGGAATTCATCAGCTTGCG 57.074 45.000 7.93 0.00 0.00 4.85
3502 4031 1.480954 CGCAGGTTAGGGAAGCTTCTA 59.519 52.381 25.05 8.78 41.49 2.10
3543 4072 0.386113 TTTAAACACCTGGCCGCAAC 59.614 50.000 0.00 0.00 0.00 4.17
3608 4137 8.726068 ACAATATCGACATCTACATCTAGTCTG 58.274 37.037 0.00 0.00 0.00 3.51
3697 4227 5.029807 TGACACACCAATCTTGAAGTGTA 57.970 39.130 15.43 6.62 41.35 2.90
3702 4232 6.295249 TGAGTAATGACACACCAATCTTGAA 58.705 36.000 0.00 0.00 0.00 2.69
3704 4234 6.748333 ATGAGTAATGACACACCAATCTTG 57.252 37.500 0.00 0.00 0.00 3.02
3707 4237 6.913170 ACAAATGAGTAATGACACACCAATC 58.087 36.000 0.00 0.00 0.00 2.67
3850 4388 8.742125 TGGATATCCTAAAGTCTGGATACATT 57.258 34.615 22.35 0.00 44.93 2.71
3890 4428 6.430000 GGTTACATTCTACTTGCTCAAAGGAA 59.570 38.462 0.00 0.00 40.51 3.36


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

AutoCloner maintained by Alex Coulton.