Multiple sequence alignment - TraesCS3B01G229300

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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 TraesCS3B01G229300 chr3B 100.000 5450 0 0 1 5450 337178085 337172636 0.000000e+00 10065
1 TraesCS3B01G229300 chr3D 97.559 3155 55 5 1749 4882 270160714 270157561 0.000000e+00 5380
2 TraesCS3B01G229300 chr3D 96.648 1044 28 5 615 1654 270162239 270161199 0.000000e+00 1727
3 TraesCS3B01G229300 chr3D 93.474 521 21 5 4883 5403 270157532 270157025 0.000000e+00 761
4 TraesCS3B01G229300 chr3D 92.131 521 37 2 1 519 270163056 270162538 0.000000e+00 732
5 TraesCS3B01G229300 chr3A 95.804 3217 77 10 1690 4882 351127742 351124560 0.000000e+00 5140
6 TraesCS3B01G229300 chr3A 96.000 950 31 5 710 1654 351129251 351128304 0.000000e+00 1537
7 TraesCS3B01G229300 chr3A 91.237 582 26 9 4883 5450 351124531 351123961 0.000000e+00 769
8 TraesCS3B01G229300 chr3A 90.289 381 31 4 1 378 351131985 351131608 1.360000e-135 494
9 TraesCS3B01G229300 chr3A 84.868 152 21 2 366 516 351131198 351131048 9.460000e-33 152
10 TraesCS3B01G229300 chr3A 93.750 96 5 1 623 718 351129596 351129502 5.690000e-30 143
11 TraesCS3B01G229300 chr4B 78.099 484 94 8 1 474 414241497 414241016 4.130000e-76 296
12 TraesCS3B01G229300 chr4B 74.477 478 113 7 1 472 25408145 25408619 1.200000e-46 198
13 TraesCS3B01G229300 chr4B 75.789 380 85 5 97 472 25413125 25413501 9.320000e-43 185
14 TraesCS3B01G229300 chr4B 73.958 480 114 8 1 472 25417913 25418389 3.350000e-42 183
15 TraesCS3B01G229300 chr2B 75.966 466 104 6 19 478 771323351 771323814 3.280000e-57 233
16 TraesCS3B01G229300 chr2B 75.966 466 104 6 19 478 771331475 771331938 3.280000e-57 233
17 TraesCS3B01G229300 chr2A 75.052 481 111 7 1 474 776178532 776179010 1.190000e-51 215


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 TraesCS3B01G229300 chr3B 337172636 337178085 5449 True 10065.0 10065 100.000000 1 5450 1 chr3B.!!$R1 5449
1 TraesCS3B01G229300 chr3D 270157025 270163056 6031 True 2150.0 5380 94.953000 1 5403 4 chr3D.!!$R1 5402
2 TraesCS3B01G229300 chr3A 351123961 351131985 8024 True 1372.5 5140 91.991333 1 5450 6 chr3A.!!$R1 5449

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
519 945 0.255318 CCCATCTCCTTGAGCAGCTT 59.745 55.000 0.00 0.0 0.00 3.74 F
1658 3953 1.028330 TGCTCATGCTAAGCCTGTGC 61.028 55.000 0.00 0.0 41.44 4.57 F
2423 5244 1.008995 CAAACAGGACGCCCAAACG 60.009 57.895 0.00 0.0 39.50 3.60 F
3777 6612 1.143838 CGGACCCGAGCATGATGAA 59.856 57.895 1.54 0.0 42.83 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 4830 0.037975 CTTTTGCTGGCGAGCCAAAT 60.038 50.000 18.08 0.0 46.63 2.32 R
2874 5695 0.604578 TAAGAAACCCAGTCCCGTCG 59.395 55.000 0.00 0.0 0.00 5.12 R
4198 7033 1.874739 CGAGACCTTTTTACGGCCACA 60.875 52.381 2.24 0.0 0.00 4.17 R
5026 7903 1.153524 TGCTCCAATGTTGCCCTGT 59.846 52.632 0.00 0.0 0.00 4.00 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
80 83 3.780294 ACTCATTGGTGACATTAGGGCTA 59.220 43.478 0.00 0.00 42.32 3.93
129 132 6.777213 TGTGCAACCCTTACTAAAGAAAAA 57.223 33.333 0.00 0.00 32.37 1.94
173 176 3.765968 TCTGACCAGAGGCACTACA 57.234 52.632 0.00 0.00 41.55 2.74
175 178 1.618837 TCTGACCAGAGGCACTACAAC 59.381 52.381 0.00 0.00 41.55 3.32
180 183 2.172717 ACCAGAGGCACTACAACAACTT 59.827 45.455 0.00 0.00 41.55 2.66
190 193 5.221048 GCACTACAACAACTTTCCAACAGAT 60.221 40.000 0.00 0.00 0.00 2.90
202 205 5.762179 TTCCAACAGATAGGACAACTCAT 57.238 39.130 0.00 0.00 32.62 2.90
206 209 5.939883 CCAACAGATAGGACAACTCATTTGA 59.060 40.000 0.00 0.00 38.73 2.69
294 298 3.462021 GCTGATGGAGCTACTCGAATTT 58.538 45.455 0.00 0.00 45.21 1.82
306 310 1.734465 CTCGAATTTCACTGAGGTGCC 59.266 52.381 0.00 0.00 42.72 5.01
336 340 4.799564 TGTTTTGTTTTCAAGAGGCACT 57.200 36.364 0.00 0.00 41.09 4.40
372 376 7.441157 CCGTTGCTAATAAGAATAGACATGGAA 59.559 37.037 0.00 0.00 0.00 3.53
431 857 1.398692 TTCTTCCAACTTGCCACCAC 58.601 50.000 0.00 0.00 0.00 4.16
444 870 2.173782 TGCCACCACTAAAAAGGACTGA 59.826 45.455 0.00 0.00 0.00 3.41
446 872 3.826729 GCCACCACTAAAAAGGACTGAAT 59.173 43.478 0.00 0.00 0.00 2.57
492 918 7.147479 CCTCATAATTAGAGAAACCCAAGGAGA 60.147 40.741 11.35 0.00 35.09 3.71
511 937 1.753073 GATGCAAACCCCATCTCCTTG 59.247 52.381 0.00 0.00 36.89 3.61
512 938 0.776810 TGCAAACCCCATCTCCTTGA 59.223 50.000 0.00 0.00 0.00 3.02
513 939 1.272092 TGCAAACCCCATCTCCTTGAG 60.272 52.381 0.00 0.00 0.00 3.02
514 940 1.467920 CAAACCCCATCTCCTTGAGC 58.532 55.000 0.00 0.00 0.00 4.26
515 941 1.075601 AAACCCCATCTCCTTGAGCA 58.924 50.000 0.00 0.00 0.00 4.26
516 942 0.622665 AACCCCATCTCCTTGAGCAG 59.377 55.000 0.00 0.00 0.00 4.24
517 943 1.153005 CCCCATCTCCTTGAGCAGC 60.153 63.158 0.00 0.00 0.00 5.25
518 944 1.633915 CCCCATCTCCTTGAGCAGCT 61.634 60.000 0.00 0.00 0.00 4.24
519 945 0.255318 CCCATCTCCTTGAGCAGCTT 59.745 55.000 0.00 0.00 0.00 3.74
520 946 1.340795 CCCATCTCCTTGAGCAGCTTT 60.341 52.381 0.00 0.00 0.00 3.51
521 947 2.444421 CCATCTCCTTGAGCAGCTTTT 58.556 47.619 0.00 0.00 0.00 2.27
522 948 2.824341 CCATCTCCTTGAGCAGCTTTTT 59.176 45.455 0.00 0.00 0.00 1.94
540 966 4.921644 TTTTTCGAGGGGTATCTCCTTT 57.078 40.909 0.00 0.00 34.21 3.11
541 967 4.921644 TTTTCGAGGGGTATCTCCTTTT 57.078 40.909 0.00 0.00 34.21 2.27
542 968 4.921644 TTTCGAGGGGTATCTCCTTTTT 57.078 40.909 0.00 0.00 34.21 1.94
614 1040 1.050421 GGGGGCCTTAGCATTTGCAT 61.050 55.000 0.84 0.00 45.16 3.96
619 1045 3.555586 GGGCCTTAGCATTTGCATAATGG 60.556 47.826 17.53 3.37 45.16 3.16
620 1046 3.555586 GGCCTTAGCATTTGCATAATGGG 60.556 47.826 17.53 12.89 45.16 4.00
621 1047 3.070015 GCCTTAGCATTTGCATAATGGGT 59.930 43.478 17.53 10.03 45.16 4.51
623 1049 4.099881 CCTTAGCATTTGCATAATGGGTGT 59.900 41.667 17.53 0.00 45.16 4.16
624 1050 3.806625 AGCATTTGCATAATGGGTGTC 57.193 42.857 17.53 6.15 45.16 3.67
625 1051 3.368248 AGCATTTGCATAATGGGTGTCT 58.632 40.909 17.53 7.69 45.16 3.41
627 1053 3.491447 GCATTTGCATAATGGGTGTCTCC 60.491 47.826 17.53 0.00 41.59 3.71
629 1055 3.281727 TTGCATAATGGGTGTCTCCTC 57.718 47.619 0.00 0.00 36.25 3.71
631 1057 1.871080 CATAATGGGTGTCTCCTCGC 58.129 55.000 0.00 0.00 36.25 5.03
822 3113 3.005539 ACCTCCACGGAGCAGCAT 61.006 61.111 7.64 0.00 40.69 3.79
1146 3438 1.538950 GACGAGTTACCCGAGAACTGT 59.461 52.381 0.00 1.84 37.27 3.55
1292 3584 6.582677 AGATTCGATCTGTTCGGATAATCT 57.417 37.500 13.41 13.41 46.28 2.40
1405 3697 4.327680 GTCTGCTGTTCTTTCTACCCATT 58.672 43.478 0.00 0.00 0.00 3.16
1438 3733 8.220898 AGTATGTATAGTATCTCCCTGAGACA 57.779 38.462 0.00 0.00 41.76 3.41
1441 3736 7.091533 TGTATAGTATCTCCCTGAGACATGA 57.908 40.000 0.00 0.00 41.76 3.07
1500 3795 9.558396 TCTATTTTTCCATTGCAAAAATCTTGT 57.442 25.926 13.02 0.00 40.81 3.16
1525 3820 5.320277 AGGCATTAGAAGGATCAATTAGGC 58.680 41.667 0.00 0.00 0.00 3.93
1554 3849 2.965671 ATTGCATCCCCTCTGTATGG 57.034 50.000 0.00 0.00 0.00 2.74
1654 3949 3.784511 ACATATGCTCATGCTAAGCCT 57.215 42.857 1.58 0.00 39.05 4.58
1655 3950 3.409570 ACATATGCTCATGCTAAGCCTG 58.590 45.455 1.58 0.00 39.05 4.85
1656 3951 3.181447 ACATATGCTCATGCTAAGCCTGT 60.181 43.478 1.58 1.97 39.05 4.00
1657 3952 1.676746 ATGCTCATGCTAAGCCTGTG 58.323 50.000 2.70 0.00 39.05 3.66
1658 3953 1.028330 TGCTCATGCTAAGCCTGTGC 61.028 55.000 0.00 0.00 41.44 4.57
1659 3954 1.722636 GCTCATGCTAAGCCTGTGCC 61.723 60.000 0.00 0.00 37.58 5.01
1660 3955 1.077501 TCATGCTAAGCCTGTGCCC 60.078 57.895 0.00 0.00 38.69 5.36
1661 3956 2.123428 CATGCTAAGCCTGTGCCCC 61.123 63.158 0.00 0.00 38.69 5.80
1662 3957 3.364907 ATGCTAAGCCTGTGCCCCC 62.365 63.158 0.00 0.00 38.69 5.40
1680 3975 2.409948 CCCCCTCTTGTCAAGCTTAG 57.590 55.000 7.78 0.52 0.00 2.18
1681 3976 1.630878 CCCCCTCTTGTCAAGCTTAGT 59.369 52.381 7.78 0.00 0.00 2.24
1682 3977 2.040412 CCCCCTCTTGTCAAGCTTAGTT 59.960 50.000 7.78 0.00 0.00 2.24
1683 3978 3.498661 CCCCCTCTTGTCAAGCTTAGTTT 60.499 47.826 7.78 0.00 0.00 2.66
1684 3979 4.263331 CCCCCTCTTGTCAAGCTTAGTTTA 60.263 45.833 7.78 0.00 0.00 2.01
1685 3980 5.501156 CCCCTCTTGTCAAGCTTAGTTTAT 58.499 41.667 7.78 0.00 0.00 1.40
1686 3981 5.355350 CCCCTCTTGTCAAGCTTAGTTTATG 59.645 44.000 7.78 0.00 0.00 1.90
1687 3982 6.173339 CCCTCTTGTCAAGCTTAGTTTATGA 58.827 40.000 7.78 0.00 0.00 2.15
1688 3983 6.825721 CCCTCTTGTCAAGCTTAGTTTATGAT 59.174 38.462 7.78 0.00 0.00 2.45
1786 4607 5.334182 GCTTCGGAAGAGAGATTTTCGTTTT 60.334 40.000 21.45 0.00 43.69 2.43
2004 4825 9.587772 GAGTATGAAGAGTGTATAGAAAAAGCA 57.412 33.333 0.00 0.00 0.00 3.91
2132 4953 4.588106 AGATGAAGATGAGATGGACGATGT 59.412 41.667 0.00 0.00 0.00 3.06
2204 5025 3.070734 GGAGCCAGCAGAATATCTTCTCA 59.929 47.826 0.00 0.00 39.78 3.27
2415 5236 4.261801 ACCTTATTGGATCAAACAGGACG 58.738 43.478 14.55 0.00 39.71 4.79
2423 5244 1.008995 CAAACAGGACGCCCAAACG 60.009 57.895 0.00 0.00 39.50 3.60
2449 5270 4.105486 GTCAAGTGCTGGTTCTTTTTCAC 58.895 43.478 0.00 0.00 0.00 3.18
2529 5350 6.162777 GCCTAGCACAAATGGAATAAACAAA 58.837 36.000 0.00 0.00 0.00 2.83
2547 5368 7.858052 AAACAAAAATAAGCAGTCTCATTCG 57.142 32.000 0.00 0.00 0.00 3.34
2874 5695 6.869315 AAACTAAAGGAAGCTGAAGTCTTC 57.131 37.500 5.58 5.58 39.26 2.87
3602 6437 3.980646 TGAAAGTTTGATGGTGGAACG 57.019 42.857 0.00 0.00 38.12 3.95
3603 6438 2.621055 TGAAAGTTTGATGGTGGAACGG 59.379 45.455 0.00 0.00 38.12 4.44
3777 6612 1.143838 CGGACCCGAGCATGATGAA 59.856 57.895 1.54 0.00 42.83 2.57
4077 6912 5.982516 TGTTGTTGTTTTGGATGATAGTTGC 59.017 36.000 0.00 0.00 0.00 4.17
4095 6930 1.623811 TGCCCTGTGGAAAGTAGAGAC 59.376 52.381 0.00 0.00 0.00 3.36
4198 7033 9.398170 CGTCACATTCATCTAAATCAAAACTTT 57.602 29.630 0.00 0.00 0.00 2.66
4324 7159 1.153745 AGCAGCCGTAGAGAAAGCG 60.154 57.895 0.00 0.00 0.00 4.68
4410 7245 7.412346 CGACTTGTTTTCAGTAGGATCAATGAG 60.412 40.741 0.00 0.00 0.00 2.90
4478 7315 5.745227 TCTGCCAGGACTTAATTAAAGAGG 58.255 41.667 0.00 0.00 38.67 3.69
4584 7421 7.786178 TGACTATTATGTGCTTGTAATCCAC 57.214 36.000 0.00 0.00 0.00 4.02
4617 7455 3.253921 GCAATTGTTACTTACCCACCGTT 59.746 43.478 7.40 0.00 0.00 4.44
4710 7548 3.956848 GCAGGGAAGGAAATAAGCAGATT 59.043 43.478 0.00 0.00 0.00 2.40
4765 7613 5.535030 GGTTTAGATTGGTGGAGAAAACACT 59.465 40.000 0.00 0.00 38.83 3.55
4842 7690 2.787601 TGTTCTGCTACGACGAACTT 57.212 45.000 0.00 0.00 38.23 2.66
4895 7771 2.593925 TGAGAGAGAGCAAGTCCTCA 57.406 50.000 0.00 0.00 34.26 3.86
4934 7811 2.690786 CCGAAAACGTAGGTTGGATCA 58.309 47.619 0.79 0.00 36.25 2.92
5026 7903 4.020617 CTCCTTGGAGGCCGCACA 62.021 66.667 9.31 0.66 34.61 4.57
5050 7927 1.547372 GGCAACATTGGAGCACATCTT 59.453 47.619 5.21 0.00 0.00 2.40
5148 8025 1.597027 CACCTCGCCGTTGGACTTT 60.597 57.895 5.98 0.00 0.00 2.66
5239 8116 1.997311 CCAGGTGGGGAGCTCATCA 60.997 63.158 17.19 10.07 0.00 3.07
5322 8199 4.029809 GCCGTTGTAGCACCCCCT 62.030 66.667 0.00 0.00 0.00 4.79
5323 8200 2.267961 CCGTTGTAGCACCCCCTC 59.732 66.667 0.00 0.00 0.00 4.30
5324 8201 2.125673 CGTTGTAGCACCCCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
5325 8202 2.436115 GTTGTAGCACCCCCTCGC 60.436 66.667 0.00 0.00 0.00 5.03
5346 8225 3.782244 GTCTTCGCCAGCAGCACG 61.782 66.667 0.00 0.00 44.04 5.34
5390 8269 2.513204 CCGCCTCCATGCTGACAG 60.513 66.667 0.00 0.00 0.00 3.51
5408 8287 2.868964 AGGCCTATTACCTGAGACCA 57.131 50.000 1.29 0.00 35.72 4.02
5413 8303 3.319689 GCCTATTACCTGAGACCAGACTC 59.680 52.174 0.00 0.00 43.02 3.36
5429 8319 0.896940 ACTCTTCACCGGTCGGCTTA 60.897 55.000 2.59 0.00 39.32 3.09
5433 8323 0.458889 TTCACCGGTCGGCTTATTCG 60.459 55.000 2.59 0.00 39.32 3.34
5440 8330 1.885157 TCGGCTTATTCGACCACGT 59.115 52.632 0.00 0.00 40.69 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 106 6.969993 TTCTTTAGTAAGGGTTGCACAAAT 57.030 33.333 0.00 0.00 32.02 2.32
129 132 8.317679 AGCATTAACTTGTCTAGATCTTCAGTT 58.682 33.333 0.00 5.38 0.00 3.16
130 133 7.846066 AGCATTAACTTGTCTAGATCTTCAGT 58.154 34.615 0.00 0.00 0.00 3.41
139 142 5.724328 TGGTCAGAGCATTAACTTGTCTAG 58.276 41.667 0.00 0.00 0.00 2.43
173 176 5.690865 TGTCCTATCTGTTGGAAAGTTGTT 58.309 37.500 0.00 0.00 33.72 2.83
175 178 5.765182 AGTTGTCCTATCTGTTGGAAAGTTG 59.235 40.000 0.00 0.00 33.72 3.16
180 183 5.762179 ATGAGTTGTCCTATCTGTTGGAA 57.238 39.130 0.00 0.00 33.72 3.53
190 193 6.070021 ACAGATGGATCAAATGAGTTGTCCTA 60.070 38.462 12.73 3.82 37.85 2.94
202 205 2.846206 AGGCCAGTACAGATGGATCAAA 59.154 45.455 5.01 0.00 40.51 2.69
206 209 2.171448 GTCAAGGCCAGTACAGATGGAT 59.829 50.000 5.01 0.00 40.51 3.41
294 298 3.933907 CATGAATCATGGCACCTCAGTGA 60.934 47.826 15.09 0.00 40.94 3.41
306 310 8.492748 CCTCTTGAAAACAAAACATGAATCATG 58.507 33.333 20.58 20.58 46.18 3.07
336 340 5.422970 TCTTATTAGCAACGGAGGACCTTAA 59.577 40.000 0.00 0.00 0.00 1.85
492 918 1.358787 TCAAGGAGATGGGGTTTGCAT 59.641 47.619 0.00 0.00 0.00 3.96
519 945 4.921644 AAAGGAGATACCCCTCGAAAAA 57.078 40.909 0.00 0.00 40.05 1.94
520 946 4.921644 AAAAGGAGATACCCCTCGAAAA 57.078 40.909 0.00 0.00 40.05 2.29
521 947 4.921644 AAAAAGGAGATACCCCTCGAAA 57.078 40.909 0.00 0.00 40.05 3.46
548 974 5.264775 GCAGCTGCTTACCCCTTAGGTTA 62.265 52.174 31.33 0.00 41.93 2.85
549 975 4.595988 GCAGCTGCTTACCCCTTAGGTT 62.596 54.545 31.33 0.00 41.93 3.50
550 976 3.134563 GCAGCTGCTTACCCCTTAGGT 62.135 57.143 31.33 0.00 44.99 3.08
551 977 0.464554 GCAGCTGCTTACCCCTTAGG 60.465 60.000 31.33 0.00 38.96 2.69
552 978 0.253044 TGCAGCTGCTTACCCCTTAG 59.747 55.000 36.61 0.00 42.66 2.18
553 979 0.918983 ATGCAGCTGCTTACCCCTTA 59.081 50.000 36.61 15.85 42.66 2.69
554 980 0.040204 AATGCAGCTGCTTACCCCTT 59.960 50.000 36.61 13.76 42.66 3.95
555 981 0.040204 AAATGCAGCTGCTTACCCCT 59.960 50.000 36.61 14.49 42.66 4.79
556 982 0.897621 AAAATGCAGCTGCTTACCCC 59.102 50.000 36.61 9.26 42.66 4.95
557 983 1.821136 AGAAAATGCAGCTGCTTACCC 59.179 47.619 36.61 22.68 42.66 3.69
558 984 3.582714 AAGAAAATGCAGCTGCTTACC 57.417 42.857 36.61 21.84 42.66 2.85
559 985 5.463061 TCAAAAAGAAAATGCAGCTGCTTAC 59.537 36.000 36.61 23.51 42.66 2.34
560 986 5.599732 TCAAAAAGAAAATGCAGCTGCTTA 58.400 33.333 36.61 20.50 42.66 3.09
606 1032 3.956199 AGGAGACACCCATTATGCAAATG 59.044 43.478 12.10 12.10 40.05 2.32
607 1033 4.210331 GAGGAGACACCCATTATGCAAAT 58.790 43.478 0.00 0.00 40.05 2.32
609 1035 2.419990 CGAGGAGACACCCATTATGCAA 60.420 50.000 0.00 0.00 40.05 4.08
614 1040 1.813859 CGCGAGGAGACACCCATTA 59.186 57.895 0.00 0.00 40.05 1.90
627 1053 3.121019 CCTCTCCTAACCCGCGAG 58.879 66.667 8.23 0.00 0.00 5.03
629 1055 4.222847 GGCCTCTCCTAACCCGCG 62.223 72.222 0.00 0.00 0.00 6.46
631 1057 2.441532 TCGGCCTCTCCTAACCCG 60.442 66.667 0.00 0.00 40.25 5.28
711 2742 1.279749 GGAAGAAGGGGTAGGGGGTG 61.280 65.000 0.00 0.00 0.00 4.61
1122 3414 0.325933 TCTCGGGTAACTCGTCCTGA 59.674 55.000 0.00 0.00 37.52 3.86
1316 3608 6.534079 GGCATCATCAGGAGAAAAGAAAATTG 59.466 38.462 0.00 0.00 0.00 2.32
1430 3725 5.710513 TTTCACCATTTTCATGTCTCAGG 57.289 39.130 0.00 0.00 0.00 3.86
1433 3728 7.040409 ACCTAGTTTTCACCATTTTCATGTCTC 60.040 37.037 0.00 0.00 0.00 3.36
1438 3733 8.650143 ATGTACCTAGTTTTCACCATTTTCAT 57.350 30.769 0.00 0.00 0.00 2.57
1441 3736 7.462571 GGATGTACCTAGTTTTCACCATTTT 57.537 36.000 0.00 0.00 35.41 1.82
1500 3795 6.942576 GCCTAATTGATCCTTCTAATGCCTTA 59.057 38.462 0.00 0.00 0.00 2.69
1525 3820 3.935203 GAGGGGATGCAATATGTATGTCG 59.065 47.826 0.00 0.00 0.00 4.35
1554 3849 1.197036 GCGTGGCACTTTTCTTCCTAC 59.803 52.381 16.72 0.00 0.00 3.18
1661 3956 1.630878 ACTAAGCTTGACAAGAGGGGG 59.369 52.381 19.51 6.71 0.00 5.40
1662 3957 3.425162 AACTAAGCTTGACAAGAGGGG 57.575 47.619 19.51 8.00 0.00 4.79
1663 3958 6.173339 TCATAAACTAAGCTTGACAAGAGGG 58.827 40.000 19.51 7.67 0.00 4.30
1664 3959 7.856145 ATCATAAACTAAGCTTGACAAGAGG 57.144 36.000 19.51 7.35 0.00 3.69
1666 3961 9.719355 TGTTATCATAAACTAAGCTTGACAAGA 57.281 29.630 19.51 0.00 0.00 3.02
1674 3969 8.552034 GCGAGAAATGTTATCATAAACTAAGCT 58.448 33.333 0.00 0.00 33.49 3.74
1675 3970 7.798982 GGCGAGAAATGTTATCATAAACTAAGC 59.201 37.037 0.00 0.00 33.49 3.09
1676 3971 9.046296 AGGCGAGAAATGTTATCATAAACTAAG 57.954 33.333 0.00 0.00 33.49 2.18
1677 3972 8.826710 CAGGCGAGAAATGTTATCATAAACTAA 58.173 33.333 0.00 0.00 33.49 2.24
1678 3973 7.441157 CCAGGCGAGAAATGTTATCATAAACTA 59.559 37.037 0.00 0.00 33.49 2.24
1679 3974 6.260936 CCAGGCGAGAAATGTTATCATAAACT 59.739 38.462 0.00 0.00 33.49 2.66
1680 3975 6.260050 TCCAGGCGAGAAATGTTATCATAAAC 59.740 38.462 0.00 0.00 33.49 2.01
1681 3976 6.353323 TCCAGGCGAGAAATGTTATCATAAA 58.647 36.000 0.00 0.00 33.49 1.40
1682 3977 5.924356 TCCAGGCGAGAAATGTTATCATAA 58.076 37.500 0.00 0.00 33.49 1.90
1683 3978 5.545063 TCCAGGCGAGAAATGTTATCATA 57.455 39.130 0.00 0.00 33.49 2.15
1684 3979 4.422073 TCCAGGCGAGAAATGTTATCAT 57.578 40.909 0.00 0.00 35.59 2.45
1685 3980 3.904800 TCCAGGCGAGAAATGTTATCA 57.095 42.857 0.00 0.00 0.00 2.15
1686 3981 4.380531 TCATCCAGGCGAGAAATGTTATC 58.619 43.478 0.00 0.00 0.00 1.75
1687 3982 4.422073 TCATCCAGGCGAGAAATGTTAT 57.578 40.909 0.00 0.00 0.00 1.89
1688 3983 3.904800 TCATCCAGGCGAGAAATGTTA 57.095 42.857 0.00 0.00 0.00 2.41
1698 4519 1.746615 CCACCAGTTCATCCAGGCG 60.747 63.158 0.00 0.00 0.00 5.52
2009 4830 0.037975 CTTTTGCTGGCGAGCCAAAT 60.038 50.000 18.08 0.00 46.63 2.32
2132 4953 5.151297 TCTGTTCTCAGATGCACACATAA 57.849 39.130 0.00 0.00 44.58 1.90
2154 4975 9.553064 CCTATGTTTCTAGAGTTTGCAGAATAT 57.447 33.333 0.00 0.00 0.00 1.28
2204 5025 2.635915 TCATACAGACCCCTTTCAACGT 59.364 45.455 0.00 0.00 0.00 3.99
2415 5236 0.310854 CACTTGACTTCCGTTTGGGC 59.689 55.000 0.00 0.00 35.24 5.36
2423 5244 2.262423 AGAACCAGCACTTGACTTCC 57.738 50.000 0.00 0.00 0.00 3.46
2529 5350 5.700832 TGTCAACGAATGAGACTGCTTATTT 59.299 36.000 0.00 0.00 39.19 1.40
2547 5368 3.113322 GGAGCGTTTCCTTTTTGTCAAC 58.887 45.455 1.38 0.00 43.16 3.18
2706 5527 7.252965 TGATTCAAACACATTCGACAGTTTA 57.747 32.000 0.00 0.00 33.30 2.01
2718 5539 4.348863 CCCCCAATTTGATTCAAACACA 57.651 40.909 13.80 0.00 36.13 3.72
2874 5695 0.604578 TAAGAAACCCAGTCCCGTCG 59.395 55.000 0.00 0.00 0.00 5.12
3254 6085 9.646522 ATGCTTAACTAAATGTGATAAATCCCT 57.353 29.630 0.00 0.00 0.00 4.20
3278 6109 9.582431 AAGAGATTGAAATAAAGAATGTGCATG 57.418 29.630 0.00 0.00 0.00 4.06
3602 6437 6.463995 TGCATTTTATTGTCCTTCCATACC 57.536 37.500 0.00 0.00 0.00 2.73
3603 6438 6.980397 CCTTGCATTTTATTGTCCTTCCATAC 59.020 38.462 0.00 0.00 0.00 2.39
3777 6612 6.899393 TGGTTGCTTAGAGTTTCAAATGAT 57.101 33.333 0.00 0.00 0.00 2.45
4077 6912 4.020218 TGATTGTCTCTACTTTCCACAGGG 60.020 45.833 0.00 0.00 0.00 4.45
4095 6930 3.256383 TGTTCTTTGCCAGATGGTGATTG 59.744 43.478 0.00 0.00 37.57 2.67
4198 7033 1.874739 CGAGACCTTTTTACGGCCACA 60.875 52.381 2.24 0.00 0.00 4.17
4410 7245 5.124457 TGATCTCACTTGAAAGCTTAATGCC 59.876 40.000 0.00 0.00 44.23 4.40
4478 7315 3.744660 AGAAATTGTATGATCGGAGGCC 58.255 45.455 0.00 0.00 0.00 5.19
4584 7421 6.560253 AAGTAACAATTGCCTACTGACTTG 57.440 37.500 17.23 0.00 0.00 3.16
4617 7455 2.684943 TGGAAGTCTCACCCAACACTA 58.315 47.619 0.00 0.00 0.00 2.74
4680 7518 2.978156 TTCCTTCCCTGCTTCAACAT 57.022 45.000 0.00 0.00 0.00 2.71
4710 7548 8.453238 ACTCTATCAGCGAAGAGAAATACTAA 57.547 34.615 12.58 0.00 41.51 2.24
4842 7690 3.536917 CCGATGGGCAGCTACCGA 61.537 66.667 0.00 0.00 0.00 4.69
4934 7811 1.877443 GACATTGTTTGTGGTAGCCGT 59.123 47.619 0.00 0.00 39.18 5.68
5026 7903 1.153524 TGCTCCAATGTTGCCCTGT 59.846 52.632 0.00 0.00 0.00 4.00
5050 7927 6.425210 TCATTCTTCTCTTTCTGGAGTTGA 57.575 37.500 0.00 0.00 35.11 3.18
5148 8025 1.901464 GCAAGCCCGGAGTTTGGAA 60.901 57.895 0.73 0.00 37.18 3.53
5239 8116 2.025321 CACAGCAAGGTTTATAGGGGGT 60.025 50.000 0.00 0.00 0.00 4.95
5390 8269 2.365941 GTCTGGTCTCAGGTAATAGGCC 59.634 54.545 0.00 0.00 41.23 5.19
5404 8283 2.352817 ACCGGTGAAGAGTCTGGTC 58.647 57.895 6.12 0.00 38.80 4.02
5405 8284 1.524863 CGACCGGTGAAGAGTCTGGT 61.525 60.000 14.63 0.00 44.82 4.00
5406 8285 1.213013 CGACCGGTGAAGAGTCTGG 59.787 63.158 14.63 0.00 36.29 3.86
5407 8286 1.213013 CCGACCGGTGAAGAGTCTG 59.787 63.158 14.63 0.00 0.00 3.51
5408 8287 2.637383 GCCGACCGGTGAAGAGTCT 61.637 63.158 14.63 0.00 37.65 3.24
5413 8303 1.287425 GAATAAGCCGACCGGTGAAG 58.713 55.000 14.63 2.45 37.65 3.02
5429 8319 1.736645 CTTGCGGACGTGGTCGAAT 60.737 57.895 0.00 0.00 40.62 3.34


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

AutoCloner maintained by Alex Coulton.